Query psy8131
Match_columns 198
No_of_seqs 232 out of 1576
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 19:23:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8131.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8131hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 100.0 7.8E-39 1.7E-43 262.1 2.5 165 1-197 291-463 (468)
2 KOG2272|consensus 100.0 8.2E-37 1.8E-41 235.0 -5.4 162 1-197 29-253 (332)
3 KOG2272|consensus 100.0 4.9E-31 1.1E-35 203.2 -0.3 159 1-195 152-311 (332)
4 KOG1703|consensus 99.9 8.4E-29 1.8E-33 214.6 4.2 160 1-193 319-478 (479)
5 KOG1044|consensus 99.9 2.3E-27 5E-32 200.8 2.9 159 1-194 80-248 (670)
6 KOG1701|consensus 99.9 2.4E-25 5.2E-30 183.0 -2.6 105 88-197 288-393 (468)
7 KOG1044|consensus 99.9 3.8E-23 8.2E-28 175.4 4.3 152 1-197 31-191 (670)
8 KOG1703|consensus 99.9 1.1E-22 2.3E-27 176.6 4.8 160 3-197 260-421 (479)
9 KOG4577|consensus 99.8 8.8E-23 1.9E-27 160.3 -4.2 109 85-196 42-153 (383)
10 KOG4577|consensus 99.7 4E-19 8.7E-24 139.8 -1.3 108 2-139 50-159 (383)
11 PF00412 LIM: LIM domain; Int 99.5 6E-15 1.3E-19 92.0 2.8 58 138-197 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.5 5.2E-14 1.1E-18 87.8 4.0 50 85-134 7-58 (58)
13 KOG1700|consensus 99.3 1.6E-13 3.5E-18 106.1 0.1 106 90-198 22-168 (200)
14 KOG1700|consensus 99.2 2.9E-12 6.2E-17 99.2 1.1 131 3-133 25-166 (200)
15 smart00132 LIM Zinc-binding do 98.8 5.8E-09 1.3E-13 59.1 3.4 38 137-176 1-38 (39)
16 smart00132 LIM Zinc-binding do 98.5 9.3E-08 2E-12 54.0 2.5 25 89-113 14-38 (39)
17 KOG0490|consensus 97.2 3.8E-05 8.2E-10 60.7 -1.9 100 92-195 13-118 (235)
18 KOG0490|consensus 96.8 0.00018 3.9E-09 56.8 -1.3 99 3-132 14-118 (235)
19 KOG1702|consensus 96.4 0.00032 6.9E-09 53.7 -2.0 44 2-45 21-64 (264)
20 KOG1702|consensus 96.2 0.00045 9.8E-09 52.9 -2.3 58 136-196 5-62 (264)
21 PF14446 Prok-RING_1: Prokaryo 91.7 0.11 2.3E-06 31.4 1.4 39 135-175 5-51 (54)
22 PF14634 zf-RING_5: zinc-RING 87.5 0.9 2E-05 26.0 3.1 39 105-143 2-44 (44)
23 PF14835 zf-RING_6: zf-RING of 86.5 0.67 1.5E-05 29.1 2.2 46 103-148 8-53 (65)
24 PF08394 Arc_trans_TRASH: Arch 84.1 0.64 1.4E-05 25.8 1.2 33 138-175 1-33 (37)
25 PF10367 Vps39_2: Vacuolar sor 81.1 1.4 3E-05 30.0 2.4 29 136-166 79-107 (109)
26 PF11781 RRN7: RNA polymerase 79.7 1.1 2.4E-05 24.7 1.2 25 13-41 9-33 (36)
27 PF01258 zf-dskA_traR: Prokary 79.2 0.4 8.6E-06 26.3 -0.8 29 15-43 6-34 (36)
28 PF10367 Vps39_2: Vacuolar sor 78.7 1.2 2.6E-05 30.4 1.4 28 14-41 80-108 (109)
29 PF14471 DUF4428: Domain of un 78.1 1.8 3.9E-05 25.9 1.8 29 14-43 1-30 (51)
30 PF10235 Cript: Microtubule-as 77.3 1.7 3.6E-05 29.3 1.6 43 97-147 39-81 (90)
31 PF13920 zf-C3HC4_3: Zinc fing 75.5 3.1 6.8E-05 24.3 2.4 43 104-147 4-49 (50)
32 cd00162 RING RING-finger (Real 75.5 4.1 8.9E-05 22.3 2.9 40 105-144 2-44 (45)
33 PF06677 Auto_anti-p27: Sjogre 75.0 1.3 2.8E-05 25.2 0.6 22 14-39 19-40 (41)
34 COG2191 Formylmethanofuran deh 74.0 1.1 2.5E-05 34.6 0.2 31 103-133 173-203 (206)
35 smart00504 Ubox Modified RING 72.9 8.5 0.00018 23.3 4.0 44 103-147 2-47 (63)
36 PF14835 zf-RING_6: zf-RING of 71.8 3.9 8.5E-05 25.7 2.2 42 13-54 8-49 (65)
37 COG1645 Uncharacterized Zn-fin 69.4 2.6 5.6E-05 30.4 1.2 22 14-40 30-51 (131)
38 PF02069 Metallothio_Pro: Prok 67.8 3.7 7.9E-05 24.6 1.4 29 14-42 9-38 (52)
39 PF06906 DUF1272: Protein of u 67.8 11 0.00024 22.9 3.5 44 104-147 7-53 (57)
40 KOG4739|consensus 66.4 4.7 0.0001 32.0 2.2 43 105-147 6-49 (233)
41 cd02249 ZZ Zinc finger, ZZ typ 65.1 4.1 8.8E-05 23.5 1.2 11 137-147 2-12 (46)
42 COG2191 Formylmethanofuran deh 63.0 3.9 8.4E-05 31.7 1.1 31 166-196 173-203 (206)
43 PF13240 zinc_ribbon_2: zinc-r 62.3 6.5 0.00014 19.2 1.5 9 138-146 2-10 (23)
44 PF10886 DUF2685: Protein of u 61.9 6.2 0.00013 23.8 1.6 25 136-163 2-26 (54)
45 PF11571 Med27: Mediator compl 61.3 4 8.8E-05 27.3 0.9 16 130-145 49-64 (90)
46 COG1645 Uncharacterized Zn-fin 60.6 6.3 0.00014 28.4 1.8 21 168-193 31-51 (131)
47 COG2888 Predicted Zn-ribbon RN 60.3 7.6 0.00017 23.9 1.8 10 45-54 9-18 (61)
48 KOG1813|consensus 59.9 5.1 0.00011 32.9 1.3 44 103-147 242-287 (313)
49 smart00291 ZnF_ZZ Zinc-binding 59.2 6.4 0.00014 22.5 1.4 12 136-147 5-16 (44)
50 PRK00807 50S ribosomal protein 58.7 6.7 0.00015 23.5 1.4 37 136-175 2-38 (52)
51 PF12773 DZR: Double zinc ribb 57.7 13 0.00027 21.6 2.5 10 137-146 31-40 (50)
52 PLN03208 E3 ubiquitin-protein 57.2 20 0.00044 27.6 4.1 45 102-147 18-80 (193)
53 KOG0320|consensus 54.1 12 0.00025 28.5 2.3 48 100-147 129-179 (187)
54 COG5152 Uncharacterized conser 54.0 5.6 0.00012 30.7 0.6 41 13-54 197-239 (259)
55 PF12674 Zn_ribbon_2: Putative 53.3 4.4 9.6E-05 26.7 0.0 29 167-195 2-35 (81)
56 PF01286 XPA_N: XPA protein N- 53.3 5.4 0.00012 21.7 0.3 25 168-192 6-30 (34)
57 COG5152 Uncharacterized conser 52.7 5.7 0.00012 30.7 0.5 44 103-147 197-242 (259)
58 PF13923 zf-C3HC4_2: Zinc fing 51.6 13 0.00028 20.3 1.8 31 15-45 1-31 (39)
59 PF13248 zf-ribbon_3: zinc-rib 51.4 12 0.00026 18.7 1.5 10 137-146 4-13 (26)
60 PRK14891 50S ribosomal protein 51.4 11 0.00025 26.9 1.8 27 136-162 5-31 (131)
61 cd00472 Ribosomal_L24e_L24 Rib 51.1 11 0.00024 22.7 1.5 27 136-162 4-30 (54)
62 cd02341 ZZ_ZZZ3 Zinc finger, Z 51.1 10 0.00023 22.2 1.4 11 137-147 2-13 (48)
63 PF07649 C1_3: C1-like domain; 50.6 7.5 0.00016 20.1 0.6 12 13-24 1-12 (30)
64 PF09943 DUF2175: Uncharacteri 50.2 5.1 0.00011 27.5 -0.1 29 137-167 4-32 (101)
65 PF13834 DUF4193: Domain of un 49.7 4.9 0.00011 27.4 -0.2 29 11-39 69-98 (99)
66 PF07191 zinc-ribbons_6: zinc- 49.5 4.9 0.00011 25.7 -0.2 39 13-56 2-41 (70)
67 COG2075 RPL24A Ribosomal prote 49.4 11 0.00024 23.6 1.4 27 136-162 4-30 (66)
68 cd02340 ZZ_NBR1_like Zinc fing 49.3 12 0.00026 21.3 1.4 11 137-147 2-12 (43)
69 PF04570 DUF581: Protein of un 49.1 8.9 0.00019 23.5 0.9 27 14-40 18-47 (58)
70 cd02336 ZZ_RSC8 Zinc finger, Z 48.9 12 0.00026 21.6 1.4 29 167-195 2-32 (45)
71 COG4847 Uncharacterized protei 47.8 6.1 0.00013 26.7 -0.0 29 137-167 8-36 (103)
72 PRK00420 hypothetical protein; 47.8 16 0.00034 25.7 2.1 13 135-147 23-35 (112)
73 PF09723 Zn-ribbon_8: Zinc rib 47.5 7.1 0.00015 22.1 0.3 29 166-194 6-34 (42)
74 PF00569 ZZ: Zinc finger, ZZ t 46.3 14 0.00031 21.2 1.4 30 13-42 5-37 (46)
75 PF12677 DUF3797: Domain of un 46.1 18 0.00038 21.3 1.7 29 136-165 14-42 (49)
76 PF09943 DUF2175: Uncharacteri 45.9 13 0.00029 25.5 1.4 32 103-134 3-35 (101)
77 KOG0320|consensus 45.6 14 0.00031 28.1 1.6 45 10-54 129-176 (187)
78 PF10083 DUF2321: Uncharacteri 45.2 19 0.00041 26.7 2.2 51 122-175 27-78 (158)
79 PF07754 DUF1610: Domain of un 44.1 17 0.00037 18.1 1.3 10 138-147 1-10 (24)
80 PRK14890 putative Zn-ribbon RN 43.6 19 0.00041 22.2 1.7 30 103-142 26-55 (59)
81 PF00645 zf-PARP: Poly(ADP-rib 43.3 3.6 7.8E-05 26.8 -1.6 12 136-147 8-19 (82)
82 smart00834 CxxC_CXXC_SSSS Puta 41.5 9.3 0.0002 21.0 0.1 8 137-144 7-14 (41)
83 cd02342 ZZ_UBA_plant Zinc fing 41.3 24 0.00052 20.3 1.8 29 14-42 2-33 (43)
84 smart00659 RPOLCX RNA polymera 40.7 18 0.00038 20.8 1.2 25 166-194 3-27 (44)
85 KOG0978|consensus 39.6 11 0.00024 34.7 0.4 43 13-56 644-689 (698)
86 KOG0978|consensus 38.8 12 0.00026 34.5 0.5 44 103-147 644-690 (698)
87 PF06827 zf-FPG_IleRS: Zinc fi 38.5 11 0.00023 19.5 0.0 12 136-147 2-13 (30)
88 PF08271 TF_Zn_Ribbon: TFIIB z 37.9 16 0.00035 20.6 0.8 25 13-39 1-25 (43)
89 PRK00398 rpoP DNA-directed RNA 37.7 13 0.00028 21.4 0.3 27 137-175 5-31 (46)
90 KOG3002|consensus 36.9 35 0.00075 28.3 2.8 45 102-147 48-92 (299)
91 cd02338 ZZ_PCMF_like Zinc fing 36.3 22 0.00047 20.8 1.2 11 137-147 2-13 (49)
92 TIGR02605 CxxC_CxxC_SSSS putat 36.2 13 0.00029 21.7 0.2 9 137-145 7-15 (52)
93 PF01246 Ribosomal_L24e: Ribos 36.1 15 0.00033 23.5 0.5 27 136-162 4-30 (71)
94 cd02335 ZZ_ADA2 Zinc finger, Z 34.5 36 0.00077 19.8 1.9 13 13-25 1-13 (49)
95 PF00096 zf-C2H2: Zinc finger, 34.4 11 0.00023 17.8 -0.3 12 13-24 1-12 (23)
96 PF13894 zf-C2H2_4: C2H2-type 34.0 15 0.00032 17.0 0.1 12 13-24 1-12 (24)
97 KOG1813|consensus 32.8 25 0.00054 29.0 1.3 47 7-55 237-285 (313)
98 PRK11595 DNA utilization prote 32.7 49 0.0011 26.0 3.0 37 104-146 7-45 (227)
99 smart00746 TRASH metallochaper 31.3 54 0.0012 16.2 2.2 25 138-162 1-25 (39)
100 PF10080 DUF2318: Predicted me 30.5 36 0.00078 23.4 1.6 25 167-195 37-61 (102)
101 PRK14559 putative protein seri 30.1 47 0.001 30.7 2.7 37 104-147 3-39 (645)
102 cd02344 ZZ_HERC2 Zinc finger, 30.1 36 0.00077 19.7 1.3 11 137-147 2-13 (45)
103 PF08209 Sgf11: Sgf11 (transcr 29.5 7.2 0.00016 21.0 -1.5 17 13-29 5-21 (33)
104 PF01927 Mut7-C: Mut7-C RNAse 29.0 28 0.0006 25.4 0.9 40 136-175 92-134 (147)
105 TIGR00570 cdk7 CDK-activating 28.8 77 0.0017 26.4 3.5 44 104-147 5-55 (309)
106 PRK12495 hypothetical protein; 28.3 33 0.00071 27.0 1.3 27 10-41 40-66 (226)
107 PF06689 zf-C4_ClpX: ClpX C4-t 27.1 35 0.00076 19.1 0.9 28 167-194 3-32 (41)
108 PF00097 zf-C3HC4: Zinc finger 26.8 60 0.0013 17.5 1.9 31 15-45 1-31 (41)
109 KOG2879|consensus 26.8 70 0.0015 26.2 2.9 44 13-56 240-287 (298)
110 KOG2932|consensus 26.7 32 0.00068 28.7 1.0 44 104-147 92-135 (389)
111 PF03107 C1_2: C1 domain; Int 26.4 45 0.00097 17.2 1.2 13 13-25 1-13 (30)
112 PRK00085 recO DNA repair prote 26.3 31 0.00067 27.2 0.8 31 10-40 147-177 (247)
113 PLN03208 E3 ubiquitin-protein 25.5 56 0.0012 25.3 2.1 27 136-166 19-45 (193)
114 KOG2893|consensus 25.5 21 0.00046 28.5 -0.2 35 135-175 10-44 (341)
115 PF14569 zf-UDP: Zinc-binding 25.2 64 0.0014 21.0 2.0 43 104-146 11-62 (80)
116 PF12855 Ecl1: Life-span regul 25.0 29 0.00062 19.9 0.3 22 15-40 9-31 (43)
117 cd02345 ZZ_dah Zinc finger, ZZ 24.5 36 0.00077 19.9 0.7 11 137-147 2-13 (49)
118 PF12171 zf-C2H2_jaz: Zinc-fin 24.5 43 0.00093 16.5 0.9 13 13-25 2-14 (27)
119 PF08792 A2L_zn_ribbon: A2L zi 24.4 48 0.001 17.7 1.1 23 14-39 5-27 (33)
120 smart00184 RING Ring finger. E 24.2 1.1E+02 0.0024 15.3 2.8 14 120-133 15-28 (39)
121 TIGR00595 priA primosomal prot 24.0 49 0.0011 29.5 1.7 28 117-144 234-262 (505)
122 PF05502 Dynactin_p62: Dynacti 23.9 54 0.0012 29.1 2.0 61 31-113 3-63 (483)
123 KOG3002|consensus 23.8 63 0.0014 26.8 2.2 43 13-56 49-91 (299)
124 PHA02610 uvsY.-2 hypothetical 23.6 62 0.0013 19.3 1.5 25 136-163 2-26 (53)
125 PF13639 zf-RING_2: Ring finge 23.6 17 0.00037 20.3 -0.8 29 137-166 2-30 (44)
126 PF14570 zf-RING_4: RING/Ubox 23.0 1E+02 0.0022 18.1 2.4 23 122-144 21-46 (48)
127 cd02334 ZZ_dystrophin Zinc fin 22.9 47 0.001 19.5 1.0 11 137-147 2-13 (49)
128 PF12156 ATPase-cat_bd: Putati 22.9 80 0.0017 20.9 2.2 34 137-174 2-35 (88)
129 PF05864 Chordopox_RPO7: Chord 22.5 20 0.00044 21.9 -0.7 16 13-28 5-20 (63)
130 TIGR02098 MJ0042_CXXC MJ0042 f 22.5 30 0.00065 18.7 0.1 10 166-175 26-35 (38)
131 PF12874 zf-met: Zinc-finger o 22.4 24 0.00051 16.9 -0.3 12 13-24 1-12 (25)
132 PHA03082 DNA-dependent RNA pol 22.3 20 0.00043 21.9 -0.7 16 13-28 5-20 (63)
133 PRK14873 primosome assembly pr 22.1 52 0.0011 30.5 1.6 38 104-144 394-431 (665)
134 PF02591 DUF164: Putative zinc 21.4 25 0.00053 21.1 -0.5 26 14-39 24-52 (56)
135 PF13912 zf-C2H2_6: C2H2-type 21.2 26 0.00056 17.1 -0.3 12 13-24 2-13 (27)
136 COG4357 Zinc finger domain con 21.1 7.2 0.00016 26.5 -3.1 12 136-147 63-74 (105)
137 PRK00085 recO DNA repair prote 20.9 56 0.0012 25.7 1.4 28 166-193 150-177 (247)
138 PF10764 Gin: Inhibitor of sig 20.8 49 0.0011 19.2 0.7 10 166-175 19-28 (46)
139 PF00130 C1_1: Phorbol esters/ 20.7 65 0.0014 18.6 1.3 12 136-147 12-23 (53)
140 KOG2462|consensus 20.6 52 0.0011 26.9 1.1 27 100-126 128-154 (279)
141 smart00355 ZnF_C2H2 zinc finge 20.2 59 0.0013 14.9 0.9 12 13-24 1-12 (26)
142 PF13719 zinc_ribbon_5: zinc-r 20.1 45 0.00098 18.2 0.5 25 168-192 5-31 (37)
143 COG4306 Uncharacterized protei 20.1 1.1E+02 0.0024 21.9 2.5 50 124-175 29-78 (160)
No 1
>KOG1701|consensus
Probab=100.00 E-value=7.8e-39 Score=262.11 Aligned_cols=165 Identities=29% Similarity=0.708 Sum_probs=151.7
Q ss_pred CccCCcccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhhcccccccccccccccccccccccCCcccccceeeee
Q psy8131 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSILFY 80 (198)
Q Consensus 1 ~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (198)
+++|++.||.+||+|..|++.|.++.||..|+++||+.||... ..+|..|++
T Consensus 291 c~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~--------------------------- 342 (468)
T KOG1701|consen 291 VEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGE--------------------------- 342 (468)
T ss_pred HHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhh---------------------------
Confidence 3689999999999999999999999999999999999999886 569999999
Q ss_pred eeeeeeccCceEeCCcCccccCCCCccCcCCCCCCceeec-CCcccchhhHhhhhccCCCCCCCCCcCCCCc---eEEee
Q psy8131 81 FLFQIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSR-EDKPFCADCFGELFAKRCYSCKKPITGIGGT---RFISF 156 (198)
Q Consensus 81 ~~~~~i~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~-~g~~yC~~c~~~~~~~~C~~C~~~I~~~~~~---~~~~~ 156 (198)
+|.+..+.+.|+.||+.||+|..|++.|++..|.++ ++++||.+||+++|+++|+.|++||.+.+|. ..|++
T Consensus 343 ----~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvva 418 (468)
T KOG1701|consen 343 ----PIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVA 418 (468)
T ss_pred ----HHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEE
Confidence 777888899999999999999999999999999876 6999999999999999999999999876544 35789
Q ss_pred CCCcccccCcccCcCCCCCC----CCceEecCCceeCcccccccC
Q psy8131 157 EDRHWHNDCFMCASCQSSLV----GRGFITDGEDIICPDCAKAKL 197 (198)
Q Consensus 157 ~~~~~H~~Cf~C~~C~~~l~----~~~~~~~~~~~~C~~C~~~~~ 197 (198)
+++.||.+|++|..|+..|+ +...+..|+.++|+.|..+++
T Consensus 419 mdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl 463 (468)
T KOG1701|consen 419 MDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRL 463 (468)
T ss_pred ccccccccceehhhcCccccccCCCCcceeccCceeechhhhhhh
Confidence 99999999999999999995 567899999999999988765
No 2
>KOG2272|consensus
Probab=100.00 E-value=8.2e-37 Score=235.04 Aligned_cols=162 Identities=28% Similarity=0.682 Sum_probs=141.5
Q ss_pred CccCCcccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhhcccccccccccccccccccccccCCcccccceeeee
Q psy8131 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSILFY 80 (198)
Q Consensus 1 ~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (198)
|..+|..||.+||+|++|..||.++.|++.+|+.||+.++..+|+|.|.+|++
T Consensus 29 vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~E--------------------------- 81 (332)
T KOG2272|consen 29 VNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGE--------------------------- 81 (332)
T ss_pred hccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhccccc---------------------------
Confidence 35689999999999999999999999999999999999999999999999999
Q ss_pred eeeeeeccCceEeCCcCccccCCCCccCcCCCCCCceeecC---------------------------------------
Q psy8131 81 FLFQIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSRE--------------------------------------- 121 (198)
Q Consensus 81 ~~~~~i~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~--------------------------------------- 121 (198)
.|-+++|.+++..|||.||+|..|++.|.+..|+-..
T Consensus 82 ----FiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d 157 (332)
T KOG2272|consen 82 ----FIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGD 157 (332)
T ss_pred ----chhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCC
Confidence 5567778888999999999888888877655443333
Q ss_pred ------------------------CcccchhhHhhhhccCCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCCCC
Q psy8131 122 ------------------------DKPFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVG 177 (198)
Q Consensus 122 ------------------------g~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 177 (198)
|.+||.+|+++.--|+|..|.+||.+ ++|.++|+.||.++|+|+.|.+|+-|
T Consensus 158 ~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIee----rvi~amgKhWHveHFvCa~CekPFlG 233 (332)
T KOG2272|consen 158 PYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEE----RVIFAMGKHWHVEHFVCAKCEKPFLG 233 (332)
T ss_pred CCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHH----HHHHHhccccchhheeehhcCCcccc
Confidence 45566666655556899999999986 78999999999999999999999999
Q ss_pred CceEecCCceeCcccccccC
Q psy8131 178 RGFITDGEDIICPDCAKAKL 197 (198)
Q Consensus 178 ~~~~~~~~~~~C~~C~~~~~ 197 (198)
-+.+...|.+||+++|.++|
T Consensus 234 HrHYEkkGlaYCe~h~~qLf 253 (332)
T KOG2272|consen 234 HRHYEKKGLAYCETHYHQLF 253 (332)
T ss_pred hhhhhhcCchhHHHHHHHHh
Confidence 99999999999999998876
No 3
>KOG2272|consensus
Probab=99.96 E-value=4.9e-31 Score=203.21 Aligned_cols=159 Identities=23% Similarity=0.643 Sum_probs=147.2
Q ss_pred CccCCcccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhhcccccccccccccccccccccccCCcccccceeeee
Q psy8131 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSILFY 80 (198)
Q Consensus 1 ~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (198)
|.+.|..||+-+|+|+.|++.|.+..- +..|++||..|+++.--|.|..|.+
T Consensus 152 l~fr~d~yH~yHFkCt~C~keL~sdaR-evk~eLyClrChD~mgipiCgaC~r--------------------------- 203 (332)
T KOG2272|consen 152 LTFRGDPYHPYHFKCTTCGKELTSDAR-EVKGELYCLRCHDKMGIPICGACRR--------------------------- 203 (332)
T ss_pred ccccCCCCCccceecccccccccchhh-hhccceeccccccccCCcccccccC---------------------------
Confidence 457889999999999999999997543 6778999999999998999999999
Q ss_pred eeeeeeccCceEeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcCCCCceEEeeCCCc
Q psy8131 81 FLFQIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRH 160 (198)
Q Consensus 81 ~~~~~i~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~~ 160 (198)
+|++++|.++|+.||.++|+|+.|.+|+-+-..+++.|..||+.+|.++|+..|..|+++|.+ .++++.++.
T Consensus 204 ----pIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G----~vv~al~Ka 275 (332)
T KOG2272|consen 204 ----PIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGG----DVVSALNKA 275 (332)
T ss_pred ----chHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCc----cHHHHhhhh
Confidence 788889999999999999999999999977779999999999999999999999999999987 678999999
Q ss_pred ccccCcccCcCCCCC-CCCceEecCCceeCcccccc
Q psy8131 161 WHNDCFMCASCQSSL-VGRGFITDGEDIICPDCAKA 195 (198)
Q Consensus 161 ~H~~Cf~C~~C~~~l-~~~~~~~~~~~~~C~~C~~~ 195 (198)
|-++||+|+.|++.| ....|+..|-.|.|+.||++
T Consensus 276 wCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 276 WCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred hccccccccccccccccccceeeeccchHHHHHHhh
Confidence 999999999999999 46689999999999999973
No 4
>KOG1703|consensus
Probab=99.95 E-value=8.4e-29 Score=214.57 Aligned_cols=160 Identities=30% Similarity=0.733 Sum_probs=150.6
Q ss_pred CccCCcccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhhcccccccccccccccccccccccCCcccccceeeee
Q psy8131 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSILFY 80 (198)
Q Consensus 1 ~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (198)
+.++++.||+.+|.|..|...+....+.+.+|.+||..|+...++|+|.+|+.
T Consensus 319 i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~--------------------------- 371 (479)
T KOG1703|consen 319 IVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLL--------------------------- 371 (479)
T ss_pred EeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCC---------------------------
Confidence 35689999999999999999999999999999999999999999999999999
Q ss_pred eeeeeeccCceEeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcCCCCceEEeeCCCc
Q psy8131 81 FLFQIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRH 160 (198)
Q Consensus 81 ~~~~~i~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~~ 160 (198)
+|.+..|.+.++.||++||.|..|+++|.+..|++.++.+||+.||.+++.++|..|.++|.. ++..+.+.+..
T Consensus 372 ----~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~--~~~~ie~~~~~ 445 (479)
T KOG1703|consen 372 ----PILEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEF--GSRQIEADGSP 445 (479)
T ss_pred ----chHHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHh--hhhHhhccCcc
Confidence 677778888899999999999999999999999999999999999999999999999999874 24789999999
Q ss_pred ccccCcccCcCCCCCCCCceEecCCceeCcccc
Q psy8131 161 WHNDCFMCASCQSSLVGRGFITDGEDIICPDCA 193 (198)
Q Consensus 161 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~C~ 193 (198)
||..||+|+.|.+.|.++.|+...++++|..|+
T Consensus 446 ~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 446 FHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred ccccceehhhhhccccCCceeecCCccccccCC
Confidence 999999999999999999999999999999985
No 5
>KOG1044|consensus
Probab=99.93 E-value=2.3e-27 Score=200.83 Aligned_cols=159 Identities=27% Similarity=0.764 Sum_probs=139.7
Q ss_pred CccCCcccCcCCcccCCCCCCCCCCC-cccCCCeecchhhHHhh-------hc-ccccccccccccccccccccccCCcc
Q psy8131 1 MEYKTRQWHEKCFACVVCKTPIGTKS-FIPREQEIYCANCYEEK-------FA-TRCVKCNKTFFRLREKGTFQSHSGRI 71 (198)
Q Consensus 1 ~~~~~~~~H~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~cy~~~-------~~-~~C~~C~~~~~~~~~~~~~~~~~~~~ 71 (198)
|.++|++||+.||+|++|+.++.... ...-+....|+.|..-. .. ..|++|++.
T Consensus 80 vsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~----------------- 142 (670)
T KOG1044|consen 80 VSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEE----------------- 142 (670)
T ss_pred EecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhh-----------------
Confidence 46899999999999999999998643 33456677888887432 12 268888884
Q ss_pred cccceeeeeeeeeeeccCceEeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcCCCCc
Q psy8131 72 NKVYSILFYFLFQIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGIGGT 151 (198)
Q Consensus 72 ~~~~~~~~~~~~~~i~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~~~ 151 (198)
+..++.+.+++++||..||+|..|...|.++ +..+||.+||+.||.+.|+.+|..|.+.|.+
T Consensus 143 -------------lk~gq~llald~qwhv~cfkc~~c~~vL~ge-y~skdg~pyce~dy~~~fgvkc~~c~~fisg---- 204 (670)
T KOG1044|consen 143 -------------LKNGQALLALDKQWHVSCFKCKSCSAVLNGE-YMSKDGVPYCEKDYQAKFGVKCEECEKFISG---- 204 (670)
T ss_pred -------------hhccceeeeeccceeeeeeehhhhcccccce-eeccCCCcchhhhhhhhcCeehHHhhhhhhh----
Confidence 5678889999999999999999999999877 9999999999999999999999999999998
Q ss_pred eEEeeCCCcccccCcccCcCCCCC-CCCceEecCCceeCccccc
Q psy8131 152 RFISFEDRHWHNDCFMCASCQSSL-VGRGFITDGEDIICPDCAK 194 (198)
Q Consensus 152 ~~~~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~~~~~C~~C~~ 194 (198)
+++.|.|++||+.|.+|+.|+..+ .|+++++.+..+|-..|-.
T Consensus 205 kvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 205 KVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred hhhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence 789999999999999999999999 7999999999999888854
No 6
>KOG1701|consensus
Probab=99.89 E-value=2.4e-25 Score=183.02 Aligned_cols=105 Identities=30% Similarity=0.747 Sum_probs=97.9
Q ss_pred cCceEeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcCCCCceEEeeCCCcccccCcc
Q psy8131 88 SGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRHWHNDCFM 167 (198)
Q Consensus 88 ~~~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~ 167 (198)
+..++++++.||..||+|..|++.|.++.||..|+++||+.||... ..+|..|+++|.+ +++.|.|+.||+.||+
T Consensus 288 ~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d----~iLrA~GkayHp~CF~ 362 (468)
T KOG1701|consen 288 GLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMD----RILRALGKAYHPGCFT 362 (468)
T ss_pred chHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHH----HHHHhcccccCCCceE
Confidence 4477899999999999999999999999999999999999999664 6999999999997 8999999999999999
Q ss_pred cCcCCCCCCCCceEec-CCceeCcccccccC
Q psy8131 168 CASCQSSLVGRGFITD-GEDIICPDCAKAKL 197 (198)
Q Consensus 168 C~~C~~~l~~~~~~~~-~~~~~C~~C~~~~~ 197 (198)
|..|++.|+|..|.++ ++++||..+|-++|
T Consensus 363 Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kf 393 (468)
T KOG1701|consen 363 CVVCARCLDGIPFTVDSQNNVYCVPDFHKKF 393 (468)
T ss_pred EEEeccccCCccccccCCCceeeehhhhhhc
Confidence 9999999999999987 77999999998775
No 7
>KOG1044|consensus
Probab=99.87 E-value=3.8e-23 Score=175.42 Aligned_cols=152 Identities=22% Similarity=0.612 Sum_probs=127.2
Q ss_pred CccCCcccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhhcccccccccccccccccccccccCCcccccceeeee
Q psy8131 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSILFY 80 (198)
Q Consensus 1 ~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (198)
|.+.++.||..||+|..|+..|+...|+.++++ +++++ ..|.+
T Consensus 31 lrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~--------------------------- 73 (670)
T KOG1044|consen 31 LRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRA--------------------------- 73 (670)
T ss_pred eEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhh---------------------------
Confidence 467899999999999999999999999988776 33343 55666
Q ss_pred eeeeeeccCceEeCCcCccccCCCCccCcCCC-CCCceeecCCcccchhhHhhh--------hccCCCCCCCCCcCCCCc
Q psy8131 81 FLFQIITSGGVTYKNEPWHRECFTCSNCSTSL-AGQRFTSREDKPFCADCFGEL--------FAKRCYSCKKPITGIGGT 151 (198)
Q Consensus 81 ~~~~~i~~~~~~~~~~~~H~~CF~C~~C~~~l-~~~~~~~~~g~~yC~~c~~~~--------~~~~C~~C~~~I~~~~~~ 151 (198)
.+++..|.++|++||++||.|+.|+.|+ .+...........|+.|..-. .-..|++|++.|..+
T Consensus 74 ----~~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~g--- 146 (670)
T KOG1044|consen 74 ----FVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNG--- 146 (670)
T ss_pred ----hccceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhcc---
Confidence 7788889999999999999999999999 455555666778899886321 124799999999763
Q ss_pred eEEeeCCCcccccCcccCcCCCCCCCCceEecCCceeCcccccccC
Q psy8131 152 RFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCAKAKL 197 (198)
Q Consensus 152 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~ 197 (198)
+++.|+++.||..||+|..|...|.|+ ++..++.|||..+|.+.|
T Consensus 147 q~llald~qwhv~cfkc~~c~~vL~ge-y~skdg~pyce~dy~~~f 191 (670)
T KOG1044|consen 147 QALLALDKQWHVSCFKCKSCSAVLNGE-YMSKDGVPYCEKDYQAKF 191 (670)
T ss_pred ceeeeeccceeeeeeehhhhcccccce-eeccCCCcchhhhhhhhc
Confidence 788999999999999999999999886 678888999999998875
No 8
>KOG1703|consensus
Probab=99.86 E-value=1.1e-22 Score=176.58 Aligned_cols=160 Identities=22% Similarity=0.427 Sum_probs=149.7
Q ss_pred cCCcccCcCCcccC-CCCCCCCCCCcccCCCeecchhhHHhhhcccccccccccccccccccccccCCcccccceeeeee
Q psy8131 3 YKTRQWHEKCFACV-VCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSILFYF 81 (198)
Q Consensus 3 ~~~~~~H~~CF~C~-~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (198)
+....||...++|. .+...|....++.+.+...+..+|.....|+|..|++
T Consensus 260 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~c~~c~~---------------------------- 311 (479)
T KOG1703|consen 260 APRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYHNVTRPLCLSCNQ---------------------------- 311 (479)
T ss_pred cccccccccccccccccchhhccccccccccccccccccccccccccccccc----------------------------
Confidence 46778999999999 8999999999999999999999998888999999999
Q ss_pred eeeeecc-CceEeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcCCCCceEEeeCCCc
Q psy8131 82 LFQIITS-GGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRH 160 (198)
Q Consensus 82 ~~~~i~~-~~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~~ 160 (198)
+|.+ ..++++++.||+.+|.|+.|...+....+...+|++||.+|+.+.++++|.+|+++|.+ .+|.+.++.
T Consensus 312 ---~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~----~~v~a~~~~ 384 (479)
T KOG1703|consen 312 ---KIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILE----EGVCALGRL 384 (479)
T ss_pred ---CcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHH----hHhhhccCe
Confidence 6777 88899999999999999999999987778899999999999999999999999999998 678889999
Q ss_pred ccccCcccCcCCCCCCCCceEecCCceeCcccccccC
Q psy8131 161 WHNDCFMCASCQSSLVGRGFITDGEDIICPDCAKAKL 197 (198)
Q Consensus 161 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~ 197 (198)
||++||.|..|+++|.+..|+..++.+||..||..++
T Consensus 385 wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~ 421 (479)
T KOG1703|consen 385 WHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLF 421 (479)
T ss_pred echhceeeecccCCCCCCcccccCCccchhhhHhhhc
Confidence 9999999999999999999999999999999999876
No 9
>KOG4577|consensus
Probab=99.83 E-value=8.8e-23 Score=160.27 Aligned_cols=109 Identities=27% Similarity=0.589 Sum_probs=95.3
Q ss_pred eeccCce-EeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcCCCCceEEeeCCCcccc
Q psy8131 85 IITSGGV-TYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRHWHN 163 (198)
Q Consensus 85 ~i~~~~~-~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~~~H~ 163 (198)
.|.+..| .++++.||..|++|+.|..+|... ++.++|.+||+++|.++|+.+|++|+..|.+. ..+..|.+..||.
T Consensus 42 ~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfGTKCsaC~~GIpPt--qVVRkAqd~VYHl 118 (383)
T KOG4577|consen 42 HILDRFILKVLDRHWHSSCLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFGTKCSACQEGIPPT--QVVRKAQDFVYHL 118 (383)
T ss_pred HHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-HhhcCCceeehHHHHHHhCCcchhhcCCCChH--HHHHHhhcceeeh
Confidence 4555543 578999999999999999999776 88999999999999999999999999999884 2456889999999
Q ss_pred cCcccCcCCCCC-CCCceEec-CCceeCccccccc
Q psy8131 164 DCFMCASCQSSL-VGRGFITD-GEDIICPDCAKAK 196 (198)
Q Consensus 164 ~Cf~C~~C~~~l-~~~~~~~~-~~~~~C~~C~~~~ 196 (198)
+||.|..|+++| +|++|++. +.+++|+.-|++.
T Consensus 119 ~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A 153 (383)
T KOG4577|consen 119 HCFACFICKRQLATGDEFYLMEDARLVCKDDYETA 153 (383)
T ss_pred hhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence 999999999999 78888875 6799999988753
No 10
>KOG4577|consensus
Probab=99.72 E-value=4e-19 Score=139.76 Aligned_cols=108 Identities=26% Similarity=0.661 Sum_probs=91.5
Q ss_pred ccCCcccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhhcccccccccccccccccccccccCCcccccceeeeee
Q psy8131 2 EYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSILFYF 81 (198)
Q Consensus 2 ~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (198)
.++++.||..|++|+.|..+|.++.| .++|.+||++++.++|+.+|.+|+.+|
T Consensus 50 Kvl~R~wHs~CLkCs~C~~qL~drCF-sR~~s~yCkedFfKrfGTKCsaC~~GI-------------------------- 102 (383)
T KOG4577|consen 50 KVLDRHWHSSCLKCSDCHDQLADRCF-SREGSVYCKEDFFKRFGTKCSACQEGI-------------------------- 102 (383)
T ss_pred HHHhhhhhhhhcchhhhhhHHHHHHh-hcCCceeehHHHHHHhCCcchhhcCCC--------------------------
Confidence 57899999999999999999999877 599999999999999999999999975
Q ss_pred eeeeeccCceEeCCcCccccCCCCccCcCCC-CCCcee-ecCCcccchhhHhhhhccCCC
Q psy8131 82 LFQIITSGGVTYKNEPWHRECFTCSNCSTSL-AGQRFT-SREDKPFCADCFGELFAKRCY 139 (198)
Q Consensus 82 ~~~~i~~~~~~~~~~~~H~~CF~C~~C~~~l-~~~~~~-~~~g~~yC~~c~~~~~~~~C~ 139 (198)
+.+.-+..+.+..||..||.|..|++.| .++.|| +.|.++.|+++|+..-..-|.
T Consensus 103 ---pPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~ 159 (383)
T KOG4577|consen 103 ---PPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCN 159 (383)
T ss_pred ---ChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhcccc
Confidence 3332233577889999999999999999 455565 568999999999876666553
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=99.52 E-value=6e-15 Score=92.03 Aligned_cols=58 Identities=31% Similarity=0.783 Sum_probs=52.0
Q ss_pred CCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCCCCCceEecCCceeCcccccccC
Q psy8131 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCAKAKL 197 (198)
Q Consensus 138 C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~ 197 (198)
|++|+++|.+. +.++.+.|+.||++||+|..|+++|.+..++..++++||..||.++|
T Consensus 1 C~~C~~~I~~~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGT--EIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSS--SEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCc--EEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 78999999973 35557999999999999999999998877999999999999998875
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=99.46 E-value=5.2e-14 Score=87.76 Aligned_cols=50 Identities=34% Similarity=0.869 Sum_probs=43.2
Q ss_pred eeccCce--EeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhhh
Q psy8131 85 IITSGGV--TYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELF 134 (198)
Q Consensus 85 ~i~~~~~--~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~ 134 (198)
+|.+..+ .++|+.||++||+|+.|+++|.+..++..+|++||+.||.++|
T Consensus 7 ~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 7 PIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 4444433 4899999999999999999998888999999999999998875
No 13
>KOG1700|consensus
Probab=99.34 E-value=1.6e-13 Score=106.14 Aligned_cols=106 Identities=22% Similarity=0.604 Sum_probs=91.0
Q ss_pred ceEeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhhhcc---------------------------------
Q psy8131 90 GVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAK--------------------------------- 136 (198)
Q Consensus 90 ~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~--------------------------------- 136 (198)
.+...|..||+.||+|..|.+.|....+...++.+||+.+|...+++
T Consensus 22 ~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 (200)
T KOG1700|consen 22 KVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKDGKSLNESKPNQSAKF 101 (200)
T ss_pred HHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcccccccccccccchhH
Confidence 34477889999999999999999888899999999999977665542
Q ss_pred --------CCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCCCCCceEecCCceeCcccccccCC
Q psy8131 137 --------RCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCAKAKLM 198 (198)
Q Consensus 137 --------~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~~ 198 (198)
.|..|++.+.+. .-+...+..||..||+|+.|+..|+...+....+.++|...+.++++
T Consensus 102 ~~~~g~~~~c~~c~k~vy~~---Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~ 168 (200)
T KOG1700|consen 102 QVFAGEKEKCARCQKTVYPL---EKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFK 168 (200)
T ss_pred Hhhhccccccccccceeeeh---HHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeec
Confidence 799999998863 44678899999999999999999999899999999999988777653
No 14
>KOG1700|consensus
Probab=99.21 E-value=2.9e-12 Score=99.23 Aligned_cols=131 Identities=21% Similarity=0.463 Sum_probs=87.8
Q ss_pred cCCcccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhhccccccccccccccccccc-------ccccCCcccccc
Q psy8131 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGT-------FQSHSGRINKVY 75 (198)
Q Consensus 3 ~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~-------~~~~~~~~~~~~ 75 (198)
..|..||+.||.|..|.+.|+...+.++++.+||+.+|...++|.-..-++.+......+. .....+......
T Consensus 25 ~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 104 (200)
T KOG1700|consen 25 KDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKDGKSLNESKPNQSAKFQVF 104 (200)
T ss_pred ccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcccccccccccccchhHHhh
Confidence 4688999999999999999999999999999999999999998876666653221111000 000000000000
Q ss_pred ee---eeeeeee-eeccCceEeCCcCccccCCCCccCcCCCCCCceeecCCcccchhhHhhh
Q psy8131 76 SI---LFYFLFQ-IITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGEL 133 (198)
Q Consensus 76 ~~---~~~~~~~-~i~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~ 133 (198)
.+ .+..+.. +.....+...+..||..||+|+.|+..|+...+...++.+||...+.++
T Consensus 105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~ 166 (200)
T KOG1700|consen 105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQL 166 (200)
T ss_pred hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhhee
Confidence 00 0001110 1111234457789999999999999999999899999999998776554
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=98.79 E-value=5.8e-09 Score=59.15 Aligned_cols=38 Identities=34% Similarity=0.869 Sum_probs=33.8
Q ss_pred CCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCCC
Q psy8131 137 RCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLV 176 (198)
Q Consensus 137 ~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 176 (198)
+|.+|+++|.+. +..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~--~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGG--ELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCC--cEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999873 36788999999999999999999985
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=98.49 E-value=9.3e-08 Score=54.04 Aligned_cols=25 Identities=36% Similarity=0.830 Sum_probs=22.2
Q ss_pred CceEeCCcCccccCCCCccCcCCCC
Q psy8131 89 GGVTYKNEPWHRECFTCSNCSTSLA 113 (198)
Q Consensus 89 ~~~~~~~~~~H~~CF~C~~C~~~l~ 113 (198)
..+.+.++.||++||+|..|+++|.
T Consensus 14 ~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 14 LVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred EEEEeCCccccccCCCCcccCCcCc
Confidence 4567889999999999999999985
No 17
>KOG0490|consensus
Probab=97.20 E-value=3.8e-05 Score=60.67 Aligned_cols=100 Identities=24% Similarity=0.547 Sum_probs=79.1
Q ss_pred EeCCcCccccCCCCccCcCCCC--CCceeecCCcccchhhHhh--hhccCCCCCCCCCcCCCCceEEeeCCCcccccCcc
Q psy8131 92 TYKNEPWHRECFTCSNCSTSLA--GQRFTSREDKPFCADCFGE--LFAKRCYSCKKPITGIGGTRFISFEDRHWHNDCFM 167 (198)
Q Consensus 92 ~~~~~~~H~~CF~C~~C~~~l~--~~~~~~~~g~~yC~~c~~~--~~~~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~ 167 (198)
...+..||..|..|..|..+|. ...+.. +|..||..+|.. .+..+|++|...|... +.+..+..+. |..||.
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql--~~ler~f~~~-h~Pd~~ 88 (235)
T KOG0490|consen 13 RVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQL--DELERAFEKV-HLPCFA 88 (235)
T ss_pred hcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHH--HHHHHhhcCC-CcCccc
Confidence 3448899999999999999996 444444 999999999988 7888999999999652 3555677777 999999
Q ss_pred cCcCCCCC-CCCceEec-CCceeCcccccc
Q psy8131 168 CASCQSSL-VGRGFITD-GEDIICPDCAKA 195 (198)
Q Consensus 168 C~~C~~~l-~~~~~~~~-~~~~~C~~C~~~ 195 (198)
|..|.+.+ .+.++.+. +.+..|...+.+
T Consensus 89 ~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 89 CRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred hHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 99999977 66666655 447777776644
No 18
>KOG0490|consensus
Probab=96.81 E-value=0.00018 Score=56.79 Aligned_cols=99 Identities=30% Similarity=0.647 Sum_probs=74.1
Q ss_pred cCCcccCcCCcccCCCCCCCC--CCCcccCCCeecchhhHHh--hhcccccccccccccccccccccccCCcccccceee
Q psy8131 3 YKTRQWHEKCFACVVCKTPIG--TKSFIPREQEIYCANCYEE--KFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSIL 78 (198)
Q Consensus 3 ~~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~--~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (198)
+.+..||..|..|..|..+|. ...|.. +|..||..+|.. .+..+|.+|...+..+
T Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql-------------------- 72 (235)
T KOG0490|consen 14 VLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQL-------------------- 72 (235)
T ss_pred cccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHH--------------------
Confidence 457889999999999999998 667766 999999999998 7778999998853211
Q ss_pred eeeeeeeeccCceEeCCcCccccCCCCccCcCCC-CCCceeecCC-cccchhhHhh
Q psy8131 79 FYFLFQIITSGGVTYKNEPWHRECFTCSNCSTSL-AGQRFTSRED-KPFCADCFGE 132 (198)
Q Consensus 79 ~~~~~~~i~~~~~~~~~~~~H~~CF~C~~C~~~l-~~~~~~~~~g-~~yC~~c~~~ 132 (198)
+....+..+. |.-||.|..|...+ ....+.+.+. +.+|...+.+
T Consensus 73 ---------~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 73 ---------DELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred ---------HHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 1111233444 98999999998866 4555666654 8888887754
No 19
>KOG1702|consensus
Probab=96.44 E-value=0.00032 Score=53.72 Aligned_cols=44 Identities=27% Similarity=0.773 Sum_probs=39.2
Q ss_pred ccCCcccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhhc
Q psy8131 2 EYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFA 45 (198)
Q Consensus 2 ~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 45 (198)
.-+++.||..||.|.+|+-+|.-+.+.-.|.++||-.+|.+..+
T Consensus 21 ~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 21 KCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred hhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 34688999999999999999998889889999999999987654
No 20
>KOG1702|consensus
Probab=96.21 E-value=0.00045 Score=52.90 Aligned_cols=58 Identities=19% Similarity=0.444 Sum_probs=47.2
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCCCCCceEecCCceeCccccccc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCAKAK 196 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~ 196 (198)
+.|..|++.+.+- .-+.-+++.||..||+|..|+.+|.-..+--.+.++||..+|...
T Consensus 5 ~n~~~cgk~vYPv---E~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 5 CNREDCGKTVYPV---EEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ 62 (264)
T ss_pred chhhhhccccccH---HHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence 4466788877762 346778999999999999999999777776678899999998754
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=91.71 E-value=0.11 Score=31.43 Aligned_cols=39 Identities=21% Similarity=0.564 Sum_probs=26.3
Q ss_pred ccCCCCCCCCCcCCCCceEE--eeCCCcccccCc----ccCc--CCCCC
Q psy8131 135 AKRCYSCKKPITGIGGTRFI--SFEDRHWHNDCF----MCAS--CQSSL 175 (198)
Q Consensus 135 ~~~C~~C~~~I~~~~~~~~~--~~~~~~~H~~Cf----~C~~--C~~~l 175 (198)
+.+|..|+++|..+ +.+| ..-+..||.+|+ .|.. |+.++
T Consensus 5 ~~~C~~Cg~~~~~~--dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG--DDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred CccChhhCCcccCC--CCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 57899999999753 2333 445788898888 4665 55544
No 22
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=87.47 E-value=0.9 Score=25.98 Aligned_cols=39 Identities=26% Similarity=0.642 Sum_probs=28.0
Q ss_pred CccCcCCC-CCCceeecC-CcccchhhHhhhh--ccCCCCCCC
Q psy8131 105 CSNCSTSL-AGQRFTSRE-DKPFCADCFGELF--AKRCYSCKK 143 (198)
Q Consensus 105 C~~C~~~l-~~~~~~~~~-g~~yC~~c~~~~~--~~~C~~C~~ 143 (198)
|..|.+.+ ....+.+.. |.++|..|..+.. ...|..|++
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 67787777 333444444 9999999998876 567888764
No 23
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=86.46 E-value=0.67 Score=29.05 Aligned_cols=46 Identities=22% Similarity=0.483 Sum_probs=24.2
Q ss_pred CCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcCC
Q psy8131 103 FTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGI 148 (198)
Q Consensus 103 F~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~ 148 (198)
++|+.|..-|........=+.+||..|-...++..|..|..|....
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~q 53 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQ 53 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-S
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHH
Confidence 6889998877654333445789999999888899999999998753
No 24
>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=84.14 E-value=0.64 Score=25.82 Aligned_cols=33 Identities=27% Similarity=0.647 Sum_probs=22.2
Q ss_pred CCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCC
Q psy8131 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL 175 (198)
Q Consensus 138 C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 175 (198)
|.-|+++|.+.+ .++...++.|| |-|..|.+.|
T Consensus 1 Cd~CG~~I~~eP--~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEP--IVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCE--EEEEECCeEEE---EECHHHHHHH
Confidence 677899998742 45677888887 4555555443
No 25
>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=81.10 E-value=1.4 Score=30.04 Aligned_cols=29 Identities=21% Similarity=0.426 Sum_probs=17.4
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCcccccCc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWHNDCF 166 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf 166 (198)
..|+.|+++|... .-++-..|..+|..|+
T Consensus 79 ~~C~vC~k~l~~~--~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNS--VFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCc--eEEEeCCCeEEecccc
Confidence 4678888887652 2333444566777665
No 26
>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=79.72 E-value=1.1 Score=24.65 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=19.1
Q ss_pred cccCCCCCCCCCCCcccCCCeecchhhHH
Q psy8131 13 FACVVCKTPIGTKSFIPREQEIYCANCYE 41 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 41 (198)
+.|.+|+.. .|...||..||..|-.
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 348888765 5778999999987753
No 27
>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=79.25 E-value=0.4 Score=26.32 Aligned_cols=29 Identities=24% Similarity=0.669 Sum_probs=23.8
Q ss_pred cCCCCCCCCCCCcccCCCeecchhhHHhh
Q psy8131 15 CVVCKTPIGTKSFIPREQEIYCANCYEEK 43 (198)
Q Consensus 15 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~ 43 (198)
|..|+.++.........+..+|.+|..+.
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 89999999988777889999999998764
No 28
>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=78.70 E-value=1.2 Score=30.39 Aligned_cols=28 Identities=25% Similarity=0.641 Sum_probs=23.4
Q ss_pred ccCCCCCCCCCCCcc-cCCCeecchhhHH
Q psy8131 14 ACVVCKTPIGTKSFI-PREQEIYCANCYE 41 (198)
Q Consensus 14 ~C~~C~~~L~~~~f~-~~~g~~yC~~cy~ 41 (198)
.|..|+++|.+..|+ ..+|.+++..|..
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 589999999988776 5778999888864
No 29
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=78.10 E-value=1.8 Score=25.86 Aligned_cols=29 Identities=24% Similarity=0.698 Sum_probs=23.5
Q ss_pred ccCCCCCCCCCCC-cccCCCeecchhhHHhh
Q psy8131 14 ACVVCKTPIGTKS-FIPREQEIYCANCYEEK 43 (198)
Q Consensus 14 ~C~~C~~~L~~~~-f~~~~g~~yC~~cy~~~ 43 (198)
.|+.|++.+.--. +...|| ..|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 4899999998533 667888 6899999886
No 30
>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=77.28 E-value=1.7 Score=29.26 Aligned_cols=43 Identities=23% Similarity=0.522 Sum_probs=30.0
Q ss_pred CccccCCCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcC
Q psy8131 97 PWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITG 147 (198)
Q Consensus 97 ~~H~~CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~ 147 (198)
.|-+.=-.|..|...+.. .|.-||..|..+. -+|+.|++.|.+
T Consensus 39 Py~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 39 PYAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred cccccCcccccccccccc------CCCccChhhhccc--CcccccCCeecc
Confidence 344433467788766532 2567999997653 699999999975
No 31
>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=75.52 E-value=3.1 Score=24.30 Aligned_cols=43 Identities=26% Similarity=0.585 Sum_probs=29.4
Q ss_pred CCccCcCCCCCCceeecCCcc-cchhhHhhh--hccCCCCCCCCCcC
Q psy8131 104 TCSNCSTSLAGQRFTSREDKP-FCADCFGEL--FAKRCYSCKKPITG 147 (198)
Q Consensus 104 ~C~~C~~~l~~~~~~~~~g~~-yC~~c~~~~--~~~~C~~C~~~I~~ 147 (198)
.|..|.....+ .....=|.. +|..|..+. ...+|..|+++|..
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred CCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 46667666543 244455777 999999776 46899999999863
No 32
>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=75.47 E-value=4.1 Score=22.29 Aligned_cols=40 Identities=20% Similarity=0.589 Sum_probs=22.7
Q ss_pred CccCcCCCCCCceeecCCcccchhhHhhhh---ccCCCCCCCC
Q psy8131 105 CSNCSTSLAGQRFTSREDKPFCADCFGELF---AKRCYSCKKP 144 (198)
Q Consensus 105 C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~---~~~C~~C~~~ 144 (198)
|..|...+........=|..+|..|..+.+ ..+|..|+..
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 556666663322222257778888876443 3467777654
No 33
>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=75.02 E-value=1.3 Score=25.21 Aligned_cols=22 Identities=36% Similarity=1.004 Sum_probs=17.2
Q ss_pred ccCCCCCCCCCCCcccCCCeecchhh
Q psy8131 14 ACVVCKTPIGTKSFIPREQEIYCANC 39 (198)
Q Consensus 14 ~C~~C~~~L~~~~f~~~~g~~yC~~c 39 (198)
.|..|+.||-. .++|+.||..|
T Consensus 19 ~Cp~C~~PL~~----~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR----DKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEE----ecCCCEECCCC
Confidence 57889888764 58899999765
No 34
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=73.96 E-value=1.1 Score=34.56 Aligned_cols=31 Identities=26% Similarity=0.575 Sum_probs=26.8
Q ss_pred CCCccCcCCCCCCceeecCCcccchhhHhhh
Q psy8131 103 FTCSNCSTSLAGQRFTSREDKPFCADCFGEL 133 (198)
Q Consensus 103 F~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~ 133 (198)
-+|+.|+..+....-...+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999999777777889999999998753
No 35
>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=72.91 E-value=8.5 Score=23.28 Aligned_cols=44 Identities=9% Similarity=0.144 Sum_probs=33.4
Q ss_pred CCCccCcCCCCCCceeecCCcccchhhHhhhh--ccCCCCCCCCCcC
Q psy8131 103 FTCSNCSTSLAGQRFTSREDKPFCADCFGELF--AKRCYSCKKPITG 147 (198)
Q Consensus 103 F~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~--~~~C~~C~~~I~~ 147 (198)
|.|..|+..+.+- .....|..||+.+..+.. ...|..|++++..
T Consensus 2 ~~Cpi~~~~~~~P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKDP-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCCC-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 5788898888664 566779999999986443 4578888888854
No 36
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=71.76 E-value=3.9 Score=25.66 Aligned_cols=42 Identities=17% Similarity=0.612 Sum_probs=23.1
Q ss_pred cccCCCCCCCCCCCcccCCCeecchhhHHhhhcccccccccc
Q psy8131 13 FACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKT 54 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~ 54 (198)
.+|+.|..-|....-...=+.++|..|..+.++..|..|+.|
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~P 49 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTP 49 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCCh
Confidence 578999888776433345577899999999999999999985
No 37
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=69.45 E-value=2.6 Score=30.37 Aligned_cols=22 Identities=36% Similarity=1.058 Sum_probs=18.1
Q ss_pred ccCCCCCCCCCCCcccCCCeecchhhH
Q psy8131 14 ACVVCKTPIGTKSFIPREQEIYCANCY 40 (198)
Q Consensus 14 ~C~~C~~~L~~~~f~~~~g~~yC~~cy 40 (198)
.|..|+.|| | .++|++||..|-
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 489999987 3 499999998875
No 38
>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=67.78 E-value=3.7 Score=24.63 Aligned_cols=29 Identities=24% Similarity=0.690 Sum_probs=17.8
Q ss_pred ccCCCCCCCCCCCcccCCCeecc-hhhHHh
Q psy8131 14 ACVVCKTPIGTKSFIPREQEIYC-ANCYEE 42 (198)
Q Consensus 14 ~C~~C~~~L~~~~f~~~~g~~yC-~~cy~~ 42 (198)
.|..|...++...-+++||+.|| +.|...
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~g 38 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACANG 38 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHHT
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhcc
Confidence 46788888887778899999999 566654
No 39
>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=67.76 E-value=11 Score=22.86 Aligned_cols=44 Identities=23% Similarity=0.619 Sum_probs=31.8
Q ss_pred CCccCcCCCCCC---ceeecCCcccchhhHhhhhccCCCCCCCCCcC
Q psy8131 104 TCSNCSTSLAGQ---RFTSREDKPFCADCFGELFAKRCYSCKKPITG 147 (198)
Q Consensus 104 ~C~~C~~~l~~~---~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~ 147 (198)
.|..|++.|..+ .+.-.=.=-||.+|....+..+|..|+..+..
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv~ 53 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELVR 53 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCcccc
Confidence 477888888433 23322345689999999889999999987765
No 40
>KOG4739|consensus
Probab=66.41 E-value=4.7 Score=32.01 Aligned_cols=43 Identities=26% Similarity=0.510 Sum_probs=31.9
Q ss_pred CccCcCCCCCCceeecC-CcccchhhHhhhhccCCCCCCCCCcC
Q psy8131 105 CSNCSTSLAGQRFTSRE-DKPFCADCFGELFAKRCYSCKKPITG 147 (198)
Q Consensus 105 C~~C~~~l~~~~~~~~~-g~~yC~~c~~~~~~~~C~~C~~~I~~ 147 (198)
|..|...-....|++.. ..++|..|.....++.|.-|+++|..
T Consensus 6 Cn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 6 CNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred eccccccCCCCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 34454444455677665 89999999987777799999999754
No 41
>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=65.10 E-value=4.1 Score=23.53 Aligned_cols=11 Identities=55% Similarity=1.201 Sum_probs=6.9
Q ss_pred CCCCCCCCCcC
Q psy8131 137 RCYSCKKPITG 147 (198)
Q Consensus 137 ~C~~C~~~I~~ 147 (198)
.|..|+++|.+
T Consensus 2 ~C~~C~~~i~g 12 (46)
T cd02249 2 SCDGCLKPIVG 12 (46)
T ss_pred CCcCCCCCCcC
Confidence 46667776654
No 42
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=62.99 E-value=3.9 Score=31.69 Aligned_cols=31 Identities=19% Similarity=0.497 Sum_probs=25.3
Q ss_pred cccCcCCCCCCCCceEecCCceeCccccccc
Q psy8131 166 FMCASCQSSLVGRGFITDGEDIICPDCAKAK 196 (198)
Q Consensus 166 f~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~ 196 (198)
-+|+.|+..+....-...+|+++|..|+...
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5788888888666677788999999998754
No 43
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=62.35 E-value=6.5 Score=19.24 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=4.2
Q ss_pred CCCCCCCCc
Q psy8131 138 CYSCKKPIT 146 (198)
Q Consensus 138 C~~C~~~I~ 146 (198)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 444444444
No 44
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=61.92 E-value=6.2 Score=23.79 Aligned_cols=25 Identities=28% Similarity=0.518 Sum_probs=17.1
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCcccc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWHN 163 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H~ 163 (198)
.+|..|++||.+. ..+...+..-|+
T Consensus 2 ~~CvVCKqpi~~a---~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDA---LVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcc---eEEEcCCCccCc
Confidence 4789999999873 445555556665
No 45
>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=61.35 E-value=4 Score=27.34 Aligned_cols=16 Identities=31% Similarity=0.831 Sum_probs=13.7
Q ss_pred HhhhhccCCCCCCCCC
Q psy8131 130 FGELFAKRCYSCKKPI 145 (198)
Q Consensus 130 ~~~~~~~~C~~C~~~I 145 (198)
|..+|...|.+|++-+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 5677889999999988
No 46
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=60.65 E-value=6.3 Score=28.41 Aligned_cols=21 Identities=33% Similarity=1.073 Sum_probs=11.3
Q ss_pred cCcCCCCCCCCceEecCCceeCcccc
Q psy8131 168 CASCQSSLVGRGFITDGEDIICPDCA 193 (198)
Q Consensus 168 C~~C~~~l~~~~~~~~~~~~~C~~C~ 193 (198)
|..|+.|| |- .+|.+||..|-
T Consensus 31 Cp~Cg~PL----F~-KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL----FR-KDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc----ee-eCCeEECCCCC
Confidence 55555555 22 55566666553
No 47
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=60.33 E-value=7.6 Score=23.90 Aligned_cols=10 Identities=20% Similarity=0.816 Sum_probs=6.7
Q ss_pred cccccccccc
Q psy8131 45 ATRCVKCNKT 54 (198)
Q Consensus 45 ~~~C~~C~~~ 54 (198)
.++|..|+..
T Consensus 9 ~~~CtSCg~~ 18 (61)
T COG2888 9 PPVCTSCGRE 18 (61)
T ss_pred CceeccCCCE
Confidence 4577777773
No 48
>KOG1813|consensus
Probab=59.86 E-value=5.1 Score=32.87 Aligned_cols=44 Identities=23% Similarity=0.649 Sum_probs=33.4
Q ss_pred CCCccCcCCCCCCceeecCCcccchhhHhhhh--ccCCCCCCCCCcC
Q psy8131 103 FTCSNCSTSLAGQRFTSREDKPFCADCFGELF--AKRCYSCKKPITG 147 (198)
Q Consensus 103 F~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~--~~~C~~C~~~I~~ 147 (198)
|.|..|++++.+. ....-+..+|+.|..+.+ +++|..|++.+.+
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 6788888877543 445567888999987655 4689999999987
No 49
>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=59.18 E-value=6.4 Score=22.47 Aligned_cols=12 Identities=50% Similarity=1.102 Sum_probs=6.8
Q ss_pred cCCCCCCCCCcC
Q psy8131 136 KRCYSCKKPITG 147 (198)
Q Consensus 136 ~~C~~C~~~I~~ 147 (198)
..|..|+++|.+
T Consensus 5 ~~C~~C~~~i~g 16 (44)
T smart00291 5 YSCDTCGKPIVG 16 (44)
T ss_pred cCCCCCCCCCcC
Confidence 456666665544
No 50
>PRK00807 50S ribosomal protein L24e; Validated
Probab=58.67 E-value=6.7 Score=23.46 Aligned_cols=37 Identities=19% Similarity=0.435 Sum_probs=26.0
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCC
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL 175 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 175 (198)
..|+.|+..|.++.|..++...|+.|. |.+..|.+.+
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~---Fcs~KC~~~f 38 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY---FCSSKCEKNY 38 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE---EeCHHHHHHH
Confidence 368899999987666666778888886 4444555533
No 51
>PF12773 DZR: Double zinc ribbon
Probab=57.71 E-value=13 Score=21.59 Aligned_cols=10 Identities=20% Similarity=0.457 Sum_probs=5.6
Q ss_pred CCCCCCCCCc
Q psy8131 137 RCYSCKKPIT 146 (198)
Q Consensus 137 ~C~~C~~~I~ 146 (198)
.|..|+..+.
T Consensus 31 ~C~~Cg~~~~ 40 (50)
T PF12773_consen 31 ICPNCGAENP 40 (50)
T ss_pred CCcCCcCCCc
Confidence 4666665544
No 52
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=57.19 E-value=20 Score=27.64 Aligned_cols=45 Identities=20% Similarity=0.521 Sum_probs=33.4
Q ss_pred CCCCccCcCCCCCCceeecCCcccchhhHhhhh------------------ccCCCCCCCCCcC
Q psy8131 102 CFTCSNCSTSLAGQRFTSREDKPFCADCFGELF------------------AKRCYSCKKPITG 147 (198)
Q Consensus 102 CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~------------------~~~C~~C~~~I~~ 147 (198)
-|.|..|...+... ....=|..||..|..+.. .++|..|+.+|..
T Consensus 18 ~~~CpICld~~~dP-VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 18 DFDCNICLDQVRDP-VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ccCCccCCCcCCCc-EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 48888998876543 445569999999985421 2579999999975
No 53
>KOG0320|consensus
Probab=54.11 E-value=12 Score=28.51 Aligned_cols=48 Identities=23% Similarity=0.657 Sum_probs=36.4
Q ss_pred ccCCCCccCcCCCCCCc-eeecCCcccchhhHhhh--hccCCCCCCCCCcC
Q psy8131 100 RECFTCSNCSTSLAGQR-FTSREDKPFCADCFGEL--FAKRCYSCKKPITG 147 (198)
Q Consensus 100 ~~CF~C~~C~~~l~~~~-~~~~~g~~yC~~c~~~~--~~~~C~~C~~~I~~ 147 (198)
..++.|-.|=.+..... +..+=|.+||..|-... .+.+|..|++.|+.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 45788888877665543 33566999999998643 46799999999875
No 54
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=53.99 E-value=5.6 Score=30.74 Aligned_cols=41 Identities=24% Similarity=0.667 Sum_probs=33.0
Q ss_pred cccCCCCCCCCCCCcccCCCeecchhhHHhhh--cccccccccc
Q psy8131 13 FACVVCKTPIGTKSFIPREQEIYCANCYEEKF--ATRCVKCNKT 54 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~--~~~C~~C~~~ 54 (198)
|.|..|.+...+. .+..=|..+|..|+-+.+ ++.|..|++.
T Consensus 197 F~C~iCKkdy~sp-vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~ 239 (259)
T COG5152 197 FLCGICKKDYESP-VVTECGHSFCSLCAIRKYQKGDECGVCGKA 239 (259)
T ss_pred eeehhchhhccch-hhhhcchhHHHHHHHHHhccCCcceecchh
Confidence 8999999888763 445668889999998765 6789999983
No 55
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=53.33 E-value=4.4 Score=26.66 Aligned_cols=29 Identities=28% Similarity=0.578 Sum_probs=17.6
Q ss_pred ccCcCCCCCCCCc-eEec-CC---ceeCcccccc
Q psy8131 167 MCASCQSSLVGRG-FITD-GE---DIICPDCAKA 195 (198)
Q Consensus 167 ~C~~C~~~l~~~~-~~~~-~~---~~~C~~C~~~ 195 (198)
.|.+|+.||..+. +... +| .-||.-||+.
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 4788888885443 3332 22 5688888753
No 56
>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=53.28 E-value=5.4 Score=21.68 Aligned_cols=25 Identities=16% Similarity=0.616 Sum_probs=8.3
Q ss_pred cCcCCCCCCCCceEecCCceeCccc
Q psy8131 168 CASCQSSLVGRGFITDGEDIICPDC 192 (198)
Q Consensus 168 C~~C~~~l~~~~~~~~~~~~~C~~C 192 (198)
|..|++++..+.....=+.+.|..|
T Consensus 6 C~eC~~~f~dSyL~~~F~~~VCD~C 30 (34)
T PF01286_consen 6 CDECGKPFMDSYLLNNFDLPVCDKC 30 (34)
T ss_dssp -TTT--EES-SSCCCCTS-S--TTT
T ss_pred HhHhCCHHHHHHHHHhCCccccccc
Confidence 4455555544433333444555554
No 57
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=52.70 E-value=5.7 Score=30.71 Aligned_cols=44 Identities=23% Similarity=0.583 Sum_probs=33.1
Q ss_pred CCCccCcCCCCCCceeecCCcccchhhHhhhh--ccCCCCCCCCCcC
Q psy8131 103 FTCSNCSTSLAGQRFTSREDKPFCADCFGELF--AKRCYSCKKPITG 147 (198)
Q Consensus 103 F~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~--~~~C~~C~~~I~~ 147 (198)
|.|..|.+...+. .+..=|..+|..|+.+.+ ++.|..|++...+
T Consensus 197 F~C~iCKkdy~sp-vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 197 FLCGICKKDYESP-VVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred eeehhchhhccch-hhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 7888888776443 444458888999987665 5789999988876
No 58
>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=51.62 E-value=13 Score=20.32 Aligned_cols=31 Identities=16% Similarity=0.554 Sum_probs=22.8
Q ss_pred cCCCCCCCCCCCcccCCCeecchhhHHhhhc
Q psy8131 15 CVVCKTPIGTKSFIPREQEIYCANCYEEKFA 45 (198)
Q Consensus 15 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 45 (198)
|..|...+.+......=|-.||++|..+...
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHH
Confidence 5678777777545677799999999987643
No 59
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.43 E-value=12 Score=18.72 Aligned_cols=10 Identities=30% Similarity=0.653 Sum_probs=4.4
Q ss_pred CCCCCCCCCc
Q psy8131 137 RCYSCKKPIT 146 (198)
Q Consensus 137 ~C~~C~~~I~ 146 (198)
.|..|+..|.
T Consensus 4 ~Cp~Cg~~~~ 13 (26)
T PF13248_consen 4 FCPNCGAEID 13 (26)
T ss_pred CCcccCCcCC
Confidence 3444444443
No 60
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=51.41 E-value=11 Score=26.92 Aligned_cols=27 Identities=22% Similarity=0.310 Sum_probs=23.3
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCccc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWH 162 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H 162 (198)
.+|+.|+.+|.++-|.++|...|+.|+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEE
Confidence 479999999998778788888888886
No 61
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=51.15 E-value=11 Score=22.74 Aligned_cols=27 Identities=15% Similarity=0.379 Sum_probs=21.8
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCccc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWH 162 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H 162 (198)
..|+-|+..|.++.|..+|...|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 468999999988777788888887775
No 62
>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=51.10 E-value=10 Score=22.22 Aligned_cols=11 Identities=55% Similarity=1.216 Sum_probs=6.9
Q ss_pred CCCCCCC-CCcC
Q psy8131 137 RCYSCKK-PITG 147 (198)
Q Consensus 137 ~C~~C~~-~I~~ 147 (198)
+|..|+. ||.+
T Consensus 2 ~Cd~C~~~pI~G 13 (48)
T cd02341 2 KCDSCGIEPIPG 13 (48)
T ss_pred CCCCCCCCcccc
Confidence 4666766 6665
No 63
>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=50.63 E-value=7.5 Score=20.13 Aligned_cols=12 Identities=42% Similarity=1.005 Sum_probs=4.4
Q ss_pred cccCCCCCCCCC
Q psy8131 13 FACVVCKTPIGT 24 (198)
Q Consensus 13 F~C~~C~~~L~~ 24 (198)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 678999999886
No 64
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=50.24 E-value=5.1 Score=27.48 Aligned_cols=29 Identities=38% Similarity=0.800 Sum_probs=15.9
Q ss_pred CCCCCCCCCcCCCCceEEeeCCCcccccCcc
Q psy8131 137 RCYSCKKPITGIGGTRFISFEDRHWHNDCFM 167 (198)
Q Consensus 137 ~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~ 167 (198)
+|..|+++|.. |..+.-..+..-|-+||+
T Consensus 4 kC~iCg~~I~~--gqlFTF~~kG~VH~~C~~ 32 (101)
T PF09943_consen 4 KCYICGKPIYE--GQLFTFTKKGPVHYECFR 32 (101)
T ss_pred EEEecCCeeee--cceEEEecCCcEeHHHHH
Confidence 46667777765 223333444555666664
No 65
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=49.69 E-value=4.9 Score=27.42 Aligned_cols=29 Identities=17% Similarity=0.432 Sum_probs=19.1
Q ss_pred CCcccCCCCCCCCC-CCcccCCCeecchhh
Q psy8131 11 KCFACVVCKTPIGT-KSFIPREQEIYCANC 39 (198)
Q Consensus 11 ~CF~C~~C~~~L~~-~~f~~~~g~~yC~~c 39 (198)
.=|+|+.|..---. +.-.+.+|.++|.+|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 44899999543321 222367899999987
No 66
>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=49.47 E-value=4.9 Score=25.65 Aligned_cols=39 Identities=15% Similarity=0.449 Sum_probs=22.8
Q ss_pred cccCCCCCCCCCCCcccCCCeecchhhHHhh-hcccccccccccc
Q psy8131 13 FACVVCKTPIGTKSFIPREQEIYCANCYEEK-FATRCVKCNKTFF 56 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~-~~~~C~~C~~~~~ 56 (198)
..|..|..+|+. .++..+|..|...- ..+.|..|++++.
T Consensus 2 ~~CP~C~~~L~~-----~~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEW-----QGGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEE-----ETTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEE-----eCCEEECccccccceecccCCCcccHHH
Confidence 368899998874 34888898887642 3458999999754
No 67
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=49.42 E-value=11 Score=23.64 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=21.1
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCccc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWH 162 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H 162 (198)
..|+-|+..|.++.|..+|.-.|+.++
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~ 30 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLR 30 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEE
Confidence 468899999988767677777777775
No 68
>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=49.25 E-value=12 Score=21.34 Aligned_cols=11 Identities=45% Similarity=1.114 Sum_probs=8.1
Q ss_pred CCCCCCCCCcC
Q psy8131 137 RCYSCKKPITG 147 (198)
Q Consensus 137 ~C~~C~~~I~~ 147 (198)
.|..|+++|.+
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 57788887766
No 69
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=49.09 E-value=8.9 Score=23.55 Aligned_cols=27 Identities=22% Similarity=0.787 Sum_probs=20.9
Q ss_pred ccCCCCCCCCC--CCcccCCCeecch-hhH
Q psy8131 14 ACVVCKTPIGT--KSFIPREQEIYCA-NCY 40 (198)
Q Consensus 14 ~C~~C~~~L~~--~~f~~~~g~~yC~-~cy 40 (198)
.|..|+++|.. ..|..++.+.+|. +|-
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR 47 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECR 47 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHH
Confidence 58899999983 4677888999995 443
No 70
>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=48.90 E-value=12 Score=21.63 Aligned_cols=29 Identities=17% Similarity=0.482 Sum_probs=16.3
Q ss_pred ccCcCCCCCCCCceEec--CCceeCcccccc
Q psy8131 167 MCASCQSSLVGRGFITD--GEDIICPDCAKA 195 (198)
Q Consensus 167 ~C~~C~~~l~~~~~~~~--~~~~~C~~C~~~ 195 (198)
.|..|+..++..+|... .+.-+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 45666666654443322 235678888765
No 71
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=47.84 E-value=6.1 Score=26.71 Aligned_cols=29 Identities=28% Similarity=0.709 Sum_probs=14.1
Q ss_pred CCCCCCCCCcCCCCceEEeeCCCcccccCcc
Q psy8131 137 RCYSCKKPITGIGGTRFISFEDRHWHNDCFM 167 (198)
Q Consensus 137 ~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~ 167 (198)
+|+.|+++|.. |..+.-.....-|-+||.
T Consensus 8 kC~VCg~~iie--GqkFTF~~kGsVH~eCl~ 36 (103)
T COG4847 8 KCYVCGGTIIE--GQKFTFTKKGSVHYECLA 36 (103)
T ss_pred eEeeeCCEeee--ccEEEEeeCCcchHHHHH
Confidence 56666666643 223333334445555553
No 72
>PRK00420 hypothetical protein; Validated
Probab=47.76 E-value=16 Score=25.67 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=8.1
Q ss_pred ccCCCCCCCCCcC
Q psy8131 135 AKRCYSCKKPITG 147 (198)
Q Consensus 135 ~~~C~~C~~~I~~ 147 (198)
+..|..|+.|+..
T Consensus 23 ~~~CP~Cg~pLf~ 35 (112)
T PRK00420 23 SKHCPVCGLPLFE 35 (112)
T ss_pred cCCCCCCCCccee
Confidence 4567777766654
No 73
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=47.48 E-value=7.1 Score=22.09 Aligned_cols=29 Identities=21% Similarity=0.702 Sum_probs=13.7
Q ss_pred cccCcCCCCCCCCceEecCCceeCccccc
Q psy8131 166 FMCASCQSSLVGRGFITDGEDIICPDCAK 194 (198)
Q Consensus 166 f~C~~C~~~l~~~~~~~~~~~~~C~~C~~ 194 (198)
|+|..|+..+.-..-...+..+.|..|..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 45666665553222122234555666544
No 74
>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=46.29 E-value=14 Score=21.24 Aligned_cols=30 Identities=23% Similarity=0.584 Sum_probs=17.8
Q ss_pred cccCCCCC-CCCCCCcc--cCCCeecchhhHHh
Q psy8131 13 FACVVCKT-PIGTKSFI--PREQEIYCANCYEE 42 (198)
Q Consensus 13 F~C~~C~~-~L~~~~f~--~~~g~~yC~~cy~~ 42 (198)
++|..|+. ++.+..|. .=.+--+|.+||.+
T Consensus 5 ~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 5 YTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp CE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred eECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 67899988 66665543 23455678888765
No 75
>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=46.06 E-value=18 Score=21.31 Aligned_cols=29 Identities=21% Similarity=0.537 Sum_probs=21.8
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCcccccC
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWHNDC 165 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H~~C 165 (198)
-.|..|+....+. ++..+.+.+..|+..|
T Consensus 14 ~~Cp~CGN~~vGn-gEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGN-GEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeec-CcceEEEeccceeeee
Confidence 4688998888774 4455678888888866
No 76
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=45.90 E-value=13 Score=25.46 Aligned_cols=32 Identities=31% Similarity=0.662 Sum_probs=24.8
Q ss_pred CCCccCcCCC-CCCceeecCCcccchhhHhhhh
Q psy8131 103 FTCSNCSTSL-AGQRFTSREDKPFCADCFGELF 134 (198)
Q Consensus 103 F~C~~C~~~l-~~~~~~~~~g~~yC~~c~~~~~ 134 (198)
.+|..|++++ .++.|....+.+.+-.|+.+..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 3688899988 6777877777888888887654
No 77
>KOG0320|consensus
Probab=45.60 E-value=14 Score=28.09 Aligned_cols=45 Identities=20% Similarity=0.733 Sum_probs=36.0
Q ss_pred cCCcccCCCCCCCCCCC-cccCCCeecchhhHHhhh--cccccccccc
Q psy8131 10 EKCFACVVCKTPIGTKS-FIPREQEIYCANCYEEKF--ATRCVKCNKT 54 (198)
Q Consensus 10 ~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~cy~~~~--~~~C~~C~~~ 54 (198)
..++.|..|-.+..... +..+=|.++|+.|.+... +.+|..|++.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kk 176 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKK 176 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccc
Confidence 46789999987777654 667889999999998764 4589999984
No 78
>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=45.17 E-value=19 Score=26.74 Aligned_cols=51 Identities=22% Similarity=0.481 Sum_probs=33.8
Q ss_pred CcccchhhHhhhhccCCCCCCCCCcCCC-CceEEeeCCCcccccCcccCcCCCCC
Q psy8131 122 DKPFCADCFGELFAKRCYSCKKPITGIG-GTRFISFEDRHWHNDCFMCASCQSSL 175 (198)
Q Consensus 122 g~~yC~~c~~~~~~~~C~~C~~~I~~~~-~~~~~~~~~~~~H~~Cf~C~~C~~~l 175 (198)
..-||..|-.+. -..|..|+.+|.|.- .+. +...+..|+.- --|..|++++
T Consensus 27 ~~~fC~kCG~~t-I~~Cp~C~~~IrG~y~v~g-v~~~g~~~~~P-sYC~~CGkpy 78 (158)
T PF10083_consen 27 REKFCSKCGAKT-ITSCPNCSTPIRGDYHVEG-VFGLGGHYEAP-SYCHNCGKPY 78 (158)
T ss_pred HHHHHHHhhHHH-HHHCcCCCCCCCCceecCC-eeeeCCCCCCC-hhHHhCCCCC
Confidence 356899997654 588999999998741 112 23345666632 2388888887
No 79
>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=44.08 E-value=17 Score=18.06 Aligned_cols=10 Identities=50% Similarity=1.182 Sum_probs=5.9
Q ss_pred CCCCCCCCcC
Q psy8131 138 CYSCKKPITG 147 (198)
Q Consensus 138 C~~C~~~I~~ 147 (198)
|.+|+.+|.+
T Consensus 1 C~sC~~~i~~ 10 (24)
T PF07754_consen 1 CTSCGRPIAP 10 (24)
T ss_pred CccCCCcccC
Confidence 4556666655
No 80
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=43.60 E-value=19 Score=22.18 Aligned_cols=30 Identities=27% Similarity=0.715 Sum_probs=15.4
Q ss_pred CCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCC
Q psy8131 103 FTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCK 142 (198)
Q Consensus 103 F~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~ 142 (198)
|.|..|++.+-.. |..|-.....-+|..|+
T Consensus 26 F~CPnCG~~~I~R----------C~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 26 FLCPNCGEVIIYR----------CEKCRKQSNPYTCPKCG 55 (59)
T ss_pred eeCCCCCCeeEee----------chhHHhcCCceECCCCC
Confidence 6666666542111 55554444444566655
No 81
>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=43.35 E-value=3.6 Score=26.81 Aligned_cols=12 Identities=42% Similarity=0.913 Sum_probs=9.2
Q ss_pred cCCCCCCCCCcC
Q psy8131 136 KRCYSCKKPITG 147 (198)
Q Consensus 136 ~~C~~C~~~I~~ 147 (198)
.+|..|++.|..
T Consensus 8 a~Ck~C~~~I~k 19 (82)
T PF00645_consen 8 AKCKGCKKKIAK 19 (82)
T ss_dssp EBETTTSCBE-T
T ss_pred ccCcccCCcCCC
Confidence 578899999975
No 82
>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=41.51 E-value=9.3 Score=21.01 Aligned_cols=8 Identities=38% Similarity=1.045 Sum_probs=3.5
Q ss_pred CCCCCCCC
Q psy8131 137 RCYSCKKP 144 (198)
Q Consensus 137 ~C~~C~~~ 144 (198)
+|..|+..
T Consensus 7 ~C~~Cg~~ 14 (41)
T smart00834 7 RCEDCGHT 14 (41)
T ss_pred EcCCCCCE
Confidence 34444443
No 83
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=41.25 E-value=24 Score=20.25 Aligned_cols=29 Identities=24% Similarity=0.604 Sum_probs=18.3
Q ss_pred ccCCCCC-CCCCCCcc--cCCCeecchhhHHh
Q psy8131 14 ACVVCKT-PIGTKSFI--PREQEIYCANCYEE 42 (198)
Q Consensus 14 ~C~~C~~-~L~~~~f~--~~~g~~yC~~cy~~ 42 (198)
+|..|+. |+.+..|. .-.+-=+|+.||.+
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~ 33 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSR 33 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhh
Confidence 5788885 77777664 33344466666654
No 84
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.72 E-value=18 Score=20.81 Aligned_cols=25 Identities=16% Similarity=0.623 Sum_probs=11.7
Q ss_pred cccCcCCCCCCCCceEecCCceeCccccc
Q psy8131 166 FMCASCQSSLVGRGFITDGEDIICPDCAK 194 (198)
Q Consensus 166 f~C~~C~~~l~~~~~~~~~~~~~C~~C~~ 194 (198)
+.|..|+..++-+ ..+.+.|..|-.
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecC----CCCceECCCCCc
Confidence 3455565544322 233455555543
No 85
>KOG0978|consensus
Probab=39.61 E-value=11 Score=34.75 Aligned_cols=43 Identities=30% Similarity=0.827 Sum_probs=33.2
Q ss_pred cccCCCCCCCCCCCcccCCCeecchhhHHhhhcc---cccccccccc
Q psy8131 13 FACVVCKTPIGTKSFIPREQEIYCANCYEEKFAT---RCVKCNKTFF 56 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~---~C~~C~~~~~ 56 (198)
.+|+.|+..-.+ ..+.+=+.++|.+|-..++.. +|.+|+.+|+
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFG 689 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 589999866554 334566889999999988865 6999999764
No 86
>KOG0978|consensus
Probab=38.84 E-value=12 Score=34.52 Aligned_cols=44 Identities=20% Similarity=0.665 Sum_probs=32.7
Q ss_pred CCCccCcCCCCCCceeecCCcccchhhHhhhhc---cCCCCCCCCCcC
Q psy8131 103 FTCSNCSTSLAGQRFTSREDKPFCADCFGELFA---KRCYSCKKPITG 147 (198)
Q Consensus 103 F~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~---~~C~~C~~~I~~ 147 (198)
++|+.|+...-+. ....=+.+||..|...++. .+|+.|+.+..+
T Consensus 644 LkCs~Cn~R~Kd~-vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNTRWKDA-VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccCchhhH-HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 6788888655332 3445589999999887764 589999999765
No 87
>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=38.48 E-value=11 Score=19.51 Aligned_cols=12 Identities=25% Similarity=0.606 Sum_probs=5.4
Q ss_pred cCCCCCCCCCcC
Q psy8131 136 KRCYSCKKPITG 147 (198)
Q Consensus 136 ~~C~~C~~~I~~ 147 (198)
.+|..|...|..
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 456667766654
No 88
>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=37.88 E-value=16 Score=20.59 Aligned_cols=25 Identities=32% Similarity=0.763 Sum_probs=13.2
Q ss_pred cccCCCCCCCCCCCcccCCCeecchhh
Q psy8131 13 FACVVCKTPIGTKSFIPREQEIYCANC 39 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~~~g~~yC~~c 39 (198)
++|..|+..- ..+-...|++.|..|
T Consensus 1 m~Cp~Cg~~~--~~~D~~~g~~vC~~C 25 (43)
T PF08271_consen 1 MKCPNCGSKE--IVFDPERGELVCPNC 25 (43)
T ss_dssp ESBTTTSSSE--EEEETTTTEEEETTT
T ss_pred CCCcCCcCCc--eEEcCCCCeEECCCC
Confidence 4688887653 122234566655443
No 89
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=37.72 E-value=13 Score=21.36 Aligned_cols=27 Identities=15% Similarity=0.449 Sum_probs=15.4
Q ss_pred CCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCC
Q psy8131 137 RCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL 175 (198)
Q Consensus 137 ~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 175 (198)
+|..|+..+...+ .. . =++|..|+.++
T Consensus 5 ~C~~CG~~~~~~~---~~----~-----~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDE---YG----T-----GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECC---CC----C-----ceECCCCCCeE
Confidence 5777777665321 01 0 26777777765
No 90
>KOG3002|consensus
Probab=36.86 E-value=35 Score=28.31 Aligned_cols=45 Identities=22% Similarity=0.632 Sum_probs=36.7
Q ss_pred CCCCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcC
Q psy8131 102 CFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITG 147 (198)
Q Consensus 102 CF~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~ 147 (198)
=+-|..|..+|..-.+.=.+|.+.|..|-.++ ..+|..|..+|..
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~-~~~CP~Cr~~~g~ 92 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRTKV-SNKCPTCRLPIGN 92 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhhhh-cccCCcccccccc
Confidence 36788888888776677788999999998554 6899999999974
No 91
>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=36.34 E-value=22 Score=20.82 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=7.3
Q ss_pred CCCCCC-CCCcC
Q psy8131 137 RCYSCK-KPITG 147 (198)
Q Consensus 137 ~C~~C~-~~I~~ 147 (198)
.|..|+ .+|.+
T Consensus 2 ~C~~C~~~~i~g 13 (49)
T cd02338 2 SCDGCGKSNFTG 13 (49)
T ss_pred CCCCCcCCCcEE
Confidence 477777 56664
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=36.18 E-value=13 Score=21.74 Aligned_cols=9 Identities=33% Similarity=0.981 Sum_probs=4.8
Q ss_pred CCCCCCCCC
Q psy8131 137 RCYSCKKPI 145 (198)
Q Consensus 137 ~C~~C~~~I 145 (198)
+|..|+...
T Consensus 7 ~C~~Cg~~f 15 (52)
T TIGR02605 7 RCTACGHRF 15 (52)
T ss_pred EeCCCCCEe
Confidence 456665543
No 93
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=36.07 E-value=15 Score=23.51 Aligned_cols=27 Identities=11% Similarity=0.204 Sum_probs=17.1
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCccc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWH 162 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H 162 (198)
..|+-|+..|.++-|..+|...|+.++
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~ 30 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFY 30 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEE
T ss_pred EEecccCCccCCCCCeEEEecCCCeEE
Confidence 468999999988777777777777765
No 94
>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=34.48 E-value=36 Score=19.82 Aligned_cols=13 Identities=23% Similarity=0.634 Sum_probs=9.6
Q ss_pred cccCCCCCCCCCC
Q psy8131 13 FACVVCKTPIGTK 25 (198)
Q Consensus 13 F~C~~C~~~L~~~ 25 (198)
++|..|++.+.+.
T Consensus 1 ~~Cd~C~~~~~~g 13 (49)
T cd02335 1 YHCDYCSKDITGT 13 (49)
T ss_pred CCCCCcCCCCCCC
Confidence 4688898887753
No 95
>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=34.36 E-value=11 Score=17.78 Aligned_cols=12 Identities=17% Similarity=0.869 Sum_probs=7.9
Q ss_pred cccCCCCCCCCC
Q psy8131 13 FACVVCKTPIGT 24 (198)
Q Consensus 13 F~C~~C~~~L~~ 24 (198)
|+|..|++.+..
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 567777776654
No 96
>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=34.02 E-value=15 Score=17.01 Aligned_cols=12 Identities=25% Similarity=0.888 Sum_probs=6.5
Q ss_pred cccCCCCCCCCC
Q psy8131 13 FACVVCKTPIGT 24 (198)
Q Consensus 13 F~C~~C~~~L~~ 24 (198)
|.|..|+..+.+
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 567777776654
No 97
>KOG1813|consensus
Probab=32.80 E-value=25 Score=28.96 Aligned_cols=47 Identities=15% Similarity=0.490 Sum_probs=35.7
Q ss_pred ccCcCCcccCCCCCCCCCCCcccCCCeecchhhHHhhh--ccccccccccc
Q psy8131 7 QWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKF--ATRCVKCNKTF 55 (198)
Q Consensus 7 ~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~--~~~C~~C~~~~ 55 (198)
.|-.. |.|..|++++.+. .+..=|-.+|+.|.-+.+ +++|..|++.+
T Consensus 237 ~~~~P-f~c~icr~~f~~p-Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 237 IELLP-FKCFICRKYFYRP-VVTKCGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred cccCC-ccccccccccccc-hhhcCCceeehhhhccccccCCcceeccccc
Confidence 44444 8899999998864 445667789999997765 46999999954
No 98
>PRK11595 DNA utilization protein GntX; Provisional
Probab=32.66 E-value=49 Score=25.96 Aligned_cols=37 Identities=30% Similarity=0.500 Sum_probs=24.7
Q ss_pred CCccCcCCCCCCceeecCCcccchhhHhhhh--ccCCCCCCCCCc
Q psy8131 104 TCSNCSTSLAGQRFTSREDKPFCADCFGELF--AKRCYSCKKPIT 146 (198)
Q Consensus 104 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~--~~~C~~C~~~I~ 146 (198)
+|..|++++... ...+|..|..+.. .+.|..|++++.
T Consensus 7 ~C~~C~~~~~~~------~~~lC~~C~~~l~~~~~~C~~Cg~~~~ 45 (227)
T PRK11595 7 LCWLCRMPLALS------HWGICSVCSRALRTLKTCCPQCGLPAT 45 (227)
T ss_pred cCccCCCccCCC------CCcccHHHHhhCCcccCcCccCCCcCC
Confidence 477777777422 1347999976542 467999998864
No 99
>smart00746 TRASH metallochaperone-like domain.
Probab=31.29 E-value=54 Score=16.23 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=12.4
Q ss_pred CCCCCCCCcCCCCceEEeeCCCccc
Q psy8131 138 CYSCKKPITGIGGTRFISFEDRHWH 162 (198)
Q Consensus 138 C~~C~~~I~~~~~~~~~~~~~~~~H 162 (198)
|+.|+..|............|+.+|
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~ 25 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFY 25 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEE
Confidence 5677777762111122235555554
No 100
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=30.50 E-value=36 Score=23.43 Aligned_cols=25 Identities=24% Similarity=0.945 Sum_probs=18.3
Q ss_pred ccCcCCCCCCCCceEecCCceeCcccccc
Q psy8131 167 MCASCQSSLVGRGFITDGEDIICPDCAKA 195 (198)
Q Consensus 167 ~C~~C~~~l~~~~~~~~~~~~~C~~C~~~ 195 (198)
.|..| .+..|+..++.+.|..|-.+
T Consensus 37 aCeiC----~~~GY~q~g~~lvC~~C~~~ 61 (102)
T PF10080_consen 37 ACEIC----GPKGYYQEGDQLVCKNCGVR 61 (102)
T ss_pred ecccc----CCCceEEECCEEEEecCCCE
Confidence 56777 56678888888888888544
No 101
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.11 E-value=47 Score=30.68 Aligned_cols=37 Identities=24% Similarity=0.608 Sum_probs=21.3
Q ss_pred CCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcC
Q psy8131 104 TCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITG 147 (198)
Q Consensus 104 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~ 147 (198)
+|..|+..... +.-||..|-..+-...|..|+..+..
T Consensus 3 ~Cp~Cg~~n~~-------~akFC~~CG~~l~~~~Cp~CG~~~~~ 39 (645)
T PRK14559 3 ICPQCQFENPN-------NNRFCQKCGTSLTHKPCPQCGTEVPV 39 (645)
T ss_pred cCCCCCCcCCC-------CCccccccCCCCCCCcCCCCCCCCCc
Confidence 46666665432 23456666544434567777777654
No 102
>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=30.09 E-value=36 Score=19.69 Aligned_cols=11 Identities=45% Similarity=1.186 Sum_probs=6.4
Q ss_pred CCCCCCC-CCcC
Q psy8131 137 RCYSCKK-PITG 147 (198)
Q Consensus 137 ~C~~C~~-~I~~ 147 (198)
.|..|+. ||.|
T Consensus 2 ~Cd~C~~~pI~G 13 (45)
T cd02344 2 TCDGCQMFPING 13 (45)
T ss_pred CCCCCCCCCCcc
Confidence 4666663 5554
No 103
>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=29.49 E-value=7.2 Score=21.02 Aligned_cols=17 Identities=29% Similarity=0.849 Sum_probs=12.4
Q ss_pred cccCCCCCCCCCCCccc
Q psy8131 13 FACVVCKTPIGTKSFIP 29 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~ 29 (198)
|.|..|++++....|+.
T Consensus 5 ~~C~nC~R~v~a~RfA~ 21 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAP 21 (33)
T ss_dssp EE-TTTSSEEEGGGHHH
T ss_pred EECCCCcCCcchhhhHH
Confidence 67888888888777763
No 104
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=28.95 E-value=28 Score=25.45 Aligned_cols=40 Identities=15% Similarity=0.417 Sum_probs=23.7
Q ss_pred cCCCCCCCCCcCCCCceE---EeeCCCcccccCcccCcCCCCC
Q psy8131 136 KRCYSCKKPITGIGGTRF---ISFEDRHWHNDCFMCASCQSSL 175 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~---~~~~~~~~H~~Cf~C~~C~~~l 175 (198)
.+|..|+.++..-+.+.+ |-..-...+.+-+.|..|++..
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 589999887754221111 1112222355667899999977
No 105
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.79 E-value=77 Score=26.42 Aligned_cols=44 Identities=23% Similarity=0.663 Sum_probs=29.2
Q ss_pred CCccCcCC--CCCC-ceeec-CCcccchhhHhhhh---ccCCCCCCCCCcC
Q psy8131 104 TCSNCSTS--LAGQ-RFTSR-EDKPFCADCFGELF---AKRCYSCKKPITG 147 (198)
Q Consensus 104 ~C~~C~~~--l~~~-~~~~~-~g~~yC~~c~~~~~---~~~C~~C~~~I~~ 147 (198)
.|..|... +... .+.+. =|..+|..|....+ ...|..|++++..
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 46677764 3322 22332 48999999998765 3479999888865
No 106
>PRK12495 hypothetical protein; Provisional
Probab=28.28 E-value=33 Score=27.05 Aligned_cols=27 Identities=22% Similarity=0.568 Sum_probs=20.1
Q ss_pred cCCcccCCCCCCCCCCCcccCCCeecchhhHH
Q psy8131 10 EKCFACVVCKTPIGTKSFIPREQEIYCANCYE 41 (198)
Q Consensus 10 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 41 (198)
..=+.|..|+.+|. ...|..+|..|-.
T Consensus 40 msa~hC~~CG~PIp-----a~pG~~~Cp~CQ~ 66 (226)
T PRK12495 40 MTNAHCDECGDPIF-----RHDGQEFCPTCQQ 66 (226)
T ss_pred cchhhcccccCccc-----CCCCeeECCCCCC
Confidence 34477999999987 4588888877754
No 107
>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=27.14 E-value=35 Score=19.14 Aligned_cols=28 Identities=21% Similarity=0.545 Sum_probs=12.1
Q ss_pred ccCcCCCCCCCC-ceEecC-CceeCccccc
Q psy8131 167 MCASCQSSLVGR-GFITDG-EDIICPDCAK 194 (198)
Q Consensus 167 ~C~~C~~~l~~~-~~~~~~-~~~~C~~C~~ 194 (198)
+|+.|+++.+.. ..+.-. +..+|..|..
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 466666666433 223222 4555666644
No 108
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=26.83 E-value=60 Score=17.54 Aligned_cols=31 Identities=16% Similarity=0.574 Sum_probs=23.0
Q ss_pred cCCCCCCCCCCCcccCCCeecchhhHHhhhc
Q psy8131 15 CVVCKTPIGTKSFIPREQEIYCANCYEEKFA 45 (198)
Q Consensus 15 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 45 (198)
|..|...+.+......=|-.||..|..+.+.
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~ 31 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLE 31 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHH
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHH
Confidence 5678787776654555688899999987654
No 109
>KOG2879|consensus
Probab=26.79 E-value=70 Score=26.18 Aligned_cols=44 Identities=25% Similarity=0.504 Sum_probs=31.9
Q ss_pred cccCCCCCCCCCCCcccCCCeecchhhHHhhhc----ccccccccccc
Q psy8131 13 FACVVCKTPIGTKSFIPREQEIYCANCYEEKFA----TRCVKCNKTFF 56 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~----~~C~~C~~~~~ 56 (198)
-+|..|+.+-.-.--...=|.+||-.|...... -+|..||.+..
T Consensus 240 ~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 240 TECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred ceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 367888887664333344678999999987765 38999999653
No 110
>KOG2932|consensus
Probab=26.72 E-value=32 Score=28.66 Aligned_cols=44 Identities=20% Similarity=0.381 Sum_probs=31.7
Q ss_pred CCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCCCcC
Q psy8131 104 TCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITG 147 (198)
Q Consensus 104 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~ 147 (198)
.|..|+.++.--.-.+-=+.+||.+|....--+.|..|..+|..
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQR 135 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHH
Confidence 58899998853223334578899999865555689999988854
No 111
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=26.45 E-value=45 Score=17.17 Aligned_cols=13 Identities=38% Similarity=0.731 Sum_probs=10.7
Q ss_pred cccCCCCCCCCCC
Q psy8131 13 FACVVCKTPIGTK 25 (198)
Q Consensus 13 F~C~~C~~~L~~~ 25 (198)
|.|..|++.+++.
T Consensus 1 ~~C~~C~~~~~~~ 13 (30)
T PF03107_consen 1 FWCDVCRRKIDGF 13 (30)
T ss_pred CCCCCCCCCcCCC
Confidence 5789999998875
No 112
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=26.27 E-value=31 Score=27.24 Aligned_cols=31 Identities=29% Similarity=0.613 Sum_probs=24.7
Q ss_pred cCCcccCCCCCCCCCCCcccCCCeecchhhH
Q psy8131 10 EKCFACVVCKTPIGTKSFIPREQEIYCANCY 40 (198)
Q Consensus 10 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy 40 (198)
|+=..|..|+++++...|...+|...|..|.
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3435799999998866677899999998886
No 113
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=25.51 E-value=56 Score=25.26 Aligned_cols=27 Identities=11% Similarity=0.366 Sum_probs=15.8
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCcccccCc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWHNDCF 166 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf 166 (198)
..|..|...+.. .+++.-|+.|+..|.
T Consensus 19 ~~CpICld~~~d----PVvT~CGH~FC~~CI 45 (193)
T PLN03208 19 FDCNICLDQVRD----PVVTLCGHLFCWPCI 45 (193)
T ss_pred cCCccCCCcCCC----cEEcCCCchhHHHHH
Confidence 346666666544 455666666655554
No 114
>KOG2893|consensus
Probab=25.46 E-value=21 Score=28.48 Aligned_cols=35 Identities=17% Similarity=0.556 Sum_probs=18.1
Q ss_pred ccCCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCC
Q psy8131 135 AKRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL 175 (198)
Q Consensus 135 ~~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 175 (198)
.+-|.-|++...++ +++.-.. -..+|+|..|++.|
T Consensus 10 kpwcwycnrefdde---kiliqhq---kakhfkchichkkl 44 (341)
T KOG2893|consen 10 KPWCWYCNREFDDE---KILIQHQ---KAKHFKCHICHKKL 44 (341)
T ss_pred Cceeeecccccchh---hhhhhhh---hhccceeeeehhhh
Confidence 34566666665542 3322211 23457777777766
No 115
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=25.15 E-value=64 Score=21.05 Aligned_cols=43 Identities=23% Similarity=0.558 Sum_probs=14.9
Q ss_pred CCccCcCCC----CCCceeec--CCcccchhhHhh---hhccCCCCCCCCCc
Q psy8131 104 TCSNCSTSL----AGQRFTSR--EDKPFCADCFGE---LFAKRCYSCKKPIT 146 (198)
Q Consensus 104 ~C~~C~~~l----~~~~~~~~--~g~~yC~~c~~~---~~~~~C~~C~~~I~ 146 (198)
.|..|+..+ .++.|+.- =+-+.|+.||+- .-...|..|+.+-.
T Consensus 11 iCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 11 ICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred ccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 466777665 23444432 267889999852 23467888875543
No 116
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=24.99 E-value=29 Score=19.90 Aligned_cols=22 Identities=36% Similarity=1.167 Sum_probs=14.7
Q ss_pred cCCCCCCCCCCCcccCCCeecch-hhH
Q psy8131 15 CVVCKTPIGTKSFIPREQEIYCA-NCY 40 (198)
Q Consensus 15 C~~C~~~L~~~~f~~~~g~~yC~-~cy 40 (198)
|..|.+.+.. ..++.+||. .|-
T Consensus 9 C~~Cdk~~~~----~~~~~lYCSe~Cr 31 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCSEECR 31 (43)
T ss_pred HHHhhccccC----CCCCccccCHHHH
Confidence 4567777654 578889994 443
No 117
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=24.49 E-value=36 Score=19.91 Aligned_cols=11 Identities=45% Similarity=1.189 Sum_probs=7.9
Q ss_pred CCCCCCC-CCcC
Q psy8131 137 RCYSCKK-PITG 147 (198)
Q Consensus 137 ~C~~C~~-~I~~ 147 (198)
.|..|.+ +|.+
T Consensus 2 ~C~~C~~~~i~g 13 (49)
T cd02345 2 SCSACRKQDISG 13 (49)
T ss_pred cCCCCCCCCceE
Confidence 4778887 7765
No 118
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=24.48 E-value=43 Score=16.52 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=9.3
Q ss_pred cccCCCCCCCCCC
Q psy8131 13 FACVVCKTPIGTK 25 (198)
Q Consensus 13 F~C~~C~~~L~~~ 25 (198)
|.|..|++.+.+.
T Consensus 2 ~~C~~C~k~f~~~ 14 (27)
T PF12171_consen 2 FYCDACDKYFSSE 14 (27)
T ss_dssp CBBTTTTBBBSSH
T ss_pred CCcccCCCCcCCH
Confidence 5678888777653
No 119
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=24.35 E-value=48 Score=17.74 Aligned_cols=23 Identities=17% Similarity=0.307 Sum_probs=14.7
Q ss_pred ccCCCCCCCCCCCcccCCCeecchhh
Q psy8131 14 ACVVCKTPIGTKSFIPREQEIYCANC 39 (198)
Q Consensus 14 ~C~~C~~~L~~~~f~~~~g~~yC~~c 39 (198)
.|..|+.++. +...++...|..|
T Consensus 5 ~C~~C~~~~i---~~~~~~~~~C~~C 27 (33)
T PF08792_consen 5 KCSKCGGNGI---VNKEDDYEVCIFC 27 (33)
T ss_pred EcCCCCCCeE---EEecCCeEEcccC
Confidence 5778887763 4356666666655
No 120
>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=24.17 E-value=1.1e+02 Score=15.33 Aligned_cols=14 Identities=21% Similarity=0.650 Sum_probs=8.4
Q ss_pred cCCcccchhhHhhh
Q psy8131 120 REDKPFCADCFGEL 133 (198)
Q Consensus 120 ~~g~~yC~~c~~~~ 133 (198)
.=|..+|..|..+.
T Consensus 15 ~C~H~~c~~C~~~~ 28 (39)
T smart00184 15 PCGHTFCRSCIRKW 28 (39)
T ss_pred cCCChHHHHHHHHH
Confidence 34566777776544
No 121
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.01 E-value=49 Score=29.52 Aligned_cols=28 Identities=29% Similarity=0.517 Sum_probs=20.4
Q ss_pred eeecCCcccchhhHh-hhhccCCCCCCCC
Q psy8131 117 FTSREDKPFCADCFG-ELFAKRCYSCKKP 144 (198)
Q Consensus 117 ~~~~~g~~yC~~c~~-~~~~~~C~~C~~~ 144 (198)
+.-.++.+.|..|-. ......|..|+..
T Consensus 234 ~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 234 YHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred EecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 445567889999954 4446789999875
No 122
>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=23.88 E-value=54 Score=29.12 Aligned_cols=61 Identities=23% Similarity=0.543 Sum_probs=0.0
Q ss_pred CCeecchhhHHhhhcccccccccccccccccccccccCCcccccceeeeeeeeeeeccCceEeCCcCccccCCCCccCcC
Q psy8131 31 EQEIYCANCYEEKFATRCVKCNKTFFRLREKGTFQSHSGRINKVYSILFYFLFQIITSGGVTYKNEPWHRECFTCSNCST 110 (198)
Q Consensus 31 ~g~~yC~~cy~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~H~~CF~C~~C~~ 110 (198)
+.-.||+.|. ..+|..|-. .++.+.++..|...+....+...+..=-.+||.|-.|..
T Consensus 3 ~~L~fC~~C~----~irc~~c~~------------------~Ei~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~ 60 (483)
T PF05502_consen 3 EELYFCEHCH----KIRCPRCVS------------------EEIDSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFS 60 (483)
T ss_pred ccceeccccc----ccCChhhcc------------------cccceeECccccccCChhhheeccceeccccccCCCCCC
Q ss_pred CCC
Q psy8131 111 SLA 113 (198)
Q Consensus 111 ~l~ 113 (198)
+|.
T Consensus 61 ~L~ 63 (483)
T PF05502_consen 61 PLS 63 (483)
T ss_pred cce
No 123
>KOG3002|consensus
Probab=23.84 E-value=63 Score=26.80 Aligned_cols=43 Identities=21% Similarity=0.596 Sum_probs=37.6
Q ss_pred cccCCCCCCCCCCCcccCCCeecchhhHHhhhcccccccccccc
Q psy8131 13 FACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFF 56 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~~~ 56 (198)
+.|.+|...|....|.=.+|-+.|..|-.++ ..+|..|..++.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~-~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKV-SNKCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhh-cccCCccccccc
Confidence 6789999999998888889999999999765 669999999775
No 124
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=23.58 E-value=62 Score=19.31 Aligned_cols=25 Identities=32% Similarity=0.527 Sum_probs=15.0
Q ss_pred cCCCCCCCCCcCCCCceEEeeCCCcccc
Q psy8131 136 KRCYSCKKPITGIGGTRFISFEDRHWHN 163 (198)
Q Consensus 136 ~~C~~C~~~I~~~~~~~~~~~~~~~~H~ 163 (198)
.+|..|++||... ..+......-|+
T Consensus 2 ~iCvvCK~Pi~~a---l~v~T~~Gpvh~ 26 (53)
T PHA02610 2 KICVVCKQPIEKA---LVVETEKGPVHP 26 (53)
T ss_pred ceeeeeCCchhhc---eEEecCCCCCCC
Confidence 4688899998652 344444444454
No 125
>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=23.57 E-value=17 Score=20.35 Aligned_cols=29 Identities=14% Similarity=0.250 Sum_probs=16.5
Q ss_pred CCCCCCCCCcCCCCceEEeeCCCcccccCc
Q psy8131 137 RCYSCKKPITGIGGTRFISFEDRHWHNDCF 166 (198)
Q Consensus 137 ~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf 166 (198)
.|..|...+... ...++..-++.||.+|+
T Consensus 2 ~C~IC~~~~~~~-~~~~~l~C~H~fh~~Ci 30 (44)
T PF13639_consen 2 ECPICLEEFEDG-EKVVKLPCGHVFHRSCI 30 (44)
T ss_dssp CETTTTCBHHTT-SCEEEETTSEEEEHHHH
T ss_pred CCcCCChhhcCC-CeEEEccCCCeeCHHHH
Confidence 466677776542 12333445777777665
No 126
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=22.95 E-value=1e+02 Score=18.13 Aligned_cols=23 Identities=26% Similarity=0.907 Sum_probs=11.4
Q ss_pred CcccchhhHhhhh---ccCCCCCCCC
Q psy8131 122 DKPFCADCFGELF---AKRCYSCKKP 144 (198)
Q Consensus 122 g~~yC~~c~~~~~---~~~C~~C~~~ 144 (198)
|--+|..||.+.. .-+|.+|+++
T Consensus 21 gf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 21 GFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp S----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 4567999987654 4689999876
No 127
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=22.93 E-value=47 Score=19.50 Aligned_cols=11 Identities=64% Similarity=1.440 Sum_probs=7.0
Q ss_pred CCCCCCC-CCcC
Q psy8131 137 RCYSCKK-PITG 147 (198)
Q Consensus 137 ~C~~C~~-~I~~ 147 (198)
.|..|++ ||.+
T Consensus 2 ~Cd~C~~~pi~g 13 (49)
T cd02334 2 KCNICKEFPITG 13 (49)
T ss_pred CCCCCCCCCcee
Confidence 4777775 5655
No 128
>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=22.85 E-value=80 Score=20.92 Aligned_cols=34 Identities=24% Similarity=0.661 Sum_probs=20.1
Q ss_pred CCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCC
Q psy8131 137 RCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSS 174 (198)
Q Consensus 137 ~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 174 (198)
.|..|+.+|... ....+.+.|..- =|.|..|...
T Consensus 2 ~C~HCg~~~p~~-~~~~~~~~g~~~---~FCC~GC~~V 35 (88)
T PF12156_consen 2 KCYHCGLPVPEG-AKITVEIDGEER---PFCCPGCQAV 35 (88)
T ss_pred CCCCCCCCCCCC-CCeeeeeCCCcc---ccccHHHHHH
Confidence 588899999642 123344555442 2777777653
No 129
>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=22.53 E-value=20 Score=21.85 Aligned_cols=16 Identities=13% Similarity=0.603 Sum_probs=12.7
Q ss_pred cccCCCCCCCCCCCcc
Q psy8131 13 FACVVCKTPIGTKSFI 28 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~ 28 (198)
.+|+.||+.|+...|.
T Consensus 5 lvCSTCGrDlSeeRy~ 20 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCCcchHHHHH
Confidence 4789999999876664
No 130
>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=22.51 E-value=30 Score=18.70 Aligned_cols=10 Identities=20% Similarity=0.637 Sum_probs=5.1
Q ss_pred cccCcCCCCC
Q psy8131 166 FMCASCQSSL 175 (198)
Q Consensus 166 f~C~~C~~~l 175 (198)
++|..|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4455555544
No 131
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=22.37 E-value=24 Score=16.91 Aligned_cols=12 Identities=25% Similarity=0.894 Sum_probs=8.0
Q ss_pred cccCCCCCCCCC
Q psy8131 13 FACVVCKTPIGT 24 (198)
Q Consensus 13 F~C~~C~~~L~~ 24 (198)
|.|..|++.+.+
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 567777776654
No 132
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=22.30 E-value=20 Score=21.87 Aligned_cols=16 Identities=13% Similarity=0.603 Sum_probs=12.5
Q ss_pred cccCCCCCCCCCCCcc
Q psy8131 13 FACVVCKTPIGTKSFI 28 (198)
Q Consensus 13 F~C~~C~~~L~~~~f~ 28 (198)
.+|+.||+.|++..|.
T Consensus 5 lVCsTCGrDlSeeRy~ 20 (63)
T PHA03082 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCcchhHHHHH
Confidence 4789999999876553
No 133
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.13 E-value=52 Score=30.50 Aligned_cols=38 Identities=26% Similarity=0.540 Sum_probs=24.4
Q ss_pred CCccCcCCCCCCceeecCCcccchhhHhhhhccCCCCCCCC
Q psy8131 104 TCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKP 144 (198)
Q Consensus 104 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~ 144 (198)
+|..|+.+|. +...++.+.|..|-.......|..|+..
T Consensus 394 ~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred ECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 3444444442 3334567889999655556799999876
No 134
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.36 E-value=25 Score=21.08 Aligned_cols=26 Identities=19% Similarity=0.724 Sum_probs=18.0
Q ss_pred ccCCCCCCCCCCCccc---CCCeecchhh
Q psy8131 14 ACVVCKTPIGTKSFIP---REQEIYCANC 39 (198)
Q Consensus 14 ~C~~C~~~L~~~~f~~---~~g~~yC~~c 39 (198)
+|..|+..|+.+.+.+ .++.++|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 7899999998776642 2355666665
No 135
>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=21.20 E-value=26 Score=17.14 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=7.7
Q ss_pred cccCCCCCCCCC
Q psy8131 13 FACVVCKTPIGT 24 (198)
Q Consensus 13 F~C~~C~~~L~~ 24 (198)
|.|..|++.+.+
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 136
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=21.11 E-value=7.2 Score=26.46 Aligned_cols=12 Identities=33% Similarity=0.595 Sum_probs=6.2
Q ss_pred cCCCCCCCCCcC
Q psy8131 136 KRCYSCKKPITG 147 (198)
Q Consensus 136 ~~C~~C~~~I~~ 147 (198)
.+|..|.+.++-
T Consensus 63 iiCGvC~~~LT~ 74 (105)
T COG4357 63 IICGVCRKLLTR 74 (105)
T ss_pred EEhhhhhhhhhH
Confidence 345555555543
No 137
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=20.94 E-value=56 Score=25.74 Aligned_cols=28 Identities=25% Similarity=0.528 Sum_probs=15.2
Q ss_pred cccCcCCCCCCCCceEecCCceeCcccc
Q psy8131 166 FMCASCQSSLVGRGFITDGEDIICPDCA 193 (198)
Q Consensus 166 f~C~~C~~~l~~~~~~~~~~~~~C~~C~ 193 (198)
..|..|++++....|...+|..+|..|.
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 3556666555433444455566666653
No 138
>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=20.80 E-value=49 Score=19.20 Aligned_cols=10 Identities=30% Similarity=1.295 Sum_probs=6.7
Q ss_pred cccCcCCCCC
Q psy8131 166 FMCASCQSSL 175 (198)
Q Consensus 166 f~C~~C~~~l 175 (198)
|-|..|.+.|
T Consensus 19 fIC~~CE~~i 28 (46)
T PF10764_consen 19 FICSDCEKEI 28 (46)
T ss_pred EehHHHHHHh
Confidence 6677776665
No 139
>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=20.69 E-value=65 Score=18.62 Aligned_cols=12 Identities=42% Similarity=0.637 Sum_probs=7.4
Q ss_pred cCCCCCCCCCcC
Q psy8131 136 KRCYSCKKPITG 147 (198)
Q Consensus 136 ~~C~~C~~~I~~ 147 (198)
..|..|++.|.+
T Consensus 12 ~~C~~C~~~i~g 23 (53)
T PF00130_consen 12 TYCDVCGKFIWG 23 (53)
T ss_dssp EB-TTSSSBECS
T ss_pred CCCcccCcccCC
Confidence 467777777743
No 140
>KOG2462|consensus
Probab=20.56 E-value=52 Score=26.88 Aligned_cols=27 Identities=19% Similarity=0.406 Sum_probs=16.4
Q ss_pred ccCCCCccCcCCCCCCceeecCCcccc
Q psy8131 100 RECFTCSNCSTSLAGQRFTSREDKPFC 126 (198)
Q Consensus 100 ~~CF~C~~C~~~l~~~~~~~~~g~~yC 126 (198)
...++|..|++.+....-..+..+.-|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~ 154 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHR 154 (279)
T ss_pred CCceeccccccccccccccchhhcccc
Confidence 346899999999865443333333333
No 141
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.19 E-value=59 Score=14.87 Aligned_cols=12 Identities=17% Similarity=0.623 Sum_probs=7.7
Q ss_pred cccCCCCCCCCC
Q psy8131 13 FACVVCKTPIGT 24 (198)
Q Consensus 13 F~C~~C~~~L~~ 24 (198)
+.|..|++.+.+
T Consensus 1 ~~C~~C~~~f~~ 12 (26)
T smart00355 1 YRCPECGKVFKS 12 (26)
T ss_pred CCCCCCcchhCC
Confidence 457777766654
No 142
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=20.15 E-value=45 Score=18.15 Aligned_cols=25 Identities=28% Similarity=0.886 Sum_probs=10.4
Q ss_pred cCcCCCCC--CCCceEecCCceeCccc
Q psy8131 168 CASCQSSL--VGRGFITDGEDIICPDC 192 (198)
Q Consensus 168 C~~C~~~l--~~~~~~~~~~~~~C~~C 192 (198)
|..|+..+ +++.....++.+-|..|
T Consensus 5 CP~C~~~f~v~~~~l~~~~~~vrC~~C 31 (37)
T PF13719_consen 5 CPNCQTRFRVPDDKLPAGGRKVRCPKC 31 (37)
T ss_pred CCCCCceEEcCHHHcccCCcEEECCCC
Confidence 44444444 22223333344445554
No 143
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.08 E-value=1.1e+02 Score=21.92 Aligned_cols=50 Identities=22% Similarity=0.435 Sum_probs=26.6
Q ss_pred ccchhhHhhhhccCCCCCCCCCcCCCCceEEeeCCCcccccCcccCcCCCCC
Q psy8131 124 PFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL 175 (198)
Q Consensus 124 ~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 175 (198)
.+|..|-.. ....|..|+.+|.+..-..-+-..|..|-+-=| |..|+.++
T Consensus 29 afcskcgea-ti~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~f 78 (160)
T COG4306 29 AFCSKCGEA-TITQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRF 78 (160)
T ss_pred HHHhhhchH-HHhcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCC
Confidence 345555433 235678888888763111113344555655333 66777766
Done!