Query psy15639
Match_columns 135
No_of_seqs 11 out of 13
Neff 1.7
Searched_HMMs 46136
Date Fri Aug 16 17:49:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15639.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15639hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02318 FYVE_2: FYVE-type zin 97.9 5.3E-06 1.2E-10 59.1 1.7 54 10-68 54-108 (118)
2 PF01363 FYVE: FYVE zinc finge 96.4 0.0011 2.3E-08 42.3 0.5 61 5-65 4-68 (69)
3 PF00628 PHD: PHD-finger; Int 95.7 0.0026 5.6E-08 38.3 -0.1 50 13-63 2-51 (51)
4 PF13639 zf-RING_2: Ring finge 94.8 0.0023 5E-08 38.0 -2.3 44 11-61 1-44 (44)
5 PF13920 zf-C3HC4_3: Zinc fing 94.8 0.0035 7.5E-08 38.2 -1.6 45 11-65 3-48 (50)
6 cd00065 FYVE FYVE domain; Zinc 94.6 0.025 5.4E-07 34.6 1.9 51 10-60 2-54 (57)
7 smart00064 FYVE Protein presen 94.1 0.061 1.3E-06 34.1 2.9 60 6-65 6-67 (68)
8 KOG2177|consensus 93.5 0.034 7.3E-07 38.2 1.0 43 10-62 13-55 (386)
9 smart00249 PHD PHD zinc finger 93.5 0.057 1.2E-06 30.1 1.8 47 12-60 1-47 (47)
10 PF14634 zf-RING_5: zinc-RING 93.1 0.026 5.7E-07 33.9 -0.0 43 13-62 2-44 (44)
11 cd00162 RING RING-finger (Real 91.6 0.019 4E-07 31.5 -1.8 44 12-63 1-44 (45)
12 KOG3799|consensus 91.6 0.082 1.8E-06 42.5 1.1 53 10-64 65-117 (169)
13 PF07649 C1_3: C1-like domain; 84.9 0.26 5.6E-06 28.0 -0.1 29 12-41 2-30 (30)
14 PLN03208 E3 ubiquitin-protein 82.2 0.31 6.7E-06 39.4 -0.8 52 10-65 18-79 (193)
15 smart00396 ZnF_UBR1 Putative z 81.2 0.5 1.1E-05 31.7 0.1 31 14-44 1-35 (71)
16 PHA02929 N1R/p28-like protein; 81.0 0.4 8.6E-06 39.3 -0.5 52 9-66 173-228 (238)
17 PF14446 Prok-RING_1: Prokaryo 78.6 0.84 1.8E-05 30.7 0.5 32 10-41 5-36 (54)
18 cd00350 rubredoxin_like Rubred 76.3 0.99 2.1E-05 26.4 0.3 10 53-62 16-25 (33)
19 KOG1729|consensus 72.3 4.1 8.9E-05 34.4 3.2 62 5-66 163-226 (288)
20 PF00097 zf-C3HC4: Zinc finger 72.2 0.85 1.8E-05 26.1 -0.7 28 13-43 1-28 (41)
21 PF13923 zf-C3HC4_2: Zinc fing 72.0 0.5 1.1E-05 27.5 -1.7 39 13-60 1-39 (39)
22 PF05715 zf-piccolo: Piccolo Z 71.2 2.8 6.1E-05 29.2 1.6 51 11-62 3-57 (61)
23 PF04810 zf-Sec23_Sec24: Sec23 71.1 1.7 3.7E-05 26.3 0.5 28 36-63 4-33 (40)
24 TIGR00622 ssl1 transcription f 70.5 2.4 5.2E-05 31.9 1.2 37 9-45 54-100 (112)
25 PF01155 HypA: Hydrogenase exp 68.9 1 2.2E-05 32.2 -1.0 23 11-33 71-93 (113)
26 PF12874 zf-met: Zinc-finger o 68.7 1 2.2E-05 23.6 -0.7 14 55-68 1-14 (25)
27 PF10497 zf-4CXXC_R1: Zinc-fin 66.9 1.7 3.7E-05 31.3 -0.2 52 9-62 6-69 (105)
28 KOG0320|consensus 66.4 1.2 2.5E-05 36.5 -1.2 50 11-68 132-181 (187)
29 TIGR00100 hypA hydrogenase nic 66.3 2.3 4.9E-05 30.7 0.4 23 11-33 71-93 (115)
30 PF03107 C1_2: C1 domain; Int 66.1 2.3 5.1E-05 24.3 0.3 29 12-41 2-30 (30)
31 PRK14559 putative protein seri 65.2 6.1 0.00013 36.4 3.0 25 53-77 40-64 (645)
32 smart00336 BBOX B-Box-type zin 65.0 2.8 6.2E-05 23.6 0.6 30 10-43 3-32 (42)
33 PF00301 Rubredoxin: Rubredoxi 63.3 2.4 5.3E-05 27.2 0.0 13 50-62 30-42 (47)
34 PRK12380 hydrogenase nickel in 63.2 2.8 6E-05 30.2 0.3 23 11-33 71-93 (113)
35 COG1571 Predicted DNA-binding 63.2 3.7 8.1E-05 36.7 1.2 59 34-99 350-408 (421)
36 PF12773 DZR: Double zinc ribb 60.5 4.6 9.9E-05 24.3 0.9 42 13-67 1-42 (50)
37 smart00661 RPOL9 RNA polymeras 60.2 5 0.00011 24.0 1.1 29 36-64 2-30 (52)
38 TIGR00570 cdk7 CDK-activating 59.6 2.5 5.4E-05 36.3 -0.5 60 11-78 4-65 (309)
39 PTZ00303 phosphatidylinositol 59.5 7.1 0.00015 39.1 2.4 56 10-65 460-530 (1374)
40 PF13831 PHD_2: PHD-finger; PD 58.1 3 6.4E-05 25.2 -0.2 32 27-61 5-36 (36)
41 PRK10422 lipopolysaccharide co 56.0 7 0.00015 31.0 1.5 25 76-100 16-40 (352)
42 PF09889 DUF2116: Uncharacteri 55.4 5.8 0.00013 26.8 0.8 14 11-24 4-17 (59)
43 KOG1985|consensus 55.3 4.5 9.7E-05 39.4 0.4 28 36-63 220-249 (887)
44 smart00109 C1 Protein kinase C 54.4 8.2 0.00018 21.9 1.3 33 8-40 9-41 (49)
45 TIGR01053 LSD1 zinc finger dom 54.1 5.9 0.00013 23.7 0.6 26 34-61 1-26 (31)
46 PRK00564 hypA hydrogenase nick 53.9 5.7 0.00012 28.7 0.7 23 11-33 72-95 (117)
47 PRK10964 ADP-heptose:LPS hepto 53.4 6.6 0.00014 30.6 0.9 24 77-100 12-35 (322)
48 TIGR02193 heptsyl_trn_I lipopo 53.1 6.3 0.00014 30.4 0.8 24 77-100 11-34 (319)
49 PF00643 zf-B_box: B-box zinc 52.2 3.3 7.1E-05 24.0 -0.7 30 11-44 4-33 (42)
50 PF07975 C1_4: TFIIH C1-like d 51.8 4.8 0.0001 26.6 -0.0 32 13-44 2-39 (51)
51 TIGR03826 YvyF flagellar opero 51.6 5.5 0.00012 30.4 0.3 24 11-35 4-27 (137)
52 TIGR02201 heptsyl_trn_III lipo 51.6 9.4 0.0002 29.9 1.6 24 77-100 11-34 (344)
53 PF06718 DUF1203: Protein of u 51.1 7 0.00015 29.1 0.7 16 11-26 2-17 (117)
54 cd00730 rubredoxin Rubredoxin; 49.9 7.6 0.00016 25.2 0.7 13 50-62 30-42 (50)
55 PF00096 zf-C2H2: Zinc finger, 49.4 6 0.00013 20.2 0.1 11 12-22 2-12 (23)
56 KOG1813|consensus 49.4 6.8 0.00015 34.3 0.5 51 8-68 239-289 (313)
57 PRK10916 ADP-heptose:LPS hepto 49.3 8.1 0.00018 30.5 0.9 24 77-100 12-35 (348)
58 PF12760 Zn_Tnp_IS1595: Transp 49.1 6 0.00013 24.2 0.1 24 36-62 20-45 (46)
59 PF13465 zf-H2C2_2: Zinc-finge 48.3 6.1 0.00013 21.7 0.0 14 8-21 12-25 (26)
60 TIGR00270 conserved hypothetic 47.5 6.2 0.00013 30.1 -0.0 34 12-46 2-36 (154)
61 PF10058 DUF2296: Predicted in 47.3 7.3 0.00016 25.5 0.3 28 35-62 23-52 (54)
62 cd02335 ZZ_ADA2 Zinc finger, Z 47.3 14 0.0003 23.0 1.6 34 12-46 2-36 (49)
63 PF13445 zf-RING_UBOX: RING-ty 46.4 5.5 0.00012 24.8 -0.4 28 13-41 1-28 (43)
64 TIGR02195 heptsyl_trn_II lipop 45.2 9.7 0.00021 29.6 0.8 24 77-100 11-34 (334)
65 PF13842 Tnp_zf-ribbon_2: DDE_ 45.1 9.3 0.0002 22.6 0.5 26 12-37 2-27 (32)
66 TIGR00599 rad18 DNA repair pro 44.8 4.9 0.00011 35.3 -1.1 50 7-66 23-72 (397)
67 COG5028 Vesicle coat complex C 44.7 6.6 0.00014 38.2 -0.3 35 35-69 200-236 (861)
68 PRK14890 putative Zn-ribbon RN 44.6 12 0.00025 25.8 1.0 36 11-63 8-45 (59)
69 PLN02189 cellulose synthase 43.9 52 0.0011 32.8 5.5 50 11-65 35-87 (1040)
70 PRK06424 transcription factor; 43.9 7.2 0.00016 29.7 -0.1 35 13-48 3-37 (144)
71 KOG2169|consensus 43.2 7 0.00015 35.5 -0.3 36 28-65 321-356 (636)
72 PF13894 zf-C2H2_4: C2H2-type 43.0 5.8 0.00013 19.4 -0.5 14 55-68 1-14 (24)
73 PF02207 zf-UBR: Putative zinc 43.0 6.8 0.00015 25.8 -0.3 26 15-40 2-31 (71)
74 PF05810 NinF: NinF protein; 42.8 6.4 0.00014 27.3 -0.5 24 7-32 15-38 (58)
75 PF09334 tRNA-synt_1g: tRNA sy 42.0 8.6 0.00019 32.5 0.0 53 12-67 122-179 (391)
76 PRK03824 hypA hydrogenase nick 41.6 9.5 0.00021 28.2 0.2 13 11-23 71-83 (135)
77 PF14569 zf-UDP: Zinc-binding 41.1 8.5 0.00018 28.0 -0.1 48 9-61 8-58 (80)
78 PRK13267 archaemetzincin-like 39.9 12 0.00027 29.0 0.6 28 40-67 147-176 (179)
79 PRK03670 competence damage-ind 39.8 18 0.00038 29.4 1.5 19 83-102 197-215 (252)
80 COG0859 RfaF ADP-heptose:LPS h 39.7 14 0.00031 29.6 1.0 24 77-100 13-36 (334)
81 KOG4739|consensus 39.6 14 0.0003 30.8 0.9 45 12-66 5-49 (233)
82 PRK08222 hydrogenase 4 subunit 39.0 11 0.00024 28.8 0.2 16 9-24 113-128 (181)
83 PRK01343 zinc-binding protein; 38.9 22 0.00048 24.1 1.6 25 5-30 4-28 (57)
84 PF14599 zinc_ribbon_6: Zinc-r 37.4 9.1 0.0002 25.9 -0.4 24 22-45 21-59 (61)
85 cd03789 GT1_LPS_heptosyltransf 36.7 17 0.00036 27.6 0.8 24 77-100 11-34 (279)
86 PF02891 zf-MIZ: MIZ/SP-RING z 36.3 3.3 7.3E-05 26.2 -2.5 31 30-62 19-49 (50)
87 KOG1245|consensus 35.6 18 0.0004 36.4 1.2 55 6-65 1104-1160(1404)
88 PHA02926 zinc finger-like prot 35.5 11 0.00024 32.0 -0.2 59 7-65 167-230 (242)
89 PLN02436 cellulose synthase A 35.3 21 0.00045 35.7 1.4 50 11-65 37-89 (1094)
90 PF13901 DUF4206: Domain of un 35.1 24 0.00053 27.4 1.6 34 28-61 144-179 (202)
91 smart00184 RING Ring finger. E 35.1 12 0.00027 19.2 -0.0 26 13-42 1-26 (39)
92 PRK04023 DNA polymerase II lar 34.8 28 0.00061 35.0 2.3 69 22-97 622-695 (1121)
93 PF08271 TF_Zn_Ribbon: TFIIB z 34.8 12 0.00027 22.4 -0.1 32 36-68 2-33 (43)
94 COG0675 Transposase and inacti 33.9 15 0.00032 27.2 0.2 24 26-64 309-332 (364)
95 cd04476 RPA1_DBD_C RPA1_DBD_C: 33.7 15 0.00032 26.7 0.2 12 53-64 50-61 (166)
96 PRK00398 rpoP DNA-directed RNA 33.6 14 0.00029 22.5 -0.1 28 36-65 5-32 (46)
97 TIGR02605 CxxC_CxxC_SSSS putat 33.4 11 0.00024 22.8 -0.5 27 36-62 7-34 (52)
98 cd02249 ZZ Zinc finger, ZZ typ 33.0 27 0.00059 21.2 1.3 32 12-45 2-34 (46)
99 PF10217 DUF2039: Uncharacteri 32.8 11 0.00025 27.5 -0.5 15 20-34 49-63 (92)
100 cd00029 C1 Protein kinase C co 32.8 20 0.00044 20.6 0.6 28 9-36 10-38 (50)
101 smart00834 CxxC_CXXC_SSSS Puta 32.7 12 0.00026 21.3 -0.3 27 37-63 8-35 (41)
102 PF00645 zf-PARP: Poly(ADP-rib 32.6 23 0.00049 23.2 0.9 50 6-68 4-53 (82)
103 PRK06260 threonine synthase; V 31.7 20 0.00044 29.8 0.7 23 12-34 5-27 (397)
104 KOG4275|consensus 31.3 21 0.00045 31.8 0.7 53 6-65 40-92 (350)
105 PRK03681 hypA hydrogenase nick 31.0 19 0.00042 25.9 0.4 16 11-26 71-86 (114)
106 PF04981 NMD3: NMD3 family ; 31.0 39 0.00085 26.5 2.1 74 13-97 1-81 (236)
107 COG5152 Uncharacterized conser 30.9 18 0.00039 31.0 0.2 47 10-68 196-244 (259)
108 KOG0311|consensus 30.5 10 0.00022 34.0 -1.3 49 12-68 45-93 (381)
109 PRK04023 DNA polymerase II lar 30.3 20 0.00043 36.0 0.5 46 11-68 627-677 (1121)
110 PRK14284 chaperone protein Dna 30.1 25 0.00055 29.7 1.0 49 8-62 156-219 (391)
111 KOG4628|consensus 30.0 24 0.00053 30.9 0.9 48 11-66 230-279 (348)
112 PRK08197 threonine synthase; V 29.7 23 0.00049 29.5 0.6 22 11-33 8-29 (394)
113 PF13912 zf-C2H2_6: C2H2-type 29.6 19 0.00041 18.9 0.1 11 12-22 3-13 (27)
114 PF13945 NST1: Salt tolerance 29.1 21 0.00045 28.9 0.3 18 53-75 140-157 (190)
115 COG1997 RPL43A Ribosomal prote 28.9 20 0.00042 26.5 0.1 31 36-68 37-67 (89)
116 COG1773 Rubredoxin [Energy pro 28.8 22 0.00049 24.0 0.4 9 54-62 3-11 (55)
117 PF01258 zf-dskA_traR: Prokary 28.8 12 0.00026 21.8 -0.8 26 10-35 3-33 (36)
118 COG5533 UBP5 Ubiquitin C-termi 28.8 16 0.00035 33.0 -0.4 30 43-72 273-302 (415)
119 PF12251 zf-SNAP50_C: snRNA-ac 28.7 36 0.00078 26.7 1.6 33 5-37 134-176 (196)
120 KOG1311|consensus 28.4 23 0.0005 28.1 0.5 29 34-68 113-141 (299)
121 PF11523 DUF3223: Protein of u 28.4 32 0.00069 23.5 1.1 19 83-101 20-40 (76)
122 KOG3214|consensus 28.3 18 0.00039 27.7 -0.2 12 11-22 48-59 (109)
123 cd08430 PBP2_IlvY The C-termin 28.2 39 0.00085 21.8 1.4 20 81-100 14-33 (199)
124 cd08471 PBP2_CrgA_like_2 The C 28.1 40 0.00086 21.9 1.5 18 83-100 17-34 (201)
125 PF13719 zinc_ribbon_5: zinc-r 27.9 19 0.00041 21.4 -0.1 27 36-62 4-33 (37)
126 PF14260 zf-C4pol: C4-type zin 27.9 40 0.00088 21.7 1.5 20 13-33 1-20 (73)
127 PF15379 DUF4606: Domain of un 27.8 30 0.00065 26.2 0.9 37 48-86 25-62 (104)
128 cd08448 PBP2_LTTR_aromatics_li 27.7 43 0.00093 21.5 1.5 20 80-99 13-32 (197)
129 PF05605 zf-Di19: Drought indu 27.5 19 0.00041 22.4 -0.2 37 11-62 3-39 (54)
130 cd08450 PBP2_HcaR The C-termin 27.4 41 0.00088 21.8 1.4 22 79-100 12-33 (196)
131 cd08452 PBP2_AlsR The C-termin 27.3 41 0.00089 22.3 1.5 17 83-99 16-32 (197)
132 KOG4477|consensus 27.3 24 0.00053 29.7 0.4 14 48-61 18-31 (228)
133 cd08451 PBP2_BudR The C-termin 27.1 42 0.00091 21.7 1.4 20 81-100 15-34 (199)
134 PF09963 DUF2197: Uncharacteri 27.1 21 0.00045 24.2 -0.0 15 12-26 4-18 (56)
135 cd08431 PBP2_HupR The C-termin 27.0 45 0.00098 21.7 1.6 20 81-100 14-33 (195)
136 PF09723 Zn-ribbon_8: Zinc rib 26.9 15 0.00032 22.3 -0.7 32 36-67 7-39 (42)
137 smart00132 LIM Zinc-binding do 26.7 24 0.00052 18.8 0.2 14 52-65 25-38 (39)
138 KOG4443|consensus 26.6 22 0.00047 34.1 -0.0 55 7-61 142-200 (694)
139 cd00021 BBOX B-Box-type zinc f 26.3 23 0.0005 19.6 0.1 20 24-43 10-29 (39)
140 PF05191 ADK_lid: Adenylate ki 26.1 20 0.00043 21.7 -0.2 16 52-67 19-34 (36)
141 PF14447 Prok-RING_4: Prokaryo 26.0 38 0.00082 23.0 1.1 21 6-26 35-55 (55)
142 PLN02638 cellulose synthase A 25.9 31 0.00067 34.4 0.9 49 11-64 18-69 (1079)
143 PF09082 DUF1922: Domain of un 25.9 62 0.0013 22.8 2.2 56 39-104 7-64 (68)
144 PF08274 PhnA_Zn_Ribbon: PhnA 25.0 30 0.00066 20.6 0.4 24 36-62 4-27 (30)
145 PRK14554 putative pseudouridyl 24.7 46 0.001 29.6 1.7 49 43-102 197-245 (422)
146 PF13834 DUF4193: Domain of un 24.5 21 0.00045 26.7 -0.4 9 33-41 91-99 (99)
147 TIGR00155 pqiA_fam integral me 24.5 39 0.00084 29.2 1.1 33 36-68 15-47 (403)
148 KOG1571|consensus 24.4 26 0.00056 31.1 0.1 44 10-67 305-349 (355)
149 cd08437 PBP2_MleR The substrat 24.4 48 0.0011 21.7 1.4 20 81-100 14-33 (198)
150 smart00868 zf-AD Zinc-finger a 24.3 31 0.00068 19.8 0.4 10 12-21 1-10 (73)
151 PRK14298 chaperone protein Dna 24.1 39 0.00085 28.5 1.1 47 9-61 140-205 (377)
152 COG1813 Predicted transcriptio 24.0 38 0.00083 27.0 0.9 40 11-51 4-43 (165)
153 cd08427 PBP2_LTTR_like_2 The C 23.8 54 0.0012 21.1 1.5 20 81-100 14-33 (195)
154 COG3880 Modulator of heat shoc 23.7 29 0.00064 28.3 0.3 9 35-43 27-35 (176)
155 PRK14282 chaperone protein Dna 23.6 37 0.0008 28.4 0.8 49 8-62 150-217 (369)
156 PRK12268 methionyl-tRNA synthe 23.6 35 0.00077 29.3 0.7 46 12-57 127-177 (556)
157 cd08478 PBP2_CrgA The C-termin 23.5 53 0.0011 21.5 1.4 18 83-100 19-36 (199)
158 PF13913 zf-C2HC_2: zinc-finge 23.5 16 0.00036 20.3 -0.9 17 11-27 3-19 (25)
159 cd08481 PBP2_GcdR_like The C-t 23.4 45 0.00097 21.4 1.0 17 83-99 16-32 (194)
160 PF12171 zf-C2H2_jaz: Zinc-fin 23.3 41 0.0009 18.1 0.7 13 12-24 3-15 (27)
161 cd08434 PBP2_GltC_like The sub 23.2 54 0.0012 20.9 1.4 20 81-100 14-33 (195)
162 PF13240 zinc_ribbon_2: zinc-r 23.2 46 0.001 18.4 0.9 20 13-34 2-21 (23)
163 TIGR03290 CoB_CoM_SS_C CoB--Co 23.1 34 0.00074 24.7 0.5 13 50-62 41-53 (144)
164 COG4068 Uncharacterized protei 22.8 37 0.00081 24.0 0.6 18 11-30 9-26 (64)
165 PRK11595 DNA utilization prote 22.6 51 0.0011 25.5 1.4 30 11-41 6-41 (227)
166 PRK08359 transcription factor; 22.5 25 0.00054 27.9 -0.3 34 11-45 7-42 (176)
167 TIGR00398 metG methionyl-tRNA 22.2 35 0.00077 29.1 0.5 50 13-65 123-177 (530)
168 PF10367 Vps39_2: Vacuolar sor 22.0 32 0.00069 22.3 0.1 31 9-41 77-107 (109)
169 cd08476 PBP2_CrgA_like_7 The C 21.6 62 0.0014 20.7 1.4 18 83-100 15-32 (197)
170 cd08449 PBP2_XapR The C-termin 21.5 61 0.0013 20.9 1.4 20 81-100 14-33 (197)
171 PF05502 Dynactin_p62: Dynacti 21.4 38 0.00083 30.0 0.5 45 26-70 5-68 (483)
172 KOG3576|consensus 21.1 29 0.00063 29.9 -0.3 110 8-124 115-246 (267)
173 PF06943 zf-LSD1: LSD1 zinc fi 21.1 38 0.00083 19.7 0.3 12 50-61 12-23 (25)
174 cd08470 PBP2_CrgA_like_1 The C 21.0 64 0.0014 21.0 1.4 19 82-100 16-34 (197)
175 KOG2041|consensus 20.9 72 0.0016 32.1 2.3 56 4-65 1111-1167(1189)
176 PLN02195 cellulose synthase A 20.9 40 0.00087 33.3 0.6 51 10-65 6-59 (977)
177 cd08444 PBP2_Cbl The C-termina 20.8 64 0.0014 21.4 1.4 20 81-100 14-33 (198)
178 PF15261 DUF4591: Domain of un 20.4 79 0.0017 24.0 2.0 21 75-95 100-120 (134)
179 PF00641 zf-RanBP: Zn-finger i 20.4 55 0.0012 18.2 0.9 10 53-62 3-12 (30)
180 PF04640 PLATZ: PLATZ transcri 20.2 73 0.0016 22.2 1.6 27 2-30 41-67 (72)
181 PF00130 C1_1: Phorbol esters/ 20.2 58 0.0013 19.4 1.0 34 8-41 9-43 (53)
182 cd00729 rubredoxin_SM Rubredox 20.1 41 0.0009 19.9 0.3 9 13-21 5-13 (34)
183 PF01586 Basic: Myogenic Basic 20.1 32 0.00069 24.9 -0.2 12 54-65 72-83 (86)
184 PLN02400 cellulose synthase 20.1 46 0.00099 33.3 0.8 49 10-63 36-87 (1085)
185 PLN02569 threonine synthase 20.1 45 0.00097 29.5 0.7 23 10-33 49-71 (484)
186 PF06827 zf-FPG_IleRS: Zinc fi 20.0 28 0.0006 19.4 -0.4 22 12-33 3-28 (30)
No 1
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=97.89 E-value=5.3e-06 Score=59.15 Aligned_cols=54 Identities=33% Similarity=0.823 Sum_probs=41.7
Q ss_pred CCCchhhccccCCCC-ccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 10 LGNCRVCLKSFKPDD-YSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 10 ~g~CRVClKsfkP~e-~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
...|-.|.+.|..-. ..+.|.+|+++||-.|..|++ ....|.|.+|......+.
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~-----~~~~WlC~vC~k~rel~~ 108 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSK-----KEPIWLCKVCQKQRELKK 108 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETS-----SSCCEEEHHHHHHHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCC-----CCCCEEChhhHHHHHHHH
Confidence 347999999987553 579999999999999999932 356899999998765443
No 2
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=96.40 E-value=0.0011 Score=42.33 Aligned_cols=61 Identities=30% Similarity=0.544 Sum_probs=37.9
Q ss_pred CCCCCCCCchhhccccCCCCccchhhhhhhhhhcccccccCCCC----CCCCCceeehhhhhhhh
Q psy15639 5 KPAARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDE----NQDENTWRCSICRRKLQ 65 (135)
Q Consensus 5 kp~~r~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~----~ed~~~WrCSvCRRK~~ 65 (135)
+|......|.+|.|.|.--.-.|.|--|.+.||.+|.++..... ......--|..|-.+++
T Consensus 4 ~~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~~~ 68 (69)
T PF01363_consen 4 VPDSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSKLQ 68 (69)
T ss_dssp SSGGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHHHH
T ss_pred CCCCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHHhc
Confidence 45667889999999998888889999999999999999876533 44445566777766654
No 3
>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=95.73 E-value=0.0026 Score=38.33 Aligned_cols=50 Identities=26% Similarity=0.591 Sum_probs=42.1
Q ss_pred chhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhh
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRK 63 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK 63 (135)
|.||.+ ...++..-.|..|.+-+=..|..++..........|.|..|++|
T Consensus 2 C~vC~~-~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~~ 51 (51)
T PF00628_consen 2 CPVCGQ-SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRPK 51 (51)
T ss_dssp BTTTTS-SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHHC
T ss_pred CcCCCC-cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcCc
Confidence 789998 67777788899999888889999988766665669999999986
No 4
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=94.81 E-value=0.0023 Score=37.99 Aligned_cols=44 Identities=20% Similarity=0.519 Sum_probs=32.3
Q ss_pred CCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICR 61 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCR 61 (135)
+.|-||+..|.+++...... |.|..|.+|..---..+ .+|.+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~------~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRN------NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHS------SB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhC------CcCCccC
Confidence 46999999999888777777 99999999964322111 2899987
No 5
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=94.80 E-value=0.0035 Score=38.23 Aligned_cols=45 Identities=27% Similarity=0.720 Sum_probs=33.2
Q ss_pred CCchhhccccCCCCccchhhhhhhh-hhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQK-VCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqk-VCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
..|.||+..++. .+-..|.|. +|.+|+.-... +..+|.+||+++.
T Consensus 3 ~~C~iC~~~~~~----~~~~pCgH~~~C~~C~~~~~~------~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPRD----VVLLPCGHLCFCEECAERLLK------RKKKCPICRQPIE 48 (50)
T ss_dssp SB-TTTSSSBSS----EEEETTCEEEEEHHHHHHHHH------TTSBBTTTTBB-S
T ss_pred CCCccCCccCCc----eEEeCCCChHHHHHHhHHhcc------cCCCCCcCChhhc
Confidence 579999997543 455679999 99999865433 6789999998875
No 6
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=94.63 E-value=0.025 Score=34.55 Aligned_cols=51 Identities=22% Similarity=0.481 Sum_probs=39.5
Q ss_pred CCCchhhccccCCCCccchhhhhhhhhhcccccccCCCCC--CCCCceeehhh
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDEN--QDENTWRCSIC 60 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~--ed~~~WrCSvC 60 (135)
...|.+|.|.|..-.-.+.|.-|...+|.+|+.+-..-.. ......-|..|
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C 54 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSC 54 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHH
Confidence 3579999999999888999999999999999998755332 22344556555
No 7
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG2177|consensus
Probab=93.54 E-value=0.034 Score=38.20 Aligned_cols=43 Identities=28% Similarity=0.708 Sum_probs=36.3
Q ss_pred CCCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhh
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRR 62 (135)
.-.|.||+--|+.- +...|.|.+|..|.-..-. ...+|.+||.
T Consensus 13 ~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~------~~~~Cp~cr~ 55 (386)
T KOG2177|consen 13 ELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE------GPLSCPVCRP 55 (386)
T ss_pred cccChhhHHHhhcC----ccccccchHhHHHHHHhcC------CCcCCcccCC
Confidence 45799999999876 7788999999999877665 5599999993
No 9
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF14634 zf-RING_5: zinc-RING finger domain
Probab=93.07 E-value=0.026 Score=33.95 Aligned_cols=43 Identities=28% Similarity=0.859 Sum_probs=32.8
Q ss_pred chhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhh
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRR 62 (135)
|.||.+.|.+++...+ -.|.|..|+.|+.-.. ...-.|.+||+
T Consensus 2 C~~C~~~~~~~~~~~l-~~CgH~~C~~C~~~~~------~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRL-TSCGHIFCEKCLKKLK------GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEE-cccCCHHHHHHHHhhc------CCCCCCcCCCC
Confidence 8899999955544333 6899999999998776 45567888874
No 11
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=91.64 E-value=0.019 Score=31.48 Aligned_cols=44 Identities=25% Similarity=0.668 Sum_probs=29.7
Q ss_pred CchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhh
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRK 63 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK 63 (135)
.|.||+..| .+. .+-..|.|..|.+|....... ...+|.+|+..
T Consensus 1 ~C~iC~~~~--~~~-~~~~~C~H~~c~~C~~~~~~~-----~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEF--REP-VVLLPCGHVFCRSCIDKWLKS-----GKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhh--hCc-eEecCCCChhcHHHHHHHHHh-----CcCCCCCCCCc
Confidence 488999888 222 233459999999998532211 46789999864
No 12
>KOG3799|consensus
Probab=91.60 E-value=0.082 Score=42.52 Aligned_cols=53 Identities=26% Similarity=0.738 Sum_probs=45.4
Q ss_pred CCCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhh
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKL 64 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~ 64 (135)
.-.|-||.|.=-+|-.-|+|.-|+-+.|--|..--.+-.+ --.|-|+.|+...
T Consensus 65 datC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsN--Kv~wvcnlc~k~q 117 (169)
T KOG3799|consen 65 DATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSN--KVMWVCNLCRKQQ 117 (169)
T ss_pred CcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccC--ceEEeccCCcHHH
Confidence 4579999999889999999999999999999887666543 6789999998753
No 13
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=84.87 E-value=0.26 Score=27.97 Aligned_cols=29 Identities=31% Similarity=0.730 Sum_probs=13.3
Q ss_pred CchhhccccCCCCccchhhhhhhhhhcccc
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECHQKVCEDCA 41 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCqqkVCEDCA 41 (135)
.|.+|.+.... ++...|.+|+--+.+.||
T Consensus 2 ~C~~C~~~~~~-~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDG-GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S---EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCC-CceEECccCCCccChhcC
Confidence 58999999888 889999999988888876
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=82.24 E-value=0.31 Score=39.37 Aligned_cols=52 Identities=17% Similarity=0.452 Sum_probs=35.7
Q ss_pred CCCchhhccccCCCCccchhhhhhhhhhccccccc-C------CCC---CCCCCceeehhhhhhhh
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYS-K------LDE---NQDENTWRCSICRRKLQ 65 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYS-k------l~~---~ed~~~WrCSvCRRK~~ 65 (135)
.-.|.||+..|+ +... ..|.|..|..|.... . ... ....+..+|.+||.++.
T Consensus 18 ~~~CpICld~~~--dPVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 18 DFDCNICLDQVR--DPVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred ccCCccCCCcCC--CcEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 357999999875 4444 379999999998521 1 000 11345689999999874
No 15
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=81.17 E-value=0.5 Score=31.72 Aligned_cols=31 Identities=26% Similarity=0.594 Sum_probs=26.7
Q ss_pred hhhccccCCCCccchhhhhhh----hhhccccccc
Q psy15639 14 RVCLKSFKPDDYSRVCYECHQ----KVCEDCASYS 44 (135)
Q Consensus 14 RVClKsfkP~e~~~tC~eCqq----kVCEDCASYS 44 (135)
.+|.+.|+.+|+...|..|+. .+|.+|+--+
T Consensus 1 ~~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~ 35 (71)
T smart00396 1 DVCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSN 35 (71)
T ss_pred CCCCCccCCCCEEEECcCCCCCCCEeEChHHCCCC
Confidence 379999999999999999985 6899998633
No 16
>PHA02929 N1R/p28-like protein; Provisional
Probab=80.97 E-value=0.4 Score=39.28 Aligned_cols=52 Identities=19% Similarity=0.586 Sum_probs=36.9
Q ss_pred CCCCchhhccccCCCCcc----chhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhc
Q psy15639 9 RLGNCRVCLKSFKPDDYS----RVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQS 66 (135)
Q Consensus 9 r~g~CRVClKsfkP~e~~----~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~s 66 (135)
....|-||+-.|...++. .+=..|+|..|.+|-.--... .=+|.+||..+++
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~------~~tCPlCR~~~~~ 228 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE------KNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc------CCCCCCCCCEeeE
Confidence 357899999988755532 234589999999998543211 2279999998764
No 17
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=78.63 E-value=0.84 Score=30.70 Aligned_cols=32 Identities=41% Similarity=0.644 Sum_probs=25.4
Q ss_pred CCCchhhccccCCCCccchhhhhhhhhhcccc
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECHQKVCEDCA 41 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCA 41 (135)
...|-+|+|-|+++|---+|.+|.--.=-+|+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 46799999999999999999999744433443
No 18
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=76.33 E-value=0.99 Score=26.36 Aligned_cols=10 Identities=30% Similarity=1.228 Sum_probs=8.0
Q ss_pred Cceeehhhhh
Q psy15639 53 NTWRCSICRR 62 (135)
Q Consensus 53 ~~WrCSvCRR 62 (135)
..|+|.+|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 6788888875
No 19
>KOG1729|consensus
Probab=72.34 E-value=4.1 Score=34.35 Aligned_cols=62 Identities=24% Similarity=0.520 Sum_probs=50.1
Q ss_pred CCCCCCCCchhhcc-ccCCCCccchhhhhhhhhhcccccc-cCCCCCCCCCceeehhhhhhhhc
Q psy15639 5 KPAARLGNCRVCLK-SFKPDDYSRVCYECHQKVCEDCASY-SKLDENQDENTWRCSICRRKLQS 66 (135)
Q Consensus 5 kp~~r~g~CRVClK-sfkP~e~~~tC~eCqqkVCEDCASY-Skl~~~ed~~~WrCSvCRRK~~s 66 (135)
.|.+.+--|++|.| -|..-+=-|.|..|..-||.-|.+- --++...+...--|+.|=..|+.
T Consensus 163 ~PD~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~el~~ 226 (288)
T KOG1729|consen 163 LPDSEATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEELEK 226 (288)
T ss_pred cCcccceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHHHhc
Confidence 57778889999999 7888888899999999999999876 23444444555589999999975
No 20
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=72.25 E-value=0.85 Score=26.11 Aligned_cols=28 Identities=29% Similarity=0.855 Sum_probs=21.8
Q ss_pred chhhccccCCCCccchhhhhhhhhhcccccc
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASY 43 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCASY 43 (135)
|.||+..|.... +=..|.|.+|.+|..-
T Consensus 1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~ 28 (41)
T PF00097_consen 1 CPICLEPFEDPV---ILLPCGHSFCRDCLRK 28 (41)
T ss_dssp ETTTSSBCSSEE---EETTTSEEEEHHHHHH
T ss_pred CCcCCccccCCC---EEecCCCcchHHHHHH
Confidence 778888776655 5578999999999753
No 21
>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=71.96 E-value=0.5 Score=27.47 Aligned_cols=39 Identities=23% Similarity=0.750 Sum_probs=25.5
Q ss_pred chhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhh
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSIC 60 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvC 60 (135)
|.||.+.+.- ..+-..|.|..|.+|+.-....+ .+|.+|
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~~------~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEKN------PKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHCT------SB-TTT
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHCc------CCCcCC
Confidence 6788876654 33578899999999976443221 577665
No 22
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=71.20 E-value=2.8 Score=29.23 Aligned_cols=51 Identities=24% Similarity=0.679 Sum_probs=37.1
Q ss_pred CCchhhcccc----CCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhh
Q psy15639 11 GNCRVCLKSF----KPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 11 g~CRVClKsf----kP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRR 62 (135)
..|.+|.... |----+.+|-+|++.||--|. ++-.++-.+-..|-|=-|.-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCG-FNP~Phl~E~~eWLCLnCQ~ 57 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCG-FNPTPHLTEVKEWLCLNCQM 57 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccC-CCCCccccccceeeeecchh
Confidence 4577776543 211135799999999999995 56667766789999988864
No 23
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=71.09 E-value=1.7 Score=26.34 Aligned_cols=28 Identities=29% Similarity=0.746 Sum_probs=14.4
Q ss_pred hhcccccccCCCC--CCCCCceeehhhhhh
Q psy15639 36 VCEDCASYSKLDE--NQDENTWRCSICRRK 63 (135)
Q Consensus 36 VCEDCASYSkl~~--~ed~~~WrCSvCRRK 63 (135)
.|..|.+|--.-- +++..+|+|..|..+
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 4667777654332 234679999999864
No 24
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.45 E-value=2.4 Score=31.87 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=28.9
Q ss_pred CCCCchhhccccCCC----------CccchhhhhhhhhhcccccccC
Q psy15639 9 RLGNCRVCLKSFKPD----------DYSRVCYECHQKVCEDCASYSK 45 (135)
Q Consensus 9 r~g~CRVClKsfkP~----------e~~~tC~eCqqkVCEDCASYSk 45 (135)
+...|.-|++.|... .--..|..|+|..|.||-.|--
T Consensus 54 ~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiH 100 (112)
T TIGR00622 54 GSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVH 100 (112)
T ss_pred CCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhh
Confidence 445799999999642 2235699999999999998853
No 25
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=68.85 E-value=1 Score=32.18 Aligned_cols=23 Identities=35% Similarity=0.948 Sum_probs=17.0
Q ss_pred CCchhhccccCCCCccchhhhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECH 33 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCq 33 (135)
..|+.|++-|.++++...|..|+
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCG 93 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSS
T ss_pred EECCCCCCEEecCCCCCCCcCCc
Confidence 46999999999999986655554
No 26
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=68.71 E-value=1 Score=23.57 Aligned_cols=14 Identities=29% Similarity=0.878 Sum_probs=11.7
Q ss_pred eeehhhhhhhhccc
Q psy15639 55 WRCSICRRKLQSRA 68 (135)
Q Consensus 55 WrCSvCRRK~~sr~ 68 (135)
|.|++|.+.+.+..
T Consensus 1 ~~C~~C~~~f~s~~ 14 (25)
T PF12874_consen 1 FYCDICNKSFSSEN 14 (25)
T ss_dssp EEETTTTEEESSHH
T ss_pred CCCCCCCCCcCCHH
Confidence 89999998887764
No 27
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=66.86 E-value=1.7 Score=31.33 Aligned_cols=52 Identities=27% Similarity=0.797 Sum_probs=32.5
Q ss_pred CCCCchhhccccCCCCccchh------hhh---hhhhhccccc--ccCC-CCCCCCCceeehhhhh
Q psy15639 9 RLGNCRVCLKSFKPDDYSRVC------YEC---HQKVCEDCAS--YSKL-DENQDENTWRCSICRR 62 (135)
Q Consensus 9 r~g~CRVClKsfkP~e~~~tC------~eC---qqkVCEDCAS--YSkl-~~~ed~~~WrCSvCRR 62 (135)
.+..|-.|++-- -++..+| ..| .-+.|.+|-. |... .+--....|.|..||-
T Consensus 6 ~g~~CHqCrqKt--~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 6 NGKTCHQCRQKT--LDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCCchhhcCCC--CCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 456788898733 3666677 777 8889999932 3321 1222345799876653
No 28
>KOG0320|consensus
Probab=66.38 E-value=1.2 Score=36.47 Aligned_cols=50 Identities=26% Similarity=0.636 Sum_probs=38.1
Q ss_pred CCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
-.|.||+-+|.-...+- .+|.|..|--|+--.- .++-.|.+||.|+--+.
T Consensus 132 ~~CPiCl~~~sek~~vs--TkCGHvFC~~Cik~al------k~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVS--TKCGHVFCSQCIKDAL------KNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cCCCceecchhhccccc--cccchhHHHHHHHHHH------HhCCCCCCcccccchhh
Confidence 57999999998777533 4899999999985432 34568999999886543
No 29
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=66.34 E-value=2.3 Score=30.66 Aligned_cols=23 Identities=26% Similarity=0.635 Sum_probs=17.1
Q ss_pred CCchhhccccCCCCccchhhhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECH 33 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCq 33 (135)
..|+.|.+-|.++++...|..|+
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cg 93 (115)
T TIGR00100 71 CECEDCSEEVSPEIDLYRCPKCH 93 (115)
T ss_pred EEcccCCCEEecCCcCccCcCCc
Confidence 56999999999998855444443
No 30
>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=66.10 E-value=2.3 Score=24.29 Aligned_cols=29 Identities=28% Similarity=0.486 Sum_probs=21.8
Q ss_pred CchhhccccCCCCccchhhhhhhhhhcccc
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECHQKVCEDCA 41 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCqqkVCEDCA 41 (135)
.|.||+|...+.. ...|.+|.-.+--.||
T Consensus 2 ~C~~C~~~~~~~~-~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCE-eEEeCCCCCeEcCccC
Confidence 5899999888877 8889888755544443
No 31
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=65.24 E-value=6.1 Score=36.43 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=20.8
Q ss_pred Cceeehhhhhhhhcccccccccccc
Q psy15639 53 NTWRCSICRRKLQSRAQPVLSQNST 77 (135)
Q Consensus 53 ~~WrCSvCRRK~~sr~qp~~~q~st 77 (135)
+.=.|..|+.++..+-+-+|++...
T Consensus 40 ~~~fC~~CG~~~~~~~~~~~~~~~~ 64 (645)
T PRK14559 40 DEAHCPNCGAETGTIWWAIIAQASP 64 (645)
T ss_pred ccccccccCCcccchhhhhcccccc
Confidence 3447999999999999999998743
No 32
>smart00336 BBOX B-Box-type zinc finger.
Probab=65.05 E-value=2.8 Score=23.62 Aligned_cols=30 Identities=20% Similarity=0.466 Sum_probs=21.0
Q ss_pred CCCchhhccccCCCCccchhhhhhhhhhcccccc
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASY 43 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASY 43 (135)
...|+.+.+ +.....|.+|+..+|..|..-
T Consensus 3 ~~~C~~h~~----~~~~~~C~~c~~~iC~~C~~~ 32 (42)
T smart00336 3 PPKCDSHGD----EPAEFFCEECGALLCRTCDEA 32 (42)
T ss_pred CCcCCCCCC----CceEEECCCCCcccccccChh
Confidence 445655543 334567999999999999854
No 33
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=63.27 E-value=2.4 Score=27.23 Aligned_cols=13 Identities=23% Similarity=0.915 Sum_probs=7.6
Q ss_pred CCCCceeehhhhh
Q psy15639 50 QDENTWRCSICRR 62 (135)
Q Consensus 50 ed~~~WrCSvCRR 62 (135)
+-+..|+|.+|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 30 DLPDDWVCPVCGA 42 (47)
T ss_dssp GS-TT-B-TTTSS
T ss_pred HCCCCCcCcCCCC
Confidence 3467899999974
No 34
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=63.23 E-value=2.8 Score=30.20 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=17.9
Q ss_pred CCchhhccccCCCCccchhhhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECH 33 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCq 33 (135)
..|+.|.+-|.++++...|..|+
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCH 93 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCC
Confidence 46999999999988777666554
No 35
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=63.22 E-value=3.7 Score=36.69 Aligned_cols=59 Identities=22% Similarity=0.486 Sum_probs=41.7
Q ss_pred hhhhcccccccCCCCCCCCCceeehhhhhhhhccccccccccccccccchHHHHHHHhhccccccc
Q psy15639 34 QKVCEDCASYSKLDENQDENTWRCSICRRKLQSRAQPVLSQNSTDSLLDVPVLEALQRRHSDVKIG 99 (135)
Q Consensus 34 qkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~qp~~~q~stds~l~vpvlealqrrhsd~klg 99 (135)
.-+|..|----| +---+-|||.-|++++.+....-++-+-.--+ |||.-. |||=-.-|+
T Consensus 350 ~p~Cp~Cg~~m~---S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~-evp~~a---rRHLskP~~ 408 (421)
T COG1571 350 NPVCPRCGGRMK---SAGRNGFRCKKCGTRARETLIKEVPRDLEPGV-EVPPVA---RRHLSKPLV 408 (421)
T ss_pred CCCCCccCCchh---hcCCCCcccccccccCCcccccccccccCCCC-cCCchh---hhhccCCcc
Confidence 346777754333 33344899999999999988777777777777 999854 688544443
No 36
>PF12773 DZR: Double zinc ribbon
Probab=60.48 E-value=4.6 Score=24.29 Aligned_cols=42 Identities=19% Similarity=0.461 Sum_probs=24.4
Q ss_pred chhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhcc
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQSR 67 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr 67 (135)
|..|.+.+.++ .+.|..|...+ . .++...+.|+.|+..+...
T Consensus 1 Cp~Cg~~~~~~--~~fC~~CG~~l--------~---~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 1 CPHCGTPNPDD--AKFCPHCGTPL--------P---PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred CCCcCCcCCcc--ccCChhhcCCh--------h---hccCCCCCCcCCcCCCcCC
Confidence 45566655544 34455554432 2 4557788888888865443
No 37
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=60.18 E-value=5 Score=24.01 Aligned_cols=29 Identities=17% Similarity=0.526 Sum_probs=19.0
Q ss_pred hhcccccccCCCCCCCCCceeehhhhhhh
Q psy15639 36 VCEDCASYSKLDENQDENTWRCSICRRKL 64 (135)
Q Consensus 36 VCEDCASYSkl~~~ed~~~WrCSvCRRK~ 64 (135)
.|.+|.+.-...+.++.+.|.|+.|+...
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 46677665544444444589999999754
No 38
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.60 E-value=2.5 Score=36.32 Aligned_cols=60 Identities=22% Similarity=0.409 Sum_probs=39.3
Q ss_pred CCchhhccc--cCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhccccccccccccc
Q psy15639 11 GNCRVCLKS--FKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQSRAQPVLSQNSTD 78 (135)
Q Consensus 11 g~CRVClKs--fkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~qp~~~q~std 78 (135)
..|.+|... +.|+--..+= +|.|+.|+-|..---. ...-.|.+|+..+..+. +-+|.-.|
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~-----~~~~~CP~C~~~lrk~~--fr~q~F~D 65 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFV-----RGSGSCPECDTPLRKNN--FRVQLFED 65 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhc-----CCCCCCCCCCCccchhh--cccccccc
Confidence 369999984 7777433333 8999999999764311 11238999998777665 44444334
No 39
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=59.46 E-value=7.1 Score=39.07 Aligned_cols=56 Identities=21% Similarity=0.553 Sum_probs=39.6
Q ss_pred CCCchhhccccCCC-----CccchhhhhhhhhhcccccccC------CC--CCCC--CCceeehhhhhhhh
Q psy15639 10 LGNCRVCLKSFKPD-----DYSRVCYECHQKVCEDCASYSK------LD--ENQD--ENTWRCSICRRKLQ 65 (135)
Q Consensus 10 ~g~CRVClKsfkP~-----e~~~tC~eCqqkVCEDCASYSk------l~--~~ed--~~~WrCSvCRRK~~ 65 (135)
+..|-.|.+.|-.. --.|-|--|.+.||..|.++.. +. +..+ +..-.|..|=+++.
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs~yp~aKLpKPgsseE~ppRRVCD~CYdq~E 530 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAKLAKPGSSDEAEERLVCDTCYKEYE 530 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCccccCccccCCcccCcccccCCCCCcccccccchhHHHHHHHH
Confidence 46799999999764 3467799999999999997542 21 1111 12236999997764
No 40
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=58.12 E-value=3 Score=25.18 Aligned_cols=32 Identities=25% Similarity=0.762 Sum_probs=14.9
Q ss_pred chhhhhhhhhhcccccccCCCCCCCCCceeehhhh
Q psy15639 27 RVCYECHQKVCEDCASYSKLDENQDENTWRCSICR 61 (135)
Q Consensus 27 ~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCR 61 (135)
-.|..|.-.|=..|......++.+ .|.|..|+
T Consensus 5 l~C~~C~v~VH~~CYGv~~~~~~~---~W~C~~C~ 36 (36)
T PF13831_consen 5 LFCDNCNVAVHQSCYGVSEVPDGD---DWLCDRCE 36 (36)
T ss_dssp EE-SSS--EEEHHHHT-SS--SS--------HHH-
T ss_pred EEeCCCCCcCChhhCCcccCCCCC---cEECCcCC
Confidence 357777777777888877776643 39999985
No 41
>PRK10422 lipopolysaccharide core biosynthesis protein; Provisional
Probab=56.01 E-value=7 Score=31.04 Aligned_cols=25 Identities=36% Similarity=0.573 Sum_probs=22.5
Q ss_pred ccccccchHHHHHHHhhcccccccc
Q psy15639 76 STDSLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 76 stds~l~vpvlealqrrhsd~klg~ 100 (135)
--|-++-.|++++|+++|++++|-.
T Consensus 16 iGD~vl~~P~l~~Lk~~~P~a~I~~ 40 (352)
T PRK10422 16 HGDMLLTTPVISSLKKNYPDAKIDV 40 (352)
T ss_pred cCceeeHHHHHHHHHHHCCCCeEEE
Confidence 3688999999999999999999964
No 42
>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=55.42 E-value=5.8 Score=26.77 Aligned_cols=14 Identities=43% Similarity=0.956 Sum_probs=11.4
Q ss_pred CCchhhccccCCCC
Q psy15639 11 GNCRVCLKSFKPDD 24 (135)
Q Consensus 11 g~CRVClKsfkP~e 24 (135)
+.|.+|+|++.|++
T Consensus 4 kHC~~CG~~Ip~~~ 17 (59)
T PF09889_consen 4 KHCPVCGKPIPPDE 17 (59)
T ss_pred CcCCcCCCcCCcch
Confidence 46889999998874
No 43
>KOG1985|consensus
Probab=55.33 E-value=4.5 Score=39.42 Aligned_cols=28 Identities=29% Similarity=0.774 Sum_probs=20.8
Q ss_pred hhcccccccCCCCCCCC--Cceeehhhhhh
Q psy15639 36 VCEDCASYSKLDENQDE--NTWRCSICRRK 63 (135)
Q Consensus 36 VCEDCASYSkl~~~ed~--~~WrCSvCRRK 63 (135)
-|+-|-+|-..--.-.. -.|||++|+|.
T Consensus 220 RCr~CRtYiNPFV~fid~gr~WrCNlC~~~ 249 (887)
T KOG1985|consen 220 RCRRCRTYINPFVEFIDQGRRWRCNLCGRV 249 (887)
T ss_pred eehhhhhhcCCeEEecCCCceeeechhhhh
Confidence 49999999765433333 48999999985
No 44
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=54.43 E-value=8.2 Score=21.92 Aligned_cols=33 Identities=27% Similarity=0.451 Sum_probs=18.0
Q ss_pred CCCCCchhhccccCCCCccchhhhhhhhhhccc
Q psy15639 8 ARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDC 40 (135)
Q Consensus 8 ~r~g~CRVClKsfkP~e~~~tC~eCqqkVCEDC 40 (135)
.++..|.+|.+.+.-......|.+|+-.|=..|
T Consensus 9 ~~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C 41 (49)
T smart00109 9 KKPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKC 41 (49)
T ss_pred CCCCCccccccccCcCCCCcCCCCCCchHHHHH
Confidence 345568888777763222455666654443333
No 45
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=54.12 E-value=5.9 Score=23.68 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=16.7
Q ss_pred hhhhcccccccCCCCCCCCCceeehhhh
Q psy15639 34 QKVCEDCASYSKLDENQDENTWRCSICR 61 (135)
Q Consensus 34 qkVCEDCASYSkl~~~ed~~~WrCSvCR 61 (135)
|.+|--|...= .--..+.++||++|.
T Consensus 1 q~~C~~C~t~L--~yP~gA~~vrCs~C~ 26 (31)
T TIGR01053 1 QVVCGGCRTLL--MYPRGASSVRCALCQ 26 (31)
T ss_pred CcCcCCCCcEe--ecCCCCCeEECCCCC
Confidence 44566665432 233468899999996
No 46
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.90 E-value=5.7 Score=28.73 Aligned_cols=23 Identities=35% Similarity=0.860 Sum_probs=16.0
Q ss_pred CCchhhccccCCCCccch-hhhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRV-CYECH 33 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~t-C~eCq 33 (135)
..|+.|++-|.+.++... |..|+
T Consensus 72 ~~C~~Cg~~~~~~~~~~~~CP~Cg 95 (117)
T PRK00564 72 LECKDCSHVFKPNALDYGVCEKCH 95 (117)
T ss_pred EEhhhCCCccccCCccCCcCcCCC
Confidence 469999999998876443 44443
No 47
>PRK10964 ADP-heptose:LPS heptosyl transferase I; Provisional
Probab=53.37 E-value=6.6 Score=30.62 Aligned_cols=24 Identities=21% Similarity=0.292 Sum_probs=21.1
Q ss_pred cccccchHHHHHHHhhcccccccc
Q psy15639 77 TDSLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 77 tds~l~vpvlealqrrhsd~klg~ 100 (135)
-|-++-.|++++|++.++|++|..
T Consensus 12 GD~v~~~p~~~~lk~~~P~a~I~~ 35 (322)
T PRK10964 12 GDVLHTLPALTDAQQAIPGIQFDW 35 (322)
T ss_pred HHHHhHHHHHHHHHHhCCCCEEEE
Confidence 467788899999999999999965
No 48
>TIGR02193 heptsyl_trn_I lipopolysaccharide heptosyltransferase I. This family consists of examples of ADP-heptose:LPS heptosyltransferase I, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.
Probab=53.08 E-value=6.3 Score=30.37 Aligned_cols=24 Identities=29% Similarity=0.468 Sum_probs=21.3
Q ss_pred cccccchHHHHHHHhhcccccccc
Q psy15639 77 TDSLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 77 tds~l~vpvlealqrrhsd~klg~ 100 (135)
-|-++-.|++.+|.++|++++|-.
T Consensus 11 GD~vl~~p~l~~Lr~~~P~a~I~~ 34 (319)
T TIGR02193 11 GDVIHTLPALTDIKRALPDVEIDW 34 (319)
T ss_pred HHHHHHHHHHHHHHHhCCCCEEEE
Confidence 477888999999999999999865
No 49
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=52.22 E-value=3.3 Score=23.99 Aligned_cols=30 Identities=20% Similarity=0.653 Sum_probs=21.9
Q ss_pred CCchhhccccCCCCccchhhhhhhhhhccccccc
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYS 44 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYS 44 (135)
..|..+.+ ......|.+|+..+|.+|+...
T Consensus 4 ~~C~~H~~----~~~~~~C~~C~~~~C~~C~~~~ 33 (42)
T PF00643_consen 4 PKCPEHPE----EPLSLFCEDCNEPLCSECTVSG 33 (42)
T ss_dssp SB-SSTTT----SBEEEEETTTTEEEEHHHHHTS
T ss_pred ccCccCCc----cceEEEecCCCCccCccCCCCC
Confidence 45555543 2378899999999999998764
No 50
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=51.76 E-value=4.8 Score=26.56 Aligned_cols=32 Identities=28% Similarity=0.706 Sum_probs=20.3
Q ss_pred chhhccccCCCC------ccchhhhhhhhhhccccccc
Q psy15639 13 CRVCLKSFKPDD------YSRVCYECHQKVCEDCASYS 44 (135)
Q Consensus 13 CRVClKsfkP~e------~~~tC~eCqqkVCEDCASYS 44 (135)
|-=|++.|.... ....|..|+|-.|-||--|-
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi 39 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFI 39 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTT
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhh
Confidence 556888888763 56899999999999998875
No 51
>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=51.59 E-value=5.5 Score=30.39 Aligned_cols=24 Identities=29% Similarity=0.629 Sum_probs=19.5
Q ss_pred CCchhhccccCCCCccchhhhhhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQK 35 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqk 35 (135)
..|+.|+|-|.-. ...+|..|.++
T Consensus 4 ~nC~~CgklF~~~-~~~iCp~C~~~ 27 (137)
T TIGR03826 4 ANCPKCGRLFVKT-GRDVCPSCYEE 27 (137)
T ss_pred ccccccchhhhhc-CCccCHHHhHH
Confidence 4799999999885 66788888763
No 52
>TIGR02201 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative. This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II.
Probab=51.56 E-value=9.4 Score=29.94 Aligned_cols=24 Identities=38% Similarity=0.599 Sum_probs=21.7
Q ss_pred cccccchHHHHHHHhhcccccccc
Q psy15639 77 TDSLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 77 tds~l~vpvlealqrrhsd~klg~ 100 (135)
-|-++-.|++.+|+++++|++|--
T Consensus 11 GD~vl~tp~l~~Lk~~~P~a~I~~ 34 (344)
T TIGR02201 11 GDMLLTTPVISSLKKNYPDAKIDV 34 (344)
T ss_pred cceeeHHHHHHHHHHHCCCCEEEE
Confidence 578899999999999999999865
No 53
>PF06718 DUF1203: Protein of unknown function (DUF1203); InterPro: IPR009593 This family consists of several hypothetical bacterial proteins of around 155 residues in length. Family members are present in Rhizobium, Agrobacterium and Streptomyces species.
Probab=51.12 E-value=7 Score=29.13 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=13.7
Q ss_pred CCchhhccccCCCCcc
Q psy15639 11 GNCRVCLKSFKPDDYS 26 (135)
Q Consensus 11 g~CRVClKsfkP~e~~ 26 (135)
-+||+|||-..++|--
T Consensus 2 ~PcR~cL~~~~~Ge~~ 17 (117)
T PF06718_consen 2 YPCRHCLRDAEPGEEL 17 (117)
T ss_pred CCcEEecccCCCCCeE
Confidence 4799999999999853
No 54
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=49.85 E-value=7.6 Score=25.17 Aligned_cols=13 Identities=23% Similarity=0.915 Sum_probs=10.4
Q ss_pred CCCCceeehhhhh
Q psy15639 50 QDENTWRCSICRR 62 (135)
Q Consensus 50 ed~~~WrCSvCRR 62 (135)
+-+..|+|.+|+-
T Consensus 30 ~Lp~~w~CP~C~a 42 (50)
T cd00730 30 DLPDDWVCPVCGA 42 (50)
T ss_pred HCCCCCCCCCCCC
Confidence 3477999999974
No 55
>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=49.41 E-value=6 Score=20.20 Aligned_cols=11 Identities=45% Similarity=1.044 Sum_probs=8.7
Q ss_pred CchhhccccCC
Q psy15639 12 NCRVCLKSFKP 22 (135)
Q Consensus 12 ~CRVClKsfkP 22 (135)
.|.+|.|+|+-
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 48899999864
No 56
>KOG1813|consensus
Probab=49.37 E-value=6.8 Score=34.26 Aligned_cols=51 Identities=24% Similarity=0.450 Sum_probs=37.9
Q ss_pred CCCCCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 8 ARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 8 ~r~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
.=+..|-||++.|.-. +=..|.|-+|+-||+-.-- .+=+|-||.+-+-+..
T Consensus 239 ~~Pf~c~icr~~f~~p----Vvt~c~h~fc~~ca~~~~q------k~~~c~vC~~~t~g~~ 289 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRP----VVTKCGHYFCEVCALKPYQ------KGEKCYVCSQQTHGSF 289 (313)
T ss_pred cCCccccccccccccc----hhhcCCceeehhhhccccc------cCCcceeccccccccc
Confidence 3456799999999644 4467999999999974322 2246999998877766
No 57
>PRK10916 ADP-heptose:LPS heptosyltransferase II; Provisional
Probab=49.26 E-value=8.1 Score=30.55 Aligned_cols=24 Identities=17% Similarity=0.277 Sum_probs=21.5
Q ss_pred cccccchHHHHHHHhhcccccccc
Q psy15639 77 TDSLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 77 tds~l~vpvlealqrrhsd~klg~ 100 (135)
-|-++-.|++.+|++.++|++|-.
T Consensus 12 GD~il~tP~l~~Lk~~~P~a~I~~ 35 (348)
T PRK10916 12 GDMMMSQSLYRTLKARYPQAIIDV 35 (348)
T ss_pred cHHHhHHHHHHHHHHHCCCCeEEE
Confidence 478899999999999999999864
No 58
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=49.13 E-value=6 Score=24.18 Aligned_cols=24 Identities=38% Similarity=0.987 Sum_probs=16.3
Q ss_pred hhccccc--ccCCCCCCCCCceeehhhhh
Q psy15639 36 VCEDCAS--YSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 36 VCEDCAS--YSkl~~~ed~~~WrCSvCRR 62 (135)
||..|.+ +..+.. ...|+|.-||+
T Consensus 20 ~CP~Cg~~~~~~~~~---~~~~~C~~C~~ 45 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKT---RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCeeeEEeCC---CCeEECCCCCC
Confidence 4555654 344444 78999999985
No 59
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=48.30 E-value=6.1 Score=21.74 Aligned_cols=14 Identities=36% Similarity=0.626 Sum_probs=10.9
Q ss_pred CCCCCchhhccccC
Q psy15639 8 ARLGNCRVCLKSFK 21 (135)
Q Consensus 8 ~r~g~CRVClKsfk 21 (135)
.++-.|.+|.|+|+
T Consensus 12 ~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 12 EKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSEEESSSSEEES
T ss_pred CCCCCCCCCcCeeC
Confidence 35578999999985
No 60
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=47.50 E-value=6.2 Score=30.11 Aligned_cols=34 Identities=24% Similarity=0.600 Sum_probs=22.5
Q ss_pred CchhhccccCCCCccch-hhhhhhhhhcccccccCC
Q psy15639 12 NCRVCLKSFKPDDYSRV-CYECHQKVCEDCASYSKL 46 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~t-C~eCqqkVCEDCASYSkl 46 (135)
.|-+|++-++ +...++ =.+=.-.||.+||-|-|.
T Consensus 2 ~CEiCG~~i~-~~~~~v~iega~l~vC~~C~k~G~~ 36 (154)
T TIGR00270 2 NCEICGRKIK-GKGFKIVIEGSEMTVCGECRKFGKE 36 (154)
T ss_pred ccccCCCccC-CCCeEEEEcCeEEehhhhHHhcCCc
Confidence 3899998886 332222 222335799999999883
No 61
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=47.33 E-value=7.3 Score=25.46 Aligned_cols=28 Identities=32% Similarity=0.729 Sum_probs=19.1
Q ss_pred hhhcccccccCCC--CCCCCCceeehhhhh
Q psy15639 35 KVCEDCASYSKLD--ENQDENTWRCSICRR 62 (135)
Q Consensus 35 kVCEDCASYSkl~--~~ed~~~WrCSvCRR 62 (135)
.+|.-|.+-.-+. +.-+.-.|+|..|+-
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCC
Confidence 4566666655555 555567999999974
No 62
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=47.26 E-value=14 Score=22.98 Aligned_cols=34 Identities=26% Similarity=0.600 Sum_probs=27.4
Q ss_pred CchhhccccCCCCccchhhhh-hhhhhcccccccCC
Q psy15639 12 NCRVCLKSFKPDDYSRVCYEC-HQKVCEDCASYSKL 46 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eC-qqkVCEDCASYSkl 46 (135)
.|..|.|.+.. .+...|.+| +-..|++|-+.-+.
T Consensus 2 ~Cd~C~~~~~~-g~r~~C~~C~d~dLC~~Cf~~g~~ 36 (49)
T cd02335 2 HCDYCSKDITG-TIRIKCAECPDFDLCLECFSAGAE 36 (49)
T ss_pred CCCCcCCCCCC-CcEEECCCCCCcchhHHhhhCcCC
Confidence 48899998863 388899999 77899999886543
No 63
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=46.41 E-value=5.5 Score=24.84 Aligned_cols=28 Identities=25% Similarity=0.875 Sum_probs=14.0
Q ss_pred chhhccccCCCCccchhhhhhhhhhcccc
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCA 41 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCA 41 (135)
|.||+. |.-++---+=--|+|-.|++|.
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl 28 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCL 28 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHH
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHH
Confidence 788988 8554443333459999999985
No 64
>TIGR02195 heptsyl_trn_II lipopolysaccharide heptosyltransferase II. This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.
Probab=45.22 E-value=9.7 Score=29.63 Aligned_cols=24 Identities=17% Similarity=0.278 Sum_probs=21.2
Q ss_pred cccccchHHHHHHHhhcccccccc
Q psy15639 77 TDSLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 77 tds~l~vpvlealqrrhsd~klg~ 100 (135)
-|-++-.|++++|++.++|++|-.
T Consensus 11 GD~i~~~p~l~~Lk~~~P~a~I~~ 34 (334)
T TIGR02195 11 GDMVMAQSLYRLLKKRYPQAVIDV 34 (334)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEE
Confidence 477888999999999999999865
No 65
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=45.07 E-value=9.3 Score=22.60 Aligned_cols=26 Identities=31% Similarity=0.844 Sum_probs=10.4
Q ss_pred CchhhccccCCCCccchhhhhhhhhh
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECHQKVC 37 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCqqkVC 37 (135)
.|.||.+.=.--+-..+|..|+.-.|
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC 27 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLC 27 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCccc
Confidence 35555552222223444444443333
No 66
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.78 E-value=4.9 Score=35.31 Aligned_cols=50 Identities=20% Similarity=0.448 Sum_probs=35.6
Q ss_pred CCCCCCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhc
Q psy15639 7 AARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQS 66 (135)
Q Consensus 7 ~~r~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~s 66 (135)
....-.|.||+.-|+ +.. --.|.|..|..|..+--.. .-.|.+|+..+..
T Consensus 23 Le~~l~C~IC~d~~~--~Pv--itpCgH~FCs~CI~~~l~~------~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 23 LDTSLRCHICKDFFD--VPV--LTSCSHTFCSLCIRRCLSN------QPKCPLCRAEDQE 72 (397)
T ss_pred cccccCCCcCchhhh--Ccc--CCCCCCchhHHHHHHHHhC------CCCCCCCCCcccc
Confidence 345568999999885 222 2589999999998753211 2379999988754
No 67
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=44.66 E-value=6.6 Score=38.22 Aligned_cols=35 Identities=31% Similarity=0.680 Sum_probs=26.2
Q ss_pred hhhcccccccCC--CCCCCCCceeehhhhhhhhcccc
Q psy15639 35 KVCEDCASYSKL--DENQDENTWRCSICRRKLQSRAQ 69 (135)
Q Consensus 35 kVCEDCASYSkl--~~~ed~~~WrCSvCRRK~~sr~q 69 (135)
--|+-|.||-.. .--++...|||.+||-|++-+..
T Consensus 200 vRCrrCrsYiNPfv~fi~~g~kw~CNiC~~kN~vp~~ 236 (861)
T COG5028 200 VRCRRCRSYINPFVQFIEQGRKWRCNICRSKNDVPEG 236 (861)
T ss_pred hhhhhhHhhcCceEEEecCCcEEEEeeccccccCccc
Confidence 468999999762 22345669999999999986653
No 68
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=44.60 E-value=12 Score=25.77 Aligned_cols=36 Identities=25% Similarity=0.718 Sum_probs=23.9
Q ss_pred CCchhhccccCCCC--ccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhh
Q psy15639 11 GNCRVCLKSFKPDD--YSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRK 63 (135)
Q Consensus 11 g~CRVClKsfkP~e--~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK 63 (135)
-.|--|..-+.|.| +...|.+|.+ ...|||.-||+-
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~-----------------~~I~RC~~CRk~ 45 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGE-----------------VIIYRCEKCRKQ 45 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCC-----------------eeEeechhHHhc
Confidence 36888888888887 4455655543 236777777753
No 69
>PLN02189 cellulose synthase
Probab=43.92 E-value=52 Score=32.83 Aligned_cols=50 Identities=26% Similarity=0.678 Sum_probs=41.1
Q ss_pred CCchhhcccc---CCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 11 GNCRVCLKSF---KPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 11 g~CRVClKsf---kP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
..|.||+--. +-+|++--|.||.--||--|-.|-+-.. +=.|..|+-.-.
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg-----~q~CpqCkt~Y~ 87 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREG-----TQNCPQCKTRYK 87 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcC-----CccCcccCCchh
Confidence 4899999765 5688999999999999999999977655 447999976554
No 70
>PRK06424 transcription factor; Provisional
Probab=43.86 E-value=7.2 Score=29.66 Aligned_cols=35 Identities=23% Similarity=0.456 Sum_probs=22.9
Q ss_pred chhhccccCCCCccchhhhhhhhhhcccccccCCCC
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDE 48 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~ 48 (135)
|-+|+|-.+-- +.-.=.+=.-.||++||-|-+...
T Consensus 3 CE~CG~~~~~~-~~v~ieg~~l~vC~~Ca~~G~~v~ 37 (144)
T PRK06424 3 CEMCGKKVPQT-TKVMIDGAILNVCDDCAKFGTPVI 37 (144)
T ss_pred ccccCcccCCc-eEEEEcCeeeehhHHHHHcCCccc
Confidence 88888877622 322223334579999999988444
No 71
>KOG2169|consensus
Probab=43.20 E-value=7 Score=35.55 Aligned_cols=36 Identities=31% Similarity=0.730 Sum_probs=29.8
Q ss_pred hhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 28 VCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 28 tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
-+..|+|.-|-|=++|- +-++.--+|+|.||-++.+
T Consensus 321 r~~~CkHlQcFD~~~~l--q~n~~~pTW~CPVC~~~~~ 356 (636)
T KOG2169|consen 321 RGHTCKHLQCFDALSYL--QMNEQKPTWRCPVCQKAAP 356 (636)
T ss_pred cccccccceecchhhhH--HhccCCCeeeCccCCcccc
Confidence 45678999999988884 4578899999999988764
No 72
>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=43.02 E-value=5.8 Score=19.39 Aligned_cols=14 Identities=29% Similarity=1.042 Sum_probs=8.3
Q ss_pred eeehhhhhhhhccc
Q psy15639 55 WRCSICRRKLQSRA 68 (135)
Q Consensus 55 WrCSvCRRK~~sr~ 68 (135)
|.|.+|.....++.
T Consensus 1 ~~C~~C~~~~~~~~ 14 (24)
T PF13894_consen 1 FQCPICGKSFRSKS 14 (24)
T ss_dssp EE-SSTS-EESSHH
T ss_pred CCCcCCCCcCCcHH
Confidence 78888887765543
No 73
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=42.95 E-value=6.8 Score=25.77 Aligned_cols=26 Identities=23% Similarity=0.713 Sum_probs=16.8
Q ss_pred hhccccCCCCccchhhhhhh----hhhccc
Q psy15639 15 VCLKSFKPDDYSRVCYECHQ----KVCEDC 40 (135)
Q Consensus 15 VClKsfkP~e~~~tC~eCqq----kVCEDC 40 (135)
.|.+.|..++....|-.|.. -+|++|
T Consensus 2 ~C~~~~~~~q~~y~C~tC~~~~~~~iC~~C 31 (71)
T PF02207_consen 2 KCTYVWTSGQIFYRCLTCSLDESSGICEEC 31 (71)
T ss_dssp SS--B--TT-EEEEETTTBSSTT-BBEHHH
T ss_pred cCCCCCcCCCEEEECccCCCCCCEEEchhh
Confidence 58888999999999999976 467777
No 74
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=42.81 E-value=6.4 Score=27.28 Aligned_cols=24 Identities=38% Similarity=0.812 Sum_probs=18.7
Q ss_pred CCCCCCchhhccccCCCCccchhhhh
Q psy15639 7 AARLGNCRVCLKSFKPDDYSRVCYEC 32 (135)
Q Consensus 7 ~~r~g~CRVClKsfkP~e~~~tC~eC 32 (135)
..|+. |+-|.|-+.|+|.. .|.+|
T Consensus 15 i~RAl-Ca~C~~~L~~~E~h-~Ce~C 38 (58)
T PF05810_consen 15 IERAL-CANCGQKLHPDETH-VCEEC 38 (58)
T ss_pred HHHHH-HhccCcccccchhh-HHHHH
Confidence 45888 99999999999973 45544
No 75
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=41.95 E-value=8.6 Score=32.51 Aligned_cols=53 Identities=23% Similarity=0.455 Sum_probs=34.7
Q ss_pred CchhhccccCCCCccchhhhhhh-----hhhcccccccCCCCCCCCCceeehhhhhhhhcc
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECHQ-----KVCEDCASYSKLDENQDENTWRCSICRRKLQSR 67 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCqq-----kVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr 67 (135)
-|.-|..-+...++..+|..|.. -.||.|..+-...+ ....+|.+|+....-|
T Consensus 122 Yc~~~e~fl~e~~v~g~CP~C~~~~a~g~~Ce~cG~~~~~~~---l~~p~~~~~g~~~~~r 179 (391)
T PF09334_consen 122 YCPSCERFLPESFVEGTCPYCGSDKARGDQCENCGRPLEPEE---LINPVCKICGSPPEVR 179 (391)
T ss_dssp EETTTTEEE-GGGETCEETTT--SSCTTTEETTTSSBEECCC---SECEEETTTS-B-EEE
T ss_pred EecCcCcccccceeeccccCcCccccCCCcccCCCCCccccc---ccCCccccccccCccc
Confidence 36667653333445578988873 47999998766544 8889999999987655
No 76
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.63 E-value=9.5 Score=28.22 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=10.2
Q ss_pred CCchhhccccCCC
Q psy15639 11 GNCRVCLKSFKPD 23 (135)
Q Consensus 11 g~CRVClKsfkP~ 23 (135)
.-|+.|++-|..+
T Consensus 71 ~~C~~CG~~~~~~ 83 (135)
T PRK03824 71 LKCRNCGNEWSLK 83 (135)
T ss_pred EECCCCCCEEecc
Confidence 4688888888776
No 77
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=41.10 E-value=8.5 Score=28.01 Aligned_cols=48 Identities=23% Similarity=0.616 Sum_probs=24.9
Q ss_pred CCCCchhhcccc---CCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhh
Q psy15639 9 RLGNCRVCLKSF---KPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICR 61 (135)
Q Consensus 9 r~g~CRVClKsf---kP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCR 61 (135)
-+..|+||+-.. .-+|+|--|.||.--||--|-.|-+-.- +-.|..|+
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg-----~q~CpqCk 58 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEG-----NQVCPQCK 58 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS------SB-TTT-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcC-----cccccccC
Confidence 456899998755 3478999999999999999999987544 34577775
No 78
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=39.93 E-value=12 Score=29.04 Aligned_cols=28 Identities=21% Similarity=0.490 Sum_probs=20.6
Q ss_pred cccc--cCCCCCCCCCceeehhhhhhhhcc
Q psy15639 40 CASY--SKLDENQDENTWRCSICRRKLQSR 67 (135)
Q Consensus 40 CASY--Skl~~~ed~~~WrCSvCRRK~~sr 67 (135)
|.-+ +.+.+.+....+-|.+|++|++..
T Consensus 147 CvM~~s~s~~e~D~k~~~lC~~C~~kL~~~ 176 (179)
T PRK13267 147 CVMNFSNSVRDVDIKEPNFCGSCQRKLERN 176 (179)
T ss_pred ccCCCCCCHHHHhCCCcccCHHHHHHHHHh
Confidence 6555 444555567889999999999764
No 79
>PRK03670 competence damage-inducible protein A; Provisional
Probab=39.78 E-value=18 Score=29.38 Aligned_cols=19 Identities=42% Similarity=0.581 Sum_probs=16.7
Q ss_pred hHHHHHHHhhccccccccCC
Q psy15639 83 VPVLEALQRRHSDVKIGSAN 102 (135)
Q Consensus 83 vpvlealqrrhsd~klg~~~ 102 (135)
.|+|++|+++|. ++|||--
T Consensus 197 a~~l~~~~~~~~-v~igSyP 215 (252)
T PRK03670 197 APILEEALERFN-VKIHSSP 215 (252)
T ss_pred HHHHHHHHHHCC-ceEecCC
Confidence 699999999995 9999944
No 80
>COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=39.74 E-value=14 Score=29.64 Aligned_cols=24 Identities=29% Similarity=0.542 Sum_probs=21.6
Q ss_pred cccccchHHHHHHHhhcccccccc
Q psy15639 77 TDSLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 77 tds~l~vpvlealqrrhsd~klg~ 100 (135)
-|-++..|++.+|++.++|++|.-
T Consensus 13 GD~vlt~p~~~~lk~~~P~a~i~~ 36 (334)
T COG0859 13 GDVVLTLPLLRTLKKAYPNAKIDV 36 (334)
T ss_pred hHHHhHHHHHHHHHHHCCCCEEEE
Confidence 367888999999999999999985
No 81
>KOG4739|consensus
Probab=39.59 E-value=14 Score=30.79 Aligned_cols=45 Identities=24% Similarity=0.712 Sum_probs=35.3
Q ss_pred CchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhc
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQS 66 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~s 66 (135)
-|-.|.+.=+++.|+-| -|.|-.|+-|...+-.+ .|..|++-+..
T Consensus 5 hCn~C~~~~~~~~f~LT--aC~HvfC~~C~k~~~~~--------~C~lCkk~ir~ 49 (233)
T KOG4739|consen 5 HCNKCFRFPSQDPFFLT--ACRHVFCEPCLKASSPD--------VCPLCKKSIRI 49 (233)
T ss_pred EeccccccCCCCceeee--echhhhhhhhcccCCcc--------ccccccceeee
Confidence 37778776667777766 79999999999887766 79999987543
No 82
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=39.04 E-value=11 Score=28.78 Aligned_cols=16 Identities=31% Similarity=0.845 Sum_probs=12.2
Q ss_pred CCCCchhhccccCCCC
Q psy15639 9 RLGNCRVCLKSFKPDD 24 (135)
Q Consensus 9 r~g~CRVClKsfkP~e 24 (135)
....|.+|+|.|.|..
T Consensus 113 ~~~~C~~Cg~~f~~~k 128 (181)
T PRK08222 113 HLQRCSRCERPFAPQK 128 (181)
T ss_pred ccCcCcccCCccCcHh
Confidence 3566999999998754
No 83
>PRK01343 zinc-binding protein; Provisional
Probab=38.86 E-value=22 Score=24.12 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=18.1
Q ss_pred CCCCCCCCchhhccccCCCCccchhh
Q psy15639 5 KPAARLGNCRVCLKSFKPDDYSRVCY 30 (135)
Q Consensus 5 kp~~r~g~CRVClKsfkP~e~~~tC~ 30 (135)
++..+...|-||.|.|.. +|.-.|.
T Consensus 4 ~~~~p~~~CP~C~k~~~~-~~rPFCS 28 (57)
T PRK01343 4 EPLRPTRPCPECGKPSTR-EAYPFCS 28 (57)
T ss_pred ccCCCCCcCCCCCCcCcC-CCCcccC
Confidence 455677899999999874 4555554
No 84
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=37.44 E-value=9.1 Score=25.86 Aligned_cols=24 Identities=38% Similarity=1.125 Sum_probs=7.7
Q ss_pred CCCccch-----hhhhhhh----------hhcccccccC
Q psy15639 22 PDDYSRV-----CYECHQK----------VCEDCASYSK 45 (135)
Q Consensus 22 P~e~~~t-----C~eCqqk----------VCEDCASYSk 45 (135)
|+||... |++|..+ -|..|.||-+
T Consensus 21 P~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT 59 (61)
T PF14599_consen 21 PEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNT 59 (61)
T ss_dssp -------EEEEEESSS--EEEEE--TT----TTTS---E
T ss_pred CHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCccc
Confidence 5555544 8888765 4888888864
No 85
>cd03789 GT1_LPS_heptosyltransferase Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=36.69 E-value=17 Score=27.61 Aligned_cols=24 Identities=38% Similarity=0.577 Sum_probs=21.5
Q ss_pred cccccchHHHHHHHhhcccccccc
Q psy15639 77 TDSLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 77 tds~l~vpvlealqrrhsd~klg~ 100 (135)
-|-++-.|++.+|++++++++|..
T Consensus 11 GD~i~~~p~l~~Lk~~~P~~~I~~ 34 (279)
T cd03789 11 GDVVLATPLLRALKARYPDARITV 34 (279)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEE
Confidence 477888999999999999999876
No 86
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=36.26 E-value=3.3 Score=26.19 Aligned_cols=31 Identities=32% Similarity=0.819 Sum_probs=13.9
Q ss_pred hhhhhhhhcccccccCCCCCCCCCceeehhhhh
Q psy15639 30 YECHQKVCEDCASYSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 30 ~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRR 62 (135)
..|+|.-|-|=.+|=.. ++..+.|+|.+|.+
T Consensus 19 ~~C~H~~CFDl~~fl~~--~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 19 KNCKHLQCFDLESFLES--NQRTPKWKCPICNK 49 (50)
T ss_dssp TT--SS--EEHHHHHHH--HHHS---B-TTT--
T ss_pred CcCcccceECHHHHHHH--hhccCCeECcCCcC
Confidence 46888888887666443 33445699999975
No 87
>KOG1245|consensus
Probab=35.62 E-value=18 Score=36.41 Aligned_cols=55 Identities=22% Similarity=0.468 Sum_probs=40.1
Q ss_pred CCCCCCCchhhccccCCCC--ccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 6 PAARLGNCRVCLKSFKPDD--YSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 6 p~~r~g~CRVClKsfkP~e--~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
..+..+-|.||++.+++++ .+.-|..+.|.-|-.=+.++....+ |-|.-||....
T Consensus 1104 ~s~~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~d-----W~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1104 RSAVNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGD-----WMCPSCRKEHR 1160 (1404)
T ss_pred cccchhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCC-----ccCCccchhhh
Confidence 4566788999999999954 3444555556667776777776653 99999987664
No 88
>PHA02926 zinc finger-like protein; Provisional
Probab=35.53 E-value=11 Score=31.95 Aligned_cols=59 Identities=19% Similarity=0.578 Sum_probs=40.8
Q ss_pred CCCCCCchhhccc-cC---CCC-ccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 7 AARLGNCRVCLKS-FK---PDD-YSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 7 ~~r~g~CRVClKs-fk---P~e-~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
.++...|-||+.. ++ |+| .+-+=..|.|-.|-+|----+....+......|.+||..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 3567889999954 44 233 45566789999999997644433334456788999998765
No 89
>PLN02436 cellulose synthase A
Probab=35.31 E-value=21 Score=35.69 Aligned_cols=50 Identities=22% Similarity=0.654 Sum_probs=41.3
Q ss_pred CCchhhcccc---CCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 11 GNCRVCLKSF---KPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 11 g~CRVClKsf---kP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
..|.||+-.. +-+|++--|.||.--||--|-.|-+-.. +=.|..|+-+-.
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg-----~~~Cpqckt~Y~ 89 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREG-----NQACPQCKTRYK 89 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcC-----CccCcccCCchh
Confidence 4899999764 6789999999999999999999977655 447999976554
No 90
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=35.14 E-value=24 Score=27.43 Aligned_cols=34 Identities=38% Similarity=0.710 Sum_probs=16.0
Q ss_pred hhhhhhhh--hhcccccccCCCCCCCCCceeehhhh
Q psy15639 28 VCYECHQK--VCEDCASYSKLDENQDENTWRCSICR 61 (135)
Q Consensus 28 tC~eCqqk--VCEDCASYSkl~~~ed~~~WrCSvCR 61 (135)
.|.-|++| +||-|.+-.-+--=+..++-+|..|.
T Consensus 144 ~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~ 179 (202)
T PF13901_consen 144 SCELCQQKGFICEICNSDDIIFPFQIDTTVRCPKCK 179 (202)
T ss_pred HhHHHHhCCCCCccCCCCCCCCCCCCCCeeeCCcCc
Confidence 34445443 55555443333333334555555554
No 91
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=35.10 E-value=12 Score=19.16 Aligned_cols=26 Identities=31% Similarity=0.931 Sum_probs=17.2
Q ss_pred chhhccccCCCCccchhhhhhhhhhccccc
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCAS 42 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCAS 42 (135)
|.||+...+ ..+-..|.|..|..|..
T Consensus 1 C~iC~~~~~----~~~~~~C~H~~c~~C~~ 26 (39)
T smart00184 1 CPICLEELK----DPVVLPCGHTFCRSCIR 26 (39)
T ss_pred CCcCccCCC----CcEEecCCChHHHHHHH
Confidence 667777632 22234699999999864
No 92
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.81 E-value=28 Score=34.97 Aligned_cols=69 Identities=17% Similarity=0.330 Sum_probs=35.3
Q ss_pred CCCccchhhhhhhh----hhcccccccCCCCCCCCCceeehhhhhhhhccccc-cccccccccccchHHHHHHHhhcccc
Q psy15639 22 PDDYSRVCYECHQK----VCEDCASYSKLDENQDENTWRCSICRRKLQSRAQP-VLSQNSTDSLLDVPVLEALQRRHSDV 96 (135)
Q Consensus 22 P~e~~~tC~eCqqk----VCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~qp-~~~q~stds~l~vpvlealqrrhsd~ 96 (135)
-+--.+.|.+|.+. .|.+|-.- ....|+|+.||.....-.-| |=..-...+...+++-+.+++-...+
T Consensus 622 VEVg~RfCpsCG~~t~~frCP~CG~~-------Te~i~fCP~CG~~~~~y~CPKCG~El~~~s~~~i~l~~~~~~A~~~l 694 (1121)
T PRK04023 622 VEIGRRKCPSCGKETFYRRCPFCGTH-------TEPVYRCPRCGIEVEEDECEKCGREPTPYSKRKIDLKELYDRALENL 694 (1121)
T ss_pred ecccCccCCCCCCcCCcccCCCCCCC-------CCcceeCccccCcCCCCcCCCCCCCCCccceEEecHHHHHHHHHHHh
Confidence 33345556666533 56666544 23456777776554421111 11222344556777777777665544
Q ss_pred c
Q psy15639 97 K 97 (135)
Q Consensus 97 k 97 (135)
.
T Consensus 695 g 695 (1121)
T PRK04023 695 G 695 (1121)
T ss_pred C
Confidence 3
No 93
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=34.79 E-value=12 Score=22.43 Aligned_cols=32 Identities=19% Similarity=0.455 Sum_probs=21.1
Q ss_pred hhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 36 VCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 36 VCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
+|..|-+.. +-.+.......|+.|+..+..+.
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLVLEENI 33 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BBEE-TT
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCEeeccc
Confidence 467777755 55556677889999987766554
No 94
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.94 E-value=15 Score=27.25 Aligned_cols=24 Identities=21% Similarity=0.531 Sum_probs=17.4
Q ss_pred cchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhh
Q psy15639 26 SRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKL 64 (135)
Q Consensus 26 ~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~ 64 (135)
|++|..|.+ .....|.|+.|+-.+
T Consensus 309 S~~C~~cg~---------------~~~r~~~C~~cg~~~ 332 (364)
T COG0675 309 SKTCPCCGH---------------LSGRLFKCPRCGFVH 332 (364)
T ss_pred cccccccCC---------------ccceeEECCCCCCee
Confidence 477887777 225689999998654
No 95
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=33.73 E-value=15 Score=26.73 Aligned_cols=12 Identities=33% Similarity=1.046 Sum_probs=9.4
Q ss_pred Cceeehhhhhhh
Q psy15639 53 NTWRCSICRRKL 64 (135)
Q Consensus 53 ~~WrCSvCRRK~ 64 (135)
..|+|..|....
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 788888887764
No 96
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=33.55 E-value=14 Score=22.46 Aligned_cols=28 Identities=29% Similarity=0.646 Sum_probs=17.6
Q ss_pred hhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 36 VCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 36 VCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
+|.+|..--..++. ...++|..|+-++-
T Consensus 5 ~C~~CG~~~~~~~~--~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 5 KCARCGREVELDEY--GTGVRCPYCGYRIL 32 (46)
T ss_pred ECCCCCCEEEECCC--CCceECCCCCCeEE
Confidence 57777654444332 23899999987654
No 97
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=33.35 E-value=11 Score=22.84 Aligned_cols=27 Identities=22% Similarity=0.602 Sum_probs=16.9
Q ss_pred hhccccc-ccCCCCCCCCCceeehhhhh
Q psy15639 36 VCEDCAS-YSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 36 VCEDCAS-YSkl~~~ed~~~WrCSvCRR 62 (135)
.|.+|.. |..+....+.....|..|+.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 3555655 55544433456788999987
No 98
>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=32.99 E-value=27 Score=21.17 Aligned_cols=32 Identities=28% Similarity=0.703 Sum_probs=25.0
Q ss_pred CchhhccccCCCCccchhhhhh-hhhhcccccccC
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECH-QKVCEDCASYSK 45 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCq-qkVCEDCASYSk 45 (135)
.|.+|.+.+. + +...|.+|. --.|.+|.+.-.
T Consensus 2 ~C~~C~~~i~-g-~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIV-G-VRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCc-C-CEEECCCCCCCcCHHHHHCcCc
Confidence 4889999554 4 778899997 678999988664
No 99
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=32.80 E-value=11 Score=27.52 Aligned_cols=15 Identities=33% Similarity=0.851 Sum_probs=7.6
Q ss_pred cCCCCccchhhhhhh
Q psy15639 20 FKPDDYSRVCYECHQ 34 (135)
Q Consensus 20 fkP~e~~~tC~eCqq 34 (135)
+||=.-...|..|+|
T Consensus 49 YKpLt~p~kC~~C~q 63 (92)
T PF10217_consen 49 YKPLTQPKKCNKCQQ 63 (92)
T ss_pred cccCCCCcccccccc
Confidence 444445555555553
No 100
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=32.80 E-value=20 Score=20.61 Aligned_cols=28 Identities=29% Similarity=0.376 Sum_probs=14.8
Q ss_pred CCCCchhhccccCCC-Cccchhhhhhhhh
Q psy15639 9 RLGNCRVCLKSFKPD-DYSRVCYECHQKV 36 (135)
Q Consensus 9 r~g~CRVClKsfkP~-e~~~tC~eCqqkV 36 (135)
++..|.+|.+.|.-. .....|..|+..|
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~~ 38 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVKC 38 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCch
Confidence 455677777766521 2333455554443
No 101
>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=32.72 E-value=12 Score=21.29 Aligned_cols=27 Identities=30% Similarity=0.732 Sum_probs=12.8
Q ss_pred hccccc-ccCCCCCCCCCceeehhhhhh
Q psy15639 37 CEDCAS-YSKLDENQDENTWRCSICRRK 63 (135)
Q Consensus 37 CEDCAS-YSkl~~~ed~~~WrCSvCRRK 63 (135)
|.+|.. |.......+.....|..|+..
T Consensus 8 C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 8 CEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred cCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 344433 333333333556667666653
No 102
>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=32.57 E-value=23 Score=23.19 Aligned_cols=50 Identities=24% Similarity=0.321 Sum_probs=31.5
Q ss_pred CCCCCCCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 6 PAARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 6 p~~r~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
+.+|+ .|+.|.+.+.-+++ |+... .++ ....-....|.=--|=.+.....
T Consensus 4 ks~Ra-~Ck~C~~~I~kg~l-RiG~~----------~~~-~~~~~~~~~W~H~~C~~~~~~~~ 53 (82)
T PF00645_consen 4 KSGRA-KCKGCKKKIAKGEL-RIGKI----------VPS-PEGDGDIPKWYHWDCFFKKQLRN 53 (82)
T ss_dssp SSSTE-BETTTSCBE-TTSE-EEEEE----------EEE-TTSSCEEEEEEEHHHHHHTTCCT
T ss_pred CCCCc-cCcccCCcCCCCCE-EEEEE----------ecc-cccCCCCCceECccccccchhhh
Confidence 34565 89999999998887 44332 111 11134567899888887776654
No 103
>PRK06260 threonine synthase; Validated
Probab=31.65 E-value=20 Score=29.81 Aligned_cols=23 Identities=35% Similarity=0.810 Sum_probs=19.9
Q ss_pred CchhhccccCCCCccchhhhhhh
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECHQ 34 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCqq 34 (135)
.|.-|.+.|.++++...|.+|..
T Consensus 5 ~C~~cg~~~~~~~~~~~Cp~cg~ 27 (397)
T PRK06260 5 KCIECGKEYDPDEIIYTCPECGG 27 (397)
T ss_pred EECCCCCCCCCCCccccCCCCCC
Confidence 48889999999999999988853
No 104
>KOG4275|consensus
Probab=31.33 E-value=21 Score=31.79 Aligned_cols=53 Identities=21% Similarity=0.669 Sum_probs=41.8
Q ss_pred CCCCCCCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 6 PAARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 6 p~~r~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
+.+-+-.|.-|+-.|.--.-.++|.+|+.-.|--|. ...+ +.-+|+-|||--|
T Consensus 40 ~~~~~p~ckacg~~f~~~~~k~~c~dckk~fc~tcs---~v~~----~lr~c~~c~r~~a 92 (350)
T KOG4275|consen 40 SSSQAPHCKACGEEFEDAQSKSDCEDCKKEFCATCS---RVSI----SLRTCTSCRRVNA 92 (350)
T ss_pred cccccchhhhhchhHhhhhhhhhhhhhhHHHHHHHH---Hhcc----cchhhhHHHHHHh
Confidence 344455899999999988889999999999888876 4433 5678999998654
No 105
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=31.04 E-value=19 Score=25.91 Aligned_cols=16 Identities=13% Similarity=0.164 Sum_probs=10.7
Q ss_pred CCchhhccccCCCCcc
Q psy15639 11 GNCRVCLKSFKPDDYS 26 (135)
Q Consensus 11 g~CRVClKsfkP~e~~ 26 (135)
..|+-|.+-|...+..
T Consensus 71 ~~C~~Cg~~~~~~~~~ 86 (114)
T PRK03681 71 CWCETCQQYVTLLTQR 86 (114)
T ss_pred EEcccCCCeeecCCcc
Confidence 4577888777665554
No 106
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=30.99 E-value=39 Score=26.50 Aligned_cols=74 Identities=19% Similarity=0.313 Sum_probs=40.2
Q ss_pred chhhccccCCCCccchhhhhhhhhhcccccccCCCC-CCCCCceeehhhhhhhhccccccccccccccccch------HH
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDE-NQDENTWRCSICRRKLQSRAQPVLSQNSTDSLLDV------PV 85 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~-~ed~~~WrCSvCRRK~~sr~qp~~~q~stds~l~v------pv 85 (135)
|-.|++...|. +..+|.+|--+. -.+.+ .+.-+.-.|..|++-+.... .+.- ...+++++ ..
T Consensus 1 C~~CG~~~~~~-~~~lC~~C~~~~-------~~i~ei~~~i~v~~C~~Cg~~~~~~~--W~~~-~~~el~~~~lk~v~~~ 69 (236)
T PF04981_consen 1 CPRCGREIEPL-IDGLCPDCYLKR-------FDIIEIPDRIEVTICPKCGRYRIGGR--WVDP-ESRELEELCLKKVERG 69 (236)
T ss_pred CCCCCCCCCCc-ccccChHHhccc-------CCeeecCCccCceECCCCCCEECCCE--eeec-CcccHHHHHHHHHHHH
Confidence 77888866654 335666665432 12222 23357788999998777622 2222 34455665 33
Q ss_pred HHHHHhhccccc
Q psy15639 86 LEALQRRHSDVK 97 (135)
Q Consensus 86 lealqrrhsd~k 97 (135)
|......|.|++
T Consensus 70 l~~~~~~~~d~~ 81 (236)
T PF04981_consen 70 LKKNIKVHVDAE 81 (236)
T ss_pred HHHhhccccccc
Confidence 333333456554
No 107
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=30.90 E-value=18 Score=30.97 Aligned_cols=47 Identities=36% Similarity=0.730 Sum_probs=38.1
Q ss_pred CCCchhhccccCCCCccchhhhhhhhhhccccc--ccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECHQKVCEDCAS--YSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCAS--YSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
+--|-||-|-|+ +.+=.+|.|-.|+-||- |-|.++ |-||+.-+--|.
T Consensus 196 PF~C~iCKkdy~----spvvt~CGH~FC~~Cai~~y~kg~~--------C~~Cgk~t~G~f 244 (259)
T COG5152 196 PFLCGICKKDYE----SPVVTECGHSFCSLCAIRKYQKGDE--------CGVCGKATYGRF 244 (259)
T ss_pred ceeehhchhhcc----chhhhhcchhHHHHHHHHHhccCCc--------ceecchhhccce
Confidence 447999999887 46678999999999995 666665 999998877665
No 108
>KOG0311|consensus
Probab=30.49 E-value=10 Score=34.00 Aligned_cols=49 Identities=31% Similarity=0.653 Sum_probs=34.5
Q ss_pred CchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
.|.|||--+|- ..|=-||-|+.|.||---+-- ...-.|.-||.++.|+-
T Consensus 45 ~c~icl~llk~---tmttkeClhrfc~~ci~~a~r-----~gn~ecptcRk~l~Skr 93 (381)
T KOG0311|consen 45 ICPICLSLLKK---TMTTKECLHRFCFDCIWKALR-----SGNNECPTCRKKLVSKR 93 (381)
T ss_pred ccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHH-----hcCCCCchHHhhccccc
Confidence 47777755542 345568999999999643321 23446999999999976
No 109
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.31 E-value=20 Score=35.96 Aligned_cols=46 Identities=24% Similarity=0.496 Sum_probs=34.3
Q ss_pred CCchhhccccCCCCccchhhhhh-----hhhhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECH-----QKVCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCq-----qkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
..|.-|++.. +...|.+|. .+.|.+|-.- ...-.|.-|+.++.+-.
T Consensus 627 RfCpsCG~~t----~~frCP~CG~~Te~i~fCP~CG~~--------~~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 627 RKCPSCGKET----FYRRCPFCGTHTEPVYRCPRCGIE--------VEEDECEKCGREPTPYS 677 (1121)
T ss_pred ccCCCCCCcC----CcccCCCCCCCCCcceeCccccCc--------CCCCcCCCCCCCCCccc
Confidence 4699999885 778999996 5799999322 22345999999876544
No 110
>PRK14284 chaperone protein DnaJ; Provisional
Probab=30.15 E-value=25 Score=29.65 Aligned_cols=49 Identities=22% Similarity=0.618 Sum_probs=35.3
Q ss_pred CCCCCchhh-ccccCCCCccchhhhhh--------------hhhhcccccccCCCCCCCCCceeehhhhh
Q psy15639 8 ARLGNCRVC-LKSFKPDDYSRVCYECH--------------QKVCEDCASYSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 8 ~r~g~CRVC-lKsfkP~e~~~tC~eCq--------------qkVCEDCASYSkl~~~ed~~~WrCSvCRR 62 (135)
.|...|..| ..+.+++.-.++|..|. +..|..|-.--+... =.|..|.-
T Consensus 156 ~r~~~C~~C~G~G~~~~~~~~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~G~~~~------~~C~~C~G 219 (391)
T PRK14284 156 SGYKSCDACSGSGANSSQGIKVCDRCKGSGQVVQSRGFFSMASTCPECGGEGRVIT------DPCSVCRG 219 (391)
T ss_pred eeeccCCCCcccccCCCCCCeecCccCCeeEEEEEeceEEEEEECCCCCCCCcccC------CcCCCCCC
Confidence 356678888 45667777678899997 348999988776543 24988874
No 111
>KOG4628|consensus
Probab=29.96 E-value=24 Score=30.85 Aligned_cols=48 Identities=23% Similarity=0.691 Sum_probs=32.4
Q ss_pred CCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCce--eehhhhhhhhc
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTW--RCSICRRKLQS 66 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~W--rCSvCRRK~~s 66 (135)
..|-||+-.|++||--++ -=|+|+.=-+|-- +- -..| .|.||.|.+..
T Consensus 230 ~~CaIClEdY~~GdklRi-LPC~H~FH~~CID-pW------L~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRI-LPCSHKFHVNCID-PW------LTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecccccCCeeeE-ecCCCchhhccch-hh------HhhcCccCCCCCCcCCC
Confidence 589999999999998887 6676654333321 11 2234 39999996543
No 112
>PRK08197 threonine synthase; Validated
Probab=29.71 E-value=23 Score=29.49 Aligned_cols=22 Identities=23% Similarity=0.773 Sum_probs=19.3
Q ss_pred CCchhhccccCCCCccchhhhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECH 33 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCq 33 (135)
-.|.-|.+.|.++++...| +|.
T Consensus 8 ~~C~~Cg~~~~~~~~~~~C-~cg 29 (394)
T PRK08197 8 LECSKCGETYDADQVHNLC-KCG 29 (394)
T ss_pred EEECCCCCCCCCCCcceec-CCC
Confidence 4699999999999998888 785
No 113
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=29.57 E-value=19 Score=18.92 Aligned_cols=11 Identities=36% Similarity=0.893 Sum_probs=8.4
Q ss_pred CchhhccccCC
Q psy15639 12 NCRVCLKSFKP 22 (135)
Q Consensus 12 ~CRVClKsfkP 22 (135)
.|.+|.+.|.-
T Consensus 3 ~C~~C~~~F~~ 13 (27)
T PF13912_consen 3 ECDECGKTFSS 13 (27)
T ss_dssp EETTTTEEESS
T ss_pred CCCccCCccCC
Confidence 48888888863
No 114
>PF13945 NST1: Salt tolerance down-regulator
Probab=29.07 E-value=21 Score=28.86 Aligned_cols=18 Identities=33% Similarity=0.883 Sum_probs=12.9
Q ss_pred Cceeehhhhhhhhcccccccccc
Q psy15639 53 NTWRCSICRRKLQSRAQPVLSQN 75 (135)
Q Consensus 53 ~~WrCSvCRRK~~sr~qp~~~q~ 75 (135)
.+-.|+||+|| |. +|-||
T Consensus 140 h~C~C~vCgr~---~~--~ie~e 157 (190)
T PF13945_consen 140 HSCSCSVCGRK---RT--AIEEE 157 (190)
T ss_pred cCcccHHHhch---hh--HHHHH
Confidence 35789999999 43 46555
No 115
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.86 E-value=20 Score=26.55 Aligned_cols=31 Identities=26% Similarity=0.618 Sum_probs=23.1
Q ss_pred hhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 36 VCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 36 VCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
+|..|.+- .-.-.-..-|.|.-|+.+.|--+
T Consensus 37 ~Cp~C~~~--~VkR~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 37 VCPFCGRT--TVKRIATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred cCCCCCCc--ceeeeccCeEEcCCCCCeecccc
Confidence 57777654 34445577899999999998765
No 116
>COG1773 Rubredoxin [Energy production and conversion]
Probab=28.77 E-value=22 Score=23.99 Aligned_cols=9 Identities=56% Similarity=1.634 Sum_probs=5.6
Q ss_pred ceeehhhhh
Q psy15639 54 TWRCSICRR 62 (135)
Q Consensus 54 ~WrCSvCRR 62 (135)
.|+|++|+-
T Consensus 3 ~~~C~~CG~ 11 (55)
T COG1773 3 RWRCSVCGY 11 (55)
T ss_pred ceEecCCce
Confidence 566666653
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=28.76 E-value=12 Score=21.83 Aligned_cols=26 Identities=23% Similarity=0.682 Sum_probs=16.2
Q ss_pred CCCchhhccccCCC-----Cccchhhhhhhh
Q psy15639 10 LGNCRVCLKSFKPD-----DYSRVCYECHQK 35 (135)
Q Consensus 10 ~g~CRVClKsfkP~-----e~~~tC~eCqqk 35 (135)
-|.|..|+..+..+ .....|.+||++
T Consensus 3 yg~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 3 YGICEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -SB-TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred CCCccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 35588888776543 467788888875
No 118
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=28.76 E-value=16 Score=33.00 Aligned_cols=30 Identities=27% Similarity=0.659 Sum_probs=21.6
Q ss_pred ccCCCCCCCCCceeehhhhhhhhccccccc
Q psy15639 43 YSKLDENQDENTWRCSICRRKLQSRAQPVL 72 (135)
Q Consensus 43 YSkl~~~ed~~~WrCSvCRRK~~sr~qp~~ 72 (135)
|++..--+-.+.|+|.+|.||-.||-+--|
T Consensus 273 f~~~e~L~g~d~W~CpkC~~k~ss~K~~~I 302 (415)
T COG5533 273 FYEEEKLEGKDAWRCPKCGRKESSRKRMEI 302 (415)
T ss_pred hhhHHhhcCcccccCchhcccccchheEEE
Confidence 333334456789999999999988875433
No 119
>PF12251 zf-SNAP50_C: snRNA-activating protein of 50kDa MW C terminal; InterPro: IPR022042 This domain family is found in eukaryotes, and is typically between 196 and 207 amino acids in length. There is a conserved CEH sequence motif. SNAP50 is part of the snRNA-activating protein complex which activates RNA polymerases II and III. There is a cysteine-histidine cluster which contains two possible zinc finger motifs.
Probab=28.71 E-value=36 Score=26.72 Aligned_cols=33 Identities=30% Similarity=0.535 Sum_probs=25.1
Q ss_pred CCCCCCCCchhhcccc----------CCCCccchhhhhhhhhh
Q psy15639 5 KPAARLGNCRVCLKSF----------KPDDYSRVCYECHQKVC 37 (135)
Q Consensus 5 kp~~r~g~CRVClKsf----------kP~e~~~tC~eCqqkVC 37 (135)
++..|...|.||.+.. .|++++..|..|-....
T Consensus 134 ~~~~~~~~C~vC~~~~A~~v~~~d~~~p~~P~~~C~~Cf~~lh 176 (196)
T PF12251_consen 134 KPRFRRRKCSVCGIYPAKWVTYNDELAPEDPCFFCDSCFRLLH 176 (196)
T ss_pred ecCcccccCCCCCCCCCEEEEECCccCCCCCchhHHHHHHHhC
Confidence 3456788999998864 68999999988865443
No 120
>KOG1311|consensus
Probab=28.43 E-value=23 Score=28.08 Aligned_cols=29 Identities=24% Similarity=0.587 Sum_probs=20.0
Q ss_pred hhhhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 34 QKVCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 34 qkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
.+.|.-|-.|.. +-+|-||+|.+=+..++
T Consensus 113 ~~~C~~C~~~rP------pRs~HCsvC~~CV~rfD 141 (299)
T KOG1311|consen 113 WKYCDTCQLYRP------PRSSHCSVCNNCVLRFD 141 (299)
T ss_pred eEEcCcCcccCC------CCcccchhhcccccccC
Confidence 367777777732 55788999887665544
No 121
>PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function. ; PDB: 2K0M_A.
Probab=28.35 E-value=32 Score=23.49 Aligned_cols=19 Identities=47% Similarity=0.684 Sum_probs=14.3
Q ss_pred hHHHHHHHhhcccc--ccccC
Q psy15639 83 VPVLEALQRRHSDV--KIGSA 101 (135)
Q Consensus 83 vpvlealqrrhsd~--klg~~ 101 (135)
-=+|++|..+||++ |+|.|
T Consensus 20 ~~~l~~ll~~HP~~~~KiG~G 40 (76)
T PF11523_consen 20 KSVLEALLKYHPEAEEKIGCG 40 (76)
T ss_dssp HHHHHHHHHTSTTHHHHHTT-
T ss_pred HHHHHHHHHhCCcHHHhhcCC
Confidence 34788999999976 77765
No 122
>KOG3214|consensus
Probab=28.30 E-value=18 Score=27.70 Aligned_cols=12 Identities=42% Similarity=1.148 Sum_probs=10.3
Q ss_pred CCchhhccccCC
Q psy15639 11 GNCRVCLKSFKP 22 (135)
Q Consensus 11 g~CRVClKsfkP 22 (135)
-+||||..||+-
T Consensus 48 ~sC~iC~esFqt 59 (109)
T KOG3214|consen 48 ASCRICEESFQT 59 (109)
T ss_pred eeeeehhhhhcc
Confidence 479999999974
No 123
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=28.19 E-value=39 Score=21.81 Aligned_cols=20 Identities=30% Similarity=0.517 Sum_probs=16.0
Q ss_pred cchHHHHHHHhhcccccccc
Q psy15639 81 LDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 81 l~vpvlealqrrhsd~klg~ 100 (135)
+=-+++.+++++|++++|=.
T Consensus 14 ~l~~~l~~~~~~~P~v~l~~ 33 (199)
T cd08430 14 FLPPILERFRAQHPQVEIKL 33 (199)
T ss_pred eccHHHHHHHHHCCCceEEE
Confidence 33688999999999887754
No 124
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=28.15 E-value=40 Score=21.91 Aligned_cols=18 Identities=11% Similarity=0.349 Sum_probs=15.3
Q ss_pred hHHHHHHHhhcccccccc
Q psy15639 83 VPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 83 vpvlealqrrhsd~klg~ 100 (135)
.+++..++++|++++|-.
T Consensus 17 ~~~l~~~~~~~P~v~i~i 34 (201)
T cd08471 17 LPIITDFLDAYPEVSVRL 34 (201)
T ss_pred HHHHHHHHHHCCCcEEEE
Confidence 478999999999988754
No 125
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=27.88 E-value=19 Score=21.43 Aligned_cols=27 Identities=19% Similarity=0.650 Sum_probs=20.0
Q ss_pred hhcccccccCCCCC---CCCCceeehhhhh
Q psy15639 36 VCEDCASYSKLDEN---QDENTWRCSICRR 62 (135)
Q Consensus 36 VCEDCASYSkl~~~---ed~~~WrCSvCRR 62 (135)
.|..|...-+++++ +....-||+.|+-
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 47778777777776 5566789999874
No 126
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=27.86 E-value=40 Score=21.68 Aligned_cols=20 Identities=30% Similarity=0.780 Sum_probs=11.0
Q ss_pred chhhccccCCCCccchhhhhh
Q psy15639 13 CRVCLKSFKPDDYSRVCYECH 33 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCq 33 (135)
|-+|++-...++ ..+|.+|.
T Consensus 1 C~~C~~~~~~~~-~~lC~~C~ 20 (73)
T PF14260_consen 1 CLVCGAKTQEGE-SPLCSNCR 20 (73)
T ss_pred CCCCCCcCCCCC-CCcCcccC
Confidence 456666666665 34444443
No 127
>PF15379 DUF4606: Domain of unknown function (DUF4606)
Probab=27.81 E-value=30 Score=26.15 Aligned_cols=37 Identities=27% Similarity=0.507 Sum_probs=23.0
Q ss_pred CCCCCCceeehhhhhhhhccccc-cccccccccccchHHH
Q psy15639 48 ENQDENTWRCSICRRKLQSRAQP-VLSQNSTDSLLDVPVL 86 (135)
Q Consensus 48 ~~ed~~~WrCSvCRRK~~sr~qp-~~~q~stds~l~vpvl 86 (135)
.-..+++|+|+-|++|.+.-+|- ++.|- -.+||-..+
T Consensus 25 ~~k~H~~s~Cp~C~kkraeLa~~~Flr~K--ktlLE~~ll 62 (104)
T PF15379_consen 25 TAKQHNSSQCPSCNKKRAELAQSAFLRRK--KTLLESLLL 62 (104)
T ss_pred cccccCcccChHHHHHHHHHHHHHHHHHH--HHHHHHHHH
Confidence 44568999999999996654432 33332 235555544
No 128
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=27.73 E-value=43 Score=21.49 Aligned_cols=20 Identities=10% Similarity=0.104 Sum_probs=16.1
Q ss_pred ccchHHHHHHHhhccccccc
Q psy15639 80 LLDVPVLEALQRRHSDVKIG 99 (135)
Q Consensus 80 ~l~vpvlealqrrhsd~klg 99 (135)
.+=.+++..++++|++++|=
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~ 32 (197)
T cd08448 13 RGLPRILRAFRAEYPGIEVA 32 (197)
T ss_pred HHHHHHHHHHHHHCCCCeEE
Confidence 34468999999999998874
No 129
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=27.53 E-value=19 Score=22.36 Aligned_cols=37 Identities=24% Similarity=0.560 Sum_probs=23.7
Q ss_pred CCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRR 62 (135)
-.|..|.|.|.-.++..-|.+-. ..+...-.|.+|..
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H---------------~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEH---------------RSESKNVVCPICSS 39 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHC---------------cCCCCCccCCCchh
Confidence 36888988777666555444322 23345678999975
No 130
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=27.45 E-value=41 Score=21.78 Aligned_cols=22 Identities=23% Similarity=0.250 Sum_probs=17.4
Q ss_pred cccchHHHHHHHhhcccccccc
Q psy15639 79 SLLDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 79 s~l~vpvlealqrrhsd~klg~ 100 (135)
..+=.+++..++++|++++|-.
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i 33 (196)
T cd08450 12 VQWLPEVLPILREEHPDLDVEL 33 (196)
T ss_pred hhhHHHHHHHHHhhCCCcEEEE
Confidence 3344688999999999988765
No 131
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=27.33 E-value=41 Score=22.26 Aligned_cols=17 Identities=18% Similarity=0.544 Sum_probs=14.8
Q ss_pred hHHHHHHHhhccccccc
Q psy15639 83 VPVLEALQRRHSDVKIG 99 (135)
Q Consensus 83 vpvlealqrrhsd~klg 99 (135)
.|++.+++++|++++|=
T Consensus 16 ~~~l~~~~~~~P~v~i~ 32 (197)
T cd08452 16 PPIVREYRKKFPSVKVE 32 (197)
T ss_pred HHHHHHHHHHCCCcEEE
Confidence 68999999999988764
No 132
>KOG4477|consensus
Probab=27.28 E-value=24 Score=29.73 Aligned_cols=14 Identities=50% Similarity=1.308 Sum_probs=11.2
Q ss_pred CCCCCCceeehhhh
Q psy15639 48 ENQDENTWRCSICR 61 (135)
Q Consensus 48 ~~ed~~~WrCSvCR 61 (135)
.++|.+-|-||||-
T Consensus 18 p~~Deg~WdCsvCT 31 (228)
T KOG4477|consen 18 PNDDEGKWDCSVCT 31 (228)
T ss_pred CccccCceeeeeee
Confidence 45788999999984
No 133
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=27.13 E-value=42 Score=21.67 Aligned_cols=20 Identities=15% Similarity=0.210 Sum_probs=15.4
Q ss_pred cchHHHHHHHhhcccccccc
Q psy15639 81 LDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 81 l~vpvlealqrrhsd~klg~ 100 (135)
+=-+++++++++|++++|=.
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i 34 (199)
T cd08451 15 LVPGLIRRFREAYPDVELTL 34 (199)
T ss_pred ccHHHHHHHHHHCCCcEEEE
Confidence 43458999999999877654
No 134
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=27.08 E-value=21 Score=24.24 Aligned_cols=15 Identities=27% Similarity=0.519 Sum_probs=9.0
Q ss_pred CchhhccccCCCCcc
Q psy15639 12 NCRVCLKSFKPDDYS 26 (135)
Q Consensus 12 ~CRVClKsfkP~e~~ 26 (135)
.|-+|.|-+.-+|-+
T Consensus 4 kC~lCdk~~~Id~~~ 18 (56)
T PF09963_consen 4 KCILCDKKEEIDEDT 18 (56)
T ss_pred EEEecCCEEEeccCC
Confidence 366677666666543
No 135
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=26.96 E-value=45 Score=21.74 Aligned_cols=20 Identities=10% Similarity=0.152 Sum_probs=16.0
Q ss_pred cchHHHHHHHhhcccccccc
Q psy15639 81 LDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 81 l~vpvlealqrrhsd~klg~ 100 (135)
+=.|++.+++++|++++|=.
T Consensus 14 ~l~~~l~~~~~~~P~v~i~i 33 (195)
T cd08431 14 PLYPLIAEFYQLNKATRIRL 33 (195)
T ss_pred HHHHHHHHHHHHCCCCceEE
Confidence 34689999999999987743
No 136
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=26.89 E-value=15 Score=22.31 Aligned_cols=32 Identities=22% Similarity=0.606 Sum_probs=19.6
Q ss_pred hhcccc-cccCCCCCCCCCceeehhhhhhhhcc
Q psy15639 36 VCEDCA-SYSKLDENQDENTWRCSICRRKLQSR 67 (135)
Q Consensus 36 VCEDCA-SYSkl~~~ed~~~WrCSvCRRK~~sr 67 (135)
.|++|. -+..+..-.+.....|..|+..-..|
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGSTEVRR 39 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEE
Confidence 355665 34444444447788999998844444
No 137
>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=26.70 E-value=24 Score=18.83 Aligned_cols=14 Identities=29% Similarity=0.795 Sum_probs=8.8
Q ss_pred CCceeehhhhhhhh
Q psy15639 52 ENTWRCSICRRKLQ 65 (135)
Q Consensus 52 ~~~WrCSvCRRK~~ 65 (135)
.+-++|+.|++.|.
T Consensus 25 ~~Cf~C~~C~~~L~ 38 (39)
T smart00132 25 PECFKCSKCGKPLG 38 (39)
T ss_pred ccCCCCcccCCcCc
Confidence 34467777776653
No 138
>KOG4443|consensus
Probab=26.62 E-value=22 Score=34.12 Aligned_cols=55 Identities=27% Similarity=0.559 Sum_probs=38.4
Q ss_pred CCCCCCchhhccccCCCCcc--chhhhhhhhhhcccccccCCCCCCCC--Cceeehhhh
Q psy15639 7 AARLGNCRVCLKSFKPDDYS--RVCYECHQKVCEDCASYSKLDENQDE--NTWRCSICR 61 (135)
Q Consensus 7 ~~r~g~CRVClKsfkP~e~~--~tC~eCqqkVCEDCASYSkl~~~ed~--~~WrCSvCR 61 (135)
..+.-.|+||++-+.-.|.- --|.-|+--+=--|-..|.....+.. ...+||.||
T Consensus 142 c~s~~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR 200 (694)
T KOG4443|consen 142 CASLSYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR 200 (694)
T ss_pred ccccccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee
Confidence 34466899999999988877 66777776655555555555443332 468999999
No 139
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=26.25 E-value=23 Score=19.56 Aligned_cols=20 Identities=25% Similarity=0.443 Sum_probs=16.2
Q ss_pred Cccchhhhhhhhhhcccccc
Q psy15639 24 DYSRVCYECHQKVCEDCASY 43 (135)
Q Consensus 24 e~~~tC~eCqqkVCEDCASY 43 (135)
.....|.+|+..+|.+|..-
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~ 29 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLS 29 (39)
T ss_pred ceEEEeCccChhhhhhcChh
Confidence 44667999999999999754
No 140
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=26.11 E-value=20 Score=21.73 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=7.4
Q ss_pred CCceeehhhhhhhhcc
Q psy15639 52 ENTWRCSICRRKLQSR 67 (135)
Q Consensus 52 ~~~WrCSvCRRK~~sr 67 (135)
.....|.+|+-+|..|
T Consensus 19 ~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 19 KVEGVCDNCGGELVQR 34 (36)
T ss_dssp SSTTBCTTTTEBEBEE
T ss_pred CCCCccCCCCCeeEeC
Confidence 3344555555444433
No 141
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=25.99 E-value=38 Score=22.99 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=17.4
Q ss_pred CCCCCCCchhhccccCCCCcc
Q psy15639 6 PAARLGNCRVCLKSFKPDDYS 26 (135)
Q Consensus 6 p~~r~g~CRVClKsfkP~e~~ 26 (135)
|..|--.|.+|.+-|.+++.+
T Consensus 35 ~~~rYngCPfC~~~~~~~~~~ 55 (55)
T PF14447_consen 35 PGERYNGCPFCGTPFEFDDPF 55 (55)
T ss_pred ChhhccCCCCCCCcccCCCCC
Confidence 567888999999999988753
No 142
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.90 E-value=31 Score=34.44 Aligned_cols=49 Identities=24% Similarity=0.611 Sum_probs=39.2
Q ss_pred CCchhhcccc---CCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhh
Q psy15639 11 GNCRVCLKSF---KPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKL 64 (135)
Q Consensus 11 g~CRVClKsf---kP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~ 64 (135)
..|+||+--. .-+|++--|.||.--||-.|-.|-+-.. +=.|..|.-.-
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG-----~q~CPqCktrY 69 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDG-----NQSCPQCKTKY 69 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcC-----CccCCccCCch
Confidence 4899998654 4578999999999999999999987655 34688896433
No 143
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=25.89 E-value=62 Score=22.78 Aligned_cols=56 Identities=21% Similarity=0.526 Sum_probs=27.9
Q ss_pred ccc--cccCCCCCCCCCceeehhhhhhhhccccccccccccccccchHHHHHHHhhccccccccCCCC
Q psy15639 39 DCA--SYSKLDENQDENTWRCSICRRKLQSRAQPVLSQNSTDSLLDVPVLEALQRRHSDVKIGSANSG 104 (135)
Q Consensus 39 DCA--SYSkl~~~ed~~~WrCSvCRRK~~sr~qp~~~q~stds~l~vpvlealqrrhsd~klg~~~~~ 104 (135)
||- +|++ |+..+-.| +|++.|.-.--+|+.+--+ .+=-..+-|+--+.+.|..+..
T Consensus 7 ~Cgr~lya~----e~~kTkkC-~CG~~l~vk~~rIl~~~~~-----~~eA~eiVrklQ~e~~G~~~ft 64 (68)
T PF09082_consen 7 DCGRYLYAK----EGAKTKKC-VCGKTLKVKERRILARAEN-----AEEASEIVRKLQEEKYGGTQFT 64 (68)
T ss_dssp TTS--EEEE----TT-SEEEE-TTTEEEE--SSS-BS--SS-----HHHHHHHHHHHSS---S-TTSS
T ss_pred cCCCEEEec----CCcceeEe-cCCCeeeeeeEEEEEecCC-----HHHHHHHHHHHHHHhccccccc
Confidence 564 4544 45688999 9999998776667765322 1222345555556677765543
No 144
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=24.96 E-value=30 Score=20.62 Aligned_cols=24 Identities=25% Similarity=0.526 Sum_probs=12.4
Q ss_pred hhcccccccCCCCCCCCCceeehhhhh
Q psy15639 36 VCEDCASYSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 36 VCEDCASYSkl~~~ed~~~WrCSvCRR 62 (135)
-|+-|.|-..+ .|...+-|+.|..
T Consensus 4 ~Cp~C~se~~y---~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY---EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E---E-SSSEEETTTTE
T ss_pred CCCCCCCccee---ccCCEEeCCcccc
Confidence 47778776666 5688888888864
No 145
>PRK14554 putative pseudouridylate synthase; Provisional
Probab=24.69 E-value=46 Score=29.64 Aligned_cols=49 Identities=29% Similarity=0.594 Sum_probs=37.0
Q ss_pred ccCCCCCCCCCceeehhhhhhhhccccccccccccccccchHHHHHHHhhccccccccCC
Q psy15639 43 YSKLDENQDENTWRCSICRRKLQSRAQPVLSQNSTDSLLDVPVLEALQRRHSDVKIGSAN 102 (135)
Q Consensus 43 YSkl~~~ed~~~WrCSvCRRK~~sr~qp~~~q~stds~l~vpvlealqrrhsd~klg~~~ 102 (135)
|-|+.-.=-.+.|-|.-|++| ..+|-+.++.=||++++. -.++++=++|
T Consensus 197 Y~Kl~R~ipQT~W~~~~g~~~---------~~~SVeelI~~~i~~~f~--~~~~~fh~aG 245 (422)
T PRK14554 197 YRKLVRGIPQTRWPCRKCKKQ---------YPESVEELIAKPVIEAFG--GEDAVFHGAG 245 (422)
T ss_pred EeeccCCCCCCccccCCCCCC---------CCCCHHHHHHHHHHHHhC--CCceEEecCC
Confidence 667776677899999999988 568889999999999886 2344444433
No 146
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=24.52 E-value=21 Score=26.69 Aligned_cols=9 Identities=56% Similarity=1.268 Sum_probs=6.8
Q ss_pred hhhhhcccc
Q psy15639 33 HQKVCEDCA 41 (135)
Q Consensus 33 qqkVCEDCA 41 (135)
.|.+|-|||
T Consensus 91 g~~iC~DCa 99 (99)
T PF13834_consen 91 GQPICRDCA 99 (99)
T ss_pred CCEeccccC
Confidence 477888886
No 147
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=24.47 E-value=39 Score=29.17 Aligned_cols=33 Identities=18% Similarity=0.405 Sum_probs=25.1
Q ss_pred hhcccccccCCCCCCCCCceeehhhhhhhhccc
Q psy15639 36 VCEDCASYSKLDENQDENTWRCSICRRKLQSRA 68 (135)
Q Consensus 36 VCEDCASYSkl~~~ed~~~WrCSvCRRK~~sr~ 68 (135)
.|++|-...+.+.-+.....+|.-|+-++..+.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~ 47 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLTVGW 47 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCcCCC
Confidence 477777666666656677899999999997665
No 148
>KOG1571|consensus
Probab=24.38 E-value=26 Score=31.06 Aligned_cols=44 Identities=27% Similarity=0.719 Sum_probs=28.0
Q ss_pred CCCchhhccccCCCCccchhhhhhhhhh-cccccccCCCCCCCCCceeehhhhhhhhcc
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECHQKVC-EDCASYSKLDENQDENTWRCSICRRKLQSR 67 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCqqkVC-EDCASYSkl~~~ed~~~WrCSvCRRK~~sr 67 (135)
...|=||+-.++--.| .+|.|..| .+|+ +.+.. |.|||+.+..-
T Consensus 305 p~lcVVcl~e~~~~~f----vpcGh~ccct~cs--~~l~~--------CPvCR~rI~~~ 349 (355)
T KOG1571|consen 305 PDLCVVCLDEPKSAVF----VPCGHVCCCTLCS--KHLPQ--------CPVCRQRIRLV 349 (355)
T ss_pred CCceEEecCCccceee----ecCCcEEEchHHH--hhCCC--------CchhHHHHHHH
Confidence 4689999977665332 45666554 4443 33333 99999988653
No 149
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=24.36 E-value=48 Score=21.65 Aligned_cols=20 Identities=10% Similarity=0.051 Sum_probs=16.0
Q ss_pred cchHHHHHHHhhcccccccc
Q psy15639 81 LDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 81 l~vpvlealqrrhsd~klg~ 100 (135)
+=.+++.+++++|++++|=.
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~ 33 (198)
T cd08437 14 YFPKLAKDLIKTGLMIQIDT 33 (198)
T ss_pred HhHHHHHHHHHhCCceEEEE
Confidence 44688999999999887654
No 150
>smart00868 zf-AD Zinc-finger associated domain (zf-AD). The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA.
Probab=24.27 E-value=31 Score=19.79 Aligned_cols=10 Identities=40% Similarity=0.919 Sum_probs=7.5
Q ss_pred CchhhccccC
Q psy15639 12 NCRVCLKSFK 21 (135)
Q Consensus 12 ~CRVClKsfk 21 (135)
.||+|++...
T Consensus 1 ~Cr~C~~~~~ 10 (73)
T smart00868 1 VCRLCLSEGE 10 (73)
T ss_pred CccccCCCCC
Confidence 4999988653
No 151
>PRK14298 chaperone protein DnaJ; Provisional
Probab=24.12 E-value=39 Score=28.55 Aligned_cols=47 Identities=26% Similarity=0.689 Sum_probs=33.2
Q ss_pred CCCCchhhc-cccCCCCccchhhhhh------------------hhhhcccccccCCCCCCCCCceeehhhh
Q psy15639 9 RLGNCRVCL-KSFKPDDYSRVCYECH------------------QKVCEDCASYSKLDENQDENTWRCSICR 61 (135)
Q Consensus 9 r~g~CRVCl-KsfkP~e~~~tC~eCq------------------qkVCEDCASYSkl~~~ed~~~WrCSvCR 61 (135)
|...|..|. ++.+++...++|..|. |..|..|..--+... =.|..|+
T Consensus 140 r~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~G~~~~------~~C~~C~ 205 (377)
T PRK14298 140 RAERCSTCSGTGAKPGTSPKRCPTCGGTGQVTTTRSTPLGQFVTTTTCSTCHGRGQVIE------SPCPVCS 205 (377)
T ss_pred eeccCCCCCCCcccCCCCCCcCCCCCCccEEEEEEecCceeEEEEEeCCCCCCCCcccC------CCCCCCC
Confidence 456677774 5667777778888886 457999988776543 1488887
No 152
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=24.01 E-value=38 Score=27.04 Aligned_cols=40 Identities=18% Similarity=0.467 Sum_probs=24.9
Q ss_pred CCchhhccccCCCCccchhhhhhhhhhcccccccCCCCCCC
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQD 51 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqkVCEDCASYSkl~~~ed 51 (135)
..|-+|++... .=+.-.=..=.-.||.|||-|-+-.....
T Consensus 4 ~~CEiCG~~i~-~~~~v~vegsel~VC~~Cak~G~~~~~~~ 43 (165)
T COG1813 4 MGCELCGREID-KPIKVKVEGAELTVCDDCAKFGTAAKTAS 43 (165)
T ss_pred cceeccccccC-CCeeEEeecceeehhHHHHHhccCccccC
Confidence 34999999887 22222223345579999998875544333
No 153
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=23.85 E-value=54 Score=21.10 Aligned_cols=20 Identities=35% Similarity=0.496 Sum_probs=16.2
Q ss_pred cchHHHHHHHhhcccccccc
Q psy15639 81 LDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 81 l~vpvlealqrrhsd~klg~ 100 (135)
+=.+++..++++|++++|=.
T Consensus 14 ~l~~~l~~~~~~~P~i~l~~ 33 (195)
T cd08427 14 LLPRALARLRRRHPDLEVHI 33 (195)
T ss_pred HhHHHHHHHHHHCCCceEEE
Confidence 34689999999999988754
No 154
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=23.69 E-value=29 Score=28.30 Aligned_cols=9 Identities=56% Similarity=1.010 Sum_probs=6.3
Q ss_pred hhhcccccc
Q psy15639 35 KVCEDCASY 43 (135)
Q Consensus 35 kVCEDCASY 43 (135)
-|||.||--
T Consensus 27 ~vCe~Ca~~ 35 (176)
T COG3880 27 YVCETCAKP 35 (176)
T ss_pred ehhhcCCCc
Confidence 378888754
No 155
>PRK14282 chaperone protein DnaJ; Provisional
Probab=23.59 E-value=37 Score=28.40 Aligned_cols=49 Identities=27% Similarity=0.651 Sum_probs=33.8
Q ss_pred CCCCCchhhc-cccCCCCccchhhhhh------------------hhhhcccccccCCCCCCCCCceeehhhhh
Q psy15639 8 ARLGNCRVCL-KSFKPDDYSRVCYECH------------------QKVCEDCASYSKLDENQDENTWRCSICRR 62 (135)
Q Consensus 8 ~r~g~CRVCl-KsfkP~e~~~tC~eCq------------------qkVCEDCASYSkl~~~ed~~~WrCSvCRR 62 (135)
.|...|..|. .+++++.-.++|..|. +..|..|...-+... =.|+.|.-
T Consensus 150 ~r~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~G~~~~------~~C~~C~G 217 (369)
T PRK14282 150 DRYETCPHCGGTGVEPGSGYVTCPKCHGTGRIREERRSFFGVFVSERTCERCGGTGKIPG------EYCHECGG 217 (369)
T ss_pred eecccCCCCCccCCCCCCCCcCCCCCCCcCEEEEEEEccCcceEEEEECCCCCCcceeCC------CCCCCCCC
Confidence 3556677774 4566666667888884 457999988777643 24999974
No 156
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=23.58 E-value=35 Score=29.30 Aligned_cols=46 Identities=11% Similarity=0.227 Sum_probs=29.5
Q ss_pred CchhhccccCCCCccchhhhhh-----hhhhcccccccCCCCCCCCCceee
Q psy15639 12 NCRVCLKSFKPDDYSRVCYECH-----QKVCEDCASYSKLDENQDENTWRC 57 (135)
Q Consensus 12 ~CRVClKsfkP~e~~~tC~eCq-----qkVCEDCASYSkl~~~ed~~~WrC 57 (135)
-|.-|...+....+.-+|..|. ...||.|+.+-+..+-.++..|+|
T Consensus 127 ~~~~~~~~l~~~~v~g~cp~c~~~~~~G~~ce~cg~~~~~~~l~~p~~~~~ 177 (556)
T PRK12268 127 YCPSDGRFLPDRYVEGTCPYCGYEGARGDQCDNCGALLDPTDLINPRSKIS 177 (556)
T ss_pred ecCCCCcCcCccceeccCCCCCCcccCCchhhhccccCChHHhcCCccccC
Confidence 3566666555555556677776 667888888766655555555554
No 157
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh
Probab=23.53 E-value=53 Score=21.50 Aligned_cols=18 Identities=17% Similarity=0.512 Sum_probs=15.4
Q ss_pred hHHHHHHHhhcccccccc
Q psy15639 83 VPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 83 vpvlealqrrhsd~klg~ 100 (135)
-+++.+++++|++++|-.
T Consensus 19 ~~~l~~f~~~~P~v~i~~ 36 (199)
T cd08478 19 APLIAKFRERYPDIELEL 36 (199)
T ss_pred HHHHHHHHHHCCCeEEEE
Confidence 468999999999988865
No 158
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=23.47 E-value=16 Score=20.27 Aligned_cols=17 Identities=29% Similarity=0.825 Sum_probs=14.0
Q ss_pred CCchhhccccCCCCccc
Q psy15639 11 GNCRVCLKSFKPDDYSR 27 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~ 27 (135)
-.|.+|+..|.|+.+.+
T Consensus 3 ~~C~~CgR~F~~~~l~~ 19 (25)
T PF13913_consen 3 VPCPICGRKFNPDRLEK 19 (25)
T ss_pred CcCCCCCCEECHHHHHH
Confidence 36999999999987654
No 159
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=23.43 E-value=45 Score=21.44 Aligned_cols=17 Identities=29% Similarity=0.671 Sum_probs=14.3
Q ss_pred hHHHHHHHhhccccccc
Q psy15639 83 VPVLEALQRRHSDVKIG 99 (135)
Q Consensus 83 vpvlealqrrhsd~klg 99 (135)
.|++.+++++|++++|=
T Consensus 16 ~~~l~~f~~~~P~i~i~ 32 (194)
T cd08481 16 IPRLPDFLARHPDITVN 32 (194)
T ss_pred HhhhhHHHHHCCCceEE
Confidence 47788999999998874
No 160
>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=23.29 E-value=41 Score=18.08 Aligned_cols=13 Identities=31% Similarity=0.797 Sum_probs=9.8
Q ss_pred CchhhccccCCCC
Q psy15639 12 NCRVCLKSFKPDD 24 (135)
Q Consensus 12 ~CRVClKsfkP~e 24 (135)
.|-+|.|.|+-+.
T Consensus 3 ~C~~C~k~f~~~~ 15 (27)
T PF12171_consen 3 YCDACDKYFSSEN 15 (27)
T ss_dssp BBTTTTBBBSSHH
T ss_pred CcccCCCCcCCHH
Confidence 5889999987543
No 161
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=23.19 E-value=54 Score=20.88 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=15.7
Q ss_pred cchHHHHHHHhhcccccccc
Q psy15639 81 LDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 81 l~vpvlealqrrhsd~klg~ 100 (135)
+=.|++..++++|++++|=.
T Consensus 14 ~l~~~l~~~~~~~P~i~i~i 33 (195)
T cd08434 14 LVPDLIRAFRKEYPNVTFEL 33 (195)
T ss_pred hhHHHHHHHHHhCCCeEEEE
Confidence 44678999999999887653
No 162
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=23.17 E-value=46 Score=18.38 Aligned_cols=20 Identities=25% Similarity=0.723 Sum_probs=11.6
Q ss_pred chhhccccCCCCccchhhhhhh
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQ 34 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqq 34 (135)
|..|++.+.++. +.|..|..
T Consensus 2 Cp~CG~~~~~~~--~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDA--KFCPNCGT 21 (23)
T ss_pred CcccCCCCCCcC--cchhhhCC
Confidence 666777765543 34666654
No 163
>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C. The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.
Probab=23.14 E-value=34 Score=24.66 Aligned_cols=13 Identities=31% Similarity=1.099 Sum_probs=10.1
Q ss_pred CCCCceeehhhhh
Q psy15639 50 QDENTWRCSICRR 62 (135)
Q Consensus 50 ed~~~WrCSvCRR 62 (135)
++...|+|..|++
T Consensus 41 ~~~~~~~C~~Cg~ 53 (144)
T TIGR03290 41 SDDDLWMCTTCYT 53 (144)
T ss_pred cCCCCCcCcCcCc
Confidence 4568899998875
No 164
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=22.78 E-value=37 Score=23.98 Aligned_cols=18 Identities=44% Similarity=0.947 Sum_probs=14.8
Q ss_pred CCchhhccccCCCCccchhh
Q psy15639 11 GNCRVCLKSFKPDDYSRVCY 30 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~ 30 (135)
.-|-||.|++-|||. +|.
T Consensus 9 ~HC~VCg~aIp~de~--~CS 26 (64)
T COG4068 9 RHCVVCGKAIPPDEQ--VCS 26 (64)
T ss_pred ccccccCCcCCCccc--hHH
Confidence 469999999999985 454
No 165
>PRK11595 DNA utilization protein GntX; Provisional
Probab=22.63 E-value=51 Score=25.49 Aligned_cols=30 Identities=23% Similarity=0.822 Sum_probs=18.7
Q ss_pred CCchhhccccCCCCccchhhhhhhh------hhcccc
Q psy15639 11 GNCRVCLKSFKPDDYSRVCYECHQK------VCEDCA 41 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~tC~eCqqk------VCEDCA 41 (135)
..|-+|.+.+...+. .+|..|..+ .|..|.
T Consensus 6 ~~C~~C~~~~~~~~~-~lC~~C~~~l~~~~~~C~~Cg 41 (227)
T PRK11595 6 GLCWLCRMPLALSHW-GICSVCSRALRTLKTCCPQCG 41 (227)
T ss_pred CcCccCCCccCCCCC-cccHHHHhhCCcccCcCccCC
Confidence 358888887654432 367777644 377775
No 166
>PRK08359 transcription factor; Validated
Probab=22.55 E-value=25 Score=27.86 Aligned_cols=34 Identities=21% Similarity=0.554 Sum_probs=23.2
Q ss_pred CCchhhccccCCCCccch-hhhhhhhhhcccc-cccC
Q psy15639 11 GNCRVCLKSFKPDDYSRV-CYECHQKVCEDCA-SYSK 45 (135)
Q Consensus 11 g~CRVClKsfkP~e~~~t-C~eCqqkVCEDCA-SYSk 45 (135)
-.|-+|++-++ +...++ =.+=.-.||.+|| -|-+
T Consensus 7 ~~CEiCG~~i~-g~~~~v~ieGael~VC~~Ca~k~G~ 42 (176)
T PRK08359 7 RYCEICGAEIR-GPGHRIRIEGAELLVCDRCYEKYGR 42 (176)
T ss_pred ceeecCCCccC-CCCeEEEEcCeEEehHHHHHHHhCC
Confidence 34999999986 443333 2233457999999 8877
No 167
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=22.17 E-value=35 Score=29.11 Aligned_cols=50 Identities=26% Similarity=0.482 Sum_probs=25.8
Q ss_pred chhhccccCCCCccchhhhhhh-----hhhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 13 CRVCLKSFKPDDYSRVCYECHQ-----KVCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 13 CRVClKsfkP~e~~~tC~eCqq-----kVCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
|..|...+...++.-+|..|.. .+||.|..+....+ ...=+|..|+..+.
T Consensus 123 ~~~~~~~l~~~~v~g~cp~c~~~~~~g~~ce~cg~~~~~~~---l~~p~~~~~~~~~e 177 (530)
T TIGR00398 123 CPECEMFLPDRYVEGTCPKCGSEDARGDHCEVCGRHLEPTE---LINPRCKICGAKPE 177 (530)
T ss_pred cCCCCcCCchhhhcCCCCCCCCcccccchhhhccccCCHHH---hcCCccccCCCcce
Confidence 3344433333334445555553 47888887654433 44445555654443
No 168
>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=21.96 E-value=32 Score=22.35 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=19.8
Q ss_pred CCCCchhhccccCCCCccchhhhhhhhhhcccc
Q psy15639 9 RLGNCRVCLKSFKPDDYSRVCYECHQKVCEDCA 41 (135)
Q Consensus 9 r~g~CRVClKsfkP~e~~~tC~eCqqkVCEDCA 41 (135)
....|.||.|.|....|....+ .+.|--.|+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~--~~v~H~~C~ 107 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPC--GHVVHYSCI 107 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCC--CeEEecccc
Confidence 3457999999998866555432 255554443
No 169
>cd08476 PBP2_CrgA_like_7 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=21.58 E-value=62 Score=20.73 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=15.1
Q ss_pred hHHHHHHHhhcccccccc
Q psy15639 83 VPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 83 vpvlealqrrhsd~klg~ 100 (135)
.|++..++++|++++|=.
T Consensus 15 ~~~l~~~~~~~P~v~i~~ 32 (197)
T cd08476 15 LPVLAAFMQRYPEIELDL 32 (197)
T ss_pred HHHHHHHHHHCCCeEEEE
Confidence 489999999999977654
No 170
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=21.50 E-value=61 Score=20.86 Aligned_cols=20 Identities=20% Similarity=0.213 Sum_probs=16.0
Q ss_pred cchHHHHHHHhhcccccccc
Q psy15639 81 LDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 81 l~vpvlealqrrhsd~klg~ 100 (135)
+=.|++..++++|++++|-.
T Consensus 14 ~l~~~l~~~~~~~P~i~i~~ 33 (197)
T cd08449 14 GLGPALRRFKRQYPNVTVRF 33 (197)
T ss_pred hHHHHHHHHHHHCCCeEEEE
Confidence 44688999999999988743
No 171
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=21.38 E-value=38 Score=30.02 Aligned_cols=45 Identities=31% Similarity=0.577 Sum_probs=27.0
Q ss_pred cchhhhhhhhhhcccccccCC-----------CC-------CCCC-Cceeehhhhhhhhccccc
Q psy15639 26 SRVCYECHQKVCEDCASYSKL-----------DE-------NQDE-NTWRCSICRRKLQSRAQP 70 (135)
Q Consensus 26 ~~tC~eCqqkVCEDCASYSkl-----------~~-------~ed~-~~WrCSvCRRK~~sr~qp 70 (135)
-..|-+|++..|.+|.+.--. +. +-=. +-|.|.+|.-.|+-+...
T Consensus 5 L~fC~~C~~irc~~c~~~Ei~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~ 68 (483)
T PF05502_consen 5 LYFCEHCHKIRCPRCVSEEIDSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVRASD 68 (483)
T ss_pred ceecccccccCChhhcccccceeECccccccCChhhheeccceeccccccCCCCCCcceeEecc
Confidence 356888888888888764211 11 1111 447777887777665533
No 172
>KOG3576|consensus
Probab=21.06 E-value=29 Score=29.85 Aligned_cols=110 Identities=24% Similarity=0.407 Sum_probs=57.4
Q ss_pred CCCCCchhhccccCCCCccchhhhhhh----hhhcccccccCCC--------CCCCCCceeehhhhhhhhcccccccccc
Q psy15639 8 ARLGNCRVCLKSFKPDDYSRVCYECHQ----KVCEDCASYSKLD--------ENQDENTWRCSICRRKLQSRAQPVLSQN 75 (135)
Q Consensus 8 ~r~g~CRVClKsfkP~e~~~tC~eCqq----kVCEDCASYSkl~--------~~ed~~~WrCSvCRRK~~sr~qp~~~q~ 75 (135)
.-.-.||||.|.|.-.-.-..=-.|.. -.|.-|.---.++ ..-.-..++|++|.+....|-
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrc------- 187 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRC------- 187 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhc-------
Confidence 334579999999975433222223332 2355554211111 112234689999998776654
Q ss_pred ccccc----cchHHHHHHHhhcccccc----ccCCCCCCC--CCCCCCCCCCccccccC
Q psy15639 76 STDSL----LDVPVLEALQRRHSDVKI----GSANSGAHP--ANQGLAPPRSPELRRHS 124 (135)
Q Consensus 76 stds~----l~vpvlealqrrhsd~kl----g~~~~~~~~--~g~glapprspelrrhs 124 (135)
|-+|- -.|+-.-|...|-..+-+ |.++..... +--.++-|-||-|++-|
T Consensus 188 sleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~SpallKfs 246 (267)
T KOG3576|consen 188 SLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPALLKFS 246 (267)
T ss_pred cHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHHHHHHH
Confidence 22332 246666666666544433 443332222 33445667777776643
No 173
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=21.06 E-value=38 Score=19.73 Aligned_cols=12 Identities=25% Similarity=0.775 Sum_probs=9.5
Q ss_pred CCCCceeehhhh
Q psy15639 50 QDENTWRCSICR 61 (135)
Q Consensus 50 ed~~~WrCSvCR 61 (135)
..+.++||++|.
T Consensus 12 ~GA~sVrCa~C~ 23 (25)
T PF06943_consen 12 RGAPSVRCACCH 23 (25)
T ss_pred CCCCCeECCccC
Confidence 347799999995
No 174
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=20.98 E-value=64 Score=20.96 Aligned_cols=19 Identities=11% Similarity=0.324 Sum_probs=15.5
Q ss_pred chHHHHHHHhhcccccccc
Q psy15639 82 DVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 82 ~vpvlealqrrhsd~klg~ 100 (135)
=.|++..++++|+++.|=.
T Consensus 16 l~~~l~~f~~~~P~v~l~i 34 (197)
T cd08470 16 IAPLVNDFMQRYPKLEVDI 34 (197)
T ss_pred HHHHHHHHHHHCCCeEEEE
Confidence 3588999999999987753
No 175
>KOG2041|consensus
Probab=20.93 E-value=72 Score=32.06 Aligned_cols=56 Identities=27% Similarity=0.635 Sum_probs=37.7
Q ss_pred CCCCCCCCCchhhccccCCCCccchhhhhhhhhhccc-ccccCCCCCCCCCceeehhhhhhhh
Q psy15639 4 DKPAARLGNCRVCLKSFKPDDYSRVCYECHQKVCEDC-ASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 4 ~kp~~r~g~CRVClKsfkP~e~~~tC~eCqqkVCEDC-ASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
-.|.+---+|-+|+--+. ++.-.|.||+-|. .-| ||=+-.++ ..-|-|++|.-...
T Consensus 1111 ~d~~~~~vdc~~cg~~i~--~~~~~c~ec~~kf-P~CiasG~pIt~---~~fWlC~~CkH~a~ 1167 (1189)
T KOG2041|consen 1111 VDPNSAKVDCSVCGAKID--PYDLQCSECQTKF-PVCIASGRPITD---NIFWLCPRCKHRAH 1167 (1189)
T ss_pred CCCCccceeeeecCCcCC--ccCCCChhhcCcC-ceeeccCCcccc---ceEEEccccccccc
Confidence 345555678999987554 5666799999885 334 34343444 55999999976543
No 176
>PLN02195 cellulose synthase A
Probab=20.92 E-value=40 Score=33.32 Aligned_cols=51 Identities=20% Similarity=0.474 Sum_probs=39.5
Q ss_pred CCCchhhcccc---CCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhhhh
Q psy15639 10 LGNCRVCLKSF---KPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQ 65 (135)
Q Consensus 10 ~g~CRVClKsf---kP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK~~ 65 (135)
+..|.||+--. +-+|++--|.||.--||--|-.|-+-+. +=.|..|.-.-.
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg-----~q~CpqCkt~Yk 59 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEG-----RKVCLRCGGPYD 59 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcC-----CccCCccCCccc
Confidence 45799998744 3468999999999999999999987655 335888865443
No 177
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=20.82 E-value=64 Score=21.45 Aligned_cols=20 Identities=15% Similarity=0.112 Sum_probs=15.9
Q ss_pred cchHHHHHHHhhcccccccc
Q psy15639 81 LDVPVLEALQRRHSDVKIGS 100 (135)
Q Consensus 81 l~vpvlealqrrhsd~klg~ 100 (135)
+=-+++.+++++|++++|-.
T Consensus 14 ~l~~~l~~~~~~~P~v~l~i 33 (198)
T cd08444 14 ALPWVVQAFKEQFPNVHLVL 33 (198)
T ss_pred hhhHHHHHHHHHCCCeEEEE
Confidence 34578999999999888754
No 178
>PF15261 DUF4591: Domain of unknown function (DUF4591)
Probab=20.40 E-value=79 Score=24.00 Aligned_cols=21 Identities=33% Similarity=0.515 Sum_probs=16.3
Q ss_pred cccccccchHHHHHHHhhccc
Q psy15639 75 NSTDSLLDVPVLEALQRRHSD 95 (135)
Q Consensus 75 ~stds~l~vpvlealqrrhsd 95 (135)
..-.++.++..||.||.||-.
T Consensus 100 ~~e~~~~~ls~Le~L~~RHe~ 120 (134)
T PF15261_consen 100 QDEASLPELSELEMLEQRHER 120 (134)
T ss_pred ccCCCcchhHHHHHHHHHHHH
Confidence 344567788899999999954
No 179
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=20.37 E-value=55 Score=18.20 Aligned_cols=10 Identities=30% Similarity=1.182 Sum_probs=8.0
Q ss_pred Cceeehhhhh
Q psy15639 53 NTWRCSICRR 62 (135)
Q Consensus 53 ~~WrCSvCRR 62 (135)
..|.|+.|.-
T Consensus 3 g~W~C~~C~~ 12 (30)
T PF00641_consen 3 GDWKCPSCTF 12 (30)
T ss_dssp SSEEETTTTE
T ss_pred cCccCCCCcC
Confidence 4799999963
No 180
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=20.25 E-value=73 Score=22.24 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCchhhccccCCCCccchhh
Q psy15639 2 KSDKPAARLGNCRVCLKSFKPDDYSRVCY 30 (135)
Q Consensus 2 ~~~kp~~r~g~CRVClKsfkP~e~~~tC~ 30 (135)
.+.++......|.+|..++. |.++.|.
T Consensus 41 q~~~~~~~~~~C~~C~R~L~--d~~~fCS 67 (72)
T PF04640_consen 41 QSRPSKGSGNICETCHRSLQ--DPYRFCS 67 (72)
T ss_pred cCCCCCCCCCccCCCCCCCC--CCCeEEe
Confidence 34444456788999999987 3366663
No 181
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=20.24 E-value=58 Score=19.39 Aligned_cols=34 Identities=21% Similarity=0.341 Sum_probs=17.0
Q ss_pred CCCCCchhhccccC-CCCccchhhhhhhhhhcccc
Q psy15639 8 ARLGNCRVCLKSFK-PDDYSRVCYECHQKVCEDCA 41 (135)
Q Consensus 8 ~r~g~CRVClKsfk-P~e~~~tC~eCqqkVCEDCA 41 (135)
..+..|.+|.|.+- ..-....|..|+-.+=.+|+
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~ 43 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCL 43 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGG
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhh
Confidence 35567888887772 22223455555554444444
No 182
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.13 E-value=41 Score=19.87 Aligned_cols=9 Identities=33% Similarity=0.678 Sum_probs=4.6
Q ss_pred chhhccccC
Q psy15639 13 CRVCLKSFK 21 (135)
Q Consensus 13 CRVClKsfk 21 (135)
|++|+--+.
T Consensus 5 C~~CG~i~~ 13 (34)
T cd00729 5 CPVCGYIHE 13 (34)
T ss_pred CCCCCCEeE
Confidence 555554444
No 183
>PF01586 Basic: Myogenic Basic domain; InterPro: IPR002546 This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding []. With 12 residues of the basic domain involved in DNA binding []. The basic domain forms an extended alpha helix in the structure.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007517 muscle organ development, 0005634 nucleus; PDB: 1MDY_C.
Probab=20.12 E-value=32 Score=24.94 Aligned_cols=12 Identities=42% Similarity=1.176 Sum_probs=1.4
Q ss_pred ceeehhhhhhhh
Q psy15639 54 TWRCSICRRKLQ 65 (135)
Q Consensus 54 ~WrCSvCRRK~~ 65 (135)
.|-|.+|.||-.
T Consensus 72 ~WACKaCKRKt~ 83 (86)
T PF01586_consen 72 LWACKACKRKTV 83 (86)
T ss_dssp -------S---T
T ss_pred HHHhHhhhccCc
Confidence 699999999854
No 184
>PLN02400 cellulose synthase
Probab=20.09 E-value=46 Score=33.32 Aligned_cols=49 Identities=29% Similarity=0.670 Sum_probs=39.3
Q ss_pred CCCchhhcccc---CCCCccchhhhhhhhhhcccccccCCCCCCCCCceeehhhhhh
Q psy15639 10 LGNCRVCLKSF---KPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRK 63 (135)
Q Consensus 10 ~g~CRVClKsf---kP~e~~~tC~eCqqkVCEDCASYSkl~~~ed~~~WrCSvCRRK 63 (135)
+..|.||+--. .-+|++--|.||.--||--|-.|-+-.. +=.|..|+-+
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeG-----nq~CPQCkTr 87 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDG-----TQCCPQCKTR 87 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchhheecccC-----CccCcccCCc
Confidence 34899998754 4578999999999999999999987655 3468889643
No 185
>PLN02569 threonine synthase
Probab=20.05 E-value=45 Score=29.48 Aligned_cols=23 Identities=9% Similarity=0.171 Sum_probs=19.7
Q ss_pred CCCchhhccccCCCCccchhhhhh
Q psy15639 10 LGNCRVCLKSFKPDDYSRVCYECH 33 (135)
Q Consensus 10 ~g~CRVClKsfkP~e~~~tC~eCq 33 (135)
.-.|.-|.+.|.++++...| +|.
T Consensus 49 ~l~C~~Cg~~y~~~~~~~~C-~cg 71 (484)
T PLN02569 49 FLECPLTGEKYSLDEVVYRS-KSG 71 (484)
T ss_pred ccEeCCCCCcCCCccccccC-CCC
Confidence 35699999999999999888 784
No 186
>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=20.03 E-value=28 Score=19.44 Aligned_cols=22 Identities=18% Similarity=0.594 Sum_probs=8.2
Q ss_pred CchhhccccCCCCc----cchhhhhh
Q psy15639 12 NCRVCLKSFKPDDY----SRVCYECH 33 (135)
Q Consensus 12 ~CRVClKsfkP~e~----~~tC~eCq 33 (135)
.|..|..-+....+ ...|..||
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 45555544433333 44555554
Done!