Query 034324
Match_columns 98
No_of_seqs 103 out of 123
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 12:14:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034324.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034324hhsearch_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 7.3E-16 1.6E-20 88.0 2.4 30 25-54 1-30 (31)
2 PF06943 zf-LSD1: LSD1 zinc fi 99.5 3.5E-15 7.7E-20 82.1 2.5 25 28-52 1-25 (25)
3 TIGR01053 LSD1 zinc finger dom 99.5 3E-15 6.6E-20 85.5 2.1 31 64-94 1-31 (31)
4 PF06943 zf-LSD1: LSD1 zinc fi 99.5 2.5E-14 5.4E-19 78.8 2.4 25 67-91 1-25 (25)
5 PF10122 Mu-like_Com: Mu-like 95.7 0.0048 1E-07 39.1 1.2 32 64-95 4-37 (51)
6 PF10122 Mu-like_Com: Mu-like 95.6 0.0068 1.5E-07 38.4 1.4 36 22-57 1-38 (51)
7 PF09788 Tmemb_55A: Transmembr 93.9 0.11 2.4E-06 41.9 4.7 36 60-95 153-190 (256)
8 PLN00209 ribosomal protein S27 92.9 0.097 2.1E-06 36.2 2.6 40 43-84 36-75 (86)
9 PTZ00083 40S ribosomal protein 92.5 0.12 2.7E-06 35.6 2.7 40 43-84 35-74 (85)
10 PRK00398 rpoP DNA-directed RNA 92.5 0.22 4.7E-06 29.4 3.4 27 64-90 3-29 (46)
11 PF01667 Ribosomal_S27e: Ribos 92.2 0.13 2.8E-06 32.8 2.3 38 43-82 7-44 (55)
12 PF11331 DUF3133: Protein of u 92.0 0.2 4.3E-06 30.9 2.9 39 39-77 2-44 (46)
13 PRK00415 rps27e 30S ribosomal 91.6 0.11 2.4E-06 33.6 1.5 37 43-81 11-47 (59)
14 PRK00398 rpoP DNA-directed RNA 91.3 0.33 7.2E-06 28.6 3.3 28 24-51 2-29 (46)
15 TIGR02098 MJ0042_CXXC MJ0042 f 90.7 0.27 5.8E-06 27.6 2.4 32 44-75 3-36 (38)
16 PRK14890 putative Zn-ribbon RN 90.7 0.23 4.9E-06 32.3 2.3 53 22-91 4-57 (59)
17 KOG1546 Metacaspase involved i 90.2 0.1 2.3E-06 43.8 0.5 30 65-96 5-34 (362)
18 COG2051 RPS27A Ribosomal prote 90.0 0.37 8E-06 32.0 2.9 38 43-82 19-56 (67)
19 PF13719 zinc_ribbon_5: zinc-r 89.0 0.5 1.1E-05 27.1 2.7 14 44-57 3-16 (37)
20 PF09788 Tmemb_55A: Transmembr 86.7 5.8 0.00012 32.2 8.3 71 22-93 62-136 (256)
21 PF13719 zinc_ribbon_5: zinc-r 86.1 0.81 1.8E-05 26.2 2.4 27 65-91 3-34 (37)
22 TIGR02098 MJ0042_CXXC MJ0042 f 85.5 1.3 2.7E-05 24.8 2.9 30 64-93 2-36 (38)
23 KOG1779 40s ribosomal protein 84.4 1.7 3.8E-05 30.0 3.7 44 43-88 34-77 (84)
24 PF12773 DZR: Double zinc ribb 84.1 0.49 1.1E-05 27.7 0.8 29 64-93 12-40 (50)
25 PF04810 zf-Sec23_Sec24: Sec23 81.8 0.98 2.1E-05 26.2 1.5 30 27-56 4-37 (40)
26 COG4357 Zinc finger domain con 80.5 0.36 7.9E-06 34.5 -0.8 27 26-52 63-89 (105)
27 PF07754 DUF1610: Domain of un 80.3 1.5 3.2E-05 23.8 1.7 22 67-89 1-23 (24)
28 PF13717 zinc_ribbon_4: zinc-r 79.4 2.1 4.5E-05 24.5 2.3 14 44-57 3-16 (36)
29 PF04690 YABBY: YABBY protein; 72.5 3.3 7.1E-05 31.5 2.4 39 43-81 12-53 (170)
30 COG2888 Predicted Zn-ribbon RN 72.1 4.2 9.1E-05 26.6 2.5 50 26-91 10-59 (61)
31 PRK14890 putative Zn-ribbon RN 71.3 3.4 7.4E-05 26.8 1.9 31 62-93 5-36 (59)
32 PRK00415 rps27e 30S ribosomal 69.6 15 0.00032 23.8 4.6 34 58-91 5-39 (59)
33 smart00661 RPOL9 RNA polymeras 65.5 6.9 0.00015 22.7 2.3 8 64-71 20-27 (52)
34 KOG1546 Metacaspase involved i 62.6 3.5 7.6E-05 34.9 0.9 27 27-55 6-32 (362)
35 PTZ00083 40S ribosomal protein 62.1 17 0.00038 25.1 4.1 36 56-91 27-63 (85)
36 PF02591 DUF164: Putative zinc 61.8 6.6 0.00014 23.8 1.8 28 25-52 22-55 (56)
37 PF05129 Elf1: Transcription e 61.1 11 0.00024 25.0 3.0 40 42-81 21-63 (81)
38 PRK14714 DNA polymerase II lar 60.7 7.4 0.00016 37.8 2.7 57 21-92 663-719 (1337)
39 PLN00209 ribosomal protein S27 60.3 20 0.00043 24.9 4.1 36 56-91 28-64 (86)
40 KOG2907 RNA polymerase I trans 59.4 3 6.6E-05 30.3 -0.0 32 65-96 8-39 (116)
41 COG1096 Predicted RNA-binding 59.3 13 0.00029 28.8 3.5 28 62-91 147-174 (188)
42 COG4416 Com Mu-like prophage p 59.2 2.2 4.8E-05 27.8 -0.7 30 65-94 5-36 (60)
43 PF09297 zf-NADH-PPase: NADH p 57.6 11 0.00023 20.6 2.0 25 66-90 5-29 (32)
44 smart00659 RPOLCX RNA polymera 56.7 14 0.00031 22.0 2.6 31 44-78 3-33 (44)
45 PF04690 YABBY: YABBY protein; 56.0 17 0.00037 27.7 3.5 35 59-93 7-47 (170)
46 PF05495 zf-CHY: CHY zinc fing 55.9 14 0.0003 23.7 2.7 27 24-50 40-68 (71)
47 COG4416 Com Mu-like prophage p 55.3 3.3 7.1E-05 27.0 -0.4 34 22-55 1-36 (60)
48 smart00731 SprT SprT homologue 52.1 21 0.00046 25.2 3.3 33 44-76 113-145 (146)
49 PF07295 DUF1451: Protein of u 51.4 17 0.00037 26.7 2.8 35 62-96 110-144 (146)
50 COG1579 Zn-ribbon protein, pos 51.1 6.8 0.00015 31.2 0.7 9 27-35 199-207 (239)
51 PF14634 zf-RING_5: zinc-RING 46.7 1.6 3.5E-05 25.1 -2.6 25 62-90 20-44 (44)
52 PF11023 DUF2614: Protein of u 46.1 9.2 0.0002 27.7 0.7 34 40-78 66-99 (114)
53 PF09082 DUF1922: Domain of un 45.9 28 0.0006 23.2 2.9 30 65-96 4-33 (68)
54 PF02150 RNA_POL_M_15KD: RNA p 45.5 11 0.00024 21.4 0.9 28 67-94 4-32 (35)
55 PRK05580 primosome assembly pr 44.5 36 0.00078 30.1 4.2 48 32-91 368-417 (679)
56 PRK14892 putative transcriptio 43.6 25 0.00054 24.5 2.5 32 42-73 20-51 (99)
57 PF12172 DUF35_N: Rubredoxin-l 43.3 18 0.00038 20.1 1.5 21 27-51 13-33 (37)
58 COG1096 Predicted RNA-binding 43.2 23 0.00049 27.6 2.5 26 26-53 150-175 (188)
59 PF00130 C1_1: Phorbol esters/ 41.8 21 0.00045 20.7 1.7 25 66-91 13-37 (53)
60 COG1996 RPC10 DNA-directed RNA 41.6 33 0.00072 21.4 2.6 29 62-90 4-32 (49)
61 COG2888 Predicted Zn-ribbon RN 41.2 26 0.00056 23.0 2.2 28 65-92 10-37 (61)
62 PF08271 TF_Zn_Ribbon: TFIIB z 40.7 38 0.00083 19.4 2.7 29 45-75 2-30 (43)
63 PRK14873 primosome assembly pr 40.4 37 0.0008 30.3 3.7 48 30-90 369-418 (665)
64 smart00109 C1 Protein kinase C 39.6 12 0.00027 20.6 0.4 24 66-91 13-36 (49)
65 TIGR00155 pqiA_fam integral me 39.6 30 0.00065 28.9 2.8 31 43-74 13-43 (403)
66 PF14369 zf-RING_3: zinc-finge 39.3 29 0.00062 19.8 1.9 24 27-50 4-28 (35)
67 PRK11827 hypothetical protein; 39.3 35 0.00076 21.9 2.5 28 25-52 8-35 (60)
68 PF14599 zinc_ribbon_6: Zinc-r 39.2 51 0.0011 21.1 3.3 34 60-93 26-59 (61)
69 cd00029 C1 Protein kinase C co 38.7 18 0.00039 20.2 1.0 25 66-91 13-37 (50)
70 PF11781 RRN7: RNA polymerase 37.8 33 0.00071 19.7 2.0 24 67-91 11-34 (36)
71 KOG3002 Zn finger protein [Gen 37.3 12 0.00025 30.5 0.1 39 44-89 49-87 (299)
72 PRK10996 thioredoxin 2; Provis 36.4 23 0.00049 24.6 1.4 32 43-75 2-33 (139)
73 smart00647 IBR In Between Ring 36.3 48 0.001 19.3 2.7 24 27-50 20-47 (64)
74 TIGR00155 pqiA_fam integral me 36.3 49 0.0011 27.7 3.6 30 25-54 13-44 (403)
75 PF13901 DUF4206: Domain of un 35.5 20 0.00044 27.0 1.2 28 66-93 154-183 (202)
76 PRK11032 hypothetical protein; 35.4 44 0.00094 25.1 2.9 35 62-96 122-156 (160)
77 PF13248 zf-ribbon_3: zinc-rib 35.4 13 0.00028 19.6 0.1 24 44-74 3-26 (26)
78 KOG4684 Uncharacterized conser 35.0 38 0.00082 27.7 2.7 47 39-86 76-125 (275)
79 PF10058 DUF2296: Predicted in 35.0 45 0.00097 20.7 2.5 8 46-53 25-32 (54)
80 PRK00423 tfb transcription ini 35.0 22 0.00048 28.3 1.3 28 45-74 13-40 (310)
81 PF05180 zf-DNL: DNL zinc fing 34.5 12 0.00026 24.5 -0.2 31 25-55 4-41 (66)
82 PRK04351 hypothetical protein; 34.2 36 0.00079 24.9 2.3 32 45-77 114-145 (149)
83 PLN00162 transport protein sec 34.0 48 0.001 30.0 3.4 34 24-57 52-89 (761)
84 PRK02935 hypothetical protein; 33.7 33 0.00072 24.8 2.0 35 39-78 66-100 (110)
85 COG4888 Uncharacterized Zn rib 33.2 34 0.00073 24.5 1.9 33 42-74 21-56 (104)
86 TIGR00100 hypA hydrogenase nic 32.4 41 0.00088 23.3 2.2 28 63-92 69-96 (115)
87 PF07191 zinc-ribbons_6: zinc- 32.0 1.4E+02 0.0031 19.8 4.6 57 25-91 1-59 (70)
88 TIGR00595 priA primosomal prot 31.1 71 0.0015 27.3 3.8 38 41-90 211-248 (505)
89 PRK12380 hydrogenase nickel in 30.7 44 0.00095 23.1 2.1 28 63-92 69-96 (113)
90 PRK11827 hypothetical protein; 30.0 74 0.0016 20.4 2.9 32 64-95 8-39 (60)
91 PRK03681 hypA hydrogenase nick 30.0 46 0.00099 23.1 2.1 29 62-92 68-97 (114)
92 TIGR01384 TFS_arch transcripti 28.9 41 0.00089 22.2 1.7 26 27-54 2-27 (104)
93 TIGR00595 priA primosomal prot 28.3 81 0.0018 26.9 3.7 27 28-54 225-251 (505)
94 PF07295 DUF1451: Protein of u 28.2 61 0.0013 23.8 2.6 36 21-56 108-143 (146)
95 cd02340 ZZ_NBR1_like Zinc fing 27.3 51 0.0011 19.3 1.7 9 81-89 13-21 (43)
96 PRK08351 DNA-directed RNA poly 27.2 30 0.00065 22.4 0.7 25 25-55 3-27 (61)
97 COG2995 PqiA Uncharacterized p 27.0 38 0.00083 29.3 1.5 35 19-56 214-248 (418)
98 PRK14559 putative protein seri 26.8 37 0.00079 30.4 1.5 36 45-93 3-38 (645)
99 PF08792 A2L_zn_ribbon: A2L zi 26.7 1.1E+02 0.0023 17.3 2.9 8 63-70 20-27 (33)
100 PF01485 IBR: IBR domain; Int 26.3 42 0.0009 19.5 1.2 26 27-52 20-49 (64)
101 PRK05580 primosome assembly pr 26.1 88 0.0019 27.7 3.6 44 27-78 392-435 (679)
102 PF07282 OrfB_Zn_ribbon: Putat 26.0 50 0.0011 20.1 1.6 33 36-72 22-54 (69)
103 KOG2907 RNA polymerase I trans 25.6 25 0.00055 25.6 0.2 34 24-57 6-39 (116)
104 PF04032 Rpr2: RNAse P Rpr2/Rp 25.5 36 0.00079 21.4 0.9 20 22-41 43-62 (85)
105 COG1405 SUA7 Transcription ini 25.3 57 0.0012 26.3 2.2 29 45-75 3-31 (285)
106 smart00782 PhnA_Zn_Ribbon PhnA 24.0 30 0.00065 21.1 0.3 28 4-34 18-45 (47)
107 PF06827 zf-FPG_IleRS: Zinc fi 23.8 63 0.0014 17.1 1.5 13 78-90 17-29 (30)
108 COG1645 Uncharacterized Zn-fin 23.8 36 0.00079 25.0 0.7 35 59-95 23-58 (131)
109 PF14835 zf-RING_6: zf-RING of 23.5 40 0.00087 22.2 0.8 43 45-93 9-51 (65)
110 PRK00564 hypA hydrogenase nick 23.3 47 0.001 23.1 1.2 28 63-92 70-98 (117)
111 PRK15103 paraquat-inducible me 22.7 63 0.0014 27.2 2.0 30 44-74 11-40 (419)
112 PF06677 Auto_anti-p27: Sjogre 22.4 1.2E+02 0.0025 18.0 2.6 27 62-89 15-41 (41)
113 PLN00162 transport protein sec 22.0 94 0.002 28.1 3.1 31 65-95 54-88 (761)
114 COG5028 Vesicle coat complex C 21.9 34 0.00074 32.0 0.4 33 65-97 200-236 (861)
115 PF13453 zf-TFIIB: Transcripti 21.9 89 0.0019 17.7 2.0 6 46-51 2-7 (41)
116 COG2191 Formylmethanofuran deh 21.2 55 0.0012 25.9 1.3 29 43-71 172-200 (206)
117 PRK06260 threonine synthase; V 20.9 72 0.0016 26.0 2.0 23 64-88 3-25 (397)
118 PRK15103 paraquat-inducible me 20.7 91 0.002 26.3 2.6 31 24-54 9-41 (419)
119 KOG1985 Vesicle coat complex C 20.7 52 0.0011 31.0 1.2 35 62-96 216-254 (887)
120 smart00547 ZnF_RBZ Zinc finger 20.5 49 0.0011 16.7 0.6 22 44-72 3-24 (26)
121 PF06107 DUF951: Bacterial pro 20.3 89 0.0019 20.1 1.9 16 63-78 30-45 (57)
122 PF04828 GFA: Glutathione-depe 20.2 1.3E+02 0.0029 18.3 2.7 19 58-76 42-60 (92)
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=99.58 E-value=7.3e-16 Score=88.02 Aligned_cols=30 Identities=60% Similarity=1.247 Sum_probs=21.0
Q ss_pred eEEcCCCCeeeeecCCCCeEecCCCCcccc
Q 034324 25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTA 54 (98)
Q Consensus 25 QlvC~gCr~lL~Yp~GA~~VrC~~C~tVn~ 54 (98)
|++|++||++|+||+||++|||+.|++||.
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~ 30 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVNL 30 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEec
Confidence 566777777777777777777777777664
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=99.54 E-value=3.5e-15 Score=82.12 Aligned_cols=25 Identities=64% Similarity=1.364 Sum_probs=17.6
Q ss_pred cCCCCeeeeecCCCCeEecCCCCcc
Q 034324 28 CSGCRNLLLYPVGATSVCCAVCNAV 52 (98)
Q Consensus 28 C~gCr~lL~Yp~GA~~VrC~~C~tV 52 (98)
|+|||++|+||+||+||||+.|++|
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 6677777777777777777777665
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=99.53 E-value=3e-15 Score=85.48 Aligned_cols=31 Identities=71% Similarity=1.338 Sum_probs=29.6
Q ss_pred EEEeCCcCceEEeecCCCeEECCCCCccccc
Q 034324 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNLA 94 (98)
Q Consensus 64 ql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v 94 (98)
|++|++||++|+||+||++|||+.|++||.|
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 6899999999999999999999999999975
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=99.47 E-value=2.5e-14 Score=78.75 Aligned_cols=25 Identities=80% Similarity=1.666 Sum_probs=24.3
Q ss_pred eCCcCceEEeecCCCeEECCCCCcc
Q 034324 67 CGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 67 Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
||+||++||||+||+||||+.|++|
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=95.75 E-value=0.0048 Score=39.05 Aligned_cols=32 Identities=28% Similarity=0.632 Sum_probs=16.7
Q ss_pred EEEeCCcCceEEee--cCCCeEECCCCCcccccc
Q 034324 64 QLVCGGCHTLLMYI--RGATSVQCSCCHTVNLAL 95 (98)
Q Consensus 64 ql~Cg~Cr~lL~yP--~GA~sVrC~~C~~Vt~v~ 95 (98)
.+.|++|+.+|+.- ..-..++|+-|.++|.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVR 37 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence 34555555555553 222355566666655554
No 6
>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=95.56 E-value=0.0068 Score=38.38 Aligned_cols=36 Identities=19% Similarity=0.488 Sum_probs=30.2
Q ss_pred CceeEEcCCCCeeeeecCCCC--eEecCCCCccccCCC
Q 034324 22 AQSQLVCSGCRNLLLYPVGAT--SVCCAVCNAVTAVPP 57 (98)
Q Consensus 22 ~~sQlvC~gCr~lL~Yp~GA~--~VrC~~C~tVn~vp~ 57 (98)
|+-++.|+.|..||...-++. .+.|+.|.++|.+.+
T Consensus 1 m~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 1 MLKEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred CCcceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 345789999999999975665 889999999998764
No 7
>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=93.88 E-value=0.11 Score=41.85 Aligned_cols=36 Identities=19% Similarity=0.536 Sum_probs=30.6
Q ss_pred CceeEEEeCCcCceEEeecCC--CeEECCCCCcccccc
Q 034324 60 TEMAQLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLAL 95 (98)
Q Consensus 60 ~~~aql~Cg~Cr~lL~yP~GA--~sVrC~~C~~Vt~v~ 95 (98)
..+.-++||+|+...+++.=. ...||+.|+.|..|-
T Consensus 153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG 190 (256)
T PF09788_consen 153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG 190 (256)
T ss_pred CCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence 357889999999999999755 567999999998875
No 8
>PLN00209 ribosomal protein S27; Provisional
Probab=92.93 E-value=0.097 Score=36.20 Aligned_cols=40 Identities=30% Similarity=0.546 Sum_probs=32.3
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEE
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ 84 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVr 84 (98)
.|+|+.|..++.+= ++....+.|.+|.++|..|.|-....
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 58999999998774 35568899999999999999876543
No 9
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=92.50 E-value=0.12 Score=35.61 Aligned_cols=40 Identities=28% Similarity=0.575 Sum_probs=31.7
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEE
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ 84 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVr 84 (98)
.|+|+.|..++.+= ++....+.|.+|.++|.-|.|-....
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 58899999988774 34567899999999999999876543
No 10
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=92.46 E-value=0.22 Score=29.38 Aligned_cols=27 Identities=22% Similarity=0.475 Sum_probs=15.9
Q ss_pred EEEeCCcCceEEeecCCCeEECCCCCc
Q 034324 64 QLVCGGCHTLLMYIRGATSVQCSCCHT 90 (98)
Q Consensus 64 ql~Cg~Cr~lL~yP~GA~sVrC~~C~~ 90 (98)
...|.+|+..+.+..+...++|+-|++
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCC
Confidence 345666666666665555666666654
No 11
>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=92.23 E-value=0.13 Score=32.75 Aligned_cols=38 Identities=24% Similarity=0.417 Sum_probs=25.6
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCe
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 82 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~s 82 (98)
.|+|+.|..++.+= .+....+.|.+|.++|.-|.|-..
T Consensus 7 ~VkCp~C~~~q~vF--Sha~t~V~C~~Cg~~L~~PtGGKa 44 (55)
T PF01667_consen 7 DVKCPGCYNIQTVF--SHAQTVVKCVVCGTVLAQPTGGKA 44 (55)
T ss_dssp EEE-TTT-SEEEEE--TT-SS-EE-SSSTSEEEEE-SSSE
T ss_pred EEECCCCCCeeEEE--ecCCeEEEcccCCCEecCCCCcCe
Confidence 58999999988773 345678999999999999988654
No 12
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=92.01 E-value=0.2 Score=30.92 Aligned_cols=39 Identities=28% Similarity=0.646 Sum_probs=27.2
Q ss_pred CCCCeEecCCCCccccCCCC----CCceeEEEeCCcCceEEee
Q 034324 39 VGATSVCCAVCNAVTAVPPP----GTEMAQLVCGGCHTLLMYI 77 (98)
Q Consensus 39 ~GA~~VrC~~C~tVn~vp~~----~~~~aql~Cg~Cr~lL~yP 77 (98)
.||+-|-|..|..+=.+|.. .....++.||.|...|.|-
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 36677777777666555532 2347899999999999874
No 13
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=91.59 E-value=0.11 Score=33.64 Aligned_cols=37 Identities=22% Similarity=0.311 Sum_probs=24.0
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCC
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGAT 81 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~ 81 (98)
.|+|+.|..++.+= ++....+.|..|.++|.-|.|-.
T Consensus 11 ~VkCp~C~n~q~vF--sha~t~V~C~~Cg~~L~~PtGGK 47 (59)
T PRK00415 11 KVKCPDCGNEQVVF--SHASTVVRCLVCGKTLAEPTGGK 47 (59)
T ss_pred EEECCCCCCeEEEE--ecCCcEEECcccCCCcccCCCcc
Confidence 46777777777542 23346677777777777777643
No 14
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.30 E-value=0.33 Score=28.57 Aligned_cols=28 Identities=21% Similarity=0.455 Sum_probs=20.2
Q ss_pred eeEEcCCCCeeeeecCCCCeEecCCCCc
Q 034324 24 SQLVCSGCRNLLLYPVGATSVCCAVCNA 51 (98)
Q Consensus 24 sQlvC~gCr~lL~Yp~GA~~VrC~~C~t 51 (98)
-...|..|...+.+..+...++|+.|.+
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCC
Confidence 3457777777777777777777777765
No 15
>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=90.74 E-value=0.27 Score=27.62 Aligned_cols=32 Identities=22% Similarity=0.571 Sum_probs=17.8
Q ss_pred EecCCCCccccCCCC--CCceeEEEeCCcCceEE
Q 034324 44 VCCAVCNAVTAVPPP--GTEMAQLVCGGCHTLLM 75 (98)
Q Consensus 44 VrC~~C~tVn~vp~~--~~~~aql~Cg~Cr~lL~ 75 (98)
+.|+.|.+.+.++.+ ..+...+.|+.|+..+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 567777776665431 11223566666666553
No 16
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.68 E-value=0.23 Score=32.25 Aligned_cols=53 Identities=21% Similarity=0.477 Sum_probs=40.7
Q ss_pred CceeEEcCCCCeeeeecCC-CCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCcc
Q 034324 22 AQSQLVCSGCRNLLLYPVG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 22 ~~sQlvC~gCr~lL~Yp~G-A~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
++.-.+|.+|...| .+++ ++..-|+.|..+... .|..||.+ +...+|+.|.+.
T Consensus 4 ~~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I~----------RC~~CRk~------~~~Y~CP~CGF~ 57 (59)
T PRK14890 4 MMEPPKCTSCGIEI-APREKAVKFLCPNCGEVIIY----------RCEKCRKQ------SNPYTCPKCGFE 57 (59)
T ss_pred cccCccccCCCCcc-cCCCccCEeeCCCCCCeeEe----------echhHHhc------CCceECCCCCCc
Confidence 44556899999988 4555 999999999876543 48899986 367889999875
No 17
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=90.23 E-value=0.1 Score=43.79 Aligned_cols=30 Identities=30% Similarity=0.627 Sum_probs=26.0
Q ss_pred EEeCCcCceEEeecCCCeEECCCCCccccccc
Q 034324 65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (98)
Q Consensus 65 l~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v~~ 96 (98)
+.|. |++.|+.|.||++ +|+.||++|.+.+
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 4565 9999999999999 9999999998763
No 18
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=89.97 E-value=0.37 Score=32.05 Aligned_cols=38 Identities=24% Similarity=0.337 Sum_probs=28.5
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCe
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 82 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~s 82 (98)
.|+|..|...+.+= ++....+.|..|..+|..|.|-..
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 48888888877663 234577889999999999888654
No 19
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.04 E-value=0.5 Score=27.08 Aligned_cols=14 Identities=29% Similarity=0.726 Sum_probs=8.2
Q ss_pred EecCCCCccccCCC
Q 034324 44 VCCAVCNAVTAVPP 57 (98)
Q Consensus 44 VrC~~C~tVn~vp~ 57 (98)
++|+.|++.-.++.
T Consensus 3 i~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 3 ITCPNCQTRFRVPD 16 (37)
T ss_pred EECCCCCceEEcCH
Confidence 45666666655543
No 20
>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=86.73 E-value=5.8 Score=32.17 Aligned_cols=71 Identities=21% Similarity=0.479 Sum_probs=50.9
Q ss_pred CceeEEcCCCCeeeeecCC--CCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCC--CCcccc
Q 034324 22 AQSQLVCSGCRNLLLYPVG--ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSC--CHTVNL 93 (98)
Q Consensus 22 ~~sQlvC~gCr~lL~Yp~G--A~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~--C~~Vt~ 93 (98)
.+.-+.|.=|+.++.-.-- =--|+|..|+-.|....+....-.+.| -|.-||+--..++.+-|+. |..|-.
T Consensus 62 ~~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRC-PCNCLLICk~sS~rIaCPRp~CkRiI~ 136 (256)
T PF09788_consen 62 GAPVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRC-PCNCLLICKSSSQRIACPRPNCKRIIN 136 (256)
T ss_pred CCceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEec-CCceEEEeecccccccCCCCCCcceEE
Confidence 3457889999988765432 234899999999986554456777888 6777777777777777776 765543
No 21
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.11 E-value=0.81 Score=26.20 Aligned_cols=27 Identities=30% Similarity=0.699 Sum_probs=14.3
Q ss_pred EEeCCcCceEEeec-----CCCeEECCCCCcc
Q 034324 65 LVCGGCHTLLMYIR-----GATSVQCSCCHTV 91 (98)
Q Consensus 65 l~Cg~Cr~lL~yP~-----GA~sVrC~~C~~V 91 (98)
+.|-+|.+..-.+. +...|||+.|+++
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 34555555555443 3455666655554
No 22
>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=85.51 E-value=1.3 Score=24.80 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=21.5
Q ss_pred EEEeCCcCceEEeec-----CCCeEECCCCCcccc
Q 034324 64 QLVCGGCHTLLMYIR-----GATSVQCSCCHTVNL 93 (98)
Q Consensus 64 ql~Cg~Cr~lL~yP~-----GA~sVrC~~C~~Vt~ 93 (98)
.+.|-+|++...++. +...|+|+.|+++-.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 467888888888774 234788888887643
No 23
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=84.39 E-value=1.7 Score=29.99 Aligned_cols=44 Identities=30% Similarity=0.562 Sum_probs=30.8
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCC
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCC 88 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C 88 (98)
.|+|+.|-.||.+=. +...-++|.+|.+.|.-|.|-..+.=..|
T Consensus 34 ~VkC~gc~~iT~vfS--HaqtvVvc~~c~~il~~~tggra~ls~~c 77 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFS--HAQTVVVCEGCSTILCQPTGGKAKLSEGC 77 (84)
T ss_pred EEEcCCceEEEEEee--cCceEEEcCCCceEEEEecCCcEEecCCC
Confidence 478888888887642 33456788888888888888776543333
No 24
>PF12773 DZR: Double zinc ribbon
Probab=84.08 E-value=0.49 Score=27.74 Aligned_cols=29 Identities=24% Similarity=0.380 Sum_probs=17.1
Q ss_pred EEEeCCcCceEEeecCCCeEECCCCCcccc
Q 034324 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (98)
Q Consensus 64 ql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~ 93 (98)
...|..|++.|. ......+.|+.|.+.+.
T Consensus 12 ~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 12 AKFCPHCGTPLP-PPDQSKKICPNCGAENP 40 (50)
T ss_pred ccCChhhcCChh-hccCCCCCCcCCcCCCc
Confidence 456666666666 44444556666666544
No 25
>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=81.76 E-value=0.98 Score=26.21 Aligned_cols=30 Identities=27% Similarity=0.727 Sum_probs=11.4
Q ss_pred EcCCCCeee----eecCCCCeEecCCCCccccCC
Q 034324 27 VCSGCRNLL----LYPVGATSVCCAVCNAVTAVP 56 (98)
Q Consensus 27 vC~gCr~lL----~Yp~GA~~VrC~~C~tVn~vp 56 (98)
.|..|+..| .+..+...-.|..|++.|.+|
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLP 37 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--EEE--
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCCcCCCC
Confidence 455555544 233445555555555555543
No 26
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=80.46 E-value=0.36 Score=34.48 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=24.8
Q ss_pred EEcCCCCeeeeecCCCCeEecCCCCcc
Q 034324 26 LVCSGCRNLLLYPVGATSVCCAVCNAV 52 (98)
Q Consensus 26 lvC~gCr~lL~Yp~GA~~VrC~~C~tV 52 (98)
++||-||.+|.+..=-..++|+.|++-
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~sp 89 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSP 89 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCC
Confidence 899999999999988888999999874
No 27
>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=80.28 E-value=1.5 Score=23.82 Aligned_cols=22 Identities=27% Similarity=0.678 Sum_probs=13.2
Q ss_pred eCCcCceEEeecC-CCeEECCCCC
Q 034324 67 CGGCHTLLMYIRG-ATSVQCSCCH 89 (98)
Q Consensus 67 Cg~Cr~lL~yP~G-A~sVrC~~C~ 89 (98)
|.+|...|. |++ +..+.|+.|.
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 445555554 666 6667777664
No 28
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=79.35 E-value=2.1 Score=24.52 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=8.5
Q ss_pred EecCCCCccccCCC
Q 034324 44 VCCAVCNAVTAVPP 57 (98)
Q Consensus 44 VrC~~C~tVn~vp~ 57 (98)
+.|+.|++.-.++.
T Consensus 3 i~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 3 ITCPNCQAKYEIDD 16 (36)
T ss_pred EECCCCCCEEeCCH
Confidence 56666666666543
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=72.48 E-value=3.3 Score=31.53 Aligned_cols=39 Identities=33% Similarity=0.581 Sum_probs=25.4
Q ss_pred eEecCCCCccccCCCCC---CceeEEEeCCcCceEEeecCCC
Q 034324 43 SVCCAVCNAVTAVPPPG---TEMAQLVCGGCHTLLMYIRGAT 81 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~---~~~aql~Cg~Cr~lL~yP~GA~ 81 (98)
.|+|.-|+||=+|--+. -++--+.||.|-.+|.+--++.
T Consensus 12 YVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~ 53 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRAL 53 (170)
T ss_pred EEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeecccc
Confidence 47777777777764332 3455678888888887655443
No 30
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=72.09 E-value=4.2 Score=26.64 Aligned_cols=50 Identities=24% Similarity=0.547 Sum_probs=38.1
Q ss_pred EEcCCCCeeeeecCCCCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCcc
Q 034324 26 LVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 26 lvC~gCr~lL~Yp~GA~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
-+|.+|...|.--.+|++.-|++|.-+.. ..|..||.+ ....+|+.|.+.
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 58999999998889999999999975443 357788875 334578888764
No 31
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.27 E-value=3.4 Score=26.79 Aligned_cols=31 Identities=26% Similarity=0.474 Sum_probs=22.3
Q ss_pred eeEEEeCCcCceEEeecC-CCeEECCCCCcccc
Q 034324 62 MAQLVCGGCHTLLMYIRG-ATSVQCSCCHTVNL 93 (98)
Q Consensus 62 ~aql~Cg~Cr~lL~yP~G-A~sVrC~~C~~Vt~ 93 (98)
+.-.+|.+|...| .|.+ +..+.|+.|..+..
T Consensus 5 ~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I 36 (59)
T PRK14890 5 MEPPKCTSCGIEI-APREKAVKFLCPNCGEVII 36 (59)
T ss_pred ccCccccCCCCcc-cCCCccCEeeCCCCCCeeE
Confidence 3445788888887 5666 88888888876643
No 32
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=69.57 E-value=15 Score=23.78 Aligned_cols=34 Identities=21% Similarity=0.632 Sum_probs=24.1
Q ss_pred CCCceeEEEeCCcCc-eEEeecCCCeEECCCCCcc
Q 034324 58 PGTEMAQLVCGGCHT-LLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 58 ~~~~~aql~Cg~Cr~-lL~yP~GA~sVrC~~C~~V 91 (98)
+....-.+.|.+|.. ..+|-+-+..|+|..|+++
T Consensus 5 p~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~ 39 (59)
T PRK00415 5 PRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKT 39 (59)
T ss_pred CCCeEEEEECCCCCCeEEEEecCCcEEECcccCCC
Confidence 445567778888864 4577777777888888764
No 33
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=65.54 E-value=6.9 Score=22.71 Aligned_cols=8 Identities=38% Similarity=1.099 Sum_probs=3.4
Q ss_pred EEEeCCcC
Q 034324 64 QLVCGGCH 71 (98)
Q Consensus 64 ql~Cg~Cr 71 (98)
+.+|..|+
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 34444444
No 34
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=62.62 E-value=3.5 Score=34.88 Aligned_cols=27 Identities=41% Similarity=0.783 Sum_probs=24.1
Q ss_pred EcCCCCeeeeecCCCCeEecCCCCccccC
Q 034324 27 VCSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (98)
Q Consensus 27 vC~gCr~lL~Yp~GA~~VrC~~C~tVn~v 55 (98)
-|. ||+-|+-|.||.. ||+.|++++..
T Consensus 6 ~~~-~~~p~~~pp~ar~-q~~~~~~~~~~ 32 (362)
T KOG1546|consen 6 GCN-CQRPMAPPPGARY-QCAGCHAVTQI 32 (362)
T ss_pred cCC-CCCCCCCCCCCcc-cccccceeeee
Confidence 355 9999999999999 99999999864
No 35
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=62.07 E-value=17 Score=25.08 Aligned_cols=36 Identities=22% Similarity=0.578 Sum_probs=24.3
Q ss_pred CCCCCceeEEEeCCcCc-eEEeecCCCeEECCCCCcc
Q 034324 56 PPPGTEMAQLVCGGCHT-LLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 56 p~~~~~~aql~Cg~Cr~-lL~yP~GA~sVrC~~C~~V 91 (98)
+.+..-...+.|.+|.. ..+|-+-+.-|.|..|+++
T Consensus 27 ~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 27 QGPNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQ 63 (85)
T ss_pred cCCCCeEEEEECCCCCCeeEEEecCceEEEccccCCE
Confidence 33445566777777753 5667777777777777765
No 36
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=61.85 E-value=6.6 Score=23.78 Aligned_cols=28 Identities=32% Similarity=0.592 Sum_probs=17.9
Q ss_pred eEEcCCCCeeeeec------CCCCeEecCCCCcc
Q 034324 25 QLVCSGCRNLLLYP------VGATSVCCAVCNAV 52 (98)
Q Consensus 25 QlvC~gCr~lL~Yp------~GA~~VrC~~C~tV 52 (98)
.-+|+||+..|.-- .|..-+.|+.|+.|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 34788888877532 44566777777653
No 37
>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=61.10 E-value=11 Score=25.02 Aligned_cols=40 Identities=18% Similarity=0.287 Sum_probs=21.2
Q ss_pred CeEecCCCCccccCCC---CCCceeEEEeCCcCceEEeecCCC
Q 034324 42 TSVCCAVCNAVTAVPP---PGTEMAQLVCGGCHTLLMYIRGAT 81 (98)
Q Consensus 42 ~~VrC~~C~tVn~vp~---~~~~~aql~Cg~Cr~lL~yP~GA~ 81 (98)
+...|+.|++-+++-- .....+.+.|+.|...-.+..+..
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L 63 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPL 63 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCcc
Confidence 5678999997776532 236799999999988777765544
No 38
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=60.65 E-value=7.4 Score=37.81 Aligned_cols=57 Identities=19% Similarity=0.354 Sum_probs=42.2
Q ss_pred CCceeEEcCCCCeeeeecCCCCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCccc
Q 034324 21 GAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (98)
Q Consensus 21 ~~~sQlvC~gCr~lL~Yp~GA~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt 92 (98)
.+.++..|-.|.+.... .+|+.|.+.+.. ...|.+|+..+-.-... +.+|+-|.+-.
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 35567899999996432 299999998742 24999999987654333 77999998644
No 39
>PLN00209 ribosomal protein S27; Provisional
Probab=60.29 E-value=20 Score=24.87 Aligned_cols=36 Identities=28% Similarity=0.684 Sum_probs=25.0
Q ss_pred CCCCCceeEEEeCCcCc-eEEeecCCCeEECCCCCcc
Q 034324 56 PPPGTEMAQLVCGGCHT-LLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 56 p~~~~~~aql~Cg~Cr~-lL~yP~GA~sVrC~~C~~V 91 (98)
+.+..-...+.|.+|.. ..+|-+-..-|.|..|+++
T Consensus 28 ~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 28 QSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred cCCCCEEEEEECCCCCCeeEEEecCceEEEccccCCE
Confidence 33445667778888864 5677777777888888765
No 40
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=59.38 E-value=3 Score=30.31 Aligned_cols=32 Identities=22% Similarity=0.401 Sum_probs=23.2
Q ss_pred EEeCCcCceEEeecCCCeEECCCCCccccccc
Q 034324 65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (98)
Q Consensus 65 l~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v~~ 96 (98)
.-|+.|+.+|.-|.-...|-|..|.++..+.+
T Consensus 8 ~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~ 39 (116)
T KOG2907|consen 8 DFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQ 39 (116)
T ss_pred chhhhhhhhcccccccCceEeccccccCCHHH
Confidence 45777777777777777777777777766553
No 41
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=59.35 E-value=13 Score=28.83 Aligned_cols=28 Identities=18% Similarity=0.515 Sum_probs=23.4
Q ss_pred eeEEEeCCcCceEEeecCCCeEECCCCCcc
Q 034324 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 62 ~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
+-.-.|..||..|++ .-...+|+.|+.+
T Consensus 147 VI~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 147 VIYARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEEEEccCCCcceEE--cCcEEECCCCCCE
Confidence 445689999999999 7788999999865
No 42
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=59.22 E-value=2.2 Score=27.79 Aligned_cols=30 Identities=30% Similarity=0.640 Sum_probs=15.7
Q ss_pred EEeCCcCceEEeecCC--CeEECCCCCccccc
Q 034324 65 LVCGGCHTLLMYIRGA--TSVQCSCCHTVNLA 94 (98)
Q Consensus 65 l~Cg~Cr~lL~yP~GA--~sVrC~~C~~Vt~v 94 (98)
+.|..|..+|.=..|. ..++|+.|..||..
T Consensus 5 iRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 5 IRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 4455555555443333 34566666666654
No 43
>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=57.62 E-value=11 Score=20.63 Aligned_cols=25 Identities=24% Similarity=0.588 Sum_probs=11.0
Q ss_pred EeCCcCceEEeecCCCeEECCCCCc
Q 034324 66 VCGGCHTLLMYIRGATSVQCSCCHT 90 (98)
Q Consensus 66 ~Cg~Cr~lL~yP~GA~sVrC~~C~~ 90 (98)
.|+.|...+..-.+-..-+|+.|..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-
T ss_pred ccCcCCccccCCCCcCEeECCCCcC
Confidence 3555666555555555566665554
No 44
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=56.67 E-value=14 Score=22.02 Aligned_cols=31 Identities=16% Similarity=0.504 Sum_probs=18.7
Q ss_pred EecCCCCccccCCCCCCceeEEEeCCcCceEEeec
Q 034324 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIR 78 (98)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~ 78 (98)
-.|..|.+.+... ....+.|..|+--++|-.
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRECGYRILYKK 33 (44)
T ss_pred EECCCCCCEeecC----CCCceECCCCCceEEEEe
Confidence 3567777655432 245677777777666644
No 45
>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=56.03 E-value=17 Score=27.66 Aligned_cols=35 Identities=20% Similarity=0.490 Sum_probs=29.0
Q ss_pred CCceeEEEeCCcCceEEeec------CCCeEECCCCCcccc
Q 034324 59 GTEMAQLVCGGCHTLLMYIR------GATSVQCSCCHTVNL 93 (98)
Q Consensus 59 ~~~~aql~Cg~Cr~lL~yP~------GA~sVrC~~C~~Vt~ 93 (98)
..+.-++.|+-|.|+|++-. ..-+|||..|..+-.
T Consensus 7 sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLS 47 (170)
T PF04690_consen 7 SEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLS 47 (170)
T ss_pred CCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceee
Confidence 56889999999999998754 677899999986543
No 46
>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=55.89 E-value=14 Score=23.69 Aligned_cols=27 Identities=19% Similarity=0.567 Sum_probs=13.1
Q ss_pred eeEEcCCCCeeeeecCCCCe--EecCCCC
Q 034324 24 SQLVCSGCRNLLLYPVGATS--VCCAVCN 50 (98)
Q Consensus 24 sQlvC~gCr~lL~Yp~GA~~--VrC~~C~ 50 (98)
.+++||-|++.+.+..-..+ ..|+.|+
T Consensus 40 ~~v~Cg~C~~~~~~~~~~c~~~~~C~~C~ 68 (71)
T PF05495_consen 40 KRVICGKCRTEQPIDEYSCGADYFCPICG 68 (71)
T ss_dssp -EEEETTT--EEES-SBTT--SEEETTTT
T ss_pred cCeECCCCCCccChhhhhcCCCccCcCcC
Confidence 37778888777776553222 3454444
No 47
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=55.27 E-value=3.3 Score=26.99 Aligned_cols=34 Identities=24% Similarity=0.518 Sum_probs=26.8
Q ss_pred CceeEEcCCCCeeeeecCCC--CeEecCCCCccccC
Q 034324 22 AQSQLVCSGCRNLLLYPVGA--TSVCCAVCNAVTAV 55 (98)
Q Consensus 22 ~~sQlvC~gCr~lL~Yp~GA--~~VrC~~C~tVn~v 55 (98)
+|--|.|..|..||.=..|- -.+.|+.|.+||..
T Consensus 1 ~~~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 1 MMQTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred CceeeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 35568899999999877665 46789999999874
No 48
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=52.06 E-value=21 Score=25.18 Aligned_cols=33 Identities=18% Similarity=0.414 Sum_probs=20.9
Q ss_pred EecCCCCccccCCCCCCceeEEEeCCcCceEEe
Q 034324 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMY 76 (98)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~y 76 (98)
-+|..|+.......-.+...+..|+.|+-.|.+
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 466667665442222344588999999988764
No 49
>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=51.37 E-value=17 Score=26.72 Aligned_cols=35 Identities=17% Similarity=0.376 Sum_probs=26.8
Q ss_pred eeEEEeCCcCceEEeecCCCeEECCCCCccccccc
Q 034324 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (98)
Q Consensus 62 ~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v~~ 96 (98)
.+.++|-+|+..+.|-.-..--.|+.|+...+.++
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHTEFTRQ 144 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCCeeeeC
Confidence 57788888888888777667777888887777665
No 50
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=51.14 E-value=6.8 Score=31.18 Aligned_cols=9 Identities=56% Similarity=1.246 Sum_probs=6.9
Q ss_pred EcCCCCeee
Q 034324 27 VCSGCRNLL 35 (98)
Q Consensus 27 vC~gCr~lL 35 (98)
+|+||+..|
T Consensus 199 ~C~GC~m~l 207 (239)
T COG1579 199 VCGGCHMKL 207 (239)
T ss_pred cccCCeeee
Confidence 688888776
No 51
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=46.75 E-value=1.6 Score=25.14 Aligned_cols=25 Identities=28% Similarity=0.723 Sum_probs=18.3
Q ss_pred eeEEEeCCcCceEEeecCCCeEECCCCCc
Q 034324 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHT 90 (98)
Q Consensus 62 ~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~ 90 (98)
=+|+.|..|-..++ ...++|+.|+.
T Consensus 20 CgH~~C~~C~~~~~----~~~~~CP~C~k 44 (44)
T PF14634_consen 20 CGHIFCEKCLKKLK----GKSVKCPICRK 44 (44)
T ss_pred cCCHHHHHHHHhhc----CCCCCCcCCCC
Confidence 46777777877777 67778888763
No 52
>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=46.15 E-value=9.2 Score=27.72 Aligned_cols=34 Identities=24% Similarity=0.302 Sum_probs=24.9
Q ss_pred CCCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeec
Q 034324 40 GATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIR 78 (98)
Q Consensus 40 GA~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~ 78 (98)
-|..|+|+.|+..|-.-- . .-.|-.|++.|-..+
T Consensus 66 kav~V~CP~C~K~TKmLG--r---~D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLG--R---VDACMHCKEPLTLDP 99 (114)
T ss_pred cceeeECCCCCChHhhhc--h---hhccCcCCCcCccCc
Confidence 468899999999997642 1 237889998875543
No 53
>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=45.91 E-value=28 Score=23.15 Aligned_cols=30 Identities=27% Similarity=0.556 Sum_probs=20.7
Q ss_pred EEeCCcCceEEeecCCCeEECCCCCccccccc
Q 034324 65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (98)
Q Consensus 65 l~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v~~ 96 (98)
..| .|+..|.-..|+.+-+| .|.....|.+
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKE 33 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEEEE--S
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCeeeeee
Confidence 568 79999999999999999 8888766654
No 54
>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=45.51 E-value=11 Score=21.37 Aligned_cols=28 Identities=25% Similarity=0.483 Sum_probs=14.0
Q ss_pred eCCcCceEEeecCCCe-EECCCCCccccc
Q 034324 67 CGGCHTLLMYIRGATS-VQCSCCHTVNLA 94 (98)
Q Consensus 67 Cg~Cr~lL~yP~GA~s-VrC~~C~~Vt~v 94 (98)
|..|..+|....+... +.|..|.++-.+
T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~~~~ 32 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRTCGYEEPI 32 (35)
T ss_dssp ETTTTSBEEEEEETTTTEEESSSS-EEE-
T ss_pred CCCCCccceEcCCCccCcCCCCCCCccCC
Confidence 5666666644443322 347777666544
No 55
>PRK05580 primosome assembly protein PriA; Validated
Probab=44.49 E-value=36 Score=30.06 Aligned_cols=48 Identities=27% Similarity=0.490 Sum_probs=29.4
Q ss_pred Ceeeeec-CC-CCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCcc
Q 034324 32 RNLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 32 r~lL~Yp-~G-A~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
++||..+ || |+.+.|..|..+- .|..|...|.|.......+|.-|.+.
T Consensus 368 qvll~~nrrGy~~~~~C~~Cg~~~------------~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 368 QVLLFLNRRGYAPFLLCRDCGWVA------------ECPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred eEEEEEcCCCCCCceEhhhCcCcc------------CCCCCCCceeEECCCCeEECCCCcCC
Confidence 3455555 44 5678888887653 35666666666666666666555544
No 56
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=43.62 E-value=25 Score=24.50 Aligned_cols=32 Identities=22% Similarity=0.499 Sum_probs=15.4
Q ss_pred CeEecCCCCccccCCCCCCceeEEEeCCcCce
Q 034324 42 TSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTL 73 (98)
Q Consensus 42 ~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~l 73 (98)
+.+.|+.|+.....-.=....+|++|..|+..
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 55677777743210000112456666666543
No 57
>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=43.33 E-value=18 Score=20.14 Aligned_cols=21 Identities=24% Similarity=0.729 Sum_probs=8.7
Q ss_pred EcCCCCeeeeecCCCCeEecCCCCc
Q 034324 27 VCSGCRNLLLYPVGATSVCCAVCNA 51 (98)
Q Consensus 27 vC~gCr~lL~Yp~GA~~VrC~~C~t 51 (98)
.|..|..+..||+ ..|+.|.+
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 4666666666666 34555543
No 58
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=43.19 E-value=23 Score=27.59 Aligned_cols=26 Identities=27% Similarity=0.583 Sum_probs=21.0
Q ss_pred EEcCCCCeeeeecCCCCeEecCCCCccc
Q 034324 26 LVCSGCRNLLLYPVGATSVCCAVCNAVT 53 (98)
Q Consensus 26 lvC~gCr~lL~Yp~GA~~VrC~~C~tVn 53 (98)
-+|..||..|++ .-....|+.|..+-
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~tE 175 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNTE 175 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCEE
Confidence 479999999999 56778899997653
No 59
>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=41.82 E-value=21 Score=20.71 Aligned_cols=25 Identities=28% Similarity=0.626 Sum_probs=14.6
Q ss_pred EeCCcCceEEeecCCCeEECCCCCcc
Q 034324 66 VCGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 66 ~Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
.|..|+..|.- .+...++|..|+.+
T Consensus 13 ~C~~C~~~i~g-~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 13 YCDVCGKFIWG-LGKQGYRCSWCGLV 37 (53)
T ss_dssp B-TTSSSBECS-SSSCEEEETTTT-E
T ss_pred CCcccCcccCC-CCCCeEEECCCCCh
Confidence 56667766633 56666777776654
No 60
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=41.58 E-value=33 Score=21.35 Aligned_cols=29 Identities=17% Similarity=0.539 Sum_probs=16.9
Q ss_pred eeEEEeCCcCceEEeecCCCeEECCCCCc
Q 034324 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHT 90 (98)
Q Consensus 62 ~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~ 90 (98)
+..-+|..|...+--.....-++|+-|++
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 34445666666665555566666666654
No 61
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=41.24 E-value=26 Score=22.98 Aligned_cols=28 Identities=25% Similarity=0.472 Sum_probs=22.0
Q ss_pred EEeCCcCceEEeecCCCeEECCCCCccc
Q 034324 65 LVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (98)
Q Consensus 65 l~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt 92 (98)
-+|.+|...|.-=.++.++.|+.|.-+.
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~ 37 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVE 37 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCcee
Confidence 4788888888777888888888887543
No 62
>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=40.66 E-value=38 Score=19.39 Aligned_cols=29 Identities=31% Similarity=0.591 Sum_probs=16.9
Q ss_pred ecCCCCccccCCCCCCceeEEEeCCcCceEE
Q 034324 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLM 75 (98)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~ 75 (98)
+|+.|.+-+.+- -.+.+.++|..|+..|-
T Consensus 2 ~Cp~Cg~~~~~~--D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKEIVF--DPERGELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSEEEE--ETTTTEEEETTT-BBEE
T ss_pred CCcCCcCCceEE--cCCCCeEECCCCCCEee
Confidence 477777755321 12357778888877664
No 63
>PRK14873 primosome assembly protein PriA; Provisional
Probab=40.37 E-value=37 Score=30.32 Aligned_cols=48 Identities=27% Similarity=0.560 Sum_probs=25.1
Q ss_pred CCCeeeeec-CC-CCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCc
Q 034324 30 GCRNLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHT 90 (98)
Q Consensus 30 gCr~lL~Yp-~G-A~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~ 90 (98)
| ++||+-+ || |+.+.|..|..+- .|..|...|-|..+....+|.-|.+
T Consensus 369 g-qvll~lnRrGyap~l~C~~Cg~~~------------~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 369 G-PVLVQVPRRGYVPSLACARCRTPA------------RCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred C-cEEEEecCCCCCCeeEhhhCcCee------------ECCCCCCceeEecCCCeeECCCCcC
Confidence 5 6666655 44 3455777776543 3445555555544444444444443
No 64
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=39.62 E-value=12 Score=20.64 Aligned_cols=24 Identities=21% Similarity=0.476 Sum_probs=14.6
Q ss_pred EeCCcCceEEeecCCCeEECCCCCcc
Q 034324 66 VCGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 66 ~Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
.|..|+..|.... ..++|+.|+.+
T Consensus 13 ~C~~C~~~i~~~~--~~~~C~~C~~~ 36 (49)
T smart00109 13 KCCVCRKSIWGSF--QGLRCSWCKVK 36 (49)
T ss_pred CccccccccCcCC--CCcCCCCCCch
Confidence 4667777665433 45677777543
No 65
>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=39.57 E-value=30 Score=28.94 Aligned_cols=31 Identities=26% Similarity=0.589 Sum_probs=14.5
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcCceE
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLL 74 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL 74 (98)
.+.|..|+.+...++ -....+..|..|+..|
T Consensus 13 ~~~C~~Cd~l~~~~~-l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 13 HILCSQCDMLVALPR-IESGQKAACPRCGTTL 43 (403)
T ss_pred eeeCCCCCCcccccC-CCCCCeeECCCCCCCC
Confidence 344555555555442 1112234455565555
No 66
>PF14369 zf-RING_3: zinc-finger
Probab=39.31 E-value=29 Score=19.75 Aligned_cols=24 Identities=21% Similarity=0.646 Sum_probs=12.1
Q ss_pred EcCCCCeeeeec-CCCCeEecCCCC
Q 034324 27 VCSGCRNLLLYP-VGATSVCCAVCN 50 (98)
Q Consensus 27 vC~gCr~lL~Yp-~GA~~VrC~~C~ 50 (98)
-|..|++.+.-. .+...+.|+.|+
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~ 28 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCH 28 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCC
Confidence 356666555542 333344466665
No 67
>PRK11827 hypothetical protein; Provisional
Probab=39.29 E-value=35 Score=21.91 Aligned_cols=28 Identities=21% Similarity=0.483 Sum_probs=18.4
Q ss_pred eEEcCCCCeeeeecCCCCeEecCCCCcc
Q 034324 25 QLVCSGCRNLLLYPVGATSVCCAVCNAV 52 (98)
Q Consensus 25 QlvC~gCr~lL~Yp~GA~~VrC~~C~tV 52 (98)
-|+|-.|+.-|.|-.++....|..|+-.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~la 35 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLA 35 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCee
Confidence 4677777777777666665556655543
No 68
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=39.24 E-value=51 Score=21.10 Aligned_cols=34 Identities=18% Similarity=0.342 Sum_probs=18.0
Q ss_pred CceeEEEeCCcCceEEeecCCCeEECCCCCcccc
Q 034324 60 TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (98)
Q Consensus 60 ~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~ 93 (98)
..+.++.|..|+..=-.+.--.-.||+.|..-|-
T Consensus 26 ~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT 59 (61)
T PF14599_consen 26 NKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNT 59 (61)
T ss_dssp --EEEEEESSS--EEEEE--TT----TTTS---E
T ss_pred CCEEEEECCCCCCccceeeeHhhhcCCCCCCccc
Confidence 4578889999998888888888889999987664
No 69
>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=38.70 E-value=18 Score=20.24 Aligned_cols=25 Identities=20% Similarity=0.538 Sum_probs=14.4
Q ss_pred EeCCcCceEEeecCCCeEECCCCCcc
Q 034324 66 VCGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 66 ~Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
.|..|+..|... +....+|+.|+.+
T Consensus 13 ~C~~C~~~i~~~-~~~~~~C~~C~~~ 37 (50)
T cd00029 13 FCDVCRKSIWGL-FKQGLRCSWCKVK 37 (50)
T ss_pred Chhhcchhhhcc-ccceeEcCCCCCc
Confidence 366666666543 4566666666543
No 70
>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=37.79 E-value=33 Score=19.66 Aligned_cols=24 Identities=17% Similarity=0.423 Sum_probs=14.1
Q ss_pred eCCcCceEEeecCCCeEECCCCCcc
Q 034324 67 CGGCHTLLMYIRGATSVQCSCCHTV 91 (98)
Q Consensus 67 Cg~Cr~lL~yP~GA~sVrC~~C~~V 91 (98)
|+.|+.. .|-......-|..|+++
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 55555555666556554
No 71
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=37.33 E-value=12 Score=30.54 Aligned_cols=39 Identities=28% Similarity=0.646 Sum_probs=24.8
Q ss_pred EecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCC
Q 034324 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCH 89 (98)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~ 89 (98)
.-|+.|---=.-|---=+.+||.|..|++ -.+.+|+.|+
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~-------~~~~~CP~Cr 87 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRT-------KVSNKCPTCR 87 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhh-------hhcccCCccc
Confidence 45776642221121113579999999998 4567898886
No 72
>PRK10996 thioredoxin 2; Provisional
Probab=36.40 E-value=23 Score=24.56 Aligned_cols=32 Identities=25% Similarity=0.618 Sum_probs=23.7
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcCceEE
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLM 75 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~ 75 (98)
+-.|..|+.+|..|++.. -.+..||+|...+.
T Consensus 2 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 33 (139)
T PRK10996 2 NTVCTSCQAINRLPDERI-EDAAKCGRCGHDLF 33 (139)
T ss_pred eEECCCCCCcCCCCCccc-cCCCcCCCCCCccC
Confidence 457999999999876543 34568998887665
No 73
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=36.35 E-value=48 Score=19.26 Aligned_cols=24 Identities=25% Similarity=0.753 Sum_probs=15.7
Q ss_pred EcC--CCCeeeeecC--CCCeEecCCCC
Q 034324 27 VCS--GCRNLLLYPV--GATSVCCAVCN 50 (98)
Q Consensus 27 vC~--gCr~lL~Yp~--GA~~VrC~~C~ 50 (98)
-|- +|..++.... |...|.|..|+
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~ 47 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCG 47 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCC
Confidence 366 7777776654 66677776664
No 74
>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=36.31 E-value=49 Score=27.68 Aligned_cols=30 Identities=23% Similarity=0.617 Sum_probs=20.9
Q ss_pred eEEcCCCCeeeeecCCC--CeEecCCCCcccc
Q 034324 25 QLVCSGCRNLLLYPVGA--TSVCCAVCNAVTA 54 (98)
Q Consensus 25 QlvC~gCr~lL~Yp~GA--~~VrC~~C~tVn~ 54 (98)
-+.|..|..+...++-+ ..-+|+.|+++=.
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 45588888888877633 3456888887754
No 75
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=35.51 E-value=20 Score=26.99 Aligned_cols=28 Identities=25% Similarity=0.605 Sum_probs=23.2
Q ss_pred EeCCcC-ceEEeecCC-CeEECCCCCcccc
Q 034324 66 VCGGCH-TLLMYIRGA-TSVQCSCCHTVNL 93 (98)
Q Consensus 66 ~Cg~Cr-~lL~yP~GA-~sVrC~~C~~Vt~ 93 (98)
+|.-|+ .-++||... ..++|..|.+|-.
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H 183 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFH 183 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCccccc
Confidence 577777 489999999 9999999998754
No 76
>PRK11032 hypothetical protein; Provisional
Probab=35.42 E-value=44 Score=25.14 Aligned_cols=35 Identities=23% Similarity=0.509 Sum_probs=27.0
Q ss_pred eeEEEeCCcCceEEeecCCCeEECCCCCccccccc
Q 034324 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (98)
Q Consensus 62 ~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v~~ 96 (98)
.+.++|-+|.-.+-|-.-..--.|+-|+...+.|+
T Consensus 122 ~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~R~ 156 (160)
T PRK11032 122 LGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQRR 156 (160)
T ss_pred cceEEecCCCCEEEecCCCcCCCCCCCCCCeeeeC
Confidence 57788888888888877777778888887776654
No 77
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.36 E-value=13 Score=19.57 Aligned_cols=24 Identities=29% Similarity=0.693 Sum_probs=14.4
Q ss_pred EecCCCCccccCCCCCCceeEEEeCCcCceE
Q 034324 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLL 74 (98)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL 74 (98)
+.|+.|.+.+. . ..-.|..|+..|
T Consensus 3 ~~Cp~Cg~~~~--~-----~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEID--P-----DAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCC--c-----ccccChhhCCCC
Confidence 46777877542 1 355677776543
No 78
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=34.98 E-value=38 Score=27.67 Aligned_cols=47 Identities=19% Similarity=0.376 Sum_probs=26.5
Q ss_pred CCCCeEecCCCCccccCCCCCCceeEEEeCCcCce---EEeecCCCeEECC
Q 034324 39 VGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTL---LMYIRGATSVQCS 86 (98)
Q Consensus 39 ~GA~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~l---L~yP~GA~sVrC~ 86 (98)
-++.-|-|..|+..-.+- --+|.--+.|+.|..- ---|.|...|||+
T Consensus 76 g~~PmvtCRVCq~~i~~e-gk~~QHVVKC~~CnEATPIrnAPpGKKYVRCP 125 (275)
T KOG4684|consen 76 GQFPMVTCRVCQVAISLE-GKNQQHVVKCHSCNEATPIRNAPPGKKYVRCP 125 (275)
T ss_pred CCCceEeehhhhHHhccc-cccceeeEeecccCccccCCCCCCCCceeecC
Confidence 355667777776544331 1234444567777542 2356677777776
No 79
>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=34.97 E-value=45 Score=20.69 Aligned_cols=8 Identities=25% Similarity=0.787 Sum_probs=3.4
Q ss_pred cCCCCccc
Q 034324 46 CAVCNAVT 53 (98)
Q Consensus 46 C~~C~tVn 53 (98)
|+.|++.|
T Consensus 25 C~~C~~hN 32 (54)
T PF10058_consen 25 CSKCFSHN 32 (54)
T ss_pred Ccccchhh
Confidence 44444444
No 80
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=34.96 E-value=22 Score=28.31 Aligned_cols=28 Identities=21% Similarity=0.630 Sum_probs=13.6
Q ss_pred ecCCCCccccCCCCCCceeEEEeCCcCceE
Q 034324 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLL 74 (98)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL 74 (98)
.|+.|...+.+- -.+.+.++|..|+..|
T Consensus 13 ~Cp~Cg~~~iv~--d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 13 VCPECGSDKLIY--DYERGEIVCADCGLVI 40 (310)
T ss_pred cCcCCCCCCeeE--ECCCCeEeecccCCcc
Confidence 455555433221 1234666666666544
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=34.48 E-value=12 Score=24.52 Aligned_cols=31 Identities=23% Similarity=0.542 Sum_probs=20.5
Q ss_pred eEEcCCCCee-------eeecCCCCeEecCCCCccccC
Q 034324 25 QLVCSGCRNL-------LLYPVGATSVCCAVCNAVTAV 55 (98)
Q Consensus 25 QlvC~gCr~l-------L~Yp~GA~~VrC~~C~tVn~v 55 (98)
+..|..|.+- .+|-+|...|+|+.|+..-..
T Consensus 4 ~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeee
Confidence 4566667543 468899999999999876544
No 82
>PRK04351 hypothetical protein; Provisional
Probab=34.24 E-value=36 Score=24.91 Aligned_cols=32 Identities=22% Similarity=0.430 Sum_probs=18.7
Q ss_pred ecCCCCccccCCCCCCceeEEEeCCcCceEEee
Q 034324 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYI 77 (98)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP 77 (98)
+|..|+.+-.-.. -....+-+||.|+..|.+-
T Consensus 114 ~C~~Cg~~~~r~R-r~n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 114 ECQSCGQQYLRKR-RINTKRYRCGKCRGKLKLI 145 (149)
T ss_pred ECCCCCCEeeeee-ecCCCcEEeCCCCcEeeec
Confidence 4555554433221 2234778899998888753
No 83
>PLN00162 transport protein sec23; Provisional
Probab=34.04 E-value=48 Score=29.96 Aligned_cols=34 Identities=29% Similarity=0.583 Sum_probs=28.9
Q ss_pred eeEEcCCCCeee----eecCCCCeEecCCCCccccCCC
Q 034324 24 SQLVCSGCRNLL----LYPVGATSVCCAVCNAVTAVPP 57 (98)
Q Consensus 24 sQlvC~gCr~lL----~Yp~GA~~VrC~~C~tVn~vp~ 57 (98)
.-++|..||..| ..-.+....+|..|+..|.+|+
T Consensus 52 ~pvRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~~P~ 89 (761)
T PLN00162 52 DPLRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNHFPP 89 (761)
T ss_pred CCCccCCCcCEECCceEEecCCCEEEccCCCCCCCCch
Confidence 458999999988 3456788999999999999875
No 84
>PRK02935 hypothetical protein; Provisional
Probab=33.69 E-value=33 Score=24.77 Aligned_cols=35 Identities=26% Similarity=0.381 Sum_probs=25.1
Q ss_pred CCCCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeec
Q 034324 39 VGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIR 78 (98)
Q Consensus 39 ~GA~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~ 78 (98)
.-|..|.|+.|+-.|-..- -.-.|-.|++.|-..+
T Consensus 66 tkavqV~CP~C~K~TKmLG-----rvD~CM~C~~PLTLd~ 100 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLG-----RVDACMHCNQPLTLDR 100 (110)
T ss_pred ccceeeECCCCCchhhhcc-----ceeecCcCCCcCCcCc
Confidence 4578899999999997652 2336888888775544
No 85
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=33.19 E-value=34 Score=24.51 Aligned_cols=33 Identities=18% Similarity=0.492 Sum_probs=24.4
Q ss_pred CeEecCCCCccccC---CCCCCceeEEEeCCcCceE
Q 034324 42 TSVCCAVCNAVTAV---PPPGTEMAQLVCGGCHTLL 74 (98)
Q Consensus 42 ~~VrC~~C~tVn~v---p~~~~~~aql~Cg~Cr~lL 74 (98)
+.+-|+.|+..+.+ ---....+-++||.|...-
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred ceEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 35679999998876 2224568999999998643
No 86
>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=32.37 E-value=41 Score=23.33 Aligned_cols=28 Identities=18% Similarity=0.450 Sum_probs=20.2
Q ss_pred eEEEeCCcCceEEeecCCCeEECCCCCccc
Q 034324 63 AQLVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (98)
Q Consensus 63 aql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt 92 (98)
+...|..|+. .|+.....++|+.|+..+
T Consensus 69 ~~~~C~~Cg~--~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 69 VECECEDCSE--EVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred cEEEcccCCC--EEecCCcCccCcCCcCCC
Confidence 6678888884 455555578899998765
No 87
>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=32.05 E-value=1.4e+02 Score=19.80 Aligned_cols=57 Identities=23% Similarity=0.529 Sum_probs=34.8
Q ss_pred eEEcCCCCeeeeecCCCCeEecCCCCccccCCCCCCceeEEEeCCcCceEEee--cCCCeEECCCCCcc
Q 034324 25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYI--RGATSVQCSCCHTV 91 (98)
Q Consensus 25 QlvC~gCr~lL~Yp~GA~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP--~GA~sVrC~~C~~V 91 (98)
++.|-.|+.-|...- ....|..|+.-- ..+..|-.|...|-.= =||...-|-.|+..
T Consensus 1 e~~CP~C~~~L~~~~--~~~~C~~C~~~~--------~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gL 59 (70)
T PF07191_consen 1 ENTCPKCQQELEWQG--GHYHCEACQKDY--------KKEAFCPDCGQPLEVLKACGAVDYFCNHCHGL 59 (70)
T ss_dssp --B-SSS-SBEEEET--TEEEETTT--EE--------EEEEE-TTT-SB-EEEEETTEEEEE-TTTT-E
T ss_pred CCcCCCCCCccEEeC--CEEECccccccc--------eecccCCCcccHHHHHHHhcccceeeccCCce
Confidence 367888999876655 788899998632 3677899999887654 48888888888764
No 88
>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=31.12 E-value=71 Score=27.25 Aligned_cols=38 Identities=21% Similarity=0.665 Sum_probs=19.1
Q ss_pred CCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCc
Q 034324 41 ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHT 90 (98)
Q Consensus 41 A~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~ 90 (98)
|+.+.|..|..+- .|..|...|-|=......+|.-|.+
T Consensus 211 a~~~~C~~Cg~~~------------~C~~C~~~l~~h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 211 SKNLLCRSCGYIL------------CCPNCDVSLTYHKKEGKLRCHYCGY 248 (505)
T ss_pred CCeeEhhhCcCcc------------CCCCCCCceEEecCCCeEEcCCCcC
Confidence 4556666666543 2444555555544444444444443
No 89
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.73 E-value=44 Score=23.14 Aligned_cols=28 Identities=29% Similarity=0.506 Sum_probs=20.3
Q ss_pred eEEEeCCcCceEEeecCCCeEECCCCCccc
Q 034324 63 AQLVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (98)
Q Consensus 63 aql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt 92 (98)
+...|..|+. .|+.......|+.|+..+
T Consensus 69 ~~~~C~~Cg~--~~~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 69 AQAWCWDCSQ--VVEIHQHDAQCPHCHGER 96 (113)
T ss_pred cEEEcccCCC--EEecCCcCccCcCCCCCC
Confidence 6788888984 455555667799998654
No 90
>PRK11827 hypothetical protein; Provisional
Probab=30.03 E-value=74 Score=20.42 Aligned_cols=32 Identities=16% Similarity=0.247 Sum_probs=19.2
Q ss_pred EEEeCCcCceEEeecCCCeEECCCCCcccccc
Q 034324 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNLAL 95 (98)
Q Consensus 64 ql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~v~ 95 (98)
-+.|-.|+.-|.|=.++....|..|+-.-.|+
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeecccc
Confidence 35666666666666566666666666554444
No 91
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=30.01 E-value=46 Score=23.09 Aligned_cols=29 Identities=21% Similarity=0.375 Sum_probs=21.2
Q ss_pred eeEEEeCCcCceEEeecCCCe-EECCCCCccc
Q 034324 62 MAQLVCGGCHTLLMYIRGATS-VQCSCCHTVN 92 (98)
Q Consensus 62 ~aql~Cg~Cr~lL~yP~GA~s-VrC~~C~~Vt 92 (98)
-+...|..|+. .|+..... .+|+.|+..+
T Consensus 68 p~~~~C~~Cg~--~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 68 EAECWCETCQQ--YVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred CcEEEcccCCC--eeecCCccCCcCcCcCCCC
Confidence 36788999985 56665554 7899999764
No 92
>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=28.91 E-value=41 Score=22.22 Aligned_cols=26 Identities=23% Similarity=0.636 Sum_probs=19.1
Q ss_pred EcCCCCeeeeecCCCCeEecCCCCcccc
Q 034324 27 VCSGCRNLLLYPVGATSVCCAVCNAVTA 54 (98)
Q Consensus 27 vC~gCr~lL~Yp~GA~~VrC~~C~tVn~ 54 (98)
.|..|..+|. +.+ ....|..|.....
T Consensus 2 fC~~Cg~~l~-~~~-~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMT-PKN-GVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccc-cCC-CeEECcCCCCccc
Confidence 5888999985 444 3788999986644
No 93
>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=28.26 E-value=81 Score=26.90 Aligned_cols=27 Identities=22% Similarity=0.524 Sum_probs=14.1
Q ss_pred cCCCCeeeeecCCCCeEecCCCCcccc
Q 034324 28 CSGCRNLLLYPVGATSVCCAVCNAVTA 54 (98)
Q Consensus 28 C~gCr~lL~Yp~GA~~VrC~~C~tVn~ 54 (98)
|..|..-|.|-+.-...+|..|.....
T Consensus 225 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 225 CPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 444555555555555555555554443
No 94
>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=28.25 E-value=61 Score=23.82 Aligned_cols=36 Identities=17% Similarity=0.298 Sum_probs=30.1
Q ss_pred CCceeEEcCCCCeeeeecCCCCeEecCCCCccccCC
Q 034324 21 GAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVP 56 (98)
Q Consensus 21 ~~~sQlvC~gCr~lL~Yp~GA~~VrC~~C~tVn~vp 56 (98)
.-.+.++|-.|...+.|..-...-.|+.|+......
T Consensus 108 ~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVELTHPERLPPCPKCGHTEFTR 143 (146)
T ss_pred ecCceEecccCCCEEEecCCCcCCCCCCCCCCeeee
Confidence 356789999999999988877788999999887654
No 95
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=27.33 E-value=51 Score=19.30 Aligned_cols=9 Identities=22% Similarity=0.741 Sum_probs=4.6
Q ss_pred CeEECCCCC
Q 034324 81 TSVQCSCCH 89 (98)
Q Consensus 81 ~sVrC~~C~ 89 (98)
...+|..|.
T Consensus 13 ~ry~C~~C~ 21 (43)
T cd02340 13 VRYKCLVCP 21 (43)
T ss_pred CeEECCCCC
Confidence 345555554
No 96
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=27.22 E-value=30 Score=22.38 Aligned_cols=25 Identities=20% Similarity=0.529 Sum_probs=17.2
Q ss_pred eEEcCCCCeeeeecCCCCeEecCCCCccccC
Q 034324 25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (98)
Q Consensus 25 QlvC~gCr~lL~Yp~GA~~VrC~~C~tVn~v 55 (98)
...|..|+.|+. .-+|+.|.+.+.+
T Consensus 3 ~kAC~~C~~i~~------~~~CP~Cgs~~~T 27 (61)
T PRK08351 3 EKACRHCHYITT------EDRCPVCGSRDLS 27 (61)
T ss_pred hhhhhhCCcccC------CCcCCCCcCCccc
Confidence 347888888872 2268888887754
No 97
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=27.02 E-value=38 Score=29.33 Aligned_cols=35 Identities=17% Similarity=0.333 Sum_probs=27.2
Q ss_pred CCCCceeEEcCCCCeeeeecCCCCeEecCCCCccccCC
Q 034324 19 ANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVP 56 (98)
Q Consensus 19 ~~~~~sQlvC~gCr~lL~Yp~GA~~VrC~~C~tVn~vp 56 (98)
.+.++++..|.+|..+..-. ...+|..|++--.+.
T Consensus 214 ~~~~~~~~~C~~C~~~~~~~---~~~~CpRC~~~Ly~r 248 (418)
T COG2995 214 TGAREGLRSCLCCHYILPHD---AEPRCPRCGSKLYVR 248 (418)
T ss_pred CCCcccceecccccccCCHh---hCCCCCCCCChhhcc
Confidence 67888999999998876554 778899998765543
No 98
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.80 E-value=37 Score=30.44 Aligned_cols=36 Identities=25% Similarity=0.455 Sum_probs=18.3
Q ss_pred ecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCcccc
Q 034324 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (98)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~ 93 (98)
.|+.|++.|.. ..-.|..|++.|-. -.|+.|.+.+.
T Consensus 3 ~Cp~Cg~~n~~-------~akFC~~CG~~l~~------~~Cp~CG~~~~ 38 (645)
T PRK14559 3 ICPQCQFENPN-------NNRFCQKCGTSLTH------KPCPQCGTEVP 38 (645)
T ss_pred cCCCCCCcCCC-------CCccccccCCCCCC------CcCCCCCCCCC
Confidence 56666666631 23356666655521 24555555443
No 99
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.67 E-value=1.1e+02 Score=17.28 Aligned_cols=8 Identities=38% Similarity=0.496 Sum_probs=3.2
Q ss_pred eEEEeCCc
Q 034324 63 AQLVCGGC 70 (98)
Q Consensus 63 aql~Cg~C 70 (98)
++.+|..|
T Consensus 20 ~~~~C~~C 27 (33)
T PF08792_consen 20 DYEVCIFC 27 (33)
T ss_pred CeEEcccC
Confidence 33444443
No 100
>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=26.30 E-value=42 Score=19.48 Aligned_cols=26 Identities=27% Similarity=0.659 Sum_probs=13.5
Q ss_pred EcCC--CCeeeeecCCCCe--EecCCCCcc
Q 034324 27 VCSG--CRNLLLYPVGATS--VCCAVCNAV 52 (98)
Q Consensus 27 vC~g--Cr~lL~Yp~GA~~--VrC~~C~tV 52 (98)
.|-+ |..++....|... |+|..|++.
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 49 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTE 49 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSE
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCc
Confidence 5644 7777777777776 777777643
No 101
>PRK05580 primosome assembly protein PriA; Validated
Probab=26.10 E-value=88 Score=27.68 Aligned_cols=44 Identities=18% Similarity=0.384 Sum_probs=25.3
Q ss_pred EcCCCCeeeeecCCCCeEecCCCCccccCCCCCCceeEEEeCCcCceEEeec
Q 034324 27 VCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIR 78 (98)
Q Consensus 27 vC~gCr~lL~Yp~GA~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~ 78 (98)
.|..|..-|.|...-....|..|......+. .|..|+-.-+...
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~--------~Cp~Cg~~~l~~~ 435 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIPK--------ACPECGSTDLVPV 435 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCCC--------CCCCCcCCeeEEe
Confidence 3555556666766666667777766554332 4666655444443
No 102
>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=25.97 E-value=50 Score=20.15 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=17.5
Q ss_pred eecCCCCeEecCCCCccccCCCCCCceeEEEeCCcCc
Q 034324 36 LYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHT 72 (98)
Q Consensus 36 ~Yp~GA~~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~ 72 (98)
.-+.+ +|-.|+.|..+.... .......|..|+.
T Consensus 22 v~~~~-TSq~C~~CG~~~~~~---~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 22 VDEAY-TSQTCPRCGHRNKKR---RSGRVFTCPNCGF 54 (69)
T ss_pred ECCCC-CccCccCcccccccc---cccceEEcCCCCC
Confidence 33444 666777777666541 1234455555544
No 103
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=25.61 E-value=25 Score=25.59 Aligned_cols=34 Identities=29% Similarity=0.538 Sum_probs=29.8
Q ss_pred eeEEcCCCCeeeeecCCCCeEecCCCCccccCCC
Q 034324 24 SQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPP 57 (98)
Q Consensus 24 sQlvC~gCr~lL~Yp~GA~~VrC~~C~tVn~vp~ 57 (98)
+-+-|+.|..||.-+.-...|-|..|.....+..
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~ 39 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQ 39 (116)
T ss_pred CcchhhhhhhhcccccccCceEeccccccCCHHH
Confidence 4567999999999999999999999999987643
No 104
>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=25.47 E-value=36 Score=21.36 Aligned_cols=20 Identities=25% Similarity=0.564 Sum_probs=11.6
Q ss_pred CceeEEcCCCCeeeeecCCC
Q 034324 22 AQSQLVCSGCRNLLLYPVGA 41 (98)
Q Consensus 22 ~~sQlvC~gCr~lL~Yp~GA 41 (98)
+..+.+|.+|.++|..-..+
T Consensus 43 ~~kr~~Ck~C~~~liPG~~~ 62 (85)
T PF04032_consen 43 EIKRTICKKCGSLLIPGVNC 62 (85)
T ss_dssp TCCCTB-TTT--B--CTTTE
T ss_pred HHhcccccCCCCEEeCCCcc
Confidence 56788999999999876654
No 105
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=25.32 E-value=57 Score=26.32 Aligned_cols=29 Identities=24% Similarity=0.670 Sum_probs=23.2
Q ss_pred ecCCCCccccCCCCCCceeEEEeCCcCceEE
Q 034324 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLM 75 (98)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~ 75 (98)
.|+.|...+.+.. .+.+..+|+.|+..|-
T Consensus 3 ~CpeCg~~~~~~d--~~~ge~VC~~CG~Vi~ 31 (285)
T COG1405 3 SCPECGSTNIITD--YERGEIVCADCGLVLE 31 (285)
T ss_pred CCCCCCCccceee--ccCCeEEeccCCEEec
Confidence 5999999977642 4579999999998774
No 106
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=24.00 E-value=30 Score=21.10 Aligned_cols=28 Identities=29% Similarity=0.726 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCCCCCCCCCceeEEcCCCCee
Q 034324 4 PLAPYPTPPAPYTPPANGAQSQLVCSGCRNL 34 (98)
Q Consensus 4 pl~p~p~~~~~~~pp~~~~~sQlvC~gCr~l 34 (98)
+|..|.=||++- .+.+.+-++|.-|+.-
T Consensus 18 ~L~vy~Vpp~~~---~~~d~~iliC~tC~~Q 45 (47)
T smart00782 18 PLVVYAVPPSSD---VTADNSVMLCDTCHSQ 45 (47)
T ss_pred CceEEecCCCCC---CCccceeeechHHHHh
Confidence 456666544443 5678899999988754
No 107
>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=23.82 E-value=63 Score=17.09 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=6.2
Q ss_pred cCCCeEECCCCCc
Q 034324 78 RGATSVQCSCCHT 90 (98)
Q Consensus 78 ~GA~sVrC~~C~~ 90 (98)
.|..++.|+.|+.
T Consensus 17 ~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 17 NGRSTYLCPRCQK 29 (30)
T ss_dssp TTEEEEE-TTTCC
T ss_pred cCCCCeECcCCcC
Confidence 3445555665553
No 108
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=23.82 E-value=36 Score=25.05 Aligned_cols=35 Identities=26% Similarity=0.433 Sum_probs=27.3
Q ss_pred CCceeEEEeCCcCceEEeecCCCeEECCCCC-cccccc
Q 034324 59 GTEMAQLVCGGCHTLLMYIRGATSVQCSCCH-TVNLAL 95 (98)
Q Consensus 59 ~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~-~Vt~v~ 95 (98)
|..|---.|-.|++.|+= =...|-|+.|. +++.+.
T Consensus 23 GAkML~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 23 GAKMLAKHCPKCGTPLFR--KDGEVFCPVCGYREVVVE 58 (131)
T ss_pred hhHHHHhhCcccCCccee--eCCeEECCCCCceEEEee
Confidence 455667789999999987 66789999999 665544
No 109
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=23.50 E-value=40 Score=22.21 Aligned_cols=43 Identities=23% Similarity=0.567 Sum_probs=14.5
Q ss_pred ecCCCCccccCCCCCCceeEEEeCCcCceEEeecCCCeEECCCCCcccc
Q 034324 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (98)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL~yP~GA~sVrC~~C~~Vt~ 93 (98)
||+.|..+=..|---..=.|+-|..|-.- -.|. +|++|++=.-
T Consensus 9 rCs~C~~~l~~pv~l~~CeH~fCs~Ci~~---~~~~---~CPvC~~Paw 51 (65)
T PF14835_consen 9 RCSICFDILKEPVCLGGCEHIFCSSCIRD---CIGS---ECPVCHTPAW 51 (65)
T ss_dssp S-SSS-S--SS-B---SSS--B-TTTGGG---GTTT---B-SSS--B-S
T ss_pred CCcHHHHHhcCCceeccCccHHHHHHhHH---hcCC---CCCCcCChHH
Confidence 56667666443321123457777777533 1222 4888876543
No 110
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.26 E-value=47 Score=23.13 Aligned_cols=28 Identities=29% Similarity=0.644 Sum_probs=17.8
Q ss_pred eEEEeCCcCceEEeecCCC-eEECCCCCccc
Q 034324 63 AQLVCGGCHTLLMYIRGAT-SVQCSCCHTVN 92 (98)
Q Consensus 63 aql~Cg~Cr~lL~yP~GA~-sVrC~~C~~Vt 92 (98)
+...|..|+.. ++.... ..+|+.|+.-+
T Consensus 70 ~~~~C~~Cg~~--~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 70 VELECKDCSHV--FKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CEEEhhhCCCc--cccCCccCCcCcCCCCCc
Confidence 67788888833 444433 34588888754
No 111
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=22.71 E-value=63 Score=27.24 Aligned_cols=30 Identities=27% Similarity=0.605 Sum_probs=15.1
Q ss_pred EecCCCCccccCCCCCCceeEEEeCCcCceE
Q 034324 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLL 74 (98)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~lL 74 (98)
+.|..|+.+...++ -..-.+-.|..|+..|
T Consensus 11 ~~C~~Cd~l~~~~~-l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPR-LEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCC-CCCCCeeECCCCCCCC
Confidence 44666666655442 1112234466666665
No 112
>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=22.44 E-value=1.2e+02 Score=17.98 Aligned_cols=27 Identities=30% Similarity=0.589 Sum_probs=16.6
Q ss_pred eeEEEeCCcCceEEeecCCCeEECCCCC
Q 034324 62 MAQLVCGGCHTLLMYIRGATSVQCSCCH 89 (98)
Q Consensus 62 ~aql~Cg~Cr~lL~yP~GA~sVrC~~C~ 89 (98)
|-.-.|..|.+.||=.++- .+.|..|.
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 4445677777777764443 46677663
No 113
>PLN00162 transport protein sec23; Provisional
Probab=22.00 E-value=94 Score=28.12 Aligned_cols=31 Identities=26% Similarity=0.357 Sum_probs=22.4
Q ss_pred EEeCCcCceE----EeecCCCeEECCCCCcccccc
Q 034324 65 LVCGGCHTLL----MYIRGATSVQCSCCHTVNLAL 95 (98)
Q Consensus 65 l~Cg~Cr~lL----~yP~GA~sVrC~~C~~Vt~v~ 95 (98)
+.|..||..| .+-.+....+|..|...|.+.
T Consensus 54 vRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~~P 88 (761)
T PLN00162 54 LRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNHFP 88 (761)
T ss_pred CccCCCcCEECCceEEecCCCEEEccCCCCCCCCc
Confidence 5566666655 234578899999999999764
No 114
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=21.89 E-value=34 Score=32.03 Aligned_cols=33 Identities=24% Similarity=0.630 Sum_probs=0.0
Q ss_pred EEeCCcCceEE----eecCCCeEECCCCCcccccccC
Q 034324 65 LVCGGCHTLLM----YIRGATSVQCSCCHTVNLALEG 97 (98)
Q Consensus 65 l~Cg~Cr~lL~----yP~GA~sVrC~~C~~Vt~v~~~ 97 (98)
++|..||.-+- +-.+.+.++|-.|+.+|++.++
T Consensus 200 vRCrrCrsYiNPfv~fi~~g~kw~CNiC~~kN~vp~~ 236 (861)
T COG5028 200 VRCRRCRSYINPFVQFIEQGRKWRCNICRSKNDVPEG 236 (861)
T ss_pred hhhhhhHhhcCceEEEecCCcEEEEeeccccccCccc
No 115
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=21.87 E-value=89 Score=17.67 Aligned_cols=6 Identities=33% Similarity=1.237 Sum_probs=3.5
Q ss_pred cCCCCc
Q 034324 46 CAVCNA 51 (98)
Q Consensus 46 C~~C~t 51 (98)
|+.|++
T Consensus 2 CP~C~~ 7 (41)
T PF13453_consen 2 CPRCGT 7 (41)
T ss_pred cCCCCc
Confidence 556655
No 116
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=21.24 E-value=55 Score=25.87 Aligned_cols=29 Identities=28% Similarity=0.512 Sum_probs=19.9
Q ss_pred eEecCCCCccccCCCCCCceeEEEeCCcC
Q 034324 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCH 71 (98)
Q Consensus 43 ~VrC~~C~tVn~vp~~~~~~aql~Cg~Cr 71 (98)
+|+|+.|.-....+......+.++|..|-
T Consensus 172 ~v~C~kCGE~~~e~~~~~~ng~~vC~~C~ 200 (206)
T COG2191 172 SVRCSKCGELFMEPRAVVLNGKPVCKPCA 200 (206)
T ss_pred eeeccccCcccccchhhhcCCceeccccc
Confidence 37888887776655445566777887774
No 117
>PRK06260 threonine synthase; Validated
Probab=20.88 E-value=72 Score=25.97 Aligned_cols=23 Identities=26% Similarity=0.483 Sum_probs=10.1
Q ss_pred EEEeCCcCceEEeecCCCeEECCCC
Q 034324 64 QLVCGGCHTLLMYIRGATSVQCSCC 88 (98)
Q Consensus 64 ql~Cg~Cr~lL~yP~GA~sVrC~~C 88 (98)
++.|-.|+.. |+.+....+|+.|
T Consensus 3 ~~~C~~cg~~--~~~~~~~~~Cp~c 25 (397)
T PRK06260 3 WLKCIECGKE--YDPDEIIYTCPEC 25 (397)
T ss_pred EEEECCCCCC--CCCCCccccCCCC
Confidence 3444444443 3444334444444
No 118
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=20.74 E-value=91 Score=26.27 Aligned_cols=31 Identities=19% Similarity=0.585 Sum_probs=20.1
Q ss_pred eeEEcCCCCeeeeecCC--CCeEecCCCCcccc
Q 034324 24 SQLVCSGCRNLLLYPVG--ATSVCCAVCNAVTA 54 (98)
Q Consensus 24 sQlvC~gCr~lL~Yp~G--A~~VrC~~C~tVn~ 54 (98)
+.+.|..|..+...++- -..-+|+.|+++=.
T Consensus 9 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 41 (419)
T PRK15103 9 KHILCPQCDMLVALPRLEHGQKAACPRCGTTLT 41 (419)
T ss_pred CcccCCCCCceeecCCCCCCCeeECCCCCCCCc
Confidence 34668888887777742 22457888877654
No 119
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.70 E-value=52 Score=31.03 Aligned_cols=35 Identities=23% Similarity=0.533 Sum_probs=26.9
Q ss_pred eeEEEeCCcCceE---E-eecCCCeEECCCCCccccccc
Q 034324 62 MAQLVCGGCHTLL---M-YIRGATSVQCSCCHTVNLALE 96 (98)
Q Consensus 62 ~aql~Cg~Cr~lL---~-yP~GA~sVrC~~C~~Vt~v~~ 96 (98)
..-++|..||+-+ . +..--+..||..|..||++.+
T Consensus 216 ~~IvRCr~CRtYiNPFV~fid~gr~WrCNlC~~~NdvP~ 254 (887)
T KOG1985|consen 216 TLIVRCRRCRTYINPFVEFIDQGRRWRCNLCGRVNDVPD 254 (887)
T ss_pred CceeeehhhhhhcCCeEEecCCCceeeechhhhhcCCcH
Confidence 4567899999865 2 334448999999999999864
No 120
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=20.51 E-value=49 Score=16.73 Aligned_cols=22 Identities=18% Similarity=0.492 Sum_probs=13.5
Q ss_pred EecCCCCccccCCCCCCceeEEEeCCcCc
Q 034324 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHT 72 (98)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~Cg~Cr~ 72 (98)
..|+.|..+|.. ....|..|++
T Consensus 3 W~C~~C~~~N~~-------~~~~C~~C~~ 24 (26)
T smart00547 3 WECPACTFLNFA-------SRSKCFACGA 24 (26)
T ss_pred ccCCCCCCcChh-------hhccccccCC
Confidence 457777777764 2345666654
No 121
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=20.27 E-value=89 Score=20.09 Aligned_cols=16 Identities=31% Similarity=0.688 Sum_probs=12.7
Q ss_pred eEEEeCCcCceEEeec
Q 034324 63 AQLVCGGCHTLLMYIR 78 (98)
Q Consensus 63 aql~Cg~Cr~lL~yP~ 78 (98)
..+.|-+|...+|.|+
T Consensus 30 ikikC~gCg~~imlpR 45 (57)
T PF06107_consen 30 IKIKCLGCGRQIMLPR 45 (57)
T ss_pred EEEEECCCCCEEEEeH
Confidence 5677888888888876
No 122
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=20.16 E-value=1.3e+02 Score=18.26 Aligned_cols=19 Identities=21% Similarity=0.550 Sum_probs=14.2
Q ss_pred CCCceeEEEeCCcCceEEe
Q 034324 58 PGTEMAQLVCGGCHTLLMY 76 (98)
Q Consensus 58 ~~~~~aql~Cg~Cr~lL~y 76 (98)
++..+.+.-|+.|++.|++
T Consensus 42 s~~~~~r~FC~~CGs~l~~ 60 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFS 60 (92)
T ss_dssp TTSSCEEEEETTT--EEEE
T ss_pred CCCcCcCcccCCCCCeeec
Confidence 3567888999999999996
Done!