Query psy3653
Match_columns 202
No_of_seqs 221 out of 1696
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 22:12:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3653.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3653hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2272|consensus 100.0 3E-40 6.6E-45 253.6 -1.9 194 9-202 10-254 (332)
2 KOG1701|consensus 100.0 9.7E-37 2.1E-41 249.6 1.3 170 13-200 276-462 (468)
3 KOG2272|consensus 100.0 1.4E-33 3.1E-38 216.9 -1.5 164 18-199 84-311 (332)
4 KOG1044|consensus 99.9 1E-27 2.2E-32 202.8 6.2 175 7-202 16-192 (670)
5 KOG1703|consensus 99.9 1.7E-27 3.6E-32 206.6 3.1 160 20-197 317-478 (479)
6 KOG1044|consensus 99.9 1.5E-24 3.3E-29 183.7 2.5 161 18-197 76-247 (670)
7 KOG1701|consensus 99.9 7.9E-25 1.7E-29 179.8 -3.1 117 67-202 275-394 (468)
8 KOG1703|consensus 99.9 2.8E-22 6.2E-27 174.0 4.5 165 20-202 256-422 (479)
9 KOG4577|consensus 99.8 6.1E-21 1.3E-25 149.8 -2.0 121 60-199 27-152 (383)
10 KOG4577|consensus 99.8 4.1E-20 8.9E-25 145.2 -0.9 97 21-118 48-148 (383)
11 PF00412 LIM: LIM domain; Int 99.6 6.5E-16 1.4E-20 96.4 4.1 56 146-201 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.4 2.2E-13 4.7E-18 84.9 2.1 44 22-65 15-58 (58)
13 KOG1700|consensus 99.3 2E-12 4.3E-17 100.1 2.0 136 65-200 6-166 (200)
14 KOG1700|consensus 99.1 1.4E-11 3E-16 95.4 1.4 107 13-119 9-162 (200)
15 smart00132 LIM Zinc-binding do 98.8 3.3E-09 7E-14 60.2 2.4 36 145-180 1-38 (39)
16 smart00132 LIM Zinc-binding do 98.6 4E-08 8.7E-13 55.6 2.1 36 68-103 1-38 (39)
17 KOG0490|consensus 97.5 2.6E-05 5.7E-10 61.7 0.1 90 21-112 11-107 (235)
18 KOG0490|consensus 97.3 8.1E-05 1.8E-09 58.8 0.9 109 72-198 2-117 (235)
19 KOG1702|consensus 97.1 5.4E-05 1.2E-09 57.8 -2.1 57 144-200 5-62 (264)
20 KOG1702|consensus 96.6 0.00051 1.1E-08 52.5 0.1 60 67-126 5-65 (264)
21 PF08394 Arc_trans_TRASH: Arch 91.6 0.071 1.5E-06 29.6 0.5 32 146-180 1-34 (37)
22 PF14835 zf-RING_6: zf-RING of 91.0 0.2 4.3E-06 31.4 2.1 48 34-81 8-55 (65)
23 PF14446 Prok-RING_1: Prokaryo 89.2 0.33 7.1E-06 29.3 2.0 38 142-179 4-51 (54)
24 KOG2462|consensus 82.8 0.81 1.8E-05 37.0 1.8 129 31-184 128-258 (279)
25 PF07503 zf-HYPF: HypF finger; 82.3 0.46 9.9E-06 26.0 0.2 32 13-44 1-32 (35)
26 PF06677 Auto_anti-p27: Sjogre 81.1 1.2 2.5E-05 25.4 1.6 28 29-60 13-40 (41)
27 PF11781 RRN7: RNA polymerase 81.1 1.2 2.5E-05 24.6 1.5 25 34-62 9-33 (36)
28 PF01258 zf-dskA_traR: Prokary 78.4 0.39 8.5E-06 26.3 -0.9 28 172-199 6-33 (36)
29 TIGR00622 ssl1 transcription f 78.3 2.1 4.5E-05 30.0 2.4 26 13-46 3-28 (112)
30 PF10367 Vps39_2: Vacuolar sor 77.8 1.6 3.5E-05 29.7 1.8 29 143-171 78-108 (109)
31 PF13240 zinc_ribbon_2: zinc-r 77.1 1.7 3.6E-05 21.4 1.2 9 146-154 2-10 (23)
32 PF14835 zf-RING_6: zf-RING of 77.1 3.8 8.3E-05 25.7 3.1 31 130-160 27-57 (65)
33 COG2191 Formylmethanofuran deh 75.7 1.3 2.9E-05 34.2 1.0 31 34-64 173-203 (206)
34 COG1645 Uncharacterized Zn-fin 75.1 1.9 4.2E-05 31.0 1.6 22 35-61 30-51 (131)
35 PF14471 DUF4428: Domain of un 74.2 2.5 5.5E-05 25.2 1.7 28 172-200 2-30 (51)
36 PF02069 Metallothio_Pro: Prok 74.1 2.1 4.7E-05 25.6 1.4 27 36-62 10-37 (52)
37 PF06827 zf-FPG_IleRS: Zinc fi 71.5 1.8 3.8E-05 22.5 0.6 15 144-158 2-16 (30)
38 PF12674 Zn_ribbon_2: Putative 71.5 1.5 3.3E-05 28.8 0.4 29 35-63 2-35 (81)
39 COG2191 Formylmethanofuran deh 71.1 1.4 3.1E-05 34.0 0.2 30 170-199 173-202 (206)
40 PF06906 DUF1272: Protein of u 68.6 4.2 9.1E-05 24.7 1.8 45 35-79 7-54 (57)
41 PF10235 Cript: Microtubule-as 68.2 3.3 7.1E-05 27.8 1.4 42 29-78 40-81 (90)
42 PF10367 Vps39_2: Vacuolar sor 67.6 4.7 0.0001 27.4 2.2 27 35-61 80-107 (109)
43 PF09943 DUF2175: Uncharacteri 65.6 1.8 3.8E-05 29.7 -0.3 27 145-171 4-32 (101)
44 PF12773 DZR: Double zinc ribb 64.5 3.7 8.1E-05 23.9 1.0 12 143-154 12-23 (50)
45 PF14634 zf-RING_5: zinc-RING 59.0 5.6 0.00012 22.6 1.1 39 36-74 2-44 (44)
46 PRK14890 putative Zn-ribbon RN 58.8 5.4 0.00012 24.5 1.0 36 35-74 9-44 (59)
47 PRK00420 hypothetical protein; 58.4 6.2 0.00013 27.7 1.4 25 34-62 24-48 (112)
48 PF13834 DUF4193: Domain of un 58.3 4 8.7E-05 27.8 0.4 29 32-60 69-98 (99)
49 PF13248 zf-ribbon_3: zinc-rib 58.1 6.6 0.00014 19.7 1.1 7 36-42 5-11 (26)
50 COG4357 Zinc finger domain con 54.9 2.1 4.6E-05 28.9 -1.3 53 69-121 38-91 (105)
51 PRK00432 30S ribosomal protein 54.0 7.6 0.00016 23.0 1.1 26 11-41 20-45 (50)
52 KOG2462|consensus 53.8 4 8.6E-05 33.1 -0.2 36 68-103 217-254 (279)
53 cd02249 ZZ Zinc finger, ZZ typ 53.7 11 0.00023 21.7 1.7 11 145-155 2-12 (46)
54 PF10083 DUF2321: Uncharacteri 52.8 5.3 0.00012 29.6 0.4 49 131-181 28-80 (158)
55 PF00645 zf-PARP: Poly(ADP-rib 52.6 4.7 0.0001 26.3 0.0 13 142-154 6-18 (82)
56 smart00291 ZnF_ZZ Zinc-binding 52.2 13 0.00028 21.2 1.8 12 144-155 5-16 (44)
57 PF03854 zf-P11: P-11 zinc fin 52.0 5.6 0.00012 23.3 0.3 29 126-154 10-46 (50)
58 PF11571 Med27: Mediator compl 51.2 5.2 0.00011 26.8 0.1 16 61-76 49-64 (90)
59 cd00162 RING RING-finger (Real 51.0 5.3 0.00012 21.8 0.1 39 36-74 2-43 (45)
60 TIGR02098 MJ0042_CXXC MJ0042 f 50.8 3.9 8.5E-05 22.4 -0.5 10 34-43 26-35 (38)
61 PF07754 DUF1610: Domain of un 50.7 12 0.00025 18.6 1.3 9 146-154 1-9 (24)
62 PRK14559 putative protein seri 50.7 20 0.00044 33.0 3.8 21 133-153 17-37 (645)
63 PRK14559 putative protein seri 50.0 16 0.00034 33.7 3.0 10 67-76 28-37 (645)
64 PF08271 TF_Zn_Ribbon: TFIIB z 49.6 6.6 0.00014 22.2 0.4 11 34-44 20-30 (43)
65 KOG0320|consensus 49.2 5 0.00011 30.5 -0.3 50 30-79 128-180 (187)
66 PF13920 zf-C3HC4_3: Zinc fing 49.2 17 0.00037 21.0 2.1 42 35-77 4-48 (50)
67 PF07191 zinc-ribbons_6: zinc- 47.8 4.4 9.5E-05 25.8 -0.6 24 53-76 16-40 (70)
68 smart00504 Ubox Modified RING 47.6 13 0.00029 22.4 1.5 29 125-153 15-45 (63)
69 PF08274 PhnA_Zn_Ribbon: PhnA 47.4 9.8 0.00021 20.0 0.8 10 14-23 5-14 (30)
70 COG4847 Uncharacterized protei 46.8 5.9 0.00013 26.7 -0.2 30 144-173 7-38 (103)
71 PF10886 DUF2685: Protein of u 44.5 13 0.00027 22.4 1.0 24 144-167 2-26 (54)
72 COG2888 Predicted Zn-ribbon RN 42.0 12 0.00026 23.0 0.7 11 35-45 11-21 (61)
73 PRK06266 transcription initiat 41.7 11 0.00024 28.6 0.6 27 13-44 119-147 (178)
74 PF13717 zinc_ribbon_4: zinc-r 41.3 11 0.00023 20.6 0.3 8 12-19 3-10 (36)
75 PF06689 zf-C4_ClpX: ClpX C4-t 40.3 27 0.00058 19.6 1.9 29 171-199 3-33 (41)
76 COG5152 Uncharacterized conser 40.2 5.8 0.00013 30.7 -1.1 45 34-79 197-243 (259)
77 PF04570 DUF581: Protein of un 39.6 18 0.0004 22.1 1.2 27 171-197 18-47 (58)
78 cd02340 ZZ_NBR1_like Zinc fing 39.5 24 0.00053 20.0 1.7 11 145-155 2-12 (43)
79 PF12760 Zn_Tnp_IS1595: Transp 39.1 13 0.00027 21.4 0.4 14 28-42 14-27 (46)
80 PF02150 RNA_POL_M_15KD: RNA p 38.9 11 0.00024 20.4 0.2 7 13-19 3-9 (35)
81 COG2075 RPL24A Ribosomal prote 38.6 22 0.00048 22.3 1.5 21 171-191 5-28 (66)
82 COG0068 HypF Hydrogenase matur 37.4 24 0.00051 32.7 2.0 84 10-102 100-183 (750)
83 smart00659 RPOLCX RNA polymera 37.4 21 0.00045 20.5 1.1 11 34-44 3-13 (44)
84 smart00834 CxxC_CXXC_SSSS Puta 37.3 12 0.00025 20.6 0.1 9 145-153 7-15 (41)
85 PF09723 Zn-ribbon_8: Zinc rib 36.6 12 0.00026 21.1 0.0 11 170-180 6-16 (42)
86 TIGR00373 conserved hypothetic 35.4 14 0.00031 27.4 0.3 27 13-44 111-139 (158)
87 PF00569 ZZ: Zinc finger, ZZ t 34.1 25 0.00053 20.2 1.1 12 144-155 5-17 (46)
88 cd02336 ZZ_RSC8 Zinc finger, Z 34.1 36 0.00077 19.6 1.8 29 171-199 2-32 (45)
89 cd02341 ZZ_ZZZ3 Zinc finger, Z 33.9 39 0.00084 19.8 2.0 11 145-155 2-13 (48)
90 PF13639 zf-RING_2: Ring finge 33.7 14 0.0003 20.7 0.0 26 145-170 2-30 (44)
91 KOG1813|consensus 32.7 27 0.00058 28.8 1.5 44 34-78 242-287 (313)
92 TIGR02605 CxxC_CxxC_SSSS putat 32.6 16 0.00035 21.4 0.2 10 144-153 6-15 (52)
93 PF05864 Chordopox_RPO7: Chord 32.3 9.9 0.00021 23.1 -0.8 16 34-49 5-20 (63)
94 PF01286 XPA_N: XPA protein N- 31.7 22 0.00047 19.3 0.6 12 35-46 5-16 (34)
95 PF09297 zf-NADH-PPase: NADH p 31.6 20 0.00044 18.7 0.4 26 12-41 4-29 (32)
96 PHA03082 DNA-dependent RNA pol 31.5 10 0.00022 23.1 -0.8 15 34-48 5-19 (63)
97 KOG0978|consensus 31.4 6.4 0.00014 36.3 -2.5 45 34-79 644-691 (698)
98 PF00096 zf-C2H2: Zinc finger, 31.3 21 0.00046 16.6 0.5 12 34-45 1-12 (23)
99 COG0266 Nei Formamidopyrimidin 31.0 30 0.00064 28.3 1.5 28 142-169 244-271 (273)
100 cd02335 ZZ_ADA2 Zinc finger, Z 30.7 44 0.00095 19.4 1.8 10 145-154 2-11 (49)
101 PF12647 RNHCP: RNHCP domain; 30.5 1.3E+02 0.0028 20.3 4.2 11 92-102 4-14 (92)
102 COG1998 RPS31 Ribosomal protei 30.0 25 0.00054 20.8 0.6 28 9-40 17-44 (51)
103 PF10764 Gin: Inhibitor of sig 29.7 47 0.001 19.2 1.8 11 170-180 19-29 (46)
104 PRK14714 DNA polymerase II lar 29.4 70 0.0015 31.9 3.8 9 145-153 711-719 (1337)
105 PF14255 Cys_rich_CPXG: Cystei 28.8 26 0.00057 20.9 0.6 8 146-153 3-10 (52)
106 PLN03208 E3 ubiquitin-protein 28.6 44 0.00096 25.8 2.0 9 172-180 71-79 (193)
107 COG1996 RPC10 DNA-directed RNA 28.4 23 0.00049 20.9 0.3 11 143-153 24-34 (49)
108 PF12677 DUF3797: Domain of un 26.9 52 0.0011 19.4 1.6 26 144-169 14-42 (49)
109 PF04945 YHS: YHS domain; Int 26.8 12 0.00026 21.5 -1.1 31 147-180 4-37 (47)
110 PHA00626 hypothetical protein 26.7 33 0.00072 20.8 0.8 38 13-50 2-40 (59)
111 PRK00807 50S ribosomal protein 26.6 50 0.0011 19.6 1.6 20 172-191 4-26 (52)
112 PF13923 zf-C3HC4_2: Zinc fing 26.4 43 0.00093 18.1 1.2 12 188-199 17-28 (39)
113 COG0068 HypF Hydrogenase matur 26.3 34 0.00073 31.8 1.1 82 68-180 103-184 (750)
114 TIGR00143 hypF [NiFe] hydrogen 26.2 42 0.0009 31.4 1.8 84 10-102 67-150 (711)
115 PF14803 Nudix_N_2: Nudix N-te 26.1 32 0.0007 18.5 0.6 9 36-44 3-11 (34)
116 smart00531 TFIIE Transcription 26.0 23 0.0005 25.9 0.0 11 34-44 124-134 (147)
117 PF08209 Sgf11: Sgf11 (transcr 25.4 19 0.00042 19.3 -0.3 16 170-185 5-20 (33)
118 TIGR00686 phnA alkylphosphonat 25.0 42 0.0009 23.3 1.2 29 13-46 4-32 (109)
119 PF02591 DUF164: Putative zinc 25.0 26 0.00057 20.9 0.2 13 67-79 23-35 (56)
120 KOG1734|consensus 25.0 54 0.0012 26.8 1.9 43 124-171 210-262 (328)
121 cd02338 ZZ_PCMF_like Zinc fing 25.0 50 0.0011 19.2 1.4 11 145-155 2-13 (49)
122 PF00130 C1_1: Phorbol esters/ 24.9 50 0.0011 19.1 1.4 13 143-155 11-23 (53)
123 PF07649 C1_3: C1-like domain; 24.8 38 0.00083 17.3 0.8 12 34-45 1-12 (30)
124 PF10571 UPF0547: Uncharacteri 24.8 48 0.001 16.7 1.1 8 14-21 3-10 (26)
125 PF13894 zf-C2H2_4: C2H2-type 24.6 34 0.00073 15.6 0.5 11 34-44 1-11 (24)
126 PRK00398 rpoP DNA-directed RNA 24.0 18 0.00039 20.7 -0.7 28 144-180 4-32 (46)
127 PF13719 zinc_ribbon_5: zinc-r 23.8 34 0.00074 18.6 0.5 7 69-75 5-11 (37)
128 PF01844 HNH: HNH endonuclease 23.7 32 0.00069 19.2 0.3 20 181-200 25-44 (47)
129 PF11077 DUF2616: Protein of u 23.6 46 0.001 25.2 1.3 36 31-66 137-172 (173)
130 PF12898 Stc1: Stc1 domain; I 23.4 13 0.00028 24.5 -1.5 27 171-197 52-82 (84)
131 KOG3002|consensus 22.8 34 0.00073 28.4 0.4 45 32-77 47-91 (299)
132 PF06524 NOA36: NOA36 protein; 22.6 1.6E+02 0.0035 24.0 4.2 13 142-154 208-220 (314)
133 PRK01103 formamidopyrimidine/5 22.6 55 0.0012 26.6 1.7 28 142-169 244-271 (274)
134 smart00184 RING Ring finger. E 22.5 38 0.00082 17.3 0.5 24 147-170 2-25 (39)
135 PF05502 Dynactin_p62: Dynacti 21.8 56 0.0012 29.0 1.7 14 167-180 50-63 (483)
136 PRK14810 formamidopyrimidine-D 21.6 59 0.0013 26.5 1.6 28 142-169 243-270 (272)
137 PF01194 RNA_pol_N: RNA polyme 21.3 61 0.0013 20.0 1.3 12 143-154 4-15 (60)
138 cd02344 ZZ_HERC2 Zinc finger, 21.1 80 0.0017 18.2 1.7 11 145-155 2-13 (45)
139 PHA02929 N1R/p28-like protein; 21.0 59 0.0013 26.0 1.5 38 143-180 174-227 (238)
140 PF12156 ATPase-cat_bd: Putati 21.0 51 0.0011 21.8 1.0 31 145-178 2-35 (88)
141 PF13912 zf-C2H2_6: C2H2-type 20.9 43 0.00093 16.3 0.5 12 34-45 2-13 (27)
142 PRK10445 endonuclease VIII; Pr 20.8 62 0.0013 26.2 1.6 28 142-169 234-261 (263)
143 PRK14714 DNA polymerase II lar 20.5 71 0.0015 31.9 2.1 23 131-153 667-689 (1337)
144 PRK10220 hypothetical protein; 20.4 63 0.0014 22.5 1.3 29 13-46 5-33 (111)
145 PRK14811 formamidopyrimidine-D 20.4 65 0.0014 26.2 1.7 25 143-167 235-259 (269)
146 PF08792 A2L_zn_ribbon: A2L zi 20.4 93 0.002 16.6 1.7 23 35-60 5-27 (33)
147 PF14149 YhfH: YhfH-like prote 20.2 13 0.00027 20.6 -1.7 18 139-156 9-26 (37)
148 TIGR00577 fpg formamidopyrimid 20.1 67 0.0015 26.1 1.7 28 142-169 244-271 (272)
No 1
>KOG2272|consensus
Probab=100.00 E-value=3e-40 Score=253.63 Aligned_cols=194 Identities=34% Similarity=0.731 Sum_probs=175.8
Q ss_pred hHHhhCcCc------ccchhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCccccccccccccc
Q psy3653 9 FDDHFSLRC------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVS 82 (202)
Q Consensus 9 ~~~~~~~~C------~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~ 82 (202)
++...|.|| .++++...+..||.+||.|+.|-.|+.++.|++.+|+.||+.|+..+|+|-|..|++.|.+++|.
T Consensus 10 ~~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVik 89 (332)
T KOG2272|consen 10 LANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIK 89 (332)
T ss_pred HHHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHH
Confidence 456789999 45788889999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCC----------------------------------------
Q psy3653 83 ALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG---------------------------------------- 122 (202)
Q Consensus 83 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~---------------------------------------- 122 (202)
+++.+||+.||+|..|++.|.+..|+...|+.+|+++-+.
T Consensus 90 amnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C 169 (332)
T KOG2272|consen 90 AMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTC 169 (332)
T ss_pred hhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccc
Confidence 9999999999999999999999999888888777544321
Q ss_pred -----CceeecCCCccccccccccCCCCCCCCCCCcccceeeecCcccccccccccccccccCCCceEeeCCcccChhhH
Q psy3653 123 -----GSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197 (202)
Q Consensus 123 -----~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~ 197 (202)
+..-+..|.+||.+|+.+..-+.|..|.+||.+++|.++|+.||.++|+|+.|.+++-+-+.+++.|.+||..+|
T Consensus 170 ~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~ 249 (332)
T KOG2272|consen 170 GKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 249 (332)
T ss_pred cccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHH
Confidence 011123567899999998889999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcC
Q psy3653 198 EKLFG 202 (202)
Q Consensus 198 ~~~fg 202 (202)
.+|||
T Consensus 250 ~qLfG 254 (332)
T KOG2272|consen 250 HQLFG 254 (332)
T ss_pred HHHhh
Confidence 99998
No 2
>KOG1701|consensus
Probab=100.00 E-value=9.7e-37 Score=249.62 Aligned_cols=170 Identities=31% Similarity=0.671 Sum_probs=154.3
Q ss_pred hCcCcccc------hhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCc
Q psy3653 13 FSLRCFQK------CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNT 86 (202)
Q Consensus 13 ~~~~C~~~------~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~ 86 (202)
.|.+|.+. .+.||++.||..||+|.+|++.|.++.||..|+++||+.||.+.. .+|..|+++|.++++.|+|+
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~d~iLrA~Gk 354 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIMDRILRALGK 354 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHHHHHHHhccc
Confidence 78899543 478999999999999999999999999999999999999997754 69999999999999999999
Q ss_pred eecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcc---cc----eee
Q psy3653 87 QWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPIT---GR----CIT 159 (202)
Q Consensus 87 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~---~~----~~~ 159 (202)
.||+.||+|..|++.|++..|.+ +.++++||..+|+++|+++|+.|++||. |+ .|+
T Consensus 355 ayHp~CF~Cv~C~r~ldgipFtv-----------------d~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvv 417 (468)
T KOG1701|consen 355 AYHPGCFTCVVCARCLDGIPFTV-----------------DSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVV 417 (468)
T ss_pred ccCCCceEEEEeccccCCccccc-----------------cCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEE
Confidence 99999999999999999988764 6788999999999999999999999993 21 378
Q ss_pred ecCcccccccccccccccccC----CCceEeeCCcccChhhHhhh
Q psy3653 160 AMFRKFHPEHFVCAFCLRQLN----KGTFKEQNDKPYCHGCFEKL 200 (202)
Q Consensus 160 ~~~~~~H~~Cf~C~~C~~~l~----~~~~~~~~~~~yC~~c~~~~ 200 (202)
++++.||.+|++|..|+..|+ +...+..||.++|+.|..+.
T Consensus 418 amdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~R 462 (468)
T KOG1701|consen 418 AMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKR 462 (468)
T ss_pred EccccccccceehhhcCccccccCCCCcceeccCceeechhhhhh
Confidence 999999999999999999998 23389999999999998765
No 3
>KOG2272|consensus
Probab=99.97 E-value=1.4e-33 Score=216.92 Aligned_cols=164 Identities=34% Similarity=0.829 Sum_probs=141.8
Q ss_pred ccchhcccccccccccccccccccccCCCceeeeCCe-------------------------------------------
Q psy3653 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGK------------------------------------------- 54 (202)
Q Consensus 18 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~------------------------------------------- 54 (202)
.|++|.||+.+||+.||+|..|++.|++..|+...|+
T Consensus 84 iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yH 163 (332)
T KOG2272|consen 84 IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYH 163 (332)
T ss_pred hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccc
Confidence 5788999999999999999999988877666544444
Q ss_pred --------------------eeccccccccCCCCCcccccccccccccccCceecccCCCCCCCCCCCCCCceeecCCcc
Q psy3653 55 --------------------PYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP 114 (202)
Q Consensus 55 --------------------~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~ 114 (202)
+||.+|+.+.-.|.|..|.++|.+++|.++|+.||.+.|+|+.|-+|+-+-
T Consensus 164 FkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGH--------- 234 (332)
T KOG2272|consen 164 FKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGH--------- 234 (332)
T ss_pred eecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccch---------
Confidence 455555554555778889999998899999999999999999998887654
Q ss_pred cCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcccceeeecCcccccccccccccccccCCCc-eEeeCCcccC
Q psy3653 115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGT-FKEQNDKPYC 193 (202)
Q Consensus 115 ~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~yC 193 (202)
..+++.|.+||+++|.++++..|..|+.+|.|.++.|+++.|.++||+|+.|++.|...+ |++.|.+|.|
T Consensus 235 ---------rHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~C 305 (332)
T KOG2272|consen 235 ---------RHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVC 305 (332)
T ss_pred ---------hhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHHhhhhhccccccccccccccccccceeeeccchHH
Confidence 345799999999999999999999999999999999999999999999999999998554 9999999999
Q ss_pred hhhHhh
Q psy3653 194 HGCFEK 199 (202)
Q Consensus 194 ~~c~~~ 199 (202)
+.||++
T Consensus 306 KkCy~r 311 (332)
T KOG2272|consen 306 KKCYDR 311 (332)
T ss_pred HHHHhh
Confidence 999974
No 4
>KOG1044|consensus
Probab=99.94 E-value=1e-27 Score=202.78 Aligned_cols=175 Identities=25% Similarity=0.543 Sum_probs=144.8
Q ss_pred hhhHHhhCcCcccchhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCc
Q psy3653 7 LFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNT 86 (202)
Q Consensus 7 ~~~~~~~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~ 86 (202)
+|+-.-.+++|.|+++.+.++.||..||+|..|+..|....|+.+++. +++++ ..|...|.+++|+++++
T Consensus 16 ~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~gevvsa~gk 85 (670)
T KOG1044|consen 16 GIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGEVVSTLGK 85 (670)
T ss_pred ceehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccceeEecccc
Confidence 344555677889999999999999999999999999999999988886 44555 77888999999999999
Q ss_pred eecccCCCCCCCCCCCCCCce-eecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCc-ccceeeecCcc
Q psy3653 87 QWHSTCFVCRDCKKPVTGKSF-YAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPI-TGRCITAMFRK 164 (202)
Q Consensus 87 ~~H~~Cf~C~~C~~~l~~~~~-~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I-~~~~~~~~~~~ 164 (202)
.||++||.|+.|+.|+...+. ...+...+|..+.+...... ........|++|++.| .|+.+.|+++.
T Consensus 86 tyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p----------~~~~~ps~cagc~~~lk~gq~llald~q 155 (670)
T KOG1044|consen 86 TYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSP----------AESYGPSTCAGCGEELKNGQALLALDKQ 155 (670)
T ss_pred eeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCc----------ccccCCccccchhhhhhccceeeeeccc
Confidence 999999999999999955444 44444566666554433321 1113456799999999 79999999999
Q ss_pred cccccccccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653 165 FHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202 (202)
Q Consensus 165 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg 202 (202)
||..||+|..|...|. ++++.+||.|||..+|.+.||
T Consensus 156 whv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fg 192 (670)
T KOG1044|consen 156 WHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFG 192 (670)
T ss_pred eeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcC
Confidence 9999999999999997 579999999999999999998
No 5
>KOG1703|consensus
Probab=99.93 E-value=1.7e-27 Score=206.58 Aligned_cols=160 Identities=43% Similarity=0.864 Sum_probs=150.6
Q ss_pred chhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCceecccCCCCCCCC
Q psy3653 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCK 99 (202)
Q Consensus 20 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~C~ 99 (202)
+.+.++++.||+.+|.|..|+..+....+...||.+||.+|+.+.+.+.|.+|.++|.++.|.|.+..||++||.|..|+
T Consensus 317 ~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~ 396 (479)
T KOG1703|consen 317 KVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALGRLWHPECFVCADCG 396 (479)
T ss_pred eeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhccCeechhceeeeccc
Confidence 78889999999999999999999988888999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcc--cceeeecCccccccccccccccc
Q psy3653 100 KPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPIT--GRCITAMFRKFHPEHFVCAFCLR 177 (202)
Q Consensus 100 ~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~--~~~~~~~~~~~H~~Cf~C~~C~~ 177 (202)
++|.+.. ++..++.+||+.+|..++..+|..|.+||. +..+.+.+..||..||+|+.|.+
T Consensus 397 ~~~~~~~------------------~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~ 458 (479)
T KOG1703|consen 397 KPLKNSS------------------FFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMK 458 (479)
T ss_pred CCCCCCc------------------ccccCCccchhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhc
Confidence 8887754 456888999999999999999999999985 78899999999999999999999
Q ss_pred ccCCCceEeeCCcccChhhH
Q psy3653 178 QLNKGTFKEQNDKPYCHGCF 197 (202)
Q Consensus 178 ~l~~~~~~~~~~~~yC~~c~ 197 (202)
.|.++.|+...++|+|.+|+
T Consensus 459 ~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 459 KLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred cccCCceeecCCccccccCC
Confidence 99999999999999999875
No 6
>KOG1044|consensus
Probab=99.89 E-value=1.5e-24 Score=183.73 Aligned_cols=161 Identities=29% Similarity=0.642 Sum_probs=138.5
Q ss_pred ccchhcccccccccccccccccccccCCCcee-eeCCeeecccccccc--------CCCCCcccccccc-cccccccCce
Q psy3653 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFH-EKDGKPYCRDDYFDL--------FAPKCGGCNRAIM-ENYVSALNTQ 87 (202)
Q Consensus 18 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~-~~~g~~yC~~c~~~~--------~~~~C~~C~~~I~-~~~v~~~~~~ 87 (202)
.++++.++|++||+.||.|++|+.+.....-. .......|+.|-.-. ....|++|++.|. ++.+.|+++.
T Consensus 76 ~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~q 155 (670)
T KOG1044|consen 76 EGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQ 155 (670)
T ss_pred cceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccc
Confidence 46789999999999999999999998765444 444457788876432 2237999999996 7889999999
Q ss_pred ecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcccceeeecCccccc
Q psy3653 88 WHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHP 167 (202)
Q Consensus 88 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~ 167 (202)
||..||+|..|...|.+ .++.++|.|||+++|.+.|+.+|..|.+-|.|.++.|.|++||+
T Consensus 156 whv~cfkc~~c~~vL~g-------------------ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag~kh~HP 216 (670)
T KOG1044|consen 156 WHVSCFKCKSCSAVLNG-------------------EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAGDKHFHP 216 (670)
T ss_pred eeeeeeehhhhcccccc-------------------eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhccCcccCc
Confidence 99999999999999977 46789999999999999999999999999999999999999999
Q ss_pred ccccccccccccCCCc-eEeeCCcccChhhH
Q psy3653 168 EHFVCAFCLRQLNKGT-FKEQNDKPYCHGCF 197 (202)
Q Consensus 168 ~Cf~C~~C~~~l~~~~-~~~~~~~~yC~~c~ 197 (202)
.|-+|+.|+..+..|+ .+.....+|=+.|-
T Consensus 217 tCARCsRCgqmF~eGEEMYlQGs~iWHP~C~ 247 (670)
T KOG1044|consen 217 TCARCSRCGQMFGEGEEMYLQGSEIWHPDCK 247 (670)
T ss_pred chhhhhhhccccccchheeeccccccCCccc
Confidence 9999999999999776 77777777766663
No 7
>KOG1701|consensus
Probab=99.88 E-value=7.9e-25 Score=179.84 Aligned_cols=117 Identities=33% Similarity=0.786 Sum_probs=105.6
Q ss_pred CCCcccccccccc--cccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCC
Q psy3653 67 PKCGGCNRAIMEN--YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGS 144 (202)
Q Consensus 67 ~~C~~C~~~I~~~--~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~ 144 (202)
.+|++|++.|++. .+.||++.||..||+|..|.+.|.++.||. .|+++||+.+|.. ..+
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~------------------v~~k~~CE~cyq~-tle 335 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQ------------------VDGKPYCEGCYQD-TLE 335 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccc------------------cCCcccchHHHHH-HHH
Confidence 3999999999854 679999999999999999999999987765 5666788888865 478
Q ss_pred CCCCCCCCcccceeeecCcccccccccccccccccCCCceEe-eCCcccChhhHhhhcC
Q psy3653 145 LCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKE-QNDKPYCHGCFEKLFG 202 (202)
Q Consensus 145 ~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~~~~yC~~c~~~~fg 202 (202)
+|..|+++|.+++|.|.|+.||+.||+|..|++.|++..|.+ .++++||..+|.++|+
T Consensus 336 kC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA 394 (468)
T KOG1701|consen 336 KCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA 394 (468)
T ss_pred HHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC
Confidence 999999999999999999999999999999999999999985 5899999999999986
No 8
>KOG1703|consensus
Probab=99.85 E-value=2.8e-22 Score=174.00 Aligned_cols=165 Identities=27% Similarity=0.490 Sum_probs=152.7
Q ss_pred chhccccccccccccccc-ccccccCCCceeeeCCeeeccccccccCCCCCccccccccc-ccccccCceecccCCCCCC
Q psy3653 20 KCVTALEKTWHTEHFFCA-QCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIME-NYVSALNTQWHSTCFVCRD 97 (202)
Q Consensus 20 ~~~~~~~~~~H~~Cf~C~-~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~-~~v~~~~~~~H~~Cf~C~~ 97 (202)
....+....||..-+++. .+...|....++.+.+.+.+..+|...+.+.|..|.+.|.+ +++.++++.||+.+|.|+.
T Consensus 256 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~ 335 (479)
T KOG1703|consen 256 PLVSAPRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYHNVTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEV 335 (479)
T ss_pred cceecccccccccccccccccchhhcccccccccccccccccccccccccccccccCcccceeEeeccccccccceeecc
Confidence 456778999999999999 88888888889999999999999999999999999999998 9999999999999999999
Q ss_pred CCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcccceeeecCccccccccccccccc
Q psy3653 98 CKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLR 177 (202)
Q Consensus 98 C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~ 177 (202)
|...+....+ ...+|.+||..++.+.+++.|.+|+++|.++.|.+.++.||++||.|..|++
T Consensus 336 ~~~~~~~~~~------------------~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~ 397 (479)
T KOG1703|consen 336 CAIVILDGGP------------------RELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALGRLWHPECFVCADCGK 397 (479)
T ss_pred ccccccCCCc------------------cccCCCccHHHHHHHhhCccccccCCchHHhHhhhccCeechhceeeecccC
Confidence 9988865433 4578899999999999999999999999999999999999999999999999
Q ss_pred ccCCCceEeeCCcccChhhHhhhcC
Q psy3653 178 QLNKGTFKEQNDKPYCHGCFEKLFG 202 (202)
Q Consensus 178 ~l~~~~~~~~~~~~yC~~c~~~~fg 202 (202)
+|.++.|+..++.|||..||.++|+
T Consensus 398 ~~~~~~~~~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 398 PLKNSSFFESDGEPYCEDHYKKLFT 422 (479)
T ss_pred CCCCCcccccCCccchhhhHhhhcc
Confidence 9999999999999999999999874
No 9
>KOG4577|consensus
Probab=99.78 E-value=6.1e-21 Score=149.79 Aligned_cols=121 Identities=29% Similarity=0.776 Sum_probs=104.4
Q ss_pred cccccCCCCCccccccccccc-ccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccc
Q psy3653 60 DYFDLFAPKCGGCNRAIMENY-VSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHY 138 (202)
Q Consensus 60 c~~~~~~~~C~~C~~~I~~~~-v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~ 138 (202)
++.....|+|++|.+.|.+++ +.++++.||..|++|+.|..+|... .|.++|..||++++
T Consensus 27 df~~~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-------------------CFsR~~s~yCkedF 87 (383)
T KOG4577|consen 27 DFSNVEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR-------------------CFSREGSVYCKEDF 87 (383)
T ss_pred cccccccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-------------------HhhcCCceeehHHH
Confidence 344445689999999999985 4899999999999999999999763 45789999999999
Q ss_pred cccCCCCCCCCCCCcccc-ee-eecCcccccccccccccccccCCCc-eE-eeCCcccChhhHhh
Q psy3653 139 HAKRGSLCAGCHKPITGR-CI-TAMFRKFHPEHFVCAFCLRQLNKGT-FK-EQNDKPYCHGCFEK 199 (202)
Q Consensus 139 ~~~~~~~C~~C~~~I~~~-~~-~~~~~~~H~~Cf~C~~C~~~l~~~~-~~-~~~~~~yC~~c~~~ 199 (202)
.++|+.+|..|+..|... +| .|.+..||..||.|..|+++|.+|+ |+ ..|.++.|+..|+.
T Consensus 88 fKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~ 152 (383)
T KOG4577|consen 88 FKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET 152 (383)
T ss_pred HHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence 999999999999999544 33 5778899999999999999999776 66 56899999999975
No 10
>KOG4577|consensus
Probab=99.76 E-value=4.1e-20 Score=145.15 Aligned_cols=97 Identities=32% Similarity=0.836 Sum_probs=84.3
Q ss_pred hhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccc-cc-cccCceecccCCCCCCC
Q psy3653 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMEN-YV-SALNTQWHSTCFVCRDC 98 (202)
Q Consensus 21 ~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~-~v-~~~~~~~H~~Cf~C~~C 98 (202)
+++++++.||..|++|++|..+|.+ .++.++|.+||+++|+++|+.+|..|...|.+. +| .|.+..||..||.|..|
T Consensus 48 ilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC 126 (383)
T KOG4577|consen 48 ILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFIC 126 (383)
T ss_pred HHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhh
Confidence 5789999999999999999999976 477999999999999999999999999999854 44 68899999999999999
Q ss_pred CCCC-CCCceeecC-CcccCCC
Q psy3653 99 KKPV-TGKSFYAME-GKPDCRQ 118 (202)
Q Consensus 99 ~~~l-~~~~~~~~~-~~~~C~~ 118 (202)
++.| ++++||.++ .+..|..
T Consensus 127 ~R~L~TGdEFYLmeD~rLvCK~ 148 (383)
T KOG4577|consen 127 KRQLATGDEFYLMEDARLVCKD 148 (383)
T ss_pred hcccccCCeeEEeccceeehhh
Confidence 9999 788888753 2444433
No 11
>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=99.61 E-value=6.5e-16 Score=96.40 Aligned_cols=56 Identities=50% Similarity=1.025 Sum_probs=51.1
Q ss_pred CCCCCCCccccee--eecCcccccccccccccccccCCCceEeeCCcccChhhHhhhc
Q psy3653 146 CAGCHKPITGRCI--TAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201 (202)
Q Consensus 146 C~~C~~~I~~~~~--~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~f 201 (202)
|++|+++|.+..+ .+.|+.||++||+|..|+++|.++.++..+++|||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 7899999964433 5999999999999999999999999999999999999999987
No 12
>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=99.37 E-value=2.2e-13 Score=84.87 Aligned_cols=44 Identities=50% Similarity=1.083 Sum_probs=40.8
Q ss_pred hcccccccccccccccccccccCCCceeeeCCeeeccccccccC
Q psy3653 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65 (202)
Q Consensus 22 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~ 65 (202)
+.++|+.||+.||+|+.|+++|.+..++..||++||++||.++|
T Consensus 15 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 15 IKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp EEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred EEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 36999999999999999999999888999999999999998764
No 13
>KOG1700|consensus
Probab=99.25 E-value=2e-12 Score=100.11 Aligned_cols=136 Identities=26% Similarity=0.542 Sum_probs=100.9
Q ss_pred CCCCCcccccccc-cccccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCC-----Cceee----------c
Q psy3653 65 FAPKCGGCNRAIM-ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG-----GSFFD----------H 128 (202)
Q Consensus 65 ~~~~C~~C~~~I~-~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~-----~~~~~----------~ 128 (202)
...+|..|++.+. .+.+...+..||+.||+|..|.+.|...+....++.++|..+... +..+. .
T Consensus 6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (200)
T KOG1700|consen 6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK 85 (200)
T ss_pred ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCc
Confidence 4568999999997 445558899999999999999999998888889999999873210 00000 0
Q ss_pred CCCcc---cccc-----ccccCCCCCCCCCCCc-ccceeeecCcccccccccccccccccCCCceEeeCCcccChhhHhh
Q psy3653 129 EGLPY---CETH-----YHAKRGSLCAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEK 199 (202)
Q Consensus 129 ~g~~~---C~~~-----~~~~~~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~ 199 (202)
++... ...- ........|.+|++.+ ..+.+...+..||+.||+|+.|+..|+.+.+...++.+||...+.+
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~ 165 (200)
T KOG1700|consen 86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQ 165 (200)
T ss_pred ccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhhe
Confidence 11110 1000 0111245799999999 5667888899999999999999999999999999999999766654
Q ss_pred h
Q psy3653 200 L 200 (202)
Q Consensus 200 ~ 200 (202)
+
T Consensus 166 ~ 166 (200)
T KOG1700|consen 166 L 166 (200)
T ss_pred e
Confidence 3
No 14
>KOG1700|consensus
Probab=99.13 E-value=1.4e-11 Score=95.41 Aligned_cols=107 Identities=29% Similarity=0.684 Sum_probs=85.6
Q ss_pred hCcCcccch-----hcccccccccccccccccccccCCCceeeeCCeeeccccccccCCC--------------------
Q psy3653 13 FSLRCFQKC-----VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAP-------------------- 67 (202)
Q Consensus 13 ~~~~C~~~~-----~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~-------------------- 67 (202)
-|++|.+.+ +...|..||+.||+|..|.+.|+...+.++++.+||+.+|...+++
T Consensus 9 kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (200)
T KOG1700|consen 9 KCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKDGK 88 (200)
T ss_pred hhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcccc
Confidence 577885433 3456899999999999999999999999999999999976444332
Q ss_pred ---------------------CCccccccccc-ccccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCC
Q psy3653 68 ---------------------KCGGCNRAIME-NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQP 119 (202)
Q Consensus 68 ---------------------~C~~C~~~I~~-~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~ 119 (202)
.|.+|++.+.+ +.+...+..||..||+|+.|+..|+..++....+.++|..+
T Consensus 89 ~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~ 162 (200)
T KOG1700|consen 89 SLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHH 162 (200)
T ss_pred cccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchh
Confidence 29999999984 56678899999999999999999988777665555555443
No 15
>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=98.80 E-value=3.3e-09 Score=60.17 Aligned_cols=36 Identities=44% Similarity=0.918 Sum_probs=32.6
Q ss_pred CCCCCCCCccc--ceeeecCcccccccccccccccccC
Q psy3653 145 LCAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLN 180 (202)
Q Consensus 145 ~C~~C~~~I~~--~~~~~~~~~~H~~Cf~C~~C~~~l~ 180 (202)
+|.+|+++|.+ ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58999999965 6788899999999999999999986
No 16
>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=98.55 E-value=4e-08 Score=55.56 Aligned_cols=36 Identities=42% Similarity=1.037 Sum_probs=32.0
Q ss_pred CCccccccccc--ccccccCceecccCCCCCCCCCCCC
Q psy3653 68 KCGGCNRAIME--NYVSALNTQWHSTCFVCRDCKKPVT 103 (202)
Q Consensus 68 ~C~~C~~~I~~--~~v~~~~~~~H~~Cf~C~~C~~~l~ 103 (202)
+|.+|+++|.+ ..+.+++..||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58899999986 5778899999999999999999885
No 17
>KOG0490|consensus
Probab=97.48 E-value=2.6e-05 Score=61.67 Aligned_cols=90 Identities=31% Similarity=0.764 Sum_probs=72.3
Q ss_pred hhcccccccccccccccccccccC--CCceeeeCCeeeccccccc--cCCCCCcccccccc--cccccccCceecccCCC
Q psy3653 21 CVTALEKTWHTEHFFCAQCGKQFG--EDGFHEKDGKPYCRDDYFD--LFAPKCGGCNRAIM--ENYVSALNTQWHSTCFV 94 (202)
Q Consensus 21 ~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~c~~~--~~~~~C~~C~~~I~--~~~v~~~~~~~H~~Cf~ 94 (202)
.+.+.+..||..|++|..|..+|. ...|.. +|..||..+|.. .+..+|.+|...+. +.+..+.... |-.||.
T Consensus 11 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~ 88 (235)
T KOG0490|consen 11 LLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFA 88 (235)
T ss_pred HhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccc
Confidence 345568999999999999999997 444445 999999999998 78889999999986 4455566666 999999
Q ss_pred CCCCCCCC-CCCceeecCC
Q psy3653 95 CRDCKKPV-TGKSFYAMEG 112 (202)
Q Consensus 95 C~~C~~~l-~~~~~~~~~~ 112 (202)
|..|.+.+ ...++.+..|
T Consensus 89 ~r~~la~~~~~~e~rVqvw 107 (235)
T KOG0490|consen 89 CRECLALLLTGDEFRVQVW 107 (235)
T ss_pred hHHHHhhcCCCCeeeeehh
Confidence 99998876 5666666555
No 18
>KOG0490|consensus
Probab=97.30 E-value=8.1e-05 Score=58.83 Aligned_cols=109 Identities=28% Similarity=0.579 Sum_probs=82.3
Q ss_pred cccccccc-cccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccc--cCCCCCCC
Q psy3653 72 CNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHA--KRGSLCAG 148 (202)
Q Consensus 72 C~~~I~~~-~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~--~~~~~C~~ 148 (202)
|+..|.+. .+.+.+..||..|..|..|..+|... ...+.++|..||..++.. .+..+|.+
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~g~~~~~~d~~~~~~~~~rr~r 64 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVG-----------------DTCFSKDGSIYCKRDYQREFKFSKRCAR 64 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccC-----------------CCcccCCCcccccccchhhhhccccccC
Confidence 56677665 34566899999999999999888611 123345888999999987 67889999
Q ss_pred CCCCc--ccceeeecCcccccccccccccccccCCCc-eEeeCC-cccChhhHh
Q psy3653 149 CHKPI--TGRCITAMFRKFHPEHFVCAFCLRQLNKGT-FKEQND-KPYCHGCFE 198 (202)
Q Consensus 149 C~~~I--~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~-~~yC~~c~~ 198 (202)
|...| .+++..+..+. |..||.|..|.+.+..++ +.+.+. +..|...+.
T Consensus 65 t~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~ 117 (235)
T KOG0490|consen 65 CKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRK 117 (235)
T ss_pred CCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhh
Confidence 99998 35555667777 999999999999876555 666555 777776654
No 19
>KOG1702|consensus
Probab=97.07 E-value=5.4e-05 Score=57.78 Aligned_cols=57 Identities=25% Similarity=0.523 Sum_probs=48.0
Q ss_pred CCCCCCCCCc-ccceeeecCcccccccccccccccccCCCceEeeCCcccChhhHhhh
Q psy3653 144 SLCAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKL 200 (202)
Q Consensus 144 ~~C~~C~~~I-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~ 200 (202)
..|..|++.+ .-+-|.-+++.||..||+|..|+.+|+-..+-..+.+|||...|.+.
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ 62 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence 3466788877 34557888999999999999999999988888889999999998654
No 20
>KOG1702|consensus
Probab=96.62 E-value=0.00051 Score=52.54 Aligned_cols=60 Identities=22% Similarity=0.546 Sum_probs=49.6
Q ss_pred CCCccccccccc-ccccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCcee
Q psy3653 67 PKCGGCNRAIME-NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFF 126 (202)
Q Consensus 67 ~~C~~C~~~I~~-~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~ 126 (202)
+.+..|++.+.+ +-+.-+++.||..||+|..|+.+|.-..+...+.+|+|...++++.+.
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at 65 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVAT 65 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceee
Confidence 456778888874 567788999999999999999999888888888899998888776554
No 21
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=91.59 E-value=0.071 Score=29.58 Aligned_cols=32 Identities=31% Similarity=0.658 Sum_probs=23.0
Q ss_pred CCCCCCCcccce--eeecCcccccccccccccccccC
Q psy3653 146 CAGCHKPITGRC--ITAMFRKFHPEHFVCAFCLRQLN 180 (202)
Q Consensus 146 C~~C~~~I~~~~--~~~~~~~~H~~Cf~C~~C~~~l~ 180 (202)
|.-|+++|.++. +...++.|+ |.|..|.+.|.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~fk 34 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQFK 34 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHHH
Confidence 677999996654 456788888 66677766553
No 22
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=91.03 E-value=0.2 Score=31.36 Aligned_cols=48 Identities=15% Similarity=0.254 Sum_probs=24.8
Q ss_pred ccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccc
Q psy3653 34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYV 81 (202)
Q Consensus 34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v 81 (202)
++|+.|..-|...-....=+..||..|..+.++..|..|+.|...+.+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~ 55 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDI 55 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS-
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHH
Confidence 678888887766544455567899999999888999999998864433
No 23
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.21 E-value=0.33 Score=29.31 Aligned_cols=38 Identities=18% Similarity=0.433 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCcc--cceee--ecCcccccccc----cccc--ccccc
Q psy3653 142 RGSLCAGCHKPIT--GRCIT--AMFRKFHPEHF----VCAF--CLRQL 179 (202)
Q Consensus 142 ~~~~C~~C~~~I~--~~~~~--~~~~~~H~~Cf----~C~~--C~~~l 179 (202)
.+.+|..|+++|. +.+|+ .-+..||++|. .|.. |+..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 3578999999993 34332 34788999997 4665 55543
No 24
>KOG2462|consensus
Probab=82.76 E-value=0.81 Score=36.98 Aligned_cols=129 Identities=17% Similarity=0.351 Sum_probs=74.2
Q ss_pred cccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCceecccCCCCCCCCCCCCCCceeec
Q psy3653 31 TEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAM 110 (202)
Q Consensus 31 ~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~ 110 (202)
...++|.+|++.++...=..+..+.-|.-+- .-+..|..|++.-.......|-..-|.-=+.|..|++.|... |..
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s--~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRP--WLL 203 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDS--KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRP--WLL 203 (279)
T ss_pred CCceeccccccccccccccchhhcccccccc--cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccch--HHh
Confidence 4568999999998765444566666665544 334589999987653322233344466567899999887531 111
Q ss_pred CCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcccce-eeec-CcccccccccccccccccCCCce
Q psy3653 111 EGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRC-ITAM-FRKFHPEHFVCAFCLRQLNKGTF 184 (202)
Q Consensus 111 ~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~-~~~~-~~~~H~~Cf~C~~C~~~l~~~~~ 184 (202)
.|+. -.+.| + ..-.|+.|++...++. +.|- ...=+.+=|.|..|++.+....+
T Consensus 204 QGHi-----------RTHTG---------E-KPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~Sy 258 (279)
T KOG2462|consen 204 QGHI-----------RTHTG---------E-KPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSY 258 (279)
T ss_pred hccc-----------ccccC---------C-CCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHH
Confidence 1110 00000 0 1235889998886642 2221 11123335788999888775443
No 25
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=82.29 E-value=0.46 Score=26.04 Aligned_cols=32 Identities=16% Similarity=0.625 Sum_probs=22.6
Q ss_pred hCcCcccchhcccccccccccccccccccccC
Q psy3653 13 FSLRCFQKCVTALEKTWHTEHFFCAQCGKQFG 44 (202)
Q Consensus 13 ~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 44 (202)
.|+.|..++....++.||..=..|..||=+++
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTTCC-SCC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCCCCCCEE
Confidence 37778888888899999999999999987663
No 26
>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=81.13 E-value=1.2 Score=25.36 Aligned_cols=28 Identities=36% Similarity=0.822 Sum_probs=19.4
Q ss_pred cccccccccccccccCCCceeeeCCeeecccc
Q psy3653 29 WHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDD 60 (202)
Q Consensus 29 ~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c 60 (202)
|-.-=-.|..|+.||- ..++|+.||..|
T Consensus 13 ~~ML~~~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 13 WTMLDEHCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred HhHhcCccCCCCCeeE----EecCCCEECCCC
Confidence 4444446778888873 368999998765
No 27
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=81.12 E-value=1.2 Score=24.58 Aligned_cols=25 Identities=32% Similarity=0.535 Sum_probs=18.9
Q ss_pred ccccccccccCCCceeeeCCeeecccccc
Q psy3653 34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62 (202)
Q Consensus 34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~ 62 (202)
+.|..|+.. .|...||..||..|-.
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 347888765 4778999999987754
No 28
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=78.38 E-value=0.39 Score=26.31 Aligned_cols=28 Identities=18% Similarity=0.453 Sum_probs=12.1
Q ss_pred ccccccccCCCceEeeCCcccChhhHhh
Q psy3653 172 CAFCLRQLNKGTFKEQNDKPYCHGCFEK 199 (202)
Q Consensus 172 C~~C~~~l~~~~~~~~~~~~yC~~c~~~ 199 (202)
|..|+.++...+....++..+|.+|+.+
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 4444444443333334455555555543
No 29
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.28 E-value=2.1 Score=30.00 Aligned_cols=26 Identities=23% Similarity=0.402 Sum_probs=18.3
Q ss_pred hCcCcccchhcccccccccccccccccccccCCC
Q psy3653 13 FSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGED 46 (202)
Q Consensus 13 ~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 46 (202)
.||||..++-..- ..|..||..|-..
T Consensus 3 ~CPrC~skvC~LP--------~~CpiCgLtLVss 28 (112)
T TIGR00622 3 FCPQCRAKVCELP--------VECPICGLTLILS 28 (112)
T ss_pred cCCCCCCCccCCC--------CcCCcCCCEEecc
Confidence 5889988775544 5678888877543
No 30
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=77.77 E-value=1.6 Score=29.74 Aligned_cols=29 Identities=17% Similarity=0.313 Sum_probs=20.2
Q ss_pred CCCCCCCCCCcccce-e-eecCccccccccc
Q psy3653 143 GSLCAGCHKPITGRC-I-TAMFRKFHPEHFV 171 (202)
Q Consensus 143 ~~~C~~C~~~I~~~~-~-~~~~~~~H~~Cf~ 171 (202)
...|+.|+++|.... + -..|..+|..|.+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 467999999995433 3 3346778888863
No 31
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.15 E-value=1.7 Score=21.36 Aligned_cols=9 Identities=33% Similarity=0.936 Sum_probs=4.6
Q ss_pred CCCCCCCcc
Q psy3653 146 CAGCHKPIT 154 (202)
Q Consensus 146 C~~C~~~I~ 154 (202)
|+.|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 455555553
No 32
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=77.15 E-value=3.8 Score=25.67 Aligned_cols=31 Identities=26% Similarity=0.415 Sum_probs=15.4
Q ss_pred CCccccccccccCCCCCCCCCCCcccceeee
Q psy3653 130 GLPYCETHYHAKRGSLCAGCHKPITGRCITA 160 (202)
Q Consensus 130 g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~ 160 (202)
...+|..|.....+..|+.|..|...+.+..
T Consensus 27 eH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~ 57 (65)
T PF14835_consen 27 EHIFCSSCIRDCIGSECPVCHTPAWIQDIQI 57 (65)
T ss_dssp S--B-TTTGGGGTTTB-SSS--B-S-SS---
T ss_pred ccHHHHHHhHHhcCCCCCCcCChHHHHHHHh
Confidence 3567777777777888999999986554443
No 33
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=75.71 E-value=1.3 Score=34.17 Aligned_cols=31 Identities=29% Similarity=0.505 Sum_probs=27.2
Q ss_pred ccccccccccCCCceeeeCCeeecccccccc
Q psy3653 34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDL 64 (202)
Q Consensus 34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~ 64 (202)
-+|+.||....+..-...+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999999887777899999999999754
No 34
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=75.10 E-value=1.9 Score=30.99 Aligned_cols=22 Identities=36% Similarity=0.910 Sum_probs=17.4
Q ss_pred cccccccccCCCceeeeCCeeeccccc
Q psy3653 35 FCAQCGKQFGEDGFHEKDGKPYCRDDY 61 (202)
Q Consensus 35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~ 61 (202)
.|..||.|| | .+||.+||..|-
T Consensus 30 hCp~Cg~PL----F-~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL----F-RKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc----e-eeCCeEECCCCC
Confidence 368899988 4 499999987764
No 35
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=74.17 E-value=2.5 Score=25.16 Aligned_cols=28 Identities=32% Similarity=0.759 Sum_probs=17.0
Q ss_pred ccccccccCCCc-eEeeCCcccChhhHhhh
Q psy3653 172 CAFCLRQLNKGT-FKEQNDKPYCHGCFEKL 200 (202)
Q Consensus 172 C~~C~~~l~~~~-~~~~~~~~yC~~c~~~~ 200 (202)
|..|+..++--. +-..|| ..|..|+.++
T Consensus 2 C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 2 CAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCccccccccccceeccCc-cchHHHHHHh
Confidence 566666665322 456666 5777777664
No 36
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=74.08 E-value=2.1 Score=25.59 Aligned_cols=27 Identities=33% Similarity=0.626 Sum_probs=16.1
Q ss_pred ccccccccCCCceeeeCCeeeccc-ccc
Q psy3653 36 CAQCGKQFGEDGFHEKDGKPYCRD-DYF 62 (202)
Q Consensus 36 C~~C~~~l~~~~~~~~~g~~yC~~-c~~ 62 (202)
|..|.-.++...-+.+||+.||.+ |..
T Consensus 10 C~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 10 CPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp STT----B-TTTSEESSS-EESSHHHHH
T ss_pred CCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 567888888777899999999964 543
No 37
>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=71.54 E-value=1.8 Score=22.53 Aligned_cols=15 Identities=27% Similarity=0.465 Sum_probs=8.2
Q ss_pred CCCCCCCCCccccee
Q psy3653 144 SLCAGCHKPITGRCI 158 (202)
Q Consensus 144 ~~C~~C~~~I~~~~~ 158 (202)
.+|.+|+.+|....+
T Consensus 2 ~~C~rC~~~~~~~~~ 16 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGI 16 (30)
T ss_dssp SB-TTT--BBEEEEE
T ss_pred CcCccCCCcceEeEe
Confidence 578899988865444
No 38
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=71.48 E-value=1.5 Score=28.84 Aligned_cols=29 Identities=38% Similarity=0.843 Sum_probs=21.4
Q ss_pred cccccccccCCCcee--eeCC---eeeccccccc
Q psy3653 35 FCAQCGKQFGEDGFH--EKDG---KPYCRDDYFD 63 (202)
Q Consensus 35 ~C~~C~~~l~~~~~~--~~~g---~~yC~~c~~~ 63 (202)
.|+.||-||+....+ +.|| .-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 489999999876533 3455 3699999865
No 39
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=71.10 E-value=1.4 Score=34.02 Aligned_cols=30 Identities=30% Similarity=0.502 Sum_probs=24.6
Q ss_pred ccccccccccCCCceEeeCCcccChhhHhh
Q psy3653 170 FVCAFCLRQLNKGTFKEQNDKPYCHGCFEK 199 (202)
Q Consensus 170 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~ 199 (202)
-+|..|+..+...+-...+|++.|..|+.+
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccchhhhcCCceeccccccc
Confidence 578888887776677788999999999974
No 40
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=68.59 E-value=4.2 Score=24.66 Aligned_cols=45 Identities=18% Similarity=0.428 Sum_probs=32.4
Q ss_pred cccccccccCCCc---eeeeCCeeeccccccccCCCCCcccccccccc
Q psy3653 35 FCAQCGKQFGEDG---FHEKDGKPYCRDDYFDLFAPKCGGCNRAIMEN 79 (202)
Q Consensus 35 ~C~~C~~~l~~~~---~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~ 79 (202)
.|..|++.|..++ ++=.-.=.||.+|....+...|..|+..+..+
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv~R 54 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELVRR 54 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccccC
Confidence 3577888886543 44344457899999988888999998877543
No 41
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=68.21 E-value=3.3 Score=27.84 Aligned_cols=42 Identities=19% Similarity=0.543 Sum_probs=25.3
Q ss_pred cccccccccccccccCCCceeeeCCeeeccccccccCCCCCccccccccc
Q psy3653 29 WHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIME 78 (202)
Q Consensus 29 ~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~ 78 (202)
|-+.=-+|..|+..+.. .|..||..|..+. -.|+-|++.|.+
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhccc--CcccccCCeecc
Confidence 33333356777665532 3566888886554 378888877753
No 42
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=67.58 E-value=4.7 Score=27.35 Aligned_cols=27 Identities=26% Similarity=0.405 Sum_probs=16.7
Q ss_pred cccccccccCCCceee-eCCeeeccccc
Q psy3653 35 FCAQCGKQFGEDGFHE-KDGKPYCRDDY 61 (202)
Q Consensus 35 ~C~~C~~~l~~~~~~~-~~g~~yC~~c~ 61 (202)
+|+.|+++|....|.. -+|..++..|.
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccc
Confidence 4777777777665553 44566655554
No 43
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=65.57 E-value=1.8 Score=29.70 Aligned_cols=27 Identities=37% Similarity=0.496 Sum_probs=19.4
Q ss_pred CCCCCCCCc-ccceeeec-Cccccccccc
Q psy3653 145 LCAGCHKPI-TGRCITAM-FRKFHPEHFV 171 (202)
Q Consensus 145 ~C~~C~~~I-~~~~~~~~-~~~~H~~Cf~ 171 (202)
+|..|+++| .|+..++. +..-|-.||+
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~ 32 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFR 32 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHH
Confidence 588899999 56665554 4556888885
No 44
>PF12773 DZR: Double zinc ribbon
Probab=64.52 E-value=3.7 Score=23.93 Aligned_cols=12 Identities=25% Similarity=0.935 Sum_probs=8.3
Q ss_pred CCCCCCCCCCcc
Q psy3653 143 GSLCAGCHKPIT 154 (202)
Q Consensus 143 ~~~C~~C~~~I~ 154 (202)
+..|..|+.++.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 456777777776
No 45
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=58.98 E-value=5.6 Score=22.55 Aligned_cols=39 Identities=23% Similarity=0.483 Sum_probs=24.2
Q ss_pred ccccccccCC--CceeeeCCeeeccccccccC--CCCCccccc
Q psy3653 36 CAQCGKQFGE--DGFHEKDGKPYCRDDYFDLF--APKCGGCNR 74 (202)
Q Consensus 36 C~~C~~~l~~--~~~~~~~g~~yC~~c~~~~~--~~~C~~C~~ 74 (202)
|..|.+.+++ ..+...=|..+|.+|..+.. ...|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 5566666622 23445667788888887776 556766653
No 46
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=58.84 E-value=5.4 Score=24.49 Aligned_cols=36 Identities=22% Similarity=0.465 Sum_probs=18.2
Q ss_pred cccccccccCCCceeeeCCeeeccccccccCCCCCccccc
Q psy3653 35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNR 74 (202)
Q Consensus 35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~ 74 (202)
+|.+||..|.+.. +.-...|.+|-... ..+|..|.+
T Consensus 9 ~CtSCg~~i~~~~---~~~~F~CPnCG~~~-I~RC~~CRk 44 (59)
T PRK14890 9 KCTSCGIEIAPRE---KAVKFLCPNCGEVI-IYRCEKCRK 44 (59)
T ss_pred cccCCCCcccCCC---ccCEeeCCCCCCee-EeechhHHh
Confidence 5778888776542 12344555553321 124555543
No 47
>PRK00420 hypothetical protein; Validated
Probab=58.39 E-value=6.2 Score=27.69 Aligned_cols=25 Identities=32% Similarity=0.572 Sum_probs=17.8
Q ss_pred ccccccccccCCCceeeeCCeeecccccc
Q psy3653 34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62 (202)
Q Consensus 34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~ 62 (202)
-.|..||.+| |-.++|+.||..|-.
T Consensus 24 ~~CP~Cg~pL----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc----eecCCCceECCCCCC
Confidence 5678898877 334888888777643
No 48
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=58.27 E-value=4 Score=27.83 Aligned_cols=29 Identities=38% Similarity=0.700 Sum_probs=19.9
Q ss_pred ccccccccccccCCC-ceeeeCCeeecccc
Q psy3653 32 EHFFCAQCGKQFGED-GFHEKDGKPYCRDD 60 (202)
Q Consensus 32 ~Cf~C~~C~~~l~~~-~~~~~~g~~yC~~c 60 (202)
.=|+|+.|-..-... .-..++|+++|.+|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 458999996544322 23367899999987
No 49
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=58.12 E-value=6.6 Score=19.68 Aligned_cols=7 Identities=43% Similarity=1.516 Sum_probs=3.0
Q ss_pred ccccccc
Q psy3653 36 CAQCGKQ 42 (202)
Q Consensus 36 C~~C~~~ 42 (202)
|..||+.
T Consensus 5 Cp~Cg~~ 11 (26)
T PF13248_consen 5 CPNCGAE 11 (26)
T ss_pred CcccCCc
Confidence 3444443
No 50
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=54.95 E-value=2.1 Score=28.92 Aligned_cols=53 Identities=19% Similarity=0.521 Sum_probs=36.7
Q ss_pred Ccccccccccc-cccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCC
Q psy3653 69 CGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121 (202)
Q Consensus 69 C~~C~~~I~~~-~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~ 121 (202)
|..|...+.+- .....-..+++.+..|..|...|+..++...+.-|+|+.+|.
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~spFN 91 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQSPFN 91 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCCCCC
Confidence 55555555432 223333567888889999999998888877777788877763
No 51
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=54.00 E-value=7.6 Score=23.00 Aligned_cols=26 Identities=27% Similarity=0.669 Sum_probs=13.0
Q ss_pred HhhCcCcccchhccccccccccccccccccc
Q psy3653 11 DHFSLRCFQKCVTALEKTWHTEHFFCAQCGK 41 (202)
Q Consensus 11 ~~~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~ 41 (202)
..+||+|... +.+.. ..=|.|..|+-
T Consensus 20 ~~fCP~Cg~~-~m~~~----~~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSG-FMAEH----LDRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcc-hhecc----CCcEECCCcCC
Confidence 3467777544 33332 23455666643
No 52
>KOG2462|consensus
Probab=53.76 E-value=4 Score=33.11 Aligned_cols=36 Identities=22% Similarity=0.515 Sum_probs=15.5
Q ss_pred CCcccccccccc-cccc-cCceecccCCCCCCCCCCCC
Q psy3653 68 KCGGCNRAIMEN-YVSA-LNTQWHSTCFVCRDCKKPVT 103 (202)
Q Consensus 68 ~C~~C~~~I~~~-~v~~-~~~~~H~~Cf~C~~C~~~l~ 103 (202)
.|..|++.+.|+ -+.| +-..=+..=|.|.+|++.|.
T Consensus 217 ~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 217 SCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFA 254 (279)
T ss_pred cCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHH
Confidence 455555555543 1221 11122223455555555544
No 53
>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=53.67 E-value=11 Score=21.70 Aligned_cols=11 Identities=64% Similarity=1.413 Sum_probs=7.2
Q ss_pred CCCCCCCCccc
Q psy3653 145 LCAGCHKPITG 155 (202)
Q Consensus 145 ~C~~C~~~I~~ 155 (202)
.|..|+++|.+
T Consensus 2 ~C~~C~~~i~g 12 (46)
T cd02249 2 SCDGCLKPIVG 12 (46)
T ss_pred CCcCCCCCCcC
Confidence 46777776655
No 54
>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=52.84 E-value=5.3 Score=29.57 Aligned_cols=49 Identities=16% Similarity=0.437 Sum_probs=32.7
Q ss_pred CccccccccccCCCCCCCCCCCcccce----eeecCcccccccccccccccccCC
Q psy3653 131 LPYCETHYHAKRGSLCAGCHKPITGRC----ITAMFRKFHPEHFVCAFCLRQLNK 181 (202)
Q Consensus 131 ~~~C~~~~~~~~~~~C~~C~~~I~~~~----~~~~~~~~H~~Cf~C~~C~~~l~~ 181 (202)
.-||.+|-.+ .-..|+.|+.||.|.. +...|..|+.-=+ |..|+++...
T Consensus 28 ~~fC~kCG~~-tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsY-C~~CGkpyPW 80 (158)
T PF10083_consen 28 EKFCSKCGAK-TITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSY-CHNCGKPYPW 80 (158)
T ss_pred HHHHHHhhHH-HHHHCcCCCCCCCCceecCCeeeeCCCCCCChh-HHhCCCCCch
Confidence 3477777654 3567999999997653 3445666664332 8888888763
No 55
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=52.57 E-value=4.7 Score=26.26 Aligned_cols=13 Identities=38% Similarity=0.871 Sum_probs=9.6
Q ss_pred CCCCCCCCCCCcc
Q psy3653 142 RGSLCAGCHKPIT 154 (202)
Q Consensus 142 ~~~~C~~C~~~I~ 154 (202)
...+|.+|++.|.
T Consensus 6 ~Ra~Ck~C~~~I~ 18 (82)
T PF00645_consen 6 GRAKCKGCKKKIA 18 (82)
T ss_dssp STEBETTTSCBE-
T ss_pred CCccCcccCCcCC
Confidence 3457999999993
No 56
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=52.17 E-value=13 Score=21.18 Aligned_cols=12 Identities=50% Similarity=1.043 Sum_probs=7.7
Q ss_pred CCCCCCCCCccc
Q psy3653 144 SLCAGCHKPITG 155 (202)
Q Consensus 144 ~~C~~C~~~I~~ 155 (202)
..|..|+.+|.+
T Consensus 5 ~~C~~C~~~i~g 16 (44)
T smart00291 5 YSCDTCGKPIVG 16 (44)
T ss_pred cCCCCCCCCCcC
Confidence 457777776654
No 57
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=52.05 E-value=5.6 Score=23.29 Aligned_cols=29 Identities=38% Similarity=0.847 Sum_probs=15.6
Q ss_pred eecCCCccccccccc--------cCCCCCCCCCCCcc
Q psy3653 126 FDHEGLPYCETHYHA--------KRGSLCAGCHKPIT 154 (202)
Q Consensus 126 ~~~~g~~~C~~~~~~--------~~~~~C~~C~~~I~ 154 (202)
+...|.+.|.++|.- ..+++|+.|++|+.
T Consensus 10 f~~k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 10 FANKGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp S--SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred hcCCCeeeecchhHHHHHHHHHhccccCCCcccCcCc
Confidence 455666677777732 24678888888874
No 58
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=51.23 E-value=5.2 Score=26.80 Aligned_cols=16 Identities=31% Similarity=0.914 Sum_probs=13.7
Q ss_pred ccccCCCCCccccccc
Q psy3653 61 YFDLFAPKCGGCNRAI 76 (202)
Q Consensus 61 ~~~~~~~~C~~C~~~I 76 (202)
|..+|...|.+|++.+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 5677888999999988
No 59
>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=50.97 E-value=5.3 Score=21.80 Aligned_cols=39 Identities=23% Similarity=0.459 Sum_probs=17.7
Q ss_pred ccccccccCCCceeeeCCeeeccccccccC---CCCCccccc
Q psy3653 36 CAQCGKQFGEDGFHEKDGKPYCRDDYFDLF---APKCGGCNR 74 (202)
Q Consensus 36 C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~---~~~C~~C~~ 74 (202)
|..|...+........=|..||..|..+.+ ..+|..|+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCC
Confidence 455555552222222245556666654332 234555544
No 60
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=50.82 E-value=3.9 Score=22.36 Aligned_cols=10 Identities=30% Similarity=1.039 Sum_probs=5.2
Q ss_pred cccccccccc
Q psy3653 34 FFCAQCGKQF 43 (202)
Q Consensus 34 f~C~~C~~~l 43 (202)
++|..|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 5555555544
No 61
>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=50.74 E-value=12 Score=18.65 Aligned_cols=9 Identities=44% Similarity=1.387 Sum_probs=4.3
Q ss_pred CCCCCCCcc
Q psy3653 146 CAGCHKPIT 154 (202)
Q Consensus 146 C~~C~~~I~ 154 (202)
|..|+.+|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 344555553
No 62
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=50.73 E-value=20 Score=32.97 Aligned_cols=21 Identities=14% Similarity=0.502 Sum_probs=9.2
Q ss_pred cccccccccCCCCCCCCCCCc
Q psy3653 133 YCETHYHAKRGSLCAGCHKPI 153 (202)
Q Consensus 133 ~C~~~~~~~~~~~C~~C~~~I 153 (202)
||..|-.......|+.|+..+
T Consensus 17 FC~~CG~~l~~~~Cp~CG~~~ 37 (645)
T PRK14559 17 FCQKCGTSLTHKPCPQCGTEV 37 (645)
T ss_pred cccccCCCCCCCcCCCCCCCC
Confidence 444444333333455555544
No 63
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=49.99 E-value=16 Score=33.69 Aligned_cols=10 Identities=20% Similarity=0.750 Sum_probs=4.6
Q ss_pred CCCccccccc
Q psy3653 67 PKCGGCNRAI 76 (202)
Q Consensus 67 ~~C~~C~~~I 76 (202)
..|..|+..+
T Consensus 28 ~~Cp~CG~~~ 37 (645)
T PRK14559 28 KPCPQCGTEV 37 (645)
T ss_pred CcCCCCCCCC
Confidence 3455554443
No 64
>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=49.65 E-value=6.6 Score=22.22 Aligned_cols=11 Identities=27% Similarity=0.918 Sum_probs=4.5
Q ss_pred ccccccccccC
Q psy3653 34 FFCAQCGKQFG 44 (202)
Q Consensus 34 f~C~~C~~~l~ 44 (202)
+.|..||..|+
T Consensus 20 ~vC~~CG~Vl~ 30 (43)
T PF08271_consen 20 LVCPNCGLVLE 30 (43)
T ss_dssp EEETTT-BBEE
T ss_pred EECCCCCCEee
Confidence 44444444443
No 65
>KOG0320|consensus
Probab=49.20 E-value=5 Score=30.45 Aligned_cols=50 Identities=22% Similarity=0.443 Sum_probs=38.6
Q ss_pred ccccccccccccccCCCc-eeeeCCeeecccccccc--CCCCCcccccccccc
Q psy3653 30 HTEHFFCAQCGKQFGEDG-FHEKDGKPYCRDDYFDL--FAPKCGGCNRAIMEN 79 (202)
Q Consensus 30 H~~Cf~C~~C~~~l~~~~-~~~~~g~~yC~~c~~~~--~~~~C~~C~~~I~~~ 79 (202)
-..+++|..|-.+.+... +..+=|.+||+.|.+.. .+.+|..|++.|..+
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 346799999977776553 55788999999998775 356899999988643
No 66
>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=49.18 E-value=17 Score=21.04 Aligned_cols=42 Identities=21% Similarity=0.314 Sum_probs=27.2
Q ss_pred cccccccccCCCceeeeCCee-ecccccccc--CCCCCcccccccc
Q psy3653 35 FCAQCGKQFGEDGFHEKDGKP-YCRDDYFDL--FAPKCGGCNRAIM 77 (202)
Q Consensus 35 ~C~~C~~~l~~~~~~~~~g~~-yC~~c~~~~--~~~~C~~C~~~I~ 77 (202)
.|..|.....+ ..+..=|.. +|..|..+. ...+|..|+++|.
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 45666665443 334455666 899998776 4568999988874
No 67
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=47.77 E-value=4.4 Score=25.85 Aligned_cols=24 Identities=21% Similarity=0.420 Sum_probs=8.0
Q ss_pred Ceeecccccccc-CCCCCccccccc
Q psy3653 53 GKPYCRDDYFDL-FAPKCGGCNRAI 76 (202)
Q Consensus 53 g~~yC~~c~~~~-~~~~C~~C~~~I 76 (202)
+..+|..|-... ..+.|..|++++
T Consensus 16 ~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp TEEEETTT--EEEEEEE-TTT-SB-
T ss_pred CEEECccccccceecccCCCcccHH
Confidence 444444443221 113455555555
No 68
>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=47.64 E-value=13 Score=22.39 Aligned_cols=29 Identities=10% Similarity=0.032 Sum_probs=13.7
Q ss_pred eeecCCCcccccccccc--CCCCCCCCCCCc
Q psy3653 125 FFDHEGLPYCETHYHAK--RGSLCAGCHKPI 153 (202)
Q Consensus 125 ~~~~~g~~~C~~~~~~~--~~~~C~~C~~~I 153 (202)
+....|..|+..+..+. ....|+.|++++
T Consensus 15 v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~ 45 (63)
T smart00504 15 VILPSGQTYERRAIEKWLLSHGTDPVTGQPL 45 (63)
T ss_pred EECCCCCEEeHHHHHHHHHHCCCCCCCcCCC
Confidence 44455555555543321 123455555555
No 69
>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=47.37 E-value=9.8 Score=19.98 Aligned_cols=10 Identities=10% Similarity=0.032 Sum_probs=1.8
Q ss_pred CcCcccchhc
Q psy3653 14 SLRCFQKCVT 23 (202)
Q Consensus 14 ~~~C~~~~~~ 23 (202)
||.|..++..
T Consensus 5 Cp~C~se~~y 14 (30)
T PF08274_consen 5 CPLCGSEYTY 14 (30)
T ss_dssp -TTT-----E
T ss_pred CCCCCCccee
Confidence 4445443333
No 70
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=46.77 E-value=5.9 Score=26.75 Aligned_cols=30 Identities=23% Similarity=0.233 Sum_probs=20.4
Q ss_pred CCCCCCCCCc-ccceeeec-Cccccccccccc
Q psy3653 144 SLCAGCHKPI-TGRCITAM-FRKFHPEHFVCA 173 (202)
Q Consensus 144 ~~C~~C~~~I-~~~~~~~~-~~~~H~~Cf~C~ 173 (202)
-+|..|+++| +|+..+.- ...-|-+||.=+
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s 38 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAES 38 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHH
Confidence 4699999998 67765543 345687887433
No 71
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=44.53 E-value=13 Score=22.45 Aligned_cols=24 Identities=25% Similarity=0.635 Sum_probs=15.8
Q ss_pred CCCCCCCCCcc-cceeeecCccccc
Q psy3653 144 SLCAGCHKPIT-GRCITAMFRKFHP 167 (202)
Q Consensus 144 ~~C~~C~~~I~-~~~~~~~~~~~H~ 167 (202)
.+|..|+.||. ...+...+..-|+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCc
Confidence 46888999994 4555555556665
No 72
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=42.00 E-value=12 Score=22.99 Aligned_cols=11 Identities=27% Similarity=1.087 Sum_probs=6.5
Q ss_pred cccccccccCC
Q psy3653 35 FCAQCGKQFGE 45 (202)
Q Consensus 35 ~C~~C~~~l~~ 45 (202)
+|.+||..|..
T Consensus 11 ~CtSCg~~i~p 21 (61)
T COG2888 11 VCTSCGREIAP 21 (61)
T ss_pred eeccCCCEecc
Confidence 45666666643
No 73
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=41.65 E-value=11 Score=28.63 Aligned_cols=27 Identities=33% Similarity=0.699 Sum_probs=14.9
Q ss_pred hCcCcccch--hcccccccccccccccccccccC
Q psy3653 13 FSLRCFQKC--VTALEKTWHTEHFFCAQCGKQFG 44 (202)
Q Consensus 13 ~~~~C~~~~--~~~~~~~~H~~Cf~C~~C~~~l~ 44 (202)
.||+|..++ ..|++. =|.|..||.+|.
T Consensus 119 ~Cp~C~~rytf~eA~~~-----~F~Cp~Cg~~L~ 147 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEY-----GFRCPQCGEMLE 147 (178)
T ss_pred ECCCCCcEEeHHHHhhc-----CCcCCCCCCCCe
Confidence 467764433 334432 377777777664
No 74
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=41.27 E-value=11 Score=20.61 Aligned_cols=8 Identities=13% Similarity=0.102 Sum_probs=4.2
Q ss_pred hhCcCccc
Q psy3653 12 HFSLRCFQ 19 (202)
Q Consensus 12 ~~~~~C~~ 19 (202)
+.||+|..
T Consensus 3 i~Cp~C~~ 10 (36)
T PF13717_consen 3 ITCPNCQA 10 (36)
T ss_pred EECCCCCC
Confidence 34666643
No 75
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=40.34 E-value=27 Score=19.61 Aligned_cols=29 Identities=28% Similarity=0.581 Sum_probs=15.4
Q ss_pred cccccccccCCCc-eE-eeCCcccChhhHhh
Q psy3653 171 VCAFCLRQLNKGT-FK-EQNDKPYCHGCFEK 199 (202)
Q Consensus 171 ~C~~C~~~l~~~~-~~-~~~~~~yC~~c~~~ 199 (202)
+|+.|+++.+... .+ ..++...|..|...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 5777777776444 33 23367778877654
No 76
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=40.22 E-value=5.8 Score=30.65 Aligned_cols=45 Identities=22% Similarity=0.617 Sum_probs=34.1
Q ss_pred ccccccccccCCCceeeeCCeeeccccccccC--CCCCcccccccccc
Q psy3653 34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF--APKCGGCNRAIMEN 79 (202)
Q Consensus 34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~--~~~C~~C~~~I~~~ 79 (202)
|.|..|++...+. .+..=|..+|..|+.+.+ ++.|..|++...+.
T Consensus 197 F~C~iCKkdy~sp-vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~ 243 (259)
T COG5152 197 FLCGICKKDYESP-VVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR 243 (259)
T ss_pred eeehhchhhccch-hhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence 7888888877553 445667888999987765 57899999877654
No 77
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=39.62 E-value=18 Score=22.15 Aligned_cols=27 Identities=30% Similarity=0.899 Sum_probs=17.3
Q ss_pred cccccccccCCCc--eEeeCCcccC-hhhH
Q psy3653 171 VCAFCLRQLNKGT--FKEQNDKPYC-HGCF 197 (202)
Q Consensus 171 ~C~~C~~~l~~~~--~~~~~~~~yC-~~c~ 197 (202)
.|..|++.|..++ |+-...+.+| .+|-
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR 47 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECR 47 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHH
Confidence 4677778887443 5556667788 3554
No 78
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=39.46 E-value=24 Score=20.00 Aligned_cols=11 Identities=55% Similarity=1.525 Sum_probs=8.0
Q ss_pred CCCCCCCCccc
Q psy3653 145 LCAGCHKPITG 155 (202)
Q Consensus 145 ~C~~C~~~I~~ 155 (202)
.|.+|+++|.|
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 47788887765
No 79
>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=39.15 E-value=13 Score=21.40 Aligned_cols=14 Identities=36% Similarity=1.198 Sum_probs=7.7
Q ss_pred ccccccccccccccc
Q psy3653 28 TWHTEHFFCAQCGKQ 42 (202)
Q Consensus 28 ~~H~~Cf~C~~C~~~ 42 (202)
.|-.+ |.|..|+..
T Consensus 14 RW~~g-~~CP~Cg~~ 27 (46)
T PF12760_consen 14 RWPDG-FVCPHCGST 27 (46)
T ss_pred cCCCC-CCCCCCCCe
Confidence 34444 666667653
No 80
>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=38.91 E-value=11 Score=20.41 Aligned_cols=7 Identities=29% Similarity=0.581 Sum_probs=4.2
Q ss_pred hCcCccc
Q psy3653 13 FSLRCFQ 19 (202)
Q Consensus 13 ~~~~C~~ 19 (202)
|||+|..
T Consensus 3 FCp~C~n 9 (35)
T PF02150_consen 3 FCPECGN 9 (35)
T ss_dssp BETTTTS
T ss_pred eCCCCCc
Confidence 5666653
No 81
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=38.56 E-value=22 Score=22.31 Aligned_cols=21 Identities=33% Similarity=0.868 Sum_probs=13.3
Q ss_pred cccccccccCCCc---eEeeCCcc
Q psy3653 171 VCAFCLRQLNKGT---FKEQNDKP 191 (202)
Q Consensus 171 ~C~~C~~~l~~~~---~~~~~~~~ 191 (202)
+|+.|+..|.+|. |+..||.+
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v 28 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKV 28 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeE
Confidence 4677777776555 55556654
No 82
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=37.44 E-value=24 Score=32.73 Aligned_cols=84 Identities=21% Similarity=0.498 Sum_probs=60.1
Q ss_pred HHhhCcCcccchhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCceec
Q psy3653 10 DDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWH 89 (202)
Q Consensus 10 ~~~~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H 89 (202)
+-..|+.|..+...-.++.||=-=-.|..||-+ |...+.-||=+.-....--+.|..|.+. +-...|+.||
T Consensus 100 D~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPR-----fTIi~alPYDR~nTsM~~F~lC~~C~~E----Y~dP~nRRfH 170 (750)
T COG0068 100 DAATCEDCLEEIFDPNSRRYLYPFINCTNCGPR-----FTIIEALPYDRENTSMADFPLCPFCDKE----YKDPLNRRFH 170 (750)
T ss_pred chhhhHHHHHHhcCCCCcceeccccccCCCCcc-----eeeeccCCCCcccCccccCcCCHHHHHH----hcCccccccc
Confidence 445788898889999999999988899999654 4455555553333333333678888763 3345688999
Q ss_pred ccCCCCCCCCCCC
Q psy3653 90 STCFVCRDCKKPV 102 (202)
Q Consensus 90 ~~Cf~C~~C~~~l 102 (202)
..=..|..|+-.+
T Consensus 171 AQp~aCp~CGP~~ 183 (750)
T COG0068 171 AQPIACPKCGPHL 183 (750)
T ss_pred cccccCcccCCCe
Confidence 9999999998765
No 83
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=37.36 E-value=21 Score=20.50 Aligned_cols=11 Identities=27% Similarity=1.162 Sum_probs=7.6
Q ss_pred ccccccccccC
Q psy3653 34 FFCAQCGKQFG 44 (202)
Q Consensus 34 f~C~~C~~~l~ 44 (202)
++|..||..++
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 56788877654
No 84
>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=37.28 E-value=12 Score=20.58 Aligned_cols=9 Identities=22% Similarity=0.785 Sum_probs=5.0
Q ss_pred CCCCCCCCc
Q psy3653 145 LCAGCHKPI 153 (202)
Q Consensus 145 ~C~~C~~~I 153 (202)
+|..|++..
T Consensus 7 ~C~~Cg~~f 15 (41)
T smart00834 7 RCEDCGHTF 15 (41)
T ss_pred EcCCCCCEE
Confidence 455665544
No 85
>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=36.61 E-value=12 Score=21.14 Aligned_cols=11 Identities=18% Similarity=0.697 Sum_probs=5.1
Q ss_pred ccccccccccC
Q psy3653 170 FVCAFCLRQLN 180 (202)
Q Consensus 170 f~C~~C~~~l~ 180 (202)
|+|..|+..+.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 34555554443
No 86
>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=35.38 E-value=14 Score=27.43 Aligned_cols=27 Identities=22% Similarity=0.498 Sum_probs=16.5
Q ss_pred hCcCcccch--hcccccccccccccccccccccC
Q psy3653 13 FSLRCFQKC--VTALEKTWHTEHFFCAQCGKQFG 44 (202)
Q Consensus 13 ~~~~C~~~~--~~~~~~~~H~~Cf~C~~C~~~l~ 44 (202)
+||+|..++ ..|++. =|+|..||.+|.
T Consensus 111 ~Cp~c~~r~tf~eA~~~-----~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 111 ICPNMCVRFTFNEAMEL-----NFTCPRCGAMLD 139 (158)
T ss_pred ECCCCCcEeeHHHHHHc-----CCcCCCCCCEee
Confidence 477775433 344442 378888887774
No 87
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=34.12 E-value=25 Score=20.20 Aligned_cols=12 Identities=50% Similarity=1.176 Sum_probs=5.9
Q ss_pred CCCCCCCC-Cccc
Q psy3653 144 SLCAGCHK-PITG 155 (202)
Q Consensus 144 ~~C~~C~~-~I~~ 155 (202)
..|.+|+. +|.+
T Consensus 5 ~~C~~C~~~~i~g 17 (46)
T PF00569_consen 5 YTCDGCGTDPIIG 17 (46)
T ss_dssp CE-SSS-SSSEES
T ss_pred eECcCCCCCcCcC
Confidence 45777766 5554
No 88
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=34.11 E-value=36 Score=19.64 Aligned_cols=29 Identities=14% Similarity=0.537 Sum_probs=14.9
Q ss_pred cccccccccCCCceEe--eCCcccChhhHhh
Q psy3653 171 VCAFCLRQLNKGTFKE--QNDKPYCHGCFEK 199 (202)
Q Consensus 171 ~C~~C~~~l~~~~~~~--~~~~~yC~~c~~~ 199 (202)
.|..|+..+..-++.- ..+.-+|.+||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 3555555554322221 1235678888854
No 89
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=33.89 E-value=39 Score=19.75 Aligned_cols=11 Identities=45% Similarity=1.084 Sum_probs=7.3
Q ss_pred CCCCCCC-Cccc
Q psy3653 145 LCAGCHK-PITG 155 (202)
Q Consensus 145 ~C~~C~~-~I~~ 155 (202)
+|.+|+. ||.|
T Consensus 2 ~Cd~C~~~pI~G 13 (48)
T cd02341 2 KCDSCGIEPIPG 13 (48)
T ss_pred CCCCCCCCcccc
Confidence 4777776 6664
No 90
>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=33.74 E-value=14 Score=20.73 Aligned_cols=26 Identities=19% Similarity=0.353 Sum_probs=15.4
Q ss_pred CCCCCCCCcc-cceeee--cCcccccccc
Q psy3653 145 LCAGCHKPIT-GRCITA--MFRKFHPEHF 170 (202)
Q Consensus 145 ~C~~C~~~I~-~~~~~~--~~~~~H~~Cf 170 (202)
.|+.|.+.+. ++.+.. -+..||.+|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci 30 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCI 30 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHH
Confidence 4777777773 333222 3667777775
No 91
>KOG1813|consensus
Probab=32.70 E-value=27 Score=28.78 Aligned_cols=44 Identities=25% Similarity=0.457 Sum_probs=30.1
Q ss_pred ccccccccccCCCceeeeCCeeeccccccccC--CCCCccccccccc
Q psy3653 34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF--APKCGGCNRAIME 78 (202)
Q Consensus 34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~--~~~C~~C~~~I~~ 78 (202)
|.|..|+++..+. ....=|..+|+.|..+.+ ++.|..|++.+.+
T Consensus 242 f~c~icr~~f~~p-Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYRP-VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred ccccccccccccc-hhhcCCceeehhhhccccccCCcceeccccccc
Confidence 6677777776543 445666778888877765 3578888887754
No 92
>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=32.61 E-value=16 Score=21.36 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=6.0
Q ss_pred CCCCCCCCCc
Q psy3653 144 SLCAGCHKPI 153 (202)
Q Consensus 144 ~~C~~C~~~I 153 (202)
-+|..|+...
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 3577776644
No 93
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 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. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=32.26 E-value=9.9 Score=23.12 Aligned_cols=16 Identities=25% Similarity=1.036 Sum_probs=11.7
Q ss_pred ccccccccccCCCcee
Q psy3653 34 FFCAQCGKQFGEDGFH 49 (202)
Q Consensus 34 f~C~~C~~~l~~~~~~ 49 (202)
+.|++||+.|++..|.
T Consensus 5 lvCSTCGrDlSeeRy~ 20 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCCcchHHHHH
Confidence 5688888888776553
No 94
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=31.75 E-value=22 Score=19.29 Aligned_cols=12 Identities=42% Similarity=1.038 Sum_probs=5.2
Q ss_pred cccccccccCCC
Q psy3653 35 FCAQCGKQFGED 46 (202)
Q Consensus 35 ~C~~C~~~l~~~ 46 (202)
.|.+|++++..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 466777777654
No 95
>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=31.58 E-value=20 Score=18.75 Aligned_cols=26 Identities=27% Similarity=0.528 Sum_probs=10.6
Q ss_pred hhCcCcccchhccccccccccccccccccc
Q psy3653 12 HFSLRCFQKCVTALEKTWHTEHFFCAQCGK 41 (202)
Q Consensus 12 ~~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~ 41 (202)
-+|++|.++...+.+ -|-..| ..|+.
T Consensus 4 rfC~~CG~~t~~~~~-g~~r~C---~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPG-GWARRC---PSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-SS-SS-EEE---SSSS-
T ss_pred cccCcCCccccCCCC-cCEeEC---CCCcC
Confidence 478888765555433 344444 55543
No 96
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=31.53 E-value=10 Score=23.09 Aligned_cols=15 Identities=27% Similarity=1.092 Sum_probs=11.3
Q ss_pred ccccccccccCCCce
Q psy3653 34 FFCAQCGKQFGEDGF 48 (202)
Q Consensus 34 f~C~~C~~~l~~~~~ 48 (202)
+.|++||+.|++..|
T Consensus 5 lVCsTCGrDlSeeRy 19 (63)
T PHA03082 5 LVCSTCGRDLSEERY 19 (63)
T ss_pred eeecccCcchhHHHH
Confidence 568888888877654
No 97
>KOG0978|consensus
Probab=31.39 E-value=6.4 Score=36.25 Aligned_cols=45 Identities=24% Similarity=0.574 Sum_probs=31.6
Q ss_pred ccccccccccCCCceeeeCCeeeccccccccCC---CCCcccccccccc
Q psy3653 34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA---PKCGGCNRAIMEN 79 (202)
Q Consensus 34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~---~~C~~C~~~I~~~ 79 (202)
++|+.|+.+.-+ ..+.+=+..||..|...++. .+|+.|+.++...
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 688888866543 24456677888888877654 4788888877643
No 98
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=31.34 E-value=21 Score=16.64 Aligned_cols=12 Identities=42% Similarity=1.132 Sum_probs=7.3
Q ss_pred ccccccccccCC
Q psy3653 34 FFCAQCGKQFGE 45 (202)
Q Consensus 34 f~C~~C~~~l~~ 45 (202)
|+|..|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 456777666543
No 99
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=30.98 E-value=30 Score=28.30 Aligned_cols=28 Identities=21% Similarity=0.377 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCcccceeeecCccccccc
Q psy3653 142 RGSLCAGCHKPITGRCITAMFRKFHPEH 169 (202)
Q Consensus 142 ~~~~C~~C~~~I~~~~~~~~~~~~H~~C 169 (202)
.+..|.+|+.+|.-..+.-.+..|.|.|
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCC
Confidence 4667999999997655555555666655
No 100
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=30.75 E-value=44 Score=19.42 Aligned_cols=10 Identities=50% Similarity=0.853 Sum_probs=6.1
Q ss_pred CCCCCCCCcc
Q psy3653 145 LCAGCHKPIT 154 (202)
Q Consensus 145 ~C~~C~~~I~ 154 (202)
.|.+|.+.|.
T Consensus 2 ~Cd~C~~~~~ 11 (49)
T cd02335 2 HCDYCSKDIT 11 (49)
T ss_pred CCCCcCCCCC
Confidence 4666766654
No 101
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=30.49 E-value=1.3e+02 Score=20.28 Aligned_cols=11 Identities=36% Similarity=0.872 Sum_probs=7.8
Q ss_pred CCCCCCCCCCC
Q psy3653 92 CFVCRDCKKPV 102 (202)
Q Consensus 92 Cf~C~~C~~~l 102 (202)
-|.|..|+...
T Consensus 4 ~F~C~~CG~~V 14 (92)
T PF12647_consen 4 SFTCVHCGLTV 14 (92)
T ss_pred ccCccccCCCc
Confidence 47777777765
No 102
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=29.99 E-value=25 Score=20.80 Aligned_cols=28 Identities=29% Similarity=0.653 Sum_probs=15.0
Q ss_pred hHHhhCcCcccchhcccccccccccccccccc
Q psy3653 9 FDDHFSLRCFQKCVTALEKTWHTEHFFCAQCG 40 (202)
Q Consensus 9 ~~~~~~~~C~~~~~~~~~~~~H~~Cf~C~~C~ 40 (202)
.-+-+||||..-++.|. |.+=+-|..||
T Consensus 17 rk~~~CPrCG~gvfmA~----H~dR~~CGkCg 44 (51)
T COG1998 17 RKNRFCPRCGPGVFMAD----HKDRWACGKCG 44 (51)
T ss_pred EccccCCCCCCcchhhh----cCceeEecccc
Confidence 34567888865455443 33334455554
No 103
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=29.73 E-value=47 Score=19.25 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=6.2
Q ss_pred ccccccccccC
Q psy3653 170 FVCAFCLRQLN 180 (202)
Q Consensus 170 f~C~~C~~~l~ 180 (202)
|-|..|.+.|.
T Consensus 19 fIC~~CE~~iv 29 (46)
T PF10764_consen 19 FICSDCEKEIV 29 (46)
T ss_pred EehHHHHHHhc
Confidence 55666655554
No 104
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=29.35 E-value=70 Score=31.89 Aligned_cols=9 Identities=22% Similarity=0.759 Sum_probs=4.9
Q ss_pred CCCCCCCCc
Q psy3653 145 LCAGCHKPI 153 (202)
Q Consensus 145 ~C~~C~~~I 153 (202)
.|+.|+.++
T Consensus 711 ~CP~CGtpl 719 (1337)
T PRK14714 711 ECPRCDVEL 719 (1337)
T ss_pred cCCCCCCcc
Confidence 455555554
No 105
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=28.78 E-value=26 Score=20.93 Aligned_cols=8 Identities=50% Similarity=1.277 Sum_probs=4.1
Q ss_pred CCCCCCCc
Q psy3653 146 CAGCHKPI 153 (202)
Q Consensus 146 C~~C~~~I 153 (202)
|+-|+++|
T Consensus 3 CPyCge~~ 10 (52)
T PF14255_consen 3 CPYCGEPI 10 (52)
T ss_pred CCCCCCee
Confidence 45555554
No 106
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=28.58 E-value=44 Score=25.81 Aligned_cols=9 Identities=22% Similarity=0.914 Sum_probs=4.0
Q ss_pred ccccccccC
Q psy3653 172 CAFCLRQLN 180 (202)
Q Consensus 172 C~~C~~~l~ 180 (202)
|..|...+.
T Consensus 71 CPvCR~~Is 79 (193)
T PLN03208 71 CPVCKSDVS 79 (193)
T ss_pred CCCCCCcCC
Confidence 444444444
No 107
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.41 E-value=23 Score=20.95 Aligned_cols=11 Identities=36% Similarity=0.718 Sum_probs=8.3
Q ss_pred CCCCCCCCCCc
Q psy3653 143 GSLCAGCHKPI 153 (202)
Q Consensus 143 ~~~C~~C~~~I 153 (202)
+.+|+.|+-.|
T Consensus 24 ~irCp~Cg~rI 34 (49)
T COG1996 24 GIRCPYCGSRI 34 (49)
T ss_pred ceeCCCCCcEE
Confidence 45788888777
No 108
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=26.94 E-value=52 Score=19.36 Aligned_cols=26 Identities=12% Similarity=0.207 Sum_probs=18.8
Q ss_pred CCCCCCCCCcc---cceeeecCccccccc
Q psy3653 144 SLCAGCHKPIT---GRCITAMFRKFHPEH 169 (202)
Q Consensus 144 ~~C~~C~~~I~---~~~~~~~~~~~H~~C 169 (202)
..|+.|+.... +..+.+.+..|++.|
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeee
Confidence 46999988762 344677788888876
No 109
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=26.83 E-value=12 Score=21.49 Aligned_cols=31 Identities=13% Similarity=0.268 Sum_probs=19.1
Q ss_pred CCCCCCc---ccceeeecCcccccccccccccccccC
Q psy3653 147 AGCHKPI---TGRCITAMFRKFHPEHFVCAFCLRQLN 180 (202)
Q Consensus 147 ~~C~~~I---~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 180 (202)
++|+..| ....+...|+.|+ |.+..|...+.
T Consensus 4 Pvcg~~v~~~~~~~~~y~G~~Y~---FCS~~C~~~F~ 37 (47)
T PF04945_consen 4 PVCGMKVPGNAAYSVEYNGRTYY---FCSEGCKEKFE 37 (47)
T ss_dssp -GGG-BE-----EEEEETTEEEE---ESSHHHHHHHH
T ss_pred CCCCCEEccCccEEEEECCEEEE---EcCHHHHHHHH
Confidence 5677777 3445677888887 77777776654
No 110
>PHA00626 hypothetical protein
Probab=26.70 E-value=33 Score=20.83 Aligned_cols=38 Identities=18% Similarity=0.408 Sum_probs=18.9
Q ss_pred hCcCccc-chhcccccccccccccccccccccCCCceee
Q psy3653 13 FSLRCFQ-KCVTALEKTWHTEHFFCAQCGKQFGEDGFHE 50 (202)
Q Consensus 13 ~~~~C~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~ 50 (202)
.||+|.. .++.-.--.=+..=++|..||-..+.+.|-+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~~ 40 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFGE 40 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhhhhh
Confidence 4788854 3433111112244467777776665444433
No 111
>PRK00807 50S ribosomal protein L24e; Validated
Probab=26.57 E-value=50 Score=19.63 Aligned_cols=20 Identities=25% Similarity=0.820 Sum_probs=8.8
Q ss_pred ccccccccCCCc---eEeeCCcc
Q psy3653 172 CAFCLRQLNKGT---FKEQNDKP 191 (202)
Q Consensus 172 C~~C~~~l~~~~---~~~~~~~~ 191 (202)
|+.|+..+.++. |+..||++
T Consensus 4 C~fcG~~I~pg~G~~~vr~Dgkv 26 (52)
T PRK00807 4 CSFCGKEIEPGTGKMYVKKDGTI 26 (52)
T ss_pred cCCCCCeEcCCCCeEEEEeCCcE
Confidence 444555544222 34445544
No 112
>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=26.37 E-value=43 Score=18.13 Aligned_cols=12 Identities=33% Similarity=0.971 Sum_probs=5.6
Q ss_pred CCcccChhhHhh
Q psy3653 188 NDKPYCHGCFEK 199 (202)
Q Consensus 188 ~~~~yC~~c~~~ 199 (202)
=|..||.+|..+
T Consensus 17 CGH~fC~~C~~~ 28 (39)
T PF13923_consen 17 CGHSFCKECIEK 28 (39)
T ss_dssp TSEEEEHHHHHH
T ss_pred CCCchhHHHHHH
Confidence 344455555443
No 113
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=26.27 E-value=34 Score=31.78 Aligned_cols=82 Identities=24% Similarity=0.486 Sum_probs=51.2
Q ss_pred CCcccccccccccccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCC
Q psy3653 68 KCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCA 147 (202)
Q Consensus 68 ~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~ 147 (202)
.|..|-+.|.+. .++.|+-.=-.|+.|+-.++. -+..||=........-+.|+
T Consensus 103 ~C~~Cl~Ei~dp----~~rrY~YPF~~CT~CGPRfTI-----------------------i~alPYDR~nTsM~~F~lC~ 155 (750)
T COG0068 103 TCEDCLEEIFDP----NSRRYLYPFINCTNCGPRFTI-----------------------IEALPYDRENTSMADFPLCP 155 (750)
T ss_pred hhHHHHHHhcCC----CCcceeccccccCCCCcceee-----------------------eccCCCCcccCccccCcCCH
Confidence 577777766543 456677666679999876543 23334433333333345677
Q ss_pred CCCCCcccceeeecCcccccccccccccccccC
Q psy3653 148 GCHKPITGRCITAMFRKFHPEHFVCAFCLRQLN 180 (202)
Q Consensus 148 ~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 180 (202)
.|.+ ++-...++.||-.=..|..|+-.+.
T Consensus 156 ~C~~----EY~dP~nRRfHAQp~aCp~CGP~~~ 184 (750)
T COG0068 156 FCDK----EYKDPLNRRFHAQPIACPKCGPHLF 184 (750)
T ss_pred HHHH----HhcCccccccccccccCcccCCCeE
Confidence 7744 4446678888888888888887653
No 114
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=26.20 E-value=42 Score=31.40 Aligned_cols=84 Identities=19% Similarity=0.489 Sum_probs=55.5
Q ss_pred HHhhCcCcccchhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCceec
Q psy3653 10 DDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWH 89 (202)
Q Consensus 10 ~~~~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H 89 (202)
+-..|+-|..+...-.++.|+=-=-.|..||=+ |.....-||=..-.....-+.|..|.+...+ ..++.||
T Consensus 67 D~a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr-----~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~----p~~rr~h 137 (711)
T TIGR00143 67 DVATCSDCLEEMLDKNDRRYLYPFISCTHCGPR-----FTIIEALPYDRENTSMADFPLCPDCAKEYKD----PLDRRFH 137 (711)
T ss_pred chhhHHHHHHHhcCCCcccccCCcccccCCCCC-----eEEeecCCCCCCCcCCCCCcCCHHHHHHhcC----CccccCC
Confidence 556788898888888899999988899999754 3333333332211111122467777665432 3567788
Q ss_pred ccCCCCCCCCCCC
Q psy3653 90 STCFVCRDCKKPV 102 (202)
Q Consensus 90 ~~Cf~C~~C~~~l 102 (202)
..=..|..|+-+|
T Consensus 138 ~~~~~C~~Cgp~l 150 (711)
T TIGR00143 138 AQPIACPRCGPQL 150 (711)
T ss_pred CCCccCCCCCcEE
Confidence 8878888888776
No 115
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.10 E-value=32 Score=18.54 Aligned_cols=9 Identities=44% Similarity=1.202 Sum_probs=3.0
Q ss_pred ccccccccC
Q psy3653 36 CAQCGKQFG 44 (202)
Q Consensus 36 C~~C~~~l~ 44 (202)
|..||.+|+
T Consensus 3 C~~CG~~l~ 11 (34)
T PF14803_consen 3 CPQCGGPLE 11 (34)
T ss_dssp -TTT--B-E
T ss_pred cccccChhh
Confidence 566666663
No 116
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.02 E-value=23 Score=25.92 Aligned_cols=11 Identities=36% Similarity=1.219 Sum_probs=6.9
Q ss_pred ccccccccccC
Q psy3653 34 FFCAQCGKQFG 44 (202)
Q Consensus 34 f~C~~C~~~l~ 44 (202)
|.|..||..|.
T Consensus 124 f~Cp~Cg~~l~ 134 (147)
T smart00531 124 FTCPRCGEELE 134 (147)
T ss_pred EECCCCCCEEE
Confidence 66666666653
No 117
>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=25.35 E-value=19 Score=19.31 Aligned_cols=16 Identities=25% Similarity=0.551 Sum_probs=9.9
Q ss_pred ccccccccccCCCceE
Q psy3653 170 FVCAFCLRQLNKGTFK 185 (202)
Q Consensus 170 f~C~~C~~~l~~~~~~ 185 (202)
|.|..|++++..++|.
T Consensus 5 ~~C~nC~R~v~a~RfA 20 (33)
T PF08209_consen 5 VECPNCGRPVAASRFA 20 (33)
T ss_dssp EE-TTTSSEEEGGGHH
T ss_pred EECCCCcCCcchhhhH
Confidence 4577777777766654
No 118
>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=25.01 E-value=42 Score=23.34 Aligned_cols=29 Identities=14% Similarity=0.347 Sum_probs=19.0
Q ss_pred hCcCcccchhcccccccccccccccccccccCCC
Q psy3653 13 FSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGED 46 (202)
Q Consensus 13 ~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 46 (202)
.||+|..++.-.++.. |.|.+|+..++..
T Consensus 4 ~CP~C~seytY~dg~~-----~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQ-----LICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEecCCe-----eECcccccccccc
Confidence 4777777666655554 6777777766543
No 119
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.00 E-value=26 Score=20.93 Aligned_cols=13 Identities=23% Similarity=0.733 Sum_probs=8.4
Q ss_pred CCCcccccccccc
Q psy3653 67 PKCGGCNRAIMEN 79 (202)
Q Consensus 67 ~~C~~C~~~I~~~ 79 (202)
..|.+|+..|.+.
T Consensus 23 ~~C~gC~~~l~~~ 35 (56)
T PF02591_consen 23 GTCSGCHMELPPQ 35 (56)
T ss_pred CccCCCCEEcCHH
Confidence 4677777777643
No 120
>KOG1734|consensus
Probab=25.00 E-value=54 Score=26.78 Aligned_cols=43 Identities=28% Similarity=0.436 Sum_probs=27.0
Q ss_pred ceeecCCCccccccccccCCCCCCCCCCCccc----ce-e-----eecCccccccccc
Q psy3653 124 SFFDHEGLPYCETHYHAKRGSLCAGCHKPITG----RC-I-----TAMFRKFHPEHFV 171 (202)
Q Consensus 124 ~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~----~~-~-----~~~~~~~H~~Cf~ 171 (202)
.+++++|.|. ..+....|+.|++.|.. +. | -.-+..||..|-|
T Consensus 210 GfYs~~glPt-----khl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIr 262 (328)
T KOG1734|consen 210 GFYSPSGLPT-----KHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIR 262 (328)
T ss_pred cccCCCCCCC-----CCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhh
Confidence 4667777762 22334679999999831 11 1 2347789988764
No 121
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=24.97 E-value=50 Score=19.23 Aligned_cols=11 Identities=45% Similarity=1.063 Sum_probs=7.3
Q ss_pred CCCCCC-CCccc
Q psy3653 145 LCAGCH-KPITG 155 (202)
Q Consensus 145 ~C~~C~-~~I~~ 155 (202)
.|.+|+ .+|.|
T Consensus 2 ~C~~C~~~~i~g 13 (49)
T cd02338 2 SCDGCGKSNFTG 13 (49)
T ss_pred CCCCCcCCCcEE
Confidence 477777 56664
No 122
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=24.93 E-value=50 Score=19.13 Aligned_cols=13 Identities=38% Similarity=0.626 Sum_probs=9.3
Q ss_pred CCCCCCCCCCccc
Q psy3653 143 GSLCAGCHKPITG 155 (202)
Q Consensus 143 ~~~C~~C~~~I~~ 155 (202)
...|..|++.|.+
T Consensus 11 ~~~C~~C~~~i~g 23 (53)
T PF00130_consen 11 PTYCDVCGKFIWG 23 (53)
T ss_dssp TEB-TTSSSBECS
T ss_pred CCCCcccCcccCC
Confidence 4579999999944
No 123
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=24.81 E-value=38 Score=17.31 Aligned_cols=12 Identities=42% Similarity=1.005 Sum_probs=3.5
Q ss_pred ccccccccccCC
Q psy3653 34 FFCAQCGKQFGE 45 (202)
Q Consensus 34 f~C~~C~~~l~~ 45 (202)
|+|..|++++++
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 467777777655
No 124
>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=24.78 E-value=48 Score=16.66 Aligned_cols=8 Identities=13% Similarity=0.231 Sum_probs=3.7
Q ss_pred CcCcccch
Q psy3653 14 SLRCFQKC 21 (202)
Q Consensus 14 ~~~C~~~~ 21 (202)
||.|..++
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 45554433
No 125
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=24.64 E-value=34 Score=15.62 Aligned_cols=11 Identities=55% Similarity=1.265 Sum_probs=5.1
Q ss_pred ccccccccccC
Q psy3653 34 FFCAQCGKQFG 44 (202)
Q Consensus 34 f~C~~C~~~l~ 44 (202)
|+|..|+..+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 45666666554
No 126
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=23.98 E-value=18 Score=20.71 Aligned_cols=28 Identities=21% Similarity=0.505 Sum_probs=17.4
Q ss_pred CCCCCCCCCcc-cceeeecCcccccccccccccccccC
Q psy3653 144 SLCAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLN 180 (202)
Q Consensus 144 ~~C~~C~~~I~-~~~~~~~~~~~H~~Cf~C~~C~~~l~ 180 (202)
-+|+.|+..+. +.... =++|..|+.++.
T Consensus 4 y~C~~CG~~~~~~~~~~---------~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGT---------GVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCC---------ceECCCCCCeEE
Confidence 36888888773 22111 267888887654
No 127
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.78 E-value=34 Score=18.63 Aligned_cols=7 Identities=29% Similarity=1.032 Sum_probs=3.0
Q ss_pred Ccccccc
Q psy3653 69 CGGCNRA 75 (202)
Q Consensus 69 C~~C~~~ 75 (202)
|..|+..
T Consensus 5 CP~C~~~ 11 (37)
T PF13719_consen 5 CPNCQTR 11 (37)
T ss_pred CCCCCce
Confidence 4444443
No 128
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=23.72 E-value=32 Score=19.24 Aligned_cols=20 Identities=25% Similarity=0.351 Sum_probs=11.6
Q ss_pred CCceEeeCCcccChhhHhhh
Q psy3653 181 KGTFKEQNDKPYCHGCFEKL 200 (202)
Q Consensus 181 ~~~~~~~~~~~yC~~c~~~~ 200 (202)
++.....+-.+.|..|..++
T Consensus 25 gg~~~~~Nl~~lC~~Ch~~k 44 (47)
T PF01844_consen 25 GGKNDLENLILLCPSCHRKK 44 (47)
T ss_dssp T---STTTEEEEEHHHHHHH
T ss_pred CCCCCHHHHHHHhHHHHHHh
Confidence 33445556688888887553
No 129
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=23.56 E-value=46 Score=25.22 Aligned_cols=36 Identities=22% Similarity=0.408 Sum_probs=22.5
Q ss_pred cccccccccccccCCCceeeeCCeeeccccccccCC
Q psy3653 31 TEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA 66 (202)
Q Consensus 31 ~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 66 (202)
..|++|+.=....+...+...|-+++|+.|...+|.
T Consensus 137 ~kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClFPLF~ 172 (173)
T PF11077_consen 137 DKCVQCSQKCENVGAKIFTYFNFNLFCKNCLFPLFD 172 (173)
T ss_pred cccCcCCCCcccccceeEEecChhhcccccCccccc
Confidence 345555533233333337788889999999887763
No 130
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=23.44 E-value=13 Score=24.53 Aligned_cols=27 Identities=22% Similarity=0.651 Sum_probs=14.5
Q ss_pred cccccccccCCCceE---eeCCcc-cChhhH
Q psy3653 171 VCAFCLRQLNKGTFK---EQNDKP-YCHGCF 197 (202)
Q Consensus 171 ~C~~C~~~l~~~~~~---~~~~~~-yC~~c~ 197 (202)
.|..|++.++-..|. ..++.+ .|..|.
T Consensus 52 ~C~~C~~~k~ld~FSK~QR~~~~~a~C~~Cv 82 (84)
T PF12898_consen 52 TCSPCGKTKPLDEFSKNQRRKPDPARCKDCV 82 (84)
T ss_pred EeccCCCCcCHHHHhHHhhcCCCcccchhhh
Confidence 566666666655554 233344 666653
No 131
>KOG3002|consensus
Probab=22.75 E-value=34 Score=28.39 Aligned_cols=45 Identities=20% Similarity=0.388 Sum_probs=37.1
Q ss_pred ccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccc
Q psy3653 32 EHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIM 77 (202)
Q Consensus 32 ~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~ 77 (202)
+=|-|..|...|....|.=.+|.+.|..|-.++ ..+|..|..+|.
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~-~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKV-SNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhhh-cccCCccccccc
Confidence 346788999999888888889999999997654 358999999986
No 132
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=22.64 E-value=1.6e+02 Score=23.99 Aligned_cols=13 Identities=15% Similarity=0.376 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCcc
Q psy3653 142 RGSLCAGCHKPIT 154 (202)
Q Consensus 142 ~~~~C~~C~~~I~ 154 (202)
.+..|+.|+-+..
T Consensus 208 k~~PCPKCg~et~ 220 (314)
T PF06524_consen 208 KPIPCPKCGYETQ 220 (314)
T ss_pred CCCCCCCCCCccc
Confidence 4567999998883
No 133
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=22.55 E-value=55 Score=26.59 Aligned_cols=28 Identities=25% Similarity=0.383 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCcccceeeecCccccccc
Q psy3653 142 RGSLCAGCHKPITGRCITAMFRKFHPEH 169 (202)
Q Consensus 142 ~~~~C~~C~~~I~~~~~~~~~~~~H~~C 169 (202)
.+..|.+|+.+|.-..+.-.+..|.|.|
T Consensus 244 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQGGRSTFFCPRC 271 (274)
T ss_pred CCCCCCCCCCeeEEEEECCCCcEECcCC
Confidence 3456888888885433332333344433
No 134
>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=22.53 E-value=38 Score=17.28 Aligned_cols=24 Identities=8% Similarity=0.135 Sum_probs=10.0
Q ss_pred CCCCCCcccceeeecCcccccccc
Q psy3653 147 AGCHKPITGRCITAMFRKFHPEHF 170 (202)
Q Consensus 147 ~~C~~~I~~~~~~~~~~~~H~~Cf 170 (202)
+.|........+..-+..||..|+
T Consensus 2 ~iC~~~~~~~~~~~C~H~~c~~C~ 25 (39)
T smart00184 2 PICLEELKDPVVLPCGHTFCRSCI 25 (39)
T ss_pred CcCccCCCCcEEecCCChHHHHHH
Confidence 334444333233334445554443
No 135
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=21.83 E-value=56 Score=29.02 Aligned_cols=14 Identities=29% Similarity=0.800 Sum_probs=8.6
Q ss_pred cccccccccccccC
Q psy3653 167 PEHFVCAFCLRQLN 180 (202)
Q Consensus 167 ~~Cf~C~~C~~~l~ 180 (202)
++||.|-.|..+|.
T Consensus 50 r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 50 RNCFDCPICFSPLS 63 (483)
T ss_pred cccccCCCCCCcce
Confidence 46666666666655
No 136
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.62 E-value=59 Score=26.46 Aligned_cols=28 Identities=21% Similarity=0.551 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCcccceeeecCccccccc
Q psy3653 142 RGSLCAGCHKPITGRCITAMFRKFHPEH 169 (202)
Q Consensus 142 ~~~~C~~C~~~I~~~~~~~~~~~~H~~C 169 (202)
.+..|.+|+.+|.-..+...+..|.|.|
T Consensus 243 ~g~pCprCG~~I~~~~~~gR~t~~CP~C 270 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVAGRSSHYCPHC 270 (272)
T ss_pred CCCcCCCCCCeeEEEEECCCccEECcCC
Confidence 3567889988885433333333455444
No 137
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=21.34 E-value=61 Score=20.02 Aligned_cols=12 Identities=33% Similarity=0.492 Sum_probs=9.1
Q ss_pred CCCCCCCCCCcc
Q psy3653 143 GSLCAGCHKPIT 154 (202)
Q Consensus 143 ~~~C~~C~~~I~ 154 (202)
..+|..||++|.
T Consensus 4 PVRCFTCGkvi~ 15 (60)
T PF01194_consen 4 PVRCFTCGKVIG 15 (60)
T ss_dssp SSS-STTTSBTC
T ss_pred ceecCCCCCChh
Confidence 568999999994
No 138
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.07 E-value=80 Score=18.19 Aligned_cols=11 Identities=55% Similarity=1.407 Sum_probs=6.4
Q ss_pred CCCCCCC-Cccc
Q psy3653 145 LCAGCHK-PITG 155 (202)
Q Consensus 145 ~C~~C~~-~I~~ 155 (202)
.|.+|+. ||.|
T Consensus 2 ~Cd~C~~~pI~G 13 (45)
T cd02344 2 TCDGCQMFPING 13 (45)
T ss_pred CCCCCCCCCCcc
Confidence 4666763 5654
No 139
>PHA02929 N1R/p28-like protein; Provisional
Probab=20.98 E-value=59 Score=26.02 Aligned_cols=38 Identities=18% Similarity=0.403 Sum_probs=26.6
Q ss_pred CCCCCCCCCCcccc--------eeeecCcccccccc--------cccccccccC
Q psy3653 143 GSLCAGCHKPITGR--------CITAMFRKFHPEHF--------VCAFCLRQLN 180 (202)
Q Consensus 143 ~~~C~~C~~~I~~~--------~~~~~~~~~H~~Cf--------~C~~C~~~l~ 180 (202)
...|+.|.+++.+. .+..-+..||..|+ .|..|.+.+.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 46799999987432 23345778888887 5777777665
No 140
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=20.98 E-value=51 Score=21.85 Aligned_cols=31 Identities=23% Similarity=0.436 Sum_probs=19.0
Q ss_pred CCCCCCCCcc-cce--eeecCcccccccccccccccc
Q psy3653 145 LCAGCHKPIT-GRC--ITAMFRKFHPEHFVCAFCLRQ 178 (202)
Q Consensus 145 ~C~~C~~~I~-~~~--~~~~~~~~H~~Cf~C~~C~~~ 178 (202)
.|..|+.||. +.. +.+.|..-. |.|..|...
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~---FCC~GC~~V 35 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERP---FCCPGCQAV 35 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccc---cccHHHHHH
Confidence 5889999994 322 344454433 667777654
No 141
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=20.86 E-value=43 Score=16.26 Aligned_cols=12 Identities=50% Similarity=1.245 Sum_probs=7.5
Q ss_pred ccccccccccCC
Q psy3653 34 FFCAQCGKQFGE 45 (202)
Q Consensus 34 f~C~~C~~~l~~ 45 (202)
|+|..|++.+..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 467777766654
No 142
>PRK10445 endonuclease VIII; Provisional
Probab=20.77 E-value=62 Score=26.17 Aligned_cols=28 Identities=18% Similarity=0.319 Sum_probs=15.7
Q ss_pred CCCCCCCCCCCcccceeeecCccccccc
Q psy3653 142 RGSLCAGCHKPITGRCITAMFRKFHPEH 169 (202)
Q Consensus 142 ~~~~C~~C~~~I~~~~~~~~~~~~H~~C 169 (202)
.+..|++|+.+|.-..+.-.+..|.|.|
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~gR~t~~CP~C 261 (263)
T PRK10445 234 DGEACERCGGIIEKTTLSSRPFYWCPGC 261 (263)
T ss_pred CCCCCCCCCCEeEEEEECCCCcEECCCC
Confidence 3567888888885433333333454443
No 143
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=20.53 E-value=71 Score=31.86 Aligned_cols=23 Identities=13% Similarity=0.271 Sum_probs=15.0
Q ss_pred CccccccccccCCCCCCCCCCCc
Q psy3653 131 LPYCETHYHAKRGSLCAGCHKPI 153 (202)
Q Consensus 131 ~~~C~~~~~~~~~~~C~~C~~~I 153 (202)
...|+.|-...+..+|+.|+.+.
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCccccccCcccCCcC
Confidence 35677776665566777777664
No 144
>PRK10220 hypothetical protein; Provisional
Probab=20.44 E-value=63 Score=22.50 Aligned_cols=29 Identities=10% Similarity=0.499 Sum_probs=18.1
Q ss_pred hCcCcccchhcccccccccccccccccccccCCC
Q psy3653 13 FSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGED 46 (202)
Q Consensus 13 ~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 46 (202)
.||.|..++.-.++.. |.|.+|+..++..
T Consensus 5 ~CP~C~seytY~d~~~-----~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYEDNGM-----YICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcCCCe-----EECCcccCcCCcc
Confidence 4777766666655554 6777777666543
No 145
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.40 E-value=65 Score=26.16 Aligned_cols=25 Identities=28% Similarity=0.571 Sum_probs=14.5
Q ss_pred CCCCCCCCCCcccceeeecCccccc
Q psy3653 143 GSLCAGCHKPITGRCITAMFRKFHP 167 (202)
Q Consensus 143 ~~~C~~C~~~I~~~~~~~~~~~~H~ 167 (202)
+..|.+|+.+|.-..+.-.+..|.+
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp 259 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCP 259 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECC
Confidence 5679999999854333322333444
No 146
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.37 E-value=93 Score=16.56 Aligned_cols=23 Identities=22% Similarity=0.363 Sum_probs=13.4
Q ss_pred cccccccccCCCceeeeCCeeecccc
Q psy3653 35 FCAQCGKQFGEDGFHEKDGKPYCRDD 60 (202)
Q Consensus 35 ~C~~C~~~l~~~~~~~~~g~~yC~~c 60 (202)
+|..|+.++ .+...++..+|..|
T Consensus 5 ~C~~C~~~~---i~~~~~~~~~C~~C 27 (33)
T PF08792_consen 5 KCSKCGGNG---IVNKEDDYEVCIFC 27 (33)
T ss_pred EcCCCCCCe---EEEecCCeEEcccC
Confidence 466676654 23356666666665
No 147
>PF14149 YhfH: YhfH-like protein
Probab=20.18 E-value=13 Score=20.61 Aligned_cols=18 Identities=22% Similarity=0.416 Sum_probs=13.2
Q ss_pred cccCCCCCCCCCCCcccc
Q psy3653 139 HAKRGSLCAGCHKPITGR 156 (202)
Q Consensus 139 ~~~~~~~C~~C~~~I~~~ 156 (202)
..+....|+.||+.|.++
T Consensus 9 rnLp~K~C~~CG~~i~EQ 26 (37)
T PF14149_consen 9 RNLPPKKCTECGKEIEEQ 26 (37)
T ss_pred HhCCCcccHHHHHHHHHH
Confidence 345567899999998643
No 148
>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=20.12 E-value=67 Score=26.09 Aligned_cols=28 Identities=25% Similarity=0.503 Sum_probs=16.5
Q ss_pred CCCCCCCCCCCcccceeeecCccccccc
Q psy3653 142 RGSLCAGCHKPITGRCITAMFRKFHPEH 169 (202)
Q Consensus 142 ~~~~C~~C~~~I~~~~~~~~~~~~H~~C 169 (202)
.+..|.+|+.+|.-..+.-.+..|.|.|
T Consensus 244 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 244 KGEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 3557999999985433333333455544
Done!