Query 047076
Match_columns 86
No_of_seqs 100 out of 477
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:22:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047076.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047076hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2858 Uncharacterized conser 99.7 2.7E-17 5.8E-22 129.9 2.9 69 16-84 14-89 (390)
2 PF04438 zf-HIT: HIT zinc fing 99.3 7.4E-13 1.6E-17 71.7 0.2 29 19-48 2-30 (30)
3 KOG2857 Predicted MYND Zn-fing 99.3 1.4E-12 3.1E-17 92.8 1.5 41 19-59 5-45 (157)
4 KOG4317 Predicted Zn-finger pr 99.1 2.2E-11 4.7E-16 95.9 -0.0 41 19-61 7-47 (383)
5 KOG3362 Predicted BBOX Zn-fing 98.8 6.6E-10 1.4E-14 79.3 0.7 46 9-56 108-153 (156)
6 PF01753 zf-MYND: MYND finger; 96.3 0.0011 2.4E-08 36.2 0.3 29 22-51 1-30 (37)
7 KOG2858 Uncharacterized conser 93.8 0.023 5.1E-07 45.8 0.7 41 20-60 186-226 (390)
8 PF07754 DUF1610: Domain of un 92.5 0.094 2E-06 27.0 1.6 14 26-39 11-24 (24)
9 PF13824 zf-Mss51: Zinc-finger 90.9 0.14 3E-06 31.2 1.3 25 21-45 1-29 (55)
10 KOG1710 MYND Zn-finger and ank 90.6 0.048 1E-06 43.7 -1.1 38 19-58 319-361 (396)
11 PRK14890 putative Zn-ribbon RN 89.2 0.15 3.3E-06 31.4 0.6 20 20-39 37-56 (59)
12 PLN03158 methionine aminopepti 88.5 0.2 4.3E-06 40.2 0.9 34 15-49 5-46 (396)
13 KOG2807 RNA polymerase II tran 88.3 0.45 9.7E-06 38.4 2.8 26 19-45 263-290 (378)
14 PHA00626 hypothetical protein 86.6 0.43 9.4E-06 29.5 1.4 40 20-70 12-51 (59)
15 TIGR00622 ssl1 transcription f 86.0 0.36 7.9E-06 33.1 1.0 14 32-45 2-15 (112)
16 COG2888 Predicted Zn-ribbon RN 84.6 0.37 8E-06 30.0 0.4 20 20-39 39-58 (61)
17 PLN00206 DEAD-box ATP-dependen 84.3 0.3 6.4E-06 39.7 -0.1 48 5-53 14-61 (518)
18 PF13842 Tnp_zf-ribbon_2: DDE_ 81.5 1.7 3.6E-05 23.3 2.2 25 21-45 2-30 (32)
19 cd00350 rubredoxin_like Rubred 80.6 0.85 1.8E-05 24.3 0.9 20 21-40 3-26 (33)
20 PRK13130 H/ACA RNA-protein com 80.4 0.92 2E-05 27.6 1.1 40 18-73 4-43 (56)
21 smart00154 ZnF_AN1 AN1-like Zi 80.2 1.4 3.1E-05 24.5 1.7 23 22-44 1-25 (39)
22 cd00729 rubredoxin_SM Rubredox 72.5 1.7 3.8E-05 23.5 0.7 20 21-40 4-27 (34)
23 PF07975 C1_4: TFIIH C1-like d 70.0 2.6 5.7E-05 25.1 1.1 29 29-58 19-48 (51)
24 PF00643 zf-B_box: B-box zinc 68.2 3.8 8.2E-05 22.1 1.5 26 19-44 3-28 (42)
25 PF10058 DUF2296: Predicted in 67.0 6.7 0.00014 23.3 2.5 23 17-39 20-52 (54)
26 PF07282 OrfB_Zn_ribbon: Putat 65.8 5.3 0.00011 23.7 1.9 23 18-40 27-55 (69)
27 smart00290 ZnF_UBP Ubiquitin C 64.7 6.3 0.00014 21.9 2.0 24 21-44 1-24 (50)
28 PF01428 zf-AN1: AN1-like Zinc 64.5 3.8 8.1E-05 22.9 1.0 20 25-44 6-26 (43)
29 PRK03824 hypA hydrogenase nick 63.7 3.1 6.7E-05 28.7 0.6 9 19-27 70-78 (135)
30 PRK12380 hydrogenase nickel in 63.3 3.2 7E-05 27.7 0.7 22 19-40 70-95 (113)
31 PF07649 C1_3: C1-like domain; 62.7 5.3 0.00012 20.5 1.3 19 21-39 2-23 (30)
32 PF13894 zf-C2H2_4: C2H2-type 62.5 2.2 4.8E-05 19.5 -0.2 20 32-51 1-20 (24)
33 PF00096 zf-C2H2: Zinc finger, 61.4 3.5 7.6E-05 19.3 0.4 18 32-49 1-18 (23)
34 PRK00420 hypothetical protein; 58.8 6.9 0.00015 26.7 1.7 29 19-50 23-56 (112)
35 TIGR02098 MJ0042_CXXC MJ0042 f 56.9 7.1 0.00015 20.8 1.2 11 31-41 2-12 (38)
36 TIGR00627 tfb4 transcription f 56.6 12 0.00026 29.0 2.8 25 20-45 243-269 (279)
37 smart00531 TFIIE Transcription 56.1 7.5 0.00016 26.8 1.5 16 28-43 96-111 (147)
38 TIGR00622 ssl1 transcription f 55.0 21 0.00045 24.5 3.5 39 20-58 56-108 (112)
39 TIGR00100 hypA hydrogenase nic 55.0 5.4 0.00012 26.7 0.6 23 19-41 70-96 (115)
40 PRK00398 rpoP DNA-directed RNA 54.2 7.6 0.00017 21.7 1.1 11 31-41 3-13 (46)
41 PF13912 zf-C2H2_6: C2H2-type 54.1 3.5 7.6E-05 20.1 -0.3 22 32-53 2-23 (27)
42 PRK00564 hypA hydrogenase nick 52.8 6.7 0.00015 26.3 0.8 22 19-40 71-97 (117)
43 PF14206 Cys_rich_CPCC: Cystei 52.6 5.9 0.00013 25.4 0.5 12 31-42 1-12 (78)
44 PF09862 DUF2089: Protein of u 52.2 12 0.00025 25.6 1.9 20 22-41 1-22 (113)
45 PF01155 HypA: Hydrogenase exp 52.1 3.5 7.5E-05 27.5 -0.7 23 19-41 70-96 (113)
46 COG0675 Transposase and inacti 50.9 15 0.00032 26.5 2.5 21 19-39 309-330 (364)
47 PF08271 TF_Zn_Ribbon: TFIIB z 50.1 7.3 0.00016 21.5 0.6 10 32-41 1-10 (43)
48 PF13240 zinc_ribbon_2: zinc-r 49.4 8.9 0.00019 19.0 0.8 6 34-39 16-21 (23)
49 PF12773 DZR: Double zinc ribb 48.8 12 0.00026 20.9 1.3 24 17-40 10-38 (50)
50 PF04640 PLATZ: PLATZ transcri 48.6 14 0.0003 23.4 1.7 23 18-46 48-70 (72)
51 smart00834 CxxC_CXXC_SSSS Puta 48.2 11 0.00023 20.0 1.0 12 30-41 4-15 (41)
52 PF01363 FYVE: FYVE zinc finge 48.1 16 0.00035 21.5 1.9 26 18-43 8-37 (69)
53 COG5195 Uncharacterized conser 47.2 16 0.00035 25.2 2.0 33 16-49 63-95 (118)
54 PRK00762 hypA hydrogenase nick 46.7 9 0.0002 26.0 0.7 21 19-40 70-101 (124)
55 PF09855 DUF2082: Nucleic-acid 46.5 7.9 0.00017 23.9 0.4 11 32-42 1-11 (64)
56 PRK04023 DNA polymerase II lar 46.4 12 0.00025 34.4 1.5 23 18-40 625-647 (1121)
57 PF05495 zf-CHY: CHY zinc fing 46.2 7.1 0.00015 24.0 0.1 24 17-40 39-70 (71)
58 PRK03681 hypA hydrogenase nick 46.0 9.8 0.00021 25.4 0.8 22 19-40 70-96 (114)
59 COG5151 SSL1 RNA polymerase II 46.0 9.5 0.00021 31.0 0.8 51 3-58 351-415 (421)
60 PF06906 DUF1272: Protein of u 45.6 5.9 0.00013 24.3 -0.3 33 6-38 16-48 (57)
61 KOG3612 PHD Zn-finger protein 45.3 4.2 9.2E-05 34.7 -1.3 32 20-53 528-559 (588)
62 COG1592 Rubrerythrin [Energy p 45.0 12 0.00027 27.0 1.2 22 19-40 134-158 (166)
63 cd02335 ZZ_ADA2 Zinc finger, Z 44.6 37 0.00079 19.3 3.0 32 21-52 2-36 (49)
64 TIGR00373 conserved hypothetic 44.4 14 0.00031 25.9 1.5 14 28-41 106-119 (158)
65 PF14949 ARF7EP_C: ARF7 effect 44.3 11 0.00024 25.4 0.8 26 20-46 61-89 (103)
66 PHA00616 hypothetical protein 43.5 3.5 7.7E-05 23.9 -1.4 21 32-52 2-22 (44)
67 PRK01343 zinc-binding protein; 43.4 11 0.00024 23.0 0.6 26 19-49 9-34 (57)
68 COG4049 Uncharacterized protei 43.2 11 0.00024 23.5 0.6 15 28-42 14-28 (65)
69 PF12387 Peptidase_C74: Pestiv 43.2 10 0.00023 28.3 0.6 28 19-46 162-190 (200)
70 PF09538 FYDLN_acid: Protein o 42.7 11 0.00024 25.3 0.6 14 31-44 9-22 (108)
71 PF03107 C1_2: C1 domain; Int 42.6 22 0.00048 18.3 1.7 18 21-38 2-22 (30)
72 COG1571 Predicted DNA-binding 42.5 13 0.00029 30.6 1.2 26 19-44 350-380 (421)
73 PF08265 YL1_C: YL1 nuclear pr 42.5 16 0.00034 19.5 1.1 28 21-49 2-29 (30)
74 TIGR00354 polC DNA polymerase, 41.7 13 0.00028 33.9 1.1 24 18-41 624-647 (1095)
75 cd01121 Sms Sms (bacterial rad 41.7 17 0.00036 28.9 1.6 19 21-39 2-22 (372)
76 PRK06266 transcription initiat 41.3 17 0.00037 26.1 1.5 14 29-42 115-128 (178)
77 TIGR01031 rpmF_bact ribosomal 41.2 23 0.0005 21.0 1.8 25 15-39 22-47 (55)
78 PF13717 zinc_ribbon_4: zinc-r 40.8 18 0.0004 19.5 1.2 10 32-41 3-12 (36)
79 PF14446 Prok-RING_1: Prokaryo 40.4 24 0.00052 21.3 1.8 23 19-41 5-31 (54)
80 PRK04023 DNA polymerase II lar 39.9 18 0.0004 33.2 1.7 23 19-41 638-661 (1121)
81 smart00109 C1 Protein kinase C 39.4 19 0.00042 19.1 1.2 21 19-39 11-35 (49)
82 KOG2807 RNA polymerase II tran 38.5 21 0.00045 29.1 1.7 43 17-59 328-373 (378)
83 PF13719 zinc_ribbon_5: zinc-r 38.1 18 0.00038 19.6 0.9 10 32-41 3-12 (37)
84 PF14353 CpXC: CpXC protein 38.1 20 0.00043 23.7 1.3 14 28-41 35-48 (128)
85 PF13005 zf-IS66: zinc-finger 38.1 20 0.00043 19.7 1.2 11 28-38 37-47 (47)
86 PF13465 zf-H2C2_2: Zinc-finge 38.0 15 0.00032 18.2 0.6 12 30-41 13-24 (26)
87 cd00065 FYVE FYVE domain; Zinc 38.0 22 0.00047 20.0 1.3 30 20-50 3-36 (57)
88 COG5151 SSL1 RNA polymerase II 37.8 18 0.00039 29.5 1.3 25 20-45 296-322 (421)
89 PRK11823 DNA repair protein Ra 37.3 23 0.0005 28.6 1.8 23 17-39 5-29 (446)
90 TIGR00416 sms DNA repair prote 36.7 24 0.00051 28.7 1.8 22 18-39 6-29 (454)
91 PRK00432 30S ribosomal protein 35.8 34 0.00074 19.9 1.9 23 19-41 20-47 (50)
92 smart00064 FYVE Protein presen 35.6 25 0.00055 20.6 1.4 25 19-43 10-38 (68)
93 PF13908 Shisa: Wnt and FGF in 35.5 35 0.00076 23.9 2.3 35 24-59 20-55 (179)
94 PRK09263 anaerobic ribonucleos 35.2 21 0.00047 30.9 1.4 22 19-40 641-668 (711)
95 TIGR02487 NrdD anaerobic ribon 35.1 25 0.00054 29.6 1.7 22 19-40 524-547 (579)
96 PRK14892 putative transcriptio 35.1 32 0.00069 22.9 1.9 12 29-40 19-30 (99)
97 PF03884 DUF329: Domain of unk 34.9 17 0.00037 22.0 0.5 11 39-49 21-31 (57)
98 PRK14704 anaerobic ribonucleos 34.9 22 0.00048 30.3 1.4 21 19-39 559-580 (618)
99 TIGR02827 RNR_anaer_Bdell anae 34.7 22 0.00047 30.3 1.3 22 18-39 531-554 (586)
100 PF02069 Metallothio_Pro: Prok 34.5 11 0.00023 22.7 -0.4 19 38-56 27-45 (52)
101 PRK03976 rpl37ae 50S ribosomal 34.1 20 0.00043 23.7 0.8 13 28-40 33-45 (90)
102 PRK15103 paraquat-inducible me 34.0 37 0.00079 27.5 2.5 25 17-41 219-245 (419)
103 smart00336 BBOX B-Box-type zin 33.9 51 0.0011 17.0 2.3 28 19-47 3-30 (42)
104 PF14835 zf-RING_6: zf-RING of 33.8 13 0.00028 23.3 -0.1 21 20-40 29-49 (65)
105 PF08792 A2L_zn_ribbon: A2L zi 33.4 40 0.00086 18.1 1.8 22 19-40 3-30 (33)
106 PRK07111 anaerobic ribonucleos 33.3 25 0.00053 30.6 1.4 21 19-39 680-701 (735)
107 PRK12496 hypothetical protein; 33.2 27 0.00059 24.7 1.4 11 31-41 127-137 (164)
108 COG1066 Sms Predicted ATP-depe 32.7 26 0.00057 29.3 1.5 22 18-39 6-29 (456)
109 TIGR00280 L37a ribosomal prote 32.6 22 0.00047 23.6 0.8 14 28-41 32-45 (91)
110 cd00021 BBOX B-Box-type zinc f 32.4 40 0.00087 17.2 1.7 26 21-47 2-27 (39)
111 PHA02942 putative transposase; 32.3 35 0.00077 27.2 2.1 22 19-40 325-351 (383)
112 PF09297 zf-NADH-PPase: NADH p 32.2 31 0.00067 17.8 1.2 22 19-40 3-30 (32)
113 PF01780 Ribosomal_L37ae: Ribo 32.1 18 0.00038 24.0 0.3 13 29-41 33-45 (90)
114 PRK08271 anaerobic ribonucleos 32.1 27 0.00058 30.0 1.4 22 18-39 565-588 (623)
115 PF09788 Tmemb_55A: Transmembr 31.8 53 0.0012 25.5 2.9 39 3-41 45-95 (256)
116 PRK12286 rpmF 50S ribosomal pr 31.2 57 0.0012 19.5 2.4 24 16-39 24-48 (57)
117 PF00301 Rubredoxin: Rubredoxi 31.1 24 0.00052 20.4 0.7 11 31-41 1-11 (47)
118 PTZ00255 60S ribosomal protein 30.8 22 0.00048 23.5 0.6 13 28-40 33-45 (90)
119 PF01783 Ribosomal_L32p: Ribos 30.5 22 0.00048 21.0 0.5 22 17-38 24-46 (56)
120 PF10609 ParA: ParA/MinD ATPas 30.4 27 0.00059 22.4 1.0 15 27-41 61-75 (81)
121 TIGR02605 CxxC_CxxC_SSSS putat 30.1 29 0.00062 19.4 0.9 14 30-43 4-17 (52)
122 PF06102 DUF947: Domain of unk 30.0 25 0.00055 25.1 0.9 25 61-85 34-59 (168)
123 PF09723 Zn-ribbon_8: Zinc rib 29.8 29 0.00064 19.1 0.9 16 30-45 4-19 (42)
124 cd02344 ZZ_HERC2 Zinc finger, 29.4 55 0.0012 18.8 2.0 32 21-52 2-36 (45)
125 PRK08270 anaerobic ribonucleos 29.3 31 0.00066 29.7 1.4 22 19-40 626-648 (656)
126 PF08189 Meleagrin: Meleagrin/ 29.1 28 0.0006 19.8 0.7 16 34-51 6-21 (39)
127 PF15135 UPF0515: Uncharacteri 28.9 42 0.00092 26.3 2.0 28 14-41 127-165 (278)
128 PF13597 NRDD: Anaerobic ribon 28.7 27 0.00058 29.2 0.9 23 19-41 491-514 (546)
129 COG4640 Predicted membrane pro 28.1 32 0.00069 28.7 1.2 25 19-43 1-27 (465)
130 PF10122 Mu-like_Com: Mu-like 27.8 31 0.00068 20.7 0.8 21 20-40 5-33 (51)
131 PF08646 Rep_fac-A_C: Replicat 27.6 34 0.00074 23.0 1.1 20 21-40 20-46 (146)
132 TIGR02300 FYDLN_acid conserved 27.5 27 0.00059 24.6 0.6 14 31-44 9-22 (129)
133 PF13909 zf-H2C2_5: C2H2-type 27.2 34 0.00074 16.1 0.8 8 32-39 1-8 (24)
134 COG1997 RPL43A Ribosomal prote 26.6 29 0.00062 23.0 0.6 14 28-41 32-45 (89)
135 cd02342 ZZ_UBA_plant Zinc fing 26.6 44 0.00095 19.3 1.3 30 21-50 2-34 (43)
136 PRK14714 DNA polymerase II lar 26.3 40 0.00086 31.7 1.6 21 21-41 681-702 (1337)
137 COG2260 Predicted Zn-ribbon RN 26.0 39 0.00085 20.8 1.1 36 31-73 5-43 (59)
138 PF04236 Transp_Tc5_C: Tc5 tra 25.7 65 0.0014 19.7 2.0 25 17-42 25-51 (63)
139 PF03833 PolC_DP2: DNA polymer 25.4 23 0.00051 31.8 0.0 23 19-41 655-677 (900)
140 TIGR01384 TFS_arch transcripti 25.4 56 0.0012 20.8 1.8 20 21-40 2-25 (104)
141 KOG4850 Uncharacterized conser 24.9 35 0.00076 25.3 0.8 29 19-48 135-166 (190)
142 PF13878 zf-C2H2_3: zinc-finge 24.6 34 0.00074 19.0 0.6 14 30-43 12-25 (41)
143 COG1594 RPB9 DNA-directed RNA 24.6 74 0.0016 21.3 2.3 21 20-40 73-109 (113)
144 cd02340 ZZ_NBR1_like Zinc fing 24.4 67 0.0014 17.9 1.8 28 21-48 2-31 (43)
145 TIGR00155 pqiA_fam integral me 24.4 77 0.0017 25.5 2.8 23 19-41 13-43 (403)
146 PRK06450 threonine synthase; V 24.4 38 0.00082 26.3 1.0 18 21-38 5-25 (338)
147 PF12172 DUF35_N: Rubredoxin-l 24.1 23 0.00051 18.7 -0.2 22 18-39 10-33 (37)
148 PRK11788 tetratricopeptide rep 24.1 58 0.0013 24.1 1.9 21 19-39 354-376 (389)
149 KOG2593 Transcription initiati 24.1 30 0.00064 28.8 0.4 21 28-48 125-145 (436)
150 PF02148 zf-UBP: Zn-finger in 24.1 41 0.00088 19.8 0.9 23 22-44 1-24 (63)
151 PF14471 DUF4428: Domain of un 24.0 11 0.00025 22.0 -1.5 21 21-41 1-30 (51)
152 PLN03144 Carbon catabolite rep 24.0 34 0.00073 29.3 0.7 30 20-49 63-100 (606)
153 PF04216 FdhE: Protein involve 24.0 19 0.00042 27.2 -0.7 7 20-26 173-179 (290)
154 PF03833 PolC_DP2: DNA polymer 23.8 26 0.00057 31.5 0.0 27 20-46 668-695 (900)
155 cd00029 C1 Protein kinase C co 23.7 66 0.0014 17.2 1.7 21 19-39 11-36 (50)
156 cd02339 ZZ_Mind_bomb Zinc fing 23.6 71 0.0015 18.1 1.8 28 21-48 2-32 (45)
157 PF05605 zf-Di19: Drought indu 23.6 22 0.00048 20.3 -0.3 22 31-53 2-23 (54)
158 PF05741 zf-nanos: Nanos RNA b 23.3 50 0.0011 19.9 1.2 11 29-39 31-41 (55)
159 KOG2907 RNA polymerase I trans 23.2 45 0.00097 23.1 1.0 22 19-40 74-111 (116)
160 PRK08579 anaerobic ribonucleos 23.1 47 0.001 28.5 1.4 23 18-40 567-591 (625)
161 PRK11032 hypothetical protein; 23.0 39 0.00085 24.3 0.8 25 16-40 121-151 (160)
162 PF01927 Mut7-C: Mut7-C RNAse 22.4 61 0.0013 22.2 1.6 11 31-41 124-134 (147)
163 COG3813 Uncharacterized protei 22.1 27 0.00058 22.7 -0.2 33 6-38 16-48 (84)
164 KOG4137 Uncharacterized conser 21.9 71 0.0015 21.7 1.8 32 17-49 48-79 (102)
165 PRK14559 putative protein seri 21.9 61 0.0013 28.0 1.8 23 18-40 14-36 (645)
166 COG1656 Uncharacterized conser 21.3 50 0.0011 24.1 1.0 11 31-41 130-140 (165)
167 cd02334 ZZ_dystrophin Zinc fin 21.2 78 0.0017 18.3 1.7 29 21-49 2-33 (49)
168 cd01675 RNR_III Class III ribo 21.1 53 0.0011 27.5 1.2 20 21-40 520-541 (555)
169 smart00355 ZnF_C2H2 zinc finge 20.8 22 0.00047 16.0 -0.7 19 32-50 1-19 (26)
170 PF14570 zf-RING_4: RING/Ubox 20.7 43 0.00093 19.6 0.5 12 30-41 36-47 (48)
171 cd00730 rubredoxin Rubredoxin; 20.5 47 0.001 19.4 0.6 12 29-40 32-43 (50)
172 cd02341 ZZ_ZZZ3 Zinc finger, Z 20.4 90 0.002 17.9 1.8 27 21-48 2-34 (48)
173 PF04606 Ogr_Delta: Ogr/Delta- 20.1 46 0.001 18.7 0.5 9 33-41 1-9 (47)
No 1
>KOG2858 consensus Uncharacterized conserved protein [General function prediction only]
Probab=99.66 E-value=2.7e-17 Score=129.91 Aligned_cols=69 Identities=36% Similarity=0.649 Sum_probs=62.1
Q ss_pred cccccccccCCCCCeeEeCCCCCcccccccccccccccccCCCCCCcceeee-cCCCCh------hhhhhhccccc
Q 047076 16 AKEAAICQECKYKVSKYKCPGCSIRTCSLACVKAHKQRTGCSGNRNVTQFVP-LSQFND------NILLSATKLSS 84 (86)
Q Consensus 16 ~~~~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g~r~~~~~v~-~~~~~~------~~l~~Dy~fLe 84 (86)
.....+|+||+.+++||+||||.+++|||+|.+.||...+|+|.|++..||| |+|+++ +.+++||+||-
T Consensus 14 ~~~~vlCgVClknE~KYkCPRCl~rtCsLeCskkHK~~dnCsG~rqp~t~Vp~l~q~d~~K~~~~q~v~~d~n~l~ 89 (390)
T KOG2858|consen 14 GLHSVLCGVCLKNEPKYKCPRCLARTCSLECSKKHKIGDNCSGSRQPPTEVPMLDQPDTEKRLAGQWVEQDVNDLP 89 (390)
T ss_pred ccchhhhhhcccCcccccCcchhhhheeccccccccccCCCcCCcCCcccccccccCCchhhhhhHHHHHHhhhhh
Confidence 3456899999999999999999999999999999999999999999999998 467765 37899999984
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=99.27 E-value=7.4e-13 Score=71.65 Aligned_cols=29 Identities=48% Similarity=1.140 Sum_probs=23.6
Q ss_pred ccccccCCCCCeeEeCCCCCcccccccccc
Q 047076 19 AAICQECKYKVSKYKCPGCSIRTCSLACVK 48 (86)
Q Consensus 19 ~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k 48 (86)
..+|.||+. +++|+||+|+++||||+|+|
T Consensus 2 ~~~C~vC~~-~~kY~Cp~C~~~~CSl~C~k 30 (30)
T PF04438_consen 2 RKLCSVCGN-PAKYRCPRCGARYCSLACYK 30 (30)
T ss_dssp -EEETSSSS-EESEE-TTT--EESSHHHHH
T ss_pred cCCCccCcC-CCEEECCCcCCceeCcEeEC
Confidence 468999998 99999999999999999986
No 3
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=99.26 E-value=1.4e-12 Score=92.80 Aligned_cols=41 Identities=41% Similarity=0.861 Sum_probs=36.9
Q ss_pred ccccccCCCCCeeEeCCCCCcccccccccccccccccCCCC
Q 047076 19 AAICQECKYKVSKYKCPGCSIRTCSLACVKAHKQRTGCSGN 59 (86)
Q Consensus 19 ~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g~ 59 (86)
+.+|.||...++|||||+|..+||||.|||+||....|...
T Consensus 5 t~tC~ic~e~~~KYKCpkC~vPYCSl~CfKiHk~tPq~~~v 45 (157)
T KOG2857|consen 5 TTTCVICLESEIKYKCPKCSVPYCSLPCFKIHKSTPQCETV 45 (157)
T ss_pred eeeehhhhcchhhccCCCCCCccccchhhhhccCCcccccc
Confidence 57899999999999999999999999999999997666543
No 4
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=99.07 E-value=2.2e-11 Score=95.95 Aligned_cols=41 Identities=34% Similarity=0.813 Sum_probs=37.2
Q ss_pred ccccccCCCCCeeEeCCCCCcccccccccccccccccCCCCCC
Q 047076 19 AAICQECKYKVSKYKCPGCSIRTCSLACVKAHKQRTGCSGNRN 61 (86)
Q Consensus 19 ~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g~r~ 61 (86)
-.+|.||+++.+.|+||||+.+||||.|||.|+++ |+.++.
T Consensus 7 ~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~h~~~--CsE~Fy 47 (383)
T KOG4317|consen 7 FLACGICGVQKREYTCPRCNLLYCSLKCYRNHKHS--CSEKFY 47 (383)
T ss_pred eeeccccccccccccCCCCCccceeeeeecCCCcc--chHHHH
Confidence 35799999999999999999999999999999995 987654
No 5
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=98.85 E-value=6.6e-10 Score=79.27 Aligned_cols=46 Identities=28% Similarity=0.681 Sum_probs=38.8
Q ss_pred CCCCCcccccccccccCCCCCeeEeCCCCCcccccccccccccccccC
Q 047076 9 STNQNPKAKEAAICQECKYKVSKYKCPGCSIRTCSLACVKAHKQRTGC 56 (86)
Q Consensus 9 s~~~~~~~~~~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C 56 (86)
+++...-++...+|.||| .+++|.|-+||.+|||+.|.++|.+. .|
T Consensus 108 ~~a~p~~KP~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~HneT-RC 153 (156)
T KOG3362|consen 108 AYAKPSFKPLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNET-RC 153 (156)
T ss_pred cccCCCCCCcchhhhhcC-CCchhHHHhcCCceeechhhhhcccc-cc
Confidence 344444456667999999 59999999999999999999999997 77
No 6
>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=96.34 E-value=0.0011 Score=36.23 Aligned_cols=29 Identities=34% Similarity=0.780 Sum_probs=23.1
Q ss_pred cccCCCCCeeEeCCCC-Cccccccccccccc
Q 047076 22 CQECKYKVSKYKCPGC-SIRTCSLACVKAHK 51 (86)
Q Consensus 22 C~vC~~~~~kY~CP~C-~~~~CSl~C~k~Hk 51 (86)
|.+|+....+ +|++| .+.|||.+|.+.|-
T Consensus 1 C~~C~~~~~~-~C~~C~~~~YCs~~Cq~~~w 30 (37)
T PF01753_consen 1 CAVCGKPALK-RCSRCKSVYYCSEECQRADW 30 (37)
T ss_dssp -TTTSSCSSE-EETTTSSSEESSHHHHHHHH
T ss_pred CcCCCCCcCC-cCCCCCCEEecCHHHHHHHH
Confidence 6788875556 99999 78899999988764
No 7
>KOG2858 consensus Uncharacterized conserved protein [General function prediction only]
Probab=93.80 E-value=0.023 Score=45.84 Aligned_cols=41 Identities=32% Similarity=0.717 Sum_probs=38.8
Q ss_pred cccccCCCCCeeEeCCCCCcccccccccccccccccCCCCC
Q 047076 20 AICQECKYKVSKYKCPGCSIRTCSLACVKAHKQRTGCSGNR 60 (86)
Q Consensus 20 ~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g~r 60 (86)
.+|..|+...++|+||+|.+..|.+++.+.|..+-.|.+.|
T Consensus 186 ~~~eTi~te~~k~~~pr~k~y~clV~e~~k~v~ql~c~~~R 226 (390)
T KOG2858|consen 186 SRCETIGTEEAKYRCPRCKRYSCLVPEVKKHVAQLTCNGVR 226 (390)
T ss_pred ccccchhhhhccccccchhhhceeccchhhhhhhhcccccc
Confidence 68899999999999999999999999999999998998877
No 8
>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=92.52 E-value=0.094 Score=27.04 Aligned_cols=14 Identities=21% Similarity=0.878 Sum_probs=10.9
Q ss_pred CCCCeeEeCCCCCc
Q 047076 26 KYKVSKYKCPGCSI 39 (86)
Q Consensus 26 ~~~~~kY~CP~C~~ 39 (86)
..+...|.||.|+.
T Consensus 11 r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 11 REQAVPFPCPNCGF 24 (24)
T ss_pred cccCceEeCCCCCC
Confidence 44567999999973
No 9
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=90.87 E-value=0.14 Score=31.20 Aligned_cols=25 Identities=40% Similarity=1.014 Sum_probs=18.4
Q ss_pred ccccCCC---CCeeEeCCCCCccc-cccc
Q 047076 21 ICQECKY---KVSKYKCPGCSIRT-CSLA 45 (86)
Q Consensus 21 ~C~vC~~---~~~kY~CP~C~~~~-CSl~ 45 (86)
+|.||.. ....|.||.||++| ||.+
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~e 29 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSEE 29 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCHH
Confidence 4667775 35799999999987 5543
No 10
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=90.62 E-value=0.048 Score=43.71 Aligned_cols=38 Identities=32% Similarity=0.723 Sum_probs=32.4
Q ss_pred ccccccCCCCCeeEeCCCCC-cccccccccccc----cccccCCC
Q 047076 19 AAICQECKYKVSKYKCPGCS-IRTCSLACVKAH----KQRTGCSG 58 (86)
Q Consensus 19 ~~~C~vC~~~~~kY~CP~C~-~~~CSl~C~k~H----k~~~~C~g 58 (86)
..+|++||...++=||..|- ..||+-+|.|.| |. .|+-
T Consensus 319 ~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~hWf~HKK--~C~~ 361 (396)
T KOG1710|consen 319 CQFCSTCGHPGAKKRCSQCKAVAYCDQECQKFHWFIHKK--VCSF 361 (396)
T ss_pred cccccccCCCCccchhhhhHHHHHHHHHHHHhhhHHHHH--HHHH
Confidence 47999999999999999999 899999998764 55 4754
No 11
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=89.22 E-value=0.15 Score=31.44 Aligned_cols=20 Identities=30% Similarity=1.024 Sum_probs=13.6
Q ss_pred cccccCCCCCeeEeCCCCCc
Q 047076 20 AICQECKYKVSKYKCPGCSI 39 (86)
Q Consensus 20 ~~C~vC~~~~~kY~CP~C~~ 39 (86)
.+|.-|.+....|+||.|+.
T Consensus 37 ~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 37 YRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred eechhHHhcCCceECCCCCC
Confidence 45666666667788887764
No 12
>PLN03158 methionine aminopeptidase; Provisional
Probab=88.47 E-value=0.2 Score=40.22 Aligned_cols=34 Identities=29% Similarity=0.696 Sum_probs=26.8
Q ss_pred ccccccccccCCCCCeeEeCCCCCc--------cccccccccc
Q 047076 15 KAKEAAICQECKYKVSKYKCPGCSI--------RTCSLACVKA 49 (86)
Q Consensus 15 ~~~~~~~C~vC~~~~~kY~CP~C~~--------~~CSl~C~k~ 49 (86)
+++.+..|.-|++ +++..||.|.. .+||-+|+|.
T Consensus 5 ~~~~~~~c~~c~~-~a~l~Cp~C~k~~~~~~~s~fCsq~CFk~ 46 (396)
T PLN03158 5 LTTSPLACARCSK-PAHLQCPKCLELKLPREGASFCSQDCFKA 46 (396)
T ss_pred cCCCcccccCCCC-cccccCccchhcCCCCCCceeECHHHHHH
Confidence 4455677999996 68899999964 5799999763
No 13
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=88.34 E-value=0.45 Score=38.40 Aligned_cols=26 Identities=35% Similarity=0.949 Sum_probs=20.7
Q ss_pred ccccccCCC--CCeeEeCCCCCccccccc
Q 047076 19 AAICQECKY--KVSKYKCPGCSIRTCSLA 45 (86)
Q Consensus 19 ~~~C~vC~~--~~~kY~CP~C~~~~CSl~ 45 (86)
+.+|. |.. ..+-|-||+|.++.|||.
T Consensus 263 ps~C~-CH~~~~~~Gy~CP~CkakvCsLP 290 (378)
T KOG2807|consen 263 PSFCA-CHSELSGGGYFCPQCKAKVCSLP 290 (378)
T ss_pred cchhe-eccccccCceeCCcccCeeecCC
Confidence 36776 764 456899999999999994
No 14
>PHA00626 hypothetical protein
Probab=86.61 E-value=0.43 Score=29.45 Aligned_cols=40 Identities=23% Similarity=0.396 Sum_probs=29.5
Q ss_pred cccccCCCCCeeEeCCCCCcccccccccccccccccCCCCCCcceeeecCC
Q 047076 20 AICQECKYKVSKYKCPGCSIRTCSLACVKAHKQRTGCSGNRNVTQFVPLSQ 70 (86)
Q Consensus 20 ~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g~r~~~~~v~~~~ 70 (86)
..|.+|......|+||.|+-.+ -|+. -|.|...+||.++.
T Consensus 12 vrcg~cr~~snrYkCkdCGY~f--------t~~~---~~~~~~~~~~~~~~ 51 (59)
T PHA00626 12 AKEKTMRGWSDDYVCCDCGYND--------SKDA---FGERGKNEFVRINK 51 (59)
T ss_pred eeeceecccCcceEcCCCCCee--------chhh---hhhccccceEEech
Confidence 4688888777899999999654 2332 46777888888764
No 15
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.02 E-value=0.36 Score=33.06 Aligned_cols=14 Identities=43% Similarity=1.231 Sum_probs=13.3
Q ss_pred EeCCCCCccccccc
Q 047076 32 YKCPGCSIRTCSLA 45 (86)
Q Consensus 32 Y~CP~C~~~~CSl~ 45 (86)
|.||+|+.++|+|.
T Consensus 2 Y~CPrC~skvC~LP 15 (112)
T TIGR00622 2 YFCPQCRAKVCELP 15 (112)
T ss_pred ccCCCCCCCccCCC
Confidence 89999999999996
No 16
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.57 E-value=0.37 Score=29.98 Aligned_cols=20 Identities=30% Similarity=0.938 Sum_probs=13.4
Q ss_pred cccccCCCCCeeEeCCCCCc
Q 047076 20 AICQECKYKVSKYKCPGCSI 39 (86)
Q Consensus 20 ~~C~vC~~~~~kY~CP~C~~ 39 (86)
.+|.-|......|+||.|+.
T Consensus 39 ~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 39 YRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred ehhhhHHHcCCceECCCcCc
Confidence 34555666667788888874
No 17
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=84.32 E-value=0.3 Score=39.65 Aligned_cols=48 Identities=25% Similarity=0.406 Sum_probs=39.9
Q ss_pred cCCCCCCCCcccccccccccCCCCCeeEeCCCCCccccccccccccccc
Q 047076 5 EGPTSTNQNPKAKEAAICQECKYKVSKYKCPGCSIRTCSLACVKAHKQR 53 (86)
Q Consensus 5 ~~p~s~~~~~~~~~~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~ 53 (86)
+...|-++.-+.++..+|.|||. -+-|-|-.=.-..|||+|...|-..
T Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (518)
T PLN00206 14 VKERSIEQREALPGEPKCVVCGR-YGEYICDETDDDICSLECKQALLRR 61 (518)
T ss_pred hhhhhHHhcCCCCCCceEEEecC-ccceeccCCCCccccHHHHHHHHHH
Confidence 34455566677778899999996 7899999999999999999999864
No 18
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=81.54 E-value=1.7 Score=23.34 Aligned_cols=25 Identities=28% Similarity=0.810 Sum_probs=19.2
Q ss_pred ccccCCCC----CeeEeCCCCCccccccc
Q 047076 21 ICQECKYK----VSKYKCPGCSIRTCSLA 45 (86)
Q Consensus 21 ~C~vC~~~----~~kY~CP~C~~~~CSl~ 45 (86)
.|.||..+ ..+|.|..|+...|--.
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 57788763 37999999998887654
No 19
>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=80.59 E-value=0.85 Score=24.32 Aligned_cols=20 Identities=30% Similarity=0.926 Sum_probs=13.9
Q ss_pred ccccCCCC----CeeEeCCCCCcc
Q 047076 21 ICQECKYK----VSKYKCPGCSIR 40 (86)
Q Consensus 21 ~C~vC~~~----~~kY~CP~C~~~ 40 (86)
.|.+||.. ....+||.|+.+
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCCc
Confidence 57888852 246788888763
No 20
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=80.40 E-value=0.92 Score=27.55 Aligned_cols=40 Identities=25% Similarity=0.517 Sum_probs=24.9
Q ss_pred cccccccCCCCCeeEeCCCCCcccccccccccccccccCCCCCCcceeeecCCCCh
Q 047076 18 EAAICQECKYKVSKYKCPGCSIRTCSLACVKAHKQRTGCSGNRNVTQFVPLSQFND 73 (86)
Q Consensus 18 ~~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g~r~~~~~v~~~~~~~ 73 (86)
.+..|..|++-.-+-.||.|+..+= ...+..|.|-..|..
T Consensus 4 ~mr~C~~CgvYTLk~~CP~CG~~t~----------------~~~P~rfSp~D~y~~ 43 (56)
T PRK13130 4 KIRKCPKCGVYTLKEICPVCGGKTK----------------NPHPPRFSPEDKYGK 43 (56)
T ss_pred cceECCCCCCEEccccCcCCCCCCC----------------CCCCCCCCCCCccHH
Confidence 4567777777555777777775532 345666666655544
No 21
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=80.22 E-value=1.4 Score=24.51 Aligned_cols=23 Identities=35% Similarity=0.842 Sum_probs=19.0
Q ss_pred cccCCCCCe--eEeCCCCCcccccc
Q 047076 22 CQECKYKVS--KYKCPGCSIRTCSL 44 (86)
Q Consensus 22 C~vC~~~~~--kY~CP~C~~~~CSl 44 (86)
|.+|+.... .++|..|+..+|+.
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 677887665 59999999999985
No 22
>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=72.55 E-value=1.7 Score=23.46 Aligned_cols=20 Identities=35% Similarity=0.874 Sum_probs=13.3
Q ss_pred ccccCCCC----CeeEeCCCCCcc
Q 047076 21 ICQECKYK----VSKYKCPGCSIR 40 (86)
Q Consensus 21 ~C~vC~~~----~~kY~CP~C~~~ 40 (86)
+|.+||.- .+-.+||.|+.+
T Consensus 4 ~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred ECCCCCCEeECCcCCCcCcCCCCc
Confidence 57888852 134688888764
No 23
>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=69.99 E-value=2.6 Score=25.10 Aligned_cols=29 Identities=38% Similarity=0.958 Sum_probs=15.1
Q ss_pred CeeEeCCCCCcccccccc-cccccccccCCC
Q 047076 29 VSKYKCPGCSIRTCSLAC-VKAHKQRTGCSG 58 (86)
Q Consensus 29 ~~kY~CP~C~~~~CSl~C-~k~Hk~~~~C~g 58 (86)
...|+||+|...+|- .| .-+|....+|.|
T Consensus 19 ~~~y~C~~C~~~FC~-dCD~fiHE~LH~CPG 48 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCI-DCDVFIHETLHNCPG 48 (51)
T ss_dssp -EEE--TTTT--B-H-HHHHTTTTTS-SSST
T ss_pred CCeEECCCCCCcccc-CcChhhhccccCCcC
Confidence 478999999999983 44 345666666655
No 24
>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=68.17 E-value=3.8 Score=22.07 Aligned_cols=26 Identities=23% Similarity=0.413 Sum_probs=21.9
Q ss_pred ccccccCCCCCeeEeCCCCCcccccc
Q 047076 19 AAICQECKYKVSKYKCPGCSIRTCSL 44 (86)
Q Consensus 19 ~~~C~vC~~~~~kY~CP~C~~~~CSl 44 (86)
...|..+......|-|..|+...|+.
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 46899999877999999999999874
No 25
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=67.00 E-value=6.7 Score=23.34 Aligned_cols=23 Identities=35% Similarity=0.870 Sum_probs=16.3
Q ss_pred ccccccccCCC----------CCeeEeCCCCCc
Q 047076 17 KEAAICQECKY----------KVSKYKCPGCSI 39 (86)
Q Consensus 17 ~~~~~C~vC~~----------~~~kY~CP~C~~ 39 (86)
+-..+|.-|.. ...+|+||.|+.
T Consensus 20 r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 20 RYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred ceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 33467888863 234899999985
No 26
>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=65.76 E-value=5.3 Score=23.72 Aligned_cols=23 Identities=22% Similarity=0.821 Sum_probs=16.3
Q ss_pred cccccccCCCCC------eeEeCCCCCcc
Q 047076 18 EAAICQECKYKV------SKYKCPGCSIR 40 (86)
Q Consensus 18 ~~~~C~vC~~~~------~kY~CP~C~~~ 40 (86)
..+.|..|+... ..|+||.|+..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 356799998633 35899988764
No 27
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=64.67 E-value=6.3 Score=21.91 Aligned_cols=24 Identities=21% Similarity=0.520 Sum_probs=20.1
Q ss_pred ccccCCCCCeeEeCCCCCcccccc
Q 047076 21 ICQECKYKVSKYKCPGCSIRTCSL 44 (86)
Q Consensus 21 ~C~vC~~~~~kY~CP~C~~~~CSl 44 (86)
.|..|+.....|.|..|+.-.|.-
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCC
Confidence 488999877899999999888844
No 28
>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=64.54 E-value=3.8 Score=22.88 Aligned_cols=20 Identities=35% Similarity=0.712 Sum_probs=11.4
Q ss_pred CCCCC-eeEeCCCCCcccccc
Q 047076 25 CKYKV-SKYKCPGCSIRTCSL 44 (86)
Q Consensus 25 C~~~~-~kY~CP~C~~~~CSl 44 (86)
|+... -.++|+.|+..||..
T Consensus 6 C~~~~~~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 6 CKKKDFLPFKCKHCGKSFCLK 26 (43)
T ss_dssp T--BCTSHEE-TTTS-EE-TT
T ss_pred CcCccCCCeECCCCCcccCcc
Confidence 66533 379999999999974
No 29
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.71 E-value=3.1 Score=28.66 Aligned_cols=9 Identities=22% Similarity=0.730 Sum_probs=6.5
Q ss_pred ccccccCCC
Q 047076 19 AAICQECKY 27 (86)
Q Consensus 19 ~~~C~vC~~ 27 (86)
...|..|+.
T Consensus 70 ~~~C~~CG~ 78 (135)
T PRK03824 70 VLKCRNCGN 78 (135)
T ss_pred EEECCCCCC
Confidence 457888885
No 30
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=63.33 E-value=3.2 Score=27.73 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=15.5
Q ss_pred ccccccCCCCC----eeEeCCCCCcc
Q 047076 19 AAICQECKYKV----SKYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~~----~kY~CP~C~~~ 40 (86)
...|..|+... ..+.||.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 70 QAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred EEEcccCCCEEecCCcCccCcCCCCC
Confidence 46798898633 34779999854
No 31
>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=62.73 E-value=5.3 Score=20.51 Aligned_cols=19 Identities=26% Similarity=0.856 Sum_probs=9.1
Q ss_pred ccccCCCCC---eeEeCCCCCc
Q 047076 21 ICQECKYKV---SKYKCPGCSI 39 (86)
Q Consensus 21 ~C~vC~~~~---~kY~CP~C~~ 39 (86)
.|.+|+... ..|.|+.|..
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp --TTTS----S--EEE-TTT--
T ss_pred cCCcCCCcCCCCceEECccCCC
Confidence 588999754 4899999874
No 32
>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=62.51 E-value=2.2 Score=19.53 Aligned_cols=20 Identities=25% Similarity=0.559 Sum_probs=12.3
Q ss_pred EeCCCCCccccccccccccc
Q 047076 32 YKCPGCSIRTCSLACVKAHK 51 (86)
Q Consensus 32 Y~CP~C~~~~CSl~C~k~Hk 51 (86)
|.|+.|+..+=+..-++.|.
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 67888887776666655554
No 33
>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=61.43 E-value=3.5 Score=19.35 Aligned_cols=18 Identities=39% Similarity=0.683 Sum_probs=11.0
Q ss_pred EeCCCCCccccccccccc
Q 047076 32 YKCPGCSIRTCSLACVKA 49 (86)
Q Consensus 32 Y~CP~C~~~~CSl~C~k~ 49 (86)
|+||.|+..+=+..=.+.
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 788888876644433333
No 34
>PRK00420 hypothetical protein; Validated
Probab=58.78 E-value=6.9 Score=26.68 Aligned_cols=29 Identities=17% Similarity=0.311 Sum_probs=20.6
Q ss_pred ccccccCCC-----CCeeEeCCCCCcccccccccccc
Q 047076 19 AAICQECKY-----KVSKYKCPGCSIRTCSLACVKAH 50 (86)
Q Consensus 19 ~~~C~vC~~-----~~~kY~CP~C~~~~CSl~C~k~H 50 (86)
...|.+|+. +.++.-||.|+. .+.+-..+
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~---~~~v~~~e 56 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGK---VYIVKSDE 56 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCC---eeeeccHH
Confidence 468999996 466788999998 44554433
No 35
>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=56.92 E-value=7.1 Score=20.75 Aligned_cols=11 Identities=27% Similarity=0.957 Sum_probs=7.8
Q ss_pred eEeCCCCCccc
Q 047076 31 KYKCPGCSIRT 41 (86)
Q Consensus 31 kY~CP~C~~~~ 41 (86)
+++||.|+..+
T Consensus 2 ~~~CP~C~~~~ 12 (38)
T TIGR02098 2 RIQCPNCKTSF 12 (38)
T ss_pred EEECCCCCCEE
Confidence 46788888753
No 36
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.57 E-value=12 Score=28.96 Aligned_cols=25 Identities=24% Similarity=0.656 Sum_probs=19.0
Q ss_pred cccccCCCCCe--eEeCCCCCccccccc
Q 047076 20 AICQECKYKVS--KYKCPGCSIRTCSLA 45 (86)
Q Consensus 20 ~~C~vC~~~~~--kY~CP~C~~~~CSl~ 45 (86)
..|. |..+.. -|.||+|...+|++.
T Consensus 243 a~Cf-Ch~k~v~~GyvCs~Clsi~C~~p 269 (279)
T TIGR00627 243 ASCF-CHHQLVSIGFVCSVCLSVLCQYT 269 (279)
T ss_pred ceee-ecCccccceEECCCccCCcCCCC
Confidence 4676 665444 599999999999874
No 37
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=56.06 E-value=7.5 Score=26.76 Aligned_cols=16 Identities=31% Similarity=0.740 Sum_probs=12.0
Q ss_pred CCeeEeCCCCCccccc
Q 047076 28 KVSKYKCPGCSIRTCS 43 (86)
Q Consensus 28 ~~~kY~CP~C~~~~CS 43 (86)
+...|.||.|+.+|=.
T Consensus 96 ~~~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 96 NNAYYKCPNCQSKYTF 111 (147)
T ss_pred CCcEEECcCCCCEeeH
Confidence 3468999999877744
No 38
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.04 E-value=21 Score=24.45 Aligned_cols=39 Identities=26% Similarity=0.539 Sum_probs=27.8
Q ss_pred cccccCCCC--------------CeeEeCCCCCcccccccccccccccccCCC
Q 047076 20 AICQECKYK--------------VSKYKCPGCSIRTCSLACVKAHKQRTGCSG 58 (86)
Q Consensus 20 ~~C~vC~~~--------------~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g 58 (86)
..|..|+.. .+.|+|++|...+|--==...|....+|.|
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPG 108 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPG 108 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcC
Confidence 469999862 347999999999984333456666666665
No 39
>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=55.02 E-value=5.4 Score=26.71 Aligned_cols=23 Identities=30% Similarity=0.839 Sum_probs=15.9
Q ss_pred ccccccCCCCC----eeEeCCCCCccc
Q 047076 19 AAICQECKYKV----SKYKCPGCSIRT 41 (86)
Q Consensus 19 ~~~C~vC~~~~----~kY~CP~C~~~~ 41 (86)
...|..|+... ..+.||+|+.+.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCCcCCC
Confidence 46788898643 256799988653
No 40
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=54.16 E-value=7.6 Score=21.70 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=8.8
Q ss_pred eEeCCCCCccc
Q 047076 31 KYKCPGCSIRT 41 (86)
Q Consensus 31 kY~CP~C~~~~ 41 (86)
.|+||+|+...
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 58999998754
No 41
>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=54.10 E-value=3.5 Score=20.13 Aligned_cols=22 Identities=27% Similarity=0.706 Sum_probs=18.8
Q ss_pred EeCCCCCccccccccccccccc
Q 047076 32 YKCPGCSIRTCSLACVKAHKQR 53 (86)
Q Consensus 32 Y~CP~C~~~~CSl~C~k~Hk~~ 53 (86)
|+|..|+..+=++.=+..|+..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCccCCccCChhHHHHHhHH
Confidence 8899999999888888888764
No 42
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.78 E-value=6.7 Score=26.34 Aligned_cols=22 Identities=23% Similarity=0.733 Sum_probs=15.0
Q ss_pred ccccccCCCCCe----eE-eCCCCCcc
Q 047076 19 AAICQECKYKVS----KY-KCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~~~----kY-~CP~C~~~ 40 (86)
...|..|+.... .| +||+|+.+
T Consensus 71 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 71 ELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred EEEhhhCCCccccCCccCCcCcCCCCC
Confidence 467999986432 24 49999865
No 43
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=52.59 E-value=5.9 Score=25.44 Aligned_cols=12 Identities=50% Similarity=1.052 Sum_probs=10.1
Q ss_pred eEeCCCCCcccc
Q 047076 31 KYKCPGCSIRTC 42 (86)
Q Consensus 31 kY~CP~C~~~~C 42 (86)
||.||-|+.++=
T Consensus 1 K~~CPCCg~~Tl 12 (78)
T PF14206_consen 1 KYPCPCCGYYTL 12 (78)
T ss_pred CccCCCCCcEEe
Confidence 789999998874
No 44
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=52.23 E-value=12 Score=25.63 Aligned_cols=20 Identities=35% Similarity=0.973 Sum_probs=14.6
Q ss_pred cccCCCC--CeeEeCCCCCccc
Q 047076 22 CQECKYK--VSKYKCPGCSIRT 41 (86)
Q Consensus 22 C~vC~~~--~~kY~CP~C~~~~ 41 (86)
|-||+.+ ..+++||.|++..
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 6788863 3489999888653
No 45
>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=52.14 E-value=3.5 Score=27.45 Aligned_cols=23 Identities=26% Similarity=0.837 Sum_probs=14.4
Q ss_pred ccccccCCCCCe----eEeCCCCCccc
Q 047076 19 AAICQECKYKVS----KYKCPGCSIRT 41 (86)
Q Consensus 19 ~~~C~vC~~~~~----kY~CP~C~~~~ 41 (86)
...|..|+.... .+.||.|+...
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred cEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 467999996432 57799998753
No 46
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.94 E-value=15 Score=26.52 Aligned_cols=21 Identities=29% Similarity=0.765 Sum_probs=15.9
Q ss_pred ccccccCCCC-CeeEeCCCCCc
Q 047076 19 AAICQECKYK-VSKYKCPGCSI 39 (86)
Q Consensus 19 ~~~C~vC~~~-~~kY~CP~C~~ 39 (86)
...|.+||.- ...++||+|+.
T Consensus 309 S~~C~~cg~~~~r~~~C~~cg~ 330 (364)
T COG0675 309 SKTCPCCGHLSGRLFKCPRCGF 330 (364)
T ss_pred cccccccCCccceeEECCCCCC
Confidence 4689999972 24799999985
No 47
>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=50.06 E-value=7.3 Score=21.53 Aligned_cols=10 Identities=40% Similarity=1.172 Sum_probs=8.2
Q ss_pred EeCCCCCccc
Q 047076 32 YKCPGCSIRT 41 (86)
Q Consensus 32 Y~CP~C~~~~ 41 (86)
|+||.|+...
T Consensus 1 m~Cp~Cg~~~ 10 (43)
T PF08271_consen 1 MKCPNCGSKE 10 (43)
T ss_dssp ESBTTTSSSE
T ss_pred CCCcCCcCCc
Confidence 7899988876
No 48
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.42 E-value=8.9 Score=19.02 Aligned_cols=6 Identities=50% Similarity=1.708 Sum_probs=2.9
Q ss_pred CCCCCc
Q 047076 34 CPGCSI 39 (86)
Q Consensus 34 CP~C~~ 39 (86)
||.|+.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555544
No 49
>PF12773 DZR: Double zinc ribbon
Probab=48.75 E-value=12 Score=20.86 Aligned_cols=24 Identities=29% Similarity=0.805 Sum_probs=16.5
Q ss_pred ccccccccCCCCCe-----eEeCCCCCcc
Q 047076 17 KEAAICQECKYKVS-----KYKCPGCSIR 40 (86)
Q Consensus 17 ~~~~~C~vC~~~~~-----kY~CP~C~~~ 40 (86)
....+|..|+.... ...||.|+..
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcCC
Confidence 34678888887443 4678888764
No 50
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=48.63 E-value=14 Score=23.44 Aligned_cols=23 Identities=35% Similarity=0.911 Sum_probs=16.4
Q ss_pred cccccccCCCCCeeEeCCCCCcccccccc
Q 047076 18 EAAICQECKYKVSKYKCPGCSIRTCSLAC 46 (86)
Q Consensus 18 ~~~~C~vC~~~~~kY~CP~C~~~~CSl~C 46 (86)
....|.+|+..-.. ..+||||.|
T Consensus 48 ~~~~C~~C~R~L~d------~~~fCSl~C 70 (72)
T PF04640_consen 48 SGNICETCHRSLQD------PYRFCSLSC 70 (72)
T ss_pred CCCccCCCCCCCCC------CCeEEeeeE
Confidence 46789999864321 268999998
No 51
>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=48.23 E-value=11 Score=20.01 Aligned_cols=12 Identities=25% Similarity=0.783 Sum_probs=9.4
Q ss_pred eeEeCCCCCccc
Q 047076 30 SKYKCPGCSIRT 41 (86)
Q Consensus 30 ~kY~CP~C~~~~ 41 (86)
..|+|+.|+..+
T Consensus 4 Y~y~C~~Cg~~f 15 (41)
T smart00834 4 YEYRCEDCGHTF 15 (41)
T ss_pred EEEEcCCCCCEE
Confidence 468999998855
No 52
>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=48.10 E-value=16 Score=21.51 Aligned_cols=26 Identities=35% Similarity=0.728 Sum_probs=14.2
Q ss_pred cccccccCCCCC----eeEeCCCCCccccc
Q 047076 18 EAAICQECKYKV----SKYKCPGCSIRTCS 43 (86)
Q Consensus 18 ~~~~C~vC~~~~----~kY~CP~C~~~~CS 43 (86)
....|.+|+..- .++.|..||..+|+
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCS 37 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEEC
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECC
Confidence 356899998743 48999999999995
No 53
>COG5195 Uncharacterized conserved protein [Function unknown]
Probab=47.23 E-value=16 Score=25.17 Aligned_cols=33 Identities=18% Similarity=0.359 Sum_probs=25.8
Q ss_pred cccccccccCCCCCeeEeCCCCCccccccccccc
Q 047076 16 AKEAAICQECKYKVSKYKCPGCSIRTCSLACVKA 49 (86)
Q Consensus 16 ~~~~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~ 49 (86)
++++..|.|=|- .+.|+||.=+++|=..+=|+.
T Consensus 63 ~P~~KyCDvTGL-~a~Yt~P~t~lrYhn~eiY~l 95 (118)
T COG5195 63 KPRMKYCDVTGL-PAPYTCPNTGLRYHNSEIYKL 95 (118)
T ss_pred ccccccccccCC-cccccCCCcCceeccHHHHHH
Confidence 466789999886 799999999999865554443
No 54
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.72 E-value=9 Score=25.96 Aligned_cols=21 Identities=33% Similarity=0.861 Sum_probs=14.2
Q ss_pred ccccccCCCCC-----e------eEeCCCCCcc
Q 047076 19 AAICQECKYKV-----S------KYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~~-----~------kY~CP~C~~~ 40 (86)
...| -|+... . .+.||.|+..
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK 101 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCC
Confidence 4679 898651 1 2679999843
No 55
>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=46.48 E-value=7.9 Score=23.91 Aligned_cols=11 Identities=45% Similarity=1.147 Sum_probs=8.6
Q ss_pred EeCCCCCcccc
Q 047076 32 YKCPGCSIRTC 42 (86)
Q Consensus 32 Y~CP~C~~~~C 42 (86)
|+||+|+-...
T Consensus 1 y~C~KCg~~~~ 11 (64)
T PF09855_consen 1 YKCPKCGNEEY 11 (64)
T ss_pred CCCCCCCCcce
Confidence 78999997543
No 56
>PRK04023 DNA polymerase II large subunit; Validated
Probab=46.37 E-value=12 Score=34.39 Aligned_cols=23 Identities=22% Similarity=0.561 Sum_probs=18.4
Q ss_pred cccccccCCCCCeeEeCCCCCcc
Q 047076 18 EAAICQECKYKVSKYKCPGCSIR 40 (86)
Q Consensus 18 ~~~~C~vC~~~~~kY~CP~C~~~ 40 (86)
..++|.-|+......+||.|+..
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~ 647 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTH 647 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCC
Confidence 35789999988788899999854
No 57
>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=46.20 E-value=7.1 Score=24.05 Aligned_cols=24 Identities=29% Similarity=0.837 Sum_probs=14.1
Q ss_pred ccccccccCCCCC--------eeEeCCCCCcc
Q 047076 17 KEAAICQECKYKV--------SKYKCPGCSIR 40 (86)
Q Consensus 17 ~~~~~C~vC~~~~--------~kY~CP~C~~~ 40 (86)
....+|++|+... ++|.||.|+..
T Consensus 39 ~~~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~~ 70 (71)
T PF05495_consen 39 VKRVICGKCRTEQPIDEYSCGADYFCPICGLY 70 (71)
T ss_dssp --EEEETTT--EEES-SBTT--SEEETTTTEE
T ss_pred ccCeECCCCCCccChhhhhcCCCccCcCcCCC
Confidence 3367899998532 35899988753
No 58
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=46.03 E-value=9.8 Score=25.44 Aligned_cols=22 Identities=27% Similarity=0.753 Sum_probs=14.8
Q ss_pred ccccccCCCCCe-----eEeCCCCCcc
Q 047076 19 AAICQECKYKVS-----KYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~~~-----kY~CP~C~~~ 40 (86)
...|..|+.... .+.||.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCcCCC
Confidence 467888986422 2569998864
No 59
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=46.00 E-value=9.5 Score=31.05 Aligned_cols=51 Identities=31% Similarity=0.565 Sum_probs=36.5
Q ss_pred cccCCCCCCCCcccccccccccCCC--------------CCeeEeCCCCCcccccccccccccccccCCC
Q 047076 3 FQEGPTSTNQNPKAKEAAICQECKY--------------KVSKYKCPGCSIRTCSLACVKAHKQRTGCSG 58 (86)
Q Consensus 3 ~~~~p~s~~~~~~~~~~~~C~vC~~--------------~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g 58 (86)
++|.|.+++. ...-|-+|+. ..+.|+|+.|-..+|+--=...|.....|-|
T Consensus 351 f~E~p~~~~~-----ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~C~g 415 (421)
T COG5151 351 FVEKPEGTNP-----KSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIG 415 (421)
T ss_pred cccccCCCCC-----CCccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHhhCCC
Confidence 4556655543 4458999985 2578999999999998655667777666655
No 60
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=45.63 E-value=5.9 Score=24.30 Aligned_cols=33 Identities=24% Similarity=0.548 Sum_probs=18.7
Q ss_pred CCCCCCCCcccccccccccCCCCCeeEeCCCCC
Q 047076 6 GPTSTNQNPKAKEAAICQECKYKVSKYKCPGCS 38 (86)
Q Consensus 6 ~p~s~~~~~~~~~~~~C~vC~~~~~kY~CP~C~ 38 (86)
+|.|.++.--.-.=.+|.-|....-...||.|+
T Consensus 16 p~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCg 48 (57)
T PF06906_consen 16 PPDSPEAYICSFECTFCADCAETMLNGVCPNCG 48 (57)
T ss_pred CCCCCcceEEeEeCcccHHHHHHHhcCcCcCCC
Confidence 344434443334446677777654467788765
No 61
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=45.33 E-value=4.2 Score=34.71 Aligned_cols=32 Identities=22% Similarity=0.445 Sum_probs=26.2
Q ss_pred cccccCCCCCeeEeCCCCCccccccccccccccc
Q 047076 20 AICQECKYKVSKYKCPGCSIRTCSLACVKAHKQR 53 (86)
Q Consensus 20 ~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~Hk~~ 53 (86)
.-|..|..+...|-|= +.-|||++|.+.|...
T Consensus 528 QWC~nC~~EAiy~CCW--NTSYCsveCQQ~HW~~ 559 (588)
T KOG3612|consen 528 QWCYNCLDEAIYHCCW--NTSYCSVECQQGHWPE 559 (588)
T ss_pred HHHHhhhHHHHHHhhc--cccccCcchhhccchh
Confidence 5699999865566666 8999999999998764
No 62
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=44.98 E-value=12 Score=27.05 Aligned_cols=22 Identities=27% Similarity=0.683 Sum_probs=15.5
Q ss_pred ccccccCCC---CCeeEeCCCCCcc
Q 047076 19 AAICQECKY---KVSKYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~---~~~kY~CP~C~~~ 40 (86)
.-+|.|||. ..+.=+||.|+.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 357888884 3556788888865
No 63
>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=44.55 E-value=37 Score=19.28 Aligned_cols=32 Identities=25% Similarity=0.589 Sum_probs=23.3
Q ss_pred ccccCCCCC---eeEeCCCCCcccccccccccccc
Q 047076 21 ICQECKYKV---SKYKCPGCSIRTCSLACVKAHKQ 52 (86)
Q Consensus 21 ~C~vC~~~~---~kY~CP~C~~~~CSl~C~k~Hk~ 52 (86)
.|.+|.... ..|+|..|.-..=.+.|+...++
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 478888644 46999999766666788876544
No 64
>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=44.39 E-value=14 Score=25.87 Aligned_cols=14 Identities=21% Similarity=0.505 Sum_probs=10.6
Q ss_pred CCeeEeCCCCCccc
Q 047076 28 KVSKYKCPGCSIRT 41 (86)
Q Consensus 28 ~~~kY~CP~C~~~~ 41 (86)
+...|.||+|+.+|
T Consensus 106 ~~~~Y~Cp~c~~r~ 119 (158)
T TIGR00373 106 NNMFFICPNMCVRF 119 (158)
T ss_pred CCCeEECCCCCcEe
Confidence 34678888888777
No 65
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=44.26 E-value=11 Score=25.43 Aligned_cols=26 Identities=35% Similarity=1.041 Sum_probs=20.6
Q ss_pred cccccCCCC---CeeEeCCCCCcccccccc
Q 047076 20 AICQECKYK---VSKYKCPGCSIRTCSLAC 46 (86)
Q Consensus 20 ~~C~vC~~~---~~kY~CP~C~~~~CSl~C 46 (86)
-+|. |... .-.|-||+|+.+-|..+|
T Consensus 61 DlCD-CL~~~C~GC~~PC~~C~S~KCG~~C 89 (103)
T PF14949_consen 61 DLCD-CLDEDCPGCHYPCPKCGSRKCGPEC 89 (103)
T ss_pred cccc-ccCCCCCCccccCCCCCCCccChhh
Confidence 4666 5542 248999999999999999
No 66
>PHA00616 hypothetical protein
Probab=43.49 E-value=3.5 Score=23.90 Aligned_cols=21 Identities=24% Similarity=0.260 Sum_probs=16.7
Q ss_pred EeCCCCCcccccccccccccc
Q 047076 32 YKCPGCSIRTCSLACVKAHKQ 52 (86)
Q Consensus 32 Y~CP~C~~~~CSl~C~k~Hk~ 52 (86)
|+||+|+..+.-..=.+.|-.
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r 22 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLL 22 (44)
T ss_pred CccchhhHHHhhHHHHHHHHH
Confidence 899999998887776666654
No 67
>PRK01343 zinc-binding protein; Provisional
Probab=43.38 E-value=11 Score=23.02 Aligned_cols=26 Identities=23% Similarity=0.450 Sum_probs=17.6
Q ss_pred ccccccCCCCCeeEeCCCCCccccccccccc
Q 047076 19 AAICQECKYKVSKYKCPGCSIRTCSLACVKA 49 (86)
Q Consensus 19 ~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~ 49 (86)
...|-||+.... . + ..++||-.|-.+
T Consensus 9 ~~~CP~C~k~~~-~--~--~rPFCS~RC~~i 34 (57)
T PRK01343 9 TRPCPECGKPST-R--E--AYPFCSERCRDI 34 (57)
T ss_pred CCcCCCCCCcCc-C--C--CCcccCHHHhhh
Confidence 567999997432 1 1 458999988544
No 68
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=43.18 E-value=11 Score=23.47 Aligned_cols=15 Identities=20% Similarity=0.505 Sum_probs=11.7
Q ss_pred CCeeEeCCCCCcccc
Q 047076 28 KVSKYKCPGCSIRTC 42 (86)
Q Consensus 28 ~~~kY~CP~C~~~~C 42 (86)
.+...+||+|+.-+=
T Consensus 14 GE~~lrCPRC~~~FR 28 (65)
T COG4049 14 GEEFLRCPRCGMVFR 28 (65)
T ss_pred CceeeeCCchhHHHH
Confidence 356899999998653
No 69
>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=43.17 E-value=10 Score=28.27 Aligned_cols=28 Identities=21% Similarity=0.651 Sum_probs=21.2
Q ss_pred ccccccCCC-CCeeEeCCCCCcccccccc
Q 047076 19 AAICQECKY-KVSKYKCPGCSIRTCSLAC 46 (86)
Q Consensus 19 ~~~C~vC~~-~~~kY~CP~C~~~~CSl~C 46 (86)
--+|.||.. ++-.=+||+|+..-=++.|
T Consensus 162 cilCtvCe~r~w~g~~CPKCGr~G~pi~C 190 (200)
T PF12387_consen 162 CILCTVCEGREWKGGNCPKCGRHGKPITC 190 (200)
T ss_pred eEEEeeeecCccCCCCCCcccCCCCCeec
Confidence 457888875 5567789999987666666
No 70
>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=42.71 E-value=11 Score=25.34 Aligned_cols=14 Identities=36% Similarity=0.871 Sum_probs=10.8
Q ss_pred eEeCCCCCcccccc
Q 047076 31 KYKCPGCSIRTCSL 44 (86)
Q Consensus 31 kY~CP~C~~~~CSl 44 (86)
|-.||.|+.||--|
T Consensus 9 KR~Cp~CG~kFYDL 22 (108)
T PF09538_consen 9 KRTCPSCGAKFYDL 22 (108)
T ss_pred cccCCCCcchhccC
Confidence 77788888888666
No 71
>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=42.60 E-value=22 Score=18.26 Aligned_cols=18 Identities=28% Similarity=0.802 Sum_probs=12.6
Q ss_pred ccccCCC--CCe-eEeCCCCC
Q 047076 21 ICQECKY--KVS-KYKCPGCS 38 (86)
Q Consensus 21 ~C~vC~~--~~~-kY~CP~C~ 38 (86)
.|+||+. +.. .|+|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 4888886 334 68887776
No 72
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=42.52 E-value=13 Score=30.58 Aligned_cols=26 Identities=19% Similarity=0.662 Sum_probs=18.4
Q ss_pred ccccccCCC---CCe--eEeCCCCCcccccc
Q 047076 19 AAICQECKY---KVS--KYKCPGCSIRTCSL 44 (86)
Q Consensus 19 ~~~C~vC~~---~~~--kY~CP~C~~~~CSl 44 (86)
..+|..|+. ..+ -||||+|+.++=+.
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 358888984 112 69999999987543
No 73
>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=42.46 E-value=16 Score=19.46 Aligned_cols=28 Identities=14% Similarity=0.290 Sum_probs=22.3
Q ss_pred ccccCCCCCeeEeCCCCCccccccccccc
Q 047076 21 ICQECKYKVSKYKCPGCSIRTCSLACVKA 49 (86)
Q Consensus 21 ~C~vC~~~~~kY~CP~C~~~~CSl~C~k~ 49 (86)
.|.|=+. +++|+-|+=+++|-+++-|+.
T Consensus 2 ~C~iTgl-pA~Y~DP~T~l~Y~n~~ayk~ 29 (30)
T PF08265_consen 2 YCDITGL-PARYRDPKTGLPYANSEAYKI 29 (30)
T ss_pred cccccCC-CccccCCCCCCcccCHHHhhc
Confidence 5777564 899999999999988876653
No 74
>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=41.74 E-value=13 Score=33.94 Aligned_cols=24 Identities=29% Similarity=0.559 Sum_probs=19.2
Q ss_pred cccccccCCCCCeeEeCCCCCccc
Q 047076 18 EAAICQECKYKVSKYKCPGCSIRT 41 (86)
Q Consensus 18 ~~~~C~vC~~~~~kY~CP~C~~~~ 41 (86)
..+.|.-|+.-..+.+||.|+.++
T Consensus 624 ~~RKCPkCG~yTlk~rCP~CG~~T 647 (1095)
T TIGR00354 624 AIRKCPQCGKESFWLKCPVCGELT 647 (1095)
T ss_pred EEEECCCCCcccccccCCCCCCcc
Confidence 357788888888888888888775
No 75
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=41.71 E-value=17 Score=28.90 Aligned_cols=19 Identities=47% Similarity=1.267 Sum_probs=15.6
Q ss_pred ccccCCCCCeeE--eCCCCCc
Q 047076 21 ICQECKYKVSKY--KCPGCSI 39 (86)
Q Consensus 21 ~C~vC~~~~~kY--~CP~C~~ 39 (86)
+|..|+....|+ +||.|+.
T Consensus 2 ~c~~cg~~~~~~~g~cp~c~~ 22 (372)
T cd01121 2 VCSECGYVSPKWLGKCPECGE 22 (372)
T ss_pred CCCCCCCCCCCccEECcCCCC
Confidence 589999877765 8999985
No 76
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=41.30 E-value=17 Score=26.11 Aligned_cols=14 Identities=36% Similarity=0.755 Sum_probs=11.2
Q ss_pred CeeEeCCCCCcccc
Q 047076 29 VSKYKCPGCSIRTC 42 (86)
Q Consensus 29 ~~kY~CP~C~~~~C 42 (86)
...|.||+|+.+|=
T Consensus 115 ~~~Y~Cp~C~~ryt 128 (178)
T PRK06266 115 NMFFFCPNCHIRFT 128 (178)
T ss_pred CCEEECCCCCcEEe
Confidence 46899999988873
No 77
>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=41.16 E-value=23 Score=21.01 Aligned_cols=25 Identities=28% Similarity=0.759 Sum_probs=18.4
Q ss_pred ccccccccccCCC-CCeeEeCCCCCc
Q 047076 15 KAKEAAICQECKY-KVSKYKCPGCSI 39 (86)
Q Consensus 15 ~~~~~~~C~vC~~-~~~kY~CP~C~~ 39 (86)
+.+....|..|++ ..+-.-||.|+.
T Consensus 22 ~~p~l~~C~~cG~~~~~H~vc~~cG~ 47 (55)
T TIGR01031 22 TAPTLVVCPNCGEFKLPHRVCPSCGY 47 (55)
T ss_pred cCCcceECCCCCCcccCeeECCccCe
Confidence 3455677999996 456788999984
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=40.77 E-value=18 Score=19.54 Aligned_cols=10 Identities=30% Similarity=1.019 Sum_probs=6.1
Q ss_pred EeCCCCCccc
Q 047076 32 YKCPGCSIRT 41 (86)
Q Consensus 32 Y~CP~C~~~~ 41 (86)
-+||+|+..|
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 4566666654
No 79
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=40.42 E-value=24 Score=21.28 Aligned_cols=23 Identities=26% Similarity=0.567 Sum_probs=17.9
Q ss_pred ccccccCCCC----CeeEeCCCCCccc
Q 047076 19 AAICQECKYK----VSKYKCPGCSIRT 41 (86)
Q Consensus 19 ~~~C~vC~~~----~~kY~CP~C~~~~ 41 (86)
...|.+|+.. ...-.||-|+++|
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcc
Confidence 4579999963 2367899999988
No 80
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.90 E-value=18 Score=33.18 Aligned_cols=23 Identities=30% Similarity=0.768 Sum_probs=16.4
Q ss_pred ccccccCCCC-CeeEeCCCCCccc
Q 047076 19 AAICQECKYK-VSKYKCPGCSIRT 41 (86)
Q Consensus 19 ~~~C~vC~~~-~~kY~CP~C~~~~ 41 (86)
...|..||.. ...|+||+|+...
T Consensus 638 ~frCP~CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 638 YRRCPFCGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred cccCCCCCCCCCcceeCccccCcC
Confidence 3578889863 3588899886543
No 81
>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=39.42 E-value=19 Score=19.09 Aligned_cols=21 Identities=19% Similarity=0.670 Sum_probs=14.2
Q ss_pred ccccccCCCCCe----eEeCCCCCc
Q 047076 19 AAICQECKYKVS----KYKCPGCSI 39 (86)
Q Consensus 19 ~~~C~vC~~~~~----kY~CP~C~~ 39 (86)
...|.+|+..-. -|+|+.|+.
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCc
Confidence 468999986333 577776654
No 82
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=38.48 E-value=21 Score=29.06 Aligned_cols=43 Identities=23% Similarity=0.590 Sum_probs=31.4
Q ss_pred ccccccccCC---CCCeeEeCCCCCcccccccccccccccccCCCC
Q 047076 17 KEAAICQECK---YKVSKYKCPGCSIRTCSLACVKAHKQRTGCSGN 59 (86)
Q Consensus 17 ~~~~~C~vC~---~~~~kY~CP~C~~~~CSl~C~k~Hk~~~~C~g~ 59 (86)
.....|-+|+ .....|+|+.|...+|.-==...|.....|.|=
T Consensus 328 ~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgC 373 (378)
T KOG2807|consen 328 NGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGC 373 (378)
T ss_pred CCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCc
Confidence 3456799993 245699999999999965445677777777663
No 83
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=38.12 E-value=18 Score=19.60 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=6.7
Q ss_pred EeCCCCCccc
Q 047076 32 YKCPGCSIRT 41 (86)
Q Consensus 32 Y~CP~C~~~~ 41 (86)
-+||.|+..|
T Consensus 3 i~CP~C~~~f 12 (37)
T PF13719_consen 3 ITCPNCQTRF 12 (37)
T ss_pred EECCCCCceE
Confidence 4678777654
No 84
>PF14353 CpXC: CpXC protein
Probab=38.08 E-value=20 Score=23.72 Aligned_cols=14 Identities=21% Similarity=0.812 Sum_probs=11.3
Q ss_pred CCeeEeCCCCCccc
Q 047076 28 KVSKYKCPGCSIRT 41 (86)
Q Consensus 28 ~~~kY~CP~C~~~~ 41 (86)
.-..|+||.|+...
T Consensus 35 ~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 35 SLFSFTCPSCGHKF 48 (128)
T ss_pred CcCEEECCCCCCce
Confidence 45689999999765
No 85
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=38.07 E-value=20 Score=19.67 Aligned_cols=11 Identities=45% Similarity=1.081 Sum_probs=8.4
Q ss_pred CCeeEeCCCCC
Q 047076 28 KVSKYKCPGCS 38 (86)
Q Consensus 28 ~~~kY~CP~C~ 38 (86)
...+|.||.|+
T Consensus 37 ~~~~y~C~~C~ 47 (47)
T PF13005_consen 37 VRHKYACPCCG 47 (47)
T ss_pred EeceEECCCCC
Confidence 34689999885
No 86
>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=38.04 E-value=15 Score=18.23 Aligned_cols=12 Identities=42% Similarity=0.916 Sum_probs=8.5
Q ss_pred eeEeCCCCCccc
Q 047076 30 SKYKCPGCSIRT 41 (86)
Q Consensus 30 ~kY~CP~C~~~~ 41 (86)
-.|.||-|+..+
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 458888887653
No 87
>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=37.97 E-value=22 Score=20.02 Aligned_cols=30 Identities=23% Similarity=0.619 Sum_probs=21.4
Q ss_pred cccccCCCC----CeeEeCCCCCcccccccccccc
Q 047076 20 AICQECKYK----VSKYKCPGCSIRTCSLACVKAH 50 (86)
Q Consensus 20 ~~C~vC~~~----~~kY~CP~C~~~~CSl~C~k~H 50 (86)
..|.+|+.. ..++.|..|+..+|+ .|...+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~-~C~~~~ 36 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCS-KCSSNR 36 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcCh-HHcCCe
Confidence 467778752 348999999999997 454433
No 88
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=37.84 E-value=18 Score=29.48 Aligned_cols=25 Identities=40% Similarity=1.084 Sum_probs=20.4
Q ss_pred cccccCCC--CCeeEeCCCCCccccccc
Q 047076 20 AICQECKY--KVSKYKCPGCSIRTCSLA 45 (86)
Q Consensus 20 ~~C~vC~~--~~~kY~CP~C~~~~CSl~ 45 (86)
.+|. |.. ..+-|-||+|-.+-|||.
T Consensus 296 s~Ca-CHs~~~~gGy~CP~CktkVCsLP 322 (421)
T COG5151 296 SVCA-CHSEVKGGGYECPVCKTKVCSLP 322 (421)
T ss_pred ccee-eeeeeccCceeCCcccceeecCC
Confidence 5777 764 456899999999999984
No 89
>PRK11823 DNA repair protein RadA; Provisional
Probab=37.27 E-value=23 Score=28.65 Aligned_cols=23 Identities=43% Similarity=0.931 Sum_probs=17.4
Q ss_pred ccccccccCCCCCee--EeCCCCCc
Q 047076 17 KEAAICQECKYKVSK--YKCPGCSI 39 (86)
Q Consensus 17 ~~~~~C~vC~~~~~k--Y~CP~C~~ 39 (86)
+..-+|..||....+ -+||.|+.
T Consensus 5 ~~~y~C~~Cg~~~~~~~g~Cp~C~~ 29 (446)
T PRK11823 5 KTAYVCQECGAESPKWLGRCPECGA 29 (446)
T ss_pred CCeEECCcCCCCCcccCeeCcCCCC
Confidence 345679999987665 48999975
No 90
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=36.70 E-value=24 Score=28.71 Aligned_cols=22 Identities=36% Similarity=0.845 Sum_probs=17.2
Q ss_pred cccccccCCCCCee--EeCCCCCc
Q 047076 18 EAAICQECKYKVSK--YKCPGCSI 39 (86)
Q Consensus 18 ~~~~C~vC~~~~~k--Y~CP~C~~ 39 (86)
..-+|..|+....+ -+||.|+.
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~ 29 (454)
T TIGR00416 6 SKFVCQHCGADSPKWQGKCPACHA 29 (454)
T ss_pred CeEECCcCCCCCccccEECcCCCC
Confidence 35679999987665 48999975
No 91
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=35.78 E-value=34 Score=19.89 Aligned_cols=23 Identities=17% Similarity=0.732 Sum_probs=16.7
Q ss_pred ccccccCCC-----CCeeEeCCCCCccc
Q 047076 19 AAICQECKY-----KVSKYKCPGCSIRT 41 (86)
Q Consensus 19 ~~~C~vC~~-----~~~kY~CP~C~~~~ 41 (86)
..+|..|+. ....+.|.+|+..+
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCCEE
Confidence 458888876 34488899988654
No 92
>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 PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=35.50 E-value=35 Score=23.87 Aligned_cols=35 Identities=23% Similarity=0.536 Sum_probs=26.6
Q ss_pred cCCCCCeeEeCCCCCcccccccccccc-cccccCCCC
Q 047076 24 ECKYKVSKYKCPGCSIRTCSLACVKAH-KQRTGCSGN 59 (86)
Q Consensus 24 vC~~~~~kY~CP~C~~~~CSl~C~k~H-k~~~~C~g~ 59 (86)
.|.+....|-|-.|..|||... .+.- .++..|+..
T Consensus 20 ~C~~~~~~~CCG~C~~ryCC~~-~~~~~~~q~~C~~~ 55 (179)
T PF13908_consen 20 NCPEGDFTFCCGTCSLRYCCSD-LKRARLDQGSCDNY 55 (179)
T ss_pred cCCCcCcceecCCccCcchhhh-hhhceecccccccc
Confidence 5777788999999999999888 5433 245578763
No 94
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=35.25 E-value=21 Score=30.87 Aligned_cols=22 Identities=27% Similarity=0.816 Sum_probs=16.0
Q ss_pred ccccccCCCCCe------eEeCCCCCcc
Q 047076 19 AAICQECKYKVS------KYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~~~------kY~CP~C~~~ 40 (86)
..+|..||...- .+.||.|+..
T Consensus 641 ~~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 641 IDECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred CcccCCCCCCccccCCCCCCcCcCCCCC
Confidence 468999997321 2799999864
No 95
>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=35.12 E-value=25 Score=29.58 Aligned_cols=22 Identities=32% Similarity=0.939 Sum_probs=16.3
Q ss_pred ccccccCCCCCee--EeCCCCCcc
Q 047076 19 AAICQECKYKVSK--YKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~~~k--Y~CP~C~~~ 40 (86)
..+|..|+..... ++||.|+..
T Consensus 524 ~~~C~~CG~~g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 524 VDVCEDCGYTGEGLNDKCPKCGSH 547 (579)
T ss_pred CccCCCCCCCCCCCCCcCcCCCCc
Confidence 4689999973333 689999974
No 96
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.11 E-value=32 Score=22.88 Aligned_cols=12 Identities=25% Similarity=0.789 Sum_probs=7.6
Q ss_pred CeeEeCCCCCcc
Q 047076 29 VSKYKCPGCSIR 40 (86)
Q Consensus 29 ~~kY~CP~C~~~ 40 (86)
+..+.||.|+..
T Consensus 19 pt~f~CP~Cge~ 30 (99)
T PRK14892 19 PKIFECPRCGKV 30 (99)
T ss_pred CcEeECCCCCCe
Confidence 446777777744
No 97
>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=34.90 E-value=17 Score=22.03 Aligned_cols=11 Identities=27% Similarity=0.356 Sum_probs=6.9
Q ss_pred ccccccccccc
Q 047076 39 IRTCSLACVKA 49 (86)
Q Consensus 39 ~~~CSl~C~k~ 49 (86)
.++||-.|-.+
T Consensus 21 rPFCS~RCk~i 31 (57)
T PF03884_consen 21 RPFCSERCKLI 31 (57)
T ss_dssp -SSSSHHHHHH
T ss_pred CCcccHhhccc
Confidence 46788888443
No 98
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=34.89 E-value=22 Score=30.34 Aligned_cols=21 Identities=33% Similarity=0.893 Sum_probs=16.1
Q ss_pred ccccccCCCC-CeeEeCCCCCc
Q 047076 19 AAICQECKYK-VSKYKCPGCSI 39 (86)
Q Consensus 19 ~~~C~vC~~~-~~kY~CP~C~~ 39 (86)
..+|..|+.. ...+.||.|+.
T Consensus 559 ~~~C~~CGy~g~~~~~CP~CG~ 580 (618)
T PRK14704 559 VDRCKCCSYHGVIGNECPSCGN 580 (618)
T ss_pred CeecCCCCCCCCcCccCcCCCC
Confidence 4689999973 23489999986
No 99
>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=34.72 E-value=22 Score=30.31 Aligned_cols=22 Identities=27% Similarity=0.766 Sum_probs=16.7
Q ss_pred cccccccCCCCC--eeEeCCCCCc
Q 047076 18 EAAICQECKYKV--SKYKCPGCSI 39 (86)
Q Consensus 18 ~~~~C~vC~~~~--~kY~CP~C~~ 39 (86)
...+|..|+.-. ..++||.|+.
T Consensus 531 ~~siC~~CGy~~g~~~~~CP~CGs 554 (586)
T TIGR02827 531 KITICNDCHHIDKRTLHRCPVCGS 554 (586)
T ss_pred CCeecCCCCCcCCCcCCcCcCCCC
Confidence 347899999732 3489999986
No 100
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=34.50 E-value=11 Score=22.65 Aligned_cols=19 Identities=32% Similarity=0.627 Sum_probs=12.9
Q ss_pred CcccccccccccccccccC
Q 047076 38 SIRTCSLACVKAHKQRTGC 56 (86)
Q Consensus 38 ~~~~CSl~C~k~Hk~~~~C 56 (86)
+..|||-+|-+.|.....|
T Consensus 27 Gk~YCS~aCA~gH~~~e~C 45 (52)
T PF02069_consen 27 GKYYCSEACANGHPNGEPC 45 (52)
T ss_dssp S-EESSHHHHHTSSS----
T ss_pred CEeeecHHHhccCCCCCCC
Confidence 6679999999999887677
No 101
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.08 E-value=20 Score=23.71 Aligned_cols=13 Identities=31% Similarity=0.549 Sum_probs=10.0
Q ss_pred CCeeEeCCCCCcc
Q 047076 28 KVSKYKCPGCSIR 40 (86)
Q Consensus 28 ~~~kY~CP~C~~~ 40 (86)
+.++|+||.|+..
T Consensus 33 q~a~y~CpfCgk~ 45 (90)
T PRK03976 33 MRAKHVCPVCGRP 45 (90)
T ss_pred HhcCccCCCCCCC
Confidence 3579999999654
No 102
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=34.01 E-value=37 Score=27.55 Aligned_cols=25 Identities=20% Similarity=0.545 Sum_probs=17.0
Q ss_pred ccccccccCCCC--CeeEeCCCCCccc
Q 047076 17 KEAAICQECKYK--VSKYKCPGCSIRT 41 (86)
Q Consensus 17 ~~~~~C~vC~~~--~~kY~CP~C~~~~ 41 (86)
.....|..|+.- ..+-+||||+..-
T Consensus 219 ~~l~~C~~Cd~l~~~~~a~CpRC~~~L 245 (419)
T PRK15103 219 QGLRSCSCCTAILPADQPVCPRCHTKG 245 (419)
T ss_pred cCCCcCCCCCCCCCCCCCCCCCCCCcC
Confidence 445569999952 2344799999763
No 103
>smart00336 BBOX B-Box-type zinc finger.
Probab=33.89 E-value=51 Score=17.05 Aligned_cols=28 Identities=18% Similarity=0.545 Sum_probs=22.1
Q ss_pred ccccccCCCCCeeEeCCCCCccccccccc
Q 047076 19 AAICQECKYKVSKYKCPGCSIRTCSLACV 47 (86)
Q Consensus 19 ~~~C~vC~~~~~kY~CP~C~~~~CSl~C~ 47 (86)
...|..+..+..+|-|..|+...| ..|.
T Consensus 3 ~~~C~~h~~~~~~~~C~~c~~~iC-~~C~ 30 (42)
T smart00336 3 PPKCDSHGDEPAEFFCEECGALLC-RTCD 30 (42)
T ss_pred CCcCCCCCCCceEEECCCCCcccc-cccC
Confidence 457888886678889999999988 4554
No 104
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=33.81 E-value=13 Score=23.33 Aligned_cols=21 Identities=24% Similarity=0.670 Sum_probs=8.9
Q ss_pred cccccCCCCCeeEeCCCCCcc
Q 047076 20 AICQECKYKVSKYKCPGCSIR 40 (86)
Q Consensus 20 ~~C~vC~~~~~kY~CP~C~~~ 40 (86)
.+|+.|-.....+.||.|..+
T Consensus 29 ~fCs~Ci~~~~~~~CPvC~~P 49 (65)
T PF14835_consen 29 IFCSSCIRDCIGSECPVCHTP 49 (65)
T ss_dssp -B-TTTGGGGTTTB-SSS--B
T ss_pred HHHHHHhHHhcCCCCCCcCCh
Confidence 456666554444556666554
No 105
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=33.45 E-value=40 Score=18.09 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=15.0
Q ss_pred ccccccCCC------CCeeEeCCCCCcc
Q 047076 19 AAICQECKY------KVSKYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~------~~~kY~CP~C~~~ 40 (86)
...|..|+. +.+.|.|+.|+.-
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 356888874 3456789988763
No 106
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=33.28 E-value=25 Score=30.64 Aligned_cols=21 Identities=38% Similarity=0.876 Sum_probs=16.8
Q ss_pred ccccccCCC-CCeeEeCCCCCc
Q 047076 19 AAICQECKY-KVSKYKCPGCSI 39 (86)
Q Consensus 19 ~~~C~vC~~-~~~kY~CP~C~~ 39 (86)
..+|..||. ..-.+.||.|+.
T Consensus 680 ~~~C~~CG~~~~~~~~CP~CG~ 701 (735)
T PRK07111 680 VDRCPVCGYLGVIEDKCPKCGS 701 (735)
T ss_pred CeecCCCCCCCCcCccCcCCCC
Confidence 468999996 334689999997
No 107
>PRK12496 hypothetical protein; Provisional
Probab=33.19 E-value=27 Score=24.71 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=5.9
Q ss_pred eEeCCCCCccc
Q 047076 31 KYKCPGCSIRT 41 (86)
Q Consensus 31 kY~CP~C~~~~ 41 (86)
+|+|++|+..|
T Consensus 127 ~~~C~gC~~~~ 137 (164)
T PRK12496 127 RKVCKGCKKKY 137 (164)
T ss_pred eEECCCCCccc
Confidence 45555555444
No 108
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=32.70 E-value=26 Score=29.25 Aligned_cols=22 Identities=50% Similarity=1.180 Sum_probs=18.6
Q ss_pred cccccccCCCCCeeE--eCCCCCc
Q 047076 18 EAAICQECKYKVSKY--KCPGCSI 39 (86)
Q Consensus 18 ~~~~C~vC~~~~~kY--~CP~C~~ 39 (86)
..-.|.-|+...+|+ +||.|+.
T Consensus 6 t~f~C~~CG~~s~KW~GkCp~Cg~ 29 (456)
T COG1066 6 TAFVCQECGYVSPKWLGKCPACGA 29 (456)
T ss_pred cEEEcccCCCCCccccccCCCCCC
Confidence 456799999988887 8999995
No 109
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=32.58 E-value=22 Score=23.59 Aligned_cols=14 Identities=43% Similarity=0.930 Sum_probs=10.5
Q ss_pred CCeeEeCCCCCccc
Q 047076 28 KVSKYKCPGCSIRT 41 (86)
Q Consensus 28 ~~~kY~CP~C~~~~ 41 (86)
+.++|+||.|+...
T Consensus 32 q~a~y~CpfCgk~~ 45 (91)
T TIGR00280 32 QKAKYVCPFCGKKT 45 (91)
T ss_pred HhcCccCCCCCCCc
Confidence 35799999997543
No 110
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=32.37 E-value=40 Score=17.22 Aligned_cols=26 Identities=19% Similarity=0.406 Sum_probs=21.0
Q ss_pred ccccCCCCCeeEeCCCCCccccccccc
Q 047076 21 ICQECKYKVSKYKCPGCSIRTCSLACV 47 (86)
Q Consensus 21 ~C~vC~~~~~kY~CP~C~~~~CSl~C~ 47 (86)
.|..++.++.+|-|..|+...| ..|.
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC-~~C~ 27 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLC-VDCD 27 (39)
T ss_pred CCCccCCcceEEEeCccChhhh-hhcC
Confidence 5788877688999999999999 4553
No 111
>PHA02942 putative transposase; Provisional
Probab=32.29 E-value=35 Score=27.18 Aligned_cols=22 Identities=27% Similarity=0.899 Sum_probs=15.3
Q ss_pred ccccccCCCCC-----eeEeCCCCCcc
Q 047076 19 AAICQECKYKV-----SKYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~~-----~kY~CP~C~~~ 40 (86)
...|..||... -.|+||.|+..
T Consensus 325 Sq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 325 SVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred CccCCCCCCccCcCCCCEEECCCCCCE
Confidence 36799998531 35889888753
No 112
>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=32.19 E-value=31 Score=17.84 Aligned_cols=22 Identities=23% Similarity=0.631 Sum_probs=10.5
Q ss_pred ccccccCCCC------CeeEeCCCCCcc
Q 047076 19 AAICQECKYK------VSKYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~------~~kY~CP~C~~~ 40 (86)
.++|..|+.. ...=+||.|+..
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 3578888742 235577777654
No 113
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=32.09 E-value=18 Score=23.95 Aligned_cols=13 Identities=38% Similarity=0.902 Sum_probs=9.7
Q ss_pred CeeEeCCCCCccc
Q 047076 29 VSKYKCPGCSIRT 41 (86)
Q Consensus 29 ~~kY~CP~C~~~~ 41 (86)
..+|+||.|+...
T Consensus 33 ~~ky~Cp~Cgk~~ 45 (90)
T PF01780_consen 33 HAKYTCPFCGKTS 45 (90)
T ss_dssp HS-BEESSSSSSE
T ss_pred hCCCcCCCCCCce
Confidence 4689999998765
No 114
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.06 E-value=27 Score=30.01 Aligned_cols=22 Identities=27% Similarity=0.779 Sum_probs=17.2
Q ss_pred cccccccCCCC--CeeEeCCCCCc
Q 047076 18 EAAICQECKYK--VSKYKCPGCSI 39 (86)
Q Consensus 18 ~~~~C~vC~~~--~~kY~CP~C~~ 39 (86)
...+|..|+.. .-.++||.|+.
T Consensus 565 ~~~iC~~CG~~~~g~~~~CP~CGs 588 (623)
T PRK08271 565 KITICNDCHHIDKRTGKRCPICGS 588 (623)
T ss_pred CCccCCCCCCcCCCCCcCCcCCCC
Confidence 34789999973 24799999986
No 115
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=31.83 E-value=53 Score=25.52 Aligned_cols=39 Identities=21% Similarity=0.347 Sum_probs=25.3
Q ss_pred cccCCCCCCCCcc----cccccccccCCC--------CCeeEeCCCCCccc
Q 047076 3 FQEGPTSTNQNPK----AKEAAICQECKY--------KVSKYKCPGCSIRT 41 (86)
Q Consensus 3 ~~~~p~s~~~~~~----~~~~~~C~vC~~--------~~~kY~CP~C~~~~ 41 (86)
..|.||.|+.... ...+..|.||+. ....-||+.|+.-|
T Consensus 45 ~~e~pppy~~~~s~~~~~~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEAT 95 (256)
T PF09788_consen 45 PGEPPPPYSPLGSPESGGAPVVTCRVCQSLIDIEGKMHQHVVKCSVCNEAT 95 (256)
T ss_pred CCCCCCCCCcccCCCCCCCceEEeecCCceecccCccceeeEECCCCCccc
Confidence 3566777774322 233678999983 23467899998766
No 116
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=31.18 E-value=57 Score=19.50 Aligned_cols=24 Identities=29% Similarity=0.699 Sum_probs=16.3
Q ss_pred cccccccccCCC-CCeeEeCCCCCc
Q 047076 16 AKEAAICQECKY-KVSKYKCPGCSI 39 (86)
Q Consensus 16 ~~~~~~C~vC~~-~~~kY~CP~C~~ 39 (86)
++....|..||+ ..+-.-||.|+.
T Consensus 24 ~~~l~~C~~CG~~~~~H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLPHRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCCeEECCCCCc
Confidence 344567888886 445677888874
No 117
>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=31.06 E-value=24 Score=20.43 Aligned_cols=11 Identities=45% Similarity=1.078 Sum_probs=7.3
Q ss_pred eEeCCCCCccc
Q 047076 31 KYKCPGCSIRT 41 (86)
Q Consensus 31 kY~CP~C~~~~ 41 (86)
||.|+.|+--|
T Consensus 1 ky~C~~CgyvY 11 (47)
T PF00301_consen 1 KYQCPVCGYVY 11 (47)
T ss_dssp EEEETTTSBEE
T ss_pred CcCCCCCCEEE
Confidence 57777777555
No 118
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.79 E-value=22 Score=23.49 Aligned_cols=13 Identities=38% Similarity=0.835 Sum_probs=10.2
Q ss_pred CCeeEeCCCCCcc
Q 047076 28 KVSKYKCPGCSIR 40 (86)
Q Consensus 28 ~~~kY~CP~C~~~ 40 (86)
+.++|+||.|+..
T Consensus 33 q~a~y~CpfCgk~ 45 (90)
T PTZ00255 33 QHAKYFCPFCGKH 45 (90)
T ss_pred HhCCccCCCCCCC
Confidence 3579999999754
No 119
>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=30.53 E-value=22 Score=20.96 Aligned_cols=22 Identities=27% Similarity=0.771 Sum_probs=16.1
Q ss_pred ccccccccCCC-CCeeEeCCCCC
Q 047076 17 KEAAICQECKY-KVSKYKCPGCS 38 (86)
Q Consensus 17 ~~~~~C~vC~~-~~~kY~CP~C~ 38 (86)
+....|..|+. ..+.+-||.|+
T Consensus 24 ~~l~~c~~cg~~~~~H~vc~~cG 46 (56)
T PF01783_consen 24 PNLVKCPNCGEPKLPHRVCPSCG 46 (56)
T ss_dssp TSEEESSSSSSEESTTSBCTTTB
T ss_pred cceeeeccCCCEecccEeeCCCC
Confidence 34567888986 44578888886
No 120
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=30.44 E-value=27 Score=22.43 Aligned_cols=15 Identities=33% Similarity=0.760 Sum_probs=8.5
Q ss_pred CCCeeEeCCCCCccc
Q 047076 27 YKVSKYKCPGCSIRT 41 (86)
Q Consensus 27 ~~~~kY~CP~C~~~~ 41 (86)
+|-+-|.||.|+.++
T Consensus 61 ENMs~~~Cp~Cg~~~ 75 (81)
T PF10609_consen 61 ENMSYFVCPHCGERI 75 (81)
T ss_dssp ECT-EEE-TTT--EE
T ss_pred ECCCccCCCCCCCee
Confidence 467899999998653
No 121
>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=30.06 E-value=29 Score=19.44 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=10.5
Q ss_pred eeEeCCCCCccccc
Q 047076 30 SKYKCPGCSIRTCS 43 (86)
Q Consensus 30 ~kY~CP~C~~~~CS 43 (86)
..|+|+.|+..+=-
T Consensus 4 Yey~C~~Cg~~fe~ 17 (52)
T TIGR02605 4 YEYRCTACGHRFEV 17 (52)
T ss_pred EEEEeCCCCCEeEE
Confidence 47999999985533
No 122
>PF06102 DUF947: Domain of unknown function (DUF947); InterPro: IPR009292 This is a family of eukaryotic proteins with unknown function.
Probab=30.00 E-value=25 Score=25.08 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=19.6
Q ss_pred CcceeeecC-CCChhhhhhhcccccC
Q 047076 61 NVTQFVPLS-QFNDNILLSATKLSSK 85 (86)
Q Consensus 61 ~~~~~v~~~-~~~~~~l~~Dy~fLe~ 85 (86)
....|-++. .|+...+.++|.||.|
T Consensus 34 rDPRFd~~~G~~~~~~f~k~Y~FL~d 59 (168)
T PF06102_consen 34 RDPRFDSLSGEFNEDLFRKNYGFLDD 59 (168)
T ss_pred CCCCcCccccccCHHHHHHhhhhHHH
Confidence 345666664 6888999999999975
No 123
>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=29.77 E-value=29 Score=19.14 Aligned_cols=16 Identities=25% Similarity=0.578 Sum_probs=11.2
Q ss_pred eeEeCCCCCccccccc
Q 047076 30 SKYKCPGCSIRTCSLA 45 (86)
Q Consensus 30 ~kY~CP~C~~~~CSl~ 45 (86)
.-|+|+.|+..+=-+.
T Consensus 4 Yey~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQ 19 (42)
T ss_pred EEEEeCCCCCEEEEEE
Confidence 4699999996664443
No 124
>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=29.42 E-value=55 Score=18.77 Aligned_cols=32 Identities=25% Similarity=0.653 Sum_probs=23.6
Q ss_pred ccccCCCCC---eeEeCCCCCcccccccccccccc
Q 047076 21 ICQECKYKV---SKYKCPGCSIRTCSLACVKAHKQ 52 (86)
Q Consensus 21 ~C~vC~~~~---~kY~CP~C~~~~CSl~C~k~Hk~ 52 (86)
.|..|+..+ ..|+|-.|.-..=...|+..-++
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~~H 36 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRKH 36 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCCCCc
Confidence 588888643 48999999977777788876443
No 125
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.33 E-value=31 Score=29.68 Aligned_cols=22 Identities=27% Similarity=0.605 Sum_probs=17.1
Q ss_pred ccccccCCC-CCeeEeCCCCCcc
Q 047076 19 AAICQECKY-KVSKYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~-~~~kY~CP~C~~~ 40 (86)
..+|..||. ..-.+.||.|+..
T Consensus 626 ~~~C~~CG~~~g~~~~CP~CG~~ 648 (656)
T PRK08270 626 FSICPKHGYLSGEHEFCPKCGEE 648 (656)
T ss_pred CcccCCCCCcCCCCCCCcCCcCc
Confidence 468999997 3347899999954
No 126
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=29.08 E-value=28 Score=19.78 Aligned_cols=16 Identities=44% Similarity=0.926 Sum_probs=12.6
Q ss_pred CCCCCccccccccccccc
Q 047076 34 CPGCSIRTCSLACVKAHK 51 (86)
Q Consensus 34 CP~C~~~~CSl~C~k~Hk 51 (86)
|| .+.|||..|.|..-
T Consensus 6 cp--kiGYCS~~CsKt~v 21 (39)
T PF08189_consen 6 CP--KIGYCSSKCSKTDV 21 (39)
T ss_pred Cc--ccceecccccccce
Confidence 67 57899999988653
No 127
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=28.89 E-value=42 Score=26.33 Aligned_cols=28 Identities=29% Similarity=0.944 Sum_probs=18.8
Q ss_pred cccccccccccCCCC-----------CeeEeCCCCCccc
Q 047076 14 PKAKEAAICQECKYK-----------VSKYKCPGCSIRT 41 (86)
Q Consensus 14 ~~~~~~~~C~vC~~~-----------~~kY~CP~C~~~~ 41 (86)
+..+....|.-|.+. -+.|+||.|+..+
T Consensus 127 p~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F 165 (278)
T PF15135_consen 127 PQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNF 165 (278)
T ss_pred CcccccccccccccccCCCccccccceeeeecccccccc
Confidence 344556677777654 3688999888665
No 128
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=28.67 E-value=27 Score=29.17 Aligned_cols=23 Identities=35% Similarity=0.846 Sum_probs=11.7
Q ss_pred ccccccCCCCCe-eEeCCCCCccc
Q 047076 19 AAICQECKYKVS-KYKCPGCSIRT 41 (86)
Q Consensus 19 ~~~C~vC~~~~~-kY~CP~C~~~~ 41 (86)
..+|..|+.... .++||.|+..-
T Consensus 491 ~~~C~~CG~~~~~~~~CP~CGs~~ 514 (546)
T PF13597_consen 491 IDICPDCGYIGGEGDKCPKCGSEN 514 (546)
T ss_dssp EEEETTT---S--EEE-CCC----
T ss_pred cccccCCCcCCCCCCCCCCCCCcc
Confidence 468999997433 69999999875
No 129
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.06 E-value=32 Score=28.71 Aligned_cols=25 Identities=20% Similarity=0.565 Sum_probs=18.6
Q ss_pred ccccccCC--CCCeeEeCCCCCccccc
Q 047076 19 AAICQECK--YKVSKYKCPGCSIRTCS 43 (86)
Q Consensus 19 ~~~C~vC~--~~~~kY~CP~C~~~~CS 43 (86)
|.+|..|| .++.-+.||.|+.+.=+
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~~t~ 27 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHKFTS 27 (465)
T ss_pred CCcccccccccccccccccccCCcCCc
Confidence 56899999 24556779999987644
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=27.81 E-value=31 Score=20.66 Aligned_cols=21 Identities=29% Similarity=0.670 Sum_probs=13.7
Q ss_pred cccccCCCC--------CeeEeCCCCCcc
Q 047076 20 AICQECKYK--------VSKYKCPGCSIR 40 (86)
Q Consensus 20 ~~C~vC~~~--------~~kY~CP~C~~~ 40 (86)
..|..|+.- .-.-+||||+..
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 457777631 236789999863
No 131
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=27.56 E-value=34 Score=22.97 Aligned_cols=20 Identities=30% Similarity=0.886 Sum_probs=12.5
Q ss_pred ccc--cCCCC-----CeeEeCCCCCcc
Q 047076 21 ICQ--ECKYK-----VSKYKCPGCSIR 40 (86)
Q Consensus 21 ~C~--vC~~~-----~~kY~CP~C~~~ 40 (86)
-|. .|+.+ .+.|+|++|+..
T Consensus 20 aC~~~~C~kKv~~~~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 20 ACPNEKCNKKVTENGDGSYRCEKCNKT 46 (146)
T ss_dssp E-TSTTTS-B-EEETTTEEEETTTTEE
T ss_pred CCCCccCCCEeecCCCcEEECCCCCCc
Confidence 466 77764 457888888855
No 132
>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=27.47 E-value=27 Score=24.57 Aligned_cols=14 Identities=29% Similarity=0.510 Sum_probs=9.6
Q ss_pred eEeCCCCCcccccc
Q 047076 31 KYKCPGCSIRTCSL 44 (86)
Q Consensus 31 kY~CP~C~~~~CSl 44 (86)
|..||.|+.|+-=|
T Consensus 9 Kr~Cp~cg~kFYDL 22 (129)
T TIGR02300 9 KRICPNTGSKFYDL 22 (129)
T ss_pred cccCCCcCcccccc
Confidence 67777777777544
No 133
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=27.25 E-value=34 Score=16.09 Aligned_cols=8 Identities=75% Similarity=1.734 Sum_probs=4.6
Q ss_pred EeCCCCCc
Q 047076 32 YKCPGCSI 39 (86)
Q Consensus 32 Y~CP~C~~ 39 (86)
|+|+-|.-
T Consensus 1 y~C~~C~y 8 (24)
T PF13909_consen 1 YKCPHCSY 8 (24)
T ss_dssp EE-SSSS-
T ss_pred CCCCCCCC
Confidence 78887764
No 134
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.64 E-value=29 Score=23.03 Aligned_cols=14 Identities=36% Similarity=0.610 Sum_probs=10.8
Q ss_pred CCeeEeCCCCCccc
Q 047076 28 KVSKYKCPGCSIRT 41 (86)
Q Consensus 28 ~~~kY~CP~C~~~~ 41 (86)
.-.+|.||.|+.+.
T Consensus 32 ~~~~~~Cp~C~~~~ 45 (89)
T COG1997 32 QRAKHVCPFCGRTT 45 (89)
T ss_pred HhcCCcCCCCCCcc
Confidence 34689999998774
No 135
>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=26.56 E-value=44 Score=19.33 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=18.6
Q ss_pred ccccCCCCC---eeEeCCCCCcccccccccccc
Q 047076 21 ICQECKYKV---SKYKCPGCSIRTCSLACVKAH 50 (86)
Q Consensus 21 ~C~vC~~~~---~kY~CP~C~~~~CSl~C~k~H 50 (86)
.|..|+..+ .+|+|-.|.-.-=.-.|++.+
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 478888644 388888876553333455444
No 136
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.30 E-value=40 Score=31.70 Aligned_cols=21 Identities=29% Similarity=0.892 Sum_probs=0.0
Q ss_pred ccccCCCCC-eeEeCCCCCccc
Q 047076 21 ICQECKYKV-SKYKCPGCSIRT 41 (86)
Q Consensus 21 ~C~vC~~~~-~kY~CP~C~~~~ 41 (86)
+|..|+... ..|.||.|+...
T Consensus 681 fCP~CGs~te~vy~CPsCGaev 702 (1337)
T PRK14714 681 RCPDCGTHTEPVYVCPDCGAEV 702 (1337)
T ss_pred cCcccCCcCCCceeCccCCCcc
No 137
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=26.03 E-value=39 Score=20.82 Aligned_cols=36 Identities=28% Similarity=0.656 Sum_probs=20.1
Q ss_pred eEeCCCCCcccccccccccccccccCCCC---CCcceeeecCCCCh
Q 047076 31 KYKCPGCSIRTCSLACVKAHKQRTGCSGN---RNVTQFVPLSQFND 73 (86)
Q Consensus 31 kY~CP~C~~~~CSl~C~k~Hk~~~~C~g~---r~~~~~v~~~~~~~ 73 (86)
-.+||+|++.|=.-.| ..|.|. -.+..|.|-..|.-
T Consensus 5 ~rkC~~cg~YTLke~C-------p~CG~~t~~~~PprFSPeD~y~k 43 (59)
T COG2260 5 IRKCPKCGRYTLKEKC-------PVCGGDTKVPHPPRFSPEDKYGK 43 (59)
T ss_pred hhcCcCCCceeecccC-------CCCCCccccCCCCCCCccchHHH
Confidence 3566777766644444 245543 44677777655543
No 138
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.66 E-value=65 Score=19.74 Aligned_cols=25 Identities=28% Similarity=0.624 Sum_probs=20.5
Q ss_pred cccccccc--CCCCCeeEeCCCCCcccc
Q 047076 17 KEAAICQE--CKYKVSKYKCPGCSIRTC 42 (86)
Q Consensus 17 ~~~~~C~v--C~~~~~kY~CP~C~~~~C 42 (86)
.....|.+ |+. .+.-+|+.|....|
T Consensus 25 ~~~~~C~~~gC~~-~s~I~C~~Ckk~~C 51 (63)
T PF04236_consen 25 NVAGDCDITGCNN-TSFIRCAYCKKSLC 51 (63)
T ss_pred CCcCcCCCCCCCC-cCEEEccccCCccc
Confidence 34577999 996 79999999998776
No 139
>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=25.44 E-value=23 Score=31.85 Aligned_cols=23 Identities=26% Similarity=0.671 Sum_probs=0.0
Q ss_pred ccccccCCCCCeeEeCCCCCccc
Q 047076 19 AAICQECKYKVSKYKCPGCSIRT 41 (86)
Q Consensus 19 ~~~C~vC~~~~~kY~CP~C~~~~ 41 (86)
...|.-|+.....-+||.|+.+|
T Consensus 655 ~r~Cp~Cg~~t~~~~Cp~CG~~T 677 (900)
T PF03833_consen 655 RRRCPKCGKETFYNRCPECGSHT 677 (900)
T ss_dssp -----------------------
T ss_pred cccCcccCCcchhhcCcccCCcc
Confidence 45677777766677777777764
No 140
>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=25.38 E-value=56 Score=20.78 Aligned_cols=20 Identities=35% Similarity=0.981 Sum_probs=13.8
Q ss_pred ccccCCC----CCeeEeCCCCCcc
Q 047076 21 ICQECKY----KVSKYKCPGCSIR 40 (86)
Q Consensus 21 ~C~vC~~----~~~kY~CP~C~~~ 40 (86)
+|..|+. ....|.||.|+..
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCc
Confidence 5777774 2357889988865
No 141
>KOG4850 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.85 E-value=35 Score=25.25 Aligned_cols=29 Identities=24% Similarity=0.819 Sum_probs=21.8
Q ss_pred ccccccCCCCC---eeEeCCCCCcccccccccc
Q 047076 19 AAICQECKYKV---SKYKCPGCSIRTCSLACVK 48 (86)
Q Consensus 19 ~~~C~vC~~~~---~kY~CP~C~~~~CSl~C~k 48 (86)
+-+|. |...+ -.|.||.|+..-|..+|-.
T Consensus 135 ~DlCD-Cl~~eCdGC~Y~C~~CGSTkCG~~CR~ 166 (190)
T KOG4850|consen 135 FDLCD-CLVVECDGCHYPCKQCGSTKCGIGCRQ 166 (190)
T ss_pred ccHHh-hhccccccceecccccccccccccccc
Confidence 35665 55433 4899999999999999943
No 142
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=24.63 E-value=34 Score=18.98 Aligned_cols=14 Identities=21% Similarity=0.643 Sum_probs=9.6
Q ss_pred eeEeCCCCCccccc
Q 047076 30 SKYKCPGCSIRTCS 43 (86)
Q Consensus 30 ~kY~CP~C~~~~CS 43 (86)
+.-+||.|+..|-.
T Consensus 12 ~~~~C~~CgM~Y~~ 25 (41)
T PF13878_consen 12 GATTCPTCGMLYSP 25 (41)
T ss_pred CCcCCCCCCCEECC
Confidence 34588888887743
No 143
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=24.55 E-value=74 Score=21.31 Aligned_cols=21 Identities=38% Similarity=0.888 Sum_probs=15.0
Q ss_pred cccccCCCCCe----------------eEeCCCCCcc
Q 047076 20 AICQECKYKVS----------------KYKCPGCSIR 40 (86)
Q Consensus 20 ~~C~vC~~~~~----------------kY~CP~C~~~ 40 (86)
..|..|+.+.+ .|+|.+|+-+
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~ 109 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYR 109 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCE
Confidence 46888887654 5788888754
No 144
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=24.41 E-value=67 Score=17.91 Aligned_cols=28 Identities=29% Similarity=0.603 Sum_probs=17.4
Q ss_pred ccccCCC--CCeeEeCCCCCcccccccccc
Q 047076 21 ICQECKY--KVSKYKCPGCSIRTCSLACVK 48 (86)
Q Consensus 21 ~C~vC~~--~~~kY~CP~C~~~~CSl~C~k 48 (86)
.|.+|+. ....|+|-.|.-..=...|+.
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~ 31 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEA 31 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhC
Confidence 5777876 345999999864332334544
No 145
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=24.41 E-value=77 Score=25.52 Aligned_cols=23 Identities=26% Similarity=0.752 Sum_probs=16.5
Q ss_pred ccccccCCC--------CCeeEeCCCCCccc
Q 047076 19 AAICQECKY--------KVSKYKCPGCSIRT 41 (86)
Q Consensus 19 ~~~C~vC~~--------~~~kY~CP~C~~~~ 41 (86)
...|..|+. ...+.+||||+..-
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 456999983 23478899999764
No 146
>PRK06450 threonine synthase; Validated
Probab=24.39 E-value=38 Score=26.34 Aligned_cols=18 Identities=22% Similarity=0.877 Sum_probs=8.7
Q ss_pred ccccCCCCCe---eEeCCCCC
Q 047076 21 ICQECKYKVS---KYKCPGCS 38 (86)
Q Consensus 21 ~C~vC~~~~~---kY~CP~C~ 38 (86)
.|.-|+..-. .|+||+|+
T Consensus 5 ~C~~Cg~~~~~~~~~~C~~cg 25 (338)
T PRK06450 5 VCMKCGKERESIYEIRCKKCG 25 (338)
T ss_pred EECCcCCcCCCcccccCCcCC
Confidence 4555553211 45566664
No 147
>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=24.15 E-value=23 Score=18.74 Aligned_cols=22 Identities=23% Similarity=0.612 Sum_probs=11.4
Q ss_pred cccccccCCC--CCeeEeCCCCCc
Q 047076 18 EAAICQECKY--KVSKYKCPGCSI 39 (86)
Q Consensus 18 ~~~~C~vC~~--~~~kY~CP~C~~ 39 (86)
....|..|+. -+....||.|+.
T Consensus 10 ~~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEEE-TTT--EEES--SEETTTT-
T ss_pred EEEEcCCCCCEecCCCcCCCCcCc
Confidence 3467888886 345778888864
No 148
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=24.14 E-value=58 Score=24.08 Aligned_cols=21 Identities=24% Similarity=0.876 Sum_probs=15.6
Q ss_pred ccccccCCCCC--eeEeCCCCCc
Q 047076 19 AAICQECKYKV--SKYKCPGCSI 39 (86)
Q Consensus 19 ~~~C~vC~~~~--~kY~CP~C~~ 39 (86)
..+|+-||... ..+.||+|+.
T Consensus 354 ~~~c~~cg~~~~~~~~~c~~c~~ 376 (389)
T PRK11788 354 RYRCRNCGFTARTLYWHCPSCKA 376 (389)
T ss_pred CEECCCCCCCCccceeECcCCCC
Confidence 36788898633 4789999975
No 149
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.11 E-value=30 Score=28.81 Aligned_cols=21 Identities=33% Similarity=0.789 Sum_probs=16.4
Q ss_pred CCeeEeCCCCCcccccccccc
Q 047076 28 KVSKYKCPGCSIRTCSLACVK 48 (86)
Q Consensus 28 ~~~kY~CP~C~~~~CSl~C~k 48 (86)
+.+-|+||.|+..|=+|.=.+
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred ccccccCCccccchhhhHHHH
Confidence 567899999999987775433
No 150
>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=24.06 E-value=41 Score=19.81 Aligned_cols=23 Identities=22% Similarity=0.639 Sum_probs=17.7
Q ss_pred cccCCCC-CeeEeCCCCCcccccc
Q 047076 22 CQECKYK-VSKYKCPGCSIRTCSL 44 (86)
Q Consensus 22 C~vC~~~-~~kY~CP~C~~~~CSl 44 (86)
|.+|+.. ...|.|-.|+...|.-
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 6778766 7899999999999984
No 151
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=24.00 E-value=11 Score=22.00 Aligned_cols=21 Identities=29% Similarity=0.752 Sum_probs=13.5
Q ss_pred ccccCCCCCeeEe---------CCCCCccc
Q 047076 21 ICQECKYKVSKYK---------CPGCSIRT 41 (86)
Q Consensus 21 ~C~vC~~~~~kY~---------CP~C~~~~ 41 (86)
.|.||+.+-+.++ |..|..+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 3788887665554 77666554
No 152
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=23.99 E-value=34 Score=29.35 Aligned_cols=30 Identities=27% Similarity=0.655 Sum_probs=21.9
Q ss_pred cccccCCCCCeeEeCCCCC--------ccccccccccc
Q 047076 20 AICQECKYKVSKYKCPGCS--------IRTCSLACVKA 49 (86)
Q Consensus 20 ~~C~vC~~~~~kY~CP~C~--------~~~CSl~C~k~ 49 (86)
.+|.|=-.+++.-.||.|. ..+||-+|+|.
T Consensus 63 ~~c~~h~~~~a~lqCp~C~k~~~~~~~s~fCsq~CFk~ 100 (606)
T PLN03144 63 AVCSVHPSEPATLQCVGCVKAKLPVSKSYHCSPKCFSD 100 (606)
T ss_pred eeEeecCCCcccccCccchhcCCCcCcceeeCHHHHHH
Confidence 4555544577889999983 56899999763
No 153
>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=23.99 E-value=19 Score=27.16 Aligned_cols=7 Identities=29% Similarity=0.933 Sum_probs=2.4
Q ss_pred cccccCC
Q 047076 20 AICQECK 26 (86)
Q Consensus 20 ~~C~vC~ 26 (86)
..|-|||
T Consensus 173 g~CPvCG 179 (290)
T PF04216_consen 173 GYCPVCG 179 (290)
T ss_dssp SS-TTT-
T ss_pred CcCCCCC
Confidence 3444444
No 154
>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=23.81 E-value=26 Score=31.55 Aligned_cols=27 Identities=33% Similarity=0.795 Sum_probs=0.0
Q ss_pred cccccCCCC-CeeEeCCCCCcccccccc
Q 047076 20 AICQECKYK-VSKYKCPGCSIRTCSLAC 46 (86)
Q Consensus 20 ~~C~vC~~~-~~kY~CP~C~~~~CSl~C 46 (86)
..|..|+.. ...|.||+|+...=.-.|
T Consensus 668 ~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C 695 (900)
T PF03833_consen 668 NRCPECGSHTEPVYVCPDCGIEVEEDEC 695 (900)
T ss_dssp ----------------------------
T ss_pred hcCcccCCccccceeccccccccCcccc
Confidence 578889874 358999999987644444
No 155
>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=23.72 E-value=66 Score=17.15 Aligned_cols=21 Identities=19% Similarity=0.751 Sum_probs=14.8
Q ss_pred ccccccCCCC-----CeeEeCCCCCc
Q 047076 19 AAICQECKYK-----VSKYKCPGCSI 39 (86)
Q Consensus 19 ~~~C~vC~~~-----~~kY~CP~C~~ 39 (86)
...|.+|+.. ..-|+|..|+.
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~ 36 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKV 36 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCC
Confidence 4579999752 35788888864
No 156
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=23.63 E-value=71 Score=18.11 Aligned_cols=28 Identities=25% Similarity=0.738 Sum_probs=18.2
Q ss_pred ccccCCCC---CeeEeCCCCCcccccccccc
Q 047076 21 ICQECKYK---VSKYKCPGCSIRTCSLACVK 48 (86)
Q Consensus 21 ~C~vC~~~---~~kY~CP~C~~~~CSl~C~k 48 (86)
.|..|++. ...|+|-.|.-..=...|+.
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~ 32 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYH 32 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhC
Confidence 57888853 45999999864433345544
No 157
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=23.60 E-value=22 Score=20.33 Aligned_cols=22 Identities=23% Similarity=0.510 Sum_probs=16.9
Q ss_pred eEeCCCCCccccccccccccccc
Q 047076 31 KYKCPGCSIRTCSLACVKAHKQR 53 (86)
Q Consensus 31 kY~CP~C~~~~CSl~C~k~Hk~~ 53 (86)
.|+||-|+. .-+..=...|-..
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED 23 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh
Confidence 589999999 8887766666544
No 158
>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=23.30 E-value=50 Score=19.90 Aligned_cols=11 Identities=45% Similarity=1.108 Sum_probs=4.7
Q ss_pred CeeEeCCCCCc
Q 047076 29 VSKYKCPGCSI 39 (86)
Q Consensus 29 ~~kY~CP~C~~ 39 (86)
--+|+||-|++
T Consensus 31 Lr~y~Cp~CgA 41 (55)
T PF05741_consen 31 LRKYVCPICGA 41 (55)
T ss_dssp GGG---TTT--
T ss_pred HhcCcCCCCcC
Confidence 46899999986
No 159
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=23.18 E-value=45 Score=23.13 Aligned_cols=22 Identities=27% Similarity=0.815 Sum_probs=15.3
Q ss_pred ccccccCCCC----------------CeeEeCCCCCcc
Q 047076 19 AAICQECKYK----------------VSKYKCPGCSIR 40 (86)
Q Consensus 19 ~~~C~vC~~~----------------~~kY~CP~C~~~ 40 (86)
...|.-||.. .-.|+||+|.-+
T Consensus 74 ~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred hccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence 3578888742 347999999765
No 160
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.10 E-value=47 Score=28.50 Aligned_cols=23 Identities=22% Similarity=0.680 Sum_probs=17.5
Q ss_pred cccccccCCC--CCeeEeCCCCCcc
Q 047076 18 EAAICQECKY--KVSKYKCPGCSIR 40 (86)
Q Consensus 18 ~~~~C~vC~~--~~~kY~CP~C~~~ 40 (86)
...+|..|+. ....+.||.|+..
T Consensus 567 ~~~~C~~CG~~~~g~~~~CP~CGs~ 591 (625)
T PRK08579 567 AITVCNKCGRSTTGLYTRCPRCGSE 591 (625)
T ss_pred CCccCCCCCCccCCCCCcCcCCCCc
Confidence 3568999996 2447899999974
No 161
>PRK11032 hypothetical protein; Provisional
Probab=23.00 E-value=39 Score=24.28 Aligned_cols=25 Identities=24% Similarity=0.786 Sum_probs=16.0
Q ss_pred cccccccccCCCCCeeEe------CCCCCcc
Q 047076 16 AKEAAICQECKYKVSKYK------CPGCSIR 40 (86)
Q Consensus 16 ~~~~~~C~vC~~~~~kY~------CP~C~~~ 40 (86)
.++.-+|.-|+.....|+ ||.|+-.
T Consensus 121 g~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 121 GLGNLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred ecceEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 345567888887655554 7777644
No 162
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=22.45 E-value=61 Score=22.15 Aligned_cols=11 Identities=36% Similarity=1.050 Sum_probs=9.6
Q ss_pred eEeCCCCCccc
Q 047076 31 KYKCPGCSIRT 41 (86)
Q Consensus 31 kY~CP~C~~~~ 41 (86)
.|.||+|+.-|
T Consensus 124 f~~C~~C~kiy 134 (147)
T PF01927_consen 124 FWRCPGCGKIY 134 (147)
T ss_pred EEECCCCCCEe
Confidence 79999999866
No 163
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.12 E-value=27 Score=22.75 Aligned_cols=33 Identities=27% Similarity=0.562 Sum_probs=20.4
Q ss_pred CCCCCCCCcccccccccccCCCCCeeEeCCCCC
Q 047076 6 GPTSTNQNPKAKEAAICQECKYKVSKYKCPGCS 38 (86)
Q Consensus 6 ~p~s~~~~~~~~~~~~C~vC~~~~~kY~CP~C~ 38 (86)
||.|..+.--+..-.+|.-|.++.-.=.||.|+
T Consensus 16 pp~s~dA~ICtfEcTFCadCae~~l~g~CPnCG 48 (84)
T COG3813 16 PPDSTDARICTFECTFCADCAENRLHGLCPNCG 48 (84)
T ss_pred CCCCCceeEEEEeeehhHhHHHHhhcCcCCCCC
Confidence 555555555555556777777665566677654
No 164
>KOG4137 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.93 E-value=71 Score=21.66 Aligned_cols=32 Identities=16% Similarity=0.230 Sum_probs=25.2
Q ss_pred ccccccccCCCCCeeEeCCCCCccccccccccc
Q 047076 17 KEAAICQECKYKVSKYKCPGCSIRTCSLACVKA 49 (86)
Q Consensus 17 ~~~~~C~vC~~~~~kY~CP~C~~~~CSl~C~k~ 49 (86)
++...|+|=|- ++.|+||.=+++|=+.+=|+.
T Consensus 48 PakKycDvTGL-papYtdP~t~Lry~naeiY~~ 79 (102)
T KOG4137|consen 48 PAKKYCDVTGL-PAPYTDPNTGLRYHNAEIYKL 79 (102)
T ss_pred cchhhccccCC-cccccCCCccceeccHHHHHH
Confidence 45679999886 799999999998876655544
No 165
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.90 E-value=61 Score=27.97 Aligned_cols=23 Identities=26% Similarity=0.811 Sum_probs=16.3
Q ss_pred cccccccCCCCCeeEeCCCCCcc
Q 047076 18 EAAICQECKYKVSKYKCPGCSIR 40 (86)
Q Consensus 18 ~~~~C~vC~~~~~kY~CP~C~~~ 40 (86)
..++|.-||..-..-.||.|+..
T Consensus 14 ~akFC~~CG~~l~~~~Cp~CG~~ 36 (645)
T PRK14559 14 NNRFCQKCGTSLTHKPCPQCGTE 36 (645)
T ss_pred CCccccccCCCCCCCcCCCCCCC
Confidence 45688888875444578888876
No 166
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=21.27 E-value=50 Score=24.06 Aligned_cols=11 Identities=36% Similarity=0.929 Sum_probs=9.5
Q ss_pred eEeCCCCCccc
Q 047076 31 KYKCPGCSIRT 41 (86)
Q Consensus 31 kY~CP~C~~~~ 41 (86)
.|+||.|+..|
T Consensus 130 f~~C~~CgkiY 140 (165)
T COG1656 130 FYRCPKCGKIY 140 (165)
T ss_pred eeECCCCcccc
Confidence 68999999876
No 167
>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=21.15 E-value=78 Score=18.29 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=20.2
Q ss_pred ccccCCC---CCeeEeCCCCCccccccccccc
Q 047076 21 ICQECKY---KVSKYKCPGCSIRTCSLACVKA 49 (86)
Q Consensus 21 ~C~vC~~---~~~kY~CP~C~~~~CSl~C~k~ 49 (86)
.|.+|+. ....|+|-.|.-.-=...|+..
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~ 33 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFS 33 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhC
Confidence 5888885 3458999988766555567643
No 168
>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=21.06 E-value=53 Score=27.48 Aligned_cols=20 Identities=40% Similarity=1.125 Sum_probs=16.0
Q ss_pred ccccCCCC--CeeEeCCCCCcc
Q 047076 21 ICQECKYK--VSKYKCPGCSIR 40 (86)
Q Consensus 21 ~C~vC~~~--~~kY~CP~C~~~ 40 (86)
+|..|+.. .-.++||.|+..
T Consensus 520 ~C~~CG~~~~~~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGEGEGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCcCCCCCCcCCCCc
Confidence 89999974 247899999965
No 169
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.81 E-value=22 Score=15.96 Aligned_cols=19 Identities=37% Similarity=0.777 Sum_probs=9.4
Q ss_pred EeCCCCCcccccccccccc
Q 047076 32 YKCPGCSIRTCSLACVKAH 50 (86)
Q Consensus 32 Y~CP~C~~~~CSl~C~k~H 50 (86)
|+|+-|+..+-+..=...|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H 19 (26)
T smart00355 1 YRCPECGKVFKSKSALKEH 19 (26)
T ss_pred CCCCCCcchhCCHHHHHHH
Confidence 4566666555444333333
No 170
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=20.65 E-value=43 Score=19.64 Aligned_cols=12 Identities=33% Similarity=0.814 Sum_probs=5.6
Q ss_pred eeEeCCCCCccc
Q 047076 30 SKYKCPGCSIRT 41 (86)
Q Consensus 30 ~kY~CP~C~~~~ 41 (86)
..=+||.|..+|
T Consensus 36 ~~g~CPgCr~~Y 47 (48)
T PF14570_consen 36 EGGRCPGCREPY 47 (48)
T ss_dssp S-SB-TTT--B-
T ss_pred cCCCCCCCCCCC
Confidence 466899998876
No 171
>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=20.51 E-value=47 Score=19.40 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=7.5
Q ss_pred CeeEeCCCCCcc
Q 047076 29 VSKYKCPGCSIR 40 (86)
Q Consensus 29 ~~kY~CP~C~~~ 40 (86)
+.-|+||.|+..
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 445677777653
No 172
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=20.41 E-value=90 Score=17.95 Aligned_cols=27 Identities=30% Similarity=0.960 Sum_probs=17.0
Q ss_pred ccccCCCC---CeeEeCCCCC---cccccccccc
Q 047076 21 ICQECKYK---VSKYKCPGCS---IRTCSLACVK 48 (86)
Q Consensus 21 ~C~vC~~~---~~kY~CP~C~---~~~CSl~C~k 48 (86)
.|.+|+.. ...|+|-.|. .-.|+ .|+.
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~-~C~~ 34 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQ-DCVV 34 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCH-HHHh
Confidence 37788863 3379999997 33343 5544
No 173
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=20.09 E-value=46 Score=18.71 Aligned_cols=9 Identities=33% Similarity=1.250 Sum_probs=6.3
Q ss_pred eCCCCCccc
Q 047076 33 KCPGCSIRT 41 (86)
Q Consensus 33 ~CP~C~~~~ 41 (86)
+||.|+.+.
T Consensus 1 ~CP~Cg~~a 9 (47)
T PF04606_consen 1 RCPHCGSKA 9 (47)
T ss_pred CcCCCCCee
Confidence 578887754
Done!