Query psy11756
Match_columns 233
No_of_seqs 173 out of 1766
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 18:07:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11756.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11756hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 100.0 1.4E-37 3E-42 265.3 0.9 181 37-218 272-466 (468)
2 KOG2272|consensus 100.0 1.2E-33 2.6E-38 226.2 -1.7 186 34-220 132-318 (332)
3 KOG2272|consensus 100.0 3.6E-33 7.9E-38 223.5 -4.6 180 37-217 71-255 (332)
4 KOG1703|consensus 100.0 3.6E-29 7.9E-34 226.5 4.4 174 38-211 302-478 (479)
5 KOG1044|consensus 99.9 5.1E-27 1.1E-31 206.9 5.3 182 37-219 14-255 (670)
6 KOG1701|consensus 99.9 5.8E-24 1.3E-28 182.1 -4.1 115 98-213 274-391 (468)
7 KOG1703|consensus 99.9 7.5E-22 1.6E-26 178.9 6.7 175 42-216 246-422 (479)
8 KOG4577|consensus 99.8 2.4E-22 5.3E-27 164.0 -1.9 137 23-160 17-158 (383)
9 KOG4577|consensus 99.8 4.2E-22 9.1E-27 162.7 -1.8 129 92-221 27-160 (383)
10 KOG1044|consensus 99.7 4.8E-18 1E-22 150.6 2.3 116 37-153 131-248 (670)
11 PF00412 LIM: LIM domain; Int 99.5 6.1E-14 1.3E-18 90.9 4.6 55 160-214 1-57 (58)
12 PF00412 LIM: LIM domain; Int 99.4 5.1E-14 1.1E-18 91.3 2.4 56 42-97 1-58 (58)
13 KOG1700|consensus 99.2 4.3E-12 9.4E-17 102.4 1.0 118 39-156 7-167 (200)
14 KOG1700|consensus 99.1 1E-11 2.2E-16 100.2 0.4 119 98-216 7-168 (200)
15 smart00132 LIM Zinc-binding do 98.7 1.9E-08 4.1E-13 59.2 3.0 36 41-76 1-38 (39)
16 smart00132 LIM Zinc-binding do 98.7 2.1E-08 4.5E-13 59.0 3.1 36 159-194 1-38 (39)
17 KOG1702|consensus 97.6 8.7E-06 1.9E-10 64.5 -1.4 60 38-97 3-63 (264)
18 KOG0490|consensus 97.5 1.4E-05 2.9E-10 66.0 -1.8 109 44-154 1-118 (235)
19 KOG0490|consensus 97.4 2.9E-05 6.3E-10 64.0 -0.8 109 104-214 2-119 (235)
20 KOG1702|consensus 95.8 0.00075 1.6E-08 53.7 -3.0 57 100-156 6-63 (264)
21 KOG2462|consensus 85.0 0.27 5.8E-06 41.3 -0.1 126 62-194 127-254 (279)
22 PF14446 Prok-RING_1: Prokaryo 84.3 0.57 1.2E-05 29.4 1.2 38 156-193 4-51 (54)
23 PF14835 zf-RING_6: zf-RING of 83.7 1.1 2.5E-05 29.1 2.4 48 125-172 8-55 (65)
24 PF14835 zf-RING_6: zf-RING of 83.3 1.1 2.4E-05 29.2 2.2 46 66-111 8-53 (65)
25 PF08394 Arc_trans_TRASH: Arch 79.0 0.81 1.8E-05 26.4 0.5 27 42-68 1-29 (37)
26 PF08394 Arc_trans_TRASH: Arch 78.3 1.5 3.2E-05 25.3 1.4 30 160-192 1-32 (37)
27 PF14471 DUF4428: Domain of un 78.1 1.4 3E-05 27.4 1.3 29 185-214 1-30 (51)
28 smart00291 ZnF_ZZ Zinc-binding 76.2 3 6.5E-05 24.9 2.5 32 186-217 7-40 (44)
29 PF11781 RRN7: RNA polymerase 74.6 2.4 5.2E-05 24.3 1.6 25 185-213 10-34 (36)
30 PF10367 Vps39_2: Vacuolar sor 72.6 3.6 7.7E-05 29.1 2.6 27 158-184 79-107 (109)
31 smart00504 Ubox Modified RING 72.5 6.2 0.00013 24.9 3.5 46 125-171 2-49 (63)
32 PF10367 Vps39_2: Vacuolar sor 72.5 3.4 7.4E-05 29.2 2.5 28 185-212 80-108 (109)
33 PF10235 Cript: Microtubule-as 72.0 2.6 5.6E-05 29.5 1.6 44 118-169 38-81 (90)
34 KOG0320|consensus 71.1 2.2 4.7E-05 33.7 1.2 49 122-170 129-180 (187)
35 PF06677 Auto_anti-p27: Sjogre 70.6 3.4 7.3E-05 24.4 1.7 21 186-210 20-40 (41)
36 cd02336 ZZ_RSC8 Zinc finger, Z 69.2 7.6 0.00017 23.4 3.0 39 185-223 2-42 (45)
37 PF14634 zf-RING_5: zinc-RING 68.1 5.8 0.00012 23.5 2.4 39 127-165 2-44 (44)
38 PF13920 zf-C3HC4_3: Zinc fing 67.8 7.6 0.00016 23.5 3.0 43 126-169 4-49 (50)
39 PF06827 zf-FPG_IleRS: Zinc fi 65.7 2.1 4.5E-05 23.2 0.1 13 158-170 2-14 (30)
40 COG1645 Uncharacterized Zn-fin 65.4 4.5 9.7E-05 30.3 1.8 22 186-212 31-52 (131)
41 PF01258 zf-dskA_traR: Prokary 65.3 0.61 1.3E-05 26.6 -2.2 28 186-213 6-33 (36)
42 PF08271 TF_Zn_Ribbon: TFIIB z 65.3 5 0.00011 23.7 1.7 39 184-225 1-39 (43)
43 PF10083 DUF2321: Uncharacteri 65.3 3.9 8.4E-05 31.5 1.5 48 144-193 27-78 (158)
44 COG2191 Formylmethanofuran deh 64.2 3 6.5E-05 33.6 0.7 31 184-214 173-203 (206)
45 PRK04023 DNA polymerase II lar 62.5 12 0.00025 37.4 4.4 76 13-110 599-675 (1121)
46 COG2191 Formylmethanofuran deh 61.0 4 8.6E-05 32.9 0.9 31 66-96 173-203 (206)
47 cd02249 ZZ Zinc finger, ZZ typ 60.0 7.6 0.00016 23.3 1.8 31 185-215 2-34 (46)
48 cd00162 RING RING-finger (Real 60.0 7.5 0.00016 22.1 1.8 40 127-166 2-44 (45)
49 KOG1813|consensus 57.8 6.7 0.00015 33.4 1.8 44 125-169 242-287 (313)
50 COG5152 Uncharacterized conser 56.7 3 6.5E-05 33.5 -0.5 46 125-171 197-244 (259)
51 PRK00420 hypothetical protein; 56.0 7.7 0.00017 28.3 1.6 27 185-215 25-51 (112)
52 PF14569 zf-UDP: Zinc-binding 54.7 5.8 0.00013 26.8 0.7 18 203-220 35-52 (80)
53 PF12773 DZR: Double zinc ribb 53.6 13 0.00029 22.4 2.2 9 159-167 31-39 (50)
54 PF09943 DUF2175: Uncharacteri 52.9 6.8 0.00015 28.0 0.9 31 184-214 3-34 (101)
55 COG1645 Uncharacterized Zn-fin 51.0 9.1 0.0002 28.7 1.4 22 126-152 30-51 (131)
56 PF06906 DUF1272: Protein of u 50.8 17 0.00037 23.0 2.3 43 68-110 8-53 (57)
57 PRK14559 putative protein seri 50.8 14 0.0003 35.5 2.8 22 146-167 16-37 (645)
58 cd02338 ZZ_PCMF_like Zinc fing 50.0 20 0.00044 21.8 2.6 15 203-217 23-37 (49)
59 TIGR00595 priA primosomal prot 49.5 14 0.00031 34.2 2.7 39 125-166 223-262 (505)
60 PF07191 zinc-ribbons_6: zinc- 49.3 5.5 0.00012 26.4 -0.0 37 67-108 3-40 (70)
61 KOG0320|consensus 48.8 7.4 0.00016 30.7 0.6 50 62-111 128-180 (187)
62 PLN03208 E3 ubiquitin-protein 48.6 23 0.0005 28.5 3.4 47 124-171 18-82 (193)
63 PRK14890 putative Zn-ribbon RN 48.3 19 0.0004 23.1 2.2 49 99-165 8-56 (59)
64 KOG2462|consensus 48.2 6 0.00013 33.4 0.0 91 35-136 126-227 (279)
65 PLN02400 cellulose synthase 47.1 20 0.00043 36.2 3.4 14 154-167 33-46 (1085)
66 PF06689 zf-C4_ClpX: ClpX C4-t 46.8 20 0.00042 21.0 2.1 31 185-215 3-35 (41)
67 cd02341 ZZ_ZZZ3 Zinc finger, Z 46.5 19 0.00042 21.9 2.1 13 203-215 25-37 (48)
68 cd02340 ZZ_NBR1_like Zinc fing 45.9 19 0.00041 21.4 1.9 10 204-213 23-32 (43)
69 PF02069 Metallothio_Pro: Prok 45.9 12 0.00026 23.3 1.1 25 67-91 9-33 (52)
70 PRK14714 DNA polymerase II lar 45.5 16 0.00035 37.4 2.5 22 145-166 667-688 (1337)
71 KOG4443|consensus 45.5 14 0.0003 35.0 1.9 86 39-136 35-127 (694)
72 PF00645 zf-PARP: Poly(ADP-rib 45.1 3.6 7.8E-05 27.9 -1.5 16 158-173 8-23 (82)
73 COG4847 Uncharacterized protei 44.3 10 0.00023 26.6 0.7 30 184-213 7-37 (103)
74 COG2888 Predicted Zn-ribbon RN 43.5 23 0.00049 22.7 2.1 10 99-108 10-19 (61)
75 cd02345 ZZ_dah Zinc finger, ZZ 43.1 28 0.0006 21.2 2.4 15 204-218 24-38 (49)
76 PLN02638 cellulose synthase A 42.7 23 0.0005 35.8 3.0 12 156-167 16-27 (1079)
77 TIGR03826 YvyF flagellar opero 42.1 18 0.00039 27.4 1.8 32 184-223 82-113 (137)
78 cd02334 ZZ_dystrophin Zinc fin 41.9 33 0.00071 21.0 2.6 34 186-219 3-39 (49)
79 KOG4443|consensus 41.7 11 0.00023 35.7 0.6 23 173-195 105-127 (694)
80 PRK14559 putative protein seri 41.2 29 0.00064 33.3 3.4 8 41-48 3-10 (645)
81 PF13923 zf-C3HC4_2: Zinc fing 41.0 13 0.00028 21.2 0.7 31 186-217 1-32 (39)
82 PF06524 NOA36: NOA36 protein; 40.6 36 0.00079 28.6 3.4 100 63-170 111-222 (314)
83 PF11571 Med27: Mediator compl 40.2 12 0.00027 26.0 0.6 16 152-167 49-64 (90)
84 KOG3816|consensus 40.0 14 0.0003 32.9 0.9 67 146-212 428-508 (526)
85 PF13248 zf-ribbon_3: zinc-rib 38.9 22 0.00048 18.5 1.3 9 159-167 4-12 (26)
86 KOG3002|consensus 37.9 30 0.00065 29.8 2.7 44 124-168 48-91 (299)
87 cd02335 ZZ_ADA2 Zinc finger, Z 37.6 63 0.0014 19.5 3.5 14 203-216 23-36 (49)
88 KOG3579|consensus 36.2 25 0.00053 30.0 1.8 61 37-108 266-327 (352)
89 KOG0978|consensus 35.4 14 0.0003 35.6 0.3 45 125-170 644-691 (698)
90 COG0266 Nei Formamidopyrimidin 35.4 25 0.00053 29.9 1.8 27 157-183 245-271 (273)
91 PF00569 ZZ: Zinc finger, ZZ t 34.9 21 0.00046 21.3 1.0 12 203-214 27-38 (46)
92 PLN02436 cellulose synthase A 34.7 36 0.00079 34.4 3.0 50 155-211 34-85 (1094)
93 PF07754 DUF1610: Domain of un 34.3 30 0.00064 17.9 1.3 10 160-169 1-10 (24)
94 PLN02189 cellulose synthase 34.1 37 0.00081 34.2 3.0 50 155-211 32-83 (1040)
95 PRK14714 DNA polymerase II lar 32.9 31 0.00068 35.4 2.3 11 39-49 667-677 (1337)
96 KOG4739|consensus 32.6 28 0.00061 28.8 1.6 34 136-169 15-49 (233)
97 PRK00398 rpoP DNA-directed RNA 32.3 21 0.00046 21.3 0.7 9 185-193 5-13 (46)
98 PRK14873 primosome assembly pr 31.8 33 0.00072 33.0 2.2 39 125-166 393-431 (665)
99 KOG1813|consensus 31.7 26 0.00055 30.0 1.3 46 65-111 241-288 (313)
100 PF13834 DUF4193: Domain of un 31.5 13 0.00029 26.3 -0.4 27 184-210 71-98 (99)
101 KOG3576|consensus 31.5 13 0.00028 30.1 -0.5 68 63-135 115-184 (267)
102 PF15227 zf-C3HC4_4: zinc fing 31.1 40 0.00086 19.7 1.7 34 186-220 1-34 (42)
103 KOG3002|consensus 30.3 35 0.00077 29.4 1.9 43 66-109 49-91 (299)
104 PF10764 Gin: Inhibitor of sig 29.8 63 0.0014 19.5 2.4 30 185-216 1-30 (46)
105 PF01844 HNH: HNH endonuclease 28.9 17 0.00038 21.2 -0.1 19 195-213 25-43 (47)
106 PRK04023 DNA polymerase II lar 28.7 80 0.0017 31.9 4.2 26 141-166 622-647 (1121)
107 PRK01103 formamidopyrimidine/5 28.7 38 0.00083 28.7 1.9 27 157-183 245-271 (274)
108 COG4357 Zinc finger domain con 28.1 6.9 0.00015 27.6 -2.2 43 42-84 38-81 (105)
109 PF05502 Dynactin_p62: Dynacti 27.8 46 0.00099 30.8 2.3 13 181-193 50-62 (483)
110 PF12674 Zn_ribbon_2: Putative 26.7 30 0.00065 23.6 0.7 30 185-214 2-36 (81)
111 PF08792 A2L_zn_ribbon: A2L zi 26.5 56 0.0012 18.2 1.7 25 185-212 5-29 (33)
112 COG5152 Uncharacterized conser 26.5 13 0.00029 29.9 -1.2 45 66-111 197-243 (259)
113 PF10529 Hist_rich_Ca-bd: Hist 26.4 42 0.00092 15.3 0.9 12 222-233 4-15 (15)
114 PF11077 DUF2616: Protein of u 26.1 49 0.0011 26.1 1.9 36 63-98 137-172 (173)
115 cd02343 ZZ_EF Zinc finger, ZZ 25.9 97 0.0021 18.9 2.8 17 203-219 22-38 (48)
116 PRK14810 formamidopyrimidine-D 25.9 45 0.00098 28.2 1.8 27 157-183 244-270 (272)
117 PRK14811 formamidopyrimidine-D 25.8 46 0.001 28.1 1.9 27 157-183 235-261 (269)
118 KOG0956|consensus 25.8 83 0.0018 30.4 3.6 129 82-221 44-191 (900)
119 PF14447 Prok-RING_4: Prokaryo 25.4 50 0.0011 20.8 1.5 28 143-170 25-52 (55)
120 PRK10445 endonuclease VIII; Pr 25.3 46 0.001 28.0 1.8 27 157-183 235-261 (263)
121 PF10080 DUF2318: Predicted me 25.2 49 0.0011 23.7 1.6 29 185-217 37-65 (102)
122 PLN03208 E3 ubiquitin-protein 25.1 43 0.00093 26.9 1.4 18 184-201 69-86 (193)
123 smart00659 RPOLCX RNA polymera 24.8 38 0.00081 20.2 0.8 26 184-213 3-28 (44)
124 KOG2893|consensus 24.3 23 0.0005 29.4 -0.2 51 158-215 11-62 (341)
125 TIGR00577 fpg formamidopyrimid 24.0 51 0.0011 27.9 1.8 27 157-183 245-271 (272)
126 cd02342 ZZ_UBA_plant Zinc fing 24.0 65 0.0014 19.2 1.7 25 192-216 10-36 (43)
127 COG0068 HypF Hydrogenase matur 24.0 21 0.00047 34.3 -0.5 81 100-193 103-183 (750)
128 cd02344 ZZ_HERC2 Zinc finger, 23.6 71 0.0015 19.2 1.9 28 186-213 3-33 (45)
129 PRK13945 formamidopyrimidine-D 23.6 52 0.0011 28.0 1.8 27 157-183 254-280 (282)
130 PF10122 Mu-like_Com: Mu-like 23.6 35 0.00076 21.1 0.5 27 184-212 5-32 (51)
131 smart00834 CxxC_CXXC_SSSS Puta 23.5 27 0.00059 19.8 0.0 11 125-135 6-16 (41)
132 PF10886 DUF2685: Protein of u 23.4 46 0.001 20.9 1.0 11 185-195 3-13 (54)
133 PRK00807 50S ribosomal protein 23.2 68 0.0015 19.8 1.8 31 185-215 3-39 (52)
134 PF09723 Zn-ribbon_8: Zinc rib 23.1 26 0.00056 20.5 -0.1 11 125-135 6-16 (42)
135 TIGR02605 CxxC_CxxC_SSSS putat 23.0 22 0.00048 21.6 -0.4 9 185-193 7-15 (52)
136 COG1997 RPL43A Ribosomal prote 21.9 1.1E+02 0.0025 21.2 2.8 36 158-201 36-71 (89)
137 PF08746 zf-RING-like: RING-li 21.7 9.9 0.00021 22.6 -2.2 25 160-184 1-28 (43)
138 PF12677 DUF3797: Domain of un 21.7 70 0.0015 19.6 1.6 26 158-183 14-42 (49)
139 KOG2932|consensus 21.4 35 0.00075 29.5 0.3 53 127-179 93-145 (389)
140 PF00097 zf-C3HC4: Zinc finger 21.4 39 0.00084 19.1 0.4 32 186-217 1-32 (41)
141 PRK14873 primosome assembly pr 20.6 82 0.0018 30.4 2.6 39 66-107 393-431 (665)
142 PF01286 XPA_N: XPA protein N- 20.6 37 0.00081 19.1 0.2 26 186-211 6-31 (34)
143 COG1198 PriA Primosomal protei 20.5 79 0.0017 30.9 2.5 39 125-166 445-484 (730)
144 smart00661 RPOL9 RNA polymeras 20.4 56 0.0012 19.6 1.0 9 204-212 20-28 (52)
145 COG0266 Nei Formamidopyrimidin 20.4 79 0.0017 26.9 2.2 27 98-124 245-271 (273)
146 TIGR00595 priA primosomal prot 20.1 96 0.0021 28.8 2.9 39 66-107 223-262 (505)
No 1
>KOG1701|consensus
Probab=100.00 E-value=1.4e-37 Score=265.27 Aligned_cols=181 Identities=31% Similarity=0.719 Sum_probs=165.7
Q ss_pred CCCCccccccccccc--cEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCccccccEEe
Q psy11756 37 TMYPKCAACQGLIQN--IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDVVVT 114 (233)
Q Consensus 37 ~~~~~C~~C~~~I~~--~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~~~~~ 114 (233)
....+|.+|++.|.+ ..+.||++.||..||+|..|++.|.++.||..++++||+.||... ..+|..|++.|.++++.
T Consensus 272 ~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d~iLr 350 (468)
T KOG1701|consen 272 DYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMDRILR 350 (468)
T ss_pred hhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHHHHHH
Confidence 445699999999988 458999999999999999999999999999999999999999875 57999999999999999
Q ss_pred cCCCeeecCCCCCCCCCcccccCceecc-CCceechhhhhhccCCCCCCCCCCcccc-------EEEEcCceecCCCCCc
Q psy11756 115 ALNQTWHPDHFVCISCGTKLLYKGFYER-EGNAFCTACYEGKFCPKCFGCGKPITET-------AIKVHDRKWHEACFRC 186 (233)
Q Consensus 115 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~g~~~C~~c~~~~~~~~C~~C~~~I~~~-------~i~~~~~~~H~~Cf~C 186 (233)
+.|+.||+.||+|.+|++.|.+..|.+. ++++||..+|++.|+++|+.|+++|... .|+++++.||.+|++|
T Consensus 351 A~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~C 430 (468)
T KOG1701|consen 351 ALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKC 430 (468)
T ss_pred hcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccceeh
Confidence 9999999999999999999999888865 7899999999999999999999999542 2789999999999999
Q ss_pred CCCCCCCC----CCceEeeCCeeeChhhhhccccCC
Q psy11756 187 GRCRRPIS----GPTFRVCEADVVCVECSEKGREEG 218 (233)
Q Consensus 187 ~~C~~~l~----~~~~~~~~~~~~C~~C~~~~~~~~ 218 (233)
-.|+..|. +..-|.+||+++|+.|+.++...+
T Consensus 431 EDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl~~~ 466 (468)
T KOG1701|consen 431 EDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRLQAG 466 (468)
T ss_pred hhcCccccccCCCCcceeccCceeechhhhhhhccc
Confidence 99999994 577888999999999999887654
No 2
>KOG2272|consensus
Probab=99.97 E-value=1.2e-33 Score=226.24 Aligned_cols=186 Identities=27% Similarity=0.635 Sum_probs=173.4
Q ss_pred CCCCCCCccccccccccccEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCccccccEE
Q psy11756 34 AASTMYPKCAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDVVV 113 (233)
Q Consensus 34 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~~~~ 113 (233)
+.+.+.-+|.+|+..|.++.|...+..||+..|+|..|++.|.+... ..+|.+||.+|+.+...++|..|+++|.++++
T Consensus 132 a~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaR-evk~eLyClrChD~mgipiCgaC~rpIeervi 210 (332)
T KOG2272|consen 132 AKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDAR-EVKGELYCLRCHDKMGIPICGACRRPIEERVI 210 (332)
T ss_pred ccccceeehhhhhhhcccccccccCCCCCccceecccccccccchhh-hhccceeccccccccCCcccccccCchHHHHH
Confidence 44566789999999999999999999999999999999999986543 66789999999999989999999999999999
Q ss_pred ecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCccccEEEEcCceecCCCCCcCCCCCCC
Q psy11756 114 TALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPI 193 (233)
Q Consensus 114 ~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~i~~~~~~~H~~Cf~C~~C~~~l 193 (233)
.++|+.||.++|+|+.|.+|+.|-..|++.|..||..+|.++++..|..|+++|.+.++.+.++.|.++||+|+.|.+.|
T Consensus 211 ~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~al~KawCv~cf~Cs~Cdkkl 290 (332)
T KOG2272|consen 211 FAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSALNKAWCVECFSCSTCDKKL 290 (332)
T ss_pred HHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHHhhhhhcccccccccccccc
Confidence 99999999999999999999999899999999999999999999999999999999999999999999999999999999
Q ss_pred C-CCceEeeCCeeeChhhhhccccCCCC
Q psy11756 194 S-GPTFRVCEADVVCVECSEKGREEGKN 220 (233)
Q Consensus 194 ~-~~~~~~~~~~~~C~~C~~~~~~~~~~ 220 (233)
+ -.+|+..|-.|.|++||++.+.+++.
T Consensus 291 ~~K~Kf~E~DmkP~CKkCy~rfp~elkk 318 (332)
T KOG2272|consen 291 TQKNKFYEFDMKPVCKKCYDRFPLELKK 318 (332)
T ss_pred ccccceeeeccchHHHHHHhhccHHHHH
Confidence 4 58899999999999999988877654
No 3
>KOG2272|consensus
Probab=99.97 E-value=3.6e-33 Score=223.45 Aligned_cols=180 Identities=28% Similarity=0.597 Sum_probs=165.3
Q ss_pred CCCCccccccccccccEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCcccccccccccc-----CCCCCCCCcccccc
Q psy11756 37 TMYPKCAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLF-----LNKCQGCRLPIKDV 111 (233)
Q Consensus 37 ~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~-----~~~C~~C~~~i~~~ 111 (233)
.-.|.|.+|++.|.|++|.+++.+|||.||+|..|++.|.+..|+-..|+.+|..|..+.. .-.|.+|+..|.+.
T Consensus 71 LfaPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~ 150 (332)
T KOG2272|consen 71 LFAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ 150 (332)
T ss_pred hhchhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc
Confidence 3458999999999999999999999999999999999999999999999999999987632 24799999999889
Q ss_pred EEecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCccccEEEEcCceecCCCCCcCCCCC
Q psy11756 112 VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITETAIKVHDRKWHEACFRCGRCRR 191 (233)
Q Consensus 112 ~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~i~~~~~~~H~~Cf~C~~C~~ 191 (233)
.+++.+..||+.+|+|..|++.|+.. -....|.+||..|++++-.|+|..|.+||++++|.++|+.||.++|+|+.|.+
T Consensus 151 ~l~fr~d~yH~yHFkCt~C~keL~sd-aRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~Cek 229 (332)
T KOG2272|consen 151 PLTFRGDPYHPYHFKCTTCGKELTSD-AREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEK 229 (332)
T ss_pred cccccCCCCCccceecccccccccch-hhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCC
Confidence 99999999999999999999999754 34568899999999999999999999999999999999999999999999999
Q ss_pred CCCCCceEeeCCeeeChhhhhccccC
Q psy11756 192 PISGPTFRVCEADVVCVECSEKGREE 217 (233)
Q Consensus 192 ~l~~~~~~~~~~~~~C~~C~~~~~~~ 217 (233)
++.|-+.+.+.|..||...|.++.-+
T Consensus 230 PFlGHrHYEkkGlaYCe~h~~qLfG~ 255 (332)
T KOG2272|consen 230 PFLGHRHYEKKGLAYCETHYHQLFGN 255 (332)
T ss_pred cccchhhhhhcCchhHHHHHHHHhhh
Confidence 99999999999999999999876543
No 4
>KOG1703|consensus
Probab=99.95 E-value=3.6e-29 Score=226.48 Aligned_cols=174 Identities=34% Similarity=0.749 Sum_probs=166.6
Q ss_pred CCCccccccccccc-cEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCccccccEEecC
Q psy11756 38 MYPKCAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDVVVTAL 116 (233)
Q Consensus 38 ~~~~C~~C~~~I~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~~~~~~~ 116 (233)
..+.|.+|++.|.+ +++.++++.||+.+|.|..|...+....+...+|++||..|+...+.+.|.+|+++|.++.|.+.
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~ 381 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCAL 381 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhc
Confidence 45899999999999 99999999999999999999999998888899999999999999999999999999999999999
Q ss_pred CCeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCcc--ccEEEEcCceecCCCCCcCCCCCCCC
Q psy11756 117 NQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPIT--ETAIKVHDRKWHEACFRCGRCRRPIS 194 (233)
Q Consensus 117 ~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~--~~~i~~~~~~~H~~Cf~C~~C~~~l~ 194 (233)
+..||+.||.|..|+++|.+..|+..+|.+||..||+.++.++|..|.++|+ +..|.+.+..||..||+|+.|.+.|.
T Consensus 382 ~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~ 461 (479)
T KOG1703|consen 382 GRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLT 461 (479)
T ss_pred cCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhcccc
Confidence 9999999999999999999899999999999999999999999999999987 56799999999999999999999999
Q ss_pred CCceEeeCCeeeChhhh
Q psy11756 195 GPTFRVCEADVVCVECS 211 (233)
Q Consensus 195 ~~~~~~~~~~~~C~~C~ 211 (233)
++.|+...++|+|++|+
T Consensus 462 ~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 462 KKTFFETLDKPLCQKHF 478 (479)
T ss_pred CCceeecCCccccccCC
Confidence 99999999999999986
No 5
>KOG1044|consensus
Probab=99.93 E-value=5.1e-27 Score=206.91 Aligned_cols=182 Identities=24% Similarity=0.573 Sum_probs=154.1
Q ss_pred CCCCccccccccccccEeeecCCCcCcCCCccCCCCCCCCCCceeeeCC-cccccccccccc------------------
Q psy11756 37 TMYPKCAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAG-SPYCVEDYASLF------------------ 97 (233)
Q Consensus 37 ~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~-~~yC~~c~~~~~------------------ 97 (233)
.....|..|.+...++++.+.++.+|..||+|..|+..|....|+.+++ ++|+........
T Consensus 14 ~~~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~ 93 (670)
T KOG1044|consen 14 KQGIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFS 93 (670)
T ss_pred ccceehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccce
Confidence 4456899999999999999999999999999999999999888888765 355542211110
Q ss_pred ---------------------------------------CCCCCCCCccc-cccEEecCCCeeecCCCCCCCCCcccccC
Q psy11756 98 ---------------------------------------LNKCQGCRLPI-KDVVVTALNQTWHPDHFVCISCGTKLLYK 137 (233)
Q Consensus 98 ---------------------------------------~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 137 (233)
-..|++|++.| .+..+.++++.||..||+|..|...|.+
T Consensus 94 cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g- 172 (670)
T KOG1044|consen 94 CSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG- 172 (670)
T ss_pred ecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-
Confidence 01589999988 5668899999999999999999999976
Q ss_pred ceeccCCceechhhhhhccCCCCCCCCCCccccEEEEcCceecCCCCCcCCCCCCCC-CCceEeeCCeeeChhhhhcccc
Q psy11756 138 GFYEREGNAFCTACYEGKFCPKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPIS-GPTFRVCEADVVCVECSEKGRE 216 (233)
Q Consensus 138 ~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~i~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~~~~~C~~C~~~~~~ 216 (233)
.|..++|.+||..+|.+.|+.+|..|.+.|.+++|.++|+.||+.|.+|.+|+.++. |++.|+....+|-..|-.....
T Consensus 173 ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa~~t 252 (670)
T KOG1044|consen 173 EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQATKT 252 (670)
T ss_pred eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhccCcccCcchhhhhhhccccccchheeeccccccCCccccccch
Confidence 588899999999999999999999999999999999999999999999999999995 5555555667999999876665
Q ss_pred CCC
Q psy11756 217 EGK 219 (233)
Q Consensus 217 ~~~ 219 (233)
|+.
T Consensus 253 E~i 255 (670)
T KOG1044|consen 253 EEI 255 (670)
T ss_pred hhc
Confidence 443
No 6
>KOG1701|consensus
Probab=99.86 E-value=5.8e-24 Score=182.08 Aligned_cols=115 Identities=30% Similarity=0.745 Sum_probs=107.3
Q ss_pred CCCCCCCCcccccc--EEecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCccccEEEEc
Q psy11756 98 LNKCQGCRLPIKDV--VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITETAIKVH 175 (233)
Q Consensus 98 ~~~C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~i~~~ 175 (233)
..+|.+|++.|.+. .+.|+++.||..||+|..|.+.|.+..||.+++++||+.||... ..+|..|+++|.++.|++.
T Consensus 274 ~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d~iLrA~ 352 (468)
T KOG1701|consen 274 FGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMDRILRAL 352 (468)
T ss_pred hhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHHHHHHhc
Confidence 34999999999765 78999999999999999999999999999999999999999654 4799999999999999999
Q ss_pred CceecCCCCCcCCCCCCCCCCceEee-CCeeeChhhhhc
Q psy11756 176 DRKWHEACFRCGRCRRPISGPTFRVC-EADVVCVECSEK 213 (233)
Q Consensus 176 ~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~C~~~ 213 (233)
|+.||+.||+|..|++.|.|..|.+. ++++||..+|-+
T Consensus 353 GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~ 391 (468)
T KOG1701|consen 353 GKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHK 391 (468)
T ss_pred ccccCCCceEEEEeccccCCccccccCCCceeeehhhhh
Confidence 99999999999999999999999998 899999999844
No 7
>KOG1703|consensus
Probab=99.85 E-value=7.5e-22 Score=178.92 Aligned_cols=175 Identities=24% Similarity=0.509 Sum_probs=163.0
Q ss_pred cccccccccccEeeecCCCcCcCCCccC-CCCCCCCCCceeeeCCccccccccccccCCCCCCCCccccc-cEEecCCCe
Q psy11756 42 CAACQGLIQNIIVQALDKTWHPEHFRCT-HCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKD-VVVTALNQT 119 (233)
Q Consensus 42 C~~C~~~I~~~~~~~~~~~~H~~Cf~C~-~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~-~~~~~~~~~ 119 (233)
|..+..++....+.+....||...++|. .+...+....++.+.+...+..+|.....++|..|.+.|.+ ..++++++.
T Consensus 246 ~~~~~~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~c~~c~~~i~~~~~i~~~~~~ 325 (479)
T KOG1703|consen 246 SASMDSPECQPLVSAPRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYHNVTRPLCLSCNQKIRSVKVIVALGKE 325 (479)
T ss_pred CcccCCCccCcceecccccccccccccccccchhhcccccccccccccccccccccccccccccccCcccceeEeecccc
Confidence 6667777777778888999999999998 89888888888899999999999988888999999999999 899999999
Q ss_pred eecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCccccEEEEcCceecCCCCCcCCCCCCCCCCceE
Q psy11756 120 WHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFR 199 (233)
Q Consensus 120 ~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~i~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 199 (233)
||+.+|.|..|...+....+...+|.+||..|+...++++|.+|+++|.++.|.+.++.||++||.|+.|++.|.+..|+
T Consensus 326 ~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~ 405 (479)
T KOG1703|consen 326 WHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFF 405 (479)
T ss_pred ccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhccCeechhceeeecccCCCCCCccc
Confidence 99999999999999987778888999999999999999999999999999999999999999999999999999999999
Q ss_pred eeCCeeeChhhhhcccc
Q psy11756 200 VCEADVVCVECSEKGRE 216 (233)
Q Consensus 200 ~~~~~~~C~~C~~~~~~ 216 (233)
..++.+||..||.++..
T Consensus 406 ~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 406 ESDGEPYCEDHYKKLFT 422 (479)
T ss_pred ccCCccchhhhHhhhcc
Confidence 99999999999998774
No 8
>KOG4577|consensus
Probab=99.83 E-value=2.4e-22 Score=164.03 Aligned_cols=137 Identities=28% Similarity=0.610 Sum_probs=114.4
Q ss_pred ccccCCCCCCCCCCCCCCccccccccccccE-eeecCCCcCcCCCccCCCCCCCCCCceeeeCCccccccccccccCCCC
Q psy11756 23 DVSEALDPPPNAASTMYPKCAACQGLIQNII-VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKC 101 (233)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C 101 (233)
+++..+.+.+.-.....++|++|.+.|.+++ ++++++.||..|++|+.|...|.+.. +.++|.+||+.+|.++|+.+|
T Consensus 17 ~~~~lLs~~~df~~~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drC-FsR~~s~yCkedFfKrfGTKC 95 (383)
T KOG4577|consen 17 DLPGLLSPQEDFSNVEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRC-FSREGSVYCKEDFFKRFGTKC 95 (383)
T ss_pred cChhhccccccccccccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHH-hhcCCceeehHHHHHHhCCcc
Confidence 3444444333333347899999999999975 78999999999999999999999754 599999999999999999999
Q ss_pred CCCCcccccc--EEecCCCeeecCCCCCCCCCcccc-cCceec-cCCceechhhhhhccCCCC
Q psy11756 102 QGCRLPIKDV--VVTALNQTWHPDHFVCISCGTKLL-YKGFYE-REGNAFCTACYEGKFCPKC 160 (233)
Q Consensus 102 ~~C~~~i~~~--~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~-~~g~~~C~~c~~~~~~~~C 160 (233)
..|...|... +..+.+..||..||.|..|+++|. |..||. .+++++|+.+|.+.-..-|
T Consensus 96 saC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 96 SACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred hhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 9999999654 445889999999999999999996 667775 5889999999987665555
No 9
>KOG4577|consensus
Probab=99.82 E-value=4.2e-22 Score=162.68 Aligned_cols=129 Identities=29% Similarity=0.669 Sum_probs=113.3
Q ss_pred ccccccCCCCCCCCcccccc-EEecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCcccc
Q psy11756 92 DYASLFLNKCQGCRLPIKDV-VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITET 170 (233)
Q Consensus 92 c~~~~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~ 170 (233)
++.....++|++|.+.|.++ ++.++++.||..|++|+.|..+|.. ..+.++|.+||..+|.++|+.+|..|...|.+.
T Consensus 27 df~~~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPt 105 (383)
T KOG4577|consen 27 DFSNVEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPT 105 (383)
T ss_pred cccccccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChH
Confidence 33333468999999999998 6679999999999999999999975 466789999999999999999999999999765
Q ss_pred E--EEEcCceecCCCCCcCCCCCCC-CCCceEee-CCeeeChhhhhccccCCCCC
Q psy11756 171 A--IKVHDRKWHEACFRCGRCRRPI-SGPTFRVC-EADVVCVECSEKGREEGKND 221 (233)
Q Consensus 171 ~--i~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~-~~~~~C~~C~~~~~~~~~~~ 221 (233)
. ..+.+..||..||.|..|+++| +|++||++ |++++|+.-|+.+.+..-+.
T Consensus 106 qVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~ 160 (383)
T KOG4577|consen 106 QVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNE 160 (383)
T ss_pred HHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccc
Confidence 4 3488999999999999999999 88999998 89999999999988766543
No 10
>KOG1044|consensus
Probab=99.69 E-value=4.8e-18 Score=150.55 Aligned_cols=116 Identities=28% Similarity=0.600 Sum_probs=106.5
Q ss_pred CCCCccccccccc-cccEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCccccccEEec
Q psy11756 37 TMYPKCAACQGLI-QNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDVVVTA 115 (233)
Q Consensus 37 ~~~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~~~~~~ 115 (233)
.....|++|++.| .|..+.|+++.||..||+|..|+..|.+ .|..++|.+||+.||...|+.+|..|.+.|.+.++.+
T Consensus 131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqa 209 (670)
T KOG1044|consen 131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQA 209 (670)
T ss_pred cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhc
Confidence 4567899999998 5599999999999999999999999885 6889999999999999999999999999999999999
Q ss_pred CCCeeecCCCCCCCCCcccc-cCceeccCCceechhhhh
Q psy11756 116 LNQTWHPDHFVCISCGTKLL-YKGFYEREGNAFCTACYE 153 (233)
Q Consensus 116 ~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~g~~~C~~c~~ 153 (233)
.++.||+.|-+|..|+++|. |+..|+.+..++.+.|-.
T Consensus 210 g~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 210 GDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred cCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence 99999999999999999997 668888888888888853
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=99.47 E-value=6.1e-14 Score=90.93 Aligned_cols=55 Identities=36% Similarity=0.922 Sum_probs=49.6
Q ss_pred CCCCCCCccccEE--EEcCceecCCCCCcCCCCCCCCCCceEeeCCeeeChhhhhcc
Q psy11756 160 CFGCGKPITETAI--KVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECSEKG 214 (233)
Q Consensus 160 C~~C~~~I~~~~i--~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~ 214 (233)
|.+|+++|.+..+ .+.|+.||++||+|..|+++|.++.|+..+|+|||..||.+.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKR 57 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhh
Confidence 7899999987654 499999999999999999999888899999999999999763
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=99.43 E-value=5.1e-14 Score=91.28 Aligned_cols=56 Identities=39% Similarity=0.915 Sum_probs=50.6
Q ss_pred cccccccccc-cE-eeecCCCcCcCCCccCCCCCCCCCCceeeeCCcccccccccccc
Q psy11756 42 CAACQGLIQN-II-VQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLF 97 (233)
Q Consensus 42 C~~C~~~I~~-~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~ 97 (233)
|.+|+++|.+ .. +.++|+.||+.||+|..|+++|.+..|+..+|++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 7899999987 33 46999999999999999999999888999999999999998764
No 13
>KOG1700|consensus
Probab=99.19 E-value=4.3e-12 Score=102.35 Aligned_cols=118 Identities=29% Similarity=0.579 Sum_probs=99.7
Q ss_pred CCccccccccccc-cEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCccccccccccccCC------------------
Q psy11756 39 YPKCAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLN------------------ 99 (233)
Q Consensus 39 ~~~C~~C~~~I~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~------------------ 99 (233)
...|.+|++.|+- +.+...|..||+.||+|..|.+.|....+..+++.+||..+|...+.+
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD 86 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence 3489999999977 555688999999999999999999988888899999999976555322
Q ss_pred -----------------------CCCCCCcccccc-EEecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhc
Q psy11756 100 -----------------------KCQGCRLPIKDV-VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGK 155 (233)
Q Consensus 100 -----------------------~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~ 155 (233)
.|..|++.+... -++..+..||..||+|..|+..|....+....|.+||..++.++
T Consensus 87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~ 166 (200)
T KOG1700|consen 87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQL 166 (200)
T ss_pred cccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhhee
Confidence 688898888643 67788999999999999999999988888889999998776554
Q ss_pred c
Q psy11756 156 F 156 (233)
Q Consensus 156 ~ 156 (233)
+
T Consensus 167 ~ 167 (200)
T KOG1700|consen 167 F 167 (200)
T ss_pred e
Confidence 4
No 14
>KOG1700|consensus
Probab=99.13 E-value=1e-11 Score=100.24 Aligned_cols=119 Identities=26% Similarity=0.600 Sum_probs=98.4
Q ss_pred CCCCCCCCcccccc-EEecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCC------------------
Q psy11756 98 LNKCQGCRLPIKDV-VVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCP------------------ 158 (233)
Q Consensus 98 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~------------------ 158 (233)
...|..|++.+.-. .+...+..||..||+|..|...|....+...++.+||..++...+++
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD 86 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence 45899999999543 55688999999999999999999877888899999999965443332
Q ss_pred -----------------------CCCCCCCCccc-cEEEEcCceecCCCCCcCCCCCCCCCCceEeeCCeeeChhhhhcc
Q psy11756 159 -----------------------KCFGCGKPITE-TAIKVHDRKWHEACFRCGRCRRPISGPTFRVCEADVVCVECSEKG 214 (233)
Q Consensus 159 -----------------------~C~~C~~~I~~-~~i~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~ 214 (233)
.|.+|.+.+.+ +.+...+..||..||+|..|++.|+.+.+....|.+||...+...
T Consensus 87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~ 166 (200)
T KOG1700|consen 87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQL 166 (200)
T ss_pred cccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhhee
Confidence 29999998865 346677889999999999999999999999999999888877664
Q ss_pred cc
Q psy11756 215 RE 216 (233)
Q Consensus 215 ~~ 216 (233)
..
T Consensus 167 ~~ 168 (200)
T KOG1700|consen 167 FK 168 (200)
T ss_pred ec
Confidence 44
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=98.66 E-value=1.9e-08 Score=59.24 Aligned_cols=36 Identities=44% Similarity=1.130 Sum_probs=32.8
Q ss_pred ccccccccccc--cEeeecCCCcCcCCCccCCCCCCCC
Q psy11756 41 KCAACQGLIQN--IIVQALDKTWHPEHFRCTHCRIPIA 76 (233)
Q Consensus 41 ~C~~C~~~I~~--~~~~~~~~~~H~~Cf~C~~C~~~l~ 76 (233)
+|.+|++.|.+ ..+.++++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58899999987 6788899999999999999999985
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=98.66 E-value=2.1e-08 Score=59.03 Aligned_cols=36 Identities=42% Similarity=1.239 Sum_probs=32.3
Q ss_pred CCCCCCCCccc--cEEEEcCceecCCCCCcCCCCCCCC
Q psy11756 159 KCFGCGKPITE--TAIKVHDRKWHEACFRCGRCRRPIS 194 (233)
Q Consensus 159 ~C~~C~~~I~~--~~i~~~~~~~H~~Cf~C~~C~~~l~ 194 (233)
+|.+|+++|.+ ..+.+.+..||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58999999987 5677899999999999999999985
No 17
>KOG1702|consensus
Probab=97.57 E-value=8.7e-06 Score=64.53 Aligned_cols=60 Identities=23% Similarity=0.549 Sum_probs=53.2
Q ss_pred CCCccccccccccc-cEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCcccccccccccc
Q psy11756 38 MYPKCAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLF 97 (233)
Q Consensus 38 ~~~~C~~C~~~I~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~ 97 (233)
.+..|..|++.++. +-|..+++.||..||+|..|+.+|....|-..+.++||..+|....
T Consensus 3 ~k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 3 KKCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred ccchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 45678899999988 7788899999999999999999999888888899999999997653
No 18
>KOG0490|consensus
Probab=97.46 E-value=1.4e-05 Score=65.98 Aligned_cols=109 Identities=27% Similarity=0.551 Sum_probs=85.1
Q ss_pred ccccccccc-EeeecCCCcCcCCCccCCCCCCCC--CCceeeeCCcccccccccc--ccCCCCCCCCcccc--ccEEecC
Q psy11756 44 ACQGLIQNI-IVQALDKTWHPEHFRCTHCRIPIA--TQKFHVHAGSPYCVEDYAS--LFLNKCQGCRLPIK--DVVVTAL 116 (233)
Q Consensus 44 ~C~~~I~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~yC~~c~~~--~~~~~C~~C~~~i~--~~~~~~~ 116 (233)
.|+..|.+. .+.+.+..||..|..|..|..+|. ...|.. +|..||..+|.. .+..+|.+|...+. +.+..+.
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f 79 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAF 79 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhh
Confidence 367788774 466779999999999999999997 555555 999999999998 77789999999983 3455566
Q ss_pred CCeeecCCCCCCCCCcccc-cCceecc-CCceechhhhhh
Q psy11756 117 NQTWHPDHFVCISCGTKLL-YKGFYER-EGNAFCTACYEG 154 (233)
Q Consensus 117 ~~~~H~~Cf~C~~C~~~l~-~~~~~~~-~g~~~C~~c~~~ 154 (233)
.+. |.-||.|..|...+. +..+.+. +.+.+|...+.+
T Consensus 80 ~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 80 EKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred cCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 666 999999999988664 4455554 447888777644
No 19
>KOG0490|consensus
Probab=97.38 E-value=2.9e-05 Score=64.01 Aligned_cols=109 Identities=25% Similarity=0.563 Sum_probs=86.7
Q ss_pred CCcccccc-EEecCCCeeecCCCCCCCCCcccc--cCceeccCCceechhhhhh--ccCCCCCCCCCCccc--cEEEEcC
Q psy11756 104 CRLPIKDV-VVTALNQTWHPDHFVCISCGTKLL--YKGFYEREGNAFCTACYEG--KFCPKCFGCGKPITE--TAIKVHD 176 (233)
Q Consensus 104 C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~~C~~c~~~--~~~~~C~~C~~~I~~--~~i~~~~ 176 (233)
|+..|.+. .+.+.+..||..|..|..|...+. ...|.. +|..||...+.. .+..+|.+|.+.|.. ....+..
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~ 80 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFE 80 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhc
Confidence 56677665 445668999999999999999997 445555 999999999987 778899999999833 2334555
Q ss_pred ceecCCCCCcCCCCCCC-CCCceEeeCC-eeeChhhhhcc
Q psy11756 177 RKWHEACFRCGRCRRPI-SGPTFRVCEA-DVVCVECSEKG 214 (233)
Q Consensus 177 ~~~H~~Cf~C~~C~~~l-~~~~~~~~~~-~~~C~~C~~~~ 214 (233)
+. |-.||.|..|...+ .+..+.+.+. +..|.+.+...
T Consensus 81 ~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 81 KV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred CC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 56 99999999999987 5677777665 89999999766
No 20
>KOG1702|consensus
Probab=95.76 E-value=0.00075 Score=53.74 Aligned_cols=57 Identities=23% Similarity=0.576 Sum_probs=45.0
Q ss_pred CCCCCCccccc-cEEecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhcc
Q psy11756 100 KCQGCRLPIKD-VVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKF 156 (233)
Q Consensus 100 ~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~ 156 (233)
.|..|++.+.. +-+.-+++.||..||+|..|+.+|.-..+-..+.++||..+|....
T Consensus 6 n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred hhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 45566666643 2466788999999999999999998767777899999999996544
No 21
>KOG2462|consensus
Probab=84.99 E-value=0.27 Score=41.28 Aligned_cols=126 Identities=16% Similarity=0.295 Sum_probs=73.0
Q ss_pred CcCCCccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCccccccEEecCCCeeecCCCCCCCCCcccccCceec
Q psy11756 62 HPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYE 141 (233)
Q Consensus 62 H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~ 141 (233)
-...++|..|++.+.+..=..+-.+..|..+-. ....|..|++.-...-...+-..-|.-=++|.+|++.|... |.
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~--ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRP-WL- 202 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSK--KAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRP-WL- 202 (279)
T ss_pred cCCceeccccccccccccccchhhccccccccc--ccccCCCCCceeeehHHHhhHhhccCCCcccccccccccch-HH-
Confidence 356789999999988643334555666665543 35689999876533211112223355557899999988633 22
Q ss_pred cCCceechhhhhhccCCCCCCCCCCccccE-EEEc-CceecCCCCCcCCCCCCCC
Q psy11756 142 REGNAFCTACYEGKFCPKCFGCGKPITETA-IKVH-DRKWHEACFRCGRCRRPIS 194 (233)
Q Consensus 142 ~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~-i~~~-~~~~H~~Cf~C~~C~~~l~ 194 (233)
..|.+-- +. ..-.-.|+.|++...++- |++. -..-+..=|.|.+|+|.+.
T Consensus 203 LQGHiRT--HT-GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 203 LQGHIRT--HT-GEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFA 254 (279)
T ss_pred hhccccc--cc-CCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHH
Confidence 2333311 11 111125888888887753 3332 1123344688999998874
No 22
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=84.25 E-value=0.57 Score=29.44 Aligned_cols=38 Identities=29% Similarity=0.561 Sum_probs=25.1
Q ss_pred cCCCCCCCCCCcc-ccEEEE---cCceecCCCC----CcCC--CCCCC
Q psy11756 156 FCPKCFGCGKPIT-ETAIKV---HDRKWHEACF----RCGR--CRRPI 193 (233)
Q Consensus 156 ~~~~C~~C~~~I~-~~~i~~---~~~~~H~~Cf----~C~~--C~~~l 193 (233)
.+.+|..|+++|. +..|++ -+..||.+|+ .|.. |+..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 3568999999995 333433 4678999997 3655 55443
No 23
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=83.74 E-value=1.1 Score=29.13 Aligned_cols=48 Identities=21% Similarity=0.352 Sum_probs=22.8
Q ss_pred CCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCccccEE
Q psy11756 125 FVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITETAI 172 (233)
Q Consensus 125 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~i 172 (233)
.+|+.|..-+...-....=+..||..|....++..|+.|+.|-....+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~ 55 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDI 55 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS-
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHH
Confidence 477888776653322234568899999888888889999988654443
No 24
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=83.31 E-value=1.1 Score=29.22 Aligned_cols=46 Identities=15% Similarity=0.256 Sum_probs=22.3
Q ss_pred CccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCcccccc
Q psy11756 66 FRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDV 111 (233)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~~ 111 (233)
++|+.|...|........=...||..|....++..|+.|+.|....
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 5788888877654333344567899998887778899998887543
No 25
>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=79.00 E-value=0.81 Score=26.41 Aligned_cols=27 Identities=30% Similarity=0.509 Sum_probs=19.2
Q ss_pred cccccccccc--cEeeecCCCcCcCCCcc
Q psy11756 42 CAACQGLIQN--IIVQALDKTWHPEHFRC 68 (233)
Q Consensus 42 C~~C~~~I~~--~~~~~~~~~~H~~Cf~C 68 (233)
|.-|+.+|.+ .++...++.||--|-.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC 29 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTC 29 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHH
Confidence 6778999987 34667788888655443
No 26
>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=78.26 E-value=1.5 Score=25.34 Aligned_cols=30 Identities=30% Similarity=0.688 Sum_probs=18.9
Q ss_pred CCCCCCCccccE--EEEcCceecCCCCCcCCCCCC
Q psy11756 160 CFGCGKPITETA--IKVHDRKWHEACFRCGRCRRP 192 (233)
Q Consensus 160 C~~C~~~I~~~~--i~~~~~~~H~~Cf~C~~C~~~ 192 (233)
|.-|++.|.++. +.+.++.|| |-|..|.+.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHH
Confidence 677888887654 446777787 444444443
No 27
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=78.09 E-value=1.4 Score=27.42 Aligned_cols=29 Identities=24% Similarity=0.694 Sum_probs=22.6
Q ss_pred CcCCCCCCCC-CCceEeeCCeeeChhhhhcc
Q psy11756 185 RCGRCRRPIS-GPTFRVCEADVVCVECSEKG 214 (233)
Q Consensus 185 ~C~~C~~~l~-~~~~~~~~~~~~C~~C~~~~ 214 (233)
.|..|++.+. -.++...|| .+|..|+.++
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 4888998883 234667788 7999999997
No 28
>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=76.20 E-value=3 Score=24.86 Aligned_cols=32 Identities=28% Similarity=0.698 Sum_probs=18.0
Q ss_pred cCCCCCCCCCCceEee--CCeeeChhhhhccccC
Q psy11756 186 CGRCRRPISGPTFRVC--EADVVCVECSEKGREE 217 (233)
Q Consensus 186 C~~C~~~l~~~~~~~~--~~~~~C~~C~~~~~~~ 217 (233)
|..|++.+.+.+|.-. .+--+|..||.+....
T Consensus 7 C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~~ 40 (44)
T smart00291 7 CDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSAG 40 (44)
T ss_pred CCCCCCCCcCCEEECCCCCCccchHHHHhCcCcC
Confidence 4445554444444332 3456899998875544
No 29
>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=74.59 E-value=2.4 Score=24.28 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=18.4
Q ss_pred CcCCCCCCCCCCceEeeCCeeeChhhhhc
Q psy11756 185 RCGRCRRPISGPTFRVCEADVVCVECSEK 213 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~~~~~~~C~~C~~~ 213 (233)
.|..|+.. .|...+|..||..|.-+
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCceE
Confidence 47777765 46777999999888643
No 30
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=72.63 E-value=3.6 Score=29.14 Aligned_cols=27 Identities=30% Similarity=0.685 Sum_probs=17.9
Q ss_pred CCCCCCCCCccccE-EEEc-CceecCCCC
Q psy11756 158 PKCFGCGKPITETA-IKVH-DRKWHEACF 184 (233)
Q Consensus 158 ~~C~~C~~~I~~~~-i~~~-~~~~H~~Cf 184 (233)
..|+.|+++|.... +++. |..+|..|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 46888888885443 4444 456887776
No 31
>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=72.55 E-value=6.2 Score=24.93 Aligned_cols=46 Identities=15% Similarity=0.143 Sum_probs=32.7
Q ss_pred CCCCCCCcccccCceeccCCceechhhhhhcc--CCCCCCCCCCccccE
Q psy11756 125 FVCISCGTKLLYKGFYEREGNAFCTACYEGKF--CPKCFGCGKPITETA 171 (233)
Q Consensus 125 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~--~~~C~~C~~~I~~~~ 171 (233)
|.|..|+..+.. +.....|..||..|..+.. ...|+.|++++....
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence 568888887764 5666789999998875433 457888888775433
No 32
>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=72.50 E-value=3.4 Score=29.24 Aligned_cols=28 Identities=29% Similarity=0.695 Sum_probs=18.0
Q ss_pred CcCCCCCCCCCCceEee-CCeeeChhhhh
Q psy11756 185 RCGRCRRPISGPTFRVC-EADVVCVECSE 212 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~~-~~~~~C~~C~~ 212 (233)
.|..|++.|.++.|.+. +|.++...|.+
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 36777777766666665 66666666653
No 33
>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=72.00 E-value=2.6 Score=29.47 Aligned_cols=44 Identities=32% Similarity=0.672 Sum_probs=30.1
Q ss_pred CeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCccc
Q psy11756 118 QTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITE 169 (233)
Q Consensus 118 ~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~ 169 (233)
..|-+.--+|..|+..+. ..|..||..|..+. -+|+.|++.|.+
T Consensus 38 nPy~~~~~~C~~CK~~v~------q~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 38 NPYAPYSSKCKICKTKVH------QPGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred CcccccCccccccccccc------cCCCccChhhhccc--CcccccCCeecc
Confidence 344444446888887653 23678899996554 389999999865
No 34
>KOG0320|consensus
Probab=71.14 E-value=2.2 Score=33.67 Aligned_cols=49 Identities=27% Similarity=0.567 Sum_probs=36.9
Q ss_pred cCCCCCCCCCcccccC-ceeccCCceechhhhhhcc--CCCCCCCCCCcccc
Q psy11756 122 PDHFVCISCGTKLLYK-GFYEREGNAFCTACYEGKF--CPKCFGCGKPITET 170 (233)
Q Consensus 122 ~~Cf~C~~C~~~l~~~-~~~~~~g~~~C~~c~~~~~--~~~C~~C~~~I~~~ 170 (233)
..+|+|..|-...... .+..+=|++||..|..... +.+|+.|++.|+.+
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 3468888888777643 3556789999999986543 57899999988764
No 35
>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=70.61 E-value=3.4 Score=24.42 Aligned_cols=21 Identities=33% Similarity=1.002 Sum_probs=12.0
Q ss_pred cCCCCCCCCCCceEeeCCeeeChhh
Q psy11756 186 CGRCRRPISGPTFRVCEADVVCVEC 210 (233)
Q Consensus 186 C~~C~~~l~~~~~~~~~~~~~C~~C 210 (233)
|..|+.+| |...+|++||..|
T Consensus 20 Cp~C~~PL----~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPL----MRDKDGKIYCVSC 40 (41)
T ss_pred cCCCCCee----EEecCCCEECCCC
Confidence 44555555 2245667777665
No 36
>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=69.15 E-value=7.6 Score=23.39 Aligned_cols=39 Identities=18% Similarity=0.387 Sum_probs=26.1
Q ss_pred CcCCCCCCCCCCceEee--CCeeeChhhhhccccCCCCCCC
Q psy11756 185 RCGRCRRPISGPTFRVC--EADVVCVECSEKGREEGKNDTS 223 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~~--~~~~~C~~C~~~~~~~~~~~~~ 223 (233)
.|..|+..++..+|... .+.-+|..||.+.+--.+-+.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G~f~~~~~s~ 42 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEGRFPSNFQSS 42 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhCcCCCCCCccc
Confidence 46777777765555544 2458999999987765555443
No 37
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=68.10 E-value=5.8 Score=23.46 Aligned_cols=39 Identities=28% Similarity=0.484 Sum_probs=25.7
Q ss_pred CCCCCcccc--cCceeccCCceechhhhhhcc--CCCCCCCCC
Q psy11756 127 CISCGTKLL--YKGFYEREGNAFCTACYEGKF--CPKCFGCGK 165 (233)
Q Consensus 127 C~~C~~~l~--~~~~~~~~g~~~C~~c~~~~~--~~~C~~C~~ 165 (233)
|..|...+. ...+...=|..+|..|..++. ...|+.|++
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 556666662 223344458899999987776 567887764
No 38
>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=67.83 E-value=7.6 Score=23.53 Aligned_cols=43 Identities=28% Similarity=0.414 Sum_probs=28.2
Q ss_pred CCCCCCcccccCceeccCCce-echhhhhhc--cCCCCCCCCCCccc
Q psy11756 126 VCISCGTKLLYKGFYEREGNA-FCTACYEGK--FCPKCFGCGKPITE 169 (233)
Q Consensus 126 ~C~~C~~~l~~~~~~~~~g~~-~C~~c~~~~--~~~~C~~C~~~I~~ 169 (233)
.|..|...... ..+..=|.. +|..|..+. ...+|+.|.++|..
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 46666665432 333456777 999998766 46789999998853
No 39
>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=65.69 E-value=2.1 Score=23.20 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=5.5
Q ss_pred CCCCCCCCCcccc
Q psy11756 158 PKCFGCGKPITET 170 (233)
Q Consensus 158 ~~C~~C~~~I~~~ 170 (233)
.+|.+|...|...
T Consensus 2 ~~C~rC~~~~~~~ 14 (30)
T PF06827_consen 2 EKCPRCWNYIEDI 14 (30)
T ss_dssp SB-TTT--BBEEE
T ss_pred CcCccCCCcceEe
Confidence 3566666665543
No 40
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=65.39 E-value=4.5 Score=30.31 Aligned_cols=22 Identities=36% Similarity=1.038 Sum_probs=18.3
Q ss_pred cCCCCCCCCCCceEeeCCeeeChhhhh
Q psy11756 186 CGRCRRPISGPTFRVCEADVVCVECSE 212 (233)
Q Consensus 186 C~~C~~~l~~~~~~~~~~~~~C~~C~~ 212 (233)
|..|+.+| |- ++|.+||..|-.
T Consensus 31 Cp~Cg~PL----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 31 CPKCGTPL----FR-KDGEVFCPVCGY 52 (131)
T ss_pred CcccCCcc----ee-eCCeEECCCCCc
Confidence 77888888 55 899999999983
No 41
>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=65.33 E-value=0.61 Score=26.60 Aligned_cols=28 Identities=32% Similarity=0.832 Sum_probs=19.3
Q ss_pred cCCCCCCCCCCceEeeCCeeeChhhhhc
Q psy11756 186 CGRCRRPISGPTFRVCEADVVCVECSEK 213 (233)
Q Consensus 186 C~~C~~~l~~~~~~~~~~~~~C~~C~~~ 213 (233)
|..|+..+...+.....+..+|..|...
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 7777777766677777788888888754
No 42
>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=65.30 E-value=5 Score=23.68 Aligned_cols=39 Identities=23% Similarity=0.417 Sum_probs=21.8
Q ss_pred CCcCCCCCCCCCCceEeeCCeeeChhhhhccccCCCCCCCCC
Q psy11756 184 FRCGRCRRPISGPTFRVCEADVVCVECSEKGREEGKNDTSSY 225 (233)
Q Consensus 184 f~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~ 225 (233)
++|..|+... -.+-...|.++|..| ...+++..++.+.+
T Consensus 1 m~Cp~Cg~~~--~~~D~~~g~~vC~~C-G~Vl~e~~i~~~~e 39 (43)
T PF08271_consen 1 MKCPNCGSKE--IVFDPERGELVCPNC-GLVLEENIIDEGPE 39 (43)
T ss_dssp ESBTTTSSSE--EEEETTTTEEEETTT--BBEE-TTBSCCCS
T ss_pred CCCcCCcCCc--eEEcCCCCeEECCCC-CCEeecccccCCcc
Confidence 4677777643 112223688999999 44555555555444
No 43
>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=65.26 E-value=3.9 Score=31.52 Aligned_cols=48 Identities=21% Similarity=0.578 Sum_probs=32.3
Q ss_pred CceechhhhhhccCCCCCCCCCCccccE----EEEcCceecCCCCCcCCCCCCC
Q psy11756 144 GNAFCTACYEGKFCPKCFGCGKPITETA----IKVHDRKWHEACFRCGRCRRPI 193 (233)
Q Consensus 144 g~~~C~~c~~~~~~~~C~~C~~~I~~~~----i~~~~~~~H~~Cf~C~~C~~~l 193 (233)
..-||..|-.+.. ..|+.|+.+|.|.+ +...+..|+.-= -|..|+++.
T Consensus 27 ~~~fC~kCG~~tI-~~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGkpy 78 (158)
T PF10083_consen 27 REKFCSKCGAKTI-TSCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGKPY 78 (158)
T ss_pred HHHHHHHhhHHHH-HHCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCCCC
Confidence 3568999976654 68999999998754 334456666322 266777665
No 44
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=64.16 E-value=3 Score=33.57 Aligned_cols=31 Identities=32% Similarity=0.677 Sum_probs=26.6
Q ss_pred CCcCCCCCCCCCCceEeeCCeeeChhhhhcc
Q psy11756 184 FRCGRCRRPISGPTFRVCEADVVCVECSEKG 214 (233)
Q Consensus 184 f~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~ 214 (233)
-+|..|+..+...+-...+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6799999998777778889999999999764
No 45
>PRK04023 DNA polymerase II large subunit; Validated
Probab=62.49 E-value=12 Score=37.43 Aligned_cols=76 Identities=16% Similarity=0.241 Sum_probs=44.8
Q ss_pred CCCCCCCCccccccCCC-CCCCCCCCCCCccccccccccccEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCcccccc
Q psy11756 13 LLGQGDETDVDVSEALD-PPPNAASTMYPKCAACQGLIQNIIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVE 91 (233)
Q Consensus 13 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~ 91 (233)
++|....+.++...+.. ...-........|..|+... .=|+|..|+..- .....|..
T Consensus 599 PiG~~GG~~R~i~~A~~~~g~~eVEVg~RfCpsCG~~t--------------~~frCP~CG~~T--------e~i~fCP~ 656 (1121)
T PRK04023 599 PIGNAGGSTRDINKAAKYKGTIEVEIGRRKCPSCGKET--------------FYRRCPFCGTHT--------EPVYRCPR 656 (1121)
T ss_pred cccccCcccccHHHHHhcCCceeecccCccCCCCCCcC--------------CcccCCCCCCCC--------CcceeCcc
Confidence 44444444444443333 12223345567899998762 227889998861 22336888
Q ss_pred ccccccCCCCCCCCccccc
Q psy11756 92 DYASLFLNKCQGCRLPIKD 110 (233)
Q Consensus 92 c~~~~~~~~C~~C~~~i~~ 110 (233)
|-.......|..|+..+..
T Consensus 657 CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 657 CGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred ccCcCCCCcCCCCCCCCCc
Confidence 8666555678888877743
No 46
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=60.98 E-value=4 Score=32.90 Aligned_cols=31 Identities=23% Similarity=0.416 Sum_probs=26.6
Q ss_pred CccCCCCCCCCCCceeeeCCccccccccccc
Q psy11756 66 FRCTHCRIPIATQKFHVHAGSPYCVEDYASL 96 (233)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~ 96 (233)
-+|+.|+..+....-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999998877777899999999998754
No 47
>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=60.03 E-value=7.6 Score=23.28 Aligned_cols=31 Identities=32% Similarity=0.777 Sum_probs=16.6
Q ss_pred CcCCCCCCCCCCceEee--CCeeeChhhhhccc
Q psy11756 185 RCGRCRRPISGPTFRVC--EADVVCVECSEKGR 215 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~~--~~~~~C~~C~~~~~ 215 (233)
.|..|++.|.|.+|.-. .+--+|..|+....
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 34455554444333322 24567888887654
No 48
>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=60.02 E-value=7.5 Score=22.07 Aligned_cols=40 Identities=23% Similarity=0.484 Sum_probs=19.9
Q ss_pred CCCCCcccccCceeccCCceechhhhhhcc---CCCCCCCCCC
Q psy11756 127 CISCGTKLLYKGFYEREGNAFCTACYEGKF---CPKCFGCGKP 166 (233)
Q Consensus 127 C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~---~~~C~~C~~~ 166 (233)
|..|...+........=|..+|..|..... ..+|+.|+..
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 455555542221222246667777764332 3457766654
No 49
>KOG1813|consensus
Probab=57.78 E-value=6.7 Score=33.45 Aligned_cols=44 Identities=23% Similarity=0.615 Sum_probs=25.7
Q ss_pred CCCCCCCcccccCceeccCCceechhhhhhcc--CCCCCCCCCCccc
Q psy11756 125 FVCISCGTKLLYKGFYEREGNAFCTACYEGKF--CPKCFGCGKPITE 169 (233)
Q Consensus 125 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~--~~~C~~C~~~I~~ 169 (233)
|.|..|++.+.. +.+..-+..+|..|..+.+ +++|..|++.+.+
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccCCcceeccccccc
Confidence 566666666542 3444556666776664444 3466666666654
No 50
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=56.67 E-value=3 Score=33.45 Aligned_cols=46 Identities=26% Similarity=0.536 Sum_probs=34.4
Q ss_pred CCCCCCCcccccCceeccCCceechhhhhhcc--CCCCCCCCCCccccE
Q psy11756 125 FVCISCGTKLLYKGFYEREGNAFCTACYEGKF--CPKCFGCGKPITETA 171 (233)
Q Consensus 125 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~--~~~C~~C~~~I~~~~ 171 (233)
|.|..|+..... +.+..=|..+|..|+.+.+ ++.|..|++...+.+
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f 244 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRF 244 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccce
Confidence 788889887753 4556678889999987665 568888888766644
No 51
>PRK00420 hypothetical protein; Validated
Probab=55.99 E-value=7.7 Score=28.31 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=18.6
Q ss_pred CcCCCCCCCCCCceEeeCCeeeChhhhhccc
Q psy11756 185 RCGRCRRPISGPTFRVCEADVVCVECSEKGR 215 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~ 215 (233)
.|..|+.+| |...+|+.||..|.....
T Consensus 25 ~CP~Cg~pL----f~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPL----FELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCcc----eecCCCceECCCCCCeee
Confidence 466677666 444788888888876443
No 52
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=54.73 E-value=5.8 Score=26.82 Aligned_cols=18 Identities=44% Similarity=0.674 Sum_probs=8.8
Q ss_pred CeeeChhhhhccccCCCC
Q psy11756 203 ADVVCVECSEKGREEGKN 220 (233)
Q Consensus 203 ~~~~C~~C~~~~~~~~~~ 220 (233)
+-|.|+.||+..+.+++.
T Consensus 35 ~fPvCr~CyEYErkeg~q 52 (80)
T PF14569_consen 35 AFPVCRPCYEYERKEGNQ 52 (80)
T ss_dssp -----HHHHHHHHHTS-S
T ss_pred CCccchhHHHHHhhcCcc
Confidence 457888888777776654
No 53
>PF12773 DZR: Double zinc ribbon
Probab=53.56 E-value=13 Score=22.41 Aligned_cols=9 Identities=33% Similarity=0.755 Sum_probs=4.3
Q ss_pred CCCCCCCCc
Q psy11756 159 KCFGCGKPI 167 (233)
Q Consensus 159 ~C~~C~~~I 167 (233)
.|..|+..+
T Consensus 31 ~C~~Cg~~~ 39 (50)
T PF12773_consen 31 ICPNCGAEN 39 (50)
T ss_pred CCcCCcCCC
Confidence 355555443
No 54
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=52.86 E-value=6.8 Score=27.97 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=22.7
Q ss_pred CCcCCCCCCC-CCCceEeeCCeeeChhhhhcc
Q psy11756 184 FRCGRCRRPI-SGPTFRVCEADVVCVECSEKG 214 (233)
Q Consensus 184 f~C~~C~~~l-~~~~~~~~~~~~~C~~C~~~~ 214 (233)
++|..|++.+ .|+.|.+..+.|..-.|+...
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 4677788777 677777777778878887653
No 55
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=51.01 E-value=9.1 Score=28.69 Aligned_cols=22 Identities=45% Similarity=1.174 Sum_probs=16.6
Q ss_pred CCCCCCcccccCceeccCCceechhhh
Q psy11756 126 VCISCGTKLLYKGFYEREGNAFCTACY 152 (233)
Q Consensus 126 ~C~~C~~~l~~~~~~~~~g~~~C~~c~ 152 (233)
.|..|+.|| | .++|.+||+.|-
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 477888776 3 389999998775
No 56
>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=50.81 E-value=17 Score=22.97 Aligned_cols=43 Identities=12% Similarity=0.436 Sum_probs=28.9
Q ss_pred cCCCCCCCCCC---ceeeeCCccccccccccccCCCCCCCCccccc
Q psy11756 68 CTHCRIPIATQ---KFHVHAGSPYCVEDYASLFLNKCQGCRLPIKD 110 (233)
Q Consensus 68 C~~C~~~l~~~---~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~ 110 (233)
|..|++.|... .+.-.-.=.||..|.......+|..|+..+..
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv~ 53 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELVR 53 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCcccc
Confidence 56667777532 23223334688999888878899999887643
No 57
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=50.78 E-value=14 Score=35.46 Aligned_cols=22 Identities=27% Similarity=0.697 Sum_probs=9.7
Q ss_pred eechhhhhhccCCCCCCCCCCc
Q psy11756 146 AFCTACYEGKFCPKCFGCGKPI 167 (233)
Q Consensus 146 ~~C~~c~~~~~~~~C~~C~~~I 167 (233)
.||..|-..+....|..|+..+
T Consensus 16 kFC~~CG~~l~~~~Cp~CG~~~ 37 (645)
T PRK14559 16 RFCQKCGTSLTHKPCPQCGTEV 37 (645)
T ss_pred ccccccCCCCCCCcCCCCCCCC
Confidence 3444444333334455555444
No 58
>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=50.00 E-value=20 Score=21.82 Aligned_cols=15 Identities=20% Similarity=0.598 Sum_probs=10.0
Q ss_pred CeeeChhhhhccccC
Q psy11756 203 ADVVCVECSEKGREE 217 (233)
Q Consensus 203 ~~~~C~~C~~~~~~~ 217 (233)
+--+|.+||......
T Consensus 23 d~dlC~~Cf~~~~~~ 37 (49)
T cd02338 23 DYDLCADCYDSGVTT 37 (49)
T ss_pred CCccchhHHhCCCcC
Confidence 455788888766543
No 59
>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=49.52 E-value=14 Score=34.23 Aligned_cols=39 Identities=26% Similarity=0.629 Sum_probs=27.4
Q ss_pred CCCCCCCcccccCceeccCCceechhhhhh-ccCCCCCCCCCC
Q psy11756 125 FVCISCGTKLLYKGFYEREGNAFCTACYEG-KFCPKCFGCGKP 166 (233)
Q Consensus 125 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~-~~~~~C~~C~~~ 166 (233)
.+|..|+.+|. |+...+.+.|+.|-.. .....|+.|+..
T Consensus 223 ~~C~~C~~~l~---~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLT---YHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceE---EecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 45677776653 5556788899999544 446689999764
No 60
>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=49.29 E-value=5.5 Score=26.44 Aligned_cols=37 Identities=19% Similarity=0.464 Sum_probs=16.1
Q ss_pred ccCCCCCCCCCCceeeeCCccccccccccc-cCCCCCCCCccc
Q psy11756 67 RCTHCRIPIATQKFHVHAGSPYCVEDYASL-FLNKCQGCRLPI 108 (233)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~-~~~~C~~C~~~i 108 (233)
.|..|+.+|. ..++..+|..|.... ..+.|..|++++
T Consensus 3 ~CP~C~~~L~-----~~~~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELE-----WQGGHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEE-----EETTEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccE-----EeCCEEECccccccceecccCCCcccHH
Confidence 4666666654 233555666654332 125677777666
No 61
>KOG0320|consensus
Probab=48.82 E-value=7.4 Score=30.73 Aligned_cols=50 Identities=20% Similarity=0.488 Sum_probs=37.6
Q ss_pred CcCCCccCCCCCCCCCCc-eeeeCCccccccccccc--cCCCCCCCCcccccc
Q psy11756 62 HPEHFRCTHCRIPIATQK-FHVHAGSPYCVEDYASL--FLNKCQGCRLPIKDV 111 (233)
Q Consensus 62 H~~Cf~C~~C~~~l~~~~-~~~~~~~~yC~~c~~~~--~~~~C~~C~~~i~~~ 111 (233)
-..+++|..|-.+..... +..+=|.+||..|.... .+..|..|++.|...
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 356799999977776543 55677999999998753 457999999988543
No 62
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=48.63 E-value=23 Score=28.45 Aligned_cols=47 Identities=26% Similarity=0.484 Sum_probs=29.1
Q ss_pred CCCCCCCCcccccCceeccCCceechhhhhhc------------------cCCCCCCCCCCccccE
Q psy11756 124 HFVCISCGTKLLYKGFYEREGNAFCTACYEGK------------------FCPKCFGCGKPITETA 171 (233)
Q Consensus 124 Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~------------------~~~~C~~C~~~I~~~~ 171 (233)
-|.|..|...+. ......=|..||..|..+. ....|+.|..+|....
T Consensus 18 ~~~CpICld~~~-dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 18 DFDCNICLDQVR-DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred ccCCccCCCcCC-CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 366777766554 2344556777777776321 2357999998886543
No 63
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=48.30 E-value=19 Score=23.07 Aligned_cols=49 Identities=29% Similarity=0.700 Sum_probs=24.8
Q ss_pred CCCCCCCccccccEEecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCC
Q psy11756 99 NKCQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGK 165 (233)
Q Consensus 99 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~ 165 (233)
+.|..|+..|.+.- +..-|.|..|+..+-. -|..|-.+...-+|..|+.
T Consensus 8 ~~CtSCg~~i~~~~--------~~~~F~CPnCG~~~I~----------RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 8 PKCTSCGIEIAPRE--------KAVKFLCPNCGEVIIY----------RCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred ccccCCCCcccCCC--------ccCEeeCCCCCCeeEe----------echhHHhcCCceECCCCCC
Confidence 45667776664321 1112566666654210 1666655555556666653
No 64
>KOG2462|consensus
Probab=48.17 E-value=6 Score=33.39 Aligned_cols=91 Identities=18% Similarity=0.299 Sum_probs=46.7
Q ss_pred CCCCCCccccccccccccEeeecCCCcC-----cCCCccCCCCCCCCCCc-eee--eCCccccccccccccCCCCCCCCc
Q psy11756 35 ASTMYPKCAACQGLIQNIIVQALDKTWH-----PEHFRCTHCRIPIATQK-FHV--HAGSPYCVEDYASLFLNKCQGCRL 106 (233)
Q Consensus 35 ~~~~~~~C~~C~~~I~~~~~~~~~~~~H-----~~Cf~C~~C~~~l~~~~-~~~--~~~~~yC~~c~~~~~~~~C~~C~~ 106 (233)
.....-.|..|++......=...-+.+| +.=|.|..|++.-.... +.+ +...+ .-.|..|++
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l----------~c~C~iCGK 195 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL----------PCECGICGK 195 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC----------Ccccccccc
Confidence 3445567888888664321112234444 55689999987543221 111 11110 236888888
Q ss_pred ccc-ccEEecCCCeeec--CCCCCCCCCccccc
Q psy11756 107 PIK-DVVVTALNQTWHP--DHFVCISCGTKLLY 136 (233)
Q Consensus 107 ~i~-~~~~~~~~~~~H~--~Cf~C~~C~~~l~~ 136 (233)
.+. .+++...- ..|. .=|.|..|++.|.+
T Consensus 196 aFSRPWLLQGHi-RTHTGEKPF~C~hC~kAFAD 227 (279)
T KOG2462|consen 196 AFSRPWLLQGHI-RTHTGEKPFSCPHCGKAFAD 227 (279)
T ss_pred cccchHHhhccc-ccccCCCCccCCcccchhcc
Confidence 773 22222111 1111 22788999988853
No 65
>PLN02400 cellulose synthase
Probab=47.12 E-value=20 Score=36.20 Aligned_cols=14 Identities=21% Similarity=0.389 Sum_probs=8.9
Q ss_pred hccCCCCCCCCCCc
Q psy11756 154 GKFCPKCFGCGKPI 167 (233)
Q Consensus 154 ~~~~~~C~~C~~~I 167 (233)
.+.+..|..|+..|
T Consensus 33 ~~~gqiCqICGD~V 46 (1085)
T PLN02400 33 NLNGQICQICGDDV 46 (1085)
T ss_pred ccCCceeeeccccc
Confidence 34455777777665
No 66
>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=46.82 E-value=20 Score=21.03 Aligned_cols=31 Identities=32% Similarity=0.602 Sum_probs=19.0
Q ss_pred CcCCCCCCCCCCceEe-eC-CeeeChhhhhccc
Q psy11756 185 RCGRCRRPISGPTFRV-CE-ADVVCVECSEKGR 215 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~-~~-~~~~C~~C~~~~~ 215 (233)
+|+.|++........+ .. +..+|..|-+...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~~ 35 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQAY 35 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHHH
Confidence 5888999885443333 34 7899999986543
No 67
>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=46.49 E-value=19 Score=21.94 Aligned_cols=13 Identities=31% Similarity=0.657 Sum_probs=8.9
Q ss_pred CeeeChhhhhccc
Q psy11756 203 ADVVCVECSEKGR 215 (233)
Q Consensus 203 ~~~~C~~C~~~~~ 215 (233)
+-=+|..|+....
T Consensus 25 d~DlC~~C~~~~~ 37 (48)
T cd02341 25 DFDLCQDCVVKGE 37 (48)
T ss_pred CCccCHHHHhCcC
Confidence 3457888887654
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=45.91 E-value=19 Score=21.35 Aligned_cols=10 Identities=30% Similarity=0.693 Sum_probs=6.0
Q ss_pred eeeChhhhhc
Q psy11756 204 DVVCVECSEK 213 (233)
Q Consensus 204 ~~~C~~C~~~ 213 (233)
--+|..|+..
T Consensus 23 ~dLC~~C~~~ 32 (43)
T cd02340 23 YDLCESCEAK 32 (43)
T ss_pred ccchHHhhCc
Confidence 4466666654
No 69
>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=45.90 E-value=12 Score=23.29 Aligned_cols=25 Identities=24% Similarity=0.614 Sum_probs=14.7
Q ss_pred ccCCCCCCCCCCceeeeCCcccccc
Q psy11756 67 RCTHCRIPIATQKFHVHAGSPYCVE 91 (233)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~yC~~ 91 (233)
-|..|...++...-+.++|+.||..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~ 33 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSE 33 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSH
T ss_pred cCCCCEeEECchHhHHhCCEeeecH
Confidence 4678888888666779999999964
No 70
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=45.52 E-value=16 Score=37.35 Aligned_cols=22 Identities=23% Similarity=0.677 Sum_probs=12.1
Q ss_pred ceechhhhhhccCCCCCCCCCC
Q psy11756 145 NAFCTACYEGKFCPKCFGCGKP 166 (233)
Q Consensus 145 ~~~C~~c~~~~~~~~C~~C~~~ 166 (233)
...|+.|-...+..+|+.|+..
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~ 688 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTH 688 (1337)
T ss_pred EEECCCCCCccccccCcccCCc
Confidence 3456666554444556666555
No 71
>KOG4443|consensus
Probab=45.46 E-value=14 Score=35.00 Aligned_cols=86 Identities=21% Similarity=0.315 Sum_probs=50.3
Q ss_pred CCccccccccccccEee------ecCCCc-CcCCCccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCcccccc
Q psy11756 39 YPKCAACQGLIQNIIVQ------ALDKTW-HPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDV 111 (233)
Q Consensus 39 ~~~C~~C~~~I~~~~~~------~~~~~~-H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~~ 111 (233)
...|..|++.-.+..+. .+.+.| -+.|-+|..|++.-+... -++|+.|-.... .-|.+|..+.
T Consensus 35 m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~gD~~k------f~~Ck~cDvsyh----~yc~~P~~~~ 104 (694)
T KOG4443|consen 35 LLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTGDPKK------FLLCKRCDVSYH----CYCQKPPNDK 104 (694)
T ss_pred chhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccCCccc------cccccccccccc----ccccCCcccc
Confidence 56788888776553222 123346 488888888884332222 246666633221 1144444443
Q ss_pred EEecCCCeeecCCCCCCCCCccccc
Q psy11756 112 VVTALNQTWHPDHFVCISCGTKLLY 136 (233)
Q Consensus 112 ~~~~~~~~~H~~Cf~C~~C~~~l~~ 136 (233)
+ ..+..+.++|++|..|...+.+
T Consensus 105 v--~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 105 V--PSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred c--cCcccccHHHHhhhhccccccc
Confidence 2 2455668889999999988876
No 72
>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=45.06 E-value=3.6 Score=27.92 Aligned_cols=16 Identities=38% Similarity=0.864 Sum_probs=10.5
Q ss_pred CCCCCCCCCccccEEE
Q psy11756 158 PKCFGCGKPITETAIK 173 (233)
Q Consensus 158 ~~C~~C~~~I~~~~i~ 173 (233)
.+|.+|+..|.-+.|+
T Consensus 8 a~Ck~C~~~I~kg~lR 23 (82)
T PF00645_consen 8 AKCKGCKKKIAKGELR 23 (82)
T ss_dssp EBETTTSCBE-TTSEE
T ss_pred ccCcccCCcCCCCCEE
Confidence 3688999999654433
No 73
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=44.30 E-value=10 Score=26.59 Aligned_cols=30 Identities=27% Similarity=0.596 Sum_probs=18.4
Q ss_pred CCcCCCCCCC-CCCceEeeCCeeeChhhhhc
Q psy11756 184 FRCGRCRRPI-SGPTFRVCEADVVCVECSEK 213 (233)
Q Consensus 184 f~C~~C~~~l-~~~~~~~~~~~~~C~~C~~~ 213 (233)
|+|..|+..+ +|++|.+...-+.--+|+..
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~ 37 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAE 37 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHH
Confidence 4566676666 56666666555555666543
No 74
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=43.52 E-value=23 Score=22.72 Aligned_cols=10 Identities=30% Similarity=0.703 Sum_probs=6.4
Q ss_pred CCCCCCCccc
Q psy11756 99 NKCQGCRLPI 108 (233)
Q Consensus 99 ~~C~~C~~~i 108 (233)
+.|..|+..|
T Consensus 10 ~~CtSCg~~i 19 (61)
T COG2888 10 PVCTSCGREI 19 (61)
T ss_pred ceeccCCCEe
Confidence 5666666666
No 75
>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=43.10 E-value=28 Score=21.23 Aligned_cols=15 Identities=40% Similarity=0.820 Sum_probs=9.8
Q ss_pred eeeChhhhhccccCC
Q psy11756 204 DVVCVECSEKGREEG 218 (233)
Q Consensus 204 ~~~C~~C~~~~~~~~ 218 (233)
--+|..||.......
T Consensus 24 ydLC~~Cf~~~~~~~ 38 (49)
T cd02345 24 YSLCLGCYTKGRETK 38 (49)
T ss_pred cCchHHHHhCCCcCC
Confidence 457888888665443
No 76
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=42.67 E-value=23 Score=35.78 Aligned_cols=12 Identities=25% Similarity=0.448 Sum_probs=7.4
Q ss_pred cCCCCCCCCCCc
Q psy11756 156 FCPKCFGCGKPI 167 (233)
Q Consensus 156 ~~~~C~~C~~~I 167 (233)
.+..|..|+..|
T Consensus 16 ~~qiCqICGD~v 27 (1079)
T PLN02638 16 GGQVCQICGDNV 27 (1079)
T ss_pred CCceeeeccccc
Confidence 345677777665
No 77
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=42.12 E-value=18 Score=27.42 Aligned_cols=32 Identities=19% Similarity=0.514 Sum_probs=22.8
Q ss_pred CCcCCCCCCCCCCceEeeCCeeeChhhhhccccCCCCCCC
Q psy11756 184 FRCGRCRRPISGPTFRVCEADVVCVECSEKGREEGKNDTS 223 (233)
Q Consensus 184 f~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~ 223 (233)
..|.+|+++|..+ -||..|...+..+.+....
T Consensus 82 ~~CE~CG~~I~~G--------r~C~~C~~~l~~~l~~~~~ 113 (137)
T TIGR03826 82 YPCERCGTSIREG--------RLCDSCAGELKRQLSAGEQ 113 (137)
T ss_pred CcccccCCcCCCC--------CccHHHHHHHHHHHHHHhc
Confidence 5699999999644 4799999777665544433
No 78
>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=41.93 E-value=33 Score=21.00 Aligned_cols=34 Identities=29% Similarity=0.642 Sum_probs=18.6
Q ss_pred cCCCCC-CCCCCceEee--CCeeeChhhhhccccCCC
Q psy11756 186 CGRCRR-PISGPTFRVC--EADVVCVECSEKGREEGK 219 (233)
Q Consensus 186 C~~C~~-~l~~~~~~~~--~~~~~C~~C~~~~~~~~~ 219 (233)
|..|++ +|.|.+|.-. .+--+|..||......++
T Consensus 3 Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~ 39 (49)
T cd02334 3 CNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKS 39 (49)
T ss_pred CCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCC
Confidence 444443 3444444433 345678999987655443
No 79
>KOG4443|consensus
Probab=41.72 E-value=11 Score=35.73 Aligned_cols=23 Identities=22% Similarity=0.547 Sum_probs=18.8
Q ss_pred EEcCceecCCCCCcCCCCCCCCC
Q psy11756 173 KVHDRKWHEACFRCGRCRRPISG 195 (233)
Q Consensus 173 ~~~~~~~H~~Cf~C~~C~~~l~~ 195 (233)
+..+..+.++|++|..|+..+.|
T Consensus 105 v~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 105 VPSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred ccCcccccHHHHhhhhccccccc
Confidence 34577788999999999998865
No 80
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=41.22 E-value=29 Score=33.25 Aligned_cols=8 Identities=38% Similarity=0.654 Sum_probs=3.3
Q ss_pred cccccccc
Q psy11756 41 KCAACQGL 48 (233)
Q Consensus 41 ~C~~C~~~ 48 (233)
.|..|+..
T Consensus 3 ~Cp~Cg~~ 10 (645)
T PRK14559 3 ICPQCQFE 10 (645)
T ss_pred cCCCCCCc
Confidence 34444433
No 81
>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=40.98 E-value=13 Score=21.18 Aligned_cols=31 Identities=26% Similarity=0.424 Sum_probs=21.4
Q ss_pred cCCCCCCCCCCce-EeeCCeeeChhhhhccccC
Q psy11756 186 CGRCRRPISGPTF-RVCEADVVCVECSEKGREE 217 (233)
Q Consensus 186 C~~C~~~l~~~~~-~~~~~~~~C~~C~~~~~~~ 217 (233)
|..|...+.+ .+ ...=|..||..|.++..++
T Consensus 1 C~iC~~~~~~-~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRD-PVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SS-EEEECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcccC-cCEECCCCCchhHHHHHHHHHC
Confidence 5667776654 43 3346999999999887766
No 82
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=40.63 E-value=36 Score=28.64 Aligned_cols=100 Identities=20% Similarity=0.211 Sum_probs=53.9
Q ss_pred cCCCccCCCCCCCCCCceeeeCCccccccccccccC--CCCCCCCccccc-cE--EecCCCeeecCCCCCCCCCcccccC
Q psy11756 63 PEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFL--NKCQGCRLPIKD-VV--VTALNQTWHPDHFVCISCGTKLLYK 137 (233)
Q Consensus 63 ~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~--~~C~~C~~~i~~-~~--~~~~~~~~H~~Cf~C~~C~~~l~~~ 137 (233)
..|+.=..|.-||.+..... |++-.+...+ -+|..|...|.. .. ..+.=+..-.+-|+|.+|++. |.
T Consensus 111 rkCl~~HaC~Cpl~da~C~E------C~R~vw~hGGrif~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrl--Gq 182 (314)
T PF06524_consen 111 RKCLSTHACTCPLQDAVCIE------CERGVWDHGGRIFKCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNRL--GQ 182 (314)
T ss_pred ccccccccccCcCCCcEeee------eecccccCCCeEEEeecCCCeeeccchhhhhhhhhhhhcccccccccccc--cc
Confidence 56777777888887543221 1111222111 257777777732 11 223444455566888888763 11
Q ss_pred ceeccCCceechhhhhh-------ccCCCCCCCCCCcccc
Q psy11756 138 GFYEREGNAFCTACYEG-------KFCPKCFGCGKPITET 170 (233)
Q Consensus 138 ~~~~~~g~~~C~~c~~~-------~~~~~C~~C~~~I~~~ 170 (233)
---++=..-||..|..+ .-++.|++|+......
T Consensus 183 ~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~et~eT 222 (314)
T PF06524_consen 183 YSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYETQET 222 (314)
T ss_pred hhhhheeeeehhhhhhhcccccccCCCCCCCCCCCccccc
Confidence 11123344566666543 2246799999988653
No 83
>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=40.16 E-value=12 Score=26.00 Aligned_cols=16 Identities=38% Similarity=0.874 Sum_probs=13.8
Q ss_pred hhhccCCCCCCCCCCc
Q psy11756 152 YEGKFCPKCFGCGKPI 167 (233)
Q Consensus 152 ~~~~~~~~C~~C~~~I 167 (233)
|..+|..+|.+|++-+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 5678889999999988
No 84
>KOG3816|consensus
Probab=40.00 E-value=14 Score=32.90 Aligned_cols=67 Identities=19% Similarity=0.524 Sum_probs=41.4
Q ss_pred eechhhhhhccCCCCCCCCCCccccEEEEcCce-ec-----CCC---CCcCCCCCCCCC-----CceEeeCCeeeChhhh
Q psy11756 146 AFCTACYEGKFCPKCFGCGKPITETAIKVHDRK-WH-----EAC---FRCGRCRRPISG-----PTFRVCEADVVCVECS 211 (233)
Q Consensus 146 ~~C~~c~~~~~~~~C~~C~~~I~~~~i~~~~~~-~H-----~~C---f~C~~C~~~l~~-----~~~~~~~~~~~C~~C~ 211 (233)
-+|..|.+..-...|..|+++.++...+.+.-. |- +-| |.|..|.++|.. ..|........|..|-
T Consensus 428 ~vC~~CL~g~~sI~C~~Ck~~wDGss~vLGTmY~YDI~aa~pCC~~R~~C~~C~k~l~~~~q~~t~~s~ys~~~~cP~c~ 507 (526)
T KOG3816|consen 428 QVCARCLWGDWSIICKNCKKDWDGSSFVLGTMYYYDIVAAGPCCPVRLVCQSCRKSLGVRDQLATQLSNYSALRICPSCK 507 (526)
T ss_pred HHHHHHhcccchHHHhhcCCCCCCcceeechhhhhhhhhcCCcchhhhhhhhhccccccHHHHHHHHhhhhcccccCCcC
Confidence 347888877777789999999877654433322 11 334 689999999942 1222224445565554
Q ss_pred h
Q psy11756 212 E 212 (233)
Q Consensus 212 ~ 212 (233)
.
T Consensus 508 ~ 508 (526)
T KOG3816|consen 508 L 508 (526)
T ss_pred c
Confidence 3
No 85
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=38.93 E-value=22 Score=18.45 Aligned_cols=9 Identities=44% Similarity=0.962 Sum_probs=4.5
Q ss_pred CCCCCCCCc
Q psy11756 159 KCFGCGKPI 167 (233)
Q Consensus 159 ~C~~C~~~I 167 (233)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 455555544
No 86
>KOG3002|consensus
Probab=37.87 E-value=30 Score=29.83 Aligned_cols=44 Identities=27% Similarity=0.477 Sum_probs=34.5
Q ss_pred CCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCcc
Q psy11756 124 HFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPIT 168 (233)
Q Consensus 124 Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~ 168 (233)
=+-|.+|...|....|.-.+|.+.|..|..+ ...+|+.|..+|.
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~-~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRTK-VSNKCPTCRLPIG 91 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhhh-hcccCCccccccc
Confidence 3567788888877777778999999999643 3468999998885
No 87
>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=37.63 E-value=63 Score=19.52 Aligned_cols=14 Identities=36% Similarity=0.693 Sum_probs=9.6
Q ss_pred CeeeChhhhhcccc
Q psy11756 203 ADVVCVECSEKGRE 216 (233)
Q Consensus 203 ~~~~C~~C~~~~~~ 216 (233)
+--+|..||.....
T Consensus 23 d~dLC~~Cf~~g~~ 36 (49)
T cd02335 23 DFDLCLECFSAGAE 36 (49)
T ss_pred CcchhHHhhhCcCC
Confidence 34578888876654
No 88
>KOG3579|consensus
Probab=36.18 E-value=25 Score=30.00 Aligned_cols=61 Identities=25% Similarity=0.402 Sum_probs=42.2
Q ss_pred CCCCccccccccccc-cEeeecCCCcCcCCCccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCccc
Q psy11756 37 TMYPKCAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPI 108 (233)
Q Consensus 37 ~~~~~C~~C~~~I~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i 108 (233)
...-.|.-|++.+.+ -+|....-.-|..||-|+ +..|..+ -..|.+||.. +.+|.--+-.|
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCS--ResIK~Q---g~sgevYCPS------GdkCPLvgS~v 327 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCS--RESIKQQ---GASGEVYCPS------GDKCPLVGSNV 327 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccC--HHHHHhh---cCCCceeCCC------CCcCcccCCcc
Confidence 344579999999988 688888888999999998 4444432 3456788875 34564444333
No 89
>KOG0978|consensus
Probab=35.42 E-value=14 Score=35.56 Aligned_cols=45 Identities=22% Similarity=0.617 Sum_probs=30.5
Q ss_pred CCCCCCCcccccCceeccCCceechhhhhhccC---CCCCCCCCCcccc
Q psy11756 125 FVCISCGTKLLYKGFYEREGNAFCTACYEGKFC---PKCFGCGKPITET 170 (233)
Q Consensus 125 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~---~~C~~C~~~I~~~ 170 (233)
.+|+.|+..... .....=|++||..|...++. .+|+.|+.+....
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 467888754432 23334578899999876664 5799999887554
No 90
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=35.35 E-value=25 Score=29.92 Aligned_cols=27 Identities=22% Similarity=0.544 Sum_probs=21.0
Q ss_pred CCCCCCCCCCccccEEEEcCceecCCC
Q psy11756 157 CPKCFGCGKPITETAIKVHDRKWHEAC 183 (233)
Q Consensus 157 ~~~C~~C~~~I~~~~i~~~~~~~H~~C 183 (233)
+..|.+|+.+|.-..+.-++..|++.|
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCC
Confidence 567889998888777777777787766
No 91
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=34.90 E-value=21 Score=21.34 Aligned_cols=12 Identities=33% Similarity=0.744 Sum_probs=7.7
Q ss_pred CeeeChhhhhcc
Q psy11756 203 ADVVCVECSEKG 214 (233)
Q Consensus 203 ~~~~C~~C~~~~ 214 (233)
+-=+|..||.+.
T Consensus 27 d~dLC~~C~~~g 38 (46)
T PF00569_consen 27 DYDLCEDCFSKG 38 (46)
T ss_dssp S-EEEHHHHHH-
T ss_pred CCchhhHHHhCc
Confidence 355788888774
No 92
>PLN02436 cellulose synthase A
Probab=34.70 E-value=36 Score=34.40 Aligned_cols=50 Identities=22% Similarity=0.525 Sum_probs=23.3
Q ss_pred ccCCCCCCCCCCccccEEEEcCceecCCCCCcCCCCCCC--CCCceEeeCCeeeChhhh
Q psy11756 155 KFCPKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPI--SGPTFRVCEADVVCVECS 211 (233)
Q Consensus 155 ~~~~~C~~C~~~I~~~~i~~~~~~~H~~Cf~C~~C~~~l--~~~~~~~~~~~~~C~~C~ 211 (233)
..+..|..|+..|-. ++.|..| -.|..|+=++ .-=+|...+|.-.|..|-
T Consensus 34 ~~~~iCqICGD~Vg~---t~dGe~F----VACn~C~fpvCr~Cyeyer~eg~~~Cpqck 85 (1094)
T PLN02436 34 LSGQTCQICGDEIEL---TVDGEPF----VACNECAFPVCRPCYEYERREGNQACPQCK 85 (1094)
T ss_pred cCCccccccccccCc---CCCCCEE----EeeccCCCccccchhhhhhhcCCccCcccC
Confidence 334578888776622 1233333 2233343333 112344456665555554
No 93
>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=34.30 E-value=30 Score=17.90 Aligned_cols=10 Identities=50% Similarity=1.404 Sum_probs=4.9
Q ss_pred CCCCCCCccc
Q psy11756 160 CFGCGKPITE 169 (233)
Q Consensus 160 C~~C~~~I~~ 169 (233)
|.+|+..|.+
T Consensus 1 C~sC~~~i~~ 10 (24)
T PF07754_consen 1 CTSCGRPIAP 10 (24)
T ss_pred CccCCCcccC
Confidence 3445555544
No 94
>PLN02189 cellulose synthase
Probab=34.06 E-value=37 Score=34.20 Aligned_cols=50 Identities=22% Similarity=0.439 Sum_probs=23.0
Q ss_pred ccCCCCCCCCCCccccEEEEcCceecCCCCCcCCCCCCC--CCCceEeeCCeeeChhhh
Q psy11756 155 KFCPKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPI--SGPTFRVCEADVVCVECS 211 (233)
Q Consensus 155 ~~~~~C~~C~~~I~~~~i~~~~~~~H~~Cf~C~~C~~~l--~~~~~~~~~~~~~C~~C~ 211 (233)
..+..|..|+..|.- ...|..| -.|..|+=++ .-=+|...+|.-.|..|-
T Consensus 32 ~~~~~C~iCgd~vg~---~~~g~~f----vaC~~C~fpvCr~Cyeyer~eg~q~CpqCk 83 (1040)
T PLN02189 32 LDGQVCEICGDEIGL---TVDGDLF----VACNECGFPVCRPCYEYERREGTQNCPQCK 83 (1040)
T ss_pred ccCccccccccccCc---CCCCCEE----EeeccCCCccccchhhhhhhcCCccCcccC
Confidence 334578888776632 1233333 2233333333 112344446665555554
No 95
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.92 E-value=31 Score=35.44 Aligned_cols=11 Identities=18% Similarity=0.573 Sum_probs=7.2
Q ss_pred CCccccccccc
Q psy11756 39 YPKCAACQGLI 49 (233)
Q Consensus 39 ~~~C~~C~~~I 49 (233)
..+|..|+..+
T Consensus 667 ~rkCPkCG~~t 677 (1337)
T PRK14714 667 RRRCPSCGTET 677 (1337)
T ss_pred EEECCCCCCcc
Confidence 45777777654
No 96
>KOG4739|consensus
Probab=32.57 E-value=28 Score=28.82 Aligned_cols=34 Identities=24% Similarity=0.449 Sum_probs=25.3
Q ss_pred cCceecc-CCceechhhhhhccCCCCCCCCCCccc
Q psy11756 136 YKGFYER-EGNAFCTACYEGKFCPKCFGCGKPITE 169 (233)
Q Consensus 136 ~~~~~~~-~g~~~C~~c~~~~~~~~C~~C~~~I~~ 169 (233)
..+|++- =..++|..|.....+..|.-|+++|..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred CCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 3455543 478899999877777799999998743
No 97
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=32.34 E-value=21 Score=21.26 Aligned_cols=9 Identities=44% Similarity=1.376 Sum_probs=4.3
Q ss_pred CcCCCCCCC
Q psy11756 185 RCGRCRRPI 193 (233)
Q Consensus 185 ~C~~C~~~l 193 (233)
+|..|+..+
T Consensus 5 ~C~~CG~~~ 13 (46)
T PRK00398 5 KCARCGREV 13 (46)
T ss_pred ECCCCCCEE
Confidence 445555444
No 98
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.81 E-value=33 Score=33.03 Aligned_cols=39 Identities=23% Similarity=0.389 Sum_probs=27.7
Q ss_pred CCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCC
Q psy11756 125 FVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKP 166 (233)
Q Consensus 125 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~ 166 (233)
++|..|+.+|. |....+.+.|+-|-.......|..|+..
T Consensus 393 ~~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 45666776664 4445678889999766666789999765
No 99
>KOG1813|consensus
Probab=31.72 E-value=26 Score=30.04 Aligned_cols=46 Identities=20% Similarity=0.392 Sum_probs=30.3
Q ss_pred CCccCCCCCCCCCCceeeeCCccccccccccccC--CCCCCCCcccccc
Q psy11756 65 HFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFL--NKCQGCRLPIKDV 111 (233)
Q Consensus 65 Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~--~~C~~C~~~i~~~ 111 (233)
=|+|-.|+++... .....-+..+|..|....+. +.|..|++.+.+.
T Consensus 241 Pf~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 241 PFKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred Ccccccccccccc-chhhcCCceeehhhhccccccCCcceecccccccc
Confidence 3677778777764 33455566778888765543 6788888777553
No 100
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=31.51 E-value=13 Score=26.34 Aligned_cols=27 Identities=19% Similarity=0.564 Sum_probs=14.9
Q ss_pred CCcCCCCCCCCCCceE-eeCCeeeChhh
Q psy11756 184 FRCGRCRRPISGPTFR-VCEADVVCVEC 210 (233)
Q Consensus 184 f~C~~C~~~l~~~~~~-~~~~~~~C~~C 210 (233)
|+|+.|=-+-...+.. ..+|++||..|
T Consensus 71 FTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 71 FTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred eeeeeeeeEechhhhccccCCCEecccc
Confidence 5555554333222333 33788888887
No 101
>KOG3576|consensus
Probab=31.47 E-value=13 Score=30.14 Aligned_cols=68 Identities=18% Similarity=0.358 Sum_probs=38.4
Q ss_pred cCCCccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCccccccEEecCCCeee--cCCCCCCCCCcccc
Q psy11756 63 PEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIKDVVVTALNQTWH--PDHFVCISCGTKLL 135 (233)
Q Consensus 63 ~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H--~~Cf~C~~C~~~l~ 135 (233)
.+=|+|..|++.+.-+.. .+-.+-|..+..+ ..|..|++...+.+-.-+-..-| ..=|+|..|.+.++
T Consensus 115 ~d~ftCrvCgK~F~lQRm--lnrh~kch~~vkr---~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaft 184 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRM--LNRHLKCHSDVKR---HLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFT 184 (267)
T ss_pred CCeeeeehhhhhhhHHHH--HHHHhhhccHHHH---HHHhhccCcccchhhhhhhhccccCccccchhhhhHHHH
Confidence 555899999987764332 2223445555443 47889999886541110001111 12367888888764
No 102
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=31.12 E-value=40 Score=19.71 Aligned_cols=34 Identities=18% Similarity=0.329 Sum_probs=22.7
Q ss_pred cCCCCCCCCCCceEeeCCeeeChhhhhccccCCCC
Q psy11756 186 CGRCRRPISGPTFRVCEADVVCVECSEKGREEGKN 220 (233)
Q Consensus 186 C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~~~~~~ 220 (233)
|..|...|. ....+.=|..+|..|..+...+.+.
T Consensus 1 CpiC~~~~~-~Pv~l~CGH~FC~~Cl~~~~~~~~~ 34 (42)
T PF15227_consen 1 CPICLDLFK-DPVSLPCGHSFCRSCLERLWKEPSG 34 (42)
T ss_dssp ETTTTSB-S-SEEE-SSSSEEEHHHHHHHHCCSSS
T ss_pred CCccchhhC-CccccCCcCHHHHHHHHHHHHccCC
Confidence 456666664 4555557899999999887765443
No 103
>KOG3002|consensus
Probab=30.25 E-value=35 Score=29.40 Aligned_cols=43 Identities=33% Similarity=0.700 Sum_probs=27.7
Q ss_pred CccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCcccc
Q psy11756 66 FRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLPIK 109 (233)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~i~ 109 (233)
+-|..|..+|....|.=.+|.+.|..|-.++ ..+|..|.++|.
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 3456666667666666666777777776433 457777777774
No 104
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=29.79 E-value=63 Score=19.50 Aligned_cols=30 Identities=13% Similarity=0.333 Sum_probs=20.9
Q ss_pred CcCCCCCCCCCCceEeeCCeeeChhhhhcccc
Q psy11756 185 RCGRCRRPISGPTFRVCEADVVCVECSEKGRE 216 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~~ 216 (233)
.|..|++.... -....|..+|..|-++.+.
T Consensus 1 ~CiiC~~~~~~--GI~I~~~fIC~~CE~~iv~ 30 (46)
T PF10764_consen 1 KCIICGKEKEE--GIHIYGKFICSDCEKEIVN 30 (46)
T ss_pred CeEeCCCcCCC--CEEEECeEehHHHHHHhcc
Confidence 36677777753 3344678999999877654
No 105
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=28.93 E-value=17 Score=21.24 Aligned_cols=19 Identities=21% Similarity=0.436 Sum_probs=11.8
Q ss_pred CCceEeeCCeeeChhhhhc
Q psy11756 195 GPTFRVCEADVVCVECSEK 213 (233)
Q Consensus 195 ~~~~~~~~~~~~C~~C~~~ 213 (233)
++.....|-.+.|..|...
T Consensus 25 gg~~~~~Nl~~lC~~Ch~~ 43 (47)
T PF01844_consen 25 GGKNDLENLILLCPSCHRK 43 (47)
T ss_dssp T---STTTEEEEEHHHHHH
T ss_pred CCCCCHHHHHHHhHHHHHH
Confidence 4555555677999999864
No 106
>PRK04023 DNA polymerase II large subunit; Validated
Probab=28.73 E-value=80 Score=31.91 Aligned_cols=26 Identities=27% Similarity=0.608 Sum_probs=17.1
Q ss_pred ccCCceechhhhhhccCCCCCCCCCC
Q psy11756 141 EREGNAFCTACYEGKFCPKCFGCGKP 166 (233)
Q Consensus 141 ~~~g~~~C~~c~~~~~~~~C~~C~~~ 166 (233)
+.-+..+|..|-...+..+|+.|+..
T Consensus 622 VEVg~RfCpsCG~~t~~frCP~CG~~ 647 (1121)
T PRK04023 622 VEIGRRKCPSCGKETFYRRCPFCGTH 647 (1121)
T ss_pred ecccCccCCCCCCcCCcccCCCCCCC
Confidence 34455677777666666677777765
No 107
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=28.67 E-value=38 Score=28.65 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=14.4
Q ss_pred CCCCCCCCCCccccEEEEcCceecCCC
Q psy11756 157 CPKCFGCGKPITETAIKVHDRKWHEAC 183 (233)
Q Consensus 157 ~~~C~~C~~~I~~~~i~~~~~~~H~~C 183 (233)
+..|.+|+.+|.-..+..++..|+|.|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRC 271 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCC
Confidence 345777777665433333444565544
No 108
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=28.07 E-value=6.9 Score=27.58 Aligned_cols=43 Identities=14% Similarity=0.398 Sum_probs=26.9
Q ss_pred cccccccccc-cEeeecCCCcCcCCCccCCCCCCCCCCceeeeC
Q psy11756 42 CAACQGLIQN-IIVQALDKTWHPEHFRCTHCRIPIATQKFHVHA 84 (233)
Q Consensus 42 C~~C~~~I~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~ 84 (233)
|..|...+.. .+....-..+++.+.-|-.|++.|+-..|.+..
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~ 81 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCG 81 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcC
Confidence 5556666655 445555566778888888887777654554333
No 109
>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=27.81 E-value=46 Score=30.79 Aligned_cols=13 Identities=38% Similarity=1.134 Sum_probs=8.8
Q ss_pred CCCCCcCCCCCCC
Q psy11756 181 EACFRCGRCRRPI 193 (233)
Q Consensus 181 ~~Cf~C~~C~~~l 193 (233)
.+||.|..|...|
T Consensus 50 r~Cf~CP~C~~~L 62 (483)
T PF05502_consen 50 RNCFDCPICFSPL 62 (483)
T ss_pred cccccCCCCCCcc
Confidence 3677777777666
No 110
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=26.75 E-value=30 Score=23.63 Aligned_cols=30 Identities=27% Similarity=0.620 Sum_probs=18.9
Q ss_pred CcCCCCCCCCCCc-eEee-CCe---eeChhhhhcc
Q psy11756 185 RCGRCRRPISGPT-FRVC-EAD---VVCVECSEKG 214 (233)
Q Consensus 185 ~C~~C~~~l~~~~-~~~~-~~~---~~C~~C~~~~ 214 (233)
.|+.|+-+|.... +... ||. -||.-||+..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G 36 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNG 36 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCC
Confidence 3788888885444 3332 443 5888888653
No 111
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.55 E-value=56 Score=18.17 Aligned_cols=25 Identities=20% Similarity=0.539 Sum_probs=14.2
Q ss_pred CcCCCCCCCCCCceEeeCCeeeChhhhh
Q psy11756 185 RCGRCRRPISGPTFRVCEADVVCVECSE 212 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~~~~~~~C~~C~~ 212 (233)
+|..|+..+ -+...++..+|..|-.
T Consensus 5 ~C~~C~~~~---i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 5 KCSKCGGNG---IVNKEDDYEVCIFCGS 29 (33)
T ss_pred EcCCCCCCe---EEEecCCeEEcccCCc
Confidence 355566544 2335567777777743
No 112
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=26.52 E-value=13 Score=29.85 Aligned_cols=45 Identities=16% Similarity=0.372 Sum_probs=26.5
Q ss_pred CccCCCCCCCCCCceeeeCCcccccccccccc--CCCCCCCCcccccc
Q psy11756 66 FRCTHCRIPIATQKFHVHAGSPYCVEDYASLF--LNKCQGCRLPIKDV 111 (233)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~--~~~C~~C~~~i~~~ 111 (233)
|.|-.|.+...+ ..+..=|..+|..|+.+.+ ++.|..|++...+.
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~ 243 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR 243 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence 667777665543 2334445667777766543 36677777665544
No 113
>PF10529 Hist_rich_Ca-bd: Histidine-rich Calcium-binding repeat region; InterPro: IPR019552 This entry represents a histidine-rich calcium-binding repeat which appears in proteins called histidine-rich-calcium binding proteins (HRC). HRC is a high capacity, low affinity Ca2+-binding protein, residing in the lumen of the sarcoplasmic reticulum. HRC binds directly to triadin. This binding interaction occurs between the histidine-rich region of HRC and multiple clusters of charged amino acids, named KEKE motifs, in the lumenal domain of triadin. This repeat is found in the acidic region of the protein, which can be long and variable. There is also a cysteine-rich region further towards the C terminus []. HRC may regulate sarcoplasmic reticular calcium transport, play a critical role in maintaining calcium homeostasis, and function in the heart. HRC is a candidate regulator of sarcoplasmic reticular calcium uptake.
Probab=26.42 E-value=42 Score=15.25 Aligned_cols=12 Identities=42% Similarity=0.554 Sum_probs=7.3
Q ss_pred CCCCCCccccCC
Q psy11756 222 TSSYFEEDEEED 233 (233)
Q Consensus 222 ~~~~~~~~~~~~ 233 (233)
+....++|||++
T Consensus 4 rgH~~eeDed~~ 15 (15)
T PF10529_consen 4 RGHREEEDEDDD 15 (15)
T ss_pred CccccccccccC
Confidence 345667777654
No 114
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=26.07 E-value=49 Score=26.11 Aligned_cols=36 Identities=14% Similarity=0.245 Sum_probs=22.3
Q ss_pred cCCCccCCCCCCCCCCceeeeCCccccccccccccC
Q psy11756 63 PEHFRCTHCRIPIATQKFHVHAGSPYCVEDYASLFL 98 (233)
Q Consensus 63 ~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~ 98 (233)
..|++|..=........++..+-+++|..|...+|.
T Consensus 137 ~kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClFPLF~ 172 (173)
T PF11077_consen 137 DKCVQCSQKCENVGAKIFTYFNFNLFCKNCLFPLFD 172 (173)
T ss_pred cccCcCCCCcccccceeEEecChhhcccccCccccc
Confidence 345555433222333347778889999999887763
No 115
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=25.94 E-value=97 Score=18.93 Aligned_cols=17 Identities=18% Similarity=0.266 Sum_probs=11.4
Q ss_pred CeeeChhhhhccccCCC
Q psy11756 203 ADVVCVECSEKGREEGK 219 (233)
Q Consensus 203 ~~~~C~~C~~~~~~~~~ 219 (233)
+--+|..|+...+..+.
T Consensus 22 d~DlC~~Cf~~g~~~~~ 38 (48)
T cd02343 22 DMDLCKTCFLGGVKPEG 38 (48)
T ss_pred CchhHHHHHhCCccCCC
Confidence 34578888887766544
No 116
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.91 E-value=45 Score=28.23 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.2
Q ss_pred CCCCCCCCCCccccEEEEcCceecCCC
Q psy11756 157 CPKCFGCGKPITETAIKVHDRKWHEAC 183 (233)
Q Consensus 157 ~~~C~~C~~~I~~~~i~~~~~~~H~~C 183 (233)
+..|.+|+.+|.-..+..+...|++.|
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~C 270 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHC 270 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCC
Confidence 456888877775444444455566655
No 117
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.82 E-value=46 Score=28.12 Aligned_cols=27 Identities=22% Similarity=0.583 Sum_probs=13.9
Q ss_pred CCCCCCCCCCccccEEEEcCceecCCC
Q psy11756 157 CPKCFGCGKPITETAIKVHDRKWHEAC 183 (233)
Q Consensus 157 ~~~C~~C~~~I~~~~i~~~~~~~H~~C 183 (233)
+..|.+|+.+|.-..+..++..|++.|
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~C 261 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQC 261 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCC
Confidence 345777766665433333444454443
No 118
>KOG0956|consensus
Probab=25.77 E-value=83 Score=30.38 Aligned_cols=129 Identities=16% Similarity=0.243 Sum_probs=64.2
Q ss_pred eeCCcccccccccccc--CCCCCCCCcccccc-EEecCCCee-ecCCCCCCCCCcccccCceecc--CCceechhhhhhc
Q psy11756 82 VHAGSPYCVEDYASLF--LNKCQGCRLPIKDV-VVTALNQTW-HPDHFVCISCGTKLLYKGFYER--EGNAFCTACYEGK 155 (233)
Q Consensus 82 ~~~~~~yC~~c~~~~~--~~~C~~C~~~i~~~-~~~~~~~~~-H~~Cf~C~~C~~~l~~~~~~~~--~g~~~C~~c~~~~ 155 (233)
+-.|.-||.+|-.+.- ..+|.-| |-.+. +....+.-| |.- |..=|.+..|..+ +.-++=..--+.+
T Consensus 44 VPtGpWfCrKCesqeraarvrCeLC--P~kdGALKkTDn~GWAHVV------CALYIPEVrFgNV~TMEPIiLq~VP~dR 115 (900)
T KOG0956|consen 44 VPTGPWFCRKCESQERAARVRCELC--PHKDGALKKTDNGGWAHVV------CALYIPEVRFGNVHTMEPIILQDVPHDR 115 (900)
T ss_pred cCCCchhhhhhhhhhhhccceeecc--cCcccceecccCCCceEEE------EEeeccceeecccccccceeeccCchhh
Confidence 4567778999865432 2456666 33333 444556667 653 3333333344432 2222222222456
Q ss_pred cCCCCCCCCCCc------cccEEEEc----CceecCCCCCcCCCCCCCCCCceEeeCCe---eeChhhhhccccCCCCC
Q psy11756 156 FCPKCFGCGKPI------TETAIKVH----DRKWHEACFRCGRCRRPISGPTFRVCEAD---VVCVECSEKGREEGKND 221 (233)
Q Consensus 156 ~~~~C~~C~~~I------~~~~i~~~----~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~---~~C~~C~~~~~~~~~~~ 221 (233)
|...|..|...= .+-.|+-. .+.||..|..= .-.|-.+.-...|+. -||+-+|.|++....++
T Consensus 116 fnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~---~GLLCEE~gn~~dNVKYCGYCk~HfsKlkk~~~~k 191 (900)
T KOG0956|consen 116 FNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQR---AGLLCEEEGNISDNVKYCGYCKYHFSKLKKSPAIK 191 (900)
T ss_pred hcceeeeecccCCccccccccceecccccchhhhhhhHhhh---hccceeccccccccceechhHHHHHHHhhcCCCcc
Confidence 667777776431 12224432 34688877421 111212222333444 36778888887766554
No 119
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=25.36 E-value=50 Score=20.82 Aligned_cols=28 Identities=29% Similarity=0.706 Sum_probs=21.4
Q ss_pred CCceechhhhhhccCCCCCCCCCCcccc
Q psy11756 143 EGNAFCTACYEGKFCPKCFGCGKPITET 170 (233)
Q Consensus 143 ~g~~~C~~c~~~~~~~~C~~C~~~I~~~ 170 (233)
=|.++|..||....-.-|+.|+++|...
T Consensus 25 CgH~I~~~~f~~~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 25 CGHLICDNCFPGERYNGCPFCGTPFEFD 52 (55)
T ss_pred ccceeeccccChhhccCCCCCCCcccCC
Confidence 4678888888766667899999888643
No 120
>PRK10445 endonuclease VIII; Provisional
Probab=25.30 E-value=46 Score=28.01 Aligned_cols=27 Identities=26% Similarity=0.583 Sum_probs=13.9
Q ss_pred CCCCCCCCCCccccEEEEcCceecCCC
Q psy11756 157 CPKCFGCGKPITETAIKVHDRKWHEAC 183 (233)
Q Consensus 157 ~~~C~~C~~~I~~~~i~~~~~~~H~~C 183 (233)
+..|.+|+.+|.-..+..++..|++.|
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~C 261 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGC 261 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCC
Confidence 345666666664433333444455544
No 121
>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=25.22 E-value=49 Score=23.72 Aligned_cols=29 Identities=17% Similarity=0.407 Sum_probs=22.4
Q ss_pred CcCCCCCCCCCCceEeeCCeeeChhhhhccccC
Q psy11756 185 RCGRCRRPISGPTFRVCEADVVCVECSEKGREE 217 (233)
Q Consensus 185 ~C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~~~ 217 (233)
.|..| .+..|+..++.+.|..|-..+..+
T Consensus 37 aCeiC----~~~GY~q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 37 ACEIC----GPKGYYQEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred ecccc----CCCceEEECCEEEEecCCCEEehh
Confidence 46677 447788889999999998876654
No 122
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=25.06 E-value=43 Score=26.93 Aligned_cols=18 Identities=22% Similarity=0.455 Sum_probs=10.8
Q ss_pred CCcCCCCCCCCCCceEee
Q psy11756 184 FRCGRCRRPISGPTFRVC 201 (233)
Q Consensus 184 f~C~~C~~~l~~~~~~~~ 201 (233)
++|..|+..+........
T Consensus 69 ~~CPvCR~~Is~~~LvPi 86 (193)
T PLN03208 69 PKCPVCKSDVSEATLVPI 86 (193)
T ss_pred CcCCCCCCcCChhcEEEe
Confidence 357788887754444433
No 123
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=24.83 E-value=38 Score=20.23 Aligned_cols=26 Identities=31% Similarity=0.676 Sum_probs=14.2
Q ss_pred CCcCCCCCCCCCCceEeeCCeeeChhhhhc
Q psy11756 184 FRCGRCRRPISGPTFRVCEADVVCVECSEK 213 (233)
Q Consensus 184 f~C~~C~~~l~~~~~~~~~~~~~C~~C~~~ 213 (233)
+.|..|+..++-. ..+.+.|..|--.
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC----CCCceECCCCCce
Confidence 3566666655322 2455677766543
No 124
>KOG2893|consensus
Probab=24.25 E-value=23 Score=29.38 Aligned_cols=51 Identities=24% Similarity=0.693 Sum_probs=26.7
Q ss_pred CCCCCCCCCccccEEEEcCceecCCCCCcCCCCCCC-CCCceEeeCCeeeChhhhhccc
Q psy11756 158 PKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPI-SGPTFRVCEADVVCVECSEKGR 215 (233)
Q Consensus 158 ~~C~~C~~~I~~~~i~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~~~~~C~~C~~~~~ 215 (233)
+-|.-|++...++.|.+..+. ..+|+|-.|++.| +|- .-.+.|+.-++..+
T Consensus 11 pwcwycnrefddekiliqhqk--akhfkchichkkl~sgp-----glsihcmqvhketi 62 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQK--AKHFKCHICHKKLFSGP-----GLSIHCMQVHKETI 62 (341)
T ss_pred ceeeecccccchhhhhhhhhh--hccceeeeehhhhccCC-----Cceeehhhhhhhhh
Confidence 346666666665544332221 2357777787777 222 22355665554433
No 125
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.05 E-value=51 Score=27.86 Aligned_cols=27 Identities=22% Similarity=0.581 Sum_probs=16.6
Q ss_pred CCCCCCCCCCccccEEEEcCceecCCC
Q psy11756 157 CPKCFGCGKPITETAIKVHDRKWHEAC 183 (233)
Q Consensus 157 ~~~C~~C~~~I~~~~i~~~~~~~H~~C 183 (233)
+..|.+|+.+|.-..+..++..|.+.|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 456788887775544444555576655
No 126
>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=24.04 E-value=65 Score=19.21 Aligned_cols=25 Identities=28% Similarity=0.631 Sum_probs=12.7
Q ss_pred CCCCCceEee--CCeeeChhhhhcccc
Q psy11756 192 PISGPTFRVC--EADVVCVECSEKGRE 216 (233)
Q Consensus 192 ~l~~~~~~~~--~~~~~C~~C~~~~~~ 216 (233)
+|.|.+|.-. .+-=+|..|+.+.-.
T Consensus 10 PI~G~RykC~~C~dyDLC~~C~~~~~n 36 (43)
T cd02342 10 PITGPRYKSKVKEDYDLCTICFSRMGN 36 (43)
T ss_pred cccccceEeCCCCCCccHHHHhhhhcC
Confidence 3344444443 233467777766543
No 127
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=24.03 E-value=21 Score=34.27 Aligned_cols=81 Identities=21% Similarity=0.395 Sum_probs=52.9
Q ss_pred CCCCCCccccccEEecCCCeeecCCCCCCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCccccEEEEcCcee
Q psy11756 100 KCQGCRLPIKDVVVTALNQTWHPDHFVCISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITETAIKVHDRKW 179 (233)
Q Consensus 100 ~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~i~~~~~~~ 179 (233)
.|..|-+.|.+ -.++.||----.|+.|+- .|......||=........-+.|..|.+- +-...++.|
T Consensus 103 ~C~~Cl~Ei~d----p~~rrY~YPF~~CT~CGP-----RfTIi~alPYDR~nTsM~~F~lC~~C~~E----Y~dP~nRRf 169 (750)
T COG0068 103 TCEDCLEEIFD----PNSRRYLYPFINCTNCGP-----RFTIIEALPYDRENTSMADFPLCPFCDKE----YKDPLNRRF 169 (750)
T ss_pred hhHHHHHHhcC----CCCcceeccccccCCCCc-----ceeeeccCCCCcccCccccCcCCHHHHHH----hcCcccccc
Confidence 45555544433 235667777778999974 45555666665444433334677777653 333578899
Q ss_pred cCCCCCcCCCCCCC
Q psy11756 180 HEACFRCGRCRRPI 193 (233)
Q Consensus 180 H~~Cf~C~~C~~~l 193 (233)
|..=..|..|+-.+
T Consensus 170 HAQp~aCp~CGP~~ 183 (750)
T COG0068 170 HAQPIACPKCGPHL 183 (750)
T ss_pred ccccccCcccCCCe
Confidence 99999999999876
No 128
>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=23.61 E-value=71 Score=19.17 Aligned_cols=28 Identities=32% Similarity=0.851 Sum_probs=14.7
Q ss_pred cCCCCC-CCCCCceEee--CCeeeChhhhhc
Q psy11756 186 CGRCRR-PISGPTFRVC--EADVVCVECSEK 213 (233)
Q Consensus 186 C~~C~~-~l~~~~~~~~--~~~~~C~~C~~~ 213 (233)
|..|+. +|.|.+|.-. .+--+|..||..
T Consensus 3 Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 3 CDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 444443 3344444433 345578888876
No 129
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.59 E-value=52 Score=27.99 Aligned_cols=27 Identities=26% Similarity=0.708 Sum_probs=14.3
Q ss_pred CCCCCCCCCCccccEEEEcCceecCCC
Q psy11756 157 CPKCFGCGKPITETAIKVHDRKWHEAC 183 (233)
Q Consensus 157 ~~~C~~C~~~I~~~~i~~~~~~~H~~C 183 (233)
+..|.+|+.+|.-..+..++..|++.|
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCC
Confidence 346777776665433333444455544
No 130
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=23.57 E-value=35 Score=21.13 Aligned_cols=27 Identities=26% Similarity=0.784 Sum_probs=14.1
Q ss_pred CCcCCCCCCCCC-CceEeeCCeeeChhhhh
Q psy11756 184 FRCGRCRRPISG-PTFRVCEADVVCVECSE 212 (233)
Q Consensus 184 f~C~~C~~~l~~-~~~~~~~~~~~C~~C~~ 212 (233)
++|..|++.|.- +.+. +..+-|..|-.
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCCCc
Confidence 456666666632 2333 33566666653
No 131
>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=23.48 E-value=27 Score=19.82 Aligned_cols=11 Identities=27% Similarity=0.893 Sum_probs=6.0
Q ss_pred CCCCCCCcccc
Q psy11756 125 FVCISCGTKLL 135 (233)
Q Consensus 125 f~C~~C~~~l~ 135 (233)
|+|..|+..+.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 45666665543
No 132
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=23.36 E-value=46 Score=20.87 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=6.3
Q ss_pred CcCCCCCCCCC
Q psy11756 185 RCGRCRRPISG 195 (233)
Q Consensus 185 ~C~~C~~~l~~ 195 (233)
.|..|+.++..
T Consensus 3 ~CvVCKqpi~~ 13 (54)
T PF10886_consen 3 ICVVCKQPIDD 13 (54)
T ss_pred eeeeeCCccCc
Confidence 35666666643
No 133
>PRK00807 50S ribosomal protein L24e; Validated
Probab=23.22 E-value=68 Score=19.85 Aligned_cols=31 Identities=16% Similarity=0.489 Sum_probs=17.5
Q ss_pred CcCCCCCCCC-C--CceEeeCCe---eeChhhhhccc
Q psy11756 185 RCGRCRRPIS-G--PTFRVCEAD---VVCVECSEKGR 215 (233)
Q Consensus 185 ~C~~C~~~l~-~--~~~~~~~~~---~~C~~C~~~~~ 215 (233)
.|..|+..+. | ..|...||+ +.+.+|.....
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f~ 39 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNYK 39 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHHH
Confidence 3777777773 2 333445776 34557766543
No 134
>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=23.13 E-value=26 Score=20.54 Aligned_cols=11 Identities=27% Similarity=0.918 Sum_probs=6.9
Q ss_pred CCCCCCCcccc
Q psy11756 125 FVCISCGTKLL 135 (233)
Q Consensus 125 f~C~~C~~~l~ 135 (233)
|+|..|+..+.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 56677776554
No 135
>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=23.04 E-value=22 Score=21.61 Aligned_cols=9 Identities=33% Similarity=0.951 Sum_probs=4.4
Q ss_pred CcCCCCCCC
Q psy11756 185 RCGRCRRPI 193 (233)
Q Consensus 185 ~C~~C~~~l 193 (233)
+|..|+..+
T Consensus 7 ~C~~Cg~~f 15 (52)
T TIGR02605 7 RCTACGHRF 15 (52)
T ss_pred EeCCCCCEe
Confidence 455555444
No 136
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.89 E-value=1.1e+02 Score=21.18 Aligned_cols=36 Identities=19% Similarity=0.649 Sum_probs=26.3
Q ss_pred CCCCCCCCCccccEEEEcCceecCCCCCcCCCCCCCCCCceEee
Q psy11756 158 PKCFGCGKPITETAIKVHDRKWHEACFRCGRCRRPISGPTFRVC 201 (233)
Q Consensus 158 ~~C~~C~~~I~~~~i~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~ 201 (233)
..|+.|++.. +.+....+| .|..|+..+.|+.|...
T Consensus 36 ~~Cp~C~~~~---VkR~a~GIW-----~C~kCg~~fAGgay~P~ 71 (89)
T COG1997 36 HVCPFCGRTT---VKRIATGIW-----KCRKCGAKFAGGAYTPV 71 (89)
T ss_pred CcCCCCCCcc---eeeeccCeE-----EcCCCCCeecccccccc
Confidence 4799998873 334555666 68899999988888764
No 137
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=21.71 E-value=9.9 Score=22.57 Aligned_cols=25 Identities=24% Similarity=0.597 Sum_probs=9.2
Q ss_pred CCCCCCCccccEEEE---cCceecCCCC
Q psy11756 160 CFGCGKPITETAIKV---HDRKWHEACF 184 (233)
Q Consensus 160 C~~C~~~I~~~~i~~---~~~~~H~~Cf 184 (233)
|..|+..++-+.+=. =+..||..|+
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~ 28 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCF 28 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHH
Confidence 445555554443322 2335777775
No 138
>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=21.66 E-value=70 Score=19.58 Aligned_cols=26 Identities=23% Similarity=0.580 Sum_probs=19.3
Q ss_pred CCCCCCCCCccc---cEEEEcCceecCCC
Q psy11756 158 PKCFGCGKPITE---TAIKVHDRKWHEAC 183 (233)
Q Consensus 158 ~~C~~C~~~I~~---~~i~~~~~~~H~~C 183 (233)
..|+.|+..+.+ +.|.+.+..|+..|
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeee
Confidence 378889877644 34788888888776
No 139
>KOG2932|consensus
Probab=21.44 E-value=35 Score=29.53 Aligned_cols=53 Identities=15% Similarity=0.286 Sum_probs=0.0
Q ss_pred CCCCCcccccCceeccCCceechhhhhhccCCCCCCCCCCccccEEEEcCcee
Q psy11756 127 CISCGTKLLYKGFYEREGNAFCTACYEGKFCPKCFGCGKPITETAIKVHDRKW 179 (233)
Q Consensus 127 C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~~C~~C~~~I~~~~i~~~~~~~ 179 (233)
|..|+.+|..-.-.+-=..+||.+|...---+.|.+|...|.--.-..+|.+|
T Consensus 93 Cd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~VqrIeq~~~g~iF 145 (389)
T KOG2932|consen 93 CDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQRIEQIMMGGIF 145 (389)
T ss_pred ecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHHHHHhcccceE
No 140
>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=21.38 E-value=39 Score=19.11 Aligned_cols=32 Identities=25% Similarity=0.539 Sum_probs=21.9
Q ss_pred cCCCCCCCCCCceEeeCCeeeChhhhhccccC
Q psy11756 186 CGRCRRPISGPTFRVCEADVVCVECSEKGREE 217 (233)
Q Consensus 186 C~~C~~~l~~~~~~~~~~~~~C~~C~~~~~~~ 217 (233)
|..|...+........=|..||..|..+....
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHH
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHh
Confidence 55666766533333445889999999888775
No 141
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.62 E-value=82 Score=30.44 Aligned_cols=39 Identities=26% Similarity=0.492 Sum_probs=25.5
Q ss_pred CccCCCCCCCCCCceeeeCCccccccccccccCCCCCCCCcc
Q psy11756 66 FRCTHCRIPIATQKFHVHAGSPYCVEDYASLFLNKCQGCRLP 107 (233)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~C~~C~~~ 107 (233)
++|..|.-+|. |....+.+.|.-|-.......|..|+..
T Consensus 393 ~~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 45566655553 4344567888888655556789999865
No 142
>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=20.61 E-value=37 Score=19.14 Aligned_cols=26 Identities=23% Similarity=0.530 Sum_probs=7.1
Q ss_pred cCCCCCCCCCCceEeeCCeeeChhhh
Q psy11756 186 CGRCRRPISGPTFRVCEADVVCVECS 211 (233)
Q Consensus 186 C~~C~~~l~~~~~~~~~~~~~C~~C~ 211 (233)
|-.|++.+...-+...=+...|..|.
T Consensus 6 C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 6 CDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp -TTT--EES-SSCCCCTS-S--TTT-
T ss_pred HhHhCCHHHHHHHHHhCCcccccccc
Confidence 44444444322222223344555553
No 143
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.52 E-value=79 Score=30.88 Aligned_cols=39 Identities=23% Similarity=0.502 Sum_probs=29.1
Q ss_pred CCCCCCCcccccCceeccCCceechhhhhh-ccCCCCCCCCCC
Q psy11756 125 FVCISCGTKLLYKGFYEREGNAFCTACYEG-KFCPKCFGCGKP 166 (233)
Q Consensus 125 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~-~~~~~C~~C~~~ 166 (233)
++|..|...+. ++...+.+.|+-|-.+ .....|+.|+-.
T Consensus 445 ~~Cp~Cd~~lt---~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLT---LHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceE---EecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 57788887764 5556688999999655 556689999876
No 144
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.44 E-value=56 Score=19.60 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=4.3
Q ss_pred eeeChhhhh
Q psy11756 204 DVVCVECSE 212 (233)
Q Consensus 204 ~~~C~~C~~ 212 (233)
...|..|--
T Consensus 20 ~~vC~~Cg~ 28 (52)
T smart00661 20 RFVCRKCGY 28 (52)
T ss_pred EEECCcCCC
Confidence 444555543
No 145
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.43 E-value=79 Score=26.91 Aligned_cols=27 Identities=19% Similarity=0.442 Sum_probs=19.2
Q ss_pred CCCCCCCCccccccEEecCCCeeecCC
Q psy11756 98 LNKCQGCRLPIKDVVVTALNQTWHPDH 124 (233)
Q Consensus 98 ~~~C~~C~~~i~~~~~~~~~~~~H~~C 124 (233)
+..|..|+.+|....+.-++..|.+.|
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCC
Confidence 467888888887666666666676655
No 146
>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=20.14 E-value=96 Score=28.80 Aligned_cols=39 Identities=18% Similarity=0.479 Sum_probs=26.0
Q ss_pred CccCCCCCCCCCCceeeeCCcccccccccc-ccCCCCCCCCcc
Q psy11756 66 FRCTHCRIPIATQKFHVHAGSPYCVEDYAS-LFLNKCQGCRLP 107 (233)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~-~~~~~C~~C~~~ 107 (233)
.+|..|.-+| +|....+.+.|..|-.. .....|..|+..
T Consensus 223 ~~C~~C~~~l---~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSL---TYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCce---EEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4555555554 45556778889988544 345689999864
Done!