Query psy8689
Match_columns 72
No_of_seqs 114 out of 637
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 16:42:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8689.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8689hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2906|consensus 100.0 1.6E-32 3.4E-37 171.8 2.6 67 4-72 39-105 (105)
2 TIGR01384 TFS_arch transcripti 99.9 1.2E-25 2.6E-30 139.5 5.1 60 11-72 43-102 (104)
3 smart00440 ZnF_C2C2 C2C2 Zinc 99.9 5E-25 1.1E-29 118.2 4.9 40 31-72 1-40 (40)
4 PF01096 TFIIS_C: Transcriptio 99.9 3.6E-24 7.8E-29 114.3 4.7 39 31-71 1-39 (39)
5 KOG2691|consensus 99.9 4.3E-23 9.3E-28 130.9 4.1 65 6-72 48-113 (113)
6 COG1594 RPB9 DNA-directed RNA 99.9 7E-22 1.5E-26 125.9 4.8 49 22-72 64-112 (113)
7 PHA02998 RNA polymerase subuni 99.8 1E-19 2.2E-24 124.2 4.5 44 26-71 138-182 (195)
8 TIGR01385 TFSII transcription 99.7 8.2E-18 1.8E-22 121.5 4.6 42 28-71 256-297 (299)
9 KOG2907|consensus 99.6 2E-16 4.3E-21 101.1 2.2 46 25-72 69-114 (116)
10 KOG1105|consensus 99.2 2.5E-11 5.5E-16 88.0 4.1 40 30-71 255-294 (296)
11 PF04606 Ogr_Delta: Ogr/Delta- 98.4 5.4E-07 1.2E-11 49.2 3.5 38 32-71 1-38 (47)
12 PRK09678 DNA-binding transcrip 98.0 6.3E-06 1.4E-10 49.1 3.2 39 31-71 2-40 (72)
13 COG4332 Uncharacterized protei 96.1 0.0051 1.1E-07 42.7 2.8 46 24-71 11-60 (203)
14 PF01396 zf-C4_Topoisom: Topoi 96.1 0.0099 2.1E-07 31.2 3.2 31 31-69 2-33 (39)
15 PF13717 zinc_ribbon_4: zinc-r 96.0 0.0085 1.8E-07 31.0 2.5 36 29-71 1-36 (36)
16 PF09855 DUF2082: Nucleic-acid 95.5 0.022 4.7E-07 33.2 3.3 15 32-46 2-16 (64)
17 PHA00626 hypothetical protein 95.3 0.014 3.1E-07 33.5 2.1 33 32-71 2-34 (59)
18 PF08274 PhnA_Zn_Ribbon: PhnA 95.2 0.0072 1.6E-07 30.4 0.4 27 32-71 4-30 (30)
19 PF12760 Zn_Tnp_IS1595: Transp 95.1 0.019 4.2E-07 30.7 2.0 28 31-69 19-46 (46)
20 TIGR02098 MJ0042_CXXC MJ0042 f 94.9 0.041 8.8E-07 28.0 2.9 35 29-71 1-36 (38)
21 PF13719 zinc_ribbon_5: zinc-r 94.9 0.03 6.6E-07 28.9 2.3 36 29-71 1-36 (37)
22 PRK00464 nrdR transcriptional 94.8 0.042 9.2E-07 36.7 3.5 36 32-71 2-39 (154)
23 TIGR00244 transcriptional regu 94.3 0.059 1.3E-06 36.1 3.3 36 32-71 2-39 (147)
24 TIGR03655 anti_R_Lar restricti 94.2 0.11 2.4E-06 28.5 3.8 34 31-69 2-35 (53)
25 PF10058 DUF2296: Predicted in 94.1 0.058 1.3E-06 30.3 2.5 48 13-68 5-52 (54)
26 COG3478 Predicted nucleic-acid 93.9 0.053 1.1E-06 32.0 2.1 35 31-69 5-49 (68)
27 PF08271 TF_Zn_Ribbon: TFIIB z 93.2 0.1 2.2E-06 27.5 2.4 28 32-70 2-29 (43)
28 COG1779 C4-type Zn-finger prot 93.1 0.16 3.5E-06 35.5 3.9 42 28-72 12-55 (201)
29 TIGR00686 phnA alkylphosphonat 92.8 0.076 1.7E-06 34.0 1.8 27 32-71 4-30 (109)
30 COG1327 Predicted transcriptio 92.7 0.065 1.4E-06 36.2 1.4 36 32-71 2-39 (156)
31 PF14354 Lar_restr_allev: Rest 92.1 0.28 6E-06 27.1 3.3 34 31-68 4-37 (61)
32 PF05876 Terminase_GpA: Phage 91.7 0.13 2.8E-06 40.1 2.2 41 30-72 200-241 (557)
33 PF09151 DUF1936: Domain of un 91.2 0.62 1.3E-05 23.9 3.7 33 31-68 2-34 (36)
34 COG2051 RPS27A Ribosomal prote 91.1 0.25 5.5E-06 29.1 2.5 29 30-69 19-47 (67)
35 PF01667 Ribosomal_S27e: Ribos 90.4 0.16 3.5E-06 28.8 1.3 30 29-69 6-35 (55)
36 PF13453 zf-TFIIB: Transcripti 90.4 0.56 1.2E-05 24.4 3.3 30 32-71 1-30 (41)
37 PRK10220 hypothetical protein; 90.3 0.19 4.2E-06 32.2 1.7 27 32-71 5-31 (111)
38 PF04216 FdhE: Protein involve 90.1 0.39 8.5E-06 34.2 3.3 36 30-71 172-208 (290)
39 PRK00415 rps27e 30S ribosomal 90.0 0.35 7.5E-06 27.8 2.4 30 29-69 10-39 (59)
40 smart00661 RPOL9 RNA polymeras 89.7 0.38 8.3E-06 25.6 2.3 12 58-71 20-31 (52)
41 PF11781 RRN7: RNA polymerase 89.6 0.37 8.1E-06 24.9 2.2 26 31-69 9-34 (36)
42 TIGR00340 zpr1_rel ZPR1-relate 89.1 0.8 1.7E-05 30.8 4.0 37 33-71 1-39 (163)
43 PF05129 Elf1: Transcription e 88.7 1.2 2.5E-05 26.7 4.2 37 29-71 21-57 (81)
44 COG1326 Uncharacterized archae 88.4 0.22 4.9E-06 34.8 1.0 36 30-71 6-41 (201)
45 COG4888 Uncharacterized Zn rib 87.1 1.9 4.1E-05 27.4 4.5 35 30-70 22-56 (104)
46 PF07282 OrfB_Zn_ribbon: Putat 86.6 0.72 1.6E-05 26.0 2.3 30 29-70 27-56 (69)
47 PTZ00083 40S ribosomal protein 86.5 0.91 2E-05 27.9 2.8 30 29-69 34-63 (85)
48 PLN00209 ribosomal protein S27 86.5 0.87 1.9E-05 28.0 2.7 30 29-69 35-64 (86)
49 PRK00432 30S ribosomal protein 86.4 0.62 1.3E-05 25.6 1.9 29 29-70 19-47 (50)
50 smart00709 Zpr1 Duplicated dom 85.5 1.6 3.5E-05 29.2 3.9 37 32-71 2-40 (160)
51 TIGR00310 ZPR1_znf ZPR1 zinc f 84.7 1.6 3.5E-05 30.0 3.7 38 32-71 2-41 (192)
52 PF08792 A2L_zn_ribbon: A2L zi 83.8 2.2 4.9E-05 21.5 3.1 29 30-70 3-31 (33)
53 PF03119 DNA_ligase_ZBD: NAD-d 83.4 0.99 2.1E-05 22.0 1.6 25 32-66 1-26 (28)
54 PRK03988 translation initiatio 83.3 2.2 4.8E-05 28.0 3.8 30 31-69 103-132 (138)
55 COG5415 Predicted integral mem 83.3 0.54 1.2E-05 33.6 0.9 36 26-69 188-223 (251)
56 PF14353 CpXC: CpXC protein 83.1 1.7 3.8E-05 27.2 3.1 11 31-41 2-12 (128)
57 PF03811 Zn_Tnp_IS1: InsA N-te 82.7 2.9 6.4E-05 21.5 3.3 32 28-63 3-34 (36)
58 TIGR00311 aIF-2beta translatio 82.6 2.4 5.1E-05 27.7 3.7 30 31-69 98-127 (133)
59 PF04216 FdhE: Protein involve 82.4 1.3 2.8E-05 31.6 2.6 39 30-71 211-249 (290)
60 PF01873 eIF-5_eIF-2B: Domain 82.1 2.4 5.2E-05 27.3 3.5 30 31-69 94-123 (125)
61 PF11792 Baculo_LEF5_C: Baculo 82.0 0.053 1.2E-06 29.4 -3.6 30 36-68 13-42 (43)
62 TIGR02443 conserved hypothetic 81.6 3.7 8E-05 23.6 3.8 32 31-70 10-41 (59)
63 PF03367 zf-ZPR1: ZPR1 zinc-fi 80.8 2.3 5.1E-05 28.3 3.2 38 31-71 2-41 (161)
64 smart00659 RPOLCX RNA polymera 80.5 1 2.2E-05 24.1 1.2 14 29-42 18-31 (44)
65 PF06044 DRP: Dam-replacing fa 80.2 1.1 2.4E-05 32.4 1.5 33 30-70 31-63 (254)
66 PF09526 DUF2387: Probable met 79.6 4.7 0.0001 23.7 3.9 33 31-71 9-41 (71)
67 PRK14892 putative transcriptio 79.3 1.1 2.4E-05 28.0 1.2 32 29-69 20-51 (99)
68 smart00653 eIF2B_5 domain pres 78.9 3.9 8.4E-05 25.8 3.6 30 31-69 81-110 (110)
69 PF06839 zf-GRF: GRF zinc fing 78.8 7.4 0.00016 20.4 4.2 37 32-71 2-42 (45)
70 PF07754 DUF1610: Domain of un 77.9 2.1 4.5E-05 20.4 1.7 10 29-38 15-24 (24)
71 PF03604 DNA_RNApol_7kD: DNA d 77.8 1.1 2.4E-05 22.6 0.7 12 30-41 17-28 (32)
72 TIGR01562 FdhE formate dehydro 77.3 1.8 3.8E-05 31.9 1.9 38 30-71 184-221 (305)
73 PRK12336 translation initiatio 76.7 4.6 9.9E-05 27.8 3.8 30 31-69 99-128 (201)
74 PRK03564 formate dehydrogenase 75.4 2.8 6.1E-05 30.9 2.6 37 30-71 187-223 (309)
75 PF12677 DUF3797: Domain of un 74.7 1.3 2.9E-05 24.6 0.5 11 31-41 14-24 (49)
76 PF14311 DUF4379: Domain of un 74.4 3.9 8.5E-05 22.2 2.4 16 54-71 24-39 (55)
77 COG1997 RPL43A Ribosomal prote 74.2 3.5 7.6E-05 25.5 2.4 31 29-71 34-64 (89)
78 PF14205 Cys_rich_KTR: Cystein 73.3 2.8 6.1E-05 23.8 1.7 11 31-41 5-15 (55)
79 COG0675 Transposase and inacti 69.1 4.3 9.4E-05 27.9 2.2 25 29-70 308-332 (364)
80 PF06353 DUF1062: Protein of u 69.0 3 6.5E-05 27.6 1.3 14 56-71 11-24 (142)
81 PF01927 Mut7-C: Mut7-C RNAse 68.9 3.7 8E-05 26.6 1.7 37 30-69 91-133 (147)
82 PRK06319 DNA topoisomerase I/S 68.6 5.9 0.00013 32.7 3.2 34 29-69 591-625 (860)
83 cd00350 rubredoxin_like Rubred 68.4 1.7 3.7E-05 21.6 0.1 16 30-45 17-32 (33)
84 COG0551 TopA Zn-finger domain 68.0 14 0.0003 23.5 4.3 38 27-70 57-95 (140)
85 PRK09710 lar restriction allev 67.1 10 0.00022 22.1 3.2 31 31-70 7-37 (64)
86 COG2824 PhnA Uncharacterized Z 66.7 4.4 9.6E-05 26.0 1.7 27 32-71 5-31 (112)
87 PF08772 NOB1_Zn_bind: Nin one 65.6 2.9 6.3E-05 24.8 0.7 14 28-41 22-35 (73)
88 PF13248 zf-ribbon_3: zinc-rib 64.8 3.2 6.8E-05 19.6 0.6 10 30-39 2-11 (26)
89 PHA02942 putative transposase; 64.0 6.2 0.00013 29.6 2.3 29 29-70 324-352 (383)
90 PF05180 zf-DNL: DNL zinc fing 63.5 3.5 7.6E-05 24.1 0.7 35 30-69 4-38 (66)
91 PF10571 UPF0547: Uncharacteri 63.2 4.4 9.6E-05 19.4 1.0 9 32-40 2-10 (26)
92 PRK00398 rpoP DNA-directed RNA 63.1 7.3 0.00016 20.4 1.9 12 30-41 21-32 (46)
93 COG1996 RPC10 DNA-directed RNA 63.0 4.1 8.9E-05 22.5 0.9 12 30-41 24-35 (49)
94 PF14803 Nudix_N_2: Nudix N-te 62.8 8.4 0.00018 19.6 2.0 30 32-69 2-31 (34)
95 PF13240 zinc_ribbon_2: zinc-r 62.4 3.8 8.2E-05 19.0 0.6 9 32-40 1-9 (23)
96 PRK14890 putative Zn-ribbon RN 60.3 10 0.00022 21.8 2.2 35 28-69 23-57 (59)
97 COG5319 Uncharacterized protei 60.2 2.7 5.9E-05 27.9 -0.1 30 12-41 13-43 (142)
98 TIGR02605 CxxC_CxxC_SSSS putat 59.4 5.1 0.00011 21.2 0.9 12 30-41 26-37 (52)
99 TIGR02159 PA_CoA_Oxy4 phenylac 59.1 3.1 6.6E-05 27.5 -0.0 36 30-70 105-140 (146)
100 PF11672 DUF3268: Protein of u 58.6 11 0.00023 23.7 2.4 34 31-67 3-38 (102)
101 TIGR01562 FdhE formate dehydro 57.7 18 0.00039 26.7 3.7 38 30-70 224-262 (305)
102 PF13408 Zn_ribbon_recom: Reco 57.5 15 0.00032 19.4 2.6 27 30-63 5-31 (58)
103 PRK07219 DNA topoisomerase I; 57.4 9.9 0.00021 31.2 2.6 33 30-69 602-635 (822)
104 cd00674 LysRS_core_class_I cat 57.0 15 0.00033 27.4 3.3 33 30-69 169-201 (353)
105 PF01780 Ribosomal_L37ae: Ribo 56.1 18 0.00038 22.4 3.0 31 29-71 34-64 (90)
106 PF04194 PDCD2_C: Programmed c 55.5 14 0.00029 24.5 2.6 35 31-66 98-145 (164)
107 cd00729 rubredoxin_SM Rubredox 52.3 12 0.00026 18.8 1.5 12 58-71 2-13 (34)
108 PF09723 Zn-ribbon_8: Zinc rib 52.1 10 0.00023 19.6 1.3 10 59-70 6-15 (42)
109 smart00834 CxxC_CXXC_SSSS Puta 51.7 10 0.00022 18.9 1.2 11 59-71 6-16 (41)
110 PF04032 Rpr2: RNAse P Rpr2/Rp 51.6 18 0.00038 20.7 2.4 35 30-68 46-85 (85)
111 PRK00423 tfb transcription ini 50.9 15 0.00032 26.6 2.4 28 31-69 12-39 (310)
112 COG0375 HybF Zn finger protein 49.7 12 0.00027 24.0 1.6 11 31-41 87-97 (115)
113 TIGR01051 topA_bact DNA topois 49.5 15 0.00032 29.1 2.4 31 31-69 575-606 (610)
114 COG3364 Zn-ribbon containing p 49.5 9.7 0.00021 24.4 1.1 21 31-51 21-41 (112)
115 PRK07220 DNA topoisomerase I; 48.6 18 0.00039 29.4 2.7 32 31-69 590-622 (740)
116 PF10122 Mu-like_Com: Mu-like 48.5 10 0.00023 21.1 1.0 14 29-42 23-36 (51)
117 PF13790 DUF4182: Domain of un 48.2 36 0.00077 17.9 3.0 31 31-68 4-35 (38)
118 PF01921 tRNA-synt_1f: tRNA sy 47.0 20 0.00043 27.1 2.6 35 30-69 174-208 (360)
119 PRK03564 formate dehydrogenase 46.9 30 0.00065 25.6 3.5 37 30-71 226-263 (309)
120 TIGR00280 L37a ribosomal prote 46.5 34 0.00075 21.1 3.2 32 28-71 33-64 (91)
121 PF02150 RNA_POL_M_15KD: RNA p 46.0 14 0.0003 18.6 1.2 28 32-70 3-30 (35)
122 PRK14973 DNA topoisomerase I; 45.7 15 0.00032 30.9 1.9 32 30-69 635-666 (936)
123 KOG2703|consensus 44.5 21 0.00046 27.8 2.5 11 31-41 69-79 (460)
124 COG3677 Transposase and inacti 44.3 18 0.00038 23.3 1.8 39 26-71 26-64 (129)
125 PF14690 zf-ISL3: zinc-finger 44.3 11 0.00023 19.4 0.6 12 31-42 3-14 (47)
126 TIGR00467 lysS_arch lysyl-tRNA 44.1 29 0.00064 27.2 3.2 32 30-69 168-199 (515)
127 KOG2767|consensus 43.8 11 0.00023 28.9 0.8 32 31-70 97-128 (400)
128 PF09538 FYDLN_acid: Protein o 43.7 13 0.00029 23.4 1.1 15 26-40 22-36 (108)
129 PRK05978 hypothetical protein; 43.5 11 0.00025 25.0 0.8 30 30-70 33-62 (148)
130 PF09845 DUF2072: Zn-ribbon co 43.4 16 0.00035 24.0 1.5 17 31-47 20-36 (131)
131 PHA02540 61 DNA primase; Provi 43.1 37 0.0008 25.4 3.5 33 29-68 26-63 (337)
132 smart00778 Prim_Zn_Ribbon Zinc 42.9 22 0.00047 18.4 1.6 14 31-44 4-17 (37)
133 smart00531 TFIIE Transcription 42.9 11 0.00023 24.5 0.5 29 30-69 99-132 (147)
134 COG3024 Uncharacterized protei 42.6 15 0.00032 21.5 1.1 14 28-41 5-18 (65)
135 PTZ00255 60S ribosomal protein 42.3 43 0.00094 20.6 3.2 32 28-71 34-65 (90)
136 PF03884 DUF329: Domain of unk 41.8 14 0.0003 21.0 0.8 13 29-41 1-13 (57)
137 PRK00750 lysK lysyl-tRNA synth 41.6 42 0.0009 26.1 3.7 35 30-70 175-209 (510)
138 PRK06599 DNA topoisomerase I; 41.1 29 0.00063 27.8 2.8 32 30-68 585-617 (675)
139 PF00684 DnaJ_CXXCXGXG: DnaJ c 40.4 67 0.0015 17.9 4.9 34 30-67 15-48 (66)
140 PF02701 zf-Dof: Dof domain, z 40.3 21 0.00047 20.7 1.5 37 30-71 5-41 (63)
141 PF10825 DUF2752: Protein of u 39.9 6.7 0.00015 21.4 -0.6 15 29-43 8-22 (52)
142 COG1656 Uncharacterized conser 39.8 12 0.00025 25.6 0.4 36 31-69 98-139 (165)
143 PF00096 zf-C2H2: Zinc finger, 39.4 26 0.00055 15.1 1.4 11 59-71 1-11 (23)
144 PRK05582 DNA topoisomerase I; 38.7 24 0.00051 28.1 2.0 31 30-68 571-602 (650)
145 TIGR03830 CxxCG_CxxCG_HTH puta 38.3 47 0.001 20.1 3.0 7 33-39 1-7 (127)
146 PRK03681 hypA hydrogenase nick 38.2 19 0.00041 22.5 1.2 10 31-40 88-97 (114)
147 KOG2462|consensus 38.1 25 0.00054 25.9 1.9 39 28-71 128-172 (279)
148 PRK11032 hypothetical protein; 38.0 18 0.0004 24.4 1.1 14 27-40 139-152 (160)
149 PRK05776 DNA topoisomerase I; 38.0 30 0.00065 27.9 2.5 35 30-69 596-634 (670)
150 COG2888 Predicted Zn-ribbon RN 37.8 22 0.00048 20.5 1.3 34 29-69 26-59 (61)
151 PF07295 DUF1451: Protein of u 37.5 20 0.00043 23.7 1.2 11 30-40 130-140 (146)
152 TIGR01057 topA_arch DNA topois 37.3 29 0.00062 27.5 2.3 29 30-66 589-618 (618)
153 TIGR00373 conserved hypothetic 37.3 21 0.00046 23.5 1.3 18 52-71 103-120 (158)
154 KOG3507|consensus 37.2 16 0.00035 21.1 0.6 27 30-69 20-46 (62)
155 COG1571 Predicted DNA-binding 36.3 20 0.00042 27.8 1.2 28 31-71 351-378 (421)
156 TIGR01206 lysW lysine biosynth 35.7 51 0.0011 18.3 2.6 7 32-38 4-10 (54)
157 COG1096 Predicted RNA-binding 35.7 19 0.00042 25.0 1.0 12 30-41 165-176 (188)
158 KOG2061|consensus 35.2 26 0.00057 26.6 1.7 54 15-68 29-91 (362)
159 COG2093 DNA-directed RNA polym 35.1 23 0.0005 20.6 1.1 12 31-42 19-30 (64)
160 TIGR00319 desulf_FeS4 desulfof 34.9 28 0.00061 17.0 1.3 11 57-69 6-16 (34)
161 PF01155 HypA: Hydrogenase exp 34.8 33 0.00072 21.3 1.9 14 30-43 86-99 (113)
162 smart00647 IBR In Between Ring 34.5 41 0.00088 17.8 2.0 8 31-38 19-28 (64)
163 PF08273 Prim_Zn_Ribbon: Zinc- 34.3 21 0.00045 18.7 0.8 13 31-43 4-16 (40)
164 cd00974 DSRD Desulforedoxin (D 34.1 29 0.00063 17.0 1.3 11 57-69 3-13 (34)
165 COG2995 PqiA Uncharacterized p 34.0 24 0.00052 27.3 1.3 19 23-41 30-49 (418)
166 PF08063 PADR1: PADR1 (NUC008) 34.0 21 0.00045 19.8 0.8 14 31-44 15-28 (55)
167 PRK00762 hypA hydrogenase nick 33.8 23 0.0005 22.5 1.0 11 31-41 93-103 (124)
168 PF13913 zf-C2HC_2: zinc-finge 33.7 19 0.00042 16.7 0.5 9 31-39 3-11 (25)
169 KOG2846|consensus 33.1 15 0.00032 27.6 0.1 35 26-68 216-250 (328)
170 PF13894 zf-C2H2_4: C2H2-type 33.0 36 0.00078 14.1 1.4 11 59-71 1-11 (24)
171 PF14952 zf-tcix: Putative tre 32.8 20 0.00043 19.5 0.5 27 31-71 12-38 (44)
172 PF11023 DUF2614: Protein of u 32.6 26 0.00056 22.6 1.1 12 30-41 69-80 (114)
173 PTZ00396 Casein kinase II subu 32.1 40 0.00087 24.3 2.2 19 19-37 137-155 (251)
174 PRK06266 transcription initiat 32.1 28 0.00061 23.4 1.3 18 52-71 111-128 (178)
175 PF10601 zf-LITAF-like: LITAF- 32.0 44 0.00096 18.9 2.0 16 28-43 56-71 (73)
176 PRK00564 hypA hydrogenase nick 32.0 33 0.00071 21.6 1.5 11 32-42 90-100 (117)
177 KOG3214|consensus 31.8 40 0.00086 21.5 1.8 37 29-71 22-58 (109)
178 PF10083 DUF2321: Uncharacteri 31.2 36 0.00078 23.1 1.7 10 29-38 38-47 (158)
179 PRK07726 DNA topoisomerase III 31.2 40 0.00087 27.0 2.2 29 31-67 611-639 (658)
180 PRK00420 hypothetical protein; 31.2 33 0.00072 21.8 1.5 11 30-40 23-33 (112)
181 PF09463 Opy2: Opy2 protein; 31.0 55 0.0012 16.8 2.0 16 32-47 10-25 (35)
182 PF14369 zf-RING_3: zinc-finge 30.8 34 0.00073 17.2 1.2 9 31-39 22-30 (35)
183 TIGR00515 accD acetyl-CoA carb 30.1 8.9 0.00019 27.9 -1.5 30 31-71 27-56 (285)
184 PRK08173 DNA topoisomerase III 29.7 48 0.001 27.6 2.5 28 30-69 726-758 (862)
185 PF06397 Desulfoferrod_N: Desu 29.3 33 0.00071 17.7 1.0 12 56-69 4-15 (36)
186 COG1645 Uncharacterized Zn-fin 29.0 35 0.00076 22.4 1.3 12 30-41 44-55 (131)
187 PF14255 Cys_rich_CPXG: Cystei 29.0 37 0.0008 18.8 1.2 14 31-44 1-14 (52)
188 COG5533 UBP5 Ubiquitin C-termi 28.9 33 0.00071 26.2 1.3 18 31-48 285-302 (415)
189 COG1998 RPS31 Ribosomal protei 28.9 24 0.00052 19.7 0.4 12 28-39 17-28 (51)
190 COG1405 SUA7 Transcription ini 28.9 47 0.001 24.2 2.1 26 32-68 3-28 (285)
191 smart00714 LITAF Possible memb 27.7 57 0.0012 18.1 1.9 16 28-43 50-65 (67)
192 PRK08351 DNA-directed RNA poly 27.6 32 0.0007 19.7 0.8 9 32-40 17-25 (61)
193 PF14122 YokU: YokU-like prote 27.0 71 0.0015 19.7 2.3 38 32-71 1-46 (87)
194 PF15135 UPF0515: Uncharacteri 26.7 31 0.00068 25.3 0.8 14 57-72 154-167 (278)
195 PF01214 CK_II_beta: Casein ki 26.6 56 0.0012 22.3 2.0 15 23-37 120-134 (184)
196 smart00401 ZnF_GATA zinc finge 26.4 30 0.00066 18.7 0.6 33 31-71 4-36 (52)
197 PRK12380 hydrogenase nickel in 26.1 40 0.00087 21.0 1.2 9 30-38 70-78 (113)
198 PF08790 zf-LYAR: LYAR-type C2 26.1 51 0.0011 16.1 1.3 11 59-71 1-11 (28)
199 COG3058 FdhE Uncharacterized p 26.0 35 0.00076 25.4 1.0 36 31-70 186-221 (308)
200 PF02591 DUF164: Putative zinc 26.0 36 0.00078 18.4 0.9 9 30-38 46-54 (56)
201 CHL00174 accD acetyl-CoA carbo 26.0 11 0.00024 27.7 -1.6 30 31-71 39-68 (296)
202 cd00730 rubredoxin Rubredoxin; 25.9 22 0.00048 19.4 -0.0 15 30-44 34-48 (50)
203 COG4640 Predicted membrane pro 25.8 38 0.00082 26.5 1.2 7 32-38 3-9 (465)
204 PF06906 DUF1272: Protein of u 25.8 33 0.00073 19.5 0.7 11 30-40 41-51 (57)
205 PRK08197 threonine synthase; V 25.6 62 0.0013 24.0 2.2 10 30-39 7-16 (394)
206 PF10080 DUF2318: Predicted me 25.4 1E+02 0.0022 19.2 2.9 27 32-71 37-63 (102)
207 COG1384 LysS Lysyl-tRNA synthe 25.3 65 0.0014 25.7 2.4 32 30-69 171-203 (521)
208 COG1885 Uncharacterized protei 25.3 35 0.00076 21.9 0.8 15 31-45 50-65 (115)
209 PF15616 TerY-C: TerY-C metal 25.2 66 0.0014 21.0 2.1 10 32-41 79-88 (131)
210 TIGR02300 FYDLN_acid conserved 25.2 39 0.00084 22.2 1.0 15 26-40 22-36 (129)
211 PHA02611 51 baseplate hub asse 24.7 72 0.0016 23.1 2.3 17 30-46 82-98 (249)
212 smart00532 LIGANc Ligase N fam 24.6 75 0.0016 24.5 2.6 28 30-67 399-426 (441)
213 PRK03976 rpl37ae 50S ribosomal 24.5 1.4E+02 0.003 18.4 3.3 32 28-71 34-65 (90)
214 KOG0006|consensus 24.3 78 0.0017 24.3 2.6 36 25-70 392-427 (446)
215 PF13465 zf-H2C2_2: Zinc-finge 24.1 64 0.0014 14.7 1.4 11 59-71 15-25 (26)
216 PF14400 Transglut_i_TM: Inact 23.7 1E+02 0.0022 20.8 2.9 22 37-61 68-89 (165)
217 cd01204 IRS_PTB Insulin recept 23.4 79 0.0017 20.1 2.1 23 33-55 52-74 (104)
218 PF01412 ArfGap: Putative GTPa 23.3 41 0.00088 20.8 0.8 29 30-68 13-41 (116)
219 COG1545 Predicted nucleic-acid 23.1 80 0.0017 20.4 2.2 9 31-39 44-52 (140)
220 PRK12286 rpmF 50S ribosomal pr 23.0 47 0.001 18.6 0.9 11 31-41 28-38 (57)
221 PRK14810 formamidopyrimidine-D 23.0 1E+02 0.0023 21.9 2.9 17 29-45 243-259 (272)
222 PF13912 zf-C2H2_6: C2H2-type 23.0 70 0.0015 14.2 1.4 11 59-71 2-12 (27)
223 PF06676 DUF1178: Protein of u 22.9 51 0.0011 21.9 1.3 14 29-42 31-44 (148)
224 COG0777 AccD Acetyl-CoA carbox 22.7 27 0.00058 25.9 -0.1 30 31-71 29-58 (294)
225 PRK00418 DNA gyrase inhibitor; 22.6 45 0.00098 19.2 0.8 13 29-41 5-17 (62)
226 PRK14724 DNA topoisomerase III 22.6 1.1E+02 0.0025 25.9 3.4 22 30-63 755-776 (987)
227 PF13878 zf-C2H2_3: zinc-finge 22.4 41 0.00089 17.4 0.6 9 30-38 13-21 (41)
228 PF09297 zf-NADH-PPase: NADH p 22.0 57 0.0012 15.6 1.1 11 31-41 4-14 (32)
229 PRK12496 hypothetical protein; 21.8 42 0.00091 22.3 0.7 10 31-40 144-153 (164)
230 TIGR00100 hypA hydrogenase nic 21.8 57 0.0012 20.4 1.2 9 30-38 70-78 (115)
231 PF00301 Rubredoxin: Rubredoxi 21.5 32 0.00069 18.6 0.0 13 30-42 34-46 (47)
232 PRK07561 DNA topoisomerase I s 21.5 1E+02 0.0022 25.6 3.0 32 30-69 587-622 (859)
233 PRK13945 formamidopyrimidine-D 21.5 1.2E+02 0.0026 21.6 3.0 16 30-45 254-269 (282)
234 KOG3277|consensus 21.4 76 0.0016 21.7 1.9 37 27-68 74-112 (165)
235 TIGR00575 dnlj DNA ligase, NAD 21.3 95 0.0021 25.1 2.7 27 31-67 393-419 (652)
236 cd00202 ZnF_GATA Zinc finger D 21.3 22 0.00047 19.6 -0.7 12 33-44 2-13 (54)
237 PF06200 tify: tify domain; I 21.2 70 0.0015 16.4 1.3 9 52-60 5-13 (36)
238 PRK06393 rpoE DNA-directed RNA 21.2 51 0.0011 19.1 0.9 9 32-40 19-27 (64)
239 PRK02935 hypothetical protein; 21.1 56 0.0012 20.9 1.1 10 30-39 70-79 (110)
240 PRK03824 hypA hydrogenase nick 21.1 70 0.0015 20.5 1.6 12 57-70 69-80 (135)
241 PRK05654 acetyl-CoA carboxylas 21.0 18 0.00039 26.4 -1.3 30 31-71 28-57 (292)
242 PRK14811 formamidopyrimidine-D 20.9 1.2E+02 0.0026 21.5 2.9 30 30-69 235-264 (269)
243 PHA02325 hypothetical protein 20.9 44 0.00096 19.7 0.6 24 30-53 3-29 (72)
244 PF06573 Churchill: Churchill 20.5 1.4E+02 0.003 19.2 2.8 14 31-44 28-41 (112)
245 COG5349 Uncharacterized protei 20.4 49 0.0011 21.7 0.7 12 30-41 21-32 (126)
246 PF13824 zf-Mss51: Zinc-finger 20.4 50 0.0011 18.6 0.7 10 29-38 13-22 (55)
247 COG4311 SoxD Sarcosine oxidase 20.2 76 0.0016 19.9 1.5 18 30-47 3-20 (97)
248 PF13917 zf-CCHC_3: Zinc knuck 20.2 46 0.001 17.6 0.5 17 30-46 4-20 (42)
249 COG2331 Uncharacterized protei 20.1 53 0.0012 19.9 0.8 13 56-70 10-22 (82)
250 KOG4080|consensus 20.1 45 0.00098 23.0 0.6 10 31-40 94-103 (176)
251 COG3880 Modulator of heat shoc 20.0 78 0.0017 21.8 1.7 33 32-68 2-34 (176)
No 1
>KOG2906|consensus
Probab=99.97 E-value=1.6e-32 Score=171.77 Aligned_cols=67 Identities=70% Similarity=1.280 Sum_probs=64.5
Q ss_pred ccCccCccccccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689 4 GRLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72 (72)
Q Consensus 4 ~~~~~~~ke~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~ 72 (72)
.|..++.|++|+|+||+++|++++.+...||+|||++|+|+|+|+||||||||+||.|++ |+|+|||
T Consensus 39 ~r~~~~~Kevd~vlgg~~a~~nv~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~--C~~~Wre 105 (105)
T KOG2906|consen 39 SRKYPKLKEVDDVLGGDEAWENVDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCK--CKHRWRE 105 (105)
T ss_pred ccccCchhhhhhhcCCcccccchhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhc--ccccccC
Confidence 356789999999999999999999999999999999999999999999999999999999 9999997
No 2
>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=99.92 E-value=1.2e-25 Score=139.49 Aligned_cols=60 Identities=47% Similarity=0.907 Sum_probs=52.2
Q ss_pred cccccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689 11 KEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72 (72)
Q Consensus 11 ke~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~ 72 (72)
++.++++.+.+..+++|++.+.||+|||++|+|+|+|+||||||||+||+|++ |||+|++
T Consensus 43 ~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~--C~~~w~~ 102 (104)
T TIGR01384 43 KIKETIIIREEDSETLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTK--CGYVWRE 102 (104)
T ss_pred ccccceeeccccccCCCcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCC--CCCeeEe
Confidence 44455544445568999999999999999999999999999999999999999 9999986
No 3
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.91 E-value=5e-25 Score=118.20 Aligned_cols=40 Identities=65% Similarity=1.290 Sum_probs=38.4
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~ 72 (72)
..||+||+++|+|+|+|+||||||||+||+|++ |||+|++
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~--C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTK--CGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCC--CCCEeCC
Confidence 369999999999999999999999999999999 9999986
No 4
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=99.90 E-value=3.6e-24 Score=114.28 Aligned_cols=39 Identities=77% Similarity=1.476 Sum_probs=35.0
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+.||+||+++++|+|+|+||||||||+||.|.+ |||+|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~--C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCN--CGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESS--STEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCC--CCCeeC
Confidence 479999999999999999999999999999999 999997
No 5
>KOG2691|consensus
Probab=99.87 E-value=4.3e-23 Score=130.90 Aligned_cols=65 Identities=43% Similarity=0.863 Sum_probs=60.4
Q ss_pred CccCccccccccCCccccccCCcc-eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689 6 LKIKPKEIDHVMGGAAAWENVDTT-EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72 (72)
Q Consensus 6 ~~~~~ke~~~v~~~~~~~~~~~~t-~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~ 72 (72)
..++.+|.+.|+.+.++||++|++ ++.||+||+++|+|||.|+|.+|+.|+|||+|++ |||+|+|
T Consensus 48 ~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~--C~h~wte 113 (113)
T KOG2691|consen 48 LSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCS--CGHRWTE 113 (113)
T ss_pred cccchhhHHHHHHhhccCCCcCccccccCCccCCcceEEEecccccccceEEEEEEecc--ccccccC
Confidence 345678999999999999999996 6899999999999999999999999999999999 9999986
No 6
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.85 E-value=7e-22 Score=125.92 Aligned_cols=49 Identities=59% Similarity=1.189 Sum_probs=44.0
Q ss_pred ccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689 22 AWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72 (72)
Q Consensus 22 ~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~ 72 (72)
..+++++..+.||+||+++|+|||.|+||||||||+||.|+. |||+|++
T Consensus 64 ~~~~~~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~--Cg~~wre 112 (113)
T COG1594 64 GAKTLPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTR--CGYRWRE 112 (113)
T ss_pred CccccccccccCCCCCCceeEEEeeehhccCCCceEEEEecc--cCCEeec
Confidence 344555667899999999999999999999999999999999 9999985
No 7
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.79 E-value=1e-19 Score=124.16 Aligned_cols=44 Identities=34% Similarity=0.639 Sum_probs=41.6
Q ss_pred CCc-ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 26 VDT-TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 26 ~~~-t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+|. +.+.||+|||++|+|+|+|+||||||||+||.|.+ |||+|+
T Consensus 138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~--CG~~wk 182 (195)
T PHA02998 138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRD--CKKHFK 182 (195)
T ss_pred cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCC--CCCccC
Confidence 566 67999999999999999999999999999999999 999997
No 8
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=99.71 E-value=8.2e-18 Score=121.54 Aligned_cols=42 Identities=52% Similarity=0.997 Sum_probs=39.7
Q ss_pred cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+..+.||+||+++++|||+|+||||||||+||+|++ |||+|+
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~--Cg~~w~ 297 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEE--CGNRWK 297 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCC--CCCeee
Confidence 345899999999999999999999999999999999 999997
No 9
>KOG2907|consensus
Probab=99.61 E-value=2e-16 Score=101.13 Aligned_cols=46 Identities=39% Similarity=0.825 Sum_probs=42.7
Q ss_pred cCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689 25 NVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72 (72)
Q Consensus 25 ~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~ 72 (72)
..+..+.+||+|||.++.|..+|+|||||+.|+||.|.+ |+|++++
T Consensus 69 ~ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~k--C~~k~~e 114 (116)
T KOG2907|consen 69 DGAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPK--CKYKFTE 114 (116)
T ss_pred cccchhccCcccCCchhhhhhhhcccccCCceEEEEcCc--cceeeec
Confidence 457778899999999999999999999999999999988 9999875
No 10
>KOG1105|consensus
Probab=99.17 E-value=2.5e-11 Score=88.02 Aligned_cols=40 Identities=55% Similarity=1.033 Sum_probs=38.7
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+.|-+|+.....|.|.|+||+|||||.|..|.+ ||++|+
T Consensus 255 ~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~e--cgnrWk 294 (296)
T KOG1105|consen 255 LFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNE--CGNRWK 294 (296)
T ss_pred ceeeccccccceeEEeeccCCCCCCcceeeeecc--cCCccc
Confidence 5899999999999999999999999999999999 999996
No 11
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=98.37 E-value=5.4e-07 Score=49.24 Aligned_cols=38 Identities=21% Similarity=0.514 Sum_probs=30.4
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.||.||++..+-...+ ..+.--.+||+|.|++|||+|+
T Consensus 1 ~CP~Cg~~a~ir~S~~--~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQ--LSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchh--hCcceEEEEEEECCCcCCCEEE
Confidence 5999999998876543 2445566999999999999996
No 12
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=98.01 E-value=6.3e-06 Score=49.13 Aligned_cols=39 Identities=21% Similarity=0.475 Sum_probs=29.4
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
..||.||+...+--..+ ..++-..+||.|.|++|||+|+
T Consensus 2 m~CP~Cg~~a~irtSr~--~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 2 FHCPLCQHAAHARTSRY--ITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred ccCCCCCCccEEEEChh--cChhhheeeeecCCCCCCCEEE
Confidence 47999999996554422 2344455999999999999996
No 13
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.15 E-value=0.0051 Score=42.72 Aligned_cols=46 Identities=22% Similarity=0.580 Sum_probs=33.2
Q ss_pred ccCCcceeeCCCCCCCceEEEEeeccCCCCC----ceEEEEecCCCCCceec
Q psy8689 24 ENVDTTEEKCPKCEHPRAYFMQIQTRSADEP----MTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 24 ~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~----mTlfy~C~~~~Cg~~w~ 71 (72)
.++|+.-+.|++||...++.=.-..|....+ .=++|.|++ |.++|-
T Consensus 11 ~~~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~--Cd~tWN 60 (203)
T COG4332 11 VGAPQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTH--CDYTWN 60 (203)
T ss_pred ccCChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeec--cCCccc
Confidence 3577778899999999987533333333333 338899999 999994
No 14
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=96.10 E-value=0.0099 Score=31.19 Aligned_cols=31 Identities=32% Similarity=0.780 Sum_probs=20.8
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~~ 69 (72)
..||.|| ...+. .+.+ -+ .|+.|.+ |+|.+.
T Consensus 2 ~~CP~Cg-~~lv~--r~~k---~g--~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 2 EKCPKCG-GPLVL--RRGK---KG--KFLGCSNYPECKYT 33 (39)
T ss_pred cCCCCCC-ceeEE--EECC---CC--CEEECCCCCCcCCe
Confidence 4799999 33322 2222 23 8999998 889875
No 15
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.95 E-value=0.0085 Score=30.97 Aligned_cols=36 Identities=19% Similarity=0.459 Sum_probs=22.2
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+.+.||+|+..-.+=-. + .. +...-..|.+ |+|.|.
T Consensus 1 M~i~Cp~C~~~y~i~d~-~--ip--~~g~~v~C~~--C~~~f~ 36 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDE-K--IP--PKGRKVRCSK--CGHVFF 36 (36)
T ss_pred CEEECCCCCCEEeCCHH-H--CC--CCCcEEECCC--CCCEeC
Confidence 45789999865432110 1 11 3335678988 999995
No 16
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=95.53 E-value=0.022 Score=33.17 Aligned_cols=15 Identities=33% Similarity=0.687 Sum_probs=8.9
Q ss_pred eCCCCCCCceEEEEe
Q psy8689 32 KCPKCEHPRAYFMQI 46 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~ 46 (72)
.||+||+.+...-++
T Consensus 2 ~C~KCg~~~~e~~~v 16 (64)
T PF09855_consen 2 KCPKCGNEEYESGEV 16 (64)
T ss_pred CCCCCCCcceecceE
Confidence 477777766554443
No 17
>PHA00626 hypothetical protein
Probab=95.34 E-value=0.014 Score=33.50 Aligned_cols=33 Identities=30% Similarity=0.674 Sum_probs=21.2
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.||+||+.+.+= -...| .+.. =|.|.+ ||+.|.
T Consensus 2 ~CP~CGS~~Ivr-cg~cr---~~sn-rYkCkd--CGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAK-EKTMR---GWSD-DYVCCD--CGYNDS 34 (59)
T ss_pred CCCCCCCceeee-eceec---ccCc-ceEcCC--CCCeec
Confidence 699999987762 11111 1122 488988 999875
No 18
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=95.16 E-value=0.0072 Score=30.41 Aligned_cols=27 Identities=33% Similarity=0.878 Sum_probs=13.5
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+||.|++...+. -...|+|-. |+|.|.
T Consensus 4 ~Cp~C~se~~y~-----------D~~~~vCp~--C~~ew~ 30 (30)
T PF08274_consen 4 KCPLCGSEYTYE-----------DGELLVCPE--CGHEWN 30 (30)
T ss_dssp --TTT-----EE------------SSSEEETT--TTEEE-
T ss_pred CCCCCCCcceec-----------cCCEEeCCc--ccccCC
Confidence 799999999872 112478966 999993
No 19
>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=95.08 E-value=0.019 Score=30.75 Aligned_cols=28 Identities=25% Similarity=0.691 Sum_probs=20.9
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.||+||+.+++.+.. ...|.|.. |+++
T Consensus 19 ~~CP~Cg~~~~~~~~~---------~~~~~C~~--C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT---------RGRYRCKA--CRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCC---------CCeEECCC--CCCc
Confidence 5699999996655442 45789998 9874
No 20
>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=94.89 E-value=0.041 Score=28.04 Aligned_cols=35 Identities=20% Similarity=0.586 Sum_probs=21.1
Q ss_pred ceeeCCCCCCCceEEEEeec-cCCCCCceEEEEecCCCCCceec
Q psy8689 29 TEEKCPKCEHPRAYFMQIQT-RSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~-rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+.+.||.|+..-. ++. ...+.+. -..|.+ |++.|.
T Consensus 1 M~~~CP~C~~~~~----v~~~~~~~~~~--~v~C~~--C~~~~~ 36 (38)
T TIGR02098 1 MRIQCPNCKTSFR----VVDSQLGANGG--KVRCGK--CGHVWY 36 (38)
T ss_pred CEEECCCCCCEEE----eCHHHcCCCCC--EEECCC--CCCEEE
Confidence 3578999987522 221 1222333 567988 999885
No 21
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.85 E-value=0.03 Score=28.92 Aligned_cols=36 Identities=19% Similarity=0.392 Sum_probs=21.8
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+.+.||+|+..-.+--. | .. .-..-..|.+ |+|.|.
T Consensus 1 M~i~CP~C~~~f~v~~~-~--l~--~~~~~vrC~~--C~~~f~ 36 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDD-K--LP--AGGRKVRCPK--CGHVFR 36 (37)
T ss_pred CEEECCCCCceEEcCHH-H--cc--cCCcEEECCC--CCcEee
Confidence 35789999865432211 1 11 2234678988 999995
No 22
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.78 E-value=0.042 Score=36.73 Aligned_cols=36 Identities=31% Similarity=0.837 Sum_probs=24.0
Q ss_pred eCCCCCCCceEEEEeeccCCCC--CceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADE--PMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE--~mTlfy~C~~~~Cg~~w~ 71 (72)
+||.||+....-.. .|...+ ..+.+|.|.+ ||.+|.
T Consensus 2 ~cp~c~~~~~~~~~--s~~~~~~~~~~~~~~c~~--c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRVID--SRPAEDGNAIRRRRECLA--CGKRFT 39 (154)
T ss_pred cCCCCCCCCCEeEe--ccccCCCCceeeeeeccc--cCCcce
Confidence 69999998742211 132334 3667899988 999874
No 23
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=94.33 E-value=0.059 Score=36.05 Aligned_cols=36 Identities=22% Similarity=0.618 Sum_probs=26.5
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEE--EEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTF--YKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlf--y~C~~~~Cg~~w~ 71 (72)
.||.|||.+.-- +-+|+++++.++= -.|.+ ||++|.
T Consensus 2 ~CP~C~~~dtkV--iDSR~~~dg~~IRRRReC~~--C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRV--LDSRLVEDGQSIRRRRECLE--CHERFT 39 (147)
T ss_pred CCCCCCCCCCEe--eeccccCCCCeeeecccCCc--cCCccc
Confidence 699999877644 3458888887754 45877 998885
No 24
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=94.22 E-value=0.11 Score=28.54 Aligned_cols=34 Identities=21% Similarity=0.688 Sum_probs=22.2
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.||.||.....+.. +..+..-.-+|.|.. ||..
T Consensus 2 kPCPfCGg~~~~~~~---~~~~~~~~~~~~C~~--Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR---GFDPLDLSHYFECST--CGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe---ccCCCCCEEEEECCC--CCCC
Confidence 479999997765532 123344455668988 9875
No 25
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=94.08 E-value=0.058 Score=30.26 Aligned_cols=48 Identities=23% Similarity=0.322 Sum_probs=29.3
Q ss_pred cccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 13 IDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 13 ~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
+-|+|-|++.-....+..+.|++|....-.+. ..|+..+-|+|.. ||+
T Consensus 5 i~d~L~G~d~~~~~~r~aLIC~~C~~hNGla~------~~~~~~i~y~C~~--Cg~ 52 (54)
T PF10058_consen 5 ILDVLLGDDPTSPSNRYALICSKCFSHNGLAP------KEEFEEIQYRCPY--CGA 52 (54)
T ss_pred HHHHHhCCCCccccCceeEECcccchhhcccc------cccCCceEEEcCC--CCC
Confidence 34455454442223334578999975555332 3567777899977 986
No 26
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=93.86 E-value=0.053 Score=31.96 Aligned_cols=35 Identities=31% Similarity=0.710 Sum_probs=21.0
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCce--------EE--EEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMT--------TF--YKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mT--------lf--y~C~~~~Cg~~ 69 (72)
.+||+||+++..--++ +...+... .| ..|.+ ||++
T Consensus 5 ~kCpKCgn~~~~ekei--~~tg~~lskifdvq~n~f~~itCk~--CgYt 49 (68)
T COG3478 5 FKCPKCGNTNYEEKEI--AATGGGLSKIFDVQNNKFIVITCKN--CGYT 49 (68)
T ss_pred ccCCCcCCcchhhcee--eccCCCcceeEEecccEEEEEEecc--CCch
Confidence 3599999987654443 33433332 23 34888 9874
No 27
>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=93.16 E-value=0.1 Score=27.46 Aligned_cols=28 Identities=36% Similarity=0.806 Sum_probs=19.2
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
.||.||+...++ - +++-.++|.+ ||...
T Consensus 2 ~Cp~Cg~~~~~~-D--------~~~g~~vC~~--CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVF-D--------PERGELVCPN--CGLVL 29 (43)
T ss_dssp SBTTTSSSEEEE-E--------TTTTEEEETT--T-BBE
T ss_pred CCcCCcCCceEE-c--------CCCCeEECCC--CCCEe
Confidence 699999988333 2 3455679988 99753
No 28
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=93.09 E-value=0.16 Score=35.51 Aligned_cols=42 Identities=19% Similarity=0.292 Sum_probs=28.6
Q ss_pred cceeeCCCCCCCceEEEEeeccCCCCC--ceEEEEecCCCCCceecC
Q psy8689 28 TTEEKCPKCEHPRAYFMQIQTRSADEP--MTTFYKCCNIKCGFRWRE 72 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~--mTlfy~C~~~~Cg~~w~~ 72 (72)
.+.+.||.||+ .....+......-.+ |-..++|.+ ||+|..+
T Consensus 12 ~~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~--CgYR~~D 55 (201)
T COG1779 12 ETRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCER--CGYRSTD 55 (201)
T ss_pred eeeecCCcccc-eeeEEEeeecCCccceEEEEEEEccc--cCCcccc
Confidence 34689999999 555555454444444 445677999 9999764
No 29
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=92.83 E-value=0.076 Score=33.95 Aligned_cols=27 Identities=33% Similarity=0.865 Sum_probs=20.1
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.||+|++..+|--. -.|+|-. |+|-|.
T Consensus 4 ~CP~C~seytY~dg-----------~~~iCpe--C~~EW~ 30 (109)
T TIGR00686 4 PCPKCNSEYTYHDG-----------TQLICPS--CLYEWN 30 (109)
T ss_pred cCCcCCCcceEecC-----------CeeECcc--cccccc
Confidence 69999998775422 1388955 999995
No 30
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=92.72 E-value=0.065 Score=36.17 Aligned_cols=36 Identities=33% Similarity=0.720 Sum_probs=25.6
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEE--EEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTF--YKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlf--y~C~~~~Cg~~w~ 71 (72)
.||.|+|...--. -.|.++++.++= -.|.+ ||++|.
T Consensus 2 ~CPfC~~~~tkVi--DSR~~edg~aIRRRReC~~--C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVI--DSRPAEEGNAIRRRRECLE--CGERFT 39 (156)
T ss_pred CCCCCCCCCCeee--ecccccccchhhhhhcccc--cccccc
Confidence 6888888877543 457888876643 45877 888875
No 31
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=92.07 E-value=0.28 Score=27.12 Aligned_cols=34 Identities=26% Similarity=0.577 Sum_probs=21.2
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
..||-||+......+. ...+..+..+..|.+ ||.
T Consensus 4 kPCPFCG~~~~~~~~~--~~~~~~~~~~V~C~~--Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQD--EGFDYGMYYYVECTD--CGA 37 (61)
T ss_pred cCCCCCCCcceEeecc--cCCCCCCEEEEEcCC--CCC
Confidence 5799997666655442 222333335666988 986
No 32
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=91.69 E-value=0.13 Score=40.12 Aligned_cols=41 Identities=24% Similarity=0.549 Sum_probs=28.5
Q ss_pred eeeCCCCCCCceEEE-EeeccCCCCCceEEEEecCCCCCceecC
Q psy8689 30 EEKCPKCEHPRAYFM-QIQTRSADEPMTTFYKCCNIKCGFRWRE 72 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~-q~Q~rsadE~mTlfy~C~~~~Cg~~w~~ 72 (72)
-+.||.||+.-..-| +++--....+.+.+|+|.. ||+.|.+
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~--Cg~~i~e 241 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPH--CGCEIEE 241 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCC--CcCCCCH
Confidence 479999998776644 3332111168899999966 9998753
No 33
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=91.15 E-value=0.62 Score=23.93 Aligned_cols=33 Identities=24% Similarity=0.525 Sum_probs=16.5
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
.-||+||-.-..-.-.| .+....|.|.||.|.+
T Consensus 2 hlcpkcgvgvl~pvy~~-----kgeikvfrcsnpacdy 34 (36)
T PF09151_consen 2 HLCPKCGVGVLEPVYNQ-----KGEIKVFRCSNPACDY 34 (36)
T ss_dssp -B-TTTSSSBEEEEE-T-----TS-EEEEEES-TT---
T ss_pred ccCCccCceEEEEeecC-----CCcEEEEEcCCCcccc
Confidence 35999987654432222 2456678899999975
No 34
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=91.06 E-value=0.25 Score=29.09 Aligned_cols=29 Identities=31% Similarity=0.734 Sum_probs=22.9
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+++||.|||...+|--.| ....|.. ||..
T Consensus 19 ~VkCpdC~N~q~vFshas---------t~V~C~~--CG~~ 47 (67)
T COG2051 19 RVKCPDCGNEQVVFSHAS---------TVVTCLI--CGTT 47 (67)
T ss_pred EEECCCCCCEEEEeccCc---------eEEEecc--cccE
Confidence 689999999999996644 3467888 8864
No 35
>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=90.43 E-value=0.16 Score=28.79 Aligned_cols=30 Identities=37% Similarity=0.738 Sum_probs=19.5
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
++++||.|++...+|-..|+ -..|.. ||..
T Consensus 6 m~VkCp~C~~~q~vFSha~t---------~V~C~~--Cg~~ 35 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQT---------VVKCVV--CGTV 35 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS----------EE-SS--STSE
T ss_pred EEEECCCCCCeeEEEecCCe---------EEEccc--CCCE
Confidence 47899999999999966553 256877 8764
No 36
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=90.40 E-value=0.56 Score=24.35 Aligned_cols=30 Identities=27% Similarity=0.654 Sum_probs=18.9
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+||+|+.. ..-.+. .. ...+.|.. |+-.|-
T Consensus 1 ~CP~C~~~-l~~~~~------~~-~~id~C~~--C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRL------GD-VEIDVCPS--CGGIWF 30 (41)
T ss_pred CcCCCCcc-cceEEE------CC-EEEEECCC--CCeEEc
Confidence 59999883 322221 12 45577977 999985
No 37
>PRK10220 hypothetical protein; Provisional
Probab=90.30 E-value=0.19 Score=32.19 Aligned_cols=27 Identities=33% Similarity=0.947 Sum_probs=19.9
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.||+|++..+|--. . -|+|-. |+|-|.
T Consensus 5 ~CP~C~seytY~d~--------~---~~vCpe--C~hEW~ 31 (111)
T PRK10220 5 HCPKCNSEYTYEDN--------G---MYICPE--CAHEWN 31 (111)
T ss_pred cCCCCCCcceEcCC--------C---eEECCc--ccCcCC
Confidence 69999988775321 1 488955 999996
No 38
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=90.13 E-value=0.39 Score=34.25 Aligned_cols=36 Identities=28% Similarity=0.732 Sum_probs=18.6
Q ss_pred eeeCCCCCCCceEEEEeeccCCC-CCceEEEEecCCCCCceec
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSAD-EPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsad-E~mTlfy~C~~~~Cg~~w~ 71 (72)
...||-||+.-..-.-.. .+ ++- .|..|.- |++.|+
T Consensus 172 ~g~CPvCGs~P~~s~l~~---~~~~G~-R~L~Cs~--C~t~W~ 208 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRG---GEREGK-RYLHCSL--CGTEWR 208 (290)
T ss_dssp -SS-TTT---EEEEEEE---------E-EEEEETT--T--EEE
T ss_pred CCcCCCCCCcCceEEEec---CCCCcc-EEEEcCC--CCCeee
Confidence 368999999876654322 22 244 8999988 999996
No 39
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=90.01 E-value=0.35 Score=27.84 Aligned_cols=30 Identities=30% Similarity=0.728 Sum_probs=23.4
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
++++||.|++...+|--.|+ -..|.. ||..
T Consensus 10 ~~VkCp~C~n~q~vFsha~t---------~V~C~~--Cg~~ 39 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHAST---------VVRCLV--CGKT 39 (59)
T ss_pred EEEECCCCCCeEEEEecCCc---------EEECcc--cCCC
Confidence 46899999999999976542 366877 8864
No 40
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.69 E-value=0.38 Score=25.60 Aligned_cols=12 Identities=25% Similarity=0.797 Sum_probs=7.5
Q ss_pred EEEecCCCCCceec
Q psy8689 58 FYKCCNIKCGFRWR 71 (72)
Q Consensus 58 fy~C~~~~Cg~~w~ 71 (72)
.|+|.. ||+.+.
T Consensus 20 ~~vC~~--Cg~~~~ 31 (52)
T smart00661 20 RFVCRK--CGYEEP 31 (52)
T ss_pred EEECCc--CCCeEE
Confidence 566755 776653
No 41
>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=89.64 E-value=0.37 Score=24.86 Aligned_cols=26 Identities=35% Similarity=0.961 Sum_probs=18.4
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
..|+.|++. +|... + =||.|.. |||.
T Consensus 9 ~~C~~C~~~---~~~~~-----d---G~~yC~~--cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR---WFYSD-----D---GFYYCDR--CGHQ 34 (36)
T ss_pred CcCCCCCCe---EeEcc-----C---CEEEhhh--CceE
Confidence 469999998 44422 2 2788988 9986
No 42
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=89.08 E-value=0.8 Score=30.83 Aligned_cols=37 Identities=24% Similarity=0.476 Sum_probs=17.0
Q ss_pred CCCCCCCceEEEEeeccCCCCC--ceEEEEecCCCCCceec
Q psy8689 33 CPKCEHPRAYFMQIQTRSADEP--MTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 33 Cp~Cg~~~a~~~q~Q~rsadE~--mTlfy~C~~~~Cg~~w~ 71 (72)
||.||++...+....+...-=. +-.-|.|-. ||++..
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~--CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEK--CGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCC--CCCchh
Confidence 6777766444422222221111 223456655 777654
No 43
>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=88.66 E-value=1.2 Score=26.75 Aligned_cols=37 Identities=22% Similarity=0.548 Sum_probs=19.6
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+.+.||.|||..++-..+- +. ..+-...|.. ||..|.
T Consensus 21 ~~F~CPfC~~~~sV~v~id-kk---~~~~~~~C~~--Cg~~~~ 57 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKID-KK---EGIGILSCRV--CGESFQ 57 (81)
T ss_dssp S----TTT--SS-EEEEEE-TT---TTEEEEEESS--S--EEE
T ss_pred ceEcCCcCCCCCeEEEEEE-cc---CCEEEEEecC--CCCeEE
Confidence 3589999999999887653 21 4555677999 998764
No 44
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=88.37 E-value=0.22 Score=34.80 Aligned_cols=36 Identities=22% Similarity=0.482 Sum_probs=22.4
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+.||.||..+..---+-.| +-..-+.|.+ ||+.|.
T Consensus 6 y~~Cp~Cg~eev~hEVik~~----g~~~lvrC~e--CG~V~~ 41 (201)
T COG1326 6 YIECPSCGSEEVSHEVIKER----GREPLVRCEE--CGTVHP 41 (201)
T ss_pred EEECCCCCcchhhHHHHHhc----CCceEEEccC--CCcEee
Confidence 47899999554411111111 2236788998 999995
No 45
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=87.07 E-value=1.9 Score=27.38 Aligned_cols=35 Identities=23% Similarity=0.584 Sum_probs=25.6
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
.+.||.|||...+--.+- -..+.-+..|.+ ||.++
T Consensus 22 ~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~--CGls~ 56 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVK----KTVNIGTAVCGN--CGLSF 56 (104)
T ss_pred eEecCccCCeeeeEEEEE----ecCceeEEEccc--CcceE
Confidence 489999999988744332 124666788999 99876
No 46
>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=86.56 E-value=0.72 Score=25.95 Aligned_cols=30 Identities=33% Similarity=0.874 Sum_probs=22.2
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
|...||.||+.... ......|.|.+ ||+.+
T Consensus 27 TSq~C~~CG~~~~~----------~~~~r~~~C~~--Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----------RRSGRVFTCPN--CGFEM 56 (69)
T ss_pred CccCccCccccccc----------ccccceEEcCC--CCCEE
Confidence 45679999998774 23445788988 99875
No 47
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=86.51 E-value=0.91 Score=27.88 Aligned_cols=30 Identities=30% Similarity=0.662 Sum_probs=23.8
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
++++||.|++...+|-..|+ -..|.. ||..
T Consensus 34 m~VkCp~C~n~q~VFShA~t---------~V~C~~--Cg~~ 63 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQT---------VVLCGG--CSSQ 63 (85)
T ss_pred EEEECCCCCCeeEEEecCce---------EEEccc--cCCE
Confidence 47899999999999987653 366877 8764
No 48
>PLN00209 ribosomal protein S27; Provisional
Probab=86.50 E-value=0.87 Score=28.02 Aligned_cols=30 Identities=27% Similarity=0.482 Sum_probs=23.7
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
++++||.|++...+|-..|+ -..|.. ||..
T Consensus 35 m~VkCp~C~n~q~VFShA~t---------~V~C~~--Cg~~ 64 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQT---------VVVCGS--CQTV 64 (86)
T ss_pred EEEECCCCCCeeEEEecCce---------EEEccc--cCCE
Confidence 46899999999999987552 366877 8764
No 49
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=86.43 E-value=0.62 Score=25.63 Aligned_cols=29 Identities=28% Similarity=0.776 Sum_probs=18.8
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
....||+||+. |.-.. . -.+.|-. ||+.+
T Consensus 19 ~~~fCP~Cg~~---~m~~~-~-------~r~~C~~--Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSG---FMAEH-L-------DRWHCGK--CGYTE 47 (50)
T ss_pred ccCcCcCCCcc---hhecc-C-------CcEECCC--cCCEE
Confidence 44689999986 22211 1 2577988 99874
No 50
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=85.47 E-value=1.6 Score=29.18 Aligned_cols=37 Identities=22% Similarity=0.473 Sum_probs=17.5
Q ss_pred eCCCCCCCceEEEEeeccCCCCCce--EEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMT--TFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mT--lfy~C~~~~Cg~~w~ 71 (72)
.||.||++.. +....+....-.-. .-|.|-. ||++..
T Consensus 2 ~Cp~C~~~~~-~~~~~~~IP~F~evii~sf~C~~--CGyk~~ 40 (160)
T smart00709 2 DCPSCGGNGT-TRMLLTSIPYFREVIIMSFECEH--CGYRNN 40 (160)
T ss_pred cCCCCCCCCE-EEEEEecCCCcceEEEEEEECCC--CCCccc
Confidence 4777776543 33323333322222 2355655 777654
No 51
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=84.72 E-value=1.6 Score=30.05 Aligned_cols=38 Identities=24% Similarity=0.506 Sum_probs=18.0
Q ss_pred eCCCCCCCceE-EEEee-ccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAY-FMQIQ-TRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~-~~q~Q-~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.||.||.+..+ ..... +---.+=+-.-|.|-. ||++..
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~--CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEH--CGYRSN 41 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCC--CCCccc
Confidence 58888765333 22212 1111111233466766 887764
No 52
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=83.79 E-value=2.2 Score=21.52 Aligned_cols=29 Identities=24% Similarity=0.524 Sum_probs=21.5
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
...|+.||++..++ +.+ -+++|.. ||..+
T Consensus 3 ~~~C~~C~~~~i~~-~~~---------~~~~C~~--Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN-KED---------DYEVCIF--CGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE-ecC---------CeEEccc--CCcEe
Confidence 36899999999765 222 2788988 99765
No 53
>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=83.43 E-value=0.99 Score=21.98 Aligned_cols=25 Identities=32% Similarity=0.677 Sum_probs=10.3
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCC-CC
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI-KC 66 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~-~C 66 (72)
.||.||+.-. |..+|. .+.|.|+ .|
T Consensus 1 ~CP~C~s~l~-------~~~~ev---~~~C~N~l~C 26 (28)
T PF03119_consen 1 TCPVCGSKLV-------REEGEV---DIRCPNPLSC 26 (28)
T ss_dssp B-TTT--BEE-------E-CCTT---CEEE--CGC-
T ss_pred CcCCCCCEeE-------cCCCCE---eEECCCCCcC
Confidence 4999998765 223333 4567775 45
No 54
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=83.31 E-value=2.2 Score=27.99 Aligned_cols=30 Identities=27% Similarity=0.674 Sum_probs=23.9
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.|+.|++.+..+.- . .-.+|..|.. ||..
T Consensus 103 VlC~~C~spdT~l~k-~------~r~~~l~C~A--CGa~ 132 (138)
T PRK03988 103 VICPECGSPDTKLIK-E------GRIWVLKCEA--CGAE 132 (138)
T ss_pred EECCCCCCCCcEEEE-c------CCeEEEEccc--CCCC
Confidence 789999999987743 2 3478889998 9974
No 55
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=83.29 E-value=0.54 Score=33.61 Aligned_cols=36 Identities=25% Similarity=0.706 Sum_probs=24.9
Q ss_pred CCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 26 VDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 26 ~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
.+.-.+.||.|.|....+ |-++-|.. =|+|.+ |+|.
T Consensus 188 ~~~~alIC~~C~hhngl~-----~~~ek~~~-efiC~~--Cn~~ 223 (251)
T COG5415 188 SPFKALICPQCHHHNGLY-----RLAEKPII-EFICPH--CNHK 223 (251)
T ss_pred Cchhhhcccccccccccc-----ccccccch-heeccc--chhh
Confidence 344458999999888766 44555555 567987 9873
No 56
>PF14353 CpXC: CpXC protein
Probab=83.08 E-value=1.7 Score=27.22 Aligned_cols=11 Identities=36% Similarity=0.911 Sum_probs=6.1
Q ss_pred eeCCCCCCCce
Q psy8689 31 EKCPKCEHPRA 41 (72)
Q Consensus 31 ~~Cp~Cg~~~a 41 (72)
+.||+||+.--
T Consensus 2 itCP~C~~~~~ 12 (128)
T PF14353_consen 2 ITCPHCGHEFE 12 (128)
T ss_pred cCCCCCCCeeE
Confidence 45666665433
No 57
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=82.72 E-value=2.9 Score=21.52 Aligned_cols=32 Identities=16% Similarity=0.469 Sum_probs=20.3
Q ss_pred cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecC
Q psy8689 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN 63 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~ 63 (72)
+.++.||.|++.+.++.--+. ..+- .=|.|.+
T Consensus 3 ~i~v~CP~C~s~~~v~k~G~~---~~G~-qryrC~~ 34 (36)
T PF03811_consen 3 KIDVHCPRCQSTEGVKKNGKS---PSGH-QRYRCKD 34 (36)
T ss_pred cEeeeCCCCCCCCcceeCCCC---CCCC-EeEecCc
Confidence 346899999999977754332 1222 3366766
No 58
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=82.64 E-value=2.4 Score=27.69 Aligned_cols=30 Identities=23% Similarity=0.708 Sum_probs=23.1
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.||.|++.+..+.- . .-..|..|.. ||..
T Consensus 98 VlC~~C~sPdT~l~k-~------~r~~~l~C~A--CGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIK-E------GRVSLLKCEA--CGAK 127 (133)
T ss_pred EECCCCCCCCcEEEE-e------CCeEEEeccc--CCCC
Confidence 789999999987653 2 3355778988 9975
No 59
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=82.40 E-value=1.3 Score=31.58 Aligned_cols=39 Identities=23% Similarity=0.448 Sum_probs=19.8
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+.||.||+.+..-+.. ....+++.-..++|-. |+.-++
T Consensus 211 R~~Cp~Cg~~~~~~l~~-~~~e~~~~~rve~C~~--C~~YlK 249 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEY-FTVEGEPAYRVEVCES--CGSYLK 249 (290)
T ss_dssp TTS-TTT---SS-EEE---------SEEEEEETT--TTEEEE
T ss_pred CCCCcCCCCCCCcceee-EecCCCCcEEEEECCc--ccchHH
Confidence 46899999887764442 2235666777889988 998664
No 60
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=82.05 E-value=2.4 Score=27.34 Aligned_cols=30 Identities=30% Similarity=0.714 Sum_probs=24.1
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.||.|++.+..+.-. .-.+|..|.. ||..
T Consensus 94 VlC~~C~spdT~l~k~-------~r~~~l~C~a--CGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE-------GRLIFLKCKA--CGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEE-------TTCCEEEETT--TSCE
T ss_pred EEcCCCCCCccEEEEc-------CCEEEEEecc--cCCc
Confidence 7899999999887653 2357889998 9975
No 61
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=82.05 E-value=0.053 Score=29.43 Aligned_cols=30 Identities=30% Similarity=0.604 Sum_probs=23.9
Q ss_pred CCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 36 CEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 36 Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
|.|.-+ ....|+|+.||..+.+-.|.. |+.
T Consensus 13 C~H~f~-~~E~Q~RAGDE~VSfI~~C~~--C~~ 42 (43)
T PF11792_consen 13 CKHKFV-TIEKQLRAGDEAVSFIKYCQK--CGQ 42 (43)
T ss_pred ceeeee-ehhhhhcccchHHHHHHHHHH--hCC
Confidence 777666 445699999999998888987 875
No 62
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=81.61 E-value=3.7 Score=23.60 Aligned_cols=32 Identities=25% Similarity=0.624 Sum_probs=21.0
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
+.||+|+....+-+=. |.-.-+..|+. |||+-
T Consensus 10 A~CP~C~~~Dtl~~~~------e~~~e~vECv~--Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWK------ENNIELVECVE--CGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEE------eCCceEEEecc--CCCcc
Confidence 5899999877763221 11224678998 99874
No 63
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=80.80 E-value=2.3 Score=28.33 Aligned_cols=38 Identities=18% Similarity=0.500 Sum_probs=17.2
Q ss_pred eeCCCCCCCceEEEEeeccCCCCC--ceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEP--MTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~--mTlfy~C~~~~Cg~~w~ 71 (72)
..||.||++...-+ ..+....=+ +-.-|.|-+ ||++..
T Consensus 2 s~Cp~C~~~~~~~~-~~~~IP~F~evii~sf~C~~--CGyk~~ 41 (161)
T PF03367_consen 2 SLCPNCGENGTTRI-LLTDIPYFKEVIIMSFECEH--CGYKNN 41 (161)
T ss_dssp EE-TTTSSCCEEEE-EEEEETTTEEEEEEEEE-TT--T--EEE
T ss_pred CcCCCCCCCcEEEE-EEEcCCCCceEEEEEeECCC--CCCEee
Confidence 36888887765433 222222112 223466877 888765
No 64
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=80.50 E-value=1 Score=24.12 Aligned_cols=14 Identities=21% Similarity=0.536 Sum_probs=11.2
Q ss_pred ceeeCCCCCCCceE
Q psy8689 29 TEEKCPKCEHPRAY 42 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~ 42 (72)
..+.||.||++-.+
T Consensus 18 ~~irC~~CG~rIly 31 (44)
T smart00659 18 DVVRCRECGYRILY 31 (44)
T ss_pred CceECCCCCceEEE
Confidence 45899999998663
No 65
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=80.19 E-value=1.1 Score=32.42 Aligned_cols=33 Identities=27% Similarity=0.703 Sum_probs=11.5
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
...||.||+....-|..-. |..=|| |.+ |+..+
T Consensus 31 n~yCP~Cg~~~L~~f~NN~-----PVaDF~-C~~--C~eey 63 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNR-----PVADFY-CPN--CNEEY 63 (254)
T ss_dssp H---TTT--SS-EE-------------EEE--TT--T--EE
T ss_pred CCcCCCCCChhHhhccCCC-----ccceeE-CCC--CchHH
Confidence 4689999999766555433 444455 888 98765
No 66
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=79.61 E-value=4.7 Score=23.68 Aligned_cols=33 Identities=27% Similarity=0.717 Sum_probs=21.4
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+.||+|+....+-+=.. + -.-+..|+. |||+-+
T Consensus 9 a~CP~C~~~D~i~~~~e-----~-~ve~vECV~--CGy~e~ 41 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRE-----N-GVEYVECVE--CGYTER 41 (71)
T ss_pred ccCCCCcCccEEEEEEe-----C-CceEEEecC--CCCeec
Confidence 58999998776532211 1 144677998 999743
No 67
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=79.34 E-value=1.1 Score=28.00 Aligned_cols=32 Identities=22% Similarity=0.609 Sum_probs=18.7
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.+.||.||+... -. -.. . .+...+|.+ ||+.
T Consensus 20 t~f~CP~Cge~~v-~v--~~~---k-~~~h~~C~~--CG~y 51 (99)
T PRK14892 20 KIFECPRCGKVSI-SV--KIK---K-NIAIITCGN--CGLY 51 (99)
T ss_pred cEeECCCCCCeEe-ee--ecC---C-CcceEECCC--CCCc
Confidence 3578999995322 11 111 1 466777877 8864
No 68
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=78.91 E-value=3.9 Score=25.85 Aligned_cols=30 Identities=33% Similarity=0.756 Sum_probs=23.2
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.|+.|++.+..+.-. .-.+|..|.. ||.+
T Consensus 81 VlC~~C~spdT~l~k~-------~r~~~l~C~a--CGa~ 110 (110)
T smart00653 81 VLCPECGSPDTELIKE-------NRLFFLKCEA--CGAR 110 (110)
T ss_pred EECCCCCCCCcEEEEe-------CCeEEEEccc--cCCC
Confidence 7899999999877542 2367888988 9964
No 69
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=78.77 E-value=7.4 Score=20.42 Aligned_cols=37 Identities=41% Similarity=1.016 Sum_probs=22.0
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCC---CCc-eec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIK---CGF-RWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~---Cg~-~w~ 71 (72)
.|+ ||..-.++.. . +..+.+=..||.|.+.. |++ .|.
T Consensus 2 ~C~-Cg~~~~~~~s-~-k~~~N~GR~Fy~C~~~~~~~C~fF~W~ 42 (45)
T PF06839_consen 2 KCP-CGEPAVRRTS-K-KTGPNPGRRFYKCPNYKDKGCNFFQWE 42 (45)
T ss_pred CCC-CCCEeEEEEE-e-CCCCCCCCcceECCCCCCCCcCCEEec
Confidence 477 7744433333 2 25667788999998644 654 343
No 70
>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=77.93 E-value=2.1 Score=20.42 Aligned_cols=10 Identities=30% Similarity=0.849 Sum_probs=7.1
Q ss_pred ceeeCCCCCC
Q psy8689 29 TEEKCPKCEH 38 (72)
Q Consensus 29 t~~~Cp~Cg~ 38 (72)
+...||+||.
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4578888874
No 71
>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=77.78 E-value=1.1 Score=22.59 Aligned_cols=12 Identities=33% Similarity=0.888 Sum_probs=8.6
Q ss_pred eeeCCCCCCCce
Q psy8689 30 EEKCPKCEHPRA 41 (72)
Q Consensus 30 ~~~Cp~Cg~~~a 41 (72)
.+.|+.||++-.
T Consensus 17 ~irC~~CG~RIl 28 (32)
T PF03604_consen 17 PIRCPECGHRIL 28 (32)
T ss_dssp TSSBSSSS-SEE
T ss_pred cEECCcCCCeEE
Confidence 479999998743
No 72
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=77.29 E-value=1.8 Score=31.90 Aligned_cols=38 Identities=21% Similarity=0.662 Sum_probs=25.3
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
...||-||+.-..-. ++....+++ -.|..|.- |++.|.
T Consensus 184 ~~~CPvCGs~P~~s~-~~~~~~~~G-~RyL~Csl--C~teW~ 221 (305)
T TIGR01562 184 RTLCPACGSPPVASM-VRQGGKETG-LRYLSCSL--CATEWH 221 (305)
T ss_pred CCcCCCCCChhhhhh-hcccCCCCC-ceEEEcCC--CCCccc
Confidence 358999998764322 122222344 57889988 999996
No 73
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=76.68 E-value=4.6 Score=27.78 Aligned_cols=30 Identities=20% Similarity=0.620 Sum_probs=23.7
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.|+.|++.+..+.. . .-++|..|.. ||..
T Consensus 99 V~C~~C~~pdT~l~k-~------~~~~~l~C~a--CGa~ 128 (201)
T PRK12336 99 VICSECGLPDTRLVK-E------DRVLMLRCDA--CGAH 128 (201)
T ss_pred EECCCCCCCCcEEEE-c------CCeEEEEccc--CCCC
Confidence 789999999987753 1 3577889988 9964
No 74
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=75.39 E-value=2.8 Score=30.93 Aligned_cols=37 Identities=19% Similarity=0.547 Sum_probs=24.8
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
...||-||+.-..-. +.. ..+++ -.|..|.- |++.|.
T Consensus 187 ~~~CPvCGs~P~~s~-v~~-~~~~G-~RyL~Csl--C~teW~ 223 (309)
T PRK03564 187 RQFCPVCGSMPVSSV-VQI-GTTQG-LRYLHCNL--CESEWH 223 (309)
T ss_pred CCCCCCCCCcchhhe-eec-cCCCC-ceEEEcCC--CCCccc
Confidence 468999998765332 122 12333 37899988 999996
No 75
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=74.75 E-value=1.3 Score=24.59 Aligned_cols=11 Identities=45% Similarity=1.105 Sum_probs=8.9
Q ss_pred eeCCCCCCCce
Q psy8689 31 EKCPKCEHPRA 41 (72)
Q Consensus 31 ~~Cp~Cg~~~a 41 (72)
..||+||+...
T Consensus 14 ~~Cp~CGN~~v 24 (49)
T PF12677_consen 14 CKCPKCGNDKV 24 (49)
T ss_pred ccCcccCCcEe
Confidence 68999998654
No 76
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=74.39 E-value=3.9 Score=22.20 Aligned_cols=16 Identities=31% Similarity=1.107 Sum_probs=9.4
Q ss_pred CceEEEEecCCCCCceec
Q psy8689 54 PMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 54 ~mTlfy~C~~~~Cg~~w~ 71 (72)
...++..|.. |||.|+
T Consensus 24 ~~~v~W~C~~--Cgh~w~ 39 (55)
T PF14311_consen 24 NKKVWWKCPK--CGHEWK 39 (55)
T ss_pred CCEEEEECCC--CCCeeE
Confidence 3445566655 666665
No 77
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=74.17 E-value=3.5 Score=25.51 Aligned_cols=31 Identities=29% Similarity=0.729 Sum_probs=22.4
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
....||.|+.+.+ = |. .+-+..|.. ||+.|.
T Consensus 34 ~~~~Cp~C~~~~V-k-----R~----a~GIW~C~k--Cg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTV-K-----RI----ATGIWKCRK--CGAKFA 64 (89)
T ss_pred cCCcCCCCCCcce-e-----ee----ccCeEEcCC--CCCeec
Confidence 3568999999843 2 32 355788987 999984
No 78
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=73.32 E-value=2.8 Score=23.79 Aligned_cols=11 Identities=27% Similarity=0.688 Sum_probs=5.3
Q ss_pred eeCCCCCCCce
Q psy8689 31 EKCPKCEHPRA 41 (72)
Q Consensus 31 ~~Cp~Cg~~~a 41 (72)
+.||.||++..
T Consensus 5 i~CP~CgnKTR 15 (55)
T PF14205_consen 5 ILCPICGNKTR 15 (55)
T ss_pred EECCCCCCccc
Confidence 34555555443
No 79
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=69.09 E-value=4.3 Score=27.87 Aligned_cols=25 Identities=40% Similarity=0.976 Sum_probs=18.2
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
|...||.||+ ....-|.|.. ||+.+
T Consensus 308 tS~~C~~cg~---------------~~~r~~~C~~--cg~~~ 332 (364)
T COG0675 308 TSKTCPCCGH---------------LSGRLFKCPR--CGFVH 332 (364)
T ss_pred CcccccccCC---------------ccceeEECCC--CCCee
Confidence 3478999999 1233588987 99865
No 80
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=69.03 E-value=3 Score=27.56 Aligned_cols=14 Identities=29% Similarity=1.118 Sum_probs=12.2
Q ss_pred eEEEEecCCCCCceec
Q psy8689 56 TTFYKCCNIKCGFRWR 71 (72)
Q Consensus 56 Tlfy~C~~~~Cg~~w~ 71 (72)
=+.|.|.. |+++|.
T Consensus 11 WLIYrC~~--C~~TwN 24 (142)
T PF06353_consen 11 WLIYRCEK--CDYTWN 24 (142)
T ss_pred EEEEEccc--CcCccc
Confidence 37899999 999995
No 81
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=68.94 E-value=3.7 Score=26.60 Aligned_cols=37 Identities=27% Similarity=0.641 Sum_probs=19.9
Q ss_pred eeeCCCCCCCceEEE------EeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFM------QIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~------q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
-..|+.|++.-..-- .++.. .-+...-|+.|.. ||..
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~-v~~~~~~f~~C~~--C~ki 133 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPY-VYETYDEFWRCPG--CGKI 133 (147)
T ss_pred CCccCCCCcEeeechhhccccccCcc-ccccCCeEEECCC--CCCE
Confidence 358999997322110 01100 1112335999987 9976
No 82
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=68.62 E-value=5.9 Score=32.69 Aligned_cols=34 Identities=29% Similarity=0.773 Sum_probs=20.9
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCce
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGFR 69 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~~ 69 (72)
+...||+||....+-.-. |. -.|+.|.+ |+|.|.
T Consensus 591 ~~~~CP~Cg~~~L~~k~g--r~-----G~Fl~Cs~yP~C~~t 625 (860)
T PRK06319 591 TEIDCPKCHKGKLVKIWA--KN-----RYFYGCSEYPECDYK 625 (860)
T ss_pred cCcccCCCCCcceeEEec--CC-----CceeeccCCcccccc
Confidence 357899998766543211 11 24888876 667653
No 83
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=68.44 E-value=1.7 Score=21.61 Aligned_cols=16 Identities=31% Similarity=0.733 Sum_probs=12.4
Q ss_pred eeeCCCCCCCceEEEE
Q psy8689 30 EEKCPKCEHPRAYFMQ 45 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q 45 (72)
...||.||.....|..
T Consensus 17 ~~~CP~Cg~~~~~F~~ 32 (33)
T cd00350 17 PWVCPVCGAPKDKFEK 32 (33)
T ss_pred CCcCcCCCCcHHHcEE
Confidence 4689999998876653
No 84
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=68.02 E-value=14 Score=23.52 Aligned_cols=38 Identities=34% Similarity=0.576 Sum_probs=23.1
Q ss_pred CcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCcee
Q psy8689 27 DTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGFRW 70 (72)
Q Consensus 27 ~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~~w 70 (72)
..+.+.||+|+....+.... | -+ +.||.|.+ |.|.+.+
T Consensus 57 ~~~~~~Cp~C~~~~~~~k~~--~---~~-~~f~~~~~~Pkc~~~~ 95 (140)
T COG0551 57 EKTGVKCPKCGKGLLVLKKG--R---FG-KNFLGCSNYPKCRFTE 95 (140)
T ss_pred ccCceeCCCCCCCceEEEec--c---CC-ceEEeecCCCcCceee
Confidence 34568999999755544331 1 11 57887763 4566654
No 85
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=67.10 E-value=10 Score=22.08 Aligned_cols=31 Identities=29% Similarity=0.474 Sum_probs=21.7
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
+.||-||...+...+. .-..+++|.. |+-.+
T Consensus 7 KPCPFCG~~~~~v~~~-------~g~~~v~C~~--CgA~~ 37 (64)
T PRK09710 7 KPCPFCGCPSVTVKAI-------SGYYRAKCNG--CESRT 37 (64)
T ss_pred cCCCCCCCceeEEEec-------CceEEEEcCC--CCcCc
Confidence 6899999998877641 2244567877 97543
No 86
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=66.66 E-value=4.4 Score=26.00 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=18.0
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.||+|+....|- -.+ -|+|-. |+|.|.
T Consensus 5 ~cp~c~sEytYe----------d~~-~~~cpe--c~~ew~ 31 (112)
T COG2824 5 PCPKCNSEYTYE----------DGG-QLICPE--CAHEWN 31 (112)
T ss_pred CCCccCCceEEe----------cCc-eEeCch--hccccc
Confidence 688888765532 122 567855 999997
No 87
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=65.62 E-value=2.9 Score=24.79 Aligned_cols=14 Identities=36% Similarity=0.823 Sum_probs=5.5
Q ss_pred cceeeCCCCCCCce
Q psy8689 28 TTEEKCPKCEHPRA 41 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a 41 (72)
.+...||+||+.-.
T Consensus 22 ~~k~FCp~CGn~TL 35 (73)
T PF08772_consen 22 MTKQFCPKCGNATL 35 (73)
T ss_dssp SS--S-SSS--S--
T ss_pred CCceeCcccCCCcc
Confidence 34578999999743
No 88
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=64.82 E-value=3.2 Score=19.57 Aligned_cols=10 Identities=40% Similarity=0.919 Sum_probs=7.7
Q ss_pred eeeCCCCCCC
Q psy8689 30 EEKCPKCEHP 39 (72)
Q Consensus 30 ~~~Cp~Cg~~ 39 (72)
...||+||..
T Consensus 2 ~~~Cp~Cg~~ 11 (26)
T PF13248_consen 2 EMFCPNCGAE 11 (26)
T ss_pred cCCCcccCCc
Confidence 4579999983
No 89
>PHA02942 putative transposase; Provisional
Probab=64.03 E-value=6.2 Score=29.55 Aligned_cols=29 Identities=28% Similarity=0.843 Sum_probs=20.0
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
|...||.||+... + .....|.|.+ ||+..
T Consensus 324 TSq~Cs~CG~~~~-------~----l~~r~f~C~~--CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMV-------E----IAHRYFHCPS--CGYEN 352 (383)
T ss_pred CCccCCCCCCccC-------c----CCCCEEECCC--CCCEe
Confidence 4567999999653 1 1123699988 99864
No 90
>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=63.49 E-value=3.5 Score=24.08 Aligned_cols=35 Identities=26% Similarity=0.397 Sum_probs=25.1
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
...|..|+++.+..+..| |-+.=+++..|-. |...
T Consensus 4 ~FTC~~C~~Rs~~~~sk~---aY~~GvViv~C~g--C~~~ 38 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQ---AYHKGVVIVQCPG--CKNR 38 (66)
T ss_dssp EEEETTTTEEEEEEEEHH---HHHTSEEEEE-TT--S--E
T ss_pred EEEcCCCCCccceeeCHH---HHhCCeEEEECCC--Ccce
Confidence 468999999999888744 5566678999966 9764
No 91
>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=63.17 E-value=4.4 Score=19.39 Aligned_cols=9 Identities=33% Similarity=1.029 Sum_probs=5.5
Q ss_pred eCCCCCCCc
Q psy8689 32 KCPKCEHPR 40 (72)
Q Consensus 32 ~Cp~Cg~~~ 40 (72)
.||.|+..-
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 467776544
No 92
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=63.12 E-value=7.3 Score=20.41 Aligned_cols=12 Identities=25% Similarity=0.584 Sum_probs=7.2
Q ss_pred eeeCCCCCCCce
Q psy8689 30 EEKCPKCEHPRA 41 (72)
Q Consensus 30 ~~~Cp~Cg~~~a 41 (72)
.+.||.||++-.
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 456777765544
No 93
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=63.04 E-value=4.1 Score=22.55 Aligned_cols=12 Identities=25% Similarity=0.617 Sum_probs=9.8
Q ss_pred eeeCCCCCCCce
Q psy8689 30 EEKCPKCEHPRA 41 (72)
Q Consensus 30 ~~~Cp~Cg~~~a 41 (72)
.+.||.||++-.
T Consensus 24 ~irCp~Cg~rIl 35 (49)
T COG1996 24 GIRCPYCGSRIL 35 (49)
T ss_pred ceeCCCCCcEEE
Confidence 479999999754
No 94
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=62.83 E-value=8.4 Score=19.56 Aligned_cols=30 Identities=30% Similarity=0.699 Sum_probs=12.4
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
.||.||+.-. + .+-..|+... ++|.. ||..
T Consensus 2 fC~~CG~~l~-~---~ip~gd~r~R--~vC~~--Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLE-R---RIPEGDDRER--LVCPA--CGFI 31 (34)
T ss_dssp B-TTT--B-E-E---E--TT-SS-E--EEETT--TTEE
T ss_pred ccccccChhh-h---hcCCCCCccc--eECCC--CCCE
Confidence 5899998832 1 1122233333 45766 8864
No 95
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=62.41 E-value=3.8 Score=18.99 Aligned_cols=9 Identities=33% Similarity=0.918 Sum_probs=6.7
Q ss_pred eCCCCCCCc
Q psy8689 32 KCPKCEHPR 40 (72)
Q Consensus 32 ~Cp~Cg~~~ 40 (72)
.||+||+.-
T Consensus 1 ~Cp~CG~~~ 9 (23)
T PF13240_consen 1 YCPNCGAEI 9 (23)
T ss_pred CCcccCCCC
Confidence 489998753
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.31 E-value=10 Score=21.81 Aligned_cols=35 Identities=26% Similarity=0.642 Sum_probs=20.0
Q ss_pred cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
.+.+.||+||.. .++.=..=|. ...-|.|-+ ||..
T Consensus 23 ~~~F~CPnCG~~-~I~RC~~CRk----~~~~Y~CP~--CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEV-IIYRCEKCRK----QSNPYTCPK--CGFE 57 (59)
T ss_pred cCEeeCCCCCCe-eEeechhHHh----cCCceECCC--CCCc
Confidence 356899999873 2332212121 224588966 9863
No 97
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.23 E-value=2.7 Score=27.87 Aligned_cols=30 Identities=20% Similarity=0.505 Sum_probs=19.7
Q ss_pred ccccccCCccccc-cCCcceeeCCCCCCCce
Q psy8689 12 EIDHVMGGAAAWE-NVDTTEEKCPKCEHPRA 41 (72)
Q Consensus 12 e~~~v~~~~~~~~-~~~~t~~~Cp~Cg~~~a 41 (72)
+-+.-|++.+... ...+--+.||.||+.++
T Consensus 13 eFEGWF~ssaDfd~Q~~rgLv~CPvCgs~~V 43 (142)
T COG5319 13 EFEGWFGSSADFDRQRERGLVTCPVCGSTEV 43 (142)
T ss_pred cccccccCchhHHHHHHcCceeCCCCCcHHH
Confidence 5556666654433 34455689999999765
No 98
>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=59.41 E-value=5.1 Score=21.25 Aligned_cols=12 Identities=25% Similarity=0.775 Sum_probs=9.3
Q ss_pred eeeCCCCCCCce
Q psy8689 30 EEKCPKCEHPRA 41 (72)
Q Consensus 30 ~~~Cp~Cg~~~a 41 (72)
.+.||.||+..+
T Consensus 26 ~~~CP~Cg~~~~ 37 (52)
T TIGR02605 26 LATCPECGGEKL 37 (52)
T ss_pred CCCCCCCCCCce
Confidence 367999998654
No 99
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=59.11 E-value=3.1 Score=27.46 Aligned_cols=36 Identities=17% Similarity=0.532 Sum_probs=22.8
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
.+.||.||+....-.. +..| .+-.-.|.|.. |...|
T Consensus 105 ~~~cp~c~s~~t~~~s-~fg~--t~cka~~~c~~--c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTITS-IFGP--TACKALYRCRA--CKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEeec-CCCC--hhhHHHhhhhh--hCCcH
Confidence 4899999998875432 2221 12334577888 87654
No 100
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=58.55 E-value=11 Score=23.70 Aligned_cols=34 Identities=26% Similarity=0.569 Sum_probs=19.2
Q ss_pred eeCCCCCCCceEEE--EeeccCCCCCceEEEEecCCCCC
Q psy8689 31 EKCPKCEHPRAYFM--QIQTRSADEPMTTFYKCCNIKCG 67 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~--q~Q~rsadE~mTlfy~C~~~~Cg 67 (72)
+.||-||.+...-- .+=.++.++.. .+|+|.+ |+
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~-~~y~C~~--C~ 38 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGP-YLYVCTP--CD 38 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCc-eeEECCC--CC
Confidence 57999997544311 11113344333 4599998 96
No 101
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=57.71 E-value=18 Score=26.67 Aligned_cols=38 Identities=18% Similarity=0.517 Sum_probs=24.7
Q ss_pred eeeCCCCCCCceE-EEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 30 EEKCPKCEHPRAY-FMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~-~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
.+.||.||+.+-. |+..-. ..+++--...+|-. |+.-+
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~-~~~~~~~r~e~C~~--C~~Yl 262 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEH-DAEKAVLKAETCDS--CQGYL 262 (305)
T ss_pred CccCCCCCCCCceeeEeecC-CCCCcceEEeeccc--cccch
Confidence 5799999987765 554421 11345566788988 98644
No 102
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=57.46 E-value=15 Score=19.35 Aligned_cols=27 Identities=22% Similarity=0.552 Sum_probs=17.8
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecC
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN 63 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~ 63 (72)
.+.|+.||+.=.. +. +. .-..||.|.+
T Consensus 5 ~l~C~~CG~~m~~--~~--~~---~~~~yy~C~~ 31 (58)
T PF13408_consen 5 LLRCGHCGSKMTR--RK--RK---GKYRYYRCSN 31 (58)
T ss_pred cEEcccCCcEeEE--EE--CC---CCceEEEcCC
Confidence 4789999987444 21 22 2338899986
No 103
>PRK07219 DNA topoisomerase I; Validated
Probab=57.41 E-value=9.9 Score=31.16 Aligned_cols=33 Identities=24% Similarity=0.594 Sum_probs=20.3
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~~ 69 (72)
...||+||+.- .... ...+ ..||.|.+ |.|.+.
T Consensus 602 ~~~CP~Cg~~l-~~r~-----~~~g-~~F~gCs~yp~C~~t 635 (822)
T PRK07219 602 IGKCPECGGDL-IIIR-----TDKG-SRFVGCSGYPDCRNT 635 (822)
T ss_pred cCcCCCCCCcc-eeee-----ccCC-ceeeecCCCcCCCCe
Confidence 46799999742 2111 1111 25899987 789864
No 104
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=57.03 E-value=15 Score=27.40 Aligned_cols=33 Identities=27% Similarity=0.568 Sum_probs=20.7
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
...|++|| .-.+-.. .-..+.-|+.|.| . |||.
T Consensus 169 ~p~c~~cg-~~~~~v~---~~d~~~~~v~y~c-~--cG~~ 201 (353)
T cd00674 169 MPYCEKCG-KDTTTVE---AYDAKAGTVTYKC-E--CGHE 201 (353)
T ss_pred eeecCCcC-cceeEEE---EEeCCCCeEEEEc-C--CCCE
Confidence 46899999 3222211 1233456899999 3 9986
No 105
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=56.06 E-value=18 Score=22.35 Aligned_cols=31 Identities=26% Similarity=0.629 Sum_probs=21.2
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
....||.||.....- + .+=+..|.. |++.|-
T Consensus 34 ~ky~Cp~Cgk~~vkR-~---------a~GIW~C~~--C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKR-V---------ATGIWKCKK--CGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEEE-E---------ETTEEEETT--TTEEEE
T ss_pred CCCcCCCCCCceeEE-e---------eeEEeecCC--CCCEEe
Confidence 356899999988421 1 233588988 998873
No 106
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=55.54 E-value=14 Score=24.47 Aligned_cols=35 Identities=29% Similarity=0.670 Sum_probs=24.1
Q ss_pred eeCCCCCCCceEEEEee------ccCC-------CCCceEEEEecCCCC
Q psy8689 31 EKCPKCEHPRAYFMQIQ------TRSA-------DEPMTTFYKCCNIKC 66 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q------~rsa-------dE~mTlfy~C~~~~C 66 (72)
-.|+.||+.+..=||+. +... |=+.-+.|.|.+ .|
T Consensus 98 p~C~~Cg~~R~FEfQlmP~li~~L~~~~~~~~~~dwgtv~VyTCs~-sC 145 (164)
T PF04194_consen 98 PKCENCGSPRVFEFQLMPQLIYYLEVDDEGSDSMDWGTVLVYTCSA-SC 145 (164)
T ss_pred CCCccCCCccEEEEEechHHHHHhhccccCCCCceeeEEEEEEehH-Hc
Confidence 37999999999988872 2222 223447899984 47
No 107
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=52.27 E-value=12 Score=18.75 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=8.7
Q ss_pred EEEecCCCCCceec
Q psy8689 58 FYKCCNIKCGFRWR 71 (72)
Q Consensus 58 fy~C~~~~Cg~~w~ 71 (72)
+|+|.+ ||+...
T Consensus 2 ~~~C~~--CG~i~~ 13 (34)
T cd00729 2 VWVCPV--CGYIHE 13 (34)
T ss_pred eEECCC--CCCEeE
Confidence 578888 887654
No 108
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=52.08 E-value=10 Score=19.64 Aligned_cols=10 Identities=40% Similarity=1.394 Sum_probs=7.4
Q ss_pred EEecCCCCCcee
Q psy8689 59 YKCCNIKCGFRW 70 (72)
Q Consensus 59 y~C~~~~Cg~~w 70 (72)
|.|.+ |||.|
T Consensus 6 y~C~~--Cg~~f 15 (42)
T PF09723_consen 6 YRCEE--CGHEF 15 (42)
T ss_pred EEeCC--CCCEE
Confidence 67877 88766
No 109
>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=51.67 E-value=10 Score=18.86 Aligned_cols=11 Identities=36% Similarity=1.301 Sum_probs=7.3
Q ss_pred EEecCCCCCceec
Q psy8689 59 YKCCNIKCGFRWR 71 (72)
Q Consensus 59 y~C~~~~Cg~~w~ 71 (72)
|.|.+ ||+.|.
T Consensus 6 y~C~~--Cg~~fe 16 (41)
T smart00834 6 YRCED--CGHTFE 16 (41)
T ss_pred EEcCC--CCCEEE
Confidence 56766 877663
No 110
>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=51.58 E-value=18 Score=20.73 Aligned_cols=35 Identities=26% Similarity=0.616 Sum_probs=17.4
Q ss_pred eeeCCCCCC-----CceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 30 EEKCPKCEH-----PRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 30 ~~~Cp~Cg~-----~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
...|.+||. ..+.. .+. +.....-.+.|.|.. |||
T Consensus 46 r~~Ck~C~~~liPG~~~~v-ri~-~~~~~~~~l~~~C~~--C~~ 85 (85)
T PF04032_consen 46 RTICKKCGSLLIPGVNCSV-RIR-KKKKKKNFLVYTCLN--CGH 85 (85)
T ss_dssp CTB-TTT--B--CTTTEEE-EEE----SSS-EEEEEETT--TTE
T ss_pred cccccCCCCEEeCCCccEE-EEE-ecCCCCCEEEEEccc--cCC
Confidence 358999996 22222 222 223334568899999 997
No 111
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=50.92 E-value=15 Score=26.62 Aligned_cols=28 Identities=21% Similarity=0.590 Sum_probs=19.5
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
..||.||+...++-. .+--++|.+ ||..
T Consensus 12 ~~Cp~Cg~~~iv~d~---------~~Ge~vC~~--CG~V 39 (310)
T PRK00423 12 LVCPECGSDKLIYDY---------ERGEIVCAD--CGLV 39 (310)
T ss_pred CcCcCCCCCCeeEEC---------CCCeEeecc--cCCc
Confidence 579999986655432 233578999 9864
No 112
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=49.66 E-value=12 Score=23.99 Aligned_cols=11 Identities=36% Similarity=0.887 Sum_probs=6.6
Q ss_pred eeCCCCCCCce
Q psy8689 31 EKCPKCEHPRA 41 (72)
Q Consensus 31 ~~Cp~Cg~~~a 41 (72)
..||+||+...
T Consensus 87 ~~CP~C~s~~~ 97 (115)
T COG0375 87 YRCPKCGSINL 97 (115)
T ss_pred eECCCCCCCce
Confidence 44666666555
No 113
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=49.53 E-value=15 Score=29.12 Aligned_cols=31 Identities=26% Similarity=0.765 Sum_probs=18.8
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~~ 69 (72)
..||+||+. .. . |+...+ .||.|.+ +.|++.
T Consensus 575 ~~CP~Cg~~-~~-~----~~~~~g--kf~gCs~y~~C~~~ 606 (610)
T TIGR01051 575 QDCPLCGRP-MV-V----KLGKYG--PFLACSNFPECKYT 606 (610)
T ss_pred CCCCCCCCe-eE-E----EecCCC--ceeeCCCCCCCCCC
Confidence 579999874 21 1 111112 4899998 778754
No 114
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=49.50 E-value=9.7 Score=24.36 Aligned_cols=21 Identities=29% Similarity=0.689 Sum_probs=14.9
Q ss_pred eeCCCCCCCceEEEEeeccCC
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSA 51 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsa 51 (72)
--||+||.+.--|.-...|.|
T Consensus 21 ~GCp~CG~nkF~yv~~e~rpa 41 (112)
T COG3364 21 SGCPKCGCNKFLYVPEEKRPA 41 (112)
T ss_pred ccCccccchheEecccccccc
Confidence 469999999887765544433
No 115
>PRK07220 DNA topoisomerase I; Validated
Probab=48.62 E-value=18 Score=29.40 Aligned_cols=32 Identities=28% Similarity=0.651 Sum_probs=18.3
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCce
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~~ 69 (72)
..||+||+.-. . |....+ ..|+.|.+ |.|.+.
T Consensus 590 ~~CP~Cg~~l~-~-----r~~r~g-~~f~gCs~yp~C~~~ 622 (740)
T PRK07220 590 GKCPLCGSDLM-V-----RRSKRG-SRFIGCEGYPECTFS 622 (740)
T ss_pred cccccCCCeee-E-----EecCCC-ceEEEcCCCCCCCce
Confidence 58999996421 1 111111 35888876 668754
No 116
>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=48.45 E-value=10 Score=21.15 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=10.5
Q ss_pred ceeeCCCCCCCceE
Q psy8689 29 TEEKCPKCEHPRAY 42 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~ 42 (72)
..++||+|+.-.-+
T Consensus 23 leIKCpRC~tiN~~ 36 (51)
T PF10122_consen 23 LEIKCPRCKTINHV 36 (51)
T ss_pred EEEECCCCCccceE
Confidence 46899999965543
No 117
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=48.20 E-value=36 Score=17.88 Aligned_cols=31 Identities=32% Similarity=0.668 Sum_probs=20.8
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEE-EecCCCCCc
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFY-KCCNIKCGF 68 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy-~C~~~~Cg~ 68 (72)
+.|..|+..-..| .+|..+++| .|.+++|.+
T Consensus 4 IvCq~C~~~Id~~-------e~ekV~~lYg~C~~~eC~~ 35 (38)
T PF13790_consen 4 IVCQHCNETIDHF-------ETEKVTTLYGKCGKCECRE 35 (38)
T ss_pred EEeccccceeeee-------cCCcEEEEEEECCCCcccc
Confidence 5788898877766 246777666 487755654
No 118
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=47.04 E-value=20 Score=27.13 Aligned_cols=35 Identities=26% Similarity=0.460 Sum_probs=19.0
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
...|++||.-..+-.. .-..+.-++.|.|.. |||.
T Consensus 174 ~piC~~cGri~tt~v~---~~d~~~~~v~Y~c~~--cG~~ 208 (360)
T PF01921_consen 174 LPICEKCGRIDTTEVT---EYDPEGGTVTYRCEE--CGHE 208 (360)
T ss_dssp EEEETTTEE--EEEEE---EE--SSSEEEEE--T--TS--
T ss_pred eeeccccCCcccceee---EeecCCCEEEEEecC--CCCE
Confidence 4689999983332222 112367899999966 9996
No 119
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=46.87 E-value=30 Score=25.59 Aligned_cols=37 Identities=19% Similarity=0.593 Sum_probs=24.0
Q ss_pred eeeCCCCCCCceE-EEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 30 EEKCPKCEHPRAY-FMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~-~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+.||.||+.+.. |+..- .+++--...+|-. |+.-+|
T Consensus 226 R~~C~~Cg~~~~l~y~~~~---~~~~~~r~e~C~~--C~~YlK 263 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSLD---SEQAAVKAESCGD--CGTYLK 263 (309)
T ss_pred CccCCCCCCCCceeeeeec---CCCcceEeeeccc--ccccce
Confidence 5789999986655 44432 2224456688988 986543
No 120
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=46.52 E-value=34 Score=21.13 Aligned_cols=32 Identities=25% Similarity=0.631 Sum_probs=22.2
Q ss_pred cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.....||.||.... - | ..+-+..|.. |+..|-
T Consensus 33 ~a~y~CpfCgk~~v-k-----R----~a~GIW~C~~--C~~~~A 64 (91)
T TIGR00280 33 KAKYVCPFCGKKTV-K-----R----GSTGIWTCRK--CGAKFA 64 (91)
T ss_pred hcCccCCCCCCCce-E-----E----EeeEEEEcCC--CCCEEe
Confidence 34578999996553 2 1 1456789988 998873
No 121
>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=46.03 E-value=14 Score=18.62 Aligned_cols=28 Identities=25% Similarity=0.632 Sum_probs=15.0
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
.||+||+-=.. + .+...+. .|.. |++..
T Consensus 3 FCp~C~nlL~p--~-----~~~~~~~--~C~~--C~Y~~ 30 (35)
T PF02150_consen 3 FCPECGNLLYP--K-----EDKEKRV--ACRT--CGYEE 30 (35)
T ss_dssp BETTTTSBEEE--E-----EETTTTE--EESS--SS-EE
T ss_pred eCCCCCccceE--c-----CCCccCc--CCCC--CCCcc
Confidence 58889875432 1 1112222 8877 88764
No 122
>PRK14973 DNA topoisomerase I; Provisional
Probab=45.72 E-value=15 Score=30.87 Aligned_cols=32 Identities=22% Similarity=0.451 Sum_probs=20.0
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+..||+||..-.... |...-|+ |+-| |+|.|.
T Consensus 635 ~~~Cp~CG~p~~~~~----r~Gr~g~--fl~C--P~C~~~ 666 (936)
T PRK14973 635 DEVCPIHHLNHVRLI----RKGARPW--DIGC--PLCSHI 666 (936)
T ss_pred CCCCCCCCCCceEEe----ecCCCcc--cccC--ccccch
Confidence 457999998733222 2233344 7778 779884
No 123
>KOG2703|consensus
Probab=44.48 E-value=21 Score=27.78 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=5.2
Q ss_pred eeCCCCCCCce
Q psy8689 31 EKCPKCEHPRA 41 (72)
Q Consensus 31 ~~Cp~Cg~~~a 41 (72)
+.||.||++..
T Consensus 69 F~CpHCG~kN~ 79 (460)
T KOG2703|consen 69 FECPHCGHKNN 79 (460)
T ss_pred eecCccCCccc
Confidence 34455554444
No 124
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.35 E-value=18 Score=23.32 Aligned_cols=39 Identities=26% Similarity=0.589 Sum_probs=24.9
Q ss_pred CCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 26 VDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 26 ~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
...+...||.|++.. +..-...+ +. --=|.|.. |+..|.
T Consensus 26 ~~~~~~~cP~C~s~~-~~k~g~~~-~~---~qRyrC~~--C~~tf~ 64 (129)
T COG3677 26 MQITKVNCPRCKSSN-VVKIGGIR-RG---HQRYKCKS--CGSTFT 64 (129)
T ss_pred hhcccCcCCCCCccc-eeeECCcc-cc---ccccccCC--cCccee
Confidence 344568899999877 44333322 21 23488988 998885
No 125
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=44.33 E-value=11 Score=19.40 Aligned_cols=12 Identities=33% Similarity=1.046 Sum_probs=9.4
Q ss_pred eeCCCCCCCceE
Q psy8689 31 EKCPKCEHPRAY 42 (72)
Q Consensus 31 ~~Cp~Cg~~~a~ 42 (72)
..||.||+...+
T Consensus 3 ~~Cp~Cg~~~~~ 14 (47)
T PF14690_consen 3 PRCPHCGSPSVH 14 (47)
T ss_pred ccCCCcCCCceE
Confidence 479999987744
No 126
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=44.12 E-value=29 Score=27.19 Aligned_cols=32 Identities=19% Similarity=0.445 Sum_probs=21.2
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
...||+||.-..... ..-++. |+.|.|. |||.
T Consensus 168 ~pic~~cGrv~~~~~---~~~~~~--~v~Y~c~---cG~~ 199 (515)
T TIGR00467 168 SVFCENCGRDTTTVN---NYDNEY--SIEYSCE---CGNQ 199 (515)
T ss_pred eeecCCcCccCceEE---EecCCc--eEEEEcC---CCCE
Confidence 468999998754222 122333 7999994 9985
No 127
>KOG2767|consensus
Probab=43.76 E-value=11 Score=28.89 Aligned_cols=32 Identities=38% Similarity=0.797 Sum_probs=25.0
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
+.||.|++.+.-++-.- ..+|-+.|.. ||++.
T Consensus 97 VlC~~C~NPETel~itk------~q~i~~~CkA--CG~r~ 128 (400)
T KOG2767|consen 97 VLCPSCENPETELIITK------KQTISLKCKA--CGFRS 128 (400)
T ss_pred eeCcCCCCCceeEEecc------cchhhhHHHH--cCCcc
Confidence 68999999999876521 3567788988 99863
No 128
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=43.71 E-value=13 Score=23.38 Aligned_cols=15 Identities=27% Similarity=0.627 Sum_probs=10.2
Q ss_pred CCcceeeCCCCCCCc
Q psy8689 26 VDTTEEKCPKCEHPR 40 (72)
Q Consensus 26 ~~~t~~~Cp~Cg~~~ 40 (72)
|.+..+.||+||..-
T Consensus 22 Lnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 22 LNKDPIVCPKCGTEF 36 (108)
T ss_pred CCCCCccCCCCCCcc
Confidence 344557899999643
No 129
>PRK05978 hypothetical protein; Provisional
Probab=43.47 E-value=11 Score=25.05 Aligned_cols=30 Identities=20% Similarity=0.669 Sum_probs=19.2
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
.-+||+||.....- ...++-=.|.. ||..+
T Consensus 33 ~grCP~CG~G~LF~---------g~Lkv~~~C~~--CG~~~ 62 (148)
T PRK05978 33 RGRCPACGEGKLFR---------AFLKPVDHCAA--CGEDF 62 (148)
T ss_pred cCcCCCCCCCcccc---------cccccCCCccc--cCCcc
Confidence 46899999887742 12333445766 87655
No 130
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=43.44 E-value=16 Score=24.01 Aligned_cols=17 Identities=18% Similarity=0.628 Sum_probs=13.3
Q ss_pred eeCCCCCCCceEEEEee
Q psy8689 31 EKCPKCEHPRAYFMQIQ 47 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q 47 (72)
.=||.||.+.-.|....
T Consensus 20 ~GCP~CGg~kF~yv~~~ 36 (131)
T PF09845_consen 20 SGCPECGGNKFQYVPEE 36 (131)
T ss_pred ccCcccCCcceEEcCCC
Confidence 45999999988886543
No 131
>PHA02540 61 DNA primase; Provisional
Probab=43.08 E-value=37 Score=25.38 Aligned_cols=33 Identities=27% Similarity=0.686 Sum_probs=24.3
Q ss_pred ceeeCCCCCC-----CceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 29 TEEKCPKCEH-----PRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 29 t~~~Cp~Cg~-----~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
-...||-||. +.+.|+-.+.+. ..||.|-+ ||.
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~-----~~~yhCFg--CGa 63 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEKKD-----GGVFKCHN--CGY 63 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEeccCC-----ceEEEecC--CCC
Confidence 4678999997 446777655332 67999999 985
No 132
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=42.94 E-value=22 Score=18.39 Aligned_cols=14 Identities=21% Similarity=0.733 Sum_probs=11.1
Q ss_pred eeCCCCCCCceEEE
Q psy8689 31 EKCPKCEHPRAYFM 44 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~ 44 (72)
..||.||.+...-|
T Consensus 4 ~pCP~CGG~DrFr~ 17 (37)
T smart00778 4 GPCPNCGGSDRFRF 17 (37)
T ss_pred cCCCCCCCcccccc
Confidence 57999999887553
No 133
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.90 E-value=11 Score=24.48 Aligned_cols=29 Identities=28% Similarity=0.608 Sum_probs=20.9
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEE-----EEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTF-----YKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlf-----y~C~~~~Cg~~ 69 (72)
...||.||. . -+.+|.+.+. |.|-+ ||..
T Consensus 99 ~Y~Cp~C~~---~------y~~~ea~~~~d~~~~f~Cp~--Cg~~ 132 (147)
T smart00531 99 YYKCPNCQS---K------YTFLEANQLLDMDGTFTCPR--CGEE 132 (147)
T ss_pred EEECcCCCC---E------eeHHHHHHhcCCCCcEECCC--CCCE
Confidence 467999972 2 3577777777 88966 9875
No 134
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.63 E-value=15 Score=21.51 Aligned_cols=14 Identities=29% Similarity=0.781 Sum_probs=11.2
Q ss_pred cceeeCCCCCCCce
Q psy8689 28 TTEEKCPKCEHPRA 41 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a 41 (72)
++.++||.||....
T Consensus 5 ~~~v~CP~Cgkpv~ 18 (65)
T COG3024 5 RITVPCPTCGKPVV 18 (65)
T ss_pred cccccCCCCCCccc
Confidence 45689999998766
No 135
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=42.28 E-value=43 Score=20.63 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=21.8
Q ss_pred cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.....||.||.... - | ..+-+..|.. |+..|-
T Consensus 34 ~a~y~CpfCgk~~v-k-----R----~a~GIW~C~~--C~~~~A 65 (90)
T PTZ00255 34 HAKYFCPFCGKHAV-K-----R----QAVGIWRCKG--CKKTVA 65 (90)
T ss_pred hCCccCCCCCCCce-e-----e----eeeEEEEcCC--CCCEEe
Confidence 34578999996553 2 1 1346788988 998763
No 136
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=41.77 E-value=14 Score=20.95 Aligned_cols=13 Identities=38% Similarity=0.884 Sum_probs=6.9
Q ss_pred ceeeCCCCCCCce
Q psy8689 29 TEEKCPKCEHPRA 41 (72)
Q Consensus 29 t~~~Cp~Cg~~~a 41 (72)
|.+.||.||....
T Consensus 1 m~v~CP~C~k~~~ 13 (57)
T PF03884_consen 1 MTVKCPICGKPVE 13 (57)
T ss_dssp -EEE-TTT--EEE
T ss_pred CcccCCCCCCeec
Confidence 3578999997654
No 137
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=41.58 E-value=42 Score=26.11 Aligned_cols=35 Identities=29% Similarity=0.458 Sum_probs=23.3
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
...||+||.-..+-.- .-..+.-|+.|.|. |||..
T Consensus 175 ~pic~~cg~~~~~~~~---~~d~~~~~v~y~~~---cG~~~ 209 (510)
T PRK00750 175 LPICPKCGKVLTTPVI---SYDAEAGTVTYDCE---CGHEG 209 (510)
T ss_pred eeeCCCCCccceEEEE---EEeCCCCEEEEEcC---CCCEE
Confidence 4689999987654432 11334458889884 99864
No 138
>PRK06599 DNA topoisomerase I; Validated
Probab=41.13 E-value=29 Score=27.83 Aligned_cols=32 Identities=25% Similarity=0.678 Sum_probs=18.4
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCc
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGF 68 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~ 68 (72)
...||+||....+... ..- ..||.|.+ +.|++
T Consensus 585 ~~~CP~C~~~~l~~k~-----~k~--g~F~~Cs~~p~C~~ 617 (675)
T PRK06599 585 DETCPKCGGGPLVLKL-----GKN--GKFLGCSGYPECKY 617 (675)
T ss_pred CccccccCCCcceEEe-----cCC--CceeeCCCCCccCC
Confidence 3689999654443321 111 13888876 66764
No 139
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=40.41 E-value=67 Score=17.87 Aligned_cols=34 Identities=21% Similarity=0.513 Sum_probs=21.0
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCC
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCG 67 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg 67 (72)
...|+.|+....+..+.| ...-.+..--.|.. |+
T Consensus 15 ~~~C~~C~G~G~~~~~~~--~~~~~~~~~~~C~~--C~ 48 (66)
T PF00684_consen 15 PKTCPQCNGSGQVTRRQQ--TPGGVFQMQQTCPK--CG 48 (66)
T ss_dssp -EE-TTSSSSSEEEEEEE--SSSTTEEEEEE-TT--TS
T ss_pred CcCCcCCCCeeEEEEEEe--CCCeEEEEEEECCC--Cc
Confidence 368999999999887755 33334445556766 74
No 140
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=40.27 E-value=21 Score=20.71 Aligned_cols=37 Identities=24% Similarity=0.665 Sum_probs=21.8
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+.||+|++...-|-=.---+...| =|.|.. |...|+
T Consensus 5 ~~~CPRC~S~nTKFcYyNNy~~~QP---R~~Ck~--C~rywT 41 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFCYYNNYNLSQP---RYFCKS--CRRYWT 41 (63)
T ss_pred CCCCCCcCCCCCEEEeecCCCCCCc---chhhHH--HHHHHH
Confidence 4689999988776532111111112 255877 877775
No 141
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=39.89 E-value=6.7 Score=21.43 Aligned_cols=15 Identities=40% Similarity=0.868 Sum_probs=11.7
Q ss_pred ceeeCCCCCCCceEE
Q psy8689 29 TEEKCPKCEHPRAYF 43 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~ 43 (72)
+.+.||.||-.+++.
T Consensus 8 tG~~CPgCG~tRa~~ 22 (52)
T PF10825_consen 8 TGIPCPGCGMTRAFI 22 (52)
T ss_pred hCCCCCCCcHHHHHH
Confidence 567899999877654
No 142
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.76 E-value=12 Score=25.57 Aligned_cols=36 Identities=22% Similarity=0.629 Sum_probs=20.5
Q ss_pred eeCCCCCCCceEE------EEeeccCCCCCceEEEEecCCCCCce
Q psy8689 31 EKCPKCEHPRAYF------MQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~------~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
..||.|+..-.-- -++. ..-......||.|.+ ||..
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp-~~~~~~~~~f~~C~~--Cgki 139 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVP-EKVYRNYEEFYRCPK--CGKI 139 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccc-hhhhhcccceeECCC--Cccc
Confidence 5899999643211 0111 001223567999988 9875
No 143
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=39.35 E-value=26 Score=15.09 Aligned_cols=11 Identities=45% Similarity=1.047 Sum_probs=7.1
Q ss_pred EEecCCCCCceec
Q psy8689 59 YKCCNIKCGFRWR 71 (72)
Q Consensus 59 y~C~~~~Cg~~w~ 71 (72)
|.|.. |+..|.
T Consensus 1 y~C~~--C~~~f~ 11 (23)
T PF00096_consen 1 YKCPI--CGKSFS 11 (23)
T ss_dssp EEETT--TTEEES
T ss_pred CCCCC--CCCccC
Confidence 56766 777664
No 144
>PRK05582 DNA topoisomerase I; Validated
Probab=38.66 E-value=24 Score=28.15 Aligned_cols=31 Identities=35% Similarity=0.680 Sum_probs=18.0
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCc
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGF 68 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~ 68 (72)
...||+||+.- + ....+. ..||.|.+ +.|++
T Consensus 571 ~~~CP~Cg~~l-~--~~~~k~-----gkf~~Cs~~~~C~~ 602 (650)
T PRK05582 571 GEDCPKCGSPM-V--IKMGRY-----GKFIACSNFPDCRN 602 (650)
T ss_pred CCCCCCCCCEe-E--EEecCC-----CceeecCCcccccc
Confidence 46899998631 1 112121 24888887 66764
No 145
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=38.26 E-value=47 Score=20.07 Aligned_cols=7 Identities=43% Similarity=1.231 Sum_probs=3.6
Q ss_pred CCCCCCC
Q psy8689 33 CPKCEHP 39 (72)
Q Consensus 33 Cp~Cg~~ 39 (72)
||.||+.
T Consensus 1 C~~C~~~ 7 (127)
T TIGR03830 1 CPICGSG 7 (127)
T ss_pred CCCCCCc
Confidence 5555543
No 146
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.17 E-value=19 Score=22.53 Aligned_cols=10 Identities=30% Similarity=1.059 Sum_probs=5.5
Q ss_pred eeCCCCCCCc
Q psy8689 31 EKCPKCEHPR 40 (72)
Q Consensus 31 ~~Cp~Cg~~~ 40 (72)
..||.||+..
T Consensus 88 ~~CP~Cgs~~ 97 (114)
T PRK03681 88 RRCPQCHGDM 97 (114)
T ss_pred CcCcCcCCCC
Confidence 3466666544
No 147
>KOG2462|consensus
Probab=38.05 E-value=25 Score=25.86 Aligned_cols=39 Identities=28% Similarity=0.557 Sum_probs=27.8
Q ss_pred cceeeCCCCCCCceEEE------EeeccCCCCCceEEEEecCCCCCceec
Q psy8689 28 TTEEKCPKCEHPRAYFM------QIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~~------q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.....|++||..-+.+. |.- |++|+ ..-+.|.. |+..++
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H-~~~~s--~ka~~C~~--C~K~Yv 172 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTH-RSLDS--KKAFSCKY--CGKVYV 172 (279)
T ss_pred CCceeccccccccccccccchhhccc-ccccc--cccccCCC--CCceee
Confidence 34578999999888875 433 77777 34467877 887765
No 148
>PRK11032 hypothetical protein; Provisional
Probab=38.04 E-value=18 Score=24.35 Aligned_cols=14 Identities=36% Similarity=0.800 Sum_probs=9.3
Q ss_pred CcceeeCCCCCCCc
Q psy8689 27 DTTEEKCPKCEHPR 40 (72)
Q Consensus 27 ~~t~~~Cp~Cg~~~ 40 (72)
|...-.||+||+.+
T Consensus 139 p~~i~pCp~C~~~~ 152 (160)
T PRK11032 139 PEVLPLCPKCGHDQ 152 (160)
T ss_pred CCcCCCCCCCCCCe
Confidence 33345799998864
No 149
>PRK05776 DNA topoisomerase I; Provisional
Probab=37.97 E-value=30 Score=27.87 Aligned_cols=35 Identities=17% Similarity=0.125 Sum_probs=21.3
Q ss_pred eeeCCCCCCCce---EEEEeeccCCCCCceEEEEecC-CCCCce
Q psy8689 30 EEKCPKCEHPRA---YFMQIQTRSADEPMTTFYKCCN-IKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a---~~~q~Q~rsadE~mTlfy~C~~-~~Cg~~ 69 (72)
...||+||+.-. +.. ..| -+-..|+.|.+ |+|.+.
T Consensus 596 ~~~Cp~Cg~~l~~~~~~~--~~~---~~~~~f~~c~~~p~c~~~ 634 (670)
T PRK05776 596 VGKCKICGREAYKDGLCK--YHY---EAKKRLVKAYEEWKERTG 634 (670)
T ss_pred CCcCCCCCCccccCceEE--ecc---cCCccceecCCCccccCC
Confidence 468999997441 221 112 12236888997 888765
No 150
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=37.84 E-value=22 Score=20.53 Aligned_cols=34 Identities=29% Similarity=0.726 Sum_probs=19.5
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
+.+.||+||+...+=-+. -| ....=|+|-+ ||..
T Consensus 26 v~F~CPnCGe~~I~Rc~~-CR----k~g~~Y~Cp~--CGF~ 59 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAK-CR----KLGNPYRCPK--CGFE 59 (61)
T ss_pred eEeeCCCCCceeeehhhh-HH----HcCCceECCC--cCcc
Confidence 458999999754432221 11 1223488976 9863
No 151
>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=37.48 E-value=20 Score=23.72 Aligned_cols=11 Identities=45% Similarity=1.078 Sum_probs=7.9
Q ss_pred eeeCCCCCCCc
Q psy8689 30 EEKCPKCEHPR 40 (72)
Q Consensus 30 ~~~Cp~Cg~~~ 40 (72)
.-.||+||+..
T Consensus 130 l~~Cp~C~~~~ 140 (146)
T PF07295_consen 130 LPPCPKCGHTE 140 (146)
T ss_pred CCCCCCCCCCe
Confidence 35788888764
No 152
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=37.34 E-value=29 Score=27.52 Aligned_cols=29 Identities=34% Similarity=0.715 Sum_probs=16.2
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCC
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKC 66 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~C 66 (72)
...||+||+.-. .+... ...||-|.+ |.|
T Consensus 589 ~~~CPkCg~~l~------~~~~k--~g~f~gCs~yp~C 618 (618)
T TIGR01057 589 VGKCPKCGGKLV------SKYAK--KGRFVGCSNYPEC 618 (618)
T ss_pred cCCCCcCCCeee------eeecC--CccEEECCCCCCC
Confidence 357999987411 01111 125899987 444
No 153
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=37.31 E-value=21 Score=23.53 Aligned_cols=18 Identities=28% Similarity=0.453 Sum_probs=11.4
Q ss_pred CCCceEEEEecCCCCCceec
Q psy8689 52 DEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 52 dE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+.-..||+|.+ |+.+|.
T Consensus 103 ~e~~~~~Y~Cp~--c~~r~t 120 (158)
T TIGR00373 103 FETNNMFFICPN--MCVRFT 120 (158)
T ss_pred hccCCCeEECCC--CCcEee
Confidence 344557777765 777663
No 154
>KOG3507|consensus
Probab=37.15 E-value=16 Score=21.14 Aligned_cols=27 Identities=22% Similarity=0.706 Sum_probs=18.0
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
.-.|..||.+... + +. =-+.|.+ |||+
T Consensus 20 iYiCgdC~~en~l----k--~~-----D~irCRe--CG~R 46 (62)
T KOG3507|consen 20 IYICGDCGQENTL----K--RG-----DVIRCRE--CGYR 46 (62)
T ss_pred EEEeccccccccc----c--CC-----CcEehhh--cchH
Confidence 4579999987652 2 22 2367887 9986
No 155
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=36.28 E-value=20 Score=27.78 Aligned_cols=28 Identities=36% Similarity=0.827 Sum_probs=19.9
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
-.||.||.. +.||.. + .|.|.. ||.+.+
T Consensus 351 p~Cp~Cg~~--------m~S~G~--~-g~rC~k--Cg~~~~ 378 (421)
T COG1571 351 PVCPRCGGR--------MKSAGR--N-GFRCKK--CGTRAR 378 (421)
T ss_pred CCCCccCCc--------hhhcCC--C-Cccccc--ccccCC
Confidence 379999964 345543 3 899987 998765
No 156
>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=35.71 E-value=51 Score=18.31 Aligned_cols=7 Identities=43% Similarity=1.459 Sum_probs=3.5
Q ss_pred eCCCCCC
Q psy8689 32 KCPKCEH 38 (72)
Q Consensus 32 ~Cp~Cg~ 38 (72)
.||.||.
T Consensus 4 ~CP~CG~ 10 (54)
T TIGR01206 4 ECPDCGA 10 (54)
T ss_pred CCCCCCC
Confidence 4555554
No 157
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=35.71 E-value=19 Score=24.98 Aligned_cols=12 Identities=33% Similarity=0.841 Sum_probs=9.5
Q ss_pred eeeCCCCCCCce
Q psy8689 30 EEKCPKCEHPRA 41 (72)
Q Consensus 30 ~~~Cp~Cg~~~a 41 (72)
...||+||+.|-
T Consensus 165 ~l~Cp~Cg~tEk 176 (188)
T COG1096 165 MLKCPNCGNTEK 176 (188)
T ss_pred EEECCCCCCEEe
Confidence 478999998765
No 158
>KOG2061|consensus
Probab=35.16 E-value=26 Score=26.62 Aligned_cols=54 Identities=24% Similarity=0.543 Sum_probs=32.8
Q ss_pred cccCCcccccc---CCc-ceeeCCCCCCCceEEEEeeccCCCCC-----ceEEEEecCCCCCc
Q psy8689 15 HVMGGAAAWEN---VDT-TEEKCPKCEHPRAYFMQIQTRSADEP-----MTTFYKCCNIKCGF 68 (72)
Q Consensus 15 ~v~~~~~~~~~---~~~-t~~~Cp~Cg~~~a~~~q~Q~rsadE~-----mTlfy~C~~~~Cg~ 68 (72)
-.+||.-+|.. ++. ....|..||+.-..-.|+---..+++ .-..|.|.++.|.-
T Consensus 29 skiGG~P~wl~~~~~p~~~~l~C~~C~~~~~lllQ~YAP~~~~~~~fhR~LyvF~C~~p~C~~ 91 (362)
T KOG2061|consen 29 SKIGGRPAWLGPDPLPNPEALLCELCGNPLSLLLQVYAPLPDIPSAFHRSLYVFGCRNPSCST 91 (362)
T ss_pred cccCCccccCCcccCCCcccccchhhcChHhhhhhhhccCCCCCCccceEEEEEEcCCCcccc
Confidence 34567665532 333 35899999999887666532113333 33346699988864
No 159
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=35.13 E-value=23 Score=20.62 Aligned_cols=12 Identities=33% Similarity=0.725 Sum_probs=9.6
Q ss_pred eeCCCCCCCceE
Q psy8689 31 EKCPKCEHPRAY 42 (72)
Q Consensus 31 ~~Cp~Cg~~~a~ 42 (72)
..||.||+.+..
T Consensus 19 e~CP~Cgs~~~t 30 (64)
T COG2093 19 EICPVCGSTDLT 30 (64)
T ss_pred ccCCCCCCcccc
Confidence 569999998654
No 160
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=34.93 E-value=28 Score=16.99 Aligned_cols=11 Identities=45% Similarity=0.908 Sum_probs=8.8
Q ss_pred EEEEecCCCCCce
Q psy8689 57 TFYKCCNIKCGFR 69 (72)
Q Consensus 57 lfy~C~~~~Cg~~ 69 (72)
-||.|.. ||+.
T Consensus 6 ~~ykC~~--Cgni 16 (34)
T TIGR00319 6 QVYKCEV--CGNI 16 (34)
T ss_pred cEEEcCC--CCcE
Confidence 4899988 9875
No 161
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=34.83 E-value=33 Score=21.29 Aligned_cols=14 Identities=29% Similarity=0.878 Sum_probs=8.8
Q ss_pred eeeCCCCCCCceEE
Q psy8689 30 EEKCPKCEHPRAYF 43 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~ 43 (72)
...||.||+.....
T Consensus 86 ~~~CP~Cgs~~~~i 99 (113)
T PF01155_consen 86 DFSCPRCGSPDVEI 99 (113)
T ss_dssp CHH-SSSSSS-EEE
T ss_pred CCCCcCCcCCCcEE
Confidence 35799999987644
No 162
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=34.53 E-value=41 Score=17.78 Aligned_cols=8 Identities=38% Similarity=1.174 Sum_probs=5.5
Q ss_pred eeCC--CCCC
Q psy8689 31 EKCP--KCEH 38 (72)
Q Consensus 31 ~~Cp--~Cg~ 38 (72)
..|| +|+.
T Consensus 19 ~~CP~~~C~~ 28 (64)
T smart00647 19 KWCPAPDCSA 28 (64)
T ss_pred cCCCCCCCcc
Confidence 4688 7854
No 163
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=34.33 E-value=21 Score=18.75 Aligned_cols=13 Identities=23% Similarity=0.649 Sum_probs=8.0
Q ss_pred eeCCCCCCCceEE
Q psy8689 31 EKCPKCEHPRAYF 43 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~ 43 (72)
..||.||.+...-
T Consensus 4 ~pCP~CGG~DrFr 16 (40)
T PF08273_consen 4 GPCPICGGKDRFR 16 (40)
T ss_dssp E--TTTT-TTTEE
T ss_pred CCCCCCcCccccc
Confidence 5799999988754
No 164
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=34.14 E-value=29 Score=16.98 Aligned_cols=11 Identities=45% Similarity=0.887 Sum_probs=8.6
Q ss_pred EEEEecCCCCCce
Q psy8689 57 TFYKCCNIKCGFR 69 (72)
Q Consensus 57 lfy~C~~~~Cg~~ 69 (72)
-||.|.. ||+.
T Consensus 3 ~~ykC~~--CGni 13 (34)
T cd00974 3 EVYKCEI--CGNI 13 (34)
T ss_pred cEEEcCC--CCcE
Confidence 4888988 8875
No 165
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=34.04 E-value=24 Score=27.32 Aligned_cols=19 Identities=26% Similarity=0.721 Sum_probs=12.6
Q ss_pred cccCCcc-eeeCCCCCCCce
Q psy8689 23 WENVDTT-EEKCPKCEHPRA 41 (72)
Q Consensus 23 ~~~~~~t-~~~Cp~Cg~~~a 41 (72)
.|.++.- ...||+|||.=.
T Consensus 30 ~P~l~~~q~A~CPRC~~~l~ 49 (418)
T COG2995 30 LPRLDSGQSAYCPRCGHTLT 49 (418)
T ss_pred cccCCCCCcccCCCCCCccc
Confidence 3445554 378999998654
No 166
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=33.98 E-value=21 Score=19.81 Aligned_cols=14 Identities=50% Similarity=1.120 Sum_probs=8.3
Q ss_pred eeCCCCCCCceEEE
Q psy8689 31 EKCPKCEHPRAYFM 44 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~ 44 (72)
..||.|++...+|-
T Consensus 15 ~~Cp~C~~~~l~~~ 28 (55)
T PF08063_consen 15 EPCPKCKGGQLYFD 28 (55)
T ss_dssp ---SSSSE-EEEEE
T ss_pred CCCCCCCCCeEEec
Confidence 58999999877774
No 167
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.82 E-value=23 Score=22.49 Aligned_cols=11 Identities=45% Similarity=1.038 Sum_probs=8.0
Q ss_pred eeCCCCCCCce
Q psy8689 31 EKCPKCEHPRA 41 (72)
Q Consensus 31 ~~Cp~Cg~~~a 41 (72)
..||.||+...
T Consensus 93 ~~CP~Cgs~~~ 103 (124)
T PRK00762 93 IECPVCGNKRA 103 (124)
T ss_pred CcCcCCCCCCC
Confidence 46888886654
No 168
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=33.69 E-value=19 Score=16.68 Aligned_cols=9 Identities=33% Similarity=0.932 Sum_probs=6.3
Q ss_pred eeCCCCCCC
Q psy8689 31 EKCPKCEHP 39 (72)
Q Consensus 31 ~~Cp~Cg~~ 39 (72)
+.||.||..
T Consensus 3 ~~C~~CgR~ 11 (25)
T PF13913_consen 3 VPCPICGRK 11 (25)
T ss_pred CcCCCCCCE
Confidence 568888753
No 169
>KOG2846|consensus
Probab=33.13 E-value=15 Score=27.58 Aligned_cols=35 Identities=20% Similarity=0.477 Sum_probs=22.6
Q ss_pred CCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 26 VDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 26 ~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
.++-.+.|+.|.+....+ |- +|..-+-|.|-. |+|
T Consensus 216 ~~ryALIC~~C~~HNGla-----~~-ee~~yi~F~C~~--Cn~ 250 (328)
T KOG2846|consen 216 NNRYALICSQCHHHNGLA-----RK-EEYEYITFRCPH--CNA 250 (328)
T ss_pred cchhhhcchhhccccCcC-----Ch-hhcCceEEECcc--ccc
Confidence 344468999998665533 32 445555567977 987
No 170
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=33.00 E-value=36 Score=14.12 Aligned_cols=11 Identities=36% Similarity=1.062 Sum_probs=5.0
Q ss_pred EEecCCCCCceec
Q psy8689 59 YKCCNIKCGFRWR 71 (72)
Q Consensus 59 y~C~~~~Cg~~w~ 71 (72)
|.|.. |+..+.
T Consensus 1 ~~C~~--C~~~~~ 11 (24)
T PF13894_consen 1 FQCPI--CGKSFR 11 (24)
T ss_dssp EE-SS--TS-EES
T ss_pred CCCcC--CCCcCC
Confidence 45655 666654
No 171
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=32.78 E-value=20 Score=19.47 Aligned_cols=27 Identities=37% Similarity=0.758 Sum_probs=18.6
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+||+||--.. +|+ ..|.|..|++.++
T Consensus 12 rkCp~CGt~NG------~R~--------~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 12 RKCPKCGTYNG------TRG--------LSCKNKSCPQVFN 38 (44)
T ss_pred ccCCcCcCccC------ccc--------ccccCCccchhhh
Confidence 58999996543 132 4688888887765
No 172
>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=32.59 E-value=26 Score=22.60 Aligned_cols=12 Identities=25% Similarity=0.872 Sum_probs=9.3
Q ss_pred eeeCCCCCCCce
Q psy8689 30 EEKCPKCEHPRA 41 (72)
Q Consensus 30 ~~~Cp~Cg~~~a 41 (72)
.+.||+|++.--
T Consensus 69 ~V~CP~C~K~TK 80 (114)
T PF11023_consen 69 QVECPNCGKQTK 80 (114)
T ss_pred eeECCCCCChHh
Confidence 578999997543
No 173
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=32.10 E-value=40 Score=24.28 Aligned_cols=19 Identities=21% Similarity=0.599 Sum_probs=13.2
Q ss_pred CccccccCCcceeeCCCCC
Q psy8689 19 GAAAWENVDTTEEKCPKCE 37 (72)
Q Consensus 19 ~~~~~~~~~~t~~~Cp~Cg 37 (72)
|....+...++.+.||+|.
T Consensus 137 GlSd~~g~~~VKlyCP~C~ 155 (251)
T PTZ00396 137 GLSDVLKTSRVKVYCPRCQ 155 (251)
T ss_pred ccCCCcCcCceeEeCCCch
Confidence 4344455666788999997
No 174
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=32.07 E-value=28 Score=23.45 Aligned_cols=18 Identities=33% Similarity=0.809 Sum_probs=13.0
Q ss_pred CCCceEEEEecCCCCCceec
Q psy8689 52 DEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 52 dE~mTlfy~C~~~~Cg~~w~ 71 (72)
.|.-..||+|.+ |+.+|.
T Consensus 111 ~e~~~~~Y~Cp~--C~~ryt 128 (178)
T PRK06266 111 EEENNMFFFCPN--CHIRFT 128 (178)
T ss_pred hccCCCEEECCC--CCcEEe
Confidence 444567899977 988874
No 175
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=32.04 E-value=44 Score=18.88 Aligned_cols=16 Identities=19% Similarity=0.482 Sum_probs=12.5
Q ss_pred cceeeCCCCCCCceEE
Q psy8689 28 TTEEKCPKCEHPRAYF 43 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~ 43 (72)
.....||+|++.-++|
T Consensus 56 d~~H~Cp~C~~~lg~~ 71 (73)
T PF10601_consen 56 DVYHYCPNCGAFLGTY 71 (73)
T ss_pred CceEECCCCCCEeEEE
Confidence 4468999999887765
No 176
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.98 E-value=33 Score=21.56 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=8.4
Q ss_pred eCCCCCCCceE
Q psy8689 32 KCPKCEHPRAY 42 (72)
Q Consensus 32 ~Cp~Cg~~~a~ 42 (72)
.||+||+....
T Consensus 90 ~CP~Cgs~~~~ 100 (117)
T PRK00564 90 VCEKCHSKNVI 100 (117)
T ss_pred cCcCCCCCceE
Confidence 59999987653
No 177
>KOG3214|consensus
Probab=31.82 E-value=40 Score=21.50 Aligned_cols=37 Identities=16% Similarity=0.336 Sum_probs=26.0
Q ss_pred ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+.+.||.|+|...+--.+- -..++-|..|.- |+..|.
T Consensus 22 t~FnClfcnHek~v~~~~D----k~~~iG~~sC~i--C~esFq 58 (109)
T KOG3214|consen 22 TQFNCLFCNHEKSVSCTLD----KKHNIGKASCRI--CEESFQ 58 (109)
T ss_pred eeeccCccccccceeeeeh----hhcCcceeeeee--hhhhhc
Confidence 3578999999987654432 234777888988 886653
No 178
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=31.23 E-value=36 Score=23.08 Aligned_cols=10 Identities=40% Similarity=1.036 Sum_probs=6.8
Q ss_pred ceeeCCCCCC
Q psy8689 29 TEEKCPKCEH 38 (72)
Q Consensus 29 t~~~Cp~Cg~ 38 (72)
+...||+|+.
T Consensus 38 tI~~Cp~C~~ 47 (158)
T PF10083_consen 38 TITSCPNCST 47 (158)
T ss_pred HHHHCcCCCC
Confidence 3457888875
No 179
>PRK07726 DNA topoisomerase III; Provisional
Probab=31.19 E-value=40 Score=27.00 Aligned_cols=29 Identities=28% Similarity=0.756 Sum_probs=17.2
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCC
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCG 67 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg 67 (72)
..||+||+.- +.. ..+ -..||.|.+..|.
T Consensus 611 ~~CP~C~~~~-~~~--~~~-----~~~f~~Cs~~~~~ 639 (658)
T PRK07726 611 PKCPDCGKPM-LKV--KGK-----NGKMLVCQDRECG 639 (658)
T ss_pred ccccccCccc-eee--ccc-----CCeeEecCCCccc
Confidence 6799999752 211 111 1358999985554
No 180
>PRK00420 hypothetical protein; Validated
Probab=31.17 E-value=33 Score=21.83 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=7.7
Q ss_pred eeeCCCCCCCc
Q psy8689 30 EEKCPKCEHPR 40 (72)
Q Consensus 30 ~~~Cp~Cg~~~ 40 (72)
...||.||..-
T Consensus 23 ~~~CP~Cg~pL 33 (112)
T PRK00420 23 SKHCPVCGLPL 33 (112)
T ss_pred cCCCCCCCCcc
Confidence 36799998543
No 181
>PF09463 Opy2: Opy2 protein; InterPro: IPR018571 Opy2p acts as a membrane anchor in the HOG signalling pathway []. This entry represents a conserved N-terminal domain.
Probab=30.95 E-value=55 Score=16.81 Aligned_cols=16 Identities=25% Similarity=0.671 Sum_probs=12.8
Q ss_pred eCCCCCCCceEEEEee
Q psy8689 32 KCPKCEHPRAYFMQIQ 47 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q 47 (72)
.||.|..++.-.+..|
T Consensus 10 ~CP~C~~ge~C~~t~~ 25 (35)
T PF09463_consen 10 SCPSCPSGEECVLTSQ 25 (35)
T ss_pred CCCCCCCCCEEEecCC
Confidence 7999999888776644
No 182
>PF14369 zf-RING_3: zinc-finger
Probab=30.80 E-value=34 Score=17.24 Aligned_cols=9 Identities=33% Similarity=1.051 Sum_probs=6.9
Q ss_pred eeCCCCCCC
Q psy8689 31 EKCPKCEHP 39 (72)
Q Consensus 31 ~~Cp~Cg~~ 39 (72)
+.||.|++.
T Consensus 22 ~~CP~C~~g 30 (35)
T PF14369_consen 22 VACPRCHGG 30 (35)
T ss_pred cCCcCCCCc
Confidence 469999863
No 183
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=30.12 E-value=8.9 Score=27.87 Aligned_cols=30 Identities=27% Similarity=0.654 Sum_probs=18.8
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+||+|+.. +| ..+ -..-+++|-+ |||-++
T Consensus 27 ~~c~~c~~~--~~-~~~------l~~~~~vc~~--c~~h~r 56 (285)
T TIGR00515 27 TKCPKCGQV--LY-TKE------LERNLEVCPK--CDHHMR 56 (285)
T ss_pred eECCCCcch--hh-HHH------HHhhCCCCCC--CCCcCc
Confidence 689999853 22 211 2234689966 999765
No 184
>PRK08173 DNA topoisomerase III; Validated
Probab=29.66 E-value=48 Score=27.62 Aligned_cols=28 Identities=36% Similarity=0.809 Sum_probs=18.5
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecC-----CCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-----IKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-----~~Cg~~ 69 (72)
...||+||+. ++ . . ..+|.|.+ +.|+++
T Consensus 726 ~g~CPkCg~~--v~---e-~------~k~y~Cs~~~~~~~~C~f~ 758 (862)
T PRK08173 726 VGACPKCGGR--VF---E-H------GMSYVCEKSVGPPKTCDFR 758 (862)
T ss_pred ccCCCCCCCe--eE---e-e------ceEEEeCCCcCCCCCCCee
Confidence 4689999875 21 1 1 12799997 678755
No 185
>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=29.27 E-value=33 Score=17.68 Aligned_cols=12 Identities=50% Similarity=1.085 Sum_probs=6.9
Q ss_pred eEEEEecCCCCCce
Q psy8689 56 TTFYKCCNIKCGFR 69 (72)
Q Consensus 56 Tlfy~C~~~~Cg~~ 69 (72)
.-||.|.. ||+.
T Consensus 4 ~~~YkC~~--CGni 15 (36)
T PF06397_consen 4 GEFYKCEH--CGNI 15 (36)
T ss_dssp TEEEE-TT--T--E
T ss_pred ccEEEccC--CCCE
Confidence 45899988 9875
No 186
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=29.03 E-value=35 Score=22.41 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=8.0
Q ss_pred eeeCCCCCCCce
Q psy8689 30 EEKCPKCEHPRA 41 (72)
Q Consensus 30 ~~~Cp~Cg~~~a 41 (72)
.+.||.||+++.
T Consensus 44 ~v~CPvC~~~~~ 55 (131)
T COG1645 44 EVFCPVCGYREV 55 (131)
T ss_pred eEECCCCCceEE
Confidence 467888886544
No 187
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=29.02 E-value=37 Score=18.75 Aligned_cols=14 Identities=29% Similarity=0.854 Sum_probs=10.8
Q ss_pred eeCCCCCCCceEEE
Q psy8689 31 EKCPKCEHPRAYFM 44 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~ 44 (72)
+.||.||+.-.+..
T Consensus 1 i~CPyCge~~~~~i 14 (52)
T PF14255_consen 1 IQCPYCGEPIEILI 14 (52)
T ss_pred CCCCCCCCeeEEEE
Confidence 46999999877654
No 188
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=28.90 E-value=33 Score=26.24 Aligned_cols=18 Identities=22% Similarity=0.584 Sum_probs=13.3
Q ss_pred eeCCCCCCCceEEEEeec
Q psy8689 31 EKCPKCEHPRAYFMQIQT 48 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~ 48 (72)
..||+|+.++..-.|+.+
T Consensus 285 W~CpkC~~k~ss~K~~~I 302 (415)
T COG5533 285 WRCPKCGRKESSRKRMEI 302 (415)
T ss_pred ccCchhcccccchheEEE
Confidence 489999988876655543
No 189
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=28.88 E-value=24 Score=19.71 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=8.6
Q ss_pred cceeeCCCCCCC
Q psy8689 28 TTEEKCPKCEHP 39 (72)
Q Consensus 28 ~t~~~Cp~Cg~~ 39 (72)
+-+..||+||..
T Consensus 17 rk~~~CPrCG~g 28 (51)
T COG1998 17 RKNRFCPRCGPG 28 (51)
T ss_pred EccccCCCCCCc
Confidence 335689999953
No 190
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=28.86 E-value=47 Score=24.16 Aligned_cols=26 Identities=23% Similarity=0.611 Sum_probs=16.0
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
.||.||....++-- ..--++|.+ ||-
T Consensus 3 ~CpeCg~~~~~~d~---------~~ge~VC~~--CG~ 28 (285)
T COG1405 3 SCPECGSTNIITDY---------ERGEIVCAD--CGL 28 (285)
T ss_pred CCCCCCCccceeec---------cCCeEEecc--CCE
Confidence 69999988444311 122467887 874
No 191
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=27.72 E-value=57 Score=18.15 Aligned_cols=16 Identities=19% Similarity=0.557 Sum_probs=12.4
Q ss_pred cceeeCCCCCCCceEE
Q psy8689 28 TTEEKCPKCEHPRAYF 43 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~ 43 (72)
.....||+||..-++|
T Consensus 50 d~~H~Cp~C~~~lg~~ 65 (67)
T smart00714 50 DVNHYCPNCGAFLGTY 65 (67)
T ss_pred CccEECCCCCCEeEEe
Confidence 3457999999877766
No 192
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=27.60 E-value=32 Score=19.72 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=7.8
Q ss_pred eCCCCCCCc
Q psy8689 32 KCPKCEHPR 40 (72)
Q Consensus 32 ~Cp~Cg~~~ 40 (72)
.||.||+..
T Consensus 17 ~CP~Cgs~~ 25 (61)
T PRK08351 17 RCPVCGSRD 25 (61)
T ss_pred cCCCCcCCc
Confidence 699999876
No 193
>PF14122 YokU: YokU-like protein
Probab=27.03 E-value=71 Score=19.67 Aligned_cols=38 Identities=24% Similarity=0.586 Sum_probs=21.8
Q ss_pred eCCCCCCC------ceEEEEeec--cCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHP------RAYFMQIQT--RSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~------~a~~~q~Q~--rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
+|.-||+. ..+||.+.. |.-.-.+|--..|.+ ||-.+.
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~--CgmvYq 46 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSN--CGMVYQ 46 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecC--CCcEEe
Confidence 36667764 346675532 222334556677888 886654
No 194
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=26.71 E-value=31 Score=25.27 Aligned_cols=14 Identities=21% Similarity=0.709 Sum_probs=11.7
Q ss_pred EEEEecCCCCCceecC
Q psy8689 57 TFYKCCNIKCGFRWRE 72 (72)
Q Consensus 57 lfy~C~~~~Cg~~w~~ 72 (72)
-+|.|.+ |+|.|+.
T Consensus 154 aef~C~~--C~h~F~G 167 (278)
T PF15135_consen 154 AEFHCPK--CRHNFRG 167 (278)
T ss_pred eeeeccc--ccccchh
Confidence 5799988 9999973
No 195
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=26.56 E-value=56 Score=22.26 Aligned_cols=15 Identities=27% Similarity=0.629 Sum_probs=8.9
Q ss_pred cccCCcceeeCCCCC
Q psy8689 23 WENVDTTEEKCPKCE 37 (72)
Q Consensus 23 ~~~~~~t~~~Cp~Cg 37 (72)
.+...++.+.||+|+
T Consensus 120 ~~g~~~vKlyCP~C~ 134 (184)
T PF01214_consen 120 TPGESTVKLYCPRCK 134 (184)
T ss_dssp STTS-BBEEEETTTT
T ss_pred CCCccceeEECCCCc
Confidence 344555667777776
No 196
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=26.36 E-value=30 Score=18.72 Aligned_cols=33 Identities=15% Similarity=0.479 Sum_probs=20.5
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
..|..|+-.+...|. ....+. -..|.. ||-.|+
T Consensus 4 ~~C~~C~~~~T~~WR----~g~~g~--~~LCna--Cgl~~~ 36 (52)
T smart00401 4 RSCSNCGTTETPLWR----RGPSGN--KTLCNA--CGLYYK 36 (52)
T ss_pred CCcCCCCCCCCCccc----cCCCCC--CcEeec--ccHHHH
Confidence 469999988876653 333333 234666 776664
No 197
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=26.09 E-value=40 Score=21.01 Aligned_cols=9 Identities=22% Similarity=0.671 Sum_probs=6.9
Q ss_pred eeeCCCCCC
Q psy8689 30 EEKCPKCEH 38 (72)
Q Consensus 30 ~~~Cp~Cg~ 38 (72)
...|+.||+
T Consensus 70 ~~~C~~Cg~ 78 (113)
T PRK12380 70 QAWCWDCSQ 78 (113)
T ss_pred EEEcccCCC
Confidence 568888883
No 198
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=26.08 E-value=51 Score=16.14 Aligned_cols=11 Identities=18% Similarity=0.890 Sum_probs=8.5
Q ss_pred EEecCCCCCceec
Q psy8689 59 YKCCNIKCGFRWR 71 (72)
Q Consensus 59 y~C~~~~Cg~~w~ 71 (72)
|.|.+ |+..|.
T Consensus 1 ~sCiD--C~~~F~ 11 (28)
T PF08790_consen 1 FSCID--CSKDFD 11 (28)
T ss_dssp EEETT--TTEEEE
T ss_pred Ceeec--CCCCcC
Confidence 57888 988764
No 199
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=26.05 E-value=35 Score=25.41 Aligned_cols=36 Identities=19% Similarity=0.564 Sum_probs=22.3
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
..||.||+.-+.-+-.+ .-+.++. .|..|.- |.--|
T Consensus 186 ~~CPvCGS~PvaSmV~~-g~~~~Gl-RYL~Csl--C~teW 221 (308)
T COG3058 186 QYCPVCGSMPVASMVQI-GETEQGL-RYLHCSL--CETEW 221 (308)
T ss_pred ccCCCcCCCCcceeeee-cCccccc-hhhhhhh--HHHHH
Confidence 58999999887766533 3344443 4566655 54444
No 200
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=26.00 E-value=36 Score=18.37 Aligned_cols=9 Identities=33% Similarity=0.862 Sum_probs=7.2
Q ss_pred eeeCCCCCC
Q psy8689 30 EEKCPKCEH 38 (72)
Q Consensus 30 ~~~Cp~Cg~ 38 (72)
.+.||.||.
T Consensus 46 i~~Cp~CgR 54 (56)
T PF02591_consen 46 IVFCPNCGR 54 (56)
T ss_pred eEECcCCCc
Confidence 478999984
No 201
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.95 E-value=11 Score=27.72 Aligned_cols=30 Identities=17% Similarity=0.553 Sum_probs=19.0
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+||+|+..- | ..+ --.-+++|.+ |+|-++
T Consensus 39 ~kc~~C~~~~--~-~~~------l~~~~~vcp~--c~~h~r 68 (296)
T CHL00174 39 VQCENCYGLN--Y-KKF------LKSKMNICEQ--CGYHLK 68 (296)
T ss_pred eECCCccchh--h-HHH------HHHcCCCCCC--CCCCcC
Confidence 6899998632 1 111 2234689966 999765
No 202
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=25.91 E-value=22 Score=19.42 Aligned_cols=15 Identities=27% Similarity=0.601 Sum_probs=11.7
Q ss_pred eeeCCCCCCCceEEE
Q psy8689 30 EEKCPKCEHPRAYFM 44 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~ 44 (72)
+..||.||.....|.
T Consensus 34 ~w~CP~C~a~K~~F~ 48 (50)
T cd00730 34 DWVCPVCGAGKDDFE 48 (50)
T ss_pred CCCCCCCCCcHHHcE
Confidence 478999998876553
No 203
>COG4640 Predicted membrane protein [Function unknown]
Probab=25.84 E-value=38 Score=26.46 Aligned_cols=7 Identities=57% Similarity=1.402 Sum_probs=4.4
Q ss_pred eCCCCCC
Q psy8689 32 KCPKCEH 38 (72)
Q Consensus 32 ~Cp~Cg~ 38 (72)
.||+||+
T Consensus 3 fC~kcG~ 9 (465)
T COG4640 3 FCPKCGS 9 (465)
T ss_pred ccccccc
Confidence 4777774
No 204
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=25.75 E-value=33 Score=19.53 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=8.3
Q ss_pred eeeCCCCCCCc
Q psy8689 30 EEKCPKCEHPR 40 (72)
Q Consensus 30 ~~~Cp~Cg~~~ 40 (72)
...||+||+.-
T Consensus 41 ~~~CPNCgGel 51 (57)
T PF06906_consen 41 NGVCPNCGGEL 51 (57)
T ss_pred cCcCcCCCCcc
Confidence 45799999753
No 205
>PRK08197 threonine synthase; Validated
Probab=25.57 E-value=62 Score=23.96 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=6.9
Q ss_pred eeeCCCCCCC
Q psy8689 30 EEKCPKCEHP 39 (72)
Q Consensus 30 ~~~Cp~Cg~~ 39 (72)
...|.+||+.
T Consensus 7 ~~~C~~Cg~~ 16 (394)
T PRK08197 7 HLECSKCGET 16 (394)
T ss_pred EEEECCCCCC
Confidence 3678888755
No 206
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=25.42 E-value=1e+02 Score=19.21 Aligned_cols=27 Identities=37% Similarity=0.904 Sum_probs=17.6
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.|.-| ....++ |.- - ..+|.+ |+.+|.
T Consensus 37 aCeiC-~~~GY~-q~g-------~--~lvC~~--C~~~~~ 63 (102)
T PF10080_consen 37 ACEIC-GPKGYY-QEG-------D--QLVCKN--CGVRFN 63 (102)
T ss_pred ecccc-CCCceE-EEC-------C--EEEEec--CCCEEe
Confidence 69999 334444 421 1 468999 999984
No 207
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=25.32 E-value=65 Score=25.71 Aligned_cols=32 Identities=28% Similarity=0.547 Sum_probs=20.9
Q ss_pred eeeCCCCCC-CceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEH-PRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~-~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
...||+||. ..+.-.. -|..-|+-|.|. |||.
T Consensus 171 ~piC~kcGri~~t~v~~-----~d~~~~v~Y~Ce---~Gh~ 203 (521)
T COG1384 171 MPICEKCGRILTTPVIE-----WDGEGTVEYRCE---CGHE 203 (521)
T ss_pred cccccccCCcceeEEEE-----ecCCceEEEEec---CCcc
Confidence 467999998 3332222 233478999997 7873
No 208
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.32 E-value=35 Score=21.92 Aligned_cols=15 Identities=40% Similarity=1.052 Sum_probs=10.1
Q ss_pred eeCCCCCCC-ceEEEE
Q psy8689 31 EKCPKCEHP-RAYFMQ 45 (72)
Q Consensus 31 ~~Cp~Cg~~-~a~~~q 45 (72)
-.||+||.. +++|.-
T Consensus 50 t~CP~Cg~~~e~~fvv 65 (115)
T COG1885 50 TSCPKCGEPFESAFVV 65 (115)
T ss_pred ccCCCCCCccceeEEE
Confidence 379999964 555543
No 209
>PF15616 TerY-C: TerY-C metal binding domain
Probab=25.21 E-value=66 Score=21.03 Aligned_cols=10 Identities=40% Similarity=1.029 Sum_probs=8.1
Q ss_pred eCCCCCCCce
Q psy8689 32 KCPKCEHPRA 41 (72)
Q Consensus 32 ~Cp~Cg~~~a 41 (72)
-||-||+.-+
T Consensus 79 gCP~CGn~~~ 88 (131)
T PF15616_consen 79 GCPHCGNQYA 88 (131)
T ss_pred CCCCCcChhc
Confidence 6999998755
No 210
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=25.20 E-value=39 Score=22.22 Aligned_cols=15 Identities=7% Similarity=0.062 Sum_probs=10.7
Q ss_pred CCcceeeCCCCCCCc
Q psy8689 26 VDTTEEKCPKCEHPR 40 (72)
Q Consensus 26 ~~~t~~~Cp~Cg~~~ 40 (72)
|.+..+.||+||..-
T Consensus 22 Lnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 22 LNRRPAVSPYTGEQF 36 (129)
T ss_pred cCCCCccCCCcCCcc
Confidence 345567899999753
No 211
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=24.66 E-value=72 Score=23.13 Aligned_cols=17 Identities=24% Similarity=0.794 Sum_probs=13.3
Q ss_pred eeeCCCCCCCceEEEEe
Q psy8689 30 EEKCPKCEHPRAYFMQI 46 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~ 46 (72)
.+.||+||+...+++.+
T Consensus 82 ~~tCp~Cg~e~~v~~~l 98 (249)
T PHA02611 82 TFTCPKCKKEKTVLFNL 98 (249)
T ss_pred EEECCCCCCceeEEEEe
Confidence 36899999997776654
No 212
>smart00532 LIGANc Ligase N family.
Probab=24.62 E-value=75 Score=24.47 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=18.1
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCC
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCG 67 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg 67 (72)
...||.||+.-... .++ ..+.|.|+.|-
T Consensus 399 P~~CP~C~s~l~~~-------~~~---~~~~C~n~~C~ 426 (441)
T smart00532 399 PTHCPSCGSELVRE-------EGE---VDIRCPNPLCP 426 (441)
T ss_pred CCCCCCCCCEeEec-------CCc---eEEEeCCCCCH
Confidence 35799999876421 122 45668887784
No 213
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=24.49 E-value=1.4e+02 Score=18.39 Aligned_cols=32 Identities=28% Similarity=0.791 Sum_probs=22.0
Q ss_pred cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.....||.||..... | ..+-+..|.. |++.|-
T Consensus 34 ~a~y~CpfCgk~~vk------R----~a~GIW~C~~--C~~~~A 65 (90)
T PRK03976 34 RAKHVCPVCGRPKVK------R----VGTGIWECRK--CGAKFA 65 (90)
T ss_pred hcCccCCCCCCCceE------E----EEEEEEEcCC--CCCEEe
Confidence 345789999765542 1 2456789988 998873
No 214
>KOG0006|consensus
Probab=24.32 E-value=78 Score=24.31 Aligned_cols=36 Identities=31% Similarity=0.828 Sum_probs=19.8
Q ss_pred cCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689 25 NVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70 (72)
Q Consensus 25 ~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w 70 (72)
+...+...||+|.-.-- . .+=-...+|+.|.||.-|
T Consensus 392 TIk~tTkpCPkChvptE--------r--nGGCmHm~Ct~~~Cg~eW 427 (446)
T KOG0006|consen 392 TIKKTTKPCPKCHVPTE--------R--NGGCMHMKCTQPQCGLEW 427 (446)
T ss_pred hhhhccCCCCCccCccc--------c--CCceEEeecCCCCCCcee
Confidence 33445678999973211 1 111234567777777665
No 215
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=24.08 E-value=64 Score=14.73 Aligned_cols=11 Identities=45% Similarity=1.089 Sum_probs=6.7
Q ss_pred EEecCCCCCceec
Q psy8689 59 YKCCNIKCGFRWR 71 (72)
Q Consensus 59 y~C~~~~Cg~~w~ 71 (72)
|.|.. |+..|.
T Consensus 15 ~~C~~--C~k~F~ 25 (26)
T PF13465_consen 15 YKCPY--CGKSFS 25 (26)
T ss_dssp EEESS--SSEEES
T ss_pred CCCCC--CcCeeC
Confidence 66655 766654
No 216
>PF14400 Transglut_i_TM: Inactive transglutaminase fused to 7 transmembrane helices
Probab=23.66 E-value=1e+02 Score=20.79 Aligned_cols=22 Identities=32% Similarity=0.539 Sum_probs=16.7
Q ss_pred CCCceEEEEeeccCCCCCceEEEEe
Q psy8689 37 EHPRAYFMQIQTRSADEPMTTFYKC 61 (72)
Q Consensus 37 g~~~a~~~q~Q~rsadE~mTlfy~C 61 (72)
+++.|.|. +|.|..+.||||.=
T Consensus 68 ~~RrA~WS---~R~A~G~QtLYYr~ 89 (165)
T PF14400_consen 68 GNRRAEWS---IRRASGPQTLYYRV 89 (165)
T ss_pred CCcEEEEe---cccCCCceEEEEEE
Confidence 46666663 48899999999974
No 217
>cd01204 IRS_PTB Insulin receptor substrate (IRS) Phosphotyrosine-binding domain(PTB). Insulin receptor substrate (IRS) Phosphotyrosine-binding domain(PTB). This domain has a PH-like fold and is found in insulin receptor substrate molecules. IRS molecules have an N-terminal PH domain , which is followed by an IRS-like PTB domain. This PTBi domain is shorter than the PTB domain which is found in SHC, Numb and other proteins. The PTBi domain binds to phosphotyrosines which are in NPXpY motifs in the insulin receptor, IGF-I receptor and the IL-4 receptor.
Probab=23.38 E-value=79 Score=20.06 Aligned_cols=23 Identities=26% Similarity=0.388 Sum_probs=18.3
Q ss_pred CCCCCCCceEEEEeeccCCCCCc
Q psy8689 33 CPKCEHPRAYFMQIQTRSADEPM 55 (72)
Q Consensus 33 Cp~Cg~~~a~~~q~Q~rsadE~m 55 (72)
=.+|||.+.+||.-=.|||--+.
T Consensus 52 IRRCGHs~~~Ff~E~GRsa~tG~ 74 (104)
T cd01204 52 IRRCGHSENFFFIEVGRSAVTGP 74 (104)
T ss_pred eeeccCcccEEEEEecccccCCC
Confidence 45899999999987888876543
No 218
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=23.32 E-value=41 Score=20.82 Aligned_cols=29 Identities=17% Similarity=0.624 Sum_probs=16.8
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
+..|-.||..+..|..+... .|+|.. |..
T Consensus 13 N~~CaDCg~~~p~w~s~~~G--------iflC~~--Cag 41 (116)
T PF01412_consen 13 NKVCADCGAPNPTWASLNYG--------IFLCLE--CAG 41 (116)
T ss_dssp CTB-TTT-SBS--EEETTTT--------EEE-HH--HHH
T ss_pred cCcCCCCCCCCCCEEEeecC--------hhhhHH--HHH
Confidence 46899999999988764422 577887 853
No 219
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=23.06 E-value=80 Score=20.40 Aligned_cols=9 Identities=44% Similarity=1.117 Sum_probs=5.7
Q ss_pred eeCCCCCCC
Q psy8689 31 EKCPKCEHP 39 (72)
Q Consensus 31 ~~Cp~Cg~~ 39 (72)
..||+|+.+
T Consensus 44 ~~Cp~C~~~ 52 (140)
T COG1545 44 AYCPKCGSE 52 (140)
T ss_pred ccCCCCCCC
Confidence 356667666
No 220
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.98 E-value=47 Score=18.56 Aligned_cols=11 Identities=36% Similarity=1.192 Sum_probs=8.6
Q ss_pred eeCCCCCCCce
Q psy8689 31 EKCPKCEHPRA 41 (72)
Q Consensus 31 ~~Cp~Cg~~~a 41 (72)
..||.||+-..
T Consensus 28 ~~C~~CG~~~~ 38 (57)
T PRK12286 28 VECPNCGEPKL 38 (57)
T ss_pred eECCCCCCccC
Confidence 68999997543
No 221
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.97 E-value=1e+02 Score=21.86 Aligned_cols=17 Identities=29% Similarity=0.591 Sum_probs=11.0
Q ss_pred ceeeCCCCCCCceEEEE
Q psy8689 29 TEEKCPKCEHPRAYFMQ 45 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~~~q 45 (72)
....||+||..=....+
T Consensus 243 ~g~pCprCG~~I~~~~~ 259 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVV 259 (272)
T ss_pred CCCcCCCCCCeeEEEEE
Confidence 35689999965543333
No 222
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=22.97 E-value=70 Score=14.17 Aligned_cols=11 Identities=27% Similarity=1.014 Sum_probs=7.6
Q ss_pred EEecCCCCCceec
Q psy8689 59 YKCCNIKCGFRWR 71 (72)
Q Consensus 59 y~C~~~~Cg~~w~ 71 (72)
|.|.. |+..|.
T Consensus 2 ~~C~~--C~~~F~ 12 (27)
T PF13912_consen 2 FECDE--CGKTFS 12 (27)
T ss_dssp EEETT--TTEEES
T ss_pred CCCCc--cCCccC
Confidence 56777 877664
No 223
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=22.90 E-value=51 Score=21.94 Aligned_cols=14 Identities=21% Similarity=0.498 Sum_probs=11.1
Q ss_pred ceeeCCCCCCCceE
Q psy8689 29 TEEKCPKCEHPRAY 42 (72)
Q Consensus 29 t~~~Cp~Cg~~~a~ 42 (72)
-.+.||-||+..+.
T Consensus 31 glv~CP~Cgs~~V~ 44 (148)
T PF06676_consen 31 GLVSCPVCGSTEVS 44 (148)
T ss_pred CCccCCCCCCCeEe
Confidence 35899999987764
No 224
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=22.70 E-value=27 Score=25.88 Aligned_cols=30 Identities=30% Similarity=0.786 Sum_probs=20.4
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+||+|++ ..| . .|-.+-+++|.+ |+|-++
T Consensus 29 ~KCp~c~~--~~y-~------~eL~~n~~vcp~--c~~h~r 58 (294)
T COG0777 29 TKCPSCGE--MLY-R------KELESNLKVCPK--CGHHMR 58 (294)
T ss_pred eECCCccc--eee-H------HHHHhhhhcccc--cCcccc
Confidence 68999985 233 1 244566788977 998654
No 225
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=22.56 E-value=45 Score=19.20 Aligned_cols=13 Identities=31% Similarity=0.879 Sum_probs=9.9
Q ss_pred ceeeCCCCCCCce
Q psy8689 29 TEEKCPKCEHPRA 41 (72)
Q Consensus 29 t~~~Cp~Cg~~~a 41 (72)
+.+.||.||....
T Consensus 5 ~~v~CP~C~k~~~ 17 (62)
T PRK00418 5 ITVNCPTCGKPVE 17 (62)
T ss_pred ccccCCCCCCccc
Confidence 3579999998643
No 226
>PRK14724 DNA topoisomerase III; Provisional
Probab=22.56 E-value=1.1e+02 Score=25.91 Aligned_cols=22 Identities=36% Similarity=0.813 Sum_probs=14.8
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecC
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN 63 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~ 63 (72)
...||+||+.- + . -..+|.|.+
T Consensus 755 ~g~CPkCg~~v--~-e---------~gk~y~Cs~ 776 (987)
T PRK14724 755 LGPCPKCGAPV--F-E---------HGSNYVCEK 776 (987)
T ss_pred ccCCCCCCCce--E-e---------ecceEEcCC
Confidence 46899998762 2 1 134789987
No 227
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=22.42 E-value=41 Score=17.39 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=7.1
Q ss_pred eeeCCCCCC
Q psy8689 30 EEKCPKCEH 38 (72)
Q Consensus 30 ~~~Cp~Cg~ 38 (72)
...|+.||-
T Consensus 13 ~~~C~~CgM 21 (41)
T PF13878_consen 13 ATTCPTCGM 21 (41)
T ss_pred CcCCCCCCC
Confidence 368999984
No 228
>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=22.04 E-value=57 Score=15.65 Aligned_cols=11 Identities=27% Similarity=0.806 Sum_probs=4.9
Q ss_pred eeCCCCCCCce
Q psy8689 31 EKCPKCEHPRA 41 (72)
Q Consensus 31 ~~Cp~Cg~~~a 41 (72)
..|++||..-.
T Consensus 4 rfC~~CG~~t~ 14 (32)
T PF09297_consen 4 RFCGRCGAPTK 14 (32)
T ss_dssp SB-TTT--BEE
T ss_pred cccCcCCcccc
Confidence 35778877544
No 229
>PRK12496 hypothetical protein; Provisional
Probab=21.85 E-value=42 Score=22.30 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=7.5
Q ss_pred eeCCCCCCCc
Q psy8689 31 EKCPKCEHPR 40 (72)
Q Consensus 31 ~~Cp~Cg~~~ 40 (72)
..||.||++-
T Consensus 144 ~~C~~CG~~~ 153 (164)
T PRK12496 144 DVCEICGSPV 153 (164)
T ss_pred CcCCCCCChh
Confidence 3599999763
No 230
>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=21.75 E-value=57 Score=20.35 Aligned_cols=9 Identities=33% Similarity=0.940 Sum_probs=6.7
Q ss_pred eeeCCCCCC
Q psy8689 30 EEKCPKCEH 38 (72)
Q Consensus 30 ~~~Cp~Cg~ 38 (72)
...|+.||+
T Consensus 70 ~~~C~~Cg~ 78 (115)
T TIGR00100 70 ECECEDCSE 78 (115)
T ss_pred EEEcccCCC
Confidence 468888883
No 231
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=21.52 E-value=32 Score=18.57 Aligned_cols=13 Identities=31% Similarity=0.836 Sum_probs=8.2
Q ss_pred eeeCCCCCCCceE
Q psy8689 30 EEKCPKCEHPRAY 42 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~ 42 (72)
+..||.|+..+..
T Consensus 34 ~w~CP~C~a~K~~ 46 (47)
T PF00301_consen 34 DWVCPVCGAPKSD 46 (47)
T ss_dssp T-B-TTTSSBGGG
T ss_pred CCcCcCCCCcccc
Confidence 3789999987643
No 232
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=21.47 E-value=1e+02 Score=25.57 Aligned_cols=32 Identities=19% Similarity=0.601 Sum_probs=19.5
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecC----CCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN----IKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~----~~Cg~~ 69 (72)
...||+||.. .+. . ..|- + .|+.|.+ +.|.+.
T Consensus 587 ~~~CP~Cg~~-l~~-r-~gr~---G--~Fl~Cs~y~~~p~C~~~ 622 (859)
T PRK07561 587 DRDCPTCGRG-MGI-R-TGKT---G--VFLGCSGYALKERCKTT 622 (859)
T ss_pred cccCcccCCc-ceE-E-ecCC---C--CeeeccCCcCCCCCCCC
Confidence 4789999975 222 1 2221 2 3888986 678763
No 233
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.45 E-value=1.2e+02 Score=21.64 Aligned_cols=16 Identities=25% Similarity=0.530 Sum_probs=11.3
Q ss_pred eeeCCCCCCCceEEEE
Q psy8689 30 EEKCPKCEHPRAYFMQ 45 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q 45 (72)
...||.||..=..-.+
T Consensus 254 g~pC~~Cg~~I~~~~~ 269 (282)
T PRK13945 254 GKPCRKCGTPIERIKL 269 (282)
T ss_pred cCCCCcCCCeeEEEEE
Confidence 4689999976554444
No 234
>KOG3277|consensus
Probab=21.42 E-value=76 Score=21.66 Aligned_cols=37 Identities=16% Similarity=0.328 Sum_probs=28.2
Q ss_pred Ccce--eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 27 DTTE--EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 27 ~~t~--~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
|++. ..|..|+.+..-.+. ..|-+.=++|..|.. |..
T Consensus 74 p~m~l~yTCkvCntRs~ktis---k~AY~~GvVivqC~g--C~~ 112 (165)
T KOG3277|consen 74 PRMQLAYTCKVCNTRSTKTIS---KQAYEKGVVIVQCPG--CKN 112 (165)
T ss_pred cceEEEEEeeccCCccccccC---hhhhhCceEEEECCC--Ccc
Confidence 4554 589999988887666 447788899999976 864
No 235
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=21.30 E-value=95 Score=25.08 Aligned_cols=27 Identities=26% Similarity=0.752 Sum_probs=17.3
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCC
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCG 67 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg 67 (72)
..||.||+.-.. ..+ - ..+.|.|+.|-
T Consensus 393 ~~CP~C~s~l~~-------~~~--~-~~~~C~n~~C~ 419 (652)
T TIGR00575 393 THCPSCGSPLVK-------IEE--E-AVIRCPNLNCP 419 (652)
T ss_pred CCCCCCCCEeEe-------cCC--c-EEEEECCCCCH
Confidence 479999987642 111 1 45668887784
No 236
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=21.30 E-value=22 Score=19.59 Aligned_cols=12 Identities=17% Similarity=0.598 Sum_probs=6.3
Q ss_pred CCCCCCCceEEE
Q psy8689 33 CPKCEHPRAYFM 44 (72)
Q Consensus 33 Cp~Cg~~~a~~~ 44 (72)
|..|+-.+...|
T Consensus 2 C~~C~~~~Tp~W 13 (54)
T cd00202 2 CSNCGTTTTPLW 13 (54)
T ss_pred CCCCCCCCCccc
Confidence 556665555433
No 237
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=21.23 E-value=70 Score=16.39 Aligned_cols=9 Identities=33% Similarity=0.674 Sum_probs=6.7
Q ss_pred CCCceEEEE
Q psy8689 52 DEPMTTFYK 60 (72)
Q Consensus 52 dE~mTlfy~ 60 (72)
...+||||-
T Consensus 5 ~~qLTIfY~ 13 (36)
T PF06200_consen 5 TAQLTIFYG 13 (36)
T ss_pred CCcEEEEEC
Confidence 346999993
No 238
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=21.19 E-value=51 Score=19.12 Aligned_cols=9 Identities=22% Similarity=0.667 Sum_probs=7.9
Q ss_pred eCCCCCCCc
Q psy8689 32 KCPKCEHPR 40 (72)
Q Consensus 32 ~Cp~Cg~~~ 40 (72)
.||.||+..
T Consensus 19 ~Cp~Cgs~~ 27 (64)
T PRK06393 19 TCPVHGDEK 27 (64)
T ss_pred cCCCCCCCc
Confidence 799999975
No 239
>PRK02935 hypothetical protein; Provisional
Probab=21.11 E-value=56 Score=20.94 Aligned_cols=10 Identities=50% Similarity=1.338 Sum_probs=8.3
Q ss_pred eeeCCCCCCC
Q psy8689 30 EEKCPKCEHP 39 (72)
Q Consensus 30 ~~~Cp~Cg~~ 39 (72)
.+.||+|++.
T Consensus 70 qV~CP~C~K~ 79 (110)
T PRK02935 70 QVICPSCEKP 79 (110)
T ss_pred eeECCCCCch
Confidence 5799999874
No 240
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.10 E-value=70 Score=20.53 Aligned_cols=12 Identities=50% Similarity=1.293 Sum_probs=8.1
Q ss_pred EEEEecCCCCCcee
Q psy8689 57 TFYKCCNIKCGFRW 70 (72)
Q Consensus 57 lfy~C~~~~Cg~~w 70 (72)
..+.|.+ ||+.|
T Consensus 69 ~~~~C~~--CG~~~ 80 (135)
T PRK03824 69 AVLKCRN--CGNEW 80 (135)
T ss_pred eEEECCC--CCCEE
Confidence 4566766 77766
No 241
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=21.05 E-value=18 Score=26.37 Aligned_cols=30 Identities=27% Similarity=0.706 Sum_probs=18.6
Q ss_pred eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689 31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~ 71 (72)
.+||+|+.. .+..+. -.-+++|-. |+|-++
T Consensus 28 ~~c~~c~~~---~~~~~l------~~~~~vc~~--c~~h~r 57 (292)
T PRK05654 28 TKCPSCGQV---LYRKEL------EANLNVCPK--CGHHMR 57 (292)
T ss_pred eECCCccch---hhHHHH------HhcCCCCCC--CCCCee
Confidence 689999863 222221 223578966 999765
No 242
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.93 E-value=1.2e+02 Score=21.54 Aligned_cols=30 Identities=27% Similarity=0.522 Sum_probs=18.2
Q ss_pred eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689 30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~ 69 (72)
...||.||..=....+.+ |+ + |.|-. |...
T Consensus 235 g~pC~~Cg~~I~~~~~~g-R~------t-y~Cp~--CQ~~ 264 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGG-RG------T-HFCPQ--CQPL 264 (269)
T ss_pred cCCCCcCCCeeEEEEECC-CC------c-EECCC--CcCC
Confidence 468999997755544432 43 3 44755 8653
No 243
>PHA02325 hypothetical protein
Probab=20.89 E-value=44 Score=19.70 Aligned_cols=24 Identities=17% Similarity=0.429 Sum_probs=14.2
Q ss_pred eeeCCCCCC---CceEEEEeeccCCCC
Q psy8689 30 EEKCPKCEH---PRAYFMQIQTRSADE 53 (72)
Q Consensus 30 ~~~Cp~Cg~---~~a~~~q~Q~rsadE 53 (72)
...||+||. ..-.||.--.+.+++
T Consensus 3 ~k~CPkC~A~WldgqhYWsgTgk~g~~ 29 (72)
T PHA02325 3 TKICPKCGARWLDGQHYWSGTGKKGNP 29 (72)
T ss_pred ccccCccCCEeEcceeeeccCCCcCCc
Confidence 367999995 344566544444443
No 244
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=20.51 E-value=1.4e+02 Score=19.18 Aligned_cols=14 Identities=14% Similarity=0.539 Sum_probs=4.0
Q ss_pred eeCCCCCCCceEEE
Q psy8689 31 EKCPKCEHPRAYFM 44 (72)
Q Consensus 31 ~~Cp~Cg~~~a~~~ 44 (72)
+-|..|+.+.-+-.
T Consensus 28 ~~Ca~C~krdfv~i 41 (112)
T PF06573_consen 28 VGCASCQKRDFVLI 41 (112)
T ss_dssp ---SSS--SS-EEE
T ss_pred hhhhccCCCCcEEE
Confidence 34555555554433
No 245
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.42 E-value=49 Score=21.68 Aligned_cols=12 Identities=33% Similarity=1.030 Sum_probs=9.3
Q ss_pred eeeCCCCCCCce
Q psy8689 30 EEKCPKCEHPRA 41 (72)
Q Consensus 30 ~~~Cp~Cg~~~a 41 (72)
.-.||+||..+-
T Consensus 21 ~grCP~CGeGrL 32 (126)
T COG5349 21 RGRCPRCGEGRL 32 (126)
T ss_pred cCCCCCCCCchh
Confidence 358999998665
No 246
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=20.41 E-value=50 Score=18.58 Aligned_cols=10 Identities=30% Similarity=0.876 Sum_probs=7.8
Q ss_pred ceeeCCCCCC
Q psy8689 29 TEEKCPKCEH 38 (72)
Q Consensus 29 t~~~Cp~Cg~ 38 (72)
.+..||.||-
T Consensus 13 v~~~Cp~cGi 22 (55)
T PF13824_consen 13 VNFECPDCGI 22 (55)
T ss_pred cCCcCCCCCC
Confidence 4578999994
No 247
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=20.20 E-value=76 Score=19.90 Aligned_cols=18 Identities=17% Similarity=0.266 Sum_probs=12.8
Q ss_pred eeeCCCCCCCceEEEEee
Q psy8689 30 EEKCPKCEHPRAYFMQIQ 47 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~Q 47 (72)
.+.||-||.+.-.=|..+
T Consensus 3 LI~CP~Cg~R~e~EFt~~ 20 (97)
T COG4311 3 LIPCPYCGERPEEEFTYA 20 (97)
T ss_pred eecCCCCCCCchhheeec
Confidence 478999998665555544
No 248
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=20.17 E-value=46 Score=17.62 Aligned_cols=17 Identities=18% Similarity=0.540 Sum_probs=12.3
Q ss_pred eeeCCCCCCCceEEEEe
Q psy8689 30 EEKCPKCEHPRAYFMQI 46 (72)
Q Consensus 30 ~~~Cp~Cg~~~a~~~q~ 46 (72)
...|.+|+..+...|+=
T Consensus 4 ~~~CqkC~~~GH~tyeC 20 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYEC 20 (42)
T ss_pred CCcCcccCCCCcchhhC
Confidence 46799998877766553
No 249
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.09 E-value=53 Score=19.95 Aligned_cols=13 Identities=46% Similarity=1.076 Sum_probs=9.9
Q ss_pred eEEEEecCCCCCcee
Q psy8689 56 TTFYKCCNIKCGFRW 70 (72)
Q Consensus 56 Tlfy~C~~~~Cg~~w 70 (72)
|.-|.|.+ |||++
T Consensus 10 tY~Y~c~~--cg~~~ 22 (82)
T COG2331 10 TYSYECTE--CGNRF 22 (82)
T ss_pred ceEEeecc--cchHH
Confidence 44588988 99875
No 250
>KOG4080|consensus
Probab=20.08 E-value=45 Score=22.97 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=7.9
Q ss_pred eeCCCCCCCc
Q psy8689 31 EKCPKCEHPR 40 (72)
Q Consensus 31 ~~Cp~Cg~~~ 40 (72)
..||.|||-.
T Consensus 94 ~~CP~CGh~k 103 (176)
T KOG4080|consen 94 NTCPACGHIK 103 (176)
T ss_pred ccCcccCccc
Confidence 5799999843
No 251
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=20.03 E-value=78 Score=21.84 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=21.7
Q ss_pred eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68 (72)
Q Consensus 32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~ 68 (72)
.|.+|+.+.|.+--.|+-. + .-+-+|+|-+ |..
T Consensus 2 iCq~CqqnpAti~~tkI~~-~-~k~e~~vCe~--Ca~ 34 (176)
T COG3880 2 ICQNCQQNPATIHFTKIIN-G-EKIELYVCET--CAK 34 (176)
T ss_pred cchhhcCCcceEEEEEeec-C-CeeEeehhhc--CCC
Confidence 5999999888764434332 2 2344899988 854
Done!