Query 033478
Match_columns 118
No_of_seqs 104 out of 135
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 02:44:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033478.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033478hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01053 LSD1 zinc finger dom 99.6 1.5E-15 3.3E-20 89.6 2.3 31 32-62 1-31 (31)
2 PF06943 zf-LSD1: LSD1 zinc fi 99.5 5.9E-15 1.3E-19 84.2 2.3 25 35-59 1-25 (25)
3 TIGR01053 LSD1 zinc finger dom 99.5 1.3E-14 2.7E-19 85.7 2.1 31 70-100 1-31 (31)
4 PF06943 zf-LSD1: LSD1 zinc fi 99.4 1.5E-13 3.2E-18 78.4 2.5 25 73-97 1-25 (25)
5 PF10122 Mu-like_Com: Mu-like 95.4 0.0087 1.9E-07 39.3 1.5 35 70-104 4-40 (51)
6 KOG1546 Metacaspase involved i 95.1 0.0082 1.8E-07 52.0 1.0 30 71-102 5-34 (362)
7 PF13719 zinc_ribbon_5: zinc-r 93.9 0.064 1.4E-06 32.0 2.6 27 71-97 3-34 (37)
8 PRK00398 rpoP DNA-directed RNA 93.8 0.14 3.1E-06 31.2 4.0 32 70-101 3-34 (46)
9 TIGR02098 MJ0042_CXXC MJ0042 f 93.6 0.094 2E-06 30.5 2.9 30 51-80 3-35 (38)
10 PF10122 Mu-like_Com: Mu-like 93.6 0.038 8.3E-07 36.3 1.3 33 31-63 3-37 (51)
11 PF09788 Tmemb_55A: Transmembr 93.4 0.1 2.3E-06 43.5 3.9 41 66-106 153-195 (256)
12 PLN00209 ribosomal protein S27 93.3 0.085 1.8E-06 37.8 2.8 40 50-90 36-75 (86)
13 PF01667 Ribosomal_S27e: Ribos 93.2 0.085 1.8E-06 34.8 2.5 39 50-89 7-45 (55)
14 PTZ00083 40S ribosomal protein 93.0 0.1 2.2E-06 37.4 2.9 40 50-90 35-74 (85)
15 PRK00415 rps27e 30S ribosomal 92.6 0.083 1.8E-06 35.5 1.9 38 50-88 11-48 (59)
16 PF13717 zinc_ribbon_4: zinc-r 92.1 0.22 4.8E-06 29.6 3.1 15 83-97 20-34 (36)
17 TIGR02098 MJ0042_CXXC MJ0042 f 91.5 0.43 9.3E-06 27.6 3.9 30 70-99 2-36 (38)
18 COG2051 RPS27A Ribosomal prote 90.7 0.3 6.4E-06 33.8 3.0 38 50-88 19-56 (67)
19 PRK14890 putative Zn-ribbon RN 90.4 0.31 6.7E-06 32.8 2.8 53 29-97 4-57 (59)
20 PF11331 DUF3133: Protein of u 90.1 0.36 7.7E-06 30.9 2.8 38 46-83 2-44 (46)
21 PF13719 zinc_ribbon_5: zinc-r 90.0 0.33 7.1E-06 28.9 2.4 30 51-80 3-35 (37)
22 PF12773 DZR: Double zinc ribb 89.4 0.2 4.4E-06 30.3 1.2 40 53-99 1-40 (50)
23 PRK00398 rpoP DNA-directed RNA 89.0 0.58 1.2E-05 28.5 3.1 25 33-57 4-28 (46)
24 KOG1779 40s ribosomal protein 86.3 1.4 3.1E-05 31.6 4.1 41 50-91 34-74 (84)
25 PF13717 zinc_ribbon_4: zinc-r 86.2 0.83 1.8E-05 27.1 2.5 29 51-79 3-34 (36)
26 PF09788 Tmemb_55A: Transmembr 85.3 1.7 3.6E-05 36.5 4.7 73 30-103 63-140 (256)
27 PF04810 zf-Sec23_Sec24: Sec23 83.5 1.1 2.4E-05 26.9 2.2 20 83-102 19-38 (40)
28 smart00661 RPOL9 RNA polymeras 79.0 2.3 5E-05 25.6 2.5 30 73-102 3-34 (52)
29 PF04690 YABBY: YABBY protein; 77.8 1.9 4.1E-05 34.0 2.4 39 50-88 12-54 (170)
30 PRK05580 primosome assembly pr 77.6 3.5 7.6E-05 37.4 4.3 51 39-100 368-420 (679)
31 PRK14714 DNA polymerase II lar 76.7 2.2 4.8E-05 42.6 3.0 57 28-98 663-719 (1337)
32 PF11331 DUF3133: Protein of u 75.5 1.4 2.9E-05 28.3 0.8 30 71-100 7-43 (46)
33 PRK14873 primosome assembly pr 75.0 5.4 0.00012 36.6 4.8 49 36-96 368-418 (665)
34 PF09297 zf-NADH-PPase: NADH p 74.7 3.2 6.8E-05 23.6 2.1 26 72-97 5-30 (32)
35 PF05495 zf-CHY: CHY zinc fing 73.5 4.7 0.0001 26.8 3.1 48 49-96 9-69 (71)
36 PF08271 TF_Zn_Ribbon: TFIIB z 72.8 1.9 4.1E-05 25.9 0.9 28 52-80 2-29 (43)
37 PF11023 DUF2614: Protein of u 72.0 2 4.3E-05 32.3 1.1 35 47-85 66-100 (114)
38 COG4357 Zinc finger domain con 71.2 0.99 2.1E-05 33.5 -0.7 27 32-58 62-88 (105)
39 TIGR00595 priA primosomal prot 71.0 5.2 0.00011 35.1 3.6 42 48-100 211-252 (505)
40 KOG4684 Uncharacterized conser 70.2 5.5 0.00012 33.6 3.4 46 47-92 77-125 (275)
41 PF07754 DUF1610: Domain of un 69.6 4.1 8.9E-05 23.0 1.8 22 73-95 1-23 (24)
42 PRK02935 hypothetical protein; 68.7 3.5 7.6E-05 30.9 1.8 36 46-85 66-101 (110)
43 KOG2907 RNA polymerase I trans 68.6 1.7 3.7E-05 32.8 0.1 38 70-107 7-44 (116)
44 PF05129 Elf1: Transcription e 64.8 8.7 0.00019 26.5 3.0 38 49-86 21-62 (81)
45 smart00659 RPOLCX RNA polymera 63.9 8.6 0.00019 23.9 2.6 30 52-84 4-33 (44)
46 COG1096 Predicted RNA-binding 63.7 6.9 0.00015 31.5 2.7 24 72-97 151-174 (188)
47 KOG1546 Metacaspase involved i 63.1 3.6 7.7E-05 36.1 1.0 26 35-62 7-32 (362)
48 PF09082 DUF1922: Domain of un 62.9 9.8 0.00021 26.3 3.0 31 71-103 4-34 (68)
49 PRK02935 hypothetical protein; 62.9 4.3 9.2E-05 30.4 1.3 26 83-111 65-90 (110)
50 PF02150 RNA_POL_M_15KD: RNA p 62.4 4.4 9.6E-05 24.0 1.1 30 73-102 4-34 (35)
51 COG4416 Com Mu-like prophage p 60.9 2.3 5E-05 28.9 -0.4 33 69-101 3-37 (60)
52 COG2888 Predicted Zn-ribbon RN 60.7 9.4 0.0002 26.0 2.5 50 33-97 10-59 (61)
53 PF15616 TerY-C: TerY-C metal 60.3 8.7 0.00019 29.1 2.6 41 18-60 73-115 (131)
54 PF13248 zf-ribbon_3: zinc-rib 58.7 3.7 8E-05 22.6 0.3 24 51-80 3-26 (26)
55 PF04690 YABBY: YABBY protein; 57.9 19 0.00042 28.3 4.2 41 63-103 5-51 (170)
56 COG1198 PriA Primosomal protei 57.6 15 0.00032 34.6 4.1 53 39-102 422-476 (730)
57 COG2051 RPS27A Ribosomal prote 56.1 21 0.00045 24.7 3.7 36 66-101 15-51 (67)
58 TIGR00155 pqiA_fam integral me 55.2 11 0.00024 32.5 2.7 31 50-80 13-43 (403)
59 COG1996 RPC10 DNA-directed RNA 52.1 17 0.00037 23.5 2.6 33 68-100 4-36 (49)
60 PF03604 DNA_RNApol_7kD: DNA d 51.0 7.2 0.00016 23.0 0.6 12 71-82 18-29 (32)
61 PRK14890 putative Zn-ribbon RN 50.5 15 0.00031 24.8 2.1 30 68-98 5-35 (59)
62 PRK14559 putative protein seri 48.9 11 0.00024 34.7 1.9 10 52-61 3-12 (645)
63 COG1096 Predicted RNA-binding 46.8 44 0.00096 27.0 4.7 49 7-60 125-175 (188)
64 PLN00209 ribosomal protein S27 46.2 20 0.00044 25.8 2.4 37 27-63 31-68 (86)
65 PTZ00083 40S ribosomal protein 45.9 21 0.00045 25.7 2.5 37 27-63 30-67 (85)
66 PRK15103 paraquat-inducible me 45.3 14 0.0003 32.1 1.8 30 51-80 11-40 (419)
67 PF01667 Ribosomal_S27e: Ribos 45.0 21 0.00046 23.5 2.2 34 31-64 6-40 (55)
68 smart00647 IBR In Between Ring 44.6 30 0.00066 20.8 2.8 26 71-96 19-48 (64)
69 TIGR01384 TFS_arch transcripti 43.8 17 0.00037 24.9 1.7 28 72-101 2-29 (104)
70 PF02591 DUF164: Putative zinc 42.8 19 0.00041 22.5 1.7 27 32-58 22-54 (56)
71 PF14634 zf-RING_5: zinc-RING 42.7 2 4.4E-05 25.6 -2.7 23 69-95 21-43 (44)
72 PF14369 zf-RING_3: zinc-finge 42.3 26 0.00056 20.7 2.1 26 71-96 3-29 (35)
73 PF14803 Nudix_N_2: Nudix N-te 42.0 23 0.0005 21.1 1.9 25 73-97 3-31 (34)
74 PF01485 IBR: IBR domain; Int 40.6 16 0.00035 21.9 1.1 25 34-58 20-48 (64)
75 PF06677 Auto_anti-p27: Sjogre 40.6 37 0.00081 20.9 2.7 27 68-95 15-41 (41)
76 PF12172 DUF35_N: Rubredoxin-l 40.3 18 0.00039 20.8 1.2 21 34-58 13-33 (37)
77 TIGR00100 hypA hydrogenase nic 39.6 35 0.00077 24.4 2.9 28 69-98 69-96 (115)
78 PRK10996 thioredoxin 2; Provis 39.0 18 0.0004 25.8 1.4 32 50-81 2-33 (139)
79 TIGR00595 priA primosomal prot 38.1 34 0.00073 30.1 3.1 22 70-96 240-261 (505)
80 PF07282 OrfB_Zn_ribbon: Putat 37.9 46 0.00099 21.0 2.9 18 43-61 22-39 (69)
81 PF05180 zf-DNL: DNL zinc fing 37.8 10 0.00022 25.8 -0.1 21 42-62 21-41 (66)
82 PRK11827 hypothetical protein; 37.7 41 0.00088 22.5 2.7 32 32-63 8-39 (60)
83 PRK04351 hypothetical protein; 36.8 31 0.00066 26.2 2.3 33 51-83 113-145 (149)
84 PF08792 A2L_zn_ribbon: A2L zi 36.6 51 0.0011 19.4 2.8 26 72-97 5-30 (33)
85 PRK11827 hypothetical protein; 36.5 48 0.001 22.1 2.9 33 70-102 8-40 (60)
86 PF07295 DUF1451: Protein of u 35.6 43 0.00094 25.5 3.0 34 68-101 110-143 (146)
87 PF00130 C1_1: Phorbol esters/ 35.1 33 0.00072 20.5 1.9 26 71-97 12-37 (53)
88 smart00109 C1 Protein kinase C 34.8 17 0.00036 20.7 0.5 23 72-96 13-35 (49)
89 TIGR00155 pqiA_fam integral me 34.3 40 0.00086 29.2 2.9 32 68-99 11-44 (403)
90 COG1579 Zn-ribbon protein, pos 34.3 18 0.00039 29.9 0.7 12 85-96 218-229 (239)
91 smart00834 CxxC_CXXC_SSSS Puta 34.2 40 0.00088 19.0 2.1 26 71-96 6-34 (41)
92 PRK00415 rps27e 30S ribosomal 34.2 71 0.0015 21.4 3.5 31 32-62 11-42 (59)
93 cd00029 C1 Protein kinase C co 34.1 24 0.00051 20.4 1.1 24 72-96 13-36 (50)
94 PF07191 zinc-ribbons_6: zinc- 33.7 1E+02 0.0023 21.2 4.3 58 33-99 2-61 (70)
95 PF14599 zinc_ribbon_6: Zinc-r 33.0 63 0.0014 21.5 3.1 33 66-98 26-58 (61)
96 PRK04023 DNA polymerase II lar 32.0 37 0.0008 33.9 2.5 54 28-100 622-675 (1121)
97 COG4888 Uncharacterized Zn rib 32.0 36 0.00078 25.4 1.9 31 50-80 22-56 (104)
98 smart00531 TFIIE Transcription 31.5 39 0.00084 24.9 2.1 45 42-86 91-139 (147)
99 cd04476 RPA1_DBD_C RPA1_DBD_C: 31.4 67 0.0015 23.5 3.3 54 58-113 23-76 (166)
100 PRK00423 tfb transcription ini 30.9 27 0.00058 28.7 1.2 13 68-80 28-40 (310)
101 smart00731 SprT SprT homologue 30.9 63 0.0014 23.5 3.1 32 51-82 113-145 (146)
102 PF10571 UPF0547: Uncharacteri 30.8 24 0.00052 19.8 0.7 9 88-96 14-22 (26)
103 PRK05580 primosome assembly pr 30.7 53 0.0011 30.0 3.2 27 35-61 393-419 (679)
104 PF11781 RRN7: RNA polymerase 30.7 51 0.0011 19.6 2.1 24 73-97 11-34 (36)
105 TIGR01206 lysW lysine biosynth 30.6 52 0.0011 21.4 2.3 31 72-102 4-36 (54)
106 PRK12380 hydrogenase nickel in 30.3 46 0.001 23.8 2.2 27 69-97 69-95 (113)
107 PF03884 DUF329: Domain of unk 30.2 35 0.00076 22.6 1.5 23 88-110 2-24 (57)
108 smart00547 ZnF_RBZ Zinc finger 30.2 25 0.00055 18.5 0.7 22 51-78 3-24 (26)
109 PF13901 DUF4206: Domain of un 30.1 30 0.00065 27.0 1.3 27 72-98 154-182 (202)
110 COG1645 Uncharacterized Zn-fin 29.9 26 0.00056 26.8 0.9 36 64-101 22-58 (131)
111 PRK03681 hypA hydrogenase nick 29.6 48 0.001 23.8 2.2 28 69-98 69-97 (114)
112 KOG2824 Glutaredoxin-related p 28.4 92 0.002 26.6 4.0 53 29-95 226-280 (281)
113 PLN00162 transport protein sec 28.3 52 0.0011 30.7 2.7 32 71-102 54-89 (761)
114 PF03119 DNA_ligase_ZBD: NAD-d 28.2 52 0.0011 18.6 1.8 21 72-92 1-21 (28)
115 COG2816 NPY1 NTP pyrophosphohy 27.3 41 0.00089 28.5 1.8 28 71-98 112-139 (279)
116 KOG2906 RNA polymerase III sub 27.0 77 0.0017 23.7 3.0 32 71-102 2-35 (105)
117 COG2995 PqiA Uncharacterized p 26.6 21 0.00045 32.0 -0.1 47 13-62 197-247 (418)
118 cd00069 GHB Glycoprotein hormo 26.6 47 0.001 24.3 1.8 33 28-61 42-90 (102)
119 PF07776 zf-AD: Zinc-finger as 26.4 15 0.00032 22.1 -0.8 25 18-43 32-56 (75)
120 PF06827 zf-FPG_IleRS: Zinc fi 26.4 55 0.0012 18.0 1.6 10 86-95 19-28 (30)
121 PRK00564 hypA hydrogenase nick 26.2 42 0.0009 24.2 1.4 28 69-98 70-98 (117)
122 PF15227 zf-C3HC4_4: zinc fing 26.1 5 0.00011 24.1 -2.9 42 53-94 1-42 (42)
123 COG1148 HdrA Heterodisulfide r 25.9 34 0.00075 32.0 1.1 44 24-79 552-595 (622)
124 PRK00241 nudC NADH pyrophospha 25.4 53 0.0012 26.5 2.0 30 70-99 99-128 (256)
125 PRK00420 hypothetical protein; 25.1 46 0.00099 24.6 1.5 34 67-101 20-53 (112)
126 COG1198 PriA Primosomal protei 25.1 85 0.0018 29.7 3.5 29 35-63 447-475 (730)
127 PF13240 zinc_ribbon_2: zinc-r 24.3 34 0.00074 18.5 0.5 21 53-79 2-22 (23)
128 PRK14873 primosome assembly pr 23.4 85 0.0018 29.1 3.2 49 31-97 382-431 (665)
129 PF02318 FYVE_2: FYVE-type zin 22.8 37 0.0008 24.2 0.6 55 29-99 51-105 (118)
130 PF08646 Rep_fac-A_C: Replicat 22.8 85 0.0018 22.5 2.5 45 68-113 16-62 (146)
131 PRK08351 DNA-directed RNA poly 22.8 39 0.00085 22.7 0.7 25 32-62 3-27 (61)
132 COG0484 DnaJ DnaJ-class molecu 22.7 1.3E+02 0.0028 26.5 3.9 83 14-101 124-210 (371)
133 KOG1985 Vesicle coat complex C 22.5 52 0.0011 32.1 1.7 37 66-102 214-254 (887)
134 PF04032 Rpr2: RNAse P Rpr2/Rp 22.5 46 0.001 21.6 1.0 44 27-77 41-84 (85)
135 PRK15103 paraquat-inducible me 22.2 76 0.0016 27.7 2.5 27 33-59 11-39 (419)
136 PRK14714 DNA polymerase II lar 21.5 71 0.0015 32.5 2.4 37 50-99 667-703 (1337)
137 PF14353 CpXC: CpXC protein 21.2 80 0.0017 22.3 2.1 18 66-83 34-51 (128)
138 KOG2907 RNA polymerase I trans 21.0 40 0.00087 25.5 0.5 33 31-63 6-38 (116)
139 PF00791 ZU5: ZU5 domain; Int 20.8 1.1E+02 0.0024 21.3 2.7 23 66-88 11-33 (103)
140 PF10058 DUF2296: Predicted in 20.6 1E+02 0.0023 19.8 2.3 8 53-60 25-32 (54)
141 COG0675 Transposase and inacti 20.4 83 0.0018 23.8 2.1 12 47-58 306-317 (364)
142 COG2995 PqiA Uncharacterized p 20.4 61 0.0013 29.1 1.6 27 71-97 19-47 (418)
143 PF03811 Zn_Tnp_IS1: InsA N-te 20.3 1.1E+02 0.0023 18.4 2.2 11 50-60 5-15 (36)
144 PF02892 zf-BED: BED zinc fing 20.2 62 0.0013 18.8 1.1 28 20-47 4-31 (45)
145 PRK14892 putative transcriptio 20.2 1.9E+02 0.0041 20.8 3.8 15 85-99 39-53 (99)
No 1
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=99.56 E-value=1.5e-15 Score=89.63 Aligned_cols=31 Identities=68% Similarity=1.339 Sum_probs=23.1
Q ss_pred eeeeccccceeeecCCCCeEEcCCCCccccc
Q 033478 32 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFV 62 (118)
Q Consensus 32 QLvCggCr~lL~YprGA~sVrC~~C~tVn~v 62 (118)
|++|++||++|+||+||++|||+.|++||.+
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVNLV 31 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEecC
Confidence 6777777777777777777777777777753
No 2
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=99.51 E-value=5.9e-15 Score=84.15 Aligned_cols=25 Identities=68% Similarity=1.578 Sum_probs=19.7
Q ss_pred eccccceeeecCCCCeEEcCCCCcc
Q 033478 35 CGSCRRLLAYPRGARHVKCSCCQTV 59 (118)
Q Consensus 35 CggCr~lL~YprGA~sVrC~~C~tV 59 (118)
|+|||++|+||+||+||||+.|++|
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 6778888888888888888888775
No 3
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=99.48 E-value=1.3e-14 Score=85.74 Aligned_cols=31 Identities=55% Similarity=1.019 Sum_probs=29.5
Q ss_pred EEEcCCCCeeeEeeCCCCeEECCCCCcccee
Q 033478 70 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 100 (118)
Q Consensus 70 ~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V 100 (118)
|++|++||++|+||+||++|||+.|++||.|
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVNLV 31 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEecC
Confidence 5899999999999999999999999999975
No 4
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=99.40 E-value=1.5e-13 Score=78.44 Aligned_cols=25 Identities=64% Similarity=1.334 Sum_probs=24.3
Q ss_pred cCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 73 CASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 73 Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
|++||++||||+||+||||+.|++|
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 8999999999999999999999987
No 5
>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=95.38 E-value=0.0087 Score=39.30 Aligned_cols=35 Identities=17% Similarity=0.541 Sum_probs=24.8
Q ss_pred EEEcCCCCeeeEee--CCCCeEECCCCCccceeccCC
Q 033478 70 QVKCASCAVLLMYP--YGAPSVRCSSCCFVTEIGVCG 104 (118)
Q Consensus 70 ~v~Cg~Crt~LmyP--~GA~SVrCs~C~tVT~V~~~n 104 (118)
.++|++|+.+|.-. ...-.++|+-|.++|.|...+
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS 40 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence 47788888888775 333478888888888877544
No 6
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=95.14 E-value=0.0082 Score=52.00 Aligned_cols=30 Identities=37% Similarity=0.702 Sum_probs=27.5
Q ss_pred EEcCCCCeeeEeeCCCCeEECCCCCccceecc
Q 033478 71 VKCASCAVLLMYPYGAPSVRCSSCCFVTEIGV 102 (118)
Q Consensus 71 v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~~ 102 (118)
+.|. |++.++.|+||+. ||+.||++|.+..
T Consensus 5 ~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~~ 34 (362)
T KOG1546|consen 5 VGCN-CQRPMAPPPGARY-QCAGCHAVTQIAQ 34 (362)
T ss_pred ccCC-CCCCCCCCCCCcc-cccccceeeeecc
Confidence 5676 9999999999999 9999999999983
No 7
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.89 E-value=0.064 Score=31.95 Aligned_cols=27 Identities=33% Similarity=0.842 Sum_probs=15.5
Q ss_pred EEcCCCCeeeEeeC-----CCCeEECCCCCcc
Q 033478 71 VKCASCAVLLMYPY-----GAPSVRCSSCCFV 97 (118)
Q Consensus 71 v~Cg~Crt~LmyP~-----GA~SVrCs~C~tV 97 (118)
+.|.+|.+..-+|. +...|||+.|+++
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 44555555554443 4567777777665
No 8
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.75 E-value=0.14 Score=31.16 Aligned_cols=32 Identities=25% Similarity=0.473 Sum_probs=22.0
Q ss_pred EEEcCCCCeeeEeeCCCCeEECCCCCccceec
Q 033478 70 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 101 (118)
Q Consensus 70 ~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~ 101 (118)
...|++|+..+.+..+...++|+-|++--.+.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILFK 34 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEEc
Confidence 45677777777777777777777777644443
No 9
>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=93.59 E-value=0.094 Score=30.48 Aligned_cols=30 Identities=27% Similarity=0.732 Sum_probs=16.1
Q ss_pred EEcCCCCcccccccc---ceeeEEEcCCCCeee
Q 033478 51 VKCSCCQTVNFVLEA---HQVGQVKCASCAVLL 80 (118)
Q Consensus 51 VrC~~C~tVn~v~~a---~q~a~v~Cg~Crt~L 80 (118)
+.|+.|.+.+.++++ .+...+.|++|+..+
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 566677766555531 122356666666554
No 10
>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=93.57 E-value=0.038 Score=36.31 Aligned_cols=33 Identities=36% Similarity=0.794 Sum_probs=28.3
Q ss_pred ceeeeccccceeeecCCCC--eEEcCCCCcccccc
Q 033478 31 AQMVCGSCRRLLAYPRGAR--HVKCSCCQTVNFVL 63 (118)
Q Consensus 31 sQLvCggCr~lL~YprGA~--sVrC~~C~tVn~v~ 63 (118)
-.+.|+.|..+|+.--++. .++|+.|.++|.+.
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVR 37 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence 4678999999999875665 88999999999876
No 11
>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=93.37 E-value=0.1 Score=43.49 Aligned_cols=41 Identities=20% Similarity=0.380 Sum_probs=33.9
Q ss_pred ceeeEEEcCCCCeeeEeeCCC--CeEECCCCCccceeccCCcc
Q 033478 66 HQVGQVKCASCAVLLMYPYGA--PSVRCSSCCFVTEIGVCGLS 106 (118)
Q Consensus 66 ~q~a~v~Cg~Crt~LmyP~GA--~SVrCs~C~tVT~V~~~n~r 106 (118)
..+..++|++|+...+++.=. ...||+.|+.|..|...-.|
T Consensus 153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~~faR 195 (256)
T PF09788_consen 153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGPRFAR 195 (256)
T ss_pred CCceeEECCCCCCcEeccCCCCCccccCCCCceeccccchHhh
Confidence 356889999999999998755 56799999999999875444
No 12
>PLN00209 ribosomal protein S27; Provisional
Probab=93.31 E-value=0.085 Score=37.85 Aligned_cols=40 Identities=33% Similarity=0.630 Sum_probs=33.1
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEE
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR 90 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVr 90 (118)
.|+|+.|..++.+= ++....|.|..|++.|..|.|-...-
T Consensus 36 ~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGGKa~l 75 (86)
T PLN00209 36 DVKCQGCFNITTVF-SHSQTVVVCGSCQTVLCQPTGGKARL 75 (86)
T ss_pred EEECCCCCCeeEEE-ecCceEEEccccCCEeeccCCCCeEe
Confidence 58999999998875 35577899999999999999976543
No 13
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=93.20 E-value=0.085 Score=34.84 Aligned_cols=39 Identities=33% Similarity=0.692 Sum_probs=26.7
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeE
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV 89 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SV 89 (118)
.|+|+.|..++.+= ++....+.|.+|++.|.-|.|-..-
T Consensus 7 ~VkCp~C~~~q~vF-Sha~t~V~C~~Cg~~L~~PtGGKa~ 45 (55)
T PF01667_consen 7 DVKCPGCYNIQTVF-SHAQTVVKCVVCGTVLAQPTGGKAR 45 (55)
T ss_dssp EEE-TTT-SEEEEE-TT-SS-EE-SSSTSEEEEE-SSSEE
T ss_pred EEECCCCCCeeEEE-ecCCeEEEcccCCCEecCCCCcCeE
Confidence 58999999998874 3556779999999999999986643
No 14
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=93.02 E-value=0.1 Score=37.36 Aligned_cols=40 Identities=30% Similarity=0.606 Sum_probs=32.8
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEE
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR 90 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVr 90 (118)
.|+|+.|..++.+= ++....|.|.+|++.|.-|.|-...-
T Consensus 35 ~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGGKa~l 74 (85)
T PTZ00083 35 DVKCPGCSQITTVF-SHAQTVVLCGGCSSQLCQPTGGKAKL 74 (85)
T ss_pred EEECCCCCCeeEEE-ecCceEEEccccCCEeeccCCCCeEe
Confidence 58999999998875 35577799999999999999976543
No 15
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=92.64 E-value=0.083 Score=35.48 Aligned_cols=38 Identities=32% Similarity=0.639 Sum_probs=27.6
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCe
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~S 88 (118)
.|+|+.|..++.+= ++-...+.|..|++.|.-|.|-..
T Consensus 11 ~VkCp~C~n~q~vF-sha~t~V~C~~Cg~~L~~PtGGKa 48 (59)
T PRK00415 11 KVKCPDCGNEQVVF-SHASTVVRCLVCGKTLAEPTGGKA 48 (59)
T ss_pred EEECCCCCCeEEEE-ecCCcEEECcccCCCcccCCCcce
Confidence 47888888887654 244566888888888888887543
No 16
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.14 E-value=0.22 Score=29.61 Aligned_cols=15 Identities=47% Similarity=0.840 Sum_probs=8.9
Q ss_pred eCCCCeEECCCCCcc
Q 033478 83 PYGAPSVRCSSCCFV 97 (118)
Q Consensus 83 P~GA~SVrCs~C~tV 97 (118)
|++...|+|+.|+.+
T Consensus 20 p~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 20 PPKGRKVRCSKCGHV 34 (36)
T ss_pred CCCCcEEECCCCCCE
Confidence 445556666666653
No 17
>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=91.53 E-value=0.43 Score=27.64 Aligned_cols=30 Identities=23% Similarity=0.540 Sum_probs=22.9
Q ss_pred EEEcCCCCeeeEeeC-----CCCeEECCCCCccce
Q 033478 70 QVKCASCAVLLMYPY-----GAPSVRCSSCCFVTE 99 (118)
Q Consensus 70 ~v~Cg~Crt~LmyP~-----GA~SVrCs~C~tVT~ 99 (118)
.+.|.+|++...++. +...|+|+.|+++-.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 578999999888884 234799999987644
No 18
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=90.71 E-value=0.3 Score=33.75 Aligned_cols=38 Identities=32% Similarity=0.624 Sum_probs=28.0
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCe
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 88 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~S 88 (118)
.|+|+.|...+-+= ++....+.|..|++.|..|.|-.+
T Consensus 19 ~VkCpdC~N~q~vF-shast~V~C~~CG~~l~~PTGGka 56 (67)
T COG2051 19 RVKCPDCGNEQVVF-SHASTVVTCLICGTTLAEPTGGKA 56 (67)
T ss_pred EEECCCCCCEEEEe-ccCceEEEecccccEEEecCCCeE
Confidence 47888887776654 344666888888888888888654
No 19
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.40 E-value=0.31 Score=32.83 Aligned_cols=53 Identities=28% Similarity=0.603 Sum_probs=41.1
Q ss_pred ccceeeeccccceeeecCC-CCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 29 EMAQMVCGSCRRLLAYPRG-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 29 ~~sQLvCggCr~lL~YprG-A~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
.+.-.+|.+|...| .|++ |+.--|+.|..+.. .+|..||.+ +...+|+.|.+.
T Consensus 4 ~~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I---------~RC~~CRk~------~~~Y~CP~CGF~ 57 (59)
T PRK14890 4 MMEPPKCTSCGIEI-APREKAVKFLCPNCGEVII---------YRCEKCRKQ------SNPYTCPKCGFE 57 (59)
T ss_pred cccCccccCCCCcc-cCCCccCEeeCCCCCCeeE---------eechhHHhc------CCceECCCCCCc
Confidence 34556899999888 5666 99999999987654 568999876 356788888764
No 20
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=90.10 E-value=0.36 Score=30.91 Aligned_cols=38 Identities=24% Similarity=0.572 Sum_probs=27.0
Q ss_pred CCCCeEEcCCCCccccccc-----cceeeEEEcCCCCeeeEee
Q 033478 46 RGARHVKCSCCQTVNFVLE-----AHQVGQVKCASCAVLLMYP 83 (118)
Q Consensus 46 rGA~sVrC~~C~tVn~v~~-----a~q~a~v~Cg~Crt~LmyP 83 (118)
.||+-|-|..|..+=..|. .....++.||.|...|.|-
T Consensus 2 GGAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 2 GGAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred CCCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence 3677777777776666653 2337789999999888764
No 21
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.03 E-value=0.33 Score=28.86 Aligned_cols=30 Identities=27% Similarity=0.583 Sum_probs=20.4
Q ss_pred EEcCCCCcccccccc---ceeeEEEcCCCCeee
Q 033478 51 VKCSCCQTVNFVLEA---HQVGQVKCASCAVLL 80 (118)
Q Consensus 51 VrC~~C~tVn~v~~a---~q~a~v~Cg~Crt~L 80 (118)
++|+.|++.-.+++. ..-..++|+.|+...
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 677888877777642 445677888887653
No 22
>PF12773 DZR: Double zinc ribbon
Probab=89.42 E-value=0.2 Score=30.31 Aligned_cols=40 Identities=25% Similarity=0.464 Sum_probs=25.9
Q ss_pred cCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCccce
Q 033478 53 CSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTE 99 (118)
Q Consensus 53 C~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~ 99 (118)
|+.|.+.+.. ....|..|++.|. +.....+.|+.|.+.+.
T Consensus 1 Cp~Cg~~~~~------~~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 1 CPHCGTPNPD------DAKFCPHCGTPLP-PPDQSKKICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCc------cccCChhhcCChh-hccCCCCCCcCCcCCCc
Confidence 5666666532 2467777777777 55566677888877643
No 23
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.05 E-value=0.58 Score=28.46 Aligned_cols=25 Identities=24% Similarity=0.623 Sum_probs=11.4
Q ss_pred eeeccccceeeecCCCCeEEcCCCC
Q 033478 33 MVCGSCRRLLAYPRGARHVKCSCCQ 57 (118)
Q Consensus 33 LvCggCr~lL~YprGA~sVrC~~C~ 57 (118)
..|..|...+.+..+....+|+.|.
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCC
Confidence 3444444444444444444444443
No 24
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=86.32 E-value=1.4 Score=31.60 Aligned_cols=41 Identities=29% Similarity=0.606 Sum_probs=32.4
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEEC
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRC 91 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrC 91 (118)
-|+|+.|--||.+-+ +...-+.|++|.+.|.-|.|-..+-=
T Consensus 34 ~VkC~gc~~iT~vfS-HaqtvVvc~~c~~il~~~tggra~ls 74 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFS-HAQTVVVCEGCSTILCQPTGGKAKLS 74 (84)
T ss_pred EEEcCCceEEEEEee-cCceEEEcCCCceEEEEecCCcEEec
Confidence 488999988888763 44566899999999999998876643
No 25
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.17 E-value=0.83 Score=27.14 Aligned_cols=29 Identities=21% Similarity=0.591 Sum_probs=21.0
Q ss_pred EEcCCCCccccccc---cceeeEEEcCCCCee
Q 033478 51 VKCSCCQTVNFVLE---AHQVGQVKCASCAVL 79 (118)
Q Consensus 51 VrC~~C~tVn~v~~---a~q~a~v~Cg~Crt~ 79 (118)
+.|+.|++.-.+++ ...-..+.|+.|+..
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 67888888877764 245667888888764
No 26
>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=85.34 E-value=1.7 Score=36.49 Aligned_cols=73 Identities=22% Similarity=0.534 Sum_probs=57.4
Q ss_pred cceeeeccccceeeecCC--CCeEEcCCCCccccccc-cceeeEEEcCCCCeeeEeeCCCCeEECCC--CCccceeccC
Q 033478 30 MAQMVCGSCRRLLAYPRG--ARHVKCSCCQTVNFVLE-AHQVGQVKCASCAVLLMYPYGAPSVRCSS--CCFVTEIGVC 103 (118)
Q Consensus 30 ~sQLvCggCr~lL~YprG--A~sVrC~~C~tVn~v~~-a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~--C~tVT~V~~~ 103 (118)
+.-+.|.=|+.++--.-- =--|+|..|+-.|+..+ ....-.++| -|..+|+....++.|-|+. |+.|......
T Consensus 63 ~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRC-PCNCLLICk~sS~rIaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 63 APVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRC-PCNCLLICKSSSQRIACPRPNCKRIINLGPS 140 (256)
T ss_pred CceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEec-CCceEEEeecccccccCCCCCCcceEEeCCc
Confidence 356789999987755432 22489999999998764 456778999 7899999999999999988 9998877655
No 27
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=83.46 E-value=1.1 Score=26.90 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=11.1
Q ss_pred eCCCCeEECCCCCccceecc
Q 033478 83 PYGAPSVRCSSCCFVTEIGV 102 (118)
Q Consensus 83 P~GA~SVrCs~C~tVT~V~~ 102 (118)
-.+..+-+|+.|.+.|.++.
T Consensus 19 ~~~~~~w~C~~C~~~N~lp~ 38 (40)
T PF04810_consen 19 DDGGKTWICNFCGTKNPLPP 38 (40)
T ss_dssp ETTTTEEEETTT--EEE--G
T ss_pred cCCCCEEECcCCCCcCCCCC
Confidence 34667777777777777764
No 28
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=79.02 E-value=2.3 Score=25.57 Aligned_cols=30 Identities=23% Similarity=0.594 Sum_probs=19.1
Q ss_pred cCCCCeeeEeeCCCC--eEECCCCCccceecc
Q 033478 73 CASCAVLLMYPYGAP--SVRCSSCCFVTEIGV 102 (118)
Q Consensus 73 Cg~Crt~LmyP~GA~--SVrCs~C~tVT~V~~ 102 (118)
|..|+.+|..+.+.. ...|+.|.++-.+.+
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeEECCC
Confidence 667777554444432 567888887766653
No 29
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=77.82 E-value=1.9 Score=33.95 Aligned_cols=39 Identities=28% Similarity=0.437 Sum_probs=25.8
Q ss_pred eEEcCCCCcccccc-c---cceeeEEEcCCCCeeeEeeCCCCe
Q 033478 50 HVKCSCCQTVNFVL-E---AHQVGQVKCASCAVLLMYPYGAPS 88 (118)
Q Consensus 50 sVrC~~C~tVn~v~-~---a~q~a~v~Cg~Crt~LmyP~GA~S 88 (118)
.|+|.-|+||=+|. | --++-.|+||.|--+|.+--++..
T Consensus 12 YVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred EEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccc
Confidence 47777777777764 1 345666778888888776555443
No 30
>PRK05580 primosome assembly protein PriA; Validated
Probab=77.60 E-value=3.5 Score=37.36 Aligned_cols=51 Identities=29% Similarity=0.559 Sum_probs=37.3
Q ss_pred cceeeec-CC-CCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCcccee
Q 033478 39 RRLLAYP-RG-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 100 (118)
Q Consensus 39 r~lL~Yp-rG-A~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V 100 (118)
+++|.-+ || |+.+.|..|..+ +.|..|...|.|.......+|.-|.+...+
T Consensus 368 qvll~~nrrGy~~~~~C~~Cg~~-----------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~ 420 (679)
T PRK05580 368 QVLLFLNRRGYAPFLLCRDCGWV-----------AECPHCDASLTLHRFQRRLRCHHCGYQEPI 420 (679)
T ss_pred eEEEEEcCCCCCCceEhhhCcCc-----------cCCCCCCCceeEECCCCeEECCCCcCCCCC
Confidence 4556666 45 678999999876 468888888888887777777777766554
No 31
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=76.65 E-value=2.2 Score=42.59 Aligned_cols=57 Identities=21% Similarity=0.364 Sum_probs=43.3
Q ss_pred cccceeeeccccceeeecCCCCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCccc
Q 033478 28 QEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVT 98 (118)
Q Consensus 28 ~~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT 98 (118)
.|.++..|..|.+.... .+|+.|.+-+.. ...|..|+..+-..... +.+|+-|.+-+
T Consensus 663 VEV~~rkCPkCG~~t~~------~fCP~CGs~te~-------vy~CPsCGaev~~des~-a~~CP~CGtpl 719 (1337)
T PRK14714 663 VEVGRRRCPSCGTETYE------NRCPDCGTHTEP-------VYVCPDCGAEVPPDESG-RVECPRCDVEL 719 (1337)
T ss_pred EEEEEEECCCCCCcccc------ccCcccCCcCCC-------ceeCccCCCccCCCccc-cccCCCCCCcc
Confidence 46778999999986432 299999998742 24899999987655434 88999999654
No 32
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=75.46 E-value=1.4 Score=28.26 Aligned_cols=30 Identities=37% Similarity=0.726 Sum_probs=20.9
Q ss_pred EEcCCCCeeeEeeCC-------CCeEECCCCCcccee
Q 033478 71 VKCASCAVLLMYPYG-------APSVRCSSCCFVTEI 100 (118)
Q Consensus 71 v~Cg~Crt~LmyP~G-------A~SVrCs~C~tVT~V 100 (118)
++|.+|..+|.+|.+ ...+||..|..|-..
T Consensus 7 v~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~ 43 (46)
T PF11331_consen 7 VVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF 43 (46)
T ss_pred eECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE
Confidence 678888888877764 346778777776543
No 33
>PRK14873 primosome assembly protein PriA; Provisional
Probab=75.01 E-value=5.4 Score=36.64 Aligned_cols=49 Identities=29% Similarity=0.601 Sum_probs=36.0
Q ss_pred ccccceeeecC-C-CCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCc
Q 033478 36 GSCRRLLAYPR-G-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCF 96 (118)
Q Consensus 36 ggCr~lL~Ypr-G-A~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~t 96 (118)
.| ++||.-+| | |+.+.|..|..+ ..|.+|...|.|..+....+|.-|.+
T Consensus 368 ~g-qvll~lnRrGyap~l~C~~Cg~~-----------~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 368 HG-PVLVQVPRRGYVPSLACARCRTP-----------ARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred cC-cEEEEecCCCCCCeeEhhhCcCe-----------eECCCCCCceeEecCCCeeECCCCcC
Confidence 57 78887664 4 567799999876 46777777777777666777777776
No 34
>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=74.66 E-value=3.2 Score=23.60 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=16.7
Q ss_pred EcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 72 KCASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 72 ~Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
.|+.|+..+..-.+-.+-+|+.|...
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 58888888888888888888888754
No 35
>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=73.45 E-value=4.7 Score=26.82 Aligned_cols=48 Identities=17% Similarity=0.321 Sum_probs=26.6
Q ss_pred CeEEcCCCCcccccc-----------ccceeeEEEcCCCCeeeEeeCCCCe--EECCCCCc
Q 033478 49 RHVKCSCCQTVNFVL-----------EAHQVGQVKCASCAVLLMYPYGAPS--VRCSSCCF 96 (118)
Q Consensus 49 ~sVrC~~C~tVn~v~-----------~a~q~a~v~Cg~Crt~LmyP~GA~S--VrCs~C~t 96 (118)
...+++.|+..-+-. .......|.||.|++.+.+..-.-+ ..|+.|+.
T Consensus 9 ~~~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 9 CAIRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp EEEEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred EEEECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 456666666554332 1233448999999998887664333 67888864
No 36
>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=72.80 E-value=1.9 Score=25.88 Aligned_cols=28 Identities=29% Similarity=0.832 Sum_probs=12.8
Q ss_pred EcCCCCccccccccceeeEEEcCCCCeee
Q 033478 52 KCSCCQTVNFVLEAHQVGQVKCASCAVLL 80 (118)
Q Consensus 52 rC~~C~tVn~v~~a~q~a~v~Cg~Crt~L 80 (118)
+|+.|.+-+.+- -.+.+.++|..|+..|
T Consensus 2 ~Cp~Cg~~~~~~-D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVF-DPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEE-ETTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEE-cCCCCeEECCCCCCEe
Confidence 355555544211 1234455666665554
No 37
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=72.00 E-value=2 Score=32.33 Aligned_cols=35 Identities=23% Similarity=0.362 Sum_probs=27.0
Q ss_pred CCCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCC
Q 033478 47 GARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYG 85 (118)
Q Consensus 47 GA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~G 85 (118)
-|..|+||.|+-.|-..--. -.|-.|+++|...+.
T Consensus 66 kav~V~CP~C~K~TKmLGr~----D~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRV----DACMHCKEPLTLDPS 100 (114)
T ss_pred cceeeECCCCCChHhhhchh----hccCcCCCcCccCch
Confidence 46889999999999764211 379999999987764
No 38
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=71.17 E-value=0.99 Score=33.54 Aligned_cols=27 Identities=33% Similarity=0.818 Sum_probs=24.3
Q ss_pred eeeeccccceeeecCCCCeEEcCCCCc
Q 033478 32 QMVCGSCRRLLAYPRGARHVKCSCCQT 58 (118)
Q Consensus 32 QLvCggCr~lL~YprGA~sVrC~~C~t 58 (118)
-++||-||.+|.|..=-..++|+.|++
T Consensus 62 ~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 62 AIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred cEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 389999999999988888889999986
No 39
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.04 E-value=5.2 Score=35.06 Aligned_cols=42 Identities=26% Similarity=0.713 Sum_probs=27.9
Q ss_pred CCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCcccee
Q 033478 48 ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 100 (118)
Q Consensus 48 A~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V 100 (118)
|+.+.|..|..+ +.|..|...|.|-......+|.-|.+...+
T Consensus 211 a~~~~C~~Cg~~-----------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~ 252 (505)
T TIGR00595 211 SKNLLCRSCGYI-----------LCCPNCDVSLTYHKKEGKLRCHYCGYQEPI 252 (505)
T ss_pred CCeeEhhhCcCc-----------cCCCCCCCceEEecCCCeEEcCCCcCcCCC
Confidence 567788888765 356677777777666666666666655544
No 40
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=70.18 E-value=5.5 Score=33.59 Aligned_cols=46 Identities=33% Similarity=0.475 Sum_probs=22.4
Q ss_pred CCCeEEcCCCCccccccccceeeEEEcCCCCeee---EeeCCCCeEECC
Q 033478 47 GARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLL---MYPYGAPSVRCS 92 (118)
Q Consensus 47 GA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~L---myP~GA~SVrCs 92 (118)
+++-|-|..|+..-.+---+|+--+.|+.|...- =.|+|...|||+
T Consensus 77 ~~PmvtCRVCq~~i~~egk~~QHVVKC~~CnEATPIrnAPpGKKYVRCP 125 (275)
T KOG4684|consen 77 QFPMVTCRVCQVAISLEGKNQQHVVKCHSCNEATPIRNAPPGKKYVRCP 125 (275)
T ss_pred CCceEeehhhhHHhccccccceeeEeecccCccccCCCCCCCCceeecC
Confidence 4455555555544333333444445555554321 235555555555
No 41
>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=69.55 E-value=4.1 Score=22.99 Aligned_cols=22 Identities=32% Similarity=0.782 Sum_probs=12.4
Q ss_pred cCCCCeeeEeeCC-CCeEECCCCC
Q 033478 73 CASCAVLLMYPYG-APSVRCSSCC 95 (118)
Q Consensus 73 Cg~Crt~LmyP~G-A~SVrCs~C~ 95 (118)
|..|+..|. |++ +....|+.|.
T Consensus 1 C~sC~~~i~-~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIA-PREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCccc-CcccCceEeCCCCC
Confidence 445555444 555 6666666664
No 42
>PRK02935 hypothetical protein; Provisional
Probab=68.69 E-value=3.5 Score=30.89 Aligned_cols=36 Identities=22% Similarity=0.376 Sum_probs=28.1
Q ss_pred CCCCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCC
Q 033478 46 RGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYG 85 (118)
Q Consensus 46 rGA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~G 85 (118)
--|..|.|+.|+-.|-..--. -.|-.|+++|-..++
T Consensus 66 tkavqV~CP~C~K~TKmLGrv----D~CM~C~~PLTLd~~ 101 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLGRV----DACMHCNQPLTLDRS 101 (110)
T ss_pred ccceeeECCCCCchhhhccce----eecCcCCCcCCcCcc
Confidence 358889999999999765222 369999999988765
No 43
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=68.60 E-value=1.7 Score=32.79 Aligned_cols=38 Identities=21% Similarity=0.357 Sum_probs=31.0
Q ss_pred EEEcCCCCeeeEeeCCCCeEECCCCCccceeccCCcce
Q 033478 70 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSL 107 (118)
Q Consensus 70 ~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~~~n~r~ 107 (118)
..-|+.|+.+|..|.-...+-|..|..+..+.+...++
T Consensus 7 ~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~ 44 (116)
T KOG2907|consen 7 LDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSGLV 44 (116)
T ss_pred cchhhhhhhhcccccccCceEeccccccCCHHHhCCee
Confidence 45688899999999988888899999988887665544
No 44
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=64.76 E-value=8.7 Score=26.47 Aligned_cols=38 Identities=16% Similarity=0.422 Sum_probs=20.7
Q ss_pred CeEEcCCCCcccccc----ccceeeEEEcCCCCeeeEeeCCC
Q 033478 49 RHVKCSCCQTVNFVL----EAHQVGQVKCASCAVLLMYPYGA 86 (118)
Q Consensus 49 ~sVrC~~C~tVn~v~----~a~q~a~v~Cg~Crt~LmyP~GA 86 (118)
+.-.|+.|+.-+.|. .....+.+.|+.|+..-.++.+.
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~ 62 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINP 62 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--S
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCc
Confidence 345799999877765 25679999999998777666544
No 45
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=63.91 E-value=8.6 Score=23.87 Aligned_cols=30 Identities=23% Similarity=0.554 Sum_probs=14.8
Q ss_pred EcCCCCccccccccceeeEEEcCCCCeeeEeeC
Q 033478 52 KCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPY 84 (118)
Q Consensus 52 rC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~ 84 (118)
.|+.|.+.+... +...+.|..|+--++|-.
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCRECGYRILYKK 33 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCCCceEEEEe
Confidence 455555544322 234455666655555543
No 46
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=63.67 E-value=6.9 Score=31.52 Aligned_cols=24 Identities=21% Similarity=0.668 Sum_probs=18.8
Q ss_pred EcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 72 KCASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 72 ~Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
.|..||..|++ .-...+|+.|.++
T Consensus 151 ~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 151 RCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EccCCCcceEE--cCcEEECCCCCCE
Confidence 48888888888 6677888888764
No 47
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=63.09 E-value=3.6 Score=36.10 Aligned_cols=26 Identities=42% Similarity=0.991 Sum_probs=24.0
Q ss_pred eccccceeeecCCCCeEEcCCCCccccc
Q 033478 35 CGSCRRLLAYPRGARHVKCSCCQTVNFV 62 (118)
Q Consensus 35 CggCr~lL~YprGA~sVrC~~C~tVn~v 62 (118)
|. ||+-++-|.||.. ||+.|++++..
T Consensus 7 ~~-~~~p~~~pp~ar~-q~~~~~~~~~~ 32 (362)
T KOG1546|consen 7 CN-CQRPMAPPPGARY-QCAGCHAVTQI 32 (362)
T ss_pred CC-CCCCCCCCCCCcc-cccccceeeee
Confidence 55 9999999999999 99999999974
No 48
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=62.90 E-value=9.8 Score=26.25 Aligned_cols=31 Identities=23% Similarity=0.522 Sum_probs=23.4
Q ss_pred EEcCCCCeeeEeeCCCCeEECCCCCccceeccC
Q 033478 71 VKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVC 103 (118)
Q Consensus 71 v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~~~ 103 (118)
.+| .|+..|....|+..-+| .|.....|.+.
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~ 34 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKER 34 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEEEE--SS
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCeeeeeeE
Confidence 679 79999999999999999 89999988754
No 49
>PRK02935 hypothetical protein; Provisional
Probab=62.88 E-value=4.3 Score=30.45 Aligned_cols=26 Identities=31% Similarity=0.332 Sum_probs=21.2
Q ss_pred eCCCCeEECCCCCccceeccCCcceeeee
Q 033478 83 PYGAPSVRCSSCCFVTEIGVCGLSLFLCM 111 (118)
Q Consensus 83 P~GA~SVrCs~C~tVT~V~~~n~r~~l~~ 111 (118)
.--|.-|.||.|+.+|.+ .+|++.||
T Consensus 65 StkavqV~CP~C~K~TKm---LGrvD~CM 90 (110)
T PRK02935 65 STKAVQVICPSCEKPTKM---LGRVDACM 90 (110)
T ss_pred cccceeeECCCCCchhhh---ccceeecC
Confidence 345677899999999984 67889988
No 50
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=62.42 E-value=4.4 Score=23.96 Aligned_cols=30 Identities=27% Similarity=0.590 Sum_probs=16.8
Q ss_pred cCCCCeeeEeeCCCCe-EECCCCCccceecc
Q 033478 73 CASCAVLLMYPYGAPS-VRCSSCCFVTEIGV 102 (118)
Q Consensus 73 Cg~Crt~LmyP~GA~S-VrCs~C~tVT~V~~ 102 (118)
|..|+.+|....+... +.|..|.++-.+..
T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRTCGYEEPISQ 34 (35)
T ss_dssp ETTTTSBEEEEEETTTTEEESSSS-EEE-SS
T ss_pred CCCCCccceEcCCCccCcCCCCCCCccCCCC
Confidence 6777776654443333 35888877766643
No 51
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=60.88 E-value=2.3 Score=28.85 Aligned_cols=33 Identities=30% Similarity=0.574 Sum_probs=21.0
Q ss_pred eEEEcCCCCeeeEeeCCC--CeEECCCCCccceec
Q 033478 69 GQVKCASCAVLLMYPYGA--PSVRCSSCCFVTEIG 101 (118)
Q Consensus 69 a~v~Cg~Crt~LmyP~GA--~SVrCs~C~tVT~V~ 101 (118)
-.++|..|..+|.=..|. .-++||.|..||.+.
T Consensus 3 ~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~~ 37 (60)
T COG4416 3 QTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEFY 37 (60)
T ss_pred eeeehHHHhHHHHhcccceeeeecCCccceeeeee
Confidence 346666666666555443 456788887777654
No 52
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=60.68 E-value=9.4 Score=26.02 Aligned_cols=50 Identities=36% Similarity=0.741 Sum_probs=37.4
Q ss_pred eeeccccceeeecCCCCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 33 MVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 33 LvCggCr~lL~YprGA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
.+|.+|-..|.=-.+|.+--|++|.-+.. .+|..||.+ ....+|+.|.+.
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~I---------~Rc~~CRk~------g~~Y~Cp~CGF~ 59 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVEI---------YRCAKCRKL------GNPYRCPKCGFE 59 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCceee---------ehhhhHHHc------CCceECCCcCcc
Confidence 58999999888888888889999975443 568888864 234577777654
No 53
>PF15616 TerY-C: TerY-C metal binding domain
Probab=60.33 E-value=8.7 Score=29.12 Aligned_cols=41 Identities=22% Similarity=0.468 Sum_probs=21.9
Q ss_pred eeeeecccC--ccccceeeeccccceeeecCCCCeEEcCCCCccc
Q 033478 18 SFWLTLTCY--HQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVN 60 (118)
Q Consensus 18 ~~~~~~~~~--~~~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn 60 (118)
|.+=.+.|| |.+.+-.+| +|..|+=|-- -..|-||-|...-
T Consensus 73 eL~g~PgCP~CGn~~~fa~C-~CGkl~Ci~g-~~~~~CPwCg~~g 115 (131)
T PF15616_consen 73 ELIGAPGCPHCGNQYAFAVC-GCGKLFCIDG-EGEVTCPWCGNEG 115 (131)
T ss_pred HhcCCCCCCCCcChhcEEEe-cCCCEEEeCC-CCCEECCCCCCee
Confidence 333345566 455555555 5666666654 3355666665443
No 54
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=58.73 E-value=3.7 Score=22.58 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=14.0
Q ss_pred EEcCCCCccccccccceeeEEEcCCCCeee
Q 033478 51 VKCSCCQTVNFVLEAHQVGQVKCASCAVLL 80 (118)
Q Consensus 51 VrC~~C~tVn~v~~a~q~a~v~Cg~Crt~L 80 (118)
+.|+.|.+.+.. ..-.|.+|++.|
T Consensus 3 ~~Cp~Cg~~~~~------~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEIDP------DAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCCc------ccccChhhCCCC
Confidence 457777775432 235677776654
No 55
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=57.89 E-value=19 Score=28.34 Aligned_cols=41 Identities=22% Similarity=0.473 Sum_probs=33.0
Q ss_pred cccceeeEEEcCCCCeeeEeeC------CCCeEECCCCCccceeccC
Q 033478 63 LEAHQVGQVKCASCAVLLMYPY------GAPSVRCSSCCFVTEIGVC 103 (118)
Q Consensus 63 ~~a~q~a~v~Cg~Crt~LmyP~------GA~SVrCs~C~tVT~V~~~ 103 (118)
.+..+.-+|.|+-|.|.|.+-- ..-+|||..|..+-.|...
T Consensus 5 ~~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~ 51 (170)
T PF04690_consen 5 SPSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMR 51 (170)
T ss_pred CCCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeecc
Confidence 4567899999999999998753 4568999999988776543
No 56
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.60 E-value=15 Score=34.61 Aligned_cols=53 Identities=26% Similarity=0.538 Sum_probs=39.1
Q ss_pred cceeeecC-C-CCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCccceecc
Q 033478 39 RRLLAYPR-G-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGV 102 (118)
Q Consensus 39 r~lL~Ypr-G-A~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~~ 102 (118)
+++|+-+| | ++.+.|..|..+- .|.+|...|.|.......+|--|++-..++.
T Consensus 422 Q~llflnRRGys~~l~C~~Cg~v~-----------~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~ 476 (730)
T COG1198 422 QVLLFLNRRGYAPLLLCRDCGYIA-----------ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQ 476 (730)
T ss_pred eEEEEEccCCccceeecccCCCcc-----------cCCCCCcceEEecCCCeeEeCCCCCCCCCCC
Confidence 34555554 4 5588899998774 5888888888888888888888887766653
No 57
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=56.11 E-value=21 Score=24.71 Aligned_cols=36 Identities=19% Similarity=0.425 Sum_probs=27.7
Q ss_pred ceeeEEEcCCCC-eeeEeeCCCCeEECCCCCccceec
Q 033478 66 HQVGQVKCASCA-VLLMYPYGAPSVRCSSCCFVTEIG 101 (118)
Q Consensus 66 ~q~a~v~Cg~Cr-t~LmyP~GA~SVrCs~C~tVT~V~ 101 (118)
.-...+.|.+|+ ...+|-.-+..|+|..|.++--.+
T Consensus 15 s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 15 SRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred ceEEEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 346778899996 567888888899999998865433
No 58
>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=55.15 E-value=11 Score=32.49 Aligned_cols=31 Identities=23% Similarity=0.541 Sum_probs=14.3
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeee
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLL 80 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~L 80 (118)
.+.|+.|+.+...|+-..-..-.|..|+..|
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 3445555555554432222233455555555
No 59
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=52.06 E-value=17 Score=23.54 Aligned_cols=33 Identities=21% Similarity=0.422 Sum_probs=23.5
Q ss_pred eeEEEcCCCCeeeEeeCCCCeEECCCCCcccee
Q 033478 68 VGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 100 (118)
Q Consensus 68 ~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V 100 (118)
+..-.|..|+..+-......-++|+-|.+=-.+
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSRILV 36 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcEEEE
Confidence 455668888888877777788888888764443
No 60
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=50.97 E-value=7.2 Score=23.01 Aligned_cols=12 Identities=25% Similarity=1.082 Sum_probs=5.0
Q ss_pred EEcCCCCeeeEe
Q 033478 71 VKCASCAVLLMY 82 (118)
Q Consensus 71 v~Cg~Crt~Lmy 82 (118)
|.|..|+--++|
T Consensus 18 irC~~CG~RIly 29 (32)
T PF03604_consen 18 IRCPECGHRILY 29 (32)
T ss_dssp SSBSSSS-SEEB
T ss_pred EECCcCCCeEEE
Confidence 444444444443
No 61
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=50.47 E-value=15 Score=24.83 Aligned_cols=30 Identities=30% Similarity=0.600 Sum_probs=20.8
Q ss_pred eeEEEcCCCCeeeEeeCC-CCeEECCCCCccc
Q 033478 68 VGQVKCASCAVLLMYPYG-APSVRCSSCCFVT 98 (118)
Q Consensus 68 ~a~v~Cg~Crt~LmyP~G-A~SVrCs~C~tVT 98 (118)
+....|..|+..| .|.+ +....|+.|..++
T Consensus 5 ~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~ 35 (59)
T PRK14890 5 MEPPKCTSCGIEI-APREKAVKFLCPNCGEVI 35 (59)
T ss_pred ccCccccCCCCcc-cCCCccCEeeCCCCCCee
Confidence 3344688888877 4555 7888888887653
No 62
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=48.91 E-value=11 Score=34.71 Aligned_cols=10 Identities=40% Similarity=0.584 Sum_probs=5.3
Q ss_pred EcCCCCcccc
Q 033478 52 KCSCCQTVNF 61 (118)
Q Consensus 52 rC~~C~tVn~ 61 (118)
.|+.|++.|+
T Consensus 3 ~Cp~Cg~~n~ 12 (645)
T PRK14559 3 ICPQCQFENP 12 (645)
T ss_pred cCCCCCCcCC
Confidence 4555555553
No 63
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=46.76 E-value=44 Score=26.97 Aligned_cols=49 Identities=24% Similarity=0.380 Sum_probs=34.2
Q ss_pred eeeeeccccceeeeeecccCccccce--eeeccccceeeecCCCCeEEcCCCCccc
Q 033478 7 SVARVNSLSQESFWLTLTCYHQEMAQ--MVCGSCRRLLAYPRGARHVKCSCCQTVN 60 (118)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~sQ--LvCggCr~lL~YprGA~sVrC~~C~tVn 60 (118)
--|||-|+- +=+.++--+.+++- -.|..||..|++ .-...+|+.|..+-
T Consensus 125 vrA~Vis~~---~~~~Lst~~~dlGVI~A~CsrC~~~L~~--~~~~l~Cp~Cg~tE 175 (188)
T COG1096 125 VRARVISTG---DPIQLSTKGNDLGVIYARCSRCRAPLVK--KGNMLKCPNCGNTE 175 (188)
T ss_pred EEEEEEecC---CCeEEEecCCcceEEEEEccCCCcceEE--cCcEEECCCCCCEE
Confidence 346776665 33444455566654 479999999999 66788999998653
No 64
>PLN00209 ribosomal protein S27; Provisional
Probab=46.21 E-value=20 Score=25.78 Aligned_cols=37 Identities=22% Similarity=0.457 Sum_probs=23.3
Q ss_pred ccccceeeeccccce-eeecCCCCeEEcCCCCcccccc
Q 033478 27 HQEMAQMVCGSCRRL-LAYPRGARHVKCSCCQTVNFVL 63 (118)
Q Consensus 27 ~~~~sQLvCggCr~l-L~YprGA~sVrC~~C~tVn~v~ 63 (118)
..-+-...|.+|..+ ..|..-.+-|.|..|+++=.-|
T Consensus 31 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 31 NSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQP 68 (86)
T ss_pred CCEEEEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 344445566666543 5677777777777777766544
No 65
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=45.94 E-value=21 Score=25.65 Aligned_cols=37 Identities=14% Similarity=0.403 Sum_probs=23.9
Q ss_pred ccccceeeeccccce-eeecCCCCeEEcCCCCcccccc
Q 033478 27 HQEMAQMVCGSCRRL-LAYPRGARHVKCSCCQTVNFVL 63 (118)
Q Consensus 27 ~~~~sQLvCggCr~l-L~YprGA~sVrC~~C~tVn~v~ 63 (118)
..-+-...|.||..+ ..|..-++-|.|..|+++=.-|
T Consensus 30 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 30 NSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQP 67 (85)
T ss_pred CCeEEEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 334445566667543 5677777778888887776554
No 66
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=45.32 E-value=14 Score=32.09 Aligned_cols=30 Identities=17% Similarity=0.480 Sum_probs=15.7
Q ss_pred EEcCCCCccccccccceeeEEEcCCCCeee
Q 033478 51 VKCSCCQTVNFVLEAHQVGQVKCASCAVLL 80 (118)
Q Consensus 51 VrC~~C~tVn~v~~a~q~a~v~Cg~Crt~L 80 (118)
+.|+.|+.+...++-..-..-.|..|+..|
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 446666666655542222234466666655
No 67
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=44.97 E-value=21 Score=23.49 Aligned_cols=34 Identities=24% Similarity=0.496 Sum_probs=19.2
Q ss_pred ceeeeccccce-eeecCCCCeEEcCCCCccccccc
Q 033478 31 AQMVCGSCRRL-LAYPRGARHVKCSCCQTVNFVLE 64 (118)
Q Consensus 31 sQLvCggCr~l-L~YprGA~sVrC~~C~tVn~v~~ 64 (118)
=...|.+|..+ ..|.+-++.|.|..|+++=.-|.
T Consensus 6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~Pt 40 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPT 40 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-
T ss_pred EEEECCCCCCeeEEEecCCeEEEcccCCCEecCCC
Confidence 34566677543 56788888888888888765553
No 68
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=44.62 E-value=30 Score=20.81 Aligned_cols=26 Identities=27% Similarity=0.742 Sum_probs=16.0
Q ss_pred EEcC--CCCeeeEeeC--CCCeEECCCCCc
Q 033478 71 VKCA--SCAVLLMYPY--GAPSVRCSSCCF 96 (118)
Q Consensus 71 v~Cg--~Crt~LmyP~--GA~SVrCs~C~t 96 (118)
..|. +|...+..+. |...|+|+.|+.
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~ 48 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGF 48 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCC
Confidence 3466 6666666653 667777766654
No 69
>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=43.80 E-value=17 Score=24.90 Aligned_cols=28 Identities=29% Similarity=0.619 Sum_probs=19.4
Q ss_pred EcCCCCeeeEeeCCCCeEECCCCCccceec
Q 033478 72 KCASCAVLLMYPYGAPSVRCSSCCFVTEIG 101 (118)
Q Consensus 72 ~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~ 101 (118)
.|..|+.+| +|.+ ..+.|+.|.+...+.
T Consensus 2 fC~~Cg~~l-~~~~-~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 2 FCPKCGSLM-TPKN-GVYVCPSCGYEKEKK 29 (104)
T ss_pred CCcccCccc-ccCC-CeEECcCCCCccccc
Confidence 477888877 4443 368888888776653
No 70
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=42.80 E-value=19 Score=22.48 Aligned_cols=27 Identities=26% Similarity=0.536 Sum_probs=13.9
Q ss_pred eeeeccccceeee------cCCCCeEEcCCCCc
Q 033478 32 QMVCGSCRRLLAY------PRGARHVKCSCCQT 58 (118)
Q Consensus 32 QLvCggCr~lL~Y------prGA~sVrC~~C~t 58 (118)
.-+|+||+..|.- .+|..-+.|+.|+.
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 3477777754432 12334555555544
No 71
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=42.68 E-value=2 Score=25.59 Aligned_cols=23 Identities=35% Similarity=0.810 Sum_probs=12.1
Q ss_pred eEEEcCCCCeeeEeeCCCCeEECCCCC
Q 033478 69 GQVKCASCAVLLMYPYGAPSVRCSSCC 95 (118)
Q Consensus 69 a~v~Cg~Crt~LmyP~GA~SVrCs~C~ 95 (118)
+|+.|..|-..++ ...++|+.|+
T Consensus 21 gH~~C~~C~~~~~----~~~~~CP~C~ 43 (44)
T PF14634_consen 21 GHIFCEKCLKKLK----GKSVKCPICR 43 (44)
T ss_pred CCHHHHHHHHhhc----CCCCCCcCCC
Confidence 3444555555555 5555555554
No 72
>PF14369 zf-RING_3: zinc-finger
Probab=42.32 E-value=26 Score=20.74 Aligned_cols=26 Identities=19% Similarity=0.434 Sum_probs=15.9
Q ss_pred EEcCCCCeeeEee-CCCCeEECCCCCc
Q 033478 71 VKCASCAVLLMYP-YGAPSVRCSSCCF 96 (118)
Q Consensus 71 v~Cg~Crt~LmyP-~GA~SVrCs~C~t 96 (118)
-.|-+|+...... .+...+.||.|+.
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 3567777766663 3444455777763
No 73
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=42.02 E-value=23 Score=21.07 Aligned_cols=25 Identities=32% Similarity=0.816 Sum_probs=9.4
Q ss_pred cCCCCeeeEe--eCC--CCeEECCCCCcc
Q 033478 73 CASCAVLLMY--PYG--APSVRCSSCCFV 97 (118)
Q Consensus 73 Cg~Crt~Lmy--P~G--A~SVrCs~C~tV 97 (118)
|.+|+..|.. |.| -.-..|+.|++|
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred cccccChhhhhcCCCCCccceECCCCCCE
Confidence 5555555443 432 233446666655
No 74
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=40.64 E-value=16 Score=21.94 Aligned_cols=25 Identities=28% Similarity=0.753 Sum_probs=11.4
Q ss_pred eecc--ccceeeecCCCCe--EEcCCCCc
Q 033478 34 VCGS--CRRLLAYPRGARH--VKCSCCQT 58 (118)
Q Consensus 34 vCgg--Cr~lL~YprGA~s--VrC~~C~t 58 (118)
.|.+ |...+....|... |+|+.|++
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 48 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGT 48 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCS
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCC
Confidence 5644 6666666666665 66666654
No 75
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=40.62 E-value=37 Score=20.93 Aligned_cols=27 Identities=26% Similarity=0.577 Sum_probs=18.0
Q ss_pred eeEEEcCCCCeeeEeeCCCCeEECCCCC
Q 033478 68 VGQVKCASCAVLLMYPYGAPSVRCSSCC 95 (118)
Q Consensus 68 ~a~v~Cg~Crt~LmyP~GA~SVrCs~C~ 95 (118)
|-.-.|..|+++||=..+- .+.|+.|.
T Consensus 15 ML~~~Cp~C~~PL~~~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 15 MLDEHCPDCGTPLMRDKDG-KIYCVSCG 41 (41)
T ss_pred HhcCccCCCCCeeEEecCC-CEECCCCC
Confidence 4445688888888875544 46777773
No 76
>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=40.33 E-value=18 Score=20.81 Aligned_cols=21 Identities=33% Similarity=0.800 Sum_probs=10.0
Q ss_pred eeccccceeeecCCCCeEEcCCCCc
Q 033478 34 VCGSCRRLLAYPRGARHVKCSCCQT 58 (118)
Q Consensus 34 vCggCr~lL~YprGA~sVrC~~C~t 58 (118)
.|..|..+..||+ ..|+.|.+
T Consensus 13 rC~~Cg~~~~pPr----~~Cp~C~s 33 (37)
T PF12172_consen 13 RCRDCGRVQFPPR----PVCPHCGS 33 (37)
T ss_dssp E-TTT--EEES------SEETTTT-
T ss_pred EcCCCCCEecCCC----cCCCCcCc
Confidence 5777777777776 35666653
No 77
>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=39.64 E-value=35 Score=24.45 Aligned_cols=28 Identities=18% Similarity=0.409 Sum_probs=17.9
Q ss_pred eEEEcCCCCeeeEeeCCCCeEECCCCCccc
Q 033478 69 GQVKCASCAVLLMYPYGAPSVRCSSCCFVT 98 (118)
Q Consensus 69 a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT 98 (118)
+...|..|+ -.++.......||.|+..+
T Consensus 69 ~~~~C~~Cg--~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 69 VECECEDCS--EEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred cEEEcccCC--CEEecCCcCccCcCCcCCC
Confidence 346677777 3445555567788888754
No 78
>PRK10996 thioredoxin 2; Provisional
Probab=38.99 E-value=18 Score=25.81 Aligned_cols=32 Identities=25% Similarity=0.591 Sum_probs=20.4
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeeeE
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLM 81 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~Lm 81 (118)
+-.|+.|+.+|.-|+..---+-.||+|...+.
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (139)
T PRK10996 2 NTVCTSCQAINRLPDERIEDAAKCGRCGHDLF 33 (139)
T ss_pred eEECCCCCCcCCCCCccccCCCcCCCCCCccC
Confidence 45688888888776532233346887776654
No 79
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.13 E-value=34 Score=30.11 Aligned_cols=22 Identities=23% Similarity=0.641 Sum_probs=10.7
Q ss_pred EEEcCCCCeeeEeeCCCCeEECCCCCc
Q 033478 70 QVKCASCAVLLMYPYGAPSVRCSSCCF 96 (118)
Q Consensus 70 ~v~Cg~Crt~LmyP~GA~SVrCs~C~t 96 (118)
.+.|..|+-.--+|. +|+.|+.
T Consensus 240 ~l~Ch~Cg~~~~~~~-----~Cp~C~s 261 (505)
T TIGR00595 240 KLRCHYCGYQEPIPK-----TCPQCGS 261 (505)
T ss_pred eEEcCCCcCcCCCCC-----CCCCCCC
Confidence 455555554433332 5555554
No 80
>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=37.87 E-value=46 Score=21.00 Aligned_cols=18 Identities=17% Similarity=0.165 Sum_probs=9.1
Q ss_pred eecCCCCeEEcCCCCcccc
Q 033478 43 AYPRGARHVKCSCCQTVNF 61 (118)
Q Consensus 43 ~YprGA~sVrC~~C~tVn~ 61 (118)
.-|.+ +|-.|+.|..++.
T Consensus 22 v~~~~-TSq~C~~CG~~~~ 39 (69)
T PF07282_consen 22 VDEAY-TSQTCPRCGHRNK 39 (69)
T ss_pred ECCCC-CccCccCcccccc
Confidence 33444 5555555555554
No 81
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=37.84 E-value=10 Score=25.79 Aligned_cols=21 Identities=29% Similarity=0.719 Sum_probs=14.9
Q ss_pred eeecCCCCeEEcCCCCccccc
Q 033478 42 LAYPRGARHVKCSCCQTVNFV 62 (118)
Q Consensus 42 L~YprGA~sVrC~~C~tVn~v 62 (118)
.+|-+|..-|||+.|+..-..
T Consensus 21 ~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 21 QAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp HHHHTSEEEEE-TTS--EEES
T ss_pred HHHhCCeEEEECCCCcceeee
Confidence 579999999999999876543
No 82
>PRK11827 hypothetical protein; Provisional
Probab=37.66 E-value=41 Score=22.45 Aligned_cols=32 Identities=16% Similarity=0.279 Sum_probs=21.9
Q ss_pred eeeeccccceeeecCCCCeEEcCCCCcccccc
Q 033478 32 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFVL 63 (118)
Q Consensus 32 QLvCggCr~lL~YprGA~sVrC~~C~tVn~v~ 63 (118)
-|+|..|+.-|.|-.++..-.|..|+-.-++.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeecccc
Confidence 46788888888887777666666666555543
No 83
>PRK04351 hypothetical protein; Provisional
Probab=36.81 E-value=31 Score=26.18 Aligned_cols=33 Identities=15% Similarity=0.358 Sum_probs=19.1
Q ss_pred EEcCCCCccccccccceeeEEEcCCCCeeeEee
Q 033478 51 VKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYP 83 (118)
Q Consensus 51 VrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP 83 (118)
-+|..|+.+-.-.-..+...-.||.|+..|..-
T Consensus 113 Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 113 YECQSCGQQYLRKRRINTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EECCCCCCEeeeeeecCCCcEEeCCCCcEeeec
Confidence 356666654433223345667788887777653
No 84
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=36.65 E-value=51 Score=19.36 Aligned_cols=26 Identities=19% Similarity=0.266 Sum_probs=12.0
Q ss_pred EcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 72 KCASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 72 ~Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
.|.+|+..+++-....--.|.-|..+
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCcE
Confidence 44445554444444444444444444
No 85
>PRK11827 hypothetical protein; Provisional
Probab=36.49 E-value=48 Score=22.13 Aligned_cols=33 Identities=15% Similarity=0.270 Sum_probs=27.0
Q ss_pred EEEcCCCCeeeEeeCCCCeEECCCCCccceecc
Q 033478 70 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGV 102 (118)
Q Consensus 70 ~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~~ 102 (118)
-+.|..|+..|.|-.++...-|..|+-.-+|+.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~d 40 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFPLRD 40 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeeccccC
Confidence 477999999999988888888998887777754
No 86
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=35.64 E-value=43 Score=25.48 Aligned_cols=34 Identities=15% Similarity=0.302 Sum_probs=20.9
Q ss_pred eeEEEcCCCCeeeEeeCCCCeEECCCCCccceec
Q 033478 68 VGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 101 (118)
Q Consensus 68 ~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~ 101 (118)
.+.++|-+|+-.+.+-.-..--.|+.|+...-.+
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHTEFTR 143 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCCeeee
Confidence 4556666666666666555566677666655443
No 87
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=35.09 E-value=33 Score=20.49 Aligned_cols=26 Identities=31% Similarity=0.686 Sum_probs=16.3
Q ss_pred EEcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 71 VKCASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 71 v~Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
..|..|+..|.- .+.+..+|+.|+.+
T Consensus 12 ~~C~~C~~~i~g-~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 12 TYCDVCGKFIWG-LGKQGYRCSWCGLV 37 (53)
T ss_dssp EB-TTSSSBECS-SSSCEEEETTTT-E
T ss_pred CCCcccCcccCC-CCCCeEEECCCCCh
Confidence 457777777733 66777777777654
No 88
>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=34.80 E-value=17 Score=20.71 Aligned_cols=23 Identities=30% Similarity=0.732 Sum_probs=11.8
Q ss_pred EcCCCCeeeEeeCCCCeEECCCCCc
Q 033478 72 KCASCAVLLMYPYGAPSVRCSSCCF 96 (118)
Q Consensus 72 ~Cg~Crt~LmyP~GA~SVrCs~C~t 96 (118)
.|..|+..|.... +..+|+.|+.
T Consensus 13 ~C~~C~~~i~~~~--~~~~C~~C~~ 35 (49)
T smart00109 13 KCCVCRKSIWGSF--QGLRCSWCKV 35 (49)
T ss_pred CccccccccCcCC--CCcCCCCCCc
Confidence 3555555554322 3556666543
No 89
>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=34.30 E-value=40 Score=29.15 Aligned_cols=32 Identities=19% Similarity=0.580 Sum_probs=23.3
Q ss_pred eeEEEcCCCCeeeEeeC--CCCeEECCCCCccce
Q 033478 68 VGQVKCASCAVLLMYPY--GAPSVRCSSCCFVTE 99 (118)
Q Consensus 68 ~a~v~Cg~Crt~LmyP~--GA~SVrCs~C~tVT~ 99 (118)
...+.|..|....-.|+ .....+|+.|+++=.
T Consensus 11 ~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 11 AKHILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred CCeeeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 34567999998888875 444567999988764
No 90
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=34.28 E-value=18 Score=29.85 Aligned_cols=12 Identities=25% Similarity=0.357 Sum_probs=5.5
Q ss_pred CCCeEECCCCCc
Q 033478 85 GAPSVRCSSCCF 96 (118)
Q Consensus 85 GA~SVrCs~C~t 96 (118)
+-.-|+||.|+.
T Consensus 218 ~d~iv~CP~CgR 229 (239)
T COG1579 218 KDEIVFCPYCGR 229 (239)
T ss_pred CCCCccCCccch
Confidence 334445555543
No 91
>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=34.25 E-value=40 Score=19.04 Aligned_cols=26 Identities=19% Similarity=0.502 Sum_probs=15.8
Q ss_pred EEcCCCCeeeEeeC--C-CCeEECCCCCc
Q 033478 71 VKCASCAVLLMYPY--G-APSVRCSSCCF 96 (118)
Q Consensus 71 v~Cg~Crt~LmyP~--G-A~SVrCs~C~t 96 (118)
..|..|+...-... + ...+.|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 46777776443332 2 45777888876
No 92
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=34.23 E-value=71 Score=21.44 Aligned_cols=31 Identities=16% Similarity=0.496 Sum_probs=14.8
Q ss_pred eeeeccccce-eeecCCCCeEEcCCCCccccc
Q 033478 32 QMVCGSCRRL-LAYPRGARHVKCSCCQTVNFV 62 (118)
Q Consensus 32 QLvCggCr~l-L~YprGA~sVrC~~C~tVn~v 62 (118)
...|.+|... ..|.+-++-|.|..|.++=.-
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 3444444432 345555555555555554433
No 93
>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=34.08 E-value=24 Score=20.39 Aligned_cols=24 Identities=25% Similarity=0.415 Sum_probs=12.7
Q ss_pred EcCCCCeeeEeeCCCCeEECCCCCc
Q 033478 72 KCASCAVLLMYPYGAPSVRCSSCCF 96 (118)
Q Consensus 72 ~Cg~Crt~LmyP~GA~SVrCs~C~t 96 (118)
.|..|+..|... +.+..+|+.|+.
T Consensus 13 ~C~~C~~~i~~~-~~~~~~C~~C~~ 36 (50)
T cd00029 13 FCDVCRKSIWGL-FKQGLRCSWCKV 36 (50)
T ss_pred Chhhcchhhhcc-ccceeEcCCCCC
Confidence 355555555432 455566666644
No 94
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=33.71 E-value=1e+02 Score=21.25 Aligned_cols=58 Identities=26% Similarity=0.568 Sum_probs=34.9
Q ss_pred eeeccccceeeecCCCCeEEcCCCCccccccccceeeEEEcCCCCeeeEee--CCCCeEECCCCCccce
Q 033478 33 MVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYP--YGAPSVRCSSCCFVTE 99 (118)
Q Consensus 33 LvCggCr~lL~YprGA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP--~GA~SVrCs~C~tVT~ 99 (118)
+.|..|+..|.- .| ..-.|..|+.-- ..+-.|..|+..|-.= =||-..-|-.||...+
T Consensus 2 ~~CP~C~~~L~~-~~-~~~~C~~C~~~~-------~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gLiS 61 (70)
T PF07191_consen 2 NTCPKCQQELEW-QG-GHYHCEACQKDY-------KKEAFCPDCGQPLEVLKACGAVDYFCNHCHGLIS 61 (70)
T ss_dssp -B-SSS-SBEEE-ET-TEEEETTT--EE-------EEEEE-TTT-SB-EEEEETTEEEEE-TTTT-EE-
T ss_pred CcCCCCCCccEE-eC-CEEECccccccc-------eecccCCCcccHHHHHHHhcccceeeccCCceee
Confidence 578888888554 44 788899998632 4457899999988664 4888899999987643
No 95
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=32.99 E-value=63 Score=21.48 Aligned_cols=33 Identities=18% Similarity=0.396 Sum_probs=15.0
Q ss_pred ceeeEEEcCCCCeeeEeeCCCCeEECCCCCccc
Q 033478 66 HQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVT 98 (118)
Q Consensus 66 ~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT 98 (118)
.....|.|..|+..=-++.----.||+.|..-|
T Consensus 26 ~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYN 58 (61)
T PF14599_consen 26 NKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYN 58 (61)
T ss_dssp --EEEEEESSS--EEEEE--TT----TTTS---
T ss_pred CCEEEEECCCCCCccceeeeHhhhcCCCCCCcc
Confidence 456677777777777777777777777776644
No 96
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.05 E-value=37 Score=33.86 Aligned_cols=54 Identities=20% Similarity=0.444 Sum_probs=39.8
Q ss_pred cccceeeeccccceeeecCCCCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCcccee
Q 033478 28 QEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 100 (118)
Q Consensus 28 ~~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V 100 (118)
.+.+.-.|.+|-... ..-+|+.|.+.|.. .-.|..|++..- ...|+.|.+.+..
T Consensus 622 VEVg~RfCpsCG~~t------~~frCP~CG~~Te~-------i~fCP~CG~~~~------~y~CPKCG~El~~ 675 (1121)
T PRK04023 622 VEIGRRKCPSCGKET------FYRRCPFCGTHTEP-------VYRCPRCGIEVE------EDECEKCGREPTP 675 (1121)
T ss_pred ecccCccCCCCCCcC------CcccCCCCCCCCCc-------ceeCccccCcCC------CCcCCCCCCCCCc
Confidence 455667899999874 55799999998632 268999977643 1349999988764
No 97
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=32.04 E-value=36 Score=25.35 Aligned_cols=31 Identities=16% Similarity=0.548 Sum_probs=23.1
Q ss_pred eEEcCCCCcccccc----ccceeeEEEcCCCCeee
Q 033478 50 HVKCSCCQTVNFVL----EAHQVGQVKCASCAVLL 80 (118)
Q Consensus 50 sVrC~~C~tVn~v~----~a~q~a~v~Cg~Crt~L 80 (118)
.--|+.|+..+.+. -....+.++||.|+..-
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 34689999888873 24568889999998643
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.50 E-value=39 Score=24.88 Aligned_cols=45 Identities=27% Similarity=0.378 Sum_probs=27.5
Q ss_pred eeecCCCCeEEcCCCCccccccccc----eeeEEEcCCCCeeeEeeCCC
Q 033478 42 LAYPRGARHVKCSCCQTVNFVLEAH----QVGQVKCASCAVLLMYPYGA 86 (118)
Q Consensus 42 L~YprGA~sVrC~~C~tVn~v~~a~----q~a~v~Cg~Crt~LmyP~GA 86 (118)
|.|-.+-....|+.|+..-...++. ..+...|..|+..|..=.++
T Consensus 91 l~~e~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~ 139 (147)
T smart00531 91 LEDETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNS 139 (147)
T ss_pred HhcccCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCch
Confidence 4455566677788887544433221 23448888888888765443
No 99
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=31.43 E-value=67 Score=23.46 Aligned_cols=54 Identities=20% Similarity=0.279 Sum_probs=34.5
Q ss_pred ccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCccceeccCCcceeeeeec
Q 033478 58 TVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCD 113 (118)
Q Consensus 58 tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~~~n~r~~l~~~~ 113 (118)
+|....+. ..-..-|..|+..+ .+.++..-+|..|+....-+..-.++.+-.-|
T Consensus 23 ~I~~I~~~-~~~Y~aC~~C~kkv-~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D 76 (166)
T cd04476 23 TIVFIKPD-NWWYPACPGCNKKV-VEEGNGTYRCEKCNKSVPNPEYRYILSLNVAD 76 (166)
T ss_pred EEEEEcCC-CeEEccccccCccc-EeCCCCcEECCCCCCcCCCccEEEEEEEEEEe
Confidence 34444333 46667788888885 46677889999998876444444555554444
No 100
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=30.93 E-value=27 Score=28.74 Aligned_cols=13 Identities=31% Similarity=1.037 Sum_probs=6.3
Q ss_pred eeEEEcCCCCeee
Q 033478 68 VGQVKCASCAVLL 80 (118)
Q Consensus 68 ~a~v~Cg~Crt~L 80 (118)
.+.++|..|+..|
T Consensus 28 ~Ge~vC~~CG~Vl 40 (310)
T PRK00423 28 RGEIVCADCGLVI 40 (310)
T ss_pred CCeEeecccCCcc
Confidence 4445555555433
No 101
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=30.86 E-value=63 Score=23.49 Aligned_cols=32 Identities=19% Similarity=0.594 Sum_probs=20.1
Q ss_pred EEcCCCCcccccc-ccceeeEEEcCCCCeeeEe
Q 033478 51 VKCSCCQTVNFVL-EAHQVGQVKCASCAVLLMY 82 (118)
Q Consensus 51 VrC~~C~tVn~v~-~a~q~a~v~Cg~Crt~Lmy 82 (118)
-+|..|+...... -.++..+..|+.|+-.|.+
T Consensus 113 y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~~ 145 (146)
T smart00731 113 YRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLIL 145 (146)
T ss_pred EECCCCCCCCceEccccCcceEEcCCCCCEEEe
Confidence 4666666654422 2344577888888887763
No 102
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.76 E-value=24 Score=19.80 Aligned_cols=9 Identities=22% Similarity=0.833 Sum_probs=4.6
Q ss_pred eEECCCCCc
Q 033478 88 SVRCSSCCF 96 (118)
Q Consensus 88 SVrCs~C~t 96 (118)
...|+.|.+
T Consensus 14 ~~~Cp~CG~ 22 (26)
T PF10571_consen 14 AKFCPHCGY 22 (26)
T ss_pred cCcCCCCCC
Confidence 345555554
No 103
>PRK05580 primosome assembly protein PriA; Validated
Probab=30.70 E-value=53 Score=29.98 Aligned_cols=27 Identities=26% Similarity=0.556 Sum_probs=13.2
Q ss_pred eccccceeeecCCCCeEEcCCCCcccc
Q 033478 35 CGSCRRLLAYPRGARHVKCSCCQTVNF 61 (118)
Q Consensus 35 CggCr~lL~YprGA~sVrC~~C~tVn~ 61 (118)
|..|..-|.|...-....|..|.....
T Consensus 393 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 393 CPHCDASLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred CCCCCCceeEECCCCeEECCCCcCCCC
Confidence 444444455555444455555554433
No 104
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=30.68 E-value=51 Score=19.61 Aligned_cols=24 Identities=17% Similarity=0.430 Sum_probs=14.3
Q ss_pred cCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 73 CASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 73 Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
|+.|+.. .+-...-..-|..|+++
T Consensus 11 C~~C~~~-~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 11 CPVCGSR-WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCCCCe-EeEccCCEEEhhhCceE
Confidence 6666666 55555556666666655
No 105
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=30.55 E-value=52 Score=21.39 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=17.4
Q ss_pred EcCCCCeeeEeeCCC--CeEECCCCCccceecc
Q 033478 72 KCASCAVLLMYPYGA--PSVRCSSCCFVTEIGV 102 (118)
Q Consensus 72 ~Cg~Crt~LmyP~GA--~SVrCs~C~tVT~V~~ 102 (118)
.|..|+..+-+|... .-|.|+.|.+-=.|..
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~ 36 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAELEVVS 36 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEEEEEe
Confidence 455666666555432 3566666666555543
No 106
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.28 E-value=46 Score=23.84 Aligned_cols=27 Identities=19% Similarity=0.406 Sum_probs=17.8
Q ss_pred eEEEcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 69 GQVKCASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 69 a~v~Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
+...|..|+. .++.......||.|+..
T Consensus 69 ~~~~C~~Cg~--~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 69 AQAWCWDCSQ--VVEIHQHDAQCPHCHGE 95 (113)
T ss_pred cEEEcccCCC--EEecCCcCccCcCCCCC
Confidence 4567888873 34555556668888864
No 107
>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=30.17 E-value=35 Score=22.56 Aligned_cols=23 Identities=22% Similarity=0.325 Sum_probs=13.0
Q ss_pred eEECCCCCccceeccCCcceeee
Q 033478 88 SVRCSSCCFVTEIGVCGLSLFLC 110 (118)
Q Consensus 88 SVrCs~C~tVT~V~~~n~r~~l~ 110 (118)
.|+|+.|+..+.....|.--|.|
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFC 24 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFC 24 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSS
T ss_pred cccCCCCCCeecccCCCCcCCcc
Confidence 57888888888887777666666
No 108
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=30.16 E-value=25 Score=18.54 Aligned_cols=22 Identities=32% Similarity=0.863 Sum_probs=14.1
Q ss_pred EEcCCCCccccccccceeeEEEcCCCCe
Q 033478 51 VKCSCCQTVNFVLEAHQVGQVKCASCAV 78 (118)
Q Consensus 51 VrC~~C~tVn~v~~a~q~a~v~Cg~Crt 78 (118)
..|+.|..+|... ...|..|++
T Consensus 3 W~C~~C~~~N~~~------~~~C~~C~~ 24 (26)
T smart00547 3 WECPACTFLNFAS------RSKCFACGA 24 (26)
T ss_pred ccCCCCCCcChhh------hccccccCC
Confidence 4577788887643 256666665
No 109
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=30.14 E-value=30 Score=26.96 Aligned_cols=27 Identities=30% Similarity=0.765 Sum_probs=20.7
Q ss_pred EcCCCC-eeeEeeCCC-CeEECCCCCccc
Q 033478 72 KCASCA-VLLMYPYGA-PSVRCSSCCFVT 98 (118)
Q Consensus 72 ~Cg~Cr-t~LmyP~GA-~SVrCs~C~tVT 98 (118)
.|.-|+ ..++||... ..++|+.|.+|-
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~ 182 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVF 182 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCcccc
Confidence 466676 478888888 888888888774
No 110
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=29.92 E-value=26 Score=26.77 Aligned_cols=36 Identities=17% Similarity=0.347 Sum_probs=27.7
Q ss_pred ccceeeEEEcCCCCeeeEeeCCCCeEECCCCC-ccceec
Q 033478 64 EAHQVGQVKCASCAVLLMYPYGAPSVRCSSCC-FVTEIG 101 (118)
Q Consensus 64 ~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~-tVT~V~ 101 (118)
.++-|--..|..|+++|.= =...|-||+|. .++-+.
T Consensus 22 ~GAkML~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 22 QGAKMLAKHCPKCGTPLFR--KDGEVFCPVCGYREVVVE 58 (131)
T ss_pred hhhHHHHhhCcccCCccee--eCCeEECCCCCceEEEee
Confidence 3555667789999999998 56679999999 555544
No 111
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.55 E-value=48 Score=23.78 Aligned_cols=28 Identities=18% Similarity=0.387 Sum_probs=18.6
Q ss_pred eEEEcCCCCeeeEeeCCCCe-EECCCCCccc
Q 033478 69 GQVKCASCAVLLMYPYGAPS-VRCSSCCFVT 98 (118)
Q Consensus 69 a~v~Cg~Crt~LmyP~GA~S-VrCs~C~tVT 98 (118)
+...|..|+. .+|..... .+||.|+...
T Consensus 69 ~~~~C~~Cg~--~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 69 AECWCETCQQ--YVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred cEEEcccCCC--eeecCCccCCcCcCcCCCC
Confidence 4567888874 45554444 7799998653
No 112
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.37 E-value=92 Score=26.64 Aligned_cols=53 Identities=36% Similarity=0.686 Sum_probs=37.4
Q ss_pred ccceeeeccccceeeecCCCCeEEcCCCCccccccc--cceeeEEEcCCCCeeeEeeCCCCeEECCCCC
Q 033478 29 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLE--AHQVGQVKCASCAVLLMYPYGAPSVRCSSCC 95 (118)
Q Consensus 29 ~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v~~--a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~ 95 (118)
..+-.+|.+|- |+.-+-|..|+.=.-+.. ..+..-++|..|.- --.|||+.|.
T Consensus 226 ~~~~~~C~~CG-------g~rFlpC~~C~GS~kv~~~~~~~~~~~rC~~CNE-------NGLvrCp~Cs 280 (281)
T KOG2824|consen 226 CEGGGVCESCG-------GARFLPCSNCHGSCKVHEEEEDDGGVLRCLECNE-------NGLVRCPVCS 280 (281)
T ss_pred CCCCCcCCCcC-------CcceEecCCCCCceeeeeeccCCCcEEECcccCC-------CCceeCCccC
Confidence 33446788886 788888999988777654 56667777777763 3457777774
No 113
>PLN00162 transport protein sec23; Provisional
Probab=28.33 E-value=52 Score=30.72 Aligned_cols=32 Identities=19% Similarity=0.449 Sum_probs=18.6
Q ss_pred EEcCCCCeee----EeeCCCCeEECCCCCccceecc
Q 033478 71 VKCASCAVLL----MYPYGAPSVRCSSCCFVTEIGV 102 (118)
Q Consensus 71 v~Cg~Crt~L----myP~GA~SVrCs~C~tVT~V~~ 102 (118)
++|..||..| .+-.+...-+|+.|...|.+++
T Consensus 54 vRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~~P~ 89 (761)
T PLN00162 54 LRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNHFPP 89 (761)
T ss_pred CccCCCcCEECCceEEecCCCEEEccCCCCCCCCch
Confidence 4455555443 2334666777777777776653
No 114
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=28.15 E-value=52 Score=18.57 Aligned_cols=21 Identities=29% Similarity=0.721 Sum_probs=11.8
Q ss_pred EcCCCCeeeEeeCCCCeEECC
Q 033478 72 KCASCAVLLMYPYGAPSVRCS 92 (118)
Q Consensus 72 ~Cg~Crt~LmyP~GA~SVrCs 92 (118)
.|.-|+..|+...|.-..+|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 367777777777777777775
No 115
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.31 E-value=41 Score=28.49 Aligned_cols=28 Identities=18% Similarity=0.318 Sum_probs=20.2
Q ss_pred EEcCCCCeeeEeeCCCCeEECCCCCccc
Q 033478 71 VKCASCAVLLMYPYGAPSVRCSSCCFVT 98 (118)
Q Consensus 71 v~Cg~Crt~LmyP~GA~SVrCs~C~tVT 98 (118)
--||+|++.+-.-.|-....|+.|....
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 4477777777777777777777777643
No 116
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=27.02 E-value=77 Score=23.66 Aligned_cols=32 Identities=25% Similarity=0.662 Sum_probs=26.9
Q ss_pred EEcCCCCeeeEeeCCCC--eEECCCCCccceecc
Q 033478 71 VKCASCAVLLMYPYGAP--SVRCSSCCFVTEIGV 102 (118)
Q Consensus 71 v~Cg~Crt~LmyP~GA~--SVrCs~C~tVT~V~~ 102 (118)
.-|..|+-+|++--|+. ..-|..|-+|-.|..
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~~ 35 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFPISR 35 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceeeEee
Confidence 35889999999999987 567999999988873
No 117
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=26.62 E-value=21 Score=31.99 Aligned_cols=47 Identities=15% Similarity=0.361 Sum_probs=30.1
Q ss_pred cccceeeeeecccC----ccccceeeeccccceeeecCCCCeEEcCCCCccccc
Q 033478 13 SLSQESFWLTLTCY----HQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFV 62 (118)
Q Consensus 13 ~~~~~~~~~~~~~~----~~~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v 62 (118)
.++.+..|-.+-|+ +.+.++..|.+|..+.... ...+|+.|++-=.+
T Consensus 197 ~~~~~~lwe~~~pq~~~~~~~~~~~~C~~C~~~~~~~---~~~~CpRC~~~Ly~ 247 (418)
T COG2995 197 CVNRRWLWERFYPQTLATGAREGLRSCLCCHYILPHD---AEPRCPRCGSKLYV 247 (418)
T ss_pred hCCHHHHHHhhccccCCCCCcccceecccccccCCHh---hCCCCCCCCChhhc
Confidence 34556666666443 6677888888888654332 66778888765433
No 118
>cd00069 GHB Glycoprotein hormone beta chain homologues. Gonadotropins; reproductive hormones consisting of two glycosylated chains (alpha and beta) of similar topology with Cysteine-knot motifs.
Probab=26.60 E-value=47 Score=24.32 Aligned_cols=33 Identities=30% Similarity=0.582 Sum_probs=24.3
Q ss_pred cccceeeec------------cccc----eeeecCCCCeEEcCCCCcccc
Q 033478 28 QEMAQMVCG------------SCRR----LLAYPRGARHVKCSCCQTVNF 61 (118)
Q Consensus 28 ~~~sQLvCg------------gCr~----lL~YprGA~sVrC~~C~tVn~ 61 (118)
....|-+|. ||.. ...|| =|.|.+|+.|++-|.
T Consensus 42 ~~~~Q~vCtY~~~~Y~tv~lpgCp~gvdp~~tYP-VAlsC~C~~C~t~~t 90 (102)
T cd00069 42 SPLPQRVCTYRELSYETVRLPGCPPGVDPGVTYP-VALSCHCGKCNTDTT 90 (102)
T ss_pred CCcccCcccCCcEEEEEEECCCCcCCCCCCEEee-eecccccCCcCCCCc
Confidence 445677776 5776 78888 488888888888663
No 119
>PF07776 zf-AD: Zinc-finger associated domain (zf-AD) ; InterPro: IPR012934 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 zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus; PDB: 1PZW_A.
Probab=26.43 E-value=15 Score=22.11 Aligned_cols=25 Identities=20% Similarity=0.480 Sum_probs=14.2
Q ss_pred eeeeecccCccccceeeeccccceee
Q 033478 18 SFWLTLTCYHQEMAQMVCGSCRRLLA 43 (118)
Q Consensus 18 ~~~~~~~~~~~~~sQLvCggCr~lL~ 43 (118)
-+++.+. +..+..+.||..|.+.|.
T Consensus 32 ~~~~~i~-~~~~lp~~IC~~C~~~l~ 56 (75)
T PF07776_consen 32 CTGIQIS-PDDDLPQQICSSCWEKLQ 56 (75)
T ss_dssp H-SS----SS-SS-SEEEHHHHHHHH
T ss_pred HhCCcCc-CCCCCHHHHHHHHHHHHH
Confidence 3455555 667778889999987664
No 120
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=26.40 E-value=55 Score=18.01 Aligned_cols=10 Identities=20% Similarity=0.627 Sum_probs=3.6
Q ss_pred CCeEECCCCC
Q 033478 86 APSVRCSSCC 95 (118)
Q Consensus 86 A~SVrCs~C~ 95 (118)
..+.-|+.|+
T Consensus 19 r~~~~C~rCq 28 (30)
T PF06827_consen 19 RSTYLCPRCQ 28 (30)
T ss_dssp EEEEE-TTTC
T ss_pred CCCeECcCCc
Confidence 3344444443
No 121
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.16 E-value=42 Score=24.22 Aligned_cols=28 Identities=18% Similarity=0.454 Sum_probs=16.5
Q ss_pred eEEEcCCCCeeeEeeCCCC-eEECCCCCccc
Q 033478 69 GQVKCASCAVLLMYPYGAP-SVRCSSCCFVT 98 (118)
Q Consensus 69 a~v~Cg~Crt~LmyP~GA~-SVrCs~C~tVT 98 (118)
+...|..|+.. ++.... ..+||.|+..+
T Consensus 70 ~~~~C~~Cg~~--~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 70 VELECKDCSHV--FKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CEEEhhhCCCc--cccCCccCCcCcCCCCCc
Confidence 45677777733 444333 34588888753
No 122
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=26.10 E-value=5 Score=24.14 Aligned_cols=42 Identities=21% Similarity=0.424 Sum_probs=16.7
Q ss_pred cCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCC
Q 033478 53 CSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSC 94 (118)
Q Consensus 53 C~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C 94 (118)
|+.|..+=..|-..+=+|.-|..|-..+.-..+.....|+.|
T Consensus 1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 344444433332333444555555555444444444555554
No 123
>COG1148 HdrA Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]
Probab=25.89 E-value=34 Score=32.01 Aligned_cols=44 Identities=23% Similarity=0.464 Sum_probs=32.7
Q ss_pred ccCccccceeeeccccceeeecCCCCeEEcCCCCccccccccceeeEEEcCCCCee
Q 033478 24 TCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVL 79 (118)
Q Consensus 24 ~~~~~~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~ 79 (118)
++-.....+.+|+||++=+.-|-||-++- . ..||+ +.|.+|++-
T Consensus 552 ~~~~a~vde~~C~gC~~C~~Cpf~ais~~-k--a~v~~---------~~C~gCG~C 595 (622)
T COG1148 552 EPFVATVDEDKCTGCGICAECPFGAISVD-K--AEVNP---------LRCKGCGIC 595 (622)
T ss_pred cccccccchhhhcCCcceeeCCCCceecc-c--cccCh---------hhhCcccch
Confidence 45556678889999999999999999987 3 33333 567777653
No 124
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.38 E-value=53 Score=26.48 Aligned_cols=30 Identities=13% Similarity=0.172 Sum_probs=22.8
Q ss_pred EEEcCCCCeeeEeeCCCCeEECCCCCccce
Q 033478 70 QVKCASCAVLLMYPYGAPSVRCSSCCFVTE 99 (118)
Q Consensus 70 ~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~ 99 (118)
+-.|+.|+..|..-.+-..-.|+.|..+--
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPHCRERYY 128 (256)
T ss_pred CccccccCCCCeecCCceeEECCCCCCEEC
Confidence 456888888888777777788888876543
No 125
>PRK00420 hypothetical protein; Validated
Probab=25.09 E-value=46 Score=24.61 Aligned_cols=34 Identities=18% Similarity=0.241 Sum_probs=20.3
Q ss_pred eeeEEEcCCCCeeeEeeCCCCeEECCCCCccceec
Q 033478 67 QVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 101 (118)
Q Consensus 67 q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~V~ 101 (118)
.|..-.|.-|++.|+=- ....+.|+.|+.+-.|.
T Consensus 20 ~ml~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 20 KMLSKHCPVCGLPLFEL-KDGEVVCPVHGKVYIVK 53 (112)
T ss_pred HHccCCCCCCCCcceec-CCCceECCCCCCeeeec
Confidence 34445677777776653 23356777777765553
No 126
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.06 E-value=85 Score=29.73 Aligned_cols=29 Identities=17% Similarity=0.544 Sum_probs=14.0
Q ss_pred eccccceeeecCCCCeEEcCCCCcccccc
Q 033478 35 CGSCRRLLAYPRGARHVKCSCCQTVNFVL 63 (118)
Q Consensus 35 CggCr~lL~YprGA~sVrC~~C~tVn~v~ 63 (118)
|-.|..-|.|.+....-+|--|..-...|
T Consensus 447 Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p 475 (730)
T COG1198 447 CPNCDSPLTLHKATGQLRCHYCGYQEPIP 475 (730)
T ss_pred CCCCCcceEEecCCCeeEeCCCCCCCCCC
Confidence 33444455555555555555555443333
No 127
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=24.28 E-value=34 Score=18.52 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=10.4
Q ss_pred cCCCCccccccccceeeEEEcCCCCee
Q 033478 53 CSCCQTVNFVLEAHQVGQVKCASCAVL 79 (118)
Q Consensus 53 C~~C~tVn~v~~a~q~a~v~Cg~Crt~ 79 (118)
|+.|..-+... ...|.+|++.
T Consensus 2 Cp~CG~~~~~~------~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIEDD------AKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCCc------CcchhhhCCc
Confidence 55665555321 1336666654
No 128
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.39 E-value=85 Score=29.05 Aligned_cols=49 Identities=22% Similarity=0.590 Sum_probs=29.9
Q ss_pred ceeeeccccceeeecCCCCeEEcCCCCc-cccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCcc
Q 033478 31 AQMVCGSCRRLLAYPRGARHVKCSCCQT-VNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFV 97 (118)
Q Consensus 31 sQLvCggCr~lL~YprGA~sVrC~~C~t-Vn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tV 97 (118)
.-+.|..|... .+|+.|+. .+.-. ....+.|..|+... . .-+|+.|+.-
T Consensus 382 p~l~C~~Cg~~---------~~C~~C~~~L~~h~---~~~~l~Ch~CG~~~-~-----p~~Cp~Cgs~ 431 (665)
T PRK14873 382 PSLACARCRTP---------ARCRHCTGPLGLPS---AGGTPRCRWCGRAA-P-----DWRCPRCGSD 431 (665)
T ss_pred CeeEhhhCcCe---------eECCCCCCceeEec---CCCeeECCCCcCCC-c-----CccCCCCcCC
Confidence 45678888743 57888873 22211 13467888888642 1 2378888764
No 129
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=22.77 E-value=37 Score=24.17 Aligned_cols=55 Identities=22% Similarity=0.492 Sum_probs=35.8
Q ss_pred ccceeeeccccceeeecCCCCeEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCccce
Q 033478 29 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTE 99 (118)
Q Consensus 29 ~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~ 99 (118)
.+++-.|.-|...+-+. +.....|..|.. -+|..|+.. -.+...-.|.+|+.-..
T Consensus 51 ~~~~~~C~~C~~~fg~l-~~~~~~C~~C~~------------~VC~~C~~~---~~~~~~WlC~vC~k~re 105 (118)
T PF02318_consen 51 KYGERHCARCGKPFGFL-FNRGRVCVDCKH------------RVCKKCGVY---SKKEPIWLCKVCQKQRE 105 (118)
T ss_dssp THCCSB-TTTS-BCSCT-STTCEEETTTTE------------EEETTSEEE---TSSSCCEEEHHHHHHHH
T ss_pred ccCCcchhhhCCccccc-CCCCCcCCcCCc------------cccCccCCc---CCCCCCEEChhhHHHHH
Confidence 34666788887766544 334477888863 678899887 55677778888765443
No 130
>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=22.77 E-value=85 Score=22.49 Aligned_cols=45 Identities=24% Similarity=0.302 Sum_probs=25.4
Q ss_pred eeEEEcC--CCCeeeEeeCCCCeEECCCCCccceeccCCcceeeeeec
Q 033478 68 VGQVKCA--SCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCD 113 (118)
Q Consensus 68 ~a~v~Cg--~Crt~LmyP~GA~SVrCs~C~tVT~V~~~n~r~~l~~~~ 113 (118)
....-|. .|+.-+..- |..+-+|..|+....-+....++.+-..|
T Consensus 16 ~~Y~aC~~~~C~kKv~~~-~~~~y~C~~C~~~~~~~~~ry~l~~~i~D 62 (146)
T PF08646_consen 16 WYYPACPNEKCNKKVTEN-GDGSYRCEKCNKTVENPKYRYRLSLKISD 62 (146)
T ss_dssp TEEEE-TSTTTS-B-EEE-TTTEEEETTTTEEESS-EEEEEEEEEEEE
T ss_pred cEECCCCCccCCCEeecC-CCcEEECCCCCCcCCCeeEEEEEEEEEEe
Confidence 4556677 788765554 66678888888765444444455544444
No 131
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=22.75 E-value=39 Score=22.67 Aligned_cols=25 Identities=16% Similarity=0.646 Sum_probs=14.5
Q ss_pred eeeeccccceeeecCCCCeEEcCCCCccccc
Q 033478 32 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFV 62 (118)
Q Consensus 32 QLvCggCr~lL~YprGA~sVrC~~C~tVn~v 62 (118)
...|..|+.++. .-+|+.|.+.+..
T Consensus 3 ~kAC~~C~~i~~------~~~CP~Cgs~~~T 27 (61)
T PRK08351 3 EKACRHCHYITT------EDRCPVCGSRDLS 27 (61)
T ss_pred hhhhhhCCcccC------CCcCCCCcCCccc
Confidence 346777776662 1157777766543
No 132
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=22.65 E-value=1.3e+02 Score=26.48 Aligned_cols=83 Identities=14% Similarity=0.226 Sum_probs=52.7
Q ss_pred ccceeeeeecccCccccceeeeccccceeeecCCCCeEEcCCCCccccccc----cceeeEEEcCCCCeeeEeeCCCCeE
Q 033478 14 LSQESFWLTLTCYHQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLE----AHQVGQVKCASCAVLLMYPYGAPSV 89 (118)
Q Consensus 14 ~~~~~~~~~~~~~~~~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v~~----a~q~a~v~Cg~Crt~LmyP~GA~SV 89 (118)
|+|||.-.--+-+-.--.+..|..|.-- =...|..-+-|+.|+.--.+.. +....+..|..|+=.=... .-
T Consensus 124 isleEa~~G~~~~i~~~~~~~C~~C~Gs-Gak~gt~~~tC~tC~G~G~v~~~~~~g~~~~~~~C~~C~G~G~~i----~~ 198 (371)
T COG0484 124 ITLEEAVFGVKKEIRVTRSVTCSTCHGS-GAKPGTDPKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGKII----KD 198 (371)
T ss_pred eEhhhhccCceeeEecceeeECCcCCCC-CCCCCCCCCcCCCCCCcCeEEEEEeeeEEEEEEECCCCccceeEC----CC
Confidence 4455544333322223356678888755 4455667779999987665442 4467888999997554443 45
Q ss_pred ECCCCCccceec
Q 033478 90 RCSSCCFVTEIG 101 (118)
Q Consensus 90 rCs~C~tVT~V~ 101 (118)
.|+.|+.--.|.
T Consensus 199 pC~~C~G~G~v~ 210 (371)
T COG0484 199 PCGKCKGKGRVK 210 (371)
T ss_pred CCCCCCCCCeEe
Confidence 799999876654
No 133
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.49 E-value=52 Score=32.13 Aligned_cols=37 Identities=19% Similarity=0.398 Sum_probs=26.6
Q ss_pred ceeeEEEcCCCCeee----EeeCCCCeEECCCCCccceecc
Q 033478 66 HQVGQVKCASCAVLL----MYPYGAPSVRCSSCCFVTEIGV 102 (118)
Q Consensus 66 ~q~a~v~Cg~Crt~L----myP~GA~SVrCs~C~tVT~V~~ 102 (118)
....-++|..||+-+ .+..--+.-||..|..+|++++
T Consensus 214 ~~~~IvRCr~CRtYiNPFV~fid~gr~WrCNlC~~~NdvP~ 254 (887)
T KOG1985|consen 214 TSTLIVRCRRCRTYINPFVEFIDQGRRWRCNLCGRVNDVPD 254 (887)
T ss_pred cCCceeeehhhhhhcCCeEEecCCCceeeechhhhhcCCcH
Confidence 444557788888754 2334447899999999999974
No 134
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=22.48 E-value=46 Score=21.57 Aligned_cols=44 Identities=18% Similarity=0.354 Sum_probs=21.5
Q ss_pred ccccceeeeccccceeeecCCCCeEEcCCCCccccccccceeeEEEcCCCC
Q 033478 27 HQEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCA 77 (118)
Q Consensus 27 ~~~~sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v~~a~q~a~v~Cg~Cr 77 (118)
.+++.+.+|.+|.++|..-..+. ||=- .-........+.|..|+
T Consensus 41 ~~~~kr~~Ck~C~~~liPG~~~~-vri~------~~~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 41 PPEIKRTICKKCGSLLIPGVNCS-VRIR------KKKKKKNFLVYTCLNCG 84 (85)
T ss_dssp STTCCCTB-TTT--B--CTTTEE-EEEE---------SSS-EEEEEETTTT
T ss_pred ChHHhcccccCCCCEEeCCCccE-EEEE------ecCCCCCEEEEEccccC
Confidence 35578889999999998776543 3322 00122335556677775
No 135
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=22.18 E-value=76 Score=27.65 Aligned_cols=27 Identities=33% Similarity=0.802 Sum_probs=11.5
Q ss_pred eeeccccceeeecCC--CCeEEcCCCCcc
Q 033478 33 MVCGSCRRLLAYPRG--ARHVKCSCCQTV 59 (118)
Q Consensus 33 LvCggCr~lL~YprG--A~sVrC~~C~tV 59 (118)
+.|..|..+...|+- -..-+|++|+++
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 39 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTT 39 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCC
Confidence 445555544444421 112345555544
No 136
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.47 E-value=71 Score=32.55 Aligned_cols=37 Identities=22% Similarity=0.617 Sum_probs=24.9
Q ss_pred eEEcCCCCccccccccceeeEEEcCCCCeeeEeeCCCCeEECCCCCccce
Q 033478 50 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTE 99 (118)
Q Consensus 50 sVrC~~C~tVn~v~~a~q~a~v~Cg~Crt~LmyP~GA~SVrCs~C~tVT~ 99 (118)
..+|+.|.+.+.. ..|..|+..+- +...|+.|+.-..
T Consensus 667 ~rkCPkCG~~t~~--------~fCP~CGs~te-----~vy~CPsCGaev~ 703 (1337)
T PRK14714 667 RRRCPSCGTETYE--------NRCPDCGTHTE-----PVYVCPDCGAEVP 703 (1337)
T ss_pred EEECCCCCCcccc--------ccCcccCCcCC-----CceeCccCCCccC
Confidence 3678888886631 27888887762 2348888887543
No 137
>PF14353 CpXC: CpXC protein
Probab=21.19 E-value=80 Score=22.26 Aligned_cols=18 Identities=17% Similarity=0.325 Sum_probs=12.4
Q ss_pred ceeeEEEcCCCCeeeEee
Q 033478 66 HQVGQVKCASCAVLLMYP 83 (118)
Q Consensus 66 ~q~a~v~Cg~Crt~LmyP 83 (118)
.+.....|.+|+....+.
T Consensus 34 g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CCcCEEECCCCCCceecC
Confidence 566778888888765543
No 138
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=21.01 E-value=40 Score=25.50 Aligned_cols=33 Identities=27% Similarity=0.464 Sum_probs=29.6
Q ss_pred ceeeeccccceeeecCCCCeEEcCCCCcccccc
Q 033478 31 AQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVL 63 (118)
Q Consensus 31 sQLvCggCr~lL~YprGA~sVrC~~C~tVn~v~ 63 (118)
+-+-|+.|-.||.-|.-+..|-|..|....++.
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~ 38 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVS 38 (116)
T ss_pred CcchhhhhhhhcccccccCceEeccccccCCHH
Confidence 456799999999999999999999999998875
No 139
>PF00791 ZU5: ZU5 domain; InterPro: IPR000906 This is a domain of unknown function, present in ZO-1 and Unc5-like netrin receptors. It is also found in different variants of ankyrin, which are responsible for attaching integral membrane proteins to cytoskeletal elements.; PDB: 4D8O_A 3G5B_A 3UD2_C 3KBT_D 3UD1_A 3KBU_D 3F59_A 2KXS_A 2KXR_A.
Probab=20.76 E-value=1.1e+02 Score=21.29 Aligned_cols=23 Identities=30% Similarity=0.463 Sum_probs=18.3
Q ss_pred ceeeEEEcCCCCeeeEeeCCCCe
Q 033478 66 HQVGQVKCASCAVLLMYPYGAPS 88 (118)
Q Consensus 66 ~q~a~v~Cg~Crt~LmyP~GA~S 88 (118)
++-+.+.....+..|..|+||-.
T Consensus 11 ~~GG~L~l~~~gv~L~IPpGAv~ 33 (103)
T PF00791_consen 11 HEGGRLRLPESGVSLSIPPGAVP 33 (103)
T ss_dssp TT-EEEESTTTTEEEEE-TTSSS
T ss_pred CCCcEEEeCCCCEEEEECCCcCC
Confidence 45678889999999999999975
No 140
>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=20.64 E-value=1e+02 Score=19.77 Aligned_cols=8 Identities=50% Similarity=0.962 Sum_probs=3.7
Q ss_pred cCCCCccc
Q 033478 53 CSCCQTVN 60 (118)
Q Consensus 53 C~~C~tVn 60 (118)
|+.|++.|
T Consensus 25 C~~C~~hN 32 (54)
T PF10058_consen 25 CSKCFSHN 32 (54)
T ss_pred Ccccchhh
Confidence 44444444
No 141
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.41 E-value=83 Score=23.84 Aligned_cols=12 Identities=25% Similarity=0.706 Sum_probs=6.7
Q ss_pred CCCeEEcCCCCc
Q 033478 47 GARHVKCSCCQT 58 (118)
Q Consensus 47 GA~sVrC~~C~t 58 (118)
--+|..|+.|..
T Consensus 306 ~~tS~~C~~cg~ 317 (364)
T COG0675 306 YYTSKTCPCCGH 317 (364)
T ss_pred CCCcccccccCC
Confidence 344566666655
No 142
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=20.35 E-value=61 Score=29.14 Aligned_cols=27 Identities=26% Similarity=0.720 Sum_probs=15.5
Q ss_pred EEcCCCCeeeEeeC--CCCeEECCCCCcc
Q 033478 71 VKCASCAVLLMYPY--GAPSVRCSSCCFV 97 (118)
Q Consensus 71 v~Cg~Crt~LmyP~--GA~SVrCs~C~tV 97 (118)
+.|.+|....-+|+ .+++..||.|++.
T Consensus 19 ~~C~eCd~~~~~P~l~~~q~A~CPRC~~~ 47 (418)
T COG2995 19 ILCPECDMLVSLPRLDSGQSAYCPRCGHT 47 (418)
T ss_pred ecCCCCCceeccccCCCCCcccCCCCCCc
Confidence 44555655555554 5556666666543
No 143
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=20.30 E-value=1.1e+02 Score=18.37 Aligned_cols=11 Identities=36% Similarity=0.930 Sum_probs=5.8
Q ss_pred eEEcCCCCccc
Q 033478 50 HVKCSCCQTVN 60 (118)
Q Consensus 50 sVrC~~C~tVn 60 (118)
.|.|+.|+.-.
T Consensus 5 ~v~CP~C~s~~ 15 (36)
T PF03811_consen 5 DVHCPRCQSTE 15 (36)
T ss_pred eeeCCCCCCCC
Confidence 35555555555
No 144
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=20.17 E-value=62 Score=18.75 Aligned_cols=28 Identities=21% Similarity=0.610 Sum_probs=13.4
Q ss_pred eeecccCccccceeeeccccceeeecCC
Q 033478 20 WLTLTCYHQEMAQMVCGSCRRLLAYPRG 47 (118)
Q Consensus 20 ~~~~~~~~~~~sQLvCggCr~lL~YprG 47 (118)
|=.|+....+.....|--|...+.|.+|
T Consensus 4 W~~F~~~~~~~~~a~C~~C~~~~~~~~~ 31 (45)
T PF02892_consen 4 WKHFTKIPGDKKKAKCKYCGKVIKYSSG 31 (45)
T ss_dssp CCCCEE--GCSS-EEETTTTEE-----S
T ss_pred cccEEEccCCcCeEEeCCCCeEEeeCCC
Confidence 5555554456677788888877777633
No 145
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.16 E-value=1.9e+02 Score=20.83 Aligned_cols=15 Identities=27% Similarity=0.674 Sum_probs=8.2
Q ss_pred CCCeEECCCCCccce
Q 033478 85 GAPSVRCSSCCFVTE 99 (118)
Q Consensus 85 GA~SVrCs~C~tVT~ 99 (118)
|-..+.|+.|++-..
T Consensus 39 ~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 39 NIAIITCGNCGLYTE 53 (99)
T ss_pred CcceEECCCCCCccC
Confidence 455566666655433
Done!