Query 033096
Match_columns 127
No_of_seqs 113 out of 140
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 09:46:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033096.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033096hhsearch_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 99.5 3.1E-15 6.6E-20 89.3 2.3 31 41-71 1-31 (31)
2 PF06943 zf-LSD1: LSD1 zinc fi 99.5 1.4E-14 3E-19 83.5 2.3 25 44-68 1-25 (25)
3 TIGR01053 LSD1 zinc finger dom 99.5 2.5E-14 5.5E-19 85.3 2.3 31 79-109 1-31 (31)
4 PF06943 zf-LSD1: LSD1 zinc fi 99.4 4.1E-13 8.9E-18 77.3 2.4 25 82-106 1-25 (25)
5 PF09788 Tmemb_55A: Transmembr 97.1 0.0021 4.5E-08 54.0 7.2 36 76-111 154-191 (256)
6 PF10122 Mu-like_Com: Mu-like 95.1 0.014 3.1E-07 38.7 1.8 34 79-112 4-39 (51)
7 KOG1546 Metacaspase involved i 95.0 0.01 2.3E-07 51.9 1.2 30 79-110 4-33 (362)
8 PF13719 zinc_ribbon_5: zinc-r 94.3 0.045 9.7E-07 33.0 2.6 30 79-108 2-36 (37)
9 PLN00209 ribosomal protein S27 94.2 0.053 1.1E-06 39.3 3.1 40 59-99 36-75 (86)
10 PF01667 Ribosomal_S27e: Ribos 94.2 0.044 9.5E-07 36.6 2.5 39 59-98 7-45 (55)
11 PF10122 Mu-like_Com: Mu-like 94.1 0.029 6.3E-07 37.2 1.5 35 39-73 2-38 (51)
12 PTZ00083 40S ribosomal protein 94.1 0.06 1.3E-06 39.0 3.2 40 59-99 35-74 (85)
13 PRK00415 rps27e 30S ribosomal 93.8 0.045 9.7E-07 37.2 2.0 38 59-97 11-48 (59)
14 PRK00398 rpoP DNA-directed RNA 93.7 0.095 2.1E-06 32.3 3.2 30 79-108 3-32 (46)
15 TIGR02098 MJ0042_CXXC MJ0042 f 92.9 0.13 2.8E-06 30.2 2.8 13 60-72 3-15 (38)
16 PF13717 zinc_ribbon_4: zinc-r 92.5 0.19 4E-06 30.3 3.1 28 79-106 2-34 (36)
17 PF11331 DUF3133: Protein of u 92.4 0.14 2.9E-06 33.2 2.5 38 55-92 2-44 (46)
18 PLN00162 transport protein sec 92.3 0.15 3.3E-06 47.4 3.8 64 10-73 2-89 (761)
19 TIGR02098 MJ0042_CXXC MJ0042 f 92.2 0.33 7.1E-06 28.5 3.9 31 79-109 2-37 (38)
20 COG2051 RPS27A Ribosomal prote 92.1 0.21 4.4E-06 34.9 3.3 39 59-98 19-57 (67)
21 KOG1779 40s ribosomal protein 91.4 0.24 5.2E-06 35.9 3.2 40 59-99 34-73 (84)
22 PF12773 DZR: Double zinc ribb 91.0 0.12 2.6E-06 31.8 1.1 39 62-107 1-39 (50)
23 PRK00398 rpoP DNA-directed RNA 89.0 0.56 1.2E-05 28.8 3.1 27 41-67 3-29 (46)
24 PF13719 zinc_ribbon_5: zinc-r 88.3 0.5 1.1E-05 28.4 2.4 30 60-89 3-35 (37)
25 PRK14890 putative Zn-ribbon RN 86.2 0.75 1.6E-05 31.3 2.6 52 39-106 5-57 (59)
26 PF04810 zf-Sec23_Sec24: Sec23 85.0 0.7 1.5E-05 28.1 1.8 30 43-72 4-37 (40)
27 PF04690 YABBY: YABBY protein; 84.1 0.77 1.7E-05 36.6 2.2 38 59-96 12-53 (170)
28 PF04810 zf-Sec23_Sec24: Sec23 83.3 1.2 2.6E-05 27.1 2.3 31 81-111 4-38 (40)
29 PF11331 DUF3133: Protein of u 83.3 0.63 1.4E-05 30.1 1.1 31 79-109 6-43 (46)
30 PF13717 zinc_ribbon_4: zinc-r 82.2 1.6 3.5E-05 26.2 2.5 29 60-88 3-34 (36)
31 PF09788 Tmemb_55A: Transmembr 80.4 2 4.3E-05 36.5 3.4 36 37-72 153-190 (256)
32 smart00661 RPOL9 RNA polymeras 78.4 2.7 5.8E-05 25.6 2.7 31 82-112 3-35 (52)
33 PF04690 YABBY: YABBY protein; 75.6 4.5 9.8E-05 32.2 4.0 41 73-113 6-52 (170)
34 PF09297 zf-NADH-PPase: NADH p 75.6 2.5 5.5E-05 24.3 1.9 27 80-106 4-30 (32)
35 PF11023 DUF2614: Protein of u 71.1 2.3 5E-05 32.3 1.3 35 56-94 66-100 (114)
36 PRK14714 DNA polymerase II lar 71.1 3.6 7.9E-05 41.6 2.9 57 37-107 663-719 (1337)
37 PF07754 DUF1610: Domain of un 70.0 4.2 9E-05 23.2 1.9 22 82-104 1-23 (24)
38 PRK14873 primosome assembly pr 68.7 7.8 0.00017 36.1 4.4 61 45-121 368-430 (665)
39 PRK05580 primosome assembly pr 68.6 7.9 0.00017 35.6 4.4 52 48-110 368-421 (679)
40 PF08271 TF_Zn_Ribbon: TFIIB z 68.5 3 6.5E-05 25.3 1.2 27 62-89 3-29 (43)
41 smart00659 RPOLCX RNA polymera 68.1 6.2 0.00013 24.8 2.6 29 61-92 4-32 (44)
42 PRK02935 hypothetical protein; 66.7 4.5 9.8E-05 30.7 2.0 35 56-94 67-101 (110)
43 COG4357 Zinc finger domain con 66.2 1.4 3.1E-05 33.0 -0.7 27 41-67 62-88 (105)
44 KOG1546 Metacaspase involved i 65.8 3 6.5E-05 37.0 1.1 26 44-71 7-32 (362)
45 TIGR00595 priA primosomal prot 65.7 8.1 0.00018 34.3 3.8 46 54-110 207-253 (505)
46 KOG2907 RNA polymerase I trans 63.8 2.7 5.9E-05 32.0 0.4 39 78-116 6-44 (116)
47 COG2995 PqiA Uncharacterized p 62.3 3.9 8.3E-05 36.9 1.1 44 24-71 204-247 (418)
48 COG1996 RPC10 DNA-directed RNA 61.7 8.9 0.00019 25.1 2.5 30 77-106 4-33 (49)
49 COG4416 Com Mu-like prophage p 61.3 2.7 5.8E-05 28.8 -0.0 32 78-109 3-36 (60)
50 PF05129 Elf1: Transcription e 58.7 12 0.00026 26.1 2.9 38 58-95 21-62 (81)
51 PF02150 RNA_POL_M_15KD: RNA p 58.7 5.4 0.00012 23.9 1.0 31 81-111 3-34 (35)
52 COG1096 Predicted RNA-binding 58.2 9.5 0.00021 31.1 2.6 26 79-106 149-174 (188)
53 PF11023 DUF2614: Protein of u 58.1 3.7 8.1E-05 31.2 0.3 32 93-124 65-96 (114)
54 PF02591 DUF164: Putative zinc 57.9 8.4 0.00018 24.4 1.9 28 79-106 22-55 (56)
55 PF09082 DUF1922: Domain of un 57.8 13 0.00029 25.9 2.9 32 79-112 3-34 (68)
56 PF05495 zf-CHY: CHY zinc fing 57.6 13 0.00029 24.9 2.9 26 41-66 41-68 (71)
57 COG1198 PriA Primosomal protei 57.3 15 0.00032 35.1 4.0 53 48-111 422-476 (730)
58 PF13248 zf-ribbon_3: zinc-rib 56.3 4.5 9.7E-05 22.5 0.3 24 60-89 3-26 (26)
59 KOG4684 Uncharacterized conser 54.8 12 0.00026 31.9 2.8 47 55-101 76-125 (275)
60 COG2051 RPS27A Ribosomal prote 53.8 20 0.00044 25.0 3.3 36 75-110 15-51 (67)
61 PF14369 zf-RING_3: zinc-finge 53.2 14 0.00029 22.2 2.1 26 80-105 3-29 (35)
62 PRK14890 putative Zn-ribbon RN 48.5 19 0.00041 24.6 2.4 30 77-107 5-35 (59)
63 smart00547 ZnF_RBZ Zinc finger 48.3 9.5 0.00021 20.5 0.8 24 59-88 2-25 (26)
64 KOG1779 40s ribosomal protein 48.2 48 0.001 24.1 4.6 45 78-122 33-78 (84)
65 TIGR00155 pqiA_fam integral me 48.1 18 0.00039 31.6 2.9 30 60-89 14-43 (403)
66 COG2888 Predicted Zn-ribbon RN 47.6 22 0.00047 24.5 2.7 50 42-106 10-59 (61)
67 PF14634 zf-RING_5: zinc-RING 47.5 1.9 4.2E-05 26.0 -2.3 25 77-105 20-44 (44)
68 PF01485 IBR: IBR domain; Int 44.4 15 0.00032 22.4 1.4 21 85-105 26-48 (64)
69 KOG1986 Vesicle coat complex C 43.3 25 0.00054 34.0 3.3 59 14-72 6-88 (745)
70 COG4416 Com Mu-like prophage p 42.0 8.4 0.00018 26.4 -0.0 33 39-71 2-36 (60)
71 PF00130 C1_1: Phorbol esters/ 41.9 22 0.00047 21.6 1.8 28 79-107 11-38 (53)
72 PRK14559 putative protein seri 41.1 16 0.00034 34.2 1.6 35 61-107 3-37 (645)
73 PF14803 Nudix_N_2: Nudix N-te 40.7 22 0.00047 21.4 1.6 25 82-106 3-31 (34)
74 smart00647 IBR In Between Ring 40.5 34 0.00074 20.8 2.6 28 79-106 18-49 (64)
75 PF05180 zf-DNL: DNL zinc fing 40.3 8.3 0.00018 26.5 -0.2 31 41-71 4-41 (66)
76 COG1579 Zn-ribbon protein, pos 40.3 13 0.00028 31.1 0.8 12 94-105 218-229 (239)
77 PRK02935 hypothetical protein; 39.9 14 0.00031 28.0 0.9 31 93-123 66-96 (110)
78 TIGR01384 TFS_arch transcripti 39.4 23 0.00049 24.6 1.8 27 81-109 2-28 (104)
79 PRK10996 thioredoxin 2; Provis 39.2 23 0.00049 25.7 1.9 32 59-90 2-33 (139)
80 PF01667 Ribosomal_S27e: Ribos 38.6 27 0.00058 23.3 2.0 35 76-110 4-39 (55)
81 cd00029 C1 Protein kinase C co 38.3 18 0.00039 21.2 1.0 25 81-106 13-37 (50)
82 COG1645 Uncharacterized Zn-fin 38.1 19 0.0004 27.9 1.3 36 73-110 22-58 (131)
83 smart00109 C1 Protein kinase C 37.7 16 0.00034 21.1 0.7 24 81-106 13-36 (49)
84 PLN00209 ribosomal protein S27 37.5 34 0.00074 24.9 2.5 37 74-110 31-68 (86)
85 PF03604 DNA_RNApol_7kD: DNA d 37.4 17 0.00037 21.6 0.8 12 80-91 18-29 (32)
86 PTZ00083 40S ribosomal protein 37.4 34 0.00074 24.8 2.5 37 74-110 30-67 (85)
87 PF14599 zinc_ribbon_6: Zinc-r 37.3 32 0.0007 23.2 2.2 34 37-70 26-59 (61)
88 KOG0117 Heterogeneous nuclear 37.0 22 0.00048 32.9 1.8 17 13-29 64-80 (506)
89 smart00834 CxxC_CXXC_SSSS Puta 36.7 33 0.00072 19.7 2.0 27 79-105 5-34 (41)
90 TIGR00100 hypA hydrogenase nic 36.5 42 0.00092 24.4 2.9 27 79-107 70-96 (115)
91 COG1096 Predicted RNA-binding 36.4 30 0.00065 28.2 2.3 26 42-69 150-175 (188)
92 PF07295 DUF1451: Protein of u 36.3 43 0.00092 25.8 3.1 29 79-107 112-140 (146)
93 PF12172 DUF35_N: Rubredoxin-l 35.8 24 0.00051 20.6 1.2 21 43-67 13-33 (37)
94 PF07282 OrfB_Zn_ribbon: Putat 34.3 49 0.0011 21.1 2.7 24 82-105 31-54 (69)
95 PF10571 UPF0547: Uncharacteri 34.3 21 0.00046 20.3 0.8 9 97-105 14-22 (26)
96 PRK15103 paraquat-inducible me 34.1 30 0.00065 30.5 2.1 30 60-89 11-40 (419)
97 PF11781 RRN7: RNA polymerase 33.8 37 0.0008 20.5 1.9 24 82-106 11-34 (36)
98 PF06397 Desulfoferrod_N: Desu 33.6 35 0.00075 21.0 1.8 26 97-122 6-32 (36)
99 PF06677 Auto_anti-p27: Sjogre 33.5 40 0.00087 21.0 2.1 28 76-104 14-41 (41)
100 PF07191 zinc-ribbons_6: zinc- 33.1 98 0.0021 21.6 4.2 58 42-108 2-61 (70)
101 PRK04351 hypothetical protein; 33.0 38 0.00082 26.0 2.3 32 61-92 114-145 (149)
102 COG4888 Uncharacterized Zn rib 32.6 33 0.00071 25.8 1.8 32 59-90 22-57 (104)
103 PRK15103 paraquat-inducible me 31.8 31 0.00067 30.4 1.8 30 36-69 216-245 (419)
104 PRK00415 rps27e 30S ribosomal 31.7 1E+02 0.0022 21.0 3.9 38 35-72 5-43 (59)
105 PRK11827 hypothetical protein; 31.6 57 0.0012 22.0 2.7 32 41-72 8-39 (60)
106 PF08792 A2L_zn_ribbon: A2L zi 31.4 71 0.0015 18.9 2.8 26 81-106 5-30 (33)
107 smart00531 TFIIE Transcription 31.4 37 0.00081 25.3 2.0 44 51-94 91-138 (147)
108 TIGR00595 priA primosomal prot 31.1 62 0.0013 28.9 3.6 22 79-105 240-261 (505)
109 COG2816 NPY1 NTP pyrophosphohy 30.7 35 0.00075 29.3 1.9 29 79-107 111-139 (279)
110 PF02318 FYVE_2: FYVE-type zin 30.7 25 0.00053 25.4 0.9 53 39-107 52-104 (118)
111 PF12528 DUF3728: Prepilin pep 30.2 31 0.00067 24.1 1.3 18 13-30 35-52 (84)
112 PF06827 zf-FPG_IleRS: Zinc fi 28.9 44 0.00096 18.6 1.6 10 95-104 19-28 (30)
113 PRK00420 hypothetical protein; 28.9 39 0.00084 25.3 1.7 36 74-110 18-53 (112)
114 PRK11827 hypothetical protein; 28.5 77 0.0017 21.4 2.9 32 79-110 8-39 (60)
115 TIGR00570 cdk7 CDK-activating 28.3 19 0.00041 31.2 -0.0 46 61-109 5-55 (309)
116 PRK14892 putative transcriptio 28.1 59 0.0013 23.7 2.5 9 58-66 20-28 (99)
117 PF13901 DUF4206: Domain of un 28.0 38 0.00083 26.7 1.6 29 81-109 154-184 (202)
118 COG5047 SEC23 Vesicle coat com 27.7 46 0.00099 32.1 2.3 64 9-72 1-89 (755)
119 PLN00162 transport protein sec 27.5 51 0.0011 31.1 2.6 34 78-111 52-89 (761)
120 PRK03681 hypA hydrogenase nick 27.2 55 0.0012 23.8 2.2 28 78-107 69-97 (114)
121 PRK00241 nudC NADH pyrophospha 27.2 46 0.001 27.2 2.0 31 79-109 99-129 (256)
122 PRK12380 hydrogenase nickel in 27.1 56 0.0012 23.7 2.2 27 78-106 69-95 (113)
123 PRK14714 DNA polymerase II lar 27.0 46 0.001 34.2 2.3 39 59-110 667-705 (1337)
124 smart00731 SprT SprT homologue 26.5 79 0.0017 23.3 3.0 33 59-91 112-145 (146)
125 PRK05580 primosome assembly pr 26.1 85 0.0018 29.0 3.7 25 44-68 393-417 (679)
126 TIGR00155 pqiA_fam integral me 25.9 71 0.0015 28.0 3.0 31 78-108 12-44 (403)
127 TIGR01206 lysW lysine biosynth 25.4 71 0.0015 21.0 2.3 29 81-109 4-34 (54)
128 PF12760 Zn_Tnp_IS1595: Transp 25.3 84 0.0018 19.2 2.5 26 60-86 19-44 (46)
129 PF15227 zf-C3HC4_4: zinc fing 25.2 8.1 0.00018 23.5 -2.1 42 62-103 1-42 (42)
130 PRK08351 DNA-directed RNA poly 25.2 34 0.00074 23.2 0.8 27 40-72 2-28 (61)
131 PRK00564 hypA hydrogenase nick 24.3 50 0.0011 24.1 1.6 28 78-107 70-98 (117)
132 PF00641 zf-RanBP: Zn-finger i 24.3 43 0.00092 18.7 0.9 23 59-87 4-26 (30)
133 PF07295 DUF1451: Protein of u 23.9 69 0.0015 24.7 2.3 34 39-72 110-143 (146)
134 PRK04023 DNA polymerase II lar 23.5 64 0.0014 32.7 2.5 54 38-110 623-676 (1121)
135 PRK00423 tfb transcription ini 23.2 47 0.001 27.7 1.4 12 77-88 28-39 (310)
136 TIGR02605 CxxC_CxxC_SSSS putat 22.2 1.1E+02 0.0023 18.6 2.5 10 96-105 25-34 (52)
137 KOG2906 RNA polymerase III sub 22.2 1.1E+02 0.0023 23.2 3.0 30 81-110 3-34 (105)
138 PRK14873 primosome assembly pr 21.6 1.1E+02 0.0025 28.6 3.7 49 40-106 382-431 (665)
139 PF10058 DUF2296: Predicted in 21.2 99 0.0021 20.1 2.3 8 62-69 25-32 (54)
140 KOG2907 RNA polymerase I trans 20.9 39 0.00084 25.9 0.4 33 40-72 6-38 (116)
141 PF13240 zinc_ribbon_2: zinc-r 20.9 44 0.00095 18.3 0.5 8 82-89 16-23 (23)
142 PF03119 DNA_ligase_ZBD: NAD-d 20.9 80 0.0017 18.0 1.7 20 82-101 2-21 (28)
143 KOG1985 Vesicle coat complex C 20.4 65 0.0014 31.9 1.8 43 68-110 207-253 (887)
144 PF04032 Rpr2: RNAse P Rpr2/Rp 20.2 57 0.0012 21.4 1.1 41 39-86 44-84 (85)
145 PHA02942 putative transposase; 20.1 1.1E+02 0.0023 26.6 2.9 20 49-69 316-335 (383)
146 PF14353 CpXC: CpXC protein 20.0 84 0.0018 22.4 2.0 18 75-92 34-51 (128)
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=99.54 E-value=3.1e-15 Score=89.25 Aligned_cols=31 Identities=68% Similarity=1.339 Sum_probs=22.8
Q ss_pred eeeeccccceeeecCCCCeEEcCCCCCcccc
Q 033096 41 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFV 71 (127)
Q Consensus 41 QLvCggCr~lL~YprGA~sVrCs~C~tVn~v 71 (127)
|++|++||++|+||+||++|||+.|++||.+
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 5677777777777777777777777777753
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=99.49 E-value=1.4e-14 Score=83.46 Aligned_cols=25 Identities=68% Similarity=1.578 Sum_probs=20.4
Q ss_pred eccccceeeecCCCCeEEcCCCCCc
Q 033096 44 CGSCRRLLAYPRGARHVKCSCCQTV 68 (127)
Q Consensus 44 CggCr~lL~YprGA~sVrCs~C~tV 68 (127)
|+|||++|+||+||+||||+.|++|
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 7788888888888888888888876
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=99.46 E-value=2.5e-14 Score=85.31 Aligned_cols=31 Identities=55% Similarity=1.019 Sum_probs=29.6
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCceee
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 109 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V 109 (127)
|++|++||++|+||+||++|||+.|++||.|
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 6899999999999999999999999999976
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=99.35 E-value=4.1e-13 Score=77.34 Aligned_cols=25 Identities=64% Similarity=1.334 Sum_probs=24.3
Q ss_pred cCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 82 CASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 82 Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
|++||++||||+||+||||+.|++|
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
>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=97.08 E-value=0.0021 Score=54.04 Aligned_cols=36 Identities=22% Similarity=0.524 Sum_probs=30.0
Q ss_pred ceeeEEcCCCCeeeeeeCCC--CeEeCCCCCCceeecc
Q 033096 76 QVGQVKCASCAVLLMYPYGA--PSVRCSSCCFVTEIGV 111 (127)
Q Consensus 76 e~a~v~Cg~Crt~L~yP~GA--~SVrCa~C~tVT~V~~ 111 (127)
.+..++|++|+...+++.=. ...||++|+.|+.|..
T Consensus 154 ~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~ 191 (256)
T PF09788_consen 154 GSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP 191 (256)
T ss_pred CceeEECCCCCCcEeccCCCCCccccCCCCceeccccc
Confidence 45688999999999998644 5679999999999984
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=95.07 E-value=0.014 Score=38.74 Aligned_cols=34 Identities=18% Similarity=0.553 Sum_probs=20.8
Q ss_pred eEEcCCCCeeeeee--CCCCeEeCCCCCCceeeccC
Q 033096 79 QVKCASCAVLLMYP--YGAPSVRCSSCCFVTEIGVC 112 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP--~GA~SVrCa~C~tVT~V~~~ 112 (127)
.++|++|+.+|+.. ...-.|+|+-|.+++.|.+.
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~ 39 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRAT 39 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEecc
Confidence 45667777666664 33346677777777766543
No 7
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=94.98 E-value=0.01 Score=51.93 Aligned_cols=30 Identities=37% Similarity=0.701 Sum_probs=27.5
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCceeec
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
.+.|. |++.++.|+||+. ||+.||+||.+.
T Consensus 4 ~~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~ 33 (362)
T KOG1546|consen 4 LVGCN-CQRPMAPPPGARY-QCAGCHAVTQIA 33 (362)
T ss_pred cccCC-CCCCCCCCCCCcc-cccccceeeeec
Confidence 45676 9999999999999 999999999987
No 8
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.35 E-value=0.045 Score=32.98 Aligned_cols=30 Identities=30% Similarity=0.723 Sum_probs=19.8
Q ss_pred eEEcCCCCeeeeee-----CCCCeEeCCCCCCcee
Q 033096 79 QVKCASCAVLLMYP-----YGAPSVRCSSCCFVTE 108 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP-----~GA~SVrCa~C~tVT~ 108 (127)
.+.|.+|.+.+-+| .+...|||+.|+++=.
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 35666666666655 3466888888877643
No 9
>PLN00209 ribosomal protein S27; Provisional
Probab=94.22 E-value=0.053 Score=39.33 Aligned_cols=40 Identities=33% Similarity=0.623 Sum_probs=33.6
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEe
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR 99 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVr 99 (127)
.|+|+.|..++.+.. +....+.|..|++.|..|.|....-
T Consensus 36 ~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~~L~~PTGGKa~l 75 (86)
T PLN00209 36 DVKCQGCFNITTVFS-HSQTVVVCGSCQTVLCQPTGGKARL 75 (86)
T ss_pred EEECCCCCCeeEEEe-cCceEEEccccCCEeeccCCCCeEe
Confidence 589999999998874 5567899999999999999977643
No 10
>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=94.18 E-value=0.044 Score=36.59 Aligned_cols=39 Identities=33% Similarity=0.684 Sum_probs=27.7
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeE
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV 98 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SV 98 (127)
.|+|+.|..++.+.. +....+.|..|++.|.-|.|-..-
T Consensus 7 ~VkCp~C~~~q~vFS-ha~t~V~C~~Cg~~L~~PtGGKa~ 45 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFS-HAQTVVKCVVCGTVLAQPTGGKAR 45 (55)
T ss_dssp EEE-TTT-SEEEEET-T-SS-EE-SSSTSEEEEE-SSSEE
T ss_pred EEECCCCCCeeEEEe-cCCeEEEcccCCCEecCCCCcCeE
Confidence 489999999998874 456788999999999999987653
No 11
>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=94.12 E-value=0.029 Score=37.24 Aligned_cols=35 Identities=34% Similarity=0.775 Sum_probs=29.1
Q ss_pred cceeeeccccceeeecCCCC--eEEcCCCCCcccccC
Q 033096 39 MAQMVCGSCRRLLAYPRGAR--HVKCSCCQTVNFVLE 73 (127)
Q Consensus 39 ~sQLvCggCr~lL~YprGA~--sVrCs~C~tVn~v~~ 73 (127)
+-.+.|+.|..||..--++. .+.|+.|.|||.+..
T Consensus 2 ~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 2 LKEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred CcceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 34689999999999865555 789999999998763
No 12
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=94.07 E-value=0.06 Score=38.95 Aligned_cols=40 Identities=30% Similarity=0.599 Sum_probs=33.5
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEe
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR 99 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVr 99 (127)
.|+|+.|..++.+.. +....+.|..|++.|.-|.|....-
T Consensus 35 ~VkCp~C~n~q~VFS-hA~t~V~C~~Cg~~L~~PTGGKa~l 74 (85)
T PTZ00083 35 DVKCPGCSQITTVFS-HAQTVVLCGGCSSQLCQPTGGKAKL 74 (85)
T ss_pred EEECCCCCCeeEEEe-cCceEEEccccCCEeeccCCCCeEe
Confidence 589999999998874 4567899999999999999977643
No 13
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=93.84 E-value=0.045 Score=37.18 Aligned_cols=38 Identities=32% Similarity=0.631 Sum_probs=30.6
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCe
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPS 97 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~S 97 (127)
.|+|+.|..++.+.. +-...+.|..|++.|.-|.|-..
T Consensus 11 ~VkCp~C~n~q~vFs-ha~t~V~C~~Cg~~L~~PtGGKa 48 (59)
T PRK00415 11 KVKCPDCGNEQVVFS-HASTVVRCLVCGKTLAEPTGGKA 48 (59)
T ss_pred EEECCCCCCeEEEEe-cCCcEEECcccCCCcccCCCcce
Confidence 488999999887763 44567889999999999988654
No 14
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.71 E-value=0.095 Score=32.33 Aligned_cols=30 Identities=27% Similarity=0.505 Sum_probs=22.0
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCcee
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTE 108 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~ 108 (127)
...|.+|+..+.+......++|+.|++--.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 456888888888877777788888876433
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=92.91 E-value=0.13 Score=30.24 Aligned_cols=13 Identities=31% Similarity=0.721 Sum_probs=6.7
Q ss_pred EEcCCCCCccccc
Q 033096 60 VKCSCCQTVNFVL 72 (127)
Q Consensus 60 VrCs~C~tVn~v~ 72 (127)
+.|+.|.+.+.++
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 4555555554444
No 16
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.45 E-value=0.19 Score=30.30 Aligned_cols=28 Identities=32% Similarity=0.695 Sum_probs=16.6
Q ss_pred eEEcCCCCeeeee-----eCCCCeEeCCCCCCc
Q 033096 79 QVKCASCAVLLMY-----PYGAPSVRCSSCCFV 106 (127)
Q Consensus 79 ~v~Cg~Crt~L~y-----P~GA~SVrCa~C~tV 106 (127)
.+.|.+|.+...+ |.+...|+|+.|+.+
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 3455555555443 455667777777764
No 17
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=92.37 E-value=0.14 Score=33.21 Aligned_cols=38 Identities=24% Similarity=0.572 Sum_probs=27.6
Q ss_pred CCCCeEEcCCCCCcccccC-----ccceeeEEcCCCCeeeeee
Q 033096 55 RGARHVKCSCCQTVNFVLE-----AHQVGQVKCASCAVLLMYP 92 (127)
Q Consensus 55 rGA~sVrCs~C~tVn~v~~-----~~e~a~v~Cg~Crt~L~yP 92 (127)
.||+.|-|..|..+=.+|. ...+..+.||.|...|.|-
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 4788888888877766663 2236788899999888763
No 18
>PLN00162 transport protein sec23; Provisional
Probab=92.28 E-value=0.15 Score=47.43 Aligned_cols=64 Identities=23% Similarity=0.389 Sum_probs=47.1
Q ss_pred hhhhhhhhcCCCCCCCCCCC-----------------CC---CCCCccccceeeecccccee----eecCCCCeEEcCCC
Q 033096 10 ENQEENEEAGPPPGWQPIPP-----------------PL---PVPSPSEMAQMVCGSCRRLL----AYPRGARHVKCSCC 65 (127)
Q Consensus 10 ~~~~~~~~~~~~~gw~~~~~-----------------~~---~~p~~~~~sQLvCggCr~lL----~YprGA~sVrCs~C 65 (127)
+-+|-|+.+|.|.-|..+|- |. +..|-.+..-+.|..||..| .+..+...++|..|
T Consensus 2 ~~~~~e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~~vp~v~~~pvRC~~CraylNPf~~~d~~~~~W~C~~C 81 (761)
T PLN00162 2 DFAELEAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLPELPVLPYDPLRCRTCRAVLNPYCRVDFQAKIWICPFC 81 (761)
T ss_pred chhhhcccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCCCCCcCCCCCCccCCCcCEECCceEEecCCCEEEccCC
Confidence 34455566999999998875 11 12233445678999999987 35568899999999
Q ss_pred CCcccccC
Q 033096 66 QTVNFVLE 73 (127)
Q Consensus 66 ~tVn~v~~ 73 (127)
...|.+|+
T Consensus 82 ~~~N~~P~ 89 (761)
T PLN00162 82 FQRNHFPP 89 (761)
T ss_pred CCCCCCch
Confidence 99998874
No 19
>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=92.22 E-value=0.33 Score=28.49 Aligned_cols=31 Identities=23% Similarity=0.514 Sum_probs=23.4
Q ss_pred eEEcCCCCeeeeeeC-----CCCeEeCCCCCCceee
Q 033096 79 QVKCASCAVLLMYPY-----GAPSVRCSSCCFVTEI 109 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~-----GA~SVrCa~C~tVT~V 109 (127)
.+.|.+|++...++. +...|+|+.|+++-.+
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 577999999888884 2347999999886543
No 20
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=92.08 E-value=0.21 Score=34.90 Aligned_cols=39 Identities=31% Similarity=0.586 Sum_probs=30.7
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeE
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSV 98 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SV 98 (127)
.|+|+.|...+-+.. +-...+.|..|+++|..|.|-.+.
T Consensus 19 ~VkCpdC~N~q~vFs-hast~V~C~~CG~~l~~PTGGka~ 57 (67)
T COG2051 19 RVKCPDCGNEQVVFS-HASTVVTCLICGTTLAEPTGGKAK 57 (67)
T ss_pred EEECCCCCCEEEEec-cCceEEEecccccEEEecCCCeEE
Confidence 488999988887763 445678899999999999887653
No 21
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=91.38 E-value=0.24 Score=35.88 Aligned_cols=40 Identities=30% Similarity=0.620 Sum_probs=33.1
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEe
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVR 99 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVr 99 (127)
-|+|+.|--||-+.+ +...-+.|.+|.+.|.-|.|.+.+-
T Consensus 34 ~VkC~gc~~iT~vfS-HaqtvVvc~~c~~il~~~tggra~l 73 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFS-HAQTVVVCEGCSTILCQPTGGKAKL 73 (84)
T ss_pred EEEcCCceEEEEEee-cCceEEEcCCCceEEEEecCCcEEe
Confidence 489999999998875 4455788999999999999988764
No 22
>PF12773 DZR: Double zinc ribbon
Probab=91.01 E-value=0.12 Score=31.76 Aligned_cols=39 Identities=26% Similarity=0.480 Sum_probs=27.7
Q ss_pred cCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096 62 CSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVT 107 (127)
Q Consensus 62 Cs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT 107 (127)
|+.|.+.+. .....|.+|++.|. ......+.|+.|++.+
T Consensus 1 Cp~Cg~~~~------~~~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 1 CPHCGTPNP------DDAKFCPHCGTPLP-PPDQSKKICPNCGAEN 39 (50)
T ss_pred CCCcCCcCC------ccccCChhhcCChh-hccCCCCCCcCCcCCC
Confidence 566777653 23566888888888 5566677888888863
No 23
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.04 E-value=0.56 Score=28.84 Aligned_cols=27 Identities=22% Similarity=0.575 Sum_probs=15.0
Q ss_pred eeeeccccceeeecCCCCeEEcCCCCC
Q 033096 41 QMVCGSCRRLLAYPRGARHVKCSCCQT 67 (127)
Q Consensus 41 QLvCggCr~lL~YprGA~sVrCs~C~t 67 (127)
...|..|...+.|......++|+.|.+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCC
Confidence 345566666665555555555555543
No 24
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.32 E-value=0.5 Score=28.39 Aligned_cols=30 Identities=27% Similarity=0.583 Sum_probs=17.7
Q ss_pred EEcCCCCCcccccCc---cceeeEEcCCCCeee
Q 033096 60 VKCSCCQTVNFVLEA---HQVGQVKCASCAVLL 89 (127)
Q Consensus 60 VrCs~C~tVn~v~~~---~e~a~v~Cg~Crt~L 89 (127)
++|+.|++.-.+++. ..-..+.|+.|+...
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 567777766665531 334466677776543
No 25
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.22 E-value=0.75 Score=31.33 Aligned_cols=52 Identities=29% Similarity=0.607 Sum_probs=38.3
Q ss_pred cceeeeccccceeeecCC-CCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 39 MAQMVCGSCRRLLAYPRG-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 39 ~sQLvCggCr~lL~YprG-A~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
+.-.+|.+|...| .|++ |+.--|+.|..+.. .+|..||..- ...+|+.|++.
T Consensus 5 ~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I---------~RC~~CRk~~------~~Y~CP~CGF~ 57 (59)
T PRK14890 5 MEPPKCTSCGIEI-APREKAVKFLCPNCGEVII---------YRCEKCRKQS------NPYTCPKCGFE 57 (59)
T ss_pred ccCccccCCCCcc-cCCCccCEeeCCCCCCeeE---------eechhHHhcC------CceECCCCCCc
Confidence 4455799999888 4555 89999999987653 3488888753 46788888764
No 26
>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=85.03 E-value=0.7 Score=28.12 Aligned_cols=30 Identities=30% Similarity=0.656 Sum_probs=11.6
Q ss_pred eecccccee----eecCCCCeEEcCCCCCccccc
Q 033096 43 VCGSCRRLL----AYPRGARHVKCSCCQTVNFVL 72 (127)
Q Consensus 43 vCggCr~lL----~YprGA~sVrCs~C~tVn~v~ 72 (127)
.|..|+..| .+..+.....|..|++.|.++
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 455555443 244455555555555555444
No 27
>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=84.14 E-value=0.77 Score=36.57 Aligned_cols=38 Identities=29% Similarity=0.473 Sum_probs=25.7
Q ss_pred eEEcCCCCCccccc----CccceeeEEcCCCCeeeeeeCCCC
Q 033096 59 HVKCSCCQTVNFVL----EAHQVGQVKCASCAVLLMYPYGAP 96 (127)
Q Consensus 59 sVrCs~C~tVn~v~----~~~e~a~v~Cg~Crt~L~yP~GA~ 96 (127)
.|+|.-|+||=+|. ....+-.|+||+|-.+|.+--++.
T Consensus 12 YVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~ 53 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRAL 53 (170)
T ss_pred EEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeecccc
Confidence 47777788777664 134556778888888887655444
No 28
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=83.29 E-value=1.2 Score=27.08 Aligned_cols=31 Identities=19% Similarity=0.502 Sum_probs=16.0
Q ss_pred EcCCCCeee----eeeCCCCeEeCCCCCCceeecc
Q 033096 81 KCASCAVLL----MYPYGAPSVRCSSCCFVTEIGV 111 (127)
Q Consensus 81 ~Cg~Crt~L----~yP~GA~SVrCa~C~tVT~V~~ 111 (127)
+|.+|++.| .+-.+..+-.|..|.+.|.++.
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp~ 38 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLPP 38 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEEEETTT--EEE--G
T ss_pred ccCCCCCEECCcceEcCCCCEEECcCCCCcCCCCC
Confidence 445555443 2335778889999999888864
No 29
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=83.29 E-value=0.63 Score=30.12 Aligned_cols=31 Identities=35% Similarity=0.674 Sum_probs=23.4
Q ss_pred eEEcCCCCeeeeeeCC-------CCeEeCCCCCCceee
Q 033096 79 QVKCASCAVLLMYPYG-------APSVRCSSCCFVTEI 109 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~G-------A~SVrCa~C~tVT~V 109 (127)
-++|.+|..+|.+|.+ ...+||..|..|-.+
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~ 43 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF 43 (46)
T ss_pred EeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE
Confidence 5778888888888853 457788888877654
No 30
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=82.17 E-value=1.6 Score=26.21 Aligned_cols=29 Identities=21% Similarity=0.591 Sum_probs=18.4
Q ss_pred EEcCCCCCcccccC---ccceeeEEcCCCCee
Q 033096 60 VKCSCCQTVNFVLE---AHQVGQVKCASCAVL 88 (127)
Q Consensus 60 VrCs~C~tVn~v~~---~~e~a~v~Cg~Crt~ 88 (127)
+.|+.|++.-.+++ ...-..+.|+.|+..
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 56777777766653 234456777777754
No 31
>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=80.41 E-value=2 Score=36.47 Aligned_cols=36 Identities=19% Similarity=0.547 Sum_probs=30.1
Q ss_pred cccceeeeccccceeeecCCC--CeEEcCCCCCccccc
Q 033096 37 SEMAQMVCGSCRRLLAYPRGA--RHVKCSCCQTVNFVL 72 (127)
Q Consensus 37 ~~~sQLvCggCr~lL~YprGA--~sVrCs~C~tVn~v~ 72 (127)
..+..++|+.|+...+|+.=. +-.||+.|..+.+|-
T Consensus 153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG 190 (256)
T PF09788_consen 153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG 190 (256)
T ss_pred CCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence 457899999999999998644 567999999998874
No 32
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=78.45 E-value=2.7 Score=25.61 Aligned_cols=31 Identities=23% Similarity=0.545 Sum_probs=20.7
Q ss_pred cCCCCeeeeeeCCCC--eEeCCCCCCceeeccC
Q 033096 82 CASCAVLLMYPYGAP--SVRCSSCCFVTEIGVC 112 (127)
Q Consensus 82 Cg~Crt~L~yP~GA~--SVrCa~C~tVT~V~~~ 112 (127)
|..|+.+|..+.+.. ...|+.|+++-++.+.
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 777777665554432 5778888887776543
No 33
>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=75.64 E-value=4.5 Score=32.24 Aligned_cols=41 Identities=22% Similarity=0.503 Sum_probs=33.2
Q ss_pred CccceeeEEcCCCCeeeeee------CCCCeEeCCCCCCceeeccCC
Q 033096 73 EAHQVGQVKCASCAVLLMYP------YGAPSVRCSSCCFVTEIGVCG 113 (127)
Q Consensus 73 ~~~e~a~v~Cg~Crt~L~yP------~GA~SVrCa~C~tVT~V~~~~ 113 (127)
+..++-+|.|+-|.|.|.+- ...-+|||++|..+-.|....
T Consensus 6 ~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~ 52 (170)
T PF04690_consen 6 PSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRA 52 (170)
T ss_pred CCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccc
Confidence 45677899999999999876 466789999999988876443
No 34
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=75.59 E-value=2.5 Score=24.30 Aligned_cols=27 Identities=26% Similarity=0.436 Sum_probs=17.1
Q ss_pred EEcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 80 VKCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 80 v~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
-.|+.|+..+..-.+-.+-+|+.|+..
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cccCcCCccccCCCCcCEeECCCCcCE
Confidence 358888888888888888888888754
No 35
>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=71.12 E-value=2.3 Score=32.30 Aligned_cols=35 Identities=23% Similarity=0.367 Sum_probs=26.1
Q ss_pred CCCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCC
Q 033096 56 GARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYG 94 (127)
Q Consensus 56 GA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~G 94 (127)
-|..|+|+.|+-.|-+.-- .-.|-+|+++|...+.
T Consensus 66 kav~V~CP~C~K~TKmLGr----~D~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGR----VDACMHCKEPLTLDPS 100 (114)
T ss_pred cceeeECCCCCChHhhhch----hhccCcCCCcCccCch
Confidence 3678999999999976531 2369999999887653
No 36
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.07 E-value=3.6 Score=41.64 Aligned_cols=57 Identities=21% Similarity=0.367 Sum_probs=42.0
Q ss_pred cccceeeeccccceeeecCCCCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096 37 SEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVT 107 (127)
Q Consensus 37 ~~~sQLvCggCr~lL~YprGA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT 107 (127)
.+.++..|..|.+.... .+|+.|.+-+.. ...|..|+..+...... +.+|+-|++-+
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 45667899999986432 299999988732 34799999987654434 88999999644
No 37
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=69.99 E-value=4.2 Score=23.21 Aligned_cols=22 Identities=32% Similarity=0.782 Sum_probs=13.7
Q ss_pred cCCCCeeeeeeCC-CCeEeCCCCC
Q 033096 82 CASCAVLLMYPYG-APSVRCSSCC 104 (127)
Q Consensus 82 Cg~Crt~L~yP~G-A~SVrCa~C~ 104 (127)
|..|+..|. |++ +....|+.|.
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 445655554 666 6677777765
No 38
>PRK14873 primosome assembly protein PriA; Provisional
Probab=68.67 E-value=7.8 Score=36.07 Aligned_cols=61 Identities=25% Similarity=0.470 Sum_probs=43.8
Q ss_pred ccccceeeecC-C-CCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCceeeccCCceEEEeec
Q 033096 45 GSCRRLLAYPR-G-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMC 121 (127)
Q Consensus 45 ggCr~lL~Ypr-G-A~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~~~~~~~~~c~~ 121 (127)
.| ++||.-+| | |+.+.|..|..+- .|.+|...|.|..+....+|..|++.. + .-+|-.|-.
T Consensus 368 ~g-qvll~lnRrGyap~l~C~~Cg~~~-----------~C~~C~~~L~~h~~~~~l~Ch~CG~~~-~---p~~Cp~Cgs 430 (665)
T PRK14873 368 HG-PVLVQVPRRGYVPSLACARCRTPA-----------RCRHCTGPLGLPSAGGTPRCRWCGRAA-P---DWRCPRCGS 430 (665)
T ss_pred cC-cEEEEecCCCCCCeeEhhhCcCee-----------ECCCCCCceeEecCCCeeECCCCcCCC-c---CccCCCCcC
Confidence 57 77777664 4 5677999998754 588899999888887888888888742 2 335555543
No 39
>PRK05580 primosome assembly protein PriA; Validated
Probab=68.62 E-value=7.9 Score=35.62 Aligned_cols=52 Identities=29% Similarity=0.535 Sum_probs=39.0
Q ss_pred cceeeec-CC-CCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCceeec
Q 033096 48 RRLLAYP-RG-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 48 r~lL~Yp-rG-A~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
++||.-+ || |+.+.|..|..+- .|.+|...|.|.......+|..|++...++
T Consensus 368 qvll~~nrrGy~~~~~C~~Cg~~~-----------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 421 (679)
T PRK05580 368 QVLLFLNRRGYAPFLLCRDCGWVA-----------ECPHCDASLTLHRFQRRLRCHHCGYQEPIP 421 (679)
T ss_pred eEEEEEcCCCCCCceEhhhCcCcc-----------CCCCCCCceeEECCCCeEECCCCcCCCCCC
Confidence 3455555 44 6789999998754 488888888888888888888888776554
No 40
>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=68.47 E-value=3 Score=25.28 Aligned_cols=27 Identities=26% Similarity=0.823 Sum_probs=11.7
Q ss_pred cCCCCCcccccCccceeeEEcCCCCeee
Q 033096 62 CSCCQTVNFVLEAHQVGQVKCASCAVLL 89 (127)
Q Consensus 62 Cs~C~tVn~v~~~~e~a~v~Cg~Crt~L 89 (127)
|+.|.+-+.+. -...+.++|..|+..|
T Consensus 3 Cp~Cg~~~~~~-D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 3 CPNCGSKEIVF-DPERGELVCPNCGLVL 29 (43)
T ss_dssp BTTTSSSEEEE-ETTTTEEEETTT-BBE
T ss_pred CcCCcCCceEE-cCCCCeEECCCCCCEe
Confidence 55555544221 1223455566555544
No 41
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=68.06 E-value=6.2 Score=24.82 Aligned_cols=29 Identities=24% Similarity=0.597 Sum_probs=13.1
Q ss_pred EcCCCCCcccccCccceeeEEcCCCCeeeeee
Q 033096 61 KCSCCQTVNFVLEAHQVGQVKCASCAVLLMYP 92 (127)
Q Consensus 61 rCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP 92 (127)
.|..|.+.+... ....+.|..|+-.++|-
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG~rIlyK 32 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCRECGYRILYK 32 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCCCceEEEE
Confidence 345555443322 12345555555555543
No 42
>PRK02935 hypothetical protein; Provisional
Probab=66.69 E-value=4.5 Score=30.65 Aligned_cols=35 Identities=23% Similarity=0.390 Sum_probs=27.1
Q ss_pred CCCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCC
Q 033096 56 GARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYG 94 (127)
Q Consensus 56 GA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~G 94 (127)
-|..|.|+.|+-.|-+.- -.-.|-+|+++|-..++
T Consensus 67 kavqV~CP~C~K~TKmLG----rvD~CM~C~~PLTLd~~ 101 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLG----RVDACMHCNQPLTLDRS 101 (110)
T ss_pred cceeeECCCCCchhhhcc----ceeecCcCCCcCCcCcc
Confidence 478899999999997763 13359999999988765
No 43
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=66.22 E-value=1.4 Score=33.04 Aligned_cols=27 Identities=33% Similarity=0.818 Sum_probs=24.0
Q ss_pred eeeeccccceeeecCCCCeEEcCCCCC
Q 033096 41 QMVCGSCRRLLAYPRGARHVKCSCCQT 67 (127)
Q Consensus 41 QLvCggCr~lL~YprGA~sVrCs~C~t 67 (127)
-++||-||.+|.|..=-..++|+.|++
T Consensus 62 ~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 62 AIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred cEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 389999999999988888888999975
No 44
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=65.75 E-value=3 Score=36.96 Aligned_cols=26 Identities=42% Similarity=0.991 Sum_probs=23.9
Q ss_pred eccccceeeecCCCCeEEcCCCCCcccc
Q 033096 44 CGSCRRLLAYPRGARHVKCSCCQTVNFV 71 (127)
Q Consensus 44 CggCr~lL~YprGA~sVrCs~C~tVn~v 71 (127)
|+ |++-|+-|.||+. ||+.|++++..
T Consensus 7 ~~-~~~p~~~pp~ar~-q~~~~~~~~~~ 32 (362)
T KOG1546|consen 7 CN-CQRPMAPPPGARY-QCAGCHAVTQI 32 (362)
T ss_pred CC-CCCCCCCCCCCcc-cccccceeeee
Confidence 55 9999999999999 99999999964
No 45
>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=65.75 E-value=8.1 Score=34.33 Aligned_cols=46 Identities=28% Similarity=0.680 Sum_probs=34.5
Q ss_pred cCC-CCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCceeec
Q 033096 54 PRG-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 54 prG-A~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
.|| |+.+.|..|..+- .|.+|...|.|-......+|..|++...++
T Consensus 207 rrGya~~~~C~~Cg~~~-----------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 253 (505)
T TIGR00595 207 RRGYSKNLLCRSCGYIL-----------CCPNCDVSLTYHKKEGKLRCHYCGYQEPIP 253 (505)
T ss_pred CCcCCCeeEhhhCcCcc-----------CCCCCCCceEEecCCCeEEcCCCcCcCCCC
Confidence 344 5778999997654 388888888888777788888887776655
No 46
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=63.76 E-value=2.7 Score=32.03 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=30.6
Q ss_pred eeEEcCCCCeeeeeeCCCCeEeCCCCCCceeeccCCceE
Q 033096 78 GQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVCGLSL 116 (127)
Q Consensus 78 a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~~~~~~~ 116 (127)
..+-|+.|+.+|..|.-+..|-|..|..+..|.+.....
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~ 44 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSGLV 44 (116)
T ss_pred CcchhhhhhhhcccccccCceEeccccccCCHHHhCCee
Confidence 355688899999999888888899998888887655443
No 47
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=62.27 E-value=3.9 Score=36.91 Aligned_cols=44 Identities=18% Similarity=0.458 Sum_probs=32.1
Q ss_pred CCCCCCCCCCCCccccceeeeccccceeeecCCCCeEEcCCCCCcccc
Q 033096 24 WQPIPPPLPVPSPSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFV 71 (127)
Q Consensus 24 w~~~~~~~~~p~~~~~sQLvCggCr~lL~YprGA~sVrCs~C~tVn~v 71 (127)
|+.+++..+. .+...++..|.+|..+.... ...+|++|++--.+
T Consensus 204 we~~~pq~~~-~~~~~~~~~C~~C~~~~~~~---~~~~CpRC~~~Ly~ 247 (418)
T COG2995 204 WERFYPQTLA-TGAREGLRSCLCCHYILPHD---AEPRCPRCGSKLYV 247 (418)
T ss_pred HHhhccccCC-CCCcccceecccccccCCHh---hCCCCCCCCChhhc
Confidence 6666665554 67788899999998876654 67788888875443
No 48
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.68 E-value=8.9 Score=25.15 Aligned_cols=30 Identities=23% Similarity=0.468 Sum_probs=21.7
Q ss_pred eeeEEcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 77 VGQVKCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 77 ~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
+..-.|..|+..+-......-++|+.|++=
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 445567788887777777778888888753
No 49
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=61.31 E-value=2.7 Score=28.82 Aligned_cols=32 Identities=31% Similarity=0.634 Sum_probs=19.2
Q ss_pred eeEEcCCCCeeeeeeCCC--CeEeCCCCCCceee
Q 033096 78 GQVKCASCAVLLMYPYGA--PSVRCSSCCFVTEI 109 (127)
Q Consensus 78 a~v~Cg~Crt~L~yP~GA--~SVrCa~C~tVT~V 109 (127)
..++|..|..+|.=.-|. .-++|+.|..|+.+
T Consensus 3 ~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 3 QTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eeeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 356666666666555443 35667777776654
No 50
>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=58.72 E-value=12 Score=26.05 Aligned_cols=38 Identities=16% Similarity=0.422 Sum_probs=20.8
Q ss_pred CeEEcCCCCCccccc----CccceeeEEcCCCCeeeeeeCCC
Q 033096 58 RHVKCSCCQTVNFVL----EAHQVGQVKCASCAVLLMYPYGA 95 (127)
Q Consensus 58 ~sVrCs~C~tVn~v~----~~~e~a~v~Cg~Crt~L~yP~GA 95 (127)
+.-.|+.|+.-++|. .....+.+.|+.|+..-.+..+.
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~ 62 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINP 62 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--S
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCc
Confidence 445799999777765 24678999999998877776544
No 51
>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=58.65 E-value=5.4 Score=23.86 Aligned_cols=31 Identities=26% Similarity=0.536 Sum_probs=17.9
Q ss_pred EcCCCCeeeeeeCCCCe-EeCCCCCCceeecc
Q 033096 81 KCASCAVLLMYPYGAPS-VRCSSCCFVTEIGV 111 (127)
Q Consensus 81 ~Cg~Crt~L~yP~GA~S-VrCa~C~tVT~V~~ 111 (127)
-|..|+.+|....+... +.|..|.++-.+..
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEPISQ 34 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE-SS
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccCCCC
Confidence 37778777755543332 35888888776653
No 52
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=58.21 E-value=9.5 Score=31.10 Aligned_cols=26 Identities=19% Similarity=0.597 Sum_probs=22.4
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
.-.|+.|+..|++ .-...+|+.|+++
T Consensus 149 ~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 149 YARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEEccCCCcceEE--cCcEEECCCCCCE
Confidence 4469999999999 7789999999875
No 53
>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=58.08 E-value=3.7 Score=31.20 Aligned_cols=32 Identities=22% Similarity=0.194 Sum_probs=25.7
Q ss_pred CCCCeEeCCCCCCceeeccCCceEEEeecccc
Q 033096 93 YGAPSVRCSSCCFVTEIGVCGLSLFLCMCDLA 124 (127)
Q Consensus 93 ~GA~SVrCa~C~tVT~V~~~~~~~~~c~~~~~ 124 (127)
.-|..|+|+.|+.+|.+--..-+|..|+-+|.
T Consensus 65 tkav~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 65 TKAVQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred ccceeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 34667899999999988777778988887763
No 54
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=57.86 E-value=8.4 Score=24.41 Aligned_cols=28 Identities=25% Similarity=0.488 Sum_probs=17.3
Q ss_pred eEEcCCCCeeeeee------CCCCeEeCCCCCCc
Q 033096 79 QVKCASCAVLLMYP------YGAPSVRCSSCCFV 106 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP------~GA~SVrCa~C~tV 106 (127)
.-.|++|++.|.-- .+..-+.|+.|+.+
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 33577777765422 45567777777754
No 55
>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=57.76 E-value=13 Score=25.91 Aligned_cols=32 Identities=22% Similarity=0.486 Sum_probs=23.7
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCceeeccC
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGVC 112 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~~~ 112 (127)
-.+| .|+..|....++..-+| .|+....|...
T Consensus 3 ifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~ 34 (68)
T PF09082_consen 3 IFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKER 34 (68)
T ss_dssp EEEE-TTS--EEEETT-SEEEE-TTTEEEE--SS
T ss_pred EEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeE
Confidence 3579 79999999999999999 99999998754
No 56
>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=57.59 E-value=13 Score=24.94 Aligned_cols=26 Identities=23% Similarity=0.586 Sum_probs=14.5
Q ss_pred eeeeccccceeeecCCCCe--EEcCCCC
Q 033096 41 QMVCGSCRRLLAYPRGARH--VKCSCCQ 66 (127)
Q Consensus 41 QLvCggCr~lL~YprGA~s--VrCs~C~ 66 (127)
+++||-|++.+.+..-..+ ..|+.|+
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~ 68 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICG 68 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTT
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcC
Confidence 8899999998887654222 3455444
No 57
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.29 E-value=15 Score=35.06 Aligned_cols=53 Identities=26% Similarity=0.506 Sum_probs=41.8
Q ss_pred cceeeecC-C-CCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCceeecc
Q 033096 48 RRLLAYPR-G-ARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIGV 111 (127)
Q Consensus 48 r~lL~Ypr-G-A~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~~ 111 (127)
++||+-+| | |+.+.|..|..|-- |.+|...|.|-......+|-.|++...++.
T Consensus 422 Q~llflnRRGys~~l~C~~Cg~v~~-----------Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~ 476 (730)
T COG1198 422 QVLLFLNRRGYAPLLLCRDCGYIAE-----------CPNCDSPLTLHKATGQLRCHYCGYQEPIPQ 476 (730)
T ss_pred eEEEEEccCCccceeecccCCCccc-----------CCCCCcceEEecCCCeeEeCCCCCCCCCCC
Confidence 34555554 4 56899999988753 889999999999999999999998877663
No 58
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=56.25 E-value=4.5 Score=22.50 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=13.4
Q ss_pred EEcCCCCCcccccCccceeeEEcCCCCeee
Q 033096 60 VKCSCCQTVNFVLEAHQVGQVKCASCAVLL 89 (127)
Q Consensus 60 VrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L 89 (127)
+.|+.|.+.+. ...-.|.+|++.|
T Consensus 3 ~~Cp~Cg~~~~------~~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEID------PDAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCC------cccccChhhCCCC
Confidence 45777777442 1244577776654
No 59
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=54.82 E-value=12 Score=31.94 Aligned_cols=47 Identities=32% Similarity=0.458 Sum_probs=30.8
Q ss_pred CCCCeEEcCCCCCcccccCccceeeEEcCCCCeee---eeeCCCCeEeCC
Q 033096 55 RGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLL---MYPYGAPSVRCS 101 (127)
Q Consensus 55 rGA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L---~yP~GA~SVrCa 101 (127)
-+++-|-|..|+..-.+---+|+--+.|+.|...- -.|+|...|||+
T Consensus 76 g~~PmvtCRVCq~~i~~egk~~QHVVKC~~CnEATPIrnAPpGKKYVRCP 125 (275)
T KOG4684|consen 76 GQFPMVTCRVCQVAISLEGKNQQHVVKCHSCNEATPIRNAPPGKKYVRCP 125 (275)
T ss_pred CCCceEeehhhhHHhccccccceeeEeecccCccccCCCCCCCCceeecC
Confidence 35667777777765554445666667777776533 346777788877
No 60
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=53.82 E-value=20 Score=25.03 Aligned_cols=36 Identities=19% Similarity=0.425 Sum_probs=26.2
Q ss_pred cceeeEEcCCCC-eeeeeeCCCCeEeCCCCCCceeec
Q 033096 75 HQVGQVKCASCA-VLLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 75 ~e~a~v~Cg~Cr-t~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
.-...+.|..|+ ...++-.-+..|+|..|.++---+
T Consensus 15 s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 15 SRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred ceEEEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 445678888886 456777778888888888765544
No 61
>PF14369 zf-RING_3: zinc-finger
Probab=53.16 E-value=14 Score=22.21 Aligned_cols=26 Identities=19% Similarity=0.434 Sum_probs=17.3
Q ss_pred EEcCCCCeeeeee-CCCCeEeCCCCCC
Q 033096 80 VKCASCAVLLMYP-YGAPSVRCSSCCF 105 (127)
Q Consensus 80 v~Cg~Crt~L~yP-~GA~SVrCa~C~t 105 (127)
-+|-+|+..+... .+...+.|+.|+.
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 4677888777774 3455556888874
No 62
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=48.53 E-value=19 Score=24.57 Aligned_cols=30 Identities=30% Similarity=0.600 Sum_probs=21.6
Q ss_pred eeeEEcCCCCeeeeeeCC-CCeEeCCCCCCce
Q 033096 77 VGQVKCASCAVLLMYPYG-APSVRCSSCCFVT 107 (127)
Q Consensus 77 ~a~v~Cg~Crt~L~yP~G-A~SVrCa~C~tVT 107 (127)
+....|..|+..| .|.+ +....|+.|..++
T Consensus 5 ~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~ 35 (59)
T PRK14890 5 MEPPKCTSCGIEI-APREKAVKFLCPNCGEVI 35 (59)
T ss_pred ccCccccCCCCcc-cCCCccCEeeCCCCCCee
Confidence 3345688888877 5666 8888888887653
No 63
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=48.28 E-value=9.5 Score=20.49 Aligned_cols=24 Identities=29% Similarity=0.765 Sum_probs=15.8
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCee
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVL 88 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~ 88 (127)
.+.|+.|..+|... ...|..|++.
T Consensus 2 ~W~C~~C~~~N~~~------~~~C~~C~~p 25 (26)
T smart00547 2 DWECPACTFLNFAS------RSKCFACGAP 25 (26)
T ss_pred cccCCCCCCcChhh------hccccccCCc
Confidence 35688888888643 4567667653
No 64
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=48.23 E-value=48 Score=24.13 Aligned_cols=45 Identities=20% Similarity=0.375 Sum_probs=22.8
Q ss_pred eeEEcCCCCe-eeeeeCCCCeEeCCCCCCceeeccCCceEEEeecc
Q 033096 78 GQVKCASCAV-LLMYPYGAPSVRCSSCCFVTEIGVCGLSLFLCMCD 122 (127)
Q Consensus 78 a~v~Cg~Crt-~L~yP~GA~SVrCa~C~tVT~V~~~~~~~~~c~~~ 122 (127)
+.+.|++|.. +-.|-.--..|-|..|.+|--++....-.+.+-|.
T Consensus 33 m~VkC~gc~~iT~vfSHaqtvVvc~~c~~il~~~tggra~ls~~cs 78 (84)
T KOG1779|consen 33 MDVKCPGCFKITTVFSHAQTVVVCEGCSTILCQPTGGKAKLSEGCS 78 (84)
T ss_pred EEEEcCCceEEEEEeecCceEEEcCCCceEEEEecCCcEEecCCCc
Confidence 3455655543 33344444455566666655555555444444443
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=48.13 E-value=18 Score=31.60 Aligned_cols=30 Identities=20% Similarity=0.493 Sum_probs=13.0
Q ss_pred EEcCCCCCcccccCccceeeEEcCCCCeee
Q 033096 60 VKCSCCQTVNFVLEAHQVGQVKCASCAVLL 89 (127)
Q Consensus 60 VrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L 89 (127)
+.|..|+.+...++...-..-.|..|++.|
T Consensus 14 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 14 ILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 345555555544432112233355555555
No 66
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=47.63 E-value=22 Score=24.52 Aligned_cols=50 Identities=36% Similarity=0.721 Sum_probs=33.1
Q ss_pred eeeccccceeeecCCCCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 42 MVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 42 LvCggCr~lL~YprGA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
-+|.+|-..|.=-.+|++--|++|.-+. -.+|..||.+ ....+|+.|.+.
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~---------I~Rc~~CRk~------g~~Y~Cp~CGF~ 59 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVE---------IYRCAKCRKL------GNPYRCPKCGFE 59 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCcee---------eehhhhHHHc------CCceECCCcCcc
Confidence 4788888888777788888888886443 3446777754 223566666653
No 67
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=47.46 E-value=1.9 Score=25.99 Aligned_cols=25 Identities=32% Similarity=0.701 Sum_probs=18.6
Q ss_pred eeeEEcCCCCeeeeeeCCCCeEeCCCCCC
Q 033096 77 VGQVKCASCAVLLMYPYGAPSVRCSSCCF 105 (127)
Q Consensus 77 ~a~v~Cg~Crt~L~yP~GA~SVrCa~C~t 105 (127)
=+|+.|..|-..++ ...+.|+.|++
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 34777777888877 77788888863
No 68
>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=44.40 E-value=15 Score=22.43 Aligned_cols=21 Identities=33% Similarity=0.657 Sum_probs=7.8
Q ss_pred CCeeeeeeCCCCe--EeCCCCCC
Q 033096 85 CAVLLMYPYGAPS--VRCSSCCF 105 (127)
Q Consensus 85 Crt~L~yP~GA~S--VrCa~C~t 105 (127)
|...+....+... |+|+.|++
T Consensus 26 C~~~~~~~~~~~~~~~~C~~C~~ 48 (64)
T PF01485_consen 26 CEYIIEKDDGCNSPIVTCPSCGT 48 (64)
T ss_dssp T---ECS-SSTTS--CCTTSCCS
T ss_pred CcccEEecCCCCCCeeECCCCCC
Confidence 4444444444444 44444443
No 69
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.33 E-value=25 Score=33.96 Aligned_cols=59 Identities=22% Similarity=0.375 Sum_probs=44.5
Q ss_pred hhhhcCCCCCCCCCCCC--------------------CCCCCccccceeeeccccceee----ecCCCCeEEcCCCCCcc
Q 033096 14 ENEEAGPPPGWQPIPPP--------------------LPVPSPSEMAQMVCGSCRRLLA----YPRGARHVKCSCCQTVN 69 (127)
Q Consensus 14 ~~~~~~~~~gw~~~~~~--------------------~~~p~~~~~sQLvCggCr~lL~----YprGA~sVrCs~C~tVn 69 (127)
-++-||++.-|...|-. -|.++.-+..-+.|..|+.+|- -.-+|.++.|.-|+.-|
T Consensus 6 ~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~~~~~~~~y~P~~C~~C~AvlNPyc~vd~~a~~W~CpfC~qrN 85 (745)
T KOG1986|consen 6 IEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKERPDLPPIQYDPLRCSKCGAVLNPYCSVDFRAKSWICPFCNQRN 85 (745)
T ss_pred cccCCCcccccccCCCcccccccccccHHHhccccccCCCCCccCCCCchhccchhhcCcceeecccCceEeccccccCC
Confidence 45678999999887762 2233556677889999998873 34589999999999988
Q ss_pred ccc
Q 033096 70 FVL 72 (127)
Q Consensus 70 ~v~ 72 (127)
.-|
T Consensus 86 ~~p 88 (745)
T KOG1986|consen 86 PFP 88 (745)
T ss_pred CCC
Confidence 655
No 70
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=41.99 E-value=8.4 Score=26.43 Aligned_cols=33 Identities=36% Similarity=0.724 Sum_probs=26.3
Q ss_pred cceeeeccccceeeecCCC--CeEEcCCCCCcccc
Q 033096 39 MAQMVCGSCRRLLAYPRGA--RHVKCSCCQTVNFV 71 (127)
Q Consensus 39 ~sQLvCggCr~lL~YprGA--~sVrCs~C~tVn~v 71 (127)
|--|.|..|..||.-..|. --+.|+.|.+||..
T Consensus 2 ~~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 2 MQTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred ceeeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 4568899999999876665 45789999999975
No 71
>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=41.93 E-value=22 Score=21.60 Aligned_cols=28 Identities=29% Similarity=0.629 Sum_probs=19.2
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVT 107 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT 107 (127)
...|..|+..|.- .+....+|..|+.+-
T Consensus 11 ~~~C~~C~~~i~g-~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 11 PTYCDVCGKFIWG-LGKQGYRCSWCGLVC 38 (53)
T ss_dssp TEB-TTSSSBECS-SSSCEEEETTTT-EE
T ss_pred CCCCcccCcccCC-CCCCeEEECCCCChH
Confidence 3468888888844 777888888887654
No 72
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=41.11 E-value=16 Score=34.19 Aligned_cols=35 Identities=26% Similarity=0.463 Sum_probs=19.3
Q ss_pred EcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096 61 KCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVT 107 (127)
Q Consensus 61 rCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT 107 (127)
.|+.|.+.|.. ..-.|..|++.|.. ..|+.|++.+
T Consensus 3 ~Cp~Cg~~n~~------~akFC~~CG~~l~~------~~Cp~CG~~~ 37 (645)
T PRK14559 3 ICPQCQFENPN------NNRFCQKCGTSLTH------KPCPQCGTEV 37 (645)
T ss_pred cCCCCCCcCCC------CCccccccCCCCCC------CcCCCCCCCC
Confidence 57777776642 23346666666631 2466666553
No 73
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=40.74 E-value=22 Score=21.42 Aligned_cols=25 Identities=32% Similarity=0.816 Sum_probs=9.8
Q ss_pred cCCCCeeeee--eCC--CCeEeCCCCCCc
Q 033096 82 CASCAVLLMY--PYG--APSVRCSSCCFV 106 (127)
Q Consensus 82 Cg~Crt~L~y--P~G--A~SVrCa~C~tV 106 (127)
|.+|+..|.+ |.| -.-..|+.|++|
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred cccccChhhhhcCCCCCccceECCCCCCE
Confidence 5566655544 432 333446666655
No 74
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=40.49 E-value=34 Score=20.85 Aligned_cols=28 Identities=25% Similarity=0.659 Sum_probs=18.8
Q ss_pred eEEcC--CCCeeeeeeC--CCCeEeCCCCCCc
Q 033096 79 QVKCA--SCAVLLMYPY--GAPSVRCSSCCFV 106 (127)
Q Consensus 79 ~v~Cg--~Crt~L~yP~--GA~SVrCa~C~tV 106 (127)
..+|. +|...+.... +...|+|+.|+..
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~ 49 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFS 49 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCe
Confidence 34577 7777776653 7778888777643
No 75
>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=40.35 E-value=8.3 Score=26.54 Aligned_cols=31 Identities=26% Similarity=0.721 Sum_probs=20.7
Q ss_pred eeeeccccce-------eeecCCCCeEEcCCCCCcccc
Q 033096 41 QMVCGSCRRL-------LAYPRGARHVKCSCCQTVNFV 71 (127)
Q Consensus 41 QLvCggCr~l-------L~YprGA~sVrCs~C~tVn~v 71 (127)
+..|..|.+- .+|-.|...|+|+.|+..-..
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 4567777543 579999999999999876543
No 76
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=40.30 E-value=13 Score=31.05 Aligned_cols=12 Identities=25% Similarity=0.357 Sum_probs=5.4
Q ss_pred CCCeEeCCCCCC
Q 033096 94 GAPSVRCSSCCF 105 (127)
Q Consensus 94 GA~SVrCa~C~t 105 (127)
+-.-|+|+.|+.
T Consensus 218 ~d~iv~CP~CgR 229 (239)
T COG1579 218 KDEIVFCPYCGR 229 (239)
T ss_pred CCCCccCCccch
Confidence 334444444443
No 77
>PRK02935 hypothetical protein; Provisional
Probab=39.87 E-value=14 Score=27.97 Aligned_cols=31 Identities=26% Similarity=0.161 Sum_probs=24.3
Q ss_pred CCCCeEeCCCCCCceeeccCCceEEEeeccc
Q 033096 93 YGAPSVRCSSCCFVTEIGVCGLSLFLCMCDL 123 (127)
Q Consensus 93 ~GA~SVrCa~C~tVT~V~~~~~~~~~c~~~~ 123 (127)
--|.-|.|+.|+.+|.+-.+.=.|..|.=.|
T Consensus 66 tkavqV~CP~C~K~TKmLGrvD~CM~C~~PL 96 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLGRVDACMHCNQPL 96 (110)
T ss_pred ccceeeECCCCCchhhhccceeecCcCCCcC
Confidence 3466789999999999887777787776554
No 78
>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=39.41 E-value=23 Score=24.58 Aligned_cols=27 Identities=30% Similarity=0.672 Sum_probs=18.3
Q ss_pred EcCCCCeeeeeeCCCCeEeCCCCCCceee
Q 033096 81 KCASCAVLLMYPYGAPSVRCSSCCFVTEI 109 (127)
Q Consensus 81 ~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V 109 (127)
.|..|+.+|. |.+ ..+.|+.|.+...+
T Consensus 2 fC~~Cg~~l~-~~~-~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMT-PKN-GVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccc-cCC-CeEECcCCCCcccc
Confidence 4777877773 443 36778888877655
No 79
>PRK10996 thioredoxin 2; Provisional
Probab=39.15 E-value=23 Score=25.68 Aligned_cols=32 Identities=25% Similarity=0.591 Sum_probs=21.5
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCeeee
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLM 90 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~ 90 (127)
+-.|+.|+.+|.-++..---+-.||+|...+.
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (139)
T PRK10996 2 NTVCTSCQAINRLPDERIEDAAKCGRCGHDLF 33 (139)
T ss_pred eEECCCCCCcCCCCCccccCCCcCCCCCCccC
Confidence 45788888888776532233456888877665
No 80
>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=38.58 E-value=27 Score=23.31 Aligned_cols=35 Identities=23% Similarity=0.426 Sum_probs=21.6
Q ss_pred ceeeEEcCCCCe-eeeeeCCCCeEeCCCCCCceeec
Q 033096 76 QVGQVKCASCAV-LLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 76 e~a~v~Cg~Crt-~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
-...+.|.+|.. ..++-.-+..|.|..|+++---+
T Consensus 4 ~Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~P 39 (55)
T PF01667_consen 4 YFMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQP 39 (55)
T ss_dssp -EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE
T ss_pred cEEEEECCCCCCeeEEEecCCeEEEcccCCCEecCC
Confidence 356788999975 45677778889999998876444
No 81
>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=38.34 E-value=18 Score=21.17 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=16.6
Q ss_pred EcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 81 KCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 81 ~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
.|..|+..|... +....+|+.|+.+
T Consensus 13 ~C~~C~~~i~~~-~~~~~~C~~C~~~ 37 (50)
T cd00029 13 FCDVCRKSIWGL-FKQGLRCSWCKVK 37 (50)
T ss_pred Chhhcchhhhcc-ccceeEcCCCCCc
Confidence 477777776653 5677777777654
No 82
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=38.12 E-value=19 Score=27.86 Aligned_cols=36 Identities=17% Similarity=0.347 Sum_probs=28.6
Q ss_pred CccceeeEEcCCCCeeeeeeCCCCeEeCCCCC-Cceeec
Q 033096 73 EAHQVGQVKCASCAVLLMYPYGAPSVRCSSCC-FVTEIG 110 (127)
Q Consensus 73 ~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~-tVT~V~ 110 (127)
.|+-|.--.|..|+++|+= =.-.|-|++|. +++-|.
T Consensus 22 ~GAkML~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 22 QGAKMLAKHCPKCGTPLFR--KDGEVFCPVCGYREVVVE 58 (131)
T ss_pred hhhHHHHhhCcccCCccee--eCCeEECCCCCceEEEee
Confidence 4667778889999999998 55589999999 555554
No 83
>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=37.66 E-value=16 Score=21.10 Aligned_cols=24 Identities=29% Similarity=0.678 Sum_probs=15.0
Q ss_pred EcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 81 KCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 81 ~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
.|..|+..|.... ...+|+.|+.+
T Consensus 13 ~C~~C~~~i~~~~--~~~~C~~C~~~ 36 (49)
T smart00109 13 KCCVCRKSIWGSF--QGLRCSWCKVK 36 (49)
T ss_pred CccccccccCcCC--CCcCCCCCCch
Confidence 4777777765433 46777777654
No 84
>PLN00209 ribosomal protein S27; Provisional
Probab=37.52 E-value=34 Score=24.90 Aligned_cols=37 Identities=24% Similarity=0.355 Sum_probs=27.4
Q ss_pred ccceeeEEcCCCCe-eeeeeCCCCeEeCCCCCCceeec
Q 033096 74 AHQVGQVKCASCAV-LLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 74 ~~e~a~v~Cg~Crt-~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
-.-+..+.|.+|.. ..+|-.-+..|.|..|+++---+
T Consensus 31 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 31 NSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQP 68 (86)
T ss_pred CCEEEEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 34566888999975 56677778888999998875444
No 85
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=37.41 E-value=17 Score=21.62 Aligned_cols=12 Identities=25% Similarity=1.082 Sum_probs=4.7
Q ss_pred EEcCCCCeeeee
Q 033096 80 VKCASCAVLLMY 91 (127)
Q Consensus 80 v~Cg~Crt~L~y 91 (127)
+.|..|+-.++|
T Consensus 18 irC~~CG~RIly 29 (32)
T PF03604_consen 18 IRCPECGHRILY 29 (32)
T ss_dssp SSBSSSS-SEEB
T ss_pred EECCcCCCeEEE
Confidence 344444444433
No 86
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=37.37 E-value=34 Score=24.83 Aligned_cols=37 Identities=19% Similarity=0.361 Sum_probs=27.6
Q ss_pred ccceeeEEcCCCCe-eeeeeCCCCeEeCCCCCCceeec
Q 033096 74 AHQVGQVKCASCAV-LLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 74 ~~e~a~v~Cg~Crt-~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
-.-...+.|.+|.. ..++-.-+..|.|..|+++---+
T Consensus 30 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 30 NSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQP 67 (85)
T ss_pred CCeEEEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 34566888999975 56777788889999998876444
No 87
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=37.33 E-value=32 Score=23.16 Aligned_cols=34 Identities=24% Similarity=0.431 Sum_probs=13.4
Q ss_pred cccceeeeccccceeeecCCCCeEEcCCCCCccc
Q 033096 37 SEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNF 70 (127)
Q Consensus 37 ~~~sQLvCggCr~lL~YprGA~sVrCs~C~tVn~ 70 (127)
.....|.|+.|+..=.=+----.-+|+.|.+-|.
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 4467777888876544444444556777766653
No 88
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=37.05 E-value=22 Score=32.89 Aligned_cols=17 Identities=47% Similarity=1.236 Sum_probs=12.9
Q ss_pred hhhhhcCCCCCCCCCCC
Q 033096 13 EENEEAGPPPGWQPIPP 29 (127)
Q Consensus 13 ~~~~~~~~~~gw~~~~~ 29 (127)
.+.++.||||||+-.++
T Consensus 64 gqrk~ggPpP~weg~~p 80 (506)
T KOG0117|consen 64 GQRKYGGPPPGWEGPPP 80 (506)
T ss_pred cccccCCCCCcccCCCC
Confidence 35567899999987654
No 89
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=36.67 E-value=33 Score=19.66 Aligned_cols=27 Identities=19% Similarity=0.486 Sum_probs=16.6
Q ss_pred eEEcCCCCeeeeeeCC---CCeEeCCCCCC
Q 033096 79 QVKCASCAVLLMYPYG---APSVRCSSCCF 105 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~G---A~SVrCa~C~t 105 (127)
...|..|+...-...+ ...+.|+.|+.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 3457777774433332 45777888876
No 90
>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=36.55 E-value=42 Score=24.35 Aligned_cols=27 Identities=19% Similarity=0.476 Sum_probs=17.2
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVT 107 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT 107 (127)
..+|..|+. .++.......||.|+..+
T Consensus 70 ~~~C~~Cg~--~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSE--EVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred EEEcccCCC--EEecCCcCccCcCCcCCC
Confidence 566777773 344444467788888654
No 91
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.39 E-value=30 Score=28.24 Aligned_cols=26 Identities=27% Similarity=0.637 Sum_probs=21.0
Q ss_pred eeeccccceeeecCCCCeEEcCCCCCcc
Q 033096 42 MVCGSCRRLLAYPRGARHVKCSCCQTVN 69 (127)
Q Consensus 42 LvCggCr~lL~YprGA~sVrCs~C~tVn 69 (127)
-+|..||..|++ .-....|+.|..+-
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 56788899997653
No 92
>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=36.32 E-value=43 Score=25.83 Aligned_cols=29 Identities=14% Similarity=0.362 Sum_probs=13.4
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVT 107 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT 107 (127)
.++|-+|+..+.+-.-..--.|+.|+...
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHTE 140 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCCe
Confidence 44455554444444434444455554443
No 93
>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=35.76 E-value=24 Score=20.56 Aligned_cols=21 Identities=33% Similarity=0.800 Sum_probs=8.8
Q ss_pred eeccccceeeecCCCCeEEcCCCCC
Q 033096 43 VCGSCRRLLAYPRGARHVKCSCCQT 67 (127)
Q Consensus 43 vCggCr~lL~YprGA~sVrCs~C~t 67 (127)
.|..|..+..||+ ..|+.|.+
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 34565543
No 94
>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=34.31 E-value=49 Score=21.12 Aligned_cols=24 Identities=21% Similarity=0.534 Sum_probs=9.9
Q ss_pred cCCCCeeeeeeCCCCeEeCCCCCC
Q 033096 82 CASCAVLLMYPYGAPSVRCSSCCF 105 (127)
Q Consensus 82 Cg~Crt~L~yP~GA~SVrCa~C~t 105 (127)
|..|+...--+...+...|+.|+.
T Consensus 31 C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 31 CPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred ccCcccccccccccceEEcCCCCC
Confidence 333333333344444444444443
No 95
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=34.28 E-value=21 Score=20.27 Aligned_cols=9 Identities=22% Similarity=0.833 Sum_probs=4.9
Q ss_pred eEeCCCCCC
Q 033096 97 SVRCSSCCF 105 (127)
Q Consensus 97 SVrCa~C~t 105 (127)
...|+.|++
T Consensus 14 ~~~Cp~CG~ 22 (26)
T PF10571_consen 14 AKFCPHCGY 22 (26)
T ss_pred cCcCCCCCC
Confidence 445666654
No 96
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=34.06 E-value=30 Score=30.49 Aligned_cols=30 Identities=17% Similarity=0.480 Sum_probs=15.1
Q ss_pred EEcCCCCCcccccCccceeeEEcCCCCeee
Q 033096 60 VKCSCCQTVNFVLEAHQVGQVKCASCAVLL 89 (127)
Q Consensus 60 VrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L 89 (127)
+.|..|+.+...++...-..-.|..|+..|
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 446666666555432222234466666655
No 97
>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=33.78 E-value=37 Score=20.47 Aligned_cols=24 Identities=17% Similarity=0.430 Sum_probs=12.7
Q ss_pred cCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 82 CASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 82 Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
|+.|+.. .+-...-..-|..|+++
T Consensus 11 C~~C~~~-~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 11 CPVCGSR-WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCCCCe-EeEccCCEEEhhhCceE
Confidence 5555555 44444445555555554
No 98
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=33.64 E-value=35 Score=21.01 Aligned_cols=26 Identities=23% Similarity=0.382 Sum_probs=14.4
Q ss_pred eEeCCCCCCceee-ccCCceEEEeecc
Q 033096 97 SVRCSSCCFVTEI-GVCGLSLFLCMCD 122 (127)
Q Consensus 97 SVrCa~C~tVT~V-~~~~~~~~~c~~~ 122 (127)
..+|..|..|-.| ......++||-=+
T Consensus 6 ~YkC~~CGniVev~~~g~g~lvCCGe~ 32 (36)
T PF06397_consen 6 FYKCEHCGNIVEVVHDGGGPLVCCGEP 32 (36)
T ss_dssp EEE-TTT--EEEEEE--SS-EEETTEE
T ss_pred EEEccCCCCEEEEEECCCCCEEeCCcc
Confidence 4689999988775 4667788888543
No 99
>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=33.51 E-value=40 Score=21.04 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=19.3
Q ss_pred ceeeEEcCCCCeeeeeeCCCCeEeCCCCC
Q 033096 76 QVGQVKCASCAVLLMYPYGAPSVRCSSCC 104 (127)
Q Consensus 76 e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~ 104 (127)
-|..-.|..|+++||=..+. .+.|..|.
T Consensus 14 ~ML~~~Cp~C~~PL~~~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 14 TMLDEHCPDCGTPLMRDKDG-KIYCVSCG 41 (41)
T ss_pred hHhcCccCCCCCeeEEecCC-CEECCCCC
Confidence 34556788888888875544 46787773
No 100
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=33.15 E-value=98 Score=21.63 Aligned_cols=58 Identities=24% Similarity=0.515 Sum_probs=36.3
Q ss_pred eeeccccceeeecCCCCeEEcCCCCCcccccCccceeeEEcCCCCeeeeee--CCCCeEeCCCCCCcee
Q 033096 42 MVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYP--YGAPSVRCSSCCFVTE 108 (127)
Q Consensus 42 LvCggCr~lL~YprGA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP--~GA~SVrCa~C~tVT~ 108 (127)
+.|-.|+.-|...- ..-.|..|+.-- ..+-.|..|+..|-.= =||-..-|-.||...+
T Consensus 2 ~~CP~C~~~L~~~~--~~~~C~~C~~~~-------~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gLiS 61 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--GHYHCEACQKDY-------KKEAFCPDCGQPLEVLKACGAVDYFCNHCHGLIS 61 (70)
T ss_dssp -B-SSS-SBEEEET--TEEEETTT--EE-------EEEEE-TTT-SB-EEEEETTEEEEE-TTTT-EE-
T ss_pred CcCCCCCCccEEeC--CEEECccccccc-------eecccCCCcccHHHHHHHhcccceeeccCCceee
Confidence 67889999977655 788899998732 3467799999988764 5888999999987643
No 101
>PRK04351 hypothetical protein; Provisional
Probab=32.96 E-value=38 Score=25.99 Aligned_cols=32 Identities=16% Similarity=0.380 Sum_probs=18.8
Q ss_pred EcCCCCCcccccCccceeeEEcCCCCeeeeee
Q 033096 61 KCSCCQTVNFVLEAHQVGQVKCASCAVLLMYP 92 (127)
Q Consensus 61 rCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP 92 (127)
+|..|..+-.-.--.....-.|+.|+..|.+-
T Consensus 114 ~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 114 ECQSCGQQYLRKRRINTKRYRCGKCRGKLKLI 145 (149)
T ss_pred ECCCCCCEeeeeeecCCCcEEeCCCCcEeeec
Confidence 55555543332212234677899999888753
No 102
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=32.57 E-value=33 Score=25.83 Aligned_cols=32 Identities=16% Similarity=0.510 Sum_probs=23.6
Q ss_pred eEEcCCCCCccccc----CccceeeEEcCCCCeeee
Q 033096 59 HVKCSCCQTVNFVL----EAHQVGQVKCASCAVLLM 90 (127)
Q Consensus 59 sVrCs~C~tVn~v~----~~~e~a~v~Cg~Crt~L~ 90 (127)
.--|+.|+..+.+. -....+.++|+.|+....
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 34688898888773 246678999999986543
No 103
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=31.77 E-value=31 Score=30.39 Aligned_cols=30 Identities=23% Similarity=0.549 Sum_probs=17.2
Q ss_pred ccccceeeeccccceeeecCCCCeEEcCCCCCcc
Q 033096 36 PSEMAQMVCGSCRRLLAYPRGARHVKCSCCQTVN 69 (127)
Q Consensus 36 ~~~~sQLvCggCr~lL~YprGA~sVrCs~C~tVn 69 (127)
+.+.+-+.|..|..+. +. ..-+|++|++.=
T Consensus 216 ~~~~~l~~C~~Cd~l~--~~--~~a~CpRC~~~L 245 (419)
T PRK15103 216 GLRQGLRSCSCCTAIL--PA--DQPVCPRCHTKG 245 (419)
T ss_pred ccccCCCcCCCCCCCC--CC--CCCCCCCCCCcC
Confidence 3344555688888763 22 223677776654
No 104
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=31.72 E-value=1e+02 Score=20.96 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=23.3
Q ss_pred Cccccceeeeccccce-eeecCCCCeEEcCCCCCccccc
Q 033096 35 SPSEMAQMVCGSCRRL-LAYPRGARHVKCSCCQTVNFVL 72 (127)
Q Consensus 35 ~~~~~sQLvCggCr~l-L~YprGA~sVrCs~C~tVn~v~ 72 (127)
|.+-+-.+.|.+|... ..|..-++-|.|..|.++=.-|
T Consensus 5 p~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~P 43 (59)
T PRK00415 5 PRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEP 43 (59)
T ss_pred CCCeEEEEECCCCCCeEEEEecCCcEEECcccCCCcccC
Confidence 3345556667777653 4666666777777776665444
No 105
>PRK11827 hypothetical protein; Provisional
Probab=31.58 E-value=57 Score=22.00 Aligned_cols=32 Identities=16% Similarity=0.279 Sum_probs=22.3
Q ss_pred eeeeccccceeeecCCCCeEEcCCCCCccccc
Q 033096 41 QMVCGSCRRLLAYPRGARHVKCSCCQTVNFVL 72 (127)
Q Consensus 41 QLvCggCr~lL~YprGA~sVrCs~C~tVn~v~ 72 (127)
-|+|-.|+.-|.|..++..-.|..|.-.-++.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeecccc
Confidence 47788888888887777766676666555443
No 106
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=31.45 E-value=71 Score=18.95 Aligned_cols=26 Identities=19% Similarity=0.266 Sum_probs=11.0
Q ss_pred EcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 81 KCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 81 ~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
.|..|+..+++-....--.|.-|..+
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCcE
Confidence 34444444444333333444444443
No 107
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.43 E-value=37 Score=25.30 Aligned_cols=44 Identities=27% Similarity=0.378 Sum_probs=25.7
Q ss_pred eeecCCCCeEEcCCCCCcccccCcc----ceeeEEcCCCCeeeeeeCC
Q 033096 51 LAYPRGARHVKCSCCQTVNFVLEAH----QVGQVKCASCAVLLMYPYG 94 (127)
Q Consensus 51 L~YprGA~sVrCs~C~tVn~v~~~~----e~a~v~Cg~Crt~L~yP~G 94 (127)
|.|-.+-....|+.|+..-....+. ..+...|..|+..|..=-+
T Consensus 91 l~~e~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 91 LEDETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDN 138 (147)
T ss_pred HhcccCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCc
Confidence 3455566677788887544332221 1234788888888876443
No 108
>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=31.07 E-value=62 Score=28.85 Aligned_cols=22 Identities=23% Similarity=0.641 Sum_probs=10.9
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCC
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCF 105 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~t 105 (127)
.+.|..|+-..-+|. +|+.|+.
T Consensus 240 ~l~Ch~Cg~~~~~~~-----~Cp~C~s 261 (505)
T TIGR00595 240 KLRCHYCGYQEPIPK-----TCPQCGS 261 (505)
T ss_pred eEEcCCCcCcCCCCC-----CCCCCCC
Confidence 455555554444332 5555554
No 109
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=30.74 E-value=35 Score=29.27 Aligned_cols=29 Identities=17% Similarity=0.321 Sum_probs=20.9
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVT 107 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT 107 (127)
+-.||+|++.+-.-.|-....|+.|+...
T Consensus 111 ~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 111 HRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred CcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 44577777777777777777777777654
No 110
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=30.68 E-value=25 Score=25.39 Aligned_cols=53 Identities=21% Similarity=0.489 Sum_probs=36.1
Q ss_pred cceeeeccccceeeecCCCCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCce
Q 033096 39 MAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVT 107 (127)
Q Consensus 39 ~sQLvCggCr~lL~YprGA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT 107 (127)
++.-.|.-|...+-|- +.+...|..|. +-+|..|+.. -.+...-.|.+|+.-.
T Consensus 52 ~~~~~C~~C~~~fg~l-~~~~~~C~~C~------------~~VC~~C~~~---~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 52 YGERHCARCGKPFGFL-FNRGRVCVDCK------------HRVCKKCGVY---SKKEPIWLCKVCQKQR 104 (118)
T ss_dssp HCCSB-TTTS-BCSCT-STTCEEETTTT------------EEEETTSEEE---TSSSCCEEEHHHHHHH
T ss_pred cCCcchhhhCCccccc-CCCCCcCCcCC------------ccccCccCCc---CCCCCCEEChhhHHHH
Confidence 3556899998877655 33448888886 6679999987 4566777888776543
No 111
>PF12528 DUF3728: Prepilin peptidase dependent protein C (DUF3728); InterPro: IPR022204 This family of proteins is found in bacteria. Proteins in this family are typically between 106 and 121 amino acids in length. The family is found in association with PF07963 from PFAM. There are two completely conserved C residues that may be functionally important. This family is frequently annotated as prepilin peptidase dependent protein C however there is little accompanying literature to confirm this.
Probab=30.23 E-value=31 Score=24.12 Aligned_cols=18 Identities=39% Similarity=0.757 Sum_probs=11.7
Q ss_pred hhhhhcCCCCCCCCCCCC
Q 033096 13 EENEEAGPPPGWQPIPPP 30 (127)
Q Consensus 13 ~~~~~~~~~~gw~~~~~~ 30 (127)
++..+.++++||+..-..
T Consensus 35 ~~~~~~~~~~gWq~~~~~ 52 (84)
T PF12528_consen 35 IPPALSGPPPGWQYSRQQ 52 (84)
T ss_pred ccccccCCCCCceeeeee
Confidence 334445699999876553
No 112
>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=28.92 E-value=44 Score=18.62 Aligned_cols=10 Identities=20% Similarity=0.627 Sum_probs=3.6
Q ss_pred CCeEeCCCCC
Q 033096 95 APSVRCSSCC 104 (127)
Q Consensus 95 A~SVrCa~C~ 104 (127)
..+.-|+.|+
T Consensus 19 r~~~~C~rCq 28 (30)
T PF06827_consen 19 RSTYLCPRCQ 28 (30)
T ss_dssp EEEEE-TTTC
T ss_pred CCCeECcCCc
Confidence 3334444443
No 113
>PRK00420 hypothetical protein; Validated
Probab=28.90 E-value=39 Score=25.27 Aligned_cols=36 Identities=17% Similarity=0.225 Sum_probs=21.5
Q ss_pred ccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCceeec
Q 033096 74 AHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 74 ~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
|..|..-.|.-|++.|+=- -...+.|+.|+.+-.|.
T Consensus 18 Ga~ml~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 18 GAKMLSKHCPVCGLPLFEL-KDGEVVCPVHGKVYIVK 53 (112)
T ss_pred HHHHccCCCCCCCCcceec-CCCceECCCCCCeeeec
Confidence 3444555677777777653 22366777777765553
No 114
>PRK11827 hypothetical protein; Provisional
Probab=28.46 E-value=77 Score=21.39 Aligned_cols=32 Identities=16% Similarity=0.309 Sum_probs=25.4
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCceeec
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
-+.|..|+..|.|=.++....|..|+-+-.|.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeecccc
Confidence 46788888888887777788888888777665
No 115
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.33 E-value=19 Score=31.18 Aligned_cols=46 Identities=26% Similarity=0.521 Sum_probs=29.3
Q ss_pred EcCCCCCcccccCc-----cceeeEEcCCCCeeeeeeCCCCeEeCCCCCCceee
Q 033096 61 KCSCCQTVNFVLEA-----HQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 109 (127)
Q Consensus 61 rCs~C~tVn~v~~~-----~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V 109 (127)
.|+.|.+-....+. ++=+|..|..|-..|.- ..+..|+.|+..-+-
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~---~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV---RGSGSCPECDTPLRK 55 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc---CCCCCCCCCCCccch
Confidence 58899885443332 23457777788888742 233589999875543
No 116
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.14 E-value=59 Score=23.72 Aligned_cols=9 Identities=22% Similarity=0.815 Sum_probs=4.8
Q ss_pred CeEEcCCCC
Q 033096 58 RHVKCSCCQ 66 (127)
Q Consensus 58 ~sVrCs~C~ 66 (127)
+.+.|+.|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 345555555
No 117
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=27.98 E-value=38 Score=26.72 Aligned_cols=29 Identities=28% Similarity=0.693 Sum_probs=23.6
Q ss_pred EcCCCC-eeeeeeCCC-CeEeCCCCCCceee
Q 033096 81 KCASCA-VLLMYPYGA-PSVRCSSCCFVTEI 109 (127)
Q Consensus 81 ~Cg~Cr-t~L~yP~GA-~SVrCa~C~tVT~V 109 (127)
+|.-|. ..++||... .+++|+.|.+|-..
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~ 184 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFHK 184 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCccccch
Confidence 577777 489999998 89999999988653
No 118
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=27.69 E-value=46 Score=32.13 Aligned_cols=64 Identities=19% Similarity=0.404 Sum_probs=46.3
Q ss_pred hhhhhhhhhcCCCCCCCCCCCC------CCCC---------Cc-----cccceeeecc-ccceee----ecCCCCeEEcC
Q 033096 9 MENQEENEEAGPPPGWQPIPPP------LPVP---------SP-----SEMAQMVCGS-CRRLLA----YPRGARHVKCS 63 (127)
Q Consensus 9 ~~~~~~~~~~~~~~gw~~~~~~------~~~p---------~~-----~~~sQLvCgg-Cr~lL~----YprGA~sVrCs 63 (127)
|+.|+-||.||.+--|...|.+ +.+| +- ...--++|.+ |+.+|. -..++.++-|+
T Consensus 1 m~fe~iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~~~~~v~~yepv~C~~pC~avlnpyC~id~r~~~W~Cp 80 (755)
T COG5047 1 MNFEIIEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHEDDALTVNYYEPVKCTAPCKAVLNPYCHIDERNQSWICP 80 (755)
T ss_pred CchhhhccccceEEEEecccCCccccccccccHHHhccccccccccCcccCCCceecccchhhcCcceeeccCCceEecc
Confidence 5566677889999999887762 2333 11 2234578999 998884 36789999999
Q ss_pred CCCCccccc
Q 033096 64 CCQTVNFVL 72 (127)
Q Consensus 64 ~C~tVn~v~ 72 (127)
-|+.-|.-|
T Consensus 81 fCnqrn~lp 89 (755)
T COG5047 81 FCNQRNTLP 89 (755)
T ss_pred eecCCCCCC
Confidence 999988655
No 119
>PLN00162 transport protein sec23; Provisional
Probab=27.47 E-value=51 Score=31.14 Aligned_cols=34 Identities=18% Similarity=0.422 Sum_probs=25.8
Q ss_pred eeEEcCCCCeee----eeeCCCCeEeCCCCCCceeecc
Q 033096 78 GQVKCASCAVLL----MYPYGAPSVRCSSCCFVTEIGV 111 (127)
Q Consensus 78 a~v~Cg~Crt~L----~yP~GA~SVrCa~C~tVT~V~~ 111 (127)
.-++|.+||+.| .+-.+...-+|..|...|.++.
T Consensus 52 ~pvRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~~P~ 89 (761)
T PLN00162 52 DPLRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNHFPP 89 (761)
T ss_pred CCCccCCCcCEECCceEEecCCCEEEccCCCCCCCCch
Confidence 457787787765 2346788999999999998874
No 120
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=27.24 E-value=55 Score=23.79 Aligned_cols=28 Identities=18% Similarity=0.387 Sum_probs=18.6
Q ss_pred eeEEcCCCCeeeeeeCCCCe-EeCCCCCCce
Q 033096 78 GQVKCASCAVLLMYPYGAPS-VRCSSCCFVT 107 (127)
Q Consensus 78 a~v~Cg~Crt~L~yP~GA~S-VrCa~C~tVT 107 (127)
+..+|..|+. .+|..... .+||.|+...
T Consensus 69 ~~~~C~~Cg~--~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 69 AECWCETCQQ--YVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred cEEEcccCCC--eeecCCccCCcCcCcCCCC
Confidence 3677888885 45554444 7799998653
No 121
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=27.18 E-value=46 Score=27.19 Aligned_cols=31 Identities=13% Similarity=0.138 Sum_probs=25.0
Q ss_pred eEEcCCCCeeeeeeCCCCeEeCCCCCCceee
Q 033096 79 QVKCASCAVLLMYPYGAPSVRCSSCCFVTEI 109 (127)
Q Consensus 79 ~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V 109 (127)
+-.|+.|+..|..-.+-..-.|+.|+.+--.
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPHCRERYYP 129 (256)
T ss_pred CccccccCCCCeecCCceeEECCCCCCEECC
Confidence 5579999999888888888889999865543
No 122
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=27.12 E-value=56 Score=23.71 Aligned_cols=27 Identities=19% Similarity=0.409 Sum_probs=17.7
Q ss_pred eeEEcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 78 GQVKCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 78 a~v~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
+..+|..|+.. ++.......|+.|+..
T Consensus 69 ~~~~C~~Cg~~--~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 69 AQAWCWDCSQV--VEIHQHDAQCPHCHGE 95 (113)
T ss_pred cEEEcccCCCE--EecCCcCccCcCCCCC
Confidence 36778888843 4444455668888864
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.00 E-value=46 Score=34.19 Aligned_cols=39 Identities=21% Similarity=0.595 Sum_probs=28.6
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCceeec
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
..+|+.|.+.+. ...|..|+..+- ....|+.|+.-..-.
T Consensus 667 ~rkCPkCG~~t~--------~~fCP~CGs~te-----~vy~CPsCGaev~~d 705 (1337)
T PRK14714 667 RRRCPSCGTETY--------ENRCPDCGTHTE-----PVYVCPDCGAEVPPD 705 (1337)
T ss_pred EEECCCCCCccc--------cccCcccCCcCC-----CceeCccCCCccCCC
Confidence 478999999764 238999998873 245899999865433
No 124
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=26.47 E-value=79 Score=23.28 Aligned_cols=33 Identities=18% Similarity=0.565 Sum_probs=20.8
Q ss_pred eEEcCCCCCccccc-CccceeeEEcCCCCeeeee
Q 033096 59 HVKCSCCQTVNFVL-EAHQVGQVKCASCAVLLMY 91 (127)
Q Consensus 59 sVrCs~C~tVn~v~-~~~e~a~v~Cg~Crt~L~y 91 (127)
..+|..|....... -.+.+....|+.|+-.|.+
T Consensus 112 ~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~~ 145 (146)
T smart00731 112 PYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLIL 145 (146)
T ss_pred EEECCCCCCCCceEccccCcceEEcCCCCCEEEe
Confidence 35677777655422 2344578889999887763
No 125
>PRK05580 primosome assembly protein PriA; Validated
Probab=26.06 E-value=85 Score=29.05 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=11.0
Q ss_pred eccccceeeecCCCCeEEcCCCCCc
Q 033096 44 CGSCRRLLAYPRGARHVKCSCCQTV 68 (127)
Q Consensus 44 CggCr~lL~YprGA~sVrCs~C~tV 68 (127)
|..|..-|.|...-....|..|...
T Consensus 393 C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 393 CPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred CCCCCCceeEECCCCeEECCCCcCC
Confidence 3334444444444444444444433
No 126
>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=25.93 E-value=71 Score=27.99 Aligned_cols=31 Identities=19% Similarity=0.597 Sum_probs=21.6
Q ss_pred eeEEcCCCCeeeeeeC--CCCeEeCCCCCCcee
Q 033096 78 GQVKCASCAVLLMYPY--GAPSVRCSSCCFVTE 108 (127)
Q Consensus 78 a~v~Cg~Crt~L~yP~--GA~SVrCa~C~tVT~ 108 (127)
..+.|..|....-.|+ .....+|+.|+++=.
T Consensus 12 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 12 KHILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred CeeeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 3566888888887775 444567888887654
No 127
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=25.43 E-value=71 Score=21.03 Aligned_cols=29 Identities=21% Similarity=0.477 Sum_probs=14.9
Q ss_pred EcCCCCeeeeeeCCC--CeEeCCCCCCceee
Q 033096 81 KCASCAVLLMYPYGA--PSVRCSSCCFVTEI 109 (127)
Q Consensus 81 ~Cg~Crt~L~yP~GA--~SVrCa~C~tVT~V 109 (127)
.|..|+..+-+|... .-|.|+.|.+--.|
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 455555555555322 24566666554444
No 128
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.28 E-value=84 Score=19.16 Aligned_cols=26 Identities=19% Similarity=0.623 Sum_probs=12.0
Q ss_pred EEcCCCCCcccccCccceeeEEcCCCC
Q 033096 60 VKCSCCQTVNFVLEAHQVGQVKCASCA 86 (127)
Q Consensus 60 VrCs~C~tVn~v~~~~e~a~v~Cg~Cr 86 (127)
+.|+.|....... ......-.|..|+
T Consensus 19 ~~CP~Cg~~~~~~-~~~~~~~~C~~C~ 44 (46)
T PF12760_consen 19 FVCPHCGSTKHYR-LKTRGRYRCKACR 44 (46)
T ss_pred CCCCCCCCeeeEE-eCCCCeEECCCCC
Confidence 5577776653222 1113344555554
No 129
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=25.24 E-value=8.1 Score=23.50 Aligned_cols=42 Identities=21% Similarity=0.424 Sum_probs=19.0
Q ss_pred cCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCC
Q 033096 62 CSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSC 103 (127)
Q Consensus 62 Cs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C 103 (127)
|+.|..+-.-|-..+=+|..|..|-..+.-..+...+.|+.|
T Consensus 1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 344444433332223345666666666665555555667665
No 130
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=25.15 E-value=34 Score=23.23 Aligned_cols=27 Identities=15% Similarity=0.556 Sum_probs=18.3
Q ss_pred ceeeeccccceeeecCCCCeEEcCCCCCccccc
Q 033096 40 AQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVL 72 (127)
Q Consensus 40 sQLvCggCr~lL~YprGA~sVrCs~C~tVn~v~ 72 (127)
....|..|+.++. .-+|+.|.+.+++.
T Consensus 2 ~~kAC~~C~~i~~------~~~CP~Cgs~~~T~ 28 (61)
T PRK08351 2 TEKACRHCHYITT------EDRCPVCGSRDLSD 28 (61)
T ss_pred chhhhhhCCcccC------CCcCCCCcCCcccc
Confidence 3447888888883 12688888877543
No 131
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.34 E-value=50 Score=24.11 Aligned_cols=28 Identities=18% Similarity=0.454 Sum_probs=17.3
Q ss_pred eeEEcCCCCeeeeeeCCCC-eEeCCCCCCce
Q 033096 78 GQVKCASCAVLLMYPYGAP-SVRCSSCCFVT 107 (127)
Q Consensus 78 a~v~Cg~Crt~L~yP~GA~-SVrCa~C~tVT 107 (127)
+..+|..|+.. ++.... ..+|+.|+..+
T Consensus 70 ~~~~C~~Cg~~--~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 70 VELECKDCSHV--FKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CEEEhhhCCCc--cccCCccCCcCcCCCCCc
Confidence 46778888843 344333 34588888753
No 132
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=24.30 E-value=43 Score=18.69 Aligned_cols=23 Identities=30% Similarity=0.730 Sum_probs=13.1
Q ss_pred eEEcCCCCCcccccCccceeeEEcCCCCe
Q 033096 59 HVKCSCCQTVNFVLEAHQVGQVKCASCAV 87 (127)
Q Consensus 59 sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt 87 (127)
...|+.|..+|... ...|..|++
T Consensus 4 ~W~C~~C~~~N~~~------~~~C~~C~~ 26 (30)
T PF00641_consen 4 DWKCPSCTFMNPAS------RSKCVACGA 26 (30)
T ss_dssp SEEETTTTEEEESS------SSB-TTT--
T ss_pred CccCCCCcCCchHH------hhhhhCcCC
Confidence 56788888888643 344666654
No 133
>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=23.93 E-value=69 Score=24.68 Aligned_cols=34 Identities=21% Similarity=0.496 Sum_probs=29.7
Q ss_pred cceeeeccccceeeecCCCCeEEcCCCCCccccc
Q 033096 39 MAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVL 72 (127)
Q Consensus 39 ~sQLvCggCr~lL~YprGA~sVrCs~C~tVn~v~ 72 (127)
.|.++|-.|-..+.|..-..--.|+.|+...+.+
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHTEFTR 143 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCCeeee
Confidence 4889999999999998877888999999888765
No 134
>PRK04023 DNA polymerase II large subunit; Validated
Probab=23.46 E-value=64 Score=32.67 Aligned_cols=54 Identities=20% Similarity=0.412 Sum_probs=37.2
Q ss_pred ccceeeeccccceeeecCCCCeEEcCCCCCcccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCceeec
Q 033096 38 EMAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 38 ~~sQLvCggCr~lL~YprGA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tVT~V~ 110 (127)
+.+.-.|.+|-... ..-+|+.|.+.|. ....|..|++..-- ..|+.|.+.+.-.
T Consensus 623 EVg~RfCpsCG~~t------~~frCP~CG~~Te-------~i~fCP~CG~~~~~------y~CPKCG~El~~~ 676 (1121)
T PRK04023 623 EIGRRKCPSCGKET------FYRRCPFCGTHTE-------PVYRCPRCGIEVEE------DECEKCGREPTPY 676 (1121)
T ss_pred cccCccCCCCCCcC------CcccCCCCCCCCC-------cceeCccccCcCCC------CcCCCCCCCCCcc
Confidence 44556888998874 4578999988852 24579999776431 3499998876643
No 135
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=23.25 E-value=47 Score=27.68 Aligned_cols=12 Identities=33% Similarity=1.046 Sum_probs=5.3
Q ss_pred eeeEEcCCCCee
Q 033096 77 VGQVKCASCAVL 88 (127)
Q Consensus 77 ~a~v~Cg~Crt~ 88 (127)
.+.++|..|+..
T Consensus 28 ~Ge~vC~~CG~V 39 (310)
T PRK00423 28 RGEIVCADCGLV 39 (310)
T ss_pred CCeEeecccCCc
Confidence 344444444443
No 136
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=22.24 E-value=1.1e+02 Score=18.64 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=6.2
Q ss_pred CeEeCCCCCC
Q 033096 96 PSVRCSSCCF 105 (127)
Q Consensus 96 ~SVrCa~C~t 105 (127)
..+.|+.|+.
T Consensus 25 ~~~~CP~Cg~ 34 (52)
T TIGR02605 25 PLATCPECGG 34 (52)
T ss_pred CCCCCCCCCC
Confidence 4556777765
No 137
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=22.17 E-value=1.1e+02 Score=23.18 Aligned_cols=30 Identities=27% Similarity=0.708 Sum_probs=26.0
Q ss_pred EcCCCCeeeeeeCCCC--eEeCCCCCCceeec
Q 033096 81 KCASCAVLLMYPYGAP--SVRCSSCCFVTEIG 110 (127)
Q Consensus 81 ~Cg~Crt~L~yP~GA~--SVrCa~C~tVT~V~ 110 (127)
-|..|+-.|+|--|+. ..-|..|-+|-.|.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 4889999999999987 56799999998887
No 138
>PRK14873 primosome assembly protein PriA; Provisional
Probab=21.61 E-value=1.1e+02 Score=28.59 Aligned_cols=49 Identities=22% Similarity=0.590 Sum_probs=30.2
Q ss_pred ceeeeccccceeeecCCCCeEEcCCCCC-cccccCccceeeEEcCCCCeeeeeeCCCCeEeCCCCCCc
Q 033096 40 AQMVCGSCRRLLAYPRGARHVKCSCCQT-VNFVLEAHQVGQVKCASCAVLLMYPYGAPSVRCSSCCFV 106 (127)
Q Consensus 40 sQLvCggCr~lL~YprGA~sVrCs~C~t-Vn~v~~~~e~a~v~Cg~Crt~L~yP~GA~SVrCa~C~tV 106 (127)
.-+.|..|... .+|+.|+. .+.-. ....+.|..|+... . .-+|+.|+.-
T Consensus 382 p~l~C~~Cg~~---------~~C~~C~~~L~~h~---~~~~l~Ch~CG~~~-~-----p~~Cp~Cgs~ 431 (665)
T PRK14873 382 PSLACARCRTP---------ARCRHCTGPLGLPS---AGGTPRCRWCGRAA-P-----DWRCPRCGSD 431 (665)
T ss_pred CeeEhhhCcCe---------eECCCCCCceeEec---CCCeeECCCCcCCC-c-----CccCCCCcCC
Confidence 45688888765 47888873 33211 12467788888642 2 2378888764
No 139
>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=21.20 E-value=99 Score=20.12 Aligned_cols=8 Identities=50% Similarity=0.962 Sum_probs=3.4
Q ss_pred cCCCCCcc
Q 033096 62 CSCCQTVN 69 (127)
Q Consensus 62 Cs~C~tVn 69 (127)
|+.|++.|
T Consensus 25 C~~C~~hN 32 (54)
T PF10058_consen 25 CSKCFSHN 32 (54)
T ss_pred Ccccchhh
Confidence 44444444
No 140
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=20.94 E-value=39 Score=25.87 Aligned_cols=33 Identities=27% Similarity=0.464 Sum_probs=29.5
Q ss_pred ceeeeccccceeeecCCCCeEEcCCCCCccccc
Q 033096 40 AQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVL 72 (127)
Q Consensus 40 sQLvCggCr~lL~YprGA~sVrCs~C~tVn~v~ 72 (127)
+-+.|+.|-.||.-|.-+..|-|..|.++..+.
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~ 38 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVS 38 (116)
T ss_pred CcchhhhhhhhcccccccCceEeccccccCCHH
Confidence 456799999999999999999999999998765
No 141
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.94 E-value=44 Score=18.30 Aligned_cols=8 Identities=38% Similarity=1.099 Sum_probs=4.5
Q ss_pred cCCCCeee
Q 033096 82 CASCAVLL 89 (127)
Q Consensus 82 Cg~Crt~L 89 (127)
|.+|++.|
T Consensus 16 C~~CG~~l 23 (23)
T PF13240_consen 16 CPNCGTPL 23 (23)
T ss_pred hhhhCCcC
Confidence 66665543
No 142
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=20.91 E-value=80 Score=17.98 Aligned_cols=20 Identities=30% Similarity=0.755 Sum_probs=10.6
Q ss_pred cCCCCeeeeeeCCCCeEeCC
Q 033096 82 CASCAVLLMYPYGAPSVRCS 101 (127)
Q Consensus 82 Cg~Crt~L~yP~GA~SVrCa 101 (127)
|.-|++.|+...|--.+||.
T Consensus 2 CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 2 CPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp -TTT--BEEE-CCTTCEEE-
T ss_pred cCCCCCEeEcCCCCEeEECC
Confidence 66677777777776677664
No 143
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.36 E-value=65 Score=31.85 Aligned_cols=43 Identities=16% Similarity=0.352 Sum_probs=0.0
Q ss_pred cccccCccceeeEEcCCCCeee----eeeCCCCeEeCCCCCCceeec
Q 033096 68 VNFVLEAHQVGQVKCASCAVLL----MYPYGAPSVRCSSCCFVTEIG 110 (127)
Q Consensus 68 Vn~v~~~~e~a~v~Cg~Crt~L----~yP~GA~SVrCa~C~tVT~V~ 110 (127)
++..+......-++|..||+.+ .+..-.+.-||..|.+||.|+
T Consensus 207 ~~~~p~~~~~~IvRCr~CRtYiNPFV~fid~gr~WrCNlC~~~NdvP 253 (887)
T KOG1985|consen 207 IDPLPVITSTLIVRCRRCRTYINPFVEFIDQGRRWRCNLCGRVNDVP 253 (887)
T ss_pred cCCCCcccCCceeeehhhhhhcCCeEEecCCCceeeechhhhhcCCc
No 144
>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=20.18 E-value=57 Score=21.41 Aligned_cols=41 Identities=17% Similarity=0.361 Sum_probs=19.6
Q ss_pred cceeeeccccceeeecCCCCeEEcCCCCCcccccCccceeeEEcCCCC
Q 033096 39 MAQMVCGSCRRLLAYPRGARHVKCSCCQTVNFVLEAHQVGQVKCASCA 86 (127)
Q Consensus 39 ~sQLvCggCr~lL~YprGA~sVrCs~C~tVn~v~~~~e~a~v~Cg~Cr 86 (127)
+.+.+|.+|.++|..-..++ ||=- .-........+.|..|+
T Consensus 44 ~kr~~Ck~C~~~liPG~~~~-vri~------~~~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 44 IKRTICKKCGSLLIPGVNCS-VRIR------KKKKKKNFLVYTCLNCG 84 (85)
T ss_dssp CCCTB-TTT--B--CTTTEE-EEEE---------SSS-EEEEEETTTT
T ss_pred HhcccccCCCCEEeCCCccE-EEEE------ecCCCCCEEEEEccccC
Confidence 57889999999998876543 3321 00112334566677765
No 145
>PHA02942 putative transposase; Provisional
Probab=20.11 E-value=1.1e+02 Score=26.64 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=9.3
Q ss_pred ceeeecCCCCeEEcCCCCCcc
Q 033096 49 RLLAYPRGARHVKCSCCQTVN 69 (127)
Q Consensus 49 ~lL~YprGA~sVrCs~C~tVn 69 (127)
.+..-|.+ ||-.|+.|..++
T Consensus 316 Vv~V~p~y-TSq~Cs~CG~~~ 335 (383)
T PHA02942 316 VEFVNPSY-SSVSCPKCGHKM 335 (383)
T ss_pred EEEECCCC-CCccCCCCCCcc
Confidence 33334444 555555555444
No 146
>PF14353 CpXC: CpXC protein
Probab=20.05 E-value=84 Score=22.43 Aligned_cols=18 Identities=17% Similarity=0.325 Sum_probs=12.6
Q ss_pred cceeeEEcCCCCeeeeee
Q 033096 75 HQVGQVKCASCAVLLMYP 92 (127)
Q Consensus 75 ~e~a~v~Cg~Crt~L~yP 92 (127)
.+.....|.+|+....+.
T Consensus 34 g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CCcCEEECCCCCCceecC
Confidence 556677888888766554
Done!