Query 045112
Match_columns 296
No_of_seqs 70 out of 72
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 09:57:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045112hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00114 LIGANc NAD+ dependent 96.8 0.0017 3.6E-08 61.8 4.7 36 72-107 3-39 (307)
2 PF01653 DNA_ligase_aden: NAD- 96.5 0.0033 7.2E-08 59.9 4.7 36 71-106 6-42 (315)
3 smart00532 LIGANc Ligase N fam 96.3 0.0049 1.1E-07 61.5 4.5 36 71-106 4-40 (441)
4 PRK07956 ligA NAD-dependent DN 96.1 0.0059 1.3E-07 63.6 4.6 36 71-106 8-44 (665)
5 PRK14351 ligA NAD-dependent DN 95.9 0.01 2.2E-07 62.3 5.1 36 71-106 35-71 (689)
6 PF13248 zf-ribbon_3: zinc-rib 95.7 0.0041 9E-08 39.5 0.9 24 227-261 3-26 (26)
7 TIGR02098 MJ0042_CXXC MJ0042 f 95.6 0.0074 1.6E-07 40.4 1.7 35 226-262 2-36 (38)
8 PRK08097 ligB NAD-dependent DN 95.5 0.015 3.3E-07 59.9 4.5 35 72-106 34-69 (562)
9 PRK00398 rpoP DNA-directed RNA 95.4 0.014 3E-07 40.9 2.8 31 228-265 5-35 (46)
10 PRK14350 ligA NAD-dependent DN 95.2 0.02 4.4E-07 60.0 4.2 38 69-106 6-44 (669)
11 TIGR00575 dnlj DNA ligase, NAD 95.1 0.019 4.2E-07 59.7 3.7 32 76-107 2-34 (652)
12 TIGR01206 lysW lysine biosynth 95.1 0.017 3.6E-07 43.1 2.4 34 226-264 2-35 (54)
13 COG2888 Predicted Zn-ribbon RN 94.5 0.016 3.5E-07 44.5 1.1 36 222-259 23-58 (61)
14 PF13240 zinc_ribbon_2: zinc-r 94.3 0.021 4.5E-07 35.8 1.0 22 229-261 2-23 (23)
15 PRK05978 hypothetical protein; 93.9 0.026 5.7E-07 49.5 1.3 32 225-264 32-65 (148)
16 smart00531 TFIIE Transcription 93.9 0.028 6.1E-07 47.8 1.4 53 213-266 86-138 (147)
17 COG2051 RPS27A Ribosomal prote 93.5 0.057 1.2E-06 42.3 2.4 36 224-265 17-52 (67)
18 PF14354 Lar_restr_allev: Rest 93.3 0.024 5.3E-07 41.0 0.1 32 228-259 5-37 (61)
19 PRK00420 hypothetical protein; 93.1 0.063 1.4E-06 45.3 2.2 44 214-265 11-54 (112)
20 PRK14890 putative Zn-ribbon RN 92.9 0.047 1E-06 41.7 1.1 33 224-259 23-56 (59)
21 PRK00415 rps27e 30S ribosomal 92.7 0.072 1.6E-06 40.7 1.9 34 224-263 9-42 (59)
22 PHA00626 hypothetical protein 92.6 0.073 1.6E-06 40.7 1.7 42 228-271 2-43 (59)
23 PF14255 Cys_rich_CPXG: Cystei 92.6 0.093 2E-06 38.9 2.2 42 228-270 2-43 (52)
24 COG5349 Uncharacterized protei 92.5 0.041 8.8E-07 47.5 0.4 31 225-263 20-52 (126)
25 COG0272 Lig NAD-dependent DNA 92.1 0.18 3.8E-06 53.4 4.4 38 70-107 9-47 (667)
26 TIGR03655 anti_R_Lar restricti 91.8 0.14 2.9E-06 37.0 2.3 36 228-263 3-38 (53)
27 PF11023 DUF2614: Protein of u 91.6 0.38 8.1E-06 41.1 5.1 34 228-270 71-104 (114)
28 PF08271 TF_Zn_Ribbon: TFIIB z 91.6 0.17 3.7E-06 35.0 2.6 38 228-271 2-39 (43)
29 PF14353 CpXC: CpXC protein 91.2 0.15 3.2E-06 41.9 2.3 41 228-268 3-55 (128)
30 PF10571 UPF0547: Uncharacteri 91.0 0.12 2.5E-06 33.4 1.1 23 228-261 2-24 (26)
31 TIGR00373 conserved hypothetic 90.8 0.096 2.1E-06 45.5 0.9 33 227-265 110-142 (158)
32 PRK09710 lar restriction allev 90.3 0.18 3.8E-06 39.2 1.8 33 227-263 7-39 (64)
33 smart00659 RPOLCX RNA polymera 90.3 0.23 4.9E-06 35.5 2.2 29 228-264 4-32 (44)
34 PF01667 Ribosomal_S27e: Ribos 89.6 0.27 5.8E-06 37.0 2.3 35 225-265 6-40 (55)
35 PF06044 DRP: Dam-replacing fa 89.4 0.091 2E-06 49.9 -0.5 58 203-267 12-69 (254)
36 PRK06266 transcription initiat 89.3 0.15 3.4E-06 45.2 0.9 47 213-265 104-150 (178)
37 smart00834 CxxC_CXXC_SSSS Puta 88.4 0.45 9.8E-06 31.6 2.5 29 228-260 7-35 (41)
38 PF01096 TFIIS_C: Transcriptio 88.4 0.31 6.7E-06 33.6 1.7 33 228-260 2-37 (39)
39 TIGR02605 CxxC_CxxC_SSSS putat 88.0 0.54 1.2E-05 33.1 2.8 39 228-275 7-45 (52)
40 PF14803 Nudix_N_2: Nudix N-te 87.4 0.33 7.1E-06 33.2 1.3 28 229-259 3-30 (34)
41 PF03604 DNA_RNApol_7kD: DNA d 87.1 0.4 8.7E-06 32.4 1.6 28 229-264 3-30 (32)
42 PF07282 OrfB_Zn_ribbon: Putat 87.0 0.39 8.5E-06 35.4 1.7 32 227-267 29-60 (69)
43 PLN00209 ribosomal protein S27 86.2 0.49 1.1E-05 38.7 2.0 36 223-264 33-68 (86)
44 smart00440 ZnF_C2C2 C2C2 Zinc 86.1 0.58 1.3E-05 32.5 2.1 32 228-259 2-36 (40)
45 PF12773 DZR: Double zinc ribb 86.1 0.36 7.8E-06 33.7 1.0 18 247-264 25-42 (50)
46 PTZ00083 40S ribosomal protein 84.5 0.67 1.5E-05 37.8 2.0 35 223-263 32-66 (85)
47 PF13719 zinc_ribbon_5: zinc-r 83.9 0.57 1.2E-05 31.9 1.2 34 226-261 2-35 (37)
48 PF05191 ADK_lid: Adenylate ki 83.6 0.64 1.4E-05 31.9 1.3 33 228-265 3-35 (36)
49 smart00661 RPOL9 RNA polymeras 83.2 0.9 1.9E-05 31.7 2.0 28 228-260 2-29 (52)
50 PF05876 Terminase_GpA: Phage 82.6 0.74 1.6E-05 47.2 1.9 50 219-268 193-246 (557)
51 PRK02935 hypothetical protein; 82.3 3.2 7E-05 35.3 5.3 35 227-270 71-105 (110)
52 COG1326 Uncharacterized archae 82.3 0.48 1E-05 43.8 0.4 34 225-260 5-39 (201)
53 PF07754 DUF1610: Domain of un 82.1 0.57 1.2E-05 30.1 0.6 11 224-234 14-24 (24)
54 PRK00432 30S ribosomal protein 81.9 0.82 1.8E-05 33.4 1.4 29 224-260 18-46 (50)
55 PF09862 DUF2089: Protein of u 81.5 0.89 1.9E-05 38.5 1.7 23 229-262 1-23 (113)
56 PRK14714 DNA polymerase II lar 81.2 1.1 2.3E-05 50.8 2.6 44 221-264 662-705 (1337)
57 COG1645 Uncharacterized Zn-fin 81.0 0.75 1.6E-05 40.0 1.1 39 212-259 14-52 (131)
58 PF09723 Zn-ribbon_8: Zinc rib 80.7 1.7 3.6E-05 30.3 2.5 28 228-259 7-34 (42)
59 PRK00464 nrdR transcriptional 79.6 1.4 2.9E-05 38.9 2.3 41 228-268 2-45 (154)
60 COG3677 Transposase and inacti 79.3 1.7 3.6E-05 37.1 2.6 45 220-266 24-68 (129)
61 PF12760 Zn_Tnp_IS1595: Transp 78.8 1.7 3.6E-05 30.5 2.1 36 214-259 10-45 (46)
62 PF10083 DUF2321: Uncharacteri 78.7 1.1 2.3E-05 40.3 1.3 34 228-261 41-78 (158)
63 PRK04023 DNA polymerase II lar 78.5 1.3 2.8E-05 49.3 2.1 41 226-266 626-678 (1121)
64 PF13717 zinc_ribbon_4: zinc-r 78.4 1.2 2.6E-05 30.3 1.3 33 226-260 2-34 (36)
65 TIGR03831 YgiT_finger YgiT-typ 76.4 1.6 3.5E-05 29.3 1.4 19 220-238 22-44 (46)
66 PF01807 zf-CHC2: CHC2 zinc fi 75.8 1.7 3.8E-05 34.7 1.7 31 225-259 32-62 (97)
67 PF05129 Elf1: Transcription e 75.7 1.8 3.9E-05 34.3 1.7 39 227-268 23-61 (81)
68 smart00778 Prim_Zn_Ribbon Zinc 73.6 1.4 3.1E-05 30.7 0.6 30 226-259 3-33 (37)
69 PRK14892 putative transcriptio 73.2 2.6 5.6E-05 34.9 2.1 31 228-262 23-53 (99)
70 PF08996 zf-DNA_Pol: DNA Polym 73.0 1.1 2.4E-05 39.7 -0.1 43 217-260 9-54 (188)
71 PRK01103 formamidopyrimidine/5 72.8 3.4 7.3E-05 38.5 3.1 35 220-259 235-273 (274)
72 PF06906 DUF1272: Protein of u 72.5 1.5 3.2E-05 33.6 0.5 13 225-237 40-52 (57)
73 COG1096 Predicted RNA-binding 71.8 2.5 5.5E-05 38.8 2.0 32 220-260 143-174 (188)
74 COG0675 Transposase and inacti 71.5 2.2 4.7E-05 37.8 1.4 22 227-260 310-331 (364)
75 PF04216 FdhE: Protein involve 70.3 4.1 9E-05 38.0 3.1 22 223-244 169-191 (290)
76 PRK14559 putative protein seri 68.8 2.7 5.9E-05 44.4 1.7 15 253-267 29-43 (645)
77 PF06677 Auto_anti-p27: Sjogre 68.0 3.5 7.5E-05 29.3 1.6 36 215-258 6-41 (41)
78 PRK12495 hypothetical protein; 68.0 3.8 8.2E-05 38.7 2.3 43 211-262 27-69 (226)
79 PF08273 Prim_Zn_Ribbon: Zinc- 67.7 2.3 5E-05 30.1 0.6 31 226-259 3-34 (40)
80 TIGR00155 pqiA_fam integral me 67.4 1.7 3.7E-05 43.1 -0.1 24 228-261 217-240 (403)
81 PF09538 FYDLN_acid: Protein o 67.3 3.7 8E-05 34.3 1.8 32 225-264 8-39 (108)
82 PRK14810 formamidopyrimidine-D 67.0 4 8.6E-05 38.2 2.2 28 227-259 245-272 (272)
83 PRK14559 putative protein seri 66.1 3.7 7.9E-05 43.5 2.0 14 248-261 38-51 (645)
84 PF10263 SprT-like: SprT-like 65.9 4.5 9.8E-05 33.6 2.1 35 224-263 121-155 (157)
85 COG3813 Uncharacterized protei 65.3 2.5 5.5E-05 34.2 0.5 15 224-238 39-53 (84)
86 PRK10445 endonuclease VIII; Pr 64.4 4.9 0.00011 37.5 2.3 28 227-259 236-263 (263)
87 PF09567 RE_MamI: MamI restric 63.8 3.1 6.8E-05 40.4 0.9 23 227-260 83-105 (314)
88 COG1405 SUA7 Transcription ini 63.6 4.4 9.5E-05 38.8 1.9 36 227-268 2-37 (285)
89 PRK14714 DNA polymerase II lar 63.3 4.2 9.2E-05 46.3 1.9 43 224-267 677-725 (1337)
90 PF09851 SHOCT: Short C-termin 63.3 5.7 0.00012 26.2 1.8 21 84-106 10-30 (31)
91 TIGR00310 ZPR1_znf ZPR1 zinc f 63.3 3.2 6.9E-05 37.7 0.8 9 251-259 30-38 (192)
92 PRK07111 anaerobic ribonucleos 63.0 4.1 8.8E-05 43.6 1.7 40 228-282 682-724 (735)
93 TIGR00244 transcriptional regu 62.8 5.2 0.00011 35.5 2.0 36 228-263 2-40 (147)
94 PF07508 Recombinase: Recombin 62.7 5.7 0.00012 30.3 2.0 20 88-107 82-101 (102)
95 TIGR00577 fpg formamidopyrimid 62.5 5.5 0.00012 37.2 2.3 34 220-258 235-272 (272)
96 KOG3134 Predicted membrane pro 61.7 2.3 5E-05 40.0 -0.4 32 228-260 2-33 (225)
97 TIGR02300 FYDLN_acid conserved 61.7 5.2 0.00011 34.9 1.8 29 225-261 8-36 (129)
98 PF04161 Arv1: Arv1-like famil 61.6 3.4 7.3E-05 37.2 0.6 31 229-260 3-33 (208)
99 PRK08579 anaerobic ribonucleos 61.0 2.8 6.1E-05 44.1 0.1 42 227-282 569-613 (625)
100 TIGR00340 zpr1_rel ZPR1-relate 60.8 3.6 7.8E-05 36.6 0.7 17 219-235 21-37 (163)
101 COG1996 RPC10 DNA-directed RNA 60.4 5.8 0.00013 29.4 1.6 30 228-264 8-37 (49)
102 PF11781 RRN7: RNA polymerase 60.0 5 0.00011 27.5 1.1 25 229-261 11-35 (36)
103 PF04280 Tim44: Tim44-like dom 59.6 8.6 0.00019 31.5 2.7 38 71-108 20-62 (147)
104 PRK13945 formamidopyrimidine-D 59.4 6.6 0.00014 36.9 2.2 27 227-258 255-281 (282)
105 PRK03988 translation initiatio 59.2 6.1 0.00013 34.3 1.8 29 228-260 104-132 (138)
106 PF05502 Dynactin_p62: Dynacti 59.1 6.8 0.00015 39.9 2.4 43 224-266 24-67 (483)
107 TIGR01054 rgy reverse gyrase. 59.0 3.6 7.7E-05 46.1 0.4 29 224-259 5-33 (1171)
108 COG3877 Uncharacterized protei 58.9 5.3 0.00011 34.4 1.3 25 227-262 7-31 (122)
109 PRK04011 peptide chain release 58.8 5.8 0.00013 39.5 1.8 36 226-264 328-363 (411)
110 TIGR01562 FdhE formate dehydro 58.4 6.6 0.00014 38.1 2.1 35 226-260 184-233 (305)
111 COG1998 RPS31 Ribosomal protei 58.3 6.4 0.00014 29.6 1.5 31 222-260 15-46 (51)
112 PRK14811 formamidopyrimidine-D 58.0 7.4 0.00016 36.5 2.3 28 228-260 237-264 (269)
113 cd00729 rubredoxin_SM Rubredox 57.6 9.7 0.00021 25.6 2.2 24 228-260 4-27 (34)
114 TIGR02827 RNR_anaer_Bdell anae 57.6 6.5 0.00014 41.2 2.0 41 228-282 534-577 (586)
115 PRK00398 rpoP DNA-directed RNA 57.3 6.6 0.00014 27.4 1.4 19 250-268 2-20 (46)
116 smart00400 ZnF_CHCC zinc finge 57.3 5.1 0.00011 28.7 0.9 30 226-259 2-31 (55)
117 smart00653 eIF2B_5 domain pres 57.3 6.7 0.00014 32.8 1.7 29 228-260 82-110 (110)
118 PF04216 FdhE: Protein involve 56.9 5.7 0.00012 37.1 1.3 37 226-262 211-249 (290)
119 TIGR01391 dnaG DNA primase, ca 56.0 8.1 0.00017 38.2 2.3 31 225-259 33-63 (415)
120 PHA02998 RNA polymerase subuni 55.5 8.3 0.00018 35.7 2.1 36 225-260 142-180 (195)
121 PHA02942 putative transposase; 54.9 8 0.00017 38.1 2.0 26 228-261 327-352 (383)
122 TIGR00311 aIF-2beta translatio 54.7 7.9 0.00017 33.4 1.7 29 228-260 99-127 (133)
123 PRK12380 hydrogenase nickel in 54.2 7.4 0.00016 32.2 1.4 30 222-260 66-95 (113)
124 PF14789 THDPS_M: Tetrahydrodi 54.2 12 0.00026 26.8 2.3 26 93-118 12-41 (41)
125 PRK13130 H/ACA RNA-protein com 54.0 5.5 0.00012 30.1 0.6 15 224-238 15-29 (56)
126 PF11331 DUF3133: Protein of u 53.9 8.1 0.00018 28.3 1.4 36 229-264 9-44 (46)
127 PF01873 eIF-5_eIF-2B: Domain 53.7 9.5 0.00021 32.5 2.0 30 227-260 94-123 (125)
128 PHA02540 61 DNA primase; Provi 53.2 14 0.00031 36.3 3.5 34 225-260 26-64 (337)
129 PF09334 tRNA-synt_1g: tRNA sy 52.9 9.9 0.00021 37.3 2.3 19 250-268 148-166 (391)
130 PF15616 TerY-C: TerY-C metal 52.8 9.3 0.0002 33.2 1.9 44 223-266 74-120 (131)
131 PRK09263 anaerobic ribonucleos 52.3 9.2 0.0002 40.9 2.1 27 227-260 642-668 (711)
132 PRK03824 hypA hydrogenase nick 51.9 11 0.00023 32.3 2.1 12 224-235 68-79 (135)
133 TIGR00100 hypA hydrogenase nic 51.6 9.5 0.00021 31.6 1.7 30 222-260 66-95 (115)
134 PRK12286 rpmF 50S ribosomal pr 51.4 8.1 0.00018 29.0 1.1 20 227-258 28-47 (57)
135 PF13597 NRDD: Anaerobic ribon 50.4 9.2 0.0002 39.4 1.7 45 227-284 492-537 (546)
136 PRK00133 metG methionyl-tRNA s 50.2 8 0.00017 40.4 1.3 40 225-266 138-184 (673)
137 PRK09678 DNA-binding transcrip 50.0 20 0.00043 28.3 3.1 47 228-276 3-54 (72)
138 PF05605 zf-Di19: Drought indu 49.4 7.7 0.00017 27.8 0.7 31 228-259 4-39 (54)
139 PRK00423 tfb transcription ini 48.7 11 0.00024 35.8 1.8 29 228-262 13-41 (310)
140 PF13453 zf-TFIIB: Transcripti 48.0 12 0.00025 25.6 1.4 28 228-260 1-28 (41)
141 PRK12336 translation initiatio 47.4 12 0.00025 34.0 1.7 35 227-265 99-133 (201)
142 COG4888 Uncharacterized Zn rib 46.5 14 0.0003 31.4 1.9 37 227-264 23-59 (104)
143 TIGR00595 priA primosomal prot 46.3 13 0.00028 37.7 2.1 12 55-66 22-33 (505)
144 PRK12496 hypothetical protein; 46.3 12 0.00025 33.0 1.5 34 220-262 121-154 (164)
145 TIGR02487 NrdD anaerobic ribon 46.0 11 0.00024 39.1 1.5 42 227-282 525-569 (579)
146 PRK03564 formate dehydrogenase 45.6 14 0.00031 36.0 2.2 35 225-259 186-234 (309)
147 PRK03681 hypA hydrogenase nick 45.1 11 0.00025 31.2 1.2 29 224-260 68-96 (114)
148 PF01155 HypA: Hydrogenase exp 44.9 7.2 0.00016 32.1 -0.0 30 222-260 66-95 (113)
149 COG1110 Reverse gyrase [DNA re 44.6 6.5 0.00014 44.3 -0.4 28 224-258 6-33 (1187)
150 PF03833 PolC_DP2: DNA polymer 44.5 7.4 0.00016 42.9 0.0 19 222-240 651-669 (900)
151 PRK00241 nudC NADH pyrophospha 44.0 14 0.00029 34.5 1.6 27 226-259 99-125 (256)
152 PRK05580 primosome assembly pr 44.0 15 0.00032 38.7 2.1 11 56-66 188-198 (679)
153 PF09889 DUF2116: Uncharacteri 44.0 9.9 0.00021 29.0 0.6 24 227-261 4-28 (59)
154 PRK08271 anaerobic ribonucleos 43.7 8.9 0.00019 40.5 0.4 22 227-259 567-588 (623)
155 PF05193 Peptidase_M16_C: Pept 43.6 33 0.00072 26.9 3.6 33 71-105 152-184 (184)
156 TIGR01405 polC_Gram_pos DNA po 43.5 14 0.00031 41.9 2.0 34 227-262 684-719 (1213)
157 TIGR03676 aRF1/eRF1 peptide ch 43.2 15 0.00032 36.6 1.9 35 226-263 320-354 (403)
158 TIGR02159 PA_CoA_Oxy4 phenylac 43.1 8.1 0.00018 33.6 0.0 35 226-263 105-142 (146)
159 COG4640 Predicted membrane pro 43.1 12 0.00026 38.4 1.2 28 228-266 3-30 (465)
160 PF06170 DUF983: Protein of un 43.0 10 0.00022 30.5 0.6 17 220-236 2-18 (86)
161 PRK05667 dnaG DNA primase; Val 43.0 17 0.00036 37.9 2.2 31 225-259 35-65 (580)
162 PF11793 FANCL_C: FANCL C-term 42.8 8.5 0.00018 29.3 0.1 18 220-237 49-66 (70)
163 PF12677 DUF3797: Domain of un 42.4 10 0.00023 28.3 0.5 11 226-236 13-23 (49)
164 PRK09401 reverse gyrase; Revie 42.4 8.1 0.00018 43.4 -0.1 29 224-259 5-33 (1176)
165 PF04502 DUF572: Family of unk 42.4 15 0.00032 35.4 1.7 45 227-271 41-97 (324)
166 COG3058 FdhE Uncharacterized p 42.2 9.1 0.0002 37.6 0.2 40 226-265 185-241 (308)
167 PRK08665 ribonucleotide-diphos 42.2 16 0.00035 39.3 2.1 24 227-259 725-748 (752)
168 TIGR01385 TFSII transcription 42.1 21 0.00046 34.5 2.7 38 226-263 258-298 (299)
169 KOG2593 Transcription initiati 41.9 8.1 0.00018 39.5 -0.1 61 212-273 114-175 (436)
170 PRK00448 polC DNA polymerase I 41.6 16 0.00034 42.3 2.0 34 227-262 909-944 (1437)
171 PRK08173 DNA topoisomerase III 41.0 15 0.00033 40.1 1.7 27 226-261 624-650 (862)
172 PF04380 BMFP: Membrane fusoge 41.0 48 0.001 26.0 4.0 38 70-107 24-61 (79)
173 TIGR01384 TFS_arch transcripti 40.6 22 0.00048 28.2 2.2 34 226-259 62-98 (104)
174 PRK08351 DNA-directed RNA poly 40.3 13 0.00027 28.7 0.7 14 228-241 17-32 (61)
175 COG4306 Uncharacterized protei 40.3 17 0.00038 32.3 1.6 36 228-263 41-80 (160)
176 PRK15103 paraquat-inducible me 40.2 11 0.00023 37.8 0.4 28 229-261 13-40 (419)
177 smart00132 LIM Zinc-binding do 40.0 17 0.00038 22.7 1.2 33 229-262 2-38 (39)
178 PRK14873 primosome assembly pr 40.0 18 0.00039 38.4 2.0 28 108-135 238-270 (665)
179 PRK04023 DNA polymerase II lar 39.9 19 0.0004 40.7 2.1 10 53-62 365-374 (1121)
180 KOG1598 Transcription initiati 39.8 30 0.00065 36.3 3.5 52 228-288 2-53 (521)
181 PHA00727 hypothetical protein 38.7 35 0.00075 32.5 3.4 41 69-109 17-70 (278)
182 COG1274 PckA Phosphoenolpyruva 37.9 28 0.00061 36.8 3.0 32 94-125 42-77 (608)
183 TIGR00155 pqiA_fam integral me 37.8 22 0.00049 35.4 2.2 30 228-262 15-44 (403)
184 PF08274 PhnA_Zn_Ribbon: PhnA 37.4 18 0.00039 24.3 1.0 26 227-260 3-28 (30)
185 PF01956 DUF106: Integral memb 37.3 2.4E+02 0.0052 24.2 8.1 62 72-155 45-106 (168)
186 TIGR00398 metG methionyl-tRNA 37.3 15 0.00033 36.7 0.9 11 225-235 135-145 (530)
187 COG3462 Predicted membrane pro 37.0 31 0.00068 29.8 2.6 23 82-106 94-116 (117)
188 PF03833 PolC_DP2: DNA polymer 36.6 12 0.00025 41.4 0.0 44 222-266 663-707 (900)
189 PF07295 DUF1451: Protein of u 36.5 22 0.00048 31.1 1.7 38 69-107 10-47 (146)
190 COG1327 Predicted transcriptio 36.0 21 0.00046 32.2 1.5 35 228-262 2-39 (156)
191 PRK15103 paraquat-inducible me 35.6 22 0.00048 35.7 1.7 23 228-261 223-245 (419)
192 COG5257 GCD11 Translation init 35.5 26 0.00057 35.6 2.2 35 220-266 53-87 (415)
193 PF02591 DUF164: Putative zinc 35.5 15 0.00033 26.5 0.5 36 224-261 20-56 (56)
194 PF00373 FERM_M: FERM central 35.1 74 0.0016 24.7 4.3 36 66-101 2-37 (126)
195 PF06221 zf-C2HC5: Putative zi 35.1 17 0.00038 27.5 0.7 13 226-238 35-47 (57)
196 TIGR00777 ahpD alkylhydroperox 35.0 18 0.00038 33.0 0.9 39 70-108 62-105 (177)
197 TIGR00354 polC DNA polymerase, 34.7 25 0.00054 39.6 2.1 27 221-260 620-646 (1095)
198 PF10058 DUF2296: Predicted in 34.6 24 0.00051 26.2 1.3 32 223-259 21-52 (54)
199 COG1579 Zn-ribbon protein, pos 34.5 9.8 0.00021 36.0 -0.8 42 225-268 196-238 (239)
200 KOG3716 Carnitine O-acyltransf 34.4 21 0.00046 38.8 1.5 22 77-104 177-198 (764)
201 COG0375 HybF Zn finger protein 34.4 18 0.0004 30.9 0.9 27 225-260 69-95 (115)
202 COG1545 Predicted nucleic-acid 33.9 75 0.0016 27.3 4.5 54 220-287 23-76 (140)
203 PF10415 FumaraseC_C: Fumarase 33.8 26 0.00057 25.9 1.5 20 82-101 18-46 (55)
204 PRK00564 hypA hydrogenase nick 33.8 24 0.00052 29.4 1.4 30 223-260 68-97 (117)
205 PRK04351 hypothetical protein; 33.7 33 0.00072 30.0 2.3 35 227-266 113-147 (149)
206 TIGR03037 anthran_nbaC 3-hydro 33.4 26 0.00055 31.4 1.6 34 226-259 114-159 (159)
207 PRK14530 adenylate kinase; Pro 33.3 56 0.0012 28.6 3.7 35 227-266 127-161 (215)
208 COG1867 TRM1 N2,N2-dimethylgua 33.1 26 0.00056 35.4 1.8 28 227-262 241-268 (380)
209 COG0143 MetG Methionyl-tRNA sy 33.1 23 0.00049 37.2 1.4 11 225-235 141-151 (558)
210 PF08209 Sgf11: Sgf11 (transcr 32.5 27 0.00059 23.8 1.3 13 250-262 3-15 (33)
211 PF15110 TMEM141: TMEM141 prot 32.4 23 0.00049 29.6 1.0 35 184-218 53-87 (94)
212 COG1198 PriA Primosomal protei 32.2 28 0.00061 37.7 2.0 90 40-135 224-326 (730)
213 COG1571 Predicted DNA-binding 32.0 24 0.00052 36.0 1.4 35 225-267 349-383 (421)
214 PF04423 Rad50_zn_hook: Rad50 31.8 20 0.00043 25.7 0.6 10 253-262 22-31 (54)
215 TIGR03142 cytochro_ccmI cytoch 31.7 45 0.00098 27.4 2.7 16 92-107 56-71 (117)
216 PRK14526 adenylate kinase; Pro 31.7 34 0.00074 30.8 2.2 35 227-266 123-157 (211)
217 COG5525 Bacteriophage tail ass 31.6 34 0.00074 36.5 2.4 50 214-263 215-271 (611)
218 PF04328 DUF466: Protein of un 31.4 83 0.0018 24.2 3.9 34 77-110 26-59 (65)
219 COG1675 TFA1 Transcription ini 31.2 18 0.00038 32.9 0.2 34 227-266 114-147 (176)
220 PRK08197 threonine synthase; V 30.6 38 0.00083 32.9 2.4 32 226-267 7-38 (394)
221 PF14952 zf-tcix: Putative tre 30.2 22 0.00049 26.0 0.6 9 228-236 13-21 (44)
222 PF03884 DUF329: Domain of unk 30.1 20 0.00043 27.3 0.3 12 226-237 2-13 (57)
223 PRK08270 anaerobic ribonucleos 29.9 33 0.00072 36.4 2.0 24 227-262 627-650 (656)
224 COG2816 NPY1 NTP pyrophosphohy 29.7 26 0.00056 34.0 1.1 29 226-261 111-139 (279)
225 PRK14701 reverse gyrase; Provi 29.5 18 0.0004 42.2 0.1 27 224-257 4-30 (1638)
226 smart00731 SprT SprT homologue 29.5 44 0.00096 28.2 2.4 34 226-263 112-145 (146)
227 PRK14715 DNA polymerase II lar 29.2 35 0.00076 39.8 2.1 27 221-260 669-695 (1627)
228 PF07295 DUF1451: Protein of u 29.1 26 0.00056 30.7 0.9 13 226-238 130-142 (146)
229 PRK14704 anaerobic ribonucleos 29.1 15 0.00032 38.8 -0.7 21 228-260 561-581 (618)
230 COG0266 Nei Formamidopyrimidin 28.9 40 0.00086 32.6 2.2 26 228-258 247-272 (273)
231 PF03367 zf-ZPR1: ZPR1 zinc-fi 28.8 26 0.00056 30.9 0.9 22 219-240 23-44 (161)
232 TIGR01562 FdhE formate dehydro 28.6 35 0.00076 33.3 1.8 37 225-261 223-262 (305)
233 PRK11823 DNA repair protein Ra 28.5 30 0.00064 34.7 1.3 15 274-288 73-87 (446)
234 PRK13264 3-hydroxyanthranilate 28.3 33 0.00072 31.2 1.5 38 225-262 119-168 (177)
235 PF14206 Cys_rich_CPCC: Cystei 28.2 24 0.00053 28.2 0.6 27 226-258 1-27 (78)
236 PLN02419 methylmalonate-semial 28.0 1.2E+02 0.0025 32.2 5.5 59 57-116 387-459 (604)
237 PLN02766 coniferyl-aldehyde de 27.9 1.1E+02 0.0025 30.8 5.3 45 72-116 315-371 (501)
238 COG2960 Uncharacterized protei 27.9 80 0.0017 26.9 3.5 35 71-105 34-68 (103)
239 PRK09521 exosome complex RNA-b 27.7 39 0.00084 29.8 1.8 31 221-259 144-174 (189)
240 PTZ00381 aldehyde dehydrogenas 27.6 1.2E+02 0.0025 30.9 5.3 43 72-115 262-313 (493)
241 PRK14973 DNA topoisomerase I; 27.5 50 0.0011 36.6 2.9 12 226-237 588-599 (936)
242 TIGR00340 zpr1_rel ZPR1-relate 27.5 33 0.00071 30.6 1.3 9 252-260 29-37 (163)
243 PF13913 zf-C2HC_2: zinc-finge 27.4 28 0.0006 21.9 0.6 8 228-235 4-11 (25)
244 smart00709 Zpr1 Duplicated dom 27.4 33 0.00071 30.3 1.3 21 219-239 22-42 (160)
245 PRK00762 hypA hydrogenase nick 27.2 35 0.00075 28.7 1.3 32 223-259 67-100 (124)
246 PF13408 Zn_ribbon_recom: Reco 26.8 50 0.0011 22.9 1.9 15 250-264 4-18 (58)
247 TIGR00108 eRF peptide chain re 26.8 39 0.00085 33.7 1.8 35 226-263 324-358 (409)
248 COG2176 PolC DNA polymerase II 26.8 46 0.00099 38.6 2.5 50 211-262 899-950 (1444)
249 TIGR00310 ZPR1_znf ZPR1 zinc f 26.7 34 0.00074 31.2 1.3 19 219-237 23-41 (192)
250 TIGR00595 priA primosomal prot 26.6 36 0.00077 34.7 1.5 27 229-262 225-251 (505)
251 PRK00893 aspartate carbamoyltr 26.5 49 0.0011 29.6 2.2 39 224-264 105-147 (152)
252 KOG2324 Prolyl-tRNA synthetase 26.4 42 0.00091 34.5 2.0 52 54-105 89-149 (457)
253 PRK11032 hypothetical protein; 26.2 42 0.0009 30.1 1.7 26 228-260 126-151 (160)
254 PF05280 FlhC: Flagellar trans 26.2 34 0.00073 30.8 1.2 34 220-259 129-162 (175)
255 COG0300 DltE Short-chain dehyd 26.2 1.9E+02 0.004 27.8 6.1 100 45-149 17-123 (265)
256 PRK04338 N(2),N(2)-dimethylgua 26.1 44 0.00096 33.0 2.0 31 224-262 242-272 (382)
257 PRK06260 threonine synthase; V 25.9 60 0.0013 31.6 2.9 28 228-264 5-32 (397)
258 PRK06393 rpoE DNA-directed RNA 25.5 31 0.00067 26.9 0.7 10 228-237 19-28 (64)
259 PLN02459 probable adenylate ki 25.4 71 0.0015 30.4 3.2 40 227-266 154-199 (261)
260 PF03119 DNA_ligase_ZBD: NAD-d 25.4 44 0.00096 21.7 1.3 10 253-262 1-10 (28)
261 PF12162 STAT1_TAZ2bind: STAT1 25.3 46 0.001 21.5 1.3 12 93-104 10-21 (23)
262 PF14577 SEO_C: Sieve element 25.1 36 0.00077 32.3 1.1 17 246-262 209-225 (235)
263 PRK06556 vitamin B12-dependent 24.8 38 0.00082 37.8 1.4 17 68-84 664-680 (953)
264 PRK14529 adenylate kinase; Pro 24.7 50 0.0011 30.4 2.0 36 226-265 126-162 (223)
265 PF14485 DUF4431: Domain of un 24.6 66 0.0014 23.4 2.2 22 92-116 5-26 (48)
266 PF14319 Zn_Tnp_IS91: Transpos 24.5 48 0.0011 27.4 1.7 29 225-260 41-69 (111)
267 COG1241 MCM2 Predicted ATPase 24.4 46 0.001 35.9 1.9 27 228-257 131-157 (682)
268 COG1594 RPB9 DNA-directed RNA 24.4 53 0.0011 27.5 1.9 35 226-260 72-109 (113)
269 cd07110 ALDH_F10_BADH Arabidop 24.3 1.5E+02 0.0033 29.1 5.3 44 73-116 277-332 (456)
270 PF09297 zf-NADH-PPase: NADH p 24.3 26 0.00056 22.8 0.0 10 228-237 23-32 (32)
271 PF09845 DUF2072: Zn-ribbon co 24.2 43 0.00093 29.4 1.4 24 221-245 15-38 (131)
272 PF05907 DUF866: Eukaryotic pr 24.1 41 0.00089 29.7 1.3 41 223-263 27-76 (161)
273 COG2023 RPR2 RNase P subunit R 24.1 35 0.00076 28.9 0.8 40 227-266 57-97 (105)
274 PRK08115 ribonucleotide-diphos 24.1 37 0.00081 37.5 1.2 28 227-262 828-855 (858)
275 PF02150 RNA_POL_M_15KD: RNA p 24.0 25 0.00054 23.8 -0.1 27 229-261 4-30 (35)
276 PRK15331 chaperone protein Sic 23.9 72 0.0016 28.8 2.8 23 70-92 32-54 (165)
277 COG3024 Uncharacterized protei 23.9 35 0.00075 26.9 0.7 14 224-237 5-18 (65)
278 PF08819 DUF1802: Domain of un 23.7 44 0.00096 30.1 1.4 18 87-104 159-176 (177)
279 cd07078 ALDH NAD(P)+ dependent 23.7 1.6E+02 0.0036 28.2 5.3 44 73-116 253-308 (432)
280 PF14446 Prok-RING_1: Prokaryo 23.6 50 0.0011 25.0 1.4 26 226-260 5-30 (54)
281 PRK03922 hypothetical protein; 23.6 38 0.00083 29.1 1.0 17 223-239 46-62 (113)
282 PF10825 DUF2752: Protein of u 23.5 35 0.00076 24.8 0.6 8 228-235 11-18 (52)
283 PF08976 DUF1880: Domain of un 23.4 39 0.00084 29.3 0.9 14 92-105 3-16 (118)
284 PF02829 3H: 3H domain; Inter 23.2 1.3E+02 0.0027 24.9 3.9 44 64-109 38-95 (98)
285 cd00114 LIGANc NAD+ dependent 23.2 38 0.00082 32.7 0.9 38 97-142 2-40 (307)
286 smart00647 IBR In Between Ring 23.2 59 0.0013 22.7 1.7 33 228-265 20-54 (64)
287 TIGR00686 phnA alkylphosphonat 23.0 49 0.0011 28.3 1.5 27 227-261 3-29 (109)
288 TIGR00416 sms DNA repair prote 22.7 43 0.00093 33.8 1.3 13 276-288 89-101 (454)
289 COG0551 TopA Zn-finger domain 22.7 91 0.002 26.1 3.0 41 223-263 14-73 (140)
290 PF01485 IBR: IBR domain; Int 22.5 58 0.0012 22.7 1.6 32 228-264 20-53 (64)
291 TIGR03844 cysteate_syn cysteat 22.5 69 0.0015 31.7 2.6 27 228-264 4-30 (398)
292 COG3464 Transposase and inacti 22.4 52 0.0011 32.8 1.7 48 224-271 36-98 (402)
293 TIGR01031 rpmF_bact ribosomal 22.4 37 0.00081 25.2 0.6 11 227-237 27-37 (55)
294 COG4260 Membrane protease subu 22.4 39 0.00084 33.6 0.9 61 53-113 127-213 (345)
295 PF05209 MinC_N: Septum format 22.4 97 0.0021 24.6 3.0 37 73-110 30-73 (99)
296 PRK12268 methionyl-tRNA synthe 22.3 67 0.0014 32.5 2.5 9 226-234 141-149 (556)
297 PF12647 RNHCP: RNHCP domain; 21.9 59 0.0013 27.0 1.7 32 228-264 6-37 (92)
298 KOG0909 Peptide:N-glycanase [P 21.8 40 0.00087 35.1 0.9 41 224-264 159-207 (500)
299 cd07107 ALDH_PhdK-like Nocardi 21.8 1.7E+02 0.0038 28.7 5.2 60 57-116 255-328 (456)
300 PF04475 DUF555: Protein of un 21.7 60 0.0013 27.6 1.7 36 203-239 24-60 (102)
301 PF01783 Ribosomal_L32p: Ribos 21.7 39 0.00084 24.9 0.5 20 227-258 27-46 (56)
302 PF14690 zf-ISL3: zinc-finger 21.5 42 0.00091 22.8 0.7 9 228-236 4-12 (47)
303 cd07113 ALDH_PADH_NahF Escheri 21.5 1.9E+02 0.0041 28.8 5.4 60 57-116 280-353 (477)
304 cd07108 ALDH_MGR_2402 Magnetos 21.4 1.7E+02 0.0037 28.8 5.0 60 57-116 256-330 (457)
305 TIGR01780 SSADH succinate-semi 21.4 2E+02 0.0042 28.4 5.5 59 58-116 258-330 (448)
306 COG4481 Uncharacterized protei 21.3 59 0.0013 25.2 1.5 39 219-262 7-45 (60)
307 PF10609 ParA: ParA/MinD ATPas 21.2 31 0.00067 27.7 -0.1 13 227-239 66-78 (81)
308 COG1885 Uncharacterized protei 21.0 50 0.0011 28.5 1.1 17 224-240 47-63 (115)
309 cd07135 ALDH_F14-YMR110C Sacch 21.0 2.3E+02 0.005 28.1 5.9 63 56-118 243-315 (436)
310 COG2093 DNA-directed RNA polym 20.9 42 0.00091 26.4 0.6 11 229-239 21-31 (64)
311 PRK03564 formate dehydrogenase 20.7 60 0.0013 31.8 1.8 35 228-262 228-263 (309)
312 COG1198 PriA Primosomal protei 20.7 48 0.0011 35.9 1.2 14 228-241 477-490 (730)
313 PF03938 OmpH: Outer membrane 20.7 1.6E+02 0.0035 24.4 4.1 36 72-107 52-87 (158)
314 cd07116 ALDH_ACDHII-AcoD Ralst 20.7 1.8E+02 0.0039 29.0 5.1 60 57-116 279-352 (479)
315 PF11290 DUF3090: Protein of u 20.6 45 0.00096 30.5 0.8 11 226-236 154-164 (171)
316 PF02701 zf-Dof: Dof domain, z 20.4 45 0.00098 26.1 0.7 33 228-260 7-39 (63)
317 PRK08329 threonine synthase; V 20.4 80 0.0017 30.3 2.5 26 228-264 3-28 (347)
318 PF09930 DUF2162: Predicted tr 20.4 45 0.00097 31.2 0.8 35 202-236 74-115 (224)
319 TIGR00357 methionine-R-sulfoxi 20.3 54 0.0012 28.7 1.2 39 228-266 42-106 (134)
320 PRK12722 transcriptional activ 20.2 75 0.0016 29.2 2.2 36 218-259 127-162 (187)
321 COG0229 Conserved domain frequ 20.2 46 0.001 29.6 0.8 34 228-261 44-101 (140)
322 TIGR01552 phd_fam prevent-host 20.2 2.4E+02 0.0052 19.4 4.3 15 92-106 36-50 (52)
323 PF05120 GvpG: Gas vesicle pro 20.1 2E+02 0.0044 23.0 4.3 25 80-106 38-62 (79)
No 1
>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=96.78 E-value=0.0017 Score=61.85 Aligned_cols=36 Identities=28% Similarity=0.437 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112 72 KETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLRW 107 (296)
Q Consensus 72 ~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~ 107 (296)
..+|+++-.++..+||. |+|+|||+|||.|..+|+.
T Consensus 3 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 39 (307)
T cd00114 3 IAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRA 39 (307)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 67899999999999887 9999999999999999973
No 2
>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=96.49 E-value=0.0033 Score=59.94 Aligned_cols=36 Identities=31% Similarity=0.534 Sum_probs=32.2
Q ss_pred cHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHh
Q 045112 71 SKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 71 t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk 106 (296)
...+|+++-.++..+||. |+|+|||+|||.|..+|+
T Consensus 6 ~i~~L~~~i~~~~~~YY~~~~p~isD~eYD~l~~~L~ 42 (315)
T PF01653_consen 6 RIEELRKEINRHNYAYYNLGEPIISDAEYDQLFRELK 42 (315)
T ss_dssp HHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 467888889999999877 899999999999999986
No 3
>smart00532 LIGANc Ligase N family.
Probab=96.26 E-value=0.0049 Score=61.53 Aligned_cols=36 Identities=28% Similarity=0.497 Sum_probs=32.6
Q ss_pred cHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHh
Q 045112 71 SKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 71 t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk 106 (296)
...+|.++-.++..+||. |+|+|||+|||+|..||+
T Consensus 4 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 40 (441)
T smart00532 4 EISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELK 40 (441)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH
Confidence 367888889999999886 999999999999999997
No 4
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.13 E-value=0.0059 Score=63.62 Aligned_cols=36 Identities=31% Similarity=0.383 Sum_probs=32.8
Q ss_pred cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHh
Q 045112 71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk 106 (296)
...+|.++-.++..+|| .|+|+|||+|||+|..+|+
T Consensus 8 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~ 44 (665)
T PRK07956 8 RIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELV 44 (665)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 36788888888999988 9999999999999999997
No 5
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.92 E-value=0.01 Score=62.31 Aligned_cols=36 Identities=28% Similarity=0.548 Sum_probs=30.3
Q ss_pred cHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHh
Q 045112 71 SKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 71 t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk 106 (296)
..++|.++-.++..+|| .|+|+|||+|||+|.++|+
T Consensus 35 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 71 (689)
T PRK14351 35 QAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQ 71 (689)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 45666777777777887 6899999999999999998
No 6
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=95.75 E-value=0.0041 Score=39.45 Aligned_cols=24 Identities=46% Similarity=1.036 Sum_probs=18.6
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
-.|||||+++ +....-|++||++|
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 33466799999875
No 7
>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=95.59 E-value=0.0074 Score=40.36 Aligned_cols=35 Identities=26% Similarity=0.507 Sum_probs=22.9
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
+-.||+|++.+.. ....-.....+++|++|+..+.
T Consensus 2 ~~~CP~C~~~~~v--~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRV--VDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEe--CHHHcCCCCCEEECCCCCCEEE
Confidence 4579999998542 2211112334899999999875
No 8
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=95.52 E-value=0.015 Score=59.93 Aligned_cols=35 Identities=29% Similarity=0.523 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHh
Q 045112 72 KETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 72 ~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk 106 (296)
..+|.++-.++..+||. |+|+|||+|||+|..||+
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 55677777777788775 999999999999999997
No 9
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.44 E-value=0.014 Score=40.88 Aligned_cols=31 Identities=32% Similarity=0.702 Sum_probs=22.7
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
-|||||+++-. +. .....+|+.||+.+.|..
T Consensus 5 ~C~~CG~~~~~----~~---~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 5 KCARCGREVEL----DE---YGTGVRCPYCGYRILFKE 35 (46)
T ss_pred ECCCCCCEEEE----CC---CCCceECCCCCCeEEEcc
Confidence 59999997643 11 112789999999999864
No 10
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.19 E-value=0.02 Score=60.00 Aligned_cols=38 Identities=26% Similarity=0.447 Sum_probs=31.7
Q ss_pred cccHHHHHHHHHHHHHHhh-cCCCccchhhhHHHHHHHh
Q 045112 69 TASKETLEALYRQARDAYY-SGKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 69 ~~t~~elE~~flqA~~AY~-~GkPimsDeeFD~LK~kLk 106 (296)
++..++|.++-.+.-.+|| .|+|+|||+|||+|..||+
T Consensus 6 ~~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~ 44 (669)
T PRK14350 6 QDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQ 44 (669)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 3456777777778888877 5899999999999999996
No 11
>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=95.08 E-value=0.019 Score=59.74 Aligned_cols=32 Identities=31% Similarity=0.473 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112 76 EALYRQARDAYYS-GKPLIVDDMFDRVELKLRW 107 (296)
Q Consensus 76 E~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~ 107 (296)
.++-.++..+||. |+|+|||+|||+|.++|+.
T Consensus 2 ~~~l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 34 (652)
T TIGR00575 2 RKLIRHHDYRYYVLDEPSISDAEYDRLYRELQE 34 (652)
T ss_pred HHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 3445667788886 9999999999999999984
No 12
>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=95.08 E-value=0.017 Score=43.09 Aligned_cols=34 Identities=29% Similarity=0.604 Sum_probs=24.4
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
+..||.||+++-- .....-..++|++||..++--
T Consensus 2 ~~~CP~CG~~iev-----~~~~~GeiV~Cp~CGaeleVv 35 (54)
T TIGR01206 2 QFECPDCGAEIEL-----ENPELGELVICDECGAELEVV 35 (54)
T ss_pred ccCCCCCCCEEec-----CCCccCCEEeCCCCCCEEEEE
Confidence 5689999998732 222223478999999998864
No 13
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.49 E-value=0.016 Score=44.51 Aligned_cols=36 Identities=28% Similarity=0.583 Sum_probs=23.3
Q ss_pred eeeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 222 LVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 222 ~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
--..+=+||||||+.- .+-..--.-.|..+|++||=
T Consensus 23 e~~v~F~CPnCGe~~I--~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 23 ETAVKFPCPNCGEVEI--YRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred CceeEeeCCCCCceee--ehhhhHHHcCCceECCCcCc
Confidence 3457889999996543 12222223457899999983
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=94.28 E-value=0.021 Score=35.76 Aligned_cols=22 Identities=45% Similarity=1.029 Sum_probs=16.3
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
|||||+|+. .+..-|++||++|
T Consensus 2 Cp~CG~~~~-----------~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIE-----------DDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCC-----------CcCcchhhhCCcC
Confidence 999999873 2233499999875
No 15
>PRK05978 hypothetical protein; Provisional
Probab=93.91 E-value=0.026 Score=49.48 Aligned_cols=32 Identities=38% Similarity=0.937 Sum_probs=23.4
Q ss_pred eecCCCCCccccc--eeeccCCCCCCCCccccCCCCcceEEe
Q 045112 225 LRGACPNCGEEVF--AFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 225 LKGpCPNCGeEv~--sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
|+|-||+||+.-. .|++ -+-.|++||..+++.
T Consensus 32 l~grCP~CG~G~LF~g~Lk--------v~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGEGKLFRAFLK--------PVDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCCCcccccccc--------cCCCccccCCccccC
Confidence 5899999999743 3333 344699999988753
No 16
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=93.87 E-value=0.028 Score=47.82 Aligned_cols=53 Identities=23% Similarity=0.452 Sum_probs=30.5
Q ss_pred HHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112 213 VLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 213 ~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
.|..-+..+.--..=-|||||.. |+|--...-...+.+..|++||..|+++..
T Consensus 86 ~L~~~l~~e~~~~~Y~Cp~C~~~-y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 86 RLEDKLEDETNNAYYKCPNCQSK-YTFLEANQLLDMDGTFTCPRCGEELEEDDN 138 (147)
T ss_pred HHHHHHhcccCCcEEECcCCCCE-eeHHHHHHhcCCCCcEECCCCCCEEEEcCc
Confidence 34443333332233459999944 445322211123566999999999988653
No 17
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=93.53 E-value=0.057 Score=42.26 Aligned_cols=36 Identities=36% Similarity=0.782 Sum_probs=29.6
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
-|+--||.||+|-..| +.+...+.|.+||+.|..-|
T Consensus 17 Fl~VkCpdC~N~q~vF------shast~V~C~~CG~~l~~PT 52 (67)
T COG2051 17 FLRVKCPDCGNEQVVF------SHASTVVTCLICGTTLAEPT 52 (67)
T ss_pred EEEEECCCCCCEEEEe------ccCceEEEecccccEEEecC
Confidence 4677799999998877 25677899999999997654
No 18
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=93.31 E-value=0.024 Score=41.02 Aligned_cols=32 Identities=22% Similarity=0.549 Sum_probs=22.8
Q ss_pred CCCCCccccceeeccCCCCCCC-CccccCCCCc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSP-HRSDCHVCGS 259 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~-n~vkChvC~t 259 (296)
|||=||.+..........+... ..+.|++||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 8999998887665533322111 7899999998
No 19
>PRK00420 hypothetical protein; Validated
Probab=93.09 E-value=0.063 Score=45.27 Aligned_cols=44 Identities=23% Similarity=0.441 Sum_probs=30.5
Q ss_pred HhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 214 LQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 214 Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
+..++.+=...|-..||.||.+.|.+ . ...+-|++||..+.=..
T Consensus 11 ~a~~Ll~Ga~ml~~~CP~Cg~pLf~l---k-----~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 11 AAELLLKGAKMLSKHCPVCGLPLFEL---K-----DGEVVCPVHGKVYIVKS 54 (112)
T ss_pred HHHHHHhHHHHccCCCCCCCCcceec---C-----CCceECCCCCCeeeecc
Confidence 44444454555789999999888765 1 23678999999766433
No 20
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=92.87 E-value=0.047 Score=41.75 Aligned_cols=33 Identities=30% Similarity=0.819 Sum_probs=21.8
Q ss_pred eeecCCCCCccc-cceeeccCCCCCCCCccccCCCCc
Q 045112 224 ALRGACPNCGEE-VFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 224 iLKGpCPNCGeE-v~sFfgtv~s~~~~n~vkChvC~t 259 (296)
..+=+|||||++ +.- -.+--.-.|.++|++||-
T Consensus 23 ~~~F~CPnCG~~~I~R---C~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR---CEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEee---chhHHhcCCceECCCCCC
Confidence 456689999998 432 111113458899999984
No 21
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=92.71 E-value=0.072 Score=40.68 Aligned_cols=34 Identities=35% Similarity=0.779 Sum_probs=28.1
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
-|+--||.|++|...| +.+...++|.+||+.|.-
T Consensus 9 F~~VkCp~C~n~q~vF------sha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 9 FLKVKCPDCGNEQVVF------SHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEEEECCCCCCeEEEE------ecCCcEEECcccCCCccc
Confidence 4677899999999888 256778999999999853
No 22
>PHA00626 hypothetical protein
Probab=92.57 E-value=0.073 Score=40.73 Aligned_cols=42 Identities=21% Similarity=0.325 Sum_probs=28.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeecc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSS 271 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~ 271 (296)
.||+||..+..==+.+. .-+++.+|+.||-...=|+-=|+-+
T Consensus 2 ~CP~CGS~~Ivrcg~cr--~~snrYkCkdCGY~ft~~~~~~~~~ 43 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR--GWSDDYVCCDCGYNDSKDAFGERGK 43 (59)
T ss_pred CCCCCCCceeeeeceec--ccCcceEcCCCCCeechhhhhhccc
Confidence 49999997655223322 2478999999998776665555443
No 23
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=92.56 E-value=0.093 Score=38.87 Aligned_cols=42 Identities=26% Similarity=0.680 Sum_probs=33.2
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeec
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQS 270 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s 270 (296)
.||.||+.+-.....-.+ .-.---+|.+|-+++.+.-.+...
T Consensus 2 ~CPyCge~~~~~iD~s~~-~Q~yiEDC~vCC~PI~~~v~~d~~ 43 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAG-DQEYIEDCQVCCRPIEVQVTVDED 43 (52)
T ss_pred CCCCCCCeeEEEEecCCC-CeeEEeehhhcCCccEEEEEECCC
Confidence 599999999887766555 444556899999999999877643
No 24
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.55 E-value=0.041 Score=47.52 Aligned_cols=31 Identities=42% Similarity=0.977 Sum_probs=23.2
Q ss_pred eecCCCCCccccc--eeeccCCCCCCCCccccCCCCcceEE
Q 045112 225 LRGACPNCGEEVF--AFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 225 LKGpCPNCGeEv~--sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
|+|-||||||--. .|.+..+ .|.+||-.+-|
T Consensus 20 l~grCP~CGeGrLF~gFLK~~p--------~C~aCG~dyg~ 52 (126)
T COG5349 20 LRGRCPRCGEGRLFRGFLKVVP--------ACEACGLDYGF 52 (126)
T ss_pred hcCCCCCCCCchhhhhhcccCc--------hhhhccccccC
Confidence 6899999999643 5555444 49999987765
No 25
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=92.05 E-value=0.18 Score=53.41 Aligned_cols=38 Identities=24% Similarity=0.372 Sum_probs=31.9
Q ss_pred ccHHHHHHHHHHHHHHhhc-CCCccchhhhHHHHHHHhH
Q 045112 70 ASKETLEALYRQARDAYYS-GKPLIVDDMFDRVELKLRW 107 (296)
Q Consensus 70 ~t~~elE~~flqA~~AY~~-GkPimsDeeFD~LK~kLk~ 107 (296)
+..++|.++-.+-...||- ++|+|+|+|||+|.+||..
T Consensus 9 ~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~~ 47 (667)
T COG0272 9 EEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQE 47 (667)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCCChHHHHHHHHHHHH
Confidence 4567777777777788776 9999999999999999974
No 26
>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=91.78 E-value=0.14 Score=37.05 Aligned_cols=36 Identities=22% Similarity=0.481 Sum_probs=25.3
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
|||-||.+...|...........-.+|..|+.....
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 899999998877532222234445699999988765
No 27
>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=91.61 E-value=0.38 Score=41.10 Aligned_cols=34 Identities=26% Similarity=0.637 Sum_probs=25.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeec
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQS 270 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s 270 (296)
.|||||.+....=+. --|..|+++|+-|-..|--
T Consensus 71 ~CP~C~K~TKmLGr~---------D~CM~C~~pLTLd~~legk 104 (114)
T PF11023_consen 71 ECPNCGKQTKMLGRV---------DACMHCKEPLTLDPSLEGK 104 (114)
T ss_pred ECCCCCChHhhhchh---------hccCcCCCcCccCchhhcc
Confidence 399999987643111 2699999999999887753
No 28
>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=91.58 E-value=0.17 Score=34.98 Aligned_cols=38 Identities=29% Similarity=0.542 Sum_probs=25.6
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeecc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSS 271 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~ 271 (296)
-||+||... ..+- ..+.+.-|.+||.-++.+.-.+..+
T Consensus 2 ~Cp~Cg~~~-~~~D-----~~~g~~vC~~CG~Vl~e~~i~~~~e 39 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-----PERGELVCPNCGLVLEENIIDEGPE 39 (43)
T ss_dssp SBTTTSSSE-EEEE-----TTTTEEEETTT-BBEE-TTBSCCCS
T ss_pred CCcCCcCCc-eEEc-----CCCCeEECCCCCCEeecccccCCcc
Confidence 499999977 3332 3456789999999998776655443
No 29
>PF14353 CpXC: CpXC protein
Probab=91.20 E-value=0.15 Score=41.88 Aligned_cols=41 Identities=27% Similarity=0.495 Sum_probs=27.8
Q ss_pred CCCCCccccceee-ccCCC-----------CCCCCccccCCCCcceEEeccee
Q 045112 228 ACPNCGEEVFAFV-NSDQT-----------KNSPHRSDCHVCGSLLEFRTKVE 268 (296)
Q Consensus 228 pCPNCGeEv~sFf-gtv~s-----------~~~~n~vkChvC~t~L~fds~ve 268 (296)
.||+||++...=+ ..+.. +++-+.+.|+.||.....+...-
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~l 55 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLL 55 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEE
Confidence 6999999765332 22222 25778999999999876655443
No 30
>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=90.99 E-value=0.12 Score=33.43 Aligned_cols=23 Identities=39% Similarity=0.912 Sum_probs=17.8
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
.||+|+++| ..+..+|+.||-..
T Consensus 2 ~CP~C~~~V-----------~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEV-----------PESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCc-----------hhhcCcCCCCCCCC
Confidence 499999998 34556899998653
No 31
>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=90.84 E-value=0.096 Score=45.49 Aligned_cols=33 Identities=27% Similarity=0.619 Sum_probs=23.9
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
=-||||+.. ++|--... +...|++||..|+++.
T Consensus 110 Y~Cp~c~~r-~tf~eA~~-----~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 110 FICPNMCVR-FTFNEAME-----LNFTCPRCGAMLDYLD 142 (158)
T ss_pred EECCCCCcE-eeHHHHHH-----cCCcCCCCCCEeeecc
Confidence 349999943 45543322 5899999999999864
No 32
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=90.32 E-value=0.18 Score=39.22 Aligned_cols=33 Identities=24% Similarity=0.518 Sum_probs=23.5
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
-|||.||++....=-+ ...-.++|+.|++.-.|
T Consensus 7 KPCPFCG~~~~~v~~~----~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 7 KPCPFCGCPSVTVKAI----SGYYRAKCNGCESRTGY 39 (64)
T ss_pred cCCCCCCCceeEEEec----CceEEEEcCCCCcCccc
Confidence 3999999998765321 23446999999996443
No 33
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.31 E-value=0.23 Score=35.46 Aligned_cols=29 Identities=28% Similarity=0.605 Sum_probs=23.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
-|.+||+|+..- ....++|+.||..+.|-
T Consensus 4 ~C~~Cg~~~~~~--------~~~~irC~~CG~rIlyK 32 (44)
T smart00659 4 ICGECGRENEIK--------SKDVVRCRECGYRILYK 32 (44)
T ss_pred ECCCCCCEeecC--------CCCceECCCCCceEEEE
Confidence 499999997632 45679999999999985
No 34
>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=89.63 E-value=0.27 Score=37.03 Aligned_cols=35 Identities=29% Similarity=0.611 Sum_probs=23.5
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
|+--||.|++|...| +.+...+.|.+|++.|.--|
T Consensus 6 m~VkCp~C~~~q~vF------Sha~t~V~C~~Cg~~L~~Pt 40 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVF------SHAQTVVKCVVCGTVLAQPT 40 (55)
T ss_dssp EEEE-TTT-SEEEEE------TT-SS-EE-SSSTSEEEEE-
T ss_pred EEEECCCCCCeeEEE------ecCCeEEEcccCCCEecCCC
Confidence 556799999999887 36778899999999986543
No 35
>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=89.38 E-value=0.091 Score=49.88 Aligned_cols=58 Identities=29% Similarity=0.515 Sum_probs=27.7
Q ss_pred hhhhhhhhHHHHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecce
Q 045112 203 GYPIASASVRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKV 267 (296)
Q Consensus 203 gyplasa~v~~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~v 267 (296)
+|-=.+-.+++||..|. .=...|||||.+..+=|+ .|+...+..|++|+...+-.|+=
T Consensus 12 ~YkS~sQ~aRVltE~Wv----~~n~yCP~Cg~~~L~~f~---NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 12 GYKSNSQIARVLTEDWV----AENMYCPNCGSKPLSKFE---NNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp HTTT-TTHHHHHHHHHH----HHH---TTT--SS-EE-----------EEE-TTT--EEEEEEEE
T ss_pred hccChhhhhHHHHHHHH----HHCCcCCCCCChhHhhcc---CCCccceeECCCCchHHhhhhhc
Confidence 44444555666776654 445789999999776664 34557789999999987766653
No 36
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.28 E-value=0.15 Score=45.22 Aligned_cols=47 Identities=26% Similarity=0.412 Sum_probs=29.7
Q ss_pred HHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 213 VLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 213 ~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
.|..-+..+.--.-=-||||+.. |+|.-.. .+...|++||..|++..
T Consensus 104 klk~~l~~e~~~~~Y~Cp~C~~r-ytf~eA~-----~~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 104 KLKEQLEEEENNMFFFCPNCHIR-FTFDEAM-----EYGFRCPQCGEMLEEYD 150 (178)
T ss_pred HHHHHhhhccCCCEEECCCCCcE-EeHHHHh-----hcCCcCCCCCCCCeecc
Confidence 34444443333333459999944 4554322 35899999999999864
No 37
>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=88.39 E-value=0.45 Score=31.60 Aligned_cols=29 Identities=21% Similarity=0.556 Sum_probs=20.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.||+||.+.-..... .+.....|+.||..
T Consensus 7 ~C~~Cg~~fe~~~~~----~~~~~~~CP~Cg~~ 35 (41)
T smart00834 7 RCEDCGHTFEVLQKI----SDDPLATCPECGGD 35 (41)
T ss_pred EcCCCCCEEEEEEec----CCCCCCCCCCCCCc
Confidence 699999965544332 22567889999984
No 38
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=88.37 E-value=0.31 Score=33.62 Aligned_cols=33 Identities=24% Similarity=0.573 Sum_probs=21.6
Q ss_pred CCCCCccccceeec--cCCCC-CCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVN--SDQTK-NSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfg--tv~s~-~~~n~vkChvC~t~ 260 (296)
+||+||.+.-.||- +.++. ..+--..|-+|+..
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 69999999998883 33332 35667889999853
No 39
>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=88.04 E-value=0.54 Score=33.11 Aligned_cols=39 Identities=23% Similarity=0.547 Sum_probs=24.9
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeeccccCC
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLG 275 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~s~~~ 275 (296)
-|++||.+.-..... .+.....|++||+ .++++-.|+++
T Consensus 7 ~C~~Cg~~fe~~~~~----~~~~~~~CP~Cg~-----~~~~r~~s~~~ 45 (52)
T TIGR02605 7 RCTACGHRFEVLQKM----SDDPLATCPECGG-----EKLRRLLSAVG 45 (52)
T ss_pred EeCCCCCEeEEEEec----CCCCCCCCCCCCC-----CceeEEecccc
Confidence 499999765444322 1245678999998 35566666553
No 40
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=87.41 E-value=0.33 Score=33.16 Aligned_cols=28 Identities=29% Similarity=0.669 Sum_probs=15.9
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
||+||.++-- .+..+.++.+.-|+.||.
T Consensus 3 C~~CG~~l~~---~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CPQCGGPLER---RIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -TTT--B-EE---E--TT-SS-EEEETTTTE
T ss_pred cccccChhhh---hcCCCCCccceECCCCCC
Confidence 9999999632 344557889999999985
No 41
>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=87.08 E-value=0.4 Score=32.38 Aligned_cols=28 Identities=29% Similarity=0.687 Sum_probs=19.9
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
|.+||+||. ++ ....++|..||..+.|-
T Consensus 3 C~~Cg~~~~-----~~---~~~~irC~~CG~RIlyK 30 (32)
T PF03604_consen 3 CGECGAEVE-----LK---PGDPIRCPECGHRILYK 30 (32)
T ss_dssp ESSSSSSE------BS---TSSTSSBSSSS-SEEBE
T ss_pred CCcCCCeeE-----cC---CCCcEECCcCCCeEEEe
Confidence 889999987 22 23458999999988773
No 42
>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=87.00 E-value=0.39 Score=35.42 Aligned_cols=32 Identities=28% Similarity=0.595 Sum_probs=24.6
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecce
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKV 267 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~v 267 (296)
-.||.||..+.. ........|++||.. +|.++
T Consensus 29 q~C~~CG~~~~~-------~~~~r~~~C~~Cg~~--~~rD~ 60 (69)
T PF07282_consen 29 QTCPRCGHRNKK-------RRSGRVFTCPNCGFE--MDRDV 60 (69)
T ss_pred cCccCccccccc-------ccccceEEcCCCCCE--ECcHH
Confidence 359999999887 356678999999976 45444
No 43
>PLN00209 ribosomal protein S27; Provisional
Probab=86.19 E-value=0.49 Score=38.67 Aligned_cols=36 Identities=19% Similarity=0.327 Sum_probs=29.9
Q ss_pred eeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 223 VALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 223 liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
--|+--||.|++|...| +.+...|.|.+|++.|.--
T Consensus 33 ~Fm~VkCp~C~n~q~VF------ShA~t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 33 FFMDVKCQGCFNITTVF------SHSQTVVVCGSCQTVLCQP 68 (86)
T ss_pred EEEEEECCCCCCeeEEE------ecCceEEEccccCCEeecc
Confidence 56788899999999887 2567789999999998643
No 44
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=86.14 E-value=0.58 Score=32.47 Aligned_cols=32 Identities=25% Similarity=0.603 Sum_probs=23.6
Q ss_pred CCCCCccccceeecc--CCCC-CCCCccccCCCCc
Q 045112 228 ACPNCGEEVFAFVNS--DQTK-NSPHRSDCHVCGS 259 (296)
Q Consensus 228 pCPNCGeEv~sFfgt--v~s~-~~~n~vkChvC~t 259 (296)
+||+||...-.||-. .++. ..+--.+|-+|+-
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~ 36 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGH 36 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCC
Confidence 699999888888752 2222 3567889999984
No 45
>PF12773 DZR: Double zinc ribbon
Probab=86.11 E-value=0.36 Score=33.68 Aligned_cols=18 Identities=17% Similarity=0.294 Sum_probs=11.7
Q ss_pred CCCCccccCCCCcceEEe
Q 045112 247 NSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 247 ~~~n~vkChvC~t~L~fd 264 (296)
.......|++||+.+.=+
T Consensus 25 ~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 25 PDQSKKICPNCGAENPPN 42 (50)
T ss_pred ccCCCCCCcCCcCCCcCC
Confidence 455567788888865433
No 46
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=84.51 E-value=0.67 Score=37.82 Aligned_cols=35 Identities=23% Similarity=0.413 Sum_probs=29.4
Q ss_pred eeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112 223 VALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 223 liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
--|+--||.|+++...| +.+...|.|.+|++.|.-
T Consensus 32 ~Fm~VkCp~C~n~q~VF------ShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 32 YFMDVKCPGCSQITTVF------SHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred eEEEEECCCCCCeeEEE------ecCceEEEccccCCEeec
Confidence 56788899999999887 266778999999999854
No 47
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=83.92 E-value=0.57 Score=31.90 Aligned_cols=34 Identities=26% Similarity=0.613 Sum_probs=20.8
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
+-.||||++.-. +...+=....-+++|++|+...
T Consensus 2 ~i~CP~C~~~f~--v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFR--VPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEE--cCHHHcccCCcEEECCCCCcEe
Confidence 346999997521 1121111344599999999764
No 48
>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=83.57 E-value=0.64 Score=31.93 Aligned_cols=33 Identities=30% Similarity=0.580 Sum_probs=23.0
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
-||+||+--...|. .....-+|.+||..|+=|.
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 39999986554443 2456679999999887654
No 49
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.18 E-value=0.9 Score=31.65 Aligned_cols=28 Identities=29% Similarity=0.720 Sum_probs=18.3
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
-||+||+-+ +.... ...+...|+.||-.
T Consensus 2 FCp~Cg~~l--~~~~~---~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNML--IPKEG---KEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCcc--ccccC---CCCCEEECCcCCCe
Confidence 399999944 22221 22358899999954
No 50
>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=82.61 E-value=0.74 Score=47.16 Aligned_cols=50 Identities=28% Similarity=0.448 Sum_probs=36.5
Q ss_pred ccceeeeecCCCCCccccceeecc---CCC-CCCCCccccCCCCcceEEeccee
Q 045112 219 RNDLVALRGACPNCGEEVFAFVNS---DQT-KNSPHRSDCHVCGSLLEFRTKVE 268 (296)
Q Consensus 219 ~~D~liLKGpCPNCGeEv~sFfgt---v~s-~~~~n~vkChvC~t~L~fds~ve 268 (296)
..|----.-|||+||++..-=|.. ... ...+....|+.||+.+.-.-+-.
T Consensus 193 ~sdqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~ 246 (557)
T PF05876_consen 193 ESDQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRR 246 (557)
T ss_pred hCCceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhh
Confidence 466677889999999987633443 222 46788899999999998665544
No 51
>PRK02935 hypothetical protein; Provisional
Probab=82.32 E-value=3.2 Score=35.34 Aligned_cols=35 Identities=23% Similarity=0.512 Sum_probs=25.8
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeec
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQS 270 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s 270 (296)
-.||||+.+..--=+.| -|-.|+++|+-|...|.-
T Consensus 71 V~CP~C~K~TKmLGrvD---------~CM~C~~PLTLd~~legk 105 (110)
T PRK02935 71 VICPSCEKPTKMLGRVD---------ACMHCNQPLTLDRSLEGK 105 (110)
T ss_pred eECCCCCchhhhcccee---------ecCcCCCcCCcCcccccc
Confidence 38999998875321111 599999999998877753
No 52
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=82.28 E-value=0.48 Score=43.82 Aligned_cols=34 Identities=32% Similarity=0.678 Sum_probs=20.2
Q ss_pred eecCCCCCc-cccceeeccCCCCCCCCccccCCCCcc
Q 045112 225 LRGACPNCG-EEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 225 LKGpCPNCG-eEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
..-+||+|| +|+..=+-.-. ...-.+.|.+||+-
T Consensus 5 iy~~Cp~Cg~eev~hEVik~~--g~~~lvrC~eCG~V 39 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIKER--GREPLVRCEECGTV 39 (201)
T ss_pred EEEECCCCCcchhhHHHHHhc--CCceEEEccCCCcE
Confidence 456899999 44421111111 12268999999973
No 53
>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=82.11 E-value=0.57 Score=30.15 Aligned_cols=11 Identities=55% Similarity=1.074 Sum_probs=8.4
Q ss_pred eeecCCCCCcc
Q 045112 224 ALRGACPNCGE 234 (296)
Q Consensus 224 iLKGpCPNCGe 234 (296)
...=+|||||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 44568999996
No 54
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=81.94 E-value=0.82 Score=33.38 Aligned_cols=29 Identities=31% Similarity=0.726 Sum_probs=20.2
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.++--||+||.+ |.... ..+..|..||-.
T Consensus 18 ~~~~fCP~Cg~~---~m~~~-----~~r~~C~~Cgyt 46 (50)
T PRK00432 18 RKNKFCPRCGSG---FMAEH-----LDRWHCGKCGYT 46 (50)
T ss_pred EccCcCcCCCcc---hhecc-----CCcEECCCcCCE
Confidence 456699999987 32221 157899999864
No 55
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=81.51 E-value=0.89 Score=38.55 Aligned_cols=23 Identities=43% Similarity=1.061 Sum_probs=16.8
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
||.||.+.. ..+.+|++|++.++
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 888887754 34678888888765
No 56
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=81.18 E-value=1.1 Score=50.79 Aligned_cols=44 Identities=23% Similarity=0.443 Sum_probs=27.3
Q ss_pred ceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 221 DLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 221 D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
++.+-.--||+||++++.+|=..=+........|+.||..+..+
T Consensus 662 eVEV~~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~d 705 (1337)
T PRK14714 662 EVEVGRRRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPPD 705 (1337)
T ss_pred EEEEEEEECCCCCCccccccCcccCCcCCCceeCccCCCccCCC
Confidence 35677788999999998876433332222334566666655444
No 57
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=81.00 E-value=0.75 Score=40.02 Aligned_cols=39 Identities=28% Similarity=0.608 Sum_probs=29.6
Q ss_pred HHHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 212 RVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 212 ~~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
+.+..|+.+=+..|--.||-||.+.|. .+-++-|++||.
T Consensus 14 k~iA~lLl~GAkML~~hCp~Cg~PLF~---------KdG~v~CPvC~~ 52 (131)
T COG1645 14 KKIAELLLQGAKMLAKHCPKCGTPLFR---------KDGEVFCPVCGY 52 (131)
T ss_pred HHHHHHHHhhhHHHHhhCcccCCccee---------eCCeEECCCCCc
Confidence 344456666667777889999999986 345788999996
No 58
>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=80.67 E-value=1.7 Score=30.28 Aligned_cols=28 Identities=29% Similarity=0.667 Sum_probs=20.2
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
-|++||.+--.+.. ..+...+.|+.||.
T Consensus 7 ~C~~Cg~~fe~~~~----~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQS----ISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEE----cCCCCCCcCCCCCC
Confidence 49999977555543 22367889999998
No 59
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=79.58 E-value=1.4 Score=38.91 Aligned_cols=41 Identities=27% Similarity=0.588 Sum_probs=26.1
Q ss_pred CCCCCccccceeeccC---CCCCCCCccccCCCCcceEEeccee
Q 045112 228 ACPNCGEEVFAFVNSD---QTKNSPHRSDCHVCGSLLEFRTKVE 268 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv---~s~~~~n~vkChvC~t~L~fds~ve 268 (296)
-||-||++-..-..+. .++..+-..+|.+||....==-+|+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVE 45 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEecc
Confidence 4999998764444443 3444444499999998765333333
No 60
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.25 E-value=1.7 Score=37.09 Aligned_cols=45 Identities=22% Similarity=0.482 Sum_probs=31.6
Q ss_pred cceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112 220 NDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 220 ~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
....+.+--||-|+.++ .+..-.......+.+|+.|++....+++
T Consensus 24 ~~~~~~~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~~~~ 68 (129)
T COG3677 24 IRMQITKVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTVETG 68 (129)
T ss_pred HhhhcccCcCCCCCccc--eeeECCccccccccccCCcCcceeeecc
Confidence 34556677899999999 3332222234789999999998876653
No 61
>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=78.76 E-value=1.7 Score=30.53 Aligned_cols=36 Identities=25% Similarity=0.579 Sum_probs=24.1
Q ss_pred HhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 214 LQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 214 Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
|..+.-+|-+ -||.||......+.+ +...+|..|+.
T Consensus 10 l~~~RW~~g~----~CP~Cg~~~~~~~~~------~~~~~C~~C~~ 45 (46)
T PF12760_consen 10 LEEIRWPDGF----VCPHCGSTKHYRLKT------RGRYRCKACRK 45 (46)
T ss_pred HHHhcCCCCC----CCCCCCCeeeEEeCC------CCeEECCCCCC
Confidence 4444445542 299999984444443 78899999975
No 62
>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=78.66 E-value=1.1 Score=40.26 Aligned_cols=34 Identities=26% Similarity=0.505 Sum_probs=22.3
Q ss_pred CCCCCccccceee--ccCC--CCCCCCccccCCCCcce
Q 045112 228 ACPNCGEEVFAFV--NSDQ--TKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 228 pCPNCGeEv~sFf--gtv~--s~~~~n~vkChvC~t~L 261 (296)
.||||++.+.-.+ .++- +.....-.-||+||...
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 5999999998432 2222 22333556899999875
No 63
>PRK04023 DNA polymerase II large subunit; Validated
Probab=78.50 E-value=1.3 Score=49.33 Aligned_cols=41 Identities=27% Similarity=0.464 Sum_probs=22.3
Q ss_pred ecCCCCCccccceeeccCCC------------CCCCCccccCCCCcceEEecc
Q 045112 226 RGACPNCGEEVFAFVNSDQT------------KNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s------------~~~~n~vkChvC~t~L~fds~ 266 (296)
.--||.||++.+.|+=..=+ ....+..+|++||..+.=.++
T Consensus 626 ~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~~s~ 678 (1121)
T PRK04023 626 RRKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTPYSK 678 (1121)
T ss_pred CccCCCCCCcCCcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCccce
Confidence 33688888876555422111 123344668888777654433
No 64
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=78.39 E-value=1.2 Score=30.31 Aligned_cols=33 Identities=21% Similarity=0.617 Sum_probs=20.5
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
+-.||||++.-. +...+=.....+++|++|+..
T Consensus 2 ~i~Cp~C~~~y~--i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 2 IITCPNCQAKYE--IDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCEEe--CCHHHCCCCCcEEECCCCCCE
Confidence 346999997522 122111145568999999975
No 65
>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=76.38 E-value=1.6 Score=29.30 Aligned_cols=19 Identities=37% Similarity=1.050 Sum_probs=13.5
Q ss_pred cceeeeec-C---CCCCccccce
Q 045112 220 NDLVALRG-A---CPNCGEEVFA 238 (296)
Q Consensus 220 ~D~liLKG-p---CPNCGeEv~s 238 (296)
...++++. | ||+|||+.++
T Consensus 22 ~~~~~i~~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 22 GELIVIENVPALVCPQCGEEYLD 44 (46)
T ss_pred CEEEEEeCCCccccccCCCEeeC
Confidence 44566644 5 9999998764
No 66
>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=75.82 E-value=1.7 Score=34.69 Aligned_cols=31 Identities=26% Similarity=0.544 Sum_probs=17.4
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
.+++||-|++.+-+|.=. .+.+..+|..||.
T Consensus 32 ~~~~CPfH~d~~pS~~i~----~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 32 YRCLCPFHDDKTPSFSIN----PDKNRFKCFGCGK 62 (97)
T ss_dssp EEE--SSS--SS--EEEE----TTTTEEEETTT--
T ss_pred EEEECcCCCCCCCceEEE----CCCCeEEECCCCC
Confidence 568899999988777543 2456899999986
No 67
>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=75.68 E-value=1.8 Score=34.32 Aligned_cols=39 Identities=33% Similarity=0.628 Sum_probs=20.9
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEeccee
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVE 268 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve 268 (296)
=.||.|+.++-.=..-++. .....+.|.+||. .|+++|.
T Consensus 23 F~CPfC~~~~sV~v~idkk-~~~~~~~C~~Cg~--~~~~~i~ 61 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKK-EGIGILSCRVCGE--SFQTKIN 61 (81)
T ss_dssp ---TTT--SS-EEEEEETT-TTEEEEEESSS----EEEEE--
T ss_pred EcCCcCCCCCeEEEEEEcc-CCEEEEEecCCCC--eEEEccC
Confidence 3799999876655554444 6778899999965 4555554
No 68
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=73.56 E-value=1.4 Score=30.67 Aligned_cols=30 Identities=37% Similarity=0.908 Sum_probs=18.6
Q ss_pred ecCCCCCccc-cceeeccCCCCCCCCccccCCCCc
Q 045112 226 RGACPNCGEE-VFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 226 KGpCPNCGeE-v~sFfgtv~s~~~~n~vkChvC~t 259 (296)
++|||+||-. -|. |..- ......-|..|+.
T Consensus 3 ~~pCP~CGG~DrFr-~~d~---~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFR-FDDK---DGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccc-cccC---CCCcCEEeCCCCC
Confidence 5899999763 445 4321 2235677888863
No 69
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=73.17 E-value=2.6 Score=34.93 Aligned_cols=31 Identities=29% Similarity=0.584 Sum_probs=19.6
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
.|||||+. ..-..-.+ ..-.+.|++||.--.
T Consensus 23 ~CP~Cge~-~v~v~~~k---~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 23 ECPRCGKV-SISVKIKK---NIAIITCGNCGLYTE 53 (99)
T ss_pred ECCCCCCe-EeeeecCC---CcceEECCCCCCccC
Confidence 59999953 22122222 467789999997643
No 70
>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=73.01 E-value=1.1 Score=39.74 Aligned_cols=43 Identities=28% Similarity=0.484 Sum_probs=23.2
Q ss_pred hhccceeeeecCCCCCccccceeeccCC---CCCCCCccccCCCCcc
Q 045112 217 LWRNDLVALRGACPNCGEEVFAFVNSDQ---TKNSPHRSDCHVCGSL 260 (296)
Q Consensus 217 l~~~D~liLKGpCPNCGeEv~sFfgtv~---s~~~~n~vkChvC~t~ 260 (296)
-.++|..-|+=.||.|++++. |=|... .........|++|++.
T Consensus 9 erf~~c~~l~~~C~~C~~~~~-f~g~~~~~~~~~~~~~~~C~~C~~~ 54 (188)
T PF08996_consen 9 ERFKDCEPLKLTCPSCGTEFE-FPGVFEEDGDDVSPSGLQCPNCSTP 54 (188)
T ss_dssp TTTTT---EEEE-TTT--EEE-E-SSS--SSEEEETTEEEETTT--B
T ss_pred HHhcCCCceEeECCCCCCCcc-ccccccCCccccccCcCcCCCCCCc
Confidence 457899999999999999863 322222 2245778999999983
No 71
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=72.85 E-value=3.4 Score=38.50 Aligned_cols=35 Identities=17% Similarity=0.443 Sum_probs=24.3
Q ss_pred cceeeeec----CCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 220 NDLVALRG----ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 220 ~D~liLKG----pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
++.+-+.| |||.||+++..-.- +.+...=|++|..
T Consensus 235 ~~~l~Vy~R~g~pC~~Cg~~I~~~~~-----~gR~t~~CP~CQ~ 273 (274)
T PRK01103 235 QQSLQVYGREGEPCRRCGTPIEKIKQ-----GGRSTFFCPRCQK 273 (274)
T ss_pred cceeEEcCCCCCCCCCCCCeeEEEEE-----CCCCcEECcCCCC
Confidence 44556664 89999999864211 2467789999975
No 72
>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=72.47 E-value=1.5 Score=33.62 Aligned_cols=13 Identities=62% Similarity=1.451 Sum_probs=10.8
Q ss_pred eecCCCCCccccc
Q 045112 225 LRGACPNCGEEVF 237 (296)
Q Consensus 225 LKGpCPNCGeEv~ 237 (296)
|.|-|||||-|..
T Consensus 40 l~~~CPNCgGelv 52 (57)
T PF06906_consen 40 LNGVCPNCGGELV 52 (57)
T ss_pred hcCcCcCCCCccc
Confidence 5899999998753
No 73
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=71.78 E-value=2.5 Score=38.78 Aligned_cols=32 Identities=25% Similarity=0.586 Sum_probs=26.8
Q ss_pred cceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 220 NDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 220 ~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
+|.=.++.-|+||+++..- .-+..+|+|||..
T Consensus 143 ~dlGVI~A~CsrC~~~L~~---------~~~~l~Cp~Cg~t 174 (188)
T COG1096 143 NDLGVIYARCSRCRAPLVK---------KGNMLKCPNCGNT 174 (188)
T ss_pred CcceEEEEEccCCCcceEE---------cCcEEECCCCCCE
Confidence 8998899999999998753 3467899999964
No 74
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=71.45 E-value=2.2 Score=37.85 Aligned_cols=22 Identities=36% Similarity=0.825 Sum_probs=16.8
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
-.||+||. .+.-..+|++||..
T Consensus 310 ~~C~~cg~------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH------------LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC------------ccceeEECCCCCCe
Confidence 36999999 23456899999974
No 75
>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=70.34 E-value=4.1 Score=38.01 Aligned_cols=22 Identities=32% Similarity=0.700 Sum_probs=9.7
Q ss_pred eeeecCCCCCccc-cceeeccCC
Q 045112 223 VALRGACPNCGEE-VFAFVNSDQ 244 (296)
Q Consensus 223 liLKGpCPNCGeE-v~sFfgtv~ 244 (296)
-=-+|-||.||.. +.+.+....
T Consensus 169 ~w~~g~CPvCGs~P~~s~l~~~~ 191 (290)
T PF04216_consen 169 GWQRGYCPVCGSPPVLSVLRGGE 191 (290)
T ss_dssp -TT-SS-TTT---EEEEEEE---
T ss_pred CccCCcCCCCCCcCceEEEecCC
Confidence 3457999999987 557776543
No 76
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=68.77 E-value=2.7 Score=44.41 Aligned_cols=15 Identities=20% Similarity=0.525 Sum_probs=7.9
Q ss_pred ccCCCCcceEEecce
Q 045112 253 DCHVCGSLLEFRTKV 267 (296)
Q Consensus 253 kChvC~t~L~fds~v 267 (296)
+|+.||+.+.-++++
T Consensus 29 ~Cp~CG~~~~~~~~f 43 (645)
T PRK14559 29 PCPQCGTEVPVDEAH 43 (645)
T ss_pred cCCCCCCCCCccccc
Confidence 455555555544443
No 77
>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=68.03 E-value=3.5 Score=29.28 Aligned_cols=36 Identities=25% Similarity=0.610 Sum_probs=24.0
Q ss_pred hhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCC
Q 045112 215 QGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCG 258 (296)
Q Consensus 215 t~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~ 258 (296)
..++.+=...|.-.||.||.+.+. + ...+.-|.+|+
T Consensus 6 ~~~LL~G~~ML~~~Cp~C~~PL~~----~----k~g~~~Cv~C~ 41 (41)
T PF06677_consen 6 GEYLLQGWTMLDEHCPDCGTPLMR----D----KDGKIYCVSCG 41 (41)
T ss_pred HHHHHHhHhHhcCccCCCCCeeEE----e----cCCCEECCCCC
Confidence 334444456778899999988764 1 22356799886
No 78
>PRK12495 hypothetical protein; Provisional
Probab=67.99 E-value=3.8 Score=38.65 Aligned_cols=43 Identities=16% Similarity=0.444 Sum_probs=32.5
Q ss_pred HHHHhhhhccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 211 VRVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 211 v~~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
.+.+..|+.+=...+---||.||.+++ .-+..+-|.+|+....
T Consensus 27 ~~~ma~lL~~gatmsa~hC~~CG~PIp---------a~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 27 TERMSELLLQGATMTNAHCDECGDPIF---------RHDGQEFCPTCQQPVT 69 (226)
T ss_pred HHHHHHHHHhhcccchhhcccccCccc---------CCCCeeECCCCCCccc
Confidence 345666777777778889999999999 2245778999997644
No 79
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=67.69 E-value=2.3 Score=30.06 Aligned_cols=31 Identities=26% Similarity=0.667 Sum_probs=15.2
Q ss_pred ecCCCCCccccc-eeeccCCCCCCCCccccCCCCc
Q 045112 226 RGACPNCGEEVF-AFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 226 KGpCPNCGeEv~-sFfgtv~s~~~~n~vkChvC~t 259 (296)
.+|||+||-.-. .-|... ..+...-|-.|+.
T Consensus 3 h~pCP~CGG~DrFri~~d~---~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGGKDRFRIFDDK---DGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT-TTTEEEETT-------S-EEETTTTB
T ss_pred CCCCCCCcCccccccCcCc---ccCCCEECCCCCC
Confidence 589999987554 424322 2236778888843
No 80
>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=67.35 E-value=1.7 Score=43.08 Aligned_cols=24 Identities=21% Similarity=0.639 Sum_probs=18.8
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
.||.|+..+ ....++.|+.|++.|
T Consensus 217 ~C~~Cd~~~----------~~~~~a~CpRC~~~L 240 (403)
T TIGR00155 217 SCSACHTTI----------LPAQEPVCPRCSTPL 240 (403)
T ss_pred cCCCCCCcc----------CCCCCcCCcCCCCcc
Confidence 499999954 124578899999999
No 81
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=67.25 E-value=3.7 Score=34.34 Aligned_cols=32 Identities=22% Similarity=0.687 Sum_probs=22.8
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
.|--||+||+--|-. ++.-+-|+.||+...=.
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 577899999986643 12346799999875443
No 82
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=67.05 E-value=4 Score=38.21 Aligned_cols=28 Identities=21% Similarity=0.450 Sum_probs=20.3
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
-|||.||+++..-.- ..+...-|++|.+
T Consensus 245 ~pCprCG~~I~~~~~-----~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPIRRVVV-----AGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCeeEEEEE-----CCCccEECcCCcC
Confidence 399999999864221 2477889999963
No 83
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=66.15 E-value=3.7 Score=43.46 Aligned_cols=14 Identities=21% Similarity=0.577 Sum_probs=10.0
Q ss_pred CCCccccCCCCcce
Q 045112 248 SPHRSDCHVCGSLL 261 (296)
Q Consensus 248 ~~n~vkChvC~t~L 261 (296)
....--|++||+.+
T Consensus 38 ~~~~~fC~~CG~~~ 51 (645)
T PRK14559 38 PVDEAHCPNCGAET 51 (645)
T ss_pred CcccccccccCCcc
Confidence 34556799999875
No 84
>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=65.94 E-value=4.5 Score=33.55 Aligned_cols=35 Identities=31% Similarity=0.540 Sum_probs=25.2
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
--.-.|++|+.++...-.. ...+..|..|+..|++
T Consensus 121 ~~~~~C~~C~~~~~r~~~~-----~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 121 KYVYRCPSCGREYKRHRRS-----KRKRYRCGRCGGPLVQ 155 (157)
T ss_pred ceEEEcCCCCCEeeeeccc-----chhhEECCCCCCEEEE
Confidence 3456799999997444332 3445889999998875
No 85
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.33 E-value=2.5 Score=34.21 Aligned_cols=15 Identities=60% Similarity=1.276 Sum_probs=12.2
Q ss_pred eeecCCCCCccccce
Q 045112 224 ALRGACPNCGEEVFA 238 (296)
Q Consensus 224 iLKGpCPNCGeEv~s 238 (296)
.|.|.|||||-|..+
T Consensus 39 ~l~g~CPnCGGelv~ 53 (84)
T COG3813 39 RLHGLCPNCGGELVA 53 (84)
T ss_pred hhcCcCCCCCchhhc
Confidence 468999999998754
No 86
>PRK10445 endonuclease VIII; Provisional
Probab=64.39 E-value=4.9 Score=37.45 Aligned_cols=28 Identities=25% Similarity=0.354 Sum_probs=19.7
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
.|||.||+++..-.= ..+...-|++|..
T Consensus 236 ~~Cp~Cg~~I~~~~~-----~gR~t~~CP~CQ~ 263 (263)
T PRK10445 236 EACERCGGIIEKTTL-----SSRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCEeEEEEE-----CCCCcEECCCCcC
Confidence 589999998863221 2366788999963
No 87
>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=63.84 E-value=3.1 Score=40.40 Aligned_cols=23 Identities=43% Similarity=1.012 Sum_probs=18.9
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
|.|-|||++|.++ +-+|++|++.
T Consensus 83 ~~C~~CGa~V~~~-----------e~~Cp~C~St 105 (314)
T PF09567_consen 83 GKCNNCGANVSRL-----------EESCPNCGST 105 (314)
T ss_pred hhhccccceeeeh-----------hhcCCCCCcc
Confidence 6799999988764 6689999975
No 88
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=63.60 E-value=4.4 Score=38.84 Aligned_cols=36 Identities=25% Similarity=0.427 Sum_probs=25.4
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEeccee
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVE 268 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve 268 (296)
..||+||..++.. . -...+..|..||.-++-+...+
T Consensus 2 ~~CpeCg~~~~~~--d----~~~ge~VC~~CG~Vi~~~~id~ 37 (285)
T COG1405 2 MSCPECGSTNIIT--D----YERGEIVCADCGLVLEDSLIDP 37 (285)
T ss_pred CCCCCCCCcccee--e----ccCCeEEeccCCEEeccccccC
Confidence 4799999994432 1 2356899999999887544443
No 89
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=63.30 E-value=4.2 Score=46.30 Aligned_cols=43 Identities=23% Similarity=0.522 Sum_probs=26.0
Q ss_pred eeecCCCCCccccc-eee----cc-CCCCCCCCccccCCCCcceEEecce
Q 045112 224 ALRGACPNCGEEVF-AFV----NS-DQTKNSPHRSDCHVCGSLLEFRTKV 267 (296)
Q Consensus 224 iLKGpCPNCGeEv~-sFf----gt-v~s~~~~n~vkChvC~t~L~fds~v 267 (296)
+-..-||+||+... .|+ |. +.+..++ ..+|+.|+++++=.+++
T Consensus 677 t~~~fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CGtplv~~~~~ 725 (1337)
T PRK14714 677 TYENRCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCDVELTPYQRR 725 (1337)
T ss_pred cccccCcccCCcCCCceeCccCCCccCCCccc-cccCCCCCCcccccceE
Confidence 34558888888753 222 11 2222334 67999999988655443
No 90
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=63.25 E-value=5.7 Score=26.18 Aligned_cols=21 Identities=19% Similarity=0.460 Sum_probs=17.4
Q ss_pred HHhhcCCCccchhhhHHHHHHHh
Q 045112 84 DAYYSGKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 84 ~AY~~GkPimsDeeFD~LK~kLk 106 (296)
.-|.+| +||+|||++.|.+|.
T Consensus 10 ~l~~~G--~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 10 ELYDKG--EISEEEYEQKKARLL 30 (31)
T ss_pred HHHHcC--CCCHHHHHHHHHHHh
Confidence 337777 799999999999984
No 91
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=63.25 E-value=3.2 Score=37.70 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=5.1
Q ss_pred ccccCCCCc
Q 045112 251 RSDCHVCGS 259 (296)
Q Consensus 251 ~vkChvC~t 259 (296)
...|..||-
T Consensus 30 sf~C~~CGy 38 (192)
T TIGR00310 30 STICEHCGY 38 (192)
T ss_pred EEECCCCCC
Confidence 455666663
No 92
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=63.01 E-value=4.1 Score=43.59 Aligned_cols=40 Identities=20% Similarity=0.434 Sum_probs=23.0
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeeccccCCce---eEEeE
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQ---WVYGR 282 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~s~~~r~---w~~GR 282 (296)
-||+||- -+.. .-+|++||.. +.+|-++..|-.|+ |..||
T Consensus 682 ~C~~CG~-----~~~~-------~~~CP~CG~~---~~~~~~Ri~GYl~~v~~wn~gK 724 (735)
T PRK07111 682 RCPVCGY-----LGVI-------EDKCPKCGST---NIQRIRRITGYLGTLDRFNSAK 724 (735)
T ss_pred ecCCCCC-----CCCc-------CccCcCCCCc---cceeeehhhhhccchhhccccc
Confidence 5999992 2222 1799999972 23444444444443 66654
No 93
>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=62.79 E-value=5.2 Score=35.51 Aligned_cols=36 Identities=19% Similarity=0.494 Sum_probs=27.9
Q ss_pred CCCCCccccceeecc---CCCCCCCCccccCCCCcceEE
Q 045112 228 ACPNCGEEVFAFVNS---DQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 228 pCPNCGeEv~sFfgt---v~s~~~~n~vkChvC~t~L~f 263 (296)
-||-||.+...=.-+ ..++.-+-+-+|.+|+...+=
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 499999998888765 344456678899999988643
No 94
>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=62.70 E-value=5.7 Score=30.34 Aligned_cols=20 Identities=35% Similarity=0.549 Sum_probs=17.1
Q ss_pred cCCCccchhhhHHHHHHHhH
Q 045112 88 SGKPLIVDDMFDRVELKLRW 107 (296)
Q Consensus 88 ~GkPimsDeeFD~LK~kLk~ 107 (296)
.-.||||+|+||+++..|+.
T Consensus 82 ~~~~IIs~~~f~~vq~~l~~ 101 (102)
T PF07508_consen 82 YHPPIISEEEFERVQKKLDE 101 (102)
T ss_pred CCCCccCHHHHHHHHHHHhc
Confidence 34799999999999999863
No 95
>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=62.52 E-value=5.5 Score=37.21 Aligned_cols=34 Identities=18% Similarity=0.431 Sum_probs=23.0
Q ss_pred cceeeeec----CCCCCccccceeeccCCCCCCCCccccCCCC
Q 045112 220 NDLVALRG----ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCG 258 (296)
Q Consensus 220 ~D~liLKG----pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~ 258 (296)
++.+-++| |||.||+++..-- + ..+...=|++|.
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 34455554 8999999987532 1 136778899994
No 96
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=61.67 E-value=2.3 Score=40.05 Aligned_cols=32 Identities=22% Similarity=0.542 Sum_probs=25.7
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.|-+||+|+.+-|.--++ +.---.||+||+..
T Consensus 2 ~CVeCg~~vksLy~~Ys~-g~irlt~C~nC~e~ 33 (225)
T KOG3134|consen 2 RCVECGSEVKSLYTQYSP-GNIRLTKCPNCQEV 33 (225)
T ss_pred cccccCchHHHHHHhcCC-CcEEEeeCCchhhH
Confidence 499999999999876555 35566899999975
No 97
>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=61.67 E-value=5.2 Score=34.92 Aligned_cols=29 Identities=17% Similarity=0.454 Sum_probs=21.5
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
.|--||+||+.-|-. .+.-+.|+.||+..
T Consensus 8 tKr~Cp~cg~kFYDL--------nk~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDL--------NRRPAVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCcccccc--------CCCCccCCCcCCcc
Confidence 477899999875532 23457899999973
No 98
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=61.55 E-value=3.4 Score=37.24 Aligned_cols=31 Identities=23% Similarity=0.594 Sum_probs=23.5
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
|=|||.+|.+-|..-++ +.---.+|++|+..
T Consensus 3 CIeCg~~v~~Ly~~Ys~-~~irLt~C~~C~~v 33 (208)
T PF04161_consen 3 CIECGHPVKSLYRQYSP-GNIRLTKCPNCGKV 33 (208)
T ss_pred eccCCCcchhhhhccCC-CcEEEeeccccCCc
Confidence 89999999877766554 44455789999864
No 99
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=61.01 E-value=2.8 Score=44.08 Aligned_cols=42 Identities=26% Similarity=0.461 Sum_probs=25.9
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeeccccCCce---eEEeE
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQ---WVYGR 282 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~s~~~r~---w~~GR 282 (296)
.-||+||.+. .....+|++||+. +.+|-++..+--|+ |.-||
T Consensus 569 ~~C~~CG~~~-----------~g~~~~CP~CGs~---~~~v~~Rv~GYl~~v~~wN~gK 613 (625)
T PRK08579 569 TVCNKCGRST-----------TGLYTRCPRCGSE---DVEVWSRIIGYYRPLKNWNPYR 613 (625)
T ss_pred ccCCCCCCcc-----------CCCCCcCcCCCCc---hhHHHHHHHhhhcccccccccc
Confidence 5699999843 1124699999974 34555555443333 76665
No 100
>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=60.84 E-value=3.6 Score=36.55 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=8.5
Q ss_pred ccceeeeecCCCCCccc
Q 045112 219 RNDLVALRGACPNCGEE 235 (296)
Q Consensus 219 ~~D~liLKGpCPNCGeE 235 (296)
+++.+|+...||+||-.
T Consensus 21 F~evii~sf~C~~CGyr 37 (163)
T TIGR00340 21 FGKIMLSTYICEKCGYR 37 (163)
T ss_pred cceEEEEEEECCCCCCc
Confidence 34555555555555543
No 101
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=60.41 E-value=5.8 Score=29.43 Aligned_cols=30 Identities=30% Similarity=0.742 Sum_probs=23.1
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
-|-+||.++ ......-.+.|+.||..+-|-
T Consensus 8 ~C~~Cg~~~-------~~~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 8 KCARCGREV-------ELDQETRGIRCPYCGSRILVK 37 (49)
T ss_pred EhhhcCCee-------ehhhccCceeCCCCCcEEEEe
Confidence 488999998 223467788999999988773
No 102
>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=59.97 E-value=5 Score=27.54 Aligned_cols=25 Identities=36% Similarity=0.810 Sum_probs=17.7
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
||.|++. +|.++.+ ..-|.-||+.+
T Consensus 11 C~~C~~~---~~~~~dG-----~~yC~~cG~~~ 35 (36)
T PF11781_consen 11 CPVCGSR---WFYSDDG-----FYYCDRCGHQS 35 (36)
T ss_pred CCCCCCe---EeEccCC-----EEEhhhCceEc
Confidence 9999987 6655555 56677777654
No 103
>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=59.64 E-value=8.6 Score=31.45 Aligned_cols=38 Identities=16% Similarity=0.472 Sum_probs=32.6
Q ss_pred cHHHHHHHHHHHHHHhhcCC-----CccchhhhHHHHHHHhHh
Q 045112 71 SKETLEALYRQARDAYYSGK-----PLIVDDMFDRVELKLRWY 108 (296)
Q Consensus 71 t~~elE~~flqA~~AY~~Gk-----PimsDeeFD~LK~kLk~~ 108 (296)
=+.+.|+.|.....||.+|+ +.+|++.|.+++.++++.
T Consensus 20 F~~~ak~~f~~i~~A~~~~D~~~l~~~~t~~~~~~~~~~i~~~ 62 (147)
T PF04280_consen 20 FLEEAKEAFLPIQEAWAKGDLEALRPLLTEELYERLQAEIKAR 62 (147)
T ss_dssp HHHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHhCHHHHHHHHHHHHHH
Confidence 35788999999889999995 899999999999999987
No 104
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=59.45 E-value=6.6 Score=36.88 Aligned_cols=27 Identities=19% Similarity=0.422 Sum_probs=19.9
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCC
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCG 258 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~ 258 (296)
-|||.||+++..-. + ..+...=|++|.
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 39999999987422 1 237788999996
No 105
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=59.15 E-value=6.1 Score=34.30 Aligned_cols=29 Identities=24% Similarity=0.681 Sum_probs=23.8
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
-||.|+.+...+... +...-.+|..||..
T Consensus 104 lC~~C~spdT~l~k~----~r~~~l~C~ACGa~ 132 (138)
T PRK03988 104 ICPECGSPDTKLIKE----GRIWVLKCEACGAE 132 (138)
T ss_pred ECCCCCCCCcEEEEc----CCeEEEEcccCCCC
Confidence 499999999888763 34678899999975
No 106
>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=59.13 E-value=6.8 Score=39.92 Aligned_cols=43 Identities=30% Similarity=0.381 Sum_probs=27.0
Q ss_pred eeecCCCCCccccceeeccCCCCC-CCCccccCCCCcceEEecc
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKN-SPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~-~~n~vkChvC~t~L~fds~ 266 (296)
|..--||||-+|+-+==-....++ .+|=.+|+.|...|.-.+.
T Consensus 24 i~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~~~ 67 (483)
T PF05502_consen 24 IDSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVRAS 67 (483)
T ss_pred cceeECccccccCChhhheeccceeccccccCCCCCCcceeEec
Confidence 444568888877653111112233 3477899999999987743
No 107
>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=59.01 E-value=3.6 Score=46.10 Aligned_cols=29 Identities=28% Similarity=0.588 Sum_probs=20.6
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
+-++.|||||.++.+. +-.+..-|..|--
T Consensus 5 ~y~~~CPnCgg~i~~~-------rl~~~~~c~~Clp 33 (1171)
T TIGR01054 5 VYSNLCPNCGGEISSE-------RLEKGLPCARCLP 33 (1171)
T ss_pred hhcCCCCCCCCccchh-------HhhcCCCccccCc
Confidence 5678999999887654 4445556788843
No 108
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.92 E-value=5.3 Score=34.43 Aligned_cols=25 Identities=24% Similarity=0.774 Sum_probs=19.3
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
-+||-||++.. .-+.+|++|++...
T Consensus 7 ~~cPvcg~~~i-----------VTeL~c~~~etTVr 31 (122)
T COG3877 7 NRCPVCGRKLI-----------VTELKCSNCETTVR 31 (122)
T ss_pred CCCCcccccce-----------eEEEecCCCCceEe
Confidence 47999998754 34788999998764
No 109
>PRK04011 peptide chain release factor 1; Provisional
Probab=58.82 E-value=5.8 Score=39.47 Aligned_cols=36 Identities=36% Similarity=0.597 Sum_probs=27.4
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
.--|||||.+..-++.... .....+|+.||..++-.
T Consensus 328 ~~~c~~c~~~~~~~~~~~~---~~~~~~c~~~~~~~~~~ 363 (411)
T PRK04011 328 TYKCPNCGYEEEKTVKRRE---ELPEKTCPKCGSELEIV 363 (411)
T ss_pred EEEcCCCCcceeeeccccc---ccccccCcccCcccccc
Confidence 4569999998877776544 35567999999987764
No 110
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=58.45 E-value=6.6 Score=38.13 Aligned_cols=35 Identities=26% Similarity=0.579 Sum_probs=22.7
Q ss_pred ecCCCCCccccc-eeecc---CCCCC-----------CCCccccCCCCcc
Q 045112 226 RGACPNCGEEVF-AFVNS---DQTKN-----------SPHRSDCHVCGSL 260 (296)
Q Consensus 226 KGpCPNCGeEv~-sFfgt---v~s~~-----------~~n~vkChvC~t~ 260 (296)
.|-||.||..=. +.+.. ..+.+ .-.+++|++||..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 569999998743 44422 22221 4568999999974
No 111
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=58.35 E-value=6.4 Score=29.62 Aligned_cols=31 Identities=35% Similarity=0.657 Sum_probs=21.2
Q ss_pred eeeeecCCCCCccccc-eeeccCCCCCCCCccccCCCCcc
Q 045112 222 LVALRGACPNCGEEVF-AFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 222 ~liLKGpCPNCGeEv~-sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
+.-++--||+||.-+| +.- .++.-|..||-.
T Consensus 15 v~rk~~~CPrCG~gvfmA~H--------~dR~~CGkCgyT 46 (51)
T COG1998 15 VKRKNRFCPRCGPGVFMADH--------KDRWACGKCGYT 46 (51)
T ss_pred EEEccccCCCCCCcchhhhc--------CceeEeccccce
Confidence 4556778999998765 322 237778888853
No 112
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=57.98 E-value=7.4 Score=36.46 Aligned_cols=28 Identities=29% Similarity=0.662 Sum_probs=20.9
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
|||.||+++..-.- ..+...=|++|...
T Consensus 237 pC~~Cg~~I~~~~~-----~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTPIEKIVV-----GGRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCeeEEEEE-----CCCCcEECCCCcCC
Confidence 89999999864321 23677899999864
No 113
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=57.63 E-value=9.7 Score=25.64 Aligned_cols=24 Identities=29% Similarity=0.821 Sum_probs=14.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
-|++||... -+... --+|++||..
T Consensus 4 ~C~~CG~i~---~g~~~------p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIH---EGEEA------PEKCPICGAP 27 (34)
T ss_pred ECCCCCCEe---ECCcC------CCcCcCCCCc
Confidence 489999542 22211 1389999874
No 114
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=57.62 E-value=6.5 Score=41.25 Aligned_cols=41 Identities=20% Similarity=0.414 Sum_probs=22.8
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeeccccCC---ceeEEeE
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLG---RQWVYGR 282 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~s~~~---r~w~~GR 282 (296)
-||.||- . ...+..+|++||.. +.++-++..+-. ++|-.||
T Consensus 534 iC~~CGy-----~------~g~~~~~CP~CGs~---~~ev~sRv~GYl~~v~~wN~gK 577 (586)
T TIGR02827 534 ICNDCHH-----I------DKRTLHRCPVCGSA---NIDYGTRVIGYLKRVSAFSKER 577 (586)
T ss_pred ecCCCCC-----c------CCCcCCcCcCCCCc---cceEEEeecceecCcccccccc
Confidence 4899985 1 12235799999963 233333333322 3366665
No 115
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=57.34 E-value=6.6 Score=27.37 Aligned_cols=19 Identities=21% Similarity=0.413 Sum_probs=16.2
Q ss_pred CccccCCCCcceEEeccee
Q 045112 250 HRSDCHVCGSLLEFRTKVE 268 (296)
Q Consensus 250 n~vkChvC~t~L~fds~ve 268 (296)
..++|.+||..++|+....
T Consensus 2 ~~y~C~~CG~~~~~~~~~~ 20 (46)
T PRK00398 2 AEYKCARCGREVELDEYGT 20 (46)
T ss_pred CEEECCCCCCEEEECCCCC
Confidence 4679999999999997764
No 116
>smart00400 ZnF_CHCC zinc finger.
Probab=57.27 E-value=5.1 Score=28.73 Aligned_cols=30 Identities=30% Similarity=0.638 Sum_probs=23.3
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
++.||-+.+++-+|-= . ..+|...|..|+.
T Consensus 2 ~~~cPfh~d~~pSf~v--~--~~kn~~~Cf~cg~ 31 (55)
T smart00400 2 KGLCPFHGEKTPSFSV--S--PDKQFFHCFGCGA 31 (55)
T ss_pred cccCcCCCCCCCCEEE--E--CCCCEEEEeCCCC
Confidence 5789999999998832 2 3468899999974
No 117
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=57.26 E-value=6.7 Score=32.81 Aligned_cols=29 Identities=28% Similarity=0.724 Sum_probs=23.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
-||.|+.+-..+... +...-.+|..||..
T Consensus 82 lC~~C~spdT~l~k~----~r~~~l~C~aCGa~ 110 (110)
T smart00653 82 LCPECGSPDTELIKE----NRLFFLKCEACGAR 110 (110)
T ss_pred ECCCCCCCCcEEEEe----CCeEEEEccccCCC
Confidence 499999999888875 34677899999963
No 118
>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=56.87 E-value=5.7 Score=37.10 Aligned_cols=37 Identities=30% Similarity=0.555 Sum_probs=15.7
Q ss_pred ecCCCCCccccceeeccC-CCCCCCCc-cccCCCCcceE
Q 045112 226 RGACPNCGEEVFAFVNSD-QTKNSPHR-SDCHVCGSLLE 262 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv-~s~~~~n~-vkChvC~t~L~ 262 (296)
..-||+||++.-.=+... .......+ .-|..|++=++
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 446999999877543332 11122333 35899987553
No 119
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=56.03 E-value=8.1 Score=38.18 Aligned_cols=31 Identities=29% Similarity=0.511 Sum_probs=24.6
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
.+|.||-|++..-+|.=.. ..+..+|..||.
T Consensus 33 ~~~~CPfh~ek~pSf~v~~----~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 33 YVGLCPFHHEKTPSFSVSP----EKQFYHCFGCGA 63 (415)
T ss_pred eEeeCCCCCCCCCeEEEEc----CCCcEEECCCCC
Confidence 4589999999998886542 356799999986
No 120
>PHA02998 RNA polymerase subunit; Provisional
Probab=55.51 E-value=8.3 Score=35.69 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=26.1
Q ss_pred eecCCCCCccccceeec--cCCCC-CCCCccccCCCCcc
Q 045112 225 LRGACPNCGEEVFAFVN--SDQTK-NSPHRSDCHVCGSL 260 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfg--tv~s~-~~~n~vkChvC~t~ 260 (296)
-..+||.||...-.|+- +.++. ..+--++|..||-.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~ 180 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKH 180 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCc
Confidence 35689999988888864 33343 34667899999854
No 121
>PHA02942 putative transposase; Provisional
Probab=54.90 E-value=8 Score=38.11 Aligned_cols=26 Identities=27% Similarity=0.727 Sum_probs=18.7
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
-||+||..+.. . +....+|.+||..+
T Consensus 327 ~Cs~CG~~~~~-----l---~~r~f~C~~CG~~~ 352 (383)
T PHA02942 327 SCPKCGHKMVE-----I---AHRYFHCPSCGYEN 352 (383)
T ss_pred cCCCCCCccCc-----C---CCCEEECCCCCCEe
Confidence 49999987631 1 22369999999865
No 122
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=54.67 E-value=7.9 Score=33.41 Aligned_cols=29 Identities=17% Similarity=0.523 Sum_probs=22.7
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
-||.|+.+-..+... +...-.+|..||..
T Consensus 99 lC~~C~sPdT~l~k~----~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 99 ICRECNRPDTRIIKE----GRVSLLKCEACGAK 127 (133)
T ss_pred ECCCCCCCCcEEEEe----CCeEEEecccCCCC
Confidence 499999999988863 22346799999974
No 123
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=54.22 E-value=7.4 Score=32.25 Aligned_cols=30 Identities=20% Similarity=0.475 Sum_probs=19.4
Q ss_pred eeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 222 LVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 222 ~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.+-+.+-|++||.+. ... .+...|+.||+.
T Consensus 66 ~vp~~~~C~~Cg~~~----~~~-----~~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVV----EIH-----QHDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEE----ecC-----CcCccCcCCCCC
Confidence 345678999999432 211 234459999964
No 124
>PF14789 THDPS_M: Tetrahydrodipicolinate N-succinyltransferase middle; PDB: 3R5A_F 3R5B_A 3R5C_B 3R5D_D 3FSY_C 3FSX_A 2RIJ_A.
Probab=54.19 E-value=12 Score=26.84 Aligned_cols=26 Identities=31% Similarity=0.535 Sum_probs=17.2
Q ss_pred cchhhhHHHHHHHhHhCCeeee----eccc
Q 045112 93 IVDDMFDRVELKLRWYGSKSVI----KYPR 118 (296)
Q Consensus 93 msDeeFD~LK~kLk~~GS~Vv~----k~Pr 118 (296)
+.-|+|++++.+||..|-.+.| |+||
T Consensus 12 ~~~~~~~~~r~~lr~~g~~~~V~~VDKFPR 41 (41)
T PF14789_consen 12 CEPEDFEENRLRLRARGRPLTVYSVDKFPR 41 (41)
T ss_dssp EEHHHHHHHHHHHHHTT----EEEEESS-B
T ss_pred cCHHHHHHHHHHHHhCCCCcEEEEEcCCCC
Confidence 3457899999999999966655 7775
No 125
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=54.03 E-value=5.5 Score=30.11 Aligned_cols=15 Identities=33% Similarity=0.833 Sum_probs=10.7
Q ss_pred eeecCCCCCccccce
Q 045112 224 ALRGACPNCGEEVFA 238 (296)
Q Consensus 224 iLKGpCPNCGeEv~s 238 (296)
-||..||+||++..+
T Consensus 15 TLk~~CP~CG~~t~~ 29 (56)
T PRK13130 15 TLKEICPVCGGKTKN 29 (56)
T ss_pred EccccCcCCCCCCCC
Confidence 357788888887654
No 126
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=53.94 E-value=8.1 Score=28.26 Aligned_cols=36 Identities=22% Similarity=0.500 Sum_probs=25.4
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
|.||-|-+.-=-+.-.+.+..++..|..|...|.|.
T Consensus 9 C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 9 CSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred CccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence 889987665322222333568899999999999884
No 127
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=53.65 E-value=9.5 Score=32.52 Aligned_cols=30 Identities=23% Similarity=0.606 Sum_probs=24.4
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
=-||.|+.+-..+... +...-.+|..||..
T Consensus 94 VlC~~C~spdT~l~k~----~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE----GRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEE----TTCCEEEETTTSCE
T ss_pred EEcCCCCCCccEEEEc----CCEEEEEecccCCc
Confidence 3599999999888766 44578999999974
No 128
>PHA02540 61 DNA primase; Provisional
Probab=53.21 E-value=14 Score=36.30 Aligned_cols=34 Identities=26% Similarity=0.411 Sum_probs=22.6
Q ss_pred eecCCCCCcccc-----ceeeccCCCCCCCCccccCCCCcc
Q 045112 225 LRGACPNCGEEV-----FAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 225 LKGpCPNCGeEv-----~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.+|.||=|++-. -+|.= .+....-..+|++||..
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V--~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWI--YEKKDGGVFKCHNCGYH 64 (337)
T ss_pred EEecCCCCCCccccCcCCcEEE--eccCCceEEEecCCCCC
Confidence 999999999943 24432 11111447899999963
No 129
>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=52.88 E-value=9.9 Score=37.34 Aligned_cols=19 Identities=26% Similarity=0.567 Sum_probs=11.4
Q ss_pred CccccCCCCcceEEeccee
Q 045112 250 HRSDCHVCGSLLEFRTKVE 268 (296)
Q Consensus 250 n~vkChvC~t~L~fds~ve 268 (296)
..-.|.+||..+.-+.-.+
T Consensus 148 ~g~~Ce~cG~~~~~~~l~~ 166 (391)
T PF09334_consen 148 RGDQCENCGRPLEPEELIN 166 (391)
T ss_dssp TTTEETTTSSBEECCCSEC
T ss_pred CCCcccCCCCCcccccccC
Confidence 3456777887777444333
No 130
>PF15616 TerY-C: TerY-C metal binding domain
Probab=52.82 E-value=9.3 Score=33.24 Aligned_cols=44 Identities=23% Similarity=0.472 Sum_probs=30.3
Q ss_pred eeeecCCCCCccc-cceee--ccCCCCCCCCccccCCCCcceEEecc
Q 045112 223 VALRGACPNCGEE-VFAFV--NSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 223 liLKGpCPNCGeE-v~sFf--gtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
++=..-||.||++ .++== |-+.=......+-|+.||....|...
T Consensus 74 L~g~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~~~~ 120 (131)
T PF15616_consen 74 LIGAPGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSFGAG 120 (131)
T ss_pred hcCCCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeeeccc
Confidence 4445889999998 33322 22222234669999999999999876
No 131
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=52.32 E-value=9.2 Score=40.86 Aligned_cols=27 Identities=22% Similarity=0.550 Sum_probs=16.1
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
--||+||- -|-+.. .....+|++||..
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 35999993 232221 1223789999964
No 132
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=51.92 E-value=11 Score=32.26 Aligned_cols=12 Identities=42% Similarity=0.805 Sum_probs=9.2
Q ss_pred eeecCCCCCccc
Q 045112 224 ALRGACPNCGEE 235 (296)
Q Consensus 224 iLKGpCPNCGeE 235 (296)
-.++-|++||.+
T Consensus 68 p~~~~C~~CG~~ 79 (135)
T PRK03824 68 EAVLKCRNCGNE 79 (135)
T ss_pred ceEEECCCCCCE
Confidence 367889999943
No 133
>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=51.61 E-value=9.5 Score=31.63 Aligned_cols=30 Identities=23% Similarity=0.553 Sum_probs=19.8
Q ss_pred eeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 222 LVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 222 ~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.+-+.+-|++||++ |... .+...|+.||+.
T Consensus 66 ~~p~~~~C~~Cg~~----~~~~-----~~~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEE----VSPE-----IDLYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCE----EecC-----CcCccCcCCcCC
Confidence 34567899999943 2221 124679999975
No 134
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=51.42 E-value=8.1 Score=29.01 Aligned_cols=20 Identities=45% Similarity=1.105 Sum_probs=14.3
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCC
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCG 258 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~ 258 (296)
-.||+||+-... -.-|.+||
T Consensus 28 ~~C~~CG~~~~~------------H~vC~~CG 47 (57)
T PRK12286 28 VECPNCGEPKLP------------HRVCPSCG 47 (57)
T ss_pred eECCCCCCccCC------------eEECCCCC
Confidence 359999987654 34588888
No 135
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=50.37 E-value=9.2 Score=39.39 Aligned_cols=45 Identities=27% Similarity=0.555 Sum_probs=17.0
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcc-eEEecceeeccccCCceeEEeEEE
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL-LEFRTKVEQSSSRLGRQWVYGRIY 284 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~-L~fds~ve~s~s~~~r~w~~GRiY 284 (296)
--|++||-.. . ..-+|++||+. ++.=+.|--=.+ +-+.|-.||.=
T Consensus 492 ~~C~~CG~~~----------~--~~~~CP~CGs~~~~~~~Rv~GYl~-~v~~~n~gK~~ 537 (546)
T PF13597_consen 492 DICPDCGYIG----------G--EGDKCPKCGSENIEVYSRVTGYLR-PVSRWNKGKQA 537 (546)
T ss_dssp EEETTT---S--------------EEE-CCC----EEEEB-SSSS-B-TTS--------
T ss_pred ccccCCCcCC----------C--CCCCCCCCCCcccceEEEeecccc-CccccCHHHHH
Confidence 3599999521 1 16789999999 665555544444 44568888753
No 136
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=50.17 E-value=8 Score=40.38 Aligned_cols=40 Identities=18% Similarity=0.455 Sum_probs=22.4
Q ss_pred eecCCCCCccccceeecc--CCC-----CCCCCccccCCCCcceEEecc
Q 045112 225 LRGACPNCGEEVFAFVNS--DQT-----KNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgt--v~s-----~~~~n~vkChvC~t~L~fds~ 266 (296)
+.|.||.|+.+. ..|. +.- ..+-.+-.|..||.++++..+
T Consensus 138 v~g~cp~C~~~d--~~g~~ce~cg~~~~~~~l~~~~~~~~g~~~e~~~~ 184 (673)
T PRK00133 138 VKGTCPKCGAED--QYGDNCEVCGATYSPTELINPKSAISGATPVLKES 184 (673)
T ss_pred eecccCCCCCcc--cCCchhhhccccCChHhhcCCccccCCCcceEEec
Confidence 469999999872 1121 000 011123457788888877654
No 137
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=49.97 E-value=20 Score=28.27 Aligned_cols=47 Identities=17% Similarity=0.366 Sum_probs=34.7
Q ss_pred CCCCCccccceeec-c--CCCCCCCCccccC--CCCcceEEecceeeccccCCc
Q 045112 228 ACPNCGEEVFAFVN-S--DQTKNSPHRSDCH--VCGSLLEFRTKVEQSSSRLGR 276 (296)
Q Consensus 228 pCPNCGeEv~sFfg-t--v~s~~~~n~vkCh--vC~t~L~fds~ve~s~s~~~r 276 (296)
.||.||..- -.. + .......-...|. +||...+-...|..+.+.|++
T Consensus 3 ~CP~Cg~~a--~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~s~tis~p~~ 54 (72)
T PRK09678 3 HCPLCQHAA--HARTSRYITDTTKERYHQCQNVNCSATFITYESVQRYIVKPGE 54 (72)
T ss_pred cCCCCCCcc--EEEEChhcChhhheeeeecCCCCCCCEEEEEEEEEEEEcCCCC
Confidence 599999987 222 2 1112345567897 999999999999999998875
No 138
>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=49.43 E-value=7.7 Score=27.79 Aligned_cols=31 Identities=29% Similarity=0.790 Sum_probs=20.3
Q ss_pred CCCCCccccceeec-----cCCCCCCCCccccCCCCc
Q 045112 228 ACPNCGEEVFAFVN-----SDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 228 pCPNCGeEv~sFfg-----tv~s~~~~n~vkChvC~t 259 (296)
+||=||+ .++.-. ...-..+..++.|+.|..
T Consensus 4 ~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 4 TCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred CCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchh
Confidence 7999999 554321 122224456899999986
No 139
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=48.67 E-value=11 Score=35.83 Aligned_cols=29 Identities=31% Similarity=0.827 Sum_probs=20.1
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
.||+||..+. +- + ...-+.-|.+||.-++
T Consensus 13 ~Cp~Cg~~~i--v~-d---~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 13 VCPECGSDKL--IY-D---YERGEIVCADCGLVIE 41 (310)
T ss_pred cCcCCCCCCe--eE-E---CCCCeEeecccCCccc
Confidence 5999997432 11 1 3466889999999663
No 140
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=48.03 E-value=12 Score=25.64 Aligned_cols=28 Identities=29% Similarity=0.706 Sum_probs=16.4
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.||.|+++...... ....--.|+.|+=.
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCeE
Confidence 38999987653322 22233458888743
No 141
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=47.38 E-value=12 Score=34.00 Aligned_cols=35 Identities=20% Similarity=0.457 Sum_probs=25.9
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
=-||.|+.+-..+... +...-.+|..||..--=++
T Consensus 99 V~C~~C~~pdT~l~k~----~~~~~l~C~aCGa~~~v~~ 133 (201)
T PRK12336 99 VICSECGLPDTRLVKE----DRVLMLRCDACGAHRPVKK 133 (201)
T ss_pred EECCCCCCCCcEEEEc----CCeEEEEcccCCCCccccc
Confidence 3499999999888764 2355679999998654443
No 142
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=46.48 E-value=14 Score=31.36 Aligned_cols=37 Identities=24% Similarity=0.475 Sum_probs=26.0
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
=.||-||.|..+-=- ++-....-.+-|.+||-..+++
T Consensus 23 FtCp~Cghe~vs~ct-vkk~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 23 FTCPRCGHEKVSSCT-VKKTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred EecCccCCeeeeEEE-EEecCceeEEEcccCcceEEEe
Confidence 469999999886322 2222455678899999877665
No 143
>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=46.33 E-value=13 Score=37.71 Aligned_cols=12 Identities=25% Similarity=0.318 Sum_probs=9.4
Q ss_pred CCCCCeeEeeCC
Q 045112 55 NEEGPSCIFVGP 66 (296)
Q Consensus 55 ~~eGpsc~~~~p 66 (296)
..+|-.++++-|
T Consensus 22 l~~g~~vLvlvP 33 (505)
T TIGR00595 22 LALGKSVLVLVP 33 (505)
T ss_pred HHcCCeEEEEeC
Confidence 456878888888
No 144
>PRK12496 hypothetical protein; Provisional
Probab=46.28 E-value=12 Score=32.96 Aligned_cols=34 Identities=21% Similarity=0.596 Sum_probs=21.5
Q ss_pred cceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 220 NDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 220 ~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
++...=+--||.||.+- .. +...-.|++||+++.
T Consensus 121 ~~~~~w~~~C~gC~~~~----~~-----~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 121 KKVIKWRKVCKGCKKKY----PE-----DYPDDVCEICGSPVK 154 (164)
T ss_pred hhheeeeEECCCCCccc----cC-----CCCCCcCCCCCChhh
Confidence 34445566799999542 21 122347999999874
No 145
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=46.01 E-value=11 Score=39.11 Aligned_cols=42 Identities=24% Similarity=0.572 Sum_probs=22.7
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeeccccC---CceeEEeE
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRL---GRQWVYGR 282 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~s~~---~r~w~~GR 282 (296)
--|++||- .|.. ..-+|++||.. |.+|-++..|- -++|..||
T Consensus 525 ~~C~~CG~-----~g~~------~~~~CP~Cgs~---~~~~~~Rv~GYl~~v~~~n~gK 569 (579)
T TIGR02487 525 DVCEDCGY-----TGEG------LNDKCPKCGSH---DIEVISRITGYLGPVENWNDGK 569 (579)
T ss_pred ccCCCCCC-----CCCC------CCCcCcCCCCc---cceehhhhhhhhcccccccccc
Confidence 35999983 2221 12689999974 23333333332 23366665
No 146
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=45.63 E-value=14 Score=35.96 Aligned_cols=35 Identities=29% Similarity=0.524 Sum_probs=24.0
Q ss_pred eecCCCCCcccc-ceee--ccCCCCC-----------CCCccccCCCCc
Q 045112 225 LRGACPNCGEEV-FAFV--NSDQTKN-----------SPHRSDCHVCGS 259 (296)
Q Consensus 225 LKGpCPNCGeEv-~sFf--gtv~s~~-----------~~n~vkChvC~t 259 (296)
-+|-||.||..= .+.. ++..+-+ .-.+++|++||.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 579999999874 3443 3332222 456899999996
No 147
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=45.12 E-value=11 Score=31.20 Aligned_cols=29 Identities=17% Similarity=0.403 Sum_probs=18.5
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
=..+-|++||+ +|... ..+...|+.||+.
T Consensus 68 p~~~~C~~Cg~----~~~~~----~~~~~~CP~Cgs~ 96 (114)
T PRK03681 68 EAECWCETCQQ----YVTLL----TQRVRRCPQCHGD 96 (114)
T ss_pred CcEEEcccCCC----eeecC----CccCCcCcCcCCC
Confidence 35678999995 33221 1123679999965
No 148
>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=44.86 E-value=7.2 Score=32.14 Aligned_cols=30 Identities=33% Similarity=0.647 Sum_probs=17.9
Q ss_pred eeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 222 LVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 222 ~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.+-+++-|++||.+-. .+.+...|+.||+.
T Consensus 66 ~~p~~~~C~~Cg~~~~---------~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 66 EVPARARCRDCGHEFE---------PDEFDFSCPRCGSP 95 (113)
T ss_dssp EE--EEEETTTS-EEE---------CHHCCHH-SSSSSS
T ss_pred ecCCcEECCCCCCEEe---------cCCCCCCCcCCcCC
Confidence 3557889999998742 12223569999987
No 149
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=44.57 E-value=6.5 Score=44.29 Aligned_cols=28 Identities=25% Similarity=0.634 Sum_probs=18.6
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCC
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCG 258 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~ 258 (296)
|-++.|||||-+ +.+.+-.+..-|..|=
T Consensus 6 iY~~~CpNCGG~-------isseRL~~glpCe~CL 33 (1187)
T COG1110 6 IYGSSCPNCGGD-------ISSERLEKGLPCERCL 33 (1187)
T ss_pred hhhccCCCCCCc-------CcHHHHhcCCCchhcc
Confidence 457889999954 4444555555577773
No 150
>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=44.52 E-value=7.4 Score=42.89 Aligned_cols=19 Identities=37% Similarity=0.707 Sum_probs=0.0
Q ss_pred eeeeecCCCCCccccceee
Q 045112 222 LVALRGACPNCGEEVFAFV 240 (296)
Q Consensus 222 ~liLKGpCPNCGeEv~sFf 240 (296)
.-|-.--||+||++.+.+.
T Consensus 651 vei~~r~Cp~Cg~~t~~~~ 669 (900)
T PF03833_consen 651 VEIGRRRCPKCGKETFYNR 669 (900)
T ss_dssp -------------------
T ss_pred EeeecccCcccCCcchhhc
Confidence 4566678999999977654
No 151
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=44.00 E-value=14 Score=34.54 Aligned_cols=27 Identities=19% Similarity=0.457 Sum_probs=19.9
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
.--||.||++.... .+...-.|+.|+.
T Consensus 99 ~~fC~~CG~~~~~~-------~~~~~~~C~~c~~ 125 (256)
T PRK00241 99 HRFCGYCGHPMHPS-------KTEWAMLCPHCRE 125 (256)
T ss_pred CccccccCCCCeec-------CCceeEECCCCCC
Confidence 56799999987642 2345667999995
No 152
>PRK05580 primosome assembly protein PriA; Validated
Probab=43.99 E-value=15 Score=38.70 Aligned_cols=11 Identities=18% Similarity=0.528 Sum_probs=8.6
Q ss_pred CCCCeeEeeCC
Q 045112 56 EEGPSCIFVGP 66 (296)
Q Consensus 56 ~eGpsc~~~~p 66 (296)
..|..++++-|
T Consensus 188 ~~g~~vLvLvP 198 (679)
T PRK05580 188 AQGKQALVLVP 198 (679)
T ss_pred HcCCeEEEEeC
Confidence 45788888888
No 153
>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=43.99 E-value=9.9 Score=28.99 Aligned_cols=24 Identities=33% Similarity=0.787 Sum_probs=16.8
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccC-CCCcce
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCH-VCGSLL 261 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkCh-vC~t~L 261 (296)
.-|||||+++- +++.-|+ .|+...
T Consensus 4 kHC~~CG~~Ip-----------~~~~fCS~~C~~~~ 28 (59)
T PF09889_consen 4 KHCPVCGKPIP-----------PDESFCSPKCREEY 28 (59)
T ss_pred CcCCcCCCcCC-----------cchhhhCHHHHHHH
Confidence 35999998864 3577784 777654
No 154
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=43.66 E-value=8.9 Score=40.54 Aligned_cols=22 Identities=27% Similarity=0.717 Sum_probs=15.3
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
--||+||-.. .....+|++||.
T Consensus 567 ~iC~~CG~~~-----------~g~~~~CP~CGs 588 (623)
T PRK08271 567 TICNDCHHID-----------KRTGKRCPICGS 588 (623)
T ss_pred ccCCCCCCcC-----------CCCCcCCcCCCC
Confidence 3599999640 123478999996
No 155
>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=43.63 E-value=33 Score=26.93 Aligned_cols=33 Identities=15% Similarity=0.177 Sum_probs=24.9
Q ss_pred cHHHHHHHHHHHHHHhhcCCCccchhhhHHHHHHH
Q 045112 71 SKETLEALYRQARDAYYSGKPLIVDDMFDRVELKL 105 (296)
Q Consensus 71 t~~elE~~flqA~~AY~~GkPimsDeeFD~LK~kL 105 (296)
..+++++.+.+-...-.++. |+++||++.|..|
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 66777788887776655552 9999999999876
No 156
>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=43.46 E-value=14 Score=41.89 Aligned_cols=34 Identities=32% Similarity=0.615 Sum_probs=23.8
Q ss_pred cCCCCCccccceee--ccCCCCCCCCccccCCCCcceE
Q 045112 227 GACPNCGEEVFAFV--NSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 227 GpCPNCGeEv~sFf--gtv~s~~~~n~vkChvC~t~L~ 262 (296)
=-||||. -..|+ +++.++=+--.-+|++||+.|.
T Consensus 684 y~c~~c~--~~ef~~~~~~~sg~dlp~k~cp~c~~~~~ 719 (1213)
T TIGR01405 684 YLCPNCK--YSEFITDGSVGSGFDLPDKDCPKCGAPLK 719 (1213)
T ss_pred ccCcccc--cccccccccccccccCccccCcccccccc
Confidence 3599996 33444 3455556777789999999875
No 157
>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=43.19 E-value=15 Score=36.63 Aligned_cols=35 Identities=37% Similarity=0.667 Sum_probs=25.3
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
.--|||||.+...++...+. .+...|+.||..|+-
T Consensus 320 ~~rc~~c~~~~~~~~~~~~~---~~~~~~~~~~~~~~~ 354 (403)
T TIGR03676 320 TFKCPNCGYEEEKTVKPEEG---DKSEACPKCGSELEI 354 (403)
T ss_pred EEEcCCCCcceeeecccccc---cccccCcccCccccc
Confidence 45699999999888854443 222679999988764
No 158
>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=43.09 E-value=8.1 Score=33.64 Aligned_cols=35 Identities=20% Similarity=0.540 Sum_probs=24.1
Q ss_pred ecCCCCCcccccee---eccCCCCCCCCccccCCCCcceEE
Q 045112 226 RGACPNCGEEVFAF---VNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 226 KGpCPNCGeEv~sF---fgtv~s~~~~n~vkChvC~t~L~f 263 (296)
.-+||.||..+..- ||+- .=+.-..|..|....+|
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 35899999888754 5532 22456788888877655
No 159
>COG4640 Predicted membrane protein [Function unknown]
Probab=43.05 E-value=12 Score=38.42 Aligned_cols=28 Identities=29% Similarity=0.784 Sum_probs=19.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
-||+||.+. ....++|..||++..=+..
T Consensus 3 fC~kcG~qk-----------~Ed~~qC~qCG~~~t~~~s 30 (465)
T COG4640 3 FCPKCGSQK-----------AEDDVQCTQCGHKFTSRQS 30 (465)
T ss_pred ccccccccc-----------ccccccccccCCcCCchhh
Confidence 499999653 2345669999998765443
No 160
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=43.03 E-value=10 Score=30.54 Aligned_cols=17 Identities=24% Similarity=0.745 Sum_probs=12.1
Q ss_pred cceeeeecCCCCCcccc
Q 045112 220 NDLVALRGACPNCGEEV 236 (296)
Q Consensus 220 ~D~liLKGpCPNCGeEv 236 (296)
+.++-++-.||+||++-
T Consensus 2 ~g~Lk~~~~C~~CG~d~ 18 (86)
T PF06170_consen 2 RGYLKVAPRCPHCGLDY 18 (86)
T ss_pred CccccCCCcccccCCcc
Confidence 34566777888888874
No 161
>PRK05667 dnaG DNA primase; Validated
Probab=42.96 E-value=17 Score=37.95 Aligned_cols=31 Identities=29% Similarity=0.590 Sum_probs=24.7
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
.+|.||-|++..-||.=+ ...+..+|..||.
T Consensus 35 ~~~~CPfH~ektpSf~V~----~~k~~~~CF~Cg~ 65 (580)
T PRK05667 35 YKGLCPFHDEKTPSFTVS----PDKQFYHCFGCGA 65 (580)
T ss_pred eeecCCCCCCCCCceEEE----CCCCeEEECCCCC
Confidence 578999999999888533 2467799999986
No 162
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=42.83 E-value=8.5 Score=29.35 Aligned_cols=18 Identities=22% Similarity=0.785 Sum_probs=10.7
Q ss_pred cceeeeecCCCCCccccc
Q 045112 220 NDLVALRGACPNCGEEVF 237 (296)
Q Consensus 220 ~D~liLKGpCPNCGeEv~ 237 (296)
+.+..+.|.||.|.+++.
T Consensus 49 ~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 49 QSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp -TTT--EEE-TTT-SEEE
T ss_pred eeecccccCCcCCCCeee
Confidence 446788999999999875
No 163
>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=42.43 E-value=10 Score=28.29 Aligned_cols=11 Identities=36% Similarity=1.081 Sum_probs=9.6
Q ss_pred ecCCCCCcccc
Q 045112 226 RGACPNCGEEV 236 (296)
Q Consensus 226 KGpCPNCGeEv 236 (296)
.+.||+||.+.
T Consensus 13 Y~~Cp~CGN~~ 23 (49)
T PF12677_consen 13 YCKCPKCGNDK 23 (49)
T ss_pred hccCcccCCcE
Confidence 78999999874
No 164
>PRK09401 reverse gyrase; Reviewed
Probab=42.43 E-value=8.1 Score=43.44 Aligned_cols=29 Identities=24% Similarity=0.690 Sum_probs=20.2
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
+-++.|||||-++- +.+--...-|+.|=-
T Consensus 5 ~y~~~cpnc~g~i~-------~~rl~~g~~c~~cl~ 33 (1176)
T PRK09401 5 IYKNSCPNCGGDIS-------DERLEKGLPCEKCLP 33 (1176)
T ss_pred hhcccCCCCCCcCc-------HhHHhcCCcChhhCC
Confidence 56789999997765 334444567888865
No 165
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=42.42 E-value=15 Score=35.45 Aligned_cols=45 Identities=22% Similarity=0.423 Sum_probs=30.7
Q ss_pred cCCCCCccccceeec--c----CCC-----C-CCCCccccCCCCcceEEecceeecc
Q 045112 227 GACPNCGEEVFAFVN--S----DQT-----K-NSPHRSDCHVCGSLLEFRTKVEQSS 271 (296)
Q Consensus 227 GpCPNCGeEv~sFfg--t----v~s-----~-~~~n~vkChvC~t~L~fds~ve~s~ 271 (296)
.-|-.||+-++.=.+ . +.+ . .=+...|||.|+..++|.|.=+.+.
T Consensus 41 i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~kTDPkn~d 97 (324)
T PF04502_consen 41 IWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIEFKTDPKNTD 97 (324)
T ss_pred CcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEeeecCCCCCC
Confidence 359999998764322 1 111 0 1345789999999999999877653
No 166
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=42.25 E-value=9.1 Score=37.55 Aligned_cols=40 Identities=30% Similarity=0.620 Sum_probs=26.0
Q ss_pred ecCCCCCcc-ccceeec---cCCCCC-----------CCCccccCCCCc--ceEEec
Q 045112 226 RGACPNCGE-EVFAFVN---SDQTKN-----------SPHRSDCHVCGS--LLEFRT 265 (296)
Q Consensus 226 KGpCPNCGe-Ev~sFfg---tv~s~~-----------~~n~vkChvC~t--~L~fds 265 (296)
.+-||-||. +|-+++- +-.|-+ .-.++||.|||. .+.|++
T Consensus 185 ~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t~~l~y~s 241 (308)
T COG3058 185 RQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQSKKLHYWS 241 (308)
T ss_pred cccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhccccccCCcccee
Confidence 357999996 5556652 444433 335889999996 355544
No 167
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=42.17 E-value=16 Score=39.29 Aligned_cols=24 Identities=42% Similarity=1.086 Sum_probs=15.1
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
+.||.||+ ...|=++ =..|++||-
T Consensus 725 ~~Cp~Cg~-~l~~~~G--------C~~C~~CG~ 748 (752)
T PRK08665 725 GACPECGS-ILEHEEG--------CVVCHSCGY 748 (752)
T ss_pred CCCCCCCc-ccEECCC--------CCcCCCCCC
Confidence 56999984 4444332 236888883
No 168
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=42.13 E-value=21 Score=34.49 Aligned_cols=38 Identities=16% Similarity=0.440 Sum_probs=26.8
Q ss_pred ecCCCCCccccceeec--cCCCC-CCCCccccCCCCcceEE
Q 045112 226 RGACPNCGEEVFAFVN--SDQTK-NSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 226 KGpCPNCGeEv~sFfg--tv~s~-~~~n~vkChvC~t~L~f 263 (296)
..+||+||...-+||- +.++. .-+--+.|.+||-.-.|
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKF 298 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeee
Confidence 3699999999888885 33332 23556789999975544
No 169
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=41.90 E-value=8.1 Score=39.53 Aligned_cols=61 Identities=23% Similarity=0.348 Sum_probs=37.8
Q ss_pred HHHhhhhccceeeeecCCCCCccccceeeccCCC-CCCCCccccCCCCcceEEecceeecccc
Q 045112 212 RVLQGLWRNDLVALRGACPNCGEEVFAFVNSDQT-KNSPHRSDCHVCGSLLEFRTKVEQSSSR 273 (296)
Q Consensus 212 ~~Lt~l~~~D~liLKGpCPNCGeEv~sFfgtv~s-~~~~n~vkChvC~t~L~fds~ve~s~s~ 273 (296)
+.|..=.++|+------||||...-.+- --.+= ...+-+..|.+|+..|+=|...-++.+.
T Consensus 114 krled~~~d~t~~~~Y~Cp~C~kkyt~L-ea~~L~~~~~~~F~C~~C~gelveDe~~~~~~e~ 175 (436)
T KOG2593|consen 114 KRLEDRLRDDTNVAGYVCPNCQKKYTSL-EALQLLDNETGEFHCENCGGELVEDENKLPSKES 175 (436)
T ss_pred HHHHHHhhhccccccccCCccccchhhh-HHHHhhcccCceEEEecCCCchhcccccCchHHH
Confidence 3344444556655566799998762221 00000 1345688999999999998877666543
No 170
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=41.59 E-value=16 Score=42.25 Aligned_cols=34 Identities=32% Similarity=0.604 Sum_probs=24.2
Q ss_pred cCCCCCccccceee--ccCCCCCCCCccccCCCCcceE
Q 045112 227 GACPNCGEEVFAFV--NSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 227 GpCPNCGeEv~sFf--gtv~s~~~~n~vkChvC~t~L~ 262 (296)
=-||||. -..|+ +++.++=+--.-+|++||+.|.
T Consensus 909 y~C~~C~--~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~ 944 (1437)
T PRK00448 909 YVCPNCK--YSEFFTDGSVGSGFDLPDKDCPKCGTKLK 944 (1437)
T ss_pred ccCcccc--cccccccccccccccCccccCcccccccc
Confidence 3499995 33444 3455656777889999999875
No 171
>PRK08173 DNA topoisomerase III; Validated
Probab=41.02 E-value=15 Score=40.07 Aligned_cols=27 Identities=33% Similarity=0.728 Sum_probs=18.0
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
.|+||.||.++. .......|++|+-.+
T Consensus 624 ~~~CP~Cg~~~~---------~~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 624 QTPCPNCGGVVK---------ENYRRFACTKCDFSI 650 (862)
T ss_pred cccCCccccccc---------ccCceeEcCCCCccc
Confidence 589999998741 112237888887544
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=41.02 E-value=48 Score=25.99 Aligned_cols=38 Identities=21% Similarity=0.233 Sum_probs=33.2
Q ss_pred ccHHHHHHHHHHHHHHhhcCCCccchhhhHHHHHHHhH
Q 045112 70 ASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRW 107 (296)
Q Consensus 70 ~t~~elE~~flqA~~AY~~GkPimsDeeFD~LK~kLk~ 107 (296)
...+|+|....+..+.-...=-+++-||||.++..|..
T Consensus 24 ~~~~e~e~~~r~~l~~~l~kldlVtREEFd~q~~~L~~ 61 (79)
T PF04380_consen 24 GPREEIEKNIRARLQSALSKLDLVTREEFDAQKAVLAR 61 (79)
T ss_pred hhHHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHH
Confidence 35678999999999998999999999999999887754
No 173
>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=40.61 E-value=22 Score=28.22 Aligned_cols=34 Identities=24% Similarity=0.579 Sum_probs=24.2
Q ss_pred ecCCCCCccccceeec--cCCCC-CCCCccccCCCCc
Q 045112 226 RGACPNCGEEVFAFVN--SDQTK-NSPHRSDCHVCGS 259 (296)
Q Consensus 226 KGpCPNCGeEv~sFfg--tv~s~-~~~n~vkChvC~t 259 (296)
.-.||+||.+--.|+- +.+.. ..+--..|-+|+-
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 4699999988877874 22222 4667788999984
No 174
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=40.29 E-value=13 Score=28.70 Aligned_cols=14 Identities=29% Similarity=0.978 Sum_probs=10.4
Q ss_pred CCCCCccccce--eec
Q 045112 228 ACPNCGEEVFA--FVN 241 (296)
Q Consensus 228 pCPNCGeEv~s--Ffg 241 (296)
-|||||.+.++ +||
T Consensus 17 ~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 17 RCPVCGSRDLSDEWFD 32 (61)
T ss_pred cCCCCcCCcccccccc
Confidence 59999998753 355
No 175
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.27 E-value=17 Score=32.31 Aligned_cols=36 Identities=28% Similarity=0.592 Sum_probs=22.8
Q ss_pred CCCCCccccc-ee-eccCCCC--CCCCccccCCCCcceEE
Q 045112 228 ACPNCGEEVF-AF-VNSDQTK--NSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 228 pCPNCGeEv~-sF-fgtv~s~--~~~n~vkChvC~t~L~f 263 (296)
.||.|-+.++ .| +-++.+- .-.--.-|||||+..-+
T Consensus 41 qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpw 80 (160)
T COG4306 41 QCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPW 80 (160)
T ss_pred cCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCc
Confidence 6999999888 44 3333322 22334579999987643
No 176
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=40.21 E-value=11 Score=37.82 Aligned_cols=28 Identities=29% Similarity=0.663 Sum_probs=19.9
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
||.|+.-+. .+.-+...++.|+.||+.|
T Consensus 13 C~~Cd~l~~-----~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 13 CPQCDMLVA-----LPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred CCCCCceee-----cCCCCCCCeeECCCCCCCC
Confidence 999997532 2222344578999999999
No 177
>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=40.00 E-value=17 Score=22.68 Aligned_cols=33 Identities=27% Similarity=0.637 Sum_probs=18.9
Q ss_pred CCCCccccce--eeccCCCCCC--CCccccCCCCcceE
Q 045112 229 CPNCGEEVFA--FVNSDQTKNS--PHRSDCHVCGSLLE 262 (296)
Q Consensus 229 CPNCGeEv~s--Ffgtv~s~~~--~n~vkChvC~t~L~ 262 (296)
|+.|++.+.. ..-. ..+.. ++=.+|+.|+..|+
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 7788887653 2211 11122 23377899988774
No 178
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.95 E-value=18 Score=38.38 Aligned_cols=28 Identities=14% Similarity=0.011 Sum_probs=16.1
Q ss_pred hCCeeeeeccceee-----eccceeecccccHH
Q 045112 108 YGSKSVIKYPRCSI-----RRQSTYADAEEDLS 135 (296)
Q Consensus 108 ~GS~Vv~k~PrCSl-----r~~~vysD~e~D~l 135 (296)
+|..-+|-|.|-.+ +=.-|..|+|-|.+
T Consensus 238 ~G~~~IViGtRSAvFaP~~~LgLIIvdEEhd~s 270 (665)
T PRK14873 238 RGQARVVVGTRSAVFAPVEDLGLVAIWDDGDDL 270 (665)
T ss_pred CCCCcEEEEcceeEEeccCCCCEEEEEcCCchh
Confidence 56555556777544 32445567776665
No 179
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.89 E-value=19 Score=40.72 Aligned_cols=10 Identities=30% Similarity=0.521 Sum_probs=6.7
Q ss_pred ccCCCCCeeE
Q 045112 53 CKNEEGPSCI 62 (296)
Q Consensus 53 ~~~~eGpsc~ 62 (296)
..+.|||-+-
T Consensus 365 vdsIegPtVr 374 (1121)
T PRK04023 365 VDSIEGPTVR 374 (1121)
T ss_pred cccCcCCeEE
Confidence 4678888653
No 180
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=39.77 E-value=30 Score=36.30 Aligned_cols=52 Identities=25% Similarity=0.599 Sum_probs=37.1
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeeccccCCceeEEeEEEEEec
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLSR 288 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~s~~~r~w~~GRiYlv~~ 288 (296)
-|+|||-.++. -+ .++.+.-|..||+-++++.=|.+-. ..+. +-|-+--+.|
T Consensus 2 ~C~~C~~s~fe---~d---~a~g~~~C~~CG~v~E~~~ivsev~--F~e~-~~G~~v~~~~ 53 (521)
T KOG1598|consen 2 VCKNCGGSNFE---RD---EATGNLYCTACGTVLEYNNIVAEVT--FVEG-AQGQFVRVGQ 53 (521)
T ss_pred cCCCCCCCCcc---cc---cccCCceeccccceeeccceeEEee--eecc-cceeEEeccc
Confidence 49999987752 22 4788899999999999987665443 3333 7777766665
No 181
>PHA00727 hypothetical protein
Probab=38.67 E-value=35 Score=32.54 Aligned_cols=41 Identities=24% Similarity=0.370 Sum_probs=32.3
Q ss_pred cccHHHHHHHHHHHHHHhhcCCCc-------------cchhhhHHHHHHHhHhC
Q 045112 69 TASKETLEALYRQARDAYYSGKPL-------------IVDDMFDRVELKLRWYG 109 (296)
Q Consensus 69 ~~t~~elE~~flqA~~AY~~GkPi-------------msDeeFD~LK~kLk~~G 109 (296)
..|.|||.|.|-||..--.+||.+ +--.+|++||++|...-
T Consensus 17 aqsleelkqkyee~qkqi~dgk~lkrlykvyekrefelk~~qf~qlkael~kkk 70 (278)
T PHA00727 17 AQSLEELKQKYEEAQKQIADGKTLKRLYKVYEKREFELKKQQFEQLKAELSKKK 70 (278)
T ss_pred cccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 358999999999999878888764 34567899999985443
No 182
>COG1274 PckA Phosphoenolpyruvate carboxykinase (GTP) [Energy production and conversion]
Probab=37.94 E-value=28 Score=36.82 Aligned_cols=32 Identities=16% Similarity=0.241 Sum_probs=27.8
Q ss_pred chhhhHHHHHHHhHhCCeeeee---ccceee-eccc
Q 045112 94 VDDMFDRVELKLRWYGSKSVIK---YPRCSI-RRQS 125 (296)
Q Consensus 94 sDeeFD~LK~kLk~~GS~Vv~k---~PrCSl-r~~~ 125 (296)
||||||.|-.++...|-.+-+. .|.|.| ++.+
T Consensus 42 S~eE~~~l~~~~v~aG~~i~Ln~~~~pn~~l~~s~p 77 (608)
T COG1274 42 SPEEYDYLCWKMVEAGEEIKLNPEKHPNSYLARSNP 77 (608)
T ss_pred CHHHHHHHHHHHHhcCceeecCcccCCCceEeecCh
Confidence 7999999999999999999885 999998 4443
No 183
>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=37.79 E-value=22 Score=35.37 Aligned_cols=30 Identities=27% Similarity=0.583 Sum_probs=21.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
.||.|+.-+.. +.-...+++.|+.||+.|.
T Consensus 15 ~C~~Cd~l~~~-----~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVAL-----PRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccc-----cCCCCCCeeECCCCCCCCc
Confidence 49999976432 2324456789999999994
No 184
>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=37.41 E-value=18 Score=24.25 Aligned_cols=26 Identities=31% Similarity=0.604 Sum_probs=11.0
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
.+||.|+.|..= .+....-|+-|+-+
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGHE 28 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTEE
T ss_pred CCCCCCCCccee--------ccCCEEeCCccccc
Confidence 368888877543 34445667777754
No 185
>PF01956 DUF106: Integral membrane protein DUF106; InterPro: IPR002809 This entry represents a group of eukaryotic and archaeal proteins that have no known function. Members are predicted to be integral membrane proteins.; GO: 0016020 membrane
Probab=37.29 E-value=2.4e+02 Score=24.15 Aligned_cols=62 Identities=2% Similarity=-0.042 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHhhcCCCccchhhhHHHHHHHhHhCCeeeeeccceeeeccceeecccccHHHHHHhHHHHHHHHHhh
Q 045112 72 KETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGSKSVIKYPRCSIRRQSTYADAEEDLSQVLALGIIWILILAFG 151 (296)
Q Consensus 72 ~~elE~~flqA~~AY~~GkPimsDeeFD~LK~kLk~~GS~Vv~k~PrCSlr~~~vysD~e~D~lkm~lL~~p~~livaLG 151 (296)
..+.|+++.+..+...+-..-...+.|++.|.+++..-+++ .++..+..-+++++-++
T Consensus 45 ~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~----------------------~~~~mK~~~~~~v~~i~ 102 (168)
T PF01956_consen 45 YQKRMKEFQKRYRELRKNGDFKKPKKLEKRQMELMEKQQEM----------------------MMMMMKPMFVTMVPQIP 102 (168)
T ss_pred HHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHHHH----------------------HHHHHHHhHHHHHHHHH
Confidence 34445555555544333444566888999999887644443 66677777777776555
Q ss_pred cccc
Q 045112 152 SSIC 155 (296)
Q Consensus 152 l~~~ 155 (296)
++.+
T Consensus 103 i~~w 106 (168)
T PF01956_consen 103 IFYW 106 (168)
T ss_pred HHHH
Confidence 5543
No 186
>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=37.27 E-value=15 Score=36.74 Aligned_cols=11 Identities=55% Similarity=1.549 Sum_probs=9.0
Q ss_pred eecCCCCCccc
Q 045112 225 LRGACPNCGEE 235 (296)
Q Consensus 225 LKGpCPNCGeE 235 (296)
++|-||.||.+
T Consensus 135 v~g~cp~c~~~ 145 (530)
T TIGR00398 135 VEGTCPKCGSE 145 (530)
T ss_pred hcCCCCCCCCc
Confidence 36899999886
No 187
>COG3462 Predicted membrane protein [Function unknown]
Probab=36.99 E-value=31 Score=29.78 Aligned_cols=23 Identities=22% Similarity=0.577 Sum_probs=20.2
Q ss_pred HHHHhhcCCCccchhhhHHHHHHHh
Q 045112 82 ARDAYYSGKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 82 A~~AY~~GkPimsDeeFD~LK~kLk 106 (296)
++.-|.+|+ +|||||.+.+++|+
T Consensus 94 lkER~AkGE--ItEEEY~r~~~~ir 116 (117)
T COG3462 94 LKERYAKGE--ITEEEYRRIIRTIR 116 (117)
T ss_pred HHHHHhcCC--CCHHHHHHHHHHhc
Confidence 466799998 89999999999986
No 188
>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=36.59 E-value=12 Score=41.44 Aligned_cols=44 Identities=20% Similarity=0.397 Sum_probs=0.0
Q ss_pred eeeeecCCCCCccccceeec-cCCCCCCCCccccCCCCcceEEecc
Q 045112 222 LVALRGACPNCGEEVFAFVN-SDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 222 ~liLKGpCPNCGeEv~sFfg-tv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
..-.+--||.||+.....+. ..=+ ...+.-+|+.|++...--++
T Consensus 663 ~~t~~~~Cp~CG~~T~~~~~Cp~C~-~~~~~~~C~~C~~~~~~~~~ 707 (900)
T PF03833_consen 663 KETFYNRCPECGSHTEPVYVCPDCG-IEVEEDECPKCGRETTSYSK 707 (900)
T ss_dssp ----------------------------------------------
T ss_pred CcchhhcCcccCCccccceeccccc-cccCccccccccccCcccce
Confidence 35567789999998764443 2222 23334499999998665444
No 189
>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=36.47 E-value=22 Score=31.14 Aligned_cols=38 Identities=18% Similarity=0.248 Sum_probs=24.5
Q ss_pred cccHHHHHHHHHHHHHHhhcCCCccchhhhHHHHHHHhH
Q 045112 69 TASKETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRW 107 (296)
Q Consensus 69 ~~t~~elE~~flqA~~AY~~GkPimsDeeFD~LK~kLk~ 107 (296)
..+..+|++.--+|+ .|..-.-=|+.||.+.+++-||.
T Consensus 10 ~~~~~~L~~~le~a~-e~~~~~~elT~eEl~lv~~ylkR 47 (146)
T PF07295_consen 10 EHSEEELQEALEKAK-EYLVAAGELTREELALVSAYLKR 47 (146)
T ss_pred hcCHHHHHHHHHHHH-HHHHHHhhcCHHHHHHHHHHHHH
Confidence 345566665544444 34444445899999998888775
No 190
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=36.03 E-value=21 Score=32.15 Aligned_cols=35 Identities=29% Similarity=0.709 Sum_probs=27.7
Q ss_pred CCCCCccccceeecc---CCCCCCCCccccCCCCcceE
Q 045112 228 ACPNCGEEVFAFVNS---DQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 228 pCPNCGeEv~sFfgt---v~s~~~~n~vkChvC~t~L~ 262 (296)
-||-|+.+-..-.-+ ..++.-+-+-+|.+|+...+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 499999998877764 55556778889999998763
No 191
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=35.57 E-value=22 Score=35.66 Aligned_cols=23 Identities=17% Similarity=0.489 Sum_probs=17.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
.||+|+.-+ + ..+..|+.|++.|
T Consensus 223 ~C~~Cd~l~-------~----~~~a~CpRC~~~L 245 (419)
T PRK15103 223 SCSCCTAIL-------P----ADQPVCPRCHTKG 245 (419)
T ss_pred cCCCCCCCC-------C----CCCCCCCCCCCcC
Confidence 499999842 1 2456899999998
No 192
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=35.54 E-value=26 Score=35.56 Aligned_cols=35 Identities=23% Similarity=0.531 Sum_probs=23.8
Q ss_pred cceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112 220 NDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 220 ~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
-|..|- -||+|... ..-+-+-+|++||++.++--.
T Consensus 53 Ad~~i~--kC~~c~~~----------~~y~~~~~C~~cg~~~~l~R~ 87 (415)
T COG5257 53 ADAKIY--KCPECYRP----------ECYTTEPKCPNCGAETELVRR 87 (415)
T ss_pred ccCceE--eCCCCCCC----------cccccCCCCCCCCCCccEEEE
Confidence 455554 49999865 234556789999998865443
No 193
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=35.49 E-value=15 Score=26.48 Aligned_cols=36 Identities=25% Similarity=0.451 Sum_probs=26.2
Q ss_pred eeecCCCCCccccc-eeeccCCCCCCCCccccCCCCcce
Q 045112 224 ALRGACPNCGEEVF-AFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 224 iLKGpCPNCGeEv~-sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
+-.|.|-.|+.++- +.+..++.+ ..-+.|++||+.|
T Consensus 20 v~~~~C~gC~~~l~~~~~~~i~~~--~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 20 VEGGTCSGCHMELPPQELNEIRKG--DEIVFCPNCGRIL 56 (56)
T ss_pred eeCCccCCCCEEcCHHHHHHHHcC--CCeEECcCCCccC
Confidence 44689999999887 445455442 5678999999865
No 194
>PF00373 FERM_M: FERM central domain; InterPro: IPR019748 The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 4DXA_B 2EMS_A 2ZPY_A 1J19_A 2D10_B 2D11_B 1GC6_A 2D2Q_A 2EMT_A 2YVC_A ....
Probab=35.13 E-value=74 Score=24.73 Aligned_cols=36 Identities=25% Similarity=0.271 Sum_probs=29.1
Q ss_pred CcccccHHHHHHHHHHHHHHhhcCCCccchhhhHHH
Q 045112 66 PLETASKETLEALYRQARDAYYSGKPLIVDDMFDRV 101 (296)
Q Consensus 66 p~e~~t~~elE~~flqA~~AY~~GkPimsDeeFD~L 101 (296)
|.+.....+++..|+|++..+.+|+=.+++|+-=.|
T Consensus 2 p~~~~d~~~~~lly~Q~~~~vl~g~~~~~~e~a~~L 37 (126)
T PF00373_consen 2 PLHIDDPITRHLLYLQARRDVLQGRLPCSEEDAIKL 37 (126)
T ss_dssp GGGTTSHHHHHHHHHHHHHHHHTTSSTS-HHHHHHH
T ss_pred CcccCCHHHHHHHHHHHHHHHHcCcCCCCHHHHHHH
Confidence 445667788999999999999999999998876544
No 195
>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=35.05 E-value=17 Score=27.52 Aligned_cols=13 Identities=38% Similarity=1.104 Sum_probs=11.4
Q ss_pred ecCCCCCccccce
Q 045112 226 RGACPNCGEEVFA 238 (296)
Q Consensus 226 KGpCPNCGeEv~s 238 (296)
.||||-||+++.+
T Consensus 35 ~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 35 LGPCPFCGTPLLS 47 (57)
T ss_pred cCcCCCCCCcccC
Confidence 7999999998875
No 196
>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=34.99 E-value=18 Score=33.00 Aligned_cols=39 Identities=28% Similarity=0.366 Sum_probs=31.6
Q ss_pred ccHHHHHHHHHHHH-HH----hhcCCCccchhhhHHHHHHHhHh
Q 045112 70 ASKETLEALYRQAR-DA----YYSGKPLIVDDMFDRVELKLRWY 108 (296)
Q Consensus 70 ~t~~elE~~flqA~-~A----Y~~GkPimsDeeFD~LK~kLk~~ 108 (296)
.|.+++++..-.|+ |+ ||+-..+++|++|+.++.+||..
T Consensus 62 ls~~~~~aa~~aas~MamnNv~Yr~~hl~~~~~y~~~pa~lrmn 105 (177)
T TIGR00777 62 LSAEARHAALGAAAIMAMNNVFYRGRHLLEGARYDDLRPGLRMN 105 (177)
T ss_pred CCHHHHHHHHHHHHHHhhhhHHHHhHhhcccchhhcCCccchhH
Confidence 46667777666665 44 99999999999999999999873
No 197
>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=34.73 E-value=25 Score=39.62 Aligned_cols=27 Identities=37% Similarity=0.880 Sum_probs=21.4
Q ss_pred ceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 221 DLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 221 D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
+..+-.--||+||++. ....|++||+.
T Consensus 620 ~vev~~RKCPkCG~yT-------------lk~rCP~CG~~ 646 (1095)
T TIGR00354 620 EVEIAIRKCPQCGKES-------------FWLKCPVCGEL 646 (1095)
T ss_pred EEEEEEEECCCCCccc-------------ccccCCCCCCc
Confidence 4677888999999874 45579999976
No 198
>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=34.56 E-value=24 Score=26.22 Aligned_cols=32 Identities=22% Similarity=0.354 Sum_probs=22.8
Q ss_pred eeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 223 VALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 223 liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
.+|- |++|..-|-...+ .........|..|+.
T Consensus 21 ~aLI--C~~C~~hNGla~~---~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 21 YALI--CSKCFSHNGLAPK---EEFEEIQYRCPYCGA 52 (54)
T ss_pred eeEE--Ccccchhhccccc---ccCCceEEEcCCCCC
Confidence 4444 9999998876662 223455899999986
No 199
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=34.52 E-value=9.8 Score=35.98 Aligned_cols=42 Identities=19% Similarity=0.311 Sum_probs=32.1
Q ss_pred eecCCCCCccccceeecc-CCCCCCCCccccCCCCcceEEeccee
Q 045112 225 LRGACPNCGEEVFAFVNS-DQTKNSPHRSDCHVCGSLLEFRTKVE 268 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgt-v~s~~~~n~vkChvC~t~L~fds~ve 268 (296)
=+..|--|+..+.+=+-+ +.. ...-+.|+.||+-|-|+...+
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~--~d~iv~CP~CgRILy~~e~~~ 238 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRK--KDEIVFCPYCGRILYYDESEE 238 (239)
T ss_pred cCCcccCCeeeecHHHHHHHhc--CCCCccCCccchHHHhhhccc
Confidence 356899999999865543 332 556789999999999987765
No 200
>KOG3716 consensus Carnitine O-acyltransferase CPTI [Lipid transport and metabolism]
Probab=34.41 E-value=21 Score=38.76 Aligned_cols=22 Identities=32% Similarity=0.607 Sum_probs=17.9
Q ss_pred HHHHHHHHHhhcCCCccchhhhHHHHHH
Q 045112 77 ALYRQARDAYYSGKPLIVDDMFDRVELK 104 (296)
Q Consensus 77 ~~flqA~~AY~~GkPimsDeeFD~LK~k 104 (296)
+.|++-+ ||||||||||+|.+-
T Consensus 177 ~rYL~Sm------kpilseEe~~~l~~l 198 (764)
T KOG3716|consen 177 TRYLDSM------KPILSEEEFDRLEEL 198 (764)
T ss_pred HHHHHhc------ccccCHHHHHHHHHH
Confidence 5677654 899999999998754
No 201
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=34.36 E-value=18 Score=30.86 Aligned_cols=27 Identities=33% Similarity=0.642 Sum_probs=19.6
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
++.-|.+|+.++- ...+...|+.|++.
T Consensus 69 ~~~~C~~C~~~~~---------~e~~~~~CP~C~s~ 95 (115)
T COG0375 69 AECWCLDCGQEVE---------LEELDYRCPKCGSI 95 (115)
T ss_pred cEEEeccCCCeec---------chhheeECCCCCCC
Confidence 4678999955432 46677789999964
No 202
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=33.94 E-value=75 Score=27.28 Aligned_cols=54 Identities=30% Similarity=0.520 Sum_probs=34.5
Q ss_pred cceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecceeeccccCCceeEEeEEEEEe
Q 045112 220 NDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKVEQSSSRLGRQWVYGRIYLLS 287 (296)
Q Consensus 220 ~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ve~s~s~~~r~w~~GRiYlv~ 287 (296)
+.--++-.-|++||. .||+ -+..|+.|++.-+. ..||- |+.|.-+.|=.+|...
T Consensus 23 ~~~kl~g~kC~~CG~---v~~P--------Pr~~Cp~C~~~~~~-E~vel--s~~G~V~t~Tv~~~~~ 76 (140)
T COG1545 23 KEGKLLGTKCKKCGR---VYFP--------PRAYCPKCGSETEL-EWVEL--SGEGKVETYTVVYVKP 76 (140)
T ss_pred hhCcEEEEEcCCCCe---EEcC--------CcccCCCCCCCCce-EEEEe--CCCeEEEEEEEEeeCC
Confidence 446778889999996 4554 35679999998511 22333 3456666666666543
No 203
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=33.79 E-value=26 Score=25.88 Aligned_cols=20 Identities=20% Similarity=0.581 Sum_probs=13.3
Q ss_pred HHHHhhcCCCc---------cchhhhHHH
Q 045112 82 ARDAYYSGKPL---------IVDDMFDRV 101 (296)
Q Consensus 82 A~~AY~~GkPi---------msDeeFD~L 101 (296)
|++|+.+|+++ |++||+|++
T Consensus 18 Ak~A~~~g~svre~v~~~g~lt~ee~d~l 46 (55)
T PF10415_consen 18 AKEALAEGRSVREVVLEEGLLTEEELDEL 46 (55)
T ss_dssp HHHHHHHT--HHHHHHHTTSS-HHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHcCCCCHHHHHHH
Confidence 45778888875 899999876
No 204
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.78 E-value=24 Score=29.43 Aligned_cols=30 Identities=17% Similarity=0.421 Sum_probs=18.7
Q ss_pred eeeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 223 VALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 223 liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
+-+.+-|++||.+ |... ..+...|+.||+.
T Consensus 68 vp~~~~C~~Cg~~----~~~~----~~~~~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSHV----FKPN----ALDYGVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCCc----cccC----CccCCcCcCCCCC
Confidence 4467889999933 2211 1123469999975
No 205
>PRK04351 hypothetical protein; Provisional
Probab=33.68 E-value=33 Score=29.99 Aligned_cols=35 Identities=20% Similarity=0.544 Sum_probs=25.9
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
=.|.+||.+... ... -++.+.-|..|+..|++-.+
T Consensus 113 Y~C~~Cg~~~~r----~Rr-~n~~~yrCg~C~g~L~~~~~ 147 (149)
T PRK04351 113 YECQSCGQQYLR----KRR-INTKRYRCGKCRGKLKLINQ 147 (149)
T ss_pred EECCCCCCEeee----eee-cCCCcEEeCCCCcEeeeccc
Confidence 469999975543 233 35688999999999998643
No 206
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=33.40 E-value=26 Score=31.41 Aligned_cols=34 Identities=26% Similarity=0.612 Sum_probs=22.2
Q ss_pred ecCCCCCccccc-eee-ccCCC----------CCCCCccccCCCCc
Q 045112 226 RGACPNCGEEVF-AFV-NSDQT----------KNSPHRSDCHVCGS 259 (296)
Q Consensus 226 KGpCPNCGeEv~-sFf-gtv~s----------~~~~n~vkChvC~t 259 (296)
-=-||||.+.++ ..| -++-. .++...-.|.+||+
T Consensus 114 ~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 114 QWFCPQCGHKLHRAEVQLENIVTDLPPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred EEECCCCCCeEEEEEEEecChhhhhHHHHHHHhCChhhccCCccCC
Confidence 345999999998 333 23211 14666778999996
No 207
>PRK14530 adenylate kinase; Provisional
Probab=33.34 E-value=56 Score=28.57 Aligned_cols=35 Identities=29% Similarity=0.621 Sum_probs=24.6
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
..||.||+....+|..- .....|.+||..|+-+.+
T Consensus 127 ~~~~~~g~~~~~~~~~p-----~~~~~~~~~~~rl~~R~d 161 (215)
T PRK14530 127 RVCPDCGANYHVEFNQP-----EEEGVCDECGGELIQRDD 161 (215)
T ss_pred CcCcccCCccccCCCCC-----cccccCcccCCcccCCCC
Confidence 57999998877666431 234468899988876654
No 208
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=33.12 E-value=26 Score=35.44 Aligned_cols=28 Identities=29% Similarity=0.552 Sum_probs=18.6
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
.-|+.||+.+. ....-+.+|+.||..+.
T Consensus 241 ~~c~~cg~~~~--------~~~~~~~~c~~Cg~~~~ 268 (380)
T COG1867 241 YHCSRCGEIVG--------SFREVDEKCPHCGGKVH 268 (380)
T ss_pred EEcccccceec--------ccccccccCCcccccce
Confidence 56999993222 24455678999998543
No 209
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=33.09 E-value=23 Score=37.17 Aligned_cols=11 Identities=55% Similarity=1.519 Sum_probs=8.3
Q ss_pred eecCCCCCccc
Q 045112 225 LRGACPNCGEE 235 (296)
Q Consensus 225 LKGpCPNCGeE 235 (296)
++|.||.||.|
T Consensus 141 v~g~cp~cg~~ 151 (558)
T COG0143 141 VEGTCPKCGGE 151 (558)
T ss_pred eeccCCCcCcc
Confidence 47888888854
No 210
>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=32.52 E-value=27 Score=23.84 Aligned_cols=13 Identities=23% Similarity=0.626 Sum_probs=7.4
Q ss_pred CccccCCCCcceE
Q 045112 250 HRSDCHVCGSLLE 262 (296)
Q Consensus 250 n~vkChvC~t~L~ 262 (296)
..++|+||++.+.
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 4567777777653
No 211
>PF15110 TMEM141: TMEM141 protein family; PDB: 2LOR_A.
Probab=32.35 E-value=23 Score=29.62 Aligned_cols=35 Identities=20% Similarity=0.410 Sum_probs=26.7
Q ss_pred ccchhhhhHHHHHHhhhhhhhhhhhhhHHHHhhhh
Q 045112 184 SGFLAAVNVILFMAVGSLIGYPIASASVRVLQGLW 218 (296)
Q Consensus 184 ~~~i~~vn~i~l~~~~~ligyplasa~v~~Lt~l~ 218 (296)
+...+.||+++-+..+.+.+|-+|+.--+.=|++|
T Consensus 53 lpYp~q~~~LVS~v~~sv~sY~vT~~et~~Cq~~W 87 (94)
T PF15110_consen 53 LPYPFQWNILVSVVVASVASYQVTRVETQKCQNLW 87 (94)
T ss_dssp SSSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCchhHHHHHHhhhhhhhhhhHHHHHHHHHH
Confidence 44667888888877888899999987766677766
No 212
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=32.25 E-value=28 Score=37.68 Aligned_cols=90 Identities=23% Similarity=0.210 Sum_probs=45.9
Q ss_pred CcCCCCCccc---cccccCCCCCeeEeeCCcccccHHHHHHHHHHHHHHhhcCCC-----ccchhhhHHHHHHHhHhCCe
Q 045112 40 GNGGGGFAAA---ATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKP-----LIVDDMFDRVELKLRWYGSK 111 (296)
Q Consensus 40 ~~~~~~~~~~---~~~~~~~eGpsc~~~~p~e~~t~~elE~~flqA~~AY~~GkP-----imsDeeFD~LK~kLk~~GS~ 111 (296)
++.|.|-++. +-.+-...|=..+++=| |-+---+|.+.|. +++.-++ -+||.|--+-=++. ..|+.
T Consensus 224 GvTGSGKTEvYl~~i~~~L~~GkqvLvLVP-EI~Ltpq~~~rf~----~rFg~~v~vlHS~Ls~~er~~~W~~~-~~G~~ 297 (730)
T COG1198 224 GVTGSGKTEVYLEAIAKVLAQGKQVLVLVP-EIALTPQLLARFK----ARFGAKVAVLHSGLSPGERYRVWRRA-RRGEA 297 (730)
T ss_pred CCCCCcHHHHHHHHHHHHHHcCCEEEEEec-cccchHHHHHHHH----HHhCCChhhhcccCChHHHHHHHHHH-hcCCc
Confidence 4445554442 22344567777777777 5454444443332 2332111 14554422211222 24777
Q ss_pred eeeeccceee-----eccceeecccccHH
Q 045112 112 SVIKYPRCSI-----RRQSTYADAEEDLS 135 (296)
Q Consensus 112 Vv~k~PrCSl-----r~~~vysD~e~D~l 135 (296)
-+|-|.|..+ .=+-|..|+|=|.+
T Consensus 298 ~vVIGtRSAlF~Pf~~LGLIIvDEEHD~s 326 (730)
T COG1198 298 RVVIGTRSALFLPFKNLGLIIVDEEHDSS 326 (730)
T ss_pred eEEEEechhhcCchhhccEEEEecccccc
Confidence 7778888666 33445578877755
No 213
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.03 E-value=24 Score=36.03 Aligned_cols=35 Identities=20% Similarity=0.538 Sum_probs=24.2
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecce
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKV 267 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~v 267 (296)
-+--||-||.-. +| ..++..+|..||+.+-.+...
T Consensus 349 ~~p~Cp~Cg~~m-------~S-~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 349 VNPVCPRCGGRM-------KS-AGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred cCCCCCccCCch-------hh-cCCCCcccccccccCCccccc
Confidence 344799999643 34 233399999999987665543
No 214
>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=31.77 E-value=20 Score=25.71 Aligned_cols=10 Identities=40% Similarity=1.042 Sum_probs=4.2
Q ss_pred ccCCCCcceE
Q 045112 253 DCHVCGSLLE 262 (296)
Q Consensus 253 kChvC~t~L~ 262 (296)
.|++|++.|.
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 6777777653
No 215
>TIGR03142 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family
Probab=31.72 E-value=45 Score=27.44 Aligned_cols=16 Identities=13% Similarity=0.179 Sum_probs=14.4
Q ss_pred ccchhhhHHHHHHHhH
Q 045112 92 LIVDDMFDRVELKLRW 107 (296)
Q Consensus 92 imsDeeFD~LK~kLk~ 107 (296)
+++++||+++|.||..
T Consensus 56 ~l~~~e~~~~~~El~r 71 (117)
T TIGR03142 56 LLDEAEAEAARAELQR 71 (117)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 8999999999998864
No 216
>PRK14526 adenylate kinase; Provisional
Probab=31.67 E-value=34 Score=30.77 Aligned_cols=35 Identities=20% Similarity=0.434 Sum_probs=24.9
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
.-||.||.--...|.. .+...+|.+|+..|+-|.+
T Consensus 123 ~~~~~~g~~y~~~~~p-----p~~~~~~~~~~~~l~~R~D 157 (211)
T PRK14526 123 RICKSCNNIFNIYTLP-----TKEKGICDVCKGDLYQRKD 157 (211)
T ss_pred CcccccCCccccccCC-----CCccCcCCCCCCeeeccCC
Confidence 5699999876655543 2345689999988876653
No 217
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=31.55 E-value=34 Score=36.52 Aligned_cols=50 Identities=22% Similarity=0.363 Sum_probs=33.9
Q ss_pred HhhhhccceeeeecCCCCCcccccee-------eccCCCCCCCCccccCCCCcceEE
Q 045112 214 LQGLWRNDLVALRGACPNCGEEVFAF-------VNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 214 Lt~l~~~D~liLKGpCPNCGeEv~sF-------fgtv~s~~~~n~vkChvC~t~L~f 263 (296)
...+-..|..=-.-|||.||||-+== ||.-.--.......||.|.+.+..
T Consensus 215 e~~y~~gd~rr~yvpCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~ 271 (611)
T COG5525 215 ERAYNAGDQRRFYVPCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRP 271 (611)
T ss_pred HHHhhhccceeEEeeCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeee
Confidence 44455568888899999999986533 332111113445589999999998
No 218
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=31.42 E-value=83 Score=24.17 Aligned_cols=34 Identities=15% Similarity=0.153 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhcCCCccchhhhHHHHHHHhHhCC
Q 045112 77 ALYRQARDAYYSGKPLIVDDMFDRVELKLRWYGS 110 (296)
Q Consensus 77 ~~flqA~~AY~~GkPimsDeeFD~LK~kLk~~GS 110 (296)
..|++=...--.|+|+||-+||-+-..+=++.+-
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 3578777778889999999999988777766543
No 219
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.18 E-value=18 Score=32.88 Aligned_cols=34 Identities=29% Similarity=0.496 Sum_probs=22.1
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecc
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~ 266 (296)
=-||||.... +|=- .-.+...|+.||..|+|...
T Consensus 114 y~C~~~~~r~-sfde-----A~~~~F~Cp~Cg~~L~~~d~ 147 (176)
T COG1675 114 YVCPNCHVKY-SFDE-----AMELGFTCPKCGEDLEEYDS 147 (176)
T ss_pred eeCCCCCCcc-cHHH-----HHHhCCCCCCCCchhhhccc
Confidence 3589998653 3311 12234899999999998653
No 220
>PRK08197 threonine synthase; Validated
Probab=30.58 E-value=38 Score=32.94 Aligned_cols=32 Identities=28% Similarity=0.594 Sum_probs=21.1
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcceEEecce
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRTKV 267 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds~v 267 (296)
+=-|++||+|- + .+.....| .|+..|..+.+.
T Consensus 7 ~~~C~~Cg~~~--------~-~~~~~~~C-~cg~~l~~~~d~ 38 (394)
T PRK08197 7 HLECSKCGETY--------D-ADQVHNLC-KCGKPLLVRYDL 38 (394)
T ss_pred EEEECCCCCCC--------C-CCCcceec-CCCCeeEEEech
Confidence 34799999883 1 22335679 799887666543
No 221
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=30.18 E-value=22 Score=26.04 Aligned_cols=9 Identities=44% Similarity=1.206 Sum_probs=8.1
Q ss_pred CCCCCcccc
Q 045112 228 ACPNCGEEV 236 (296)
Q Consensus 228 pCPNCGeEv 236 (296)
.||.||+.|
T Consensus 13 kCp~CGt~N 21 (44)
T PF14952_consen 13 KCPKCGTYN 21 (44)
T ss_pred cCCcCcCcc
Confidence 699999987
No 222
>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=30.09 E-value=20 Score=27.25 Aligned_cols=12 Identities=42% Similarity=0.852 Sum_probs=4.6
Q ss_pred ecCCCCCccccc
Q 045112 226 RGACPNCGEEVF 237 (296)
Q Consensus 226 KGpCPNCGeEv~ 237 (296)
|-+||.||.++.
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 345666665543
No 223
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.91 E-value=33 Score=36.44 Aligned_cols=24 Identities=29% Similarity=0.581 Sum_probs=16.4
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
--|++||-. . -..-+|++||..++
T Consensus 627 ~~C~~CG~~-----~-------g~~~~CP~CG~~~~ 650 (656)
T PRK08270 627 SICPKHGYL-----S-------GEHEFCPKCGEETE 650 (656)
T ss_pred cccCCCCCc-----C-------CCCCCCcCCcCccc
Confidence 359999952 1 12478999998744
No 224
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.68 E-value=26 Score=34.01 Aligned_cols=29 Identities=21% Similarity=0.497 Sum_probs=20.0
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
.--||.||++++.-=+ --...|++|+...
T Consensus 111 ~RFCg~CG~~~~~~~~-------g~~~~C~~cg~~~ 139 (279)
T COG2816 111 HRFCGRCGTKTYPREG-------GWARVCPKCGHEH 139 (279)
T ss_pred CcCCCCCCCcCccccC-------ceeeeCCCCCCcc
Confidence 3459999999875433 2345799998753
No 225
>PRK14701 reverse gyrase; Provisional
Probab=29.54 E-value=18 Score=42.20 Aligned_cols=27 Identities=26% Similarity=0.751 Sum_probs=18.2
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCC
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVC 257 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC 257 (296)
+-++.|||||-++-+. +--...-|..|
T Consensus 4 ~y~~~cpnc~g~~~~~-------rl~~g~~c~~c 30 (1638)
T PRK14701 4 IYKEMCPNCGGDITDE-------RLAEKGVCEKC 30 (1638)
T ss_pred hhcccCCCCCCccchh-------HHhcCCCchhh
Confidence 5678999999776432 33344568888
No 226
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=29.48 E-value=44 Score=28.19 Aligned_cols=34 Identities=26% Similarity=0.617 Sum_probs=24.0
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
.-.|.+||+... ..-+. .++.+..|..|+..|++
T Consensus 112 ~y~C~~C~~~~~---~~rr~-~~~~~y~C~~C~g~l~~ 145 (146)
T smart00731 112 PYRCTGCGQRYL---RVRRS-NNVSRYRCGKCGGKLIL 145 (146)
T ss_pred EEECCCCCCCCc---eEccc-cCcceEEcCCCCCEEEe
Confidence 557989998753 22233 33478999999998875
No 227
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=29.18 E-value=35 Score=39.83 Aligned_cols=27 Identities=30% Similarity=0.616 Sum_probs=22.1
Q ss_pred ceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 221 DLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 221 D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
+.-+-..-||+||++- ....|+.||+.
T Consensus 669 ~vei~~~~Cp~Cg~~~-------------~~~~Cp~CG~~ 695 (1627)
T PRK14715 669 DIEIAFFKCPKCGKVG-------------LYHVCPFCGTR 695 (1627)
T ss_pred eEEEEeeeCCCCCCcc-------------ccccCcccCCc
Confidence 4568899999999874 35689999998
No 228
>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=29.07 E-value=26 Score=30.75 Aligned_cols=13 Identities=38% Similarity=1.037 Sum_probs=10.1
Q ss_pred ecCCCCCccccce
Q 045112 226 RGACPNCGEEVFA 238 (296)
Q Consensus 226 KGpCPNCGeEv~s 238 (296)
--|||+||...|+
T Consensus 130 l~~Cp~C~~~~F~ 142 (146)
T PF07295_consen 130 LPPCPKCGHTEFT 142 (146)
T ss_pred CCCCCCCCCCeee
Confidence 3699999987664
No 229
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.05 E-value=15 Score=38.78 Aligned_cols=21 Identities=24% Similarity=0.691 Sum_probs=14.3
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
-|++||-. |. +..+|++||..
T Consensus 561 ~C~~CGy~-----g~-------~~~~CP~CG~~ 581 (618)
T PRK14704 561 RCKCCSYH-----GV-------IGNECPSCGNE 581 (618)
T ss_pred ecCCCCCC-----CC-------cCccCcCCCCC
Confidence 49999831 11 13789999974
No 230
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=28.93 E-value=40 Score=32.59 Aligned_cols=26 Identities=23% Similarity=0.557 Sum_probs=17.9
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCC
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCG 258 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~ 258 (296)
||+.||+.+..=. . ..++..=|++|.
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 8999998876321 1 345667888886
No 231
>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=28.76 E-value=26 Score=30.87 Aligned_cols=22 Identities=14% Similarity=0.360 Sum_probs=16.1
Q ss_pred ccceeeeecCCCCCccccceee
Q 045112 219 RNDLVALRGACPNCGEEVFAFV 240 (296)
Q Consensus 219 ~~D~liLKGpCPNCGeEv~sFf 240 (296)
+++.+|+...||+||-.+....
T Consensus 23 F~evii~sf~C~~CGyk~~ev~ 44 (161)
T PF03367_consen 23 FKEVIIMSFECEHCGYKNNEVK 44 (161)
T ss_dssp TEEEEEEEEE-TTT--EEEEEE
T ss_pred CceEEEEEeECCCCCCEeeeEE
Confidence 5899999999999998887544
No 232
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=28.58 E-value=35 Score=33.26 Aligned_cols=37 Identities=22% Similarity=0.627 Sum_probs=21.6
Q ss_pred eecCCCCCccccc-eeeccCCC-CCCCCcc-ccCCCCcce
Q 045112 225 LRGACPNCGEEVF-AFVNSDQT-KNSPHRS-DCHVCGSLL 261 (296)
Q Consensus 225 LKGpCPNCGeEv~-sFfgtv~s-~~~~n~v-kChvC~t~L 261 (296)
...-||+||++-. .||..+.. .....++ -|..|++=+
T Consensus 223 ~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~Yl 262 (305)
T TIGR01562 223 VRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYL 262 (305)
T ss_pred cCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccch
Confidence 3567999999764 34433321 1223333 489998754
No 233
>PRK11823 DNA repair protein RadA; Provisional
Probab=28.48 E-value=30 Score=34.68 Aligned_cols=15 Identities=33% Similarity=0.507 Sum_probs=9.5
Q ss_pred CCceeEEeEEEEEec
Q 045112 274 LGRQWVYGRIYLLSR 288 (296)
Q Consensus 274 ~~r~w~~GRiYlv~~ 288 (296)
++.-++.|.++|+..
T Consensus 73 LgGGi~~Gs~~lI~G 87 (446)
T PRK11823 73 LGGGLVPGSVVLIGG 87 (446)
T ss_pred hcCCccCCEEEEEEC
Confidence 345566677777765
No 234
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=28.26 E-value=33 Score=31.25 Aligned_cols=38 Identities=24% Similarity=0.462 Sum_probs=24.8
Q ss_pred eecCCCCCccccc-eee-ccCCC----------CCCCCccccCCCCcceE
Q 045112 225 LRGACPNCGEEVF-AFV-NSDQT----------KNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 225 LKGpCPNCGeEv~-sFf-gtv~s----------~~~~n~vkChvC~t~L~ 262 (296)
|-=-|+||.+.++ .+| -++-. .++...-.|.+||+.+.
T Consensus 119 ~~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~CG~v~~ 168 (177)
T PRK13264 119 FQWYCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDNCGTVHP 168 (177)
T ss_pred eEEECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCcCCcccC
Confidence 3445999999998 333 22211 14666778999998653
No 235
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=28.25 E-value=24 Score=28.21 Aligned_cols=27 Identities=26% Similarity=0.584 Sum_probs=16.2
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCC
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCG 258 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~ 258 (296)
|-+||.||..++. ....-.---|++|.
T Consensus 1 K~~CPCCg~~Tl~------~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 1 KYPCPCCGYYTLE------ERGEGTYDICPVCF 27 (78)
T ss_pred CccCCCCCcEEec------cCCCcCceECCCCC
Confidence 5689999977652 11111144688886
No 236
>PLN02419 methylmalonate-semialdehyde dehydrogenase [acylating]
Probab=27.96 E-value=1.2e+02 Score=32.20 Aligned_cols=59 Identities=15% Similarity=0.211 Sum_probs=42.5
Q ss_pred CCCeeEeeCCc--ccccHHHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHhH---hCCeeeeec
Q 045112 57 EGPSCIFVGPL--ETASKETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLRW---YGSKSVIKY 116 (296)
Q Consensus 57 eGpsc~~~~p~--e~~t~~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk~---~GS~Vv~k~ 116 (296)
.|..|+-.+++ +.. .+++.+.++++...+.-|. |+++.+.+|+++.-+.. +|.+++.-+
T Consensus 387 aGQ~C~A~~Rv~V~~~-~d~f~e~l~~~~~~l~vG~p~d~~t~~GPlis~~~~~~v~~~i~~A~~~GAkvl~GG 459 (604)
T PLN02419 387 AGQRCMALSTVVFVGD-AKSWEDKLVERAKALKVTCGSEPDADLGPVISKQAKERICRLIQSGVDDGAKLLLDG 459 (604)
T ss_pred CCCCcCCCCEEEEeCc-HHHHHHHHHHHHHHhccCCCCCCCCCccCCCCHHHHHHHHHHHHHHHhcCCEEEeCC
Confidence 47777644441 222 5888888999888887776 68899999999877754 588887744
No 237
>PLN02766 coniferyl-aldehyde dehydrogenase
Probab=27.92 E-value=1.1e+02 Score=30.80 Aligned_cols=45 Identities=9% Similarity=0.170 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHhH---hCCeeeeec
Q 045112 72 KETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLRW---YGSKSVIKY 116 (296)
Q Consensus 72 ~~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk~---~GS~Vv~k~ 116 (296)
.+++.+.+.++...+.-|. |+++.+.+|+++.-+.. +|.+|+.-+
T Consensus 315 ~d~f~~~l~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~v~~~i~~a~~~Ga~v~~gG 371 (501)
T PLN02766 315 YDEFVKKLVEKAKDWVVGDPFDPRARQGPQVDKQQFEKILSYIEHGKREGATLLTGG 371 (501)
T ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCEEEeCC
Confidence 4556666666666666665 57888999998877754 477777644
No 238
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.87 E-value=80 Score=26.86 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=30.1
Q ss_pred cHHHHHHHHHHHHHHhhcCCCccchhhhHHHHHHH
Q 045112 71 SKETLEALYRQARDAYYSGKPLIVDDMFDRVELKL 105 (296)
Q Consensus 71 t~~elE~~flqA~~AY~~GkPimsDeeFD~LK~kL 105 (296)
..+|+|..|.+-+++-+.-=-+++-||||-..+=|
T Consensus 34 ~~~evE~~~r~~~q~~lnkLDlVsREEFdvq~qvl 68 (103)
T COG2960 34 VRAEVEKAFRAQLQRQLNKLDLVSREEFDVQRQVL 68 (103)
T ss_pred hHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHH
Confidence 45799999999999999999999999999765543
No 239
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=27.75 E-value=39 Score=29.82 Aligned_cols=31 Identities=23% Similarity=0.610 Sum_probs=21.9
Q ss_pred ceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 221 DLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 221 D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
++=.|..-||.||++. ++ .+-++.+|.+|+.
T Consensus 144 ~lGvv~a~~~~~g~~~------~~--~~~~~~~c~~~~~ 174 (189)
T PRK09521 144 DLGVIYAMCSRCRTPL------VK--KGENELKCPNCGN 174 (189)
T ss_pred CceEEEEEccccCCce------EE--CCCCEEECCCCCC
Confidence 3445566799999887 22 3447899999994
No 240
>PTZ00381 aldehyde dehydrogenase family protein; Provisional
Probab=27.55 E-value=1.2e+02 Score=30.86 Aligned_cols=43 Identities=16% Similarity=0.277 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHhHhCCeeeee
Q 045112 72 KETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLRWYGSKSVIK 115 (296)
Q Consensus 72 ~~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk~~GS~Vv~k 115 (296)
.+++-+.+.++...++ |. |+++++.||+++.-++.+|.+++.-
T Consensus 262 ~d~f~~~l~~~~~~~~-g~~~~~~~~~gpli~~~~~~ri~~~i~~~ga~~~~g 313 (493)
T PTZ00381 262 KDKFIEALKEAIKEFF-GEDPKKSEDYSRIVNEFHTKRLAELIKDHGGKVVYG 313 (493)
T ss_pred HHHHHHHHHHHHHHHh-CCCCccCCCcCCCCCHHHHHHHHHHHHhCCCcEEEC
Confidence 4555555555555655 43 5789999999999998888888763
No 241
>PRK14973 DNA topoisomerase I; Provisional
Probab=27.53 E-value=50 Score=36.64 Aligned_cols=12 Identities=42% Similarity=1.165 Sum_probs=9.4
Q ss_pred ecCCCCCccccc
Q 045112 226 RGACPNCGEEVF 237 (296)
Q Consensus 226 KGpCPNCGeEv~ 237 (296)
.|+||.||.++.
T Consensus 588 ~~~CP~CG~~l~ 599 (936)
T PRK14973 588 IGPCPVCGKDLR 599 (936)
T ss_pred cccCCcccccce
Confidence 489999997653
No 242
>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=27.49 E-value=33 Score=30.59 Aligned_cols=9 Identities=33% Similarity=0.685 Sum_probs=5.6
Q ss_pred cccCCCCcc
Q 045112 252 SDCHVCGSL 260 (296)
Q Consensus 252 vkChvC~t~ 260 (296)
..|..||-.
T Consensus 29 f~C~~CGyr 37 (163)
T TIGR00340 29 YICEKCGYR 37 (163)
T ss_pred EECCCCCCc
Confidence 467777744
No 243
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=27.40 E-value=28 Score=21.91 Aligned_cols=8 Identities=50% Similarity=1.510 Sum_probs=5.3
Q ss_pred CCCCCccc
Q 045112 228 ACPNCGEE 235 (296)
Q Consensus 228 pCPNCGeE 235 (296)
+||+||..
T Consensus 4 ~C~~CgR~ 11 (25)
T PF13913_consen 4 PCPICGRK 11 (25)
T ss_pred cCCCCCCE
Confidence 67777753
No 244
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=27.39 E-value=33 Score=30.34 Aligned_cols=21 Identities=14% Similarity=0.384 Sum_probs=18.4
Q ss_pred ccceeeeecCCCCCcccccee
Q 045112 219 RNDLVALRGACPNCGEEVFAF 239 (296)
Q Consensus 219 ~~D~liLKGpCPNCGeEv~sF 239 (296)
+++.+|+...||+||-.+...
T Consensus 22 F~evii~sf~C~~CGyk~~ev 42 (160)
T smart00709 22 FREVIIMSFECEHCGYRNNEV 42 (160)
T ss_pred cceEEEEEEECCCCCCccceE
Confidence 689999999999999887744
No 245
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.19 E-value=35 Score=28.74 Aligned_cols=32 Identities=28% Similarity=0.651 Sum_probs=17.8
Q ss_pred eeeecCCCCCccccceeeccCCCCCC--CCccccCCCCc
Q 045112 223 VALRGACPNCGEEVFAFVNSDQTKNS--PHRSDCHVCGS 259 (296)
Q Consensus 223 liLKGpCPNCGeEv~sFfgtv~s~~~--~n~vkChvC~t 259 (296)
+-+++-| +||.+ |........ .....|+.||+
T Consensus 67 vp~~~~C-~Cg~~----~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 67 IPVEIEC-ECGYE----GVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred cCeeEEe-eCcCc----ccccccchhccccCCcCcCCCC
Confidence 4567899 99943 222111011 11356999995
No 246
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=26.79 E-value=50 Score=22.88 Aligned_cols=15 Identities=33% Similarity=0.545 Sum_probs=12.3
Q ss_pred CccccCCCCcceEEe
Q 045112 250 HRSDCHVCGSLLEFR 264 (296)
Q Consensus 250 n~vkChvC~t~L~fd 264 (296)
..+.|+.||..|...
T Consensus 4 g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRR 18 (58)
T ss_pred CcEEcccCCcEeEEE
Confidence 467899999999884
No 247
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=26.77 E-value=39 Score=33.72 Aligned_cols=35 Identities=20% Similarity=0.459 Sum_probs=21.6
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcceEE
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEF 263 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~f 263 (296)
.--|||||.+ .++...+. .+....+|+.||..+.-
T Consensus 324 ~~r~~~~~~~--~~~~~~~~-~~~~~~~c~~~~~~~~~ 358 (409)
T TIGR00108 324 TYKCAECGEV--IEKTVREL-KDKKFAICPACGQEMDV 358 (409)
T ss_pred EEEcCCCCce--eecccccc-cccccccCcccCccccc
Confidence 4579999984 33333222 22234489999998753
No 248
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=26.75 E-value=46 Score=38.58 Aligned_cols=50 Identities=24% Similarity=0.458 Sum_probs=33.1
Q ss_pred HHHHhhhhccceeeeecCCCCCccccceeec--cCCCCCCCCccccCCCCcceE
Q 045112 211 VRVLQGLWRNDLVALRGACPNCGEEVFAFVN--SDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 211 v~~Lt~l~~~D~liLKGpCPNCGeEv~sFfg--tv~s~~~~n~vkChvC~t~L~ 262 (296)
|-.+++.--=|-|.=---||||.- +-|+. ++-++=+--.-.|+.||++|.
T Consensus 899 VAtm~gITEVNPL~PHY~Cp~Cky--~Ef~~d~svgsGfDLpdK~CPkCg~pl~ 950 (1444)
T COG2176 899 VATMIGITEVNPLPPHYLCPECKY--SEFIDDGSVGSGFDLPDKDCPKCGTPLK 950 (1444)
T ss_pred HHHhhcccccCCCCccccCCCCce--eeeecCCCcCCCCCCCCCCCCcCCCccc
Confidence 333444433355666667999963 45665 566666777789999999965
No 249
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=26.72 E-value=34 Score=31.16 Aligned_cols=19 Identities=16% Similarity=0.422 Sum_probs=17.0
Q ss_pred ccceeeeecCCCCCccccc
Q 045112 219 RNDLVALRGACPNCGEEVF 237 (296)
Q Consensus 219 ~~D~liLKGpCPNCGeEv~ 237 (296)
+++.+|+...||+||-.+.
T Consensus 23 F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 23 FGEVLETSTICEHCGYRSN 41 (192)
T ss_pred cceEEEEEEECCCCCCccc
Confidence 5899999999999997765
No 250
>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=26.62 E-value=36 Score=34.67 Aligned_cols=27 Identities=30% Similarity=0.806 Sum_probs=14.4
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
||||.... +|- ...|..+||-||....
T Consensus 225 C~~C~~~l-~~h------~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 225 CPNCDVSL-TYH------KKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCce-EEe------cCCCeEEcCCCcCcCC
Confidence 88886543 222 2345566666665443
No 251
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=26.50 E-value=49 Score=29.59 Aligned_cols=39 Identities=23% Similarity=0.353 Sum_probs=28.9
Q ss_pred eeecCCCCCc----cccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 224 ALRGACPNCG----EEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 224 iLKGpCPNCG----eEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
++|=|=|||= |++.+.|--+ ...+...+|+=|++.+.++
T Consensus 105 i~kC~Np~CITn~~E~v~~~F~v~--~~~~~~~rC~YCe~~~~~~ 147 (152)
T PRK00893 105 VLKCPNPNCITNTNEPVESRFYVV--DKEPIKLRCKYCEKEFSED 147 (152)
T ss_pred eEECCCCCCcCCCCcCcCcEEEEE--eCCCCEEEeeCCCCEechh
Confidence 3566667884 4577777664 3677899999999998865
No 252
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=26.36 E-value=42 Score=34.47 Aligned_cols=52 Identities=13% Similarity=0.054 Sum_probs=26.5
Q ss_pred cCCC--CCeeEeeCCcc------cccHHHHHHHHHHHHHH-hhcCCCccchhhhHHHHHHH
Q 045112 54 KNEE--GPSCIFVGPLE------TASKETLEALYRQARDA-YYSGKPLIVDDMFDRVELKL 105 (296)
Q Consensus 54 ~~~e--Gpsc~~~~p~e------~~t~~elE~~flqA~~A-Y~~GkPimsDeeFD~LK~kL 105 (296)
.+|+ ||--..+..-. +.|-||.=.+-+..... =|+.=||..=..=.+-++||
T Consensus 89 gRw~~~gsEl~rl~Dr~gkq~cL~pThEE~iT~lmat~~~lsykqlPi~vYQigrKfRDEl 149 (457)
T KOG2324|consen 89 GRWDAMGSELFRLHDRKGKQMCLTPTHEEDITALMATYIPLSYKQLPIRVYQIGRKFRDEL 149 (457)
T ss_pred CcccccchhheEeeccCCCEeccCCchHHHHHHHHHhcCccccccCcEEeeeechhhhhcc
Confidence 4666 66666554321 22555554433333333 35566776655444555555
No 253
>PRK11032 hypothetical protein; Provisional
Probab=26.25 E-value=42 Score=30.09 Aligned_cols=26 Identities=19% Similarity=0.496 Sum_probs=18.6
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
-|-|||.+.--++.+.-+ .|+.|+..
T Consensus 126 vC~~Cg~~~~~~~p~~i~-------pCp~C~~~ 151 (160)
T PRK11032 126 VCEKCHHHLAFYTPEVLP-------LCPKCGHD 151 (160)
T ss_pred EecCCCCEEEecCCCcCC-------CCCCCCCC
Confidence 499999998655554322 49999975
No 254
>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=26.23 E-value=34 Score=30.76 Aligned_cols=34 Identities=18% Similarity=0.518 Sum_probs=14.3
Q ss_pred cceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 220 NDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 220 ~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
.+. +---+|+.||.+..+-. +...+..+|+-|.-
T Consensus 129 sg~-l~l~~C~~C~~~fv~~~-----~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 129 SGM-LQLAPCRRCGGHFVTHA-----HDPRHSFVCPFCQP 162 (175)
T ss_dssp TTS-EEEEE-TTT--EEEEES-----S--SS----TT---
T ss_pred cCC-ccccCCCCCCCCeECcC-----CCCCcCcCCCCCCC
Confidence 443 44568999999876542 24468899999983
No 255
>COG0300 DltE Short-chain dehydrogenases of various substrate specificities [General function prediction only]
Probab=26.16 E-value=1.9e+02 Score=27.76 Aligned_cols=100 Identities=19% Similarity=0.226 Sum_probs=68.3
Q ss_pred CCccccccccCCCCCeeEeeCCcccccHHHHHHHHHHHHHHhhcCCC------ccchhhhHHHHHHHhHhCCeeeeeccc
Q 045112 45 GFAAAATMCKNEEGPSCIFVGPLETASKETLEALYRQARDAYYSGKP------LIVDDMFDRVELKLRWYGSKSVIKYPR 118 (296)
Q Consensus 45 ~~~~~~~~~~~~eGpsc~~~~p~e~~t~~elE~~flqA~~AY~~GkP------imsDeeFD~LK~kLk~~GS~Vv~k~Pr 118 (296)
|........++.+|=..+.+.+. ++-||+++-|=.+.+ ..+. +=.+++-.+|..+|+..|-+|-+.=--
T Consensus 17 GIG~~~A~~lA~~g~~liLvaR~----~~kL~~la~~l~~~~-~v~v~vi~~DLs~~~~~~~l~~~l~~~~~~IdvLVNN 91 (265)
T COG0300 17 GIGAELAKQLARRGYNLILVARR----EDKLEALAKELEDKT-GVEVEVIPADLSDPEALERLEDELKERGGPIDVLVNN 91 (265)
T ss_pred hHHHHHHHHHHHCCCEEEEEeCc----HHHHHHHHHHHHHhh-CceEEEEECcCCChhHHHHHHHHHHhcCCcccEEEEC
Confidence 34445556789999999999885 577888777777666 3333 445688899999999987666664333
Q ss_pred eeeeccceeecccccHH-HHHHhHHHHHHHHH
Q 045112 119 CSIRRQSTYADAEEDLS-QVLALGIIWILILA 149 (296)
Q Consensus 119 CSlr~~~vysD~e~D~l-km~lL~~p~~liva 149 (296)
+-+-...-+.|.+.|.. +|+-+|+.+.+.+.
T Consensus 92 AG~g~~g~f~~~~~~~~~~mi~lN~~a~~~LT 123 (265)
T COG0300 92 AGFGTFGPFLELSLDEEEEMIQLNILALTRLT 123 (265)
T ss_pred CCcCCccchhhCChHHHHHHHHHHHHHHHHHH
Confidence 33322233466666554 88899999886653
No 256
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=26.10 E-value=44 Score=32.96 Aligned_cols=31 Identities=23% Similarity=0.368 Sum_probs=20.2
Q ss_pred eeecCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
=.-+-|++||..-.... ....+|+.||..+.
T Consensus 242 g~~~~C~~c~~~~~~~~--------~~~~~C~~c~~~~~ 272 (382)
T PRK04338 242 GYVYYCPKCLYREEVEG--------LPPEECPVCGGKFG 272 (382)
T ss_pred eeEEECCCCCcEEEecC--------CCCCCCCCCCCcce
Confidence 34567999997554321 23457999998553
No 257
>PRK06260 threonine synthase; Validated
Probab=25.87 E-value=60 Score=31.63 Aligned_cols=28 Identities=36% Similarity=0.662 Sum_probs=19.2
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
-|++||++-- .+.....|+.|+..|..+
T Consensus 5 ~C~~cg~~~~---------~~~~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 5 KCIECGKEYD---------PDEIIYTCPECGGLLEVI 32 (397)
T ss_pred EECCCCCCCC---------CCCccccCCCCCCeEEEE
Confidence 5999998731 222346799999886554
No 258
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=25.51 E-value=31 Score=26.93 Aligned_cols=10 Identities=40% Similarity=0.840 Sum_probs=8.7
Q ss_pred CCCCCccccc
Q 045112 228 ACPNCGEEVF 237 (296)
Q Consensus 228 pCPNCGeEv~ 237 (296)
-||+||.+.+
T Consensus 19 ~Cp~Cgs~~~ 28 (64)
T PRK06393 19 TCPVHGDEKT 28 (64)
T ss_pred cCCCCCCCcC
Confidence 7999999875
No 259
>PLN02459 probable adenylate kinase
Probab=25.40 E-value=71 Score=30.41 Aligned_cols=40 Identities=20% Similarity=0.258 Sum_probs=22.9
Q ss_pred cCCCCCccccceee-c--c---CCCCCCCCccccCCCCcceEEecc
Q 045112 227 GACPNCGEEVFAFV-N--S---DQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 227 GpCPNCGeEv~sFf-g--t---v~s~~~~n~vkChvC~t~L~fds~ 266 (296)
.-||.||.--...+ . + +.+...+....|.+|+..|+-|.+
T Consensus 154 ~~~~~~g~~Yn~~~~~~~~~~~~~~~~~~p~~~~~~~~~~L~~R~D 199 (261)
T PLN02459 154 RICSECGKNFNVADIDLKGEDGRPGIVMPPLLPPPECASKLITRAD 199 (261)
T ss_pred ccccccCccccccccccccccccccccCCCCCCCcccccccccCCC
Confidence 34999998655433 1 1 111123334457789888876554
No 260
>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=25.36 E-value=44 Score=21.71 Aligned_cols=10 Identities=60% Similarity=1.135 Sum_probs=4.7
Q ss_pred ccCCCCcceE
Q 045112 253 DCHVCGSLLE 262 (296)
Q Consensus 253 kChvC~t~L~ 262 (296)
.|++|+++++
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4777777776
No 261
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=25.34 E-value=46 Score=21.51 Aligned_cols=12 Identities=25% Similarity=0.404 Sum_probs=9.3
Q ss_pred cchhhhHHHHHH
Q 045112 93 IVDDMFDRVELK 104 (296)
Q Consensus 93 msDeeFD~LK~k 104 (296)
||-|+||+|+.-
T Consensus 10 MSPddy~~l~~~ 21 (23)
T PF12162_consen 10 MSPDDYDELERM 21 (23)
T ss_dssp S-HHHHHHHHHH
T ss_pred CCHHHHHHHHHh
Confidence 899999999863
No 262
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=25.05 E-value=36 Score=32.35 Aligned_cols=17 Identities=29% Similarity=0.608 Sum_probs=15.1
Q ss_pred CCCCCccccCCCCcceE
Q 045112 246 KNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 246 ~~~~n~vkChvC~t~L~ 262 (296)
+..+.+++|++|++.|+
T Consensus 209 g~ipe~i~CpeC~R~ME 225 (235)
T PF14577_consen 209 GRIPETIVCPECGRPME 225 (235)
T ss_pred cCCCceeECCCCCCchh
Confidence 47788999999999997
No 263
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=24.84 E-value=38 Score=37.80 Aligned_cols=17 Identities=29% Similarity=0.478 Sum_probs=14.9
Q ss_pred ccccHHHHHHHHHHHHH
Q 045112 68 ETASKETLEALYRQARD 84 (296)
Q Consensus 68 e~~t~~elE~~flqA~~ 84 (296)
+.+|.++++..|++|-.
T Consensus 664 ~~at~edv~~~y~~Awk 680 (953)
T PRK06556 664 EDATVEDIEEVYLEGWK 680 (953)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 56899999999999975
No 264
>PRK14529 adenylate kinase; Provisional
Probab=24.65 E-value=50 Score=30.36 Aligned_cols=36 Identities=31% Similarity=0.612 Sum_probs=23.0
Q ss_pred ecCCCCCccccc-eeeccCCCCCCCCccccCCCCcceEEec
Q 045112 226 RGACPNCGEEVF-AFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 226 KGpCPNCGeEv~-sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
..-||+||.-.+ .|+.. + .....+|.+|+.+|+-|+
T Consensus 126 R~~c~~~~~~~~~~~~~~--p--~~~~~~cd~~~~~l~~R~ 162 (223)
T PRK14529 126 RRLCKNDNNHPNNIFIDA--I--KPDGDVCRVCGGELSTRA 162 (223)
T ss_pred CccccccCCcccccccCC--C--cccCCcCcCcCCccccCC
Confidence 356999887555 44331 1 112348999999887765
No 265
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=24.59 E-value=66 Score=23.38 Aligned_cols=22 Identities=5% Similarity=0.268 Sum_probs=17.9
Q ss_pred ccchhhhHHHHHHHhHhCCeeeeec
Q 045112 92 LIVDDMFDRVELKLRWYGSKSVIKY 116 (296)
Q Consensus 92 imsDeeFD~LK~kLk~~GS~Vv~k~ 116 (296)
++++|+|+.+|. ..|..|.|.|
T Consensus 5 ~l~~~~~~~~~~---~~Gk~V~V~G 26 (48)
T PF14485_consen 5 ILSEEDYSYLKS---LLGKRVSVTG 26 (48)
T ss_pred EeChhhhHHHHH---hcCCeEEEEE
Confidence 468999999887 6899988864
No 266
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=24.55 E-value=48 Score=27.42 Aligned_cols=29 Identities=28% Similarity=0.706 Sum_probs=20.7
Q ss_pred eecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 225 LRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 225 LKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
..-.|++||.+-+.++ +=.|+ -|+.|+..
T Consensus 41 ~~~~C~~Cg~~~~~~~------SCk~R-~CP~C~~~ 69 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYN------SCKNR-HCPSCQAK 69 (111)
T ss_pred ceeecCCCCceEEecC------cccCc-CCCCCCCh
Confidence 3457999999987765 23334 69999875
No 267
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=24.40 E-value=46 Score=35.87 Aligned_cols=27 Identities=30% Similarity=0.673 Sum_probs=20.7
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCC
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVC 257 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC 257 (296)
-||+||.++..++.... -.-...|++|
T Consensus 131 ~C~~Cg~~~~~~~~~~~---~~~~~~C~~~ 157 (682)
T COG1241 131 ECPKCGREVEVEQSEFR---VEPPRECENC 157 (682)
T ss_pred EcCCCCCEEEEEecccc---ccCCccCCCc
Confidence 49999999999886533 3345679999
No 268
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=24.37 E-value=53 Score=27.50 Aligned_cols=35 Identities=20% Similarity=0.584 Sum_probs=24.5
Q ss_pred ecCCCCCccccceeec--cCCCCC-CCCccccCCCCcc
Q 045112 226 RGACPNCGEEVFAFVN--SDQTKN-SPHRSDCHVCGSL 260 (296)
Q Consensus 226 KGpCPNCGeEv~sFfg--tv~s~~-~~n~vkChvC~t~ 260 (296)
+.-||.||.+=-.|+- +.++.. .+-=.+|-.||-.
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~ 109 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYR 109 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCE
Confidence 4569999998888875 344432 3444799999864
No 269
>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=24.28 E-value=1.5e+02 Score=29.07 Aligned_cols=44 Identities=16% Similarity=0.237 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHhH---hCCeeeeec
Q 045112 73 ETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLRW---YGSKSVIKY 116 (296)
Q Consensus 73 ~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk~---~GS~Vv~k~ 116 (296)
+++-+.+.+....+.-|. |+++.+.+++++.-+.+ +|.+++..+
T Consensus 277 d~f~~~l~~~~~~~~~g~p~~~~~~~Gpli~~~~~~~~~~~v~~a~~~Ga~~~~gg 332 (456)
T cd07110 277 DAFLERLATAAEAIRVGDPLEEGVRLGPLVSQAQYEKVLSFIARGKEEGARLLCGG 332 (456)
T ss_pred HHHHHHHHHHHHhcCCCCCCCCCCCcCCCCCHHHHHHHHHHHHHHHhCCCEEEeCC
Confidence 344444444444454443 46677777877776654 566666544
No 270
>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=24.26 E-value=26 Score=22.83 Aligned_cols=10 Identities=50% Similarity=1.484 Sum_probs=5.1
Q ss_pred CCCCCccccc
Q 045112 228 ACPNCGEEVF 237 (296)
Q Consensus 228 pCPNCGeEv~ 237 (296)
-||+||.+.|
T Consensus 23 ~C~~Cg~~~y 32 (32)
T PF09297_consen 23 RCPSCGHEHY 32 (32)
T ss_dssp EESSSS-EE-
T ss_pred ECCCCcCEeC
Confidence 4677776643
No 271
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.19 E-value=43 Score=29.39 Aligned_cols=24 Identities=33% Similarity=0.852 Sum_probs=18.9
Q ss_pred ceeeeecCCCCCccccceeeccCCC
Q 045112 221 DLVALRGACPNCGEEVFAFVNSDQT 245 (296)
Q Consensus 221 D~liLKGpCPNCGeEv~sFfgtv~s 245 (296)
+..||+| ||+||---|.|.+....
T Consensus 15 s~eil~G-CP~CGg~kF~yv~~~~~ 38 (131)
T PF09845_consen 15 SKEILSG-CPECGGNKFQYVPEEKD 38 (131)
T ss_pred cHHHHcc-CcccCCcceEEcCCCcc
Confidence 3357777 99999999999986444
No 272
>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=24.13 E-value=41 Score=29.67 Aligned_cols=41 Identities=17% Similarity=0.373 Sum_probs=21.0
Q ss_pred eeeecCCCCCccccc--eeecc-----CCCCC--CCCccccCCCCcceEE
Q 045112 223 VALRGACPNCGEEVF--AFVNS-----DQTKN--SPHRSDCHVCGSLLEF 263 (296)
Q Consensus 223 liLKGpCPNCGeEv~--sFfgt-----v~s~~--~~n~vkChvC~t~L~f 263 (296)
-.+|=.|.||||+.- .++-. +++++ +.--.||..|++...-
T Consensus 27 ~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si 76 (161)
T PF05907_consen 27 WFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSI 76 (161)
T ss_dssp EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEE
T ss_pred EEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEE
Confidence 467888999999764 44431 33332 3233499999987654
No 273
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=24.12 E-value=35 Score=28.94 Aligned_cols=40 Identities=15% Similarity=0.349 Sum_probs=26.2
Q ss_pred cCCCCCccccceeecc-CCCCCCCCccccCCCCcceEEecc
Q 045112 227 GACPNCGEEVFAFVNS-DQTKNSPHRSDCHVCGSLLEFRTK 266 (296)
Q Consensus 227 GpCPNCGeEv~sFfgt-v~s~~~~n~vkChvC~t~L~fds~ 266 (296)
.-|++|.+...-...- +.--.....+.|+.||..+-|.-.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEeccc
Confidence 4699999865433321 222123378899999999988654
No 274
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=24.11 E-value=37 Score=37.52 Aligned_cols=28 Identities=29% Similarity=0.721 Sum_probs=18.5
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
--||-|++....=.|+-. -|.||+.+|+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--------~c~~c~~~~~ 855 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--------TCTNCGAQLK 855 (858)
T ss_pred CCCCccCCCceeecCCCc--------cccchhhhhc
Confidence 368999886655444332 4888888764
No 275
>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=24.00 E-value=25 Score=23.85 Aligned_cols=27 Identities=30% Similarity=0.853 Sum_probs=14.9
Q ss_pred CCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 229 CPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 229 CPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
||.||.=.+ ...+. ..+. .|..|+-.-
T Consensus 4 Cp~C~nlL~--p~~~~---~~~~-~C~~C~Y~~ 30 (35)
T PF02150_consen 4 CPECGNLLY--PKEDK---EKRV-ACRTCGYEE 30 (35)
T ss_dssp ETTTTSBEE--EEEET---TTTE-EESSSS-EE
T ss_pred CCCCCccce--EcCCC---ccCc-CCCCCCCcc
Confidence 888887553 22222 2222 899998643
No 276
>PRK15331 chaperone protein SicA; Provisional
Probab=23.94 E-value=72 Score=28.77 Aligned_cols=23 Identities=22% Similarity=0.468 Sum_probs=20.7
Q ss_pred ccHHHHHHHHHHHHHHhhcCCCc
Q 045112 70 ASKETLEALYRQARDAYYSGKPL 92 (296)
Q Consensus 70 ~t~~elE~~flqA~~AY~~GkPi 92 (296)
-|.++||+.|-.|-+.|..||--
T Consensus 32 is~~~le~iY~~Ay~~y~~Gk~~ 54 (165)
T PRK15331 32 IPQDMMDGLYAHAYEFYNQGRLD 54 (165)
T ss_pred CCHHHHHHHHHHHHHHHHCCCHH
Confidence 47899999999999999999853
No 277
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.89 E-value=35 Score=26.89 Aligned_cols=14 Identities=36% Similarity=0.973 Sum_probs=10.1
Q ss_pred eeecCCCCCccccc
Q 045112 224 ALRGACPNCGEEVF 237 (296)
Q Consensus 224 iLKGpCPNCGeEv~ 237 (296)
.++-+||-||..|-
T Consensus 5 ~~~v~CP~Cgkpv~ 18 (65)
T COG3024 5 RITVPCPTCGKPVV 18 (65)
T ss_pred cccccCCCCCCccc
Confidence 35668888888764
No 278
>PF08819 DUF1802: Domain of unknown function (DUF1802); InterPro: IPR014923 The function of this family is unknown. This region is found associated with a IPR007560 from INTERPRO suggesting they could be part of a restriction modification system.
Probab=23.72 E-value=44 Score=30.13 Aligned_cols=18 Identities=22% Similarity=0.447 Sum_probs=15.2
Q ss_pred hcCCCccchhhhHHHHHH
Q 045112 87 YSGKPLIVDDMFDRVELK 104 (296)
Q Consensus 87 ~~GkPimsDeeFD~LK~k 104 (296)
-.++|++||++|++...+
T Consensus 159 ~~~~PVlsD~~f~~~~~~ 176 (177)
T PF08819_consen 159 EGSKPVLSDEEFAQRAAE 176 (177)
T ss_pred CCCCCcCCHHHHHHHHhc
Confidence 456999999999998765
No 279
>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=23.71 E-value=1.6e+02 Score=28.17 Aligned_cols=44 Identities=23% Similarity=0.200 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhhcCCC---------ccchhhhHHHHHHHhH---hCCeeeeec
Q 045112 73 ETLEALYRQARDAYYSGKP---------LIVDDMFDRVELKLRW---YGSKSVIKY 116 (296)
Q Consensus 73 ~elE~~flqA~~AY~~GkP---------imsDeeFD~LK~kLk~---~GS~Vv~k~ 116 (296)
+++-+...++...+.-|.| +++.+.+++++..+.. +|.+++.-+
T Consensus 253 ~~~~~~L~~~l~~~~~g~p~~~~~~~~~~~~~~~~~~~~~~i~~~~~~g~~~~~gg 308 (432)
T cd07078 253 DEFVERLVERVKALKVGNPLDPDTDMGPLISAAQLDRVLAYIEDAKAEGAKLLCGG 308 (432)
T ss_pred HHHHHHHHHHHHccCcCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCEEEeCC
Confidence 3444444445555665544 7888889999887765 566676644
No 280
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=23.64 E-value=50 Score=25.01 Aligned_cols=26 Identities=27% Similarity=0.670 Sum_probs=16.3
Q ss_pred ecCCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 226 RGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 226 KGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
++.||-||+++. ...--|-|+.||++
T Consensus 5 ~~~C~~Cg~~~~---------~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 5 GCKCPVCGKKFK---------DGDDIVVCPECGAP 30 (54)
T ss_pred CccChhhCCccc---------CCCCEEECCCCCCc
Confidence 567888887753 12334667777764
No 281
>PRK03922 hypothetical protein; Provisional
Probab=23.62 E-value=38 Score=29.14 Aligned_cols=17 Identities=29% Similarity=0.495 Sum_probs=12.6
Q ss_pred eeeecCCCCCcccccee
Q 045112 223 VALRGACPNCGEEVFAF 239 (296)
Q Consensus 223 liLKGpCPNCGeEv~sF 239 (296)
-+=.-.||.||+|.-+=
T Consensus 46 evG~~~cP~cge~~~~a 62 (113)
T PRK03922 46 EVGLTICPKCGEPFDSA 62 (113)
T ss_pred ecCcccCCCCCCcCCcE
Confidence 34456899999998843
No 282
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=23.53 E-value=35 Score=24.83 Aligned_cols=8 Identities=50% Similarity=1.489 Sum_probs=6.7
Q ss_pred CCCCCccc
Q 045112 228 ACPNCGEE 235 (296)
Q Consensus 228 pCPNCGeE 235 (296)
+||.||..
T Consensus 11 ~CPgCG~t 18 (52)
T PF10825_consen 11 PCPGCGMT 18 (52)
T ss_pred CCCCCcHH
Confidence 89999963
No 283
>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=23.36 E-value=39 Score=29.28 Aligned_cols=14 Identities=29% Similarity=0.641 Sum_probs=8.9
Q ss_pred ccchhhhHHHHHHH
Q 045112 92 LIVDDMFDRVELKL 105 (296)
Q Consensus 92 imsDeeFD~LK~kL 105 (296)
|++||+||+|=.|+
T Consensus 3 iLtDeQFdrLW~e~ 16 (118)
T PF08976_consen 3 ILTDEQFDRLWNEM 16 (118)
T ss_dssp ---HHHHHHHHTTS
T ss_pred cccHHHhhhhhhhC
Confidence 78999999986554
No 284
>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=23.20 E-value=1.3e+02 Score=24.88 Aligned_cols=44 Identities=23% Similarity=0.393 Sum_probs=30.0
Q ss_pred eCCcccccHHHHHHHHHHHHHHhhcCCCcc--------------chhhhHHHHHHHhHhC
Q 045112 64 VGPLETASKETLEALYRQARDAYYSGKPLI--------------VDDMFDRVELKLRWYG 109 (296)
Q Consensus 64 ~~p~e~~t~~elE~~flqA~~AY~~GkPim--------------sDeeFD~LK~kLk~~G 109 (296)
-++..-+|..+. +.|++.+..+ .++|+. ++|.+|+.+++|+.+|
T Consensus 38 ~~~L~i~sr~Dv-~~Fi~~l~~~-~~~~Ls~LT~GvH~HtI~a~~~e~l~~I~~~L~~~G 95 (98)
T PF02829_consen 38 TGNLNISSRRDV-DKFIEKLEKS-KAKPLSSLTGGVHYHTIEAPDEEDLDKIEEALKKKG 95 (98)
T ss_dssp EEEEEE-SHHHH-HHHHHHHHH---S--STTGGGGEEEEEEEESSHHHHHHHHHHHHHTT
T ss_pred EEEEecCCHHHH-HHHHHHHhcc-CCcchHHhcCCEeeEEEEECCHHHHHHHHHHHHHCC
Confidence 344455566666 4699988887 888875 4689999999999988
No 285
>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=23.17 E-value=38 Score=32.66 Aligned_cols=38 Identities=13% Similarity=-0.077 Sum_probs=29.1
Q ss_pred hhHHHHHHHhHhCCeeeeeccceee-eccceeecccccHHHHHHhHH
Q 045112 97 MFDRVELKLRWYGSKSVIKYPRCSI-RRQSTYADAEEDLSQVLALGI 142 (296)
Q Consensus 97 eFD~LK~kLk~~GS~Vv~k~PrCSl-r~~~vysD~e~D~lkm~lL~~ 142 (296)
+.++|.++|+. .-+.+. .+.|+.||+|+|.+.-.|..+
T Consensus 2 ~i~~L~~~i~~--------~~~~YY~~~~p~IsD~eYD~L~~~L~~l 40 (307)
T cd00114 2 RIAELRELLNK--------HDYRYYVLDEPSVSDAEYDRLYRELRAL 40 (307)
T ss_pred HHHHHHHHHHH--------HHHHHHhCCCCCCChHHHHHHHHHHHHH
Confidence 57888888876 556654 599999999999996665543
No 286
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=23.17 E-value=59 Score=22.72 Aligned_cols=33 Identities=27% Similarity=0.714 Sum_probs=22.2
Q ss_pred CCC--CCccccceeeccCCCCCCCCccccCCCCcceEEec
Q 045112 228 ACP--NCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFRT 265 (296)
Q Consensus 228 pCP--NCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fds 265 (296)
.|| +|+.-+..- . +.....++|+.|+...=|.=
T Consensus 20 ~CP~~~C~~~~~~~---~--~~~~~~v~C~~C~~~fC~~C 54 (64)
T smart00647 20 WCPAPDCSAAIIVT---E--EEGCNRVTCPKCGFSFCFRC 54 (64)
T ss_pred CCCCCCCcceEEec---C--CCCCCeeECCCCCCeECCCC
Confidence 799 997755431 1 23557899999987765543
No 287
>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=23.02 E-value=49 Score=28.32 Aligned_cols=27 Identities=22% Similarity=0.561 Sum_probs=17.7
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCCcce
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLL 261 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L 261 (296)
-+||.|+.|. +| .+.+..-|+-|+-.-
T Consensus 3 p~CP~C~sey-tY-------~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEY-TY-------HDGTQLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcc-eE-------ecCCeeECccccccc
Confidence 4799999874 33 244456788887543
No 288
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=22.73 E-value=43 Score=33.75 Aligned_cols=13 Identities=23% Similarity=0.289 Sum_probs=7.1
Q ss_pred ceeEEeEEEEEec
Q 045112 276 RQWVYGRIYLLSR 288 (296)
Q Consensus 276 r~w~~GRiYlv~~ 288 (296)
.-++.|.++|+..
T Consensus 89 GGi~~GsvilI~G 101 (454)
T TIGR00416 89 GGIVPGSLILIGG 101 (454)
T ss_pred CCccCCeEEEEEc
Confidence 3455566666554
No 289
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=22.68 E-value=91 Score=26.05 Aligned_cols=41 Identities=22% Similarity=0.545 Sum_probs=26.1
Q ss_pred eeeecCCCCCccccceeecc--------CCC----------CCCCCccccCCCCc-ceEE
Q 045112 223 VALRGACPNCGEEVFAFVNS--------DQT----------KNSPHRSDCHVCGS-LLEF 263 (296)
Q Consensus 223 liLKGpCPNCGeEv~sFfgt--------v~s----------~~~~n~vkChvC~t-~L~f 263 (296)
....+.||-||.+...+++- +.+ ....-.++|+.|+. .++.
T Consensus 14 ~~~~~~Cp~Cg~~m~~~~~~~g~f~gCs~yP~C~~~~~~~~~~~~~~~~Cp~C~~~~~~~ 73 (140)
T COG0551 14 LKTGQICPKCGKNMVKKFGKYGIFLGCSNYPKCDYYEPEKAIAEKTGVKCPKCGKGLLVL 73 (140)
T ss_pred cccCccCCcCCCeeEEEEccCCeEEEeCCCCCCCCCcccccccccCceeCCCCCCCceEE
Confidence 34579999999998766542 111 12233488999995 4443
No 290
>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=22.51 E-value=58 Score=22.71 Aligned_cols=32 Identities=28% Similarity=0.603 Sum_probs=14.1
Q ss_pred CCCC--CccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 228 ACPN--CGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 228 pCPN--CGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
.||+ |+.-+.. ..+ .....+.|..|+...=|.
T Consensus 20 ~Cp~~~C~~~~~~----~~~-~~~~~~~C~~C~~~fC~~ 53 (64)
T PF01485_consen 20 WCPNPDCEYIIEK----DDG-CNSPIVTCPSCGTEFCFK 53 (64)
T ss_dssp --TTSST---ECS-----SS-TTS--CCTTSCCSEECSS
T ss_pred CCCCCCCcccEEe----cCC-CCCCeeECCCCCCcCccc
Confidence 8988 9864321 111 111158999999765443
No 291
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=22.48 E-value=69 Score=31.75 Aligned_cols=27 Identities=33% Similarity=0.684 Sum_probs=17.2
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
-|++||++- . + . ...+|+.|+..|..+
T Consensus 4 ~C~~Cg~~~----~-~---~--~~~~C~~c~g~l~~~ 30 (398)
T TIGR03844 4 RCPGCGEVL----P-D---H--YTLSCPLDCGLLRAE 30 (398)
T ss_pred EeCCCCCcc----C-C---c--cccCCCCCCCceEEe
Confidence 599999873 2 1 1 146798887665433
No 292
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.44 E-value=52 Score=32.77 Aligned_cols=48 Identities=23% Similarity=0.389 Sum_probs=29.4
Q ss_pred eeecCCCCCccccceeecc----CC---CC-------CCCCccccCCCCcce-EEecceeecc
Q 045112 224 ALRGACPNCGEEVFAFVNS----DQ---TK-------NSPHRSDCHVCGSLL-EFRTKVEQSS 271 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgt----v~---s~-------~~~n~vkChvC~t~L-~fds~ve~s~ 271 (296)
+.|..||.||+.+-.--++ +. =. -..-+++|+.|+... +...-|+++.
T Consensus 36 ~~~~~CP~Cg~~~~~~~~~~~~~I~~L~~~~~~~~L~~r~rR~~c~~c~~~~~~~~~~v~~~~ 98 (402)
T COG3464 36 PRKHRCPECGQRTIRRHGWRIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKRFAEKVDFVDRAQ 98 (402)
T ss_pred cccCCCCCCCCcceeccccceeeeeecccCCeeEEEEeccceeecccCCCCcccchhhhhccc
Confidence 3459999999997333211 00 00 244578999999987 5555555443
No 293
>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=22.43 E-value=37 Score=25.22 Aligned_cols=11 Identities=55% Similarity=1.144 Sum_probs=8.3
Q ss_pred cCCCCCccccc
Q 045112 227 GACPNCGEEVF 237 (296)
Q Consensus 227 GpCPNCGeEv~ 237 (296)
..|||||+...
T Consensus 27 ~~C~~cG~~~~ 37 (55)
T TIGR01031 27 VVCPNCGEFKL 37 (55)
T ss_pred eECCCCCCccc
Confidence 34999998654
No 294
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=22.39 E-value=39 Score=33.64 Aligned_cols=61 Identities=18% Similarity=0.176 Sum_probs=37.9
Q ss_pred ccCCCCCeeEee-----------CCcccccHHHHHHHH----HHHHHH--hhcCCCcc---------chhhhHHHHHHHh
Q 045112 53 CKNEEGPSCIFV-----------GPLETASKETLEALY----RQARDA--YYSGKPLI---------VDDMFDRVELKLR 106 (296)
Q Consensus 53 ~~~~eGpsc~~~-----------~p~e~~t~~elE~~f----lqA~~A--Y~~GkPim---------sDeeFD~LK~kLk 106 (296)
-++.+|-+-+-+ +..+--+++++|++| ++|+++ =-+|+|+. |.-+=+.|-+.++
T Consensus 127 ~lRa~Gtys~kvtDpi~fi~~I~g~~dvy~v~di~~q~ls~~m~al~tai~q~G~~~~~ltan~~elsk~m~e~Ld~q~~ 206 (345)
T COG4260 127 FLRAHGTYSIKVTDPILFIQQIPGNRDVYTVDDINQQYLSEFMGALATAINQSGVRFSFLTANQMELSKYMAEVLDEQWT 206 (345)
T ss_pred EEeecceEEEEecCHHHHHHhccCCCceEEHHHHHHHHHHHHHHHHHHHHHhcCceehhhhhhHHHHHHHHHHHHhHHHH
Confidence 356677665533 223445888999876 467755 34588863 4455566777777
Q ss_pred HhCCeee
Q 045112 107 WYGSKSV 113 (296)
Q Consensus 107 ~~GS~Vv 113 (296)
..|=.|.
T Consensus 207 q~Gm~v~ 213 (345)
T COG4260 207 QYGMAVD 213 (345)
T ss_pred hhCceEe
Confidence 7776443
No 295
>PF05209 MinC_N: Septum formation inhibitor MinC, N-terminal domain; InterPro: IPR007874 In Escherichia coli FtsZ (P0A9A6 from SWISSPROT) assembles into a Z ring at midcell. Its assembly at polar sites is prevented by the min system. MinC P18196 from SWISSPROT, a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with the MinDE proteins. MinC is an oligomer, probably a dimer []. The C-terminal half of MinC is the most conserved and interacts with MinD. The N-terminal half is thought to interact with FtsZ. MinC rapidly oscillates between the poles of the cell to destabilise FtsZ filaments that have formed before they mature into polar Z rings; GO: 0051302 regulation of cell division; PDB: 3GHF_A 1HF2_C.
Probab=22.37 E-value=97 Score=24.58 Aligned_cols=37 Identities=24% Similarity=0.382 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHhhcCCCccch-------hhhHHHHHHHhHhCC
Q 045112 73 ETLEALYRQARDAYYSGKPLIVD-------DMFDRVELKLRWYGS 110 (296)
Q Consensus 73 ~elE~~flqA~~AY~~GkPimsD-------eeFD~LK~kLk~~GS 110 (296)
++|.+..-||-+ +++|.|++-| .+|..|+.-++..|=
T Consensus 30 ~~L~~ki~~ap~-FF~~~pvvldl~~l~~~~dl~~L~~~l~~~gl 73 (99)
T PF05209_consen 30 QALDEKIAQAPD-FFKNAPVVLDLSNLPDELDLAALVELLRRHGL 73 (99)
T ss_dssp HHHHHHHHHTHH-HCTTTEEEEEEEEEETTHHHHHHHHHHHCCCH
T ss_pred HHHHHHHHhChH-hHcCCCeEEehhhcCChhhHHHHHHHHHHcCC
Confidence 344444444443 7799998766 789999999987774
No 296
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=22.31 E-value=67 Score=32.45 Aligned_cols=9 Identities=56% Similarity=1.505 Sum_probs=7.1
Q ss_pred ecCCCCCcc
Q 045112 226 RGACPNCGE 234 (296)
Q Consensus 226 KGpCPNCGe 234 (296)
+|.||.|+.
T Consensus 141 ~g~cp~c~~ 149 (556)
T PRK12268 141 EGTCPYCGY 149 (556)
T ss_pred eccCCCCCC
Confidence 488999984
No 297
>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=21.88 E-value=59 Score=27.02 Aligned_cols=32 Identities=34% Similarity=0.645 Sum_probs=24.1
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
.|++||.+|-. .+..+.++--|++|=..+--|
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 59999998743 233667888899998877776
No 298
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=21.84 E-value=40 Score=35.11 Aligned_cols=41 Identities=20% Similarity=0.439 Sum_probs=28.5
Q ss_pred eeecCCCCCccccceeeccCCCC--------CCCCccccCCCCcceEEe
Q 045112 224 ALRGACPNCGEEVFAFVNSDQTK--------NSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFfgtv~s~--------~~~n~vkChvC~t~L~fd 264 (296)
.=+-||+-||.|..+=.|.-.++ +...-.+|..|++...|-
T Consensus 159 vN~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFP 207 (500)
T KOG0909|consen 159 VNNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFP 207 (500)
T ss_pred cCCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCc
Confidence 44678999999998555542222 234456899999998874
No 299
>cd07107 ALDH_PhdK-like Nocardioides 2-carboxybenzaldehyde dehydrogenase, PhdK-like. Nocardioides sp. strain KP72-carboxybenzaldehyde dehydrogenase (PhdK), an enzyme involved in phenanthrene degradation, and other similar sequences, are present in this CD.
Probab=21.78 E-value=1.7e+02 Score=28.74 Aligned_cols=60 Identities=22% Similarity=0.221 Sum_probs=40.0
Q ss_pred CCCeeEeeCC--cccccHHHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHhH---hCCeeeeec
Q 045112 57 EGPSCIFVGP--LETASKETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLRW---YGSKSVIKY 116 (296)
Q Consensus 57 eGpsc~~~~p--~e~~t~~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk~---~GS~Vv~k~ 116 (296)
.|..|+-.++ .+..-.+++-+.+.++...+.-|. |+++.+.+|+++.-+.. +|.+++.-+
T Consensus 255 ~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~l~~g~p~~~~~~~Gpli~~~~~~~v~~~i~~a~~~Ga~v~~gG 328 (456)
T cd07107 255 CGQSCGSTSRLFVHESIYDEVLARVVERVAAIKVGDPTDPATTMGPLVSRQQYDRVMHYIDSAKREGARLVTGG 328 (456)
T ss_pred CCCCCcCCcEEEEcHHHHHHHHHHHHHHHHhCCCCCCCCCCCCcCcccCHHHHHHHHHHHHHHHHCCCEEEeCC
Confidence 4766654333 122344667777777777777665 56888999999887753 587877654
No 300
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=21.74 E-value=60 Score=27.55 Aligned_cols=36 Identities=33% Similarity=0.497 Sum_probs=20.3
Q ss_pred hhhhhhhhHHHHhh-hhccceeeeecCCCCCcccccee
Q 045112 203 GYPIASASVRVLQG-LWRNDLVALRGACPNCGEEVFAF 239 (296)
Q Consensus 203 gyplasa~v~~Lt~-l~~~D~liLKGpCPNCGeEv~sF 239 (296)
+..++-++-+ |.. +-+=|.-+=.-.||.||+|..+=
T Consensus 24 ~iAIseaGkr-Ln~~~~~VeIevG~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 24 GIAISEAGKR-LNPDLDYVEIEVGDTICPKCGEELDSA 60 (102)
T ss_pred HHHHHHHHHh-hCCCCCeEEEecCcccCCCCCCccCce
Confidence 4445555543 333 32233334455899999998843
No 301
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=21.68 E-value=39 Score=24.90 Aligned_cols=20 Identities=45% Similarity=1.076 Sum_probs=13.5
Q ss_pred cCCCCCccccceeeccCCCCCCCCccccCCCC
Q 045112 227 GACPNCGEEVFAFVNSDQTKNSPHRSDCHVCG 258 (296)
Q Consensus 227 GpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~ 258 (296)
..||+||+-.. ...-|.+||
T Consensus 27 ~~c~~cg~~~~------------~H~vc~~cG 46 (56)
T PF01783_consen 27 VKCPNCGEPKL------------PHRVCPSCG 46 (56)
T ss_dssp EESSSSSSEES------------TTSBCTTTB
T ss_pred eeeccCCCEec------------ccEeeCCCC
Confidence 57999997432 224577887
No 302
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=21.47 E-value=42 Score=22.75 Aligned_cols=9 Identities=44% Similarity=1.350 Sum_probs=5.6
Q ss_pred CCCCCcccc
Q 045112 228 ACPNCGEEV 236 (296)
Q Consensus 228 pCPNCGeEv 236 (296)
.||+||.+.
T Consensus 4 ~Cp~Cg~~~ 12 (47)
T PF14690_consen 4 RCPHCGSPS 12 (47)
T ss_pred cCCCcCCCc
Confidence 466666555
No 303
>cd07113 ALDH_PADH_NahF Escherichia coli NAD+-dependent phenylacetaldehyde dehydrogenase PadA-like. NAD+-dependent, homodimeric, phenylacetaldehyde dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia coli involved in the catabolism of 2-phenylethylamine, and other related sequences, are present in this CD. Also included is the Pseudomonas fluorescens ST StyD PADH involved in styrene catabolism, the Sphingomonas sp. LB126 FldD protein involved in fluorene degradation, and the Novosphingobium aromaticivorans NahF salicylaldehyde dehydrogenase involved in the NAD+-dependent conversion of salicylaldehyde to salicylate.
Probab=21.46 E-value=1.9e+02 Score=28.82 Aligned_cols=60 Identities=23% Similarity=0.267 Sum_probs=34.9
Q ss_pred CCCeeEeeCC--cccccHHHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHhH---hCCeeeeec
Q 045112 57 EGPSCIFVGP--LETASKETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLRW---YGSKSVIKY 116 (296)
Q Consensus 57 eGpsc~~~~p--~e~~t~~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk~---~GS~Vv~k~ 116 (296)
.|..|+-.++ .+..-.+++-+.+.++...+.-|. |+++.+.||+++.-+.. +|.+++.-+
T Consensus 280 ~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~gpli~~~~~~~~~~~i~~a~~~Ga~~l~gg 353 (477)
T cd07113 280 QGQVCAAPERFYVHRSKFDELVTKLKQALSSFQVGSPMDESVMFGPLANQPHFDKVCSYLDDARAEGDEIVRGG 353 (477)
T ss_pred CCCCCcCCcEEEECHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCcCHHHHHHHHHHHHHHHHCCCEEEeCC
Confidence 4555543333 122233556666666666665554 46777888888877764 577766544
No 304
>cd07108 ALDH_MGR_2402 Magnetospirillum NAD(P)+-dependent aldehyde dehydrogenase MSR-1-like. NAD(P)+-dependent aldehyde dehydrogenase of Magnetospirillum gryphiswaldense MSR-1 (MGR_2402) , and other similar sequences, are present in this CD.
Probab=21.41 E-value=1.7e+02 Score=28.77 Aligned_cols=60 Identities=13% Similarity=0.138 Sum_probs=37.1
Q ss_pred CCCeeEeeCC--cccccHHHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHhH----hCCeeeeec
Q 045112 57 EGPSCIFVGP--LETASKETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLRW----YGSKSVIKY 116 (296)
Q Consensus 57 eGpsc~~~~p--~e~~t~~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk~----~GS~Vv~k~ 116 (296)
.|..|+-.++ .+..-.+++.+.+.++...+.-|. |+++.+.+|+++.-+.. +|.+++.-+
T Consensus 256 ~GQ~C~a~~rv~V~~~i~~~f~~~l~~~~~~~~vg~p~~~~~~~gpli~~~~~~~~~~~i~~a~~~~ga~vl~gG 330 (457)
T cd07108 256 QGQSCTAGSRLFVHEDIYDAFLEKLVAKLSKLKIGDPLDEATDIGAIISEKQFAKVCGYIDLGLSTSGATVLRGG 330 (457)
T ss_pred CCCCCCCCeEEEEehHHHHHHHHHHHHHHhhCCCCCCCCCCCCcCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCC
Confidence 4566643322 122234666666667666666564 57888889998877764 677777644
No 305
>TIGR01780 SSADH succinate-semialdehyde dehydrogenase. SSADH enzyme belongs to the aldehyde dehydrogenase family (pfam00171), sharing a common evolutionary origin and enzymatic mechanism with lactaldehyde dehydrogenase. Like in lactaldehyde dehydrogenase and succinate semialdehyde dehydrogenase, the mammalian catalytic glutamic acid and cysteine residues are conserved in all the enzymes of this family (PS00687, PS00070).
Probab=21.38 E-value=2e+02 Score=28.39 Aligned_cols=59 Identities=20% Similarity=0.326 Sum_probs=38.7
Q ss_pred CCeeEeeCC--cccccHHHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHhH---hCCeeeeec
Q 045112 58 GPSCIFVGP--LETASKETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLRW---YGSKSVIKY 116 (296)
Q Consensus 58 Gpsc~~~~p--~e~~t~~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk~---~GS~Vv~k~ 116 (296)
|..|+-..+ .+..-.+++-+.+.++...+.-|. |+++.+.+|+++..+.. +|.+++.-+
T Consensus 258 GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~l~~G~p~~~~~~~gpli~~~~~~~v~~~i~~a~~~Ga~il~gg 330 (448)
T TIGR01780 258 GQTCVCANRLYVHDGIYDEFAKKLAEAVKKLKVGNGLDEGVTQGPLINEKAVEKVEKHIADAVEKGAKVVTGG 330 (448)
T ss_pred CCcccCCceeechHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEeCC
Confidence 666665444 122234566666777777776665 48888899999887754 587776644
No 306
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.32 E-value=59 Score=25.19 Aligned_cols=39 Identities=18% Similarity=0.463 Sum_probs=26.4
Q ss_pred ccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCcceE
Q 045112 219 RNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLE 262 (296)
Q Consensus 219 ~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~ 262 (296)
.+|++-+|-|=| ||+.-+- -+.- ++.-+.||.|||..+.
T Consensus 7 l~~~VEMKK~H~-Cg~Nrwk---IiRv-GaDIkikC~nC~h~vm 45 (60)
T COG4481 7 LGDIVEMKKPHA-CGTNRWK---IIRV-GADIKIKCENCGHSVM 45 (60)
T ss_pred ccchheecCCCc-cccceEE---EEEe-cCcEEEEecCCCcEEE
Confidence 478889998876 7772222 1222 4667899999998754
No 307
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=21.24 E-value=31 Score=27.69 Aligned_cols=13 Identities=46% Similarity=1.323 Sum_probs=7.6
Q ss_pred cCCCCCcccccee
Q 045112 227 GACPNCGEEVFAF 239 (296)
Q Consensus 227 GpCPNCGeEv~sF 239 (296)
-.||+||++..-|
T Consensus 66 ~~Cp~Cg~~~~iF 78 (81)
T PF10609_consen 66 FVCPHCGERIYIF 78 (81)
T ss_dssp EE-TTT--EEETT
T ss_pred cCCCCCCCeecCC
Confidence 4799999987655
No 308
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.02 E-value=50 Score=28.46 Aligned_cols=17 Identities=29% Similarity=0.622 Sum_probs=12.7
Q ss_pred eeecCCCCCccccceee
Q 045112 224 ALRGACPNCGEEVFAFV 240 (296)
Q Consensus 224 iLKGpCPNCGeEv~sFf 240 (296)
+=.-.||.||++.-+-|
T Consensus 47 ~G~t~CP~Cg~~~e~~f 63 (115)
T COG1885 47 VGSTSCPKCGEPFESAF 63 (115)
T ss_pred cccccCCCCCCccceeE
Confidence 34468999999988544
No 309
>cd07135 ALDH_F14-YMR110C Saccharomyces cerevisiae aldehyde dehydrogenase family 14 and related proteins. Aldehyde dehydrogenase family 14 (ALDH14), isolated mainly from the mitochondrial outer membrane of Saccharomyces cerevisiae (YMR110C) and most closely related to the plant and animal ALDHs and fatty ALDHs family 3 members, and similar fungal sequences, are present in this CD.
Probab=20.96 E-value=2.3e+02 Score=28.09 Aligned_cols=63 Identities=17% Similarity=0.288 Sum_probs=39.1
Q ss_pred CCCCeeEeeCCc--ccccHHHHHHHHHHHHHHhhcCC--------CccchhhhHHHHHHHhHhCCeeeeeccc
Q 045112 56 EEGPSCIFVGPL--ETASKETLEALYRQARDAYYSGK--------PLIVDDMFDRVELKLRWYGSKSVIKYPR 118 (296)
Q Consensus 56 ~eGpsc~~~~p~--e~~t~~elE~~flqA~~AY~~Gk--------PimsDeeFD~LK~kLk~~GS~Vv~k~Pr 118 (296)
..|..|.-.++. +..-.+++-+.+.++...+.-|. |+++.+.+|+++.-+...|.+++.-+++
T Consensus 243 ~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~gpli~~~~~~~i~~~v~~ag~~v~~gg~~ 315 (436)
T cd07135 243 NAGQICVAPDYVLVDPSVYDEFVEELKKVLDEFYPGGANASPDYTRIVNPRHFNRLKSLLDTTKGKVVIGGEM 315 (436)
T ss_pred cCCceecCCCEEeccHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHHHHHHHHhcCCeEEECCCc
Confidence 346666644441 22234455555555555566676 6788889999998887767777665543
No 310
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=20.89 E-value=42 Score=26.38 Aligned_cols=11 Identities=36% Similarity=0.936 Sum_probs=9.0
Q ss_pred CCCCcccccee
Q 045112 229 CPNCGEEVFAF 239 (296)
Q Consensus 229 CPNCGeEv~sF 239 (296)
||+||.+-+++
T Consensus 21 CP~Cgs~~~te 31 (64)
T COG2093 21 CPVCGSTDLTE 31 (64)
T ss_pred CCCCCCcccch
Confidence 99999986654
No 311
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.73 E-value=60 Score=31.81 Aligned_cols=35 Identities=23% Similarity=0.502 Sum_probs=18.8
Q ss_pred CCCCCccccceeeccCCCCCCCCc-cccCCCCcceE
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHR-SDCHVCGSLLE 262 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~-vkChvC~t~L~ 262 (296)
-||+||+.-.--|-++.+.....+ --|..|++=++
T Consensus 228 ~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 228 KCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred cCCCCCCCCceeeeeecCCCcceEeeecccccccce
Confidence 488888754322334444333333 34788877554
No 312
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.70 E-value=48 Score=35.95 Aligned_cols=14 Identities=43% Similarity=1.044 Sum_probs=8.7
Q ss_pred CCCCCccccceeec
Q 045112 228 ACPNCGEEVFAFVN 241 (296)
Q Consensus 228 pCPNCGeEv~sFfg 241 (296)
.||+||.+...++|
T Consensus 477 ~Cp~Cgs~~L~~~G 490 (730)
T COG1198 477 SCPECGSEHLRAVG 490 (730)
T ss_pred CCCCCCCCeeEEec
Confidence 46677766655554
No 313
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=20.69 E-value=1.6e+02 Score=24.45 Aligned_cols=36 Identities=8% Similarity=0.093 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHhhcCCCccchhhhHHHHHHHhH
Q 045112 72 KETLEALYRQARDAYYSGKPLIVDDMFDRVELKLRW 107 (296)
Q Consensus 72 ~~elE~~flqA~~AY~~GkPimsDeeFD~LK~kLk~ 107 (296)
..++++++-.-...|-+..+.||+++++.+..+|..
T Consensus 52 l~~~~~el~~~~~~l~~~~~~ls~~~~~~~~~~l~~ 87 (158)
T PF03938_consen 52 LQAKQKELQKLQQKLQSQKATLSEEERQKRQQELQQ 87 (158)
T ss_dssp HHHHHHHHHHHHHHHTTS----SSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHH
Confidence 446666676666779999999999999888888754
No 314
>cd07116 ALDH_ACDHII-AcoD Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like. Included in this CD is the NAD+-dependent, acetaldehyde dehydrogenase II (AcDHII, AcoD, EC=1.2.1.3) from Ralstonia (Alcaligenes) eutrophus H16 involved in the catabolism of acetoin and ethanol, and similar proteins, such as, the dimeric dihydrolipoamide dehydrogenase of the acetoin dehydrogenase enzyme system of Klebsiella pneumonia. Also included are sequences similar to the NAD+-dependent chloroacetaldehyde dehydrogenases (AldA and AldB) of Xanthobacter autotrophicus GJ10 which are involved in the degradation of 1,2-dichloroethane. These proteins apparently require RpoN factors for expression.
Probab=20.68 E-value=1.8e+02 Score=28.95 Aligned_cols=60 Identities=8% Similarity=0.094 Sum_probs=32.6
Q ss_pred CCCeeEeeCC--cccccHHHHHHHHHHHHHHhhcCC---------CccchhhhHHHHHHHh---HhCCeeeeec
Q 045112 57 EGPSCIFVGP--LETASKETLEALYRQARDAYYSGK---------PLIVDDMFDRVELKLR---WYGSKSVIKY 116 (296)
Q Consensus 57 eGpsc~~~~p--~e~~t~~elE~~flqA~~AY~~Gk---------PimsDeeFD~LK~kLk---~~GS~Vv~k~ 116 (296)
.|..|+-.++ .+..-.+++-+.+.++...+.-|. |+++.+.+|+++.-+. .+|.+++.-+
T Consensus 279 ~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~l~~G~p~~~~~~~Gpli~~~~~~~v~~~i~~a~~~Ga~~~~gg 352 (479)
T cd07116 279 QGEVCTCPSRALIQESIYDRFMERALERVKAIKQGNPLDTETMIGAQASLEQLEKILSYIDIGKEEGAEVLTGG 352 (479)
T ss_pred CCCCCCCCeEEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCEEEeCC
Confidence 4565543333 122234455555555555555564 6777777777776654 3566655433
No 315
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=20.62 E-value=45 Score=30.45 Aligned_cols=11 Identities=55% Similarity=1.286 Sum_probs=8.9
Q ss_pred ecCCCCCcccc
Q 045112 226 RGACPNCGEEV 236 (296)
Q Consensus 226 KGpCPNCGeEv 236 (296)
.-+||.||++.
T Consensus 154 RP~CPlCg~Pl 164 (171)
T PF11290_consen 154 RPPCPLCGEPL 164 (171)
T ss_pred CCCCCCCCCCC
Confidence 35899999875
No 316
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.40 E-value=45 Score=26.12 Aligned_cols=33 Identities=24% Similarity=0.503 Sum_probs=23.8
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcc
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSL 260 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~ 260 (296)
+||-|...+.-|=-=+.-+.+.-+..|..|.+-
T Consensus 7 ~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~ry 39 (63)
T PF02701_consen 7 PCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRY 39 (63)
T ss_pred CCCCcCCCCCEEEeecCCCCCCcchhhHHHHHH
Confidence 799999999877443333356667889888653
No 317
>PRK08329 threonine synthase; Validated
Probab=20.39 E-value=80 Score=30.27 Aligned_cols=26 Identities=27% Similarity=0.617 Sum_probs=17.5
Q ss_pred CCCCCccccceeeccCCCCCCCCccccCCCCcceEEe
Q 045112 228 ACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGSLLEFR 264 (296)
Q Consensus 228 pCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t~L~fd 264 (296)
-|+.||+|-- .+.. ..| .|+-.|...
T Consensus 3 ~C~~Cg~~~~---------~~~~-~~C-~c~~~l~~~ 28 (347)
T PRK08329 3 RCTKCGRTYE---------EKFK-LRC-DCGGTLLVE 28 (347)
T ss_pred CcCCCCCCcC---------CCCc-eec-CCCCcEEEE
Confidence 5999998741 1122 679 698876655
No 318
>PF09930 DUF2162: Predicted transporter (DUF2162); InterPro: IPR017199 This group represents a predicted membrane transporter, MTH672 type.
Probab=20.38 E-value=45 Score=31.19 Aligned_cols=35 Identities=20% Similarity=0.401 Sum_probs=22.7
Q ss_pred hhhhhhhhhHHHHhhh-------hccceeeeecCCCCCcccc
Q 045112 202 IGYPIASASVRVLQGL-------WRNDLVALRGACPNCGEEV 236 (296)
Q Consensus 202 igyplasa~v~~Lt~l-------~~~D~liLKGpCPNCGeEv 236 (296)
++..+..++...+.+- -.+.++++--|||.|-+-+
T Consensus 74 mal~li~~Gi~ti~~W~~~~~~~s~~t~lal~~PCPvCl~Ai 115 (224)
T PF09930_consen 74 MALLLIYAGIYTIKKWKKSGKDSSRRTFLALSLPCPVCLTAI 115 (224)
T ss_pred HHHHHHHHHHHHHHHHcccCCCCcccchhhhhcCchHHHHHH
Confidence 3555566666544331 2455799999999997654
No 319
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=20.35 E-value=54 Score=28.75 Aligned_cols=39 Identities=23% Similarity=0.452 Sum_probs=27.0
Q ss_pred CCCCCccccce-------------eeccCCCC-----------CCCCccccCCCCcce--EEecc
Q 045112 228 ACPNCGEEVFA-------------FVNSDQTK-----------NSPHRSDCHVCGSLL--EFRTK 266 (296)
Q Consensus 228 pCPNCGeEv~s-------------Ffgtv~s~-----------~~~n~vkChvC~t~L--~fds~ 266 (296)
-|-.||++.|+ |+..+..+ -.+-++.|.+|+.-| +|+-.
T Consensus 42 ~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D~s~gm~RtEv~C~~Cg~HLGHVF~DG 106 (134)
T TIGR00357 42 VDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDESHGMIRTEVRCRNCDAHLGHVFDDG 106 (134)
T ss_pred EccCCCCccccccchhcCCCCCcCcCcccCCCceEEeecCCCCcEEEEEEecCCCCccCcccCCC
Confidence 59999999874 44444222 245679999999987 67653
No 320
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.23 E-value=75 Score=29.23 Aligned_cols=36 Identities=14% Similarity=0.375 Sum_probs=24.0
Q ss_pred hccceeeeecCCCCCccccceeeccCCCCCCCCccccCCCCc
Q 045112 218 WRNDLVALRGACPNCGEEVFAFVNSDQTKNSPHRSDCHVCGS 259 (296)
Q Consensus 218 ~~~D~liLKGpCPNCGeEv~sFfgtv~s~~~~n~vkChvC~t 259 (296)
...+ .+=--+|..||.+-.+-. ....+..+|+.|.-
T Consensus 127 ~~s~-~L~l~~C~~Cgg~fv~~~-----~e~~~~f~CplC~~ 162 (187)
T PRK12722 127 VDSG-MLQLSSCNCCGGHFVTHA-----HDPVGSFVCGLCQP 162 (187)
T ss_pred HhcC-cEeeccCCCCCCCeeccc-----cccCCCCcCCCCCC
Confidence 3344 334458999999854222 24578899999986
No 321
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=20.20 E-value=46 Score=29.60 Aligned_cols=34 Identities=29% Similarity=0.595 Sum_probs=24.7
Q ss_pred CCCCCccccce-------------eeccCCC-----------CCCCCccccCCCCcce
Q 045112 228 ACPNCGEEVFA-------------FVNSDQT-----------KNSPHRSDCHVCGSLL 261 (296)
Q Consensus 228 pCPNCGeEv~s-------------Ffgtv~s-----------~~~~n~vkChvC~t~L 261 (296)
-|-.||++.|+ |+..+.. +-.+-++.|.+|++-|
T Consensus 44 ~c~~cg~pLF~S~~KfdSgcGWPSF~~pi~~~~I~~~~D~S~gM~RtEVrc~~c~sHL 101 (140)
T COG0229 44 VCIVCGEPLFSSEDKFDSGCGWPSFTKPISPDAITYKEDRSHGMVRTEVRCANCDSHL 101 (140)
T ss_pred EeecCCCccccccccccCCCCCccccccCCcccceEeeccCCCcEEEEEEecCCCCcc
Confidence 48889999873 5655433 2356789999999877
No 322
>TIGR01552 phd_fam prevent-host-death family protein. This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family.
Probab=20.17 E-value=2.4e+02 Score=19.40 Aligned_cols=15 Identities=33% Similarity=0.589 Sum_probs=11.6
Q ss_pred ccchhhhHHHHHHHh
Q 045112 92 LIVDDMFDRVELKLR 106 (296)
Q Consensus 92 imsDeeFD~LK~kLk 106 (296)
+|+-++|++|++.|.
T Consensus 36 lv~~~~y~~l~~~~~ 50 (52)
T TIGR01552 36 LVSAADYDRLQETLR 50 (52)
T ss_pred EeeHHHHHHHHHHhc
Confidence 468888999888763
No 323
>PF05120 GvpG: Gas vesicle protein G ; InterPro: IPR007804 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are involved in the formation of gas vesicles [].
Probab=20.09 E-value=2e+02 Score=23.04 Aligned_cols=25 Identities=28% Similarity=0.456 Sum_probs=19.8
Q ss_pred HHHHHHhhcCCCccchhhhHHHHHHHh
Q 045112 80 RQARDAYYSGKPLIVDDMFDRVELKLR 106 (296)
Q Consensus 80 lqA~~AY~~GkPimsDeeFD~LK~kLk 106 (296)
.+.-++|-.|+ ||.||||+-+.+|-
T Consensus 38 ~~L~~~~e~GE--IseeEf~~~E~eLL 62 (79)
T PF05120_consen 38 AELQEALEAGE--ISEEEFERREDELL 62 (79)
T ss_pred HHHHHHHHcCC--CCHHHHHHHHHHHH
Confidence 33446788887 89999999998874
Done!