Query psy271
Match_columns 191
No_of_seqs 210 out of 1911
Neff 8.7
Searched_HMMs 46136
Date Fri Aug 16 23:14:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy271.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/271hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812|consensus 99.9 2.8E-24 6.1E-29 180.3 6.3 108 65-173 234-357 (384)
2 KOG1814|consensus 99.9 9.6E-23 2.1E-27 166.9 3.9 148 18-170 230-416 (445)
3 KOG1815|consensus 99.8 2.2E-21 4.7E-26 166.5 6.5 150 23-175 119-283 (444)
4 COG1157 FliI Flagellar biosynt 99.6 2.3E-16 4.9E-21 131.2 6.6 100 2-101 64-164 (441)
5 KOG0006|consensus 99.6 5.2E-16 1.1E-20 123.9 4.8 118 37-159 292-437 (446)
6 TIGR03324 alt_F1F0_F1_al alter 99.5 5.9E-15 1.3E-19 126.7 6.0 102 1-102 62-164 (497)
7 CHL00059 atpA ATP synthase CF1 99.5 1.1E-14 2.4E-19 124.5 6.5 101 1-101 41-142 (485)
8 PRK13343 F0F1 ATP synthase sub 99.5 1.1E-14 2.4E-19 125.4 5.9 101 1-101 62-163 (502)
9 PRK07165 F0F1 ATP synthase sub 99.5 1.2E-14 2.7E-19 124.7 5.8 102 1-102 38-145 (507)
10 TIGR01040 V-ATPase_V1_B V-type 99.5 1.3E-14 2.9E-19 123.3 5.6 101 2-102 41-143 (466)
11 PRK04196 V-type ATP synthase s 99.5 2.3E-14 5E-19 122.9 6.3 101 1-101 42-144 (460)
12 PRK08972 fliI flagellum-specif 99.5 2.7E-14 5.8E-19 121.2 6.3 94 2-95 63-156 (444)
13 PRK09281 F0F1 ATP synthase sub 99.5 2.4E-14 5.1E-19 123.8 5.9 102 1-102 62-164 (502)
14 TIGR03305 alt_F1F0_F1_bet alte 99.5 3.1E-14 6.7E-19 121.3 6.3 99 2-100 38-138 (449)
15 PTZ00185 ATPase alpha subunit; 99.5 2.9E-14 6.3E-19 122.2 5.9 101 1-101 81-190 (574)
16 PRK06936 type III secretion sy 99.5 2.2E-14 4.9E-19 121.9 5.2 94 2-95 63-156 (439)
17 PRK07960 fliI flagellum-specif 99.5 2.7E-14 5.9E-19 121.5 5.5 94 2-95 69-169 (455)
18 TIGR00962 atpA proton transloc 99.5 3.3E-14 7.2E-19 122.9 5.8 101 1-101 61-162 (501)
19 PRK05922 type III secretion sy 99.5 4.7E-14 1E-18 119.9 6.1 94 2-95 58-151 (434)
20 TIGR01041 ATP_syn_B_arch ATP s 99.5 4.7E-14 1E-18 120.8 6.0 100 1-100 40-141 (458)
21 PRK09099 type III secretion sy 99.5 4.7E-14 1E-18 120.3 5.8 94 2-95 64-157 (441)
22 PRK05688 fliI flagellum-specif 99.5 3.8E-14 8.3E-19 120.8 5.2 94 2-95 69-162 (451)
23 PRK02118 V-type ATP synthase s 99.5 5E-14 1.1E-18 119.4 5.7 99 2-101 42-141 (436)
24 PRK07196 fliI flagellum-specif 99.5 5.1E-14 1.1E-18 119.7 5.5 94 2-95 56-149 (434)
25 CHL00060 atpB ATP synthase CF1 99.5 6.5E-14 1.4E-18 120.2 6.0 100 2-101 61-162 (494)
26 PRK08927 fliI flagellum-specif 99.5 6.1E-14 1.3E-18 119.3 5.5 98 2-99 58-157 (442)
27 PRK09280 F0F1 ATP synthase sub 99.5 6.7E-14 1.5E-18 119.6 5.6 100 2-101 44-145 (463)
28 TIGR01039 atpD ATP synthase, F 99.4 9.4E-14 2E-18 118.4 5.8 99 2-100 43-143 (461)
29 TIGR03498 FliI_clade3 flagella 99.4 1.2E-13 2.5E-18 117.3 5.5 94 1-94 39-133 (418)
30 TIGR02546 III_secr_ATP type II 99.4 1.6E-13 3.4E-18 117.1 5.6 94 2-95 44-139 (422)
31 PRK12597 F0F1 ATP synthase sub 99.4 1.8E-13 3.8E-18 117.3 5.9 99 2-100 43-143 (461)
32 PRK08472 fliI flagellum-specif 99.4 1.3E-13 2.9E-18 117.2 4.9 94 2-95 58-151 (434)
33 PRK06820 type III secretion sy 99.4 2.6E-13 5.6E-18 115.6 6.0 97 2-99 65-162 (440)
34 COG0056 AtpA F0F1-type ATP syn 99.4 1.9E-13 4.1E-18 114.4 4.9 94 1-94 62-155 (504)
35 TIGR03496 FliI_clade1 flagella 99.4 2.3E-13 4.9E-18 115.5 5.2 94 2-95 38-131 (411)
36 PRK07721 fliI flagellum-specif 99.4 3.2E-13 6.9E-18 115.5 6.0 94 2-95 59-152 (438)
37 TIGR03497 FliI_clade2 flagella 99.4 2.2E-13 4.9E-18 115.6 5.0 94 2-95 38-131 (413)
38 TIGR01026 fliI_yscN ATPase Fli 99.4 4.4E-13 9.5E-18 114.7 6.5 94 2-95 63-157 (440)
39 PRK06315 type III secretion sy 99.4 2.3E-13 4.9E-18 116.1 4.7 94 2-95 62-158 (442)
40 PRK07594 type III secretion sy 99.4 7.6E-13 1.6E-17 112.6 6.2 93 2-95 57-149 (433)
41 PRK06793 fliI flagellum-specif 99.3 1.5E-12 3.3E-17 110.7 6.2 93 2-94 57-149 (432)
42 PRK08149 ATP synthase SpaL; Va 99.3 2.5E-12 5.5E-17 109.3 5.9 94 2-95 48-145 (428)
43 TIGR01043 ATP_syn_A_arch ATP s 99.3 5.4E-12 1.2E-16 110.0 6.5 56 2-57 37-92 (578)
44 PRK06002 fliI flagellum-specif 99.3 4.5E-12 9.7E-17 108.1 5.7 93 2-95 66-159 (450)
45 TIGR01042 V-ATPase_V1_A V-type 99.2 9.1E-12 2E-16 108.3 5.6 56 2-57 38-93 (591)
46 PRK04192 V-type ATP synthase s 99.2 4.7E-11 1E-15 104.3 6.1 57 2-58 40-96 (586)
47 COG1156 NtpB Archaeal/vacuolar 99.1 9.6E-11 2.1E-15 97.3 5.9 98 2-99 46-144 (463)
48 COG0055 AtpD F0F1-type ATP syn 99.0 2.9E-10 6.3E-15 93.8 4.1 91 3-93 47-139 (468)
49 KOG1350|consensus 98.8 1.8E-09 4E-14 87.6 3.4 90 3-92 93-182 (521)
50 KOG1351|consensus 98.8 5.8E-09 1.3E-13 83.9 4.8 94 2-95 63-157 (489)
51 smart00647 IBR In Between Ring 98.7 1.2E-08 2.7E-13 64.3 4.2 47 112-158 7-59 (64)
52 PRK14698 V-type ATP synthase s 98.7 1.9E-08 4.1E-13 93.6 4.6 56 2-57 40-95 (1017)
53 PF01485 IBR: IBR domain; Int 98.6 2.1E-08 4.6E-13 63.2 1.8 39 120-158 17-59 (64)
54 cd01135 V_A-ATPase_B V/A-type 98.5 3.7E-08 8.1E-13 79.3 1.9 69 33-101 1-70 (276)
55 cd01133 F1-ATPase_beta F1 ATP 98.5 7.7E-08 1.7E-12 77.6 2.1 68 33-100 1-69 (274)
56 COG1155 NtpA Archaeal/vacuolar 98.5 1.8E-07 4E-12 80.2 4.4 56 2-57 38-93 (588)
57 KOG1353|consensus 98.4 2.1E-07 4.6E-12 73.4 3.6 84 2-93 56-139 (340)
58 cd01132 F1_ATPase_alpha F1 ATP 98.4 1.3E-07 2.8E-12 76.3 1.6 68 34-101 2-70 (274)
59 KOG1352|consensus 98.3 4.6E-07 1E-11 75.6 2.5 76 2-78 57-132 (618)
60 cd01136 ATPase_flagellum-secre 97.9 2.5E-06 5.4E-11 70.7 0.7 63 33-95 1-63 (326)
61 PF02874 ATP-synt_ab_N: ATP sy 97.5 0.00014 3.1E-09 46.3 3.4 31 1-31 39-69 (69)
62 PF01485 IBR: IBR domain; Int 97.4 0.0001 2.2E-09 46.0 2.5 37 61-97 15-64 (64)
63 smart00647 IBR In Between Ring 97.2 0.00025 5.5E-09 44.3 2.4 36 62-97 16-64 (64)
64 PF10571 UPF0547: Uncharacteri 96.6 0.001 2.2E-08 34.1 1.1 24 122-149 1-24 (26)
65 COG0056 AtpA F0F1-type ATP syn 96.1 0.0033 7.2E-08 53.7 2.0 35 157-191 114-148 (504)
66 PRK12608 transcription termina 95.7 0.007 1.5E-07 51.2 2.3 70 18-94 56-126 (380)
67 PHA00626 hypothetical protein 95.0 0.023 5E-07 34.3 2.4 27 123-149 2-33 (59)
68 smart00661 RPOL9 RNA polymeras 94.5 0.033 7.2E-07 33.1 2.3 28 122-149 1-30 (52)
69 KOG0823|consensus 94.2 0.016 3.6E-07 45.2 0.5 25 140-166 62-86 (230)
70 TIGR02098 MJ0042_CXXC MJ0042 f 94.1 0.053 1.2E-06 30.1 2.4 27 122-149 3-35 (38)
71 PF08274 PhnA_Zn_Ribbon: PhnA 94.0 0.052 1.1E-06 28.7 2.1 27 122-149 3-29 (30)
72 PF13719 zinc_ribbon_5: zinc-r 93.9 0.059 1.3E-06 29.9 2.3 28 122-149 3-35 (37)
73 PF09297 zf-NADH-PPase: NADH p 93.6 0.13 2.7E-06 27.6 3.2 29 120-148 2-30 (32)
74 PF13248 zf-ribbon_3: zinc-rib 93.6 0.042 9.1E-07 28.0 1.2 13 121-133 2-14 (26)
75 PRK00398 rpoP DNA-directed RNA 93.5 0.083 1.8E-06 30.8 2.6 30 122-151 4-33 (46)
76 PRK00432 30S ribosomal protein 93.1 0.089 1.9E-06 31.4 2.3 28 120-149 19-47 (50)
77 PF13240 zinc_ribbon_2: zinc-r 92.9 0.061 1.3E-06 26.6 1.1 22 123-148 1-22 (23)
78 PF13717 zinc_ribbon_4: zinc-r 92.6 0.13 2.8E-06 28.4 2.3 28 122-149 3-35 (36)
79 KOG1815|consensus 92.4 0.094 2E-06 45.5 2.4 39 121-160 158-199 (444)
80 KOG1814|consensus 91.9 0.088 1.9E-06 44.6 1.6 41 119-159 271-313 (445)
81 PRK05654 acetyl-CoA carboxylas 91.3 0.042 9.1E-07 45.0 -0.8 29 121-149 27-56 (292)
82 PF13923 zf-C3HC4_2: Zinc fing 91.3 0.051 1.1E-06 30.4 -0.3 21 140-160 12-32 (39)
83 PRK08665 ribonucleotide-diphos 91.1 0.14 3E-06 47.4 2.2 27 122-150 725-751 (752)
84 PLN03208 E3 ubiquitin-protein 90.9 0.045 9.8E-07 41.9 -1.0 34 120-159 17-50 (193)
85 PF07282 OrfB_Zn_ribbon: Putat 90.7 0.22 4.7E-06 31.5 2.2 30 120-149 27-56 (69)
86 PF06677 Auto_anti-p27: Sjogre 90.4 0.54 1.2E-05 26.7 3.4 24 121-146 17-41 (41)
87 PF09538 FYDLN_acid: Protein o 90.3 0.18 4E-06 35.1 1.7 27 122-149 10-36 (108)
88 CHL00174 accD acetyl-CoA carbo 90.1 0.058 1.3E-06 44.2 -1.0 30 121-150 38-68 (296)
89 KOG2906|consensus 90.0 0.26 5.6E-06 33.4 2.2 28 123-150 3-32 (105)
90 PRK14714 DNA polymerase II lar 89.8 0.29 6.4E-06 47.1 3.2 18 173-190 750-767 (1337)
91 PF00097 zf-C3HC4: Zinc finger 89.8 0.074 1.6E-06 29.8 -0.5 32 124-160 1-32 (41)
92 TIGR00515 accD acetyl-CoA carb 89.8 0.067 1.5E-06 43.7 -0.9 30 121-150 26-56 (285)
93 PF14952 zf-tcix: Putative tre 89.6 0.29 6.3E-06 28.0 1.8 25 115-143 5-29 (44)
94 PF02150 RNA_POL_M_15KD: RNA p 88.7 0.5 1.1E-05 25.8 2.4 28 122-149 2-30 (35)
95 KOG0317|consensus 88.6 0.086 1.9E-06 42.6 -1.1 36 120-161 238-273 (293)
96 COG0777 AccD Acetyl-CoA carbox 88.5 0.14 3.1E-06 41.3 0.1 31 120-150 27-58 (294)
97 TIGR00686 phnA alkylphosphonat 88.4 0.39 8.5E-06 33.2 2.2 30 122-160 3-32 (109)
98 PRK14559 putative protein seri 88.1 0.26 5.6E-06 44.8 1.5 33 120-158 14-52 (645)
99 PRK09710 lar restriction allev 87.8 0.61 1.3E-05 29.1 2.6 30 119-148 4-36 (64)
100 cd00162 RING RING-finger (Real 87.8 0.21 4.6E-06 27.8 0.5 32 124-160 2-33 (45)
101 PRK04023 DNA polymerase II lar 87.7 0.63 1.4E-05 43.9 3.7 33 119-157 624-661 (1121)
102 PF07191 zinc-ribbons_6: zinc- 87.2 0.59 1.3E-05 29.8 2.3 35 123-159 3-42 (70)
103 PF12760 Zn_Tnp_IS1595: Transp 87.0 2.1 4.6E-05 24.7 4.5 29 120-148 17-46 (46)
104 PF14803 Nudix_N_2: Nudix N-te 86.9 0.73 1.6E-05 25.1 2.3 26 122-147 1-30 (34)
105 PF14835 zf-RING_6: zf-RING of 86.8 0.36 7.8E-06 30.2 1.1 25 121-145 7-34 (65)
106 TIGR03655 anti_R_Lar restricti 86.8 0.64 1.4E-05 27.9 2.3 31 121-151 1-38 (53)
107 PF03119 DNA_ligase_ZBD: NAD-d 86.7 0.72 1.6E-05 23.9 2.1 21 123-143 1-21 (28)
108 PRK10220 hypothetical protein; 86.3 0.65 1.4E-05 32.1 2.3 30 122-160 4-33 (111)
109 COG1997 RPL43A Ribosomal prote 85.9 0.75 1.6E-05 30.5 2.3 31 120-150 34-64 (89)
110 PRK00420 hypothetical protein; 84.4 1.1 2.3E-05 31.5 2.7 25 121-147 23-48 (112)
111 COG1998 RPS31 Ribosomal protei 84.2 0.78 1.7E-05 27.1 1.6 27 121-147 19-45 (51)
112 PF13639 zf-RING_2: Ring finge 83.6 0.29 6.3E-06 27.9 -0.3 34 124-160 3-36 (44)
113 COG1645 Uncharacterized Zn-fin 83.3 0.97 2.1E-05 32.5 2.2 25 121-147 28-52 (131)
114 PF15227 zf-C3HC4_4: zinc fing 83.1 0.39 8.5E-06 27.3 0.1 21 140-161 12-32 (42)
115 KOG0006|consensus 83.0 0.78 1.7E-05 37.8 1.8 48 113-160 306-357 (446)
116 TIGR01384 TFS_arch transcripti 82.3 0.99 2.1E-05 30.9 1.9 24 123-148 2-25 (104)
117 PRK14892 putative transcriptio 82.3 1.2 2.6E-05 30.5 2.2 30 120-149 20-52 (99)
118 PF08792 A2L_zn_ribbon: A2L zi 82.2 1.7 3.6E-05 23.5 2.4 29 121-149 3-31 (33)
119 smart00184 RING Ring finger. E 81.9 0.51 1.1E-05 25.1 0.3 16 144-159 15-30 (39)
120 TIGR01206 lysW lysine biosynth 81.8 1.7 3.7E-05 26.3 2.6 28 122-149 3-32 (54)
121 TIGR02300 FYDLN_acid conserved 81.2 1.1 2.3E-05 32.1 1.7 27 122-149 10-36 (129)
122 CHL00059 atpA ATP synthase CF1 80.5 1.6 3.5E-05 38.4 2.9 32 160-191 96-127 (485)
123 PF01599 Ribosomal_S27: Riboso 79.7 1.3 2.7E-05 26.0 1.4 27 121-147 18-46 (47)
124 PF08271 TF_Zn_Ribbon: TFIIB z 79.6 2.4 5.3E-05 24.0 2.7 24 123-146 2-26 (43)
125 TIGR03324 alt_F1F0_F1_al alter 79.5 1.4 3.1E-05 38.8 2.4 32 160-191 117-148 (497)
126 COG1198 PriA Primosomal protei 78.4 2.1 4.5E-05 39.6 3.1 35 122-156 445-484 (730)
127 COG1594 RPB9 DNA-directed RNA 78.4 1.8 4E-05 30.3 2.2 28 122-149 3-32 (113)
128 PF13453 zf-TFIIB: Transcripti 78.2 1.8 3.8E-05 24.4 1.7 31 123-159 1-31 (41)
129 PF14353 CpXC: CpXC protein 78.1 2.3 5.1E-05 30.2 2.8 18 120-137 37-54 (128)
130 PRK13343 F0F1 ATP synthase sub 76.7 1.9 4.1E-05 38.1 2.3 32 160-191 117-148 (502)
131 PF14354 Lar_restr_allev: Rest 76.6 2.4 5.2E-05 25.9 2.2 28 120-147 2-37 (61)
132 PF01363 FYVE: FYVE zinc finge 76.5 2.8 6E-05 26.2 2.5 37 120-158 8-44 (69)
133 PF12773 DZR: Double zinc ribb 76.4 1.4 3.1E-05 25.8 1.0 13 120-132 11-23 (50)
134 PF15616 TerY-C: TerY-C metal 76.3 1.9 4E-05 31.1 1.8 26 120-152 76-101 (131)
135 PTZ00185 ATPase alpha subunit; 75.8 2.6 5.6E-05 37.5 2.9 24 168-191 152-175 (574)
136 PF03833 PolC_DP2: DNA polymer 75.6 0.89 1.9E-05 42.2 0.0 17 174-190 733-749 (900)
137 PF01396 zf-C4_Topoisom: Topoi 75.6 3.8 8.2E-05 22.9 2.6 22 122-144 2-26 (39)
138 TIGR02443 conserved hypothetic 75.1 3.5 7.6E-05 25.3 2.5 28 122-149 10-41 (59)
139 PF14634 zf-RING_5: zinc-RING 75.1 1.9 4.2E-05 24.5 1.3 33 123-158 1-33 (44)
140 PF14569 zf-UDP: Zinc-binding 75.0 1.9 4.1E-05 28.0 1.4 40 83-139 30-69 (80)
141 PF14149 YhfH: YhfH-like prote 74.7 0.21 4.6E-06 27.7 -2.6 27 119-145 11-37 (37)
142 PRK11827 hypothetical protein; 73.9 3.4 7.3E-05 25.6 2.3 27 121-147 8-34 (60)
143 PF05715 zf-piccolo: Piccolo Z 73.4 1.3 2.9E-05 27.1 0.4 38 122-159 3-42 (61)
144 smart00659 RPOLCX RNA polymera 73.4 3.9 8.4E-05 23.6 2.3 25 123-148 4-28 (44)
145 PRK14559 putative protein seri 72.5 3.6 7.9E-05 37.5 3.1 56 122-182 2-61 (645)
146 PF12861 zf-Apc11: Anaphase-pr 72.2 2.2 4.8E-05 28.3 1.2 35 122-160 33-67 (85)
147 PF07754 DUF1610: Domain of un 72.0 3.5 7.5E-05 20.6 1.6 6 123-128 18-23 (24)
148 COG2824 PhnA Uncharacterized Z 71.1 3.6 7.8E-05 28.4 2.1 30 121-159 3-32 (112)
149 PF06827 zf-FPG_IleRS: Zinc fi 71.0 3.5 7.6E-05 21.4 1.6 25 122-146 2-28 (30)
150 KOG3612|consensus 70.6 2.3 5E-05 37.5 1.3 26 164-191 561-586 (588)
151 PF10122 Mu-like_Com: Mu-like 70.3 1.7 3.7E-05 25.8 0.4 26 122-147 5-32 (51)
152 TIGR01053 LSD1 zinc finger dom 70.2 6 0.00013 21.0 2.4 26 122-147 2-27 (31)
153 PRK09281 F0F1 ATP synthase sub 69.9 3.6 7.8E-05 36.5 2.4 31 161-191 118-148 (502)
154 PRK09521 exosome complex RNA-b 69.1 4.3 9.4E-05 31.0 2.5 26 123-149 151-176 (189)
155 TIGR00595 priA primosomal prot 69.1 4.7 0.0001 35.7 3.0 35 122-156 223-262 (505)
156 PRK12286 rpmF 50S ribosomal pr 69.0 3.3 7.2E-05 25.3 1.5 24 119-147 25-48 (57)
157 COG2816 NPY1 NTP pyrophosphohy 68.7 5.9 0.00013 32.3 3.2 30 120-149 110-139 (279)
158 TIGR00962 atpA proton transloc 68.3 4 8.8E-05 36.1 2.4 29 163-191 119-147 (501)
159 PF03604 DNA_RNApol_7kD: DNA d 67.7 3.3 7.1E-05 22.2 1.1 23 124-147 3-25 (32)
160 PRK07165 F0F1 ATP synthase sub 67.4 4.7 0.0001 35.7 2.6 24 168-191 106-129 (507)
161 COG1096 Predicted RNA-binding 67.0 4.3 9.3E-05 31.0 2.0 25 122-148 150-174 (188)
162 PF11781 RRN7: RNA polymerase 67.0 4.8 0.0001 22.1 1.7 27 120-148 7-34 (36)
163 PF06044 DRP: Dam-replacing fa 66.7 6.1 0.00013 31.5 2.8 37 111-149 22-63 (254)
164 PF04216 FdhE: Protein involve 66.3 3.3 7.2E-05 33.8 1.4 35 122-156 173-220 (290)
165 PF06943 zf-LSD1: LSD1 zinc fi 66.3 8.5 0.00018 19.4 2.3 24 124-147 1-24 (25)
166 PF05129 Elf1: Transcription e 66.1 3.6 7.8E-05 27.0 1.3 29 121-149 22-56 (81)
167 smart00834 CxxC_CXXC_SSSS Puta 65.9 4.1 9E-05 22.5 1.4 11 122-132 27-37 (41)
168 cd00065 FYVE FYVE domain; Zinc 65.9 4 8.7E-05 24.3 1.4 36 121-158 2-37 (57)
169 PF14369 zf-RING_3: zinc-finge 65.4 6.7 0.00015 21.3 2.1 10 124-133 5-14 (35)
170 PRK08332 ribonucleotide-diphos 65.4 4.5 9.9E-05 40.9 2.3 28 122-151 1705-1738(1740)
171 smart00440 ZnF_C2C2 C2C2 Zinc 65.1 7.5 0.00016 21.8 2.3 8 123-130 2-9 (40)
172 PF09526 DUF2387: Probable met 64.4 7.1 0.00015 25.0 2.4 27 122-148 9-39 (71)
173 PRK12495 hypothetical protein; 64.3 7 0.00015 30.6 2.7 28 121-158 42-69 (226)
174 PHA02929 N1R/p28-like protein; 64.0 4 8.7E-05 32.5 1.4 40 121-161 174-216 (238)
175 PF07975 C1_4: TFIIH C1-like d 63.9 2.3 5E-05 25.4 0.0 17 138-154 20-36 (51)
176 PRK14873 primosome assembly pr 63.6 6.1 0.00013 36.3 2.7 35 122-156 393-431 (665)
177 PRK14714 DNA polymerase II lar 63.5 4.4 9.4E-05 39.5 1.8 33 121-159 667-704 (1337)
178 smart00154 ZnF_AN1 AN1-like Zi 63.0 5.6 0.00012 22.2 1.5 25 124-152 1-25 (39)
179 PRK08115 ribonucleotide-diphos 62.8 4.1 8.9E-05 38.3 1.5 25 122-148 828-853 (858)
180 PRK14890 putative Zn-ribbon RN 62.0 6.8 0.00015 24.1 1.8 31 122-152 8-38 (59)
181 COG0266 Nei Formamidopyrimidin 61.2 8.6 0.00019 31.3 2.8 27 120-146 244-272 (273)
182 TIGR00599 rad18 DNA repair pro 61.1 4.1 8.9E-05 34.9 1.1 34 121-160 26-59 (397)
183 PF14446 Prok-RING_1: Prokaryo 61.1 4.1 8.9E-05 24.6 0.8 11 121-131 21-31 (54)
184 PF03966 Trm112p: Trm112p-like 60.9 8.5 0.00018 24.1 2.3 10 139-148 53-62 (68)
185 PRK05580 primosome assembly pr 60.8 8.2 0.00018 35.5 3.0 35 122-156 391-430 (679)
186 PLN03086 PRLI-interacting fact 59.9 5.8 0.00013 35.6 1.8 30 120-149 432-463 (567)
187 PF02318 FYVE_2: FYVE-type zin 59.5 8.8 0.00019 26.9 2.4 36 120-156 53-88 (118)
188 PRK00241 nudC NADH pyrophospha 59.0 8.6 0.00019 30.9 2.5 31 119-149 97-127 (256)
189 PF13920 zf-C3HC4_3: Zinc fing 58.7 8 0.00017 22.4 1.8 14 120-133 36-49 (50)
190 PRK14811 formamidopyrimidine-D 58.7 10 0.00022 30.7 2.9 27 120-154 234-262 (269)
191 TIGR00570 cdk7 CDK-activating 58.1 6.7 0.00015 32.4 1.8 35 122-157 4-38 (309)
192 PF14205 Cys_rich_KTR: Cystein 57.0 5 0.00011 24.2 0.6 29 120-148 3-37 (55)
193 PF10083 DUF2321: Uncharacteri 56.9 4.1 8.9E-05 30.1 0.3 14 120-133 38-51 (158)
194 PRK01103 formamidopyrimidine/5 56.1 12 0.00025 30.4 2.8 15 120-134 244-258 (274)
195 TIGR01031 rpmF_bact ribosomal 56.0 8.9 0.00019 23.2 1.7 23 120-147 25-47 (55)
196 PLN02638 cellulose synthase A 55.8 8.2 0.00018 37.2 2.1 40 84-140 39-78 (1079)
197 PF13445 zf-RING_UBOX: RING-ty 55.4 5.9 0.00013 22.6 0.8 35 124-161 1-35 (43)
198 PRK10445 endonuclease VIII; Pr 55.2 12 0.00026 30.2 2.8 17 120-136 234-252 (263)
199 COG5574 PEX10 RING-finger-cont 55.2 3.4 7.4E-05 33.2 -0.3 34 122-161 216-250 (271)
200 PHA02926 zinc finger-like prot 54.8 7.2 0.00016 30.7 1.4 41 120-160 169-212 (242)
201 PRK14810 formamidopyrimidine-D 54.6 12 0.00027 30.3 2.8 14 120-133 243-256 (272)
202 PF01783 Ribosomal_L32p: Ribos 53.8 8.3 0.00018 23.3 1.3 22 120-146 25-46 (56)
203 TIGR00577 fpg formamidopyrimid 53.8 13 0.00028 30.1 2.8 14 121-134 245-258 (272)
204 KOG0320|consensus 53.6 4 8.7E-05 30.9 -0.2 36 120-159 130-165 (187)
205 PRK04196 V-type ATP synthase s 53.3 14 0.0003 32.4 3.1 30 162-191 100-129 (460)
206 PF15135 UPF0515: Uncharacteri 53.0 9.4 0.0002 30.5 1.8 37 121-157 132-184 (278)
207 smart00064 FYVE Protein presen 52.5 9.3 0.0002 23.7 1.4 36 121-158 10-45 (68)
208 COG1996 RPC10 DNA-directed RNA 52.0 8.6 0.00019 22.7 1.1 11 121-131 24-34 (49)
209 PRK13130 H/ACA RNA-protein com 52.0 6.2 0.00013 24.0 0.5 13 120-132 4-16 (56)
210 PRK13945 formamidopyrimidine-D 51.5 15 0.00032 30.0 2.8 17 120-136 253-271 (282)
211 PF08646 Rep_fac-A_C: Replicat 51.5 14 0.0003 26.8 2.4 26 122-148 19-46 (146)
212 TIGR03305 alt_F1F0_F1_bet alte 51.4 14 0.0003 32.4 2.7 32 160-191 93-124 (449)
213 COG2888 Predicted Zn-ribbon RN 50.0 12 0.00027 23.0 1.6 31 123-153 11-41 (61)
214 PRK12380 hydrogenase nickel in 49.4 9.6 0.00021 26.6 1.2 8 123-130 88-95 (113)
215 PRK08972 fliI flagellum-specif 49.1 16 0.00035 31.9 2.7 32 160-191 117-148 (444)
216 PF01873 eIF-5_eIF-2B: Domain 49.0 21 0.00046 25.5 2.9 27 122-148 94-123 (125)
217 PF14570 zf-RING_4: RING/Ubox 48.5 7.1 0.00015 23.0 0.4 34 124-159 1-34 (48)
218 cd04476 RPA1_DBD_C RPA1_DBD_C: 48.3 14 0.00031 27.3 2.1 26 122-148 35-60 (166)
219 COG0675 Transposase and inacti 48.2 13 0.00028 30.3 2.0 27 120-159 308-334 (364)
220 COG1656 Uncharacterized conser 46.4 11 0.00025 28.1 1.3 16 120-135 96-111 (165)
221 PF13490 zf-HC2: Putative zinc 45.8 6.7 0.00015 21.0 -0.0 32 97-128 1-35 (36)
222 CHL00060 atpB ATP synthase CF1 45.7 18 0.00039 32.0 2.5 31 161-191 117-147 (494)
223 TIGR01040 V-ATPase_V1_B V-type 45.7 16 0.00036 32.0 2.3 33 159-191 95-127 (466)
224 PHA02942 putative transposase; 45.7 17 0.00038 31.0 2.4 29 120-149 324-352 (383)
225 PRK03564 formate dehydrogenase 45.6 14 0.0003 30.6 1.8 34 122-155 188-234 (309)
226 KOG1812|consensus 45.6 11 0.00025 32.2 1.3 21 140-160 259-279 (384)
227 PF01780 Ribosomal_L37ae: Ribo 45.3 15 0.00033 24.6 1.6 31 120-150 34-64 (90)
228 KOG0824|consensus 44.3 7.3 0.00016 32.0 -0.1 14 144-157 24-37 (324)
229 TIGR01562 FdhE formate dehydro 44.1 15 0.00033 30.4 1.8 34 123-156 186-233 (305)
230 PF01428 zf-AN1: AN1-like Zinc 43.6 13 0.00029 21.0 1.0 19 138-156 12-30 (43)
231 TIGR00100 hypA hydrogenase nic 43.5 14 0.0003 25.9 1.3 9 122-130 87-95 (115)
232 PLN02400 cellulose synthase 43.5 13 0.00028 35.9 1.4 40 84-140 58-97 (1085)
233 COG4640 Predicted membrane pro 43.4 14 0.00029 31.7 1.4 24 122-149 2-25 (465)
234 TIGR01041 ATP_syn_B_arch ATP s 41.0 26 0.00056 30.8 2.8 25 167-191 103-127 (458)
235 PRK12496 hypothetical protein; 41.0 15 0.00032 27.5 1.1 28 122-159 128-155 (164)
236 TIGR00622 ssl1 transcription f 41.0 25 0.00054 24.6 2.2 34 121-154 55-96 (112)
237 PHA02325 hypothetical protein 41.0 14 0.0003 23.1 0.8 12 120-131 2-13 (72)
238 PLN02189 cellulose synthase 40.5 21 0.00045 34.4 2.3 40 84-140 56-95 (1040)
239 PTZ00303 phosphatidylinositol 40.0 21 0.00046 33.5 2.1 36 121-156 460-498 (1374)
240 PF08746 zf-RING-like: RING-li 39.7 10 0.00022 21.6 0.1 12 86-99 18-29 (43)
241 PRK08927 fliI flagellum-specif 38.6 26 0.00056 30.6 2.4 24 168-191 121-144 (442)
242 COG1571 Predicted DNA-binding 38.5 18 0.00039 31.3 1.4 27 122-149 351-377 (421)
243 smart00531 TFIIE Transcription 38.4 12 0.00027 27.3 0.4 13 121-133 99-111 (147)
244 TIGR00280 L37a ribosomal prote 38.4 36 0.00079 22.9 2.6 31 120-150 34-64 (91)
245 smart00132 LIM Zinc-binding do 38.3 21 0.00045 18.8 1.3 23 123-145 1-30 (39)
246 KOG2879|consensus 37.6 31 0.00067 28.1 2.5 31 121-156 239-269 (298)
247 PF10497 zf-4CXXC_R1: Zinc-fin 37.4 18 0.0004 24.9 1.1 35 120-158 6-49 (105)
248 cd01134 V_A-ATPase_A V/A-type 37.2 9.6 0.00021 32.3 -0.4 28 163-191 116-143 (369)
249 PHA02998 RNA polymerase subuni 37.0 37 0.00079 25.8 2.7 38 120-161 142-185 (195)
250 PRK03681 hypA hydrogenase nick 36.0 21 0.00046 24.9 1.2 15 122-136 88-103 (114)
251 TIGR01039 atpD ATP synthase, F 35.9 29 0.00063 30.5 2.3 32 160-191 98-129 (461)
252 COG3529 Predicted nucleic-acid 35.9 12 0.00026 23.1 -0.1 27 123-149 12-42 (66)
253 COG3024 Uncharacterized protei 35.6 19 0.00042 22.4 0.9 16 120-135 6-21 (65)
254 COG4888 Uncharacterized Zn rib 35.5 34 0.00074 23.4 2.1 28 122-149 23-56 (104)
255 PF09862 DUF2089: Protein of u 35.3 36 0.00077 23.9 2.3 21 124-148 1-21 (113)
256 PRK05688 fliI flagellum-specif 35.0 31 0.00068 30.2 2.4 30 162-191 125-154 (451)
257 PRK09099 type III secretion sy 35.0 35 0.00075 29.9 2.6 29 163-191 121-149 (441)
258 PTZ00255 60S ribosomal protein 35.0 48 0.001 22.2 2.8 31 120-150 35-65 (90)
259 PRK03976 rpl37ae 50S ribosomal 34.7 44 0.00096 22.4 2.5 31 120-150 35-65 (90)
260 KOG2907|consensus 34.6 16 0.00035 25.5 0.5 24 123-146 9-32 (116)
261 PRK06386 replication factor A; 34.5 18 0.00039 30.7 0.8 13 121-133 236-248 (358)
262 PF08882 Acetone_carb_G: Aceto 34.5 20 0.00043 25.0 0.9 23 138-162 23-45 (112)
263 KOG2164|consensus 34.4 13 0.00029 32.7 0.0 32 121-158 186-217 (513)
264 PF01927 Mut7-C: Mut7-C RNAse 34.2 33 0.00071 25.0 2.1 14 121-134 91-104 (147)
265 PF04981 NMD3: NMD3 family ; 34.2 28 0.00062 27.5 1.9 13 138-150 34-46 (236)
266 PRK11088 rrmA 23S rRNA methylt 34.1 26 0.00057 28.1 1.7 24 123-149 4-27 (272)
267 PRK07960 fliI flagellum-specif 34.0 31 0.00067 30.3 2.2 33 159-191 129-161 (455)
268 KOG0978|consensus 33.9 12 0.00025 34.5 -0.4 35 119-159 641-675 (698)
269 KOG4218|consensus 33.9 15 0.00031 31.0 0.2 47 84-130 18-76 (475)
270 PLN02436 cellulose synthase A 33.9 30 0.00066 33.5 2.2 40 84-140 58-97 (1094)
271 PF00643 zf-B_box: B-box zinc 33.8 35 0.00075 18.7 1.7 29 122-156 4-32 (42)
272 PF03884 DUF329: Domain of unk 33.6 13 0.00028 22.7 -0.1 19 121-139 2-20 (57)
273 PRK07218 replication factor A; 33.3 19 0.00041 31.3 0.8 13 121-133 297-309 (423)
274 PRK00423 tfb transcription ini 32.3 45 0.00098 27.5 2.8 27 121-147 11-38 (310)
275 PF13821 DUF4187: Domain of un 32.2 21 0.00045 21.6 0.6 17 144-160 24-40 (55)
276 PF09151 DUF1936: Domain of un 32.1 24 0.00051 18.7 0.7 9 123-131 3-11 (36)
277 smart00504 Ubox Modified RING 31.6 21 0.00045 21.4 0.6 32 123-160 3-34 (63)
278 PRK06936 type III secretion sy 31.3 40 0.00086 29.5 2.4 25 167-191 124-148 (439)
279 PLN02915 cellulose synthase A 31.1 35 0.00075 33.0 2.1 39 84-139 37-75 (1044)
280 PF09723 Zn-ribbon_8: Zinc rib 31.0 35 0.00075 19.2 1.4 13 121-133 26-39 (42)
281 PF08209 Sgf11: Sgf11 (transcr 30.6 29 0.00063 18.6 0.9 13 122-134 5-17 (33)
282 PF14996 RMP: Retinal Maintena 30.4 37 0.0008 24.9 1.7 38 135-172 64-101 (146)
283 smart00653 eIF2B_5 domain pres 30.0 46 0.001 23.1 2.1 26 122-147 81-109 (110)
284 PRK12597 F0F1 ATP synthase sub 29.7 39 0.00085 29.7 2.1 29 163-191 101-129 (461)
285 PF13451 zf-trcl: Probable zin 29.6 31 0.00067 20.4 1.0 17 139-155 4-20 (49)
286 TIGR03498 FliI_clade3 flagella 29.4 40 0.00087 29.2 2.1 23 169-191 104-126 (418)
287 PF13913 zf-C2HC_2: zinc-finge 28.5 40 0.00086 16.6 1.2 10 122-131 3-12 (25)
288 PRK03988 translation initiatio 28.2 52 0.0011 23.9 2.2 28 121-148 102-132 (138)
289 COG3677 Transposase and inacti 28.2 79 0.0017 22.6 3.1 33 121-153 30-67 (129)
290 PF06397 Desulfoferrod_N: Desu 28.2 49 0.0011 18.2 1.6 25 121-147 6-31 (36)
291 TIGR00311 aIF-2beta translatio 28.1 52 0.0011 23.7 2.2 27 122-148 98-127 (133)
292 PF02470 MCE: mce related prot 27.8 1.2E+02 0.0026 19.2 3.8 24 10-33 4-27 (81)
293 COG5432 RAD18 RING-finger-cont 27.8 20 0.00043 29.5 -0.0 16 144-159 42-57 (391)
294 PRK00464 nrdR transcriptional 27.6 58 0.0013 24.1 2.4 7 123-129 2-8 (154)
295 PRK09280 F0F1 ATP synthase sub 27.4 41 0.0009 29.6 1.9 29 163-191 102-130 (463)
296 KOG1994|consensus 27.1 14 0.00031 29.1 -0.9 25 144-168 236-260 (268)
297 COG1040 ComFC Predicted amidop 27.1 12 0.00025 29.5 -1.4 27 122-160 25-51 (225)
298 PF11023 DUF2614: Protein of u 26.9 27 0.00059 24.4 0.5 11 121-131 69-79 (114)
299 PRK05922 type III secretion sy 26.6 53 0.0012 28.7 2.4 26 166-191 118-143 (434)
300 TIGR00155 pqiA_fam integral me 26.0 52 0.0011 28.4 2.2 28 121-148 13-42 (403)
301 PRK01110 rpmF 50S ribosomal pr 25.9 55 0.0012 20.1 1.7 12 120-131 26-37 (60)
302 PF02080 TrkA_C: TrkA-C domain 25.8 57 0.0012 19.8 1.9 41 2-50 30-70 (71)
303 PF13878 zf-C2H2_3: zinc-finge 25.8 44 0.00096 18.7 1.2 13 121-133 13-25 (41)
304 COG4416 Com Mu-like prophage p 25.6 34 0.00073 20.6 0.7 11 122-132 25-35 (60)
305 TIGR00627 tfb4 transcription f 25.4 38 0.00082 27.7 1.2 12 140-151 256-267 (279)
306 COG5152 Uncharacterized conser 25.3 17 0.00037 28.1 -0.7 13 144-156 213-225 (259)
307 TIGR02605 CxxC_CxxC_SSSS putat 25.3 48 0.001 19.2 1.3 13 121-133 26-39 (52)
308 PF14319 Zn_Tnp_IS91: Transpos 25.1 53 0.0011 22.8 1.7 27 122-156 43-69 (111)
309 PF09889 DUF2116: Uncharacteri 25.0 33 0.00072 21.1 0.6 25 122-158 4-29 (59)
310 KOG3795|consensus 24.8 45 0.00097 25.4 1.4 14 144-157 23-36 (230)
311 PLN02195 cellulose synthase A 24.8 53 0.0011 31.6 2.1 11 121-131 48-58 (977)
312 PRK01343 zinc-binding protein; 24.6 40 0.00087 20.6 0.9 13 120-132 8-20 (57)
313 KOG2932|consensus 24.5 30 0.00066 28.7 0.5 53 120-177 122-177 (389)
314 KOG4739|consensus 24.4 23 0.00051 28.1 -0.2 24 135-158 21-48 (233)
315 PRK11595 DNA utilization prote 24.0 26 0.00057 27.4 0.1 8 124-131 8-15 (227)
316 KOG2691|consensus 24.0 26 0.00056 24.3 -0.0 11 120-130 72-82 (113)
317 PTZ00368 universal minicircle 23.9 75 0.0016 22.9 2.5 16 83-98 54-69 (148)
318 PRK00418 DNA gyrase inhibitor; 23.8 44 0.00094 20.8 1.0 14 121-134 6-19 (62)
319 COG1675 TFA1 Transcription ini 23.5 18 0.00039 27.5 -0.9 28 120-147 112-140 (176)
320 PRK12336 translation initiatio 23.3 67 0.0015 24.8 2.2 31 122-152 99-132 (201)
321 COG5175 MOT2 Transcriptional r 23.3 21 0.00047 29.9 -0.6 34 123-158 16-49 (480)
322 TIGR02546 III_secr_ATP type II 23.0 65 0.0014 28.0 2.2 23 169-191 109-131 (422)
323 KOG0297|consensus 22.8 70 0.0015 27.4 2.4 34 122-160 22-55 (391)
324 PF04423 Rad50_zn_hook: Rad50 22.6 70 0.0015 18.8 1.7 10 123-132 22-31 (54)
325 TIGR00320 dfx_rbo desulfoferro 22.4 78 0.0017 22.5 2.2 22 121-142 7-29 (125)
326 PRK06315 type III secretion sy 22.4 61 0.0013 28.4 2.0 24 168-191 127-150 (442)
327 PF00412 LIM: LIM domain; Int 22.4 43 0.00092 19.6 0.8 9 124-132 1-9 (58)
328 PF14255 Cys_rich_CPXG: Cystei 22.3 54 0.0012 19.6 1.2 11 123-133 2-12 (52)
329 PRK12366 replication factor A; 22.2 45 0.00098 30.6 1.2 25 121-147 532-556 (637)
330 COG1885 Uncharacterized protei 22.1 48 0.001 22.9 1.0 13 120-132 48-60 (115)
331 PRK06393 rpoE DNA-directed RNA 22.0 22 0.00047 22.3 -0.6 13 120-132 4-16 (64)
332 COG0333 RpmF Ribosomal protein 21.9 75 0.0016 19.4 1.7 23 120-147 26-48 (57)
333 PRK04023 DNA polymerase II lar 21.9 66 0.0014 31.2 2.1 19 172-190 702-720 (1121)
334 PF10013 DUF2256: Uncharacteri 21.8 49 0.0011 18.9 0.8 12 121-132 8-19 (42)
335 PF05876 Terminase_GpA: Phage 21.8 59 0.0013 29.3 1.8 13 122-134 201-213 (557)
336 TIGR00373 conserved hypothetic 21.8 29 0.00062 25.7 -0.1 27 122-148 110-137 (158)
337 KOG1356|consensus 21.7 49 0.0011 31.2 1.3 31 124-158 232-262 (889)
338 COG3478 Predicted nucleic-acid 21.3 49 0.0011 20.7 0.8 11 138-148 39-49 (68)
339 KOG1873|consensus 21.2 51 0.0011 30.8 1.3 56 95-154 43-108 (877)
340 PF06844 DUF1244: Protein of u 21.1 18 0.00039 22.7 -1.1 12 148-159 11-22 (68)
341 COG3809 Uncharacterized protei 20.9 92 0.002 20.4 2.0 34 122-161 2-35 (88)
342 PF04236 Transp_Tc5_C: Tc5 tra 20.8 64 0.0014 20.1 1.3 20 135-154 33-55 (63)
343 COG2176 PolC DNA polymerase II 20.8 48 0.001 32.7 1.0 15 121-135 939-953 (1444)
344 cd02249 ZZ Zinc finger, ZZ typ 20.6 71 0.0015 18.1 1.4 30 123-156 2-32 (46)
345 COG1326 Uncharacterized archae 20.6 49 0.0011 25.5 0.9 28 122-149 7-40 (201)
346 PF12678 zf-rbx1: RING-H2 zinc 20.6 30 0.00065 22.0 -0.2 18 144-161 49-66 (73)
347 PF04606 Ogr_Delta: Ogr/Delta- 20.4 51 0.0011 18.9 0.8 10 123-132 1-10 (47)
348 COG4260 Membrane protease subu 20.3 46 0.00099 27.4 0.7 11 121-131 306-316 (345)
349 PF14690 zf-ISL3: zinc-finger 20.3 71 0.0015 17.9 1.4 12 122-133 3-14 (47)
350 PF01667 Ribosomal_S27e: Ribos 20.0 1.3E+02 0.0028 18.2 2.4 30 123-152 9-39 (55)
No 1
>KOG1812|consensus
Probab=99.90 E-value=2.8e-24 Score=180.32 Aligned_cols=108 Identities=27% Similarity=0.554 Sum_probs=94.2
Q ss_pred cCCCCCCCCCeeecCC----------------CCCccccCCcccCccchHHHHHHHhhccChHHHHHHHHhcCCCCCCCC
Q psy271 65 RFRVGIKAPGIIPRIS----------------VREPMQSGIEYHAPTDCAVIKKWLTKCADDSETANYISAHTKDCPKCH 128 (191)
Q Consensus 65 ~~Cp~~~C~~~~~r~~----------------~~~C~~Cgv~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~ 128 (191)
.|||.++|+..+.... ..+|.+|+++||.+.+|++|+++......+..++++++++|++||+|+
T Consensus 234 ~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la~~wr~CpkC~ 313 (384)
T KOG1812|consen 234 VYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLAKRWRQCPKCK 313 (384)
T ss_pred ccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHHHhcCcCcccc
Confidence 3999999987655322 123999999999999999999999877788889999999999999999
Q ss_pred cceEecCCcCceEeCCCCcceecccccccccCCCCCCCCCCcccC
Q psy271 129 ICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDGKGPLKTTTRFRVG 173 (191)
Q Consensus 129 ~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~~~~~~~~~~~~~~ 173 (191)
..|+|++|||||+|. ||++|||.|+.+|..+...|.++.+..-+
T Consensus 314 ~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~~r~~~~ 357 (384)
T KOG1812|consen 314 FMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYECCRYKES 357 (384)
T ss_pred eeeeecCCcceEEee-ccccchhhcCcchhhCCccccCccccccc
Confidence 999999999999995 99999999999999988878777775543
No 2
>KOG1814|consensus
Probab=99.86 E-value=9.6e-23 Score=166.91 Aligned_cols=148 Identities=21% Similarity=0.390 Sum_probs=111.7
Q ss_pred CCCCCCCCeEEecCCccccccchhHHHHHHhh-cCCcccCCCCCcccccCCCCCCCCCeeecCCC-----------CCcc
Q psy271 18 DRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDA-LGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV-----------REPM 85 (191)
Q Consensus 18 ~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~-~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~-----------~~C~ 85 (191)
..-+.+++.-..+-..++-.||++|+.||... +.+.++.+ ++..|||++.|..+.-+++. .+|.
T Consensus 230 l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~lqk~l~~m----sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCt 305 (445)
T KOG1814|consen 230 LKCPDPKCGSVAPPGQVKELVGDELFARYEKLMLQKTLELM----SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCT 305 (445)
T ss_pred ecCCCCCCcccCCchHHHHHHHHHHHHHHHHHHHHHHHHhh----cccccCChhhccCccccCchhhhhhhccCccHHHH
Confidence 34445555544444578889999999999877 55666665 57789999999988644433 2399
Q ss_pred ccCCcccCccchHHH--------HHHHh-------------------hccChHHHHHHHHhcCCCCCCCCcceEecCCcC
Q psy271 86 QSGIEYHAPTDCAVI--------KKWLT-------------------KCADDSETANYISAHTKDCPKCHICIEKNGGCN 138 (191)
Q Consensus 86 ~Cgv~~H~~~~C~~~--------~~~~~-------------------~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~ 138 (191)
.|+..||+...|+.- ..|.+ ...++.++.+|+..|.|+||+|++.|||++|||
T Consensus 306 lCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCn 385 (445)
T KOG1814|consen 306 LCKLTWHGVSPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCN 385 (445)
T ss_pred HHHHhhcCCCcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCcc
Confidence 999999999999642 11211 111244566899999999999999999999999
Q ss_pred ceEeCCCCcceecccccccccCCCCCCCCCCc
Q psy271 139 HMQCYHCKHEFCWMCLGNTIDGKGPLKTTTRF 170 (191)
Q Consensus 139 ~m~C~~C~~~fC~~C~~~~~~~~~~~~~~~~~ 170 (191)
||+|.+|++.|||.|+.... ...||.|.+.-
T Consensus 386 KM~C~~c~~~fc~~c~~~l~-~~nPYkHF~e~ 416 (445)
T KOG1814|consen 386 KMHCTKCGTYFCWICAELLY-PENPYKHFSEP 416 (445)
T ss_pred ceeeccccccceeehhhhcC-CCChhhhhcCC
Confidence 99999999999999987644 46788887653
No 3
>KOG1815|consensus
Probab=99.84 E-value=2.2e-21 Score=166.50 Aligned_cols=150 Identities=33% Similarity=0.566 Sum_probs=120.4
Q ss_pred CCCeEEecCCccccccch-hHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecC-----------CCCCccccCCc
Q psy271 23 EGDIVKRTGAIVDVPVGE-DLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRI-----------SVREPMQSGIE 90 (191)
Q Consensus 23 ~G~~v~~~g~~~~v~v~~-~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~-----------~~~~C~~Cgv~ 90 (191)
.++.+...+..+...+++ ++..+|...+-+..... ....+|||.++|+.++... ...+|+.|+..
T Consensus 119 ~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~---~~~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~ 195 (444)
T KOG1815|consen 119 HGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVED---NVPLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEE 195 (444)
T ss_pred CCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhc---CCccccCCCCCCCceeeccCCCccceeCCCCchhHhhcccc
Confidence 555555555666666666 36666666544333222 1237899999999987741 11249999999
Q ss_pred ccCccchHHHHHHHhhccChHHHHHHHHhcCCCCCCCCcceEecCCcCceEeCC--CCcceecccccccccCCCC-CCCC
Q psy271 91 YHAPTDCAVIKKWLTKCADDSETANYISAHTKDCPKCHICIEKNGGCNHMQCYH--CKHEFCWMCLGNTIDGKGP-LKTT 167 (191)
Q Consensus 91 ~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~~m~C~~--C~~~fC~~C~~~~~~~~~~-~~~~ 167 (191)
||++.+|....+|+.+..++++...|+..++++||+|..+|||++|||||+|.. |+++|||.|++.|..|+.. ++.+
T Consensus 196 ~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c 275 (444)
T KOG1815|consen 196 SHSPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSC 275 (444)
T ss_pred ccCCCcccchHHHHHhhhhhhhhhhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccccccceeee
Confidence 999999999999999999998888899999999999999999999999999976 9999999999999998755 8899
Q ss_pred CCcccCcc
Q psy271 168 TRFRVGIK 175 (191)
Q Consensus 168 ~~~~~~~~ 175 (191)
+++..+..
T Consensus 276 ~~~~~~~~ 283 (444)
T KOG1815|consen 276 NRYVDGKS 283 (444)
T ss_pred eeeechhh
Confidence 99887664
No 4
>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=99.65 E-value=2.3e-16 Score=131.19 Aligned_cols=100 Identities=29% Similarity=0.482 Sum_probs=93.6
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
||+|+++.+.++||++..|+.+|+.|.+++..+++++|++|||||+|++|+|||+.+.+.....+.....+++|+.|..+
T Consensus 64 Vvgf~~~~~~L~p~~~~~gv~~g~~V~~~~~~~~v~~g~~lLGRVld~~G~plDg~~~~~~~~~~~l~~~pp~pm~R~~I 143 (441)
T COG1157 64 VVGFNEERVLLMPFEPVEGVSPGAEVVPTGRPLSVPVGDALLGRVLDGLGRPLDGGGLPDGTERRPLDAPPPNPLKRRPI 143 (441)
T ss_pred EEEEcCCeEEEeccCccccCCCCCEEEecCCccccccChhhhhhhhccCCCcCcCCCCCCCcccccccCCCCCchhcccc
Confidence 89999999999999999999999999999999999999999999999999999997777666667888899999999999
Q ss_pred CCccccCCcccCc-cchHHHH
Q psy271 82 REPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 82 ~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
.+.+.+|++++++ .+|..-|
T Consensus 144 ~~~l~tGVRaIDgllT~G~GQ 164 (441)
T COG1157 144 EEPLDTGVRAIDGLLTCGKGQ 164 (441)
T ss_pred cccccccceeeecccccccCc
Confidence 9999999999999 6887754
No 5
>KOG0006|consensus
Probab=99.61 E-value=5.2e-16 Score=123.87 Aligned_cols=118 Identities=24% Similarity=0.400 Sum_probs=83.3
Q ss_pred ccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCCC------------CccccCCcccCccchHH-----
Q psy271 37 PVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISVR------------EPMQSGIEYHAPTDCAV----- 99 (191)
Q Consensus 37 ~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~~------------~C~~Cgv~~H~~~~C~~----- 99 (191)
.++++-+.||.....+...-. ..-+.||+++|+.-+...+.. +|..|...+|.+ .|.+
T Consensus 292 ilg~e~Y~rYQr~atEe~vlq----~gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh~g-eC~~~~~as 366 (446)
T KOG0006|consen 292 ILGEEQYNRYQRYATEECVLQ----MGGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYHEG-ECSAVFEAS 366 (446)
T ss_pred ecchhHHHHHHHhhhhhheee----cCCEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhccc-cceeeeccc
Confidence 367777888876543322211 123579999998866554432 277777777765 3431
Q ss_pred ------HH--H-HHhhccChHHHHHHHHhcCCCCCCCCcceEecCCcCceEeCC--CCcceeccccccccc
Q psy271 100 ------IK--K-WLTKCADDSETANYISAHTKDCPKCHICIEKNGGCNHMQCYH--CKHEFCWMCLGNTID 159 (191)
Q Consensus 100 ------~~--~-~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~~m~C~~--C~~~fC~~C~~~~~~ 159 (191)
|. . .-+...-|+++...|++.+|+||+|+++.||+|||+||.|++ ||.+|||.|+.+|..
T Consensus 367 ~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 367 GTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred cccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 10 0 111122366777889999999999999999999999999997 999999999999985
No 6
>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.
Probab=99.55 E-value=5.9e-15 Score=126.71 Aligned_cols=102 Identities=41% Similarity=0.739 Sum_probs=93.1
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
.|++|+++.+.+++|+++.||+.|+.|.++|+.++|++|++|||||+|++|+|||+++++....+|......++++.|.+
T Consensus 62 ~Vi~l~~~~v~~~~l~~~~gi~~G~~V~~tg~~~~vpvg~~llGRVvd~lG~PiDg~~~~~~~~~~~i~~~~p~~~~R~~ 141 (497)
T TIGR03324 62 IAFNVDEDEVGVVLLGEYSHLQAGDEVERTGRVMDVPVGDGLLGRVVDPLGRPLDGGGPLASSPRLPIERPAPPIMDRAP 141 (497)
T ss_pred EEEEEcCCeEEEEEecCCcCCcCCCEEEECCCCCeEECCHhhCcCEECCCCCCcCCCCCCCCCceeehhccCcCccccCC
Confidence 48999999999999999999999999999999999999999999999999999999987766666788888999999999
Q ss_pred CCCccccCCcccCc-cchHHHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVIKK 102 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~~~ 102 (191)
+.+++.||+++.|. .++...++
T Consensus 142 v~epl~TGI~aID~l~pigrGQR 164 (497)
T TIGR03324 142 VTVPLQTGLKVIDALIPIGRGQR 164 (497)
T ss_pred CCchhhcCCEEEeccCCcccCCE
Confidence 99999999999988 46765543
No 7
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=99.53 E-value=1.1e-14 Score=124.53 Aligned_cols=101 Identities=46% Similarity=0.690 Sum_probs=92.2
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
+|++|+++.+.+++|++++||+.|+.|.++++.++|++|++|||||+|++|+|||+++++.....+......++++.|.+
T Consensus 41 ~vi~~~~~~v~~~~l~~~~gi~~G~~V~~tg~~~~vpvg~~llGRVvd~lG~piDg~~~~~~~~~~~i~~~ap~~~~R~~ 120 (485)
T CHL00059 41 IALNLESNNVGVVLMGDGLMIQEGSSVKATGKIAQIPVSEAYLGRVVNALAKPIDGKGEISASESRLIESPAPGIISRRS 120 (485)
T ss_pred EEEEEcCCEEEEEEeeCCCCCCCCCEEEECCCcceEEcCHhhcCCEECCCCCeeCCCCCcCCCccccccCCCCCchhccC
Confidence 48999999999999999999999999999999999999999999999999999999877665556777888999999999
Q ss_pred CCCccccCCcccCc-cchHHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
+.+++.||+++.|. .++...+
T Consensus 121 v~epl~TGI~aID~l~pigrGQ 142 (485)
T CHL00059 121 VYEPLQTGLIAIDSMIPIGRGQ 142 (485)
T ss_pred CCcccccCceeeccccccccCC
Confidence 99999999999987 4676544
No 8
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=99.52 E-value=1.1e-14 Score=125.45 Aligned_cols=101 Identities=43% Similarity=0.674 Sum_probs=92.5
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
+|++|+++.+.+++|++++||..|+.|.++|+.++|++|+++||||+|++|+|||+++++....++......++++.|..
T Consensus 62 ~V~~l~~~~v~~~~l~~~~gi~~G~~V~~tg~~~~vpvg~~llGRVid~lG~piDg~~~i~~~~~~~i~~~ap~~~~R~~ 141 (502)
T PRK13343 62 FAFNLEEELVGAVLLDDTADILAGTEVRRTGRVLEVPVGDGLLGRVIDPLGRPLDGGGPLQATARRPLERPAPAIIERDF 141 (502)
T ss_pred EEEEecCCeEEEEEeeCCCCCCCCCEeEecCCcceeecCHHhcCCEECCCCCcccCCCCCCCCceecccCCCcChhhcCC
Confidence 48999999999999999999999999999999999999999999999999999999987766666788889999999999
Q ss_pred CCCccccCCcccCc-cchHHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
+.+++.||+++.|. .++...+
T Consensus 142 v~epl~TGIkaID~l~pigrGQ 163 (502)
T PRK13343 142 VTEPLQTGIKVVDALIPIGRGQ 163 (502)
T ss_pred CCcccccCCceeccccccccCC
Confidence 99999999999987 4665543
No 9
>PRK07165 F0F1 ATP synthase subunit alpha; Validated
Probab=99.52 E-value=1.2e-14 Score=124.74 Aligned_cols=102 Identities=15% Similarity=0.158 Sum_probs=90.3
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcc-----cccCCCCCCCCCe
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKT-----TTRFRVGIKAPGI 75 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~-----~~~~Cp~~~C~~~ 75 (191)
+|++++++.+.+++|+++.||..|+.|.++|+.++|++|++|||||+|++|+|||+++++.. ...+.....++++
T Consensus 38 ~V~~~~~~~v~~~~l~~~~gi~~G~~V~~tg~~~~vpvg~~lLGRVvd~lG~piDg~g~i~~~~~~~~~~~~i~~~ap~~ 117 (507)
T PRK07165 38 FVISATEDKAYLLINNEKGKIKINDELIELNNTNKVKTSKEYFGKIIDIDGNIIYPEAQNPLSKKFLPNTSSIFNLAHGL 117 (507)
T ss_pred EEEEEeCCeEEEEEccCccCCCCCCEEEECCCccEEECCccccCCEECCCCcccCCCCCCCcccccccccccccCCCCCc
Confidence 48999999999999999999999999999999999999999999999999999999876544 3345667789999
Q ss_pred eecCCCCCccccCCcccCc-cchHHHHH
Q psy271 76 IPRISVREPMQSGIEYHAP-TDCAVIKK 102 (191)
Q Consensus 76 ~~r~~~~~C~~Cgv~~H~~-~~C~~~~~ 102 (191)
+.|..+.+++.||+++.|. .++...|+
T Consensus 118 ~~R~~v~epL~TGIkaID~l~pigrGQR 145 (507)
T PRK07165 118 MTVKTLNEQLYTGIIAIDLLIPIGKGQR 145 (507)
T ss_pred hhhCCCCceeecCchhhhhcCCcccCCE
Confidence 9999999999999999988 46655443
No 10
>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.
Probab=99.52 E-value=1.3e-14 Score=123.32 Aligned_cols=101 Identities=28% Similarity=0.342 Sum_probs=92.2
Q ss_pred eeeecCCeEEEEEecCCCCCCC-CCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKE-GDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~-G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|++|+++.+.+++|++++||.+ |+.|.++++.++|++|+++||||+|++|+|||+.+++.....+......++++.|..
T Consensus 41 Vi~~~~~~~~l~~~~~~~gi~~~g~~V~~t~~~~~v~vg~~lLGRVid~~G~piD~~~~~~~~~~~~i~~~~~~~~~R~~ 120 (466)
T TIGR01040 41 VLEVSGNKAVVQVFEGTSGIDAKKTTCEFTGDILRTPVSEDMLGRVFNGSGKPIDKGPPVLAEDYLDINGQPINPYARIY 120 (466)
T ss_pred EEEEeCCeEEEEEcCCCCCcccCCCEEEECCCccEEEcCcccccCEECccccccCCCCCCCCCceeeccCCCCChhHcCC
Confidence 8999999999999999999997 999999999999999999999999999999999877655656788889999999999
Q ss_pred CCCccccCCcccCc-cchHHHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVIKK 102 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~~~ 102 (191)
+.+.+.||+++.|. .++...|+
T Consensus 121 i~e~l~TGI~aID~l~~ig~GQR 143 (466)
T TIGR01040 121 PEEMIQTGISAIDVMNSIARGQK 143 (466)
T ss_pred CCCeeecCcEEEeccCccccCCe
Confidence 99999999999998 56766543
No 11
>PRK04196 V-type ATP synthase subunit B; Provisional
Probab=99.51 E-value=2.3e-14 Score=122.93 Aligned_cols=101 Identities=27% Similarity=0.361 Sum_probs=91.8
Q ss_pred CeeeecCCeEEEEEecCCCCCC-CCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIK-EGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRI 79 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~-~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~ 79 (191)
.|++|++|.+.+++|++++||+ .|+.|.++|+.++|++|++||||++|++|+|||+++++.....+.+....++++.|.
T Consensus 42 eVi~~~~~~~~l~~~~~t~gl~i~G~~V~~tg~~~~V~vg~~lLGRVvD~~G~PlD~~~~i~~~~~~~i~~~ap~~l~R~ 121 (460)
T PRK04196 42 QVLEVSEDKAVVQVFEGTTGLDLKDTKVRFTGEPLKLPVSEDMLGRIFDGLGRPIDGGPEIIPEKRLDINGAPINPVARE 121 (460)
T ss_pred EEEEEeCCeEEEEEccCCCCCCCCCCEEEeCCCccEEEcCcccccCEECccCCCccCCCCCCCCccCcccCCCCChhhcC
Confidence 3899999999999999999999 899999999999999999999999999999999988776565678888999999999
Q ss_pred CCCCccccCCcccCc-cchHHHH
Q psy271 80 SVREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 80 ~~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
.+.+.+.||+++.|. .++..-+
T Consensus 122 ~i~epl~TGi~~ID~l~pig~GQ 144 (460)
T PRK04196 122 YPEEFIQTGISAIDGLNTLVRGQ 144 (460)
T ss_pred CCCccccCCeEEEeccCcccCCC
Confidence 999999999999987 4665443
No 12
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=99.50 E-value=2.7e-14 Score=121.19 Aligned_cols=94 Identities=28% Similarity=0.440 Sum_probs=87.5
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
||+++++.+.+++|++++||+.|+.|.++|+.++|++|++|||||+|++|+|||+++++.....|......++++.|..+
T Consensus 63 Vv~~~~~~~~l~~~~~~~gi~~g~~V~~tg~~~~v~vg~~llGRVid~~G~plD~~~~~~~~~~~~i~~~~~~p~~R~~i 142 (444)
T PRK08972 63 VVGFDGDLLYLMPIEELRGVLPGARVTPLGEQSGLPVGMSLLGRVIDGVGNPLDGLGPIYTDQRASRHSPPINPLSRRPI 142 (444)
T ss_pred EEEecCCEEEEEECCCcCCCCCCCEEEECCCccEEEcChhhcCCeECCCCCCcCCCCCCCCCccccccCCCCChhhcCCC
Confidence 89999999999999999999999999999999999999999999999999999998877666567888889999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.+..
T Consensus 143 ~e~l~TGi~aID~l 156 (444)
T PRK08972 143 TEPLDVGVRAINAM 156 (444)
T ss_pred CCcccccceeecce
Confidence 99999999997763
No 13
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=99.50 E-value=2.4e-14 Score=123.85 Aligned_cols=102 Identities=55% Similarity=0.834 Sum_probs=93.1
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
.|++++++.+.+++|+++.||..|+.|.++|+++++++|++|||||+|++|+|||+++++....++......++++.|..
T Consensus 62 ~Vi~~~~~~~~~~~~~~~~gi~~g~~V~~~~~~~~v~vg~~llGrv~d~~G~pid~~~~~~~~~~~~i~~~~p~~~~R~~ 141 (502)
T PRK09281 62 IALNLEEDNVGAVILGDYEDIKEGDTVKRTGRILEVPVGEALLGRVVNPLGQPIDGKGPIEATETRPVERKAPGVIDRKS 141 (502)
T ss_pred EEEEEcCCeEEEEEecCcccccCCCeeeecCCceEEecCHHhcCCEEccCCCCcCCCCCCCCCceecccCCCcCccccCC
Confidence 48999999999999999999999999999999999999999999999999999999877766666788889999999999
Q ss_pred CCCccccCCcccCc-cchHHHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVIKK 102 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~~~ 102 (191)
+.+.+.||+++.|. .++...++
T Consensus 142 ~~~~l~TGi~~ID~l~pigrGQr 164 (502)
T PRK09281 142 VHEPLQTGIKAIDAMIPIGRGQR 164 (502)
T ss_pred ccceeecCCeeeecccccccCcE
Confidence 99999999999988 46765543
No 14
>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.
Probab=99.50 E-value=3.1e-14 Score=121.32 Aligned_cols=99 Identities=26% Similarity=0.357 Sum_probs=89.5
Q ss_pred eee-ecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 2 ALN-LEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~-l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|+. |+++.+.+++|++++||+.|+.|.+++..++|++|+++|||++|++|+|||+++++....++......++++.|..
T Consensus 38 Vv~~l~~~~v~l~~l~~t~Gi~~G~~V~~tg~~~~VpVg~~lLGRVlD~~G~PiD~~~~~~~~~~~~i~~~ap~~~~R~~ 117 (449)
T TIGR03305 38 VLSQLDAHHVRGIALTPTQGLARGMPVRDSGGPLKAPVGKPTLSRMFDVFGNTIDRREPPKDVEWRSVHQAPPTLTRRSS 117 (449)
T ss_pred eeeEecCCeEEEEEccCcccCCCCCEEEecCCceEEEcChhhcCCEEccCccccCCCCCCCCccccchhcCCCCchhccc
Confidence 455 9999999999999999999999999999999999999999999999999999877655556788889999999999
Q ss_pred CCCccccCCcccCc-cchHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVI 100 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~ 100 (191)
+.+.+.||+++.|. .++..-
T Consensus 118 i~e~L~TGIr~ID~l~pigkG 138 (449)
T TIGR03305 118 KSEVFETGIKAIDVLVPLERG 138 (449)
T ss_pred CCcccccCceeeccccccccC
Confidence 99999999999987 455543
No 15
>PTZ00185 ATPase alpha subunit; Provisional
Probab=99.49 E-value=2.9e-14 Score=122.22 Aligned_cols=101 Identities=28% Similarity=0.462 Sum_probs=88.8
Q ss_pred CeeeecCC-eEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCC------CCCccc-ccCCCCCCC
Q psy271 1 MALNLEPD-NVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGK------GPLKTT-TRFRVGIKA 72 (191)
Q Consensus 1 ~v~~l~~~-~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~------~~~~~~-~~~Cp~~~C 72 (191)
+|++|++| .+.+++|++++||+.|+.|.++|+.++|++|+++||||+|++|+|||++ +++..+ ..+......
T Consensus 81 ~vlnl~~d~~v~~v~lg~~~gI~~G~~V~~tg~~~~VpVG~~lLGRVvD~lG~PIDg~~~~~~~g~i~~~~~~~pIe~~a 160 (574)
T PTZ00185 81 LVFNLEKDGRIGIILMDNITEVQSGQKVMATGKLLYIPVGAGVLGKVVNPLGHEVPVGLLTRSRALLESEQTLGKVDAGA 160 (574)
T ss_pred EEEEecCCCeEEEEEecCccCCCCCCEEEECCCccEEECCcccccCEECCCCcccCCCCccccCCCCCcccccccccCCC
Confidence 58999999 6999999999999999999999999999999999999999999999987 333333 345778899
Q ss_pred CCeeecCCCCCccccCCcccCc-cchHHHH
Q psy271 73 PGIIPRISVREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 73 ~~~~~r~~~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
++++.|..+.+++.||+++.|. .++...+
T Consensus 161 p~~~~R~~v~epL~TGIkaID~LiPIGRGQ 190 (574)
T PTZ00185 161 PNIVSRSPVNYNLLTGFKAVDTMIPIGRGQ 190 (574)
T ss_pred cChhhcCCCCCcCcCCceeeeccccccCCC
Confidence 9999999999999999999987 4665543
No 16
>PRK06936 type III secretion system ATPase; Provisional
Probab=99.49 E-value=2.2e-14 Score=121.85 Aligned_cols=94 Identities=28% Similarity=0.429 Sum_probs=87.1
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++++++.+.+++|++++||+.|+.|.++|+.++|++|++||||++|++|+|||+++++....++......++++.|..+
T Consensus 63 Vv~~~~~~~~l~~~~~~~gi~~g~~V~~tg~~~~v~vg~~lLGRV~d~~G~plD~~~~~~~~~~~pi~~~~p~p~~R~~i 142 (439)
T PRK06936 63 VIGFAQHQALLTPLGEMYGISSNTEVSPTGTMHQVGVGEHLLGRVLDGLGQPFDGGHPPEPAAWYPVYADAPAPMSRRLI 142 (439)
T ss_pred EEEEECCeEEEEecCCCCCCCCCCEEEeCCCceEEEeCccccCCEECCCCCccCCCCCCCccceeeccCCCCChHHcccc
Confidence 78999999999999999999999999999999999999999999999999999998776555556778889999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+++.+|+++.+..
T Consensus 143 ~~~l~TGi~vid~l 156 (439)
T PRK06936 143 ETPLSLGVRVIDGL 156 (439)
T ss_pred CCCCcCCcceeeee
Confidence 99999999998764
No 17
>PRK07960 fliI flagellum-specific ATP synthase; Validated
Probab=99.49 E-value=2.7e-14 Score=121.48 Aligned_cols=94 Identities=18% Similarity=0.230 Sum_probs=87.4
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEec-------CCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRT-------GAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPG 74 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~-------g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~ 74 (191)
||+|+++.+.+++|++++||..|+.|.++ +..+++++|++|||||+|++|+|||+++++....++......++
T Consensus 69 Vvg~~~~~~~l~~~~~~~gi~~g~~v~~~~~~~~~~~~~~~v~vg~~llGRvid~~G~piDg~~~~~~~~~~~i~~~~~~ 148 (455)
T PRK07960 69 VVGFNGQRLFLMPLEEVEGILPGARVYARNISGEGLQSGKQLPLGPALLGRVLDGSGKPLDGLPAPDTGETGALITPPFN 148 (455)
T ss_pred EEEecCCEEEEEECCCccCCCCCCEEEECCcccccCCCceEEECCcccccCEECCCccccCCCCCCCCCccccccCCCcC
Confidence 78999999999999999999999999998 99999999999999999999999999877655555788889999
Q ss_pred eeecCCCCCccccCCcccCcc
Q psy271 75 IIPRISVREPMQSGIEYHAPT 95 (191)
Q Consensus 75 ~~~r~~~~~C~~Cgv~~H~~~ 95 (191)
++.|..+.+.+.+|+++.+..
T Consensus 149 p~~R~~i~e~l~TGiraID~l 169 (455)
T PRK07960 149 PLQRTPIEHVLDTGVRAINAL 169 (455)
T ss_pred hHHhcccccchhccceeeeec
Confidence 999999999999999998863
No 18
>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.
Probab=99.49 E-value=3.3e-14 Score=122.91 Aligned_cols=101 Identities=49% Similarity=0.768 Sum_probs=91.1
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
+|++++++.+.+++|+++.||..|+.|.++|+.++|++|+++||||+|++|+|||+++++.....+......++++.|..
T Consensus 61 ~Vi~~~~~~~~~~~~~~~~gi~~G~~V~~tg~~~~v~vg~~llGRV~d~~G~pld~~~~~~~~~~~~i~~~~p~~~~R~~ 140 (501)
T TIGR00962 61 IALNLEEDSVGAVIMGDYSNIREGSTVKRTGRILKVPVGDGLLGRVVNALGQPIDGKGPIDSDEFRPIEKIAPGVMERKS 140 (501)
T ss_pred EEEEecCCeEEEEEecCCcCCCCCCeeEecCCccEEecChHhcCCEeCCCCCeeCCCCCcCCCCceeeecCCCChhhcCC
Confidence 48999999999999999999999999999999999999999999999999999999877655555677778899999999
Q ss_pred CCCccccCCcccCc-cchHHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
+.+++.||+++.|. .++...+
T Consensus 141 i~~pl~TGi~aID~l~pigrGQ 162 (501)
T TIGR00962 141 VHEPLQTGIKAIDAMIPIGRGQ 162 (501)
T ss_pred cCceeccCCceeeccCCcccCC
Confidence 99999999999988 4666544
No 19
>PRK05922 type III secretion system ATPase; Validated
Probab=99.48 E-value=4.7e-14 Score=119.88 Aligned_cols=94 Identities=21% Similarity=0.294 Sum_probs=86.9
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++|+++++.+++|++++||++|+.|.+++.++++++|++||||++|++|+|||+.+++.....+......++++.|..+
T Consensus 58 Vv~~~~~~~~l~~~~~~~gi~~G~~V~~~~~~~~v~vg~~llGrv~d~~G~pld~~~~~~~~~~~pi~~~~~~~~~R~~i 137 (434)
T PRK05922 58 VIGFHNRTTLLMSLSPIHYVALGAEVLPLRRPPSLHLSDHLLGRVLDGFGNPLDGKEQLPKTHLKPLFSSPPSPMSRQPI 137 (434)
T ss_pred EEEEeCCeEEEEEccCCCCCCCCCEEEeCCCCcEEEcChhhcCCEeCCCCCccCCCCCCCccceeecccCCCChhhcCCc
Confidence 89999999999999999999999999999999999999999999999999999998766555556677788999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.+..
T Consensus 138 ~e~l~TGIr~ID~l 151 (434)
T PRK05922 138 QEIFPTGIKAIDAF 151 (434)
T ss_pred ceecCCCceeecce
Confidence 99999999998873
No 20
>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=99.48 E-value=4.7e-14 Score=120.80 Aligned_cols=100 Identities=24% Similarity=0.275 Sum_probs=90.7
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCe-EEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDI-VKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRI 79 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~-v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~ 79 (191)
.|++|+++.+.+++|+++.||+.|+. |.+++++++|++|++|||||+|++|+|||+++++..+.+|......++++.|.
T Consensus 40 eVv~~~~~~~~l~~~~~t~gi~~g~~~V~~tg~~~~v~vg~~lLGRViD~~G~plD~~~~~~~~~~~~i~~~~~~~~~R~ 119 (458)
T TIGR01041 40 QVLDSSEGLAVVQVFEGTTGLDPTGTKVRFTGETLKLPVSEDMLGRILNGSGEPIDGGPEIVPDERRDINGAPINPYARE 119 (458)
T ss_pred EEEEEECCEEEEEEecCCcCcCCCCcEEEECCCceEEEcChhhccCEEccCCcccCCCCCCCccceeeccCCCCChhhcC
Confidence 38999999999999999999999987 99999999999999999999999999999987766665678888999999999
Q ss_pred CCCCccccCCcccCc-cchHHH
Q psy271 80 SVREPMQSGIEYHAP-TDCAVI 100 (191)
Q Consensus 80 ~~~~C~~Cgv~~H~~-~~C~~~ 100 (191)
.+.+.+.||+++.|. .++..-
T Consensus 120 ~~~~~l~TGi~~ID~l~pig~G 141 (458)
T TIGR01041 120 YPEEFIQTGISAIDGMNTLVRG 141 (458)
T ss_pred CCCCcCCCCeEEEEccCccccC
Confidence 999999999999987 456544
No 21
>PRK09099 type III secretion system ATPase; Provisional
Probab=99.47 E-value=4.7e-14 Score=120.25 Aligned_cols=94 Identities=32% Similarity=0.486 Sum_probs=87.0
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++|+++.+.+++|+++.||+.|+.|.+++++++|++|++||||++|++|+|||+.+++.....+.....+++++.|..+
T Consensus 64 Vv~~~~~~~~l~~~~~t~gi~~g~~V~~tg~~~~v~vg~~lLGrV~d~~G~piD~~~~~~~~~~~~i~~~~p~p~~R~~i 143 (441)
T PRK09099 64 VVGFSRDVALLSPFGELGGLSRGTRVIGLGRPLSVPVGPALLGRVIDGLGEPIDGGGPLDCDELVPVIAAPPDPMSRRMV 143 (441)
T ss_pred EEEEECCEEEEEEccCCcCCCCCCEEEeCCCccEEEeccccccCEEcccCCccCCCCCCccccccccccCCCChhhcCCc
Confidence 89999999999999999999999999999999999999999999999999999998776555556778899999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.++.
T Consensus 144 ~e~l~TGi~~ID~l 157 (441)
T PRK09099 144 EAPLPTGVRIVDGL 157 (441)
T ss_pred ccccCCCceeccce
Confidence 99999999998764
No 22
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=99.47 E-value=3.8e-14 Score=120.81 Aligned_cols=94 Identities=27% Similarity=0.411 Sum_probs=86.8
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++|+++.+.+++|+++.||+.|+.|.++++.++|++|++|||||+|++|+|||+++++....++......++++.|..+
T Consensus 69 Vv~~~~~~~~l~~~~~~~gi~~g~~V~~tg~~~~v~vg~~llGRV~d~~G~plD~~~~~~~~~~~~i~~~~~~p~~R~~i 148 (451)
T PRK05688 69 VMGFSGDKVFLMPVGSVAGIAPGARVVPLADTGRLPMGMSMLGRVLDGAGRALDGKGPMKAEDWVPMDGPTINPLNRHPI 148 (451)
T ss_pred EEEEcCCEEEEEEccCccCCCCCCEEEECCCccEEEecccccCCEEeccCceecCCCCCCccceecccCCCCCHHHcccc
Confidence 78999999999999999999999999999999999999999999999999999998776555455777888999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+++.+|+++.+..
T Consensus 149 ~~~l~TGi~aID~l 162 (451)
T PRK05688 149 SEPLDVGIRSINGL 162 (451)
T ss_pred cCCcccceeeecce
Confidence 99999999998774
No 23
>PRK02118 V-type ATP synthase subunit B; Provisional
Probab=99.47 E-value=5e-14 Score=119.41 Aligned_cols=99 Identities=30% Similarity=0.415 Sum_probs=88.6
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++|+++.+.+++|++++||..|+.|.++|++++|++|+++|||++|++|+|||+.+++..+ .+......++++.|..+
T Consensus 42 Vi~~~~~~v~~~~~~~t~Gl~~g~~V~~tg~~~~vpvg~~lLGRV~d~~G~PiD~~~~~~~~-~~~i~~~~~~p~~R~~~ 120 (436)
T PRK02118 42 VIRLDGDKVTLQVFGGTRGISTGDEVVFLGRPMQVTYSESLLGRRFNGSGKPIDGGPELEGE-PIEIGGPSVNPVKRIVP 120 (436)
T ss_pred EEEEcCCEEEEEEecCCcCCCCCCEEEeCCCceEEEcCccccCCEEccCCcccCCCCCCCcc-eeecCCCCCChHHcCCc
Confidence 78999999999999999999999999999999999999999999999999999987766444 36677788899999999
Q ss_pred CCccccCCcccCc-cchHHHH
Q psy271 82 REPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 82 ~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
.+.+.||+++.|. .++..-+
T Consensus 121 ~e~l~TGIkaID~l~pl~rGQ 141 (436)
T PRK02118 121 REMIRTGIPMIDVFNTLVESQ 141 (436)
T ss_pred ccccccCcEEeecccccccCC
Confidence 9999999999988 4565443
No 24
>PRK07196 fliI flagellum-specific ATP synthase; Validated
Probab=99.47 E-value=5.1e-14 Score=119.74 Aligned_cols=94 Identities=22% Similarity=0.360 Sum_probs=86.1
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
||+++++.+.+++|++++||+.|+.|.++++.+++++|++||||++|++|+|||+++++..+..+......++++.|..+
T Consensus 56 Vv~~~~~~~~l~~~~~~~gi~~g~~v~~~~~~~~v~vg~~llGrv~d~~G~pld~~~~~~~~~~~~~~~~~~~p~~R~~~ 135 (434)
T PRK07196 56 VVGFDRDITYLMPFKHPGGVLGGARVFPSEQDGELLIGDSWLGRVINGLGEPLDGKGQLGGSTPLQQQLPQIHPLQRRAV 135 (434)
T ss_pred EEEecCCEEEEEECCCccCCCCCCEEEECCCccEEEcCccccCCeeCcCCCCcCCCCCCCCCceeeccCCCCChHHhccc
Confidence 89999999999999999999999999999999999999999999999999999998766555555666788889999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.++.
T Consensus 136 ~~~l~TGi~aID~l 149 (434)
T PRK07196 136 DTPLDVGVNAINGL 149 (434)
T ss_pred ccccccceeeccce
Confidence 99999999998775
No 25
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=99.47 E-value=6.5e-14 Score=120.15 Aligned_cols=100 Identities=27% Similarity=0.334 Sum_probs=90.3
Q ss_pred eeeecC-CeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 2 ALNLEP-DNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~l~~-~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|+++.+ +.+.+++|++++||+.|+.|.++++.++|++|+++||||+|++|++||+++++.....+......++++.|.+
T Consensus 61 Vvg~~~~~~v~~~~l~~~~gi~~G~~V~~tg~~~~vpvg~~lLGRVid~~G~piDg~~~~~~~~~~pi~~~~p~~~~R~~ 140 (494)
T CHL00060 61 VQQLLGNNRVRAVAMSATDGLMRGMEVIDTGAPLSVPVGGATLGRIFNVLGEPVDNLGPVDTRTTSPIHRSAPAFIQLDT 140 (494)
T ss_pred EEEEeCCCeEEEEeccCccCCCCCCEEEeCCCcceeecchhhcCCEEeecCcccCCCCCCCCCccccccCCCcCchhccc
Confidence 788888 9999999999999999999999999999999999999999999999999877655556778889999999999
Q ss_pred CCCccccCCcccCc-cchHHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
+.+.+.||+++.|. .++..-+
T Consensus 141 i~e~L~TGIraID~l~pigkGQ 162 (494)
T CHL00060 141 KLSIFETGIKVVDLLAPYRRGG 162 (494)
T ss_pred ccceeecCceeeeccCCcccCC
Confidence 99999999999988 4665543
No 26
>PRK08927 fliI flagellum-specific ATP synthase; Validated
Probab=99.46 E-value=6.1e-14 Score=119.32 Aligned_cols=98 Identities=29% Similarity=0.438 Sum_probs=88.8
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCccc-ccCCCCCCCCCeeecCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTT-TRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~-~~~Cp~~~C~~~~~r~~ 80 (191)
|++++++.+.+++|+++.||..|+.|.++++.++|++|+++|||++|++|+|||+++++... .++......++++.|..
T Consensus 58 Vv~~~~~~~~l~~~~~~~gi~~g~~V~~tg~~~~v~vg~~llGRVid~~G~piDg~~~~~~~~~~~~i~~~~p~~~~R~~ 137 (442)
T PRK08927 58 VVGFRGDRALLMPFGPLEGVRRGCRAVIANAAAAVRPSRAWLGRVVNALGEPIDGKGPLPQGPVPYPLRAPPPPAHSRAR 137 (442)
T ss_pred EEEEcCCeEEEEEccCccCCCCCCEEEeCCCccEEECChhhCCCEEccCCCCccCCCCCCCCcccccccCCCcChHHcCC
Confidence 89999999999999999999999999999999999999999999999999999998766443 45788889999999999
Q ss_pred CCCccccCCcccCcc-chHH
Q psy271 81 VREPMQSGIEYHAPT-DCAV 99 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~~-~C~~ 99 (191)
+.+.+.+|+++.|.. ++..
T Consensus 138 ~~~~l~TGir~ID~l~~i~~ 157 (442)
T PRK08927 138 VGEPLDLGVRALNTFLTCCR 157 (442)
T ss_pred cccccccceEEEeeeeEEcC
Confidence 999999999998873 4443
No 27
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=99.46 E-value=6.7e-14 Score=119.56 Aligned_cols=100 Identities=30% Similarity=0.426 Sum_probs=90.6
Q ss_pred eee-ecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 2 ALN-LEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~-l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|++ ++++.+.+++|++++||..|+.|.++++++++++|+++|||++|++|+|||+.+++....+|......++++.|..
T Consensus 44 Vv~~~~~~~~~~~~~~~~~gi~~G~~V~~tg~~~~v~vg~~lLGRViD~~G~pld~~~~~~~~~~~pi~~~~~~~~~R~~ 123 (463)
T PRK09280 44 VAQHLGDGVVRTIAMGSTDGLVRGMEVIDTGAPISVPVGKATLGRIFNVLGEPIDEKGPIGAEERWPIHRKAPSFEELST 123 (463)
T ss_pred eeEEecCCeEEEEEecCccCCCCCCEEEeCCCceEEEcChhhcCCEEeeeccccCCCCCcCccceecccCCCCChHHhCC
Confidence 566 9999999999999999999999999999999999999999999999999999877665666888889999999999
Q ss_pred CCCccccCCcccCc-cchHHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
+.+.+.+|+++.|. .++..-+
T Consensus 124 ~~~~l~TGiraID~l~pigkGQ 145 (463)
T PRK09280 124 KTEILETGIKVIDLLAPYAKGG 145 (463)
T ss_pred ccceeccCCeeecccCCcccCC
Confidence 99999999999988 4665543
No 28
>TIGR01039 atpD ATP synthase, F1 beta subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.
Probab=99.45 E-value=9.4e-14 Score=118.40 Aligned_cols=99 Identities=31% Similarity=0.474 Sum_probs=89.5
Q ss_pred eee-ecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 2 ALN-LEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~-l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|++ |+++.+.+++|+++.||+.|+.|.++++.+++++|+++|||++|++|+|||+++++....+|......++++.|..
T Consensus 43 Vv~~~~~~~v~l~~l~~~~gi~~G~~V~~t~~~~~i~vg~~lLGRViD~~G~pid~~~~~~~~~~~pi~~~~p~~~~R~~ 122 (461)
T TIGR01039 43 VAQHLGDDTVRTIAMGSTDGLVRGLEVIDTGAPISVPVGKETLGRIFNVLGEPIDEKGPIPAKERWPIHRKAPSFEEQST 122 (461)
T ss_pred eeeeeCCCeEEEEEccCcccCCCCCEEEeCCCceEEEcChhhcCCEEccCCcccCCCCCCCCCcccccccCCCChhHcCC
Confidence 455 9999999999999999999999999999999999999999999999999999876655556788889999999999
Q ss_pred CCCccccCCcccCc-cchHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVI 100 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~ 100 (191)
+.+.+.+|+++.|. .++..-
T Consensus 123 ~~e~l~TGiraID~l~pig~G 143 (461)
T TIGR01039 123 KVEILETGIKVIDLLAPYAKG 143 (461)
T ss_pred cccccccCceeecccCCcccC
Confidence 99999999999987 456544
No 29
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=99.44 E-value=1.2e-13 Score=117.32 Aligned_cols=94 Identities=29% Similarity=0.434 Sum_probs=85.8
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCccc-ccCCCCCCCCCeeecC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTT-TRFRVGIKAPGIIPRI 79 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~-~~~Cp~~~C~~~~~r~ 79 (191)
.|++|+++.+.+++|++++||..|+.|.+++.+++|++|+++||||+|++|+|||+++++... ..+......++++.|.
T Consensus 39 eVv~~~~~~v~l~~~~~~~gi~~G~~V~~tg~~~~i~vg~~lLGRViD~lG~plD~~~~~~~~~~~~~i~~~~p~~~~R~ 118 (418)
T TIGR03498 39 EVVGFNGDRVLLMPFEPLEGVGLGCAVFAREGPLAVRPHPSWLGRVINALGEPIDGKGPLPQGERRYPLRASPPPAMSRA 118 (418)
T ss_pred EEEEEcCCeEEEEEccCCcCCCCCCEEEECCCccEEEeChhhcCCEECCCCCccCCCCCCCCCcceechhhcCCChhhcc
Confidence 389999999999999999999999999999999999999999999999999999998765444 3467777899999999
Q ss_pred CCCCccccCCcccCc
Q psy271 80 SVREPMQSGIEYHAP 94 (191)
Q Consensus 80 ~~~~C~~Cgv~~H~~ 94 (191)
.+.+.+.+|+++.+.
T Consensus 119 ~i~~~l~tGi~aiD~ 133 (418)
T TIGR03498 119 RVGEPLDTGVRVIDT 133 (418)
T ss_pred CcccccCCccEEEee
Confidence 999999999999875
No 30
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=99.43 E-value=1.6e-13 Score=117.05 Aligned_cols=94 Identities=28% Similarity=0.453 Sum_probs=86.4
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccc--cCCCCCCCCCeeecC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTT--RFRVGIKAPGIIPRI 79 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~--~~Cp~~~C~~~~~r~ 79 (191)
|++++++.+.+++|++++||+.|+.|.++|+.+++++|+++||||+|++|+|||+++++.... .|.....+++++.|.
T Consensus 44 Vi~~~~~~~~l~~~~~~~gl~~G~~V~~tg~~~~v~vg~~lLGrViD~~G~plD~~~~~~~~~~~~~pi~~~~~~~~~R~ 123 (422)
T TIGR02546 44 VVGFTGDEALLSPLGELHGISPGSEVIPTGRPLSIRVGEALLGRVLDGFGRPLDGKGELPAGEIETRPLDADPPPPMSRQ 123 (422)
T ss_pred EEEEcCCcEEEEEccCccCCCCCCEEEECCCCceEEeChhhccCEeCCCCCcccCCCCCCCCCceeeeccCCCcCHHHcc
Confidence 899999999999999999999999999999999999999999999999999999987665442 577888999999999
Q ss_pred CCCCccccCCcccCcc
Q psy271 80 SVREPMQSGIEYHAPT 95 (191)
Q Consensus 80 ~~~~C~~Cgv~~H~~~ 95 (191)
.+.+.+.+|+++.+..
T Consensus 124 ~i~~~l~tG~~~id~l 139 (422)
T TIGR02546 124 PIDQPLPTGVRAIDGL 139 (422)
T ss_pred CcccccCCCceeehhh
Confidence 9999999999987764
No 31
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=99.43 E-value=1.8e-13 Score=117.28 Aligned_cols=99 Identities=28% Similarity=0.462 Sum_probs=89.9
Q ss_pred eeee-cCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 2 ALNL-EPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~l-~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|+++ +++.+.+++++++.||+.|+.|.+++.+++|++|+++||||+|++|+|||+.+++....+|......++++.|..
T Consensus 43 Vv~~l~~~~v~l~~~~~~~gl~~G~~V~~tg~~~~v~vg~~llGRVid~~G~plD~~~~~~~~~~~~i~~~~p~~~~R~~ 122 (461)
T PRK12597 43 VKQHLDETTVRAIALGSTSGLARGDEVRNTGGPIEVPVGEAVLGRLLDVLGEPLDGGPPLPAEERRPIHSTIPPLAEQDT 122 (461)
T ss_pred EEEEcCCCeEEEEEecCccCCCCCCEEEeCCCceEEEcChhhcCCEEeeccccccCCCCCCCcceeeccCCCcChhhcCC
Confidence 6777 999999999999999999999999999999999999999999999999999877655556788888999999999
Q ss_pred CCCccccCCcccCc-cchHHH
Q psy271 81 VREPMQSGIEYHAP-TDCAVI 100 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~-~~C~~~ 100 (191)
+.+.+.+|+++.|. .++..-
T Consensus 123 ~~e~l~TGir~ID~l~pigkG 143 (461)
T PRK12597 123 STEILETGIKVIDLLCPIAKG 143 (461)
T ss_pred cCcceecCCeeecccCccccC
Confidence 99999999999988 466554
No 32
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=99.42 E-value=1.3e-13 Score=117.25 Aligned_cols=94 Identities=29% Similarity=0.395 Sum_probs=86.2
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++|+++.+.+++|++++||+.|+.|.++++.++|++|++||||++|++|+|||+++++.....+.+....++++.|..+
T Consensus 58 Vv~~~~~~~~l~~~~~t~gl~~G~~V~~tg~~~~v~vg~~llGRViD~~G~plD~~g~~~~~~~~~i~~~~~~~~~R~~i 137 (434)
T PRK08472 58 VVVIEKEQFGISPFSFIEGFKIGDKVFISKEGLNIPVGRNLLGRVVDPLGRPIDGKGAIDYERYAPIMKAPIAAMKRGLI 137 (434)
T ss_pred EEEEeCCeEEEEEccCCCCCCCCCEEEeCCCceEEEcChhhcCCEECCCCCcccCCCCCCcccccccccCCCCHHHcCCc
Confidence 89999999999999999999999999999999999999999999999999999998776555556778889999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.+..
T Consensus 138 ~~~l~tgi~aid~l 151 (434)
T PRK08472 138 DEVFSVGVKSIDGL 151 (434)
T ss_pred ceeccchhHHhhhc
Confidence 99999998876654
No 33
>PRK06820 type III secretion system ATPase; Validated
Probab=99.41 E-value=2.6e-13 Score=115.63 Aligned_cols=97 Identities=27% Similarity=0.457 Sum_probs=86.7
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++++++.+.+++|++++||+.|+.|.++|+.+++++|++|||||+|++|+|||+.+.+ ...++......++++.|..+
T Consensus 65 Vv~~~~~~~~l~~~~~~~gi~~g~~v~~tg~~~~v~vg~~llGrv~d~~G~pld~~~~~-~~~~~~i~~~~p~p~~R~~~ 143 (440)
T PRK06820 65 VVSIEQEMALLSPFASSDGLRCGQWVTPLGHMHQVQVGADLAGRILDGLGAPIDGGPPL-TGQWRELDCPPPSPLTRQPI 143 (440)
T ss_pred EEEEeCCeEEEEEccCccCCCCCCEEEECCCCcEEEechhhcCCEECccCCccCCCCCC-CcccccccCCCCChhhcCCc
Confidence 89999999999999999999999999999999999999999999999999999998655 33345677789999999999
Q ss_pred CCccccCCcccCcc-chHH
Q psy271 82 REPMQSGIEYHAPT-DCAV 99 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~-~C~~ 99 (191)
.+.+.+|+++.+.. +...
T Consensus 144 ~~~l~TGi~aID~l~~i~~ 162 (440)
T PRK06820 144 EQMLTTGIRAIDGILSCGE 162 (440)
T ss_pred hhhccCCCceecceEEecC
Confidence 99999999998763 4443
No 34
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=99.41 E-value=1.9e-13 Score=114.37 Aligned_cols=94 Identities=62% Similarity=0.937 Sum_probs=88.3
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|+++|++|.|.++.+++...|..|+.|..||+.+.|++|++++|||+|++|+|+|+++++..+.........|+++.|..
T Consensus 62 ~alnle~d~VG~vi~g~~~~i~eG~~v~~Tg~i~~Vpvg~~llGRVVn~lG~pidgkg~i~~~~~~~~e~~Apgv~~Rks 141 (504)
T COG0056 62 MALNLEEDSVGAVILGDYSDIKEGDEVKRTGRILEVPVGEELLGRVVDALGNPIDGKGPIDATKTRPVEKKAPGVMDRKS 141 (504)
T ss_pred EEEeccccceeEEEecCCccccCCcEEEeeCceEEEecchhhcceeecCCCCccCCCCCccccccCccccccCceecccc
Confidence 57899999999999999999999999999999999999999999999999999999999887776777778999999999
Q ss_pred CCCccccCCcccCc
Q psy271 81 VREPMQSGIEYHAP 94 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~ 94 (191)
+.+++.||+.+.|-
T Consensus 142 V~ePlqTGikaIDa 155 (504)
T COG0056 142 VNEPLQTGIKAIDA 155 (504)
T ss_pred cCchhhhhhHHHhh
Confidence 99999999998764
No 35
>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=99.41 E-value=2.3e-13 Score=115.50 Aligned_cols=94 Identities=28% Similarity=0.469 Sum_probs=87.5
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++++++.+.+++|++++||+.|+.|.++|+.+++++|+++||||+|++|++||+.+++.....|......++++.|..+
T Consensus 38 Vv~~~~~~v~l~~~~~t~gl~~G~~V~~tg~~~~v~vg~~llGrVid~~G~pld~~~~~~~~~~~~i~~~~~~~~~R~~~ 117 (411)
T TIGR03496 38 VVGFRGDRVLLMPLEDVEGLRPGARVFPLEGPLRLPVGDSLLGRVIDGLGRPLDGKGPLDAGERVPLYAPPINPLKRAPI 117 (411)
T ss_pred EEEecCCEEEEEEccCccCCCCCCEEEECCCccEEEcchhhcCCEECCCCCCcCCCCCCCcccccccccCCCCHHhccCc
Confidence 89999999999999999999999999999999999999999999999999999998776556667888899999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.+..
T Consensus 118 ~~~~~tGi~~id~l 131 (411)
T TIGR03496 118 DEPLDVGVRAINGL 131 (411)
T ss_pred ceEeeeeEEeecce
Confidence 99999999988764
No 36
>PRK07721 fliI flagellum-specific ATP synthase; Validated
Probab=99.40 E-value=3.2e-13 Score=115.48 Aligned_cols=94 Identities=28% Similarity=0.468 Sum_probs=84.7
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++++++.+.+++|++++||+.|+.|.++|+.++|++|++||||++|++|+|||+.+.......+.....+++++.|..+
T Consensus 59 Vi~~~~~~~~l~~~~~~~gl~~g~~V~~tg~~~~v~vg~~llGRv~d~~G~plD~~~~~~~~~~~~i~~~~p~p~~R~~i 138 (438)
T PRK07721 59 VVGFKDEHVLLMPYTEVAEIAPGCLVEATGKPLEVKVGSGLIGQVLDALGEPLDGSALPKGLAPVSTDQDPPNPLKRPPI 138 (438)
T ss_pred EEEEcCCEEEEEEccCccCCCCCCEEEECCCccEEEechhhcCCEECcCCCccCCCCCCCccccCCccCCCCChhhccCc
Confidence 89999999999999999999999999999999999999999999999999999987643333446778899999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.+..
T Consensus 139 ~~~l~tg~~vid~l 152 (438)
T PRK07721 139 REPMEVGVRAIDSL 152 (438)
T ss_pred ccccccchhhhhee
Confidence 99999999987764
No 37
>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=99.40 E-value=2.2e-13 Score=115.61 Aligned_cols=94 Identities=30% Similarity=0.562 Sum_probs=86.9
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++++++.+.+++|+++.||+.|+.|.++|+++++++|+++|||++|++|+|||+++++.....|......++++.|..+
T Consensus 38 Vi~~~~~~v~l~~~~~t~gl~~G~~V~~tg~~~~vpvg~~lLGRVid~~G~plD~~~~~~~~~~~~i~~~~p~~~~R~~~ 117 (413)
T TIGR03497 38 VVGFKEENVLLMPLGEVEGIGPGSLVIATGRPLAIKVGKGLLGRVLDGLGRPLDGEGPIIGEEPYPLDNPPPNPLKRPRI 117 (413)
T ss_pred EEEEcCCeEEEEEccCccCCCCCCEEEEcCCeeEEEcchhhcCCEEcCCCCcccCCCCCCCCccccccCCCcChHHccch
Confidence 88999999999999999999999999999999999999999999999999999998776555567888889999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.+..
T Consensus 118 ~~~~~tGi~~iD~l 131 (413)
T TIGR03497 118 RDPLETGIKAIDGL 131 (413)
T ss_pred hhhccccceeeeeE
Confidence 99999999987764
No 38
>TIGR01026 fliI_yscN ATPase FliI/YscN family. This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.
Probab=99.40 E-value=4.4e-13 Score=114.68 Aligned_cols=94 Identities=27% Similarity=0.396 Sum_probs=84.9
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCC-CCcccccCCCCCCCCCeeecCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKG-PLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~-~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|++++++.+.+++|++++||++|+.|.++|.++++++|+++|||++|++|+|||+.+ .+.....+......++++.|..
T Consensus 63 Vi~~~~~~v~l~~~~~t~gl~~G~~V~~tg~~~~v~vg~~llGRVid~~G~plD~~~~~~~~~~~~~i~~~~~~p~~R~~ 142 (440)
T TIGR01026 63 VVGFNGEFVFLMPYEEVEGVRPGSKVLATGEGLSIKVGDGLLGRVLDGLGKPIDGKGKFLDNVETEGLITAPINPLKRAP 142 (440)
T ss_pred EEEecCCEEEEEEccCCcCCCCCCEEEeCCCccEEEcChhhhhceecCCCcccCCCCCCCCCccccccccCCCChHHccC
Confidence 899999999999999999999999999999999999999999999999999999886 4433444567778899999999
Q ss_pred CCCccccCCcccCcc
Q psy271 81 VREPMQSGIEYHAPT 95 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~~ 95 (191)
+.+.+.+|+++.+..
T Consensus 143 ~~e~l~TGi~~iD~l 157 (440)
T TIGR01026 143 IREILSTGVRSIDGL 157 (440)
T ss_pred ccccccceeeeeeec
Confidence 999999999987764
No 39
>PRK06315 type III secretion system ATPase; Provisional
Probab=99.40 E-value=2.3e-13 Score=116.07 Aligned_cols=94 Identities=24% Similarity=0.399 Sum_probs=84.8
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccC--CCCCc-ccccCCCCCCCCCeeec
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDG--KGPLK-TTTRFRVGIKAPGIIPR 78 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~--~~~~~-~~~~~Cp~~~C~~~~~r 78 (191)
|++++++.+.+++|+++.||.+|+.|.++|..++|++|++||||++|++|+|||+ ++++. .+..|......++++.|
T Consensus 62 Vv~~~~~~~~l~~~~~~~gi~~g~~V~~~g~~~~v~vg~~llGrv~d~~G~pld~~~~~~~~~~~~~~~i~~~~~~~~~R 141 (442)
T PRK06315 62 VVGFTQNFVFLSPLGELTGVSPSSEVIPTGLPLHIRAGNGLLGRVLNGLGEPIDTETKGPLENVDETYPIFRAPPDPLHR 141 (442)
T ss_pred EEEEcCCeEEEEEccCCcCCCCCCEEEeCCCccEEEecccccCCEEeccCcccccccCCCcccccceeeeecCCCChHHc
Confidence 8999999999999999999999999999999999999999999999999999997 55543 33346667788999999
Q ss_pred CCCCCccccCCcccCcc
Q psy271 79 ISVREPMQSGIEYHAPT 95 (191)
Q Consensus 79 ~~~~~C~~Cgv~~H~~~ 95 (191)
..+.+.+.+|+++.++.
T Consensus 142 ~~~~e~l~TGi~aID~~ 158 (442)
T PRK06315 142 AKLRTILSTGVRCIDGM 158 (442)
T ss_pred ccccccccceEEEEecc
Confidence 99999999999998764
No 40
>PRK07594 type III secretion system ATPase SsaN; Validated
Probab=99.37 E-value=7.6e-13 Score=112.61 Aligned_cols=93 Identities=24% Similarity=0.359 Sum_probs=84.3
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++++++.+.+++|++++||+.|+.|.++|+.+++++|+++|||++|++|++||+++.. ....+......++++.|..+
T Consensus 57 Vv~~~~~~~~l~~~~~~~gi~~g~~V~~tg~~~~v~vg~~llGrVid~~G~pld~~~~~-~~~~~~i~~~~p~~~~r~~v 135 (433)
T PRK07594 57 VVGINGSKALLSPFTSTIGLHCGQQVMALRRRHQVPVGEALLGRVIDGFGRPLDGRELP-DVCWKDYDAMPPPAMVRQPI 135 (433)
T ss_pred EEEEcCCeEEEEEccCCcCCCCCCEEEeCCCccEEEeChhhccCEEcccCCCcCCCCCC-cccccccccCCCCceeccCH
Confidence 89999999999999999999999999999999999999999999999999999987653 33345667788999999999
Q ss_pred CCccccCCcccCcc
Q psy271 82 REPMQSGIEYHAPT 95 (191)
Q Consensus 82 ~~C~~Cgv~~H~~~ 95 (191)
.+.+.+|+++.+..
T Consensus 136 ~~~l~tGi~aID~l 149 (433)
T PRK07594 136 TQPLMTGIRAIDSV 149 (433)
T ss_pred hheeCCCceeeeee
Confidence 99999999998764
No 41
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=99.34 E-value=1.5e-12 Score=110.74 Aligned_cols=93 Identities=19% Similarity=0.318 Sum_probs=84.5
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
|++++++.+.+++|++++||+.|+.|.+++..++|++|+++||||+|++|+|+|+++.+.....+.+....++++.|..+
T Consensus 57 V~~~~~~~~~~~~~~~~~gi~~g~~v~~~~~~~~v~vg~~~lGrV~d~~G~piD~~~~~~~~~~~~i~~~~~~~~~r~~i 136 (432)
T PRK06793 57 VIAIEKENNMLLPFEQTEKVCYGDSVTLIAEDVVIPRGNHLLGKVLSANGEVLNEEAENIPLQKIKLDAPPIHAFEREEI 136 (432)
T ss_pred EEEecCCcEEEEEccCccCCCCCCEEEECCCccEEEcCHhhccCEECcCCccCCCCCCCCCcccccccCCCCCchheech
Confidence 89999999999999999999999999999999999999999999999999999988655444456777788899999999
Q ss_pred CCccccCCcccCc
Q psy271 82 REPMQSGIEYHAP 94 (191)
Q Consensus 82 ~~C~~Cgv~~H~~ 94 (191)
.+.+.+|+++.+.
T Consensus 137 ~~~l~TGiraID~ 149 (432)
T PRK06793 137 TDVFETGIKSIDS 149 (432)
T ss_pred hhccCCCCEEEec
Confidence 9999999988776
No 42
>PRK08149 ATP synthase SpaL; Validated
Probab=99.31 E-value=2.5e-12 Score=109.30 Aligned_cols=94 Identities=23% Similarity=0.398 Sum_probs=83.9
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCC--CCc--ccccCCCCCCCCCeee
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKG--PLK--TTTRFRVGIKAPGIIP 77 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~--~~~--~~~~~Cp~~~C~~~~~ 77 (191)
|++++++.+.+++|++++||..|+.|.++++.+++++|++++||++|++|+++|+.+ ... ...++......++++.
T Consensus 48 vv~~~~~~~~l~~~~~~~gi~~g~~v~~~~~~~~v~vg~~llGrv~d~~G~piD~~~~~~~~~~~~~~~~i~~~~~~~~~ 127 (428)
T PRK08149 48 VVGFQRERTILSLIGNAQGLSRQVVLKPTGKPLSVWVGEALLGAVLDPTGKIVERFDAPPTVGPISEERVIDVAPPSYAE 127 (428)
T ss_pred EEEeeCcEEEEEECCCccCCCCCCEEEEcCCcCEEEeChhhcCCeeCCCCCCcCCCCCCcccccccceeehhccCCcchh
Confidence 789999999999999999999999999999999999999999999999999999875 221 1334677788899999
Q ss_pred cCCCCCccccCCcccCcc
Q psy271 78 RISVREPMQSGIEYHAPT 95 (191)
Q Consensus 78 r~~~~~C~~Cgv~~H~~~ 95 (191)
|..+.+.+.+|+++.+..
T Consensus 128 R~~i~e~l~tGi~aid~l 145 (428)
T PRK08149 128 RRPIREPLITGVRAIDGL 145 (428)
T ss_pred ccCccccccCCcEEEeee
Confidence 999999999999987664
No 43
>TIGR01043 ATP_syn_A_arch ATP synthase archaeal, A subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=99.28 E-value=5.4e-12 Score=110.00 Aligned_cols=56 Identities=30% Similarity=0.443 Sum_probs=54.9
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGK 57 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~ 57 (191)
|++|++|.+.+++|+++.||++|+.|.++|++++|++|+.||||++|++|+|||+.
T Consensus 37 Vi~~~~d~a~iqvye~t~Gl~~G~~V~~tg~plsV~lGpglLGrV~DgigrPLd~~ 92 (578)
T TIGR01043 37 IIRIEGDKAFIQVYEETSGIKPGEPVVGTGAPLSVELGPGLLGSIYDGVQRPLDVL 92 (578)
T ss_pred EEEEcCCeEEEEECCCCCCCCCCCEEEECCCccEEEcCHHHhcceeccCCccccCc
Confidence 89999999999999999999999999999999999999999999999999999976
No 44
>PRK06002 fliI flagellum-specific ATP synthase; Validated
Probab=99.28 E-value=4.5e-12 Score=108.13 Aligned_cols=93 Identities=30% Similarity=0.452 Sum_probs=84.0
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccc-cCCCCCCCCCeeecCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTT-RFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~-~~Cp~~~C~~~~~r~~ 80 (191)
|++|+++.+.+++|++++||+.|+.|.+ +..+++++|++|||||+|++|+|||+.+++.... .+......++++.+..
T Consensus 66 Vv~~~~~~~~l~~~~~~~gi~~g~~v~~-~~~~~v~vg~~llGRV~d~~G~piDg~~~~~~~~~~~~i~~~~p~~~~r~~ 144 (450)
T PRK06002 66 VVRVDPDGVTVKPFEPRIEIGLGDAVFR-KGPLRIRPDPSWKGRVINALGEPIDGLGPLAPGTRPMSIDATAPPAMTRAR 144 (450)
T ss_pred EEEEeCCeEEEEEccCCcCCCCCCEEEe-CCCceeecCcccccCEECCCCcCCCCCCCCCCCcceeeccCCCCCCeEeec
Confidence 8999999999999999999999999999 6689999999999999999999999987665433 4577889999999999
Q ss_pred CCCccccCCcccCcc
Q psy271 81 VREPMQSGIEYHAPT 95 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~~ 95 (191)
+.+.+.+|+++.+..
T Consensus 145 v~~~l~TGi~aID~L 159 (450)
T PRK06002 145 VETGLRTGVRVIDIF 159 (450)
T ss_pred ceEEcCCCcEEeeee
Confidence 999999999988764
No 45
>TIGR01042 V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.
Probab=99.24 E-value=9.1e-12 Score=108.32 Aligned_cols=56 Identities=27% Similarity=0.474 Sum_probs=54.7
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGK 57 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~ 57 (191)
||+|++|.+.+++|+++.||++|+.|..+|.+++|++|+.||||++|++|+|||+.
T Consensus 38 VI~l~~d~a~iq~ye~t~Gl~~G~~V~~tg~~lsv~lGpglLG~V~DgigrPLd~~ 93 (591)
T TIGR01042 38 IIRLEGDKATIQVYEETSGLTVGDPVLRTGKPLSVELGPGILGNIFDGIQRPLKAI 93 (591)
T ss_pred EEEEcCCeEEEEEccCccCCCCCCEEEeCCCccEEEcCHHHhhcccCcCCCchHHH
Confidence 89999999999999999999999999999999999999999999999999999965
No 46
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=99.16 E-value=4.7e-11 Score=104.34 Aligned_cols=57 Identities=28% Similarity=0.479 Sum_probs=55.3
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKG 58 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~ 58 (191)
|++++++.+.+++|+++.||++|+.|.++|++++|++|+.||||++|++|+|||+.+
T Consensus 40 Vi~~~~d~a~iqv~e~T~Gl~~G~~V~~tg~plsv~lGpglLGrv~Dg~grPLd~~~ 96 (586)
T PRK04192 40 IIRIEGDKATIQVYEETSGIKPGEPVEFTGEPLSVELGPGLLGSIFDGIQRPLDELA 96 (586)
T ss_pred EEEEeCCceEEEEecCCcCCCCCCEEEeCCCccEEEcCHHhcCCeecCCCCcccccc
Confidence 899999999999999999999999999999999999999999999999999999764
No 47
>COG1156 NtpB Archaeal/vacuolar-type H+-ATPase subunit B [Energy production and conversion]
Probab=99.12 E-value=9.6e-11 Score=97.29 Aligned_cols=98 Identities=29% Similarity=0.399 Sum_probs=90.3
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCe-EEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDI-VKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~-v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|+.++.+.+.++.|+.+.|+...+. |.++|..++++++++|+||++|++|+|||+.+.+.++...-.+....||..|..
T Consensus 46 Vle~~~~~a~vQVfegT~Gl~~~~t~vrF~g~~l~i~vs~dllGRifnG~G~PiDggp~i~~e~~~dI~g~~~NP~aR~y 125 (463)
T COG1156 46 VLEVRGDKAVVQVFEGTSGLDTKGTTVRFTGETLKIPVSEDLLGRIFNGSGKPIDGGPEIVPEDRLDINGAPINPYARIY 125 (463)
T ss_pred EeeccCceEEEEEeecccCCCCCCceEEEeCceEEEeecHHhhhhhhcCCCCcCCCCCcCCCCcccccCCCCCCchhhhC
Confidence 7889999999999999999996666 999999999999999999999999999999988877767788889999999999
Q ss_pred CCCccccCCcccCccchHH
Q psy271 81 VREPMQSGIEYHAPTDCAV 99 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~~~C~~ 99 (191)
..+.+.+|++++++.++-.
T Consensus 126 P~efIqTgIsaIDg~NtLv 144 (463)
T COG1156 126 PEEFIQTGISAIDGMNTLV 144 (463)
T ss_pred hhhHhhcCccHHhhhhhhh
Confidence 9999999999999987754
No 48
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=99.00 E-value=2.9e-10 Score=93.85 Aligned_cols=91 Identities=31% Similarity=0.500 Sum_probs=83.1
Q ss_pred eeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCccc--ccCCCCCCCCCeeecCC
Q psy271 3 LNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTT--TRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 3 ~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~--~~~Cp~~~C~~~~~r~~ 80 (191)
..|.++.|..++++.++|+..|..|..+|.+++||||+..+||++|.+|++||+.+++... .+|..+...|...+...
T Consensus 47 q~lg~~~VR~Iam~~t~gl~rg~~v~dtg~pi~VPVG~~~lgri~nvlG~~iD~~~~~~~~~~~~~~Ih~~~p~~~e~~~ 126 (468)
T COG0055 47 QHLGDNVVRTIAMGSTDGLVRGLEVIDTGKPISVPVGKGTLGRIFNVLGEPIDEKGPIKAEDFEKWPIHRKAPSFEELST 126 (468)
T ss_pred HHhCCCeEEEEEecCccCcccCcEEecCCCceEEecchhhcccchhccCCcccccCCCCccccceeeccCCCCchhhccc
Confidence 4678899999999999999999999999999999999999999999999999998887654 67888889888888888
Q ss_pred CCCccccCCcccC
Q psy271 81 VREPMQSGIEYHA 93 (191)
Q Consensus 81 ~~~C~~Cgv~~H~ 93 (191)
..+-+.+|++..|
T Consensus 127 ~~EIleTGIKVID 139 (468)
T COG0055 127 KTEILETGIKVID 139 (468)
T ss_pred chhhhhhCceEEE
Confidence 8889999999876
No 49
>KOG1350|consensus
Probab=98.85 E-value=1.8e-09 Score=87.61 Aligned_cols=90 Identities=26% Similarity=0.476 Sum_probs=80.1
Q ss_pred eeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCCC
Q psy271 3 LNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISVR 82 (191)
Q Consensus 3 ~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~~ 82 (191)
.+|.++.|..++++.++|+..|..|..+|.+++|+||.+.|||++|..|+|+|+.+++....+..+..+.|.+.+-....
T Consensus 93 qhlG~n~VR~iAMdgTEGLvRG~~VlDtG~Pi~ipVG~~tLGRI~NViGePiDerGpi~s~~~~~IHaeaP~f~e~s~~~ 172 (521)
T KOG1350|consen 93 QHLGENTVRTIAMDGTEGLVRGQKVLDTGYPISIPVGPETLGRIMNVIGEPIDERGPIKSKKYSPIHAEAPEFVEMSVEQ 172 (521)
T ss_pred HHhCcCeEEEEEecCchhhhcCcccccCCCceeeecCHHHHhhHHHhcCCcccccCCcccccccccccCChhHhhhcccH
Confidence 46889999999999999999999999999999999999999999999999999999998887677788888888777666
Q ss_pred CccccCCccc
Q psy271 83 EPMQSGIEYH 92 (191)
Q Consensus 83 ~C~~Cgv~~H 92 (191)
+-+.+|++..
T Consensus 173 eIl~TGIKVv 182 (521)
T KOG1350|consen 173 EILVTGIKVV 182 (521)
T ss_pred HHHhhcceee
Confidence 6777777653
No 50
>KOG1351|consensus
Probab=98.80 E-value=5.8e-09 Score=83.92 Aligned_cols=94 Identities=28% Similarity=0.382 Sum_probs=84.9
Q ss_pred eeeecCCeEEEEEecCCCCCC-CCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIK-EGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRIS 80 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~-~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~ 80 (191)
|+.++++++.+..|+.+.||- .-..+.++|..++.+|++++|||++|+.|+|||..+++.++...-++..+.+|..|..
T Consensus 63 vlev~g~kavvqvfegtsgid~k~t~~eftg~~lr~pvsedmlgrifngsgkpid~gp~vl~edyldi~gqpinp~~riy 142 (489)
T KOG1351|consen 63 VLEVSGEKAVVQVFEGTSGIDAKKTTVEFTGEILRTPVSEDMLGRIFNGSGKPIDKGPPVLAEDYLDINGQPINPYARIY 142 (489)
T ss_pred EEEecCCeeEEEEeccccccccccceEEEecccccccccHHHhhhhhcCCCCccCCCCCcChHHhhccCCCcCCcccccC
Confidence 788999999999999999998 6778999999999999999999999999999999988877766778888999999988
Q ss_pred CCCccccCCcccCcc
Q psy271 81 VREPMQSGIEYHAPT 95 (191)
Q Consensus 81 ~~~C~~Cgv~~H~~~ 95 (191)
..+-+.+|+.+++.+
T Consensus 143 peemiqtgis~idvm 157 (489)
T KOG1351|consen 143 PEEMIQTGISAIDVM 157 (489)
T ss_pred hHHHHHhCchHHhhh
Confidence 888889998877654
No 51
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.75 E-value=1.2e-08 Score=64.26 Aligned_cols=47 Identities=30% Similarity=0.706 Sum_probs=39.7
Q ss_pred HHHHHHHh--cCCCCC--CCCcceEecC--CcCceEeCCCCcceecccccccc
Q psy271 112 ETANYISA--HTKDCP--KCHICIEKNG--GCNHMQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 112 ~~~~~~~~--~~k~CP--~C~~~i~k~~--GC~~m~C~~C~~~fC~~C~~~~~ 158 (191)
.+..++.. +++.|| +|...|+..+ +..+++|..|++.|||.|+.+|-
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 34455554 578899 9999999975 99999998899999999999984
No 52
>PRK14698 V-type ATP synthase subunit A; Provisional
Probab=98.67 E-value=1.9e-08 Score=93.63 Aligned_cols=56 Identities=25% Similarity=0.414 Sum_probs=54.0
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGK 57 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~ 57 (191)
||+|+++.+.+++|+++.||.+|++|.+++.++++++|++|||||+|++|+||+..
T Consensus 40 VIg~~~d~a~iq~~e~t~Gl~~G~~V~~tg~~l~V~lG~~LLGRV~DGlGrPL~~~ 95 (1017)
T PRK14698 40 IIRLEGDKAVIQVYEETAGLKPGEPVEGTGSSLSVELGPGLLTSIYDGIQRPLEVI 95 (1017)
T ss_pred EEEEeCCEEEEEECCCCCCCCCCCEEEEcCCcceeecCHHHhhcccCCCCChHHHH
Confidence 89999999999999999999999999999999999999999999999999998753
No 53
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.59 E-value=2.1e-08 Score=63.16 Aligned_cols=39 Identities=38% Similarity=0.912 Sum_probs=29.8
Q ss_pred cCCCCCC--CCcceEecCCcCc--eEeCCCCcceecccccccc
Q psy271 120 HTKDCPK--CHICIEKNGGCNH--MQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 120 ~~k~CP~--C~~~i~k~~GC~~--m~C~~C~~~fC~~C~~~~~ 158 (191)
+.+.||+ |...+++.++.++ |+|..|++.|||.|+.+|-
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWH 59 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESC
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccC
Confidence 4679987 9999999999999 9998899999999999983
No 54
>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.
Probab=98.52 E-value=3.7e-08 Score=79.34 Aligned_cols=69 Identities=26% Similarity=0.371 Sum_probs=59.5
Q ss_pred ccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCCCCccccCCcccCc-cchHHHH
Q psy271 33 IVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISVREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 33 ~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
+++|++|+++|||++|++|++||+++++....++......++++.|..+.+.+.||+++.|. .++..-|
T Consensus 1 ~~~Vpvg~~lLGRVvd~lG~piD~~~~~~~~~~~~i~~~ap~~~~R~~i~e~l~TGIkaID~l~pig~GQ 70 (276)
T cd01135 1 TLKVPVSEDMLGRIFNGSGKPIDGGPEILAEEYLDINGPPINPVARIYPEEMIQTGISAIDGMNTLVRGQ 70 (276)
T ss_pred CcEEECChhhcCCEECCCCCCCCCCCCCCCCceeeccCCCcCchhcCCcccccccCcEeeecccccccCC
Confidence 36899999999999999999999987765555677888999999999999999999999988 4666544
No 55
>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.
Probab=98.45 E-value=7.7e-08 Score=77.62 Aligned_cols=68 Identities=31% Similarity=0.542 Sum_probs=58.8
Q ss_pred ccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCCCCccccCCcccCcc-chHHH
Q psy271 33 IVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISVREPMQSGIEYHAPT-DCAVI 100 (191)
Q Consensus 33 ~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~~~C~~Cgv~~H~~~-~C~~~ 100 (191)
+++|++|+++|||++|++|++||+++++....+|......++++.|..+.+.+.||+++.|.. ++..-
T Consensus 1 ~~~vpvg~~llGRv~d~~G~piD~~~~~~~~~~~~i~~~~p~~~~R~~~~e~L~TGIr~ID~l~pig~G 69 (274)
T cd01133 1 PISVPVGPETLGRIFNVLGEPIDERGPIKTKKTWPIHREAPEFVEQSTKTEILETGIKVIDLLAPYAKG 69 (274)
T ss_pred CcEEecChhhcCCEECCCCCccCCCCCCCccccccccCCCCCchhhcCcCcccccCceeeeccCCcccC
Confidence 468999999999999999999999877655556888889999999999999999999999884 55443
No 56
>COG1155 NtpA Archaeal/vacuolar-type H+-ATPase subunit A [Energy production and conversion]
Probab=98.45 E-value=1.8e-07 Score=80.21 Aligned_cols=56 Identities=23% Similarity=0.422 Sum_probs=53.9
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGK 57 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~ 57 (191)
||++++|++.++.|+++.||++|++|..||.++++.+|+.||+.+.|++++||+..
T Consensus 38 iI~i~gd~a~iQVyE~T~Gi~~Ge~V~~Tg~pLsvELGPGll~~IyDGiQrPL~~i 93 (588)
T COG1155 38 IIRIEGNRATIQVYEDTAGIRPGEKVENTGRPLSVELGPGLLKSIYDGIQRPLDVI 93 (588)
T ss_pred EEEEeCCeEEEEEEeecCCCCCCCeeecCCCceEEEeCccHHhhhhhhccChHHHH
Confidence 78999999999999999999999999999999999999999999999999998753
No 57
>KOG1353|consensus
Probab=98.41 E-value=2.1e-07 Score=73.38 Aligned_cols=84 Identities=63% Similarity=0.894 Sum_probs=70.8
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCC
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISV 81 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~ 81 (191)
.++++.+.+.++.|++..-++.|+.|..++....+++++.|+||+.|++|+++|+++++....+. ++.|...
T Consensus 56 alnle~~~vg~v~~g~d~~ikeg~~VkrTgaIvDVpvg~~LlgrvvdAlGn~idgkG~i~~~~~~--------ii~r~Sv 127 (340)
T KOG1353|consen 56 ALNLEGENVGVVVFGEDSLIKEGDTVKRTAAISDVPPLKALLGRVGCALGEPIDGNGKISAKERR--------IIPRASV 127 (340)
T ss_pred hccccCCceEEEEEcCcceeccCceEEeeeeeeccCchHHHhhhhhhhhcCeecCCCCccccccc--------cccceee
Confidence 46788999999999999999999999999999999999999999999999999999887554332 5556666
Q ss_pred CCccccCCcccC
Q psy271 82 REPMQSGIEYHA 93 (191)
Q Consensus 82 ~~C~~Cgv~~H~ 93 (191)
.++..+|.++-+
T Consensus 128 ~epmqtg~KAvd 139 (340)
T KOG1353|consen 128 DEPMQTGLKAVD 139 (340)
T ss_pred echhhhhhhHhh
Confidence 666677766543
No 58
>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.
Probab=98.38 E-value=1.3e-07 Score=76.25 Aligned_cols=68 Identities=59% Similarity=0.880 Sum_probs=58.5
Q ss_pred cccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCCCCccccCCcccCc-cchHHHH
Q psy271 34 VDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISVREPMQSGIEYHAP-TDCAVIK 101 (191)
Q Consensus 34 ~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~~~C~~Cgv~~H~~-~~C~~~~ 101 (191)
++|++|+++|||++|++|++||+++++.....|......++++.|..+.+.+.||+++.|. .++..-|
T Consensus 2 ~~vpvg~~lLGRvld~~G~piD~~~~~~~~~~~~i~~~~p~~~~R~~i~e~L~TGI~~ID~l~pigrGQ 70 (274)
T cd01132 2 ADVPVGEALLGRVVDALGNPIDGKGPIETKERRPIESKAPGIIPRKSVNEPLQTGIKAIDAMIPIGRGQ 70 (274)
T ss_pred eEEECCHhhCCCEEccCCCCccCCCCcCcCceeeccCCCCChhhcCCcccccccCCEEeeccCCcccCC
Confidence 5799999999999999999999987765566678888999999999999999999999887 3555433
No 59
>KOG1352|consensus
Probab=98.26 E-value=4.6e-07 Score=75.59 Aligned_cols=76 Identities=21% Similarity=0.331 Sum_probs=61.8
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeec
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPR 78 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r 78 (191)
||+|++|.++++.|+++.|++.|++|..||+++++.+|+.++|.++|+.++||........+ .|-|..---.++.|
T Consensus 57 iIrlegD~aTIQVYEeTsG~tVgDpvlrTgkPLsvELGPGimgsIfDGIQRPLk~I~~~s~s-iyiPkGv~~~aL~r 132 (618)
T KOG1352|consen 57 IIRLEGDMATIQVYEETSGLTVGDPVLRTGKPLSVELGPGIMGSIFDGIQRPLKDISELSQS-IYIPKGVNTPALDR 132 (618)
T ss_pred eeEecCceeEEEEEeccCCcccCCchhhcCCcceEeeCcchhhhhhhhhhhhHHHHHHhcCc-EeccCCCCccccCc
Confidence 78999999999999999999999999999999999999999999999999998765443333 35554433333333
No 60
>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
Probab=97.94 E-value=2.5e-06 Score=70.66 Aligned_cols=63 Identities=37% Similarity=0.659 Sum_probs=54.8
Q ss_pred ccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCCCCccccCCcccCcc
Q psy271 33 IVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISVREPMQSGIEYHAPT 95 (191)
Q Consensus 33 ~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~~~C~~Cgv~~H~~~ 95 (191)
+++|++|+++|||++|++|+|||+.+++....++......++++.|..+.+.+.+|+++.+..
T Consensus 1 ~~~v~vg~~~lGrv~d~~G~pid~~~~~~~~~~~~i~~~~~~~~~R~~~~~~l~tGi~aiD~l 63 (326)
T cd01136 1 PLSVPVGDALLGRVLDAFGEPLDGKGPLGKEVRYPLLRTPPNPLKRRPIDEVLPTGVRAIDGL 63 (326)
T ss_pred CceeeCCcccccCEECCCCcccCCCCCCCCCccccccCCCcCHHHhccceeEcCCCcEEEeee
Confidence 368999999999999999999999876655556778888899999999999999999987764
No 61
>PF02874 ATP-synt_ab_N: ATP synthase alpha/beta family, beta-barrel domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR004100 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the N-terminal domain, which forms a closed beta-barrel with Greek-key topology. ; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015992 proton transport, 0046034 ATP metabolic process, 0016469 proton-transporting two-sector ATPase complex; PDB: 1W0K_A 1H8H_B 2WSS_A 1EFR_A 2JIZ_H 1E1Q_A 2V7Q_B 1E79_B 1E1R_C 2XND_C ....
Probab=97.46 E-value=0.00014 Score=46.35 Aligned_cols=31 Identities=32% Similarity=0.508 Sum_probs=29.2
Q ss_pred CeeeecCCeEEEEEecCCCCCCCCCeEEecC
Q psy271 1 MALNLEPDNVGVVVFGNDRLIKEGDIVKRTG 31 (191)
Q Consensus 1 ~v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g 31 (191)
.|++|++|.+.+++|++++||++|+.|.+||
T Consensus 39 ~Vv~~~~~~v~~~~~~~t~Gl~~G~~V~~tG 69 (69)
T PF02874_consen 39 EVVGLDEDEVRLQVFGSTDGLSRGTEVRFTG 69 (69)
T ss_dssp EEEEEETTEEEEEESSSGTTSBTTCEEEEEE
T ss_pred eecccCccEEEEEEecCCCCCCCCCEEEcCc
Confidence 3899999999999999999999999999885
No 62
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=97.44 E-value=0.0001 Score=46.01 Aligned_cols=37 Identities=16% Similarity=0.183 Sum_probs=21.9
Q ss_pred cccccCCCCCCCCCeeecCCCC-------------CccccCCcccCccch
Q psy271 61 KTTTRFRVGIKAPGIIPRISVR-------------EPMQSGIEYHAPTDC 97 (191)
Q Consensus 61 ~~~~~~Cp~~~C~~~~~r~~~~-------------~C~~Cgv~~H~~~~C 97 (191)
..+.+|||+++|..++...... .|+.|+.+||.+.+|
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 3466799999999988764332 299999999999887
No 63
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=97.22 E-value=0.00025 Score=44.26 Aligned_cols=36 Identities=11% Similarity=0.225 Sum_probs=29.0
Q ss_pred ccccCCCCCCCCCeeecCC--C-----------CCccccCCcccCccch
Q psy271 62 TTTRFRVGIKAPGIIPRIS--V-----------REPMQSGIEYHAPTDC 97 (191)
Q Consensus 62 ~~~~~Cp~~~C~~~~~r~~--~-----------~~C~~Cgv~~H~~~~C 97 (191)
.+.+|||.++|..++.... . ..|+.|+.+||.+.+|
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4678999999998877752 1 2399999999999887
No 64
>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=96.60 E-value=0.001 Score=34.15 Aligned_cols=24 Identities=33% Similarity=0.861 Sum_probs=17.4
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
|.||.|+..|..+ -..|..|||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 6799999998543 24566688776
No 65
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=96.08 E-value=0.0033 Score=53.73 Aligned_cols=35 Identities=51% Similarity=0.827 Sum_probs=32.4
Q ss_pred cccCCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 157 TIDGKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
..++.++-....+.+++..||||++|.+|.|||+|
T Consensus 114 pidgkg~i~~~~~~~~e~~Apgv~~RksV~ePlqT 148 (504)
T COG0056 114 PIDGKGPIDATKTRPVEKKAPGVMDRKSVNEPLQT 148 (504)
T ss_pred ccCCCCCccccccCccccccCceecccccCchhhh
Confidence 46677899999999999999999999999999998
No 66
>PRK12608 transcription termination factor Rho; Provisional
Probab=95.67 E-value=0.007 Score=51.16 Aligned_cols=70 Identities=11% Similarity=0.034 Sum_probs=52.6
Q ss_pred CCCCCCCCeEEecCCccccccchhHHHHHHhhcCCcccCCCCCcccccCCCCCCCCCeeecCCCCCcc-ccCCcccCc
Q psy271 18 DRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDALGNTIDGKGPLKTTTRFRVGIKAPGIIPRISVREPM-QSGIEYHAP 94 (191)
Q Consensus 18 ~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~g~~ld~~~~~~~~~~~Cp~~~C~~~~~r~~~~~C~-~Cgv~~H~~ 94 (191)
..||+.|+.|..+++. +++..+||||+|.+|+++|+.. ...+-....++++..|..+.... .+++++.+.
T Consensus 56 ~~~l~~Gd~V~~~~r~---~~~~~~LgrV~~~~G~p~d~~~----~~~~~~~~~pi~p~~R~~ie~~~~~~~~RvID~ 126 (380)
T PRK12608 56 RFNLRTGDVVEGVARP---RERYRVLVRVDSVNGTDPEKLA----RRPHFDDLTPLHPRERLRLETGSDDLSMRVVDL 126 (380)
T ss_pred HhCCCCCCEEEeccCC---CCChhheEEEeccCCcCchhcc----cccCcCcCCCCCccccccccccCcchhHhhhhh
Confidence 3579999999999887 9999999999999999998762 11223344666777777776655 666666654
No 67
>PHA00626 hypothetical protein
Probab=95.01 E-value=0.023 Score=34.33 Aligned_cols=27 Identities=30% Similarity=0.587 Sum_probs=21.9
Q ss_pred CCCCCCc-ceEecCCcCc----eEeCCCCcce
Q psy271 123 DCPKCHI-CIEKNGGCNH----MQCYHCKHEF 149 (191)
Q Consensus 123 ~CP~C~~-~i~k~~GC~~----m~C~~C~~~f 149 (191)
.||+|+. .|.|.+-|+. -.|..||+.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 5999999 5889888766 6687788777
No 68
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.54 E-value=0.033 Score=33.15 Aligned_cols=28 Identities=32% Similarity=0.594 Sum_probs=21.5
Q ss_pred CCCCCCCcceEecCC--cCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKNGG--CNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~~G--C~~m~C~~C~~~f 149 (191)
+-||.|+.++...++ -++..|..|++.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 359999999976543 4689999898763
No 69
>KOG0823|consensus
Probab=94.16 E-value=0.016 Score=45.24 Aligned_cols=25 Identities=32% Similarity=0.753 Sum_probs=19.3
Q ss_pred eEeCCCCcceecccccccccCCCCCCC
Q psy271 140 MQCYHCKHEFCWMCLGNTIDGKGPLKT 166 (191)
Q Consensus 140 m~C~~C~~~fC~~C~~~~~~~~~~~~~ 166 (191)
+|| |||-|||-|+-.|......-..
T Consensus 62 vTl--CGHLFCWpClyqWl~~~~~~~~ 86 (230)
T KOG0823|consen 62 VTL--CGHLFCWPCLYQWLQTRPNSKE 86 (230)
T ss_pred Eee--cccceehHHHHHHHhhcCCCee
Confidence 666 9999999999999875433333
No 70
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=94.07 E-value=0.053 Score=30.12 Aligned_cols=27 Identities=26% Similarity=0.803 Sum_probs=20.0
Q ss_pred CCCCCCCcceEec------CCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKN------GGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~------~GC~~m~C~~C~~~f 149 (191)
..||+|+..+.-. .| ..+.|++|++.|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~-~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG-GKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC-CEEECCCCCCEE
Confidence 4699999977654 22 379999888776
No 71
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=94.04 E-value=0.052 Score=28.73 Aligned_cols=27 Identities=30% Similarity=0.688 Sum_probs=14.5
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
-+||+|+.-....+|. .|.|..|+++|
T Consensus 3 p~Cp~C~se~~y~D~~-~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGE-LLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SS-SEEETTTTEEE
T ss_pred CCCCCCCCcceeccCC-EEeCCcccccC
Confidence 3799999999998775 47898888876
No 72
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.88 E-value=0.059 Score=29.94 Aligned_cols=28 Identities=29% Similarity=0.787 Sum_probs=21.4
Q ss_pred CCCCCCCcceEec-----CCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKN-----GGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~-----~GC~~m~C~~C~~~f 149 (191)
..||+|+...... .+=-.+.|++|++.|
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4799999988653 233489999999877
No 73
>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=93.60 E-value=0.13 Score=27.55 Aligned_cols=29 Identities=24% Similarity=0.509 Sum_probs=19.6
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~ 148 (191)
+.+-||.|+.+.+...+=..|.|..|+++
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 45779999999999888788999989875
No 74
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=93.59 E-value=0.042 Score=28.01 Aligned_cols=13 Identities=31% Similarity=0.674 Sum_probs=9.6
Q ss_pred CCCCCCCCcceEe
Q psy271 121 TKDCPKCHICIEK 133 (191)
Q Consensus 121 ~k~CP~C~~~i~k 133 (191)
.+.||+|+..++.
T Consensus 2 ~~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 2 EMFCPNCGAEIDP 14 (26)
T ss_pred cCCCcccCCcCCc
Confidence 4679999997743
No 75
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.50 E-value=0.083 Score=30.76 Aligned_cols=30 Identities=17% Similarity=0.420 Sum_probs=22.9
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceec
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCW 151 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~ 151 (191)
-+||+|+..++....=..++|..||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 469999999987655447899888876654
No 76
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=93.09 E-value=0.089 Score=31.36 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=21.1
Q ss_pred cCCCCCCCCc-ceEecCCcCceEeCCCCcce
Q psy271 120 HTKDCPKCHI-CIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 120 ~~k~CP~C~~-~i~k~~GC~~m~C~~C~~~f 149 (191)
..+-||+|+. .+.... +.+.|.+||+.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 4568999998 443333 699999999875
No 77
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=92.85 E-value=0.061 Score=26.61 Aligned_cols=22 Identities=32% Similarity=0.729 Sum_probs=13.3
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~ 148 (191)
.||+|+..|+.. ...|..||+.
T Consensus 1 ~Cp~CG~~~~~~----~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD----AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc----CcchhhhCCc
Confidence 488999888543 2345555543
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.55 E-value=0.13 Score=28.39 Aligned_cols=28 Identities=29% Similarity=0.725 Sum_probs=20.7
Q ss_pred CCCCCCCcceEec-----CCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKN-----GGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~-----~GC~~m~C~~C~~~f 149 (191)
..||+|+..++.. ++=-.+.|++|++.|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4699999998753 222368999998876
No 79
>KOG1815|consensus
Probab=92.37 E-value=0.094 Score=45.54 Aligned_cols=39 Identities=28% Similarity=0.705 Sum_probs=32.7
Q ss_pred CCCCC--CCCcceEe-cCCcCceEeCCCCcceecccccccccC
Q psy271 121 TKDCP--KCHICIEK-NGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 121 ~k~CP--~C~~~i~k-~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
.|-|| .|+..+.. .+.+..+.| .|++.|||.|+.+|...
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C-~~g~~FC~~C~~~~H~p 199 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDC-GCGHEFCFACGEESHSP 199 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeC-CCCchhHhhccccccCC
Confidence 45565 79999987 888999999 59999999999887653
No 80
>KOG1814|consensus
Probab=91.86 E-value=0.088 Score=44.59 Aligned_cols=41 Identities=22% Similarity=0.629 Sum_probs=37.0
Q ss_pred hcCCCCCC--CCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 119 AHTKDCPK--CHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 119 ~~~k~CP~--C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
.+.+-||. |..+.-...|++-..|++|.+.||..|...|-.
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG 313 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG 313 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC
Confidence 35789998 999996789999999999999999999998864
No 81
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=91.33 E-value=0.042 Score=45.03 Aligned_cols=29 Identities=24% Similarity=0.565 Sum_probs=24.0
Q ss_pred CCCCCCCCcceEe-cCCcCceEeCCCCcce
Q psy271 121 TKDCPKCHICIEK-NGGCNHMQCYHCKHEF 149 (191)
Q Consensus 121 ~k~CP~C~~~i~k-~~GC~~m~C~~C~~~f 149 (191)
|.+||+|+..+-+ .-.=|.+.|.+|+|+|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 8899999999875 3445678999999998
No 82
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=91.32 E-value=0.051 Score=30.37 Aligned_cols=21 Identities=24% Similarity=0.691 Sum_probs=17.2
Q ss_pred eEeCCCCcceecccccccccC
Q psy271 140 MQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 140 m~C~~C~~~fC~~C~~~~~~~ 160 (191)
+.-..|||.||+.|...|...
T Consensus 12 ~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 12 VVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp EEECTTSEEEEHHHHHHHHHC
T ss_pred CEECCCCCchhHHHHHHHHHC
Confidence 345579999999999998765
No 83
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=91.07 E-value=0.14 Score=47.37 Aligned_cols=27 Identities=33% Similarity=0.904 Sum_probs=24.4
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCccee
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC 150 (191)
..||.|+..+...+||. +|..||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 36999999999999998 8999999876
No 84
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=90.90 E-value=0.045 Score=41.91 Aligned_cols=34 Identities=26% Similarity=0.606 Sum_probs=25.0
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
..-.||-|...+.. -+. +.|||.|||.|...|..
T Consensus 17 ~~~~CpICld~~~d-----PVv-T~CGH~FC~~CI~~wl~ 50 (193)
T PLN03208 17 GDFDCNICLDQVRD-----PVV-TLCGHLFCWPCIHKWTY 50 (193)
T ss_pred CccCCccCCCcCCC-----cEE-cCCCchhHHHHHHHHHH
Confidence 34679999876531 123 46999999999999853
No 85
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=90.72 E-value=0.22 Score=31.47 Aligned_cols=30 Identities=23% Similarity=0.606 Sum_probs=24.1
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
+++.||.|+....+...=..++|..||+.+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEE
Confidence 578999999999995555678898787653
No 86
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=90.41 E-value=0.54 Score=26.73 Aligned_cols=24 Identities=25% Similarity=0.841 Sum_probs=18.4
Q ss_pred CCCCCCCCcceEe-cCCcCceEeCCCC
Q psy271 121 TKDCPKCHICIEK-NGGCNHMQCYHCK 146 (191)
Q Consensus 121 ~k~CP~C~~~i~k-~~GC~~m~C~~C~ 146 (191)
...||+|+.+..+ .+| .+.|..|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCCCC
Confidence 4689999999998 455 67787664
No 87
>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=90.29 E-value=0.18 Score=35.09 Aligned_cols=27 Identities=26% Similarity=0.683 Sum_probs=19.2
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
+.||+|+....=-.- +.++|..||+.|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 469999988864333 788898666554
No 88
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=90.13 E-value=0.058 Score=44.17 Aligned_cols=30 Identities=17% Similarity=0.149 Sum_probs=22.2
Q ss_pred CCCCCCCCcceEe-cCCcCceEeCCCCccee
Q psy271 121 TKDCPKCHICIEK-NGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 121 ~k~CP~C~~~i~k-~~GC~~m~C~~C~~~fC 150 (191)
|.+||+|+..+.+ .-.=|.+.|.+|+|+|=
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 7788888888865 34456778888888763
No 89
>KOG2906|consensus
Probab=90.05 E-value=0.26 Score=33.37 Aligned_cols=28 Identities=29% Similarity=0.682 Sum_probs=21.9
Q ss_pred CCCCCCcceEe--cCCcCceEeCCCCccee
Q psy271 123 DCPKCHICIEK--NGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 123 ~CP~C~~~i~k--~~GC~~m~C~~C~~~fC 150 (191)
-||.|+..+.- .+.||...|..|.|.|=
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 49999987654 44599999998998774
No 90
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=89.84 E-value=0.29 Score=47.09 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=14.5
Q ss_pred CccCCCccccCCCCCCCC
Q psy271 173 GIKAPGIIPRISVREPMQ 190 (191)
Q Consensus 173 ~~~a~~i~~r~~~~~~~~ 190 (191)
=+..-|+++++.+-|||+
T Consensus 750 ~KgVkgl~S~~k~~EplE 767 (1337)
T PRK14714 750 LKGVKGLTSREKIPEPLE 767 (1337)
T ss_pred cccceecccCCCCCcchH
Confidence 355778999999999985
No 91
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=89.83 E-value=0.074 Score=29.85 Aligned_cols=32 Identities=31% Similarity=0.681 Sum_probs=21.6
Q ss_pred CCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
||-|....+... +=..|+|.||..|...|...
T Consensus 1 C~iC~~~~~~~~-----~~~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 1 CPICLEPFEDPV-----ILLPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp ETTTSSBCSSEE-----EETTTSEEEEHHHHHHHHHH
T ss_pred CCcCCccccCCC-----EEecCCCcchHHHHHHHHHh
Confidence 445555443322 34479999999999998764
No 92
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=89.79 E-value=0.067 Score=43.70 Aligned_cols=30 Identities=27% Similarity=0.516 Sum_probs=23.9
Q ss_pred CCCCCCCCcceEec-CCcCceEeCCCCccee
Q psy271 121 TKDCPKCHICIEKN-GGCNHMQCYHCKHEFC 150 (191)
Q Consensus 121 ~k~CP~C~~~i~k~-~GC~~m~C~~C~~~fC 150 (191)
|.+||+|+..+.+. -.=|.+.|.+|+|+|=
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 88999999999764 4456689999999863
No 93
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=89.56 E-value=0.29 Score=28.05 Aligned_cols=25 Identities=24% Similarity=0.554 Sum_probs=18.2
Q ss_pred HHHHhcCCCCCCCCcceEecCCcCceEeC
Q psy271 115 NYISAHTKDCPKCHICIEKNGGCNHMQCY 143 (191)
Q Consensus 115 ~~~~~~~k~CP~C~~~i~k~~GC~~m~C~ 143 (191)
.+.....++||+|++.- |+.-+.|.
T Consensus 5 k~TlRGirkCp~CGt~N----G~R~~~CK 29 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN----GTRGLSCK 29 (44)
T ss_pred hhhHhccccCCcCcCcc----Cccccccc
Confidence 34556789999999876 66666664
No 94
>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=88.73 E-value=0.5 Score=25.84 Aligned_cols=28 Identities=21% Similarity=0.486 Sum_probs=17.3
Q ss_pred CCCCCCCcceEe-cCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEK-NGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k-~~GC~~m~C~~C~~~f 149 (191)
+=||.|+.+..- .+.=.+..|..|+|++
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 349999988764 3333333888888764
No 95
>KOG0317|consensus
Probab=88.56 E-value=0.086 Score=42.62 Aligned_cols=36 Identities=28% Similarity=0.638 Sum_probs=25.8
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcceecccccccccCC
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDGK 161 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~~ 161 (191)
++.+|--|-... .|-+|+=|||-|||-|...|-...
T Consensus 238 a~~kC~LCLe~~------~~pSaTpCGHiFCWsCI~~w~~ek 273 (293)
T KOG0317|consen 238 ATRKCSLCLENR------SNPSATPCGHIFCWSCILEWCSEK 273 (293)
T ss_pred CCCceEEEecCC------CCCCcCcCcchHHHHHHHHHHccc
Confidence 345566665544 245777899999999999997543
No 96
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=88.52 E-value=0.14 Score=41.25 Aligned_cols=31 Identities=23% Similarity=0.471 Sum_probs=25.8
Q ss_pred cCCCCCCCCcceEe-cCCcCceEeCCCCccee
Q psy271 120 HTKDCPKCHICIEK-NGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 120 ~~k~CP~C~~~i~k-~~GC~~m~C~~C~~~fC 150 (191)
-|.+||+|+..+.+ .-+=|.+.|.+|+|+|=
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCcccc
Confidence 47899999999875 56778899999999874
No 97
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=88.39 E-value=0.39 Score=33.17 Aligned_cols=30 Identities=27% Similarity=0.569 Sum_probs=22.3
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
-+||+|+.-+.-..|=+ +.|. .|+.+|...
T Consensus 3 p~CP~C~seytY~dg~~-~iCp--------eC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICP--------SCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceEecCCe-eECc--------ccccccccc
Confidence 47999999998888854 6777 555666543
No 98
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=88.12 E-value=0.26 Score=44.78 Aligned_cols=33 Identities=30% Similarity=0.658 Sum_probs=24.4
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcc------eecccccccc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHE------FCWMCLGNTI 158 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~------fC~~C~~~~~ 158 (191)
+.|-||+|+..+. +..|.+||+. ||-.||.+..
T Consensus 14 ~akFC~~CG~~l~------~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 14 NNRFCQKCGTSLT------HKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CCccccccCCCCC------CCcCCCCCCCCCcccccccccCCccc
Confidence 3567888888773 3568888877 9999998644
No 99
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=87.83 E-value=0.61 Score=29.11 Aligned_cols=30 Identities=23% Similarity=0.521 Sum_probs=21.6
Q ss_pred hcCCCCCCCCcceEe---cCCcCceEeCCCCcc
Q psy271 119 AHTKDCPKCHICIEK---NGGCNHMQCYHCKHE 148 (191)
Q Consensus 119 ~~~k~CP~C~~~i~k---~~GC~~m~C~~C~~~ 148 (191)
.+.|+||-|+..+.+ .+|=....|-+|+..
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 357999999988765 466555677666664
No 100
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=87.82 E-value=0.21 Score=27.81 Aligned_cols=32 Identities=25% Similarity=0.650 Sum_probs=22.0
Q ss_pred CCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
||-|...+ =+-+.-..|+|.||+.|+..|...
T Consensus 2 C~iC~~~~-----~~~~~~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 2 CPICLEEF-----REPVVLLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred CCcCchhh-----hCceEecCCCChhcHHHHHHHHHh
Confidence 66666655 123344459999999999988754
No 101
>PRK04023 DNA polymerase II large subunit; Validated
Probab=87.70 E-value=0.63 Score=43.94 Aligned_cols=33 Identities=21% Similarity=0.402 Sum_probs=25.1
Q ss_pred hcCCCCCCCCcceEecCCcCceEeCCCCc-----ceeccccccc
Q psy271 119 AHTKDCPKCHICIEKNGGCNHMQCYHCKH-----EFCWMCLGNT 157 (191)
Q Consensus 119 ~~~k~CP~C~~~i~k~~GC~~m~C~~C~~-----~fC~~C~~~~ 157 (191)
...+.||+|+... ....|..||. .||-.|+..-
T Consensus 624 Vg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred ccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcC
Confidence 3578999999985 5578888885 4888887654
No 102
>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=87.25 E-value=0.59 Score=29.80 Aligned_cols=35 Identities=34% Similarity=0.769 Sum_probs=22.9
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcc-----eeccccccccc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHE-----FCWMCLGNTID 159 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~-----fC~~C~~~~~~ 159 (191)
.||.|+..++..+ .+..|..|... ||-.|++++..
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHHH
Confidence 5999999999988 68889989876 48888887653
No 103
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=86.98 E-value=2.1 Score=24.74 Aligned_cols=29 Identities=17% Similarity=0.442 Sum_probs=18.0
Q ss_pred cCCCCCCCCcc-eEecCCcCceEeCCCCcc
Q psy271 120 HTKDCPKCHIC-IEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 120 ~~k~CP~C~~~-i~k~~GC~~m~C~~C~~~ 148 (191)
+.-.||+|+.. +-...+=....|..|+++
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 44579999984 333344345677777653
No 104
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=86.87 E-value=0.73 Score=25.08 Aligned_cols=26 Identities=31% Similarity=0.715 Sum_probs=14.9
Q ss_pred CCCCCCCcceEec--CCcCc--eEeCCCCc
Q psy271 122 KDCPKCHICIEKN--GGCNH--MQCYHCKH 147 (191)
Q Consensus 122 k~CP~C~~~i~k~--~GC~~--m~C~~C~~ 147 (191)
|-||+|+.+++.. .|=++ +.|..|++
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 3599999999874 45444 88988875
No 105
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=86.81 E-value=0.36 Score=30.24 Aligned_cols=25 Identities=32% Similarity=0.923 Sum_probs=10.1
Q ss_pred CCCCCCCCcceEec---CCcCceEeCCC
Q psy271 121 TKDCPKCHICIEKN---GGCNHMQCYHC 145 (191)
Q Consensus 121 ~k~CP~C~~~i~k~---~GC~~m~C~~C 145 (191)
.-+|++|....... +||.|+.|+.|
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~C 34 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSC 34 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHH
Confidence 46899998876442 56665555533
No 106
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=86.79 E-value=0.64 Score=27.86 Aligned_cols=31 Identities=23% Similarity=0.272 Sum_probs=19.2
Q ss_pred CCCCCCCCcceEe------cCCcCce-EeCCCCcceec
Q psy271 121 TKDCPKCHICIEK------NGGCNHM-QCYHCKHEFCW 151 (191)
Q Consensus 121 ~k~CP~C~~~i~k------~~GC~~m-~C~~C~~~fC~ 151 (191)
.|+||.|+..-+. +.+..++ .|..|+....+
T Consensus 1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 3899999987762 2234444 37666666543
No 107
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=86.72 E-value=0.72 Score=23.89 Aligned_cols=21 Identities=24% Similarity=0.648 Sum_probs=13.7
Q ss_pred CCCCCCcceEecCCcCceEeC
Q psy271 123 DCPKCHICIEKNGGCNHMQCY 143 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~ 143 (191)
.||.|+..+.+.+|=-...|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 499999999999887777775
No 108
>PRK10220 hypothetical protein; Provisional
Probab=86.26 E-value=0.65 Score=32.13 Aligned_cols=30 Identities=23% Similarity=0.416 Sum_probs=22.2
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
-.||+|..-+.-..|=+ +.|. .|+.+|...
T Consensus 4 P~CP~C~seytY~d~~~-~vCp--------eC~hEW~~~ 33 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGM-YICP--------ECAHEWNDA 33 (111)
T ss_pred CcCCCCCCcceEcCCCe-EECC--------cccCcCCcc
Confidence 57999999998887754 6677 566667654
No 109
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=85.87 E-value=0.75 Score=30.53 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=23.9
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCccee
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC 150 (191)
.-..||.|+....|..+=---.|.+||+.|=
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 3568999999998877766677777777663
No 110
>PRK00420 hypothetical protein; Validated
Probab=84.42 E-value=1.1 Score=31.48 Aligned_cols=25 Identities=24% Similarity=0.600 Sum_probs=17.8
Q ss_pred CCCCCCCCcceEe-cCCcCceEeCCCCc
Q psy271 121 TKDCPKCHICIEK-NGGCNHMQCYHCKH 147 (191)
Q Consensus 121 ~k~CP~C~~~i~k-~~GC~~m~C~~C~~ 147 (191)
...||.|+.+..+ .+| +..|..||.
T Consensus 23 ~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~ 48 (112)
T PRK00420 23 SKHCPVCGLPLFELKDG--EVVCPVHGK 48 (112)
T ss_pred cCCCCCCCCcceecCCC--ceECCCCCC
Confidence 5799999999987 555 555654443
No 111
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=84.22 E-value=0.78 Score=27.07 Aligned_cols=27 Identities=19% Similarity=0.461 Sum_probs=18.3
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
.+.||+|+--+....-=+.-.|.+||+
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 478999996444433334778888886
No 112
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=83.64 E-value=0.29 Score=27.92 Aligned_cols=34 Identities=26% Similarity=0.579 Sum_probs=23.4
Q ss_pred CCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
||-|...++. +=.-... .|++.||+.|...|...
T Consensus 3 C~IC~~~~~~--~~~~~~l-~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 3 CPICLEEFED--GEKVVKL-PCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp ETTTTCBHHT--TSCEEEE-TTSEEEEHHHHHHHHHH
T ss_pred CcCCChhhcC--CCeEEEc-cCCCeeCHHHHHHHHHh
Confidence 5666665543 2233445 49999999999999864
No 113
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=83.30 E-value=0.97 Score=32.46 Aligned_cols=25 Identities=32% Similarity=0.746 Sum_probs=17.5
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
.+-||.|+.+..+..| .+.|..|++
T Consensus 28 ~~hCp~Cg~PLF~KdG--~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFRKDG--EVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcceeeCC--eEECCCCCc
Confidence 4689999999988665 455554443
No 114
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=83.11 E-value=0.39 Score=27.35 Aligned_cols=21 Identities=29% Similarity=0.672 Sum_probs=16.0
Q ss_pred eEeCCCCcceecccccccccCC
Q psy271 140 MQCYHCKHEFCWMCLGNTIDGK 161 (191)
Q Consensus 140 m~C~~C~~~fC~~C~~~~~~~~ 161 (191)
++= .|||.||..|+..|....
T Consensus 12 v~l-~CGH~FC~~Cl~~~~~~~ 32 (42)
T PF15227_consen 12 VSL-PCGHSFCRSCLERLWKEP 32 (42)
T ss_dssp EE--SSSSEEEHHHHHHHHCCS
T ss_pred ccc-CCcCHHHHHHHHHHHHcc
Confidence 444 599999999999887543
No 115
>KOG0006|consensus
Probab=83.02 E-value=0.78 Score=37.82 Aligned_cols=48 Identities=21% Similarity=0.455 Sum_probs=37.3
Q ss_pred HHHHHH-hcCCCCC--CCCcceEecCCcCceEeCC-CCcceecccccccccC
Q psy271 113 TANYIS-AHTKDCP--KCHICIEKNGGCNHMQCYH-CKHEFCWMCLGNTIDG 160 (191)
Q Consensus 113 ~~~~~~-~~~k~CP--~C~~~i~k~~GC~~m~C~~-C~~~fC~~C~~~~~~~ 160 (191)
+++++. ....-|| .|+.-+--..-|.++||-. |++.||-.|...|..+
T Consensus 306 tEe~vlq~gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh~g 357 (446)
T KOG0006|consen 306 TEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYHEG 357 (446)
T ss_pred hhhheeecCCEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhccc
Confidence 344443 3556676 8999998888999999986 9999999998876543
No 116
>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=82.30 E-value=0.99 Score=30.91 Aligned_cols=24 Identities=33% Similarity=0.701 Sum_probs=19.3
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~ 148 (191)
-||.|+.++...++ .+.|..|++.
T Consensus 2 fC~~Cg~~l~~~~~--~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNG--VYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCC--eEECcCCCCc
Confidence 59999999977653 7888877776
No 117
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=82.26 E-value=1.2 Score=30.52 Aligned_cols=30 Identities=17% Similarity=0.378 Sum_probs=20.1
Q ss_pred cCCCCCCCCcceE---ecCCcCceEeCCCCcce
Q psy271 120 HTKDCPKCHICIE---KNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 120 ~~k~CP~C~~~i~---k~~GC~~m~C~~C~~~f 149 (191)
+.-.||+|+.... +..|=-|..|..||++|
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 3457999994332 23355689999888775
No 118
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=82.16 E-value=1.7 Score=23.46 Aligned_cols=29 Identities=28% Similarity=0.411 Sum_probs=19.3
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
.+.|+.|+....-+.-=..+.|..|+..|
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 46788898877664444567776666544
No 119
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=81.90 E-value=0.51 Score=25.13 Aligned_cols=16 Identities=31% Similarity=0.929 Sum_probs=14.3
Q ss_pred CCCcceeccccccccc
Q psy271 144 HCKHEFCWMCLGNTID 159 (191)
Q Consensus 144 ~C~~~fC~~C~~~~~~ 159 (191)
.|++.||+.|.+.|..
T Consensus 15 ~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 15 PCGHTFCRSCIRKWLK 30 (39)
T ss_pred cCCChHHHHHHHHHHH
Confidence 6999999999998875
No 120
>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=81.80 E-value=1.7 Score=26.27 Aligned_cols=28 Identities=29% Similarity=0.602 Sum_probs=20.1
Q ss_pred CCCCCCCcceEecCCc--CceEeCCCCcce
Q psy271 122 KDCPKCHICIEKNGGC--NHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC--~~m~C~~C~~~f 149 (191)
-.||.|+..|+..+.= ..+.|..||..+
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 4799999999886432 357888676655
No 121
>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=81.25 E-value=1.1 Score=32.06 Aligned_cols=27 Identities=11% Similarity=0.086 Sum_probs=19.2
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
+.||+|+....--.- +-++|..||+.|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 469999988864333 778998666653
No 122
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=80.46 E-value=1.6 Score=38.35 Aligned_cols=32 Identities=44% Similarity=0.671 Sum_probs=25.5
Q ss_pred CCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 160 GKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 160 ~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+.++.....+++++..+|++++|..|++||+|
T Consensus 96 g~~~~~~~~~~~i~~~ap~~~~R~~v~epl~T 127 (485)
T CHL00059 96 GKGEISASESRLIESPAPGIISRRSVYEPLQT 127 (485)
T ss_pred CCCCcCCCccccccCCCCCchhccCCCccccc
Confidence 33344344567899999999999999999997
No 123
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=79.67 E-value=1.3 Score=26.01 Aligned_cols=27 Identities=22% Similarity=0.536 Sum_probs=20.0
Q ss_pred CCCCC--CCCcceEecCCcCceEeCCCCc
Q psy271 121 TKDCP--KCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 121 ~k~CP--~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
.+.|| .|+.-+--..--+...|.+|++
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 46899 9999776666667899998875
No 124
>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=79.64 E-value=2.4 Score=24.05 Aligned_cols=24 Identities=21% Similarity=0.524 Sum_probs=13.7
Q ss_pred CCCCCCcce-EecCCcCceEeCCCC
Q psy271 123 DCPKCHICI-EKNGGCNHMQCYHCK 146 (191)
Q Consensus 123 ~CP~C~~~i-~k~~GC~~m~C~~C~ 146 (191)
.||.|+..- .-...=.-+.|..||
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-
T ss_pred CCcCCcCCceEEcCCCCeEECCCCC
Confidence 589998864 333333345776444
No 125
>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.
Probab=79.51 E-value=1.4 Score=38.77 Aligned_cols=32 Identities=38% Similarity=0.687 Sum_probs=26.3
Q ss_pred CCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 160 GKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 160 ~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+.++.....+++++..+|++++|..|++||+|
T Consensus 117 g~~~~~~~~~~~i~~~~p~~~~R~~v~epl~T 148 (497)
T TIGR03324 117 GGGPLASSPRLPIERPAPPIMDRAPVTVPLQT 148 (497)
T ss_pred CCCCCCCCceeehhccCcCccccCCCCchhhc
Confidence 44455555677899999999999999999987
No 126
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=78.37 E-value=2.1 Score=39.63 Aligned_cols=35 Identities=20% Similarity=0.599 Sum_probs=30.4
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcc-----eecccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHE-----FCWMCLGN 156 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~-----fC~~C~~~ 156 (191)
-.||+|..+..-...=+.|.|-.||++ .|..||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 469999999987666699999889998 89999887
No 127
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=78.36 E-value=1.8 Score=30.31 Aligned_cols=28 Identities=25% Similarity=0.558 Sum_probs=20.8
Q ss_pred CCCCCCCcceEe--cCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEK--NGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k--~~GC~~m~C~~C~~~f 149 (191)
+-||+|+.++.- .++=+.+.|.+||+++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 569999999875 2233389999888875
No 128
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=78.25 E-value=1.8 Score=24.39 Aligned_cols=31 Identities=26% Similarity=0.532 Sum_probs=17.8
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
+||+|+...+...- ..+ ....|-.|++-|.+
T Consensus 1 ~CP~C~~~l~~~~~-~~~-----~id~C~~C~G~W~d 31 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GDV-----EIDVCPSCGGIWFD 31 (41)
T ss_pred CcCCCCcccceEEE-CCE-----EEEECCCCCeEEcc
Confidence 59999998876433 111 12234466666654
No 129
>PF14353 CpXC: CpXC protein
Probab=78.07 E-value=2.3 Score=30.18 Aligned_cols=18 Identities=17% Similarity=0.288 Sum_probs=11.3
Q ss_pred cCCCCCCCCcceEecCCc
Q psy271 120 HTKDCPKCHICIEKNGGC 137 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC 137 (191)
+...||+|+..+..+..+
T Consensus 37 ~~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPL 54 (128)
T ss_pred CEEECCCCCCceecCCCE
Confidence 356788887777554443
No 130
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=76.67 E-value=1.9 Score=38.11 Aligned_cols=32 Identities=47% Similarity=0.677 Sum_probs=26.1
Q ss_pred CCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 160 GKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 160 ~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+.++.....+++++..+|++++|..|++||.|
T Consensus 117 g~~~i~~~~~~~i~~~ap~~~~R~~v~epl~T 148 (502)
T PRK13343 117 GGGPLQATARRPLERPAPAIIERDFVTEPLQT 148 (502)
T ss_pred CCCCCCCCceecccCCCcChhhcCCCCccccc
Confidence 44454455677888999999999999999987
No 131
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=76.63 E-value=2.4 Score=25.87 Aligned_cols=28 Identities=21% Similarity=0.385 Sum_probs=17.3
Q ss_pred cCCCCCCCCcceEec--CCc------CceEeCCCCc
Q psy271 120 HTKDCPKCHICIEKN--GGC------NHMQCYHCKH 147 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~--~GC------~~m~C~~C~~ 147 (191)
..|+||-|+...... ..- .++.|..||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 368999999665432 111 4577766655
No 132
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=76.54 E-value=2.8 Score=26.24 Aligned_cols=37 Identities=19% Similarity=0.444 Sum_probs=20.8
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcceecccccccc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~ 158 (191)
....|+.|+..... --..-.|..||.-||..|.....
T Consensus 8 ~~~~C~~C~~~F~~--~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 8 EASNCMICGKKFSL--FRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp G-SB-TTT--B-BS--SS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCcCcCcCCcCCC--ceeeEccCCCCCEECCchhCCEE
Confidence 46789999999843 34567899999999999987544
No 133
>PF12773 DZR: Double zinc ribbon
Probab=76.43 E-value=1.4 Score=25.75 Aligned_cols=13 Identities=31% Similarity=0.720 Sum_probs=8.3
Q ss_pred cCCCCCCCCcceE
Q psy271 120 HTKDCPKCHICIE 132 (191)
Q Consensus 120 ~~k~CP~C~~~i~ 132 (191)
+.+.||+|+..+.
T Consensus 11 ~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 11 DAKFCPHCGTPLP 23 (50)
T ss_pred cccCChhhcCChh
Confidence 3566777776665
No 134
>PF15616 TerY-C: TerY-C metal binding domain
Probab=76.26 E-value=1.9 Score=31.12 Aligned_cols=26 Identities=27% Similarity=0.667 Sum_probs=18.5
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcceecc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFCWM 152 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~ 152 (191)
..--||.|+... ....| .||.-|||.
T Consensus 76 g~PgCP~CGn~~------~fa~C-~CGkl~Ci~ 101 (131)
T PF15616_consen 76 GAPGCPHCGNQY------AFAVC-GCGKLFCID 101 (131)
T ss_pred CCCCCCCCcChh------cEEEe-cCCCEEEeC
Confidence 346799999886 34566 577777763
No 135
>PTZ00185 ATPase alpha subunit; Provisional
Probab=75.77 E-value=2.6 Score=37.53 Aligned_cols=24 Identities=29% Similarity=0.326 Sum_probs=21.9
Q ss_pred CCcccCccCCCccccCCCCCCCCC
Q psy271 168 TRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 168 ~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
.+++++..||++++|.+|++||+|
T Consensus 152 ~~~pIe~~ap~~~~R~~v~epL~T 175 (574)
T PTZ00185 152 TLGKVDAGAPNIVSRSPVNYNLLT 175 (574)
T ss_pred ccccccCCCcChhhcCCCCCcCcC
Confidence 356899999999999999999998
No 136
>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=75.65 E-value=0.89 Score=42.23 Aligned_cols=17 Identities=18% Similarity=0.462 Sum_probs=0.0
Q ss_pred ccCCCccccCCCCCCCC
Q psy271 174 IKAPGIIPRISVREPMQ 190 (191)
Q Consensus 174 ~~a~~i~~r~~~~~~~~ 190 (191)
+..-|+++++.+-|||+
T Consensus 733 KGVkgl~S~~k~pEPlE 749 (900)
T PF03833_consen 733 KGVKGLTSKEKIPEPLE 749 (900)
T ss_dssp -----------------
T ss_pred hhHHhhhccccCcchHH
Confidence 34568888988888885
No 137
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=75.65 E-value=3.8 Score=22.86 Aligned_cols=22 Identities=27% Similarity=0.680 Sum_probs=15.2
Q ss_pred CCCCCCCcceEe---cCCcCceEeCC
Q psy271 122 KDCPKCHICIEK---NGGCNHMQCYH 144 (191)
Q Consensus 122 k~CP~C~~~i~k---~~GC~~m~C~~ 144 (191)
+.||+|+..+.. ..| ..+.|++
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~Cs~ 26 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGCSN 26 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEECCC
Confidence 579999987754 345 6677763
No 138
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=75.11 E-value=3.5 Score=25.32 Aligned_cols=28 Identities=21% Similarity=0.457 Sum_probs=21.0
Q ss_pred CCCCCCCcce----EecCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICI----EKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i----~k~~GC~~m~C~~C~~~f 149 (191)
-.||+|+.+= -+..|=.++.|..|||..
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 4699998753 346777889999888753
No 139
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=75.07 E-value=1.9 Score=24.54 Aligned_cols=33 Identities=24% Similarity=0.488 Sum_probs=23.3
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcceecccccccc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~ 158 (191)
.|+.|...+..+.. ..=..|||.||..|...+.
T Consensus 1 ~C~~C~~~~~~~~~---~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 1 HCNICFEKYSEERR---PRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCcCcCccccCCCC---eEEcccCCHHHHHHHHhhc
Confidence 37888888833333 2223699999999998877
No 140
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=75.04 E-value=1.9 Score=28.03 Aligned_cols=40 Identities=13% Similarity=0.357 Sum_probs=15.4
Q ss_pred CccccCCcccCccchHHHHHHHhhccChHHHHHHHHhcCCCCCCCCcceEecCCcCc
Q psy271 83 EPMQSGIEYHAPTDCAVIKKWLTKCADDSETANYISAHTKDCPKCHICIEKNGGCNH 139 (191)
Q Consensus 83 ~C~~Cgv~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~~ 139 (191)
.|-.|+.+.-. +|.+|.. +...+-||+|++.+.+..|+..
T Consensus 30 AC~eC~fPvCr--~CyEYEr---------------keg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 30 ACHECAFPVCR--PCYEYER---------------KEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp S-SSS-----H--HHHHHHH---------------HTS-SB-TTT--B----TT---
T ss_pred EEcccCCccch--hHHHHHh---------------hcCcccccccCCCcccccCCCC
Confidence 37777776533 5666533 2467899999999988887654
No 141
>PF14149 YhfH: YhfH-like protein
Probab=74.65 E-value=0.21 Score=27.65 Aligned_cols=27 Identities=30% Similarity=0.710 Sum_probs=22.3
Q ss_pred hcCCCCCCCCcceEecCCcCceEeCCC
Q psy271 119 AHTKDCPKCHICIEKNGGCNHMQCYHC 145 (191)
Q Consensus 119 ~~~k~CP~C~~~i~k~~GC~~m~C~~C 145 (191)
...|.|+.|+..|+-..-|..++|.+|
T Consensus 11 Lp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred CCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 467999999999988877888888765
No 142
>PRK11827 hypothetical protein; Provisional
Probab=73.94 E-value=3.4 Score=25.55 Aligned_cols=27 Identities=19% Similarity=0.256 Sum_probs=20.1
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
.-.||.|+...+-...=+...|..|+-
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCe
Confidence 457999999998766556688875553
No 143
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=73.44 E-value=1.3 Score=27.14 Aligned_cols=38 Identities=26% Similarity=0.551 Sum_probs=29.3
Q ss_pred CCCCCCCcceEec--CCcCceEeCCCCcceeccccccccc
Q psy271 122 KDCPKCHICIEKN--GGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 122 k~CP~C~~~i~k~--~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
..||-|+.-.... +-=|+-+|+.|+..-|-.||=....
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP~P 42 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNPTP 42 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCCCCc
Confidence 5699999877332 3358899999999999999966433
No 144
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=73.39 E-value=3.9 Score=23.57 Aligned_cols=25 Identities=20% Similarity=0.438 Sum_probs=14.0
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~ 148 (191)
.|..|+..++...+ .-+.|..||+.
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecCCC-CceECCCCCce
Confidence 36666666665533 44666555554
No 145
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=72.47 E-value=3.6 Score=37.55 Aligned_cols=56 Identities=20% Similarity=0.274 Sum_probs=34.1
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcc----eecccccccccCCCCCCCCCCcccCccCCCcccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHE----FCWMCLGNTIDGKGPLKTTTRFRVGIKAPGIIPR 182 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~----fC~~C~~~~~~~~~~~~~~~~~~~~~~a~~i~~r 182 (191)
+.||+|+..+... .-.|.+||+. +|-.||.+...+..-+-.|.... +.....|++.
T Consensus 2 ~~Cp~Cg~~n~~~----akFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~~~-~~~~~~~~~~ 61 (645)
T PRK14559 2 LICPQCQFENPNN----NRFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGAET-GTIWWAIIAQ 61 (645)
T ss_pred CcCCCCCCcCCCC----CccccccCCCCCCCcCCCCCCCCCcccccccccCCcc-cchhhhhccc
Confidence 5799999987443 2367778876 58888888655444333444332 2334455543
No 146
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=72.24 E-value=2.2 Score=28.32 Aligned_cols=35 Identities=23% Similarity=0.604 Sum_probs=29.0
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
-.||.|+.+ .+.|.-+.. .|++.|=..|...|...
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g-~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWG-KCSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeec-cCccHHHHHHHHHHHcc
Confidence 358888887 477888888 59999999999999864
No 147
>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=71.98 E-value=3.5 Score=20.57 Aligned_cols=6 Identities=50% Similarity=1.625 Sum_probs=3.4
Q ss_pred CCCCCC
Q psy271 123 DCPKCH 128 (191)
Q Consensus 123 ~CP~C~ 128 (191)
.||+|+
T Consensus 18 ~CPnCG 23 (24)
T PF07754_consen 18 PCPNCG 23 (24)
T ss_pred eCCCCC
Confidence 566664
No 148
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=71.15 E-value=3.6 Score=28.38 Aligned_cols=30 Identities=23% Similarity=0.501 Sum_probs=20.9
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
.-+||+|..-+.-.+|= .|.|. .|+.+|..
T Consensus 3 lp~cp~c~sEytYed~~-~~~cp--------ec~~ew~~ 32 (112)
T COG2824 3 LPPCPKCNSEYTYEDGG-QLICP--------ECAHEWNE 32 (112)
T ss_pred CCCCCccCCceEEecCc-eEeCc--------hhcccccc
Confidence 35799998877665443 88888 56666664
No 149
>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=70.98 E-value=3.5 Score=21.36 Aligned_cols=25 Identities=32% Similarity=0.824 Sum_probs=13.9
Q ss_pred CCCCCCCcceEec--CCcCceEeCCCC
Q psy271 122 KDCPKCHICIEKN--GGCNHMQCYHCK 146 (191)
Q Consensus 122 k~CP~C~~~i~k~--~GC~~m~C~~C~ 146 (191)
++||.|...|++. +|=+...|.+|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 6899999999763 444456666554
No 150
>KOG3612|consensus
Probab=70.60 E-value=2.3 Score=37.54 Aligned_cols=26 Identities=27% Similarity=0.346 Sum_probs=20.5
Q ss_pred CCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 164 LKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 164 ~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
-.+|.+...+.+||++ -+.+.+||++
T Consensus 561 ~ksCrrk~~~~~aps~--~~~~~~~~~~ 586 (588)
T KOG3612|consen 561 RKSCRRKKTNQGAPSE--PQPLNKPMQG 586 (588)
T ss_pred hhhhcccCCCCCCCCC--CCcccCCCCC
Confidence 3458888888999999 7778888764
No 151
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=70.34 E-value=1.7 Score=25.83 Aligned_cols=26 Identities=27% Similarity=0.688 Sum_probs=15.0
Q ss_pred CCCCCCCcceEecCCcC--ceEeCCCCc
Q psy271 122 KDCPKCHICIEKNGGCN--HMQCYHCKH 147 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~--~m~C~~C~~ 147 (191)
.+|++|+...-+.++=. .+.|.+|++
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 36777777666643322 366666654
No 152
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=70.16 E-value=6 Score=20.97 Aligned_cols=26 Identities=19% Similarity=0.539 Sum_probs=22.4
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
..|..|+..+.--.|=..+.|+.|..
T Consensus 2 ~~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 2 VVCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred cCcCCCCcEeecCCCCCeEECCCCCe
Confidence 36999999999999999999987754
No 153
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=69.94 E-value=3.6 Score=36.45 Aligned_cols=31 Identities=52% Similarity=0.790 Sum_probs=25.3
Q ss_pred CCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 161 KGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 161 ~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
..+.....+++++..+|++++|..+++||.|
T Consensus 118 ~~~~~~~~~~~i~~~~p~~~~R~~~~~~l~T 148 (502)
T PRK09281 118 KGPIEATETRPVERKAPGVIDRKSVHEPLQT 148 (502)
T ss_pred CCCCCCCceecccCCCcCccccCCccceeec
Confidence 3344445677899999999999999999987
No 154
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=69.15 E-value=4.3 Score=30.97 Aligned_cols=26 Identities=27% Similarity=0.662 Sum_probs=21.5
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcce
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
.|++|+.+..+.+ .+.|.|..|++..
T Consensus 151 ~~~~~g~~~~~~~-~~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVKKG-ENELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEECC-CCEEECCCCCCEE
Confidence 6999999998854 4999999888653
No 155
>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=69.10 E-value=4.7 Score=35.71 Aligned_cols=35 Identities=20% Similarity=0.575 Sum_probs=27.7
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcc-----eecccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHE-----FCWMCLGN 156 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~-----fC~~C~~~ 156 (191)
-+||+|.....-...=+.+.|..||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 369999988875555568999999988 59999774
No 156
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=69.00 E-value=3.3 Score=25.28 Aligned_cols=24 Identities=25% Similarity=0.508 Sum_probs=16.7
Q ss_pred hcCCCCCCCCcceEecCCcCceEeCCCCc
Q psy271 119 AHTKDCPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 119 ~~~k~CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
.+.-.||+|+..... |-.|..||+
T Consensus 25 ~~l~~C~~CG~~~~~-----H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPKLP-----HRVCPSCGY 48 (57)
T ss_pred CcceECCCCCCccCC-----eEECCCCCc
Confidence 345679999998844 666665664
No 157
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=68.71 E-value=5.9 Score=32.25 Aligned_cols=30 Identities=23% Similarity=0.429 Sum_probs=26.3
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
+-+=||+|+...+-..|=-.+.|.+|++.+
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 457899999999999998999999888765
No 158
>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.
Probab=68.28 E-value=4 Score=36.12 Aligned_cols=29 Identities=34% Similarity=0.596 Sum_probs=23.6
Q ss_pred CCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 163 PLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 163 ~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+.....+++++..+|++++|..|++||.|
T Consensus 119 ~~~~~~~~~i~~~~p~~~~R~~i~~pl~T 147 (501)
T TIGR00962 119 PIDSDEFRPIEKIAPGVMERKSVHEPLQT 147 (501)
T ss_pred CcCCCCceeeecCCCChhhcCCcCceecc
Confidence 33334566888899999999999999987
No 159
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=67.68 E-value=3.3 Score=22.16 Aligned_cols=23 Identities=30% Similarity=0.842 Sum_probs=8.6
Q ss_pred CCCCCcceEecCCcCceEeCCCCc
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
|..|+..++...+ .-+.|..||+
T Consensus 3 C~~Cg~~~~~~~~-~~irC~~CG~ 25 (32)
T PF03604_consen 3 CGECGAEVELKPG-DPIRCPECGH 25 (32)
T ss_dssp ESSSSSSE-BSTS-STSSBSSSS-
T ss_pred CCcCCCeeEcCCC-CcEECCcCCC
Confidence 4444444443322 2344444443
No 160
>PRK07165 F0F1 ATP synthase subunit alpha; Validated
Probab=67.42 E-value=4.7 Score=35.70 Aligned_cols=24 Identities=13% Similarity=0.128 Sum_probs=21.8
Q ss_pred CCcccCccCCCccccCCCCCCCCC
Q psy271 168 TRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 168 ~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
.+.+++..||++++|.++.+||+|
T Consensus 106 ~~~~i~~~ap~~~~R~~v~epL~T 129 (507)
T PRK07165 106 NTSSIFNLAHGLMTVKTLNEQLYT 129 (507)
T ss_pred ccccccCCCCCchhhCCCCceeec
Confidence 466888899999999999999998
No 161
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=66.97 E-value=4.3 Score=31.00 Aligned_cols=25 Identities=24% Similarity=0.680 Sum_probs=20.8
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~ 148 (191)
-+|++|+...++ .=+.|.|.+||+.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCE
Confidence 379999999999 5578999988764
No 162
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=66.95 E-value=4.8 Score=22.10 Aligned_cols=27 Identities=26% Similarity=0.616 Sum_probs=17.8
Q ss_pred cCCCCCCCCcceEe-cCCcCceEeCCCCcc
Q psy271 120 HTKDCPKCHICIEK-NGGCNHMQCYHCKHE 148 (191)
Q Consensus 120 ~~k~CP~C~~~i~k-~~GC~~m~C~~C~~~ 148 (191)
...+|+.|+...-. ++| ...|.+||+.
T Consensus 7 ~~~~C~~C~~~~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 7 PNEPCPVCGSRWFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred CCCcCCCCCCeEeEccCC--EEEhhhCceE
Confidence 34569999887543 455 6677667764
No 163
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=66.75 E-value=6.1 Score=31.48 Aligned_cols=37 Identities=24% Similarity=0.608 Sum_probs=15.0
Q ss_pred HHHHHHHHhcCCCCCCCCcc-eEecCCcCc----eEeCCCCcce
Q psy271 111 SETANYISAHTKDCPKCHIC-IEKNGGCNH----MQCYHCKHEF 149 (191)
Q Consensus 111 ~~~~~~~~~~~k~CP~C~~~-i~k~~GC~~----m~C~~C~~~f 149 (191)
..++.|+..+ .-||.|+.. +.+- +-|. ..|..|+.+|
T Consensus 22 VltE~Wv~~n-~yCP~Cg~~~L~~f-~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 22 VLTEDWVAEN-MYCPNCGSKPLSKF-ENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp HHHHHHHHHH----TTT--SS-EE---------EEE-TTT--EE
T ss_pred HHHHHHHHHC-CcCCCCCChhHhhc-cCCCccceeECCCCchHH
Confidence 3567788765 469999998 5554 3333 4555444443
No 164
>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=66.30 E-value=3.3 Score=33.82 Aligned_cols=35 Identities=26% Similarity=0.574 Sum_probs=16.7
Q ss_pred CCCCCCCcce-----EecC--CcCceEeCCCCcce------ecccccc
Q psy271 122 KDCPKCHICI-----EKNG--GCNHMQCYHCKHEF------CWMCLGN 156 (191)
Q Consensus 122 k~CP~C~~~i-----~k~~--GC~~m~C~~C~~~f------C~~C~~~ 156 (191)
-.||-|+..= ...+ |=.++.|+.|+++| |-.||..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 5799999873 2233 78899999888887 6667654
No 165
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=66.29 E-value=8.5 Score=19.37 Aligned_cols=24 Identities=21% Similarity=0.618 Sum_probs=19.8
Q ss_pred CCCCCcceEecCCcCceEeCCCCc
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
|-+|+..+.--.|=.++.|+.|.+
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 668888888888988999987764
No 166
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=66.11 E-value=3.6 Score=27.04 Aligned_cols=29 Identities=34% Similarity=0.866 Sum_probs=15.1
Q ss_pred CCCCCCCC----cc--eEecCCcCceEeCCCCcce
Q psy271 121 TKDCPKCH----IC--IEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 121 ~k~CP~C~----~~--i~k~~GC~~m~C~~C~~~f 149 (191)
.=.||.|+ +. |.|..|=-++.|..|+..|
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 45799999 22 3446677778898776655
No 167
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=65.89 E-value=4.1 Score=22.46 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=5.3
Q ss_pred CCCCCCCcceE
Q psy271 122 KDCPKCHICIE 132 (191)
Q Consensus 122 k~CP~C~~~i~ 132 (191)
..||.|+..++
T Consensus 27 ~~CP~Cg~~~~ 37 (41)
T smart00834 27 ATCPECGGDVR 37 (41)
T ss_pred CCCCCCCCcce
Confidence 34555555443
No 168
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=65.88 E-value=4 Score=24.33 Aligned_cols=36 Identities=25% Similarity=0.589 Sum_probs=25.4
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCcceecccccccc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~ 158 (191)
...|+.|+....... ..-.|..||..||..|.....
T Consensus 2 ~~~C~~C~~~F~~~~--rk~~Cr~Cg~~~C~~C~~~~~ 37 (57)
T cd00065 2 ASSCMGCGKPFTLTR--RRHHCRNCGRIFCSKCSSNRI 37 (57)
T ss_pred cCcCcccCccccCCc--cccccCcCcCCcChHHcCCee
Confidence 356888887665422 345677899999999977543
No 169
>PF14369 zf-RING_3: zinc-finger
Probab=65.44 E-value=6.7 Score=21.34 Aligned_cols=10 Identities=20% Similarity=0.760 Sum_probs=5.0
Q ss_pred CCCCCcceEe
Q psy271 124 CPKCHICIEK 133 (191)
Q Consensus 124 CP~C~~~i~k 133 (191)
|.+|...|..
T Consensus 5 Ch~C~~~V~~ 14 (35)
T PF14369_consen 5 CHQCNRFVRI 14 (35)
T ss_pred CccCCCEeEe
Confidence 4455555544
No 170
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=65.43 E-value=4.5 Score=40.90 Aligned_cols=28 Identities=29% Similarity=0.707 Sum_probs=24.3
Q ss_pred CCCCCCCcc------eEecCCcCceEeCCCCcceec
Q psy271 122 KDCPKCHIC------IEKNGGCNHMQCYHCKHEFCW 151 (191)
Q Consensus 122 k~CP~C~~~------i~k~~GC~~m~C~~C~~~fC~ 151 (191)
..||.|+.. +...+||. +|..||+.=|-
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s~c~ 1738 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCCcccc
Confidence 349999999 78899997 89999998774
No 171
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=65.10 E-value=7.5 Score=21.77 Aligned_cols=8 Identities=50% Similarity=1.111 Sum_probs=5.7
Q ss_pred CCCCCCcc
Q psy271 123 DCPKCHIC 130 (191)
Q Consensus 123 ~CP~C~~~ 130 (191)
+||+|+..
T Consensus 2 ~Cp~C~~~ 9 (40)
T smart00440 2 PCPKCGNR 9 (40)
T ss_pred cCCCCCCC
Confidence 68888753
No 172
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=64.41 E-value=7.1 Score=24.99 Aligned_cols=27 Identities=26% Similarity=0.660 Sum_probs=20.7
Q ss_pred CCCCCCCcce----EecCCcCceEeCCCCcc
Q psy271 122 KDCPKCHICI----EKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 122 k~CP~C~~~i----~k~~GC~~m~C~~C~~~ 148 (191)
-.||+|+.+= -+..|=.++.|..|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 4699998763 34577888999988875
No 173
>PRK12495 hypothetical protein; Provisional
Probab=64.26 E-value=7 Score=30.62 Aligned_cols=28 Identities=29% Similarity=0.571 Sum_probs=19.8
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCcceecccccccc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~ 158 (191)
.+-|+.|+.+|-+..|+ .||-.|.+...
T Consensus 42 a~hC~~CG~PIpa~pG~----------~~Cp~CQ~~~~ 69 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ----------EFCPTCQQPVT 69 (226)
T ss_pred hhhcccccCcccCCCCe----------eECCCCCCccc
Confidence 57899999999865553 45667765543
No 174
>PHA02929 N1R/p28-like protein; Provisional
Probab=63.96 E-value=4 Score=32.50 Aligned_cols=40 Identities=25% Similarity=0.488 Sum_probs=28.5
Q ss_pred CCCCCCCCcceEecCCcC---ceEeCCCCcceecccccccccCC
Q psy271 121 TKDCPKCHICIEKNGGCN---HMQCYHCKHEFCWMCLGNTIDGK 161 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~---~m~C~~C~~~fC~~C~~~~~~~~ 161 (191)
...||-|...+.....-+ -+.- .|+|.||..|...|....
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~-~C~H~FC~~CI~~Wl~~~ 216 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILS-NCNHVFCIECIDIWKKEK 216 (238)
T ss_pred CCCCccCCcccccCccccccceecC-CCCCcccHHHHHHHHhcC
Confidence 468999999876543222 1333 599999999999998643
No 175
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=63.92 E-value=2.3 Score=25.38 Aligned_cols=17 Identities=35% Similarity=0.966 Sum_probs=9.5
Q ss_pred CceEeCCCCcceecccc
Q psy271 138 NHMQCYHCKHEFCWMCL 154 (191)
Q Consensus 138 ~~m~C~~C~~~fC~~C~ 154 (191)
..-.|.+|+..||..|-
T Consensus 20 ~~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EEE--TTTT--B-HHHH
T ss_pred CeEECCCCCCccccCcC
Confidence 34678899999999993
No 176
>PRK14873 primosome assembly protein PriA; Provisional
Probab=63.61 E-value=6.1 Score=36.29 Aligned_cols=35 Identities=17% Similarity=0.405 Sum_probs=26.9
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcc----eecccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHE----FCWMCLGN 156 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~----fC~~C~~~ 156 (191)
-+||+|..+.....+=+.+.|..||+. .|-.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 469999988887555578999889884 47777664
No 177
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=63.55 E-value=4.4 Score=39.54 Aligned_cols=33 Identities=24% Similarity=0.575 Sum_probs=23.0
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCcce-----eccccccccc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKHEF-----CWMCLGNTID 159 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~~f-----C~~C~~~~~~ 159 (191)
..+||+|+..+... .|..||.+. |-.|+.....
T Consensus 667 ~rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~~ 704 (1337)
T PRK14714 667 RRRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVPP 704 (1337)
T ss_pred EEECCCCCCccccc------cCcccCCcCCCceeCccCCCccCC
Confidence 37899999976432 777787663 7777776543
No 178
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=63.03 E-value=5.6 Score=22.21 Aligned_cols=25 Identities=28% Similarity=0.716 Sum_probs=16.0
Q ss_pred CCCCCcceEecCCcCceEeCCCCcceecc
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKHEFCWM 152 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~~fC~~ 152 (191)
|-.|+...... -+.|..|+..||-.
T Consensus 1 C~~C~~~~~l~----~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLT----GFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCccccc----CeECCccCCccccc
Confidence 33455554443 47887799999864
No 179
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=62.82 E-value=4.1 Score=38.33 Aligned_cols=25 Identities=40% Similarity=1.083 Sum_probs=20.2
Q ss_pred CCCCCCCcc-eEecCCcCceEeCCCCcc
Q psy271 122 KDCPKCHIC-IEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 122 k~CP~C~~~-i~k~~GC~~m~C~~C~~~ 148 (191)
-.||-|+.- |+..|||| ||++|+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 479999975 56799999 68888765
No 180
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=61.99 E-value=6.8 Score=24.07 Aligned_cols=31 Identities=19% Similarity=0.476 Sum_probs=20.5
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWM 152 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~ 152 (191)
..|-+|+..|.-.+.--++.|.+||..-=|.
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~R 38 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYR 38 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEee
Confidence 3577777777666666777777777663333
No 181
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=61.24 E-value=8.6 Score=31.29 Aligned_cols=27 Identities=33% Similarity=0.706 Sum_probs=19.6
Q ss_pred cCCCCCCCCcceEec--CCcCceEeCCCC
Q psy271 120 HTKDCPKCHICIEKN--GGCNHMQCYHCK 146 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~--~GC~~m~C~~C~ 146 (191)
..++|+.|+..|+|. +|=+-..|.+|.
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 467999999999984 665555555553
No 182
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.11 E-value=4.1 Score=34.94 Aligned_cols=34 Identities=21% Similarity=0.642 Sum_probs=23.7
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
.-.||-|.-.+. +.++ ..|+|.||+.|...|...
T Consensus 26 ~l~C~IC~d~~~-----~Pvi-tpCgH~FCs~CI~~~l~~ 59 (397)
T TIGR00599 26 SLRCHICKDFFD-----VPVL-TSCSHTFCSLCIRRCLSN 59 (397)
T ss_pred ccCCCcCchhhh-----CccC-CCCCCchhHHHHHHHHhC
Confidence 458999987663 2232 368888888888877654
No 183
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=61.08 E-value=4.1 Score=24.60 Aligned_cols=11 Identities=27% Similarity=0.624 Sum_probs=6.3
Q ss_pred CCCCCCCCcce
Q psy271 121 TKDCPKCHICI 131 (191)
Q Consensus 121 ~k~CP~C~~~i 131 (191)
.-.||.|++++
T Consensus 21 iVvCp~Cgapy 31 (54)
T PF14446_consen 21 IVVCPECGAPY 31 (54)
T ss_pred EEECCCCCCcc
Confidence 34566666665
No 184
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=60.85 E-value=8.5 Score=24.13 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=4.4
Q ss_pred ceEeCCCCcc
Q psy271 139 HMQCYHCKHE 148 (191)
Q Consensus 139 ~m~C~~C~~~ 148 (191)
.+.|..|+..
T Consensus 53 ~L~Cp~c~r~ 62 (68)
T PF03966_consen 53 ELICPECGRE 62 (68)
T ss_dssp EEEETTTTEE
T ss_pred EEEcCCCCCE
Confidence 3444444443
No 185
>PRK05580 primosome assembly protein PriA; Validated
Probab=60.76 E-value=8.2 Score=35.54 Aligned_cols=35 Identities=23% Similarity=0.638 Sum_probs=27.4
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcc-----eecccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHE-----FCWMCLGN 156 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~-----fC~~C~~~ 156 (191)
-+||+|..+..-...=+.+.|..||+. .|-.|+..
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 369999998875444578999999987 59999765
No 186
>PLN03086 PRLI-interacting factor K; Provisional
Probab=59.94 E-value=5.8 Score=35.61 Aligned_cols=30 Identities=33% Similarity=0.840 Sum_probs=25.7
Q ss_pred cCCCCCC--CCcceEecCCcCceEeCCCCcce
Q psy271 120 HTKDCPK--CHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 120 ~~k~CP~--C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
+...||+ |+..+.+...=+|..|..|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCCCCCCcc
Confidence 5678995 99999999999999999898766
No 187
>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=59.51 E-value=8.8 Score=26.92 Aligned_cols=36 Identities=22% Similarity=0.428 Sum_probs=26.7
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcceecccccc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGN 156 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~ 156 (191)
+.+.|..|+.+.-...+.. ..|..|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 4578999998876554444 78989999999999865
No 188
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=58.97 E-value=8.6 Score=30.91 Aligned_cols=31 Identities=19% Similarity=0.436 Sum_probs=24.2
Q ss_pred hcCCCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 119 AHTKDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 119 ~~~k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
.+.+-||.|+.+++...+=..+.|..|+..+
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCCEE
Confidence 3568899999999876555778999888543
No 189
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=58.74 E-value=8 Score=22.45 Aligned_cols=14 Identities=43% Similarity=0.861 Sum_probs=11.2
Q ss_pred cCCCCCCCCcceEe
Q psy271 120 HTKDCPKCHICIEK 133 (191)
Q Consensus 120 ~~k~CP~C~~~i~k 133 (191)
..+.||-|+..|++
T Consensus 36 ~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 36 RKKKCPICRQPIES 49 (50)
T ss_dssp TTSBBTTTTBB-SE
T ss_pred cCCCCCcCChhhcC
Confidence 67899999999875
No 190
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=58.66 E-value=10 Score=30.74 Aligned_cols=27 Identities=41% Similarity=0.848 Sum_probs=19.5
Q ss_pred cCCCCCCCCcceEec--CCcCceEeCCCCcceecccc
Q psy271 120 HTKDCPKCHICIEKN--GGCNHMQCYHCKHEFCWMCL 154 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~--~GC~~m~C~~C~~~fC~~C~ 154 (191)
..++||.|+..|+|. +| =+++||-.|-
T Consensus 234 ~g~pC~~Cg~~I~~~~~~g--------R~ty~Cp~CQ 262 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVVGG--------RGTHFCPQCQ 262 (269)
T ss_pred CcCCCCcCCCeeEEEEECC--------CCcEECCCCc
Confidence 357999999999973 44 4566666663
No 191
>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=58.11 E-value=6.7 Score=32.44 Aligned_cols=35 Identities=26% Similarity=0.615 Sum_probs=24.7
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceeccccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNT 157 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~ 157 (191)
..||.|+.-...+..=..|.= .|||.||-.|...+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l 38 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL 38 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHH
Confidence 469999997655544333333 58999999998874
No 192
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=57.04 E-value=5 Score=24.20 Aligned_cols=29 Identities=24% Similarity=0.387 Sum_probs=14.1
Q ss_pred cCCCCCCCCcce----Eec--CCcCceEeCCCCcc
Q psy271 120 HTKDCPKCHICI----EKN--GGCNHMQCYHCKHE 148 (191)
Q Consensus 120 ~~k~CP~C~~~i----~k~--~GC~~m~C~~C~~~ 148 (191)
.|..||.|+... -.+ ---.-+.|.+|+++
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred eEEECCCCCCccceeeecCceeccccccCCCCCce
Confidence 355677777332 111 11333566666654
No 193
>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=56.93 E-value=4.1 Score=30.14 Aligned_cols=14 Identities=29% Similarity=0.726 Sum_probs=11.3
Q ss_pred cCCCCCCCCcceEe
Q psy271 120 HTKDCPKCHICIEK 133 (191)
Q Consensus 120 ~~k~CP~C~~~i~k 133 (191)
....||+|+.+|.-
T Consensus 38 tI~~Cp~C~~~IrG 51 (158)
T PF10083_consen 38 TITSCPNCSTPIRG 51 (158)
T ss_pred HHHHCcCCCCCCCC
Confidence 45689999999954
No 194
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=56.12 E-value=12 Score=30.44 Aligned_cols=15 Identities=33% Similarity=0.611 Sum_probs=12.5
Q ss_pred cCCCCCCCCcceEec
Q psy271 120 HTKDCPKCHICIEKN 134 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~ 134 (191)
..++||.|+..|+|.
T Consensus 244 ~g~pC~~Cg~~I~~~ 258 (274)
T PRK01103 244 EGEPCRRCGTPIEKI 258 (274)
T ss_pred CCCCCCCCCCeeEEE
Confidence 357899999999973
No 195
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=56.04 E-value=8.9 Score=23.18 Aligned_cols=23 Identities=26% Similarity=0.508 Sum_probs=15.0
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
+...||.|+.+. =.|-.|..||+
T Consensus 25 ~l~~C~~cG~~~-----~~H~vc~~cG~ 47 (55)
T TIGR01031 25 TLVVCPNCGEFK-----LPHRVCPSCGY 47 (55)
T ss_pred cceECCCCCCcc-----cCeeECCccCe
Confidence 456799999877 24555655553
No 196
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=55.75 E-value=8.2 Score=37.17 Aligned_cols=40 Identities=13% Similarity=0.316 Sum_probs=29.0
Q ss_pred ccccCCcccCccchHHHHHHHhhccChHHHHHHHHhcCCCCCCCCcceEecCCcCce
Q psy271 84 PMQSGIEYHAPTDCAVIKKWLTKCADDSETANYISAHTKDCPKCHICIEKNGGCNHM 140 (191)
Q Consensus 84 C~~Cgv~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~~m 140 (191)
|-.|+.+... +|.+|... ...+.||+|++.+.+--|+..+
T Consensus 39 C~eC~FPVCr--pCYEYEr~---------------eG~q~CPqCktrYkr~kgsprv 78 (1079)
T PLN02638 39 CDVCAFPVCR--PCYEYERK---------------DGNQSCPQCKTKYKRHKGSPAI 78 (1079)
T ss_pred eccCCCcccc--chhhhhhh---------------cCCccCCccCCchhhhcCCCCc
Confidence 8888888765 67776432 4578899999999876666654
No 197
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=55.45 E-value=5.9 Score=22.64 Aligned_cols=35 Identities=29% Similarity=0.535 Sum_probs=18.1
Q ss_pred CCCCCcceEecCCcCceEeCCCCcceecccccccccCC
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDGK 161 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~~ 161 (191)
||-|+. +.+.--..|.= .|||-||..|+..+...+
T Consensus 1 CpIc~e--~~~~~n~P~~L-~CGH~~c~~cl~~l~~~~ 35 (43)
T PF13445_consen 1 CPICKE--FSTEENPPMVL-PCGHVFCKDCLQKLSKKS 35 (43)
T ss_dssp -TTT------TTSS-EEE--SSS-EEEHHHHHHHHHH-
T ss_pred CCcccc--ccCCCCCCEEE-eCccHHHHHHHHHHHhcC
Confidence 566655 22222234443 499999999999887643
No 198
>PRK10445 endonuclease VIII; Provisional
Probab=55.24 E-value=12 Score=30.19 Aligned_cols=17 Identities=29% Similarity=0.530 Sum_probs=13.7
Q ss_pred cCCCCCCCCcceEe--cCC
Q psy271 120 HTKDCPKCHICIEK--NGG 136 (191)
Q Consensus 120 ~~k~CP~C~~~i~k--~~G 136 (191)
..++||.|+..|++ .+|
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~g 252 (263)
T PRK10445 234 DGEACERCGGIIEKTTLSS 252 (263)
T ss_pred CCCCCCCCCCEeEEEEECC
Confidence 35899999999997 355
No 199
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.20 E-value=3.4 Score=33.20 Aligned_cols=34 Identities=32% Similarity=0.494 Sum_probs=24.7
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccc-cccCC
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGN-TIDGK 161 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~-~~~~~ 161 (191)
.+|+-|-...++ -.|+-|||-|||.|+-. |-...
T Consensus 216 ~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~~~t~~k 250 (271)
T COG5574 216 YKCFLCLEEPEV------PSCTPCGHLFCLSCLLISWTKKK 250 (271)
T ss_pred cceeeeecccCC------cccccccchhhHHHHHHHHHhhc
Confidence 348877766643 45778999999999887 76544
No 200
>PHA02926 zinc finger-like protein; Provisional
Probab=54.81 E-value=7.2 Score=30.74 Aligned_cols=41 Identities=22% Similarity=0.376 Sum_probs=26.8
Q ss_pred cCCCCCCCCcceE-ec-CCcCc-eEeCCCCcceecccccccccC
Q psy271 120 HTKDCPKCHICIE-KN-GGCNH-MQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 120 ~~k~CP~C~~~i~-k~-~GC~~-m~C~~C~~~fC~~C~~~~~~~ 160 (191)
.-+.|+=|-..+- |. .++.. -.=..|+|.||+.|-..|...
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~ 212 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRT 212 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHh
Confidence 3578999997763 32 22211 011258899999999999864
No 201
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=54.59 E-value=12 Score=30.29 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=12.3
Q ss_pred cCCCCCCCCcceEe
Q psy271 120 HTKDCPKCHICIEK 133 (191)
Q Consensus 120 ~~k~CP~C~~~i~k 133 (191)
..++||.|+..|++
T Consensus 243 ~g~pCprCG~~I~~ 256 (272)
T PRK14810 243 TGEPCLNCKTPIRR 256 (272)
T ss_pred CCCcCCCCCCeeEE
Confidence 35799999999987
No 202
>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=53.79 E-value=8.3 Score=23.33 Aligned_cols=22 Identities=27% Similarity=0.584 Sum_probs=13.9
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCC
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCK 146 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~ 146 (191)
+...||.|+.+.. .|..|..||
T Consensus 25 ~l~~c~~cg~~~~-----~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-----PHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEES-----TTSBCTTTB
T ss_pred ceeeeccCCCEec-----ccEeeCCCC
Confidence 4567999987662 355555554
No 203
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.78 E-value=13 Score=30.13 Aligned_cols=14 Identities=36% Similarity=0.645 Sum_probs=12.2
Q ss_pred CCCCCCCCcceEec
Q psy271 121 TKDCPKCHICIEKN 134 (191)
Q Consensus 121 ~k~CP~C~~~i~k~ 134 (191)
.++||.|+..|+|.
T Consensus 245 g~pC~~Cg~~I~~~ 258 (272)
T TIGR00577 245 GEPCRRCGTPIEKI 258 (272)
T ss_pred CCCCCCCCCeeEEE
Confidence 56999999999983
No 204
>KOG0320|consensus
Probab=53.64 E-value=4 Score=30.92 Aligned_cols=36 Identities=25% Similarity=0.631 Sum_probs=26.7
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
..-.||-|-..+++..- .=++|||-||-.|.+....
T Consensus 130 ~~~~CPiCl~~~sek~~----vsTkCGHvFC~~Cik~alk 165 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVP----VSTKCGHVFCSQCIKDALK 165 (187)
T ss_pred cccCCCceecchhhccc----cccccchhHHHHHHHHHHH
Confidence 45679999988887543 2237999999999887654
No 205
>PRK04196 V-type ATP synthase subunit B; Provisional
Probab=53.30 E-value=14 Score=32.42 Aligned_cols=30 Identities=13% Similarity=0.089 Sum_probs=24.2
Q ss_pred CCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 162 GPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 162 ~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
.+.....+++++..+|..++|..+.+||.|
T Consensus 100 ~~i~~~~~~~i~~~ap~~l~R~~i~epl~T 129 (460)
T PRK04196 100 PEIIPEKRLDINGAPINPVAREYPEEFIQT 129 (460)
T ss_pred CCCCCCccCcccCCCCChhhcCCCCccccC
Confidence 333334567889999999999999999987
No 206
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=53.02 E-value=9.4 Score=30.52 Aligned_cols=37 Identities=30% Similarity=0.762 Sum_probs=26.3
Q ss_pred CCCCCCCCcceE-----ecCCcCceEeCCCCcce-----------eccccccc
Q psy271 121 TKDCPKCHICIE-----KNGGCNHMQCYHCKHEF-----------CWMCLGNT 157 (191)
Q Consensus 121 ~k~CP~C~~~i~-----k~~GC~~m~C~~C~~~f-----------C~~C~~~~ 157 (191)
..+|-+|+..++ |..|=....|.+|++.| ||.|+.+.
T Consensus 132 VSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v 184 (278)
T PF15135_consen 132 VSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNPV 184 (278)
T ss_pred cccccccccccCCCccccccceeeeecccccccchhhhhcCCCCCccCCCCcc
Confidence 457778877764 45666667788888887 77887654
No 207
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=52.03 E-value=8.6 Score=22.73 Aligned_cols=11 Identities=36% Similarity=0.715 Sum_probs=6.6
Q ss_pred CCCCCCCCcce
Q psy271 121 TKDCPKCHICI 131 (191)
Q Consensus 121 ~k~CP~C~~~i 131 (191)
..+||.|+..|
T Consensus 24 ~irCp~Cg~rI 34 (49)
T COG1996 24 GIRCPYCGSRI 34 (49)
T ss_pred ceeCCCCCcEE
Confidence 45666666655
No 209
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=51.98 E-value=6.2 Score=24.03 Aligned_cols=13 Identities=31% Similarity=0.892 Sum_probs=9.9
Q ss_pred cCCCCCCCCcceE
Q psy271 120 HTKDCPKCHICIE 132 (191)
Q Consensus 120 ~~k~CP~C~~~i~ 132 (191)
..+.||+|++..-
T Consensus 4 ~mr~C~~CgvYTL 16 (56)
T PRK13130 4 KIRKCPKCGVYTL 16 (56)
T ss_pred cceECCCCCCEEc
Confidence 4578998888874
No 210
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=51.55 E-value=15 Score=29.99 Aligned_cols=17 Identities=41% Similarity=0.700 Sum_probs=13.7
Q ss_pred cCCCCCCCCcceEe--cCC
Q psy271 120 HTKDCPKCHICIEK--NGG 136 (191)
Q Consensus 120 ~~k~CP~C~~~i~k--~~G 136 (191)
..++||.|+..|+| .+|
T Consensus 253 ~g~pC~~Cg~~I~~~~~~g 271 (282)
T PRK13945 253 TGKPCRKCGTPIERIKLAG 271 (282)
T ss_pred CcCCCCcCCCeeEEEEECC
Confidence 35799999999987 355
No 211
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=51.52 E-value=14 Score=26.79 Aligned_cols=26 Identities=31% Similarity=0.824 Sum_probs=16.0
Q ss_pred CCCC--CCCcceEecCCcCceEeCCCCcc
Q psy271 122 KDCP--KCHICIEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 122 k~CP--~C~~~i~k~~GC~~m~C~~C~~~ 148 (191)
..|| +|+..+... +=+...|.+|+..
T Consensus 19 ~aC~~~~C~kKv~~~-~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 19 PACPNEKCNKKVTEN-GDGSYRCEKCNKT 46 (146)
T ss_dssp EE-TSTTTS-B-EEE-TTTEEEETTTTEE
T ss_pred CCCCCccCCCEeecC-CCcEEECCCCCCc
Confidence 4699 999998877 3345777766654
No 212
>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.
Probab=51.42 E-value=14 Score=32.38 Aligned_cols=32 Identities=22% Similarity=0.230 Sum_probs=25.8
Q ss_pred CCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 160 GKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 160 ~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+..+.....+++++..+|..++|..+++||.|
T Consensus 93 ~~~~~~~~~~~~i~~~ap~~~~R~~i~e~L~T 124 (449)
T TIGR03305 93 RREPPKDVEWRSVHQAPPTLTRRSSKSEVFET 124 (449)
T ss_pred CCCCCCCccccchhcCCCCchhcccCCccccc
Confidence 34444445567899999999999999999987
No 213
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=49.98 E-value=12 Score=22.99 Aligned_cols=31 Identities=19% Similarity=0.464 Sum_probs=16.3
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcceeccc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHEFCWMC 153 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C 153 (191)
.|-+|+..|.-.++=-++-|.+||...=|.|
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc 41 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGEVEIYRC 41 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCceeeehh
Confidence 4555555555555555555555555444444
No 214
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=49.38 E-value=9.6 Score=26.62 Aligned_cols=8 Identities=50% Similarity=1.273 Sum_probs=5.5
Q ss_pred CCCCCCcc
Q psy271 123 DCPKCHIC 130 (191)
Q Consensus 123 ~CP~C~~~ 130 (191)
.||+|+..
T Consensus 88 ~CP~Cgs~ 95 (113)
T PRK12380 88 QCPHCHGE 95 (113)
T ss_pred cCcCCCCC
Confidence 48888754
No 215
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=49.07 E-value=16 Score=31.90 Aligned_cols=32 Identities=25% Similarity=0.381 Sum_probs=25.0
Q ss_pred CCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 160 GKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 160 ~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+..+.....+++++..+|..++|..+++||.|
T Consensus 117 ~~~~~~~~~~~~i~~~~~~p~~R~~i~e~l~T 148 (444)
T PRK08972 117 GLGPIYTDQRASRHSPPINPLSRRPITEPLDV 148 (444)
T ss_pred CCCCCCCCccccccCCCCChhhcCCCCCcccc
Confidence 33344444567888899999999999999987
No 216
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=49.03 E-value=21 Score=25.45 Aligned_cols=27 Identities=26% Similarity=0.592 Sum_probs=22.0
Q ss_pred CCCCCCCcc---eEecCCcCceEeCCCCcc
Q psy271 122 KDCPKCHIC---IEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 122 k~CP~C~~~---i~k~~GC~~m~C~~C~~~ 148 (191)
-.||.|+.+ +.|.++=..+.|..||..
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 569999976 567788899999888864
No 217
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=48.53 E-value=7.1 Score=22.96 Aligned_cols=34 Identities=21% Similarity=0.773 Sum_probs=16.3
Q ss_pred CCCCCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
||-|-..+ -..|=+..-| .|++++|..|......
T Consensus 1 cp~C~e~~-d~~d~~~~PC-~Cgf~IC~~C~~~i~~ 34 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPC-ECGFQICRFCYHDILE 34 (48)
T ss_dssp -TTTS-B---CCCTT--SS-TTS----HHHHHHHTT
T ss_pred CCCccccc-ccCCCccccC-cCCCcHHHHHHHHHHh
Confidence 56666666 3334466778 5999999999776654
No 218
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=48.32 E-value=14 Score=27.27 Aligned_cols=26 Identities=23% Similarity=0.758 Sum_probs=17.5
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~ 148 (191)
..||+|+..+...+. ....|.+|+..
T Consensus 35 ~aC~~C~kkv~~~~~-~~~~C~~C~~~ 60 (166)
T cd04476 35 PACPGCNKKVVEEGN-GTYRCEKCNKS 60 (166)
T ss_pred ccccccCcccEeCCC-CcEECCCCCCc
Confidence 579999999887654 44555555543
No 219
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.18 E-value=13 Score=30.28 Aligned_cols=27 Identities=22% Similarity=0.250 Sum_probs=19.3
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
+++.||.|+. -.++..+|+.||..+..
T Consensus 308 tS~~C~~cg~-------------~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 308 TSKTCPCCGH-------------LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred CcccccccCC-------------ccceeEECCCCCCeehh
Confidence 3589999998 24677777777765443
No 220
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=46.38 E-value=11 Score=28.12 Aligned_cols=16 Identities=31% Similarity=0.652 Sum_probs=12.8
Q ss_pred cCCCCCCCCcceEecC
Q psy271 120 HTKDCPKCHICIEKNG 135 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~ 135 (191)
...+||.|+..+.|-.
T Consensus 96 e~~RCp~CN~~L~~vs 111 (165)
T COG1656 96 EFSRCPECNGELEKVS 111 (165)
T ss_pred ccccCcccCCEeccCc
Confidence 3578999999998853
No 221
>PF13490 zf-HC2: Putative zinc-finger; PDB: 2Z2S_F 2Q1Z_B 3HUG_T.
Probab=45.82 E-value=6.7 Score=21.03 Aligned_cols=32 Identities=28% Similarity=0.696 Sum_probs=16.5
Q ss_pred hHHHHHHHhhccCh---HHHHHHHHhcCCCCCCCC
Q psy271 97 CAVIKKWLTKCADD---SETANYISAHTKDCPKCH 128 (191)
Q Consensus 97 C~~~~~~~~~~~~~---~~~~~~~~~~~k~CP~C~ 128 (191)
|++++..+....+. ......+..+...||.|+
T Consensus 1 C~~~~~~l~~y~dg~L~~~~~~~~~~HL~~C~~C~ 35 (36)
T PF13490_consen 1 CEEVRELLSAYLDGELSPEERARLEAHLASCPSCR 35 (36)
T ss_dssp ----HHHHHHHHCT-S-HHHHHHHHHHHCT-HHHH
T ss_pred ChHHHHHHHHHHcCCCCHHHHHHHHHHHHcCHHhc
Confidence 45555555443333 334456777889999885
No 222
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=45.70 E-value=18 Score=32.04 Aligned_cols=31 Identities=23% Similarity=0.260 Sum_probs=24.8
Q ss_pred CCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 161 KGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 161 ~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
..+.....+++++..+|..++|..+++||.|
T Consensus 117 ~~~~~~~~~~pi~~~~p~~~~R~~i~e~L~T 147 (494)
T CHL00060 117 LGPVDTRTTSPIHRSAPAFIQLDTKLSIFET 147 (494)
T ss_pred CCCCCCCccccccCCCcCchhcccccceeec
Confidence 3344444567888899999999999999987
No 223
>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.
Probab=45.69 E-value=16 Score=32.00 Aligned_cols=33 Identities=18% Similarity=0.179 Sum_probs=25.8
Q ss_pred cCCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 159 DGKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 159 ~~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
++..+.....+++++..+|..++|..+.+||.|
T Consensus 95 D~~~~~~~~~~~~i~~~~~~~~~R~~i~e~l~T 127 (466)
T TIGR01040 95 DKGPPVLAEDYLDINGQPINPYARIYPEEMIQT 127 (466)
T ss_pred CCCCCCCCCceeeccCCCCChhHcCCCCCeeec
Confidence 334444444567899999999999999999987
No 224
>PHA02942 putative transposase; Provisional
Probab=45.69 E-value=17 Score=31.00 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=18.8
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
+++.||.|+..... -+=....|..||+..
T Consensus 324 TSq~Cs~CG~~~~~-l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVE-IAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCc-CCCCEEECCCCCCEe
Confidence 46889999986532 122357787677653
No 225
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=45.64 E-value=14 Score=30.65 Aligned_cols=34 Identities=26% Similarity=0.735 Sum_probs=26.3
Q ss_pred CCCCCCCcc-----eE--ecCCcCceEeCCCCcce------eccccc
Q psy271 122 KDCPKCHIC-----IE--KNGGCNHMQCYHCKHEF------CWMCLG 155 (191)
Q Consensus 122 k~CP~C~~~-----i~--k~~GC~~m~C~~C~~~f------C~~C~~ 155 (191)
..||-|+.. |. -.+|=.++.|+.|+++| |-.|+.
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 579999987 21 14788899999999887 667875
No 226
>KOG1812|consensus
Probab=45.58 E-value=11 Score=32.16 Aligned_cols=21 Identities=24% Similarity=0.523 Sum_probs=18.3
Q ss_pred eEeCCCCcceecccccccccC
Q psy271 140 MQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 140 m~C~~C~~~fC~~C~~~~~~~ 160 (191)
-.|..|+..||..|..+|..+
T Consensus 259 ~~C~~C~~~fCv~C~~~wh~~ 279 (384)
T KOG1812|consen 259 RPCVKCHELFCVKCKVPWHAN 279 (384)
T ss_pred cccccCCCceeecCCCcCCCC
Confidence 357789999999999999875
No 227
>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=45.31 E-value=15 Score=24.65 Aligned_cols=31 Identities=23% Similarity=0.489 Sum_probs=23.4
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCccee
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC 150 (191)
....||.|+..-.|..+----.|.+|+..|=
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CCCcCCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 3468999999998877666678887777663
No 228
>KOG0824|consensus
Probab=44.31 E-value=7.3 Score=32.02 Aligned_cols=14 Identities=36% Similarity=1.269 Sum_probs=11.8
Q ss_pred CCCcceeccccccc
Q psy271 144 HCKHEFCWMCLGNT 157 (191)
Q Consensus 144 ~C~~~fC~~C~~~~ 157 (191)
-|+|.|||.|.+.-
T Consensus 24 ~C~HkFCyiCiKGs 37 (324)
T KOG0824|consen 24 YCFHKFCYICIKGS 37 (324)
T ss_pred cccchhhhhhhcch
Confidence 49999999998753
No 229
>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=44.13 E-value=15 Score=30.37 Aligned_cols=34 Identities=26% Similarity=0.709 Sum_probs=26.3
Q ss_pred CCCCCCcc-----eEe---cCCcCceEeCCCCcce------ecccccc
Q psy271 123 DCPKCHIC-----IEK---NGGCNHMQCYHCKHEF------CWMCLGN 156 (191)
Q Consensus 123 ~CP~C~~~-----i~k---~~GC~~m~C~~C~~~f------C~~C~~~ 156 (191)
.||-|+.. |.. .+|=.++.|+.|+++| |-.|+..
T Consensus 186 ~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 186 LCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred cCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 79999986 222 4788899999899887 6678763
No 230
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=43.59 E-value=13 Score=21.00 Aligned_cols=19 Identities=26% Similarity=0.583 Sum_probs=12.1
Q ss_pred CceEeCCCCcceecccccc
Q psy271 138 NHMQCYHCKHEFCWMCLGN 156 (191)
Q Consensus 138 ~~m~C~~C~~~fC~~C~~~ 156 (191)
.-+.|..|+..||-.=..+
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST
T ss_pred CCeECCCCCcccCccccCc
Confidence 4689988999999876544
No 231
>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=43.53 E-value=14 Score=25.89 Aligned_cols=9 Identities=56% Similarity=1.176 Sum_probs=6.2
Q ss_pred CCCCCCCcc
Q psy271 122 KDCPKCHIC 130 (191)
Q Consensus 122 k~CP~C~~~ 130 (191)
..||+|+..
T Consensus 87 ~~CP~Cgs~ 95 (115)
T TIGR00100 87 YRCPKCHGI 95 (115)
T ss_pred ccCcCCcCC
Confidence 468888764
No 232
>PLN02400 cellulose synthase
Probab=43.46 E-value=13 Score=35.92 Aligned_cols=40 Identities=15% Similarity=0.338 Sum_probs=25.9
Q ss_pred ccccCCcccCccchHHHHHHHhhccChHHHHHHHHhcCCCCCCCCcceEecCCcCce
Q psy271 84 PMQSGIEYHAPTDCAVIKKWLTKCADDSETANYISAHTKDCPKCHICIEKNGGCNHM 140 (191)
Q Consensus 84 C~~Cgv~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~~m 140 (191)
|-.|+.+... +|.+|... ...+.||+|++.+.+..|+..+
T Consensus 58 C~eCaFPVCR--pCYEYERk---------------eGnq~CPQCkTrYkR~KgsprV 97 (1085)
T PLN02400 58 CNECAFPVCR--PCYEYERK---------------DGTQCCPQCKTRYRRHKGSPRV 97 (1085)
T ss_pred EccCCCcccc--chhheecc---------------cCCccCcccCCccccccCCCCC
Confidence 7777777654 56665332 3467788888888766666554
No 233
>COG4640 Predicted membrane protein [Function unknown]
Probab=43.40 E-value=14 Score=31.69 Aligned_cols=24 Identities=46% Similarity=0.960 Sum_probs=15.5
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
+-||+|+.. +.++ -|.|.+||+.|
T Consensus 2 ~fC~kcG~q--k~Ed--~~qC~qCG~~~ 25 (465)
T COG4640 2 KFCPKCGSQ--KAED--DVQCTQCGHKF 25 (465)
T ss_pred Ccccccccc--cccc--cccccccCCcC
Confidence 468888842 3333 35588888876
No 234
>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=41.04 E-value=26 Score=30.78 Aligned_cols=25 Identities=16% Similarity=0.003 Sum_probs=21.9
Q ss_pred CCCcccCccCCCccccCCCCCCCCC
Q psy271 167 TTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 167 ~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
..+++++..+|..++|..+.+||.|
T Consensus 103 ~~~~~i~~~~~~~~~R~~~~~~l~T 127 (458)
T TIGR01041 103 DERRDINGAPINPYAREYPEEFIQT 127 (458)
T ss_pred cceeeccCCCCChhhcCCCCCcCCC
Confidence 3456888889999999999999987
No 235
>PRK12496 hypothetical protein; Provisional
Probab=40.98 E-value=15 Score=27.52 Aligned_cols=28 Identities=18% Similarity=0.382 Sum_probs=16.5
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
++|+.|+..+..+. ...||-.||.+.+.
T Consensus 128 ~~C~gC~~~~~~~~----------~~~~C~~CG~~~~r 155 (164)
T PRK12496 128 KVCKGCKKKYPEDY----------PDDVCEICGSPVKR 155 (164)
T ss_pred EECCCCCccccCCC----------CCCcCCCCCChhhh
Confidence 35888887764321 12456688877653
No 236
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.98 E-value=25 Score=24.63 Aligned_cols=34 Identities=26% Similarity=0.536 Sum_probs=23.6
Q ss_pred CCCCCCCCcceEecC--------CcCceEeCCCCcceecccc
Q psy271 121 TKDCPKCHICIEKNG--------GCNHMQCYHCKHEFCWMCL 154 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~--------GC~~m~C~~C~~~fC~~C~ 154 (191)
.+.|-.|+..+.... .=..-.|.+|+..||..|-
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD 96 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCD 96 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccc
Confidence 356999988764311 1125669999999999994
No 237
>PHA02325 hypothetical protein
Probab=40.95 E-value=14 Score=23.10 Aligned_cols=12 Identities=50% Similarity=0.830 Sum_probs=8.0
Q ss_pred cCCCCCCCCcce
Q psy271 120 HTKDCPKCHICI 131 (191)
Q Consensus 120 ~~k~CP~C~~~i 131 (191)
++|.||+|++.-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 357788887654
No 238
>PLN02189 cellulose synthase
Probab=40.46 E-value=21 Score=34.43 Aligned_cols=40 Identities=18% Similarity=0.424 Sum_probs=27.8
Q ss_pred ccccCCcccCccchHHHHHHHhhccChHHHHHHHHhcCCCCCCCCcceEecCCcCce
Q psy271 84 PMQSGIEYHAPTDCAVIKKWLTKCADDSETANYISAHTKDCPKCHICIEKNGGCNHM 140 (191)
Q Consensus 84 C~~Cgv~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~~m 140 (191)
|-.|+.+... +|.+|... ...+.||+|+..+.+--|++.+
T Consensus 56 C~~C~fpvCr--~Cyeyer~---------------eg~q~CpqCkt~Y~r~kgs~~v 95 (1040)
T PLN02189 56 CNECGFPVCR--PCYEYERR---------------EGTQNCPQCKTRYKRLKGSPRV 95 (1040)
T ss_pred eccCCCcccc--chhhhhhh---------------cCCccCcccCCchhhccCCCCc
Confidence 7777777654 67766332 3467899999998876676664
No 239
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=39.95 E-value=21 Score=33.48 Aligned_cols=36 Identities=22% Similarity=0.701 Sum_probs=29.3
Q ss_pred CCCCCCCCcceE---ecCCcCceEeCCCCcceecccccc
Q psy271 121 TKDCPKCHICIE---KNGGCNHMQCYHCKHEFCWMCLGN 156 (191)
Q Consensus 121 ~k~CP~C~~~i~---k~~GC~~m~C~~C~~~fC~~C~~~ 156 (191)
.+.|..|+.... |.-+...=.|.+||.-||-.|...
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSn 498 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITK 498 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCccccCccccCC
Confidence 367999998873 456777888999999999999754
No 240
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=39.71 E-value=10 Score=21.60 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=5.3
Q ss_pred ccCCcccCccchHH
Q psy271 86 QSGIEYHAPTDCAV 99 (191)
Q Consensus 86 ~Cgv~~H~~~~C~~ 99 (191)
.|+++||. .|.+
T Consensus 18 ~C~~r~H~--~C~~ 29 (43)
T PF08746_consen 18 DCNVRLHD--DCFK 29 (43)
T ss_dssp -S--EE-H--HHHH
T ss_pred ccCchHHH--HHHH
Confidence 47888887 5553
No 241
>PRK08927 fliI flagellum-specific ATP synthase; Validated
Probab=38.64 E-value=26 Score=30.64 Aligned_cols=24 Identities=21% Similarity=0.353 Sum_probs=22.0
Q ss_pred CCcccCccCCCccccCCCCCCCCC
Q psy271 168 TRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 168 ~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
.+++++..+|..++|..+.+||.|
T Consensus 121 ~~~~i~~~~p~~~~R~~~~~~l~T 144 (442)
T PRK08927 121 VPYPLRAPPPPAHSRARVGEPLDL 144 (442)
T ss_pred ccccccCCCcChHHcCCccccccc
Confidence 467899999999999999999987
No 242
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=38.53 E-value=18 Score=31.29 Aligned_cols=27 Identities=30% Similarity=0.702 Sum_probs=19.9
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcce
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
-.||.|+... |+.|=|-..|.+||+.+
T Consensus 351 p~Cp~Cg~~m-~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 351 PVCPRCGGRM-KSAGRNGFRCKKCGTRA 377 (421)
T ss_pred CCCCccCCch-hhcCCCCcccccccccC
Confidence 3799999987 44454488898777654
No 243
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=38.39 E-value=12 Score=27.27 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=9.6
Q ss_pred CCCCCCCCcceEe
Q psy271 121 TKDCPKCHICIEK 133 (191)
Q Consensus 121 ~k~CP~C~~~i~k 133 (191)
.-.||.|+..+.-
T Consensus 99 ~Y~Cp~C~~~y~~ 111 (147)
T smart00531 99 YYKCPNCQSKYTF 111 (147)
T ss_pred EEECcCCCCEeeH
Confidence 3469999988764
No 244
>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=38.38 E-value=36 Score=22.87 Aligned_cols=31 Identities=26% Similarity=0.523 Sum_probs=22.9
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCccee
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC 150 (191)
....||.|+..-.|..+----.|..|+..|=
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEEe
Confidence 4568999988877776666677777777663
No 245
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=38.34 E-value=21 Score=18.76 Aligned_cols=23 Identities=30% Similarity=0.758 Sum_probs=13.0
Q ss_pred CCCCCCcceEe-------cCCcCceEeCCC
Q psy271 123 DCPKCHICIEK-------NGGCNHMQCYHC 145 (191)
Q Consensus 123 ~CP~C~~~i~k-------~~GC~~m~C~~C 145 (191)
+|+.|+..|.- .+..-|..|..|
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C 30 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKC 30 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCC
Confidence 46777766532 345666666543
No 246
>KOG2879|consensus
Probab=37.62 E-value=31 Score=28.12 Aligned_cols=31 Identities=23% Similarity=0.725 Sum_probs=19.7
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCcceecccccc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGN 156 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~ 156 (191)
.+.||-|+..=.- =.+|- .|+|-|||.|.+.
T Consensus 239 ~~~C~~Cg~~Pti---P~~~~--~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 239 DTECPVCGEPPTI---PHVIG--KCGHIYCYYCIAT 269 (298)
T ss_pred CceeeccCCCCCC---Ceeec--cccceeehhhhhh
Confidence 4679999875321 01222 3888888899764
No 247
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=37.37 E-value=18 Score=24.92 Aligned_cols=35 Identities=29% Similarity=0.598 Sum_probs=22.8
Q ss_pred cCCCCCCCCcceEecCCcCceEe------CCC---Ccceecccccccc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQC------YHC---KHEFCWMCLGNTI 158 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C------~~C---~~~fC~~C~~~~~ 158 (191)
+.+.|.+|+..-. =.+|.| ..| .-.||+.|+....
T Consensus 6 ~g~~CHqCrqKt~----~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ry 49 (105)
T PF10497_consen 6 NGKTCHQCRQKTL----DFKTICTGHWKNSSCRGCRGKFCGGCLRNRY 49 (105)
T ss_pred CCCCchhhcCCCC----CCceEcCCCCCCCCCccCcceehHhHHHHHH
Confidence 4567777776332 123555 566 8999999976544
No 248
>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.
Probab=37.23 E-value=9.6 Score=32.34 Aligned_cols=28 Identities=14% Similarity=0.317 Sum_probs=23.6
Q ss_pred CCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 163 PLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 163 ~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
.+.-..++++...+|.. .|..+.+||.|
T Consensus 116 ~~~~~~~~Pv~~~~P~~-~r~~~~~pL~T 143 (369)
T cd01134 116 EITMVQKWPVRQPRPVK-EKLPPNEPLLT 143 (369)
T ss_pred ccccceeeecccCCCcc-ccCCCCCchhc
Confidence 55556678999988888 99999999987
No 249
>PHA02998 RNA polymerase subunit; Provisional
Probab=36.99 E-value=37 Score=25.85 Aligned_cols=38 Identities=18% Similarity=0.322 Sum_probs=21.9
Q ss_pred cCCCCCCCCcc------eEecCCcCceEeCCCCcceecccccccccCC
Q psy271 120 HTKDCPKCHIC------IEKNGGCNHMQCYHCKHEFCWMCLGNTIDGK 161 (191)
Q Consensus 120 ~~k~CP~C~~~------i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~~ 161 (191)
...+||+|+.. +|-.++=--||= +..|-.|+..|....
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~----FYkC~~CG~~wkppk 185 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLV----RHACRDCKKHFKPPK 185 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceE----EEEcCCCCCccCCcc
Confidence 45789999853 344444444541 233446777777644
No 250
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=36.03 E-value=21 Score=24.92 Aligned_cols=15 Identities=27% Similarity=0.718 Sum_probs=9.0
Q ss_pred CCCCCCCcc-eEecCC
Q psy271 122 KDCPKCHIC-IEKNGG 136 (191)
Q Consensus 122 k~CP~C~~~-i~k~~G 136 (191)
.+||+|+.. ++..+|
T Consensus 88 ~~CP~Cgs~~~~i~~G 103 (114)
T PRK03681 88 RRCPQCHGDMLRIVAD 103 (114)
T ss_pred CcCcCcCCCCcEEccC
Confidence 458888854 444444
No 251
>TIGR01039 atpD ATP synthase, F1 beta subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.
Probab=35.93 E-value=29 Score=30.49 Aligned_cols=32 Identities=25% Similarity=0.439 Sum_probs=25.5
Q ss_pred CCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 160 GKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 160 ~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+..+.....++++...+|..+.|..+++||.|
T Consensus 98 ~~~~~~~~~~~pi~~~~p~~~~R~~~~e~l~T 129 (461)
T TIGR01039 98 EKGPIPAKERWPIHRKAPSFEEQSTKVEILET 129 (461)
T ss_pred CCCCCCCCcccccccCCCChhHcCCccccccc
Confidence 33444444677888899999999999999987
No 252
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.86 E-value=12 Score=23.11 Aligned_cols=27 Identities=22% Similarity=0.706 Sum_probs=16.8
Q ss_pred CCCCCCcceE----ecCCcCceEeCCCCcce
Q psy271 123 DCPKCHICIE----KNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 123 ~CP~C~~~i~----k~~GC~~m~C~~C~~~f 149 (191)
.||.|+..=. ...+=.+.-|..||++.
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 4666654322 24556678888888876
No 253
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.55 E-value=19 Score=22.44 Aligned_cols=16 Identities=25% Similarity=0.403 Sum_probs=12.8
Q ss_pred cCCCCCCCCcceEecC
Q psy271 120 HTKDCPKCHICIEKNG 135 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~ 135 (191)
.+.+||.|+.+++...
T Consensus 6 ~~v~CP~Cgkpv~w~~ 21 (65)
T COG3024 6 ITVPCPTCGKPVVWGE 21 (65)
T ss_pred ccccCCCCCCcccccc
Confidence 3678999999998743
No 254
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.48 E-value=34 Score=23.43 Aligned_cols=28 Identities=25% Similarity=0.592 Sum_probs=17.3
Q ss_pred CCCCCCCcc------eEecCCcCceEeCCCCcce
Q psy271 122 KDCPKCHIC------IEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~~------i~k~~GC~~m~C~~C~~~f 149 (191)
-.||.|+.. +-|..+=-..+|..||..|
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 358888764 2334444457787777665
No 255
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=35.28 E-value=36 Score=23.89 Aligned_cols=21 Identities=29% Similarity=0.738 Sum_probs=11.7
Q ss_pred CCCCCcceEecCCcCceEeCCCCcc
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~~ 148 (191)
||.|+....-+ .+.|.+|++.
T Consensus 1 CPvCg~~l~vt----~l~C~~C~t~ 21 (113)
T PF09862_consen 1 CPVCGGELVVT----RLKCPSCGTE 21 (113)
T ss_pred CCCCCCceEEE----EEEcCCCCCE
Confidence 67777665432 2555556543
No 256
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=35.02 E-value=31 Score=30.21 Aligned_cols=30 Identities=20% Similarity=0.360 Sum_probs=23.7
Q ss_pred CCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 162 GPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 162 ~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
.+.....+.+++..+|..++|..+++||.|
T Consensus 125 ~~~~~~~~~~i~~~~~~p~~R~~i~~~l~T 154 (451)
T PRK05688 125 GPMKAEDWVPMDGPTINPLNRHPISEPLDV 154 (451)
T ss_pred CCCCccceecccCCCCCHHHcccccCCccc
Confidence 343344456788889999999999999987
No 257
>PRK09099 type III secretion system ATPase; Provisional
Probab=35.01 E-value=35 Score=29.86 Aligned_cols=29 Identities=24% Similarity=0.357 Sum_probs=23.1
Q ss_pred CCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 163 PLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 163 ~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+.....+++++..+|..++|..+++||.|
T Consensus 121 ~~~~~~~~~i~~~~p~p~~R~~i~e~l~T 149 (441)
T PRK09099 121 PLDCDELVPVIAAPPDPMSRRMVEAPLPT 149 (441)
T ss_pred CCccccccccccCCCChhhcCCcccccCC
Confidence 33333456788899999999999999987
No 258
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=34.98 E-value=48 Score=22.23 Aligned_cols=31 Identities=23% Similarity=0.410 Sum_probs=22.9
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCccee
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC 150 (191)
....||.|+..-.|..+----.|..|+..|=
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCceeeeeeEEEEcCCCCCEEe
Confidence 4568999988877776666677877777663
No 259
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.67 E-value=44 Score=22.42 Aligned_cols=31 Identities=26% Similarity=0.525 Sum_probs=23.3
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCccee
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKHEFC 150 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC 150 (191)
....||.|+..-.|..+----.|..|+..|=
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 3568999988888877666677777777664
No 260
>KOG2907|consensus
Probab=34.59 E-value=16 Score=25.50 Aligned_cols=24 Identities=25% Similarity=0.647 Sum_probs=13.2
Q ss_pred CCCCCCcceEecCCcCceEeCCCC
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCK 146 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~ 146 (191)
-|+.|+..++..+-=.-..|.+|+
T Consensus 9 FC~~CG~ll~~~~~~~~~~C~~Ck 32 (116)
T KOG2907|consen 9 FCSDCGSLLEEPSAQSTVLCIRCK 32 (116)
T ss_pred hhhhhhhhcccccccCceEecccc
Confidence 367777777654443444454443
No 261
>PRK06386 replication factor A; Reviewed
Probab=34.54 E-value=18 Score=30.69 Aligned_cols=13 Identities=31% Similarity=0.672 Sum_probs=11.5
Q ss_pred CCCCCCCCcceEe
Q psy271 121 TKDCPKCHICIEK 133 (191)
Q Consensus 121 ~k~CP~C~~~i~k 133 (191)
.++||.|+..+++
T Consensus 236 i~rCP~C~R~l~~ 248 (358)
T PRK06386 236 FTKCSVCNKIIED 248 (358)
T ss_pred EecCcCCCeEccC
Confidence 3799999999985
No 262
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=34.52 E-value=20 Score=25.00 Aligned_cols=23 Identities=35% Similarity=0.572 Sum_probs=16.8
Q ss_pred CceEeCCCCcceecccccccccCCC
Q psy271 138 NHMQCYHCKHEFCWMCLGNTIDGKG 162 (191)
Q Consensus 138 ~~m~C~~C~~~fC~~C~~~~~~~~~ 162 (191)
..+.| .|||.||-.= .+|+.+.-
T Consensus 23 k~vkc-~CGh~f~d~r-~NwK~~al 45 (112)
T PF08882_consen 23 KVVKC-DCGHEFCDAR-ENWKLGAL 45 (112)
T ss_pred ceeec-cCCCeecChh-cChhhCcE
Confidence 36889 7999999763 67776543
No 263
>KOG2164|consensus
Probab=34.41 E-value=13 Score=32.67 Aligned_cols=32 Identities=25% Similarity=0.492 Sum_probs=22.4
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCcceecccccccc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~ 158 (191)
-.+||-|-..-. +..|| .|||-|||-|+-.|-
T Consensus 186 ~~~CPICL~~~~----~p~~t--~CGHiFC~~CiLqy~ 217 (513)
T KOG2164|consen 186 DMQCPICLEPPS----VPVRT--NCGHIFCGPCILQYW 217 (513)
T ss_pred CCcCCcccCCCC----ccccc--ccCceeeHHHHHHHH
Confidence 678999976532 33333 499999999986554
No 264
>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=34.24 E-value=33 Score=24.97 Aligned_cols=14 Identities=29% Similarity=0.605 Sum_probs=11.6
Q ss_pred CCCCCCCCcceEec
Q psy271 121 TKDCPKCHICIEKN 134 (191)
Q Consensus 121 ~k~CP~C~~~i~k~ 134 (191)
..+||.|+..+++.
T Consensus 91 ~sRC~~CN~~L~~v 104 (147)
T PF01927_consen 91 FSRCPKCNGPLRPV 104 (147)
T ss_pred CCccCCCCcEeeec
Confidence 57899999988764
No 265
>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=34.19 E-value=28 Score=27.48 Aligned_cols=13 Identities=15% Similarity=0.243 Sum_probs=6.5
Q ss_pred CceEeCCCCccee
Q psy271 138 NHMQCYHCKHEFC 150 (191)
Q Consensus 138 ~~m~C~~C~~~fC 150 (191)
+...|..||..|-
T Consensus 34 ~v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 34 EVTICPKCGRYRI 46 (236)
T ss_pred CceECCCCCCEEC
Confidence 4455555555444
No 266
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=34.14 E-value=26 Score=28.07 Aligned_cols=24 Identities=33% Similarity=0.740 Sum_probs=18.6
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcce
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHEF 149 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~f 149 (191)
.||.|+.++...+ +...|. .+|.|
T Consensus 4 ~CP~C~~~l~~~~--~~~~C~-~~h~f 27 (272)
T PRK11088 4 QCPLCHQPLTLEE--NSWICP-QNHQF 27 (272)
T ss_pred cCCCCCcchhcCC--CEEEcC-CCCCC
Confidence 6999999997654 568885 47776
No 267
>PRK07960 fliI flagellum-specific ATP synthase; Validated
Probab=34.02 E-value=31 Score=30.29 Aligned_cols=33 Identities=12% Similarity=0.065 Sum_probs=26.5
Q ss_pred cCCCCCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 159 DGKGPLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 159 ~~~~~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
++..+.....+++++..+|..+.|..+.+||.|
T Consensus 129 Dg~~~~~~~~~~~i~~~~~~p~~R~~i~e~l~T 161 (455)
T PRK07960 129 DGLPAPDTGETGALITPPFNPLQRTPIEHVLDT 161 (455)
T ss_pred CCCCCCCCCccccccCCCcChHHhcccccchhc
Confidence 344455455677899999999999999999987
No 268
>KOG0978|consensus
Probab=33.89 E-value=12 Score=34.50 Aligned_cols=35 Identities=23% Similarity=0.548 Sum_probs=22.9
Q ss_pred hcCCCCCCCCcceEecCCcCceEeCCCCcceeccccccccc
Q psy271 119 AHTKDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTID 159 (191)
Q Consensus 119 ~~~k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~ 159 (191)
...-.||-|...- |+ +.=++|+|-||+.|.++...
T Consensus 641 K~~LkCs~Cn~R~-Kd-----~vI~kC~H~FC~~Cvq~r~e 675 (698)
T KOG0978|consen 641 KELLKCSVCNTRW-KD-----AVITKCGHVFCEECVQTRYE 675 (698)
T ss_pred HhceeCCCccCch-hh-----HHHHhcchHHHHHHHHHHHH
Confidence 3567899997421 11 11126899999999887764
No 269
>KOG4218|consensus
Probab=33.86 E-value=15 Score=30.97 Aligned_cols=47 Identities=23% Similarity=0.418 Sum_probs=25.2
Q ss_pred ccccCCcc---cCc-cchHHHHHHHhhccCh------HHHHH--HHHhcCCCCCCCCcc
Q psy271 84 PMQSGIEY---HAP-TDCAVIKKWLTKCADD------SETAN--YISAHTKDCPKCHIC 130 (191)
Q Consensus 84 C~~Cgv~~---H~~-~~C~~~~~~~~~~~~~------~~~~~--~~~~~~k~CP~C~~~ 130 (191)
|.-||-+. |.| .+|+..+....+...+ .+.++ .-+...|+||.|+..
T Consensus 18 CPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQ 76 (475)
T KOG4218|consen 18 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQ 76 (475)
T ss_pred cccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHH
Confidence 67777654 777 6888766554322111 11111 112346889988654
No 270
>PLN02436 cellulose synthase A
Probab=33.85 E-value=30 Score=33.49 Aligned_cols=40 Identities=13% Similarity=0.337 Sum_probs=26.5
Q ss_pred ccccCCcccCccchHHHHHHHhhccChHHHHHHHHhcCCCCCCCCcceEecCCcCce
Q psy271 84 PMQSGIEYHAPTDCAVIKKWLTKCADDSETANYISAHTKDCPKCHICIEKNGGCNHM 140 (191)
Q Consensus 84 C~~Cgv~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~~m 140 (191)
|-.|+.+... +|.+|... ...+.||+|+..+.+--|++.+
T Consensus 58 Cn~C~fpvCr--~Cyeyer~---------------eg~~~Cpqckt~Y~r~kgs~~~ 97 (1094)
T PLN02436 58 CNECAFPVCR--PCYEYERR---------------EGNQACPQCKTRYKRIKGSPRV 97 (1094)
T ss_pred eccCCCcccc--chhhhhhh---------------cCCccCcccCCchhhccCCCCc
Confidence 7777777654 56665332 3467888888888766666553
No 271
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=33.78 E-value=35 Score=18.73 Aligned_cols=29 Identities=21% Similarity=0.505 Sum_probs=21.2
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGN 156 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~ 156 (191)
..|+.+.... ..+.|..|+..+|..|...
T Consensus 4 ~~C~~H~~~~------~~~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 4 PKCPEHPEEP------LSLFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SB-SSTTTSB------EEEEETTTTEEEEHHHHHT
T ss_pred ccCccCCccc------eEEEecCCCCccCccCCCC
Confidence 4577776551 2688999999999999764
No 272
>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=33.62 E-value=13 Score=22.72 Aligned_cols=19 Identities=26% Similarity=0.389 Sum_probs=9.5
Q ss_pred CCCCCCCCcceEecCCcCc
Q psy271 121 TKDCPKCHICIEKNGGCNH 139 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~ 139 (191)
+.+||.|+..++-+.+-.+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~ 20 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPF 20 (57)
T ss_dssp EEE-TTT--EEE-SSSSS-
T ss_pred cccCCCCCCeecccCCCCc
Confidence 3578989888887555444
No 273
>PRK07218 replication factor A; Provisional
Probab=33.27 E-value=19 Score=31.25 Aligned_cols=13 Identities=38% Similarity=0.953 Sum_probs=11.5
Q ss_pred CCCCCCCCcceEe
Q psy271 121 TKDCPKCHICIEK 133 (191)
Q Consensus 121 ~k~CP~C~~~i~k 133 (191)
.++||.|+..+++
T Consensus 297 i~rCP~C~r~v~~ 309 (423)
T PRK07218 297 IERCPECGRVIQK 309 (423)
T ss_pred eecCcCccccccC
Confidence 4899999999977
No 274
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=32.27 E-value=45 Score=27.52 Aligned_cols=27 Identities=19% Similarity=0.422 Sum_probs=14.9
Q ss_pred CCCCCCCCc-ceEecCCcCceEeCCCCc
Q psy271 121 TKDCPKCHI-CIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 121 ~k~CP~C~~-~i~k~~GC~~m~C~~C~~ 147 (191)
...||.|+. .|..+..=--+.|..||.
T Consensus 11 ~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 11 KLVCPECGSDKLIYDYERGEIVCADCGL 38 (310)
T ss_pred CCcCcCCCCCCeeEECCCCeEeecccCC
Confidence 467999987 343332212366664543
No 275
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=32.19 E-value=21 Score=21.59 Aligned_cols=17 Identities=24% Similarity=0.587 Sum_probs=13.0
Q ss_pred CCCcceecccccccccC
Q psy271 144 HCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 144 ~C~~~fC~~C~~~~~~~ 160 (191)
+=.+.||+-|+..+.+.
T Consensus 24 R~~~~YC~~Cg~~Y~d~ 40 (55)
T PF13821_consen 24 REEHNYCFWCGTKYDDE 40 (55)
T ss_pred HhhCceeeeeCCccCCH
Confidence 46788889998887764
No 276
>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=32.07 E-value=24 Score=18.67 Aligned_cols=9 Identities=44% Similarity=1.206 Sum_probs=6.3
Q ss_pred CCCCCCcce
Q psy271 123 DCPKCHICI 131 (191)
Q Consensus 123 ~CP~C~~~i 131 (191)
-||+|+.-+
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 599999765
No 277
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=31.58 E-value=21 Score=21.43 Aligned_cols=32 Identities=6% Similarity=0.087 Sum_probs=23.8
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
.||-|+..+.- .+. ..||+.||..|...|...
T Consensus 3 ~Cpi~~~~~~~-----Pv~-~~~G~v~~~~~i~~~~~~ 34 (63)
T smart00504 3 LCPISLEVMKD-----PVI-LPSGQTYERRAIEKWLLS 34 (63)
T ss_pred CCcCCCCcCCC-----CEE-CCCCCEEeHHHHHHHHHH
Confidence 48888887642 244 369999999999998753
No 278
>PRK06936 type III secretion system ATPase; Provisional
Probab=31.30 E-value=40 Score=29.48 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=21.7
Q ss_pred CCCcccCccCCCccccCCCCCCCCC
Q psy271 167 TTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 167 ~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
..+++++..+|..++|..+++||.|
T Consensus 124 ~~~~pi~~~~p~p~~R~~i~~~l~T 148 (439)
T PRK06936 124 AAWYPVYADAPAPMSRRLIETPLSL 148 (439)
T ss_pred cceeeccCCCCChHHccccCCCCcC
Confidence 3456788889999999999999987
No 279
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=31.07 E-value=35 Score=33.01 Aligned_cols=39 Identities=18% Similarity=0.463 Sum_probs=26.6
Q ss_pred ccccCCcccCccchHHHHHHHhhccChHHHHHHHHhcCCCCCCCCcceEecCCcCc
Q psy271 84 PMQSGIEYHAPTDCAVIKKWLTKCADDSETANYISAHTKDCPKCHICIEKNGGCNH 139 (191)
Q Consensus 84 C~~Cgv~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i~k~~GC~~ 139 (191)
|-.|+.+... +|.+|... ...+.||+|+..+.+-.|++.
T Consensus 37 C~eC~fpvCr--~cyeye~~---------------~g~~~cp~c~t~y~~~~~~~~ 75 (1044)
T PLN02915 37 CHVCGFPVCK--PCYEYERS---------------EGNQCCPQCNTRYKRHKGCPR 75 (1044)
T ss_pred eccCCCcccc--chhhhhhh---------------cCCccCCccCCchhhhcCCCC
Confidence 7778777654 57665332 346789999988876556555
No 280
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=31.01 E-value=35 Score=19.15 Aligned_cols=13 Identities=23% Similarity=0.756 Sum_probs=10.0
Q ss_pred CCCCCCCCc-ceEe
Q psy271 121 TKDCPKCHI-CIEK 133 (191)
Q Consensus 121 ~k~CP~C~~-~i~k 133 (191)
...||+|+. .++|
T Consensus 26 ~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 26 PVPCPECGSTEVRR 39 (42)
T ss_pred CCcCCCCCCCceEE
Confidence 568999998 6655
No 281
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=30.58 E-value=29 Score=18.63 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=8.9
Q ss_pred CCCCCCCcceEec
Q psy271 122 KDCPKCHICIEKN 134 (191)
Q Consensus 122 k~CP~C~~~i~k~ 134 (191)
-.||+|+..|.-+
T Consensus 5 ~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 5 VECPNCGRPVAAS 17 (33)
T ss_dssp EE-TTTSSEEEGG
T ss_pred EECCCCcCCcchh
Confidence 3699999988643
No 282
>PF14996 RMP: Retinal Maintenance
Probab=30.39 E-value=37 Score=24.94 Aligned_cols=38 Identities=11% Similarity=0.170 Sum_probs=28.9
Q ss_pred CCcCceEeCCCCcceecccccccccCCCCCCCCCCccc
Q psy271 135 GGCNHMQCYHCKHEFCWMCLGNTIDGKGPLKTTTRFRV 172 (191)
Q Consensus 135 ~GC~~m~C~~C~~~fC~~C~~~~~~~~~~~~~~~~~~~ 172 (191)
.+|+++.|..|.+.---.=+..|...-......|.++.
T Consensus 64 r~C~~LrC~~CDf~V~~f~~~~W~~~~DYLFfRNn~P~ 101 (146)
T PF14996_consen 64 RACDNLRCTKCDFRVVRFDDYKWDKSCDYLFFRNNYPD 101 (146)
T ss_pred ccCCCCEEecCCcEEEEeCCCccCCCCCEEEEecCCCc
Confidence 67999999999988887778889876655555555554
No 283
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=29.96 E-value=46 Score=23.14 Aligned_cols=26 Identities=23% Similarity=0.521 Sum_probs=19.4
Q ss_pred CCCCCCCcc---eEecCCcCceEeCCCCc
Q psy271 122 KDCPKCHIC---IEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 122 k~CP~C~~~---i~k~~GC~~m~C~~C~~ 147 (191)
-.||.|+.+ ++|+++=..+.|..||.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 469999876 56676666688987875
No 284
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=29.72 E-value=39 Score=29.69 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=23.5
Q ss_pred CCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 163 PLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 163 ~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+.....++++...+|..++|..+++||.|
T Consensus 101 ~~~~~~~~~i~~~~p~~~~R~~~~e~l~T 129 (461)
T PRK12597 101 PLPAEERRPIHSTIPPLAEQDTSTEILET 129 (461)
T ss_pred CCCCcceeeccCCCcChhhcCCcCcceec
Confidence 33334567888889999999999999987
No 285
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=29.55 E-value=31 Score=20.38 Aligned_cols=17 Identities=24% Similarity=0.604 Sum_probs=12.7
Q ss_pred ceEeCCCCcceeccccc
Q psy271 139 HMQCYHCKHEFCWMCLG 155 (191)
Q Consensus 139 ~m~C~~C~~~fC~~C~~ 155 (191)
+++|..||.+|-|.=+.
T Consensus 4 ~l~C~dCg~~FvfTa~E 20 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGE 20 (49)
T ss_pred eEEcccCCCeEEEehhH
Confidence 47888888888886543
No 286
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=29.38 E-value=40 Score=29.22 Aligned_cols=23 Identities=26% Similarity=0.579 Sum_probs=20.8
Q ss_pred CcccCccCCCccccCCCCCCCCC
Q psy271 169 RFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 169 ~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
.++++..+|..++|..+++||.|
T Consensus 104 ~~~i~~~~p~~~~R~~i~~~l~t 126 (418)
T TIGR03498 104 RYPLRASPPPAMSRARVGEPLDT 126 (418)
T ss_pred eechhhcCCChhhccCcccccCC
Confidence 46888899999999999999987
No 287
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=28.55 E-value=40 Score=16.64 Aligned_cols=10 Identities=30% Similarity=0.683 Sum_probs=5.4
Q ss_pred CCCCCCCcce
Q psy271 122 KDCPKCHICI 131 (191)
Q Consensus 122 k~CP~C~~~i 131 (191)
.+||.|+...
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 3566665544
No 288
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=28.24 E-value=52 Score=23.90 Aligned_cols=28 Identities=29% Similarity=0.557 Sum_probs=20.4
Q ss_pred CCCCCCCCcc---eEecCCcCceEeCCCCcc
Q psy271 121 TKDCPKCHIC---IEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 121 ~k~CP~C~~~---i~k~~GC~~m~C~~C~~~ 148 (191)
--.||.|+.+ ++|.+.=..+.|..||+.
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3569999976 566666566889878765
No 289
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.18 E-value=79 Score=22.61 Aligned_cols=33 Identities=27% Similarity=0.644 Sum_probs=22.3
Q ss_pred CCCCCCCCcce-EecCC----cCceEeCCCCcceeccc
Q psy271 121 TKDCPKCHICI-EKNGG----CNHMQCYHCKHEFCWMC 153 (191)
Q Consensus 121 ~k~CP~C~~~i-~k~~G----C~~m~C~~C~~~fC~~C 153 (191)
-..||.|+... .|.++ =.+-.|..|+..|=..=
T Consensus 30 ~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 30 KVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred cCcCCCCCccceeeECCccccccccccCCcCcceeeec
Confidence 37899999887 55544 34467877777765443
No 290
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=28.15 E-value=49 Score=18.16 Aligned_cols=25 Identities=24% Similarity=0.638 Sum_probs=13.0
Q ss_pred CCCCCCCCcceEe-cCCcCceEeCCCCc
Q psy271 121 TKDCPKCHICIEK-NGGCNHMQCYHCKH 147 (191)
Q Consensus 121 ~k~CP~C~~~i~k-~~GC~~m~C~~C~~ 147 (191)
.-+|..|+..++. .+|=--+.| ||.
T Consensus 6 ~YkC~~CGniVev~~~g~g~lvC--CGe 31 (36)
T PF06397_consen 6 FYKCEHCGNIVEVVHDGGGPLVC--CGE 31 (36)
T ss_dssp EEE-TTT--EEEEEE--SS-EEE--TTE
T ss_pred EEEccCCCCEEEEEECCCCCEEe--CCc
Confidence 3479999999985 444446777 654
No 291
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=28.10 E-value=52 Score=23.72 Aligned_cols=27 Identities=26% Similarity=0.576 Sum_probs=19.3
Q ss_pred CCCCCCCcc---eEecCCcCceEeCCCCcc
Q psy271 122 KDCPKCHIC---IEKNGGCNHMQCYHCKHE 148 (191)
Q Consensus 122 k~CP~C~~~---i~k~~GC~~m~C~~C~~~ 148 (191)
-.||.|+.+ +.|.+.=..+.|..||+.
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 569999976 556655455789878765
No 292
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=27.80 E-value=1.2e+02 Score=19.20 Aligned_cols=24 Identities=21% Similarity=0.227 Sum_probs=19.3
Q ss_pred EEEEEecCCCCCCCCCeEEecCCc
Q psy271 10 VGVVVFGNDRLIKEGDIVKRTGAI 33 (191)
Q Consensus 10 ~~~~~~~~~~gi~~G~~v~~~g~~ 33 (191)
..-+.|++..||.+|+.|...|-.
T Consensus 4 ~v~~~~~~~~GL~~gs~V~~~Gv~ 27 (81)
T PF02470_consen 4 TVTVYFDDAGGLSVGSPVRYRGVE 27 (81)
T ss_pred EEEEEECCcCCCCCcCEEEECCEE
Confidence 345778899999999999887633
No 293
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=27.77 E-value=20 Score=29.50 Aligned_cols=16 Identities=31% Similarity=1.045 Sum_probs=12.3
Q ss_pred CCCcceeccccccccc
Q psy271 144 HCKHEFCWMCLGNTID 159 (191)
Q Consensus 144 ~C~~~fC~~C~~~~~~ 159 (191)
.|||-||++|-+.+..
T Consensus 42 tCgHtFCslCIR~hL~ 57 (391)
T COG5432 42 TCGHTFCSLCIRRHLG 57 (391)
T ss_pred ccccchhHHHHHHHhc
Confidence 4899999999776553
No 294
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=27.60 E-value=58 Score=24.11 Aligned_cols=7 Identities=43% Similarity=1.113 Sum_probs=5.4
Q ss_pred CCCCCCc
Q psy271 123 DCPKCHI 129 (191)
Q Consensus 123 ~CP~C~~ 129 (191)
+||.|+.
T Consensus 2 ~cp~c~~ 8 (154)
T PRK00464 2 RCPFCGH 8 (154)
T ss_pred cCCCCCC
Confidence 5888885
No 295
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=27.40 E-value=41 Score=29.57 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=23.9
Q ss_pred CCCCCCCcccCccCCCccccCCCCCCCCC
Q psy271 163 PLKTTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 163 ~~~~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+.....+++++..+|..++|..+++||.|
T Consensus 102 ~~~~~~~~pi~~~~~~~~~R~~~~~~l~T 130 (463)
T PRK09280 102 PIGAEERWPIHRKAPSFEELSTKTEILET 130 (463)
T ss_pred CcCccceecccCCCCChHHhCCccceecc
Confidence 33334567899999999999999999987
No 296
>KOG1994|consensus
Probab=27.15 E-value=14 Score=29.13 Aligned_cols=25 Identities=16% Similarity=0.398 Sum_probs=20.8
Q ss_pred CCCcceecccccccccCCCCCCCCC
Q psy271 144 HCKHEFCWMCLGNTIDGKGPLKTTT 168 (191)
Q Consensus 144 ~C~~~fC~~C~~~~~~~~~~~~~~~ 168 (191)
+=++.+|..||..|++...-|.||.
T Consensus 236 R~eh~YC~fCG~~y~~~edl~ehCP 260 (268)
T KOG1994|consen 236 RSEHYYCFFCGIKYKDEEDLYEHCP 260 (268)
T ss_pred hccceEEEEeccccCCHHHHHHhCC
Confidence 5788999999999998877777764
No 297
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=27.12 E-value=12 Score=29.52 Aligned_cols=27 Identities=19% Similarity=0.346 Sum_probs=18.2
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
.-|+.|+..+++.++ +|+.|+.+...+
T Consensus 25 ~~C~~C~~~~~~~~~------------~C~~C~~~l~~~ 51 (225)
T COG1040 25 GLCSGCQADLPLIGN------------LCPLCGLPLSSH 51 (225)
T ss_pred CcChhhhhchhHHHh------------hhHhhhChhccc
Confidence 468888888776665 566776665544
No 298
>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=26.89 E-value=27 Score=24.41 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=8.6
Q ss_pred CCCCCCCCcce
Q psy271 121 TKDCPKCHICI 131 (191)
Q Consensus 121 ~k~CP~C~~~i 131 (191)
.-.||+|+...
T Consensus 69 ~V~CP~C~K~T 79 (114)
T PF11023_consen 69 QVECPNCGKQT 79 (114)
T ss_pred eeECCCCCChH
Confidence 45799999876
No 299
>PRK05922 type III secretion system ATPase; Validated
Probab=26.59 E-value=53 Score=28.66 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=21.9
Q ss_pred CCCCcccCccCCCccccCCCCCCCCC
Q psy271 166 TTTRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 166 ~~~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
...+.++...+|..+.|..+++||.|
T Consensus 118 ~~~~~pi~~~~~~~~~R~~i~e~l~T 143 (434)
T PRK05922 118 KTHLKPLFSSPPSPMSRQPIQEIFPT 143 (434)
T ss_pred ccceeecccCCCChhhcCCcceecCC
Confidence 34456788889999999999999987
No 300
>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=25.97 E-value=52 Score=28.37 Aligned_cols=28 Identities=14% Similarity=0.439 Sum_probs=18.1
Q ss_pred CCCCCCCCcceEecC--CcCceEeCCCCcc
Q psy271 121 TKDCPKCHICIEKNG--GCNHMQCYHCKHE 148 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~--GC~~m~C~~C~~~ 148 (191)
...||.|+..+++.. .=..-.|.+||+.
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTT 42 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCC
Confidence 457999999887642 2235667766654
No 301
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=25.94 E-value=55 Score=20.12 Aligned_cols=12 Identities=0% Similarity=-0.424 Sum_probs=9.3
Q ss_pred cCCCCCCCCcce
Q psy271 120 HTKDCPKCHICI 131 (191)
Q Consensus 120 ~~k~CP~C~~~i 131 (191)
+.-.||+|+..+
T Consensus 26 ~~~~c~~cg~~~ 37 (60)
T PRK01110 26 TLSVDKTTGEYH 37 (60)
T ss_pred ceeEcCCCCcee
Confidence 345799999887
No 302
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=25.83 E-value=57 Score=19.84 Aligned_cols=41 Identities=17% Similarity=0.336 Sum_probs=21.4
Q ss_pred eeeecCCeEEEEEecCCCCCCCCCeEEecCCccccccchhHHHHHHhhc
Q psy271 2 ALNLEPDNVGVVVFGNDRLIKEGDIVKRTGAIVDVPVGEDLLGRVVDAL 50 (191)
Q Consensus 2 v~~l~~~~~~~~~~~~~~gi~~G~~v~~~g~~~~v~v~~~llgrv~d~~ 50 (191)
|+++..+...+.|.+ ..-+.+|+.+...| ..+-+.++.+.+
T Consensus 30 i~~i~R~~~~~~p~~-~~~l~~gD~l~v~g-------~~~~i~~~~~~~ 70 (71)
T PF02080_consen 30 IVAIKRGGEIIIPDG-DTVLQAGDILIVVG-------DPEDIERFRELF 70 (71)
T ss_dssp EEEEEETEEEES--T-T-BE-TTEEEEEEE-------EHHHHHHHHHHT
T ss_pred EEEEEECCEEECCCC-CCEECCCCEEEEEE-------CHHHHHHHHHhh
Confidence 556666655555555 44477777776665 344455555444
No 303
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=25.78 E-value=44 Score=18.71 Aligned_cols=13 Identities=23% Similarity=0.766 Sum_probs=9.8
Q ss_pred CCCCCCCCcceEe
Q psy271 121 TKDCPKCHICIEK 133 (191)
Q Consensus 121 ~k~CP~C~~~i~k 133 (191)
...||.|+..+..
T Consensus 13 ~~~C~~CgM~Y~~ 25 (41)
T PF13878_consen 13 ATTCPTCGMLYSP 25 (41)
T ss_pred CcCCCCCCCEECC
Confidence 4689999887754
No 304
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=25.58 E-value=34 Score=20.61 Aligned_cols=11 Identities=45% Similarity=1.081 Sum_probs=9.1
Q ss_pred CCCCCCCcceE
Q psy271 122 KDCPKCHICIE 132 (191)
Q Consensus 122 k~CP~C~~~i~ 132 (191)
+.||+|+..-+
T Consensus 25 ~KCPrCK~vN~ 35 (60)
T COG4416 25 KKCPRCKEVNE 35 (60)
T ss_pred ecCCccceeee
Confidence 78999998765
No 305
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.43 E-value=38 Score=27.70 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=7.4
Q ss_pred eEeCCCCcceec
Q psy271 140 MQCYHCKHEFCW 151 (191)
Q Consensus 140 m~C~~C~~~fC~ 151 (191)
..|+.|...||-
T Consensus 256 yvCs~Clsi~C~ 267 (279)
T TIGR00627 256 FVCSVCLSVLCQ 267 (279)
T ss_pred EECCCccCCcCC
Confidence 556666666664
No 306
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=25.32 E-value=17 Score=28.11 Aligned_cols=13 Identities=38% Similarity=1.053 Sum_probs=10.5
Q ss_pred CCCcceecccccc
Q psy271 144 HCKHEFCWMCLGN 156 (191)
Q Consensus 144 ~C~~~fC~~C~~~ 156 (191)
.|||+||-.|-..
T Consensus 213 ~CGH~FC~~Cai~ 225 (259)
T COG5152 213 ECGHSFCSLCAIR 225 (259)
T ss_pred hcchhHHHHHHHH
Confidence 6999999998653
No 307
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=25.26 E-value=48 Score=19.22 Aligned_cols=13 Identities=23% Similarity=0.700 Sum_probs=10.0
Q ss_pred CCCCCCCCc-ceEe
Q psy271 121 TKDCPKCHI-CIEK 133 (191)
Q Consensus 121 ~k~CP~C~~-~i~k 133 (191)
...||.|+. .++|
T Consensus 26 ~~~CP~Cg~~~~~r 39 (52)
T TIGR02605 26 LATCPECGGEKLRR 39 (52)
T ss_pred CCCCCCCCCCceeE
Confidence 457999998 6665
No 308
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=25.09 E-value=53 Score=22.79 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=16.8
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGN 156 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~ 156 (191)
-.|+.|+..- ...-.|+..||-.|+..
T Consensus 43 ~~C~~Cg~~~--------~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 43 YRCEDCGHEK--------IVYNSCKNRHCPSCQAK 69 (111)
T ss_pred eecCCCCceE--------EecCcccCcCCCCCCCh
Confidence 3577766544 33335777788888764
No 309
>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=25.04 E-value=33 Score=21.07 Aligned_cols=25 Identities=32% Similarity=0.651 Sum_probs=17.2
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceec-ccccccc
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCW-MCLGNTI 158 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~-~C~~~~~ 158 (191)
|-||.|+.+|.- ...||- .|.+.|.
T Consensus 4 kHC~~CG~~Ip~------------~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKPIPP------------DESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCcCCc------------chhhhCHHHHHHHH
Confidence 679999999964 345663 6666554
No 310
>KOG3795|consensus
Probab=24.83 E-value=45 Score=25.35 Aligned_cols=14 Identities=21% Similarity=0.572 Sum_probs=10.6
Q ss_pred CCCcceeccccccc
Q psy271 144 HCKHEFCWMCLGNT 157 (191)
Q Consensus 144 ~C~~~fC~~C~~~~ 157 (191)
+-+..|||.|--+-
T Consensus 23 ~SRkFfCY~C~VPV 36 (230)
T KOG3795|consen 23 SSRKFFCYDCRVPV 36 (230)
T ss_pred CcceEEEEeecccc
Confidence 46778999997664
No 311
>PLN02195 cellulose synthase A
Probab=24.83 E-value=53 Score=31.62 Aligned_cols=11 Identities=27% Similarity=0.419 Sum_probs=5.2
Q ss_pred CCCCCCCCcce
Q psy271 121 TKDCPKCHICI 131 (191)
Q Consensus 121 ~k~CP~C~~~i 131 (191)
.+-||+|+..+
T Consensus 48 ~q~CpqCkt~Y 58 (977)
T PLN02195 48 RKVCLRCGGPY 58 (977)
T ss_pred CccCCccCCcc
Confidence 34455554444
No 312
>PRK01343 zinc-binding protein; Provisional
Probab=24.65 E-value=40 Score=20.58 Aligned_cols=13 Identities=31% Similarity=0.685 Sum_probs=10.5
Q ss_pred cCCCCCCCCcceE
Q psy271 120 HTKDCPKCHICIE 132 (191)
Q Consensus 120 ~~k~CP~C~~~i~ 132 (191)
-.++||.|+....
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3688999999875
No 313
>KOG2932|consensus
Probab=24.46 E-value=30 Score=28.69 Aligned_cols=53 Identities=15% Similarity=0.236 Sum_probs=29.1
Q ss_pred cCCCCCCCCcceEecCCcCc---eEeCCCCcceecccccccccCCCCCCCCCCcccCccCC
Q psy271 120 HTKDCPKCHICIEKNGGCNH---MQCYHCKHEFCWMCLGNTIDGKGPLKTTTRFRVGIKAP 177 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~---m~C~~C~~~fC~~C~~~~~~~~~~~~~~~~~~~~~~a~ 177 (191)
..|.||.|.-.|+|.+-|.. +.|+ -=-.|+..|.....--.|.|..+....+|
T Consensus 122 ~dK~Cp~C~d~VqrIeq~~~g~iFmC~-----~~~GC~RTyLsqrDlqAHInhrH~~~~~p 177 (389)
T KOG2932|consen 122 SDKICPLCDDRVQRIEQIMMGGIFMCA-----APHGCLRTYLSQRDLQAHINHRHGSLLQP 177 (389)
T ss_pred ccccCcCcccHHHHHHHhcccceEEee-----cchhHHHHHhhHHHHHHHhhhhhccccCC
Confidence 35778888888877776633 2332 00136666665544455555555544433
No 314
>KOG4739|consensus
Probab=24.43 E-value=23 Score=28.07 Aligned_cols=24 Identities=25% Similarity=0.702 Sum_probs=18.2
Q ss_pred CCcCceEeCCCC----cceecccccccc
Q psy271 135 GGCNHMQCYHCK----HEFCWMCLGNTI 158 (191)
Q Consensus 135 ~GC~~m~C~~C~----~~fC~~C~~~~~ 158 (191)
..|.||.|..|- ..+|..|.++..
T Consensus 21 TaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 21 TACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred eechhhhhhhhcccCCccccccccceee
Confidence 569999998664 349999988743
No 315
>PRK11595 DNA utilization protein GntX; Provisional
Probab=24.04 E-value=26 Score=27.42 Aligned_cols=8 Identities=25% Similarity=0.779 Sum_probs=3.4
Q ss_pred CCCCCcce
Q psy271 124 CPKCHICI 131 (191)
Q Consensus 124 CP~C~~~i 131 (191)
|+-|+..+
T Consensus 8 C~~C~~~~ 15 (227)
T PRK11595 8 CWLCRMPL 15 (227)
T ss_pred CccCCCcc
Confidence 44444433
No 316
>KOG2691|consensus
Probab=24.00 E-value=26 Score=24.31 Aligned_cols=11 Identities=45% Similarity=0.951 Sum_probs=8.7
Q ss_pred cCCCCCCCCcc
Q psy271 120 HTKDCPKCHIC 130 (191)
Q Consensus 120 ~~k~CP~C~~~ 130 (191)
.-|.||+|+..
T Consensus 72 s~~~C~~C~~~ 82 (113)
T KOG2691|consen 72 SDKHCPKCGHR 82 (113)
T ss_pred ccccCCccCCc
Confidence 45889999864
No 317
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=23.90 E-value=75 Score=22.93 Aligned_cols=16 Identities=19% Similarity=0.368 Sum_probs=9.6
Q ss_pred CccccCCcccCccchH
Q psy271 83 EPMQSGIEYHAPTDCA 98 (191)
Q Consensus 83 ~C~~Cgv~~H~~~~C~ 98 (191)
.|+.|+..-|....|.
T Consensus 54 ~C~~Cg~~GH~~~~Cp 69 (148)
T PTZ00368 54 SCYNCGKTGHLSRECP 69 (148)
T ss_pred ccCCCCCcCcCcccCC
Confidence 4666666666655554
No 318
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=23.78 E-value=44 Score=20.80 Aligned_cols=14 Identities=36% Similarity=0.731 Sum_probs=11.0
Q ss_pred CCCCCCCCcceEec
Q psy271 121 TKDCPKCHICIEKN 134 (191)
Q Consensus 121 ~k~CP~C~~~i~k~ 134 (191)
..+||.|+..++-.
T Consensus 6 ~v~CP~C~k~~~w~ 19 (62)
T PRK00418 6 TVNCPTCGKPVEWG 19 (62)
T ss_pred cccCCCCCCccccc
Confidence 56899999988643
No 319
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.46 E-value=18 Score=27.47 Aligned_cols=28 Identities=21% Similarity=0.591 Sum_probs=19.6
Q ss_pred cCCCCCCCCcceEecCCcCc-eEeCCCCc
Q psy271 120 HTKDCPKCHICIEKNGGCNH-MQCYHCKH 147 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~-m~C~~C~~ 147 (191)
+.-.||.|...+.-...+.+ .+|+.||.
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~ 140 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMELGFTCPKCGE 140 (176)
T ss_pred CceeCCCCCCcccHHHHHHhCCCCCCCCc
Confidence 34578999988887766655 77775553
No 320
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=23.30 E-value=67 Score=24.82 Aligned_cols=31 Identities=16% Similarity=0.314 Sum_probs=22.0
Q ss_pred CCCCCCCcc---eEecCCcCceEeCCCCcceecc
Q psy271 122 KDCPKCHIC---IEKNGGCNHMQCYHCKHEFCWM 152 (191)
Q Consensus 122 k~CP~C~~~---i~k~~GC~~m~C~~C~~~fC~~ 152 (191)
-.||.|+.+ +.|.++=..+.|..||+.-.-.
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~ 132 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAHRPVK 132 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCcccc
Confidence 469999976 5677766678898677765443
No 321
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=23.25 E-value=21 Score=29.92 Aligned_cols=34 Identities=26% Similarity=0.684 Sum_probs=25.5
Q ss_pred CCCCCCcceEecCCcCceEeCCCCcceecccccccc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~ 158 (191)
-||-|-.++.-++- |..-| .|||+.|-.|.....
T Consensus 16 ~cplcie~mditdk-nf~pc-~cgy~ic~fc~~~ir 49 (480)
T COG5175 16 YCPLCIEPMDITDK-NFFPC-PCGYQICQFCYNNIR 49 (480)
T ss_pred cCcccccccccccC-CcccC-CcccHHHHHHHHHHH
Confidence 39999888876654 67789 599988777765543
No 322
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=23.03 E-value=65 Score=27.96 Aligned_cols=23 Identities=13% Similarity=0.339 Sum_probs=21.0
Q ss_pred CcccCccCCCccccCCCCCCCCC
Q psy271 169 RFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 169 ~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
+++++..+|..++|..+++||.|
T Consensus 109 ~~pi~~~~~~~~~R~~i~~~l~t 131 (422)
T TIGR02546 109 TRPLDADPPPPMSRQPIDQPLPT 131 (422)
T ss_pred eeeccCCCcCHHHccCcccccCC
Confidence 56888899999999999999986
No 323
>KOG0297|consensus
Probab=22.81 E-value=70 Score=27.44 Aligned_cols=34 Identities=29% Similarity=0.667 Sum_probs=25.5
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccccccC
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDG 160 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~ 160 (191)
..||.|...+ +....=+.||+.||..|...|...
T Consensus 22 l~C~~C~~vl-----~~p~~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 22 LLCPICMSVL-----RDPVQTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred ccCccccccc-----cCCCCCCCCCCcccccccchhhcc
Confidence 4688887777 333332579999999999999876
No 324
>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=22.63 E-value=70 Score=18.81 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=5.3
Q ss_pred CCCCCCcceE
Q psy271 123 DCPKCHICIE 132 (191)
Q Consensus 123 ~CP~C~~~i~ 132 (191)
.||-|+..+.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 8999998874
No 325
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=22.44 E-value=78 Score=22.54 Aligned_cols=22 Identities=27% Similarity=0.653 Sum_probs=16.7
Q ss_pred CCCCCCCCcceEe-cCCcCceEe
Q psy271 121 TKDCPKCHICIEK-NGGCNHMQC 142 (191)
Q Consensus 121 ~k~CP~C~~~i~k-~~GC~~m~C 142 (191)
.-+|+.|+..++. ..|-.-++|
T Consensus 7 fYkC~~CGniv~v~~~g~~~l~C 29 (125)
T TIGR00320 7 VYKCEVCGNIVEVLNAGIGQLVC 29 (125)
T ss_pred EEECCCCCcEEEEEECCCcceee
Confidence 4579999999974 455566888
No 326
>PRK06315 type III secretion system ATPase; Provisional
Probab=22.41 E-value=61 Score=28.37 Aligned_cols=24 Identities=13% Similarity=0.257 Sum_probs=20.9
Q ss_pred CCcccCccCCCccccCCCCCCCCC
Q psy271 168 TRFRVGIKAPGIIPRISVREPMQS 191 (191)
Q Consensus 168 ~~~~~~~~a~~i~~r~~~~~~~~~ 191 (191)
.++++...+|..++|..+++||.|
T Consensus 127 ~~~~i~~~~~~~~~R~~~~e~l~T 150 (442)
T PRK06315 127 ETYPIFRAPPDPLHRAKLRTILST 150 (442)
T ss_pred ceeeeecCCCChHHcccccccccc
Confidence 456778889999999999999987
No 327
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=22.40 E-value=43 Score=19.58 Aligned_cols=9 Identities=33% Similarity=0.766 Sum_probs=6.7
Q ss_pred CCCCCcceE
Q psy271 124 CPKCHICIE 132 (191)
Q Consensus 124 CP~C~~~i~ 132 (191)
|.+|+.+|.
T Consensus 1 C~~C~~~I~ 9 (58)
T PF00412_consen 1 CARCGKPIY 9 (58)
T ss_dssp BTTTSSBES
T ss_pred CCCCCCCcc
Confidence 677887776
No 328
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=22.32 E-value=54 Score=19.56 Aligned_cols=11 Identities=45% Similarity=0.839 Sum_probs=9.6
Q ss_pred CCCCCCcceEe
Q psy271 123 DCPKCHICIEK 133 (191)
Q Consensus 123 ~CP~C~~~i~k 133 (191)
.||.|+..++.
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 69999999876
No 329
>PRK12366 replication factor A; Reviewed
Probab=22.16 E-value=45 Score=30.58 Aligned_cols=25 Identities=28% Similarity=0.673 Sum_probs=17.1
Q ss_pred CCCCCCCCcceEecCCcCceEeCCCCc
Q psy271 121 TKDCPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
...||.|+..+...+| .-.|..|+.
T Consensus 532 y~aCp~CnkKv~~~~g--~~~C~~c~~ 556 (637)
T PRK12366 532 LYLCPNCRKRVEEVDG--EYICEFCGE 556 (637)
T ss_pred EecccccCeEeEcCCC--cEECCCCCC
Confidence 4789999999987554 334555554
No 330
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.10 E-value=48 Score=22.86 Aligned_cols=13 Identities=38% Similarity=0.817 Sum_probs=10.5
Q ss_pred cCCCCCCCCcceE
Q psy271 120 HTKDCPKCHICIE 132 (191)
Q Consensus 120 ~~k~CP~C~~~i~ 132 (191)
+...||+|+..++
T Consensus 48 G~t~CP~Cg~~~e 60 (115)
T COG1885 48 GSTSCPKCGEPFE 60 (115)
T ss_pred ccccCCCCCCccc
Confidence 4678999998875
No 331
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=22.01 E-value=22 Score=22.27 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=8.5
Q ss_pred cCCCCCCCCcceE
Q psy271 120 HTKDCPKCHICIE 132 (191)
Q Consensus 120 ~~k~CP~C~~~i~ 132 (191)
.-+.|-+|+..++
T Consensus 4 ~~~AC~~C~~i~~ 16 (64)
T PRK06393 4 QYRACKKCKRLTP 16 (64)
T ss_pred hhhhHhhCCcccC
Confidence 3456777777773
No 332
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.89 E-value=75 Score=19.39 Aligned_cols=23 Identities=26% Similarity=0.576 Sum_probs=15.2
Q ss_pred cCCCCCCCCcceEecCCcCceEeCCCCc
Q psy271 120 HTKDCPKCHICIEKNGGCNHMQCYHCKH 147 (191)
Q Consensus 120 ~~k~CP~C~~~i~k~~GC~~m~C~~C~~ 147 (191)
+...||+|+.... .|-.|..||+
T Consensus 26 ~~~~c~~cG~~~l-----~Hrvc~~cg~ 48 (57)
T COG0333 26 TLSVCPNCGEYKL-----PHRVCLKCGY 48 (57)
T ss_pred cceeccCCCCccc-----CceEcCCCCC
Confidence 4578999988773 3555655654
No 333
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.86 E-value=66 Score=31.17 Aligned_cols=19 Identities=16% Similarity=0.303 Sum_probs=15.5
Q ss_pred cCccCCCccccCCCCCCCC
Q psy271 172 VGIKAPGIIPRISVREPMQ 190 (191)
Q Consensus 172 ~~~~a~~i~~r~~~~~~~~ 190 (191)
.-+..-|+++++.+-|||+
T Consensus 702 ~~KGVkgl~S~~k~~EPlE 720 (1121)
T PRK04023 702 EVKGVKGLTSKDKIPEPLE 720 (1121)
T ss_pred ccccceecccCCCCCcchH
Confidence 3455779999999999985
No 334
>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=21.80 E-value=49 Score=18.86 Aligned_cols=12 Identities=33% Similarity=0.661 Sum_probs=8.9
Q ss_pred CCCCCCCCcceE
Q psy271 121 TKDCPKCHICIE 132 (191)
Q Consensus 121 ~k~CP~C~~~i~ 132 (191)
.|.||.|+.++.
T Consensus 8 ~K~C~~C~rpf~ 19 (42)
T PF10013_consen 8 SKICPVCGRPFT 19 (42)
T ss_pred CCcCcccCCcch
Confidence 578888887763
No 335
>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=21.76 E-value=59 Score=29.28 Aligned_cols=13 Identities=23% Similarity=0.429 Sum_probs=10.4
Q ss_pred CCCCCCCcceEec
Q psy271 122 KDCPKCHICIEKN 134 (191)
Q Consensus 122 k~CP~C~~~i~k~ 134 (191)
-+||+|+......
T Consensus 201 vpCPhCg~~~~l~ 213 (557)
T PF05876_consen 201 VPCPHCGEEQVLE 213 (557)
T ss_pred ccCCCCCCCcccc
Confidence 5899999887664
No 336
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=21.76 E-value=29 Score=25.73 Aligned_cols=27 Identities=19% Similarity=0.322 Sum_probs=15.8
Q ss_pred CCCCCCCcceEecCC-cCceEeCCCCcc
Q psy271 122 KDCPKCHICIEKNGG-CNHMQCYHCKHE 148 (191)
Q Consensus 122 k~CP~C~~~i~k~~G-C~~m~C~~C~~~ 148 (191)
-.||.|+..+.-.+- =+..+|..||..
T Consensus 110 Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred EECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 359999977754211 134777755543
No 337
>KOG1356|consensus
Probab=21.69 E-value=49 Score=31.18 Aligned_cols=31 Identities=23% Similarity=0.558 Sum_probs=25.0
Q ss_pred CCCCCcceEecCCcCceEeCCCCcceecccccccc
Q psy271 124 CPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTI 158 (191)
Q Consensus 124 CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~ 158 (191)
|-.|. ++.+-.|-.|.+|++.+|--|.+.|.
T Consensus 232 C~~C~----~tlfn~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 232 CDRCE----TTLFNIHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred hhhhc----ccccceeEEccccCCeeeecchhhcc
Confidence 55553 44455699999999999999999995
No 338
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.33 E-value=49 Score=20.74 Aligned_cols=11 Identities=18% Similarity=0.498 Sum_probs=8.4
Q ss_pred CceEeCCCCcc
Q psy271 138 NHMQCYHCKHE 148 (191)
Q Consensus 138 ~~m~C~~C~~~ 148 (191)
.+++|.+||+.
T Consensus 39 ~~itCk~CgYt 49 (68)
T COG3478 39 IVITCKNCGYT 49 (68)
T ss_pred EEEEeccCCch
Confidence 35889989874
No 339
>KOG1873|consensus
Probab=21.15 E-value=51 Score=30.75 Aligned_cols=56 Identities=23% Similarity=0.355 Sum_probs=34.9
Q ss_pred cchHHHHHHHhhccChHHHHHHHH-hcCCCCCCCCcceEecCC--------cCc-eEeCCCCcceecccc
Q psy271 95 TDCAVIKKWLTKCADDSETANYIS-AHTKDCPKCHICIEKNGG--------CNH-MQCYHCKHEFCWMCL 154 (191)
Q Consensus 95 ~~C~~~~~~~~~~~~~~~~~~~~~-~~~k~CP~C~~~i~k~~G--------C~~-m~C~~C~~~fC~~C~ 154 (191)
..|..+++.+.. .-....++ ..|..|-.|..-.-..+| =+- -.|.+||+++|-.-.
T Consensus 43 ~~C~Hi~Kav~l----~~lk~~iks~~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~~~ 108 (877)
T KOG1873|consen 43 VECQHIKKAVDL----SHLKRAIKSLLWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGRNS 108 (877)
T ss_pred cccchHHhhhcH----HHHHHHHHHHHHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCCCc
Confidence 458887766431 11222222 246779999988877665 222 459999999886543
No 340
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=21.09 E-value=18 Score=22.72 Aligned_cols=12 Identities=33% Similarity=0.725 Sum_probs=8.4
Q ss_pred ceeccccccccc
Q psy271 148 EFCWMCLGNTID 159 (191)
Q Consensus 148 ~fC~~C~~~~~~ 159 (191)
.||-.|+.+|..
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 599999999974
No 341
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.85 E-value=92 Score=20.37 Aligned_cols=34 Identities=21% Similarity=0.404 Sum_probs=21.2
Q ss_pred CCCCCCCcceEecCCcCceEeCCCCcceecccccccccCC
Q psy271 122 KDCPKCHICIEKNGGCNHMQCYHCKHEFCWMCLGNTIDGK 161 (191)
Q Consensus 122 k~CP~C~~~i~k~~GC~~m~C~~C~~~fC~~C~~~~~~~~ 161 (191)
+-||.|++...-+.- +.--..+|-.|++-|.+.+
T Consensus 2 llCP~C~v~l~~~~r------s~vEiD~CPrCrGVWLDrG 35 (88)
T COG3809 2 LLCPICGVELVMSVR------SGVEIDYCPRCRGVWLDRG 35 (88)
T ss_pred cccCcCCceeeeeee------cCceeeeCCccccEeecch
Confidence 469999988754321 1233445668888887644
No 342
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.80 E-value=64 Score=20.08 Aligned_cols=20 Identities=35% Similarity=1.069 Sum_probs=14.2
Q ss_pred CCcCc---eEeCCCCcceecccc
Q psy271 135 GGCNH---MQCYHCKHEFCWMCL 154 (191)
Q Consensus 135 ~GC~~---m~C~~C~~~fC~~C~ 154 (191)
.||+. +.|..|+..+|....
T Consensus 33 ~gC~~~s~I~C~~Ckk~~Cf~Hf 55 (63)
T PF04236_consen 33 TGCNNTSFIRCAYCKKSLCFNHF 55 (63)
T ss_pred CCCCCcCEEEccccCCcccccce
Confidence 44555 678889998887653
No 343
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=20.78 E-value=48 Score=32.74 Aligned_cols=15 Identities=53% Similarity=1.167 Sum_probs=8.8
Q ss_pred CCCCCCCCcceEecC
Q psy271 121 TKDCPKCHICIEKNG 135 (191)
Q Consensus 121 ~k~CP~C~~~i~k~~ 135 (191)
-|.||+|+.+..|.|
T Consensus 939 dK~CPkCg~pl~kDG 953 (1444)
T COG2176 939 DKDCPKCGTPLKKDG 953 (1444)
T ss_pred CCCCCcCCCccccCC
Confidence 356666666655543
No 344
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=20.62 E-value=71 Score=18.13 Aligned_cols=30 Identities=27% Similarity=0.767 Sum_probs=23.1
Q ss_pred CCCCCCcceEecCCcCceEeCCCC-cceecccccc
Q psy271 123 DCPKCHICIEKNGGCNHMQCYHCK-HEFCWMCLGN 156 (191)
Q Consensus 123 ~CP~C~~~i~k~~GC~~m~C~~C~-~~fC~~C~~~ 156 (191)
.|-.|+.+|. | .+..|..|. +..|-.|-..
T Consensus 2 ~C~~C~~~i~---g-~r~~C~~C~d~dLC~~Cf~~ 32 (46)
T cd02249 2 SCDGCLKPIV---G-VRYHCLVCEDFDLCSSCYAK 32 (46)
T ss_pred CCcCCCCCCc---C-CEEECCCCCCCcCHHHHHCc
Confidence 4778888653 4 789999998 8888888654
No 345
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=20.59 E-value=49 Score=25.53 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=14.2
Q ss_pred CCCCCCCc-----ceEecCCc-CceEeCCCCcce
Q psy271 122 KDCPKCHI-----CIEKNGGC-NHMQCYHCKHEF 149 (191)
Q Consensus 122 k~CP~C~~-----~i~k~~GC-~~m~C~~C~~~f 149 (191)
..||+|+. -+-|..|= .-..|..||+-|
T Consensus 7 ~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 7 IECPSCGSEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EECCCCCcchhhHHHHHhcCCceEEEccCCCcEe
Confidence 35888871 11233333 335676565544
No 346
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=20.59 E-value=30 Score=21.96 Aligned_cols=18 Identities=22% Similarity=0.660 Sum_probs=15.5
Q ss_pred CCCcceecccccccccCC
Q psy271 144 HCKHEFCWMCLGNTIDGK 161 (191)
Q Consensus 144 ~C~~~fC~~C~~~~~~~~ 161 (191)
.|||.|-..|+..|....
T Consensus 49 ~C~H~FH~~Ci~~Wl~~~ 66 (73)
T PF12678_consen 49 PCGHIFHFHCISQWLKQN 66 (73)
T ss_dssp TTSEEEEHHHHHHHHTTS
T ss_pred ccCCCEEHHHHHHHHhcC
Confidence 699999999999998644
No 347
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=20.39 E-value=51 Score=18.93 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=7.8
Q ss_pred CCCCCCcceE
Q psy271 123 DCPKCHICIE 132 (191)
Q Consensus 123 ~CP~C~~~i~ 132 (191)
.||.|+....
T Consensus 1 ~CP~Cg~~a~ 10 (47)
T PF04606_consen 1 RCPHCGSKAR 10 (47)
T ss_pred CcCCCCCeeE
Confidence 5999998654
No 348
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=20.31 E-value=46 Score=27.40 Aligned_cols=11 Identities=27% Similarity=0.519 Sum_probs=7.8
Q ss_pred CCCCCCCCcce
Q psy271 121 TKDCPKCHICI 131 (191)
Q Consensus 121 ~k~CP~C~~~i 131 (191)
+-+||.|..+-
T Consensus 306 t~~~~r~~k~n 316 (345)
T COG4260 306 TWPCARCAKLN 316 (345)
T ss_pred cCcchhccccc
Confidence 45788887765
No 349
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=20.25 E-value=71 Score=17.90 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=7.7
Q ss_pred CCCCCCCcceEe
Q psy271 122 KDCPKCHICIEK 133 (191)
Q Consensus 122 k~CP~C~~~i~k 133 (191)
..||.|+..-.+
T Consensus 3 ~~Cp~Cg~~~~~ 14 (47)
T PF14690_consen 3 PRCPHCGSPSVH 14 (47)
T ss_pred ccCCCcCCCceE
Confidence 358888866533
No 350
>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=20.05 E-value=1.3e+02 Score=18.23 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=13.0
Q ss_pred CCCCCCcceEe-cCCcCceEeCCCCcceecc
Q psy271 123 DCPKCHICIEK-NGGCNHMQCYHCKHEFCWM 152 (191)
Q Consensus 123 ~CP~C~~~i~k-~~GC~~m~C~~C~~~fC~~ 152 (191)
+||.|...-.- +--=.-+.|..|+...|--
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~L~~P 39 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTVLAQP 39 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSEEEEE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCEecCC
Confidence 57777643322 3333446666666655543
Done!