Query 020974
Match_columns 319
No_of_seqs 214 out of 1030
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 06:37:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020974.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020974hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01385 TFSII transcription 100.0 1.3E-67 2.8E-72 496.5 24.6 286 7-310 3-299 (299)
2 KOG1105 Transcription elongati 100.0 1.8E-61 4E-66 448.5 21.9 287 9-310 3-296 (296)
3 smart00510 TFS2M Domain in the 99.9 2.5E-27 5.5E-32 190.7 10.9 102 135-244 1-102 (102)
4 PF07500 TFIIS_M: Transcriptio 99.9 6E-27 1.3E-31 192.6 6.2 114 133-255 1-114 (115)
5 smart00440 ZnF_C2C2 C2C2 Zinc 99.8 6.5E-19 1.4E-23 118.2 3.9 39 271-309 1-40 (40)
6 PF01096 TFIIS_C: Transcriptio 99.7 2.5E-18 5.4E-23 114.7 4.0 38 271-308 1-39 (39)
7 smart00509 TFS2N Domain in the 99.7 2E-17 4.3E-22 126.1 5.3 74 8-84 1-74 (75)
8 KOG2906 RNA polymerase III sub 99.7 1.4E-17 3.1E-22 129.9 1.7 43 267-309 62-105 (105)
9 COG1594 RPB9 DNA-directed RNA 99.6 4E-16 8.6E-21 127.8 3.9 44 267-310 69-113 (113)
10 cd00183 TFIIS_I N-terminal dom 99.6 2E-15 4.2E-20 115.4 5.9 72 10-84 5-76 (76)
11 PHA02998 RNA polymerase subuni 99.5 3.4E-15 7.3E-20 128.7 4.4 45 269-313 142-187 (195)
12 TIGR01384 TFS_arch transcripti 99.5 3.6E-15 7.9E-20 120.3 4.4 43 268-310 60-103 (104)
13 PF08711 Med26: TFIIS helical 99.4 1.5E-13 3.3E-18 97.7 2.2 52 33-84 1-53 (53)
14 KOG1634 Predicted transcriptio 99.3 4.8E-13 1E-17 137.7 3.9 82 167-249 266-348 (778)
15 KOG2691 RNA polymerase II subu 99.3 1.1E-12 2.4E-17 104.3 3.4 44 266-309 69-113 (113)
16 KOG2907 RNA polymerase I trans 99.2 4.7E-12 1E-16 101.6 1.7 43 268-310 72-115 (116)
17 KOG2821 RNA polymerase II tran 96.9 0.00045 9.8E-09 68.2 2.0 74 5-86 7-80 (433)
18 PF11467 LEDGF: Lens epitheliu 96.8 0.0011 2.4E-08 53.8 3.0 78 2-84 1-80 (106)
19 KOG1793 Uncharacterized conser 95.9 0.0092 2E-07 58.3 4.5 61 26-86 230-293 (417)
20 PF09855 DUF2082: Nucleic-acid 95.4 0.017 3.6E-07 42.7 3.3 36 271-306 1-45 (64)
21 PRK09678 DNA-binding transcrip 95.1 0.017 3.8E-07 43.6 2.5 40 270-310 1-42 (72)
22 PF04606 Ogr_Delta: Ogr/Delta- 94.8 0.027 5.7E-07 38.9 2.7 37 272-310 1-40 (47)
23 COG5139 Uncharacterized conser 94.2 0.067 1.5E-06 50.5 4.7 59 26-84 227-287 (397)
24 PF13717 zinc_ribbon_4: zinc-r 94.0 0.031 6.7E-07 36.4 1.5 35 270-308 2-36 (36)
25 PF08274 PhnA_Zn_Ribbon: PhnA 93.1 0.051 1.1E-06 34.0 1.3 28 271-308 3-30 (30)
26 TIGR02098 MJ0042_CXXC MJ0042 f 92.9 0.086 1.9E-06 34.3 2.2 35 270-309 2-37 (38)
27 COG3478 Predicted nucleic-acid 92.9 0.1 2.3E-06 38.3 2.8 36 269-306 3-49 (68)
28 TIGR00686 phnA alkylphosphonat 92.5 0.075 1.6E-06 43.0 1.8 30 271-310 3-32 (109)
29 PF12760 Zn_Tnp_IS1595: Transp 92.3 0.14 3E-06 35.0 2.8 29 270-306 18-46 (46)
30 PF13719 zinc_ribbon_5: zinc-r 92.0 0.097 2.1E-06 34.2 1.6 35 270-309 2-37 (37)
31 PHA00626 hypothetical protein 91.6 0.19 4.1E-06 36.0 2.8 36 272-315 2-39 (59)
32 PRK10220 hypothetical protein; 91.3 0.14 3.1E-06 41.5 2.1 31 271-311 4-34 (111)
33 COG4888 Uncharacterized Zn rib 91.1 0.27 5.8E-06 39.3 3.5 37 269-309 21-58 (104)
34 PF08271 TF_Zn_Ribbon: TFIIB z 90.4 0.31 6.7E-06 32.8 2.9 31 271-309 1-31 (43)
35 COG2051 RPS27A Ribosomal prote 89.9 0.21 4.7E-06 36.9 1.8 29 269-306 18-47 (67)
36 TIGR00244 transcriptional regu 89.2 0.3 6.5E-06 41.8 2.5 39 271-309 1-40 (147)
37 PF05129 Elf1: Transcription e 88.6 0.58 1.2E-05 36.1 3.6 40 267-310 19-59 (81)
38 PF14354 Lar_restr_allev: Rest 88.2 0.75 1.6E-05 32.9 3.7 35 269-305 2-37 (61)
39 TIGR02443 conserved hypothetic 88.0 0.69 1.5E-05 33.5 3.3 36 271-311 10-45 (59)
40 PF11792 Baculo_LEF5_C: Baculo 87.9 0.043 9.4E-07 37.1 -2.7 30 276-305 13-42 (43)
41 TIGR03655 anti_R_Lar restricti 87.4 0.96 2.1E-05 31.8 3.8 34 271-306 2-35 (53)
42 COG4332 Uncharacterized protei 87.1 0.34 7.5E-06 42.7 1.6 42 267-310 14-62 (203)
43 KOG3507 DNA-directed RNA polym 87.0 0.37 8E-06 34.8 1.5 31 266-306 16-46 (62)
44 PF05876 Terminase_GpA: Phage 86.8 0.53 1.1E-05 48.8 3.1 40 270-309 200-241 (557)
45 PF09526 DUF2387: Probable met 85.8 0.97 2.1E-05 34.0 3.3 35 271-310 9-43 (71)
46 PRK03988 translation initiatio 85.8 0.84 1.8E-05 38.8 3.3 33 269-307 101-133 (138)
47 PF04216 FdhE: Protein involve 85.2 0.73 1.6E-05 43.7 3.0 41 270-312 172-212 (290)
48 COG2888 Predicted Zn-ribbon RN 85.1 0.43 9.3E-06 34.6 1.0 33 268-305 25-58 (61)
49 PF03604 DNA_RNApol_7kD: DNA d 83.9 0.77 1.7E-05 29.2 1.7 26 271-306 1-26 (32)
50 PF05180 zf-DNL: DNL zinc fing 83.4 0.38 8.3E-06 35.7 0.2 34 270-306 4-38 (66)
51 COG1779 C4-type Zn-finger prot 82.5 1.4 3.1E-05 39.5 3.4 42 266-308 10-54 (201)
52 smart00659 RPOLCX RNA polymera 82.3 1 2.3E-05 30.6 2.0 27 270-306 2-28 (44)
53 KOG1886 BAH domain proteins [T 82.3 0.54 1.2E-05 47.3 0.8 171 131-319 238-414 (464)
54 PF09723 Zn-ribbon_8: Zinc rib 82.3 1.6 3.4E-05 29.3 2.8 30 269-305 4-34 (42)
55 PRK14892 putative transcriptio 81.7 1 2.3E-05 36.1 2.1 36 267-308 18-53 (99)
56 COG1997 RPL43A Ribosomal prote 81.4 1.1 2.5E-05 34.9 2.1 31 269-308 34-64 (89)
57 TIGR01562 FdhE formate dehydro 81.1 0.92 2E-05 43.6 1.9 43 269-312 183-225 (305)
58 smart00653 eIF2B_5 domain pres 80.9 1.8 3.9E-05 35.3 3.3 32 269-306 79-110 (110)
59 PF01873 eIF-5_eIF-2B: Domain 80.8 1.9 4.1E-05 36.0 3.5 31 270-306 93-123 (125)
60 PF14353 CpXC: CpXC protein 80.5 1.4 3E-05 36.4 2.6 38 271-308 2-49 (128)
61 PLN00209 ribosomal protein S27 80.3 1.7 3.7E-05 33.8 2.7 59 230-307 6-65 (86)
62 PRK03564 formate dehydrogenase 80.0 1.4 3.1E-05 42.3 2.8 42 269-312 186-227 (309)
63 PRK00415 rps27e 30S ribosomal 79.6 1.4 3E-05 32.0 1.9 30 269-307 10-40 (59)
64 TIGR00311 aIF-2beta translatio 79.6 2 4.4E-05 36.2 3.3 33 269-307 96-128 (133)
65 PRK00398 rpoP DNA-directed RNA 79.3 1.5 3.2E-05 29.8 2.0 29 270-307 3-31 (46)
66 PTZ00083 40S ribosomal protein 78.6 2.1 4.5E-05 33.3 2.7 30 269-307 34-64 (85)
67 PRK09710 lar restriction allev 78.4 2.9 6.3E-05 30.8 3.3 35 269-309 5-39 (64)
68 PF13453 zf-TFIIB: Transcripti 78.2 2.7 5.9E-05 27.8 2.9 30 272-308 1-30 (41)
69 PF10571 UPF0547: Uncharacteri 78.1 1.1 2.4E-05 27.0 0.9 11 298-308 15-25 (26)
70 TIGR02159 PA_CoA_Oxy4 phenylac 77.0 1.5 3.3E-05 37.6 1.8 36 270-307 105-140 (146)
71 smart00661 RPOL9 RNA polymeras 76.9 2.4 5.3E-05 29.1 2.6 33 272-311 2-34 (52)
72 PF01667 Ribosomal_S27e: Ribos 74.8 1.6 3.4E-05 31.3 1.1 28 270-306 7-35 (55)
73 PRK12336 translation initiatio 74.6 3.2 6.8E-05 37.4 3.3 33 269-307 97-129 (201)
74 smart00834 CxxC_CXXC_SSSS Puta 74.3 3.7 8E-05 26.7 2.7 29 270-305 5-34 (41)
75 smart00531 TFIIE Transcription 74.1 1.1 2.4E-05 38.2 0.2 40 267-310 96-136 (147)
76 PLN02976 amine oxidase 74.0 3 6.4E-05 48.0 3.5 60 29-88 1301-1361(1713)
77 PF07282 OrfB_Zn_ribbon: Putat 73.9 2.1 4.6E-05 31.3 1.7 31 267-307 26-56 (69)
78 PF04216 FdhE: Protein involve 72.7 2.8 6.1E-05 39.7 2.6 42 270-311 211-252 (290)
79 PRK06266 transcription initiat 71.7 1.1 2.4E-05 39.6 -0.3 34 267-308 114-147 (178)
80 PF02701 zf-Dof: Dof domain, z 71.6 1.6 3.4E-05 32.0 0.5 39 269-310 4-43 (63)
81 KOG3277 Uncharacterized conser 71.3 2.1 4.5E-05 36.9 1.2 35 269-306 78-113 (165)
82 PRK14890 putative Zn-ribbon RN 71.2 2.5 5.5E-05 30.6 1.5 35 268-306 23-57 (59)
83 TIGR02605 CxxC_CxxC_SSSS putat 69.3 5.1 0.00011 27.6 2.7 29 270-305 5-34 (52)
84 TIGR00373 conserved hypothetic 68.6 1.4 3E-05 38.2 -0.5 33 267-307 106-138 (158)
85 KOG4274 Positive cofactor 2 (P 68.2 9.2 0.0002 39.6 5.2 61 134-209 8-68 (742)
86 PF11781 RRN7: RNA polymerase 68.1 3.8 8.2E-05 26.6 1.7 27 270-306 8-34 (36)
87 COG2835 Uncharacterized conser 67.8 5.3 0.00012 29.0 2.5 38 269-317 7-45 (60)
88 PRK00432 30S ribosomal protein 67.0 2.8 6E-05 29.3 0.9 29 270-308 20-48 (50)
89 PF01396 zf-C4_Topoisom: Topoi 66.8 7.2 0.00016 25.7 2.9 29 271-306 2-33 (39)
90 COG2824 PhnA Uncharacterized Z 66.6 4.1 8.9E-05 33.0 1.9 31 270-310 3-33 (112)
91 PF03811 Zn_Tnp_IS1: InsA N-te 63.1 5.2 0.00011 26.0 1.6 30 270-303 5-35 (36)
92 COG1996 RPC10 DNA-directed RNA 62.9 4 8.6E-05 28.5 1.1 32 267-307 3-34 (49)
93 PF09538 FYDLN_acid: Protein o 62.8 5 0.00011 32.7 1.8 32 269-310 8-39 (108)
94 TIGR01206 lysW lysine biosynth 62.2 6.5 0.00014 28.0 2.1 33 270-309 2-34 (54)
95 PF04032 Rpr2: RNAse P Rpr2/Rp 59.6 7.7 0.00017 29.4 2.3 36 269-305 45-85 (85)
96 TIGR02300 FYDLN_acid conserved 59.6 4.8 0.0001 33.7 1.2 32 269-310 8-39 (129)
97 PF14726 RTTN_N: Rotatin, an a 58.9 8.8 0.00019 30.7 2.6 64 13-77 33-96 (98)
98 PRK05978 hypothetical protein; 58.9 5.3 0.00011 34.4 1.4 36 270-313 33-68 (148)
99 PRK12286 rpmF 50S ribosomal pr 57.6 8.3 0.00018 27.7 2.0 26 266-305 23-48 (57)
100 PF08792 A2L_zn_ribbon: A2L zi 57.0 12 0.00026 23.8 2.5 29 269-306 2-30 (33)
101 PF14311 DUF4379: Domain of un 56.9 10 0.00022 26.6 2.3 18 293-310 24-41 (55)
102 TIGR00280 L37a ribosomal prote 56.9 8.9 0.00019 30.3 2.2 31 269-308 34-64 (91)
103 PRK03976 rpl37ae 50S ribosomal 56.5 9.2 0.0002 30.1 2.2 32 269-309 35-66 (90)
104 smart00778 Prim_Zn_Ribbon Zinc 56.1 9.1 0.0002 25.1 1.8 30 271-305 4-33 (37)
105 PF07754 DUF1610: Domain of un 55.9 5.1 0.00011 23.8 0.5 11 268-278 14-24 (24)
106 PF01780 Ribosomal_L37ae: Ribo 55.8 6.2 0.00013 31.1 1.2 32 269-309 34-65 (90)
107 PRK03954 ribonuclease P protei 54.4 14 0.0003 30.7 3.1 38 269-309 63-105 (121)
108 TIGR01031 rpmF_bact ribosomal 53.6 9.8 0.00021 27.1 1.8 26 266-305 22-47 (55)
109 PF10058 DUF2296: Predicted in 52.8 11 0.00023 26.8 1.9 32 269-305 21-52 (54)
110 COG2023 RPR2 RNase P subunit R 52.7 10 0.00022 30.7 2.0 37 269-309 55-94 (105)
111 PTZ00255 60S ribosomal protein 51.6 13 0.00029 29.3 2.4 31 269-308 35-65 (90)
112 PRK11032 hypothetical protein; 51.4 8.2 0.00018 33.6 1.4 38 266-314 120-158 (160)
113 PF09332 Mcm10: Mcm10 replicat 51.3 5.7 0.00012 38.8 0.4 15 292-306 280-294 (344)
114 KOG2462 C2H2-type Zn-finger pr 50.5 8 0.00017 36.5 1.2 39 267-307 127-171 (279)
115 cd00674 LysRS_core_class_I cat 49.9 18 0.0004 35.4 3.7 36 270-309 169-204 (353)
116 PF09332 Mcm10: Mcm10 replicat 49.6 4.4 9.5E-05 39.6 -0.7 33 266-308 281-315 (344)
117 KOG3623 Homeobox transcription 49.4 5.7 0.00012 42.2 0.1 39 269-311 280-323 (1007)
118 PHA02942 putative transposase; 47.7 9.1 0.0002 37.9 1.2 29 268-307 324-352 (383)
119 PF00684 DnaJ_CXXCXGXG: DnaJ c 47.3 42 0.00092 24.4 4.5 38 267-306 12-50 (66)
120 PF01921 tRNA-synt_1f: tRNA sy 46.1 18 0.00039 35.6 2.9 39 270-310 174-212 (360)
121 COG0675 Transposase and inacti 45.7 13 0.00028 34.7 1.9 24 270-307 309-332 (364)
122 PF14803 Nudix_N_2: Nudix N-te 45.5 17 0.00037 23.3 1.8 29 272-305 2-30 (34)
123 PF10080 DUF2318: Predicted me 45.2 14 0.00031 29.7 1.8 36 267-313 32-68 (102)
124 COG1656 Uncharacterized conser 45.0 9.2 0.0002 33.4 0.7 45 268-312 95-146 (165)
125 COG3058 FdhE Uncharacterized p 44.9 6.3 0.00014 37.3 -0.4 39 269-308 184-222 (308)
126 TIGR00467 lysS_arch lysyl-tRNA 44.5 19 0.00041 37.1 3.0 34 270-308 168-201 (515)
127 COG3677 Transposase and inacti 43.6 15 0.00033 30.7 1.8 38 267-309 27-65 (129)
128 smart00531 TFIIE Transcription 43.4 7.7 0.00017 33.0 -0.0 22 289-310 91-112 (147)
129 KOG1779 40s ribosomal protein 43.1 21 0.00045 27.4 2.2 55 231-304 5-60 (84)
130 PF05207 zf-CSL: CSL zinc fing 41.9 12 0.00026 26.5 0.8 33 269-306 17-49 (55)
131 PRK11827 hypothetical protein; 41.7 18 0.00039 26.3 1.7 39 269-317 7-45 (60)
132 TIGR00373 conserved hypothetic 41.6 13 0.00027 32.2 1.0 20 291-310 103-122 (158)
133 PRK06266 transcription initiat 41.4 13 0.00028 32.9 1.0 19 292-310 112-130 (178)
134 PF14949 ARF7EP_C: ARF7 effect 41.1 12 0.00026 30.3 0.7 13 270-282 74-86 (103)
135 KOG0909 Peptide:N-glycanase [P 40.9 30 0.00064 34.9 3.5 96 207-311 104-208 (500)
136 PF07295 DUF1451: Protein of u 40.5 12 0.00027 32.0 0.8 33 266-307 108-140 (146)
137 PRK00420 hypothetical protein; 40.3 16 0.00035 30.0 1.4 29 271-309 24-52 (112)
138 PF13408 Zn_ribbon_recom: Reco 40.0 26 0.00057 24.1 2.3 32 268-305 3-34 (58)
139 TIGR01562 FdhE formate dehydro 39.9 32 0.00068 33.1 3.5 40 270-310 224-265 (305)
140 COG2816 NPY1 NTP pyrophosphohy 38.8 19 0.00041 34.2 1.8 27 272-307 113-139 (279)
141 PF01927 Mut7-C: Mut7-C RNAse 38.1 24 0.00051 29.9 2.2 41 270-310 91-138 (147)
142 KOG2462 C2H2-type Zn-finger pr 38.0 7.6 0.00016 36.6 -1.0 34 270-307 215-253 (279)
143 smart00401 ZnF_GATA zinc finge 37.9 14 0.0003 25.9 0.5 34 271-309 4-37 (52)
144 PF09297 zf-NADH-PPase: NADH p 37.8 33 0.00071 21.3 2.2 26 272-306 5-30 (32)
145 PRK14714 DNA polymerase II lar 37.7 18 0.00039 41.0 1.6 36 269-306 666-701 (1337)
146 PF11672 DUF3268: Protein of u 37.6 31 0.00068 27.8 2.6 32 271-304 3-38 (102)
147 PLN03119 putative ADP-ribosyla 36.9 31 0.00067 36.0 3.0 28 269-304 22-50 (648)
148 PF06397 Desulfoferrod_N: Desu 35.0 22 0.00048 23.2 1.1 16 294-309 3-18 (36)
149 COG0777 AccD Acetyl-CoA carbox 34.4 14 0.00031 34.9 0.2 36 267-310 25-60 (294)
150 COG1571 Predicted DNA-binding 34.0 21 0.00045 35.9 1.3 33 269-311 349-381 (421)
151 PF06044 DRP: Dam-replacing fa 33.4 19 0.00042 33.4 0.9 33 269-307 30-63 (254)
152 PF03589 Antiterm: Antitermina 33.0 11 0.00024 29.9 -0.7 34 272-306 7-41 (95)
153 cd00974 DSRD Desulforedoxin (D 33.0 26 0.00056 22.1 1.2 14 295-308 2-15 (34)
154 PRK00750 lysK lysyl-tRNA synth 32.3 50 0.0011 34.0 3.8 38 270-310 175-212 (510)
155 TIGR00319 desulf_FeS4 desulfof 31.9 28 0.0006 21.9 1.2 13 296-308 6-18 (34)
156 PRK03564 formate dehydrogenase 31.6 53 0.0011 31.7 3.6 38 270-310 226-265 (309)
157 COG5415 Predicted integral mem 30.9 23 0.00049 32.3 0.9 32 269-305 191-222 (251)
158 PF01783 Ribosomal_L32p: Ribos 30.7 15 0.00032 26.2 -0.3 22 269-304 25-46 (56)
159 PF02172 KIX: KIX domain; Int 29.8 90 0.0019 24.1 3.9 66 133-203 10-75 (81)
160 PF08209 Sgf11: Sgf11 (transcr 29.7 31 0.00068 22.0 1.1 17 296-312 3-19 (33)
161 PF02150 RNA_POL_M_15KD: RNA p 29.6 40 0.00087 21.6 1.7 28 272-308 3-31 (35)
162 PF03833 PolC_DP2: DNA polymer 29.3 18 0.00039 39.3 0.0 40 266-307 651-690 (900)
163 PF09606 Med15: ARC105 or Med1 29.0 73 0.0016 34.7 4.5 51 140-205 2-52 (799)
164 TIGR00100 hypA hydrogenase nic 28.8 25 0.00054 28.7 0.7 29 266-305 66-94 (115)
165 PRK03824 hypA hydrogenase nick 28.8 35 0.00076 28.7 1.7 38 268-306 68-116 (135)
166 TIGR03830 CxxCG_CxxCG_HTH puta 28.4 40 0.00086 27.2 1.9 14 296-309 30-43 (127)
167 PF10562 CaM_bdg_C0: Calmoduli 27.8 57 0.0012 20.2 2.0 18 66-83 11-28 (29)
168 COG0484 DnaJ DnaJ-class molecu 27.8 58 0.0013 32.2 3.2 38 266-306 155-192 (371)
169 TIGR00515 accD acetyl-CoA carb 27.5 13 0.00029 35.3 -1.2 31 269-309 25-57 (285)
170 PRK12775 putative trifunctiona 27.3 44 0.00096 37.3 2.6 51 266-318 792-842 (1006)
171 PRK14810 formamidopyrimidine-D 27.3 53 0.0012 30.8 2.8 28 270-304 244-271 (272)
172 PRK10445 endonuclease VIII; Pr 27.2 54 0.0012 30.6 2.8 29 270-305 235-263 (263)
173 PF06254 DUF1019: Protein of u 27.0 41 0.00088 26.5 1.6 50 180-229 12-61 (89)
174 PF04194 PDCD2_C: Programmed c 26.8 65 0.0014 27.9 3.1 34 270-303 97-145 (164)
175 COG3809 Uncharacterized protei 26.8 61 0.0013 25.0 2.4 31 271-308 2-32 (88)
176 COG1645 Uncharacterized Zn-fin 26.7 40 0.00086 28.5 1.6 30 267-308 26-55 (131)
177 PF10083 DUF2321: Uncharacteri 25.8 49 0.0011 28.7 2.0 13 298-310 69-83 (158)
178 PRK05654 acetyl-CoA carboxylas 25.8 15 0.00033 35.1 -1.2 32 269-310 26-59 (292)
179 PF08273 Prim_Zn_Ribbon: Zinc- 25.8 41 0.00089 22.4 1.2 31 271-305 4-34 (40)
180 KOG2593 Transcription initiati 25.5 22 0.00048 35.6 -0.2 38 267-307 125-163 (436)
181 PRK14811 formamidopyrimidine-D 25.4 61 0.0013 30.4 2.8 29 271-306 236-264 (269)
182 KOG2041 WD40 repeat protein [G 25.4 78 0.0017 34.2 3.7 17 290-306 1147-1165(1189)
183 PF10955 DUF2757: Protein of u 25.4 42 0.00091 25.6 1.4 13 294-306 1-13 (76)
184 cd00729 rubredoxin_SM Rubredox 25.4 40 0.00087 21.4 1.1 13 297-309 2-14 (34)
185 COG4049 Uncharacterized protei 25.3 26 0.00056 25.3 0.2 10 269-278 16-25 (65)
186 PF15135 UPF0515: Uncharacteri 24.9 40 0.00088 31.5 1.4 12 297-308 155-166 (278)
187 PRK01103 formamidopyrimidine/5 24.9 65 0.0014 30.2 2.9 29 270-305 245-273 (274)
188 PF11023 DUF2614: Protein of u 24.4 25 0.00055 28.8 0.0 30 267-308 66-96 (114)
189 smart00099 btg1 tob/btg1 famil 24.4 57 0.0012 26.6 2.1 62 170-233 27-92 (108)
190 COG2331 Uncharacterized protei 24.3 36 0.00077 26.1 0.8 14 295-308 10-23 (82)
191 CHL00174 accD acetyl-CoA carbo 24.2 16 0.00035 35.0 -1.3 31 269-309 37-69 (296)
192 PF08996 zf-DNA_Pol: DNA Polym 23.9 26 0.00055 31.1 -0.1 37 270-306 18-54 (188)
193 PF14122 YokU: YokU-like prote 23.8 50 0.0011 25.8 1.5 36 272-307 1-45 (87)
194 PLN03131 hypothetical protein; 23.6 71 0.0015 33.7 3.0 28 269-304 22-50 (705)
195 PRK04860 hypothetical protein; 23.6 23 0.0005 30.8 -0.4 41 268-311 117-157 (160)
196 COG5349 Uncharacterized protei 23.5 30 0.00066 28.8 0.3 13 270-282 21-33 (126)
197 PRK12277 50S ribosomal protein 23.3 1.8E+02 0.0039 22.5 4.5 45 35-85 36-80 (83)
198 COG3364 Zn-ribbon containing p 23.1 41 0.00088 27.2 1.0 21 270-290 20-41 (112)
199 PHA00616 hypothetical protein 23.1 29 0.00063 23.7 0.1 13 271-283 2-14 (44)
200 PRK06599 DNA topoisomerase I; 22.8 1.1E+02 0.0025 32.5 4.6 15 213-227 543-557 (675)
201 PRK04179 rpl37e 50S ribosomal 22.5 36 0.00078 24.9 0.5 25 269-305 16-40 (62)
202 PF09845 DUF2072: Zn-ribbon co 22.5 43 0.00094 28.2 1.1 17 270-286 19-36 (131)
203 PRK13945 formamidopyrimidine-D 22.2 78 0.0017 29.9 2.9 29 270-305 254-282 (282)
204 PF06827 zf-FPG_IleRS: Zinc fi 21.9 78 0.0017 19.1 1.9 28 271-305 2-29 (30)
205 COG4734 ArdA Antirestriction p 21.8 6.8 0.00015 34.3 -4.0 41 270-311 16-61 (193)
206 TIGR03831 YgiT_finger YgiT-typ 21.7 80 0.0017 20.5 2.1 11 298-308 33-43 (46)
207 COG1198 PriA Primosomal protei 21.4 78 0.0017 34.2 2.9 16 220-235 386-401 (730)
208 KOG2767 Translation initiation 21.3 37 0.0008 33.3 0.4 33 270-307 96-128 (400)
209 COG4888 Uncharacterized Zn rib 21.2 70 0.0015 25.8 1.9 23 286-308 11-33 (104)
210 COG1675 TFA1 Transcription ini 21.2 22 0.00048 31.5 -1.0 33 266-306 109-141 (176)
211 PF05443 ROS_MUCR: ROS/MUCR tr 21.0 43 0.00093 28.3 0.7 14 296-309 71-84 (132)
212 TIGR00577 fpg formamidopyrimid 20.4 88 0.0019 29.3 2.8 27 271-304 246-272 (272)
213 COG5179 TAF1 Transcription ini 20.3 61 0.0013 34.2 1.8 42 231-278 904-945 (968)
214 COG1096 Predicted RNA-binding 20.3 67 0.0014 28.7 1.8 25 271-306 150-174 (188)
No 1
>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=100.00 E-value=1.3e-67 Score=496.51 Aligned_cols=286 Identities=30% Similarity=0.435 Sum_probs=224.0
Q ss_pred HHHHHHHHHHHHHHhhcCCccHHHHHHHHHHhhcCCCCHHhhhcccceeecccccCCCCHHHHHHHHHHHHHHHhhcccc
Q 020974 7 DLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWDV 86 (319)
Q Consensus 7 el~~~~~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~lv~~WK~~v~~~ 86 (319)
|+...++ +++.+.. + .+++.|+++|++|+.++||.++|++|+||++||+||||++++|+.+|+.||+.||++|..+
T Consensus 3 ei~~~~k-~L~k~~~--~-~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~ 78 (299)
T TIGR01385 3 EVASHAK-ALDKNKS--S-KNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKN 78 (299)
T ss_pred HHHHHHH-Hhhhhcc--C-CCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhh
Confidence 4444444 4455422 2 5788999999999999999999999999999999999999999999999999999999875
Q ss_pred cchhhhhhccccc-----cccccccccc--c-CCccccCCCCCCCCC--CcccccCCChHHHHHHHHHHHHHHhhhhhhc
Q 020974 87 EDVEYVAVTKKAK-----LVENVKVEEV--T-NGEERRHDSGNVPKK--SISCMIKCNDSFREIVREKLYDALSKVSDEA 156 (319)
Q Consensus 87 ~~~~~~~~~~~~~-----~s~~~~~~~~--~-~~~~s~~~~~~~ps~--~~~~~~~~~d~vR~k~r~~L~~aL~~~~~e~ 156 (319)
...... ..++.. ++.+.+.+.. + ........++..+.. ....++.++|++|++||++|++||....++.
T Consensus 79 k~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~ 157 (299)
T TIGR01385 79 KSDHPG-GNPEDKTTVGESVNSVKQEAKSQSDKIEQPKYVSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHP 157 (299)
T ss_pred cccCcc-cccccccccCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhhcCCCC
Confidence 332111 100000 0000000000 0 000000000111111 1223458999999999999999999754322
Q ss_pred hhhhhhhhhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhcCCCCCHHHHHHHhcCCCChhhhhcCChhhcCch
Q 020974 157 ADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASD 236 (319)
Q Consensus 157 ~~~~~~~~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~lv~Ms~eElas~ 236 (319)
+ ..+++..+|.+||.+||..|+.....|++++|+|+|||||++||+||++|++|+|+|++||.|+++||||+
T Consensus 158 ~--------~~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~ 229 (299)
T TIGR01385 158 P--------QSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASA 229 (299)
T ss_pred c--------cccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCH
Confidence 1 23467889999999999999988889999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhhchhhhhcCCCCccccccccccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 237 KIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 237 e~k~~~~~~~~~e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
+++++++++ .+++|+++|++ .... +.|++|+|++||+++|+| |+|||+||||||+||+|.+|||+|+||
T Consensus 230 e~k~~~e~~-~ke~l~~~~~~---~~~~-~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~fc 299 (299)
T TIGR01385 230 ELKQEREEI-TKENLFEAQGA---KIQK-AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKFC 299 (299)
T ss_pred HHHHHHHHH-HHHHHHHHHhh---hhhc-CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeeeC
Confidence 999999999 99999999944 3344 899999999999999999 999999999999999999999999998
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=1.8e-61 Score=448.54 Aligned_cols=287 Identities=28% Similarity=0.424 Sum_probs=225.2
Q ss_pred HHHHHHHHHHHH-hhcCCccHHHHHHHHHHhhcCCCCHHhhhcccceeecc-cccCCCCHHHHHHHHHHHHHHHhhcccc
Q 020974 9 CEAAKRAAVAAV-WKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLL-PMLKHPSQKIQKLAYDLISSWRDMCWDV 86 (319)
Q Consensus 9 ~~~~~k~~~~a~-~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~IG~~V~-~Lrkh~~~~I~~~Ak~lv~~WK~~v~~~ 86 (319)
++.+.++|+.-. +..+ ++.+.++++|.+|++.|||.++|++|+||+.|| .|.+|+|++|.++|+.||+.||++|...
T Consensus 3 ~e~~~r~ak~l~~~~~~-~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~ 81 (296)
T KOG1105|consen 3 EEEALRAAKALEKDKQS-KNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKS 81 (296)
T ss_pred cHHHHHHHHHHHhhccc-ccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcc
Confidence 444555555532 1222 788999999999999999999999999999999 5567899999999999999999999864
Q ss_pred cc---hhhhhhccccccccccccccccCCccccCCCCCCCCCC-cccccCCChHHHHHHHHHHHHHHhhhhhhchhhhhh
Q 020974 87 ED---VEYVAVTKKAKLVENVKVEEVTNGEERRHDSGNVPKKS-ISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTI 162 (319)
Q Consensus 87 ~~---~~~~~~~~~~~~s~~~~~~~~~~~~~s~~~~~~~ps~~-~~~~~~~~d~vR~k~r~~L~~aL~~~~~e~~~~~~~ 162 (319)
+. ++..+.+.|+..+..+.+..... .++...+...+..+ .+..+.++|++|++|++||++||.....
T Consensus 82 ~~~~k~~~~~~~~p~~~~~~~~s~~~~~-~ks~~~~~~~~~~~~~~~~~~~~d~~r~k~~e~l~~al~~~~~-------- 152 (296)
T KOG1105|consen 82 PGREKSGDNKSHDPGEASSKSPSGAKQP-EKSRGDSKRDKHSGSKDPVPITNDPVRDKCRELLYAALTTEDD-------- 152 (296)
T ss_pred cccccCccccCCCCCcCCcCCccCCCCc-cccccccccccccCcCCCCCCCCchHHHHHHHHHHHHhccccc--------
Confidence 11 11111222222211111000000 00000000000000 0123457899999999999999984221
Q ss_pred hhhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhcCCCCCHHHHHHHhcCCCChhhhhcCChhhcCchHHHHHh
Q 020974 163 DLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWN 242 (319)
Q Consensus 163 ~~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~lv~Ms~eElas~e~k~~~ 242 (319)
+....+++..+|.+||.+||..++.+..+|+.++||++|||+|++||+||++||.|+|+|++|+.|+++||||+++++++
T Consensus 153 ~~~~~~~~~~~a~~iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~ 232 (296)
T KOG1105|consen 153 SRVTGADPLELAVQIEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKEER 232 (296)
T ss_pred ccccCCCHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHHHH
Confidence 22356778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhchhhhhcCCCCccccccccccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 243 HHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 243 ~~~~~~e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
+++ .+++|+++|++..++ +.|+.|.|++|+.++|+| |+||||+||||||||+|.+|||+|+||
T Consensus 233 ~k~-~keal~~~q~~~~~g----t~td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnrWkfc 296 (296)
T KOG1105|consen 233 QKL-TKEALREHQMAKIQG----TQTDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNRWKFC 296 (296)
T ss_pred HHH-HHHHHHHHhhccccc----ccccceeeccccccceeEEeeccCCCCCCcceeeeecccCCccccC
Confidence 999 999999999765555 899999999999999999 999999999999999999999999998
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.95 E-value=2.5e-27 Score=190.70 Aligned_cols=102 Identities=38% Similarity=0.657 Sum_probs=91.9
Q ss_pred hHHHHHHHHHHHHHHhhhhhhchhhhhhhhhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhcCCCCCHHHHHH
Q 020974 135 DSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRK 214 (319)
Q Consensus 135 d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~ 214 (319)
|++|++|+++|+++|..+....+ ...++..+|.+||.+||..|+.....|++++|+|+|||||++||+||++
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~--------~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~ 72 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEE--------IELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRK 72 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCc--------ccccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 57999999999999997654322 2245778999999999999988788999999999999999999999999
Q ss_pred HhcCCCChhhhhcCChhhcCchHHHHHhhh
Q 020974 215 VLLGHVKPETIINMSAKEMASDKIQLWNHH 244 (319)
Q Consensus 215 vl~G~i~p~~lv~Ms~eElas~e~k~~~~~ 244 (319)
|++|+|+|++||.||++||||+++|+++++
T Consensus 73 vl~G~i~p~~lv~Ms~~ElAs~elk~~~e~ 102 (102)
T smart00510 73 VLNGEITPEKLATMTAEELASAELKEKREK 102 (102)
T ss_pred HHcCCCCHHHHhcCCHHHcCCHHHHHHHhC
Confidence 999999999999999999999999999874
No 4
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. 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. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=99.93 E-value=6e-27 Score=192.58 Aligned_cols=114 Identities=36% Similarity=0.646 Sum_probs=103.9
Q ss_pred CChHHHHHHHHHHHHHHhhhhhhchhhhhhhhhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhcCCCCCHHHH
Q 020974 133 CNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFR 212 (319)
Q Consensus 133 ~~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr 212 (319)
|++++|++++++|+++|.....+ .+ ...++..+|.+||.+||..|+..+..|++++|+|+|||||++||.|+
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~-------~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~ 72 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QD-------DPEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLR 72 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CC-------CTCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHH
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-cc-------chhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHH
Confidence 57899999999999999986543 11 34567899999999999999877899999999999999999999999
Q ss_pred HHHhcCCCChhhhhcCChhhcCchHHHHHhhhhhhchhhhhcC
Q 020974 213 RKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGH 255 (319)
Q Consensus 213 ~~vl~G~i~p~~lv~Ms~eElas~e~k~~~~~~~~~e~l~~~q 255 (319)
.+|++|+|+|.+||.|+++||||++++++++++ .+++++++|
T Consensus 73 ~~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~-~~~~l~~~~ 114 (115)
T PF07500_consen 73 RRILSGEISPEELVTMSPEELASEELKEEREKI-RKESLKQSQ 114 (115)
T ss_dssp HHHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCH-HHHHHHHTB
T ss_pred HHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHH-HHHHHHHhh
Confidence 999999999999999999999999999999999 999999887
No 5
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.75 E-value=6.5e-19 Score=118.15 Aligned_cols=39 Identities=23% Similarity=0.617 Sum_probs=37.4
Q ss_pred ccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCccee
Q 020974 271 YECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 271 ~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
++||+||+++++| |+|+||||||||+||+|.+|||+|+.
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 5799999999999 99999999999999999999999974
No 6
>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=99.73 E-value=2.5e-18 Score=114.74 Aligned_cols=38 Identities=32% Similarity=0.730 Sum_probs=34.0
Q ss_pred ccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcce
Q 020974 271 YECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 271 ~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
++||+||+++++| |.|+|+||||||+||+|.+|||+|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 5799999999999 9999999999999999999999996
No 7
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.69 E-value=2e-17 Score=126.08 Aligned_cols=74 Identities=36% Similarity=0.566 Sum_probs=66.8
Q ss_pred HHHHHHHHHHHHHhhcCCccHHHHHHHHHHhhcCCCCHHhhhcccceeecccccCCCCHHHHHHHHHHHHHHHhhcc
Q 020974 8 LCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCW 84 (319)
Q Consensus 8 l~~~~~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~lv~~WK~~v~ 84 (319)
|++.++++.+.++. + ++.+.|+++|++|+.++||.++|++|+||++||+||||+|++|+.+|+.||+.||+.|+
T Consensus 1 ~~~~~k~~~k~~~~--~-~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 1 LLRAAKKLDKVANN--G-KEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred ChHHHHHHHHHhcC--C-CCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 46777777777743 2 56889999999999999999999999999999999999999999999999999999985
No 8
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=99.67 E-value=1.4e-17 Score=129.88 Aligned_cols=43 Identities=23% Similarity=0.542 Sum_probs=39.5
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCccee
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
.....+||+||+.+++| |+||||||||||+||.|.+|+|+|+.
T Consensus 62 ~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wre 105 (105)
T KOG2906|consen 62 DQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWRE 105 (105)
T ss_pred hhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhcccccccC
Confidence 33456999999999999 99999999999999999999999984
No 9
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.60 E-value=4e-16 Score=127.79 Aligned_cols=44 Identities=25% Similarity=0.503 Sum_probs=40.8
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
.+..+.||+||++++.| |+|+||||||||+||+|..|||+|++.
T Consensus 69 ~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre~ 113 (113)
T COG1594 69 PTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWREY 113 (113)
T ss_pred ccccccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeecC
Confidence 34478999999999999 999999999999999999999999874
No 10
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=99.59 E-value=2e-15 Score=115.40 Aligned_cols=72 Identities=29% Similarity=0.384 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHhhcCCccHHHHHHHHHHhhcCCCCHHhhhcccceeecccccCCCCHHHHHHHHHHHHHHHhhcc
Q 020974 10 EAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCW 84 (319)
Q Consensus 10 ~~~~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~lv~~WK~~v~ 84 (319)
..+++.++.... + ++.+.|+++|+.|+.+|||.++|++|+||+.||+||||++++|+.+|+.||++||+.|+
T Consensus 5 ~r~~~~l~~~~~--~-~~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 5 LRAKKKLEKKDS--N-EEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred HHHHHHhhcccc--C-CCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence 344455555421 2 68899999999999999999999999999999999999999999999999999999874
No 11
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.55 E-value=3.4e-15 Score=128.67 Aligned_cols=45 Identities=11% Similarity=0.218 Sum_probs=41.2
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceecccc
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVSTNLS 313 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~~~~ 313 (319)
...+||+||+++++| |+||||||||||+||.|.+|||+|+--++-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkppkf~ 187 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPPKFR 187 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCcccc
Confidence 457999999999999 999999999999999999999999866553
No 12
>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=99.55 E-value=3.6e-15 Score=120.34 Aligned_cols=43 Identities=28% Similarity=0.572 Sum_probs=40.0
Q ss_pred cccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 268 SDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
+....||+||+++++| |+|+||||||||+||+|.+|||+|+..
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 3458999999999999 999999999999999999999999863
No 13
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=99.38 E-value=1.5e-13 Score=97.65 Aligned_cols=52 Identities=31% Similarity=0.468 Sum_probs=47.3
Q ss_pred HHHHHhhcCCCCHHhhhcccceeecccccCC-CCHHHHHHHHHHHHHHHhhcc
Q 020974 33 DALDQIKNSSITYQLLVSTQVIRHLLPMLKH-PSQKIQKLAYDLISSWRDMCW 84 (319)
Q Consensus 33 ~~L~~L~~~~it~~~L~~T~IG~~V~~Lrkh-~~~~I~~~Ak~lv~~WK~~v~ 84 (319)
++|+.|..+|||.++|++|+||++|++|+|| .+++|+.+|+.|+++||++|+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 5799999999999999999999999999999 899999999999999999874
No 14
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.34 E-value=4.8e-13 Score=137.72 Aligned_cols=82 Identities=30% Similarity=0.528 Sum_probs=75.4
Q ss_pred cCChHHHHHHHHHHHHHHhc-cCchhHHHHHHHHHHhcCCCCCHHHHHHHhcCCCChhhhhcCChhhcCchHHHHHhhhh
Q 020974 167 ACDPIQVAILVESAMYEKWC-RSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHL 245 (319)
Q Consensus 167 ~~d~~~lA~~IE~~lf~~~~-~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~lv~Ms~eElas~e~k~~~~~~ 245 (319)
..++.-++..||..+|..|| +.+..|+.|+|+|+|||||++||.||.+|..|+|+|++|+.|+++|||+.++.+|+++.
T Consensus 266 ~~d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rEek 345 (778)
T KOG1634|consen 266 LQDPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWREEK 345 (778)
T ss_pred ccchhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHHHH
Confidence 34566778899999999998 77789999999999999999999999999999999999999999999999999999988
Q ss_pred hhch
Q 020974 246 DKDG 249 (319)
Q Consensus 246 ~~~e 249 (319)
.++
T Consensus 346 -~ee 348 (778)
T KOG1634|consen 346 -AEE 348 (778)
T ss_pred -HHH
Confidence 544
No 15
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=99.31 E-value=1.1e-12 Score=104.28 Aligned_cols=44 Identities=20% Similarity=0.528 Sum_probs=41.6
Q ss_pred cccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCccee
Q 020974 266 IVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
..|.+..||+||+++++| |.|+|.+|+.|+.||+|.+|||+|.+
T Consensus 69 Prts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 69 PRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred CccccccCCccCCcceEEEecccccccceEEEEEEeccccccccC
Confidence 677889999999999999 99999999999999999999999964
No 16
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=99.20 E-value=4.7e-12 Score=101.60 Aligned_cols=43 Identities=26% Similarity=0.468 Sum_probs=39.2
Q ss_pred cccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 268 SDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
+-...||+||+.+..| .+|+|||||+.|+||+|.+|+++.++.
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeecc
Confidence 3457999999999999 999999999999999999999988653
No 17
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=96.89 E-value=0.00045 Score=68.18 Aligned_cols=74 Identities=18% Similarity=0.312 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHHHHHHhhcCCccHHHHHHHHHHhhcCCCCHHhhhcccceeecccccCCCCHHHHHHHHHHHHHHHhhcc
Q 020974 5 VMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCW 84 (319)
Q Consensus 5 ~~el~~~~~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~lv~~WK~~v~ 84 (319)
.++..+.++..+... .++.+.+..|..|.++|++++.|.+|.+|++|+.|++|. .+..+|..|+..||++|.
T Consensus 7 ~l~~Vr~lQ~~l~~~------~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~ 78 (433)
T KOG2821|consen 7 GLGAVRKLQARLENR------IDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVL 78 (433)
T ss_pred hHHHHHHHHHHHHhC------ccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcc
Confidence 445555555555555 689999999999999999999999999999999999998 699999999999999996
Q ss_pred cc
Q 020974 85 DV 86 (319)
Q Consensus 85 ~~ 86 (319)
..
T Consensus 79 ~d 80 (433)
T KOG2821|consen 79 VD 80 (433)
T ss_pred cc
Confidence 54
No 18
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=96.78 E-value=0.0011 Score=53.78 Aligned_cols=78 Identities=21% Similarity=0.382 Sum_probs=56.9
Q ss_pred hhhHHHHHHHHHHHHHHHHhhcCCccHHHHHHHHHHhhcCCCCHHhhhccc-ceeecccccCC-CCHHHHHHHHHHHHHH
Q 020974 2 EKKVMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQ-VIRHLLPMLKH-PSQKIQKLAYDLISSW 79 (319)
Q Consensus 2 ~~~~~el~~~~~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~-IG~~V~~Lrkh-~~~~I~~~Ak~lv~~W 79 (319)
|..|++|-.-.+-++... + +++.+|+++|.+|..++||..+|.... +--++.++|+. .|..|++.|..|+.+.
T Consensus 1 E~~L~~l~~~Ik~~L~~~----~-~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkf 75 (106)
T PF11467_consen 1 ERRLQELHSEIKSSLKVD----N-PDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKF 75 (106)
T ss_dssp HHHHHHHHHHHHHTCETT----E-E-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHHHcCC----C-CCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 556666664444333222 2 789999999999999999999888654 77788888987 5799999999999999
Q ss_pred Hhhcc
Q 020974 80 RDMCW 84 (319)
Q Consensus 80 K~~v~ 84 (319)
|.++.
T Consensus 76 K~~f~ 80 (106)
T PF11467_consen 76 KSLFL 80 (106)
T ss_dssp HHHHH
T ss_pred HHHhC
Confidence 99985
No 19
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.92 E-value=0.0092 Score=58.25 Aligned_cols=61 Identities=18% Similarity=0.266 Sum_probs=51.6
Q ss_pred ccHHHHHHHHHHhhcCCCCH-HhhhcccceeecccccCCCC--HHHHHHHHHHHHHHHhhcccc
Q 020974 26 VEEARCIDALDQIKNSSITY-QLLVSTQVIRHLLPMLKHPS--QKIQKLAYDLISSWRDMCWDV 86 (319)
Q Consensus 26 ~~~~~~l~~L~~L~~~~it~-~~L~~T~IG~~V~~Lrkh~~--~~I~~~Ak~lv~~WK~~v~~~ 86 (319)
|+..-=..+|..|.++||-. +.|+..+||++|-.|.||+. ..++.+|..||..|-+-+...
T Consensus 230 Pal~Ir~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI~~~ 293 (417)
T KOG1793|consen 230 PALNIRKSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPIFKL 293 (417)
T ss_pred cchHHHHHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccccCC
Confidence 34444456778888889988 99999999999999999975 789999999999999988644
No 20
>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=95.45 E-value=0.017 Score=42.70 Aligned_cols=36 Identities=25% Similarity=0.548 Sum_probs=25.3
Q ss_pred ccccCCCCcceEE-EEec-cCC-----CCC--ceeEEEccCCCCc
Q 020974 271 YECGRCGHNKISY-QHSS-ILD-----DYN--LTRHVTCLNCNQY 306 (319)
Q Consensus 271 ~~C~~C~~~~~~~-q~q~-rsa-----de~--mt~f~~C~~C~~~ 306 (319)
+.||+||+++... ++|. +.. |-. .-+.++|.+||++
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 5799999998887 7764 211 212 2267899999987
No 21
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=95.09 E-value=0.017 Score=43.56 Aligned_cols=40 Identities=20% Similarity=0.519 Sum_probs=27.8
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEcc--CCCCcceec
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCL--NCNQYWVST 310 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~--~C~~~w~~~ 310 (319)
++.||.||+....-..+ +..|.--..|+.|. +|||+|...
T Consensus 1 mm~CP~Cg~~a~irtSr-~~s~~~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 1 MFHCPLCQHAAHARTSR-YITDTTKERYHQCQNVNCSATFITY 42 (72)
T ss_pred CccCCCCCCccEEEECh-hcChhhheeeeecCCCCCCCEEEEE
Confidence 47899999987443221 12344455999999 799999753
No 22
>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=94.80 E-value=0.027 Score=38.89 Aligned_cols=37 Identities=19% Similarity=0.447 Sum_probs=26.0
Q ss_pred cccCCCCcceEE-EEeccCCCCCceeEEEccC--CCCcceec
Q 020974 272 ECGRCGHNKISY-QHSSILDDYNLTRHVTCLN--CNQYWVST 310 (319)
Q Consensus 272 ~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~--C~~~w~~~ 310 (319)
.||.||++-... ..+. .+.--..|+.|.| |||+|...
T Consensus 1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQL--SPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhh--CcceEEEEEEECCCcCCCEEEEE
Confidence 599999976554 2221 3334459999998 99999753
No 23
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=94.20 E-value=0.067 Score=50.51 Aligned_cols=59 Identities=19% Similarity=0.167 Sum_probs=48.4
Q ss_pred ccHHHHHHHHHHhhcCCCCHHhhhcccceeecccccCC--CCHHHHHHHHHHHHHHHhhcc
Q 020974 26 VEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKH--PSQKIQKLAYDLISSWRDMCW 84 (319)
Q Consensus 26 ~~~~~~l~~L~~L~~~~it~~~L~~T~IG~~V~~Lrkh--~~~~I~~~Ak~lv~~WK~~v~ 84 (319)
|+..---.+|..|..+||-.+.|.+.+||+.|-...+. ..+.|+.+|++||..|-.-+-
T Consensus 227 P~~~IqksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpIi 287 (397)
T COG5139 227 PNIKIQKSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPII 287 (397)
T ss_pred cchHHHHHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhcccc
Confidence 33333345666777899999999999999999998765 468999999999999998664
No 24
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.03 E-value=0.031 Score=36.43 Aligned_cols=35 Identities=20% Similarity=0.399 Sum_probs=22.0
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
.+.|++|+..-..-..+.+ +-..-+.|.+|||.|+
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip----~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIP----PKGRKVRCSKCGHVFF 36 (36)
T ss_pred EEECCCCCCEEeCCHHHCC----CCCcEEECCCCCCEeC
Confidence 4689999763222122221 3345689999999995
No 25
>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=93.10 E-value=0.051 Score=34.05 Aligned_cols=28 Identities=25% Similarity=0.675 Sum_probs=14.3
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
-.|+.|++..+. .|.. .++|..|+|.|.
T Consensus 3 p~Cp~C~se~~y-------~D~~---~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY-------EDGE---LLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E-------E-SS---SEEETTTTEEE-
T ss_pred CCCCCCCCccee-------ccCC---EEeCCcccccCC
Confidence 379999996655 3333 379999999994
No 26
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=92.89 E-value=0.086 Score=34.33 Aligned_cols=35 Identities=20% Similarity=0.589 Sum_probs=22.8
Q ss_pred cccccCCCCcceEEEEecc-CCCCCceeEEEccCCCCccee
Q 020974 270 IYECGRCGHNKISYQHSSI-LDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~r-sade~mt~f~~C~~C~~~w~~ 309 (319)
.+.||+|+.. |.++.. -.+.+ ..+.|.+||+.|..
T Consensus 2 ~~~CP~C~~~---~~v~~~~~~~~~--~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 2 RIQCPNCKTS---FRVVDSQLGANG--GKVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCE---EEeCHHHcCCCC--CEEECCCCCCEEEe
Confidence 3789999974 433321 12222 26899999999974
No 27
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=92.85 E-value=0.1 Score=38.27 Aligned_cols=36 Identities=22% Similarity=0.594 Sum_probs=23.9
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCce----------eEEEccCCCCc
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLT----------RHVTCLNCNQY 306 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt----------~f~~C~~C~~~ 306 (319)
..+.||+||.++..- +++. ..+... +.++|.+||.+
T Consensus 3 ~~~kCpKCgn~~~~ekei~~--tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 3 NAFKCPKCGNTNYEEKEIAA--TGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred ccccCCCcCCcchhhceeec--cCCCcceeEEecccEEEEEEeccCCch
Confidence 346799999987555 5543 333322 44789999965
No 28
>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=92.45 E-value=0.075 Score=43.01 Aligned_cols=30 Identities=23% Similarity=0.672 Sum_probs=21.7
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceec
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
-.||+|++.- +|+ |.. .+.|..|+|.|...
T Consensus 3 p~CP~C~sey-tY~------dg~---~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEY-TYH------DGT---QLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcc-eEe------cCC---eeECcccccccccc
Confidence 4799999954 442 222 38999999999644
No 29
>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=92.34 E-value=0.14 Score=35.02 Aligned_cols=29 Identities=21% Similarity=0.611 Sum_probs=21.2
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.+.||+||+. ..|.+.+ ...|.|..|+++
T Consensus 18 g~~CP~Cg~~-~~~~~~~-------~~~~~C~~C~~q 46 (46)
T PF12760_consen 18 GFVCPHCGST-KHYRLKT-------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCe-eeEEeCC-------CCeEECCCCCCc
Confidence 3889999998 3334432 566899999974
No 30
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.97 E-value=0.097 Score=34.24 Aligned_cols=35 Identities=23% Similarity=0.528 Sum_probs=22.1
Q ss_pred cccccCCCCcceEEEEec-cCCCCCceeEEEccCCCCccee
Q 020974 270 IYECGRCGHNKISYQHSS-ILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~-rsade~mt~f~~C~~C~~~w~~ 309 (319)
..+||.|+. .|.+.. +-. +-..-+.|.+|+|.|.+
T Consensus 2 ~i~CP~C~~---~f~v~~~~l~--~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 2 IITCPNCQT---RFRVPDDKLP--AGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EEECCCCCc---eEEcCHHHcc--cCCcEEECCCCCcEeeC
Confidence 368999986 442211 111 12346999999999964
No 31
>PHA00626 hypothetical protein
Probab=91.62 E-value=0.19 Score=35.97 Aligned_cols=36 Identities=22% Similarity=0.534 Sum_probs=23.1
Q ss_pred cccCCCCcceEE--EEeccCCCCCceeEEEccCCCCcceecccccc
Q 020974 272 ECGRCGHNKISY--QHSSILDDYNLTRHVTCLNCNQYWVSTNLSFG 315 (319)
Q Consensus 272 ~C~~C~~~~~~~--q~q~rsade~mt~f~~C~~C~~~w~~~~~~~~ 315 (319)
.||+||+.+.+- ... - ...-|.|..||+++ +.+.|+
T Consensus 2 ~CP~CGS~~Ivrcg~cr--~----~snrYkCkdCGY~f--t~~~~~ 39 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR--G----WSDDYVCCDCGYND--SKDAFG 39 (59)
T ss_pred CCCCCCCceeeeeceec--c----cCcceEcCCCCCee--chhhhh
Confidence 699999976654 221 1 12338999999876 444443
No 32
>PRK10220 hypothetical protein; Provisional
Probab=91.29 E-value=0.14 Score=41.49 Aligned_cols=31 Identities=23% Similarity=0.697 Sum_probs=22.5
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceecc
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~ 311 (319)
-.||.|++.-+ | .|.. .+.|..|+|.|....
T Consensus 4 P~CP~C~seyt-Y------~d~~---~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYT-Y------EDNG---MYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcce-E------cCCC---eEECCcccCcCCccc
Confidence 47999999554 4 2222 489999999997543
No 33
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=91.09 E-value=0.27 Score=39.32 Aligned_cols=37 Identities=27% Similarity=0.555 Sum_probs=28.6
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCccee
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
..|.||+||+.+.+- .+-. -.+.-+..|-+||.++.+
T Consensus 21 k~FtCp~Cghe~vs~ctvkk----~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKK----TVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred ceEecCccCCeeeeEEEEEe----cCceeEEEcccCcceEEE
Confidence 469999999999886 4422 256778999999988753
No 34
>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=90.40 E-value=0.31 Score=32.77 Aligned_cols=31 Identities=23% Similarity=0.616 Sum_probs=20.8
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
|.||.||++...+- +++-.++|.+||.-...
T Consensus 1 m~Cp~Cg~~~~~~D--------~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIVFD--------PERGELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEEEE--------TTTTEEEETTT-BBEE-
T ss_pred CCCcCCcCCceEEc--------CCCCeEECCCCCCEeec
Confidence 58999999874322 44556899999965543
No 35
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=89.86 E-value=0.21 Score=36.88 Aligned_cols=29 Identities=31% Similarity=0.703 Sum_probs=24.0
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCc
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~ 306 (319)
-..+||.||+..+.| -.| +.|+|..||..
T Consensus 18 l~VkCpdC~N~q~vFshas---------t~V~C~~CG~~ 47 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHAS---------TVVTCLICGTT 47 (67)
T ss_pred EEEECCCCCCEEEEeccCc---------eEEEecccccE
Confidence 357999999999999 665 35899999965
No 36
>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=89.19 E-value=0.3 Score=41.82 Aligned_cols=39 Identities=21% Similarity=0.566 Sum_probs=24.0
Q ss_pred ccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCccee
Q 020974 271 YECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 271 ~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
..||.||+.++.. -...-........==.|.+||+||..
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 3799999988775 33110000012245689999999873
No 37
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=88.65 E-value=0.58 Score=36.13 Aligned_cols=40 Identities=15% Similarity=0.450 Sum_probs=22.0
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
....|.||.|++.++.- .+-. . .++-.+.|..||..|.+.
T Consensus 19 l~~~F~CPfC~~~~sV~v~idk-k---~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVKIDK-K---EGIGILSCRVCGESFQTK 59 (81)
T ss_dssp -SS----TTT--SS-EEEEEET-T---TTEEEEEESSS--EEEEE
T ss_pred CCceEcCCcCCCCCeEEEEEEc-c---CCEEEEEecCCCCeEEEc
Confidence 33679999999988887 6632 2 567789999999888654
No 38
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=88.16 E-value=0.75 Score=32.95 Aligned_cols=35 Identities=26% Similarity=0.568 Sum_probs=23.7
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCC
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~ 305 (319)
.+.+||-||.....+ +.- ..+..+..+|.|.+||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~--~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDE--GFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeeccc--CCCCCCEEEEEcCCCCC
Confidence 467999997766665 422 22333338889999997
No 39
>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=88.01 E-value=0.69 Score=33.51 Aligned_cols=36 Identities=17% Similarity=0.303 Sum_probs=25.6
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceecc
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~ 311 (319)
..||+|+.-+..-.++. .-.-+++|..|||+-.-..
T Consensus 10 A~CP~C~~~Dtl~~~~e-----~~~e~vECv~Cg~~~~~~~ 45 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKE-----NNIELVECVECGYQEQQKD 45 (59)
T ss_pred ccCCCCcCccEEEEEEe-----CCceEEEeccCCCccccCC
Confidence 58999999888764432 1235689999999865443
No 40
>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=87.88 E-value=0.043 Score=37.09 Aligned_cols=30 Identities=20% Similarity=0.401 Sum_probs=24.7
Q ss_pred CCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 276 CGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 276 C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
|.+.-.+-..|+|++||....+-.|..||.
T Consensus 13 C~H~f~~~E~Q~RAGDE~VSfI~~C~~C~~ 42 (43)
T PF11792_consen 13 CKHKFVTIEKQLRAGDEAVSFIKYCQKCGQ 42 (43)
T ss_pred ceeeeeehhhhhcccchHHHHHHHHHHhCC
Confidence 666555448999999999888888999985
No 41
>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=87.37 E-value=0.96 Score=31.79 Aligned_cols=34 Identities=21% Similarity=0.508 Sum_probs=22.5
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.+||-||++...+.... .|-.-.-++.|..||..
T Consensus 2 kPCPfCGg~~~~~~~~~--~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGF--DPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEecc--CCCCCEEEEECCCCCCC
Confidence 58999999777663222 22233445589999976
No 42
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.09 E-value=0.34 Score=42.73 Aligned_cols=42 Identities=17% Similarity=0.359 Sum_probs=30.5
Q ss_pred ccccccccCCCCcceEE-------EEeccCCCCCceeEEEccCCCCcceec
Q 020974 267 VSDIYECGRCGHNKISY-------QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-------q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
+.-...|++||....+- -.|.+.-|- =.+|.|.+|.++|.++
T Consensus 14 pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDv--WlIYkC~~Cd~tWN~~ 62 (203)
T COG4332 14 PQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDV--WLIYKCTHCDYTWNIS 62 (203)
T ss_pred ChhhhhCcccCCcceeeecCcEEEcCCCcEEEE--EEEEEeeccCCccchh
Confidence 34567999999988753 234444443 4789999999999865
No 43
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=86.99 E-value=0.37 Score=34.76 Aligned_cols=31 Identities=29% Similarity=0.689 Sum_probs=24.3
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
+.+..|.|+.||+.+.- .+.|- +.|..||||
T Consensus 16 ~~~miYiCgdC~~en~l-----k~~D~-----irCReCG~R 46 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTL-----KRGDV-----IRCRECGYR 46 (62)
T ss_pred cccEEEEeccccccccc-----cCCCc-----EehhhcchH
Confidence 57788999999998764 23333 799999997
No 44
>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=86.80 E-value=0.53 Score=48.83 Aligned_cols=40 Identities=15% Similarity=0.301 Sum_probs=30.2
Q ss_pred cccccCCCCcceE-E-EEeccCCCCCceeEEEccCCCCccee
Q 020974 270 IYECGRCGHNKIS-Y-QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 270 ~~~C~~C~~~~~~-~-q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
..+||.||+...- | +++--....|.+.+|+|..||..|..
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 4689999998774 3 66552222688999999999998864
No 45
>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=85.84 E-value=0.97 Score=34.03 Aligned_cols=35 Identities=14% Similarity=0.271 Sum_probs=25.1
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceec
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
..||+|+.-++...++. . + .-+++|..|||+-.-.
T Consensus 9 a~CP~C~~~D~i~~~~e--~-~--ve~vECV~CGy~e~~~ 43 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRE--N-G--VEYVECVECGYTERQP 43 (71)
T ss_pred ccCCCCcCccEEEEEEe--C-C--ceEEEecCCCCeeccC
Confidence 58999999886654432 1 1 4679999999986543
No 46
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=85.81 E-value=0.84 Score=38.81 Aligned_cols=33 Identities=15% Similarity=0.347 Sum_probs=26.4
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
.-..|+.||+.++.+... .-+.|..|..||.+-
T Consensus 101 ~yVlC~~C~spdT~l~k~------~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 101 EYVICPECGSPDTKLIKE------GRIWVLKCEACGAET 133 (138)
T ss_pred hcEECCCCCCCCcEEEEc------CCeEEEEcccCCCCC
Confidence 347999999999998543 337899999999764
No 47
>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=85.18 E-value=0.73 Score=43.67 Aligned_cols=41 Identities=17% Similarity=0.273 Sum_probs=20.1
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceeccc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNL 312 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~~ 312 (319)
.-.||-||+.-..-.+..... ++ ..|..|.-||+.|.+-|.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~-~G-~R~L~Cs~C~t~W~~~R~ 212 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGER-EG-KRYLHCSLCGTEWRFVRI 212 (290)
T ss_dssp -SS-TTT---EEEEEEE--------EEEEEETTT--EEE--TT
T ss_pred CCcCCCCCCcCceEEEecCCC-Cc-cEEEEcCCCCCeeeecCC
Confidence 369999999654434442221 23 499999999999998775
No 48
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=85.05 E-value=0.43 Score=34.58 Aligned_cols=33 Identities=18% Similarity=0.385 Sum_probs=21.0
Q ss_pred cccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCC
Q 020974 268 SDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~ 305 (319)
-..|.||+||.....- +.= |.-. .-|+|.+||.
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~C-Rk~g----~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKC-RKLG----NPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeeehhhhH-HHcC----CceECCCcCc
Confidence 3579999999755443 322 2221 2389999995
No 49
>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=83.92 E-value=0.77 Score=29.17 Aligned_cols=26 Identities=31% Similarity=0.758 Sum_probs=13.8
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
+.|++||...- ....| + +.|.+||||
T Consensus 1 Y~C~~Cg~~~~-----~~~~~-~----irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVE-----LKPGD-P----IRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE------BSTSS-T----SSBSSSS-S
T ss_pred CCCCcCCCeeE-----cCCCC-c----EECCcCCCe
Confidence 45777776433 11222 2 578888876
No 50
>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=83.38 E-value=0.38 Score=35.71 Aligned_cols=34 Identities=18% Similarity=0.475 Sum_probs=22.9
Q ss_pred cccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCc
Q 020974 270 IYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.|+|..|+.+..-- ..| |=+--++++.|.+|+++
T Consensus 4 ~FTC~~C~~Rs~~~~sk~---aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQ---AYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEEETTTTEEEEEEEEHH---HHHTSEEEEE-TTS--E
T ss_pred EEEcCCCCCccceeeCHH---HHhCCeEEEECCCCcce
Confidence 48999999988765 333 33344699999999865
No 51
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=82.54 E-value=1.4 Score=39.52 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=29.5
Q ss_pred cccccccccCCCCcceEE-EEeccCC--CCCceeEEEccCCCCcce
Q 020974 266 IVSDIYECGRCGHNKISY-QHSSILD--DYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~-q~q~rsa--de~mt~f~~C~~C~~~w~ 308 (319)
..+....||-||+ .+.+ +....-. .+-|-..+.|.+||.|..
T Consensus 10 ~~~~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 10 EFETRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeeeeecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 4556789999999 5554 4444322 344678899999999865
No 52
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.30 E-value=1 Score=30.63 Aligned_cols=27 Identities=37% Similarity=0.854 Sum_probs=16.8
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.|.|++||.. +.+. +.|. +.|.+|||+
T Consensus 2 ~Y~C~~Cg~~---~~~~--~~~~-----irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRE---NEIK--SKDV-----VRCRECGYR 28 (44)
T ss_pred EEECCCCCCE---eecC--CCCc-----eECCCCCce
Confidence 3788888883 2111 2222 688889887
No 53
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=82.26 E-value=0.54 Score=47.29 Aligned_cols=171 Identities=10% Similarity=-0.021 Sum_probs=105.0
Q ss_pred cCCChHHHHHHHHHHHHHHhhhhhhchhhh-hhh--hhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhcCCCC
Q 020974 131 IKCNDSFREIVREKLYDALSKVSDEAADKV-TID--LVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPE 207 (319)
Q Consensus 131 ~~~~d~vR~k~r~~L~~aL~~~~~e~~~~~-~~~--~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NLkd~k 207 (319)
+.+++.-|++++.-++..+..++.-..... .-+ ..-..+....+..||...|+.+..+...|..+...+.++|+ .
T Consensus 238 ~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~~~~~~~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k--~ 315 (464)
T KOG1886|consen 238 LLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPAGDQGSLWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLK--G 315 (464)
T ss_pred CCCCcccccccccccchhhccccccccccCCCcccccCCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhc--c
Confidence 568899999999999999865443221110 000 11223467788999999999887777899999999999998 4
Q ss_pred CHHHHHHHhcC-CCChhhhhcCChhhcCchHHHHHhhhhhhchhhhhcCCCCccccccccccccccccCCCCcceEE-EE
Q 020974 208 NQDFRRKVLLG-HVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY-QH 285 (319)
Q Consensus 208 N~~Lr~~vl~G-~i~p~~lv~Ms~eElas~e~k~~~~~~~~~e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~~~~~~-q~ 285 (319)
---|+.+.++| +..|+-.+.|.+-.+-+...-..-.+. ...+-+ . ..-+.-.|..|=..-+.- ++
T Consensus 316 ~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~~~~~~~~----~~d~~~----~-----l~~~~~~~~~~~~~~~g~~~~ 382 (464)
T KOG1886|consen 316 QALLKPEPLNPGETKPEPKQELHPPSFPDGQSSPSSMKL----NDDDYD----G-----LCVGLELTAGSLYLYCGQEGL 382 (464)
T ss_pred hhhhccccCCCcccCchhhhhccCCCCCCCccCcccccc----CchhHH----H-----HHHhhhhhccchhhhcccccc
Confidence 46788888998 499999998877666555431111111 000000 0 111122333222222222 11
Q ss_pred -eccCCCCCceeEEEccCCCCcceeccccccccCC
Q 020974 286 -SSILDDYNLTRHVTCLNCNQYWVSTNLSFGVLPI 319 (319)
Q Consensus 286 -q~rsade~mt~f~~C~~C~~~w~~~~~~~~~~~~ 319 (319)
+..-.+-+| .-|..|+..|-..|+...++|+
T Consensus 383 ~~~~~~~~~~---~~~v~~~~~a~~~~~~~~~~~~ 414 (464)
T KOG1886|consen 383 ICAGHLPCPM---LPEVKLSPVAAVHREGLLLAPS 414 (464)
T ss_pred eeccccCCCC---CCCcCcccccccchhhhcccce
Confidence 222223334 5788899999999998888774
No 54
>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=82.25 E-value=1.6 Score=29.27 Aligned_cols=30 Identities=37% Similarity=0.816 Sum_probs=20.3
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCC
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~ 305 (319)
=.|.|..||+ .| .+|.-+.+.+ ..|..||.
T Consensus 4 Yey~C~~Cg~---~fe~~~~~~~~~~----~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGH---EFEVLQSISEDDP----VPCPECGS 34 (42)
T ss_pred EEEEeCCCCC---EEEEEEEcCCCCC----CcCCCCCC
Confidence 3589999997 45 5554333232 58999997
No 55
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=81.72 E-value=1 Score=36.07 Aligned_cols=36 Identities=36% Similarity=0.665 Sum_probs=24.0
Q ss_pred ccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 267 VSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
....|.||.||+....--+ .| .+.+++|.+||....
T Consensus 18 lpt~f~CP~Cge~~v~v~~-~k-----~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 18 LPKIFECPRCGKVSISVKI-KK-----NIAIITCGNCGLYTE 53 (99)
T ss_pred CCcEeECCCCCCeEeeeec-CC-----CcceEECCCCCCccC
Confidence 3468999999963222211 12 478899999997643
No 56
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=81.38 E-value=1.1 Score=34.89 Aligned_cols=31 Identities=19% Similarity=0.463 Sum_probs=23.0
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
+.+.||.||.+.+- |.+ +-++.|..||+.|.
T Consensus 34 ~~~~Cp~C~~~~Vk-----R~a----~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTVK-----RIA----TGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCccee-----eec----cCeEEcCCCCCeec
Confidence 56899999998332 222 45799999998874
No 57
>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=81.11 E-value=0.92 Score=43.56 Aligned_cols=43 Identities=16% Similarity=0.335 Sum_probs=30.8
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceeccc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNL 312 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~~ 312 (319)
..-.||-||+.-+.-.++....+++ -.|..|.-|++.|.+-|.
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G-~RyL~CslC~teW~~~R~ 225 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETG-LRYLSCSLCATEWHYVRV 225 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCC-ceEEEcCCCCCcccccCc
Confidence 3459999999764325544333344 689999999999998764
No 58
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=80.94 E-value=1.8 Score=35.34 Aligned_cols=32 Identities=16% Similarity=0.404 Sum_probs=25.2
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.-..|+.|++.++.+.... -+.|..|..||.+
T Consensus 79 ~yVlC~~C~spdT~l~k~~------r~~~l~C~aCGa~ 110 (110)
T smart00653 79 EYVLCPECGSPDTELIKEN------RLFFLKCEACGAR 110 (110)
T ss_pred hcEECCCCCCCCcEEEEeC------CeEEEEccccCCC
Confidence 3478999999999985432 2688999999964
No 59
>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=80.85 E-value=1.9 Score=36.00 Aligned_cols=31 Identities=16% Similarity=0.398 Sum_probs=25.0
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
-..|+.|++.++.+... .-..|..|..||.+
T Consensus 93 yVlC~~C~spdT~l~k~------~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKE------GRLIFLKCKACGAS 123 (125)
T ss_dssp HSSCTSTSSSSEEEEEE------TTCCEEEETTTSCE
T ss_pred EEEcCCCCCCccEEEEc------CCEEEEEecccCCc
Confidence 36899999999999554 22488999999975
No 60
>PF14353 CpXC: CpXC protein
Probab=80.49 E-value=1.4 Score=36.44 Aligned_cols=38 Identities=26% Similarity=0.430 Sum_probs=22.4
Q ss_pred ccccCCCCcceEEEEec-cCCCCC-c--------eeEEEccCCCCcce
Q 020974 271 YECGRCGHNKISYQHSS-ILDDYN-L--------TRHVTCLNCNQYWV 308 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~-rsade~-m--------t~f~~C~~C~~~w~ 308 (319)
.+||.||+.-..-.... =...+| | -..++|.+||+...
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCcee
Confidence 58999998655321111 111122 1 24689999999874
No 61
>PLN00209 ribosomal protein S27; Provisional
Probab=80.33 E-value=1.7 Score=33.84 Aligned_cols=59 Identities=15% Similarity=0.207 Sum_probs=37.8
Q ss_pred hhhcCchHHHHHhhhhhhchhhhhcCCCCccccccccccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcc
Q 020974 230 AKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 230 ~eElas~e~k~~~~~~~~~e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w 307 (319)
..||..+....+..+. +.+.|-... . ..=-...|+.|++-.+.| ..|+ -|.|..||..-
T Consensus 6 ~~DLl~P~~~~e~~kh-K~k~Lv~~P--------n-S~Fm~VkCp~C~n~q~VFShA~t---------~V~C~~Cg~~L 65 (86)
T PLN00209 6 DIDLLNPPAELEKRKH-KLKRLVQSP--------N-SFFMDVKCQGCFNITTVFSHSQT---------VVVCGSCQTVL 65 (86)
T ss_pred chhccCCCHHHHHhhh-hceeeecCC--------C-CEEEEEECCCCCCeeEEEecCce---------EEEccccCCEe
Confidence 3466666656566555 433332211 1 222467999999999999 7764 48999999653
No 62
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=79.98 E-value=1.4 Score=42.32 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=30.4
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceeccc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNL 312 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~~ 312 (319)
..-.||-||+.-+.-.++.+ .++ --.|..|.-|++.|.+-|.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~-~~~-G~RyL~CslC~teW~~~R~ 227 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIG-TTQ-GLRYLHCNLCESEWHVVRV 227 (309)
T ss_pred CCCCCCCCCCcchhheeecc-CCC-CceEEEcCCCCCcccccCc
Confidence 45799999997654344432 233 3589999999999998764
No 63
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=79.63 E-value=1.4 Score=31.99 Aligned_cols=30 Identities=27% Similarity=0.688 Sum_probs=24.4
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcc
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w 307 (319)
-..+|+.|++..+.| -.|+ -|.|..||..-
T Consensus 10 ~~VkCp~C~n~q~vFsha~t---------~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHAST---------VVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCCCeEEEEecCCc---------EEECcccCCCc
Confidence 357999999999999 6653 48999999763
No 64
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=79.58 E-value=2 Score=36.22 Aligned_cols=33 Identities=12% Similarity=0.292 Sum_probs=25.8
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
.-..|+.||+.++.+... .-..|..|..||.+-
T Consensus 96 ~yVlC~~C~sPdT~l~k~------~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKE------GRVSLLKCEACGAKA 128 (133)
T ss_pred heEECCCCCCCCcEEEEe------CCeEEEecccCCCCC
Confidence 447899999999998543 235688999999763
No 65
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.30 E-value=1.5 Score=29.80 Aligned_cols=29 Identities=34% Similarity=0.644 Sum_probs=17.5
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
.|.|++||..- .| ++.++ -+.|..||++-
T Consensus 3 ~y~C~~CG~~~-~~-------~~~~~-~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREV-EL-------DEYGT-GVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEE-EE-------CCCCC-ceECCCCCCeE
Confidence 47888888732 22 11112 46888888764
No 66
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=78.56 E-value=2.1 Score=33.30 Aligned_cols=30 Identities=17% Similarity=0.401 Sum_probs=24.9
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcc
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w 307 (319)
-...|+.|++-.+.| ..|+ -|.|..||..-
T Consensus 34 m~VkCp~C~n~q~VFShA~t---------~V~C~~Cg~~L 64 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQT---------VVLCGGCSSQL 64 (85)
T ss_pred EEEECCCCCCeeEEEecCce---------EEEccccCCEe
Confidence 468999999999999 7764 48999999653
No 67
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=78.41 E-value=2.9 Score=30.78 Aligned_cols=35 Identities=14% Similarity=0.310 Sum_probs=25.5
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
...+||-||....+...+ .-..++.|..||-+|-.
T Consensus 5 ~lKPCPFCG~~~~~v~~~------~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAI------SGYYRAKCNGCESRTGY 39 (64)
T ss_pred cccCCCCCCCceeEEEec------CceEEEEcCCCCcCccc
Confidence 356999999988887322 11456999999987654
No 68
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=78.21 E-value=2.7 Score=27.81 Aligned_cols=30 Identities=23% Similarity=0.620 Sum_probs=20.6
Q ss_pred cccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 272 ECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 272 ~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
.||+|+..=..+.+ ++ .....|.+||--|-
T Consensus 1 ~CP~C~~~l~~~~~-----~~--~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GD--VEIDVCPSCGGIWF 30 (41)
T ss_pred CcCCCCcccceEEE-----CC--EEEEECCCCCeEEc
Confidence 59999884332233 22 56678999999995
No 69
>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=78.08 E-value=1.1 Score=27.03 Aligned_cols=11 Identities=18% Similarity=0.473 Sum_probs=8.4
Q ss_pred EEccCCCCcce
Q 020974 298 VTCLNCNQYWV 308 (319)
Q Consensus 298 ~~C~~C~~~w~ 308 (319)
-.|.+|||.|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 47888888774
No 70
>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=77.05 E-value=1.5 Score=37.59 Aligned_cols=36 Identities=17% Similarity=0.354 Sum_probs=26.2
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
...||+||+.++.-..|-.|. +=.-.|.|..|...+
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t--~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPT--ACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEeecCCCCh--hhHHHhhhhhhCCcH
Confidence 479999999998875555443 334678899887654
No 71
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=76.92 E-value=2.4 Score=29.08 Aligned_cols=33 Identities=18% Similarity=0.439 Sum_probs=20.1
Q ss_pred cccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceecc
Q 020974 272 ECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 272 ~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~ 311 (319)
-||.||+ ..| .+ .++. ..++.|..||+.+....
T Consensus 2 FCp~Cg~--~l~---~~-~~~~-~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGN--MLI---PK-EGKE-KRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCC--ccc---cc-cCCC-CCEEECCcCCCeEECCC
Confidence 4899988 222 11 1111 23778999999887653
No 72
>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=74.76 E-value=1.6 Score=31.28 Aligned_cols=28 Identities=18% Similarity=0.496 Sum_probs=19.6
Q ss_pred cccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCc
Q 020974 270 IYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~ 306 (319)
..+|+.|++..+.| ..|+ -|.|..||..
T Consensus 7 ~VkCp~C~~~q~vFSha~t---------~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQT---------VVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS----------EE-SSSTSE
T ss_pred EEECCCCCCeeEEEecCCe---------EEEcccCCCE
Confidence 47999999999999 7774 3899999964
No 73
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=74.64 E-value=3.2 Score=37.45 Aligned_cols=33 Identities=15% Similarity=0.385 Sum_probs=25.8
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
.-..|+.|++.++.+... .-+.|..|..||..-
T Consensus 97 ~yV~C~~C~~pdT~l~k~------~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 97 EYVICSECGLPDTRLVKE------DRVLMLRCDACGAHR 129 (201)
T ss_pred heEECCCCCCCCcEEEEc------CCeEEEEcccCCCCc
Confidence 447899999999988543 247889999999753
No 74
>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=74.25 E-value=3.7 Score=26.66 Aligned_cols=29 Identities=38% Similarity=0.869 Sum_probs=19.0
Q ss_pred cccccCCCCcceEE-EEeccCCCCCceeEEEccCCCC
Q 020974 270 IYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~ 305 (319)
.|.|+.||+ .| .++..+.+ ....|..||.
T Consensus 5 ~y~C~~Cg~---~fe~~~~~~~~----~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGH---TFEVLQKISDD----PLATCPECGG 34 (41)
T ss_pred EEEcCCCCC---EEEEEEecCCC----CCCCCCCCCC
Confidence 589999998 45 44432222 2358999997
No 75
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.08 E-value=1.1 Score=38.24 Aligned_cols=40 Identities=23% Similarity=0.502 Sum_probs=25.0
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
....|.||+||. ..++ ..+. ..| + +..++|.+||..-...
T Consensus 96 ~~~~Y~Cp~C~~-~y~~~ea~~-~~d-~-~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 96 NNAYYKCPNCQS-KYTFLEANQ-LLD-M-DGTFTCPRCGEELEED 136 (147)
T ss_pred CCcEEECcCCCC-EeeHHHHHH-hcC-C-CCcEECCCCCCEEEEc
Confidence 446799999984 3334 3322 122 2 4548999999876543
No 76
>PLN02976 amine oxidase
Probab=73.99 E-value=3 Score=48.00 Aligned_cols=60 Identities=13% Similarity=0.155 Sum_probs=50.3
Q ss_pred HHHHHHHHHhhcCCCCHHhhhcccceeecc-cccCCCCHHHHHHHHHHHHHHHhhcccccc
Q 020974 29 ARCIDALDQIKNSSITYQLLVSTQVIRHLL-PMLKHPSQKIQKLAYDLISSWRDMCWDVED 88 (319)
Q Consensus 29 ~~~l~~L~~L~~~~it~~~L~~T~IG~~V~-~Lrkh~~~~I~~~Ak~lv~~WK~~v~~~~~ 88 (319)
+-+..+|+-|--++.++..|+..+||++|. ++.-|.+++|+.+|+.++..|-..+..+..
T Consensus 1301 ~l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~ 1361 (1713)
T PLN02976 1301 QLLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKA 1361 (1713)
T ss_pred HHHHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 344566666777888889999999999985 567899999999999999999999976655
No 77
>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=73.92 E-value=2.1 Score=31.31 Aligned_cols=31 Identities=32% Similarity=0.602 Sum_probs=21.8
Q ss_pred ccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 267 VSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
-|+. .|+.||+..-. ......+.|.+||..+
T Consensus 26 ~TSq-~C~~CG~~~~~---------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 26 YTSQ-TCPRCGHRNKK---------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCcc-CccCccccccc---------ccccceEEcCCCCCEE
Confidence 3554 89999997654 1223458999999875
No 78
>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=72.70 E-value=2.8 Score=39.67 Aligned_cols=42 Identities=17% Similarity=0.362 Sum_probs=22.3
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceecc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~ 311 (319)
...|+.||+.+..-.......+++.-...+|..|+..+|.-.
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence 467999998877531112235667778899999999998654
No 79
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=71.72 E-value=1.1 Score=39.59 Aligned_cols=34 Identities=15% Similarity=0.379 Sum_probs=24.6
Q ss_pred ccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 267 VSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
...-|.||+|+. +.+ .+|.|...++|..||..-.
T Consensus 114 ~~~~Y~Cp~C~~-ryt-------f~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHI-RFT-------FDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCc-EEe-------HHHHhhcCCcCCCCCCCCe
Confidence 446799999995 333 3456667799999997644
No 80
>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=71.61 E-value=1.6 Score=31.96 Aligned_cols=39 Identities=18% Similarity=0.485 Sum_probs=26.6
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
....||+|++.++-| =----+...|- +.|..|...|..-
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~~Ck~C~rywT~G 43 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPR---YFCKSCRRYWTHG 43 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcc---hhhHHHHHHHHhc
Confidence 457999999999865 33222233343 6899999999753
No 81
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.33 E-value=2.1 Score=36.95 Aligned_cols=35 Identities=17% Similarity=0.307 Sum_probs=26.8
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCc
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~ 306 (319)
=.|+|..|+.+..-- ..| |=+.-|+||+|..|.+.
T Consensus 78 l~yTCkvCntRs~ktisk~---AY~~GvVivqC~gC~~~ 113 (165)
T KOG3277|consen 78 LAYTCKVCNTRSTKTISKQ---AYEKGVVIVQCPGCKNH 113 (165)
T ss_pred EEEEeeccCCccccccChh---hhhCceEEEECCCCccc
Confidence 359999999988743 333 55667999999999865
No 82
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.18 E-value=2.5 Score=30.59 Aligned_cols=35 Identities=20% Similarity=0.348 Sum_probs=20.6
Q ss_pred cccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 268 SDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
-..|.||.||.....-=..-|.. -.-|+|.+||..
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~----~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQ----SNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhc----CCceECCCCCCc
Confidence 35799999998422211111211 134899999953
No 83
>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=69.33 E-value=5.1 Score=27.63 Aligned_cols=29 Identities=31% Similarity=0.772 Sum_probs=19.0
Q ss_pred cccccCCCCcceEE-EEeccCCCCCceeEEEccCCCC
Q 020974 270 IYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~ 305 (319)
.|.|..||+ .| .+|. ..|+ ....|..||.
T Consensus 5 ey~C~~Cg~---~fe~~~~-~~~~---~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGH---RFEVLQK-MSDD---PLATCPECGG 34 (52)
T ss_pred EEEeCCCCC---EeEEEEe-cCCC---CCCCCCCCCC
Confidence 589999996 45 4442 2332 2367999997
No 84
>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=68.60 E-value=1.4 Score=38.23 Aligned_cols=33 Identities=12% Similarity=0.293 Sum_probs=23.7
Q ss_pred ccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 267 VSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
...-|.||+|+. +.+ -+|.|...++|..||..-
T Consensus 106 ~~~~Y~Cp~c~~-r~t-------f~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 106 NNMFFICPNMCV-RFT-------FNEAMELNFTCPRCGAML 138 (158)
T ss_pred CCCeEECCCCCc-Eee-------HHHHHHcCCcCCCCCCEe
Confidence 456799999994 333 345555678999999764
No 85
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=68.23 E-value=9.2 Score=39.57 Aligned_cols=61 Identities=23% Similarity=0.247 Sum_probs=46.4
Q ss_pred ChHHHHHHHHHHHHHHhhhhhhchhhhhhhhhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhcCCCCCH
Q 020974 134 NDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQ 209 (319)
Q Consensus 134 ~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~ 209 (319)
+-+.|.+++.-|.+.|.....+.. .-|..+|++||.+.. +..+|-..+-.|+.+++|-.|.
T Consensus 8 S~kFRq~vIsried~l~~n~q~~~--------------k~a~~mE~hVF~K~~-tkDEYl~lvAkli~h~~d~s~~ 68 (742)
T KOG4274|consen 8 SPKFRQHVISRIEDELRKNGQAHS--------------KSAKDMESHVFLKAK-TKDEYLSLVAKLIIHFRDISNK 68 (742)
T ss_pred cHHHHHHHHHHhhhhhhhhhhccC--------------cchHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHhhhhh
Confidence 357899999999999986432111 238899999998764 3569999998899999986653
No 86
>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=68.11 E-value=3.8 Score=26.64 Aligned_cols=27 Identities=22% Similarity=0.458 Sum_probs=19.2
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.++|+.|+++ .|.. ++ -|+.|..|||.
T Consensus 8 ~~~C~~C~~~--~~~~-----~d---G~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR--WFYS-----DD---GFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe--EeEc-----cC---CEEEhhhCceE
Confidence 3579999998 4322 23 36899999984
No 87
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=67.75 E-value=5.3 Score=29.04 Aligned_cols=38 Identities=18% Similarity=0.383 Sum_probs=28.8
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceecccccccc
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVL 317 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~~~~~~~~ 317 (319)
+...||-|+++=... +.| -..|..|+ +|.-.++.++||
T Consensus 7 eiLaCP~~kg~L~~~~~~~----------~L~c~~~~-~aYpI~dGIPvl 45 (60)
T COG2835 7 EILACPVCKGPLVYDEEKQ----------ELICPRCK-LAYPIRDGIPVL 45 (60)
T ss_pred eeeeccCcCCcceEeccCC----------EEEecccC-ceeecccCcccc
Confidence 567899999982222 333 37899997 888899999886
No 88
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=67.00 E-value=2.8 Score=29.33 Aligned_cols=29 Identities=21% Similarity=0.456 Sum_probs=19.0
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
...||+||+. +..... ..+.|..||.++.
T Consensus 20 ~~fCP~Cg~~---~m~~~~-------~r~~C~~Cgyt~~ 48 (50)
T PRK00432 20 NKFCPRCGSG---FMAEHL-------DRWHCGKCGYTEF 48 (50)
T ss_pred cCcCcCCCcc---hheccC-------CcEECCCcCCEEe
Confidence 3489999985 411110 3479999998753
No 89
>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=66.82 E-value=7.2 Score=25.67 Aligned_cols=29 Identities=21% Similarity=0.567 Sum_probs=19.5
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccC---CCCc
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLN---CNQY 306 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~---C~~~ 306 (319)
..||.||+ ... +.++|.+ .|+.|.+ |.+.
T Consensus 2 ~~CP~Cg~-~lv-~r~~k~g-----~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 2 EKCPKCGG-PLV-LRRGKKG-----KFLGCSNYPECKYT 33 (39)
T ss_pred cCCCCCCc-eeE-EEECCCC-----CEEECCCCCCcCCe
Confidence 47999993 211 4444444 8999996 8765
No 90
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=66.58 E-value=4.1 Score=33.01 Aligned_cols=31 Identities=23% Similarity=0.747 Sum_probs=21.6
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceec
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
+-.||+|.+ +.+|. |- + .+.|..|+|.|...
T Consensus 3 lp~cp~c~s-EytYe------d~--~-~~~cpec~~ew~~~ 33 (112)
T COG2824 3 LPPCPKCNS-EYTYE------DG--G-QLICPECAHEWNEN 33 (112)
T ss_pred CCCCCccCC-ceEEe------cC--c-eEeCchhccccccc
Confidence 347999987 44551 11 1 47999999999844
No 91
>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=63.10 E-value=5.2 Score=26.03 Aligned_cols=30 Identities=20% Similarity=0.399 Sum_probs=21.5
Q ss_pred cccccCCCCcceEE-EEeccCCCCCceeEEEccCC
Q 020974 270 IYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNC 303 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C 303 (319)
...||+|++.+-+| --+..++- .-|.|..|
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~----qryrC~~C 35 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGH----QRYRCKDC 35 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCC----EeEecCcC
Confidence 46999999999777 66543332 34788888
No 92
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=62.90 E-value=4 Score=28.52 Aligned_cols=32 Identities=28% Similarity=0.605 Sum_probs=20.3
Q ss_pred ccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 267 VSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
.+..|.|.+||..- . ..| -+.-+.|..|||+-
T Consensus 3 ~~~~Y~C~~Cg~~~-~-~~~-------~~~~irCp~Cg~rI 34 (49)
T COG1996 3 AMMEYKCARCGREV-E-LDQ-------ETRGIRCPYCGSRI 34 (49)
T ss_pred ceEEEEhhhcCCee-e-hhh-------ccCceeCCCCCcEE
Confidence 34568899998743 0 222 24557899999873
No 93
>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=62.77 E-value=5 Score=32.69 Aligned_cols=32 Identities=19% Similarity=0.516 Sum_probs=22.9
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceec
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
....|+.||.+ +|-+.. .| ++|..||..|.-.
T Consensus 8 tKR~Cp~CG~k--FYDLnk----~P----ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAK--FYDLNK----DP----IVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcch--hccCCC----CC----ccCCCCCCccCcc
Confidence 34689999975 454432 35 4899999999655
No 94
>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=62.24 E-value=6.5 Score=28.00 Aligned_cols=33 Identities=24% Similarity=0.535 Sum_probs=21.3
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
.|.||.||..- .+- .+ ..--.+.|..||.....
T Consensus 2 ~~~CP~CG~~i---ev~---~~-~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAEI---ELE---NP-ELGELVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCEE---ecC---CC-ccCCEEeCCCCCCEEEE
Confidence 47999999932 221 11 11346899999987653
No 95
>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=59.64 E-value=7.7 Score=29.35 Aligned_cols=36 Identities=25% Similarity=0.391 Sum_probs=18.6
Q ss_pred ccccccCCCC-----cceEEEEeccCCCCCceeEEEccCCCC
Q 020974 269 DIYECGRCGH-----NKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 269 ~~~~C~~C~~-----~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
...-|.+||. ..++..+. +..-..-...|+|..|||
T Consensus 45 kr~~Ck~C~~~liPG~~~~vri~-~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCSVRIR-KKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CCTB-TTT--B--CTTTEEEEEE----SSS-EEEEEETTTTE
T ss_pred hcccccCCCCEEeCCCccEEEEE-ecCCCCCEEEEEccccCC
Confidence 4568999997 23444222 112222358899999996
No 96
>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=59.60 E-value=4.8 Score=33.70 Aligned_cols=32 Identities=9% Similarity=0.115 Sum_probs=22.3
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceec
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
....||.||.+ +|-+.. .| ++|..||..|...
T Consensus 8 tKr~Cp~cg~k--FYDLnk----~p----~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSK--FYDLNR----RP----AVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCcc--ccccCC----CC----ccCCCcCCccCcc
Confidence 34689999975 454431 24 4899999999644
No 97
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=58.88 E-value=8.8 Score=30.69 Aligned_cols=64 Identities=14% Similarity=0.126 Sum_probs=48.8
Q ss_pred HHHHHHHHhhcCCccHHHHHHHHHHhhcCCCCHHhhhcccceeecccccCCCCHHHHHHHHHHHH
Q 020974 13 KRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLIS 77 (319)
Q Consensus 13 ~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~lv~ 77 (319)
++...|=+-.. ++.+++++++|.+|-..|....+|..-+.-..+++||++-++..+...-.|++
T Consensus 33 ~~LleWFnf~~-~~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 33 KQLLEWFNFPP-VPMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred HHHHHHhCCCC-CccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 44445543222 37789999999999999999999998776666999999888777776666654
No 98
>PRK05978 hypothetical protein; Provisional
Probab=58.87 E-value=5.3 Score=34.38 Aligned_cols=36 Identities=19% Similarity=0.370 Sum_probs=25.0
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceecccc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLS 313 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~~~ 313 (319)
.-+||+||+-+..- ...+.--.|..||..+..-+-+
T Consensus 33 ~grCP~CG~G~LF~--------g~Lkv~~~C~~CG~~~~~~~a~ 68 (148)
T PRK05978 33 RGRCPACGEGKLFR--------AFLKPVDHCAACGEDFTHHRAD 68 (148)
T ss_pred cCcCCCCCCCcccc--------cccccCCCccccCCccccCCcc
Confidence 45899999987752 1223334899999998866443
No 99
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=57.59 E-value=8.3 Score=27.72 Aligned_cols=26 Identities=27% Similarity=0.662 Sum_probs=19.5
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
.......|+.||+ +...+..|.+||.
T Consensus 23 ~~~~l~~C~~CG~--------------~~~~H~vC~~CG~ 48 (57)
T PRK12286 23 KAPGLVECPNCGE--------------PKLPHRVCPSCGY 48 (57)
T ss_pred cCCcceECCCCCC--------------ccCCeEECCCCCc
Confidence 3456789999998 4445789999984
No 100
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=57.02 E-value=12 Score=23.80 Aligned_cols=29 Identities=24% Similarity=0.679 Sum_probs=20.7
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
+...|..||+....+.-| -++.|..||..
T Consensus 2 ~~~~C~~C~~~~i~~~~~---------~~~~C~~Cg~~ 30 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVNKED---------DYEVCIFCGSS 30 (33)
T ss_pred CceEcCCCCCCeEEEecC---------CeEEcccCCcE
Confidence 346899999988765222 24799999864
No 101
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=56.89 E-value=10 Score=26.62 Aligned_cols=18 Identities=22% Similarity=0.593 Sum_probs=13.8
Q ss_pred CceeEEEccCCCCcceec
Q 020974 293 NLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 293 ~mt~f~~C~~C~~~w~~~ 310 (319)
.......|..|||.|+..
T Consensus 24 ~~~v~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWKAS 41 (55)
T ss_pred CCEEEEECCCCCCeeEcc
Confidence 445778899999998764
No 102
>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=56.88 E-value=8.9 Score=30.28 Aligned_cols=31 Identities=26% Similarity=0.554 Sum_probs=22.5
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
..+.||.||...+. | ..+-++.|..||..|-
T Consensus 34 a~y~CpfCgk~~vk-----R----~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTVK-----R----GSTGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCceE-----E----EeeEEEEcCCCCCEEe
Confidence 46899999975543 1 1256799999998864
No 103
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=56.46 E-value=9.2 Score=30.14 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=23.1
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
..+.||.||...+.- ..+-++.|..||..|--
T Consensus 35 a~y~CpfCgk~~vkR---------~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKR---------VGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEE---------EEEEEEEcCCCCCEEeC
Confidence 569999998655541 22567999999988743
No 104
>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=56.07 E-value=9.1 Score=25.11 Aligned_cols=30 Identities=23% Similarity=0.407 Sum_probs=19.3
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
.+||.||++.-.- -.|-..+--+.|..|+.
T Consensus 4 ~pCP~CGG~DrFr-----~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFR-----FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccc-----cccCCCCcCEEeCCCCC
Confidence 4899999977653 12223344468888874
No 105
>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=55.95 E-value=5.1 Score=23.80 Aligned_cols=11 Identities=27% Similarity=0.860 Sum_probs=9.0
Q ss_pred cccccccCCCC
Q 020974 268 SDIYECGRCGH 278 (319)
Q Consensus 268 t~~~~C~~C~~ 278 (319)
...|.||+||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45799999984
No 106
>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=55.85 E-value=6.2 Score=31.11 Aligned_cols=32 Identities=22% Similarity=0.556 Sum_probs=22.0
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
..|.||.||...+--+ + +-++.|..||..|--
T Consensus 34 ~ky~Cp~Cgk~~vkR~-----a----~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRV-----A----TGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEEE-----E----TTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEEe-----e----eEEeecCCCCCEEeC
Confidence 4589999999774311 1 345899999988743
No 107
>PRK03954 ribonuclease P protein component 4; Validated
Probab=54.41 E-value=14 Score=30.73 Aligned_cols=38 Identities=18% Similarity=0.301 Sum_probs=23.9
Q ss_pred ccccccCCCCc-----ceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 269 DIYECGRCGHN-----KISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 269 ~~~~C~~C~~~-----~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
-..-|.+|+.- .++..+ +....+ .+.++|+.||+.-++
T Consensus 63 KR~~CK~C~t~LiPG~n~~vRi--~~~~~~-~vvitCl~CG~~kR~ 105 (121)
T PRK03954 63 KRRYCKRCHSFLVPGVNARVRL--RQKRMP-HVVITCLECGHIMRY 105 (121)
T ss_pred HHHHhhcCCCeeecCCceEEEE--ecCCcc-eEEEECccCCCEEee
Confidence 35689999765 444422 222122 378899999987654
No 108
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=53.55 E-value=9.8 Score=27.11 Aligned_cols=26 Identities=23% Similarity=0.581 Sum_probs=19.4
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
.......|+.||. +...+..|.+||.
T Consensus 22 ~~p~l~~C~~cG~--------------~~~~H~vc~~cG~ 47 (55)
T TIGR01031 22 TAPTLVVCPNCGE--------------FKLPHRVCPSCGY 47 (55)
T ss_pred cCCcceECCCCCC--------------cccCeeECCccCe
Confidence 3456678999997 5556788999983
No 109
>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=52.81 E-value=11 Score=26.83 Aligned_cols=32 Identities=13% Similarity=0.199 Sum_probs=23.6
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
-...|++|.+..-.+- ..|+..+-|.|..||+
T Consensus 21 ~aLIC~~C~~hNGla~-----~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 21 YALICSKCFSHNGLAP-----KEEFEEIQYRCPYCGA 52 (54)
T ss_pred eeEECcccchhhcccc-----cccCCceEEEcCCCCC
Confidence 3568999998777652 2355566889999995
No 110
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=52.66 E-value=10 Score=30.70 Aligned_cols=37 Identities=19% Similarity=0.243 Sum_probs=24.0
Q ss_pred ccccccCCCCcceEE---EEeccCCCCCceeEEEccCCCCccee
Q 020974 269 DIYECGRCGHNKISY---QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~---q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
-...|++|...=..+ .+..+++- +-++|..||+--++
T Consensus 55 KR~~CkkC~t~Lvpg~n~rvR~~~~~----v~vtC~~CG~~~R~ 94 (105)
T COG2023 55 KRTICKKCYTPLVPGKNARVRLRKGR----VVVTCLECGTIRRY 94 (105)
T ss_pred HHHhccccCcccccCcceEEEEcCCe----EEEEecCCCcEEEe
Confidence 346899999843333 33333332 78899999986544
No 111
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=51.63 E-value=13 Score=29.25 Aligned_cols=31 Identities=19% Similarity=0.419 Sum_probs=22.4
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
..+.||.||..... |. .+-++.|..|+..|-
T Consensus 35 a~y~CpfCgk~~vk-----R~----a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHAVK-----RQ----AVGIWRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCcee-----ee----eeEEEEcCCCCCEEe
Confidence 56999999975543 11 246799999998764
No 112
>PRK11032 hypothetical protein; Provisional
Probab=51.40 E-value=8.2 Score=33.64 Aligned_cols=38 Identities=18% Similarity=0.347 Sum_probs=27.4
Q ss_pred cccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceeccccc
Q 020974 266 IVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVSTNLSF 314 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~~~~~ 314 (319)
.-.+.+.|-+||+.-+.| -- ..--|.+|||.- |.|.+|
T Consensus 120 vg~G~LvC~~Cg~~~~~~~p~----------~i~pCp~C~~~~-F~R~~~ 158 (160)
T PRK11032 120 VGLGNLVCEKCHHHLAFYTPE----------VLPLCPKCGHDQ-FQRRPF 158 (160)
T ss_pred eecceEEecCCCCEEEecCCC----------cCCCCCCCCCCe-eeeCCC
Confidence 455789999999988776 22 234799999875 556554
No 113
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=51.32 E-value=5.7 Score=38.80 Aligned_cols=15 Identities=20% Similarity=0.578 Sum_probs=8.8
Q ss_pred CCceeEEEccCCCCc
Q 020974 292 YNLTRHVTCLNCNQY 306 (319)
Q Consensus 292 e~mt~f~~C~~C~~~ 306 (319)
+....|+.|.+||+|
T Consensus 280 ~a~KRFFkC~~C~~R 294 (344)
T PF09332_consen 280 DAVKRFFKCKDCGNR 294 (344)
T ss_dssp EEE-EEEE-T-TS-E
T ss_pred eeeeeeEECCCCCCe
Confidence 345689999999988
No 114
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=50.49 E-value=8 Score=36.50 Aligned_cols=39 Identities=18% Similarity=0.476 Sum_probs=23.3
Q ss_pred ccccccccCCCCcceEE-E----Eec-cCCCCCceeEEEccCCCCcc
Q 020974 267 VSDIYECGRCGHNKISY-Q----HSS-ILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q----~q~-rsade~mt~f~~C~~C~~~w 307 (319)
..+.+.|++||..-.++ - .|| |++|++ .-..|..||+.+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~--ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSK--KAFSCKYCGKVY 171 (279)
T ss_pred cCCceeccccccccccccccchhhccccccccc--ccccCCCCCcee
Confidence 34567777777776666 2 255 566663 234666666554
No 115
>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=49.91 E-value=18 Score=35.43 Aligned_cols=36 Identities=17% Similarity=0.311 Sum_probs=22.1
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
.-.|++|| +-.+-..- ... +.-|+.|.| .|||.-..
T Consensus 169 ~p~c~~cg-~~~~~v~~-~d~-~~~~v~y~c-~cG~~g~~ 204 (353)
T cd00674 169 MPYCEKCG-KDTTTVEA-YDA-KAGTVTYKC-ECGHEETV 204 (353)
T ss_pred eeecCCcC-cceeEEEE-EeC-CCCeEEEEc-CCCCEEEE
Confidence 45799999 43332211 123 345788899 59987554
No 116
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=49.59 E-value=4.4 Score=39.57 Aligned_cols=33 Identities=30% Similarity=0.768 Sum_probs=15.7
Q ss_pred cccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCc-ce
Q 020974 266 IVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQY-WV 308 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~-w~ 308 (319)
+..--|.|+.||.+-++| .+ |. ..|.+||.. |.
T Consensus 281 a~KRFFkC~~C~~Rt~sl~r~-------P~---~~C~~Cg~~~we 315 (344)
T PF09332_consen 281 AVKRFFKCKDCGNRTISLERL-------PK---KHCSNCGSSKWE 315 (344)
T ss_dssp EE-EEEE-T-TS-EEEESSSS------------S--TTT-S---E
T ss_pred eeeeeEECCCCCCeeeecccC-------CC---CCCCcCCcCcee
Confidence 344578999999997776 33 22 489999853 64
No 117
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=49.45 E-value=5.7 Score=42.22 Aligned_cols=39 Identities=15% Similarity=0.403 Sum_probs=29.6
Q ss_pred ccccccCCCCcceE---E--EEeccCCCCCceeEEEccCCCCcceecc
Q 020974 269 DIYECGRCGHNKIS---Y--QHSSILDDYNLTRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 269 ~~~~C~~C~~~~~~---~--q~q~rsade~mt~f~~C~~C~~~w~~~~ 311 (319)
-.|+|..||+.=-+ . -+.+.|++-| |.|.+|++|+..++
T Consensus 280 RKFKCtECgKAFKfKHHLKEHlRIHSGEKP----feCpnCkKRFSHSG 323 (1007)
T KOG3623|consen 280 RKFKCTECGKAFKFKHHLKEHLRIHSGEKP----FECPNCKKRFSHSG 323 (1007)
T ss_pred ccccccccchhhhhHHHHHhhheeecCCCC----cCCcccccccccCC
Confidence 47999999974322 1 3467788887 79999999997765
No 118
>PHA02942 putative transposase; Provisional
Probab=47.75 E-value=9.1 Score=37.90 Aligned_cols=29 Identities=28% Similarity=0.612 Sum_probs=19.9
Q ss_pred cccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 268 SDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
|+ -.|+.||+.... .-...+.|.+||+.+
T Consensus 324 TS-q~Cs~CG~~~~~----------l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SS-VSCPKCGHKMVE----------IAHRYFHCPSCGYEN 352 (383)
T ss_pred CC-ccCCCCCCccCc----------CCCCEEECCCCCCEe
Confidence 55 489999985421 112368999999865
No 119
>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=47.30 E-value=42 Score=24.35 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=27.1
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCc
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~ 306 (319)
......|+.|+...... ..| ...-.+....+|..|+-+
T Consensus 12 ~~~~~~C~~C~G~G~~~~~~~--~~~~~~~~~~~C~~C~G~ 50 (66)
T PF00684_consen 12 GKKPKTCPQCNGSGQVTRRQQ--TPGGVFQMQQTCPKCGGT 50 (66)
T ss_dssp TTT-EE-TTSSSSSEEEEEEE--SSSTTEEEEEE-TTTSSS
T ss_pred CCCCcCCcCCCCeeEEEEEEe--CCCeEEEEEEECCCCcce
Confidence 44567999999999988 555 566677788899999754
No 120
>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=46.12 E-value=18 Score=35.62 Aligned_cols=39 Identities=18% Similarity=0.275 Sum_probs=19.5
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceec
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
.-.|++||.=.++-... . -.+.-++.|.|..|||.-..+
T Consensus 174 ~piC~~cGri~tt~v~~-~-d~~~~~v~Y~c~~cG~~g~~~ 212 (360)
T PF01921_consen 174 LPICEKCGRIDTTEVTE-Y-DPEGGTVTYRCEECGHEGEVD 212 (360)
T ss_dssp EEEETTTEE--EEEEEE-E---SSSEEEEE--TTS---EEE
T ss_pred eeeccccCCcccceeeE-e-ecCCCEEEEEecCCCCEEEEe
Confidence 45799999833333111 1 224457899999999986554
No 121
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.65 E-value=13 Score=34.74 Aligned_cols=24 Identities=29% Similarity=0.657 Sum_probs=18.0
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
--.|+.||+ .+ ...+.|.+||+.+
T Consensus 309 S~~C~~cg~---------~~-----~r~~~C~~cg~~~ 332 (364)
T COG0675 309 SKTCPCCGH---------LS-----GRLFKCPRCGFVH 332 (364)
T ss_pred cccccccCC---------cc-----ceeEECCCCCCee
Confidence 358999999 11 3447999999875
No 122
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=45.46 E-value=17 Score=23.32 Aligned_cols=29 Identities=21% Similarity=0.465 Sum_probs=12.9
Q ss_pred cccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 272 ECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 272 ~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
-|+.||+. ..+ .+=..|+. .-.+|..||.
T Consensus 2 fC~~CG~~-l~~--~ip~gd~r--~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGP-LER--RIPEGDDR--ERLVCPACGF 30 (34)
T ss_dssp B-TTT--B--EE--E--TT-SS---EEEETTTTE
T ss_pred ccccccCh-hhh--hcCCCCCc--cceECCCCCC
Confidence 38999987 333 11123442 3357999984
No 123
>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=45.22 E-value=14 Score=29.72 Aligned_cols=36 Identities=25% Similarity=0.553 Sum_probs=23.8
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceecccc
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVSTNLS 313 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~~~~ 313 (319)
.+..-.|--|+ ...| |. .|. ++|.+||.+|...+.-
T Consensus 32 ~va~daCeiC~--~~GY~q~----g~~-----lvC~~C~~~~~~~~ig 68 (102)
T PF10080_consen 32 RVAFDACEICG--PKGYYQE----GDQ-----LVCKNCGVRFNLPTIG 68 (102)
T ss_pred EEEEEeccccC--CCceEEE----CCE-----EEEecCCCEEehhhcc
Confidence 44455799993 3445 33 333 7999999999765543
No 124
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=44.98 E-value=9.2 Score=33.44 Aligned_cols=45 Identities=13% Similarity=0.350 Sum_probs=26.3
Q ss_pred cccccccCCCCcceEE---EEecc---CCCCCceeEEEccCCCCc-ceeccc
Q 020974 268 SDIYECGRCGHNKISY---QHSSI---LDDYNLTRHVTCLNCNQY-WVSTNL 312 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~---q~q~r---sade~mt~f~~C~~C~~~-w~~~~~ 312 (319)
...-.||.|+..=.-. .+-.+ .-...-.-|++|.+||.- |+.+-|
T Consensus 95 ~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 95 PEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHW 146 (165)
T ss_pred cccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCchHH
Confidence 3456899999853322 11000 011233579999999975 776654
No 125
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=44.87 E-value=6.3 Score=37.30 Aligned_cols=39 Identities=18% Similarity=0.339 Sum_probs=25.7
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
...-||-||+.-++-.+|..-+.++ -+|..|.-|---|.
T Consensus 184 ~~~~CPvCGS~PvaSmV~~g~~~~G-lRYL~CslC~teW~ 222 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQIGETEQG-LRYLHCSLCETEWH 222 (308)
T ss_pred ccccCCCcCCCCcceeeeecCcccc-chhhhhhhHHHHHH
Confidence 5678999999999885554333343 46666665555553
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=44.48 E-value=19 Score=37.14 Aligned_cols=34 Identities=18% Similarity=0.515 Sum_probs=22.5
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
.-.|++||.=.++.. ...++. |+.|.| .|||.=.
T Consensus 168 ~pic~~cGrv~~~~~--~~~~~~--~v~Y~c-~cG~~g~ 201 (515)
T TIGR00467 168 SVFCENCGRDTTTVN--NYDNEY--SIEYSC-ECGNQES 201 (515)
T ss_pred eeecCCcCccCceEE--EecCCc--eEEEEc-CCCCEEE
Confidence 457999998644322 334444 788899 5998743
No 127
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.65 E-value=15 Score=30.74 Aligned_cols=38 Identities=13% Similarity=0.295 Sum_probs=27.0
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCccee
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
......||.|++.. ++ --..+.. -.-|.|..|+..|..
T Consensus 27 ~~~~~~cP~C~s~~-~~k~g~~~~~----~qRyrC~~C~~tf~~ 65 (129)
T COG3677 27 QITKVNCPRCKSSN-VVKIGGIRRG----HQRYKCKSCGSTFTV 65 (129)
T ss_pred hcccCcCCCCCccc-eeeECCcccc----ccccccCCcCcceee
Confidence 44557999999988 66 4444443 234799999988863
No 128
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.45 E-value=7.7 Score=33.01 Aligned_cols=22 Identities=23% Similarity=0.398 Sum_probs=17.5
Q ss_pred CCCCCceeEEEccCCCCcceec
Q 020974 289 LDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 289 sade~mt~f~~C~~C~~~w~~~ 310 (319)
-..+....||.|.+||.+|.+-
T Consensus 91 l~~e~~~~~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 91 LEDETNNAYYKCPNCQSKYTFL 112 (147)
T ss_pred HhcccCCcEEECcCCCCEeeHH
Confidence 3455567899999999999864
No 129
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=43.08 E-value=21 Score=27.42 Aligned_cols=55 Identities=16% Similarity=0.203 Sum_probs=35.0
Q ss_pred hhcCchHHHHHhhhhhhchhhhhcCCCCccccccccccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCC
Q 020974 231 KEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCN 304 (319)
Q Consensus 231 eElas~e~k~~~~~~~~~e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~ 304 (319)
.||+-+..+++..+. +.+.|.++. + .--...+|+.|-+--+.| -.|| -|+|.+|+
T Consensus 5 ~dllhPs~e~e~r~h-K~krLvq~~-------n--syFm~VkC~gc~~iT~vfSHaqt---------vVvc~~c~ 60 (84)
T KOG1779|consen 5 KDLLHPSPEKEKRKH-KLKRLVQSP-------N--SYFMDVKCPGCFKITTVFSHAQT---------VVVCEGCS 60 (84)
T ss_pred hhhcCCCHHHHhhhh-hhhhheeCC-------C--ceEEEEEcCCceEEEEEeecCce---------EEEcCCCc
Confidence 355555555555555 445554433 1 122457999999999999 7774 47888885
No 130
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=41.93 E-value=12 Score=26.54 Aligned_cols=33 Identities=27% Similarity=0.562 Sum_probs=19.0
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
=.+.| |||.. |.+.-.-..+. ...+.|..|.-.
T Consensus 17 ~~y~C-RCG~~---f~i~e~~l~~~-~~iv~C~sCSL~ 49 (55)
T PF05207_consen 17 YSYPC-RCGGE---FEISEEDLEEG-EVIVQCDSCSLW 49 (55)
T ss_dssp EEEEE-TTSSE---EEEEHHHHHCT---EEEETTTTEE
T ss_pred EEEcC-CCCCE---EEEcchhccCc-CEEEECCCCccE
Confidence 46899 99998 52211111111 678999999843
No 131
>PRK11827 hypothetical protein; Provisional
Probab=41.74 E-value=18 Score=26.33 Aligned_cols=39 Identities=21% Similarity=0.356 Sum_probs=25.1
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceecccccccc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVL 317 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~~~~~~~ 317 (319)
+...||.|++.= .|. .+ ..-.+|..||-.+-. ++.++||
T Consensus 7 eILaCP~ckg~L-~~~-----~~---~~~Lic~~~~laYPI-~dgIPVl 45 (60)
T PRK11827 7 EIIACPVCNGKL-WYN-----QE---KQELICKLDNLAFPL-RDGIPVL 45 (60)
T ss_pred hheECCCCCCcC-eEc-----CC---CCeEECCccCeeccc-cCCcccc
Confidence 567899998843 341 01 113679999877644 7777775
No 132
>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=41.57 E-value=13 Score=32.22 Aligned_cols=20 Identities=10% Similarity=-0.051 Sum_probs=15.6
Q ss_pred CCCceeEEEccCCCCcceec
Q 020974 291 DYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 291 de~mt~f~~C~~C~~~w~~~ 310 (319)
.+.-..||.|.+|+.+|.|-
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~ 122 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFN 122 (158)
T ss_pred hccCCCeEECCCCCcEeeHH
Confidence 34446899999999999763
No 133
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=41.40 E-value=13 Score=32.87 Aligned_cols=19 Identities=16% Similarity=0.258 Sum_probs=15.0
Q ss_pred CCceeEEEccCCCCcceec
Q 020974 292 YNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 292 e~mt~f~~C~~C~~~w~~~ 310 (319)
|.-..||.|.+||.+|.|-
T Consensus 112 e~~~~~Y~Cp~C~~rytf~ 130 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFD 130 (178)
T ss_pred ccCCCEEECCCCCcEEeHH
Confidence 3345899999999999763
No 134
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=41.13 E-value=12 Score=30.29 Aligned_cols=13 Identities=38% Similarity=0.984 Sum_probs=11.7
Q ss_pred cccccCCCCcceE
Q 020974 270 IYECGRCGHNKIS 282 (319)
Q Consensus 270 ~~~C~~C~~~~~~ 282 (319)
-|+|++||+++|.
T Consensus 74 ~~PC~~C~S~KCG 86 (103)
T PF14949_consen 74 HYPCPKCGSRKCG 86 (103)
T ss_pred cccCCCCCCCccC
Confidence 5899999999985
No 135
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=40.88 E-value=30 Score=34.90 Aligned_cols=96 Identities=11% Similarity=0.138 Sum_probs=52.7
Q ss_pred CCHHHHHHHhcCCCChhhhhcCChhhcCchHHHHHhhhhhhc---hhhhhcCCCCccccccccccccccccCCCCcceEE
Q 020974 207 ENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKD---GALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY 283 (319)
Q Consensus 207 kN~~Lr~~vl~G~i~p~~lv~Ms~eElas~e~k~~~~~~~~~---e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~~~~~~ 283 (319)
.||.|....+ .-|+.++|..+..++++--+=+...+.+..+ -..++.+.. .=-+.-+|++||++-..-
T Consensus 104 EDP~lq~~Al-s~iPvdEL~~kA~ekla~~eg~ki~kdy~i~leLL~WFKq~FF--------~WvN~PpC~~CG~et~~~ 174 (500)
T KOG0909|consen 104 EDPVLQAKAL-STIPVDELKEKASEKLAKAEGEKIYKDYLIKLELLNWFKQDFF--------KWVNNPPCNKCGGETSSG 174 (500)
T ss_pred cCHHHHHHHH-hcCCHHHHHHHHHHhhcccchhhhhcchHHHHHHHHHHHHhhh--------eecCCCCccccccccccc
Confidence 5787755544 4577799998888888851111111111010 111223311 112446899999966432
Q ss_pred -EEeccCCCC-----CceeEEEccCCCCcceecc
Q 020974 284 -QHSSILDDY-----NLTRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 284 -q~q~rsade-----~mt~f~~C~~C~~~w~~~~ 311 (319)
+-|--..+| .-.-.|.|..||+.=+|-|
T Consensus 175 l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPR 208 (500)
T KOG0909|consen 175 LGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPR 208 (500)
T ss_pred ccCCCCchhHhhcCCceEEEEEecCCCCcccCcc
Confidence 333222333 1235789999999877765
No 136
>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=40.55 E-value=12 Score=32.02 Aligned_cols=33 Identities=21% Similarity=0.442 Sum_probs=23.9
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
.-.+.+.|-+||+.-..+. | +..--|.+||+.-
T Consensus 108 ~g~G~l~C~~Cg~~~~~~~--------~-~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVELTH--------P-ERLPPCPKCGHTE 140 (146)
T ss_pred ecCceEecccCCCEEEecC--------C-CcCCCCCCCCCCe
Confidence 5668899999999766641 1 2235799999874
No 137
>PRK00420 hypothetical protein; Validated
Probab=40.33 E-value=16 Score=29.98 Aligned_cols=29 Identities=17% Similarity=0.359 Sum_probs=18.7
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
..||.||..-..+ +.+ -+.|.+||.....
T Consensus 24 ~~CP~Cg~pLf~l----k~g------~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPLFEL----KDG------EVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcceec----CCC------ceECCCCCCeeee
Confidence 5899999654332 111 1589999986543
No 138
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=39.99 E-value=26 Score=24.11 Aligned_cols=32 Identities=25% Similarity=0.485 Sum_probs=20.6
Q ss_pred cccccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 268 SDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
++.+.|+.||++=.. +++. .-..+|.|.++..
T Consensus 3 ~g~l~C~~CG~~m~~---~~~~---~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTR---RKRK---GKYRYYRCSNRRR 34 (58)
T ss_pred CCcEEcccCCcEeEE---EECC---CCceEEEcCCCcC
Confidence 467899999985333 3333 2228899987643
No 139
>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=39.89 E-value=32 Score=33.15 Aligned_cols=40 Identities=20% Similarity=0.402 Sum_probs=27.3
Q ss_pred cccccCCCCcceE-E-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 270 IYECGRCGHNKIS-Y-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 270 ~~~C~~C~~~~~~-~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
...|+.||+.+-- | .+-. ..+++-....+|..|+.-+|.-
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~-~~~~~~~r~e~C~~C~~YlK~~ 265 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEH-DAEKAVLKAETCDSCQGYLKIL 265 (305)
T ss_pred CccCCCCCCCCceeeEeecC-CCCCcceEEeeccccccchhhh
Confidence 5689999987643 4 4321 1134556778999999998864
No 140
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=38.81 E-value=19 Score=34.17 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=17.2
Q ss_pred cccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 272 ECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 272 ~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
-|++||++..... ++ .-..|.+|||.-
T Consensus 113 FCg~CG~~~~~~~------~g---~~~~C~~cg~~~ 139 (279)
T COG2816 113 FCGRCGTKTYPRE------GG---WARVCPKCGHEH 139 (279)
T ss_pred CCCCCCCcCcccc------Cc---eeeeCCCCCCcc
Confidence 5999998654421 11 235899998764
No 141
>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=38.12 E-value=24 Score=29.95 Aligned_cols=41 Identities=12% Similarity=0.307 Sum_probs=23.1
Q ss_pred cccccCCCCcceEE-EEeccC-----CCCCceeEEEccCCCCc-ceec
Q 020974 270 IYECGRCGHNKISY-QHSSIL-----DDYNLTRHVTCLNCNQY-WVST 310 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q~rs-----ade~mt~f~~C~~C~~~-w~~~ 310 (319)
.-.|+.|++.=..- --+.+. .-+....|+.|..||.- |..+
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGS 138 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccc
Confidence 46999999932222 111110 11122359999999975 6544
No 142
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=38.02 E-value=7.6 Score=36.63 Aligned_cols=34 Identities=18% Similarity=0.458 Sum_probs=26.2
Q ss_pred cccccCCCCcceEE-----EEeccCCCCCceeEEEccCCCCcc
Q 020974 270 IYECGRCGHNKISY-----QHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-----q~q~rsade~mt~f~~C~~C~~~w 307 (319)
-|.|+.|+..=+-- -+||.+.+.+ |.|..||+++
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQTHS~~K~----~qC~~C~KsF 253 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQTHSDVKK----HQCPRCGKSF 253 (279)
T ss_pred CccCCcccchhcchHHHHHHHHhhcCCcc----ccCcchhhHH
Confidence 68999998765432 4589898885 7999999875
No 143
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=37.88 E-value=14 Score=25.90 Aligned_cols=34 Identities=18% Similarity=0.467 Sum_probs=22.5
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCccee
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
..|..|+..++.. + |...... -..|+.||-.|+-
T Consensus 4 ~~C~~C~~~~T~~-W--R~g~~g~--~~LCnaCgl~~~k 37 (52)
T smart00401 4 RSCSNCGTTETPL-W--RRGPSGN--KTLCNACGLYYKK 37 (52)
T ss_pred CCcCCCCCCCCCc-c--ccCCCCC--CcEeecccHHHHH
Confidence 5899999766543 3 3332222 3689999999864
No 144
>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=37.81 E-value=33 Score=21.26 Aligned_cols=26 Identities=27% Similarity=0.549 Sum_probs=11.8
Q ss_pred cccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 272 ECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 272 ~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
-|++||+.-..- .++ .--.|..||+.
T Consensus 5 fC~~CG~~t~~~------~~g---~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPA------PGG---WARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-------SSS---S-EEESSSS-E
T ss_pred ccCcCCccccCC------CCc---CEeECCCCcCE
Confidence 488998854331 112 22478888864
No 145
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.74 E-value=18 Score=40.97 Aligned_cols=36 Identities=17% Similarity=0.385 Sum_probs=21.5
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
..+.||+||.. +|+..=.....+++.-|.|.+||..
T Consensus 666 ~~rkCPkCG~~--t~~~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 666 GRRRCPSCGTE--TYENRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EEEECCCCCCc--cccccCcccCCcCCCceeCccCCCc
Confidence 45899999984 2222222344455555688888774
No 146
>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=37.61 E-value=31 Score=27.80 Aligned_cols=32 Identities=19% Similarity=0.302 Sum_probs=20.5
Q ss_pred ccccCCCCcceEE----EEeccCCCCCceeEEEccCCC
Q 020974 271 YECGRCGHNKISY----QHSSILDDYNLTRHVTCLNCN 304 (319)
Q Consensus 271 ~~C~~C~~~~~~~----q~q~rsade~mt~f~~C~~C~ 304 (319)
..|+.||.. +.+ .+--+..|+.. .+|.|..|+
T Consensus 3 ~~CpYCg~~-~~l~~~~~iYg~~~~~~~-~~y~C~~C~ 38 (102)
T PF11672_consen 3 IICPYCGGP-AELVDGSEIYGHRYDDGP-YLYVCTPCD 38 (102)
T ss_pred cccCCCCCe-eEEcccchhcCccCCCCc-eeEECCCCC
Confidence 479999984 444 33334444332 459999997
No 147
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=36.88 E-value=31 Score=35.97 Aligned_cols=28 Identities=18% Similarity=0.465 Sum_probs=19.9
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCC
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCN 304 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~ 304 (319)
+.-.|..||.....| -+- .-+ ++|..|.
T Consensus 22 gNk~CADCgs~~P~WASiN-------lGI-FICi~CS 50 (648)
T PLN03119 22 PNRRCINCNSLGPQYVCTT-------FWT-FVCMACS 50 (648)
T ss_pred CCCccccCCCCCCCceeec-------cce-EEeccch
Confidence 335899999999888 442 223 5899884
No 148
>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=34.98 E-value=22 Score=23.17 Aligned_cols=16 Identities=13% Similarity=0.260 Sum_probs=9.2
Q ss_pred ceeEEEccCCCCccee
Q 020974 294 LTRHVTCLNCNQYWVS 309 (319)
Q Consensus 294 mt~f~~C~~C~~~w~~ 309 (319)
+..||.|..|||--..
T Consensus 3 ~~~~YkC~~CGniVev 18 (36)
T PF06397_consen 3 KGEFYKCEHCGNIVEV 18 (36)
T ss_dssp TTEEEE-TTT--EEEE
T ss_pred cccEEEccCCCCEEEE
Confidence 3468999999986543
No 149
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=34.42 E-value=14 Score=34.93 Aligned_cols=36 Identities=17% Similarity=0.350 Sum_probs=24.8
Q ss_pred ccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceec
Q 020974 267 VSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
+.-..+||.||. ..|. .|=+..+.+|.+|+|-.+.+
T Consensus 25 e~lw~KCp~c~~--~~y~------~eL~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 25 EGLWTKCPSCGE--MLYR------KELESNLKVCPKCGHHMRIS 60 (294)
T ss_pred CCceeECCCccc--eeeH------HHHHhhhhcccccCcccccC
Confidence 445789999996 5551 12235678999999976643
No 150
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.97 E-value=21 Score=35.87 Aligned_cols=33 Identities=24% Similarity=0.304 Sum_probs=23.1
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceecc
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~ 311 (319)
..-.||+||.+- .|+... .|.|..||.+....+
T Consensus 349 ~~p~Cp~Cg~~m-------~S~G~~---g~rC~kCg~~~~~~~ 381 (421)
T COG1571 349 VNPVCPRCGGRM-------KSAGRN---GFRCKKCGTRARETL 381 (421)
T ss_pred cCCCCCccCCch-------hhcCCC---CcccccccccCCccc
Confidence 334899999853 355442 689999998876544
No 151
>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=33.39 E-value=19 Score=33.43 Aligned_cols=33 Identities=24% Similarity=0.705 Sum_probs=11.2
Q ss_pred ccccccCCCCcceE-EEEeccCCCCCceeEEEccCCCCcc
Q 020974 269 DIYECGRCGHNKIS-YQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 269 ~~~~C~~C~~~~~~-~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
..+-||.||+..-. |.-=. |.-- +.|.+|++.+
T Consensus 30 ~n~yCP~Cg~~~L~~f~NN~-----PVaD-F~C~~C~eey 63 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKFENNR-----PVAD-FYCPNCNEEY 63 (254)
T ss_dssp HH---TTT--SS-EE-------------E-EE-TTT--EE
T ss_pred HCCcCCCCCChhHhhccCCC-----ccce-eECCCCchHH
Confidence 45689999998443 33322 3333 4799998775
No 152
>PF03589 Antiterm: Antitermination protein; InterPro: IPR003222 This entry consists of antitermination proteins found in bacteriophages, such as protein Q from phage lambda, and some bacterial homologues. Protein Q positively regulates expression of the phage late gene operon by binding to the bacterial host RNA polymerase (RNAP) and modifying it. The modified RNAP transcribes through termination sites that otherwise prevent expression of the regulated genes [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=32.97 E-value=11 Score=29.90 Aligned_cols=34 Identities=18% Similarity=0.478 Sum_probs=27.7
Q ss_pred cccCCCCcceEE-EEeccCCCCCceeEEEccCCCCc
Q 020974 272 ECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 272 ~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.|.+|+++.... ..|++.. -+|..|-+|..||.+
T Consensus 7 ~c~~c~g~g~al~~~~s~~~-~G~pvfk~c~rcgg~ 41 (95)
T PF03589_consen 7 SCRRCAGDGAALDMKQSKAQ-FGVPVFKDCERCGGR 41 (95)
T ss_pred CcCccCCcceeccHHHhHhc-cCCchhhhhhhhcCC
Confidence 799999999998 8887554 256789999999865
No 153
>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=32.97 E-value=26 Score=22.08 Aligned_cols=14 Identities=14% Similarity=0.226 Sum_probs=11.1
Q ss_pred eeEEEccCCCCcce
Q 020974 295 TRHVTCLNCNQYWV 308 (319)
Q Consensus 295 t~f~~C~~C~~~w~ 308 (319)
-.||.|..||+.-.
T Consensus 2 ~~~ykC~~CGniv~ 15 (34)
T cd00974 2 LEVYKCEICGNIVE 15 (34)
T ss_pred CcEEEcCCCCcEEE
Confidence 35899999998754
No 154
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=32.34 E-value=50 Score=33.96 Aligned_cols=38 Identities=21% Similarity=0.247 Sum_probs=24.2
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceec
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
.-.|++||.=.++-.. .. -.+.-|+.|.|. |||....+
T Consensus 175 ~pic~~cg~~~~~~~~-~~-d~~~~~v~y~~~-cG~~~~~~ 212 (510)
T PRK00750 175 LPICPKCGKVLTTPVI-SY-DAEAGTVTYDCE-CGHEGEVP 212 (510)
T ss_pred eeeCCCCCccceEEEE-EE-eCCCCEEEEEcC-CCCEEEEe
Confidence 4579999987655522 11 223347788885 99986543
No 155
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=31.94 E-value=28 Score=21.88 Aligned_cols=13 Identities=15% Similarity=0.319 Sum_probs=10.6
Q ss_pred eEEEccCCCCcce
Q 020974 296 RHVTCLNCNQYWV 308 (319)
Q Consensus 296 ~f~~C~~C~~~w~ 308 (319)
.||.|..||+.-.
T Consensus 6 ~~ykC~~Cgniv~ 18 (34)
T TIGR00319 6 QVYKCEVCGNIVE 18 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 5999999998653
No 156
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=31.58 E-value=53 Score=31.70 Aligned_cols=38 Identities=16% Similarity=0.408 Sum_probs=26.3
Q ss_pred cccccCCCCcce-EE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974 270 IYECGRCGHNKI-SY-QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 270 ~~~C~~C~~~~~-~~-q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
...|+.||+.+- .| .+ ..+++-....+|..|+.-+|.-
T Consensus 226 R~~C~~Cg~~~~l~y~~~---~~~~~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSL---DSEQAAVKAESCGDCGTYLKIL 265 (309)
T ss_pred CccCCCCCCCCceeeeee---cCCCcceEeeecccccccceec
Confidence 568999998643 34 33 2333456778999999999864
No 157
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=30.90 E-value=23 Score=32.29 Aligned_cols=32 Identities=25% Similarity=0.601 Sum_probs=22.6
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
....|+.|.+..-.| |-+.-|.- -|.|.+|+|
T Consensus 191 ~alIC~~C~hhngl~----~~~ek~~~-efiC~~Cn~ 222 (251)
T COG5415 191 KALICPQCHHHNGLY----RLAEKPII-EFICPHCNH 222 (251)
T ss_pred hhhcccccccccccc----ccccccch-heecccchh
Confidence 357899999988877 22333433 379999986
No 158
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=30.74 E-value=15 Score=26.19 Aligned_cols=22 Identities=27% Similarity=0.827 Sum_probs=16.1
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCC
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCN 304 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~ 304 (319)
....|+.||. +......|.+||
T Consensus 25 ~l~~c~~cg~--------------~~~~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGE--------------PKLPHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSS--------------EESTTSBCTTTB
T ss_pred ceeeeccCCC--------------EecccEeeCCCC
Confidence 6789999996 223346888897
No 159
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=29.82 E-value=90 Score=24.07 Aligned_cols=66 Identities=21% Similarity=0.196 Sum_probs=40.0
Q ss_pred CChHHHHHHHHHHHHHHhhhhhhchhhhhhhhhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhc
Q 020974 133 CNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNI 203 (319)
Q Consensus 133 ~~d~vR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NL 203 (319)
-...+|+..+.-|..++...-+ +.. .. ...-.+....|..||..+|.... +..+|=..+-..++++
T Consensus 10 vt~~lR~hlV~KLv~aI~P~pd--p~a-~~-d~rm~~l~~yarkvE~~~fe~A~-sreeYY~llA~kiy~i 75 (81)
T PF02172_consen 10 VTPDLRNHLVHKLVQAIFPTPD--PNA-MN-DPRMKNLIEYARKVEKDMFETAQ-SREEYYHLLAEKIYKI 75 (81)
T ss_dssp T-HHHHHHHHHHHHHHHS-SSS--CCC-CC-SHHHHHHHHHHHHHHHHHHHC-S-SHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhCCCCC--hhh-hh-hHHHHHHHHHHHHHHHHHHHHhc-cHHHHHHHHHHHHHHH
Confidence 4578999999999888875311 000 00 01112356889999999998643 3457766666666665
No 160
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=29.73 E-value=31 Score=22.01 Aligned_cols=17 Identities=24% Similarity=0.509 Sum_probs=10.1
Q ss_pred eEEEccCCCCcceeccc
Q 020974 296 RHVTCLNCNQYWVSTNL 312 (319)
Q Consensus 296 ~f~~C~~C~~~w~~~~~ 312 (319)
.+|+|.+|+..-..+|+
T Consensus 3 ~~~~C~nC~R~v~a~Rf 19 (33)
T PF08209_consen 3 PYVECPNCGRPVAASRF 19 (33)
T ss_dssp -EEE-TTTSSEEEGGGH
T ss_pred CeEECCCCcCCcchhhh
Confidence 56788888876555543
No 161
>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=29.55 E-value=40 Score=21.59 Aligned_cols=28 Identities=29% Similarity=0.634 Sum_probs=14.9
Q ss_pred cccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcce
Q 020974 272 ECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 272 ~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
-||.||+ .-| +- ..+ +.. .|..||....
T Consensus 3 FCp~C~n--lL~p~~----~~~--~~~-~C~~C~Y~~~ 31 (35)
T PF02150_consen 3 FCPECGN--LLYPKE----DKE--KRV-ACRTCGYEEP 31 (35)
T ss_dssp BETTTTS--BEEEEE----ETT--TTE-EESSSS-EEE
T ss_pred eCCCCCc--cceEcC----CCc--cCc-CCCCCCCccC
Confidence 5888886 223 21 111 222 8999987543
No 162
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=29.25 E-value=18 Score=39.26 Aligned_cols=40 Identities=13% Similarity=0.296 Sum_probs=0.0
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
.+...+.|+.||.. +|...-.......+..|.|..||+.-
T Consensus 651 vei~~r~Cp~Cg~~--t~~~~Cp~CG~~T~~~~~Cp~C~~~~ 690 (900)
T PF03833_consen 651 VEIGRRRCPKCGKE--TFYNRCPECGSHTEPVYVCPDCGIEV 690 (900)
T ss_dssp ------------------------------------------
T ss_pred EeeecccCcccCCc--chhhcCcccCCccccceecccccccc
Confidence 34567899999975 33222234566667788999998764
No 163
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=29.05 E-value=73 Score=34.71 Aligned_cols=51 Identities=22% Similarity=0.251 Sum_probs=33.9
Q ss_pred HHHHHHHHHHhhhhhhchhhhhhhhhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhcCC
Q 020974 140 IVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISD 205 (319)
Q Consensus 140 k~r~~L~~aL~~~~~e~~~~~~~~~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NLkd 205 (319)
+++.-|.++|+....... .=|.++|++||.+.. +..+|-..+-.|+.+++|
T Consensus 2 ~vi~~ie~a~~~~~~~~~--------------k~a~emE~hvF~Ka~-tkdEYl~~varli~h~r~ 52 (799)
T PF09606_consen 2 KVISKIEEAMRKNGQNTP--------------KSAREMENHVFQKAK-TKDEYLSLVARLILHIRD 52 (799)
T ss_dssp HHHHHHHHHHHHH----S--------------S-HHHHHHHHHHH-S-SHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHhCCCCC--------------CCHHHHHHHHHHhhc-cHHHHHHHHHHHHHHHHH
Confidence 566667777775332111 227899999998854 457999888888888875
No 164
>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=28.83 E-value=25 Score=28.72 Aligned_cols=29 Identities=17% Similarity=0.356 Sum_probs=17.8
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
.....+.|+.||. .|... ..++.|..||.
T Consensus 66 ~~p~~~~C~~Cg~---~~~~~--------~~~~~CP~Cgs 94 (115)
T TIGR00100 66 DEPVECECEDCSE---EVSPE--------IDLYRCPKCHG 94 (115)
T ss_pred eeCcEEEcccCCC---EEecC--------CcCccCcCCcC
Confidence 3445689999993 23110 12578999984
No 165
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.77 E-value=35 Score=28.67 Aligned_cols=38 Identities=16% Similarity=0.319 Sum_probs=20.7
Q ss_pred cccccccCCCCcceEEEEeccCCCC---------Cc--eeEEEccCCCCc
Q 020974 268 SDIYECGRCGHNKISYQHSSILDDY---------NL--TRHVTCLNCNQY 306 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~q~q~rsade---------~m--t~f~~C~~C~~~ 306 (319)
...+.|+.||..-..-+.| ++-|+ |- ..|+.|..||..
T Consensus 68 p~~~~C~~CG~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVK-ESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ceEEECCCCCCEEeccccc-ccccccccccccccccccccCcCCcCCCCC
Confidence 3678999999421110212 12222 11 356789999954
No 166
>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=28.38 E-value=40 Score=27.16 Aligned_cols=14 Identities=14% Similarity=0.349 Sum_probs=10.2
Q ss_pred eEEEccCCCCccee
Q 020974 296 RHVTCLNCNQYWVS 309 (319)
Q Consensus 296 ~f~~C~~C~~~w~~ 309 (319)
..+.|..||..+..
T Consensus 30 ~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 30 PGWYCPACGEELLD 43 (127)
T ss_pred eeeECCCCCCEEEc
Confidence 45689999987643
No 167
>PF10562 CaM_bdg_C0: Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; InterPro: IPR018882 This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue [].
Probab=27.76 E-value=57 Score=20.20 Aligned_cols=18 Identities=33% Similarity=0.425 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHhhc
Q 020974 66 QKIQKLAYDLISSWRDMC 83 (319)
Q Consensus 66 ~~I~~~Ak~lv~~WK~~v 83 (319)
.+--.+|+..+++|+..+
T Consensus 11 qk~~elAr~a~dkWR~~i 28 (29)
T PF10562_consen 11 QKQLELARHAADKWRGNI 28 (29)
T ss_pred HHHHHHHHHHHHHHHhhc
Confidence 345679999999999875
No 168
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=27.76 E-value=58 Score=32.22 Aligned_cols=38 Identities=18% Similarity=0.202 Sum_probs=27.0
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.-++...|+.|+++..+.+.| |+ --+..-.+|..|+-+
T Consensus 155 ~gt~~~tC~tC~G~G~v~~~~-~~--g~~~~~~~C~~C~G~ 192 (371)
T COG0484 155 PGTDPKTCPTCNGSGQVRTVQ-RT--GFFSFQQTCPTCNGT 192 (371)
T ss_pred CCCCCCcCCCCCCcCeEEEEE-ee--eEEEEEEECCCCccc
Confidence 455788999999998887333 12 456677889988644
No 169
>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=27.48 E-value=13 Score=35.31 Aligned_cols=31 Identities=19% Similarity=0.537 Sum_probs=22.0
Q ss_pred ccccccCCCCcceEE--EEeccCCCCCceeEEEccCCCCccee
Q 020974 269 DIYECGRCGHNKISY--QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~--q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
-...|+.|+. ..| ++. ..+++|.+|||.++.
T Consensus 25 ~~~~c~~c~~--~~~~~~l~--------~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 25 VWTKCPKCGQ--VLYTKELE--------RNLEVCPKCDHHMRM 57 (285)
T ss_pred CeeECCCCcc--hhhHHHHH--------hhCCCCCCCCCcCcC
Confidence 3689999986 344 221 356899999998764
No 170
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=27.32 E-value=44 Score=37.34 Aligned_cols=51 Identities=12% Similarity=0.277 Sum_probs=34.8
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceeccccccccC
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVLP 318 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~~~~~~~~ 318 (319)
.+|...+||+|+..--.-..-.=-| ..+..|.|..||+..--..++|++-|
T Consensus 792 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~ 842 (1006)
T PRK12775 792 AETGVATCPKCHRPLEGDEEYVCCA--TSELQWRCDDCGKVSEGFAFPYGMCP 842 (1006)
T ss_pred ccCCCccCcccCCCCCCCceeEEec--CcceeeehhhhccccccccCCcCcCc
Confidence 5778889999987532110000012 23567899999999988899998877
No 171
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.28 E-value=53 Score=30.83 Aligned_cols=28 Identities=14% Similarity=0.230 Sum_probs=17.2
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCC
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCN 304 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~ 304 (319)
..+|++||..-..-.+-. ..-|-|..|.
T Consensus 244 g~pCprCG~~I~~~~~~g-------R~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAG-------RSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECC-------CccEECcCCc
Confidence 359999996433322211 3347899996
No 172
>PRK10445 endonuclease VIII; Provisional
Probab=27.22 E-value=54 Score=30.63 Aligned_cols=29 Identities=28% Similarity=0.409 Sum_probs=17.9
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
.-+||+||..-..-.+-. ..-|-|.+|..
T Consensus 235 g~~Cp~Cg~~I~~~~~~g-------R~t~~CP~CQ~ 263 (263)
T PRK10445 235 GEACERCGGIIEKTTLSS-------RPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCEeEEEEECC-------CCcEECCCCcC
Confidence 358999997543332222 23378999963
No 173
>PF06254 DUF1019: Protein of unknown function (DUF1019); InterPro: IPR009364 This entry is represented by Bacteriophage phi-80, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3C4R_C.
Probab=27.04 E-value=41 Score=26.49 Aligned_cols=50 Identities=12% Similarity=0.051 Sum_probs=28.5
Q ss_pred HHHHHhccCchhHHHHHHHHHHhcCCCCCHHHHHHHhcCCCChhhhhcCC
Q 020974 180 AMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMS 229 (319)
Q Consensus 180 ~lf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~lv~Ms 229 (319)
.||..+.+++..|+.+++.|.-.+-..--++++.+|.+|.=...-|+.+-
T Consensus 12 ~iFRwl~~ds~~~~~~~~~L~PAI~aAlP~E~rarl~~~~~~~~~la~~~ 61 (89)
T PF06254_consen 12 KIFRWLDNDSPAYREKIMQLSPAILAALPPERRARLSSGDSTMYLLASAA 61 (89)
T ss_dssp HHHHHHH--SHHHHHHHHHHHHHHHHHS-HHHHHHHHCTT-HHH------
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHhCCHHHHhhccCCCCchhhhhHhH
Confidence 57766666677888888888776655445678888877755554454443
No 174
>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=26.84 E-value=65 Score=27.86 Aligned_cols=34 Identities=29% Similarity=0.573 Sum_probs=22.0
Q ss_pred cccccCCCCcceEE-EEe------ccCC-------CCCceeEEEcc-CC
Q 020974 270 IYECGRCGHNKISY-QHS------SILD-------DYNLTRHVTCL-NC 303 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q------~rsa-------de~mt~f~~C~-~C 303 (319)
.-.|++||+..+.= |+. .+.. |=+....|||. +|
T Consensus 97 ip~C~~Cg~~R~FEfQlmP~li~~L~~~~~~~~~~dwgtv~VyTCs~sC 145 (164)
T PF04194_consen 97 IPKCENCGSPRVFEFQLMPQLIYYLEVDDEGSDSMDWGTVLVYTCSASC 145 (164)
T ss_pred CCCCccCCCccEEEEEechHHHHHhhccccCCCCceeeEEEEEEehHHc
Confidence 56899999988764 651 1112 22334789999 48
No 175
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.75 E-value=61 Score=24.99 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=20.7
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
.-||.|+- ..++-.|+.-| |-.|..|+--|-
T Consensus 2 llCP~C~v---~l~~~~rs~vE----iD~CPrCrGVWL 32 (88)
T COG3809 2 LLCPICGV---ELVMSVRSGVE----IDYCPRCRGVWL 32 (88)
T ss_pred cccCcCCc---eeeeeeecCce----eeeCCccccEee
Confidence 46888874 33444456655 567999988884
No 176
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=26.75 E-value=40 Score=28.46 Aligned_cols=30 Identities=27% Similarity=0.510 Sum_probs=18.6
Q ss_pred ccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcce
Q 020974 267 VSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
.++ .+||+||-.-- +. ..+ +.|..||++-.
T Consensus 26 ML~-~hCp~Cg~PLF--~K----dG~-----v~CPvC~~~~~ 55 (131)
T COG1645 26 MLA-KHCPKCGTPLF--RK----DGE-----VFCPVCGYREV 55 (131)
T ss_pred HHH-hhCcccCCcce--ee----CCe-----EECCCCCceEE
Confidence 444 68999987543 21 112 67999997643
No 177
>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=25.84 E-value=49 Score=28.73 Aligned_cols=13 Identities=31% Similarity=0.915 Sum_probs=9.8
Q ss_pred EEccCCCCc--ceec
Q 020974 298 VTCLNCNQY--WVST 310 (319)
Q Consensus 298 ~~C~~C~~~--w~~~ 310 (319)
..|.+||+. |...
T Consensus 69 sYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 69 SYCHNCGKPYPWTEN 83 (158)
T ss_pred hhHHhCCCCCchHHH
Confidence 469999987 6544
No 178
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=25.83 E-value=15 Score=35.06 Aligned_cols=32 Identities=19% Similarity=0.477 Sum_probs=22.4
Q ss_pred ccccccCCCCcceEE--EEeccCCCCCceeEEEccCCCCcceec
Q 020974 269 DIYECGRCGHNKISY--QHSSILDDYNLTRHVTCLNCNQYWVST 310 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~--q~q~rsade~mt~f~~C~~C~~~w~~~ 310 (319)
-..+|+.|+. ..| ++. ..+++|.+|||.++.+
T Consensus 26 ~~~~c~~c~~--~~~~~~l~--------~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 26 LWTKCPSCGQ--VLYRKELE--------ANLNVCPKCGHHMRIS 59 (292)
T ss_pred CeeECCCccc--hhhHHHHH--------hcCCCCCCCCCCeeCC
Confidence 3789999987 344 332 2357999999988753
No 179
>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=25.79 E-value=41 Score=22.40 Aligned_cols=31 Identities=19% Similarity=0.314 Sum_probs=14.2
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
.+||.||++.-.-... |..-+--+.|..|+.
T Consensus 4 ~pCP~CGG~DrFri~~----d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFD----DKDGRGTWICRQCGG 34 (40)
T ss_dssp E--TTTT-TTTEEEET----T----S-EEETTTTB
T ss_pred CCCCCCcCccccccCc----CcccCCCEECCCCCC
Confidence 4899999976542221 211223468999943
No 180
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=25.55 E-value=22 Score=35.64 Aligned_cols=38 Identities=24% Similarity=0.277 Sum_probs=26.3
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcc
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w 307 (319)
....|.||.|..+=... -.|. =.+++..+.|.+||-.-
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccccCCccccchhhhHHHHh---hcccCceEEEecCCCch
Confidence 34569999999865555 4443 23556778999998643
No 181
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.41 E-value=61 Score=30.41 Aligned_cols=29 Identities=21% Similarity=0.406 Sum_probs=18.5
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.+|++||..-....+-.| .-|-|..|...
T Consensus 236 ~pC~~Cg~~I~~~~~~gR-------~ty~Cp~CQ~~ 264 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGR-------GTHFCPQCQPL 264 (269)
T ss_pred CCCCcCCCeeEEEEECCC-------CcEECCCCcCC
Confidence 489999975444322223 33789999854
No 182
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=25.41 E-value=78 Score=34.19 Aligned_cols=17 Identities=18% Similarity=0.354 Sum_probs=12.9
Q ss_pred CCCCce--eEEEccCCCCc
Q 020974 290 DDYNLT--RHVTCLNCNQY 306 (319)
Q Consensus 290 ade~mt--~f~~C~~C~~~ 306 (319)
...|.| +|+.|..|.|+
T Consensus 1147 sG~pIt~~~fWlC~~CkH~ 1165 (1189)
T KOG2041|consen 1147 SGRPITDNIFWLCPRCKHR 1165 (1189)
T ss_pred cCCccccceEEEccccccc
Confidence 445555 79999999886
No 183
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=25.40 E-value=42 Score=25.63 Aligned_cols=13 Identities=23% Similarity=0.623 Sum_probs=11.3
Q ss_pred ceeEEEccCCCCc
Q 020974 294 LTRHVTCLNCNQY 306 (319)
Q Consensus 294 mt~f~~C~~C~~~ 306 (319)
|.++|.|..||..
T Consensus 1 Mai~Y~CRHCg~~ 13 (76)
T PF10955_consen 1 MAIHYYCRHCGTK 13 (76)
T ss_pred CceEEEecCCCCE
Confidence 7789999999965
No 184
>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=25.37 E-value=40 Score=21.41 Aligned_cols=13 Identities=15% Similarity=0.248 Sum_probs=10.7
Q ss_pred EEEccCCCCccee
Q 020974 297 HVTCLNCNQYWVS 309 (319)
Q Consensus 297 f~~C~~C~~~w~~ 309 (319)
+|.|..||+....
T Consensus 2 ~~~C~~CG~i~~g 14 (34)
T cd00729 2 VWVCPVCGYIHEG 14 (34)
T ss_pred eEECCCCCCEeEC
Confidence 6899999988754
No 185
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=25.35 E-value=26 Score=25.25 Aligned_cols=10 Identities=40% Similarity=1.182 Sum_probs=8.4
Q ss_pred ccccccCCCC
Q 020974 269 DIYECGRCGH 278 (319)
Q Consensus 269 ~~~~C~~C~~ 278 (319)
..+.||+||.
T Consensus 16 ~~lrCPRC~~ 25 (65)
T COG4049 16 EFLRCPRCGM 25 (65)
T ss_pred eeeeCCchhH
Confidence 5789999985
No 186
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=24.92 E-value=40 Score=31.49 Aligned_cols=12 Identities=17% Similarity=0.650 Sum_probs=6.5
Q ss_pred EEEccCCCCcce
Q 020974 297 HVTCLNCNQYWV 308 (319)
Q Consensus 297 f~~C~~C~~~w~ 308 (319)
+|.|.+|+|.|+
T Consensus 155 ef~C~~C~h~F~ 166 (278)
T PF15135_consen 155 EFHCPKCRHNFR 166 (278)
T ss_pred eeecccccccch
Confidence 455555555554
No 187
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=24.89 E-value=65 Score=30.20 Aligned_cols=29 Identities=21% Similarity=0.494 Sum_probs=17.9
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
..+|++||..-..-.+-. ..-|-|..|..
T Consensus 245 g~pC~~Cg~~I~~~~~~g-------R~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGG-------RSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEECC-------CCcEECcCCCC
Confidence 358999997533322222 23378999975
No 188
>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=24.44 E-value=25 Score=28.79 Aligned_cols=30 Identities=20% Similarity=0.514 Sum_probs=19.2
Q ss_pred ccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcce
Q 020974 267 VSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 267 ~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~ 308 (319)
..-+..||.|++.--.. .. ..|..|++.-.
T Consensus 66 kav~V~CP~C~K~TKmLGr~------------D~CM~C~~pLT 96 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRV------------DACMHCKEPLT 96 (114)
T ss_pred cceeeECCCCCChHhhhchh------------hccCcCCCcCc
Confidence 44567899999854433 22 26888887543
No 189
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=24.43 E-value=57 Score=26.59 Aligned_cols=62 Identities=13% Similarity=0.111 Sum_probs=47.3
Q ss_pred hHHHHHHHHHHHHHHhcc----CchhHHHHHHHHHHhcCCCCCHHHHHHHhcCCCChhhhhcCChhhc
Q 020974 170 PIQVAILVESAMYEKWCR----SNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEM 233 (319)
Q Consensus 170 ~~~lA~~IE~~lf~~~~~----~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~lv~Ms~eEl 233 (319)
...++..++..|..+|.+ .....-+.+|.|..| ++..|-|...-..--|+.++|..+=|.||
T Consensus 27 v~~F~~~L~~~L~~~y~~HWyP~~P~kGqayRCIrIn--~~~Dp~l~~Aa~~sGl~~~~l~~~LP~el 92 (108)
T smart00099 27 VEIFAEKLTRLLKEKYKNHWYPEKPYKGSGFRCIRIN--QKVDPVIEQACKESGLDIDDLGGNLPKEL 92 (108)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCCCCcceEEEEEC--CcCCHHHHHHHHHhCCCHHHHHHhCCccc
Confidence 457899999999999853 234455667888888 67889998888887788888876655555
No 190
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.32 E-value=36 Score=26.06 Aligned_cols=14 Identities=21% Similarity=0.522 Sum_probs=10.9
Q ss_pred eeEEEccCCCCcce
Q 020974 295 TRHVTCLNCNQYWV 308 (319)
Q Consensus 295 t~f~~C~~C~~~w~ 308 (319)
|.-|.|.+|||++-
T Consensus 10 tY~Y~c~~cg~~~d 23 (82)
T COG2331 10 TYSYECTECGNRFD 23 (82)
T ss_pred ceEEeecccchHHH
Confidence 45689999999863
No 191
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=24.23 E-value=16 Score=34.98 Aligned_cols=31 Identities=16% Similarity=0.353 Sum_probs=21.9
Q ss_pred ccccccCCCCcceEE--EEeccCCCCCceeEEEccCCCCccee
Q 020974 269 DIYECGRCGHNKISY--QHSSILDDYNLTRHVTCLNCNQYWVS 309 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~--q~q~rsade~mt~f~~C~~C~~~w~~ 309 (319)
-..+|+.|+. ..| ++. ..+++|.+|||-++.
T Consensus 37 lw~kc~~C~~--~~~~~~l~--------~~~~vcp~c~~h~rl 69 (296)
T CHL00174 37 LWVQCENCYG--LNYKKFLK--------SKMNICEQCGYHLKM 69 (296)
T ss_pred CeeECCCccc--hhhHHHHH--------HcCCCCCCCCCCcCC
Confidence 3789999986 334 321 356899999997764
No 192
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=23.87 E-value=26 Score=31.10 Aligned_cols=37 Identities=19% Similarity=0.203 Sum_probs=16.8
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.+.||.||+....-.+..-..+........|.+|++.
T Consensus 18 ~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~ 54 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTP 54 (188)
T ss_dssp EEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B
T ss_pred EeECCCCCCCccccccccCCccccccCcCcCCCCCCc
Confidence 5899999985444322211122222357899999873
No 193
>PF14122 YokU: YokU-like protein
Probab=23.78 E-value=50 Score=25.80 Aligned_cols=36 Identities=22% Similarity=0.542 Sum_probs=22.3
Q ss_pred cccCCCCcce------EE-EEec--cCCCCCceeEEEccCCCCcc
Q 020974 272 ECGRCGHNKI------SY-QHSS--ILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 272 ~C~~C~~~~~------~~-q~q~--rsade~mt~f~~C~~C~~~w 307 (319)
.|.-||+.++ +| .+-. |.-.=++|.-+.|.+||-.+
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvY 45 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVY 45 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEE
Confidence 4777887654 44 4432 33333556678999999654
No 194
>PLN03131 hypothetical protein; Provisional
Probab=23.61 E-value=71 Score=33.71 Aligned_cols=28 Identities=14% Similarity=0.428 Sum_probs=19.8
Q ss_pred ccccccCCCCcceEE-EEeccCCCCCceeEEEccCCC
Q 020974 269 DIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCN 304 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~ 304 (319)
+.-.|..||.....| -+- .-+ +.|..|.
T Consensus 22 gNk~CADCga~~P~WASiN-------lGI-FICi~CS 50 (705)
T PLN03131 22 PNRRCINCNSLGPQFVCTN-------FWT-FICMTCS 50 (705)
T ss_pred CCCccccCCCCCCCeeEec-------cce-EEchhch
Confidence 345899999998888 442 223 5899995
No 195
>PRK04860 hypothetical protein; Provisional
Probab=23.57 E-value=23 Score=30.81 Aligned_cols=41 Identities=15% Similarity=0.347 Sum_probs=23.7
Q ss_pred cccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcceecc
Q 020974 268 SDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 268 t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~~~ 311 (319)
+=.|.|. |+.....+....|.-.. +..|.|..|+.......
T Consensus 117 ~~~Y~C~-C~~~~~~~rrH~ri~~g--~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 117 TFPYRCK-CQEHQLTVRRHNRVVRG--EAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEEcC-CCCeeCHHHHHHHHhcC--CccEECCCCCceeEEec
Confidence 3469998 98722222111111111 24589999999887654
No 196
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.47 E-value=30 Score=28.76 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=9.7
Q ss_pred cccccCCCCcceE
Q 020974 270 IYECGRCGHNKIS 282 (319)
Q Consensus 270 ~~~C~~C~~~~~~ 282 (319)
.-.||+||.-+-.
T Consensus 21 ~grCP~CGeGrLF 33 (126)
T COG5349 21 RGRCPRCGEGRLF 33 (126)
T ss_pred cCCCCCCCCchhh
Confidence 4589999986643
No 197
>PRK12277 50S ribosomal protein L13e; Provisional
Probab=23.26 E-value=1.8e+02 Score=22.54 Aligned_cols=45 Identities=2% Similarity=0.022 Sum_probs=31.8
Q ss_pred HHHhhcCCCCHHhhhcccceeecccccCCCCHHHHHHHHHHHHHHHhhccc
Q 020974 35 LDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWD 85 (319)
Q Consensus 35 L~~L~~~~it~~~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~lv~~WK~~v~~ 85 (319)
|.+|+...|+..... .||.+|..=|++.+++ -. .-++.|+..+..
T Consensus 36 l~ELkaaGi~~~~Ar--tiGI~VD~RRrn~~~e---NV-erLk~y~skL~~ 80 (83)
T PRK12277 36 IGELEAAGLDIKNAR--KLGIRVDKRRKTVHEE---NV-EALKKFLEQLGN 80 (83)
T ss_pred HHHHHHcCCCHHHhc--ccCeeecccccCCCHH---HH-HHHHHHHHHhcc
Confidence 667777888877765 6999999999998765 22 234557766543
No 198
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=23.11 E-value=41 Score=27.20 Aligned_cols=21 Identities=29% Similarity=0.615 Sum_probs=15.5
Q ss_pred cccccCCCCcceEE-EEeccCC
Q 020974 270 IYECGRCGHNKISY-QHSSILD 290 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q~rsa 290 (319)
+--||+||.++-.| -.-.|.|
T Consensus 20 l~GCp~CG~nkF~yv~~e~rpa 41 (112)
T COG3364 20 LSGCPKCGCNKFLYVPEEKRPA 41 (112)
T ss_pred HccCccccchheEecccccccc
Confidence 44699999999999 4444543
No 199
>PHA00616 hypothetical protein
Probab=23.07 E-value=29 Score=23.67 Aligned_cols=13 Identities=38% Similarity=0.705 Sum_probs=9.1
Q ss_pred ccccCCCCcceEE
Q 020974 271 YECGRCGHNKISY 283 (319)
Q Consensus 271 ~~C~~C~~~~~~~ 283 (319)
++|++||..=..+
T Consensus 2 YqC~~CG~~F~~~ 14 (44)
T PHA00616 2 YQCLRCGGIFRKK 14 (44)
T ss_pred CccchhhHHHhhH
Confidence 6888888754444
No 200
>PRK06599 DNA topoisomerase I; Validated
Probab=22.82 E-value=1.1e+02 Score=32.49 Aligned_cols=15 Identities=7% Similarity=0.191 Sum_probs=12.0
Q ss_pred HHHhcCCCChhhhhc
Q 020974 213 RKVLLGHVKPETIIN 227 (319)
Q Consensus 213 ~~vl~G~i~p~~lv~ 227 (319)
..|..|+.++++|+.
T Consensus 543 ~~I~~G~~~~~~~l~ 557 (675)
T PRK06599 543 DEIAEGKKDWKPVLR 557 (675)
T ss_pred HHHHcCCCCHHHHHH
Confidence 567789998888866
No 201
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=22.51 E-value=36 Score=24.93 Aligned_cols=25 Identities=32% Similarity=0.759 Sum_probs=17.9
Q ss_pred ccccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 269 DIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 269 ~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
+-..|.+||.+ .|-+|- -+|-.||.
T Consensus 16 tHt~CrRCG~~--syh~qK----------~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRH--SYNVRK----------KYCAACGF 40 (62)
T ss_pred ccchhcccCcc--cccccc----------cchhhcCC
Confidence 45689999986 563332 27999987
No 202
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=22.47 E-value=43 Score=28.20 Aligned_cols=17 Identities=35% Similarity=0.852 Sum_probs=13.6
Q ss_pred cccccCCCCcceEE-EEe
Q 020974 270 IYECGRCGHNKISY-QHS 286 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q 286 (319)
.-=||.||+++-.| .-.
T Consensus 19 l~GCP~CGg~kF~yv~~~ 36 (131)
T PF09845_consen 19 LSGCPECGGNKFQYVPEE 36 (131)
T ss_pred HccCcccCCcceEEcCCC
Confidence 44699999999999 443
No 203
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.16 E-value=78 Score=29.85 Aligned_cols=29 Identities=21% Similarity=0.448 Sum_probs=18.1
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
..+|++||..-..-.+-. ..-|-|..|..
T Consensus 254 g~pC~~Cg~~I~~~~~~g-------R~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAG-------RSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEECC-------CccEECCCCcC
Confidence 359999997544332222 33378999973
No 204
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=21.91 E-value=78 Score=19.12 Aligned_cols=28 Identities=21% Similarity=0.379 Sum_probs=12.9
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCC
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQ 305 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~ 305 (319)
.+|++|+..-..... .-...+.|..|.+
T Consensus 2 ~~C~rC~~~~~~~~~-------~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGI-------NGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEE-------TTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEe-------cCCCCeECcCCcC
Confidence 379999986444311 1123367888864
No 205
>COG4734 ArdA Antirestriction protein [General function prediction only]
Probab=21.76 E-value=6.8 Score=34.30 Aligned_cols=41 Identities=20% Similarity=0.369 Sum_probs=31.2
Q ss_pred cccccCCCCcceEE-EEeccCCCCCc----eeEEEccCCCCcceecc
Q 020974 270 IYECGRCGHNKISY-QHSSILDDYNL----TRHVTCLNCNQYWVSTN 311 (319)
Q Consensus 270 ~~~C~~C~~~~~~~-q~q~rsade~m----t~f~~C~~C~~~w~~~~ 311 (319)
.+.|=.||+--+.+ |.| ||++.-. .++|.|.||.-+|..|-
T Consensus 16 ~y~~y~~gsi~t~~fqe~-vsaml~~srfPnvmVkCpnceg~~e~Ct 61 (193)
T COG4734 16 TYHKYNCGSIFTKWFQET-VSAMLFDSRFPNVMVKCPNCEGFYEACT 61 (193)
T ss_pred hcceeeccccccHHHHHH-HHHHHHhhcCccceeeccchhhHHHHHH
Confidence 57888999988888 776 4444432 37899999999998774
No 206
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=21.71 E-value=80 Score=20.50 Aligned_cols=11 Identities=18% Similarity=0.863 Sum_probs=7.8
Q ss_pred EEccCCCCcce
Q 020974 298 VTCLNCNQYWV 308 (319)
Q Consensus 298 ~~C~~C~~~w~ 308 (319)
+.|.+||..+-
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 36888887653
No 207
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=21.43 E-value=78 Score=34.19 Aligned_cols=16 Identities=19% Similarity=0.360 Sum_probs=12.3
Q ss_pred CChhhhhcCChhhcCc
Q 020974 220 VKPETIINMSAKEMAS 235 (319)
Q Consensus 220 i~p~~lv~Ms~eElas 235 (319)
++.-.++.|..+.+..
T Consensus 386 ~p~v~iiDmr~e~~~~ 401 (730)
T COG1198 386 LPRVEIIDMRKEPLET 401 (730)
T ss_pred CCcceEEecccccccc
Confidence 5666788998888776
No 208
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=21.27 E-value=37 Score=33.29 Aligned_cols=33 Identities=15% Similarity=0.313 Sum_probs=24.1
Q ss_pred cccccCCCCcceEEEEeccCCCCCceeEEEccCCCCcc
Q 020974 270 IYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYW 307 (319)
Q Consensus 270 ~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 307 (319)
-..|+.|++.++.+.+- . .-|+-+.|..||.+-
T Consensus 96 FVlC~~C~NPETel~it---k--~q~i~~~CkACG~r~ 128 (400)
T KOG2767|consen 96 FVLCPSCENPETELIIT---K--KQTISLKCKACGFRS 128 (400)
T ss_pred heeCcCCCCCceeEEec---c--cchhhhHHHHcCCcc
Confidence 36899999999998331 1 224567899999774
No 209
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=21.21 E-value=70 Score=25.79 Aligned_cols=23 Identities=22% Similarity=0.235 Sum_probs=15.9
Q ss_pred eccCCCCCceeEEEccCCCCcce
Q 020974 286 SSILDDYNLTRHVTCLNCNQYWV 308 (319)
Q Consensus 286 q~rsade~mt~f~~C~~C~~~w~ 308 (319)
++|.---+..+.++|..|||.--
T Consensus 11 ~ik~~~~~L~k~FtCp~Cghe~v 33 (104)
T COG4888 11 IIKRRPQVLPKTFTCPRCGHEKV 33 (104)
T ss_pred cCcccCccCCceEecCccCCeee
Confidence 34444445677889999999744
No 210
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=21.19 E-value=22 Score=31.47 Aligned_cols=33 Identities=24% Similarity=0.466 Sum_probs=21.9
Q ss_pred cccccccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 266 IVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 266 ~~t~~~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
.....|.||.|+-+ .+ -||.|..-++|..||.-
T Consensus 109 ~~~~~y~C~~~~~r-~s-------fdeA~~~~F~Cp~Cg~~ 141 (176)
T COG1675 109 TENNYYVCPNCHVK-YS-------FDEAMELGFTCPKCGED 141 (176)
T ss_pred ccCCceeCCCCCCc-cc-------HHHHHHhCCCCCCCCch
Confidence 45567999777653 33 34455555899999954
No 211
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=20.99 E-value=43 Score=28.26 Aligned_cols=14 Identities=21% Similarity=0.740 Sum_probs=7.7
Q ss_pred eEEEccCCCCccee
Q 020974 296 RHVTCLNCNQYWVS 309 (319)
Q Consensus 296 ~f~~C~~C~~~w~~ 309 (319)
.+++|+.||..++.
T Consensus 71 d~i~clecGk~~k~ 84 (132)
T PF05443_consen 71 DYIICLECGKKFKT 84 (132)
T ss_dssp S-EE-TBT--EESB
T ss_pred CeeEEccCCcccch
Confidence 57899999987764
No 212
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.40 E-value=88 Score=29.35 Aligned_cols=27 Identities=22% Similarity=0.470 Sum_probs=16.8
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCC
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCN 304 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~ 304 (319)
.+|++||..-....+-.| .-|-|..|.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR-------~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGR-------GTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCeeEEEEECCC-------CCEECCCCC
Confidence 489999975433333222 336799995
No 213
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=20.28 E-value=61 Score=34.25 Aligned_cols=42 Identities=14% Similarity=0.245 Sum_probs=22.9
Q ss_pred hhcCchHHHHHhhhhhhchhhhhcCCCCccccccccccccccccCCCC
Q 020974 231 KEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGH 278 (319)
Q Consensus 231 eElas~e~k~~~~~~~~~e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~ 278 (319)
.|||.-+.-.+|... ++.+-+-.. .++..+ ..|. -+|+.||+
T Consensus 904 ~ELAn~eKs~qRR~A-R~~sk~G~d---L~G~GR-K~Tt-r~C~nCGQ 945 (968)
T COG5179 904 LELANLEKSQQRRAA-RQNSKNGSD---LAGKGR-KNTT-RTCGNCGQ 945 (968)
T ss_pred HHHHhhhhhHHHHHH-Hhhhccccc---ccCCCC-CCcc-eecccccc
Confidence 366666655555555 443333333 333344 4444 48999997
No 214
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=20.26 E-value=67 Score=28.75 Aligned_cols=25 Identities=28% Similarity=0.658 Sum_probs=14.8
Q ss_pred ccccCCCCcceEEEEeccCCCCCceeEEEccCCCCc
Q 020974 271 YECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQY 306 (319)
Q Consensus 271 ~~C~~C~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 306 (319)
..|.+|++.=.. ++. ...|.+||++
T Consensus 150 A~CsrC~~~L~~--------~~~---~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--------KGN---MLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--------cCc---EEECCCCCCE
Confidence 478888773221 111 2578888876
Done!