Query psy2284
Match_columns 175
No_of_seqs 141 out of 209
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 20:45:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2284.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2284hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3362|consensus 100.0 2E-53 4.3E-58 340.3 4.2 154 2-173 3-156 (156)
2 PF04438 zf-HIT: HIT zinc fing 99.2 1.3E-12 2.9E-17 79.8 -0.3 30 134-163 1-30 (30)
3 COG5195 Uncharacterized conser 97.3 0.00013 2.7E-09 56.8 2.3 57 102-158 32-89 (118)
4 KOG4137|consensus 97.3 0.00026 5.5E-09 54.3 3.6 44 117-160 32-75 (102)
5 PF01753 zf-MYND: MYND finger; 95.6 0.0037 8E-08 38.8 0.2 29 138-166 1-30 (37)
6 KOG1710|consensus 94.4 0.0072 1.6E-07 54.9 -1.2 35 133-167 317-353 (396)
7 PF13824 zf-Mss51: Zinc-finger 93.3 0.045 9.7E-07 38.0 1.3 27 137-163 1-32 (55)
8 cd00350 rubredoxin_like Rubred 92.4 0.061 1.3E-06 32.9 1.0 20 136-155 2-26 (33)
9 cd00729 rubredoxin_SM Rubredox 86.9 0.29 6.2E-06 30.4 0.8 20 136-155 3-27 (34)
10 cd00730 rubredoxin Rubredoxin; 83.3 0.66 1.4E-05 31.3 1.3 10 146-155 34-43 (50)
11 PF12387 Peptidase_C74: Pestiv 83.2 0.62 1.4E-05 39.5 1.4 58 105-164 132-193 (200)
12 PF00301 Rubredoxin: Rubredoxi 83.2 0.5 1.1E-05 31.5 0.7 12 144-155 32-43 (47)
13 PLN00206 DEAD-box ATP-dependen 82.8 0.54 1.2E-05 43.8 1.0 34 133-166 26-59 (518)
14 PRK00420 hypothetical protein; 81.0 0.94 2E-05 35.3 1.6 21 136-156 24-50 (112)
15 TIGR02487 NrdD anaerobic ribon 80.9 0.86 1.9E-05 43.7 1.6 25 131-155 520-547 (579)
16 PF13248 zf-ribbon_3: zinc-rib 80.4 0.8 1.7E-05 26.6 0.8 20 136-155 3-25 (26)
17 PRK14704 anaerobic ribonucleos 79.3 0.94 2E-05 44.1 1.3 24 131-154 555-580 (618)
18 PF09297 zf-NADH-PPase: NADH p 78.6 0.86 1.9E-05 27.4 0.5 21 135-155 3-30 (32)
19 PRK03824 hypA hydrogenase nick 78.5 0.87 1.9E-05 35.9 0.7 12 131-142 66-77 (135)
20 PRK01343 zinc-binding protein; 77.9 1.5 3.2E-05 30.7 1.6 28 134-165 8-35 (57)
21 smart00290 ZnF_UBP Ubiquitin C 76.6 1.7 3.8E-05 27.8 1.6 23 137-159 1-24 (50)
22 PRK12380 hydrogenase nickel in 76.6 1.4 3.1E-05 33.7 1.4 25 131-155 66-95 (113)
23 smart00661 RPOL9 RNA polymeras 76.3 1.6 3.5E-05 28.1 1.4 19 136-154 1-28 (52)
24 PRK07111 anaerobic ribonucleos 76.2 1.4 3.1E-05 43.7 1.5 24 131-154 676-701 (735)
25 PHA00626 hypothetical protein 76.1 1.7 3.6E-05 30.7 1.4 21 136-156 12-33 (59)
26 PRK09263 anaerobic ribonucleos 75.2 1.5 3.3E-05 43.3 1.5 24 132-155 638-668 (711)
27 PF10013 DUF2256: Uncharacteri 74.6 0.51 1.1E-05 31.2 -1.3 30 134-163 7-40 (42)
28 PF07754 DUF1610: Domain of un 74.4 2.1 4.5E-05 25.1 1.3 11 144-154 14-24 (24)
29 COG0675 Transposase and inacti 73.6 2.3 5E-05 35.3 2.0 24 131-154 305-330 (364)
30 PRK03681 hypA hydrogenase nick 73.0 1.7 3.6E-05 33.4 0.9 25 131-155 66-96 (114)
31 PRK00762 hypA hydrogenase nick 71.1 1.9 4.2E-05 33.5 0.9 24 131-155 66-101 (124)
32 smart00154 ZnF_AN1 AN1-like Zi 71.0 2.9 6.2E-05 26.6 1.5 22 138-159 1-25 (39)
33 PF01155 HypA: Hydrogenase exp 71.0 1.1 2.3E-05 34.2 -0.5 26 131-156 66-96 (113)
34 PF03884 DUF329: Domain of unk 70.5 1.4 3.1E-05 30.6 0.0 10 155-164 22-31 (57)
35 PF08265 YL1_C: YL1 nuclear pr 70.4 2.6 5.5E-05 25.8 1.1 28 136-163 1-28 (30)
36 TIGR02827 RNR_anaer_Bdell anae 69.9 2.4 5.3E-05 41.1 1.5 24 132-155 529-555 (586)
37 PRK12496 hypothetical protein; 69.2 2.4 5.2E-05 34.5 1.1 21 135-155 127-152 (164)
38 PRK00432 30S ribosomal protein 69.1 3.1 6.8E-05 27.9 1.5 27 131-157 16-48 (50)
39 PRK05452 anaerobic nitric oxid 69.1 2.9 6.3E-05 39.1 1.8 29 127-155 417-467 (479)
40 TIGR01031 rpmF_bact ribosomal 69.0 3.2 7E-05 28.3 1.5 23 132-154 23-47 (55)
41 PRK13130 H/ACA RNA-protein com 68.6 2.2 4.7E-05 29.6 0.7 23 135-157 5-28 (56)
42 PF11682 DUF3279: Protein of u 67.8 4.4 9.5E-05 32.4 2.3 29 128-156 90-120 (128)
43 PRK14890 putative Zn-ribbon RN 67.4 2.1 4.5E-05 30.2 0.4 9 146-154 48-56 (59)
44 COG3024 Uncharacterized protei 67.1 2.2 4.8E-05 30.6 0.4 11 155-165 27-37 (65)
45 TIGR00100 hypA hydrogenase nic 67.1 2.6 5.7E-05 32.3 0.9 26 131-156 66-96 (115)
46 PF14446 Prok-RING_1: Prokaryo 67.1 3.5 7.6E-05 28.5 1.4 22 135-156 5-31 (54)
47 PF13240 zinc_ribbon_2: zinc-r 66.8 2.7 5.9E-05 24.0 0.7 19 137-155 1-22 (23)
48 PRK00564 hypA hydrogenase nick 66.7 2.9 6.3E-05 32.2 1.1 25 131-155 67-97 (117)
49 PF07282 OrfB_Zn_ribbon: Putat 66.4 3.3 7.2E-05 28.2 1.2 22 134-155 27-55 (69)
50 PF12172 DUF35_N: Rubredoxin-l 66.2 2 4.4E-05 26.4 0.1 18 137-154 13-33 (37)
51 smart00109 C1 Protein kinase C 65.1 3.8 8.3E-05 25.2 1.2 22 133-154 9-35 (49)
52 PRK00418 DNA gyrase inhibitor; 65.1 4.1 9E-05 28.9 1.5 32 133-164 4-35 (62)
53 PRK08271 anaerobic ribonucleos 64.6 3.6 7.7E-05 40.3 1.5 24 132-155 563-589 (623)
54 PF09538 FYDLN_acid: Protein o 63.6 3.2 6.8E-05 32.0 0.7 24 133-156 7-36 (108)
55 PRK12495 hypothetical protein; 63.2 4.4 9.5E-05 35.3 1.6 25 132-156 39-68 (226)
56 PRK08270 anaerobic ribonucleos 63.1 4.1 8.8E-05 40.0 1.6 24 132-155 623-648 (656)
57 PF09862 DUF2089: Protein of u 62.6 3.2 6.9E-05 32.5 0.6 19 138-156 1-22 (113)
58 PRK12286 rpmF 50S ribosomal pr 62.6 5.9 0.00013 27.3 1.9 23 132-154 24-48 (57)
59 PRK11788 tetratricopeptide rep 61.9 5.3 0.00012 34.0 1.9 25 131-155 350-377 (389)
60 COG1592 Rubrerythrin [Energy p 61.3 4.5 9.7E-05 33.6 1.3 21 135-155 134-158 (166)
61 PF11781 RRN7: RNA polymerase 60.9 4.2 9.2E-05 25.6 0.8 20 135-154 8-33 (36)
62 cd07160 NR_DBD_LXR DNA-binding 60.8 6 0.00013 30.0 1.8 31 126-156 9-45 (101)
63 PF08271 TF_Zn_Ribbon: TFIIB z 60.6 3.7 8E-05 26.1 0.6 18 137-154 2-27 (43)
64 PHA02942 putative transposase; 60.4 6.2 0.00013 36.1 2.1 22 134-155 324-351 (383)
65 PF01783 Ribosomal_L32p: Ribos 59.2 4.6 0.0001 27.4 0.9 20 134-153 25-46 (56)
66 PF13597 NRDD: Anaerobic ribon 59.0 3.6 7.9E-05 39.3 0.4 25 132-156 488-514 (546)
67 PF01428 zf-AN1: AN1-like Zinc 58.7 5.8 0.00013 25.3 1.2 22 138-159 1-26 (43)
68 TIGR00269 conserved hypothetic 58.5 4.3 9.2E-05 30.4 0.7 21 134-154 79-100 (104)
69 cd01675 RNR_III Class III ribo 58.1 5.7 0.00012 38.0 1.6 24 132-156 516-542 (555)
70 smart00064 FYVE Protein presen 58.0 6 0.00013 26.7 1.3 24 135-158 10-38 (68)
71 PF13842 Tnp_zf-ribbon_2: DDE_ 57.5 8.9 0.00019 23.4 1.8 24 137-160 2-30 (32)
72 PF13878 zf-C2H2_3: zinc-finge 57.1 5.6 0.00012 25.5 0.9 15 144-158 11-25 (41)
73 cd00065 FYVE FYVE domain; Zinc 56.5 6.7 0.00015 25.5 1.3 26 136-162 3-33 (57)
74 PLN02294 cytochrome c oxidase 56.4 10 0.00022 31.9 2.6 29 128-156 109-151 (174)
75 COG4068 Uncharacterized protei 56.2 4.1 8.9E-05 29.0 0.2 28 132-164 5-32 (64)
76 PRK04023 DNA polymerase II lar 55.8 6.5 0.00014 41.0 1.6 6 137-142 628-633 (1121)
77 PRK08579 anaerobic ribonucleos 55.4 5.8 0.00013 38.8 1.2 25 131-155 564-591 (625)
78 cd00029 C1 Protein kinase C co 55.1 7 0.00015 24.3 1.1 22 134-155 10-37 (50)
79 TIGR01384 TFS_arch transcripti 54.8 7 0.00015 28.7 1.3 21 136-156 1-26 (104)
80 COG1571 Predicted DNA-binding 54.4 5.9 0.00013 37.3 1.0 25 135-159 350-380 (421)
81 KOG3612|consensus 53.8 2.9 6.4E-05 40.6 -1.1 31 135-167 527-558 (588)
82 smart00547 ZnF_RBZ Zinc finger 52.7 6.4 0.00014 22.1 0.6 20 136-155 3-25 (26)
83 PRK14892 putative transcriptio 52.7 8.2 0.00018 29.5 1.4 25 132-156 18-52 (99)
84 PRK14714 DNA polymerase II lar 52.6 9.8 0.00021 40.5 2.3 20 136-155 680-701 (1337)
85 PF01363 FYVE: FYVE zinc finge 51.6 7.6 0.00016 26.3 1.0 25 135-159 9-38 (69)
86 PF08792 A2L_zn_ribbon: A2L zi 50.7 10 0.00022 23.5 1.3 21 135-155 3-30 (33)
87 COG4338 Uncharacterized protei 50.6 0.9 2E-05 31.2 -3.7 34 131-164 8-45 (54)
88 PRK00241 nudC NADH pyrophospha 49.6 9.5 0.00021 32.9 1.5 25 132-156 96-127 (256)
89 PF00096 zf-C2H2: Zinc finger, 49.4 7.3 0.00016 20.9 0.5 18 147-164 1-18 (23)
90 PF00641 zf-RanBP: Zn-finger i 48.8 8.8 0.00019 22.5 0.8 22 134-155 3-27 (30)
91 COG1645 Uncharacterized Zn-fin 47.6 11 0.00023 30.4 1.3 18 137-154 30-52 (131)
92 PF14803 Nudix_N_2: Nudix N-te 47.6 8.1 0.00018 24.1 0.5 6 137-142 2-7 (34)
93 KOG2807|consensus 47.2 32 0.00068 32.0 4.4 27 134-160 262-290 (378)
94 PF09889 DUF2116: Uncharacteri 46.6 7.4 0.00016 27.2 0.3 24 136-164 4-27 (59)
95 COG2888 Predicted Zn-ribbon RN 46.6 7.2 0.00016 27.7 0.2 12 132-143 24-35 (61)
96 COG2816 NPY1 NTP pyrophosphohy 45.7 12 0.00026 33.5 1.5 25 132-156 108-139 (279)
97 PF14949 ARF7EP_C: ARF7 effect 45.3 11 0.00025 29.0 1.1 16 146-161 74-89 (103)
98 PF02148 zf-UBP: Zn-finger in 45.2 9.1 0.0002 26.0 0.5 22 138-159 1-24 (63)
99 TIGR02098 MJ0042_CXXC MJ0042 f 44.4 12 0.00026 22.7 1.0 11 146-156 2-12 (38)
100 PF03833 PolC_DP2: DNA polymer 43.6 7.8 0.00017 39.6 0.0 37 135-171 667-705 (900)
101 PF04216 FdhE: Protein involve 43.2 7.2 0.00016 33.8 -0.2 22 21-42 11-32 (290)
102 COG1545 Predicted nucleic-acid 42.9 13 0.00029 29.4 1.3 20 136-155 30-52 (140)
103 PF13894 zf-C2H2_4: C2H2-type 42.7 7.5 0.00016 20.2 -0.1 20 147-166 1-20 (24)
104 PRK14891 50S ribosomal protein 42.6 8.4 0.00018 31.1 0.1 42 133-174 2-53 (131)
105 smart00659 RPOLCX RNA polymera 42.6 17 0.00037 23.7 1.5 19 137-155 4-28 (44)
106 COG4888 Uncharacterized Zn rib 41.9 16 0.00036 28.4 1.6 28 129-156 16-56 (104)
107 PF03107 C1_2: C1 domain; Int 41.4 18 0.00039 21.4 1.4 17 137-153 2-22 (30)
108 TIGR00622 ssl1 transcription f 41.1 28 0.00061 27.3 2.8 38 118-157 40-92 (112)
109 PF12773 DZR: Double zinc ribb 41.1 15 0.00033 23.4 1.1 22 133-154 10-37 (50)
110 PF13696 zf-CCHC_2: Zinc knuck 38.8 24 0.00052 22.0 1.7 21 131-151 4-26 (32)
111 PF00643 zf-B_box: B-box zinc 38.4 16 0.00034 22.4 0.8 25 135-159 3-28 (42)
112 PRK04023 DNA polymerase II lar 38.1 24 0.00052 37.0 2.4 21 134-154 637-659 (1121)
113 PF14569 zf-UDP: Zinc-binding 37.7 15 0.00032 27.4 0.7 12 145-156 50-61 (80)
114 PRK01110 rpmF 50S ribosomal pr 37.4 20 0.00044 24.8 1.3 19 135-154 27-47 (60)
115 PF05495 zf-CHY: CHY zinc fing 37.1 11 0.00024 26.5 -0.0 21 135-155 41-70 (71)
116 PF07975 C1_4: TFIIH C1-like d 37.1 18 0.00039 24.6 1.0 14 145-158 20-33 (51)
117 PHA00616 hypothetical protein 37.1 5.9 0.00013 26.3 -1.3 15 146-160 1-15 (44)
118 cd07173 NR_DBD_AR DNA-binding 36.7 8.5 0.00019 28.0 -0.7 22 133-154 1-28 (82)
119 PRK00398 rpoP DNA-directed RNA 36.1 19 0.00042 23.0 1.0 11 146-156 3-13 (46)
120 PLN02195 cellulose synthase A 36.0 18 0.00039 37.5 1.2 22 136-157 26-59 (977)
121 smart00647 IBR In Between Ring 35.6 29 0.00062 22.5 1.8 16 146-162 40-55 (64)
122 PF07649 C1_3: C1-like domain; 35.6 18 0.00039 21.2 0.7 19 136-154 1-23 (30)
123 PF14353 CpXC: CpXC protein 35.4 23 0.0005 26.9 1.5 15 142-156 34-48 (128)
124 PRK03564 formate dehydrogenase 35.3 19 0.0004 32.6 1.1 23 20-42 27-49 (309)
125 smart00834 CxxC_CXXC_SSSS Puta 35.3 20 0.00043 21.7 0.9 11 146-156 5-15 (41)
126 PF11239 DUF3040: Protein of u 34.9 16 0.00034 26.2 0.5 18 30-47 7-24 (82)
127 TIGR01562 FdhE formate dehydro 34.3 20 0.00044 32.2 1.2 26 19-44 22-47 (305)
128 PF09855 DUF2082: Nucleic-acid 34.1 17 0.00037 25.7 0.5 10 147-156 1-10 (64)
129 PLN02189 cellulose synthase 33.9 20 0.00044 37.4 1.2 13 145-157 75-87 (1040)
130 PF10122 Mu-like_Com: Mu-like 33.8 19 0.00042 24.7 0.7 20 136-155 5-33 (51)
131 TIGR02300 FYDLN_acid conserved 33.4 24 0.00053 28.4 1.3 25 132-156 6-36 (129)
132 smart00531 TFIIE Transcription 33.2 21 0.00045 28.2 0.9 13 145-157 98-110 (147)
133 COG3364 Zn-ribbon containing p 33.2 20 0.00043 28.2 0.8 21 135-155 2-29 (112)
134 COG0333 RpmF Ribosomal protein 32.8 32 0.00069 24.0 1.7 20 135-154 27-48 (57)
135 PF08461 HTH_12: Ribonuclease 32.8 41 0.00089 23.3 2.3 23 22-44 27-49 (66)
136 PLN02638 cellulose synthase A 32.2 22 0.00048 37.3 1.1 22 136-157 37-70 (1079)
137 PF14753 DUF4475: Domain of un 32.2 24 0.00052 30.2 1.2 18 138-156 125-143 (196)
138 PLN02436 cellulose synthase A 30.9 24 0.00052 37.0 1.2 11 146-156 78-88 (1094)
139 PF13719 zinc_ribbon_5: zinc-r 30.5 28 0.0006 21.6 1.0 10 147-156 3-12 (37)
140 cd02334 ZZ_dystrophin Zinc fin 30.4 31 0.00066 23.0 1.3 31 137-167 2-36 (49)
141 TIGR00373 conserved hypothetic 29.8 26 0.00056 28.2 0.9 10 147-156 110-119 (158)
142 PF10571 UPF0547: Uncharacteri 29.7 30 0.00065 20.3 1.0 6 149-154 17-22 (26)
143 PF04640 PLATZ: PLATZ transcri 29.6 25 0.00054 25.5 0.8 24 134-162 48-71 (72)
144 PF13717 zinc_ribbon_4: zinc-r 29.5 29 0.00063 21.5 1.0 10 147-156 3-12 (36)
145 smart00291 ZnF_ZZ Zinc-binding 29.1 37 0.0008 21.6 1.4 29 136-164 5-36 (44)
146 TIGR00627 tfb4 transcription f 29.1 29 0.00062 30.8 1.2 20 137-156 257-279 (279)
147 cd02335 ZZ_ADA2 Zinc finger, Z 29.0 40 0.00086 22.0 1.6 31 137-167 2-36 (49)
148 PRK06266 transcription initiat 28.9 27 0.00058 28.8 0.9 17 28-44 51-67 (178)
149 PF05741 zf-nanos: Nanos RNA b 28.9 28 0.00061 24.1 0.9 18 134-154 24-41 (55)
150 cd02345 ZZ_dah Zinc finger, ZZ 28.8 31 0.00068 22.7 1.1 31 137-167 2-36 (49)
151 PLN02915 cellulose synthase A 28.4 28 0.00062 36.4 1.2 22 136-157 35-68 (1044)
152 PF03604 DNA_RNApol_7kD: DNA d 27.9 36 0.00079 20.9 1.2 9 147-155 18-26 (32)
153 PF10083 DUF2321: Uncharacteri 27.9 9.5 0.00021 31.6 -1.9 25 131-155 24-48 (158)
154 PF00130 C1_1: Phorbol esters/ 27.8 24 0.00052 22.6 0.4 24 132-155 8-37 (53)
155 PF13465 zf-H2C2_2: Zinc-finge 27.8 25 0.00054 20.0 0.4 11 146-156 14-24 (26)
156 KOG4850|consensus 27.5 29 0.00063 29.3 0.9 16 146-161 149-164 (190)
157 PF02132 RecR: RecR protein; 27.2 16 0.00035 23.1 -0.5 18 134-151 16-34 (41)
158 KOG1356|consensus 27.1 30 0.00065 35.5 1.1 35 130-165 224-261 (889)
159 COG2260 Predicted Zn-ribbon RN 27.1 28 0.00061 24.6 0.6 20 136-155 6-26 (59)
160 PF14447 Prok-RING_4: Prokaryo 26.9 35 0.00075 23.8 1.0 20 137-156 29-49 (55)
161 PRK00807 50S ribosomal protein 26.8 31 0.00068 23.2 0.8 39 136-174 2-50 (52)
162 COG4306 Uncharacterized protei 26.4 19 0.0004 29.5 -0.4 21 135-155 28-48 (160)
163 COG1998 RPS31 Ribosomal protei 26.2 40 0.00086 23.2 1.2 24 131-154 15-45 (51)
164 PF03833 PolC_DP2: DNA polymer 25.8 23 0.00049 36.4 0.0 38 134-171 654-696 (900)
165 PLN02400 cellulose synthase 25.1 34 0.00074 35.9 1.1 11 146-156 78-88 (1085)
166 PF06677 Auto_anti-p27: Sjogre 24.9 49 0.0011 21.4 1.4 9 145-153 33-41 (41)
167 PF06524 NOA36: NOA36 protein; 24.8 26 0.00057 31.7 0.2 24 136-159 172-195 (314)
168 PF01412 ArfGap: Putative GTPa 24.8 21 0.00045 27.1 -0.4 35 132-167 10-45 (116)
169 PF05129 Elf1: Transcription e 24.7 27 0.00059 25.4 0.2 26 131-156 18-56 (81)
170 COG1885 Uncharacterized protei 24.5 36 0.00077 26.9 0.9 25 115-156 35-59 (115)
171 PF10263 SprT-like: SprT-like 24.0 40 0.00087 25.9 1.1 10 145-154 142-151 (157)
172 TIGR00155 pqiA_fam integral me 23.7 42 0.0009 31.0 1.3 22 135-156 215-240 (403)
173 PF05715 zf-piccolo: Piccolo Z 23.6 36 0.00079 24.2 0.7 27 114-145 14-40 (61)
174 TIGR02605 CxxC_CxxC_SSSS putat 23.5 41 0.00088 21.6 0.9 11 146-156 5-15 (52)
175 COG4391 Uncharacterized protei 23.5 73 0.0016 22.7 2.2 27 129-156 32-58 (62)
176 PF00628 PHD: PHD-finger; Int 23.5 42 0.00092 21.1 0.9 20 137-156 1-24 (51)
177 KOG2807|consensus 23.1 64 0.0014 30.1 2.3 32 127-158 322-357 (378)
178 KOG1802|consensus 22.9 38 0.00082 34.6 0.9 29 132-160 57-88 (935)
179 PF14392 zf-CCHC_4: Zinc knuck 22.7 38 0.00082 22.0 0.6 12 135-146 31-42 (49)
180 PF07966 A1_Propeptide: A1 Pro 22.7 30 0.00066 20.6 0.1 24 87-110 4-27 (29)
181 cd06970 NR_DBD_PNR DNA-binding 22.6 36 0.00078 25.3 0.5 24 133-156 4-33 (92)
182 PLN03119 putative ADP-ribosyla 22.4 48 0.001 32.9 1.4 36 132-168 20-56 (648)
183 TIGR00354 polC DNA polymerase, 21.7 44 0.00094 35.1 1.1 22 134-155 624-646 (1095)
184 PRK05978 hypothetical protein; 21.5 46 0.00099 27.1 1.0 23 134-156 32-62 (148)
185 KOG2907|consensus 21.5 43 0.00092 26.6 0.8 11 146-156 102-112 (116)
186 KOG4602|consensus 21.4 37 0.00081 30.7 0.5 16 145-160 267-290 (318)
187 TIGR00595 priA primosomal prot 21.2 45 0.00098 31.5 1.0 23 133-155 238-262 (505)
188 cd02344 ZZ_HERC2 Zinc finger, 21.2 61 0.0013 21.3 1.3 28 137-164 2-33 (45)
189 PF09723 Zn-ribbon_8: Zinc rib 21.1 49 0.0011 20.9 0.9 11 146-156 5-15 (42)
190 cd02342 ZZ_UBA_plant Zinc fing 21.1 49 0.0011 21.9 0.9 29 137-165 2-34 (43)
191 PF02318 FYVE_2: FYVE-type zin 20.9 50 0.0011 25.1 1.0 31 134-165 53-89 (118)
192 PF12855 Ecl1: Life-span regul 20.6 31 0.00067 22.7 -0.2 30 136-167 7-36 (43)
193 cd06966 NR_DBD_CAR DNA-binding 20.5 44 0.00096 24.8 0.7 20 137-156 2-27 (94)
194 PRK09521 exosome complex RNA-b 20.5 62 0.0013 26.4 1.6 22 135-156 149-176 (189)
195 PF13912 zf-C2H2_6: C2H2-type 20.5 29 0.00062 19.2 -0.3 24 147-170 2-25 (27)
196 cd02249 ZZ Zinc finger, ZZ typ 20.3 58 0.0013 20.8 1.1 28 137-164 2-32 (46)
197 PRK14714 DNA polymerase II lar 20.2 53 0.0012 35.3 1.3 22 135-156 667-689 (1337)
198 PRK13844 recombination protein 20.2 52 0.0011 28.1 1.1 23 132-154 54-77 (200)
No 1
>KOG3362|consensus
Probab=100.00 E-value=2e-53 Score=340.32 Aligned_cols=154 Identities=51% Similarity=0.909 Sum_probs=139.9
Q ss_pred cccccccccccccccccccCCHHHHHHHHHHHHHhhhCCCCCCCCCccccccccCCcchhhhcccccccccccchhHHHH
Q psy2284 2 TTMANRLSGRIKDANKQRVLDEATRQRRARKALESLESDNFHDDPHADLVMNKKAPKFQETLDAKSGSRKKKSKSAEYYK 81 (175)
Q Consensus 2 ~~~~~R~s~R~k~~~~~rvlD~~~R~rr~~~rLdaLE~DN~~ddp~a~l~~~k~~pkf~d~~~~~~~~kkkk~k~~~~~k 81 (175)
+.|..|.|.|+++.+++|+||+++|+++.+++||+||+|||+|||||+|+|.+..|+|.+.+.++ ..+++++.++++++
T Consensus 3 ~~~e~r~s~r~~~~~~rRvlD~~ar~rr~~r~l~~Le~Dn~~ddpha~l~~~k~~p~f~d~l~~G-kr~~~~~~~~~~~~ 81 (156)
T KOG3362|consen 3 HSFEERASQRIKDQEQRRVLDLNARQRRDNRNLEALEQDNFHDDPHASLVKPKQLPKFDDDLMGG-KRKKQKSYKSEKFK 81 (156)
T ss_pred cchHHHHHHHHhhhhhccccchHHHHhhhhhhhHHHhhhccCCCcccccccccccccccHHHhcc-hhhhccccccchhh
Confidence 45678999999999999999999999999999999999999999999999999999999998754 22333445567776
Q ss_pred hhhhhcccccccchhhhhhccccHHHHHHHhhhccCCCCCccccccCCCCCCCcccceecCCCCceecCCCCCccccccc
Q psy2284 82 LKTMEGLFHKTNQQNYIFRFRKSLAQMIEEDKALNSQGSAYENAEAKPSKFPNRHFCAVCGFPSNYTCVPCGARYCCVRC 161 (175)
Q Consensus 82 ~~~~~~~~~~~~~~~~ilr~rKnf~~lleE~~~~~~~~p~Y~~a~a~ps~~P~r~~C~VCG~~~~YtC~~Cg~ryCS~~C 161 (175)
+ ++||||++||||+.+.-...|+|.++.|+|+.+|.|+||+||||||+|+|++||++|||+.|
T Consensus 82 ~-----------------~~RKnf~~~Ldea~~~~~k~~~Y~~~~a~p~~KP~r~fCaVCG~~S~ysC~~CG~kyCsv~C 144 (156)
T KOG3362|consen 82 L-----------------RFRKNFQALLDEALLNLMKNPNYHTAYAKPSFKPLRKFCAVCGYDSKYSCVNCGTKYCSVRC 144 (156)
T ss_pred h-----------------hHHHHHHHHHHccchhhhhccchhhcccCCCCCCcchhhhhcCCCchhHHHhcCCceeechh
Confidence 5 99999999999998744578999999999999999999999999999999999999999999
Q ss_pred cccccccccccc
Q psy2284 162 LGTHQDTRCLKW 173 (175)
Q Consensus 162 ~~~H~etRC~K~ 173 (175)
.++|+||||+||
T Consensus 145 ~~~HneTRC~kw 156 (156)
T KOG3362|consen 145 LKTHNETRCMKW 156 (156)
T ss_pred hhhccccccccC
Confidence 999999999999
No 2
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=99.22 E-value=1.3e-12 Score=79.81 Aligned_cols=30 Identities=50% Similarity=1.326 Sum_probs=23.9
Q ss_pred CcccceecCCCCceecCCCCCccccccccc
Q psy2284 134 NRHFCAVCGFPSNYTCVPCGARYCCVRCLG 163 (175)
Q Consensus 134 ~r~~C~VCG~~~~YtC~~Cg~ryCS~~C~~ 163 (175)
++.+|+|||++++|+||+||.+|||+.|++
T Consensus 1 ~~~~C~vC~~~~kY~Cp~C~~~~CSl~C~k 30 (30)
T PF04438_consen 1 PRKLCSVCGNPAKYRCPRCGARYCSLACYK 30 (30)
T ss_dssp --EEETSSSSEESEE-TTT--EESSHHHHH
T ss_pred CcCCCccCcCCCEEECCCcCCceeCcEeEC
Confidence 578999999999999999999999999974
No 3
>COG5195 Uncharacterized conserved protein [Function unknown]
Probab=97.34 E-value=0.00013 Score=56.83 Aligned_cols=57 Identities=39% Similarity=0.598 Sum_probs=47.2
Q ss_pred cccHHHHHHHhhhcc-CCCCCccccccCCCCCCCcccceecCCCCceecCCCCCcccc
Q psy2284 102 RKSLAQMIEEDKALN-SQGSAYENAEAKPSKFPNRHFCAVCGFPSNYTCVPCGARYCC 158 (175)
Q Consensus 102 rKnf~~lleE~~~~~-~~~p~Y~~a~a~ps~~P~r~~C~VCG~~~~YtC~~Cg~ryCS 158 (175)
-|++.+||..+.+++ +.--+|+.+.||||..|.-++|-|=|-++-||||.=|.||=-
T Consensus 32 ~ktlrQli~~~~i~ne~sk~~Y~sieappSv~P~~KyCDvTGL~a~Yt~P~t~lrYhn 89 (118)
T COG5195 32 FKTLRQLIPRLTIENESSKHRYLSIEAPPSVKPRMKYCDVTGLPAPYTCPNTGLRYHN 89 (118)
T ss_pred hhhHHHHccccccccccccceeEeecCCCccccccccccccCCcccccCCCcCceecc
Confidence 456667777665543 234589999999999999999999999999999999999843
No 4
>KOG4137|consensus
Probab=97.30 E-value=0.00026 Score=54.26 Aligned_cols=44 Identities=34% Similarity=0.611 Sum_probs=40.1
Q ss_pred CCCCCccccccCCCCCCCcccceecCCCCceecCCCCCcccccc
Q psy2284 117 SQGSAYENAEAKPSKFPNRHFCAVCGFPSNYTCVPCGARYCCVR 160 (175)
Q Consensus 117 ~~~p~Y~~a~a~ps~~P~r~~C~VCG~~~~YtC~~Cg~ryCS~~ 160 (175)
..-++|++..||||..|.-+.|-|=|-++-|+||.=|.||=+..
T Consensus 32 ~~k~tYfsi~appSv~PakKycDvTGLpapYtdP~t~Lry~nae 75 (102)
T KOG4137|consen 32 EKKHTYFSIEAPPSVKPAKKYCDVTGLPAPYTDPNTGLRYHNAE 75 (102)
T ss_pred cccCceEEecCCCccccchhhccccCCcccccCCCccceeccHH
Confidence 45689999999999999999999999999999999999986544
No 5
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=95.59 E-value=0.0037 Score=38.78 Aligned_cols=29 Identities=38% Similarity=0.923 Sum_probs=24.2
Q ss_pred ceecCCCCceecCCC-CCcccccccccccc
Q psy2284 138 CAVCGFPSNYTCVPC-GARYCCVRCLGTHQ 166 (175)
Q Consensus 138 C~VCG~~~~YtC~~C-g~ryCS~~C~~~H~ 166 (175)
|.+||..+.-.|++| ...|||..|...|.
T Consensus 1 C~~C~~~~~~~C~~C~~~~YCs~~Cq~~~w 30 (37)
T PF01753_consen 1 CAVCGKPALKRCSRCKSVYYCSEECQRADW 30 (37)
T ss_dssp -TTTSSCSSEEETTTSSSEESSHHHHHHHH
T ss_pred CcCCCCCcCCcCCCCCCEEecCHHHHHHHH
Confidence 788998776699999 66899999998775
No 6
>KOG1710|consensus
Probab=94.41 E-value=0.0072 Score=54.90 Aligned_cols=35 Identities=31% Similarity=0.821 Sum_probs=29.4
Q ss_pred CCcccceecCCCC-ceecCCCC-Cccccccccccccc
Q psy2284 133 PNRHFCAVCGFPS-NYTCVPCG-ARYCCVRCLGTHQD 167 (175)
Q Consensus 133 P~r~~C~VCG~~~-~YtC~~Cg-~ryCS~~C~~~H~e 167 (175)
..-.||++||-+| +-+|..|- .-||+..|.+.|.-
T Consensus 317 ~d~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~hWf 353 (396)
T KOG1710|consen 317 ADCQFCSTCGHPGAKKRCSQCKAVAYCDQECQKFHWF 353 (396)
T ss_pred EecccccccCCCCccchhhhhHHHHHHHHHHHHhhhH
Confidence 3457999999776 66699998 78999999999964
No 7
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=93.28 E-value=0.045 Score=37.98 Aligned_cols=27 Identities=30% Similarity=0.759 Sum_probs=22.2
Q ss_pred cceecCC----CCceecCCCCCc-cccccccc
Q psy2284 137 FCAVCGF----PSNYTCVPCGAR-YCCVRCLG 163 (175)
Q Consensus 137 ~C~VCG~----~~~YtC~~Cg~r-yCS~~C~~ 163 (175)
+|.||+. ...|.||.||.+ |||..-..
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~ 32 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSEEHWE 32 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCHHHHH
Confidence 6899998 889999999997 58876543
No 8
>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=92.41 E-value=0.061 Score=32.91 Aligned_cols=20 Identities=40% Similarity=1.090 Sum_probs=15.9
Q ss_pred ccceecCCC-----CceecCCCCCc
Q psy2284 136 HFCAVCGFP-----SNYTCVPCGAR 155 (175)
Q Consensus 136 ~~C~VCG~~-----~~YtC~~Cg~r 155 (175)
..|.||||. ....||.||..
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCCc
Confidence 579999954 46789999974
No 9
>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=86.85 E-value=0.29 Score=30.36 Aligned_cols=20 Identities=40% Similarity=0.978 Sum_probs=15.3
Q ss_pred ccceecCCC--C---ceecCCCCCc
Q psy2284 136 HFCAVCGFP--S---NYTCVPCGAR 155 (175)
Q Consensus 136 ~~C~VCG~~--~---~YtC~~Cg~r 155 (175)
..|.||||. + ...||.||..
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 579999954 3 3689999974
No 10
>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=83.33 E-value=0.66 Score=31.28 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=7.0
Q ss_pred ceecCCCCCc
Q psy2284 146 NYTCVPCGAR 155 (175)
Q Consensus 146 ~YtC~~Cg~r 155 (175)
.++||.||..
T Consensus 34 ~w~CP~C~a~ 43 (50)
T cd00730 34 DWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCc
Confidence 5678888763
No 11
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=83.25 E-value=0.62 Score=39.47 Aligned_cols=58 Identities=22% Similarity=0.247 Sum_probs=40.0
Q ss_pred HHHHHHHhhhccCCCCCcccc--ccCCCCCCCcccceecC--CCCceecCCCCCcccccccccc
Q psy2284 105 LAQMIEEDKALNSQGSAYENA--EAKPSKFPNRHFCAVCG--FPSNYTCVPCGARYCCVRCLGT 164 (175)
Q Consensus 105 f~~lleE~~~~~~~~p~Y~~a--~a~ps~~P~r~~C~VCG--~~~~YtC~~Cg~ryCS~~C~~~ 164 (175)
...+++|+.. +.-|.-.+. ++.-+.-+.--+|.||- .|-.-+||+||..-=++.|.-+
T Consensus 132 v~~Wf~EeEv--yGmpKi~~iika~tLsk~~hcilCtvCe~r~w~g~~CPKCGr~G~pi~CGmt 193 (200)
T PF12387_consen 132 VASWFGEEEV--YGMPKIITIIKAATLSKSKHCILCTVCEGREWKGGNCPKCGRHGKPITCGMT 193 (200)
T ss_pred HHHHcccccc--cCcchhhhhhhHHhccCCCceEEEeeeecCccCCCCCCcccCCCCCeecccC
Confidence 3467888765 344433332 34556666677999998 8888999999998777777533
No 12
>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=83.19 E-value=0.5 Score=31.51 Aligned_cols=12 Identities=42% Similarity=1.162 Sum_probs=5.8
Q ss_pred CCceecCCCCCc
Q psy2284 144 PSNYTCVPCGAR 155 (175)
Q Consensus 144 ~~~YtC~~Cg~r 155 (175)
+..|+||.||+.
T Consensus 32 p~~w~CP~C~a~ 43 (47)
T PF00301_consen 32 PDDWVCPVCGAP 43 (47)
T ss_dssp -TT-B-TTTSSB
T ss_pred CCCCcCcCCCCc
Confidence 345677777753
No 13
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=82.81 E-value=0.54 Score=43.79 Aligned_cols=34 Identities=26% Similarity=0.638 Sum_probs=29.5
Q ss_pred CCcccceecCCCCceecCCCCCcccccccccccc
Q psy2284 133 PNRHFCAVCGFPSNYTCVPCGARYCCVRCLGTHQ 166 (175)
Q Consensus 133 P~r~~C~VCG~~~~YtC~~Cg~ryCS~~C~~~H~ 166 (175)
|.-..|-|||--|.|-|-.=....||++|...|-
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 (518)
T PLN00206 26 PGEPKCVVCGRYGEYICDETDDDICSLECKQALL 59 (518)
T ss_pred CCCceEEEecCccceeccCCCCccccHHHHHHHH
Confidence 3334599999999999999999999999998875
No 14
>PRK00420 hypothetical protein; Validated
Probab=81.04 E-value=0.94 Score=35.34 Aligned_cols=21 Identities=33% Similarity=0.855 Sum_probs=16.6
Q ss_pred ccceecCC------CCceecCCCCCcc
Q psy2284 136 HFCAVCGF------PSNYTCVPCGARY 156 (175)
Q Consensus 136 ~~C~VCG~------~~~YtC~~Cg~ry 156 (175)
.-|.+||+ .|.+-||.||..+
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCee
Confidence 56999993 4678899999854
No 15
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=80.90 E-value=0.86 Score=43.74 Aligned_cols=25 Identities=28% Similarity=0.776 Sum_probs=20.8
Q ss_pred CCCCcccceecCCCCce---ecCCCCCc
Q psy2284 131 KFPNRHFCAVCGFPSNY---TCVPCGAR 155 (175)
Q Consensus 131 ~~P~r~~C~VCG~~~~Y---tC~~Cg~r 155 (175)
..|+...|..|||.+.. .||.||..
T Consensus 520 ~n~~~~~C~~CG~~g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 520 INPPVDVCEDCGYTGEGLNDKCPKCGSH 547 (579)
T ss_pred eccCCccCCCCCCCCCCCCCcCcCCCCc
Confidence 35778899999998865 79999965
No 16
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=80.37 E-value=0.8 Score=26.57 Aligned_cols=20 Identities=40% Similarity=1.047 Sum_probs=13.6
Q ss_pred ccceecCC--CCcee-cCCCCCc
Q psy2284 136 HFCAVCGF--PSNYT-CVPCGAR 155 (175)
Q Consensus 136 ~~C~VCG~--~~~Yt-C~~Cg~r 155 (175)
.+|.-||. ....+ |+.||.+
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 57888883 33444 8888875
No 17
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=79.29 E-value=0.94 Score=44.07 Aligned_cols=24 Identities=21% Similarity=0.551 Sum_probs=20.5
Q ss_pred CCCCcccceecCCCCc--eecCCCCC
Q psy2284 131 KFPNRHFCAVCGFPSN--YTCVPCGA 154 (175)
Q Consensus 131 ~~P~r~~C~VCG~~~~--YtC~~Cg~ 154 (175)
..|+...|-.|||.+. ++||.||.
T Consensus 555 in~~~~~C~~CGy~g~~~~~CP~CG~ 580 (618)
T PRK14704 555 INHPVDRCKCCSYHGVIGNECPSCGN 580 (618)
T ss_pred eCCCCeecCCCCCCCCcCccCcCCCC
Confidence 4688889999999875 68999995
No 18
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=78.60 E-value=0.86 Score=27.42 Aligned_cols=21 Identities=38% Similarity=1.088 Sum_probs=11.1
Q ss_pred cccceecCCCC-------ceecCCCCCc
Q psy2284 135 RHFCAVCGFPS-------NYTCVPCGAR 155 (175)
Q Consensus 135 r~~C~VCG~~~-------~YtC~~Cg~r 155 (175)
-.||+.||.+- .-.|+.||..
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 36999999432 2348888864
No 19
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=78.49 E-value=0.87 Score=35.95 Aligned_cols=12 Identities=25% Similarity=0.448 Sum_probs=10.4
Q ss_pred CCCCcccceecC
Q psy2284 131 KFPNRHFCAVCG 142 (175)
Q Consensus 131 ~~P~r~~C~VCG 142 (175)
..|.+..|..||
T Consensus 66 ~~p~~~~C~~CG 77 (135)
T PRK03824 66 EEEAVLKCRNCG 77 (135)
T ss_pred ecceEEECCCCC
Confidence 467889999999
No 20
>PRK01343 zinc-binding protein; Provisional
Probab=77.93 E-value=1.5 Score=30.67 Aligned_cols=28 Identities=29% Similarity=0.654 Sum_probs=20.0
Q ss_pred CcccceecCCCCceecCCCCCccccccccccc
Q psy2284 134 NRHFCAVCGFPSNYTCVPCGARYCCVRCLGTH 165 (175)
Q Consensus 134 ~r~~C~VCG~~~~YtC~~Cg~ryCS~~C~~~H 165 (175)
+.+.|-|||.+.... ..+|||.+|..+.
T Consensus 8 p~~~CP~C~k~~~~~----~rPFCS~RC~~iD 35 (57)
T PRK01343 8 PTRPCPECGKPSTRE----AYPFCSERCRDID 35 (57)
T ss_pred CCCcCCCCCCcCcCC----CCcccCHHHhhhh
Confidence 457899999655421 3489999997653
No 21
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=76.57 E-value=1.7 Score=27.76 Aligned_cols=23 Identities=35% Similarity=0.940 Sum_probs=19.5
Q ss_pred cceecC-CCCceecCCCCCccccc
Q psy2284 137 FCAVCG-FPSNYTCVPCGARYCCV 159 (175)
Q Consensus 137 ~C~VCG-~~~~YtC~~Cg~ryCS~ 159 (175)
.|++|+ ....|.|..|+.-+|..
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCC
Confidence 499999 55699999999999864
No 22
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=76.57 E-value=1.4 Score=33.71 Aligned_cols=25 Identities=20% Similarity=0.509 Sum_probs=19.2
Q ss_pred CCCCcccceecCC-C----CceecCCCCCc
Q psy2284 131 KFPNRHFCAVCGF-P----SNYTCVPCGAR 155 (175)
Q Consensus 131 ~~P~r~~C~VCG~-~----~~YtC~~Cg~r 155 (175)
..|.+-.|..||. + ..+.||.||..
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 4788999999993 2 23569999965
No 23
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=76.25 E-value=1.6 Score=28.07 Aligned_cols=19 Identities=42% Similarity=1.308 Sum_probs=13.0
Q ss_pred ccceecC---CCC------ceecCCCCC
Q psy2284 136 HFCAVCG---FPS------NYTCVPCGA 154 (175)
Q Consensus 136 ~~C~VCG---~~~------~YtC~~Cg~ 154 (175)
+||.-|| +.. .|.|+.||-
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCC
Confidence 4788888 222 477888885
No 24
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=76.16 E-value=1.4 Score=43.66 Aligned_cols=24 Identities=29% Similarity=0.708 Sum_probs=20.0
Q ss_pred CCCCcccceecCCCC--ceecCCCCC
Q psy2284 131 KFPNRHFCAVCGFPS--NYTCVPCGA 154 (175)
Q Consensus 131 ~~P~r~~C~VCG~~~--~YtC~~Cg~ 154 (175)
..|+..+|.+|||.+ .+.||.||.
T Consensus 676 in~~~~~C~~CG~~~~~~~~CP~CG~ 701 (735)
T PRK07111 676 INHPVDRCPVCGYLGVIEDKCPKCGS 701 (735)
T ss_pred eCCCCeecCCCCCCCCcCccCcCCCC
Confidence 468888999999866 468999995
No 25
>PHA00626 hypothetical protein
Probab=76.08 E-value=1.7 Score=30.67 Aligned_cols=21 Identities=24% Similarity=0.268 Sum_probs=16.4
Q ss_pred ccceecCCCC-ceecCCCCCcc
Q psy2284 136 HFCAVCGFPS-NYTCVPCGARY 156 (175)
Q Consensus 136 ~~C~VCG~~~-~YtC~~Cg~ry 156 (175)
..|.+|-.|+ .|.|+.||-.|
T Consensus 12 vrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 12 AKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred eeeceecccCcceEcCCCCCee
Confidence 4677777654 89999999876
No 26
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=75.21 E-value=1.5 Score=43.29 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=19.1
Q ss_pred CCCcccceecCCCCc-------eecCCCCCc
Q psy2284 132 FPNRHFCAVCGFPSN-------YTCVPCGAR 155 (175)
Q Consensus 132 ~P~r~~C~VCG~~~~-------YtC~~Cg~r 155 (175)
-|+..+|-+|||.|. +.||.||..
T Consensus 638 n~~~~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 638 NTPIDECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred CCCCcccCCCCCCccccCCCCCCcCcCCCCC
Confidence 367789999999753 589999953
No 27
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=74.58 E-value=0.51 Score=31.20 Aligned_cols=30 Identities=33% Similarity=0.832 Sum_probs=17.8
Q ss_pred CcccceecCCCC--ceecCCC--CCccccccccc
Q psy2284 134 NRHFCAVCGFPS--NYTCVPC--GARYCCVRCLG 163 (175)
Q Consensus 134 ~r~~C~VCG~~~--~YtC~~C--g~ryCS~~C~~ 163 (175)
|.++|.|||-+- .-+=-+| ...|||-.|..
T Consensus 7 p~K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR~ 40 (42)
T PF10013_consen 7 PSKICPVCGRPFTWRKKWARCWDEVKYCSDRCRR 40 (42)
T ss_pred CCCcCcccCCcchHHHHHHHhchhhccHHHHhcc
Confidence 347888888322 2222344 45799999853
No 28
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=74.40 E-value=2.1 Score=25.15 Aligned_cols=11 Identities=27% Similarity=0.854 Sum_probs=8.7
Q ss_pred CCceecCCCCC
Q psy2284 144 PSNYTCVPCGA 154 (175)
Q Consensus 144 ~~~YtC~~Cg~ 154 (175)
-..|.||.||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 44799999984
No 29
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.61 E-value=2.3 Score=35.29 Aligned_cols=24 Identities=25% Similarity=0.753 Sum_probs=19.1
Q ss_pred CCCCcccceecCCC--CceecCCCCC
Q psy2284 131 KFPNRHFCAVCGFP--SNYTCVPCGA 154 (175)
Q Consensus 131 ~~P~r~~C~VCG~~--~~YtC~~Cg~ 154 (175)
..+.-..|++||++ ..+.|+.||.
T Consensus 305 ~~~tS~~C~~cg~~~~r~~~C~~cg~ 330 (364)
T COG0675 305 PYYTSKTCPCCGHLSGRLFKCPRCGF 330 (364)
T ss_pred CCCCcccccccCCccceeEECCCCCC
Confidence 45666899999964 3688999997
No 30
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=73.02 E-value=1.7 Score=33.41 Aligned_cols=25 Identities=16% Similarity=0.517 Sum_probs=18.7
Q ss_pred CCCCcccceecC--CCC---c-eecCCCCCc
Q psy2284 131 KFPNRHFCAVCG--FPS---N-YTCVPCGAR 155 (175)
Q Consensus 131 ~~P~r~~C~VCG--~~~---~-YtC~~Cg~r 155 (175)
..|.+-.|.-|| ++. . +.||.||..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 468899999999 322 1 449999965
No 31
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.07 E-value=1.9 Score=33.51 Aligned_cols=24 Identities=29% Similarity=0.794 Sum_probs=17.8
Q ss_pred CCCCcccceecCCC------C------ceecCCCCCc
Q psy2284 131 KFPNRHFCAVCGFP------S------NYTCVPCGAR 155 (175)
Q Consensus 131 ~~P~r~~C~VCG~~------~------~YtC~~Cg~r 155 (175)
..|.+-.| -||.. . .+.||.||..
T Consensus 66 ~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 66 MIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK 101 (124)
T ss_pred ecCeeEEe-eCcCcccccccchhccccCCcCcCCCCC
Confidence 46888999 99933 1 1579999953
No 32
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=71.01 E-value=2.9 Score=26.61 Aligned_cols=22 Identities=27% Similarity=0.892 Sum_probs=17.7
Q ss_pred ceecC-CCC--ceecCCCCCccccc
Q psy2284 138 CAVCG-FPS--NYTCVPCGARYCCV 159 (175)
Q Consensus 138 C~VCG-~~~--~YtC~~Cg~ryCS~ 159 (175)
|.+|+ .++ .++|..|+..||+.
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 77888 333 68899999999985
No 33
>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=70.98 E-value=1.1 Score=34.23 Aligned_cols=26 Identities=31% Similarity=0.834 Sum_probs=16.3
Q ss_pred CCCCcccceecCCCC-----ceecCCCCCcc
Q psy2284 131 KFPNRHFCAVCGFPS-----NYTCVPCGARY 156 (175)
Q Consensus 131 ~~P~r~~C~VCG~~~-----~YtC~~Cg~ry 156 (175)
..|.+..|..||+.. .+.||.||...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp EE--EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred ecCCcEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 468889999999332 35699999863
No 34
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=70.48 E-value=1.4 Score=30.64 Aligned_cols=10 Identities=30% Similarity=0.766 Sum_probs=8.0
Q ss_pred cccccccccc
Q psy2284 155 RYCCVRCLGT 164 (175)
Q Consensus 155 ryCS~~C~~~ 164 (175)
+|||.+|..+
T Consensus 22 PFCS~RCk~i 31 (57)
T PF03884_consen 22 PFCSERCKLI 31 (57)
T ss_dssp SSSSHHHHHH
T ss_pred CcccHhhccc
Confidence 5899999754
No 35
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=70.36 E-value=2.6 Score=25.83 Aligned_cols=28 Identities=21% Similarity=0.577 Sum_probs=24.6
Q ss_pred ccceecCCCCceecCCCCCccccccccc
Q psy2284 136 HFCAVCGFPSNYTCVPCGARYCCVRCLG 163 (175)
Q Consensus 136 ~~C~VCG~~~~YtC~~Cg~ryCS~~C~~ 163 (175)
++|.|=|.+++|+.|.=|.+|-++.-++
T Consensus 1 k~C~iTglpA~Y~DP~T~l~Y~n~~ayk 28 (30)
T PF08265_consen 1 KYCDITGLPARYRDPKTGLPYANSEAYK 28 (30)
T ss_pred CcccccCCCccccCCCCCCcccCHHHhh
Confidence 5799999999999999999998876554
No 36
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=69.91 E-value=2.4 Score=41.14 Aligned_cols=24 Identities=21% Similarity=0.468 Sum_probs=19.1
Q ss_pred CCCcccceecCCC-Cc--eecCCCCCc
Q psy2284 132 FPNRHFCAVCGFP-SN--YTCVPCGAR 155 (175)
Q Consensus 132 ~P~r~~C~VCG~~-~~--YtC~~Cg~r 155 (175)
-|+-.+|.+|||. +. +.||.||..
T Consensus 529 n~~~siC~~CGy~~g~~~~~CP~CGs~ 555 (586)
T TIGR02827 529 NIKITICNDCHHIDKRTLHRCPVCGSA 555 (586)
T ss_pred CCCCeecCCCCCcCCCcCCcCcCCCCc
Confidence 4677899999984 52 789999953
No 37
>PRK12496 hypothetical protein; Provisional
Probab=69.19 E-value=2.4 Score=34.48 Aligned_cols=21 Identities=38% Similarity=1.140 Sum_probs=16.3
Q ss_pred cccceecC--CCCcee---cCCCCCc
Q psy2284 135 RHFCAVCG--FPSNYT---CVPCGAR 155 (175)
Q Consensus 135 r~~C~VCG--~~~~Yt---C~~Cg~r 155 (175)
+..|.-|| |+..|. ||.||.+
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~ 152 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSP 152 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCCh
Confidence 36799999 765554 9999975
No 38
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=69.13 E-value=3.1 Score=27.89 Aligned_cols=27 Identities=26% Similarity=0.618 Sum_probs=20.4
Q ss_pred CCCCcccceecCC------CCceecCCCCCccc
Q psy2284 131 KFPNRHFCAVCGF------PSNYTCVPCGARYC 157 (175)
Q Consensus 131 ~~P~r~~C~VCG~------~~~YtC~~Cg~ryC 157 (175)
..+.+.||..||. ...+.|.+||..+-
T Consensus 16 v~~~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 16 VKRKNKFCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred EEEccCcCcCCCcchheccCCcEECCCcCCEEe
Confidence 3466789999996 33788999997653
No 39
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=69.05 E-value=2.9 Score=39.07 Aligned_cols=29 Identities=24% Similarity=0.695 Sum_probs=21.9
Q ss_pred cCCCCCCCcccceecC--CCC--------------------ceecCCCCCc
Q psy2284 127 AKPSKFPNRHFCAVCG--FPS--------------------NYTCVPCGAR 155 (175)
Q Consensus 127 a~ps~~P~r~~C~VCG--~~~--------------------~YtC~~Cg~r 155 (175)
..|+....+..|.+|| |-. .++||.||..
T Consensus 417 ~~~~~~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 417 TTTADLGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred ccccCCCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 3455577788999999 443 5899999974
No 40
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=68.96 E-value=3.2 Score=28.33 Aligned_cols=23 Identities=30% Similarity=0.719 Sum_probs=17.7
Q ss_pred CCCcccceecC--CCCceecCCCCC
Q psy2284 132 FPNRHFCAVCG--FPSNYTCVPCGA 154 (175)
Q Consensus 132 ~P~r~~C~VCG--~~~~YtC~~Cg~ 154 (175)
.|....|..|| ..+..-|+.||.
T Consensus 23 ~p~l~~C~~cG~~~~~H~vc~~cG~ 47 (55)
T TIGR01031 23 APTLVVCPNCGEFKLPHRVCPSCGY 47 (55)
T ss_pred CCcceECCCCCCcccCeeECCccCe
Confidence 35667899999 556777999994
No 41
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=68.62 E-value=2.2 Score=29.59 Aligned_cols=23 Identities=26% Similarity=0.699 Sum_probs=18.4
Q ss_pred cccceecC-CCCceecCCCCCccc
Q psy2284 135 RHFCAVCG-FPSNYTCVPCGARYC 157 (175)
Q Consensus 135 r~~C~VCG-~~~~YtC~~Cg~ryC 157 (175)
.+.|..|| |--+..||.||..+-
T Consensus 5 mr~C~~CgvYTLk~~CP~CG~~t~ 28 (56)
T PRK13130 5 IRKCPKCGVYTLKEICPVCGGKTK 28 (56)
T ss_pred ceECCCCCCEEccccCcCCCCCCC
Confidence 46799999 666888999998653
No 42
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=67.78 E-value=4.4 Score=32.38 Aligned_cols=29 Identities=24% Similarity=0.698 Sum_probs=23.8
Q ss_pred CCCCCCCcccceecC--CCCceecCCCCCcc
Q psy2284 128 KPSKFPNRHFCAVCG--FPSNYTCVPCGARY 156 (175)
Q Consensus 128 ~ps~~P~r~~C~VCG--~~~~YtC~~Cg~ry 156 (175)
+|...+...+|.-|| |.|.=-|+.|+.-.
T Consensus 90 ~pv~~~~~W~Cv~C~~~Y~GeK~C~~C~tGi 120 (128)
T PF11682_consen 90 DPVPRKTDWHCVMCGNHYHGEKYCPKCGTGI 120 (128)
T ss_pred CCCCcCceEEEecCCCccCcCEecCCCCCcc
Confidence 444478888999999 89987799999854
No 43
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=67.37 E-value=2.1 Score=30.17 Aligned_cols=9 Identities=56% Similarity=1.268 Sum_probs=6.5
Q ss_pred ceecCCCCC
Q psy2284 146 NYTCVPCGA 154 (175)
Q Consensus 146 ~YtC~~Cg~ 154 (175)
.|+||.||-
T Consensus 48 ~Y~CP~CGF 56 (59)
T PRK14890 48 PYTCPKCGF 56 (59)
T ss_pred ceECCCCCC
Confidence 677777774
No 44
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.12 E-value=2.2 Score=30.63 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=9.0
Q ss_pred ccccccccccc
Q psy2284 155 RYCCVRCLGTH 165 (175)
Q Consensus 155 ryCS~~C~~~H 165 (175)
+|||.+|..+.
T Consensus 27 PFCSkRCklID 37 (65)
T COG3024 27 PFCSKRCKLID 37 (65)
T ss_pred cchhHhhhhcc
Confidence 68999998764
No 45
>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=67.12 E-value=2.6 Score=32.32 Aligned_cols=26 Identities=27% Similarity=0.461 Sum_probs=19.1
Q ss_pred CCCCcccceecCC-CC----ceecCCCCCcc
Q psy2284 131 KFPNRHFCAVCGF-PS----NYTCVPCGARY 156 (175)
Q Consensus 131 ~~P~r~~C~VCG~-~~----~YtC~~Cg~ry 156 (175)
..|.+-.|..||. ++ .+.||.||..-
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred eeCcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 4678899999992 21 34599999753
No 46
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.06 E-value=3.5 Score=28.51 Aligned_cols=22 Identities=45% Similarity=1.004 Sum_probs=16.7
Q ss_pred cccceecC--C--CC-ceecCCCCCcc
Q psy2284 135 RHFCAVCG--F--PS-NYTCVPCGARY 156 (175)
Q Consensus 135 r~~C~VCG--~--~~-~YtC~~Cg~ry 156 (175)
...|.+|| + .. ...||-||++|
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcc
Confidence 35799999 3 22 56699999987
No 47
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=66.76 E-value=2.7 Score=23.99 Aligned_cols=19 Identities=32% Similarity=0.920 Sum_probs=10.4
Q ss_pred cceecCC--C-CceecCCCCCc
Q psy2284 137 FCAVCGF--P-SNYTCVPCGAR 155 (175)
Q Consensus 137 ~C~VCG~--~-~~YtC~~Cg~r 155 (175)
+|.-||. . ..--|+.||..
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 4667772 1 22237777764
No 48
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=66.71 E-value=2.9 Score=32.19 Aligned_cols=25 Identities=20% Similarity=0.490 Sum_probs=18.8
Q ss_pred CCCCcccceecC-CCC----cee-cCCCCCc
Q psy2284 131 KFPNRHFCAVCG-FPS----NYT-CVPCGAR 155 (175)
Q Consensus 131 ~~P~r~~C~VCG-~~~----~Yt-C~~Cg~r 155 (175)
..|.+-+|..|| .+. .|. ||.||.+
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 468899999999 332 243 9999975
No 49
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=66.44 E-value=3.3 Score=28.18 Aligned_cols=22 Identities=32% Similarity=0.871 Sum_probs=15.9
Q ss_pred CcccceecCCCC-------ceecCCCCCc
Q psy2284 134 NRHFCAVCGFPS-------NYTCVPCGAR 155 (175)
Q Consensus 134 ~r~~C~VCG~~~-------~YtC~~Cg~r 155 (175)
.-..|++||... .+.|+.||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 456799999433 3679999875
No 50
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=66.19 E-value=2 Score=26.38 Aligned_cols=18 Identities=44% Similarity=1.163 Sum_probs=9.5
Q ss_pred cceecC---CCCceecCCCCC
Q psy2284 137 FCAVCG---FPSNYTCVPCGA 154 (175)
Q Consensus 137 ~C~VCG---~~~~YtC~~Cg~ 154 (175)
.|.-|| |+....|+.||.
T Consensus 13 rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 13 RCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp E-TTT--EEES--SEETTTT-
T ss_pred EcCCCCCEecCCCcCCCCcCc
Confidence 577777 566777888864
No 51
>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=65.15 E-value=3.8 Score=25.21 Aligned_cols=22 Identities=23% Similarity=0.519 Sum_probs=16.1
Q ss_pred CCcccceecC--CCC---ceecCCCCC
Q psy2284 133 PNRHFCAVCG--FPS---NYTCVPCGA 154 (175)
Q Consensus 133 P~r~~C~VCG--~~~---~YtC~~Cg~ 154 (175)
....+|.+|+ .|+ .|.|..|+.
T Consensus 9 ~~~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 9 KKPTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCCCccccccccCcCCCCcCCCCCCc
Confidence 4456899998 554 688888865
No 52
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=65.13 E-value=4.1 Score=28.87 Aligned_cols=32 Identities=22% Similarity=0.463 Sum_probs=19.4
Q ss_pred CCcccceecCCCCceecCCCCCcccccccccc
Q psy2284 133 PNRHFCAVCGFPSNYTCVPCGARYCCVRCLGT 164 (175)
Q Consensus 133 P~r~~C~VCG~~~~YtC~~Cg~ryCS~~C~~~ 164 (175)
+....|-+||....+.=..=..+|||.+|..+
T Consensus 4 ~~~v~CP~C~k~~~w~~~~~~rPFCS~RCk~I 35 (62)
T PRK00418 4 TITVNCPTCGKPVEWGEISPFRPFCSKRCQLI 35 (62)
T ss_pred CccccCCCCCCcccccCCCCcCCcccHHHHhh
Confidence 44567888886543321112347899999765
No 53
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=64.64 E-value=3.6 Score=40.29 Aligned_cols=24 Identities=21% Similarity=0.480 Sum_probs=19.3
Q ss_pred CCCcccceecCCC--C-ceecCCCCCc
Q psy2284 132 FPNRHFCAVCGFP--S-NYTCVPCGAR 155 (175)
Q Consensus 132 ~P~r~~C~VCG~~--~-~YtC~~Cg~r 155 (175)
-|+...|.+|||. + .+.||.||..
T Consensus 563 n~~~~iC~~CG~~~~g~~~~CP~CGs~ 589 (623)
T PRK08271 563 NVKITICNDCHHIDKRTGKRCPICGSE 589 (623)
T ss_pred CCCCccCCCCCCcCCCCCcCCcCCCCc
Confidence 4677899999985 3 6779999964
No 54
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=63.61 E-value=3.2 Score=32.04 Aligned_cols=24 Identities=29% Similarity=0.902 Sum_probs=12.2
Q ss_pred CCcccceecC--CCC----ceecCCCCCcc
Q psy2284 133 PNRHFCAVCG--FPS----NYTCVPCGARY 156 (175)
Q Consensus 133 P~r~~C~VCG--~~~----~YtC~~Cg~ry 156 (175)
-.-++|--|| |-- ...||.||+-|
T Consensus 7 GtKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred CCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 3445666666 332 23366666544
No 55
>PRK12495 hypothetical protein; Provisional
Probab=63.16 E-value=4.4 Score=35.30 Aligned_cols=25 Identities=20% Similarity=0.483 Sum_probs=18.0
Q ss_pred CCCcccceecC-----CCCceecCCCCCcc
Q psy2284 132 FPNRHFCAVCG-----FPSNYTCVPCGARY 156 (175)
Q Consensus 132 ~P~r~~C~VCG-----~~~~YtC~~Cg~ry 156 (175)
.+...+|.+|| ++|...|+.|+..+
T Consensus 39 tmsa~hC~~CG~PIpa~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 39 TMTNAHCDECGDPIFRHDGQEFCPTCQQPV 68 (226)
T ss_pred ccchhhcccccCcccCCCCeeECCCCCCcc
Confidence 44567899999 45777788887654
No 56
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=63.13 E-value=4.1 Score=39.98 Aligned_cols=24 Identities=29% Similarity=0.664 Sum_probs=18.9
Q ss_pred CCCcccceecCCCC--ceecCCCCCc
Q psy2284 132 FPNRHFCAVCGFPS--NYTCVPCGAR 155 (175)
Q Consensus 132 ~P~r~~C~VCG~~~--~YtC~~Cg~r 155 (175)
-|+-..|..|||.. .+.||.||..
T Consensus 623 n~~~~~C~~CG~~~g~~~~CP~CG~~ 648 (656)
T PRK08270 623 TPTFSICPKHGYLSGEHEFCPKCGEE 648 (656)
T ss_pred CCCCcccCCCCCcCCCCCCCcCCcCc
Confidence 47778999999743 4679999964
No 57
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=62.60 E-value=3.2 Score=32.48 Aligned_cols=19 Identities=37% Similarity=1.086 Sum_probs=15.0
Q ss_pred ceecC---CCCceecCCCCCcc
Q psy2284 138 CAVCG---FPSNYTCVPCGARY 156 (175)
Q Consensus 138 C~VCG---~~~~YtC~~Cg~ry 156 (175)
|.||| ....+.|+.|++-.
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE
Confidence 88999 34578899999853
No 58
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=62.57 E-value=5.9 Score=27.31 Aligned_cols=23 Identities=30% Similarity=0.660 Sum_probs=16.1
Q ss_pred CCCcccceecC--CCCceecCCCCC
Q psy2284 132 FPNRHFCAVCG--FPSNYTCVPCGA 154 (175)
Q Consensus 132 ~P~r~~C~VCG--~~~~YtC~~Cg~ 154 (175)
.|....|.-|| ..+..-|+.||.
T Consensus 24 ~~~l~~C~~CG~~~~~H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLPHRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCCeEECCCCCc
Confidence 45557788888 445666888884
No 59
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=61.92 E-value=5.3 Score=34.04 Aligned_cols=25 Identities=36% Similarity=0.753 Sum_probs=18.4
Q ss_pred CCCCcccceecCCCC---ceecCCCCCc
Q psy2284 131 KFPNRHFCAVCGFPS---NYTCVPCGAR 155 (175)
Q Consensus 131 ~~P~r~~C~VCG~~~---~YtC~~Cg~r 155 (175)
...|...|+-||+-+ -+-||+||..
T Consensus 350 ~~~p~~~c~~cg~~~~~~~~~c~~c~~~ 377 (389)
T PRK11788 350 KRKPRYRCRNCGFTARTLYWHCPSCKAW 377 (389)
T ss_pred hCCCCEECCCCCCCCccceeECcCCCCc
Confidence 345568899999655 3459999974
No 60
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=61.35 E-value=4.5 Score=33.56 Aligned_cols=21 Identities=38% Similarity=0.952 Sum_probs=16.9
Q ss_pred cccceecCCC----CceecCCCCCc
Q psy2284 135 RHFCAVCGFP----SNYTCVPCGAR 155 (175)
Q Consensus 135 r~~C~VCG~~----~~YtC~~Cg~r 155 (175)
...|-||||. +.-.||.||.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 7899999964 35569999975
No 61
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=60.94 E-value=4.2 Score=25.55 Aligned_cols=20 Identities=40% Similarity=0.886 Sum_probs=14.8
Q ss_pred cccceecC------CCCceecCCCCC
Q psy2284 135 RHFCAVCG------FPSNYTCVPCGA 154 (175)
Q Consensus 135 r~~C~VCG------~~~~YtC~~Cg~ 154 (175)
+.-|.||| ..|.|.|.+||.
T Consensus 8 ~~~C~~C~~~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSRWFYSDDGFYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCeEeEccCCEEEhhhCce
Confidence 34599999 236788999985
No 62
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=60.84 E-value=6 Score=30.04 Aligned_cols=31 Identities=23% Similarity=0.597 Sum_probs=19.0
Q ss_pred ccCCCCCCCcccceecCCC------CceecCCCCCcc
Q psy2284 126 EAKPSKFPNRHFCAVCGFP------SNYTCVPCGARY 156 (175)
Q Consensus 126 ~a~ps~~P~r~~C~VCG~~------~~YtC~~Cg~ry 156 (175)
..|++.......|.|||.. |.++|-.|...|
T Consensus 9 ~~~~~~~~~~~~C~VCg~~a~g~hyGv~sC~aCk~FF 45 (101)
T cd07160 9 KGPAPKMLGNEVCSVCGDKASGFHYNVLSCEGCKGFF 45 (101)
T ss_pred CCCCCcccCCCCCeecCCcCcceEECcceehhhhhhh
Confidence 3445555556789999843 344577776643
No 63
>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=60.63 E-value=3.7 Score=26.06 Aligned_cols=18 Identities=33% Similarity=0.883 Sum_probs=11.1
Q ss_pred cceecCC--------CCceecCCCCC
Q psy2284 137 FCAVCGF--------PSNYTCVPCGA 154 (175)
Q Consensus 137 ~C~VCG~--------~~~YtC~~Cg~ 154 (175)
.|..||. .|.+.|+.||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 4667772 35677888875
No 64
>PHA02942 putative transposase; Provisional
Probab=60.37 E-value=6.2 Score=36.08 Aligned_cols=22 Identities=27% Similarity=0.803 Sum_probs=17.0
Q ss_pred CcccceecCCC------CceecCCCCCc
Q psy2284 134 NRHFCAVCGFP------SNYTCVPCGAR 155 (175)
Q Consensus 134 ~r~~C~VCG~~------~~YtC~~Cg~r 155 (175)
.-..|++||.. -.|.|+.||..
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCE
Confidence 55899999954 25889999863
No 65
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=59.24 E-value=4.6 Score=27.40 Aligned_cols=20 Identities=35% Similarity=0.773 Sum_probs=15.5
Q ss_pred CcccceecC--CCCceecCCCC
Q psy2284 134 NRHFCAVCG--FPSNYTCVPCG 153 (175)
Q Consensus 134 ~r~~C~VCG--~~~~YtC~~Cg 153 (175)
....|..|| ..+.+-|+.||
T Consensus 25 ~l~~c~~cg~~~~~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEESTTSBCTTTB
T ss_pred ceeeeccCCCEecccEeeCCCC
Confidence 447899999 55677899997
No 66
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=59.00 E-value=3.6 Score=39.27 Aligned_cols=25 Identities=28% Similarity=0.767 Sum_probs=12.4
Q ss_pred CCCcccceecCCCC--ceecCCCCCcc
Q psy2284 132 FPNRHFCAVCGFPS--NYTCVPCGARY 156 (175)
Q Consensus 132 ~P~r~~C~VCG~~~--~YtC~~Cg~ry 156 (175)
-|+...|..|||.+ ...||.||..-
T Consensus 488 n~~~~~C~~CG~~~~~~~~CP~CGs~~ 514 (546)
T PF13597_consen 488 NPPIDICPDCGYIGGEGDKCPKCGSEN 514 (546)
T ss_dssp E--EEEETTT---S--EEE-CCC----
T ss_pred ecCcccccCCCcCCCCCCCCCCCCCcc
Confidence 46778999999655 46899999864
No 67
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=58.68 E-value=5.8 Score=25.30 Aligned_cols=22 Identities=27% Similarity=0.857 Sum_probs=12.5
Q ss_pred cee--cC--CCCceecCCCCCccccc
Q psy2284 138 CAV--CG--FPSNYTCVPCGARYCCV 159 (175)
Q Consensus 138 C~V--CG--~~~~YtC~~Cg~ryCS~ 159 (175)
|++ |+ -.-.+.|..|+..||..
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSFCLK 26 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE-TT
T ss_pred CccCcCcCccCCCeECCCCCcccCcc
Confidence 556 77 22468899999999974
No 68
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=58.51 E-value=4.3 Score=30.39 Aligned_cols=21 Identities=29% Similarity=0.716 Sum_probs=16.0
Q ss_pred CcccceecCCCCcee-cCCCCC
Q psy2284 134 NRHFCAVCGFPSNYT-CVPCGA 154 (175)
Q Consensus 134 ~r~~C~VCG~~~~Yt-C~~Cg~ 154 (175)
....|.+||+++.-. |.-|-.
T Consensus 79 ~~~~C~~CG~pss~~iC~~C~l 100 (104)
T TIGR00269 79 DLRRCERCGEPTSGRICKACKF 100 (104)
T ss_pred cCCcCCcCcCcCCccccHhhhh
Confidence 466899999998655 877754
No 69
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=58.13 E-value=5.7 Score=38.01 Aligned_cols=24 Identities=29% Similarity=0.890 Sum_probs=18.4
Q ss_pred CCCcccceecCCCC---ceecCCCCCcc
Q psy2284 132 FPNRHFCAVCGFPS---NYTCVPCGARY 156 (175)
Q Consensus 132 ~P~r~~C~VCG~~~---~YtC~~Cg~ry 156 (175)
.|.- .|..|||.+ .++||.||..-
T Consensus 516 ~p~~-~C~~CG~~~~~~~~~CP~CGs~~ 542 (555)
T cd01675 516 TPID-ICNDCGYIGEGEGFKCPKCGSED 542 (555)
T ss_pred cCCc-cCCCCCCCCcCCCCCCcCCCCcC
Confidence 3444 999999864 57899999753
No 70
>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 PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=57.47 E-value=8.9 Score=23.44 Aligned_cols=24 Identities=29% Similarity=0.801 Sum_probs=18.8
Q ss_pred cceecCCC-----CceecCCCCCcccccc
Q psy2284 137 FCAVCGFP-----SNYTCVPCGARYCCVR 160 (175)
Q Consensus 137 ~C~VCG~~-----~~YtC~~Cg~ryCS~~ 160 (175)
-|.||... .+|.|..|+...|-..
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~~ 30 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVEP 30 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCCC
Confidence 47788754 7899999998887654
No 72
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=57.09 E-value=5.6 Score=25.49 Aligned_cols=15 Identities=33% Similarity=0.594 Sum_probs=10.7
Q ss_pred CCceecCCCCCcccc
Q psy2284 144 PSNYTCVPCGARYCC 158 (175)
Q Consensus 144 ~~~YtC~~Cg~ryCS 158 (175)
++..+|+.||+-|-.
T Consensus 11 ~~~~~C~~CgM~Y~~ 25 (41)
T PF13878_consen 11 FGATTCPTCGMLYSP 25 (41)
T ss_pred cCCcCCCCCCCEECC
Confidence 345678888887754
No 73
>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=56.48 E-value=6.7 Score=25.46 Aligned_cols=26 Identities=31% Similarity=0.892 Sum_probs=19.0
Q ss_pred ccceecC-----CCCceecCCCCCcccccccc
Q psy2284 136 HFCAVCG-----FPSNYTCVPCGARYCCVRCL 162 (175)
Q Consensus 136 ~~C~VCG-----~~~~YtC~~Cg~ryCS~~C~ 162 (175)
..|.+|+ +..++.|..||..+|+ .|.
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~-~C~ 33 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCS-KCS 33 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcCh-HHc
Confidence 4688887 2337789999999987 443
No 74
>PLN02294 cytochrome c oxidase subunit Vb
Probab=56.44 E-value=10 Score=31.93 Aligned_cols=29 Identities=17% Similarity=0.334 Sum_probs=22.7
Q ss_pred CCCCCCCcccceecCCCC--------------ceecCCCCCcc
Q psy2284 128 KPSKFPNRHFCAVCGFPS--------------NYTCVPCGARY 156 (175)
Q Consensus 128 ~ps~~P~r~~C~VCG~~~--------------~YtC~~Cg~ry 156 (175)
-||....|...++||+.. .+.|+.||..|
T Consensus 109 VpS~~d~RiVGCtg~~~eDsh~v~Wf~L~kGkp~RCpeCG~~f 151 (174)
T PLN02294 109 VKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYF 151 (174)
T ss_pred eccCCCceEEeeCCCCCCCCceeEEEEecCCCceeCCCCCCEE
Confidence 378899999999996432 35699999866
No 75
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=56.24 E-value=4.1 Score=29.02 Aligned_cols=28 Identities=21% Similarity=0.466 Sum_probs=19.5
Q ss_pred CCCcccceecCCCCceecCCCCCcccccccccc
Q psy2284 132 FPNRHFCAVCGFPSNYTCVPCGARYCCVRCLGT 164 (175)
Q Consensus 132 ~P~r~~C~VCG~~~~YtC~~Cg~ryCS~~C~~~ 164 (175)
.+|-+-|-|||..=. =+.++||-+|..+
T Consensus 5 v~PH~HC~VCg~aIp-----~de~~CSe~C~ei 32 (64)
T COG4068 5 VVPHRHCVVCGKAIP-----PDEQVCSEECGEI 32 (64)
T ss_pred CCCCccccccCCcCC-----CccchHHHHHHHH
Confidence 466677888884321 1678999999754
No 76
>PRK04023 DNA polymerase II large subunit; Validated
Probab=55.80 E-value=6.5 Score=40.96 Aligned_cols=6 Identities=50% Similarity=1.420 Sum_probs=2.4
Q ss_pred cceecC
Q psy2284 137 FCAVCG 142 (175)
Q Consensus 137 ~C~VCG 142 (175)
||.-||
T Consensus 628 fCpsCG 633 (1121)
T PRK04023 628 KCPSCG 633 (1121)
T ss_pred cCCCCC
Confidence 444444
No 77
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=55.41 E-value=5.8 Score=38.82 Aligned_cols=25 Identities=28% Similarity=0.674 Sum_probs=19.5
Q ss_pred CCCCcccceecCCC--C-ceecCCCCCc
Q psy2284 131 KFPNRHFCAVCGFP--S-NYTCVPCGAR 155 (175)
Q Consensus 131 ~~P~r~~C~VCG~~--~-~YtC~~Cg~r 155 (175)
..|+..+|..||+. + ...||.||..
T Consensus 564 inp~~~~C~~CG~~~~g~~~~CP~CGs~ 591 (625)
T PRK08579 564 YTPAITVCNKCGRSTTGLYTRCPRCGSE 591 (625)
T ss_pred eCCCCccCCCCCCccCCCCCcCcCCCCc
Confidence 35788899999972 3 5679999964
No 78
>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=55.08 E-value=7 Score=24.33 Aligned_cols=22 Identities=27% Similarity=0.709 Sum_probs=16.2
Q ss_pred CcccceecC--CC----CceecCCCCCc
Q psy2284 134 NRHFCAVCG--FP----SNYTCVPCGAR 155 (175)
Q Consensus 134 ~r~~C~VCG--~~----~~YtC~~Cg~r 155 (175)
...+|.+|+ .| ..|.|..|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCc
Confidence 456899998 55 56889888653
No 79
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=54.80 E-value=7 Score=28.74 Aligned_cols=21 Identities=43% Similarity=1.133 Sum_probs=15.7
Q ss_pred ccceecC---CC--CceecCCCCCcc
Q psy2284 136 HFCAVCG---FP--SNYTCVPCGARY 156 (175)
Q Consensus 136 ~~C~VCG---~~--~~YtC~~Cg~ry 156 (175)
.||..|| ++ +.+.|+.||..+
T Consensus 1 ~fC~~Cg~~l~~~~~~~~C~~C~~~~ 26 (104)
T TIGR01384 1 KFCPKCGSLMTPKNGVYVCPSCGYEK 26 (104)
T ss_pred CCCcccCcccccCCCeEECcCCCCcc
Confidence 3899999 23 478899998653
No 80
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=54.40 E-value=5.9 Score=37.29 Aligned_cols=25 Identities=28% Similarity=0.741 Sum_probs=18.8
Q ss_pred cccceecC----CCC--ceecCCCCCccccc
Q psy2284 135 RHFCAVCG----FPS--NYTCVPCGARYCCV 159 (175)
Q Consensus 135 r~~C~VCG----~~~--~YtC~~Cg~ryCS~ 159 (175)
-..|..|| ..| -|+|++||.++=+.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCcc
Confidence 34899999 233 58999999987553
No 81
>KOG3612|consensus
Probab=53.85 E-value=2.9 Score=40.63 Aligned_cols=31 Identities=32% Similarity=0.859 Sum_probs=27.1
Q ss_pred cccceecCCCCceecCCC-CCccccccccccccc
Q psy2284 135 RHFCAVCGFPSNYTCVPC-GARYCCVRCLGTHQD 167 (175)
Q Consensus 135 r~~C~VCG~~~~YtC~~C-g~ryCS~~C~~~H~e 167 (175)
-..|--|-..+.|-| | .+-|||+.|...|.-
T Consensus 527 KQWC~nC~~EAiy~C--CWNTSYCsveCQQ~HW~ 558 (588)
T KOG3612|consen 527 KQWCYNCLDEAIYHC--CWNTSYCSVECQQGHWP 558 (588)
T ss_pred HHHHHhhhHHHHHHh--hccccccCcchhhccch
Confidence 348999999999886 5 889999999999975
No 82
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=52.66 E-value=6.4 Score=22.11 Aligned_cols=20 Identities=40% Similarity=0.951 Sum_probs=14.0
Q ss_pred ccceecC---CCCceecCCCCCc
Q psy2284 136 HFCAVCG---FPSNYTCVPCGAR 155 (175)
Q Consensus 136 ~~C~VCG---~~~~YtC~~Cg~r 155 (175)
..|..|+ +.....|..|+.+
T Consensus 3 W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 3 WECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred ccCCCCCCcChhhhccccccCCc
Confidence 3588887 4456678888864
No 83
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=52.65 E-value=8.2 Score=29.47 Aligned_cols=25 Identities=32% Similarity=0.632 Sum_probs=16.8
Q ss_pred CCCcccceecCCC----------CceecCCCCCcc
Q psy2284 132 FPNRHFCAVCGFP----------SNYTCVPCGARY 156 (175)
Q Consensus 132 ~P~r~~C~VCG~~----------~~YtC~~Cg~ry 156 (175)
.|....|..||.. +...|+.||.+|
T Consensus 18 lpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 18 LPKIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CCcEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 4556678888822 256788888865
No 84
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=52.65 E-value=9.8 Score=40.47 Aligned_cols=20 Identities=40% Similarity=0.977 Sum_probs=16.5
Q ss_pred ccceecCCCC--ceecCCCCCc
Q psy2284 136 HFCAVCGFPS--NYTCVPCGAR 155 (175)
Q Consensus 136 ~~C~VCG~~~--~YtC~~Cg~r 155 (175)
.||..||.+. .|.|+.||..
T Consensus 680 ~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 680 NRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred ccCcccCCcCCCceeCccCCCc
Confidence 4999999554 8899999985
No 85
>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=51.56 E-value=7.6 Score=26.31 Aligned_cols=25 Identities=32% Similarity=0.871 Sum_probs=13.5
Q ss_pred cccceecC--C---CCceecCCCCCccccc
Q psy2284 135 RHFCAVCG--F---PSNYTCVPCGARYCCV 159 (175)
Q Consensus 135 r~~C~VCG--~---~~~YtC~~Cg~ryCS~ 159 (175)
...|.+|+ | ..++.|..||.-+|+.
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSS 38 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECC
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCc
Confidence 46799998 2 3377899999999863
No 86
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=50.70 E-value=10 Score=23.48 Aligned_cols=21 Identities=29% Similarity=0.678 Sum_probs=15.2
Q ss_pred cccceecCCCCc-------eecCCCCCc
Q psy2284 135 RHFCAVCGFPSN-------YTCVPCGAR 155 (175)
Q Consensus 135 r~~C~VCG~~~~-------YtC~~Cg~r 155 (175)
...|.+||-.+- |.|+.||.-
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 357999995554 469999864
No 87
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.61 E-value=0.9 Score=31.25 Aligned_cols=34 Identities=26% Similarity=0.608 Sum_probs=22.4
Q ss_pred CCCCcccceecCCCC--ceecCCC--CCcccccccccc
Q psy2284 131 KFPNRHFCAVCGFPS--NYTCVPC--GARYCCVRCLGT 164 (175)
Q Consensus 131 ~~P~r~~C~VCG~~~--~YtC~~C--g~ryCS~~C~~~ 164 (175)
..-+-++|.|||-+- .-+=.+| ...|||-+|...
T Consensus 8 a~lp~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCrr~ 45 (54)
T COG4338 8 ATLPDKICPVCQRPFSWRKKWARCWDEVKYCSERCRRL 45 (54)
T ss_pred cccchhhhhhhcCchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355678999999443 2234445 457999999743
No 88
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=49.62 E-value=9.5 Score=32.95 Aligned_cols=25 Identities=36% Similarity=1.023 Sum_probs=17.6
Q ss_pred CCCcccceecCCCCce-------ecCCCCCcc
Q psy2284 132 FPNRHFCAVCGFPSNY-------TCVPCGARY 156 (175)
Q Consensus 132 ~P~r~~C~VCG~~~~Y-------tC~~Cg~ry 156 (175)
.-.-+||+.||.+-.. .|+.||..+
T Consensus 96 ~~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 96 YRSHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred hhcCccccccCCCCeecCCceeEECCCCCCEE
Confidence 3456799999965332 399998765
No 89
>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=49.35 E-value=7.3 Score=20.87 Aligned_cols=18 Identities=28% Similarity=0.682 Sum_probs=11.9
Q ss_pred eecCCCCCcccccccccc
Q psy2284 147 YTCVPCGARYCCVRCLGT 164 (175)
Q Consensus 147 YtC~~Cg~ryCS~~C~~~ 164 (175)
|.|+.||..|=+..=+..
T Consensus 1 y~C~~C~~~f~~~~~l~~ 18 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKR 18 (23)
T ss_dssp EEETTTTEEESSHHHHHH
T ss_pred CCCCCCCCccCCHHHHHH
Confidence 789999887755443333
No 90
>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=48.80 E-value=8.8 Score=22.49 Aligned_cols=22 Identities=36% Similarity=0.745 Sum_probs=13.5
Q ss_pred CcccceecC---CCCceecCCCCCc
Q psy2284 134 NRHFCAVCG---FPSNYTCVPCGAR 155 (175)
Q Consensus 134 ~r~~C~VCG---~~~~YtC~~Cg~r 155 (175)
..-.|.+|+ +...-.|..||..
T Consensus 3 g~W~C~~C~~~N~~~~~~C~~C~~~ 27 (30)
T PF00641_consen 3 GDWKCPSCTFMNPASRSKCVACGAP 27 (30)
T ss_dssp SSEEETTTTEEEESSSSB-TTT--B
T ss_pred cCccCCCCcCCchHHhhhhhCcCCC
Confidence 345788998 4556679999864
No 91
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=47.57 E-value=11 Score=30.42 Aligned_cols=18 Identities=33% Similarity=0.850 Sum_probs=11.0
Q ss_pred cceecC-----CCCceecCCCCC
Q psy2284 137 FCAVCG-----FPSNYTCVPCGA 154 (175)
Q Consensus 137 ~C~VCG-----~~~~YtC~~Cg~ 154 (175)
-|.+|| +.|..-||.||.
T Consensus 30 hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcceeeCCeEECCCCCc
Confidence 466676 345566777764
No 92
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=47.56 E-value=8.1 Score=24.12 Aligned_cols=6 Identities=67% Similarity=1.962 Sum_probs=2.2
Q ss_pred cceecC
Q psy2284 137 FCAVCG 142 (175)
Q Consensus 137 ~C~VCG 142 (175)
||..||
T Consensus 2 fC~~CG 7 (34)
T PF14803_consen 2 FCPQCG 7 (34)
T ss_dssp B-TTT-
T ss_pred cccccc
Confidence 555555
No 93
>KOG2807|consensus
Probab=47.19 E-value=32 Score=32.01 Aligned_cols=27 Identities=30% Similarity=0.714 Sum_probs=20.1
Q ss_pred CcccceecC--CCCceecCCCCCcccccc
Q psy2284 134 NRHFCAVCG--FPSNYTCVPCGARYCCVR 160 (175)
Q Consensus 134 ~r~~C~VCG--~~~~YtC~~Cg~ryCS~~ 160 (175)
.+.||+-=+ .-+.|-||+|++++||+.
T Consensus 262 ~ps~C~CH~~~~~~Gy~CP~CkakvCsLP 290 (378)
T KOG2807|consen 262 TPSFCACHSELSGGGYFCPQCKAKVCSLP 290 (378)
T ss_pred CcchheeccccccCceeCCcccCeeecCC
Confidence 346775333 456899999999999964
No 94
>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=46.60 E-value=7.4 Score=27.21 Aligned_cols=24 Identities=29% Similarity=0.808 Sum_probs=14.5
Q ss_pred ccceecCCCCceecCCCCCcccccccccc
Q psy2284 136 HFCAVCGFPSNYTCVPCGARYCCVRCLGT 164 (175)
Q Consensus 136 ~~C~VCG~~~~YtC~~Cg~ryCS~~C~~~ 164 (175)
+-|-|||.+=.- ...|||-.|.+.
T Consensus 4 kHC~~CG~~Ip~-----~~~fCS~~C~~~ 27 (59)
T PF09889_consen 4 KHCPVCGKPIPP-----DESFCSPKCREE 27 (59)
T ss_pred CcCCcCCCcCCc-----chhhhCHHHHHH
Confidence 446666633221 357999999654
No 95
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=46.56 E-value=7.2 Score=27.71 Aligned_cols=12 Identities=25% Similarity=0.514 Sum_probs=6.8
Q ss_pred CCCcccceecCC
Q psy2284 132 FPNRHFCAVCGF 143 (175)
Q Consensus 132 ~P~r~~C~VCG~ 143 (175)
.-....|--||.
T Consensus 24 ~~v~F~CPnCGe 35 (61)
T COG2888 24 TAVKFPCPNCGE 35 (61)
T ss_pred ceeEeeCCCCCc
Confidence 344456667773
No 96
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=45.73 E-value=12 Score=33.50 Aligned_cols=25 Identities=28% Similarity=0.820 Sum_probs=18.0
Q ss_pred CCCcccceecCCC-----C--ceecCCCCCcc
Q psy2284 132 FPNRHFCAVCGFP-----S--NYTCVPCGARY 156 (175)
Q Consensus 132 ~P~r~~C~VCG~~-----~--~YtC~~Cg~ry 156 (175)
.-.-+||+-||.. + ++-|+.||..+
T Consensus 108 ~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 108 YRSHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HhhCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 3456799999932 2 44599999865
No 97
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=45.31 E-value=11 Score=29.01 Aligned_cols=16 Identities=44% Similarity=1.240 Sum_probs=15.0
Q ss_pred ceecCCCCCccccccc
Q psy2284 146 NYTCVPCGARYCCVRC 161 (175)
Q Consensus 146 ~YtC~~Cg~ryCS~~C 161 (175)
.|-|++||.+-|+..|
T Consensus 74 ~~PC~~C~S~KCG~~C 89 (103)
T PF14949_consen 74 HYPCPKCGSRKCGPEC 89 (103)
T ss_pred cccCCCCCCCccChhh
Confidence 6779999999999999
No 98
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=45.16 E-value=9.1 Score=26.01 Aligned_cols=22 Identities=36% Similarity=0.966 Sum_probs=17.0
Q ss_pred ceecC-C-CCceecCCCCCccccc
Q psy2284 138 CAVCG-F-PSNYTCVPCGARYCCV 159 (175)
Q Consensus 138 C~VCG-~-~~~YtC~~Cg~ryCS~ 159 (175)
|++|+ . ...|.|..||.-.|..
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETT
T ss_pred CCCCCCcCCceEEeCCCCcccccC
Confidence 78888 4 5689999999999985
No 99
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=44.42 E-value=12 Score=22.74 Aligned_cols=11 Identities=18% Similarity=0.736 Sum_probs=8.2
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
+++||.||+.|
T Consensus 2 ~~~CP~C~~~~ 12 (38)
T TIGR02098 2 RIQCPNCKTSF 12 (38)
T ss_pred EEECCCCCCEE
Confidence 36789998865
No 100
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=43.56 E-value=7.8 Score=39.63 Aligned_cols=37 Identities=24% Similarity=0.507 Sum_probs=0.0
Q ss_pred cccceecCCC--CceecCCCCCccccccccccccccccc
Q psy2284 135 RHFCAVCGFP--SNYTCVPCGARYCCVRCLGTHQDTRCL 171 (175)
Q Consensus 135 r~~C~VCG~~--~~YtC~~Cg~ryCS~~C~~~H~etRC~ 171 (175)
...|..||.+ ..|.|+.||..+=.-.|-+-..++.|.
T Consensus 667 ~~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~~~ 705 (900)
T PF03833_consen 667 YNRCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETTSY 705 (900)
T ss_dssp ---------------------------------------
T ss_pred hhcCcccCCccccceeccccccccCccccccccccCccc
Confidence 3456666633 456666666665444554444444443
No 101
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=43.23 E-value=7.2 Score=33.83 Aligned_cols=22 Identities=27% Similarity=0.200 Sum_probs=13.6
Q ss_pred CCHHHHHHHHHHHHHhhhCCCC
Q psy2284 21 LDEATRQRRARKALESLESDNF 42 (175)
Q Consensus 21 lD~~~R~rr~~~rLdaLE~DN~ 42 (175)
-|.++.-.+..+||.+|.+++.
T Consensus 11 ~~~~~~~~~ra~rl~~La~~~p 32 (290)
T PF04216_consen 11 PDPATLFARRAERLRALAEKHP 32 (290)
T ss_dssp ---TTHHHHHHHHHHHHHTT-T
T ss_pred CCHhhHHHHHHHHHHHHHHhCC
Confidence 3566666666778888888866
No 102
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=42.87 E-value=13 Score=29.38 Aligned_cols=20 Identities=40% Similarity=1.062 Sum_probs=12.7
Q ss_pred ccceecC---CCCceecCCCCCc
Q psy2284 136 HFCAVCG---FPSNYTCVPCGAR 155 (175)
Q Consensus 136 ~~C~VCG---~~~~YtC~~Cg~r 155 (175)
.-|..|| |+..--|+.||.+
T Consensus 30 ~kC~~CG~v~~PPr~~Cp~C~~~ 52 (140)
T COG1545 30 TKCKKCGRVYFPPRAYCPKCGSE 52 (140)
T ss_pred EEcCCCCeEEcCCcccCCCCCCC
Confidence 3566777 5566667777655
No 103
>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=42.70 E-value=7.5 Score=20.22 Aligned_cols=20 Identities=25% Similarity=0.597 Sum_probs=11.4
Q ss_pred eecCCCCCcccccccccccc
Q psy2284 147 YTCVPCGARYCCVRCLGTHQ 166 (175)
Q Consensus 147 YtC~~Cg~ryCS~~C~~~H~ 166 (175)
|.|+-||..|=+..-+..|.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 56777877776655555543
No 104
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=42.62 E-value=8.4 Score=31.07 Aligned_cols=42 Identities=21% Similarity=0.343 Sum_probs=25.6
Q ss_pred CCcccceecC---CCCceec--CCC--CCcccccccccccc---cccccccc
Q psy2284 133 PNRHFCAVCG---FPSNYTC--VPC--GARYCCVRCLGTHQ---DTRCLKWT 174 (175)
Q Consensus 133 P~r~~C~VCG---~~~~YtC--~~C--g~ryCS~~C~~~H~---etRC~K~~ 174 (175)
+....|+.|| |||.-+- .+= -.+|||.+|.+.+. .-|=++||
T Consensus 2 m~~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~~kRnPRKlkWT 53 (131)
T PRK14891 2 VETRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYDLGREARDLEWT 53 (131)
T ss_pred CceeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHHccCCCccchhH
Confidence 3456899999 6664221 111 23689999986553 35666665
No 105
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=42.61 E-value=17 Score=23.72 Aligned_cols=19 Identities=37% Similarity=0.912 Sum_probs=12.7
Q ss_pred cceecCC------CCceecCCCCCc
Q psy2284 137 FCAVCGF------PSNYTCVPCGAR 155 (175)
Q Consensus 137 ~C~VCG~------~~~YtC~~Cg~r 155 (175)
.|+-||. .....|+.||-+
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCce
Confidence 5777872 234668888865
No 106
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=41.90 E-value=16 Score=28.37 Aligned_cols=28 Identities=29% Similarity=0.819 Sum_probs=19.6
Q ss_pred CCCCCCcccceecCCCC-------------ceecCCCCCcc
Q psy2284 129 PSKFPNRHFCAVCGFPS-------------NYTCVPCGARY 156 (175)
Q Consensus 129 ps~~P~r~~C~VCG~~~-------------~YtC~~Cg~ry 156 (175)
|+.+|...-|-+||... ...|-.||++|
T Consensus 16 ~~~L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 16 PQVLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred CccCCceEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 45577888888888432 23588888875
No 107
>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=41.43 E-value=18 Score=21.40 Aligned_cols=17 Identities=35% Similarity=0.856 Sum_probs=12.2
Q ss_pred cceecC---CCC-ceecCCCC
Q psy2284 137 FCAVCG---FPS-NYTCVPCG 153 (175)
Q Consensus 137 ~C~VCG---~~~-~YtC~~Cg 153 (175)
.|.||+ .+. -|+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 589998 333 68887776
No 108
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.10 E-value=28 Score=27.27 Aligned_cols=38 Identities=24% Similarity=0.682 Sum_probs=24.7
Q ss_pred CCCCccccccCCCCCCCcccceecCC--C-------------CceecCCCCCccc
Q psy2284 118 QGSAYENAEAKPSKFPNRHFCAVCGF--P-------------SNYTCVPCGARYC 157 (175)
Q Consensus 118 ~~p~Y~~a~a~ps~~P~r~~C~VCG~--~-------------~~YtC~~Cg~ryC 157 (175)
+.++|..... +....-..|-.|+. + +.|.|++|..-||
T Consensus 40 Pl~~f~ev~~--~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC 92 (112)
T TIGR00622 40 PLKAFQEIPL--EEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFC 92 (112)
T ss_pred CCcccccccc--cccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccc
Confidence 5566655422 12222356999983 3 4699999999998
No 109
>PF12773 DZR: Double zinc ribbon
Probab=41.06 E-value=15 Score=23.42 Aligned_cols=22 Identities=41% Similarity=1.016 Sum_probs=13.3
Q ss_pred CCcccceecCCCC------ceecCCCCC
Q psy2284 133 PNRHFCAVCGFPS------NYTCVPCGA 154 (175)
Q Consensus 133 P~r~~C~VCG~~~------~YtC~~Cg~ 154 (175)
+...||.-||..- ...|+.||.
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcC
Confidence 3456777777322 245777776
No 110
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=38.79 E-value=24 Score=21.98 Aligned_cols=21 Identities=29% Similarity=0.659 Sum_probs=15.8
Q ss_pred CCCCcccceecCCCCcee--cCC
Q psy2284 131 KFPNRHFCAVCGFPSNYT--CVP 151 (175)
Q Consensus 131 ~~P~r~~C~VCG~~~~Yt--C~~ 151 (175)
..|+-..|-+|+..|.|. ||.
T Consensus 4 ~pP~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 4 KPPPGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCCCCEeecCCCCCccHhHCCC
Confidence 356667899999888776 764
No 111
>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=38.43 E-value=16 Score=22.43 Aligned_cols=25 Identities=16% Similarity=0.332 Sum_probs=20.1
Q ss_pred cccceecCCC-CceecCCCCCccccc
Q psy2284 135 RHFCAVCGFP-SNYTCVPCGARYCCV 159 (175)
Q Consensus 135 r~~C~VCG~~-~~YtC~~Cg~ryCS~ 159 (175)
..+|..|+.. ..|-|..|+..+|+.
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~ 28 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSE 28 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHH
T ss_pred CccCccCCccceEEEecCCCCccCcc
Confidence 4689999966 899999999988864
No 112
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.06 E-value=24 Score=37.02 Aligned_cols=21 Identities=33% Similarity=0.811 Sum_probs=11.7
Q ss_pred CcccceecCCC--CceecCCCCC
Q psy2284 134 NRHFCAVCGFP--SNYTCVPCGA 154 (175)
Q Consensus 134 ~r~~C~VCG~~--~~YtC~~Cg~ 154 (175)
...+|..||.. ..|.|+.||.
T Consensus 637 ~~frCP~CG~~Te~i~fCP~CG~ 659 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRCGI 659 (1121)
T ss_pred CcccCCCCCCCCCcceeCccccC
Confidence 34566666633 4555666655
No 113
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=37.72 E-value=15 Score=27.40 Aligned_cols=12 Identities=42% Similarity=0.985 Sum_probs=4.2
Q ss_pred CceecCCCCCcc
Q psy2284 145 SNYTCVPCGARY 156 (175)
Q Consensus 145 ~~YtC~~Cg~ry 156 (175)
+.-.|++|+++|
T Consensus 50 g~q~CpqCkt~y 61 (80)
T PF14569_consen 50 GNQVCPQCKTRY 61 (80)
T ss_dssp S-SB-TTT--B-
T ss_pred CcccccccCCCc
Confidence 444566776666
No 114
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=37.43 E-value=20 Score=24.85 Aligned_cols=19 Identities=11% Similarity=-0.048 Sum_probs=10.0
Q ss_pred cccceecC--CCCceecCCCCC
Q psy2284 135 RHFCAVCG--FPSNYTCVPCGA 154 (175)
Q Consensus 135 r~~C~VCG--~~~~YtC~~Cg~ 154 (175)
...|.-|| ......|+ ||.
T Consensus 27 ~~~c~~cg~~~~pH~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGEYHLPHHVSP-KGY 47 (60)
T ss_pred eeEcCCCCceeccceecC-Ccc
Confidence 35566666 33344566 653
No 115
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=37.14 E-value=11 Score=26.54 Aligned_cols=21 Identities=33% Similarity=0.781 Sum_probs=13.4
Q ss_pred cccceecC---CC------CceecCCCCCc
Q psy2284 135 RHFCAVCG---FP------SNYTCVPCGAR 155 (175)
Q Consensus 135 r~~C~VCG---~~------~~YtC~~Cg~r 155 (175)
+.+|++|+ .. +.|.|+.|+..
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~~ 70 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICGLY 70 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTTEE
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcCCC
Confidence 78999998 23 34677777654
No 116
>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=37.11 E-value=18 Score=24.60 Aligned_cols=14 Identities=36% Similarity=1.080 Sum_probs=7.4
Q ss_pred CceecCCCCCcccc
Q psy2284 145 SNYTCVPCGARYCC 158 (175)
Q Consensus 145 ~~YtC~~Cg~ryCS 158 (175)
+.|.|++|+.-||-
T Consensus 20 ~~y~C~~C~~~FC~ 33 (51)
T PF07975_consen 20 SRYRCPKCKNHFCI 33 (51)
T ss_dssp EEE--TTTT--B-H
T ss_pred CeEECCCCCCcccc
Confidence 57999999999973
No 117
>PHA00616 hypothetical protein
Probab=37.09 E-value=5.9 Score=26.28 Aligned_cols=15 Identities=27% Similarity=0.784 Sum_probs=11.7
Q ss_pred ceecCCCCCcccccc
Q psy2284 146 NYTCVPCGARYCCVR 160 (175)
Q Consensus 146 ~YtC~~Cg~ryCS~~ 160 (175)
.|.|++||..+.-..
T Consensus 1 pYqC~~CG~~F~~~s 15 (44)
T PHA00616 1 MYQCLRCGGIFRKKK 15 (44)
T ss_pred CCccchhhHHHhhHH
Confidence 389999999876544
No 118
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=36.68 E-value=8.5 Score=28.02 Aligned_cols=22 Identities=32% Similarity=0.840 Sum_probs=14.3
Q ss_pred CCcccceecCCCC------ceecCCCCC
Q psy2284 133 PNRHFCAVCGFPS------NYTCVPCGA 154 (175)
Q Consensus 133 P~r~~C~VCG~~~------~YtC~~Cg~ 154 (175)
|++..|.|||..+ .++|-.|.+
T Consensus 1 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~ 28 (82)
T cd07173 1 PPQKTCLICGDEASGCHYGALTCGSCKV 28 (82)
T ss_pred CCCCCCeecCCcCcceEECcchhhhHHH
Confidence 5677899998433 334666655
No 119
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=36.11 E-value=19 Score=22.98 Aligned_cols=11 Identities=36% Similarity=1.099 Sum_probs=8.2
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
.|.|++||..+
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 48888888753
No 120
>PLN02195 cellulose synthase A
Probab=35.99 E-value=18 Score=37.53 Aligned_cols=22 Identities=32% Similarity=0.945 Sum_probs=16.6
Q ss_pred ccceecCCC------------CceecCCCCCccc
Q psy2284 136 HFCAVCGFP------------SNYTCVPCGARYC 157 (175)
Q Consensus 136 ~~C~VCG~~------------~~YtC~~Cg~ryC 157 (175)
.-|.+|||+ |+-.||.|++||=
T Consensus 26 vaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 26 VACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred EEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 458888765 5667999998884
No 121
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=35.64 E-value=29 Score=22.48 Aligned_cols=16 Identities=44% Similarity=1.190 Sum_probs=9.8
Q ss_pred ceecCCCCCcccccccc
Q psy2284 146 NYTCVPCGARYCCVRCL 162 (175)
Q Consensus 146 ~YtC~~Cg~ryCS~~C~ 162 (175)
..+|+.||..|| ..|.
T Consensus 40 ~v~C~~C~~~fC-~~C~ 55 (64)
T smart00647 40 RVTCPKCGFSFC-FRCK 55 (64)
T ss_pred eeECCCCCCeEC-CCCC
Confidence 455777777776 4443
No 122
>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=35.55 E-value=18 Score=21.18 Aligned_cols=19 Identities=37% Similarity=0.892 Sum_probs=8.9
Q ss_pred ccceecCCC----CceecCCCCC
Q psy2284 136 HFCAVCGFP----SNYTCVPCGA 154 (175)
Q Consensus 136 ~~C~VCG~~----~~YtC~~Cg~ 154 (175)
+.|.+||.. ..|.|..|.-
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp ---TTTS----S--EEE-TTT--
T ss_pred CcCCcCCCcCCCCceEECccCCC
Confidence 368999933 3788998863
No 123
>PF14353 CpXC: CpXC protein
Probab=35.42 E-value=23 Score=26.87 Aligned_cols=15 Identities=33% Similarity=0.941 Sum_probs=10.6
Q ss_pred CCCCceecCCCCCcc
Q psy2284 142 GFPSNYTCVPCGARY 156 (175)
Q Consensus 142 G~~~~YtC~~Cg~ry 156 (175)
|..-.|+||.||..+
T Consensus 34 g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKF 48 (128)
T ss_pred CCcCEEECCCCCCce
Confidence 345578899998753
No 124
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.34 E-value=19 Score=32.59 Aligned_cols=23 Identities=17% Similarity=0.145 Sum_probs=15.2
Q ss_pred cCCHHHHHHHHHHHHHhhhCCCC
Q psy2284 20 VLDEATRQRRARKALESLESDNF 42 (175)
Q Consensus 20 vlD~~~R~rr~~~rLdaLE~DN~ 42 (175)
..|..+--.+..+||..|=.+|.
T Consensus 27 ~p~~~~lf~~RA~Rl~~LA~~~p 49 (309)
T PRK03564 27 FANLKNLYNRRAERLRQLAENNP 49 (309)
T ss_pred cCCcccHHHHHHHHHHHHHhcCC
Confidence 34666666677777777776654
No 125
>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=35.29 E-value=20 Score=21.69 Aligned_cols=11 Identities=36% Similarity=1.198 Sum_probs=8.6
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
.|.|+.||..|
T Consensus 5 ~y~C~~Cg~~f 15 (41)
T smart00834 5 EYRCEDCGHTF 15 (41)
T ss_pred EEEcCCCCCEE
Confidence 47899999865
No 126
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=34.92 E-value=16 Score=26.23 Aligned_cols=18 Identities=33% Similarity=0.540 Sum_probs=14.7
Q ss_pred HHHHHHhhhCCCCCCCCC
Q psy2284 30 ARKALESLESDNFHDDPH 47 (175)
Q Consensus 30 ~~~rLdaLE~DN~~ddp~ 47 (175)
-+++|++||+.=+.|||+
T Consensus 7 E~r~L~eiEr~L~~~DP~ 24 (82)
T PF11239_consen 7 EQRRLEEIERQLRADDPR 24 (82)
T ss_pred HHHHHHHHHHHHHhcCcH
Confidence 456899999998888874
No 127
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=34.29 E-value=20 Score=32.22 Aligned_cols=26 Identities=12% Similarity=-0.121 Sum_probs=19.2
Q ss_pred ccCCHHHHHHHHHHHHHhhhCCCCCC
Q psy2284 19 RVLDEATRQRRARKALESLESDNFHD 44 (175)
Q Consensus 19 rvlD~~~R~rr~~~rLdaLE~DN~~d 44 (175)
...|..+--.+..+||..|-++|+..
T Consensus 22 ~~p~~~~lf~~RA~RL~~LA~~~pl~ 47 (305)
T TIGR01562 22 LHPPLRDLFNRRAERLLQLAEGHPLG 47 (305)
T ss_pred ecCChhhHHHHHHHHHHHHhccCCHH
Confidence 34577777778888888888777764
No 128
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=34.14 E-value=17 Score=25.67 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=7.9
Q ss_pred eecCCCCCcc
Q psy2284 147 YTCVPCGARY 156 (175)
Q Consensus 147 YtC~~Cg~ry 156 (175)
|.||+||..-
T Consensus 1 y~C~KCg~~~ 10 (64)
T PF09855_consen 1 YKCPKCGNEE 10 (64)
T ss_pred CCCCCCCCcc
Confidence 7899998753
No 129
>PLN02189 cellulose synthase
Probab=33.89 E-value=20 Score=37.38 Aligned_cols=13 Identities=31% Similarity=0.767 Sum_probs=7.5
Q ss_pred CceecCCCCCccc
Q psy2284 145 SNYTCVPCGARYC 157 (175)
Q Consensus 145 ~~YtC~~Cg~ryC 157 (175)
|+-.||+|+++|=
T Consensus 75 g~q~CpqCkt~Y~ 87 (1040)
T PLN02189 75 GTQNCPQCKTRYK 87 (1040)
T ss_pred CCccCcccCCchh
Confidence 4445666666664
No 130
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=33.81 E-value=19 Score=24.68 Aligned_cols=20 Identities=20% Similarity=0.487 Sum_probs=12.7
Q ss_pred ccceecC---CC------CceecCCCCCc
Q psy2284 136 HFCAVCG---FP------SNYTCVPCGAR 155 (175)
Q Consensus 136 ~~C~VCG---~~------~~YtC~~Cg~r 155 (175)
.-|..|+ .. -..+||+||+-
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 3577776 22 24569999873
No 131
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=33.37 E-value=24 Score=28.39 Aligned_cols=25 Identities=16% Similarity=0.422 Sum_probs=15.3
Q ss_pred CCCcccceecC--C----CCceecCCCCCcc
Q psy2284 132 FPNRHFCAVCG--F----PSNYTCVPCGARY 156 (175)
Q Consensus 132 ~P~r~~C~VCG--~----~~~YtC~~Cg~ry 156 (175)
.-..+.|-.|| | .....||.||.-|
T Consensus 6 lGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred hCccccCCCcCccccccCCCCccCCCcCCcc
Confidence 34456777777 2 2345577777755
No 132
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=33.18 E-value=21 Score=28.17 Aligned_cols=13 Identities=31% Similarity=0.973 Sum_probs=9.9
Q ss_pred CceecCCCCCccc
Q psy2284 145 SNYTCVPCGARYC 157 (175)
Q Consensus 145 ~~YtC~~Cg~ryC 157 (175)
..|.||.||.+|=
T Consensus 98 ~~Y~Cp~C~~~y~ 110 (147)
T smart00531 98 AYYKCPNCQSKYT 110 (147)
T ss_pred cEEECcCCCCEee
Confidence 4688999988763
No 133
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.16 E-value=20 Score=28.17 Aligned_cols=21 Identities=38% Similarity=0.944 Sum_probs=15.1
Q ss_pred cccceecC--CCC-----ceecCCCCCc
Q psy2284 135 RHFCAVCG--FPS-----NYTCVPCGAR 155 (175)
Q Consensus 135 r~~C~VCG--~~~-----~YtC~~Cg~r 155 (175)
.|.|.-|| |.. ---||.||-+
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~n 29 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGCN 29 (112)
T ss_pred CceecccccccccccHHHHccCccccch
Confidence 47899999 444 1349999865
No 134
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=32.78 E-value=32 Score=23.98 Aligned_cols=20 Identities=30% Similarity=0.803 Sum_probs=10.8
Q ss_pred cccceecC--CCCceecCCCCC
Q psy2284 135 RHFCAVCG--FPSNYTCVPCGA 154 (175)
Q Consensus 135 r~~C~VCG--~~~~YtC~~Cg~ 154 (175)
-..|..|| ..+.-.|+.||.
T Consensus 27 ~~~c~~cG~~~l~Hrvc~~cg~ 48 (57)
T COG0333 27 LSVCPNCGEYKLPHRVCLKCGY 48 (57)
T ss_pred ceeccCCCCcccCceEcCCCCC
Confidence 44566666 334455666663
No 135
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=32.75 E-value=41 Score=23.32 Aligned_cols=23 Identities=22% Similarity=0.419 Sum_probs=19.0
Q ss_pred CHHHHHHHHHHHHHhhhCCCCCC
Q psy2284 22 DEATRQRRARKALESLESDNFHD 44 (175)
Q Consensus 22 D~~~R~rr~~~rLdaLE~DN~~d 44 (175)
+.+.-.+..+++|.+||+|.|..
T Consensus 27 g~~~se~avRrrLr~me~~Glt~ 49 (66)
T PF08461_consen 27 GEELSEEAVRRRLRAMERDGLTR 49 (66)
T ss_pred ChhhhHHHHHHHHHHHHHCCCcc
Confidence 55566788999999999999765
No 136
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=32.23 E-value=22 Score=37.26 Aligned_cols=22 Identities=41% Similarity=1.046 Sum_probs=18.0
Q ss_pred ccceecCCC------------CceecCCCCCccc
Q psy2284 136 HFCAVCGFP------------SNYTCVPCGARYC 157 (175)
Q Consensus 136 ~~C~VCG~~------------~~YtC~~Cg~ryC 157 (175)
.-|..|||+ |+-.||.|++||=
T Consensus 37 VAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 37 VACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred EEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 568888876 6678999999995
No 137
>PF14753 DUF4475: Domain of unknown function (DUF4475)
Probab=32.19 E-value=24 Score=30.18 Aligned_cols=18 Identities=33% Similarity=1.113 Sum_probs=14.4
Q ss_pred ceecC-CCCceecCCCCCcc
Q psy2284 138 CAVCG-FPSNYTCVPCGARY 156 (175)
Q Consensus 138 C~VCG-~~~~YtC~~Cg~ry 156 (175)
|+.|+ |.+.|+|. ||.++
T Consensus 125 ~~~C~~F~S~f~C~-Cd~~~ 143 (196)
T PF14753_consen 125 CCGCSGFESSFLCA-CDQPW 143 (196)
T ss_pred CCCCCCCCCCceec-CcCch
Confidence 45777 99999995 99764
No 138
>PLN02436 cellulose synthase A
Probab=30.94 E-value=24 Score=37.01 Aligned_cols=11 Identities=45% Similarity=1.081 Sum_probs=5.5
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
+-.||+|+++|
T Consensus 78 ~~~Cpqckt~Y 88 (1094)
T PLN02436 78 NQACPQCKTRY 88 (1094)
T ss_pred CccCcccCCch
Confidence 33455555555
No 139
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=30.46 E-value=28 Score=21.61 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=7.5
Q ss_pred eecCCCCCcc
Q psy2284 147 YTCVPCGARY 156 (175)
Q Consensus 147 YtC~~Cg~ry 156 (175)
.+||.|+..|
T Consensus 3 i~CP~C~~~f 12 (37)
T PF13719_consen 3 ITCPNCQTRF 12 (37)
T ss_pred EECCCCCceE
Confidence 4688888766
No 140
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=30.45 E-value=31 Score=23.02 Aligned_cols=31 Identities=23% Similarity=0.626 Sum_probs=22.5
Q ss_pred cceecCC---CC-ceecCCCCCccccccccccccc
Q psy2284 137 FCAVCGF---PS-NYTCVPCGARYCCVRCLGTHQD 167 (175)
Q Consensus 137 ~C~VCG~---~~-~YtC~~Cg~ryCS~~C~~~H~e 167 (175)
.|.+|+. .| .|+|..|-...-...|+....+
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~ 36 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRT 36 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCc
Confidence 4888882 33 8999999888777788754433
No 141
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=29.77 E-value=26 Score=28.24 Aligned_cols=10 Identities=20% Similarity=0.677 Sum_probs=5.2
Q ss_pred eecCCCCCcc
Q psy2284 147 YTCVPCGARY 156 (175)
Q Consensus 147 YtC~~Cg~ry 156 (175)
|.||.|+.+|
T Consensus 110 Y~Cp~c~~r~ 119 (158)
T TIGR00373 110 FICPNMCVRF 119 (158)
T ss_pred EECCCCCcEe
Confidence 4555555544
No 142
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=29.71 E-value=30 Score=20.31 Aligned_cols=6 Identities=50% Similarity=1.359 Sum_probs=3.6
Q ss_pred cCCCCC
Q psy2284 149 CVPCGA 154 (175)
Q Consensus 149 C~~Cg~ 154 (175)
||.||-
T Consensus 17 Cp~CG~ 22 (26)
T PF10571_consen 17 CPHCGY 22 (26)
T ss_pred CCCCCC
Confidence 666664
No 143
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=29.60 E-value=25 Score=25.48 Aligned_cols=24 Identities=21% Similarity=0.629 Sum_probs=14.8
Q ss_pred CcccceecCCCCceecCCCCCcccccccc
Q psy2284 134 NRHFCAVCGFPSNYTCVPCGARYCCVRCL 162 (175)
Q Consensus 134 ~r~~C~VCG~~~~YtC~~Cg~ryCS~~C~ 162 (175)
.-..|.+|+-+=.- ..+|||+.|-
T Consensus 48 ~~~~C~~C~R~L~d-----~~~fCSl~CK 71 (72)
T PF04640_consen 48 SGNICETCHRSLQD-----PYRFCSLSCK 71 (72)
T ss_pred CCCccCCCCCCCCC-----CCeEEeeeEE
Confidence 44577777732221 1589999994
No 144
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.53 E-value=29 Score=21.50 Aligned_cols=10 Identities=50% Similarity=1.132 Sum_probs=7.6
Q ss_pred eecCCCCCcc
Q psy2284 147 YTCVPCGARY 156 (175)
Q Consensus 147 YtC~~Cg~ry 156 (175)
.+|++|++.|
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 4688888876
No 145
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=29.11 E-value=37 Score=21.58 Aligned_cols=29 Identities=28% Similarity=0.787 Sum_probs=21.8
Q ss_pred ccceecC---CCCceecCCCCCcccccccccc
Q psy2284 136 HFCAVCG---FPSNYTCVPCGARYCCVRCLGT 164 (175)
Q Consensus 136 ~~C~VCG---~~~~YtC~~Cg~ryCS~~C~~~ 164 (175)
..|.+|| ....|+|..|....=...|+..
T Consensus 5 ~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 5 YSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred cCCCCCCCCCcCCEEECCCCCCccchHHHHhC
Confidence 4588998 3348999999887777777754
No 146
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.08 E-value=29 Score=30.84 Aligned_cols=20 Identities=35% Similarity=0.957 Sum_probs=0.0
Q ss_pred cceecC-CCCcee--cCCCCCcc
Q psy2284 137 FCAVCG-FPSNYT--CVPCGARY 156 (175)
Q Consensus 137 ~C~VCG-~~~~Yt--C~~Cg~ry 156 (175)
+|+||. ....+. |+.||.+|
T Consensus 257 vCs~Clsi~C~~p~~C~~Cgt~f 279 (279)
T TIGR00627 257 VCSVCLSVLCQYTPICKTCKTAF 279 (279)
T ss_pred ECCCccCCcCCCCCCCCCCCCCC
No 147
>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=29.02 E-value=40 Score=21.98 Aligned_cols=31 Identities=19% Similarity=0.594 Sum_probs=23.0
Q ss_pred cceecC-CC---CceecCCCCCccccccccccccc
Q psy2284 137 FCAVCG-FP---SNYTCVPCGARYCCVRCLGTHQD 167 (175)
Q Consensus 137 ~C~VCG-~~---~~YtC~~Cg~ryCS~~C~~~H~e 167 (175)
-|.+|+ .. -.|.|..|....-...|+....+
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~ 36 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAE 36 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCC
Confidence 388888 22 25899999888777888876655
No 148
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.86 E-value=27 Score=28.79 Aligned_cols=17 Identities=29% Similarity=0.323 Sum_probs=10.8
Q ss_pred HHHHHHHHhhhCCCCCC
Q psy2284 28 RRARKALESLESDNFHD 44 (175)
Q Consensus 28 rr~~~rLdaLE~DN~~d 44 (175)
...|+.|-.|+.|+...
T Consensus 51 ~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 51 NTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHHHHHHHCCCeE
Confidence 45667777777776533
No 149
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=28.86 E-value=28 Score=24.07 Aligned_cols=18 Identities=44% Similarity=0.922 Sum_probs=7.1
Q ss_pred CcccceecCCCCceecCCCCC
Q psy2284 134 NRHFCAVCGFPSNYTCVPCGA 154 (175)
Q Consensus 134 ~r~~C~VCG~~~~YtC~~Cg~ 154 (175)
.+..|.| --.|+|+-||+
T Consensus 24 G~v~CPv---Lr~y~Cp~CgA 41 (55)
T PF05741_consen 24 GRVTCPV---LRKYVCPICGA 41 (55)
T ss_dssp S-B--TT---GGG---TTT--
T ss_pred CCEeCHH---HhcCcCCCCcC
Confidence 3444544 78899999987
No 150
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=28.76 E-value=31 Score=22.67 Aligned_cols=31 Identities=19% Similarity=0.669 Sum_probs=23.5
Q ss_pred cceecCC---CC-ceecCCCCCccccccccccccc
Q psy2284 137 FCAVCGF---PS-NYTCVPCGARYCCVRCLGTHQD 167 (175)
Q Consensus 137 ~C~VCG~---~~-~YtC~~Cg~ryCS~~C~~~H~e 167 (175)
.|++|+. .+ .|+|..|....-...|+....+
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~ 36 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRE 36 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCc
Confidence 4788884 23 7899999988888889876644
No 151
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=28.44 E-value=28 Score=36.36 Aligned_cols=22 Identities=50% Similarity=1.153 Sum_probs=17.6
Q ss_pred ccceecCCC------------CceecCCCCCccc
Q psy2284 136 HFCAVCGFP------------SNYTCVPCGARYC 157 (175)
Q Consensus 136 ~~C~VCG~~------------~~YtC~~Cg~ryC 157 (175)
.-|.+|||+ |+-.||+|+++|=
T Consensus 35 VAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 35 VACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred EEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 568888775 5667999999995
No 152
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=27.95 E-value=36 Score=20.93 Aligned_cols=9 Identities=44% Similarity=1.121 Sum_probs=5.1
Q ss_pred eecCCCCCc
Q psy2284 147 YTCVPCGAR 155 (175)
Q Consensus 147 YtC~~Cg~r 155 (175)
..|+.||-|
T Consensus 18 irC~~CG~R 26 (32)
T PF03604_consen 18 IRCPECGHR 26 (32)
T ss_dssp SSBSSSS-S
T ss_pred EECCcCCCe
Confidence 457777755
No 153
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.86 E-value=9.5 Score=31.65 Aligned_cols=25 Identities=24% Similarity=0.618 Sum_probs=20.3
Q ss_pred CCCCcccceecCCCCceecCCCCCc
Q psy2284 131 KFPNRHFCAVCGFPSNYTCVPCGAR 155 (175)
Q Consensus 131 ~~P~r~~C~VCG~~~~YtC~~Cg~r 155 (175)
.-+...||+-||..-.-.||.|+..
T Consensus 24 p~~~~~fC~kCG~~tI~~Cp~C~~~ 48 (158)
T PF10083_consen 24 PELREKFCSKCGAKTITSCPNCSTP 48 (158)
T ss_pred chHHHHHHHHhhHHHHHHCcCCCCC
Confidence 3456679999998888899999764
No 154
>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=27.81 E-value=24 Score=22.57 Aligned_cols=24 Identities=38% Similarity=0.963 Sum_probs=16.1
Q ss_pred CCCcccceecC--CC----CceecCCCCCc
Q psy2284 132 FPNRHFCAVCG--FP----SNYTCVPCGAR 155 (175)
Q Consensus 132 ~P~r~~C~VCG--~~----~~YtC~~Cg~r 155 (175)
+....+|.+|+ .| ..|.|..|+..
T Consensus 8 ~~~~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 8 FSKPTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp SSSTEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCCCCcccCcccCCCCCCeEEECCCCCh
Confidence 46677999999 32 27889988863
No 155
>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=27.80 E-value=25 Score=19.98 Aligned_cols=11 Identities=36% Similarity=1.096 Sum_probs=7.1
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
.|.|+.|+..|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 37777777554
No 156
>KOG4850|consensus
Probab=27.50 E-value=29 Score=29.32 Aligned_cols=16 Identities=38% Similarity=1.221 Sum_probs=15.2
Q ss_pred ceecCCCCCccccccc
Q psy2284 146 NYTCVPCGARYCCVRC 161 (175)
Q Consensus 146 ~YtC~~Cg~ryCS~~C 161 (175)
-|.|+.||.--|...|
T Consensus 149 ~Y~C~~CGSTkCG~~C 164 (190)
T KOG4850|consen 149 HYPCKQCGSTKCGIGC 164 (190)
T ss_pred eecccccccccccccc
Confidence 6899999999999999
No 157
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=27.22 E-value=16 Score=23.12 Aligned_cols=18 Identities=39% Similarity=0.829 Sum_probs=8.2
Q ss_pred CcccceecCCCCc-eecCC
Q psy2284 134 NRHFCAVCGFPSN-YTCVP 151 (175)
Q Consensus 134 ~r~~C~VCG~~~~-YtC~~ 151 (175)
..++|.+||+++. -.|.=
T Consensus 16 ~i~~C~~C~nlse~~~C~I 34 (41)
T PF02132_consen 16 NIKFCSICGNLSEEDPCEI 34 (41)
T ss_dssp H-EE-SSS--EESSSS-HH
T ss_pred cCCccCCCCCcCCCCcCcC
Confidence 3579999997663 33543
No 158
>KOG1356|consensus
Probab=27.13 E-value=30 Score=35.50 Aligned_cols=35 Identities=26% Similarity=0.695 Sum_probs=26.7
Q ss_pred CCCCCcccceecC---CCCceecCCCCCccccccccccc
Q psy2284 130 SKFPNRHFCAVCG---FPSNYTCVPCGARYCCVRCLGTH 165 (175)
Q Consensus 130 s~~P~r~~C~VCG---~~~~YtC~~Cg~ryCS~~C~~~H 165 (175)
+.+-.+..|.+|. |.-...|++||.+|| +.|++.-
T Consensus 224 a~~g~~~mC~~C~~tlfn~hw~C~~C~~~~C-l~C~r~~ 261 (889)
T KOG1356|consen 224 AVKGIREMCDRCETTLFNIHWRCPRCGFGVC-LDCYRKW 261 (889)
T ss_pred cccCcchhhhhhcccccceeEEccccCCeee-ecchhhc
Confidence 4467788999999 333567999999977 6777654
No 159
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=27.07 E-value=28 Score=24.59 Aligned_cols=20 Identities=30% Similarity=0.883 Sum_probs=14.5
Q ss_pred ccceecC-CCCceecCCCCCc
Q psy2284 136 HFCAVCG-FPSNYTCVPCGAR 155 (175)
Q Consensus 136 ~~C~VCG-~~~~YtC~~Cg~r 155 (175)
..|.-|| |.=+-+||.||..
T Consensus 6 rkC~~cg~YTLke~Cp~CG~~ 26 (59)
T COG2260 6 RKCPKCGRYTLKEKCPVCGGD 26 (59)
T ss_pred hcCcCCCceeecccCCCCCCc
Confidence 4577788 6666778888864
No 160
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=26.87 E-value=35 Score=23.75 Aligned_cols=20 Identities=30% Similarity=0.808 Sum_probs=13.5
Q ss_pred cceecCCCCcee-cCCCCCcc
Q psy2284 137 FCAVCGFPSNYT-CVPCGARY 156 (175)
Q Consensus 137 ~C~VCG~~~~Yt-C~~Cg~ry 156 (175)
+|--|=--.+|. ||=||.++
T Consensus 29 I~~~~f~~~rYngCPfC~~~~ 49 (55)
T PF14447_consen 29 ICDNCFPGERYNGCPFCGTPF 49 (55)
T ss_pred eeccccChhhccCCCCCCCcc
Confidence 444443444888 99999875
No 161
>PRK00807 50S ribosomal protein L24e; Validated
Probab=26.84 E-value=31 Score=23.20 Aligned_cols=39 Identities=28% Similarity=0.562 Sum_probs=21.8
Q ss_pred ccceecC---CCCcee--cCCC--CCccccccccccc---ccccccccc
Q psy2284 136 HFCAVCG---FPSNYT--CVPC--GARYCCVRCLGTH---QDTRCLKWT 174 (175)
Q Consensus 136 ~~C~VCG---~~~~Yt--C~~C--g~ryCS~~C~~~H---~etRC~K~~ 174 (175)
+.|++|| ++|.-. =..= -.+|||.+|...+ ..-|=++||
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f~~~~nprk~~WT 50 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNYKLGRVPRKLKWT 50 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHHHccCCCCccccc
Confidence 5799999 544311 1111 1257999998743 335555554
No 162
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.38 E-value=19 Score=29.50 Aligned_cols=21 Identities=33% Similarity=0.793 Sum_probs=17.1
Q ss_pred cccceecCCCCceecCCCCCc
Q psy2284 135 RHFCAVCGFPSNYTCVPCGAR 155 (175)
Q Consensus 135 r~~C~VCG~~~~YtC~~Cg~r 155 (175)
-.||+-||..-.-.||.|.+.
T Consensus 28 eafcskcgeati~qcp~csas 48 (160)
T COG4306 28 EAFCSKCGEATITQCPICSAS 48 (160)
T ss_pred HHHHhhhchHHHhcCCccCCc
Confidence 459999998888889999763
No 163
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=26.21 E-value=40 Score=23.22 Aligned_cols=24 Identities=33% Similarity=0.892 Sum_probs=16.3
Q ss_pred CCCCcccceecC---CC----CceecCCCCC
Q psy2284 131 KFPNRHFCAVCG---FP----SNYTCVPCGA 154 (175)
Q Consensus 131 ~~P~r~~C~VCG---~~----~~YtC~~Cg~ 154 (175)
..-..+||.-|| |- -.|.|-+||-
T Consensus 15 v~rk~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 15 VKRKNRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred EEEccccCCCCCCcchhhhcCceeEeccccc
Confidence 345667888888 22 2677888874
No 164
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=25.81 E-value=23 Score=36.42 Aligned_cols=38 Identities=32% Similarity=0.827 Sum_probs=0.0
Q ss_pred CcccceecCCCCcee-cCCCCCc----cccccccccccccccc
Q psy2284 134 NRHFCAVCGFPSNYT-CVPCGAR----YCCVRCLGTHQDTRCL 171 (175)
Q Consensus 134 ~r~~C~VCG~~~~Yt-C~~Cg~r----yCS~~C~~~H~etRC~ 171 (175)
.+..|.-||..+-+. |+.||.+ |=+-.|.....+..|.
T Consensus 654 ~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~ 696 (900)
T PF03833_consen 654 GRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVEEDECP 696 (900)
T ss_dssp -------------------------------------------
T ss_pred ecccCcccCCcchhhcCcccCCccccceeccccccccCccccc
Confidence 466899999777554 9999986 3334576665555554
No 165
>PLN02400 cellulose synthase
Probab=25.13 E-value=34 Score=35.94 Aligned_cols=11 Identities=36% Similarity=0.948 Sum_probs=5.6
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
+-.||.|.+||
T Consensus 78 nq~CPQCkTrY 88 (1085)
T PLN02400 78 TQCCPQCKTRY 88 (1085)
T ss_pred CccCcccCCcc
Confidence 33455555555
No 166
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=24.89 E-value=49 Score=21.40 Aligned_cols=9 Identities=44% Similarity=1.184 Sum_probs=4.4
Q ss_pred CceecCCCC
Q psy2284 145 SNYTCVPCG 153 (175)
Q Consensus 145 ~~YtC~~Cg 153 (175)
++..|+.|+
T Consensus 33 g~~~Cv~C~ 41 (41)
T PF06677_consen 33 GKIYCVSCG 41 (41)
T ss_pred CCEECCCCC
Confidence 344455553
No 167
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=24.77 E-value=26 Score=31.69 Aligned_cols=24 Identities=25% Similarity=0.750 Sum_probs=20.3
Q ss_pred ccceecCCCCceecCCCCCccccc
Q psy2284 136 HFCAVCGFPSNYTCVPCGARYCCV 159 (175)
Q Consensus 136 ~~C~VCG~~~~YtC~~Cg~ryCS~ 159 (175)
.-|..|+..|.|+|.+|-+-||--
T Consensus 172 ~KC~SCNrlGq~sCLRCK~cfCdd 195 (314)
T PF06524_consen 172 FKCQSCNRLGQYSCLRCKICFCDD 195 (314)
T ss_pred ccccccccccchhhhheeeeehhh
Confidence 358889999999999999988853
No 168
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=24.75 E-value=21 Score=27.06 Aligned_cols=35 Identities=29% Similarity=0.731 Sum_probs=22.6
Q ss_pred CCCcccceecC-CCCceecCCCCCccccccccccccc
Q psy2284 132 FPNRHFCAVCG-FPSNYTCVPCGARYCCVRCLGTHQD 167 (175)
Q Consensus 132 ~P~r~~C~VCG-~~~~YtC~~Cg~ryCS~~C~~~H~e 167 (175)
.|.-+.|.-|| ..+.|.|+.=|...| ..|-.+|+.
T Consensus 10 ~~~N~~CaDCg~~~p~w~s~~~GiflC-~~Cag~HR~ 45 (116)
T PF01412_consen 10 KPGNKVCADCGAPNPTWASLNYGIFLC-LECAGIHRS 45 (116)
T ss_dssp STTCTB-TTT-SBS--EEETTTTEEE--HHHHHHHHH
T ss_pred CcCcCcCCCCCCCCCCEEEeecChhhh-HHHHHHHHH
Confidence 46678999999 445888888776655 578888876
No 169
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=24.68 E-value=27 Score=25.44 Aligned_cols=26 Identities=27% Similarity=0.677 Sum_probs=10.7
Q ss_pred CCCCcccceecC-------------CCCceecCCCCCcc
Q psy2284 131 KFPNRHFCAVCG-------------FPSNYTCVPCGARY 156 (175)
Q Consensus 131 ~~P~r~~C~VCG-------------~~~~YtC~~Cg~ry 156 (175)
.+|...-|-.|| ..|..+|-.||..|
T Consensus 18 ~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 18 KLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp --SS----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred CCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 355566677777 23456677777765
No 170
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.52 E-value=36 Score=26.86 Aligned_cols=25 Identities=28% Similarity=0.632 Sum_probs=18.4
Q ss_pred ccCCCCCccccccCCCCCCCcccceecCCCCceecCCCCCcc
Q psy2284 115 LNSQGSAYENAEAKPSKFPNRHFCAVCGFPSNYTCVPCGARY 156 (175)
Q Consensus 115 ~~~~~p~Y~~a~a~ps~~P~r~~C~VCG~~~~YtC~~Cg~ry 156 (175)
+|.+..+|..... |.+.||.||..+
T Consensus 35 Ln~~~LdyV~ie~-----------------G~t~CP~Cg~~~ 59 (115)
T COG1885 35 LNKPDLDYVEIEV-----------------GSTSCPKCGEPF 59 (115)
T ss_pred hccCCCCeEEEec-----------------ccccCCCCCCcc
Confidence 5667788988873 556788888765
No 171
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=23.97 E-value=40 Score=25.86 Aligned_cols=10 Identities=40% Similarity=1.129 Sum_probs=5.9
Q ss_pred CceecCCCCC
Q psy2284 145 SNYTCVPCGA 154 (175)
Q Consensus 145 ~~YtC~~Cg~ 154 (175)
..|.|+.||.
T Consensus 142 ~~~~C~~C~~ 151 (157)
T PF10263_consen 142 KRYRCGRCGG 151 (157)
T ss_pred hhEECCCCCC
Confidence 3566666664
No 172
>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=23.72 E-value=42 Score=31.04 Aligned_cols=22 Identities=18% Similarity=0.529 Sum_probs=15.9
Q ss_pred cccceecCC----CCceecCCCCCcc
Q psy2284 135 RHFCAVCGF----PSNYTCVPCGARY 156 (175)
Q Consensus 135 r~~C~VCG~----~~~YtC~~Cg~ry 156 (175)
...|..||. .....|||||...
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L 240 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPL 240 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcc
Confidence 445999995 2355699999864
No 173
>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=23.59 E-value=36 Score=24.19 Aligned_cols=27 Identities=19% Similarity=0.472 Sum_probs=18.2
Q ss_pred hccCCCCCccccccCCCCCCCcccceecCCCC
Q psy2284 114 ALNSQGSAYENAEAKPSKFPNRHFCAVCGFPS 145 (175)
Q Consensus 114 ~~~~~~p~Y~~a~a~ps~~P~r~~C~VCG~~~ 145 (175)
....+.|||.+.. -=....|..|||..
T Consensus 14 ~gsk~~pNyntCT-----~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 14 VGSKDPPNYNTCT-----ECKSQVCNLCGFNP 40 (61)
T ss_pred cCCCCCCCccHHH-----HHhhhhhcccCCCC
Confidence 3445778998876 23445789999654
No 174
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=23.50 E-value=41 Score=21.60 Aligned_cols=11 Identities=45% Similarity=1.434 Sum_probs=8.4
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
.|.|..||..|
T Consensus 5 ey~C~~Cg~~f 15 (52)
T TIGR02605 5 EYRCTACGHRF 15 (52)
T ss_pred EEEeCCCCCEe
Confidence 47888898854
No 175
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.48 E-value=73 Score=22.71 Aligned_cols=27 Identities=30% Similarity=0.559 Sum_probs=22.7
Q ss_pred CCCCCCcccceecCCCCceecCCCCCcc
Q psy2284 129 PSKFPNRHFCAVCGFPSNYTCVPCGARY 156 (175)
Q Consensus 129 ps~~P~r~~C~VCG~~~~YtC~~Cg~ry 156 (175)
++.--+|.|=.+ |..+...||=||++|
T Consensus 32 ~p~~HPrV~L~m-g~~gev~CPYC~t~y 58 (62)
T COG4391 32 PPNDHPRVFLDM-GDEGEVVCPYCSTRY 58 (62)
T ss_pred CCCCCCEEEEEc-CCCCcEecCccccEE
Confidence 336678888888 999999999999987
No 176
>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=23.47 E-value=42 Score=21.13 Aligned_cols=20 Identities=35% Similarity=1.004 Sum_probs=11.0
Q ss_pred cceecCCCC----ceecCCCCCcc
Q psy2284 137 FCAVCGFPS----NYTCVPCGARY 156 (175)
Q Consensus 137 ~C~VCG~~~----~YtC~~Cg~ry 156 (175)
+|.|||... -..|-.|+..|
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEE
T ss_pred eCcCCCCcCCCCCeEEcCCCChhh
Confidence 477777421 33377776543
No 177
>KOG2807|consensus
Probab=23.07 E-value=64 Score=30.08 Aligned_cols=32 Identities=22% Similarity=0.747 Sum_probs=26.2
Q ss_pred cCCCCCCCcccceecC----CCCceecCCCCCcccc
Q psy2284 127 AKPSKFPNRHFCAVCG----FPSNYTCVPCGARYCC 158 (175)
Q Consensus 127 a~ps~~P~r~~C~VCG----~~~~YtC~~Cg~ryCS 158 (175)
.|...++.-.+|-+|+ -.+.|+|..|-.-||.
T Consensus 322 ip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCl 357 (378)
T KOG2807|consen 322 IPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCL 357 (378)
T ss_pred ccccccCCCcceeeeccccCCCCcEEchhccceeec
Confidence 4566788888999993 5569999999999885
No 178
>KOG1802|consensus
Probab=22.87 E-value=38 Score=34.57 Aligned_cols=29 Identities=34% Similarity=0.764 Sum_probs=22.8
Q ss_pred CCCcccceecC-CC--CceecCCCCCcccccc
Q psy2284 132 FPNRHFCAVCG-FP--SNYTCVPCGARYCCVR 160 (175)
Q Consensus 132 ~P~r~~C~VCG-~~--~~YtC~~Cg~ryCS~~ 160 (175)
.-+++.|.-|| .. ....|+.||.++|-.+
T Consensus 57 ~~~~~~c~Ycgi~~p~~v~kc~~c~Kwfcn~r 88 (935)
T KOG1802|consen 57 KLPEHACAYCGISEPACVIKCNTCGKWFCNSR 88 (935)
T ss_pred ccchhhhhhccCCCchheeeccccCceeecCC
Confidence 56789999999 33 3556999999999654
No 179
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=22.73 E-value=38 Score=22.04 Aligned_cols=12 Identities=33% Similarity=0.772 Sum_probs=9.3
Q ss_pred cccceecCCCCc
Q psy2284 135 RHFCAVCGFPSN 146 (175)
Q Consensus 135 r~~C~VCG~~~~ 146 (175)
..||..||..|.
T Consensus 31 p~~C~~C~~~gH 42 (49)
T PF14392_consen 31 PRFCFHCGRIGH 42 (49)
T ss_pred ChhhcCCCCcCc
Confidence 468999997764
No 180
>PF07966 A1_Propeptide: A1 Propeptide ; InterPro: IPR012848 Most eukaryotic endopeptidases (MEROPS peptidase family A1) are synthesised with signal and propeptides. The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide. The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residue in the propeptide. This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions [, ]. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1AVF_Q 1HTR_P 3PSG_A 2PSG_A 3VCM_Q 1TZS_P.
Probab=22.69 E-value=30 Score=20.60 Aligned_cols=24 Identities=13% Similarity=0.155 Sum_probs=14.7
Q ss_pred cccccccchhhhhhccccHHHHHH
Q psy2284 87 GLFHKTNQQNYIFRFRKSLAQMIE 110 (175)
Q Consensus 87 ~~~~~~~~~~~ilr~rKnf~~lle 110 (175)
=+||+.+|-|..|+..-.+..+|.
T Consensus 4 IPL~K~kS~R~~L~e~g~~~~flk 27 (29)
T PF07966_consen 4 IPLKKFKSMRETLREKGTLEEFLK 27 (29)
T ss_dssp EEEEE---HHHHHHHTT-HHHHHC
T ss_pred EeccCCchHHHHHHHcCchHHHHH
Confidence 368888888888887777766654
No 181
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=22.57 E-value=36 Score=25.30 Aligned_cols=24 Identities=29% Similarity=0.740 Sum_probs=15.3
Q ss_pred CCcccceecCCC------CceecCCCCCcc
Q psy2284 133 PNRHFCAVCGFP------SNYTCVPCGARY 156 (175)
Q Consensus 133 P~r~~C~VCG~~------~~YtC~~Cg~ry 156 (175)
+|...|.|||.+ |.++|-.|...|
T Consensus 4 ~p~~~C~VCg~~a~g~hyGv~sC~aCk~FF 33 (92)
T cd06970 4 NPGLLCRVCGDTSSGKHYGIYACNGCSGFF 33 (92)
T ss_pred CCCCCCeecCCcCcccEECccEEeeeeeEe
Confidence 445579999843 344577776643
No 182
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=22.41 E-value=48 Score=32.94 Aligned_cols=36 Identities=25% Similarity=0.695 Sum_probs=29.6
Q ss_pred CCCcccceecC-CCCceecCCCCCcccccccccccccc
Q psy2284 132 FPNRHFCAVCG-FPSNYTCVPCGARYCCVRCLGTHQDT 168 (175)
Q Consensus 132 ~P~r~~C~VCG-~~~~YtC~~Cg~ryCS~~C~~~H~et 168 (175)
.|.-+.|.-|| ....|.|...|...| +.|-.+|+..
T Consensus 20 lPgNk~CADCgs~~P~WASiNlGIFIC-i~CSGIHRsL 56 (648)
T PLN03119 20 LPPNRRCINCNSLGPQYVCTTFWTFVC-MACSGIHREF 56 (648)
T ss_pred CcCCCccccCCCCCCCceeeccceEEe-ccchhhhccC
Confidence 56678999999 556899999999888 5899999873
No 183
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=21.65 E-value=44 Score=35.06 Aligned_cols=22 Identities=27% Similarity=0.561 Sum_probs=17.6
Q ss_pred CcccceecC-CCCceecCCCCCc
Q psy2284 134 NRHFCAVCG-FPSNYTCVPCGAR 155 (175)
Q Consensus 134 ~r~~C~VCG-~~~~YtC~~Cg~r 155 (175)
.++.|.-|| +--...||.||.+
T Consensus 624 ~~RKCPkCG~yTlk~rCP~CG~~ 646 (1095)
T TIGR00354 624 AIRKCPQCGKESFWLKCPVCGEL 646 (1095)
T ss_pred EEEECCCCCcccccccCCCCCCc
Confidence 457899999 5557779999986
No 184
>PRK05978 hypothetical protein; Provisional
Probab=21.54 E-value=46 Score=27.13 Aligned_cols=23 Identities=30% Similarity=0.765 Sum_probs=15.4
Q ss_pred CcccceecCC----CC----ceecCCCCCcc
Q psy2284 134 NRHFCAVCGF----PS----NYTCVPCGARY 156 (175)
Q Consensus 134 ~r~~C~VCG~----~~----~YtC~~Cg~ry 156 (175)
-+..|-.||. .+ +-+|+.||..|
T Consensus 32 l~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 32 FRGRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred HcCcCCCCCCCcccccccccCCCccccCCcc
Confidence 3567888882 22 33599998876
No 185
>KOG2907|consensus
Probab=21.45 E-value=43 Score=26.58 Aligned_cols=11 Identities=36% Similarity=0.978 Sum_probs=8.8
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
-|+|++|+-++
T Consensus 102 FYTC~kC~~k~ 112 (116)
T KOG2907|consen 102 FYTCPKCKYKF 112 (116)
T ss_pred EEEcCccceee
Confidence 48999998764
No 186
>KOG4602|consensus
Probab=21.35 E-value=37 Score=30.70 Aligned_cols=16 Identities=44% Similarity=1.169 Sum_probs=12.5
Q ss_pred CceecCCCCC--------cccccc
Q psy2284 145 SNYTCVPCGA--------RYCCVR 160 (175)
Q Consensus 145 ~~YtC~~Cg~--------ryCS~~ 160 (175)
-.|.||-||+ +||.+.
T Consensus 267 R~YVCPiCGATgDnAHTiKyCPl~ 290 (318)
T KOG4602|consen 267 RSYVCPICGATGDNAHTIKYCPLA 290 (318)
T ss_pred hhhcCccccccCCcccceeccccc
Confidence 3589999997 688765
No 187
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.25 E-value=45 Score=31.47 Aligned_cols=23 Identities=30% Similarity=0.853 Sum_probs=14.8
Q ss_pred CCcccceecCCCC--ceecCCCCCc
Q psy2284 133 PNRHFCAVCGFPS--NYTCVPCGAR 155 (175)
Q Consensus 133 P~r~~C~VCG~~~--~YtC~~Cg~r 155 (175)
...-.|.-||+.. ...||.||..
T Consensus 238 ~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 238 EGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 3455788888554 3458888763
No 188
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.18 E-value=61 Score=21.35 Aligned_cols=28 Identities=25% Similarity=0.715 Sum_probs=20.6
Q ss_pred cceecC---CC-CceecCCCCCcccccccccc
Q psy2284 137 FCAVCG---FP-SNYTCVPCGARYCCVRCLGT 164 (175)
Q Consensus 137 ~C~VCG---~~-~~YtC~~Cg~ryCS~~C~~~ 164 (175)
.|..|+ .. ..|+|..|.-..-...|+..
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 477787 33 38999999887777777754
No 189
>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=21.14 E-value=49 Score=20.94 Aligned_cols=11 Identities=36% Similarity=1.222 Sum_probs=8.3
Q ss_pred ceecCCCCCcc
Q psy2284 146 NYTCVPCGARY 156 (175)
Q Consensus 146 ~YtC~~Cg~ry 156 (175)
.|.|..||..+
T Consensus 5 ey~C~~Cg~~f 15 (42)
T PF09723_consen 5 EYRCEECGHEF 15 (42)
T ss_pred EEEeCCCCCEE
Confidence 47899999654
No 190
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=21.10 E-value=49 Score=21.95 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=19.0
Q ss_pred cceecCC---CC-ceecCCCCCccccccccccc
Q psy2284 137 FCAVCGF---PS-NYTCVPCGARYCCVRCLGTH 165 (175)
Q Consensus 137 ~C~VCG~---~~-~YtC~~Cg~ryCS~~C~~~H 165 (175)
.|-.||. .| .|+|..|.-..-...|+.-+
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 4778882 23 88899887765555565443
No 191
>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=20.89 E-value=50 Score=25.10 Aligned_cols=31 Identities=32% Similarity=0.648 Sum_probs=21.1
Q ss_pred CcccceecCC----C--CceecCCCCCccccccccccc
Q psy2284 134 NRHFCAVCGF----P--SNYTCVPCGARYCCVRCLGTH 165 (175)
Q Consensus 134 ~r~~C~VCG~----~--~~YtC~~Cg~ryCS~~C~~~H 165 (175)
..+.|..|+. . ..-.|..|+.+.|+. |...+
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~-C~~~~ 89 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKK-CGVYS 89 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETT-SEEET
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCc-cCCcC
Confidence 4558999972 2 356699999999976 65543
No 192
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=20.57 E-value=31 Score=22.65 Aligned_cols=30 Identities=27% Similarity=0.595 Sum_probs=19.1
Q ss_pred ccceecCCCCceecCCCCCccccccccccccc
Q psy2284 136 HFCAVCGFPSNYTCVPCGARYCCVRCLGTHQD 167 (175)
Q Consensus 136 ~~C~VCG~~~~YtC~~Cg~ryCS~~C~~~H~e 167 (175)
-||.||+..-.- +.=+.-|||-.|.....+
T Consensus 7 ~yC~~Cdk~~~~--~~~~~lYCSe~Cr~~D~~ 36 (43)
T PF12855_consen 7 DYCIVCDKQIDP--PDDGSLYCSEECRLKDQE 36 (43)
T ss_pred hHHHHhhccccC--CCCCccccCHHHHhHhhh
Confidence 488999832211 222678999999765443
No 193
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=20.52 E-value=44 Score=24.82 Aligned_cols=20 Identities=40% Similarity=0.941 Sum_probs=12.5
Q ss_pred cceecCCC------CceecCCCCCcc
Q psy2284 137 FCAVCGFP------SNYTCVPCGARY 156 (175)
Q Consensus 137 ~C~VCG~~------~~YtC~~Cg~ry 156 (175)
.|.|||.+ |-++|-.|.+.|
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FF 27 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFF 27 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehhee
Confidence 58899843 234577776643
No 194
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=20.50 E-value=62 Score=26.37 Aligned_cols=22 Identities=23% Similarity=0.619 Sum_probs=17.2
Q ss_pred cccceecCC------CCceecCCCCCcc
Q psy2284 135 RHFCAVCGF------PSNYTCVPCGARY 156 (175)
Q Consensus 135 r~~C~VCG~------~~~YtC~~Cg~ry 156 (175)
..+|..||- |..-.|+.||.++
T Consensus 149 ~a~~~~~g~~~~~~~~~~~~c~~~~~~e 176 (189)
T PRK09521 149 YAMCSRCRTPLVKKGENELKCPNCGNIE 176 (189)
T ss_pred EEEccccCCceEECCCCEEECCCCCCEE
Confidence 347999994 6677899999865
No 195
>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=20.47 E-value=29 Score=19.19 Aligned_cols=24 Identities=25% Similarity=0.856 Sum_probs=16.7
Q ss_pred eecCCCCCcccccccccccccccc
Q psy2284 147 YTCVPCGARYCCVRCLGTHQDTRC 170 (175)
Q Consensus 147 YtC~~Cg~ryCS~~C~~~H~etRC 170 (175)
|.|..|+..|-+..=+..|..+-|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 788888888877666655554433
No 196
>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=20.27 E-value=58 Score=20.75 Aligned_cols=28 Identities=25% Similarity=0.655 Sum_probs=19.0
Q ss_pred cceecC--CC-CceecCCCCCcccccccccc
Q psy2284 137 FCAVCG--FP-SNYTCVPCGARYCCVRCLGT 164 (175)
Q Consensus 137 ~C~VCG--~~-~~YtC~~Cg~ryCS~~C~~~ 164 (175)
.|.+|+ .+ -.|.|..|....-...|+..
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~ 32 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAK 32 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCc
Confidence 478888 23 37889999876655666543
No 197
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=20.20 E-value=53 Score=35.27 Aligned_cols=22 Identities=32% Similarity=0.841 Sum_probs=14.1
Q ss_pred cccceecCCCC-ceecCCCCCcc
Q psy2284 135 RHFCAVCGFPS-NYTCVPCGARY 156 (175)
Q Consensus 135 r~~C~VCG~~~-~YtC~~Cg~ry 156 (175)
+..|.-||... ...|+.||.+.
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCccccccCcccCCcC
Confidence 56788888332 33688888663
No 198
>PRK13844 recombination protein RecR; Provisional
Probab=20.20 E-value=52 Score=28.11 Aligned_cols=23 Identities=22% Similarity=0.470 Sum_probs=16.2
Q ss_pred CCCcccceecCCCC-ceecCCCCC
Q psy2284 132 FPNRHFCAVCGFPS-NYTCVPCGA 154 (175)
Q Consensus 132 ~P~r~~C~VCG~~~-~YtC~~Cg~ 154 (175)
.-..++|++||+.+ .-.|+=|.-
T Consensus 54 ~~~i~~C~~C~~lte~~~C~IC~d 77 (200)
T PRK13844 54 TANIKKCVYCQALTEDDVCNICSN 77 (200)
T ss_pred HHhCCcCCCCCCCCCCCCCCCCCC
Confidence 34567999999666 445887753
Done!