Query 016386
Match_columns 390
No_of_seqs 262 out of 2052
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 06:23:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016386.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016386hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2084 Predicted histone tail 99.9 1.2E-22 2.5E-27 207.3 20.5 341 3-372 32-385 (482)
2 PF00856 SET: SET domain; Int 99.3 7.6E-13 1.7E-17 113.9 4.3 50 173-222 109-162 (162)
3 smart00317 SET SET (Su(var)3-9 99.1 9.7E-11 2.1E-15 95.8 4.5 46 176-221 67-116 (116)
4 PF01753 zf-MYND: MYND finger; 98.8 2.5E-09 5.5E-14 69.8 1.3 37 30-67 1-37 (37)
5 KOG2589 Histone tail methylase 98.7 7.7E-09 1.7E-13 98.1 4.5 79 162-251 176-256 (453)
6 COG2940 Proteins containing SE 97.9 7E-06 1.5E-10 84.4 2.8 69 182-250 405-477 (480)
7 KOG1080 Histone H3 (Lys4) meth 97.7 2.9E-05 6.3E-10 84.6 3.9 42 182-223 939-984 (1005)
8 KOG4442 Clathrin coat binding 97.6 3.3E-05 7.1E-10 79.5 3.3 45 183-227 194-242 (729)
9 KOG1710 MYND Zn-finger and ank 97.3 9.6E-05 2.1E-09 68.9 1.5 44 27-70 319-362 (396)
10 KOG1082 Histone H3 (Lys9) meth 96.8 0.00077 1.7E-08 66.9 3.1 43 184-226 274-324 (364)
11 PF13824 zf-Mss51: Zinc-finger 96.3 0.0067 1.5E-07 42.6 4.2 45 30-74 2-49 (55)
12 KOG1141 Predicted histone meth 96.1 0.0031 6.8E-08 66.2 2.4 55 184-246 1191-1253(1262)
13 KOG1337 N-methyltransferase [G 96.1 0.0087 1.9E-07 61.5 5.8 89 148-242 197-291 (472)
14 KOG1083 Putative transcription 95.7 0.007 1.5E-07 65.3 3.1 39 184-222 1252-1294(1306)
15 KOG1085 Predicted methyltransf 95.6 0.0086 1.9E-07 55.9 2.8 44 183-226 334-381 (392)
16 PLN03158 methionine aminopepti 92.5 0.084 1.8E-06 52.9 2.6 39 26-65 8-53 (396)
17 KOG1079 Transcriptional repres 91.7 0.17 3.6E-06 52.7 3.7 41 183-223 666-710 (739)
18 KOG1338 Uncharacterized conser 90.6 0.87 1.9E-05 44.8 7.1 79 147-225 173-262 (466)
19 KOG2857 Predicted MYND Zn-fing 90.0 0.1 2.2E-06 43.7 0.3 38 27-69 5-44 (157)
20 PF04438 zf-HIT: HIT zinc fing 89.5 0.17 3.6E-06 31.1 0.9 28 28-57 3-30 (30)
21 PF13424 TPR_12: Tetratricopep 89.0 1.8 3.8E-05 32.1 6.5 52 315-367 13-64 (78)
22 PF10579 Rapsyn_N: Rapsyn N-te 85.1 5.4 0.00012 30.4 7.0 55 306-365 5-59 (80)
23 PF09889 DUF2116: Uncharacteri 83.9 0.94 2E-05 32.5 2.3 28 27-61 3-30 (59)
24 KOG1081 Transcription factor N 82.9 0.58 1.2E-05 47.9 1.3 51 174-224 362-417 (463)
25 PF13374 TPR_10: Tetratricopep 80.9 3.7 7.9E-05 26.0 4.3 32 315-346 10-41 (42)
26 PRK00418 DNA gyrase inhibitor; 78.7 1.4 3.1E-05 31.9 1.7 11 49-59 26-36 (62)
27 PRK01343 zinc-binding protein; 75.9 2.2 4.7E-05 30.3 2.0 27 27-59 9-35 (57)
28 PRK00398 rpoP DNA-directed RNA 72.6 3.2 6.9E-05 28.0 2.2 30 265-296 3-32 (46)
29 KOG3612 PHD Zn-finger protein 72.0 1 2.2E-05 46.0 -0.6 42 27-71 527-568 (588)
30 PF13512 TPR_18: Tetratricopep 70.4 13 0.00028 31.7 5.8 50 310-364 13-62 (142)
31 TIGR02795 tol_pal_ybgF tol-pal 68.7 14 0.00029 29.0 5.5 46 317-367 49-94 (119)
32 PF13414 TPR_11: TPR repeat; P 68.0 12 0.00026 26.7 4.7 46 310-363 6-51 (69)
33 PF13432 TPR_16: Tetratricopep 67.9 16 0.00036 25.7 5.3 46 313-366 3-48 (65)
34 PF13525 YfiO: Outer membrane 67.9 21 0.00044 32.1 7.1 53 308-365 6-58 (203)
35 cd02680 MIT_calpain7_2 MIT: do 66.7 32 0.0007 25.9 6.7 35 305-339 4-38 (75)
36 KOG0553 TPR repeat-containing 65.5 17 0.00036 34.9 6.1 51 305-363 79-129 (304)
37 PF14559 TPR_19: Tetratricopep 65.5 10 0.00023 26.9 3.9 42 319-368 3-44 (68)
38 PF12855 Ecl1: Life-span regul 63.0 4 8.8E-05 27.3 1.1 30 28-61 7-36 (43)
39 KOG4317 Predicted Zn-finger pr 62.9 2.5 5.4E-05 40.3 0.1 38 26-68 6-43 (383)
40 PF02748 PyrI_C: Aspartate car 62.6 6 0.00013 27.6 1.9 37 265-301 6-51 (52)
41 PF04810 zf-Sec23_Sec24: Sec23 61.4 3.9 8.4E-05 26.8 0.8 29 266-296 3-35 (40)
42 PLN03144 Carbon catabolite rep 60.8 5.3 0.00011 42.3 2.0 27 39-65 74-107 (606)
43 COG4105 ComL DNA uptake lipopr 60.2 28 0.0006 32.7 6.4 55 307-366 34-88 (254)
44 cd02678 MIT_VPS4 MIT: domain c 59.3 65 0.0014 23.9 7.3 36 305-340 4-39 (75)
45 TIGR02059 swm_rep_I cyanobacte 58.7 19 0.00041 28.7 4.3 28 198-225 70-99 (101)
46 PRK10866 outer membrane biogen 58.5 33 0.00071 31.9 6.8 51 310-365 35-85 (243)
47 PF09986 DUF2225: Uncharacteri 58.0 28 0.0006 31.9 6.0 80 284-364 47-133 (214)
48 PF03884 DUF329: Domain of unk 58.0 6.1 0.00013 28.1 1.3 12 48-59 21-32 (57)
49 PF01485 IBR: IBR domain; Int 56.6 7.6 0.00017 27.5 1.7 29 266-294 19-49 (64)
50 PF07754 DUF1610: Domain of un 56.6 8.4 0.00018 22.3 1.5 22 272-293 3-24 (24)
51 PF08189 Meleagrin: Meleagrin/ 54.7 2.7 5.9E-05 26.7 -0.8 19 45-63 6-25 (39)
52 cd02684 MIT_2 MIT: domain cont 54.0 84 0.0018 23.5 7.1 36 305-340 4-39 (75)
53 PF08271 TF_Zn_Ribbon: TFIIB z 53.4 8.4 0.00018 25.5 1.4 28 267-296 2-30 (43)
54 KOG3362 Predicted BBOX Zn-fing 52.6 6 0.00013 33.5 0.7 31 26-58 117-147 (156)
55 PRK10803 tol-pal system protei 52.5 40 0.00087 31.8 6.3 47 320-371 193-239 (263)
56 PF13512 TPR_18: Tetratricopep 52.2 42 0.00091 28.6 5.7 47 311-362 51-97 (142)
57 TIGR02795 tol_pal_ybgF tol-pal 52.1 42 0.00091 26.1 5.7 51 310-365 5-55 (119)
58 TIGR03302 OM_YfiO outer membra 51.9 22 0.00048 32.2 4.4 52 311-367 37-88 (235)
59 cd02681 MIT_calpain7_1 MIT: do 51.3 1E+02 0.0022 23.2 7.5 35 305-339 4-38 (76)
60 COG3024 Uncharacterized protei 49.3 9.1 0.0002 27.7 1.1 11 49-59 27-37 (65)
61 cd02656 MIT MIT: domain contai 48.6 1.1E+02 0.0023 22.6 7.5 36 306-341 5-40 (75)
62 KOG1840 Kinesin light chain [C 46.1 82 0.0018 32.8 7.9 49 317-365 335-383 (508)
63 PRK11827 hypothetical protein; 46.0 13 0.00028 26.8 1.5 35 261-297 4-38 (60)
64 PF08666 SAF: SAF domain; Int 44.8 14 0.00031 26.1 1.6 17 204-220 3-19 (63)
65 PF13174 TPR_6: Tetratricopept 44.8 35 0.00075 20.0 3.2 24 314-337 7-30 (33)
66 PF09297 zf-NADH-PPase: NADH p 44.4 17 0.00037 22.3 1.7 26 267-294 5-30 (32)
67 cd02683 MIT_1 MIT: domain cont 43.9 1.3E+02 0.0028 22.6 6.8 35 306-340 5-39 (77)
68 PF04071 zf-like: Cysteine-ric 43.3 89 0.0019 24.2 5.8 45 272-316 37-82 (86)
69 KOG2461 Transcription factor B 43.2 12 0.00025 37.6 1.2 25 200-224 121-145 (396)
70 PF04212 MIT: MIT (microtubule 42.0 1.3E+02 0.0028 21.7 7.0 32 306-337 4-35 (69)
71 PLN03098 LPA1 LOW PSII ACCUMUL 40.2 86 0.0019 32.0 6.7 54 311-369 79-132 (453)
72 KOG2738 Putative methionine am 40.1 15 0.00032 35.2 1.3 34 31-65 12-50 (369)
73 PF10516 SHNi-TPR: SHNi-TPR; 38.5 40 0.00086 21.8 2.7 25 319-343 13-37 (38)
74 KOG1840 Kinesin light chain [C 38.4 61 0.0013 33.7 5.6 48 318-365 252-299 (508)
75 PRK00420 hypothetical protein; 38.3 85 0.0018 25.6 5.3 29 265-296 23-51 (112)
76 PF09862 DUF2089: Protein of u 38.0 79 0.0017 25.9 5.0 11 286-296 13-23 (113)
77 COG4068 Uncharacterized protei 37.5 21 0.00046 25.4 1.4 24 27-57 8-31 (64)
78 COG1781 PyrI Aspartate carbamo 37.5 21 0.00046 30.6 1.7 37 265-301 106-151 (153)
79 PF00856 SET: SET domain; Int 37.4 19 0.00042 29.7 1.5 21 3-23 8-28 (162)
80 PF04423 Rad50_zn_hook: Rad50 36.5 54 0.0012 22.7 3.4 28 287-314 22-49 (54)
81 KOG2782 Putative SAM dependent 36.3 51 0.0011 30.4 4.0 46 340-385 90-145 (303)
82 smart00661 RPOL9 RNA polymeras 35.4 27 0.00058 23.8 1.7 27 268-296 3-31 (52)
83 cd02682 MIT_AAA_Arch MIT: doma 35.1 2E+02 0.0043 21.7 6.8 43 305-347 4-48 (75)
84 PF13176 TPR_7: Tetratricopept 35.0 89 0.0019 19.3 4.0 20 319-338 11-30 (36)
85 KOG4236 Serine/threonine prote 34.2 23 0.00051 36.8 1.7 53 3-57 120-189 (888)
86 COG1997 RPL43A Ribosomal prote 34.0 28 0.0006 27.0 1.7 30 265-296 35-64 (89)
87 PRK10803 tol-pal system protei 33.8 99 0.0021 29.2 5.8 33 319-356 229-261 (263)
88 COG1729 Uncharacterized protei 33.8 84 0.0018 29.7 5.2 51 310-365 144-194 (262)
89 PF07719 TPR_2: Tetratricopept 33.6 1E+02 0.0022 18.0 4.5 25 313-337 7-31 (34)
90 smart00745 MIT Microtubule Int 33.5 1.9E+02 0.0042 21.2 7.6 35 305-339 6-40 (77)
91 PF08646 Rep_fac-A_C: Replicat 33.4 22 0.00047 30.2 1.2 27 267-294 20-46 (146)
92 PF10013 DUF2256: Uncharacteri 33.0 13 0.00027 24.7 -0.3 29 27-57 8-40 (42)
93 PRK00893 aspartate carbamoyltr 32.8 32 0.00069 29.7 2.1 20 281-300 130-149 (152)
94 PF09976 TPR_21: Tetratricopep 32.7 1.6E+02 0.0035 24.4 6.5 57 307-368 48-104 (145)
95 PRK02603 photosystem I assembl 32.5 1.5E+02 0.0032 25.4 6.5 51 311-366 39-89 (172)
96 KOG4234 TPR repeat-containing 32.4 1.3E+02 0.0029 27.5 5.9 35 305-339 93-127 (271)
97 smart00154 ZnF_AN1 AN1-like Zi 32.3 27 0.00058 22.7 1.2 23 30-53 1-25 (39)
98 PRK06266 transcription initiat 31.5 36 0.00079 30.1 2.3 19 147-165 47-65 (178)
99 PF13428 TPR_14: Tetratricopep 31.2 1.5E+02 0.0032 19.1 5.1 26 317-347 11-36 (44)
100 smart00647 IBR In Between Ring 31.2 44 0.00095 23.4 2.4 29 266-294 19-49 (64)
101 COG1675 TFA1 Transcription ini 31.2 1.3E+02 0.0028 26.6 5.7 41 230-278 103-143 (176)
102 PF10571 UPF0547: Uncharacteri 31.0 38 0.00082 20.0 1.6 20 29-48 2-23 (26)
103 PF14949 ARF7EP_C: ARF7 effect 30.4 18 0.00039 29.1 0.2 25 39-64 74-99 (103)
104 CHL00033 ycf3 photosystem I as 30.0 2E+02 0.0044 24.4 6.8 47 314-365 42-88 (168)
105 PF13525 YfiO: Outer membrane 29.5 1.7E+02 0.0036 26.1 6.4 48 311-363 46-93 (203)
106 PF07282 OrfB_Zn_ribbon: Putat 28.2 50 0.0011 23.9 2.2 33 264-298 27-59 (69)
107 KOG2807 RNA polymerase II tran 28.1 25 0.00055 34.0 0.7 41 15-57 317-361 (378)
108 PF11781 RRN7: RNA polymerase 28.0 40 0.00087 21.5 1.4 27 266-295 9-35 (36)
109 PF01780 Ribosomal_L37ae: Ribo 28.0 55 0.0012 25.6 2.4 30 265-296 35-64 (90)
110 PLN03088 SGT1, suppressor of 27.8 1.4E+02 0.0031 29.3 6.1 40 319-366 48-87 (356)
111 COG1998 RPS31 Ribosomal protei 27.6 32 0.0007 23.7 1.0 25 267-294 21-46 (51)
112 cd02677 MIT_SNX15 MIT: domain 27.4 2.7E+02 0.0058 20.8 7.0 35 305-339 4-38 (75)
113 PF08772 NOB1_Zn_bind: Nin one 27.3 31 0.00066 25.9 0.9 22 27-48 9-33 (73)
114 PF07975 C1_4: TFIIH C1-like d 26.8 34 0.00075 23.7 1.0 26 29-56 1-36 (51)
115 PRK10866 outer membrane biogen 26.8 1.8E+02 0.0039 26.9 6.3 42 317-363 79-120 (243)
116 PF05030 SSXT: SSXT protein (N 26.7 1.3E+02 0.0027 22.1 4.0 35 294-328 5-39 (65)
117 TIGR03302 OM_YfiO outer membra 26.4 1.8E+02 0.0039 26.1 6.1 48 315-367 174-221 (235)
118 PF14561 TPR_20: Tetratricopep 26.0 2.2E+02 0.0048 22.0 5.6 29 308-336 23-51 (90)
119 PF14803 Nudix_N_2: Nudix N-te 26.0 18 0.00038 22.9 -0.5 22 29-50 2-33 (34)
120 PF14853 Fis1_TPR_C: Fis1 C-te 25.9 2.3E+02 0.005 19.6 6.7 41 314-359 8-48 (53)
121 PF09538 FYDLN_acid: Protein o 25.8 48 0.001 26.9 1.9 23 26-48 8-35 (108)
122 PF00515 TPR_1: Tetratricopept 25.6 1.5E+02 0.0033 17.4 4.3 26 312-337 6-31 (34)
123 PF09082 DUF1922: Domain of un 25.4 15 0.00033 27.1 -1.0 31 266-300 4-34 (68)
124 PF12760 Zn_Tnp_IS1595: Transp 24.9 73 0.0016 21.2 2.4 29 263-293 16-45 (46)
125 TIGR03830 CxxCG_CxxCG_HTH puta 24.4 74 0.0016 25.9 2.8 33 283-315 29-62 (127)
126 TIGR00373 conserved hypothetic 24.4 33 0.00071 29.8 0.7 18 148-165 40-57 (158)
127 PF01599 Ribosomal_S27: Riboso 24.2 43 0.00092 22.9 1.1 27 266-293 19-46 (47)
128 smart00659 RPOLCX RNA polymera 24.2 61 0.0013 21.7 1.8 9 285-293 19-27 (44)
129 COG2158 Uncharacterized protei 23.6 1.2E+02 0.0026 24.4 3.7 32 277-308 54-85 (112)
130 cd00189 TPR Tetratricopeptide 23.3 2.4E+02 0.0052 19.4 5.3 38 321-366 48-85 (100)
131 PF12895 Apc3: Anaphase-promot 23.2 2E+02 0.0044 21.1 4.9 19 348-366 57-75 (84)
132 PF03194 LUC7: LUC7 N_terminus 23.1 2.1E+02 0.0046 26.8 6.0 41 297-337 122-162 (254)
133 PF12688 TPR_5: Tetratrico pep 23.1 3.1E+02 0.0068 22.4 6.3 24 312-335 6-29 (120)
134 PF02150 RNA_POL_M_15KD: RNA p 23.0 40 0.00088 21.3 0.8 27 268-296 4-31 (35)
135 PF08792 A2L_zn_ribbon: A2L zi 22.8 56 0.0012 20.4 1.3 28 266-295 4-31 (33)
136 PRK14890 putative Zn-ribbon RN 22.0 36 0.00079 24.3 0.4 18 30-47 39-56 (59)
137 KOG0006 E3 ubiquitin-protein l 21.9 34 0.00073 33.0 0.3 26 39-69 335-361 (446)
138 TIGR00240 ATCase_reg aspartate 21.9 34 0.00073 29.4 0.3 16 284-299 131-146 (150)
139 PF09577 Spore_YpjB: Sporulati 21.8 3.4E+02 0.0073 25.2 6.9 35 305-339 3-37 (232)
140 smart00858 SAF This domain fam 21.8 59 0.0013 22.7 1.5 16 204-219 3-18 (64)
141 PRK00415 rps27e 30S ribosomal 21.8 58 0.0013 23.4 1.4 32 262-295 8-40 (59)
142 PRK06266 transcription initiat 21.4 1.8E+02 0.0039 25.7 4.8 11 147-157 36-46 (178)
143 PF03604 DNA_RNApol_7kD: DNA d 21.3 77 0.0017 19.7 1.7 9 286-294 18-26 (32)
144 KOG0006 E3 ubiquitin-protein l 20.7 54 0.0012 31.7 1.4 34 263-296 313-347 (446)
145 COG1996 RPC10 DNA-directed RNA 20.5 51 0.0011 22.7 0.9 7 244-250 8-14 (49)
146 COG2888 Predicted Zn-ribbon RN 20.4 58 0.0013 23.3 1.2 32 27-59 9-48 (61)
147 cd02679 MIT_spastin MIT: domai 20.3 2E+02 0.0044 21.8 4.3 32 304-335 5-36 (79)
148 TIGR00373 conserved hypothetic 20.3 1.9E+02 0.0041 25.0 4.7 18 141-158 22-39 (158)
149 smart00109 C1 Protein kinase C 20.3 1E+02 0.0023 20.0 2.5 32 25-58 9-44 (49)
150 COG2835 Uncharacterized conser 20.2 53 0.0011 23.6 0.9 35 261-297 4-38 (60)
No 1
>KOG2084 consensus Predicted histone tail methylase containing SET domain [Chromatin structure and dynamics]
Probab=99.90 E-value=1.2e-22 Score=207.33 Aligned_cols=341 Identities=24% Similarity=0.359 Sum_probs=205.8
Q ss_pred CCCCCCCEEEEeCCeeeeecCCCCCcccccccCcCCCCCCCCCCccccCCHHHHHHhhhhhHHHHHHhhhhhhhhcccCC
Q 016386 3 SFHVSGEVIISQEPYVCVPNNSSSISRCDGCFASSNLKKCSACQVVWYCGSNCQKLDWKLHRLECQVLSRLDKEKRKSVT 82 (390)
Q Consensus 3 ~~I~~Ge~Il~e~P~~~~~~~~~~~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~~~~H~~EC~~l~~l~~~~~~~~~ 82 (390)
.+|++|++|+.|.|++.+|.. ..|..|+.. ....|..|....+|+..++...|..|+++|.. .........
T Consensus 32 ~~i~~g~~i~~e~p~~~~p~~----~~~~~c~~~-~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--- 102 (482)
T KOG2084|consen 32 QAIEAGEVILEEEPLVVGPAS----KSCSRCLGC-SCDHCRRCLEAIECNKCQQRGWALCGKFACSA-DLAKLECEP--- 102 (482)
T ss_pred cccCCCceEEecCcceeeecc----cCCcccccc-chhhhhcCCccHhhhhhhccCccccchhhcch-hhccccccc---
Confidence 479999999999999999986 344455443 44567788888888754444444567777765 322111000
Q ss_pred HHHHHHHHHHH-HHHhcCCCCCCCCCCCchHH--HHHhhcccCCCChHH--HHHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 016386 83 PSIRLMLKLYL-RRKLQNDNVIPSTTTDNYSL--VEALVAHMSDIDEKQ--LLLYAQIANLVNLILQWPEISINEIAENF 157 (390)
Q Consensus 83 ~~~~l~lR~l~-~~~~~~~~~~~~~~~~~~~~--v~~L~sh~~~~~~~~--~~~~~~~~~l~~~~l~~~~~~~~ei~~~~ 157 (390)
.........+. ....... ..+.+.. +..+....+...... ...+...+................+..++
T Consensus 103 ~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 176 (482)
T KOG2084|consen 103 LKLVGAPEECLALSSLHEE------SREAIVLLSLLEECSLSAEKPRLRLDLSYLEHGATEDDQSHLLLVLAADCISKLF 176 (482)
T ss_pred hhhccchHHHHHhhcCCcc------ccchHHHHHHHHHhhhhcccccHhHHHhhHHHHhhHHhhccccchhHHHHHHHHH
Confidence 00000000000 0000000 0111111 111111111111100 00111111100000001111222334445
Q ss_pred hHhhccccccccCCCC----CCcccccccccccCCCCCCCeEEEEeCCEEEEEEccccCCCC-eeeEeccCCCCCHHHHH
Q 016386 158 SKLACNAHTICNSELR----PLGTGLYPVISIINHSCLPNAVLVFEGRLAVVRAVQHVPKGA-EVLISYIETAGSTMTRQ 232 (390)
Q Consensus 158 ~~l~~Naf~i~~~~~~----~~g~glyp~~S~~NHSC~PN~~~~f~~~~~~vrA~r~I~~Ge-ei~isY~~~~~~~~~Rr 232 (390)
..+..+++.+.+.... ..|.|+||..+++||||.||+...|++....+++...+.+++ +++++|++..+++..||
T Consensus 177 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~hsC~pn~~~~~~~~~~~~~~~~~~~~~~~~l~~~y~~~~~~~~~r~ 256 (482)
T KOG2084|consen 177 PSLLCNSITNASSLRVPEPLFLGRGLFPGSSLFNHSCFPNISVIFDGRGLALLVPAGIDAGEEELTISYTDPLLSTASRQ 256 (482)
T ss_pred HHHHHhhhhhhhhhhccccccceeeecccchhcccCCCCCeEEEECCceeEEEeecccCCCCCEEEEeecccccCHHHHH
Confidence 5555666655544333 489999999999999999999999999998888888888877 99999999999999999
Q ss_pred HHHhccCCeEeeCcccCCCCCCCCccchhhhhccccCCCCCcceeeeCCC---CCccccCcCCCccCHHHHHHHHHHHHH
Q 016386 233 KALKEQYLFTCTCPRCIKLGQFDDIQESAILEGYRCKDDGCSGFLLRDSD---DKGFTCQQCGLVRSKEEIKKIASEVNI 309 (390)
Q Consensus 233 ~~L~~~~~F~C~C~rC~~~~~~~~~~~~~~l~~~~C~~~~C~g~~~~~~~---~~~~~C~~C~~~~~~~~v~~~~~~~~~ 309 (390)
+.|+..|.|.|.|.||.+| ++ .+.++.+++|.+..|.+.+.+... ...|.|..|.......++.........
T Consensus 257 ~~l~~~~~f~c~c~rc~d~-~~----~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~ 331 (482)
T KOG2084|consen 257 KQLRQSKLFSCQCPRCLDP-TE----LGTFLSSLRCENCTCGGLLGTSFLDKEDLQWPCTECALVRLKAYVVESREELQN 331 (482)
T ss_pred HHHhhccceeeecCCCCCC-Cc----cccchhhhhhcCCCCCCccCCCcccccCCCccccccccchhHHHHHHHHHHHHh
Confidence 9999999999999999985 33 345667789988888766544333 358999999999887777766655443
Q ss_pred HHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhccccce
Q 016386 310 LSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCLGCSII 372 (390)
Q Consensus 310 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~~~~~~ 372 (390)
. .. ...++ ....+.+...+....|+++.........+..++..+...-..|+.+
T Consensus 332 ~---~~--~~~~~----~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~il~~~~~~~~~~~~~ 385 (482)
T KOG2084|consen 332 E---LL--DAFSD----LLIEELLLLRQESLELPNDFEVLLLKLHLLFILGSLLGAFLSCSPN 385 (482)
T ss_pred h---cc--ccCCh----hhhHHHHHHHHHhhhCcchHHHHHHHHHHHHHHHHHHhhhhccchh
Confidence 2 00 01111 1222234456667789999988888888888777665544455543
No 2
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=99.33 E-value=7.6e-13 Score=113.93 Aligned_cols=50 Identities=44% Similarity=0.767 Sum_probs=44.9
Q ss_pred CCCcccccccccccCCCCCCCeEEEEe----CCEEEEEEccccCCCCeeeEecc
Q 016386 173 RPLGTGLYPVISIINHSCLPNAVLVFE----GRLAVVRAVQHVPKGAEVLISYI 222 (390)
Q Consensus 173 ~~~g~glyp~~S~~NHSC~PN~~~~f~----~~~~~vrA~r~I~~Geei~isY~ 222 (390)
...+.+|||.++++||||.||+.+.|+ ++.++++|.|||++||||+|||+
T Consensus 109 ~~~~~~l~p~~d~~NHsc~pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 109 DRDGIALYPFADMLNHSCDPNCEVSFDFDGDGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp EEEEEEEETGGGGSEEESSTSEEEEEEEETTTTEEEEEESS-B-TTSBEEEEST
T ss_pred cccccccCcHhHheccccccccceeeEeecccceEEEEECCccCCCCEEEEEEC
Confidence 356899999999999999999999998 78999999999999999999996
No 3
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=99.08 E-value=9.7e-11 Score=95.79 Aligned_cols=46 Identities=33% Similarity=0.512 Sum_probs=40.5
Q ss_pred cccccccccccCCCCCCCeEEEEeC--C--EEEEEEccccCCCCeeeEec
Q 016386 176 GTGLYPVISIINHSCLPNAVLVFEG--R--LAVVRAVQHVPKGAEVLISY 221 (390)
Q Consensus 176 g~glyp~~S~~NHSC~PN~~~~f~~--~--~~~vrA~r~I~~Geei~isY 221 (390)
+..++|.++++||||.||+...+.. + .+.++|+|+|++|||||++|
T Consensus 67 ~~~~~~~~~~iNHsc~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 67 ARRKGNIARFINHSCEPNCELLFVEVNGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred CCccCcHHHeeCCCCCCCEEEEEEEECCCcEEEEEECCCcCCCCEEeecC
Confidence 4458899999999999999987653 3 59999999999999999999
No 4
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=98.76 E-value=2.5e-09 Score=69.77 Aligned_cols=37 Identities=46% Similarity=1.245 Sum_probs=32.2
Q ss_pred cccccCcCCCCCCCCCCccccCCHHHHHHhhhhhHHHH
Q 016386 30 CDGCFASSNLKKCSACQVVWYCGSNCQKLDWKLHRLEC 67 (390)
Q Consensus 30 C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~~~~H~~EC 67 (390)
|.+|++.. +.+|++|+.++|||++||+++|..|+.||
T Consensus 1 C~~C~~~~-~~~C~~C~~~~YCs~~Cq~~~w~~Hk~~C 37 (37)
T PF01753_consen 1 CAVCGKPA-LKRCSRCKSVYYCSEECQRADWPYHKFEC 37 (37)
T ss_dssp -TTTSSCS-SEEETTTSSSEESSHHHHHHHHHHHCCTH
T ss_pred CcCCCCCc-CCcCCCCCCEEecCHHHHHHHHHHHhhhC
Confidence 77888853 34999999999999999999999999987
No 5
>KOG2589 consensus Histone tail methylase [Chromatin structure and dynamics]
Probab=98.74 E-value=7.7e-09 Score=98.10 Aligned_cols=79 Identities=24% Similarity=0.373 Sum_probs=62.7
Q ss_pred ccccccccCCCCCCccccccc-ccccCCCCCCCeEEEEeC-CEEEEEEccccCCCCeeeEeccCCCCCHHHHHHHHhccC
Q 016386 162 CNAHTICNSELRPLGTGLYPV-ISIINHSCLPNAVLVFEG-RLAVVRAVQHVPKGAEVLISYIETAGSTMTRQKALKEQY 239 (390)
Q Consensus 162 ~Naf~i~~~~~~~~g~glyp~-~S~~NHSC~PN~~~~f~~-~~~~vrA~r~I~~Geei~isY~~~~~~~~~Rr~~L~~~~ 239 (390)
-|-|.|+-+... .-.-||.. ++++||+|.||+.++-.| +++.|+++|||++|||||.=|++.+.+ ..
T Consensus 176 ~nDFSvmyStRk-~caqLwLGPaafINHDCrpnCkFvs~g~~tacvkvlRDIePGeEITcFYgs~fFG----------~~ 244 (453)
T KOG2589|consen 176 GNDFSVMYSTRK-RCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKVLRDIEPGEEITCFYGSGFFG----------EN 244 (453)
T ss_pred CCceeeeeeccc-chhhheeccHHhhcCCCCCCceeecCCCceeeeehhhcCCCCceeEEeecccccC----------CC
Confidence 466776654322 22345554 789999999999988877 789999999999999999999988776 34
Q ss_pred CeEeeCcccCCC
Q 016386 240 LFTCTCPRCIKL 251 (390)
Q Consensus 240 ~F~C~C~rC~~~ 251 (390)
.-+|.|..|..-
T Consensus 245 N~~CeC~TCER~ 256 (453)
T KOG2589|consen 245 NEECECVTCERR 256 (453)
T ss_pred CceeEEeecccc
Confidence 568999999884
No 6
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=97.87 E-value=7e-06 Score=84.39 Aligned_cols=69 Identities=25% Similarity=0.375 Sum_probs=57.3
Q ss_pred cccccCCCCCCCeEEEEeCC----EEEEEEccccCCCCeeeEeccCCCCCHHHHHHHHhccCCeEeeCcccCC
Q 016386 182 VISIINHSCLPNAVLVFEGR----LAVVRAVQHVPKGAEVLISYIETAGSTMTRQKALKEQYLFTCTCPRCIK 250 (390)
Q Consensus 182 ~~S~~NHSC~PN~~~~f~~~----~~~vrA~r~I~~Geei~isY~~~~~~~~~Rr~~L~~~~~F~C~C~rC~~ 250 (390)
.+.++||||.||+..+..+. .+..+|++||.+||||+..|....+....+...+...+...|.+.+|..
T Consensus 405 ~~r~~nHS~~pN~~~~~~~~~g~~~~~~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 477 (480)
T COG2940 405 VARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSH 477 (480)
T ss_pred ccceeecCCCCCcceecccccccceeeecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCC
Confidence 45689999999998876543 6889999999999999999988765544456677778999999999987
No 7
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=97.68 E-value=2.9e-05 Score=84.57 Aligned_cols=42 Identities=31% Similarity=0.521 Sum_probs=34.6
Q ss_pred cccccCCCCCCCeEE---EEeCC-EEEEEEccccCCCCeeeEeccC
Q 016386 182 VISIINHSCLPNAVL---VFEGR-LAVVRAVQHVPKGAEVLISYIE 223 (390)
Q Consensus 182 ~~S~~NHSC~PN~~~---~f~~~-~~~vrA~r~I~~Geei~isY~~ 223 (390)
.+.++||||.|||.. +.+|. +|+|.|.|+|.+|||||..|-.
T Consensus 939 iAr~InHsC~PNCyakvi~V~g~~~IvIyakr~I~~~EElTYDYkF 984 (1005)
T KOG1080|consen 939 IARFINHSCNPNCYAKVITVEGDKRIVIYSKRDIAAGEELTYDYKF 984 (1005)
T ss_pred hhheeecccCCCceeeEEEecCeeEEEEEEecccccCceeeeeccc
Confidence 367899999999954 34454 6999999999999999998843
No 8
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.64 E-value=3.3e-05 Score=79.52 Aligned_cols=45 Identities=27% Similarity=0.317 Sum_probs=34.8
Q ss_pred ccccCCCCCCCeEE---EEeC-CEEEEEEccccCCCCeeeEeccCCCCC
Q 016386 183 ISIINHSCLPNAVL---VFEG-RLAVVRAVQHVPKGAEVLISYIETAGS 227 (390)
Q Consensus 183 ~S~~NHSC~PN~~~---~f~~-~~~~vrA~r~I~~Geei~isY~~~~~~ 227 (390)
+-++||||+|||.+ +..| -++=+.|.++|++|||||.-|-....+
T Consensus 194 aRFiNHSC~PNa~~~KWtV~~~lRvGiFakk~I~~GEEITFDYqf~rYG 242 (729)
T KOG4442|consen 194 ARFINHSCDPNAEVQKWTVPDELRVGIFAKKVIKPGEEITFDYQFDRYG 242 (729)
T ss_pred HHhhcCCCCCCceeeeeeeCCeeEEEEeEecccCCCceeeEeccccccc
Confidence 34789999999964 3333 256688999999999999999665444
No 9
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=97.30 E-value=9.6e-05 Score=68.86 Aligned_cols=44 Identities=36% Similarity=0.890 Sum_probs=40.6
Q ss_pred CcccccccCcCCCCCCCCCCccccCCHHHHHHhhhhhHHHHHHh
Q 016386 27 ISRCDGCFASSNLKKCSACQVVWYCGSNCQKLDWKLHRLECQVL 70 (390)
Q Consensus 27 ~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~~~~H~~EC~~l 70 (390)
...|..|..+.+..+|+.|+.+.||+++||+-+|-.|+--|+.+
T Consensus 319 ~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~hWf~HKK~C~~L 362 (396)
T KOG1710|consen 319 CQFCSTCGHPGAKKRCSQCKAVAYCDQECQKFHWFIHKKVCSFL 362 (396)
T ss_pred cccccccCCCCccchhhhhHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 56788888888889999999999999999999999999999987
No 10
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=96.83 E-value=0.00077 Score=66.86 Aligned_cols=43 Identities=28% Similarity=0.476 Sum_probs=35.0
Q ss_pred cccCCCCCCCeEEE--EeCC------EEEEEEccccCCCCeeeEeccCCCC
Q 016386 184 SIINHSCLPNAVLV--FEGR------LAVVRAVQHVPKGAEVLISYIETAG 226 (390)
Q Consensus 184 S~~NHSC~PN~~~~--f~~~------~~~vrA~r~I~~Geei~isY~~~~~ 226 (390)
-++||||.||+.+. +.+. .+.+.|+++|++|+|+|.-|+....
T Consensus 274 RfinHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~~~ 324 (364)
T KOG1082|consen 274 RFINHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKAYK 324 (364)
T ss_pred ccccCCCCccceeeeeeecCCccchheeeeeeccccCCCcccchhhccccc
Confidence 37899999999764 3442 4678899999999999999987644
No 11
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=96.34 E-value=0.0067 Score=42.62 Aligned_cols=45 Identities=22% Similarity=0.491 Sum_probs=37.2
Q ss_pred cccccCc---CCCCCCCCCCccccCCHHHHHHhhhhhHHHHHHhhhhh
Q 016386 30 CDGCFAS---SNLKKCSACQVVWYCGSNCQKLDWKLHRLECQVLSRLD 74 (390)
Q Consensus 30 C~~C~~~---~~~~~C~~C~~~~yCS~~C~~~~~~~H~~EC~~l~~l~ 74 (390)
|..|... ...+.|+.|+++.|||++=...+..+|+--|..|+...
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~D~e~H~~~c~~LRqvN 49 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIPTHCSEEHWEDDYEEHRQLCERLRQVN 49 (55)
T ss_pred CCCCccccccccCCcCCCCCCcCccCHHHHHHhHHHHHHHHHHHHHhc
Confidence 6666664 23689999999999999988888789999999998754
No 12
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=96.12 E-value=0.0031 Score=66.20 Aligned_cols=55 Identities=29% Similarity=0.464 Sum_probs=39.6
Q ss_pred cccCCCCCCCeEE--EEeCC---E---EEEEEccccCCCCeeeEeccCCCCCHHHHHHHHhccCCeEeeCc
Q 016386 184 SIINHSCLPNAVL--VFEGR---L---AVVRAVQHVPKGAEVLISYIETAGSTMTRQKALKEQYLFTCTCP 246 (390)
Q Consensus 184 S~~NHSC~PN~~~--~f~~~---~---~~vrA~r~I~~Geei~isY~~~~~~~~~Rr~~L~~~~~F~C~C~ 246 (390)
-++||||+||..+ +|.+. + +...|.+-|++|.|||.-|......+. .+-..|+|-
T Consensus 1191 RfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~g~v~--------~keL~C~CG 1253 (1262)
T KOG1141|consen 1191 RFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQGQVA--------TKELTCHCG 1253 (1262)
T ss_pred hhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccccccc--------cceEEEecC
Confidence 4689999999865 55442 1 345678899999999999977644332 455778774
No 13
>KOG1337 consensus N-methyltransferase [General function prediction only]
Probab=96.12 E-value=0.0087 Score=61.53 Aligned_cols=89 Identities=20% Similarity=0.202 Sum_probs=61.6
Q ss_pred CCHHHHHHHHhHhhccccccccCC-----CCCCcccccccccccCCCCCCCeEEEEe-CCEEEEEEccccCCCCeeeEec
Q 016386 148 ISINEIAENFSKLACNAHTICNSE-----LRPLGTGLYPVISIINHSCLPNAVLVFE-GRLAVVRAVQHVPKGAEVLISY 221 (390)
Q Consensus 148 ~~~~ei~~~~~~l~~Naf~i~~~~-----~~~~g~glyp~~S~~NHSC~PN~~~~f~-~~~~~vrA~r~I~~Geei~isY 221 (390)
++...+.-.+..+.+.+|.+.... ....-.++.|..-+.||++.+.....+. +..+.+++.++|.+||||+|+|
T Consensus 197 ~~~~~~~w~~~~~~sr~~~~~~~~~~~~~~~~~~~~L~P~~D~~NH~~~~~~~~~~~~d~~~~l~~~~~v~~geevfi~Y 276 (472)
T KOG1337|consen 197 FTFSAFKWAYSIVNSRAFYLPSLQRLTAGDPDDNEALAPLIDLLNHSPEVIKAGYNQEDEAVELVAERDVSAGEEVFINY 276 (472)
T ss_pred cchHHHHHHHHHHhhhhhccccccccccCCCCcchhhhhhHHhhccCchhccccccCCCCcEEEEEeeeecCCCeEEEec
Confidence 334445556666666666543221 1123368999999999999994433333 3478999999999999999999
Q ss_pred cCCCCCHHHHHHHHhccCCeE
Q 016386 222 IETAGSTMTRQKALKEQYLFT 242 (390)
Q Consensus 222 ~~~~~~~~~Rr~~L~~~~~F~ 242 (390)
++.. ...|...|||.
T Consensus 277 G~~~------N~eLL~~YGFv 291 (472)
T KOG1337|consen 277 GPKS------NAELLLHYGFV 291 (472)
T ss_pred CCCc------hHHHHHhcCCC
Confidence 9842 23455589997
No 14
>KOG1083 consensus Putative transcription factor ASH1/LIN-59 [Transcription]
Probab=95.74 E-value=0.007 Score=65.27 Aligned_cols=39 Identities=36% Similarity=0.628 Sum_probs=32.4
Q ss_pred cccCCCCCCCeEE---EEeCC-EEEEEEccccCCCCeeeEecc
Q 016386 184 SIINHSCLPNAVL---VFEGR-LAVVRAVQHVPKGAEVLISYI 222 (390)
Q Consensus 184 S~~NHSC~PN~~~---~f~~~-~~~vrA~r~I~~Geei~isY~ 222 (390)
-++||||.||+-. ..+|. ++.|.|+|||.+||||+.-|-
T Consensus 1252 RfinhscKPNc~~qkwSVNG~~Rv~L~A~rDi~kGEELtYDYN 1294 (1306)
T KOG1083|consen 1252 RFINHSCKPNCEMQKWSVNGEYRVGLFALRDLPKGEELTYDYN 1294 (1306)
T ss_pred cccccccCCCCccccccccceeeeeeeecCCCCCCceEEEecc
Confidence 4679999999853 44553 688999999999999999984
No 15
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=95.60 E-value=0.0086 Score=55.88 Aligned_cols=44 Identities=25% Similarity=0.355 Sum_probs=36.3
Q ss_pred ccccCCCCCCCeEE---EEeCC-EEEEEEccccCCCCeeeEeccCCCC
Q 016386 183 ISIINHSCLPNAVL---VFEGR-LAVVRAVQHVPKGAEVLISYIETAG 226 (390)
Q Consensus 183 ~S~~NHSC~PN~~~---~f~~~-~~~vrA~r~I~~Geei~isY~~~~~ 226 (390)
.-++|||=.+|+.. .++|. .+++.|.|||.+||||+.-|+|-..
T Consensus 334 GRLINHS~~gNl~TKvv~Idg~pHLiLvA~rdIa~GEELlYDYGDRSk 381 (392)
T KOG1085|consen 334 GRLINHSVRGNLKTKVVEIDGSPHLILVARRDIAQGEELLYDYGDRSK 381 (392)
T ss_pred hhhhcccccCcceeeEEEecCCceEEEEeccccccchhhhhhccccch
Confidence 34799999999864 34554 5999999999999999999998643
No 16
>PLN03158 methionine aminopeptidase; Provisional
Probab=92.48 E-value=0.084 Score=52.91 Aligned_cols=39 Identities=26% Similarity=0.694 Sum_probs=30.6
Q ss_pred CCcccccccCcCCCCCCCCCC-------ccccCCHHHHHHhhhhhHH
Q 016386 26 SISRCDGCFASSNLKKCSACQ-------VVWYCGSNCQKLDWKLHRL 65 (390)
Q Consensus 26 ~~~~C~~C~~~~~~~~C~~C~-------~~~yCS~~C~~~~~~~H~~ 65 (390)
....|.+|.++.. ..|+.|. ..+|||++|.+.+|+.||.
T Consensus 8 ~~~~c~~c~~~a~-l~Cp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~ 53 (396)
T PLN03158 8 SPLACARCSKPAH-LQCPKCLELKLPREGASFCSQDCFKAAWSSHKS 53 (396)
T ss_pred CcccccCCCCccc-ccCccchhcCCCCCCceeECHHHHHHHHHHHHH
Confidence 3456999988754 7888883 2679999999999987753
No 17
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=91.73 E-value=0.17 Score=52.74 Aligned_cols=41 Identities=27% Similarity=0.388 Sum_probs=33.0
Q ss_pred ccccCCCCCCCeEE--EE-eC-CEEEEEEccccCCCCeeeEeccC
Q 016386 183 ISIINHSCLPNAVL--VF-EG-RLAVVRAVQHVPKGAEVLISYIE 223 (390)
Q Consensus 183 ~S~~NHSC~PN~~~--~f-~~-~~~~vrA~r~I~~Geei~isY~~ 223 (390)
+-+.|||=.||+.. .+ .| .++-++|.|.|.+|||||.-|-.
T Consensus 666 ~rFANHS~nPNCYAkvm~V~GdhRIGifAkRaIeagEELffDYrY 710 (739)
T KOG1079|consen 666 IRFANHSFNPNCYAKVMMVAGDHRIGIFAKRAIEAGEELFFDYRY 710 (739)
T ss_pred hhhccCCCCCCcEEEEEEecCCcceeeeehhhcccCceeeeeecc
Confidence 45789999999853 22 23 46889999999999999999964
No 18
>KOG1338 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.58 E-value=0.87 Score=44.85 Aligned_cols=79 Identities=23% Similarity=0.227 Sum_probs=60.8
Q ss_pred CCCHHHHHHHHhHhhccccccc----------cCCCCCCcccccccccccCCCCC-CCeEEEEeCCEEEEEEccccCCCC
Q 016386 147 EISINEIAENFSKLACNAHTIC----------NSELRPLGTGLYPVISIINHSCL-PNAVLVFEGRLAVVRAVQHVPKGA 215 (390)
Q Consensus 147 ~~~~~ei~~~~~~l~~Naf~i~----------~~~~~~~g~glyp~~S~~NHSC~-PN~~~~f~~~~~~vrA~r~I~~Ge 215 (390)
.++.+.++.+.+.+..=+|.+- +.+-...|-..-|.+-++||.=. -|+...++++-+.+.|.|+|++|+
T Consensus 173 ~~slEdF~y~~Al~laysfdve~~~s~~~~eee~e~e~ngk~m~p~ad~lNhd~~k~nanl~y~~NcL~mva~r~iekgd 252 (466)
T KOG1338|consen 173 RPSLEDFMYAYALGLAYSFDVEFLLSLDNLEEESEIECNGKLMTPIADFLNHDGLKANANLRYEDNCLEMVADRNIEKGD 252 (466)
T ss_pred ccCHHHHHHHHHHHHHHheeeehhcchhhhhhhhccccCcccccchhhhhccchhhcccceeccCcceeeeecCCCCCcc
Confidence 4667777777766655555442 11234678899999999999876 777778888999999999999999
Q ss_pred eeeEeccCCC
Q 016386 216 EVLISYIETA 225 (390)
Q Consensus 216 ei~isY~~~~ 225 (390)
|+..+|+-..
T Consensus 253 ev~n~dg~~p 262 (466)
T KOG1338|consen 253 EVDNSDGLKP 262 (466)
T ss_pred ccccccccCc
Confidence 9999997443
No 19
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=90.03 E-value=0.1 Score=43.66 Aligned_cols=38 Identities=34% Similarity=0.831 Sum_probs=30.8
Q ss_pred CcccccccCcCCCCCCCCCCccccCCHHHHHHhhhhhHH--HHHH
Q 016386 27 ISRCDGCFASSNLKKCSACQVVWYCGSNCQKLDWKLHRL--ECQV 69 (390)
Q Consensus 27 ~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~~~~H~~--EC~~ 69 (390)
...|.-|.+....++|+.|.++ |||-.|. +.|+. +|+.
T Consensus 5 t~tC~ic~e~~~KYKCpkC~vP-YCSl~Cf----KiHk~tPq~~~ 44 (157)
T KOG2857|consen 5 TTTCVICLESEIKYKCPKCSVP-YCSLPCF----KIHKSTPQCET 44 (157)
T ss_pred eeeehhhhcchhhccCCCCCCc-cccchhh----hhccCCccccc
Confidence 4678999988778999999985 9999996 46876 6754
No 20
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=89.51 E-value=0.17 Score=31.13 Aligned_cols=28 Identities=29% Similarity=0.731 Sum_probs=20.1
Q ss_pred cccccccCcCCCCCCCCCCccccCCHHHHH
Q 016386 28 SRCDGCFASSNLKKCSACQVVWYCGSNCQK 57 (390)
Q Consensus 28 ~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~ 57 (390)
..|..|.. .....|++|+.. |||-+|.+
T Consensus 3 ~~C~vC~~-~~kY~Cp~C~~~-~CSl~C~k 30 (30)
T PF04438_consen 3 KLCSVCGN-PAKYRCPRCGAR-YCSLACYK 30 (30)
T ss_dssp EEETSSSS-EESEE-TTT--E-ESSHHHHH
T ss_pred CCCccCcC-CCEEECCCcCCc-eeCcEeEC
Confidence 46888887 567899999985 99999963
No 21
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=89.02 E-value=1.8 Score=32.13 Aligned_cols=52 Identities=12% Similarity=0.026 Sum_probs=42.5
Q ss_pred HhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhc
Q 016386 315 LALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCL 367 (390)
Q Consensus 315 ~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~ 367 (390)
.-....|++++|++.|++++.. ...+.+.|..+..+...++.+|..+|+...
T Consensus 13 ~~~~~~~~~~~A~~~~~~al~~-~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~ 64 (78)
T PF13424_consen 13 RVYRELGRYDEALDYYEKALDI-EEQLGDDHPDTANTLNNLGECYYRLGDYEE 64 (78)
T ss_dssp HHHHHTT-HHHHHHHHHHHHHH-HHHTTTHHHHHHHHHHHHHHHHHHTTHHHH
T ss_pred HHHHHcCCHHHHHHHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHHHcCCHHH
Confidence 3344678999999999999988 566677888899999999999999998743
No 22
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=85.08 E-value=5.4 Score=30.41 Aligned_cols=55 Identities=11% Similarity=0.048 Sum_probs=44.1
Q ss_pred HHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcch
Q 016386 306 EVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSIL 365 (390)
Q Consensus 306 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~ 365 (390)
.+...+++..+++...+.++|+.+.+.++++.. +.....++.-.|+++|+++|..
T Consensus 5 ~ak~~ie~GlkLY~~~~~~~Al~~W~~aL~k~~-----~~~~rf~~lG~l~qA~~e~Gky 59 (80)
T PF10579_consen 5 QAKQQIEKGLKLYHQNETQQALQKWRKALEKIT-----DREDRFRVLGYLIQAHMEWGKY 59 (80)
T ss_pred HHHHHHHHHHHHhccchHHHHHHHHHHHHhhcC-----ChHHHHHHHHHHHHHHHHHHHH
Confidence 344566778888888889999999998887663 3446889999999999999976
No 23
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=83.88 E-value=0.94 Score=32.49 Aligned_cols=28 Identities=18% Similarity=0.370 Sum_probs=20.6
Q ss_pred CcccccccCcCCCCCCCCCCccccCCHHHHHHhhh
Q 016386 27 ISRCDGCFASSNLKKCSACQVVWYCGSNCQKLDWK 61 (390)
Q Consensus 27 ~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~~~ 61 (390)
..+|..|.++.++- -.|||++|++..++
T Consensus 3 HkHC~~CG~~Ip~~-------~~fCS~~C~~~~~k 30 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD-------ESFCSPKCREEYRK 30 (59)
T ss_pred CCcCCcCCCcCCcc-------hhhhCHHHHHHHHH
Confidence 46899998886542 25999999976443
No 24
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=82.93 E-value=0.58 Score=47.93 Aligned_cols=51 Identities=24% Similarity=0.281 Sum_probs=39.0
Q ss_pred CCccccccccc-ccCCCCCCCeEEEE---e-CCEEEEEEccccCCCCeeeEeccCC
Q 016386 174 PLGTGLYPVIS-IINHSCLPNAVLVF---E-GRLAVVRAVQHVPKGAEVLISYIET 224 (390)
Q Consensus 174 ~~g~glyp~~S-~~NHSC~PN~~~~f---~-~~~~~vrA~r~I~~Geei~isY~~~ 224 (390)
.+-.+-+...| ++||||.||+.-.- . .....+.|.+.|+.|+|+|.+|.-.
T Consensus 362 ~id~~~~~n~sr~~nh~~~~~v~~~k~~~~~~t~~~~~a~~~i~~g~e~t~~~n~~ 417 (463)
T KOG1081|consen 362 IIDAGPKGNYSRFLNHSCQPNVETEKWQVIGDTRVGLFAPRQIEAGEELTFNYNGN 417 (463)
T ss_pred ccccccccchhhhhcccCCCceeechhheecccccccccccccccchhhhheeecc
Confidence 34456667666 78999999997532 2 2357899999999999999999654
No 25
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=80.91 E-value=3.7 Score=26.01 Aligned_cols=32 Identities=16% Similarity=0.183 Sum_probs=18.4
Q ss_pred HhhhcCCCHHHHHHHHHHHHHhhhcccCCCch
Q 016386 315 LALTSCGNHQEVVSTYKMIEKLQKKLYHPFSV 346 (390)
Q Consensus 315 ~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~ 346 (390)
.-....|++++|+.++++++..++.++-|.|+
T Consensus 10 ~~~~~~g~~~~A~~~~~~al~~~~~~~G~~Hp 41 (42)
T PF13374_consen 10 NAYRAQGRYEEALELLEEALEIRERLLGPDHP 41 (42)
T ss_dssp HHHHHCT-HHHHHHHHHHHHHHH---------
T ss_pred HHHHhhhhcchhhHHHHHHHHHHHHHhccccc
Confidence 33446789999999999999999999888876
No 26
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=78.65 E-value=1.4 Score=31.86 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=9.4
Q ss_pred ccCCHHHHHHh
Q 016386 49 WYCGSNCQKLD 59 (390)
Q Consensus 49 ~yCS~~C~~~~ 59 (390)
.|||+.|+.-|
T Consensus 26 PFCS~RCk~ID 36 (62)
T PRK00418 26 PFCSKRCQLID 36 (62)
T ss_pred CcccHHHHhhh
Confidence 69999999764
No 27
>PRK01343 zinc-binding protein; Provisional
Probab=75.93 E-value=2.2 Score=30.33 Aligned_cols=27 Identities=22% Similarity=0.609 Sum_probs=16.8
Q ss_pred CcccccccCcCCCCCCCCCCccccCCHHHHHHh
Q 016386 27 ISRCDGCFASSNLKKCSACQVVWYCGSNCQKLD 59 (390)
Q Consensus 27 ~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~ 59 (390)
...|-.|-++... .+..|||+.|+.-|
T Consensus 9 ~~~CP~C~k~~~~------~~rPFCS~RC~~iD 35 (57)
T PRK01343 9 TRPCPECGKPSTR------EAYPFCSERCRDID 35 (57)
T ss_pred CCcCCCCCCcCcC------CCCcccCHHHhhhh
Confidence 3456666655211 24479999999765
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.62 E-value=3.2 Score=27.98 Aligned_cols=30 Identities=27% Similarity=0.596 Sum_probs=19.9
Q ss_pred ccccCCCCCcceeeeCCCCCccccCcCCCccC
Q 016386 265 GYRCKDDGCSGFLLRDSDDKGFTCQQCGLVRS 296 (390)
Q Consensus 265 ~~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~~ 296 (390)
-++|+ +|++.+..+.....+.|+.||....
T Consensus 3 ~y~C~--~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCA--RCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECC--CCCCEEEECCCCCceECCCCCCeEE
Confidence 36786 6877665444444788999987654
No 29
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=71.99 E-value=1 Score=46.01 Aligned_cols=42 Identities=26% Similarity=0.622 Sum_probs=31.1
Q ss_pred CcccccccCcCCCCCCCCCCccccCCHHHHHHhhhhhHHHHHHhh
Q 016386 27 ISRCDGCFASSNLKKCSACQVVWYCGSNCQKLDWKLHRLECQVLS 71 (390)
Q Consensus 27 ~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~~~~H~~EC~~l~ 71 (390)
..=|++|..+.-..- |=...|||-+||+.+|..|+--|..-+
T Consensus 527 KQWC~nC~~EAiy~C---CWNTSYCsveCQQ~HW~~H~ksCrrk~ 568 (588)
T KOG3612|consen 527 KQWCYNCLDEAIYHC---CWNTSYCSVECQQGHWPEHRKSCRRKK 568 (588)
T ss_pred HHHHHhhhHHHHHHh---hccccccCcchhhccchhHhhhhcccC
Confidence 456888887643332 333569999999999999999997543
No 30
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=70.38 E-value=13 Score=31.73 Aligned_cols=50 Identities=18% Similarity=0.230 Sum_probs=22.3
Q ss_pred HHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcc
Q 016386 310 LSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSI 364 (390)
Q Consensus 310 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~ 364 (390)
++.++...+..|+|++|++.++.+..+ +|...+--++.-.|+.+|-+-+.
T Consensus 13 ly~~a~~~l~~~~Y~~A~~~le~L~~r-----yP~g~ya~qAqL~l~yayy~~~~ 62 (142)
T PF13512_consen 13 LYQEAQEALQKGNYEEAIKQLEALDTR-----YPFGEYAEQAQLDLAYAYYKQGD 62 (142)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHhc-----CCCCcccHHHHHHHHHHHHHccC
Confidence 344444444455555555555444332 24444444444444444444333
No 31
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=68.66 E-value=14 Score=29.04 Aligned_cols=46 Identities=13% Similarity=-0.043 Sum_probs=30.6
Q ss_pred hhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhc
Q 016386 317 LTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCL 367 (390)
Q Consensus 317 ~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~ 367 (390)
....+++++|++.++.++. .+|.+.....+...++.+|..+|....
T Consensus 49 ~~~~~~~~~A~~~~~~~~~-----~~p~~~~~~~~~~~~~~~~~~~~~~~~ 94 (119)
T TIGR02795 49 YYAQGKYADAAKAFLAVVK-----KYPKSPKAPDALLKLGMSLQELGDKEK 94 (119)
T ss_pred HHhhccHHHHHHHHHHHHH-----HCCCCCcccHHHHHHHHHHHHhCChHH
Confidence 3455677777777766654 347776667777777777777776643
No 32
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=68.02 E-value=12 Score=26.66 Aligned_cols=46 Identities=13% Similarity=0.140 Sum_probs=34.8
Q ss_pred HHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhc
Q 016386 310 LSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSS 363 (390)
Q Consensus 310 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~ 363 (390)
....+......+++++|+..|++++.. .|+|.. +...++.+|..+|
T Consensus 6 ~~~~g~~~~~~~~~~~A~~~~~~ai~~-----~p~~~~---~~~~~g~~~~~~~ 51 (69)
T PF13414_consen 6 WYNLGQIYFQQGDYEEAIEYFEKAIEL-----DPNNAE---AYYNLGLAYMKLG 51 (69)
T ss_dssp HHHHHHHHHHTTHHHHHHHHHHHHHHH-----STTHHH---HHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHc-----CCCCHH---HHHHHHHHHHHhC
Confidence 345555666788999999999988764 466544 7778888888888
No 33
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=67.93 E-value=16 Score=25.65 Aligned_cols=46 Identities=15% Similarity=0.043 Sum_probs=33.6
Q ss_pred HHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchh
Q 016386 313 KTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILC 366 (390)
Q Consensus 313 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~ 366 (390)
.+...+..|++++|++.|+.+++.. |. -..+...+..+|...|.+.
T Consensus 3 ~a~~~~~~g~~~~A~~~~~~~l~~~-----P~---~~~a~~~lg~~~~~~g~~~ 48 (65)
T PF13432_consen 3 LARALYQQGDYDEAIAAFEQALKQD-----PD---NPEAWYLLGRILYQQGRYD 48 (65)
T ss_dssp HHHHHHHCTHHHHHHHHHHHHHCCS-----TT---HHHHHHHHHHHHHHTT-HH
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHC-----CC---CHHHHHHHHHHHHHcCCHH
Confidence 4455667889999999999887533 43 5667888888888888764
No 34
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=67.91 E-value=21 Score=32.11 Aligned_cols=53 Identities=19% Similarity=0.180 Sum_probs=34.2
Q ss_pred HHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcch
Q 016386 308 NILSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSIL 365 (390)
Q Consensus 308 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~ 365 (390)
+.+++++......|++.+|++.|+.+... +|++....++.-.++.+|-..|+.
T Consensus 6 ~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~-----~P~s~~a~~A~l~la~a~y~~~~y 58 (203)
T PF13525_consen 6 EALYQKALEALQQGDYEEAIKLFEKLIDR-----YPNSPYAPQAQLMLAYAYYKQGDY 58 (203)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHHHHHHHH------TTSTTHHHHHHHHHHHHHHTT-H
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHH-----CCCChHHHHHHHHHHHHHHHcCCH
Confidence 45566666666777777777777776543 477777777777777777666654
No 35
>cd02680 MIT_calpain7_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=66.69 E-value=32 Score=25.93 Aligned_cols=35 Identities=17% Similarity=0.250 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKK 339 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 339 (390)
+++..++.+|......|++++|+++|...+.+...
T Consensus 4 ~kai~Lv~~A~~eD~~gny~eA~~lY~~ale~~~~ 38 (75)
T cd02680 4 ERAHFLVTQAFDEDEKGNAEEAIELYTEAVELCIN 38 (75)
T ss_pred HHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHHH
Confidence 34556667777777789999999999988776644
No 36
>KOG0553 consensus TPR repeat-containing protein [General function prediction only]
Probab=65.53 E-value=17 Score=34.90 Aligned_cols=51 Identities=18% Similarity=0.166 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSS 363 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~ 363 (390)
.+++.+-.+..+++..++|++|+.+|..++. |.|+|..++.-| +++|..||
T Consensus 79 ~~AE~LK~eGN~~m~~~~Y~eAv~kY~~AI~-----l~P~nAVyycNR---AAAy~~Lg 129 (304)
T KOG0553|consen 79 ALAESLKNEGNKLMKNKDYQEAVDKYTEAIE-----LDPTNAVYYCNR---AAAYSKLG 129 (304)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh-----cCCCcchHHHHH---HHHHHHhc
Confidence 3455566677778888899999999998876 558887766544 34555555
No 37
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=65.49 E-value=10 Score=26.86 Aligned_cols=42 Identities=14% Similarity=0.148 Sum_probs=30.6
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhcc
Q 016386 319 SCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCLG 368 (390)
Q Consensus 319 ~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~~ 368 (390)
..|++++|++.|+.++.. +|.+ ..++..|+++|...|.+..+
T Consensus 3 ~~~~~~~A~~~~~~~l~~-----~p~~---~~~~~~la~~~~~~g~~~~A 44 (68)
T PF14559_consen 3 KQGDYDEAIELLEKALQR-----NPDN---PEARLLLAQCYLKQGQYDEA 44 (68)
T ss_dssp HTTHHHHHHHHHHHHHHH-----TTTS---HHHHHHHHHHHHHTT-HHHH
T ss_pred hccCHHHHHHHHHHHHHH-----CCCC---HHHHHHHHHHHHHcCCHHHH
Confidence 467899999999888754 3543 44666899999999988654
No 38
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=62.98 E-value=4 Score=27.28 Aligned_cols=30 Identities=20% Similarity=0.377 Sum_probs=18.9
Q ss_pred cccccccCcCCCCCCCCCCccccCCHHHHHHhhh
Q 016386 28 SRCDGCFASSNLKKCSACQVVWYCGSNCQKLDWK 61 (390)
Q Consensus 28 ~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~~~ 61 (390)
..|..|-+.... .-....|||++|+..++.
T Consensus 7 ~yC~~Cdk~~~~----~~~~~lYCSe~Cr~~D~~ 36 (43)
T PF12855_consen 7 DYCIVCDKQIDP----PDDGSLYCSEECRLKDQE 36 (43)
T ss_pred hHHHHhhccccC----CCCCccccCHHHHhHhhh
Confidence 456666665311 123457999999988763
No 39
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=62.91 E-value=2.5 Score=40.34 Aligned_cols=38 Identities=26% Similarity=0.711 Sum_probs=29.5
Q ss_pred CCcccccccCcCCCCCCCCCCccccCCHHHHHHhhhhhHHHHH
Q 016386 26 SISRCDGCFASSNLKKCSACQVVWYCGSNCQKLDWKLHRLECQ 68 (390)
Q Consensus 26 ~~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~~~~~H~~EC~ 68 (390)
..-.|.-|-....-+.||.|+. .|||-.|-+ .|+.-|.
T Consensus 6 ~~~~C~ic~vq~~~YtCPRCn~-~YCsl~CYr----~h~~~Cs 43 (383)
T KOG4317|consen 6 SFLACGICGVQKREYTCPRCNL-LYCSLKCYR----NHKHSCS 43 (383)
T ss_pred ceeeccccccccccccCCCCCc-cceeeeeec----CCCccch
Confidence 3456888888765699999998 499999975 4666674
No 40
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=62.56 E-value=6 Score=27.61 Aligned_cols=37 Identities=19% Similarity=0.481 Sum_probs=22.4
Q ss_pred ccccCCCCCcc----ee-----eeCCCCCccccCcCCCccCHHHHH
Q 016386 265 GYRCKDDGCSG----FL-----LRDSDDKGFTCQQCGLVRSKEEIK 301 (390)
Q Consensus 265 ~~~C~~~~C~g----~~-----~~~~~~~~~~C~~C~~~~~~~~v~ 301 (390)
-++|+|++|-. ++ +.+.+....+|..|++..+.++|.
T Consensus 6 vl~C~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~~~~eI~ 51 (52)
T PF02748_consen 6 VLKCPNPNCITNSNEPVESRFYVIDKEPIKLRCHYCERIITEDEIW 51 (52)
T ss_dssp SSE-SSTTBTTT-TSSS--EEEEEETTTCEEEETTT--EEEHHHHH
T ss_pred EEEcCCCCcccCCCCCCCceEEEEeCCCCEEEeeCCCCEecccEEe
Confidence 46888888832 11 223345678999999998877653
No 41
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=61.44 E-value=3.9 Score=26.78 Aligned_cols=29 Identities=31% Similarity=0.801 Sum_probs=15.6
Q ss_pred cccCCCCCcceeee----CCCCCccccCcCCCccC
Q 016386 266 YRCKDDGCSGFLLR----DSDDKGFTCQQCGLVRS 296 (390)
Q Consensus 266 ~~C~~~~C~g~~~~----~~~~~~~~C~~C~~~~~ 296 (390)
++|. .|++++-| +.+...|.|.-|+....
T Consensus 3 ~rC~--~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 3 VRCR--RCRAYLNPFCQFDDGGKTWICNFCGTKNP 35 (40)
T ss_dssp -B-T--TT--BS-TTSEEETTTTEEEETTT--EEE
T ss_pred cccC--CCCCEECCcceEcCCCCEEECcCCCCcCC
Confidence 5785 68777644 34567899999998643
No 42
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=60.80 E-value=5.3 Score=42.29 Aligned_cols=27 Identities=26% Similarity=0.822 Sum_probs=21.0
Q ss_pred CCCCCCC---C----ccccCCHHHHHHhhhhhHH
Q 016386 39 LKKCSAC---Q----VVWYCGSNCQKLDWKLHRL 65 (390)
Q Consensus 39 ~~~C~~C---~----~~~yCS~~C~~~~~~~H~~ 65 (390)
...|+.| + ..+|||++|.+.+|+.||.
T Consensus 74 ~lqCp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~ 107 (606)
T PLN03144 74 TLQCVGCVKAKLPVSKSYHCSPKCFSDAWRHHRV 107 (606)
T ss_pred cccCccchhcCCCcCcceeeCHHHHHHHHHHHHH
Confidence 4677777 2 2579999999999998864
No 43
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=60.17 E-value=28 Score=32.71 Aligned_cols=55 Identities=22% Similarity=0.282 Sum_probs=44.2
Q ss_pred HHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchh
Q 016386 307 VNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILC 366 (390)
Q Consensus 307 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~ 366 (390)
...+++++......|++.+|.+.|+.+.. -||.+.+--++.-.|+.++..-+...
T Consensus 34 ~~~LY~~g~~~L~~gn~~~A~~~fe~l~~-----~~p~s~~~~qa~l~l~yA~Yk~~~y~ 88 (254)
T COG4105 34 ASELYNEGLTELQKGNYEEAIKYFEALDS-----RHPFSPYSEQAQLDLAYAYYKNGEYD 88 (254)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCCcccHHHHHHHHHHHHhcccHH
Confidence 34567777777778999999999988864 57999998999999988887766554
No 44
>cd02678 MIT_VPS4 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
Probab=59.30 E-value=65 Score=23.93 Aligned_cols=36 Identities=19% Similarity=0.208 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKL 340 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 340 (390)
+.+..++.+|......|++++|+.+|...+......
T Consensus 4 ~~A~~l~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~ 39 (75)
T cd02678 4 QKAIELVKKAIEEDNAGNYEEALRLYQHALEYFMHA 39 (75)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 455667777777788999999999999877665443
No 45
>TIGR02059 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803.
Probab=58.66 E-value=19 Score=28.68 Aligned_cols=28 Identities=29% Similarity=0.443 Sum_probs=23.4
Q ss_pred EeCC--EEEEEEccccCCCCeeeEeccCCC
Q 016386 198 FEGR--LAVVRAVQHVPKGAEVLISYIETA 225 (390)
Q Consensus 198 f~~~--~~~vrA~r~I~~Geei~isY~~~~ 225 (390)
.++. ++.+--.++|..|++++++|.++.
T Consensus 70 V~~s~ktVTLTL~~~V~~Gq~VTVsYt~ps 99 (101)
T TIGR02059 70 LGGSNTTITLTLAQVVEDGDEVTLSYTKNS 99 (101)
T ss_pred EcCcccEEEEEecccccCCCEEEEEeeCCC
Confidence 4454 788888999999999999998764
No 46
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=58.47 E-value=33 Score=31.91 Aligned_cols=51 Identities=18% Similarity=0.264 Sum_probs=28.7
Q ss_pred HHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcch
Q 016386 310 LSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSIL 365 (390)
Q Consensus 310 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~ 365 (390)
.++++......|++++|++.|+.++. .+|......++...|+.+|-.+++.
T Consensus 35 ~Y~~A~~~~~~g~y~~Ai~~f~~l~~-----~yP~s~~a~~a~l~la~ayy~~~~y 85 (243)
T PRK10866 35 IYATAQQKLQDGNWKQAITQLEALDN-----RYPFGPYSQQVQLDLIYAYYKNADL 85 (243)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHH-----hCCCChHHHHHHHHHHHHHHhcCCH
Confidence 44555555556666666666665544 3455555555555555555555443
No 47
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=58.01 E-value=28 Score=31.85 Aligned_cols=80 Identities=13% Similarity=0.189 Sum_probs=48.1
Q ss_pred CccccCcCCCccCHHHHHHHHH----HHHHHHHHHH---hhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHH
Q 016386 284 KGFTCQQCGLVRSKEEIKKIAS----EVNILSKKTL---ALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLI 356 (390)
Q Consensus 284 ~~~~C~~C~~~~~~~~v~~~~~----~~~~~~~~~~---~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~ 356 (390)
..|.|+.||......+...+-. .+.+.+.... ......++++|++.|+.++.- ..+....+..++.+-..|+
T Consensus 47 ~V~vCP~CgyA~~~~~F~~l~~~~~~~i~~~i~~~~~~~~~~~~Rt~~~ai~~YkLAll~-~~~~~~~~s~~A~l~LrlA 125 (214)
T PF09986_consen 47 EVWVCPHCGYAAFEEDFEKLSPEQKEKIKENISSRWKPRDFSGERTLEEAIESYKLALLC-AQIKKEKPSKKAGLCLRLA 125 (214)
T ss_pred eEEECCCCCCcccccccccCCHHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHHHH-HHHhCCCHHHHHHHHHHHH
Confidence 4589999998765443332221 1222212111 233445799999988876543 3444555667777888888
Q ss_pred HHHHHhcc
Q 016386 357 KGYIHSSI 364 (390)
Q Consensus 357 ~~y~~~~~ 364 (390)
=+|-++|+
T Consensus 126 WlyR~~~~ 133 (214)
T PF09986_consen 126 WLYRDLGD 133 (214)
T ss_pred HHhhccCC
Confidence 88877776
No 48
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=57.97 E-value=6.1 Score=28.14 Aligned_cols=12 Identities=25% Similarity=0.803 Sum_probs=9.3
Q ss_pred cccCCHHHHHHh
Q 016386 48 VWYCGSNCQKLD 59 (390)
Q Consensus 48 ~~yCS~~C~~~~ 59 (390)
-.|||+.|+.-+
T Consensus 21 rPFCS~RCk~iD 32 (57)
T PF03884_consen 21 RPFCSERCKLID 32 (57)
T ss_dssp -SSSSHHHHHHH
T ss_pred CCcccHhhcccC
Confidence 359999999764
No 49
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=56.63 E-value=7.6 Score=27.48 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=16.2
Q ss_pred cccCCCCCcceeeeCCCCCc--cccCcCCCc
Q 016386 266 YRCKDDGCSGFLLRDSDDKG--FTCQQCGLV 294 (390)
Q Consensus 266 ~~C~~~~C~g~~~~~~~~~~--~~C~~C~~~ 294 (390)
..||++.|.+.+........ ..|..|+..
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 49 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTE 49 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCc
Confidence 37998889887766555444 788888764
No 50
>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=56.61 E-value=8.4 Score=22.35 Aligned_cols=22 Identities=23% Similarity=0.676 Sum_probs=12.1
Q ss_pred CCcceeeeCCCCCccccCcCCC
Q 016386 272 GCSGFLLRDSDDKGFTCQQCGL 293 (390)
Q Consensus 272 ~C~g~~~~~~~~~~~~C~~C~~ 293 (390)
.|+..+.|......+.|++||.
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCcccCceEeCCCCCC
Confidence 3444444444355667777763
No 51
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=54.72 E-value=2.7 Score=26.70 Aligned_cols=19 Identities=42% Similarity=1.144 Sum_probs=14.2
Q ss_pred CCccccCCHHHHHHh-hhhh
Q 016386 45 CQVVWYCGSNCQKLD-WKLH 63 (390)
Q Consensus 45 C~~~~yCS~~C~~~~-~~~H 63 (390)
|..+-|||..|.+.+ |.+|
T Consensus 6 cpkiGYCS~~CsKt~vWa~s 25 (39)
T PF08189_consen 6 CPKIGYCSSKCSKTDVWAFS 25 (39)
T ss_pred Ccccceecccccccceeeec
Confidence 455679999999864 7655
No 52
>cd02684 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear.
Probab=54.04 E-value=84 Score=23.51 Aligned_cols=36 Identities=11% Similarity=0.045 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKL 340 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 340 (390)
+++..++.+|......|++++|+.+|...+......
T Consensus 4 ~~Ai~lv~~Av~~D~~g~y~eA~~lY~~ale~~~~~ 39 (75)
T cd02684 4 EKAIALVVQAVKKDQRGDAAAALSLYCSALQYFVPA 39 (75)
T ss_pred HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Confidence 345566777777778899999999999877665543
No 53
>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=53.39 E-value=8.4 Score=25.49 Aligned_cols=28 Identities=29% Similarity=0.796 Sum_probs=16.0
Q ss_pred ccCCCCCcc-eeeeCCCCCccccCcCCCccC
Q 016386 267 RCKDDGCSG-FLLRDSDDKGFTCQQCGLVRS 296 (390)
Q Consensus 267 ~C~~~~C~g-~~~~~~~~~~~~C~~C~~~~~ 296 (390)
+|| .|++ .+..+.....+.|..||..++
T Consensus 2 ~Cp--~Cg~~~~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp SBT--TTSSSEEEEETTTTEEEETTT-BBEE
T ss_pred CCc--CCcCCceEEcCCCCeEECCCCCCEee
Confidence 575 5643 234444556678888887654
No 54
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=52.62 E-value=6 Score=33.49 Aligned_cols=31 Identities=26% Similarity=0.538 Sum_probs=25.9
Q ss_pred CCcccccccCcCCCCCCCCCCccccCCHHHHHH
Q 016386 26 SISRCDGCFASSNLKKCSACQVVWYCGSNCQKL 58 (390)
Q Consensus 26 ~~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~~ 58 (390)
....|..|. -.....|.+|+. .|||..|.+.
T Consensus 117 ~r~fCaVCG-~~S~ysC~~CG~-kyCsv~C~~~ 147 (156)
T KOG3362|consen 117 LRKFCAVCG-YDSKYSCVNCGT-KYCSVRCLKT 147 (156)
T ss_pred cchhhhhcC-CCchhHHHhcCC-ceeechhhhh
Confidence 467899998 556889999998 6999999864
No 55
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=52.51 E-value=40 Score=31.83 Aligned_cols=47 Identities=11% Similarity=-0.018 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhccccc
Q 016386 320 CGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCLGCSI 371 (390)
Q Consensus 320 ~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~~~~~ 371 (390)
.+++++|+..|+.+++ .+|.|.....+...++.+|.++|+...+...
T Consensus 193 ~g~~~~A~~~f~~vv~-----~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~ 239 (263)
T PRK10803 193 KGKKDDAAYYFASVVK-----NYPKSPKAADAMFKVGVIMQDKGDTAKAKAV 239 (263)
T ss_pred cCCHHHHHHHHHHHHH-----HCCCCcchhHHHHHHHHHHHHcCCHHHHHHH
Confidence 4455555555555443 2466677777777777777777666655443
No 56
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=52.20 E-value=42 Score=28.65 Aligned_cols=47 Identities=17% Similarity=0.171 Sum_probs=32.1
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHh
Q 016386 311 SKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHS 362 (390)
Q Consensus 311 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~ 362 (390)
++-+...+..+++++|+..+.++++ |||.|..+--+.....-++.+.
T Consensus 51 L~l~yayy~~~~y~~A~a~~~rFir-----LhP~hp~vdYa~Y~~gL~~~~~ 97 (142)
T PF13512_consen 51 LDLAYAYYKQGDYEEAIAAYDRFIR-----LHPTHPNVDYAYYMRGLSYYEQ 97 (142)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHH-----hCCCCCCccHHHHHHHHHHHHH
Confidence 3344445567899999999988876 7899997766555544444433
No 57
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=52.11 E-value=42 Score=26.10 Aligned_cols=51 Identities=14% Similarity=0.146 Sum_probs=29.6
Q ss_pred HHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcch
Q 016386 310 LSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSIL 365 (390)
Q Consensus 310 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~ 365 (390)
.+..+......+++++|++.+..++.. +|.+.....+...++.+|...|..
T Consensus 5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~~~~l~~~~~~~~~~ 55 (119)
T TIGR02795 5 YYDAALLVLKAGDYADAIQAFQAFLKK-----YPKSTYAPNAHYWLGEAYYAQGKY 55 (119)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHH-----CCCccccHHHHHHHHHHHHhhccH
Confidence 344455555566777777777766543 355554455555566666655554
No 58
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=51.89 E-value=22 Score=32.17 Aligned_cols=52 Identities=19% Similarity=0.229 Sum_probs=27.5
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhc
Q 016386 311 SKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCL 367 (390)
Q Consensus 311 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~ 367 (390)
+..+......+++++|+..++.++. .+|.+.....+...++.+|...|.+..
T Consensus 37 ~~~g~~~~~~~~~~~A~~~~~~~~~-----~~p~~~~~~~a~~~la~~~~~~~~~~~ 88 (235)
T TIGR03302 37 YEEAKEALDSGDYTEAIKYFEALES-----RYPFSPYAEQAQLDLAYAYYKSGDYAE 88 (235)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHH-----hCCCchhHHHHHHHHHHHHHhcCCHHH
Confidence 3334444445566666666655543 335555555555555666665555543
No 59
>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=51.33 E-value=1e+02 Score=23.20 Aligned_cols=35 Identities=17% Similarity=0.141 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKK 339 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 339 (390)
..+.++..+|......|++++|+..|+..+.....
T Consensus 4 ~~Ai~~a~~Ave~D~~g~y~eA~~~Y~~aie~l~~ 38 (76)
T cd02681 4 RDAVQFARLAVQRDQEGRYSEAVFYYKEAAQLLIY 38 (76)
T ss_pred HHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHH
Confidence 34455667777788899999999999987665544
No 60
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.33 E-value=9.1 Score=27.75 Aligned_cols=11 Identities=27% Similarity=0.933 Sum_probs=9.1
Q ss_pred ccCCHHHHHHh
Q 016386 49 WYCGSNCQKLD 59 (390)
Q Consensus 49 ~yCS~~C~~~~ 59 (390)
.|||+.|+.-+
T Consensus 27 PFCSkRCklID 37 (65)
T COG3024 27 PFCSKRCKLID 37 (65)
T ss_pred cchhHhhhhcc
Confidence 59999999754
No 61
>cd02656 MIT MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear.
Probab=48.61 E-value=1.1e+02 Score=22.57 Aligned_cols=36 Identities=19% Similarity=0.185 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhccc
Q 016386 306 EVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKLY 341 (390)
Q Consensus 306 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~l 341 (390)
.+..+..+|......|++++|+..|...+......+
T Consensus 5 ~a~~l~~~Av~~D~~g~~~~Al~~Y~~a~e~l~~~~ 40 (75)
T cd02656 5 QAKELIKQAVKEDEDGNYEEALELYKEALDYLLQAL 40 (75)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence 344456666667778999999999998776655543
No 62
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=46.07 E-value=82 Score=32.81 Aligned_cols=49 Identities=18% Similarity=0.103 Sum_probs=44.3
Q ss_pred hhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcch
Q 016386 317 LTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSIL 365 (390)
Q Consensus 317 ~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~ 365 (390)
....+.+++|+.+++..++.+..++-+.|+.+..++-.|+.+|..+|..
T Consensus 335 ~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~ 383 (508)
T KOG1840|consen 335 LQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKY 383 (508)
T ss_pred HHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcch
Confidence 3345689999999999999999999999999999999999999999876
No 63
>PRK11827 hypothetical protein; Provisional
Probab=46.05 E-value=13 Score=26.77 Aligned_cols=35 Identities=23% Similarity=0.423 Sum_probs=27.1
Q ss_pred hhhhccccCCCCCcceeeeCCCCCccccCcCCCccCH
Q 016386 261 AILEGYRCKDDGCSGFLLRDSDDKGFTCQQCGLVRSK 297 (390)
Q Consensus 261 ~~l~~~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~~~ 297 (390)
.+++-+.|| .|+|.+..+.+.....|..|+.....
T Consensus 4 ~LLeILaCP--~ckg~L~~~~~~~~Lic~~~~laYPI 38 (60)
T PRK11827 4 RLLEIIACP--VCNGKLWYNQEKQELICKLDNLAFPL 38 (60)
T ss_pred HHHhheECC--CCCCcCeEcCCCCeEECCccCeeccc
Confidence 356778997 79999877665666789999987664
No 64
>PF08666 SAF: SAF domain; InterPro: IPR013974 This entry includes a range of different proteins, such as antifreeze proteins, flagellar FlgA proteins, and CpaB pilus proteins. ; PDB: 1C89_A 3NLA_A 3RDN_A 1C8A_A 3FRN_A 1WVO_A 3K3S_H 3G8R_B 1XUU_A 1XUZ_A ....
Probab=44.82 E-value=14 Score=26.06 Aligned_cols=17 Identities=29% Similarity=0.511 Sum_probs=12.4
Q ss_pred EEEEccccCCCCeeeEe
Q 016386 204 VVRAVQHVPKGAEVLIS 220 (390)
Q Consensus 204 ~vrA~r~I~~Geei~is 220 (390)
++.|.++|++|+.|+-.
T Consensus 3 vvVA~~di~~G~~i~~~ 19 (63)
T PF08666_consen 3 VVVAARDIPAGTVITAE 19 (63)
T ss_dssp EEEESSTB-TT-BECTT
T ss_pred EEEEeCccCCCCEEccC
Confidence 57899999999998544
No 65
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=44.78 E-value=35 Score=20.01 Aligned_cols=24 Identities=13% Similarity=0.175 Sum_probs=17.2
Q ss_pred HHhhhcCCCHHHHHHHHHHHHHhh
Q 016386 314 TLALTSCGNHQEVVSTYKMIEKLQ 337 (390)
Q Consensus 314 ~~~~~~~~~~~~a~~~~~~~~~~~ 337 (390)
+.-....|++++|++.++.++..+
T Consensus 7 a~~~~~~g~~~~A~~~~~~~~~~~ 30 (33)
T PF13174_consen 7 ARCYYKLGDYDEAIEYFQRLIKRY 30 (33)
T ss_dssp HHHHHHHCHHHHHHHHHHHHHHHS
T ss_pred HHHHHHccCHHHHHHHHHHHHHHC
Confidence 333334578999999999887754
No 66
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=44.36 E-value=17 Score=22.32 Aligned_cols=26 Identities=19% Similarity=0.389 Sum_probs=15.5
Q ss_pred ccCCCCCcceeeeCCCCCccccCcCCCc
Q 016386 267 RCKDDGCSGFLLRDSDDKGFTCQQCGLV 294 (390)
Q Consensus 267 ~C~~~~C~g~~~~~~~~~~~~C~~C~~~ 294 (390)
.|+ .|++...+.......+|..|+..
T Consensus 5 fC~--~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCG--RCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-T--TT--BEEE-SSSS-EEESSSS-E
T ss_pred ccC--cCCccccCCCCcCEeECCCCcCE
Confidence 375 78888887777677789999875
No 67
>cd02683 MIT_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with unknown function, co-occuring with an as yet undescribed domain. The molecular function of the MIT domain is unclear.
Probab=43.87 E-value=1.3e+02 Score=22.60 Aligned_cols=35 Identities=20% Similarity=0.247 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcc
Q 016386 306 EVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKL 340 (390)
Q Consensus 306 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 340 (390)
.+..++.+|......|++++|+..|...+.....+
T Consensus 5 ~a~~l~~~Ave~D~~g~y~eAl~~Y~~aie~l~~~ 39 (77)
T cd02683 5 AAKEVLKRAVELDQEGRFQEALVCYQEGIDLLMQV 39 (77)
T ss_pred HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Confidence 34456677777778899999999999877665543
No 68
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=43.27 E-value=89 Score=24.25 Aligned_cols=45 Identities=18% Similarity=0.398 Sum_probs=31.6
Q ss_pred CCcce-eeeCCCCCccccCcCCCccCHHHHHHHHHHHHHHHHHHHh
Q 016386 272 GCSGF-LLRDSDDKGFTCQQCGLVRSKEEIKKIASEVNILSKKTLA 316 (390)
Q Consensus 272 ~C~g~-~~~~~~~~~~~C~~C~~~~~~~~v~~~~~~~~~~~~~~~~ 316 (390)
.|.|- +...++...|.|..|...-..+.+..+++.+.+..+...+
T Consensus 37 ~~~G~~~~~~~G~~vw~C~~C~~~H~~e~~~~i~~~~~~~~~~~k~ 82 (86)
T PF04071_consen 37 ECGGNFIYTKNGSKVWDCSDCTLPHRPENYDYIIRKLKEIIEELKK 82 (86)
T ss_pred CCCccEEEcCCCCeeeECccCCCccCHHHHHHHHHHHHHHHHHHHH
Confidence 45454 3333445689999999999888888888777766665443
No 69
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=43.17 E-value=12 Score=37.64 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=22.2
Q ss_pred CCEEEEEEccccCCCCeeeEeccCC
Q 016386 200 GRLAVVRAVQHVPKGAEVLISYIET 224 (390)
Q Consensus 200 ~~~~~vrA~r~I~~Geei~isY~~~ 224 (390)
++.+-.||+|+|++||||.+=|++.
T Consensus 121 ~~~Ifyrt~r~I~p~eELlVWY~~e 145 (396)
T KOG2461|consen 121 GENIFYRTIRDIRPNEELLVWYGSE 145 (396)
T ss_pred cCceEEEecccCCCCCeEEEEeccc
Confidence 4568899999999999999999865
No 70
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=41.97 E-value=1.3e+02 Score=21.67 Aligned_cols=32 Identities=25% Similarity=0.269 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhh
Q 016386 306 EVNILSKKTLALTSCGNHQEVVSTYKMIEKLQ 337 (390)
Q Consensus 306 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~ 337 (390)
.+-.++.+|......|++++|++.|...+...
T Consensus 4 ~A~~~~~~Av~~D~~g~~~~A~~~Y~~ai~~l 35 (69)
T PF04212_consen 4 KAIELIKKAVEADEAGNYEEALELYKEAIEYL 35 (69)
T ss_dssp HHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44456677777888999999999999776554
No 71
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=40.15 E-value=86 Score=32.02 Aligned_cols=54 Identities=9% Similarity=-0.041 Sum_probs=41.3
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhccc
Q 016386 311 SKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCLGC 369 (390)
Q Consensus 311 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~~~ 369 (390)
+..+..+...+++++|+..|++.+. +.|++.....+.+.++-+|..+|....+-
T Consensus 79 ~NLG~AL~~lGryeEAIa~f~rALe-----L~Pd~aeA~~A~yNLAcaya~LGr~dEAl 132 (453)
T PLN03098 79 VNLGLSLFSKGRVKDALAQFETALE-----LNPNPDEAQAAYYNKACCHAYREEGKKAA 132 (453)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHh-----hCCCchHHHHHHHHHHHHHHHcCCHHHHH
Confidence 3445556678899999999998876 45877666667889999999999875543
No 72
>KOG2738 consensus Putative methionine aminopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=40.07 E-value=15 Score=35.20 Aligned_cols=34 Identities=24% Similarity=0.756 Sum_probs=23.6
Q ss_pred ccccCcCCCCCCCCC-----CccccCCHHHHHHhhhhhHH
Q 016386 31 DGCFASSNLKKCSAC-----QVVWYCGSNCQKLDWKLHRL 65 (390)
Q Consensus 31 ~~C~~~~~~~~C~~C-----~~~~yCS~~C~~~~~~~H~~ 65 (390)
..|.++.. ..|+.| .-.+||+++|.+..|..|+.
T Consensus 12 ~~c~~~a~-l~Cp~c~~~~i~~~~fc~q~cf~~~w~~hK~ 50 (369)
T KOG2738|consen 12 LQCGSEAS-LQCPTCLKLGIKSAYFCAQECFKNSWLSHKK 50 (369)
T ss_pred cccCChhh-ccCchhhhcCCCcccccCchhhhcchhhhhh
Confidence 55666533 566666 22469999999999987653
No 73
>PF10516 SHNi-TPR: SHNi-TPR; InterPro: IPR019544 The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. This entry represents SHNi-TPR (Sim3-Hif1-NASP interrupted TPR), a sequence that is an interrupted form of TPR repeat [].
Probab=38.53 E-value=40 Score=21.81 Aligned_cols=25 Identities=20% Similarity=0.424 Sum_probs=20.8
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCC
Q 016386 319 SCGNHQEVVSTYKMIEKLQKKLYHP 343 (390)
Q Consensus 319 ~~~~~~~a~~~~~~~~~~~~~~lhp 343 (390)
..+++++|++-|++++..++.++.|
T Consensus 13 e~e~f~qA~~D~~~aL~i~~~l~~~ 37 (38)
T PF10516_consen 13 ENENFEQAIEDYEKALEIQEELLPP 37 (38)
T ss_pred HhccHHHHHHHHHHHHHHHHHhcCC
Confidence 4668999999999999888877765
No 74
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=38.40 E-value=61 Score=33.73 Aligned_cols=48 Identities=17% Similarity=0.209 Sum_probs=44.3
Q ss_pred hcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcch
Q 016386 318 TSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSIL 365 (390)
Q Consensus 318 ~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~ 365 (390)
...+.+.+|+.+|+.++.....++-+.|+.+..+...|+.+|...|+.
T Consensus 252 ~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf 299 (508)
T KOG1840|consen 252 RSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKF 299 (508)
T ss_pred HHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCCh
Confidence 356789999999999999999999999999999999999999988886
No 75
>PRK00420 hypothetical protein; Validated
Probab=38.27 E-value=85 Score=25.64 Aligned_cols=29 Identities=24% Similarity=0.332 Sum_probs=16.8
Q ss_pred ccccCCCCCcceeeeCCCCCccccCcCCCccC
Q 016386 265 GYRCKDDGCSGFLLRDSDDKGFTCQQCGLVRS 296 (390)
Q Consensus 265 ~~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~~ 296 (390)
+-.|| .|+.++... .+....|+.||....
T Consensus 23 ~~~CP--~Cg~pLf~l-k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCP--VCGLPLFEL-KDGEVVCPVHGKVYI 51 (112)
T ss_pred cCCCC--CCCCcceec-CCCceECCCCCCeee
Confidence 34575 576665432 233567888887554
No 76
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=38.03 E-value=79 Score=25.86 Aligned_cols=11 Identities=27% Similarity=0.797 Sum_probs=6.1
Q ss_pred cccCcCCCccC
Q 016386 286 FTCQQCGLVRS 296 (390)
Q Consensus 286 ~~C~~C~~~~~ 296 (390)
..|+.|+..+.
T Consensus 13 l~C~~C~t~i~ 23 (113)
T PF09862_consen 13 LKCPSCGTEIE 23 (113)
T ss_pred EEcCCCCCEEE
Confidence 45666665543
No 77
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=37.52 E-value=21 Score=25.38 Aligned_cols=24 Identities=17% Similarity=0.349 Sum_probs=17.4
Q ss_pred CcccccccCcCCCCCCCCCCccccCCHHHHH
Q 016386 27 ISRCDGCFASSNLKKCSACQVVWYCGSNCQK 57 (390)
Q Consensus 27 ~~~C~~C~~~~~~~~C~~C~~~~yCS~~C~~ 57 (390)
..+|-.|.+..+.- -.+||++|+.
T Consensus 8 H~HC~VCg~aIp~d-------e~~CSe~C~e 31 (64)
T COG4068 8 HRHCVVCGKAIPPD-------EQVCSEECGE 31 (64)
T ss_pred CccccccCCcCCCc-------cchHHHHHHH
Confidence 46788888875532 2489999985
No 78
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=37.50 E-value=21 Score=30.56 Aligned_cols=37 Identities=19% Similarity=0.461 Sum_probs=23.4
Q ss_pred ccccCCCCCc---c-ee-----eeCCCCCccccCcCCCccCHHHHH
Q 016386 265 GYRCKDDGCS---G-FL-----LRDSDDKGFTCQQCGLVRSKEEIK 301 (390)
Q Consensus 265 ~~~C~~~~C~---g-~~-----~~~~~~~~~~C~~C~~~~~~~~v~ 301 (390)
-++|+|++|- . ++ ..+......+|..|++..+.+++.
T Consensus 106 vlkCpN~nCITn~e~pv~s~F~~~~~~~~~lrC~YCe~~~~~~~v~ 151 (153)
T COG1781 106 VLRCPNPNCITNAEEPVESKFYVVSKEPLALRCKYCEKTFSEDEVL 151 (153)
T ss_pred EEEcCCCCcccCCCccCCccEEEEecCCcEEEEEecCcEechhhhh
Confidence 4688888882 1 21 112223458999999998866553
No 79
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=37.40 E-value=19 Score=29.70 Aligned_cols=21 Identities=29% Similarity=0.461 Sum_probs=14.9
Q ss_pred CCCCCCCEEEEeCCeeeeecC
Q 016386 3 SFHVSGEVIISQEPYVCVPNN 23 (390)
Q Consensus 3 ~~I~~Ge~Il~e~P~~~~~~~ 23 (390)
++|++||+|+.+.|++..+..
T Consensus 8 ~dI~~Ge~I~~p~~~~~~~~~ 28 (162)
T PF00856_consen 8 RDIKAGEVILIPRPAILTPDE 28 (162)
T ss_dssp S-B-TTEEEEEESEEEEEHHH
T ss_pred ccCCCCCEEEEECcceEEehh
Confidence 799999999977777766653
No 80
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=36.47 E-value=54 Score=22.68 Aligned_cols=28 Identities=14% Similarity=0.297 Sum_probs=17.9
Q ss_pred ccCcCCCccCHHHHHHHHHHHHHHHHHH
Q 016386 287 TCQQCGLVRSKEEIKKIASEVNILSKKT 314 (390)
Q Consensus 287 ~C~~C~~~~~~~~v~~~~~~~~~~~~~~ 314 (390)
.|+.|+..++.+....++.+.+..++..
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~~~i~~~ 49 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYKSEIEEL 49 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHhh
Confidence 7999999999887777777776655543
No 81
>KOG2782 consensus Putative SAM dependent methyltransferases [General function prediction only]
Probab=36.32 E-value=51 Score=30.39 Aligned_cols=46 Identities=30% Similarity=0.420 Sum_probs=30.0
Q ss_pred ccCCCchhHHHHHHHHHHHHHHhcch---------hccccceecccc-ccceeeec
Q 016386 340 LYHPFSVNLMQTREKLIKGYIHSSIL---------CLGCSIIPVGNL-NGFLVTQK 385 (390)
Q Consensus 340 ~lhp~~~~~~~~~~~l~~~y~~~~~~---------~~~~~~~~~~~~-~~~~~~~~ 385 (390)
++||.=..++.--..+-.+.++.|+. +.|||||.|-|- .||-|.|.
T Consensus 90 l~~~~l~a~Lg~Fs~~~~l~~~~gl~~~~vDGiLmDlGcSSMQ~d~peRGFSv~~d 145 (303)
T KOG2782|consen 90 LMHPTLKAVLGNFSYIKSLIADTGLLDVGVDGILMDLGCSSMQVDNPERGFSVLQD 145 (303)
T ss_pred hcchhHHHHHhhhHHHHHHHHHhCCCcCCcceEEeecCccccccCCccccceeecc
Confidence 44554333443334455566666655 899999999885 58988774
No 82
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.38 E-value=27 Score=23.75 Aligned_cols=27 Identities=26% Similarity=0.877 Sum_probs=17.4
Q ss_pred cCCCCCcceeeeCCCC--CccccCcCCCccC
Q 016386 268 CKDDGCSGFLLRDSDD--KGFTCQQCGLVRS 296 (390)
Q Consensus 268 C~~~~C~g~~~~~~~~--~~~~C~~C~~~~~ 296 (390)
|+ .|+..+.+.... ..|.|..||....
T Consensus 3 Cp--~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 3 CP--KCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CC--CCCCccccccCCCCCEEECCcCCCeEE
Confidence 65 677666554332 3688999997643
No 83
>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.
Probab=35.12 E-value=2e+02 Score=21.71 Aligned_cols=43 Identities=14% Similarity=0.200 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcc--cCCCchh
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKL--YHPFSVN 347 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~--lhp~~~~ 347 (390)
+.+.....+|......|++++|+..|+........+ ..|.+..
T Consensus 4 ~~A~~~a~~AVe~D~~gr~~eAi~~Y~~aIe~L~q~~~~~pD~~~ 48 (75)
T cd02682 4 EMARKYAINAVKAEKEGNAEDAITNYKKAIEVLSQIVKNYPDSPT 48 (75)
T ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHhCCChHH
Confidence 344555667777888899999999998876665554 3344443
No 84
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=35.03 E-value=89 Score=19.28 Aligned_cols=20 Identities=15% Similarity=0.323 Sum_probs=15.3
Q ss_pred cCCCHHHHHHHHHHHHHhhh
Q 016386 319 SCGNHQEVVSTYKMIEKLQK 338 (390)
Q Consensus 319 ~~~~~~~a~~~~~~~~~~~~ 338 (390)
..|++++|++.|++.+.+..
T Consensus 11 ~~g~~~~Ai~~y~~aL~l~~ 30 (36)
T PF13176_consen 11 QQGDYEKAIEYYEQALALAR 30 (36)
T ss_dssp HCT-HHHHHHHHHHHHHHHH
T ss_pred HcCCHHHHHHHHHHHHHhcc
Confidence 57899999999999775543
No 85
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=34.16 E-value=23 Score=36.82 Aligned_cols=53 Identities=23% Similarity=0.385 Sum_probs=36.2
Q ss_pred CCCCCCCEE---EE---------eCCeeeeecCCCCCcccccccCcC-----CCCCCCCCCccccCCHHHHH
Q 016386 3 SFHVSGEVI---IS---------QEPYVCVPNNSSSISRCDGCFASS-----NLKKCSACQVVWYCGSNCQK 57 (390)
Q Consensus 3 ~~I~~Ge~I---l~---------e~P~~~~~~~~~~~~~C~~C~~~~-----~~~~C~~C~~~~yCS~~C~~ 57 (390)
+||..|++| +. -.|.+.-+......+.|++|...+ ...+|.+|+.- |= +.|..
T Consensus 120 sdI~eG~lvEvvl~~~at~ed~~i~PH~l~vhSY~~PtFCD~CGEmL~GLvrQGlKC~gCglN-yH-KRCa~ 189 (888)
T KOG4236|consen 120 SDITEGDLVEVVLSASATFEDFQIRPHTLFVHSYKAPTFCDFCGEMLFGLVRQGLKCEGCGLN-YH-KRCAF 189 (888)
T ss_pred cccccCceEEEEeeccccccceeeecceeeeecccCchHHHHHHHHHHHHHHccccccCCCCc-Hh-hhhhh
Confidence 578888754 33 245555555556789999999873 47899999974 43 45543
No 86
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=34.00 E-value=28 Score=26.99 Aligned_cols=30 Identities=17% Similarity=0.397 Sum_probs=19.9
Q ss_pred ccccCCCCCcceeeeCCCCCccccCcCCCccC
Q 016386 265 GYRCKDDGCSGFLLRDSDDKGFTCQQCGLVRS 296 (390)
Q Consensus 265 ~~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~~ 296 (390)
...|| .|+.....-....-|.|.+||....
T Consensus 35 ~~~Cp--~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCP--FCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCC--CCCCcceeeeccCeEEcCCCCCeec
Confidence 45675 6754443334456799999998764
No 87
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=33.77 E-value=99 Score=29.18 Aligned_cols=33 Identities=18% Similarity=0.234 Sum_probs=19.4
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHH
Q 016386 319 SCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLI 356 (390)
Q Consensus 319 ~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~ 356 (390)
..+++.+|+..|+.+++. +|.+..--.++..|.
T Consensus 229 ~~g~~~~A~~~~~~vi~~-----yP~s~~a~~A~~rL~ 261 (263)
T PRK10803 229 DKGDTAKAKAVYQQVIKK-----YPGTDGAKQAQKRLN 261 (263)
T ss_pred HcCCHHHHHHHHHHHHHH-----CcCCHHHHHHHHHHh
Confidence 455666666666665543 366666555555553
No 88
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.76 E-value=84 Score=29.72 Aligned_cols=51 Identities=18% Similarity=0.087 Sum_probs=38.6
Q ss_pred HHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcch
Q 016386 310 LSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSIL 365 (390)
Q Consensus 310 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~ 365 (390)
+++.|..++-.++|.+|...|...++++ |++.+..+++.-|-++|-..|+-
T Consensus 144 ~Y~~A~~~~ksgdy~~A~~~F~~fi~~Y-----P~s~~~~nA~yWLGe~~y~qg~y 194 (262)
T COG1729 144 LYNAALDLYKSGDYAEAEQAFQAFIKKY-----PNSTYTPNAYYWLGESLYAQGDY 194 (262)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcC-----CCCcccchhHHHHHHHHHhcccc
Confidence 6777777777788888888888888766 77777777777777777666654
No 89
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=33.57 E-value=1e+02 Score=18.01 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=17.6
Q ss_pred HHHhhhcCCCHHHHHHHHHHHHHhh
Q 016386 313 KTLALTSCGNHQEVVSTYKMIEKLQ 337 (390)
Q Consensus 313 ~~~~~~~~~~~~~a~~~~~~~~~~~ 337 (390)
.+.-....+++++|++.+++++.+.
T Consensus 7 lg~~~~~~~~~~~A~~~~~~al~l~ 31 (34)
T PF07719_consen 7 LGQAYYQLGNYEEAIEYFEKALELD 31 (34)
T ss_dssp HHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHC
Confidence 3344556789999999999887644
No 90
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=33.54 E-value=1.9e+02 Score=21.17 Aligned_cols=35 Identities=23% Similarity=0.271 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKK 339 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 339 (390)
.++..++.+|......|++++|+..|...+.....
T Consensus 6 ~~A~~li~~Av~~d~~g~~~eAl~~Y~~a~e~l~~ 40 (77)
T smart00745 6 SKAKELISKALKADEAGDYEEALELYKKAIEYLLE 40 (77)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 44555667777777789999999999987655443
No 91
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=33.37 E-value=22 Score=30.16 Aligned_cols=27 Identities=19% Similarity=0.725 Sum_probs=11.4
Q ss_pred ccCCCCCcceeeeCCCCCccccCcCCCc
Q 016386 267 RCKDDGCSGFLLRDSDDKGFTCQQCGLV 294 (390)
Q Consensus 267 ~C~~~~C~g~~~~~~~~~~~~C~~C~~~ 294 (390)
.|++..|...+.+. ++..|.|.+|+..
T Consensus 20 aC~~~~C~kKv~~~-~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 20 ACPNEKCNKKVTEN-GDGSYRCEKCNKT 46 (146)
T ss_dssp E-TSTTTS-B-EEE-TTTEEEETTTTEE
T ss_pred CCCCccCCCEeecC-CCcEEECCCCCCc
Confidence 35444454444333 2334566666654
No 92
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=32.96 E-value=13 Score=24.70 Aligned_cols=29 Identities=24% Similarity=0.599 Sum_probs=17.6
Q ss_pred CcccccccCcCC----CCCCCCCCccccCCHHHHH
Q 016386 27 ISRCDGCFASSN----LKKCSACQVVWYCGSNCQK 57 (390)
Q Consensus 27 ~~~C~~C~~~~~----~~~C~~C~~~~yCS~~C~~ 57 (390)
...|..|.++.. -..|= ..|.|||+.|+.
T Consensus 8 ~K~C~~C~rpf~WRKKW~~~W--d~VkYCS~rCR~ 40 (42)
T PF10013_consen 8 SKICPVCGRPFTWRKKWARCW--DEVKYCSDRCRR 40 (42)
T ss_pred CCcCcccCCcchHHHHHHHhc--hhhccHHHHhcc
Confidence 456888877732 11110 246799999975
No 93
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=32.83 E-value=32 Score=29.68 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=14.9
Q ss_pred CCCCccccCcCCCccCHHHH
Q 016386 281 SDDKGFTCQQCGLVRSKEEI 300 (390)
Q Consensus 281 ~~~~~~~C~~C~~~~~~~~v 300 (390)
.+...++|..|++..+.+++
T Consensus 130 ~~~~~~rC~YCe~~~~~~~~ 149 (152)
T PRK00893 130 KEPIKLRCKYCEKEFSEDIV 149 (152)
T ss_pred CCCCEEEeeCCCCEechhhh
Confidence 34457899999999876554
No 94
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=32.70 E-value=1.6e+02 Score=24.42 Aligned_cols=57 Identities=11% Similarity=-0.067 Sum_probs=0.0
Q ss_pred HHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhcc
Q 016386 307 VNILSKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCLG 368 (390)
Q Consensus 307 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~~ 368 (390)
....+..+......|++++|+..|+.++... |....-.-++..|+.++...|....+
T Consensus 48 ~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~-----~d~~l~~~a~l~LA~~~~~~~~~d~A 104 (145)
T PF09976_consen 48 ALAALQLAKAAYEQGDYDEAKAALEKALANA-----PDPELKPLARLRLARILLQQGQYDEA 104 (145)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC-----CCHHHHHHHHHHHHHHHHHcCCHHHH
No 95
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=32.52 E-value=1.5e+02 Score=25.43 Aligned_cols=51 Identities=12% Similarity=0.014 Sum_probs=28.6
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchh
Q 016386 311 SKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILC 366 (390)
Q Consensus 311 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~ 366 (390)
+..+......|++++|+..+++++... |.+.....+...++.+|..+|...
T Consensus 39 ~~lg~~~~~~g~~~~A~~~~~~al~~~-----~~~~~~~~~~~~la~~~~~~g~~~ 89 (172)
T PRK02603 39 YRDGMSAQADGEYAEALENYEEALKLE-----EDPNDRSYILYNMGIIYASNGEHD 89 (172)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHh-----hccchHHHHHHHHHHHHHHcCCHH
Confidence 334444445677777777777665432 222223445566666666666653
No 96
>KOG4234 consensus TPR repeat-containing protein [General function prediction only]
Probab=32.44 E-value=1.3e+02 Score=27.54 Aligned_cols=35 Identities=20% Similarity=0.177 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKK 339 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 339 (390)
.++..+-.+...+...|+|++|.+.|..++.....
T Consensus 93 ~kad~lK~EGN~~F~ngdyeeA~skY~~Ale~cp~ 127 (271)
T KOG4234|consen 93 EKADSLKKEGNELFKNGDYEEANSKYQEALESCPS 127 (271)
T ss_pred HHHHHHHHHHHHhhhcccHHHHHHHHHHHHHhCcc
Confidence 34444445555677889999999999998876543
No 97
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=32.29 E-value=27 Score=22.72 Aligned_cols=23 Identities=30% Similarity=0.777 Sum_probs=17.3
Q ss_pred cccccCcCC--CCCCCCCCccccCCH
Q 016386 30 CDGCFASSN--LKKCSACQVVWYCGS 53 (390)
Q Consensus 30 C~~C~~~~~--~~~C~~C~~~~yCS~ 53 (390)
|+.|-+... ++.|..|+.. ||+.
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~-FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNL-FCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCc-cccc
Confidence 667777732 6789999985 9973
No 98
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=31.53 E-value=36 Score=30.15 Aligned_cols=19 Identities=21% Similarity=0.174 Sum_probs=12.0
Q ss_pred CCCHHHHHHHHhHhhcccc
Q 016386 147 EISINEIAENFSKLACNAH 165 (390)
Q Consensus 147 ~~~~~ei~~~~~~l~~Naf 165 (390)
.++..++.+++.++.-++.
T Consensus 47 gi~~~~VRk~L~~L~e~gL 65 (178)
T PRK06266 47 GIKLNTVRKILYKLYDARL 65 (178)
T ss_pred CCCHHHHHHHHHHHHHCCC
Confidence 3466677777777765544
No 99
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=31.24 E-value=1.5e+02 Score=19.09 Aligned_cols=26 Identities=12% Similarity=0.074 Sum_probs=20.7
Q ss_pred hhcCCCHHHHHHHHHHHHHhhhcccCCCchh
Q 016386 317 LTSCGNHQEVVSTYKMIEKLQKKLYHPFSVN 347 (390)
Q Consensus 317 ~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~ 347 (390)
....|++++|++.|+++++ .+|.|..
T Consensus 11 ~~~~G~~~~A~~~~~~~l~-----~~P~~~~ 36 (44)
T PF13428_consen 11 YRRLGQPDEAERLLRRALA-----LDPDDPE 36 (44)
T ss_pred HHHcCCHHHHHHHHHHHHH-----HCcCCHH
Confidence 4468899999999999876 4587764
No 100
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=31.22 E-value=44 Score=23.44 Aligned_cols=29 Identities=24% Similarity=0.612 Sum_probs=18.1
Q ss_pred cccCCCCCcceeeeCC--CCCccccCcCCCc
Q 016386 266 YRCKDDGCSGFLLRDS--DDKGFTCQQCGLV 294 (390)
Q Consensus 266 ~~C~~~~C~g~~~~~~--~~~~~~C~~C~~~ 294 (390)
..||.+.|...+.... ......|..|+..
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~ 49 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFS 49 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCe
Confidence 3588888876665432 3455677777654
No 101
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.19 E-value=1.3e+02 Score=26.64 Aligned_cols=41 Identities=22% Similarity=0.447 Sum_probs=25.5
Q ss_pred HHHHHHhccCCeEeeCcccCCCCCCCCccchhhhhccccCCCCCcceee
Q 016386 230 TRQKALKEQYLFTCTCPRCIKLGQFDDIQESAILEGYRCKDDGCSGFLL 278 (390)
Q Consensus 230 ~Rr~~L~~~~~F~C~C~rC~~~~~~~~~~~~~~l~~~~C~~~~C~g~~~ 278 (390)
.+.+...++-+|.| +.|.-.- +...++...|.|| .|++.+.
T Consensus 103 ~~le~~~~~~~y~C--~~~~~r~----sfdeA~~~~F~Cp--~Cg~~L~ 143 (176)
T COG1675 103 RKLEKETENNYYVC--PNCHVKY----SFDEAMELGFTCP--KCGEDLE 143 (176)
T ss_pred HHHHhhccCCceeC--CCCCCcc----cHHHHHHhCCCCC--CCCchhh
Confidence 44556677888888 7776641 2233455667886 6766654
No 102
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.99 E-value=38 Score=19.98 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=15.5
Q ss_pred ccccccCcCC--CCCCCCCCcc
Q 016386 29 RCDGCFASSN--LKKCSACQVV 48 (390)
Q Consensus 29 ~C~~C~~~~~--~~~C~~C~~~ 48 (390)
.|-.|.+..+ ...|+.|++.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCC
Confidence 5888888854 6789999875
No 103
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=30.43 E-value=18 Score=29.08 Aligned_cols=25 Identities=24% Similarity=0.705 Sum_probs=18.4
Q ss_pred CCCCCCCCccccCCHHHHH-HhhhhhH
Q 016386 39 LKKCSACQVVWYCGSNCQK-LDWKLHR 64 (390)
Q Consensus 39 ~~~C~~C~~~~yCS~~C~~-~~~~~H~ 64 (390)
..||+.|+.. -|+.+|+. .-|.|-.
T Consensus 74 ~~PC~~C~S~-KCG~~CR~nRkw~ye~ 99 (103)
T PF14949_consen 74 HYPCPKCGSR-KCGPECRCNRKWVYES 99 (103)
T ss_pred cccCCCCCCC-ccChhhCcCCceeeee
Confidence 4689999985 79999985 3455433
No 104
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=29.97 E-value=2e+02 Score=24.40 Aligned_cols=47 Identities=11% Similarity=-0.069 Sum_probs=25.9
Q ss_pred HHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcch
Q 016386 314 TLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSIL 365 (390)
Q Consensus 314 ~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~ 365 (390)
+......+++++|+..++.++.. .|.+.....+...++.+|..+|..
T Consensus 42 g~~~~~~g~~~~A~~~~~~al~l-----~~~~~~~~~~~~~lg~~~~~~g~~ 88 (168)
T CHL00033 42 GMSAQSEGEYAEALQNYYEAMRL-----EIDPYDRSYILYNIGLIHTSNGEH 88 (168)
T ss_pred HHHHHHcCCHHHHHHHHHHHHhc-----cccchhhHHHHHHHHHHHHHcCCH
Confidence 33344556777777777666543 233333444555666666655554
No 105
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=29.53 E-value=1.7e+02 Score=26.14 Aligned_cols=48 Identities=19% Similarity=0.103 Sum_probs=34.3
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhc
Q 016386 311 SKKTLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSS 363 (390)
Q Consensus 311 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~ 363 (390)
+..+......+++++|+..++.+++ .||.|...-.+...+..++..+.
T Consensus 46 l~la~a~y~~~~y~~A~~~~~~fi~-----~yP~~~~~~~A~Y~~g~~~~~~~ 93 (203)
T PF13525_consen 46 LMLAYAYYKQGDYEEAIAAYERFIK-----LYPNSPKADYALYMLGLSYYKQI 93 (203)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHH-----H-TT-TTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHH-----HCCCCcchhhHHHHHHHHHHHhC
Confidence 3344445567899999999998876 56999998888888888776653
No 106
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.17 E-value=50 Score=23.90 Aligned_cols=33 Identities=21% Similarity=0.572 Sum_probs=22.5
Q ss_pred hccccCCCCCcceeeeCCCCCccccCcCCCccCHH
Q 016386 264 EGYRCKDDGCSGFLLRDSDDKGFTCQQCGLVRSKE 298 (390)
Q Consensus 264 ~~~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~~~~ 298 (390)
.+-.|+ .|+...........|.|..||...+.+
T Consensus 27 TSq~C~--~CG~~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 27 TSQTCP--RCGHRNKKRRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred CccCcc--CcccccccccccceEEcCCCCCEECcH
Confidence 455675 676554443455679999999987654
No 107
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=28.14 E-value=25 Score=33.97 Aligned_cols=41 Identities=24% Similarity=0.720 Sum_probs=28.9
Q ss_pred CCeeeeecCC-CCCcccccccCcC---CCCCCCCCCccccCCHHHHH
Q 016386 15 EPYVCVPNNS-SSISRCDGCFASS---NLKKCSACQVVWYCGSNCQK 57 (390)
Q Consensus 15 ~P~~~~~~~~-~~~~~C~~C~~~~---~~~~C~~C~~~~yCS~~C~~ 57 (390)
+||+-+|... ....+|..|+... ..++|..|+.+ ||. .|-.
T Consensus 317 ~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~-FCl-dCDv 361 (378)
T KOG2807|consen 317 KPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNV-FCL-DCDV 361 (378)
T ss_pred cchhhccccccCCCcceeeeccccCCCCcEEchhccce-eec-cchH
Confidence 4555555543 3567799997663 47899999996 997 6854
No 108
>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=28.04 E-value=40 Score=21.51 Aligned_cols=27 Identities=30% Similarity=0.535 Sum_probs=19.1
Q ss_pred cccCCCCCcceeeeCCCCCccccCcCCCcc
Q 016386 266 YRCKDDGCSGFLLRDSDDKGFTCQQCGLVR 295 (390)
Q Consensus 266 ~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~ 295 (390)
+.|+ .|++. ....++..+.|..||+..
T Consensus 9 ~~C~--~C~~~-~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 9 EPCP--VCGSR-WFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred CcCC--CCCCe-EeEccCCEEEhhhCceEc
Confidence 3486 58777 444556678999999864
No 109
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=28.02 E-value=55 Score=25.63 Aligned_cols=30 Identities=20% Similarity=0.516 Sum_probs=18.2
Q ss_pred ccccCCCCCcceeeeCCCCCccccCcCCCccC
Q 016386 265 GYRCKDDGCSGFLLRDSDDKGFTCQQCGLVRS 296 (390)
Q Consensus 265 ~~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~~ 296 (390)
.+.|| .|+..-+......-|+|..|+..+.
T Consensus 35 ky~Cp--~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCP--FCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEES--SSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CCcCC--CCCCceeEEeeeEEeecCCCCCEEe
Confidence 46675 6754333333345699999997654
No 110
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=27.77 E-value=1.4e+02 Score=29.30 Aligned_cols=40 Identities=15% Similarity=0.077 Sum_probs=18.6
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchh
Q 016386 319 SCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILC 366 (390)
Q Consensus 319 ~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~ 366 (390)
..+++++|+..+.+++.+ .|.+. .+...++.+|..+|+..
T Consensus 48 ~~g~~~eAl~~~~~Al~l-----~P~~~---~a~~~lg~~~~~lg~~~ 87 (356)
T PLN03088 48 KLGNFTEAVADANKAIEL-----DPSLA---KAYLRKGTACMKLEEYQ 87 (356)
T ss_pred HcCCHHHHHHHHHHHHHh-----CcCCH---HHHHHHHHHHHHhCCHH
Confidence 344555555555544432 23322 23444555555555544
No 111
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.57 E-value=32 Score=23.65 Aligned_cols=25 Identities=32% Similarity=0.966 Sum_probs=17.8
Q ss_pred ccCCCCCc-ceeeeCCCCCccccCcCCCc
Q 016386 267 RCKDDGCS-GFLLRDSDDKGFTCQQCGLV 294 (390)
Q Consensus 267 ~C~~~~C~-g~~~~~~~~~~~~C~~C~~~ 294 (390)
.|| .|+ |.++....+ .|.|-+||..
T Consensus 21 ~CP--rCG~gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 21 FCP--RCGPGVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred cCC--CCCCcchhhhcCc-eeEeccccce
Confidence 486 685 666655444 8999999975
No 112
>cd02677 MIT_SNX15 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.
Probab=27.40 E-value=2.7e+02 Score=20.84 Aligned_cols=35 Identities=17% Similarity=0.148 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKK 339 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 339 (390)
.++..++.+|......+++++|+..|...+.....
T Consensus 4 ~~A~~l~~~Ave~d~~~~y~eA~~~Y~~~i~~~~~ 38 (75)
T cd02677 4 EQAAELIRLALEKEEEGDYEAAFEFYRAGVDLLLK 38 (75)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 34455666777777788999999999987766544
No 113
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=27.25 E-value=31 Score=25.92 Aligned_cols=22 Identities=27% Similarity=0.794 Sum_probs=9.8
Q ss_pred CcccccccCcC---CCCCCCCCCcc
Q 016386 27 ISRCDGCFASS---NLKKCSACQVV 48 (390)
Q Consensus 27 ~~~C~~C~~~~---~~~~C~~C~~~ 48 (390)
-..|+.||... ....||.|+..
T Consensus 9 vlrC~aCf~~t~~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 9 VLRCHACFKITKDMTKQFCPKCGNA 33 (73)
T ss_dssp EEE-SSS--EES-SS--S-SSS--S
T ss_pred eEEccccccCcCCCCceeCcccCCC
Confidence 45799999983 36678888753
No 114
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=26.83 E-value=34 Score=23.75 Aligned_cols=26 Identities=27% Similarity=0.834 Sum_probs=14.4
Q ss_pred ccccccCcCC----------CCCCCCCCccccCCHHHH
Q 016386 29 RCDGCFASSN----------LKKCSACQVVWYCGSNCQ 56 (390)
Q Consensus 29 ~C~~C~~~~~----------~~~C~~C~~~~yCS~~C~ 56 (390)
.|.+|.++.+ .+.|+.|+.. || .+|-
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~-FC-~dCD 36 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNH-FC-IDCD 36 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT---B--HHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCc-cc-cCcC
Confidence 3778887732 3789999985 89 4674
No 115
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=26.79 E-value=1.8e+02 Score=26.93 Aligned_cols=42 Identities=5% Similarity=-0.135 Sum_probs=33.2
Q ss_pred hhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhc
Q 016386 317 LTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSS 363 (390)
Q Consensus 317 ~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~ 363 (390)
....+++++|+..++++++ .||+|...-.+...++.++..++
T Consensus 79 yy~~~~y~~A~~~~e~fi~-----~~P~~~~~~~a~Y~~g~~~~~~~ 120 (243)
T PRK10866 79 YYKNADLPLAQAAIDRFIR-----LNPTHPNIDYVLYMRGLTNMALD 120 (243)
T ss_pred HHhcCCHHHHHHHHHHHHH-----hCcCCCchHHHHHHHHHhhhhcc
Confidence 3456789999988888876 67999999888888887765554
No 116
>PF05030 SSXT: SSXT protein (N-terminal region); InterPro: IPR007726 SSXT (also known as SYT or SS18) appears to function synergistically with RBM14 as a transcriptional coactivator []. The SSXT protein is involved in synovial sarcoma in humans. A SYT-SSX fusion gene resulting from the chromosomal translocation t(X;18) (p11;q11) is characteristic of synovial sarcomas. This translocation fuses the SSXT (SYT) gene from chromosome 18 to either of two homologous genes at Xp11, SSX1 or SSX2 []. This entry also includes SS18-like protein 1, a transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons [],[].
Probab=26.73 E-value=1.3e+02 Score=22.13 Aligned_cols=35 Identities=26% Similarity=0.268 Sum_probs=28.9
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHhhhcCCCHHHHHH
Q 016386 294 VRSKEEIKKIASEVNILSKKTLALTSCGNHQEVVS 328 (390)
Q Consensus 294 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~a~~ 328 (390)
.++.+.+.++++|=..++..+......|...++..
T Consensus 5 ~~~~~~IQk~LdEN~~LI~~I~e~qn~Gr~~Ec~q 39 (65)
T PF05030_consen 5 QITTEQIQKMLDENDQLIQCIQEYQNKGRAQECVQ 39 (65)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence 45678899999998889998888888888888874
No 117
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=26.45 E-value=1.8e+02 Score=26.06 Aligned_cols=48 Identities=10% Similarity=0.164 Sum_probs=38.8
Q ss_pred HhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchhc
Q 016386 315 LALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILCL 367 (390)
Q Consensus 315 ~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~~ 367 (390)
.-....|++++|+..++.++.. .|+++...++...+..+|..+|+...
T Consensus 174 ~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~a~~~l~~~~~~lg~~~~ 221 (235)
T TIGR03302 174 RFYLKRGAYVAAINRFETVVEN-----YPDTPATEEALARLVEAYLKLGLKDL 221 (235)
T ss_pred HHHHHcCChHHHHHHHHHHHHH-----CCCCcchHHHHHHHHHHHHHcCCHHH
Confidence 3344678999999999888764 47778889999999999999998754
No 118
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=26.00 E-value=2.2e+02 Score=21.98 Aligned_cols=29 Identities=14% Similarity=0.114 Sum_probs=20.0
Q ss_pred HHHHHHHHhhhcCCCHHHHHHHHHHHHHh
Q 016386 308 NILSKKTLALTSCGNHQEVVSTYKMIEKL 336 (390)
Q Consensus 308 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~ 336 (390)
...++-+..+...|++++|++.+-.+++.
T Consensus 23 ~ar~~lA~~~~~~g~~e~Al~~Ll~~v~~ 51 (90)
T PF14561_consen 23 DARYALADALLAAGDYEEALDQLLELVRR 51 (90)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence 34455566677789999999888777654
No 119
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=25.98 E-value=18 Score=22.88 Aligned_cols=22 Identities=27% Similarity=0.631 Sum_probs=12.3
Q ss_pred ccccccCcCC----------CCCCCCCCcccc
Q 016386 29 RCDGCFASSN----------LKKCSACQVVWY 50 (390)
Q Consensus 29 ~C~~C~~~~~----------~~~C~~C~~~~y 50 (390)
.|..|..++. -..|+.|+++.|
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE-
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEEe
Confidence 5788887731 356999998866
No 120
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=25.85 E-value=2.3e+02 Score=19.63 Aligned_cols=41 Identities=7% Similarity=0.047 Sum_probs=29.9
Q ss_pred HHhhhcCCCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHH
Q 016386 314 TLALTSCGNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGY 359 (390)
Q Consensus 314 ~~~~~~~~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y 359 (390)
|...+-.++|++|++....+++ ..|.|.....++..+..--
T Consensus 8 Aig~ykl~~Y~~A~~~~~~lL~-----~eP~N~Qa~~L~~~i~~~i 48 (53)
T PF14853_consen 8 AIGHYKLGEYEKARRYCDALLE-----IEPDNRQAQSLKELIEDKI 48 (53)
T ss_dssp HHHHHHTT-HHHHHHHHHHHHH-----HTTS-HHHHHHHHHHHHHH
T ss_pred HHHHHHhhhHHHHHHHHHHHHh-----hCCCcHHHHHHHHHHHHHH
Confidence 4444567899999999988887 4599999888888776644
No 121
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=25.78 E-value=48 Score=26.89 Aligned_cols=23 Identities=22% Similarity=0.481 Sum_probs=18.2
Q ss_pred CCcccccccCc---C--CCCCCCCCCcc
Q 016386 26 SISRCDGCFAS---S--NLKKCSACQVV 48 (390)
Q Consensus 26 ~~~~C~~C~~~---~--~~~~C~~C~~~ 48 (390)
...+|..|.++ + .++.||.|+..
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCc
Confidence 46789999998 2 47889988865
No 122
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=25.64 E-value=1.5e+02 Score=17.44 Aligned_cols=26 Identities=19% Similarity=0.203 Sum_probs=18.2
Q ss_pred HHHHhhhcCCCHHHHHHHHHHHHHhh
Q 016386 312 KKTLALTSCGNHQEVVSTYKMIEKLQ 337 (390)
Q Consensus 312 ~~~~~~~~~~~~~~a~~~~~~~~~~~ 337 (390)
..+.-....+++++|+..|+++++..
T Consensus 6 ~~g~~~~~~~~~~~A~~~~~~al~~~ 31 (34)
T PF00515_consen 6 NLGNAYFQLGDYEEALEYYQRALELD 31 (34)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHHhCCchHHHHHHHHHHHHC
Confidence 34444556789999999999887754
No 123
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=25.37 E-value=15 Score=27.06 Aligned_cols=31 Identities=29% Similarity=0.697 Sum_probs=20.1
Q ss_pred cccCCCCCcceeeeCCCCCccccCcCCCccCHHHH
Q 016386 266 YRCKDDGCSGFLLRDSDDKGFTCQQCGLVRSKEEI 300 (390)
Q Consensus 266 ~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~~~~~v 300 (390)
|+| .|+.++....+...-+| .||..+..+++
T Consensus 4 frC---~Cgr~lya~e~~kTkkC-~CG~~l~vk~~ 34 (68)
T PF09082_consen 4 FRC---DCGRYLYAKEGAKTKKC-VCGKTLKVKER 34 (68)
T ss_dssp EEE---TTS--EEEETT-SEEEE-TTTEEEE--SS
T ss_pred EEe---cCCCEEEecCCcceeEe-cCCCeeeeeeE
Confidence 678 58888877777777889 99998876543
No 124
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=24.95 E-value=73 Score=21.25 Aligned_cols=29 Identities=21% Similarity=0.602 Sum_probs=17.8
Q ss_pred hhccccCCCCCcce-eeeCCCCCccccCcCCC
Q 016386 263 LEGYRCKDDGCSGF-LLRDSDDKGFTCQQCGL 293 (390)
Q Consensus 263 l~~~~C~~~~C~g~-~~~~~~~~~~~C~~C~~ 293 (390)
-.++.|| .|+.. .........|+|..|++
T Consensus 16 ~~g~~CP--~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 16 PDGFVCP--HCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCC--CCCCeeeEEeCCCCeEECCCCCC
Confidence 3467787 67542 22223356799999986
No 125
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.37 E-value=74 Score=25.87 Aligned_cols=33 Identities=24% Similarity=0.379 Sum_probs=21.2
Q ss_pred CCccccCcCCCcc-CHHHHHHHHHHHHHHHHHHH
Q 016386 283 DKGFTCQQCGLVR-SKEEIKKIASEVNILSKKTL 315 (390)
Q Consensus 283 ~~~~~C~~C~~~~-~~~~v~~~~~~~~~~~~~~~ 315 (390)
...|.|+.||... +.+........+.+.+.+..
T Consensus 29 ~~~~~C~~CGe~~~~~e~~~~~~~~i~~~~~~~~ 62 (127)
T TIGR03830 29 VPGWYCPACGEELLDPEESKRNSAALADFYRKVD 62 (127)
T ss_pred eeeeECCCCCCEEEcHHHHHHHHHHHHHHHHHcc
Confidence 3568999999875 45555555555555555443
No 126
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=24.37 E-value=33 Score=29.78 Aligned_cols=18 Identities=22% Similarity=0.266 Sum_probs=10.1
Q ss_pred CCHHHHHHHHhHhhcccc
Q 016386 148 ISINEIAENFSKLACNAH 165 (390)
Q Consensus 148 ~~~~ei~~~~~~l~~Naf 165 (390)
++..++.+++.++.-+.+
T Consensus 40 i~~~~VRk~L~~L~e~~L 57 (158)
T TIGR00373 40 IKLNEVRKALYALYDAGL 57 (158)
T ss_pred CCHHHHHHHHHHHHHCCC
Confidence 455566666666654443
No 127
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=24.20 E-value=43 Score=22.88 Aligned_cols=27 Identities=22% Similarity=0.758 Sum_probs=17.8
Q ss_pred cccCCCCCc-ceeeeCCCCCccccCcCCC
Q 016386 266 YRCKDDGCS-GFLLRDSDDKGFTCQQCGL 293 (390)
Q Consensus 266 ~~C~~~~C~-g~~~~~~~~~~~~C~~C~~ 293 (390)
-.||++.|+ |.++.... ..|.|-+||.
T Consensus 19 k~CP~~~CG~GvFMA~H~-dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHK-DRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-S-SEEEETTTSS
T ss_pred hcCCCcccCCceEeeecC-CCccCCCccc
Confidence 359988995 65555443 4789999985
No 128
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=24.19 E-value=61 Score=21.69 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=4.2
Q ss_pred ccccCcCCC
Q 016386 285 GFTCQQCGL 293 (390)
Q Consensus 285 ~~~C~~C~~ 293 (390)
...|..||.
T Consensus 19 ~irC~~CG~ 27 (44)
T smart00659 19 VVRCRECGY 27 (44)
T ss_pred ceECCCCCc
Confidence 344555554
No 129
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=23.64 E-value=1.2e+02 Score=24.38 Aligned_cols=32 Identities=22% Similarity=0.467 Sum_probs=22.8
Q ss_pred eeeCCCCCccccCcCCCccCHHHHHHHHHHHH
Q 016386 277 LLRDSDDKGFTCQQCGLVRSKEEIKKIASEVN 308 (390)
Q Consensus 277 ~~~~~~~~~~~C~~C~~~~~~~~v~~~~~~~~ 308 (390)
+...++...|.|..|....+.+-++.++.++.
T Consensus 54 i~~~~G~~VwSC~dC~~iH~ke~~~~ilr~ll 85 (112)
T COG2158 54 ISDSNGRKVWSCSDCHWIHRKEGAEEILRELL 85 (112)
T ss_pred eEcCCCCEEeeccccceecccchHHHHHHHHH
Confidence 44444567899999998887777776665553
No 130
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=23.33 E-value=2.4e+02 Score=19.37 Aligned_cols=38 Identities=16% Similarity=0.173 Sum_probs=18.5
Q ss_pred CCHHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHhcchh
Q 016386 321 GNHQEVVSTYKMIEKLQKKLYHPFSVNLMQTREKLIKGYIHSSILC 366 (390)
Q Consensus 321 ~~~~~a~~~~~~~~~~~~~~lhp~~~~~~~~~~~l~~~y~~~~~~~ 366 (390)
+++++|++.++..+. ..|.+. .+...++.+|...|...
T Consensus 48 ~~~~~a~~~~~~~~~-----~~~~~~---~~~~~~~~~~~~~~~~~ 85 (100)
T cd00189 48 GKYEEALEDYEKALE-----LDPDNA---KAYYNLGLAYYKLGKYE 85 (100)
T ss_pred HHHHHHHHHHHHHHh-----CCCcch---hHHHHHHHHHHHHHhHH
Confidence 345555555544433 223333 44555666666666543
No 131
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=23.25 E-value=2e+02 Score=21.15 Aligned_cols=19 Identities=5% Similarity=-0.151 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHhcchh
Q 016386 348 LMQTREKLIKGYIHSSILC 366 (390)
Q Consensus 348 ~~~~~~~l~~~y~~~~~~~ 366 (390)
....+..++++|.++|.++
T Consensus 57 ~~~~~~l~a~~~~~l~~y~ 75 (84)
T PF12895_consen 57 NPDIHYLLARCLLKLGKYE 75 (84)
T ss_dssp HHHHHHHHHHHHHHTT-HH
T ss_pred CHHHHHHHHHHHHHhCCHH
Confidence 3566667788888888764
No 132
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=23.12 E-value=2.1e+02 Score=26.83 Aligned_cols=41 Identities=24% Similarity=0.344 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhh
Q 016386 297 KEEIKKIASEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQ 337 (390)
Q Consensus 297 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~ 337 (390)
.+.+..+..+|..+++++..+-..|++++|..+...+..+.
T Consensus 122 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk 162 (254)
T PF03194_consen 122 AEKIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEKLK 162 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46678888899999999999999999999998888776553
No 133
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=23.11 E-value=3.1e+02 Score=22.42 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=12.0
Q ss_pred HHHHhhhcCCCHHHHHHHHHHHHH
Q 016386 312 KKTLALTSCGNHQEVVSTYKMIEK 335 (390)
Q Consensus 312 ~~~~~~~~~~~~~~a~~~~~~~~~ 335 (390)
+.+......|+.++|+..|++.+.
T Consensus 6 ~~A~a~d~~G~~~~Ai~~Y~~Al~ 29 (120)
T PF12688_consen 6 ELAWAHDSLGREEEAIPLYRRALA 29 (120)
T ss_pred HHHHHHHhcCCHHHHHHHHHHHHH
Confidence 344444445555555555555443
No 134
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=23.01 E-value=40 Score=21.30 Aligned_cols=27 Identities=26% Similarity=0.792 Sum_probs=17.2
Q ss_pred cCCCCCcceeeeCCCCCc-cccCcCCCccC
Q 016386 268 CKDDGCSGFLLRDSDDKG-FTCQQCGLVRS 296 (390)
Q Consensus 268 C~~~~C~g~~~~~~~~~~-~~C~~C~~~~~ 296 (390)
|| .|++.+.|..+... ..|..|+....
T Consensus 4 Cp--~C~nlL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 4 CP--ECGNLLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp ET--TTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred CC--CCCccceEcCCCccCcCCCCCCCccC
Confidence 75 78888877554322 25999997654
No 135
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.76 E-value=56 Score=20.43 Aligned_cols=28 Identities=25% Similarity=0.525 Sum_probs=18.5
Q ss_pred cccCCCCCcceeeeCCCCCccccCcCCCcc
Q 016386 266 YRCKDDGCSGFLLRDSDDKGFTCQQCGLVR 295 (390)
Q Consensus 266 ~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~ 295 (390)
.+|. .|++..+...+.....|..||...
T Consensus 4 ~~C~--~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCS--KCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcC--CCCCCeEEEecCCeEEcccCCcEe
Confidence 3675 687666553444567899999763
No 136
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=21.96 E-value=36 Score=24.34 Aligned_cols=18 Identities=33% Similarity=0.833 Sum_probs=8.6
Q ss_pred cccccCcCCCCCCCCCCc
Q 016386 30 CDGCFASSNLKKCSACQV 47 (390)
Q Consensus 30 C~~C~~~~~~~~C~~C~~ 47 (390)
|..|-+..+.+.|+.|++
T Consensus 39 C~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 39 CEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred chhHHhcCCceECCCCCC
Confidence 344433334555555554
No 137
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=21.91 E-value=34 Score=32.96 Aligned_cols=26 Identities=27% Similarity=0.857 Sum_probs=20.7
Q ss_pred CCCCCC-CCccccCCHHHHHHhhhhhHHHHHH
Q 016386 39 LKKCSA-CQVVWYCGSNCQKLDWKLHRLECQV 69 (390)
Q Consensus 39 ~~~C~~-C~~~~yCS~~C~~~~~~~H~~EC~~ 69 (390)
.+.|++ |+++ || ++|.+. ||.-||..
T Consensus 335 kvtC~~gCgf~-FC-R~C~e~---yh~geC~~ 361 (446)
T KOG0006|consen 335 KVTCEGGCGFA-FC-RECKEA---YHEGECSA 361 (446)
T ss_pred cccCCCCchhH-hH-HHHHhh---hcccccee
Confidence 567875 9996 99 689864 99999973
No 138
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=21.86 E-value=34 Score=29.43 Aligned_cols=16 Identities=13% Similarity=0.260 Sum_probs=12.1
Q ss_pred CccccCcCCCccCHHH
Q 016386 284 KGFTCQQCGLVRSKEE 299 (390)
Q Consensus 284 ~~~~C~~C~~~~~~~~ 299 (390)
..++|..|++..+.++
T Consensus 131 ~~lrC~YCe~~~~~~~ 146 (150)
T TIGR00240 131 IALRCYYCEKEIEHNV 146 (150)
T ss_pred eEEEEECCCCEEecce
Confidence 4689999999876443
No 139
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=21.85 E-value=3.4e+02 Score=25.20 Aligned_cols=35 Identities=20% Similarity=0.259 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhhhc
Q 016386 305 SEVNILSKKTLALTSCGNHQEVVSTYKMIEKLQKK 339 (390)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 339 (390)
+++..+.+++..+..+|++++|+.++..+.+....
T Consensus 3 ~eLd~~sd~~lqlvk~~~yeeA~q~l~~fs~~f~~ 37 (232)
T PF09577_consen 3 KELDQLSDEALQLVKQGKYEEAKQLLEYFSEQFTS 37 (232)
T ss_pred HHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHhh
Confidence 34555666777777899999999888877655443
No 140
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=21.76 E-value=59 Score=22.70 Aligned_cols=16 Identities=31% Similarity=0.499 Sum_probs=13.9
Q ss_pred EEEEccccCCCCeeeE
Q 016386 204 VVRAVQHVPKGAEVLI 219 (390)
Q Consensus 204 ~vrA~r~I~~Geei~i 219 (390)
+++|.++|++|+.|+-
T Consensus 3 v~va~~~i~~G~~i~~ 18 (64)
T smart00858 3 VVVAARDLPAGEVITA 18 (64)
T ss_pred EEEEeCccCCCCCcch
Confidence 4678999999999985
No 141
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=21.75 E-value=58 Score=23.35 Aligned_cols=32 Identities=16% Similarity=0.395 Sum_probs=22.0
Q ss_pred hhhccccCCCCCcc-eeeeCCCCCccccCcCCCcc
Q 016386 262 ILEGYRCKDDGCSG-FLLRDSDDKGFTCQQCGLVR 295 (390)
Q Consensus 262 ~l~~~~C~~~~C~g-~~~~~~~~~~~~C~~C~~~~ 295 (390)
++-.++|+ .|.. -+..+.......|..||..+
T Consensus 8 ~F~~VkCp--~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 8 RFLKVKCP--DCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred eEEEEECC--CCCCeEEEEecCCcEEECcccCCCc
Confidence 44578897 6853 33445566677899999875
No 142
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.40 E-value=1.8e+02 Score=25.74 Aligned_cols=11 Identities=45% Similarity=0.528 Sum_probs=5.6
Q ss_pred CCCHHHHHHHH
Q 016386 147 EISINEIAENF 157 (390)
Q Consensus 147 ~~~~~ei~~~~ 157 (390)
..+.++|...+
T Consensus 36 ~~tdeeLA~~L 46 (178)
T PRK06266 36 EVTDEEIAEQT 46 (178)
T ss_pred CcCHHHHHHHH
Confidence 44555555444
No 143
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=21.29 E-value=77 Score=19.68 Aligned_cols=9 Identities=33% Similarity=1.036 Sum_probs=4.0
Q ss_pred cccCcCCCc
Q 016386 286 FTCQQCGLV 294 (390)
Q Consensus 286 ~~C~~C~~~ 294 (390)
..|..||..
T Consensus 18 irC~~CG~R 26 (32)
T PF03604_consen 18 IRCPECGHR 26 (32)
T ss_dssp SSBSSSS-S
T ss_pred EECCcCCCe
Confidence 445555543
No 144
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=20.67 E-value=54 Score=31.65 Aligned_cols=34 Identities=32% Similarity=0.768 Sum_probs=26.2
Q ss_pred hhccccCCCCCcceeeeCCCCCccccCc-CCCccC
Q 016386 263 LEGYRCKDDGCSGFLLRDSDDKGFTCQQ-CGLVRS 296 (390)
Q Consensus 263 l~~~~C~~~~C~g~~~~~~~~~~~~C~~-C~~~~~ 296 (390)
+.++.||++.|+..+++.++.....|.. ||..+-
T Consensus 313 ~gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FC 347 (446)
T KOG0006|consen 313 MGGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFC 347 (446)
T ss_pred cCCEecCCCCCCcccccCCCCCcccCCCCchhHhH
Confidence 3478999999986667777777788886 887654
No 145
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.48 E-value=51 Score=22.71 Aligned_cols=7 Identities=43% Similarity=1.251 Sum_probs=3.7
Q ss_pred eCcccCC
Q 016386 244 TCPRCIK 250 (390)
Q Consensus 244 ~C~rC~~ 250 (390)
.|.+|..
T Consensus 8 ~C~~Cg~ 14 (49)
T COG1996 8 KCARCGR 14 (49)
T ss_pred EhhhcCC
Confidence 4555555
No 146
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.37 E-value=58 Score=23.35 Aligned_cols=32 Identities=28% Similarity=0.724 Sum_probs=23.0
Q ss_pred CcccccccCcC-C-----CCCCCCCC-c-cccCCHHHHHHh
Q 016386 27 ISRCDGCFASS-N-----LKKCSACQ-V-VWYCGSNCQKLD 59 (390)
Q Consensus 27 ~~~C~~C~~~~-~-----~~~C~~C~-~-~~yCS~~C~~~~ 59 (390)
...|..|...+ + .++|++|+ . .+-| ..|++..
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc-~~CRk~g 48 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRC-AKCRKLG 48 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehh-hhHHHcC
Confidence 57899998885 2 57899999 3 3345 6788764
No 147
>cd02679 MIT_spastin MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
Probab=20.33 E-value=2e+02 Score=21.82 Aligned_cols=32 Identities=13% Similarity=0.154 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHH
Q 016386 304 ASEVNILSKKTLALTSCGNHQEVVSTYKMIEK 335 (390)
Q Consensus 304 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 335 (390)
.+.+-..+++|.+..+.|+.++|+..|+..+.
T Consensus 5 ~~~A~~~I~kaL~~dE~g~~e~Al~~Y~~gi~ 36 (79)
T cd02679 5 YKQAFEEISKALRADEWGDKEQALAHYRKGLR 36 (79)
T ss_pred HHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHH
Confidence 34556677888888888999999999997553
No 148
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=20.30 E-value=1.9e+02 Score=24.97 Aligned_cols=18 Identities=17% Similarity=0.034 Sum_probs=10.0
Q ss_pred HHhCCCCCCHHHHHHHHh
Q 016386 141 LILQWPEISINEIAENFS 158 (390)
Q Consensus 141 ~~l~~~~~~~~ei~~~~~ 158 (390)
.++.....+.++|.+.++
T Consensus 22 aL~~~~~~tdEeLa~~Lg 39 (158)
T TIGR00373 22 SLGIKGEFTDEEISLELG 39 (158)
T ss_pred HHhccCCCCHHHHHHHHC
Confidence 344344566677766554
No 149
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=20.30 E-value=1e+02 Score=19.99 Aligned_cols=32 Identities=28% Similarity=0.558 Sum_probs=23.2
Q ss_pred CCCcccccccCcCC----CCCCCCCCccccCCHHHHHH
Q 016386 25 SSISRCDGCFASSN----LKKCSACQVVWYCGSNCQKL 58 (390)
Q Consensus 25 ~~~~~C~~C~~~~~----~~~C~~C~~~~yCS~~C~~~ 58 (390)
...+.|..|.+... ..+|+.|+. .+-..|...
T Consensus 9 ~~~~~C~~C~~~i~~~~~~~~C~~C~~--~~H~~C~~~ 44 (49)
T smart00109 9 KKPTKCCVCRKSIWGSFQGLRCSWCKV--KCHKKCAEK 44 (49)
T ss_pred CCCCCccccccccCcCCCCcCCCCCCc--hHHHHHHhh
Confidence 34678999988842 678988886 377777654
No 150
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=20.16 E-value=53 Score=23.63 Aligned_cols=35 Identities=29% Similarity=0.617 Sum_probs=27.4
Q ss_pred hhhhccccCCCCCcceeeeCCCCCccccCcCCCccCH
Q 016386 261 AILEGYRCKDDGCSGFLLRDSDDKGFTCQQCGLVRSK 297 (390)
Q Consensus 261 ~~l~~~~C~~~~C~g~~~~~~~~~~~~C~~C~~~~~~ 297 (390)
.+++-+.|| .|+|++....+.....|..|+.....
T Consensus 4 ~LLeiLaCP--~~kg~L~~~~~~~~L~c~~~~~aYpI 38 (60)
T COG2835 4 RLLEILACP--VCKGPLVYDEEKQELICPRCKLAYPI 38 (60)
T ss_pred hhheeeecc--CcCCcceEeccCCEEEecccCceeec
Confidence 456778897 89999877777777889999987653
Done!