Query 018197
Match_columns 359
No_of_seqs 121 out of 208
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 06:57:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018197.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018197hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13240 zinc_ribbon_2: zinc-r 98.3 2.7E-07 5.8E-12 59.0 1.6 23 333-356 1-23 (23)
2 PF13248 zf-ribbon_3: zinc-rib 98.2 5.2E-07 1.1E-11 58.4 1.8 25 331-356 2-26 (26)
3 COG4260 Membrane protease subu 97.7 2.1E-05 4.7E-10 76.9 2.5 54 130-189 188-241 (345)
4 PF10571 UPF0547: Uncharacteri 97.2 0.0002 4.4E-09 47.3 1.5 24 332-356 1-24 (26)
5 PF12773 DZR: Double zinc ribb 96.8 0.0007 1.5E-08 48.0 2.1 25 331-355 12-38 (50)
6 PF12773 DZR: Double zinc ribb 96.5 0.0018 3.9E-08 45.9 2.4 25 328-353 26-50 (50)
7 PF09297 zf-NADH-PPase: NADH p 96.0 0.0023 5E-08 42.8 0.6 26 330-355 2-30 (32)
8 KOG3940 Uncharacterized conser 95.8 0.0044 9.4E-08 61.5 1.6 28 331-358 322-350 (351)
9 smart00661 RPOL9 RNA polymeras 95.4 0.011 2.3E-07 41.9 2.1 24 332-355 1-29 (52)
10 PRK00420 hypothetical protein; 95.4 0.0084 1.8E-07 51.3 1.7 26 331-356 23-50 (112)
11 PF14803 Nudix_N_2: Nudix N-te 94.9 0.0069 1.5E-07 42.3 -0.1 23 332-354 1-30 (34)
12 PF09538 FYDLN_acid: Protein o 93.8 0.046 1E-06 46.2 2.6 27 330-356 7-36 (108)
13 COG1645 Uncharacterized Zn-fin 93.3 0.031 6.8E-07 49.3 0.7 25 331-355 28-53 (131)
14 PRK00398 rpoP DNA-directed RNA 93.1 0.04 8.7E-07 39.2 1.0 24 334-357 6-32 (46)
15 PRK07418 acetolactate synthase 92.6 0.065 1.4E-06 54.7 2.0 27 329-356 590-616 (616)
16 PRK14714 DNA polymerase II lar 92.4 0.088 1.9E-06 59.8 2.8 25 333-357 694-720 (1337)
17 COG2816 NPY1 NTP pyrophosphohy 92.0 0.075 1.6E-06 51.7 1.5 27 329-355 109-138 (279)
18 PRK00241 nudC NADH pyrophospha 91.7 0.088 1.9E-06 49.3 1.6 27 329-355 97-126 (256)
19 PRK04023 DNA polymerase II lar 91.5 0.11 2.4E-06 58.1 2.2 39 67-105 420-458 (1121)
20 PRK04023 DNA polymerase II lar 90.9 0.12 2.7E-06 57.7 2.0 23 331-356 651-673 (1121)
21 PRK12496 hypothetical protein; 90.8 0.15 3.2E-06 45.3 2.0 25 332-356 128-153 (164)
22 PF13240 zinc_ribbon_2: zinc-r 90.8 0.1 2.2E-06 33.5 0.7 13 329-341 11-23 (23)
23 PRK12495 hypothetical protein; 90.6 0.12 2.7E-06 49.1 1.4 27 330-356 41-68 (226)
24 PF06677 Auto_anti-p27: Sjogre 90.5 0.14 3E-06 37.2 1.3 23 331-353 17-41 (41)
25 PF13248 zf-ribbon_3: zinc-rib 90.4 0.11 2.5E-06 33.6 0.7 13 329-341 14-26 (26)
26 PF02150 RNA_POL_M_15KD: RNA p 90.1 0.086 1.9E-06 36.6 -0.1 24 332-355 2-29 (35)
27 PRK14714 DNA polymerase II lar 89.8 0.16 3.6E-06 57.7 1.8 22 332-355 680-701 (1337)
28 smart00659 RPOLCX RNA polymera 89.4 0.18 3.8E-06 36.8 1.1 24 334-357 5-30 (44)
29 PRK00432 30S ribosomal protein 89.1 0.21 4.5E-06 37.2 1.3 26 330-355 19-46 (50)
30 TIGR02098 MJ0042_CXXC MJ0042 f 88.8 0.16 3.6E-06 34.4 0.5 24 334-357 5-36 (38)
31 PRK14890 putative Zn-ribbon RN 87.8 0.33 7.1E-06 38.1 1.7 25 330-354 23-56 (59)
32 PRK12380 hydrogenase nickel in 87.8 0.23 4.9E-06 41.7 0.9 27 329-355 68-95 (113)
33 PF09889 DUF2116: Uncharacteri 87.6 0.16 3.5E-06 39.4 -0.1 25 330-355 2-27 (59)
34 COG1545 Predicted nucleic-acid 87.5 0.26 5.6E-06 42.8 1.1 24 331-355 29-52 (140)
35 PRK00564 hypA hydrogenase nick 87.2 0.27 5.8E-06 41.5 1.0 32 325-356 65-98 (117)
36 COG0675 Transposase and inacti 87.2 0.34 7.3E-06 42.9 1.6 28 326-355 304-331 (364)
37 PF14803 Nudix_N_2: Nudix N-te 87.0 0.23 4.9E-06 34.8 0.4 10 347-356 1-10 (34)
38 PF14446 Prok-RING_1: Prokaryo 86.7 0.31 6.8E-06 37.5 1.0 25 331-355 5-30 (54)
39 TIGR00100 hypA hydrogenase nic 86.3 0.32 7E-06 40.8 1.0 28 329-356 68-96 (115)
40 PF03604 DNA_RNApol_7kD: DNA d 85.8 0.4 8.6E-06 33.2 1.1 24 334-357 3-28 (32)
41 smart00834 CxxC_CXXC_SSSS Puta 85.8 0.54 1.2E-05 31.7 1.7 24 333-356 7-36 (41)
42 PRK03681 hypA hydrogenase nick 85.3 0.38 8.2E-06 40.4 1.0 28 329-356 68-97 (114)
43 PF08271 TF_Zn_Ribbon: TFIIB z 84.4 0.31 6.6E-06 34.3 0.0 24 333-356 2-29 (43)
44 COG2888 Predicted Zn-ribbon RN 84.0 0.63 1.4E-05 36.9 1.6 27 329-355 24-59 (61)
45 PF07282 OrfB_Zn_ribbon: Putat 83.9 0.7 1.5E-05 34.5 1.7 34 323-356 20-56 (69)
46 PF10083 DUF2321: Uncharacteri 83.3 0.54 1.2E-05 42.9 1.1 11 346-356 68-78 (158)
47 PF14319 Zn_Tnp_IS91: Transpos 82.0 0.66 1.4E-05 38.9 1.1 25 332-356 43-70 (111)
48 PF11781 RRN7: RNA polymerase 81.9 0.49 1.1E-05 33.3 0.2 23 334-356 11-35 (36)
49 PRK03824 hypA hydrogenase nick 81.6 0.64 1.4E-05 40.1 0.9 15 329-343 68-82 (135)
50 PF05191 ADK_lid: Adenylate ki 81.4 0.44 9.6E-06 33.5 -0.1 25 333-357 3-32 (36)
51 PRK13130 H/ACA RNA-protein com 80.8 0.86 1.9E-05 35.2 1.3 23 331-356 5-27 (56)
52 PF09567 RE_MamI: MamI restric 79.8 1 2.2E-05 44.5 1.7 53 302-355 38-105 (314)
53 PF08772 NOB1_Zn_bind: Nin one 79.7 0.73 1.6E-05 37.0 0.6 23 333-355 11-33 (73)
54 COG1439 Predicted nucleic acid 79.6 0.87 1.9E-05 42.1 1.1 24 332-356 140-163 (177)
55 PHA02942 putative transposase; 77.8 1.8 3.8E-05 43.0 2.7 35 322-356 316-352 (383)
56 PRK11788 tetratricopeptide rep 77.7 1.3 2.8E-05 40.5 1.6 27 328-355 351-377 (389)
57 PF01155 HypA: Hydrogenase exp 77.3 0.42 9.1E-06 39.9 -1.5 28 329-356 68-96 (113)
58 TIGR00577 fpg formamidopyrimid 76.1 1.5 3.3E-05 41.3 1.7 23 330-352 244-271 (272)
59 PRK01343 zinc-binding protein; 75.9 2.5 5.4E-05 33.0 2.5 26 326-351 4-29 (57)
60 PRK06266 transcription initiat 75.7 1.2 2.6E-05 40.2 0.8 24 334-357 120-147 (178)
61 PRK10445 endonuclease VIII; Pr 75.7 1.5 3.3E-05 41.2 1.5 24 330-353 234-262 (263)
62 smart00531 TFIIE Transcription 75.5 1.3 2.8E-05 38.2 1.0 23 334-356 102-133 (147)
63 PRK01103 formamidopyrimidine/5 75.3 1.6 3.4E-05 41.1 1.5 25 330-354 244-273 (274)
64 PRK14810 formamidopyrimidine-D 75.0 1.6 3.5E-05 41.2 1.5 23 331-353 244-271 (272)
65 TIGR00373 conserved hypothetic 74.2 1.1 2.5E-05 39.4 0.3 24 334-357 112-139 (158)
66 TIGR01031 rpmF_bact ribosomal 74.2 1.6 3.4E-05 33.2 1.0 23 330-354 25-47 (55)
67 TIGR02420 dksA RNA polymerase- 74.0 1.3 2.8E-05 36.6 0.6 23 332-354 81-109 (110)
68 PF12172 DUF35_N: Rubredoxin-l 73.7 0.93 2E-05 30.9 -0.3 23 332-355 12-34 (37)
69 TIGR03826 YvyF flagellar opero 73.5 1.9 4.2E-05 38.1 1.6 34 321-356 70-104 (137)
70 PF07754 DUF1610: Domain of un 73.4 2.1 4.5E-05 28.4 1.3 21 334-354 1-24 (24)
71 COG1592 Rubrerythrin [Energy p 73.2 2.3 5E-05 38.8 2.0 26 331-356 134-159 (166)
72 PRK12286 rpmF 50S ribosomal pr 73.0 1.9 4.1E-05 33.0 1.2 25 329-355 25-49 (57)
73 PF09723 Zn-ribbon_8: Zinc rib 73.0 2.2 4.7E-05 30.3 1.4 21 334-354 8-34 (42)
74 TIGR01206 lysW lysine biosynth 72.9 1.4 3.1E-05 33.6 0.5 24 333-356 4-32 (54)
75 PRK14811 formamidopyrimidine-D 72.9 2 4.2E-05 40.7 1.5 26 330-355 234-264 (269)
76 PF11682 DUF3279: Protein of u 72.8 2 4.4E-05 37.9 1.5 28 327-356 93-120 (128)
77 cd00350 rubredoxin_like Rubred 72.8 2.5 5.4E-05 28.6 1.6 23 334-356 4-27 (33)
78 KOG3507 DNA-directed RNA polym 72.7 1.5 3.3E-05 34.9 0.6 29 329-357 17-48 (62)
79 PRK09521 exosome complex RNA-b 72.5 1.5 3.3E-05 39.0 0.7 24 332-355 150-175 (189)
80 PF01783 Ribosomal_L32p: Ribos 72.0 2 4.3E-05 32.3 1.1 24 330-355 25-48 (56)
81 PRK10778 dksA RNA polymerase-b 71.2 1.6 3.5E-05 38.7 0.6 25 331-355 111-141 (151)
82 PRK13945 formamidopyrimidine-D 71.1 2.3 5.1E-05 40.3 1.6 23 331-353 254-281 (282)
83 COG0266 Nei Formamidopyrimidin 70.4 2.1 4.6E-05 41.6 1.2 25 329-353 243-272 (273)
84 TIGR00155 pqiA_fam integral me 69.5 3.3 7.1E-05 41.6 2.3 24 333-356 217-240 (403)
85 TIGR02605 CxxC_CxxC_SSSS putat 69.2 3.2 6.8E-05 29.7 1.6 22 333-354 7-34 (52)
86 COG1579 Zn-ribbon protein, pos 69.0 2.3 5E-05 40.7 1.1 24 331-354 197-229 (239)
87 PRK08665 ribonucleotide-diphos 69.0 3.4 7.5E-05 44.7 2.5 24 332-355 725-749 (752)
88 PF13421 Band_7_1: SPFH domain 68.4 5.1 0.00011 36.9 3.1 41 137-180 168-208 (211)
89 PF14369 zf-RING_3: zinc-finge 68.3 3.3 7.2E-05 28.9 1.5 25 332-356 3-31 (35)
90 COG1996 RPC10 DNA-directed RNA 68.2 2.1 4.5E-05 32.5 0.5 24 334-357 9-35 (49)
91 TIGR02419 C4_traR_proteo phage 68.0 3.1 6.8E-05 32.1 1.5 24 331-354 31-60 (63)
92 PRK13715 conjugal transfer pro 67.9 2.6 5.6E-05 33.6 1.0 24 331-354 34-63 (73)
93 PHA00080 DksA-like zinc finger 67.9 2.7 5.9E-05 33.3 1.1 24 331-354 31-60 (72)
94 TIGR02890 spore_yteA sporulati 66.2 2.2 4.8E-05 38.2 0.4 23 333-355 88-116 (159)
95 PF13719 zinc_ribbon_5: zinc-r 65.9 2.9 6.4E-05 29.0 0.9 23 333-355 4-34 (37)
96 PRK14890 putative Zn-ribbon RN 65.8 4.7 0.0001 31.8 2.1 25 331-355 7-34 (59)
97 CHL00174 accD acetyl-CoA carbo 65.8 2.3 5E-05 41.8 0.4 23 333-355 40-66 (296)
98 PF13005 zf-IS66: zinc-finger 64.8 3.2 7E-05 29.0 0.9 11 331-341 2-12 (47)
99 PLN02976 amine oxidase 64.3 4 8.6E-05 48.2 2.0 29 43-82 384-412 (1713)
100 COG1656 Uncharacterized conser 63.1 3 6.5E-05 38.3 0.6 11 331-341 97-107 (165)
101 PRK00415 rps27e 30S ribosomal 63.1 4.3 9.3E-05 31.9 1.4 31 326-356 2-40 (59)
102 PRK11019 hypothetical protein; 63.0 3 6.6E-05 34.6 0.6 25 331-355 36-66 (88)
103 PF01258 zf-dskA_traR: Prokary 61.9 2.1 4.6E-05 29.2 -0.4 23 332-354 4-32 (36)
104 PRK00762 hypA hydrogenase nick 61.5 4 8.6E-05 34.8 1.1 27 329-356 68-102 (124)
105 PF08792 A2L_zn_ribbon: A2L zi 61.2 4.1 8.9E-05 28.3 0.9 25 331-355 3-30 (33)
106 cd00729 rubredoxin_SM Rubredox 61.2 5.6 0.00012 27.4 1.6 24 333-356 4-28 (34)
107 PRK08579 anaerobic ribonucleos 60.8 6.4 0.00014 42.0 2.6 26 329-355 566-591 (625)
108 PF07191 zinc-ribbons_6: zinc- 60.6 2 4.3E-05 34.7 -0.9 21 334-356 20-40 (70)
109 PF10083 DUF2321: Uncharacteri 60.6 5.3 0.00011 36.7 1.7 34 309-342 44-79 (158)
110 PRK06386 replication factor A; 60.2 4.4 9.6E-05 40.7 1.3 21 332-355 237-257 (358)
111 PRK05978 hypothetical protein; 59.8 5.9 0.00013 35.6 1.8 25 332-356 34-62 (148)
112 PRK15103 paraquat-inducible me 59.5 6.5 0.00014 39.8 2.3 25 331-356 221-245 (419)
113 KOG2462 C2H2-type Zn-finger pr 59.5 53 0.0012 32.7 8.4 28 329-356 127-171 (279)
114 PF07295 DUF1451: Protein of u 59.5 4.4 9.5E-05 36.1 1.0 27 329-355 110-139 (146)
115 KOG4470 Proteasome activator s 59.4 7.5 0.00016 37.8 2.6 39 30-68 59-97 (246)
116 COG1096 Predicted RNA-binding 59.4 3.9 8.4E-05 38.3 0.7 24 332-355 150-174 (188)
117 PF13717 zinc_ribbon_4: zinc-r 59.2 4.4 9.6E-05 28.2 0.8 22 334-355 5-34 (36)
118 COG1998 RPS31 Ribosomal protei 59.1 5.2 0.00011 30.9 1.2 25 330-354 18-45 (51)
119 PRK01110 rpmF 50S ribosomal pr 57.9 4.7 0.0001 31.1 0.8 21 331-354 27-47 (60)
120 PRK07111 anaerobic ribonucleos 57.5 6.4 0.00014 42.6 2.0 25 328-354 677-701 (735)
121 TIGR00595 priA primosomal prot 57.2 6.5 0.00014 40.2 1.9 24 331-356 240-263 (505)
122 KOG0856 Predicted pilin-like t 57.0 5.2 0.00011 36.4 1.0 27 329-355 51-78 (146)
123 COG1198 PriA Primosomal protei 57.0 10 0.00022 41.5 3.3 23 331-355 462-484 (730)
124 PF03119 DNA_ligase_ZBD: NAD-d 56.7 3.5 7.7E-05 27.5 -0.0 18 333-350 1-21 (28)
125 PRK11032 hypothetical protein; 56.3 5.5 0.00012 36.2 1.1 20 72-91 4-23 (160)
126 PF08274 PhnA_Zn_Ribbon: PhnA 56.0 3.9 8.5E-05 28.1 0.1 22 333-354 4-27 (30)
127 cd04476 RPA1_DBD_C RPA1_DBD_C: 55.8 5.2 0.00011 34.3 0.8 23 334-356 37-61 (166)
128 PF02591 DUF164: Putative zinc 55.0 5.5 0.00012 29.3 0.7 23 332-354 23-54 (56)
129 COG4260 Membrane protease subu 53.4 6.7 0.00015 39.5 1.2 29 328-356 312-344 (345)
130 PRK14873 primosome assembly pr 53.4 8.1 0.00017 41.4 1.9 23 331-356 410-432 (665)
131 COG0333 RpmF Ribosomal protein 53.3 8.2 0.00018 30.1 1.5 25 329-355 25-49 (57)
132 PRK08271 anaerobic ribonucleos 53.1 9.9 0.00021 40.7 2.5 27 328-355 563-589 (623)
133 TIGR00354 polC DNA polymerase, 52.8 7.4 0.00016 44.2 1.6 22 332-356 626-647 (1095)
134 COG1110 Reverse gyrase [DNA re 52.7 5.4 0.00012 45.6 0.5 27 329-356 692-718 (1187)
135 COG2093 DNA-directed RNA polym 52.2 6.9 0.00015 31.4 0.9 24 331-355 4-27 (64)
136 TIGR03037 anthran_nbaC 3-hydro 51.9 6.8 0.00015 35.6 0.9 24 331-354 114-159 (159)
137 TIGR02487 NrdD anaerobic ribon 51.6 11 0.00024 39.6 2.5 27 328-355 521-547 (579)
138 PF03833 PolC_DP2: DNA polymer 50.9 5.1 0.00011 44.7 0.0 8 348-355 694-701 (900)
139 COG4306 Uncharacterized protei 50.8 8.7 0.00019 35.0 1.4 14 329-342 66-79 (160)
140 PF01529 zf-DHHC: DHHC palmito 50.5 8.6 0.00019 32.3 1.3 26 329-355 46-71 (174)
141 PF05876 Terminase_GpA: Phage 49.8 9.9 0.00021 39.6 1.8 8 334-341 203-210 (557)
142 PRK07218 replication factor A; 49.3 9.3 0.0002 39.1 1.6 21 332-355 298-318 (423)
143 PF14354 Lar_restr_allev: Rest 48.4 12 0.00027 27.3 1.7 24 331-354 3-37 (61)
144 PF03833 PolC_DP2: DNA polymer 48.3 5.9 0.00013 44.2 0.0 20 333-355 657-676 (900)
145 TIGR00354 polC DNA polymerase, 48.2 9.5 0.00021 43.4 1.5 29 329-357 1009-1039(1095)
146 PF04828 GFA: Glutathione-depe 48.2 4.8 0.0001 30.0 -0.5 10 347-356 49-58 (92)
147 PF03983 SHD1: SLA1 homology d 47.8 11 0.00023 30.5 1.3 40 142-182 28-68 (70)
148 PRK13264 3-hydroxyanthranilate 47.5 8.2 0.00018 35.7 0.8 25 331-355 120-166 (177)
149 PRK08351 DNA-directed RNA poly 46.9 11 0.00024 29.7 1.3 21 332-355 4-24 (61)
150 PRK08270 anaerobic ribonucleos 46.5 14 0.00031 39.5 2.5 26 329-356 624-649 (656)
151 PF13597 NRDD: Anaerobic ribon 46.2 5.7 0.00012 41.3 -0.5 25 329-355 489-513 (546)
152 PRK08332 ribonucleotide-diphos 45.2 10 0.00022 45.1 1.2 24 333-356 1706-1736(1740)
153 PF10013 DUF2256: Uncharacteri 45.1 10 0.00022 28.3 0.8 23 329-351 6-36 (42)
154 KOG1883 Cofactor required for 44.8 8 0.00017 44.8 0.4 21 65-85 1199-1219(1517)
155 TIGR00375 conserved hypothetic 44.8 10 0.00023 38.2 1.1 23 333-356 242-268 (374)
156 TIGR03831 YgiT_finger YgiT-typ 44.7 11 0.00024 25.6 0.9 17 326-342 27-43 (46)
157 TIGR02827 RNR_anaer_Bdell anae 44.5 15 0.00033 39.1 2.3 26 329-355 530-555 (586)
158 PF13453 zf-TFIIB: Transcripti 44.4 8.1 0.00018 27.0 0.2 21 334-354 2-27 (41)
159 PF11023 DUF2614: Protein of u 43.8 11 0.00024 33.2 0.9 25 331-356 69-95 (114)
160 COG1571 Predicted DNA-binding 43.7 13 0.00028 38.5 1.6 24 333-356 352-377 (421)
161 PRK14892 putative transcriptio 43.6 10 0.00022 32.1 0.7 26 331-356 20-52 (99)
162 PRK12366 replication factor A; 43.5 9.5 0.00021 40.4 0.6 24 332-355 533-557 (637)
163 PRK05580 primosome assembly pr 43.5 15 0.00031 39.1 2.0 23 332-356 409-431 (679)
164 KOG2463 Predicted RNA-binding 42.9 9.1 0.0002 39.1 0.4 24 333-356 244-267 (376)
165 COG0375 HybF Zn finger protein 42.9 9.1 0.0002 33.4 0.3 28 329-356 68-96 (115)
166 PF06827 zf-FPG_IleRS: Zinc fi 42.6 6.3 0.00014 25.8 -0.5 22 332-353 2-28 (30)
167 COG1503 eRF1 Peptide chain rel 42.6 13 0.00027 38.5 1.3 25 332-356 327-358 (411)
168 PRK06393 rpoE DNA-directed RNA 42.1 14 0.00029 29.6 1.1 22 331-355 5-26 (64)
169 PRK09710 lar restriction allev 41.0 15 0.00032 29.5 1.2 27 329-355 4-36 (64)
170 TIGR01405 polC_Gram_pos DNA po 40.6 22 0.00047 40.9 2.9 35 323-357 675-719 (1213)
171 PF13824 zf-Mss51: Zinc-finger 40.6 22 0.00048 27.7 2.0 23 333-355 1-23 (55)
172 COG1379 PHP family phosphoeste 40.5 8.6 0.00019 39.4 -0.2 23 334-356 249-275 (403)
173 cd01675 RNR_III Class III ribo 40.4 18 0.00039 37.7 2.1 22 333-355 520-541 (555)
174 COG1997 RPL43A Ribosomal prote 40.3 15 0.00033 31.1 1.2 25 333-357 37-64 (89)
175 PF09538 FYDLN_acid: Protein o 39.9 21 0.00045 30.4 2.0 24 321-344 7-39 (108)
176 PF14205 Cys_rich_KTR: Cystein 39.6 17 0.00038 28.5 1.4 23 333-355 6-37 (55)
177 PRK09263 anaerobic ribonucleos 39.5 23 0.00049 38.4 2.7 27 329-355 639-668 (711)
178 KOG0257 Kynurenine aminotransf 39.4 7.1 0.00015 40.4 -1.0 27 74-100 212-240 (420)
179 COG3024 Uncharacterized protei 39.1 22 0.00047 28.8 1.8 15 328-342 4-18 (65)
180 PHA00626 hypothetical protein 39.0 16 0.00034 29.1 1.1 23 333-355 2-32 (59)
181 KOG3623 Homeobox transcription 38.7 16 0.00034 41.0 1.4 28 329-356 278-319 (1007)
182 PF14569 zf-UDP: Zinc-binding 38.7 12 0.00025 31.3 0.3 22 334-355 31-60 (80)
183 COG0846 SIR2 NAD-dependent pro 38.6 15 0.00032 35.2 1.0 24 332-355 123-155 (250)
184 COG1328 NrdD Oxygen-sensitive 38.6 19 0.00042 39.3 2.0 26 329-355 639-664 (700)
185 PF07105 DUF1367: Protein of u 38.5 90 0.002 29.7 6.1 92 75-180 71-164 (196)
186 COG1579 Zn-ribbon protein, pos 38.5 16 0.00034 35.2 1.2 13 329-341 219-231 (239)
187 PRK02935 hypothetical protein; 38.5 17 0.00037 31.9 1.3 26 331-356 70-96 (110)
188 TIGR03655 anti_R_Lar restricti 37.8 17 0.00036 26.7 1.0 24 332-355 2-35 (53)
189 KOG2582 COP9 signalosome, subu 37.4 55 0.0012 34.2 4.9 75 76-160 276-357 (422)
190 COG5273 Uncharacterized protei 37.3 19 0.00042 35.1 1.6 28 327-355 105-132 (309)
191 PRK14715 DNA polymerase II lar 37.1 18 0.00038 42.7 1.5 20 334-356 677-696 (1627)
192 PF03884 DUF329: Domain of unk 36.7 11 0.00024 29.2 -0.1 20 332-351 3-26 (57)
193 COG4306 Uncharacterized protei 36.3 21 0.00046 32.6 1.6 12 346-357 68-79 (160)
194 PRK00448 polC DNA polymerase I 35.2 29 0.00064 40.6 2.8 35 323-357 900-944 (1437)
195 COG2023 RPR2 RNase P subunit R 35.0 14 0.00031 31.9 0.3 32 325-356 50-92 (105)
196 PF13174 TPR_6: Tetratricopept 34.7 29 0.00062 21.1 1.6 17 103-119 17-33 (33)
197 PRK07217 replication factor A; 34.1 23 0.0005 35.4 1.6 22 331-355 188-211 (311)
198 PLN00209 ribosomal protein S27 34.0 18 0.00039 30.5 0.7 31 326-356 27-65 (86)
199 PRK00241 nudC NADH pyrophospha 34.0 18 0.00039 34.2 0.8 12 345-356 98-109 (256)
200 PF09855 DUF2082: Nucleic-acid 34.0 17 0.00038 28.6 0.6 8 347-354 37-44 (64)
201 PF12596 Tnp_P_element_C: 87kD 34.0 25 0.00053 30.4 1.5 27 101-127 78-105 (106)
202 smart00109 C1 Protein kinase C 34.0 37 0.0008 22.7 2.2 26 330-355 10-36 (49)
203 PF09420 Nop16: Ribosome bioge 33.8 21 0.00045 31.5 1.1 30 162-196 112-141 (164)
204 PRK00504 rpmG 50S ribosomal pr 33.7 17 0.00038 27.4 0.5 23 333-355 9-43 (50)
205 PLN02638 cellulose synthase A 33.5 21 0.00045 40.9 1.3 22 334-355 39-68 (1079)
206 PF06906 DUF1272: Protein of u 33.5 11 0.00024 29.7 -0.6 23 332-357 30-52 (57)
207 KOG0162 Myosin class I heavy c 33.4 31 0.00067 38.9 2.5 32 173-204 854-885 (1106)
208 COG5257 GCD11 Translation init 33.1 28 0.00061 36.0 2.0 28 329-356 53-82 (415)
209 KOG3084 NADH pyrophosphatase I 32.9 24 0.00052 35.9 1.5 14 329-342 148-161 (345)
210 COG1773 Rubredoxin [Energy pro 31.6 26 0.00056 27.3 1.2 9 347-355 37-45 (55)
211 PRK14715 DNA polymerase II lar 31.5 25 0.00054 41.6 1.5 26 331-357 1541-1568(1627)
212 KOG3362 Predicted BBOX Zn-fing 31.5 17 0.00037 33.4 0.2 24 329-356 116-139 (156)
213 PLN02569 threonine synthase 31.4 27 0.00058 36.1 1.6 24 332-356 50-74 (484)
214 PF01396 zf-C4_Topoisom: Topoi 31.4 19 0.00041 25.4 0.4 16 332-347 2-17 (39)
215 PRK14704 anaerobic ribonucleos 30.9 34 0.00073 36.7 2.3 25 329-355 557-581 (618)
216 PF09334 tRNA-synt_1g: tRNA sy 30.5 21 0.00046 35.4 0.7 23 72-94 16-38 (391)
217 PHA02768 hypothetical protein; 30.4 27 0.00059 27.1 1.1 23 333-355 7-40 (55)
218 PLN02189 cellulose synthase 30.2 27 0.00059 39.9 1.5 25 331-355 51-85 (1040)
219 PRK12267 methionyl-tRNA synthe 30.1 26 0.00057 36.6 1.3 27 330-356 124-153 (648)
220 COG2816 NPY1 NTP pyrophosphohy 29.7 24 0.00051 34.9 0.9 13 344-356 109-121 (279)
221 COG3791 Uncharacterized conser 29.7 22 0.00048 30.4 0.6 11 346-356 69-79 (133)
222 PTZ00083 40S ribosomal protein 29.4 24 0.00051 29.7 0.7 31 326-356 26-64 (85)
223 PF12674 Zn_ribbon_2: Putative 29.3 19 0.0004 29.2 0.1 11 332-342 1-11 (81)
224 PRK04338 N(2),N(2)-dimethylgua 29.2 28 0.00061 34.7 1.3 36 161-197 131-167 (382)
225 KOG3084 NADH pyrophosphatase I 29.1 24 0.00051 36.0 0.8 11 346-356 150-160 (345)
226 PRK04136 rpl40e 50S ribosomal 29.0 40 0.00086 25.9 1.8 26 330-356 13-38 (48)
227 PF00301 Rubredoxin: Rubredoxi 28.7 21 0.00045 26.6 0.2 7 349-355 37-43 (47)
228 COG4068 Uncharacterized protei 28.6 28 0.00061 28.0 0.9 24 329-353 6-30 (64)
229 PLN02915 cellulose synthase A 28.4 30 0.00064 39.6 1.4 22 334-355 37-66 (1044)
230 PF06221 zf-C2HC5: Putative zi 28.4 37 0.0008 26.4 1.5 27 331-357 18-46 (57)
231 COG2260 Predicted Zn-ribbon RN 28.3 31 0.00067 27.4 1.1 21 332-355 6-26 (59)
232 COG0272 Lig NAD-dependent DNA 28.3 41 0.0009 36.8 2.4 27 329-355 402-434 (667)
233 PF01927 Mut7-C: Mut7-C RNAse 27.9 26 0.00057 30.2 0.7 8 334-341 94-101 (147)
234 TIGR00308 TRM1 tRNA(guanine-26 27.7 37 0.0008 34.0 1.8 25 332-356 234-262 (374)
235 PRK05452 anaerobic nitric oxid 27.6 29 0.00062 35.5 1.1 28 329-356 422-468 (479)
236 TIGR03847 conserved hypothetic 27.4 41 0.00088 31.6 1.9 21 329-350 154-174 (177)
237 KOG2932 E3 ubiquitin ligase in 27.4 24 0.00051 36.2 0.4 11 331-341 90-100 (389)
238 PF10263 SprT-like: SprT-like 26.9 23 0.00049 29.7 0.2 24 334-357 126-154 (157)
239 smart00401 ZnF_GATA zinc finge 26.7 53 0.0011 24.4 2.1 25 331-355 3-34 (52)
240 PLN02436 cellulose synthase A 26.4 35 0.00075 39.3 1.5 25 331-355 53-87 (1094)
241 PF09139 Mmp37: Mitochondrial 26.1 1.3E+02 0.0028 30.3 5.2 93 56-149 176-298 (330)
242 PF10122 Mu-like_Com: Mu-like 25.8 25 0.00053 27.2 0.2 23 333-355 6-33 (51)
243 PRK05417 glutathione-dependent 25.6 30 0.00066 32.1 0.8 9 348-356 95-103 (191)
244 KOG0712 Molecular chaperone (D 25.5 40 0.00086 34.1 1.6 24 107-142 23-47 (337)
245 PRK05508 methionine sulfoxide 25.5 42 0.00091 29.6 1.6 24 332-355 34-57 (119)
246 PF14260 zf-C4pol: C4-type zin 25.3 50 0.0011 25.1 1.8 22 334-355 1-22 (73)
247 cd00202 ZnF_GATA Zinc finger D 25.2 30 0.00064 26.1 0.5 23 333-355 1-30 (54)
248 PF13388 DUF4106: Protein of u 24.9 1.8E+02 0.0038 30.1 5.9 35 226-268 189-223 (422)
249 cd00817 ValRS_core catalytic c 24.5 35 0.00076 33.5 1.0 24 331-356 140-163 (382)
250 COG2331 Uncharacterized protei 24.4 23 0.0005 29.7 -0.2 22 334-355 15-42 (82)
251 cd01410 SIRT7 SIRT7: Eukaryoti 24.3 76 0.0017 28.9 3.1 54 303-356 67-130 (206)
252 PRK06556 vitamin B12-dependent 24.3 39 0.00084 38.2 1.4 27 329-355 922-949 (953)
253 PF01408 GFO_IDH_MocA: Oxidore 24.1 1.2E+02 0.0027 23.5 3.8 45 139-185 54-115 (120)
254 PRK00085 recO DNA repair prote 23.9 42 0.0009 30.2 1.3 23 331-353 149-177 (247)
255 KOG2807 RNA polymerase II tran 23.9 40 0.00087 34.7 1.3 10 332-341 277-286 (378)
256 PRK04011 peptide chain release 23.6 46 0.00099 33.7 1.6 24 333-356 330-360 (411)
257 TIGR02820 formald_GSH S-(hydro 23.5 35 0.00075 31.6 0.7 10 347-356 90-99 (182)
258 PF01485 IBR: IBR domain; Int 23.4 52 0.0011 23.2 1.5 11 331-341 18-30 (64)
259 PRK00481 NAD-dependent deacety 22.7 62 0.0014 29.8 2.2 18 151-169 15-32 (242)
260 PRK00750 lysK lysyl-tRNA synth 22.6 32 0.0007 35.5 0.4 25 331-355 175-208 (510)
261 PRK12268 methionyl-tRNA synthe 22.6 45 0.00098 33.9 1.4 11 331-341 125-135 (556)
262 PF14206 Cys_rich_CPCC: Cystei 22.5 49 0.0011 27.1 1.3 21 334-354 4-28 (78)
263 COG1734 DksA DnaK suppressor p 22.3 27 0.00059 30.4 -0.2 23 333-355 82-110 (120)
264 smart00532 LIGANc Ligase N fam 22.3 55 0.0012 33.7 1.9 26 330-355 398-428 (441)
265 PF14311 DUF4379: Domain of un 22.1 54 0.0012 23.9 1.4 20 333-352 30-55 (55)
266 PLN02400 cellulose synthase 21.9 46 0.001 38.3 1.4 22 334-355 58-87 (1085)
267 COG2126 RPL37A Ribosomal prote 21.9 43 0.00093 26.9 0.8 26 331-356 16-41 (61)
268 PF10235 Cript: Microtubule-as 21.8 46 0.00099 28.1 1.0 22 331-352 44-65 (90)
269 PRK08402 replication factor A; 21.8 39 0.00085 33.9 0.8 23 332-354 213-238 (355)
270 COG5349 Uncharacterized protei 21.6 38 0.00082 30.4 0.6 24 333-356 23-50 (126)
271 COG2176 PolC DNA polymerase II 21.6 63 0.0014 38.1 2.4 34 324-357 907-950 (1444)
272 PHA00732 hypothetical protein 21.5 66 0.0014 25.9 1.8 22 334-355 4-36 (79)
273 PRK11893 methionyl-tRNA synthe 21.1 64 0.0014 32.1 2.1 27 330-356 121-151 (511)
274 PRK00418 DNA gyrase inhibitor; 21.0 80 0.0017 25.1 2.2 21 331-351 6-30 (62)
275 TIGR03676 aRF1/eRF1 peptide ch 20.8 58 0.0012 33.0 1.7 24 333-356 322-352 (403)
276 PF01780 Ribosomal_L37ae: Ribo 20.8 16 0.00035 30.7 -1.8 25 333-357 37-64 (90)
277 PF13408 Zn_ribbon_recom: Reco 20.4 37 0.00079 23.9 0.2 13 330-342 4-16 (58)
278 PF02146 SIR2: Sir2 family; I 20.4 35 0.00076 29.6 0.1 25 332-356 106-139 (178)
279 COG2401 ABC-type ATPase fused 20.3 47 0.001 35.7 1.0 24 332-356 131-154 (593)
280 PF04809 HupH_C: HupH hydrogen 20.1 64 0.0014 27.8 1.6 25 167-191 35-59 (120)
281 PF04216 FdhE: Protein involve 20.1 29 0.00064 32.8 -0.5 22 333-355 199-220 (290)
No 1
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=98.31 E-value=2.7e-07 Score=59.04 Aligned_cols=23 Identities=39% Similarity=1.091 Sum_probs=20.7
Q ss_pred CCCcCCCCCCCCCCCCCcccCCcC
Q 018197 333 FCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~~~~AKFCpECGtKr 356 (359)
||++||+++. ++++||++||+++
T Consensus 1 ~Cp~CG~~~~-~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIE-DDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCC-CcCcchhhhCCcC
Confidence 7999999997 4699999999975
No 2
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=98.24 E-value=5.2e-07 Score=58.42 Aligned_cols=25 Identities=44% Similarity=1.054 Sum_probs=21.4
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
.++|++||+.+ ..+++||+.||+++
T Consensus 2 ~~~Cp~Cg~~~-~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEI-DPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcC-CcccccChhhCCCC
Confidence 47899999965 46799999999985
No 3
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=97.67 E-value=2.1e-05 Score=76.94 Aligned_cols=54 Identities=19% Similarity=0.156 Sum_probs=43.3
Q ss_pred hhhhhhhccchhhhHhhheeEeEEEeecceeeccCCCCChhhHHHHHHHhcccccccccc
Q 018197 130 ATSLETRTRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTGRNEVAISAQ 189 (359)
Q Consensus 130 Ats~etrt~fpelv~~EekrvrfvVVnGl~IVE~p~Nlp~eDqewfkRLtgr~EVai~g~ 189 (359)
|.++|--..+.|+++..-+++|+.|+++- |- ++|+|+|-|.-|++ |+--++.||
T Consensus 188 an~~elsk~m~e~Ld~q~~q~Gm~v~sfq--va-Sisypde~Q~lin~---r~s~~M~gD 241 (345)
T COG4260 188 ANQMELSKYMAEVLDEQWTQYGMAVDSFQ--VA-SISYPDESQALINM---RNSGAMLGD 241 (345)
T ss_pred hhHHHHHHHHHHHHhHHHHhhCceEeeEE--EE-EecCcHHHHHHHHh---hcccccccC
Confidence 34555556778999999999999999988 77 89999999988776 444677776
No 4
>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=97.16 E-value=0.0002 Score=47.28 Aligned_cols=24 Identities=46% Similarity=0.996 Sum_probs=20.6
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 332 KFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
|-||+||+.++. .+|+||.||...
T Consensus 1 K~CP~C~~~V~~-~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPE-SAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchh-hcCcCCCCCCCC
Confidence 679999999875 599999999754
No 5
>PF12773 DZR: Double zinc ribbon
Probab=96.84 E-value=0.0007 Score=47.99 Aligned_cols=25 Identities=44% Similarity=1.161 Sum_probs=11.3
Q ss_pred CCCCCcCCCCCC--CCCCCCCcccCCc
Q 018197 331 AKFCDECGAPYL--RETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~--~~~AKFCpECGtK 355 (359)
++||+.||+++. ....++|+.||+.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCC
Confidence 445555555544 3333444444443
No 6
>PF12773 DZR: Double zinc ribbon
Probab=96.52 E-value=0.0018 Score=45.86 Aligned_cols=25 Identities=40% Similarity=0.990 Sum_probs=21.1
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCcccC
Q 018197 328 ASPAKFCDECGAPYLRETSKFCSECG 353 (359)
Q Consensus 328 ~~~sKFCpeCGt~l~~~~AKFCpECG 353 (359)
....++|+.||+.+. .+++||++||
T Consensus 26 ~~~~~~C~~Cg~~~~-~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENP-PNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCc-CCcCccCccc
Confidence 455789999999965 5699999998
No 7
>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=96.01 E-value=0.0023 Score=42.80 Aligned_cols=26 Identities=35% Similarity=0.879 Sum_probs=17.6
Q ss_pred CCCCCCcCCCCC---CCCCCCCCcccCCc
Q 018197 330 PAKFCDECGAPY---LRETSKFCSECGVK 355 (359)
Q Consensus 330 ~sKFCpeCGt~l---~~~~AKFCpECGtK 355 (359)
+.+||+.||.++ ..+|++-|+.||..
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 468999999997 45689999999963
No 8
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.76 E-value=0.0044 Score=61.46 Aligned_cols=28 Identities=18% Similarity=0.364 Sum_probs=24.8
Q ss_pred CCCCCcCCCCCC-CCCCCCCcccCCcCcC
Q 018197 331 AKFCDECGAPYL-RETSKFCSECGVKRLG 358 (359)
Q Consensus 331 sKFCpeCGt~l~-~~~AKFCpECGtKr~~ 358 (359)
.+|||+||..+. ..|+|||++|+..++.
T Consensus 322 ~~~Cp~cg~r~~~~~~ak~~~~c~~r~~i 350 (351)
T KOG3940|consen 322 YVQCPHCGRRFNEQAAAKHIPKCVNRVHI 350 (351)
T ss_pred cccCccccccchHHHHHhhcccccccccc
Confidence 599999999997 6799999999988653
No 9
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=95.41 E-value=0.011 Score=41.94 Aligned_cols=24 Identities=33% Similarity=0.928 Sum_probs=18.2
Q ss_pred CCCCcCCCCCCCC-C----CCCCcccCCc
Q 018197 332 KFCDECGAPYLRE-T----SKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~-~----AKFCpECGtK 355 (359)
+|||+||..+... + -..|+.||..
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCe
Confidence 6999999988433 2 3569999975
No 10
>PRK00420 hypothetical protein; Validated
Probab=95.37 E-value=0.0084 Score=51.32 Aligned_cols=26 Identities=27% Similarity=0.675 Sum_probs=22.7
Q ss_pred CCCCCcCCCCCC--CCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYL--RETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~--~~~AKFCpECGtKr 356 (359)
+.-||.||+++. ..+..|||.||...
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCee
Confidence 588999999996 57899999999864
No 11
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=94.91 E-value=0.0069 Score=42.27 Aligned_cols=23 Identities=43% Similarity=1.190 Sum_probs=12.4
Q ss_pred CCCCcCCCCC---CCC----CCCCCcccCC
Q 018197 332 KFCDECGAPY---LRE----TSKFCSECGV 354 (359)
Q Consensus 332 KFCpeCGt~l---~~~----~AKFCpECGt 354 (359)
|||+.||.++ +++ .-.+|+.||.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 7999999998 221 2568999985
No 12
>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=93.81 E-value=0.046 Score=46.24 Aligned_cols=27 Identities=33% Similarity=0.840 Sum_probs=20.2
Q ss_pred CCCC-CCcCCCCC--CCCCCCCCcccCCcC
Q 018197 330 PAKF-CDECGAPY--LRETSKFCSECGVKR 356 (359)
Q Consensus 330 ~sKF-CpeCGt~l--~~~~AKFCpECGtKr 356 (359)
+.|. |++||+++ +...-.-||.||+-.
T Consensus 7 GtKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred CCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 4454 99999997 333567799999864
No 13
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=93.29 E-value=0.031 Score=49.27 Aligned_cols=25 Identities=44% Similarity=1.162 Sum_probs=20.9
Q ss_pred CCCCCcCCCCCCC-CCCCCCcccCCc
Q 018197 331 AKFCDECGAPYLR-ETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~~-~~AKFCpECGtK 355 (359)
++-||.||+++.. .|--|||-||.+
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCCce
Confidence 6789999999964 467799999965
No 14
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.14 E-value=0.04 Score=39.21 Aligned_cols=24 Identities=33% Similarity=0.703 Sum_probs=18.4
Q ss_pred CCcCCCCCC---CCCCCCCcccCCcCc
Q 018197 334 CDECGAPYL---RETSKFCSECGVKRL 357 (359)
Q Consensus 334 CpeCGt~l~---~~~AKFCpECGtKr~ 357 (359)
|++||+.+. ......||.||.++.
T Consensus 6 C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 6 CARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred CCCCCCEEEECCCCCceECCCCCCeEE
Confidence 999999872 222689999999853
No 15
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=92.62 E-value=0.065 Score=54.66 Aligned_cols=27 Identities=41% Similarity=0.966 Sum_probs=22.1
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
...++|++||+.+. ..+|||++||.++
T Consensus 590 ~~~~~~~~~~~~~~-~~~~f~~~~g~~~ 616 (616)
T PRK07418 590 AELIYCSNCGAKNP-STHRFCPECGTKL 616 (616)
T ss_pred cCcccCCCCCCcCc-cccccchhhCCCC
Confidence 35678999999854 5699999999875
No 16
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=92.41 E-value=0.088 Score=59.77 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=15.8
Q ss_pred CCCcCCCCCCCC--CCCCCcccCCcCc
Q 018197 333 FCDECGAPYLRE--TSKFCSECGVKRL 357 (359)
Q Consensus 333 FCpeCGt~l~~~--~AKFCpECGtKr~ 357 (359)
+|+.||+.+... ++.|||.||+++.
T Consensus 694 ~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 694 VCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred eCccCCCccCCCccccccCCCCCCccc
Confidence 355555554322 3779999998864
No 17
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=92.03 E-value=0.075 Score=51.70 Aligned_cols=27 Identities=26% Similarity=0.784 Sum_probs=23.5
Q ss_pred CCCCCCCcCCCCC---CCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPY---LRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l---~~~~AKFCpECGtK 355 (359)
...+||+.||+++ ..++++-|+.||..
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCc
Confidence 6689999999998 35689999999986
No 18
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=91.72 E-value=0.088 Score=49.32 Aligned_cols=27 Identities=30% Similarity=0.815 Sum_probs=22.6
Q ss_pred CCCCCCCcCCCCCC---CCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYL---RETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~---~~~AKFCpECGtK 355 (359)
...+||+.||+++. ....+.|+.||..
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCCE
Confidence 66899999999973 4568999999965
No 19
>PRK04023 DNA polymerase II large subunit; Validated
Probab=91.47 E-value=0.11 Score=58.10 Aligned_cols=39 Identities=13% Similarity=0.158 Sum_probs=17.2
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhccccchhhhhHHHHhh
Q 018197 67 LPLMYVANMYETLVNDVNLRLASFNGIREKTIGVALEAA 105 (359)
Q Consensus 67 LPLmyvANlyetlv~~vn~rlasl~g~~ekt~gvaleaa 105 (359)
+|--|+---|+..+...+.......++-+-|.--||+.|
T Consensus 420 ~Ps~y~~EWW~qe~~~~~~~~~~~~~l~~p~~~eA~~~s 458 (1121)
T PRK04023 420 LPSSYCEEWWIQELEAAGAEYEPEFDLENPSQEEALKIS 458 (1121)
T ss_pred CCccccHHHHHHHHHhcccccCccccccCCCHHHHHHHH
Confidence 444455444444443333333223333344555666543
No 20
>PRK04023 DNA polymerase II large subunit; Validated
Probab=90.94 E-value=0.12 Score=57.66 Aligned_cols=23 Identities=26% Similarity=0.652 Sum_probs=11.2
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
.+||+.||+... ...||+||.+.
T Consensus 651 i~fCP~CG~~~~---~y~CPKCG~El 673 (1121)
T PRK04023 651 VYRCPRCGIEVE---EDECEKCGREP 673 (1121)
T ss_pred ceeCccccCcCC---CCcCCCCCCCC
Confidence 445555555432 24455555553
No 21
>PRK12496 hypothetical protein; Provisional
Probab=90.81 E-value=0.15 Score=45.33 Aligned_cols=25 Identities=28% Similarity=0.691 Sum_probs=19.9
Q ss_pred CCCCcCCCCCCC-CCCCCCcccCCcC
Q 018197 332 KFCDECGAPYLR-ETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~-~~AKFCpECGtKr 356 (359)
+.|+.||..+.. ....|||.||.++
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChh
Confidence 349999999964 2468999999985
No 22
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.79 E-value=0.1 Score=33.53 Aligned_cols=13 Identities=54% Similarity=1.290 Sum_probs=11.3
Q ss_pred CCCCCCCcCCCCC
Q 018197 329 SPAKFCDECGAPY 341 (359)
Q Consensus 329 ~~sKFCpeCGt~l 341 (359)
.+++||+.||+++
T Consensus 11 ~~~~fC~~CG~~l 23 (23)
T PF13240_consen 11 DDAKFCPNCGTPL 23 (23)
T ss_pred CcCcchhhhCCcC
Confidence 5689999999975
No 23
>PRK12495 hypothetical protein; Provisional
Probab=90.59 E-value=0.12 Score=49.14 Aligned_cols=27 Identities=37% Similarity=0.971 Sum_probs=22.5
Q ss_pred CCCCCCcCCCCCCC-CCCCCCcccCCcC
Q 018197 330 PAKFCDECGAPYLR-ETSKFCSECGVKR 356 (359)
Q Consensus 330 ~sKFCpeCGt~l~~-~~AKFCpECGtKr 356 (359)
..++|+.||.+++. +|..||+.|+...
T Consensus 41 sa~hC~~CG~PIpa~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 41 TNAHCDECGDPIFRHDGQEFCPTCQQPV 68 (226)
T ss_pred chhhcccccCcccCCCCeeECCCCCCcc
Confidence 37889999999963 4789999999763
No 24
>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=90.55 E-value=0.14 Score=37.17 Aligned_cols=23 Identities=30% Similarity=1.152 Sum_probs=19.5
Q ss_pred CCCCCcCCCCCC--CCCCCCCcccC
Q 018197 331 AKFCDECGAPYL--RETSKFCSECG 353 (359)
Q Consensus 331 sKFCpeCGt~l~--~~~AKFCpECG 353 (359)
+..||.||.++. ..+..||+.|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCCCEECCCCC
Confidence 678999999984 45788999997
No 25
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=90.39 E-value=0.11 Score=33.61 Aligned_cols=13 Identities=54% Similarity=1.124 Sum_probs=11.4
Q ss_pred CCCCCCCcCCCCC
Q 018197 329 SPAKFCDECGAPY 341 (359)
Q Consensus 329 ~~sKFCpeCGt~l 341 (359)
.+.+||+.||++|
T Consensus 14 ~~~~fC~~CG~~L 26 (26)
T PF13248_consen 14 PDAKFCPNCGAKL 26 (26)
T ss_pred cccccChhhCCCC
Confidence 5689999999985
No 26
>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=90.08 E-value=0.086 Score=36.61 Aligned_cols=24 Identities=33% Similarity=0.905 Sum_probs=15.8
Q ss_pred CCCCcCCCCCCCC----CCCCCcccCCc
Q 018197 332 KFCDECGAPYLRE----TSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~----~AKFCpECGtK 355 (359)
+|||+||.-|.+. ....|..||..
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCc
Confidence 7999999998322 12259999864
No 27
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=89.85 E-value=0.16 Score=57.72 Aligned_cols=22 Identities=27% Similarity=0.819 Sum_probs=10.7
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCc
Q 018197 332 KFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtK 355 (359)
+||++||++... .-+||.||.+
T Consensus 680 ~fCP~CGs~te~--vy~CPsCGae 701 (1337)
T PRK14714 680 NRCPDCGTHTEP--VYVCPDCGAE 701 (1337)
T ss_pred ccCcccCCcCCC--ceeCccCCCc
Confidence 355555555422 1255555554
No 28
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.35 E-value=0.18 Score=36.78 Aligned_cols=24 Identities=38% Similarity=0.823 Sum_probs=19.1
Q ss_pred CCcCCCCCC--CCCCCCCcccCCcCc
Q 018197 334 CDECGAPYL--RETSKFCSECGVKRL 357 (359)
Q Consensus 334 CpeCGt~l~--~~~AKFCpECGtKr~ 357 (359)
|.+||+.+. ..+.--||+||.+++
T Consensus 5 C~~Cg~~~~~~~~~~irC~~CG~rIl 30 (44)
T smart00659 5 CGECGRENEIKSKDVVRCRECGYRIL 30 (44)
T ss_pred CCCCCCEeecCCCCceECCCCCceEE
Confidence 999999873 235788999998864
No 29
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=89.13 E-value=0.21 Score=37.24 Aligned_cols=26 Identities=31% Similarity=0.732 Sum_probs=19.4
Q ss_pred CCCCCCcCCC-CC-CCCCCCCCcccCCc
Q 018197 330 PAKFCDECGA-PY-LRETSKFCSECGVK 355 (359)
Q Consensus 330 ~sKFCpeCGt-~l-~~~~AKFCpECGtK 355 (359)
..+|||.||. -+ ...+..-|..||..
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGYT 46 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCCE
Confidence 3679999999 44 33457789999964
No 30
>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=88.76 E-value=0.16 Score=34.40 Aligned_cols=24 Identities=21% Similarity=0.614 Sum_probs=17.2
Q ss_pred CCcCCCCCC------C--CCCCCCcccCCcCc
Q 018197 334 CDECGAPYL------R--ETSKFCSECGVKRL 357 (359)
Q Consensus 334 CpeCGt~l~------~--~~AKFCpECGtKr~ 357 (359)
||+||+.+- . ...-.||.||+.+.
T Consensus 5 CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 5 CPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred CCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 999999761 1 11248999998764
No 31
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.78 E-value=0.33 Score=38.12 Aligned_cols=25 Identities=32% Similarity=0.937 Sum_probs=16.0
Q ss_pred CCCC-CCcCCCCCC--------CCCCCCCcccCC
Q 018197 330 PAKF-CDECGAPYL--------RETSKFCSECGV 354 (359)
Q Consensus 330 ~sKF-CpeCGt~l~--------~~~AKFCpECGt 354 (359)
.++| ||+||+.++ ....--||+||.
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence 4666 888888732 233556888875
No 32
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=87.78 E-value=0.23 Score=41.70 Aligned_cols=27 Identities=15% Similarity=0.423 Sum_probs=19.6
Q ss_pred CCCCCCCcCCCCCCCC-CCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRE-TSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~-~AKFCpECGtK 355 (359)
+..-+|..||...... .-..||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 4456799999887554 33349999975
No 33
>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=87.58 E-value=0.16 Score=39.42 Aligned_cols=25 Identities=40% Similarity=0.962 Sum_probs=20.4
Q ss_pred CCCCCCcCCCCCCCCCCCCCc-ccCCc
Q 018197 330 PAKFCDECGAPYLRETSKFCS-ECGVK 355 (359)
Q Consensus 330 ~sKFCpeCGt~l~~~~AKFCp-ECGtK 355 (359)
+-|-|+.||++++. +-.||+ +|+..
T Consensus 2 ~HkHC~~CG~~Ip~-~~~fCS~~C~~~ 27 (59)
T PF09889_consen 2 PHKHCPVCGKPIPP-DESFCSPKCREE 27 (59)
T ss_pred CCCcCCcCCCcCCc-chhhhCHHHHHH
Confidence 35779999999985 499995 99865
No 34
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=87.53 E-value=0.26 Score=42.76 Aligned_cols=24 Identities=29% Similarity=0.978 Sum_probs=20.8
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
+.-|.+||.-+.++ ..+||.||.+
T Consensus 29 g~kC~~CG~v~~PP-r~~Cp~C~~~ 52 (140)
T COG1545 29 GTKCKKCGRVYFPP-RAYCPKCGSE 52 (140)
T ss_pred EEEcCCCCeEEcCC-cccCCCCCCC
Confidence 45699999999766 8999999988
No 35
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=87.21 E-value=0.27 Score=41.50 Aligned_cols=32 Identities=16% Similarity=0.425 Sum_probs=22.2
Q ss_pred cCCCCCCCCCCcCCCCCCCC-CCCC-CcccCCcC
Q 018197 325 VMPASPAKFCDECGAPYLRE-TSKF-CSECGVKR 356 (359)
Q Consensus 325 i~p~~~sKFCpeCGt~l~~~-~AKF-CpECGtKr 356 (359)
+---+..-+|..||...... ...+ ||.||...
T Consensus 65 Ie~vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 65 IVDEKVELECKDCSHVFKPNALDYGVCEKCHSKN 98 (117)
T ss_pred EEecCCEEEhhhCCCccccCCccCCcCcCCCCCc
Confidence 33334556799999887554 3455 99999863
No 36
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.15 E-value=0.34 Score=42.94 Aligned_cols=28 Identities=32% Similarity=0.611 Sum_probs=22.4
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 326 MPASPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 326 ~p~~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
.|..+++-|+.||. .....-+||.||..
T Consensus 304 ~~~~tS~~C~~cg~--~~~r~~~C~~cg~~ 331 (364)
T COG0675 304 PPYYTSKTCPCCGH--LSGRLFKCPRCGFV 331 (364)
T ss_pred CCCCCcccccccCC--ccceeEECCCCCCe
Confidence 35788999999999 33345689999986
No 37
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=87.01 E-value=0.23 Score=34.77 Aligned_cols=10 Identities=50% Similarity=1.192 Sum_probs=4.8
Q ss_pred CCCcccCCcC
Q 018197 347 KFCSECGVKR 356 (359)
Q Consensus 347 KFCpECGtKr 356 (359)
||||+||.++
T Consensus 1 kfC~~CG~~l 10 (34)
T PF14803_consen 1 KFCPQCGGPL 10 (34)
T ss_dssp -B-TTT--B-
T ss_pred CccccccChh
Confidence 8999999986
No 38
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.67 E-value=0.31 Score=37.52 Aligned_cols=25 Identities=28% Similarity=0.731 Sum_probs=20.1
Q ss_pred CCCCCcCCCCCC-CCCCCCCcccCCc
Q 018197 331 AKFCDECGAPYL-RETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~-~~~AKFCpECGtK 355 (359)
..-|+.||.++. .+..-.||+||++
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAP 30 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCc
Confidence 456999999984 5668899999987
No 39
>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=86.29 E-value=0.32 Score=40.84 Aligned_cols=28 Identities=18% Similarity=0.332 Sum_probs=20.4
Q ss_pred CCCCCCCcCCCCCCCCC-CCCCcccCCcC
Q 018197 329 SPAKFCDECGAPYLRET-SKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~-AKFCpECGtKr 356 (359)
+..-+|..||..+.... ..-||.||...
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 68 PVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 44567999998886543 44499999864
No 40
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=85.82 E-value=0.4 Score=33.21 Aligned_cols=24 Identities=42% Similarity=0.841 Sum_probs=17.6
Q ss_pred CCcCCCCCC--CCCCCCCcccCCcCc
Q 018197 334 CDECGAPYL--RETSKFCSECGVKRL 357 (359)
Q Consensus 334 CpeCGt~l~--~~~AKFCpECGtKr~ 357 (359)
|.+||+... ...+--|++||.+++
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECGHRIL 28 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS-SEE
T ss_pred CCcCCCeeEcCCCCcEECCcCCCeEE
Confidence 889999872 334678999998865
No 41
>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=85.81 E-value=0.54 Score=31.71 Aligned_cols=24 Identities=29% Similarity=0.833 Sum_probs=17.1
Q ss_pred CCCcCCCCCC------CCCCCCCcccCCcC
Q 018197 333 FCDECGAPYL------RETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~------~~~AKFCpECGtKr 356 (359)
.|++||..+- .....-||+||...
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 3999999761 13356799999853
No 42
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=85.31 E-value=0.38 Score=40.44 Aligned_cols=28 Identities=14% Similarity=0.402 Sum_probs=20.1
Q ss_pred CCCCCCCcCCCCCCCC-CC-CCCcccCCcC
Q 018197 329 SPAKFCDECGAPYLRE-TS-KFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~-~A-KFCpECGtKr 356 (359)
+..-+|..||..+... .. ..||.||...
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence 4556799999887643 33 3399999763
No 43
>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=84.43 E-value=0.31 Score=34.34 Aligned_cols=24 Identities=25% Similarity=0.747 Sum_probs=16.5
Q ss_pred CCCcCCCCCC----CCCCCCCcccCCcC
Q 018197 333 FCDECGAPYL----RETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~----~~~AKFCpECGtKr 356 (359)
.||.||...+ ..+--.|++||.-+
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 4999999862 23455899999764
No 44
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.02 E-value=0.63 Score=36.92 Aligned_cols=27 Identities=30% Similarity=0.806 Sum_probs=17.2
Q ss_pred CCCCC-CCcCCCCCC--------CCCCCCCcccCCc
Q 018197 329 SPAKF-CDECGAPYL--------RETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKF-CpeCGt~l~--------~~~AKFCpECGtK 355 (359)
..++| ||+||..++ ..+---||+||..
T Consensus 24 ~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 24 TAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred ceeEeeCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence 34667 888886653 2334568888853
No 45
>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=83.87 E-value=0.7 Score=34.52 Aligned_cols=34 Identities=24% Similarity=0.519 Sum_probs=25.6
Q ss_pred cccCCCCCCCCCCcCCCCCCC---CCCCCCcccCCcC
Q 018197 323 LHVMPASPAKFCDECGAPYLR---ETSKFCSECGVKR 356 (359)
Q Consensus 323 ~~i~p~~~sKFCpeCGt~l~~---~~AKFCpECGtKr 356 (359)
..+.|.-+++-|+.||..... ...-.|++||...
T Consensus 20 ~~v~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 20 VEVDEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred EEECCCCCccCccCcccccccccccceEEcCCCCCEE
Confidence 345677789999999999854 2355799999874
No 46
>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=83.29 E-value=0.54 Score=42.92 Aligned_cols=11 Identities=27% Similarity=0.963 Sum_probs=6.8
Q ss_pred CCCCcccCCcC
Q 018197 346 SKFCSECGVKR 356 (359)
Q Consensus 346 AKFCpECGtKr 356 (359)
..||.+||++.
T Consensus 68 PsYC~~CGkpy 78 (158)
T PF10083_consen 68 PSYCHNCGKPY 78 (158)
T ss_pred ChhHHhCCCCC
Confidence 45666666654
No 47
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=81.96 E-value=0.66 Score=38.94 Aligned_cols=25 Identities=24% Similarity=0.711 Sum_probs=18.6
Q ss_pred CCCCcCCCCCCCC---CCCCCcccCCcC
Q 018197 332 KFCDECGAPYLRE---TSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~~---~AKFCpECGtKr 356 (359)
-.|++||...... ..+|||.||.+.
T Consensus 43 ~~C~~Cg~~~~~~~SCk~R~CP~C~~~~ 70 (111)
T PF14319_consen 43 YRCEDCGHEKIVYNSCKNRHCPSCQAKA 70 (111)
T ss_pred eecCCCCceEEecCcccCcCCCCCCChH
Confidence 3488898876432 488999999874
No 48
>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=81.89 E-value=0.49 Score=33.26 Aligned_cols=23 Identities=26% Similarity=0.876 Sum_probs=19.7
Q ss_pred CCcCCCCC--CCCCCCCCcccCCcC
Q 018197 334 CDECGAPY--LRETSKFCSECGVKR 356 (359)
Q Consensus 334 CpeCGt~l--~~~~AKFCpECGtKr 356 (359)
|+.||+.. ..+|-.||-+||+..
T Consensus 11 C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 11 CPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred CCCCCCeEeEccCCEEEhhhCceEc
Confidence 99999986 567899999999864
No 49
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.60 E-value=0.64 Score=40.15 Aligned_cols=15 Identities=20% Similarity=0.543 Sum_probs=10.9
Q ss_pred CCCCCCCcCCCCCCC
Q 018197 329 SPAKFCDECGAPYLR 343 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~ 343 (359)
+...+|..||.....
T Consensus 68 p~~~~C~~CG~~~~~ 82 (135)
T PRK03824 68 EAVLKCRNCGNEWSL 82 (135)
T ss_pred ceEEECCCCCCEEec
Confidence 345669999977644
No 50
>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=81.41 E-value=0.44 Score=33.47 Aligned_cols=25 Identities=28% Similarity=0.818 Sum_probs=18.5
Q ss_pred CCCcCCCCC-----CCCCCCCCcccCCcCc
Q 018197 333 FCDECGAPY-----LRETSKFCSECGVKRL 357 (359)
Q Consensus 333 FCpeCGt~l-----~~~~AKFCpECGtKr~ 357 (359)
.|+.||+.| ++.....|..||.++.
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGELV 32 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBEB
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCeeE
Confidence 599999987 3445789999998753
No 51
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=80.80 E-value=0.86 Score=35.17 Aligned_cols=23 Identities=35% Similarity=0.839 Sum_probs=17.3
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
.+.|+.||.--+ .+.||+||.+.
T Consensus 5 mr~C~~CgvYTL---k~~CP~CG~~t 27 (56)
T PRK13130 5 IRKCPKCGVYTL---KEICPVCGGKT 27 (56)
T ss_pred ceECCCCCCEEc---cccCcCCCCCC
Confidence 466888887765 67888888774
No 52
>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=79.81 E-value=1 Score=44.48 Aligned_cols=53 Identities=34% Similarity=0.601 Sum_probs=33.0
Q ss_pred CCccCCcccc-ccCCCCCcccccc--cCCCC------------CCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 302 PTISQHMACL-QPLTGGHVGERLH--VMPAS------------PAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 302 ~~i~qh~~yl-qP~tgG~~gG~~~--i~p~~------------~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
.||.||++.+ +=..||..|-|+. ++|.. ...-|.+||+.+. .+-+-||+||..
T Consensus 38 GYigQHLaSlVTG~PG~~SGARG~DL~~~n~d~sEiKsC~rvDQl~~C~~CGa~V~-~~e~~Cp~C~St 105 (314)
T PF09567_consen 38 GYIGQHLASLVTGYPGGGSGARGDDLVMNNDDGSEIKSCYRVDQLGKCNNCGANVS-RLEESCPNCGST 105 (314)
T ss_pred ccHHHhhhhheecCCCCccccccccccccCCCcchhhhhhhhhhhhhhccccceee-ehhhcCCCCCcc
Confidence 4788999886 3233333333322 33331 2245899999975 467899999975
No 53
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=79.70 E-value=0.73 Score=37.04 Aligned_cols=23 Identities=30% Similarity=0.658 Sum_probs=10.4
Q ss_pred CCCcCCCCCCCCCCCCCcccCCc
Q 018197 333 FCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~~~~AKFCpECGtK 355 (359)
.|..|=+-....+-.|||.||.+
T Consensus 11 rC~aCf~~t~~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 11 RCHACFKITKDMTKQFCPKCGNA 33 (73)
T ss_dssp E-SSS--EES-SS--S-SSS--S
T ss_pred EccccccCcCCCCceeCcccCCC
Confidence 47888666666667888888887
No 54
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=79.57 E-value=0.87 Score=42.07 Aligned_cols=24 Identities=29% Similarity=0.703 Sum_probs=20.4
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 332 KFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
+-|..|+..++ ...+|||-||.++
T Consensus 140 ~rC~GC~~~f~-~~~~~Cp~CG~~~ 163 (177)
T COG1439 140 LRCHGCKRIFP-EPKDFCPICGSPL 163 (177)
T ss_pred EEEecCceecC-CCCCcCCCCCCce
Confidence 45999999998 4599999999884
No 55
>PHA02942 putative transposase; Provisional
Probab=77.84 E-value=1.8 Score=43.03 Aligned_cols=35 Identities=23% Similarity=0.543 Sum_probs=24.7
Q ss_pred ccccCCCCCCCCCCcCCCCCCCCC-CC-CCcccCCcC
Q 018197 322 RLHVMPASPAKFCDECGAPYLRET-SK-FCSECGVKR 356 (359)
Q Consensus 322 ~~~i~p~~~sKFCpeCGt~l~~~~-AK-FCpECGtKr 356 (359)
...+.|.-+++.|+.||....... -. -|++||...
T Consensus 316 Vv~V~p~yTSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 316 VEFVNPSYSSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred EEEECCCCCCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 344567789999999998764221 22 489999864
No 56
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=77.74 E-value=1.3 Score=40.50 Aligned_cols=27 Identities=22% Similarity=0.458 Sum_probs=21.7
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 328 ASPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 328 ~~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
..+...|.+||.... .|.-.||.||+-
T Consensus 351 ~~p~~~c~~cg~~~~-~~~~~c~~c~~~ 377 (389)
T PRK11788 351 RKPRYRCRNCGFTAR-TLYWHCPSCKAW 377 (389)
T ss_pred CCCCEECCCCCCCCc-cceeECcCCCCc
Confidence 344566999999875 689999999973
No 57
>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=77.29 E-value=0.42 Score=39.87 Aligned_cols=28 Identities=21% Similarity=0.619 Sum_probs=16.9
Q ss_pred CCCCCCCcCCCCCCCC-CCCCCcccCCcC
Q 018197 329 SPAKFCDECGAPYLRE-TSKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~-~AKFCpECGtKr 356 (359)
+...+|..||..+... ...-||.||...
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp --EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred CCcEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 3345699999998433 234599999873
No 58
>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=76.07 E-value=1.5 Score=41.30 Aligned_cols=23 Identities=30% Similarity=0.930 Sum_probs=18.6
Q ss_pred CCCCCCcCCCCCC-----CCCCCCCccc
Q 018197 330 PAKFCDECGAPYL-----RETSKFCSEC 352 (359)
Q Consensus 330 ~sKFCpeCGt~l~-----~~~AKFCpEC 352 (359)
..+.|+.||+++. .-+.-|||.|
T Consensus 244 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 244 KGEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 3678999999982 2358899999
No 59
>PRK01343 zinc-binding protein; Provisional
Probab=75.87 E-value=2.5 Score=32.99 Aligned_cols=26 Identities=50% Similarity=1.005 Sum_probs=20.7
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCcc
Q 018197 326 MPASPAKFCDECGAPYLRETSKFCSE 351 (359)
Q Consensus 326 ~p~~~sKFCpeCGt~l~~~~AKFCpE 351 (359)
.+....+.||.||++.....-.||++
T Consensus 4 ~~~~p~~~CP~C~k~~~~~~rPFCS~ 29 (57)
T PRK01343 4 EPLRPTRPCPECGKPSTREAYPFCSE 29 (57)
T ss_pred ccCCCCCcCCCCCCcCcCCCCcccCH
Confidence 34456789999999987677889985
No 60
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=75.73 E-value=1.2 Score=40.17 Aligned_cols=24 Identities=25% Similarity=0.573 Sum_probs=17.9
Q ss_pred CCcCCCCCC----CCCCCCCcccCCcCc
Q 018197 334 CDECGAPYL----RETSKFCSECGVKRL 357 (359)
Q Consensus 334 CpeCGt~l~----~~~AKFCpECGtKr~ 357 (359)
||.||.++. -...=-||.||..+.
T Consensus 120 Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 120 CPNCHIRFTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred CCCCCcEEeHHHHhhcCCcCCCCCCCCe
Confidence 999998882 234566999998864
No 61
>PRK10445 endonuclease VIII; Provisional
Probab=75.71 E-value=1.5 Score=41.20 Aligned_cols=24 Identities=21% Similarity=0.645 Sum_probs=19.0
Q ss_pred CCCCCCcCCCCCC-----CCCCCCCcccC
Q 018197 330 PAKFCDECGAPYL-----RETSKFCSECG 353 (359)
Q Consensus 330 ~sKFCpeCGt~l~-----~~~AKFCpECG 353 (359)
..+-|+.||+++. .-+.-|||.|=
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 234 DGEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 3678999999983 33688999994
No 62
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.46 E-value=1.3 Score=38.20 Aligned_cols=23 Identities=26% Similarity=0.715 Sum_probs=16.6
Q ss_pred CCcCCCCCC--------CCCC-CCCcccCCcC
Q 018197 334 CDECGAPYL--------RETS-KFCSECGVKR 356 (359)
Q Consensus 334 CpeCGt~l~--------~~~A-KFCpECGtKr 356 (359)
||.||..+. ...+ --||.||..+
T Consensus 102 Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 102 CPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred CcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 999998872 1233 4499999886
No 63
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=75.32 E-value=1.6 Score=41.11 Aligned_cols=25 Identities=28% Similarity=0.786 Sum_probs=19.4
Q ss_pred CCCCCCcCCCCCC-----CCCCCCCcccCC
Q 018197 330 PAKFCDECGAPYL-----RETSKFCSECGV 354 (359)
Q Consensus 330 ~sKFCpeCGt~l~-----~~~AKFCpECGt 354 (359)
..+.|+.||+++. .-+.-|||.|=.
T Consensus 244 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 3678999999983 235889999954
No 64
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=74.95 E-value=1.6 Score=41.20 Aligned_cols=23 Identities=26% Similarity=0.777 Sum_probs=18.6
Q ss_pred CCCCCcCCCCCC-----CCCCCCCcccC
Q 018197 331 AKFCDECGAPYL-----RETSKFCSECG 353 (359)
Q Consensus 331 sKFCpeCGt~l~-----~~~AKFCpECG 353 (359)
.+-|+.||+++. .-+.-|||.|=
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 678999999982 23588999994
No 65
>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=74.18 E-value=1.1 Score=39.39 Aligned_cols=24 Identities=21% Similarity=0.427 Sum_probs=16.8
Q ss_pred CCcCCCCCC----CCCCCCCcccCCcCc
Q 018197 334 CDECGAPYL----RETSKFCSECGVKRL 357 (359)
Q Consensus 334 CpeCGt~l~----~~~AKFCpECGtKr~ 357 (359)
||.||.++. -...=-||+||..+.
T Consensus 112 Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 112 CPNMCVRFTFNEAMELNFTCPRCGAMLD 139 (158)
T ss_pred CCCCCcEeeHHHHHHcCCcCCCCCCEee
Confidence 999998872 123456999998763
No 66
>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=74.16 E-value=1.6 Score=33.17 Aligned_cols=23 Identities=30% Similarity=0.811 Sum_probs=18.2
Q ss_pred CCCCCCcCCCCCCCCCCCCCcccCC
Q 018197 330 PAKFCDECGAPYLRETSKFCSECGV 354 (359)
Q Consensus 330 ~sKFCpeCGt~l~~~~AKFCpECGt 354 (359)
.--.|++||+.... -..|+.||.
T Consensus 25 ~l~~C~~cG~~~~~--H~vc~~cG~ 47 (55)
T TIGR01031 25 TLVVCPNCGEFKLP--HRVCPSCGY 47 (55)
T ss_pred cceECCCCCCcccC--eeECCccCe
Confidence 34559999998764 578999996
No 67
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=73.99 E-value=1.3 Score=36.64 Aligned_cols=23 Identities=35% Similarity=1.016 Sum_probs=19.4
Q ss_pred CCCCcCCCCC------CCCCCCCCcccCC
Q 018197 332 KFCDECGAPY------LRETSKFCSECGV 354 (359)
Q Consensus 332 KFCpeCGt~l------~~~~AKFCpECGt 354 (359)
-+|-.||.++ ..+|+++|-+|=+
T Consensus 81 G~C~~Cge~I~~~RL~a~P~a~~Cv~Cq~ 109 (110)
T TIGR02420 81 GYCEECGEEIGLRRLEARPTATLCIDCKT 109 (110)
T ss_pred CchhccCCcccHHHHhhCCCccccHHhHc
Confidence 3799999998 3579999999954
No 68
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=73.66 E-value=0.93 Score=30.88 Aligned_cols=23 Identities=26% Similarity=0.811 Sum_probs=13.5
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCc
Q 018197 332 KFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtK 355 (359)
..|..||....++ .-+||.||..
T Consensus 12 ~rC~~Cg~~~~pP-r~~Cp~C~s~ 34 (37)
T PF12172_consen 12 QRCRDCGRVQFPP-RPVCPHCGSD 34 (37)
T ss_dssp EE-TTT--EEES---SEETTTT--
T ss_pred EEcCCCCCEecCC-CcCCCCcCcc
Confidence 4599999997655 6899999964
No 69
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=73.48 E-value=1.9 Score=38.06 Aligned_cols=34 Identities=21% Similarity=0.540 Sum_probs=23.1
Q ss_pred cccccCCC-CCCCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 321 ERLHVMPA-SPAKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 321 G~~~i~p~-~~sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
|++.+.+. .-.--|..||+++. .++||++|=.++
T Consensus 70 GRL~~~~~~nl~~~CE~CG~~I~--~Gr~C~~C~~~l 104 (137)
T TIGR03826 70 GRLQLKHFPNLGYPCERCGTSIR--EGRLCDSCAGEL 104 (137)
T ss_pred CCeeccCCCCCcCcccccCCcCC--CCCccHHHHHHH
Confidence 44444443 33445999999986 469999996543
No 70
>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=73.36 E-value=2.1 Score=28.39 Aligned_cols=21 Identities=33% Similarity=0.961 Sum_probs=12.9
Q ss_pred CCcCCCCCCCC--CCC-CCcccCC
Q 018197 334 CDECGAPYLRE--TSK-FCSECGV 354 (359)
Q Consensus 334 CpeCGt~l~~~--~AK-FCpECGt 354 (359)
|..||..+.+. +.. -||+||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 67787777422 233 3888874
No 71
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=73.24 E-value=2.3 Score=38.77 Aligned_cols=26 Identities=27% Similarity=0.654 Sum_probs=21.3
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
..-|+.||.....+....||-||.+.
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k 159 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPK 159 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChH
Confidence 45599999998667788999999763
No 72
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=73.01 E-value=1.9 Score=33.04 Aligned_cols=25 Identities=32% Similarity=0.800 Sum_probs=19.1
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
..--.|++||+.... -.-|+.||.=
T Consensus 25 ~~l~~C~~CG~~~~~--H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP--HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC--eEECCCCCcC
Confidence 334569999999864 5789999964
No 73
>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=72.98 E-value=2.2 Score=30.26 Aligned_cols=21 Identities=38% Similarity=1.081 Sum_probs=16.0
Q ss_pred CCcCCCCC------CCCCCCCCcccCC
Q 018197 334 CDECGAPY------LRETSKFCSECGV 354 (359)
Q Consensus 334 CpeCGt~l------~~~~AKFCpECGt 354 (359)
|.+||..+ ......-||+||.
T Consensus 8 C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 8 CEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred eCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 99999765 2235778999998
No 74
>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=72.92 E-value=1.4 Score=33.60 Aligned_cols=24 Identities=38% Similarity=0.797 Sum_probs=17.3
Q ss_pred CCCcCCCCCCCC-----CCCCCcccCCcC
Q 018197 333 FCDECGAPYLRE-----TSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~~~-----~AKFCpECGtKr 356 (359)
-||.||+.+-.+ .--=|++||..+
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 399999997221 234699999874
No 75
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=72.91 E-value=2 Score=40.67 Aligned_cols=26 Identities=27% Similarity=0.760 Sum_probs=20.1
Q ss_pred CCCCCCcCCCCCC-----CCCCCCCcccCCc
Q 018197 330 PAKFCDECGAPYL-----RETSKFCSECGVK 355 (359)
Q Consensus 330 ~sKFCpeCGt~l~-----~~~AKFCpECGtK 355 (359)
..+-|+.||+++. .-+.-|||.|=..
T Consensus 234 ~g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CcCCCCcCCCeeEEEEECCCCcEECCCCcCC
Confidence 3678999999983 2358899999654
No 76
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=72.85 E-value=2 Score=37.85 Aligned_cols=28 Identities=32% Similarity=0.805 Sum_probs=23.2
Q ss_pred CCCCCCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 327 PASPAKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 327 p~~~sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
+.....+|..||.-+- |-|+|+.||+-+
T Consensus 93 ~~~~~W~Cv~C~~~Y~--GeK~C~~C~tGi 120 (128)
T PF11682_consen 93 PRKTDWHCVMCGNHYH--GEKYCPKCGTGI 120 (128)
T ss_pred CcCceEEEecCCCccC--cCEecCCCCCcc
Confidence 3456788999999984 679999999875
No 77
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=72.75 E-value=2.5 Score=28.65 Aligned_cols=23 Identities=35% Similarity=0.819 Sum_probs=17.3
Q ss_pred CCcCCCCCCCC-CCCCCcccCCcC
Q 018197 334 CDECGAPYLRE-TSKFCSECGVKR 356 (359)
Q Consensus 334 CpeCGt~l~~~-~AKFCpECGtKr 356 (359)
|..||..+... ...-||.||.+.
T Consensus 4 C~~CGy~y~~~~~~~~CP~Cg~~~ 27 (33)
T cd00350 4 CPVCGYIYDGEEAPWVCPVCGAPK 27 (33)
T ss_pred CCCCCCEECCCcCCCcCcCCCCcH
Confidence 88999886433 466899999864
No 78
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=72.74 E-value=1.5 Score=34.90 Aligned_cols=29 Identities=31% Similarity=0.753 Sum_probs=21.7
Q ss_pred CCCCC-CCcCCCCC--CCCCCCCCcccCCcCc
Q 018197 329 SPAKF-CDECGAPY--LRETSKFCSECGVKRL 357 (359)
Q Consensus 329 ~~sKF-CpeCGt~l--~~~~AKFCpECGtKr~ 357 (359)
+...+ |.+||+.. -...+--|-|||.+++
T Consensus 17 ~~miYiCgdC~~en~lk~~D~irCReCG~RIl 48 (62)
T KOG3507|consen 17 ATMIYICGDCGQENTLKRGDVIRCRECGYRIL 48 (62)
T ss_pred ccEEEEeccccccccccCCCcEehhhcchHHH
Confidence 44455 99999996 3445788999998754
No 79
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=72.49 E-value=1.5 Score=38.96 Aligned_cols=24 Identities=25% Similarity=0.804 Sum_probs=19.0
Q ss_pred CCCCcCCCCCCC-C-CCCCCcccCCc
Q 018197 332 KFCDECGAPYLR-E-TSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~-~-~AKFCpECGtK 355 (359)
..|++||.++.+ . +.-.|++||+.
T Consensus 150 a~~~~~g~~~~~~~~~~~~c~~~~~~ 175 (189)
T PRK09521 150 AMCSRCRTPLVKKGENELKCPNCGNI 175 (189)
T ss_pred EEccccCCceEECCCCEEECCCCCCE
Confidence 469999999843 3 46789999975
No 80
>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=71.95 E-value=2 Score=32.33 Aligned_cols=24 Identities=33% Similarity=0.845 Sum_probs=18.4
Q ss_pred CCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 330 PAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 330 ~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
..-.|++||+.... -..|++||.-
T Consensus 25 ~l~~c~~cg~~~~~--H~vc~~cG~y 48 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP--HRVCPSCGYY 48 (56)
T ss_dssp SEEESSSSSSEEST--TSBCTTTBBS
T ss_pred ceeeeccCCCEecc--cEeeCCCCeE
Confidence 44679999987653 5789999853
No 81
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=71.24 E-value=1.6 Score=38.71 Aligned_cols=25 Identities=28% Similarity=0.838 Sum_probs=20.3
Q ss_pred CCCCCcCCCCC------CCCCCCCCcccCCc
Q 018197 331 AKFCDECGAPY------LRETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l------~~~~AKFCpECGtK 355 (359)
--+|-.||.++ ..+++.+|-+|=..
T Consensus 111 YG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~ 141 (151)
T PRK10778 111 FGYCESCGVEIGIRRLEARPTADLCIDCKTL 141 (151)
T ss_pred CceeccCCCcccHHHHhcCCCccccHHHHHH
Confidence 34699999998 36799999999553
No 82
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=71.11 E-value=2.3 Score=40.26 Aligned_cols=23 Identities=30% Similarity=0.941 Sum_probs=18.5
Q ss_pred CCCCCcCCCCCC-----CCCCCCCcccC
Q 018197 331 AKFCDECGAPYL-----RETSKFCSECG 353 (359)
Q Consensus 331 sKFCpeCGt~l~-----~~~AKFCpECG 353 (359)
.+-|+.||+++. .-+.-|||.|=
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 678999999983 23588999994
No 83
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=70.37 E-value=2.1 Score=41.64 Aligned_cols=25 Identities=24% Similarity=0.761 Sum_probs=19.9
Q ss_pred CCCCCCCcCCCCCC-----CCCCCCCcccC
Q 018197 329 SPAKFCDECGAPYL-----RETSKFCSECG 353 (359)
Q Consensus 329 ~~sKFCpeCGt~l~-----~~~AKFCpECG 353 (359)
...+.|..||+.+. .-+.-|||.|-
T Consensus 243 R~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 243 RAGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 34889999999982 33688999994
No 84
>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=69.46 E-value=3.3 Score=41.60 Aligned_cols=24 Identities=21% Similarity=0.605 Sum_probs=18.7
Q ss_pred CCCcCCCCCCCCCCCCCcccCCcC
Q 018197 333 FCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~~~~AKFCpECGtKr 356 (359)
-|++||..+.....--||.||.++
T Consensus 217 ~C~~Cd~~~~~~~~a~CpRC~~~L 240 (403)
T TIGR00155 217 SCSACHTTILPAQEPVCPRCSTPL 240 (403)
T ss_pred cCCCCCCccCCCCCcCCcCCCCcc
Confidence 499999977555566799999875
No 85
>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=69.20 E-value=3.2 Score=29.66 Aligned_cols=22 Identities=32% Similarity=0.835 Sum_probs=14.4
Q ss_pred CCCcCCCCCC------CCCCCCCcccCC
Q 018197 333 FCDECGAPYL------RETSKFCSECGV 354 (359)
Q Consensus 333 FCpeCGt~l~------~~~AKFCpECGt 354 (359)
.|.+||..+- .....-||+||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 3899998551 112346999997
No 86
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=69.02 E-value=2.3 Score=40.70 Aligned_cols=24 Identities=25% Similarity=0.760 Sum_probs=17.0
Q ss_pred CCCCCcCCCCCC---------CCCCCCCcccCC
Q 018197 331 AKFCDECGAPYL---------RETSKFCSECGV 354 (359)
Q Consensus 331 sKFCpeCGt~l~---------~~~AKFCpECGt 354 (359)
+.-|.-|+..++ .....|||+||.
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccch
Confidence 445888888773 234788888885
No 87
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=68.95 E-value=3.4 Score=44.66 Aligned_cols=24 Identities=33% Similarity=0.761 Sum_probs=20.1
Q ss_pred CCCCcCCCCCC-CCCCCCCcccCCc
Q 018197 332 KFCDECGAPYL-RETSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~-~~~AKFCpECGtK 355 (359)
..||+||..+. .+|=.-|..||-.
T Consensus 725 ~~Cp~Cg~~l~~~~GC~~C~~CG~s 749 (752)
T PRK08665 725 GACPECGSILEHEEGCVVCHSCGYS 749 (752)
T ss_pred CCCCCCCcccEECCCCCcCCCCCCC
Confidence 47999998874 5688999999964
No 88
>PF13421 Band_7_1: SPFH domain-Band 7 family
Probab=68.36 E-value=5.1 Score=36.90 Aligned_cols=41 Identities=17% Similarity=0.118 Sum_probs=35.0
Q ss_pred ccchhhhHhhheeEeEEEeecceeeccCCCCChhhHHHHHHHhc
Q 018197 137 TRFPELVIQEEKRVRFVVVNGLDIVEKPNNMPIEDAEWFKRLTG 180 (359)
Q Consensus 137 t~fpelv~~EekrvrfvVVnGl~IVE~p~Nlp~eDqewfkRLtg 180 (359)
+.+.+.+..+..++|+.++++- |+ ++++|+|+++-+++...
T Consensus 168 ~~~~~~l~~~~~~~Gi~l~~f~--I~-~i~~pee~~~~i~~~~~ 208 (211)
T PF13421_consen 168 EALKEKLNPEFERYGIELVDFG--IE-SISFPEEVQKAIDKRAS 208 (211)
T ss_pred HHHHHHHHHHHHhcCcEEEEEE--EE-eecCCHHHHHHHHHHHh
Confidence 3456678889999999999999 88 99999999999887654
No 89
>PF14369 zf-RING_3: zinc-finger
Probab=68.26 E-value=3.3 Score=28.88 Aligned_cols=25 Identities=16% Similarity=0.453 Sum_probs=17.5
Q ss_pred CCCCcCCCCCC----CCCCCCCcccCCcC
Q 018197 332 KFCDECGAPYL----RETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~----~~~AKFCpECGtKr 356 (359)
-||.+|...+- .....+||.|+...
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 47999987662 23456799998653
No 90
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=68.21 E-value=2.1 Score=32.52 Aligned_cols=24 Identities=29% Similarity=0.701 Sum_probs=19.1
Q ss_pred CCcCCCCCC---CCCCCCCcccCCcCc
Q 018197 334 CDECGAPYL---RETSKFCSECGVKRL 357 (359)
Q Consensus 334 CpeCGt~l~---~~~AKFCpECGtKr~ 357 (359)
|..||+.+- ....--||.||.+++
T Consensus 9 C~~Cg~~~~~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 9 CARCGREVELDQETRGIRCPYCGSRIL 35 (49)
T ss_pred hhhcCCeeehhhccCceeCCCCCcEEE
Confidence 999999983 335778999999864
No 91
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=68.02 E-value=3.1 Score=32.06 Aligned_cols=24 Identities=25% Similarity=0.675 Sum_probs=19.9
Q ss_pred CCCCCcCCCCCC------CCCCCCCcccCC
Q 018197 331 AKFCDECGAPYL------RETSKFCSECGV 354 (359)
Q Consensus 331 sKFCpeCGt~l~------~~~AKFCpECGt 354 (359)
..||-.||.+++ .+++.+|-+|-+
T Consensus 31 ~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~ 60 (63)
T TIGR02419 31 LRECEDCGEPIPEARREALPGVTRCVSCQE 60 (63)
T ss_pred CCeeccCCCcChHHHHhhcCCcCCcHHHHh
Confidence 568999999984 468999999954
No 92
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=67.88 E-value=2.6 Score=33.57 Aligned_cols=24 Identities=29% Similarity=0.800 Sum_probs=19.8
Q ss_pred CCCCCcCCCCCC------CCCCCCCcccCC
Q 018197 331 AKFCDECGAPYL------RETSKFCSECGV 354 (359)
Q Consensus 331 sKFCpeCGt~l~------~~~AKFCpECGt 354 (359)
..+|-+||.+++ .+++.+|-+|-+
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~ 63 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQA 63 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHH
Confidence 358999999984 468999999954
No 93
>PHA00080 DksA-like zinc finger domain containing protein
Probab=67.87 E-value=2.7 Score=33.30 Aligned_cols=24 Identities=33% Similarity=0.818 Sum_probs=19.9
Q ss_pred CCCCCcCCCCCC------CCCCCCCcccCC
Q 018197 331 AKFCDECGAPYL------RETSKFCSECGV 354 (359)
Q Consensus 331 sKFCpeCGt~l~------~~~AKFCpECGt 354 (359)
..+|-.||.+++ .+++.+|-+|-+
T Consensus 31 ~~~C~~Cg~~Ip~~Rl~a~P~~~~Cv~Cq~ 60 (72)
T PHA00080 31 ATHCEECGDPIPEARREAVPGCRTCVSCQE 60 (72)
T ss_pred CCEecCCCCcCcHHHHHhCCCccCcHHHHH
Confidence 458999999984 568999999954
No 94
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=66.16 E-value=2.2 Score=38.16 Aligned_cols=23 Identities=35% Similarity=0.875 Sum_probs=19.3
Q ss_pred CCCcCCCCC------CCCCCCCCcccCCc
Q 018197 333 FCDECGAPY------LRETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l------~~~~AKFCpECGtK 355 (359)
+|-.||.++ ..+++.+|-+|=..
T Consensus 88 ~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~ 116 (159)
T TIGR02890 88 ICEVCGKPIPYERLEAIPTATTCVECQNR 116 (159)
T ss_pred eecccCCcccHHHHhhCCCcchhHHHHHH
Confidence 699999998 45789999999553
No 95
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=65.90 E-value=2.9 Score=29.03 Aligned_cols=23 Identities=22% Similarity=0.613 Sum_probs=16.2
Q ss_pred CCCcCCCCCCC--------CCCCCCcccCCc
Q 018197 333 FCDECGAPYLR--------ETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~~--------~~AKFCpECGtK 355 (359)
-||+|++.+.. ...--|+.||..
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 39999999821 123459999975
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=65.78 E-value=4.7 Score=31.78 Aligned_cols=25 Identities=28% Similarity=0.728 Sum_probs=18.8
Q ss_pred CCCCCcCCCCCCCC--CCC-CCcccCCc
Q 018197 331 AKFCDECGAPYLRE--TSK-FCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~~~--~AK-FCpECGtK 355 (359)
...|..||..+.+. .++ .||+||+-
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCe
Confidence 44799999998532 344 49999986
No 97
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=65.75 E-value=2.3 Score=41.79 Aligned_cols=23 Identities=26% Similarity=0.800 Sum_probs=18.8
Q ss_pred CCCcCCCCC----CCCCCCCCcccCCc
Q 018197 333 FCDECGAPY----LRETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l----~~~~AKFCpECGtK 355 (359)
-|++||+.+ ...+.+.||+||.-
T Consensus 40 kc~~C~~~~~~~~l~~~~~vcp~c~~h 66 (296)
T CHL00174 40 QCENCYGLNYKKFLKSKMNICEQCGYH 66 (296)
T ss_pred ECCCccchhhHHHHHHcCCCCCCCCCC
Confidence 399999987 34568999999975
No 98
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=64.77 E-value=3.2 Score=29.02 Aligned_cols=11 Identities=27% Similarity=0.978 Sum_probs=8.9
Q ss_pred CCCCCcCCCCC
Q 018197 331 AKFCDECGAPY 341 (359)
Q Consensus 331 sKFCpeCGt~l 341 (359)
...|+.||..|
T Consensus 2 ~~~C~~Cg~~l 12 (47)
T PF13005_consen 2 PRACPDCGGEL 12 (47)
T ss_pred CCcCCCCCcee
Confidence 46788888887
No 99
>PLN02976 amine oxidase
Probab=64.27 E-value=4 Score=48.19 Aligned_cols=29 Identities=48% Similarity=0.690 Sum_probs=24.1
Q ss_pred CCCcccccccccCCccccCCCcchhhHHHHHHHHHHHHHH
Q 018197 43 QPGQDKLSKRKNRDVQYEGDPRFALPLMYVANMYETLVND 82 (359)
Q Consensus 43 ~~~~dk~~KRk~~ev~YEGdprf~LPLmyvANlyetlv~~ 82 (359)
+-+..|.+|||.+|+-||||+. ||+||+|
T Consensus 384 ~R~~r~~kk~~~~d~~~egd~~-----------w~~l~~~ 412 (1713)
T PLN02976 384 QRVTRKAKKRKLGDMAYEGDAD-----------WETLINE 412 (1713)
T ss_pred cccccccccccccccccccCcc-----------HHHHhcc
Confidence 3444678899999999999987 6889887
No 100
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=63.09 E-value=3 Score=38.32 Aligned_cols=11 Identities=27% Similarity=0.634 Sum_probs=8.9
Q ss_pred CCCCCcCCCCC
Q 018197 331 AKFCDECGAPY 341 (359)
Q Consensus 331 sKFCpeCGt~l 341 (359)
-.-||+|+.++
T Consensus 97 ~~RCp~CN~~L 107 (165)
T COG1656 97 FSRCPECNGEL 107 (165)
T ss_pred cccCcccCCEe
Confidence 34599999998
No 101
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=63.07 E-value=4.3 Score=31.93 Aligned_cols=31 Identities=29% Similarity=0.743 Sum_probs=23.0
Q ss_pred CCCCCCCC----CCcCCCCCC----CCCCCCCcccCCcC
Q 018197 326 MPASPAKF----CDECGAPYL----RETSKFCSECGVKR 356 (359)
Q Consensus 326 ~p~~~sKF----CpeCGt~l~----~~~AKFCpECGtKr 356 (359)
.|...++| |+.|+.... ......|..||+.+
T Consensus 2 i~~p~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 2 IPQPRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred CCCCCCeEEEEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 35566777 999998762 34578899999876
No 102
>PRK11019 hypothetical protein; Provisional
Probab=62.99 E-value=3 Score=34.62 Aligned_cols=25 Identities=28% Similarity=0.745 Sum_probs=20.5
Q ss_pred CCCCCcCCCCCC------CCCCCCCcccCCc
Q 018197 331 AKFCDECGAPYL------RETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~------~~~AKFCpECGtK 355 (359)
..||-.||.+++ .+++.+|-+|-+.
T Consensus 36 yg~C~~CG~~Ip~~Rl~A~P~a~~Cv~Cq~~ 66 (88)
T PRK11019 36 LTECEECGEPIPEARRKAIPGVRLCVACQQE 66 (88)
T ss_pred CCeeCcCCCcCcHHHHhhcCCccccHHHHHH
Confidence 468999999984 4689999999553
No 103
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=61.89 E-value=2.1 Score=29.19 Aligned_cols=23 Identities=30% Similarity=0.911 Sum_probs=16.3
Q ss_pred CCCCcCCCCC------CCCCCCCCcccCC
Q 018197 332 KFCDECGAPY------LRETSKFCSECGV 354 (359)
Q Consensus 332 KFCpeCGt~l------~~~~AKFCpECGt 354 (359)
.+|..||.++ ..+++.+|-+|-.
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQE 32 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhC
Confidence 3599999998 3468999999854
No 104
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.52 E-value=4 Score=34.84 Aligned_cols=27 Identities=33% Similarity=0.597 Sum_probs=17.5
Q ss_pred CCCCCCCcCCCCCCCCC--------CCCCcccCCcC
Q 018197 329 SPAKFCDECGAPYLRET--------SKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~--------AKFCpECGtKr 356 (359)
+...+| .||......+ ..-||.||...
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKR 102 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCC
Confidence 445679 9998854221 12399999653
No 105
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=61.24 E-value=4.1 Score=28.27 Aligned_cols=25 Identities=28% Similarity=0.719 Sum_probs=19.1
Q ss_pred CCCCCcCCCCCC---CCCCCCCcccCCc
Q 018197 331 AKFCDECGAPYL---RETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~---~~~AKFCpECGtK 355 (359)
-+-|..||..++ ..+--||++||.-
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 456999999874 3467899999963
No 106
>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=61.15 E-value=5.6 Score=27.40 Aligned_cols=24 Identities=29% Similarity=0.671 Sum_probs=17.2
Q ss_pred CCCcCCCCCCCC-CCCCCcccCCcC
Q 018197 333 FCDECGAPYLRE-TSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~~~-~AKFCpECGtKr 356 (359)
-|..||.-+... .-.-||-||.+.
T Consensus 4 ~C~~CG~i~~g~~~p~~CP~Cg~~~ 28 (34)
T cd00729 4 VCPVCGYIHEGEEAPEKCPICGAPK 28 (34)
T ss_pred ECCCCCCEeECCcCCCcCcCCCCch
Confidence 399999776322 347899999864
No 107
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=60.79 E-value=6.4 Score=42.03 Aligned_cols=26 Identities=23% Similarity=0.682 Sum_probs=19.7
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
.+...|++||..+. .-...||.||..
T Consensus 566 p~~~~C~~CG~~~~-g~~~~CP~CGs~ 591 (625)
T PRK08579 566 PAITVCNKCGRSTT-GLYTRCPRCGSE 591 (625)
T ss_pred CCCccCCCCCCccC-CCCCcCcCCCCc
Confidence 35678999999653 336799999954
No 108
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=60.60 E-value=2 Score=34.71 Aligned_cols=21 Identities=33% Similarity=1.066 Sum_probs=7.4
Q ss_pred CCcCCCCCCCCCCCCCcccCCcC
Q 018197 334 CDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 334 CpeCGt~l~~~~AKFCpECGtKr 356 (359)
|..|+..+.. .-|||+||.++
T Consensus 20 C~~C~~~~~~--~a~CPdC~~~L 40 (70)
T PF07191_consen 20 CEACQKDYKK--EAFCPDCGQPL 40 (70)
T ss_dssp ETTT--EEEE--EEE-TTT-SB-
T ss_pred Ccccccccee--cccCCCcccHH
Confidence 4444444321 24566666554
No 109
>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=60.56 E-value=5.3 Score=36.67 Aligned_cols=34 Identities=29% Similarity=0.755 Sum_probs=21.4
Q ss_pred cccccCCCC-Cccccccc-CCCCCCCCCCcCCCCCC
Q 018197 309 ACLQPLTGG-HVGERLHV-MPASPAKFCDECGAPYL 342 (359)
Q Consensus 309 ~ylqP~tgG-~~gG~~~i-~p~~~sKFCpeCGt~l~ 342 (359)
.|..|..|. ++-|.... .+...+.||.+||+++|
T Consensus 44 ~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 44 NCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred CCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 445553333 34454444 34467899999999995
No 110
>PRK06386 replication factor A; Reviewed
Probab=60.20 E-value=4.4 Score=40.70 Aligned_cols=21 Identities=14% Similarity=0.305 Sum_probs=17.5
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCc
Q 018197 332 KFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtK 355 (359)
+-||+|+..+.. .+|++||..
T Consensus 237 ~rCP~C~R~l~~---g~C~~HG~v 257 (358)
T PRK06386 237 TKCSVCNKIIED---GVCKDHPDA 257 (358)
T ss_pred ecCcCCCeEccC---CcCCCCCCC
Confidence 679999998863 399999974
No 111
>PRK05978 hypothetical protein; Provisional
Probab=59.81 E-value=5.9 Score=35.60 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=18.5
Q ss_pred CCCCcCCCCCC----CCCCCCCcccCCcC
Q 018197 332 KFCDECGAPYL----RETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~----~~~AKFCpECGtKr 356 (359)
--||.||+--. -.-..-|+.||.+.
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCcc
Confidence 35999998753 12367899999985
No 112
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=59.49 E-value=6.5 Score=39.76 Aligned_cols=25 Identities=24% Similarity=0.561 Sum_probs=18.5
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
..-|++||.-...+ ..-||.||.++
T Consensus 221 l~~C~~Cd~l~~~~-~a~CpRC~~~L 245 (419)
T PRK15103 221 LRSCSCCTAILPAD-QPVCPRCHTKG 245 (419)
T ss_pred CCcCCCCCCCCCCC-CCCCCCCCCcC
Confidence 34599999976433 44799999976
No 113
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=59.49 E-value=53 Score=32.67 Aligned_cols=28 Identities=29% Similarity=0.752 Sum_probs=21.3
Q ss_pred CCCCC-CCcCCCCCCC----------------CCCCCCcccCCcC
Q 018197 329 SPAKF-CDECGAPYLR----------------ETSKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKF-CpeCGt~l~~----------------~~AKFCpECGtKr 356 (359)
...++ |++||+.|.. .-++-|+.||+--
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVY 171 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCcee
Confidence 44566 9999999932 3488999999863
No 114
>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=59.47 E-value=4.4 Score=36.05 Aligned_cols=27 Identities=26% Similarity=0.626 Sum_probs=18.5
Q ss_pred CCCCCCCcCCCCCC---CCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYL---RETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~---~~~AKFCpECGtK 355 (359)
.+.-.|.+||..+. +.---=||+||..
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 33456999999871 1224459999976
No 115
>KOG4470 consensus Proteasome activator subunit [Posttranslational modification, protein turnover, chaperones]
Probab=59.40 E-value=7.5 Score=37.78 Aligned_cols=39 Identities=28% Similarity=0.417 Sum_probs=33.6
Q ss_pred eeeccCCCCcccCCCCcccccccccCCccccCCCcchhh
Q 018197 30 VIEVTDSGAEYSQQPGQDKLSKRKNRDVQYEGDPRFALP 68 (359)
Q Consensus 30 vi~v~~~~~~~~~~~~~dk~~KRk~~ev~YEGdprf~LP 68 (359)
-|+|+|....+..-.+.|-..|++.-|...+|+|-|+||
T Consensus 59 ~ipvpdp~~~~~~~d~~~~~~~~~~~d~~~~g~~~~~~p 97 (246)
T KOG4470|consen 59 NIPVPDPELLKNELDSDDQAVKKQRVDEKKKGAPVFGLP 97 (246)
T ss_pred CCCCCCchhhcccCccccchhhhhhhhhhccCCcccCCC
Confidence 488888877777777777778888899999999999999
No 116
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=59.35 E-value=3.9 Score=38.32 Aligned_cols=24 Identities=29% Similarity=0.798 Sum_probs=19.0
Q ss_pred CCCCcCCCCCCCC-CCCCCcccCCc
Q 018197 332 KFCDECGAPYLRE-TSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~-~AKFCpECGtK 355 (359)
..|++||+.|... ..-.||+||.-
T Consensus 150 A~CsrC~~~L~~~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVKKGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEEcCcEEECCCCCCE
Confidence 4599999999544 46789999964
No 117
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=59.17 E-value=4.4 Score=28.18 Aligned_cols=22 Identities=36% Similarity=0.798 Sum_probs=15.8
Q ss_pred CCcCCCCCC-------CCC-CCCCcccCCc
Q 018197 334 CDECGAPYL-------RET-SKFCSECGVK 355 (359)
Q Consensus 334 CpeCGt~l~-------~~~-AKFCpECGtK 355 (359)
||+|++.+. ..+ .--|+.||..
T Consensus 5 Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 5 CPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred CCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 999999982 222 3469999975
No 118
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=59.11 E-value=5.2 Score=30.93 Aligned_cols=25 Identities=28% Similarity=0.805 Sum_probs=16.2
Q ss_pred CCCCCCcCCCC--CCC-CCCCCCcccCC
Q 018197 330 PAKFCDECGAP--YLR-ETSKFCSECGV 354 (359)
Q Consensus 330 ~sKFCpeCGt~--l~~-~~AKFCpECGt 354 (359)
.-+|||.||.- |.. ..---|-.||-
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccc
Confidence 46899999953 321 12446888885
No 119
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=57.86 E-value=4.7 Score=31.14 Aligned_cols=21 Identities=14% Similarity=0.072 Sum_probs=16.5
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGV 354 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGt 354 (359)
.-.|++||+...+. .-|+ ||.
T Consensus 27 ~~~c~~cg~~~~pH--~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGEYHLPH--HVSP-KGY 47 (60)
T ss_pred eeEcCCCCceeccc--eecC-Ccc
Confidence 45699999998754 4599 995
No 120
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=57.46 E-value=6.4 Score=42.65 Aligned_cols=25 Identities=28% Similarity=0.691 Sum_probs=17.9
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCcccCC
Q 018197 328 ASPAKFCDECGAPYLRETSKFCSECGV 354 (359)
Q Consensus 328 ~~~sKFCpeCGt~l~~~~AKFCpECGt 354 (359)
..+.-.|++||..-. -...||.||.
T Consensus 677 n~~~~~C~~CG~~~~--~~~~CP~CG~ 701 (735)
T PRK07111 677 NHPVDRCPVCGYLGV--IEDKCPKCGS 701 (735)
T ss_pred CCCCeecCCCCCCCC--cCccCcCCCC
Confidence 355677999995332 2478999995
No 121
>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=57.22 E-value=6.5 Score=40.22 Aligned_cols=24 Identities=29% Similarity=0.623 Sum_probs=18.0
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
.-.|+-||..... ...||+||...
T Consensus 240 ~l~Ch~Cg~~~~~--~~~Cp~C~s~~ 263 (505)
T TIGR00595 240 KLRCHYCGYQEPI--PKTCPQCGSED 263 (505)
T ss_pred eEEcCCCcCcCCC--CCCCCCCCCCe
Confidence 3468888888653 46899999863
No 122
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=56.99 E-value=5.2 Score=36.39 Aligned_cols=27 Identities=37% Similarity=0.870 Sum_probs=23.0
Q ss_pred CCCCC-CCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKF-CDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKF-CpeCGt~l~~~~AKFCpECGtK 355 (359)
..+-| |--||++|.....||++.||=+
T Consensus 51 e~GvY~C~~C~~pLykS~tKfdsgcGWP 78 (146)
T KOG0856|consen 51 EEGVYVCAGCGTPLYKSTTKFDSGCGWP 78 (146)
T ss_pred CCceEEEeecCCccccccccccCCCCCc
Confidence 44445 9999999998899999999976
No 123
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=56.96 E-value=10 Score=41.46 Aligned_cols=23 Identities=30% Similarity=0.677 Sum_probs=18.9
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
.-+|+-||.... -...||+||..
T Consensus 462 ~L~CH~Cg~~~~--~p~~Cp~Cgs~ 484 (730)
T COG1198 462 QLRCHYCGYQEP--IPQSCPECGSE 484 (730)
T ss_pred eeEeCCCCCCCC--CCCCCCCCCCC
Confidence 457999999953 36899999987
No 124
>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=56.68 E-value=3.5 Score=27.53 Aligned_cols=18 Identities=28% Similarity=0.682 Sum_probs=8.3
Q ss_pred CCCcCCCCCC---CCCCCCCc
Q 018197 333 FCDECGAPYL---RETSKFCS 350 (359)
Q Consensus 333 FCpeCGt~l~---~~~AKFCp 350 (359)
+||.||+++. .+-.-||+
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 5888888874 22355554
No 125
>PRK11032 hypothetical protein; Provisional
Probab=56.26 E-value=5.5 Score=36.19 Aligned_cols=20 Identities=35% Similarity=0.438 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHhhhhhcc
Q 018197 72 VANMYETLVNDVNLRLASFN 91 (359)
Q Consensus 72 vANlyetlv~~vn~rlasl~ 91 (359)
++-.|+.|+.+|..+|...+
T Consensus 4 ~~~~Y~~ll~~v~~~l~~~~ 23 (160)
T PRK11032 4 VAQYYRELVASLTERLRNGE 23 (160)
T ss_pred HHHHHHHHHHHHHHHHHhCH
Confidence 46789999999999997665
No 126
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=56.02 E-value=3.9 Score=28.13 Aligned_cols=22 Identities=36% Similarity=0.828 Sum_probs=11.3
Q ss_pred CCCcCCCCC--CCCCCCCCcccCC
Q 018197 333 FCDECGAPY--LRETSKFCSECGV 354 (359)
Q Consensus 333 FCpeCGt~l--~~~~AKFCpECGt 354 (359)
-|+.||..+ .....--||+||.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCcceeccCCEEeCCcccc
Confidence 499999987 3444566999985
No 127
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=55.79 E-value=5.2 Score=34.34 Aligned_cols=23 Identities=22% Similarity=0.608 Sum_probs=19.1
Q ss_pred CCcCCCCCCCC--CCCCCcccCCcC
Q 018197 334 CDECGAPYLRE--TSKFCSECGVKR 356 (359)
Q Consensus 334 CpeCGt~l~~~--~AKFCpECGtKr 356 (359)
|+.|..++... +.-+|+.|++..
T Consensus 37 C~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 37 CPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccCcccEeCCCCcEECCCCCCcC
Confidence 99999998654 578999999873
No 128
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=54.97 E-value=5.5 Score=29.31 Aligned_cols=23 Identities=26% Similarity=0.703 Sum_probs=17.2
Q ss_pred CCCCcCCCCCC---------CCCCCCCcccCC
Q 018197 332 KFCDECGAPYL---------RETSKFCSECGV 354 (359)
Q Consensus 332 KFCpeCGt~l~---------~~~AKFCpECGt 354 (359)
.-|.-|+..++ ...--|||+||.
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 47999998884 224679999985
No 129
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=53.39 E-value=6.7 Score=39.52 Aligned_cols=29 Identities=34% Similarity=0.856 Sum_probs=21.9
Q ss_pred CCCCCCCCcCC-CC---CCCCCCCCCcccCCcC
Q 018197 328 ASPAKFCDECG-AP---YLRETSKFCSECGVKR 356 (359)
Q Consensus 328 ~~~sKFCpeCG-t~---l~~~~AKFCpECGtKr 356 (359)
+...+||++|| .. +...-+|||||||++.
T Consensus 312 ~~k~nfc~ncG~~~t~~~~ng~a~fcp~cgq~~ 344 (345)
T COG4260 312 CAKLNFCLNCGCGTTADFDNGKAKFCPECGQGF 344 (345)
T ss_pred ccccccccccCcccccCCccchhhhChhhcCCC
Confidence 35677999999 32 2344699999999975
No 130
>PRK14873 primosome assembly protein PriA; Provisional
Probab=53.38 E-value=8.1 Score=41.37 Aligned_cols=23 Identities=30% Similarity=0.658 Sum_probs=17.9
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
.-.|+-||.... ...||+||.+.
T Consensus 410 ~l~Ch~CG~~~~---p~~Cp~Cgs~~ 432 (665)
T PRK14873 410 TPRCRWCGRAAP---DWRCPRCGSDR 432 (665)
T ss_pred eeECCCCcCCCc---CccCCCCcCCc
Confidence 346999998752 57999999874
No 131
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=53.30 E-value=8.2 Score=30.10 Aligned_cols=25 Identities=28% Similarity=0.737 Sum_probs=19.8
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
.....|++||...+. -.-|+.||.-
T Consensus 25 ~~~~~c~~cG~~~l~--Hrvc~~cg~Y 49 (57)
T COG0333 25 PTLSVCPNCGEYKLP--HRVCLKCGYY 49 (57)
T ss_pred ccceeccCCCCcccC--ceEcCCCCCc
Confidence 335789999999864 5789999974
No 132
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=53.07 E-value=9.9 Score=40.70 Aligned_cols=27 Identities=26% Similarity=0.586 Sum_probs=19.4
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 328 ASPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 328 ~~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
+.+.-.|++||.... ....-||.||..
T Consensus 563 n~~~~iC~~CG~~~~-g~~~~CP~CGs~ 589 (623)
T PRK08271 563 NVKITICNDCHHIDK-RTGKRCPICGSE 589 (623)
T ss_pred CCCCccCCCCCCcCC-CCCcCCcCCCCc
Confidence 345677999997632 236889999954
No 133
>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=52.84 E-value=7.4 Score=44.19 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=17.9
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 332 KFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
..||.||+.-. ...||.||.+.
T Consensus 626 RKCPkCG~yTl---k~rCP~CG~~T 647 (1095)
T TIGR00354 626 RKCPQCGKESF---WLKCPVCGELT 647 (1095)
T ss_pred EECCCCCcccc---cccCCCCCCcc
Confidence 56999999854 56899999873
No 134
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=52.69 E-value=5.4 Score=45.56 Aligned_cols=27 Identities=26% Similarity=0.842 Sum_probs=23.1
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
+.-|-|..||..+... .++||.||.+.
T Consensus 692 ~tIKrC~dcg~q~~~~-~~~cP~Cgs~~ 718 (1187)
T COG1110 692 DTIKRCRDCGEQFVDS-EDKCPRCGSRN 718 (1187)
T ss_pred HHHHHHhhcCceeccc-cccCCCCCCcc
Confidence 5668899999999865 88999999864
No 135
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=52.20 E-value=6.9 Score=31.45 Aligned_cols=24 Identities=29% Similarity=0.717 Sum_probs=18.8
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
-|-|..|..-++ +..+-||.||..
T Consensus 4 ~kAC~~Ck~l~~-~d~e~CP~Cgs~ 27 (64)
T COG2093 4 EKACKNCKRLTP-EDTEICPVCGST 27 (64)
T ss_pred hHHHhhccccCC-CCCccCCCCCCc
Confidence 456999977665 458999999986
No 136
>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=51.85 E-value=6.8 Score=35.61 Aligned_cols=24 Identities=33% Similarity=0.895 Sum_probs=18.7
Q ss_pred CCCCCcCCCCC----------------------CCCCCCCCcccCC
Q 018197 331 AKFCDECGAPY----------------------LRETSKFCSECGV 354 (359)
Q Consensus 331 sKFCpeCGt~l----------------------~~~~AKFCpECGt 354 (359)
-.||++|+..+ ..+..+-|+.||+
T Consensus 114 ~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 114 QWFCPQCGHKLHRAEVQLENIVTDLPPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred EEECCCCCCeEEEEEEEecChhhhhHHHHHHHhCChhhccCCccCC
Confidence 36799999887 1235899999996
No 137
>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=51.56 E-value=11 Score=39.55 Aligned_cols=27 Identities=26% Similarity=0.791 Sum_probs=18.0
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 328 ASPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 328 ~~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
..+.-.|.+||.. -......||.||.+
T Consensus 521 n~~~~~C~~CG~~-g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 521 NPPVDVCEDCGYT-GEGLNDKCPKCGSH 547 (579)
T ss_pred ccCCccCCCCCCC-CCCCCCcCcCCCCc
Confidence 3456789999972 11112589999965
No 138
>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=50.92 E-value=5.1 Score=44.73 Aligned_cols=8 Identities=38% Similarity=1.103 Sum_probs=0.0
Q ss_pred CCcccCCc
Q 018197 348 FCSECGVK 355 (359)
Q Consensus 348 FCpECGtK 355 (359)
+||.||.+
T Consensus 694 ~C~~C~~~ 701 (900)
T PF03833_consen 694 ECPKCGRE 701 (900)
T ss_dssp --------
T ss_pred cccccccc
Confidence 66666665
No 139
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.82 E-value=8.7 Score=34.98 Aligned_cols=14 Identities=36% Similarity=1.168 Sum_probs=8.9
Q ss_pred CCCCCCCcCCCCCC
Q 018197 329 SPAKFCDECGAPYL 342 (359)
Q Consensus 329 ~~sKFCpeCGt~l~ 342 (359)
..+.||++||.+++
T Consensus 66 e~psfchncgs~fp 79 (160)
T COG4306 66 EPPSFCHNCGSRFP 79 (160)
T ss_pred CCcchhhcCCCCCC
Confidence 44567777777663
No 140
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=50.53 E-value=8.6 Score=32.30 Aligned_cols=26 Identities=23% Similarity=0.516 Sum_probs=21.7
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
...++|+.|....+.. ++.|..||+=
T Consensus 46 ~~~~~C~~C~~~kp~R-s~HC~~C~~C 71 (174)
T PF01529_consen 46 GELKYCSTCKIIKPPR-SHHCRVCNRC 71 (174)
T ss_pred CCCEECcccCCcCCCc-ceeccccccc
Confidence 4578999998887754 9999999864
No 141
>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=49.77 E-value=9.9 Score=39.56 Aligned_cols=8 Identities=38% Similarity=1.128 Sum_probs=5.8
Q ss_pred CCcCCCCC
Q 018197 334 CDECGAPY 341 (359)
Q Consensus 334 CpeCGt~l 341 (359)
||.||...
T Consensus 203 CPhCg~~~ 210 (557)
T PF05876_consen 203 CPHCGEEQ 210 (557)
T ss_pred CCCCCCCc
Confidence 77777765
No 142
>PRK07218 replication factor A; Provisional
Probab=49.33 E-value=9.3 Score=39.10 Aligned_cols=21 Identities=29% Similarity=0.635 Sum_probs=17.4
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCc
Q 018197 332 KFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtK 355 (359)
+-||+|+..+.. -.|++||..
T Consensus 298 ~rCP~C~r~v~~---~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRVIQK---GQCRSHGAV 318 (423)
T ss_pred ecCcCccccccC---CcCCCCCCc
Confidence 679999999843 589999975
No 143
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=48.35 E-value=12 Score=27.27 Aligned_cols=24 Identities=29% Similarity=0.627 Sum_probs=16.2
Q ss_pred CCCCCcCCCCCCC-----C------CCCCCcccCC
Q 018197 331 AKFCDECGAPYLR-----E------TSKFCSECGV 354 (359)
Q Consensus 331 sKFCpeCGt~l~~-----~------~AKFCpECGt 354 (359)
-|-||-||..-+. . ..-+|.+||.
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4779999977521 1 1245999987
No 144
>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=48.31 E-value=5.9 Score=44.25 Aligned_cols=20 Identities=35% Similarity=0.916 Sum_probs=0.0
Q ss_pred CCCcCCCCCCCCCCCCCcccCCc
Q 018197 333 FCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~~~~AKFCpECGtK 355 (359)
-||+||..-. ...||+||+.
T Consensus 657 ~Cp~Cg~~t~---~~~Cp~CG~~ 676 (900)
T PF03833_consen 657 RCPKCGKETF---YNRCPECGSH 676 (900)
T ss_dssp -----------------------
T ss_pred cCcccCCcch---hhcCcccCCc
Confidence 3777776632 3455555554
No 145
>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=48.22 E-value=9.5 Score=43.38 Aligned_cols=29 Identities=24% Similarity=0.539 Sum_probs=21.1
Q ss_pred CCCCC-CCcCCCCCC-CCCCCCCcccCCcCc
Q 018197 329 SPAKF-CDECGAPYL-RETSKFCSECGVKRL 357 (359)
Q Consensus 329 ~~sKF-CpeCGt~l~-~~~AKFCpECGtKr~ 357 (359)
+.-+| |..||++|- .+-+--|++||.++.
T Consensus 1009 srQ~fRC~kC~~kYRR~PL~G~C~kCGg~li 1039 (1095)
T TIGR00354 1009 SRQEVRCTKCNTKYRRIPLVGKCLKCGNNLT 1039 (1095)
T ss_pred hccceeecccCCccccCCCCCcccccCCeEE
Confidence 34466 999999982 123567999999863
No 146
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=48.18 E-value=4.8 Score=30.04 Aligned_cols=10 Identities=40% Similarity=1.032 Sum_probs=4.2
Q ss_pred CCCcccCCcC
Q 018197 347 KFCSECGVKR 356 (359)
Q Consensus 347 KFCpECGtKr 356 (359)
.||++||+.+
T Consensus 49 ~FC~~CGs~l 58 (92)
T PF04828_consen 49 YFCPTCGSPL 58 (92)
T ss_dssp EEETTT--EE
T ss_pred cccCCCCCee
Confidence 4555555543
No 147
>PF03983 SHD1: SLA1 homology domain 1, SHD1 ; InterPro: IPR007131 The SLA1 homology domain is found in the cytoskeleton assembly control protein SLA1, which is responsible for the correct formation of the actin cytoskeleton.; GO: 0008092 cytoskeletal protein binding, 0030674 protein binding, bridging, 0042802 identical protein binding, 0043130 ubiquitin binding; PDB: 2HBP_A.
Probab=47.84 E-value=11 Score=30.48 Aligned_cols=40 Identities=28% Similarity=0.550 Sum_probs=26.3
Q ss_pred hhHhhheeEeEEEeecceeeccC-CCCChhhHHHHHHHhccc
Q 018197 142 LVIQEEKRVRFVVVNGLDIVEKP-NNMPIEDAEWFKRLTGRN 182 (359)
Q Consensus 142 lv~~EekrvrfvVVnGl~IVE~p-~Nlp~eDqewfkRLtgr~ 182 (359)
+|--...+|.+.=.||-.| +-| +.|..+|++|++++||.+
T Consensus 28 fv~~~dgkV~L~k~nG~~i-~VP~~kLS~~D~~yve~~tg~s 68 (70)
T PF03983_consen 28 FVGVNDGKVHLHKTNGVKI-AVPLEKLSDEDQEYVEKITGKS 68 (70)
T ss_dssp EEEEETTEEEEE-TTS-EE-EEETTSB-HHHHHHHHHHHS--
T ss_pred EEEeeCCEEEEEecCCeEE-EeEhHHcCHHHHHHHHHHhccC
Confidence 3344567888888899754 333 469999999999999954
No 148
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=47.52 E-value=8.2 Score=35.73 Aligned_cols=25 Identities=32% Similarity=0.805 Sum_probs=19.4
Q ss_pred CCCCCcCCCCC----------------------CCCCCCCCcccCCc
Q 018197 331 AKFCDECGAPY----------------------LRETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l----------------------~~~~AKFCpECGtK 355 (359)
-.||++|+..+ ..+..+-|+.||+-
T Consensus 120 ~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~CG~v 166 (177)
T PRK13264 120 QWYCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDNCGTV 166 (177)
T ss_pred EEECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCcCCcc
Confidence 36799999887 13358999999984
No 149
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=46.89 E-value=11 Score=29.68 Aligned_cols=21 Identities=33% Similarity=0.725 Sum_probs=15.3
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCc
Q 018197 332 KFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtK 355 (359)
|-|.+|..-. ..+.||.||..
T Consensus 4 kAC~~C~~i~---~~~~CP~Cgs~ 24 (61)
T PRK08351 4 KACRHCHYIT---TEDRCPVCGSR 24 (61)
T ss_pred hhhhhCCccc---CCCcCCCCcCC
Confidence 4688887665 35689999875
No 150
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=46.47 E-value=14 Score=39.54 Aligned_cols=26 Identities=23% Similarity=0.632 Sum_probs=18.8
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
.+.-.|++||.. ..-..-||.||...
T Consensus 624 ~~~~~C~~CG~~--~g~~~~CP~CG~~~ 649 (656)
T PRK08270 624 PTFSICPKHGYL--SGEHEFCPKCGEET 649 (656)
T ss_pred CCCcccCCCCCc--CCCCCCCcCCcCcc
Confidence 345679999973 23367899999763
No 151
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=46.20 E-value=5.7 Score=41.30 Aligned_cols=25 Identities=28% Similarity=0.747 Sum_probs=11.8
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
.+...|.+||.... ...-||.||.+
T Consensus 489 ~~~~~C~~CG~~~~--~~~~CP~CGs~ 513 (546)
T PF13597_consen 489 PPIDICPDCGYIGG--EGDKCPKCGSE 513 (546)
T ss_dssp --EEEETTT---S----EEE-CCC---
T ss_pred cCcccccCCCcCCC--CCCCCCCCCCc
Confidence 44567999998753 26789999987
No 152
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=45.22 E-value=10 Score=45.14 Aligned_cols=24 Identities=21% Similarity=0.681 Sum_probs=19.6
Q ss_pred CCCcCCCC------C-CCCCCCCCcccCCcC
Q 018197 333 FCDECGAP------Y-LRETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~------l-~~~~AKFCpECGtKr 356 (359)
.||+||.+ + ..+|-.-||.||-..
T Consensus 1706 ~cp~c~~~~~~~~~~~~~~gc~~c~~cg~s~ 1736 (1740)
T PRK08332 1706 YCPVCYEKEGKLVELRMESGCATCPVCGWSK 1736 (1740)
T ss_pred CCCCCCCCCCcceeeEecCCceeCCCCCCcc
Confidence 49999999 3 467888999999753
No 153
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=45.07 E-value=10 Score=28.32 Aligned_cols=23 Identities=39% Similarity=1.061 Sum_probs=17.3
Q ss_pred CCCCCCCcCCCCCC--------CCCCCCCcc
Q 018197 329 SPAKFCDECGAPYL--------RETSKFCSE 351 (359)
Q Consensus 329 ~~sKFCpeCGt~l~--------~~~AKFCpE 351 (359)
-+.|.|+-||.++. =+..|||++
T Consensus 6 lp~K~C~~C~rpf~WRKKW~~~Wd~VkYCS~ 36 (42)
T PF10013_consen 6 LPSKICPVCGRPFTWRKKWARCWDEVKYCSD 36 (42)
T ss_pred CCCCcCcccCCcchHHHHHHHhchhhccHHH
Confidence 35799999999982 234888886
No 154
>KOG1883 consensus Cofactor required for Sp1 transcriptional activation, subunit 3 [Transcription]
Probab=44.84 E-value=8 Score=44.77 Aligned_cols=21 Identities=29% Similarity=0.262 Sum_probs=18.6
Q ss_pred chhhHHHHHHHHHHHHHHHHh
Q 018197 65 FALPLMYVANMYETLVNDVNL 85 (359)
Q Consensus 65 f~LPLmyvANlyetlv~~vn~ 85 (359)
-|||--|-+-+|..||.=++.
T Consensus 1199 taLP~~y~~~l~d~lv~vivn 1219 (1517)
T KOG1883|consen 1199 TALPEPYWNALHDRLVAVIVN 1219 (1517)
T ss_pred hcCCcHHHHHHHHHHHHHHcC
Confidence 479999999999999998876
No 155
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=44.78 E-value=10 Score=38.24 Aligned_cols=23 Identities=35% Similarity=0.930 Sum_probs=17.5
Q ss_pred CCCcCCCCCCCCC----CCCCcccCCcC
Q 018197 333 FCDECGAPYLRET----SKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~~~~----AKFCpECGtKr 356 (359)
.|..||..+.... .--|| ||.++
T Consensus 242 ~c~~C~~~~~~~~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 242 ACEACGEPAVSEDAETACANCP-CGGRI 268 (374)
T ss_pred hhcccCCcCCchhhhhcCCCCC-CCCcc
Confidence 4999999985332 25699 99985
No 156
>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=44.70 E-value=11 Score=25.57 Aligned_cols=17 Identities=41% Similarity=0.991 Sum_probs=9.2
Q ss_pred CCCCCCCCCCcCCCCCC
Q 018197 326 MPASPAKFCDECGAPYL 342 (359)
Q Consensus 326 ~p~~~sKFCpeCGt~l~ 342 (359)
...-++.+|++||..+.
T Consensus 27 i~~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 27 IENVPALVCPQCGEEYL 43 (46)
T ss_pred EeCCCccccccCCCEee
Confidence 33444556666666553
No 157
>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=44.51 E-value=15 Score=39.11 Aligned_cols=26 Identities=23% Similarity=0.572 Sum_probs=17.4
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
.+.-.|++||.. ..+....||.||.+
T Consensus 530 ~~~siC~~CGy~-~g~~~~~CP~CGs~ 555 (586)
T TIGR02827 530 IKITICNDCHHI-DKRTLHRCPVCGSA 555 (586)
T ss_pred CCCeecCCCCCc-CCCcCCcCcCCCCc
Confidence 345669999972 11223799999954
No 158
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=44.37 E-value=8.1 Score=26.96 Aligned_cols=21 Identities=29% Similarity=0.784 Sum_probs=14.0
Q ss_pred CCcCCCCCCC-----CCCCCCcccCC
Q 018197 334 CDECGAPYLR-----ETSKFCSECGV 354 (359)
Q Consensus 334 CpeCGt~l~~-----~~AKFCpECGt 354 (359)
||.|+..|.. -...-|+.||-
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G 27 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGG 27 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCe
Confidence 8999887721 12455888874
No 159
>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=43.82 E-value=11 Score=33.15 Aligned_cols=25 Identities=24% Similarity=0.503 Sum_probs=18.2
Q ss_pred CCCCCcCCCCC--CCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPY--LRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l--~~~~AKFCpECGtKr 356 (359)
.--||+||..- .. -.--|+.|++++
T Consensus 69 ~V~CP~C~K~TKmLG-r~D~CM~C~~pL 95 (114)
T PF11023_consen 69 QVECPNCGKQTKMLG-RVDACMHCKEPL 95 (114)
T ss_pred eeECCCCCChHhhhc-hhhccCcCCCcC
Confidence 34499999875 32 245799999986
No 160
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.71 E-value=13 Score=38.50 Aligned_cols=24 Identities=25% Similarity=0.726 Sum_probs=18.7
Q ss_pred CCCcCCCCCCCCC--CCCCcccCCcC
Q 018197 333 FCDECGAPYLRET--SKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~~~~--AKFCpECGtKr 356 (359)
-||.||..+...| .--|+.||++.
T Consensus 352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 352 VCPRCGGRMKSAGRNGFRCKKCGTRA 377 (421)
T ss_pred CCCccCCchhhcCCCCcccccccccC
Confidence 5999999995443 44699999985
No 161
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=43.55 E-value=10 Score=32.08 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=17.7
Q ss_pred CCC-CCcCCCCCCC------CCCCCCcccCCcC
Q 018197 331 AKF-CDECGAPYLR------ETSKFCSECGVKR 356 (359)
Q Consensus 331 sKF-CpeCGt~l~~------~~AKFCpECGtKr 356 (359)
.-| ||.||...+. -.-.-|+.||...
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 344 9999965432 1256799999863
No 162
>PRK12366 replication factor A; Reviewed
Probab=43.52 E-value=9.5 Score=40.43 Aligned_cols=24 Identities=21% Similarity=0.497 Sum_probs=18.5
Q ss_pred CCCCcCCCCCCCC-CCCCCcccCCc
Q 018197 332 KFCDECGAPYLRE-TSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~-~AKFCpECGtK 355 (359)
+-||+|..++... +.-.|+.||+.
T Consensus 533 ~aCp~CnkKv~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRKRVEEVDGEYICEFCGEV 557 (637)
T ss_pred ecccccCeEeEcCCCcEECCCCCCC
Confidence 3499999998642 45589999985
No 163
>PRK05580 primosome assembly protein PriA; Validated
Probab=43.47 E-value=15 Score=39.09 Aligned_cols=23 Identities=35% Similarity=0.710 Sum_probs=16.1
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 332 KFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
-.|+-||..... ...||+||...
T Consensus 409 l~Ch~Cg~~~~~--~~~Cp~Cg~~~ 431 (679)
T PRK05580 409 LRCHHCGYQEPI--PKACPECGSTD 431 (679)
T ss_pred EECCCCcCCCCC--CCCCCCCcCCe
Confidence 358888877643 35799998763
No 164
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=42.91 E-value=9.1 Score=39.08 Aligned_cols=24 Identities=29% Similarity=0.639 Sum_probs=18.9
Q ss_pred CCCcCCCCCCCCCCCCCcccCCcC
Q 018197 333 FCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~~~~AKFCpECGtKr 356 (359)
-|+.|=+-...-+-+|||.||.+-
T Consensus 244 RCh~Cfsit~~m~k~FCp~CG~~T 267 (376)
T KOG2463|consen 244 RCHGCFSITSEMPKDFCPSCGHKT 267 (376)
T ss_pred EeeeeeEecCccchhcccccCCCe
Confidence 399996666655688999999883
No 165
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=42.90 E-value=9.1 Score=33.36 Aligned_cols=28 Identities=25% Similarity=0.614 Sum_probs=20.3
Q ss_pred CCCCCCCcCCCCCC-CCCCCCCcccCCcC
Q 018197 329 SPAKFCDECGAPYL-RETSKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~-~~~AKFCpECGtKr 356 (359)
+..-.|..||..+. ..+.-.||.||...
T Consensus 68 p~~~~C~~C~~~~~~e~~~~~CP~C~s~~ 96 (115)
T COG0375 68 PAECWCLDCGQEVELEELDYRCPKCGSIN 96 (115)
T ss_pred ccEEEeccCCCeecchhheeECCCCCCCc
Confidence 44556999998874 33555599999764
No 166
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=42.62 E-value=6.3 Score=25.80 Aligned_cols=22 Identities=18% Similarity=0.538 Sum_probs=12.5
Q ss_pred CCCCcCCCCCCC-----CCCCCCcccC
Q 018197 332 KFCDECGAPYLR-----ETSKFCSECG 353 (359)
Q Consensus 332 KFCpeCGt~l~~-----~~AKFCpECG 353 (359)
+-|+.||..+.. ....||+.|=
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 569999998732 2468999884
No 167
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=42.56 E-value=13 Score=38.51 Aligned_cols=25 Identities=40% Similarity=1.015 Sum_probs=17.9
Q ss_pred CC-CCcCCCCCC-----CCCCCC-CcccCCcC
Q 018197 332 KF-CDECGAPYL-----RETSKF-CSECGVKR 356 (359)
Q Consensus 332 KF-CpeCGt~l~-----~~~AKF-CpECGtKr 356 (359)
.| |++||.... .++++| ||+||...
T Consensus 327 ~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~ 358 (411)
T COG1503 327 TYKCPTCGYENLKSKREFEQKRFRCPECGSEM 358 (411)
T ss_pred eecCCCcchhhhhcccccccccccCccccccc
Confidence 45 999999872 123455 99999864
No 168
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=42.08 E-value=14 Score=29.56 Aligned_cols=22 Identities=23% Similarity=0.484 Sum_probs=16.2
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
-+-|.+|..-. ..+.||.||..
T Consensus 5 ~~AC~~C~~i~---~~~~Cp~Cgs~ 26 (64)
T PRK06393 5 YRACKKCKRLT---PEKTCPVHGDE 26 (64)
T ss_pred hhhHhhCCccc---CCCcCCCCCCC
Confidence 35588997665 36799999975
No 169
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=41.05 E-value=15 Score=29.45 Aligned_cols=27 Identities=26% Similarity=0.586 Sum_probs=19.6
Q ss_pred CCCCCCCcCCCCCCC------CCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLR------ETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~------~~AKFCpECGtK 355 (359)
..-|.||-||...+. -..-+|..||..
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 457899999998631 124679999974
No 170
>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=40.60 E-value=22 Score=40.94 Aligned_cols=35 Identities=26% Similarity=0.587 Sum_probs=23.6
Q ss_pred cccCCCCCCCCCCcCCCCCC-CC---------CCCCCcccCCcCc
Q 018197 323 LHVMPASPAKFCDECGAPYL-RE---------TSKFCSECGVKRL 357 (359)
Q Consensus 323 ~~i~p~~~sKFCpeCGt~l~-~~---------~AKFCpECGtKr~ 357 (359)
..+.|-.+--.||+|...-. .. -.|-||.||+++.
T Consensus 675 TeVdPL~phy~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~~~ 719 (1213)
T TIGR01405 675 TEVNPLPPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLK 719 (1213)
T ss_pred CCcCCCcccccCcccccccccccccccccccCccccCcccccccc
Confidence 34556666678999965421 10 1689999999864
No 171
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=40.60 E-value=22 Score=27.67 Aligned_cols=23 Identities=22% Similarity=0.675 Sum_probs=14.7
Q ss_pred CCCcCCCCCCCCCCCCCcccCCc
Q 018197 333 FCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~~~~AKFCpECGtK 355 (359)
+||-|+..+.....--||.||-+
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIP 23 (55)
T ss_pred CCCCCccccccccCCcCCCCCCc
Confidence 47777776544444557777765
No 172
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=40.54 E-value=8.6 Score=39.45 Aligned_cols=23 Identities=39% Similarity=0.817 Sum_probs=17.7
Q ss_pred CCcCCCCCCCCCCC----CCcccCCcC
Q 018197 334 CDECGAPYLRETSK----FCSECGVKR 356 (359)
Q Consensus 334 CpeCGt~l~~~~AK----FCpECGtKr 356 (359)
|..|++.+..+.|+ -||+||.++
T Consensus 249 C~rC~t~y~le~A~~~~wrCpkCGg~i 275 (403)
T COG1379 249 CSRCYTRYSLEEAKSLRWRCPKCGGKI 275 (403)
T ss_pred HHHhhhccCcchhhhhcccCcccccch
Confidence 99999998544343 599999864
No 173
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=40.41 E-value=18 Score=37.74 Aligned_cols=22 Identities=27% Similarity=0.730 Sum_probs=16.9
Q ss_pred CCCcCCCCCCCCCCCCCcccCCc
Q 018197 333 FCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~~~~AKFCpECGtK 355 (359)
.|.+||.... ...--||.||..
T Consensus 520 ~C~~CG~~~~-~~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGE-GEGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCc-CCCCCCcCCCCc
Confidence 8999997542 235789999965
No 174
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=40.34 E-value=15 Score=31.11 Aligned_cols=25 Identities=28% Similarity=0.582 Sum_probs=19.1
Q ss_pred CCCcCCCCCC---CCCCCCCcccCCcCc
Q 018197 333 FCDECGAPYL---RETSKFCSECGVKRL 357 (359)
Q Consensus 333 FCpeCGt~l~---~~~AKFCpECGtKr~ 357 (359)
-||.||.+-+ ..+---|..||.+..
T Consensus 37 ~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 37 VCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 4999999863 345667999998864
No 175
>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=39.86 E-value=21 Score=30.44 Aligned_cols=24 Identities=33% Similarity=0.724 Sum_probs=15.4
Q ss_pred cccccCCCCCCCC---------CCcCCCCCCCC
Q 018197 321 ERLHVMPASPAKF---------CDECGAPYLRE 344 (359)
Q Consensus 321 G~~~i~p~~~sKF---------CpeCGt~l~~~ 344 (359)
|+=.+||+-+.|| ||.||+.+...
T Consensus 7 GtKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 3334566544444 99999998543
No 176
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=39.55 E-value=17 Score=28.46 Aligned_cols=23 Identities=26% Similarity=0.832 Sum_probs=16.1
Q ss_pred CCCcCCCCC---------CCCCCCCCcccCCc
Q 018197 333 FCDECGAPY---------LRETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l---------~~~~AKFCpECGtK 355 (359)
.||-||.+- +..-.-|||.|-+.
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCce
Confidence 499999764 12236799999765
No 177
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=39.46 E-value=23 Score=38.44 Aligned_cols=27 Identities=33% Similarity=0.687 Sum_probs=17.3
Q ss_pred CCCCCCCcCCCCC---CCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPY---LRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l---~~~~AKFCpECGtK 355 (359)
.+.-.|++||..= .....--||.||.+
T Consensus 639 ~~~~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 639 TPIDECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred CCCcccCCCCCCccccCCCCCCcCcCCCCC
Confidence 4567899999730 11112469999953
No 178
>KOG0257 consensus Kynurenine aminotransferase, glutamine transaminase K [Amino acid transport and metabolism]
Probab=39.40 E-value=7.1 Score=40.43 Aligned_cols=27 Identities=52% Similarity=0.741 Sum_probs=24.5
Q ss_pred HHHHHHHHHHH--hhhhhccccchhhhhH
Q 018197 74 NMYETLVNDVN--LRLASFNGIREKTIGV 100 (359)
Q Consensus 74 Nlyetlv~~vn--~rlasl~g~~ekt~gv 100 (359)
+.||-||.|=| .|+|||+|+.|.||-|
T Consensus 212 evYe~~v~d~~~h~r~aslPgm~ertitv 240 (420)
T KOG0257|consen 212 EVYEWLVYDGNKHIRIASLPGMYERTITV 240 (420)
T ss_pred hHhHHHhhCCCcceeeecCCchhheEEEe
Confidence 56999999999 9999999999998754
No 179
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.08 E-value=22 Score=28.77 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=11.5
Q ss_pred CCCCCCCCcCCCCCC
Q 018197 328 ASPAKFCDECGAPYL 342 (359)
Q Consensus 328 ~~~sKFCpeCGt~l~ 342 (359)
.....-||.||++..
T Consensus 4 ~~~~v~CP~Cgkpv~ 18 (65)
T COG3024 4 LRITVPCPTCGKPVV 18 (65)
T ss_pred ccccccCCCCCCccc
Confidence 344567999999985
No 180
>PHA00626 hypothetical protein
Probab=39.04 E-value=16 Score=29.06 Aligned_cols=23 Identities=26% Similarity=0.846 Sum_probs=15.1
Q ss_pred CCCcCCCC-CCC-------CCCCCCcccCCc
Q 018197 333 FCDECGAP-YLR-------ETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~-l~~-------~~AKFCpECGtK 355 (359)
.||.||.. +.. ..---|+.||..
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ 32 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYN 32 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCe
Confidence 59999985 321 234458999865
No 181
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=38.73 E-value=16 Score=40.98 Aligned_cols=28 Identities=29% Similarity=0.715 Sum_probs=20.0
Q ss_pred CCCCC-CCcCCCCC-----------CCCC--CCCCcccCCcC
Q 018197 329 SPAKF-CDECGAPY-----------LRET--SKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKF-CpeCGt~l-----------~~~~--AKFCpECGtKr 356 (359)
..-|| |+|||+-+ +-.| .-=|++|+++.
T Consensus 278 ~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRF 319 (1007)
T KOG3623|consen 278 LLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRF 319 (1007)
T ss_pred hhccccccccchhhhhHHHHHhhheeecCCCCcCCccccccc
Confidence 44699 99999986 2222 33599999875
No 182
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=38.72 E-value=12 Score=31.29 Aligned_cols=22 Identities=32% Similarity=0.967 Sum_probs=10.9
Q ss_pred CCcCCCCC--------CCCCCCCCcccCCc
Q 018197 334 CDECGAPY--------LRETSKFCSECGVK 355 (359)
Q Consensus 334 CpeCGt~l--------~~~~AKFCpECGtK 355 (359)
|.+|+.++ ..++.+-||.|+++
T Consensus 31 C~eC~fPvCr~CyEYErkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 31 CHECAFPVCRPCYEYERKEGNQVCPQCKTR 60 (80)
T ss_dssp -SSS-----HHHHHHHHHTS-SB-TTT--B
T ss_pred EcccCCccchhHHHHHhhcCcccccccCCC
Confidence 99999998 35689999999987
No 183
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=38.61 E-value=15 Score=35.20 Aligned_cols=24 Identities=33% Similarity=0.843 Sum_probs=15.5
Q ss_pred CCCCcCCCCCCCC-C----C----CCCcccCCc
Q 018197 332 KFCDECGAPYLRE-T----S----KFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~-~----A----KFCpECGtK 355 (359)
..|..||..+... . . --|+.||.+
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 123 VRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence 3499998887411 1 1 239999984
No 184
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=38.59 E-value=19 Score=39.30 Aligned_cols=26 Identities=27% Similarity=0.816 Sum_probs=18.5
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
..--.|..||..+-....+ ||.||..
T Consensus 639 ~~i~~C~~cg~~~~~~~~~-Cp~CG~~ 664 (700)
T COG1328 639 TPISVCNRCGYSGEGLRTR-CPKCGSE 664 (700)
T ss_pred CCceeeccCCccccccccc-CCCCCCc
Confidence 4456799999987432233 9999965
No 185
>PF07105 DUF1367: Protein of unknown function (DUF1367); InterPro: IPR009797 This entry is represented by Bacteriophage VT2phi_272, P37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=38.53 E-value=90 Score=29.67 Aligned_cols=92 Identities=24% Similarity=0.162 Sum_probs=69.8
Q ss_pred HHHHHHHHHHhhhhhccccchhhhhHHHHhhcchhHHHHhhCCCCCccceehhhhhhhhhhhccchhhhHhhheeEeEEE
Q 018197 75 MYETLVNDVNLRLASFNGIREKTIGVALEAAGGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKRVRFVV 154 (359)
Q Consensus 75 lyetlv~~vn~rlasl~g~~ekt~gvaleaagglyr~l~kkfpkkg~c~fkRRElAts~etrt~fpelv~~EekrvrfvV 154 (359)
-=+.||+.+=.+||...|-. ++-.|+|-..-.++++|= +.--+...+.+.|+.-|+-|---+-++.
T Consensus 71 ~E~~lv~g~v~~la~~~g~~----~~l~~~A~~yL~~va~~R----------~~~~~~~k~feafR~wvti~AG~yd~~~ 136 (196)
T PF07105_consen 71 AERKLVRGFVKFLASYAGSE----DALQEAADQYLAKVAKKR----------ARDIEAEKSFEAFRKWVTIEAGFYDIVP 136 (196)
T ss_pred HHHHHHHHHHHHHHHHhCCH----HHHHHHHHHHHHHHHHHh----------hccchhhhCHHHHHHHHHHhcccceeee
Confidence 34679999999999999976 788899999888998863 2233566667779999998876666443
Q ss_pred -eec-ceeeccCCCCChhhHHHHHHHhc
Q 018197 155 -VNG-LDIVEKPNNMPIEDAEWFKRLTG 180 (359)
Q Consensus 155 -VnG-l~IVE~p~Nlp~eDqewfkRLtg 180 (359)
++| +..+-|++++-+=|+++|+++-.
T Consensus 137 ~pdG~~~~~pkSISFa~Mdq~eF~~lY~ 164 (196)
T PF07105_consen 137 NPDGGVRKEPKSISFANMDQEEFEELYK 164 (196)
T ss_pred CCCCcEeeccccCcccccCHHHHHHHHH
Confidence 456 66667788888888888888754
No 186
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=38.53 E-value=16 Score=35.17 Aligned_cols=13 Identities=31% Similarity=0.705 Sum_probs=10.7
Q ss_pred CCCCCCCcCCCCC
Q 018197 329 SPAKFCDECGAPY 341 (359)
Q Consensus 329 ~~sKFCpeCGt~l 341 (359)
....|||+||.-+
T Consensus 219 d~iv~CP~CgRIL 231 (239)
T COG1579 219 DEIVFCPYCGRIL 231 (239)
T ss_pred CCCccCCccchHH
Confidence 6678999999865
No 187
>PRK02935 hypothetical protein; Provisional
Probab=38.49 E-value=17 Score=31.87 Aligned_cols=26 Identities=19% Similarity=0.526 Sum_probs=18.8
Q ss_pred CCCCCcCCCCC-CCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPY-LRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l-~~~~AKFCpECGtKr 356 (359)
.--||+|++.- .-.-.--|..|++++
T Consensus 70 qV~CP~C~K~TKmLGrvD~CM~C~~PL 96 (110)
T PRK02935 70 QVICPSCEKPTKMLGRVDACMHCNQPL 96 (110)
T ss_pred eeECCCCCchhhhccceeecCcCCCcC
Confidence 34699999774 112366899999986
No 188
>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=37.85 E-value=17 Score=26.70 Aligned_cols=24 Identities=38% Similarity=0.740 Sum_probs=13.8
Q ss_pred CCCCcCCCCCC--C-------CCCC-CCcccCCc
Q 018197 332 KFCDECGAPYL--R-------ETSK-FCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~--~-------~~AK-FCpECGtK 355 (359)
|-||-||..-. . .+.- .|..||..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 56888887632 0 1122 48888764
No 189
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=37.41 E-value=55 Score=34.18 Aligned_cols=75 Identities=24% Similarity=0.423 Sum_probs=51.2
Q ss_pred HHHHHHHHHhhhhhccccchhhhhHHHHhhcchhH----HHHhhCCCCCccceehhhhhh--hhhhhccchhhhHhhh-e
Q 018197 76 YETLVNDVNLRLASFNGIREKTIGVALEAAGGLYR----SLAKKFPKKGSCTYKRRELAT--SLETRTRFPELVIQEE-K 148 (359)
Q Consensus 76 yetlv~~vn~rlasl~g~~ekt~gvaleaagglyr----~l~kkfpkkg~c~fkRRElAt--s~etrt~fpelv~~Ee-k 148 (359)
-||||.+-+.|+ .+++.+|+|+.|+--||. ||+|+|- |.+=.++|. -|..+.+.-+.|.|=. .
T Consensus 276 Lr~lVk~~~~rF-----~kDnnt~l~k~av~sl~k~nI~rltktF~-----sLsL~dIA~~vQLa~~qevek~Ilqmie~ 345 (422)
T KOG2582|consen 276 LRTLVKKHSERF-----TKDNNTGLAKQAVSSLYKKNIQRLTKTFL-----SLSLSDIASRVQLASAQEVEKYILQMIED 345 (422)
T ss_pred HHHHHHHHHHHH-----hhcCcHHHHHHHHHHHHHHHHHHHHHHHH-----HhhHHHHHHHHHhcchHHHHHHHHHHhcc
Confidence 467777777777 479999999999999996 5777774 455555555 4444444444444422 2
Q ss_pred eEeEEEeeccee
Q 018197 149 RVRFVVVNGLDI 160 (359)
Q Consensus 149 rvrfvVVnGl~I 160 (359)
.=-|.++|||.+
T Consensus 346 ~~i~a~iNG~v~ 357 (422)
T KOG2582|consen 346 GEIFASINGMVF 357 (422)
T ss_pred CceEEEecceEE
Confidence 335899999944
No 190
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=37.31 E-value=19 Score=35.08 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=22.1
Q ss_pred CCCCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 327 PASPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 327 p~~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
+....+||.+|-.-.+ +.+|.|+.|+.=
T Consensus 105 ~~~~~~~C~~C~~~KP-~RS~HC~~Cn~C 132 (309)
T COG5273 105 KFGTENFCSTCNIYKP-PRSHHCSICNRC 132 (309)
T ss_pred ccccceeccccccccC-CCCccchhhcch
Confidence 3467899999976665 569999999863
No 191
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=37.07 E-value=18 Score=42.72 Aligned_cols=20 Identities=35% Similarity=0.891 Sum_probs=16.8
Q ss_pred CCcCCCCCCCCCCCCCcccCCcC
Q 018197 334 CDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 334 CpeCGt~l~~~~AKFCpECGtKr 356 (359)
||.||+.-+ ..-||.||++.
T Consensus 677 Cp~Cg~~~~---~~~Cp~CG~~~ 696 (1627)
T PRK14715 677 CPKCGKVGL---YHVCPFCGTRV 696 (1627)
T ss_pred CCCCCCccc---cccCcccCCcc
Confidence 999999854 56899999874
No 192
>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=36.65 E-value=11 Score=29.24 Aligned_cols=20 Identities=40% Similarity=0.728 Sum_probs=9.5
Q ss_pred CCCCcCCCCCCC----CCCCCCcc
Q 018197 332 KFCDECGAPYLR----ETSKFCSE 351 (359)
Q Consensus 332 KFCpeCGt~l~~----~~AKFCpE 351 (359)
..||.||++... ..--||++
T Consensus 3 v~CP~C~k~~~~~~~n~~rPFCS~ 26 (57)
T PF03884_consen 3 VKCPICGKPVEWSPENPFRPFCSE 26 (57)
T ss_dssp EE-TTT--EEE-SSSSS--SSSSH
T ss_pred ccCCCCCCeecccCCCCcCCcccH
Confidence 359999999854 34557764
No 193
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.28 E-value=21 Score=32.58 Aligned_cols=12 Identities=33% Similarity=0.944 Sum_probs=10.2
Q ss_pred CCCCcccCCcCc
Q 018197 346 SKFCSECGVKRL 357 (359)
Q Consensus 346 AKFCpECGtKr~ 357 (359)
.-||.+||.+..
T Consensus 68 psfchncgs~fp 79 (160)
T COG4306 68 PSFCHNCGSRFP 79 (160)
T ss_pred cchhhcCCCCCC
Confidence 679999999864
No 194
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=35.16 E-value=29 Score=40.64 Aligned_cols=35 Identities=29% Similarity=0.604 Sum_probs=23.7
Q ss_pred cccCCCCCCCCCCcCCCCCC-CC---------CCCCCcccCCcCc
Q 018197 323 LHVMPASPAKFCDECGAPYL-RE---------TSKFCSECGVKRL 357 (359)
Q Consensus 323 ~~i~p~~~sKFCpeCGt~l~-~~---------~AKFCpECGtKr~ 357 (359)
..+.|-.+--.||+|...-. .. -.|-||+||+++.
T Consensus 900 TeVdPL~phy~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~ 944 (1437)
T PRK00448 900 TEVNPLPPHYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLK 944 (1437)
T ss_pred CCcCCCCccccCcccccccccccccccccccCccccCcccccccc
Confidence 34556677778999965431 11 1688999999964
No 195
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=35.02 E-value=14 Score=31.94 Aligned_cols=32 Identities=25% Similarity=0.568 Sum_probs=22.1
Q ss_pred cCCCCCCCCCCcCCCCCCCCC-----------CCCCcccCCcC
Q 018197 325 VMPASPAKFCDECGAPYLRET-----------SKFCSECGVKR 356 (359)
Q Consensus 325 i~p~~~sKFCpeCGt~l~~~~-----------AKFCpECGtKr 356 (359)
+.+.-.--||..|.+.|.++. .--|.+||...
T Consensus 50 lp~~iKR~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 50 LPREIKRTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIR 92 (105)
T ss_pred cCHHHHHHhccccCcccccCcceEEEEcCCeEEEEecCCCcEE
Confidence 344455578999999985331 34699999863
No 196
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=34.73 E-value=29 Score=21.08 Aligned_cols=17 Identities=24% Similarity=0.561 Sum_probs=13.4
Q ss_pred HhhcchhHHHHhhCCCC
Q 018197 103 EAAGGLYRSLAKKFPKK 119 (359)
Q Consensus 103 eaagglyr~l~kkfpkk 119 (359)
+.|-..|+++.++||++
T Consensus 17 ~~A~~~~~~~~~~~P~s 33 (33)
T PF13174_consen 17 DEAIEYFQRLIKRYPDS 33 (33)
T ss_dssp HHHHHHHHHHHHHSTTS
T ss_pred HHHHHHHHHHHHHCcCC
Confidence 34556899999999974
No 197
>PRK07217 replication factor A; Reviewed
Probab=34.09 E-value=23 Score=35.44 Aligned_cols=22 Identities=36% Similarity=0.534 Sum_probs=17.7
Q ss_pred CCCCCc--CCCCCCCCCCCCCcccCCc
Q 018197 331 AKFCDE--CGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpe--CGt~l~~~~AKFCpECGtK 355 (359)
-+-||+ |+..+.. -.|++||.-
T Consensus 188 I~rCP~~~C~Rvl~~---g~C~~HG~v 211 (311)
T PRK07217 188 IKRCPEEDCTRVLQN---GRCSEHGKV 211 (311)
T ss_pred eecCCccccCccccC---CCCCCCCCc
Confidence 477999 9998843 489999964
No 198
>PLN00209 ribosomal protein S27; Provisional
Probab=34.03 E-value=18 Score=30.48 Aligned_cols=31 Identities=19% Similarity=0.417 Sum_probs=23.4
Q ss_pred CCCCCCCC----CCcCCCCCC----CCCCCCCcccCCcC
Q 018197 326 MPASPAKF----CDECGAPYL----RETSKFCSECGVKR 356 (359)
Q Consensus 326 ~p~~~sKF----CpeCGt~l~----~~~AKFCpECGtKr 356 (359)
.|.+.++| |+.|+.... ......|..||+.+
T Consensus 27 v~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L 65 (86)
T PLN00209 27 VQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVL 65 (86)
T ss_pred ecCCCCEEEEEECCCCCCeeEEEecCceEEEccccCCEe
Confidence 56777887 999988752 34577899999875
No 199
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=33.98 E-value=18 Score=34.15 Aligned_cols=12 Identities=33% Similarity=0.944 Sum_probs=10.6
Q ss_pred CCCCCcccCCcC
Q 018197 345 TSKFCSECGVKR 356 (359)
Q Consensus 345 ~AKFCpECGtKr 356 (359)
.-+||+.||+++
T Consensus 98 ~~~fC~~CG~~~ 109 (256)
T PRK00241 98 SHRFCGYCGHPM 109 (256)
T ss_pred cCccccccCCCC
Confidence 489999999985
No 200
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=33.98 E-value=17 Score=28.58 Aligned_cols=8 Identities=38% Similarity=1.099 Sum_probs=4.7
Q ss_pred CCCcccCC
Q 018197 347 KFCSECGV 354 (359)
Q Consensus 347 KFCpECGt 354 (359)
.-|++||-
T Consensus 37 v~C~~CGY 44 (64)
T PF09855_consen 37 VSCTNCGY 44 (64)
T ss_pred EECCCCCC
Confidence 34666664
No 201
>PF12596 Tnp_P_element_C: 87kDa Transposase; InterPro: IPR022242 This domain family is found in eukaryotes, and is typically between 78 and 110 amino acids in length. The family is found in association with PF05485 from PFAM. There are two completely conserved residues (D and G) that may be functionally important. This family is an 87kDa transposase protein which catalyses both the precise and imprecise excision of a nonautonomous P transposable element.
Probab=33.97 E-value=25 Score=30.43 Aligned_cols=27 Identities=30% Similarity=0.507 Sum_probs=23.7
Q ss_pred HHH-hhcchhHHHHhhCCCCCccceehh
Q 018197 101 ALE-AAGGLYRSLAKKFPKKGSCTYKRR 127 (359)
Q Consensus 101 ale-aagglyr~l~kkfpkkg~c~fkRR 127 (359)
||| .||=+-||+.+|||-=|.|+++-+
T Consensus 78 ~l~YiaGyVa~k~~~k~p~L~~~t~~~~ 105 (106)
T PF12596_consen 78 GLEYIAGYVAKKFRNKYPNLGDYTCNSN 105 (106)
T ss_pred HHHHHHHHHHHHHHhcCCchhheeeccC
Confidence 677 789999999999999999998744
No 202
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=33.95 E-value=37 Score=22.73 Aligned_cols=26 Identities=27% Similarity=0.420 Sum_probs=19.7
Q ss_pred CCCCCCcCCCCCCCC-CCCCCcccCCc
Q 018197 330 PAKFCDECGAPYLRE-TSKFCSECGVK 355 (359)
Q Consensus 330 ~sKFCpeCGt~l~~~-~AKFCpECGtK 355 (359)
.+.||.-|+..+... .+..|..|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~ 36 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVK 36 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCch
Confidence 356899999988542 27889999865
No 203
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=33.80 E-value=21 Score=31.51 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=23.6
Q ss_pred ccCCCCChhhHHHHHHHhccccccccccccccccc
Q 018197 162 EKPNNMPIEDAEWFKRLTGRNEVAISAQDYKFYSP 196 (359)
Q Consensus 162 E~p~Nlp~eDqewfkRLtgr~EVai~g~DYkfys~ 196 (359)
.++.-|+..|.+|+.+|.. =+|+||+.-+-
T Consensus 112 ~~~~~ls~~e~~~i~~Li~-----KhGdDy~aMar 141 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIE-----KHGDDYKAMAR 141 (164)
T ss_pred cCCCCCCHHHHHHHHHHHH-----HHCccHHHHhc
Confidence 4466799999999999966 56799876543
No 204
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=33.69 E-value=17 Score=27.44 Aligned_cols=23 Identities=35% Similarity=0.785 Sum_probs=14.9
Q ss_pred CCCcCCCCC-C-----------CCCCCCCcccCCc
Q 018197 333 FCDECGAPY-L-----------RETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l-~-----------~~~AKFCpECGtK 355 (359)
-|.+||... . -+--||||.|+.-
T Consensus 9 ~C~~c~~rnY~t~KNk~~~~~rLelkKycp~c~kh 43 (50)
T PRK00504 9 ACTECKSRNYTTTKNKKNTPERLELKKFCPRCNKH 43 (50)
T ss_pred EEcCCCCccEeEcCCCCCCCceEEEECcCCCCCCe
Confidence 388888663 0 0126899998864
No 205
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=33.52 E-value=21 Score=40.90 Aligned_cols=22 Identities=32% Similarity=0.899 Sum_probs=19.5
Q ss_pred CCcCCCCC--------CCCCCCCCcccCCc
Q 018197 334 CDECGAPY--------LRETSKFCSECGVK 355 (359)
Q Consensus 334 CpeCGt~l--------~~~~AKFCpECGtK 355 (359)
|.|||-++ -.++.+-||.|+|+
T Consensus 39 C~eC~FPVCrpCYEYEr~eG~q~CPqCktr 68 (1079)
T PLN02638 39 CDVCAFPVCRPCYEYERKDGNQSCPQCKTK 68 (1079)
T ss_pred eccCCCccccchhhhhhhcCCccCCccCCc
Confidence 99999998 35689999999997
No 206
>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=33.50 E-value=11 Score=29.73 Aligned_cols=23 Identities=30% Similarity=0.944 Sum_probs=16.5
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCcCc
Q 018197 332 KFCDECGAPYLRETSKFCSECGVKRL 357 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtKr~ 357 (359)
-||..|-+.++ ..-||+||-.+.
T Consensus 30 TFC~~C~e~~l---~~~CPNCgGelv 52 (57)
T PF06906_consen 30 TFCADCAETML---NGVCPNCGGELV 52 (57)
T ss_pred cccHHHHHHHh---cCcCcCCCCccc
Confidence 57888877665 357999997653
No 207
>KOG0162 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=33.41 E-value=31 Score=38.94 Aligned_cols=32 Identities=16% Similarity=0.174 Sum_probs=15.6
Q ss_pred HHHHHHhccccccccccccccccccccccccc
Q 018197 173 EWFKRLTGRNEVAISAQDYKFYSPRHKYRRVA 204 (359)
Q Consensus 173 ewfkRLtgr~EVai~g~DYkfys~Rhk~RR~~ 204 (359)
|++-.|..|.|-.+-+.=--.+++-+-|++.+
T Consensus 854 Ef~t~L~k~~~e~~n~~l~l~~~~tie~~~K~ 885 (1106)
T KOG0162|consen 854 EFITLLKKRYEERTNRKLQLKFGSTIEYSKKK 885 (1106)
T ss_pred HHHHHHHHHHHHhhcCceeEEeccceEEEecc
Confidence 44555555555555444333444444444433
No 208
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=33.09 E-value=28 Score=36.04 Aligned_cols=28 Identities=36% Similarity=0.721 Sum_probs=20.5
Q ss_pred CCCCC--CCcCCCCCCCCCCCCCcccCCcC
Q 018197 329 SPAKF--CDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKF--CpeCGt~l~~~~AKFCpECGtKr 356 (359)
.+.++ |++|+.+-.-....-|++||...
T Consensus 53 Ad~~i~kC~~c~~~~~y~~~~~C~~cg~~~ 82 (415)
T COG5257 53 ADAKIYKCPECYRPECYTTEPKCPNCGAET 82 (415)
T ss_pred ccCceEeCCCCCCCcccccCCCCCCCCCCc
Confidence 34555 99999865444578899999863
No 209
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=32.86 E-value=24 Score=35.93 Aligned_cols=14 Identities=50% Similarity=1.009 Sum_probs=12.0
Q ss_pred CCCCCCCcCCCCCC
Q 018197 329 SPAKFCDECGAPYL 342 (359)
Q Consensus 329 ~~sKFCpeCGt~l~ 342 (359)
..-||||.||.+..
T Consensus 148 skykFCp~CG~~tk 161 (345)
T KOG3084|consen 148 SKYKFCPGCGSPTK 161 (345)
T ss_pred HHhccCcccCCCcc
Confidence 56799999999984
No 210
>COG1773 Rubredoxin [Energy production and conversion]
Probab=31.56 E-value=26 Score=27.33 Aligned_cols=9 Identities=56% Similarity=1.202 Sum_probs=5.2
Q ss_pred CCCcccCCc
Q 018197 347 KFCSECGVK 355 (359)
Q Consensus 347 KFCpECGtK 355 (359)
--||+||..
T Consensus 37 w~CP~Cg~~ 45 (55)
T COG1773 37 WVCPECGVG 45 (55)
T ss_pred cCCCCCCCC
Confidence 347777743
No 211
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=31.52 E-value=25 Score=41.61 Aligned_cols=26 Identities=38% Similarity=0.924 Sum_probs=19.2
Q ss_pred CCC-CCcCCCCCC-CCCCCCCcccCCcCc
Q 018197 331 AKF-CDECGAPYL-RETSKFCSECGVKRL 357 (359)
Q Consensus 331 sKF-CpeCGt~l~-~~~AKFCpECGtKr~ 357 (359)
-+| | .||+++- .+-.--|++||.++.
T Consensus 1541 Q~~RC-kC~~kyRR~PL~G~C~kCGg~~i 1568 (1627)
T PRK14715 1541 QEFRC-KCGAKYRRVPLKGKCPKCGSKLI 1568 (1627)
T ss_pred cceee-cCCCccccCCCCCcCcccCCeEE
Confidence 356 9 9999982 123567999999864
No 212
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=31.48 E-value=17 Score=33.41 Aligned_cols=24 Identities=38% Similarity=0.830 Sum_probs=16.9
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
+.-+||.-||.. +---|-+||++.
T Consensus 116 P~r~fCaVCG~~----S~ysC~~CG~ky 139 (156)
T KOG3362|consen 116 PLRKFCAVCGYD----SKYSCVNCGTKY 139 (156)
T ss_pred CcchhhhhcCCC----chhHHHhcCCce
Confidence 556999999932 223488999884
No 213
>PLN02569 threonine synthase
Probab=31.36 E-value=27 Score=36.11 Aligned_cols=24 Identities=17% Similarity=0.115 Sum_probs=17.5
Q ss_pred CCCCcCCCCCCCCCCC-CCcccCCcC
Q 018197 332 KFCDECGAPYLRETSK-FCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~~~AK-FCpECGtKr 356 (359)
-.|..||+.++..... .| +||..+
T Consensus 50 l~C~~Cg~~y~~~~~~~~C-~cgg~l 74 (484)
T PLN02569 50 LECPLTGEKYSLDEVVYRS-KSGGLL 74 (484)
T ss_pred cEeCCCCCcCCCccccccC-CCCCeE
Confidence 4499999999655443 46 899665
No 214
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=31.36 E-value=19 Score=25.39 Aligned_cols=16 Identities=31% Similarity=0.823 Sum_probs=10.9
Q ss_pred CCCCcCCCCCCCCCCC
Q 018197 332 KFCDECGAPYLRETSK 347 (359)
Q Consensus 332 KFCpeCGt~l~~~~AK 347 (359)
..||.||..|+.-.+|
T Consensus 2 ~~CP~Cg~~lv~r~~k 17 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGK 17 (39)
T ss_pred cCCCCCCceeEEEECC
Confidence 5699999888543333
No 215
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.94 E-value=34 Score=36.68 Aligned_cols=25 Identities=24% Similarity=0.566 Sum_probs=16.6
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpECGtK 355 (359)
.+.-.|++||..- +-.--||.||.+
T Consensus 557 ~~~~~C~~CGy~g--~~~~~CP~CG~~ 581 (618)
T PRK14704 557 HPVDRCKCCSYHG--VIGNECPSCGNE 581 (618)
T ss_pred CCCeecCCCCCCC--CcCccCcCCCCC
Confidence 4456799999731 112459999954
No 216
>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=30.52 E-value=21 Score=35.43 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHhhhhhccccc
Q 018197 72 VANMYETLVNDVNLRLASFNGIR 94 (359)
Q Consensus 72 vANlyetlv~~vn~rlasl~g~~ 94 (359)
|-.+|.+|..||-.|-..+.|-.
T Consensus 16 lGH~~~~l~ADv~aR~~r~~G~~ 38 (391)
T PF09334_consen 16 LGHLYPYLAADVLARYLRLRGHD 38 (391)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-E
T ss_pred CChhHHHHHHHHHHHHHhhcccc
Confidence 45778888888888887776643
No 217
>PHA02768 hypothetical protein; Provisional
Probab=30.42 E-value=27 Score=27.07 Aligned_cols=23 Identities=30% Similarity=0.570 Sum_probs=16.4
Q ss_pred CCCcCCCCCCC----------C-CCCCCcccCCc
Q 018197 333 FCDECGAPYLR----------E-TSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~~----------~-~AKFCpECGtK 355 (359)
-|++||..+.. - ...-|.+||.-
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~ 40 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRI 40 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcCCcccCCcccce
Confidence 49999999821 1 25669999874
No 218
>PLN02189 cellulose synthase
Probab=30.19 E-value=27 Score=39.91 Aligned_cols=25 Identities=40% Similarity=1.010 Sum_probs=20.8
Q ss_pred CCC--CCcCCCCC--------CCCCCCCCcccCCc
Q 018197 331 AKF--CDECGAPY--------LRETSKFCSECGVK 355 (359)
Q Consensus 331 sKF--CpeCGt~l--------~~~~AKFCpECGtK 355 (359)
-.| |.+||-++ -.++.+-||.|+++
T Consensus 51 ~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~ 85 (1040)
T PLN02189 51 DLFVACNECGFPVCRPCYEYERREGTQNCPQCKTR 85 (1040)
T ss_pred CEEEeeccCCCccccchhhhhhhcCCccCcccCCc
Confidence 355 99999998 35689999999997
No 219
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=30.11 E-value=26 Score=36.64 Aligned_cols=27 Identities=19% Similarity=0.596 Sum_probs=20.6
Q ss_pred CCCCCCcCCCCCCCCC---CCCCcccCCcC
Q 018197 330 PAKFCDECGAPYLRET---SKFCSECGVKR 356 (359)
Q Consensus 330 ~sKFCpeCGt~l~~~~---AKFCpECGtKr 356 (359)
...+|+.|++-+.... ..+|+.||++.
T Consensus 124 ~~~yc~~~~~~l~~~~l~~~~~c~~cg~~~ 153 (648)
T PRK12267 124 EGWYCVSCETFFTESQLVDGGKCPDCGREV 153 (648)
T ss_pred EEeecCCCCccCChHHhccCCcCCCCCCcC
Confidence 3678999999986531 25899999985
No 220
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.73 E-value=24 Score=34.88 Aligned_cols=13 Identities=38% Similarity=1.147 Sum_probs=11.2
Q ss_pred CCCCCCcccCCcC
Q 018197 344 ETSKFCSECGVKR 356 (359)
Q Consensus 344 ~~AKFCpECGtKr 356 (359)
..-+||+.||+|.
T Consensus 109 ~~~RFCg~CG~~~ 121 (279)
T COG2816 109 RSHRFCGRCGTKT 121 (279)
T ss_pred hhCcCCCCCCCcC
Confidence 3589999999996
No 221
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=29.68 E-value=22 Score=30.38 Aligned_cols=11 Identities=36% Similarity=0.963 Sum_probs=7.1
Q ss_pred CCCCcccCCcC
Q 018197 346 SKFCSECGVKR 356 (359)
Q Consensus 346 AKFCpECGtKr 356 (359)
-.||+.||+.+
T Consensus 69 r~FC~~CGs~l 79 (133)
T COG3791 69 RGFCPTCGSPL 79 (133)
T ss_pred CeecccCCCce
Confidence 45777777664
No 222
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=29.42 E-value=24 Score=29.72 Aligned_cols=31 Identities=19% Similarity=0.512 Sum_probs=22.7
Q ss_pred CCCCCCCC----CCcCCCCCC----CCCCCCCcccCCcC
Q 018197 326 MPASPAKF----CDECGAPYL----RETSKFCSECGVKR 356 (359)
Q Consensus 326 ~p~~~sKF----CpeCGt~l~----~~~AKFCpECGtKr 356 (359)
.|.+.++| |+.|+.... ......|..||+-+
T Consensus 26 v~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L 64 (85)
T PTZ00083 26 VQGPNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQL 64 (85)
T ss_pred ecCCCCeEEEEECCCCCCeeEEEecCceEEEccccCCEe
Confidence 56677777 999987752 34577899998865
No 223
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=29.27 E-value=19 Score=29.23 Aligned_cols=11 Identities=55% Similarity=1.383 Sum_probs=9.4
Q ss_pred CCCCcCCCCCC
Q 018197 332 KFCDECGAPYL 342 (359)
Q Consensus 332 KFCpeCGt~l~ 342 (359)
|||-.||.|+.
T Consensus 1 k~CQSCGMPl~ 11 (81)
T PF12674_consen 1 KFCQSCGMPLS 11 (81)
T ss_pred CcCCcCcCccC
Confidence 78999999984
No 224
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=29.19 E-value=28 Score=34.71 Aligned_cols=36 Identities=11% Similarity=0.151 Sum_probs=22.4
Q ss_pred eccCCCCChhhHHH-HHHHhcccccccccccccccccc
Q 018197 161 VEKPNNMPIEDAEW-FKRLTGRNEVAISAQDYKFYSPR 197 (359)
Q Consensus 161 VE~p~Nlp~eDqew-fkRLtgr~EVai~g~DYkfys~R 197 (359)
+| |.-.|.+=.++ +..+..+.=+.|+++|-+..+-.
T Consensus 131 lD-P~Gs~~~~l~~al~~~~~~gilyvSAtD~~~L~g~ 167 (382)
T PRK04338 131 ID-PFGSPAPFLDSAIRSVKRGGLLCVTATDTAPLCGA 167 (382)
T ss_pred EC-CCCCcHHHHHHHHHHhcCCCEEEEEecCchhhcCC
Confidence 44 44555444444 66666667777887777777654
No 225
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=29.06 E-value=24 Score=35.96 Aligned_cols=11 Identities=45% Similarity=1.081 Sum_probs=10.0
Q ss_pred CCCCcccCCcC
Q 018197 346 SKFCSECGVKR 356 (359)
Q Consensus 346 AKFCpECGtKr 356 (359)
-||||.||.+.
T Consensus 150 ykFCp~CG~~t 160 (345)
T KOG3084|consen 150 YKFCPGCGSPT 160 (345)
T ss_pred hccCcccCCCc
Confidence 79999999985
No 226
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=28.97 E-value=40 Score=25.87 Aligned_cols=26 Identities=31% Similarity=0.649 Sum_probs=21.6
Q ss_pred CCCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 330 PAKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 330 ~sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
+-+.|-.|++.++. .|.-|-.||.+-
T Consensus 13 ~k~ICrkC~ARnp~-~A~~CRKCg~~~ 38 (48)
T PRK04136 13 NKKICMRCNARNPW-RATKCRKCGYKN 38 (48)
T ss_pred cccchhcccCCCCc-cccccccCCCCC
Confidence 45789999999975 499999999863
No 227
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=28.66 E-value=21 Score=26.60 Aligned_cols=7 Identities=43% Similarity=1.312 Sum_probs=2.8
Q ss_pred CcccCCc
Q 018197 349 CSECGVK 355 (359)
Q Consensus 349 CpECGtK 355 (359)
||.||..
T Consensus 37 CP~C~a~ 43 (47)
T PF00301_consen 37 CPVCGAP 43 (47)
T ss_dssp -TTTSSB
T ss_pred CcCCCCc
Confidence 5555443
No 228
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=28.62 E-value=28 Score=28.03 Aligned_cols=24 Identities=38% Similarity=0.922 Sum_probs=19.4
Q ss_pred CCCCCCCcCCCCCCCCCCCCCcc-cC
Q 018197 329 SPAKFCDECGAPYLRETSKFCSE-CG 353 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCpE-CG 353 (359)
.+-+-|+-||+.++. +..||+| ||
T Consensus 6 ~PH~HC~VCg~aIp~-de~~CSe~C~ 30 (64)
T COG4068 6 VPHRHCVVCGKAIPP-DEQVCSEECG 30 (64)
T ss_pred CCCccccccCCcCCC-ccchHHHHHH
Confidence 346789999999975 5899985 77
No 229
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=28.44 E-value=30 Score=39.63 Aligned_cols=22 Identities=32% Similarity=0.942 Sum_probs=19.4
Q ss_pred CCcCCCCC--------CCCCCCCCcccCCc
Q 018197 334 CDECGAPY--------LRETSKFCSECGVK 355 (359)
Q Consensus 334 CpeCGt~l--------~~~~AKFCpECGtK 355 (359)
|.+||-++ ..++.+-||.|+++
T Consensus 37 C~eC~fpvCr~cyeye~~~g~~~cp~c~t~ 66 (1044)
T PLN02915 37 CHVCGFPVCKPCYEYERSEGNQCCPQCNTR 66 (1044)
T ss_pred eccCCCccccchhhhhhhcCCccCCccCCc
Confidence 99999998 35689999999997
No 230
>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=28.40 E-value=37 Score=26.44 Aligned_cols=27 Identities=33% Similarity=0.532 Sum_probs=20.4
Q ss_pred CCCCCcCCCCC-CCCC-CCCCcccCCcCc
Q 018197 331 AKFCDECGAPY-LRET-SKFCSECGVKRL 357 (359)
Q Consensus 331 sKFCpeCGt~l-~~~~-AKFCpECGtKr~ 357 (359)
..-|.+||.-+ ..++ ..-|+-||+++.
T Consensus 18 ~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~ 46 (57)
T PF06221_consen 18 APNCLNCGKIICEQEGPLGPCPFCGTPLL 46 (57)
T ss_pred cccccccChhhcccccCcCcCCCCCCccc
Confidence 45699999887 4455 688999998764
No 231
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=28.29 E-value=31 Score=27.43 Aligned_cols=21 Identities=33% Similarity=0.854 Sum_probs=11.0
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCc
Q 018197 332 KFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtK 355 (359)
+-|++||.=-+. --||.||..
T Consensus 6 rkC~~cg~YTLk---e~Cp~CG~~ 26 (59)
T COG2260 6 RKCPKCGRYTLK---EKCPVCGGD 26 (59)
T ss_pred hcCcCCCceeec---ccCCCCCCc
Confidence 346666654332 256666654
No 232
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=28.25 E-value=41 Score=36.82 Aligned_cols=27 Identities=22% Similarity=0.593 Sum_probs=20.3
Q ss_pred CCCCCCCcCCCCCC---CCCCCCCcc---cCCc
Q 018197 329 SPAKFCDECGAPYL---RETSKFCSE---CGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~---~~~AKFCpE---CGtK 355 (359)
..+.+||.||+.+. .+-.-||++ |-..
T Consensus 402 ~~P~~CP~C~s~l~r~~~e~~~rC~n~~~C~aq 434 (667)
T COG0272 402 PFPTHCPVCGSELVREEGEVVIRCTNGLNCPAQ 434 (667)
T ss_pred CCCCCCCCCCCeeEeccCceeEecCCCCCChHH
Confidence 35778999999986 345788987 7544
No 233
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=27.86 E-value=26 Score=30.21 Aligned_cols=8 Identities=38% Similarity=1.331 Sum_probs=4.7
Q ss_pred CCcCCCCC
Q 018197 334 CDECGAPY 341 (359)
Q Consensus 334 CpeCGt~l 341 (359)
|+.|+..+
T Consensus 94 C~~CN~~L 101 (147)
T PF01927_consen 94 CPKCNGPL 101 (147)
T ss_pred cCCCCcEe
Confidence 66666555
No 234
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=27.71 E-value=37 Score=33.96 Aligned_cols=25 Identities=24% Similarity=0.480 Sum_probs=17.2
Q ss_pred CCCCcCCCCCCC----CCCCCCcccCCcC
Q 018197 332 KFCDECGAPYLR----ETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~----~~AKFCpECGtKr 356 (359)
..|+.||..... .....|++||.+.
T Consensus 234 ~~C~~c~~~~~~~~~~~~~~~C~~c~~~~ 262 (374)
T TIGR00308 234 YHCSRCLHNKPVNGISQRKGRCKECGGEY 262 (374)
T ss_pred EECCCcccccccccccCCCCCCCCCCCcc
Confidence 459999876432 2345799999874
No 235
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=27.63 E-value=29 Score=35.46 Aligned_cols=28 Identities=21% Similarity=0.622 Sum_probs=18.6
Q ss_pred CCCCC-CCcCCCCCC----------CCCCCC--------CcccCCcC
Q 018197 329 SPAKF-CDECGAPYL----------RETSKF--------CSECGVKR 356 (359)
Q Consensus 329 ~~sKF-CpeCGt~l~----------~~~AKF--------CpECGtKr 356 (359)
...++ |..||..|. +++..| ||.||...
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~k 468 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGK 468 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCcH
Confidence 33455 999998873 233344 99999763
No 236
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=27.44 E-value=41 Score=31.57 Aligned_cols=21 Identities=24% Similarity=0.613 Sum_probs=17.1
Q ss_pred CCCCCCCcCCCCCCCCCCCCCc
Q 018197 329 SPAKFCDECGAPYLRETSKFCS 350 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~AKFCp 350 (359)
.+-..||-||.++-++ +-|||
T Consensus 154 AGRP~CPlCg~PldP~-GH~Cp 174 (177)
T TIGR03847 154 AGRPPCPLCGRPIDPD-GHICP 174 (177)
T ss_pred CCCCCCCCCCCCCCCC-CccCC
Confidence 4567899999999654 89997
No 237
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=27.38 E-value=24 Score=36.17 Aligned_cols=11 Identities=45% Similarity=1.225 Sum_probs=8.5
Q ss_pred CCCCCcCCCCC
Q 018197 331 AKFCDECGAPY 341 (359)
Q Consensus 331 sKFCpeCGt~l 341 (359)
..||..||.++
T Consensus 90 VHfCd~Cd~PI 100 (389)
T KOG2932|consen 90 VHFCDRCDFPI 100 (389)
T ss_pred eEeecccCCcc
Confidence 57888888876
No 238
>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=26.85 E-value=23 Score=29.67 Aligned_cols=24 Identities=33% Similarity=0.833 Sum_probs=16.7
Q ss_pred CCcCCCCCCC----CC-CCCCcccCCcCc
Q 018197 334 CDECGAPYLR----ET-SKFCSECGVKRL 357 (359)
Q Consensus 334 CpeCGt~l~~----~~-AKFCpECGtKr~ 357 (359)
|+.||..+.. .+ ...|+.||.++.
T Consensus 126 C~~C~~~~~r~~~~~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 126 CPSCGREYKRHRRSKRKRYRCGRCGGPLV 154 (157)
T ss_pred cCCCCCEeeeecccchhhEECCCCCCEEE
Confidence 9999977621 22 237999998764
No 239
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=26.68 E-value=53 Score=24.37 Aligned_cols=25 Identities=24% Similarity=0.783 Sum_probs=17.6
Q ss_pred CCCCCcCCCCCCC------CC-CCCCcccCCc
Q 018197 331 AKFCDECGAPYLR------ET-SKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~~------~~-AKFCpECGtK 355 (359)
...|.+||+.-.. .+ .-+|..||-.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHH
Confidence 5679999987632 22 4889999854
No 240
>PLN02436 cellulose synthase A
Probab=26.40 E-value=35 Score=39.29 Aligned_cols=25 Identities=36% Similarity=0.955 Sum_probs=20.8
Q ss_pred CCC--CCcCCCCC--------CCCCCCCCcccCCc
Q 018197 331 AKF--CDECGAPY--------LRETSKFCSECGVK 355 (359)
Q Consensus 331 sKF--CpeCGt~l--------~~~~AKFCpECGtK 355 (359)
-.| |.+||-++ -.++.+-||.|+++
T Consensus 53 e~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~ 87 (1094)
T PLN02436 53 EPFVACNECAFPVCRPCYEYERREGNQACPQCKTR 87 (1094)
T ss_pred CEEEeeccCCCccccchhhhhhhcCCccCcccCCc
Confidence 345 99999998 35689999999997
No 241
>PF09139 Mmp37: Mitochondrial matrix Mmp37; InterPro: IPR015222 MMp37 is a mitochondrial matrix protein that functions in the translocation of proteins across the mitochondrial inner membrane [].
Probab=26.12 E-value=1.3e+02 Score=30.33 Aligned_cols=93 Identities=20% Similarity=0.330 Sum_probs=51.0
Q ss_pred CccccCCCcchhh--------------HHHHHHHHHHHHHHHHhh-hhhc---------ccc--chhhhhHHHH----hh
Q 018197 56 DVQYEGDPRFALP--------------LMYVANMYETLVNDVNLR-LASF---------NGI--REKTIGVALE----AA 105 (359)
Q Consensus 56 ev~YEGdprf~LP--------------LmyvANlyetlv~~vn~r-lasl---------~g~--~ekt~gvale----aa 105 (359)
-+-|-||+|.+++ +-..-+||+.++.+.... +-.. ++. ++++...-.+ -=
T Consensus 176 ~LSY~GD~RM~~~gEn~~KV~nIV~~q~~~Fr~LY~p~l~~~~~~~~~~~~~~~~~~~~~~~~~qd~s~~~~~~~l~~LP 255 (330)
T PF09139_consen 176 SLSYMGDFRMAIFGENPNKVRNIVSGQLDNFRELYSPLLQELPNVVYLGSSVWTSDDSGNGTFEQDKSPSARAHLLRRLP 255 (330)
T ss_pred ccccccccccccCccCHHHHHHHHhccHHHHHHHHHHHHHhcccceeccccccCCCccccceEEeCCCHHHHHHHHHHCC
Confidence 3579999998653 455678999999998443 2221 111 2222222111 22
Q ss_pred cchhHHHHhhCCCCCccceehhhhhhhhhhhccchhhhHhhhee
Q 018197 106 GGLYRSLAKKFPKKGSCTYKRRELATSLETRTRFPELVIQEEKR 149 (359)
Q Consensus 106 gglyr~l~kkfpkkg~c~fkRRElAts~etrt~fpelv~~Eekr 149 (359)
..|.++|..++.+++.- =.-.|...++....++++.|.+-.++
T Consensus 256 ~~~~~~l~~~~~~~~~~-~d~~~~~~~ia~d~~~~~~v~~aI~~ 298 (330)
T PF09139_consen 256 KTLRSRLYRQYDRKGRN-RDGEEFLRAIASDPDLREVVRRAIRR 298 (330)
T ss_pred HHHHHHHHHHhccCCCc-cchhHHHHHHhcChhHHHHHHHHHHh
Confidence 45667788888877700 01122334455555666666665554
No 242
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=25.81 E-value=25 Score=27.22 Aligned_cols=23 Identities=17% Similarity=0.491 Sum_probs=14.2
Q ss_pred CCCcCCCCCCCCC-----CCCCcccCCc
Q 018197 333 FCDECGAPYLRET-----SKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~~~~-----AKFCpECGtK 355 (359)
-|..|+..|...+ ..-||-||+=
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCcc
Confidence 3788877764421 3358888763
No 243
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=25.60 E-value=30 Score=32.11 Aligned_cols=9 Identities=56% Similarity=1.232 Sum_probs=6.4
Q ss_pred CCcccCCcC
Q 018197 348 FCSECGVKR 356 (359)
Q Consensus 348 FCpECGtKr 356 (359)
||++||+.+
T Consensus 95 FC~~CGS~L 103 (191)
T PRK05417 95 ACKECGVHM 103 (191)
T ss_pred eCCCCCCcc
Confidence 777777765
No 244
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=25.54 E-value=40 Score=34.09 Aligned_cols=24 Identities=38% Similarity=0.650 Sum_probs=19.3
Q ss_pred chhHHHHhhC-CCCCccceehhhhhhhhhhhccchhh
Q 018197 107 GLYRSLAKKF-PKKGSCTYKRRELATSLETRTRFPEL 142 (359)
Q Consensus 107 glyr~l~kkf-pkkg~c~fkRRElAts~etrt~fpel 142 (359)
--||||++|| |.|.+- ++++|+|.
T Consensus 23 kayrkla~k~HpDkn~~------------~~ekfkei 47 (337)
T KOG0712|consen 23 KAYRKLALKYHPDKNPD------------AGEKFKEI 47 (337)
T ss_pred HHHHHHHHHhCCCCCcc------------HHHHHHHH
Confidence 3599999998 888876 67788774
No 245
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=25.51 E-value=42 Score=29.56 Aligned_cols=24 Identities=46% Similarity=0.955 Sum_probs=21.3
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCc
Q 018197 332 KFCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtK 355 (359)
-.|.-||++|.....||=+.||=+
T Consensus 34 Y~C~~Cg~pLF~S~~KfdSg~GWP 57 (119)
T PRK05508 34 YVCKQCGAPLYRSEDKFKSGCGWP 57 (119)
T ss_pred EEecCCCCccccccccccCCCCCc
Confidence 349999999998899999999965
No 246
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=25.34 E-value=50 Score=25.06 Aligned_cols=22 Identities=36% Similarity=0.753 Sum_probs=16.3
Q ss_pred CCcCCCCCCCCCCCCCcccCCc
Q 018197 334 CDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 334 CpeCGt~l~~~~AKFCpECGtK 355 (359)
|..||+++......+|.+|-..
T Consensus 1 C~~C~~~~~~~~~~lC~~C~~~ 22 (73)
T PF14260_consen 1 CLVCGAKTQEGESPLCSNCRSD 22 (73)
T ss_pred CCCCCCcCCCCCCCcCcccCcC
Confidence 7788888865545888888743
No 247
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=25.19 E-value=30 Score=26.07 Aligned_cols=23 Identities=30% Similarity=0.849 Sum_probs=14.8
Q ss_pred CCCcCCCCCC-------CCCCCCCcccCCc
Q 018197 333 FCDECGAPYL-------RETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~-------~~~AKFCpECGtK 355 (359)
.|.+||+... ..+...|..||..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~ 30 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLY 30 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHH
Confidence 4778887652 2346678888754
No 248
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=24.90 E-value=1.8e+02 Score=30.11 Aligned_cols=35 Identities=23% Similarity=0.339 Sum_probs=20.3
Q ss_pred eeecCCccCCCCCccccCCCCcCCCCCCCCCCccccccccccc
Q 018197 226 MVTAQGFHTISEPQNQQQTPSKHHMQPLSHQPQFHHIHNNHHQ 268 (359)
Q Consensus 226 ~~~~~gfrs~~e~q~q~~~~~k~~~~~l~~qp~~h~~~q~~~~ 268 (359)
..+++|-|--.-||..||+.-. +|++.+.|||+.+
T Consensus 189 FTSSHGHRHrhAPQPtQQPTVQ--------NPaqQ~tvQNp~q 223 (422)
T PF13388_consen 189 FTSSHGHRHRHAPQPTQQPTVQ--------NPAQQPTVQNPNQ 223 (422)
T ss_pred hhhccccccccCCCCCCCCCCC--------CCCCCCCcCCccc
Confidence 3444888876666644443332 3666677776544
No 249
>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=24.51 E-value=35 Score=33.51 Aligned_cols=24 Identities=17% Similarity=0.337 Sum_probs=17.3
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
.-||+.|++.+... --|..||+++
T Consensus 140 ~~yc~~~~t~l~~~--evc~~cg~~~ 163 (382)
T cd00817 140 VNWCPKLRTAISDI--EVCSRSGDVI 163 (382)
T ss_pred EeecCCcCCCCCcc--hhcccCCCeE
Confidence 45788888888543 3488888875
No 250
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.41 E-value=23 Score=29.66 Aligned_cols=22 Identities=36% Similarity=1.064 Sum_probs=13.9
Q ss_pred CCcCCCCC------CCCCCCCCcccCCc
Q 018197 334 CDECGAPY------LRETSKFCSECGVK 355 (359)
Q Consensus 334 CpeCGt~l------~~~~AKFCpECGtK 355 (359)
|.+||..+ ...----|++||.+
T Consensus 15 c~~cg~~~dvvq~~~ddplt~ce~c~a~ 42 (82)
T COG2331 15 CTECGNRFDVVQAMTDDPLTTCEECGAR 42 (82)
T ss_pred ecccchHHHHHHhcccCccccChhhChH
Confidence 78888775 12224568888875
No 251
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=24.33 E-value=76 Score=28.91 Aligned_cols=54 Identities=28% Similarity=0.453 Sum_probs=27.2
Q ss_pred CccCCccccccCCCCCcccccccCCCCCCCCCCcCCCCCCC----------CCCCCCcccCCcC
Q 018197 303 TISQHMACLQPLTGGHVGERLHVMPASPAKFCDECGAPYLR----------ETSKFCSECGVKR 356 (359)
Q Consensus 303 ~i~qh~~ylqP~tgG~~gG~~~i~p~~~sKFCpeCGt~l~~----------~~AKFCpECGtKr 356 (359)
-|.|-+|.|-..+|-..--..++=.+-..-.|..||..+.. ....-|+.||..+
T Consensus 67 viTQNID~Lh~~AG~~~~~vielHG~~~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~l 130 (206)
T cd01410 67 VISQNVDGLHLRSGLPREKLSELHGNMFIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGIL 130 (206)
T ss_pred EEecCccchHhHcCcCcccEEEecCCcCcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCcc
Confidence 35666777644444211001111111223359999987631 1235599999764
No 252
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=24.29 E-value=39 Score=38.21 Aligned_cols=27 Identities=30% Similarity=0.806 Sum_probs=20.6
Q ss_pred CCCCCCCcCCCCCCCCC-CCCCcccCCc
Q 018197 329 SPAKFCDECGAPYLRET-SKFCSECGVK 355 (359)
Q Consensus 329 ~~sKFCpeCGt~l~~~~-AKFCpECGtK 355 (359)
.++.-|+.||+++...| ---|-+||..
T Consensus 922 ~~~~~c~~c~~~~~~~g~c~~c~~cg~t 949 (953)
T PRK06556 922 ADAPLCPTCGTKMVRNGSCYVCEGCGST 949 (953)
T ss_pred ccCCcCCCccCeeeECCceEeccCCCCC
Confidence 45667999999996554 4668999974
No 253
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=24.09 E-value=1.2e+02 Score=23.50 Aligned_cols=45 Identities=29% Similarity=0.383 Sum_probs=32.6
Q ss_pred chhhhHhhheeEeEEEeecc-----------------eeeccCCCCChhhHHHHHHHhcccccc
Q 018197 139 FPELVIQEEKRVRFVVVNGL-----------------DIVEKPNNMPIEDAEWFKRLTGRNEVA 185 (359)
Q Consensus 139 fpelv~~EekrvrfvVVnGl-----------------~IVE~p~Nlp~eDqewfkRLtgr~EVa 185 (359)
+.+++..+ ++-++++..- .++|||.-+..+|++.+.++-.++.+.
T Consensus 54 ~~~ll~~~--~~D~V~I~tp~~~h~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~~~~~ 115 (120)
T PF01408_consen 54 LEELLADE--DVDAVIIATPPSSHAEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKEKGVK 115 (120)
T ss_dssp HHHHHHHT--TESEEEEESSGGGHHHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHHHTSC
T ss_pred HHHHHHhh--cCCEEEEecCCcchHHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHHhCCE
Confidence 55566555 4556655443 679999999999999999888765544
No 254
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=23.93 E-value=42 Score=30.18 Aligned_cols=23 Identities=48% Similarity=1.028 Sum_probs=18.0
Q ss_pred CCCCCcCCCCC------CCCCCCCCcccC
Q 018197 331 AKFCDECGAPY------LRETSKFCSECG 353 (359)
Q Consensus 331 sKFCpeCGt~l------~~~~AKFCpECG 353 (359)
-..|..||++. +..++-.|..|+
T Consensus 149 l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCCceEEecccCCccccccc
Confidence 35699999875 456788899997
No 255
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=23.88 E-value=40 Score=34.66 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=5.8
Q ss_pred CCCCcCCCCC
Q 018197 332 KFCDECGAPY 341 (359)
Q Consensus 332 KFCpeCGt~l 341 (359)
-|||.|++++
T Consensus 277 y~CP~Ckakv 286 (378)
T KOG2807|consen 277 YFCPQCKAKV 286 (378)
T ss_pred eeCCcccCee
Confidence 4566666654
No 256
>PRK04011 peptide chain release factor 1; Provisional
Probab=23.59 E-value=46 Score=33.68 Aligned_cols=24 Identities=29% Similarity=0.645 Sum_probs=17.6
Q ss_pred CCCcCCCCCC-------CCCCCCCcccCCcC
Q 018197 333 FCDECGAPYL-------RETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~-------~~~AKFCpECGtKr 356 (359)
.|+.||..-. ....+.||+||..+
T Consensus 330 ~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~~ 360 (411)
T PRK04011 330 KCPNCGYEEEKTVKRREELPEKTCPKCGSEL 360 (411)
T ss_pred EcCCCCcceeeecccccccccccCcccCccc
Confidence 3999998641 23478999999774
No 257
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=23.50 E-value=35 Score=31.63 Aligned_cols=10 Identities=30% Similarity=0.870 Sum_probs=7.1
Q ss_pred CCCcccCCcC
Q 018197 347 KFCSECGVKR 356 (359)
Q Consensus 347 KFCpECGtKr 356 (359)
.||+.||+.+
T Consensus 90 ~FC~~CGS~L 99 (182)
T TIGR02820 90 HACKGCGTHM 99 (182)
T ss_pred ecCCCCCCcc
Confidence 3777777765
No 258
>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=23.44 E-value=52 Score=23.22 Aligned_cols=11 Identities=18% Similarity=0.679 Sum_probs=3.3
Q ss_pred CCCCCc--CCCCC
Q 018197 331 AKFCDE--CGAPY 341 (359)
Q Consensus 331 sKFCpe--CGt~l 341 (359)
.++||. |+..+
T Consensus 18 ~~~Cp~~~C~~~~ 30 (64)
T PF01485_consen 18 IRWCPNPDCEYII 30 (64)
T ss_dssp CC--TTSST---E
T ss_pred ccCCCCCCCcccE
Confidence 356655 66665
No 259
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=22.70 E-value=62 Score=29.76 Aligned_cols=18 Identities=33% Similarity=0.564 Sum_probs=11.5
Q ss_pred eEEEeecceeeccCCCCCh
Q 018197 151 RFVVVNGLDIVEKPNNMPI 169 (359)
Q Consensus 151 rfvVVnGl~IVE~p~Nlp~ 169 (359)
+++|..|.||=- ++.||.
T Consensus 15 ~ivi~tGAGiS~-~sGip~ 32 (242)
T PRK00481 15 RIVVLTGAGISA-ESGIPD 32 (242)
T ss_pred CEEEEeCCcccc-ccCCCC
Confidence 467777777644 556763
No 260
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=22.63 E-value=32 Score=35.55 Aligned_cols=25 Identities=32% Similarity=0.711 Sum_probs=18.1
Q ss_pred CCCCCcCCCCCC-------CC--CCCCCcccCCc
Q 018197 331 AKFCDECGAPYL-------RE--TSKFCSECGVK 355 (359)
Q Consensus 331 sKFCpeCGt~l~-------~~--~AKFCpECGtK 355 (359)
.-.|++||.-.- .+ ...|+++||..
T Consensus 175 ~pic~~cg~~~~~~~~~~d~~~~~v~y~~~cG~~ 208 (510)
T PRK00750 175 LPICPKCGKVLTTPVISYDAEAGTVTYDCECGHE 208 (510)
T ss_pred eeeCCCCCccceEEEEEEeCCCCEEEEEcCCCCE
Confidence 356999998861 11 35899999976
No 261
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=22.60 E-value=45 Score=33.90 Aligned_cols=11 Identities=18% Similarity=0.440 Sum_probs=5.7
Q ss_pred CCCCCcCCCCC
Q 018197 331 AKFCDECGAPY 341 (359)
Q Consensus 331 sKFCpeCGt~l 341 (359)
.-||+.|++-+
T Consensus 125 ~~~~~~~~~~l 135 (556)
T PRK12268 125 QAYCPSDGRFL 135 (556)
T ss_pred EEecCCCCcCc
Confidence 34555555544
No 262
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=22.47 E-value=49 Score=27.11 Aligned_cols=21 Identities=33% Similarity=0.668 Sum_probs=15.2
Q ss_pred CCcCCCCCCCCCC----CCCcccCC
Q 018197 334 CDECGAPYLRETS----KFCSECGV 354 (359)
Q Consensus 334 CpeCGt~l~~~~A----KFCpECGt 354 (359)
||=||...+.... -.|+-|+=
T Consensus 4 CPCCg~~Tl~~~~~~~ydIC~VC~W 28 (78)
T PF14206_consen 4 CPCCGYYTLEERGEGTYDICPVCFW 28 (78)
T ss_pred CCCCCcEEeccCCCcCceECCCCCc
Confidence 9999988754433 37999973
No 263
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=22.35 E-value=27 Score=30.38 Aligned_cols=23 Identities=43% Similarity=1.138 Sum_probs=19.3
Q ss_pred CCCcCCCCCC------CCCCCCCcccCCc
Q 018197 333 FCDECGAPYL------RETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~------~~~AKFCpECGtK 355 (359)
+|-+||.+++ .++|.-|-+|...
T Consensus 82 ~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~ 110 (120)
T COG1734 82 ICEECGEPIPEARLEARPTARLCIECQER 110 (120)
T ss_pred chhccCCcCCHHHHhhCcchHHHHHHHHH
Confidence 6999999984 5689999999764
No 264
>smart00532 LIGANc Ligase N family.
Probab=22.30 E-value=55 Score=33.72 Aligned_cols=26 Identities=27% Similarity=0.733 Sum_probs=17.5
Q ss_pred CCCCCCcCCCCCCCC---CCCCCcc--cCCc
Q 018197 330 PAKFCDECGAPYLRE---TSKFCSE--CGVK 355 (359)
Q Consensus 330 ~sKFCpeCGt~l~~~---~AKFCpE--CGtK 355 (359)
.+.+||.||+++... ..-||++ |-..
T Consensus 398 ~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq 428 (441)
T smart00532 398 MPTHCPSCGSELVREEGEVDIRCPNPLCPAQ 428 (441)
T ss_pred CCCCCCCCCCEeEecCCceEEEeCCCCCHHH
Confidence 468899999998522 2446874 7543
No 265
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=22.10 E-value=54 Score=23.93 Aligned_cols=20 Identities=30% Similarity=0.776 Sum_probs=15.2
Q ss_pred CCCcCCCCCC------CCCCCCCccc
Q 018197 333 FCDECGAPYL------RETSKFCSEC 352 (359)
Q Consensus 333 FCpeCGt~l~------~~~AKFCpEC 352 (359)
.|+.||-.+. ....+-||.|
T Consensus 30 ~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 30 KCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred ECCCCCCeeEccHhhhccCCCCCCCC
Confidence 3999999872 1358889988
No 266
>PLN02400 cellulose synthase
Probab=21.86 E-value=46 Score=38.29 Aligned_cols=22 Identities=27% Similarity=0.976 Sum_probs=19.3
Q ss_pred CCcCCCCC--------CCCCCCCCcccCCc
Q 018197 334 CDECGAPY--------LRETSKFCSECGVK 355 (359)
Q Consensus 334 CpeCGt~l--------~~~~AKFCpECGtK 355 (359)
|.+||.++ -.++..-||.|+|+
T Consensus 58 C~eCaFPVCRpCYEYERkeGnq~CPQCkTr 87 (1085)
T PLN02400 58 CNECAFPVCRPCYEYERKDGTQCCPQCKTR 87 (1085)
T ss_pred EccCCCccccchhheecccCCccCcccCCc
Confidence 99999998 35689999999997
No 267
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=21.86 E-value=43 Score=26.85 Aligned_cols=26 Identities=31% Similarity=0.788 Sum_probs=20.4
Q ss_pred CCCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 331 AKFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
---|-.||..-...--|.|..||..+
T Consensus 16 H~~CRRCGr~syhv~k~~CaaCGfgr 41 (61)
T COG2126 16 HIRCRRCGRRSYHVRKKYCAACGFGR 41 (61)
T ss_pred eehhhhccchheeeccceecccCCCC
Confidence 34599999886555589999999874
No 268
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=21.79 E-value=46 Score=28.08 Aligned_cols=22 Identities=23% Similarity=0.712 Sum_probs=15.0
Q ss_pred CCCCCcCCCCCCCCCCCCCccc
Q 018197 331 AKFCDECGAPYLRETSKFCSEC 352 (359)
Q Consensus 331 sKFCpeCGt~l~~~~AKFCpEC 352 (359)
..-|-.|-+.+-..+++||..|
T Consensus 44 ~~~C~~CK~~v~q~g~~YCq~C 65 (90)
T PF10235_consen 44 SSKCKICKTKVHQPGAKYCQTC 65 (90)
T ss_pred CccccccccccccCCCccChhh
Confidence 3457777777765567777776
No 269
>PRK08402 replication factor A; Reviewed
Probab=21.76 E-value=39 Score=33.89 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=17.4
Q ss_pred CCCCcCCCCCC-C--CCCCCCcccCC
Q 018197 332 KFCDECGAPYL-R--ETSKFCSECGV 354 (359)
Q Consensus 332 KFCpeCGt~l~-~--~~AKFCpECGt 354 (359)
.-||+|..++. . .+.-.|.+||.
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 34999999985 2 24568999994
No 270
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.64 E-value=38 Score=30.35 Aligned_cols=24 Identities=29% Similarity=0.710 Sum_probs=17.3
Q ss_pred CCCcCCCCCCC----CCCCCCcccCCcC
Q 018197 333 FCDECGAPYLR----ETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~~----~~AKFCpECGtKr 356 (359)
-||.||+-..- .-+.-|..||...
T Consensus 23 rCP~CGeGrLF~gFLK~~p~C~aCG~dy 50 (126)
T COG5349 23 RCPRCGEGRLFRGFLKVVPACEACGLDY 50 (126)
T ss_pred CCCCCCCchhhhhhcccCchhhhccccc
Confidence 59999987521 2377899999753
No 271
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=21.63 E-value=63 Score=38.11 Aligned_cols=34 Identities=29% Similarity=0.596 Sum_probs=23.1
Q ss_pred ccCCCCCCCCCCcCCCCC-CC---------CCCCCCcccCCcCc
Q 018197 324 HVMPASPAKFCDECGAPY-LR---------ETSKFCSECGVKRL 357 (359)
Q Consensus 324 ~i~p~~~sKFCpeCGt~l-~~---------~~AKFCpECGtKr~ 357 (359)
.+.|-.+---||+|-..= .. ---|-||.||+|+.
T Consensus 907 EVNPL~PHY~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~pl~ 950 (1444)
T COG2176 907 EVNPLPPHYLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTPLK 950 (1444)
T ss_pred ccCCCCccccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCccc
Confidence 344566677799996552 11 02689999999963
No 272
>PHA00732 hypothetical protein
Probab=21.46 E-value=66 Score=25.87 Aligned_cols=22 Identities=27% Similarity=0.638 Sum_probs=13.2
Q ss_pred CCcCCCCCC-----------CCCCCCCcccCCc
Q 018197 334 CDECGAPYL-----------RETSKFCSECGVK 355 (359)
Q Consensus 334 CpeCGt~l~-----------~~~AKFCpECGtK 355 (359)
|..||..+. .....-|++||+.
T Consensus 4 C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKs 36 (79)
T PHA00732 4 CPICGFTTVTLFALKQHARRNHTLTKCPVCNKS 36 (79)
T ss_pred CCCCCCccCCHHHHHHHhhcccCCCccCCCCCE
Confidence 777777652 1123457888765
No 273
>PRK11893 methionyl-tRNA synthetase; Reviewed
Probab=21.13 E-value=64 Score=32.13 Aligned_cols=27 Identities=22% Similarity=0.437 Sum_probs=19.5
Q ss_pred CCCCCCcCCCCCC----CCCCCCCcccCCcC
Q 018197 330 PAKFCDECGAPYL----RETSKFCSECGVKR 356 (359)
Q Consensus 330 ~sKFCpeCGt~l~----~~~AKFCpECGtKr 356 (359)
..-||+.||+-+. .+...+|..||+++
T Consensus 121 ~~~~~~~~~~~l~~~~l~~~~p~~~~~~~~~ 151 (511)
T PRK11893 121 EGWYCVRCEEFYTESELIEDGYRCPPTGAPV 151 (511)
T ss_pred eeeccccccccCCHHHhcCCCCCCCCCCCcc
Confidence 3678999998863 12225899999985
No 274
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=21.05 E-value=80 Score=25.12 Aligned_cols=21 Identities=33% Similarity=0.732 Sum_probs=14.2
Q ss_pred CCCCCcCCCCCC----CCCCCCCcc
Q 018197 331 AKFCDECGAPYL----RETSKFCSE 351 (359)
Q Consensus 331 sKFCpeCGt~l~----~~~AKFCpE 351 (359)
...||.||++.. ...--||++
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~ 30 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSK 30 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccH
Confidence 456999999963 223457875
No 275
>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=20.84 E-value=58 Score=33.02 Aligned_cols=24 Identities=29% Similarity=0.700 Sum_probs=16.4
Q ss_pred CCCcCCCCCC-------CCCCCCCcccCCcC
Q 018197 333 FCDECGAPYL-------RETSKFCSECGVKR 356 (359)
Q Consensus 333 FCpeCGt~l~-------~~~AKFCpECGtKr 356 (359)
-|+.||.... .....|||+||..+
T Consensus 322 rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (403)
T TIGR03676 322 KCPNCGYEEEKTVKPEEGDKSEACPKCGSEL 352 (403)
T ss_pred EcCCCCcceeeecccccccccccCcccCccc
Confidence 3999998642 11247899999774
No 276
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=20.83 E-value=16 Score=30.73 Aligned_cols=25 Identities=28% Similarity=0.534 Sum_probs=18.2
Q ss_pred CCCcCCCCCC---CCCCCCCcccCCcCc
Q 018197 333 FCDECGAPYL---RETSKFCSECGVKRL 357 (359)
Q Consensus 333 FCpeCGt~l~---~~~AKFCpECGtKr~ 357 (359)
+||.||..-+ ..+---|..||.+..
T Consensus 37 ~Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 37 TCPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp EESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred cCCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 4999998863 234567999998754
No 277
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=20.41 E-value=37 Score=23.90 Aligned_cols=13 Identities=23% Similarity=0.539 Sum_probs=10.2
Q ss_pred CCCCCCcCCCCCC
Q 018197 330 PAKFCDECGAPYL 342 (359)
Q Consensus 330 ~sKFCpeCGt~l~ 342 (359)
+--+|..||..|.
T Consensus 4 g~l~C~~CG~~m~ 16 (58)
T PF13408_consen 4 GLLRCGHCGSKMT 16 (58)
T ss_pred CcEEcccCCcEeE
Confidence 3458999999983
No 278
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=20.36 E-value=35 Score=29.63 Aligned_cols=25 Identities=32% Similarity=0.707 Sum_probs=17.5
Q ss_pred CCCCcCCCCCC---------CCCCCCCcccCCcC
Q 018197 332 KFCDECGAPYL---------RETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~---------~~~AKFCpECGtKr 356 (359)
-.|..||..+. .....-|+.||..+
T Consensus 106 ~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~l 139 (178)
T PF02146_consen 106 LRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLL 139 (178)
T ss_dssp EEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBE
T ss_pred eeecCCCccccchhhcccccccccccccccCccC
Confidence 35999999762 12345899999864
No 279
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=20.33 E-value=47 Score=35.67 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=16.9
Q ss_pred CCCCcCCCCCCCCCCCCCcccCCcC
Q 018197 332 KFCDECGAPYLRETSKFCSECGVKR 356 (359)
Q Consensus 332 KFCpeCGt~l~~~~AKFCpECGtKr 356 (359)
.-|+.||..+-...---| +||...
T Consensus 131 w~c~~cg~~iean~kp~c-~cg~~~ 154 (593)
T COG2401 131 WRCEKCGTIIEANTKPEC-KCGSHV 154 (593)
T ss_pred EecchhchhhhhcCCccc-CCCCce
Confidence 459999998744434467 999853
No 280
>PF04809 HupH_C: HupH hydrogenase expression protein, C-terminal conserved region; InterPro: IPR006894 This entry represents the C-terminal conserved domain found in bacterial hydrogenase expression proteins (HupH), which are necessary for hydrogenase synthesis. The precise function of HupH is unknown [].; PDB: 3SB1_A.
Probab=20.11 E-value=64 Score=27.83 Aligned_cols=25 Identities=24% Similarity=0.430 Sum_probs=17.5
Q ss_pred CChhhHHHHHHHhcccccccccccc
Q 018197 167 MPIEDAEWFKRLTGRNEVAISAQDY 191 (359)
Q Consensus 167 lp~eDqewfkRLtgr~EVai~g~DY 191 (359)
|..+|.+||...+|+-||+|..+.|
T Consensus 35 Ls~~D~~~L~~~LGeGeVsi~~~g~ 59 (120)
T PF04809_consen 35 LSPADRALLDETLGEGEVSILSRGY 59 (120)
T ss_dssp --HHHHHHHHHHH---SEEEEEE--
T ss_pred CCHHHHHHHHHHcCCCcEEEEEcCC
Confidence 6799999999999999999988877
No 281
>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=20.06 E-value=29 Score=32.78 Aligned_cols=22 Identities=27% Similarity=0.662 Sum_probs=7.9
Q ss_pred CCCcCCCCCCCCCCCCCcccCCc
Q 018197 333 FCDECGAPYLRETSKFCSECGVK 355 (359)
Q Consensus 333 FCpeCGt~l~~~~AKFCpECGtK 355 (359)
+|.-||+.-... ---||.||..
T Consensus 199 ~Cs~C~t~W~~~-R~~Cp~Cg~~ 220 (290)
T PF04216_consen 199 HCSLCGTEWRFV-RIKCPYCGNT 220 (290)
T ss_dssp EETTT--EEE---TTS-TTT---
T ss_pred EcCCCCCeeeec-CCCCcCCCCC
Confidence 477777765322 2237777764
Done!