Query psy15437
Match_columns 143
No_of_seqs 168 out of 1957
Neff 10.3
Searched_HMMs 46136
Date Fri Aug 16 21:02:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15437.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15437hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4577|consensus 100.0 1.3E-30 2.8E-35 176.2 4.8 127 2-142 90-217 (383)
2 TIGR01565 homeo_ZF_HD homeobox 99.8 4.7E-19 1E-23 94.5 5.4 51 93-143 2-56 (58)
3 KOG0843|consensus 99.7 5.5E-18 1.2E-22 108.0 3.6 52 91-142 101-152 (197)
4 KOG0842|consensus 99.7 2.4E-17 5.2E-22 114.7 5.7 56 87-142 148-203 (307)
5 KOG0484|consensus 99.7 2E-18 4.4E-23 100.4 -0.1 54 89-142 14-67 (125)
6 KOG0850|consensus 99.7 1.6E-17 3.5E-22 109.7 3.8 57 86-142 116-172 (245)
7 KOG0490|consensus 99.7 1.5E-17 3.3E-22 114.1 1.7 110 10-143 2-111 (235)
8 KOG0485|consensus 99.6 3.8E-16 8.2E-21 102.5 3.3 55 88-142 100-154 (268)
9 KOG0489|consensus 99.6 2.3E-16 5E-21 109.4 1.9 53 90-142 157-209 (261)
10 PF00412 LIM: LIM domain; Int 99.6 2.1E-15 4.5E-20 81.8 5.0 58 7-65 1-58 (58)
11 KOG0493|consensus 99.6 8.5E-16 1.9E-20 103.4 3.2 51 92-142 246-296 (342)
12 KOG0488|consensus 99.6 1.6E-15 3.5E-20 107.0 4.4 55 88-142 168-222 (309)
13 KOG0494|consensus 99.6 3E-15 6.5E-20 100.7 4.2 54 89-142 137-191 (332)
14 PF00046 Homeobox: Homeobox do 99.6 1.5E-15 3.2E-20 82.1 2.0 50 93-142 1-50 (57)
15 KOG0848|consensus 99.5 9.7E-16 2.1E-20 103.4 1.1 54 89-142 196-249 (317)
16 KOG2251|consensus 99.5 4.8E-15 1E-19 97.7 4.3 56 87-142 32-87 (228)
17 COG5576 Homeodomain-containing 99.5 9E-15 2E-19 93.5 4.7 59 84-142 43-101 (156)
18 KOG0487|consensus 99.5 4.4E-15 9.5E-20 103.5 3.3 53 90-142 233-285 (308)
19 KOG1701|consensus 99.5 2E-16 4.4E-21 112.9 -3.6 105 4-128 334-440 (468)
20 KOG0492|consensus 99.5 8.7E-15 1.9E-19 95.5 4.1 52 91-142 143-194 (246)
21 KOG1701|consensus 99.5 9.7E-16 2.1E-20 109.4 -1.8 77 3-80 273-349 (468)
22 smart00389 HOX Homeodomain. DN 99.5 6.4E-14 1.4E-18 75.4 3.3 49 94-142 2-50 (56)
23 cd00086 homeodomain Homeodomai 99.4 1.4E-13 3.1E-18 74.8 3.1 49 94-142 2-50 (59)
24 KOG0490|consensus 99.3 9E-13 2E-17 90.4 3.8 139 3-142 58-203 (235)
25 KOG0844|consensus 99.3 1E-12 2.2E-17 90.6 1.9 54 89-142 178-231 (408)
26 KOG0491|consensus 99.3 2.3E-13 4.9E-18 85.8 -1.8 50 93-142 101-150 (194)
27 KOG0483|consensus 99.2 7E-12 1.5E-16 83.0 2.7 49 94-142 52-100 (198)
28 KOG4577|consensus 99.2 6.9E-13 1.5E-17 90.7 -3.3 69 5-76 34-103 (383)
29 KOG3802|consensus 99.1 5.7E-11 1.2E-15 85.0 5.0 52 91-142 293-344 (398)
30 KOG0486|consensus 99.1 3E-11 6.5E-16 83.7 2.8 54 89-142 109-162 (351)
31 KOG0847|consensus 99.1 4.9E-11 1.1E-15 78.8 1.3 51 92-142 167-217 (288)
32 KOG0849|consensus 99.0 4.8E-10 1E-14 81.1 3.5 55 89-143 173-227 (354)
33 smart00132 LIM Zinc-binding do 98.9 8.4E-10 1.8E-14 54.6 2.7 38 6-43 1-38 (39)
34 KOG2272|consensus 98.9 9.9E-10 2.1E-14 74.2 1.9 100 5-129 13-113 (332)
35 KOG1703|consensus 98.8 8.6E-10 1.9E-14 83.0 0.9 100 2-126 361-461 (479)
36 KOG2272|consensus 98.8 5.2E-10 1.1E-14 75.6 -0.8 75 4-81 195-270 (332)
37 KOG1044|consensus 98.8 1.7E-09 3.7E-14 80.6 0.9 69 5-76 134-203 (670)
38 KOG1168|consensus 98.6 3.6E-08 7.7E-13 68.0 2.2 53 90-142 307-359 (385)
39 PF05920 Homeobox_KN: Homeobox 98.3 9.1E-08 2E-12 47.4 -0.5 30 113-142 7-36 (40)
40 KOG2252|consensus 98.2 1.4E-06 3E-11 65.2 3.7 57 86-142 414-470 (558)
41 KOG0775|consensus 98.1 4.1E-06 8.8E-11 57.6 3.5 44 99-142 183-226 (304)
42 KOG0774|consensus 98.0 7.5E-06 1.6E-10 56.0 3.4 50 93-142 189-241 (334)
43 KOG1700|consensus 98.0 1.4E-06 3E-11 58.5 -0.1 59 5-65 109-167 (200)
44 KOG1703|consensus 97.9 9.6E-06 2.1E-10 61.4 2.5 78 3-82 302-380 (479)
45 KOG1044|consensus 97.8 4.4E-06 9.5E-11 62.9 0.6 60 2-63 190-249 (670)
46 KOG1700|consensus 97.8 4.4E-06 9.5E-11 56.1 0.3 61 4-66 7-67 (200)
47 KOG1146|consensus 97.6 2.8E-05 6.1E-10 63.6 2.1 50 93-142 904-953 (1406)
48 KOG1702|consensus 97.4 6.9E-06 1.5E-10 54.3 -3.3 59 5-65 5-63 (264)
49 PF11569 Homez: Homeodomain le 97.3 4.7E-05 1E-09 40.1 -0.0 37 104-140 10-46 (56)
50 KOG3623|consensus 96.3 0.0023 5E-08 50.2 1.7 39 104-142 568-606 (1007)
51 KOG0773|consensus 96.2 0.0057 1.2E-07 44.6 3.5 52 92-143 239-293 (342)
52 PF04218 CENP-B_N: CENP-B N-te 93.2 0.13 2.7E-06 27.0 2.7 45 93-142 1-45 (53)
53 PF08394 Arc_trans_TRASH: Arch 91.6 0.11 2.4E-06 25.0 1.1 26 7-32 1-26 (37)
54 PF14446 Prok-RING_1: Prokaryo 89.6 0.16 3.4E-06 26.7 0.7 31 3-33 4-36 (54)
55 PF09943 DUF2175: Uncharacteri 88.7 0.15 3.3E-06 30.3 0.3 12 6-17 4-15 (101)
56 PF04967 HTH_10: HTH DNA bindi 88.3 0.58 1.3E-05 24.5 2.3 38 99-136 1-40 (53)
57 COG1645 Uncharacterized Zn-fin 87.4 0.41 8.9E-06 29.9 1.6 24 33-62 29-52 (131)
58 PRK08359 transcription factor; 87.2 0.87 1.9E-05 30.1 3.1 28 34-62 8-38 (176)
59 PF13240 zinc_ribbon_2: zinc-r 84.4 0.69 1.5E-05 19.7 1.1 10 6-15 1-10 (23)
60 PF13248 zf-ribbon_3: zinc-rib 82.9 1 2.2E-05 19.7 1.4 11 5-15 3-13 (26)
61 PF10668 Phage_terminase: Phag 82.1 0.45 9.6E-06 25.6 0.1 18 122-139 25-42 (60)
62 PF06677 Auto_anti-p27: Sjogre 81.7 1.1 2.5E-05 22.0 1.4 22 34-60 19-40 (41)
63 KOG2893|consensus 78.0 0.81 1.7E-05 31.7 0.3 54 5-67 11-64 (341)
64 PRK00420 hypothetical protein; 77.6 1.4 3.1E-05 26.8 1.3 25 33-62 24-48 (112)
65 PF11781 RRN7: RNA polymerase 77.1 2.2 4.7E-05 20.4 1.6 23 34-61 10-32 (36)
66 TIGR00270 conserved hypothetic 76.6 3.8 8.1E-05 26.6 3.1 19 122-140 85-103 (154)
67 PRK00807 50S ribosomal protein 73.5 2.5 5.3E-05 22.0 1.3 23 6-28 3-27 (52)
68 COG1813 Predicted transcriptio 73.4 12 0.00025 24.6 4.6 19 121-139 94-112 (165)
69 PF11516 DUF3220: Protein of u 72.5 0.31 6.6E-06 27.5 -2.3 9 135-143 32-40 (106)
70 PF07754 DUF1610: Domain of un 72.1 3.4 7.4E-05 17.8 1.4 12 7-18 1-12 (24)
71 cd02413 40S_S3_KH K homology R 72.0 4.3 9.3E-05 23.2 2.2 23 121-143 55-77 (81)
72 PF00645 zf-PARP: Poly(ADP-rib 71.0 1.5 3.2E-05 25.0 0.2 14 5-18 8-21 (82)
73 PF09943 DUF2175: Uncharacteri 70.5 4.7 0.0001 24.1 2.2 34 33-66 3-36 (101)
74 PF06827 zf-FPG_IleRS: Zinc fi 70.3 5 0.00011 18.0 1.9 12 4-15 1-12 (30)
75 COG3413 Predicted DNA binding 69.7 4.6 0.0001 27.5 2.4 38 98-135 155-194 (215)
76 PF10367 Vps39_2: Vacuolar sor 69.4 3.2 7E-05 24.6 1.5 27 34-61 80-107 (109)
77 COG4847 Uncharacterized protei 67.9 4.1 8.8E-05 24.0 1.5 29 33-61 7-35 (103)
78 PRK06424 transcription factor; 67.6 10 0.00022 24.3 3.4 20 122-141 100-119 (144)
79 COG4367 Uncharacterized protei 66.6 5.8 0.00013 23.0 2.0 37 98-134 2-38 (97)
80 PF11571 Med27: Mediator compl 66.0 1.7 3.6E-05 25.4 -0.3 13 2-14 52-64 (90)
81 PF06056 Terminase_5: Putative 65.4 2.2 4.7E-05 22.7 0.1 19 122-140 16-34 (58)
82 PF14569 zf-UDP: Zinc-binding 64.3 6.3 0.00014 22.3 1.8 14 2-15 7-20 (80)
83 PF14471 DUF4428: Domain of un 63.8 6.7 0.00014 20.3 1.8 29 35-64 2-30 (51)
84 TIGR03826 YvyF flagellar opero 63.0 7.3 0.00016 24.7 2.1 18 122-139 49-66 (137)
85 PF08281 Sigma70_r4_2: Sigma-7 62.5 5 0.00011 20.5 1.2 38 99-141 11-48 (54)
86 COG2075 RPL24A Ribosomal prote 61.1 5.1 0.00011 21.9 1.0 12 6-17 5-16 (66)
87 PF13411 MerR_1: MerR HTH fami 60.9 2.7 5.9E-05 22.7 -0.0 18 122-139 3-20 (69)
88 cd04761 HTH_MerR-SF Helix-Turn 60.9 2.4 5.1E-05 21.1 -0.3 20 122-141 3-22 (49)
89 PF01527 HTH_Tnp_1: Transposas 60.8 5.9 0.00013 21.8 1.4 40 95-139 3-43 (76)
90 KOG0320|consensus 60.6 5.3 0.00012 26.5 1.2 37 30-66 129-165 (187)
91 PRK14891 50S ribosomal protein 60.0 5.8 0.00013 24.8 1.3 26 4-29 4-31 (131)
92 PF10083 DUF2321: Uncharacteri 59.1 39 0.00084 22.0 4.9 77 53-129 27-110 (158)
93 PF10170 C6_DPF: Cysteine-rich 58.9 9.3 0.0002 22.7 2.0 35 32-66 49-83 (97)
94 cd00472 Ribosomal_L24e_L24 Rib 58.4 7.6 0.00016 20.4 1.4 24 5-28 4-29 (54)
95 PRK14890 putative Zn-ribbon RN 57.7 8.6 0.00019 20.6 1.5 28 4-41 7-34 (59)
96 PF13936 HTH_38: Helix-turn-he 57.6 7.7 0.00017 19.2 1.3 36 97-137 3-38 (44)
97 PF00376 MerR: MerR family reg 56.6 3.2 7E-05 20.0 -0.2 17 123-139 3-19 (38)
98 KOG3623|consensus 56.1 10 0.00022 31.0 2.3 52 91-142 625-676 (1007)
99 PF04545 Sigma70_r4: Sigma-70, 55.8 10 0.00022 19.0 1.7 37 98-139 4-40 (50)
100 KOG0823|consensus 54.9 24 0.00052 24.5 3.7 47 29-77 44-96 (230)
101 cd01176 IPT_RBP-Jkappa IPT dom 53.7 5.4 0.00012 23.4 0.4 9 135-143 32-40 (97)
102 PF04570 DUF581: Protein of un 53.2 11 0.00024 20.1 1.5 27 34-60 18-45 (58)
103 PF06689 zf-C4_ClpX: ClpX C4-t 52.2 28 0.00061 16.9 3.9 32 34-65 3-35 (41)
104 KOG1146|consensus 51.9 24 0.00053 30.8 3.9 53 90-142 703-755 (1406)
105 PRK00398 rpoP DNA-directed RNA 51.7 7.9 0.00017 19.3 0.8 27 6-42 5-31 (46)
106 PHA03236 DNA packaging protein 51.4 15 0.00032 22.9 2.1 20 124-143 26-46 (127)
107 PF13518 HTH_28: Helix-turn-he 50.0 6.4 0.00014 19.7 0.3 20 122-141 15-34 (52)
108 PF09607 BrkDBD: Brinker DNA-b 49.8 13 0.00028 19.9 1.4 18 124-141 30-47 (58)
109 cd06171 Sigma70_r4 Sigma70, re 49.5 15 0.00033 17.9 1.8 38 99-141 11-48 (55)
110 KOG3579|consensus 49.3 8.9 0.00019 27.5 1.0 31 6-37 270-300 (352)
111 cd04763 HTH_MlrA-like Helix-Tu 47.0 5.2 0.00011 21.7 -0.4 20 122-141 3-22 (68)
112 cd04764 HTH_MlrA-like_sg1 Heli 46.6 6.7 0.00014 21.1 0.0 20 122-141 3-22 (67)
113 smart00504 Ubox Modified RING 46.6 32 0.00068 17.9 2.8 32 33-66 2-33 (63)
114 cd00569 HTH_Hin_like Helix-tur 45.8 28 0.0006 15.0 2.8 36 99-139 6-41 (42)
115 PF01246 Ribosomal_L24e: Ribos 45.2 11 0.00023 21.0 0.7 23 6-28 5-29 (71)
116 PHA00626 hypothetical protein 44.5 15 0.00032 19.5 1.1 40 6-52 2-42 (59)
117 PF01258 zf-dskA_traR: Prokary 43.4 4 8.6E-05 19.3 -1.1 9 7-15 6-14 (36)
118 smart00834 CxxC_CXXC_SSSS Puta 43.0 27 0.00059 16.5 2.0 14 2-15 3-16 (41)
119 PF02796 HTH_7: Helix-turn-hel 42.5 22 0.00047 17.5 1.6 34 99-137 6-39 (45)
120 COG2191 Formylmethanofuran deh 42.5 11 0.00024 25.6 0.6 30 33-63 173-202 (206)
121 cd02249 ZZ Zinc finger, ZZ typ 41.7 22 0.00047 17.7 1.5 8 55-62 24-31 (46)
122 TIGR02098 MJ0042_CXXC MJ0042 f 41.7 9.7 0.00021 18.0 0.2 32 6-42 4-35 (38)
123 PF01927 Mut7-C: Mut7-C RNAse 41.3 16 0.00036 23.3 1.2 43 4-46 91-138 (147)
124 PF13384 HTH_23: Homeodomain-l 41.1 8 0.00017 19.3 -0.2 21 121-141 19-39 (50)
125 PF09292 Neil1-DNA_bind: Endon 40.8 10 0.00022 18.2 0.2 6 137-142 27-32 (39)
126 TIGR00373 conserved hypothetic 40.5 5.8 0.00013 25.8 -0.9 29 6-43 111-139 (158)
127 PF06971 Put_DNA-bind_N: Putat 40.4 10 0.00023 19.5 0.2 16 122-137 31-46 (50)
128 PRK12495 hypothetical protein; 40.4 14 0.00031 25.4 0.9 23 33-61 43-65 (226)
129 PF00196 GerE: Bacterial regul 40.1 8.6 0.00019 20.0 -0.2 38 98-141 3-40 (58)
130 PF02069 Metallothio_Pro: Prok 39.9 23 0.00051 18.4 1.4 25 34-59 9-33 (52)
131 COG3149 PulM Type II secretory 39.9 12 0.00026 24.7 0.5 14 130-143 123-136 (181)
132 PRK09710 lar restriction allev 39.7 21 0.00045 19.5 1.3 29 5-40 7-35 (64)
133 KOG0978|consensus 39.3 6.4 0.00014 31.8 -1.0 39 33-73 644-686 (698)
134 cd04762 HTH_MerR-trunc Helix-T 38.6 8.5 0.00018 18.6 -0.3 19 123-141 4-22 (49)
135 PF04502 DUF572: Family of unk 38.2 18 0.00038 26.5 1.1 40 3-43 39-88 (324)
136 PRK06266 transcription initiat 38.1 7.8 0.00017 25.7 -0.6 29 6-43 119-147 (178)
137 TIGR03879 near_KaiC_dom probab 38.0 9.1 0.0002 21.5 -0.3 22 121-142 34-55 (73)
138 cd01104 HTH_MlrA-CarA Helix-Tu 37.5 11 0.00024 20.1 -0.0 20 122-141 3-22 (68)
139 PF12824 MRP-L20: Mitochondria 37.1 77 0.0017 20.8 3.8 40 95-136 82-121 (164)
140 smart00291 ZnF_ZZ Zinc-binding 36.5 30 0.00064 17.0 1.5 9 54-62 27-35 (44)
141 PF00130 C1_1: Phorbol esters/ 36.0 22 0.00047 18.0 1.0 11 5-15 12-22 (53)
142 PRK09413 IS2 repressor TnpA; R 35.0 66 0.0014 19.6 3.2 41 96-140 10-50 (121)
143 PF11388 DotA: Phagosome traff 34.8 14 0.0003 21.7 0.1 8 136-143 32-39 (105)
144 PF10886 DUF2685: Protein of u 34.8 37 0.0008 17.8 1.7 10 6-15 3-12 (54)
145 PF05502 Dynactin_p62: Dynacti 34.5 23 0.0005 27.5 1.3 36 6-43 28-63 (483)
146 PHA02768 hypothetical protein; 34.3 12 0.00027 19.7 -0.1 39 3-43 4-42 (55)
147 PF10122 Mu-like_Com: Mu-like 34.2 20 0.00044 18.5 0.7 13 4-16 4-16 (51)
148 PF07503 zf-HYPF: HypF finger; 33.9 37 0.00079 16.0 1.5 21 23-43 12-32 (35)
149 PHA03225 DNA packaging protein 32.9 39 0.00084 21.1 1.8 10 134-143 41-50 (125)
150 smart00659 RPOLCX RNA polymera 32.8 28 0.00061 17.3 1.0 10 6-15 4-13 (44)
151 PLN02638 cellulose synthase A 32.8 21 0.00045 30.5 0.8 51 2-61 15-66 (1079)
152 PF13717 zinc_ribbon_4: zinc-r 32.5 18 0.00039 17.1 0.3 30 6-40 4-33 (36)
153 PF10078 DUF2316: Uncharacteri 32.4 15 0.00032 21.5 -0.0 28 105-136 13-40 (89)
154 PF00628 PHD: PHD-finger; Int 31.9 36 0.00078 17.0 1.4 29 6-34 1-30 (51)
155 PLN02400 cellulose synthase 31.9 35 0.00075 29.3 1.9 49 3-60 35-84 (1085)
156 smart00422 HTH_MERR helix_turn 31.5 15 0.00031 19.7 -0.1 18 123-140 4-21 (70)
157 PRK10072 putative transcriptio 31.1 53 0.0011 19.4 2.2 37 98-141 32-68 (96)
158 PF14279 HNH_5: HNH endonuclea 30.7 18 0.00038 20.1 0.1 36 7-43 1-41 (71)
159 PRK04016 DNA-directed RNA poly 30.5 25 0.00054 19.0 0.7 9 6-14 6-14 (62)
160 COG1998 RPS31 Ribosomal protei 30.4 32 0.0007 17.7 1.0 14 49-62 32-45 (51)
161 PF00569 ZZ: Zinc finger, ZZ t 30.2 51 0.0011 16.4 1.8 11 53-63 27-37 (46)
162 PF03107 C1_2: C1 domain; Int 29.7 54 0.0012 14.6 1.6 10 6-15 2-11 (30)
163 PRK06759 RNA polymerase factor 29.2 45 0.00097 20.9 1.8 37 99-140 107-143 (154)
164 PF12773 DZR: Double zinc ribb 29.1 57 0.0012 16.2 1.9 9 34-42 31-39 (50)
165 cd01392 HTH_LacI Helix-turn-he 29.0 12 0.00025 18.8 -0.8 19 124-142 2-20 (52)
166 PHA02955 hypothetical protein; 29.0 83 0.0018 21.6 3.1 41 102-142 61-102 (213)
167 smart00421 HTH_LUXR helix_turn 28.8 76 0.0017 15.5 2.4 36 99-140 4-39 (58)
168 PF01194 RNA_pol_N: RNA polyme 28.2 35 0.00075 18.4 1.0 9 6-14 6-14 (60)
169 PF13404 HTH_AsnC-type: AsnC-t 28.0 22 0.00048 17.4 0.2 16 122-137 20-35 (42)
170 PF08280 HTH_Mga: M protein tr 28.0 37 0.00079 17.8 1.1 31 103-137 7-37 (59)
171 cd02341 ZZ_ZZZ3 Zinc finger, Z 27.8 49 0.0011 16.8 1.5 9 55-63 27-35 (48)
172 PLN03208 E3 ubiquitin-protein 27.6 68 0.0015 21.7 2.4 31 31-63 17-47 (193)
173 PTZ00044 ubiquitin; Provisiona 27.6 56 0.0012 17.8 1.8 22 121-142 26-47 (76)
174 PF13223 DUF4031: Protein of u 27.1 55 0.0012 18.9 1.7 18 121-142 25-42 (83)
175 PF13923 zf-C3HC4_2: Zinc fing 27.1 79 0.0017 14.7 2.1 30 35-66 1-31 (39)
176 PF08279 HTH_11: HTH domain; 26.9 23 0.00049 18.0 0.1 17 121-137 17-33 (55)
177 cd02336 ZZ_RSC8 Zinc finger, Z 26.7 62 0.0013 16.2 1.7 29 34-63 2-32 (45)
178 COG1656 Uncharacterized conser 26.6 23 0.0005 23.3 0.1 43 4-46 97-144 (165)
179 PF00096 zf-C2H2: Zinc finger, 26.5 25 0.00054 14.1 0.2 11 33-43 1-11 (23)
180 PF08792 A2L_zn_ribbon: A2L zi 26.5 69 0.0015 14.8 1.7 8 52-59 19-26 (33)
181 cd01793 Fubi Fubi ubiquitin-li 26.5 60 0.0013 17.7 1.8 22 121-142 24-45 (74)
182 PF13730 HTH_36: Helix-turn-he 26.4 42 0.00091 17.0 1.1 19 121-139 27-45 (55)
183 COG4357 Zinc finger domain con 26.4 5 0.00011 23.7 -2.6 15 28-42 58-72 (105)
184 PRK15183 Vi polysaccharide bio 26.0 77 0.0017 19.2 2.2 39 96-134 93-131 (143)
185 KOG0773|consensus 25.6 34 0.00073 25.1 0.8 32 111-142 116-147 (342)
186 PRK03681 hypA hydrogenase nick 25.6 71 0.0015 19.5 2.1 7 6-12 72-78 (114)
187 PF13309 HTH_22: HTH domain 25.5 1E+02 0.0022 16.5 2.6 34 103-136 26-59 (64)
188 PF14229 DUF4332: Domain of un 25.3 33 0.00071 21.2 0.6 23 117-139 27-49 (122)
189 PRK12537 RNA polymerase sigma 25.1 73 0.0016 20.7 2.3 20 121-140 151-170 (182)
190 PHA03229 DNA packaging protein 25.1 79 0.0017 19.9 2.2 10 134-143 43-52 (132)
191 PF13834 DUF4193: Domain of un 25.0 25 0.00053 21.0 0.0 28 33-60 71-98 (99)
192 PF13894 zf-C2H2_4: C2H2-type 24.9 31 0.00067 13.6 0.3 10 33-42 1-10 (24)
193 PRK00118 putative DNA-binding 24.9 67 0.0014 19.4 1.9 37 99-140 18-54 (104)
194 PRK09646 RNA polymerase sigma 24.9 68 0.0015 21.2 2.2 37 99-140 143-179 (194)
195 cd01796 DDI1_N DNA damage indu 24.7 67 0.0015 17.5 1.8 22 121-142 25-46 (71)
196 PF12874 zf-met: Zinc-finger o 24.4 34 0.00074 14.0 0.5 11 33-43 1-11 (25)
197 COG1997 RPL43A Ribosomal prote 24.4 89 0.0019 18.2 2.2 35 5-50 36-70 (89)
198 PF06032 DUF917: Protein of un 24.4 29 0.00064 25.7 0.4 11 132-142 267-277 (353)
199 PF15227 zf-C3HC4_4: zinc fing 24.2 96 0.0021 15.0 2.1 29 35-65 1-29 (42)
200 cd01798 parkin_N amino-termina 24.1 71 0.0015 17.1 1.8 22 121-142 24-45 (70)
201 PF00325 Crp: Bacterial regula 23.9 40 0.00086 15.6 0.6 16 121-136 4-19 (32)
202 PRK00085 recO DNA repair prote 23.7 44 0.00095 23.1 1.1 32 29-61 146-177 (247)
203 PLN02436 cellulose synthase A 23.5 44 0.00095 28.7 1.2 12 4-15 36-47 (1094)
204 smart00531 TFIIE Transcription 23.5 21 0.00045 22.8 -0.5 33 6-42 101-133 (147)
205 PF13719 zinc_ribbon_5: zinc-r 23.5 35 0.00077 16.1 0.4 12 6-17 4-15 (37)
206 PF14255 Cys_rich_CPXG: Cystei 23.5 31 0.00067 17.9 0.2 29 6-35 2-30 (52)
207 PLN03123 poly [ADP-ribose] pol 23.3 52 0.0011 28.1 1.6 30 5-34 18-57 (981)
208 cd06170 LuxR_C_like C-terminal 23.0 27 0.00057 17.4 -0.1 20 121-140 17-36 (57)
209 PF12171 zf-C2H2_jaz: Zinc-fin 22.9 66 0.0014 13.6 1.2 11 33-43 2-12 (27)
210 cd01769 UBL Ubiquitin-like dom 22.8 90 0.002 16.2 2.1 21 121-141 23-43 (69)
211 PTZ00397 macrophage migration 22.6 64 0.0014 19.5 1.6 23 121-143 81-103 (116)
212 cd01797 NIRF_N amino-terminal 22.6 81 0.0017 17.6 1.9 22 121-142 28-49 (78)
213 PF09889 DUF2116: Uncharacteri 22.6 45 0.00097 17.9 0.8 9 35-43 6-14 (59)
214 KOG3002|consensus 22.4 62 0.0013 23.5 1.6 45 31-76 47-91 (299)
215 PRK12530 RNA polymerase sigma 22.4 67 0.0014 21.1 1.7 20 121-140 152-171 (189)
216 PF08880 QLQ: QLQ; InterPro: 22.3 1.1E+02 0.0023 14.6 2.0 13 98-110 2-14 (37)
217 PLN00032 DNA-directed RNA poly 22.3 48 0.001 18.5 0.8 9 6-14 6-14 (71)
218 TIGR02989 Sig-70_gvs1 RNA poly 22.2 75 0.0016 19.9 1.9 37 99-140 112-148 (159)
219 PF10764 Gin: Inhibitor of sig 22.0 1.1E+02 0.0023 15.4 2.0 12 52-63 16-27 (46)
220 PRK12526 RNA polymerase sigma 21.8 52 0.0011 22.0 1.1 21 121-141 171-191 (206)
221 PF13443 HTH_26: Cro/C1-type H 21.4 1.2E+02 0.0025 15.7 2.3 29 107-135 27-56 (63)
222 TIGR00613 reco DNA repair prot 21.3 81 0.0018 21.6 2.0 33 28-61 143-175 (241)
223 COG2888 Predicted Zn-ribbon RN 21.3 71 0.0015 17.2 1.3 27 4-40 9-35 (61)
224 PF12244 DUF3606: Protein of u 21.2 62 0.0013 17.0 1.1 17 120-136 21-37 (57)
225 PF14634 zf-RING_5: zinc-RING 21.2 72 0.0016 15.4 1.3 13 52-64 20-32 (44)
226 PRK12514 RNA polymerase sigma 21.2 74 0.0016 20.5 1.8 21 121-141 147-167 (179)
227 PF12677 DUF3797: Domain of un 21.2 84 0.0018 16.1 1.5 27 6-32 15-42 (49)
228 PF02042 RWP-RK: RWP-RK domain 21.1 98 0.0021 16.1 1.8 24 105-135 8-31 (52)
229 PLN02915 cellulose synthase A 21.0 48 0.001 28.4 1.0 50 3-61 14-64 (1044)
230 PF14835 zf-RING_6: zf-RING of 20.7 44 0.00095 18.3 0.5 8 6-13 9-16 (65)
231 PRK04217 hypothetical protein; 20.6 70 0.0015 19.5 1.4 38 97-139 41-78 (110)
232 KOG4543|consensus 20.6 95 0.0021 20.8 2.0 35 32-66 156-190 (208)
233 PLN02189 cellulose synthase 20.5 53 0.0012 28.2 1.1 12 4-15 34-45 (1040)
234 PF11212 DUF2999: Protein of u 20.5 1.6E+02 0.0034 16.5 2.6 35 98-136 12-46 (82)
235 PRK09652 RNA polymerase sigma 20.5 77 0.0017 20.2 1.7 37 99-140 129-165 (182)
236 TIGR01764 excise DNA binding d 20.5 35 0.00076 16.4 0.1 18 123-140 5-22 (49)
237 TIGR02959 SigZ RNA polymerase 20.4 83 0.0018 20.2 1.9 36 99-139 101-136 (170)
238 PF10080 DUF2318: Predicted me 20.3 1.2E+02 0.0026 18.2 2.4 33 26-63 29-61 (102)
239 COG1427 Predicted periplasmic 20.3 54 0.0012 23.2 1.0 25 119-143 198-222 (252)
240 PF06573 Churchill: Churchill 20.2 68 0.0015 19.5 1.2 34 7-40 2-35 (112)
No 1
>KOG4577|consensus
Probab=99.96 E-value=1.3e-30 Score=176.23 Aligned_cols=127 Identities=36% Similarity=0.731 Sum_probs=112.8
Q ss_pred CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEee-CCeeechhhHHHHHHHhhccCCCCCCccc
Q psy15437 2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIK-QGQLFCRPDYEKEVEMLQGYAQGIPFDLI 80 (143)
Q Consensus 2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~-~~~~~C~~~~~~~~~~~~~~~~~~~~~~~ 80 (143)
.|+.+|..|...|-+...+..+.+.+||..||.|..|+++|.+|++||.. ++++.|..+|...-. ..+.
T Consensus 90 rfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~--k~~~-------- 159 (383)
T KOG4577|consen 90 RFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQ--KHCN-------- 159 (383)
T ss_pred HhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHh--cccc--------
Confidence 48899999999999888778899999999999999999999999999765 789999999987433 2222
Q ss_pred cCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 81 TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 81 ~~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+-++....||+||.+++.|+++|+..|...+.|....|++|+.++||..++|||||||
T Consensus 160 ----~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQN 217 (383)
T KOG4577|consen 160 ----ELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQN 217 (383)
T ss_pred ----ccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhh
Confidence 2235566789999999999999999999999999999999999999999999999999
No 2
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.78 E-value=4.7e-19 Score=94.48 Aligned_cols=51 Identities=18% Similarity=0.174 Sum_probs=49.5
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCC----CCHHHHHHHHHHhCCCcccceecccCC
Q psy15437 93 KRPRTILTTQQRRAFKASFEISPK----PCRKVREGLARDTGLSVRIVQSRPIPV 143 (143)
Q Consensus 93 ~r~R~~~~~~q~~~L~~~f~~~~~----p~~~~~~~la~~~~l~~~~vkvWFQn~ 143 (143)
+|.||.||.+|+..|+..|+.++| |+..++++||..+||++++|||||||.
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~ 56 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN 56 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence 689999999999999999999999 999999999999999999999999994
No 3
>KOG0843|consensus
Probab=99.71 E-value=5.5e-18 Score=108.02 Aligned_cols=52 Identities=29% Similarity=0.232 Sum_probs=51.1
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+++|.||.|+.+|+..|+..|+.++|....+|++||..|+|++.||||||||
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQN 152 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQN 152 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhh
Confidence 7889999999999999999999999999999999999999999999999999
No 4
>KOG0842|consensus
Probab=99.70 E-value=2.4e-17 Score=114.65 Aligned_cols=56 Identities=20% Similarity=0.205 Sum_probs=52.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 87 DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.+.+++|+.|..|+..|...||+.|....|.+..+|++||..|+|++.||||||||
T Consensus 148 t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQN 203 (307)
T KOG0842|consen 148 TGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQN 203 (307)
T ss_pred cccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeec
Confidence 34566677888999999999999999999999999999999999999999999999
No 5
>KOG0484|consensus
Probab=99.69 E-value=2e-18 Score=100.36 Aligned_cols=54 Identities=26% Similarity=0.240 Sum_probs=51.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.++.+|.||.|+..|+..|++.|.+.+||++..|++||.++.|+++.|||||||
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQN 67 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQN 67 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHh
Confidence 456778999999999999999999999999999999999999999999999999
No 6
>KOG0850|consensus
Probab=99.69 E-value=1.6e-17 Score=109.75 Aligned_cols=57 Identities=23% Similarity=0.252 Sum_probs=53.7
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 86 HDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 86 ~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.++.++.++.||+++..||+.|++.|++.+|....+|++||..|||+..||||||||
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQN 172 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQN 172 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhh
Confidence 456677778999999999999999999999999999999999999999999999999
No 7
>KOG0490|consensus
Probab=99.67 E-value=1.5e-17 Score=114.06 Aligned_cols=110 Identities=25% Similarity=0.448 Sum_probs=91.5
Q ss_pred cCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhhccCCCCCCccccCCCCCCCC
Q psy15437 10 CSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSSKSHDGR 89 (143)
Q Consensus 10 C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (143)
|+..|. +.......+..||..|..|..|...+..+...+..++..||..++.+ ...
T Consensus 2 ~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~-----------------------~~~ 57 (235)
T KOG0490|consen 2 CGRQIL-DRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQR-----------------------EFK 57 (235)
T ss_pred CCcccc-chHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchh-----------------------hhh
Confidence 566665 34445666889999999999999999533445444999999888865 123
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccCC
Q psy15437 90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIPV 143 (143)
Q Consensus 90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn~ 143 (143)
.+.++.|+.++..|+..|++.|+..|||+..+++.||..+++++..|+|||||.
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnr 111 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNR 111 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhh
Confidence 456789999999999999999999999999999999999999999999999995
No 8
>KOG0485|consensus
Probab=99.61 E-value=3.8e-16 Score=102.46 Aligned_cols=55 Identities=24% Similarity=0.271 Sum_probs=52.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+..++|+.||+|+..|+..||..|+...|....+|..||.+|.|++.||||||||
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQN 154 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQN 154 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhh
Confidence 4557788999999999999999999999999999999999999999999999999
No 9
>KOG0489|consensus
Probab=99.60 E-value=2.3e-16 Score=109.42 Aligned_cols=53 Identities=23% Similarity=0.184 Sum_probs=51.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.+.+|.||.||..|+..||+.|+.|.|.+...|.++|..|.|+++||||||||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQN 209 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQN 209 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHH
Confidence 44788999999999999999999999999999999999999999999999999
No 10
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.60 E-value=2.1e-15 Score=81.85 Aligned_cols=58 Identities=33% Similarity=0.843 Sum_probs=51.7
Q ss_pred ccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437 7 CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV 65 (143)
Q Consensus 7 C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~ 65 (143)
|.+|+++|.+.+.++.+.++.||++||+|..|+.+|..+. ++..++.+||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD-FYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS-EEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe-eEeECCEEECHHHHhhhC
Confidence 7899999997777668999999999999999999996444 999999999999998764
No 11
>KOG0493|consensus
Probab=99.58 E-value=8.5e-16 Score=103.39 Aligned_cols=51 Identities=29% Similarity=0.363 Sum_probs=49.3
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
-||.||.|+.+|++.|+..|+.|.|.+...|.+||.+|+|.+.||||||||
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQN 296 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQN 296 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhh
Confidence 357899999999999999999999999999999999999999999999999
No 12
>KOG0488|consensus
Probab=99.58 E-value=1.6e-15 Score=107.02 Aligned_cols=55 Identities=20% Similarity=0.154 Sum_probs=51.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
..++.++.||+||+.|+..||+.|+...|....+|++||..|||+..|||+||||
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQN 222 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQN 222 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhh
Confidence 3466667899999999999999999999999999999999999999999999999
No 13
>KOG0494|consensus
Probab=99.56 E-value=3e-15 Score=100.69 Aligned_cols=54 Identities=28% Similarity=0.271 Sum_probs=49.6
Q ss_pred CCCCCCC-CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 89 RRGPKRP-RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 89 ~~~~~r~-R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+.+++|. ||+||..|+..||..|.+.+||+...|+.||.+|.|++..|+|||||
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQN 191 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQN 191 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhh
Confidence 3334444 99999999999999999999999999999999999999999999999
No 14
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.55 E-value=1.5e-15 Score=82.12 Aligned_cols=50 Identities=34% Similarity=0.492 Sum_probs=48.3
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
++.|+.++.+|+..|+..|..+++|+..+++.||..+||+..+|++||||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHH
Confidence 46789999999999999999999999999999999999999999999998
No 15
>KOG0848|consensus
Probab=99.55 E-value=9.7e-16 Score=103.40 Aligned_cols=54 Identities=26% Similarity=0.242 Sum_probs=50.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.+.+.+.|.++|+.|+..||+.|+-++|.++..+.+||..|+|+++||||||||
T Consensus 196 tRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQN 249 (317)
T KOG0848|consen 196 TRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQN 249 (317)
T ss_pred eecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhh
Confidence 344556788999999999999999999999999999999999999999999999
No 16
>KOG2251|consensus
Probab=99.55 E-value=4.8e-15 Score=97.67 Aligned_cols=56 Identities=30% Similarity=0.276 Sum_probs=54.2
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 87 DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.++++.+|.||.|+..|++.||..|.+..||+...|++||.+|+|++.+|||||-|
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKN 87 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKN 87 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhcc
Confidence 67788999999999999999999999999999999999999999999999999988
No 17
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.54 E-value=9e-15 Score=93.50 Aligned_cols=59 Identities=27% Similarity=0.305 Sum_probs=54.5
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 84 KSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 84 ~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
...++....++.|+..+..|+..|++.|.++++|+...|..|+..++|+++.|||||||
T Consensus 43 ~~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQN 101 (156)
T COG5576 43 RKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQN 101 (156)
T ss_pred hcccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhch
Confidence 34556677788899999999999999999999999999999999999999999999999
No 18
>KOG0487|consensus
Probab=99.53 E-value=4.4e-15 Score=103.51 Aligned_cols=53 Identities=21% Similarity=0.176 Sum_probs=50.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
++.+++|..+|..|+..||+.|..|-|.+..-|.+|+..|+|+++||||||||
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQN 285 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQN 285 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehh
Confidence 55667889999999999999999999999999999999999999999999999
No 19
>KOG1701|consensus
Probab=99.53 E-value=2e-16 Score=112.85 Aligned_cols=105 Identities=27% Similarity=0.594 Sum_probs=86.1
Q ss_pred CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEee-CCeeechhhHHHHHH-HhhccCCCCCCcccc
Q psy15437 4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIK-QGQLFCRPDYEKEVE-MLQGYAQGIPFDLIT 81 (143)
Q Consensus 4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~-~~~~~C~~~~~~~~~-~~~~~~~~~~~~~~~ 81 (143)
..+|..|++.|. |++++|+|+.||+.||+|..|.+.| +|..|... ++++||..||.+.|+ +|..|..+|.
T Consensus 334 lekC~~Cg~~I~--d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~----- 405 (468)
T KOG1701|consen 334 LEKCNKCGEPIM--DRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPIL----- 405 (468)
T ss_pred HHHHhhhhhHHH--HHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhcCcchhhccCCcc-----
Confidence 468999999998 7789999999999999999999999 68889765 789999999999997 7888888887
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHH
Q psy15437 82 SSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARD 128 (143)
Q Consensus 82 ~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~ 128 (143)
+.++....=| +..|-+.||.+.|-+..++.+|+.+
T Consensus 406 ---P~~G~~etvR---------vvamdr~fHv~CY~CEDCg~~LS~e 440 (468)
T KOG1701|consen 406 ---PRDGKDETVR---------VVAMDRDFHVNCYKCEDCGLLLSSE 440 (468)
T ss_pred ---CCCCCcceEE---------EEEccccccccceehhhcCcccccc
Confidence 2333332211 2347889999999999999888743
No 20
>KOG0492|consensus
Probab=99.53 E-value=8.7e-15 Score=95.48 Aligned_cols=52 Identities=23% Similarity=0.165 Sum_probs=49.5
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
..+..||.||..|+..||+.|...+|..+.+|.+++..|.|++.||||||||
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQN 194 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQN 194 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhh
Confidence 3456899999999999999999999999999999999999999999999999
No 21
>KOG1701|consensus
Probab=99.50 E-value=9.7e-16 Score=109.42 Aligned_cols=77 Identities=27% Similarity=0.637 Sum_probs=70.5
Q ss_pred CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhhccCCCCCCccc
Q psy15437 3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLI 80 (143)
Q Consensus 3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~ 80 (143)
|...|.+|++.|.+++..++|+++.||..||+|..|.++| .|..||..+++.||+.||...+++|..|+..|.+.++
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L-~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~iL 349 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQL-AGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDRIL 349 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhh-ccccccccCCcccchHHHHHHHHHHhhhhhHHHHHHH
Confidence 4458999999999999999999999999999999999999 6999999999999999999999999999988775443
No 22
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.45 E-value=6.4e-14 Score=75.38 Aligned_cols=49 Identities=37% Similarity=0.452 Sum_probs=47.0
Q ss_pred CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+.|+.++..++..|+..|..+++|+..++..||..+||+..+|+.||+|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQN 50 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHH
Confidence 4677899999999999999999999999999999999999999999998
No 23
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.42 E-value=1.4e-13 Score=74.76 Aligned_cols=49 Identities=37% Similarity=0.488 Sum_probs=47.0
Q ss_pred CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+.|+.++..++..|+..|..+++|+..+++.||..+||+..+|++||+|
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 4678899999999999999999999999999999999999999999998
No 24
>KOG0490|consensus
Probab=99.34 E-value=9e-13 Score=90.44 Aligned_cols=139 Identities=27% Similarity=0.422 Sum_probs=103.5
Q ss_pred CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCC-eeechhhHHHHHHHhhccCCCCCCc---
Q psy15437 3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQG-QLFCRPDYEKEVEMLQGYAQGIPFD--- 78 (143)
Q Consensus 3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~-~~~C~~~~~~~~~~~~~~~~~~~~~--- 78 (143)
+..+|.+|...+...+.+..++.+. |.-||.|..|...+..+.++.+... ...|..++...-.....-..+....
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~ 136 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAP 136 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCC
Confidence 5679999999997667777788887 9999999999998878888876644 7788777654310111111111110
Q ss_pred ---cccCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 79 ---LITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 79 ---~~~~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
............+.++.|+.+...++..+...|...++|+...++.|+..+|++++.|+|||||
T Consensus 137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~ 203 (235)
T KOG0490|consen 137 PSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQN 203 (235)
T ss_pred ccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhccc
Confidence 0111112233455667899999999999999999999999999999999999999999999998
No 25
>KOG0844|consensus
Probab=99.29 E-value=1e-12 Score=90.55 Aligned_cols=54 Identities=20% Similarity=0.106 Sum_probs=50.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
....+|.||.|+.+|+..||+.|-+..|...+.|=+||..|+|++..|||||||
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQN 231 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQN 231 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhh
Confidence 344568999999999999999999999999999999999999999999999999
No 26
>KOG0491|consensus
Probab=99.27 E-value=2.3e-13 Score=85.84 Aligned_cols=50 Identities=22% Similarity=0.233 Sum_probs=48.1
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
++.||+|+..|+..|++.|+...|....++.+||..|+|++.|||.||||
T Consensus 101 ~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQN 150 (194)
T KOG0491|consen 101 RKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQN 150 (194)
T ss_pred hhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHH
Confidence 34799999999999999999999999999999999999999999999999
No 27
>KOG0483|consensus
Probab=99.21 E-value=7e-12 Score=82.96 Aligned_cols=49 Identities=27% Similarity=0.260 Sum_probs=46.0
Q ss_pred CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+.+..++.+|...|+..|+.+.+.....+..||.+|||.++||.|||||
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQN 100 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQN 100 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhh
Confidence 4456789999999999999999999999999999999999999999999
No 28
>KOG4577|consensus
Probab=99.18 E-value=6.9e-13 Score=90.72 Aligned_cols=69 Identities=28% Similarity=0.741 Sum_probs=63.4
Q ss_pred ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCC
Q psy15437 5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIP 76 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~ 76 (143)
+.|+.|.+.|. +.++..+.++.||..|++|+.|..+|. +.++.+++.+||..+|.++|+ +|..|..+|+
T Consensus 34 p~CagC~q~Il-DrFilKvl~R~wHs~CLkCs~C~~qL~--drCFsR~~s~yCkedFfKrfGTKCsaC~~GIp 103 (383)
T KOG4577|consen 34 PICAGCDQHIL-DRFILKVLDRHWHSSCLKCSDCHDQLA--DRCFSREGSVYCKEDFFKRFGTKCSACQEGIP 103 (383)
T ss_pred ccccchHHHHH-HHHHHHHHhhhhhhhhcchhhhhhHHH--HHHhhcCCceeehHHHHHHhCCcchhhcCCCC
Confidence 58999999998 677889999999999999999999994 678999999999999999997 7889999998
No 29
>KOG3802|consensus
Probab=99.15 E-value=5.7e-11 Score=84.96 Aligned_cols=52 Identities=21% Similarity=0.270 Sum_probs=49.7
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
++|++||.+....+..||+.|.+|+.|+..++.+||.+|+|.+.+|+|||=|
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCN 344 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCN 344 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeec
Confidence 5677899999999999999999999999999999999999999999999966
No 30
>KOG0486|consensus
Probab=99.13 E-value=3e-11 Score=83.67 Aligned_cols=54 Identities=28% Similarity=0.234 Sum_probs=51.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
-++++|.||.|+..|++.||..|.+|.||++..|+++|+-++|++..|+|||-|
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfkn 162 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKN 162 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhccc
Confidence 446778999999999999999999999999999999999999999999999987
No 31
>KOG0847|consensus
Probab=99.06 E-value=4.9e-11 Score=78.79 Aligned_cols=51 Identities=20% Similarity=0.164 Sum_probs=48.0
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.+..|..|+..|+..|++.|+...|+-..++.+||..+|+.+.+|+|||||
T Consensus 167 rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQN 217 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQN 217 (288)
T ss_pred ccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhc
Confidence 344678899999999999999999999999999999999999999999999
No 32
>KOG0849|consensus
Probab=98.96 E-value=4.8e-10 Score=81.06 Aligned_cols=55 Identities=35% Similarity=0.401 Sum_probs=51.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccCC
Q psy15437 89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIPV 143 (143)
Q Consensus 89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn~ 143 (143)
.++.+|.||.++..|+..|+..|+.++||++..|+.||.++++++..|+|||||.
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nr 227 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNR 227 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhh
Confidence 4555667999999999999999999999999999999999999999999999994
No 33
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.93 E-value=8.4e-10 Score=54.58 Aligned_cols=38 Identities=42% Similarity=0.996 Sum_probs=33.8
Q ss_pred cccccCccccCCcceEEecCcccccCCcccccCCcccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQ 43 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 43 (143)
+|..|+++|.+.+..+.+.+..||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58999999986656788999999999999999999883
No 34
>KOG2272|consensus
Probab=98.86 E-value=9.9e-10 Score=74.24 Aligned_cols=100 Identities=22% Similarity=0.397 Sum_probs=75.7
Q ss_pred ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhhc-cCCCCCCccccCC
Q psy15437 5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQG-YAQGIPFDLITSS 83 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~-~~~~~~~~~~~~~ 83 (143)
..|.+|.....+.|.++...+..||..||.|..|-.++. +..|+..+|+.||..||..++++++. |++=+.+.
T Consensus 13 ~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~-~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGr----- 86 (332)
T KOG2272|consen 13 MVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFP-DGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGR----- 86 (332)
T ss_pred HHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCC-CceeEEecCcccccccchhhhchhhcccccchhhH-----
Confidence 469999999999999999999999999999999999994 66699999999999999999987654 33333222
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHh
Q psy15437 84 KSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDT 129 (143)
Q Consensus 84 ~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~ 129 (143)
-+..+..+|+...+.+..+.++||...
T Consensus 87 -------------------VikamnnSwHp~CF~Cd~Cn~~Lad~g 113 (332)
T KOG2272|consen 87 -------------------VIKAMNNSWHPACFRCDLCNKHLADQG 113 (332)
T ss_pred -------------------HHHhhccccCcccchhHHHHHHHhhhh
Confidence 233345555556666666666655443
No 35
>KOG1703|consensus
Probab=98.83 E-value=8.6e-10 Score=82.97 Aligned_cols=100 Identities=22% Similarity=0.422 Sum_probs=72.9
Q ss_pred CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCCCccc
Q psy15437 2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIPFDLI 80 (143)
Q Consensus 2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~~~~~ 80 (143)
.++..|.+|+.+|. +.++.+.+..||++||.|..|.+.+ .+..|+.+++.+||..||..++. ++..+..++
T Consensus 361 ~~~p~C~~C~~~i~--~~~v~a~~~~wH~~cf~C~~C~~~~-~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~----- 432 (479)
T KOG1703|consen 361 PFRPNCKRCLLPIL--EEGVCALGRLWHPECFVCADCGKPL-KNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPV----- 432 (479)
T ss_pred hhCccccccCCchH--HhHhhhccCeechhceeeecccCCC-CCCcccccCCccchhhhHhhhccccchhccchh-----
Confidence 36789999999998 3367888999999999999998888 57779999999999999999886 333332221
Q ss_pred cCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHH
Q psy15437 81 TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLA 126 (143)
Q Consensus 81 ~~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la 126 (143)
.+-..++..+...|+...|-+..+...|.
T Consensus 433 -----------------~~~~~~ie~~~~~~h~~~F~c~~c~~~l~ 461 (479)
T KOG1703|consen 433 -----------------EFGSRQIEADGSPFHGDCFRCANCMKKLT 461 (479)
T ss_pred -----------------HhhhhHhhccCccccccceehhhhhcccc
Confidence 12233455556666666666665554443
No 36
>KOG2272|consensus
Probab=98.81 E-value=5.2e-10 Score=75.55 Aligned_cols=75 Identities=23% Similarity=0.456 Sum_probs=63.4
Q ss_pred CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH-hhccCCCCCCcccc
Q psy15437 4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM-LQGYAQGIPFDLIT 81 (143)
Q Consensus 4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~-~~~~~~~~~~~~~~ 81 (143)
-+.|..|.++|. +.++.++++.||.+.|.|..|.+++ -|.+.|.+.|..||..+|.++++. |=.|+..+.++++.
T Consensus 195 ipiCgaC~rpIe--ervi~amgKhWHveHFvCa~CekPF-lGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~ 270 (332)
T KOG2272|consen 195 IPICGACRRPIE--ERVIFAMGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVS 270 (332)
T ss_pred CcccccccCchH--HHHHHHhccccchhheeehhcCCcc-cchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHH
Confidence 367899999997 6678999999999999999999999 478889999999999999999974 44666666665543
No 37
>KOG1044|consensus
Probab=98.77 E-value=1.7e-09 Score=80.59 Aligned_cols=69 Identities=29% Similarity=0.691 Sum_probs=57.1
Q ss_pred ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCC
Q psy15437 5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIP 76 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~ 76 (143)
..|++|++.|..+. ++.+.++.||..||+|..|..-|. .++..+++.+||..||...|+ +|..|..=|.
T Consensus 134 s~cagc~~~lk~gq-~llald~qwhv~cfkc~~c~~vL~--gey~skdg~pyce~dy~~~fgvkc~~c~~fis 203 (670)
T KOG1044|consen 134 STCAGCGEELKNGQ-ALLALDKQWHVSCFKCKSCSAVLN--GEYMSKDGVPYCEKDYQAKFGVKCEECEKFIS 203 (670)
T ss_pred ccccchhhhhhccc-eeeeeccceeeeeeehhhhccccc--ceeeccCCCcchhhhhhhhcCeehHHhhhhhh
Confidence 47999999998544 678999999999999999999994 458899999999999998886 5555554443
No 38
>KOG1168|consensus
Probab=98.55 E-value=3.6e-08 Score=68.04 Aligned_cols=53 Identities=23% Similarity=0.379 Sum_probs=49.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
..+||+||.+.+-....||..|...+.|....++.+|.+|+|.+-+|+|||=|
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCN 359 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCN 359 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeec
Confidence 34678999999999999999999999999999999999999999999999976
No 39
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.30 E-value=9.1e-08 Score=47.36 Aligned_cols=30 Identities=33% Similarity=0.505 Sum_probs=25.4
Q ss_pred cCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 113 ISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 113 ~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.+|||+..+++.||.++|++..||..||=|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~N 36 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFIN 36 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 479999999999999999999999999976
No 40
>KOG2252|consensus
Probab=98.21 E-value=1.4e-06 Score=65.19 Aligned_cols=57 Identities=25% Similarity=0.422 Sum_probs=52.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 86 HDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 86 ~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.+..-.+|+.|.+|+..|+..|...|..+++|+..+.+.|+.+|+|....|..||=|
T Consensus 414 ~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmN 470 (558)
T KOG2252|consen 414 DDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMN 470 (558)
T ss_pred ccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHh
Confidence 445556777899999999999999999999999999999999999999999999977
No 41
>KOG0775|consensus
Probab=98.07 E-value=4.1e-06 Score=57.64 Aligned_cols=44 Identities=20% Similarity=0.329 Sum_probs=39.5
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
|...-+..|+..|..++||...++.+||..|||+..||-.||-|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKN 226 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKN 226 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhh
Confidence 44445668888999999999999999999999999999999988
No 42
>KOG0774|consensus
Probab=97.98 E-value=7.5e-06 Score=56.02 Aligned_cols=50 Identities=22% Similarity=0.320 Sum_probs=46.2
Q ss_pred CCCCCCCCHHHHHHHHHhh---hcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 93 KRPRTILTTQQRRAFKASF---EISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 93 ~r~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+|+|..|+....++|...| ..|+||+..++++||.+.+++-.||-.||.|
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgn 241 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGN 241 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcccccc
Confidence 4678899999999999998 4678999999999999999999999999988
No 43
>KOG1700|consensus
Probab=97.98 E-value=1.4e-06 Score=58.47 Aligned_cols=59 Identities=27% Similarity=0.687 Sum_probs=49.8
Q ss_pred ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437 5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV 65 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~ 65 (143)
..|.+|.+.+++.+. +...+..||..||+|..|+..|.+ ..+....+.++|..++...+
T Consensus 109 ~~c~~c~k~vy~~Ek-~~~~~~~~hk~cfrc~~~~~~ls~-~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 109 EKCARCQKTVYPLEK-VTGNGLEFHKSCFRCTHCGKKLSP-KNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred cccccccceeeehHH-HhhhhhhhhhhheeecccccccCC-cchhhcCCccccchhhheee
Confidence 579999999998876 568889999999999999999964 55888888999877776654
No 44
>KOG1703|consensus
Probab=97.85 E-value=9.6e-06 Score=61.41 Aligned_cols=78 Identities=19% Similarity=0.352 Sum_probs=64.1
Q ss_pred CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCCCcccc
Q psy15437 3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIPFDLIT 81 (143)
Q Consensus 3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~~~~~~ 81 (143)
....|..|...|... .++.++++.||+.+|.|..|...+..+. +...+|.+||..|+...+. .|..|..+|.+..+.
T Consensus 302 ~~p~c~~c~~~i~~~-~~i~~~~~~~h~~~~~c~~~~~~~~~~~-~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~ 379 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSV-KVIVALGKEWHPEHFSCEVCAIVILDGG-PRELDGKILCHECFHAPFRPNCKRCLLPILEEGVC 379 (479)
T ss_pred ccccccccccCcccc-eeEeeccccccccceeeccccccccCCC-ccccCCCccHHHHHHHhhCccccccCCchHHhHhh
Confidence 357899999999842 5788999999999999999999997554 5677899999999988775 788888888866554
Q ss_pred C
Q psy15437 82 S 82 (143)
Q Consensus 82 ~ 82 (143)
+
T Consensus 380 a 380 (479)
T KOG1703|consen 380 A 380 (479)
T ss_pred h
Confidence 4
No 45
>KOG1044|consensus
Probab=97.85 E-value=4.4e-06 Score=62.92 Aligned_cols=60 Identities=22% Similarity=0.493 Sum_probs=53.3
Q ss_pred CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437 2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63 (143)
Q Consensus 2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~ 63 (143)
.|+.+|..|.+-|. ..++.+.++.||+.|-.|+.|+..+..|.+-|+.+..+|...|-+.
T Consensus 190 ~fgvkc~~c~~fis--gkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa 249 (670)
T KOG1044|consen 190 KFGVKCEECEKFIS--GKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQA 249 (670)
T ss_pred hcCeehHHhhhhhh--hhhhhccCcccCcchhhhhhhccccccchheeeccccccCCccccc
Confidence 58899999999998 4478999999999999999999999999999999999988777543
No 46
>KOG1700|consensus
Probab=97.83 E-value=4.4e-06 Score=56.12 Aligned_cols=61 Identities=21% Similarity=0.426 Sum_probs=50.6
Q ss_pred CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437 4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE 66 (143)
Q Consensus 4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~ 66 (143)
..+|..|++.++..+. +...+..||..||.|..|...|. ...+..+++.+||..+|...++
T Consensus 7 ~~kc~~c~k~vy~~e~-~~~~g~~~hk~c~~c~~~~k~l~-~~~~~~~e~~~yc~~~~~~~~~ 67 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEK-VQKDGVDFHKECFKCEKCKKTLT-LSGYSEHEGVPYCKNCHVAQFG 67 (200)
T ss_pred cchhhhccCcchHHHH-HhccCcchhhhHHhccccccccc-cccccccccccccccchHhhhC
Confidence 4589999999997775 45889999999999999999995 4557779999999997655554
No 47
>KOG1146|consensus
Probab=97.63 E-value=2.8e-05 Score=63.64 Aligned_cols=50 Identities=26% Similarity=0.253 Sum_probs=47.7
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
++.|+.++..|+..|+..|....+|...+.+.|...++++.++|+|||||
T Consensus 904 ~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qn 953 (1406)
T KOG1146|consen 904 RAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQN 953 (1406)
T ss_pred hhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhh
Confidence 45799999999999999999999999999999999999999999999998
No 48
>KOG1702|consensus
Probab=97.40 E-value=6.9e-06 Score=54.35 Aligned_cols=59 Identities=36% Similarity=0.706 Sum_probs=46.8
Q ss_pred ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437 5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV 65 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~ 65 (143)
.-|..|++.+++.|. +.-.+++||..||+|..|+..|.. ..+--.+.++||..+|...+
T Consensus 5 ~n~~~cgk~vYPvE~-v~cldk~whk~cfkce~c~mtlnm-KnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEE-VKCLDKVWHKQCFKCEVCGMTLNM-KNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHHH-HhhHHHHHHHHhheeeeccCChhh-hhccccccCCCcCcccccce
Confidence 347789999998875 567889999999999999998863 22444578899999997653
No 49
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.33 E-value=4.7e-05 Score=40.08 Aligned_cols=37 Identities=8% Similarity=0.036 Sum_probs=28.3
Q ss_pred HHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437 104 RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 104 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF 140 (143)
+..|+..|.....+.......|..+++|+..+|+.||
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WF 46 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWF 46 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHH
Confidence 4569999999999999999999999999999999999
No 50
>KOG3623|consensus
Probab=96.26 E-value=0.0023 Score=50.20 Aligned_cols=39 Identities=18% Similarity=0.274 Sum_probs=36.7
Q ss_pred HHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 104 RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 104 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
+..|+..|..|..|...+...+|.+.|++.++||+||++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~ 606 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFED 606 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHh
Confidence 567888999999999999999999999999999999987
No 51
>KOG0773|consensus
Probab=96.22 E-value=0.0057 Score=44.56 Aligned_cols=52 Identities=27% Similarity=0.284 Sum_probs=41.2
Q ss_pred CCCCCCCCCHHHHHHHHHhh---hcCCCCCHHHHHHHHHHhCCCcccceecccCC
Q psy15437 92 PKRPRTILTTQQRRAFKASF---EISPKPCRKVREGLARDTGLSVRIVQSRPIPV 143 (143)
Q Consensus 92 ~~r~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn~ 143 (143)
..|.+..+.......|+... ...+||...++..|+.++||+..||..||-|.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINa 293 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINA 293 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhc
Confidence 44455577777777777552 23579999999999999999999999999883
No 52
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.23 E-value=0.13 Score=26.97 Aligned_cols=45 Identities=24% Similarity=0.285 Sum_probs=32.9
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
++.|..+|.++...+-..++... ....+|..+|++..+|.-|.-|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHC
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHh
Confidence 46788999999988888888886 4668999999999998877543
No 53
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=91.57 E-value=0.11 Score=25.02 Aligned_cols=26 Identities=23% Similarity=0.547 Sum_probs=17.4
Q ss_pred ccccCccccCCcceEEecCcccccCC
Q psy15437 7 CLGCSEKLGPDELVMKTLDNVFHVQC 32 (143)
Q Consensus 7 C~~C~~~i~~~~~~~~~~~~~~h~~c 32 (143)
|..||..|.++-.++...++.||.-|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC 26 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCC 26 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEEC
Confidence 67788888755455566777775443
No 54
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.65 E-value=0.16 Score=26.69 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=22.0
Q ss_pred CCccccccCccccCCcceE--EecCcccccCCc
Q psy15437 3 YVKKCLGCSEKLGPDELVM--KTLDNVFHVQCF 33 (143)
Q Consensus 3 ~~~~C~~C~~~i~~~~~~~--~~~~~~~h~~cf 33 (143)
.+.+|..|++.+.+.+-++ ..=+..||.+|+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 4679999999996443233 345777888887
No 55
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=88.70 E-value=0.15 Score=30.32 Aligned_cols=12 Identities=25% Similarity=0.587 Sum_probs=5.9
Q ss_pred cccccCccccCC
Q psy15437 6 KCLGCSEKLGPD 17 (143)
Q Consensus 6 ~C~~C~~~i~~~ 17 (143)
+|..|+++|+.+
T Consensus 4 kC~iCg~~I~~g 15 (101)
T PF09943_consen 4 KCYICGKPIYEG 15 (101)
T ss_pred EEEecCCeeeec
Confidence 355555555533
No 56
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=88.29 E-value=0.58 Score=24.49 Aligned_cols=38 Identities=39% Similarity=0.514 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHhhhcCCC--CCHHHHHHHHHHhCCCcccc
Q psy15437 99 LTTQQRRAFKASFEISPK--PCRKVREGLARDTGLSVRIV 136 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~--p~~~~~~~la~~~~l~~~~v 136 (143)
+|..|...|...++..-| |-......||..+|+++..+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 467899999999888876 55556778999999998643
No 57
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=87.40 E-value=0.41 Score=29.95 Aligned_cols=24 Identities=38% Similarity=0.701 Sum_probs=19.5
Q ss_pred cccccCCccccCCCceEeeCCeeechhhHH
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYE 62 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~ 62 (143)
-.|..|+.+| |- ++|.+||..|-.
T Consensus 29 ~hCp~Cg~PL-----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPL-----FR-KDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcc-----ee-eCCeEECCCCCc
Confidence 3588888888 65 899999988863
No 58
>PRK08359 transcription factor; Validated
Probab=87.20 E-value=0.87 Score=30.14 Aligned_cols=28 Identities=39% Similarity=0.884 Sum_probs=17.3
Q ss_pred ccccCCccccCCCceEe-eCCe--eechhhHH
Q psy15437 34 VCVVCGSRLQRGEQFVI-KQGQ--LFCRPDYE 62 (143)
Q Consensus 34 ~C~~C~~~l~~~~~~~~-~~~~--~~C~~~~~ 62 (143)
.|..|+..+ .|..+.. .+|. ..|..|+.
T Consensus 8 ~CEiCG~~i-~g~~~~v~ieGael~VC~~Ca~ 38 (176)
T PRK08359 8 YCEICGAEI-RGPGHRIRIEGAELLVCDRCYE 38 (176)
T ss_pred eeecCCCcc-CCCCeEEEEcCeEEehHHHHHH
Confidence 388888888 4564533 3442 34888873
No 59
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.43 E-value=0.69 Score=19.70 Aligned_cols=10 Identities=20% Similarity=0.753 Sum_probs=6.5
Q ss_pred cccccCcccc
Q psy15437 6 KCLGCSEKLG 15 (143)
Q Consensus 6 ~C~~C~~~i~ 15 (143)
+|..|+..|.
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 3667776665
No 60
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.90 E-value=1 Score=19.73 Aligned_cols=11 Identities=18% Similarity=0.634 Sum_probs=7.2
Q ss_pred ccccccCcccc
Q psy15437 5 KKCLGCSEKLG 15 (143)
Q Consensus 5 ~~C~~C~~~i~ 15 (143)
..|..|+..+.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 46777777554
No 61
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=82.10 E-value=0.45 Score=25.62 Aligned_cols=18 Identities=17% Similarity=0.278 Sum_probs=16.0
Q ss_pred HHHHHHHhCCCcccceec
Q psy15437 122 REGLARDTGLSVRIVQSR 139 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvW 139 (143)
...+|.+||+++.+|+.|
T Consensus 25 lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 457899999999999988
No 62
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=81.65 E-value=1.1 Score=22.05 Aligned_cols=22 Identities=32% Similarity=0.759 Sum_probs=14.6
Q ss_pred ccccCCccccCCCceEeeCCeeechhh
Q psy15437 34 VCVVCGSRLQRGEQFVIKQGQLFCRPD 60 (143)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~ 60 (143)
.|..|+.+| +-.+++..||..|
T Consensus 19 ~Cp~C~~PL-----~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPL-----MRDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCee-----EEecCCCEECCCC
Confidence 466777776 4456778888655
No 63
>KOG2893|consensus
Probab=77.97 E-value=0.81 Score=31.68 Aligned_cols=54 Identities=19% Similarity=0.500 Sum_probs=34.2
Q ss_pred ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH
Q psy15437 5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM 67 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~ 67 (143)
.-|..|+...- +|.++....+ ...|+|..|.+.|-+|.... +.|-+-+..+..+
T Consensus 11 pwcwycnrefd-dekiliqhqk---akhfkchichkkl~sgpgls-----ihcmqvhketid~ 64 (341)
T KOG2893|consen 11 PWCWYCNREFD-DEKILIQHQK---AKHFKCHICHKKLFSGPGLS-----IHCMQVHKETIDK 64 (341)
T ss_pred ceeeecccccc-hhhhhhhhhh---hccceeeeehhhhccCCCce-----eehhhhhhhhhhc
Confidence 35889998876 4554433332 35689999999886666443 4566666555543
No 64
>PRK00420 hypothetical protein; Validated
Probab=77.59 E-value=1.4 Score=26.85 Aligned_cols=25 Identities=36% Similarity=0.740 Sum_probs=18.4
Q ss_pred cccccCCccccCCCceEeeCCeeechhhHH
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYE 62 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~ 62 (143)
-.|..|+.+| |..++|..+|..|-.
T Consensus 24 ~~CP~Cg~pL-----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL-----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc-----eecCCCceECCCCCC
Confidence 4677888877 555788899977743
No 65
>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=77.10 E-value=2.2 Score=20.38 Aligned_cols=23 Identities=39% Similarity=0.772 Sum_probs=16.0
Q ss_pred ccccCCccccCCCceEeeCCeeechhhH
Q psy15437 34 VCVVCGSRLQRGEQFVIKQGQLFCRPDY 61 (143)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~ 61 (143)
.|..|+..+ +...+|..||..|.
T Consensus 10 ~C~~C~~~~-----~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 10 PCPVCGSRW-----FYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCCCCeE-----eEccCCEEEhhhCc
Confidence 466776643 67778889996664
No 66
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=76.56 E-value=3.8 Score=26.56 Aligned_cols=19 Identities=16% Similarity=0.211 Sum_probs=12.3
Q ss_pred HHHHHHHhCCCcccceecc
Q psy15437 122 REGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvWF 140 (143)
.++||..+|++...|.-|-
T Consensus 85 qeeLA~~lgvs~s~IsriE 103 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIE 103 (154)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 4567777777776665554
No 67
>PRK00807 50S ribosomal protein L24e; Validated
Probab=73.53 E-value=2.5 Score=22.02 Aligned_cols=23 Identities=17% Similarity=0.530 Sum_probs=13.6
Q ss_pred cccccCccccCCc--ceEEecCccc
Q psy15437 6 KCLGCSEKLGPDE--LVMKTLDNVF 28 (143)
Q Consensus 6 ~C~~C~~~i~~~~--~~~~~~~~~~ 28 (143)
.|..|+..|.+++ ..+..++++|
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~ 27 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTIL 27 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEE
Confidence 5777777777553 2234555555
No 68
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=73.37 E-value=12 Score=24.62 Aligned_cols=19 Identities=21% Similarity=0.242 Sum_probs=13.1
Q ss_pred HHHHHHHHhCCCcccceec
Q psy15437 121 VREGLARDTGLSVRIVQSR 139 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvW 139 (143)
.++.||.+++....+|+-|
T Consensus 94 SqedLA~ki~ek~svI~~i 112 (165)
T COG1813 94 SQEDLAAKLKEKVSVIRRI 112 (165)
T ss_pred CHHHHHHHhcccHHHHHHH
Confidence 4667888888777766543
No 69
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=72.47 E-value=0.31 Score=27.52 Aligned_cols=9 Identities=11% Similarity=-0.178 Sum_probs=6.9
Q ss_pred cceecccCC
Q psy15437 135 IVQSRPIPV 143 (143)
Q Consensus 135 ~vkvWFQn~ 143 (143)
-||||.||+
T Consensus 32 dvkvwmqnl 40 (106)
T PF11516_consen 32 DVKVWMQNL 40 (106)
T ss_dssp HHHHHHHHH
T ss_pred cHHHHHHHH
Confidence 378998884
No 70
>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=72.08 E-value=3.4 Score=17.83 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=6.8
Q ss_pred ccccCccccCCc
Q psy15437 7 CLGCSEKLGPDE 18 (143)
Q Consensus 7 C~~C~~~i~~~~ 18 (143)
|..|+..|.+.+
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 556666665443
No 71
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=72.02 E-value=4.3 Score=23.20 Aligned_cols=23 Identities=9% Similarity=-0.013 Sum_probs=19.2
Q ss_pred HHHHHHHHhCCCcccceecccCC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIPV 143 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn~ 143 (143)
.++.|...++|.+.+++||+..|
T Consensus 55 L~~~L~k~~~~~~~~i~v~~~~v 77 (81)
T cd02413 55 LTSLVQKRFNFPEGSVELYAEKV 77 (81)
T ss_pred HHHHHHHHhCCCCCeEEEEEEEc
Confidence 45678889999999999998754
No 72
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=70.99 E-value=1.5 Score=24.96 Aligned_cols=14 Identities=43% Similarity=0.980 Sum_probs=10.5
Q ss_pred ccccccCccccCCc
Q psy15437 5 KKCLGCSEKLGPDE 18 (143)
Q Consensus 5 ~~C~~C~~~i~~~~ 18 (143)
..|..|++.|..++
T Consensus 8 a~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 8 AKCKGCKKKIAKGE 21 (82)
T ss_dssp EBETTTSCBE-TTS
T ss_pred ccCcccCCcCCCCC
Confidence 47999999997665
No 73
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=70.55 E-value=4.7 Score=24.09 Aligned_cols=34 Identities=15% Similarity=0.468 Sum_probs=27.6
Q ss_pred cccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE 66 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~ 66 (143)
++|..|+..+-.|..|.+-.+.+....|+.+...
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKAS 36 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence 5899999999888889877777888888876543
No 74
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=70.34 E-value=5 Score=17.97 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=6.9
Q ss_pred CccccccCcccc
Q psy15437 4 VKKCLGCSEKLG 15 (143)
Q Consensus 4 ~~~C~~C~~~i~ 15 (143)
+.+|.+|+..|.
T Consensus 1 G~~C~rC~~~~~ 12 (30)
T PF06827_consen 1 GEKCPRCWNYIE 12 (30)
T ss_dssp TSB-TTT--BBE
T ss_pred CCcCccCCCcce
Confidence 468999998876
No 75
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=69.69 E-value=4.6 Score=27.47 Aligned_cols=38 Identities=24% Similarity=0.341 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHhhhcCCC--CCHHHHHHHHHHhCCCccc
Q psy15437 98 ILTTQQRRAFKASFEISPK--PCRKVREGLARDTGLSVRI 135 (143)
Q Consensus 98 ~~~~~q~~~L~~~f~~~~~--p~~~~~~~la~~~~l~~~~ 135 (143)
.+|..|+..|...|+..-| |-....+.||.++|+++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 7999999999999998886 6666677899999999864
No 76
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=69.42 E-value=3.2 Score=24.56 Aligned_cols=27 Identities=30% Similarity=0.532 Sum_probs=16.1
Q ss_pred ccccCCccccCCCceE-eeCCeeechhhH
Q psy15437 34 VCVVCGSRLQRGEQFV-IKQGQLFCRPDY 61 (143)
Q Consensus 34 ~C~~C~~~l~~~~~~~-~~~~~~~C~~~~ 61 (143)
.|..|+++|.. ..|+ ..+|.++...|.
T Consensus 80 ~C~vC~k~l~~-~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGN-SVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CccCcCCcCCC-ceEEEeCCCeEEecccc
Confidence 57788888853 4453 335666655554
No 77
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=67.89 E-value=4.1 Score=23.98 Aligned_cols=29 Identities=21% Similarity=0.504 Sum_probs=15.1
Q ss_pred cccccCCccccCCCceEeeCCeeechhhH
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~ 61 (143)
|+|..|+.++-.|..|.+-........|+
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl 35 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECL 35 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHH
Confidence 45666666665566564443333334444
No 78
>PRK06424 transcription factor; Provisional
Probab=67.59 E-value=10 Score=24.32 Aligned_cols=20 Identities=15% Similarity=0.012 Sum_probs=13.4
Q ss_pred HHHHHHHhCCCcccceeccc
Q psy15437 122 REGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvWFQ 141 (143)
.++||..+|++...|.-|-.
T Consensus 100 Q~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 100 QADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHC
Confidence 45678888877766666643
No 79
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.56 E-value=5.8 Score=23.05 Aligned_cols=37 Identities=16% Similarity=0.195 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcc
Q psy15437 98 ILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVR 134 (143)
Q Consensus 98 ~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~ 134 (143)
+++.+|...-+..|+.|--.+....+++|..|+.++-
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~ 38 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEV 38 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHH
Confidence 4567777766666666665566677888999998874
No 80
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=66.02 E-value=1.7 Score=25.42 Aligned_cols=13 Identities=31% Similarity=0.792 Sum_probs=10.9
Q ss_pred CCCccccccCccc
Q psy15437 2 LYVKKCLGCSEKL 14 (143)
Q Consensus 2 ~~~~~C~~C~~~i 14 (143)
+|...|.+|++.+
T Consensus 52 lfs~pC~~C~klL 64 (90)
T PF11571_consen 52 LFSTPCKKCGKLL 64 (90)
T ss_pred hccchhhHHHhHh
Confidence 5778899998888
No 81
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=65.43 E-value=2.2 Score=22.74 Aligned_cols=19 Identities=21% Similarity=0.225 Sum_probs=16.4
Q ss_pred HHHHHHHhCCCcccceecc
Q psy15437 122 REGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvWF 140 (143)
..++|..||++...|..|=
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWK 34 (58)
T ss_pred HHHHHHHHCCChHHHHHHH
Confidence 5578999999999998884
No 82
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=64.33 E-value=6.3 Score=22.34 Aligned_cols=14 Identities=29% Similarity=0.657 Sum_probs=4.4
Q ss_pred CCCccccccCcccc
Q psy15437 2 LYVKKCLGCSEKLG 15 (143)
Q Consensus 2 ~~~~~C~~C~~~i~ 15 (143)
+.++.|.-|+..|.
T Consensus 7 ~~~qiCqiCGD~VG 20 (80)
T PF14569_consen 7 LNGQICQICGDDVG 20 (80)
T ss_dssp -SS-B-SSS--B--
T ss_pred cCCcccccccCccc
Confidence 34566777766664
No 83
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=63.77 E-value=6.7 Score=20.28 Aligned_cols=29 Identities=31% Similarity=0.754 Sum_probs=18.1
Q ss_pred cccCCccccCCCceEeeCCeeechhhHHHH
Q psy15437 35 CVVCGSRLQRGEQFVIKQGQLFCRPDYEKE 64 (143)
Q Consensus 35 C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~ 64 (143)
|..|+..++.-..+-..+| ..|..|+.+.
T Consensus 2 C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 2 CAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCccccccccccceeccCc-cchHHHHHHh
Confidence 6677776643233445566 5788888664
No 84
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=63.00 E-value=7.3 Score=24.75 Aligned_cols=18 Identities=17% Similarity=0.344 Sum_probs=14.6
Q ss_pred HHHHHHHhCCCcccceec
Q psy15437 122 REGLARDTGLSVRIVQSR 139 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvW 139 (143)
..+++..||++..+|..|
T Consensus 49 i~eV~e~tgVs~~~I~~~ 66 (137)
T TIGR03826 49 VSEIVEETGVSEKLILKF 66 (137)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 446789999999888777
No 85
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=62.51 E-value=5 Score=20.49 Aligned_cols=38 Identities=24% Similarity=0.219 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceeccc
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQ 141 (143)
++..+...+...|-.+ ...+++|..+|+++..|+.|.+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHH
Confidence 3445555555444333 3577899999999999988764
No 86
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=61.13 E-value=5.1 Score=21.90 Aligned_cols=12 Identities=33% Similarity=0.791 Sum_probs=6.9
Q ss_pred cccccCccccCC
Q psy15437 6 KCLGCSEKLGPD 17 (143)
Q Consensus 6 ~C~~C~~~i~~~ 17 (143)
+|..|+..|.++
T Consensus 5 ~CsFcG~~I~PG 16 (66)
T COG2075 5 VCSFCGKKIEPG 16 (66)
T ss_pred EecCcCCccCCC
Confidence 456666666555
No 87
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=60.88 E-value=2.7 Score=22.69 Aligned_cols=18 Identities=17% Similarity=0.135 Sum_probs=15.6
Q ss_pred HHHHHHHhCCCcccceec
Q psy15437 122 REGLARDTGLSVRIVQSR 139 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvW 139 (143)
..++|..+|++...|+.|
T Consensus 3 i~eva~~~gvs~~tlr~y 20 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYY 20 (69)
T ss_dssp HHHHHHHTTTTHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 357899999999999988
No 88
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=60.87 E-value=2.4 Score=21.11 Aligned_cols=20 Identities=25% Similarity=0.140 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCcccceeccc
Q psy15437 122 REGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvWFQ 141 (143)
..++|..+|+++..|+.|-+
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35678999999999988854
No 89
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=60.79 E-value=5.9 Score=21.76 Aligned_cols=40 Identities=15% Similarity=0.178 Sum_probs=25.1
Q ss_pred CCCCCCHHHHHHHHHhh-hcCCCCCHHHHHHHHHHhCCCcccceec
Q psy15437 95 PRTILTTQQRRAFKASF-EISPKPCRKVREGLARDTGLSVRIVQSR 139 (143)
Q Consensus 95 ~R~~~~~~q~~~L~~~f-~~~~~p~~~~~~~la~~~~l~~~~vkvW 139 (143)
.|..|+.++...+-... ... .....+|..+|+++.++..|
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W 43 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNW 43 (76)
T ss_dssp SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHH
Confidence 45677888777665554 332 36778999999999988888
No 90
>KOG0320|consensus
Probab=60.62 E-value=5.3 Score=26.48 Aligned_cols=37 Identities=16% Similarity=0.426 Sum_probs=28.6
Q ss_pred cCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437 30 VQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE 66 (143)
Q Consensus 30 ~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~ 66 (143)
..+++|..|......-..+.-+-|.+||..|....+.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk 165 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK 165 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHH
Confidence 3579999999887533346677899999999987664
No 91
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=60.04 E-value=5.8 Score=24.75 Aligned_cols=26 Identities=19% Similarity=0.461 Sum_probs=18.5
Q ss_pred CccccccCccccCCc--ceEEecCcccc
Q psy15437 4 VKKCLGCSEKLGPDE--LVMKTLDNVFH 29 (143)
Q Consensus 4 ~~~C~~C~~~i~~~~--~~~~~~~~~~h 29 (143)
...|..|+..|+++. ++++..|++|+
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEE
Confidence 347889999988874 55566677763
No 92
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=59.13 E-value=39 Score=21.99 Aligned_cols=77 Identities=12% Similarity=-0.009 Sum_probs=43.4
Q ss_pred CeeechhhHHHHHHHhhccCCCCCCccc-----cCCCCCCCCCC--CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHH
Q psy15437 53 GQLFCRPDYEKEVEMLQGYAQGIPFDLI-----TSSKSHDGRRG--PKRPRTILTTQQRRAFKASFEISPKPCRKVREGL 125 (143)
Q Consensus 53 ~~~~C~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~--~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~l 125 (143)
..-||..|-.++...|+.|+.+|.++.- .-..+...+.- .-...-.++...+..+...-+..--.+..+++.|
T Consensus 27 ~~~fC~kCG~~tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~~L~aa~el~ee~eeLs~deke~~ 106 (158)
T PF10083_consen 27 REKFCSKCGAKTITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTENALEAANELIEEDEELSPDEKEQF 106 (158)
T ss_pred HHHHHHHhhHHHHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHHHHHHHHHHHHHHhhcCCHHHHHHH
Confidence 4567888888888888888888874321 11111111111 1123445666666666655555555666677766
Q ss_pred HHHh
Q psy15437 126 ARDT 129 (143)
Q Consensus 126 a~~~ 129 (143)
...+
T Consensus 107 ~~sl 110 (158)
T PF10083_consen 107 KESL 110 (158)
T ss_pred Hhhh
Confidence 5544
No 93
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=58.87 E-value=9.3 Score=22.68 Aligned_cols=35 Identities=20% Similarity=0.506 Sum_probs=27.3
Q ss_pred CcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437 32 CFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE 66 (143)
Q Consensus 32 cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~ 66 (143)
--.|+.|++..-.|..+.+-..+-+|.+|..+...
T Consensus 49 Ga~CS~C~~~VC~~~~CSlFYtkrFC~pC~~~~~~ 83 (97)
T PF10170_consen 49 GAPCSICGKPVCVGQDCSLFYTKRFCLPCVKRNLK 83 (97)
T ss_pred CccccccCCceEcCCCccEEeeCceeHHHHHHHHH
Confidence 34689999988777777777788899999876554
No 94
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=58.40 E-value=7.6 Score=20.40 Aligned_cols=24 Identities=29% Similarity=0.580 Sum_probs=16.2
Q ss_pred ccccccCccccCCc--ceEEecCccc
Q psy15437 5 KKCLGCSEKLGPDE--LVMKTLDNVF 28 (143)
Q Consensus 5 ~~C~~C~~~i~~~~--~~~~~~~~~~ 28 (143)
..|..|+..|+++. +++..+++++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~ 29 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVF 29 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEE
Confidence 46888888888773 4455556555
No 95
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=57.67 E-value=8.6 Score=20.57 Aligned_cols=28 Identities=32% Similarity=0.778 Sum_probs=18.9
Q ss_pred CccccccCccccCCcceEEecCcccccCCcccccCCcc
Q psy15437 4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSR 41 (143)
Q Consensus 4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~ 41 (143)
..+|..|+..|.+.+..+ -|.|..|+..
T Consensus 7 ~~~CtSCg~~i~~~~~~~----------~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAV----------KFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCccC----------EeeCCCCCCe
Confidence 357999999998665322 1667777765
No 96
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=57.58 E-value=7.7 Score=19.18 Aligned_cols=36 Identities=25% Similarity=0.259 Sum_probs=16.3
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccce
Q psy15437 97 TILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137 (143)
Q Consensus 97 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vk 137 (143)
..++.++...++..+... ....++|..+|.++..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~ 38 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVS 38 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHH
Confidence 346667777777766544 245678999999987664
No 97
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=56.56 E-value=3.2 Score=19.96 Aligned_cols=17 Identities=24% Similarity=0.247 Sum_probs=13.3
Q ss_pred HHHHHHhCCCcccceec
Q psy15437 123 EGLARDTGLSVRIVQSR 139 (143)
Q Consensus 123 ~~la~~~~l~~~~vkvW 139 (143)
.++|..+|++.+.|+.|
T Consensus 3 ~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCCCHHHHHHH
Confidence 46789999999888877
No 98
>KOG3623|consensus
Probab=56.12 E-value=10 Score=30.96 Aligned_cols=52 Identities=13% Similarity=0.224 Sum_probs=34.4
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.+.+.++.+..++-..|...++.+-.+...+--..+..+...+.+|+|||++
T Consensus 625 ~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhs 676 (1007)
T KOG3623|consen 625 RPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHS 676 (1007)
T ss_pred CCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccC
Confidence 3445566666666667777776666555444444455567777889999987
No 99
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=55.77 E-value=10 Score=19.02 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceec
Q psy15437 98 ILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSR 139 (143)
Q Consensus 98 ~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvW 139 (143)
.++..+...+...|-.+. .-+++|..+|++...|+.+
T Consensus 4 ~L~~~er~vi~~~y~~~~-----t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL-----TLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC-----CHHHHHHHHCCcHHHHHHH
Confidence 356778888888883332 4668899999999877643
No 100
>KOG0823|consensus
Probab=54.95 E-value=24 Score=24.48 Aligned_cols=47 Identities=19% Similarity=0.303 Sum_probs=33.1
Q ss_pred ccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH------HhhccCCCCCC
Q psy15437 29 HVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE------MLQGYAQGIPF 77 (143)
Q Consensus 29 h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~------~~~~~~~~~~~ 77 (143)
...+|-|..|-..- .+...---|.+||.+|..+-+. -|++|...+..
T Consensus 44 ~~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 34568888887765 3557777899999999987653 24666665553
No 101
>cd01176 IPT_RBP-Jkappa IPT domain of the recombination signal Jkappa binding protein (RBP-Jkappa). RBP-J kappa, was initially considered to be involved in V(D)J recombination because of its DNA binding specificity and structural similarity to site-specific recombinases known as the integrase family. Further studies indicated that RBP-J kappa functions as a repressor of transcription, via destabilization of the general transcription factor IID and recruitment of histone deacetylase complexes.
Probab=53.66 E-value=5.4 Score=23.36 Aligned_cols=9 Identities=11% Similarity=-0.282 Sum_probs=6.4
Q ss_pred cceecccCC
Q psy15437 135 IVQSRPIPV 143 (143)
Q Consensus 135 ~vkvWFQn~ 143 (143)
.+||||.+|
T Consensus 32 nLkVWFG~v 40 (97)
T cd01176 32 NLKVWFGDV 40 (97)
T ss_pred CceEEECCc
Confidence 368888765
No 102
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=53.20 E-value=11 Score=20.13 Aligned_cols=27 Identities=22% Similarity=0.780 Sum_probs=18.5
Q ss_pred ccccCCccccCCCceEe-eCCeeechhh
Q psy15437 34 VCVVCGSRLQRGEQFVI-KQGQLFCRPD 60 (143)
Q Consensus 34 ~C~~C~~~l~~~~~~~~-~~~~~~C~~~ 60 (143)
.|..|++.|..+...++ ++...||...
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~E 45 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEE 45 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHH
Confidence 47788999975555554 4678888443
No 103
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=52.16 E-value=28 Score=16.93 Aligned_cols=32 Identities=19% Similarity=0.424 Sum_probs=15.8
Q ss_pred ccccCCccccCCCceEeeC-CeeechhhHHHHH
Q psy15437 34 VCVVCGSRLQRGEQFVIKQ-GQLFCRPDYEKEV 65 (143)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~-~~~~C~~~~~~~~ 65 (143)
.|+.|+++.........-. +..+|..|.....
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~~ 35 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQAY 35 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHHH
Confidence 4667777664333333333 5677877765543
No 104
>KOG1146|consensus
Probab=51.91 E-value=24 Score=30.81 Aligned_cols=53 Identities=15% Similarity=0.029 Sum_probs=47.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
-..++.++.+-.++...|.+.|-.+-.|....+.-|...-..+.+++++||+|
T Consensus 703 ~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~ 755 (1406)
T KOG1146|consen 703 PRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHN 755 (1406)
T ss_pred cccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcc
Confidence 33456788888899999999999999999999999999999999999999997
No 105
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=51.69 E-value=7.9 Score=19.29 Aligned_cols=27 Identities=33% Similarity=0.717 Sum_probs=17.1
Q ss_pred cccccCccccCCcceEEecCcccccCCcccccCCccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL 42 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l 42 (143)
+|..|+..+..++.. . -+.|..|+..+
T Consensus 5 ~C~~CG~~~~~~~~~----~------~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYG----T------GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCC----C------ceECCCCCCeE
Confidence 688888777533211 1 26788888766
No 106
>PHA03236 DNA packaging protein UL33; Provisional
Probab=51.36 E-value=15 Score=22.92 Aligned_cols=20 Identities=5% Similarity=-0.384 Sum_probs=13.1
Q ss_pred HHHHHh-CCCcccceecccCC
Q psy15437 124 GLARDT-GLSVRIVQSRPIPV 143 (143)
Q Consensus 124 ~la~~~-~l~~~~vkvWFQn~ 143 (143)
.|..++ .-+...+.|||.++
T Consensus 26 ~L~~~Y~~~~~~~~~iwFE~l 46 (127)
T PHA03236 26 ALEEKYLIDDDFQYRIWFEYL 46 (127)
T ss_pred HHHHHhccCCccceeeeeccc
Confidence 444444 33557899999875
No 107
>PF13518 HTH_28: Helix-turn-helix domain
Probab=49.96 E-value=6.4 Score=19.74 Aligned_cols=20 Identities=25% Similarity=0.202 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCcccceeccc
Q psy15437 122 REGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvWFQ 141 (143)
..++|..+|++..+|..|-+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHH
Confidence 45689999999999999865
No 108
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=49.79 E-value=13 Score=19.87 Aligned_cols=18 Identities=28% Similarity=0.193 Sum_probs=14.5
Q ss_pred HHHHHhCCCcccceeccc
Q psy15437 124 GLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 124 ~la~~~~l~~~~vkvWFQ 141 (143)
..|.+.|+++.+|+-|-+
T Consensus 30 Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 30 AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp HHHHHTTS-HHHHHHHHT
T ss_pred HHHHHhCccHHHHHHHHH
Confidence 359999999999999965
No 109
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=49.54 E-value=15 Score=17.87 Aligned_cols=38 Identities=24% Similarity=0.232 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceeccc
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQ 141 (143)
++..+...+...+... .....+|..+|++...|+.|..
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~ 48 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 4555666666555322 2356789999999998877753
No 110
>KOG3579|consensus
Probab=49.25 E-value=8.9 Score=27.47 Aligned_cols=31 Identities=26% Similarity=0.479 Sum_probs=18.5
Q ss_pred cccccCccccCCcceEEecCcccccCCccccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVV 37 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~ 37 (143)
+|..|++.+.... +++--.-.-|+-||-|+.
T Consensus 270 cCTLC~ERLEDTH-FVQCPSVp~HKFCFPCSR 300 (352)
T KOG3579|consen 270 CCTLCHERLEDTH-FVQCPSVPSHKFCFPCSR 300 (352)
T ss_pred eehhhhhhhccCc-eeecCCCcccceecccCH
Confidence 5667777776333 344445555777776654
No 111
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=47.03 E-value=5.2 Score=21.66 Aligned_cols=20 Identities=15% Similarity=0.132 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCcccceeccc
Q psy15437 122 REGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvWFQ 141 (143)
..++|..+|+++..++.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999998865
No 112
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=46.62 E-value=6.7 Score=21.10 Aligned_cols=20 Identities=5% Similarity=0.012 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCcccceeccc
Q psy15437 122 REGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvWFQ 141 (143)
..++|..+|+++..++.|-+
T Consensus 3 i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999998864
No 113
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=46.57 E-value=32 Score=17.93 Aligned_cols=32 Identities=22% Similarity=0.442 Sum_probs=23.3
Q ss_pred cccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE 66 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~ 66 (143)
|.|..|...+. .......|..||..+....+.
T Consensus 2 ~~Cpi~~~~~~--~Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMK--DPVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCC--CCEECCCCCEEeHHHHHHHHH
Confidence 46777777774 346666789999998887665
No 114
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=45.82 E-value=28 Score=14.98 Aligned_cols=36 Identities=19% Similarity=0.170 Sum_probs=22.4
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceec
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSR 139 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvW 139 (143)
++......+...+.... ....++..++++...|..|
T Consensus 6 ~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHh
Confidence 34555555555554332 3557788999998877666
No 115
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=45.16 E-value=11 Score=21.05 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=10.0
Q ss_pred cccccCccccCCc--ceEEecCccc
Q psy15437 6 KCLGCSEKLGPDE--LVMKTLDNVF 28 (143)
Q Consensus 6 ~C~~C~~~i~~~~--~~~~~~~~~~ 28 (143)
.|..|+..|+++. +++..+|+++
T Consensus 5 ~C~Fsg~~I~PG~G~~~Vr~DG~v~ 29 (71)
T PF01246_consen 5 KCSFSGYKIYPGHGKMYVRNDGKVF 29 (71)
T ss_dssp E-TTT-SEE-SSSSEEEE-TTS-EE
T ss_pred EecccCCccCCCCCeEEEecCCCeE
Confidence 5777777776663 3334444444
No 116
>PHA00626 hypothetical protein
Probab=44.53 E-value=15 Score=19.46 Aligned_cols=40 Identities=20% Similarity=0.518 Sum_probs=22.6
Q ss_pred cccccCc-cccCCcceEEecCcccccCCcccccCCccccCCCceEeeC
Q psy15437 6 KCLGCSE-KLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQ 52 (143)
Q Consensus 6 ~C~~C~~-~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~ 52 (143)
.|..|+. .|..... +.- |.+-+.|..|+-..+ .+.|..+.
T Consensus 2 ~CP~CGS~~Ivrcg~-cr~-----~snrYkCkdCGY~ft-~~~~~~~~ 42 (59)
T PHA00626 2 SCPKCGSGNIAKEKT-MRG-----WSDDYVCCDCGYNDS-KDAFGERG 42 (59)
T ss_pred CCCCCCCceeeeece-ecc-----cCcceEcCCCCCeec-hhhhhhcc
Confidence 5888887 3442222 111 344578999988773 44455443
No 117
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=43.36 E-value=4 Score=19.25 Aligned_cols=9 Identities=33% Similarity=0.922 Sum_probs=4.9
Q ss_pred ccccCcccc
Q psy15437 7 CLGCSEKLG 15 (143)
Q Consensus 7 C~~C~~~i~ 15 (143)
|..|+++|.
T Consensus 6 C~~CGe~I~ 14 (36)
T PF01258_consen 6 CEDCGEPIP 14 (36)
T ss_dssp -TTTSSBEE
T ss_pred ccccCChHH
Confidence 666666665
No 118
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=43.05 E-value=27 Score=16.48 Aligned_cols=14 Identities=21% Similarity=0.755 Sum_probs=9.8
Q ss_pred CCCccccccCcccc
Q psy15437 2 LYVKKCLGCSEKLG 15 (143)
Q Consensus 2 ~~~~~C~~C~~~i~ 15 (143)
.|.-+|..|+..+.
T Consensus 3 ~Y~y~C~~Cg~~fe 16 (41)
T smart00834 3 IYEYRCEDCGHTFE 16 (41)
T ss_pred CEEEEcCCCCCEEE
Confidence 45667888887664
No 119
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=42.54 E-value=22 Score=17.54 Aligned_cols=34 Identities=21% Similarity=0.221 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccce
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vk 137 (143)
++.++...+...+.... ....+|..+|++...|.
T Consensus 6 ~~~~~~~~i~~l~~~G~-----si~~IA~~~gvsr~Tvy 39 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEGM-----SIAEIAKQFGVSRSTVY 39 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHH
T ss_pred CCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHH
Confidence 44545555555565552 46688999999987654
No 120
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=42.49 E-value=11 Score=25.59 Aligned_cols=30 Identities=30% Similarity=0.616 Sum_probs=22.9
Q ss_pred cccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~ 63 (143)
-.|+.|+-.. ....-...+|++.|..|+..
T Consensus 173 v~C~kCGE~~-~e~~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELF-MEPRAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCccc-ccchhhhcCCceeccccccc
Confidence 4788999877 34545667899999999864
No 121
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=41.68 E-value=22 Score=17.68 Aligned_cols=8 Identities=25% Similarity=0.596 Sum_probs=4.3
Q ss_pred eechhhHH
Q psy15437 55 LFCRPDYE 62 (143)
Q Consensus 55 ~~C~~~~~ 62 (143)
.+|..||.
T Consensus 24 dLC~~Cf~ 31 (46)
T cd02249 24 DLCSSCYA 31 (46)
T ss_pred cCHHHHHC
Confidence 44555554
No 122
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=41.66 E-value=9.7 Score=17.96 Aligned_cols=32 Identities=16% Similarity=0.365 Sum_probs=16.9
Q ss_pred cccccCccccCCcceEEecCcccccCCcccccCCccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL 42 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l 42 (143)
.|..|+..+...+..+...+. -+.|..|+..+
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 578888766533221211111 25677777655
No 123
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=41.33 E-value=16 Score=23.26 Aligned_cols=43 Identities=21% Similarity=0.454 Sum_probs=24.5
Q ss_pred CccccccCccccCCcce-E--EecCccc--ccCCcccccCCccccCCC
Q psy15437 4 VKKCLGCSEKLGPDELV-M--KTLDNVF--HVQCFVCVVCGSRLQRGE 46 (143)
Q Consensus 4 ~~~C~~C~~~i~~~~~~-~--~~~~~~~--h~~cf~C~~C~~~l~~~~ 46 (143)
..+|..|+..+...+.- + .....++ +...+.|..|++-...|+
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGS 138 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccc
Confidence 35899999877433211 0 1112222 445678888888776554
No 124
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=41.12 E-value=8 Score=19.34 Aligned_cols=21 Identities=19% Similarity=0.090 Sum_probs=16.2
Q ss_pred HHHHHHHHhCCCcccceeccc
Q psy15437 121 VREGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQ 141 (143)
...++|..+|++...|.-|..
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 466889999999999988854
No 125
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=40.78 E-value=10 Score=18.17 Aligned_cols=6 Identities=0% Similarity=-0.590 Sum_probs=3.7
Q ss_pred eecccC
Q psy15437 137 QSRPIP 142 (143)
Q Consensus 137 kvWFQn 142 (143)
.||||.
T Consensus 27 TiWFqG 32 (39)
T PF09292_consen 27 TIWFQG 32 (39)
T ss_dssp EEEESS
T ss_pred EEEeeC
Confidence 567763
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=40.54 E-value=5.8 Score=25.77 Aligned_cols=29 Identities=28% Similarity=0.574 Sum_probs=19.5
Q ss_pred cccccCccccCCcceEEecCcccccCCcccccCCcccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQ 43 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 43 (143)
.|..|+...+.++. + . .-|.|..|+..|-
T Consensus 111 ~Cp~c~~r~tf~eA-~---~-----~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 111 ICPNMCVRFTFNEA-M---E-----LNFTCPRCGAMLD 139 (158)
T ss_pred ECCCCCcEeeHHHH-H---H-----cCCcCCCCCCEee
Confidence 48888877764442 2 2 2489999998873
No 127
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=40.42 E-value=10 Score=19.50 Aligned_cols=16 Identities=25% Similarity=0.364 Sum_probs=12.2
Q ss_pred HHHHHHHhCCCcccce
Q psy15437 122 REGLARDTGLSVRIVQ 137 (143)
Q Consensus 122 ~~~la~~~~l~~~~vk 137 (143)
-.+||..+|+++.||+
T Consensus 31 S~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 31 SQELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHhc
Confidence 4578999999998875
No 128
>PRK12495 hypothetical protein; Provisional
Probab=40.36 E-value=14 Score=25.38 Aligned_cols=23 Identities=30% Similarity=0.561 Sum_probs=11.1
Q ss_pred cccccCCccccCCCceEeeCCeeechhhH
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~ 61 (143)
+.|..|+.+|. ...|..+|..|-
T Consensus 43 ~hC~~CG~PIp------a~pG~~~Cp~CQ 65 (226)
T PRK12495 43 AHCDECGDPIF------RHDGQEFCPTCQ 65 (226)
T ss_pred hhcccccCccc------CCCCeeECCCCC
Confidence 44555555551 124555555553
No 129
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=40.08 E-value=8.6 Score=20.03 Aligned_cols=38 Identities=18% Similarity=0.212 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceeccc
Q psy15437 98 ILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 98 ~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQ 141 (143)
.+|..+...|....... ...++|..+++++..|+.+..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~ 40 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRR 40 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHH
Confidence 46667777666544444 366789999999888776544
No 130
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=39.93 E-value=23 Score=18.42 Aligned_cols=25 Identities=24% Similarity=0.697 Sum_probs=13.2
Q ss_pred ccccCCccccCCCceEeeCCeeechh
Q psy15437 34 VCVVCGSRLQRGEQFVIKQGQLFCRP 59 (143)
Q Consensus 34 ~C~~C~~~l~~~~~~~~~~~~~~C~~ 59 (143)
.|..|...++ ...-..++|+.||..
T Consensus 9 aC~~C~C~V~-~~~Ai~~dGk~YCS~ 33 (52)
T PF02069_consen 9 ACPSCSCVVS-EEEAIQKDGKYYCSE 33 (52)
T ss_dssp SSTT----B--TTTSEESSS-EESSH
T ss_pred cCCCCEeEEC-chHhHHhCCEeeecH
Confidence 5777888774 344677899999843
No 131
>COG3149 PulM Type II secretory pathway, component PulM [Intracellular trafficking and secretion]
Probab=39.88 E-value=12 Score=24.65 Aligned_cols=14 Identities=29% Similarity=0.079 Sum_probs=10.5
Q ss_pred CCCcccceecccCC
Q psy15437 130 GLSVRIVQSRPIPV 143 (143)
Q Consensus 130 ~l~~~~vkvWFQn~ 143 (143)
......||||||.|
T Consensus 123 ~~~ge~vQV~i~pv 136 (181)
T COG3149 123 DNRGEAVQVWIQPV 136 (181)
T ss_pred cCCCceEEEEeccC
Confidence 33556799999975
No 132
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=39.72 E-value=21 Score=19.49 Aligned_cols=29 Identities=24% Similarity=0.439 Sum_probs=18.4
Q ss_pred ccccccCccccCCcceEEecCcccccCCcccccCCc
Q psy15437 5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGS 40 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~ 40 (143)
.-|..|+..+. .+.+.+..|- +.|..|+.
T Consensus 7 KPCPFCG~~~~----~v~~~~g~~~---v~C~~CgA 35 (64)
T PRK09710 7 KPCPFCGCPSV----TVKAISGYYR---AKCNGCES 35 (64)
T ss_pred cCCCCCCCcee----EEEecCceEE---EEcCCCCc
Confidence 57999998776 3455565554 44555555
No 133
>KOG0978|consensus
Probab=39.26 E-value=6.4 Score=31.77 Aligned_cols=39 Identities=23% Similarity=0.510 Sum_probs=17.8
Q ss_pred cccccCCccccCCCceEeeCCeeechhhHHHHHH----HhhccCC
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE----MLQGYAQ 73 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~----~~~~~~~ 73 (143)
.+|+.|+..- -+.....-+.+||..|...+.+ +|+.|+.
T Consensus 644 LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~ 686 (698)
T KOG0978|consen 644 LKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETRQRKCPKCNA 686 (698)
T ss_pred eeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCC
Confidence 3555555321 1222333455666666554443 3555543
No 134
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=38.58 E-value=8.5 Score=18.65 Aligned_cols=19 Identities=16% Similarity=0.043 Sum_probs=14.0
Q ss_pred HHHHHHhCCCcccceeccc
Q psy15437 123 EGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 123 ~~la~~~~l~~~~vkvWFQ 141 (143)
.++|..+|++...|.-|-+
T Consensus 4 ~e~a~~lgvs~~tl~~~~~ 22 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVK 22 (49)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4678888888887777743
No 135
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=38.22 E-value=18 Score=26.50 Aligned_cols=40 Identities=13% Similarity=0.312 Sum_probs=24.6
Q ss_pred CCccccccCccccCCcceEEec-----Ccccc-----cCCcccccCCcccc
Q psy15437 3 YVKKCLGCSEKLGPDELVMKTL-----DNVFH-----VQCFVCVVCGSRLQ 43 (143)
Q Consensus 3 ~~~~C~~C~~~i~~~~~~~~~~-----~~~~h-----~~cf~C~~C~~~l~ 43 (143)
|..+|..|+..|+.+.. +.+. +-.|| .--++|..|...|.
T Consensus 39 f~i~C~~C~~~I~kG~r-FNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~ 88 (324)
T PF04502_consen 39 FNIWCNTCGEYIYKGVR-FNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIE 88 (324)
T ss_pred ccCcCCCCcccccccee-eeeeeEecCCCccccceEEEEEEEcCCCCCEEe
Confidence 77899999999975532 2222 21132 22467888887763
No 136
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=38.08 E-value=7.8 Score=25.73 Aligned_cols=29 Identities=31% Similarity=0.700 Sum_probs=18.8
Q ss_pred cccccCccccCCcceEEecCcccccCCcccccCCcccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQ 43 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 43 (143)
.|..|+.....++ |+. .-|.|..|+..|-
T Consensus 119 ~Cp~C~~rytf~e----A~~-----~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 119 FCPNCHIRFTFDE----AME-----YGFRCPQCGEMLE 147 (178)
T ss_pred ECCCCCcEEeHHH----Hhh-----cCCcCCCCCCCCe
Confidence 4778877776444 221 2488888888883
No 137
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=38.05 E-value=9.1 Score=21.47 Aligned_cols=22 Identities=14% Similarity=0.170 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCcccceecccC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn 142 (143)
..+++|..+|+++..|+.|+-+
T Consensus 34 S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 34 TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CHHHHHHHHCcCHHHHHHHHhc
Confidence 4678999999999999988643
No 138
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=37.46 E-value=11 Score=20.15 Aligned_cols=20 Identities=25% Similarity=0.210 Sum_probs=16.1
Q ss_pred HHHHHHHhCCCcccceeccc
Q psy15437 122 REGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 122 ~~~la~~~~l~~~~vkvWFQ 141 (143)
..++|..+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 34678999999999888864
No 139
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 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 entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=37.08 E-value=77 Score=20.83 Aligned_cols=40 Identities=20% Similarity=0.164 Sum_probs=32.4
Q ss_pred CCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccc
Q psy15437 95 PRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIV 136 (143)
Q Consensus 95 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v 136 (143)
....++.+++..+.+.-..+ |....+..||.+.|++..-|
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV 121 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFV 121 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHH
Confidence 34689999999998877776 56678999999999987543
No 140
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=36.50 E-value=30 Score=17.03 Aligned_cols=9 Identities=11% Similarity=0.430 Sum_probs=5.4
Q ss_pred eeechhhHH
Q psy15437 54 QLFCRPDYE 62 (143)
Q Consensus 54 ~~~C~~~~~ 62 (143)
..+|..||.
T Consensus 27 ~dlC~~Cf~ 35 (44)
T smart00291 27 YDLCQSCFA 35 (44)
T ss_pred ccchHHHHh
Confidence 345666665
No 141
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=35.99 E-value=22 Score=18.01 Aligned_cols=11 Identities=18% Similarity=0.329 Sum_probs=6.9
Q ss_pred ccccccCcccc
Q psy15437 5 KKCLGCSEKLG 15 (143)
Q Consensus 5 ~~C~~C~~~i~ 15 (143)
..|..|++.|.
T Consensus 12 ~~C~~C~~~i~ 22 (53)
T PF00130_consen 12 TYCDVCGKFIW 22 (53)
T ss_dssp EB-TTSSSBEC
T ss_pred CCCcccCcccC
Confidence 46777777773
No 142
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=34.98 E-value=66 Score=19.65 Aligned_cols=41 Identities=20% Similarity=0.041 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437 96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF 140 (143)
|..++.+....+-.....+.. ....+|..+|+++.+|.-|-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHH
Confidence 445666655433332222222 34578999999999998884
No 143
>PF11388 DotA: Phagosome trafficking protein DotA; InterPro: IPR021528 DotA is essential for intracellular growth in Legionella []. DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake [].
Probab=34.85 E-value=14 Score=21.72 Aligned_cols=8 Identities=0% Similarity=-0.371 Sum_probs=5.1
Q ss_pred ceecccCC
Q psy15437 136 VQSRPIPV 143 (143)
Q Consensus 136 vkvWFQn~ 143 (143)
+=+||||+
T Consensus 32 LC~WF~~~ 39 (105)
T PF11388_consen 32 LCTWFQNK 39 (105)
T ss_pred HHHHHccC
Confidence 44677774
No 144
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=34.81 E-value=37 Score=17.81 Aligned_cols=10 Identities=20% Similarity=0.783 Sum_probs=5.1
Q ss_pred cccccCcccc
Q psy15437 6 KCLGCSEKLG 15 (143)
Q Consensus 6 ~C~~C~~~i~ 15 (143)
+|..|+.+|.
T Consensus 3 ~CvVCKqpi~ 12 (54)
T PF10886_consen 3 ICVVCKQPID 12 (54)
T ss_pred eeeeeCCccC
Confidence 4555555554
No 145
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=34.50 E-value=23 Score=27.50 Aligned_cols=36 Identities=28% Similarity=0.554 Sum_probs=23.4
Q ss_pred cccccCccccCCcceEEecCcccccCCcccccCCcccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQ 43 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 43 (143)
.|..|-..+...+ ....+..-..+||.|-.|...|.
T Consensus 28 yCp~CL~~~p~~e--~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 28 YCPNCLFEVPSSE--ARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred ECccccccCChhh--heeccceeccccccCCCCCCcce
Confidence 4666665554332 23344445679999999999885
No 146
>PHA02768 hypothetical protein; Provisional
Probab=34.31 E-value=12 Score=19.71 Aligned_cols=39 Identities=15% Similarity=0.118 Sum_probs=24.0
Q ss_pred CCccccccCccccCCcceEEecCcccccCCcccccCCcccc
Q psy15437 3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQ 43 (143)
Q Consensus 3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 43 (143)
.+-.|..|++.....+....-+. -|..=++|..|++...
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r--~H~k~~kc~~C~k~f~ 42 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLR--KHNTNLKLSNCKRISL 42 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHH--hcCCcccCCcccceec
Confidence 45589999988874432221222 2555678888888654
No 147
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=34.17 E-value=20 Score=18.54 Aligned_cols=13 Identities=23% Similarity=0.508 Sum_probs=8.8
Q ss_pred CccccccCccccC
Q psy15437 4 VKKCLGCSEKLGP 16 (143)
Q Consensus 4 ~~~C~~C~~~i~~ 16 (143)
-.+|..|++.+..
T Consensus 4 eiRC~~CnklLa~ 16 (51)
T PF10122_consen 4 EIRCGHCNKLLAK 16 (51)
T ss_pred ceeccchhHHHhh
Confidence 4577888777753
No 148
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=33.89 E-value=37 Score=16.02 Aligned_cols=21 Identities=33% Similarity=0.714 Sum_probs=13.4
Q ss_pred ecCcccccCCcccccCCcccc
Q psy15437 23 TLDNVFHVQCFVCVVCGSRLQ 43 (143)
Q Consensus 23 ~~~~~~h~~cf~C~~C~~~l~ 43 (143)
..++.||-.-..|..|+..+.
T Consensus 12 p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 12 PSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp TTSTTTT-TT--BTTCC-SCC
T ss_pred CCCCcccCcCccCCCCCCCEE
Confidence 346788999889999998774
No 149
>PHA03225 DNA packaging protein UL33; Provisional
Probab=32.90 E-value=39 Score=21.07 Aligned_cols=10 Identities=0% Similarity=-0.256 Sum_probs=8.2
Q ss_pred ccceecccCC
Q psy15437 134 RIVQSRPIPV 143 (143)
Q Consensus 134 ~~vkvWFQn~ 143 (143)
..+.|||.++
T Consensus 41 ~~~~iwFe~m 50 (125)
T PHA03225 41 PRYEIWFFDL 50 (125)
T ss_pred ceEEEEeccc
Confidence 5789999875
No 150
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=32.79 E-value=28 Score=17.32 Aligned_cols=10 Identities=20% Similarity=0.464 Sum_probs=6.5
Q ss_pred cccccCcccc
Q psy15437 6 KCLGCSEKLG 15 (143)
Q Consensus 6 ~C~~C~~~i~ 15 (143)
+|+.|+..+.
T Consensus 4 ~C~~Cg~~~~ 13 (44)
T smart00659 4 ICGECGRENE 13 (44)
T ss_pred ECCCCCCEee
Confidence 4777776654
No 151
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=32.76 E-value=21 Score=30.53 Aligned_cols=51 Identities=22% Similarity=0.346 Sum_probs=29.4
Q ss_pred CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCC-ceEeeCCeeechhhH
Q psy15437 2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGE-QFVIKQGQLFCRPDY 61 (143)
Q Consensus 2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~-~~~~~~~~~~C~~~~ 61 (143)
+.++.|.-||..|. +.+.|..| -.|..|+-++-..+ +|-.++|.-.|.+|-
T Consensus 15 ~~~qiCqICGD~vg-----~~~~Ge~F----VAC~eC~FPVCrpCYEYEr~eG~q~CPqCk 66 (1079)
T PLN02638 15 GGGQVCQICGDNVG-----KTVDGEPF----VACDVCAFPVCRPCYEYERKDGNQSCPQCK 66 (1079)
T ss_pred cCCceeeecccccC-----cCCCCCEE----EEeccCCCccccchhhhhhhcCCccCCccC
Confidence 34568888887775 34556555 45666666664222 122345666666653
No 152
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.51 E-value=18 Score=17.09 Aligned_cols=30 Identities=23% Similarity=0.529 Sum_probs=14.8
Q ss_pred cccccCccccCCcceEEecCcccccCCcccccCCc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGS 40 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~ 40 (143)
.|..|+.....++..+...+.. .+|+.|+.
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~-----v~C~~C~~ 33 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRK-----VRCSKCGH 33 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcE-----EECCCCCC
Confidence 4777776554443333333321 45666654
No 153
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=32.44 E-value=15 Score=21.50 Aligned_cols=28 Identities=32% Similarity=0.414 Sum_probs=18.6
Q ss_pred HHHHHhhhcCCCCCHHHHHHHHHHhCCCcccc
Q psy15437 105 RAFKASFEISPKPCRKVREGLARDTGLSVRIV 136 (143)
Q Consensus 105 ~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v 136 (143)
..|+..|...-+. .+.+|..|++++..|
T Consensus 13 ~ELq~nf~~~~ls----~~~ia~dL~~s~~~l 40 (89)
T PF10078_consen 13 QELQANFELSGLS----LEQIAADLGTSPEHL 40 (89)
T ss_pred HHHHHHHHHcCCC----HHHHHHHhCCCHHHH
Confidence 3566667666544 567788888887544
No 154
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=31.93 E-value=36 Score=16.96 Aligned_cols=29 Identities=14% Similarity=0.468 Sum_probs=14.6
Q ss_pred cccccCccccCCcceE-EecCcccccCCcc
Q psy15437 6 KCLGCSEKLGPDELVM-KTLDNVFHVQCFV 34 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~-~~~~~~~h~~cf~ 34 (143)
+|..|+..-..++++. ..=+..||..|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTST
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCC
Confidence 3667777333223222 2224567777754
No 155
>PLN02400 cellulose synthase
Probab=31.85 E-value=35 Score=29.31 Aligned_cols=49 Identities=22% Similarity=0.477 Sum_probs=25.9
Q ss_pred CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCC-ceEeeCCeeechhh
Q psy15437 3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGE-QFVIKQGQLFCRPD 60 (143)
Q Consensus 3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~-~~~~~~~~~~C~~~ 60 (143)
.++.|.-|+..|. +++.|..| -.|..|.-++-..+ +|-.++|.-.|.+|
T Consensus 35 ~gqiCqICGD~VG-----~t~dGe~F----VAC~eCaFPVCRpCYEYERkeGnq~CPQC 84 (1085)
T PLN02400 35 NGQICQICGDDVG-----VTETGDVF----VACNECAFPVCRPCYEYERKDGTQCCPQC 84 (1085)
T ss_pred CCceeeecccccC-----cCCCCCEE----EEEccCCCccccchhheecccCCccCccc
Confidence 4567888877664 23455554 34555555553222 22333566666555
No 156
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=31.50 E-value=15 Score=19.73 Aligned_cols=18 Identities=28% Similarity=0.355 Sum_probs=14.4
Q ss_pred HHHHHHhCCCcccceecc
Q psy15437 123 EGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 123 ~~la~~~~l~~~~vkvWF 140 (143)
.++|..+|+++..++.|-
T Consensus 4 ~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 467888999998888773
No 157
>PRK10072 putative transcriptional regulator; Provisional
Probab=31.13 E-value=53 Score=19.44 Aligned_cols=37 Identities=16% Similarity=0.194 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceeccc
Q psy15437 98 ILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 98 ~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQ 141 (143)
..+...+..|...-.. ...+||..+|++...|.-|.+
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHc
Confidence 4466656665443222 256789999999999998875
No 158
>PF14279 HNH_5: HNH endonuclease
Probab=30.66 E-value=18 Score=20.13 Aligned_cols=36 Identities=17% Similarity=0.595 Sum_probs=21.6
Q ss_pred ccccCccccCC-----cceEEecCcccccCCcccccCCcccc
Q psy15437 7 CLGCSEKLGPD-----ELVMKTLDNVFHVQCFVCVVCGSRLQ 43 (143)
Q Consensus 7 C~~C~~~i~~~-----~~~~~~~~~~~h~~cf~C~~C~~~l~ 43 (143)
|..|++..... ..+..+.|..++... .|..|+..++
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~-vC~~CN~~~g 41 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN-VCDKCNNKFG 41 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc-hhHHHhHHHh
Confidence 66777766422 223345566666665 7777777773
No 159
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=30.46 E-value=25 Score=19.04 Aligned_cols=9 Identities=22% Similarity=1.084 Sum_probs=4.0
Q ss_pred cccccCccc
Q psy15437 6 KCLGCSEKL 14 (143)
Q Consensus 6 ~C~~C~~~i 14 (143)
+|..||+.|
T Consensus 6 RCFTCGkvi 14 (62)
T PRK04016 6 RCFTCGKVI 14 (62)
T ss_pred EecCCCCCh
Confidence 444444444
No 160
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=30.37 E-value=32 Score=17.70 Aligned_cols=14 Identities=7% Similarity=-0.069 Sum_probs=7.5
Q ss_pred EeeCCeeechhhHH
Q psy15437 49 VIKQGQLFCRPDYE 62 (143)
Q Consensus 49 ~~~~~~~~C~~~~~ 62 (143)
+.+.++.+|..|..
T Consensus 32 A~H~dR~~CGkCgy 45 (51)
T COG1998 32 ADHKDRWACGKCGY 45 (51)
T ss_pred hhcCceeEeccccc
Confidence 44455666655543
No 161
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=30.24 E-value=51 Score=16.35 Aligned_cols=11 Identities=18% Similarity=0.392 Sum_probs=7.3
Q ss_pred CeeechhhHHH
Q psy15437 53 GQLFCRPDYEK 63 (143)
Q Consensus 53 ~~~~C~~~~~~ 63 (143)
+..+|..||..
T Consensus 27 d~dLC~~C~~~ 37 (46)
T PF00569_consen 27 DYDLCEDCFSK 37 (46)
T ss_dssp S-EEEHHHHHH
T ss_pred CCchhhHHHhC
Confidence 35678888865
No 162
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=29.72 E-value=54 Score=14.57 Aligned_cols=10 Identities=30% Similarity=0.617 Sum_probs=6.3
Q ss_pred cccccCcccc
Q psy15437 6 KCLGCSEKLG 15 (143)
Q Consensus 6 ~C~~C~~~i~ 15 (143)
.|..|++.+.
T Consensus 2 ~C~~C~~~~~ 11 (30)
T PF03107_consen 2 WCDVCRRKID 11 (30)
T ss_pred CCCCCCCCcC
Confidence 4667766665
No 163
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=29.21 E-value=45 Score=20.86 Aligned_cols=37 Identities=14% Similarity=0.096 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF 140 (143)
++..+...+...|-.+. ..+++|..+|++...|+.|.
T Consensus 107 L~~~~r~ii~l~~~~~~-----s~~EIA~~l~is~~tV~~~~ 143 (154)
T PRK06759 107 LDEKEKYIIFERFFVGK-----TMGEIALETEMTYYQVRWIY 143 (154)
T ss_pred CCHHHHHHHHHHHhcCC-----CHHHHHHHHCCCHHHHHHHH
Confidence 44455555544443332 46688999999999888764
No 164
>PF12773 DZR: Double zinc ribbon
Probab=29.10 E-value=57 Score=16.22 Aligned_cols=9 Identities=33% Similarity=1.006 Sum_probs=3.9
Q ss_pred ccccCCccc
Q psy15437 34 VCVVCGSRL 42 (143)
Q Consensus 34 ~C~~C~~~l 42 (143)
.|..|+..+
T Consensus 31 ~C~~Cg~~~ 39 (50)
T PF12773_consen 31 ICPNCGAEN 39 (50)
T ss_pred CCcCCcCCC
Confidence 344444443
No 165
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=29.00 E-value=12 Score=18.78 Aligned_cols=19 Identities=32% Similarity=0.314 Sum_probs=13.1
Q ss_pred HHHHHhCCCcccceecccC
Q psy15437 124 GLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 124 ~la~~~~l~~~~vkvWFQn 142 (143)
.||..+|++...|.-|+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 4677778877777666554
No 166
>PHA02955 hypothetical protein; Provisional
Probab=29.00 E-value=83 Score=21.64 Aligned_cols=41 Identities=10% Similarity=0.094 Sum_probs=28.7
Q ss_pred HHHHHHHHhhhcC-CCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 102 QQRRAFKASFEIS-PKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 102 ~q~~~L~~~f~~~-~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
.++..|-..+.+. -..+..+++.++.++|.....|.-||++
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 3455555555443 3455667889999999999777888875
No 167
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=28.81 E-value=76 Score=15.52 Aligned_cols=36 Identities=19% Similarity=0.347 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF 140 (143)
++..+...+.. +... ....++|..++++...|..|.
T Consensus 4 l~~~e~~i~~~-~~~g-----~s~~eia~~l~is~~tv~~~~ 39 (58)
T smart00421 4 LTPREREVLRL-LAEG-----LTNKEIAERLGISEKTVKTHL 39 (58)
T ss_pred CCHHHHHHHHH-HHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 45566665544 3222 135678999999998877664
No 168
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=28.20 E-value=35 Score=18.37 Aligned_cols=9 Identities=22% Similarity=1.084 Sum_probs=3.5
Q ss_pred cccccCccc
Q psy15437 6 KCLGCSEKL 14 (143)
Q Consensus 6 ~C~~C~~~i 14 (143)
+|..||+.|
T Consensus 6 RCFTCGkvi 14 (60)
T PF01194_consen 6 RCFTCGKVI 14 (60)
T ss_dssp S-STTTSBT
T ss_pred ecCCCCCCh
Confidence 444444444
No 169
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=28.03 E-value=22 Score=17.38 Aligned_cols=16 Identities=38% Similarity=0.430 Sum_probs=11.6
Q ss_pred HHHHHHHhCCCcccce
Q psy15437 122 REGLARDTGLSVRIVQ 137 (143)
Q Consensus 122 ~~~la~~~~l~~~~vk 137 (143)
-..||..+|+++..|.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 4578999999987653
No 170
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=28.00 E-value=37 Score=17.83 Aligned_cols=31 Identities=16% Similarity=0.190 Sum_probs=19.8
Q ss_pred HHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccce
Q psy15437 103 QRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137 (143)
Q Consensus 103 q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vk 137 (143)
|+..|+--+. +..... ..||..++++++.|+
T Consensus 7 q~~Ll~~L~~-~~~~~~---~ela~~l~~S~rti~ 37 (59)
T PF08280_consen 7 QLKLLELLLK-NKWITL---KELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHH-HTSBBH---HHHHHHCTS-HHHHH
T ss_pred HHHHHHHHHc-CCCCcH---HHHHHHHCCCHHHHH
Confidence 4555555566 444433 378999999998765
No 171
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=27.77 E-value=49 Score=16.79 Aligned_cols=9 Identities=22% Similarity=0.272 Sum_probs=5.3
Q ss_pred eechhhHHH
Q psy15437 55 LFCRPDYEK 63 (143)
Q Consensus 55 ~~C~~~~~~ 63 (143)
.+|..||..
T Consensus 27 DlC~~C~~~ 35 (48)
T cd02341 27 DLCQDCVVK 35 (48)
T ss_pred ccCHHHHhC
Confidence 456666653
No 172
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=27.63 E-value=68 Score=21.74 Aligned_cols=31 Identities=32% Similarity=0.663 Sum_probs=21.1
Q ss_pred CCcccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437 31 QCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63 (143)
Q Consensus 31 ~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~ 63 (143)
..|.|..|...+. +.....-|..||..|...
T Consensus 17 ~~~~CpICld~~~--dPVvT~CGH~FC~~CI~~ 47 (193)
T PLN03208 17 GDFDCNICLDQVR--DPVVTLCGHLFCWPCIHK 47 (193)
T ss_pred CccCCccCCCcCC--CcEEcCCCchhHHHHHHH
Confidence 3477788877663 335555788888888764
No 173
>PTZ00044 ubiquitin; Provisional
Probab=27.62 E-value=56 Score=17.79 Aligned_cols=22 Identities=18% Similarity=0.258 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCcccceecccC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn 142 (143)
-++.++..+|++....+.||..
T Consensus 26 lK~~i~~~~gi~~~~q~L~~~g 47 (76)
T PTZ00044 26 VKMALQEKEGIDVKQIRLIYSG 47 (76)
T ss_pred HHHHHHHHHCCCHHHeEEEECC
Confidence 4566888999999888888863
No 174
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=27.13 E-value=55 Score=18.89 Aligned_cols=18 Identities=11% Similarity=-0.032 Sum_probs=13.7
Q ss_pred HHHHHHHHhCCCcccceecccC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn 142 (143)
+.-.+|..+|++. -|||.
T Consensus 25 ELHafA~riGv~r----r~fq~ 42 (83)
T PF13223_consen 25 ELHAFAARIGVPR----RWFQR 42 (83)
T ss_pred HHHHHHHHcCCCH----HHHcC
Confidence 4445799999998 58885
No 175
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=27.09 E-value=79 Score=14.75 Aligned_cols=30 Identities=33% Similarity=0.675 Sum_probs=17.7
Q ss_pred cccCCccccCCCc-eEeeCCeeechhhHHHHHH
Q psy15437 35 CVVCGSRLQRGEQ-FVIKQGQLFCRPDYEKEVE 66 (143)
Q Consensus 35 C~~C~~~l~~~~~-~~~~~~~~~C~~~~~~~~~ 66 (143)
|..|...+. .. ....-|..||..|..+.+.
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHH
Confidence 344555442 23 3445688899888877664
No 176
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=26.90 E-value=23 Score=18.02 Aligned_cols=17 Identities=29% Similarity=0.497 Sum_probs=12.3
Q ss_pred HHHHHHHHhCCCcccce
Q psy15437 121 VREGLARDTGLSVRIVQ 137 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vk 137 (143)
..++||..++++.+.|+
T Consensus 17 t~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 17 TAKELAEELGVSRRTIR 33 (55)
T ss_dssp EHHHHHHHCTS-HHHHH
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 35578999999987654
No 177
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=26.66 E-value=62 Score=16.21 Aligned_cols=29 Identities=21% Similarity=0.572 Sum_probs=15.6
Q ss_pred ccccCCccccCCCceE-ee-CCeeechhhHHH
Q psy15437 34 VCVVCGSRLQRGEQFV-IK-QGQLFCRPDYEK 63 (143)
Q Consensus 34 ~C~~C~~~l~~~~~~~-~~-~~~~~C~~~~~~ 63 (143)
.|..|+.-+. ...+. .+ .+..+|..||.+
T Consensus 2 ~C~~Cg~D~t-~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCT-RVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccC-ceEEEecCCCccccChHHHhC
Confidence 4556666553 22232 11 246778888864
No 178
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=26.62 E-value=23 Score=23.26 Aligned_cols=43 Identities=26% Similarity=0.480 Sum_probs=25.8
Q ss_pred CccccccCccccCC--cceE-EecCcc--cccCCcccccCCccccCCC
Q psy15437 4 VKKCLGCSEKLGPD--ELVM-KTLDNV--FHVQCFVCVVCGSRLQRGE 46 (143)
Q Consensus 4 ~~~C~~C~~~i~~~--~~~~-~~~~~~--~h~~cf~C~~C~~~l~~~~ 46 (143)
..+|..|+..+... +.+. .....+ .|..+..|..|++.-..|.
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~Gs 144 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGS 144 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCch
Confidence 35899999888532 1111 111112 3667788999988776655
No 179
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=26.55 E-value=25 Score=14.10 Aligned_cols=11 Identities=27% Similarity=1.102 Sum_probs=6.8
Q ss_pred cccccCCcccc
Q psy15437 33 FVCVVCGSRLQ 43 (143)
Q Consensus 33 f~C~~C~~~l~ 43 (143)
|.|..|++...
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 45677776653
No 180
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.54 E-value=69 Score=14.82 Aligned_cols=8 Identities=13% Similarity=0.081 Sum_probs=3.3
Q ss_pred CCeeechh
Q psy15437 52 QGQLFCRP 59 (143)
Q Consensus 52 ~~~~~C~~ 59 (143)
++..+|..
T Consensus 19 ~~~~~C~~ 26 (33)
T PF08792_consen 19 DDYEVCIF 26 (33)
T ss_pred CCeEEccc
Confidence 34444433
No 181
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=26.52 E-value=60 Score=17.74 Aligned_cols=22 Identities=14% Similarity=0.024 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCcccceecccC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn 142 (143)
-++.++...|++..+.+.||..
T Consensus 24 lK~~i~~~~gip~~~q~Li~~G 45 (74)
T cd01793 24 IKAHVAGLEGIDVEDQVLLLAG 45 (74)
T ss_pred HHHHHHhhhCCCHHHEEEEECC
Confidence 4556888889999888888864
No 182
>PF13730 HTH_36: Helix-turn-helix domain
Probab=26.37 E-value=42 Score=16.96 Aligned_cols=19 Identities=47% Similarity=0.588 Sum_probs=15.1
Q ss_pred HHHHHHHHhCCCcccceec
Q psy15437 121 VREGLARDTGLSVRIVQSR 139 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvW 139 (143)
..+.||..+|++.+.|+-+
T Consensus 27 S~~~la~~~g~s~~Tv~~~ 45 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRA 45 (55)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5668999999998877644
No 183
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=26.35 E-value=5 Score=23.70 Aligned_cols=15 Identities=33% Similarity=0.811 Sum_probs=6.3
Q ss_pred cccCCcccccCCccc
Q psy15437 28 FHVQCFVCVVCGSRL 42 (143)
Q Consensus 28 ~h~~cf~C~~C~~~l 42 (143)
+++.+..|..|...|
T Consensus 58 ~~~~~iiCGvC~~~L 72 (105)
T COG4357 58 FNPKAIICGVCRKLL 72 (105)
T ss_pred cCCccEEhhhhhhhh
Confidence 344444444444444
No 184
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=25.98 E-value=77 Score=19.19 Aligned_cols=39 Identities=18% Similarity=0.204 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcc
Q psy15437 96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVR 134 (143)
Q Consensus 96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~ 134 (143)
+-.++....+.|+..|-..+..--..|+++|.+.|+.+.
T Consensus 93 kyflsesgmeelqdrfmns~st~yrwrke~a~kfgvr~p 131 (143)
T PRK15183 93 KYFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREP 131 (143)
T ss_pred hhhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCC
Confidence 345677777888888888877777789999999998764
No 185
>KOG0773|consensus
Probab=25.63 E-value=34 Score=25.09 Aligned_cols=32 Identities=22% Similarity=0.176 Sum_probs=27.4
Q ss_pred hhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437 111 FEISPKPCRKVREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 111 f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn 142 (143)
-..++|+...+...++..+.++..++.+||=|
T Consensus 116 ~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~ 147 (342)
T KOG0773|consen 116 HRLNPYPSKLEKILLAVITKLTLTQVSTWFAN 147 (342)
T ss_pred hhhccCchHHHHHHHHHHHHhhhhhHHHHHHH
Confidence 45688999999999999999999998899843
No 186
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.63 E-value=71 Score=19.48 Aligned_cols=7 Identities=29% Similarity=0.833 Sum_probs=4.0
Q ss_pred cccccCc
Q psy15437 6 KCLGCSE 12 (143)
Q Consensus 6 ~C~~C~~ 12 (143)
+|..|+.
T Consensus 72 ~C~~Cg~ 78 (114)
T PRK03681 72 WCETCQQ 78 (114)
T ss_pred EcccCCC
Confidence 4666654
No 187
>PF13309 HTH_22: HTH domain
Probab=25.52 E-value=1e+02 Score=16.51 Aligned_cols=34 Identities=18% Similarity=0.164 Sum_probs=23.9
Q ss_pred HHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccc
Q psy15437 103 QRRAFKASFEISPKPCRKVREGLARDTGLSVRIV 136 (143)
Q Consensus 103 q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v 136 (143)
.+..+...++..-|--......+|..||+++..|
T Consensus 26 k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TV 59 (64)
T PF13309_consen 26 KKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATV 59 (64)
T ss_pred HHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHH
Confidence 3445555566666666667888999999998654
No 188
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=25.29 E-value=33 Score=21.19 Aligned_cols=23 Identities=26% Similarity=0.255 Sum_probs=19.2
Q ss_pred CCHHHHHHHHHHhCCCcccceec
Q psy15437 117 PCRKVREGLARDTGLSVRIVQSR 139 (143)
Q Consensus 117 p~~~~~~~la~~~~l~~~~vkvW 139 (143)
++...|+.||..++++...|.-|
T Consensus 27 ~~~~~r~~La~~~~i~~~~l~~w 49 (122)
T PF14229_consen 27 DTPLGRKALAKKLGISERNLLKW 49 (122)
T ss_pred CCHHHHHHHHHhcCCCHHHHHHH
Confidence 55567888999999999988887
No 189
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=25.08 E-value=73 Score=20.70 Aligned_cols=20 Identities=15% Similarity=0.197 Sum_probs=16.3
Q ss_pred HHHHHHHHhCCCcccceecc
Q psy15437 121 VREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWF 140 (143)
..+++|..+|++...|++|-
T Consensus 151 s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred CHHHHHHHHCCChhhHHHHH
Confidence 45678999999999888764
No 190
>PHA03229 DNA packaging protein UL33; Provisional
Probab=25.06 E-value=79 Score=19.92 Aligned_cols=10 Identities=0% Similarity=-0.426 Sum_probs=7.6
Q ss_pred ccceecccCC
Q psy15437 134 RIVQSRPIPV 143 (143)
Q Consensus 134 ~~vkvWFQn~ 143 (143)
....|||.++
T Consensus 43 ~~~~iwFE~l 52 (132)
T PHA03229 43 GDAAVWFEDL 52 (132)
T ss_pred cceeeeeccc
Confidence 4678999874
No 191
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=25.01 E-value=25 Score=21.00 Aligned_cols=28 Identities=32% Similarity=0.484 Sum_probs=13.7
Q ss_pred cccccCCccccCCCceEeeCCeeechhh
Q psy15437 33 FVCVVCGSRLQRGEQFVIKQGQLFCRPD 60 (143)
Q Consensus 33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~ 60 (143)
|+|+.|=---.....-...+|.++|..|
T Consensus 71 FTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 71 FTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred eeeeeeeeEechhhhccccCCCEecccc
Confidence 6666664322111111234577777665
No 192
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=24.93 E-value=31 Score=13.55 Aligned_cols=10 Identities=40% Similarity=1.275 Sum_probs=4.8
Q ss_pred cccccCCccc
Q psy15437 33 FVCVVCGSRL 42 (143)
Q Consensus 33 f~C~~C~~~l 42 (143)
|.|..|+..+
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 4566676655
No 193
>PRK00118 putative DNA-binding protein; Validated
Probab=24.93 E-value=67 Score=19.36 Aligned_cols=37 Identities=19% Similarity=0.122 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF 140 (143)
++..+...+...|.... ...++|..+|+++..|..|.
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L 54 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNI 54 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHH
Confidence 45556666655544432 45678999999998887764
No 194
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=24.92 E-value=68 Score=21.15 Aligned_cols=37 Identities=19% Similarity=0.219 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF 140 (143)
++..+...+...|-.+ ..-+++|..+|++...|+++.
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l 179 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRM 179 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHH
Confidence 4455555554443322 245678999999999888764
No 195
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=24.74 E-value=67 Score=17.46 Aligned_cols=22 Identities=9% Similarity=-0.035 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCcccceecccC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn 142 (143)
.++.++...|++..+.+.||..
T Consensus 25 lK~~I~~~~gip~~~q~Li~~G 46 (71)
T cd01796 25 FKALCEAESGIPASQQQLIYNG 46 (71)
T ss_pred HHHHHHHHhCCCHHHeEEEECC
Confidence 4556788889999888888863
No 196
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=24.45 E-value=34 Score=14.02 Aligned_cols=11 Identities=27% Similarity=0.957 Sum_probs=7.2
Q ss_pred cccccCCcccc
Q psy15437 33 FVCVVCGSRLQ 43 (143)
Q Consensus 33 f~C~~C~~~l~ 43 (143)
|.|..|+..+.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 45777777664
No 197
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.43 E-value=89 Score=18.24 Aligned_cols=35 Identities=17% Similarity=0.523 Sum_probs=22.3
Q ss_pred ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEe
Q psy15437 5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVI 50 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~ 50 (143)
..|..|+.... ......+| .|..|+..+ .|..+..
T Consensus 36 ~~Cp~C~~~~V-----kR~a~GIW-----~C~kCg~~f-AGgay~P 70 (89)
T COG1997 36 HVCPFCGRTTV-----KRIATGIW-----KCRKCGAKF-AGGAYTP 70 (89)
T ss_pred CcCCCCCCcce-----eeeccCeE-----EcCCCCCee-ccccccc
Confidence 46899988753 23333444 788898888 4554544
No 198
>PF06032 DUF917: Protein of unknown function (DUF917); InterPro: IPR010318 This family consists of hypothetical bacterial and archaeal proteins of unknown function.; PDB: 2O3I_B.
Probab=24.42 E-value=29 Score=25.75 Aligned_cols=11 Identities=9% Similarity=-0.112 Sum_probs=8.4
Q ss_pred CcccceecccC
Q psy15437 132 SVRIVQSRPIP 142 (143)
Q Consensus 132 ~~~~vkvWFQn 142 (143)
..+.++|||||
T Consensus 267 ~~~~~~i~fqN 277 (353)
T PF06032_consen 267 KGRTLRIEFQN 277 (353)
T ss_dssp TTEEEEEEESS
T ss_pred CCCEEEEEEEc
Confidence 45668899998
No 199
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=24.23 E-value=96 Score=14.99 Aligned_cols=29 Identities=24% Similarity=0.576 Sum_probs=18.4
Q ss_pred cccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437 35 CVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV 65 (143)
Q Consensus 35 C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~ 65 (143)
|..|...+. +.....-|..||..|..+..
T Consensus 1 CpiC~~~~~--~Pv~l~CGH~FC~~Cl~~~~ 29 (42)
T PF15227_consen 1 CPICLDLFK--DPVSLPCGHSFCRSCLERLW 29 (42)
T ss_dssp ETTTTSB-S--SEEE-SSSSEEEHHHHHHHH
T ss_pred CCccchhhC--CccccCCcCHHHHHHHHHHH
Confidence 445666553 45666778889988877654
No 200
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=24.12 E-value=71 Score=17.13 Aligned_cols=22 Identities=14% Similarity=0.152 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCcccceecccC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn 142 (143)
-++.++.+.|++..+.+.||..
T Consensus 24 lK~~i~~~~gi~~~~q~Li~~G 45 (70)
T cd01798 24 LKEVVAKRQGVPPDQLRVIFAG 45 (70)
T ss_pred HHHHHHHHHCCCHHHeEEEECC
Confidence 4566888999998888888753
No 201
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=23.91 E-value=40 Score=15.56 Aligned_cols=16 Identities=31% Similarity=0.430 Sum_probs=10.6
Q ss_pred HHHHHHHHhCCCcccc
Q psy15437 121 VREGLARDTGLSVRIV 136 (143)
Q Consensus 121 ~~~~la~~~~l~~~~v 136 (143)
.++.+|..+|++...|
T Consensus 4 tr~diA~~lG~t~ETV 19 (32)
T PF00325_consen 4 TRQDIADYLGLTRETV 19 (32)
T ss_dssp -HHHHHHHHTS-HHHH
T ss_pred CHHHHHHHhCCcHHHH
Confidence 3677899999887543
No 202
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=23.74 E-value=44 Score=23.06 Aligned_cols=32 Identities=25% Similarity=0.384 Sum_probs=21.6
Q ss_pred ccCCcccccCCccccCCCceEeeCCeeechhhH
Q psy15437 29 HVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61 (143)
Q Consensus 29 h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~ 61 (143)
-++-..|..|+..+. ...|...+|.++|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~-~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGD-HRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCC-ceEEecccCCccccccc
Confidence 344457888888773 34456678888887774
No 203
>PLN02436 cellulose synthase A
Probab=23.54 E-value=44 Score=28.74 Aligned_cols=12 Identities=17% Similarity=0.598 Sum_probs=6.9
Q ss_pred CccccccCcccc
Q psy15437 4 VKKCLGCSEKLG 15 (143)
Q Consensus 4 ~~~C~~C~~~i~ 15 (143)
++.|.-|+..|.
T Consensus 36 ~~iCqICGD~Vg 47 (1094)
T PLN02436 36 GQTCQICGDEIE 47 (1094)
T ss_pred CccccccccccC
Confidence 346666665553
No 204
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.53 E-value=21 Score=22.79 Aligned_cols=33 Identities=36% Similarity=0.634 Sum_probs=17.6
Q ss_pred cccccCccccCCcceEEecCcccccCCcccccCCccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL 42 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l 42 (143)
.|..|+......+. +...+ . ..-|.|..|+..|
T Consensus 101 ~Cp~C~~~y~~~ea-~~~~d--~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 101 KCPNCQSKYTFLEA-NQLLD--M-DGTFTCPRCGEEL 133 (147)
T ss_pred ECcCCCCEeeHHHH-HHhcC--C-CCcEECCCCCCEE
Confidence 47777766654331 11111 0 2227777777776
No 205
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.47 E-value=35 Score=16.10 Aligned_cols=12 Identities=17% Similarity=0.625 Sum_probs=7.1
Q ss_pred cccccCccccCC
Q psy15437 6 KCLGCSEKLGPD 17 (143)
Q Consensus 6 ~C~~C~~~i~~~ 17 (143)
.|..|+......
T Consensus 4 ~CP~C~~~f~v~ 15 (37)
T PF13719_consen 4 TCPNCQTRFRVP 15 (37)
T ss_pred ECCCCCceEEcC
Confidence 477776655433
No 206
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=23.46 E-value=31 Score=17.94 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=16.4
Q ss_pred cccccCccccCCcceEEecCcccccCCccc
Q psy15437 6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVC 35 (143)
Q Consensus 6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C 35 (143)
.|..||..+... .-....++.|-..|-.|
T Consensus 2 ~CPyCge~~~~~-iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEIL-IDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEEE-EecCCCCeeEEeehhhc
Confidence 588899888522 11133355566666544
No 207
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=23.35 E-value=52 Score=28.12 Aligned_cols=30 Identities=23% Similarity=0.469 Sum_probs=19.8
Q ss_pred ccccccCccccCCcceEEe-------c---CcccccCCcc
Q psy15437 5 KKCLGCSEKLGPDELVMKT-------L---DNVFHVQCFV 34 (143)
Q Consensus 5 ~~C~~C~~~i~~~~~~~~~-------~---~~~~h~~cf~ 34 (143)
..|..|...|..++.-+.. . ...||..||.
T Consensus 18 s~Ck~C~~~I~K~~lRi~~~v~~~~~dg~~~~W~H~~Cf~ 57 (981)
T PLN03123 18 SSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCIL 57 (981)
T ss_pred ccccccCCcccCCCeEEEEeecccccCCCCCeeecccccc
Confidence 4799999999866522211 1 2356899985
No 208
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=22.98 E-value=27 Score=17.43 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCCcccceecc
Q psy15437 121 VREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWF 140 (143)
...++|..++++...|+.|.
T Consensus 17 s~~eia~~l~~s~~tv~~~~ 36 (57)
T cd06170 17 TNKEIADILGISEKTVKTHL 36 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 45678999999998887663
No 209
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=22.89 E-value=66 Score=13.62 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=7.7
Q ss_pred cccccCCcccc
Q psy15437 33 FVCVVCGSRLQ 43 (143)
Q Consensus 33 f~C~~C~~~l~ 43 (143)
|.|..|++.+.
T Consensus 2 ~~C~~C~k~f~ 12 (27)
T PF12171_consen 2 FYCDACDKYFS 12 (27)
T ss_dssp CBBTTTTBBBS
T ss_pred CCcccCCCCcC
Confidence 56777777764
No 210
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=22.75 E-value=90 Score=16.16 Aligned_cols=21 Identities=10% Similarity=0.090 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCCcccceeccc
Q psy15437 121 VREGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQ 141 (143)
.++.++..++++...++.||.
T Consensus 23 lK~~i~~~~~~~~~~~~l~~~ 43 (69)
T cd01769 23 LKAKIAAKEGVPPEQQRLIYA 43 (69)
T ss_pred HHHHHHHHHCcChHHEEEEEC
Confidence 455678888888877777775
No 211
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=22.64 E-value=64 Score=19.47 Aligned_cols=23 Identities=13% Similarity=-0.049 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCcccceecccCC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIPV 143 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn~ 143 (143)
--+.|+..||+++..|-|-|+++
T Consensus 81 i~~~l~~~lgi~~~rv~I~f~~~ 103 (116)
T PTZ00397 81 ITKILASHLKVKSERVYIEFKDC 103 (116)
T ss_pred HHHHHHHHhCcCcccEEEEEEEC
Confidence 34567889999999999988764
No 212
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=22.63 E-value=81 Score=17.63 Aligned_cols=22 Identities=9% Similarity=-0.099 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCcccceecccC
Q psy15437 121 VREGLARDTGLSVRIVQSRPIP 142 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQn 142 (143)
-++.++...|++..+.+.||..
T Consensus 28 lK~~i~~~~gi~~~~QrLi~~G 49 (78)
T cd01797 28 LREKIQELFNVEPECQRLFYRG 49 (78)
T ss_pred HHHHHHHHhCCCHHHeEEEeCC
Confidence 4566788889999888888864
No 213
>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=22.62 E-value=45 Score=17.86 Aligned_cols=9 Identities=44% Similarity=1.221 Sum_probs=5.5
Q ss_pred cccCCcccc
Q psy15437 35 CVVCGSRLQ 43 (143)
Q Consensus 35 C~~C~~~l~ 43 (143)
|-.|+.++.
T Consensus 6 C~~CG~~Ip 14 (59)
T PF09889_consen 6 CPVCGKPIP 14 (59)
T ss_pred CCcCCCcCC
Confidence 556666664
No 214
>KOG3002|consensus
Probab=22.42 E-value=62 Score=23.55 Aligned_cols=45 Identities=22% Similarity=0.260 Sum_probs=34.5
Q ss_pred CCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhhccCCCCC
Q psy15437 31 QCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIP 76 (143)
Q Consensus 31 ~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~ 76 (143)
.-+.|..|-..|. -..+.-.+|.+.|..|-.++..+|+.|..++.
T Consensus 47 ~lleCPvC~~~l~-~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLS-PPIFQCDNGHLACSSCRTKVSNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCc-ccceecCCCcEehhhhhhhhcccCCccccccc
Confidence 4467888888885 34577788999999998777778888877665
No 215
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.40 E-value=67 Score=21.13 Aligned_cols=20 Identities=10% Similarity=0.135 Sum_probs=16.1
Q ss_pred HHHHHHHHhCCCcccceecc
Q psy15437 121 VREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWF 140 (143)
..+++|..+|+++..|+++.
T Consensus 152 s~~EIA~~lgis~~tVk~~l 171 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLL 171 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 45678999999999887753
No 216
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.31 E-value=1.1e+02 Score=14.64 Aligned_cols=13 Identities=23% Similarity=0.286 Sum_probs=10.6
Q ss_pred CCCHHHHHHHHHh
Q psy15437 98 ILTTQQRRAFKAS 110 (143)
Q Consensus 98 ~~~~~q~~~L~~~ 110 (143)
.||..|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5889999999864
No 217
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=22.29 E-value=48 Score=18.48 Aligned_cols=9 Identities=22% Similarity=1.084 Sum_probs=3.7
Q ss_pred cccccCccc
Q psy15437 6 KCLGCSEKL 14 (143)
Q Consensus 6 ~C~~C~~~i 14 (143)
+|-.||+.|
T Consensus 6 RCFTCGkvi 14 (71)
T PLN00032 6 RCFTCGKVI 14 (71)
T ss_pred eecCCCCCc
Confidence 344444433
No 218
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=22.21 E-value=75 Score=19.89 Aligned_cols=37 Identities=22% Similarity=0.259 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF 140 (143)
++..+...+...|-.. ...+++|..+|++...|+++.
T Consensus 112 L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l 148 (159)
T TIGR02989 112 LPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKAL 148 (159)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHH
Confidence 4455555554433222 245678999999998887653
No 219
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=21.98 E-value=1.1e+02 Score=15.44 Aligned_cols=12 Identities=17% Similarity=0.459 Sum_probs=6.3
Q ss_pred CCeeechhhHHH
Q psy15437 52 QGQLFCRPDYEK 63 (143)
Q Consensus 52 ~~~~~C~~~~~~ 63 (143)
.+..+|..|-..
T Consensus 16 ~~~fIC~~CE~~ 27 (46)
T PF10764_consen 16 YGKFICSDCEKE 27 (46)
T ss_pred ECeEehHHHHHH
Confidence 455556555443
No 220
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=21.84 E-value=52 Score=22.02 Aligned_cols=21 Identities=29% Similarity=0.327 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCcccceeccc
Q psy15437 121 VREGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQ 141 (143)
..+++|..+|++...|+++..
T Consensus 171 s~~EIA~~lgis~~tV~~~l~ 191 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLR 191 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 466889999999998887643
No 221
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.36 E-value=1.2e+02 Score=15.67 Aligned_cols=29 Identities=14% Similarity=0.106 Sum_probs=15.7
Q ss_pred HHHhhhcC-CCCCHHHHHHHHHHhCCCccc
Q psy15437 107 FKASFEIS-PKPCRKVREGLARDTGLSVRI 135 (143)
Q Consensus 107 L~~~f~~~-~~p~~~~~~~la~~~~l~~~~ 135 (143)
+.+.+... ..+.......||..+++++..
T Consensus 27 l~~~~~~~~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 27 LSRILNGKPSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp HHHHHTTT-----HHHHHHHHHHHT--HHH
T ss_pred HHHHHhcccccccHHHHHHHHHHcCCCHHH
Confidence 34444444 468888888889999888754
No 222
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=21.32 E-value=81 Score=21.65 Aligned_cols=33 Identities=27% Similarity=0.478 Sum_probs=20.6
Q ss_pred cccCCcccccCCccccCCCceEeeCCeeechhhH
Q psy15437 28 FHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61 (143)
Q Consensus 28 ~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~ 61 (143)
|-+.-..|..|+. ......|...+|...|..|.
T Consensus 143 ~~p~l~~C~~cg~-~~~~~~fs~~~gg~~C~~c~ 175 (241)
T TIGR00613 143 YALDLDKCAVCGS-KEDLIYFSMTYGGALCRQCG 175 (241)
T ss_pred CCcccCccCCCCC-cCCCceEchhcCeEEChhhC
Confidence 3445557778876 43333456668888887664
No 223
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=21.30 E-value=71 Score=17.18 Aligned_cols=27 Identities=33% Similarity=0.854 Sum_probs=18.5
Q ss_pred CccccccCccccCCcceEEecCcccccCCcccccCCc
Q psy15437 4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGS 40 (143)
Q Consensus 4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~ 40 (143)
..+|..|+..|.+.+..+. |.|..|+.
T Consensus 9 ~~~CtSCg~~i~p~e~~v~----------F~CPnCGe 35 (61)
T COG2888 9 PPVCTSCGREIAPGETAVK----------FPCPNCGE 35 (61)
T ss_pred CceeccCCCEeccCCceeE----------eeCCCCCc
Confidence 3589999999966664431 56677764
No 224
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=21.25 E-value=62 Score=17.03 Aligned_cols=17 Identities=12% Similarity=0.014 Sum_probs=11.4
Q ss_pred HHHHHHHHHhCCCcccc
Q psy15437 120 KVREGLARDTGLSVRIV 136 (143)
Q Consensus 120 ~~~~~la~~~~l~~~~v 136 (143)
.+...++.++|+++.++
T Consensus 21 ~ev~ywa~~~gvt~~~L 37 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQL 37 (57)
T ss_pred HHHHHHHHHHCcCHHHH
Confidence 35666777777777654
No 225
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=21.21 E-value=72 Score=15.44 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=7.1
Q ss_pred CCeeechhhHHHH
Q psy15437 52 QGQLFCRPDYEKE 64 (143)
Q Consensus 52 ~~~~~C~~~~~~~ 64 (143)
=|..+|..|....
T Consensus 20 CgH~~C~~C~~~~ 32 (44)
T PF14634_consen 20 CGHIFCEKCLKKL 32 (44)
T ss_pred cCCHHHHHHHHhh
Confidence 3556666665443
No 226
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.21 E-value=74 Score=20.52 Aligned_cols=21 Identities=10% Similarity=0.096 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCcccceeccc
Q psy15437 121 VREGLARDTGLSVRIVQSRPI 141 (143)
Q Consensus 121 ~~~~la~~~~l~~~~vkvWFQ 141 (143)
..+++|..+|++...|+++.+
T Consensus 147 s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 356789999999999887653
No 227
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=21.20 E-value=84 Score=16.12 Aligned_cols=27 Identities=22% Similarity=0.481 Sum_probs=15.7
Q ss_pred cccccCccccCC-cceEEecCcccccCC
Q psy15437 6 KCLGCSEKLGPD-ELVMKTLDNVFHVQC 32 (143)
Q Consensus 6 ~C~~C~~~i~~~-~~~~~~~~~~~h~~c 32 (143)
.|..|+-....+ +-.+....-.|+..|
T Consensus 15 ~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 15 KCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred cCcccCCcEeecCcceEEEeccceeeee
Confidence 577777655433 334455555666665
No 228
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=21.07 E-value=98 Score=16.08 Aligned_cols=24 Identities=21% Similarity=0.379 Sum_probs=14.0
Q ss_pred HHHHHhhhcCCCCCHHHHHHHHHHhCCCccc
Q psy15437 105 RAFKASFEISPKPCRKVREGLARDTGLSVRI 135 (143)
Q Consensus 105 ~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~ 135 (143)
..|...|+.. ..+.|..+|++...
T Consensus 8 ~~L~~~fhlp-------~~eAA~~Lgv~~T~ 31 (52)
T PF02042_consen 8 EDLSQYFHLP-------IKEAAKELGVSVTT 31 (52)
T ss_pred HHHHHHhCCC-------HHHHHHHhCCCHHH
Confidence 4566666644 33456777776654
No 229
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=21.04 E-value=48 Score=28.40 Aligned_cols=50 Identities=24% Similarity=0.517 Sum_probs=29.1
Q ss_pred CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCC-ceEeeCCeeechhhH
Q psy15437 3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGE-QFVIKQGQLFCRPDY 61 (143)
Q Consensus 3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~-~~~~~~~~~~C~~~~ 61 (143)
.++.|.-||..|. +.+.|..| -.|..|+-++-..+ +|-.++|.-.|..|-
T Consensus 14 ~~~~c~iCGd~vg-----~~~~Ge~F----VAC~eC~fpvCr~cyeye~~~g~~~cp~c~ 64 (1044)
T PLN02915 14 DAKTCRVCGDEVG-----VKEDGQPF----VACHVCGFPVCKPCYEYERSEGNQCCPQCN 64 (1044)
T ss_pred CcchhhccccccC-----cCCCCCEE----EEeccCCCccccchhhhhhhcCCccCCccC
Confidence 4568888988775 34556555 45666666654222 233446666665553
No 230
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=20.72 E-value=44 Score=18.29 Aligned_cols=8 Identities=25% Similarity=0.704 Sum_probs=2.4
Q ss_pred cccccCcc
Q psy15437 6 KCLGCSEK 13 (143)
Q Consensus 6 ~C~~C~~~ 13 (143)
+|..|...
T Consensus 9 rCs~C~~~ 16 (65)
T PF14835_consen 9 RCSICFDI 16 (65)
T ss_dssp S-SSS-S-
T ss_pred CCcHHHHH
Confidence 45555443
No 231
>PRK04217 hypothetical protein; Provisional
Probab=20.64 E-value=70 Score=19.50 Aligned_cols=38 Identities=16% Similarity=0.088 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceec
Q psy15437 97 TILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSR 139 (143)
Q Consensus 97 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvW 139 (143)
..++.++...+...+...- ..+++|..+|++...|+..
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~ 78 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRA 78 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHH
Confidence 4567777777766654433 4667899999999877654
No 232
>KOG4543|consensus
Probab=20.56 E-value=95 Score=20.79 Aligned_cols=35 Identities=26% Similarity=0.456 Sum_probs=26.8
Q ss_pred CcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437 32 CFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE 66 (143)
Q Consensus 32 cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~ 66 (143)
-..|+.|++.+.+...+....+..+|..|..+...
T Consensus 156 Gt~cs~c~~~vc~~~acs~~~~Atfc~pC~kre~~ 190 (208)
T KOG4543|consen 156 GTVCSPCGAAVCPRGACSQLGAATFCGPCSKREVQ 190 (208)
T ss_pred CCccccccCccccCCceeeeeecccccchhHHHHH
Confidence 35789999988766666777788899999877654
No 233
>PLN02189 cellulose synthase
Probab=20.55 E-value=53 Score=28.16 Aligned_cols=12 Identities=25% Similarity=0.720 Sum_probs=6.8
Q ss_pred CccccccCcccc
Q psy15437 4 VKKCLGCSEKLG 15 (143)
Q Consensus 4 ~~~C~~C~~~i~ 15 (143)
+..|.-|+..|.
T Consensus 34 ~~~C~iCgd~vg 45 (1040)
T PLN02189 34 GQVCEICGDEIG 45 (1040)
T ss_pred CccccccccccC
Confidence 345666665553
No 234
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=20.54 E-value=1.6e+02 Score=16.52 Aligned_cols=35 Identities=9% Similarity=0.139 Sum_probs=22.4
Q ss_pred CCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccc
Q psy15437 98 ILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIV 136 (143)
Q Consensus 98 ~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v 136 (143)
.++.+++..|-..+-.|+.- -..+..++|+++..+
T Consensus 12 nvsd~qi~elFq~lT~NPl~----AMa~i~qLGip~eKL 46 (82)
T PF11212_consen 12 NVSDEQINELFQALTQNPLA----AMATIQQLGIPQEKL 46 (82)
T ss_pred CCCHHHHHHHHHHHhhCHHH----HHHHHHHcCCCHHHH
Confidence 46778888887777777632 334456677776543
No 235
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=20.48 E-value=77 Score=20.22 Aligned_cols=37 Identities=24% Similarity=0.156 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF 140 (143)
++..+...+...|-.+ ..-+.+|..+|++...|+.|.
T Consensus 129 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l 165 (182)
T PRK09652 129 LPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRI 165 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 4455555554443222 134578999999999887764
No 236
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=20.47 E-value=35 Score=16.38 Aligned_cols=18 Identities=28% Similarity=0.095 Sum_probs=11.7
Q ss_pred HHHHHHhCCCcccceecc
Q psy15437 123 EGLARDTGLSVRIVQSRP 140 (143)
Q Consensus 123 ~~la~~~~l~~~~vkvWF 140 (143)
+++|..+|++...|.-|-
T Consensus 5 ~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 5 EEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 456777777777665553
No 237
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=20.35 E-value=83 Score=20.22 Aligned_cols=36 Identities=25% Similarity=0.269 Sum_probs=21.9
Q ss_pred CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceec
Q psy15437 99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSR 139 (143)
Q Consensus 99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvW 139 (143)
++..+...+...|-.+. ..+++|..+|+++..|+++
T Consensus 101 L~~~~r~v~~l~~~~g~-----s~~eIA~~lgis~~tV~~~ 136 (170)
T TIGR02959 101 LPDEYREAIRLTELEGL-----SQQEIAEKLGLSLSGAKSR 136 (170)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHH
Confidence 44444444444332222 4567899999999887765
No 238
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=20.32 E-value=1.2e+02 Score=18.19 Aligned_cols=33 Identities=21% Similarity=0.492 Sum_probs=22.9
Q ss_pred cccccCCcccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437 26 NVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63 (143)
Q Consensus 26 ~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~ 63 (143)
..+...--.|..|+ +..|+..++.+.|..|-.+
T Consensus 29 g~~~va~daCeiC~-----~~GY~q~g~~lvC~~C~~~ 61 (102)
T PF10080_consen 29 GSYRVAFDACEICG-----PKGYYQEGDQLVCKNCGVR 61 (102)
T ss_pred CCEEEEEEeccccC-----CCceEEECCEEEEecCCCE
Confidence 33444445788882 3558889999999988643
No 239
>COG1427 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=20.28 E-value=54 Score=23.20 Aligned_cols=25 Identities=16% Similarity=0.151 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhCCCcccceecccCC
Q psy15437 119 RKVREGLARDTGLSVRIVQSRPIPV 143 (143)
Q Consensus 119 ~~~~~~la~~~~l~~~~vkvWFQn~ 143 (143)
....++++..+|++.+.++-+|.|.
T Consensus 198 ~ei~~~~a~~lglp~~~~~eYy~~~ 222 (252)
T COG1427 198 AEILKEAAKRLGLPRSDVEEYYTNI 222 (252)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 5567788999999999999988773
No 240
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=20.17 E-value=68 Score=19.47 Aligned_cols=34 Identities=21% Similarity=0.378 Sum_probs=10.0
Q ss_pred ccccCccccCCcceEEecCcccccCCcccccCCc
Q psy15437 7 CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGS 40 (143)
Q Consensus 7 C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~ 40 (143)
|..|-+..+++.--.-..+.+|..+--.|..|++
T Consensus 2 C~~CV~~~yPdRg~~CLe~GSyllN~~~Ca~C~k 35 (112)
T PF06573_consen 2 CGDCVKKEYPDRGNTCLENGSYLLNFVGCASCQK 35 (112)
T ss_dssp --TTBSSSS---TT---SS---TTTB---SSS--
T ss_pred chhhccCcCCCCCCEeecCcceeeechhhhccCC
Confidence 4555555555532233455556666555666665
Done!