Query 020384
Match_columns 327
No_of_seqs 71 out of 73
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 09:18:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020384.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020384hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00398 rpoP DNA-directed RNA 96.1 0.0057 1.2E-07 43.5 3.1 37 274-320 5-41 (46)
2 COG2051 RPS27A Ribosomal prote 95.3 0.018 3.8E-07 45.6 3.2 45 270-323 17-61 (67)
3 PF11023 DUF2614: Protein of u 95.2 0.018 3.9E-07 49.5 3.4 65 241-317 36-102 (114)
4 PRK00420 hypothetical protein; 95.2 0.019 4.2E-07 49.0 3.3 47 257-314 8-54 (112)
5 PRK08097 ligB NAD-dependent DN 95.1 0.023 5E-07 59.5 4.4 50 125-174 8-70 (562)
6 TIGR01206 lysW lysine biosynth 95.1 0.024 5.1E-07 42.8 3.3 37 271-315 1-37 (54)
7 PF13248 zf-ribbon_3: zinc-rib 95.0 0.0099 2.1E-07 38.2 0.9 24 273-310 3-26 (26)
8 TIGR02098 MJ0042_CXXC MJ0042 f 94.8 0.023 4.9E-07 38.6 2.2 36 272-312 2-37 (38)
9 PF13240 zinc_ribbon_2: zinc-r 94.7 0.015 3.2E-07 36.9 1.0 22 275-310 2-23 (23)
10 cd00114 LIGANc NAD+ dependent 94.7 0.032 7E-07 54.0 3.8 29 146-174 10-39 (307)
11 PF01653 DNA_ligase_aden: NAD- 93.9 0.062 1.4E-06 52.2 4.1 26 148-173 16-42 (315)
12 smart00532 LIGANc Ligase N fam 93.1 0.093 2E-06 53.4 3.9 27 148-174 14-41 (441)
13 COG2888 Predicted Zn-ribbon RN 93.0 0.043 9.3E-07 42.7 1.1 37 267-308 22-58 (61)
14 PRK09710 lar restriction allev 93.0 0.062 1.3E-06 42.2 1.9 35 273-314 7-41 (64)
15 PRK05978 hypothetical protein; 92.9 0.048 1E-06 48.5 1.4 35 271-314 32-66 (148)
16 TIGR00575 dnlj DNA ligase, NAD 92.9 0.1 2.3E-06 55.3 4.1 29 146-174 5-34 (652)
17 PRK07956 ligA NAD-dependent DN 92.9 0.1 2.2E-06 55.5 4.0 27 148-174 18-45 (665)
18 PRK00415 rps27e 30S ribosomal 92.9 0.082 1.8E-06 40.9 2.4 41 269-318 8-48 (59)
19 PHA00626 hypothetical protein 92.4 0.098 2.1E-06 40.5 2.2 35 274-313 2-36 (59)
20 PF06044 DRP: Dam-replacing fa 92.3 0.054 1.2E-06 52.0 1.0 46 265-316 24-69 (254)
21 PRK14890 putative Zn-ribbon RN 92.1 0.076 1.6E-06 41.1 1.3 33 270-308 23-56 (59)
22 PF14255 Cys_rich_CPXG: Cystei 92.1 0.11 2.3E-06 39.0 2.1 37 274-314 2-38 (52)
23 smart00531 TFIIE Transcription 92.0 0.08 1.7E-06 45.8 1.6 55 259-317 86-140 (147)
24 PF01667 Ribosomal_S27e: Ribos 91.2 0.32 7E-06 37.1 3.9 42 270-320 5-46 (55)
25 PF14354 Lar_restr_allev: Rest 90.6 0.2 4.3E-06 36.8 2.2 33 274-308 5-37 (61)
26 PRK14351 ligA NAD-dependent DN 90.0 0.31 6.7E-06 52.3 4.0 28 147-174 44-72 (689)
27 smart00659 RPOLCX RNA polymera 89.9 0.4 8.8E-06 34.6 3.3 35 274-319 4-39 (44)
28 cd00114 LIGANc NAD+ dependent 89.8 0.39 8.4E-06 46.7 4.2 35 96-130 4-38 (307)
29 TIGR00373 conserved hypothetic 89.8 0.099 2.1E-06 46.1 0.1 52 259-319 96-147 (158)
30 PF14353 CpXC: CpXC protein 89.2 0.35 7.6E-06 40.4 2.9 40 274-313 3-51 (128)
31 PF08271 TF_Zn_Ribbon: TFIIB z 89.2 0.28 6E-06 34.4 2.0 32 274-314 2-33 (43)
32 PRK02935 hypothetical protein; 89.1 0.39 8.5E-06 41.2 3.1 39 269-319 67-105 (110)
33 PF10571 UPF0547: Uncharacteri 89.0 0.22 4.7E-06 32.6 1.2 23 274-310 2-24 (26)
34 PF14803 Nudix_N_2: Nudix N-te 88.6 0.3 6.4E-06 33.8 1.7 29 275-309 3-31 (34)
35 smart00834 CxxC_CXXC_SSSS Puta 88.5 0.36 7.8E-06 32.6 2.1 29 274-309 7-35 (41)
36 PRK14350 ligA NAD-dependent DN 87.8 0.58 1.3E-05 50.1 4.1 26 148-173 18-44 (669)
37 PF01653 DNA_ligase_aden: NAD- 87.8 0.69 1.5E-05 45.1 4.3 36 95-130 7-42 (315)
38 PLN00209 ribosomal protein S27 87.7 0.59 1.3E-05 38.7 3.2 44 266-318 30-73 (86)
39 smart00532 LIGANc Ligase N fam 87.6 0.59 1.3E-05 47.7 3.8 36 95-130 5-40 (441)
40 PRK06266 transcription initiat 87.2 0.17 3.6E-06 45.7 -0.3 54 257-319 102-155 (178)
41 smart00661 RPOL9 RNA polymeras 86.9 0.52 1.1E-05 33.4 2.2 34 274-315 2-35 (52)
42 PF05876 Terminase_GpA: Phage 86.8 0.41 8.8E-06 49.8 2.2 54 264-317 192-246 (557)
43 PTZ00083 40S ribosomal protein 86.7 0.75 1.6E-05 38.0 3.3 45 266-319 29-73 (85)
44 COG1645 Uncharacterized Zn-fin 86.5 0.45 9.7E-06 41.9 2.0 40 259-310 15-54 (131)
45 PRK08097 ligB NAD-dependent DN 85.8 0.76 1.7E-05 48.5 3.7 36 95-130 34-69 (562)
46 PF07282 OrfB_Zn_ribbon: Putat 85.0 0.64 1.4E-05 34.8 2.0 28 272-309 28-55 (69)
47 TIGR03655 anti_R_Lar restricti 85.0 0.79 1.7E-05 33.6 2.4 36 274-312 3-38 (53)
48 PRK14351 ligA NAD-dependent DN 84.7 1.1 2.3E-05 48.3 4.2 36 95-130 36-71 (689)
49 PF01096 TFIIS_C: Transcriptio 84.6 0.69 1.5E-05 32.3 1.9 34 274-309 2-37 (39)
50 PRK07956 ligA NAD-dependent DN 84.6 1.1 2.3E-05 48.0 4.2 36 95-130 9-44 (665)
51 PF10083 DUF2321: Uncharacteri 84.3 0.54 1.2E-05 42.7 1.5 36 274-310 41-78 (158)
52 PF09723 Zn-ribbon_8: Zinc rib 84.2 0.79 1.7E-05 32.3 2.0 28 274-308 7-34 (42)
53 PF05191 ADK_lid: Adenylate ki 84.0 0.63 1.4E-05 32.4 1.4 33 274-314 3-35 (36)
54 COG5349 Uncharacterized protei 83.8 0.4 8.8E-06 42.0 0.5 35 271-314 20-54 (126)
55 smart00440 ZnF_C2C2 C2C2 Zinc 83.6 0.94 2E-05 31.9 2.2 34 274-309 2-37 (40)
56 PF09862 DUF2089: Protein of u 83.6 0.84 1.8E-05 39.2 2.3 23 275-311 1-23 (113)
57 PF09538 FYDLN_acid: Protein o 83.1 0.87 1.9E-05 38.6 2.2 32 271-313 8-39 (108)
58 PF03367 zf-ZPR1: ZPR1 zinc-fi 82.2 0.63 1.4E-05 41.5 1.1 20 265-284 23-42 (161)
59 TIGR00575 dnlj DNA ligase, NAD 80.7 1.5 3.3E-05 46.8 3.5 27 104-130 7-33 (652)
60 TIGR02300 FYDLN_acid conserved 80.6 1.1 2.5E-05 39.4 2.1 32 271-313 8-39 (129)
61 smart00778 Prim_Zn_Ribbon Zinc 80.6 1.4 3.1E-05 31.0 2.2 30 272-308 3-33 (37)
62 PF01807 zf-CHC2: CHC2 zinc fi 80.4 0.84 1.8E-05 37.1 1.2 32 271-309 32-63 (97)
63 TIGR02605 CxxC_CxxC_SSSS putat 80.2 1.7 3.7E-05 31.1 2.5 28 274-308 7-34 (52)
64 COG0272 Lig NAD-dependent DNA 79.6 1.9 4.1E-05 46.6 3.8 25 150-174 22-47 (667)
65 PF12773 DZR: Double zinc ribb 79.3 0.93 2E-05 32.1 1.0 14 297-310 26-39 (50)
66 PF03604 DNA_RNApol_7kD: DNA d 79.1 1.3 2.9E-05 30.2 1.6 27 275-312 3-29 (32)
67 PRK14350 ligA NAD-dependent DN 79.0 1.7 3.8E-05 46.6 3.3 36 95-130 9-44 (669)
68 PF13719 zinc_ribbon_5: zinc-r 78.9 1.5 3.2E-05 30.3 1.8 35 272-311 2-36 (37)
69 PF04216 FdhE: Protein involve 78.8 1.8 4E-05 41.0 3.1 65 246-314 146-211 (290)
70 PRK14714 DNA polymerase II lar 78.5 1.6 3.6E-05 50.0 3.0 47 267-316 662-708 (1337)
71 PF07754 DUF1610: Domain of un 78.5 0.91 2E-05 29.5 0.6 11 270-280 14-24 (24)
72 PRK00432 30S ribosomal protein 78.4 1.4 3.1E-05 32.6 1.7 29 270-309 18-46 (50)
73 smart00709 Zpr1 Duplicated dom 77.9 1.2 2.7E-05 39.8 1.5 53 264-323 21-81 (160)
74 PRK00464 nrdR transcriptional 77.4 1.8 3.9E-05 38.7 2.4 37 274-310 2-38 (154)
75 PF13717 zinc_ribbon_4: zinc-r 75.3 2.3 4.9E-05 29.4 1.9 34 272-310 2-35 (36)
76 PRK14892 putative transcriptio 75.0 2.2 4.7E-05 35.9 2.1 32 274-312 23-54 (99)
77 PRK00398 rpoP DNA-directed RNA 72.9 3.5 7.5E-05 29.2 2.5 25 299-323 2-26 (46)
78 COG3677 Transposase and inacti 71.8 5 0.00011 34.7 3.7 48 266-318 24-71 (129)
79 TIGR00244 transcriptional regu 71.1 2.8 6.1E-05 37.7 2.0 38 274-311 2-39 (147)
80 PF09567 RE_MamI: MamI restric 71.0 1.8 3.9E-05 42.5 0.9 24 273-310 83-106 (314)
81 TIGR03831 YgiT_finger YgiT-typ 70.6 2.4 5.2E-05 28.9 1.2 18 267-284 23-44 (46)
82 PF12760 Zn_Tnp_IS1595: Transp 70.2 3.8 8.1E-05 29.2 2.2 36 260-308 10-45 (46)
83 PF06906 DUF1272: Protein of u 69.9 1.9 4.2E-05 33.4 0.7 13 270-282 39-51 (57)
84 PF05129 Elf1: Transcription e 68.6 4 8.6E-05 32.9 2.2 37 273-313 23-59 (81)
85 COG0675 Transposase and inacti 68.3 3.2 6.8E-05 37.6 1.8 23 273-310 310-332 (364)
86 smart00400 ZnF_CHCC zinc finge 68.2 2.9 6.4E-05 30.4 1.3 30 272-308 2-31 (55)
87 PF09851 SHOCT: Short C-termin 68.1 7 0.00015 26.1 3.0 26 103-130 5-30 (31)
88 PRK01103 formamidopyrimidine/5 67.6 4.5 9.7E-05 38.3 2.7 35 266-308 235-273 (274)
89 PF06677 Auto_anti-p27: Sjogre 67.5 5.4 0.00012 28.7 2.5 38 259-307 4-41 (41)
90 COG1998 RPS31 Ribosomal protei 66.7 4 8.7E-05 31.0 1.7 31 268-309 15-46 (51)
91 PF08996 zf-DNA_Pol: DNA Polym 66.0 2.5 5.5E-05 38.1 0.7 46 264-310 10-55 (188)
92 PRK12495 hypothetical protein; 65.8 5.4 0.00012 38.2 2.9 42 258-311 28-69 (226)
93 PRK04023 DNA polymerase II lar 65.8 4.1 9E-05 46.2 2.4 14 272-285 626-639 (1121)
94 PF10263 SprT-like: SprT-like 65.2 5.4 0.00012 33.7 2.5 36 269-312 120-155 (157)
95 COG1096 Predicted RNA-binding 64.7 4.8 0.0001 37.6 2.2 41 265-322 142-182 (188)
96 PRK14810 formamidopyrimidine-D 64.2 4.6 0.0001 38.4 2.1 28 273-308 245-272 (272)
97 COG3877 Uncharacterized protei 63.3 5.3 0.00011 34.8 2.1 26 272-311 6-31 (122)
98 PRK10445 endonuclease VIII; Pr 63.1 5.3 0.00011 37.8 2.3 27 273-307 236-262 (263)
99 COG3813 Uncharacterized protei 62.1 3.3 7.2E-05 33.9 0.6 15 270-284 39-53 (84)
100 PF08273 Prim_Zn_Ribbon: Zinc- 61.5 3.5 7.7E-05 29.5 0.6 31 272-308 3-34 (40)
101 COG4306 Uncharacterized protei 61.0 5 0.00011 36.0 1.6 38 274-312 41-80 (160)
102 PRK14559 putative protein seri 60.9 4.6 0.0001 43.4 1.6 12 299-310 40-51 (645)
103 TIGR00577 fpg formamidopyrimid 60.7 5.9 0.00013 37.6 2.2 34 266-307 235-272 (272)
104 PRK00448 polC DNA polymerase I 60.6 5.1 0.00011 46.7 2.0 36 274-312 910-945 (1437)
105 COG1675 TFA1 Transcription ini 59.3 2.4 5.3E-05 38.8 -0.6 39 273-320 114-152 (176)
106 TIGR01405 polC_Gram_pos DNA po 58.9 5.6 0.00012 45.6 1.9 36 274-312 685-720 (1213)
107 TIGR00100 hypA hydrogenase nic 58.1 5.8 0.00013 33.4 1.5 32 267-310 65-96 (115)
108 PHA02540 61 DNA primase; Provi 58.0 13 0.00027 37.3 4.0 34 271-309 26-64 (337)
109 PRK03824 hypA hydrogenase nick 57.7 6.1 0.00013 34.2 1.6 16 299-314 106-122 (135)
110 TIGR01391 dnaG DNA primase, ca 57.5 6.3 0.00014 39.6 1.8 31 271-308 33-63 (415)
111 PRK13945 formamidopyrimidine-D 57.2 7.3 0.00016 37.2 2.1 27 273-307 255-281 (282)
112 COG0272 Lig NAD-dependent DNA 57.0 12 0.00027 40.6 3.9 38 93-130 9-46 (667)
113 PRK04011 peptide chain release 56.9 4.8 0.0001 40.7 0.9 36 272-313 328-363 (411)
114 PRK03988 translation initiatio 56.6 6.9 0.00015 34.5 1.7 32 273-311 103-134 (138)
115 PHA02998 RNA polymerase subuni 56.5 9 0.00019 35.9 2.5 37 271-309 142-180 (195)
116 PF15616 TerY-C: TerY-C metal 56.1 10 0.00022 33.5 2.6 47 267-316 72-121 (131)
117 PRK14714 DNA polymerase II lar 55.7 6.7 0.00015 45.4 1.9 12 300-311 709-720 (1337)
118 PHA02942 putative transposase; 55.1 8.3 0.00018 38.6 2.2 27 273-310 326-352 (383)
119 PRK14811 formamidopyrimidine-D 55.0 8.1 0.00017 36.8 2.0 28 274-309 237-264 (269)
120 PRK08665 ribonucleotide-diphos 54.2 13 0.00027 40.7 3.5 24 273-308 725-748 (752)
121 COG1779 C4-type Zn-finger prot 53.2 6.6 0.00014 37.0 1.1 33 269-308 11-51 (201)
122 PF04502 DUF572: Family of unk 53.0 9.9 0.00021 37.2 2.3 19 297-315 74-92 (324)
123 PF11746 DUF3303: Protein of u 52.9 10 0.00023 30.8 2.1 70 96-165 11-89 (91)
124 TIGR00595 priA primosomal prot 52.8 8.9 0.00019 39.5 2.1 27 275-311 225-251 (505)
125 PF13453 zf-TFIIB: Transcripti 52.1 11 0.00023 26.3 1.7 27 274-308 1-27 (41)
126 PF14206 Cys_rich_CPCC: Cystei 52.1 11 0.00024 30.6 2.1 27 272-307 1-27 (78)
127 COG4888 Uncharacterized Zn rib 51.7 12 0.00025 32.2 2.2 38 273-314 23-60 (104)
128 TIGR03830 CxxCG_CxxCG_HTH puta 51.4 11 0.00024 30.6 2.0 36 275-310 1-41 (127)
129 PF02150 RNA_POL_M_15KD: RNA p 51.2 6.4 0.00014 27.1 0.5 28 275-311 4-31 (35)
130 PF07508 Recombinase: Recombin 51.1 13 0.00028 28.9 2.3 20 155-174 82-101 (102)
131 TIGR00354 polC DNA polymerase, 50.9 7.9 0.00017 43.9 1.4 28 267-310 620-647 (1095)
132 TIGR00311 aIF-2beta translatio 50.7 9.5 0.00021 33.4 1.6 32 272-310 97-128 (133)
133 PRK12380 hydrogenase nickel in 50.6 8.9 0.00019 32.3 1.4 35 267-313 65-100 (113)
134 PRK05667 dnaG DNA primase; Val 50.5 9.5 0.00021 40.3 1.9 31 271-308 35-65 (580)
135 PRK13130 H/ACA RNA-protein com 49.5 7.8 0.00017 29.7 0.8 13 271-283 16-28 (56)
136 PRK12286 rpmF 50S ribosomal pr 49.4 11 0.00024 28.7 1.6 20 273-307 28-47 (57)
137 COG1996 RPC10 DNA-directed RNA 48.8 13 0.00028 28.0 1.8 30 274-313 8-37 (49)
138 TIGR00097 HMP-P_kinase phospho 48.7 65 0.0014 29.4 6.8 57 120-184 115-172 (254)
139 COG1327 Predicted transcriptio 48.5 10 0.00022 34.5 1.6 38 274-311 2-39 (156)
140 PF05502 Dynactin_p62: Dynacti 48.0 11 0.00023 39.2 1.7 45 269-316 23-68 (483)
141 TIGR00155 pqiA_fam integral me 47.9 10 0.00023 38.3 1.7 27 274-313 217-243 (403)
142 COG1867 TRM1 N2,N2-dimethylgua 47.4 10 0.00023 38.7 1.6 48 117-165 84-136 (380)
143 PRK05580 primosome assembly pr 46.9 13 0.00027 39.8 2.2 28 274-311 392-419 (679)
144 TIGR01031 rpmF_bact ribosomal 46.9 12 0.00026 28.2 1.4 13 273-285 27-39 (55)
145 COG5525 Bacteriophage tail ass 46.8 15 0.00033 39.6 2.7 60 261-320 216-279 (611)
146 PRK04023 DNA polymerase II lar 45.8 11 0.00024 43.0 1.5 39 270-312 636-675 (1121)
147 smart00653 eIF2B_5 domain pres 45.1 13 0.00028 31.6 1.5 28 274-308 82-109 (110)
148 COG5257 GCD11 Translation init 45.1 16 0.00035 37.4 2.5 43 266-323 53-95 (415)
149 PF01873 eIF-5_eIF-2B: Domain 44.7 17 0.00037 31.5 2.2 31 272-309 93-123 (125)
150 PF09889 DUF2116: Uncharacteri 43.1 11 0.00023 29.2 0.7 25 273-311 4-29 (59)
151 PRK14873 primosome assembly pr 43.1 15 0.00033 39.5 2.1 67 120-188 175-251 (665)
152 PRK03681 hypA hydrogenase nick 43.0 13 0.00028 31.4 1.2 30 269-309 67-96 (114)
153 cd02661 Peptidase_C19E A subfa 43.0 26 0.00055 31.7 3.2 26 298-323 180-205 (304)
154 PF09297 zf-NADH-PPase: NADH p 42.9 19 0.00042 23.8 1.8 26 274-309 5-30 (32)
155 COG3058 FdhE Uncharacterized p 41.9 20 0.00043 35.7 2.5 38 272-309 185-234 (308)
156 PRK14715 DNA polymerase II lar 41.4 19 0.00042 42.3 2.6 35 265-315 667-701 (1627)
157 TIGR00398 metG methionyl-tRNA 41.1 19 0.0004 36.7 2.3 42 272-317 136-183 (530)
158 PRK00241 nudC NADH pyrophospha 40.5 18 0.00039 34.3 1.9 28 272-309 99-126 (256)
159 PRK12336 translation initiatio 40.4 20 0.00044 33.0 2.2 37 272-315 98-134 (201)
160 PRK00133 metG methionyl-tRNA s 40.4 14 0.00029 39.4 1.2 45 271-317 138-186 (673)
161 PF09334 tRNA-synt_1g: tRNA sy 40.3 17 0.00038 36.3 1.9 15 300-314 166-180 (391)
162 TIGR01054 rgy reverse gyrase. 40.2 12 0.00026 42.8 0.7 17 269-285 4-20 (1171)
163 PRK03564 formate dehydrogenase 39.4 39 0.00084 33.6 4.1 13 271-283 186-198 (309)
164 TIGR00155 pqiA_fam integral me 39.4 22 0.00048 36.0 2.5 32 274-313 15-46 (403)
165 PF14205 Cys_rich_KTR: Cystein 39.4 43 0.00093 25.9 3.4 43 275-321 7-49 (55)
166 COG1198 PriA Primosomal protei 39.3 19 0.00041 39.6 2.0 68 120-188 232-307 (730)
167 TIGR01384 TFS_arch transcripti 39.0 25 0.00054 28.4 2.3 37 272-308 62-98 (104)
168 PF11793 FANCL_C: FANCL C-term 38.7 11 0.00024 29.1 0.2 19 265-283 48-66 (70)
169 cd00674 LysRS_core_class_I cat 37.9 25 0.00054 35.2 2.5 44 266-314 163-206 (353)
170 smart00709 Zpr1 Duplicated dom 37.2 33 0.00071 30.8 2.9 29 274-309 2-38 (160)
171 PF12677 DUF3797: Domain of un 37.2 15 0.00032 27.8 0.6 12 272-283 13-24 (49)
172 PF04380 BMFP: Membrane fusoge 36.9 55 0.0012 26.0 3.9 36 94-130 25-60 (79)
173 PRK05654 acetyl-CoA carboxylas 36.7 8.3 0.00018 37.6 -1.0 38 273-319 28-65 (292)
174 PF04216 FdhE: Protein involve 36.4 20 0.00043 34.1 1.5 41 270-311 209-249 (290)
175 PRK03564 formate dehydrogenase 36.1 26 0.00057 34.7 2.4 38 271-312 225-264 (309)
176 cd02674 Peptidase_C19R A subfa 35.8 36 0.00079 29.7 3.0 26 298-323 102-127 (230)
177 PF05416 Peptidase_C37: Southa 35.6 12 0.00027 39.2 0.0 43 116-166 252-297 (535)
178 PF04423 Rad50_zn_hook: Rad50 35.5 21 0.00045 26.0 1.2 10 302-311 22-31 (54)
179 TIGR03676 aRF1/eRF1 peptide ch 35.5 23 0.00049 35.9 1.8 36 272-313 320-355 (403)
180 PF05907 DUF866: Eukaryotic pr 35.1 22 0.00047 31.9 1.5 45 269-313 27-77 (161)
181 KOG2906 RNA polymerase III sub 35.0 22 0.00048 30.5 1.4 32 274-313 3-34 (105)
182 PRK12496 hypothetical protein; 35.0 22 0.00047 31.8 1.4 36 266-313 121-156 (164)
183 CHL00174 accD acetyl-CoA carbo 35.0 7.8 0.00017 38.2 -1.4 37 274-319 40-76 (296)
184 PF14577 SEO_C: Sieve element 34.9 20 0.00043 34.5 1.2 19 293-311 207-225 (235)
185 PF06107 DUF951: Bacterial pro 34.7 45 0.00097 25.9 2.9 44 263-314 2-45 (57)
186 COG0143 MetG Methionyl-tRNA sy 34.5 20 0.00042 38.2 1.2 12 271-282 141-152 (558)
187 TIGR00310 ZPR1_znf ZPR1 zinc f 34.3 37 0.00081 31.4 2.9 19 265-283 23-41 (192)
188 PF03367 zf-ZPR1: ZPR1 zinc-fi 34.2 29 0.00063 31.0 2.1 29 274-309 3-39 (161)
189 PRK12412 pyridoxal kinase; Rev 34.1 1.4E+02 0.0031 27.6 6.7 57 119-183 119-176 (268)
190 TIGR00515 accD acetyl-CoA carb 34.1 8.6 0.00019 37.4 -1.3 36 274-318 28-63 (285)
191 PLN00049 carboxyl-terminal pro 34.1 79 0.0017 31.5 5.3 71 95-172 2-80 (389)
192 cd07110 ALDH_F10_BADH Arabidop 33.4 1.2E+02 0.0026 30.4 6.4 70 116-185 238-334 (456)
193 PRK04351 hypothetical protein; 33.3 36 0.00079 30.2 2.6 34 273-314 113-146 (149)
194 COG4443 Uncharacterized protei 33.2 27 0.00057 28.2 1.5 18 113-130 52-70 (72)
195 COG1241 MCM2 Predicted ATPase 33.0 34 0.00073 37.4 2.7 26 275-306 132-157 (682)
196 PF06170 DUF983: Protein of un 32.8 19 0.00041 29.4 0.6 17 267-283 3-19 (86)
197 PRK08351 DNA-directed RNA poly 32.7 21 0.00045 27.9 0.8 16 274-289 17-34 (61)
198 smart00132 LIM Zinc-binding do 32.7 30 0.00065 22.0 1.5 35 275-311 2-38 (39)
199 PLN02919 haloacid dehalogenase 32.7 3.2E+02 0.007 31.2 10.3 30 94-123 85-114 (1057)
200 PF09855 DUF2082: Nucleic-acid 32.2 45 0.00097 26.1 2.6 42 274-316 2-52 (64)
201 COG2176 PolC DNA polymerase II 32.0 31 0.00068 40.3 2.4 40 269-311 911-950 (1444)
202 PF10058 DUF2296: Predicted in 31.9 29 0.00063 26.1 1.5 32 269-308 21-52 (54)
203 PRK15103 paraquat-inducible me 31.9 26 0.00056 35.7 1.6 26 274-313 223-248 (419)
204 COG2816 NPY1 NTP pyrophosphohy 31.8 26 0.00056 34.5 1.5 29 272-310 111-139 (279)
205 PF06221 zf-C2HC5: Putative zi 31.5 23 0.0005 27.2 0.9 13 272-284 35-47 (57)
206 PRK08173 DNA topoisomerase III 31.3 28 0.00061 38.7 1.8 27 272-310 624-650 (862)
207 PF09986 DUF2225: Uncharacteri 31.2 36 0.00079 31.4 2.3 11 273-283 6-16 (214)
208 cd01169 HMPP_kinase 4-amino-5- 31.1 2.1E+02 0.0046 25.3 7.1 53 123-183 119-172 (242)
209 PF04280 Tim44: Tim44-like dom 30.3 26 0.00056 29.2 1.1 37 139-175 21-62 (147)
210 PHA02768 hypothetical protein; 30.2 26 0.00057 26.8 1.0 42 273-321 6-50 (55)
211 COG1545 Predicted nucleic-acid 30.1 36 0.00079 29.6 2.0 32 265-310 22-53 (140)
212 COG0551 TopA Zn-finger domain 30.1 57 0.0012 27.7 3.1 45 269-313 14-74 (140)
213 PF05605 zf-Di19: Drought indu 29.8 19 0.00042 26.1 0.2 34 274-309 4-40 (54)
214 KOG2593 Transcription initiati 29.6 26 0.00056 36.5 1.2 58 256-316 112-169 (436)
215 PRK14973 DNA topoisomerase I; 29.6 39 0.00085 38.0 2.6 12 272-283 588-599 (936)
216 COG0266 Nei Formamidopyrimidin 29.5 37 0.00081 33.2 2.2 26 274-307 247-272 (273)
217 COG0777 AccD Acetyl-CoA carbox 29.5 13 0.00027 36.9 -1.0 38 274-320 30-67 (294)
218 TIGR01385 TFSII transcription 29.5 47 0.001 32.7 2.9 39 272-312 258-298 (299)
219 PRK09678 DNA-binding transcrip 29.4 80 0.0017 25.3 3.6 49 274-324 3-54 (72)
220 PF11331 DUF3133: Protein of u 29.0 38 0.00083 25.1 1.6 37 274-313 8-44 (46)
221 PRK09263 anaerobic ribonucleos 28.9 40 0.00087 36.7 2.5 27 273-309 642-668 (711)
222 PRK00564 hypA hydrogenase nick 28.6 28 0.00061 29.5 1.0 30 269-309 68-97 (117)
223 PF09863 DUF2090: Uncharacteri 28.6 1.5E+02 0.0032 29.9 6.1 49 94-142 188-246 (311)
224 PF07295 DUF1451: Protein of u 28.5 46 0.001 29.6 2.4 32 275-316 115-146 (146)
225 PF12647 RNHCP: RNHCP domain; 28.4 36 0.00079 28.6 1.6 32 274-313 6-37 (92)
226 PF14319 Zn_Tnp_IS91: Transpos 28.4 36 0.00078 28.6 1.6 28 272-309 42-69 (111)
227 PRK14526 adenylate kinase; Pro 28.3 45 0.00097 30.5 2.4 34 273-314 123-156 (211)
228 PF12767 SAGA-Tad1: Transcript 28.2 59 0.0013 30.4 3.2 36 92-130 19-55 (252)
229 PF01155 HypA: Hydrogenase exp 28.2 15 0.00032 30.8 -0.7 36 267-314 65-101 (113)
230 PRK14529 adenylate kinase; Pro 28.2 40 0.00086 31.5 2.0 38 272-315 126-163 (223)
231 PRK08176 pdxK pyridoxal-pyrido 28.0 1.5E+02 0.0032 27.8 5.8 53 123-183 143-196 (281)
232 smart00731 SprT SprT homologue 27.9 61 0.0013 27.8 3.0 34 272-312 112-145 (146)
233 PF08274 PhnA_Zn_Ribbon: PhnA 27.9 45 0.00099 22.6 1.7 27 273-310 3-29 (30)
234 PF11781 RRN7: RNA polymerase 27.7 38 0.00082 23.6 1.4 25 275-310 11-35 (36)
235 PF08209 Sgf11: Sgf11 (transcr 27.7 41 0.00089 23.3 1.5 13 299-311 3-15 (33)
236 PRK11032 hypothetical protein; 27.6 35 0.00076 31.0 1.5 23 275-307 127-149 (160)
237 COG3478 Predicted nucleic-acid 27.3 33 0.00072 27.5 1.2 43 272-315 4-55 (68)
238 PRK09521 exosome complex RNA-b 27.3 48 0.001 29.7 2.3 28 270-308 147-174 (189)
239 cd07114 ALDH_DhaS Uncharacteri 27.1 1.7E+02 0.0037 29.2 6.4 69 116-184 237-332 (457)
240 KOG0909 Peptide:N-glycanase [P 27.0 23 0.0005 37.2 0.3 52 272-323 161-217 (500)
241 PF03317 ELF: ELF protein; In 27.0 1.5E+02 0.0032 28.8 5.6 106 50-177 144-255 (284)
242 COG1571 Predicted DNA-binding 26.9 33 0.00072 35.6 1.4 32 272-314 350-381 (421)
243 TIGR00595 priA primosomal prot 26.8 43 0.00094 34.6 2.2 20 300-319 222-241 (505)
244 PF02829 3H: 3H domain; Inter 26.5 1E+02 0.0023 25.7 4.0 32 144-176 50-95 (98)
245 PF03833 PolC_DP2: DNA polymer 26.0 22 0.00049 39.9 0.0 20 267-286 650-669 (900)
246 PF03884 DUF329: Domain of unk 25.8 25 0.00054 27.0 0.2 12 272-283 2-13 (57)
247 PF02591 DUF164: Putative zinc 25.6 35 0.00075 25.0 0.9 37 269-310 19-56 (56)
248 PRK09401 reverse gyrase; Revie 25.2 29 0.00063 39.9 0.7 16 269-284 4-19 (1176)
249 COG1656 Uncharacterized conser 25.2 30 0.00065 31.8 0.6 24 159-182 9-32 (165)
250 PTZ00381 aldehyde dehydrogenas 25.1 1.7E+02 0.0036 30.3 6.0 67 116-183 224-314 (493)
251 PF09082 DUF1922: Domain of un 25.1 46 0.001 26.7 1.6 29 274-314 5-33 (68)
252 PF12207 DUF3600: Domain of un 25.0 32 0.0007 31.5 0.8 66 91-156 72-159 (162)
253 PF05193 Peptidase_M16_C: Pept 24.9 1.2E+02 0.0025 24.3 3.9 33 94-129 152-184 (184)
254 smart00547 ZnF_RBZ Zinc finger 24.8 40 0.00087 20.9 1.0 22 274-309 4-25 (26)
255 TIGR02159 PA_CoA_Oxy4 phenylac 24.7 21 0.00045 31.6 -0.4 35 272-312 105-142 (146)
256 PF12674 Zn_ribbon_2: Putative 24.5 25 0.00055 28.3 0.0 32 274-309 2-35 (81)
257 COG2023 RPR2 RNase P subunit R 24.4 50 0.0011 28.4 1.8 39 273-313 57-95 (105)
258 TIGR00686 phnA alkylphosphonat 24.3 53 0.0011 28.5 1.9 27 273-310 3-29 (109)
259 cd07120 ALDH_PsfA-ACA09737 Pse 24.1 2.2E+02 0.0048 28.8 6.6 70 116-185 236-332 (455)
260 COG4481 Uncharacterized protei 24.0 62 0.0013 25.4 2.0 43 264-314 6-48 (60)
261 PF14485 DUF4431: Domain of un 24.0 65 0.0014 23.7 2.1 22 159-183 5-26 (48)
262 PRK08270 anaerobic ribonucleos 23.7 45 0.00098 36.0 1.7 24 273-311 627-650 (656)
263 COG1499 NMD3 NMD protein affec 23.7 51 0.0011 33.3 2.0 49 270-321 4-61 (355)
264 PRK15398 aldehyde dehydrogenas 23.6 1.6E+02 0.0035 30.2 5.6 59 116-176 247-316 (465)
265 PF13058 DUF3920: Protein of u 23.6 35 0.00076 30.1 0.7 47 84-130 30-81 (126)
266 TIGR00340 zpr1_rel ZPR1-relate 23.3 39 0.00085 30.5 1.0 20 264-283 20-39 (163)
267 PF05280 FlhC: Flagellar trans 23.2 38 0.00082 30.9 0.9 32 269-308 131-162 (175)
268 PF14952 zf-tcix: Putative tre 23.2 37 0.0008 25.2 0.7 9 274-282 13-21 (44)
269 PF09930 DUF2162: Predicted tr 23.1 70 0.0015 30.4 2.7 36 246-282 72-115 (224)
270 PRK06427 bifunctional hydroxy- 23.1 3E+02 0.0066 25.0 6.7 54 123-184 124-179 (266)
271 PF01921 tRNA-synt_1f: tRNA sy 23.1 48 0.001 33.7 1.7 51 261-314 163-213 (360)
272 KOG3457 Sec61 protein transloc 23.1 49 0.0011 27.7 1.5 29 219-247 47-75 (88)
273 PF13408 Zn_ribbon_recom: Reco 23.0 59 0.0013 22.9 1.7 17 299-315 4-20 (58)
274 KOG2906 RNA polymerase III sub 22.9 49 0.0011 28.5 1.4 42 265-308 58-101 (105)
275 PF08976 DUF1880: Domain of un 22.8 39 0.00084 29.7 0.8 19 115-133 2-22 (118)
276 PF13913 zf-C2HC_2: zinc-finge 22.7 39 0.00084 21.5 0.6 8 274-281 4-11 (25)
277 cd07078 ALDH NAD(P)+ dependent 22.7 2.5E+02 0.0054 27.5 6.4 68 117-184 215-309 (432)
278 PF04475 DUF555: Protein of un 22.5 40 0.00087 28.9 0.9 15 270-284 45-59 (102)
279 KOG1372 GDP-mannose 4,6 dehydr 22.5 46 0.00099 33.4 1.4 39 99-137 257-309 (376)
280 COG3024 Uncharacterized protei 22.3 41 0.00089 26.8 0.8 14 270-283 5-18 (65)
281 PRK14873 primosome assembly pr 22.2 60 0.0013 35.2 2.3 40 141-182 172-220 (665)
282 PF12207 DUF3600: Domain of un 22.2 68 0.0015 29.5 2.3 65 112-176 35-122 (162)
283 cd07092 ALDH_ABALDH-YdcW Esche 21.9 2.7E+02 0.0058 27.7 6.5 68 116-183 235-328 (450)
284 PF03119 DNA_ligase_ZBD: NAD-d 21.7 67 0.0015 21.2 1.6 9 275-283 2-10 (28)
285 PRK04338 N(2),N(2)-dimethylgua 21.7 58 0.0013 32.7 1.9 32 270-312 242-273 (382)
286 PF04328 DUF466: Protein of un 21.7 1.7E+02 0.0037 22.8 4.1 34 144-177 26-59 (65)
287 COG1579 Zn-ribbon protein, pos 21.7 25 0.00054 33.8 -0.6 40 271-314 196-235 (239)
288 COG2960 Uncharacterized protei 21.6 1.1E+02 0.0024 26.3 3.3 51 92-151 32-82 (103)
289 PF10122 Mu-like_Com: Mu-like 21.5 58 0.0012 24.9 1.4 34 274-315 6-39 (51)
290 PF12419 DUF3670: SNF2 Helicas 21.4 1.8E+02 0.004 25.0 4.7 40 115-158 82-125 (141)
291 cd07105 ALDH_SaliADH Salicylal 21.4 2.6E+02 0.0056 27.8 6.4 70 116-185 219-310 (432)
292 TIGR00777 ahpD alkylhydroperox 21.3 49 0.0011 30.6 1.2 26 150-175 79-105 (177)
293 PF06750 DiS_P_DiS: Bacterial 21.2 48 0.001 27.1 1.0 13 271-283 57-69 (92)
294 PRK03922 hypothetical protein; 21.1 45 0.00098 29.1 0.9 15 270-284 47-61 (113)
295 PF10751 DUF2535: Protein of u 21.0 95 0.0021 25.9 2.7 40 136-175 21-68 (83)
296 COG1885 Uncharacterized protei 20.8 49 0.0011 28.8 1.0 17 270-286 47-63 (115)
297 PRK07111 anaerobic ribonucleos 20.6 52 0.0011 36.1 1.4 21 273-308 681-701 (735)
298 PF01485 IBR: IBR domain; Int 20.6 70 0.0015 22.7 1.7 31 274-312 20-52 (64)
299 PLN02278 succinic semialdehyde 20.5 2.8E+02 0.0061 28.4 6.6 68 116-183 278-372 (498)
300 PLN02766 coniferyl-aldehyde de 20.5 2.6E+02 0.0056 28.8 6.3 69 116-184 277-372 (501)
301 PRK12413 phosphomethylpyrimidi 20.4 3.8E+02 0.0082 24.2 6.7 45 131-182 127-172 (253)
302 PRK08579 anaerobic ribonucleos 20.2 57 0.0012 35.2 1.6 24 272-309 568-591 (625)
303 COG0375 HybF Zn finger protein 20.1 85 0.0018 27.3 2.4 27 271-309 69-95 (115)
No 1
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.12 E-value=0.0057 Score=43.48 Aligned_cols=37 Identities=19% Similarity=0.572 Sum_probs=26.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceeee
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLIT 320 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~it 320 (327)
-|||||.++-.- + .....+|+.||..+.|...+++|.
T Consensus 5 ~C~~CG~~~~~~-------~---~~~~~~Cp~CG~~~~~~~~~~~v~ 41 (46)
T PRK00398 5 KCARCGREVELD-------E---YGTGVRCPYCGYRILFKERPPVVK 41 (46)
T ss_pred ECCCCCCEEEEC-------C---CCCceECCCCCCeEEEccCCCcce
Confidence 599999975431 1 112789999999999986665543
No 2
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=95.32 E-value=0.018 Score=45.57 Aligned_cols=45 Identities=31% Similarity=0.672 Sum_probs=36.7
Q ss_pred eeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceeeecCC
Q 020384 270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE 323 (327)
Q Consensus 270 iLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~itl~~ 323 (327)
-|+--||.||.|--.| + .+...+.|.+||+.|..-+..++...++
T Consensus 17 Fl~VkCpdC~N~q~vF-------s--hast~V~C~~CG~~l~~PTGGka~i~~~ 61 (67)
T COG2051 17 FLRVKCPDCGNEQVVF-------S--HASTVVTCLICGTTLAEPTGGKAKISGK 61 (67)
T ss_pred EEEEECCCCCCEEEEe-------c--cCceEEEecccccEEEecCCCeEEeeee
Confidence 4667799999999888 2 3677899999999999988777766554
No 3
>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=95.25 E-value=0.018 Score=49.53 Aligned_cols=65 Identities=20% Similarity=0.476 Sum_probs=40.4
Q ss_pred hHHHHHHhhhhHHHHHHHHHHHhhhc--cceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccce
Q 020384 241 SFIFTWFAAVPLIVYLSQSLTKLIVR--ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTR 317 (327)
Q Consensus 241 ~fi~t~~~~~P~i~~~a~~Lt~l~~~--D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R 317 (327)
.++.+.|+.+.++..+++...=.|.+ -.-+.--.|||||.+.... |. . --|..|+++|+.|+...
T Consensus 36 ~~im~ifmllG~L~~l~S~~VYfwIGmlStkav~V~CP~C~K~TKmL-Gr----------~-D~CM~C~~pLTLd~~le 102 (114)
T PF11023_consen 36 PIIMVIFMLLGLLAILASTAVYFWIGMLSTKAVQVECPNCGKQTKML-GR----------V-DACMHCKEPLTLDPSLE 102 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcccceeeECCCCCChHhhh-ch----------h-hccCcCCCcCccCchhh
Confidence 34555566666665555554444332 1223333499999998765 11 1 27999999999997654
No 4
>PRK00420 hypothetical protein; Validated
Probab=95.17 E-value=0.019 Score=48.98 Aligned_cols=47 Identities=19% Similarity=0.463 Sum_probs=35.2
Q ss_pred HHHHHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 257 SQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 257 a~~Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
+..+..++++=...|-..||.||.+.|.+- ....-|++||..+....
T Consensus 8 ~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~lk-----------~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 8 VKKAAELLLKGAKMLSKHCPVCGLPLFELK-----------DGEVVCPVHGKVYIVKS 54 (112)
T ss_pred HHHHHHHHHhHHHHccCCCCCCCCcceecC-----------CCceECCCCCCeeeecc
Confidence 345566666666668899999999988762 23678999999877653
No 5
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=95.12 E-value=0.023 Score=59.52 Aligned_cols=50 Identities=34% Similarity=0.492 Sum_probs=35.2
Q ss_pred hHhhhhhcCCe---eEEeChhh--HH--HH-----HHHHhhhc-CCCccChHHHHHHHHHHhh
Q 020384 125 LKEELMWEGSS---VVMLSSAE--QK--FL-----EASMAYVA-GKPIMSDEEYDKLKQKLKM 174 (327)
Q Consensus 125 LkEeL~weGSs---vv~L~~~E--q~--fL-----EA~~AY~s-GkPimsDeeFD~LK~kLk~ 174 (327)
|---|.|..|- |.+++..| ++ .| ++-.+||. |+|+|||+|||+|..+|+.
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 34457888876 56666654 11 22 22446775 9999999999999999973
No 6
>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=95.11 E-value=0.024 Score=42.85 Aligned_cols=37 Identities=24% Similarity=0.534 Sum_probs=26.5
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEecc
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 315 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~ 315 (327)
|+..||.||+++-- .....-..++|++||..++.-+.
T Consensus 1 ~~~~CP~CG~~iev--------~~~~~GeiV~Cp~CGaeleVv~~ 37 (54)
T TIGR01206 1 MQFECPDCGAEIEL--------ENPELGELVICDECGAELEVVSL 37 (54)
T ss_pred CccCCCCCCCEEec--------CCCccCCEEeCCCCCCEEEEEeC
Confidence 36789999998732 22122347899999999999753
No 7
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=95.03 E-value=0.0099 Score=38.21 Aligned_cols=24 Identities=42% Similarity=0.973 Sum_probs=18.0
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
-.|||||.+| +....-|++||++|
T Consensus 3 ~~Cp~Cg~~~--------------~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEI--------------DPDAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcC--------------CcccccChhhCCCC
Confidence 3699999976 23355799999875
No 8
>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=94.79 E-value=0.023 Score=38.57 Aligned_cols=36 Identities=22% Similarity=0.541 Sum_probs=23.3
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
+-.||+||+.+..== + .+. ....++.|++||..+..
T Consensus 2 ~~~CP~C~~~~~v~~-~--~~~--~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 2 RIQCPNCKTSFRVVD-S--QLG--ANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEEEeCH-H--HcC--CCCCEEECCCCCCEEEe
Confidence 457999999854321 1 111 22348999999998764
No 9
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=94.66 E-value=0.015 Score=36.91 Aligned_cols=22 Identities=50% Similarity=1.177 Sum_probs=16.3
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
||+||.+|.. +..-|++||+.|
T Consensus 2 Cp~CG~~~~~--------------~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIED--------------DAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCC--------------cCcchhhhCCcC
Confidence 9999998742 223399999875
No 10
>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=94.65 E-value=0.032 Score=54.04 Aligned_cols=29 Identities=31% Similarity=0.586 Sum_probs=24.1
Q ss_pred HHHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 020384 146 FLEASMAYVA-GKPIMSDEEYDKLKQKLKM 174 (327)
Q Consensus 146 fLEA~~AY~s-GkPimsDeeFD~LK~kLk~ 174 (327)
.-++..+||. |+|+|||+|||.|..+|+.
T Consensus 10 i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 39 (307)
T cd00114 10 LNKHDYRYYVLDEPSVSDAEYDRLYRELRA 39 (307)
T ss_pred HHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 3344567887 9999999999999999974
No 11
>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=93.94 E-value=0.062 Score=52.21 Aligned_cols=26 Identities=50% Similarity=0.847 Sum_probs=22.2
Q ss_pred HHHHhhhc-CCCccChHHHHHHHHHHh
Q 020384 148 EASMAYVA-GKPIMSDEEYDKLKQKLK 173 (327)
Q Consensus 148 EA~~AY~s-GkPimsDeeFD~LK~kLk 173 (327)
++..+||. |+|+|||+|||.|..+|+
T Consensus 16 ~~~~~YY~~~~p~isD~eYD~l~~~L~ 42 (315)
T PF01653_consen 16 RHNYAYYNLGEPIISDAEYDQLFRELK 42 (315)
T ss_dssp HHHHHHHTTSSSSSSHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 34557877 899999999999999986
No 12
>smart00532 LIGANc Ligase N family.
Probab=93.10 E-value=0.093 Score=53.40 Aligned_cols=27 Identities=41% Similarity=0.703 Sum_probs=23.0
Q ss_pred HHHHhhhc-CCCccChHHHHHHHHHHhh
Q 020384 148 EASMAYVA-GKPIMSDEEYDKLKQKLKM 174 (327)
Q Consensus 148 EA~~AY~s-GkPimsDeeFD~LK~kLk~ 174 (327)
++..+||. |+|+|||+|||+|..+|+.
T Consensus 14 ~~~~~YY~~~~p~IsD~eYD~L~~eL~~ 41 (441)
T smart00532 14 KHDYRYYVLDAPIISDAEYDRLMRELKE 41 (441)
T ss_pred HHHHHHHhcCCCCCChHHHHHHHHHHHH
Confidence 44567886 9999999999999999973
No 13
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.04 E-value=0.043 Score=42.74 Aligned_cols=37 Identities=30% Similarity=0.643 Sum_probs=23.2
Q ss_pred cceeeecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 267 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 267 D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
+--+.+=+||||||++-- +-. ..-.-.|..+|++||=
T Consensus 22 ~e~~v~F~CPnCGe~~I~--Rc~---~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 22 GETAVKFPCPNCGEVEIY--RCA---KCRKLGNPYRCPKCGF 58 (61)
T ss_pred CCceeEeeCCCCCceeee--hhh---hHHHcCCceECCCcCc
Confidence 334677899999955431 111 2234567889999983
No 14
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=93.02 E-value=0.062 Score=42.21 Aligned_cols=35 Identities=26% Similarity=0.640 Sum_probs=26.2
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
-|||.||.++... .-.+..-.++|+.|+..--|..
T Consensus 7 KPCPFCG~~~~~v-------~~~~g~~~v~C~~CgA~~~~~~ 41 (64)
T PRK09710 7 KPCPFCGCPSVTV-------KAISGYYRAKCNGCESRTGYGG 41 (64)
T ss_pred cCCCCCCCceeEE-------EecCceEEEEcCCCCcCccccc
Confidence 3999999998765 2223455799999999877663
No 15
>PRK05978 hypothetical protein; Provisional
Probab=92.95 E-value=0.048 Score=48.54 Aligned_cols=35 Identities=29% Similarity=0.831 Sum_probs=25.5
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
|+|-||+||+.- .|.+-+ +..-.|++||..+++.+
T Consensus 32 l~grCP~CG~G~--LF~g~L-------kv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 32 FRGRCPACGEGK--LFRAFL-------KPVDHCAACGEDFTHHR 66 (148)
T ss_pred HcCcCCCCCCCc--cccccc-------ccCCCccccCCccccCC
Confidence 689999999864 333333 34568999999988753
No 16
>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=92.92 E-value=0.1 Score=55.27 Aligned_cols=29 Identities=31% Similarity=0.556 Sum_probs=24.7
Q ss_pred HHHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 020384 146 FLEASMAYVA-GKPIMSDEEYDKLKQKLKM 174 (327)
Q Consensus 146 fLEA~~AY~s-GkPimsDeeFD~LK~kLk~ 174 (327)
.-++..+||. |+|+|||+|||+|.++|+.
T Consensus 5 l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 34 (652)
T TIGR00575 5 IRHHDYRYYVLDEPSISDAEYDRLYRELQE 34 (652)
T ss_pred HHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 3455677887 9999999999999999974
No 17
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=92.89 E-value=0.1 Score=55.52 Aligned_cols=27 Identities=37% Similarity=0.597 Sum_probs=23.6
Q ss_pred HHHHhhh-cCCCccChHHHHHHHHHHhh
Q 020384 148 EASMAYV-AGKPIMSDEEYDKLKQKLKM 174 (327)
Q Consensus 148 EA~~AY~-sGkPimsDeeFD~LK~kLk~ 174 (327)
++-.+|| .|+|+|||+|||.|..+|+.
T Consensus 18 ~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 45 (665)
T PRK07956 18 HHAYAYYVLDAPSISDAEYDRLYRELVA 45 (665)
T ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 4466788 99999999999999999973
No 18
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=92.87 E-value=0.082 Score=40.90 Aligned_cols=41 Identities=34% Similarity=0.750 Sum_probs=32.1
Q ss_pred eeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEecccee
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 318 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~ 318 (327)
--|+--||.|+.|...| + .+...++|.+||+.|.--+..+.
T Consensus 8 ~F~~VkCp~C~n~q~vF-------s--ha~t~V~C~~Cg~~L~~PtGGKa 48 (59)
T PRK00415 8 RFLKVKCPDCGNEQVVF-------S--HASTVVRCLVCGKTLAEPTGGKA 48 (59)
T ss_pred eEEEEECCCCCCeEEEE-------e--cCCcEEECcccCCCcccCCCcce
Confidence 34677899999999988 1 36778999999999976654443
No 19
>PHA00626 hypothetical protein
Probab=92.35 E-value=0.098 Score=40.49 Aligned_cols=35 Identities=31% Similarity=0.711 Sum_probs=25.0
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.||+||..+..==|.+. .-+++.+|+.||-..+-|
T Consensus 2 ~CP~CGS~~Ivrcg~cr-----~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR-----GWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceec-----ccCcceEcCCCCCeechh
Confidence 59999996554433332 347999999999776655
No 20
>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=92.35 E-value=0.054 Score=52.05 Aligned_cols=46 Identities=24% Similarity=0.519 Sum_probs=21.8
Q ss_pred hccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccc
Q 020384 265 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 316 (327)
Q Consensus 265 ~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~ 316 (327)
..+.|.=.+.|||||.+..+=| ++|+......|++|+...+..++.
T Consensus 24 tE~Wv~~n~yCP~Cg~~~L~~f------~NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 24 TEDWVAENMYCPNCGSKPLSKF------ENNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp HHHHHHHH---TTT--SS-EE--------------EEE-TTT--EEEEEEEE
T ss_pred HHHHHHHCCcCCCCCChhHhhc------cCCCccceeECCCCchHHhhhhhc
Confidence 3344455678999999966555 666677899999999999888765
No 21
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=92.10 E-value=0.076 Score=41.13 Aligned_cols=33 Identities=30% Similarity=0.594 Sum_probs=21.4
Q ss_pred eeecCCCCCccc-cceeccccccccCCCCccceeCCCCCc
Q 020384 270 ILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 270 iLKGpCPNCGeE-v~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
+.+=.|||||++ +.-=- +--.-.|.++|++||-
T Consensus 23 ~~~F~CPnCG~~~I~RC~------~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCE------KCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeech------hHHhcCCceECCCCCC
Confidence 455689999988 44211 2223457889999983
No 22
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=92.08 E-value=0.11 Score=39.05 Aligned_cols=37 Identities=22% Similarity=0.518 Sum_probs=28.4
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
.||.||+.+-...-. +.+.-.---+|.+|-+++.|.-
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 599999999988633 3334455668999999999873
No 23
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=92.05 E-value=0.08 Score=45.80 Aligned_cols=55 Identities=24% Similarity=0.470 Sum_probs=31.8
Q ss_pred HHHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccce
Q 020384 259 SLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTR 317 (327)
Q Consensus 259 ~Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R 317 (327)
.|..-...+.--..=-|||||.. |+|- ..... ...+.+..|++||..|++.-...
T Consensus 86 ~L~~~l~~e~~~~~Y~Cp~C~~~-y~~~-ea~~~--~d~~~~f~Cp~Cg~~l~~~dn~~ 140 (147)
T smart00531 86 RLEDKLEDETNNAYYKCPNCQSK-YTFL-EANQL--LDMDGTFTCPRCGEELEEDDNSE 140 (147)
T ss_pred HHHHHHhcccCCcEEECcCCCCE-eeHH-HHHHh--cCCCCcEECCCCCCEEEEcCchh
Confidence 34444333333334459999954 4453 22111 12356699999999999885443
No 24
>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=91.20 E-value=0.32 Score=37.08 Aligned_cols=42 Identities=21% Similarity=0.522 Sum_probs=27.5
Q ss_pred eeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceeee
Q 020384 270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLIT 320 (327)
Q Consensus 270 iLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~it 320 (327)
-|+--||.|+++...| + .+...+.|.+|++.|.--+..+...
T Consensus 5 Fm~VkCp~C~~~q~vF-------S--ha~t~V~C~~Cg~~L~~PtGGKa~l 46 (55)
T PF01667_consen 5 FMDVKCPGCYNIQTVF-------S--HAQTVVKCVVCGTVLAQPTGGKARL 46 (55)
T ss_dssp EEEEE-TTT-SEEEEE-------T--T-SS-EE-SSSTSEEEEE-SSSEEE
T ss_pred EEEEECCCCCCeeEEE-------e--cCCeEEEcccCCCEecCCCCcCeEE
Confidence 3566799999999988 2 3778899999999998776554443
No 25
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=90.60 E-value=0.2 Score=36.84 Aligned_cols=33 Identities=30% Similarity=0.652 Sum_probs=22.0
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
|||=||.+........... .+....+.|+.||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~--~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFD--YGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCC--CCCEEEEEcCCCCC
Confidence 8999999888765332110 00117799999998
No 26
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=90.03 E-value=0.31 Score=52.30 Aligned_cols=28 Identities=29% Similarity=0.553 Sum_probs=23.1
Q ss_pred HHHHHhhh-cCCCccChHHHHHHHHHHhh
Q 020384 147 LEASMAYV-AGKPIMSDEEYDKLKQKLKM 174 (327)
Q Consensus 147 LEA~~AY~-sGkPimsDeeFD~LK~kLk~ 174 (327)
-++-.+|| .|+|+|||+|||.|.++|+.
T Consensus 44 ~~~~~~YY~~~~p~IsD~eYD~L~~eL~~ 72 (689)
T PRK14351 44 REHDHRYYVEADPVIADRAYDALFARLQA 72 (689)
T ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 34455787 57999999999999999973
No 27
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.90 E-value=0.4 Score=34.64 Aligned_cols=35 Identities=31% Similarity=0.825 Sum_probs=26.3
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe-ccceee
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD-SNTRLI 319 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~-s~~R~i 319 (327)
-|.+||.||..- ....++|+.||..+.|- ++.|.+
T Consensus 4 ~C~~Cg~~~~~~-----------~~~~irC~~CG~rIlyK~R~~~~~ 39 (44)
T smart00659 4 ICGECGRENEIK-----------SKDVVRCRECGYRILYKKRTKRLV 39 (44)
T ss_pred ECCCCCCEeecC-----------CCCceECCCCCceEEEEeCCCceE
Confidence 499999997532 34679999999999997 444443
No 28
>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=89.85 E-value=0.39 Score=46.70 Aligned_cols=35 Identities=26% Similarity=0.366 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 96 GELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 96 ge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
-++...--.+=..||..+.+++||+|||.|.++|.
T Consensus 4 ~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~ 38 (307)
T cd00114 4 AELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELR 38 (307)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 34555555556678888999999999999999984
No 29
>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=89.79 E-value=0.099 Score=46.12 Aligned_cols=52 Identities=23% Similarity=0.397 Sum_probs=32.4
Q ss_pred HHHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceee
Q 020384 259 SLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 319 (327)
Q Consensus 259 ~Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~i 319 (327)
.|...+-.+.--.-=-||||+.. ++|.-.+ .+...|++||..|++.-.+..|
T Consensus 96 ~lk~~l~~e~~~~~Y~Cp~c~~r-~tf~eA~--------~~~F~Cp~Cg~~L~~~dn~~~i 147 (158)
T TIGR00373 96 KLREKLEFETNNMFFICPNMCVR-FTFNEAM--------ELNFTCPRCGAMLDYLDNSEAI 147 (158)
T ss_pred HHHHHHhhccCCCeEECCCCCcE-eeHHHHH--------HcCCcCCCCCCEeeeccCHHHH
Confidence 34443333332333459999943 5664222 2689999999999998655544
No 30
>PF14353 CpXC: CpXC protein
Probab=89.24 E-value=0.35 Score=40.39 Aligned_cols=40 Identities=28% Similarity=0.563 Sum_probs=25.6
Q ss_pred CCCCCccccceeccc-cccccC--------CCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGT-ILSISS--------GGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGt-ilsv~s--------~~~~~~~kChvC~t~L~f~ 313 (327)
.||+||++...=+=+ |.+... +++-+.+.|+.||.....+
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 699999986633322 221111 3456899999999876554
No 31
>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=89.19 E-value=0.28 Score=34.45 Aligned_cols=32 Identities=31% Similarity=0.827 Sum_probs=22.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
-||+||.....| + ..+.+.-|.+||..++.+.
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 499999977322 1 3667889999999988764
No 32
>PRK02935 hypothetical protein; Provisional
Probab=89.05 E-value=0.39 Score=41.25 Aligned_cols=39 Identities=15% Similarity=0.326 Sum_probs=28.1
Q ss_pred eeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceee
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 319 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~i 319 (327)
-+..-.||||+.+.+--=+. --|-.|+++|+.|....-.
T Consensus 67 kavqV~CP~C~K~TKmLGrv------------D~CM~C~~PLTLd~~legk 105 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRV------------DACMHCNQPLTLDRSLEGK 105 (110)
T ss_pred cceeeECCCCCchhhhccce------------eecCcCCCcCCcCcccccc
Confidence 34445899999998754211 2599999999999765433
No 33
>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=89.01 E-value=0.22 Score=32.59 Aligned_cols=23 Identities=35% Similarity=0.949 Sum_probs=17.2
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
.||+|+++|- .+-..|+.||-..
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 4999999983 3346799998653
No 34
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=88.59 E-value=0.3 Score=33.80 Aligned_cols=29 Identities=31% Similarity=0.808 Sum_probs=17.0
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
||+||.++-- .|..+.++.+.-|+.||..
T Consensus 3 C~~CG~~l~~------~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLER------RIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EE------E--TT-SS-EEEETTTTEE
T ss_pred cccccChhhh------hcCCCCCccceECCCCCCE
Confidence 9999999632 3466789999999999963
No 35
>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=88.54 E-value=0.36 Score=32.60 Aligned_cols=29 Identities=21% Similarity=0.524 Sum_probs=20.6
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.||+||.+.-...+ ..+.....|+.||..
T Consensus 7 ~C~~Cg~~fe~~~~-------~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 7 RCEDCGHTFEVLQK-------ISDDPLATCPECGGD 35 (41)
T ss_pred EcCCCCCEEEEEEe-------cCCCCCCCCCCCCCc
Confidence 69999996655532 123677889999984
No 36
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=87.81 E-value=0.58 Score=50.13 Aligned_cols=26 Identities=27% Similarity=0.397 Sum_probs=21.7
Q ss_pred HHHHhhh-cCCCccChHHHHHHHHHHh
Q 020384 148 EASMAYV-AGKPIMSDEEYDKLKQKLK 173 (327)
Q Consensus 148 EA~~AY~-sGkPimsDeeFD~LK~kLk 173 (327)
+.-.+|| .|+|+|||++||.|..+|+
T Consensus 18 ~~~~~YY~~~~p~IsD~~YD~L~~eL~ 44 (669)
T PRK14350 18 KWDKEYYVDSSPSVEDFTYDKALLRLQ 44 (669)
T ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 3355677 5799999999999999996
No 37
>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=87.81 E-value=0.69 Score=45.08 Aligned_cols=36 Identities=33% Similarity=0.553 Sum_probs=28.3
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
+-++...-..+=..||..+.++|||+|||.|.++|.
T Consensus 7 i~~L~~~i~~~~~~YY~~~~p~isD~eYD~l~~~L~ 42 (315)
T PF01653_consen 7 IEELRKEINRHNYAYYNLGEPIISDAEYDQLFRELK 42 (315)
T ss_dssp HHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 344555555666789999999999999999998864
No 38
>PLN00209 ribosomal protein S27; Provisional
Probab=87.74 E-value=0.59 Score=38.68 Aligned_cols=44 Identities=18% Similarity=0.449 Sum_probs=34.4
Q ss_pred ccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEecccee
Q 020384 266 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 318 (327)
Q Consensus 266 ~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~ 318 (327)
.|---|+--||.|+.+...| + .+...+.|.+||+.|.--+..+.
T Consensus 30 PnS~Fm~VkCp~C~n~q~VF-------S--hA~t~V~C~~Cg~~L~~PTGGKa 73 (86)
T PLN00209 30 PNSFFMDVKCQGCFNITTVF-------S--HSQTVVVCGSCQTVLCQPTGGKA 73 (86)
T ss_pred CCCEEEEEECCCCCCeeEEE-------e--cCceEEEccccCCEeeccCCCCe
Confidence 34456788899999999988 1 36778999999999987665444
No 39
>smart00532 LIGANc Ligase N family.
Probab=87.57 E-value=0.59 Score=47.73 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=28.7
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
+-++...-..+-..||..+.+++||+|||.|.++|.
T Consensus 5 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 40 (441)
T smart00532 5 ISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELK 40 (441)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH
Confidence 445555555566678889999999999999999995
No 40
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=87.15 E-value=0.17 Score=45.70 Aligned_cols=54 Identities=24% Similarity=0.417 Sum_probs=33.6
Q ss_pred HHHHHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceee
Q 020384 257 SQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 319 (327)
Q Consensus 257 a~~Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~i 319 (327)
...|...+-.+.--.-=-||||+.. |+|.-. -.+...|++||..|++.-.+..|
T Consensus 102 ~~klk~~l~~e~~~~~Y~Cp~C~~r-ytf~eA--------~~~~F~Cp~Cg~~L~~~dn~~~~ 155 (178)
T PRK06266 102 LKKLKEQLEEEENNMFFFCPNCHIR-FTFDEA--------MEYGFRCPQCGEMLEEYDNSELI 155 (178)
T ss_pred HHHHHHHhhhccCCCEEECCCCCcE-EeHHHH--------hhcCCcCCCCCCCCeecccHHHH
Confidence 3344444443333344459999954 566422 23689999999999997554443
No 41
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=86.94 E-value=0.52 Score=33.38 Aligned_cols=34 Identities=24% Similarity=0.579 Sum_probs=21.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEecc
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 315 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~ 315 (327)
-||+||+-+ +. +.....+...|+.||-..--+++
T Consensus 2 FCp~Cg~~l--~~------~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNML--IP------KEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCcc--cc------ccCCCCCEEECCcCCCeEECCCc
Confidence 399999843 22 22233468899999976544433
No 42
>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=86.76 E-value=0.41 Score=49.80 Aligned_cols=54 Identities=22% Similarity=0.407 Sum_probs=38.9
Q ss_pred hhccceeeecCCCCCccccceeccccccccC-CCCccceeCCCCCceeEEeccce
Q 020384 264 IVRESLILKGPCPNCGTENVSFFGTILSISS-GGTTNTINCSNCGTTMVYDSNTR 317 (327)
Q Consensus 264 ~~~D~liLKGpCPNCGeEv~aFfGtilsv~s-~~~~~~~kChvC~t~L~f~s~~R 317 (327)
...|----.-|||+||++..-=|..+.--++ ...+....|+.||+.+.=.-+.+
T Consensus 192 ~~sdqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~ 246 (557)
T PF05876_consen 192 EESDQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRR 246 (557)
T ss_pred HhCCceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhh
Confidence 4466667889999999987755666543222 46778899999999987654443
No 43
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=86.68 E-value=0.75 Score=38.01 Aligned_cols=45 Identities=18% Similarity=0.490 Sum_probs=35.0
Q ss_pred ccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceee
Q 020384 266 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 319 (327)
Q Consensus 266 ~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~i 319 (327)
.|---|+--||.|+.+...| + .+...+.|.+||+.|.--+..+..
T Consensus 29 PnS~Fm~VkCp~C~n~q~VF-------S--hA~t~V~C~~Cg~~L~~PTGGKa~ 73 (85)
T PTZ00083 29 PNSYFMDVKCPGCSQITTVF-------S--HAQTVVLCGGCSSQLCQPTGGKAK 73 (85)
T ss_pred CCCeEEEEECCCCCCeeEEE-------e--cCceEEEccccCCEeeccCCCCeE
Confidence 34456788899999999988 1 367789999999999876655543
No 44
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=86.48 E-value=0.45 Score=41.92 Aligned_cols=40 Identities=28% Similarity=0.635 Sum_probs=30.4
Q ss_pred HHHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 259 SLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 259 ~Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
.|.+++++=+..|--.||-||++.|..=| ++-|++||..-
T Consensus 15 ~iA~lLl~GAkML~~hCp~Cg~PLF~KdG------------~v~CPvC~~~~ 54 (131)
T COG1645 15 KIAELLLQGAKMLAKHCPKCGTPLFRKDG------------EVFCPVCGYRE 54 (131)
T ss_pred HHHHHHHhhhHHHHhhCcccCCcceeeCC------------eEECCCCCceE
Confidence 34466777777788899999999998533 46799999643
No 45
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=85.80 E-value=0.76 Score=48.46 Aligned_cols=36 Identities=28% Similarity=0.535 Sum_probs=28.5
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
+-++...-..+=..||..+.+++||+|||.|.+||.
T Consensus 34 i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 69 (562)
T PRK08097 34 IAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLT 69 (562)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 444555555556679999999999999999999985
No 46
>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=85.00 E-value=0.64 Score=34.83 Aligned_cols=28 Identities=32% Similarity=0.841 Sum_probs=22.3
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.-.||.||..+.. ........|++||..
T Consensus 28 Sq~C~~CG~~~~~----------~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----------RRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCccCccccccc----------ccccceEEcCCCCCE
Confidence 3469999998877 236678999999976
No 47
>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=84.99 E-value=0.79 Score=33.57 Aligned_cols=36 Identities=28% Similarity=0.630 Sum_probs=24.4
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
|||-||.+...|.-. ........-.+|..||.....
T Consensus 3 PCPfCGg~~~~~~~~---~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRG---FDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEec---cCCCCCEEEEECCCCCCCccc
Confidence 899999988866311 012234445699999988766
No 48
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=84.68 E-value=1.1 Score=48.33 Aligned_cols=36 Identities=19% Similarity=0.390 Sum_probs=30.2
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
+-++...--.+=..||..+.+++||+|||.|.++|.
T Consensus 36 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 71 (689)
T PRK14351 36 AEQLREAIREHDHRYYVEADPVIADRAYDALFARLQ 71 (689)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 556666666666779999999999999999999996
No 49
>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=84.64 E-value=0.69 Score=32.33 Aligned_cols=34 Identities=35% Similarity=0.786 Sum_probs=20.7
Q ss_pred CCCCCccccceeccccccccCC--CCccceeCCCCCce
Q 020384 274 PCPNCGTENVSFFGTILSISSG--GTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~--~~~~~~kChvC~t~ 309 (327)
.||+||...-.|| ..-..+. ..+--..|-+||..
T Consensus 2 ~Cp~Cg~~~a~~~--~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHNEAVFF--QIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SSEEEEE--EESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCCCeEEEE--EeeccCCCCCCeEEEEeCCCCCe
Confidence 6999999998888 2222222 34556789999864
No 50
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=84.63 E-value=1.1 Score=47.97 Aligned_cols=36 Identities=31% Similarity=0.504 Sum_probs=28.2
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
+-++...--.+=..||..+.+++||+|||.|.++|.
T Consensus 9 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~ 44 (665)
T PRK07956 9 IEELREELNHHAYAYYVLDAPSISDAEYDRLYRELV 44 (665)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 344444455555678889999999999999999986
No 51
>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=84.33 E-value=0.54 Score=42.65 Aligned_cols=36 Identities=28% Similarity=0.672 Sum_probs=23.8
Q ss_pred CCCCCccccce--eccccccccCCCCccceeCCCCCcee
Q 020384 274 PCPNCGTENVS--FFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 274 pCPNCGeEv~a--FfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
.||||++.+.- ++-+++.+- +....-.-||+||.+.
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g-~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLG-GHYEAPSYCHNCGKPY 78 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeC-CCCCCChhHHhCCCCC
Confidence 59999999983 233444442 2333556799999875
No 52
>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=84.22 E-value=0.79 Score=32.34 Aligned_cols=28 Identities=29% Similarity=0.723 Sum_probs=21.0
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
-|++||.+.-.+. +..+...+.|++||.
T Consensus 7 ~C~~Cg~~fe~~~-------~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQ-------SISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEE-------EcCCCCCCcCCCCCC
Confidence 4999998766663 223478899999998
No 53
>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=83.95 E-value=0.63 Score=32.37 Aligned_cols=33 Identities=30% Similarity=0.580 Sum_probs=23.6
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
-||+||.--...|. -....-+|.+||..|+-|.
T Consensus 3 ~C~~Cg~~Yh~~~~--------pP~~~~~Cd~cg~~L~qR~ 35 (36)
T PF05191_consen 3 ICPKCGRIYHIEFN--------PPKVEGVCDNCGGELVQRK 35 (36)
T ss_dssp EETTTTEEEETTTB----------SSTTBCTTTTEBEBEEG
T ss_pred CcCCCCCccccccC--------CCCCCCccCCCCCeeEeCC
Confidence 39999986555552 2567789999999887654
No 54
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.83 E-value=0.4 Score=42.02 Aligned_cols=35 Identities=31% Similarity=0.819 Sum_probs=24.2
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
|+|-||+|||--. |..-+ +..-.|.+||-.+-|..
T Consensus 20 l~grCP~CGeGrL--F~gFL-------K~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 20 LRGRCPRCGEGRL--FRGFL-------KVVPACEACGLDYGFAD 54 (126)
T ss_pred hcCCCCCCCCchh--hhhhc-------ccCchhhhccccccCCc
Confidence 7899999998643 22222 22347999999888763
No 55
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=83.62 E-value=0.94 Score=31.88 Aligned_cols=34 Identities=35% Similarity=0.854 Sum_probs=23.2
Q ss_pred CCCCCccccceeccccccccCC--CCccceeCCCCCce
Q 020384 274 PCPNCGTENVSFFGTILSISSG--GTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~--~~~~~~kChvC~t~ 309 (327)
+||+||...-.||-. -..+. ..+--..|-+|+-.
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 22332 34556889999853
No 56
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=83.57 E-value=0.84 Score=39.23 Aligned_cols=23 Identities=43% Similarity=1.096 Sum_probs=18.1
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
||.||.+.. ..+.+|.+|++.++
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 999998753 24689999999886
No 57
>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=83.09 E-value=0.87 Score=38.57 Aligned_cols=32 Identities=31% Similarity=0.797 Sum_probs=25.2
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.|--||+||+.-|-. .+.-+-|+.||+...-.
T Consensus 8 tKR~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 577899999986655 33557899999988776
No 58
>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=82.15 E-value=0.63 Score=41.49 Aligned_cols=20 Identities=30% Similarity=0.680 Sum_probs=11.1
Q ss_pred hccceeeecCCCCCccccce
Q 020384 265 VRESLILKGPCPNCGTENVS 284 (327)
Q Consensus 265 ~~D~liLKGpCPNCGeEv~a 284 (327)
+++.+|+...||+||-.+..
T Consensus 23 F~evii~sf~C~~CGyk~~e 42 (161)
T PF03367_consen 23 FKEVIIMSFECEHCGYKNNE 42 (161)
T ss_dssp TEEEEEEEEE-TTT--EEEE
T ss_pred CceEEEEEeECCCCCCEeee
Confidence 56667777777777766553
No 59
>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=80.72 E-value=1.5 Score=46.75 Aligned_cols=27 Identities=26% Similarity=0.411 Sum_probs=23.0
Q ss_pred HHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 104 QALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 104 ~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
.+-..||..+.+++||+|||.|.++|.
T Consensus 7 ~~~~~YY~~~~p~IsD~eYD~L~~~L~ 33 (652)
T TIGR00575 7 HHDYRYYVLDEPSISDAEYDRLYRELQ 33 (652)
T ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 344568888999999999999999985
No 60
>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=80.65 E-value=1.1 Score=39.43 Aligned_cols=32 Identities=19% Similarity=0.319 Sum_probs=24.5
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.|--||+||+.-|-. .+.-+.|+.||+...-.
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 477899999976554 34678899999986544
No 61
>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=80.58 E-value=1.4 Score=31.04 Aligned_cols=30 Identities=43% Similarity=0.978 Sum_probs=19.3
Q ss_pred ecCCCCCccc-cceeccccccccCCCCccceeCCCCCc
Q 020384 272 KGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 272 KGpCPNCGeE-v~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
++|||+||-. -|. |-+ .......-|..|+.
T Consensus 3 ~~pCP~CGG~DrFr-~~d------~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFR-FDD------KDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccc-ccc------CCCCcCEEeCCCCC
Confidence 5899999763 445 322 22346678888863
No 62
>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=80.45 E-value=0.84 Score=37.06 Aligned_cols=32 Identities=28% Similarity=0.568 Sum_probs=18.2
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
..+.||-|++.+-+|. + . .+++..+|+.||..
T Consensus 32 ~~~~CPfH~d~~pS~~--i---~--~~k~~~~Cf~Cg~~ 63 (97)
T PF01807_consen 32 YRCLCPFHDDKTPSFS--I---N--PDKNRFKCFGCGKG 63 (97)
T ss_dssp EEE--SSS--SS--EE--E---E--TTTTEEEETTT--E
T ss_pred EEEECcCCCCCCCceE--E---E--CCCCeEEECCCCCC
Confidence 5688999999988874 2 2 36789999999963
No 63
>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=80.15 E-value=1.7 Score=31.06 Aligned_cols=28 Identities=21% Similarity=0.623 Sum_probs=18.7
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
-|++||.+.-.+. ++ .+.....|++||.
T Consensus 7 ~C~~Cg~~fe~~~----~~---~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQ----KM---SDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEE----ec---CCCCCCCCCCCCC
Confidence 4999997554442 11 1245678999998
No 64
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=79.64 E-value=1.9 Score=46.56 Aligned_cols=25 Identities=36% Similarity=0.616 Sum_probs=21.6
Q ss_pred HHhhhc-CCCccChHHHHHHHHHHhh
Q 020384 150 SMAYVA-GKPIMSDEEYDKLKQKLKM 174 (327)
Q Consensus 150 ~~AY~s-GkPimsDeeFD~LK~kLk~ 174 (327)
..+||- ++|+|+|+|||+|.++|..
T Consensus 22 ~~~Yyv~d~P~VsD~eYD~L~reL~~ 47 (667)
T COG0272 22 DYRYYVLDAPSVSDAEYDQLYRELQE 47 (667)
T ss_pred HHHHhccCCCCCChHHHHHHHHHHHH
Confidence 456666 9999999999999999975
No 65
>PF12773 DZR: Double zinc ribbon
Probab=79.32 E-value=0.93 Score=32.09 Aligned_cols=14 Identities=29% Similarity=0.672 Sum_probs=8.3
Q ss_pred CccceeCCCCCcee
Q 020384 297 TTNTINCSNCGTTM 310 (327)
Q Consensus 297 ~~~~~kChvC~t~L 310 (327)
......|++||+.+
T Consensus 26 ~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 26 DQSKKICPNCGAEN 39 (50)
T ss_pred cCCCCCCcCCcCCC
Confidence 34455677777653
No 66
>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=79.11 E-value=1.3 Score=30.25 Aligned_cols=27 Identities=33% Similarity=0.977 Sum_probs=19.3
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
|..||.+|. + + ....+.|..||..+.|
T Consensus 3 C~~Cg~~~~--~------~---~~~~irC~~CG~RIly 29 (32)
T PF03604_consen 3 CGECGAEVE--L------K---PGDPIRCPECGHRILY 29 (32)
T ss_dssp ESSSSSSE---B------S---TSSTSSBSSSS-SEEB
T ss_pred CCcCCCeeE--c------C---CCCcEECCcCCCeEEE
Confidence 889999987 1 2 2345799999998876
No 67
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=79.04 E-value=1.7 Score=46.62 Aligned_cols=36 Identities=11% Similarity=0.200 Sum_probs=27.1
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
+-++...--..=..||..+.|++||+|||.|.+||.
T Consensus 9 i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~ 44 (669)
T PRK14350 9 ILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQ 44 (669)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 444444444445568889999999999999999984
No 68
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=78.87 E-value=1.5 Score=30.28 Aligned_cols=35 Identities=23% Similarity=0.472 Sum_probs=21.2
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
+-.||||++.-.- ++--+ ....-+++|++|+....
T Consensus 2 ~i~CP~C~~~f~v---~~~~l--~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 2 IITCPNCQTRFRV---PDDKL--PAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EEECCCCCceEEc---CHHHc--ccCCcEEECCCCCcEee
Confidence 3469999975321 11111 13445899999998654
No 69
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=78.85 E-value=1.8 Score=41.02 Aligned_cols=65 Identities=25% Similarity=0.494 Sum_probs=27.5
Q ss_pred HHhhhhHHHHHHHHHHHhhhccceeeecCCCCCccc-cceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 246 WFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 246 ~~~~~P~i~~~a~~Lt~l~~~D~liLKGpCPNCGeE-v~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
|.+.-|+.-..+..+..-+.....-.+|-||.||.. +.+.+... .. ...--.-|+.|++.=.|.+
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 WAALQPFLAALAAALDAALLPPEGWQRGYCPVCGSPPVLSVLRGG---ER-EGKRYLHCSLCGTEWRFVR 211 (290)
T ss_dssp HHHHHHHHHHHHHT--TTSSS---TT-SS-TTT---EEEEEEE----------EEEEEETTT--EEE--T
T ss_pred HHHHHHHHHHHHHhccccccccCCccCCcCCCCCCcCceEEEecC---CC-CccEEEEcCCCCCeeeecC
Confidence 444446666666555444444444567999999987 55665331 11 1224456777777766654
No 70
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=78.47 E-value=1.6 Score=50.05 Aligned_cols=47 Identities=26% Similarity=0.428 Sum_probs=31.0
Q ss_pred cceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccc
Q 020384 267 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 316 (327)
Q Consensus 267 D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~ 316 (327)
++.+-.--||+||++++.+|=..= +........|+.||..+..+..+
T Consensus 662 eVEV~~rkCPkCG~~t~~~fCP~C---Gs~te~vy~CPsCGaev~~des~ 708 (1337)
T PRK14714 662 EVEVGRRRCPSCGTETYENRCPDC---GTHTEPVYVCPDCGAEVPPDESG 708 (1337)
T ss_pred EEEEEEEECCCCCCccccccCccc---CCcCCCceeCccCCCccCCCccc
Confidence 466778899999999988764431 22223345788888877666433
No 71
>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=78.46 E-value=0.91 Score=29.54 Aligned_cols=11 Identities=55% Similarity=1.259 Sum_probs=8.3
Q ss_pred eeecCCCCCcc
Q 020384 270 ILKGPCPNCGT 280 (327)
Q Consensus 270 iLKGpCPNCGe 280 (327)
+..=+|||||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 44568999995
No 72
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=78.38 E-value=1.4 Score=32.60 Aligned_cols=29 Identities=31% Similarity=0.802 Sum_probs=20.4
Q ss_pred eeecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 270 iLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.+.--||+||.+ |... ...+..|..||-.
T Consensus 18 ~~~~fCP~Cg~~---~m~~--------~~~r~~C~~Cgyt 46 (50)
T PRK00432 18 RKNKFCPRCGSG---FMAE--------HLDRWHCGKCGYT 46 (50)
T ss_pred EccCcCcCCCcc---hhec--------cCCcEECCCcCCE
Confidence 456699999987 3211 2268899999965
No 73
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=77.91 E-value=1.2 Score=39.79 Aligned_cols=53 Identities=28% Similarity=0.384 Sum_probs=30.6
Q ss_pred hhccceeeecCCCCCcccccee--ccccccccCCCCcc--ceeCCCCCce----eEEeccceeeecCC
Q 020384 264 IVRESLILKGPCPNCGTENVSF--FGTILSISSGGTTN--TINCSNCGTT----MVYDSNTRLITLPE 323 (327)
Q Consensus 264 ~~~D~liLKGpCPNCGeEv~aF--fGtilsv~s~~~~~--~~kChvC~t~----L~f~s~~R~itl~~ 323 (327)
-+++.+|+...||+||-.+... .|. ..+. +...++.... -++++.+-.|.+||
T Consensus 21 ~F~evii~sf~C~~CGyk~~ev~~~~~-------~~p~G~r~~l~V~~~~DL~r~VvkS~ta~i~IPE 81 (160)
T smart00709 21 YFREVIIMSFECEHCGYRNNEVKSGGA-------IEPKGTRITLKVESPEDLNRDVVKSETATISIPE 81 (160)
T ss_pred CcceEEEEEEECCCCCCccceEEECcc-------cCCCceEEEEEECChhhccceEEEcCCcEEEeee
Confidence 4678888888888888776643 222 1333 4555555432 34445555555554
No 74
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=77.40 E-value=1.8 Score=38.70 Aligned_cols=37 Identities=19% Similarity=0.533 Sum_probs=22.1
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
-||-||.+-..-.-+..--+|+..+-...|.+||+..
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 4999998653332222111333444459999999864
No 75
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=75.25 E-value=2.3 Score=29.38 Aligned_cols=34 Identities=26% Similarity=0.563 Sum_probs=21.2
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
+-.||||++.-. . ++.-| +....+++|++|+...
T Consensus 2 ~i~Cp~C~~~y~-i--~d~~i--p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYE-I--DDEKI--PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEe-C--CHHHC--CCCCcEEECCCCCCEe
Confidence 446999997632 1 11112 2455689999999753
No 76
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=75.01 E-value=2.2 Score=35.88 Aligned_cols=32 Identities=31% Similarity=0.805 Sum_probs=20.9
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
.|||||+... +|.-....-.+.|++||.--..
T Consensus 23 ~CP~Cge~~v-------~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 23 ECPRCGKVSI-------SVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred ECCCCCCeEe-------eeecCCCcceEECCCCCCccCE
Confidence 5999995322 2222335678899999986443
No 77
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.88 E-value=3.5 Score=29.23 Aligned_cols=25 Identities=20% Similarity=0.457 Sum_probs=20.9
Q ss_pred cceeCCCCCceeEEeccceeeecCC
Q 020384 299 NTINCSNCGTTMVYDSNTRLITLPE 323 (327)
Q Consensus 299 ~~~kChvC~t~L~f~s~~R~itl~~ 323 (327)
..++|.+||..++++.....++.|.
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~ 26 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPY 26 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCC
Confidence 4689999999999997766777775
No 78
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=71.82 E-value=5 Score=34.73 Aligned_cols=48 Identities=23% Similarity=0.471 Sum_probs=33.6
Q ss_pred ccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEecccee
Q 020384 266 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 318 (327)
Q Consensus 266 ~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~ 318 (327)
....+.+--||-|+.++ .+- . + ......-+.+|+.|+...+....+++
T Consensus 24 ~~~~~~~~~cP~C~s~~-~~k-~--g-~~~~~~qRyrC~~C~~tf~~~~~~~~ 71 (129)
T COG3677 24 IRMQITKVNCPRCKSSN-VVK-I--G-GIRRGHQRYKCKSCGSTFTVETGSPL 71 (129)
T ss_pred HhhhcccCcCCCCCccc-eee-E--C-CccccccccccCCcCcceeeeccCcc
Confidence 44556677899999999 331 1 1 11223788999999999999876544
No 79
>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=71.06 E-value=2.8 Score=37.68 Aligned_cols=38 Identities=18% Similarity=0.444 Sum_probs=29.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
-||-||.+...-.-+=.+-.++.-+-+-+|.+||...+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 49999998887776655556666778899999998653
No 80
>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=71.04 E-value=1.8 Score=42.48 Aligned_cols=24 Identities=42% Similarity=1.003 Sum_probs=20.2
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
|.|-|||++|.++ +-+|++|++.=
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 7899999999887 45799999863
No 81
>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=70.60 E-value=2.4 Score=28.87 Aligned_cols=18 Identities=39% Similarity=1.141 Sum_probs=12.3
Q ss_pred cceeeec-C---CCCCccccce
Q 020384 267 ESLILKG-P---CPNCGTENVS 284 (327)
Q Consensus 267 D~liLKG-p---CPNCGeEv~a 284 (327)
..+++++ | ||+|||+.++
T Consensus 23 ~~~~i~~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 23 ELIVIENVPALVCPQCGEEYLD 44 (46)
T ss_pred EEEEEeCCCccccccCCCEeeC
Confidence 3455544 5 9999998763
No 82
>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=70.18 E-value=3.8 Score=29.18 Aligned_cols=36 Identities=22% Similarity=0.647 Sum_probs=23.8
Q ss_pred HHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 260 LTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 260 Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
|..+.+.|-++ ||.||......+ + .+...+|..|+.
T Consensus 10 l~~~RW~~g~~----CP~Cg~~~~~~~------~---~~~~~~C~~C~~ 45 (46)
T PF12760_consen 10 LEEIRWPDGFV----CPHCGSTKHYRL------K---TRGRYRCKACRK 45 (46)
T ss_pred HHHhcCCCCCC----CCCCCCeeeEEe------C---CCCeEECCCCCC
Confidence 45554555422 999999833332 2 278999999975
No 83
>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=69.91 E-value=1.9 Score=33.35 Aligned_cols=13 Identities=62% Similarity=1.347 Sum_probs=10.7
Q ss_pred eeecCCCCCcccc
Q 020384 270 ILKGPCPNCGTEN 282 (327)
Q Consensus 270 iLKGpCPNCGeEv 282 (327)
.|.|-|||||-|.
T Consensus 39 ~l~~~CPNCgGel 51 (57)
T PF06906_consen 39 MLNGVCPNCGGEL 51 (57)
T ss_pred HhcCcCcCCCCcc
Confidence 3589999999875
No 84
>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=68.58 E-value=4 Score=32.85 Aligned_cols=37 Identities=22% Similarity=0.481 Sum_probs=20.0
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
=.||.|+.+.-.=. .+........+.|.+||..-++.
T Consensus 23 F~CPfC~~~~sV~v----~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 23 FDCPFCNHEKSVSV----KIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp ---TTT--SS-EEE----EEETTTTEEEEEESSS--EEEEE
T ss_pred EcCCcCCCCCeEEE----EEEccCCEEEEEecCCCCeEEEc
Confidence 36999997765443 22444678899999998766554
No 85
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=68.25 E-value=3.2 Score=37.58 Aligned_cols=23 Identities=30% Similarity=0.928 Sum_probs=17.3
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
-.||+||. + ..-..+|++||...
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 46999999 1 34568999999753
No 86
>smart00400 ZnF_CHCC zinc finger.
Probab=68.21 E-value=2.9 Score=30.44 Aligned_cols=30 Identities=40% Similarity=0.803 Sum_probs=24.0
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
+|.||-+.+.+-+| .|. ..+|...|..||.
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 232 3578899999974
No 87
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=68.09 E-value=7 Score=26.10 Aligned_cols=26 Identities=35% Similarity=0.684 Sum_probs=21.4
Q ss_pred HHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 103 LQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 103 l~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
+..|...|..| .+|+|||...|..|+
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 46677888777 699999999999874
No 88
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=67.55 E-value=4.5 Score=38.32 Aligned_cols=35 Identities=34% Similarity=0.695 Sum_probs=24.8
Q ss_pred ccceeeec----CCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 266 RESLILKG----PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 266 ~D~liLKG----pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
++.+.+.| |||.||+++.... + +.+..+=|++|..
T Consensus 235 ~~~l~Vy~R~g~pC~~Cg~~I~~~~-----~---~gR~t~~CP~CQ~ 273 (274)
T PRK01103 235 QQSLQVYGREGEPCRRCGTPIEKIK-----Q---GGRSTFFCPRCQK 273 (274)
T ss_pred cceeEEcCCCCCCCCCCCCeeEEEE-----E---CCCCcEECcCCCC
Confidence 44455664 8999999987431 1 2478899999974
No 89
>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=67.47 E-value=5.4 Score=28.67 Aligned_cols=38 Identities=26% Similarity=0.674 Sum_probs=26.8
Q ss_pred HHHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCC
Q 020384 259 SLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 307 (327)
Q Consensus 259 ~Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~ 307 (327)
.+.++.++=...|--.||.||.+.+.= ...+.-|.+|+
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 345556666777888999999887651 12356799986
No 90
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=66.67 E-value=4 Score=31.03 Aligned_cols=31 Identities=26% Similarity=0.547 Sum_probs=22.4
Q ss_pred ceeeecCCCCCccccc-eeccccccccCCCCccceeCCCCCce
Q 020384 268 SLILKGPCPNCGTENV-SFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 268 ~liLKGpCPNCGeEv~-aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
+.-++--||+||.-+| +. -.++.-|..||-.
T Consensus 15 v~rk~~~CPrCG~gvfmA~-----------H~dR~~CGkCgyT 46 (51)
T COG1998 15 VKRKNRFCPRCGPGVFMAD-----------HKDRWACGKCGYT 46 (51)
T ss_pred EEEccccCCCCCCcchhhh-----------cCceeEeccccce
Confidence 3456678999999776 44 2337889999864
No 91
>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=65.99 E-value=2.5 Score=38.07 Aligned_cols=46 Identities=30% Similarity=0.580 Sum_probs=23.3
Q ss_pred hhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 264 IVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 264 ~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
-++|..-|+=.||.|++++. |=|...+...........|++|+..+
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 67888999999999999863 32222222233356789999999843
No 92
>PRK12495 hypothetical protein; Provisional
Probab=65.84 E-value=5.4 Score=38.16 Aligned_cols=42 Identities=14% Similarity=0.501 Sum_probs=32.7
Q ss_pred HHHHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 258 QSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 258 ~~Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
+.+..|+++=...+---||.||.+++.+ +...-|.+|+....
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 4466777887888888999999999944 34567999997654
No 93
>PRK04023 DNA polymerase II large subunit; Validated
Probab=65.79 E-value=4.1 Score=46.15 Aligned_cols=14 Identities=36% Similarity=0.914 Sum_probs=8.4
Q ss_pred ecCCCCCcccccee
Q 020384 272 KGPCPNCGTENVSF 285 (327)
Q Consensus 272 KGpCPNCGeEv~aF 285 (327)
.--||.||++.+.|
T Consensus 626 ~RfCpsCG~~t~~f 639 (1121)
T PRK04023 626 RRKCPSCGKETFYR 639 (1121)
T ss_pred CccCCCCCCcCCcc
Confidence 33677777775444
No 94
>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=65.19 E-value=5.4 Score=33.70 Aligned_cols=36 Identities=25% Similarity=0.532 Sum_probs=25.9
Q ss_pred eeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
-.-.-.|++|+.++...-. ....+..|..|+..|++
T Consensus 120 ~~~~~~C~~C~~~~~r~~~--------~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRR--------SKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcCCCCCEeeeecc--------cchhhEECCCCCCEEEE
Confidence 3446679999999865531 14456889999998875
No 95
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=64.65 E-value=4.8 Score=37.56 Aligned_cols=41 Identities=24% Similarity=0.545 Sum_probs=31.2
Q ss_pred hccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceeeecC
Q 020384 265 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLP 322 (327)
Q Consensus 265 ~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~itl~ 322 (327)
.+|+=.++.-|+||+++..- .-+..+|+|||. +.+|.|-.+
T Consensus 142 ~~dlGVI~A~CsrC~~~L~~------------~~~~l~Cp~Cg~-----tEkRKia~~ 182 (188)
T COG1096 142 GNDLGVIYARCSRCRAPLVK------------KGNMLKCPNCGN-----TEKRKIAKD 182 (188)
T ss_pred CCcceEEEEEccCCCcceEE------------cCcEEECCCCCC-----EEeeeeccc
Confidence 58888899999999998754 235689999995 456666544
No 96
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=64.20 E-value=4.6 Score=38.40 Aligned_cols=28 Identities=25% Similarity=0.573 Sum_probs=21.1
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
-|||.||+++..-. . +.+..+-|++|..
T Consensus 245 ~pCprCG~~I~~~~------~--~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPIRRVV------V--AGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCeeEEEE------E--CCCccEECcCCcC
Confidence 39999999996542 1 2488899999963
No 97
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.31 E-value=5.3 Score=34.81 Aligned_cols=26 Identities=38% Similarity=0.888 Sum_probs=19.9
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
--+||.||++... -+.+|++|++...
T Consensus 6 ~~~cPvcg~~~iV--------------TeL~c~~~etTVr 31 (122)
T COG3877 6 INRCPVCGRKLIV--------------TELKCSNCETTVR 31 (122)
T ss_pred CCCCCccccccee--------------EEEecCCCCceEe
Confidence 3589999987532 3679999999864
No 98
>PRK10445 endonuclease VIII; Provisional
Probab=63.14 E-value=5.3 Score=37.82 Aligned_cols=27 Identities=19% Similarity=0.445 Sum_probs=20.6
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCC
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 307 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~ 307 (327)
.+||.||.++..-. + +.+..+-|++|.
T Consensus 236 ~~Cp~Cg~~I~~~~-----~---~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTT-----L---SSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEE-----E---CCCCcEECCCCc
Confidence 58999999987442 2 247888999996
No 99
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.11 E-value=3.3 Score=33.91 Aligned_cols=15 Identities=60% Similarity=1.143 Sum_probs=12.4
Q ss_pred eeecCCCCCccccce
Q 020384 270 ILKGPCPNCGTENVS 284 (327)
Q Consensus 270 iLKGpCPNCGeEv~a 284 (327)
.|.|-|||||-|..+
T Consensus 39 ~l~g~CPnCGGelv~ 53 (84)
T COG3813 39 RLHGLCPNCGGELVA 53 (84)
T ss_pred hhcCcCCCCCchhhc
Confidence 478999999988754
No 100
>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=61.52 E-value=3.5 Score=29.51 Aligned_cols=31 Identities=35% Similarity=0.886 Sum_probs=15.4
Q ss_pred ecCCCCCccccc-eeccccccccCCCCccceeCCCCCc
Q 020384 272 KGPCPNCGTENV-SFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 272 KGpCPNCGeEv~-aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
.+|||+||-.-. ..|.+ .......-|-.|+.
T Consensus 3 h~pCP~CGG~DrFri~~d------~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGGKDRFRIFDD------KDGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT-TTTEEEETT----------S-EEETTTTB
T ss_pred CCCCCCCcCccccccCcC------cccCCCEECCCCCC
Confidence 589999987554 53322 13447788988943
No 101
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.03 E-value=5 Score=36.02 Aligned_cols=38 Identities=24% Similarity=0.645 Sum_probs=25.4
Q ss_pred CCCCCccccc--eeccccccccCCCCccceeCCCCCceeEE
Q 020384 274 PCPNCGTENV--SFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 274 pCPNCGeEv~--aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
.||.|-+.++ -|+-++++.- +.-.--.-|||||+..-+
T Consensus 41 qcp~csasirgd~~vegvlglg-~dye~psfchncgs~fpw 80 (160)
T COG4306 41 QCPICSASIRGDYYVEGVLGLG-GDYEPPSFCHNCGSRFPW 80 (160)
T ss_pred cCCccCCcccccceeeeeeccC-CCCCCcchhhcCCCCCCc
Confidence 5999999998 3455555442 223334579999997654
No 102
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.93 E-value=4.6 Score=43.36 Aligned_cols=12 Identities=33% Similarity=1.005 Sum_probs=7.4
Q ss_pred cceeCCCCCcee
Q 020384 299 NTINCSNCGTTM 310 (327)
Q Consensus 299 ~~~kChvC~t~L 310 (327)
...-|++||+.+
T Consensus 40 ~~~fC~~CG~~~ 51 (645)
T PRK14559 40 DEAHCPNCGAET 51 (645)
T ss_pred ccccccccCCcc
Confidence 334577777764
No 103
>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=60.69 E-value=5.9 Score=37.62 Aligned_cols=34 Identities=32% Similarity=0.712 Sum_probs=23.9
Q ss_pred ccceeeec----CCCCCccccceeccccccccCCCCccceeCCCCC
Q 020384 266 RESLILKG----PCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 307 (327)
Q Consensus 266 ~D~liLKG----pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~ 307 (327)
++-+-++| |||.||+++...- + +.+..+=|++|.
T Consensus 235 ~~~~~Vy~r~g~pC~~Cg~~I~~~~-----~---~gR~t~~CP~CQ 272 (272)
T TIGR00577 235 QQELQVYGRKGEPCRRCGTPIEKIK-----V---GGRGTHFCPQCQ 272 (272)
T ss_pred cceeEEeCCCCCCCCCCCCeeEEEE-----E---CCCCCEECCCCC
Confidence 34445554 8999999997642 1 247888999994
No 104
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=60.58 E-value=5.1 Score=46.74 Aligned_cols=36 Identities=39% Similarity=0.597 Sum_probs=28.2
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
-||||. ++=|-++-++.||=+--.-+|++||+.|.=
T Consensus 910 ~C~~C~---~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~k 945 (1437)
T PRK00448 910 VCPNCK---YSEFFTDGSVGSGFDLPDKDCPKCGTKLKK 945 (1437)
T ss_pred cCcccc---cccccccccccccccCccccCccccccccc
Confidence 399996 444445667888888899999999998753
No 105
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=59.35 E-value=2.4 Score=38.85 Aligned_cols=39 Identities=26% Similarity=0.502 Sum_probs=26.9
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceeee
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLIT 320 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~it 320 (327)
=-||||+... +|=- .-.+...|+.||..|++...++.|+
T Consensus 114 y~C~~~~~r~-sfde--------A~~~~F~Cp~Cg~~L~~~d~s~~i~ 152 (176)
T COG1675 114 YVCPNCHVKY-SFDE--------AMELGFTCPKCGEDLEEYDSSEEIE 152 (176)
T ss_pred eeCCCCCCcc-cHHH--------HHHhCCCCCCCCchhhhccchHHHH
Confidence 3599998764 3411 1234489999999999987776654
No 106
>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=58.88 E-value=5.6 Score=45.62 Aligned_cols=36 Identities=36% Similarity=0.581 Sum_probs=27.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
-||||. ++-|-++.++.||=+--.-+|++||+.|.=
T Consensus 685 ~c~~c~---~~ef~~~~~~~sg~dlp~k~cp~c~~~~~~ 720 (1213)
T TIGR01405 685 LCPNCK---YSEFITDGSVGSGFDLPDKDCPKCGAPLKK 720 (1213)
T ss_pred cCcccc---cccccccccccccccCccccCccccccccc
Confidence 499996 444445567788888888999999998753
No 107
>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=58.14 E-value=5.8 Score=33.40 Aligned_cols=32 Identities=25% Similarity=0.513 Sum_probs=20.6
Q ss_pred cceeeecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 267 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 267 D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
+.+-+.+-|++||.+. .. ..+...|+.||+.-
T Consensus 65 ~~~p~~~~C~~Cg~~~-~~-----------~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 65 EDEPVECECEDCSEEV-SP-----------EIDLYRCPKCHGIM 96 (115)
T ss_pred EeeCcEEEcccCCCEE-ec-----------CCcCccCcCCcCCC
Confidence 3455678999999332 11 12246799999853
No 108
>PHA02540 61 DNA primase; Provisional
Probab=58.00 E-value=13 Score=37.27 Aligned_cols=34 Identities=26% Similarity=0.594 Sum_probs=23.3
Q ss_pred eecCCCCCcccc-----ceeccccccccCCCCccceeCCCCCce
Q 020384 271 LKGPCPNCGTEN-----VSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 271 LKGpCPNCGeEv-----~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.+|.||=||+-. -+|. + ......-..+|++||..
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~--V---~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGW--I---YEKKDGGVFKCHNCGYH 64 (337)
T ss_pred EEecCCCCCCccccCcCCcEE--E---eccCCceEEEecCCCCC
Confidence 999999999944 2563 2 22122447899999963
No 109
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.69 E-value=6.1 Score=34.20 Aligned_cols=16 Identities=19% Similarity=0.613 Sum_probs=11.1
Q ss_pred cceeCCCCCce-eEEec
Q 020384 299 NTINCSNCGTT-MVYDS 314 (327)
Q Consensus 299 ~~~kChvC~t~-L~f~s 314 (327)
....|+.||+. +....
T Consensus 106 ~~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 106 AFLKCPKCGSRDFEIVK 122 (135)
T ss_pred cCcCCcCCCCCCcEEec
Confidence 44679999975 55544
No 110
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=57.47 E-value=6.3 Score=39.55 Aligned_cols=31 Identities=29% Similarity=0.566 Sum_probs=24.7
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
.+|.||-|++..-+|. |. ...+..+|+.||.
T Consensus 33 ~~~~CPfh~ek~pSf~-----v~--~~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 33 YVGLCPFHHEKTPSFS-----VS--PEKQFYHCFGCGA 63 (415)
T ss_pred eEeeCCCCCCCCCeEE-----EE--cCCCcEEECCCCC
Confidence 4589999999998884 22 2567899999986
No 111
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=57.24 E-value=7.3 Score=37.20 Aligned_cols=27 Identities=33% Similarity=0.699 Sum_probs=20.9
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCC
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 307 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~ 307 (327)
-|||.||+++..-. + +.+..+=|++|.
T Consensus 255 ~pC~~Cg~~I~~~~-----~---~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIK-----L---AGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEE-----E---CCCccEECCCCc
Confidence 39999999987542 2 247889999996
No 112
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=56.99 E-value=12 Score=40.65 Aligned_cols=38 Identities=24% Similarity=0.358 Sum_probs=30.8
Q ss_pred cchhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 93 KSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 93 ~slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
+-+.++.+.-.+.-.+||..+.|.++|.|||.|..||.
T Consensus 9 ~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~ 46 (667)
T COG0272 9 EEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQ 46 (667)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCCChHHHHHHHHHHH
Confidence 34566666666667789999999999999999988874
No 113
>PRK04011 peptide chain release factor 1; Provisional
Probab=56.89 E-value=4.8 Score=40.67 Aligned_cols=36 Identities=25% Similarity=0.545 Sum_probs=27.4
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.--||+||.+..-++ ..........|+.||..++..
T Consensus 328 ~~~c~~c~~~~~~~~------~~~~~~~~~~c~~~~~~~~~~ 363 (411)
T PRK04011 328 TYKCPNCGYEEEKTV------KRREELPEKTCPKCGSELEIV 363 (411)
T ss_pred EEEcCCCCcceeeec------ccccccccccCcccCcccccc
Confidence 456999998887775 333466778999999988764
No 114
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=56.57 E-value=6.9 Score=34.48 Aligned_cols=32 Identities=25% Similarity=0.737 Sum_probs=24.3
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
--||.||.+-..+... +...-.+|..||..-.
T Consensus 103 VlC~~C~spdT~l~k~-------~r~~~l~C~ACGa~~~ 134 (138)
T PRK03988 103 VICPECGSPDTKLIKE-------GRIWVLKCEACGAETP 134 (138)
T ss_pred EECCCCCCCCcEEEEc-------CCeEEEEcccCCCCCc
Confidence 3499999999888422 3467899999997643
No 115
>PHA02998 RNA polymerase subunit; Provisional
Probab=56.48 E-value=9 Score=35.92 Aligned_cols=37 Identities=22% Similarity=0.647 Sum_probs=27.1
Q ss_pred eecCCCCCccccceeccccccccCCCCccc--eeCCCCCce
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNT--INCSNCGTT 309 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~--~kChvC~t~ 309 (327)
....||.||...-.|+ .+-+.|...+.. ++|..||-.
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 3578999998888876 455566665544 689999854
No 116
>PF15616 TerY-C: TerY-C metal binding domain
Probab=56.09 E-value=10 Score=33.48 Aligned_cols=47 Identities=23% Similarity=0.632 Sum_probs=32.0
Q ss_pred cceeeecCCCCCccc-ccee--ccccccccCCCCccceeCCCCCceeEEeccc
Q 020384 267 ESLILKGPCPNCGTE-NVSF--FGTILSISSGGTTNTINCSNCGTTMVYDSNT 316 (327)
Q Consensus 267 D~liLKGpCPNCGeE-v~aF--fGtilsv~s~~~~~~~kChvC~t~L~f~s~~ 316 (327)
+-+|=..-||.||++ .++- =|-++=+. ..+.+-|+.||....|....
T Consensus 72 seL~g~PgCP~CGn~~~fa~C~CGkl~Ci~---g~~~~~CPwCg~~g~~~~~~ 121 (131)
T PF15616_consen 72 SELIGAPGCPHCGNQYAFAVCGCGKLFCID---GEGEVTCPWCGNEGSFGAGD 121 (131)
T ss_pred HHhcCCCCCCCCcChhcEEEecCCCEEEeC---CCCCEECCCCCCeeeecccC
Confidence 334455899999998 3322 13333343 45699999999999998653
No 117
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=55.68 E-value=6.7 Score=45.39 Aligned_cols=12 Identities=17% Similarity=0.841 Sum_probs=10.2
Q ss_pred ceeCCCCCceeE
Q 020384 300 TINCSNCGTTMV 311 (327)
Q Consensus 300 ~~kChvC~t~L~ 311 (327)
..+|+.||+.++
T Consensus 709 a~~CP~CGtplv 720 (1337)
T PRK14714 709 RVECPRCDVELT 720 (1337)
T ss_pred cccCCCCCCccc
Confidence 668999999875
No 118
>PHA02942 putative transposase; Provisional
Probab=55.06 E-value=8.3 Score=38.61 Aligned_cols=27 Identities=30% Similarity=0.837 Sum_probs=19.1
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
--||+||..+.. + +....+|.+||..+
T Consensus 326 q~Cs~CG~~~~~-----l------~~r~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKMVE-----I------AHRYFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCccCc-----C------CCCEEECCCCCCEe
Confidence 349999987631 1 12369999999865
No 119
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=55.03 E-value=8.1 Score=36.79 Aligned_cols=28 Identities=36% Similarity=0.851 Sum_probs=21.7
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
|||.||+++..-. + +.+..+-|++|...
T Consensus 237 pC~~Cg~~I~~~~-----~---~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTPIEKIV-----V---GGRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCeeEEEE-----E---CCCCcEECCCCcCC
Confidence 8999999987542 1 24788999999864
No 120
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=54.21 E-value=13 Score=40.70 Aligned_cols=24 Identities=33% Similarity=0.987 Sum_probs=16.0
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
+.||.||+ ...|= . -=..|++||-
T Consensus 725 ~~Cp~Cg~-~l~~~-------~----GC~~C~~CG~ 748 (752)
T PRK08665 725 GACPECGS-ILEHE-------E----GCVVCHSCGY 748 (752)
T ss_pred CCCCCCCc-ccEEC-------C----CCCcCCCCCC
Confidence 56999994 55552 2 2347999984
No 121
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=53.16 E-value=6.6 Score=36.98 Aligned_cols=33 Identities=33% Similarity=0.757 Sum_probs=23.3
Q ss_pred eeeecCCCCCccccc--------eeccccccccCCCCccceeCCCCCc
Q 020384 269 LILKGPCPNCGTENV--------SFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 269 liLKGpCPNCGeEv~--------aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
..-...||.||.... -|||.++ -...-|.+||-
T Consensus 11 ~~~~~~CPvCg~~l~~~~~~~~IPyFG~V~-------i~t~~C~~CgY 51 (201)
T COG1779 11 FETRIDCPVCGGTLKAHMYLYDIPYFGEVL-------ISTGVCERCGY 51 (201)
T ss_pred eeeeecCCcccceeeEEEeeecCCccceEE-------EEEEEccccCC
Confidence 445679999998644 3677764 34578999984
No 122
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=52.99 E-value=9.9 Score=37.20 Aligned_cols=19 Identities=16% Similarity=0.564 Sum_probs=16.4
Q ss_pred CccceeCCCCCceeEEecc
Q 020384 297 TTNTINCSNCGTTMVYDSN 315 (327)
Q Consensus 297 ~~~~~kChvC~t~L~f~s~ 315 (327)
=+...+||.|+..++|+|+
T Consensus 74 ~rF~~kC~~C~~~i~~kTD 92 (324)
T PF04502_consen 74 YRFYIKCPRCSNEIEFKTD 92 (324)
T ss_pred EEEEEEcCCCCCEEeeecC
Confidence 4678899999999999973
No 123
>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=52.95 E-value=10 Score=30.81 Aligned_cols=70 Identities=27% Similarity=0.307 Sum_probs=49.3
Q ss_pred hHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhhh-cCCeeEEeChhhHHHHHHHHh-hhcC-------CCccChHHH
Q 020384 96 GELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMW-EGSSVVMLSSAEQKFLEASMA-YVAG-------KPIMSDEEY 165 (327)
Q Consensus 96 ge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~w-eGSsvv~L~~~Eq~fLEA~~A-Y~sG-------kPimsDeeF 165 (327)
++..+.--+++.+|+..|++...-|.|..|..=..= .|..++.+..+..+-|-+-.+ ..+. .|+|+|+|+
T Consensus 11 ~~~~~~~~~~~~~~~~~G~~~~~peG~~~l~rw~~~~~g~g~~i~eadd~~~l~~~~~~W~~~fg~~~ei~Pv~~d~e~ 89 (91)
T PF11746_consen 11 GESQQEAYKAFERFMESGAPGDPPEGFKVLGRWHDPGGGRGFAIVEADDAKALFKHFAPWRDLFGMEFEITPVMTDEEA 89 (91)
T ss_pred cccchhHHHHHHHHHhcCCCCCCCCCEEEEEEEEecCCCcEEEEEEeCCHHHHHHHHhhhhhccCceEEEEecccHHHh
Confidence 455566778999999999887777777665442222 667777777777666666554 4444 699999997
No 124
>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=52.80 E-value=8.9 Score=39.55 Aligned_cols=27 Identities=26% Similarity=0.673 Sum_probs=16.9
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
||||+....-. ...+..+||.||....
T Consensus 225 C~~C~~~l~~h----------~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 225 CPNCDVSLTYH----------KKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCceEEe----------cCCCeEEcCCCcCcCC
Confidence 88886543222 2456788888886654
No 125
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=52.13 E-value=11 Score=26.26 Aligned_cols=27 Identities=37% Similarity=0.762 Sum_probs=16.8
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
.||.|+.+.....- ....-..|+.|+=
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 39999997664421 1233345999974
No 126
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=52.12 E-value=11 Score=30.58 Aligned_cols=27 Identities=33% Similarity=0.600 Sum_probs=17.0
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCC
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 307 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~ 307 (327)
|-+||+||..++.= .....---|+||.
T Consensus 1 K~~CPCCg~~Tl~~---------~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 1 KYPCPCCGYYTLEE---------RGEGTYDICPVCF 27 (78)
T ss_pred CccCCCCCcEEecc---------CCCcCceECCCCC
Confidence 56899999866532 1111245699996
No 127
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=51.74 E-value=12 Score=32.22 Aligned_cols=38 Identities=32% Similarity=0.646 Sum_probs=29.1
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
=.||-||.|..+-= +|.-......+-|.+||-..+++.
T Consensus 23 FtCp~Cghe~vs~c----tvkk~~~~g~~~Cg~CGls~e~ev 60 (104)
T COG4888 23 FTCPRCGHEKVSSC----TVKKTVNIGTAVCGNCGLSFECEV 60 (104)
T ss_pred EecCccCCeeeeEE----EEEecCceeEEEcccCcceEEEec
Confidence 36999999988632 345556777899999999888763
No 128
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=51.37 E-value=11 Score=30.58 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=18.5
Q ss_pred CCCCcc-ccceeccccc-cccCC---CCccceeCCCCCcee
Q 020384 275 CPNCGT-ENVSFFGTIL-SISSG---GTTNTINCSNCGTTM 310 (327)
Q Consensus 275 CPNCGe-Ev~aFfGtil-sv~s~---~~~~~~kChvC~t~L 310 (327)
||.||. +...-+.+.. +..+- -..+-..|+.||..+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 999994 3332222211 11111 134556899999863
No 129
>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=51.17 E-value=6.4 Score=27.09 Aligned_cols=28 Identities=25% Similarity=0.625 Sum_probs=17.0
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
||.||.=.+ ++.+...+. .|..|+-.-.
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 899986443 344444444 8999986543
No 130
>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=51.13 E-value=13 Score=28.90 Aligned_cols=20 Identities=35% Similarity=0.717 Sum_probs=17.1
Q ss_pred cCCCccChHHHHHHHHHHhh
Q 020384 155 AGKPIMSDEEYDKLKQKLKM 174 (327)
Q Consensus 155 sGkPimsDeeFD~LK~kLk~ 174 (327)
.-.|||++++|+++...|+.
T Consensus 82 ~~~~IIs~~~f~~vq~~l~~ 101 (102)
T PF07508_consen 82 YHPPIISEEEFERVQKKLDE 101 (102)
T ss_pred CCCCccCHHHHHHHHHHHhc
Confidence 34699999999999999863
No 131
>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=50.92 E-value=7.9 Score=43.87 Aligned_cols=28 Identities=36% Similarity=0.795 Sum_probs=22.5
Q ss_pred cceeeecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 267 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 267 D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
+..+-.--||+||++.+.+ .|++||+.-
T Consensus 620 ~vev~~RKCPkCG~yTlk~----------------rCP~CG~~T 647 (1095)
T TIGR00354 620 EVEIAIRKCPQCGKESFWL----------------KCPVCGELT 647 (1095)
T ss_pred EEEEEEEECCCCCcccccc----------------cCCCCCCcc
Confidence 5778888999999985544 699999773
No 132
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=50.67 E-value=9.5 Score=33.42 Aligned_cols=32 Identities=19% Similarity=0.590 Sum_probs=23.4
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
.--||.|+.+-..+... +...-.+|..||..-
T Consensus 97 yVlC~~C~sPdT~l~k~-------~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 97 YVICRECNRPDTRIIKE-------GRVSLLKCEACGAKA 128 (133)
T ss_pred eEECCCCCCCCcEEEEe-------CCeEEEecccCCCCC
Confidence 33499999999888532 234567999999753
No 133
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=50.62 E-value=8.9 Score=32.27 Aligned_cols=35 Identities=17% Similarity=0.317 Sum_probs=21.4
Q ss_pred cceeeecCCCCCccccceeccccccccCCCCccceeCCCCCce-eEEe
Q 020384 267 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT-MVYD 313 (327)
Q Consensus 267 D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~-L~f~ 313 (327)
+.+-+.+-|++||.+.- + ..+...|+.||+. ....
T Consensus 65 ~~vp~~~~C~~Cg~~~~--------~----~~~~~~CP~Cgs~~~~i~ 100 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVE--------I----HQHDAQCPHCHGERLRVD 100 (113)
T ss_pred EeeCcEEEcccCCCEEe--------c----CCcCccCcCCCCCCcEEc
Confidence 34557889999994321 1 1234459999964 3443
No 134
>PRK05667 dnaG DNA primase; Validated
Probab=50.46 E-value=9.5 Score=40.31 Aligned_cols=31 Identities=32% Similarity=0.642 Sum_probs=25.2
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
.+|.||-|++..-+|. |. ..++..+|..||.
T Consensus 35 ~~~~CPfH~ektpSf~-----V~--~~k~~~~CF~Cg~ 65 (580)
T PRK05667 35 YKGLCPFHDEKTPSFT-----VS--PDKQFYHCFGCGA 65 (580)
T ss_pred eeecCCCCCCCCCceE-----EE--CCCCeEEECCCCC
Confidence 5799999999998983 33 2577899999986
No 135
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=49.54 E-value=7.8 Score=29.69 Aligned_cols=13 Identities=46% Similarity=0.966 Sum_probs=8.4
Q ss_pred eecCCCCCccccc
Q 020384 271 LKGPCPNCGTENV 283 (327)
Q Consensus 271 LKGpCPNCGeEv~ 283 (327)
||..||+||++..
T Consensus 16 Lk~~CP~CG~~t~ 28 (56)
T PRK13130 16 LKEICPVCGGKTK 28 (56)
T ss_pred ccccCcCCCCCCC
Confidence 4666777776654
No 136
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=49.37 E-value=11 Score=28.69 Aligned_cols=20 Identities=40% Similarity=1.095 Sum_probs=15.0
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCC
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 307 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~ 307 (327)
-.||+||+-...- .-|.+||
T Consensus 28 ~~C~~CG~~~~~H---------------~vC~~CG 47 (57)
T PRK12286 28 VECPNCGEPKLPH---------------RVCPSCG 47 (57)
T ss_pred eECCCCCCccCCe---------------EECCCCC
Confidence 4599999876553 3588998
No 137
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=48.77 E-value=13 Score=27.96 Aligned_cols=30 Identities=30% Similarity=0.801 Sum_probs=22.9
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
-|-.||.++ .+ ....-.+.|+.||..+-|-
T Consensus 8 ~C~~Cg~~~-----~~-----~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 8 KCARCGREV-----EL-----DQETRGIRCPYCGSRILVK 37 (49)
T ss_pred EhhhcCCee-----eh-----hhccCceeCCCCCcEEEEe
Confidence 488999988 21 1356678999999998886
No 138
>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=48.74 E-value=65 Score=29.39 Aligned_cols=57 Identities=21% Similarity=0.388 Sum_probs=40.2
Q ss_pred HHHhhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhcCCc-eeeecC
Q 020384 120 EEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSE-IVVEGP 184 (327)
Q Consensus 120 eefd~LkEeL~weGSsvv~L~~~Eq~fLEA~~AY~sGkPimsDeeFD~LK~kLk~~GS~-VVvk~P 184 (327)
+..+.++++| .....+++.+..|-+.| .|.++-+.++..+.-.+|...|-+ |++++-
T Consensus 115 ~~~~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~a~~l~~~g~~~Vvvt~G 172 (254)
T TIGR00097 115 EAIEALRKRL-LPLATLITPNLPEAEAL-------LGTKIRTEQDMIKAAKKLRELGPKAVLIKGG 172 (254)
T ss_pred HHHHHHHHhc-cccccEecCCHHHHHHH-------hCCCCCCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 3445566654 35677999999998877 356666767777777888877865 777754
No 139
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=48.48 E-value=10 Score=34.51 Aligned_cols=38 Identities=21% Similarity=0.566 Sum_probs=31.2
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
-||-|+.+-..-.-+-.+-.|+..+-+-+|.+||...+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 49999999888776666667778888999999998653
No 140
>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=48.02 E-value=11 Score=39.19 Aligned_cols=45 Identities=22% Similarity=0.281 Sum_probs=30.5
Q ss_pred eeeecCCCCCccccceeccccccccCCCCc-cceeCCCCCceeEEeccc
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTT-NTINCSNCGTTMVYDSNT 316 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~-~~~kChvC~t~L~f~s~~ 316 (327)
.|..--||||-+++-+= ......++-. |=..|++|...|...+..
T Consensus 23 Ei~~~yCp~CL~~~p~~---e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~ 68 (483)
T PF05502_consen 23 EIDSYYCPNCLFEVPSS---EARSEKNRCSRNCFDCPICFSPLSVRASD 68 (483)
T ss_pred ccceeECccccccCChh---hheeccceeccccccCCCCCCcceeEecc
Confidence 44556799999888642 1111344444 778999999999988543
No 141
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=47.90 E-value=10 Score=38.26 Aligned_cols=27 Identities=22% Similarity=0.533 Sum_probs=20.1
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.||.|+.-+ + ...++.|+.||+.|.-+
T Consensus 217 ~C~~Cd~~~----------~---~~~~a~CpRC~~~L~~~ 243 (403)
T TIGR00155 217 SCSACHTTI----------L---PAQEPVCPRCSTPLYVR 243 (403)
T ss_pred cCCCCCCcc----------C---CCCCcCCcCCCCcccCC
Confidence 499999944 1 23578899999999444
No 142
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=47.35 E-value=10 Score=38.67 Aligned_cols=48 Identities=15% Similarity=0.241 Sum_probs=27.1
Q ss_pred cChHHHhhhHhhhhhc-CCeeEEeChhhHHHHHHH--H--hhhcCCCccChHHH
Q 020384 117 MSNEEFDNLKEELMWE-GSSVVMLSSAEQKFLEAS--M--AYVAGKPIMSDEEY 165 (327)
Q Consensus 117 ~sdeefd~LkEeL~we-GSsvv~L~~~Eq~fLEA~--~--AY~sGkPimsDeeF 165 (327)
+|.+-++.+|+++.-+ |.....++ ++.-.|-.. . .|.+=.|-=|-..|
T Consensus 84 isp~Avelik~Nv~~N~~~~~~v~n-~DAN~lm~~~~~~fd~IDiDPFGSPaPF 136 (380)
T COG1867 84 ISPKAVELIKENVRLNSGEDAEVIN-KDANALLHELHRAFDVIDIDPFGSPAPF 136 (380)
T ss_pred CCHHHHHHHHHHHHhcCcccceeec-chHHHHHHhcCCCccEEecCCCCCCchH
Confidence 3456778888887777 77766666 333322222 1 25555555555555
No 143
>PRK05580 primosome assembly protein PriA; Validated
Probab=46.90 E-value=13 Score=39.79 Aligned_cols=28 Identities=21% Similarity=0.685 Sum_probs=17.2
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
-||||+... .|- ...+...||.||....
T Consensus 392 ~C~~C~~~l-~~h---------~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 392 ECPHCDASL-TLH---------RFQRRLRCHHCGYQEP 419 (679)
T ss_pred CCCCCCCce-eEE---------CCCCeEECCCCcCCCC
Confidence 588887743 332 1356677888876543
No 144
>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=46.85 E-value=12 Score=28.22 Aligned_cols=13 Identities=38% Similarity=0.892 Sum_probs=9.2
Q ss_pred cCCCCCcccccee
Q 020384 273 GPCPNCGTENVSF 285 (327)
Q Consensus 273 GpCPNCGeEv~aF 285 (327)
..||+||+....-
T Consensus 27 ~~C~~cG~~~~~H 39 (55)
T TIGR01031 27 VVCPNCGEFKLPH 39 (55)
T ss_pred eECCCCCCcccCe
Confidence 3499999965543
No 145
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=46.77 E-value=15 Score=39.60 Aligned_cols=60 Identities=23% Similarity=0.392 Sum_probs=36.3
Q ss_pred HHhhhccceeeecCCCCCccccceeccccccccCCC----CccceeCCCCCceeEEeccceeee
Q 020384 261 TKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG----TTNTINCSNCGTTMVYDSNTRLIT 320 (327)
Q Consensus 261 t~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~----~~~~~kChvC~t~L~f~s~~R~it 320 (327)
..+...|..=-.-+||.||++-.==|+...+-.+.. .....-||.|++.+......|=|-
T Consensus 216 ~~y~~gd~rr~yvpCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~~~~~~gv~ 279 (611)
T COG5525 216 RAYNAGDQRRFYVPCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPKLNGRGVC 279 (611)
T ss_pred HHhhhccceeEEeeCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeeeeccCccch
Confidence 334566888888999999997653332221111111 334458999999998843333333
No 146
>PRK04023 DNA polymerase II large subunit; Validated
Probab=45.75 E-value=11 Score=43.00 Aligned_cols=39 Identities=23% Similarity=0.485 Sum_probs=25.7
Q ss_pred eeecCCCCCccccc-eeccccccccCCCCccceeCCCCCceeEE
Q 020384 270 ILKGPCPNCGTENV-SFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 270 iLKGpCPNCGeEv~-aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
...-.||+||+... .+|=. .-+...+..+|++||..+.=
T Consensus 636 t~~frCP~CG~~Te~i~fCP----~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 636 TFYRRCPFCGTHTEPVYRCP----RCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred CCcccCCCCCCCCCcceeCc----cccCcCCCCcCCCCCCCCCc
Confidence 36679999998743 33433 22334455779999998763
No 147
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=45.12 E-value=13 Score=31.62 Aligned_cols=28 Identities=25% Similarity=0.813 Sum_probs=22.2
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
-||.|+.+-..+... +...-.+|..||.
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 499999998877532 3567889999996
No 148
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=45.09 E-value=16 Score=37.42 Aligned_cols=43 Identities=23% Similarity=0.529 Sum_probs=31.0
Q ss_pred ccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceeeecCC
Q 020384 266 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE 323 (327)
Q Consensus 266 ~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~itl~~ 323 (327)
-|..|- -||+|..+ -. -+-+-+|++||+..++-+..-.+..|+
T Consensus 53 Ad~~i~--kC~~c~~~-~~------------y~~~~~C~~cg~~~~l~R~VSfVDaPG 95 (415)
T COG5257 53 ADAKIY--KCPECYRP-EC------------YTTEPKCPNCGAETELVRRVSFVDAPG 95 (415)
T ss_pred ccCceE--eCCCCCCC-cc------------cccCCCCCCCCCCccEEEEEEEeeCCc
Confidence 455444 59999876 22 234568999999999988777777665
No 149
>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=44.66 E-value=17 Score=31.48 Aligned_cols=31 Identities=26% Similarity=0.761 Sum_probs=24.1
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.--||.|+.+-..+... +...-.+|..||..
T Consensus 93 yVlC~~C~spdT~l~k~-------~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKE-------GRLIFLKCKACGAS 123 (125)
T ss_dssp HSSCTSTSSSSEEEEEE-------TTCCEEEETTTSCE
T ss_pred EEEcCCCCCCccEEEEc-------CCEEEEEecccCCc
Confidence 34599999998777533 46688999999975
No 150
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=43.13 E-value=11 Score=29.18 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=17.1
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCC-CCCceeE
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCS-NCGTTMV 311 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kCh-vC~t~L~ 311 (327)
.-|||||+++- +++.-|+ .|+....
T Consensus 4 kHC~~CG~~Ip--------------~~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKPIP--------------PDESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCcCC--------------cchhhhCHHHHHHHH
Confidence 36999998764 3566784 7776543
No 151
>PRK14873 primosome assembly protein PriA; Provisional
Probab=43.12 E-value=15 Score=39.50 Aligned_cols=67 Identities=13% Similarity=0.271 Sum_probs=37.7
Q ss_pred HHHhhhHhhhhhcCCeeEEeChh---hHHHHHHHHhhhcCCCc------cChHH-HHHHHHHHhhcCCceeeecCeeee
Q 020384 120 EEFDNLKEELMWEGSSVVMLSSA---EQKFLEASMAYVAGKPI------MSDEE-YDKLKQKLKMEGSEIVVEGPRCSL 188 (327)
Q Consensus 120 eefd~LkEeL~weGSsvv~L~~~---Eq~fLEA~~AY~sGkPi------msDee-FD~LK~kLk~~GS~VVvk~PrCsl 188 (327)
|-|-.+=++...+|.++++|=|+ -.++.++..++|.+.++ +++.+ |+.- .+++ .|..-+|-|.|-.+
T Consensus 175 evyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w-~~~~-~G~~~IViGtRSAv 251 (665)
T PRK14873 175 RRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRW-LAVL-RGQARVVVGTRSAV 251 (665)
T ss_pred HHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHH-HHHh-CCCCcEEEEcceeE
Confidence 44666666667788775555544 25667777778863444 44443 3332 2232 67655566666433
No 152
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.05 E-value=13 Score=31.35 Aligned_cols=30 Identities=17% Similarity=0.350 Sum_probs=18.9
Q ss_pred eeeecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
+=..+-|++||. +|.. ...+...|+.||+.
T Consensus 67 ~p~~~~C~~Cg~----~~~~-------~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQ----YVTL-------LTQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCC----eeec-------CCccCCcCcCcCCC
Confidence 346788999995 3311 01223679999975
No 153
>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=43.03 E-value=26 Score=31.73 Aligned_cols=26 Identities=15% Similarity=0.408 Sum_probs=17.2
Q ss_pred ccceeCCCCCceeEEeccceeeecCC
Q 020384 298 TNTINCSNCGTTMVYDSNTRLITLPE 323 (327)
Q Consensus 298 ~~~~kChvC~t~L~f~s~~R~itl~~ 323 (327)
.+..+|..|+..-......+..++|+
T Consensus 180 ~~~~~C~~C~~~~~~~~~~~i~~~P~ 205 (304)
T cd02661 180 ENKYKCERCKKKVKASKQLTIHRAPN 205 (304)
T ss_pred CCCeeCCCCCCccceEEEEEEecCCc
Confidence 34578999998765555555556664
No 154
>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=42.89 E-value=19 Score=23.77 Aligned_cols=26 Identities=23% Similarity=0.553 Sum_probs=12.0
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
-||.||.+...- ..-..-.|+.|+..
T Consensus 5 fC~~CG~~t~~~----------~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPA----------PGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-----------SSSS-EEESSSS-E
T ss_pred ccCcCCccccCC----------CCcCEeECCCCcCE
Confidence 478888776543 12345667777753
No 155
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=41.87 E-value=20 Score=35.71 Aligned_cols=38 Identities=24% Similarity=0.430 Sum_probs=21.4
Q ss_pred ecCCCCCcc-ccceeccccccccCCCC-----------ccceeCCCCCce
Q 020384 272 KGPCPNCGT-ENVSFFGTILSISSGGT-----------TNTINCSNCGTT 309 (327)
Q Consensus 272 KGpCPNCGe-Ev~aFfGtilsv~s~~~-----------~~~~kChvC~t~ 309 (327)
-+-||-||. +|-+++-.--+-+|-+= -.++||.|||..
T Consensus 185 ~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t 234 (308)
T COG3058 185 RQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQS 234 (308)
T ss_pred cccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhcccccc
Confidence 468999996 55566421101111111 247899999864
No 156
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=41.35 E-value=19 Score=42.29 Aligned_cols=35 Identities=26% Similarity=0.496 Sum_probs=26.8
Q ss_pred hccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEecc
Q 020384 265 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 315 (327)
Q Consensus 265 ~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~ 315 (327)
.-+..+-..-||+||++-+ ...|++||+..+-...
T Consensus 667 ~~~vei~~~~Cp~Cg~~~~----------------~~~Cp~CG~~~~~~~~ 701 (1627)
T PRK14715 667 TDDIEIAFFKCPKCGKVGL----------------YHVCPFCGTRVELKPY 701 (1627)
T ss_pred cceEEEEeeeCCCCCCccc----------------cccCcccCCcccCCCc
Confidence 3467789999999998743 3469999999766643
No 157
>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=41.12 E-value=19 Score=36.72 Aligned_cols=42 Identities=26% Similarity=0.582 Sum_probs=23.9
Q ss_pred ecCCCCCccccceeccccccccCCCC------ccceeCCCCCceeEEeccce
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGT------TNTINCSNCGTTMVYDSNTR 317 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~------~~~~kChvC~t~L~f~s~~R 317 (327)
+|-||.||.+- -+|++- +..+. -..-.|.-||+.++++.+..
T Consensus 136 ~g~cp~c~~~~--~~g~~c--e~cg~~~~~~~l~~p~~~~~~~~~e~~~~~~ 183 (530)
T TIGR00398 136 EGTCPKCGSED--ARGDHC--EVCGRHLEPTELINPRCKICGAKPELRDSEH 183 (530)
T ss_pred cCCCCCCCCcc--cccchh--hhccccCCHHHhcCCccccCCCcceEEecce
Confidence 58899998862 223332 11111 12235778888888875443
No 158
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=40.49 E-value=18 Score=34.29 Aligned_cols=28 Identities=21% Similarity=0.431 Sum_probs=20.5
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.--||.||.+.... .....-.|+.|+..
T Consensus 99 ~~fC~~CG~~~~~~----------~~~~~~~C~~c~~~ 126 (256)
T PRK00241 99 HRFCGYCGHPMHPS----------KTEWAMLCPHCRER 126 (256)
T ss_pred CccccccCCCCeec----------CCceeEECCCCCCE
Confidence 56799999987643 23456679999954
No 159
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=40.44 E-value=20 Score=32.98 Aligned_cols=37 Identities=16% Similarity=0.450 Sum_probs=27.8
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEecc
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 315 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~ 315 (327)
.--||.|+.+-..+... +...-.+|..||..-..++.
T Consensus 98 yV~C~~C~~pdT~l~k~-------~~~~~l~C~aCGa~~~v~~~ 134 (201)
T PRK12336 98 YVICSECGLPDTRLVKE-------DRVLMLRCDACGAHRPVKKR 134 (201)
T ss_pred eEECCCCCCCCcEEEEc-------CCeEEEEcccCCCCcccccc
Confidence 33499999999888532 24556899999998877754
No 160
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=40.40 E-value=14 Score=39.38 Aligned_cols=45 Identities=27% Similarity=0.516 Sum_probs=25.1
Q ss_pred eecCCCCCccccceecccccccc----CCCCccceeCCCCCceeEEeccce
Q 020384 271 LKGPCPNCGTENVSFFGTILSIS----SGGTTNTINCSNCGTTMVYDSNTR 317 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~----s~~~~~~~kChvC~t~L~f~s~~R 317 (327)
+.|.||.||.+. ..|+.--.- ...+-....|..||..+++..+..
T Consensus 138 v~g~cp~C~~~d--~~g~~ce~cg~~~~~~~l~~~~~~~~g~~~e~~~~~~ 186 (673)
T PRK00133 138 VKGTCPKCGAED--QYGDNCEVCGATYSPTELINPKSAISGATPVLKESEH 186 (673)
T ss_pred eecccCCCCCcc--cCCchhhhccccCChHhhcCCccccCCCcceEEecce
Confidence 359999999872 123311000 001112346888999999886543
No 161
>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=40.30 E-value=17 Score=36.26 Aligned_cols=15 Identities=20% Similarity=0.417 Sum_probs=8.4
Q ss_pred ceeCCCCCceeEEec
Q 020384 300 TINCSNCGTTMVYDS 314 (327)
Q Consensus 300 ~~kChvC~t~L~f~s 314 (327)
...|..||...+++.
T Consensus 166 ~p~~~~~g~~~~~r~ 180 (391)
T PF09334_consen 166 NPVCKICGSPPEVRE 180 (391)
T ss_dssp CEEETTTS-B-EEEE
T ss_pred CCccccccccCcccc
Confidence 356777777776773
No 162
>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=40.15 E-value=12 Score=42.82 Aligned_cols=17 Identities=41% Similarity=0.747 Sum_probs=13.7
Q ss_pred eeeecCCCCCcccccee
Q 020384 269 LILKGPCPNCGTENVSF 285 (327)
Q Consensus 269 liLKGpCPNCGeEv~aF 285 (327)
.+-++.|||||-++.+.
T Consensus 4 ~~y~~~CPnCgg~i~~~ 20 (1171)
T TIGR01054 4 AVYSNLCPNCGGEISSE 20 (1171)
T ss_pred chhcCCCCCCCCccchh
Confidence 35688999999998764
No 163
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=39.41 E-value=39 Score=33.58 Aligned_cols=13 Identities=38% Similarity=0.853 Sum_probs=10.6
Q ss_pred eecCCCCCccccc
Q 020384 271 LKGPCPNCGTENV 283 (327)
Q Consensus 271 LKGpCPNCGeEv~ 283 (327)
-+|-||.||..=.
T Consensus 186 ~~~~CPvCGs~P~ 198 (309)
T PRK03564 186 QRQFCPVCGSMPV 198 (309)
T ss_pred CCCCCCCCCCcch
Confidence 5799999998743
No 164
>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=39.40 E-value=22 Score=35.99 Aligned_cols=32 Identities=22% Similarity=0.484 Sum_probs=22.6
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.||.|+.-+.. ..-....++.|+.||+.|.-+
T Consensus 15 ~C~~Cd~l~~~--------~~l~~g~~a~CpRCg~~L~~~ 46 (403)
T TIGR00155 15 LCSQCDMLVAL--------PRIESGQKAACPRCGTTLTVG 46 (403)
T ss_pred eCCCCCCcccc--------cCCCCCCeeECCCCCCCCcCC
Confidence 49999975432 222355578999999999544
No 165
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=39.36 E-value=43 Score=25.93 Aligned_cols=43 Identities=21% Similarity=0.441 Sum_probs=29.1
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceeeec
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL 321 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~itl 321 (327)
||-||.-.+.=.+.+--. ...-.-|+.|+..-..+-+.-.|++
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 999997665433332111 3345689999999988877777665
No 166
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=39.27 E-value=19 Score=39.55 Aligned_cols=68 Identities=22% Similarity=0.278 Sum_probs=36.9
Q ss_pred HHHhhhHhhhhhcCCeeEEeChh---hHHHHHHHHhhhcCCCc-----cChHHHHHHHHHHhhcCCceeeecCeeee
Q 020384 120 EEFDNLKEELMWEGSSVVMLSSA---EQKFLEASMAYVAGKPI-----MSDEEYDKLKQKLKMEGSEIVVEGPRCSL 188 (327)
Q Consensus 120 eefd~LkEeL~weGSsvv~L~~~---Eq~fLEA~~AY~sGkPi-----msDeeFD~LK~kLk~~GS~VVvk~PrCsl 188 (327)
|=|=.+=++..-.|..+++|=|+ -.++++...++|.-++. ++|.|--..=++. ..|+--+|-|.|..+
T Consensus 232 EvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~-~~G~~~vVIGtRSAl 307 (730)
T COG1198 232 EVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRA-RRGEARVVIGTRSAL 307 (730)
T ss_pred HHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHH-hcCCceEEEEechhh
Confidence 55666666666677776655554 35566666666663332 3454422211222 147766777777554
No 167
>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=38.97 E-value=25 Score=28.36 Aligned_cols=37 Identities=22% Similarity=0.576 Sum_probs=24.1
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
...||+||.+--.||-.-..-+.-..+--..|-+|+-
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 5699999988877873222112234555678988874
No 168
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=38.72 E-value=11 Score=29.15 Aligned_cols=19 Identities=21% Similarity=0.518 Sum_probs=11.4
Q ss_pred hccceeeecCCCCCccccc
Q 020384 265 VRESLILKGPCPNCGTENV 283 (327)
Q Consensus 265 ~~D~liLKGpCPNCGeEv~ 283 (327)
.+.+..+.|.||.|.+++.
T Consensus 48 ~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 48 RQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp S-TTT--EEE-TTT-SEEE
T ss_pred CeeecccccCCcCCCCeee
Confidence 4557788999999999875
No 169
>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=37.89 E-value=25 Score=35.17 Aligned_cols=44 Identities=23% Similarity=0.408 Sum_probs=27.9
Q ss_pred ccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 266 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 266 ~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
.|-.-..--||+|| +.+ -++..+.....+-+.+|. ||..-+.+-
T Consensus 163 ~~~~P~~p~c~~cg--~~~--~~v~~~d~~~~~v~y~c~-cG~~g~~~~ 206 (353)
T cd00674 163 ETWYPFMPYCEKCG--KDT--TTVEAYDAKAGTVTYKCE-CGHEETVDI 206 (353)
T ss_pred CCceeeeeecCCcC--cce--eEEEEEeCCCCeEEEEcC-CCCEEEEee
Confidence 44556677799999 222 223344444556788895 888777764
No 170
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=37.23 E-value=33 Score=30.80 Aligned_cols=29 Identities=28% Similarity=0.969 Sum_probs=21.3
Q ss_pred CCCCCccccc--------eeccccccccCCCCccceeCCCCCce
Q 020384 274 PCPNCGTENV--------SFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~--------aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.|||||++.. -|||.++ -....|..||-.
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evi-------i~sf~C~~CGyk 38 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVI-------IMSFECEHCGYR 38 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEE-------EEEEECCCCCCc
Confidence 6999997754 3677765 346789999954
No 171
>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=37.20 E-value=15 Score=27.83 Aligned_cols=12 Identities=42% Similarity=1.129 Sum_probs=10.1
Q ss_pred ecCCCCCccccc
Q 020384 272 KGPCPNCGTENV 283 (327)
Q Consensus 272 KGpCPNCGeEv~ 283 (327)
++.||+||.+..
T Consensus 13 Y~~Cp~CGN~~v 24 (49)
T PF12677_consen 13 YCKCPKCGNDKV 24 (49)
T ss_pred hccCcccCCcEe
Confidence 789999998753
No 172
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=36.89 E-value=55 Score=26.04 Aligned_cols=36 Identities=28% Similarity=0.344 Sum_probs=30.5
Q ss_pred chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 94 slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
...|.|..+-..+++.+.. ....|.||||.+++.|.
T Consensus 25 ~~~e~e~~~r~~l~~~l~k-ldlVtREEFd~q~~~L~ 60 (79)
T PF04380_consen 25 PREEIEKNIRARLQSALSK-LDLVTREEFDAQKAVLA 60 (79)
T ss_pred hHHHHHHHHHHHHHHHHHH-CCCCcHHHHHHHHHHHH
Confidence 4467899999999999875 77899999999999854
No 173
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=36.72 E-value=8.3 Score=37.61 Aligned_cols=38 Identities=32% Similarity=0.568 Sum_probs=26.6
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceee
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 319 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~i 319 (327)
-.||+|++.++.= .+ ..|..-|+.|+.-+...+..|+-
T Consensus 28 ~~c~~c~~~~~~~---~l------~~~~~vc~~c~~h~rl~areRi~ 65 (292)
T PRK05654 28 TKCPSCGQVLYRK---EL------EANLNVCPKCGHHMRISARERLD 65 (292)
T ss_pred eECCCccchhhHH---HH------HhcCCCCCCCCCCeeCCHHHHHH
Confidence 3699999988743 22 34456899999988766655543
No 174
>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=36.41 E-value=20 Score=34.14 Aligned_cols=41 Identities=17% Similarity=0.507 Sum_probs=17.3
Q ss_pred eeecCCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 270 iLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
..-.-||+||++.-.=+..+ .+.....-.-.-|..|++=++
T Consensus 209 ~~R~~Cp~Cg~~~~~~l~~~-~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 209 FVRIKCPYCGNTDHEKLEYF-TVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp --TTS-TTT---SS-EEE---------SEEEEEETTTTEEEE
T ss_pred ecCCCCcCCCCCCCcceeeE-ecCCCCcEEEEECCcccchHH
Confidence 34567999999877433222 223333334456999998654
No 175
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=36.13 E-value=26 Score=34.72 Aligned_cols=38 Identities=24% Similarity=0.621 Sum_probs=22.4
Q ss_pred eecCCCCCccccc-eeccccccccCCCCccc-eeCCCCCceeEE
Q 020384 271 LKGPCPNCGTENV-SFFGTILSISSGGTTNT-INCSNCGTTMVY 312 (327)
Q Consensus 271 LKGpCPNCGeEv~-aFfGtilsv~s~~~~~~-~kChvC~t~L~f 312 (327)
.-.-||+||+.-. .|| ++.+.....+ --|..|++=++-
T Consensus 225 ~R~~C~~Cg~~~~l~y~----~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 225 VRVKCSNCEQSGKLHYW----SLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred cCccCCCCCCCCceeee----eecCCCcceEeeeccccccccee
Confidence 4667999997533 343 3344333333 358999986543
No 176
>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=35.75 E-value=36 Score=29.69 Aligned_cols=26 Identities=19% Similarity=0.438 Sum_probs=18.8
Q ss_pred ccceeCCCCCceeEEeccceeeecCC
Q 020384 298 TNTINCSNCGTTMVYDSNTRLITLPE 323 (327)
Q Consensus 298 ~~~~kChvC~t~L~f~s~~R~itl~~ 323 (327)
.+..+|..|+..-...+..+..++|+
T Consensus 102 ~~~~~C~~C~~~~~~~~~~~i~~lP~ 127 (230)
T cd02674 102 DNAWKCPKCKKKRKATKKLTISRLPK 127 (230)
T ss_pred CCceeCCCCCCccceEEEEEEecCCh
Confidence 45688999998776666666666664
No 177
>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=35.59 E-value=12 Score=39.24 Aligned_cols=43 Identities=26% Similarity=0.382 Sum_probs=0.0
Q ss_pred ccChHHHhh---hHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHH
Q 020384 116 VMSNEEFDN---LKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYD 166 (327)
Q Consensus 116 ~~sdeefd~---LkEeL~weGSsvv~L~~~Eq~fLEA~~AY~sGkPimsDeeFD 166 (327)
-|||||||. |||| |.|.-- =|+|||.++-||..-.+..-.++|
T Consensus 252 GLSDEEYDEyKkiREe--r~g~YS------IeEYLqdReRy~Eela~~~a~~~~ 297 (535)
T PF05416_consen 252 GLSDEEYDEYKKIREE--RGGKYS------IEEYLQDRERYEEELAEAQATEED 297 (535)
T ss_dssp ------------------------------------------------------
T ss_pred CCChhHHHHHHHHHHH--hcCCcc------HHHHHHHHHHHHHHhhhhhhhhcc
Confidence 399999885 5666 655421 279999999999877766544444
No 178
>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=35.50 E-value=21 Score=26.02 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=4.5
Q ss_pred eCCCCCceeE
Q 020384 302 NCSNCGTTMV 311 (327)
Q Consensus 302 kChvC~t~L~ 311 (327)
.|++|++.|.
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 7788877764
No 179
>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=35.47 E-value=23 Score=35.95 Aligned_cols=36 Identities=25% Similarity=0.548 Sum_probs=25.0
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.--|||||.+...++.. ....+...|+.||..++..
T Consensus 320 ~~rc~~c~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~ 355 (403)
T TIGR03676 320 TFKCPNCGYEEEKTVKP------EEGDKSEACPKCGSELEIV 355 (403)
T ss_pred EEEcCCCCcceeeeccc------ccccccccCcccCcccccc
Confidence 45699999998877632 2223336799999987754
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=35.11 E-value=22 Score=31.88 Aligned_cols=45 Identities=20% Similarity=0.472 Sum_probs=22.1
Q ss_pred eeeecCCCCCccccc--eecccc----ccccCCCCccceeCCCCCceeEEe
Q 020384 269 LILKGPCPNCGTENV--SFFGTI----LSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 269 liLKGpCPNCGeEv~--aFfGti----lsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
-.+|-.|.||||+.- .++-.. .+...+.+..-.||..|++....+
T Consensus 27 ~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si~ 77 (161)
T PF05907_consen 27 WFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSID 77 (161)
T ss_dssp EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEEE
T ss_pred EEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEEE
Confidence 457888999999754 443321 222223333445999999988774
No 181
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=35.01 E-value=22 Score=30.53 Aligned_cols=32 Identities=31% Similarity=0.795 Sum_probs=25.4
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
-||.||. +|-|+++...|+..|.-|.-.....
T Consensus 3 FCP~Cgn--------~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGN--------MLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCC--------EEEEecCCeEeeEEcCCCCceeeEe
Confidence 3999985 5667888889999999998665554
No 182
>PRK12496 hypothetical protein; Provisional
Probab=34.97 E-value=22 Score=31.82 Aligned_cols=36 Identities=14% Similarity=0.462 Sum_probs=22.0
Q ss_pred ccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 266 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 266 ~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
+....-+--|+.||.+ | .. ....-.|++||.++.=.
T Consensus 121 ~~~~~w~~~C~gC~~~---~-------~~--~~~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 121 KKVIKWRKVCKGCKKK---Y-------PE--DYPDDVCEICGSPVKRK 156 (164)
T ss_pred hhheeeeEECCCCCcc---c-------cC--CCCCCcCCCCCChhhhc
Confidence 3444445679999953 2 10 11224699999998544
No 183
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=34.97 E-value=7.8 Score=38.17 Aligned_cols=37 Identities=27% Similarity=0.510 Sum_probs=26.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceee
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI 319 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~i 319 (327)
-||+|++-++.= .+ ..|...|+.|+--+...+..|+-
T Consensus 40 kc~~C~~~~~~~---~l------~~~~~vcp~c~~h~rltAreRI~ 76 (296)
T CHL00174 40 QCENCYGLNYKK---FL------KSKMNICEQCGYHLKMSSSDRIE 76 (296)
T ss_pred ECCCccchhhHH---HH------HHcCCCCCCCCCCcCCCHHHHHH
Confidence 599999998743 22 45667899999877766655543
No 184
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=34.94 E-value=20 Score=34.50 Aligned_cols=19 Identities=42% Similarity=0.821 Sum_probs=16.3
Q ss_pred cCCCCccceeCCCCCceeE
Q 020384 293 SSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 293 ~s~~~~~~~kChvC~t~L~ 311 (327)
..+..+.+++|++|++.|+
T Consensus 207 ~~g~ipe~i~CpeC~R~ME 225 (235)
T PF14577_consen 207 SAGRIPETIVCPECGRPME 225 (235)
T ss_pred cccCCCceeECCCCCCchh
Confidence 4566789999999999997
No 185
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=34.68 E-value=45 Score=25.91 Aligned_cols=44 Identities=25% Similarity=0.548 Sum_probs=32.8
Q ss_pred hhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 263 LIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 263 l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
+-++|.+-||-|=| ||+-...- -.-++.-+.+|..||..+...+
T Consensus 2 ~~vgDiV~mKK~HP-CG~~~Wei-------~R~GaDikikC~gCg~~imlpR 45 (57)
T PF06107_consen 2 YEVGDIVEMKKPHP-CGSNEWEI-------IRIGADIKIKCLGCGRQIMLPR 45 (57)
T ss_pred ccCCCEEEEcCCCC-CCCCEEEE-------EEccCcEEEEECCCCCEEEEeH
Confidence 34689999999888 67644433 2336788999999999988764
No 186
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=34.49 E-value=20 Score=38.19 Aligned_cols=12 Identities=50% Similarity=1.453 Sum_probs=9.2
Q ss_pred eecCCCCCcccc
Q 020384 271 LKGPCPNCGTEN 282 (327)
Q Consensus 271 LKGpCPNCGeEv 282 (327)
++|.||.||.+.
T Consensus 141 v~g~cp~cg~~~ 152 (558)
T COG0143 141 VEGTCPKCGGED 152 (558)
T ss_pred eeccCCCcCccc
Confidence 489999998543
No 187
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=34.26 E-value=37 Score=31.38 Aligned_cols=19 Identities=26% Similarity=0.450 Sum_probs=12.0
Q ss_pred hccceeeecCCCCCccccc
Q 020384 265 VRESLILKGPCPNCGTENV 283 (327)
Q Consensus 265 ~~D~liLKGpCPNCGeEv~ 283 (327)
|++.+|+...||+||-.+.
T Consensus 23 F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 23 FGEVLETSTICEHCGYRSN 41 (192)
T ss_pred cceEEEEEEECCCCCCccc
Confidence 5666666666666665554
No 188
>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=34.20 E-value=29 Score=31.02 Aligned_cols=29 Identities=31% Similarity=1.011 Sum_probs=18.3
Q ss_pred CCCCCccccce--------eccccccccCCCCccceeCCCCCce
Q 020384 274 PCPNCGTENVS--------FFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~a--------FfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.|||||++... |||.++ -....|+.||-.
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 577764 345799999954
No 189
>PRK12412 pyridoxal kinase; Reviewed
Probab=34.08 E-value=1.4e+02 Score=27.60 Aligned_cols=57 Identities=26% Similarity=0.334 Sum_probs=42.2
Q ss_pred hHHHhhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhcCCc-eeeec
Q 020384 119 NEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSE-IVVEG 183 (327)
Q Consensus 119 deefd~LkEeL~weGSsvv~L~~~Eq~fLEA~~AY~sGkPimsDeeFD~LK~kLk~~GS~-VVvk~ 183 (327)
++..+.++++|. ....+++.+..|-+.| .|.++-++++..+.-.+|...|-+ |++++
T Consensus 119 ~~~~~~~~~~ll-~~advitpN~~Ea~~L-------~g~~~~~~~~~~~aa~~l~~~g~~~ViIt~ 176 (268)
T PRK12412 119 PETNDCLRDVLV-PKALVVTPNLFEAYQL-------SGVKINSLEDMKEAAKKIHALGAKYVLIKG 176 (268)
T ss_pred hHHHHHHHHhhh-ccceEEcCCHHHHHHH-------hCcCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence 345567787765 5678999999998877 477777777777777888777864 66664
No 190
>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=34.07 E-value=8.6 Score=37.40 Aligned_cols=36 Identities=31% Similarity=0.625 Sum_probs=24.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEecccee
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL 318 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~ 318 (327)
.||+|++-++.= .+ ..|-.-|+.|+.-+...+..|+
T Consensus 28 ~c~~c~~~~~~~---~l------~~~~~vc~~c~~h~rl~areRi 63 (285)
T TIGR00515 28 KCPKCGQVLYTK---EL------ERNLEVCPKCDHHMRMDARERI 63 (285)
T ss_pred ECCCCcchhhHH---HH------HhhCCCCCCCCCcCcCCHHHHH
Confidence 599999988742 11 3455689999987665544443
No 191
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=34.06 E-value=79 Score=31.48 Aligned_cols=71 Identities=17% Similarity=0.270 Sum_probs=45.2
Q ss_pred hhHHHHHHHHH---HHHhhhcCccccChHHHhhhHhhhhhcCCeeEEeChhhHHHHHH---HHh-hhcCCC-ccChHHHH
Q 020384 95 LGELEQEFLQA---LQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEA---SMA-YVAGKP-IMSDEEYD 166 (327)
Q Consensus 95 lge~E~~fl~A---l~~fY~~gk~~~sdeefd~LkEeL~weGSsvv~L~~~Eq~fLEA---~~A-Y~sGkP-imsDeeFD 166 (327)
+-|..|+|.+| ++.+||+.+ |...+|+.++|...|.- . +...+ ++..| |.+ .-+.-- .++-++|.
T Consensus 2 ~~~~~~~f~e~w~~v~~~~~d~~--~~g~dW~~~~e~y~~~~-~---~~~~~-~~~~~i~~ml~~L~D~hs~y~~~~~~~ 74 (389)
T PLN00049 2 LTEENLLFLEAWRTVDRAYVDKT--FNGQSWFRYRENALKNE-P---MNTRE-ETYAAIRKMLATLDDPFTRFLEPEKFK 74 (389)
T ss_pred CccHHHHHHHHHHHHHHHHcCcc--ccccCHHHHHHHHhhcc-C---CCcHH-HHHHHHHHHHhhCCCCcccCcCHHHHH
Confidence 34678999998 567888765 89999999999999964 2 22222 33333 222 111111 66788888
Q ss_pred HHHHHH
Q 020384 167 KLKQKL 172 (327)
Q Consensus 167 ~LK~kL 172 (327)
.+....
T Consensus 75 ~~~~~~ 80 (389)
T PLN00049 75 SLRSGT 80 (389)
T ss_pred HHHHhc
Confidence 776543
No 192
>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=33.45 E-value=1.2e+02 Score=30.35 Aligned_cols=70 Identities=24% Similarity=0.492 Sum_probs=47.5
Q ss_pred ccChHHHhhhHhhhhhc-----CC-----eeEEeChh-hHHHHHHHHh----hhcCC---------CccChHHHHHHHHH
Q 020384 116 VMSNEEFDNLKEELMWE-----GS-----SVVMLSSA-EQKFLEASMA----YVAGK---------PIMSDEEYDKLKQK 171 (327)
Q Consensus 116 ~~sdeefd~LkEeL~we-----GS-----svv~L~~~-Eq~fLEA~~A----Y~sGk---------PimsDeeFD~LK~k 171 (327)
++.|.+.|..-+.+.|. |. +.+.+-+. -.+|++++.+ +.-|. |+++.+.+++++.-
T Consensus 238 V~~dadl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~Gpli~~~~~~~~~~~ 317 (456)
T cd07110 238 VFDDADLEKAVEWAMFGCFWNNGQICSATSRLLVHESIADAFLERLATAAEAIRVGDPLEEGVRLGPLVSQAQYEKVLSF 317 (456)
T ss_pred ECCCCCHHHHHHHHHHHHHhcCCCCCCCCceEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcCCCCCHHHHHHHHHH
Confidence 45678888888888873 43 33444433 5678887654 33343 68899999999988
Q ss_pred Hhh---cCCceeeecCe
Q 020384 172 LKM---EGSEIVVEGPR 185 (327)
Q Consensus 172 Lk~---~GS~VVvk~Pr 185 (327)
+++ .|.+++.-|.+
T Consensus 318 v~~a~~~Ga~~~~gg~~ 334 (456)
T cd07110 318 IARGKEEGARLLCGGRR 334 (456)
T ss_pred HHHHHhCCCEEEeCCCc
Confidence 865 68787775543
No 193
>PRK04351 hypothetical protein; Provisional
Probab=33.28 E-value=36 Score=30.18 Aligned_cols=34 Identities=21% Similarity=0.499 Sum_probs=24.9
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
=.|.+||.+... +..+ ++.+.-|..|+..|.+-.
T Consensus 113 Y~C~~Cg~~~~r----~Rr~----n~~~yrCg~C~g~L~~~~ 146 (149)
T PRK04351 113 YECQSCGQQYLR----KRRI----NTKRYRCGKCRGKLKLIN 146 (149)
T ss_pred EECCCCCCEeee----eeec----CCCcEEeCCCCcEeeecc
Confidence 469999975543 2333 568899999999998863
No 194
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.22 E-value=27 Score=28.22 Aligned_cols=18 Identities=50% Similarity=0.772 Sum_probs=15.0
Q ss_pred Ccc-ccChHHHhhhHhhhh
Q 020384 113 GKA-VMSNEEFDNLKEELM 130 (327)
Q Consensus 113 gk~-~~sdeefd~LkEeL~ 130 (327)
||- +||||||..||+.|+
T Consensus 52 GKGiTLt~eE~~~l~d~l~ 70 (72)
T COG4443 52 GKGITLTNEEFKALKDLLN 70 (72)
T ss_pred cCceeecHHHHHHHHHHHh
Confidence 444 899999999999874
No 195
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=33.04 E-value=34 Score=37.43 Aligned_cols=26 Identities=31% Similarity=0.622 Sum_probs=20.5
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCC
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNC 306 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC 306 (327)
||+||.++..++.. ..-.-...|++|
T Consensus 132 C~~Cg~~~~~~~~~------~~~~~~~~C~~~ 157 (682)
T COG1241 132 CPKCGREVEVEQSE------FRVEPPRECENC 157 (682)
T ss_pred cCCCCCEEEEEecc------ccccCCccCCCc
Confidence 99999999999843 234456789999
No 196
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=32.85 E-value=19 Score=29.41 Aligned_cols=17 Identities=29% Similarity=0.696 Sum_probs=11.7
Q ss_pred cceeeecCCCCCccccc
Q 020384 267 ESLILKGPCPNCGTENV 283 (327)
Q Consensus 267 D~liLKGpCPNCGeEv~ 283 (327)
.++-+.-.||+||++-.
T Consensus 3 g~Lk~~~~C~~CG~d~~ 19 (86)
T PF06170_consen 3 GYLKVAPRCPHCGLDYS 19 (86)
T ss_pred ccccCCCcccccCCccc
Confidence 34556777888887754
No 197
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=32.74 E-value=21 Score=27.92 Aligned_cols=16 Identities=31% Similarity=1.097 Sum_probs=11.9
Q ss_pred CCCCCccccc--eecccc
Q 020384 274 PCPNCGTENV--SFFGTI 289 (327)
Q Consensus 274 pCPNCGeEv~--aFfGti 289 (327)
-|||||.+.+ .+||-+
T Consensus 17 ~CP~Cgs~~~T~~W~G~v 34 (61)
T PRK08351 17 RCPVCGSRDLSDEWFDLV 34 (61)
T ss_pred cCCCCcCCccccccccEE
Confidence 5999999875 566643
No 198
>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=32.69 E-value=30 Score=21.95 Aligned_cols=35 Identities=23% Similarity=0.468 Sum_probs=19.6
Q ss_pred CCCCccccceeccccccccCCCCccc--eeCCCCCceeE
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNT--INCSNCGTTMV 311 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~--~kChvC~t~L~ 311 (327)
|+.|++.+..--..+. ..+..-|. .+|+.|+..|+
T Consensus 2 C~~C~~~i~~~~~~~~--~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLR--ALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEE--eCCccccccCCCCcccCCcCc
Confidence 7888887654100011 12233333 77899998874
No 199
>PLN02919 haloacid dehalogenase-like hydrolase family protein
Probab=32.65 E-value=3.2e+02 Score=31.17 Aligned_cols=30 Identities=20% Similarity=0.135 Sum_probs=14.8
Q ss_pred chhHHHHHHHHHHHHhhhcCccccChHHHh
Q 020384 94 SLGELEQEFLQALQAFYYEGKAVMSNEEFD 123 (327)
Q Consensus 94 slge~E~~fl~Al~~fY~~gk~~~sdeefd 123 (327)
||-+-|..+.+|++..+.+---.++.+++.
T Consensus 85 TLiDS~~~~~~a~~~~~~~~G~~it~e~~~ 114 (1057)
T PLN02919 85 VLCNSEEPSRRAAVDVFAEMGVEVTVEDFV 114 (1057)
T ss_pred CeEeChHHHHHHHHHHHHHcCCCCCHHHHH
Confidence 444445555566555554322234555553
No 200
>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=32.24 E-value=45 Score=26.09 Aligned_cols=42 Identities=33% Similarity=0.781 Sum_probs=27.8
Q ss_pred CCCCCccccce---------eccccccccCCCCccceeCCCCCceeEEeccc
Q 020384 274 PCPNCGTENVS---------FFGTILSISSGGTTNTINCSNCGTTMVYDSNT 316 (327)
Q Consensus 274 pCPNCGeEv~a---------FfGtilsv~s~~~~~~~kChvC~t~L~f~s~~ 316 (327)
-||-||.+.+. .|+.++-|+... --.+-|.+||=.=.|.+++
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 344445554432 3356799999987777544
No 201
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=32.02 E-value=31 Score=40.29 Aligned_cols=40 Identities=30% Similarity=0.522 Sum_probs=28.6
Q ss_pred eeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
+.=---||||.- +-|+ ++-++-+|=+--.-.|+.||++|.
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 344456999963 4454 334677778888889999999964
No 202
>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=31.93 E-value=29 Score=26.09 Aligned_cols=32 Identities=22% Similarity=0.344 Sum_probs=23.3
Q ss_pred eeeecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
.+|- |++|..-|-...+. ........|..||.
T Consensus 21 ~aLI--C~~C~~hNGla~~~------~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 21 YALI--CSKCFSHNGLAPKE------EFEEIQYRCPYCGA 52 (54)
T ss_pred eeEE--Ccccchhhcccccc------cCCceEEEcCCCCC
Confidence 3444 99999999877522 23555999999986
No 203
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=31.89 E-value=26 Score=35.74 Aligned_cols=26 Identities=19% Similarity=0.425 Sum_probs=18.7
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.||.|+.-+ + ..++.|+.||+.|.-+
T Consensus 223 ~C~~Cd~l~----------~----~~~a~CpRC~~~L~~~ 248 (419)
T PRK15103 223 SCSCCTAIL----------P----ADQPVCPRCHTKGYVR 248 (419)
T ss_pred cCCCCCCCC----------C----CCCCCCCCCCCcCcCC
Confidence 499999842 1 1355899999999433
No 204
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.77 E-value=26 Score=34.53 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=21.1
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
.--||.||++++.-=|.. ...|++||...
T Consensus 111 ~RFCg~CG~~~~~~~~g~----------~~~C~~cg~~~ 139 (279)
T COG2816 111 HRFCGRCGTKTYPREGGW----------ARVCPKCGHEH 139 (279)
T ss_pred CcCCCCCCCcCccccCce----------eeeCCCCCCcc
Confidence 456999999998764332 45699999753
No 205
>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=31.52 E-value=23 Score=27.23 Aligned_cols=13 Identities=62% Similarity=1.260 Sum_probs=11.5
Q ss_pred ecCCCCCccccce
Q 020384 272 KGPCPNCGTENVS 284 (327)
Q Consensus 272 KGpCPNCGeEv~a 284 (327)
.||||-||+++.+
T Consensus 35 ~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 35 LGPCPFCGTPLLS 47 (57)
T ss_pred cCcCCCCCCcccC
Confidence 7999999998875
No 206
>PRK08173 DNA topoisomerase III; Validated
Probab=31.33 E-value=28 Score=38.67 Aligned_cols=27 Identities=30% Similarity=0.830 Sum_probs=18.1
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
.|+||.||.++ . . ......|++|+-.+
T Consensus 624 ~~~CP~Cg~~~---~------~---~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 624 QTPCPNCGGVV---K------E---NYRRFACTKCDFSI 650 (862)
T ss_pred cccCCcccccc---c------c---cCceeEcCCCCccc
Confidence 58999999864 1 1 12237899987554
No 207
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=31.17 E-value=36 Score=31.43 Aligned_cols=11 Identities=45% Similarity=0.893 Sum_probs=8.8
Q ss_pred cCCCCCccccc
Q 020384 273 GPCPNCGTENV 283 (327)
Q Consensus 273 GpCPNCGeEv~ 283 (327)
=.||.|+++..
T Consensus 6 ~~CPvC~~~F~ 16 (214)
T PF09986_consen 6 ITCPVCGKEFK 16 (214)
T ss_pred eECCCCCCeee
Confidence 36999998865
No 208
>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=31.11 E-value=2.1e+02 Score=25.32 Aligned_cols=53 Identities=23% Similarity=0.394 Sum_probs=37.0
Q ss_pred hhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhcCC-ceeeec
Q 020384 123 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEG 183 (327)
Q Consensus 123 d~LkEeL~weGSsvv~L~~~Eq~fLEA~~AY~sGkPimsDeeFD~LK~kLk~~GS-~VVvk~ 183 (327)
+.++++| +....+++.+..|-+.| .|.++-++++-.+...+|...|- .|++++
T Consensus 119 ~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~~~~l~~~g~~~Vvit~ 172 (242)
T cd01169 119 EALRELL-LPLATLITPNLPEAELL-------TGLEIATEEDMMKAAKALLALGAKAVLIKG 172 (242)
T ss_pred HHHHHHh-hccCeEEeCCHHHHHHH-------hCCCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence 4566654 67788999999998877 36666666555556677777775 466664
No 209
>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=30.34 E-value=26 Score=29.15 Aligned_cols=37 Identities=30% Similarity=0.668 Sum_probs=29.8
Q ss_pred eChhhHHHHHHHHhhhcCC-----CccChHHHHHHHHHHhhc
Q 020384 139 LSSAEQKFLEASMAYVAGK-----PIMSDEEYDKLKQKLKME 175 (327)
Q Consensus 139 L~~~Eq~fLEA~~AY~sGk-----PimsDeeFD~LK~kLk~~ 175 (327)
+...++.|+....||.+|+ +++++++|..++.++++.
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 3456777888777899985 899999999999999988
No 210
>PHA02768 hypothetical protein; Provisional
Probab=30.21 E-value=26 Score=26.81 Aligned_cols=42 Identities=21% Similarity=0.430 Sum_probs=26.1
Q ss_pred cCCCCCccccc---eeccccccccCCCCccceeCCCCCceeEEeccceeeec
Q 020384 273 GPCPNCGTENV---SFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL 321 (327)
Q Consensus 273 GpCPNCGeEv~---aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~itl 321 (327)
=.||-||..-. ++.+-.... ....+|.+|+. .|.++..+|.+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H-----~k~~kc~~C~k--~f~~~s~l~~~ 50 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKH-----NTNLKLSNCKR--ISLRTGEYIEI 50 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhc-----CCcccCCcccc--eecccceeEEE
Confidence 38999997533 222222111 13679999999 55677777765
No 211
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=30.13 E-value=36 Score=29.64 Aligned_cols=32 Identities=28% Similarity=0.828 Sum_probs=24.3
Q ss_pred hccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 265 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 265 ~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
++.--++-.-|++||. .|| +-+..|+.|++.-
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 4446788889999996 455 4467899999884
No 212
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=30.09 E-value=57 Score=27.74 Aligned_cols=45 Identities=27% Similarity=0.585 Sum_probs=28.1
Q ss_pred eeeecCCCCCccccceeccc--------ccccc-------CCCCccceeCCCCCc-eeEEe
Q 020384 269 LILKGPCPNCGTENVSFFGT--------ILSIS-------SGGTTNTINCSNCGT-TMVYD 313 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGt--------ilsv~-------s~~~~~~~kChvC~t-~L~f~ 313 (327)
....+.||-||.+...+++. +.+.- .....-.++|+.|+. .+..+
T Consensus 14 ~~~~~~Cp~Cg~~m~~~~~~~g~f~gCs~yP~C~~~~~~~~~~~~~~~~Cp~C~~~~~~~k 74 (140)
T COG0551 14 LKTGQICPKCGKNMVKKFGKYGIFLGCSNYPKCDYYEPEKAIAEKTGVKCPKCGKGLLVLK 74 (140)
T ss_pred cccCccCCcCCCeeEEEEccCCeEEEeCCCCCCCCCcccccccccCceeCCCCCCCceEEE
Confidence 35579999999998877766 11111 111233488999995 44444
No 213
>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=29.78 E-value=19 Score=26.12 Aligned_cols=34 Identities=21% Similarity=0.505 Sum_probs=20.6
Q ss_pred CCCCCcccccee---ccccccccCCCCccceeCCCCCce
Q 020384 274 PCPNCGTENVSF---FGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~aF---fGtilsv~s~~~~~~~kChvC~t~ 309 (327)
+||=||+ .++. ..-+. .+-..+...+.|+.|...
T Consensus 4 ~CP~C~~-~~~~~~L~~H~~-~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 4 TCPYCGK-GFSESSLVEHCE-DEHRSESKNVVCPICSSR 40 (54)
T ss_pred CCCCCCC-ccCHHHHHHHHH-hHCcCCCCCccCCCchhh
Confidence 7999999 5542 11111 122334567999999863
No 214
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.56 E-value=26 Score=36.50 Aligned_cols=58 Identities=26% Similarity=0.543 Sum_probs=36.1
Q ss_pred HHHHHHHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccc
Q 020384 256 LSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 316 (327)
Q Consensus 256 ~a~~Lt~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~ 316 (327)
+.+-|-+-..+|+-.----||||...-.+- ..+.+= ...+-+..|.+|+..|+=|...
T Consensus 112 m~krled~~~d~t~~~~Y~Cp~C~kkyt~L--ea~~L~-~~~~~~F~C~~C~gelveDe~~ 169 (436)
T KOG2593|consen 112 MRKRLEDRLRDDTNVAGYVCPNCQKKYTSL--EALQLL-DNETGEFHCENCGGELVEDENK 169 (436)
T ss_pred HHHHHHHHhhhccccccccCCccccchhhh--HHHHhh-cccCceEEEecCCCchhccccc
Confidence 444455656677766667799999863221 000000 1135678999999999988543
No 215
>PRK14973 DNA topoisomerase I; Provisional
Probab=29.56 E-value=39 Score=38.05 Aligned_cols=12 Identities=50% Similarity=1.245 Sum_probs=9.4
Q ss_pred ecCCCCCccccc
Q 020384 272 KGPCPNCGTENV 283 (327)
Q Consensus 272 KGpCPNCGeEv~ 283 (327)
.|+||.||.++.
T Consensus 588 ~~~CP~CG~~l~ 599 (936)
T PRK14973 588 IGPCPVCGKDLR 599 (936)
T ss_pred cccCCcccccce
Confidence 489999997653
No 216
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=29.51 E-value=37 Score=33.24 Aligned_cols=26 Identities=35% Similarity=0.745 Sum_probs=19.9
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCC
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCG 307 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~ 307 (327)
||+.||+.+..=. - +.++..=|++|.
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 8999999987431 1 367788999996
No 217
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=29.50 E-value=13 Score=36.93 Aligned_cols=38 Identities=32% Similarity=0.605 Sum_probs=29.2
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEeccceeee
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLIT 320 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~it 320 (327)
-||.||+=+|.= ++ ..|-.-|++|+--+...+..|+-.
T Consensus 30 KCp~c~~~~y~~---eL------~~n~~vcp~c~~h~ri~A~~Ri~~ 67 (294)
T COG0777 30 KCPSCGEMLYRK---EL------ESNLKVCPKCGHHMRISARERLEA 67 (294)
T ss_pred ECCCccceeeHH---HH------HhhhhcccccCcccccCHHHHHHH
Confidence 499999877632 33 567888999999998888777643
No 218
>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=29.50 E-value=47 Score=32.67 Aligned_cols=39 Identities=18% Similarity=0.583 Sum_probs=26.9
Q ss_pred ecCCCCCccccceeccccccccCCCCc--cceeCCCCCceeEE
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTT--NTINCSNCGTTMVY 312 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~--~~~kChvC~t~L~f 312 (327)
...||.||...-.||- .-..+...+ --+.|.+||-.-.|
T Consensus 258 ~~~C~~C~~~~~~~~q--~QtrsaDEpmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQ--LQTRSADEPMTTFVTCEECGNRWKF 298 (299)
T ss_pred cccCCCCCCccceEEE--ecccCCCCCCeEEEEcCCCCCeeee
Confidence 4799999988888873 233444444 34689999976554
No 219
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=29.40 E-value=80 Score=25.28 Aligned_cols=49 Identities=27% Similarity=0.409 Sum_probs=30.3
Q ss_pred CCCCCccccceeccccccccCCCCccceeCC--CCCceeEEe-ccceeeecCCC
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCS--NCGTTMVYD-SNTRLITLPEG 324 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kCh--vC~t~L~f~-s~~R~itl~~~ 324 (327)
.||.||..-. ..+-.-+..+...-...|. +||...+.. +-.|.|.-|..
T Consensus 3 ~CP~Cg~~a~--irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~s~tis~p~~ 54 (72)
T PRK09678 3 HCPLCQHAAH--ARTSRYITDTTKERYHQCQNVNCSATFITYESVQRYIVKPGE 54 (72)
T ss_pred cCCCCCCccE--EEEChhcChhhheeeeecCCCCCCCEEEEEEEEEEEEcCCCC
Confidence 5999999873 2222222333455667897 888887766 45666665543
No 220
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=28.96 E-value=38 Score=25.12 Aligned_cols=37 Identities=16% Similarity=0.424 Sum_probs=25.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
-|.||-+-+.- .....+ +.+..++..|..|...|.|.
T Consensus 8 ~C~~C~~lLql--P~~~~~-~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 8 VCSSCFELLQL--PAKFSL-SKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred ECccHHHHHcC--CCccCC-CccceeEEeCCCCceeEEEe
Confidence 38899876653 222222 33458899999999999885
No 221
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.85 E-value=40 Score=36.73 Aligned_cols=27 Identities=30% Similarity=0.765 Sum_probs=17.2
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
--|++||- -|.+.. ......|++||..
T Consensus 642 ~~C~~CG~-----~Ge~~~-----~~~~~~CP~CG~~ 668 (711)
T PRK09263 642 DECYECGF-----TGEFEC-----TEKGFTCPKCGNH 668 (711)
T ss_pred cccCCCCC-----CccccC-----CCCCCcCcCCCCC
Confidence 46999993 344422 1223789999963
No 222
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.60 E-value=28 Score=29.47 Aligned_cols=30 Identities=13% Similarity=0.339 Sum_probs=18.7
Q ss_pred eeeecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
+-+.+-|++||.+ +.. . ..+...|+.||+.
T Consensus 68 vp~~~~C~~Cg~~-~~~-------~---~~~~~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSHV-FKP-------N---ALDYGVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCCc-ccc-------C---CccCCcCcCCCCC
Confidence 4567889999932 111 1 1223469999985
No 223
>PF09863 DUF2090: Uncharacterized protein conserved in bacteria (DUF2090); InterPro: IPR018659 This domain, found in various prokaryotic carbohydrate kinases, has no known function.
Probab=28.57 E-value=1.5e+02 Score=29.93 Aligned_cols=49 Identities=16% Similarity=0.276 Sum_probs=40.4
Q ss_pred chhHHHHHHHHHHHHhhhcCc-------cccChHHHhhhHhhhhhcCCe---eEEeChh
Q 020384 94 SLGELEQEFLQALQAFYYEGK-------AVMSNEEFDNLKEELMWEGSS---VVMLSSA 142 (327)
Q Consensus 94 slge~E~~fl~Al~~fY~~gk-------~~~sdeefd~LkEeL~weGSs---vv~L~~~ 142 (327)
+....+.-|..+|++||+-|- +-||.+.|.++-+...=.++- ||+||.+
T Consensus 188 ~~~~~~~~~~~ai~r~Y~lGI~PDWWKLep~s~~~W~~i~~~I~~~Dp~crGvVvLGLd 246 (311)
T PF09863_consen 188 DMPVDDDTYARAIERFYNLGIKPDWWKLEPLSAAAWQAIEALIEERDPYCRGVVVLGLD 246 (311)
T ss_pred CCCCChHHHHHHHHHHHHcCCCCCeeccCCCCHHHHHHHHHHHHHhCCCceeEEEecCC
Confidence 345568899999999999874 467999999999888777774 8899876
No 224
>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=28.49 E-value=46 Score=29.63 Aligned_cols=32 Identities=31% Similarity=0.545 Sum_probs=0.0
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCceeEEeccc
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT 316 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~ 316 (327)
|-|||.++--...+.++- |+.||..---|...
T Consensus 115 C~~Cg~~~~~~~~~~l~~----------Cp~C~~~~F~R~~~ 146 (146)
T PF07295_consen 115 CENCGHEVELTHPERLPP----------CPKCGHTEFTRQPL 146 (146)
T ss_pred cccCCCEEEecCCCcCCC----------CCCCCCCeeeeCCC
No 225
>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=28.39 E-value=36 Score=28.61 Aligned_cols=32 Identities=22% Similarity=0.623 Sum_probs=25.6
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.|++||.+|-. .+.++.++--|++|=..+-.|
T Consensus 6 ~C~~CG~~V~p--------~~~g~~~RNHCP~CL~S~Hvd 37 (92)
T PF12647_consen 6 TCVHCGLTVSP--------LAAGSAHRNHCPSCLSSLHVD 37 (92)
T ss_pred CccccCCCccc--------CCCCCCccCcCcccccccccC
Confidence 59999998754 345678899999998887776
No 226
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=28.35 E-value=36 Score=28.61 Aligned_cols=28 Identities=25% Similarity=0.787 Sum_probs=21.2
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.-.|++||.+-+.++ .=+|+ -|+.|+..
T Consensus 42 ~~~C~~Cg~~~~~~~---------SCk~R-~CP~C~~~ 69 (111)
T PF14319_consen 42 RYRCEDCGHEKIVYN---------SCKNR-HCPSCQAK 69 (111)
T ss_pred eeecCCCCceEEecC---------cccCc-CCCCCCCh
Confidence 347999999998885 23445 79999975
No 227
>PRK14526 adenylate kinase; Provisional
Probab=28.31 E-value=45 Score=30.54 Aligned_cols=34 Identities=15% Similarity=0.243 Sum_probs=25.0
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
.-||.||.---..|.. .+...+|.+|+..|+-|.
T Consensus 123 ~~~~~~g~~y~~~~~p--------p~~~~~~~~~~~~l~~R~ 156 (211)
T PRK14526 123 RICKSCNNIFNIYTLP--------TKEKGICDVCKGDLYQRK 156 (211)
T ss_pred CcccccCCccccccCC--------CCccCcCCCCCCeeeccC
Confidence 5699999876655532 344678999999888765
No 228
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=28.21 E-value=59 Score=30.43 Aligned_cols=36 Identities=31% Similarity=0.544 Sum_probs=30.8
Q ss_pred ccchh-HHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 020384 92 KKSLG-ELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (327)
Q Consensus 92 k~slg-e~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~ 130 (327)
.+.|| |....|.+.|..|+-. -+|.+|||.+=..+.
T Consensus 19 ~~~LG~~~~~~Y~~~l~~fl~~---klsk~Efd~~~~~~L 55 (252)
T PF12767_consen 19 QKRLGPDRWKKYFQSLKRFLSG---KLSKEEFDKECRRIL 55 (252)
T ss_pred HHHHChHHHHHHHHHHHHHHHh---ccCHHHHHHHHHHHh
Confidence 45789 9999999999999985 489999999877754
No 229
>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=28.20 E-value=15 Score=30.79 Aligned_cols=36 Identities=25% Similarity=0.529 Sum_probs=20.0
Q ss_pred cceeeecCCCCCccccceeccccccccCCCCccceeCCCCCcee-EEec
Q 020384 267 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM-VYDS 314 (327)
Q Consensus 267 D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L-~f~s 314 (327)
+.+-+++-|++||.+... ..+...|+.||+.- ...+
T Consensus 65 e~~p~~~~C~~Cg~~~~~------------~~~~~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 65 EEVPARARCRDCGHEFEP------------DEFDFSCPRCGSPDVEIIS 101 (113)
T ss_dssp EEE--EEEETTTS-EEEC------------HHCCHH-SSSSSS-EEEEE
T ss_pred EecCCcEECCCCCCEEec------------CCCCCCCcCCcCCCcEEcc
Confidence 335578899999987431 22335699999973 4443
No 230
>PRK14529 adenylate kinase; Provisional
Probab=28.16 E-value=40 Score=31.51 Aligned_cols=38 Identities=16% Similarity=0.302 Sum_probs=23.8
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEecc
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 315 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~ 315 (327)
..-||+||.-.+..|-. .+ .....+|.+||..|+-|.+
T Consensus 126 R~~c~~~~~~~~~~~~~-----~p-~~~~~~cd~~~~~l~~R~D 163 (223)
T PRK14529 126 RRLCKNDNNHPNNIFID-----AI-KPDGDVCRVCGGELSTRAD 163 (223)
T ss_pred CccccccCCcccccccC-----CC-cccCCcCcCcCCccccCCC
Confidence 35699998766543311 11 1123489999999887763
No 231
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=28.02 E-value=1.5e+02 Score=27.84 Aligned_cols=53 Identities=15% Similarity=0.142 Sum_probs=39.6
Q ss_pred hhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhcCC-ceeeec
Q 020384 123 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEG 183 (327)
Q Consensus 123 d~LkEeL~weGSsvv~L~~~Eq~fLEA~~AY~sGkPimsDeeFD~LK~kLk~~GS-~VVvk~ 183 (327)
..+|++| .....+++.+..|-++| .|.++.++++..+.-.+|...|. .|++++
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 4566655 57788999999998887 47787777777777777877785 466764
No 232
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=27.86 E-value=61 Score=27.80 Aligned_cols=34 Identities=18% Similarity=0.610 Sum_probs=24.1
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
.--|.+||+....- .....+.+..|..|+-.|.+
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 45798999876422 33334478999999998875
No 233
>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=27.85 E-value=45 Score=22.62 Aligned_cols=27 Identities=30% Similarity=0.722 Sum_probs=11.8
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
.+||.|+.+..=. +..-.-|+-|+-..
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 4699999875432 34456788887643
No 234
>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=27.74 E-value=38 Score=23.57 Aligned_cols=25 Identities=32% Similarity=0.930 Sum_probs=16.2
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
|+.||+. +|-. ..-..-|.-||+..
T Consensus 11 C~~C~~~---~~~~--------~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 11 CPVCGSR---WFYS--------DDGFYYCDRCGHQS 35 (36)
T ss_pred CCCCCCe---EeEc--------cCCEEEhhhCceEc
Confidence 9999988 3322 23356777777754
No 235
>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=27.71 E-value=41 Score=23.29 Aligned_cols=13 Identities=31% Similarity=0.938 Sum_probs=7.2
Q ss_pred cceeCCCCCceeE
Q 020384 299 NTINCSNCGTTMV 311 (327)
Q Consensus 299 ~~~kChvC~t~L~ 311 (327)
..+.|+||++.+.
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 3467777777653
No 236
>PRK11032 hypothetical protein; Provisional
Probab=27.58 E-value=35 Score=30.99 Aligned_cols=23 Identities=26% Similarity=0.849 Sum_probs=0.0
Q ss_pred CCCCccccceeccccccccCCCCccceeCCCCC
Q 020384 275 CPNCGTENVSFFGTILSISSGGTTNTINCSNCG 307 (327)
Q Consensus 275 CPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~ 307 (327)
|-|||.+.--++.+.++- |+.||
T Consensus 127 C~~Cg~~~~~~~p~~i~p----------Cp~C~ 149 (160)
T PRK11032 127 CEKCHHHLAFYTPEVLPL----------CPKCG 149 (160)
T ss_pred ecCCCCEEEecCCCcCCC----------CCCCC
No 237
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.35 E-value=33 Score=27.50 Aligned_cols=43 Identities=30% Similarity=0.654 Sum_probs=26.5
Q ss_pred ecCCCCCccccce---------eccccccccCCCCccceeCCCCCceeEEecc
Q 020384 272 KGPCPNCGTENVS---------FFGTILSISSGGTTNTINCSNCGTTMVYDSN 315 (327)
Q Consensus 272 KGpCPNCGeEv~a---------FfGtilsv~s~~~~~~~kChvC~t~L~f~s~ 315 (327)
++.||-||.-++. ++..++-|+.+.= --+-|.+||-.=-|+++
T Consensus 4 ~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f-~~itCk~CgYtEfY~a~ 55 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKF-IVITCKNCGYTEFYSAK 55 (68)
T ss_pred cccCCCcCCcchhhceeeccCCCcceeEEecccEE-EEEEeccCCchhheecc
Confidence 4559999987762 3333444443222 23579999988777754
No 238
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=27.25 E-value=48 Score=29.70 Aligned_cols=28 Identities=32% Similarity=0.790 Sum_probs=17.8
Q ss_pred eeecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 270 iLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
.|..-|+.||++.. . .+.++.+|.+|+.
T Consensus 147 vv~a~~~~~g~~~~---------~--~~~~~~~c~~~~~ 174 (189)
T PRK09521 147 VIYAMCSRCRTPLV---------K--KGENELKCPNCGN 174 (189)
T ss_pred EEEEEccccCCceE---------E--CCCCEEECCCCCC
Confidence 34556888887761 1 2446788888884
No 239
>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=27.06 E-value=1.7e+02 Score=29.23 Aligned_cols=69 Identities=16% Similarity=0.421 Sum_probs=47.7
Q ss_pred ccChHHHhhhHhhhhh-----cCCee-----EEeCh-hhHHHHHHHHhhh----cC---------CCccChHHHHHHHHH
Q 020384 116 VMSNEEFDNLKEELMW-----EGSSV-----VMLSS-AEQKFLEASMAYV----AG---------KPIMSDEEYDKLKQK 171 (327)
Q Consensus 116 ~~sdeefd~LkEeL~w-----eGSsv-----v~L~~-~Eq~fLEA~~AY~----sG---------kPimsDeeFD~LK~k 171 (327)
++.|.+.|..=+.+.| .|..| |.+-+ .-.+|++++.... -| -|+++.+.+|+++..
T Consensus 237 V~~dAdl~~aa~~i~~~~~~~~GQ~C~a~~~v~V~~~v~~~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~ 316 (457)
T cd07114 237 VFDDADLDAAVNGVVAGIFAAAGQTCVAGSRLLVQRSIYDEFVERLVARARAIRVGDPLDPETQMGPLATERQLEKVERY 316 (457)
T ss_pred ECCCCCHHHHHHHHHHHHHhccCCCCCCCceEEEcHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCcCHHHHHHHHHH
Confidence 4568888888888877 45544 34433 3467888866543 23 378899999999998
Q ss_pred Hhhc---CCceeeecC
Q 020384 172 LKME---GSEIVVEGP 184 (327)
Q Consensus 172 Lk~~---GS~VVvk~P 184 (327)
+... |.+++.-|.
T Consensus 317 i~~a~~~ga~~l~gg~ 332 (457)
T cd07114 317 VARAREEGARVLTGGE 332 (457)
T ss_pred HHHHHHCCCEEEeCCC
Confidence 8754 888766543
No 240
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=26.97 E-value=23 Score=37.25 Aligned_cols=52 Identities=29% Similarity=0.554 Sum_probs=35.4
Q ss_pred ecCCCCCccccceeccccccc--c---CCCCccceeCCCCCceeEEeccceeeecCC
Q 020384 272 KGPCPNCGTENVSFFGTILSI--S---SGGTTNTINCSNCGTTMVYDSNTRLITLPE 323 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv--~---s~~~~~~~kChvC~t~L~f~s~~R~itl~~ 323 (327)
+-||+-||.+..+=.|.-.+- + +.+...-.+|..||+...|-+.+..+.|=+
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPRYNdp~kLLe 217 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPRYNDPIKLLE 217 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCcccCCHHHHHh
Confidence 568999999987554442111 1 222344578999999999998887776643
No 241
>PF03317 ELF: ELF protein; InterPro: IPR004990 This is a family of hypothetical proteins from cereal crops.
Probab=26.97 E-value=1.5e+02 Score=28.83 Aligned_cols=106 Identities=20% Similarity=0.248 Sum_probs=67.5
Q ss_pred ccccccccccCccccccccCccccccccccccccccccccccccchhHHHHHHHHHHHHhhhcCccccC----hHHHhhh
Q 020384 50 FTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMS----NEEFDNL 125 (327)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~i~~yCsiD~~~k~slge~E~~fl~Al~~fY~~gk~~~s----deefd~L 125 (327)
++-|-|+|++..+-+.-.+.-++|=-...+++++|--|..- .-.+|+.+|-..=.++.+ ..-|..|
T Consensus 144 IPGRLrLFLMEE~~S~~R~DliQefvalY~r~g~~LPiEPY----------lleealrSYlD~i~atD~fsiLqAaYQdL 213 (284)
T PF03317_consen 144 IPGRLRLFLMEEKLSSMRQDLIQEFVALYQRSGPVLPIEPY----------LLEEALRSYLDHIHATDSFSILQAAYQDL 213 (284)
T ss_pred CcchhhhhhhHhHHHHHHHHHHHHHHHHHHccCCcccccHH----------HHHHHHHHHHHhhcccccHHHHHHHHHHH
Confidence 34566777777666655555555543456666666554321 223466666555333333 7889999
Q ss_pred HhhhhhcCCeeEEeChh--hHHHHHHHHhhhcCCCccChHHHHHHHHHHhhcCC
Q 020384 126 KEELMWEGSSVVMLSSA--EQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS 177 (327)
Q Consensus 126 kEeL~weGSsvv~L~~~--Eq~fLEA~~AY~sGkPimsDeeFD~LK~kLk~~GS 177 (327)
+|. +|-|+.+..-- .|.||||-.+- .-+-+++++.+|+|-
T Consensus 214 ren---e~GS~FF~~~VSHNrD~LeA~ss~---------Rr~~Eveqrirw~~I 255 (284)
T PF03317_consen 214 REN---EEGSVFFRDVVSHNRDFLEAESSA---------RRCLEVEQRIRWEEI 255 (284)
T ss_pred Hhc---CCCcEEeHhhhhccHhHHHHHhhh---------hHHHHHHHHhhhhhh
Confidence 998 78777766544 59999996543 346788999999873
No 242
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.89 E-value=33 Score=35.56 Aligned_cols=32 Identities=31% Similarity=0.700 Sum_probs=22.5
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
+--||-||.-. +|.+.. ..+|..||+.+--..
T Consensus 350 ~p~Cp~Cg~~m----------~S~G~~-g~rC~kCg~~~~~~~ 381 (421)
T COG1571 350 NPVCPRCGGRM----------KSAGRN-GFRCKKCGTRARETL 381 (421)
T ss_pred CCCCCccCCch----------hhcCCC-CcccccccccCCccc
Confidence 44799999654 333444 899999999865443
No 243
>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=26.80 E-value=43 Score=34.64 Aligned_cols=20 Identities=20% Similarity=0.679 Sum_probs=15.6
Q ss_pred ceeCCCCCceeEEeccceee
Q 020384 300 TINCSNCGTTMVYDSNTRLI 319 (327)
Q Consensus 300 ~~kChvC~t~L~f~s~~R~i 319 (327)
.++|++|+..|+|....+..
T Consensus 222 ~~~C~~C~~~l~~h~~~~~l 241 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEGKL 241 (505)
T ss_pred ccCCCCCCCceEEecCCCeE
Confidence 35899999999998655543
No 244
>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=26.54 E-value=1e+02 Score=25.74 Aligned_cols=32 Identities=34% Similarity=0.618 Sum_probs=24.7
Q ss_pred HHHHHHHHhhhcCCCcc--------------ChHHHHHHHHHHhhcC
Q 020384 144 QKFLEASMAYVAGKPIM--------------SDEEYDKLKQKLKMEG 176 (327)
Q Consensus 144 q~fLEA~~AY~sGkPim--------------sDeeFD~LK~kLk~~G 176 (327)
++|++.+..+ .++|+. +.+.+|+++++|+.+|
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 7899999888 788875 4689999999999988
No 245
>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=26.04 E-value=22 Score=39.86 Aligned_cols=20 Identities=35% Similarity=0.572 Sum_probs=0.0
Q ss_pred cceeeecCCCCCccccceec
Q 020384 267 ESLILKGPCPNCGTENVSFF 286 (327)
Q Consensus 267 D~liLKGpCPNCGeEv~aFf 286 (327)
+..|-.--||+||++.+.+.
T Consensus 650 ~vei~~r~Cp~Cg~~t~~~~ 669 (900)
T PF03833_consen 650 EVEIGRRRCPKCGKETFYNR 669 (900)
T ss_dssp --------------------
T ss_pred EEeeecccCcccCCcchhhc
Confidence 34667778999999877654
No 246
>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=25.77 E-value=25 Score=27.04 Aligned_cols=12 Identities=33% Similarity=0.725 Sum_probs=4.9
Q ss_pred ecCCCCCccccc
Q 020384 272 KGPCPNCGTENV 283 (327)
Q Consensus 272 KGpCPNCGeEv~ 283 (327)
+-+||.||.++.
T Consensus 2 ~v~CP~C~k~~~ 13 (57)
T PF03884_consen 2 TVKCPICGKPVE 13 (57)
T ss_dssp EEE-TTT--EEE
T ss_pred cccCCCCCCeec
Confidence 445666666543
No 247
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.64 E-value=35 Score=25.03 Aligned_cols=37 Identities=27% Similarity=0.627 Sum_probs=26.2
Q ss_pred eeeecCCCCCccccc-eeccccccccCCCCccceeCCCCCcee
Q 020384 269 LILKGPCPNCGTENV-SFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 269 liLKGpCPNCGeEv~-aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
.+-.|.|-.|+.++- +.+-.+ ..+ ..-+.|++||+.|
T Consensus 19 ~v~~~~C~gC~~~l~~~~~~~i---~~~--~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 19 RVEGGTCSGCHMELPPQELNEI---RKG--DEIVFCPNCGRIL 56 (56)
T ss_pred EeeCCccCCCCEEcCHHHHHHH---HcC--CCeEECcCCCccC
Confidence 344689999999987 444333 332 5678999999865
No 248
>PRK09401 reverse gyrase; Reviewed
Probab=25.23 E-value=29 Score=39.87 Aligned_cols=16 Identities=44% Similarity=0.960 Sum_probs=12.1
Q ss_pred eeeecCCCCCccccce
Q 020384 269 LILKGPCPNCGTENVS 284 (327)
Q Consensus 269 liLKGpCPNCGeEv~a 284 (327)
.+-++.|||||-++-+
T Consensus 4 ~~y~~~cpnc~g~i~~ 19 (1176)
T PRK09401 4 AIYKNSCPNCGGDISD 19 (1176)
T ss_pred hhhcccCCCCCCcCcH
Confidence 3567889999987753
No 249
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=25.18 E-value=30 Score=31.81 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=20.5
Q ss_pred ccChHHHHHHHHHHhhcCCceeee
Q 020384 159 IMSDEEYDKLKQKLKMEGSEIVVE 182 (327)
Q Consensus 159 imsDeeFD~LK~kLk~~GS~VVvk 182 (327)
.+.|.|--+|=+-||-.|-+++.-
T Consensus 9 F~vD~mLG~LARwLRllGydt~~~ 32 (165)
T COG1656 9 FVVDAMLGKLARWLRLLGYDTVYS 32 (165)
T ss_pred eeHHHhHHHHHHHHHHcCCceeee
Confidence 568999999999999999887763
No 250
>PTZ00381 aldehyde dehydrogenase family protein; Provisional
Probab=25.15 E-value=1.7e+02 Score=30.27 Aligned_cols=67 Identities=24% Similarity=0.471 Sum_probs=47.5
Q ss_pred ccChHHHhhhHhhhhhc-----CCee-----EEe-ChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHH
Q 020384 116 VMSNEEFDNLKEELMWE-----GSSV-----VML-SSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQK 171 (327)
Q Consensus 116 ~~sdeefd~LkEeL~we-----GSsv-----v~L-~~~Eq~fLEA~~A----Y~sGk---------PimsDeeFD~LK~k 171 (327)
++.|.+.|.--+.+.|. |-.| +.+ .....+|++++.+ ++ |. |+++++.|++++.-
T Consensus 224 V~~dAdl~~Aa~~i~~g~~~naGQ~C~A~~~vlV~~~i~d~f~~~l~~~~~~~~-g~~~~~~~~~gpli~~~~~~ri~~~ 302 (493)
T PTZ00381 224 VDKSCNLKVAARRIAWGKFLNAGQTCVAPDYVLVHRSIKDKFIEALKEAIKEFF-GEDPKKSEDYSRIVNEFHTKRLAEL 302 (493)
T ss_pred EcCCCCHHHHHHHHHHHHHhhcCCcCCCCCEEEEeHHHHHHHHHHHHHHHHHHh-CCCCccCCCcCCCCCHHHHHHHHHH
Confidence 55688888888888883 5443 333 3345678887543 44 43 67999999999999
Q ss_pred HhhcCCceeeec
Q 020384 172 LKMEGSEIVVEG 183 (327)
Q Consensus 172 Lk~~GS~VVvk~ 183 (327)
++.+|.+++.-|
T Consensus 303 i~~~ga~~~~gG 314 (493)
T PTZ00381 303 IKDHGGKVVYGG 314 (493)
T ss_pred HHhCCCcEEECC
Confidence 988898887644
No 251
>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=25.10 E-value=46 Score=26.66 Aligned_cols=29 Identities=28% Similarity=0.611 Sum_probs=17.1
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
-| .||.-.++= .+....+| +||..|....
T Consensus 5 rC-~Cgr~lya~----------e~~kTkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 5 RC-DCGRYLYAK----------EGAKTKKC-VCGKTLKVKE 33 (68)
T ss_dssp EE-TTS--EEEE----------TT-SEEEE-TTTEEEE--S
T ss_pred Ee-cCCCEEEec----------CCcceeEe-cCCCeeeeee
Confidence 36 677655443 35667899 9999998764
No 252
>PF12207 DUF3600: Domain of unknown function (DUF3600); InterPro: IPR022019 This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C-terminal of the putative ecf-type sigma factor negative effector. ; PDB: 3FGG_A 3FH3_A.
Probab=24.98 E-value=32 Score=31.50 Aligned_cols=66 Identities=32% Similarity=0.438 Sum_probs=38.2
Q ss_pred cccchhHHHHHH--HHHHHHhhh------cCccccChHHHhhhHhhhhh-------cCCe-eEEeChh----hHHHHHHH
Q 020384 91 EKKSLGELEQEF--LQALQAFYY------EGKAVMSNEEFDNLKEELMW-------EGSS-VVMLSSA----EQKFLEAS 150 (327)
Q Consensus 91 ~k~slge~E~~f--l~Al~~fY~------~gk~~~sdeefd~LkEeL~w-------eGSs-vv~L~~~----Eq~fLEA~ 150 (327)
++-|.+|.|+.= .--||-||. ..|.+|+++|||.-+|.||= .||+ -+++... -++|++|.
T Consensus 72 e~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~vlt~~E~d~y~eALm~~e~v~vk~~~~~~~~ve~vpe~~~e~f~~a~ 151 (162)
T PF12207_consen 72 EKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEVLTQEEYDQYIEALMTYETVRVKTKSSGGITVEEVPEAYKERFIKAE 151 (162)
T ss_dssp GGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHHS-HHHHHHHHHHHHHHHHHHHHCT-SS---GGGS-HHHHHHHHHHH
T ss_pred HhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhhcCHHHHHHHHHHHhhhheeeeeccCCCCCcHHhccHHHHHHHHHHH
Confidence 455666666432 223566664 34669999999999999986 3433 3333322 37899885
Q ss_pred H--hhhcC
Q 020384 151 M--AYVAG 156 (327)
Q Consensus 151 ~--AY~sG 156 (327)
+ -|.++
T Consensus 152 ~~~~yv~~ 159 (162)
T PF12207_consen 152 QFMEYVNE 159 (162)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 4 47654
No 253
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=24.87 E-value=1.2e+02 Score=24.30 Aligned_cols=33 Identities=33% Similarity=0.493 Sum_probs=26.1
Q ss_pred chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 020384 94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL 129 (327)
Q Consensus 94 slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL 129 (327)
.+.+.+..+++-+...=.+| ++++||++.|+.|
T Consensus 152 ~~~~~~~~~~~~l~~l~~~~---~s~~el~~~k~~L 184 (184)
T PF05193_consen 152 NLDEAIEAILQELKRLREGG---ISEEELERAKNQL 184 (184)
T ss_dssp GHHHHHHHHHHHHHHHHHHC---S-HHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHcC---CCHHHHHHHHhcC
Confidence 56777778888887777765 9999999999876
No 254
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.81 E-value=40 Score=20.86 Aligned_cols=22 Identities=32% Similarity=0.786 Sum_probs=15.5
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
.|+.|+..|++- +.+|..|+++
T Consensus 4 ~C~~C~~~N~~~--------------~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFAS--------------RSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChhh--------------hccccccCCc
Confidence 588888666543 4578888874
No 255
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=24.70 E-value=21 Score=31.58 Aligned_cols=35 Identities=26% Similarity=0.766 Sum_probs=23.6
Q ss_pred ecCCCCCccccce---eccccccccCCCCccceeCCCCCceeEE
Q 020384 272 KGPCPNCGTENVS---FFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 272 KGpCPNCGeEv~a---FfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
.-+||.||..+.. =||.- .=+.-..|..|..+..|
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 3689999988764 44432 13466789888877654
No 256
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=24.50 E-value=25 Score=28.31 Aligned_cols=32 Identities=31% Similarity=0.612 Sum_probs=25.3
Q ss_pred CCCCCccccc--eeccccccccCCCCccceeCCCCCce
Q 020384 274 PCPNCGTENV--SFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 274 pCPNCGeEv~--aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
-|-+||.+.. ..+|| +.+++.|+--|.-|=..
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 4899999987 56788 67788999889888443
No 257
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=24.41 E-value=50 Score=28.42 Aligned_cols=39 Identities=23% Similarity=0.327 Sum_probs=26.6
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeEEe
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD 313 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~ 313 (327)
.-|++|.+...-.. ...|.--.....+.|+.||...-|.
T Consensus 57 ~~CkkC~t~Lvpg~--n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 57 TICKKCYTPLVPGK--NARVRLRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred HhccccCcccccCc--ceEEEEcCCeEEEEecCCCcEEEec
Confidence 56999998644332 2233333344788999999998886
No 258
>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=24.27 E-value=53 Score=28.50 Aligned_cols=27 Identities=26% Similarity=0.794 Sum_probs=19.0
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCcee
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM 310 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L 310 (327)
-+||.|+.|. +|- +.+..-|+-|+-.-
T Consensus 3 p~CP~C~sey-tY~----------dg~~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEY-TYH----------DGTQLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcc-eEe----------cCCeeECccccccc
Confidence 4799999874 552 44557899998543
No 259
>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=24.09 E-value=2.2e+02 Score=28.81 Aligned_cols=70 Identities=21% Similarity=0.403 Sum_probs=48.3
Q ss_pred ccChHHHhhhHhhhhh-----cCC-----eeEEeC-hhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHH
Q 020384 116 VMSNEEFDNLKEELMW-----EGS-----SVVMLS-SAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQK 171 (327)
Q Consensus 116 ~~sdeefd~LkEeL~w-----eGS-----svv~L~-~~Eq~fLEA~~A----Y~sGk---------PimsDeeFD~LK~k 171 (327)
++.|.+.|..-+.+.| .|- +.|.+- ..-.+|+|++.+ ..-|. |+++.+.+|+++.-
T Consensus 236 V~~daDl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~~~f~~~l~~~~~~l~~G~p~~~~~~~gpli~~~~~~~~~~~ 315 (455)
T cd07120 236 VFDDADLDAALPKLERALTIFAGQFCMAGSRVLVQRSIADEVRDRLAARLAAVKVGPGLDPASDMGPLIDRANVDRVDRM 315 (455)
T ss_pred ECCCCCHHHHHHHHHHHHHHhCCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhcCcCCCCCCCCCcCCccCHHHHHHHHHH
Confidence 5568889998888888 353 233443 445778888654 33343 68999999999987
Q ss_pred Hhh---cCCceeeecCe
Q 020384 172 LKM---EGSEIVVEGPR 185 (327)
Q Consensus 172 Lk~---~GS~VVvk~Pr 185 (327)
+.. +|.+++..|.+
T Consensus 316 i~~a~~~ga~~~~~g~~ 332 (455)
T cd07120 316 VERAIAAGAEVVLRGGP 332 (455)
T ss_pred HHHHHHCCCEEEeCCcc
Confidence 765 68888876643
No 260
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.03 E-value=62 Score=25.37 Aligned_cols=43 Identities=26% Similarity=0.541 Sum_probs=30.1
Q ss_pred hhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 264 IVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 264 ~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
-++|++-+|-|=| ||+--+-- -.-+..-+.||.|||..+..-+
T Consensus 6 ~l~~~VEMKK~H~-Cg~NrwkI-------iRvGaDIkikC~nC~h~vm~pR 48 (60)
T COG4481 6 DLGDIVEMKKPHA-CGTNRWKI-------IRVGADIKIKCENCGHSVMMPR 48 (60)
T ss_pred cccchheecCCCc-cccceEEE-------EEecCcEEEEecCCCcEEEecH
Confidence 4688999998876 77732222 2235777899999999876543
No 261
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=23.97 E-value=65 Score=23.75 Aligned_cols=22 Identities=41% Similarity=0.768 Sum_probs=18.3
Q ss_pred ccChHHHHHHHHHHhhcCCceeeec
Q 020384 159 IMSDEEYDKLKQKLKMEGSEIVVEG 183 (327)
Q Consensus 159 imsDeeFD~LK~kLk~~GS~VVvk~ 183 (327)
++++++|+.++. +.|..|.|.|
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 6899999875
No 262
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.71 E-value=45 Score=36.03 Aligned_cols=24 Identities=25% Similarity=0.563 Sum_probs=16.7
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCceeE
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV 311 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~ 311 (327)
--|++||-. +. ...+|++||..++
T Consensus 627 ~~C~~CG~~-----~g----------~~~~CP~CG~~~~ 650 (656)
T PRK08270 627 SICPKHGYL-----SG----------EHEFCPKCGEETE 650 (656)
T ss_pred cccCCCCCc-----CC----------CCCCCcCCcCccc
Confidence 469999942 11 1378999998754
No 263
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=23.67 E-value=51 Score=33.35 Aligned_cols=49 Identities=22% Similarity=0.375 Sum_probs=30.3
Q ss_pred eeecCCCCCccccc---------eeccccccccCCCCccceeCCCCCceeEEeccceeeec
Q 020384 270 ILKGPCPNCGTENV---------SFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL 321 (327)
Q Consensus 270 iLKGpCPNCGeEv~---------aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~~R~itl 321 (327)
+-.+.||.||.++- =||-+...+.=+...|-.-|+.|| .+....|-+..
T Consensus 4 ~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg---a~~~~~~W~~~ 61 (355)
T COG1499 4 ASTILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCG---AYRIRGRWVDE 61 (355)
T ss_pred CcccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCC---CccCCCcceec
Confidence 45678999999983 244433233444467778899999 34444444443
No 264
>PRK15398 aldehyde dehydrogenase EutE; Provisional
Probab=23.63 E-value=1.6e+02 Score=30.17 Aligned_cols=59 Identities=12% Similarity=0.294 Sum_probs=44.8
Q ss_pred ccChHHHhhhHhhhhh-----cCCee------EEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhcC
Q 020384 116 VMSNEEFDNLKEELMW-----EGSSV------VMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 176 (327)
Q Consensus 116 ~~sdeefd~LkEeL~w-----eGSsv------v~L~~~Eq~fLEA~~AY~sGkPimsDeeFD~LK~kLk~~G 176 (327)
++.|.+.|.--+.+.| .|..| ++=...-.+|++++.+. +.|+++.+++|+++.-+...|
T Consensus 247 V~~dADld~Aa~~i~~g~~~n~GQ~C~A~~rvlV~~si~d~f~~~l~~~--~~~li~~~~~~~v~~~l~~~~ 316 (465)
T PRK15398 247 VDETADIEKAARDIVKGASFDNNLPCIAEKEVIVVDSVADELMRLMEKN--GAVLLTAEQAEKLQKVVLKNG 316 (465)
T ss_pred EecCCCHHHHHHHHHHhcccCCCCcCCCCceEEEeHHHHHHHHHHHHHc--CCccCCHHHHHHHHHHHhhcc
Confidence 4457788888888888 45543 34444457899998887 789999999999998877554
No 265
>PF13058 DUF3920: Protein of unknown function (DUF3920)
Probab=23.55 E-value=35 Score=30.07 Aligned_cols=47 Identities=32% Similarity=0.531 Sum_probs=35.7
Q ss_pred cccccccc--ccchhHHHHHHHHHHHHhhhcCccc---cChHHHhhhHhhhh
Q 020384 84 YCSIDKKE--KKSLGELEQEFLQALQAFYYEGKAV---MSNEEFDNLKEELM 130 (327)
Q Consensus 84 yCsiD~~~--k~slge~E~~fl~Al~~fY~~gk~~---~sdeefd~LkEeL~ 130 (327)
+|..=+.. -.+|||.|-+||.++..||-..|.+ .-=|||+.+=+.|.
T Consensus 30 FcdTc~an~vl~~LgeeeeefLf~~~g~y~kek~~iFv~~we~y~qvlktll 81 (126)
T PF13058_consen 30 FCDTCDANKVLLSLGEEEEEFLFPAGGFYHKEKQLIFVCMWEEYEQVLKTLL 81 (126)
T ss_pred EecccchhHHHHHhccchhhhccccchhhhccccEEEEEehHHHHHHHHHHH
Confidence 55443333 3389999999999999999998873 34788988877764
No 266
>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=23.26 E-value=39 Score=30.55 Aligned_cols=20 Identities=15% Similarity=0.403 Sum_probs=18.1
Q ss_pred hhccceeeecCCCCCccccc
Q 020384 264 IVRESLILKGPCPNCGTENV 283 (327)
Q Consensus 264 ~~~D~liLKGpCPNCGeEv~ 283 (327)
-|++.+|+...||+||-.+.
T Consensus 20 ~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 20 YFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CcceEEEEEEECCCCCCchh
Confidence 48999999999999998776
No 267
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=23.24 E-value=38 Score=30.92 Aligned_cols=32 Identities=22% Similarity=0.596 Sum_probs=13.9
Q ss_pred eeeecCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 269 liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
++---+|+.||.+..+-. +...+..+|+-|.-
T Consensus 131 ~l~l~~C~~C~~~fv~~~--------~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 131 MLQLAPCRRCGGHFVTHA--------HDPRHSFVCPFCQP 162 (175)
T ss_dssp SEEEEE-TTT--EEEEES--------S--SS----TT---
T ss_pred CccccCCCCCCCCeECcC--------CCCCcCcCCCCCCC
Confidence 455568999999876542 23478899999984
No 268
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=23.22 E-value=37 Score=25.24 Aligned_cols=9 Identities=67% Similarity=1.516 Sum_probs=8.0
Q ss_pred CCCCCcccc
Q 020384 274 PCPNCGTEN 282 (327)
Q Consensus 274 pCPNCGeEv 282 (327)
.||.||+.|
T Consensus 13 kCp~CGt~N 21 (44)
T PF14952_consen 13 KCPKCGTYN 21 (44)
T ss_pred cCCcCcCcc
Confidence 699999987
No 269
>PF09930 DUF2162: Predicted transporter (DUF2162); InterPro: IPR017199 This group represents a predicted membrane transporter, MTH672 type.
Probab=23.15 E-value=70 Score=30.38 Aligned_cols=36 Identities=33% Similarity=0.354 Sum_probs=23.7
Q ss_pred HHhhhhHHHHHHHHHHHhh--------hccceeeecCCCCCcccc
Q 020384 246 WFAAVPLIVYLSQSLTKLI--------VRESLILKGPCPNCGTEN 282 (327)
Q Consensus 246 ~~~~~P~i~~~a~~Lt~l~--------~~D~liLKGpCPNCGeEv 282 (327)
..+++=+++|.-..+.+ | .+..+++--|||.|-+-+
T Consensus 72 ~imal~li~~Gi~ti~~-W~~~~~~~s~~t~lal~~PCPvCl~Ai 115 (224)
T PF09930_consen 72 LIMALLLIYAGIYTIKK-WKKSGKDSSRRTFLALSLPCPVCLTAI 115 (224)
T ss_pred HHHHHHHHHHHHHHHHH-HcccCCCCcccchhhhhcCchHHHHHH
Confidence 34455556566555544 4 355789999999997654
No 270
>PRK06427 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed
Probab=23.13 E-value=3e+02 Score=25.01 Aligned_cols=54 Identities=22% Similarity=0.388 Sum_probs=36.2
Q ss_pred hhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHH-HHHHHHHHhhcCC-ceeeecC
Q 020384 123 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEE-YDKLKQKLKMEGS-EIVVEGP 184 (327)
Q Consensus 123 d~LkEeL~weGSsvv~L~~~Eq~fLEA~~AY~sGkPimsDee-FD~LK~kLk~~GS-~VVvk~P 184 (327)
+.++++| .....+++.+..|-+.| .|.++-++++ ..+.-.+|...|- .|++++-
T Consensus 124 ~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~~a~~l~~~g~~~Vvit~g 179 (266)
T PRK06427 124 AALRERL-LPLATLITPNLPEAEAL-------TGLPIADTEDEMKAAARALHALGCKAVLIKGG 179 (266)
T ss_pred HHHHHhh-hCcCeEEcCCHHHHHHH-------hCCCCCCcHHHHHHHHHHHHhcCCCEEEEcCC
Confidence 4566654 35677999999998877 3666655554 5566667777775 5666653
No 271
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=23.13 E-value=48 Score=33.68 Aligned_cols=51 Identities=20% Similarity=0.307 Sum_probs=26.0
Q ss_pred HHhhhccceeeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 261 TKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 261 t~l~~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
+.-...+-.-..--||+||.=..+= +..+.....+-+..|+.||-.-+.+-
T Consensus 163 ~~~~~~~y~Pf~piC~~cGri~tt~---v~~~d~~~~~v~Y~c~~cG~~g~~~i 213 (360)
T PF01921_consen 163 GRERPETYSPFLPICEKCGRIDTTE---VTEYDPEGGTVTYRCEECGHEGEVDI 213 (360)
T ss_dssp HHT--TT--SEEEEETTTEE--EEE---EEEE--SSSEEEEE--TTS---EEET
T ss_pred CcCCCCCeeeeeeeccccCCcccce---eeEeecCCCEEEEEecCCCCEEEEec
Confidence 3335566677788899999822211 12224446788999999999988873
No 272
>KOG3457 consensus Sec61 protein translocation complex, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=23.06 E-value=49 Score=27.73 Aligned_cols=29 Identities=28% Similarity=0.500 Sum_probs=20.6
Q ss_pred hhccccccceeeeeeccCCCChhHHHHHH
Q 020384 219 FFFLDDITGFEITYLLELPEPFSFIFTWF 247 (327)
Q Consensus 219 ~~~ldd~~Gf~i~~~~~lpeP~~fi~t~~ 247 (327)
.|+-||+.|+.|.....|-=.++||+.++
T Consensus 47 kfYTDda~GlKV~PvvVLvmSvgFIasV~ 75 (88)
T KOG3457|consen 47 KFYTDDAPGLKVDPVVVLVMSVGFIASVF 75 (88)
T ss_pred EEeecCCCCceeCCeeehhhhHHHHHHHH
Confidence 45669999999876665555577777554
No 273
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.05 E-value=59 Score=22.89 Aligned_cols=17 Identities=24% Similarity=0.737 Sum_probs=13.4
Q ss_pred cceeCCCCCceeEEecc
Q 020384 299 NTINCSNCGTTMVYDSN 315 (327)
Q Consensus 299 ~~~kChvC~t~L~f~s~ 315 (327)
..+.|+.||..|.....
T Consensus 4 g~l~C~~CG~~m~~~~~ 20 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRRKR 20 (58)
T ss_pred CcEEcccCCcEeEEEEC
Confidence 45789999999988753
No 274
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=22.89 E-value=49 Score=28.52 Aligned_cols=42 Identities=26% Similarity=0.537 Sum_probs=28.8
Q ss_pred hccceeeecCCCCCccccceeccccccccCCCCccc--eeCCCCCc
Q 020384 265 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNT--INCSNCGT 308 (327)
Q Consensus 265 ~~D~liLKGpCPNCGeEv~aFfGtilsv~s~~~~~~--~kChvC~t 308 (327)
+.|+---..+||-||.+--.|| -+-+.|...+.. .||-+|+-
T Consensus 58 ~~nv~~t~~~Cp~Cgh~rayF~--qlQtRSADEPmT~FYkC~~C~~ 101 (105)
T KOG2906|consen 58 WENVDQTEATCPTCGHERAYFM--QLQTRSADEPMTTFYKCCKCKH 101 (105)
T ss_pred ccchhhccCcCCCCCCCceEEE--EeeeccCCCcHhHhhhhhcccc
Confidence 3444455678999999876666 345666666654 68988874
No 275
>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=22.75 E-value=39 Score=29.66 Aligned_cols=19 Identities=32% Similarity=0.623 Sum_probs=11.3
Q ss_pred cccChHHHhhhHhh--hhhcC
Q 020384 115 AVMSNEEFDNLKEE--LMWEG 133 (327)
Q Consensus 115 ~~~sdeefd~LkEe--L~weG 133 (327)
++|+||+||+|=.| |+|.|
T Consensus 2 qiLtDeQFdrLW~e~Pvn~~G 22 (118)
T PF08976_consen 2 QILTDEQFDRLWNEMPVNAKG 22 (118)
T ss_dssp ----HHHHHHHHTTS-B-TTS
T ss_pred ccccHHHhhhhhhhCcCCccC
Confidence 58999999999777 35555
No 276
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=22.73 E-value=39 Score=21.53 Aligned_cols=8 Identities=63% Similarity=1.788 Sum_probs=5.6
Q ss_pred CCCCCccc
Q 020384 274 PCPNCGTE 281 (327)
Q Consensus 274 pCPNCGeE 281 (327)
+||+||..
T Consensus 4 ~C~~CgR~ 11 (25)
T PF13913_consen 4 PCPICGRK 11 (25)
T ss_pred cCCCCCCE
Confidence 68888753
No 277
>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=22.67 E-value=2.5e+02 Score=27.46 Aligned_cols=68 Identities=19% Similarity=0.429 Sum_probs=44.2
Q ss_pred cChHHHhhhHhhhhh-----cCC-----eeEE-eChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHH
Q 020384 117 MSNEEFDNLKEELMW-----EGS-----SVVM-LSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKL 172 (327)
Q Consensus 117 ~sdeefd~LkEeL~w-----eGS-----svv~-L~~~Eq~fLEA~~A----Y~sGk---------PimsDeeFD~LK~kL 172 (327)
+.+.+++..-+.+.| .|- ..+. .+..-.+|++++.. +.-|. |+++.+.+++++..+
T Consensus 215 ~~~ad~~~aa~~i~~~~~~~~Gq~C~a~~~i~v~~~~~~~~~~~L~~~l~~~~~g~p~~~~~~~~~~~~~~~~~~~~~~i 294 (432)
T cd07078 215 FDDADLDAAVKGAVFGAFGNAGQVCTAASRLLVHESIYDEFVERLVERVKALKVGNPLDPDTDMGPLISAAQLDRVLAYI 294 (432)
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCccCCceEEEcHHHHHHHHHHHHHHHHccCcCCCCCCCCCCCCCCCHHHHHHHHHHH
Confidence 556677776666555 453 2333 34444678887543 55454 488999999999888
Q ss_pred hh---cCCceeeecC
Q 020384 173 KM---EGSEIVVEGP 184 (327)
Q Consensus 173 k~---~GS~VVvk~P 184 (327)
.. .|.+++.-++
T Consensus 295 ~~~~~~g~~~~~gg~ 309 (432)
T cd07078 295 EDAKAEGAKLLCGGK 309 (432)
T ss_pred HHHHhCCCEEEeCCc
Confidence 76 5777776543
No 278
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=22.55 E-value=40 Score=28.92 Aligned_cols=15 Identities=40% Similarity=0.740 Sum_probs=11.5
Q ss_pred eeecCCCCCccccce
Q 020384 270 ILKGPCPNCGTENVS 284 (327)
Q Consensus 270 iLKGpCPNCGeEv~a 284 (327)
+=.-.||.||+|..+
T Consensus 45 vG~~~cP~Cge~~~~ 59 (102)
T PF04475_consen 45 VGDTICPKCGEELDS 59 (102)
T ss_pred cCcccCCCCCCccCc
Confidence 334579999999873
No 279
>KOG1372 consensus GDP-mannose 4,6 dehydratase [Carbohydrate transport and metabolism]
Probab=22.50 E-value=46 Score=33.43 Aligned_cols=39 Identities=28% Similarity=0.444 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhhcCccc---------cChHHHhh-----hHhhhhhcCCeeE
Q 020384 99 EQEFLQALQAFYYEGKAV---------MSNEEFDN-----LKEELMWEGSSVV 137 (327)
Q Consensus 99 E~~fl~Al~~fY~~gk~~---------~sdeefd~-----LkEeL~weGSsvv 137 (327)
-.+|.+|||.--...+|. -|-+||++ +-|+|+|+|..|=
T Consensus 257 A~dYVEAMW~mLQ~d~PdDfViATge~hsVrEF~~~aF~~ig~~l~Weg~gv~ 309 (376)
T KOG1372|consen 257 AGDYVEAMWLMLQQDSPDDFVIATGEQHSVREFCNLAFAEIGEVLNWEGEGVD 309 (376)
T ss_pred hHHHHHHHHHHHhcCCCCceEEecCCcccHHHHHHHHHHhhCcEEeecccccc
Confidence 358999999988877662 24556655 5799999987653
No 280
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.33 E-value=41 Score=26.83 Aligned_cols=14 Identities=43% Similarity=1.030 Sum_probs=10.8
Q ss_pred eeecCCCCCccccc
Q 020384 270 ILKGPCPNCGTENV 283 (327)
Q Consensus 270 iLKGpCPNCGeEv~ 283 (327)
.++-+||-||.+|-
T Consensus 5 ~~~v~CP~Cgkpv~ 18 (65)
T COG3024 5 RITVPCPTCGKPVV 18 (65)
T ss_pred cccccCCCCCCccc
Confidence 45678999998874
No 281
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.22 E-value=60 Score=35.16 Aligned_cols=40 Identities=20% Similarity=0.250 Sum_probs=24.1
Q ss_pred hhhHHHHHHHHh-hhcCCCcc--------ChHHHHHHHHHHhhcCCceeee
Q 020384 141 SAEQKFLEASMA-YVAGKPIM--------SDEEYDKLKQKLKMEGSEIVVE 182 (327)
Q Consensus 141 ~~Eq~fLEA~~A-Y~sGkPim--------sDeeFD~LK~kLk~~GS~VVvk 182 (327)
-+...||+++.+ ...|+.++ .....++|+.++- +..|++.
T Consensus 172 GKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~l 220 (665)
T PRK14873 172 DWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLG--AGDVAVL 220 (665)
T ss_pred cHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcC--CCcEEEE
Confidence 356678888766 56677654 4566666665551 2456663
No 282
>PF12207 DUF3600: Domain of unknown function (DUF3600); InterPro: IPR022019 This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C-terminal of the putative ecf-type sigma factor negative effector. ; PDB: 3FGG_A 3FH3_A.
Probab=22.20 E-value=68 Score=29.48 Aligned_cols=65 Identities=29% Similarity=0.406 Sum_probs=41.3
Q ss_pred cCccccChHHHhhhHhhhhh-----------cCCe-eEEeChhhHHHHHH----HHhhhc-------CCCccChHHHHHH
Q 020384 112 EGKAVMSNEEFDNLKEELMW-----------EGSS-VVMLSSAEQKFLEA----SMAYVA-------GKPIMSDEEYDKL 168 (327)
Q Consensus 112 ~gk~~~sdeefd~LkEeL~w-----------eGSs-vv~L~~~Eq~fLEA----~~AY~s-------GkPimsDeeFD~L 168 (327)
.-|..|+.+||..-++.|-= +|-- -=-|++.||+.... ++-||+ -|-|++++|||.-
T Consensus 35 qAK~~lgeeEfeef~~lLK~lt~~kLkygD~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~vlt~~E~d~y 114 (162)
T PF12207_consen 35 QAKGELGEEEFEEFKELLKKLTNAKLKYGDKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEVLTQEEYDQY 114 (162)
T ss_dssp HHHHCS-HHHHHHHHHHHHHHHHHHHHHB-TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHHS-HHHHHHH
T ss_pred HHHHhhhHHHHHHHHHHHHHHHHhHHhhcccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhhcCHHHHHHH
Confidence 45789999999888877632 3322 22366778776666 333774 3568999999988
Q ss_pred HHHHhhcC
Q 020384 169 KQKLKMEG 176 (327)
Q Consensus 169 K~kLk~~G 176 (327)
+.-|+.+-
T Consensus 115 ~eALm~~e 122 (162)
T PF12207_consen 115 IEALMTYE 122 (162)
T ss_dssp HHHHHHHH
T ss_pred HHHHhhhh
Confidence 88776553
No 283
>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=21.86 E-value=2.7e+02 Score=27.73 Aligned_cols=68 Identities=16% Similarity=0.314 Sum_probs=46.0
Q ss_pred ccChHHHhhhHhhhhh-----cCCe-----eEEe-ChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHH
Q 020384 116 VMSNEEFDNLKEELMW-----EGSS-----VVML-SSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQK 171 (327)
Q Consensus 116 ~~sdeefd~LkEeL~w-----eGSs-----vv~L-~~~Eq~fLEA~~A----Y~sGk---------PimsDeeFD~LK~k 171 (327)
++.|.+.|..=+.+.| .|-. .|.+ ...-.+|++++.+ +.-|. |+++.+.+++++.-
T Consensus 235 V~~dAdl~~aa~~iv~~~~~~~GQ~C~a~~~v~V~~~i~~~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~i~~~ 314 (450)
T cd07092 235 VFDDADLDAAVAGIATAGYYNAGQDCTAACRVYVHESVYDEFVAALVEAVSAIRVGDPDDEDTEMGPLNSAAQRERVAGF 314 (450)
T ss_pred ECCCCCHHHHHHHHHHHHHhhCCCCCCCCcEEEEeHHHHHHHHHHHHHHHhhCCcCCCCCCCCccCcccCHHHHHHHHHH
Confidence 4568888888888888 4443 3333 3445789988665 33453 57888999999986
Q ss_pred Hhh--cCCceeeec
Q 020384 172 LKM--EGSEIVVEG 183 (327)
Q Consensus 172 Lk~--~GS~VVvk~ 183 (327)
+.. +|.+++.-|
T Consensus 315 i~~a~~ga~~~~gg 328 (450)
T cd07092 315 VERAPAHARVLTGG 328 (450)
T ss_pred HHHHHcCCEEEeCC
Confidence 654 377776644
No 284
>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=21.74 E-value=67 Score=21.16 Aligned_cols=9 Identities=56% Similarity=1.409 Sum_probs=3.6
Q ss_pred CCCCccccc
Q 020384 275 CPNCGTENV 283 (327)
Q Consensus 275 CPNCGeEv~ 283 (327)
||.||+++.
T Consensus 2 CP~C~s~l~ 10 (28)
T PF03119_consen 2 CPVCGSKLV 10 (28)
T ss_dssp -TTT--BEE
T ss_pred cCCCCCEeE
Confidence 666666655
No 285
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=21.73 E-value=58 Score=32.67 Aligned_cols=32 Identities=19% Similarity=0.214 Sum_probs=21.5
Q ss_pred eeecCCCCCccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 270 iLKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
=.-+-|++||..-.... ....+|+.||..+..
T Consensus 242 g~~~~C~~c~~~~~~~~-----------~~~~~C~~c~~~~~~ 273 (382)
T PRK04338 242 GYVYYCPKCLYREEVEG-----------LPPEECPVCGGKFGT 273 (382)
T ss_pred eeEEECCCCCcEEEecC-----------CCCCCCCCCCCccee
Confidence 34578999997554321 234579999987654
No 286
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=21.69 E-value=1.7e+02 Score=22.79 Aligned_cols=34 Identities=18% Similarity=0.332 Sum_probs=28.3
Q ss_pred HHHHHHHHhhhcCCCccChHHHHHHHHHHhhcCC
Q 020384 144 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS 177 (327)
Q Consensus 144 q~fLEA~~AY~sGkPimsDeeFD~LK~kLk~~GS 177 (327)
..|||=..+--.|+|+||-+||-+-..+=++.|-
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 5688888888899999999999988777776553
No 287
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.67 E-value=25 Score=33.81 Aligned_cols=40 Identities=20% Similarity=0.445 Sum_probs=30.0
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCceeEEec
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS 314 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s 314 (327)
=.+.|-.|+..+.+=| +..|.. .-.-+.|+.||+.|-|+-
T Consensus 196 ~g~~C~GC~m~l~~~~--~~~V~~--~d~iv~CP~CgRILy~~e 235 (239)
T COG1579 196 EGRVCGGCHMKLPSQT--LSKVRK--KDEIVFCPYCGRILYYDE 235 (239)
T ss_pred cCCcccCCeeeecHHH--HHHHhc--CCCCccCCccchHHHhhh
Confidence 3578999999998654 334443 556789999999988774
No 288
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.57 E-value=1.1e+02 Score=26.35 Aligned_cols=51 Identities=27% Similarity=0.346 Sum_probs=38.8
Q ss_pred ccchhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhhhcCCeeEEeChhhHHHHHHHH
Q 020384 92 KKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASM 151 (327)
Q Consensus 92 k~slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~weGSsvv~L~~~Eq~fLEA~~ 151 (327)
+..-+|.|.-|-+-+|+.++ .....+.||||..++.|.= .+++-+-|||+.
T Consensus 32 ~~~~~evE~~~r~~~q~~ln-kLDlVsREEFdvq~qvl~r--------tR~kl~~Leari 82 (103)
T COG2960 32 QEVRAEVEKAFRAQLQRQLN-KLDLVSREEFDVQRQVLLR--------TREKLAALEARI 82 (103)
T ss_pred hhhHHHHHHHHHHHHHHHHh-hhhhhhHHHHHHHHHHHHH--------HHHHHHHHHHHH
Confidence 34558999999999999986 5789999999999998643 344555555554
No 289
>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=21.52 E-value=58 Score=24.87 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=22.4
Q ss_pred CCCCCccccceeccccccccCCCCccceeCCCCCceeEEecc
Q 020384 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN 315 (327)
Q Consensus 274 pCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f~s~ 315 (327)
-|++|+-=...- +.-..-+.||+-|++.-.+++.
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 488887543321 1224568899999998888754
No 290
>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=21.43 E-value=1.8e+02 Score=25.02 Aligned_cols=40 Identities=25% Similarity=0.470 Sum_probs=28.7
Q ss_pred cccChHHHhhhHhhhhhcCCeeEEeChh----hHHHHHHHHhhhcCCC
Q 020384 115 AVMSNEEFDNLKEELMWEGSSVVMLSSA----EQKFLEASMAYVAGKP 158 (327)
Q Consensus 115 ~~~sdeefd~LkEeL~weGSsvv~L~~~----Eq~fLEA~~AY~sGkP 158 (327)
..||.|||+.|=++ +.++|.++-. ..+.++++.+|....+
T Consensus 82 ~~Ls~eEf~~L~~~----~~~LV~~rg~WV~ld~~~l~~~~~~~~~~~ 125 (141)
T PF12419_consen 82 EELSEEEFEQLVEQ----KRPLVRFRGRWVELDPEELRRALAFLEKAP 125 (141)
T ss_pred EECCHHHHHHHHHc----CCCeEEECCEEEEECHHHHHHHHHHHHhcc
Confidence 68999999998875 6777776644 4666777777665544
No 291
>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=21.39 E-value=2.6e+02 Score=27.82 Aligned_cols=70 Identities=23% Similarity=0.435 Sum_probs=47.0
Q ss_pred ccChHHHhhhHhhhhh-----cCCe-----eEEeC-hhhHHHHHHHHhh----hcC----CCccChHHHHHHHHHHhh--
Q 020384 116 VMSNEEFDNLKEELMW-----EGSS-----VVMLS-SAEQKFLEASMAY----VAG----KPIMSDEEYDKLKQKLKM-- 174 (327)
Q Consensus 116 ~~sdeefd~LkEeL~w-----eGSs-----vv~L~-~~Eq~fLEA~~AY----~sG----kPimsDeeFD~LK~kLk~-- 174 (327)
++.|.+.|.--+.+.| .|-. .+.+- ..-.+|+|++... .-| -|+++...+++++.-+..
T Consensus 219 V~~dadl~~aa~~i~~~~~~~~GQ~C~a~~~v~V~~~i~~~f~~~l~~~~~~~~~g~~~~gp~i~~~~~~~~~~~i~~a~ 298 (432)
T cd07105 219 VLEDADLDAAANAALFGAFLNSGQICMSTERIIVHESIADEFVEKLKAAAEKLFAGPVVLGSLVSAAAADRVKELVDDAL 298 (432)
T ss_pred ECCCCCHHHHHHHHHHHHHhcCCCCCcCCceEEEcHHHHHHHHHHHHHHHHhhcCCCCcccccCCHHHHHHHHHHHHHHH
Confidence 4557788888777777 3433 23333 3345788886653 222 389999999999988765
Q ss_pred -cCCceeeecCe
Q 020384 175 -EGSEIVVEGPR 185 (327)
Q Consensus 175 -~GS~VVvk~Pr 185 (327)
.|.+++.-|.+
T Consensus 299 ~~ga~~~~gg~~ 310 (432)
T cd07105 299 SKGAKLVVGGLA 310 (432)
T ss_pred HCCCEEEeCCCc
Confidence 58887775544
No 292
>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=21.28 E-value=49 Score=30.63 Aligned_cols=26 Identities=23% Similarity=0.569 Sum_probs=23.1
Q ss_pred HHh-hhcCCCccChHHHHHHHHHHhhc
Q 020384 150 SMA-YVAGKPIMSDEEYDKLKQKLKME 175 (327)
Q Consensus 150 ~~A-Y~sGkPimsDeeFD~LK~kLk~~ 175 (327)
|.- ||+...+++|++|+.++.+||..
T Consensus 79 mnNv~Yr~~hl~~~~~y~~~pa~lrmn 105 (177)
T TIGR00777 79 MNNVFYRGRHLLEGARYDDLRPGLRMN 105 (177)
T ss_pred hhhHHHHhHhhcccchhhcCCccchhH
Confidence 444 99999999999999999999876
No 293
>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=21.20 E-value=48 Score=27.11 Aligned_cols=13 Identities=38% Similarity=0.902 Sum_probs=7.4
Q ss_pred eecCCCCCccccc
Q 020384 271 LKGPCPNCGTENV 283 (327)
Q Consensus 271 LKGpCPNCGeEv~ 283 (327)
+||-|.+|++.+-
T Consensus 57 lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 57 LRGRCRYCGAPIP 69 (92)
T ss_pred hCCCCcccCCCCC
Confidence 5566666665543
No 294
>PRK03922 hypothetical protein; Provisional
Probab=21.15 E-value=45 Score=29.07 Aligned_cols=15 Identities=33% Similarity=0.589 Sum_probs=11.6
Q ss_pred eeecCCCCCccccce
Q 020384 270 ILKGPCPNCGTENVS 284 (327)
Q Consensus 270 iLKGpCPNCGeEv~a 284 (327)
+=.-.||.||+|..+
T Consensus 47 vG~~~cP~cge~~~~ 61 (113)
T PRK03922 47 VGLTICPKCGEPFDS 61 (113)
T ss_pred cCcccCCCCCCcCCc
Confidence 344579999999873
No 295
>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=21.04 E-value=95 Score=25.86 Aligned_cols=40 Identities=25% Similarity=0.213 Sum_probs=28.2
Q ss_pred eEEeChhh------HHHHHHHHh--hhcCCCccChHHHHHHHHHHhhc
Q 020384 136 VVMLSSAE------QKFLEASMA--YVAGKPIMSDEEYDKLKQKLKME 175 (327)
Q Consensus 136 vv~L~~~E------q~fLEA~~A--Y~sGkPimsDeeFD~LK~kLk~~ 175 (327)
+++|.+++ |.-||+.++ |.+..|--+=.-=|-||+.|||.
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 34555555 567888776 77766666666667799999996
No 296
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.79 E-value=49 Score=28.84 Aligned_cols=17 Identities=35% Similarity=0.733 Sum_probs=12.4
Q ss_pred eeecCCCCCccccceec
Q 020384 270 ILKGPCPNCGTENVSFF 286 (327)
Q Consensus 270 iLKGpCPNCGeEv~aFf 286 (327)
+=.-.||.||++.-+-|
T Consensus 47 ~G~t~CP~Cg~~~e~~f 63 (115)
T COG1885 47 VGSTSCPKCGEPFESAF 63 (115)
T ss_pred cccccCCCCCCccceeE
Confidence 33458999999987443
No 297
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.61 E-value=52 Score=36.08 Aligned_cols=21 Identities=43% Similarity=1.285 Sum_probs=14.3
Q ss_pred cCCCCCccccceeccccccccCCCCccceeCCCCCc
Q 020384 273 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT 308 (327)
Q Consensus 273 GpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t 308 (327)
--||+|| |-|.+ ..+|++||.
T Consensus 681 ~~C~~CG-----~~~~~----------~~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCG-----YLGVI----------EDKCPKCGS 701 (735)
T ss_pred eecCCCC-----CCCCc----------CccCcCCCC
Confidence 4599999 32221 168999995
No 298
>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=20.57 E-value=70 Score=22.66 Aligned_cols=31 Identities=29% Similarity=0.689 Sum_probs=14.0
Q ss_pred CCCC--CccccceeccccccccCCCCccceeCCCCCceeEE
Q 020384 274 PCPN--CGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 312 (327)
Q Consensus 274 pCPN--CGeEv~aFfGtilsv~s~~~~~~~kChvC~t~L~f 312 (327)
.||+ |+.-+..- .+.....+.|..|+...=|
T Consensus 20 ~Cp~~~C~~~~~~~--------~~~~~~~~~C~~C~~~fC~ 52 (64)
T PF01485_consen 20 WCPNPDCEYIIEKD--------DGCNSPIVTCPSCGTEFCF 52 (64)
T ss_dssp --TTSST---ECS---------SSTTS--CCTTSCCSEECS
T ss_pred CCCCCCCcccEEec--------CCCCCCeeECCCCCCcCcc
Confidence 8988 98754322 1111115999999976533
No 299
>PLN02278 succinic semialdehyde dehydrogenase
Probab=20.50 E-value=2.8e+02 Score=28.45 Aligned_cols=68 Identities=19% Similarity=0.434 Sum_probs=46.8
Q ss_pred ccChHHHhhhHhhhhh-----cCCe------eEEeChhhHHHHHHHHhhh----cCC---------CccChHHHHHHHHH
Q 020384 116 VMSNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMAYV----AGK---------PIMSDEEYDKLKQK 171 (327)
Q Consensus 116 ~~sdeefd~LkEeL~w-----eGSs------vv~L~~~Eq~fLEA~~AY~----sGk---------PimsDeeFD~LK~k 171 (327)
++.|.+.|.--+.+.| .|-. +++-...-.+|+|++.+.. -|. |+++...+|+++.-
T Consensus 278 V~~dAdl~~aa~~i~~~~f~~~GQ~C~a~~rv~V~~~i~~~f~~~L~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~v~~~ 357 (498)
T PLN02278 278 VFDDADLDVAVKGALASKFRNSGQTCVCANRILVQEGIYDKFAEAFSKAVQKLVVGDGFEEGVTQGPLINEAAVQKVESH 357 (498)
T ss_pred ECCCCCHHHHHHHHHHHHhccCCCCCcCCcEEEEeHHHHHHHHHHHHHHHHhcCCCCCCCCCCcCCCccCHHHHHHHHHH
Confidence 5568888888788777 3432 3444444678999866533 343 68999999999987
Q ss_pred Hh---hcCCceeeec
Q 020384 172 LK---MEGSEIVVEG 183 (327)
Q Consensus 172 Lk---~~GS~VVvk~ 183 (327)
+. .+|.+++.-|
T Consensus 358 i~~a~~~Ga~vl~gG 372 (498)
T PLN02278 358 VQDAVSKGAKVLLGG 372 (498)
T ss_pred HHHHHhCCCEEEeCC
Confidence 65 4788887754
No 300
>PLN02766 coniferyl-aldehyde dehydrogenase
Probab=20.48 E-value=2.6e+02 Score=28.82 Aligned_cols=69 Identities=17% Similarity=0.446 Sum_probs=44.8
Q ss_pred ccChHHHhhhHhhhhh-----cCC-----eeEEe-ChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHH
Q 020384 116 VMSNEEFDNLKEELMW-----EGS-----SVVML-SSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQK 171 (327)
Q Consensus 116 ~~sdeefd~LkEeL~w-----eGS-----svv~L-~~~Eq~fLEA~~A----Y~sGk---------PimsDeeFD~LK~k 171 (327)
++.|.+.|..=+.+.| .|- +.|.+ ...-.+|+|++.+ +.-|. |+++.+.+|+++.-
T Consensus 277 V~~dADl~~Aa~~i~~g~f~n~GQ~C~a~~ri~V~~si~d~f~~~l~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~v~~~ 356 (501)
T PLN02766 277 IFDDADVDMAVDLALLGIFYNKGEICVASSRVYVQEGIYDEFVKKLVEKAKDWVVGDPFDPRARQGPQVDKQQFEKILSY 356 (501)
T ss_pred ECCCCCHHHHHHHHHHHHHhhcCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCHHHHHHHHHH
Confidence 4456677766666666 333 33333 4445678877544 55454 68999999999987
Q ss_pred Hhh---cCCceeeecC
Q 020384 172 LKM---EGSEIVVEGP 184 (327)
Q Consensus 172 Lk~---~GS~VVvk~P 184 (327)
+.. +|.+|+.-|.
T Consensus 357 i~~a~~~Ga~v~~gG~ 372 (501)
T PLN02766 357 IEHGKREGATLLTGGK 372 (501)
T ss_pred HHHHHhCCCEEEeCCC
Confidence 754 5888876553
No 301
>PRK12413 phosphomethylpyrimidine kinase; Provisional
Probab=20.42 E-value=3.8e+02 Score=24.19 Aligned_cols=45 Identities=24% Similarity=0.371 Sum_probs=33.5
Q ss_pred hcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhcCCc-eeee
Q 020384 131 WEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSE-IVVE 182 (327)
Q Consensus 131 weGSsvv~L~~~Eq~fLEA~~AY~sGkPimsDeeFD~LK~kLk~~GS~-VVvk 182 (327)
.....+++.+..|-+.| .|.++-+.++..+.-.+|...|-+ |+++
T Consensus 127 l~~~dli~pN~~E~~~L-------~g~~~~~~~~~~~~a~~l~~~g~~~Vvvt 172 (253)
T PRK12413 127 FPYVTVITPNLVEAELL-------SGKEIKTLEDMKEAAKKLYDLGAKAVVIK 172 (253)
T ss_pred hccCcEECCCHHHHHHH-------hCcCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 34457999999988776 478887778787877788878875 5555
No 302
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.16 E-value=57 Score=35.20 Aligned_cols=24 Identities=25% Similarity=0.685 Sum_probs=16.5
Q ss_pred ecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 272 KGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
-.-|++||.+. . .....|++||+.
T Consensus 568 ~~~C~~CG~~~----~----------g~~~~CP~CGs~ 591 (625)
T PRK08579 568 ITVCNKCGRST----T----------GLYTRCPRCGSE 591 (625)
T ss_pred CccCCCCCCcc----C----------CCCCcCcCCCCc
Confidence 45799999833 1 113689999964
No 303
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=20.12 E-value=85 Score=27.29 Aligned_cols=27 Identities=26% Similarity=0.565 Sum_probs=19.0
Q ss_pred eecCCCCCccccceeccccccccCCCCccceeCCCCCce
Q 020384 271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT 309 (327)
Q Consensus 271 LKGpCPNCGeEv~aFfGtilsv~s~~~~~~~kChvC~t~ 309 (327)
+.+-|.+|+.++- ...+...|+.|++.
T Consensus 69 ~~~~C~~C~~~~~------------~e~~~~~CP~C~s~ 95 (115)
T COG0375 69 AECWCLDCGQEVE------------LEELDYRCPKCGSI 95 (115)
T ss_pred cEEEeccCCCeec------------chhheeECCCCCCC
Confidence 5678999955432 25677789999953
Done!