Query 010400
Match_columns 511
No_of_seqs 192 out of 369
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 00:05:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010400.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010400hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2613 NMD protein affecting 100.0 7E-163 1E-167 1239.6 32.2 479 15-503 13-491 (502)
2 COG1499 NMD3 NMD protein affec 100.0 1.4E-69 3.1E-74 559.3 31.3 341 13-387 3-353 (355)
3 PF04981 NMD3: NMD3 family ; 100.0 2.2E-63 4.7E-68 490.7 21.8 223 19-248 1-236 (236)
4 cd04467 S1_aIF5A S1_aIF5A: Arc 94.6 0.055 1.2E-06 43.0 4.3 30 272-301 5-34 (57)
5 PRK14714 DNA polymerase II lar 90.6 0.22 4.9E-06 59.8 3.9 67 16-89 667-741 (1337)
6 PRK04023 DNA polymerase II lar 90.3 0.26 5.7E-06 58.0 4.0 69 14-89 624-695 (1121)
7 COG1579 Zn-ribbon protein, pos 89.2 0.067 1.5E-06 53.9 -1.6 44 23-66 189-233 (239)
8 COG3809 Uncharacterized protei 88.7 0.32 6.9E-06 41.0 2.3 24 50-80 17-40 (88)
9 PF12773 DZR: Double zinc ribb 87.8 0.27 5.8E-06 37.1 1.2 40 19-65 1-40 (50)
10 PF13240 zinc_ribbon_2: zinc-r 87.3 0.31 6.8E-06 31.7 1.2 20 18-38 1-20 (23)
11 PF14803 Nudix_N_2: Nudix N-te 87.3 0.26 5.7E-06 35.2 0.8 31 17-65 1-33 (34)
12 PF13453 zf-TFIIB: Transcripti 87.0 0.4 8.7E-06 35.1 1.7 19 50-74 15-33 (41)
13 PF02591 DUF164: Putative zinc 86.3 0.15 3.4E-06 39.7 -0.9 40 24-64 15-56 (56)
14 PF13248 zf-ribbon_3: zinc-rib 85.4 0.45 9.7E-06 31.7 1.2 21 16-37 2-22 (26)
15 COG1656 Uncharacterized conser 85.0 0.38 8.2E-06 45.9 0.9 48 16-73 97-149 (165)
16 PF12773 DZR: Double zinc ribb 84.7 0.5 1.1E-05 35.6 1.3 39 14-61 10-50 (50)
17 PRK14559 putative protein seri 82.6 0.66 1.4E-05 53.0 1.7 40 16-67 15-54 (645)
18 TIGR01206 lysW lysine biosynth 80.0 1.1 2.4E-05 35.2 1.7 30 18-65 4-33 (54)
19 PF09297 zf-NADH-PPase: NADH p 79.9 0.5 1.1E-05 32.8 -0.2 24 16-39 3-29 (32)
20 PF01927 Mut7-C: Mut7-C RNAse 79.1 1.3 2.8E-05 41.1 2.2 20 53-72 123-142 (147)
21 PRK00398 rpoP DNA-directed RNA 79.0 1 2.2E-05 33.8 1.1 29 17-65 4-32 (46)
22 PF03833 PolC_DP2: DNA polymer 74.1 1 2.2E-05 52.5 0.0 68 14-88 653-723 (900)
23 smart00661 RPOL9 RNA polymeras 73.4 2.9 6.2E-05 31.5 2.3 32 17-66 1-32 (52)
24 PRK11595 DNA utilization prote 72.8 2.4 5.2E-05 42.0 2.3 37 18-63 7-43 (227)
25 PF02318 FYVE_2: FYVE-type zin 72.6 2.4 5.2E-05 38.0 2.0 44 13-71 51-96 (118)
26 PF04161 Arv1: Arv1-like famil 68.9 3.1 6.7E-05 40.9 2.0 41 17-74 1-41 (208)
27 COG2888 Predicted Zn-ribbon RN 67.1 2.1 4.5E-05 34.4 0.3 13 50-62 46-58 (61)
28 PF09889 DUF2116: Uncharacteri 67.0 2.6 5.5E-05 33.8 0.8 22 17-39 4-26 (59)
29 PF12647 RNHCP: RNHCP domain; 66.7 6.7 0.00015 34.2 3.4 49 18-66 6-79 (92)
30 PRK14890 putative Zn-ribbon RN 66.5 2.8 6E-05 33.7 0.9 45 18-62 9-56 (59)
31 PF09855 DUF2082: Nucleic-acid 66.4 4.4 9.6E-05 33.0 2.1 42 18-62 2-44 (64)
32 PF07754 DUF1610: Domain of un 65.3 4.5 9.8E-05 26.9 1.6 10 52-61 14-23 (24)
33 PHA00626 hypothetical protein 64.3 3.4 7.3E-05 32.9 1.0 34 17-66 1-35 (59)
34 PRK00241 nudC NADH pyrophospha 62.8 14 0.00031 37.5 5.5 31 14-44 97-130 (256)
35 COG1996 RPC10 DNA-directed RNA 60.2 4.1 8.8E-05 31.6 0.8 26 18-63 8-33 (49)
36 PHA02998 RNA polymerase subuni 58.5 8.1 0.00018 37.6 2.7 52 6-67 133-184 (195)
37 COG4888 Uncharacterized Zn rib 58.4 8.1 0.00018 34.2 2.4 38 14-65 19-57 (104)
38 PF10571 UPF0547: Uncharacteri 57.8 4.3 9.3E-05 27.3 0.5 19 18-37 2-20 (26)
39 COG1734 DksA DnaK suppressor p 57.7 3.3 7.2E-05 37.7 -0.0 24 16-39 80-109 (120)
40 PTZ00218 40S ribosomal protein 57.7 8.1 0.00017 30.5 2.1 30 13-43 13-46 (54)
41 PF07862 Nif11: Nitrogen fixat 57.5 8.3 0.00018 29.0 2.1 27 442-468 3-29 (49)
42 PF10083 DUF2321: Uncharacteri 57.2 1.9 4.2E-05 40.8 -1.7 60 14-82 26-93 (158)
43 PRK00420 hypothetical protein; 57.1 4.5 9.8E-05 36.4 0.7 29 17-66 24-52 (112)
44 TIGR03826 YvyF flagellar opero 56.9 2.9 6.3E-05 38.9 -0.6 32 17-48 4-35 (137)
45 PTZ00255 60S ribosomal protein 55.5 23 0.00049 30.9 4.6 25 50-75 50-74 (90)
46 COG2816 NPY1 NTP pyrophosphohy 55.0 9 0.0002 39.7 2.5 32 15-46 110-144 (279)
47 TIGR01384 TFS_arch transcripti 53.9 11 0.00025 32.6 2.7 24 139-166 62-85 (104)
48 PF12172 DUF35_N: Rubredoxin-l 53.5 11 0.00023 26.9 2.0 19 50-68 7-25 (37)
49 PF07503 zf-HYPF: HypF finger; 53.2 3.4 7.4E-05 29.7 -0.6 30 33-63 1-30 (35)
50 TIGR00038 efp translation elon 52.3 78 0.0017 30.7 8.4 30 272-301 68-97 (184)
51 PF06677 Auto_anti-p27: Sjogre 51.9 5.3 0.00011 29.7 0.2 21 17-37 18-40 (41)
52 TIGR02098 MJ0042_CXXC MJ0042 f 50.5 9.9 0.00021 27.0 1.5 12 53-64 24-35 (38)
53 PF04216 FdhE: Protein involve 50.3 10 0.00023 38.9 2.2 34 32-65 212-249 (290)
54 TIGR03054 photo_alph_chp1 puta 50.3 28 0.00061 32.4 4.7 33 266-298 90-122 (135)
55 PRK04179 rpl37e 50S ribosomal 49.1 13 0.00028 30.1 2.0 39 1-39 1-40 (62)
56 TIGR00570 cdk7 CDK-activating 47.8 11 0.00023 39.7 1.8 43 18-68 5-57 (309)
57 TIGR00280 L37a ribosomal prote 47.8 32 0.00068 30.0 4.3 24 51-75 50-73 (91)
58 TIGR03826 YvyF flagellar opero 47.5 10 0.00023 35.3 1.5 28 13-42 78-105 (137)
59 PF14353 CpXC: CpXC protein 47.4 6.9 0.00015 35.2 0.3 13 51-63 35-47 (128)
60 cd05705 S1_Rrp5_repeat_hs14 S1 46.8 91 0.002 25.4 6.8 51 276-326 11-67 (74)
61 PF11672 DUF3268: Protein of u 46.1 12 0.00027 33.1 1.7 39 16-64 2-41 (102)
62 TIGR02420 dksA RNA polymerase- 45.8 7.7 0.00017 34.3 0.3 24 15-38 79-108 (110)
63 PRK03999 translation initiatio 45.6 27 0.00059 32.0 3.9 28 272-299 74-101 (129)
64 PF14471 DUF4428: Domain of un 44.8 10 0.00022 29.4 0.8 24 18-41 1-30 (51)
65 KOG2879 Predicted E3 ubiquitin 44.8 15 0.00033 38.0 2.2 46 13-65 236-287 (298)
66 COG1545 Predicted nucleic-acid 44.7 12 0.00026 34.8 1.4 45 14-60 27-72 (140)
67 PF07191 zinc-ribbons_6: zinc- 44.4 12 0.00026 31.1 1.3 39 17-65 2-41 (70)
68 PF10892 DUF2688: Protein of u 43.3 5 0.00011 31.9 -1.1 27 15-41 9-48 (60)
69 PF07282 OrfB_Zn_ribbon: Putat 43.3 22 0.00049 28.3 2.6 32 15-66 27-58 (69)
70 COG1779 C4-type Zn-finger prot 42.7 19 0.00042 35.5 2.5 45 7-64 5-53 (201)
71 PRK12495 hypothetical protein; 42.6 11 0.00024 37.8 0.9 32 13-66 39-70 (226)
72 PRK00464 nrdR transcriptional 42.5 18 0.00039 34.3 2.3 13 54-66 28-40 (154)
73 PF13719 zinc_ribbon_5: zinc-r 41.8 19 0.0004 25.9 1.7 17 48-64 19-35 (37)
74 PF14260 zf-C4pol: C4-type zin 41.7 14 0.00029 30.1 1.1 23 19-41 1-23 (73)
75 PF05810 NinF: NinF protein; 41.4 4.9 0.00011 31.9 -1.4 29 12-40 13-41 (58)
76 PF04032 Rpr2: RNAse P Rpr2/Rp 41.4 6.8 0.00015 32.4 -0.7 20 48-67 40-59 (85)
77 PF14446 Prok-RING_1: Prokaryo 41.2 10 0.00022 30.0 0.3 22 51-73 18-39 (54)
78 smart00709 Zpr1 Duplicated dom 40.9 20 0.00043 34.2 2.3 33 18-63 2-38 (160)
79 TIGR00595 priA primosomal prot 40.6 24 0.00052 39.3 3.3 17 15-37 212-228 (505)
80 PF14149 YhfH: YhfH-like prote 40.6 3.8 8.2E-05 30.0 -2.0 25 13-37 10-37 (37)
81 COG2126 RPL37A Ribosomal prote 40.3 17 0.00037 29.2 1.5 38 1-38 1-38 (61)
82 PF01780 Ribosomal_L37ae: Ribo 40.1 11 0.00025 32.7 0.5 34 53-88 52-85 (90)
83 COG1499 NMD3 NMD protein affec 40.0 33 0.00073 36.7 4.1 67 223-299 265-331 (355)
84 PRK02290 3-dehydroquinate synt 39.3 4.3E+02 0.0094 28.4 12.0 79 194-292 138-216 (344)
85 PF05191 ADK_lid: Adenylate ki 39.1 16 0.00034 26.4 1.0 23 17-39 2-29 (36)
86 TIGR02890 spore_yteA sporulati 38.9 11 0.00024 35.8 0.3 25 15-39 85-115 (159)
87 PF13005 zf-IS66: zinc-finger 38.5 29 0.00062 25.6 2.4 39 17-61 3-47 (47)
88 PRK13674 putative GTP cyclohyd 38.5 3.1E+02 0.0067 28.4 10.6 47 113-162 127-175 (271)
89 PTZ00073 60S ribosomal protein 38.4 23 0.0005 30.8 2.1 38 1-38 1-38 (91)
90 PF05876 Terminase_GpA: Phage 38.3 25 0.00054 39.7 3.0 52 15-75 199-258 (557)
91 COG2995 PqiA Uncharacterized p 38.1 20 0.00043 38.9 2.0 44 13-74 15-58 (418)
92 COG3058 FdhE Uncharacterized p 37.8 7.1 0.00015 40.4 -1.3 9 17-25 186-194 (308)
93 PF01132 EFP: Elongation facto 37.7 45 0.00097 25.9 3.4 34 273-306 4-38 (55)
94 PF01783 Ribosomal_L32p: Ribos 37.5 20 0.00043 28.2 1.4 29 15-45 25-54 (56)
95 PRK00415 rps27e 30S ribosomal 37.0 15 0.00032 29.6 0.7 20 50-69 26-45 (59)
96 PF08772 NOB1_Zn_bind: Nin one 36.8 12 0.00026 31.3 0.1 23 32-62 10-32 (73)
97 smart00259 ZnF_A20 A20-like zi 36.8 18 0.0004 24.4 1.0 22 18-39 3-26 (26)
98 PF11009 DUF2847: Protein of u 36.3 28 0.00061 31.0 2.4 48 193-243 48-95 (105)
99 smart00659 RPOLCX RNA polymera 36.1 18 0.00038 27.3 0.9 11 53-63 18-28 (44)
100 TIGR00340 zpr1_rel ZPR1-relate 35.7 27 0.00059 33.4 2.3 33 205-239 121-153 (163)
101 PF13550 Phage-tail_3: Putativ 35.7 47 0.001 30.1 3.9 51 197-262 100-151 (164)
102 PHA00080 DksA-like zinc finger 35.6 16 0.00034 30.3 0.7 26 14-39 29-60 (72)
103 COG0846 SIR2 NAD-dependent pro 35.6 30 0.00066 35.3 2.8 63 11-88 117-180 (250)
104 TIGR00201 comF comF family pro 35.4 18 0.00038 34.7 1.0 21 19-40 1-21 (190)
105 COG0068 HypF Hydrogenase matur 35.2 44 0.00096 38.9 4.2 51 13-64 120-183 (750)
106 COG3478 Predicted nucleic-acid 35.0 29 0.00063 28.5 2.0 13 50-62 36-48 (68)
107 KOG3475 60S ribosomal protein 34.0 13 0.00028 31.9 -0.1 36 2-37 2-37 (92)
108 COG1545 Predicted nucleic-acid 32.9 1.1E+02 0.0024 28.3 5.9 22 50-71 25-46 (140)
109 KOG3507 DNA-directed RNA polym 32.7 31 0.00066 27.9 1.8 13 50-62 33-45 (62)
110 PF14599 zinc_ribbon_6: Zinc-r 32.7 9.4 0.0002 30.8 -1.1 17 48-64 42-58 (61)
111 PF04423 Rad50_zn_hook: Rad50 32.6 12 0.00026 28.8 -0.5 11 18-28 22-32 (54)
112 PLN02915 cellulose synthase A 32.3 29 0.00063 41.9 2.3 55 12-74 11-79 (1044)
113 COG2051 RPS27A Ribosomal prote 32.3 23 0.00051 29.1 1.1 18 50-67 34-51 (67)
114 COG4338 Uncharacterized protei 32.2 22 0.00047 27.7 0.8 15 12-26 8-22 (54)
115 PRK13715 conjugal transfer pro 32.1 16 0.00035 30.4 0.2 23 17-39 35-63 (73)
116 PF13717 zinc_ribbon_4: zinc-r 32.1 26 0.00057 25.1 1.2 17 48-64 19-35 (36)
117 PRK11019 hypothetical protein; 31.9 17 0.00038 31.4 0.3 26 16-41 36-67 (88)
118 KOG2932 E3 ubiquitin ligase in 31.6 22 0.00047 37.5 1.0 35 17-62 91-131 (389)
119 PF01258 zf-dskA_traR: Prokary 31.4 15 0.00033 26.0 -0.1 23 18-40 5-33 (36)
120 KOG3084 NADH pyrophosphatase I 31.0 32 0.00069 36.4 2.1 71 15-87 149-234 (345)
121 PTZ00083 40S ribosomal protein 30.9 29 0.00062 29.9 1.4 31 33-67 37-67 (85)
122 PF06827 zf-FPG_IleRS: Zinc fi 30.8 12 0.00025 25.4 -0.7 21 18-38 3-28 (30)
123 TIGR02419 C4_traR_proteo phage 30.6 21 0.00045 28.8 0.5 26 14-39 29-60 (63)
124 PLN00209 ribosomal protein S27 30.5 29 0.00063 30.0 1.4 31 33-67 38-68 (86)
125 PF01667 Ribosomal_S27e: Ribos 30.1 15 0.00032 29.2 -0.4 31 33-67 9-39 (55)
126 PF08271 TF_Zn_Ribbon: TFIIB z 30.1 24 0.00051 25.9 0.8 11 56-66 21-31 (43)
127 PF00924 MS_channel: Mechanose 30.0 1.4E+02 0.0031 28.2 6.3 64 250-324 60-125 (206)
128 TIGR00143 hypF [NiFe] hydrogen 29.4 29 0.00063 40.4 1.7 51 13-64 87-150 (711)
129 TIGR02174 CXXU_selWTH selT/sel 29.4 8.4 0.00018 31.6 -2.0 14 52-66 1-14 (72)
130 COG1110 Reverse gyrase [DNA re 29.3 22 0.00047 43.0 0.6 27 17-43 9-38 (1187)
131 COG3024 Uncharacterized protei 29.3 28 0.00061 28.5 1.1 16 13-28 4-19 (65)
132 PF10013 DUF2256: Uncharacteri 29.0 27 0.00057 26.3 0.8 15 13-27 5-19 (42)
133 PF03884 DUF329: Domain of unk 28.9 22 0.00048 28.4 0.4 13 16-28 2-14 (57)
134 cd04463 S1_EF_like S1_EF_like: 28.7 68 0.0015 24.5 3.1 27 274-300 4-30 (55)
135 TIGR03798 ocin_TIGR03798 bacte 28.3 43 0.00094 26.7 2.0 26 443-468 2-27 (64)
136 PRK00432 30S ribosomal protein 27.4 26 0.00056 27.1 0.6 11 15-25 19-29 (50)
137 PRK00529 elongation factor P; 27.2 2.3E+02 0.0049 27.5 7.2 29 272-300 69-97 (186)
138 PF09538 FYDLN_acid: Protein o 26.8 25 0.00053 31.5 0.4 28 33-66 11-38 (108)
139 COG1645 Uncharacterized Zn-fin 26.6 25 0.00054 32.6 0.4 10 17-26 29-38 (131)
140 PRK03564 formate dehydrogenase 26.0 64 0.0014 34.0 3.3 34 32-66 227-264 (309)
141 PF02701 zf-Dof: Dof domain, z 25.6 12 0.00026 30.4 -1.6 41 16-69 5-45 (63)
142 KOG4080 Mitochondrial ribosoma 25.5 12 0.00026 35.9 -1.9 32 17-50 94-125 (176)
143 TIGR00310 ZPR1_znf ZPR1 zinc f 25.5 52 0.0011 32.3 2.4 39 17-63 1-39 (192)
144 TIGR02276 beta_rpt_yvtn 40-res 25.1 1E+02 0.0022 21.2 3.3 23 272-294 5-27 (42)
145 TIGR00155 pqiA_fam integral me 24.8 56 0.0012 35.5 2.7 15 53-67 32-46 (403)
146 PF13913 zf-C2HC_2: zinc-finge 24.8 25 0.00055 23.1 0.1 13 54-66 2-14 (25)
147 PF03367 zf-ZPR1: ZPR1 zinc-fi 24.8 45 0.00098 31.7 1.8 38 17-63 2-39 (161)
148 COG1997 RPL43A Ribosomal prote 24.6 84 0.0018 27.3 3.2 22 52-74 51-72 (89)
149 COG1998 RPS31 Ribosomal protei 24.2 30 0.00065 27.0 0.4 12 14-25 17-28 (51)
150 TIGR00100 hypA hydrogenase nic 24.0 40 0.00087 30.2 1.2 15 14-28 68-82 (115)
151 PF02478 Pneumo_phosprot: Pneu 23.6 38 0.00083 34.5 1.1 61 194-260 1-61 (279)
152 PF14279 HNH_5: HNH endonuclea 23.6 28 0.0006 28.8 0.1 47 19-75 1-48 (71)
153 TIGR02219 phage_NlpC_fam putat 23.1 99 0.0022 28.1 3.6 60 245-309 71-130 (134)
154 PF07295 DUF1451: Protein of u 23.0 31 0.00068 32.4 0.4 15 13-27 109-123 (146)
155 TIGR00269 conserved hypothetic 22.7 41 0.00088 29.4 1.0 22 16-40 80-101 (104)
156 PF09151 DUF1936: Domain of un 22.7 36 0.00078 24.1 0.5 10 17-26 2-11 (36)
157 TIGR01562 FdhE formate dehydro 22.6 79 0.0017 33.3 3.2 54 32-86 225-286 (305)
158 COG4031 Predicted metal-bindin 22.6 51 0.0011 32.5 1.7 22 18-42 2-23 (227)
159 PF11023 DUF2614: Protein of u 22.5 30 0.00066 31.3 0.1 15 13-27 66-80 (114)
160 PLN02638 cellulose synthase A 22.5 56 0.0012 39.8 2.3 56 12-75 13-82 (1079)
161 COG1198 PriA Primosomal protei 22.4 87 0.0019 36.8 3.8 12 15-26 434-445 (730)
162 PRK11827 hypothetical protein; 22.3 45 0.00098 26.9 1.1 32 17-49 9-43 (60)
163 KOG2462 C2H2-type Zn-finger pr 22.2 25 0.00055 36.3 -0.5 56 16-74 130-205 (279)
164 COG0231 Efp Translation elonga 22.2 1E+02 0.0022 28.5 3.5 29 272-300 71-99 (131)
165 smart00531 TFIIE Transcription 22.2 30 0.00064 32.1 0.0 12 55-66 124-135 (147)
166 cd01407 SIR2-fam SIR2 family o 22.2 55 0.0012 32.1 1.9 64 10-89 103-166 (218)
167 PF02150 RNA_POL_M_15KD: RNA p 22.1 32 0.00069 24.6 0.2 12 55-66 2-13 (35)
168 PRK03954 ribonuclease P protei 22.1 16 0.00036 33.3 -1.6 21 47-67 57-77 (121)
169 PTZ00328 eukaryotic initiation 21.9 2.3E+02 0.0049 27.5 5.9 81 236-325 13-99 (166)
170 PF10058 DUF2296: Predicted in 21.7 60 0.0013 25.5 1.7 10 54-63 44-53 (54)
171 PRK01343 zinc-binding protein; 21.5 69 0.0015 25.7 1.9 15 13-27 6-20 (57)
172 COG5254 ARV1 Predicted membran 21.3 34 0.00074 34.0 0.3 36 17-66 1-36 (239)
173 COG1107 Archaea-specific RecJ- 21.1 47 0.001 37.9 1.3 26 17-42 81-106 (715)
174 TIGR02300 FYDLN_acid conserved 20.9 36 0.00079 31.4 0.3 28 33-66 11-38 (129)
175 PF01907 Ribosomal_L37e: Ribos 20.7 39 0.00085 26.8 0.4 26 13-38 12-37 (55)
176 cd04470 S1_EF-P_repeat_1 S1_EF 20.1 1.4E+02 0.003 23.7 3.5 29 273-301 5-33 (61)
177 PRK03681 hypA hydrogenase nick 20.1 55 0.0012 29.3 1.3 12 14-25 68-79 (114)
178 TIGR00270 conserved hypothetic 20.1 46 0.001 31.5 0.8 28 184-216 96-123 (154)
No 1
>KOG2613 consensus NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.6e-163 Score=1239.64 Aligned_cols=479 Identities=55% Similarity=0.989 Sum_probs=452.0
Q ss_pred ceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCCCceeeCCcChHHHHHHHHHHhcccccc
Q 010400 15 GSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPRTWIKAQLESKELLTFCVKRLKNLNRV 94 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~~Wv~~~les~ELL~~~Lkki~gl~kv 94 (511)
+.++||.||.||+||++|||.+|++.++||++|||++++|.+||.|.||++||+.|+.+++||+|||++||||+|||++|
T Consensus 13 ~~ILCCeCGvpi~Pn~anMC~~Clrs~VDITegipr~~~i~~Cr~CeRYlqPP~~Wi~a~leSrELLaiclkklK~L~~V 92 (502)
T KOG2613|consen 13 ATILCCECGVPIEPNPANMCVDCLRSEVDITEGIPRQATISFCRECERYLQPPKTWIRAELESRELLAICLKKLKGLNKV 92 (502)
T ss_pred cEEEEecCCCcCCCchHHHHHHHhheeeehhcCCcchhhhhhccccceecCCcHHHhhhhhccHHHHHHHHHhhcCccee
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeccceEEecccCceEEEEEEEEEEEecCeeEEEEEEEEEEEeccCCchhhhhccCCcceEEEEEEeeccCchhhHHHH
Q 010400 95 RLVNAEFIWTEPHSKRIKVKLKVQKEVLNGAILEQSYVVEYVQQDHMCDSCSRVQANPDQWVAAVQLRQHVTHRRTFFYL 174 (511)
Q Consensus 95 klvda~fiwtEphs~r~kvkltvq~ev~~g~~lqq~~~Ve~~v~~~~C~~C~R~~~~~~~w~AiVQVRq~~~~krt~~~L 174 (511)
+|+||+||||||||+||+||||||||+++|+++||+|+|||+|+++|||+|+|..++ ++|+|+|||||++.|||||+||
T Consensus 93 rLvDA~FVwTEpHSkRIkVKLTVq~E~~~~tilqQ~f~Vey~V~~~~C~DC~R~eak-dfW~a~vQvRQr~~hkrTF~YL 171 (502)
T KOG2613|consen 93 RLVDANFVWTEPHSKRIKVKLTVQKEVFTNTILQQSFVVEYTVRNQQCPDCARVEAK-DFWRALVQVRQRAEHKRTFFYL 171 (502)
T ss_pred EEeccceEeccCCCceEEEEEEEEhhhcCCceeeeeEEEEEEEecccCchhhhhhhh-HHHHHHHHHHhhcccchhhHHH
Confidence 999999999999999999999999999999999999999999999999999999995 8999999999999999999999
Q ss_pred HHHHhhccccccccceeecCCceeEEEcChhHHHHHHHHhcccCCeEEeecCceeeecCCCCeeeEEEEEEEEEcccCCC
Q 010400 175 EQLILKHDAAARAIRITQMDQGIDFFFGNRSHAVKFVEFVGKVAPVRSRHDKQLVSHDPKSNNFNYKYTFSVEISPICRE 254 (511)
Q Consensus 175 EqlilK~~~~~~i~~I~e~kdGlDfyf~s~~~Ark~v~fl~s~~p~~vkeS~kLVg~D~~~g~~~yr~T~SVrIppickg 254 (511)
|||||||++|.++++|++.++||||||++++||+|||+||+.++|++++.|++|||||.|+|+++|||||||+|+||||+
T Consensus 172 EQLILKh~ah~~t~~Ik~~~~GlDFyy~~k~hA~kmVeFL~~vvP~ryk~se~LIS~D~hsn~ynYK~t~SVEIvPiCkD 251 (502)
T KOG2613|consen 172 EQLILKHNAHGNTINIKEVKDGLDFYYANKNHAVKMVEFLQTVVPIRYKVSERLISHDVHSNTYNYKFTYSVEIVPICKD 251 (502)
T ss_pred HHHHHhcchhhcccccccccCCcceeeccHHHHHHHHHHHHhhceeEEecchhhhhhhcccCcccceeeeEEEEeeeccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CEEEcCchhhhhcCCCCCEEEEEEeCCeEEEEcCCCCeEEEecCccccccccccccCccceeEEEEEEeeeeccccccCC
Q 010400 255 DLICLPPKVAVSLGNLGPLVICMKVTNSIALLDPFTLRHCFLDADQYWRSSFKSLLTSRQLVEYIVLDVEVVSSEVNVGG 334 (511)
Q Consensus 255 DlV~l~~k~a~~lG~i~~~~lv~kv~~~I~llDP~T~~~~~l~~~~yw~~pf~~l~~~~~l~ef~Vldve~~~~~~~~~~ 334 (511)
|+||||+++|+++||||+++||+||+++|+||||.|+|+++|+++.|||+||++|++++||+||+|+||++++.-.+ .|
T Consensus 252 dlVcLpkkva~~lGNi~qlvvc~kVs~~I~llDP~tlq~adl~~s~yWr~pF~sl~~~kqL~ef~V~dv~~v~~~~~-~g 330 (502)
T KOG2613|consen 252 DLVCLPKKVAQSLGNISQLVVCTKVSNTITLLDPRTLQTADLTGSVYWRAPFNSLCDPKQLTEFIVLDVDPVGEAGG-KG 330 (502)
T ss_pred ceEEcCHHHHHhcCCccceEEEEEecCceEEeCCcceeeeecccceeecCcchhhcChhhheEEEEEEEecccccCC-cc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999874211 24
Q ss_pred CceeEEEEEEEeecCCCCCccEEEEccccCCcCCCCCeeeeeecCCCCCCChhhhhhcCCCCCceEEEehhhHHHHhhhc
Q 010400 335 SKYVLADAQVARVSDFGKNDTIFSIRTHLGHLLNPGDYALGYDLYSANNNDMELDKYKGLVLPETILIKKSYEEKRLRKR 414 (511)
Q Consensus 335 ~k~~la~~~v~r~~d~g~~~~~~~~rtHLg~~l~~Gd~v~gydl~~~n~n~~~~~~~~~~~~pdvilvkk~~~~~~~~~~ 414 (511)
.||.||||||+|+||+|+||..+++||||||||+|||+||||||+++|+||+++++|..+.+||||||||.|++. +
T Consensus 331 ~kh~l~dv~v~r~sd~g~nd~~~~~RtHLGhil~~gD~vlgydl~~~N~N~~~~d~~~~d~vPdvvlVkK~y~r~----~ 406 (502)
T KOG2613|consen 331 QKHALADVWVARSSDLGMNDKFHYARTHLGHILKPGDLVLGYDLANANLNDEEFDKLNIDGVPDVVLVKKMYDRT----K 406 (502)
T ss_pred ceeeeeeEEEEEcCccCcccceeeehhhccccCCCCCeeeeeeeccCccchhhhhhhcccCCCcEEEEEcccccc----c
Confidence 489999999999999999999999999999999999999999999999999999999999999999999999742 2
Q ss_pred CCCCCceeeeecccccCCCCcchhhhhHHHHHHHHHHhhcCHhhhhhccccccCCCCCCCCCCCCCCCCCCCCChhhhcc
Q 010400 415 SKPRSWKLKSLDMEVDDSKGRTDQEKMNKEYEEFLRDLEENPELRFNISLYRNKDYQPSEMASVTDGEDVPSVPLDELLA 494 (511)
Q Consensus 415 ~~~r~wklk~l~~~~~~~~~~~~~~~~e~d~e~F~~dleeD~elr~~i~lyk~~~~~~~~~~~~~~~~~~p~~~l~ell~ 494 (511)
++.|+||||+|+++.. .++.+.++.+.||++||+|||||+|||++|||||++++. .+.+ .++++|+|+|+|+||||
T Consensus 407 r~~r~WKlK~l~~e~~--~~~~~~~~~~~eY~~FledlEEd~elr~~vnlyrd~~~~-~~~d-~d~~ed~p~i~ldElLe 482 (502)
T KOG2613|consen 407 RKSRNWKLKRLAMEMS--RGKNESERTEKEYELFLEDLEEDPELRQGVNLYRDKEKP-TESD-TDDAEDAPQITLDELLE 482 (502)
T ss_pred hhccceehhhhhhhhc--cccccchhhHHHHHHHHHhhhcCHHHHhcceeeeccCCC-Cccc-cccccCCCCCCHHHHHh
Confidence 3559999999998752 356677788999999999999999999999999998762 2222 22348899999999999
Q ss_pred ccCCCCCCC
Q 010400 495 DLDLKSDDG 503 (511)
Q Consensus 495 ~~~~~~~~~ 503 (511)
||++..+++
T Consensus 483 dl~~~~~e~ 491 (502)
T KOG2613|consen 483 DLKLSFEED 491 (502)
T ss_pred hhhcchhhc
Confidence 998875433
No 2
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-69 Score=559.33 Aligned_cols=341 Identities=23% Similarity=0.391 Sum_probs=314.4
Q ss_pred ccceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCCCceeeCCcChHHHHHHHHHHhcccc
Q 010400 13 TVGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPRTWIKAQLESKELLTFCVKRLKNLN 92 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~~Wv~~~les~ELL~~~Lkki~gl~ 92 (511)
..+++|||.||++++|++++||.+||.+.+++.+ ||+.+++.+|++||+++.| ++|++.+.+++.|.+.+.+..+.+.
T Consensus 3 ~~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~-ip~~~~v~~C~~Cga~~~~-~~W~~~~~~~~~l~~~~~~~~~~~~ 80 (355)
T COG1499 3 DASTILCVRCGRSVDPLIDGLCGDCYVETTPLIE-IPDEVNVEVCRHCGAYRIR-GRWVDEEGANRLLEALEDEVLRRLE 80 (355)
T ss_pred CCcccEeccCCCcCchhhccccHHHHhccCcccc-CCCceEEEECCcCCCccCC-CcceeccccchHHHHHHHHHhhhhh
Confidence 4678999999999999999999999999999998 9999999999999977777 8999976677777777888777888
Q ss_pred ccc-eeccceEEecccCceEEEEEEEEEEEec-CeeEEEEEEEEEEEeccCCchhhhhccCCcceEEEEEEeeccCchh-
Q 010400 93 RVR-LVNAEFIWTEPHSKRIKVKLKVQKEVLN-GAILEQSYVVEYVQQDHMCDSCSRVQANPDQWVAAVQLRQHVTHRR- 169 (511)
Q Consensus 93 kvk-lvda~fiwtEphs~r~kvkltvq~ev~~-g~~lqq~~~Ve~~v~~~~C~~C~R~~~~~~~w~AiVQVRq~~~~kr- 169 (511)
++. .++++|+|++|+++|+.++++++++-+- |++++|++.|+|.+++.+||+|+|.+++ ||+|+||||+.+++..
T Consensus 81 ~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~~~~~~~~~~~v~~~v~~~~Cp~C~r~~~~--y~eAivQvR~~~r~~~~ 158 (355)
T COG1499 81 KVNEAVEVEFAFEEPKSRRLTVRVTIKGRGHVRGTPRTQLVEVTVEVRRTLCPRCSRFTGG--YYEAIVQVRAKGRELTE 158 (355)
T ss_pred hhccccccceeeeccCCCceEEEEEEEEeeecCCCceeEEEEEEEEEEEeEChhhhccccc--eeEEEEEEEeccCcccc
Confidence 887 8999999999999999999999976654 8999999999999999999999998776 9999999999999876
Q ss_pred ----hHHHHHHHHhhc---cccccccceeecCCceeEEEcChhHHHHHHHHhcccCCeEEeecCceeeecCCCCeeeEEE
Q 010400 170 ----TFFYLEQLILKH---DAAARAIRITQMDQGIDFFFGNRSHAVKFVEFVGKVAPVRSRHDKQLVSHDPKSNNFNYKY 242 (511)
Q Consensus 170 ----t~~~LEqlilK~---~~~~~i~~I~e~kdGlDfyf~s~~~Ark~v~fl~s~~p~~vkeS~kLVg~D~~~g~~~yr~ 242 (511)
.++++|++++|+ ++.+||+++++.++||||||+|+++|+|+++||.+.+|+.+++|++|+|+|.++|+.+||+
T Consensus 159 eee~~~~~ve~~v~k~~~~d~~~fIs~~~ek~eGiD~y~gs~~~arkva~~i~~~~~~~v~eS~~Lvg~d~~tgk~~yR~ 238 (355)
T COG1499 159 EEEEAFLFVEEIVLKRKKRDRMAFISDTEEKKEGIDIYLGSRNAARKVARFILEKFGGEVKESEKLVGRDRFTGKRVYRF 238 (355)
T ss_pred hhHHHHHHHHHHHHhhhccccccchhhhcccccceEEEEeccchHHHHHHHHHHHcCcEEEecceeEEEecCCCceEEEE
Confidence 799999999754 5678999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEcccCCCCEEEcCchhhhhcCCCCCEEEEEEeCCeEEEEcCCCCeEEEecCccccccccccccCccceeEEEEEE
Q 010400 243 TFSVEISPICREDLICLPPKVAVSLGNLGPLVICMKVTNSIALLDPFTLRHCFLDADQYWRSSFKSLLTSRQLVEYIVLD 322 (511)
Q Consensus 243 T~SVrIppickgDlV~l~~k~a~~lG~i~~~~lv~kv~~~I~llDP~T~~~~~l~~~~yw~~pf~~l~~~~~l~ef~Vld 322 (511)
|||||||+||+||||.+++ +++++|.+.++.|.++|+.|++++.++.+.||+++|..+....+|+.|+|++
T Consensus 239 t~Svrip~~~~gDiV~~~~---------~~~~~v~~~~~~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~~~~~~~vvs 309 (355)
T COG1499 239 TYSVRIPEFRPGDIVSVRG---------RQLVLVRSIGKGIVVLDLETGEPVEITWSVYKRNEGKVAVKEPRLKKAVVVS 309 (355)
T ss_pred EEEEECCCCCCCCEEEECC---------CeEEEEEEecCceEEEecccCCccccChhhcccCcceeeeccccceEEEEEe
Confidence 9999999999999999998 4789999999999999999999999999999999999999999999999999
Q ss_pred eeeeccccccCCCceeEEEEEEEeecCCCCCccEEEEccccCCcCCCCCeeeeeecCCCCCCChh
Q 010400 323 VEVVSSEVNVGGSKYVLADAQVARVSDFGKNDTIFSIRTHLGHLLNPGDYALGYDLYSANNNDME 387 (511)
Q Consensus 323 ve~~~~~~~~~~~k~~la~~~v~r~~d~g~~~~~~~~rtHLg~~l~~Gd~v~gydl~~~n~n~~~ 387 (511)
.++. ..++.|. ++|.++||+|..|++||+|++|.+++.||+.++
T Consensus 310 ~~~~---------~~~v~d~------------et~e~~~~~~~~~~~g~~v~v~~~~~~~~~~~~ 353 (355)
T COG1499 310 RDPS---------AIQVLDP------------ETYEARTVKGPSLEEGDEVKVFKVRGRNYVVEE 353 (355)
T ss_pred cCCC---------ceEEEec------------ceEEEEeccCCCCCCCCEEEEEEEeceEEeecc
Confidence 7762 3444444 579999999999999999999999999997654
No 3
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=100.00 E-value=2.2e-63 Score=490.72 Aligned_cols=223 Identities=39% Similarity=0.700 Sum_probs=214.3
Q ss_pred ccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCCCceeeCCcChHHHHHHHHHHh-ccccccc--
Q 010400 19 CCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPRTWIKAQLESKELLTFCVKRL-KNLNRVR-- 95 (511)
Q Consensus 19 C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~~Wv~~~les~ELL~~~Lkki-~gl~kvk-- 95 (511)
||+||++++|+++|||++||+++++|++ ||+++++.+||.||||+.+ |+|+++ +++||+..|++++ +++++..
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~e-i~~~i~v~~C~~Cg~~~~~-~~W~~~--~~~el~~~~lk~v~~~l~~~~~~ 76 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIE-IPDRIEVTICPKCGRYRIG-GRWVDP--ESRELEELCLKKVERGLKKNIKV 76 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeee-cCCccCceECCCCCCEECC-CEeeec--CcccHHHHHHHHHHHHHHHhhcc
Confidence 9999999999999999999999999999 9999999999999999999 799999 7899999999998 6777766
Q ss_pred eeccceEEecccCceEEEEEEEEEEEecCeeEEEEEEEEEEEeccCCchhhhhccCCcceEEEEEEeec----------c
Q 010400 96 LVNAEFIWTEPHSKRIKVKLKVQKEVLNGAILEQSYVVEYVQQDHMCDSCSRVQANPDQWVAAVQLRQH----------V 165 (511)
Q Consensus 96 lvda~fiwtEphs~r~kvkltvq~ev~~g~~lqq~~~Ve~~v~~~~C~~C~R~~~~~~~w~AiVQVRq~----------~ 165 (511)
++|++|+||||||+|++++|+|++++++|++++|++.|+|++++++||+|+|.+++ ||+|+|||||+ .
T Consensus 77 ~~d~~~v~~e~~~~r~~v~v~v~~~v~~~~~~~~~~~v~~~v~~~~C~~C~r~~~~--~~eaiVQvR~~~r~~~~~e~~~ 154 (236)
T PF04981_consen 77 HVDAEFVWTEPHSKRIKVKVTVQGEVHGGTPVEQEYEVEVRVKRQQCPDCSRIAGG--YYEAIVQVRQRGRKLTEEEKEV 154 (236)
T ss_pred cccccEEEEEeeCCEEEEEEEEEEEEcccceEEEEEEEEEEEEcCCChhHHhhhCC--CccEEEEEEecCCCCCHHHHHH
Confidence 89999999999999999999999999866999999999999999999999999977 99999999999 4
Q ss_pred CchhhHHHHHHHHhhccccccccceeecCCceeEEEcChhHHHHHHHHhcccCCeEEeecCceeeecCCCCeeeEEEEEE
Q 010400 166 THRRTFFYLEQLILKHDAAARAIRITQMDQGIDFFFGNRSHAVKFVEFVGKVAPVRSRHDKQLVSHDPKSNNFNYKYTFS 245 (511)
Q Consensus 166 ~~krt~~~LEqlilK~~~~~~i~~I~e~kdGlDfyf~s~~~Ark~v~fl~s~~p~~vkeS~kLVg~D~~~g~~~yr~T~S 245 (511)
.|++++++|||+++|+++++||++|++.+|||||||+|+++|++|++||.+.+|+++++|+||||+|.+ |+++||+|||
T Consensus 155 ~~~~~~~~le~l~~k~~~~~~i~~i~e~keGlD~y~~s~~~Arki~~~i~~~~~~~v~eS~klvg~~~~-gk~~yr~T~s 233 (236)
T PF04981_consen 155 IHKIVFEILEQLILKGDRHAFISDIEEVKEGLDFYFGSKNAARKIVSFIHSKFGGRVKESYKLVGRDDS-GKDVYRYTIS 233 (236)
T ss_pred HHHHHHHHHHHHHhhccchhcccceEECCCCEEEEECCHHHHHHHHHHHHHhcCeEEEECceeeeEeCC-CCeEEEEEEE
Confidence 466789999999999999999999999999999999999999999999999999999999999999988 9999999999
Q ss_pred EEE
Q 010400 246 VEI 248 (511)
Q Consensus 246 VrI 248 (511)
|||
T Consensus 234 Vrl 236 (236)
T PF04981_consen 234 VRL 236 (236)
T ss_pred EEC
Confidence 997
No 4
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=94.59 E-value=0.055 Score=42.96 Aligned_cols=30 Identities=10% Similarity=-0.012 Sum_probs=27.3
Q ss_pred CEEEEEEeCCeEEEEcCCCCeEEEecCccc
Q 010400 272 PLVICMKVTNSIALLDPFTLRHCFLDADQY 301 (511)
Q Consensus 272 ~~~lv~kv~~~I~llDP~T~~~~~l~~~~y 301 (511)
...|++..++.+|||||+||++.+++.+.+
T Consensus 5 ~aqVisi~g~~vQlMD~eTYeT~ev~~p~~ 34 (57)
T cd04467 5 TGQVLSIMGDVVQLMDLETYETFEVPIPEE 34 (57)
T ss_pred EEEEEEEcCCEEEEeccccceeEEEecchh
Confidence 568999999999999999999999999854
No 5
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=90.62 E-value=0.22 Score=59.81 Aligned_cols=67 Identities=21% Similarity=0.335 Sum_probs=39.5
Q ss_pred eecccccCcccCCCCcccchhhhcccccccccc--------CceEEEEeCCCCCceecCCCceeeCCcChHHHHHHHHHH
Q 010400 16 SVLCCKCGIPMAPNAANMCVACLRSEVDITEGL--------QKHVIISHCPECDCYLQPPRTWIKAQLESKELLTFCVKR 87 (511)
Q Consensus 16 ~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egI--------p~~~~v~~C~~Cgry~~~p~~Wv~~~les~ELL~~~Lkk 87 (511)
...||.||.++. .+.|+.|=........ + +...+-.+|+.||..+.+ ..|..-. .++++..++++
T Consensus 667 ~rkCPkCG~~t~---~~fCP~CGs~te~vy~-CPsCGaev~~des~a~~CP~CGtplv~-~~~~~i~--~~~~~~~A~~~ 739 (1337)
T PRK14714 667 RRRCPSCGTETY---ENRCPDCGTHTEPVYV-CPDCGAEVPPDESGRVECPRCDVELTP-YQRRTIN--VKEEYRSALEN 739 (1337)
T ss_pred EEECCCCCCccc---cccCcccCCcCCCcee-CccCCCccCCCccccccCCCCCCcccc-cceEEec--HHHHHHHHHHH
Confidence 355666666543 2355555544322211 1 111124589999999988 5777665 47788888876
Q ss_pred hc
Q 010400 88 LK 89 (511)
Q Consensus 88 i~ 89 (511)
+.
T Consensus 740 ~g 741 (1337)
T PRK14714 740 VG 741 (1337)
T ss_pred hC
Confidence 64
No 6
>PRK04023 DNA polymerase II large subunit; Validated
Probab=90.34 E-value=0.26 Score=58.03 Aligned_cols=69 Identities=22% Similarity=0.315 Sum_probs=44.6
Q ss_pred cceecccccCcccCCCCcccchhhhccccccccccC---ceEEEEeCCCCCceecCCCceeeCCcChHHHHHHHHHHhc
Q 010400 14 VGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQ---KHVIISHCPECDCYLQPPRTWIKAQLESKELLTFCVKRLK 89 (511)
Q Consensus 14 ~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp---~~~~v~~C~~Cgry~~~p~~Wv~~~les~ELL~~~Lkki~ 89 (511)
.+..+|+.||..+. ...|+.|=.....+-. +| .+..-..|++||+-..+ +.|..-. .++++..+++++.
T Consensus 624 Vg~RfCpsCG~~t~---~frCP~CG~~Te~i~f-CP~CG~~~~~y~CPKCG~El~~-~s~~~i~--l~~~~~~A~~~lg 695 (1121)
T PRK04023 624 IGRRKCPSCGKETF---YRRCPFCGTHTEPVYR-CPRCGIEVEEDECEKCGREPTP-YSKRKID--LKELYDRALENLG 695 (1121)
T ss_pred ccCccCCCCCCcCC---cccCCCCCCCCCccee-CccccCcCCCCcCCCCCCCCCc-cceEEec--HHHHHHHHHHHhC
Confidence 44567877777642 4566666554333322 22 23334669999999988 6888876 4778888888764
No 7
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=89.24 E-value=0.067 Score=53.85 Aligned_cols=44 Identities=25% Similarity=0.416 Sum_probs=32.3
Q ss_pred CcccCCCCcccchhhhcccccccc-ccCceEEEEeCCCCCceecC
Q 010400 23 GIPMAPNAANMCVACLRSEVDITE-GLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 23 G~~i~~~~~~mC~~C~~~~~dI~e-gIp~~~~v~~C~~Cgry~~~ 66 (511)
|.-+.|.-++-|..|...-..-+. .|-+.-.+.+||+|||+++-
T Consensus 189 g~gvvpl~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy~ 233 (239)
T COG1579 189 GVGVVPLEGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILYY 233 (239)
T ss_pred CceEEeecCCcccCCeeeecHHHHHHHhcCCCCccCCccchHHHh
Confidence 445566778999999876543322 35556789999999999973
No 8
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.72 E-value=0.32 Score=41.04 Aligned_cols=24 Identities=33% Similarity=0.757 Sum_probs=17.6
Q ss_pred ceEEEEeCCCCCceecCCCceeeCCcChHHH
Q 010400 50 KHVIISHCPECDCYLQPPRTWIKAQLESKEL 80 (511)
Q Consensus 50 ~~~~v~~C~~Cgry~~~p~~Wv~~~les~EL 80 (511)
..++|.+||.|+ |.|.+-+ |...|
T Consensus 17 s~vEiD~CPrCr------GVWLDrG-ELdKl 40 (88)
T COG3809 17 SGVEIDYCPRCR------GVWLDRG-ELDKL 40 (88)
T ss_pred cCceeeeCCccc------cEeecch-hHHHH
Confidence 457999999996 5788876 44434
No 9
>PF12773 DZR: Double zinc ribbon
Probab=87.81 E-value=0.27 Score=37.12 Aligned_cols=40 Identities=25% Similarity=0.571 Sum_probs=19.9
Q ss_pred ccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceec
Q 010400 19 CCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQ 65 (511)
Q Consensus 19 C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~ 65 (511)
|+.||.++++. +..|+.|=..-. +......+|+.||+...
T Consensus 1 Cp~Cg~~~~~~-~~fC~~CG~~l~------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 1 CPHCGTPNPDD-AKFCPHCGTPLP------PPDQSKKICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCcc-ccCChhhcCChh------hccCCCCCCcCCcCCCc
Confidence 55555554432 445555544333 12334556666666543
No 10
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.34 E-value=0.31 Score=31.72 Aligned_cols=20 Identities=30% Similarity=0.813 Sum_probs=14.6
Q ss_pred cccccCcccCCCCcccchhhh
Q 010400 18 LCCKCGIPMAPNAANMCVACL 38 (511)
Q Consensus 18 ~C~~CG~~i~~~~~~mC~~C~ 38 (511)
+|+.||.++++ .+..|+.|=
T Consensus 1 ~Cp~CG~~~~~-~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIED-DAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCC-cCcchhhhC
Confidence 59999998864 356777773
No 11
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=87.28 E-value=0.26 Score=35.18 Aligned_cols=31 Identities=23% Similarity=0.540 Sum_probs=15.4
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccC--ceEEEEeCCCCCceec
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQ--KHVIISHCPECDCYLQ 65 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp--~~~~v~~C~~Cgry~~ 65 (511)
.||+.||.+++. .|| +.-.=.+|+.||...+
T Consensus 1 kfC~~CG~~l~~------------------~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGPLER------------------RIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B-EE------------------E--TT-SS-EEEETTTTEEE-
T ss_pred CccccccChhhh------------------hcCCCCCccceECCCCCCEEe
Confidence 489999998652 144 5566778888887654
No 12
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=86.96 E-value=0.4 Score=35.11 Aligned_cols=19 Identities=37% Similarity=0.858 Sum_probs=14.7
Q ss_pred ceEEEEeCCCCCceecCCCceeeCC
Q 010400 50 KHVIISHCPECDCYLQPPRTWIKAQ 74 (511)
Q Consensus 50 ~~~~v~~C~~Cgry~~~p~~Wv~~~ 74 (511)
..+.+..|+.|| |.|++.+
T Consensus 15 ~~~~id~C~~C~------G~W~d~~ 33 (41)
T PF13453_consen 15 GDVEIDVCPSCG------GIWFDAG 33 (41)
T ss_pred CCEEEEECCCCC------eEEccHH
Confidence 458999999998 4577654
No 13
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=86.25 E-value=0.15 Score=39.71 Aligned_cols=40 Identities=25% Similarity=0.541 Sum_probs=26.4
Q ss_pred cccCCCCcccchhhhcccc--ccccccCceEEEEeCCCCCcee
Q 010400 24 IPMAPNAANMCVACLRSEV--DITEGLQKHVIISHCPECDCYL 64 (511)
Q Consensus 24 ~~i~~~~~~mC~~C~~~~~--dI~egIp~~~~v~~C~~Cgry~ 64 (511)
..+.+..++.|..|..+-- .+.+ |...-.+.+|++|||++
T Consensus 15 ~~va~v~~~~C~gC~~~l~~~~~~~-i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 15 VAVARVEGGTCSGCHMELPPQELNE-IRKGDEIVFCPNCGRIL 56 (56)
T ss_pred cEEEEeeCCccCCCCEEcCHHHHHH-HHcCCCeEECcCCCccC
Confidence 3344455678888876532 2333 54556899999999985
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.43 E-value=0.45 Score=31.69 Aligned_cols=21 Identities=33% Similarity=1.031 Sum_probs=14.8
Q ss_pred eecccccCcccCCCCcccchhh
Q 010400 16 SVLCCKCGIPMAPNAANMCVAC 37 (511)
Q Consensus 16 ~i~C~~CG~~i~~~~~~mC~~C 37 (511)
+++|+.||.++++ .+..|+.|
T Consensus 2 ~~~Cp~Cg~~~~~-~~~fC~~C 22 (26)
T PF13248_consen 2 EMFCPNCGAEIDP-DAKFCPNC 22 (26)
T ss_pred cCCCcccCCcCCc-ccccChhh
Confidence 4789999997653 35566666
No 15
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=85.02 E-value=0.38 Score=45.92 Aligned_cols=48 Identities=15% Similarity=0.348 Sum_probs=31.6
Q ss_pred eecccccCcccCCCCcccchhhhccccccccccCc-----eEEEEeCCCCCceecCCCceeeC
Q 010400 16 SVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQK-----HVIISHCPECDCYLQPPRTWIKA 73 (511)
Q Consensus 16 ~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~-----~~~v~~C~~Cgry~~~p~~Wv~~ 73 (511)
...||.|+.++.+... -.+.+.+|. .-....|++||+++=+|++|-.-
T Consensus 97 ~~RCp~CN~~L~~vs~----------eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m 149 (165)
T COG1656 97 FSRCPECNGELEKVSR----------EEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRM 149 (165)
T ss_pred cccCcccCCEeccCcH----------HHHhhccchhhhhcccceeECCCCcccccCchHHHHH
Confidence 3469999998764321 122222442 35677899999999888888543
No 16
>PF12773 DZR: Double zinc ribbon
Probab=84.71 E-value=0.5 Score=35.63 Aligned_cols=39 Identities=23% Similarity=0.699 Sum_probs=28.5
Q ss_pred cceecccccCcccC--CCCcccchhhhccccccccccCceEEEEeCCCCC
Q 010400 14 VGSVLCCKCGIPMA--PNAANMCVACLRSEVDITEGLQKHVIISHCPECD 61 (511)
Q Consensus 14 ~~~i~C~~CG~~i~--~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cg 61 (511)
....||+.||.++. ......|+.|-.. -.....||+.||
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~---------~~~~~~fC~~CG 50 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGAE---------NPPNAKFCPNCG 50 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcCC---------CcCCcCccCccc
Confidence 34579999999987 4445789999874 123557899987
No 17
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.55 E-value=0.66 Score=53.05 Aligned_cols=40 Identities=28% Similarity=0.658 Sum_probs=25.5
Q ss_pred eecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCC
Q 010400 16 SVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPP 67 (511)
Q Consensus 16 ~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p 67 (511)
..||+.||.+.. ..-|+.|-.. +| ..-.||+.||..+...
T Consensus 15 akFC~~CG~~l~---~~~Cp~CG~~-------~~--~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 15 NRFCQKCGTSLT---HKPCPQCGTE-------VP--VDEAHCPNCGAETGTI 54 (645)
T ss_pred CccccccCCCCC---CCcCCCCCCC-------CC--cccccccccCCcccch
Confidence 356777776654 2357777544 22 3456999999988763
No 18
>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=80.01 E-value=1.1 Score=35.24 Aligned_cols=30 Identities=23% Similarity=0.458 Sum_probs=20.4
Q ss_pred cccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceec
Q 010400 18 LCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQ 65 (511)
Q Consensus 18 ~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~ 65 (511)
-||.||.+++- ++.+ .-.+..|+.||+.+.
T Consensus 4 ~CP~CG~~iev-~~~~-----------------~GeiV~Cp~CGaele 33 (54)
T TIGR01206 4 ECPDCGAEIEL-ENPE-----------------LGELVICDECGAELE 33 (54)
T ss_pred CCCCCCCEEec-CCCc-----------------cCCEEeCCCCCCEEE
Confidence 59999998751 1111 134779999999874
No 19
>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=79.94 E-value=0.5 Score=32.80 Aligned_cols=24 Identities=29% Similarity=0.848 Sum_probs=13.4
Q ss_pred eecccccCcccCCCCc---ccchhhhc
Q 010400 16 SVLCCKCGIPMAPNAA---NMCVACLR 39 (511)
Q Consensus 16 ~i~C~~CG~~i~~~~~---~mC~~C~~ 39 (511)
..||++||.++.+..+ ..|++|=.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 4699999999876544 36776644
No 20
>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=79.15 E-value=1.3 Score=41.09 Aligned_cols=20 Identities=20% Similarity=0.521 Sum_probs=17.1
Q ss_pred EEEeCCCCCceecCCCceee
Q 010400 53 IISHCPECDCYLQPPRTWIK 72 (511)
Q Consensus 53 ~v~~C~~Cgry~~~p~~Wv~ 72 (511)
...+|+.||+++=+|++|..
T Consensus 123 ~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred eEEECCCCCCEecccccHHH
Confidence 48999999999988788854
No 21
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.04 E-value=1 Score=33.76 Aligned_cols=29 Identities=24% Similarity=0.579 Sum_probs=19.0
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceec
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQ 65 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~ 65 (511)
..|+.||..++ ++.......||.||..+.
T Consensus 4 y~C~~CG~~~~--------------------~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVE--------------------LDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEE--------------------ECCCCCceECCCCCCeEE
Confidence 45888888765 222333678999987543
No 22
>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=74.08 E-value=1 Score=52.46 Aligned_cols=68 Identities=25% Similarity=0.378 Sum_probs=0.0
Q ss_pred cceecccccCcccCCCCcccchhhhccccccccccCc---eEEEEeCCCCCceecCCCceeeCCcChHHHHHHHHHHh
Q 010400 14 VGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQK---HVIISHCPECDCYLQPPRTWIKAQLESKELLTFCVKRL 88 (511)
Q Consensus 14 ~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~---~~~v~~C~~Cgry~~~p~~Wv~~~les~ELL~~~Lkki 88 (511)
.+...|+.||..+- ...|+.|=..+..+-. +|+ +++-..|++||+...+ ..|..-.+ ++++..+++++
T Consensus 653 i~~r~Cp~Cg~~t~---~~~Cp~CG~~T~~~~~-Cp~C~~~~~~~~C~~C~~~~~~-~~~~~i~l--~~~~~~A~e~l 723 (900)
T PF03833_consen 653 IGRRRCPKCGKETF---YNRCPECGSHTEPVYV-CPDCGIEVEEDECPKCGRETTS-YSKQKIDL--KEEYDRALENL 723 (900)
T ss_dssp ------------------------------------------------------------------------------
T ss_pred eecccCcccCCcch---hhcCcccCCcccccee-ccccccccCccccccccccCcc-cceeecCH--HHHHHHHHHhh
Confidence 45567888887744 5677777666554443 322 2334489999998877 46766653 55666666654
No 23
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=73.39 E-value=2.9 Score=31.53 Aligned_cols=32 Identities=25% Similarity=0.445 Sum_probs=20.7
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecC
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~ 66 (511)
.|||.||..+.+... .+....+|+.||....-
T Consensus 1 ~FCp~Cg~~l~~~~~------------------~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 1 KFCPKCGNMLIPKEG------------------KEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCCccccccC------------------CCCCEEECCcCCCeEEC
Confidence 389999987543110 01136789999977665
No 24
>PRK11595 DNA utilization protein GntX; Provisional
Probab=72.77 E-value=2.4 Score=42.00 Aligned_cols=37 Identities=32% Similarity=0.776 Sum_probs=26.8
Q ss_pred cccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCce
Q 010400 18 LCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCY 63 (511)
Q Consensus 18 ~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry 63 (511)
.|..||.++.....++|..|...-.- + -..|+.||+-
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~----~-----~~~C~~Cg~~ 43 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRT----L-----KTCCPQCGLP 43 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCc----c-----cCcCccCCCc
Confidence 59999998865555799999875321 1 1479999964
No 25
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=72.57 E-value=2.4 Score=37.97 Aligned_cols=44 Identities=30% Similarity=0.825 Sum_probs=31.2
Q ss_pred ccceecccccCcccCC--CCcccchhhhccccccccccCceEEEEeCCCCCceecCCCcee
Q 010400 13 TVGSVLCCKCGIPMAP--NAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPRTWI 71 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~--~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~~Wv 71 (511)
......|.+||.+... |.+..|.+|- ..+|+.|+.+..+.+.|+
T Consensus 51 ~~~~~~C~~C~~~fg~l~~~~~~C~~C~---------------~~VC~~C~~~~~~~~~Wl 96 (118)
T PF02318_consen 51 KYGERHCARCGKPFGFLFNRGRVCVDCK---------------HRVCKKCGVYSKKEPIWL 96 (118)
T ss_dssp THCCSB-TTTS-BCSCTSTTCEEETTTT---------------EEEETTSEEETSSSCCEE
T ss_pred ccCCcchhhhCCcccccCCCCCcCCcCC---------------ccccCccCCcCCCCCCEE
Confidence 3456689999998643 4568999995 368999999965445786
No 26
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=68.86 E-value=3.1 Score=40.93 Aligned_cols=41 Identities=20% Similarity=0.603 Sum_probs=29.0
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCCCceeeCC
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPRTWIKAQ 74 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~~Wv~~~ 74 (511)
+.|..||.|++.++. ++ =|..+.++.|++||+.-.+ .+..+
T Consensus 1 miCIeCg~~v~~Ly~---------~Y-----s~~~irLt~C~~C~~vaDk---YiE~d 41 (208)
T PF04161_consen 1 MICIECGHPVKSLYR---------QY-----SPGNIRLTKCPNCGKVADK---YIEYD 41 (208)
T ss_pred CEeccCCCcchhhhh---------cc-----CCCcEEEeeccccCCcccc---eeccc
Confidence 469999999764432 22 1467899999999987643 66555
No 27
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=67.07 E-value=2.1 Score=34.45 Aligned_cols=13 Identities=31% Similarity=0.575 Sum_probs=9.2
Q ss_pred ceEEEEeCCCCCc
Q 010400 50 KHVIISHCPECDC 62 (511)
Q Consensus 50 ~~~~v~~C~~Cgr 62 (511)
++.+.+.|++||-
T Consensus 46 k~g~~Y~Cp~CGF 58 (61)
T COG2888 46 KLGNPYRCPKCGF 58 (61)
T ss_pred HcCCceECCCcCc
Confidence 4456788888883
No 28
>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=66.95 E-value=2.6 Score=33.84 Aligned_cols=22 Identities=32% Similarity=0.920 Sum_probs=16.1
Q ss_pred ecccccCcccCCCCcccc-hhhhc
Q 010400 17 VLCCKCGIPMAPNAANMC-VACLR 39 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC-~~C~~ 39 (511)
.-|+.||.+++++ ...| .+|-.
T Consensus 4 kHC~~CG~~Ip~~-~~fCS~~C~~ 26 (59)
T PF09889_consen 4 KHCPVCGKPIPPD-ESFCSPKCRE 26 (59)
T ss_pred CcCCcCCCcCCcc-hhhhCHHHHH
Confidence 4599999999864 5577 46643
No 29
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=66.74 E-value=6.7 Score=34.17 Aligned_cols=49 Identities=29% Similarity=0.587 Sum_probs=33.6
Q ss_pred cccccCcccCCC-----Ccccchhhhcccccc-cccc-------------------CceEEEEeCCCCCceecC
Q 010400 18 LCCKCGIPMAPN-----AANMCVACLRSEVDI-TEGL-------------------QKHVIISHCPECDCYLQP 66 (511)
Q Consensus 18 ~C~~CG~~i~~~-----~~~mC~~C~~~~~dI-~egI-------------------p~~~~v~~C~~Cgry~~~ 66 (511)
.|..||..+.|. .-|-|+.|+-+.+-- ..|= -.=+.|..|..||.....
T Consensus 6 ~C~~CG~~V~p~~~g~~~RNHCP~CL~S~Hvd~~pGDRas~C~g~M~Pi~v~~~~~g~w~iiHrC~~Cg~l~~N 79 (92)
T PF12647_consen 6 TCVHCGLTVSPLAAGSAHRNHCPSCLSSLHVDIVPGDRASDCGGRMEPIAVWVRRDGEWMIIHRCTRCGELRSN 79 (92)
T ss_pred CccccCCCcccCCCCCCccCcCcccccccccCCCCCCccccCCCeeeEEEEEEEcCCCEEEEEecCCCCCcccC
Confidence 599999998774 347899999886632 1111 112567889999887654
No 30
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.48 E-value=2.8 Score=33.66 Aligned_cols=45 Identities=29% Similarity=0.613 Sum_probs=22.3
Q ss_pred cccccCcccCCCC---cccchhhhccccccccccCceEEEEeCCCCCc
Q 010400 18 LCCKCGIPMAPNA---ANMCVACLRSEVDITEGLQKHVIISHCPECDC 62 (511)
Q Consensus 18 ~C~~CG~~i~~~~---~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgr 62 (511)
.|-.||+++.|.. .=.|++|=...+-=-...-++...+.||.||-
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence 4666666655432 22566653221100111234567788888884
No 31
>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=66.40 E-value=4.4 Score=32.98 Aligned_cols=42 Identities=21% Similarity=0.398 Sum_probs=24.3
Q ss_pred cccccCcccCCC-CcccchhhhccccccccccCceEEEEeCCCCCc
Q 010400 18 LCCKCGIPMAPN-AANMCVACLRSEVDITEGLQKHVIISHCPECDC 62 (511)
Q Consensus 18 ~C~~CG~~i~~~-~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgr 62 (511)
-||+||...-.. .-.+-..=+.+-+||-. ++..+..|++||-
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~---~~f~~v~C~~CGY 44 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQN---KKFTTVSCTNCGY 44 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecC---cEEEEEECCCCCC
Confidence 399999863211 00111111223356555 6789999999996
No 32
>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=65.30 E-value=4.5 Score=26.85 Aligned_cols=10 Identities=30% Similarity=0.943 Sum_probs=6.1
Q ss_pred EEEEeCCCCC
Q 010400 52 VIISHCPECD 61 (511)
Q Consensus 52 ~~v~~C~~Cg 61 (511)
.....||+||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 5556666665
No 33
>PHA00626 hypothetical protein
Probab=64.26 E-value=3.4 Score=32.90 Aligned_cols=34 Identities=21% Similarity=0.238 Sum_probs=23.7
Q ss_pred ecccccCcc-cCCCCcccchhhhccccccccccCceEEEEeCCCCCceecC
Q 010400 17 VLCCKCGIP-MAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 17 i~C~~CG~~-i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~ 66 (511)
+.||.||.. +. .|..|. ++.....|+.||-.+..
T Consensus 1 m~CP~CGS~~Iv-----rcg~cr-----------~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 1 MSCPKCGSGNIA-----KEKTMR-----------GWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCCceee-----eeceec-----------ccCcceEcCCCCCeech
Confidence 579999984 33 444432 33567899999988865
No 34
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=62.76 E-value=14 Score=37.49 Aligned_cols=31 Identities=29% Similarity=0.594 Sum_probs=22.7
Q ss_pred cceecccccCcccCCCC---cccchhhhcccccc
Q 010400 14 VGSVLCCKCGIPMAPNA---ANMCVACLRSEVDI 44 (511)
Q Consensus 14 ~~~i~C~~CG~~i~~~~---~~mC~~C~~~~~dI 44 (511)
....||+.||.++.... ...|..|-...++-
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRERYYPR 130 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCCEECCC
Confidence 34579999999976543 34799998777754
No 35
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=60.22 E-value=4.1 Score=31.57 Aligned_cols=26 Identities=27% Similarity=0.697 Sum_probs=17.8
Q ss_pred cccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCce
Q 010400 18 LCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCY 63 (511)
Q Consensus 18 ~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry 63 (511)
.|.+||+.++ +........||.||.-
T Consensus 8 ~C~~Cg~~~~--------------------~~~~~~~irCp~Cg~r 33 (49)
T COG1996 8 KCARCGREVE--------------------LDQETRGIRCPYCGSR 33 (49)
T ss_pred EhhhcCCeee--------------------hhhccCceeCCCCCcE
Confidence 5888888753 3344566788888863
No 36
>PHA02998 RNA polymerase subunit; Provisional
Probab=58.46 E-value=8.1 Score=37.55 Aligned_cols=52 Identities=15% Similarity=0.330 Sum_probs=31.9
Q ss_pred CCCcccCccceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCC
Q 010400 6 GMFTVPQTVGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPP 67 (511)
Q Consensus 6 ~~~~~~~~~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p 67 (511)
.||...++.....||.||..- ++.-+..+-..=-.......|..||..+.||
T Consensus 133 ~yfnvlpkkt~v~CPkCg~~~----------A~f~qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 133 DYFNVLDEKYNTPCPNCKSKN----------TTPMMIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred hheeccCcccCCCCCCCCCCc----------eEEEEEeeccCCCCceEEEEcCCCCCccCCc
Confidence 355555554567788888651 2222222222112357889999999988887
No 37
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=58.38 E-value=8.1 Score=34.21 Aligned_cols=38 Identities=18% Similarity=0.523 Sum_probs=25.6
Q ss_pred cceec-ccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceec
Q 010400 14 VGSVL-CCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQ 65 (511)
Q Consensus 14 ~~~i~-C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~ 65 (511)
..+.| ||.||.+.. ..|. ++. ...+-+..|..||.++.
T Consensus 19 L~k~FtCp~Cghe~v----s~ct------vkk----~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKV----SSCT------VKK----TVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeee----eEEE------EEe----cCceeEEEcccCcceEE
Confidence 44554 999999854 2333 333 33567889999999874
No 38
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=57.75 E-value=4.3 Score=27.30 Aligned_cols=19 Identities=32% Similarity=0.950 Sum_probs=10.8
Q ss_pred cccccCcccCCCCcccchhh
Q 010400 18 LCCKCGIPMAPNAANMCVAC 37 (511)
Q Consensus 18 ~C~~CG~~i~~~~~~mC~~C 37 (511)
-||.||..+. .....|+.|
T Consensus 2 ~CP~C~~~V~-~~~~~Cp~C 20 (26)
T PF10571_consen 2 TCPECGAEVP-ESAKFCPHC 20 (26)
T ss_pred cCCCCcCCch-hhcCcCCCC
Confidence 4788887653 334455544
No 39
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=57.74 E-value=3.3 Score=37.67 Aligned_cols=24 Identities=29% Similarity=0.879 Sum_probs=18.4
Q ss_pred eecccccCcccCCC------Ccccchhhhc
Q 010400 16 SVLCCKCGIPMAPN------AANMCVACLR 39 (511)
Q Consensus 16 ~i~C~~CG~~i~~~------~~~mC~~C~~ 39 (511)
...|..||.||+.- .+-||++|--
T Consensus 80 YG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~ 109 (120)
T COG1734 80 YGICEECGEPIPEARLEARPTARLCIECQE 109 (120)
T ss_pred ccchhccCCcCCHHHHhhCcchHHHHHHHH
Confidence 35799999999752 4579999953
No 40
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=57.66 E-value=8.1 Score=30.54 Aligned_cols=30 Identities=27% Similarity=0.538 Sum_probs=21.6
Q ss_pred ccceecccccCcccCCC----Ccccchhhhccccc
Q 010400 13 TVGSVLCCKCGIPMAPN----AANMCVACLRSEVD 43 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~~----~~~mC~~C~~~~~d 43 (511)
..+...|..||++- .. --+||-.||++...
T Consensus 13 GkGsr~C~vCg~~~-gliRkygL~~CRqCFRe~A~ 46 (54)
T PTZ00218 13 GKGSRQCRVCSNRH-GLIRKYGLNVCRQCFRENAE 46 (54)
T ss_pred CCCCCeeecCCCcc-hhhhhcCcchhhHHHHHhhH
Confidence 34457899999973 22 23699999998653
No 41
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=57.52 E-value=8.3 Score=29.03 Aligned_cols=27 Identities=26% Similarity=0.491 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhhcCHhhhhhccccccC
Q 010400 442 NKEYEEFLRDLEENPELRFNISLYRNK 468 (511)
Q Consensus 442 e~d~e~F~~dleeD~elr~~i~lyk~~ 468 (511)
..+.+.|++.++.||+||.+++-.+++
T Consensus 3 ~~~l~~Fl~~~~~d~~l~~~l~~~~~~ 29 (49)
T PF07862_consen 3 IESLKAFLEKVKSDPELREQLKACQNP 29 (49)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHhcCCH
Confidence 457899999999999999999866554
No 42
>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=57.17 E-value=1.9 Score=40.80 Aligned_cols=60 Identities=25% Similarity=0.540 Sum_probs=37.7
Q ss_pred cceecccccCcccCCCCcccchhhhccccccccccCceEEE-------EeCCCCCceecCCCceeeCCcCh-HHHHH
Q 010400 14 VGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVII-------SHCPECDCYLQPPRTWIKAQLES-KELLT 82 (511)
Q Consensus 14 ~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v-------~~C~~Cgry~~~p~~Wv~~~les-~ELL~ 82 (511)
..+.||-+||..+- --|++|-..-..=-. +|..+.+ .+|.+||..+ | |....+++ +||+.
T Consensus 26 ~~~~fC~kCG~~tI----~~Cp~C~~~IrG~y~-v~gv~~~g~~~~~PsYC~~CGkpy-P---Wt~~~L~aa~el~e 93 (158)
T PF10083_consen 26 LREKFCSKCGAKTI----TSCPNCSTPIRGDYH-VEGVFGLGGHYEAPSYCHNCGKPY-P---WTENALEAANELIE 93 (158)
T ss_pred HHHHHHHHhhHHHH----HHCcCCCCCCCCcee-cCCeeeeCCCCCCChhHHhCCCCC-c---hHHHHHHHHHHHHH
Confidence 45579999998743 268888554332222 3333333 7999999874 3 99887754 44433
No 43
>PRK00420 hypothetical protein; Validated
Probab=57.07 E-value=4.5 Score=36.44 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=18.6
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecC
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~ 66 (511)
..||.||.|.-.+ .-.-.+||.||....-
T Consensus 24 ~~CP~Cg~pLf~l---------------------k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPLFEL---------------------KDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcceec---------------------CCCceECCCCCCeeee
Confidence 4688998875421 1234678888886654
No 44
>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=56.88 E-value=2.9 Score=38.89 Aligned_cols=32 Identities=25% Similarity=0.533 Sum_probs=26.6
Q ss_pred ecccccCcccCCCCcccchhhhcccccccccc
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGL 48 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egI 48 (511)
.-|++||+....+...+|++|+.+.-+.++.|
T Consensus 4 ~nC~~CgklF~~~~~~iCp~C~~~~e~~f~kV 35 (137)
T TIGR03826 4 ANCPKCGRLFVKTGRDVCPSCYEEEEREFEKV 35 (137)
T ss_pred ccccccchhhhhcCCccCHHHhHHHHHHHHHH
Confidence 46999999977666679999999988888845
No 45
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=55.50 E-value=23 Score=30.88 Aligned_cols=25 Identities=20% Similarity=0.377 Sum_probs=20.5
Q ss_pred ceEEEEeCCCCCceecCCCceeeCCc
Q 010400 50 KHVIISHCPECDCYLQPPRTWIKAQL 75 (511)
Q Consensus 50 ~~~~v~~C~~Cgry~~~p~~Wv~~~l 75 (511)
..+-|-.|+.|+..+-+ |.|....+
T Consensus 50 ~a~GIW~C~~C~~~~AG-GAy~~~T~ 74 (90)
T PTZ00255 50 QAVGIWRCKGCKKTVAG-GAWTLSTP 74 (90)
T ss_pred eeeEEEEcCCCCCEEeC-Cccccccc
Confidence 34578899999999999 79987764
No 46
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=54.98 E-value=9 Score=39.67 Aligned_cols=32 Identities=19% Similarity=0.558 Sum_probs=26.9
Q ss_pred ceecccccCcccCCCCc---ccchhhhcccccccc
Q 010400 15 GSVLCCKCGIPMAPNAA---NMCVACLRSEVDITE 46 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~~~---~mC~~C~~~~~dI~e 46 (511)
..+||++||.++.+..+ ..|++|-...++-+.
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~fPR~d 144 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEHFPRID 144 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCccCCCCC
Confidence 45799999999988754 489999999998877
No 47
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=53.90 E-value=11 Score=32.57 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=16.3
Q ss_pred ccCCchhhhhccCCcceEEEEEEeeccC
Q 010400 139 DHMCDSCSRVQANPDQWVAAVQLRQHVT 166 (511)
Q Consensus 139 ~~~C~~C~R~~~~~~~w~AiVQVRq~~~ 166 (511)
...||.|....+- || .+|.|+...
T Consensus 62 ~~~Cp~Cg~~~a~--f~--~~Q~RsadE 85 (104)
T TIGR01384 62 RVECPKCGHKEAY--YW--LLQTRRADE 85 (104)
T ss_pred cCCCCCCCCCeeE--EE--EeccCCCCC
Confidence 4699999765542 44 369997543
No 48
>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=53.47 E-value=11 Score=26.87 Aligned_cols=19 Identities=26% Similarity=0.662 Sum_probs=11.8
Q ss_pred ceEEEEeCCCCCceecCCC
Q 010400 50 KHVIISHCPECDCYLQPPR 68 (511)
Q Consensus 50 ~~~~v~~C~~Cgry~~~p~ 68 (511)
.++.+..|+.||++..||.
T Consensus 7 ~~l~~~rC~~Cg~~~~pPr 25 (37)
T PF12172_consen 7 GRLLGQRCRDCGRVQFPPR 25 (37)
T ss_dssp T-EEEEE-TTT--EEES--
T ss_pred CEEEEEEcCCCCCEecCCC
Confidence 4688999999999999983
No 49
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=53.21 E-value=3.4 Score=29.70 Aligned_cols=30 Identities=23% Similarity=0.541 Sum_probs=18.4
Q ss_pred cchhhhccccccccccCceEEEEeCCCCCce
Q 010400 33 MCVACLRSEVDITEGLQKHVIISHCPECDCY 63 (511)
Q Consensus 33 mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry 63 (511)
||.+|..+-.+... ---.+..+-|+.||-.
T Consensus 1 lC~~C~~Ey~~p~~-RR~~~~~isC~~CGPr 30 (35)
T PF07503_consen 1 LCDDCLKEYFDPSN-RRFHYQFISCTNCGPR 30 (35)
T ss_dssp --HHHHHHHCSTTS-TTTT-TT--BTTCC-S
T ss_pred CCHHHHHHHcCCCC-CcccCcCccCCCCCCC
Confidence 79999998887776 4445777889999843
No 50
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=52.28 E-value=78 Score=30.67 Aligned_cols=30 Identities=20% Similarity=0.138 Sum_probs=26.4
Q ss_pred CEEEEEEeCCeEEEEcCCCCeEEEecCccc
Q 010400 272 PLVICMKVTNSIALLDPFTLRHCFLDADQY 301 (511)
Q Consensus 272 ~~~lv~kv~~~I~llDP~T~~~~~l~~~~y 301 (511)
+..+.+..++.++||||+|++..+|+.+..
T Consensus 68 ~~q~ly~dgd~~~fMD~etyeq~~i~~~~l 97 (184)
T TIGR00038 68 EMQYLYKDGDSYVFMDTETYEQIELPKDLL 97 (184)
T ss_pred EEEEEEECCCEEEEeCCCCccceEcCHHHH
Confidence 668888888899999999999999998754
No 51
>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=51.92 E-value=5.3 Score=29.74 Aligned_cols=21 Identities=33% Similarity=0.923 Sum_probs=12.4
Q ss_pred ecccccCcccCCC--Ccccchhh
Q 010400 17 VLCCKCGIPMAPN--AANMCVAC 37 (511)
Q Consensus 17 i~C~~CG~~i~~~--~~~mC~~C 37 (511)
-.|+.||.|.-.+ -.-+|+.|
T Consensus 18 ~~Cp~C~~PL~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDGKIYCVSC 40 (41)
T ss_pred CccCCCCCeeEEecCCCEECCCC
Confidence 4588888875432 22356655
No 52
>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=50.55 E-value=9.9 Score=26.98 Aligned_cols=12 Identities=17% Similarity=0.351 Sum_probs=8.6
Q ss_pred EEEeCCCCCcee
Q 010400 53 IISHCPECDCYL 64 (511)
Q Consensus 53 ~v~~C~~Cgry~ 64 (511)
....|++||.-+
T Consensus 24 ~~v~C~~C~~~~ 35 (38)
T TIGR02098 24 GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEE
Confidence 356788888765
No 53
>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=50.27 E-value=10 Score=38.89 Aligned_cols=34 Identities=21% Similarity=0.410 Sum_probs=19.8
Q ss_pred ccchhhhccccccccc----cCceEEEEeCCCCCceec
Q 010400 32 NMCVACLRSEVDITEG----LQKHVIISHCPECDCYLQ 65 (511)
Q Consensus 32 ~mC~~C~~~~~dI~eg----Ip~~~~v~~C~~Cgry~~ 65 (511)
..|+.|--+...-.+. -.....+..|..|++|+.
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 4688887776653222 234689999999999985
No 54
>TIGR03054 photo_alph_chp1 putative photosynthetic complex assembly protein. In twenty or so anoxygenic photosynthetic alpha-Proteobacteria known so far, a gene for a member of this protein family is present and is found in the vicinity of puhA, which encodes a component of the photosynthetic reaction center, and other genes associated with photosynthesis. This protein family is suggested, consequently, as a probable assembly factor for the photosynthetic reaction center, but its seems its actual function has not yet been demonstrated.
Probab=50.25 E-value=28 Score=32.43 Aligned_cols=33 Identities=21% Similarity=0.183 Sum_probs=28.7
Q ss_pred hcCCCCCEEEEEEeCCeEEEEcCCCCeEEEecC
Q 010400 266 SLGNLGPLVICMKVTNSIALLDPFTLRHCFLDA 298 (511)
Q Consensus 266 ~lG~i~~~~lv~kv~~~I~llDP~T~~~~~l~~ 298 (511)
.++.-.|+.|+-..+..+.|.||.|++.++|.+
T Consensus 90 gv~~~~Pf~L~r~~dGrltL~Dp~Tg~~i~L~a 122 (135)
T TIGR03054 90 GVAAEPPFRLTRYDNGRLTLTDPATGWSIELNA 122 (135)
T ss_pred CCCCCCCEEEEEEeCCcEEEEcCCCCcEEEEee
Confidence 345555999999999999999999999999875
No 55
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=49.10 E-value=13 Score=30.14 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=24.4
Q ss_pred CCCCCCCCcccCc-cceecccccCcccCCCCcccchhhhc
Q 010400 1 MAQDAGMFTVPQT-VGSVLCCKCGIPMAPNAANMCVACLR 39 (511)
Q Consensus 1 ~~~~~~~~~~~~~-~~~i~C~~CG~~i~~~~~~mC~~C~~ 39 (511)
|..+.+.|.--.. ...++|-+||+..--..-..|..|=.
T Consensus 1 MtKGT~SfGKr~~k~tHt~CrRCG~~syh~qK~~CasCGy 40 (62)
T PRK04179 1 MSKGTPSMGKRNKGKTHIRCRRCGRHSYNVRKKYCAACGF 40 (62)
T ss_pred CCCCCcccccccCCcccchhcccCcccccccccchhhcCC
Confidence 4444555544444 36789999999754444567777743
No 56
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=47.82 E-value=11 Score=39.66 Aligned_cols=43 Identities=26% Similarity=0.554 Sum_probs=30.0
Q ss_pred cccccCcccCCC----------CcccchhhhccccccccccCceEEEEeCCCCCceecCCC
Q 010400 18 LCCKCGIPMAPN----------AANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPR 68 (511)
Q Consensus 18 ~C~~CG~~i~~~----------~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~ 68 (511)
.||.|....-.| ...+|..|+..-+.-.. ..||.|+..+.+.+
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~--------~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGS--------GSCPECDTPLRKNN 57 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCC--------CCCCCCCCccchhh
Confidence 599999853322 23699999988642211 17999999998843
No 57
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=47.81 E-value=32 Score=30.05 Aligned_cols=24 Identities=13% Similarity=0.252 Sum_probs=20.1
Q ss_pred eEEEEeCCCCCceecCCCceeeCCc
Q 010400 51 HVIISHCPECDCYLQPPRTWIKAQL 75 (511)
Q Consensus 51 ~~~v~~C~~Cgry~~~p~~Wv~~~l 75 (511)
.+-|-.|+.||..+-+ |-|....+
T Consensus 50 a~GIW~C~~C~~~~AG-GAy~p~T~ 73 (91)
T TIGR00280 50 STGIWTCRKCGAKFAG-GAYTPVTP 73 (91)
T ss_pred eeEEEEcCCCCCEEeC-Cccccccc
Confidence 4678899999999999 79987764
No 58
>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=47.51 E-value=10 Score=35.26 Aligned_cols=28 Identities=18% Similarity=0.469 Sum_probs=22.1
Q ss_pred ccceecccccCcccCCCCcccchhhhcccc
Q 010400 13 TVGSVLCCKCGIPMAPNAANMCVACLRSEV 42 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~~~~~mC~~C~~~~~ 42 (511)
......|-+||.+|.. +.+|..|..+-.
T Consensus 78 ~nl~~~CE~CG~~I~~--Gr~C~~C~~~l~ 105 (137)
T TIGR03826 78 PNLGYPCERCGTSIRE--GRLCDSCAGELK 105 (137)
T ss_pred CCCcCcccccCCcCCC--CCccHHHHHHHH
Confidence 3555789999999874 689999987643
No 59
>PF14353 CpXC: CpXC protein
Probab=47.40 E-value=6.9 Score=35.17 Aligned_cols=13 Identities=23% Similarity=0.646 Sum_probs=7.0
Q ss_pred eEEEEeCCCCCce
Q 010400 51 HVIISHCPECDCY 63 (511)
Q Consensus 51 ~~~v~~C~~Cgry 63 (511)
++....||.||..
T Consensus 35 ~l~~~~CP~Cg~~ 47 (128)
T PF14353_consen 35 SLFSFTCPSCGHK 47 (128)
T ss_pred CcCEEECCCCCCc
Confidence 3445556666553
No 60
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=46.76 E-value=91 Score=25.39 Aligned_cols=51 Identities=14% Similarity=0.077 Sum_probs=33.4
Q ss_pred EEEeCCeEEEEcCCCCeEEEec----Cccccccc--cccccCccceeEEEEEEeeee
Q 010400 276 CMKVTNSIALLDPFTLRHCFLD----ADQYWRSS--FKSLLTSRQLVEYIVLDVEVV 326 (511)
Q Consensus 276 v~kv~~~I~llDP~T~~~~~l~----~~~yw~~p--f~~l~~~~~l~ef~Vldve~~ 326 (511)
|.++++.-.+++...+-...|+ ...+|++| +...+...+.+++.|++|++-
T Consensus 11 V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~ 67 (74)
T cd05705 11 VSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSE 67 (74)
T ss_pred EEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECC
Confidence 3444444445666556666666 23455666 445677889999999999983
No 61
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=46.13 E-value=12 Score=33.11 Aligned_cols=39 Identities=23% Similarity=0.542 Sum_probs=22.4
Q ss_pred eecccccCcccCCCCcccchhhhccccccccccCce-EEEEeCCCCCcee
Q 010400 16 SVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKH-VIISHCPECDCYL 64 (511)
Q Consensus 16 ~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~-~~v~~C~~Cgry~ 64 (511)
.+.|+.||.++.- ..| -.|--..+.. --+.+|+.|++|-
T Consensus 2 p~~CpYCg~~~~l-~~~---------~~iYg~~~~~~~~~y~C~~C~AyV 41 (102)
T PF11672_consen 2 PIICPYCGGPAEL-VDG---------SEIYGHRYDDGPYLYVCTPCDAYV 41 (102)
T ss_pred CcccCCCCCeeEE-ccc---------chhcCccCCCCceeEECCCCCcee
Confidence 4689999998651 122 1111111111 2359999999986
No 62
>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=45.76 E-value=7.7 Score=34.34 Aligned_cols=24 Identities=25% Similarity=0.689 Sum_probs=18.2
Q ss_pred ceecccccCcccCCC------Ccccchhhh
Q 010400 15 GSVLCCKCGIPMAPN------AANMCVACL 38 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~------~~~mC~~C~ 38 (511)
...+|-.||.||++. .+-+|+.|-
T Consensus 79 ~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 79 EYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 345899999999752 356899994
No 63
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=45.62 E-value=27 Score=32.03 Aligned_cols=28 Identities=11% Similarity=0.011 Sum_probs=25.6
Q ss_pred CEEEEEEeCCeEEEEcCCCCeEEEecCc
Q 010400 272 PLVICMKVTNSIALLDPFTLRHCFLDAD 299 (511)
Q Consensus 272 ~~~lv~kv~~~I~llDP~T~~~~~l~~~ 299 (511)
+..+.+..++.++||||+||+..+|+.+
T Consensus 74 ~~qylY~dg~~~~fMd~eTyeq~~i~~~ 101 (129)
T PRK03999 74 TGQVLSIMGDVVQLMDLETYETFEIPIP 101 (129)
T ss_pred EEEEEEecCCEEEEecCCCceEEEecCC
Confidence 6688888899999999999999999987
No 64
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=44.76 E-value=10 Score=29.36 Aligned_cols=24 Identities=25% Similarity=0.654 Sum_probs=17.1
Q ss_pred cccccCcccCCC------Ccccchhhhccc
Q 010400 18 LCCKCGIPMAPN------AANMCVACLRSE 41 (511)
Q Consensus 18 ~C~~CG~~i~~~------~~~mC~~C~~~~ 41 (511)
.|+.||.++--. .+.+|.+|+.+-
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 499999986432 235899998664
No 65
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.75 E-value=15 Score=38.00 Aligned_cols=46 Identities=22% Similarity=0.496 Sum_probs=31.2
Q ss_pred ccceecccccCcc-cCCCCc-----ccchhhhccccccccccCceEEEEeCCCCCceec
Q 010400 13 TVGSVLCCKCGIP-MAPNAA-----NMCVACLRSEVDITEGLQKHVIISHCPECDCYLQ 65 (511)
Q Consensus 13 ~~~~i~C~~CG~~-i~~~~~-----~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~ 65 (511)
+...+-|+.||.+ +-|-.. ..|.-|+++.....- -..|+.||.--.
T Consensus 236 ~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~a-------sf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDA-------SFTCPLCGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchh-------hcccCccCCCCc
Confidence 4445679999975 344333 589999988775433 247999997543
No 66
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=44.70 E-value=12 Score=34.76 Aligned_cols=45 Identities=22% Similarity=0.378 Sum_probs=34.1
Q ss_pred cceecccccCcccCCCCcccchhhhcc-ccccccccCceEEEEeCCCC
Q 010400 14 VGSVLCCKCGIPMAPNAANMCVACLRS-EVDITEGLQKHVIISHCPEC 60 (511)
Q Consensus 14 ~~~i~C~~CG~~i~~~~~~mC~~C~~~-~~dI~egIp~~~~v~~C~~C 60 (511)
.....|.+||+-.-| +-..|+.|..+ .....+ ++..-.|.-....
T Consensus 27 l~g~kC~~CG~v~~P-Pr~~Cp~C~~~~~~E~ve-ls~~G~V~t~Tv~ 72 (140)
T COG1545 27 LLGTKCKKCGRVYFP-PRAYCPKCGSETELEWVE-LSGEGKVETYTVV 72 (140)
T ss_pred EEEEEcCCCCeEEcC-CcccCCCCCCCCceEEEE-eCCCeEEEEEEEE
Confidence 344579999996433 47899999999 668888 9888777766544
No 67
>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=44.41 E-value=12 Score=31.06 Aligned_cols=39 Identities=26% Similarity=0.536 Sum_probs=19.4
Q ss_pred ecccccCcccCCCC-cccchhhhccccccccccCceEEEEeCCCCCceec
Q 010400 17 VLCCKCGIPMAPNA-ANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQ 65 (511)
Q Consensus 17 i~C~~CG~~i~~~~-~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~ 65 (511)
..||.|+.++++.. .-.|..|-.. -...-+||.|+.-+.
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~----------~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKD----------YKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--E----------EEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeCCEEECcccccc----------ceecccCCCcccHHH
Confidence 46888888877654 3468887652 223456777766543
No 68
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=43.31 E-value=5 Score=31.93 Aligned_cols=27 Identities=22% Similarity=0.620 Sum_probs=20.1
Q ss_pred ceecccccCcccCCC-------------Ccccchhhhccc
Q 010400 15 GSVLCCKCGIPMAPN-------------AANMCVACLRSE 41 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~-------------~~~mC~~C~~~~ 41 (511)
.+..|-+||+++..+ .+++|.+|+..+
T Consensus 9 V~t~CrRCGk~i~tl~~SL~Gad~lr~klG~IC~~CitpE 48 (60)
T PF10892_consen 9 VETPCRRCGKSIRTLSRSLIGADDLRVKLGGICGDCITPE 48 (60)
T ss_pred eeehhhhhCccHHHHHHHhhChHHHHHHHcchhhccCCHH
Confidence 445799999997532 458999998754
No 69
>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=43.28 E-value=22 Score=28.29 Aligned_cols=32 Identities=22% Similarity=0.526 Sum_probs=21.4
Q ss_pred ceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecC
Q 010400 15 GSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~ 66 (511)
....|+.||..... +.......|+.||.....
T Consensus 27 TSq~C~~CG~~~~~--------------------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--------------------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCccccccc--------------------ccccceEEcCCCCCEECc
Confidence 34457777776541 345578899999887543
No 70
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=42.74 E-value=19 Score=35.55 Aligned_cols=45 Identities=16% Similarity=0.390 Sum_probs=27.9
Q ss_pred CCcccCccceecccccCcccCCCCcccchhhhccccccccccCce----EEEEeCCCCCcee
Q 010400 7 MFTVPQTVGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKH----VIISHCPECDCYL 64 (511)
Q Consensus 7 ~~~~~~~~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~----~~v~~C~~Cgry~ 64 (511)
+++.......+-||.||... ....-+.+ ||=- +...+|.+||-.+
T Consensus 5 ~~~~~~~~~~~~CPvCg~~l------------~~~~~~~~-IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 5 MFPKEEFETRIDCPVCGGTL------------KAHMYLYD-IPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred cccceeeeeeecCCccccee------------eEEEeeec-CCccceEEEEEEEccccCCcc
Confidence 34445556778899999842 22333334 5543 5678899999654
No 71
>PRK12495 hypothetical protein; Provisional
Probab=42.61 E-value=11 Score=37.77 Aligned_cols=32 Identities=25% Similarity=0.550 Sum_probs=21.6
Q ss_pred ccceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecC
Q 010400 13 TVGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~ 66 (511)
+....+|+.||.||.. +| -+.+|+.|+.+...
T Consensus 39 tmsa~hC~~CG~PIpa-------------------~p---G~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 39 TMTNAHCDECGDPIFR-------------------HD---GQEFCPTCQQPVTE 70 (226)
T ss_pred ccchhhcccccCcccC-------------------CC---CeeECCCCCCcccc
Confidence 3455689999999762 22 45677777776554
No 72
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=42.51 E-value=18 Score=34.29 Aligned_cols=13 Identities=15% Similarity=0.414 Sum_probs=10.5
Q ss_pred EEeCCCCCceecC
Q 010400 54 ISHCPECDCYLQP 66 (511)
Q Consensus 54 v~~C~~Cgry~~~ 66 (511)
...|+.||.-+..
T Consensus 28 ~~~c~~c~~~f~~ 40 (154)
T PRK00464 28 RRECLACGKRFTT 40 (154)
T ss_pred eeeccccCCcceE
Confidence 3899999988764
No 73
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=41.76 E-value=19 Score=25.92 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=13.0
Q ss_pred cCceEEEEeCCCCCcee
Q 010400 48 LQKHVIISHCPECDCYL 64 (511)
Q Consensus 48 Ip~~~~v~~C~~Cgry~ 64 (511)
||....-..|+.|+-.+
T Consensus 19 l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 19 LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred cccCCcEEECCCCCcEe
Confidence 66677788899998654
No 74
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=41.67 E-value=14 Score=30.07 Aligned_cols=23 Identities=22% Similarity=0.673 Sum_probs=18.3
Q ss_pred ccccCcccCCCCcccchhhhccc
Q 010400 19 CCKCGIPMAPNAANMCVACLRSE 41 (511)
Q Consensus 19 C~~CG~~i~~~~~~mC~~C~~~~ 41 (511)
|..||..+..+...+|.+|....
T Consensus 1 C~~C~~~~~~~~~~lC~~C~~~~ 23 (73)
T PF14260_consen 1 CLVCGAKTQEGESPLCSNCRSDP 23 (73)
T ss_pred CCCCCCcCCCCCCCcCcccCcCh
Confidence 88999998866668999998533
No 75
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=41.43 E-value=4.9 Score=31.91 Aligned_cols=29 Identities=28% Similarity=0.841 Sum_probs=24.2
Q ss_pred CccceecccccCcccCCCCcccchhhhcc
Q 010400 12 QTVGSVLCCKCGIPMAPNAANMCVACLRS 40 (511)
Q Consensus 12 ~~~~~i~C~~CG~~i~~~~~~mC~~C~~~ 40 (511)
++..+-+|+.||.+..+...-.|..|..+
T Consensus 13 ~Si~RAlCa~C~~~L~~~E~h~Ce~C~~E 41 (58)
T PF05810_consen 13 QSIERALCANCGQKLHPDETHVCEECCAE 41 (58)
T ss_pred HHHHHHHHhccCcccccchhhHHHHHHHH
Confidence 35556679999999998888899999876
No 76
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=41.39 E-value=6.8 Score=32.41 Aligned_cols=20 Identities=25% Similarity=0.557 Sum_probs=12.7
Q ss_pred cCceEEEEeCCCCCceecCC
Q 010400 48 LQKHVIISHCPECDCYLQPP 67 (511)
Q Consensus 48 Ip~~~~v~~C~~Cgry~~~p 67 (511)
+|+.+.-.+|+.||..+.||
T Consensus 40 l~~~~kr~~Ck~C~~~liPG 59 (85)
T PF04032_consen 40 LPPEIKRTICKKCGSLLIPG 59 (85)
T ss_dssp -STTCCCTB-TTT--B--CT
T ss_pred CChHHhcccccCCCCEEeCC
Confidence 78888999999999999995
No 77
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=41.18 E-value=10 Score=29.99 Aligned_cols=22 Identities=36% Similarity=0.625 Sum_probs=16.2
Q ss_pred eEEEEeCCCCCceecCCCceeeC
Q 010400 51 HVIISHCPECDCYLQPPRTWIKA 73 (511)
Q Consensus 51 ~~~v~~C~~Cgry~~~p~~Wv~~ 73 (511)
+-.+++|+.||+..++ .=|...
T Consensus 18 ~dDiVvCp~CgapyHR-~C~~~~ 39 (54)
T PF14446_consen 18 GDDIVVCPECGAPYHR-DCWEKA 39 (54)
T ss_pred CCCEEECCCCCCcccH-HHHhhC
Confidence 4467899999998887 466444
No 78
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=40.95 E-value=20 Score=34.18 Aligned_cols=33 Identities=21% Similarity=0.465 Sum_probs=21.0
Q ss_pred cccccCcccCCCCcccchhhhccccccccccCce----EEEEeCCCCCce
Q 010400 18 LCCKCGIPMAPNAANMCVACLRSEVDITEGLQKH----VIISHCPECDCY 63 (511)
Q Consensus 18 ~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~----~~v~~C~~Cgry 63 (511)
.||.||.+.. ..|| +++ ||-- +....|++||--
T Consensus 2 ~Cp~C~~~~~---~~~~---------~~~-IP~F~evii~sf~C~~CGyk 38 (160)
T smart00709 2 DCPSCGGNGT---TRML---------LTS-IPYFREVIIMSFECEHCGYR 38 (160)
T ss_pred cCCCCCCCCE---EEEE---------Eec-CCCcceEEEEEEECCCCCCc
Confidence 5999997633 4444 344 6533 345789999953
No 79
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.61 E-value=24 Score=39.28 Aligned_cols=17 Identities=35% Similarity=1.030 Sum_probs=11.8
Q ss_pred ceecccccCcccCCCCcccchhh
Q 010400 15 GSVLCCKCGIPMAPNAANMCVAC 37 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~~~~mC~~C 37 (511)
+.+.|..||... .|+.|
T Consensus 212 ~~~~C~~Cg~~~------~C~~C 228 (505)
T TIGR00595 212 KNLLCRSCGYIL------CCPNC 228 (505)
T ss_pred CeeEhhhCcCcc------CCCCC
Confidence 446788888753 47777
No 80
>PF14149 YhfH: YhfH-like protein
Probab=40.56 E-value=3.8 Score=29.96 Aligned_cols=25 Identities=24% Similarity=0.631 Sum_probs=19.0
Q ss_pred ccceecccccCcccCCC---Ccccchhh
Q 010400 13 TVGSVLCCKCGIPMAPN---AANMCVAC 37 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~~---~~~mC~~C 37 (511)
+.+..-|+.||..|+.- +.+.|..|
T Consensus 10 nLp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 10 NLPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred hCCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 45667899999998653 66778776
No 81
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=40.34 E-value=17 Score=29.19 Aligned_cols=38 Identities=21% Similarity=0.415 Sum_probs=23.7
Q ss_pred CCCCCCCCcccCccceecccccCcccCCCCcccchhhh
Q 010400 1 MAQDAGMFTVPQTVGSVLCCKCGIPMAPNAANMCVACL 38 (511)
Q Consensus 1 ~~~~~~~~~~~~~~~~i~C~~CG~~i~~~~~~mC~~C~ 38 (511)
|..+.+.+.-......+.|-+||+-.----.+.|..|=
T Consensus 1 MskGT~S~GKrnk~tH~~CRRCGr~syhv~k~~CaaCG 38 (61)
T COG2126 1 MSKGTPSFGKRNKKTHIRCRRCGRRSYHVRKKYCAACG 38 (61)
T ss_pred CCCCCccccccCCcceehhhhccchheeeccceecccC
Confidence 44555555555556668899999875423346666663
No 82
>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=40.08 E-value=11 Score=32.66 Aligned_cols=34 Identities=15% Similarity=0.309 Sum_probs=22.1
Q ss_pred EEEeCCCCCceecCCCceeeCCcChHHHHHHHHHHh
Q 010400 53 IISHCPECDCYLQPPRTWIKAQLESKELLTFCVKRL 88 (511)
Q Consensus 53 ~v~~C~~Cgry~~~p~~Wv~~~les~ELL~~~Lkki 88 (511)
-|-.|+.||..+-+ |.|..... +-..+...++++
T Consensus 52 GIW~C~~C~~~~AG-GAy~~~T~-~~~t~~~~i~rl 85 (90)
T PF01780_consen 52 GIWKCKKCGKKFAG-GAYTPSTP-AAKTVKRAIRRL 85 (90)
T ss_dssp TEEEETTTTEEEE--BSSSSS-H-HHHHHHHHHHHH
T ss_pred EEeecCCCCCEEeC-CCccccch-HHHHHHHHHHHH
Confidence 46889999999998 68987763 333444455544
No 83
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=39.96 E-value=33 Score=36.74 Aligned_cols=67 Identities=19% Similarity=0.197 Sum_probs=44.5
Q ss_pred eecCceeeecCCCCeeeEEEEEEEEEcccCCCCEEEcCchhhhhcCCCCCEEEEEEeCCeEEEEcCCCCeEEEecCc
Q 010400 223 RHDKQLVSHDPKSNNFNYKYTFSVEISPICREDLICLPPKVAVSLGNLGPLVICMKVTNSIALLDPFTLRHCFLDAD 299 (511)
Q Consensus 223 keS~kLVg~D~~~g~~~yr~T~SVrIppickgDlV~l~~k~a~~lG~i~~~~lv~kv~~~I~llDP~T~~~~~l~~~ 299 (511)
+.+..+.+.|.-++ ..++.++++=. -..|..+.....++ .++|+++.++.++++||.|+.+.++..+
T Consensus 265 ~~~~~~~~~dl~t~-e~~~~~~~~~~--~~~~~~~~~~~~~~-------~~~vvs~~~~~~~v~d~et~e~~~~~~~ 331 (355)
T COG1499 265 SIGKGIVVLDLETG-EPVEITWSVYK--RNEGKVAVKEPRLK-------KAVVVSRDPSAIQVLDPETYEARTVKGP 331 (355)
T ss_pred EecCceEEEecccC-CccccChhhcc--cCcceeeeccccce-------EEEEEecCCCceEEEecceEEEEeccCC
Confidence 34555677777777 56666655421 11123333333222 6899999999999999999999988886
No 84
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=39.33 E-value=4.3e+02 Score=28.41 Aligned_cols=79 Identities=18% Similarity=0.223 Sum_probs=51.3
Q ss_pred CCceeEEEcChhHHHHHHHHhcccCCeEEeecCceeeecCCCCeeeEEEEEEEEEcccCCCCEEEcCchhhhhcCCCCCE
Q 010400 194 DQGIDFFFGNRSHAVKFVEFVGKVAPVRSRHDKQLVSHDPKSNNFNYKYTFSVEISPICREDLICLPPKVAVSLGNLGPL 273 (511)
Q Consensus 194 kdGlDfyf~s~~~Ark~v~fl~s~~p~~vkeS~kLVg~D~~~g~~~yr~T~SVrIppickgDlV~l~~k~a~~lG~i~~~ 273 (511)
-+|+=|--.+.+..++++..+.+- .++-+|+- .| -.++-|+--||-||+.-- ++=+.+.-
T Consensus 138 ~dGVvl~~~d~~ei~~~~~~~~~~-----~~~l~L~~-----------a~-Vt~V~~vG~GdRVCVDtc---sll~~gEG 197 (344)
T PRK02290 138 VDGVLLDPDDPNEIKAIVALIEEA-----REKLELVP-----------AT-VTRVEPVGMGDRVCVDTC---SLMEEGEG 197 (344)
T ss_pred CCeEEECCCCHHHHHHHHHHHhcc-----CCcceeEE-----------EE-EEEEEEcCCccEEEEEcc---ccCCCCce
Confidence 345545555566677777777651 12333333 12 247889999999999852 22233466
Q ss_pred EEEEEeCCeEEEEcCCCCe
Q 010400 274 VICMKVTNSIALLDPFTLR 292 (511)
Q Consensus 274 ~lv~kv~~~I~llDP~T~~ 292 (511)
+||-..+++.-|+..+|..
T Consensus 198 mLVGs~s~glfLVhsEt~~ 216 (344)
T PRK02290 198 MLVGSSSRGMFLVHAETEE 216 (344)
T ss_pred EEEcccCCcEEEEeccccc
Confidence 8888889999999988863
No 85
>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=39.13 E-value=16 Score=26.41 Aligned_cols=23 Identities=30% Similarity=0.732 Sum_probs=14.9
Q ss_pred ecccccCccc-----CCCCcccchhhhc
Q 010400 17 VLCCKCGIPM-----APNAANMCVACLR 39 (511)
Q Consensus 17 i~C~~CG~~i-----~~~~~~mC~~C~~ 39 (511)
..|+.||+.- .|...+.|..|--
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 5799999852 3456778877743
No 86
>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=38.88 E-value=11 Score=35.83 Aligned_cols=25 Identities=32% Similarity=0.740 Sum_probs=19.1
Q ss_pred ceecccccCcccCCC------Ccccchhhhc
Q 010400 15 GSVLCCKCGIPMAPN------AANMCVACLR 39 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~------~~~mC~~C~~ 39 (511)
...+|..||.+|++. .+.+|+.|-.
T Consensus 85 ~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~ 115 (159)
T TIGR02890 85 TYGICEVCGKPIPYERLEAIPTATTCVECQN 115 (159)
T ss_pred CCCeecccCCcccHHHHhhCCCcchhHHHHH
Confidence 345899999999752 4579999955
No 87
>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=38.52 E-value=29 Score=25.63 Aligned_cols=39 Identities=21% Similarity=0.442 Sum_probs=23.0
Q ss_pred ecccccCcccCCCCcc-cchhhhccccccccccCce-----EEEEeCCCCC
Q 010400 17 VLCCKCGIPMAPNAAN-MCVACLRSEVDITEGLQKH-----VIISHCPECD 61 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~-mC~~C~~~~~dI~egIp~~-----~~v~~C~~Cg 61 (511)
..|+.||..+.+.... . ++..+|.. ..-. .....|+.||
T Consensus 3 ~~C~~Cg~~l~~ig~~~~-----~q~l~~~p-~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 3 RACPDCGGELKEIGEEKV-----RQVLDLPP-AKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred CcCCCCCceeeECCceee-----EEEEeecc-cceEEEEEEeceEECCCCC
Confidence 3699999987642221 2 66666655 3222 2356788886
No 88
>PRK13674 putative GTP cyclohydrolase; Provisional
Probab=38.47 E-value=3.1e+02 Score=28.40 Aligned_cols=47 Identities=15% Similarity=0.373 Sum_probs=24.8
Q ss_pred EEEEEEEEEecCeeEEEEEEEEEEEeccCCchhhhhcc--CCcceEEEEEEe
Q 010400 113 VKLKVQKEVLNGAILEQSYVVEYVQQDHMCDSCSRVQA--NPDQWVAAVQLR 162 (511)
Q Consensus 113 vkltvq~ev~~g~~lqq~~~Ve~~v~~~~C~~C~R~~~--~~~~w~AiVQVR 162 (511)
..+++.++..+| .+.-...|++.+ .+.|| |++..+ ++|.=++.+.|.
T Consensus 127 Y~~~~~a~~~~~-~~~~~l~v~V~~-~T~CP-CS~~is~~~~HnQRs~~~i~ 175 (271)
T PRK13674 127 YPVTLEAELRDG-VFRLELKVEVPV-SSLCP-CSKAISRYTAHSQRSVATVK 175 (271)
T ss_pred EEEEEEEEEcCC-cEEEEEEEEEEE-EECCc-ChHhHccCCCccccEEEEEE
Confidence 455566665333 244455555554 68899 988632 223334444443
No 89
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=38.43 E-value=23 Score=30.79 Aligned_cols=38 Identities=24% Similarity=0.484 Sum_probs=23.0
Q ss_pred CCCCCCCCcccCccceecccccCcccCCCCcccchhhh
Q 010400 1 MAQDAGMFTVPQTVGSVLCCKCGIPMAPNAANMCVACL 38 (511)
Q Consensus 1 ~~~~~~~~~~~~~~~~i~C~~CG~~i~~~~~~mC~~C~ 38 (511)
|..+.+.+.--.....++|-+||+..--..-..|..|-
T Consensus 1 MtKGT~SfGKr~~ktHtlCrRCG~~syH~qK~~CasCG 38 (91)
T PTZ00073 1 MTKGTGSFGKRHGKTHTLCRRCGKRSFHVQKKRCASCG 38 (91)
T ss_pred CCCCCcccccccCcCcchhcccCccccccccccchhcC
Confidence 44455555544556678999999875433344555554
No 90
>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=38.34 E-value=25 Score=39.70 Aligned_cols=52 Identities=21% Similarity=0.467 Sum_probs=32.3
Q ss_pred ceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecC--------CCceeeCCc
Q 010400 15 GSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQP--------PRTWIKAQL 75 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~--------p~~Wv~~~l 75 (511)
=.+.||.||......-++ +...++-........|+.||..... .|+|+...+
T Consensus 199 ~~vpCPhCg~~~~l~~~~---------l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~~~~ 258 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWEN---------LKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVATNP 258 (557)
T ss_pred EEccCCCCCCCccccccc---------eeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEeccc
Confidence 346799999986643333 2222210346788999999986652 256766654
No 91
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=38.14 E-value=20 Score=38.94 Aligned_cols=44 Identities=20% Similarity=0.472 Sum_probs=31.5
Q ss_pred ccceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCCCceeeCC
Q 010400 13 TVGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPRTWIKAQ 74 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~~Wv~~~ 74 (511)
....+.|+.||-.++ ++ . + ++..--+||+||..+..+++|-...
T Consensus 15 ~~~~~~C~eCd~~~~--------------~P--~-l-~~~q~A~CPRC~~~l~~~~~~sl~r 58 (418)
T COG2995 15 PGHLILCPECDMLVS--------------LP--R-L-DSGQSAYCPRCGHTLTRGGDWSLQR 58 (418)
T ss_pred ccceecCCCCCceec--------------cc--c-C-CCCCcccCCCCCCccccCCCCCccc
Confidence 456678999987654 11 1 2 3566789999999999988886655
No 92
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=37.83 E-value=7.1 Score=40.39 Aligned_cols=9 Identities=33% Similarity=0.707 Sum_probs=7.4
Q ss_pred ecccccCcc
Q 010400 17 VLCCKCGIP 25 (511)
Q Consensus 17 i~C~~CG~~ 25 (511)
-+||.||..
T Consensus 186 ~~CPvCGS~ 194 (308)
T COG3058 186 QYCPVCGSM 194 (308)
T ss_pred ccCCCcCCC
Confidence 489999964
No 93
>PF01132 EFP: Elongation factor P (EF-P) OB domain; InterPro: IPR001059 Elongation factor P (EF-P) is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet []. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. This entry reresents the central domain of elongation factor P and its homologues. It forms an oligonucleotide-binding (OB) fold, though it is not clear if this region is involved in binding nucleic acids [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation; PDB: 1YBY_A 3A5Z_H 3TRE_A 1UEB_B 3HUW_V 3HUY_V 3OYY_B.
Probab=37.69 E-value=45 Score=25.94 Aligned_cols=34 Identities=18% Similarity=0.127 Sum_probs=24.8
Q ss_pred EEEEEEeCCeEEEEcCCCCeEEEecCccc-ccccc
Q 010400 273 LVICMKVTNSIALLDPFTLRHCFLDADQY-WRSSF 306 (511)
Q Consensus 273 ~~lv~kv~~~I~llDP~T~~~~~l~~~~y-w~~pf 306 (511)
.....+.+...++||+.|+..+.|+.+.+ +..+|
T Consensus 4 ~qylY~dgd~~~FMd~etyeQi~v~~~~~g~~~~~ 38 (55)
T PF01132_consen 4 MQYLYKDGDNYVFMDTETYEQIEVPKDQLGDALKF 38 (55)
T ss_dssp EEEEEEESSEEEEEETTT--EEEEEHHHHTTTGCC
T ss_pred EEEEEeCCCEEEEecCCCceEEEecHHHhChHHhh
Confidence 34567788899999999999999998875 43333
No 94
>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=37.47 E-value=20 Score=28.19 Aligned_cols=29 Identities=24% Similarity=0.596 Sum_probs=19.6
Q ss_pred ceecccccCcccCCCCcccchhh-hccccccc
Q 010400 15 GSVLCCKCGIPMAPNAANMCVAC-LRSEVDIT 45 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~~~~mC~~C-~~~~~dI~ 45 (511)
.-..|+.||...- +-.+|..| |-+.-.++
T Consensus 25 ~l~~c~~cg~~~~--~H~vc~~cG~y~~r~v~ 54 (56)
T PF01783_consen 25 NLVKCPNCGEPKL--PHRVCPSCGYYKGRQVI 54 (56)
T ss_dssp SEEESSSSSSEES--TTSBCTTTBBSSSSSSS
T ss_pred ceeeeccCCCEec--ccEeeCCCCeECCEEEe
Confidence 4467999997644 37899999 54444433
No 95
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=37.02 E-value=15 Score=29.56 Aligned_cols=20 Identities=20% Similarity=0.413 Sum_probs=15.8
Q ss_pred ceEEEEeCCCCCceecCCCc
Q 010400 50 KHVIISHCPECDCYLQPPRT 69 (511)
Q Consensus 50 ~~~~v~~C~~Cgry~~~p~~ 69 (511)
...+...|..||+.+-.|..
T Consensus 26 ha~t~V~C~~Cg~~L~~PtG 45 (59)
T PRK00415 26 HASTVVRCLVCGKTLAEPTG 45 (59)
T ss_pred cCCcEEECcccCCCcccCCC
Confidence 35688899999999977643
No 96
>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=36.79 E-value=12 Score=31.28 Aligned_cols=23 Identities=35% Similarity=0.882 Sum_probs=10.7
Q ss_pred ccchhhhccccccccccCceEEEEeCCCCCc
Q 010400 32 NMCVACLRSEVDITEGLQKHVIISHCPECDC 62 (511)
Q Consensus 32 ~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgr 62 (511)
-.|..||.-..+.+. .|||.||-
T Consensus 10 lrC~aCf~~t~~~~k--------~FCp~CGn 32 (73)
T PF08772_consen 10 LRCHACFKITKDMTK--------QFCPKCGN 32 (73)
T ss_dssp EE-SSS--EES-SS----------S-SSS--
T ss_pred EEccccccCcCCCCc--------eeCcccCC
Confidence 358899887665544 79999995
No 97
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=36.78 E-value=18 Score=24.35 Aligned_cols=22 Identities=27% Similarity=0.833 Sum_probs=17.5
Q ss_pred ccc--ccCcccCCCCcccchhhhc
Q 010400 18 LCC--KCGIPMAPNAANMCVACLR 39 (511)
Q Consensus 18 ~C~--~CG~~i~~~~~~mC~~C~~ 39 (511)
+|. .||-.-.|...|||..||+
T Consensus 3 ~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 3 KCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred ccccCCCCCcCChhhcccCHhhcC
Confidence 566 7887767777899999985
No 98
>PF11009 DUF2847: Protein of unknown function (DUF2847); InterPro: IPR022551 Members of this protein family, including YtxJ from Bacillus subtilis, occur in species that encode proteins for synthesizing bacillithiol. The protein is described as thioredoxin-like, while another bacillithiol-associated protein, YpdA (TIGR04018 from TIGRFAMS), is described as thioredoxin reductase-like. ; PDB: 3IV4_A.
Probab=36.30 E-value=28 Score=31.04 Aligned_cols=48 Identities=8% Similarity=0.094 Sum_probs=34.7
Q ss_pred cCCceeEEEcChhHHHHHHHHhcccCCeEEeecCceeeecCCCCeeeEEEE
Q 010400 193 MDQGIDFFFGNRSHAVKFVEFVGKVAPVRSRHDKQLVSHDPKSNNFNYKYT 243 (511)
Q Consensus 193 ~kdGlDfyf~s~~~Ark~v~fl~s~~p~~vkeS~kLVg~D~~~g~~~yr~T 243 (511)
..+++++||..--.+|-+++.|.+.+|++- +|++++= .++|+-.|.-+
T Consensus 48 ~~~~~~~y~l~v~~~R~vSn~IAe~~~V~H-eSPQ~il--i~~g~~v~~aS 95 (105)
T PF11009_consen 48 SPDEIPVYYLDVIEYRPVSNAIAEDFGVKH-ESPQVIL--IKNGKVVWHAS 95 (105)
T ss_dssp HT----EEEEEGGGGHHHHHHHHHHHT-----SSEEEE--EETTEEEEEEE
T ss_pred CCccceEEEEEEEeCchhHHHHHHHhCCCc-CCCcEEE--EECCEEEEECc
Confidence 445699999999999999999999999986 8888888 48898887643
No 99
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.07 E-value=18 Score=27.27 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=8.0
Q ss_pred EEEeCCCCCce
Q 010400 53 IISHCPECDCY 63 (511)
Q Consensus 53 ~v~~C~~Cgry 63 (511)
....||.||..
T Consensus 18 ~~irC~~CG~r 28 (44)
T smart00659 18 DVVRCRECGYR 28 (44)
T ss_pred CceECCCCCce
Confidence 45689999863
No 100
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=35.75 E-value=27 Score=33.40 Aligned_cols=33 Identities=18% Similarity=0.276 Sum_probs=18.0
Q ss_pred hHHHHHHHHhcccCCeEEeecCceeeecCCCCeee
Q 010400 205 SHAVKFVEFVGKVAPVRSRHDKQLVSHDPKSNNFN 239 (511)
Q Consensus 205 ~~Ark~v~fl~s~~p~~vkeS~kLVg~D~~~g~~~ 239 (511)
..+..|.+.|.+..-+ +.+..||=.|...|.+.
T Consensus 121 ~k~~~~l~kL~~~~~g--~~pfTlIldDP~GNS~I 153 (163)
T TIGR00340 121 KKCEEILKRIREVIEG--KFKFTLIIEDPFGNSFI 153 (163)
T ss_pred HHHHHHHHHHHHHHhC--CCCeEEEEECCCCCeee
Confidence 3445555666655444 23566666666555443
No 101
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=35.68 E-value=47 Score=30.12 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=37.4
Q ss_pred eeE-EEcChhHHHHHHHHhcccCCeEEeecCceeeecCCCCeeeEEEEEEEEEcccCCCCEEEcCch
Q 010400 197 IDF-FFGNRSHAVKFVEFVGKVAPVRSRHDKQLVSHDPKSNNFNYKYTFSVEISPICREDLICLPPK 262 (511)
Q Consensus 197 lDf-yf~s~~~Ark~v~fl~s~~p~~vkeS~kLVg~D~~~g~~~yr~T~SVrIppickgDlV~l~~k 262 (511)
++| .+.+...|++++..+.... ...+..+.|+...+-..+.+||+|.+...
T Consensus 100 ~~~~~v~~~~qA~r~a~~~l~~~---------------~~~r~t~~f~~~~~~~~l~pGDvi~l~~~ 151 (164)
T PF13550_consen 100 VDLPGVTDASQAQRLAERLLRRS---------------RYERRTVSFTLPPDGLALEPGDVIALSDD 151 (164)
T ss_pred EEEeeECCHHHHHHHHHHHHHHh---------------hccceEEEEEEChhhccCCCCCEEEEEeC
Confidence 443 4677899999999886544 23444567777777788999999999864
No 102
>PHA00080 DksA-like zinc finger domain containing protein
Probab=35.63 E-value=16 Score=30.30 Aligned_cols=26 Identities=27% Similarity=0.749 Sum_probs=19.0
Q ss_pred cceecccccCcccCCC------Ccccchhhhc
Q 010400 14 VGSVLCCKCGIPMAPN------AANMCVACLR 39 (511)
Q Consensus 14 ~~~i~C~~CG~~i~~~------~~~mC~~C~~ 39 (511)
....+|-.||.+|++. ...+|++|-.
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a~P~~~~Cv~Cq~ 60 (72)
T PHA00080 29 PSATHCEECGDPIPEARREAVPGCRTCVSCQE 60 (72)
T ss_pred CCCCEecCCCCcCcHHHHHhCCCccCcHHHHH
Confidence 3445899999999752 3468999954
No 103
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=35.58 E-value=30 Score=35.26 Aligned_cols=63 Identities=24% Similarity=0.544 Sum_probs=38.0
Q ss_pred cCccceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCc-eecCCCceeeCCcChHHHHHHHHHHh
Q 010400 11 PQTVGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDC-YLQPPRTWIKAQLESKELLTFCVKRL 88 (511)
Q Consensus 11 ~~~~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgr-y~~~p~~Wv~~~les~ELL~~~Lkki 88 (511)
+.......|..||.....+. +...+ +...+..|+.||. .+.|.-.|.--.+..+ .+..+++.+
T Consensus 117 HGsl~~~~C~~C~~~~~~~~-------------~~~~~-~~~~~p~C~~Cg~~~lrP~VV~fGE~lp~~-~~~~~~~~~ 180 (250)
T COG0846 117 HGSLKRVRCSKCGNQYYDED-------------VIKFI-EDGLIPRCPKCGGPVLRPDVVWFGEPLPAS-FLDEALEAL 180 (250)
T ss_pred ccceeeeEeCCCcCccchhh-------------hhhhc-ccCCCCcCccCCCccccCCEEEeCCCCCHH-HHHHHHHHh
Confidence 34566677999988765322 11101 1125668999999 7777655777665433 355566654
No 104
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=35.36 E-value=18 Score=34.74 Aligned_cols=21 Identities=29% Similarity=0.717 Sum_probs=16.9
Q ss_pred ccccCcccCCCCcccchhhhcc
Q 010400 19 CCKCGIPMAPNAANMCVACLRS 40 (511)
Q Consensus 19 C~~CG~~i~~~~~~mC~~C~~~ 40 (511)
|+.||+++.+. ..+|.+|...
T Consensus 1 C~~C~~~~~~~-~~~C~~C~~~ 21 (190)
T TIGR00201 1 CSLCGRPYQSV-HALCRQCGSW 21 (190)
T ss_pred CCccccccccc-cCCchhhCCc
Confidence 99999987653 5799999765
No 105
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=35.24 E-value=44 Score=38.87 Aligned_cols=51 Identities=22% Similarity=0.390 Sum_probs=37.1
Q ss_pred ccceecccccCcc---cCCC----------CcccchhhhccccccccccCceEEEEeCCCCCcee
Q 010400 13 TVGSVLCCKCGIP---MAPN----------AANMCVACLRSEVDITEGLQKHVIISHCPECDCYL 64 (511)
Q Consensus 13 ~~~~i~C~~CG~~---i~~~----------~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~ 64 (511)
.++-+-|-.||-- ++.+ .--||..|-.+..|... =-=++.-.-||.||=++
T Consensus 120 ~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~n-RRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 120 LYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLN-RRFHAQPIACPKCGPHL 183 (750)
T ss_pred eccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccc-cccccccccCcccCCCe
Confidence 3555779999953 2221 12599999999999988 33458889999999654
No 106
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.02 E-value=29 Score=28.48 Aligned_cols=13 Identities=23% Similarity=0.754 Sum_probs=10.9
Q ss_pred ceEEEEeCCCCCc
Q 010400 50 KHVIISHCPECDC 62 (511)
Q Consensus 50 ~~~~v~~C~~Cgr 62 (511)
+...+..|++||-
T Consensus 36 n~f~~itCk~CgY 48 (68)
T COG3478 36 NKFIVITCKNCGY 48 (68)
T ss_pred cEEEEEEeccCCc
Confidence 5678899999995
No 107
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=34.01 E-value=13 Score=31.93 Aligned_cols=36 Identities=19% Similarity=0.477 Sum_probs=19.3
Q ss_pred CCCCCCCcccCccceecccccCcccCCCCcccchhh
Q 010400 2 AQDAGMFTVPQTVGSVLCCKCGIPMAPNAANMCVAC 37 (511)
Q Consensus 2 ~~~~~~~~~~~~~~~i~C~~CG~~i~~~~~~mC~~C 37 (511)
.-+...|........-+|.+||+..--..-+.|..|
T Consensus 2 tKGT~sFGKr~nkshtlC~RCG~~syH~QKstC~~C 37 (92)
T KOG3475|consen 2 TKGTSSFGKRHNKSHTLCRRCGRRSYHIQKSTCSSC 37 (92)
T ss_pred CCcccchhhccccchHHHHHhCchhhhhhccccccc
Confidence 334444544444455678888886432223445444
No 108
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=32.85 E-value=1.1e+02 Score=28.31 Aligned_cols=22 Identities=23% Similarity=0.652 Sum_probs=18.5
Q ss_pred ceEEEEeCCCCCceecCCCcee
Q 010400 50 KHVIISHCPECDCYLQPPRTWI 71 (511)
Q Consensus 50 ~~~~v~~C~~Cgry~~~p~~Wv 71 (511)
..+.-..|++||+++.||..|-
T Consensus 25 ~kl~g~kC~~CG~v~~PPr~~C 46 (140)
T COG1545 25 GKLLGTKCKKCGRVYFPPRAYC 46 (140)
T ss_pred CcEEEEEcCCCCeEEcCCcccC
Confidence 3678899999999999996664
No 109
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=32.67 E-value=31 Score=27.86 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=8.9
Q ss_pred ceEEEEeCCCCCc
Q 010400 50 KHVIISHCPECDC 62 (511)
Q Consensus 50 ~~~~v~~C~~Cgr 62 (511)
+.-.+..|+.||-
T Consensus 33 k~~D~irCReCG~ 45 (62)
T KOG3507|consen 33 KRGDVIRCRECGY 45 (62)
T ss_pred cCCCcEehhhcch
Confidence 3456778888883
No 110
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=32.66 E-value=9.4 Score=30.82 Aligned_cols=17 Identities=24% Similarity=0.626 Sum_probs=5.5
Q ss_pred cCceEEEEeCCCCCcee
Q 010400 48 LQKHVIISHCPECDCYL 64 (511)
Q Consensus 48 Ip~~~~v~~C~~Cgry~ 64 (511)
++-++--..|..||+|-
T Consensus 42 v~fH~lg~KC~~C~SYN 58 (61)
T PF14599_consen 42 VPFHFLGHKCSHCGSYN 58 (61)
T ss_dssp EE--TT----TTTS---
T ss_pred eeeeHhhhcCCCCCCcc
Confidence 44455566788888884
No 111
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=32.62 E-value=12 Score=28.78 Aligned_cols=11 Identities=36% Similarity=0.911 Sum_probs=5.0
Q ss_pred cccccCcccCC
Q 010400 18 LCCKCGIPMAP 28 (511)
Q Consensus 18 ~C~~CG~~i~~ 28 (511)
-||.||+++++
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 68888887653
No 112
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=32.28 E-value=29 Score=41.93 Aligned_cols=55 Identities=22% Similarity=0.553 Sum_probs=38.0
Q ss_pred CccceecccccCcccCCCCc------------ccchhhhccccccccccCceEEEEeCCCCCceec--CCCceeeCC
Q 010400 12 QTVGSVLCCKCGIPMAPNAA------------NMCVACLRSEVDITEGLQKHVIISHCPECDCYLQ--PPRTWIKAQ 74 (511)
Q Consensus 12 ~~~~~i~C~~CG~~i~~~~~------------~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~--~p~~Wv~~~ 74 (511)
+....-.|-.||-.+..+.+ -+|..|| +++.-|| -..||.|+-.+. .|.-|+..+
T Consensus 11 ~~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy--eye~~~g------~~~cp~c~t~y~~~~~~~~~~~d 79 (1044)
T PLN02915 11 QSADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY--EYERSEG------NQCCPQCNTRYKRHKGCPRVEGD 79 (1044)
T ss_pred cCCCcchhhccccccCcCCCCCEEEEeccCCCccccchh--hhhhhcC------CccCCccCCchhhhcCCCCccCC
Confidence 44555679999988654322 3899999 7777663 357999986543 235588886
No 113
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=32.27 E-value=23 Score=29.14 Aligned_cols=18 Identities=22% Similarity=0.493 Sum_probs=14.6
Q ss_pred ceEEEEeCCCCCceecCC
Q 010400 50 KHVIISHCPECDCYLQPP 67 (511)
Q Consensus 50 ~~~~v~~C~~Cgry~~~p 67 (511)
...+...|..||+.+-.|
T Consensus 34 hast~V~C~~CG~~l~~P 51 (67)
T COG2051 34 HASTVVTCLICGTTLAEP 51 (67)
T ss_pred cCceEEEecccccEEEec
Confidence 356888999999998765
No 114
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.20 E-value=22 Score=27.65 Aligned_cols=15 Identities=27% Similarity=0.625 Sum_probs=10.7
Q ss_pred CccceecccccCccc
Q 010400 12 QTVGSVLCCKCGIPM 26 (511)
Q Consensus 12 ~~~~~i~C~~CG~~i 26 (511)
.+.+..+||.||+|.
T Consensus 8 a~lp~KICpvCqRPF 22 (54)
T COG4338 8 ATLPDKICPVCQRPF 22 (54)
T ss_pred cccchhhhhhhcCch
Confidence 356667788888875
No 115
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=32.13 E-value=16 Score=30.36 Aligned_cols=23 Identities=35% Similarity=0.924 Sum_probs=17.4
Q ss_pred ecccccCcccCCC-----C-cccchhhhc
Q 010400 17 VLCCKCGIPMAPN-----A-ANMCVACLR 39 (511)
Q Consensus 17 i~C~~CG~~i~~~-----~-~~mC~~C~~ 39 (511)
.+|..||.+|++- | ..+|+.|-.
T Consensus 35 ~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~ 63 (73)
T PRK13715 35 YLCEACGNPIPEARRKIFPGVTLCVECQA 63 (73)
T ss_pred ccHhhcCCcCCHHHHhcCCCcCCCHHHHH
Confidence 4899999999752 3 468999943
No 116
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.09 E-value=26 Score=25.09 Aligned_cols=17 Identities=12% Similarity=0.368 Sum_probs=13.9
Q ss_pred cCceEEEEeCCCCCcee
Q 010400 48 LQKHVIISHCPECDCYL 64 (511)
Q Consensus 48 Ip~~~~v~~C~~Cgry~ 64 (511)
||....-..|+.||-.+
T Consensus 19 ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 19 IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred CCCCCcEEECCCCCCEe
Confidence 78888889999998654
No 117
>PRK11019 hypothetical protein; Provisional
Probab=31.91 E-value=17 Score=31.38 Aligned_cols=26 Identities=31% Similarity=0.815 Sum_probs=19.5
Q ss_pred eecccccCcccCCC------Ccccchhhhccc
Q 010400 16 SVLCCKCGIPMAPN------AANMCVACLRSE 41 (511)
Q Consensus 16 ~i~C~~CG~~i~~~------~~~mC~~C~~~~ 41 (511)
.-+|..||.+|+.- ...+|++|-...
T Consensus 36 yg~C~~CG~~Ip~~Rl~A~P~a~~Cv~Cq~~~ 67 (88)
T PRK11019 36 LTECEECGEPIPEARRKAIPGVRLCVACQQEK 67 (88)
T ss_pred CCeeCcCCCcCcHHHHhhcCCccccHHHHHHH
Confidence 45899999998752 346899997643
No 118
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=31.63 E-value=22 Score=37.52 Aligned_cols=35 Identities=34% Similarity=0.818 Sum_probs=23.3
Q ss_pred ecccccCcccCCC------CcccchhhhccccccccccCceEEEEeCCCCCc
Q 010400 17 VLCCKCGIPMAPN------AANMCVACLRSEVDITEGLQKHVIISHCPECDC 62 (511)
Q Consensus 17 i~C~~CG~~i~~~------~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgr 62 (511)
-||-+||.+|.-- .--.|.+|-+..- ..+|+.|.-
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~-----------dK~Cp~C~d 131 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKHVFCLECARSDS-----------DKICPLCDD 131 (389)
T ss_pred EeecccCCcceeeecccccchhhhhhhhhcCc-----------cccCcCccc
Confidence 4899999997521 2246888877654 456777753
No 119
>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=31.39 E-value=15 Score=26.00 Aligned_cols=23 Identities=35% Similarity=1.002 Sum_probs=16.0
Q ss_pred cccccCcccCCC------Ccccchhhhcc
Q 010400 18 LCCKCGIPMAPN------AANMCVACLRS 40 (511)
Q Consensus 18 ~C~~CG~~i~~~------~~~mC~~C~~~ 40 (511)
+|-.||.+|... ...+|.+|...
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 499999998652 45799999754
No 120
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=30.98 E-value=32 Score=36.42 Aligned_cols=71 Identities=24% Similarity=0.362 Sum_probs=37.8
Q ss_pred ceecccccCcccCCCCcc---cch--hhhc--ccccccc------ccCceEEEEeCCCCCceecCCCceeeCC--cChHH
Q 010400 15 GSVLCCKCGIPMAPNAAN---MCV--ACLR--SEVDITE------GLQKHVIISHCPECDCYLQPPRTWIKAQ--LESKE 79 (511)
Q Consensus 15 ~~i~C~~CG~~i~~~~~~---mC~--~C~~--~~~dI~e------gIp~~~~v~~C~~Cgry~~~p~~Wv~~~--les~E 79 (511)
-..|||-||.++.|..+| .|. .|-. ..+.=+. =|......--|.. ..+++||-|.-.. +|.-|
T Consensus 149 kykFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~dPvVIm~li~~d~~~~LL~R--~~r~~~gl~t~lAGFlEpGE 226 (345)
T KOG3084|consen 149 KYKFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTDPVVIMLLIDHDGKHALLGR--QKRYPPGLWTCLAGFLEPGE 226 (345)
T ss_pred HhccCcccCCCcccccCCccceeecccCCcCCeeccCCCCeEEEEEEcCCCCEeeeec--ccCCCCchhhhhhccCCccc
Confidence 347999999998776443 576 5652 2222111 0111112222333 2335556786654 47777
Q ss_pred HHHHHHHH
Q 010400 80 LLTFCVKR 87 (511)
Q Consensus 80 LL~~~Lkk 87 (511)
-+++|..+
T Consensus 227 S~eeav~R 234 (345)
T KOG3084|consen 227 SIEEAVRR 234 (345)
T ss_pred cHHHHHHH
Confidence 77776654
No 121
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=30.90 E-value=29 Score=29.93 Aligned_cols=31 Identities=19% Similarity=0.488 Sum_probs=21.5
Q ss_pred cchhhhccccccccccCceEEEEeCCCCCceecCC
Q 010400 33 MCVACLRSEVDITEGLQKHVIISHCPECDCYLQPP 67 (511)
Q Consensus 33 mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p 67 (511)
-|++|+..++ |+. ...++..|..||..|-.|
T Consensus 37 kCp~C~n~q~-VFS---hA~t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 37 KCPGCSQITT-VFS---HAQTVVLCGGCSSQLCQP 67 (85)
T ss_pred ECCCCCCeeE-EEe---cCceEEEccccCCEeecc
Confidence 4666665554 333 456899999999999665
No 122
>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=30.78 E-value=12 Score=25.45 Aligned_cols=21 Identities=19% Similarity=0.504 Sum_probs=9.6
Q ss_pred cccccCcccCCC-----Ccccchhhh
Q 010400 18 LCCKCGIPMAPN-----AANMCVACL 38 (511)
Q Consensus 18 ~C~~CG~~i~~~-----~~~mC~~C~ 38 (511)
.|++||..+... ...+|+.|.
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 588888876532 224666663
No 123
>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=30.56 E-value=21 Score=28.80 Aligned_cols=26 Identities=27% Similarity=0.657 Sum_probs=18.9
Q ss_pred cceecccccCcccCCC-----C-cccchhhhc
Q 010400 14 VGSVLCCKCGIPMAPN-----A-ANMCVACLR 39 (511)
Q Consensus 14 ~~~i~C~~CG~~i~~~-----~-~~mC~~C~~ 39 (511)
.+..+|-.||.+|++- | ...|++|-.
T Consensus 29 ~s~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~ 60 (63)
T TIGR02419 29 PSLRECEDCGEPIPEARREALPGVTRCVSCQE 60 (63)
T ss_pred CCCCeeccCCCcChHHHHhhcCCcCCcHHHHh
Confidence 3456999999999752 3 367999843
No 124
>PLN00209 ribosomal protein S27; Provisional
Probab=30.49 E-value=29 Score=29.96 Aligned_cols=31 Identities=19% Similarity=0.543 Sum_probs=21.3
Q ss_pred cchhhhccccccccccCceEEEEeCCCCCceecCC
Q 010400 33 MCVACLRSEVDITEGLQKHVIISHCPECDCYLQPP 67 (511)
Q Consensus 33 mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p 67 (511)
-|++|+..++ |+. ...++..|..||..+-.|
T Consensus 38 kCp~C~n~q~-VFS---hA~t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 38 KCQGCFNITT-VFS---HSQTVVVCGSCQTVLCQP 68 (86)
T ss_pred ECCCCCCeeE-EEe---cCceEEEccccCCEeecc
Confidence 4666665554 333 456889999999999665
No 125
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=30.14 E-value=15 Score=29.16 Aligned_cols=31 Identities=19% Similarity=0.485 Sum_probs=17.7
Q ss_pred cchhhhccccccccccCceEEEEeCCCCCceecCC
Q 010400 33 MCVACLRSEVDITEGLQKHVIISHCPECDCYLQPP 67 (511)
Q Consensus 33 mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p 67 (511)
-|++|+..++= +. ...++..|..||..|-.|
T Consensus 9 kCp~C~~~q~v-FS---ha~t~V~C~~Cg~~L~~P 39 (55)
T PF01667_consen 9 KCPGCYNIQTV-FS---HAQTVVKCVVCGTVLAQP 39 (55)
T ss_dssp E-TTT-SEEEE-ET---T-SS-EE-SSSTSEEEEE
T ss_pred ECCCCCCeeEE-Ee---cCCeEEEcccCCCEecCC
Confidence 36666655543 33 456788999999999665
No 126
>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=30.14 E-value=24 Score=25.94 Aligned_cols=11 Identities=36% Similarity=0.975 Sum_probs=7.0
Q ss_pred eCCCCCceecC
Q 010400 56 HCPECDCYLQP 66 (511)
Q Consensus 56 ~C~~Cgry~~~ 66 (511)
+|+.||..+..
T Consensus 21 vC~~CG~Vl~e 31 (43)
T PF08271_consen 21 VCPNCGLVLEE 31 (43)
T ss_dssp EETTT-BBEE-
T ss_pred ECCCCCCEeec
Confidence 88888877754
No 127
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=29.96 E-value=1.4e+02 Score=28.21 Aligned_cols=64 Identities=13% Similarity=-0.029 Sum_probs=40.2
Q ss_pred ccCCCCEEEcCchhhhhcCCCCCEEEEEEeC-CeEEEEcCCCCeEEEecCccccccccccccC-ccceeEEEEEEee
Q 010400 250 PICREDLICLPPKVAVSLGNLGPLVICMKVT-NSIALLDPFTLRHCFLDADQYWRSSFKSLLT-SRQLVEYIVLDVE 324 (511)
Q Consensus 250 pickgDlV~l~~k~a~~lG~i~~~~lv~kv~-~~I~llDP~T~~~~~l~~~~yw~~pf~~l~~-~~~l~ef~Vldve 324 (511)
||..||.|.+++ ....|..++ .+..+.++ +++.+.+|...++++++..... +......+-+.+.
T Consensus 60 pf~vGD~I~i~~----------~~G~V~~I~l~~t~l~~~-~g~~v~IPNs~l~~~~i~N~s~~~~~~~~~v~~~v~ 125 (206)
T PF00924_consen 60 PFKVGDRIEIGG----------VEGRVEEIGLRSTRLRTW-DGEIVIIPNSKLISSPIVNYSRSSPYRRVVVEIPVD 125 (206)
T ss_dssp SS-TT-EEESSS-----------EEEEEEE-SSEEEEEET-TS-EEEEEHHHHHCS-EEETTT-SSEEEEEEEEEE-
T ss_pred CccCCCEEEEEE----------eehHHHhcCcceeeeecC-CCCEEEEEchheeeEEEEEeeccCCceeeeeeeeEe
Confidence 899999999994 334555555 46666654 7999999999999999987665 3444444444443
No 128
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=29.42 E-value=29 Score=40.44 Aligned_cols=51 Identities=24% Similarity=0.474 Sum_probs=37.1
Q ss_pred ccceecccccCccc---CC------C----CcccchhhhccccccccccCceEEEEeCCCCCcee
Q 010400 13 TVGSVLCCKCGIPM---AP------N----AANMCVACLRSEVDITEGLQKHVIISHCPECDCYL 64 (511)
Q Consensus 13 ~~~~i~C~~CG~~i---~~------~----~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~ 64 (511)
.++-+-|-.||=.. .. + .-.||.+|..+-.+... =--+...+-|+.||=.+
T Consensus 87 ~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~-rr~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 87 LYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLD-RRFHAQPIACPRCGPQL 150 (711)
T ss_pred cCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCcc-ccCCCCCccCCCCCcEE
Confidence 46667799999541 11 1 22699999999988877 33457899999999655
No 129
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=29.39 E-value=8.4 Score=31.59 Aligned_cols=14 Identities=36% Similarity=0.691 Sum_probs=11.0
Q ss_pred EEEEeCCCCCceecC
Q 010400 52 VIISHCPECDCYLQP 66 (511)
Q Consensus 52 ~~v~~C~~Cgry~~~ 66 (511)
++|.+|..|| |+..
T Consensus 1 V~IeyC~~C~-y~~R 14 (72)
T TIGR02174 1 VEIEYCGSCG-YKPR 14 (72)
T ss_pred CEEEECCCCC-ChHH
Confidence 4789999999 5544
No 130
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=29.30 E-value=22 Score=42.96 Aligned_cols=27 Identities=22% Similarity=0.642 Sum_probs=21.0
Q ss_pred ecccccCcccCC--CCccc-chhhhccccc
Q 010400 17 VLCCKCGIPMAP--NAANM-CVACLRSEVD 43 (511)
Q Consensus 17 i~C~~CG~~i~~--~~~~m-C~~C~~~~~d 43 (511)
..||.||-+++. +..|+ |..|+-....
T Consensus 9 ~~CpNCGG~isseRL~~glpCe~CLp~~~~ 38 (1187)
T COG1110 9 SSCPNCGGDISSERLEKGLPCERCLPEDTE 38 (1187)
T ss_pred ccCCCCCCcCcHHHHhcCCCchhccCCccc
Confidence 479999998754 45666 9999987664
No 131
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.26 E-value=28 Score=28.50 Aligned_cols=16 Identities=31% Similarity=0.492 Sum_probs=12.3
Q ss_pred ccceecccccCcccCC
Q 010400 13 TVGSVLCCKCGIPMAP 28 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~ 28 (511)
...++.||.||+++.-
T Consensus 4 ~~~~v~CP~Cgkpv~w 19 (65)
T COG3024 4 LRITVPCPTCGKPVVW 19 (65)
T ss_pred ccccccCCCCCCcccc
Confidence 3456789999999763
No 132
>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=29.01 E-value=27 Score=26.33 Aligned_cols=15 Identities=33% Similarity=0.804 Sum_probs=10.8
Q ss_pred ccceecccccCcccC
Q 010400 13 TVGSVLCCKCGIPMA 27 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~ 27 (511)
..+...|+.||+|+.
T Consensus 5 ~lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 5 NLPSKICPVCGRPFT 19 (42)
T ss_pred cCCCCcCcccCCcch
Confidence 456677888888864
No 133
>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=28.87 E-value=22 Score=28.36 Aligned_cols=13 Identities=38% Similarity=0.751 Sum_probs=7.4
Q ss_pred eecccccCcccCC
Q 010400 16 SVLCCKCGIPMAP 28 (511)
Q Consensus 16 ~i~C~~CG~~i~~ 28 (511)
++.||.||+++..
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 5789999998765
No 134
>cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication.
Probab=28.68 E-value=68 Score=24.48 Aligned_cols=27 Identities=7% Similarity=-0.140 Sum_probs=23.0
Q ss_pred EEEEEeCCeEEEEcCCCCeEEEecCcc
Q 010400 274 VICMKVTNSIALLDPFTLRHCFLDADQ 300 (511)
Q Consensus 274 ~lv~kv~~~I~llDP~T~~~~~l~~~~ 300 (511)
-...+.++.+++||++|+....++.+.
T Consensus 4 qylY~dg~~~~fMd~etyeq~~v~~~~ 30 (55)
T cd04463 4 QVLDIQGSKPVTMDLETYEVVQVPPPV 30 (55)
T ss_pred EEEEcCCCEeEEecCCCceEEEeCHHH
Confidence 455677889999999999999998865
No 135
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=28.35 E-value=43 Score=26.68 Aligned_cols=26 Identities=19% Similarity=0.494 Sum_probs=21.6
Q ss_pred HHHHHHHHHhhcCHhhhhhccccccC
Q 010400 443 KEYEEFLRDLEENPELRFNISLYRNK 468 (511)
Q Consensus 443 ~d~e~F~~dleeD~elr~~i~lyk~~ 468 (511)
.+...|++.+..||+||.++.-..++
T Consensus 2 e~l~~Fl~~~~~d~~L~~~l~~~~~~ 27 (64)
T TIGR03798 2 EQLKAFLEKVKTDPDLREKLKAAEDP 27 (64)
T ss_pred HHHHHHHHHHHcCHHHHHHHHHcCCH
Confidence 36789999999999999999855443
No 136
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.43 E-value=26 Score=27.06 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=8.3
Q ss_pred ceecccccCcc
Q 010400 15 GSVLCCKCGIP 25 (511)
Q Consensus 15 ~~i~C~~CG~~ 25 (511)
...+||+||..
T Consensus 19 ~~~fCP~Cg~~ 29 (50)
T PRK00432 19 KNKFCPRCGSG 29 (50)
T ss_pred ccCcCcCCCcc
Confidence 34599999973
No 137
>PRK00529 elongation factor P; Validated
Probab=27.20 E-value=2.3e+02 Score=27.49 Aligned_cols=29 Identities=17% Similarity=0.150 Sum_probs=25.3
Q ss_pred CEEEEEEeCCeEEEEcCCCCeEEEecCcc
Q 010400 272 PLVICMKVTNSIALLDPFTLRHCFLDADQ 300 (511)
Q Consensus 272 ~~~lv~kv~~~I~llDP~T~~~~~l~~~~ 300 (511)
+..+.+..++.++||||+|++..+|+.+.
T Consensus 69 ~~q~ly~dgd~~~fMD~etyeq~~l~~~~ 97 (186)
T PRK00529 69 EMQYLYNDGDGYVFMDTETYEQIEVPADQ 97 (186)
T ss_pred EEEEEEECCCEEEEecCCCceeeEcCHHH
Confidence 66788888889999999999999999863
No 138
>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=26.78 E-value=25 Score=31.50 Aligned_cols=28 Identities=25% Similarity=0.609 Sum_probs=17.1
Q ss_pred cchhhhccccccccccCceEEEEeCCCCCceecC
Q 010400 33 MCVACLRSEVDITEGLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 33 mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~ 66 (511)
.|++|=.+=++|-. =| .+||+||.-+.+
T Consensus 11 ~Cp~CG~kFYDLnk-~P-----ivCP~CG~~~~~ 38 (108)
T PF09538_consen 11 TCPSCGAKFYDLNK-DP-----IVCPKCGTEFPP 38 (108)
T ss_pred cCCCCcchhccCCC-CC-----ccCCCCCCccCc
Confidence 34444444556655 22 569999998776
No 139
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=26.58 E-value=25 Score=32.60 Aligned_cols=10 Identities=50% Similarity=1.195 Sum_probs=7.9
Q ss_pred ecccccCccc
Q 010400 17 VLCCKCGIPM 26 (511)
Q Consensus 17 i~C~~CG~~i 26 (511)
.-||.||.|.
T Consensus 29 ~hCp~Cg~PL 38 (131)
T COG1645 29 KHCPKCGTPL 38 (131)
T ss_pred hhCcccCCcc
Confidence 3499999984
No 140
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.02 E-value=64 Score=34.02 Aligned_cols=34 Identities=26% Similarity=0.540 Sum_probs=21.9
Q ss_pred ccchhhhcccccccc-ccC---ceEEEEeCCCCCceecC
Q 010400 32 NMCVACLRSEVDITE-GLQ---KHVIISHCPECDCYLQP 66 (511)
Q Consensus 32 ~mC~~C~~~~~dI~e-gIp---~~~~v~~C~~Cgry~~~ 66 (511)
..|+.|--. -+|.= .++ ..+.+..|..|++|+.-
T Consensus 227 ~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 227 VKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred ccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 467888643 23221 122 35789999999999864
No 141
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=25.63 E-value=12 Score=30.40 Aligned_cols=41 Identities=17% Similarity=0.450 Sum_probs=31.0
Q ss_pred eecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCCCc
Q 010400 16 SVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPRT 69 (511)
Q Consensus 16 ~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~~ 69 (511)
...||+|+..-. .-||-....+.. | -.+|+.|-||+..+|.
T Consensus 5 ~~~CPRC~S~nT-------KFcYyNNy~~~Q--P----R~~Ck~C~rywT~GG~ 45 (63)
T PF02701_consen 5 PLPCPRCDSTNT-------KFCYYNNYNLSQ--P----RYFCKSCRRYWTHGGT 45 (63)
T ss_pred CCCCCCcCCCCC-------EEEeecCCCCCC--c----chhhHHHHHHHHhcce
Confidence 457999997533 468889888877 3 4789999999776543
No 142
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=25.54 E-value=12 Score=35.91 Aligned_cols=32 Identities=25% Similarity=0.442 Sum_probs=24.0
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccCc
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQK 50 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~ 50 (511)
.-||.||--=. ..-+|.-||.+-..+++.|.+
T Consensus 94 ~~CP~CGh~k~--a~~LC~~Cy~kV~ket~ei~~ 125 (176)
T KOG4080|consen 94 NTCPACGHIKP--AHTLCDYCYAKVHKETSEIKK 125 (176)
T ss_pred ccCcccCcccc--ccccHHHHHHHHHHHHHHHHH
Confidence 35999997422 256999999998887775644
No 143
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=25.52 E-value=52 Score=32.30 Aligned_cols=39 Identities=15% Similarity=0.294 Sum_probs=21.7
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCce
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCY 63 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry 63 (511)
+-||.||.+.. ..||.-- ..+-+..| -+....|++||--
T Consensus 1 ~~Cp~C~~~~~---~~~~~~~---~IP~F~ev--ii~sf~C~~CGyr 39 (192)
T TIGR00310 1 IDCPSCGGECE---TVMKTVN---DIPYFGEV--LETSTICEHCGYR 39 (192)
T ss_pred CcCCCCCCCCE---EEEEEEc---CCCCcceE--EEEEEECCCCCCc
Confidence 35999998643 5566211 02222211 2456789999954
No 144
>TIGR02276 beta_rpt_yvtn 40-residue YVTN family beta-propeller repeat. This repeat of about 40 amino acids is found in up to 14 copies per protein. Archaea Methanosarcina mazei and Methanosarcina acetivorans each have over 10 genes that encode tandem copies of this repeat, which is also found in other species. PSIPRED predicts with high confidence that each 40-residue repeats contains four beta strands. This model overlaps somewhat with the NHL repeat (Pfam pfam01436) and also shows sequence similarity to the WD domain, G-beta repeat (Pfam pfam00400).
Probab=25.12 E-value=1e+02 Score=21.24 Aligned_cols=23 Identities=17% Similarity=0.244 Sum_probs=18.3
Q ss_pred CEEEEEEeCCeEEEEcCCCCeEE
Q 010400 272 PLVICMKVTNSIALLDPFTLRHC 294 (511)
Q Consensus 272 ~~~lv~kv~~~I~llDP~T~~~~ 294 (511)
.+.++.+.+++|.++|+.|++..
T Consensus 5 ~lyv~~~~~~~v~~id~~~~~~~ 27 (42)
T TIGR02276 5 KLYVTNSGSNTVSVIDTATNKVI 27 (42)
T ss_pred EEEEEeCCCCEEEEEECCCCeEE
Confidence 46666777889999999988753
No 145
>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=24.82 E-value=56 Score=35.53 Aligned_cols=15 Identities=27% Similarity=0.569 Sum_probs=12.2
Q ss_pred EEEeCCCCCceecCC
Q 010400 53 IISHCPECDCYLQPP 67 (511)
Q Consensus 53 ~v~~C~~Cgry~~~p 67 (511)
+.-.|++||+.++..
T Consensus 32 ~~a~CpRCg~~L~~~ 46 (403)
T TIGR00155 32 QKAACPRCGTTLTVG 46 (403)
T ss_pred CeeECCCCCCCCcCC
Confidence 356799999999874
No 146
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=24.80 E-value=25 Score=23.12 Aligned_cols=13 Identities=31% Similarity=0.889 Sum_probs=9.7
Q ss_pred EEeCCCCCceecC
Q 010400 54 ISHCPECDCYLQP 66 (511)
Q Consensus 54 v~~C~~Cgry~~~ 66 (511)
+..|+.|||.+.+
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 3568889988854
No 147
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=24.78 E-value=45 Score=31.69 Aligned_cols=38 Identities=16% Similarity=0.431 Sum_probs=17.1
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCce
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCY 63 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry 63 (511)
..||.||.+.. ..|| ....+-+..| -+....|++||--
T Consensus 2 s~Cp~C~~~~~---~~~~----~~~IP~F~ev--ii~sf~C~~CGyk 39 (161)
T PF03367_consen 2 SLCPNCGENGT---TRIL----LTDIPYFKEV--IIMSFECEHCGYK 39 (161)
T ss_dssp EE-TTTSSCCE---EEEE----EEEETTTEEE--EEEEEE-TTT--E
T ss_pred CcCCCCCCCcE---EEEE----EEcCCCCceE--EEEEeECCCCCCE
Confidence 47999998743 3331 1222222211 2445689999954
No 148
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.59 E-value=84 Score=27.32 Aligned_cols=22 Identities=14% Similarity=0.326 Sum_probs=18.3
Q ss_pred EEEEeCCCCCceecCCCceeeCC
Q 010400 52 VIISHCPECDCYLQPPRTWIKAQ 74 (511)
Q Consensus 52 ~~v~~C~~Cgry~~~p~~Wv~~~ 74 (511)
.-|-.|+.||.-+-+ +.|....
T Consensus 51 ~GIW~C~kCg~~fAG-gay~P~t 72 (89)
T COG1997 51 TGIWKCRKCGAKFAG-GAYTPVT 72 (89)
T ss_pred cCeEEcCCCCCeecc-ccccccc
Confidence 457899999999998 5888765
No 149
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=24.21 E-value=30 Score=27.01 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=8.9
Q ss_pred cceecccccCcc
Q 010400 14 VGSVLCCKCGIP 25 (511)
Q Consensus 14 ~~~i~C~~CG~~ 25 (511)
.-..+||+||--
T Consensus 17 rk~~~CPrCG~g 28 (51)
T COG1998 17 RKNRFCPRCGPG 28 (51)
T ss_pred EccccCCCCCCc
Confidence 445799999953
No 150
>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=24.04 E-value=40 Score=30.17 Aligned_cols=15 Identities=20% Similarity=0.452 Sum_probs=9.5
Q ss_pred cceecccccCcccCC
Q 010400 14 VGSVLCCKCGIPMAP 28 (511)
Q Consensus 14 ~~~i~C~~CG~~i~~ 28 (511)
.+...|..||...++
T Consensus 68 p~~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 68 PVECECEDCSEEVSP 82 (115)
T ss_pred CcEEEcccCCCEEec
Confidence 345668888866543
No 151
>PF02478 Pneumo_phosprot: Pneumovirus phosphoprotein; InterPro: IPR003487 This family represents a phosphoprotein from Paramyxoviridae, which could be a putative RNA polymerase alpha subunit that may function in template binding [].; GO: 0003968 RNA-directed RNA polymerase activity
Probab=23.62 E-value=38 Score=34.50 Aligned_cols=61 Identities=20% Similarity=0.319 Sum_probs=45.7
Q ss_pred CCceeEEEcChhHHHHHHHHhcccCCeEEeecCceeeecCCCCeeeEEEEEEEEEcccCCCCEEEcC
Q 010400 194 DQGIDFFFGNRSHAVKFVEFVGKVAPVRSRHDKQLVSHDPKSNNFNYKYTFSVEISPICREDLICLP 260 (511)
Q Consensus 194 kdGlDfyf~s~~~Ark~v~fl~s~~p~~vkeS~kLVg~D~~~g~~~yr~T~SVrIppickgDlV~l~ 260 (511)
.+|.|+.|.-..+|++--.|+.+.-+..-+.++.++|. +.++ ..=+|.||++|+---+-.|
T Consensus 1 ~E~~~~~f~G~eA~k~Ae~f~~s~k~~s~kr~qsI~ge--~v~t----vset~~LPti~kpak~T~p 61 (279)
T PF02478_consen 1 PEGKDILFMGEEAAKRAEAFQKSLKNPSHKRTQSIVGE--KVNT----VSETVELPTISKPAKLTTP 61 (279)
T ss_pred CCCcchhhcchHHHHHHHHHHHHhcccCcCccccCCCC--cchh----hhhcccCCCCccccccCCC
Confidence 47899999888777777779988877777777878885 3333 6678999999986644443
No 152
>PF14279 HNH_5: HNH endonuclease
Probab=23.59 E-value=28 Score=28.80 Aligned_cols=47 Identities=23% Similarity=0.425 Sum_probs=26.9
Q ss_pred ccccCcccCCCCcccchhhhccccccccccCceEEEE-eCCCCCceecCCCceeeCCc
Q 010400 19 CCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIIS-HCPECDCYLQPPRTWIKAQL 75 (511)
Q Consensus 19 C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~-~C~~Cgry~~~p~~Wv~~~l 75 (511)
|..|+.+.++.... .++=|-+.|--...+. +|..|+.++- ++++..+
T Consensus 1 Ci~C~~~~~~~~~s-------~EHIIP~sLGG~~~~~~vC~~CN~~~g---~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFS-------EEHIIPESLGGKLKINNVCDKCNNKFG---SKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCC-------ccccCchhcCCcccccchhHHHhHHHh---HHHHHHH
Confidence 78888876542111 2333333232232222 9999999984 5777765
No 153
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=23.07 E-value=99 Score=28.10 Aligned_cols=60 Identities=12% Similarity=0.020 Sum_probs=34.1
Q ss_pred EEEEcccCCCCEEEcCchhhhhcCCCCCEEEEEEeCCeEEEEcCCCCeEEEecCccccccccccc
Q 010400 245 SVEISPICREDLICLPPKVAVSLGNLGPLVICMKVTNSIALLDPFTLRHCFLDADQYWRSSFKSL 309 (511)
Q Consensus 245 SVrIppickgDlV~l~~k~a~~lG~i~~~~lv~kv~~~I~llDP~T~~~~~l~~~~yw~~pf~~l 309 (511)
+|..-.+.+||||++.... =+.++.+.|..-.+..||-. .+...+.-....||+.-|...
T Consensus 71 ~v~~~~~qpGDlvff~~~~---~~~~~HvGIy~G~g~~iHa~--~~~~v~~~~~~~yw~~r~~~a 130 (134)
T TIGR02219 71 PVPCDAAQPGDVLVFRWRP---GAAAKHAAIAASPTRFIHAY--DGAAVVESALVPWWRRRLAGA 130 (134)
T ss_pred ccchhcCCCCCEEEEeeCC---CCCCcEEEEEeCCCcEEEEC--CCCCEEEeCCcHHHHHHhhhe
Confidence 3444468999999996310 01245666666444455543 233334444469998877543
No 154
>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=23.00 E-value=31 Score=32.41 Aligned_cols=15 Identities=27% Similarity=0.780 Sum_probs=11.1
Q ss_pred ccceecccccCcccC
Q 010400 13 TVGSVLCCKCGIPMA 27 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~ 27 (511)
..++..|-.||..+.
T Consensus 109 g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE 123 (146)
T ss_pred cCceEecccCCCEEE
Confidence 466778999998754
No 155
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=22.69 E-value=41 Score=29.44 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=18.0
Q ss_pred eecccccCcccCCCCcccchhhhcc
Q 010400 16 SVLCCKCGIPMAPNAANMCVACLRS 40 (511)
Q Consensus 16 ~i~C~~CG~~i~~~~~~mC~~C~~~ 40 (511)
...|-.||-|+. +.+|..|...
T Consensus 80 ~~~C~~CG~pss---~~iC~~C~l~ 101 (104)
T TIGR00269 80 LRRCERCGEPTS---GRICKACKFL 101 (104)
T ss_pred CCcCCcCcCcCC---ccccHhhhhh
Confidence 457999999877 7899999753
No 156
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=22.65 E-value=36 Score=24.10 Aligned_cols=10 Identities=50% Similarity=1.158 Sum_probs=6.4
Q ss_pred ecccccCccc
Q 010400 17 VLCCKCGIPM 26 (511)
Q Consensus 17 i~C~~CG~~i 26 (511)
-+||+||.-+
T Consensus 2 hlcpkcgvgv 11 (36)
T PF09151_consen 2 HLCPKCGVGV 11 (36)
T ss_dssp -B-TTTSSSB
T ss_pred ccCCccCceE
Confidence 3799999864
No 157
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.61 E-value=79 Score=33.26 Aligned_cols=54 Identities=19% Similarity=0.365 Sum_probs=30.7
Q ss_pred ccchhhhcccccccc-ccC-----ceEEEEeCCCCCceecCC--CceeeCCcChHHHHHHHHH
Q 010400 32 NMCVACLRSEVDITE-GLQ-----KHVIISHCPECDCYLQPP--RTWIKAQLESKELLTFCVK 86 (511)
Q Consensus 32 ~mC~~C~~~~~dI~e-gIp-----~~~~v~~C~~Cgry~~~p--~~Wv~~~les~ELL~~~Lk 86 (511)
..|+.|--+. +|.- .+. ..+.+..|..|++|+.-- .++-..++..++|-++.|.
T Consensus 225 ~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~~~adDlaSL~LD 286 (305)
T TIGR01562 225 VKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQEKDPHADAVADDLASLALD 286 (305)
T ss_pred ccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchhhhccccCCccCchHHHHhhhHhh
Confidence 4688886543 3421 122 248899999999998531 1233333344555555443
No 158
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=22.58 E-value=51 Score=32.49 Aligned_cols=22 Identities=27% Similarity=0.988 Sum_probs=13.6
Q ss_pred cccccCcccCCCCcccchhhhcccc
Q 010400 18 LCCKCGIPMAPNAANMCVACLRSEV 42 (511)
Q Consensus 18 ~C~~CG~~i~~~~~~mC~~C~~~~~ 42 (511)
.| +||.+.+ .+ ..|..|-+.+.
T Consensus 2 ~C-rCG~~l~-~p-~~Cl~Cg~~~a 23 (227)
T COG4031 2 IC-RCGAELS-SP-AFCLNCGRRHA 23 (227)
T ss_pred cc-ccCCccc-cc-chhcccCCcce
Confidence 45 7887765 23 56777766643
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=22.48 E-value=30 Score=31.27 Aligned_cols=15 Identities=27% Similarity=0.483 Sum_probs=11.6
Q ss_pred ccceecccccCcccC
Q 010400 13 TVGSVLCCKCGIPMA 27 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~ 27 (511)
....+.||.||+++.
T Consensus 66 kav~V~CP~C~K~TK 80 (114)
T PF11023_consen 66 KAVQVECPNCGKQTK 80 (114)
T ss_pred cceeeECCCCCChHh
Confidence 355678999999865
No 160
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.46 E-value=56 Score=39.79 Aligned_cols=56 Identities=21% Similarity=0.507 Sum_probs=37.7
Q ss_pred CccceecccccCcccCCCCc------------ccchhhhccccccccccCceEEEEeCCCCCceec--CCCceeeCCc
Q 010400 12 QTVGSVLCCKCGIPMAPNAA------------NMCVACLRSEVDITEGLQKHVIISHCPECDCYLQ--PPRTWIKAQL 75 (511)
Q Consensus 12 ~~~~~i~C~~CG~~i~~~~~------------~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~--~p~~Wv~~~l 75 (511)
+....-.|-.||-.+.-..+ -+|..|| +++.-|| -..||.|+-.+. +|.-|+..+.
T Consensus 13 ~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY--EYEr~eG------~q~CPqCktrYkr~kgsprv~gDe 82 (1079)
T PLN02638 13 KHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY--EYERKDG------NQSCPQCKTKYKRHKGSPAILGDE 82 (1079)
T ss_pred cccCCceeeecccccCcCCCCCEEEEeccCCCccccchh--hhhhhcC------CccCCccCCchhhhcCCCCcCccc
Confidence 34444579999988654322 2899999 7777774 357999986543 3345888863
No 161
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.37 E-value=87 Score=36.82 Aligned_cols=12 Identities=33% Similarity=0.722 Sum_probs=7.9
Q ss_pred ceecccccCccc
Q 010400 15 GSVLCCKCGIPM 26 (511)
Q Consensus 15 ~~i~C~~CG~~i 26 (511)
+.+.|..||-..
T Consensus 434 ~~l~C~~Cg~v~ 445 (730)
T COG1198 434 PLLLCRDCGYIA 445 (730)
T ss_pred ceeecccCCCcc
Confidence 356788888653
No 162
>PRK11827 hypothetical protein; Provisional
Probab=22.29 E-value=45 Score=26.89 Aligned_cols=32 Identities=16% Similarity=0.336 Sum_probs=18.0
Q ss_pred ecccccCcccCCC---CcccchhhhccccccccccC
Q 010400 17 VLCCKCGIPMAPN---AANMCVACLRSEVDITEGLQ 49 (511)
Q Consensus 17 i~C~~CG~~i~~~---~~~mC~~C~~~~~dI~egIp 49 (511)
.-||.|+.+..-. ..-.|..| .-.++|-+|||
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~-~laYPI~dgIP 43 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLD-NLAFPLRDGIP 43 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCcc-CeeccccCCcc
Confidence 4599998875422 12345555 34455555555
No 163
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=22.21 E-value=25 Score=36.33 Aligned_cols=56 Identities=23% Similarity=0.533 Sum_probs=38.6
Q ss_pred eecccccCcccC--C--------------CCcccchhhhccccccccccCceEEE----EeCCCCCceecCCCceeeCC
Q 010400 16 SVLCCKCGIPMA--P--------------NAANMCVACLRSEVDITEGLQKHVII----SHCPECDCYLQPPRTWIKAQ 74 (511)
Q Consensus 16 ~i~C~~CG~~i~--~--------------~~~~mC~~C~~~~~dI~egIp~~~~v----~~C~~Cgry~~~p~~Wv~~~ 74 (511)
.--|+.||+.-. . -.+.-|..|=+..+.+-. +.-.+.. -.|..||.-|.+| |.--+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpA-LkMHirTH~l~c~C~iCGKaFSRP--WLLQG 205 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPA-LKMHIRTHTLPCECGICGKAFSRP--WLLQG 205 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHH-HhhHhhccCCCcccccccccccch--HHhhc
Confidence 346999999632 1 134689999888887766 5444443 3599999999887 85443
No 164
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=22.20 E-value=1e+02 Score=28.46 Aligned_cols=29 Identities=17% Similarity=0.014 Sum_probs=26.0
Q ss_pred CEEEEEEeCCeEEEEcCCCCeEEEecCcc
Q 010400 272 PLVICMKVTNSIALLDPFTLRHCFLDADQ 300 (511)
Q Consensus 272 ~~~lv~kv~~~I~llDP~T~~~~~l~~~~ 300 (511)
++.+.+..++.++|||++|+...+|+.+.
T Consensus 71 ~~q~lY~dg~~~~FMD~etyeq~~v~~~~ 99 (131)
T COG0231 71 TAQYLYIDGDFYVFMDLETYEQYELPKDQ 99 (131)
T ss_pred eEEEEEcCCCeEEEccCCCceEEEecchh
Confidence 55778888999999999999999999875
No 165
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.19 E-value=30 Score=32.14 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=10.6
Q ss_pred EeCCCCCceecC
Q 010400 55 SHCPECDCYLQP 66 (511)
Q Consensus 55 ~~C~~Cgry~~~ 66 (511)
..||.||.-+..
T Consensus 124 f~Cp~Cg~~l~~ 135 (147)
T smart00531 124 FTCPRCGEELEE 135 (147)
T ss_pred EECCCCCCEEEE
Confidence 899999998865
No 166
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=22.17 E-value=55 Score=32.08 Aligned_cols=64 Identities=20% Similarity=0.464 Sum_probs=35.9
Q ss_pred ccCccceecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecCCCceeeCCcChHHHHHHHHHHhc
Q 010400 10 VPQTVGSVLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQPPRTWIKAQLESKELLTFCVKRLK 89 (511)
Q Consensus 10 ~~~~~~~i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~p~~Wv~~~les~ELL~~~Lkki~ 89 (511)
.+.+.....|..||...... .+. ..++ ...+..|+.||..+.|.=.|..-.++.. +..+.+.+.
T Consensus 103 lHG~~~~~~C~~C~~~~~~~--~~~-----------~~~~-~~~~p~C~~Cg~~lrP~Vv~fgE~~p~~--~~~a~~~~~ 166 (218)
T cd01407 103 LHGSLFRVRCTKCGKEYPRD--ELQ-----------ADID-REEVPRCPKCGGLLRPDVVFFGESLPEE--LDEAAEALA 166 (218)
T ss_pred CcCCcCcceeCCCcCCCcHH--HHh-----------Hhhc-cCCCCcCCCCCCccCCCeEECCCCCcHH--HHHHHHHHh
Confidence 33466677788888764321 000 1011 1235569999999998544555444333 555666543
No 167
>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=22.15 E-value=32 Score=24.57 Aligned_cols=12 Identities=50% Similarity=1.168 Sum_probs=8.5
Q ss_pred EeCCCCCceecC
Q 010400 55 SHCPECDCYLQP 66 (511)
Q Consensus 55 ~~C~~Cgry~~~ 66 (511)
.|||.||..|++
T Consensus 2 ~FCp~C~nlL~p 13 (35)
T PF02150_consen 2 RFCPECGNLLYP 13 (35)
T ss_dssp -BETTTTSBEEE
T ss_pred eeCCCCCccceE
Confidence 578888887765
No 168
>PRK03954 ribonuclease P protein component 4; Validated
Probab=22.08 E-value=16 Score=33.31 Aligned_cols=21 Identities=24% Similarity=0.531 Sum_probs=19.2
Q ss_pred ccCceEEEEeCCCCCceecCC
Q 010400 47 GLQKHVIISHCPECDCYLQPP 67 (511)
Q Consensus 47 gIp~~~~v~~C~~Cgry~~~p 67 (511)
.+|+++.-.+|+.|.++|.||
T Consensus 57 rlp~~~KR~~CK~C~t~LiPG 77 (121)
T PRK03954 57 KLPRKWKRRYCKRCHSFLVPG 77 (121)
T ss_pred CCCHHHHHHHhhcCCCeeecC
Confidence 389999999999999999995
No 169
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=21.92 E-value=2.3e+02 Score=27.45 Aligned_cols=81 Identities=17% Similarity=0.197 Sum_probs=50.0
Q ss_pred CeeeEEEEEEEEEcccCCCCEEEcCchhhhhcCCCCCEEEEEEeCC------eEEEEcCCCCeEEEecCccccccccccc
Q 010400 236 NNFNYKYTFSVEISPICREDLICLPPKVAVSLGNLGPLVICMKVTN------SIALLDPFTLRHCFLDADQYWRSSFKSL 309 (511)
Q Consensus 236 g~~~yr~T~SVrIppickgDlV~l~~k~a~~lG~i~~~~lv~kv~~------~I~llDP~T~~~~~l~~~~yw~~pf~~l 309 (511)
|...-..||.+..-.+++|+.|.+.++..+... +-+++.++ .|.=+|.+|++..+...+.-- +-.-|+
T Consensus 13 ~~~gas~t~p~q~~~LkkG~yvvIkGrPCKIve-----istSKtGKHGhAK~~ivaidIFTgkK~edi~Ps~h-nv~VP~ 86 (166)
T PTZ00328 13 GGDNASKTYPLPAGALKKGGYVCINGRPCKVID-----LSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTH-NVEVPF 86 (166)
T ss_pred CCCCCCceecccccceeECCEEEECCeeeEEEE-----EecCCCCcCCceEEEEEEEecCCCCEEeeecCccc-eeEeee
Confidence 444456799999999999999999987764321 11122221 266789999998777654311 001111
Q ss_pred cCccceeEEEEEEeee
Q 010400 310 LTSRQLVEYIVLDVEV 325 (511)
Q Consensus 310 ~~~~~l~ef~Vldve~ 325 (511)
. .-.+|-||||+.
T Consensus 87 V---~r~~yqli~I~~ 99 (166)
T PTZ00328 87 V---KTFTYSVLDIQP 99 (166)
T ss_pred E---EeeEEEEEEEcC
Confidence 1 123688888865
No 170
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.74 E-value=60 Score=25.47 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=8.6
Q ss_pred EEeCCCCCce
Q 010400 54 ISHCPECDCY 63 (511)
Q Consensus 54 v~~C~~Cgry 63 (511)
..+|+.||.+
T Consensus 44 ~y~C~~Cg~~ 53 (54)
T PF10058_consen 44 QYRCPYCGAL 53 (54)
T ss_pred EEEcCCCCCc
Confidence 8899999864
No 171
>PRK01343 zinc-binding protein; Provisional
Probab=21.49 E-value=69 Score=25.68 Aligned_cols=15 Identities=27% Similarity=0.549 Sum_probs=11.7
Q ss_pred ccceecccccCcccC
Q 010400 13 TVGSVLCCKCGIPMA 27 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~ 27 (511)
....+.||.||++..
T Consensus 6 ~~p~~~CP~C~k~~~ 20 (57)
T PRK01343 6 LRPTRPCPECGKPST 20 (57)
T ss_pred CCCCCcCCCCCCcCc
Confidence 346688999999865
No 172
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=21.34 E-value=34 Score=33.99 Aligned_cols=36 Identities=22% Similarity=0.626 Sum_probs=25.5
Q ss_pred ecccccCcccCCCCcccchhhhccccccccccCceEEEEeCCCCCceecC
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEVDITEGLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~ 66 (511)
+.|..||++.+.+... +. + ..+.+..||.|.+.-.+
T Consensus 1 mvCIeCg~~vdsLyt~---------ys-t----s~iqls~Cp~C~~~~Dk 36 (239)
T COG5254 1 MVCIECGSRVDSLYTR---------YS-T----SAIQLSRCPSCNRKMDK 36 (239)
T ss_pred CeeeEcCCccceeeee---------cc-C----cceehhcCchHHHHHHH
Confidence 4699999998865431 11 2 46788999999987643
No 173
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=21.12 E-value=47 Score=37.91 Aligned_cols=26 Identities=27% Similarity=0.639 Sum_probs=22.8
Q ss_pred ecccccCcccCCCCcccchhhhcccc
Q 010400 17 VLCCKCGIPMAPNAANMCVACLRSEV 42 (511)
Q Consensus 17 i~C~~CG~~i~~~~~~mC~~C~~~~~ 42 (511)
..|..||..+.++..++|.+|.++..
T Consensus 81 ~~c~~cG~~~~~~~~~lc~~c~~~~~ 106 (715)
T COG1107 81 LTCDICGDIIVPWEEGLCPECRRKPK 106 (715)
T ss_pred EeeccccceecCcccccChhHhhCCc
Confidence 56999999998888889999999877
No 174
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.94 E-value=36 Score=31.44 Aligned_cols=28 Identities=14% Similarity=0.165 Sum_probs=15.2
Q ss_pred cchhhhccccccccccCceEEEEeCCCCCceecC
Q 010400 33 MCVACLRSEVDITEGLQKHVIISHCPECDCYLQP 66 (511)
Q Consensus 33 mC~~C~~~~~dI~egIp~~~~v~~C~~Cgry~~~ 66 (511)
+|+.|-.+-++|.. .-.+||+||..+.+
T Consensus 11 ~Cp~cg~kFYDLnk------~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 11 ICPNTGSKFYDLNR------RPAVSPYTGEQFPP 38 (129)
T ss_pred cCCCcCccccccCC------CCccCCCcCCccCc
Confidence 34444444455554 23578888877543
No 175
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=20.68 E-value=39 Score=26.85 Aligned_cols=26 Identities=23% Similarity=0.516 Sum_probs=17.1
Q ss_pred ccceecccccCcccCCCCcccchhhh
Q 010400 13 TVGSVLCCKCGIPMAPNAANMCVACL 38 (511)
Q Consensus 13 ~~~~i~C~~CG~~i~~~~~~mC~~C~ 38 (511)
....++|.+||+..--.--..|..|=
T Consensus 12 ~ktH~~CrRCG~~syH~qK~~CasCG 37 (55)
T PF01907_consen 12 NKTHTLCRRCGRRSYHIQKKTCASCG 37 (55)
T ss_dssp S-SEEE-TTTSSEEEETTTTEETTTB
T ss_pred CccEeeecccCCeeeecCCCcccccC
Confidence 44668999999975444457788773
No 176
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=20.10 E-value=1.4e+02 Score=23.72 Aligned_cols=29 Identities=14% Similarity=0.126 Sum_probs=24.2
Q ss_pred EEEEEEeCCeEEEEcCCCCeEEEecCccc
Q 010400 273 LVICMKVTNSIALLDPFTLRHCFLDADQY 301 (511)
Q Consensus 273 ~~lv~kv~~~I~llDP~T~~~~~l~~~~y 301 (511)
.....+.+...++||+.|+..+.|+.+..
T Consensus 5 ~qylY~dg~~~~FMd~etyeQ~~i~~~~i 33 (61)
T cd04470 5 MQYLYKDGDNYVFMDTETYEQIELPKEAL 33 (61)
T ss_pred EEEEEeCCCEEEEeCCCCceEEEECHHHh
Confidence 44567778899999999999999998754
No 177
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.10 E-value=55 Score=29.30 Aligned_cols=12 Identities=17% Similarity=0.340 Sum_probs=7.3
Q ss_pred cceecccccCcc
Q 010400 14 VGSVLCCKCGIP 25 (511)
Q Consensus 14 ~~~i~C~~CG~~ 25 (511)
.+...|..||..
T Consensus 68 p~~~~C~~Cg~~ 79 (114)
T PRK03681 68 EAECWCETCQQY 79 (114)
T ss_pred CcEEEcccCCCe
Confidence 344567777754
No 178
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.09 E-value=46 Score=31.47 Aligned_cols=28 Identities=7% Similarity=0.029 Sum_probs=16.5
Q ss_pred cccccceeecCCceeEEEcChhHHHHHHHHhcc
Q 010400 184 AARAIRITQMDQGIDFFFGNRSHAVKFVEFVGK 216 (511)
Q Consensus 184 ~~~i~~I~e~kdGlDfyf~s~~~Ark~v~fl~s 216 (511)
...+++|+.-. ...+...+.++++++.-
T Consensus 96 ~s~IsriE~G~-----~~Ps~~~l~kLa~~Lgv 123 (154)
T TIGR00270 96 ESLIKKIENAE-----IEPEPKVVEKLEKLLKI 123 (154)
T ss_pred HHHHHHHHCCC-----CCCCHHHHHHHHHHhCC
Confidence 34555555322 34566778888887743
Done!