Query 028248
Match_columns 211
No_of_seqs 72 out of 74
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:33:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028248.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028248hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00420 hypothetical protein; 97.6 7.7E-05 1.7E-09 59.7 3.7 48 141-199 8-55 (112)
2 PF11023 DUF2614: Protein of u 97.0 0.00069 1.5E-08 54.6 3.8 63 126-200 37-101 (114)
3 PRK00398 rpoP DNA-directed RNA 96.9 0.00091 2E-08 44.8 3.1 36 158-203 5-40 (46)
4 COG2051 RPS27A Ribosomal prote 96.7 0.0019 4.2E-08 47.7 3.6 44 155-207 18-61 (67)
5 TIGR01206 lysW lysine biosynth 96.7 0.0029 6.2E-08 44.8 4.3 44 156-207 2-47 (54)
6 TIGR02098 MJ0042_CXXC MJ0042 f 96.5 0.0025 5.4E-08 40.7 2.5 36 156-196 2-37 (38)
7 PF06044 DRP: Dam-replacing fa 96.4 0.0028 6E-08 57.1 3.2 50 140-200 19-69 (254)
8 PF13240 zinc_ribbon_2: zinc-r 96.3 0.0017 3.8E-08 38.4 0.9 22 159-194 2-23 (23)
9 PF13248 zf-ribbon_3: zinc-rib 96.2 0.002 4.3E-08 38.8 0.8 24 157-194 3-26 (26)
10 PRK00415 rps27e 30S ribosomal 96.1 0.0047 1E-07 44.6 2.6 42 155-205 10-51 (59)
11 cd00114 LIGANc NAD+ dependent 95.7 0.013 2.8E-07 53.6 4.2 27 32-58 12-39 (307)
12 COG2888 Predicted Zn-ribbon RN 95.7 0.0054 1.2E-07 44.5 1.4 36 151-191 22-57 (61)
13 PF01667 Ribosomal_S27e: Ribos 95.7 0.02 4.4E-07 40.7 4.3 44 155-207 6-49 (55)
14 PF09538 FYDLN_acid: Protein o 95.5 0.009 1.9E-07 47.4 2.1 33 155-198 8-40 (108)
15 PRK08097 ligB NAD-dependent DN 95.4 0.014 3.1E-07 57.6 3.8 50 9-58 8-70 (562)
16 smart00531 TFIIE Transcription 95.3 0.0093 2E-07 48.7 1.9 43 156-202 99-141 (147)
17 PF01653 DNA_ligase_aden: NAD- 95.2 0.025 5.4E-07 51.9 4.4 26 33-58 17-43 (315)
18 PLN00209 ribosomal protein S27 94.8 0.036 7.8E-07 42.8 3.6 45 154-207 34-78 (86)
19 smart00834 CxxC_CXXC_SSSS Puta 94.8 0.025 5.5E-07 36.0 2.3 30 157-193 6-35 (41)
20 PRK09710 lar restriction allev 94.8 0.02 4.2E-07 42.1 2.0 35 157-198 7-41 (64)
21 COG1645 Uncharacterized Zn-fin 94.7 0.029 6.3E-07 46.3 3.0 39 143-193 15-53 (131)
22 TIGR00575 dnlj DNA ligase, NAD 94.6 0.037 8E-07 55.4 4.1 29 30-58 5-34 (652)
23 PTZ00083 40S ribosomal protein 94.6 0.045 9.8E-07 42.2 3.6 46 153-207 32-77 (85)
24 PF08271 TF_Zn_Ribbon: TFIIB z 94.5 0.029 6.2E-07 37.0 2.2 32 158-198 2-33 (43)
25 smart00532 LIGANc Ligase N fam 94.5 0.036 7.8E-07 53.2 3.8 26 33-58 15-41 (441)
26 PRK07956 ligA NAD-dependent DN 94.5 0.043 9.3E-07 55.1 4.3 26 33-58 19-45 (665)
27 PRK05978 hypothetical protein; 94.5 0.018 3.9E-07 48.2 1.3 35 155-198 32-66 (148)
28 PRK02935 hypothetical protein; 94.5 0.049 1.1E-06 43.7 3.7 36 154-201 68-103 (110)
29 PF14353 CpXC: CpXC protein 94.3 0.038 8.2E-07 43.6 2.8 40 158-197 3-51 (128)
30 TIGR02300 FYDLN_acid conserved 94.1 0.031 6.7E-07 46.0 2.0 32 155-197 8-39 (129)
31 PRK06266 transcription initiat 94.1 0.011 2.4E-07 50.2 -0.6 38 156-202 117-154 (178)
32 PHA00626 hypothetical protein 94.0 0.041 8.8E-07 39.7 2.3 36 158-198 2-37 (59)
33 PF14803 Nudix_N_2: Nudix N-te 94.0 0.042 9.1E-07 35.5 2.1 29 159-193 3-31 (34)
34 PRK14890 putative Zn-ribbon RN 93.9 0.03 6.4E-07 40.5 1.4 33 154-192 23-56 (59)
35 PF14255 Cys_rich_CPXG: Cystei 93.8 0.051 1.1E-06 38.2 2.4 37 158-198 2-38 (52)
36 smart00659 RPOLCX RNA polymera 93.8 0.063 1.4E-06 36.3 2.7 30 158-198 4-33 (44)
37 PF09723 Zn-ribbon_8: Zinc rib 93.6 0.057 1.2E-06 35.7 2.3 28 158-192 7-34 (42)
38 PF10571 UPF0547: Uncharacteri 93.5 0.039 8.5E-07 33.6 1.2 23 158-194 2-24 (26)
39 TIGR00373 conserved hypothetic 93.5 0.024 5.1E-07 47.2 0.3 38 157-203 110-147 (158)
40 PF09862 DUF2089: Protein of u 93.1 0.074 1.6E-06 42.8 2.6 23 159-195 1-23 (113)
41 PF13719 zinc_ribbon_5: zinc-r 93.1 0.069 1.5E-06 34.5 2.0 34 157-195 3-36 (37)
42 PRK14351 ligA NAD-dependent DN 92.8 0.13 2.7E-06 52.1 4.2 24 35-58 48-72 (689)
43 PF14354 Lar_restr_allev: Rest 92.6 0.095 2.1E-06 36.3 2.3 33 158-192 5-37 (61)
44 TIGR02605 CxxC_CxxC_SSSS putat 92.3 0.14 3.1E-06 34.4 2.8 28 158-192 7-34 (52)
45 PF05191 ADK_lid: Adenylate ki 91.6 0.097 2.1E-06 34.0 1.2 33 158-198 3-35 (36)
46 PRK14350 ligA NAD-dependent DN 91.5 0.21 4.5E-06 50.5 4.0 24 34-57 20-44 (669)
47 PF06677 Auto_anti-p27: Sjogre 91.2 0.23 5.1E-06 33.3 2.8 38 143-191 4-41 (41)
48 PF05876 Terminase_GpA: Phage 91.1 0.13 2.8E-06 50.5 2.1 49 151-199 195-244 (557)
49 PF13717 zinc_ribbon_4: zinc-r 91.0 0.17 3.7E-06 32.7 2.0 33 157-194 3-35 (36)
50 PF07282 OrfB_Zn_ribbon: Putat 90.9 0.17 3.7E-06 35.7 2.1 27 157-193 29-55 (69)
51 smart00661 RPOL9 RNA polymeras 90.9 0.26 5.6E-06 32.9 2.8 34 158-199 2-35 (52)
52 COG5349 Uncharacterized protei 90.5 0.093 2E-06 43.1 0.4 33 155-198 20-54 (126)
53 PRK00464 nrdR transcriptional 89.8 0.24 5.3E-06 41.5 2.4 37 158-194 2-38 (154)
54 COG3877 Uncharacterized protei 89.7 0.29 6.2E-06 39.7 2.6 37 156-206 6-44 (122)
55 PF03367 zf-ZPR1: ZPR1 zinc-fi 89.6 0.16 3.4E-06 42.6 1.1 21 149-169 23-43 (161)
56 PF03604 DNA_RNApol_7kD: DNA d 89.4 0.22 4.9E-06 31.7 1.5 29 158-197 2-30 (32)
57 TIGR03655 anti_R_Lar restricti 89.1 0.36 7.9E-06 33.1 2.5 36 158-196 3-38 (53)
58 smart00709 Zpr1 Duplicated dom 88.6 0.24 5.1E-06 41.7 1.5 22 148-169 21-42 (160)
59 PF01096 TFIIS_C: Transcriptio 88.4 0.37 8.1E-06 31.5 2.0 34 158-193 2-37 (39)
60 PRK00432 30S ribosomal protein 88.4 0.33 7.2E-06 33.6 1.8 28 155-193 19-46 (50)
61 PF12773 DZR: Double zinc ribb 88.2 0.22 4.7E-06 33.2 0.9 25 159-194 15-39 (50)
62 smart00440 ZnF_C2C2 C2C2 Zinc 87.6 0.52 1.1E-05 31.0 2.3 34 158-193 2-37 (40)
63 PF10083 DUF2321: Uncharacteri 87.6 0.28 6.1E-06 41.7 1.3 38 157-195 40-79 (158)
64 PRK12495 hypothetical protein; 87.5 0.43 9.4E-06 42.6 2.5 42 142-195 28-69 (226)
65 PRK14892 putative transcriptio 86.9 0.51 1.1E-05 37.1 2.3 31 158-195 23-53 (99)
66 COG0272 Lig NAD-dependent DNA 86.8 0.67 1.5E-05 47.0 3.7 25 35-59 23-48 (667)
67 PF04216 FdhE: Protein involve 85.9 0.92 2E-05 40.6 3.8 65 130-198 146-211 (290)
68 PRK14714 DNA polymerase II lar 85.9 0.49 1.1E-05 51.0 2.3 46 152-200 663-708 (1337)
69 PF07754 DUF1610: Domain of un 85.9 0.33 7.2E-06 29.3 0.6 11 154-164 14-24 (24)
70 COG1096 Predicted RNA-binding 85.8 0.62 1.3E-05 40.6 2.5 43 149-208 142-184 (188)
71 PRK03824 hypA hydrogenase nick 85.5 0.89 1.9E-05 37.0 3.2 18 182-199 105-123 (135)
72 COG1675 TFA1 Transcription ini 84.5 0.2 4.4E-06 43.0 -1.0 37 158-203 115-151 (176)
73 PF09567 RE_MamI: MamI restric 84.4 0.43 9.2E-06 43.9 0.9 24 157-194 83-106 (314)
74 smart00778 Prim_Zn_Ribbon Zinc 84.1 0.93 2E-05 29.8 2.2 30 156-192 3-33 (37)
75 COG1779 C4-type Zn-finger prot 83.6 0.58 1.2E-05 41.2 1.4 31 155-192 13-51 (201)
76 PRK01103 formamidopyrimidine/5 83.0 1.1 2.4E-05 40.0 2.9 35 150-192 235-273 (274)
77 PF09851 SHOCT: Short C-termin 83.0 1.9 4.1E-05 26.9 3.2 25 31-57 5-30 (31)
78 PF05129 Elf1: Transcription e 82.9 1.1 2.3E-05 33.8 2.4 37 157-197 23-59 (81)
79 COG0675 Transposase and inacti 82.8 0.74 1.6E-05 39.5 1.7 23 157-194 310-332 (364)
80 PF01155 HypA: Hydrogenase exp 82.6 0.69 1.5E-05 36.4 1.3 35 154-200 68-103 (113)
81 PF01807 zf-CHC2: CHC2 zinc fi 82.2 0.69 1.5E-05 35.3 1.2 31 155-192 32-62 (97)
82 PRK00398 rpoP DNA-directed RNA 82.2 1.3 2.9E-05 29.3 2.4 25 183-207 2-26 (46)
83 PRK03681 hypA hydrogenase nick 82.1 1.2 2.6E-05 35.2 2.6 34 155-199 69-103 (114)
84 TIGR00100 hypA hydrogenase nic 82.0 0.81 1.8E-05 36.2 1.5 33 155-199 69-102 (115)
85 TIGR00244 transcriptional regu 81.9 0.95 2.1E-05 38.1 2.0 37 158-194 2-38 (147)
86 PF15616 TerY-C: TerY-C metal 81.7 1.6 3.4E-05 36.1 3.1 44 154-200 75-121 (131)
87 COG3677 Transposase and inacti 80.4 1.6 3.5E-05 35.4 2.8 49 149-202 23-71 (129)
88 cd00729 rubredoxin_SM Rubredox 79.7 1.2 2.7E-05 28.3 1.5 24 158-193 4-27 (34)
89 PRK12380 hydrogenase nickel in 79.4 1.1 2.4E-05 35.4 1.5 33 155-199 69-102 (113)
90 PRK14810 formamidopyrimidine-D 79.3 1.4 3.1E-05 39.4 2.4 27 157-191 245-271 (272)
91 PF12760 Zn_Tnp_IS1595: Transp 79.3 1.8 3.9E-05 28.8 2.3 25 159-192 21-45 (46)
92 PF10263 SprT-like: SprT-like 79.2 1.7 3.8E-05 34.6 2.6 34 155-196 122-155 (157)
93 PHA02942 putative transposase; 78.9 1.4 3E-05 41.5 2.2 26 158-194 327-352 (383)
94 PRK10445 endonuclease VIII; Pr 78.7 1.6 3.4E-05 38.9 2.5 27 157-191 236-262 (263)
95 PRK14559 putative protein seri 78.4 1.1 2.4E-05 45.2 1.6 13 182-194 39-51 (645)
96 TIGR03831 YgiT_finger YgiT-typ 78.4 1.3 2.8E-05 28.4 1.3 9 186-194 34-42 (46)
97 cd00350 rubredoxin_like Rubred 78.3 1.4 3E-05 27.7 1.4 23 158-192 3-25 (33)
98 COG1998 RPS31 Ribosomal protei 77.3 1.3 2.9E-05 31.2 1.2 29 154-193 17-46 (51)
99 TIGR00577 fpg formamidopyrimid 77.2 1.8 3.8E-05 38.8 2.3 34 150-191 235-272 (272)
100 PF08274 PhnA_Zn_Ribbon: PhnA 76.4 2.2 4.7E-05 26.9 1.9 27 157-194 3-29 (30)
101 smart00400 ZnF_CHCC zinc finge 76.4 1.4 3.1E-05 30.1 1.2 30 156-192 2-31 (55)
102 PF09297 zf-NADH-PPase: NADH p 76.3 2.2 4.9E-05 26.4 2.0 26 158-193 5-30 (32)
103 PF06906 DUF1272: Protein of u 76.2 1.2 2.5E-05 32.2 0.7 13 155-167 40-52 (57)
104 PF09986 DUF2225: Uncharacteri 75.8 2.2 4.7E-05 37.1 2.4 11 158-168 7-17 (214)
105 PF14206 Cys_rich_CPCC: Cystei 75.7 1.9 4.2E-05 32.6 1.8 27 156-191 1-27 (78)
106 PRK04023 DNA polymerase II lar 75.6 1.8 4E-05 46.0 2.2 33 2-34 477-514 (1121)
107 PRK13945 formamidopyrimidine-D 75.6 2 4.4E-05 38.6 2.3 26 158-191 256-281 (282)
108 TIGR00155 pqiA_fam integral me 75.3 4.7 0.0001 38.3 4.8 28 158-198 217-244 (403)
109 PRK00241 nudC NADH pyrophospha 75.2 4.2 9E-05 36.2 4.1 27 157-193 100-126 (256)
110 COG5257 GCD11 Translation init 75.0 2.2 4.9E-05 40.8 2.5 38 157-207 58-95 (415)
111 PF08996 zf-DNA_Pol: DNA Polym 75.0 1.3 2.8E-05 37.6 0.8 46 148-194 10-55 (188)
112 COG1867 TRM1 N2,N2-dimethylgua 74.2 1.7 3.7E-05 41.5 1.5 30 156-196 240-269 (380)
113 COG3813 Uncharacterized protei 74.2 1.3 2.8E-05 33.8 0.6 15 155-169 40-54 (84)
114 PRK14811 formamidopyrimidine-D 74.1 2.3 5.1E-05 38.0 2.3 28 158-193 237-264 (269)
115 PRK04011 peptide chain release 73.2 1.5 3.2E-05 41.7 0.8 35 157-197 329-363 (411)
116 PF08273 Prim_Zn_Ribbon: Zinc- 72.9 1.5 3.3E-05 29.2 0.6 31 156-192 3-34 (40)
117 PRK12286 rpmF 50S ribosomal pr 72.5 2.5 5.4E-05 30.1 1.6 20 157-191 28-47 (57)
118 TIGR00354 polC DNA polymerase, 72.5 1.9 4.1E-05 45.8 1.4 28 151-194 620-647 (1095)
119 PF14205 Cys_rich_KTR: Cystein 72.2 5.3 0.00011 28.7 3.2 43 159-205 7-49 (55)
120 COG4306 Uncharacterized protei 71.3 2.5 5.5E-05 35.4 1.7 38 158-196 41-80 (160)
121 PRK14890 putative Zn-ribbon RN 71.3 3.8 8.2E-05 29.7 2.4 32 157-198 8-39 (59)
122 PRK14714 DNA polymerase II lar 71.3 2.3 5E-05 46.1 1.8 13 184-196 709-721 (1337)
123 COG4888 Uncharacterized Zn rib 71.0 3.9 8.5E-05 32.7 2.6 39 157-199 23-61 (104)
124 PF09334 tRNA-synt_1g: tRNA sy 70.7 1.7 3.6E-05 40.9 0.6 9 155-163 135-143 (391)
125 TIGR00595 priA primosomal prot 70.6 3 6.4E-05 40.5 2.3 28 158-195 224-251 (505)
126 PRK12496 hypothetical protein; 70.1 2.1 4.6E-05 35.9 1.0 32 155-198 126-157 (164)
127 PRK04023 DNA polymerase II lar 70.1 2.3 4.9E-05 45.4 1.4 17 44-60 476-492 (1121)
128 COG1996 RPC10 DNA-directed RNA 69.7 3.7 7.9E-05 28.7 2.0 31 158-198 8-38 (49)
129 COG0143 MetG Methionyl-tRNA sy 69.5 2.1 4.5E-05 42.7 0.9 17 149-166 136-152 (558)
130 COG1327 Predicted transcriptio 69.5 2.7 5.8E-05 35.8 1.5 37 158-194 2-38 (156)
131 TIGR01031 rpmF_bact ribosomal 69.0 3.1 6.8E-05 29.3 1.5 20 157-191 27-46 (55)
132 COG5525 Bacteriophage tail ass 68.6 3.9 8.4E-05 41.3 2.6 61 148-208 219-283 (611)
133 COG3058 FdhE Uncharacterized p 68.5 4.2 9E-05 37.9 2.6 37 157-193 186-234 (308)
134 COG1545 Predicted nucleic-acid 68.4 3.9 8.5E-05 33.4 2.2 32 149-194 22-53 (140)
135 TIGR00311 aIF-2beta translatio 68.3 3 6.6E-05 34.2 1.5 32 158-196 99-130 (133)
136 PRK08665 ribonucleotide-diphos 68.2 5.6 0.00012 40.8 3.7 24 157-192 725-748 (752)
137 PHA02540 61 DNA primase; Provi 68.1 6.7 0.00015 36.8 3.9 40 149-193 20-64 (337)
138 PRK00448 polC DNA polymerase I 67.8 3.1 6.8E-05 45.6 1.9 37 159-198 911-947 (1437)
139 PRK03988 translation initiatio 67.0 3.1 6.8E-05 34.3 1.4 32 158-196 104-135 (138)
140 TIGR01405 polC_Gram_pos DNA po 67.0 3.3 7.2E-05 44.7 1.9 38 158-198 685-722 (1213)
141 PF05502 Dynactin_p62: Dynacti 66.8 3.3 7.1E-05 40.4 1.7 44 154-200 24-68 (483)
142 PF13453 zf-TFIIB: Transcripti 66.6 4.4 9.4E-05 26.3 1.7 27 158-192 1-27 (41)
143 TIGR03830 CxxCG_CxxCG_HTH puta 66.6 4.9 0.00011 30.8 2.3 14 181-194 28-41 (127)
144 COG0375 HybF Zn finger protein 66.1 5.6 0.00012 32.2 2.6 34 155-200 69-103 (115)
145 PRK00564 hypA hydrogenase nick 65.7 4.4 9.6E-05 32.2 2.0 34 155-199 70-104 (117)
146 TIGR01384 TFS_arch transcripti 65.7 3.9 8.4E-05 31.1 1.6 27 158-196 2-28 (104)
147 TIGR00686 phnA alkylphosphonat 65.7 4.7 0.0001 32.5 2.1 27 157-194 3-29 (109)
148 COG2816 NPY1 NTP pyrophosphohy 64.9 8.1 0.00017 35.6 3.7 40 139-193 99-138 (279)
149 PRK05580 primosome assembly pr 64.5 4.6 9.9E-05 40.6 2.2 27 158-194 392-418 (679)
150 PF07508 Recombinase: Recombin 64.4 5.6 0.00012 29.1 2.2 19 40-58 83-101 (102)
151 TIGR00155 pqiA_fam integral me 64.0 5.2 0.00011 38.1 2.4 33 158-198 15-47 (403)
152 smart00653 eIF2B_5 domain pres 64.0 4 8.7E-05 32.4 1.4 28 158-192 82-109 (110)
153 PRK13130 H/ACA RNA-protein com 63.8 3.2 6.9E-05 29.7 0.7 11 156-166 17-27 (56)
154 PHA02998 RNA polymerase subuni 63.4 6.5 0.00014 34.5 2.7 37 155-193 142-180 (195)
155 PRK12336 translation initiatio 62.7 5.3 0.00011 34.6 2.0 36 158-200 100-135 (201)
156 PF01873 eIF-5_eIF-2B: Domain 62.6 5 0.00011 32.5 1.8 29 158-193 95-123 (125)
157 smart00709 Zpr1 Duplicated dom 62.1 8.5 0.00018 32.4 3.1 28 158-192 2-37 (160)
158 PF11781 RRN7: RNA polymerase 62.1 5 0.00011 26.0 1.4 26 158-194 10-35 (36)
159 TIGR01391 dnaG DNA primase, ca 62.0 5.5 0.00012 37.7 2.2 31 155-192 33-63 (415)
160 PF03367 zf-ZPR1: ZPR1 zinc-fi 61.6 6.1 0.00013 33.1 2.2 29 158-193 3-39 (161)
161 COG1198 PriA Primosomal protei 61.2 5.7 0.00012 40.9 2.3 73 11-84 239-324 (730)
162 PRK14873 primosome assembly pr 61.0 5.8 0.00013 40.2 2.3 67 5-72 176-251 (665)
163 PF04423 Rad50_zn_hook: Rad50 60.2 5.2 0.00011 27.3 1.3 10 186-195 22-31 (54)
164 PF12647 RNHCP: RNHCP domain; 60.0 5.5 0.00012 31.2 1.5 32 158-197 6-37 (92)
165 COG1592 Rubrerythrin [Energy p 59.8 5.6 0.00012 34.0 1.7 25 156-193 134-158 (166)
166 COG0551 TopA Zn-finger domain 59.0 12 0.00025 30.0 3.3 48 150-198 12-75 (140)
167 PRK14715 DNA polymerase II lar 58.9 6 0.00013 43.6 2.0 33 151-199 669-701 (1627)
168 PF06170 DUF983: Protein of un 57.4 4.4 9.6E-05 30.9 0.6 20 150-169 2-21 (86)
169 PRK10220 hypothetical protein; 57.4 8.1 0.00018 31.3 2.1 27 157-194 4-30 (111)
170 PRK09521 exosome complex RNA-b 57.3 9.1 0.0002 32.3 2.5 27 155-192 148-174 (189)
171 PF05605 zf-Di19: Drought indu 56.7 4.1 9E-05 27.7 0.3 35 158-193 4-40 (54)
172 PF11331 DUF3133: Protein of u 56.5 7.8 0.00017 26.7 1.6 37 158-197 8-44 (46)
173 PRK05667 dnaG DNA primase; Val 56.3 7.8 0.00017 38.5 2.3 31 155-192 35-65 (580)
174 COG1656 Uncharacterized conser 56.2 4.7 0.0001 34.6 0.6 24 43-66 9-32 (165)
175 PF14446 Prok-RING_1: Prokaryo 55.9 7.2 0.00016 27.8 1.4 27 155-193 4-30 (54)
176 PF12677 DUF3797: Domain of un 55.5 6.8 0.00015 27.5 1.2 13 156-168 13-25 (49)
177 PRK15103 paraquat-inducible me 55.3 7.3 0.00016 37.3 1.8 26 158-197 223-248 (419)
178 cd07110 ALDH_F10_BADH Arabidop 55.0 37 0.00081 31.9 6.4 68 2-69 240-334 (456)
179 PF09889 DUF2116: Uncharacteri 54.5 5.6 0.00012 28.6 0.7 25 157-195 4-29 (59)
180 PF05907 DUF866: Eukaryotic pr 54.3 7.9 0.00017 32.5 1.6 44 154-197 28-77 (161)
181 PRK01110 rpmF 50S ribosomal pr 54.1 7.4 0.00016 27.9 1.2 19 157-191 28-46 (60)
182 cd02661 Peptidase_C19E A subfa 53.9 15 0.00032 31.4 3.3 25 183-207 181-205 (304)
183 PRK08270 anaerobic ribonucleos 53.9 7.5 0.00016 39.3 1.7 25 157-196 627-651 (656)
184 TIGR02159 PA_CoA_Oxy4 phenylac 53.9 4.8 0.0001 33.4 0.3 35 156-196 105-142 (146)
185 PRK00133 metG methionyl-tRNA s 53.7 6.2 0.00013 39.5 1.1 44 155-200 138-185 (673)
186 COG0266 Nei Formamidopyrimidin 53.6 10 0.00022 34.8 2.3 26 158-191 247-272 (273)
187 PF08209 Sgf11: Sgf11 (transcr 53.4 9.9 0.00021 24.4 1.6 13 183-195 3-15 (33)
188 PF14577 SEO_C: Sieve element 53.0 7 0.00015 35.2 1.2 19 177-195 207-225 (235)
189 PF14319 Zn_Tnp_IS91: Transpos 52.5 9.4 0.0002 30.1 1.7 29 155-193 41-69 (111)
190 PHA02768 hypothetical protein; 52.3 7.9 0.00017 27.6 1.1 43 156-205 5-50 (55)
191 PRK03564 formate dehydrogenase 52.2 19 0.00041 33.6 3.9 13 155-167 186-198 (309)
192 PF02150 RNA_POL_M_15KD: RNA p 51.8 8.1 0.00018 24.7 1.0 28 159-195 4-31 (35)
193 TIGR03676 aRF1/eRF1 peptide ch 51.6 9.7 0.00021 36.3 2.0 36 157-198 321-356 (403)
194 KOG2593 Transcription initiati 51.5 7.1 0.00015 38.0 1.1 49 149-200 121-169 (436)
195 COG3809 Uncharacterized protei 51.3 11 0.00023 29.3 1.8 28 158-193 3-30 (88)
196 PRK14526 adenylate kinase; Pro 51.1 12 0.00027 32.1 2.4 35 157-199 123-157 (211)
197 TIGR00097 HMP-P_kinase phospho 50.8 54 0.0012 28.2 6.3 55 6-68 117-172 (254)
198 PF11793 FANCL_C: FANCL C-term 50.7 5.9 0.00013 28.7 0.3 18 150-167 49-66 (70)
199 PRK09678 DNA-binding transcrip 50.6 27 0.00059 26.0 3.8 47 158-206 3-52 (72)
200 PRK05654 acetyl-CoA carboxylas 50.5 3.4 7.3E-05 37.9 -1.2 37 157-202 28-64 (292)
201 cd02674 Peptidase_C19R A subfa 50.5 17 0.00037 30.0 3.0 26 182-207 102-127 (230)
202 PRK08579 anaerobic ribonucleos 50.5 7.9 0.00017 39.1 1.3 24 156-193 568-591 (625)
203 PF10058 DUF2296: Predicted in 49.9 10 0.00022 26.6 1.4 28 159-192 25-52 (54)
204 TIGR01384 TFS_arch transcripti 49.6 15 0.00032 27.8 2.4 37 156-192 62-98 (104)
205 smart00547 ZnF_RBZ Zinc finger 49.6 8.9 0.00019 22.2 0.9 22 158-193 4-25 (26)
206 cd07114 ALDH_DhaS Uncharacteri 49.5 52 0.0011 30.9 6.5 67 2-68 239-332 (457)
207 CHL00174 accD acetyl-CoA carbo 49.3 3.4 7.3E-05 38.2 -1.4 36 158-202 40-75 (296)
208 COG1241 MCM2 Predicted ATPase 49.1 15 0.00033 37.7 3.0 27 158-190 131-157 (682)
209 TIGR00515 accD acetyl-CoA carb 49.1 3.7 8E-05 37.5 -1.2 33 158-199 28-60 (285)
210 smart00064 FYVE Protein presen 49.0 9.9 0.00022 26.5 1.2 37 147-197 3-39 (68)
211 PF01783 Ribosomal_L32p: Ribos 48.8 10 0.00022 26.5 1.3 20 157-191 27-46 (56)
212 PRK08176 pdxK pyridoxal-pyrido 48.8 43 0.00094 29.5 5.5 53 7-67 143-196 (281)
213 COG0777 AccD Acetyl-CoA carbox 48.4 2.9 6.3E-05 38.7 -2.0 39 158-205 30-68 (294)
214 PF10122 Mu-like_Com: Mu-like 48.4 9.5 0.00021 27.0 1.0 34 158-199 6-39 (51)
215 PF01396 zf-C4_Topoisom: Topoi 47.6 13 0.00028 24.2 1.5 17 185-201 2-18 (39)
216 PRK04351 hypothetical protein; 47.6 18 0.00039 30.1 2.8 34 157-198 113-146 (149)
217 COG1571 Predicted DNA-binding 47.3 9.9 0.00021 36.9 1.3 33 155-198 349-381 (421)
218 COG3357 Predicted transcriptio 47.2 10 0.00022 30.0 1.2 44 139-193 42-85 (97)
219 PRK07591 threonine synthase; V 46.6 14 0.00031 34.9 2.3 31 155-198 17-47 (421)
220 PRK08173 DNA topoisomerase III 46.1 12 0.00026 39.0 1.8 27 156-194 624-650 (862)
221 TIGR00310 ZPR1_znf ZPR1 zinc f 45.8 11 0.00023 32.8 1.2 22 148-169 22-43 (192)
222 smart00132 LIM Zinc-binding do 45.7 14 0.0003 22.0 1.4 36 158-195 1-38 (39)
223 PF02829 3H: 3H domain; Inter 45.4 50 0.0011 25.8 4.8 32 28-60 50-95 (98)
224 COG4530 Uncharacterized protei 45.3 12 0.00026 30.7 1.3 29 155-194 8-36 (129)
225 TIGR00340 zpr1_rel ZPR1-relate 45.2 11 0.00023 32.0 1.0 21 148-168 20-40 (163)
226 PF13597 NRDD: Anaerobic ribon 45.2 11 0.00023 37.3 1.2 25 157-196 492-517 (546)
227 PRK14973 DNA topoisomerase I; 45.1 22 0.00048 37.6 3.5 12 156-167 588-599 (936)
228 PF04502 DUF572: Family of unk 44.7 16 0.00035 33.6 2.3 18 182-199 75-92 (324)
229 PF01363 FYVE: FYVE zinc finge 44.7 14 0.00031 25.7 1.5 39 156-206 9-47 (69)
230 COG1655 Uncharacterized protei 44.6 12 0.00027 34.1 1.4 35 158-192 21-70 (267)
231 COG3478 Predicted nucleic-acid 44.3 11 0.00023 28.1 0.8 43 156-199 4-55 (68)
232 COG1198 PriA Primosomal protei 44.3 17 0.00038 37.5 2.6 39 25-66 229-276 (730)
233 PF03119 DNA_ligase_ZBD: NAD-d 44.2 17 0.00036 22.3 1.5 10 159-168 2-11 (28)
234 PTZ00381 aldehyde dehydrogenas 44.1 55 0.0012 31.7 5.9 65 2-67 226-314 (493)
235 cd07092 ALDH_ABALDH-YdcW Esche 44.0 77 0.0017 29.6 6.7 67 2-68 237-329 (450)
236 cd07120 ALDH_PsfA-ACA09737 Pse 43.9 73 0.0016 30.3 6.6 68 2-69 238-332 (455)
237 smart00731 SprT SprT homologue 43.8 26 0.00056 28.2 3.1 34 156-196 112-145 (146)
238 COG2176 PolC DNA polymerase II 43.6 16 0.00035 40.1 2.3 40 153-195 911-950 (1444)
239 PF08976 DUF1880: Domain of un 43.4 11 0.00024 30.8 0.8 17 1-17 4-22 (118)
240 PLN02766 coniferyl-aldehyde de 43.4 69 0.0015 30.9 6.4 67 2-68 279-372 (501)
241 cd07078 ALDH NAD(P)+ dependent 42.9 80 0.0017 29.0 6.5 66 3-68 217-309 (432)
242 smart00647 IBR In Between Ring 42.9 27 0.00058 23.4 2.6 31 158-196 20-52 (64)
243 PF03833 PolC_DP2: DNA polymer 42.9 8.1 0.00018 40.7 0.0 47 2-48 497-555 (900)
244 PRK08351 DNA-directed RNA poly 42.7 11 0.00025 27.3 0.8 14 158-171 17-32 (61)
245 TIGR01054 rgy reverse gyrase. 42.4 10 0.00022 40.8 0.7 16 154-169 5-20 (1171)
246 TIGR01385 TFSII transcription 42.4 24 0.00051 32.6 2.9 39 156-196 258-298 (299)
247 PF04280 Tim44: Tim44-like dom 42.4 16 0.00034 28.6 1.6 37 23-59 21-62 (147)
248 cd07105 ALDH_SaliADH Salicylal 42.3 79 0.0017 29.6 6.5 68 2-69 221-310 (432)
249 smart00734 ZnF_Rad18 Rad18-lik 42.3 12 0.00026 22.5 0.7 10 158-167 3-12 (26)
250 TIGR00398 metG methionyl-tRNA 42.2 18 0.00039 34.7 2.2 43 155-199 135-181 (530)
251 PRK09263 anaerobic ribonucleos 42.2 19 0.00041 36.9 2.5 26 157-192 642-667 (711)
252 cd01169 HMPP_kinase 4-amino-5- 42.1 1E+02 0.0022 25.7 6.5 54 6-67 118-172 (242)
253 KOG2807 RNA polymerase II tran 41.9 15 0.00033 35.0 1.6 27 158-198 278-304 (378)
254 PF02591 DUF164: Putative zinc 41.4 12 0.00027 25.6 0.7 36 154-194 20-56 (56)
255 PRK12412 pyridoxal kinase; Rev 41.2 88 0.0019 27.3 6.2 56 4-67 120-176 (268)
256 TIGR02827 RNR_anaer_Bdell anae 40.9 17 0.00038 36.5 2.0 22 157-192 533-554 (586)
257 TIGR00595 priA primosomal prot 40.9 20 0.00043 34.9 2.3 18 184-201 222-239 (505)
258 COG0333 RpmF Ribosomal protein 40.6 17 0.00037 26.1 1.4 9 158-166 29-37 (57)
259 cd07115 ALDH_HMSADH_HapE Pseud 40.5 91 0.002 29.3 6.6 66 2-67 237-329 (453)
260 cd00730 rubredoxin Rubredoxin; 40.0 27 0.00058 24.2 2.2 36 158-193 3-43 (50)
261 PLN02278 succinic semialdehyde 39.9 90 0.002 30.1 6.6 66 2-67 280-372 (498)
262 PRK06427 bifunctional hydroxy- 39.9 1E+02 0.0023 26.3 6.4 53 7-67 124-178 (266)
263 PF00641 zf-RanBP: Zn-finger i 39.9 13 0.00028 22.4 0.6 22 158-193 6-27 (30)
264 cd07135 ALDH_F14-YMR110C Sacch 39.7 87 0.0019 29.6 6.4 68 2-69 225-315 (436)
265 PF04328 DUF466: Protein of un 39.3 59 0.0013 23.6 4.1 34 28-61 26-59 (65)
266 PF07295 DUF1451: Protein of u 39.3 19 0.00041 30.0 1.7 30 28-57 17-46 (146)
267 PF06750 DiS_P_DiS: Bacterial 39.3 14 0.0003 28.3 0.8 26 129-167 44-69 (92)
268 TIGR01053 LSD1 zinc finger dom 39.3 24 0.00051 22.3 1.7 11 182-192 17-27 (31)
269 cd07143 ALDH_AldA_AN0554 Asper 39.0 96 0.0021 29.7 6.6 67 2-68 265-358 (481)
270 PF13408 Zn_ribbon_recom: Reco 38.9 24 0.00051 23.4 1.8 18 182-199 3-20 (58)
271 COG1499 NMD3 NMD protein affec 38.7 19 0.0004 34.2 1.7 37 155-191 5-50 (355)
272 cd07144 ALDH_ALD2-YMR170C Sacc 38.6 1.1E+02 0.0023 29.2 6.8 67 2-68 264-358 (484)
273 PF14311 DUF4379: Domain of un 38.3 18 0.00039 24.6 1.2 29 155-190 27-55 (55)
274 COG2991 Uncharacterized protei 38.0 38 0.00082 25.8 2.9 31 126-160 4-34 (77)
275 PRK15398 aldehyde dehydrogenas 38.0 69 0.0015 30.8 5.4 57 2-60 249-316 (465)
276 PF10751 DUF2535: Protein of u 37.9 35 0.00076 26.4 2.8 40 20-59 21-68 (83)
277 PF05280 FlhC: Flagellar trans 37.7 35 0.00075 29.2 3.0 35 149-192 128-162 (175)
278 COG2995 PqiA Uncharacterized p 37.6 22 0.00048 34.5 2.0 33 158-198 20-52 (418)
279 PF13913 zf-C2HC_2: zinc-finge 37.5 16 0.00035 21.6 0.7 9 158-166 4-12 (25)
280 PF01485 IBR: IBR domain; Int 37.4 28 0.00061 23.2 2.0 29 158-194 20-50 (64)
281 PF09855 DUF2082: Nucleic-acid 37.4 38 0.00083 24.6 2.8 42 158-200 2-52 (64)
282 PRK04338 N(2),N(2)-dimethylgua 37.3 22 0.00048 33.5 2.0 32 155-197 243-274 (382)
283 PF06676 DUF1178: Protein of u 37.3 10 0.00022 31.9 -0.2 39 158-197 7-45 (148)
284 cd07089 ALDH_CddD-AldA-like Rh 37.1 1.1E+02 0.0023 29.1 6.5 67 2-68 243-336 (459)
285 PF01921 tRNA-synt_1f: tRNA sy 37.1 21 0.00045 34.0 1.8 45 148-199 166-214 (360)
286 PRK03922 hypothetical protein; 37.0 16 0.00035 29.6 0.9 13 156-168 49-61 (113)
287 PRK08271 anaerobic ribonucleos 36.7 21 0.00045 36.2 1.8 22 157-192 567-588 (623)
288 PRK00762 hypA hydrogenase nick 36.5 30 0.00066 27.7 2.4 38 155-199 69-108 (124)
289 PF06221 zf-C2HC5: Putative zi 36.5 17 0.00037 26.0 0.8 13 156-168 35-47 (57)
290 PF04475 DUF555: Protein of un 36.4 17 0.00037 29.1 0.9 13 156-168 47-59 (102)
291 PRK07111 anaerobic ribonucleos 36.3 21 0.00046 36.7 1.8 21 157-192 681-701 (735)
292 cd07119 ALDH_BADH-GbsA Bacillu 36.1 1.1E+02 0.0023 29.1 6.4 67 2-68 254-347 (482)
293 PF06827 zf-FPG_IleRS: Zinc fi 36.1 26 0.00057 21.1 1.5 26 158-191 3-28 (30)
294 COG4260 Membrane protease subu 36.1 16 0.00036 34.3 0.9 46 19-64 153-213 (345)
295 cd00674 LysRS_core_class_I cat 36.0 30 0.00065 32.5 2.6 44 150-198 163-206 (353)
296 PF09082 DUF1922: Domain of un 36.0 28 0.0006 26.0 1.9 30 158-199 5-34 (68)
297 PRK08115 ribonucleotide-diphos 35.8 18 0.00038 38.1 1.2 29 156-195 827-855 (858)
298 KOG2324 Prolyl-tRNA synthetase 35.7 21 0.00046 34.7 1.6 32 150-192 224-255 (457)
299 PF04135 Nop10p: Nucleolar RNA 35.7 19 0.0004 25.5 0.9 13 155-167 16-28 (53)
300 PF14485 DUF4431: Domain of un 35.5 34 0.00073 23.5 2.2 22 43-67 5-26 (48)
301 cd00065 FYVE FYVE domain; Zinc 35.1 23 0.0005 23.6 1.3 27 158-196 4-30 (57)
302 cd07098 ALDH_F15-22 Aldehyde d 34.9 1.3E+02 0.0027 28.5 6.6 67 1-67 242-335 (465)
303 cd07139 ALDH_AldA-Rv0768 Mycob 34.8 1.4E+02 0.003 28.2 6.9 67 2-68 256-349 (471)
304 KOG2767 Translation initiation 34.8 21 0.00046 34.3 1.4 38 158-201 98-135 (400)
305 cd00114 LIGANc NAD+ dependent 34.6 22 0.00047 32.7 1.4 14 1-14 25-38 (307)
306 PF09930 DUF2162: Predicted tr 34.3 37 0.0008 30.2 2.8 35 131-166 73-115 (224)
307 COG1885 Uncharacterized protei 34.2 21 0.00045 29.0 1.1 14 156-169 49-62 (115)
308 cd07145 ALDH_LactADH_F420-Bios 34.1 1.3E+02 0.0028 28.3 6.5 68 2-69 243-337 (456)
309 PF03833 PolC_DP2: DNA polymer 34.0 14 0.00029 39.1 0.0 18 152-169 651-668 (900)
310 PRK14704 anaerobic ribonucleos 33.9 21 0.00046 36.0 1.3 22 157-193 560-581 (618)
311 PRK14873 primosome assembly pr 33.8 32 0.00068 35.0 2.5 39 25-65 172-219 (665)
312 PF06107 DUF951: Bacterial pro 33.4 41 0.00089 24.3 2.4 45 148-200 3-47 (57)
313 COG1503 eRF1 Peptide chain rel 33.4 22 0.00047 34.5 1.3 34 156-196 327-360 (411)
314 cd04476 RPA1_DBD_C RPA1_DBD_C: 33.4 29 0.00063 28.2 1.8 30 154-194 32-61 (166)
315 PF08063 PADR1: PADR1 (NUC008) 33.3 17 0.00037 25.5 0.4 13 157-169 15-27 (55)
316 cd07100 ALDH_SSADH1_GabD1 Myco 33.3 1.3E+02 0.0029 28.1 6.5 66 2-67 215-307 (429)
317 TIGR02487 NrdD anaerobic ribon 33.3 23 0.0005 35.2 1.5 23 157-193 525-547 (579)
318 PRK11032 hypothetical protein; 33.1 27 0.00058 29.7 1.6 23 159-191 127-149 (160)
319 PRK10090 aldehyde dehydrogenas 33.1 1.3E+02 0.0028 28.4 6.3 68 2-69 191-286 (409)
320 PRK10246 exonuclease subunit S 33.0 18 0.00038 38.3 0.6 9 157-165 504-512 (1047)
321 PF04216 FdhE: Protein involve 33.0 25 0.00053 31.5 1.5 39 156-195 211-249 (290)
322 PRK06393 rpoE DNA-directed RNA 32.6 20 0.00044 26.3 0.7 10 158-167 19-28 (64)
323 PF09332 Mcm10: Mcm10 replicat 32.6 22 0.00048 33.6 1.2 32 158-200 287-318 (344)
324 PRK14530 adenylate kinase; Pro 32.5 26 0.00057 29.3 1.5 35 157-199 127-161 (215)
325 COG3024 Uncharacterized protei 32.4 21 0.00046 26.4 0.8 13 155-167 6-18 (65)
326 PF14789 THDPS_M: Tetrahydrodi 32.3 48 0.001 22.4 2.4 22 45-66 13-34 (41)
327 COG4481 Uncharacterized protei 32.1 10 0.00023 27.5 -0.8 47 148-202 6-52 (60)
328 KOG2906 RNA polymerase III sub 31.9 44 0.00096 26.8 2.6 34 158-199 3-36 (105)
329 COG2260 Predicted Zn-ribbon RN 31.8 23 0.0005 25.7 0.9 10 186-195 19-28 (59)
330 PF14952 zf-tcix: Putative tre 31.8 22 0.00047 24.5 0.7 9 158-166 13-21 (44)
331 COG1579 Zn-ribbon protein, pos 31.7 12 0.00026 33.7 -0.7 48 148-199 186-236 (239)
332 COG3462 Predicted membrane pro 31.5 48 0.001 27.1 2.7 20 36-57 97-116 (117)
333 cd07109 ALDH_AAS00426 Uncharac 31.4 1.6E+02 0.0035 27.7 6.7 67 2-68 237-329 (454)
334 cd01675 RNR_III Class III ribo 31.4 26 0.00057 34.6 1.5 22 158-193 520-541 (555)
335 cd07106 ALDH_AldA-AAD23400 Str 31.2 1.6E+02 0.0035 27.5 6.7 67 2-68 232-325 (446)
336 PRK11613 folP dihydropteroate 31.0 2.4E+02 0.0051 25.8 7.5 104 3-113 72-191 (282)
337 TIGR00108 eRF peptide chain re 31.0 29 0.00063 33.1 1.7 36 157-198 325-360 (409)
338 PRK12860 transcriptional activ 30.9 59 0.0013 28.4 3.4 38 145-191 124-161 (189)
339 PRK11788 tetratricopeptide rep 30.9 29 0.00063 30.5 1.6 21 159-193 357-377 (389)
340 PRK09407 gabD2 succinic semial 30.9 1.5E+02 0.0033 28.7 6.6 67 2-68 272-365 (524)
341 PRK14290 chaperone protein Dna 30.8 51 0.0011 30.7 3.2 27 184-210 205-232 (365)
342 smart00504 Ubox Modified RING 30.4 41 0.0009 22.5 2.0 19 143-166 27-45 (63)
343 PF05120 GvpG: Gas vesicle pro 30.4 84 0.0018 23.8 3.7 27 28-56 34-61 (79)
344 TIGR01222 minC septum site-det 30.4 66 0.0014 27.8 3.7 16 47-62 57-72 (217)
345 PRK06556 vitamin B12-dependent 30.3 30 0.00066 36.8 1.8 23 159-193 927-949 (953)
346 PRK14529 adenylate kinase; Pro 29.9 37 0.00079 29.8 2.0 37 157-199 127-163 (223)
347 PRK12722 transcriptional activ 29.9 73 0.0016 27.8 3.8 39 145-192 124-162 (187)
348 PF13824 zf-Mss51: Zinc-finger 29.4 38 0.00082 24.2 1.6 22 159-193 2-23 (55)
349 smart00746 TRASH metallochaper 29.3 27 0.00058 19.4 0.7 9 159-167 1-9 (39)
350 KOG3457 Sec61 protein transloc 29.2 36 0.00079 26.5 1.6 26 104-129 48-73 (88)
351 PF01653 DNA_ligase_aden: NAD- 29.1 31 0.00067 31.8 1.5 14 1-14 29-42 (315)
352 PF04606 Ogr_Delta: Ogr/Delta- 29.0 31 0.00068 23.0 1.1 14 186-199 1-14 (47)
353 PF10825 DUF2752: Protein of u 29.0 25 0.00054 24.2 0.6 8 158-165 11-18 (52)
354 PLN02674 adenylate kinase 28.9 34 0.00074 30.5 1.7 34 158-199 160-193 (244)
355 PRK12366 replication factor A; 28.8 50 0.0011 33.3 3.0 39 149-203 526-564 (637)
356 PF14471 DUF4428: Domain of un 28.7 16 0.00035 25.2 -0.3 30 158-194 1-30 (51)
357 PF02146 SIR2: Sir2 family; I 28.6 25 0.00054 28.9 0.7 35 157-195 106-140 (178)
358 KOG0435 Leucyl-tRNA synthetase 28.6 31 0.00067 36.1 1.5 46 157-202 437-495 (876)
359 COG2093 DNA-directed RNA polym 28.5 26 0.00056 25.9 0.7 9 159-167 21-29 (64)
360 KOG2703 C4-type Zn-finger prot 28.4 27 0.00058 34.2 1.0 22 149-170 61-82 (460)
361 KOG3716 Carnitine O-acyltransf 28.4 33 0.00072 35.6 1.6 23 28-56 177-199 (764)
362 PRK09457 astD succinylglutamic 28.3 1.9E+02 0.004 27.8 6.6 68 2-69 254-350 (487)
363 COG1594 RPB9 DNA-directed RNA 28.2 46 0.001 26.4 2.2 33 158-198 4-36 (113)
364 PF12162 STAT1_TAZ2bind: STAT1 28.2 43 0.00094 20.2 1.5 12 44-55 10-21 (23)
365 cd07141 ALDH_F1AB_F2_RALDH1 NA 27.8 1.9E+02 0.0041 27.6 6.5 67 2-68 266-359 (481)
366 smart00532 LIGANc Ligase N fam 27.8 33 0.00071 33.3 1.4 22 40-61 166-187 (441)
367 PF03884 DUF329: Domain of unk 27.7 37 0.00079 24.3 1.3 10 157-166 3-12 (57)
368 cd07133 ALDH_CALDH_CalB Conife 27.6 1.9E+02 0.0041 27.3 6.4 68 2-69 218-310 (434)
369 PF05391 Lsm_interact: Lsm int 27.5 34 0.00073 20.2 0.9 9 1-9 10-18 (21)
370 PF05416 Peptidase_C37: Southa 27.5 20 0.00044 35.4 0.0 42 1-50 253-297 (535)
371 cd07101 ALDH_SSADH2_GabD2 Myco 27.4 2E+02 0.0044 27.1 6.6 67 2-68 236-329 (454)
372 TIGR00777 ahpD alkylhydroperox 27.4 16 0.00034 31.7 -0.7 23 37-59 83-105 (177)
373 COG2331 Uncharacterized protei 27.2 13 0.00027 28.6 -1.2 31 157-194 13-43 (82)
374 PF03563 Bunya_G2: Bunyavirus 27.2 54 0.0012 30.4 2.6 53 132-203 214-267 (285)
375 PF12419 DUF3670: SNF2 Helicas 27.1 1.3E+02 0.0029 24.2 4.7 38 1-42 84-125 (141)
376 TIGR00622 ssl1 transcription f 26.8 44 0.00096 27.0 1.8 24 159-196 4-27 (112)
377 PRK14562 haloacid dehalogenase 26.7 89 0.0019 27.0 3.8 42 4-49 58-107 (204)
378 cd07148 ALDH_RL0313 Uncharacte 26.7 2.1E+02 0.0045 27.1 6.6 68 2-69 242-336 (455)
379 cd07097 ALDH_KGSADH-YcbD Bacil 26.5 2.1E+02 0.0046 27.1 6.6 66 2-67 255-347 (473)
380 PF14768 RPA_interact_C: Repli 26.4 48 0.001 24.7 1.8 33 159-205 2-34 (82)
381 TIGR01562 FdhE formate dehydro 26.3 44 0.00096 31.0 2.0 38 156-193 184-233 (305)
382 PRK03564 formate dehydrogenase 26.3 59 0.0013 30.3 2.8 37 156-196 226-264 (309)
383 PF08646 Rep_fac-A_C: Replicat 26.1 49 0.0011 26.3 2.0 29 155-194 17-47 (146)
384 cd07102 ALDH_EDX86601 Uncharac 26.0 2.4E+02 0.0053 26.3 6.9 67 2-68 235-328 (452)
385 cd07112 ALDH_GABALDH-PuuC Esch 25.8 2.3E+02 0.0049 26.9 6.6 65 3-67 246-338 (462)
386 PRK13252 betaine aldehyde dehy 25.6 2.1E+02 0.0046 27.3 6.5 66 2-67 261-353 (488)
387 KOG0909 Peptide:N-glycanase [P 25.6 37 0.00081 33.6 1.4 62 144-205 147-215 (500)
388 PF02005 TRM: N2,N2-dimethylgu 25.6 26 0.00057 33.1 0.3 35 152-197 236-272 (377)
389 cd02663 Peptidase_C19G A subfa 25.3 86 0.0019 27.5 3.5 26 182-207 165-190 (300)
390 PRK12616 pyridoxal kinase; Rev 25.3 2.4E+02 0.0052 24.6 6.3 54 6-67 124-179 (270)
391 PRK08332 ribonucleotide-diphos 25.2 46 0.001 37.7 2.2 32 155-192 1703-1734(1740)
392 cd07091 ALDH_F1-2_Ald2-like AL 25.2 2.4E+02 0.0052 26.7 6.7 67 2-68 262-355 (476)
393 COG0272 Lig NAD-dependent DNA 25.2 35 0.00075 35.1 1.2 25 38-62 169-193 (667)
394 COG0419 SbcC ATPase involved i 25.2 32 0.00069 35.6 0.9 12 156-167 457-468 (908)
395 PF11290 DUF3090: Protein of u 25.1 34 0.00073 29.6 0.9 10 157-166 155-164 (171)
396 PRK12268 methionyl-tRNA synthe 24.9 37 0.00081 32.8 1.3 15 185-199 172-186 (556)
397 TIGR00308 TRM1 tRNA(guanine-26 24.9 50 0.0011 31.2 2.1 33 155-196 232-264 (374)
398 PF01599 Ribosomal_S27: Riboso 24.9 51 0.0011 22.8 1.6 30 153-192 15-46 (47)
399 PF12674 Zn_ribbon_2: Putative 24.5 24 0.00052 26.6 -0.1 32 158-193 2-35 (81)
400 PRK09847 gamma-glutamyl-gamma- 24.4 2.2E+02 0.0048 27.4 6.4 65 2-67 278-370 (494)
401 TIGR01496 DHPS dihydropteroate 24.2 2.3E+02 0.005 25.2 6.0 61 3-66 57-124 (257)
402 PRK05582 DNA topoisomerase I; 24.1 80 0.0017 31.7 3.4 14 185-198 612-625 (650)
403 PF09845 DUF2072: Zn-ribbon co 24.1 39 0.00085 28.1 1.1 19 153-172 17-35 (131)
404 PRK06319 DNA topoisomerase I/S 24.0 81 0.0018 33.0 3.5 16 184-199 645-660 (860)
405 cd07118 ALDH_SNDH Gluconobacte 23.8 2.6E+02 0.0055 26.5 6.6 67 2-68 239-332 (454)
406 cd07113 ALDH_PADH_NahF Escheri 23.8 2.4E+02 0.0052 26.8 6.5 67 2-68 261-354 (477)
407 PF04828 GFA: Glutathione-depe 23.7 56 0.0012 23.0 1.7 20 178-197 42-61 (92)
408 TIGR00575 dnlj DNA ligase, NAD 23.7 42 0.00092 34.0 1.4 14 1-14 20-33 (652)
409 PF02748 PyrI_C: Aspartate car 23.6 31 0.00068 24.0 0.3 38 155-197 7-48 (52)
410 COG5319 Uncharacterized protei 23.4 26 0.00056 29.4 -0.1 31 163-193 11-41 (142)
411 cd07130 ALDH_F7_AASADH NAD+-de 23.4 2.7E+02 0.0059 26.5 6.7 68 2-69 255-349 (474)
412 PRK00279 adk adenylate kinase; 23.3 52 0.0011 27.5 1.7 34 157-198 128-161 (215)
413 KOG1779 40s ribosomal protein 23.3 1.3E+02 0.0027 23.4 3.6 45 154-207 32-76 (84)
414 PRK07956 ligA NAD-dependent DN 23.3 44 0.00094 34.0 1.4 24 39-62 170-193 (665)
415 PRK05452 anaerobic nitric oxid 23.3 51 0.0011 31.9 1.8 37 157-193 426-467 (479)
416 TIGR01780 SSADH succinate-semi 23.3 2.4E+02 0.0051 26.6 6.2 67 2-68 238-331 (448)
417 PRK09401 reverse gyrase; Revie 23.3 32 0.0007 37.2 0.5 15 154-168 5-19 (1176)
418 cd07099 ALDH_DDALDH Methylomon 23.2 2.8E+02 0.006 26.0 6.7 68 2-69 237-331 (453)
419 COG1105 FruK Fructose-1-phosph 23.0 74 0.0016 29.7 2.8 54 42-95 109-180 (310)
420 PRK07218 replication factor A; 23.0 42 0.00091 32.5 1.2 21 157-193 298-318 (423)
421 PF08194 DIM: DIM protein; In 23.0 63 0.0014 21.4 1.7 14 149-162 22-35 (36)
422 PRK05756 pyridoxamine kinase; 22.9 2.1E+02 0.0046 24.9 5.6 53 7-67 129-182 (286)
423 cd07142 ALDH_F2BC Arabidosis a 22.8 2.7E+02 0.0058 26.5 6.5 67 2-68 262-355 (476)
424 TIGR00357 methionine-R-sulfoxi 22.8 53 0.0011 27.3 1.6 37 158-194 42-99 (134)
425 PF07295 DUF1451: Protein of u 22.7 60 0.0013 27.0 1.9 25 159-193 115-139 (146)
426 PRK10996 thioredoxin 2; Provis 22.7 62 0.0013 25.6 2.0 31 157-195 3-33 (139)
427 PF10609 ParA: ParA/MinD ATPas 22.7 30 0.00065 26.3 0.1 13 157-169 66-78 (81)
428 PRK14292 chaperone protein Dna 22.7 93 0.002 28.9 3.4 28 183-210 196-224 (371)
429 PRK08402 replication factor A; 22.6 86 0.0019 29.6 3.2 28 155-192 211-238 (355)
430 PLN02419 methylmalonate-semial 22.6 2.3E+02 0.005 28.6 6.3 66 2-67 368-459 (604)
431 TIGR03216 OH_muco_semi_DH 2-hy 22.6 2.6E+02 0.0056 26.7 6.4 66 2-67 260-352 (481)
432 PRK04860 hypothetical protein; 22.5 51 0.0011 27.7 1.5 19 182-200 141-159 (160)
433 cd07140 ALDH_F1L_FTFDH 10-form 22.4 2.7E+02 0.0059 26.8 6.6 68 2-69 268-362 (486)
434 PF07191 zinc-ribbons_6: zinc- 22.4 86 0.0019 23.4 2.5 39 158-196 3-42 (70)
435 PRK14287 chaperone protein Dna 22.4 1E+02 0.0022 28.9 3.5 28 183-210 194-222 (371)
436 COG4008 Predicted metal-bindin 22.3 66 0.0014 27.1 2.1 18 42-59 89-106 (153)
437 PF12172 DUF35_N: Rubredoxin-l 22.3 59 0.0013 20.3 1.4 28 152-193 7-34 (37)
438 PRK08097 ligB NAD-dependent DN 22.3 47 0.001 33.3 1.4 14 1-14 56-69 (562)
439 KOG2589 Histone tail methylase 22.2 43 0.00093 32.7 1.1 30 163-195 229-258 (453)
440 TIGR03847 conserved hypothetic 22.2 41 0.00089 29.3 0.9 10 157-166 157-166 (177)
441 KOG0393 Ras-related small GTPa 22.2 1.3E+02 0.0029 26.3 4.0 44 40-90 135-178 (198)
442 TIGR03374 ABALDH 1-pyrroline d 22.2 2.7E+02 0.0059 26.6 6.5 67 2-68 256-350 (472)
443 PF05491 RuvB_C: Holliday junc 22.2 68 0.0015 24.3 2.0 22 23-44 6-27 (76)
444 TIGR01562 FdhE formate dehydro 22.1 59 0.0013 30.2 1.9 37 156-196 224-264 (305)
445 KOG1296 Uncharacterized conser 22.0 67 0.0015 27.5 2.1 45 153-197 27-77 (161)
446 COG1773 Rubredoxin [Energy pro 21.8 72 0.0016 22.8 1.9 36 157-192 4-44 (55)
447 PF09237 GAGA: GAGA factor; I 21.8 66 0.0014 23.0 1.7 29 171-199 11-39 (54)
448 PF05209 MinC_N: Septum format 21.7 88 0.0019 23.6 2.5 29 37-65 42-78 (99)
449 PF08863 YolD: YolD-like prote 21.7 2.2E+02 0.0048 20.4 4.6 30 38-67 17-49 (92)
450 COG2023 RPR2 RNase P subunit R 21.6 62 0.0013 26.0 1.7 40 158-199 58-97 (105)
451 COG1341 Predicted GTPase or GT 21.5 62 0.0013 31.3 2.0 108 2-118 236-350 (398)
452 PRK00222 methionine sulfoxide 21.5 56 0.0012 27.4 1.5 37 158-194 45-102 (142)
453 PRK07219 DNA topoisomerase I; 21.4 95 0.0021 32.2 3.4 15 184-198 688-702 (822)
454 COG3502 Uncharacterized protei 21.3 80 0.0017 25.7 2.3 61 2-65 11-81 (115)
455 TIGR01351 adk adenylate kinase 21.3 62 0.0013 27.0 1.8 34 157-198 125-158 (210)
456 PF14690 zf-ISL3: zinc-finger 21.3 71 0.0015 20.5 1.7 10 186-195 4-13 (47)
457 PLN03086 PRLI-interacting fact 21.2 51 0.0011 33.3 1.4 10 158-167 409-418 (567)
458 PLN02569 threonine synthase 21.2 67 0.0015 31.4 2.2 29 157-198 50-78 (484)
459 PF10415 FumaraseC_C: Fumarase 21.2 65 0.0014 22.5 1.6 20 33-52 18-46 (55)
460 PRK00750 lysK lysyl-tRNA synth 21.1 85 0.0018 30.8 2.9 46 149-198 168-213 (510)
461 PRK11241 gabD succinate-semial 21.0 3.1E+02 0.0067 26.4 6.7 67 2-68 266-359 (482)
462 cd00739 DHPS DHPS subgroup of 21.0 4E+02 0.0086 23.7 6.9 62 3-66 58-126 (257)
463 COG4827 Predicted transporter 21.0 1.2E+02 0.0026 27.5 3.6 14 152-165 107-120 (239)
464 PF12653 DUF3785: Protein of u 20.9 41 0.00089 28.1 0.6 9 157-165 121-129 (138)
465 PRK09406 gabD1 succinic semial 20.8 3.1E+02 0.0067 26.1 6.5 68 2-69 242-336 (457)
466 PRK11827 hypothetical protein; 20.8 82 0.0018 22.8 2.1 30 158-197 10-39 (60)
467 cd07117 ALDH_StaphAldA1 Unchar 20.8 2.9E+02 0.0064 26.4 6.4 66 2-67 255-347 (475)
468 cd00740 MeTr MeTr subgroup of 20.8 1.9E+02 0.004 25.8 4.7 49 19-67 71-126 (252)
469 PF06054 CoiA: Competence prot 20.7 63 0.0014 30.4 1.9 15 158-172 32-46 (375)
470 cd01413 SIR2_Af2 SIR2_Af2: Arc 20.7 46 0.001 28.7 0.9 10 185-194 137-146 (222)
471 PF14129 DUF4296: Domain of un 20.6 91 0.002 23.1 2.4 29 31-59 53-81 (87)
472 PF11746 DUF3303: Protein of u 20.6 1E+02 0.0022 23.5 2.6 34 16-49 48-89 (91)
473 PRK14351 ligA NAD-dependent DN 20.6 53 0.0012 33.6 1.4 23 40-62 195-217 (689)
474 PF04504 DUF573: Protein of un 20.5 1.5E+02 0.0032 22.8 3.6 38 24-61 9-50 (98)
475 PF02701 zf-Dof: Dof domain, z 20.5 31 0.00068 25.4 -0.2 47 158-209 7-53 (63)
476 cd01412 SIRT5_Af1_CobB SIRT5_A 20.5 58 0.0013 27.8 1.4 30 158-194 111-140 (224)
477 PF13597 NRDD: Anaerobic ribon 20.4 41 0.00089 33.2 0.6 17 156-172 504-527 (546)
478 PF01408 GFO_IDH_MocA: Oxidore 20.4 1.5E+02 0.0032 21.8 3.5 61 6-66 51-119 (120)
479 COG1326 Uncharacterized archae 20.4 41 0.00088 29.8 0.5 12 155-166 5-17 (201)
480 COG4311 SoxD Sarcosine oxidase 20.1 46 0.00099 26.4 0.7 10 156-165 3-12 (97)
481 cd02660 Peptidase_C19D A subfa 20.1 93 0.002 27.3 2.7 23 185-207 196-218 (328)
No 1
>PRK00420 hypothetical protein; Validated
Probab=97.56 E-value=7.7e-05 Score=59.69 Aligned_cols=48 Identities=19% Similarity=0.492 Sum_probs=38.9
Q ss_pred HHHHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 141 SQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 141 a~~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
++.+.++.++-...|...||.||.+.|.+ ...+..||+||..+.....
T Consensus 8 ~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~l-----------k~g~~~Cp~Cg~~~~v~~~ 55 (112)
T PRK00420 8 VKKAAELLLKGAKMLSKHCPVCGLPLFEL-----------KDGEVVCPVHGKVYIVKSD 55 (112)
T ss_pred HHHHHHHHHhHHHHccCCCCCCCCcceec-----------CCCceECCCCCCeeeeccH
Confidence 34456667777766889999999999988 5779999999998887653
No 2
>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=97.04 E-value=0.00069 Score=54.56 Aligned_cols=63 Identities=19% Similarity=0.435 Sum_probs=40.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhcc--ceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 126 FIFTWFAAVPLIVYLSQSLTKLIVRE--SLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 126 ~i~~~~~~~Pvi~~~a~~lt~~~~~d--~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
++.+.++++.++..+++...=+|.+= .-++-=.|||||.+.... .+. -.|..|+++|+.|++.
T Consensus 37 ~im~ifmllG~L~~l~S~~VYfwIGmlStkav~V~CP~C~K~TKmL-----------Gr~-D~CM~C~~pLTLd~~l 101 (114)
T PF11023_consen 37 IIMVIFMLLGLLAILASTAVYFWIGMLSTKAVQVECPNCGKQTKML-----------GRV-DACMHCKEPLTLDPSL 101 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcccceeeECCCCCChHhhh-----------chh-hccCcCCCcCccCchh
Confidence 44444555566655555444444322 223444599999998877 223 3899999999999864
No 3
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.93 E-value=0.00091 Score=44.76 Aligned_cols=36 Identities=19% Similarity=0.587 Sum_probs=26.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 203 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i 203 (211)
.|||||.++..- + .....+||.||..+.+...+..+
T Consensus 5 ~C~~CG~~~~~~-------~---~~~~~~Cp~CG~~~~~~~~~~~v 40 (46)
T PRK00398 5 KCARCGREVELD-------E---YGTGVRCPYCGYRILFKERPPVV 40 (46)
T ss_pred ECCCCCCEEEEC-------C---CCCceECCCCCCeEEEccCCCcc
Confidence 599999976542 1 12279999999999988765544
No 4
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.70 E-value=0.0019 Score=47.67 Aligned_cols=44 Identities=32% Similarity=0.680 Sum_probs=37.3
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
|+-.||.||.|-..| + .++..+.|++||+.|.--+..++.+.++
T Consensus 18 l~VkCpdC~N~q~vF-------s--hast~V~C~~CG~~l~~PTGGka~i~~~ 61 (67)
T COG2051 18 LRVKCPDCGNEQVVF-------S--HASTVVTCLICGTTLAEPTGGKAKISGK 61 (67)
T ss_pred EEEECCCCCCEEEEe-------c--cCceEEEecccccEEEecCCCeEEeeee
Confidence 677899999999998 2 2688999999999999998888777654
No 5
>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=96.70 E-value=0.0029 Score=44.78 Aligned_cols=44 Identities=30% Similarity=0.544 Sum_probs=30.1
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC--ceeEeCCC
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN--TRLITLPE 207 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~--~r~i~~pe 207 (211)
+..||.||+++.- .....--.+.|++||..+++-+. .|+-..|+
T Consensus 2 ~~~CP~CG~~iev--------~~~~~GeiV~Cp~CGaeleVv~~~p~~L~~ap~ 47 (54)
T TIGR01206 2 QFECPDCGAEIEL--------ENPELGELVICDECGAELEVVSLDPLRLEAAPE 47 (54)
T ss_pred ccCCCCCCCEEec--------CCCccCCEEeCCCCCCEEEEEeCCCCEEEeCcc
Confidence 5689999998742 11112347899999999999874 44444443
No 6
>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=96.46 E-value=0.0025 Score=40.71 Aligned_cols=36 Identities=25% Similarity=0.569 Sum_probs=23.7
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
+-.||+||+.+..= ...-.....+++|++||..+..
T Consensus 2 ~~~CP~C~~~~~v~-----~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 2 RIQCPNCKTSFRVV-----DSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEEEeC-----HHHcCCCCCEEECCCCCCEEEe
Confidence 44799999986532 1111123348999999998865
No 7
>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=96.37 E-value=0.0028 Score=57.09 Aligned_cols=50 Identities=28% Similarity=0.593 Sum_probs=25.5
Q ss_pred HHHHHHHhhhccceeeecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 140 LSQSLTKLIVRESLILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 140 ~a~~lt~~~~~d~liLkG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
.|..||.-|...+. .|||||.+ ...| +.|+......|++|++.-+..++.
T Consensus 19 ~aRVltE~Wv~~n~----yCP~Cg~~~L~~f-------~NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 19 IARVLTEDWVAENM----YCPNCGSKPLSKF-------ENNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp HHHHHHHHHHHHH-------TTT--SS-EE---------------EEE-TTT--EEEEEEEE
T ss_pred hhHHHHHHHHHHCC----cCCCCCChhHhhc-------cCCCccceeECCCCchHHhhhhhc
Confidence 45566776666554 89999999 4455 666777889999999999998864
No 8
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.27 E-value=0.0017 Score=38.41 Aligned_cols=22 Identities=50% Similarity=1.170 Sum_probs=16.7
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
||+||.|+. .+..-|++||++|
T Consensus 2 Cp~CG~~~~--------------~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIE--------------DDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCC--------------CcCcchhhhCCcC
Confidence 999999974 2233499999875
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.19 E-value=0.002 Score=38.81 Aligned_cols=24 Identities=42% Similarity=0.973 Sum_probs=18.4
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
-.|||||+++ .....-|++||++|
T Consensus 3 ~~Cp~Cg~~~--------------~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEI--------------DPDAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcC--------------CcccccChhhCCCC
Confidence 3699999975 24456799999875
No 10
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.10 E-value=0.0047 Score=44.62 Aligned_cols=42 Identities=31% Similarity=0.689 Sum_probs=34.2
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeC
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL 205 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~ 205 (211)
++=.||.|+.|...| ..++..++|.+||+.|.--+..+....
T Consensus 10 ~~VkCp~C~n~q~vF---------sha~t~V~C~~Cg~~L~~PtGGKa~i~ 51 (59)
T PRK00415 10 LKVKCPDCGNEQVVF---------SHASTVVRCLVCGKTLAEPTGGKAKIK 51 (59)
T ss_pred EEEECCCCCCeEEEE---------ecCCcEEECcccCCCcccCCCcceeee
Confidence 677899999999999 126889999999999987776555544
No 11
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=95.66 E-value=0.013 Score=53.58 Aligned_cols=27 Identities=33% Similarity=0.641 Sum_probs=23.1
Q ss_pred HHHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248 32 EASMAYVA-GKPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 32 eA~~aY~~-G~Pi~sD~efD~Lk~~Lk~ 58 (211)
++-.+||. |+|+|||+|||+|.++|+.
T Consensus 12 ~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 39 (307)
T cd00114 12 KHDYRYYVLDEPSVSDAEYDRLYRELRA 39 (307)
T ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 34567887 9999999999999999974
No 12
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.66 E-value=0.0054 Score=44.55 Aligned_cols=36 Identities=31% Similarity=0.660 Sum_probs=22.4
Q ss_pred cceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 151 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 151 d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
+--+++=+|||||++.-.= - -..-.-.|..+|++||
T Consensus 22 ~e~~v~F~CPnCGe~~I~R--c---~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYR--C---AKCRKLGNPYRCPKCG 57 (61)
T ss_pred CCceeEeeCCCCCceeeeh--h---hhHHHcCCceECCCcC
Confidence 3345788999999554321 1 1222346788999998
No 13
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=95.66 E-value=0.02 Score=40.74 Aligned_cols=44 Identities=18% Similarity=0.458 Sum_probs=30.4
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
++=.||.|+.+...| ..++..+.|.+|++.|.--+..+.+...+
T Consensus 6 m~VkCp~C~~~q~vF---------Sha~t~V~C~~Cg~~L~~PtGGKa~l~~~ 49 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVF---------SHAQTVVKCVVCGTVLAQPTGGKARLTEG 49 (55)
T ss_dssp EEEE-TTT-SEEEEE---------TT-SS-EE-SSSTSEEEEE-SSSEEESSS
T ss_pred EEEECCCCCCeeEEE---------ecCCeEEEcccCCCEecCCCCcCeEEeCC
Confidence 566799999999998 23688999999999998888776665543
No 14
>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=95.47 E-value=0.009 Score=47.43 Aligned_cols=33 Identities=30% Similarity=0.777 Sum_probs=28.5
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.|--||+||+.+|-+ ++.-+.||.||+...-..
T Consensus 8 tKR~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPEP 40 (108)
T ss_pred CcccCCCCcchhccC-----------CCCCccCCCCCCccCccc
Confidence 467899999999998 667788999999988774
No 15
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=95.43 E-value=0.014 Score=57.60 Aligned_cols=50 Identities=34% Similarity=0.529 Sum_probs=33.7
Q ss_pred HHhhhcccCCeeEE---eChhh--H--HHHHH-----HHhhhc-CCCccChHHHHHHHHHHhh
Q 028248 9 LKEELMWEGSSVVM---LSSAE--Q--KFLEA-----SMAYVA-GKPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 9 lkeel~weGssv~~---l~~~E--q--~fLeA-----~~aY~~-G~Pi~sD~efD~Lk~~Lk~ 58 (211)
|---|.|..|--.+ ++..| + +.|.+ -.+||. |+|+|||+|||+|..+|+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~~ 70 (562)
T PRK08097 8 LISLLLWSSSAWAVCPDWSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQ 70 (562)
T ss_pred HHHHHHhcccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 44557888876444 44443 1 11222 246775 9999999999999999973
No 16
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=95.34 E-value=0.0093 Score=48.67 Aligned_cols=43 Identities=26% Similarity=0.583 Sum_probs=28.1
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 202 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~ 202 (211)
.=-||+||.... |- ......+ .+.+..||+||..|+...+...
T Consensus 99 ~Y~Cp~C~~~y~-~~-ea~~~~d--~~~~f~Cp~Cg~~l~~~dn~~~ 141 (147)
T smart00531 99 YYKCPNCQSKYT-FL-EANQLLD--MDGTFTCPRCGEELEEDDNSEP 141 (147)
T ss_pred EEECcCCCCEee-HH-HHHHhcC--CCCcEECCCCCCEEEEcCchhh
Confidence 345999996665 32 2111111 3566999999999999876543
No 17
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=95.20 E-value=0.025 Score=51.86 Aligned_cols=26 Identities=50% Similarity=0.833 Sum_probs=22.0
Q ss_pred HHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248 33 ASMAYVA-GKPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 33 A~~aY~~-G~Pi~sD~efD~Lk~~Lk~ 58 (211)
+..+||. |+|+|||+|||+|.++|+.
T Consensus 17 ~~~~YY~~~~p~isD~eYD~l~~~L~~ 43 (315)
T PF01653_consen 17 HNYAYYNLGEPIISDAEYDQLFRELKA 43 (315)
T ss_dssp HHHHHHTTSSSSSSHHHHHHHHHHHHH
T ss_pred HHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence 3457777 8999999999999999863
No 18
>PLN00209 ribosomal protein S27; Provisional
Probab=94.78 E-value=0.036 Score=42.80 Aligned_cols=45 Identities=13% Similarity=0.348 Sum_probs=36.8
Q ss_pred eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248 154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
-++-.||.|+.+...| ..++..+.|.+||+.|.--+..+...+++
T Consensus 34 Fm~VkCp~C~n~q~VF---------ShA~t~V~C~~Cg~~L~~PTGGKa~l~~g 78 (86)
T PLN00209 34 FMDVKCQGCFNITTVF---------SHSQTVVVCGSCQTVLCQPTGGKARLTEG 78 (86)
T ss_pred EEEEECCCCCCeeEEE---------ecCceEEEccccCCEeeccCCCCeEecCC
Confidence 4788899999999999 12688999999999998888776665543
No 19
>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=94.78 E-value=0.025 Score=36.03 Aligned_cols=30 Identities=20% Similarity=0.462 Sum_probs=22.1
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-.||.||.++....+ ........||.||..
T Consensus 6 y~C~~Cg~~fe~~~~-------~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQK-------ISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEe-------cCCCCCCCCCCCCCc
Confidence 369999998776632 123678889999984
No 20
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=94.76 E-value=0.02 Score=42.08 Aligned_cols=35 Identities=26% Similarity=0.640 Sum_probs=26.4
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-|||.||++.... +..+..-.+.|+-|+..--|..
T Consensus 7 KPCPFCG~~~~~v-------~~~~g~~~v~C~~CgA~~~~~~ 41 (64)
T PRK09710 7 KPCPFCGCPSVTV-------KAISGYYRAKCNGCESRTGYGG 41 (64)
T ss_pred cCCCCCCCceeEE-------EecCceEEEEcCCCCcCccccc
Confidence 4999999998876 2223466799999999766554
No 21
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=94.66 E-value=0.029 Score=46.25 Aligned_cols=39 Identities=26% Similarity=0.654 Sum_probs=32.0
Q ss_pred HHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 143 SLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 143 ~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.+.++.++-+..|--.||-||.+.|-. +.++-||+||..
T Consensus 15 ~iA~lLl~GAkML~~hCp~Cg~PLF~K------------dG~v~CPvC~~~ 53 (131)
T COG1645 15 KIAELLLQGAKMLAKHCPKCGTPLFRK------------DGEVFCPVCGYR 53 (131)
T ss_pred HHHHHHHhhhHHHHhhCcccCCcceee------------CCeEECCCCCce
Confidence 445777888877888999999999885 567889999953
No 22
>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=94.61 E-value=0.037 Score=55.40 Aligned_cols=29 Identities=31% Similarity=0.556 Sum_probs=24.5
Q ss_pred HHHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248 30 FLEASMAYVA-GKPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 30 fLeA~~aY~~-G~Pi~sD~efD~Lk~~Lk~ 58 (211)
.-++..+||. |+|+|||+|||+|.++|+.
T Consensus 5 l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 34 (652)
T TIGR00575 5 IRHHDYRYYVLDEPSISDAEYDRLYRELQE 34 (652)
T ss_pred HHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 3445677887 9999999999999999974
No 23
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=94.55 E-value=0.045 Score=42.18 Aligned_cols=46 Identities=13% Similarity=0.423 Sum_probs=37.3
Q ss_pred eeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248 153 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 153 liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
--++-.||.|+.+...| ..++..+.|.+||+.|.--+..+.+.+++
T Consensus 32 ~Fm~VkCp~C~n~q~VF---------ShA~t~V~C~~Cg~~L~~PTGGKa~l~~g 77 (85)
T PTZ00083 32 YFMDVKCPGCSQITTVF---------SHAQTVVLCGGCSSQLCQPTGGKAKLTEG 77 (85)
T ss_pred eEEEEECCCCCCeeEEE---------ecCceEEEccccCCEeeccCCCCeEecCC
Confidence 34788899999999999 12688999999999998888777766543
No 24
>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=94.55 E-value=0.029 Score=37.02 Aligned_cols=32 Identities=31% Similarity=0.827 Sum_probs=23.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-||+||.....+ + ..+.+.-|++||..+.-+.
T Consensus 2 ~Cp~Cg~~~~~~------D---~~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 2 KCPNCGSKEIVF------D---PERGELVCPNCGLVLEENI 33 (43)
T ss_dssp SBTTTSSSEEEE------E---TTTTEEEETTT-BBEE-TT
T ss_pred CCcCCcCCceEE------c---CCCCeEECCCCCCEeeccc
Confidence 499999987433 1 2578889999999998654
No 25
>smart00532 LIGANc Ligase N family.
Probab=94.54 E-value=0.036 Score=53.19 Aligned_cols=26 Identities=42% Similarity=0.714 Sum_probs=22.4
Q ss_pred HHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248 33 ASMAYVA-GKPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 33 A~~aY~~-G~Pi~sD~efD~Lk~~Lk~ 58 (211)
+-.+||. |+|+|||+|||+|.++|+.
T Consensus 15 ~~~~YY~~~~p~IsD~eYD~L~~eL~~ 41 (441)
T smart00532 15 HDYRYYVLDAPIISDAEYDRLMRELKE 41 (441)
T ss_pred HHHHHHhcCCCCCChHHHHHHHHHHHH
Confidence 3456886 9999999999999999973
No 26
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.47 E-value=0.043 Score=55.09 Aligned_cols=26 Identities=38% Similarity=0.615 Sum_probs=22.8
Q ss_pred HHHhhh-cCCCccChHHHHHHHHHHhh
Q 028248 33 ASMAYV-AGKPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 33 A~~aY~-~G~Pi~sD~efD~Lk~~Lk~ 58 (211)
+-.+|| .|+|+|||+|||+|.++|+.
T Consensus 19 ~~~~YY~~~~p~IsD~eYD~L~~~L~~ 45 (665)
T PRK07956 19 HAYAYYVLDAPSISDAEYDRLYRELVA 45 (665)
T ss_pred HHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 345788 99999999999999999973
No 27
>PRK05978 hypothetical protein; Provisional
Probab=94.46 E-value=0.018 Score=48.17 Aligned_cols=35 Identities=29% Similarity=0.829 Sum_probs=26.1
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
++|-||+||+.=. |++-+ +-+-.|++||..+++.+
T Consensus 32 l~grCP~CG~G~L--F~g~L-------kv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 32 FRGRCPACGEGKL--FRAFL-------KPVDHCAACGEDFTHHR 66 (148)
T ss_pred HcCcCCCCCCCcc--ccccc-------ccCCCccccCCccccCC
Confidence 7899999998632 33222 45678999999998765
No 28
>PRK02935 hypothetical protein; Provisional
Probab=94.45 E-value=0.049 Score=43.68 Aligned_cols=36 Identities=19% Similarity=0.553 Sum_probs=27.4
Q ss_pred eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCce
Q 028248 154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTR 201 (211)
Q Consensus 154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r 201 (211)
++.-.||||+.+..-. | -.--|..|+++|+.|+...
T Consensus 68 avqV~CP~C~K~TKmL-G-----------rvD~CM~C~~PLTLd~~le 103 (110)
T PRK02935 68 AVQVICPSCEKPTKML-G-----------RVDACMHCNQPLTLDRSLE 103 (110)
T ss_pred ceeeECCCCCchhhhc-c-----------ceeecCcCCCcCCcCcccc
Confidence 4455899999998866 1 1236999999999988654
No 29
>PF14353 CpXC: CpXC protein
Probab=94.30 E-value=0.038 Score=43.58 Aligned_cols=40 Identities=28% Similarity=0.563 Sum_probs=26.2
Q ss_pred CCCCCcccceeeccc-cccccC--------CCCcCceeCCCCCceeEEe
Q 028248 158 PCPNCGTENVSFFGT-ILSISS--------GGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~-i~~v~s--------~~~~~~~kC~~C~~~L~f~ 197 (211)
.||+||++...=+=+ |.+... +++-+.+.||+||....++
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 699999987744323 221111 3455799999999986654
No 30
>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=94.12 E-value=0.031 Score=46.02 Aligned_cols=32 Identities=19% Similarity=0.319 Sum_probs=27.3
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
.|-.||+||+.+|-. ++.-+.||.||+...-.
T Consensus 8 tKr~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 467899999999988 67889999999986555
No 31
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=94.11 E-value=0.011 Score=50.15 Aligned_cols=38 Identities=24% Similarity=0.388 Sum_probs=27.3
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 202 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~ 202 (211)
-=-||||+...... - . -.+...||+||..|++..++..
T Consensus 117 ~Y~Cp~C~~rytf~-e------A--~~~~F~Cp~Cg~~L~~~dn~~~ 154 (178)
T PRK06266 117 FFFCPNCHIRFTFD-E------A--MEYGFRCPQCGEMLEEYDNSEL 154 (178)
T ss_pred EEECCCCCcEEeHH-H------H--hhcCCcCCCCCCCCeecccHHH
Confidence 34599999665433 1 1 2468999999999999876544
No 32
>PHA00626 hypothetical protein
Probab=94.04 E-value=0.041 Score=39.74 Aligned_cols=36 Identities=31% Similarity=0.701 Sum_probs=24.7
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.||+||.....==|.+. .-+++.+|+.||-..+=++
T Consensus 2 ~CP~CGS~~Ivrcg~cr-----~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR-----GWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeeceec-----ccCcceEcCCCCCeechhh
Confidence 59999996544433322 2378999999997766543
No 33
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=94.04 E-value=0.042 Score=35.48 Aligned_cols=29 Identities=31% Similarity=0.773 Sum_probs=17.1
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
||+||.++.-= +..+.++.+..|+.||..
T Consensus 3 C~~CG~~l~~~------ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERR------IPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE--------TT-SS-EEEETTTTEE
T ss_pred cccccChhhhh------cCCCCCccceECCCCCCE
Confidence 99999996433 456678999999999964
No 34
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.95 E-value=0.03 Score=40.54 Aligned_cols=33 Identities=30% Similarity=0.606 Sum_probs=20.1
Q ss_pred eeecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCc
Q 028248 154 ILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 154 iLkG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
+++=.|||||++ +.-= -+--.-.|..+||+||-
T Consensus 23 ~~~F~CPnCG~~~I~RC------~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRC------EKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeec------hhHHhcCCceECCCCCC
Confidence 356688999887 4321 11222357788888873
No 35
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=93.83 E-value=0.051 Score=38.18 Aligned_cols=37 Identities=22% Similarity=0.518 Sum_probs=27.3
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.||.||+.+....-. +.+.-.---+|++|-+++.|+-
T Consensus 2 ~CPyCge~~~~~iD~----s~~~Q~yiEDC~vCC~PI~~~v 38 (52)
T PF14255_consen 2 QCPYCGEPIEILIDP----SAGDQEYIEDCQVCCRPIEVQV 38 (52)
T ss_pred CCCCCCCeeEEEEec----CCCCeeEEeehhhcCCccEEEE
Confidence 599999999988533 2222344458999999998864
No 36
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=93.78 E-value=0.063 Score=36.32 Aligned_cols=30 Identities=30% Similarity=0.829 Sum_probs=24.7
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-|.+||.||..- ....++|++||..+.|-.
T Consensus 4 ~C~~Cg~~~~~~-----------~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 4 ICGECGRENEIK-----------SKDVVRCRECGYRILYKK 33 (44)
T ss_pred ECCCCCCEeecC-----------CCCceECCCCCceEEEEe
Confidence 499999997643 356799999999999876
No 37
>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=93.62 E-value=0.057 Score=35.71 Aligned_cols=28 Identities=29% Similarity=0.723 Sum_probs=22.1
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.|+.||.++-.+. +..+...+.||+||.
T Consensus 7 ~C~~Cg~~fe~~~-------~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQ-------SISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEE-------EcCCCCCCcCCCCCC
Confidence 4999999888773 223378899999998
No 38
>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=93.51 E-value=0.039 Score=33.63 Aligned_cols=23 Identities=35% Similarity=0.949 Sum_probs=17.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.||+|+++|- .+.-.||.||-..
T Consensus 2 ~CP~C~~~V~--------------~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVP--------------ESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCch--------------hhcCcCCCCCCCC
Confidence 5999999983 4456899999653
No 39
>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=93.49 E-value=0.024 Score=47.17 Aligned_cols=38 Identities=26% Similarity=0.479 Sum_probs=27.1
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeE
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 203 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i 203 (211)
=-||+|+.... |--. -.+...||+||..|++..++..|
T Consensus 110 Y~Cp~c~~r~t-f~eA--------~~~~F~Cp~Cg~~L~~~dn~~~i 147 (158)
T TIGR00373 110 FICPNMCVRFT-FNEA--------MELNFTCPRCGAMLDYLDNSEAI 147 (158)
T ss_pred EECCCCCcEee-HHHH--------HHcCCcCCCCCCEeeeccCHHHH
Confidence 35999996544 4211 13689999999999998776543
No 40
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=93.12 E-value=0.074 Score=42.79 Aligned_cols=23 Identities=43% Similarity=1.096 Sum_probs=19.2
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
||+||.+.. ..+.+|++|++.++
T Consensus 1 CPvCg~~l~--------------vt~l~C~~C~t~i~ 23 (113)
T PF09862_consen 1 CPVCGGELV--------------VTRLKCPSCGTEIE 23 (113)
T ss_pred CCCCCCceE--------------EEEEEcCCCCCEEE
Confidence 999998764 35789999999885
No 41
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.11 E-value=0.069 Score=34.54 Aligned_cols=34 Identities=24% Similarity=0.465 Sum_probs=21.8
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
=.||||++...-= ..+=....-+++|++|+....
T Consensus 3 i~CP~C~~~f~v~-----~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVP-----DDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcC-----HHHcccCCcEEECCCCCcEee
Confidence 4699999864321 111123456999999998754
No 42
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=92.77 E-value=0.13 Score=52.09 Aligned_cols=24 Identities=29% Similarity=0.629 Sum_probs=21.1
Q ss_pred Hhhh-cCCCccChHHHHHHHHHHhh
Q 028248 35 MAYV-AGKPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 35 ~aY~-~G~Pi~sD~efD~Lk~~Lk~ 58 (211)
.+|| .|+|+|||++||+|.++|+.
T Consensus 48 ~~YY~~~~p~IsD~eYD~L~~eL~~ 72 (689)
T PRK14351 48 HRYYVEADPVIADRAYDALFARLQA 72 (689)
T ss_pred HHHHhCCCCCCChHHHHHHHHHHHH
Confidence 4687 57999999999999999973
No 43
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=92.63 E-value=0.095 Score=36.26 Aligned_cols=33 Identities=27% Similarity=0.611 Sum_probs=21.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
|||=||......-.......+ ....+.|++||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~--~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYG--MYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCC--CEEEEEcCCCCC
Confidence 899999988877432110000 006799999998
No 44
>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=92.32 E-value=0.14 Score=34.41 Aligned_cols=28 Identities=21% Similarity=0.572 Sum_probs=20.1
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.|++||.++-.+... .+.....||+||.
T Consensus 7 ~C~~Cg~~fe~~~~~-------~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKM-------SDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEec-------CCCCCCCCCCCCC
Confidence 599999877766311 1246678999998
No 45
>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=91.57 E-value=0.097 Score=34.04 Aligned_cols=33 Identities=30% Similarity=0.597 Sum_probs=24.2
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-||+||.--...|.. ....-+|.+||..|.-|.
T Consensus 3 ~C~~Cg~~Yh~~~~p--------P~~~~~Cd~cg~~L~qR~ 35 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNP--------PKVEGVCDNCGGELVQRK 35 (36)
T ss_dssp EETTTTEEEETTTB----------SSTTBCTTTTEBEBEEG
T ss_pred CcCCCCCccccccCC--------CCCCCccCCCCCeeEeCC
Confidence 399999876665533 677889999999887554
No 46
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=91.50 E-value=0.21 Score=50.45 Aligned_cols=24 Identities=29% Similarity=0.463 Sum_probs=20.8
Q ss_pred HHhhh-cCCCccChHHHHHHHHHHh
Q 028248 34 SMAYV-AGKPIMSDEEYDKLKQKLK 57 (211)
Q Consensus 34 ~~aY~-~G~Pi~sD~efD~Lk~~Lk 57 (211)
-.+|| .|+|+|||++||+|.++|+
T Consensus 20 ~~~YY~~~~p~IsD~~YD~L~~eL~ 44 (669)
T PRK14350 20 DKEYYVDSSPSVEDFTYDKALLRLQ 44 (669)
T ss_pred HHHHHhCCCCCCChHHHHHHHHHHH
Confidence 35677 4799999999999999996
No 47
>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=91.16 E-value=0.23 Score=33.25 Aligned_cols=38 Identities=26% Similarity=0.674 Sum_probs=27.8
Q ss_pred HHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 143 SLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 143 ~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
.+.++.++--..|...||.||.+.+.- .+.+.-|++|+
T Consensus 4 ~m~~~LL~G~~ML~~~Cp~C~~PL~~~-----------k~g~~~Cv~C~ 41 (41)
T PF06677_consen 4 KMGEYLLQGWTMLDEHCPDCGTPLMRD-----------KDGKIYCVSCG 41 (41)
T ss_pred HHHHHHHHhHhHhcCccCCCCCeeEEe-----------cCCCEECCCCC
Confidence 345566666666889999999887652 35578899996
No 48
>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=91.11 E-value=0.13 Score=50.48 Aligned_cols=49 Identities=22% Similarity=0.450 Sum_probs=35.4
Q ss_pred cceeeecCCCCCcccceeeccccccccC-CCCcCceeCCCCCceeEEecC
Q 028248 151 ESLILKGPCPNCGTENVSFFGTILSISS-GGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 151 d~liLkG~CPnCg~Ev~aFfg~i~~v~s-~~~~~~~kC~~C~~~L~f~~~ 199 (211)
|----.-|||.||++..-=|..+.-.+. ...+....|+.||+.+.=.-+
T Consensus 195 dqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k 244 (557)
T PF05876_consen 195 DQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDK 244 (557)
T ss_pred CceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHH
Confidence 3334677999999998755666654333 457788999999998875443
No 49
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.05 E-value=0.17 Score=32.65 Aligned_cols=33 Identities=24% Similarity=0.514 Sum_probs=21.4
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
=.||||++...-= .-+=+....+++|++|+...
T Consensus 3 i~Cp~C~~~y~i~-----d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEID-----DEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCC-----HHHCCCCCcEEECCCCCCEe
Confidence 4699999864321 11122456689999999753
No 50
>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=90.94 E-value=0.17 Score=35.75 Aligned_cols=27 Identities=33% Similarity=0.871 Sum_probs=22.0
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-.||+||..+.. ..+.....|++||..
T Consensus 29 q~C~~CG~~~~~----------~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKK----------RRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCccccccc----------ccccceEEcCCCCCE
Confidence 459999999887 236788999999986
No 51
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=90.88 E-value=0.26 Score=32.86 Aligned_cols=34 Identities=24% Similarity=0.591 Sum_probs=22.1
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
-||.||.-+ + .+....++...|+.||-..-.+.+
T Consensus 2 FCp~Cg~~l--~------~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNML--I------PKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCcc--c------cccCCCCCEEECCcCCCeEECCCc
Confidence 399999843 2 222223468899999987655444
No 52
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.49 E-value=0.093 Score=43.05 Aligned_cols=33 Identities=30% Similarity=0.825 Sum_probs=25.7
Q ss_pred eecCCCCCcccc--eeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 155 LKGPCPNCGTEN--VSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 155 LkG~CPnCg~Ev--~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
++|-||+||+-- .+|. +..-.|.+||..+-|.+
T Consensus 20 l~grCP~CGeGrLF~gFL-----------K~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 20 LRGRCPRCGEGRLFRGFL-----------KVVPACEACGLDYGFAD 54 (126)
T ss_pred hcCCCCCCCCchhhhhhc-----------ccCchhhhccccccCCc
Confidence 789999999863 3563 34557999999998865
No 53
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.83 E-value=0.24 Score=41.52 Aligned_cols=37 Identities=19% Similarity=0.533 Sum_probs=23.1
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.||-||.+-+.-.-+..--+++..+-..+|++||...
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 4999999775543222211333444449999999864
No 54
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.67 E-value=0.29 Score=39.69 Aligned_cols=37 Identities=27% Similarity=0.600 Sum_probs=26.4
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE--EecCceeEeCC
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV--YDSNTRLITLP 206 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~--f~~~~r~i~~p 206 (211)
--+||.||.+.- ..+.+|++|++... |+...+...+|
T Consensus 6 ~~~cPvcg~~~i--------------VTeL~c~~~etTVrg~F~~s~F~~Lt~ 44 (122)
T COG3877 6 INRCPVCGRKLI--------------VTELKCSNCETTVRGNFKMSKFEYLTS 44 (122)
T ss_pred CCCCCcccccce--------------eEEEecCCCCceEecceecccccccCH
Confidence 358999999753 35789999999874 55555554444
No 55
>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=89.57 E-value=0.16 Score=42.62 Aligned_cols=21 Identities=29% Similarity=0.649 Sum_probs=13.0
Q ss_pred hccceeeecCCCCCcccceee
Q 028248 149 VRESLILKGPCPNCGTENVSF 169 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aF 169 (211)
+++.+|+...||+||+.+.-.
T Consensus 23 F~evii~sf~C~~CGyk~~ev 43 (161)
T PF03367_consen 23 FKEVIIMSFECEHCGYKNNEV 43 (161)
T ss_dssp TEEEEEEEEE-TTT--EEEEE
T ss_pred CceEEEEEeECCCCCCEeeeE
Confidence 677777777777777777644
No 56
>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=89.42 E-value=0.22 Score=31.71 Aligned_cols=29 Identities=31% Similarity=0.886 Sum_probs=20.4
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
-|..||.+|. + + ....++|++||..+.|.
T Consensus 2 ~C~~Cg~~~~-~-------~---~~~~irC~~CG~RIlyK 30 (32)
T PF03604_consen 2 ICGECGAEVE-L-------K---PGDPIRCPECGHRILYK 30 (32)
T ss_dssp BESSSSSSE--B-------S---TSSTSSBSSSS-SEEBE
T ss_pred CCCcCCCeeE-c-------C---CCCcEECCcCCCeEEEe
Confidence 3889999998 2 2 34568999999887763
No 57
>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=89.15 E-value=0.36 Score=33.14 Aligned_cols=36 Identities=28% Similarity=0.630 Sum_probs=24.1
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
|||-||.+-..|-.. ........-.+|+.||....+
T Consensus 3 PCPfCGg~~~~~~~~---~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRG---FDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEec---cCCCCCEEEEECCCCCCCccc
Confidence 899999988866310 012223445589999988765
No 58
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=88.60 E-value=0.24 Score=41.68 Aligned_cols=22 Identities=32% Similarity=0.628 Sum_probs=17.8
Q ss_pred hhccceeeecCCCCCcccceee
Q 028248 148 IVRESLILKGPCPNCGTENVSF 169 (211)
Q Consensus 148 ~~~d~liLkG~CPnCg~Ev~aF 169 (211)
.+++.+++...||+||+.+.-.
T Consensus 21 ~F~evii~sf~C~~CGyk~~ev 42 (160)
T smart00709 21 YFREVIIMSFECEHCGYRNNEV 42 (160)
T ss_pred CcceEEEEEEECCCCCCccceE
Confidence 4788888888899998887755
No 59
>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=88.38 E-value=0.37 Score=31.48 Aligned_cols=34 Identities=35% Similarity=0.805 Sum_probs=20.4
Q ss_pred CCCCCcccceeeccccccccCC--CCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSG--GTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~--~~~~~~kC~~C~~~ 193 (211)
+||+||.+...|| . .-..+. ..+--..|-+||..
T Consensus 2 ~Cp~Cg~~~a~~~-~-~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHNEAVFF-Q-IQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SSEEEEE-E-ESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCCCeEEEE-E-eeccCCCCCCeEEEEeCCCCCe
Confidence 6999999999887 2 112222 23556789999864
No 60
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=88.35 E-value=0.33 Score=33.60 Aligned_cols=28 Identities=32% Similarity=0.859 Sum_probs=20.0
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
+.--||+||.+ |... ...+..|..||-.
T Consensus 19 ~~~fCP~Cg~~---~m~~--------~~~r~~C~~Cgyt 46 (50)
T PRK00432 19 KNKFCPRCGSG---FMAE--------HLDRWHCGKCGYT 46 (50)
T ss_pred ccCcCcCCCcc---hhec--------cCCcEECCCcCCE
Confidence 45589999987 3211 2368899999965
No 61
>PF12773 DZR: Double zinc ribbon
Probab=88.20 E-value=0.22 Score=33.17 Aligned_cols=25 Identities=36% Similarity=0.808 Sum_probs=14.6
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
||+||+.+. ........|++||+.+
T Consensus 15 C~~CG~~l~-----------~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 15 CPHCGTPLP-----------PPDQSKKICPNCGAEN 39 (50)
T ss_pred ChhhcCChh-----------hccCCCCCCcCCcCCC
Confidence 666666655 1134556677777754
No 62
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=87.62 E-value=0.52 Score=31.02 Aligned_cols=34 Identities=35% Similarity=0.854 Sum_probs=22.9
Q ss_pred CCCCCcccceeeccccccccCC--CCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSG--GTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~--~~~~~~kC~~C~~~ 193 (211)
+||+||...-.||-. -..|. ..+--.+|.+|+-.
T Consensus 2 ~Cp~C~~~~a~~~q~--Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQL--QTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEE--cccCCCCCCeEEEEeCCCCCE
Confidence 699999888888732 22222 23556789999853
No 63
>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=87.59 E-value=0.28 Score=41.69 Aligned_cols=38 Identities=26% Similarity=0.617 Sum_probs=25.1
Q ss_pred cCCCCCcccceeec--cccccccCCCCcCceeCCCCCceeE
Q 028248 157 GPCPNCGTENVSFF--GTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 157 G~CPnCg~Ev~aFf--g~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
-.||||++.+.+.+ -+++.. ++...--.-|||||.+.-
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~-g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGL-GGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHCcCCCCCCCCceecCCeeee-CCCCCCChhHHhCCCCCc
Confidence 36999999998543 234433 233445678999998753
No 64
>PRK12495 hypothetical protein; Provisional
Probab=87.49 E-value=0.43 Score=42.61 Aligned_cols=42 Identities=14% Similarity=0.501 Sum_probs=34.0
Q ss_pred HHHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 142 QSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 142 ~~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
+.+.++.+|-...+---||.||.+++.+ +....|++|++...
T Consensus 28 ~~ma~lL~~gatmsa~hC~~CG~PIpa~------------pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 28 ERMSELLLQGATMTNAHCDECGDPIFRH------------DGQEFCPTCQQPVT 69 (226)
T ss_pred HHHHHHHHhhcccchhhcccccCcccCC------------CCeeECCCCCCccc
Confidence 3456677777777888999999999955 67788999998765
No 65
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=86.91 E-value=0.51 Score=37.11 Aligned_cols=31 Identities=32% Similarity=0.776 Sum_probs=20.7
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
.|||||+... ++.-....-.+.|++||.--.
T Consensus 23 ~CP~Cge~~v-------~v~~~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 23 ECPRCGKVSI-------SVKIKKNIAIITCGNCGLYTE 53 (99)
T ss_pred ECCCCCCeEe-------eeecCCCcceEECCCCCCccC
Confidence 5999995322 223333577899999997643
No 66
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=86.75 E-value=0.67 Score=47.03 Aligned_cols=25 Identities=36% Similarity=0.573 Sum_probs=21.6
Q ss_pred Hhhhc-CCCccChHHHHHHHHHHhhh
Q 028248 35 MAYVA-GKPIMSDEEYDKLKQKLKME 59 (211)
Q Consensus 35 ~aY~~-G~Pi~sD~efD~Lk~~Lk~~ 59 (211)
.+||- ++|+|+|+|||+|.++|+.-
T Consensus 23 ~~Yyv~d~P~VsD~eYD~L~reL~~l 48 (667)
T COG0272 23 YRYYVLDAPSVSDAEYDQLYRELQEL 48 (667)
T ss_pred HHHhccCCCCCChHHHHHHHHHHHHH
Confidence 46666 99999999999999999753
No 67
>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=85.94 E-value=0.92 Score=40.59 Aligned_cols=65 Identities=25% Similarity=0.494 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhccceeeecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 130 WFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 130 ~~~~~Pvi~~~a~~lt~~~~~d~liLkG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
|.++-|+....+..+..-+....---+|-||+||.. +.+.+.. ... ...-...|+.|++.=.|.+
T Consensus 146 ~aaL~~~~~~~a~~l~~~~~~~~~w~~g~CPvCGs~P~~s~l~~---~~~-~G~R~L~Cs~C~t~W~~~R 211 (290)
T PF04216_consen 146 WAALQPFLAALAAALDAALLPPEGWQRGYCPVCGSPPVLSVLRG---GER-EGKRYLHCSLCGTEWRFVR 211 (290)
T ss_dssp HHHHHHHHHHHHHT--TTSSS---TT-SS-TTT---EEEEEEE----------EEEEEETTT--EEE--T
T ss_pred HHHHHHHHHHHHHhccccccccCCccCCcCCCCCCcCceEEEec---CCC-CccEEEEcCCCCCeeeecC
Confidence 455557776666544333333333356999999987 5566422 111 1234456777776665554
No 68
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=85.92 E-value=0.49 Score=51.04 Aligned_cols=46 Identities=24% Similarity=0.411 Sum_probs=27.8
Q ss_pred ceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 152 SLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 152 ~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
.-+-.-.||+||++++..|=..= +........|++||..+..+..+
T Consensus 663 VEV~~rkCPkCG~~t~~~fCP~C---Gs~te~vy~CPsCGaev~~des~ 708 (1337)
T PRK14714 663 VEVGRRRCPSCGTETYENRCPDC---GTHTEPVYVCPDCGAEVPPDESG 708 (1337)
T ss_pred EEEEEEECCCCCCccccccCccc---CCcCCCceeCccCCCccCCCccc
Confidence 45566789999999887653321 11122345677777766655433
No 69
>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=85.86 E-value=0.33 Score=29.33 Aligned_cols=11 Identities=55% Similarity=1.259 Sum_probs=8.7
Q ss_pred eeecCCCCCcc
Q 028248 154 ILKGPCPNCGT 164 (211)
Q Consensus 154 iLkG~CPnCg~ 164 (211)
++.=+|||||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45678999996
No 70
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=85.77 E-value=0.62 Score=40.61 Aligned_cols=43 Identities=28% Similarity=0.557 Sum_probs=32.3
Q ss_pred hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCCC
Q 028248 149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPEG 208 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~peg 208 (211)
.+|.=.++.-|++|+++..- .-++.+|||||.. .+|.|-.+=+
T Consensus 142 ~~dlGVI~A~CsrC~~~L~~------------~~~~l~Cp~Cg~t-----EkRKia~~y~ 184 (188)
T COG1096 142 GNDLGVIYARCSRCRAPLVK------------KGNMLKCPNCGNT-----EKRKIAKDYG 184 (188)
T ss_pred CCcceEEEEEccCCCcceEE------------cCcEEECCCCCCE-----Eeeeeccccc
Confidence 68887799999999998754 2568899999963 4566655433
No 71
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=85.54 E-value=0.89 Score=36.99 Aligned_cols=18 Identities=17% Similarity=0.547 Sum_probs=12.6
Q ss_pred cCceeCCCCCce-eEEecC
Q 028248 182 TNTINCSNCGTT-MVYDSN 199 (211)
Q Consensus 182 ~~~~kC~~C~~~-L~f~~~ 199 (211)
.....||.||+. +.....
T Consensus 105 ~~~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 105 HAFLKCPKCGSRDFEIVKG 123 (135)
T ss_pred ccCcCCcCCCCCCcEEecC
Confidence 345679999975 666654
No 72
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=84.48 E-value=0.2 Score=42.98 Aligned_cols=37 Identities=24% Similarity=0.551 Sum_probs=27.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 203 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i 203 (211)
.||||...+. |= +. ..+...||.||..|++..+.+.|
T Consensus 115 ~C~~~~~r~s-fd------eA--~~~~F~Cp~Cg~~L~~~d~s~~i 151 (176)
T COG1675 115 VCPNCHVKYS-FD------EA--MELGFTCPKCGEDLEEYDSSEEI 151 (176)
T ss_pred eCCCCCCccc-HH------HH--HHhCCCCCCCCchhhhccchHHH
Confidence 5999987754 30 11 25668999999999998877654
No 73
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=84.35 E-value=0.43 Score=43.86 Aligned_cols=24 Identities=42% Similarity=1.003 Sum_probs=20.7
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
|.|-|||.+|..+ +..||||++.=
T Consensus 83 ~~C~~CGa~V~~~--------------e~~Cp~C~Stn 106 (314)
T PF09567_consen 83 GKCNNCGANVSRL--------------EESCPNCGSTN 106 (314)
T ss_pred hhhccccceeeeh--------------hhcCCCCCccc
Confidence 7899999999888 56899999763
No 74
>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=84.12 E-value=0.93 Score=29.81 Aligned_cols=30 Identities=43% Similarity=0.978 Sum_probs=18.7
Q ss_pred ecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCc
Q 028248 156 KGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 156 kG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.+|||+||-. -|.| .+ ...+...-|..|+.
T Consensus 3 ~~pCP~CGG~DrFr~-~d------~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRF-DD------KDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCcccccc-cc------CCCCcCEEeCCCCC
Confidence 5899999763 3343 11 12346678888863
No 75
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=83.62 E-value=0.58 Score=41.20 Aligned_cols=31 Identities=35% Similarity=0.821 Sum_probs=22.8
Q ss_pred eecCCCCCccccee--------eccccccccCCCCcCceeCCCCCc
Q 028248 155 LKGPCPNCGTENVS--------FFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 155 LkG~CPnCg~Ev~a--------Ffg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
-...||+||....+ |||.++ -....|.+||-
T Consensus 13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~-------i~t~~C~~CgY 51 (201)
T COG1779 13 TRIDCPVCGGTLKAHMYLYDIPYFGEVL-------ISTGVCERCGY 51 (201)
T ss_pred eeecCCcccceeeEEEeeecCCccceEE-------EEEEEccccCC
Confidence 56789999986543 677765 45678999984
No 76
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=83.00 E-value=1.1 Score=40.01 Aligned_cols=35 Identities=31% Similarity=0.637 Sum_probs=24.9
Q ss_pred ccceeeec----CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 150 RESLILKG----PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 150 ~d~liLkG----~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
++.+-+.| |||+||+.+.... +. .+...=||+|..
T Consensus 235 ~~~l~Vy~R~g~pC~~Cg~~I~~~~-----~~---gR~t~~CP~CQ~ 273 (274)
T PRK01103 235 QQSLQVYGREGEPCRRCGTPIEKIK-----QG---GRSTFFCPRCQK 273 (274)
T ss_pred cceeEEcCCCCCCCCCCCCeeEEEE-----EC---CCCcEECcCCCC
Confidence 44455665 7999999987541 11 478889999974
No 77
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=82.99 E-value=1.9 Score=26.88 Aligned_cols=25 Identities=40% Similarity=0.590 Sum_probs=19.8
Q ss_pred HHHHHh-hhcCCCccChHHHHHHHHHHh
Q 028248 31 LEASMA-YVAGKPIMSDEEYDKLKQKLK 57 (211)
Q Consensus 31 LeA~~a-Y~~G~Pi~sD~efD~Lk~~Lk 57 (211)
|+.+.. |.+| +||++||++.|.+|.
T Consensus 5 L~~L~~l~~~G--~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 5 LEKLKELYDKG--EISEEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHHcC--CCCHHHHHHHHHHHh
Confidence 455555 7777 799999999999884
No 78
>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=82.88 E-value=1.1 Score=33.84 Aligned_cols=37 Identities=22% Similarity=0.470 Sum_probs=20.2
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
=.||.|+.+...=.. +........+.|.+||..-+++
T Consensus 23 F~CPfC~~~~sV~v~----idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVK----IDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp ---TTT--SS-EEEE----EETTTTEEEEEESSS--EEEEE
T ss_pred EcCCcCCCCCeEEEE----EEccCCEEEEEecCCCCeEEEc
Confidence 379999966554432 2444678899999998776654
No 79
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.82 E-value=0.74 Score=39.49 Aligned_cols=23 Identities=30% Similarity=0.928 Sum_probs=18.1
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
-.||+||. + +.....|++||...
T Consensus 310 ~~C~~cg~----~-----------~~r~~~C~~cg~~~ 332 (364)
T COG0675 310 KTCPCCGH----L-----------SGRLFKCPRCGFVH 332 (364)
T ss_pred ccccccCC----c-----------cceeEECCCCCCee
Confidence 45999999 2 45678999999764
No 80
>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=82.57 E-value=0.69 Score=36.38 Aligned_cols=35 Identities=23% Similarity=0.451 Sum_probs=21.0
Q ss_pred eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCcee-EEecCc
Q 028248 154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM-VYDSNT 200 (211)
Q Consensus 154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L-~f~~~~ 200 (211)
-+++-|++||.+...= .+...||.||+.- ...+..
T Consensus 68 p~~~~C~~Cg~~~~~~------------~~~~~CP~Cgs~~~~i~~G~ 103 (113)
T PF01155_consen 68 PARARCRDCGHEFEPD------------EFDFSCPRCGSPDVEIISGR 103 (113)
T ss_dssp --EEEETTTS-EEECH------------HCCHH-SSSSSS-EEEEESS
T ss_pred CCcEECCCCCCEEecC------------CCCCCCcCCcCCCcEEccCC
Confidence 3678899999986422 3346799999973 555543
No 81
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=82.23 E-value=0.69 Score=35.31 Aligned_cols=31 Identities=29% Similarity=0.598 Sum_probs=17.6
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
..+.||-|++...+|. |. .+.+..+|+.||.
T Consensus 32 ~~~~CPfH~d~~pS~~-----i~--~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 32 YRCLCPFHDDKTPSFS-----IN--PDKNRFKCFGCGK 62 (97)
T ss_dssp EEE--SSS--SS--EE-----EE--TTTTEEEETTT--
T ss_pred EEEECcCCCCCCCceE-----EE--CCCCeEEECCCCC
Confidence 5789999999888773 32 2567899999996
No 82
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.17 E-value=1.3 Score=29.34 Aligned_cols=25 Identities=20% Similarity=0.457 Sum_probs=20.7
Q ss_pred CceeCCCCCceeEEecCceeEeCCC
Q 028248 183 NTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 183 ~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
...+|++||..++++.....++-|.
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~ 26 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPY 26 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCC
Confidence 3579999999999998766777775
No 83
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=82.14 E-value=1.2 Score=35.21 Aligned_cols=34 Identities=15% Similarity=0.323 Sum_probs=21.1
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce-eEEecC
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT-MVYDSN 199 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~-L~f~~~ 199 (211)
..+-|++||+++..- ..+...||.||.. +...+.
T Consensus 69 ~~~~C~~Cg~~~~~~-----------~~~~~~CP~Cgs~~~~i~~G 103 (114)
T PRK03681 69 AECWCETCQQYVTLL-----------TQRVRRCPQCHGDMLRIVAD 103 (114)
T ss_pred cEEEcccCCCeeecC-----------CccCCcCcCcCCCCcEEccC
Confidence 567899999632211 1233679999975 444443
No 84
>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=81.95 E-value=0.81 Score=36.21 Aligned_cols=33 Identities=15% Similarity=0.450 Sum_probs=21.7
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce-eEEecC
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT-MVYDSN 199 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~-L~f~~~ 199 (211)
+.+-|++||++.. . ..+...||.||.. ....+.
T Consensus 69 ~~~~C~~Cg~~~~-~-----------~~~~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 69 VECECEDCSEEVS-P-----------EIDLYRCPKCHGIMLQVRAG 102 (115)
T ss_pred cEEEcccCCCEEe-c-----------CCcCccCcCCcCCCcEEecC
Confidence 6789999994332 2 2335679999985 355544
No 85
>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=81.85 E-value=0.95 Score=38.09 Aligned_cols=37 Identities=19% Similarity=0.456 Sum_probs=28.8
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.||-||.+...-.-+=.+..++.-+-+-+|.+||...
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 4999999988876555555666667788999999864
No 86
>PF15616 TerY-C: TerY-C metal binding domain
Probab=81.68 E-value=1.6 Score=36.07 Aligned_cols=44 Identities=23% Similarity=0.641 Sum_probs=29.9
Q ss_pred eeecCCCCCccc-ceee--ccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 154 ILKGPCPNCGTE-NVSF--FGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 154 iLkG~CPnCg~E-v~aF--fg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
+=..-||.||.+ .++- =|-++=+. ....+-||.||....|....
T Consensus 75 ~g~PgCP~CGn~~~fa~C~CGkl~Ci~---g~~~~~CPwCg~~g~~~~~~ 121 (131)
T PF15616_consen 75 IGAPGCPHCGNQYAFAVCGCGKLFCID---GEGEVTCPWCGNEGSFGAGD 121 (131)
T ss_pred cCCCCCCCCcChhcEEEecCCCEEEeC---CCCCEECCCCCCeeeecccC
Confidence 344889999998 2221 12233333 36699999999999998853
No 87
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=80.36 E-value=1.6 Score=35.41 Aligned_cols=49 Identities=22% Similarity=0.477 Sum_probs=33.9
Q ss_pred hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248 149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 202 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~ 202 (211)
-....+.+=.||-|+.++ .. .. + .......+.+||.|+...+.+.++.+
T Consensus 23 ~~~~~~~~~~cP~C~s~~-~~-k~--g-~~~~~~qRyrC~~C~~tf~~~~~~~~ 71 (129)
T COG3677 23 AIRMQITKVNCPRCKSSN-VV-KI--G-GIRRGHQRYKCKSCGSTFTVETGSPL 71 (129)
T ss_pred HHhhhcccCcCCCCCccc-ee-eE--C-CccccccccccCCcCcceeeeccCcc
Confidence 344555677899999999 33 11 1 11223778999999999999887544
No 88
>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=79.71 E-value=1.2 Score=28.32 Aligned_cols=24 Identities=29% Similarity=0.696 Sum_probs=15.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-|++||+....- ..--+||+||..
T Consensus 4 ~C~~CG~i~~g~------------~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIHEGE------------EAPEKCPICGAP 27 (34)
T ss_pred ECCCCCCEeECC------------cCCCcCcCCCCc
Confidence 499999654321 122389999974
No 89
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=79.40 E-value=1.1 Score=35.39 Aligned_cols=33 Identities=15% Similarity=0.382 Sum_probs=21.3
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce-eEEecC
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT-MVYDSN 199 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~-L~f~~~ 199 (211)
+.+-|++||++... ..+...||.||.. ......
T Consensus 69 ~~~~C~~Cg~~~~~------------~~~~~~CP~Cgs~~~~i~~G 102 (113)
T PRK12380 69 AQAWCWDCSQVVEI------------HQHDAQCPHCHGERLRVDTG 102 (113)
T ss_pred cEEEcccCCCEEec------------CCcCccCcCCCCCCcEEccC
Confidence 67889999954321 2344569999964 455544
No 90
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=79.34 E-value=1.4 Score=39.43 Aligned_cols=27 Identities=26% Similarity=0.651 Sum_probs=20.8
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
-|||.||.++.... + + .+...=||+|.
T Consensus 245 ~pCprCG~~I~~~~-----~-~--gR~t~~CP~CQ 271 (272)
T PRK14810 245 EPCLNCKTPIRRVV-----V-A--GRSSHYCPHCQ 271 (272)
T ss_pred CcCCCCCCeeEEEE-----E-C--CCccEECcCCc
Confidence 39999999997551 2 2 48889999996
No 91
>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=79.26 E-value=1.8 Score=28.82 Aligned_cols=25 Identities=28% Similarity=0.794 Sum_probs=18.5
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
||.||......+ + ++...+|..|+.
T Consensus 21 CP~Cg~~~~~~~------~---~~~~~~C~~C~~ 45 (46)
T PF12760_consen 21 CPHCGSTKHYRL------K---TRGRYRCKACRK 45 (46)
T ss_pred CCCCCCeeeEEe------C---CCCeEECCCCCC
Confidence 999999833332 2 378999999985
No 92
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=79.19 E-value=1.7 Score=34.59 Aligned_cols=34 Identities=26% Similarity=0.615 Sum_probs=25.4
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
-.-.|+.|+.++...-.. ...+..|..|+..|++
T Consensus 122 ~~~~C~~C~~~~~r~~~~--------~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRS--------KRKRYRCGRCGGPLVQ 155 (157)
T ss_pred eEEEcCCCCCEeeeeccc--------chhhEECCCCCCEEEE
Confidence 456799999998666211 4556889999998875
No 93
>PHA02942 putative transposase; Provisional
Probab=78.89 E-value=1.4 Score=41.55 Aligned_cols=26 Identities=31% Similarity=0.888 Sum_probs=18.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.||+||..+... +.....|++||..+
T Consensus 327 ~Cs~CG~~~~~l-----------~~r~f~C~~CG~~~ 352 (383)
T PHA02942 327 SCPKCGHKMVEI-----------AHRYFHCPSCGYEN 352 (383)
T ss_pred cCCCCCCccCcC-----------CCCEEECCCCCCEe
Confidence 399999876421 23368999999875
No 94
>PRK10445 endonuclease VIII; Provisional
Probab=78.69 E-value=1.6 Score=38.94 Aligned_cols=27 Identities=22% Similarity=0.468 Sum_probs=20.4
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
.+||+||.++..-. +. .+...=||+|.
T Consensus 236 ~~Cp~Cg~~I~~~~-----~~---gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTT-----LS---SRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEE-----EC---CCCcEECCCCc
Confidence 58999999987552 22 47888999995
No 95
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=78.38 E-value=1.1 Score=45.16 Aligned_cols=13 Identities=31% Similarity=0.928 Sum_probs=7.9
Q ss_pred cCceeCCCCCcee
Q 028248 182 TNTINCSNCGTTM 194 (211)
Q Consensus 182 ~~~~kC~~C~~~L 194 (211)
....-|++||+.+
T Consensus 39 ~~~~fC~~CG~~~ 51 (645)
T PRK14559 39 VDEAHCPNCGAET 51 (645)
T ss_pred cccccccccCCcc
Confidence 3344677777764
No 96
>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=78.37 E-value=1.3 Score=28.40 Aligned_cols=9 Identities=33% Similarity=1.040 Sum_probs=5.5
Q ss_pred eCCCCCcee
Q 028248 186 NCSNCGTTM 194 (211)
Q Consensus 186 kC~~C~~~L 194 (211)
.|++||+..
T Consensus 34 ~C~~CGE~~ 42 (46)
T TIGR03831 34 VCPQCGEEY 42 (46)
T ss_pred ccccCCCEe
Confidence 477776653
No 97
>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=78.33 E-value=1.4 Score=27.69 Aligned_cols=23 Identities=30% Similarity=0.651 Sum_probs=15.5
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.|++||.....- ...-.||+||.
T Consensus 3 ~C~~CGy~y~~~------------~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGE------------EAPWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCC------------cCCCcCcCCCC
Confidence 489999543322 25568999987
No 98
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=77.30 E-value=1.3 Score=31.24 Aligned_cols=29 Identities=28% Similarity=0.620 Sum_probs=21.3
Q ss_pred eeecCCCCCcccce-eeccccccccCCCCcCceeCCCCCce
Q 028248 154 ILKGPCPNCGTENV-SFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 154 iLkG~CPnCg~Ev~-aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-++--||+||.-+| +. -.++.-|.-||-.
T Consensus 17 rk~~~CPrCG~gvfmA~-----------H~dR~~CGkCgyT 46 (51)
T COG1998 17 RKNRFCPRCGPGVFMAD-----------HKDRWACGKCGYT 46 (51)
T ss_pred EccccCCCCCCcchhhh-----------cCceeEeccccce
Confidence 35667999998776 44 3448889999865
No 99
>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=77.19 E-value=1.8 Score=38.77 Aligned_cols=34 Identities=29% Similarity=0.651 Sum_probs=24.1
Q ss_pred ccceeeec----CCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 150 RESLILKG----PCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 150 ~d~liLkG----~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
++-+-+.| |||.||+++...- +. .+...=||+|.
T Consensus 235 ~~~~~Vy~r~g~pC~~Cg~~I~~~~-----~~---gR~t~~CP~CQ 272 (272)
T TIGR00577 235 QQELQVYGRKGEPCRRCGTPIEKIK-----VG---GRGTHFCPQCQ 272 (272)
T ss_pred cceeEEeCCCCCCCCCCCCeeEEEE-----EC---CCCCEECCCCC
Confidence 34455664 8999999998651 22 47888999994
No 100
>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=76.39 E-value=2.2 Score=26.93 Aligned_cols=27 Identities=30% Similarity=0.722 Sum_probs=13.9
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.+||.|+.|..=. +....-|+-|+-+.
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 4799999987653 56778899998653
No 101
>smart00400 ZnF_CHCC zinc finger.
Probab=76.36 E-value=1.4 Score=30.07 Aligned_cols=30 Identities=40% Similarity=0.803 Sum_probs=23.9
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
++.||-+.+..-+| .|. .+++...|..||+
T Consensus 2 ~~~cPfh~d~~pSf-----~v~--~~kn~~~Cf~cg~ 31 (55)
T smart00400 2 KGLCPFHGEKTPSF-----SVS--PDKQFFHCFGCGA 31 (55)
T ss_pred cccCcCCCCCCCCE-----EEE--CCCCEEEEeCCCC
Confidence 57899999999998 332 2568899999984
No 102
>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=76.31 E-value=2.2 Score=26.36 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=13.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
=||.||.+...- . .-..-.|+.|+..
T Consensus 5 fC~~CG~~t~~~-------~---~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPA-------P---GGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE--------S---SSS-EEESSSS-E
T ss_pred ccCcCCccccCC-------C---CcCEeECCCCcCE
Confidence 388888877654 1 2466778888754
No 103
>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=76.15 E-value=1.2 Score=32.22 Aligned_cols=13 Identities=69% Similarity=1.370 Sum_probs=10.6
Q ss_pred eecCCCCCcccce
Q 028248 155 LKGPCPNCGTENV 167 (211)
Q Consensus 155 LkG~CPnCg~Ev~ 167 (211)
|.|-|||||-|..
T Consensus 40 l~~~CPNCgGelv 52 (57)
T PF06906_consen 40 LNGVCPNCGGELV 52 (57)
T ss_pred hcCcCcCCCCccc
Confidence 5889999998754
No 104
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=75.78 E-value=2.2 Score=37.06 Aligned_cols=11 Identities=45% Similarity=1.075 Sum_probs=9.5
Q ss_pred CCCCCccccee
Q 028248 158 PCPNCGTENVS 168 (211)
Q Consensus 158 ~CPnCg~Ev~a 168 (211)
.||+|+.++.+
T Consensus 7 ~CPvC~~~F~~ 17 (214)
T PF09986_consen 7 TCPVCGKEFKT 17 (214)
T ss_pred ECCCCCCeeee
Confidence 69999999874
No 105
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=75.69 E-value=1.9 Score=32.62 Aligned_cols=27 Identities=33% Similarity=0.600 Sum_probs=17.5
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
|-+||+||+.++.= .....---|++|.
T Consensus 1 K~~CPCCg~~Tl~~---------~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 1 KYPCPCCGYYTLEE---------RGEGTYDICPVCF 27 (78)
T ss_pred CccCCCCCcEEecc---------CCCcCceECCCCC
Confidence 45899999876532 1122245799996
No 106
>PRK04023 DNA polymerase II large subunit; Validated
Probab=75.61 E-value=1.8 Score=46.03 Aligned_cols=33 Identities=36% Similarity=0.464 Sum_probs=15.8
Q ss_pred ChHHHHhHHhhhc-----ccCCeeEEeChhhHHHHHHH
Q 028248 2 SNEEFDNLKEELM-----WEGSSVVMLSSAEQKFLEAS 34 (211)
Q Consensus 2 s~eefd~lkeel~-----weGssv~~l~~~Eq~fLeA~ 34 (211)
|-||+..|.+-+. |++.=++-++..-++.||-+
T Consensus 477 s~ee~~~L~~~~~~~~~~~~~~l~~~~~~~~k~~LE~L 514 (1121)
T PRK04023 477 SKEELEALRNALAGGGILEEGVLVLDLSEGVKRILEKL 514 (1121)
T ss_pred CHHHHHHHHHHHHhcCcCcCCeEEecCcHHHHHHHHHh
Confidence 5566666666332 22222333333345666665
No 107
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=75.56 E-value=2 Score=38.55 Aligned_cols=26 Identities=35% Similarity=0.747 Sum_probs=20.3
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
|||.||+++..-. +. .++..=||+|.
T Consensus 256 pC~~Cg~~I~~~~-----~~---gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTPIERIK-----LA---GRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCeeEEEE-----EC---CCccEECCCCc
Confidence 9999999987542 22 48889999995
No 108
>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=75.34 E-value=4.7 Score=38.32 Aligned_cols=28 Identities=21% Similarity=0.511 Sum_probs=20.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.||.|+.-+ + ...++.|+.||+.|.-+.
T Consensus 217 ~C~~Cd~~~----------~---~~~~a~CpRC~~~L~~~~ 244 (403)
T TIGR00155 217 SCSACHTTI----------L---PAQEPVCPRCSTPLYVRR 244 (403)
T ss_pred cCCCCCCcc----------C---CCCCcCCcCCCCcccCCC
Confidence 499999943 1 246789999999994443
No 109
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=75.20 E-value=4.2 Score=36.25 Aligned_cols=27 Identities=22% Similarity=0.439 Sum_probs=19.8
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
--||.||.+.... .....-.|+.|+..
T Consensus 100 ~fC~~CG~~~~~~----------~~~~~~~C~~c~~~ 126 (256)
T PRK00241 100 RFCGYCGHPMHPS----------KTEWAMLCPHCRER 126 (256)
T ss_pred ccccccCCCCeec----------CCceeEECCCCCCE
Confidence 3599999987653 13566789999954
No 110
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=75.04 E-value=2.2 Score=40.78 Aligned_cols=38 Identities=24% Similarity=0.580 Sum_probs=27.9
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
..||+|... -.| ..+-+|++||+..++-+..-.+..|+
T Consensus 58 ~kC~~c~~~-~~y------------~~~~~C~~cg~~~~l~R~VSfVDaPG 95 (415)
T COG5257 58 YKCPECYRP-ECY------------TTEPKCPNCGAETELVRRVSFVDAPG 95 (415)
T ss_pred EeCCCCCCC-ccc------------ccCCCCCCCCCCccEEEEEEEeeCCc
Confidence 469999987 344 55678999999998887655555443
No 111
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=74.98 E-value=1.3 Score=37.65 Aligned_cols=46 Identities=30% Similarity=0.580 Sum_probs=22.8
Q ss_pred hhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 148 IVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 148 ~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
-++|-.-|+=.||.|++++. |=|...+.......+...|++|+..+
T Consensus 10 rf~~c~~l~~~C~~C~~~~~-f~g~~~~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 10 RFKDCEPLKLTCPSCGTEFE-FPGVFEEDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp TTTT---EEEE-TTT--EEE-E-SSS--SSEEEETTEEEETTT--B-
T ss_pred HhcCCCceEeECCCCCCCcc-ccccccCCccccccCcCcCCCCCCcC
Confidence 46777778899999999864 22221222233356789999999843
No 112
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=74.23 E-value=1.7 Score=41.49 Aligned_cols=30 Identities=27% Similarity=0.550 Sum_probs=23.1
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
-.-|+.||+.+.+| ...+.+|++||..+.+
T Consensus 240 ~~~c~~cg~~~~~~-----------~~~~~~c~~Cg~~~~~ 269 (380)
T COG1867 240 IYHCSRCGEIVGSF-----------REVDEKCPHCGGKVHL 269 (380)
T ss_pred EEEcccccceeccc-----------ccccccCCccccccee
Confidence 35799999666666 6778899999985543
No 113
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.22 E-value=1.3 Score=33.78 Aligned_cols=15 Identities=60% Similarity=1.125 Sum_probs=12.6
Q ss_pred eecCCCCCcccceee
Q 028248 155 LKGPCPNCGTENVSF 169 (211)
Q Consensus 155 LkG~CPnCg~Ev~aF 169 (211)
|.|.|||||-|..+=
T Consensus 40 l~g~CPnCGGelv~R 54 (84)
T COG3813 40 LHGLCPNCGGELVAR 54 (84)
T ss_pred hcCcCCCCCchhhcC
Confidence 789999999987653
No 114
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=74.09 E-value=2.3 Score=38.03 Aligned_cols=28 Identities=32% Similarity=0.777 Sum_probs=21.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
|||.||+.+.... +. .+...=||+|...
T Consensus 237 pC~~Cg~~I~~~~-----~~---gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTPIEKIV-----VG---GRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCeeEEEE-----EC---CCCcEECCCCcCC
Confidence 8999999987551 22 4888999999754
No 115
>PRK04011 peptide chain release factor 1; Provisional
Probab=73.21 E-value=1.5 Score=41.72 Aligned_cols=35 Identities=26% Similarity=0.560 Sum_probs=26.9
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
--||+||.+..-++ +.........|+.||..++..
T Consensus 329 ~~c~~c~~~~~~~~------~~~~~~~~~~c~~~~~~~~~~ 363 (411)
T PRK04011 329 YKCPNCGYEEEKTV------KRREELPEKTCPKCGSELEIV 363 (411)
T ss_pred EEcCCCCcceeeec------ccccccccccCcccCcccccc
Confidence 35999999987775 334456778999999998774
No 116
>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=72.92 E-value=1.5 Score=29.21 Aligned_cols=31 Identities=35% Similarity=0.858 Sum_probs=14.9
Q ss_pred ecCCCCCcccce-eeccccccccCCCCcCceeCCCCCc
Q 028248 156 KGPCPNCGTENV-SFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 156 kG~CPnCg~Ev~-aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.+|||+||-.-. ..|. .+ ..+...-|-.|+.
T Consensus 3 h~pCP~CGG~DrFri~~----d~--~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGGKDRFRIFD----DK--DGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT-TTTEEEET----T------S-EEETTTTB
T ss_pred CCCCCCCcCccccccCc----Cc--ccCCCEECCCCCC
Confidence 589999986543 5232 12 2457788988843
No 117
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=72.47 E-value=2.5 Score=30.06 Aligned_cols=20 Identities=40% Similarity=1.095 Sum_probs=15.0
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
-.||+||+-...- .-|++||
T Consensus 28 ~~C~~CG~~~~~H---------------~vC~~CG 47 (57)
T PRK12286 28 VECPNCGEPKLPH---------------RVCPSCG 47 (57)
T ss_pred eECCCCCCccCCe---------------EECCCCC
Confidence 3599999865543 4699999
No 118
>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=72.45 E-value=1.9 Score=45.79 Aligned_cols=28 Identities=36% Similarity=0.795 Sum_probs=21.8
Q ss_pred cceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 151 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 151 d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
+..+-.--||+||++.+.+ .|++||+.-
T Consensus 620 ~vev~~RKCPkCG~yTlk~----------------rCP~CG~~T 647 (1095)
T TIGR00354 620 EVEIAIRKCPQCGKESFWL----------------KCPVCGELT 647 (1095)
T ss_pred EEEEEEEECCCCCcccccc----------------cCCCCCCcc
Confidence 4566778999999975444 799999873
No 119
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=72.20 E-value=5.3 Score=28.67 Aligned_cols=43 Identities=21% Similarity=0.441 Sum_probs=29.5
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeC
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL 205 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~ 205 (211)
||.||.-...=.+.+--. .+.-.-||.|...-..+-+...|++
T Consensus 7 CP~CgnKTR~kir~DT~L----kNfPlyCpKCK~EtlI~v~~~~i~v 49 (55)
T PF14205_consen 7 CPICGNKTRLKIREDTVL----KNFPLYCPKCKQETLIDVKQLKITV 49 (55)
T ss_pred CCCCCCccceeeecCcee----ccccccCCCCCceEEEEeeccEEEE
Confidence 999996554332221111 4566789999999999988777765
No 120
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.34 E-value=2.5 Score=35.42 Aligned_cols=38 Identities=21% Similarity=0.611 Sum_probs=25.0
Q ss_pred CCCCCccccee--eccccccccCCCCcCceeCCCCCceeEE
Q 028248 158 PCPNCGTENVS--FFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 158 ~CPnCg~Ev~a--Ffg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
+||.|.+.++. |+-++++.-+ .-.--.-|||||...-.
T Consensus 41 qcp~csasirgd~~vegvlglg~-dye~psfchncgs~fpw 80 (160)
T COG4306 41 QCPICSASIRGDYYVEGVLGLGG-DYEPPSFCHNCGSRFPW 80 (160)
T ss_pred cCCccCCcccccceeeeeeccCC-CCCCcchhhcCCCCCCc
Confidence 79999999883 4445554422 22334579999987654
No 121
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.33 E-value=3.8 Score=29.74 Aligned_cols=32 Identities=28% Similarity=0.715 Sum_probs=23.2
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-.|-+||.++.-- ..-.+..|||||+.+.+|-
T Consensus 8 ~~CtSCg~~i~~~----------~~~~~F~CPnCG~~~I~RC 39 (59)
T PRK14890 8 PKCTSCGIEIAPR----------EKAVKFLCPNCGEVIIYRC 39 (59)
T ss_pred ccccCCCCcccCC----------CccCEeeCCCCCCeeEeec
Confidence 3588898776432 2356789999999877775
No 122
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.28 E-value=2.3 Score=46.15 Aligned_cols=13 Identities=15% Similarity=0.698 Sum_probs=10.6
Q ss_pred ceeCCCCCceeEE
Q 028248 184 TINCSNCGTTMVY 196 (211)
Q Consensus 184 ~~kC~~C~~~L~f 196 (211)
..+|+.||+.+.=
T Consensus 709 a~~CP~CGtplv~ 721 (1337)
T PRK14714 709 RVECPRCDVELTP 721 (1337)
T ss_pred cccCCCCCCcccc
Confidence 6689999988753
No 123
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=71.02 E-value=3.9 Score=32.69 Aligned_cols=39 Identities=31% Similarity=0.616 Sum_probs=29.8
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
=.||-||.|..+- -+|+-..+...+-|.|||-..+++-+
T Consensus 23 FtCp~Cghe~vs~----ctvkk~~~~g~~~Cg~CGls~e~ev~ 61 (104)
T COG4888 23 FTCPRCGHEKVSS----CTVKKTVNIGTAVCGNCGLSFECEVP 61 (104)
T ss_pred EecCccCCeeeeE----EEEEecCceeEEEcccCcceEEEecc
Confidence 3699999998873 13455567888999999988777653
No 124
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 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. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=70.73 E-value=1.7 Score=40.88 Aligned_cols=9 Identities=56% Similarity=1.682 Sum_probs=6.3
Q ss_pred eecCCCCCc
Q 028248 155 LKGPCPNCG 163 (211)
Q Consensus 155 LkG~CPnCg 163 (211)
++|.||.||
T Consensus 135 v~g~CP~C~ 143 (391)
T PF09334_consen 135 VEGTCPYCG 143 (391)
T ss_dssp ETCEETTT-
T ss_pred eeccccCcC
Confidence 568888888
No 125
>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=70.58 E-value=3 Score=40.50 Aligned_cols=28 Identities=25% Similarity=0.612 Sum_probs=18.5
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
.||+|+-..+-. ...+..+||.||....
T Consensus 224 ~C~~C~~~l~~h----------~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 224 CCPNCDVSLTYH----------KKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCCceEEe----------cCCCeEEcCCCcCcCC
Confidence 488887665433 1466788888886654
No 126
>PRK12496 hypothetical protein; Provisional
Probab=70.12 E-value=2.1 Score=35.88 Aligned_cols=32 Identities=16% Similarity=0.377 Sum_probs=20.7
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
=+--||.||.+.-. +...-.||+||.++.=..
T Consensus 126 w~~~C~gC~~~~~~------------~~~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 126 WRKVCKGCKKKYPE------------DYPDDVCEICGSPVKRKM 157 (164)
T ss_pred eeEECCCCCccccC------------CCCCCcCCCCCChhhhcc
Confidence 44569999954321 123346999999985444
No 127
>PRK04023 DNA polymerase II large subunit; Validated
Probab=70.10 E-value=2.3 Score=45.38 Aligned_cols=17 Identities=35% Similarity=0.542 Sum_probs=10.5
Q ss_pred cChHHHHHHHHHHhhhC
Q 028248 44 MSDEEYDKLKQKLKMEG 60 (211)
Q Consensus 44 ~sD~efD~Lk~~Lk~~G 60 (211)
+|-+++..|-.-+...|
T Consensus 476 is~ee~~~L~~~~~~~~ 492 (1121)
T PRK04023 476 ISKEELEALRNALAGGG 492 (1121)
T ss_pred CCHHHHHHHHHHHHhcC
Confidence 56666766666665543
No 128
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=69.74 E-value=3.7 Score=28.73 Aligned_cols=31 Identities=29% Similarity=0.706 Sum_probs=23.8
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-|-.||.++-. ........|+.||..+.|..
T Consensus 8 ~C~~Cg~~~~~----------~~~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 8 KCARCGREVEL----------DQETRGIRCPYCGSRILVKE 38 (49)
T ss_pred EhhhcCCeeeh----------hhccCceeCCCCCcEEEEec
Confidence 48899999821 12577899999999988865
No 129
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=69.55 E-value=2.1 Score=42.66 Aligned_cols=17 Identities=35% Similarity=1.093 Sum_probs=12.3
Q ss_pred hccceeeecCCCCCcccc
Q 028248 149 VRESLILKGPCPNCGTEN 166 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev 166 (211)
+-|-- ++|.||.||.+.
T Consensus 136 l~dr~-v~g~cp~cg~~~ 152 (558)
T COG0143 136 LPDRY-VEGTCPKCGGED 152 (558)
T ss_pred ccchh-eeccCCCcCccc
Confidence 44444 689999999654
No 130
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=69.50 E-value=2.7 Score=35.79 Aligned_cols=37 Identities=22% Similarity=0.582 Sum_probs=30.4
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
-||-|+.+-..-.-+=.+..++.-+-+-+|++||...
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 4999999998887666666777778889999999864
No 131
>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=68.96 E-value=3.1 Score=29.26 Aligned_cols=20 Identities=40% Similarity=1.017 Sum_probs=14.2
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
..||+||+-...- .-|++||
T Consensus 27 ~~C~~cG~~~~~H---------------~vc~~cG 46 (55)
T TIGR01031 27 VVCPNCGEFKLPH---------------RVCPSCG 46 (55)
T ss_pred eECCCCCCcccCe---------------eECCccC
Confidence 3499999854433 4689998
No 132
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=68.59 E-value=3.9 Score=41.30 Aligned_cols=61 Identities=26% Similarity=0.441 Sum_probs=35.4
Q ss_pred hhccceeeecCCCCCcccceeeccccccccCCC----CcCceeCCCCCceeEEecCceeEeCCCC
Q 028248 148 IVRESLILKGPCPNCGTENVSFFGTILSISSGG----TTNTINCSNCGTTMVYDSNTRLITLPEG 208 (211)
Q Consensus 148 ~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~----~~~~~kC~~C~~~L~f~~~~r~i~~peg 208 (211)
...|..=-.=+||.||++..==|+...+-.+.. +.-...||.|++.+....+.|-+-+-+|
T Consensus 219 ~~gd~rr~yvpCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~~~~~~gv~~~~g 283 (611)
T COG5525 219 NAGDQRRFYVPCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPKLNGRGVCLRTG 283 (611)
T ss_pred hhccceeEEeeCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeeeeccCccchhccC
Confidence 344555566799999997653332221111111 3344589999999988444554444443
No 133
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=68.46 E-value=4.2 Score=37.86 Aligned_cols=37 Identities=24% Similarity=0.432 Sum_probs=21.2
Q ss_pred cCCCCCcc-cceeeccccccccCCC-----------CcCceeCCCCCce
Q 028248 157 GPCPNCGT-ENVSFFGTILSISSGG-----------TTNTINCSNCGTT 193 (211)
Q Consensus 157 G~CPnCg~-Ev~aFfg~i~~v~s~~-----------~~~~~kC~~C~~~ 193 (211)
+-||.||. +|.+++-.--+-+|-+ .-.++||.|||..
T Consensus 186 ~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t 234 (308)
T COG3058 186 QYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQS 234 (308)
T ss_pred ccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhcccccc
Confidence 57999996 5666642210111111 1247899999864
No 134
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=68.37 E-value=3.9 Score=33.43 Aligned_cols=32 Identities=28% Similarity=0.828 Sum_probs=25.2
Q ss_pred hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
++..-++-..|++||. .|| +-+..|+.|++.-
T Consensus 22 l~~~kl~g~kC~~CG~---v~~-----------PPr~~Cp~C~~~~ 53 (140)
T COG1545 22 LKEGKLLGTKCKKCGR---VYF-----------PPRAYCPKCGSET 53 (140)
T ss_pred hhhCcEEEEEcCCCCe---EEc-----------CCcccCCCCCCCC
Confidence 5555668999999996 454 6788999999883
No 135
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=68.27 E-value=3 Score=34.20 Aligned_cols=32 Identities=19% Similarity=0.628 Sum_probs=23.8
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
-||.|+.+-+.+... +...-.+|..||..=.+
T Consensus 99 lC~~C~sPdT~l~k~-------~r~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 99 ICRECNRPDTRIIKE-------GRVSLLKCEACGAKAPL 130 (133)
T ss_pred ECCCCCCCCcEEEEe-------CCeEEEecccCCCCCcc
Confidence 499999999999532 23456799999976433
No 136
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=68.19 E-value=5.6 Score=40.81 Aligned_cols=24 Identities=33% Similarity=1.039 Sum_probs=15.6
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
+.||.||+ ...| + -.=..|++||-
T Consensus 725 ~~Cp~Cg~-~l~~-------~----~GC~~C~~CG~ 748 (752)
T PRK08665 725 GACPECGS-ILEH-------E----EGCVVCHSCGY 748 (752)
T ss_pred CCCCCCCc-ccEE-------C----CCCCcCCCCCC
Confidence 56999994 4555 2 23447899983
No 137
>PHA02540 61 DNA primase; Provisional
Probab=68.06 E-value=6.7 Score=36.80 Aligned_cols=40 Identities=30% Similarity=0.585 Sum_probs=25.4
Q ss_pred hccceeeecCCCCCcccc-----eeeccccccccCCCCcCceeCCCCCce
Q 028248 149 VRESLILKGPCPNCGTEN-----VSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev-----~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
++.....+|.||=||+-- .+|. |......-..+|++||..
T Consensus 20 ~~~~~~~~~~CPf~~ds~~~~~kpsF~-----V~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 20 VRRSSFYNFRCPICGDSQKDKNKARGW-----IYEKKDGGVFKCHNCGYH 64 (337)
T ss_pred eccCceEEecCCCCCCccccCcCCcEE-----EeccCCceEEEecCCCCC
Confidence 444433899999999944 2552 322112347899999963
No 138
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=67.79 E-value=3.1 Score=45.65 Aligned_cols=37 Identities=38% Similarity=0.661 Sum_probs=27.8
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
||+|..-- |-+.-++.||=+--.-+||+||+.|.=|.
T Consensus 911 C~~C~~~e---f~~~~~~~sG~Dlpdk~Cp~Cg~~~~kdg 947 (1437)
T PRK00448 911 CPNCKYSE---FFTDGSVGSGFDLPDKDCPKCGTKLKKDG 947 (1437)
T ss_pred Cccccccc---ccccccccccccCccccCccccccccccC
Confidence 99997433 33455677777888889999999986555
No 139
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=66.98 E-value=3.1 Score=34.34 Aligned_cols=32 Identities=25% Similarity=0.759 Sum_probs=24.8
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
-||.|+.+-+.+... +.....+|..||..-.+
T Consensus 104 lC~~C~spdT~l~k~-------~r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 104 ICPECGSPDTKLIKE-------GRIWVLKCEACGAETPV 135 (138)
T ss_pred ECCCCCCCCcEEEEc-------CCeEEEEcccCCCCCcC
Confidence 599999999999422 34678999999986443
No 140
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=66.97 E-value=3.3 Score=44.73 Aligned_cols=38 Identities=34% Similarity=0.613 Sum_probs=27.3
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-||+|..-- |-+.-++.|+=+--.-+||+||+.|.=+.
T Consensus 685 ~c~~c~~~e---f~~~~~~~sg~dlp~k~cp~c~~~~~~dg 722 (1213)
T TIGR01405 685 LCPNCKYSE---FITDGSVGSGFDLPDKDCPKCGAPLKKDG 722 (1213)
T ss_pred cCccccccc---ccccccccccccCccccCccccccccccC
Confidence 399997533 23445567777777889999999977555
No 141
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=66.84 E-value=3.3 Score=40.37 Aligned_cols=44 Identities=23% Similarity=0.308 Sum_probs=29.7
Q ss_pred eeecCCCCCcccceeeccccccccCCCCc-CceeCCCCCceeEEecCc
Q 028248 154 ILKGPCPNCGTENVSFFGTILSISSGGTT-NTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~-~~~kC~~C~~~L~f~~~~ 200 (211)
|..--||||-+++-+= ....+.++-. |=.+||.|...|..+...
T Consensus 24 i~~~yCp~CL~~~p~~---e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~ 68 (483)
T PF05502_consen 24 IDSYYCPNCLFEVPSS---EARSEKNRCSRNCFDCPICFSPLSVRASD 68 (483)
T ss_pred cceeECccccccCChh---hheeccceeccccccCCCCCCcceeEecc
Confidence 3455699999888643 1111333443 668899999999998754
No 142
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=66.61 E-value=4.4 Score=26.32 Aligned_cols=27 Identities=37% Similarity=0.762 Sum_probs=17.3
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.||.|+.+....-- ..-.--.|+.|+=
T Consensus 1 ~CP~C~~~l~~~~~--------~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGTELEPVRL--------GDVEIDVCPSCGG 27 (41)
T ss_pred CcCCCCcccceEEE--------CCEEEEECCCCCe
Confidence 59999997765421 1233445999974
No 143
>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=66.59 E-value=4.9 Score=30.78 Aligned_cols=14 Identities=21% Similarity=0.620 Sum_probs=10.3
Q ss_pred CcCceeCCCCCcee
Q 028248 181 TTNTINCSNCGTTM 194 (211)
Q Consensus 181 ~~~~~kC~~C~~~L 194 (211)
+.+-..|+.||...
T Consensus 28 ~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 28 GVPGWYCPACGEEL 41 (127)
T ss_pred eeeeeECCCCCCEE
Confidence 34566899999874
No 144
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=66.09 E-value=5.6 Score=32.23 Aligned_cols=34 Identities=21% Similarity=0.433 Sum_probs=23.5
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCC-ceeEEecCc
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG-TTMVYDSNT 200 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~-~~L~f~~~~ 200 (211)
++.-|.+|+.++.. ..+...||.|+ -.+..+...
T Consensus 69 ~~~~C~~C~~~~~~------------e~~~~~CP~C~s~~~~i~~G~ 103 (115)
T COG0375 69 AECWCLDCGQEVEL------------EELDYRCPKCGSINLRIIGGD 103 (115)
T ss_pred cEEEeccCCCeecc------------hhheeECCCCCCCceEEecCC
Confidence 56789999665543 46778899999 445555543
No 145
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=65.74 E-value=4.4 Score=32.16 Aligned_cols=34 Identities=12% Similarity=0.361 Sum_probs=20.6
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce-eEEecC
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT-MVYDSN 199 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~-L~f~~~ 199 (211)
+.+-|+.||.+. .. . ..+...||.||+. +...+.
T Consensus 70 ~~~~C~~Cg~~~-~~-------~---~~~~~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 70 VELECKDCSHVF-KP-------N---ALDYGVCEKCHSKNVIITQG 104 (117)
T ss_pred CEEEhhhCCCcc-cc-------C---CccCCcCcCCCCCceEEecC
Confidence 567899999432 22 0 1233469999985 444443
No 146
>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=65.72 E-value=3.9 Score=31.05 Aligned_cols=27 Identities=26% Similarity=0.651 Sum_probs=18.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
-||+||.-..- ..+...|+.|+....-
T Consensus 2 fC~~Cg~~l~~------------~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTP------------KNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCccccc------------CCCeEECcCCCCcccc
Confidence 49999877631 1357999999976543
No 147
>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=65.67 E-value=4.7 Score=32.52 Aligned_cols=27 Identities=26% Similarity=0.689 Sum_probs=20.2
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
-+||.|+.|.+=- +....-||-|+-.-
T Consensus 3 p~CP~C~seytY~-----------dg~~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYH-----------DGTQLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEe-----------cCCeeECccccccc
Confidence 4799999986543 46678999998543
No 148
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=64.94 E-value=8.1 Score=35.61 Aligned_cols=40 Identities=20% Similarity=0.361 Sum_probs=27.7
Q ss_pred HHHHHHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 139 YLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 139 ~~a~~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.-|.+|..|....-. ||.||++.+.-= .--...|++||..
T Consensus 99 ~~a~~l~~w~~~~RF-----Cg~CG~~~~~~~----------~g~~~~C~~cg~~ 138 (279)
T COG2816 99 ARAVQLLEWYRSHRF-----CGRCGTKTYPRE----------GGWARVCPKCGHE 138 (279)
T ss_pred HHHHHHHHHHhhCcC-----CCCCCCcCcccc----------CceeeeCCCCCCc
Confidence 445556665555545 999999998762 2345689999975
No 149
>PRK05580 primosome assembly protein PriA; Validated
Probab=64.50 E-value=4.6 Score=40.61 Aligned_cols=27 Identities=22% Similarity=0.663 Sum_probs=16.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.||+|+....-. ...+...||.||...
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 588888755432 135667777777654
No 150
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=64.39 E-value=5.6 Score=29.10 Aligned_cols=19 Identities=37% Similarity=0.793 Sum_probs=16.6
Q ss_pred CCCccChHHHHHHHHHHhh
Q 028248 40 GKPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 40 G~Pi~sD~efD~Lk~~Lk~ 58 (211)
-.||||+++|+++...|+.
T Consensus 83 ~~~IIs~~~f~~vq~~l~~ 101 (102)
T PF07508_consen 83 HPPIISEEEFERVQKKLDE 101 (102)
T ss_pred CCCccCHHHHHHHHHHHhc
Confidence 3699999999999999863
No 151
>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=63.99 E-value=5.2 Score=38.05 Aligned_cols=33 Identities=21% Similarity=0.436 Sum_probs=23.2
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.||.|+.-+.- ..-....++.|+.||+.|.-+.
T Consensus 15 ~C~~Cd~l~~~--------~~l~~g~~a~CpRCg~~L~~~~ 47 (403)
T TIGR00155 15 LCSQCDMLVAL--------PRIESGQKAACPRCGTTLTVGW 47 (403)
T ss_pred eCCCCCCcccc--------cCCCCCCeeECCCCCCCCcCCC
Confidence 59999975432 2223466899999999995443
No 152
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=63.97 E-value=4 Score=32.45 Aligned_cols=28 Identities=25% Similarity=0.813 Sum_probs=22.7
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
-||.|+.+-+.+... +.....+|..||.
T Consensus 82 lC~~C~spdT~l~k~-------~r~~~l~C~aCGa 109 (110)
T smart00653 82 LCPECGSPDTELIKE-------NRLFFLKCEACGA 109 (110)
T ss_pred ECCCCCCCCcEEEEe-------CCeEEEEccccCC
Confidence 499999999999432 3477899999996
No 153
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=63.75 E-value=3.2 Score=29.66 Aligned_cols=11 Identities=45% Similarity=1.072 Sum_probs=5.7
Q ss_pred ecCCCCCcccc
Q 028248 156 KGPCPNCGTEN 166 (211)
Q Consensus 156 kG~CPnCg~Ev 166 (211)
|..||+||++.
T Consensus 17 k~~CP~CG~~t 27 (56)
T PRK13130 17 KEICPVCGGKT 27 (56)
T ss_pred cccCcCCCCCC
Confidence 55555555543
No 154
>PHA02998 RNA polymerase subunit; Provisional
Probab=63.44 E-value=6.5 Score=34.46 Aligned_cols=37 Identities=22% Similarity=0.645 Sum_probs=25.9
Q ss_pred eecCCCCCcccceeeccccccccCCCCc--CceeCCCCCce
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTT--NTINCSNCGTT 193 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~--~~~kC~~C~~~ 193 (211)
...+||.||.....|+ .+-+.|...+ .-.+|.+||-.
T Consensus 142 t~v~CPkCg~~~A~f~--qlQTRSADEPmT~FYkC~~CG~~ 180 (195)
T PHA02998 142 YNTPCPNCKSKNTTPM--MIQTRAADEPPLVRHACRDCKKH 180 (195)
T ss_pred cCCCCCCCCCCceEEE--EEeeccCCCCceEEEEcCCCCCc
Confidence 4578999998888775 3344544443 45699999864
No 155
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=62.70 E-value=5.3 Score=34.57 Aligned_cols=36 Identities=17% Similarity=0.513 Sum_probs=28.4
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
-||.|+.+-+.+... +...-.+|..||..-.+++.+
T Consensus 100 ~C~~C~~pdT~l~k~-------~~~~~l~C~aCGa~~~v~~~~ 135 (201)
T PRK12336 100 ICSECGLPDTRLVKE-------DRVLMLRCDACGAHRPVKKRK 135 (201)
T ss_pred ECCCCCCCCcEEEEc-------CCeEEEEcccCCCCccccccc
Confidence 599999999999432 245678999999998888753
No 156
>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=62.57 E-value=5 Score=32.51 Aligned_cols=29 Identities=28% Similarity=0.875 Sum_probs=23.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-||.|+.+-+.+... +.....+|..||..
T Consensus 95 lC~~C~spdT~l~k~-------~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 95 LCPECGSPDTELIKE-------GRLIFLKCKACGAS 123 (125)
T ss_dssp SCTSTSSSSEEEEEE-------TTCCEEEETTTSCE
T ss_pred EcCCCCCCccEEEEc-------CCEEEEEecccCCc
Confidence 599999999998433 45788999999975
No 157
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=62.14 E-value=8.5 Score=32.36 Aligned_cols=28 Identities=29% Similarity=1.006 Sum_probs=21.0
Q ss_pred CCCCCcccce--------eeccccccccCCCCcCceeCCCCCc
Q 028248 158 PCPNCGTENV--------SFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 158 ~CPnCg~Ev~--------aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.|||||++.. -|||.|+ -....|+.||-
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evi-------i~sf~C~~CGy 37 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVI-------IMSFECEHCGY 37 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEE-------EEEEECCCCCC
Confidence 6999998765 3577766 34678999984
No 158
>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=62.13 E-value=5 Score=25.99 Aligned_cols=26 Identities=35% Similarity=0.991 Sum_probs=17.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
+||+||.. +|-. +.-..-|-.||++.
T Consensus 10 ~C~~C~~~---~~~~--------~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSR---WFYS--------DDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCe---EeEc--------cCCEEEhhhCceEc
Confidence 39999988 3222 45667788888764
No 159
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=62.03 E-value=5.5 Score=37.66 Aligned_cols=31 Identities=29% Similarity=0.588 Sum_probs=24.5
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.+|.||-|++..-+|. |.. ..+...|..||.
T Consensus 33 ~~~~CPfh~ek~pSf~-----v~~--~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 33 YVGLCPFHHEKTPSFS-----VSP--EKQFYHCFGCGA 63 (415)
T ss_pred eEeeCCCCCCCCCeEE-----EEc--CCCcEEECCCCC
Confidence 4689999999998883 332 467799999986
No 160
>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=61.56 E-value=6.1 Score=33.11 Aligned_cols=29 Identities=31% Similarity=1.011 Sum_probs=18.4
Q ss_pred CCCCCccccee--------eccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVS--------FFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~a--------Ffg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.|||||++... |||.++ -....|+.||-.
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evi-------i~sf~C~~CGyk 39 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVI-------IMSFECEHCGYK 39 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEE-------EEEEE-TTT--E
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEE-------EEEeECCCCCCE
Confidence 59999998654 567766 445799999953
No 161
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=61.21 E-value=5.7 Score=40.87 Aligned_cols=73 Identities=22% Similarity=0.247 Sum_probs=33.0
Q ss_pred hhhcccCCeeEEeChh---hHHHHHHHHhhhcCCCc-----cChHHHHHHHHHHhhhCCeeeeeccceeec-----Ccce
Q 028248 11 EELMWEGSSVVMLSSA---EQKFLEASMAYVAGKPI-----MSDEEYDKLKQKLKMEGSEIVVEGPRCSLR-----SRKV 77 (211)
Q Consensus 11 eel~weGssv~~l~~~---Eq~fLeA~~aY~~G~Pi-----~sD~efD~Lk~~Lk~~GS~vv~~~prCslr-----~~~~ 77 (211)
++.--+|-++++|=|+ ..+.++...+++.-++. +||.|--+.=++. ..|+--+|-|.|..+- =+-+
T Consensus 239 ~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~-~~G~~~vVIGtRSAlF~Pf~~LGLI 317 (730)
T COG1198 239 AKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRA-RRGEARVVIGTRSALFLPFKNLGLI 317 (730)
T ss_pred HHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHH-hcCCceEEEEechhhcCchhhccEE
Confidence 3344455555555444 24455555555542222 3443322211111 1366666667775552 2334
Q ss_pred eeccchh
Q 028248 78 YSDLSVD 84 (211)
Q Consensus 78 ysD~e~D 84 (211)
..|+|-|
T Consensus 318 IvDEEHD 324 (730)
T COG1198 318 IVDEEHD 324 (730)
T ss_pred EEecccc
Confidence 4555544
No 162
>PRK14873 primosome assembly protein PriA; Provisional
Probab=61.05 E-value=5.8 Score=40.17 Aligned_cols=67 Identities=12% Similarity=0.185 Sum_probs=37.4
Q ss_pred HHHhHHhhhcccCCeeEEeChh---hHHHHHHHHhhhcCCCc------cChHHHHHHHHHHhhhCCeeeeeccceee
Q 028248 5 EFDNLKEELMWEGSSVVMLSSA---EQKFLEASMAYVAGKPI------MSDEEYDKLKQKLKMEGSEIVVEGPRCSL 72 (211)
Q Consensus 5 efd~lkeel~weGssv~~l~~~---Eq~fLeA~~aY~~G~Pi------~sD~efD~Lk~~Lk~~GS~vv~~~prCsl 72 (211)
-|-.+-++...+|-++++|=++ -.++.+++.+++.+.++ +++.+--+.=.+++ .|..-+|-|.|-.+
T Consensus 176 vyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~-~G~~~IViGtRSAv 251 (665)
T PRK14873 176 RLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVL-RGQARVVVGTRSAV 251 (665)
T ss_pred HHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHh-CCCCcEEEEcceeE
Confidence 3555666666778777666655 25666777777753444 44443222222232 67655566666444
No 163
>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=60.17 E-value=5.2 Score=27.31 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=3.9
Q ss_pred eCCCCCceeE
Q 028248 186 NCSNCGTTMV 195 (211)
Q Consensus 186 kC~~C~~~L~ 195 (211)
.||+|++.|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 6666666653
No 164
>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=60.04 E-value=5.5 Score=31.20 Aligned_cols=32 Identities=22% Similarity=0.666 Sum_probs=25.8
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
.|++||.+|... ++++.++--||+|=..+-++
T Consensus 6 ~C~~CG~~V~p~--------~~g~~~RNHCP~CL~S~Hvd 37 (92)
T PF12647_consen 6 TCVHCGLTVSPL--------AAGSAHRNHCPSCLSSLHVD 37 (92)
T ss_pred CccccCCCcccC--------CCCCCccCcCcccccccccC
Confidence 599999998654 44577899999998887776
No 165
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=59.81 E-value=5.6 Score=33.98 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=16.9
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.=-||.||+-... ..--+||+||.+
T Consensus 134 ~~vC~vCGy~~~g-------------e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEG-------------EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccC-------------CCCCcCCCCCCh
Confidence 3569999864322 334589999964
No 166
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=58.99 E-value=12 Score=30.00 Aligned_cols=48 Identities=23% Similarity=0.544 Sum_probs=30.2
Q ss_pred ccceeeecCCCCCcccceeeccc--------cccc-------cCCCCcCceeCCCCCc-eeEEec
Q 028248 150 RESLILKGPCPNCGTENVSFFGT--------ILSI-------SSGGTTNTINCSNCGT-TMVYDS 198 (211)
Q Consensus 150 ~d~liLkG~CPnCg~Ev~aFfg~--------i~~v-------~s~~~~~~~kC~~C~~-~L~f~~ 198 (211)
+++. ..+.||.||.+...+++. +.+. ......-..+|++|+. .+..+.
T Consensus 12 ~~~~-~~~~Cp~Cg~~m~~~~~~~g~f~gCs~yP~C~~~~~~~~~~~~~~~~Cp~C~~~~~~~k~ 75 (140)
T COG0551 12 KDLK-TGQICPKCGKNMVKKFGKYGIFLGCSNYPKCDYYEPEKAIAEKTGVKCPKCGKGLLVLKK 75 (140)
T ss_pred cccc-cCccCCcCCCeeEEEEccCCeEEEeCCCCCCCCCcccccccccCceeCCCCCCCceEEEe
Confidence 4444 789999999998877765 1111 1122233589999995 444444
No 167
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=58.85 E-value=6 Score=43.58 Aligned_cols=33 Identities=27% Similarity=0.529 Sum_probs=25.5
Q ss_pred cceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 151 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 151 d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
+.-+-...||+||++-+ ...|+.||+..+-...
T Consensus 669 ~vei~~~~Cp~Cg~~~~----------------~~~Cp~CG~~~~~~~~ 701 (1627)
T PRK14715 669 DIEIAFFKCPKCGKVGL----------------YHVCPFCGTRVELKPY 701 (1627)
T ss_pred eEEEEeeeCCCCCCccc----------------cccCcccCCcccCCCc
Confidence 56678899999998743 3479999998665554
No 168
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=57.45 E-value=4.4 Score=30.92 Aligned_cols=20 Identities=30% Similarity=0.629 Sum_probs=13.2
Q ss_pred ccceeeecCCCCCcccceee
Q 028248 150 RESLILKGPCPNCGTENVSF 169 (211)
Q Consensus 150 ~d~liLkG~CPnCg~Ev~aF 169 (211)
+..+-+...||+||++....
T Consensus 2 ~g~Lk~~~~C~~CG~d~~~~ 21 (86)
T PF06170_consen 2 RGYLKVAPRCPHCGLDYSHA 21 (86)
T ss_pred CccccCCCcccccCCccccC
Confidence 34556777888888876543
No 169
>PRK10220 hypothetical protein; Provisional
Probab=57.36 E-value=8.1 Score=31.27 Aligned_cols=27 Identities=22% Similarity=0.583 Sum_probs=19.9
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
-+||.|+.|.+=- +....-||-|+-.-
T Consensus 4 P~CP~C~seytY~-----------d~~~~vCpeC~hEW 30 (111)
T PRK10220 4 PHCPKCNSEYTYE-----------DNGMYICPECAHEW 30 (111)
T ss_pred CcCCCCCCcceEc-----------CCCeEECCcccCcC
Confidence 4899999885432 46678999998543
No 170
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=57.34 E-value=9.1 Score=32.25 Aligned_cols=27 Identities=33% Similarity=0.754 Sum_probs=18.3
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
|..-||.||....-. +-++.+|++|+.
T Consensus 148 v~a~~~~~g~~~~~~-----------~~~~~~c~~~~~ 174 (189)
T PRK09521 148 IYAMCSRCRTPLVKK-----------GENELKCPNCGN 174 (189)
T ss_pred EEEEccccCCceEEC-----------CCCEEECCCCCC
Confidence 445688888877322 347788888884
No 171
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=56.71 E-value=4.1 Score=27.73 Aligned_cols=35 Identities=20% Similarity=0.495 Sum_probs=20.4
Q ss_pred CCCCCcccce--eeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENV--SFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~--aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
+||-||++.. ++..-+. .+-..+...+.||.|...
T Consensus 4 ~CP~C~~~~~~~~L~~H~~-~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 4 TCPYCGKGFSESSLVEHCE-DEHRSESKNVVCPICSSR 40 (54)
T ss_pred CCCCCCCccCHHHHHHHHH-hHCcCCCCCccCCCchhh
Confidence 7999999422 2221111 122234557999999873
No 172
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=56.51 E-value=7.8 Score=26.72 Aligned_cols=37 Identities=16% Similarity=0.380 Sum_probs=24.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
-|.||-+-+.- ..... -+.++.++.+|..|.+.+.|.
T Consensus 8 ~C~~C~~lLql--P~~~~-~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 8 VCSSCFELLQL--PAKFS-LSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred ECccHHHHHcC--CCccC-CCccceeEEeCCCCceeEEEe
Confidence 38888765542 11112 234458999999999999885
No 173
>PRK05667 dnaG DNA primase; Validated
Probab=56.26 E-value=7.8 Score=38.55 Aligned_cols=31 Identities=32% Similarity=0.703 Sum_probs=25.2
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
..|.||-|++..-+| +|.. ..+...|..||.
T Consensus 35 ~~~~CPfH~ektpSf-----~V~~--~k~~~~CF~Cg~ 65 (580)
T PRK05667 35 YKGLCPFHDEKTPSF-----TVSP--DKQFYHCFGCGA 65 (580)
T ss_pred eeecCCCCCCCCCce-----EEEC--CCCeEEECCCCC
Confidence 579999999999898 3433 467799999986
No 174
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=56.18 E-value=4.7 Score=34.58 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=20.3
Q ss_pred ccChHHHHHHHHHHhhhCCeeeee
Q 028248 43 IMSDEEYDKLKQKLKMEGSEIVVE 66 (211)
Q Consensus 43 i~sD~efD~Lk~~Lk~~GS~vv~~ 66 (211)
.+.|.|--+|=+-||-.|=+++.-
T Consensus 9 F~vD~mLG~LARwLRllGydt~~~ 32 (165)
T COG1656 9 FVVDAMLGKLARWLRLLGYDTVYS 32 (165)
T ss_pred eeHHHhHHHHHHHHHHcCCceeee
Confidence 568999999999999999887753
No 175
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=55.95 E-value=7.2 Score=27.78 Aligned_cols=27 Identities=26% Similarity=0.722 Sum_probs=19.3
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.++.||.||..++- ..--+.|+.||++
T Consensus 4 ~~~~C~~Cg~~~~~------------~dDiVvCp~Cgap 30 (54)
T PF14446_consen 4 EGCKCPVCGKKFKD------------GDDIVVCPECGAP 30 (54)
T ss_pred cCccChhhCCcccC------------CCCEEECCCCCCc
Confidence 35789999988642 1345789999875
No 176
>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=55.53 E-value=6.8 Score=27.51 Aligned_cols=13 Identities=38% Similarity=1.053 Sum_probs=10.2
Q ss_pred ecCCCCCccccee
Q 028248 156 KGPCPNCGTENVS 168 (211)
Q Consensus 156 kG~CPnCg~Ev~a 168 (211)
.+.||+||.+...
T Consensus 13 Y~~Cp~CGN~~vG 25 (49)
T PF12677_consen 13 YCKCPKCGNDKVG 25 (49)
T ss_pred hccCcccCCcEee
Confidence 7889999987643
No 177
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=55.30 E-value=7.3 Score=37.28 Aligned_cols=26 Identities=19% Similarity=0.422 Sum_probs=18.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
.||.|+.-+ ...++.|+.||..|.-+
T Consensus 223 ~C~~Cd~l~--------------~~~~a~CpRC~~~L~~~ 248 (419)
T PRK15103 223 SCSCCTAIL--------------PADQPVCPRCHTKGYVR 248 (419)
T ss_pred cCCCCCCCC--------------CCCCCCCCCCCCcCcCC
Confidence 499999842 12456899999999433
No 178
>cd07110 ALDH_F10_BADH Arabidopsis betaine aldehyde dehydrogenase 1 and 2, ALDH family 10A8 and 10A9-like. Present in this CD are the Arabidopsis betaine aldehyde dehydrogenase (BADH) 1 (chloroplast) and 2 (mitochondria), also known as, aldehyde dehydrogenase family 10 member A8 and aldehyde dehydrogenase family 10 member A9, respectively, and are putative dehydration- and salt-inducible BADHs (EC 1.2.1.8) that catalyze the oxidation of betaine aldehyde to the compatible solute glycine betaine.
Probab=55.05 E-value=37 Score=31.89 Aligned_cols=68 Identities=22% Similarity=0.481 Sum_probs=45.6
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEeChh-hHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VMLSSA-EQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l~~~-Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
+|.+.|.-.+.+.| .|..| +.+.+. -.+|++++.+ +.-|. |+++.+.+++++..++
T Consensus 240 ~dadl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~Gpli~~~~~~~~~~~v~ 319 (456)
T cd07110 240 DDADLEKAVEWAMFGCFWNNGQICSATSRLLVHESIADAFLERLATAAEAIRVGDPLEEGVRLGPLVSQAQYEKVLSFIA 319 (456)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCCCceEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcCCCCCHHHHHHHHHHHH
Confidence 56677777777777 34433 334333 5678887654 43443 6889999999998886
Q ss_pred h---hCCeeeeeccc
Q 028248 58 M---EGSEIVVEGPR 69 (211)
Q Consensus 58 ~---~GS~vv~~~pr 69 (211)
. .|.+++..|.+
T Consensus 320 ~a~~~Ga~~~~gg~~ 334 (456)
T cd07110 320 RGKEEGARLLCGGRR 334 (456)
T ss_pred HHHhCCCEEEeCCCc
Confidence 5 68787776543
No 179
>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=54.49 E-value=5.6 Score=28.64 Aligned_cols=25 Identities=24% Similarity=0.612 Sum_probs=17.5
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeC-CCCCceeE
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINC-SNCGTTMV 195 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC-~~C~~~L~ 195 (211)
.-|||||+++- +++.-| +.|+....
T Consensus 4 kHC~~CG~~Ip--------------~~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKPIP--------------PDESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCcCC--------------cchhhhCHHHHHHHH
Confidence 36999998763 457778 48876543
No 180
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=54.34 E-value=7.9 Score=32.52 Aligned_cols=44 Identities=20% Similarity=0.496 Sum_probs=21.8
Q ss_pred eeecCCCCCccccee--ecccc----ccccCCCCcCceeCCCCCceeEEe
Q 028248 154 ILKGPCPNCGTENVS--FFGTI----LSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 154 iLkG~CPnCg~Ev~a--Ffg~i----~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
.+|=.|.|||++... ++-.. .+...+..+.-.||..|++....+
T Consensus 28 ~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si~ 77 (161)
T PF05907_consen 28 FFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSID 77 (161)
T ss_dssp EEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEEE
T ss_pred EEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEEE
Confidence 477889999997643 33211 122333344456999999988763
No 181
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=54.12 E-value=7.4 Score=27.89 Aligned_cols=19 Identities=11% Similarity=0.177 Sum_probs=13.5
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
-.|||||+-.. +|.+ |+ ||
T Consensus 28 ~~c~~cg~~~~--------------pH~v-c~-cG 46 (60)
T PRK01110 28 SVDKTTGEYHL--------------PHHV-SP-KG 46 (60)
T ss_pred eEcCCCCceec--------------ccee-cC-Cc
Confidence 45999998542 5555 88 88
No 182
>cd02661 Peptidase_C19E A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=53.93 E-value=15 Score=31.44 Aligned_cols=25 Identities=16% Similarity=0.425 Sum_probs=17.2
Q ss_pred CceeCCCCCceeEEecCceeEeCCC
Q 028248 183 NTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 183 ~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
++.+|++|+..-......+...+|+
T Consensus 181 ~~~~C~~C~~~~~~~~~~~i~~~P~ 205 (304)
T cd02661 181 NKYKCERCKKKVKASKQLTIHRAPN 205 (304)
T ss_pred CCeeCCCCCCccceEEEEEEecCCc
Confidence 4468999998766655555556664
No 183
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=53.90 E-value=7.5 Score=39.34 Aligned_cols=25 Identities=24% Similarity=0.526 Sum_probs=17.6
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
.-|++||.. + ...-+||+||..++.
T Consensus 627 ~~C~~CG~~-----~----------g~~~~CP~CG~~~~v 651 (656)
T PRK08270 627 SICPKHGYL-----S----------GEHEFCPKCGEETEV 651 (656)
T ss_pred cccCCCCCc-----C----------CCCCCCcCCcCccce
Confidence 579999973 1 113789999988543
No 184
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=53.86 E-value=4.8 Score=33.36 Aligned_cols=35 Identities=26% Similarity=0.766 Sum_probs=24.2
Q ss_pred ecCCCCCcccceee---ccccccccCCCCcCceeCCCCCceeEE
Q 028248 156 KGPCPNCGTENVSF---FGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 156 kG~CPnCg~Ev~aF---fg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
.-+||.||..++.- ||.- .=+.-..|..|.++..|
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t------~cka~~~c~~c~epf~~ 142 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPT------ACKALYRCRACKEPFEY 142 (146)
T ss_pred CCcCCCCCCCCcEeecCCCCh------hhHHHhhhhhhCCcHhh
Confidence 35899999988854 3331 12567789999887654
No 185
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=53.69 E-value=6.2 Score=39.50 Aligned_cols=44 Identities=27% Similarity=0.508 Sum_probs=24.3
Q ss_pred eecCCCCCcccceeeccccccc----cCCCCcCceeCCCCCceeEEecCc
Q 028248 155 LKGPCPNCGTENVSFFGTILSI----SSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v----~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
+.|.||.|+.+- -.|+.--. -....-.+..|..||.+++++...
T Consensus 138 v~g~cp~C~~~d--~~g~~ce~cg~~~~~~~l~~~~~~~~g~~~e~~~~~ 185 (673)
T PRK00133 138 VKGTCPKCGAED--QYGDNCEVCGATYSPTELINPKSAISGATPVLKESE 185 (673)
T ss_pred eecccCCCCCcc--cCCchhhhccccCChHhhcCCccccCCCcceEEecc
Confidence 579999999872 11221000 000011134688899999887743
No 186
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=53.57 E-value=10 Score=34.84 Aligned_cols=26 Identities=35% Similarity=0.745 Sum_probs=19.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
||+.||+.+..-. - +.++..=||+|.
T Consensus 247 pC~~CGt~I~k~~------~--~gR~t~~CP~CQ 272 (273)
T COG0266 247 PCRRCGTPIEKIK------L--GGRSTFYCPVCQ 272 (273)
T ss_pred CCCccCCEeEEEE------E--cCCcCEeCCCCC
Confidence 8999999887541 1 247788899995
No 187
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=53.39 E-value=9.9 Score=24.43 Aligned_cols=13 Identities=31% Similarity=0.938 Sum_probs=8.0
Q ss_pred CceeCCCCCceeE
Q 028248 183 NTINCSNCGTTMV 195 (211)
Q Consensus 183 ~~~kC~~C~~~L~ 195 (211)
..+.|+||++++.
T Consensus 3 ~~~~C~nC~R~v~ 15 (33)
T PF08209_consen 3 PYVECPNCGRPVA 15 (33)
T ss_dssp -EEE-TTTSSEEE
T ss_pred CeEECCCCcCCcc
Confidence 3567888888764
No 188
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=52.98 E-value=7 Score=35.18 Aligned_cols=19 Identities=42% Similarity=0.821 Sum_probs=16.0
Q ss_pred cCCCCcCceeCCCCCceeE
Q 028248 177 SSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 177 ~s~~~~~~~kC~~C~~~L~ 195 (211)
..+..+.+++|++|+++|+
T Consensus 207 ~~g~ipe~i~CpeC~R~ME 225 (235)
T PF14577_consen 207 SAGRIPETIVCPECGRPME 225 (235)
T ss_pred cccCCCceeECCCCCCchh
Confidence 3455789999999999997
No 189
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=52.54 E-value=9.4 Score=30.07 Aligned_cols=29 Identities=24% Similarity=0.738 Sum_probs=21.7
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
..-.|++||.+-+.++. =.|+ -||.|+..
T Consensus 41 ~~~~C~~Cg~~~~~~~S---------Ck~R-~CP~C~~~ 69 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYNS---------CKNR-HCPSCQAK 69 (111)
T ss_pred ceeecCCCCceEEecCc---------ccCc-CCCCCCCh
Confidence 34579999999988852 2455 79999975
No 190
>PHA02768 hypothetical protein; Provisional
Probab=52.27 E-value=7.9 Score=27.60 Aligned_cols=43 Identities=21% Similarity=0.383 Sum_probs=26.0
Q ss_pred ecCCCCCcccce---eeccccccccCCCCcCceeCCCCCceeEEecCceeEeC
Q 028248 156 KGPCPNCGTENV---SFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL 205 (211)
Q Consensus 156 kG~CPnCg~Ev~---aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~ 205 (211)
-=.||-||..+. ++.+-.+.- +...+|.+|+.. |.++.-+|.+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H-----~k~~kc~~C~k~--f~~~s~l~~~ 50 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKH-----NTNLKLSNCKRI--SLRTGEYIEI 50 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhc-----CCcccCCcccce--ecccceeEEE
Confidence 348999998765 232222211 135799999994 4455555543
No 191
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=52.22 E-value=19 Score=33.56 Aligned_cols=13 Identities=38% Similarity=0.853 Sum_probs=10.4
Q ss_pred eecCCCCCcccce
Q 028248 155 LKGPCPNCGTENV 167 (211)
Q Consensus 155 LkG~CPnCg~Ev~ 167 (211)
-+|-||+||..=.
T Consensus 186 ~~~~CPvCGs~P~ 198 (309)
T PRK03564 186 QRQFCPVCGSMPV 198 (309)
T ss_pred CCCCCCCCCCcch
Confidence 4789999998743
No 192
>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=51.80 E-value=8.1 Score=24.74 Aligned_cols=28 Identities=25% Similarity=0.625 Sum_probs=16.2
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
||.||.=.+ ++.+...+. .|.+|+-.-.
T Consensus 4 Cp~C~nlL~--------p~~~~~~~~-~C~~C~Y~~~ 31 (35)
T PF02150_consen 4 CPECGNLLY--------PKEDKEKRV-ACRTCGYEEP 31 (35)
T ss_dssp ETTTTSBEE--------EEEETTTTE-EESSSS-EEE
T ss_pred CCCCCccce--------EcCCCccCc-CCCCCCCccC
Confidence 888875443 233334444 8999986544
No 193
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=51.63 E-value=9.7 Score=36.29 Aligned_cols=36 Identities=25% Similarity=0.549 Sum_probs=24.9
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
--|||||.+...++.. ........|+.||..+....
T Consensus 321 ~rc~~c~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~ 356 (403)
T TIGR03676 321 FKCPNCGYEEEKTVKP------EEGDKSEACPKCGSELEIVE 356 (403)
T ss_pred EEcCCCCcceeeeccc------ccccccccCcccCcccccch
Confidence 5799999999887522 11223356999999877543
No 194
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=51.53 E-value=7.1 Score=38.04 Aligned_cols=49 Identities=29% Similarity=0.582 Sum_probs=31.0
Q ss_pred hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
++|+-.--=-||||.....+. ..+.+= ...+-...|.+|+..|+-+.+.
T Consensus 121 ~d~t~~~~Y~Cp~C~kkyt~L--ea~~L~-~~~~~~F~C~~C~gelveDe~~ 169 (436)
T KOG2593|consen 121 RDDTNVAGYVCPNCQKKYTSL--EALQLL-DNETGEFHCENCGGELVEDENK 169 (436)
T ss_pred hhccccccccCCccccchhhh--HHHHhh-cccCceEEEecCCCchhccccc
Confidence 445543445699999986554 111110 0135688999999999988754
No 195
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.30 E-value=11 Score=29.30 Aligned_cols=28 Identities=29% Similarity=0.573 Sum_probs=18.4
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-||+|+-+...=.+. +..--.||.|.-.
T Consensus 3 lCP~C~v~l~~~~rs--------~vEiD~CPrCrGV 30 (88)
T COG3809 3 LCPICGVELVMSVRS--------GVEIDYCPRCRGV 30 (88)
T ss_pred ccCcCCceeeeeeec--------CceeeeCCccccE
Confidence 399999988765322 2334569999643
No 196
>PRK14526 adenylate kinase; Provisional
Probab=51.08 E-value=12 Score=32.13 Aligned_cols=35 Identities=14% Similarity=0.257 Sum_probs=25.8
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
.-||.||.-....|.. .+....|.+|+..|.-|.+
T Consensus 123 ~~~~~~g~~y~~~~~p--------p~~~~~~~~~~~~l~~R~D 157 (211)
T PRK14526 123 RICKSCNNIFNIYTLP--------TKEKGICDVCKGDLYQRKD 157 (211)
T ss_pred CcccccCCccccccCC--------CCccCcCCCCCCeeeccCC
Confidence 4599999887766533 3456789999998887664
No 197
>TIGR00097 HMP-P_kinase phosphomethylpyrimidine kinase. This model represents phosphomethylpyrimidine kinase, the ThiD protein of thiamine biosynthesis. The protein is commonly observed within operons containing other thiamine biosynthesis genes. Numerous examples are fusion proteins with other thiamine-biosynthetic domains. Saccaromyces has three recent paralogs, two of which are isofunctional and score above the trusted cutoff. The third shows a longer branch length in a phylogenetic tree and scores below the trusted cutoff, as do putative second copies in a number of species.
Probab=50.85 E-value=54 Score=28.18 Aligned_cols=55 Identities=20% Similarity=0.380 Sum_probs=37.8
Q ss_pred HHhHHhhhcccCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCCe-eeeecc
Q 028248 6 FDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSE-IVVEGP 68 (211)
Q Consensus 6 fd~lkeel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~GS~-vv~~~p 68 (211)
.+.+|++| .....+++.+..|-+.| .|.++-+.++..+.-.+|...|-+ |++++-
T Consensus 117 ~~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~a~~l~~~g~~~Vvvt~G 172 (254)
T TIGR00097 117 IEALRKRL-LPLATLITPNLPEAEAL-------LGTKIRTEQDMIKAAKKLRELGPKAVLIKGG 172 (254)
T ss_pred HHHHHHhc-cccccEecCCHHHHHHH-------hCCCCCCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 34455554 35677888888887766 466666777777778888877765 777753
No 198
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=50.65 E-value=5.9 Score=28.72 Aligned_cols=18 Identities=22% Similarity=0.584 Sum_probs=10.5
Q ss_pred ccceeeecCCCCCcccce
Q 028248 150 RESLILKGPCPNCGTENV 167 (211)
Q Consensus 150 ~d~liLkG~CPnCg~Ev~ 167 (211)
+.+..+.|.||.|.+++.
T Consensus 49 ~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 49 QSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp -TTT--EEE-TTT-SEEE
T ss_pred eeecccccCCcCCCCeee
Confidence 445668899999999875
No 199
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=50.60 E-value=27 Score=26.00 Aligned_cols=47 Identities=26% Similarity=0.446 Sum_probs=27.1
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCC--CCCceeEEecC-ceeEeCC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCS--NCGTTMVYDSN-TRLITLP 206 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~--~C~~~L~f~~~-~r~i~~p 206 (211)
.||.||..-. .++=.........-..+|. +||...+-... .|.|.-|
T Consensus 3 ~CP~Cg~~a~--irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~s~tis~p 52 (72)
T PRK09678 3 HCPLCQHAAH--ARTSRYITDTTKERYHQCQNVNCSATFITYESVQRYIVKP 52 (72)
T ss_pred cCCCCCCccE--EEEChhcChhhheeeeecCCCCCCCEEEEEEEEEEEEcCC
Confidence 5999999873 2222222333455678898 78776665543 3444333
No 200
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=50.50 E-value=3.4 Score=37.86 Aligned_cols=37 Identities=32% Similarity=0.617 Sum_probs=25.8
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 202 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~ 202 (211)
-.||+|++-++.= .+ ..|...|+.|+.-+...+..|.
T Consensus 28 ~~c~~c~~~~~~~---~l------~~~~~vc~~c~~h~rl~areRi 64 (292)
T PRK05654 28 TKCPSCGQVLYRK---EL------EANLNVCPKCGHHMRISARERL 64 (292)
T ss_pred eECCCccchhhHH---HH------HhcCCCCCCCCCCeeCCHHHHH
Confidence 3699999988743 12 3455789999998876554443
No 201
>cd02674 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=50.48 E-value=17 Score=29.96 Aligned_cols=26 Identities=19% Similarity=0.438 Sum_probs=19.2
Q ss_pred cCceeCCCCCceeEEecCceeEeCCC
Q 028248 182 TNTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 182 ~~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
.+..+|+.|+..-...+..+...+|+
T Consensus 102 ~~~~~C~~C~~~~~~~~~~~i~~lP~ 127 (230)
T cd02674 102 DNAWKCPKCKKKRKATKKLTISRLPK 127 (230)
T ss_pred CCceeCCCCCCccceEEEEEEecCCh
Confidence 45689999998877666666666664
No 202
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=50.48 E-value=7.9 Score=39.05 Aligned_cols=24 Identities=25% Similarity=0.721 Sum_probs=17.0
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-.-||+||.+... ....||+||+.
T Consensus 568 ~~~C~~CG~~~~g--------------~~~~CP~CGs~ 591 (625)
T PRK08579 568 ITVCNKCGRSTTG--------------LYTRCPRCGSE 591 (625)
T ss_pred CccCCCCCCccCC--------------CCCcCcCCCCc
Confidence 3679999994411 14689999963
No 203
>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=49.92 E-value=10 Score=26.58 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=20.9
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
|++|..-|-... +......+..|+.||.
T Consensus 25 C~~C~~hNGla~------~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 25 CSKCFSHNGLAP------KEEFEEIQYRCPYCGA 52 (54)
T ss_pred Ccccchhhcccc------cccCCceEEEcCCCCC
Confidence 999999887664 2222556999999986
No 204
>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=49.58 E-value=15 Score=27.82 Aligned_cols=37 Identities=22% Similarity=0.576 Sum_probs=23.5
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.-.||+||.+--.|+-.-..-+.-..+--..|.+|+-
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~ 98 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY 98 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCC
Confidence 5699999988877872211112223455678888874
No 205
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=49.56 E-value=8.9 Score=22.20 Aligned_cols=22 Identities=32% Similarity=0.786 Sum_probs=16.2
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.||.|+..|++- +..|..|+++
T Consensus 4 ~C~~C~~~N~~~--------------~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFAS--------------RSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChhh--------------hccccccCCc
Confidence 589998776543 5578888874
No 206
>cd07114 ALDH_DhaS Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like. Uncharacterized aldehyde dehydrogenase from Candidatus pelagibacter (DhaS) and other related sequences are present in this CD.
Probab=49.51 E-value=52 Score=30.94 Aligned_cols=67 Identities=15% Similarity=0.409 Sum_probs=45.2
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEeCh-hhHHHHHHHHhhh----cC---------CCccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VMLSS-AEQKFLEASMAYV----AG---------KPIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l~~-~Eq~fLeA~~aY~----~G---------~Pi~sD~efD~Lk~~Lk 57 (211)
+|.+.|.--+.+.| .|.+| +.+.+ .-.+|++++.... -| -|+++.+.+|+++..++
T Consensus 239 ~dAdl~~aa~~i~~~~~~~~GQ~C~a~~~v~V~~~v~~~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~i~ 318 (457)
T cd07114 239 DDADLDAAVNGVVAGIFAAAGQTCVAGSRLLVQRSIYDEFVERLVARARAIRVGDPLDPETQMGPLATERQLEKVERYVA 318 (457)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCCCceEEEcHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 45667777777777 55555 34433 3467888876533 33 37889999999999887
Q ss_pred hh---CCeeeeecc
Q 028248 58 ME---GSEIVVEGP 68 (211)
Q Consensus 58 ~~---GS~vv~~~p 68 (211)
.. |.+++.-|.
T Consensus 319 ~a~~~ga~~l~gg~ 332 (457)
T cd07114 319 RAREEGARVLTGGE 332 (457)
T ss_pred HHHHCCCEEEeCCC
Confidence 54 888776553
No 207
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=49.33 E-value=3.4 Score=38.22 Aligned_cols=36 Identities=28% Similarity=0.549 Sum_probs=25.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 202 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~ 202 (211)
.||+|++-++.= .+ ..|...||.|+--+...+..|.
T Consensus 40 kc~~C~~~~~~~---~l------~~~~~vcp~c~~h~rltAreRI 75 (296)
T CHL00174 40 QCENCYGLNYKK---FL------KSKMNICEQCGYHLKMSSSDRI 75 (296)
T ss_pred ECCCccchhhHH---HH------HHcCCCCCCCCCCcCCCHHHHH
Confidence 599999988743 12 4667889999987665554443
No 208
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=49.10 E-value=15 Score=37.65 Aligned_cols=27 Identities=30% Similarity=0.593 Sum_probs=20.7
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNC 190 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C 190 (211)
-||+||.++..++.. ..-.-...|++|
T Consensus 131 ~C~~Cg~~~~~~~~~------~~~~~~~~C~~~ 157 (682)
T COG1241 131 ECPKCGREVEVEQSE------FRVEPPRECENC 157 (682)
T ss_pred EcCCCCCEEEEEecc------ccccCCccCCCc
Confidence 499999999999643 224455789999
No 209
>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=49.09 E-value=3.7 Score=37.53 Aligned_cols=33 Identities=30% Similarity=0.607 Sum_probs=23.2
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
.||+|++-++.= .+ ..|...||.|+.-+...+.
T Consensus 28 ~c~~c~~~~~~~---~l------~~~~~vc~~c~~h~rl~ar 60 (285)
T TIGR00515 28 KCPKCGQVLYTK---EL------ERNLEVCPKCDHHMRMDAR 60 (285)
T ss_pred ECCCCcchhhHH---HH------HhhCCCCCCCCCcCcCCHH
Confidence 599999988753 11 3556789999987654443
No 210
>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 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=48.82 E-value=10 Score=26.49 Aligned_cols=20 Identities=40% Similarity=1.017 Sum_probs=14.1
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
..||+||+-. ....-|++||
T Consensus 27 ~~c~~cg~~~---------------~~H~vc~~cG 46 (56)
T PF01783_consen 27 VKCPNCGEPK---------------LPHRVCPSCG 46 (56)
T ss_dssp EESSSSSSEE---------------STTSBCTTTB
T ss_pred eeeccCCCEe---------------cccEeeCCCC
Confidence 5799999622 3335699998
No 212
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=48.81 E-value=43 Score=29.52 Aligned_cols=53 Identities=15% Similarity=0.142 Sum_probs=38.5
Q ss_pred HhHHhhhcccCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC-eeeeec
Q 028248 7 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEG 67 (211)
Q Consensus 7 d~lkeel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~GS-~vv~~~ 67 (211)
+.+|++| .....+++.+..|-++| .|.++-++++..+.-.+|...|. .|++++
T Consensus 143 ~~~~~~L-l~~advitPN~~Ea~~L-------~g~~~~~~~~~~~~~~~l~~~g~~~VvIT~ 196 (281)
T PRK08176 143 EAYRQHL-LPLAQGLTPNIFELEIL-------TGKPCRTLDSAIAAAKSLLSDTLKWVVITS 196 (281)
T ss_pred HHHHHHh-HhhcCEeCCCHHHHHHH-------hCCCCCCHHHHHHHHHHHHhcCCCEEEEee
Confidence 4566555 47788888888887776 47787777777777777877785 466664
No 213
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=48.39 E-value=2.9 Score=38.74 Aligned_cols=39 Identities=33% Similarity=0.623 Sum_probs=30.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL 205 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~ 205 (211)
.||.|++=+|.= .+ ..|...|++|+--+...+..|+..+
T Consensus 30 KCp~c~~~~y~~---eL------~~n~~vcp~c~~h~ri~A~~Ri~~l 68 (294)
T COG0777 30 KCPSCGEMLYRK---EL------ESNLKVCPKCGHHMRISARERLEAL 68 (294)
T ss_pred ECCCccceeeHH---HH------HhhhhcccccCcccccCHHHHHHHh
Confidence 599999877642 33 5788899999999988887776544
No 214
>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=48.36 E-value=9.5 Score=26.97 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=23.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
-|++|+.=..-- +.-..-+.|||-|++.-.+++.
T Consensus 6 RC~~CnklLa~~--------g~~~~leIKCpRC~tiN~~~a~ 39 (51)
T PF10122_consen 6 RCGHCNKLLAKA--------GEVIELEIKCPRCKTINHVRAT 39 (51)
T ss_pred eccchhHHHhhh--------cCccEEEEECCCCCccceEecc
Confidence 488887644321 1224568999999998888774
No 215
>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=47.60 E-value=13 Score=24.24 Aligned_cols=17 Identities=24% Similarity=0.722 Sum_probs=12.5
Q ss_pred eeCCCCCceeEEecCce
Q 028248 185 INCSNCGTTMVYDSNTR 201 (211)
Q Consensus 185 ~kC~~C~~~L~f~~~~r 201 (211)
.+||.||..|..+...+
T Consensus 2 ~~CP~Cg~~lv~r~~k~ 18 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKK 18 (39)
T ss_pred cCCCCCCceeEEEECCC
Confidence 36888888888877543
No 216
>PRK04351 hypothetical protein; Provisional
Probab=47.57 E-value=18 Score=30.07 Aligned_cols=34 Identities=21% Similarity=0.487 Sum_probs=25.5
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
=.|.+||.+...- ..+ ++.+..|..|+..|.+-.
T Consensus 113 Y~C~~Cg~~~~r~----Rr~----n~~~yrCg~C~g~L~~~~ 146 (149)
T PRK04351 113 YECQSCGQQYLRK----RRI----NTKRYRCGKCRGKLKLIN 146 (149)
T ss_pred EECCCCCCEeeee----eec----CCCcEEeCCCCcEeeecc
Confidence 4799999765432 333 578999999999998864
No 217
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.25 E-value=9.9 Score=36.92 Aligned_cols=33 Identities=30% Similarity=0.651 Sum_probs=23.0
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.+--||-||....+= +.+ -.+|+.||+.+--..
T Consensus 349 ~~p~Cp~Cg~~m~S~----------G~~-g~rC~kCg~~~~~~~ 381 (421)
T COG1571 349 VNPVCPRCGGRMKSA----------GRN-GFRCKKCGTRARETL 381 (421)
T ss_pred cCCCCCccCCchhhc----------CCC-CcccccccccCCccc
Confidence 344799999765443 333 899999999765443
No 218
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=47.20 E-value=10 Score=29.96 Aligned_cols=44 Identities=20% Similarity=0.435 Sum_probs=27.9
Q ss_pred HHHHHHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 139 YLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 139 ~~a~~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-+|.+|.+- -+.+++.-..|-+||.|.+.- . -+--.+||-|++.
T Consensus 42 hiak~lkr~-g~~Llv~Pa~CkkCGfef~~~-----~-----ik~pSRCP~CKSE 85 (97)
T COG3357 42 HIAKSLKRK-GKRLLVRPARCKKCGFEFRDD-----K-----IKKPSRCPKCKSE 85 (97)
T ss_pred HHHHHHHhC-CceEEecChhhcccCcccccc-----c-----cCCcccCCcchhh
Confidence 455544432 234566778899999886551 1 1334689999875
No 219
>PRK07591 threonine synthase; Validated
Probab=46.58 E-value=14 Score=34.89 Aligned_cols=31 Identities=19% Similarity=0.348 Sum_probs=22.6
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.+=.|+.||.+.-. +.. ..|+.||..|.++-
T Consensus 17 ~~l~C~~Cg~~~~~------------~~~-~~C~~cg~~l~~~y 47 (421)
T PRK07591 17 VALKCRECGAEYPL------------GPI-HVCEECFGPLEVAY 47 (421)
T ss_pred eEEEeCCCCCcCCC------------CCC-ccCCCCCCeEEEEe
Confidence 35679999988321 223 78999999998774
No 220
>PRK08173 DNA topoisomerase III; Validated
Probab=46.13 E-value=12 Score=39.03 Aligned_cols=27 Identities=30% Similarity=0.850 Sum_probs=18.4
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.|+||.||.++. . ......|++|+-.+
T Consensus 624 ~~~CP~Cg~~~~---------~---~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 624 QTPCPNCGGVVK---------E---NYRRFACTKCDFSI 650 (862)
T ss_pred cccCCccccccc---------c---cCceeEcCCCCccc
Confidence 488999998641 1 13348899987554
No 221
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=45.78 E-value=11 Score=32.78 Aligned_cols=22 Identities=23% Similarity=0.388 Sum_probs=18.9
Q ss_pred hhccceeeecCCCCCcccceee
Q 028248 148 IVRESLILKGPCPNCGTENVSF 169 (211)
Q Consensus 148 ~~~d~liLkG~CPnCg~Ev~aF 169 (211)
.+++.+|+...||+||+.+..-
T Consensus 22 ~F~evii~sf~C~~CGyr~~ev 43 (192)
T TIGR00310 22 YFGEVLETSTICEHCGYRSNDV 43 (192)
T ss_pred CcceEEEEEEECCCCCCcccee
Confidence 3789999999999999998743
No 222
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=45.68 E-value=14 Score=22.02 Aligned_cols=36 Identities=22% Similarity=0.449 Sum_probs=19.8
Q ss_pred CCCCCcccceeeccccccccCCCCcCc--eeCCCCCceeE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNT--INCSNCGTTMV 195 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~--~kC~~C~~~L~ 195 (211)
.|+.|++.+..--..+. ..+..-|. .+|+.|++.|.
T Consensus 1 ~C~~C~~~i~~~~~~~~--~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLR--ALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEE--eCCccccccCCCCcccCCcCc
Confidence 38888887764100011 12223333 67899998774
No 223
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=45.42 E-value=50 Score=25.78 Aligned_cols=32 Identities=34% Similarity=0.618 Sum_probs=24.7
Q ss_pred HHHHHHHHhhhcCCCcc--------------ChHHHHHHHHHHhhhC
Q 028248 28 QKFLEASMAYVAGKPIM--------------SDEEYDKLKQKLKMEG 60 (211)
Q Consensus 28 q~fLeA~~aY~~G~Pi~--------------sD~efD~Lk~~Lk~~G 60 (211)
++|++.+..+ .++|+. +.+.+|+++++|+.+|
T Consensus 50 ~~Fi~~l~~~-~~~~Ls~LT~GvH~HtI~a~~~e~l~~I~~~L~~~G 95 (98)
T PF02829_consen 50 DKFIEKLEKS-KAKPLSSLTGGVHYHTIEAPDEEDLDKIEEALKKKG 95 (98)
T ss_dssp HHHHHHHHH---S--STTGGGGEEEEEEEESSHHHHHHHHHHHHHTT
T ss_pred HHHHHHHhcc-CCcchHHhcCCEeeEEEEECCHHHHHHHHHHHHHCC
Confidence 8999999887 778875 4689999999999988
No 224
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.27 E-value=12 Score=30.69 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=24.3
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
-|--||+||.-+|-. ++.-+.||-||.+.
T Consensus 8 tKridPetg~KFYDL-----------NrdPiVsPytG~s~ 36 (129)
T COG4530 8 TKRIDPETGKKFYDL-----------NRDPIVSPYTGKSY 36 (129)
T ss_pred ccccCccccchhhcc-----------CCCccccCcccccc
Confidence 466799999998877 77788999999865
No 225
>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=45.24 E-value=11 Score=32.02 Aligned_cols=21 Identities=14% Similarity=0.392 Sum_probs=18.8
Q ss_pred hhccceeeecCCCCCccccee
Q 028248 148 IVRESLILKGPCPNCGTENVS 168 (211)
Q Consensus 148 ~~~d~liLkG~CPnCg~Ev~a 168 (211)
.+++.+|+...||+||+.+.-
T Consensus 20 ~F~evii~sf~C~~CGyr~~e 40 (163)
T TIGR00340 20 YFGKIMLSTYICEKCGYRSTD 40 (163)
T ss_pred CcceEEEEEEECCCCCCchhh
Confidence 489999999999999998873
No 226
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=45.18 E-value=11 Score=37.29 Aligned_cols=25 Identities=28% Similarity=0.788 Sum_probs=11.6
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCce-eEE
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT-MVY 196 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~-L~f 196 (211)
.-|++||... . . .-+||+||.. ++.
T Consensus 492 ~~C~~CG~~~-----~---------~-~~~CP~CGs~~~~~ 517 (546)
T PF13597_consen 492 DICPDCGYIG-----G---------E-GDKCPKCGSENIEV 517 (546)
T ss_dssp EEETTT---S-----------------EEE-CCC----EEE
T ss_pred ccccCCCcCC-----C---------C-CCCCCCCCCcccce
Confidence 4699999621 1 2 5679999998 443
No 227
>PRK14973 DNA topoisomerase I; Provisional
Probab=45.12 E-value=22 Score=37.62 Aligned_cols=12 Identities=50% Similarity=1.245 Sum_probs=9.4
Q ss_pred ecCCCCCcccce
Q 028248 156 KGPCPNCGTENV 167 (211)
Q Consensus 156 kG~CPnCg~Ev~ 167 (211)
.|+||.||.++.
T Consensus 588 ~~~CP~CG~~l~ 599 (936)
T PRK14973 588 IGPCPVCGKDLR 599 (936)
T ss_pred cccCCcccccce
Confidence 489999997653
No 228
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=44.74 E-value=16 Score=33.61 Aligned_cols=18 Identities=17% Similarity=0.630 Sum_probs=16.0
Q ss_pred cCceeCCCCCceeEEecC
Q 028248 182 TNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 182 ~~~~kC~~C~~~L~f~~~ 199 (211)
....+||.|+..++|+|+
T Consensus 75 rF~~kC~~C~~~i~~kTD 92 (324)
T PF04502_consen 75 RFYIKCPRCSNEIEFKTD 92 (324)
T ss_pred EEEEEcCCCCCEEeeecC
Confidence 567899999999999994
No 229
>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=44.72 E-value=14 Score=25.73 Aligned_cols=39 Identities=31% Similarity=0.705 Sum_probs=18.3
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCC
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLP 206 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~p 206 (211)
...|+.|+..+ ++| +.+.-|..||..+==+=....+.+|
T Consensus 9 ~~~C~~C~~~F-~~~-----------~rrhhCr~CG~~vC~~Cs~~~~~~~ 47 (69)
T PF01363_consen 9 ASNCMICGKKF-SLF-----------RRRHHCRNCGRVVCSSCSSQRIPLP 47 (69)
T ss_dssp -SB-TTT--B--BSS-----------S-EEE-TTT--EEECCCS-EEEEET
T ss_pred CCcCcCcCCcC-CCc-----------eeeEccCCCCCEECCchhCCEEccc
Confidence 35799999997 553 6788999999865433334444333
No 230
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.56 E-value=12 Score=34.08 Aligned_cols=35 Identities=26% Similarity=0.438 Sum_probs=24.7
Q ss_pred CCCCCcccce---eeccccccccCCCC------------cCceeCCCCCc
Q 028248 158 PCPNCGTENV---SFFGTILSISSGGT------------TNTINCSNCGT 192 (211)
Q Consensus 158 ~CPnCg~Ev~---aFfg~i~~v~s~~~------------~~~~kC~~C~~ 192 (211)
.||+|++-+. .++|.|..+++.-+ -+-+.||+|.-
T Consensus 21 eCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 21 ECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred ccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 6999998765 57777776665322 25578999973
No 231
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=44.33 E-value=11 Score=28.13 Aligned_cols=43 Identities=30% Similarity=0.655 Sum_probs=24.9
Q ss_pred ecCCCCCcccce---------eeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 156 KGPCPNCGTENV---------SFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 156 kG~CPnCg~Ev~---------aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
...||-||.-++ .++..|.-|+.+. ---.-|.+||-.=-|+++
T Consensus 4 ~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~-f~~itCk~CgYtEfY~a~ 55 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNK-FIVITCKNCGYTEFYSAK 55 (68)
T ss_pred cccCCCcCCcchhhceeeccCCCcceeEEecccE-EEEEEeccCCchhheecc
Confidence 456999997665 2333333343321 123569999977666654
No 232
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=44.32 E-value=17 Score=37.47 Aligned_cols=39 Identities=21% Similarity=0.445 Sum_probs=22.8
Q ss_pred hhhHHHHHHHHh-hhcCCCcc--------ChHHHHHHHHHHhhhCCeeeee
Q 028248 25 SAEQKFLEASMA-YVAGKPIM--------SDEEYDKLKQKLKMEGSEIVVE 66 (211)
Q Consensus 25 ~~Eq~fLeA~~a-Y~~G~Pi~--------sD~efD~Lk~~Lk~~GS~vv~~ 66 (211)
-+.-.||+|... -..||.++ .+.+.+++|.+. |.+|++.
T Consensus 229 GKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rF---g~~v~vl 276 (730)
T COG1198 229 GKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARF---GAKVAVL 276 (730)
T ss_pred cHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHh---CCChhhh
Confidence 344566666655 55665543 466677776665 3666653
No 233
>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=44.16 E-value=17 Score=22.28 Aligned_cols=10 Identities=50% Similarity=1.261 Sum_probs=4.3
Q ss_pred CCCCccccee
Q 028248 159 CPNCGTENVS 168 (211)
Q Consensus 159 CPnCg~Ev~a 168 (211)
||.||.++..
T Consensus 2 CP~C~s~l~~ 11 (28)
T PF03119_consen 2 CPVCGSKLVR 11 (28)
T ss_dssp -TTT--BEEE
T ss_pred cCCCCCEeEc
Confidence 6666666653
No 234
>PTZ00381 aldehyde dehydrogenase family protein; Provisional
Probab=44.13 E-value=55 Score=31.68 Aligned_cols=65 Identities=23% Similarity=0.488 Sum_probs=45.1
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE-----Ee-ChhhHHHHHHHH----hhhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV-----ML-SSAEQKFLEASM----AYVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~-----~l-~~~Eq~fLeA~~----aY~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.-.+.+.| .|-.|+ .+ .....+|++++. .++ |. |+++++.|++++.-++
T Consensus 226 ~dAdl~~Aa~~i~~g~~~naGQ~C~A~~~vlV~~~i~d~f~~~l~~~~~~~~-g~~~~~~~~~gpli~~~~~~ri~~~i~ 304 (493)
T PTZ00381 226 KSCNLKVAARRIAWGKFLNAGQTCVAPDYVLVHRSIKDKFIEALKEAIKEFF-GEDPKKSEDYSRIVNEFHTKRLAELIK 304 (493)
T ss_pred CCCCHHHHHHHHHHHHHhhcCCcCCCCCEEEEeHHHHHHHHHHHHHHHHHHh-CCCCccCCCcCCCCCHHHHHHHHHHHH
Confidence 45667777777877 365543 33 333567888764 344 43 6799999999999998
Q ss_pred hhCCeeeeec
Q 028248 58 MEGSEIVVEG 67 (211)
Q Consensus 58 ~~GS~vv~~~ 67 (211)
.+|.+++.-|
T Consensus 305 ~~ga~~~~gG 314 (493)
T PTZ00381 305 DHGGKVVYGG 314 (493)
T ss_pred hCCCcEEECC
Confidence 8898887644
No 235
>cd07092 ALDH_ABALDH-YdcW Escherichia coli NAD+-dependent gamma-aminobutyraldehyde dehydrogenase YdcW-like. NAD+-dependent, tetrameric, gamma-aminobutyraldehyde dehydrogenase (ABALDH), YdcW of Escherichia coli K12, catalyzes the oxidation of gamma-aminobutyraldehyde to gamma-aminobutyric acid. ABALDH can also oxidize n-alkyl medium-chain aldehydes, but with a lower catalytic efficiency.
Probab=43.99 E-value=77 Score=29.62 Aligned_cols=67 Identities=15% Similarity=0.297 Sum_probs=44.6
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEeC-hhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VMLS-SAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l~-~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|.+| +.+. ..-.+|++++.+ +.-|. |+++.+.+++++.-+.
T Consensus 237 ~dAdl~~aa~~iv~~~~~~~GQ~C~a~~~v~V~~~i~~~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~i~~~i~ 316 (450)
T cd07092 237 DDADLDAAVAGIATAGYYNAGQDCTAACRVYVHESVYDEFVAALVEAVSAIRVGDPDDEDTEMGPLNSAAQRERVAGFVE 316 (450)
T ss_pred CCCCHHHHHHHHHHHHHhhCCCCCCCCcEEEEeHHHHHHHHHHHHHHHhhCCcCCCCCCCCccCcccCHHHHHHHHHHHH
Confidence 46677888888888 45444 3333 345789988754 33453 5788899999998665
Q ss_pred hh--CCeeeeecc
Q 028248 58 ME--GSEIVVEGP 68 (211)
Q Consensus 58 ~~--GS~vv~~~p 68 (211)
.. |.+++.-|.
T Consensus 317 ~a~~ga~~~~gg~ 329 (450)
T cd07092 317 RAPAHARVLTGGR 329 (450)
T ss_pred HHHcCCEEEeCCC
Confidence 54 777766543
No 236
>cd07120 ALDH_PsfA-ACA09737 Pseudomonas putida aldehyde dehydrogenase PsfA (ACA09737)-like. Included in this CD is the aldehyde dehydrogenase (PsfA, locus ACA09737) of Pseudomonas putida involved in furoic acid metabolism. Transcription of psfA was induced in response to 2-furoic acid, furfuryl alcohol, and furfural.
Probab=43.90 E-value=73 Score=30.27 Aligned_cols=68 Identities=19% Similarity=0.360 Sum_probs=45.9
Q ss_pred ChHHHHhHHhhhcc-----cCCe------eEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGss------v~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
+|.+.|...+.+.| .|-+ +++-+..-.+|+|++.+ ..-|. |+++.+.+|+++.-+.
T Consensus 238 ~daDl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~~~f~~~l~~~~~~l~~G~p~~~~~~~gpli~~~~~~~~~~~i~ 317 (455)
T cd07120 238 DDADLDAALPKLERALTIFAGQFCMAGSRVLVQRSIADEVRDRLAARLAAVKVGPGLDPASDMGPLIDRANVDRVDRMVE 317 (455)
T ss_pred CCCCHHHHHHHHHHHHHHhCCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhcCcCCCCCCCCCcCCccCHHHHHHHHHHHH
Confidence 46677888888877 3433 33333445788888654 33343 6899999999998776
Q ss_pred h---hCCeeeeeccc
Q 028248 58 M---EGSEIVVEGPR 69 (211)
Q Consensus 58 ~---~GS~vv~~~pr 69 (211)
. +|.+++..|.+
T Consensus 318 ~a~~~ga~~~~~g~~ 332 (455)
T cd07120 318 RAIAAGAEVVLRGGP 332 (455)
T ss_pred HHHHCCCEEEeCCcc
Confidence 5 68888876643
No 237
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=43.76 E-value=26 Score=28.23 Aligned_cols=34 Identities=18% Similarity=0.610 Sum_probs=24.3
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
.-.|..||+....- ....+..+..|..|+..|.+
T Consensus 112 ~y~C~~C~~~~~~~-------rr~~~~~~y~C~~C~g~l~~ 145 (146)
T smart00731 112 PYRCTGCGQRYLRV-------RRSNNVSRYRCGKCGGKLIL 145 (146)
T ss_pred EEECCCCCCCCceE-------ccccCcceEEcCCCCCEEEe
Confidence 45799999886422 33334488999999998875
No 238
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=43.55 E-value=16 Score=40.09 Aligned_cols=40 Identities=30% Similarity=0.522 Sum_probs=27.3
Q ss_pred eeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 153 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 153 liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
|.=-=-||+|.+ +-|+ ++-++-++=+--.-.||.||++|.
T Consensus 911 L~PHY~Cp~Cky--~Ef~-~d~svgsGfDLpdK~CPkCg~pl~ 950 (1444)
T COG2176 911 LPPHYLCPECKY--SEFI-DDGSVGSGFDLPDKDCPKCGTPLK 950 (1444)
T ss_pred CCccccCCCCce--eeee-cCCCcCCCCCCCCCCCCcCCCccc
Confidence 444556999986 3343 223566666777789999999964
No 239
>PF08976 DUF1880: Domain of unknown function (DUF1880); InterPro: IPR015070 This entry represents EF-hand calcium-binding domain-containing protein 6 that negatively regulates the androgen receptor by recruiting histone deacetylase complex, and protein DJ-1 antagonises this inhibition by abrogation of this complex [].; PDB: 1WLZ_C.
Probab=43.40 E-value=11 Score=30.83 Aligned_cols=17 Identities=35% Similarity=0.640 Sum_probs=11.4
Q ss_pred CChHHHHhHHhh--hcccC
Q 028248 1 MSNEEFDNLKEE--LMWEG 17 (211)
Q Consensus 1 ~s~eefd~lkee--l~weG 17 (211)
|||||||+|=.| |+|+|
T Consensus 4 LtDeQFdrLW~e~Pvn~~G 22 (118)
T PF08976_consen 4 LTDEQFDRLWNEMPVNAKG 22 (118)
T ss_dssp --HHHHHHHHTTS-B-TTS
T ss_pred ccHHHhhhhhhhCcCCccC
Confidence 799999999776 45666
No 240
>PLN02766 coniferyl-aldehyde dehydrogenase
Probab=43.37 E-value=69 Score=30.93 Aligned_cols=67 Identities=16% Similarity=0.426 Sum_probs=43.9
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEe-ChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VML-SSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l-~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+...| .|-+| +.+ ...-.+|+|++.+ +.-|. |+++.+.+|+++.-+.
T Consensus 279 ~dADl~~Aa~~i~~g~f~n~GQ~C~a~~ri~V~~si~d~f~~~l~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~v~~~i~ 358 (501)
T PLN02766 279 DDADVDMAVDLALLGIFYNKGEICVASSRVYVQEGIYDEFVKKLVEKAKDWVVGDPFDPRARQGPQVDKQQFEKILSYIE 358 (501)
T ss_pred CCCCHHHHHHHHHHHHHhhcCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Confidence 45566666666666 34433 333 4445678887643 55454 6899999999998875
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+|+.-|.
T Consensus 359 ~a~~~Ga~v~~gG~ 372 (501)
T PLN02766 359 HGKREGATLLTGGK 372 (501)
T ss_pred HHHhCCCEEEeCCC
Confidence 4 4888877554
No 241
>cd07078 ALDH NAD(P)+ dependent aldehyde dehydrogenase family. The aldehyde dehydrogenase family (ALDH) of NAD(P)+ dependent enzymes, in general, oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or as osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer
Probab=42.91 E-value=80 Score=29.03 Aligned_cols=66 Identities=20% Similarity=0.450 Sum_probs=41.0
Q ss_pred hHHHHhHHhhhcc-----cCC-----eeEEeCh-hhHHHHHHHH----hhhcCC---------CccChHHHHHHHHHHhh
Q 028248 3 NEEFDNLKEELMW-----EGS-----SVVMLSS-AEQKFLEASM----AYVAGK---------PIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 3 ~eefd~lkeel~w-----eGs-----sv~~l~~-~Eq~fLeA~~----aY~~G~---------Pi~sD~efD~Lk~~Lk~ 58 (211)
|.++|...+.+.| .|- +.+.+.+ .-.+|++++. .+.-|. |+++.+.+++++..+..
T Consensus 217 ~ad~~~aa~~i~~~~~~~~Gq~C~a~~~i~v~~~~~~~~~~~L~~~l~~~~~g~p~~~~~~~~~~~~~~~~~~~~~~i~~ 296 (432)
T cd07078 217 DADLDAAVKGAVFGAFGNAGQVCTAASRLLVHESIYDEFVERLVERVKALKVGNPLDPDTDMGPLISAAQLDRVLAYIED 296 (432)
T ss_pred CCCHHHHHHHHHHHHHhccCCCccCCceEEEcHHHHHHHHHHHHHHHHccCcCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Confidence 3445555555444 453 3344443 3467888754 355554 48899999999988876
Q ss_pred ---hCCeeeeecc
Q 028248 59 ---EGSEIVVEGP 68 (211)
Q Consensus 59 ---~GS~vv~~~p 68 (211)
.|.+++..++
T Consensus 297 ~~~~g~~~~~gg~ 309 (432)
T cd07078 297 AKAEGAKLLCGGK 309 (432)
T ss_pred HHhCCCEEEeCCc
Confidence 5777876543
No 242
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=42.88 E-value=27 Score=23.36 Aligned_cols=31 Identities=23% Similarity=0.719 Sum_probs=21.4
Q ss_pred CCC--CCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 158 PCP--NCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 158 ~CP--nCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
.|| +|+.-+..- . +.....++|+.|+...=|
T Consensus 20 ~CP~~~C~~~~~~~-------~-~~~~~~v~C~~C~~~fC~ 52 (64)
T smart00647 20 WCPAPDCSAAIIVT-------E-EEGCNRVTCPKCGFSFCF 52 (64)
T ss_pred CCCCCCCcceEEec-------C-CCCCCeeECCCCCCeECC
Confidence 799 998765442 1 235678999999876544
No 243
>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=42.87 E-value=8.1 Score=40.65 Aligned_cols=47 Identities=30% Similarity=0.482 Sum_probs=0.0
Q ss_pred ChHHHHhHHhhhc-----ccC---CeeEEeCh--hhHHHHHHHHh--hhcCCCccChHH
Q 028248 2 SNEEFDNLKEELM-----WEG---SSVVMLSS--AEQKFLEASMA--YVAGKPIMSDEE 48 (211)
Q Consensus 2 s~eefd~lkeel~-----weG---ssv~~l~~--~Eq~fLeA~~a--Y~~G~Pi~sD~e 48 (211)
|-||+..|++-+. |++ ..++.+.. .-++.||.+-- ...++-|+-++.
T Consensus 497 s~ee~~~L~~~v~~~~~~~~~~~~~~~l~l~~~~~~K~iLE~L~v~H~v~~~~iii~~~ 555 (900)
T PF03833_consen 497 SPEELNKLAEAVSEAEIEWSGEDNKGVLVLPYDEKIKRILEKLLVPHKVRDGKIIIEEW 555 (900)
T ss_dssp -----------------------------------------------------------
T ss_pred CHHHHHHHHHHHHhccccccccccceeEecCCcHHHHHHHHHhCCcEEEcCCeEEEecc
Confidence 5567777776654 433 23444444 34667777542 555555555533
No 244
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=42.73 E-value=11 Score=27.31 Aligned_cols=14 Identities=36% Similarity=1.210 Sum_probs=10.3
Q ss_pred CCCCCcccce--eecc
Q 028248 158 PCPNCGTENV--SFFG 171 (211)
Q Consensus 158 ~CPnCg~Ev~--aFfg 171 (211)
.|||||.+-+ .+||
T Consensus 17 ~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 17 RCPVCGSRDLSDEWFD 32 (61)
T ss_pred cCCCCcCCcccccccc
Confidence 6999998774 3455
No 245
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=42.40 E-value=10 Score=40.83 Aligned_cols=16 Identities=44% Similarity=0.818 Sum_probs=13.1
Q ss_pred eeecCCCCCcccceee
Q 028248 154 ILKGPCPNCGTENVSF 169 (211)
Q Consensus 154 iLkG~CPnCg~Ev~aF 169 (211)
+-++.|||||-++++.
T Consensus 5 ~y~~~CPnCgg~i~~~ 20 (1171)
T TIGR01054 5 VYSNLCPNCGGEISSE 20 (1171)
T ss_pred hhcCCCCCCCCccchh
Confidence 4688999999988764
No 246
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=42.36 E-value=24 Score=32.60 Aligned_cols=39 Identities=18% Similarity=0.558 Sum_probs=26.1
Q ss_pred ecCCCCCcccceeeccccccccCCCC--cCceeCCCCCceeEE
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGT--TNTINCSNCGTTMVY 196 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~--~~~~kC~~C~~~L~f 196 (211)
..+||.||...-.||-. -..+... +--+.|.+||-.-.|
T Consensus 258 ~~~C~~C~~~~~~~~q~--QtrsaDEpmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQL--QTRSADEPMTTFVTCEECGNRWKF 298 (299)
T ss_pred cccCCCCCCccceEEEe--cccCCCCCCeEEEEcCCCCCeeee
Confidence 36999999988888732 2233333 334589999976554
No 247
>PF04280 Tim44: Tim44-like domain; InterPro: IPR007379 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane []. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005744 mitochondrial inner membrane presequence translocase complex; PDB: 2CW9_A 2FXT_A 3QK9_A.
Probab=42.36 E-value=16 Score=28.65 Aligned_cols=37 Identities=30% Similarity=0.668 Sum_probs=29.5
Q ss_pred eChhhHHHHHHHHhhhcCC-----CccChHHHHHHHHHHhhh
Q 028248 23 LSSAEQKFLEASMAYVAGK-----PIMSDEEYDKLKQKLKME 59 (211)
Q Consensus 23 l~~~Eq~fLeA~~aY~~G~-----Pi~sD~efD~Lk~~Lk~~ 59 (211)
+...++.|+....||.+|+ +.+++++|..++.++++.
T Consensus 21 ~~~ak~~f~~i~~A~~~~D~~~l~~~~t~~~~~~~~~~i~~~ 62 (147)
T PF04280_consen 21 LEEAKEAFLPIQEAWAKGDLEALRPLLTEELYERLQAEIKAR 62 (147)
T ss_dssp HHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHhCHHHHHHHHHHHHHH
Confidence 3455777888777899985 899999999999999988
No 248
>cd07105 ALDH_SaliADH Salicylaldehyde dehydrogenase, DoxF-like. Salicylaldehyde dehydrogenase (DoxF, SaliADH, EC=1.2.1.65) involved in the upper naphthalene catabolic pathway of Pseudomonas strain C18 and other similar sequences are present in this CD.
Probab=42.32 E-value=79 Score=29.55 Aligned_cols=68 Identities=22% Similarity=0.438 Sum_probs=45.1
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEeC-hhhHHHHHHHHh----hhcC----CCccChHHHHHHHHHHhh---h
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VMLS-SAEQKFLEASMA----YVAG----KPIMSDEEYDKLKQKLKM---E 59 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l~-~~Eq~fLeA~~a----Y~~G----~Pi~sD~efD~Lk~~Lk~---~ 59 (211)
.|.+.|.--+.+.| .|-+| +.+. ..-.+|+|++.+ +.-| -|+++.+.+++++.-+.. .
T Consensus 221 ~dadl~~aa~~i~~~~~~~~GQ~C~a~~~v~V~~~i~~~f~~~l~~~~~~~~~g~~~~gp~i~~~~~~~~~~~i~~a~~~ 300 (432)
T cd07105 221 EDADLDAAANAALFGAFLNSGQICMSTERIIVHESIADEFVEKLKAAAEKLFAGPVVLGSLVSAAAADRVKELVDDALSK 300 (432)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCcCCceEEEcHHHHHHHHHHHHHHHHhhcCCCCcccccCCHHHHHHHHHHHHHHHHC
Confidence 45667777777777 35433 3333 334578888654 3222 389999999999988765 5
Q ss_pred CCeeeeeccc
Q 028248 60 GSEIVVEGPR 69 (211)
Q Consensus 60 GS~vv~~~pr 69 (211)
|.+++.-+++
T Consensus 301 ga~~~~gg~~ 310 (432)
T cd07105 301 GAKLVVGGLA 310 (432)
T ss_pred CCEEEeCCCc
Confidence 8888776554
No 249
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=42.26 E-value=12 Score=22.46 Aligned_cols=10 Identities=40% Similarity=0.746 Sum_probs=8.0
Q ss_pred CCCCCcccce
Q 028248 158 PCPNCGTENV 167 (211)
Q Consensus 158 ~CPnCg~Ev~ 167 (211)
+||.|++.+.
T Consensus 3 ~CPiC~~~v~ 12 (26)
T smart00734 3 QCPVCFREVP 12 (26)
T ss_pred cCCCCcCccc
Confidence 6899988873
No 250
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=42.18 E-value=18 Score=34.73 Aligned_cols=43 Identities=23% Similarity=0.556 Sum_probs=22.5
Q ss_pred eecCCCCCcccceeecccccccc----CCCCcCceeCCCCCceeEEecC
Q 028248 155 LKGPCPNCGTENVSFFGTILSIS----SGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~----s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
++|.||.||++- -+|++--.- ....-..-.|.-||++++++..
T Consensus 135 v~g~cp~c~~~~--~~g~~ce~cg~~~~~~~l~~p~~~~~~~~~e~~~~ 181 (530)
T TIGR00398 135 VEGTCPKCGSED--ARGDHCEVCGRHLEPTELINPRCKICGAKPELRDS 181 (530)
T ss_pred hcCCCCCCCCcc--cccchhhhccccCCHHHhcCCccccCCCcceEEec
Confidence 568999998861 122221000 0001122347778888887764
No 251
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=42.16 E-value=19 Score=36.87 Aligned_cols=26 Identities=27% Similarity=0.759 Sum_probs=16.5
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.-||+||. -|-+..+ .....||+||.
T Consensus 642 ~~C~~CG~-----~Ge~~~~-----~~~~~CP~CG~ 667 (711)
T PRK09263 642 DECYECGF-----TGEFECT-----EKGFTCPKCGN 667 (711)
T ss_pred cccCCCCC-----CccccCC-----CCCCcCcCCCC
Confidence 57999996 2332211 22368999996
No 252
>cd01169 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
Probab=42.13 E-value=1e+02 Score=25.73 Aligned_cols=54 Identities=22% Similarity=0.393 Sum_probs=37.5
Q ss_pred HHhHHhhhcccCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC-eeeeec
Q 028248 6 FDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEG 67 (211)
Q Consensus 6 fd~lkeel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~GS-~vv~~~ 67 (211)
.+.++++| +....+++.+..|-+.| .|+++-++++-.+..++|...|- .|++++
T Consensus 118 ~~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~~~~l~~~g~~~Vvit~ 172 (242)
T cd01169 118 IEALRELL-LPLATLITPNLPEAELL-------TGLEIATEEDMMKAAKALLALGAKAVLIKG 172 (242)
T ss_pred HHHHHHHh-hccCeEEeCCHHHHHHH-------hCCCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence 34566665 67889999999998776 46666666655556677777775 466664
No 253
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=41.92 E-value=15 Score=34.99 Aligned_cols=27 Identities=33% Similarity=0.773 Sum_probs=22.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-||+|++-|=+. -.+|+.|+..|+-..
T Consensus 278 ~CP~CkakvCsL--------------P~eCpiC~ltLVss~ 304 (378)
T KOG2807|consen 278 FCPQCKAKVCSL--------------PIECPICSLTLVSSP 304 (378)
T ss_pred eCCcccCeeecC--------------CccCCccceeEecch
Confidence 499999998877 357999999998644
No 254
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=41.39 E-value=12 Score=25.61 Aligned_cols=36 Identities=25% Similarity=0.593 Sum_probs=25.4
Q ss_pred eeecCCCCCcccce-eeccccccccCCCCcCceeCCCCCcee
Q 028248 154 ILKGPCPNCGTENV-SFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 154 iLkG~CPnCg~Ev~-aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
+-.|.|-.|+.++. +.+-. +.+ ...-+.|++||+.|
T Consensus 20 v~~~~C~gC~~~l~~~~~~~---i~~--~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 20 VEGGTCSGCHMELPPQELNE---IRK--GDEIVFCPNCGRIL 56 (56)
T ss_pred eeCCccCCCCEEcCHHHHHH---HHc--CCCeEECcCCCccC
Confidence 34688999999987 44333 232 25678999999865
No 255
>PRK12412 pyridoxal kinase; Reviewed
Probab=41.25 E-value=88 Score=27.26 Aligned_cols=56 Identities=27% Similarity=0.322 Sum_probs=41.0
Q ss_pred HHHHhHHhhhcccCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC-eeeeec
Q 028248 4 EEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEG 67 (211)
Q Consensus 4 eefd~lkeel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~GS-~vv~~~ 67 (211)
+..+.+|++|. ....+++.+..|-+.| .|.++-++++..+.-++|...|- .|++++
T Consensus 120 ~~~~~~~~~ll-~~advitpN~~Ea~~L-------~g~~~~~~~~~~~aa~~l~~~g~~~ViIt~ 176 (268)
T PRK12412 120 ETNDCLRDVLV-PKALVVTPNLFEAYQL-------SGVKINSLEDMKEAAKKIHALGAKYVLIKG 176 (268)
T ss_pred HHHHHHHHhhh-ccceEEcCCHHHHHHH-------hCcCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence 34466777764 5788999999998766 47777777777777788887786 466664
No 256
>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=40.89 E-value=17 Score=36.49 Aligned_cols=22 Identities=23% Similarity=0.635 Sum_probs=15.6
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.-||+||. .- ..+...||+||.
T Consensus 533 siC~~CGy----~~----------g~~~~~CP~CGs 554 (586)
T TIGR02827 533 TICNDCHH----ID----------KRTLHRCPVCGS 554 (586)
T ss_pred eecCCCCC----cC----------CCcCCcCcCCCC
Confidence 46999997 11 134579999995
No 257
>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=40.87 E-value=20 Score=34.88 Aligned_cols=18 Identities=22% Similarity=0.741 Sum_probs=14.7
Q ss_pred ceeCCCCCceeEEecCce
Q 028248 184 TINCSNCGTTMVYDSNTR 201 (211)
Q Consensus 184 ~~kC~~C~~~L~f~~~~r 201 (211)
.++|++|+..|+|-.+..
T Consensus 222 ~~~C~~C~~~l~~h~~~~ 239 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEG 239 (505)
T ss_pred ccCCCCCCCceEEecCCC
Confidence 468999999999987544
No 258
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=40.62 E-value=17 Score=26.13 Aligned_cols=9 Identities=56% Similarity=1.376 Sum_probs=6.8
Q ss_pred CCCCCcccc
Q 028248 158 PCPNCGTEN 166 (211)
Q Consensus 158 ~CPnCg~Ev 166 (211)
.|||||+-.
T Consensus 29 ~c~~cG~~~ 37 (57)
T COG0333 29 VCPNCGEYK 37 (57)
T ss_pred eccCCCCcc
Confidence 589998743
No 259
>cd07115 ALDH_HMSADH_HapE Pseudomonas fluorescens 4-hydroxymuconic semialdehyde dehydrogenase-like. 4-hydroxymuconic semialdehyde dehydrogenase (HapE, EC=1.2.1.61) of Pseudomonas fluorescens ACB involved in 4-hydroxyacetophenone degradation, and putative hydroxycaproate semialdehyde dehydrogenase (ChnE) of Brachymonas petroleovorans involved in cyclohexane metabolism, and other similar sequences, are present in this CD.
Probab=40.54 E-value=91 Score=29.28 Aligned_cols=66 Identities=20% Similarity=0.413 Sum_probs=42.9
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE------EeChhhHHHHHHHHh----hhcC---------CCccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV------MLSSAEQKFLEASMA----YVAG---------KPIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~------~l~~~Eq~fLeA~~a----Y~~G---------~Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|..|. +-+....+|++++.+ ++-| -|+++.+.+++++..+.
T Consensus 237 ~dAdl~~aa~~i~~~~~~~~GQ~C~a~~~v~V~~~i~~~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~i~ 316 (453)
T cd07115 237 ADADLDAAVRAAATGIFYNQGQMCTAGSRLLVHESIYDEFLERFTSLARSLRPGDPLDPKTQMGPLVSQAQFDRVLDYVD 316 (453)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCCCeEEEEcHHHHHHHHHHHHHHHhcCCcCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 45667777777766 454443 333335678888654 3333 36899999999997775
Q ss_pred h---hCCeeeeec
Q 028248 58 M---EGSEIVVEG 67 (211)
Q Consensus 58 ~---~GS~vv~~~ 67 (211)
. .|.+++.-|
T Consensus 317 ~a~~~Ga~v~~gg 329 (453)
T cd07115 317 VGREEGARLLTGG 329 (453)
T ss_pred HHHHCCCEEEeCC
Confidence 4 588877644
No 260
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=40.01 E-value=27 Score=24.19 Aligned_cols=36 Identities=25% Similarity=0.435 Sum_probs=20.6
Q ss_pred CCCCCcccceeeccccc-cccCC----CCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTIL-SISSG----GTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~-~v~s~----~~~~~~kC~~C~~~ 193 (211)
.|+.||+.---=.|+-. +|+.+ .-+..-.||+|+..
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 59999976554434311 11111 13556799999864
No 261
>PLN02278 succinic semialdehyde dehydrogenase
Probab=39.94 E-value=90 Score=30.08 Aligned_cols=66 Identities=18% Similarity=0.414 Sum_probs=44.4
Q ss_pred ChHHHHhHHhhhcc-----cCCe------eEEeChhhHHHHHHHHhh----hcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMAY----VAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGss------v~~l~~~Eq~fLeA~~aY----~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.-.+.+.| .|-+ +++-...-.+|+|++.+. .-|. |+++...+|+++..+.
T Consensus 280 ~dAdl~~aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~~~f~~~L~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~v~~~i~ 359 (498)
T PLN02278 280 DDADLDVAVKGALASKFRNSGQTCVCANRILVQEGIYDKFAEAFSKAVQKLVVGDGFEEGVTQGPLINEAAVQKVESHVQ 359 (498)
T ss_pred CCCCHHHHHHHHHHHHhccCCCCCcCCcEEEEeHHHHHHHHHHHHHHHHhcCCCCCCCCCCcCCCccCHHHHHHHHHHHH
Confidence 46677777777766 3433 333444467899987553 3343 6899999999998765
Q ss_pred h---hCCeeeeec
Q 028248 58 M---EGSEIVVEG 67 (211)
Q Consensus 58 ~---~GS~vv~~~ 67 (211)
. +|.+++.-|
T Consensus 360 ~a~~~Ga~vl~gG 372 (498)
T PLN02278 360 DAVSKGAKVLLGG 372 (498)
T ss_pred HHHhCCCEEEeCC
Confidence 4 688887754
No 262
>PRK06427 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed
Probab=39.93 E-value=1e+02 Score=26.34 Aligned_cols=53 Identities=23% Similarity=0.406 Sum_probs=34.5
Q ss_pred HhHHhhhcccCCeeEEeChhhHHHHHHHHhhhcCCCccChHH-HHHHHHHHhhhCC-eeeeec
Q 028248 7 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEE-YDKLKQKLKMEGS-EIVVEG 67 (211)
Q Consensus 7 d~lkeel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~e-fD~Lk~~Lk~~GS-~vv~~~ 67 (211)
+.+|++| .....+++.+..|-+.| .|.++-++++ ..+.-.+|...|- .|++++
T Consensus 124 ~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~~a~~l~~~g~~~Vvit~ 178 (266)
T PRK06427 124 AALRERL-LPLATLITPNLPEAEAL-------TGLPIADTEDEMKAAARALHALGCKAVLIKG 178 (266)
T ss_pred HHHHHhh-hCcCeEEcCCHHHHHHH-------hCCCCCCcHHHHHHHHHHHHhcCCCEEEEcC
Confidence 3455554 35577888888887766 4666655554 5566677777774 566665
No 263
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=39.86 E-value=13 Score=22.44 Aligned_cols=22 Identities=32% Similarity=0.813 Sum_probs=13.5
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.||.|...|++- ..+|..|++.
T Consensus 6 ~C~~C~~~N~~~--------------~~~C~~C~~~ 27 (30)
T PF00641_consen 6 KCPSCTFMNPAS--------------RSKCVACGAP 27 (30)
T ss_dssp EETTTTEEEESS--------------SSB-TTT--B
T ss_pred cCCCCcCCchHH--------------hhhhhCcCCC
Confidence 488888777543 5679899864
No 264
>cd07135 ALDH_F14-YMR110C Saccharomyces cerevisiae aldehyde dehydrogenase family 14 and related proteins. Aldehyde dehydrogenase family 14 (ALDH14), isolated mainly from the mitochondrial outer membrane of Saccharomyces cerevisiae (YMR110C) and most closely related to the plant and animal ALDHs and fatty ALDHs family 3 members, and similar fungal sequences, are present in this CD.
Probab=39.72 E-value=87 Score=29.64 Aligned_cols=68 Identities=21% Similarity=0.491 Sum_probs=46.5
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE-----Ee-ChhhHHHHHHHHh----hhcCC--------CccChHHHHHHHHHHhh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV-----ML-SSAEQKFLEASMA----YVAGK--------PIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~-----~l-~~~Eq~fLeA~~a----Y~~G~--------Pi~sD~efD~Lk~~Lk~ 58 (211)
.|.+.|.--+.+.| .|-.|. .+ +..-.+|++++.+ +.-|. |+++.+.+|+++.-+..
T Consensus 225 ~dADl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~gpli~~~~~~~i~~~v~~ 304 (436)
T cd07135 225 KNADLELAAKRILWGKFGNAGQICVAPDYVLVDPSVYDEFVEELKKVLDEFYPGGANASPDYTRIVNPRHFNRLKSLLDT 304 (436)
T ss_pred CCCCHHHHHHHHHHHHhccCCceecCCCEEeccHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHHHHHHHHh
Confidence 45667777777766 454443 23 3334578888654 44465 78999999999999988
Q ss_pred hCCeeeeeccc
Q 028248 59 EGSEIVVEGPR 69 (211)
Q Consensus 59 ~GS~vv~~~pr 69 (211)
.|.+++.-|++
T Consensus 305 ag~~v~~gg~~ 315 (436)
T cd07135 305 TKGKVVIGGEM 315 (436)
T ss_pred cCCeEEECCCc
Confidence 78888776654
No 265
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=39.33 E-value=59 Score=23.58 Aligned_cols=34 Identities=18% Similarity=0.332 Sum_probs=28.2
Q ss_pred HHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC
Q 028248 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS 61 (211)
Q Consensus 28 q~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~GS 61 (211)
..|||=..+--.|+|+||-+||-+-..+=++.|-
T Consensus 26 e~Yv~H~~~~HP~~p~ms~~eF~r~r~~~r~~~~ 59 (65)
T PF04328_consen 26 ERYVEHMRRHHPDEPPMSEREFFRERQDARYGNP 59 (65)
T ss_pred HHHHHHHHHHCcCCCCCCHHHHHHHHHHHHhcCC
Confidence 5788888888899999999999988777766553
No 266
>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=39.31 E-value=19 Score=29.98 Aligned_cols=30 Identities=27% Similarity=0.330 Sum_probs=18.6
Q ss_pred HHHHHHHHhhhcCCCccChHHHHHHHHHHh
Q 028248 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLK 57 (211)
Q Consensus 28 q~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk 57 (211)
++.++....|..-.-=|+.+|.+.++.-||
T Consensus 17 ~~~le~a~e~~~~~~elT~eEl~lv~~ylk 46 (146)
T PF07295_consen 17 QEALEKAKEYLVAAGELTREELALVSAYLK 46 (146)
T ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence 344444455666666678888877665554
No 267
>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=39.31 E-value=14 Score=28.26 Aligned_cols=26 Identities=35% Similarity=0.999 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccceeeecCCCCCcccce
Q 028248 129 TWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENV 167 (211)
Q Consensus 129 ~~~~~~Pvi~~~a~~lt~~~~~d~liLkG~CPnCg~Ev~ 167 (211)
.|.-..|+++++- +||.|.+|++.+-
T Consensus 44 ~~~~lIPi~S~l~-------------lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 44 SWWDLIPILSYLL-------------LRGRCRYCGAPIP 69 (92)
T ss_pred cccccchHHHHHH-------------hCCCCcccCCCCC
Confidence 3555667777665 7788888877654
No 268
>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=39.27 E-value=24 Score=22.28 Aligned_cols=11 Identities=27% Similarity=0.878 Sum_probs=6.1
Q ss_pred cCceeCCCCCc
Q 028248 182 TNTINCSNCGT 192 (211)
Q Consensus 182 ~~~~kC~~C~~ 192 (211)
-..++|+.|.+
T Consensus 17 A~~vrCs~C~~ 27 (31)
T TIGR01053 17 ASSVRCALCQT 27 (31)
T ss_pred CCeEECCCCCe
Confidence 34566666654
No 269
>cd07143 ALDH_AldA_AN0554 Aspergillus nidulans aldehyde dehydrogenase, AldA (AN0554)-like. NAD(P)+-dependent aldehyde dehydrogenase (AldA) of Aspergillus nidulans (locus AN0554), and other similar sequences, are present in this CD.
Probab=38.95 E-value=96 Score=29.71 Aligned_cols=67 Identities=15% Similarity=0.310 Sum_probs=44.7
Q ss_pred ChHHHHhHHhhhcc-----cCCee------EEeChhhHHHHHHHHhh----hcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV------VMLSSAEQKFLEASMAY----VAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv------~~l~~~Eq~fLeA~~aY----~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.-.+.+.| .|..| ++-+..-.+|++++.+. .-|. |+++...+|+++..+.
T Consensus 265 ~dADl~~Aa~~i~~~~~~naGQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~G~p~~~~~~~gpli~~~~~~~~~~~i~ 344 (481)
T cd07143 265 DDADLESAVVWTAYGIFFNHGQVCCAGSRIYVQEGIYDKFVKRFKEKAKKLKVGDPFAEDTFQGPQVSQIQYERIMSYIE 344 (481)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCCCcEEEEeHhHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 45667777776666 44443 33344456788887543 3343 6899999999998886
Q ss_pred ---hhCCeeeeecc
Q 028248 58 ---MEGSEIVVEGP 68 (211)
Q Consensus 58 ---~~GS~vv~~~p 68 (211)
.+|.+++.-|.
T Consensus 345 ~a~~~ga~v~~gg~ 358 (481)
T cd07143 345 SGKAEGATVETGGK 358 (481)
T ss_pred HHHhCCCEEEeCCC
Confidence 46888876553
No 270
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=38.89 E-value=24 Score=23.35 Aligned_cols=18 Identities=22% Similarity=0.724 Sum_probs=14.0
Q ss_pred cCceeCCCCCceeEEecC
Q 028248 182 TNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 182 ~~~~kC~~C~~~L~f~~~ 199 (211)
+..+.|+.||..|..+..
T Consensus 3 ~g~l~C~~CG~~m~~~~~ 20 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKR 20 (58)
T ss_pred CCcEEcccCCcEeEEEEC
Confidence 356789999999888764
No 271
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=38.75 E-value=19 Score=34.18 Aligned_cols=37 Identities=24% Similarity=0.420 Sum_probs=26.0
Q ss_pred eecCCCCCcccce---------eeccccccccCCCCcCceeCCCCC
Q 028248 155 LKGPCPNCGTENV---------SFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 155 LkG~CPnCg~Ev~---------aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
-+..||.||.++- .||-+-..++=+...+-.-|+.||
T Consensus 5 ~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg 50 (355)
T COG1499 5 STILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCG 50 (355)
T ss_pred cccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCC
Confidence 4678999999983 455433334444567788899999
No 272
>cd07144 ALDH_ALD2-YMR170C Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c)-like. NAD(P)+-dependent Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c, ALD5, EC=1.2.1.5) and other similar sequences, are present in this CD.
Probab=38.62 E-value=1.1e+02 Score=29.23 Aligned_cols=67 Identities=24% Similarity=0.433 Sum_probs=43.8
Q ss_pred ChHHHHhHHhhhcc-----cCCeeEE-----e-ChhhHHHHHHHHh-----hhcCCC---------ccChHHHHHHHHHH
Q 028248 2 SNEEFDNLKEELMW-----EGSSVVM-----L-SSAEQKFLEASMA-----YVAGKP---------IMSDEEYDKLKQKL 56 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~~-----l-~~~Eq~fLeA~~a-----Y~~G~P---------i~sD~efD~Lk~~L 56 (211)
.|.+.|.--+...| .|..|.- + ...-.+|++++.+ |.-|.| +++.+.+|+++..+
T Consensus 264 ~dADl~~Aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~~G~p~~~~~~~gpli~~~~~~~~~~~i 343 (484)
T cd07144 264 EDADLDQAVKWAAAGIMYNSGQNCTATSRIYVQESIYDKFVEKFVEHVKQNYKVGSPFDDDTVVGPQVSKTQYDRVLSYI 343 (484)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCCCceEEEcHHHHHHHHHHHHHHHHhhCCcCCCCCCCCcCCCCcCHHHHHHHHHHH
Confidence 45667777776666 4554433 3 3334678887654 323654 78999999999888
Q ss_pred hh---hCCeeeeecc
Q 028248 57 KM---EGSEIVVEGP 68 (211)
Q Consensus 57 k~---~GS~vv~~~p 68 (211)
+. +|.+++.-+.
T Consensus 344 ~~a~~~ga~v~~gg~ 358 (484)
T cd07144 344 EKGKKEGAKLVYGGE 358 (484)
T ss_pred HHHHHCCCEEEeCCC
Confidence 76 6888776543
No 273
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=38.34 E-value=18 Score=24.64 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=15.9
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCC
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNC 190 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C 190 (211)
+-=.||.||.|-.+=+.. +......||.|
T Consensus 27 v~W~C~~Cgh~w~~~v~~-------R~~~~~~CP~C 55 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASVND-------RTRRGKGCPYC 55 (55)
T ss_pred EEEECCCCCCeeEccHhh-------hccCCCCCCCC
Confidence 344577777765544211 12456667766
No 274
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.01 E-value=38 Score=25.80 Aligned_cols=31 Identities=26% Similarity=0.457 Sum_probs=19.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhccceeeecCCC
Q 028248 126 FIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCP 160 (211)
Q Consensus 126 ~i~~~~~~~Pvi~~~a~~lt~~~~~d~liLkG~CP 160 (211)
+++|+.+.+-+|...+ .+++.++-. ++|+|-
T Consensus 4 ~lltFg~Fllvi~gMs---iG~I~krk~-I~GSCG 34 (77)
T COG2991 4 FLLTFGIFLLVIAGMS---IGYIFKRKS-IKGSCG 34 (77)
T ss_pred HHHHHHHHHHHHHHHh---Hhhheeccc-cccccc
Confidence 3444444344444444 778899988 899984
No 275
>PRK15398 aldehyde dehydrogenase EutE; Provisional
Probab=37.97 E-value=69 Score=30.85 Aligned_cols=57 Identities=11% Similarity=0.302 Sum_probs=42.4
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE------EeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhC
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV------MLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~------~l~~~Eq~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~G 60 (211)
.|.+.|.-.+...| .|..|. +=...-.+|++++.+. +.|+++.+++|+++.-+...|
T Consensus 249 ~dADld~Aa~~i~~g~~~n~GQ~C~A~~rvlV~~si~d~f~~~l~~~--~~~li~~~~~~~v~~~l~~~~ 316 (465)
T PRK15398 249 ETADIEKAARDIVKGASFDNNLPCIAEKEVIVVDSVADELMRLMEKN--GAVLLTAEQAEKLQKVVLKNG 316 (465)
T ss_pred cCCCHHHHHHHHHHhcccCCCCcCCCCceEEEeHHHHHHHHHHHHHc--CCccCCHHHHHHHHHHHhhcc
Confidence 35567777777877 565554 3344457899999887 789999999999998887554
No 276
>PF10751 DUF2535: Protein of unknown function (DUF2535); InterPro: IPR019687 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=37.91 E-value=35 Score=26.38 Aligned_cols=40 Identities=25% Similarity=0.213 Sum_probs=28.7
Q ss_pred eEEeChhh------HHHHHHHHh--hhcCCCccChHHHHHHHHHHhhh
Q 028248 20 VVMLSSAE------QKFLEASMA--YVAGKPIMSDEEYDKLKQKLKME 59 (211)
Q Consensus 20 v~~l~~~E------q~fLeA~~a--Y~~G~Pi~sD~efD~Lk~~Lk~~ 59 (211)
+++|.+++ |.-||+.++ |.+-+|--+=.-=|-||+.|||.
T Consensus 21 IPVL~ed~p~~Fmi~~rLq~fi~~vy~~~~~~~vYSFreYlKr~lKW~ 68 (83)
T PF10751_consen 21 IPVLEEDNPYYFMIQLRLQLFIAKVYNSKSPRKVYSFREYLKRVLKWP 68 (83)
T ss_pred cceecCCCceEeeHHHHHHHHHHHHHhCCCCCceeeHHHHHHHhcCcH
Confidence 35566665 667888766 77766666666667799999996
No 277
>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=37.67 E-value=35 Score=29.21 Aligned_cols=35 Identities=20% Similarity=0.469 Sum_probs=15.9
Q ss_pred hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
..+. +---+|+.||.+..+-.. ...+...|+-|.-
T Consensus 128 ~sg~-l~l~~C~~C~~~fv~~~~--------~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 128 DSGM-LQLAPCRRCGGHFVTHAH--------DPRHSFVCPFCQP 162 (175)
T ss_dssp HTTS-EEEEE-TTT--EEEEESS----------SS----TT---
T ss_pred hcCC-ccccCCCCCCCCeECcCC--------CCCcCcCCCCCCC
Confidence 3444 466789999999876632 2478899999984
No 278
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=37.57 E-value=22 Score=34.55 Aligned_cols=33 Identities=21% Similarity=0.515 Sum_probs=24.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-||-|+.-+.. ..-.+.+.+.||-||++|+-..
T Consensus 20 ~C~eCd~~~~~--------P~l~~~q~A~CPRC~~~l~~~~ 52 (418)
T COG2995 20 LCPECDMLVSL--------PRLDSGQSAYCPRCGHTLTRGG 52 (418)
T ss_pred cCCCCCceecc--------ccCCCCCcccCCCCCCccccCC
Confidence 59999987643 2334678899999999997555
No 279
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=37.48 E-value=16 Score=21.60 Aligned_cols=9 Identities=56% Similarity=1.475 Sum_probs=6.5
Q ss_pred CCCCCcccc
Q 028248 158 PCPNCGTEN 166 (211)
Q Consensus 158 ~CPnCg~Ev 166 (211)
+||.||..+
T Consensus 4 ~C~~CgR~F 12 (25)
T PF13913_consen 4 PCPICGRKF 12 (25)
T ss_pred cCCCCCCEE
Confidence 688888654
No 280
>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=37.44 E-value=28 Score=23.18 Aligned_cols=29 Identities=31% Similarity=0.678 Sum_probs=13.3
Q ss_pred CCCC--CcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPN--CGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPn--Cg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.||+ |+.-+..- .+.+...+.|+.|+...
T Consensus 20 ~Cp~~~C~~~~~~~--------~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 20 WCPNPDCEYIIEKD--------DGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp --TTSST---ECS---------SSTTS--CCTTSCCSEE
T ss_pred CCCCCCCcccEEec--------CCCCCCeeECCCCCCcC
Confidence 8988 98754432 11112249999999764
No 281
>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=37.41 E-value=38 Score=24.63 Aligned_cols=42 Identities=33% Similarity=0.781 Sum_probs=26.3
Q ss_pred CCCCCccccee---------eccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 158 PCPNCGTENVS---------FFGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 158 ~CPnCg~Ev~a---------Ffg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
-||-||.+.+. .|+.+..|+.+. -.-+-|++||=.=.|++++
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~-f~~v~C~~CGYTE~Y~~~~ 52 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKK-FTTVSCTNCGYTEFYKAKT 52 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcE-EEEEECCCCCCEEEEeecC
Confidence 49999987653 344444444432 2345799999887776653
No 282
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=37.34 E-value=22 Score=33.47 Aligned_cols=32 Identities=19% Similarity=0.258 Sum_probs=22.0
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
.-+.|++||..-.... ....+|+.||..+..-
T Consensus 243 ~~~~C~~c~~~~~~~~-----------~~~~~C~~c~~~~~~~ 274 (382)
T PRK04338 243 YVYYCPKCLYREEVEG-----------LPPEECPVCGGKFGTA 274 (382)
T ss_pred eEEECCCCCcEEEecC-----------CCCCCCCCCCCcceec
Confidence 4578999998655431 2345799999876543
No 283
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=37.33 E-value=10 Score=31.88 Aligned_cols=39 Identities=23% Similarity=0.491 Sum_probs=28.3
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
.|. ||-++-+.|++--.-..-.....+.||+||+.-+-+
T Consensus 7 ~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~~V~K 45 (148)
T PF06676_consen 7 RCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGSTEVSK 45 (148)
T ss_pred ecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCCeEee
Confidence 466 888888999775544444557789999999875544
No 284
>cd07089 ALDH_CddD-AldA-like Rhodococcus ruber 6-oxolauric acid dehydrogenase-like and related proteins. The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid; and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and also, the Mycobacterium tuberculosis H37Rv ALDH AldA (locus Rv0768) sequence; and other similar sequences, are included in this CD.
Probab=37.11 E-value=1.1e+02 Score=29.07 Aligned_cols=67 Identities=19% Similarity=0.368 Sum_probs=43.9
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEeC-hhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VMLS-SAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l~-~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
+|.+.|..-+.+.| .|-+| +.+. ..-.+|+|++.+ +.-|. |+++.+.+++++..++
T Consensus 243 ~dadl~~aa~~i~~~~~~~sGQ~C~a~~~v~V~~~v~~~f~~~l~~~~~~~~~g~p~~~~~~~gp~i~~~~~~~v~~~i~ 322 (459)
T cd07089 243 DDADLAAAAPAAVGVCMHNAGQGCALTTRLLVPRSRYDEVVEALAAAFEALPVGDPADPGTVMGPLISAAQRDRVEGYIA 322 (459)
T ss_pred CCCCHHHHHHHHHHHHHHhcCCcccCCeEEEEcHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 46677777777777 35443 3333 334678877543 44453 5789999999998765
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+++.-|.
T Consensus 323 ~a~~~Ga~~l~gg~ 336 (459)
T cd07089 323 RGRDEGARLVTGGG 336 (459)
T ss_pred HHHHCCCEEEeCCC
Confidence 4 6888876553
No 285
>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=37.07 E-value=21 Score=33.97 Aligned_cols=45 Identities=24% Similarity=0.422 Sum_probs=24.7
Q ss_pred hhccceeeecCCCCCcc----cceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 148 IVRESLILKGPCPNCGT----ENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 148 ~~~d~liLkG~CPnCg~----Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
...+-.-..--||+||. ++..| .....+-+.+|+.||..-+.+-.
T Consensus 166 ~~~~y~Pf~piC~~cGri~tt~v~~~-------d~~~~~v~Y~c~~cG~~g~~~i~ 214 (360)
T PF01921_consen 166 RPETYSPFLPICEKCGRIDTTEVTEY-------DPEGGTVTYRCEECGHEGEVDIT 214 (360)
T ss_dssp --TT--SEEEEETTTEE--EEEEEEE---------SSSEEEEE--TTS---EEETT
T ss_pred CCCCeeeeeeeccccCCcccceeeEe-------ecCCCEEEEEecCCCCEEEEecC
Confidence 44454566778999998 33344 43457889999999998887754
No 286
>PRK03922 hypothetical protein; Provisional
Probab=37.04 E-value=16 Score=29.63 Aligned_cols=13 Identities=38% Similarity=0.713 Sum_probs=10.6
Q ss_pred ecCCCCCccccee
Q 028248 156 KGPCPNCGTENVS 168 (211)
Q Consensus 156 kG~CPnCg~Ev~a 168 (211)
.-.||.||+|.-+
T Consensus 49 ~~~cP~cge~~~~ 61 (113)
T PRK03922 49 LTICPKCGEPFDS 61 (113)
T ss_pred cccCCCCCCcCCc
Confidence 4579999999874
No 287
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=36.66 E-value=21 Score=36.21 Aligned_cols=22 Identities=23% Similarity=0.676 Sum_probs=15.7
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.-||+||... ......||+||.
T Consensus 567 ~iC~~CG~~~--------------~g~~~~CP~CGs 588 (623)
T PRK08271 567 TICNDCHHID--------------KRTGKRCPICGS 588 (623)
T ss_pred ccCCCCCCcC--------------CCCCcCCcCCCC
Confidence 5699999751 113478999995
No 288
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.54 E-value=30 Score=27.66 Aligned_cols=38 Identities=26% Similarity=0.449 Sum_probs=19.6
Q ss_pred eecCCCCCcccceee-ccccccccCCCCcCceeCCCCCc-eeEEecC
Q 028248 155 LKGPCPNCGTENVSF-FGTILSISSGGTTNTINCSNCGT-TMVYDSN 199 (211)
Q Consensus 155 LkG~CPnCg~Ev~aF-fg~i~~v~s~~~~~~~kC~~C~~-~L~f~~~ 199 (211)
+.+-| .||.+...= +. +. .-.....||.||. .+.....
T Consensus 69 ~~~~C-~Cg~~~~~~~~~----~~--~~~~~~~CP~Cgs~~~~i~~G 108 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDE----ID--HYAAVIECPVCGNKRAHILGG 108 (124)
T ss_pred eeEEe-eCcCcccccccc----hh--ccccCCcCcCCCCCCCEEecC
Confidence 67889 999552110 00 00 0011356999994 4454443
No 289
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=36.52 E-value=17 Score=26.03 Aligned_cols=13 Identities=62% Similarity=1.260 Sum_probs=11.2
Q ss_pred ecCCCCCccccee
Q 028248 156 KGPCPNCGTENVS 168 (211)
Q Consensus 156 kG~CPnCg~Ev~a 168 (211)
.||||-||+++.+
T Consensus 35 ~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 35 LGPCPFCGTPLLS 47 (57)
T ss_pred cCcCCCCCCcccC
Confidence 6899999988865
No 290
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=36.41 E-value=17 Score=29.06 Aligned_cols=13 Identities=46% Similarity=0.887 Sum_probs=10.4
Q ss_pred ecCCCCCccccee
Q 028248 156 KGPCPNCGTENVS 168 (211)
Q Consensus 156 kG~CPnCg~Ev~a 168 (211)
.-.||.||+|..+
T Consensus 47 ~~~cP~Cge~~~~ 59 (102)
T PF04475_consen 47 DTICPKCGEELDS 59 (102)
T ss_pred cccCCCCCCccCc
Confidence 3479999999873
No 291
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=36.31 E-value=21 Score=36.70 Aligned_cols=21 Identities=33% Similarity=0.937 Sum_probs=14.4
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.-||+||... .+ .-+||+||.
T Consensus 681 ~~C~~CG~~~-~~--------------~~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYLG-VI--------------EDKCPKCGS 701 (735)
T ss_pred eecCCCCCCC-Cc--------------CccCcCCCC
Confidence 5699999421 11 168999995
No 292
>cd07119 ALDH_BADH-GbsA Bacillus subtilis NAD+-dependent betaine aldehyde dehydrogenase-like. Included in this CD is the NAD+-dependent, betaine aldehyde dehydrogenase (BADH, GbsA, EC=1.2.1.8) of Bacillus subtilis involved in the synthesis of the osmoprotectant glycine betaine from choline or glycine betaine aldehyde.
Probab=36.10 E-value=1.1e+02 Score=29.12 Aligned_cols=67 Identities=22% Similarity=0.437 Sum_probs=43.4
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE------EeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV------MLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~------~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
+|.+.|.--+.+.| .|-+|. +-+..-.+|+|++.+ +.-|. |+++.+.+|+++.-++
T Consensus 254 ~dADl~~Aa~~i~~~~~~~~GQ~C~a~~~v~V~~~i~d~f~~~l~~~~~~~~~G~~~~~~~~~gpli~~~~~~~~~~~i~ 333 (482)
T cd07119 254 ADADFETAVDQALNGVFFNAGQVCSAGSRLLVEESIHDKFVAALAERAKKIKLGNGLDADTEMGPLVSAEHREKVLSYIQ 333 (482)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCcCCCCCCHHHHHHHHHHHH
Confidence 45667766666666 455443 333334678888654 44343 6888999999998666
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. .|.+++.-|.
T Consensus 334 ~a~~~Ga~v~~gg~ 347 (482)
T cd07119 334 LGKEEGARLVCGGK 347 (482)
T ss_pred HHHHCCCEEEeCCc
Confidence 4 5888876553
No 293
>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=36.08 E-value=26 Score=21.07 Aligned_cols=26 Identities=23% Similarity=0.420 Sum_probs=15.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
+||.|+..+...- ....+..-|+.|-
T Consensus 3 ~C~rC~~~~~~~~--------~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIG--------INGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEE--------ETTEEEEE-TTTC
T ss_pred cCccCCCcceEeE--------ecCCCCeECcCCc
Confidence 6999998876552 1357778888885
No 294
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=36.05 E-value=16 Score=34.33 Aligned_cols=46 Identities=17% Similarity=0.190 Sum_probs=28.8
Q ss_pred eeEEeChhhHH----HHHHHHh--hhcCCCcc---------ChHHHHHHHHHHhhhCCeee
Q 028248 19 SVVMLSSAEQK----FLEASMA--YVAGKPIM---------SDEEYDKLKQKLKMEGSEIV 64 (211)
Q Consensus 19 sv~~l~~~Eq~----fLeA~~a--Y~~G~Pi~---------sD~efD~Lk~~Lk~~GS~vv 64 (211)
.++++..++|+ |+.|+++ =-+|+|+. +.-+=+.|-..++.+|=.|.
T Consensus 153 dvy~v~di~~q~ls~~m~al~tai~q~G~~~~~ltan~~elsk~m~e~Ld~q~~q~Gm~v~ 213 (345)
T COG4260 153 DVYTVDDINQQYLSEFMGALATAINQSGVRFSFLTANQMELSKYMAEVLDEQWTQYGMAVD 213 (345)
T ss_pred ceEEHHHHHHHHHHHHHHHHHHHHHhcCceehhhhhhHHHHHHHHHHHHhHHHHhhCceEe
Confidence 46777777765 4556654 33488763 44455667777888876544
No 295
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=36.00 E-value=30 Score=32.54 Aligned_cols=44 Identities=20% Similarity=0.414 Sum_probs=26.2
Q ss_pred ccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 150 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 150 ~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.+-.-..--||+||- ..+- +..+.....+-+.+|. ||..-+.+-
T Consensus 163 ~~~~P~~p~c~~cg~-~~~~---v~~~d~~~~~v~y~c~-cG~~g~~~~ 206 (353)
T cd00674 163 ETWYPFMPYCEKCGK-DTTT---VEAYDAKAGTVTYKCE-CGHEETVDI 206 (353)
T ss_pred CCceeeeeecCCcCc-ceeE---EEEEeCCCCeEEEEcC-CCCEEEEee
Confidence 444556778999992 2222 2333433456677884 887766654
No 296
>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=36.00 E-value=28 Score=25.97 Aligned_cols=30 Identities=27% Similarity=0.594 Sum_probs=17.6
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
-| .||.-.++= .+....+| +||..|.+..-
T Consensus 5 rC-~Cgr~lya~----------e~~kTkkC-~CG~~l~vk~~ 34 (68)
T PF09082_consen 5 RC-DCGRYLYAK----------EGAKTKKC-VCGKTLKVKER 34 (68)
T ss_dssp EE-TTS--EEEE----------TT-SEEEE-TTTEEEE--SS
T ss_pred Ee-cCCCEEEec----------CCcceeEe-cCCCeeeeeeE
Confidence 36 577655443 25677899 99999988753
No 297
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=35.79 E-value=18 Score=38.12 Aligned_cols=29 Identities=31% Similarity=0.780 Sum_probs=20.7
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
.--||.|++....=-| +=.-|.||+.+|+
T Consensus 827 ~~~cp~c~~~~~~~~~-----------~c~~c~~c~~~~~ 855 (858)
T PRK08115 827 GNTCPVCREGTVEEIG-----------GCNTCTNCGAQLK 855 (858)
T ss_pred CCCCCccCCCceeecC-----------CCccccchhhhhc
Confidence 3479999997665532 2346999998875
No 298
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=35.67 E-value=21 Score=34.70 Aligned_cols=32 Identities=25% Similarity=0.704 Sum_probs=18.5
Q ss_pred ccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 150 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 150 ~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.|++ -.||+||++-..= .+. -+--+.|++|..
T Consensus 224 ED~l---~~C~~C~~s~n~e-----~~~---~sk~~~Cp~C~~ 255 (457)
T KOG2324|consen 224 EDTL---MSCPSCGYSKNSE-----DLD---LSKIASCPKCNE 255 (457)
T ss_pred ccce---eecCcCCccCchh-----hhc---CCccccCCcccC
Confidence 4555 3799999543221 111 122288999998
No 299
>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=35.66 E-value=19 Score=25.53 Aligned_cols=13 Identities=46% Similarity=1.025 Sum_probs=5.9
Q ss_pred eecCCCCCcccce
Q 028248 155 LKGPCPNCGTENV 167 (211)
Q Consensus 155 LkG~CPnCg~Ev~ 167 (211)
||..||.||.+..
T Consensus 16 Lk~~cp~cG~~T~ 28 (53)
T PF04135_consen 16 LKDKCPPCGGPTE 28 (53)
T ss_dssp SSSBBTTTSSBSE
T ss_pred CCCccCCCCCCCc
Confidence 3444444444433
No 300
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=35.50 E-value=34 Score=23.46 Aligned_cols=22 Identities=41% Similarity=0.768 Sum_probs=18.3
Q ss_pred ccChHHHHHHHHHHhhhCCeeeeec
Q 028248 43 IMSDEEYDKLKQKLKMEGSEIVVEG 67 (211)
Q Consensus 43 i~sD~efD~Lk~~Lk~~GS~vv~~~ 67 (211)
++++++|+.++. ..|+.|.|.|
T Consensus 5 ~l~~~~~~~~~~---~~Gk~V~V~G 26 (48)
T PF14485_consen 5 ILSEEDYSYLKS---LLGKRVSVTG 26 (48)
T ss_pred EeChhhhHHHHH---hcCCeEEEEE
Confidence 458999999887 6899999876
No 301
>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=35.06 E-value=23 Score=23.57 Aligned_cols=27 Identities=26% Similarity=0.632 Sum_probs=19.1
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
.|+.|+.++..| .-+..|..||..+=-
T Consensus 4 ~C~~C~~~F~~~------------~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 4 SCMGCGKPFTLT------------RRRHHCRNCGRIFCS 30 (57)
T ss_pred cCcccCccccCC------------ccccccCcCcCCcCh
Confidence 689999766654 456778888876543
No 302
>cd07098 ALDH_F15-22 Aldehyde dehydrogenase family 15A1 and 22A1-like. Aldehyde dehydrogenase family members ALDH15A1 (Saccharomyces cerevisiae YHR039C) and ALDH22A1 (Arabidopsis thaliana, EC=1.2.1.3), and similar sequences, are in this CD. Significant improvement of stress tolerance in tobacco plants was observed by overexpressing the ALDH22A1 gene from maize (Zea mays) and was accompanied by a reduction of malondialdehyde derived from cellular lipid peroxidation.
Probab=34.90 E-value=1.3e+02 Score=28.46 Aligned_cols=67 Identities=21% Similarity=0.469 Sum_probs=46.0
Q ss_pred CChHHHHhHHhhhcc-----cCC-----eeEEeCh-hhHHHHHHHHh----hhcCCC---------ccChHHHHHHHHHH
Q 028248 1 MSNEEFDNLKEELMW-----EGS-----SVVMLSS-AEQKFLEASMA----YVAGKP---------IMSDEEYDKLKQKL 56 (211)
Q Consensus 1 ~s~eefd~lkeel~w-----eGs-----sv~~l~~-~Eq~fLeA~~a----Y~~G~P---------i~sD~efD~Lk~~L 56 (211)
++|.++|..-+.+.| .|- +.+.+.+ .-.+|++++.. +.-|.| +++.+.+|+++.-+
T Consensus 242 ~~dadl~~a~~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~L~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~~~~~i 321 (465)
T cd07098 242 LDDADLDQIASIIMRGTFQSSGQNCIGIERVIVHEKIYDKLLEILTDRVQALRQGPPLDGDVDVGAMISPARFDRLEELV 321 (465)
T ss_pred CCCCCHHHHHHHHHHHHHhcCCCCCcCCcEEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcCCCCCHHHHHHHHHHH
Confidence 356778888888877 342 2334433 45678877643 556765 79999999999887
Q ss_pred hh---hCCeeeeec
Q 028248 57 KM---EGSEIVVEG 67 (211)
Q Consensus 57 k~---~GS~vv~~~ 67 (211)
.. .|.+++..+
T Consensus 322 ~~a~~~Ga~~~~gg 335 (465)
T cd07098 322 ADAVEKGARLLAGG 335 (465)
T ss_pred HHHHHCCCEEEeCC
Confidence 64 588877754
No 303
>cd07139 ALDH_AldA-Rv0768 Mycobacterium tuberculosis aldehyde dehydrogenase AldA-like. The Mycobacterium tuberculosis NAD+-dependent, aldehyde dehydrogenase PDB structure, 3B4W, and the Mycobacterium tuberculosis H37Rv aldehyde dehydrogenase AldA (locus Rv0768) sequence, as well as the Rhodococcus rhodochrous ALDH involved in haloalkane catabolism, and other similar sequences, are included in this CD.
Probab=34.81 E-value=1.4e+02 Score=28.19 Aligned_cols=67 Identities=21% Similarity=0.366 Sum_probs=44.6
Q ss_pred ChHHHHhHHhhhcc-----cCCe------eEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGss------v~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.-.+.+.| .|.. +++-+..-.+|++++.. +.-|. |+++.+.+++++.-++
T Consensus 256 ~dADl~~aa~~i~~~~~~~~GQ~C~a~~~v~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~i~ 335 (471)
T cd07139 256 DDADLDAAVPGLVPASLMNNGQVCVALTRILVPRSRYDEVVEALAAAVAALKVGDPLDPATQIGPLASARQRERVEGYIA 335 (471)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCcCCcEEEEeHhHHHHHHHHHHHHHHhCCcCCCCCCCCCCCCCCCHHHHHHHHHHHH
Confidence 45677888888888 3443 33344445677777643 43333 7889999999998775
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+++..|.
T Consensus 336 ~a~~~ga~v~~gg~ 349 (471)
T cd07139 336 KGRAEGARLVTGGG 349 (471)
T ss_pred HHHHCCCEEEeCCC
Confidence 4 6888876553
No 304
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=34.75 E-value=21 Score=34.33 Aligned_cols=38 Identities=24% Similarity=0.611 Sum_probs=29.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTR 201 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r 201 (211)
.||.|+.+=+-++ |.. ..+-..+|-.||..-..|..+.
T Consensus 98 lC~~C~NPETel~-----itk-~q~i~~~CkACG~r~~~d~rhK 135 (400)
T KOG2767|consen 98 LCPSCENPETELI-----ITK-KQTISLKCKACGFRSDMDLRHK 135 (400)
T ss_pred eCcCCCCCceeEE-----ecc-cchhhhHHHHcCCcccccchhh
Confidence 4999999988874 222 4567789999999888887433
No 305
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=34.65 E-value=22 Score=32.72 Aligned_cols=14 Identities=43% Similarity=0.665 Sum_probs=12.8
Q ss_pred CChHHHHhHHhhhc
Q 028248 1 MSNEEFDNLKEELM 14 (211)
Q Consensus 1 ~s~eefd~lkeel~ 14 (211)
|||+|||.|.+||.
T Consensus 25 IsD~eYD~L~~~L~ 38 (307)
T cd00114 25 VSDAEYDRLYRELR 38 (307)
T ss_pred CChHHHHHHHHHHH
Confidence 69999999999985
No 306
>PF09930 DUF2162: Predicted transporter (DUF2162); InterPro: IPR017199 This group represents a predicted membrane transporter, MTH672 type.
Probab=34.28 E-value=37 Score=30.19 Aligned_cols=35 Identities=34% Similarity=0.371 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHHHHhh--------hccceeeecCCCCCcccc
Q 028248 131 FAAVPLIVYLSQSLTKLI--------VRESLILKGPCPNCGTEN 166 (211)
Q Consensus 131 ~~~~Pvi~~~a~~lt~~~--------~~d~liLkG~CPnCg~Ev 166 (211)
.+++=.+++.-..+.+ | .+..+++--|||+|-.-+
T Consensus 73 imal~li~~Gi~ti~~-W~~~~~~~s~~t~lal~~PCPvCl~Ai 115 (224)
T PF09930_consen 73 IMALLLIYAGIYTIKK-WKKSGKDSSRRTFLALSLPCPVCLTAI 115 (224)
T ss_pred HHHHHHHHHHHHHHHH-HcccCCCCcccchhhhhcCchHHHHHH
Confidence 3444455444444433 5 445688999999997543
No 307
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.18 E-value=21 Score=28.98 Aligned_cols=14 Identities=36% Similarity=0.755 Sum_probs=10.9
Q ss_pred ecCCCCCcccceee
Q 028248 156 KGPCPNCGTENVSF 169 (211)
Q Consensus 156 kG~CPnCg~Ev~aF 169 (211)
.-.||.||+++-+-
T Consensus 49 ~t~CP~Cg~~~e~~ 62 (115)
T COG1885 49 STSCPKCGEPFESA 62 (115)
T ss_pred cccCCCCCCcccee
Confidence 45799999998643
No 308
>cd07145 ALDH_LactADH_F420-Bios Methanocaldococcus jannaschii NAD+-dependent lactaldehyde dehydrogenase-like. NAD+-dependent, lactaldehyde dehydrogenase (EC=1.2.1.22) involved the biosynthesis of coenzyme F(420) in Methanocaldococcus jannaschii through the oxidation of lactaldehyde to lactate and generation of NAPH, and similar sequences are included in this CD.
Probab=34.14 E-value=1.3e+02 Score=28.31 Aligned_cols=68 Identities=18% Similarity=0.405 Sum_probs=44.1
Q ss_pred ChHHHHhHHhhhcc-----cCC-----eeEEeC-hhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGS-----SVVMLS-SAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGs-----sv~~l~-~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|- +.+.+. ..-.+|++++.+ +.-|. |+++.+.+++++..+.
T Consensus 243 ~dAdl~~aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~i~ 322 (456)
T cd07145 243 KDADLERAVSIAVRGRFENAGQVCNAVKRILVEEEVYDKFLKLLVEKVKKLKVGDPLDESTDLGPLISPEAVERMENLVN 322 (456)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCccCeeEEEcHHHHHHHHHHHHHHHhcCCcCCCCCCCCCcCCCcCHHHHHHHHHHHH
Confidence 45566766666666 343 233333 445688888654 44454 4889999999998876
Q ss_pred h---hCCeeeeeccc
Q 028248 58 M---EGSEIVVEGPR 69 (211)
Q Consensus 58 ~---~GS~vv~~~pr 69 (211)
. +|.+++.-+.+
T Consensus 323 ~a~~~ga~vl~gg~~ 337 (456)
T cd07145 323 DAVEKGGKILYGGKR 337 (456)
T ss_pred HHHHCCCEEEeCCCC
Confidence 4 58887766543
No 309
>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=33.97 E-value=14 Score=39.06 Aligned_cols=18 Identities=33% Similarity=0.628 Sum_probs=0.0
Q ss_pred ceeeecCCCCCcccceee
Q 028248 152 SLILKGPCPNCGTENVSF 169 (211)
Q Consensus 152 ~liLkG~CPnCg~Ev~aF 169 (211)
.-|-.--||+||++.+.+
T Consensus 651 vei~~r~Cp~Cg~~t~~~ 668 (900)
T PF03833_consen 651 VEIGRRRCPKCGKETFYN 668 (900)
T ss_dssp ------------------
T ss_pred EeeecccCcccCCcchhh
Confidence 345566799999987655
No 310
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=33.93 E-value=21 Score=36.01 Aligned_cols=22 Identities=27% Similarity=0.770 Sum_probs=15.2
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.-|++||.. |. +..+||+||..
T Consensus 560 ~~C~~CGy~-----g~----------~~~~CP~CG~~ 581 (618)
T PRK14704 560 DRCKCCSYH-----GV----------IGNECPSCGNE 581 (618)
T ss_pred eecCCCCCC-----CC----------cCccCcCCCCC
Confidence 569999962 11 13789999964
No 311
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.83 E-value=32 Score=35.01 Aligned_cols=39 Identities=21% Similarity=0.280 Sum_probs=24.8
Q ss_pred hhhHHHHHHHHh-hhcCCCcc--------ChHHHHHHHHHHhhhCCeeee
Q 028248 25 SAEQKFLEASMA-YVAGKPIM--------SDEEYDKLKQKLKMEGSEIVV 65 (211)
Q Consensus 25 ~~Eq~fLeA~~a-Y~~G~Pi~--------sD~efD~Lk~~Lk~~GS~vv~ 65 (211)
-+...|++++.+ ...|+.++ .....++|+.++- +.+|++
T Consensus 172 GKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~ 219 (665)
T PRK14873 172 DWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLG--AGDVAV 219 (665)
T ss_pred cHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcC--CCcEEE
Confidence 366778888766 66787764 4666666666551 255666
No 312
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=33.45 E-value=41 Score=24.26 Aligned_cols=45 Identities=24% Similarity=0.564 Sum_probs=32.7
Q ss_pred hhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 148 IVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 148 ~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
-++|.+-+|-|=| ||.-...-. .-+..-+.+|..||..+...+..
T Consensus 3 ~vgDiV~mKK~HP-CG~~~Wei~-------R~GaDikikC~gCg~~imlpR~~ 47 (57)
T PF06107_consen 3 EVGDIVEMKKPHP-CGSNEWEII-------RIGADIKIKCLGCGRQIMLPRSK 47 (57)
T ss_pred cCCCEEEEcCCCC-CCCCEEEEE-------EccCcEEEEECCCCCEEEEeHHH
Confidence 4678888888877 666444432 22467899999999999887753
No 313
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=33.42 E-value=22 Score=34.52 Aligned_cols=34 Identities=29% Similarity=0.605 Sum_probs=21.9
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
+-.||+|+.|+.-=- ..+... +..|+-||..+..
T Consensus 327 ~~~c~~~~~e~~~t~------~~~~~~-~~~~~~~~~e~~~ 360 (411)
T COG1503 327 TYKCPTCGYENLKSK------REFEQK-RFRCPECGSEMEE 360 (411)
T ss_pred eecCCCcchhhhhcc------cccccc-cccCccccccccc
Confidence 557999999985321 111122 3399999987653
No 314
>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=33.41 E-value=29 Score=28.20 Aligned_cols=30 Identities=23% Similarity=0.598 Sum_probs=22.8
Q ss_pred eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
...-.||+|..-+..- ......|..|+...
T Consensus 32 ~~Y~aC~~C~kkv~~~-----------~~~~~~C~~C~~~~ 61 (166)
T cd04476 32 WWYPACPGCNKKVVEE-----------GNGTYRCEKCNKSV 61 (166)
T ss_pred eEEccccccCcccEeC-----------CCCcEECCCCCCcC
Confidence 3688999998876543 12678999999875
No 315
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=33.30 E-value=17 Score=25.52 Aligned_cols=13 Identities=38% Similarity=1.096 Sum_probs=7.5
Q ss_pred cCCCCCcccceee
Q 028248 157 GPCPNCGTENVSF 169 (211)
Q Consensus 157 G~CPnCg~Ev~aF 169 (211)
++||.|+....-|
T Consensus 15 ~~Cp~C~~~~l~~ 27 (55)
T PF08063_consen 15 EPCPKCKGGQLYF 27 (55)
T ss_dssp ---SSSSE-EEEE
T ss_pred CCCCCCCCCeEEe
Confidence 6999999976666
No 316
>cd07100 ALDH_SSADH1_GabD1 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like. Succinate-semialdehyde dehydrogenase 1 (SSADH1, GabD1, EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde (SSA) to succinate. SSADH activity in Mycobacterium tuberculosis (Mtb) is encoded by both gabD1 (Rv0234c) and gabD2 (Rv1731). The Mtb GabD1 SSADH1 reportedly is an enzyme of the gamma-aminobutyrate shunt, which forms a functional link between two TCA half-cycles by converting alpha-ketoglutarate to succinate.
Probab=33.28 E-value=1.3e+02 Score=28.07 Aligned_cols=66 Identities=17% Similarity=0.391 Sum_probs=43.4
Q ss_pred ChHHHHhHHhhhcc-----cC------CeeEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHH-
Q 028248 2 SNEEFDNLKEELMW-----EG------SSVVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKL- 56 (211)
Q Consensus 2 s~eefd~lkeel~w-----eG------ssv~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~L- 56 (211)
.|.+.|.--+.+.| .| +.+++-++.-.+|++++.+ +.-|. |+++...+++++..+
T Consensus 215 ~daDl~~aa~~i~~~~~~~~GQ~C~a~~rv~v~~~i~~~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~v~~~i~ 294 (429)
T cd07100 215 DDADLDKAVKTAVKGRLQNAGQSCIAAKRFIVHEDVYDEFLEKFVEAMAALKVGDPMDEDTDLGPLARKDLRDELHEQVE 294 (429)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhccCCCCccCCCCccCCCCHHHHHHHHHHHH
Confidence 45566777777766 33 3344444556788888754 44454 578999999999755
Q ss_pred --hhhCCeeeeec
Q 028248 57 --KMEGSEIVVEG 67 (211)
Q Consensus 57 --k~~GS~vv~~~ 67 (211)
+.+|.+++.-|
T Consensus 295 ~a~~~Ga~~~~gg 307 (429)
T cd07100 295 EAVAAGATLLLGG 307 (429)
T ss_pred HHHHCCCEEEeCC
Confidence 45788887644
No 317
>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=33.26 E-value=23 Score=35.20 Aligned_cols=23 Identities=30% Similarity=0.832 Sum_probs=15.4
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
.-|++||. .|. .+.-+||+||..
T Consensus 525 ~~C~~CG~-----~g~---------~~~~~CP~Cgs~ 547 (579)
T TIGR02487 525 DVCEDCGY-----TGE---------GLNDKCPKCGSH 547 (579)
T ss_pred ccCCCCCC-----CCC---------CCCCcCcCCCCc
Confidence 56999995 222 112689999954
No 318
>PRK11032 hypothetical protein; Provisional
Probab=33.14 E-value=27 Score=29.71 Aligned_cols=23 Identities=22% Similarity=0.593 Sum_probs=0.0
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
|-+||.+..=++ ..+--.||.||
T Consensus 127 C~~Cg~~~~~~~----------p~~i~pCp~C~ 149 (160)
T PRK11032 127 CEKCHHHLAFYT----------PEVLPLCPKCG 149 (160)
T ss_pred ecCCCCEEEecC----------CCcCCCCCCCC
No 319
>PRK10090 aldehyde dehydrogenase A; Provisional
Probab=33.14 E-value=1.3e+02 Score=28.37 Aligned_cols=68 Identities=15% Similarity=0.306 Sum_probs=45.1
Q ss_pred ChHHHHhHHhhhcc-----cCCeeEE------eChhhHHHHHHHHh----hhcCC----------CccChHHHHHHHHHH
Q 028248 2 SNEEFDNLKEELMW-----EGSSVVM------LSSAEQKFLEASMA----YVAGK----------PIMSDEEYDKLKQKL 56 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~~------l~~~Eq~fLeA~~a----Y~~G~----------Pi~sD~efD~Lk~~L 56 (211)
.|.+.|.--+...| .|..|.- -+..-.+|++++.+ +.-|. |+++.+.+|+++.-+
T Consensus 191 ~dADld~aa~~iv~~~f~~~GQ~C~a~~rv~V~~~i~~~f~~~l~~~~~~~~~G~p~~~~~~~~gpli~~~~~~~~~~~i 270 (409)
T PRK10090 191 DDADLDLAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKV 270 (409)
T ss_pred CCCCHHHHHHHHHHHHHHhcCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhcCCCCCCCcccCccccccCHHHHHHHHHHH
Confidence 45667777777777 5544433 33345789888643 44453 677888999998888
Q ss_pred hh---hCCeeeeeccc
Q 028248 57 KM---EGSEIVVEGPR 69 (211)
Q Consensus 57 k~---~GS~vv~~~pr 69 (211)
.. +|.+++.-|.+
T Consensus 271 ~~a~~~Ga~~~~gg~~ 286 (409)
T PRK10090 271 ARAVEEGARVALGGKA 286 (409)
T ss_pred HHHHHCCCEEEeCCCc
Confidence 64 58888776644
No 320
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=33.05 E-value=18 Score=38.31 Aligned_cols=9 Identities=56% Similarity=1.560 Sum_probs=5.6
Q ss_pred cCCCCCccc
Q 028248 157 GPCPNCGTE 165 (211)
Q Consensus 157 G~CPnCg~E 165 (211)
-|||+||..
T Consensus 504 ePCPVCGS~ 512 (1047)
T PRK10246 504 QPCPLCGST 512 (1047)
T ss_pred CCcCCCCcc
Confidence 467777654
No 321
>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=33.00 E-value=25 Score=31.51 Aligned_cols=39 Identities=18% Similarity=0.509 Sum_probs=15.7
Q ss_pred ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
-..||+||.+.-.=+..+ .++....-.-.-|..|++=++
T Consensus 211 R~~Cp~Cg~~~~~~l~~~-~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYF-TVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TTS-TTT---SS-EEE---------SEEEEEETTTTEEEE
T ss_pred CCCCcCCCCCCCcceeeE-ecCCCCcEEEEECCcccchHH
Confidence 345999998776433222 122222333345888887664
No 322
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=32.62 E-value=20 Score=26.32 Aligned_cols=10 Identities=40% Similarity=0.889 Sum_probs=8.6
Q ss_pred CCCCCcccce
Q 028248 158 PCPNCGTENV 167 (211)
Q Consensus 158 ~CPnCg~Ev~ 167 (211)
.||+||.+.+
T Consensus 19 ~Cp~Cgs~~~ 28 (64)
T PRK06393 19 TCPVHGDEKT 28 (64)
T ss_pred cCCCCCCCcC
Confidence 7999999874
No 323
>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=32.59 E-value=22 Score=33.59 Aligned_cols=32 Identities=31% Similarity=0.846 Sum_probs=15.1
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~ 200 (211)
.|++|+....+|.. + +. ..|++||.. .|++..
T Consensus 287 kC~~C~~Rt~sl~r--~-------P~-~~C~~Cg~~-~wer~~ 318 (344)
T PF09332_consen 287 KCKDCGNRTISLER--L-------PK-KHCSNCGSS-KWERTG 318 (344)
T ss_dssp E-T-TS-EEEESSS--S----------S--TTT-S----EEE-
T ss_pred ECCCCCCeeeeccc--C-------CC-CCCCcCCcC-ceeehh
Confidence 79999999999842 2 22 479999975 566643
No 324
>PRK14530 adenylate kinase; Provisional
Probab=32.47 E-value=26 Score=29.34 Aligned_cols=35 Identities=23% Similarity=0.645 Sum_probs=25.1
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
..||.||+....+|.. ......|.+||..|+-+.+
T Consensus 127 ~~~~~~g~~~~~~~~~--------p~~~~~~~~~~~rl~~R~d 161 (215)
T PRK14530 127 RVCPDCGANYHVEFNQ--------PEEEGVCDECGGELIQRDD 161 (215)
T ss_pred CcCcccCCccccCCCC--------CcccccCcccCCcccCCCC
Confidence 5789999987777633 2344569999988876664
No 325
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.44 E-value=21 Score=26.41 Aligned_cols=13 Identities=46% Similarity=1.170 Sum_probs=10.4
Q ss_pred eecCCCCCcccce
Q 028248 155 LKGPCPNCGTENV 167 (211)
Q Consensus 155 LkG~CPnCg~Ev~ 167 (211)
++-+||-||..|.
T Consensus 6 ~~v~CP~Cgkpv~ 18 (65)
T COG3024 6 ITVPCPTCGKPVV 18 (65)
T ss_pred ccccCCCCCCccc
Confidence 5678999998875
No 326
>PF14789 THDPS_M: Tetrahydrodipicolinate N-succinyltransferase middle; PDB: 3R5A_F 3R5B_A 3R5C_B 3R5D_D 3FSY_C 3FSX_A 2RIJ_A.
Probab=32.32 E-value=48 Score=22.37 Aligned_cols=22 Identities=18% Similarity=0.477 Sum_probs=15.2
Q ss_pred ChHHHHHHHHHHhhhCCeeeee
Q 028248 45 SDEEYDKLKQKLKMEGSEIVVE 66 (211)
Q Consensus 45 sD~efD~Lk~~Lk~~GS~vv~~ 66 (211)
.-|+|++++.+||..|-.+.|.
T Consensus 13 ~~~~~~~~r~~lr~~g~~~~V~ 34 (41)
T PF14789_consen 13 EPEDFEENRLRLRARGRPLTVY 34 (41)
T ss_dssp EHHHHHHHHHHHHHTT----EE
T ss_pred CHHHHHHHHHHHHhCCCCcEEE
Confidence 4578999999999999766663
No 327
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.08 E-value=10 Score=27.45 Aligned_cols=47 Identities=23% Similarity=0.443 Sum_probs=31.8
Q ss_pred hhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248 148 IVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 202 (211)
Q Consensus 148 ~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~ 202 (211)
-++|.+-+|-|=| ||+--.-. -.-+..-+.||.|||..+..-+..+.
T Consensus 6 ~l~~~VEMKK~H~-Cg~NrwkI-------iRvGaDIkikC~nC~h~vm~pR~~Fe 52 (60)
T COG4481 6 DLGDIVEMKKPHA-CGTNRWKI-------IRVGADIKIKCENCGHSVMMPRYDFE 52 (60)
T ss_pred cccchheecCCCc-cccceEEE-------EEecCcEEEEecCCCcEEEecHHHHH
Confidence 3677777888766 77733332 12235778999999999887776543
No 328
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=31.92 E-value=44 Score=26.81 Aligned_cols=34 Identities=29% Similarity=0.755 Sum_probs=26.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
-||.||. +|-|+++.+.|+..|.-|.-.....++
T Consensus 3 FCP~Cgn--------~Live~g~~~~rf~C~tCpY~~~I~~e 36 (105)
T KOG2906|consen 3 FCPTCGN--------MLIVESGESCNRFSCRTCPYVFPISRE 36 (105)
T ss_pred ccCCCCC--------EEEEecCCeEeeEEcCCCCceeeEeee
Confidence 3999975 556788888999999999987776654
No 329
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=31.79 E-value=23 Score=25.75 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=5.5
Q ss_pred eCCCCCceeE
Q 028248 186 NCSNCGTTMV 195 (211)
Q Consensus 186 kC~~C~~~L~ 195 (211)
+|++||....
T Consensus 19 ~Cp~CG~~t~ 28 (59)
T COG2260 19 KCPVCGGDTK 28 (59)
T ss_pred cCCCCCCccc
Confidence 5666665443
No 330
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=31.77 E-value=22 Score=24.50 Aligned_cols=9 Identities=67% Similarity=1.516 Sum_probs=8.0
Q ss_pred CCCCCcccc
Q 028248 158 PCPNCGTEN 166 (211)
Q Consensus 158 ~CPnCg~Ev 166 (211)
.||.||+.|
T Consensus 13 kCp~CGt~N 21 (44)
T PF14952_consen 13 KCPKCGTYN 21 (44)
T ss_pred cCCcCcCcc
Confidence 699999877
No 331
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=31.75 E-value=12 Score=33.67 Aligned_cols=48 Identities=17% Similarity=0.344 Sum_probs=33.5
Q ss_pred hhcccee---eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 148 IVRESLI---LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 148 ~~~d~li---LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
|-++..| -...|--|+..+.+=+ +..|.. ..+-+.||.||+.|-++..
T Consensus 186 ~~kg~gvvpl~g~~C~GC~m~l~~~~--~~~V~~--~d~iv~CP~CgRILy~~e~ 236 (239)
T COG1579 186 NKKGVGVVPLEGRVCGGCHMKLPSQT--LSKVRK--KDEIVFCPYCGRILYYDES 236 (239)
T ss_pred cCCCceEEeecCCcccCCeeeecHHH--HHHHhc--CCCCccCCccchHHHhhhc
Confidence 4444433 3568999999998543 333443 6778999999999877654
No 332
>COG3462 Predicted membrane protein [Function unknown]
Probab=31.47 E-value=48 Score=27.07 Aligned_cols=20 Identities=25% Similarity=0.777 Sum_probs=18.1
Q ss_pred hhhcCCCccChHHHHHHHHHHh
Q 028248 36 AYVAGKPIMSDEEYDKLKQKLK 57 (211)
Q Consensus 36 aY~~G~Pi~sD~efD~Lk~~Lk 57 (211)
-|.+|+ +|||||.+.++++|
T Consensus 97 R~AkGE--ItEEEY~r~~~~ir 116 (117)
T COG3462 97 RYAKGE--ITEEEYRRIIRTIR 116 (117)
T ss_pred HHhcCC--CCHHHHHHHHHHhc
Confidence 499998 89999999999986
No 333
>cd07109 ALDH_AAS00426 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like. Uncharacterized aldehyde dehydrogenase of Saccharopolyspora spinosa (AAS00426) and other similar sequences, are present in this CD.
Probab=31.36 E-value=1.6e+02 Score=27.68 Aligned_cols=67 Identities=18% Similarity=0.356 Sum_probs=43.7
Q ss_pred ChHHHHhHHhhhcc-----cCCe------eEEeChhhHHHHHHHHh----hhcC--------CCccChHHHHHHHHHHhh
Q 028248 2 SNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMA----YVAG--------KPIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGss------v~~l~~~Eq~fLeA~~a----Y~~G--------~Pi~sD~efD~Lk~~Lk~ 58 (211)
+|.+.|.--+.+.| .|-. +++-+..-.+|++++.. +.-| -|+++.+.+|+++.-+..
T Consensus 237 ~daDl~~Aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~~~f~~~l~~~~~~~~~G~p~~~~~~gpli~~~~~~~~~~~i~~ 316 (454)
T cd07109 237 ADADLEAALPVVVNAIIQNAGQTCSAGSRLLVHRSIYDEVLERLVERFRALRVGPGLEDPDLGPLISAKQLDRVEGFVAR 316 (454)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCccCcEEEEcHHHHHHHHHHHHHHHHhCCCCCCcccCcCCCccCHHHHHHHHHHHHH
Confidence 45566666677776 3333 33333445678888654 4434 468899999999888765
Q ss_pred ---hCCeeeeecc
Q 028248 59 ---EGSEIVVEGP 68 (211)
Q Consensus 59 ---~GS~vv~~~p 68 (211)
.|.+++..+.
T Consensus 317 a~~~ga~~l~gg~ 329 (454)
T cd07109 317 ARARGARIVAGGR 329 (454)
T ss_pred HHhCCCEEEeCCC
Confidence 4888877654
No 334
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=31.36 E-value=26 Score=34.60 Aligned_cols=22 Identities=27% Similarity=0.832 Sum_probs=15.9
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-|++||.... ....+||+||..
T Consensus 520 ~C~~CG~~~~--------------~~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGE--------------GEGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCc--------------CCCCCCcCCCCc
Confidence 8999997432 123789999965
No 335
>cd07106 ALDH_AldA-AAD23400 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like. Putative aldehyde dehydrogenase, AldA, from Streptomyces aureofaciens (locus AAD23400) and other similar sequences are present in this CD.
Probab=31.23 E-value=1.6e+02 Score=27.55 Aligned_cols=67 Identities=27% Similarity=0.546 Sum_probs=44.8
Q ss_pred ChHHHHhHHhhhcc-----cCCee------EEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV------VMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv------~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|..| ++-+..-.+|++++.. +.-|. |+++.+.+|+++..+.
T Consensus 232 ~dADl~~aa~~iv~~~~~~~GQ~C~a~~rv~V~~~v~d~f~~~l~~~~~~~~~G~p~~~~~~~gpli~~~~~~~i~~~i~ 311 (446)
T cd07106 232 PDVDIDAVAPKLFWGAFINSGQVCAAIKRLYVHESIYDEFCEALVALAKAAVVGDGLDPGTTLGPVQNKMQYDKVKELVE 311 (446)
T ss_pred CCCCHHHHHHHHHHHHHHhcCCCCCCCcEEEEccccHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Confidence 45677777788877 45444 3333435678887644 44464 5788999999997765
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. .|.+++.-|.
T Consensus 312 ~a~~~ga~~~~gg~ 325 (446)
T cd07106 312 DAKAKGAKVLAGGE 325 (446)
T ss_pred HHHHCCCEEEeCCC
Confidence 4 6888876553
No 336
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=31.00 E-value=2.4e+02 Score=25.83 Aligned_cols=104 Identities=16% Similarity=0.250 Sum_probs=54.6
Q ss_pred hHHHHhHH---hhhcccCCeeEEeChhhHHHHHHHHhhhcCCCcc-------ChHHHHHHHHHHhhhCCeeeeeccc---
Q 028248 3 NEEFDNLK---EELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIM-------SDEEYDKLKQKLKMEGSEIVVEGPR--- 69 (211)
Q Consensus 3 ~eefd~lk---eel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~-------sD~efD~Lk~~Lk~~GS~vv~~~pr--- 69 (211)
.||++++. ++|..+-...+.+.+.--+-+|+.... |.+|+ ++++++. ++.+|-.+++.--+
T Consensus 72 eeE~~Rv~pvI~~l~~~~~~~ISIDT~~~~va~~AL~~--GadiINDI~g~~d~~~~~~----~a~~~~~vVlmh~~g~p 145 (282)
T PRK11613 72 EEELDRVIPVVEAIAQRFEVWISVDTSKPEVIRESAKA--GAHIINDIRSLSEPGALEA----AAETGLPVCLMHMQGNP 145 (282)
T ss_pred HHHHHHHHHHHHHHHhcCCCeEEEECCCHHHHHHHHHc--CCCEEEECCCCCCHHHHHH----HHHcCCCEEEEcCCCCC
Confidence 47888876 555544234466666666666654433 88888 3334544 56678888875321
Q ss_pred eeecCcceeeccchhHHHHHhhhhhhHHHHhhh---hhhccccccce
Q 028248 70 CSLRSRKVYSDLSVDYLKMLLLNVPATVVALGL---FFFLDDITGFE 113 (211)
Q Consensus 70 Cslr~~~~ysD~e~D~~km~ll~~~~~~~~lGl---~~~~~d~~gf~ 113 (211)
=.......|.|-..+ .+-++...-......|+ -..+|.-+||.
T Consensus 146 ~~~~~~~~y~dv~~~-v~~~l~~~i~~a~~~GI~~~~IilDPGiGF~ 191 (282)
T PRK11613 146 KTMQEAPKYDDVFAE-VNRYFIEQIARCEAAGIAKEKLLLDPGFGFG 191 (282)
T ss_pred CccccCCCcccHHHH-HHHHHHHHHHHHHHcCCChhhEEEeCCCCcC
Confidence 011122334444433 33333333444556676 34556655653
No 337
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=31.00 E-value=29 Score=33.07 Aligned_cols=36 Identities=19% Similarity=0.316 Sum_probs=21.9
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
--||+||++ .++. .+...+.....|+.||..+....
T Consensus 325 ~r~~~~~~~--~~~~----~~~~~~~~~~~c~~~~~~~~~~~ 360 (409)
T TIGR00108 325 YKCAECGEV--IEKT----VRELKDKKFAICPACGQEMDVVE 360 (409)
T ss_pred EEcCCCCce--eecc----cccccccccccCcccCccccchh
Confidence 569999984 3321 12112223458999999886543
No 338
>PRK12860 transcriptional activator FlhC; Provisional
Probab=30.93 E-value=59 Score=28.42 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=27.2
Q ss_pred HHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248 145 TKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 191 (211)
Q Consensus 145 t~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~ 191 (211)
.+....+ .+---+|..||.+..+-.. ...+..+|+.|.
T Consensus 124 vRf~~s~-~L~l~~C~~Cgg~fv~~~~--------e~~~~f~CplC~ 161 (189)
T PRK12860 124 VRFFDAG-MLQLARCCRCGGKFVTHAH--------DLRHNFVCGLCQ 161 (189)
T ss_pred HHHhcCC-CeeeccCCCCCCCeecccc--------ccCCCCcCCCCC
Confidence 3444555 3466799999998775532 467899999998
No 339
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=30.93 E-value=29 Score=30.51 Aligned_cols=21 Identities=29% Similarity=0.781 Sum_probs=16.3
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
|.+||.-...+ ...||+||+-
T Consensus 357 c~~cg~~~~~~--------------~~~c~~c~~~ 377 (389)
T PRK11788 357 CRNCGFTARTL--------------YWHCPSCKAW 377 (389)
T ss_pred CCCCCCCCccc--------------eeECcCCCCc
Confidence 99999766555 4679999973
No 340
>PRK09407 gabD2 succinic semialdehyde dehydrogenase; Reviewed
Probab=30.89 E-value=1.5e+02 Score=28.71 Aligned_cols=67 Identities=13% Similarity=0.342 Sum_probs=43.9
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEeChh-hHHHHHHHHhh----hcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VMLSSA-EQKFLEASMAY----VAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l~~~-Eq~fLeA~~aY----~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.-.+.+.| .|-.| +.+.+. -.+|++++.+. .-|. |+++.+.+|+++.-+.
T Consensus 272 ~dADl~~Aa~~i~~~~f~~sGQ~C~a~~rv~V~~~v~d~f~~~L~~~~~~l~~G~~~~~~~~~Gpli~~~~~~~v~~~i~ 351 (524)
T PRK09407 272 DDADLDKAAAGAVRACFSNAGQLCISIERIYVHESIYDEFVRAFVAAVRAMRLGAGYDYSADMGSLISEAQLETVSAHVD 351 (524)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCCCcEEEEcHHHHHHHHHHHHHHHHhcCCCCCCCcCCccCCCCCHHHHHHHHHHHH
Confidence 45667777777777 34433 334333 46788886543 3353 6899999999998775
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
+ +|.+++.-|.
T Consensus 352 ~a~~~Ga~vl~gG~ 365 (524)
T PRK09407 352 DAVAKGATVLAGGK 365 (524)
T ss_pred HHHhCCCEEEeCCc
Confidence 4 5788876553
No 341
>PRK14290 chaperone protein DnaJ; Provisional
Probab=30.75 E-value=51 Score=30.67 Aligned_cols=27 Identities=22% Similarity=0.519 Sum_probs=18.7
Q ss_pred ceeCCCCC-ceeEEecCceeEeCCCCCC
Q 028248 184 TINCSNCG-TTMVYDSNTRLITLPEGSE 210 (211)
Q Consensus 184 ~~kC~~C~-~~L~f~~~~r~i~~peg~~ 210 (211)
+-.|+.|. ...+-+.++..+.+|.|..
T Consensus 205 ~~~C~~C~G~g~v~~~~~~~V~Ip~G~~ 232 (365)
T PRK14290 205 EEKCPRCNGTGTVVVNEDISVKIPKGAT 232 (365)
T ss_pred cCCCCCCCCceeEEEeeEEEEEECCCCC
Confidence 44688885 4444555788889998864
No 342
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=30.42 E-value=41 Score=22.47 Aligned_cols=19 Identities=21% Similarity=0.401 Sum_probs=12.8
Q ss_pred HHHHhhhccceeeecCCCCCcccc
Q 028248 143 SLTKLIVRESLILKGPCPNCGTEN 166 (211)
Q Consensus 143 ~lt~~~~~d~liLkG~CPnCg~Ev 166 (211)
.+.+++.+ ++.||.|+++.
T Consensus 27 ~i~~~~~~-----~~~cP~~~~~~ 45 (63)
T smart00504 27 AIEKWLLS-----HGTDPVTGQPL 45 (63)
T ss_pred HHHHHHHH-----CCCCCCCcCCC
Confidence 34555544 57899999876
No 343
>PF05120 GvpG: Gas vesicle protein G ; InterPro: IPR007804 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are involved in the formation of gas vesicles [].
Probab=30.37 E-value=84 Score=23.82 Aligned_cols=27 Identities=30% Similarity=0.521 Sum_probs=21.5
Q ss_pred HHHHHHHH-hhhcCCCccChHHHHHHHHHH
Q 028248 28 QKFLEASM-AYVAGKPIMSDEEYDKLKQKL 56 (211)
Q Consensus 28 q~fLeA~~-aY~~G~Pi~sD~efD~Lk~~L 56 (211)
|+-|.+++ +|-.|+ ||.+|||+-+.+|
T Consensus 34 ~~~L~~L~~~~e~GE--IseeEf~~~E~eL 61 (79)
T PF05120_consen 34 RRELAELQEALEAGE--ISEEEFERREDEL 61 (79)
T ss_pred HHHHHHHHHHHHcCC--CCHHHHHHHHHHH
Confidence 45566665 599998 9999999988877
No 344
>TIGR01222 minC septum site-determining protein MinC. The minC protein assists in correct placement of the septum for cell division by inhibiting septum formation at other sites. Homologs from Deinocoocus, Synechocystis PCC 6803, and Helicobacter pylori do not hit the full length of the model and score between the trusted and noise cutoffs.
Probab=30.36 E-value=66 Score=27.79 Aligned_cols=16 Identities=25% Similarity=0.418 Sum_probs=9.3
Q ss_pred HHHHHHHHHHhhhCCe
Q 028248 47 EEYDKLKQKLKMEGSE 62 (211)
Q Consensus 47 ~efD~Lk~~Lk~~GS~ 62 (211)
+++.+|...|+.+|-.
T Consensus 57 ~~~~~l~~~l~~~gl~ 72 (217)
T TIGR01222 57 KDLPALVSELRRHGLE 72 (217)
T ss_pred HHHHHHHHHHHHCCCE
Confidence 3566666666666543
No 345
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=30.30 E-value=30 Score=36.80 Aligned_cols=23 Identities=43% Similarity=1.064 Sum_probs=14.8
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
||+||+-.. . +-+=..|++||+.
T Consensus 927 c~~c~~~~~---------~---~g~c~~c~~cg~t 949 (953)
T PRK06556 927 CPTCGTKMV---------R---NGSCYVCEGCGST 949 (953)
T ss_pred CCCccCeee---------E---CCceEeccCCCCC
Confidence 888886332 1 3455678888865
No 346
>PRK14529 adenylate kinase; Provisional
Probab=29.93 E-value=37 Score=29.81 Aligned_cols=37 Identities=16% Similarity=0.286 Sum_probs=23.0
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
.-||+||.-.+..|-. .+ .....+|.+||..|+=|.+
T Consensus 127 ~~c~~~~~~~~~~~~~-----~p-~~~~~~cd~~~~~l~~R~D 163 (223)
T PRK14529 127 RLCKNDNNHPNNIFID-----AI-KPDGDVCRVCGGELSTRAD 163 (223)
T ss_pred ccccccCCcccccccC-----CC-cccCCcCcCcCCccccCCC
Confidence 4599998765543311 11 1123489999999887774
No 347
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.90 E-value=73 Score=27.80 Aligned_cols=39 Identities=18% Similarity=0.413 Sum_probs=27.1
Q ss_pred HHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 145 TKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 145 t~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.+....+.+ ---+|..||.+..+-.. ...+..+|+.|.-
T Consensus 124 vRf~~s~~L-~l~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ 162 (187)
T PRK12722 124 VRFVDSGML-QLSSCNCCGGHFVTHAH--------DPVGSFVCGLCQP 162 (187)
T ss_pred HHHHhcCcE-eeccCCCCCCCeecccc--------ccCCCCcCCCCCC
Confidence 333444544 55689999998775532 3578899999986
No 348
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.37 E-value=38 Score=24.22 Aligned_cols=22 Identities=27% Similarity=0.874 Sum_probs=14.3
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
||.|+..- ....+..|+-||=+
T Consensus 2 Cpv~~~~~-------------~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 2 CPVCKKDL-------------PAHVNFECPDCGIP 23 (55)
T ss_pred CCCCcccc-------------ccccCCcCCCCCCc
Confidence 77777654 24566778888743
No 349
>smart00746 TRASH metallochaperone-like domain.
Probab=29.28 E-value=27 Score=19.37 Aligned_cols=9 Identities=33% Similarity=0.955 Sum_probs=7.4
Q ss_pred CCCCcccce
Q 028248 159 CPNCGTENV 167 (211)
Q Consensus 159 CPnCg~Ev~ 167 (211)
||.||..+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 888888875
No 350
>KOG3457 consensus Sec61 protein translocation complex, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=29.19 E-value=36 Score=26.53 Aligned_cols=26 Identities=27% Similarity=0.543 Sum_probs=17.9
Q ss_pred hhccccccceeeeeccCCCchhhHHH
Q 028248 104 FFLDDITGFEITYLLELPEPFSFIFT 129 (211)
Q Consensus 104 ~~~~d~~gf~i~~~~~~~~p~~~i~~ 129 (211)
|+-||+.|+.|.....+-=+++||+.
T Consensus 48 fYTDda~GlKV~PvvVLvmSvgFIas 73 (88)
T KOG3457|consen 48 FYTDDAPGLKVDPVVVLVMSVGFIAS 73 (88)
T ss_pred EeecCCCCceeCCeeehhhhHHHHHH
Confidence 45599999998666555555666654
No 351
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=29.07 E-value=31 Score=31.81 Aligned_cols=14 Identities=43% Similarity=0.674 Sum_probs=12.4
Q ss_pred CChHHHHhHHhhhc
Q 028248 1 MSNEEFDNLKEELM 14 (211)
Q Consensus 1 ~s~eefd~lkeel~ 14 (211)
|||+|||.|.++|.
T Consensus 29 isD~eYD~l~~~L~ 42 (315)
T PF01653_consen 29 ISDAEYDQLFRELK 42 (315)
T ss_dssp SSHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH
Confidence 79999999998874
No 352
>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=28.98 E-value=31 Score=23.05 Aligned_cols=14 Identities=21% Similarity=0.757 Sum_probs=9.7
Q ss_pred eCCCCCceeEEecC
Q 028248 186 NCSNCGTTMVYDSN 199 (211)
Q Consensus 186 kC~~C~~~L~f~~~ 199 (211)
+||.||..+..++.
T Consensus 1 ~CP~Cg~~a~ir~S 14 (47)
T PF04606_consen 1 RCPHCGSKARIRTS 14 (47)
T ss_pred CcCCCCCeeEEEEc
Confidence 47777777777664
No 353
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=28.96 E-value=25 Score=24.22 Aligned_cols=8 Identities=63% Similarity=1.850 Sum_probs=6.5
Q ss_pred CCCCCccc
Q 028248 158 PCPNCGTE 165 (211)
Q Consensus 158 ~CPnCg~E 165 (211)
+||.||..
T Consensus 11 ~CPgCG~t 18 (52)
T PF10825_consen 11 PCPGCGMT 18 (52)
T ss_pred CCCCCcHH
Confidence 79999963
No 354
>PLN02674 adenylate kinase
Probab=28.92 E-value=34 Score=30.47 Aligned_cols=34 Identities=12% Similarity=0.122 Sum_probs=24.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
-||.||.-....|.. .+....|..||+.|+-|.+
T Consensus 160 ~~~~~g~~yn~~~~p--------p~~~~~~~~~g~~L~~R~D 193 (244)
T PLN02674 160 IHPSSGRTYHTKFAP--------PKVPGVDDVTGEPLIQRKD 193 (244)
T ss_pred cccccCCccccccCC--------CcccCcccccCCccccCCC
Confidence 499999876655432 2345579999999887664
No 355
>PRK12366 replication factor A; Reviewed
Probab=28.82 E-value=50 Score=33.29 Aligned_cols=39 Identities=23% Similarity=0.549 Sum_probs=26.2
Q ss_pred hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeE
Q 028248 149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 203 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i 203 (211)
..++. +.-.||+|..-+. + ......|+.|+.. +.+.|.+
T Consensus 526 ~~~~~-~y~aCp~CnkKv~---------~---~~g~~~C~~c~~~---~p~~~~~ 564 (637)
T PRK12366 526 RKQKI-ILYLCPNCRKRVE---------E---VDGEYICEFCGEV---EPNELLM 564 (637)
T ss_pred eCCCE-EEecccccCeEeE---------c---CCCcEECCCCCCC---CCcEEEE
Confidence 34554 6789999977553 1 2467899999987 4455543
No 356
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=28.75 E-value=16 Score=25.21 Aligned_cols=30 Identities=23% Similarity=0.510 Sum_probs=21.5
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
+|+.||.|+--|-+- -+ ....-|..|-..+
T Consensus 1 ~C~iCg~kigl~~~~--k~-----~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRF--KI-----KDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccce--ec-----cCccchHHHHHHh
Confidence 599999999887431 12 3336899998776
No 357
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=28.61 E-value=25 Score=28.91 Aligned_cols=35 Identities=26% Similarity=0.502 Sum_probs=19.2
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
-.|..|+.+...- ++. .........+|+.|+..|.
T Consensus 106 ~~C~~C~~~~~~~--~~~--~~~~~~~~~~C~~C~~~lr 140 (178)
T PF02146_consen 106 LRCSKCGKEYDRE--DIV--DSIDEEEPPRCPKCGGLLR 140 (178)
T ss_dssp EEETTTSBEEEGH--HHH--HHHHTTSSCBCTTTSCBEE
T ss_pred eeecCCCccccch--hhc--ccccccccccccccCccCC
Confidence 4688999866421 111 1111233348999988654
No 358
>KOG0435 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.57 E-value=31 Score=36.09 Aligned_cols=46 Identities=22% Similarity=0.422 Sum_probs=30.3
Q ss_pred cCCCCCcc-------------cceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248 157 GPCPNCGT-------------ENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 202 (211)
Q Consensus 157 G~CPnCg~-------------Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~ 202 (211)
-.|++||. |...|-+.=-+.+....-.++.||.||.+=+.+++++-
T Consensus 437 vhc~~cG~vpVpes~LPV~LP~l~~~~~kG~Pls~~~e~vn~~cP~cg~pAkRETDTMD 495 (876)
T KOG0435|consen 437 VHCDDCGAVPVPESELPVTLPELNDFTPKGPPLSKADEWVNVDCPRCGEPAKRETDTMD 495 (876)
T ss_pred EEcCCCCcccCcHHHCCcccccccccCCCCCcccchhhheeccCccCCCcccccccccc
Confidence 36999994 22333333223333356678999999999998887753
No 359
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=28.48 E-value=26 Score=25.89 Aligned_cols=9 Identities=44% Similarity=1.494 Sum_probs=7.4
Q ss_pred CCCCcccce
Q 028248 159 CPNCGTENV 167 (211)
Q Consensus 159 CPnCg~Ev~ 167 (211)
||+||.+-+
T Consensus 21 CP~Cgs~~~ 29 (64)
T COG2093 21 CPVCGSTDL 29 (64)
T ss_pred CCCCCCccc
Confidence 999998844
No 360
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=28.40 E-value=27 Score=34.19 Aligned_cols=22 Identities=36% Similarity=0.756 Sum_probs=11.2
Q ss_pred hccceeeecCCCCCcccceeec
Q 028248 149 VRESLILKGPCPNCGTENVSFF 170 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aFf 170 (211)
+..++|..=.||.||.-|.-|+
T Consensus 61 fREvVimSF~CpHCG~kN~eiQ 82 (460)
T KOG2703|consen 61 FREVVIMSFECPHCGHKNNEIQ 82 (460)
T ss_pred hheeeeEEeecCccCCcccccc
Confidence 3344445555555555555443
No 361
>KOG3716 consensus Carnitine O-acyltransferase CPTI [Lipid transport and metabolism]
Probab=28.38 E-value=33 Score=35.57 Aligned_cols=23 Identities=39% Similarity=0.839 Sum_probs=17.7
Q ss_pred HHHHHHHHhhhcCCCccChHHHHHHHHHH
Q 028248 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKL 56 (211)
Q Consensus 28 q~fLeA~~aY~~G~Pi~sD~efD~Lk~~L 56 (211)
++||+- =|||||||||++|.+-=
T Consensus 177 ~rYL~S------mkpilseEe~~~l~~la 199 (764)
T KOG3716|consen 177 TRYLDS------MKPILSEEEFDRLEELA 199 (764)
T ss_pred HHHHHh------cccccCHHHHHHHHHHH
Confidence 566654 48999999999987543
No 362
>PRK09457 astD succinylglutamic semialdehyde dehydrogenase; Reviewed
Probab=28.28 E-value=1.9e+02 Score=27.77 Aligned_cols=68 Identities=18% Similarity=0.313 Sum_probs=44.9
Q ss_pred ChHHHHhHHhhhcc-----cCCe------eEEeChhh-HHHHHHHHh----hhcCC----------CccChHHHHHHHH-
Q 028248 2 SNEEFDNLKEELMW-----EGSS------VVMLSSAE-QKFLEASMA----YVAGK----------PIMSDEEYDKLKQ- 54 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGss------v~~l~~~E-q~fLeA~~a----Y~~G~----------Pi~sD~efD~Lk~- 54 (211)
.|.++|.--+.+.| .|-. +++-...- .+|++++.+ +.-|. |+++.+.+|+++.
T Consensus 254 ~dADl~~aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~~d~f~~~l~~~~~~~~vG~p~~~~~~~~Gpli~~~~~~~v~~~ 333 (487)
T PRK09457 254 EVADIDAAVHLIIQSAFISAGQRCTCARRLLVPQGAQGDAFLARLVAVAKRLTVGRWDAEPQPFMGAVISEQAAQGLVAA 333 (487)
T ss_pred CCCCHHHHHHHHHHHHhhccCCCCCCCceEEEeccccHHHHHHHHHHHHhcCcCCCCCcCCCCccCCCcCHHHHHHHHHH
Confidence 56677777777777 3433 33444443 778887643 44554 4688999999987
Q ss_pred --HHhhhCCeeeeeccc
Q 028248 55 --KLKMEGSEIVVEGPR 69 (211)
Q Consensus 55 --~Lk~~GS~vv~~~pr 69 (211)
+.+.+|.+++.-+.+
T Consensus 334 i~~a~~~Ga~~~~gg~~ 350 (487)
T PRK09457 334 QAQLLALGGKSLLEMTQ 350 (487)
T ss_pred HHHHHHCCCEEEeCCCc
Confidence 555679888876544
No 363
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=28.18 E-value=46 Score=26.40 Aligned_cols=33 Identities=21% Similarity=0.506 Sum_probs=22.8
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
-||.||.=...- +. ......+|..||-...+..
T Consensus 4 FCp~Cgsll~p~-------~~-~~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 4 FCPKCGSLLYPK-------KD-DEGGKLVCRKCGYEEEASN 36 (113)
T ss_pred ccCCccCeeEEe-------Ec-CCCcEEECCCCCcchhccc
Confidence 499998765543 11 1233899999998887775
No 364
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=28.17 E-value=43 Score=20.16 Aligned_cols=12 Identities=42% Similarity=0.839 Sum_probs=9.4
Q ss_pred cChHHHHHHHHH
Q 028248 44 MSDEEYDKLKQK 55 (211)
Q Consensus 44 ~sD~efD~Lk~~ 55 (211)
||-|+||+|++-
T Consensus 10 MSPddy~~l~~~ 21 (23)
T PF12162_consen 10 MSPDDYDELERM 21 (23)
T ss_dssp S-HHHHHHHHHH
T ss_pred CCHHHHHHHHHh
Confidence 789999999864
No 365
>cd07141 ALDH_F1AB_F2_RALDH1 NAD+-dependent retinal dehydrogenase 1, ALDH families 1A, 1B, and 2-like. NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36) also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1) in humans, is a homotetrameric, cytosolic enzyme that catalyzes the oxidation of retinaldehyde to retinoic acid. Human ALDH1B1 and ALDH2 are also in this cluster; both are mitochrondrial homotetramers which play important roles in acetaldehyde oxidation; ALDH1B1 in response to UV light exposure and ALDH2 during ethanol metabolism.
Probab=27.82 E-value=1.9e+02 Score=27.60 Aligned_cols=67 Identities=21% Similarity=0.409 Sum_probs=44.2
Q ss_pred ChHHHHhHHhhhcc-----cCC------eeEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGS------SVVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGs------sv~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.++|.-.+.+.| .|- .+++-+..-.+|++++.+ +.-|. |+++.+.+|+++..++
T Consensus 266 ~dADl~~A~~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~G~p~~~~~~~gpli~~~~~~~~~~~i~ 345 (481)
T cd07141 266 ADADLDYAVEQAHEALFFNMGQCCCAGSRTFVQESIYDEFVKRSVERAKKRVVGNPFDPKTEQGPQIDEEQFKKILELIE 345 (481)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCcccCCeEEEEcHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCcCCCCHHHHHHHHHHHH
Confidence 45667776777666 443 344444445778888643 44454 5889999999998665
Q ss_pred ---hhCCeeeeecc
Q 028248 58 ---MEGSEIVVEGP 68 (211)
Q Consensus 58 ---~~GS~vv~~~p 68 (211)
..|.+++..|.
T Consensus 346 ~a~~~Ga~v~~gg~ 359 (481)
T cd07141 346 SGKKEGAKLECGGK 359 (481)
T ss_pred HHHHCCCEEEeCCC
Confidence 46888876553
No 366
>smart00532 LIGANc Ligase N family.
Probab=27.78 E-value=33 Score=33.26 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=16.4
Q ss_pred CCCccChHHHHHHHHHHhhhCC
Q 028248 40 GKPIMSDEEYDKLKQKLKMEGS 61 (211)
Q Consensus 40 G~Pi~sD~efD~Lk~~Lk~~GS 61 (211)
|+=+|+.++|++|..+....|.
T Consensus 166 GEv~~~~~~F~~ln~~~~~~g~ 187 (441)
T smart00532 166 GEVFMPKEDFLALNEELEEEGE 187 (441)
T ss_pred ceEEEEHHHHHHHHHHHHhcCC
Confidence 6667888899998887665553
No 367
>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=27.71 E-value=37 Score=24.33 Aligned_cols=10 Identities=40% Similarity=0.929 Sum_probs=3.4
Q ss_pred cCCCCCcccc
Q 028248 157 GPCPNCGTEN 166 (211)
Q Consensus 157 G~CPnCg~Ev 166 (211)
-+||.||.++
T Consensus 3 v~CP~C~k~~ 12 (57)
T PF03884_consen 3 VKCPICGKPV 12 (57)
T ss_dssp EE-TTT--EE
T ss_pred ccCCCCCCee
Confidence 3455555544
No 368
>cd07133 ALDH_CALDH_CalB Coniferyl aldehyde dehydrogenase-like. Coniferyl aldehyde dehydrogenase (CALDH, EC=1.2.1.68) of Pseudomonas sp. strain HR199 (CalB) which catalyzes the NAD+-dependent oxidation of coniferyl aldehyde to ferulic acid, and similar sequences, are present in this CD.
Probab=27.57 E-value=1.9e+02 Score=27.30 Aligned_cols=68 Identities=18% Similarity=0.445 Sum_probs=43.2
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEeChh-hHHHHHHHHh----hhcC-------CCccChHHHHHHHHHHh--
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VMLSSA-EQKFLEASMA----YVAG-------KPIMSDEEYDKLKQKLK-- 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l~~~-Eq~fLeA~~a----Y~~G-------~Pi~sD~efD~Lk~~Lk-- 57 (211)
.|.+.|.--+.+.| .|-+| +.+.+. -.+|++++.+ ++-| -|+++.+.+++++..+.
T Consensus 218 ~dadl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~~~f~~~l~~~~~~~~~g~~~~~~~gpli~~~~~~~v~~~i~~a 297 (434)
T cd07133 218 PDADLAKAAERIAFGKLLNAGQTCVAPDYVLVPEDKLEEFVAAAKAAVAKMYPTLADNPDYTSIINERHYARLQGLLEDA 297 (434)
T ss_pred CCCCHHHHHHHHHHHHhccCCCcccCCCEEEEcHHHHHHHHHHHHHHHHHhcCCCCCCCCcCCCCCHHHHHHHHHHHHHH
Confidence 34556666666665 34333 344443 4678888654 3323 28899999999997664
Q ss_pred -hhCCeeeeeccc
Q 028248 58 -MEGSEIVVEGPR 69 (211)
Q Consensus 58 -~~GS~vv~~~pr 69 (211)
..|.+++.-|++
T Consensus 298 ~~~Ga~v~~gg~~ 310 (434)
T cd07133 298 RAKGARVIELNPA 310 (434)
T ss_pred HhCCCEEEecCCC
Confidence 468888776654
No 369
>PF05391 Lsm_interact: Lsm interaction motif; InterPro: IPR008669 This short motif is found at the C terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation [].
Probab=27.49 E-value=34 Score=20.20 Aligned_cols=9 Identities=33% Similarity=0.752 Sum_probs=7.5
Q ss_pred CChHHHHhH
Q 028248 1 MSNEEFDNL 9 (211)
Q Consensus 1 ~s~eefd~l 9 (211)
|||+||.+|
T Consensus 10 ~SNddFrkm 18 (21)
T PF05391_consen 10 KSNDDFRKM 18 (21)
T ss_pred cchHHHHHH
Confidence 799999875
No 370
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=27.46 E-value=20 Score=35.42 Aligned_cols=42 Identities=26% Similarity=0.417 Sum_probs=0.0
Q ss_pred CChHHHHh---HHhhhcccCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHH
Q 028248 1 MSNEEFDN---LKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYD 50 (211)
Q Consensus 1 ~s~eefd~---lkeel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~efD 50 (211)
|||||||. +||| |.|--- =|+|||.++-||..-.+..-.++|
T Consensus 253 LSDEEYDEyKkiREe--r~g~YS------IeEYLqdReRy~Eela~~~a~~~~ 297 (535)
T PF05416_consen 253 LSDEEYDEYKKIREE--RGGKYS------IEEYLQDRERYEEELAEAQATEED 297 (535)
T ss_dssp -----------------------------------------------------
T ss_pred CChhHHHHHHHHHHH--hcCCcc------HHHHHHHHHHHHHHhhhhhhhhcc
Confidence 68998885 5555 444211 289999999999877666544444
No 371
>cd07101 ALDH_SSADH2_GabD2 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 2-like. Succinate-semialdehyde dehydrogenase 2 (SSADH2) and similar proteins are in this CD. SSADH1 (GabD1, EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde to succinate. SSADH activity in Mycobacterium tuberculosis is encoded by both gabD1 (Rv0234c) and gabD2 (Rv1731), however ,the Vmax of GabD1 was shown to be much higher than that of GabD2, and GabD2 (SSADH2) is likely to serve physiologically as a dehydrogenase for a different aldehyde(s).
Probab=27.41 E-value=2e+02 Score=27.05 Aligned_cols=67 Identities=15% Similarity=0.351 Sum_probs=43.4
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE-----EeChh-hHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV-----MLSSA-EQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~-----~l~~~-Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
+|.+.|.--+.+.| .|-.|. .+.++ -.+|++++.. +.-|. |+++.+.+++++..+.
T Consensus 236 ~dAdl~~a~~~i~~~~~~~sGQ~C~a~~rv~V~~~i~d~f~~~L~~~~~~~~~G~~~~~~~~~gpli~~~~~~~v~~~v~ 315 (454)
T cd07101 236 EDADLDKAAAGAVRACFSNAGQLCVSIERIYVHESVYDEFVRRFVARTRALRLGAALDYGPDMGSLISQAQLDRVTAHVD 315 (454)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCcccCeEEEEcHHHHHHHHHHHHHHHhhCCCCCCCCCCCCcCCCCCHHHHHHHHHHHH
Confidence 45666776677766 454443 34333 3678887643 44453 6899999999997766
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+++..|.
T Consensus 316 ~a~~~Ga~vl~gg~ 329 (454)
T cd07101 316 DAVAKGATVLAGGR 329 (454)
T ss_pred HHHHCCCEEEeCCC
Confidence 4 6777776553
No 372
>TIGR00777 ahpD alkylhydroperoxidase, AhpD family. Members of this family are alkylhydroperoxidases, which catalyze the reduction of peroxides to their corresponding alcohols via oxidation of cysteine residues. In these alkylhydroperoxidases, the cysteines are located in a conserved -CXXC- motif located towards the COOH terminus. In Mycobacterium tuberculosis, two non-homologous alkylhydroperoxidases, AhpD and AhpC, are found in the same operon.
Probab=27.39 E-value=16 Score=31.68 Aligned_cols=23 Identities=26% Similarity=0.699 Sum_probs=21.9
Q ss_pred hhcCCCccChHHHHHHHHHHhhh
Q 028248 37 YVAGKPIMSDEEYDKLKQKLKME 59 (211)
Q Consensus 37 Y~~G~Pi~sD~efD~Lk~~Lk~~ 59 (211)
||+...+++|++|+.++.+||..
T Consensus 83 ~Yr~~hl~~~~~y~~~pa~lrmn 105 (177)
T TIGR00777 83 FYRGRHLLEGARYDDLRPGLRMN 105 (177)
T ss_pred HHHhHhhcccchhhcCCccchhH
Confidence 99999999999999999999876
No 373
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.24 E-value=13 Score=28.63 Aligned_cols=31 Identities=19% Similarity=0.521 Sum_probs=22.2
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
=.|-+||++.-.- +..++.-...|+-|+..+
T Consensus 13 Y~c~~cg~~~dvv-------q~~~ddplt~ce~c~a~~ 43 (82)
T COG2331 13 YECTECGNRFDVV-------QAMTDDPLTTCEECGARL 43 (82)
T ss_pred EeecccchHHHHH-------HhcccCccccChhhChHH
Confidence 3588898875433 555577788999998754
No 374
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=27.16 E-value=54 Score=30.44 Aligned_cols=53 Identities=26% Similarity=0.573 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeC-CCCCceeEEecCceeE
Q 028248 132 AAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINC-SNCGTTMVYDSNTRLI 203 (211)
Q Consensus 132 ~~~Pvi~~~a~~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC-~~C~~~L~f~~~~r~i 203 (211)
+..|+.+++|+ +-+|..|..- -.|||||=..--| ..| ..|=+.+.|++..|.+
T Consensus 214 lliPiF~P~~~-~Yg~~ynk~c---k~C~nC~La~HPF---------------tnC~s~CvCG~~f~~sd~mk 267 (285)
T PF03563_consen 214 LLIPIFYPIAY-LYGWLYNKSC---KKCKNCGLAYHPF---------------TNCGSHCVCGMKFETSDRMK 267 (285)
T ss_pred HHHHHHHHHHH-HHHHHHHHHh---hhCcccCeeccCC---------------CCCCCeeeccccccchHHHH
Confidence 34577776663 3455566644 4699999887777 235 3455667788865544
No 375
>PF12419 DUF3670: SNF2 Helicase protein ; InterPro: IPR022138 This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00271 from PFAM, PF00176 from PFAM. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.
Probab=27.09 E-value=1.3e+02 Score=24.22 Aligned_cols=38 Identities=26% Similarity=0.511 Sum_probs=23.4
Q ss_pred CChHHHHhHHhhhcccCCeeEEeChh----hHHHHHHHHhhhcCCC
Q 028248 1 MSNEEFDNLKEELMWEGSSVVMLSSA----EQKFLEASMAYVAGKP 42 (211)
Q Consensus 1 ~s~eefd~lkeel~weGssv~~l~~~----Eq~fLeA~~aY~~G~P 42 (211)
||.|||+.|-+ ++.++|.++-. ..+-++++.+|.+..+
T Consensus 84 Ls~eEf~~L~~----~~~~LV~~rg~WV~ld~~~l~~~~~~~~~~~ 125 (141)
T PF12419_consen 84 LSEEEFEQLVE----QKRPLVRFRGRWVELDPEELRRALAFLEKAP 125 (141)
T ss_pred CCHHHHHHHHH----cCCCeEEECCEEEEECHHHHHHHHHHHHhcc
Confidence 57788887766 56666666544 4555666666555433
No 376
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.79 E-value=44 Score=26.97 Aligned_cols=24 Identities=29% Similarity=0.978 Sum_probs=14.7
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
||.|+.-|-.. -++|++||-.|+-
T Consensus 4 CPrC~skvC~L--------------P~~CpiCgLtLVs 27 (112)
T TIGR00622 4 CPQCRAKVCEL--------------PVECPICGLTLIL 27 (112)
T ss_pred CCCCCCCccCC--------------CCcCCcCCCEEec
Confidence 77777666544 1467777766654
No 377
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=26.72 E-value=89 Score=27.04 Aligned_cols=42 Identities=33% Similarity=0.410 Sum_probs=31.5
Q ss_pred HHHHhHHhhhc------ccCCeeEEeChhhHHHHHHH--HhhhcCCCccChHHH
Q 028248 4 EEFDNLKEELM------WEGSSVVMLSSAEQKFLEAS--MAYVAGKPIMSDEEY 49 (211)
Q Consensus 4 eefd~lkeel~------weGssv~~l~~~Eq~fLeA~--~aY~~G~Pi~sD~ef 49 (211)
+.++.||+.+. |.| ..+...|+|.||+ ..|..++.+++-+++
T Consensus 58 ~~~~~l~~~~~~~~~~~y~~----~~~~~lQEyvEA~~f~~~l~~~~l~s~eel 107 (204)
T PRK14562 58 ELVKELKELLKDHPELYYAG----YVGTALQEYVEALLVYSLLFENKIPSPEEL 107 (204)
T ss_pred HHHHHHHHHhccCchhhhhh----hcchHHHHHHHHHHHHHHHcCCCCCCHHHc
Confidence 45667777663 333 4577899999995 569999999999884
No 378
>cd07148 ALDH_RL0313 Uncharacterized ALDH ( RL0313) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1. Uncharacterized aldehyde dehydrogenase (locus RL0313) with sequence similarity to the moss Tortula ruralis aldehyde dehydrogenase ALDH21A1 (RNP123) believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and similar sequences are included in this CD.
Probab=26.70 E-value=2.1e+02 Score=27.08 Aligned_cols=68 Identities=21% Similarity=0.445 Sum_probs=43.9
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE-----EeC-hhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV-----MLS-SAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~-----~l~-~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|..|. .+. ..-.+|++++.+ +.-|. |+++.+.+|+++..++
T Consensus 242 ~dADl~~aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~i~ 321 (455)
T cd07148 242 RSADLDAMIPPLVKGGFYHAGQVCVSVQRVFVPAEIADDFAQRLAAAAEKLVVGDPTDPDTEVGPLIRPREVDRVEEWVN 321 (455)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCccCCeEEEEcHhHHHHHHHHHHHHHhcCCCCCCCCCCCcCCCCcCHHHHHHHHHHHH
Confidence 46677777777777 454443 333 334578887654 33333 7889999999988765
Q ss_pred ---hhCCeeeeeccc
Q 028248 58 ---MEGSEIVVEGPR 69 (211)
Q Consensus 58 ---~~GS~vv~~~pr 69 (211)
.+|.+++.-|.+
T Consensus 322 ~a~~~Ga~vl~gg~~ 336 (455)
T cd07148 322 EAVAAGARLLCGGKR 336 (455)
T ss_pred HHHhCCCEEEeCCcc
Confidence 468888775543
No 379
>cd07097 ALDH_KGSADH-YcbD Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like. Kinetic studies of the Bacillus subtilis ALDH-like ycbD protein, which is involved in d-glucarate/d-galactarate utilization, reveal that it is a NADP+-dependent, alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). KGSADHs (EC 1.2.1.26) catalyze the NAD(P)+-dependent conversion of KGSA to alpha-ketoglutarate. Interestingly, the NADP+-dependent, tetrameric, 2,5-dioxopentanoate dehydrogenase (EC=1.2.1.26), an enzyme involved in the catabolic pathway for D-arabinose in Sulfolobus solfataricus, also clusters in this group. This CD shows a distant phylogenetic relationship to the Azospirillum brasilense KGSADH-II (-III) group.
Probab=26.46 E-value=2.1e+02 Score=27.10 Aligned_cols=66 Identities=21% Similarity=0.438 Sum_probs=42.9
Q ss_pred ChHHHHhHHhhhcc-----cCC------eeEEeChhhHHHHHHHHh----hhcC---------CCccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGS------SVVMLSSAEQKFLEASMA----YVAG---------KPIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGs------sv~~l~~~Eq~fLeA~~a----Y~~G---------~Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|- .+++-+..-.+|++++.+ +.-| -|+++.+.+|+++.-++
T Consensus 255 ~dadl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~Gpli~~~~~~~v~~~i~ 334 (473)
T cd07097 255 DDADLDLAVECAVQGAFFSTGQRCTASSRLIVTEGIHDRFVEALVERTKALKVGDALDEGVDIGPVVSERQLEKDLRYIE 334 (473)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCcCCeeEEEehhHHHHHHHHHHHHHHhCCCCCCCCCCCcCCCCCCHHHHHHHHHHHH
Confidence 45567777777776 343 333444444678877643 4444 36789999999998775
Q ss_pred h---hCCeeeeec
Q 028248 58 M---EGSEIVVEG 67 (211)
Q Consensus 58 ~---~GS~vv~~~ 67 (211)
. +|.+++.-|
T Consensus 335 ~a~~~Ga~v~~gg 347 (473)
T cd07097 335 IARSEGAKLVYGG 347 (473)
T ss_pred HHHHCCCEEEeCC
Confidence 4 588877655
No 380
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=26.37 E-value=48 Score=24.65 Aligned_cols=33 Identities=36% Similarity=0.829 Sum_probs=23.4
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeC
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL 205 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~ 205 (211)
||.|..-+... +.+...|+ || +.+++.+..+++
T Consensus 2 CPVC~~~~L~~-----------~~~~i~C~-Cg--l~l~~~~~~~tl 34 (82)
T PF14768_consen 2 CPVCQKGNLRE-----------NSNVISCS-CG--LRLNTQQDELTL 34 (82)
T ss_pred CCccCCCcccc-----------cCCeEECC-Cc--cEEecCCCCCCH
Confidence 99998877666 56778884 44 777777555554
No 381
>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=26.32 E-value=44 Score=31.03 Aligned_cols=38 Identities=24% Similarity=0.474 Sum_probs=20.5
Q ss_pred ecCCCCCcccce-eeccccccccCCC-----------CcCceeCCCCCce
Q 028248 156 KGPCPNCGTENV-SFFGTILSISSGG-----------TTNTINCSNCGTT 193 (211)
Q Consensus 156 kG~CPnCg~Ev~-aFfg~i~~v~s~~-----------~~~~~kC~~C~~~ 193 (211)
.|-||+||..=. +....--+..+.+ .-.+++|++||..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 468999998743 3321100001100 2347899999974
No 382
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.28 E-value=59 Score=30.32 Aligned_cols=37 Identities=24% Similarity=0.622 Sum_probs=19.1
Q ss_pred ecCCCCCcccce-eeccccccccCCCCcCc-eeCCCCCceeEE
Q 028248 156 KGPCPNCGTENV-SFFGTILSISSGGTTNT-INCSNCGTTMVY 196 (211)
Q Consensus 156 kG~CPnCg~Ev~-aFfg~i~~v~s~~~~~~-~kC~~C~~~L~f 196 (211)
-..||+||+.-. .|+ ++.+.....+ --|..|++=++.
T Consensus 226 R~~C~~Cg~~~~l~y~----~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 226 RVKCSNCEQSGKLHYW----SLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred CccCCCCCCCCceeee----eecCCCcceEeeeccccccccee
Confidence 345888886422 232 2333222223 347888876554
No 383
>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=26.08 E-value=49 Score=26.35 Aligned_cols=29 Identities=21% Similarity=0.617 Sum_probs=19.4
Q ss_pred eecCCC--CCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 155 LKGPCP--NCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 155 LkG~CP--nCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
-.-.|| .|+.-+..- ......|..|+...
T Consensus 17 ~Y~aC~~~~C~kKv~~~-----------~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 17 YYPACPNEKCNKKVTEN-----------GDGSYRCEKCNKTV 47 (146)
T ss_dssp EEEE-TSTTTS-B-EEE-----------TTTEEEETTTTEEE
T ss_pred EECCCCCccCCCEeecC-----------CCcEEECCCCCCcC
Confidence 567899 999876544 23568999999875
No 384
>cd07102 ALDH_EDX86601 Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (EDX86601). Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (locus EDX86601) and other similar sequences, are present in this CD.
Probab=25.95 E-value=2.4e+02 Score=26.32 Aligned_cols=67 Identities=24% Similarity=0.460 Sum_probs=43.3
Q ss_pred ChHHHHhHHhhhcc-----cCC------eeEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGS------SVVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGs------sv~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.-.+.+.| .|- .+++-+..-.+|++++.+ +.-|. |+++...+|+++..++
T Consensus 235 ~dADl~~aa~~i~~~~~~~~GQ~C~a~~~v~V~~~v~~~f~~~L~~~~~~l~vg~p~~~~~~~gpli~~~~~~~i~~~i~ 314 (452)
T cd07102 235 PDADLDAAAESLVDGAFFNSGQSCCSIERIYVHESIYDAFVEAFVAVVKGYKLGDPLDPSTTLGPVVSARAADFVRAQIA 314 (452)
T ss_pred CCCCHHHHHHHHHHHHHHhCCCCCcCCcEEEEeHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 45667777777777 443 333433445778887643 44565 4788889999997654
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. .|.++..-+.
T Consensus 315 ~a~~~ga~vl~gg~ 328 (452)
T cd07102 315 DAIAKGARALIDGA 328 (452)
T ss_pred HHHhCCCEEEeCCC
Confidence 3 5888877553
No 385
>cd07112 ALDH_GABALDH-PuuC Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like. NADP+-dependent, gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (GABALDH) PuuC of Escherichia coli which catalyzes the conversion of putrescine to 4-aminobutanoate and other similar sequences are present in this CD.
Probab=25.75 E-value=2.3e+02 Score=26.91 Aligned_cols=65 Identities=23% Similarity=0.499 Sum_probs=43.0
Q ss_pred hH-HHHhHHhhhcc-----cCCee-----EEeCh-hhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 3 NE-EFDNLKEELMW-----EGSSV-----VMLSS-AEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 3 ~e-efd~lkeel~w-----eGssv-----~~l~~-~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
|. +.|..-+.+.| .|..| +.+.+ ...+|++++.+ +.-|. |+++.+.+|+++..+.
T Consensus 246 da~dl~~aa~~i~~~~~~~~GQ~C~a~~~v~V~~~v~~~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~v~~~v~ 325 (462)
T cd07112 246 DAPDLDAAAEAAAAGIFWNQGEVCSAGSRLLVHESIKDEFLEKVVAAAREWKPGDPLDPATRMGALVSEAHFDKVLGYIE 325 (462)
T ss_pred CCcCHHHHHHHHHHHHHhccCCCCCCCeeEEEcHHHHHHHHHHHHHHHhcCCcCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 44 67777777776 34433 44443 35678888654 33454 5889999999998666
Q ss_pred h---hCCeeeeec
Q 028248 58 M---EGSEIVVEG 67 (211)
Q Consensus 58 ~---~GS~vv~~~ 67 (211)
. +|.+++.-|
T Consensus 326 ~a~~~Ga~v~~gg 338 (462)
T cd07112 326 SGKAEGARLVAGG 338 (462)
T ss_pred HHHHCCCEEEeCC
Confidence 5 788887654
No 386
>PRK13252 betaine aldehyde dehydrogenase; Provisional
Probab=25.64 E-value=2.1e+02 Score=27.30 Aligned_cols=66 Identities=20% Similarity=0.359 Sum_probs=42.2
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE-----Ee-ChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV-----ML-SSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~-----~l-~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+...| .|..|. .+ .+.-.+|++++.+ +.-|. |+++.+.+|+++.-+.
T Consensus 261 ~dAdl~~A~~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~i~ 340 (488)
T PRK13252 261 DDADLDRAADIAMLANFYSSGQVCTNGTRVFVQKSIKAAFEARLLERVERIRIGDPMDPATNFGPLVSFAHRDKVLGYIE 340 (488)
T ss_pred CCCCHHHHHHHHHHHHHhhcCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCHHHHHHHHHHHH
Confidence 45566666666666 355443 33 3334678887643 44454 6899999999997765
Q ss_pred ---hhCCeeeeec
Q 028248 58 ---MEGSEIVVEG 67 (211)
Q Consensus 58 ---~~GS~vv~~~ 67 (211)
.+|.+++.-|
T Consensus 341 ~a~~~Ga~vl~gg 353 (488)
T PRK13252 341 KGKAEGARLLCGG 353 (488)
T ss_pred HHHHCCCEEEeCC
Confidence 3577876644
No 387
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=25.62 E-value=37 Score=33.58 Aligned_cols=62 Identities=24% Similarity=0.474 Sum_probs=37.8
Q ss_pred HHHhhhccc--eeeecCCCCCcccceeeccccccc--c---CCCCcCceeCCCCCceeEEecCceeEeC
Q 028248 144 LTKLIVRES--LILKGPCPNCGTENVSFFGTILSI--S---SGGTTNTINCSNCGTTMVYDSNTRLITL 205 (211)
Q Consensus 144 lt~~~~~d~--liLkG~CPnCg~Ev~aFfg~i~~v--~---s~~~~~~~kC~~C~~~L~f~~~~r~i~~ 205 (211)
|-+|+-+|+ -.=+-||+.||.|..+=.|.-.+- + +.+...-.+|..||+...|-+....+.|
T Consensus 147 LL~WFKq~FF~WvN~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPRYNdp~kL 215 (500)
T KOG0909|consen 147 LLNWFKQDFFKWVNNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPRYNDPIKL 215 (500)
T ss_pred HHHHHHHhhheecCCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCcccCCHHHH
Confidence 445555553 233568999999986443331111 1 1222334689999999999887665554
No 388
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=25.57 E-value=26 Score=33.07 Aligned_cols=35 Identities=23% Similarity=0.526 Sum_probs=20.0
Q ss_pred ceeeecCCCCCccc--ceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 152 SLILKGPCPNCGTE--NVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 152 ~liLkG~CPnCg~E--v~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
.+-.-..|++|+.. +..+ ...+.+|+.||..+.+-
T Consensus 236 ~~G~v~~C~~C~~~~~~~~~-----------~~~~~~c~~cg~~~~~~ 272 (377)
T PF02005_consen 236 KLGYVYYCPSCGYREEVKGL-----------QKLKSKCPECGSKLHIS 272 (377)
T ss_dssp TEEEEEEETTT--EECCT-G-----------CC--CEETTT-SCCCEE
T ss_pred heeEEEECCCccccccccCc-----------cccCCcCCCCCCcccee
Confidence 34566899999643 2222 22348999999988764
No 389
>cd02663 Peptidase_C19G A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=25.28 E-value=86 Score=27.54 Aligned_cols=26 Identities=19% Similarity=0.508 Sum_probs=17.4
Q ss_pred cCceeCCCCCceeEEecCceeEeCCC
Q 028248 182 TNTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 182 ~~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
.++.+|..|+..-......+...+|+
T Consensus 165 ~~~~~C~~C~~~~~a~k~~~i~~lP~ 190 (300)
T cd02663 165 RNKFYCDECCSLQEAEKRMKIKKLPK 190 (300)
T ss_pred CCcEECCCCCCceeEEEEEEeccCCc
Confidence 45688999998765555555555554
No 390
>PRK12616 pyridoxal kinase; Reviewed
Probab=25.25 E-value=2.4e+02 Score=24.63 Aligned_cols=54 Identities=24% Similarity=0.359 Sum_probs=38.6
Q ss_pred HHhHHhhhcccCCeeEEeChhhHHHHHHHHhhhcCC-CccChHHHHHHHHHHhhhCCe-eeeec
Q 028248 6 FDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGK-PIMSDEEYDKLKQKLKMEGSE-IVVEG 67 (211)
Q Consensus 6 fd~lkeel~weGssv~~l~~~Eq~fLeA~~aY~~G~-Pi~sD~efD~Lk~~Lk~~GS~-vv~~~ 67 (211)
-+.+|++|. .-..+++.+..|-+.| .|. ++-+.++..+.-.+|...|.+ |++++
T Consensus 124 ~~~l~~~L~-~~advitpN~~Ea~~L-------~g~~~~~~~~~~~~aa~~l~~~G~~~VvVt~ 179 (270)
T PRK12616 124 AEALREQLA-PLATVITPNLFEAGQL-------SGMGEIKTVEQMKEAAKKIHELGAQYVVITG 179 (270)
T ss_pred HHHHHHHhh-ccceEecCCHHHHHHH-------cCCCCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence 456676553 4577888888887766 355 566778888888888888864 66664
No 391
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=25.21 E-value=46 Score=37.73 Aligned_cols=32 Identities=19% Similarity=0.380 Sum_probs=18.8
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
..+.||.||+.--..+--+. ...=+.||+||=
T Consensus 1703 ~~~~cp~c~~~~~~~~~~~~------~~gc~~c~~cg~ 1734 (1740)
T PRK08332 1703 GVVYCPVCYEKEGKLVELRM------ESGCATCPVCGW 1734 (1740)
T ss_pred ccCCCCCCCCCCCcceeeEe------cCCceeCCCCCC
Confidence 45559999998422221111 234468999983
No 392
>cd07091 ALDH_F1-2_Ald2-like ALDH subfamily: ALDH families 1and 2, including 10-formyltetrahydrofolate dehydrogenase, NAD+-dependent retinal dehydrogenase 1 and related proteins. ALDH subfamily which includes the NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36), also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1), in humans, a homotetrameric, cytosolic enzyme that catalyzes the oxidation of retinaldehyde to retinoic acid. Human ALDH1B1 and ALDH2 are also in this cluster; both are mitochrondrial homotetramers which play important roles in acetaldehyde oxidation; ALDH1B1 in response to UV light exposure and ALDH2 during ethanol metabolism. 10-formyltetrahydrofolate dehydrogenase (FTHFDH, EC=1.5.1.6), also known as aldehyde dehydrogenase family 1 member L1 (ALDH1L1), in humans, a multi-domain homotetramer with an N-terminal formyl transferase domain and a C-terminal ALDH domain. FTHFDH catalyzes an NADP+-dependent dehydrogenase reaction resulting in the co
Probab=25.19 E-value=2.4e+02 Score=26.73 Aligned_cols=67 Identities=24% Similarity=0.449 Sum_probs=42.9
Q ss_pred ChHHHHhHHhhhcc-----cCCe------eEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGss------v~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.-.+.+.| .|-. |++-+..-.+|++++.+ +.-|. |+++...++++...+.
T Consensus 262 ~dADl~~Aa~~i~~~~~~~~GQ~C~a~~rv~V~~~v~~~f~~~L~~~~~~~~~g~p~~~~~~~gpli~~~~~~~v~~~i~ 341 (476)
T cd07091 262 DDADLDKAVEWAAFGIFFNQGQCCCAGSRIFVQESIYDEFVEKFKARAEKRVVGDPFDPDTFQGPQVSKAQFDKILSYIE 341 (476)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCcCCcEEEEeHHHHHHHHHHHHHHHhhCCCCCCCCCCCcCCCCcCHHHHHHHHHHHH
Confidence 45667777777777 3433 33333344678888654 44454 4688889999986554
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. .|.+++.-|.
T Consensus 342 ~a~~~ga~vl~gg~ 355 (476)
T cd07091 342 SGKKEGATLLTGGE 355 (476)
T ss_pred HHHHCCCEEEeCCC
Confidence 4 6888877553
No 393
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=25.18 E-value=35 Score=35.10 Aligned_cols=25 Identities=28% Similarity=0.601 Sum_probs=18.3
Q ss_pred hcCCCccChHHHHHHHHHHhhhCCe
Q 028248 38 VAGKPIMSDEEYDKLKQKLKMEGSE 62 (211)
Q Consensus 38 ~~G~Pi~sD~efD~Lk~~Lk~~GS~ 62 (211)
.+|+-.|+-+.|.+|..+....|-+
T Consensus 169 VRGEvfm~k~~F~~lN~~~~~~g~~ 193 (667)
T COG0272 169 VRGEVFMPKEDFEALNEEREEEGEK 193 (667)
T ss_pred EEeEEEEeHHHHHHHHHHHHHhCCC
Confidence 3566778888888888777766654
No 394
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=25.18 E-value=32 Score=35.59 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=9.7
Q ss_pred ecCCCCCcccce
Q 028248 156 KGPCPNCGTENV 167 (211)
Q Consensus 156 kG~CPnCg~Ev~ 167 (211)
.++||.||.+..
T Consensus 457 ~~~CPvCg~~l~ 468 (908)
T COG0419 457 GEKCPVCGQELP 468 (908)
T ss_pred CCCCCCCCCCCC
Confidence 579999997764
No 395
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.09 E-value=34 Score=29.61 Aligned_cols=10 Identities=50% Similarity=1.218 Sum_probs=8.4
Q ss_pred cCCCCCcccc
Q 028248 157 GPCPNCGTEN 166 (211)
Q Consensus 157 G~CPnCg~Ev 166 (211)
-+||.||+++
T Consensus 155 P~CPlCg~Pl 164 (171)
T PF11290_consen 155 PPCPLCGEPL 164 (171)
T ss_pred CCCCCCCCCC
Confidence 4899999975
No 396
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=24.92 E-value=37 Score=32.82 Aligned_cols=15 Identities=13% Similarity=0.157 Sum_probs=10.3
Q ss_pred eeCCCCCceeEEecC
Q 028248 185 INCSNCGTTMVYDSN 199 (211)
Q Consensus 185 ~kC~~C~~~L~f~~~ 199 (211)
..|.-||+.++++..
T Consensus 172 p~~~~~~~~~e~~~~ 186 (556)
T PRK12268 172 PRSKISGSTPEFRET 186 (556)
T ss_pred CccccCCCcCeEEec
Confidence 357777788777664
No 397
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=24.90 E-value=50 Score=31.17 Aligned_cols=33 Identities=15% Similarity=0.342 Sum_probs=20.3
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f 196 (211)
.-+.||+|+.... ++. ......+|+.|+..+..
T Consensus 232 ~v~~C~~c~~~~~--~~~-------~~~~~~~C~~c~~~~~~ 264 (374)
T TIGR00308 232 YTYHCSRCLHNKP--VNG-------ISQRKGRCKECGGEYHL 264 (374)
T ss_pred eEEECCCcccccc--ccc-------ccCCCCCCCCCCCccee
Confidence 4567999976422 221 12234579999987754
No 398
>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=24.88 E-value=51 Score=22.83 Aligned_cols=30 Identities=27% Similarity=0.721 Sum_probs=19.3
Q ss_pred eeeecCCC--CCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 153 LILKGPCP--NCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 153 liLkG~CP--nCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
.-+.-.|| .||..+| ... -.++.-|..|+-
T Consensus 15 ~r~rk~CP~~~CG~GvF--MA~--------H~dR~~CGKCg~ 46 (47)
T PF01599_consen 15 KRLRKECPSPRCGAGVF--MAE--------HKDRHYCGKCGY 46 (47)
T ss_dssp EESSEE-TSTTTTSSSE--EEE---------SSEEEETTTSS
T ss_pred EEhhhcCCCcccCCceE--eee--------cCCCccCCCccc
Confidence 34678899 8999884 211 246788888874
No 399
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=24.52 E-value=24 Score=26.59 Aligned_cols=32 Identities=31% Similarity=0.612 Sum_probs=24.7
Q ss_pred CCCCCcccce--eeccccccccCCCCcCceeCCCCCce
Q 028248 158 PCPNCGTENV--SFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 158 ~CPnCg~Ev~--aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
-|-+||.+.. ..+|| +.+++.|+-=|.-|=..
T Consensus 2 ~CQSCGMPl~~~~~~Gt----e~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGT----EADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCcccccc----ccCCCCchhHHHHHhcC
Confidence 3889999887 46777 77778888889888443
No 400
>PRK09847 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional
Probab=24.44 E-value=2.2e+02 Score=27.40 Aligned_cols=65 Identities=14% Similarity=0.349 Sum_probs=43.6
Q ss_pred ChH-HHHhHHhhhcc-----cCCeeEE-----e-ChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHH
Q 028248 2 SNE-EFDNLKEELMW-----EGSSVVM-----L-SSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKL 56 (211)
Q Consensus 2 s~e-efd~lkeel~w-----eGssv~~-----l-~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~L 56 (211)
.|. ++|.-.+.+.| .|..|.- + ...-.+|++++.+ +.-|. |+++.+.+|+++.-+
T Consensus 278 ~daaDl~~Aa~~i~~~~~~~aGQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~v~~~v 357 (494)
T PRK09847 278 ADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFI 357 (494)
T ss_pred CCccCHHHHHHHHHHHHHhcCCCCCCCCcEEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCcCCCCcCHHHHHHHHHHH
Confidence 354 78888888887 5555443 3 2234678888643 44465 788999999999877
Q ss_pred h---hhCCeeeeec
Q 028248 57 K---MEGSEIVVEG 67 (211)
Q Consensus 57 k---~~GS~vv~~~ 67 (211)
. ..| +++.-|
T Consensus 358 ~~a~~~G-~i~~gg 370 (494)
T PRK09847 358 REGESKG-QLLLDG 370 (494)
T ss_pred HHHHHCC-eEEECC
Confidence 5 467 666644
No 401
>TIGR01496 DHPS dihydropteroate synthase. This model represents dihydropteroate synthase, the enzyme that catalyzes the second to last step in folic acid biosynthesis. The gene is usually designated folP (folic acid biosynthsis) or sul (sulfanilamide resistance). This model represents one branch of the family of pterin-binding enzymes (pfam00809) and of a cluster of dihydropteroate synthase and related enzymes (COG0294). Other members of pfam00809 and COG0294 are represented by TIGR00284.
Probab=24.21 E-value=2.3e+02 Score=25.16 Aligned_cols=61 Identities=15% Similarity=0.197 Sum_probs=37.6
Q ss_pred hHHHHhHH---hhhccc-CCeeEEeChhhHHHHHHHHhhhcCCCccChHH---HHHHHHHHhhhCCeeeee
Q 028248 3 NEEFDNLK---EELMWE-GSSVVMLSSAEQKFLEASMAYVAGKPIMSDEE---YDKLKQKLKMEGSEIVVE 66 (211)
Q Consensus 3 ~eefd~lk---eel~we-Gssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~e---fD~Lk~~Lk~~GS~vv~~ 66 (211)
+||+++|+ +.+..+ +- .+.+-+..-+-+++.... |.++|.|-- .+++-.-++.+|-.+++.
T Consensus 57 ~~E~~rl~~~v~~~~~~~~~-plsiDT~~~~vi~~al~~--G~~iINsis~~~~~~~~~l~~~~~~~vV~m 124 (257)
T TIGR01496 57 EEELNRVVPVIKALRDQPDV-PISVDTYRAEVARAALEA--GADIINDVSGGQDPAMLEVAAEYGVPLVLM 124 (257)
T ss_pred HHHHHHHHHHHHHHHhcCCC-eEEEeCCCHHHHHHHHHc--CCCEEEECCCCCCchhHHHHHHcCCcEEEE
Confidence 35777777 555544 43 356666666666654444 888887522 233444477889888884
No 402
>PRK05582 DNA topoisomerase I; Validated
Probab=24.07 E-value=80 Score=31.75 Aligned_cols=14 Identities=29% Similarity=0.871 Sum_probs=10.7
Q ss_pred eeCCCCCceeEEec
Q 028248 185 INCSNCGTTMVYDS 198 (211)
Q Consensus 185 ~kC~~C~~~L~f~~ 198 (211)
..|+.|+..+..+.
T Consensus 612 ~~CP~C~~~l~l~k 625 (650)
T PRK05582 612 VKCPKCGGQIVERK 625 (650)
T ss_pred CCCCCCCCceEEEc
Confidence 57999988777654
No 403
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.06 E-value=39 Score=28.07 Aligned_cols=19 Identities=37% Similarity=0.954 Sum_probs=15.7
Q ss_pred eeeecCCCCCcccceeeccc
Q 028248 153 LILKGPCPNCGTENVSFFGT 172 (211)
Q Consensus 153 liLkG~CPnCg~Ev~aFfg~ 172 (211)
.||+| ||+||---|.|...
T Consensus 17 eil~G-CP~CGg~kF~yv~~ 35 (131)
T PF09845_consen 17 EILSG-CPECGGNKFQYVPE 35 (131)
T ss_pred HHHcc-CcccCCcceEEcCC
Confidence 45666 99999999999765
No 404
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=24.03 E-value=81 Score=33.01 Aligned_cols=16 Identities=25% Similarity=0.511 Sum_probs=12.3
Q ss_pred ceeCCCCCceeEEecC
Q 028248 184 TINCSNCGTTMVYDSN 199 (211)
Q Consensus 184 ~~kC~~C~~~L~f~~~ 199 (211)
..+||.||..|..+..
T Consensus 645 ~~~CP~Cg~~m~lK~g 660 (860)
T PRK06319 645 DSPCPLCGGEMKVRHG 660 (860)
T ss_pred CCcCccCCCeeEEecC
Confidence 4479999988887653
No 405
>cd07118 ALDH_SNDH Gluconobacter oxydans L-sorbosone dehydrogenase-like. Included in this CD is the L-sorbosone dehydrogenase (SNDH) from Gluconobacter oxydans UV10. In G. oxydans, D-sorbitol is converted to 2-keto-L-gulonate (a precursor of L-ascorbic acid) in sequential oxidation steps catalyzed by a FAD-dependent, L-sorbose dehydrogenase and an NAD(P)+-dependent, L-sorbosone dehydrogenase.
Probab=23.80 E-value=2.6e+02 Score=26.48 Aligned_cols=67 Identities=18% Similarity=0.474 Sum_probs=44.0
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EEeC-hhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VMLS-SAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~l~-~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|..-+.+.| .|-+| +.+- +.-.+|++++.. +.-|. |+++...+|+++.-++
T Consensus 239 ~dAdl~~aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~d~f~~~L~~~~~~l~~g~p~~~~~~~gpli~~~~~~~~~~~i~ 318 (454)
T cd07118 239 ADADLDAAADAVVFGVYFNAGECCNSGSRLLVHESIADAFVAAVVARSRKVRVGDPLDPETKVGAIINEAQLAKITDYVD 318 (454)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCCCceEEEcHHHHHHHHHHHHHHHHhcCcCCCCCCCCcCCCCcCHHHHHHHHHHHH
Confidence 46667777777777 24333 4443 335678888654 33343 5788899999998876
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+++.-|.
T Consensus 319 ~a~~~ga~v~~gg~ 332 (454)
T cd07118 319 AGRAEGATLLLGGE 332 (454)
T ss_pred HHHhCCCEEEeCCC
Confidence 4 5778877654
No 406
>cd07113 ALDH_PADH_NahF Escherichia coli NAD+-dependent phenylacetaldehyde dehydrogenase PadA-like. NAD+-dependent, homodimeric, phenylacetaldehyde dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia coli involved in the catabolism of 2-phenylethylamine, and other related sequences, are present in this CD. Also included is the Pseudomonas fluorescens ST StyD PADH involved in styrene catabolism, the Sphingomonas sp. LB126 FldD protein involved in fluorene degradation, and the Novosphingobium aromaticivorans NahF salicylaldehyde dehydrogenase involved in the NAD+-dependent conversion of salicylaldehyde to salicylate.
Probab=23.76 E-value=2.4e+02 Score=26.83 Aligned_cols=67 Identities=22% Similarity=0.395 Sum_probs=44.0
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE-----EeCh-hhHHHHHHHH----hhhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV-----MLSS-AEQKFLEASM----AYVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~-----~l~~-~Eq~fLeA~~----aY~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+...| .|-.|+ .+-+ .-.+|++++. ++.-|. |+++.+.+|+++.-++
T Consensus 261 ~dAdl~~aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~i~ 340 (477)
T cd07113 261 KDADIDWVVEGLLTAGFLHQGQVCAAPERFYVHRSKFDELVTKLKQALSSFQVGSPMDESVMFGPLANQPHFDKVCSYLD 340 (477)
T ss_pred CCCCHHHHHHHHHHHHHhhCCCCCcCCcEEEECHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 45677777777777 344443 3333 2356777753 344454 6889999999998886
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+++.-+.
T Consensus 341 ~a~~~Ga~~l~gg~ 354 (477)
T cd07113 341 DARAEGDEIVRGGE 354 (477)
T ss_pred HHHHCCCEEEeCCC
Confidence 5 6888876554
No 407
>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=23.74 E-value=56 Score=22.98 Aligned_cols=20 Identities=25% Similarity=0.655 Sum_probs=14.6
Q ss_pred CCCCcCceeCCCCCceeEEe
Q 028248 178 SGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 178 s~~~~~~~kC~~C~~~L~f~ 197 (211)
++....+.-|++||+.|-++
T Consensus 42 s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp TTSSCEEEEETTT--EEEEE
T ss_pred CCCcCcCcccCCCCCeeecc
Confidence 56677888999999999874
No 408
>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=23.68 E-value=42 Score=34.00 Aligned_cols=14 Identities=43% Similarity=0.702 Sum_probs=12.8
Q ss_pred CChHHHHhHHhhhc
Q 028248 1 MSNEEFDNLKEELM 14 (211)
Q Consensus 1 ~s~eefd~lkeel~ 14 (211)
|||+|||.|.+||.
T Consensus 20 IsD~eYD~L~~~L~ 33 (652)
T TIGR00575 20 ISDAEYDRLYRELQ 33 (652)
T ss_pred CChHHHHHHHHHHH
Confidence 69999999999985
No 409
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=23.60 E-value=31 Score=24.02 Aligned_cols=38 Identities=29% Similarity=0.427 Sum_probs=21.3
Q ss_pred eecCCCCCc----ccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 155 LKGPCPNCG----TENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 155 LkG~CPnCg----~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
|+=+=|||= +++.+-|.- ....+...+|+=|++.++.+
T Consensus 7 l~C~Np~CITn~~E~v~~~F~v-----~~~~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 7 LKCPNPNCITNSNEPVESRFYV-----IDKEPIKLRCHYCERIITED 48 (52)
T ss_dssp SE-SSTTBTTT-TSSS--EEEE-----EETTTCEEEETTT--EEEHH
T ss_pred EEcCCCCcccCCCCCCCceEEE-----EeCCCCEEEeeCCCCEeccc
Confidence 444446784 455444422 22368999999999998764
No 410
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.39 E-value=26 Score=29.36 Aligned_cols=31 Identities=26% Similarity=0.592 Sum_probs=22.3
Q ss_pred cccceeeccccccccCCCCcCceeCCCCCce
Q 028248 163 GTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 163 g~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
|-|+-.+||+..-..+-..+.-+.||+||.+
T Consensus 11 ~HeFEGWF~ssaDfd~Q~~rgLv~CPvCgs~ 41 (142)
T COG5319 11 GHEFEGWFGSSADFDRQRERGLVTCPVCGST 41 (142)
T ss_pred CCcccccccCchhHHHHHHcCceeCCCCCcH
Confidence 4566778877665566666777889999874
No 411
>cd07130 ALDH_F7_AASADH NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B. Alpha-aminoadipic semialdehyde dehydrogenase (AASADH, EC=1.2.1.31), also known as ALDH7A1, Antiquitin-1, ALDH7B, or delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH), is a NAD+-dependent ALDH. Human ALDH7A1 is involved in the pipecolic acid pathway of lysine catabolism, catalyzing the oxidation of alpha-aminoadipic semialdehyde to alpha-aminoadipate. Arabidopsis thaliana ALDH7B4 appears to be an osmotic-stress-inducible ALDH gene encoding a turgor-responsive or stress-inducible ALDH. The Streptomyces clavuligerus P6CDH appears to be involved in cephamycin biosynthesis, catalyzing the second stage of the two-step conversion of lysine to alpha-aminoadipic acid. The ALDH7A1 enzyme and others in this group have been observed as tetramers, yet the bacterial P6CDH enzyme has been reported as a monomer.
Probab=23.39 E-value=2.7e+02 Score=26.51 Aligned_cols=68 Identities=15% Similarity=0.298 Sum_probs=43.1
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE------EeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV------MLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~------~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+...| .|-.|. +-...-.+|++++.+ ..-|. |+++...+|+++.-++
T Consensus 255 ~dadl~~Aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~l~~g~p~~~~~~~Gpli~~~~~~~~~~~i~ 334 (474)
T cd07130 255 EDADLDLAVRAVLFAAVGTAGQRCTTTRRLIVHESIYDEVLERLKKAYKQVRIGDPLDDGTLVGPLHTKAAVDNYLAAIE 334 (474)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCcCCeEEEEcHhHHHHHHHHHHHHHhcCCcCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 45667777677776 444433 334445778888643 23343 6778888888877654
Q ss_pred ---hhCCeeeeeccc
Q 028248 58 ---MEGSEIVVEGPR 69 (211)
Q Consensus 58 ---~~GS~vv~~~pr 69 (211)
.+|.+++..|.+
T Consensus 335 ~a~~~Ga~v~~gg~~ 349 (474)
T cd07130 335 EAKSQGGTVLFGGKV 349 (474)
T ss_pred HHHHCCCEEEECCCc
Confidence 458888776654
No 412
>PRK00279 adk adenylate kinase; Reviewed
Probab=23.33 E-value=52 Score=27.50 Aligned_cols=34 Identities=24% Similarity=0.586 Sum_probs=23.6
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.-||.||.-....+.. .+...+|..||..++=+.
T Consensus 128 ~~~~~~g~~~~~~~~~--------p~~~~~~~~~~~~l~~r~ 161 (215)
T PRK00279 128 RICPACGRTYHVKFNP--------PKVEGKCDVCGEELIQRA 161 (215)
T ss_pred cccCccCCcccccCCC--------CCCcCcCcCCCCcccCCC
Confidence 5699999876554322 345678999998776554
No 413
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=23.32 E-value=1.3e+02 Score=23.36 Aligned_cols=45 Identities=18% Similarity=0.406 Sum_probs=35.1
Q ss_pred eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248 154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
-+.-.||-|-.-...| | -++..+-|++|++.+---+..|....++
T Consensus 32 Fm~VkC~gc~~iT~vf-----S----HaqtvVvc~~c~~il~~~tggra~ls~~ 76 (84)
T KOG1779|consen 32 FMDVKCPGCFKITTVF-----S----HAQTVVVCEGCSTILCQPTGGKAKLSEG 76 (84)
T ss_pred EEEEEcCCceEEEEEe-----e----cCceEEEcCCCceEEEEecCCcEEecCC
Confidence 3556799998766666 1 2688899999999998888888877665
No 414
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=23.30 E-value=44 Score=34.03 Aligned_cols=24 Identities=21% Similarity=0.549 Sum_probs=16.9
Q ss_pred cCCCccChHHHHHHHHHHhhhCCe
Q 028248 39 AGKPIMSDEEYDKLKQKLKMEGSE 62 (211)
Q Consensus 39 ~G~Pi~sD~efD~Lk~~Lk~~GS~ 62 (211)
+|+=+|+.++|++|..+....|.+
T Consensus 170 RGEv~m~~~~F~~lN~~~~~~g~~ 193 (665)
T PRK07956 170 RGEVFMPKADFEALNEERREEGEK 193 (665)
T ss_pred EEEEEEEHHHHHHHHHHHHhcCCC
Confidence 355568888888887776666653
No 415
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=23.29 E-value=51 Score=31.90 Aligned_cols=37 Identities=16% Similarity=0.375 Sum_probs=20.7
Q ss_pred cCCCCCcccceeeccccc-cccCC----CCcCceeCCCCCce
Q 028248 157 GPCPNCGTENVSFFGTIL-SISSG----GTTNTINCSNCGTT 193 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~-~v~s~----~~~~~~kC~~C~~~ 193 (211)
-.|+.||+.--.=.|+-. +++.+ .-+..-.||+||..
T Consensus 426 ~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 426 MQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred EEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 359999976554444311 11111 12346789999864
No 416
>TIGR01780 SSADH succinate-semialdehyde dehydrogenase. SSADH enzyme belongs to the aldehyde dehydrogenase family (pfam00171), sharing a common evolutionary origin and enzymatic mechanism with lactaldehyde dehydrogenase. Like in lactaldehyde dehydrogenase and succinate semialdehyde dehydrogenase, the mammalian catalytic glutamic acid and cysteine residues are conserved in all the enzymes of this family (PS00687, PS00070).
Probab=23.27 E-value=2.4e+02 Score=26.61 Aligned_cols=67 Identities=18% Similarity=0.409 Sum_probs=44.4
Q ss_pred ChHHHHhHHhhhcc-----cCCeeEE-----eChh-hHHHHHHHH----hhhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVVM-----LSSA-EQKFLEASM----AYVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~~-----l~~~-Eq~fLeA~~----aY~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|..-+...| .|-.|.- +.+. -.+|++++. ++.-|. |+++.+.+|+++..++
T Consensus 238 ~dadl~~aa~~iv~~~f~~sGQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~l~~G~p~~~~~~~gpli~~~~~~~v~~~i~ 317 (448)
T TIGR01780 238 DDADIDQAVEGAMASKFRNAGQTCVCANRLYVHDGIYDEFAKKLAEAVKKLKVGNGLDEGVTQGPLINEKAVEKVEKHIA 317 (448)
T ss_pred CCCCHHHHHHHHHHHHHHhcCCcccCCceeechHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Confidence 46677777777777 3554443 3333 356777753 355465 5899999999998876
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+++.-|.
T Consensus 318 ~a~~~Ga~il~gg~ 331 (448)
T TIGR01780 318 DAVEKGAKVVTGGK 331 (448)
T ss_pred HHHHCCCEEEeCCC
Confidence 5 6888877553
No 417
>PRK09401 reverse gyrase; Reviewed
Probab=23.26 E-value=32 Score=37.22 Aligned_cols=15 Identities=47% Similarity=1.050 Sum_probs=11.4
Q ss_pred eeecCCCCCccccee
Q 028248 154 ILKGPCPNCGTENVS 168 (211)
Q Consensus 154 iLkG~CPnCg~Ev~a 168 (211)
+-++.|||||-++.+
T Consensus 5 ~y~~~cpnc~g~i~~ 19 (1176)
T PRK09401 5 IYKNSCPNCGGDISD 19 (1176)
T ss_pred hhcccCCCCCCcCcH
Confidence 467889999987763
No 418
>cd07099 ALDH_DDALDH Methylomonas sp. 4,4'-diapolycopene-dialdehyde dehydrogenase-like. The 4,4'-diapolycopene-dialdehyde dehydrogenase (DDALDH) involved in C30 carotenoid synthesis in Methylomonas sp. strain 16a and other similar sequences are present in this CD. DDALDH converts 4,4'-diapolycopene-dialdehyde into 4,4'-diapolycopene-diacid.
Probab=23.23 E-value=2.8e+02 Score=25.96 Aligned_cols=68 Identities=13% Similarity=0.434 Sum_probs=43.6
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE-----EeCh-hhHHHHHHHH----hhhcCCC---------ccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV-----MLSS-AEQKFLEASM----AYVAGKP---------IMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~-----~l~~-~Eq~fLeA~~----aY~~G~P---------i~sD~efD~Lk~~Lk 57 (211)
+|.+.|.--+.+.| .|-.|+ .+.+ .-.+|++++. +++-|.| +++...+|+++..++
T Consensus 237 ~dadl~~a~~~i~~~~~~~~GQ~C~a~~ri~V~~~i~d~f~~~l~~~~~~l~~G~~~~~~~~~gp~i~~~~~~~~~~~i~ 316 (453)
T cd07099 237 ADADLERAAAAAVWGAMVNAGQTCISVERVYVHESVYDEFVARLVAKARALRPGADDIGDADIGPMTTARQLDIVRRHVD 316 (453)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCCCcEEEEcHHHHHHHHHHHHHHHHhccCCCCCCCCCcccCCcCHHHHHHHHHHHH
Confidence 45566666666666 555443 3333 3367888764 3555754 688899999988655
Q ss_pred ---hhCCeeeeeccc
Q 028248 58 ---MEGSEIVVEGPR 69 (211)
Q Consensus 58 ---~~GS~vv~~~pr 69 (211)
..|.+++.-|.+
T Consensus 317 ~a~~~ga~~~~gg~~ 331 (453)
T cd07099 317 DAVAKGAKALTGGAR 331 (453)
T ss_pred HHHhCCCEEEeCCCc
Confidence 578888776544
No 419
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=23.02 E-value=74 Score=29.71 Aligned_cols=54 Identities=28% Similarity=0.281 Sum_probs=37.3
Q ss_pred CccChHHHHHHHHHHhh-hCC--eeeeec---------------cceeecCcceeeccchhHHHHHhhhhhh
Q 028248 42 PIMSDEEYDKLKQKLKM-EGS--EIVVEG---------------PRCSLRSRKVYSDLSVDYLKMLLLNVPA 95 (211)
Q Consensus 42 Pi~sD~efD~Lk~~Lk~-~GS--~vv~~~---------------prCslr~~~~ysD~e~D~~km~ll~~~~ 95 (211)
|.+++++++.+..+++. -.+ -||+-| .+|..++.++.-|.+-+.|+.-+.+-|+
T Consensus 109 p~is~~~~~~~l~~~~~~l~~~d~VvlsGSlP~g~~~d~y~~li~~~~~~g~~vilD~Sg~~L~~~L~~~P~ 180 (310)
T COG1105 109 PEISEAELEQFLEQLKALLESDDIVVLSGSLPPGVPPDAYAELIRILRQQGAKVILDTSGEALLAALEAKPW 180 (310)
T ss_pred CCCCHHHHHHHHHHHHHhcccCCEEEEeCCCCCCCCHHHHHHHHHHHHhcCCeEEEECChHHHHHHHccCCc
Confidence 78888888888888877 332 344444 2266778888888888887766555454
No 420
>PRK07218 replication factor A; Provisional
Probab=23.00 E-value=42 Score=32.49 Aligned_cols=21 Identities=29% Similarity=0.705 Sum_probs=15.1
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
--||+|+.-+.- -.|+.||..
T Consensus 298 ~rCP~C~r~v~~----------------~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRVIQK----------------GQCRSHGAV 318 (423)
T ss_pred ecCcCccccccC----------------CcCCCCCCc
Confidence 469999876521 479999965
No 421
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=22.97 E-value=63 Score=21.36 Aligned_cols=14 Identities=29% Similarity=0.885 Sum_probs=12.2
Q ss_pred hccceeeecCCCCC
Q 028248 149 VRESLILKGPCPNC 162 (211)
Q Consensus 149 ~~d~liLkG~CPnC 162 (211)
.-.++++.|.|-.|
T Consensus 22 ~pG~ViING~C~dC 35 (36)
T PF08194_consen 22 TPGNVIINGKCIDC 35 (36)
T ss_pred CCCeEEECceeeeC
Confidence 37789999999998
No 422
>PRK05756 pyridoxamine kinase; Validated
Probab=22.94 E-value=2.1e+02 Score=24.92 Aligned_cols=53 Identities=17% Similarity=0.347 Sum_probs=35.7
Q ss_pred HhHHhhhcccCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCCe-eeeec
Q 028248 7 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSE-IVVEG 67 (211)
Q Consensus 7 d~lkeel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~GS~-vv~~~ 67 (211)
+.++++| .....+++.+..|-++| .|.++-+.++-.+.-++|...|-+ |++++
T Consensus 129 ~~~~~~l-l~~adiitpN~~Ea~~L-------~g~~~~~~~~~~~~~~~l~~~g~~~Vvvt~ 182 (286)
T PRK05756 129 EFLRDRA-LPAADIITPNLFELEWL-------SGRPVETLEDAVAAARALIARGPKIVLVTS 182 (286)
T ss_pred HHHHHhh-cccccEecCCHHHHHHH-------hCCCcCCHHHHHHHHHHHHHhCCCEEEEec
Confidence 4455555 46788888888887766 467766666666666677777854 66664
No 423
>cd07142 ALDH_F2BC Arabidosis aldehyde dehydrogenase family 2 B4, B7, C4-like. Included in this CD is the Arabidosis aldehyde dehydrogenase family 2 members B4 and B7 (EC=1.2.1.3), which are mitochondrial homotetramers that oxidize acetaldehyde and glycolaldehyde, but not L-lactaldehyde. Also in this group, is the Arabidosis cytosolic, homotetramer ALDH2C4 (EC=1.2.1.3), an enzyme involved in the oxidation of sinapalehyde and coniferaldehyde.
Probab=22.81 E-value=2.7e+02 Score=26.53 Aligned_cols=67 Identities=22% Similarity=0.450 Sum_probs=42.7
Q ss_pred ChHHHHhHHhhhcc-----cCCe------eEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGss------v~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|-. +++-...-.+|++++.+ +.-|. |+++.+.+++++.-++
T Consensus 262 ~dADl~~Aa~~i~~~~f~~aGQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~G~p~~~~~~~Gpli~~~~~~~v~~~v~ 341 (476)
T cd07142 262 EDADVDKAVELAHFALFFNQGQCCCAGSRTFVHESIYDEFVEKAKARALKRVVGDPFRKGVEQGPQVDKEQFEKILSYIE 341 (476)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCCCCCCeeEEEeHHHHHHHHHHHHHHHHhcCCCCCCCCCCcCCcCcCHHHHHHHHHHHH
Confidence 45566666666666 2433 33333334678887644 33343 6889999999998775
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+++.-|.
T Consensus 342 ~a~~~Ga~v~~gg~ 355 (476)
T cd07142 342 HGKEEGATLITGGD 355 (476)
T ss_pred HHHhCCCEEEecCC
Confidence 4 5888877543
No 424
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=22.80 E-value=53 Score=27.29 Aligned_cols=37 Identities=27% Similarity=0.518 Sum_probs=25.7
Q ss_pred CCCCCcccce-------------eecccccc-------ccC-CCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENV-------------SFFGTILS-------ISS-GGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~-------------aFfg~i~~-------v~s-~~~~~~~kC~~C~~~L 194 (211)
-|-+||++.| +|+..|.+ +.+ +-.+.++.|.+|+.-|
T Consensus 42 ~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D~s~gm~RtEv~C~~Cg~HL 99 (134)
T TIGR00357 42 VDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDESHGMIRTEVRCRNCDAHL 99 (134)
T ss_pred EccCCCCccccccchhcCCCCCcCcCcccCCCceEEeecCCCCcEEEEEEecCCCCcc
Confidence 5999999886 47766621 122 3356779999999876
No 425
>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=22.71 E-value=60 Score=27.04 Aligned_cols=25 Identities=36% Similarity=0.749 Sum_probs=15.7
Q ss_pred CCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
|-+||.++.=.. ...--.||.||..
T Consensus 115 C~~Cg~~~~~~~----------~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 115 CENCGHEVELTH----------PERLPPCPKCGHT 139 (146)
T ss_pred cccCCCEEEecC----------CCcCCCCCCCCCC
Confidence 778887766442 2334568888765
No 426
>PRK10996 thioredoxin 2; Provisional
Probab=22.70 E-value=62 Score=25.57 Aligned_cols=31 Identities=19% Similarity=0.467 Sum_probs=19.7
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
-.||.|..++..= . ...--+++|+-|+..+-
T Consensus 3 ~~~~~~~~~~~~~------~--~~~~~~~~~~~~~~~~~ 33 (139)
T PRK10996 3 TVCTSCQAINRLP------D--ERIEDAAKCGRCGHDLF 33 (139)
T ss_pred EECCCCCCcCCCC------C--ccccCCCcCCCCCCccC
Confidence 4688888877632 1 12345678888877653
No 427
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=22.67 E-value=30 Score=26.29 Aligned_cols=13 Identities=38% Similarity=0.846 Sum_probs=7.9
Q ss_pred cCCCCCcccceee
Q 028248 157 GPCPNCGTENVSF 169 (211)
Q Consensus 157 G~CPnCg~Ev~aF 169 (211)
-.||+||++..-|
T Consensus 66 ~~Cp~Cg~~~~iF 78 (81)
T PF10609_consen 66 FVCPHCGERIYIF 78 (81)
T ss_dssp EE-TTT--EEETT
T ss_pred cCCCCCCCeecCC
Confidence 4799999988766
No 428
>PRK14292 chaperone protein DnaJ; Provisional
Probab=22.66 E-value=93 Score=28.91 Aligned_cols=28 Identities=25% Similarity=0.440 Sum_probs=19.2
Q ss_pred CceeCCCCC-ceeEEecCceeEeCCCCCC
Q 028248 183 NTINCSNCG-TTMVYDSNTRLITLPEGSE 210 (211)
Q Consensus 183 ~~~kC~~C~-~~L~f~~~~r~i~~peg~~ 210 (211)
.+-.|+.|. ...+-+.++..+.+|.|..
T Consensus 196 ~~~~C~~C~G~g~v~~~~~~~V~Ip~G~~ 224 (371)
T PRK14292 196 ITDPCTVCRGRGRTLKAETVKVKLPRGID 224 (371)
T ss_pred cCCCCCCCCCceEEeecceEEEEECCCCC
Confidence 345688885 4555566778888888863
No 429
>PRK08402 replication factor A; Reviewed
Probab=22.64 E-value=86 Score=29.61 Aligned_cols=28 Identities=25% Similarity=0.474 Sum_probs=18.8
Q ss_pred eecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248 155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 192 (211)
Q Consensus 155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~ 192 (211)
+.-.||+|..-+..= .....-.|++|+.
T Consensus 211 ~y~aCp~CnKkv~~~----------~~~~~~~Ce~~~~ 238 (355)
T PRK08402 211 VYDACPECRRKVDYD----------PATDTWICPEHGE 238 (355)
T ss_pred eEecCCCCCeEEEEe----------cCCCCEeCCCCCC
Confidence 456899998765411 1245678999985
No 430
>PLN02419 methylmalonate-semialdehyde dehydrogenase [acylating]
Probab=22.62 E-value=2.3e+02 Score=28.62 Aligned_cols=66 Identities=17% Similarity=0.406 Sum_probs=41.3
Q ss_pred ChHHHHhHHhhhcc-----cCCeeE------EeCh---hhHHHHHHHHhhhcCC---------CccChHHHHHHHHHHhh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVV------MLSS---AEQKFLEASMAYVAGK---------PIMSDEEYDKLKQKLKM 58 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~------~l~~---~Eq~fLeA~~aY~~G~---------Pi~sD~efD~Lk~~Lk~ 58 (211)
+|.+.|.--+.+.| .|-.|+ +... -.+++++++..+.-|. |+++.+.+|+++.-++.
T Consensus 368 ~DADld~Aa~~iv~g~f~naGQ~C~A~~Rv~V~~~~d~f~e~l~~~~~~l~vG~p~d~~t~~GPlis~~~~~~v~~~i~~ 447 (604)
T PLN02419 368 PDANIDATLNALLAAGFGAAGQRCMALSTVVFVGDAKSWEDKLVERAKALKVTCGSEPDADLGPVISKQAKERICRLIQS 447 (604)
T ss_pred CCCCHHHHHHHHHHHHHhhCCCCcCCCCEEEEeCcHHHHHHHHHHHHHHhccCCCCCCCCCccCCCCHHHHHHHHHHHHH
Confidence 45555665566666 454443 3222 1244555555566665 68999999999987755
Q ss_pred ---hCCeeeeec
Q 028248 59 ---EGSEIVVEG 67 (211)
Q Consensus 59 ---~GS~vv~~~ 67 (211)
+|.+++.-|
T Consensus 448 A~~~GAkvl~GG 459 (604)
T PLN02419 448 GVDDGAKLLLDG 459 (604)
T ss_pred HHhcCCEEEeCC
Confidence 588888755
No 431
>TIGR03216 OH_muco_semi_DH 2-hydroxymuconic semialdehyde dehydrogenase. Members of this protein family are 2-hydroxymuconic semialdehyde dehydrogenase. Many aromatic compounds are catabolized by way of the catechol, via the meta-cleavage pathway, to pyruvate and acetyl-CoA. This enzyme performs the second of seven steps in that pathway for catechol degradation.
Probab=22.60 E-value=2.6e+02 Score=26.66 Aligned_cols=66 Identities=24% Similarity=0.384 Sum_probs=43.1
Q ss_pred ChHHHHhHHhhhcc-----cCCeeEE-----eCh-hhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSVVM-----LSS-AEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv~~-----l~~-~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.++|.--+.+.| .|..|.- +.+ .-.+|++++.+ +.-|. |+++.+.+++++.-++
T Consensus 260 ~dadl~~aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~~~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~v~~~i~ 339 (481)
T TIGR03216 260 ADCDFDAAVAGILRSAFLNTGQVCLGTERVYVERPIFDRFVAALKARAESLKIGVPDDPATNMGPLISAEHRDKVLSYYA 339 (481)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCcCCCCCCHHHHHHHHHHHH
Confidence 45677777777766 4655543 333 23678888654 33354 5788889999986554
Q ss_pred ---hhCCeeeeec
Q 028248 58 ---MEGSEIVVEG 67 (211)
Q Consensus 58 ---~~GS~vv~~~ 67 (211)
.+|.+++.-|
T Consensus 340 ~a~~~Ga~v~~gg 352 (481)
T TIGR03216 340 LAVEEGATVVTGG 352 (481)
T ss_pred HHHHCCCEEEeCC
Confidence 5688887755
No 432
>PRK04860 hypothetical protein; Provisional
Probab=22.48 E-value=51 Score=27.73 Aligned_cols=19 Identities=26% Similarity=0.779 Sum_probs=15.5
Q ss_pred cCceeCCCCCceeEEecCc
Q 028248 182 TNTINCSNCGTTMVYDSNT 200 (211)
Q Consensus 182 ~~~~kC~~C~~~L~f~~~~ 200 (211)
....+|..|+..|.+....
T Consensus 141 ~~~YrC~~C~~~l~~~~~~ 159 (160)
T PRK04860 141 EAVYRCRRCGETLVFKGEQ 159 (160)
T ss_pred CccEECCCCCceeEEeccc
Confidence 4568999999999987654
No 433
>cd07140 ALDH_F1L_FTFDH 10-formyltetrahydrofolate dehydrogenase, ALDH family 1L. 10-formyltetrahydrofolate dehydrogenase (FTHFDH, EC=1.5.1.6), also known as aldehyde dehydrogenase family 1 member L1 (ALDH1L1) in humans, is a multi-domain homotetramer with an N-terminal formyl transferase domain and a C-terminal ALDH domain. FTHFDH catalyzes an NADP+-dependent dehydrogenase reaction resulting in the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. The ALDH domain is also capable of the oxidation of short chain aldehydes to their corresponding acids.
Probab=22.45 E-value=2.7e+02 Score=26.78 Aligned_cols=68 Identities=21% Similarity=0.307 Sum_probs=43.9
Q ss_pred ChHHHHhHHhhhcc-----cCCee------EEeChhhHHHHHHHH----hhhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV------VMLSSAEQKFLEASM----AYVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv------~~l~~~Eq~fLeA~~----aY~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|..| ++-+..-.+|+|++. ++.-|. |+++.+.||+++..++
T Consensus 268 ~dadl~~a~~~i~~~~~~~~GQ~C~a~~rl~V~~~i~~~f~~~l~~~~~~l~~g~p~~~~~~~Gpli~~~~~~~v~~~i~ 347 (486)
T cd07140 268 ADCDMDKAVRMGMSSVFFNKGENCIAAGRLFVEESIHDEFVRRVVEEVKKMKIGDPLDRSTDHGPQNHKAHLDKLVEYCE 347 (486)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCCCcEEEEcHHHHHHHHHHHHHHHHhCCccCCCCCCCcCCCCcCHHHHHHHHHHHH
Confidence 45566666666665 45433 333334467888753 354454 6788899999998886
Q ss_pred h---hCCeeeeeccc
Q 028248 58 M---EGSEIVVEGPR 69 (211)
Q Consensus 58 ~---~GS~vv~~~pr 69 (211)
+ +|.+++..|.+
T Consensus 348 ~a~~~Ga~vl~gg~~ 362 (486)
T cd07140 348 RGVKEGATLVYGGKQ 362 (486)
T ss_pred HHHHCCCEEEeCCCC
Confidence 4 58888876643
No 434
>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=22.39 E-value=86 Score=23.44 Aligned_cols=39 Identities=21% Similarity=0.399 Sum_probs=13.7
Q ss_pred CCCCCcccceeecccccccc-CCCCcCceeCCCCCceeEE
Q 028248 158 PCPNCGTENVSFFGTILSIS-SGGTTNTINCSNCGTTMVY 196 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~-s~~~~~~~kC~~C~~~L~f 196 (211)
.||.|+.|..-=-|...=.. ...-+-.+-||.|+.+|+.
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHH
Confidence 48888888442200000000 0001334567777766654
No 435
>PRK14287 chaperone protein DnaJ; Provisional
Probab=22.37 E-value=1e+02 Score=28.89 Aligned_cols=28 Identities=18% Similarity=0.424 Sum_probs=19.6
Q ss_pred CceeCCCCCceeEEec-CceeEeCCCCCC
Q 028248 183 NTINCSNCGTTMVYDS-NTRLITLPEGSE 210 (211)
Q Consensus 183 ~~~kC~~C~~~L~f~~-~~r~i~~peg~~ 210 (211)
.+-.|+.|+-.-.... ++-.+.+|+|.+
T Consensus 194 ~~~~C~~C~G~g~v~~~~~l~V~Ip~G~~ 222 (371)
T PRK14287 194 IKQKCATCGGKGKVRKRKKINVKVPAGID 222 (371)
T ss_pred ccccCCCCCCeeEEeeeEEEEEEECCcCC
Confidence 3456888887766654 467778888763
No 436
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=22.34 E-value=66 Score=27.07 Aligned_cols=18 Identities=44% Similarity=0.421 Sum_probs=15.6
Q ss_pred CccChHHHHHHHHHHhhh
Q 028248 42 PIMSDEEYDKLKQKLKME 59 (211)
Q Consensus 42 Pi~sD~efD~Lk~~Lk~~ 59 (211)
-=||++||=+||.+|..+
T Consensus 89 i~mS~~EYM~lKkqLae~ 106 (153)
T COG4008 89 INMSPEEYMELKKQLAEY 106 (153)
T ss_pred cCCCHHHHHHHHHHHHHH
Confidence 359999999999999765
No 437
>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=22.33 E-value=59 Score=20.34 Aligned_cols=28 Identities=29% Similarity=0.772 Sum_probs=14.7
Q ss_pred ceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248 152 SLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 193 (211)
Q Consensus 152 ~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~ 193 (211)
--++-.-|++||.= .| +-+.-|++|+..
T Consensus 7 ~~l~~~rC~~Cg~~--~~------------pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 7 GRLLGQRCRDCGRV--QF------------PPRPVCPHCGSD 34 (37)
T ss_dssp T-EEEEE-TTT--E--EE------------S--SEETTTT--
T ss_pred CEEEEEEcCCCCCE--ec------------CCCcCCCCcCcc
Confidence 33467789999974 33 456889999853
No 438
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=22.27 E-value=47 Score=33.34 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=12.8
Q ss_pred CChHHHHhHHhhhc
Q 028248 1 MSNEEFDNLKEELM 14 (211)
Q Consensus 1 ~s~eefd~lkeel~ 14 (211)
+||+|||.|.+||.
T Consensus 56 IsD~eYD~L~~eL~ 69 (562)
T PRK08097 56 VDDEVYDQLRARLT 69 (562)
T ss_pred CChHHHHHHHHHHH
Confidence 69999999999985
No 439
>KOG2589 consensus Histone tail methylase [Chromatin structure and dynamics]
Probab=22.24 E-value=43 Score=32.66 Aligned_cols=30 Identities=20% Similarity=0.406 Sum_probs=23.5
Q ss_pred cccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248 163 GTENVSFFGTILSISSGGTTNTINCSNCGTTMV 195 (211)
Q Consensus 163 g~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~ 195 (211)
|+|++.|+|...=. .++-.++|+-|++..+
T Consensus 229 GeEITcFYgs~fFG---~~N~~CeC~TCER~g~ 258 (453)
T KOG2589|consen 229 GEEITCFYGSGFFG---ENNEECECVTCERRGT 258 (453)
T ss_pred CceeEEeecccccC---CCCceeEEeecccccc
Confidence 79999999885533 3567899999998765
No 440
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=22.22 E-value=41 Score=29.27 Aligned_cols=10 Identities=50% Similarity=1.222 Sum_probs=8.6
Q ss_pred cCCCCCcccc
Q 028248 157 GPCPNCGTEN 166 (211)
Q Consensus 157 G~CPnCg~Ev 166 (211)
-+||.||+++
T Consensus 157 P~CPlCg~Pl 166 (177)
T TIGR03847 157 PPCPLCGRPI 166 (177)
T ss_pred CCCCCCCCCC
Confidence 4899999986
No 441
>KOG0393 consensus Ras-related small GTPase, Rho type [General function prediction only]
Probab=22.21 E-value=1.3e+02 Score=26.34 Aligned_cols=44 Identities=18% Similarity=0.077 Sum_probs=27.0
Q ss_pred CCCccChHHHHHHHHHHhhhCCeeeeeccceeecCcceeeccchhHHHHHh
Q 028248 40 GKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLL 90 (211)
Q Consensus 40 G~Pi~sD~efD~Lk~~Lk~~GS~vv~~~prCslr~~~~ysD~e~D~~km~l 90 (211)
|+-.++-++...|..++.. ++|-.||...+.- ....+|.--..+
T Consensus 135 ~~~~Vt~~~g~~lA~~iga------~~y~EcSa~tq~~-v~~vF~~a~~~~ 178 (198)
T KOG0393|consen 135 GLEPVTYEQGLELAKEIGA------VKYLECSALTQKG-VKEVFDEAIRAA 178 (198)
T ss_pred cCCcccHHHHHHHHHHhCc------ceeeeehhhhhCC-cHHHHHHHHHHH
Confidence 5556666677777776643 6777788887766 444444433333
No 442
>TIGR03374 ABALDH 1-pyrroline dehydrogenase. Members of this protein family are 1-pyrroline dehydrogenase (1.5.1.35), also called gamma-aminobutyraldehyde dehydrogenase. This enzyme can follow putrescine transaminase (EC 2.6.1.82) for a two-step conversion of putrescine to gamma-aminobutyric acid (GABA). The member from Escherichia coli is characterized as a homotetramer that binds one NADH per momomer. This enzyme belongs to the medium-chain aldehyde dehydrogenases, and is quite similar in sequence to the betaine aldehyde dehydrogenase (EC 1.2.1.8) family.
Probab=22.21 E-value=2.7e+02 Score=26.64 Aligned_cols=67 Identities=15% Similarity=0.264 Sum_probs=41.4
Q ss_pred ChHHHHhHHhhhcc-----cCCee------EEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV------VMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv------~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
+|.+.|.--+.+.| .|-+| ++-...-.+|+|++.+ +.-|. |+++...+|+++..++
T Consensus 256 ~dadl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~~~f~~~l~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~v~~~i~ 335 (472)
T TIGR03374 256 DDADIDAVVEGVRTFGFYNAGQDCTAACRIYAQRGIYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVMKAVE 335 (472)
T ss_pred CCCCHHHHHHHHHHHHHhhcCCccccCCEEEEcHHHHHHHHHHHHHHHhcCCCCCCCCCCCcCCCCCCHHHHHHHHHHHH
Confidence 45667777777776 24333 3333334678888643 33344 6788999999996554
Q ss_pred ---hhC-Ceeeeecc
Q 028248 58 ---MEG-SEIVVEGP 68 (211)
Q Consensus 58 ---~~G-S~vv~~~p 68 (211)
.+| .+++.-+.
T Consensus 336 ~a~~~G~a~v~~gg~ 350 (472)
T TIGR03374 336 EAKALGHIKVITGGE 350 (472)
T ss_pred HHHHcCCeEEEeCCc
Confidence 445 56665553
No 443
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=22.18 E-value=68 Score=24.27 Aligned_cols=22 Identities=18% Similarity=0.496 Sum_probs=17.2
Q ss_pred eChhhHHHHHHHHhhhcCCCcc
Q 028248 23 LSSAEQKFLEASMAYVAGKPIM 44 (211)
Q Consensus 23 l~~~Eq~fLeA~~aY~~G~Pi~ 44 (211)
|.+.++++|+++.--|+|.|+=
T Consensus 6 Ld~~D~~yL~~l~~~f~ggPvG 27 (76)
T PF05491_consen 6 LDELDRRYLKTLIENFKGGPVG 27 (76)
T ss_dssp -BHHHHHHHHHHHHCSTTS-B-
T ss_pred CCHHHHHHHHHHHHHcCCCCee
Confidence 5677899999999999999974
No 444
>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=22.08 E-value=59 Score=30.21 Aligned_cols=37 Identities=14% Similarity=0.468 Sum_probs=22.0
Q ss_pred ecCCCCCcccce-eeccccccccCC--CCcCce-eCCCCCceeEE
Q 028248 156 KGPCPNCGTENV-SFFGTILSISSG--GTTNTI-NCSNCGTTMVY 196 (211)
Q Consensus 156 kG~CPnCg~Ev~-aFfg~i~~v~s~--~~~~~~-kC~~C~~~L~f 196 (211)
-..||+||++-. .|| ++.+. ....++ -|..|++=++.
T Consensus 224 R~~C~~Cg~~~~l~y~----~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 224 RVKCSHCEESKHLAYL----SLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred CccCCCCCCCCceeeE----eecCCCCCcceEEeeccccccchhh
Confidence 456999998753 233 44441 223333 58999986653
No 445
>KOG1296 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.99 E-value=67 Score=27.52 Aligned_cols=45 Identities=20% Similarity=0.432 Sum_probs=28.0
Q ss_pred eeeecCCCCCcccce--eecccccccc----CCCCcCceeCCCCCceeEEe
Q 028248 153 LILKGPCPNCGTENV--SFFGTILSIS----SGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 153 liLkG~CPnCg~Ev~--aFfg~i~~v~----s~~~~~~~kC~~C~~~L~f~ 197 (211)
..+|-.|-||||--- ++....-.++ .+....--||--|++...++
T Consensus 27 f~~kLkCtnCgE~~dkw~~I~l~E~~~~pg~Rgta~~v~KCK~C~Rensv~ 77 (161)
T KOG1296|consen 27 FYLKLKCTNCGELSDKWQYITLNEEVAMPGSRGTASFVMKCKFCSRENSVT 77 (161)
T ss_pred eEEEeccccccccCCceEEEEeeeeecCCCCcchhhHhhhhhhhcccCcEE
Confidence 568999999998543 3332222222 23334445899999987654
No 446
>COG1773 Rubredoxin [Energy production and conversion]
Probab=21.84 E-value=72 Score=22.82 Aligned_cols=36 Identities=25% Similarity=0.385 Sum_probs=20.0
Q ss_pred cCCCCCcccceeeccccccccCCCC-----cCceeCCCCCc
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGT-----TNTINCSNCGT 192 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~-----~~~~kC~~C~~ 192 (211)
=.|.+||..--.=-|+-...-.++. +..-.||.||.
T Consensus 4 ~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 4 WRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred eEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCCC
Confidence 3588888765544444222222222 34567999995
No 447
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=21.79 E-value=66 Score=23.03 Aligned_cols=29 Identities=21% Similarity=0.361 Sum_probs=12.6
Q ss_pred cccccccCCCCcCceeCCCCCceeEEecC
Q 028248 171 GTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 171 g~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
++...-+-..+.+-+.||.|+..+.-.++
T Consensus 11 ~~~~~k~~~~S~~PatCP~C~a~~~~srn 39 (54)
T PF09237_consen 11 STKKPKSKSQSEQPATCPICGAVIRQSRN 39 (54)
T ss_dssp -----CCCCTTS--EE-TTT--EESSHHH
T ss_pred hhhHHHHhhccCCCCCCCcchhhccchhh
Confidence 33333344556778899999988765444
No 448
>PF05209 MinC_N: Septum formation inhibitor MinC, N-terminal domain; InterPro: IPR007874 In Escherichia coli FtsZ (P0A9A6 from SWISSPROT) assembles into a Z ring at midcell. Its assembly at polar sites is prevented by the min system. MinC P18196 from SWISSPROT, a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with the MinDE proteins. MinC is an oligomer, probably a dimer []. The C-terminal half of MinC is the most conserved and interacts with MinD. The N-terminal half is thought to interact with FtsZ. MinC rapidly oscillates between the poles of the cell to destabilise FtsZ filaments that have formed before they mature into polar Z rings; GO: 0051302 regulation of cell division; PDB: 3GHF_A 1HF2_C.
Probab=21.72 E-value=88 Score=23.57 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=23.3
Q ss_pred hhcCCCccCh-------HHHHHHHHHHhhhCC-eeee
Q 028248 37 YVAGKPIMSD-------EEYDKLKQKLKMEGS-EIVV 65 (211)
Q Consensus 37 Y~~G~Pi~sD-------~efD~Lk~~Lk~~GS-~vv~ 65 (211)
+|+|.|++-| .+|..|+.-+|..|= .|.+
T Consensus 42 FF~~~pvvldl~~l~~~~dl~~L~~~l~~~gl~~vgv 78 (99)
T PF05209_consen 42 FFKNAPVVLDLSNLPDELDLAALVELLRRHGLRPVGV 78 (99)
T ss_dssp HCTTTEEEEEEEEEETTHHHHHHHHHHHCCCHCCCCE
T ss_pred hHcCCCeEEehhhcCChhhHHHHHHHHHHcCCEEEEe
Confidence 8999998766 789999999988883 4444
No 449
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=21.69 E-value=2.2e+02 Score=20.41 Aligned_cols=30 Identities=17% Similarity=0.395 Sum_probs=24.2
Q ss_pred hcCCCccChHHHHHHHHHHhh---hCCeeeeec
Q 028248 38 VAGKPIMSDEEYDKLKQKLKM---EGSEIVVEG 67 (211)
Q Consensus 38 ~~G~Pi~sD~efD~Lk~~Lk~---~GS~vv~~~ 67 (211)
.--+|.+|+++.+.+-.+|.. .+..|.+.|
T Consensus 17 k~~kp~Lde~~leei~~~l~~a~~~~~~v~ity 49 (92)
T PF08863_consen 17 KVEKPELDEQQLEEINEKLSEAYQENQPVTITY 49 (92)
T ss_pred ccCCCCCcHHHHHHHHHHHHHHhcCCCEEEEEE
Confidence 334999999999999999964 577887754
No 450
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=21.62 E-value=62 Score=25.98 Aligned_cols=40 Identities=23% Similarity=0.316 Sum_probs=25.7
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 199 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~ 199 (211)
-|++|.+...--. ...|..-.+.-.+-|+.||...-|.-.
T Consensus 58 ~CkkC~t~Lvpg~--n~rvR~~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 58 ICKKCYTPLVPGK--NARVRLRKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred hccccCcccccCc--ceEEEEcCCeEEEEecCCCcEEEeccc
Confidence 4999998643221 222333334477899999999888643
No 451
>COG1341 Predicted GTPase or GTP-binding protein [General function prediction only]
Probab=21.48 E-value=62 Score=31.35 Aligned_cols=108 Identities=31% Similarity=0.378 Sum_probs=62.4
Q ss_pred ChHHHHhHHhhhcc---cCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCCeeeeeccceeecCccee
Q 028248 2 SNEEFDNLKEELMW---EGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVY 78 (211)
Q Consensus 2 s~eefd~lkeel~w---eGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~GS~vv~~~prCslr~~~~y 78 (211)
|-+|.-.+|+|.-| +||....++.++..-.-|. ++.|+|+=..++ .+..++-..| ....-.|-.+-..+-
T Consensus 236 sR~ER~~~R~e~~~ryf~~~~~~~v~~~~~~i~g~~--if~~~~i~~~~~--~~l~~~i~~~---~l~~~~~~~~~~~V~ 308 (398)
T COG1341 236 SREERKELREEKYRRYFEGSKIRTVDLDDVRIQGTP--IFQGEPIDDEEE--KLLEKLIKKG---ILHAEKCGGRPYVVK 308 (398)
T ss_pred ChhHHHHHHHHHHHHhccCCceEEecchhceeeccc--ccCCCccchhHH--Hhhhhhhhhc---cccceecCCceEEEe
Confidence 55788899999888 8999999988875544443 788888744433 3334433333 444455555555555
Q ss_pred eccchhHH----HHHhhhhhhHHHHhhhhhhccccccceeeeec
Q 028248 79 SDLSVDYL----KMLLLNVPATVVALGLFFFLDDITGFEITYLL 118 (211)
Q Consensus 79 sD~e~D~~----km~ll~~~~~~~~lGl~~~~~d~~gf~i~~~~ 118 (211)
+|.+ +-- +-..+.++..- .-|+..++.|-.|+-|..++
T Consensus 309 ~d~~-~~~r~~~~~~~~~v~~~~-l~gll~gl~d~~~~~iGlGv 350 (398)
T COG1341 309 SDLE-EGPRLVSGNDVRVVPSEE-LKGLLVGLIDNDGFCIGLGV 350 (398)
T ss_pred eccc-ccceeecCCcEEEEChhH-hccceEEEecCCCcEEEEEE
Confidence 6665 111 11111122211 56777777776666665544
No 452
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=21.47 E-value=56 Score=27.38 Aligned_cols=37 Identities=30% Similarity=0.617 Sum_probs=24.5
Q ss_pred CCCCCcccce-------------eecccccc--ccC------CCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENV-------------SFFGTILS--ISS------GGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~-------------aFfg~i~~--v~s------~~~~~~~kC~~C~~~L 194 (211)
-|-+||++.| +|+..|.+ |.- +..+.++.|.+|+.-|
T Consensus 45 ~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~V~~~~D~s~gm~RtEv~C~~Cg~HL 102 (142)
T PRK00222 45 VCIVCGEPLFSSDTKFDSGCGWPSFTKPIDEEAIRELRDTSHGMVRTEVRCANCDSHL 102 (142)
T ss_pred EecCCCchhcCCcccccCCCCCcCcCcccCCCceEEeeccCCCceEEEEEeCCCCCcc
Confidence 4888888876 47766631 211 2235679999999876
No 453
>PRK07219 DNA topoisomerase I; Validated
Probab=21.37 E-value=95 Score=32.23 Aligned_cols=15 Identities=20% Similarity=0.589 Sum_probs=11.3
Q ss_pred ceeCCCCCceeEEec
Q 028248 184 TINCSNCGTTMVYDS 198 (211)
Q Consensus 184 ~~kC~~C~~~L~f~~ 198 (211)
...||.|+..|..+.
T Consensus 688 ~~~CP~Cg~~l~~k~ 702 (822)
T PRK07219 688 IGPCPKCGGELAIKQ 702 (822)
T ss_pred cccCCCCCCeeEEEc
Confidence 467999988777654
No 454
>COG3502 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.33 E-value=80 Score=25.74 Aligned_cols=61 Identities=23% Similarity=0.193 Sum_probs=45.7
Q ss_pred ChHHHHhHHhhhcccCCee------EEeChhhHHHHHHHHhhhcCCCc----cChHHHHHHHHHHhhhCCeeee
Q 028248 2 SNEEFDNLKEELMWEGSSV------VMLSSAEQKFLEASMAYVAGKPI----MSDEEYDKLKQKLKMEGSEIVV 65 (211)
Q Consensus 2 s~eefd~lkeel~weGssv------~~l~~~Eq~fLeA~~aY~~G~Pi----~sD~efD~Lk~~Lk~~GS~vv~ 65 (211)
+-.+|+.=|+..+.+|+|| |-+|..+|.-.- ..-.|+||-= ..|. +.|+.+||||-|.=..
T Consensus 11 ~~~~W~~A~~~G~f~~~svd~~dGfIH~St~~Qv~~t-Aar~f~GQ~dLlLl~iD~--aaLg~~lryE~srgg~ 81 (115)
T COG3502 11 PRALWAAARAAGSFEGASVDDADGFIHLSTAAQVRET-AARHFRGQADLLLLAIDP--AALGDELRYEPSRGGA 81 (115)
T ss_pred CHHHHHHHHHcCCcCCCCcccccceEEechHHHHHHH-HHHHhcCCcceEEEEecH--HHcCCcceeecCCCCc
Confidence 3578999999999999996 889999886443 3448888862 2233 5899999999886443
No 455
>TIGR01351 adk adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
Probab=21.31 E-value=62 Score=26.97 Aligned_cols=34 Identities=18% Similarity=0.268 Sum_probs=23.2
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
.-||.||.....-|.. .....+|.+|+..|+-+.
T Consensus 125 ~~~~~~g~~y~~~~~~--------p~~~~~~~~~~~~l~~R~ 158 (210)
T TIGR01351 125 RICPSCGRVYHLKFNP--------PKVPGCDDCTGELLIQRE 158 (210)
T ss_pred CccCCcCCccccccCC--------CccCCcCcccCCccccCC
Confidence 5699999986655422 223457888988887655
No 456
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=21.26 E-value=71 Score=20.47 Aligned_cols=10 Identities=40% Similarity=1.169 Sum_probs=5.2
Q ss_pred eCCCCCceeE
Q 028248 186 NCSNCGTTMV 195 (211)
Q Consensus 186 kC~~C~~~L~ 195 (211)
.||.||....
T Consensus 4 ~Cp~Cg~~~~ 13 (47)
T PF14690_consen 4 RCPHCGSPSV 13 (47)
T ss_pred cCCCcCCCce
Confidence 3555555543
No 457
>PLN03086 PRLI-interacting factor K; Provisional
Probab=21.24 E-value=51 Score=33.28 Aligned_cols=10 Identities=30% Similarity=0.557 Sum_probs=6.6
Q ss_pred CCCCCcccce
Q 028248 158 PCPNCGTENV 167 (211)
Q Consensus 158 ~CPnCg~Ev~ 167 (211)
.||||...+.
T Consensus 409 ~C~NC~~~i~ 418 (567)
T PLN03086 409 ECRNCKHYIP 418 (567)
T ss_pred ECCCCCCccc
Confidence 4777776654
No 458
>PLN02569 threonine synthase
Probab=21.19 E-value=67 Score=31.37 Aligned_cols=29 Identities=17% Similarity=0.255 Sum_probs=20.4
Q ss_pred cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
=.|+.||++. .- +.....| .||..|.+.-
T Consensus 50 l~C~~Cg~~y-~~-----------~~~~~~C-~cgg~l~~~~ 78 (484)
T PLN02569 50 LECPLTGEKY-SL-----------DEVVYRS-KSGGLLDVRH 78 (484)
T ss_pred cEeCCCCCcC-CC-----------ccccccC-CCCCeEEEec
Confidence 3799999873 11 3445689 6999997764
No 459
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=21.15 E-value=65 Score=22.45 Aligned_cols=20 Identities=35% Similarity=0.665 Sum_probs=12.1
Q ss_pred HHHhhhcCCCc---------cChHHHHHH
Q 028248 33 ASMAYVAGKPI---------MSDEEYDKL 52 (211)
Q Consensus 33 A~~aY~~G~Pi---------~sD~efD~L 52 (211)
|..|+..|+++ |+++++|++
T Consensus 18 Ak~A~~~g~svre~v~~~g~lt~ee~d~l 46 (55)
T PF10415_consen 18 AKEALAEGRSVREVVLEEGLLTEEELDEL 46 (55)
T ss_dssp HHHHHHHT--HHHHHHHTTSS-HHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHcCCCCHHHHHHH
Confidence 34567777664 888888875
No 460
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=21.08 E-value=85 Score=30.77 Aligned_cols=46 Identities=22% Similarity=0.348 Sum_probs=26.3
Q ss_pred hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248 149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 198 (211)
Q Consensus 149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~ 198 (211)
..+-.-..--||+||.-.++-. .++.....+-+.+|. ||..-+.+-
T Consensus 168 ~~~~~P~~pic~~cg~~~~~~~---~~~d~~~~~v~y~~~-cG~~~~~~~ 213 (510)
T PRK00750 168 QATYSPFLPICPKCGKVLTTPV---ISYDAEAGTVTYDCE-CGHEGEVPV 213 (510)
T ss_pred CCCeeeeeeeCCCCCccceEEE---EEEeCCCCEEEEEcC-CCCEEEEec
Confidence 3444556777999998877553 122222224455664 777665543
No 461
>PRK11241 gabD succinate-semialdehyde dehydrogenase I; Provisional
Probab=21.02 E-value=3.1e+02 Score=26.42 Aligned_cols=67 Identities=16% Similarity=0.372 Sum_probs=42.1
Q ss_pred ChHHHHhHHhhhcc-----cCCee------EEeChhhHHHHHHHH----hhhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSSV------VMLSSAEQKFLEASM----AYVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv------~~l~~~Eq~fLeA~~----aY~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.--+.+.| .|-.| ++-.+.-.+|++++. ++.-|. |+++.+.+++++..+.
T Consensus 266 ~dADld~aa~~i~~~~f~~aGQ~C~a~~ri~V~~~i~d~f~~~l~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~v~~~i~ 345 (482)
T PRK11241 266 DDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAEKLQQAVSKLHIGDGLEKGVTIGPLIDEKAVAKVEEHIA 345 (482)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCccCeEEEEeHHHHHHHHHHHHHHHhhCCCCCCCCCCCCcCCCCCHHHHHHHHHHHH
Confidence 34556666666666 34333 333333467777753 344454 6788899999998776
Q ss_pred h---hCCeeeeecc
Q 028248 58 M---EGSEIVVEGP 68 (211)
Q Consensus 58 ~---~GS~vv~~~p 68 (211)
. +|.+++.-|.
T Consensus 346 ~a~~~Ga~vl~GG~ 359 (482)
T PRK11241 346 DALEKGARVVCGGK 359 (482)
T ss_pred HHHhCCCEEEecCC
Confidence 5 5888877653
No 462
>cd00739 DHPS DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS.
Probab=20.99 E-value=4e+02 Score=23.68 Aligned_cols=62 Identities=18% Similarity=0.232 Sum_probs=39.7
Q ss_pred hHHHHhHH---hhhcccCCeeEEeChhhHHHHHHHHhhhcCCCccChH---HH-HHHHHHHhhhCCeeeee
Q 028248 3 NEEFDNLK---EELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDE---EY-DKLKQKLKMEGSEIVVE 66 (211)
Q Consensus 3 ~eefd~lk---eel~weGssv~~l~~~Eq~fLeA~~aY~~G~Pi~sD~---ef-D~Lk~~Lk~~GS~vv~~ 66 (211)
.||+++|+ +.+..+-.-.+.+.+...+-+|+...+ |.+++.|= .. +++-.-++.+|-.+++.
T Consensus 58 ~~E~~rl~~~v~~i~~~~~~plSIDT~~~~v~e~al~~--G~~iINdisg~~~~~~~~~l~~~~~~~vV~m 126 (257)
T cd00739 58 EEELERVIPVLEALRGELDVLISVDTFRAEVARAALEA--GADIINDVSGGSDDPAMLEVAAEYGAPLVLM 126 (257)
T ss_pred HHHHHHHHHHHHHHHhcCCCcEEEeCCCHHHHHHHHHh--CCCEEEeCCCCCCChHHHHHHHHcCCCEEEE
Confidence 47788876 445555344577777777777766554 78888752 22 44444466788888873
No 463
>COG4827 Predicted transporter [General function prediction only]
Probab=20.96 E-value=1.2e+02 Score=27.47 Aligned_cols=14 Identities=36% Similarity=0.721 Sum_probs=11.4
Q ss_pred ceeeecCCCCCccc
Q 028248 152 SLILKGPCPNCGTE 165 (211)
Q Consensus 152 ~liLkG~CPnCg~E 165 (211)
.+++.-|||+|=.-
T Consensus 107 ~~ais~PCPvCl~a 120 (239)
T COG4827 107 FLAISMPCPVCLGA 120 (239)
T ss_pred eEEEecCCcHHHHH
Confidence 58899999999543
No 464
>PF12653 DUF3785: Protein of unknown function (DUF3785); InterPro: IPR024210 This family of proteins is functionally uncharacterised. Proteins in this family are approximately 140 amino acids in length and share two CXXC motifs suggesting these are zinc binding proteins. In clostridia proteins are found in an operon with three signalling proteins, suggesting that they are involved in DNA-binding transcription regulator downstream of an as yet unknown signalling pathway.
Probab=20.92 E-value=41 Score=28.13 Aligned_cols=9 Identities=56% Similarity=1.202 Sum_probs=6.9
Q ss_pred cCCCCCccc
Q 028248 157 GPCPNCGTE 165 (211)
Q Consensus 157 G~CPnCg~E 165 (211)
--|||||+=
T Consensus 121 ~VC~nCG~y 129 (138)
T PF12653_consen 121 IVCPNCGNY 129 (138)
T ss_pred EECCCCCce
Confidence 459999973
No 465
>PRK09406 gabD1 succinic semialdehyde dehydrogenase; Reviewed
Probab=20.85 E-value=3.1e+02 Score=26.11 Aligned_cols=68 Identities=21% Similarity=0.408 Sum_probs=42.3
Q ss_pred ChHHHHhHHhhhcc-----cCCee-----EE-eChhhHHHHHHHH----hhhcCC---------CccChHHHHHHHHHH-
Q 028248 2 SNEEFDNLKEELMW-----EGSSV-----VM-LSSAEQKFLEASM----AYVAGK---------PIMSDEEYDKLKQKL- 56 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGssv-----~~-l~~~Eq~fLeA~~----aY~~G~---------Pi~sD~efD~Lk~~L- 56 (211)
.|.+.|.--+...| .|-.| +. -+..-.+|++++. ++.-|. |+++...+|+++.-+
T Consensus 242 ~dadl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~l~~g~p~~~~~~~Gpli~~~~~~~~~~~i~ 321 (457)
T PRK09406 242 PSADLDRAAETAVTARVQNNGQSCIAAKRFIVHADVYDAFAEKFVARMAALRVGDPTDPDTDVGPLATEQGRDEVEKQVD 321 (457)
T ss_pred CCCCHHHHHHHHHHHHhhCCCCcccCCeEEEEcHHHHHHHHHHHHHHHhhCCCCCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 45666666666666 34333 33 3333466777753 354454 678888999888765
Q ss_pred --hhhCCeeeeeccc
Q 028248 57 --KMEGSEIVVEGPR 69 (211)
Q Consensus 57 --k~~GS~vv~~~pr 69 (211)
+.+|.+++.-|.+
T Consensus 322 ~a~~~Ga~~l~gg~~ 336 (457)
T PRK09406 322 DAVAAGATILCGGKR 336 (457)
T ss_pred HHHHCCCEEEeCCCc
Confidence 4578888775543
No 466
>PRK11827 hypothetical protein; Provisional
Probab=20.80 E-value=82 Score=22.76 Aligned_cols=30 Identities=13% Similarity=0.332 Sum_probs=20.2
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 197 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~ 197 (211)
.||.|..+.. +. ...++.-|..|+-.--.+
T Consensus 10 aCP~ckg~L~-~~---------~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 10 ACPVCNGKLW-YN---------QEKQELICKLDNLAFPLR 39 (60)
T ss_pred ECCCCCCcCe-Ec---------CCCCeEECCccCeecccc
Confidence 5999988875 31 135678899987554443
No 467
>cd07117 ALDH_StaphAldA1 Uncharacterized Staphylococcus aureus AldA1 (SACOL0154) aldehyde dehydrogenase-like. Uncharacterized aldehyde dehydrogenase from Staphylococcus aureus (AldA1, locus SACOL0154) and other similar sequences are present in this CD.
Probab=20.79 E-value=2.9e+02 Score=26.39 Aligned_cols=66 Identities=17% Similarity=0.333 Sum_probs=42.6
Q ss_pred ChHHHHhHHhhhcc-----cCCe------eEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHHh
Q 028248 2 SNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKLK 57 (211)
Q Consensus 2 s~eefd~lkeel~w-----eGss------v~~l~~~Eq~fLeA~~a----Y~~G~---------Pi~sD~efD~Lk~~Lk 57 (211)
.|.+.|.-.+.+.| .|-. +++-.+.-.+|+|++.+ +.-|. |+++.+.+++++.-+.
T Consensus 255 ~dADl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~l~~g~p~~~~~~~gpli~~~~~~~v~~~v~ 334 (475)
T cd07117 255 DDANWDKALEGAQLGILFNQGQVCCAGSRIFVQEGIYDEFVAKLKEKFENVKVGNPLDPDTQMGAQVNKDQLDKILSYVD 334 (475)
T ss_pred CCCChHHHHHHHHHHHhhccCCCCCCCeEEEEeHHHHHHHHHHHHHHHHhccCCCCCCCCCcccCcCCHHHHHHHHHHHH
Confidence 46677777777766 3333 33334446778888643 44344 5678889999996554
Q ss_pred ---hhCCeeeeec
Q 028248 58 ---MEGSEIVVEG 67 (211)
Q Consensus 58 ---~~GS~vv~~~ 67 (211)
.+|.+++.-+
T Consensus 335 ~a~~~Ga~v~~gg 347 (475)
T cd07117 335 IAKEEGAKILTGG 347 (475)
T ss_pred HHHHCCCEEEeCC
Confidence 4688887655
No 468
>cd00740 MeTr MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH.
Probab=20.78 E-value=1.9e+02 Score=25.76 Aligned_cols=49 Identities=27% Similarity=0.400 Sum_probs=34.9
Q ss_pred eeEEeChhhHHHHHHHHhhhcCCCccCh-------HHHHHHHHHHhhhCCeeeeec
Q 028248 19 SVVMLSSAEQKFLEASMAYVAGKPIMSD-------EEYDKLKQKLKMEGSEIVVEG 67 (211)
Q Consensus 19 sv~~l~~~Eq~fLeA~~aY~~G~Pi~sD-------~efD~Lk~~Lk~~GS~vv~~~ 67 (211)
..+.+.+..-+-+||...+|.|.+++.| ++++++-.-++.+|-.+|+.-
T Consensus 71 ~piSIDT~~~~v~e~aL~~~~G~~iINsIs~~~~~e~~~~~~~~~~~~~~~vV~m~ 126 (252)
T cd00740 71 VPLMLDSTNWEVIEAGLKCCQGKCVVNSINLEDGEERFLKVARLAKEHGAAVVVLA 126 (252)
T ss_pred CcEEeeCCcHHHHHHHHhhCCCCcEEEeCCCCCCccccHHHHHHHHHhCCCEEEec
Confidence 3466777777777877776679999876 235666555788998888853
No 469
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=20.73 E-value=63 Score=30.39 Aligned_cols=15 Identities=33% Similarity=0.713 Sum_probs=9.6
Q ss_pred CCCCCcccceeeccc
Q 028248 158 PCPNCGTENVSFFGT 172 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~ 172 (211)
-||.||++|.-=-|.
T Consensus 32 ~CP~C~~~v~lk~G~ 46 (375)
T PF06054_consen 32 FCPGCGEPVILKKGK 46 (375)
T ss_pred ECCCCCCeeEEEEcC
Confidence 477777777654443
No 470
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=20.66 E-value=46 Score=28.69 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=6.0
Q ss_pred eeCCCCCcee
Q 028248 185 INCSNCGTTM 194 (211)
Q Consensus 185 ~kC~~C~~~L 194 (211)
-+|++||..|
T Consensus 137 p~C~~Cgg~l 146 (222)
T cd01413 137 PRCPKCGGII 146 (222)
T ss_pred CcCCCCCCcc
Confidence 4577776554
No 471
>PF14129 DUF4296: Domain of unknown function (DUF4296)
Probab=20.63 E-value=91 Score=23.10 Aligned_cols=29 Identities=31% Similarity=0.568 Sum_probs=24.7
Q ss_pred HHHHHhhhcCCCccChHHHHHHHHHHhhh
Q 028248 31 LEASMAYVAGKPIMSDEEYDKLKQKLKME 59 (211)
Q Consensus 31 LeA~~aY~~G~Pi~sD~efD~Lk~~Lk~~ 59 (211)
.+.++.||...|-.=.+.|+++..||..+
T Consensus 53 f~~S~~YY~~~p~~~~~Iy~~V~~rL~~~ 81 (87)
T PF14129_consen 53 FDSSMVYYSRNPEEYEKIYDKVIERLEKE 81 (87)
T ss_pred HHHHHHHHHhCHHHHHHHHHHHHHHHHHH
Confidence 44466799999999999999999999764
No 472
>PF11746 DUF3303: Protein of unknown function (DUF3303); InterPro: IPR021734 Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature.
Probab=20.60 E-value=1e+02 Score=23.47 Aligned_cols=34 Identities=26% Similarity=0.414 Sum_probs=25.7
Q ss_pred cCCeeEEeChhhHHHHHHHHh-hhcC-------CCccChHHH
Q 028248 16 EGSSVVMLSSAEQKFLEASMA-YVAG-------KPIMSDEEY 49 (211)
Q Consensus 16 eGssv~~l~~~Eq~fLeA~~a-Y~~G-------~Pi~sD~ef 49 (211)
.|..++.+..+..+-|-+-.+ ..+. .|+|+|+|+
T Consensus 48 ~g~g~~i~eadd~~~l~~~~~~W~~~fg~~~ei~Pv~~d~e~ 89 (91)
T PF11746_consen 48 GGRGFAIVEADDAKALFKHFAPWRDLFGMEFEITPVMTDEEA 89 (91)
T ss_pred CCcEEEEEEeCCHHHHHHHHhhhhhccCceEEEEecccHHHh
Confidence 788888888887777766555 4444 699999986
No 473
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=20.58 E-value=53 Score=33.65 Aligned_cols=23 Identities=17% Similarity=0.390 Sum_probs=18.3
Q ss_pred CCCccChHHHHHHHHHHhhhCCe
Q 028248 40 GKPIMSDEEYDKLKQKLKMEGSE 62 (211)
Q Consensus 40 G~Pi~sD~efD~Lk~~Lk~~GS~ 62 (211)
|+=.|+.++|.++..+....|-+
T Consensus 195 GEv~m~~~~F~~lN~~~~~~g~~ 217 (689)
T PRK14351 195 GEVYMPKDAFQAYNRERIERGEE 217 (689)
T ss_pred EEEEEEHHHHHHHHHHHHHcCCC
Confidence 66678999999999888776643
No 474
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=20.52 E-value=1.5e+02 Score=22.85 Aligned_cols=38 Identities=29% Similarity=0.383 Sum_probs=28.0
Q ss_pred ChhhHHHHHHHHhhhc--CC-Ccc-ChHHHHHHHHHHhhhCC
Q 028248 24 SSAEQKFLEASMAYVA--GK-PIM-SDEEYDKLKQKLKMEGS 61 (211)
Q Consensus 24 ~~~Eq~fLeA~~aY~~--G~-Pi~-sD~efD~Lk~~Lk~~GS 61 (211)
.++|...||++.+|.. |. |.- .++-||.++..|...-|
T Consensus 9 ~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s 50 (98)
T PF04504_consen 9 EEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVS 50 (98)
T ss_pred chHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCC
Confidence 4789999999999965 64 322 25789999888855444
No 475
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.47 E-value=31 Score=25.40 Aligned_cols=47 Identities=23% Similarity=0.486 Sum_probs=30.3
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCCCC
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPEGS 209 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~peg~ 209 (211)
+||-|...++-|=- =-.-+.++-+..|.+|.+--+ ....++-+|-|.
T Consensus 7 ~CPRC~S~nTKFcY---yNNy~~~QPR~~Ck~C~rywT--~GG~lRnVPvgg 53 (63)
T PF02701_consen 7 PCPRCDSTNTKFCY---YNNYNLSQPRYFCKSCRRYWT--HGGTLRNVPVGG 53 (63)
T ss_pred CCCCcCCCCCEEEe---ecCCCCCCcchhhHHHHHHHH--hcceecCCccCC
Confidence 79999999886521 112334677889999987544 344555556553
No 476
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=20.46 E-value=58 Score=27.81 Aligned_cols=30 Identities=23% Similarity=0.604 Sum_probs=15.0
Q ss_pred CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248 158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 194 (211)
Q Consensus 158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L 194 (211)
.|+.|+.+...- .. +. ...--+|+.||..|
T Consensus 111 ~C~~C~~~~~~~-~~---~~---~~~~p~C~~Cgg~l 140 (224)
T cd01412 111 RCSSCGYVGENN-EE---IP---EEELPRCPKCGGLL 140 (224)
T ss_pred ccCCCCCCCCcc-hh---hh---ccCCCCCCCCCCcc
Confidence 588887764321 00 00 11234688887654
No 477
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=20.44 E-value=41 Score=33.25 Aligned_cols=17 Identities=29% Similarity=0.899 Sum_probs=8.5
Q ss_pred ecCCCCCccc-------ceeeccc
Q 028248 156 KGPCPNCGTE-------NVSFFGT 172 (211)
Q Consensus 156 kG~CPnCg~E-------v~aFfg~ 172 (211)
...||+||.+ |..|++.
T Consensus 504 ~~~CP~CGs~~~~~~~Rv~GYl~~ 527 (546)
T PF13597_consen 504 GDKCPKCGSENIEVYSRVTGYLRP 527 (546)
T ss_dssp EEE-CCC----EEEEB-SSSS-BT
T ss_pred CCCCCCCCCcccceEEEeeccccC
Confidence 6689999999 5566664
No 478
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=20.40 E-value=1.5e+02 Score=21.77 Aligned_cols=61 Identities=26% Similarity=0.348 Sum_probs=39.4
Q ss_pred HHhHHhhhcccCCeeEEeChh-hHHHHHHHHhhhcCCCcc-------ChHHHHHHHHHHhhhCCeeeee
Q 028248 6 FDNLKEELMWEGSSVVMLSSA-EQKFLEASMAYVAGKPIM-------SDEEYDKLKQKLKMEGSEIVVE 66 (211)
Q Consensus 6 fd~lkeel~weGssv~~l~~~-Eq~fLeA~~aY~~G~Pi~-------sD~efD~Lk~~Lk~~GS~vv~~ 66 (211)
|+.+.|.|.-+..-+|++..- ...+=-+..+--.|++++ +-+|.++|.+..+..|..+.|-
T Consensus 51 ~~~~~~ll~~~~~D~V~I~tp~~~h~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~~~~~~~Vg 119 (120)
T PF01408_consen 51 YTDLEELLADEDVDAVIIATPPSSHAEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKEKGVKVMVG 119 (120)
T ss_dssp ESSHHHHHHHTTESEEEEESSGGGHHHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHHHTSCEEEE
T ss_pred hhHHHHHHHhhcCCEEEEecCCcchHHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHHhCCEEEEe
Confidence 556677777666666666544 333333344455565544 5588999999999999887653
No 479
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=20.38 E-value=41 Score=29.83 Aligned_cols=12 Identities=42% Similarity=0.974 Sum_probs=7.9
Q ss_pred eecCCCCCc-ccc
Q 028248 155 LKGPCPNCG-TEN 166 (211)
Q Consensus 155 LkG~CPnCg-~Ev 166 (211)
..-+||+|| +|+
T Consensus 5 iy~~Cp~Cg~eev 17 (201)
T COG1326 5 IYIECPSCGSEEV 17 (201)
T ss_pred EEEECCCCCcchh
Confidence 345788888 444
No 480
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=20.13 E-value=46 Score=26.43 Aligned_cols=10 Identities=50% Similarity=1.235 Sum_probs=7.7
Q ss_pred ecCCCCCccc
Q 028248 156 KGPCPNCGTE 165 (211)
Q Consensus 156 kG~CPnCg~E 165 (211)
-=+||.||+.
T Consensus 3 LI~CP~Cg~R 12 (97)
T COG4311 3 LIPCPYCGER 12 (97)
T ss_pred eecCCCCCCC
Confidence 3489999973
No 481
>cd02660 Peptidase_C19D A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=20.07 E-value=93 Score=27.26 Aligned_cols=23 Identities=30% Similarity=0.615 Sum_probs=14.8
Q ss_pred eeCCCCCceeEEecCceeEeCCC
Q 028248 185 INCSNCGTTMVYDSNTRLITLPE 207 (211)
Q Consensus 185 ~kC~~C~~~L~f~~~~r~i~~pe 207 (211)
.+|+.|+..-......+...+|+
T Consensus 196 ~~C~~C~~~~~~~~~~~i~~lP~ 218 (328)
T cd02660 196 YKCSGCGSTQEATKQLSIKKLPP 218 (328)
T ss_pred ccCCCCCCccceEEEEEecCCCc
Confidence 47999998755444444555554
Done!