Query 035641
Match_columns 314
No_of_seqs 257 out of 1118
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 04:52:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035641.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035641hhsearch_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-70 2.9E-75 514.9 27.7 291 6-314 2-298 (299)
2 KOG1105 Transcription elongati 100.0 6.6E-63 1.4E-67 456.6 25.0 289 8-314 2-295 (296)
3 smart00510 TFS2M Domain in the 100.0 2.5E-28 5.5E-33 195.8 10.6 101 143-252 1-101 (102)
4 PF07500 TFIIS_M: Transcriptio 99.9 2.5E-27 5.4E-32 194.2 6.4 115 141-264 1-115 (115)
5 smart00440 ZnF_C2C2 C2C2 Zinc 99.8 3.7E-20 8.1E-25 123.7 4.4 39 275-313 1-39 (40)
6 PF01096 TFIIS_C: Transcriptio 99.8 7.9E-20 1.7E-24 121.5 4.0 39 275-313 1-39 (39)
7 smart00509 TFS2N Domain in the 99.7 4.4E-18 9.6E-23 129.2 5.4 74 8-86 1-74 (75)
8 KOG2906 RNA polymerase III sub 99.7 1E-18 2.2E-23 135.7 1.4 43 271-313 62-104 (105)
9 COG1594 RPB9 DNA-directed RNA 99.7 4.1E-17 9E-22 133.1 4.3 43 272-314 70-112 (113)
10 TIGR01384 TFS_arch transcripti 99.7 9.6E-17 2.1E-21 129.1 4.8 43 271-313 59-101 (104)
11 PHA02998 RNA polymerase subuni 99.6 4.3E-16 9.3E-21 133.6 4.7 41 273-313 142-182 (195)
12 cd00183 TFIIS_I N-terminal dom 99.6 1.3E-15 2.8E-20 116.0 6.0 73 7-85 3-75 (76)
13 KOG2691 RNA polymerase II subu 99.5 3.9E-15 8.4E-20 117.7 4.0 48 266-313 64-112 (113)
14 PF08711 Med26: TFIIS helical 99.4 2.9E-13 6.2E-18 95.9 2.3 52 34-86 1-53 (53)
15 KOG1634 Predicted transcriptio 99.3 1.3E-12 2.7E-17 134.2 5.2 83 177-259 267-350 (778)
16 KOG2907 RNA polymerase I trans 99.3 1.5E-12 3.2E-17 104.1 1.9 45 269-313 69-113 (116)
17 PF11467 LEDGF: Lens epitheliu 96.6 0.0038 8.3E-08 50.5 5.2 78 2-86 1-80 (106)
18 KOG1793 Uncharacterized conser 95.9 0.01 2.2E-07 57.7 4.6 53 33-86 236-291 (417)
19 PF08274 PhnA_Zn_Ribbon: PhnA 95.8 0.0026 5.6E-08 39.7 0.1 28 275-313 3-30 (30)
20 PF09855 DUF2082: Nucleic-acid 95.6 0.015 3.3E-07 42.7 3.6 37 275-311 1-45 (64)
21 KOG2821 RNA polymerase II tran 95.3 0.0047 1E-07 60.9 0.1 57 27-86 22-78 (433)
22 PRK09678 DNA-binding transcrip 95.1 0.02 4.2E-07 43.1 2.8 37 274-313 1-40 (72)
23 PF13717 zinc_ribbon_4: zinc-r 95.0 0.016 3.6E-07 37.6 2.0 32 274-313 2-36 (36)
24 PF13719 zinc_ribbon_5: zinc-r 94.6 0.024 5.2E-07 37.0 1.9 33 274-314 2-37 (37)
25 COG5139 Uncharacterized conser 94.6 0.05 1.1E-06 51.2 4.6 53 33-86 233-287 (397)
26 PHA00626 hypothetical protein 94.6 0.026 5.6E-07 40.1 2.1 33 276-313 2-34 (59)
27 TIGR02098 MJ0042_CXXC MJ0042 f 94.5 0.032 7E-07 36.3 2.4 35 274-314 2-37 (38)
28 COG3478 Predicted nucleic-acid 94.1 0.039 8.4E-07 40.3 2.3 36 274-311 4-49 (68)
29 PF08271 TF_Zn_Ribbon: TFIIB z 94.0 0.042 9.1E-07 36.9 2.2 28 275-311 1-28 (43)
30 PF04606 Ogr_Delta: Ogr/Delta- 94.0 0.053 1.2E-06 37.2 2.7 36 276-313 1-38 (47)
31 PF12760 Zn_Tnp_IS1595: Transp 94.0 0.05 1.1E-06 37.1 2.6 28 275-311 19-46 (46)
32 COG4888 Uncharacterized Zn rib 92.8 0.12 2.7E-06 41.1 3.3 38 272-313 20-57 (104)
33 TIGR00373 conserved hypothetic 91.8 0.11 2.3E-06 45.0 2.1 32 271-311 106-137 (158)
34 COG2051 RPS27A Ribosomal prote 91.3 0.14 3.1E-06 37.6 2.0 29 274-311 19-47 (67)
35 PF11781 RRN7: RNA polymerase 90.5 0.21 4.6E-06 32.4 2.0 27 274-311 8-34 (36)
36 PF05876 Terminase_GpA: Phage 90.2 0.22 4.8E-06 51.4 3.1 38 275-313 201-240 (557)
37 smart00661 RPOL9 RNA polymeras 89.9 0.32 6.9E-06 33.5 2.7 29 277-313 3-31 (52)
38 smart00531 TFIIE Transcription 89.4 0.27 5.9E-06 41.8 2.4 37 271-311 96-132 (147)
39 PF14354 Lar_restr_allev: Rest 89.2 0.52 1.1E-05 33.7 3.5 36 273-310 2-37 (61)
40 TIGR03655 anti_R_Lar restricti 88.9 0.66 1.4E-05 32.5 3.8 34 275-311 2-35 (53)
41 PLN00209 ribosomal protein S27 88.9 0.46 9.9E-06 36.8 3.1 58 240-311 7-64 (86)
42 PTZ00083 40S ribosomal protein 88.5 0.51 1.1E-05 36.5 3.1 31 272-311 33-63 (85)
43 PF09526 DUF2387: Probable met 88.4 0.41 8.8E-06 35.9 2.5 33 274-312 8-40 (71)
44 PRK06266 transcription initiat 87.5 0.28 6.1E-06 43.2 1.4 33 270-311 113-145 (178)
45 PF05129 Elf1: Transcription e 87.5 0.64 1.4E-05 35.7 3.2 38 272-313 20-57 (81)
46 PF05180 zf-DNL: DNL zinc fing 87.3 0.25 5.4E-06 36.5 0.8 35 274-311 4-38 (66)
47 PF04216 FdhE: Protein involve 87.2 0.45 9.7E-06 45.0 2.7 38 274-314 172-209 (290)
48 PF13453 zf-TFIIB: Transcripti 86.9 0.79 1.7E-05 30.3 3.0 29 276-312 1-29 (41)
49 TIGR02443 conserved hypothetic 86.5 0.72 1.6E-05 33.3 2.7 32 274-312 9-41 (59)
50 PRK00415 rps27e 30S ribosomal 85.7 0.72 1.6E-05 33.3 2.4 29 274-311 11-39 (59)
51 PRK06266 transcription initiat 85.5 1.2 2.7E-05 39.2 4.3 76 226-314 34-129 (178)
52 PF01667 Ribosomal_S27e: Ribos 84.5 0.63 1.4E-05 33.2 1.7 29 274-311 7-35 (55)
53 PF09538 FYDLN_acid: Protein o 83.8 0.53 1.2E-05 38.2 1.2 29 274-313 9-37 (108)
54 PRK00432 30S ribosomal protein 83.7 0.73 1.6E-05 32.1 1.7 28 274-312 20-47 (50)
55 PRK00398 rpoP DNA-directed RNA 83.0 1.2 2.6E-05 30.2 2.5 28 274-311 3-30 (46)
56 PRK03988 translation initiatio 82.9 1.2 2.6E-05 37.8 3.0 32 274-312 102-133 (138)
57 PF07282 OrfB_Zn_ribbon: Putat 82.6 0.93 2E-05 33.1 2.0 29 274-312 28-56 (69)
58 PF10571 UPF0547: Uncharacteri 82.6 0.67 1.4E-05 27.9 1.0 24 276-313 2-25 (26)
59 PLN02976 amine oxidase 82.2 1.3 2.9E-05 50.5 3.8 59 30-90 1301-1360(1713)
60 PRK09710 lar restriction allev 81.6 2.2 4.8E-05 31.3 3.5 33 274-313 6-38 (64)
61 PRK14892 putative transcriptio 81.4 1.5 3.3E-05 35.0 2.9 34 272-312 19-52 (99)
62 KOG3507 DNA-directed RNA polym 81.2 1.3 2.8E-05 31.9 2.2 32 269-311 15-46 (62)
63 PF03811 Zn_Tnp_IS1: InsA N-te 81.1 1.6 3.5E-05 28.3 2.5 33 272-308 3-35 (36)
64 PF01873 eIF-5_eIF-2B: Domain 80.7 1.8 4E-05 36.0 3.3 31 274-311 93-123 (125)
65 COG2888 Predicted Zn-ribbon RN 80.6 0.88 1.9E-05 32.8 1.2 36 270-310 23-58 (61)
66 TIGR00311 aIF-2beta translatio 80.5 2.2 4.7E-05 35.9 3.7 32 274-312 97-128 (133)
67 PF10058 DUF2296: Predicted in 79.4 3 6.6E-05 29.5 3.6 32 273-310 21-52 (54)
68 smart00653 eIF2B_5 domain pres 79.1 1.8 3.9E-05 35.2 2.7 31 274-311 80-110 (110)
69 TIGR01562 FdhE formate dehydro 78.8 1.4 2.9E-05 42.3 2.2 39 274-314 184-222 (305)
70 KOG3277 Uncharacterized conser 77.6 1.5 3.2E-05 37.7 1.8 35 274-311 79-113 (165)
71 smart00659 RPOLCX RNA polymera 77.2 2 4.4E-05 29.1 2.1 27 274-311 2-28 (44)
72 PF08792 A2L_zn_ribbon: A2L zi 77.1 3.7 8E-05 26.1 3.2 30 273-312 2-31 (33)
73 PRK03564 formate dehydrogenase 76.3 2.1 4.6E-05 41.0 2.7 39 273-314 186-224 (309)
74 PF09723 Zn-ribbon_8: Zinc rib 75.9 3.5 7.5E-05 27.4 2.9 31 273-310 4-34 (42)
75 PRK12336 translation initiatio 75.7 2.5 5.5E-05 37.9 3.0 31 274-311 98-128 (201)
76 PRK14890 putative Zn-ribbon RN 75.5 2.6 5.7E-05 30.4 2.4 35 272-311 23-57 (59)
77 PF01396 zf-C4_Topoisom: Topoi 75.3 3.9 8.5E-05 26.8 3.0 29 275-311 2-33 (39)
78 PF03604 DNA_RNApol_7kD: DNA d 75.2 1.6 3.5E-05 27.6 1.1 26 275-311 1-26 (32)
79 smart00531 TFIIE Transcription 74.4 5.1 0.00011 34.0 4.4 22 293-314 90-111 (147)
80 COG1997 RPL43A Ribosomal prote 73.9 3.1 6.7E-05 32.4 2.6 32 272-313 33-64 (89)
81 smart00834 CxxC_CXXC_SSSS Puta 73.5 4.3 9.2E-05 26.2 2.9 31 273-310 4-34 (41)
82 COG1645 Uncharacterized Zn-fin 72.6 1.5 3.3E-05 36.7 0.6 32 269-312 23-54 (131)
83 COG1996 RPC10 DNA-directed RNA 70.9 2.4 5.3E-05 29.5 1.3 30 272-311 4-33 (49)
84 smart00401 ZnF_GATA zinc finge 69.7 2 4.4E-05 30.0 0.7 34 274-313 3-36 (52)
85 TIGR01206 lysW lysine biosynth 69.5 3.6 7.8E-05 29.2 1.9 31 274-312 2-32 (54)
86 PF14803 Nudix_N_2: Nudix N-te 68.3 4 8.6E-05 26.2 1.7 29 277-311 3-31 (34)
87 COG0675 Transposase and inacti 67.6 7.7 0.00017 36.1 4.4 26 272-312 307-332 (364)
88 PF13240 zinc_ribbon_2: zinc-r 67.3 3.2 6.9E-05 24.1 1.1 7 305-311 16-22 (23)
89 PF04216 FdhE: Protein involve 66.1 4.2 9.1E-05 38.4 2.2 39 274-313 211-249 (290)
90 PF11792 Baculo_LEF5_C: Baculo 65.9 0.4 8.7E-06 32.3 -3.3 30 280-310 13-42 (43)
91 PF01921 tRNA-synt_1f: tRNA sy 65.1 4.9 0.00011 39.3 2.6 35 274-312 174-209 (360)
92 KOG0909 Peptide:N-glycanase [P 64.6 9.7 0.00021 38.1 4.4 94 216-314 104-206 (500)
93 PRK05978 hypothetical protein; 64.1 3.4 7.5E-05 35.4 1.1 31 274-313 33-63 (148)
94 COG3677 Transposase and inacti 64.0 7 0.00015 32.6 2.9 38 271-313 27-64 (129)
95 PF06044 DRP: Dam-replacing fa 63.7 3.8 8.3E-05 37.8 1.4 33 274-312 31-63 (254)
96 PRK12495 hypothetical protein; 62.8 8.1 0.00018 35.2 3.3 31 270-312 38-68 (226)
97 PHA02942 putative transposase; 62.6 5 0.00011 39.6 2.1 28 274-312 325-352 (383)
98 PF07754 DUF1610: Domain of un 62.5 5.2 0.00011 23.6 1.4 10 272-281 14-23 (24)
99 PF04032 Rpr2: RNAse P Rpr2/Rp 60.8 12 0.00025 28.2 3.5 36 273-310 45-85 (85)
100 KOG1779 40s ribosomal protein 60.5 11 0.00025 28.7 3.2 57 240-310 5-61 (84)
101 TIGR00373 conserved hypothetic 59.6 4.2 9.1E-05 35.0 0.9 19 296-314 103-121 (158)
102 PRK12286 rpmF 50S ribosomal pr 59.1 9 0.0002 27.4 2.4 25 271-310 24-48 (57)
103 KOG4274 Positive cofactor 2 (P 58.4 16 0.00035 37.7 4.8 60 143-218 9-68 (742)
104 smart00778 Prim_Zn_Ribbon Zinc 58.2 7.8 0.00017 25.3 1.8 31 274-310 3-33 (37)
105 PF14311 DUF4379: Domain of un 58.2 9.1 0.0002 26.7 2.3 16 298-313 24-39 (55)
106 COG1675 TFA1 Transcription ini 57.6 4.1 9E-05 35.9 0.5 32 270-310 109-140 (176)
107 PF11672 DUF3268: Protein of u 56.7 12 0.00026 30.1 3.0 34 275-309 3-38 (102)
108 cd00674 LysRS_core_class_I cat 55.8 13 0.00028 36.3 3.7 33 274-311 169-201 (353)
109 TIGR00280 L37a ribosomal prote 55.7 28 0.00061 27.4 4.8 30 273-312 34-63 (91)
110 PRK00420 hypothetical protein; 54.7 8.2 0.00018 31.5 1.8 28 274-312 23-50 (112)
111 PRK11032 hypothetical protein; 54.7 6.2 0.00014 34.2 1.1 30 272-311 122-151 (160)
112 PF13248 zf-ribbon_3: zinc-rib 54.2 5.4 0.00012 23.7 0.5 23 275-311 3-25 (26)
113 TIGR00467 lysS_arch lysyl-tRNA 53.9 12 0.00025 38.6 3.1 32 274-311 168-199 (515)
114 PF15135 UPF0515: Uncharacteri 53.8 9.3 0.0002 35.4 2.2 13 301-313 154-166 (278)
115 PF06290 PsiB: Plasmid SOS inh 53.7 16 0.00036 30.9 3.4 76 227-306 3-79 (143)
116 TIGR01031 rpmF_bact ribosomal 53.4 12 0.00025 26.6 2.2 24 272-310 24-47 (55)
117 PF02701 zf-Dof: Dof domain, z 52.9 5.7 0.00012 28.9 0.5 38 273-313 4-41 (63)
118 PF02150 RNA_POL_M_15KD: RNA p 52.8 10 0.00022 24.3 1.6 28 276-312 3-30 (35)
119 TIGR02605 CxxC_CxxC_SSSS putat 52.8 8.6 0.00019 26.3 1.4 30 274-310 5-34 (52)
120 TIGR01562 FdhE formate dehydro 52.7 17 0.00038 34.8 3.9 40 273-313 223-263 (305)
121 COG2023 RPR2 RNase P subunit R 52.4 9 0.00019 30.9 1.6 37 274-314 56-94 (105)
122 COG4332 Uncharacterized protei 52.0 8.2 0.00018 34.1 1.4 16 299-314 46-61 (203)
123 PF01780 Ribosomal_L37ae: Ribo 51.6 13 0.00029 29.2 2.4 30 273-312 34-63 (90)
124 PTZ00255 60S ribosomal protein 51.3 36 0.00079 26.7 4.8 31 272-312 34-64 (90)
125 PF14726 RTTN_N: Rotatin, an a 51.0 14 0.00031 29.3 2.6 52 27-78 45-96 (98)
126 PF04194 PDCD2_C: Programmed c 50.5 14 0.0003 32.0 2.6 35 274-308 97-145 (164)
127 PRK03976 rpl37ae 50S ribosomal 50.5 37 0.00081 26.6 4.7 30 273-312 35-64 (90)
128 PF09332 Mcm10: Mcm10 replicat 50.3 5.9 0.00013 38.6 0.3 13 299-311 282-294 (344)
129 COG1656 Uncharacterized conser 50.2 6.8 0.00015 34.1 0.7 40 271-311 94-139 (165)
130 KOG1886 BAH domain proteins [T 50.2 8.1 0.00017 38.9 1.3 103 139-243 238-343 (464)
131 CHL00174 accD acetyl-CoA carbo 49.5 3.4 7.3E-05 39.4 -1.4 31 274-313 38-68 (296)
132 KOG2767 Translation initiation 49.2 6.7 0.00015 38.1 0.5 32 275-312 97-128 (400)
133 PRK13701 psiB plasmid SOS inhi 47.7 59 0.0013 27.5 5.8 29 227-257 3-31 (144)
134 KOG2462 C2H2-type Zn-finger pr 47.2 11 0.00023 35.6 1.5 39 272-312 128-171 (279)
135 PF07295 DUF1451: Protein of u 47.1 20 0.00043 30.7 3.0 31 271-311 109-139 (146)
136 PRK12380 hydrogenase nickel in 46.5 9.6 0.00021 31.0 1.0 28 271-310 67-94 (113)
137 TIGR00100 hypA hydrogenase nic 46.3 11 0.00025 30.6 1.4 28 271-310 67-94 (115)
138 PF01927 Mut7-C: Mut7-C RNAse 45.3 17 0.00037 30.7 2.4 40 272-311 89-133 (147)
139 COG5349 Uncharacterized protei 44.6 8.2 0.00018 31.9 0.3 11 275-285 22-32 (126)
140 PF00684 DnaJ_CXXCXGXG: DnaJ c 44.4 50 0.0011 23.9 4.5 36 272-309 13-48 (66)
141 TIGR03831 YgiT_finger YgiT-typ 44.2 24 0.00052 23.0 2.5 10 303-312 33-42 (46)
142 TIGR02159 PA_CoA_Oxy4 phenylac 44.1 14 0.00029 31.6 1.6 36 274-312 105-140 (146)
143 PF14205 Cys_rich_KTR: Cystein 43.7 19 0.00041 25.6 1.9 34 273-310 3-36 (55)
144 TIGR01051 topA_bact DNA topois 43.5 46 0.00099 34.9 5.7 15 222-236 535-549 (610)
145 COG1571 Predicted DNA-binding 43.1 12 0.00026 37.4 1.2 30 273-313 349-378 (421)
146 COG5415 Predicted integral mem 43.1 12 0.00027 33.8 1.2 34 271-310 189-222 (251)
147 PF09297 zf-NADH-PPase: NADH p 42.9 18 0.0004 22.3 1.7 26 276-311 5-30 (32)
148 TIGR00354 polC DNA polymerase, 42.7 13 0.00028 40.7 1.4 23 273-311 624-646 (1095)
149 PF05605 zf-Di19: Drought indu 42.7 5.5 0.00012 27.7 -0.9 36 274-312 2-41 (54)
150 PF10080 DUF2318: Predicted me 42.6 20 0.00044 28.7 2.2 28 275-313 36-63 (102)
151 PRK08173 DNA topoisomerase III 42.1 45 0.00098 36.5 5.5 15 222-236 581-595 (862)
152 PRK03954 ribonuclease P protei 41.8 27 0.0006 28.9 3.0 37 274-314 64-105 (121)
153 PRK07219 DNA topoisomerase I; 40.8 45 0.00097 36.3 5.3 18 221-238 549-566 (822)
154 PF13408 Zn_ribbon_recom: Reco 40.5 38 0.00083 23.2 3.2 30 272-308 3-32 (58)
155 KOG3286 Selenoprotein T [Gener 40.2 17 0.00037 32.7 1.6 33 280-312 46-84 (226)
156 PRK03564 formate dehydrogenase 40.2 33 0.00072 33.0 3.7 38 273-313 225-263 (309)
157 COG3529 Predicted nucleic-acid 39.8 7.5 0.00016 28.2 -0.5 32 274-311 10-41 (66)
158 PF14122 YokU: YokU-like prote 39.7 21 0.00046 27.7 1.9 37 276-312 1-45 (87)
159 COG2816 NPY1 NTP pyrophosphohy 37.6 23 0.00049 33.5 2.1 31 271-312 109-139 (279)
160 KOG2593 Transcription initiati 37.3 14 0.0003 36.9 0.6 38 270-310 124-161 (436)
161 PF09332 Mcm10: Mcm10 replicat 37.2 9 0.00019 37.3 -0.7 30 273-312 284-314 (344)
162 PRK13130 H/ACA RNA-protein com 36.4 23 0.00051 25.3 1.5 9 274-282 5-13 (56)
163 PF15616 TerY-C: TerY-C metal 36.2 23 0.0005 29.7 1.7 11 275-285 78-88 (131)
164 cd00729 rubredoxin_SM Rubredox 36.2 20 0.00044 22.7 1.1 11 302-312 2-12 (34)
165 PRK04023 DNA polymerase II lar 35.9 22 0.00048 39.2 1.9 14 66-79 246-259 (1121)
166 KOG2879 Predicted E3 ubiquitin 35.8 22 0.00048 33.5 1.7 21 271-291 236-256 (298)
167 PRK03681 hypA hydrogenase nick 35.5 18 0.00038 29.5 0.9 29 271-310 67-95 (114)
168 PF00096 zf-C2H2: Zinc finger, 35.0 20 0.00043 19.9 0.8 10 303-312 1-10 (23)
169 PRK14715 DNA polymerase II lar 34.5 21 0.00046 40.5 1.5 23 274-312 674-696 (1627)
170 PRK00564 hypA hydrogenase nick 34.2 15 0.00032 30.0 0.3 28 272-310 69-96 (117)
171 cd00974 DSRD Desulforedoxin (D 34.2 25 0.00054 22.0 1.3 12 300-311 2-13 (34)
172 PF06573 Churchill: Churchill 34.1 34 0.00074 27.7 2.3 38 274-311 27-67 (112)
173 PRK00750 lysK lysyl-tRNA synth 34.0 41 0.00088 34.5 3.4 35 274-312 175-209 (510)
174 PRK08665 ribonucleotide-diphos 33.7 19 0.00041 38.7 1.1 25 275-311 725-749 (752)
175 PF05207 zf-CSL: CSL zinc fing 33.7 20 0.00044 25.3 0.9 33 273-311 17-49 (55)
176 KOG2907 RNA polymerase I trans 33.5 26 0.00056 28.7 1.5 24 263-286 91-114 (116)
177 TIGR00319 desulf_FeS4 desulfof 33.3 27 0.00059 21.8 1.3 12 300-311 5-16 (34)
178 PF06397 Desulfoferrod_N: Desu 33.2 26 0.00057 22.7 1.2 13 299-311 3-15 (36)
179 PF03589 Antiterm: Antitermina 32.6 13 0.00027 29.4 -0.4 36 275-311 6-41 (95)
180 PRK14714 DNA polymerase II lar 32.4 28 0.0006 39.4 2.0 14 66-79 248-261 (1337)
181 PRK05582 DNA topoisomerase I; 32.4 98 0.0021 32.7 6.1 16 222-237 529-544 (650)
182 PF14949 ARF7EP_C: ARF7 effect 32.3 21 0.00045 28.8 0.8 13 274-286 74-86 (103)
183 PRK06599 DNA topoisomerase I; 32.1 88 0.0019 33.2 5.7 15 222-236 543-557 (675)
184 PF03966 Trm112p: Trm112p-like 31.5 35 0.00076 24.9 1.9 17 297-313 48-64 (68)
185 PF14206 Cys_rich_CPCC: Cystei 31.5 35 0.00077 26.0 1.9 26 275-309 2-27 (78)
186 PF02172 KIX: KIX domain; Int 30.5 1.9E+02 0.004 22.2 5.7 66 141-212 10-75 (81)
187 PF13894 zf-C2H2_4: C2H2-type 30.1 30 0.00065 18.7 1.0 10 303-312 1-10 (24)
188 PRK07726 DNA topoisomerase III 30.0 1.1E+02 0.0024 32.4 6.0 15 222-236 569-583 (658)
189 PF01783 Ribosomal_L32p: Ribos 29.8 11 0.00024 26.7 -1.0 23 273-310 25-47 (56)
190 PRK06319 DNA topoisomerase I/S 29.6 67 0.0014 35.2 4.4 19 221-239 552-570 (860)
191 PHA02540 61 DNA primase; Provi 29.6 53 0.0011 32.0 3.2 34 273-311 26-64 (337)
192 PRK14973 DNA topoisomerase I; 29.6 33 0.00071 37.9 2.0 32 274-311 635-666 (936)
193 COG4391 Uncharacterized protei 29.1 46 0.001 24.2 2.1 16 295-313 44-59 (62)
194 PF06827 zf-FPG_IleRS: Zinc fi 29.0 61 0.0013 19.5 2.4 28 275-310 2-29 (30)
195 PRK04023 DNA polymerase II lar 29.0 30 0.00065 38.3 1.6 11 273-283 637-647 (1121)
196 PF10083 DUF2321: Uncharacteri 28.9 38 0.00083 29.3 1.9 10 302-311 68-77 (158)
197 COG1384 LysS Lysyl-tRNA synthe 28.9 59 0.0013 33.4 3.5 33 273-311 170-203 (521)
198 COG5189 SFP1 Putative transcri 28.5 33 0.00071 33.1 1.6 41 273-313 348-409 (423)
199 PF00320 GATA: GATA zinc finge 28.2 5.9 0.00013 25.4 -2.5 31 277-313 1-31 (36)
200 PF14255 Cys_rich_CPXG: Cystei 27.7 68 0.0015 22.5 2.7 34 275-312 1-34 (52)
201 PF10609 ParA: ParA/MinD ATPas 27.5 19 0.0004 27.7 -0.2 47 234-285 29-76 (81)
202 KOG3214 Uncharacterized Zn rib 27.4 42 0.00091 26.9 1.7 38 272-313 21-58 (109)
203 PF14319 Zn_Tnp_IS91: Transpos 27.2 74 0.0016 25.7 3.2 30 272-311 40-69 (111)
204 COG1198 PriA Primosomal protei 27.0 45 0.00097 35.8 2.4 16 229-244 386-401 (730)
205 KOG2462 C2H2-type Zn-finger pr 26.8 17 0.00037 34.2 -0.6 35 274-312 215-253 (279)
206 KOG3623 Homeobox transcription 26.8 19 0.00041 38.4 -0.4 35 274-312 281-319 (1007)
207 TIGR03829 YokU_near_AblA uncha 26.7 32 0.0007 26.9 1.0 11 302-312 35-45 (89)
208 COG2956 Predicted N-acetylgluc 26.7 46 0.001 32.4 2.2 27 271-312 351-377 (389)
209 smart00099 btg1 tob/btg1 famil 26.3 56 0.0012 26.5 2.3 61 180-242 28-92 (108)
210 PF03833 PolC_DP2: DNA polymer 26.2 22 0.00048 38.5 0.0 37 272-311 653-689 (900)
211 PF12677 DUF3797: Domain of un 26.0 62 0.0013 22.5 2.1 13 274-286 13-25 (49)
212 PF08256 Antimicrobial20: Aure 26.0 56 0.0012 16.5 1.4 9 8-16 2-10 (13)
213 KOG2703 C4-type Zn-finger prot 25.9 48 0.001 33.0 2.2 14 274-287 68-81 (460)
214 cd00350 rubredoxin_like Rubred 25.9 28 0.0006 21.8 0.4 16 273-288 16-31 (33)
215 PF08273 Prim_Zn_Ribbon: Zinc- 25.2 65 0.0014 21.3 2.1 29 275-309 4-33 (40)
216 PRK07220 DNA topoisomerase I; 24.3 73 0.0016 34.3 3.5 32 273-310 634-665 (740)
217 cd03031 GRX_GRX_like Glutaredo 24.1 81 0.0018 26.8 3.1 33 273-310 109-141 (147)
218 PF13465 zf-H2C2_2: Zinc-finge 24.0 40 0.00086 19.7 0.8 7 275-281 15-21 (26)
219 COG0484 DnaJ DnaJ-class molecu 24.0 77 0.0017 31.3 3.3 34 272-309 157-190 (371)
220 PRK11788 tetratricopeptide rep 23.6 53 0.0011 31.1 2.1 22 274-309 354-375 (389)
221 PRK01103 formamidopyrimidine/5 23.5 74 0.0016 29.7 3.0 29 274-310 245-273 (274)
222 PF06107 DUF951: Bacterial pro 23.3 1.1E+02 0.0024 21.9 3.1 14 298-311 27-40 (57)
223 PRK03824 hypA hydrogenase nick 23.3 43 0.00094 28.0 1.2 11 300-310 105-115 (135)
224 PRK11827 hypothetical protein; 23.1 71 0.0015 23.1 2.1 30 274-313 8-37 (60)
225 PRK00241 nudC NADH pyrophospha 22.6 66 0.0014 29.9 2.4 33 269-312 95-127 (256)
226 COG2331 Uncharacterized protei 22.5 16 0.00034 27.8 -1.4 36 270-312 8-43 (82)
227 PRK14284 chaperone protein Dna 22.5 83 0.0018 31.0 3.2 31 273-309 174-204 (391)
228 PRK00762 hypA hydrogenase nick 22.4 36 0.00078 28.1 0.6 31 271-309 67-99 (124)
229 KOG2846 Predicted membrane pro 22.3 43 0.00094 32.3 1.1 33 272-310 218-250 (328)
230 KOG2041 WD40 repeat protein [G 21.9 1.7E+02 0.0037 31.6 5.4 33 274-311 1131-1165(1189)
231 PRK07220 DNA topoisomerase I; 21.9 1.8E+02 0.0039 31.4 5.8 18 221-238 540-557 (740)
232 PF14353 CpXC: CpXC protein 21.8 52 0.0011 26.8 1.4 11 273-283 37-47 (128)
233 PF03833 PolC_DP2: DNA polymer 21.8 30 0.00066 37.5 0.0 15 270-284 663-677 (900)
234 cd00202 ZnF_GATA Zinc finger D 21.7 21 0.00046 25.1 -0.8 32 276-313 1-32 (54)
235 COG3364 Zn-ribbon containing p 21.6 43 0.00094 26.9 0.8 17 274-290 20-36 (112)
236 PRK04860 hypothetical protein; 21.4 29 0.00062 30.1 -0.2 14 300-313 141-154 (160)
237 COG5595 Zn-ribbon-containing, 21.2 42 0.00091 30.2 0.7 35 271-314 215-255 (256)
238 PRK04338 N(2),N(2)-dimethylgua 21.1 43 0.00093 33.0 0.9 29 274-313 244-272 (382)
239 PF01412 ArfGap: Putative GTPa 20.8 43 0.00094 27.0 0.7 30 272-309 11-40 (116)
240 PLN03165 chaperone protein dna 20.7 1.2E+02 0.0027 24.6 3.4 30 275-309 53-82 (111)
241 COG1579 Zn-ribbon protein, pos 20.6 24 0.00053 32.6 -0.9 36 271-310 194-229 (239)
242 PF00301 Rubredoxin: Rubredoxi 20.6 46 0.001 22.8 0.7 16 272-287 32-47 (47)
243 PF07742 BTG: BTG family; Int 20.5 1.1E+02 0.0024 25.0 3.1 63 180-242 28-94 (118)
244 COG3809 Uncharacterized protei 20.5 93 0.002 23.9 2.4 30 275-312 2-31 (88)
245 PRK14724 DNA topoisomerase III 20.5 1.9E+02 0.004 32.4 5.7 15 222-236 600-614 (987)
246 KOG3352 Cytochrome c oxidase, 20.5 85 0.0018 27.0 2.4 31 275-313 112-144 (153)
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-70 Score=514.93 Aligned_cols=291 Identities=37% Similarity=0.595 Sum_probs=236.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHhcCCCCCHHhhhcCcceeecccccCCCCHHHHHHHHHHHHHHHHhhh
Q 035641 6 VTLFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIV 85 (314)
Q Consensus 6 ~el~~~a~k~~~~~~~~~~~~~~~~~~~~~L~~L~~~~~t~~~L~~T~iG~~V~~Lrkh~~~~i~~~Ak~Li~~WK~~~v 85 (314)
.|+..+++++.++++ + .+++.|+++|++|+.++||+++|++|+||++||+||||++++|+.+|+.||+.||+ +|
T Consensus 2 ~ei~~~~k~L~k~~~----~-~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~-~v 75 (299)
T TIGR01385 2 AEVASHAKALDKNKS----S-KNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKK-VV 75 (299)
T ss_pred hHHHHHHHHhhhhcc----C-CCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHH-HH
Confidence 467788888877773 2 47789999999999999999999999999999999999999999999999999999 98
Q ss_pred cccccCCCCCCCCCCCc--ccccccCC--CCCccccCCCCcccccccCCCCCCCCCC--CCCCcHHHHHHHHHHHHHHHh
Q 035641 86 LGKETNGNKRNGSKLSV--DEKFQKQT--SDSNAVKSGCSTAKEKKATASIRKPSHA--DQAKDSMRDKIRKDLEKALSR 159 (314)
Q Consensus 86 ~~~~~~~~~~~~~~~~~--~~~~~~~~--~ss~s~k~~~~~~~~~~~~~~~~~~~~~--~~~~d~~R~k~~~~L~~aL~~ 159 (314)
. .+........++... ..++.+.. +++++.+ ...+..+++++++..++++ +.++|++|++|+++||+||..
T Consensus 76 ~-~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~ 152 (299)
T TIGR01385 76 D-KNKSDHPGGNPEDKTTVGESVNSVKQEAKSQSDK--IEQPKYVSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAK 152 (299)
T ss_pred h-hhcccCcccccccccccCCCCCCCCccccCCccc--ccCCCCCCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhh
Confidence 7 432211100000000 00000000 0000000 0011122233444444544 589999999999999999998
Q ss_pred hhccccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCChhhHhHHHhHHhhcCCCCChhhhhhhhcCCCChhhhhcCCh
Q 035641 160 VASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTP 239 (314)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~~~yk~k~Rsl~~NLkd~~Np~Lr~~vl~G~i~p~~lv~Ms~ 239 (314)
+..+.++ .+++..||.+||.+||..|+.+++.|+++||||+|||||++||+||++|++|+|+|++||.|++
T Consensus 153 ~~~~~~~---------~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~ 223 (299)
T TIGR01385 153 DSDHPPQ---------SIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTA 223 (299)
T ss_pred cCCCCcc---------ccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCH
Confidence 7543322 2467889999999999999988889999999999999999999999999999999999999999
Q ss_pred hhcCcHHHHHHHHHHHHhhhhhhccccccCCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcccC
Q 035641 240 EELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 240 eEmas~e~k~~~~~~~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
+||||++++++++++.+++|++++++....+.|+.|+||+||+++|+|||+|+|+||||||+||+|++|||+|+|
T Consensus 224 eEmas~e~k~~~e~~~ke~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 224 EEMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKF 298 (299)
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeee
Confidence 999999999999999999999999999888999999999999999999999999999999999999999999998
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=6.6e-63 Score=456.55 Aligned_cols=289 Identities=38% Similarity=0.585 Sum_probs=230.9
Q ss_pred HHHHHHHHHHHHHHhcCCCccHHHHHHHHHHhcCCCCCHHhhhcCcceeecc-cccCCCCHHHHHHHHHHHHHHHHhhhc
Q 035641 8 LFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLR-HLKKHPCEKVQNAASELLHIWKQKIVL 86 (314)
Q Consensus 8 l~~~a~k~~~~~~~~~~~~~~~~~~~~~L~~L~~~~~t~~~L~~T~iG~~V~-~Lrkh~~~~i~~~Ak~Li~~WK~~~v~ 86 (314)
+|+.+.++|+.....-++ ++.+.++++|.+|+++|||+++|++|+||+.|| .|++|+|++|.++|+.||+.||+ ++.
T Consensus 2 ~~e~~~r~ak~l~~~~~~-~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk-~~~ 79 (296)
T KOG1105|consen 2 LEEEALRAAKALEKDKQS-KNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKK-LVD 79 (296)
T ss_pred ccHHHHHHHHHHHhhccc-ccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH-Hhh
Confidence 455666666665444355 789999999999999999999999999999999 57789999999999999999999 998
Q ss_pred ccccCCCC----CCCCCCCcccccccCCCCCccccCCCCcccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhhhc
Q 035641 87 GKETNGNK----RNGSKLSVDEKFQKQTSDSNAVKSGCSTAKEKKATASIRKPSHADQAKDSMRDKIRKDLEKALSRVAS 162 (314)
Q Consensus 87 ~~~~~~~~----~~~~~~~~~~~~~~~~~ss~s~k~~~~~~~~~~~~~~~~~~~~~~~~~d~~R~k~~~~L~~aL~~~~~ 162 (314)
+...+.. ..+.|... +.++.+++ ..+ .+.+.+....+.....+.++.++|++|++|++|||.||..+..
T Consensus 80 -~~~~~~k~~~~~~~~p~~~---~~~~~s~~--~~~-~ks~~~~~~~~~~~~~~~~~~~~d~~r~k~~e~l~~al~~~~~ 152 (296)
T KOG1105|consen 80 -KSPGREKSGDNKSHDPGEA---SSKSPSGA--KQP-EKSRGDSKRDKHSGSKDPVPITNDPVRDKCRELLYAALTTEDD 152 (296)
T ss_pred -cccccccCccccCCCCCcC---CcCCccCC--CCc-cccccccccccccCcCCCCCCCCchHHHHHHHHHHHHhccccc
Confidence 3211111 01111100 00000000 000 0000000000111112345677999999999999999985421
Q ss_pred cccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCChhhHhHHHhHHhhcCCCCChhhhhhhhcCCCChhhhhcCChhhc
Q 035641 163 EAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEEL 242 (314)
Q Consensus 163 ~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~~~yk~k~Rsl~~NLkd~~Np~Lr~~vl~G~i~p~~lv~Ms~eEm 242 (314)
++...+++..+|.+||.+||..++.+.++|+++|||++|||+|++||+||++||.|+|+|++|+.|+++||
T Consensus 153 ---------~~~~~~~~~~~a~~iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEM 223 (296)
T KOG1105|consen 153 ---------SRVTGADPLELAVQIEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEM 223 (296)
T ss_pred ---------ccccCCCHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhh
Confidence 22345788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHHHHHHHHHhhhhhhccccccCCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcccC
Q 035641 243 ASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 243 as~e~k~~~~~~~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
||++++++++++.+++|+++|++...+++|+.|.|++|+.++|+|+|+|+||+|||||+|++|..||++|+|
T Consensus 224 aS~~lk~~~~k~~keal~~~q~~~~~gt~td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnrWkf 295 (296)
T KOG1105|consen 224 ASEELKEERQKLTKEALREHQMAKIQGTQTDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNRWKF 295 (296)
T ss_pred ccHHHHHHHHHHHHHHHHHHhhcccccccccceeeccccccceeEEeeccCCCCCCcceeeeecccCCcccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999998
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.95 E-value=2.5e-28 Score=195.79 Aligned_cols=101 Identities=47% Similarity=0.682 Sum_probs=92.0
Q ss_pred cHHHHHHHHHHHHHHHhhhccccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCChhhHhHHHhHHhhcCCCCChhhhh
Q 035641 143 DSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRR 222 (314)
Q Consensus 143 d~~R~k~~~~L~~aL~~~~~~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~~~yk~k~Rsl~~NLkd~~Np~Lr~ 222 (314)
|++|++|+++|+++|..+....+. ..++..+|.+||.+||..|+..++.|++|+|||+|||||++||+||.
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~~---------~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~ 71 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEEI---------ELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRR 71 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCcc---------cccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHH
Confidence 689999999999999988654332 23577899999999999999888899999999999999999999999
Q ss_pred hhhcCCCChhhhhcCChhhcCcHHHHHHHH
Q 035641 223 RVLIGEVTPERLATMTPEELASDERRQENE 252 (314)
Q Consensus 223 ~vl~G~i~p~~lv~Ms~eEmas~e~k~~~~ 252 (314)
+|++|+|+|++||.||++||||++++++++
T Consensus 72 ~vl~G~i~p~~lv~Ms~~ElAs~elk~~~e 101 (102)
T smart00510 72 KVLNGEITPEKLATMTAEELASAELKEKRE 101 (102)
T ss_pred HHHcCCCCHHHHhcCCHHHcCCHHHHHHHh
Confidence 999999999999999999999999999875
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=99.94 E-value=2.5e-27 Score=194.17 Aligned_cols=115 Identities=46% Similarity=0.738 Sum_probs=104.0
Q ss_pred CCcHHHHHHHHHHHHHHHhhhccccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCChhhHhHHHhHHhhcCCCCChhh
Q 035641 141 AKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDL 220 (314)
Q Consensus 141 ~~d~~R~k~~~~L~~aL~~~~~~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~~~yk~k~Rsl~~NLkd~~Np~L 220 (314)
|++++|++++++|+++|.....+ .+. ..++..+|.+||.+||..|+.....|++++|+|+|||||++||+|
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~~--------~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L 71 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QDD--------PEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDL 71 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CCC--------TCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCH
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-ccc--------hhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHH
Confidence 57899999999999999988654 221 245679999999999999988788999999999999999999999
Q ss_pred hhhhhcCCCChhhhhcCChhhcCcHHHHHHHHHHHHhhhhhhcc
Q 035641 221 RRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEV 264 (314)
Q Consensus 221 r~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~~~~~~~~l~~~~~ 264 (314)
+.+|++|+|+|.+||.|+++||||++++++++++.++++.++|+
T Consensus 72 ~~~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~~~l~~~~~ 115 (115)
T PF07500_consen 72 RRRILSGEISPEELVTMSPEELASEELKEEREKIRKESLKQSQM 115 (115)
T ss_dssp HHHHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHHHHHHHTB-
T ss_pred HHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999998774
No 5
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.80 E-value=3.7e-20 Score=123.70 Aligned_cols=39 Identities=46% Similarity=1.098 Sum_probs=37.9
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
++||+||+++++|||+|+||||||||+||+|.+|||+|+
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 479999999999999999999999999999999999997
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=99.79 E-value=7.9e-20 Score=121.51 Aligned_cols=39 Identities=49% Similarity=1.128 Sum_probs=35.1
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
++||+||+++++|+|+|+||||||||+||+|.+|||+|+
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 579999999999999999999999999999999999996
No 7
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.72 E-value=4.4e-18 Score=129.20 Aligned_cols=74 Identities=42% Similarity=0.701 Sum_probs=68.4
Q ss_pred HHHHHHHHHHHHHHhcCCCccHHHHHHHHHHhcCCCCCHHhhhcCcceeecccccCCCCHHHHHHHHHHHHHHHHhhhc
Q 035641 8 LFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIVL 86 (314)
Q Consensus 8 l~~~a~k~~~~~~~~~~~~~~~~~~~~~L~~L~~~~~t~~~L~~T~iG~~V~~Lrkh~~~~i~~~Ak~Li~~WK~~~v~ 86 (314)
||+++++++++++. + ++++.|+++|+.|+.++||.++|++|+||++||.||+|++++|+.+|+.||+.||+ +++
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-KEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKK-LVY 74 (75)
T ss_pred ChHHHHHHHHHhcC---C-CCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHH-Hhc
Confidence 58899999999832 2 46889999999999999999999999999999999999999999999999999999 875
No 8
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=99.72 E-value=1e-18 Score=135.69 Aligned_cols=43 Identities=44% Similarity=0.998 Sum_probs=40.6
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
+.+..+||+||+.+++|+|+|+||||||||+||.|++|+|+||
T Consensus 62 ~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 62 DQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 3456899999999999999999999999999999999999997
No 9
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.67 E-value=4.1e-17 Score=133.11 Aligned_cols=43 Identities=47% Similarity=0.933 Sum_probs=40.8
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcccC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
+..+.||+||+++++|||+|+||||||||+||+|..|||+|++
T Consensus 70 ~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 70 TAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 3478999999999999999999999999999999999999985
No 10
>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=99.65 E-value=9.6e-17 Score=129.12 Aligned_cols=43 Identities=37% Similarity=0.876 Sum_probs=40.8
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
+++...||+||+++++|+|+|+||||||||+||+|++|||+|+
T Consensus 59 ~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 59 PTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred CcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 4557999999999999999999999999999999999999997
No 11
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.61 E-value=4.3e-16 Score=133.64 Aligned_cols=41 Identities=34% Similarity=0.641 Sum_probs=39.6
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
...+||+||+++++|+|+|+||||||||+||.|..|||+|+
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 56899999999999999999999999999999999999996
No 12
>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=99.60 E-value=1.3e-15 Score=115.97 Aligned_cols=73 Identities=34% Similarity=0.598 Sum_probs=63.1
Q ss_pred HHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHhcCCCCCHHhhhcCcceeecccccCCCCHHHHHHHHHHHHHHHHhhh
Q 035641 7 TLFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIV 85 (314)
Q Consensus 7 el~~~a~k~~~~~~~~~~~~~~~~~~~~~L~~L~~~~~t~~~L~~T~iG~~V~~Lrkh~~~~i~~~Ak~Li~~WK~~~v 85 (314)
|+..+.+++.++. ++ ++.+.|+++|+.|+.+|||.++|++|+||+.||+||+|++++|+.+|+.||+.||+ ++
T Consensus 3 ev~r~~~~l~~~~----~~-~~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~-~v 75 (76)
T cd00183 3 EVLRAKKKLEKKD----SN-EEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKK-LV 75 (76)
T ss_pred HHHHHHHHhhccc----cC-CCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHH-hc
Confidence 3445555555444 22 58899999999999999999999999999999999999999999999999999999 76
No 13
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=99.54 E-value=3.9e-15 Score=117.68 Aligned_cols=48 Identities=33% Similarity=0.729 Sum_probs=43.5
Q ss_pred cccCCC-ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 266 EKKKGT-TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 266 ~~~~~~-t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.++..+ |....||+||+++++|||.|+|.+|+.|++||+|++|||+|+
T Consensus 64 ~DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 64 SDPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred cCCCcCccccccCCccCCcceEEEecccccccceEEEEEEecccccccc
Confidence 455544 578999999999999999999999999999999999999996
No 14
>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=99.36 E-value=2.9e-13 Score=95.88 Aligned_cols=52 Identities=40% Similarity=0.693 Sum_probs=47.1
Q ss_pred HHHHHhcCCCCCHHhhhcCcceeecccccCC-CCHHHHHHHHHHHHHHHHhhhc
Q 035641 34 DALKHLQAFPVTYDLLVSTQVGKSLRHLKKH-PCEKVQNAASELLHIWKQKIVL 86 (314)
Q Consensus 34 ~~L~~L~~~~~t~~~L~~T~iG~~V~~Lrkh-~~~~i~~~Ak~Li~~WK~~~v~ 86 (314)
++|+.|..+|||.++|++|+||++|+.|+|| .+++|+.+|+.|+++||+ +++
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~-~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKR-IVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHH-HH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhH-hcC
Confidence 5799999999999999999999999999999 899999999999999999 763
No 15
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.32 E-value=1.3e-12 Score=134.21 Aligned_cols=83 Identities=37% Similarity=0.576 Sum_probs=75.4
Q ss_pred CChHHHHHHHHHHHHHhhc-CCChhhHhHHHhHHhhcCCCCChhhhhhhhcCCCChhhhhcCChhhcCcHHHHHHHHHHH
Q 035641 177 RDPKQVAASVERVMFEKLR-PMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIK 255 (314)
Q Consensus 177 ~d~~~lA~~IE~alf~~~~-~~~~~yk~k~Rsl~~NLkd~~Np~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~~~~~ 255 (314)
.++..++..||..+|..|| +-+..|+.|+|+|+|||||++||.||.+|..|+|+|++||.|+++|||+.++...+++..
T Consensus 267 ~d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rEek~ 346 (778)
T KOG1634|consen 267 QDPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWREEKA 346 (778)
T ss_pred cchhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHHHHH
Confidence 4566788899999999999 667889999999999999999999999999999999999999999999999998887776
Q ss_pred Hhhh
Q 035641 256 AKFM 259 (314)
Q Consensus 256 ~~~l 259 (314)
++..
T Consensus 347 ee~~ 350 (778)
T KOG1634|consen 347 EEMN 350 (778)
T ss_pred HHHH
Confidence 6544
No 16
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=99.26 E-value=1.5e-12 Score=104.05 Aligned_cols=45 Identities=40% Similarity=0.829 Sum_probs=41.6
Q ss_pred CCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 269 KGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 269 ~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.+.+....||+|||.++.|..+|+|||||+.|+||+|.+|+|+++
T Consensus 69 ~ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 69 DGAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred cccchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 345778899999999999999999999999999999999999875
No 17
>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=96.64 E-value=0.0038 Score=50.47 Aligned_cols=78 Identities=26% Similarity=0.483 Sum_probs=55.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHhcCCCCCHHhhhcC-cceeecccccCCC-CHHHHHHHHHHHHH
Q 035641 2 EKKLVTLFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVST-QVGKSLRHLKKHP-CEKVQNAASELLHI 79 (314)
Q Consensus 2 ~~~~~el~~~a~k~~~~~~~~~~~~~~~~~~~~~L~~L~~~~~t~~~L~~T-~iG~~V~~Lrkh~-~~~i~~~Ak~Li~~ 79 (314)
|+.|++|..--|-+ ...+. +++..|+++|..|..++||..+|+.- .+--++.+||+.. +..|...|..|+.+
T Consensus 1 E~~L~~l~~~Ik~~-----L~~~~-~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnk 74 (106)
T PF11467_consen 1 ERRLQELHSEIKSS-----LKVDN-PDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNK 74 (106)
T ss_dssp HHHHHHHHHHHHHT-----CETTE-E-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHH-----HcCCC-CCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence 45566665444221 11233 79999999999999999999877754 4778889999985 88999999999999
Q ss_pred HHHhhhc
Q 035641 80 WKQKIVL 86 (314)
Q Consensus 80 WK~~~v~ 86 (314)
.|. ++.
T Consensus 75 fK~-~f~ 80 (106)
T PF11467_consen 75 FKS-LFL 80 (106)
T ss_dssp HHH-HHH
T ss_pred HHH-HhC
Confidence 999 874
No 18
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.88 E-value=0.01 Score=57.74 Aligned_cols=53 Identities=23% Similarity=0.464 Sum_probs=47.7
Q ss_pred HHHHHHhcCCCCCH-HhhhcCcceeecccccCCC--CHHHHHHHHHHHHHHHHhhhc
Q 035641 33 ADALKHLQAFPVTY-DLLVSTQVGKSLRHLKKHP--CEKVQNAASELLHIWKQKIVL 86 (314)
Q Consensus 33 ~~~L~~L~~~~~t~-~~L~~T~iG~~V~~Lrkh~--~~~i~~~Ak~Li~~WK~~~v~ 86 (314)
..+|..|..+||-. +.|...+||++|=.|.||+ ...++.+|..||..|-. .+.
T Consensus 236 ~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsR-pI~ 291 (417)
T KOG1793|consen 236 KSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSR-PIF 291 (417)
T ss_pred HHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhc-ccc
Confidence 45677888899988 9999999999999999997 57799999999999999 776
No 19
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=95.79 E-value=0.0026 Score=39.72 Aligned_cols=28 Identities=29% Similarity=0.711 Sum_probs=14.9
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
-+||.|+...++. ....|+|..|+|.|.
T Consensus 3 p~Cp~C~se~~y~-----------D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTYE-----------DGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----EE------------SSSEEETTTTEEE-
T ss_pred CCCCCCCCcceec-----------cCCEEeCCcccccCC
Confidence 4799999988761 334689999999994
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=95.61 E-value=0.015 Score=42.69 Aligned_cols=37 Identities=24% Similarity=0.641 Sum_probs=25.1
Q ss_pred eecCCCCCCceEEEeeeccCC------C--CCCeEEEEcCCCCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSA------D--EPMTTYVTCAECNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsa------d--e~mt~f~~C~~C~~~ 311 (314)
+.||+||+++...-+++.--. | ...-+.++|.+|||.
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 479999999877665543211 1 123467899999986
No 21
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=95.33 E-value=0.0047 Score=60.94 Aligned_cols=57 Identities=30% Similarity=0.533 Sum_probs=54.2
Q ss_pred ccHHHHHHHHHHhcCCCCCHHhhhcCcceeecccccCCCCHHHHHHHHHHHHHHHHhhhc
Q 035641 27 PEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIVL 86 (314)
Q Consensus 27 ~~~~~~~~~L~~L~~~~~t~~~L~~T~iG~~V~~Lrkh~~~~i~~~Ak~Li~~WK~~~v~ 86 (314)
.++.+.+..|..|..+|++++.|.+|.||++|+.|++|. .|..+|..|+..||+ ++.
T Consensus 22 ~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~-~v~ 78 (433)
T KOG2821|consen 22 IDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKD-LVL 78 (433)
T ss_pred ccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHH-hcc
Confidence 578999999999999999999999999999999999998 689999999999999 886
No 22
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=95.08 E-value=0.02 Score=43.12 Aligned_cols=37 Identities=19% Similarity=0.569 Sum_probs=25.8
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCC-eEEEEcC--CCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPM-TTYVTCA--ECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~m-t~f~~C~--~C~~~w~ 313 (314)
++.||.||+.--+ .. +|..++.. -.++.|. +|||+|+
T Consensus 1 mm~CP~Cg~~a~i-rt--Sr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 1 MFHCPLCQHAAHA-RT--SRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred CccCCCCCCccEE-EE--ChhcChhhheeeeecCCCCCCCEEE
Confidence 4789999998733 22 23333333 4899998 8999985
No 23
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.04 E-value=0.016 Score=37.58 Aligned_cols=32 Identities=25% Similarity=0.609 Sum_probs=22.6
Q ss_pred ceecCCCCCCceEEEeeeccCCCC---CCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADE---PMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade---~mt~f~~C~~C~~~w~ 313 (314)
.+.||+|+..-. + .|+ +-..-+.|.+|||.|+
T Consensus 2 ~i~Cp~C~~~y~----i----~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 2 IITCPNCQAKYE----I----DDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EEECCCCCCEEe----C----CHHHCCCCCcEEECCCCCCEeC
Confidence 378999986422 2 333 3446799999999995
No 24
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.60 E-value=0.024 Score=36.99 Aligned_cols=33 Identities=18% Similarity=0.566 Sum_probs=22.6
Q ss_pred ceecCCCCCCceEEEeeeccCCCC---CCeEEEEcCCCCCcccC
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADE---PMTTYVTCAECNKRWKC 314 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade---~mt~f~~C~~C~~~w~~ 314 (314)
.+.||.|+..- .+ .|+ +-..-+.|..|+|.|.|
T Consensus 2 ~i~CP~C~~~f----~v----~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 2 IITCPNCQTRF----RV----PDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EEECCCCCceE----Ec----CHHHcccCCcEEECCCCCcEeeC
Confidence 36899998632 22 222 22358999999999986
No 25
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=94.57 E-value=0.05 Score=51.18 Aligned_cols=53 Identities=21% Similarity=0.425 Sum_probs=45.6
Q ss_pred HHHHHHhcCCCCCHHhhhcCcceeecccccC--CCCHHHHHHHHHHHHHHHHhhhc
Q 035641 33 ADALKHLQAFPVTYDLLVSTQVGKSLRHLKK--HPCEKVQNAASELLHIWKQKIVL 86 (314)
Q Consensus 33 ~~~L~~L~~~~~t~~~L~~T~iG~~V~~Lrk--h~~~~i~~~Ak~Li~~WK~~~v~ 86 (314)
-.+|..|..+||-.+.|.+.+||+.|-..+. ...+.|+.+|+.||..|-. -+-
T Consensus 233 ksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtr-pIi 287 (397)
T COG5139 233 KSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTR-PII 287 (397)
T ss_pred HHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhc-ccc
Confidence 4567778889999999999999999988654 5688999999999999999 554
No 26
>PHA00626 hypothetical protein
Probab=94.57 E-value=0.026 Score=40.12 Aligned_cols=33 Identities=21% Similarity=0.496 Sum_probs=21.6
Q ss_pred ecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 276 KCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 276 ~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.||+||+.+.+-- -.-| ....-|.|..||+.|.
T Consensus 2 ~CP~CGS~~Ivrc-g~cr----~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKE-KTMR----GWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeee-ceec----ccCcceEcCCCCCeec
Confidence 5999999876521 1111 1134699999999874
No 27
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=94.51 E-value=0.032 Score=36.25 Aligned_cols=35 Identities=20% Similarity=0.610 Sum_probs=22.7
Q ss_pred ceecCCCCCCceEEEeeecc-CCCCCCeEEEEcCCCCCcccC
Q 035641 274 QFKCSGCGKSNCSYHQMQTR-SADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~r-sade~mt~f~~C~~C~~~w~~ 314 (314)
.+.||.|+.. |.++.. -.+.+ ..+.|.+||+.|.+
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 3789999975 223321 12223 37899999999963
No 28
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=94.12 E-value=0.039 Score=40.30 Aligned_cols=36 Identities=25% Similarity=0.697 Sum_probs=23.5
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCe----------EEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMT----------TYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt----------~f~~C~~C~~~ 311 (314)
.++||+||+++..--+++. ..+... +-++|.+||++
T Consensus 4 ~~kCpKCgn~~~~ekei~~--tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAA--TGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred cccCCCcCCcchhhceeec--cCCCcceeEEecccEEEEEEeccCCch
Confidence 4679999998765544432 323322 34689999985
No 29
>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=94.03 E-value=0.042 Score=36.90 Aligned_cols=28 Identities=25% Similarity=0.692 Sum_probs=20.5
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
+.||.||+.. .++. +++-.++|..||.-
T Consensus 1 m~Cp~Cg~~~-~~~D--------~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFD--------PERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSE-EEEE--------TTTTEEEETTT-BB
T ss_pred CCCcCCcCCc-eEEc--------CCCCeEECCCCCCE
Confidence 5799999988 4443 35668899999963
No 30
>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=93.98 E-value=0.053 Score=37.21 Aligned_cols=36 Identities=19% Similarity=0.506 Sum_probs=23.1
Q ss_pred ecCCCCCCceEEEeeeccCCCCCCeEEEEcCC--CCCccc
Q 035641 276 KCSGCGKSNCSYHQMQTRSADEPMTTYVTCAE--CNKRWK 313 (314)
Q Consensus 276 ~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~--C~~~w~ 313 (314)
.||.||.+-....-.+. .+.--..+|.|.+ |||+|.
T Consensus 1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQL--SPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhh--CcceEEEEEEECCCcCCCEEE
Confidence 49999987654321111 1122238999998 999985
No 31
>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=93.96 E-value=0.05 Score=37.08 Aligned_cols=28 Identities=25% Similarity=0.637 Sum_probs=21.1
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
+.||+||+.+.+.... ...|.|..|+++
T Consensus 19 ~~CP~Cg~~~~~~~~~---------~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT---------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCC---------CCeEECCCCCCc
Confidence 8899999995443321 567999999975
No 32
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=92.79 E-value=0.12 Score=41.06 Aligned_cols=38 Identities=18% Similarity=0.532 Sum_probs=28.9
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
...|.||.||+...+.-.+- -..+.-+.+|-+||.++-
T Consensus 20 ~k~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEE
Confidence 34599999999998754432 224778999999998864
No 33
>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=91.79 E-value=0.11 Score=44.99 Aligned_cols=32 Identities=22% Similarity=0.462 Sum_probs=21.7
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
....|.||.|+.+ | +-+|.|..-|+|..||..
T Consensus 106 ~~~~Y~Cp~c~~r---~------tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVR---F------TFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcE---e------eHHHHHHcCCcCCCCCCE
Confidence 4556789988832 2 245566778889999863
No 34
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=91.31 E-value=0.14 Score=37.61 Aligned_cols=29 Identities=31% Similarity=0.780 Sum_probs=23.4
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
..+||.||+..++|--.| +.+.|..||..
T Consensus 19 ~VkCpdC~N~q~vFshas---------t~V~C~~CG~~ 47 (67)
T COG2051 19 RVKCPDCGNEQVVFSHAS---------TVVTCLICGTT 47 (67)
T ss_pred EEECCCCCCEEEEeccCc---------eEEEecccccE
Confidence 469999999999996544 45999999863
No 35
>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=90.48 E-value=0.21 Score=32.43 Aligned_cols=27 Identities=22% Similarity=0.737 Sum_probs=20.6
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.++|+.|+.. +|. .+++ ||.|..|||.
T Consensus 8 ~~~C~~C~~~---~~~-----~~dG---~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFY-----SDDG---FYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeE-----ccCC---EEEhhhCceE
Confidence 3679999998 333 4555 8999999985
No 36
>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=90.25 E-value=0.22 Score=51.40 Aligned_cols=38 Identities=18% Similarity=0.468 Sum_probs=27.7
Q ss_pred eecCCCCCCceEEE-eeeccCCC-CCCeEEEEcCCCCCccc
Q 035641 275 FKCSGCGKSNCSYH-QMQTRSAD-EPMTTYVTCAECNKRWK 313 (314)
Q Consensus 275 ~~C~~C~~~~~~~~-q~q~rsad-e~mt~f~~C~~C~~~w~ 313 (314)
.+||.||+.-..-| +++- ..+ .|.+..|+|..||+.|.
T Consensus 201 vpCPhCg~~~~l~~~~l~w-~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKW-DKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred ccCCCCCCCccccccceee-cCCCCccceEEECCCCcCCCC
Confidence 59999998765432 3433 222 68899999999999874
No 37
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.90 E-value=0.32 Score=33.50 Aligned_cols=29 Identities=17% Similarity=0.501 Sum_probs=17.8
Q ss_pred cCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 277 CSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 277 C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
||.||+- .|. + .++. ..+++|..||+.|+
T Consensus 3 Cp~Cg~~--l~~----~-~~~~-~~~~vC~~Cg~~~~ 31 (52)
T smart00661 3 CPKCGNM--LIP----K-EGKE-KRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCc--ccc----c-cCCC-CCEEECCcCCCeEE
Confidence 9999882 121 1 1111 23788999998765
No 38
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.38 E-value=0.27 Score=41.83 Aligned_cols=37 Identities=22% Similarity=0.606 Sum_probs=21.7
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
....+.||.||.. -+|...+. -.| ++..|+|..||..
T Consensus 96 ~~~~Y~Cp~C~~~-y~~~ea~~-~~d--~~~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCPNCQSK-YTFLEANQ-LLD--MDGTFTCPRCGEE 132 (147)
T ss_pred CCcEEECcCCCCE-eeHHHHHH-hcC--CCCcEECCCCCCE
Confidence 4557999999842 22222211 112 2444999999974
No 39
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=89.19 E-value=0.52 Score=33.65 Aligned_cols=36 Identities=28% Similarity=0.565 Sum_probs=24.2
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
...+||-||.....+.+.- .-+..+..++.|..||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~--~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDE--GFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeeccc--CCCCCCEEEEEcCCCCC
Confidence 3578999977777665532 22333447888999986
No 40
>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=88.90 E-value=0.66 Score=32.49 Aligned_cols=34 Identities=18% Similarity=0.466 Sum_probs=21.9
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.+||-||+....+. . +..+-.-.-+|.|..||..
T Consensus 2 kPCPfCGg~~~~~~-~--~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLR-R--GFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeE-e--ccCCCCCEEEEECCCCCCC
Confidence 58999999666442 1 1223334455689999975
No 41
>PLN00209 ribosomal protein S27; Provisional
Probab=88.87 E-value=0.46 Score=36.79 Aligned_cols=58 Identities=22% Similarity=0.380 Sum_probs=35.5
Q ss_pred hhcCcHHHHHHHHHHHHhhhhhhccccccCCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 240 EELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 240 eEmas~e~k~~~~~~~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.||..+....|..+...+.|- +.+..-=-..+||.|++..++|-..|+ -+.|..||..
T Consensus 7 ~DLl~P~~~~e~~khK~k~Lv-----~~PnS~Fm~VkCp~C~n~q~VFShA~t---------~V~C~~Cg~~ 64 (86)
T PLN00209 7 IDLLNPPAELEKRKHKLKRLV-----QSPNSFFMDVKCQGCFNITTVFSHSQT---------VVVCGSCQTV 64 (86)
T ss_pred hhccCCCHHHHHhhhhceeee-----cCCCCEEEEEECCCCCCeeEEEecCce---------EEEccccCCE
Confidence 355555444444443333221 223332345799999999999976654 6899999864
No 42
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=88.47 E-value=0.51 Score=36.46 Aligned_cols=31 Identities=29% Similarity=0.698 Sum_probs=25.1
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
=-+.+||.|++..++|-..|+ -+.|..||..
T Consensus 33 Fm~VkCp~C~n~q~VFShA~t---------~V~C~~Cg~~ 63 (85)
T PTZ00083 33 FMDVKCPGCSQITTVFSHAQT---------VVLCGGCSSQ 63 (85)
T ss_pred EEEEECCCCCCeeEEEecCce---------EEEccccCCE
Confidence 345799999999999977654 5899999864
No 43
>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=88.36 E-value=0.41 Score=35.94 Aligned_cols=33 Identities=21% Similarity=0.438 Sum_probs=22.7
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
...||+|+.-....+ ..-+ + .-++.|+.|||+-
T Consensus 8 Ga~CP~C~~~D~i~~----~~e~-~-ve~vECV~CGy~e 40 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMM----WREN-G-VEYVECVECGYTE 40 (71)
T ss_pred CccCCCCcCccEEEE----EEeC-C-ceEEEecCCCCee
Confidence 468999998775432 1111 2 6689999999963
No 44
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=87.53 E-value=0.28 Score=43.23 Aligned_cols=33 Identities=24% Similarity=0.447 Sum_probs=24.7
Q ss_pred CCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 270 GTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 270 ~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.....|.||.||.+-. .+|.|...|.|..||..
T Consensus 113 ~~~~~Y~Cp~C~~ryt---------f~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 113 ENNMFFFCPNCHIRFT---------FDEAMEYGFRCPQCGEM 145 (178)
T ss_pred cCCCEEECCCCCcEEe---------HHHHhhcCCcCCCCCCC
Confidence 3456799999994322 45678889999999964
No 45
>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=87.46 E-value=0.64 Score=35.73 Aligned_cols=38 Identities=13% Similarity=0.471 Sum_probs=21.2
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
...|.||-|++..++---+-.. .++-.+.|..||..|.
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk----~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKK----EGIGILSCRVCGESFQ 57 (81)
T ss_dssp SS----TTT--SS-EEEEEETT----TTEEEEEESSS--EEE
T ss_pred CceEcCCcCCCCCeEEEEEEcc----CCEEEEEecCCCCeEE
Confidence 4569999999998887555322 4678899999998774
No 46
>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=87.31 E-value=0.25 Score=36.54 Aligned_cols=35 Identities=29% Similarity=0.634 Sum_probs=25.6
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.|+|..|+.+....+-.| |-+.=++++.|.+|.++
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 589999999988777554 45556899999999764
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=87.24 E-value=0.45 Score=44.95 Aligned_cols=38 Identities=21% Similarity=0.597 Sum_probs=17.8
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcccC
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
.-.||-||+.-.. -.+..... ++ ..|..|.-||+.|+|
T Consensus 172 ~g~CPvCGs~P~~-s~l~~~~~-~G-~R~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 172 RGYCPVCGSPPVL-SVLRGGER-EG-KRYLHCSLCGTEWRF 209 (290)
T ss_dssp -SS-TTT---EEE-EEEE--------EEEEEETTT--EEE-
T ss_pred CCcCCCCCCcCce-EEEecCCC-Cc-cEEEEcCCCCCeeee
Confidence 4689999986443 33322211 24 489999999999986
No 48
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=86.94 E-value=0.79 Score=30.30 Aligned_cols=29 Identities=24% Similarity=0.660 Sum_probs=20.1
Q ss_pred ecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 276 KCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 276 ~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.||+|+. ...-.++ +-.....|.+||=.|
T Consensus 1 ~CP~C~~-~l~~~~~-------~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGT-ELEPVRL-------GDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCc-ccceEEE-------CCEEEEECCCCCeEE
Confidence 5999988 3332222 236678899999888
No 49
>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=86.50 E-value=0.72 Score=33.26 Aligned_cols=32 Identities=22% Similarity=0.444 Sum_probs=22.4
Q ss_pred ceecCCCCCCceEE-EeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSY-HQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~-~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
...||+|+.-.... |+ |.-.-++.|+.|||+-
T Consensus 9 GA~CP~C~~~Dtl~~~~-------e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWK-------ENNIELVECVECGYQE 41 (59)
T ss_pred cccCCCCcCccEEEEEE-------eCCceEEEeccCCCcc
Confidence 46899999877653 21 1223579999999973
No 50
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=85.73 E-value=0.72 Score=33.30 Aligned_cols=29 Identities=31% Similarity=0.794 Sum_probs=23.6
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
..+||.|++...+|--.| +-+.|..||+.
T Consensus 11 ~VkCp~C~n~q~vFsha~---------t~V~C~~Cg~~ 39 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHAS---------TVVRCLVCGKT 39 (59)
T ss_pred EEECCCCCCeEEEEecCC---------cEEECcccCCC
Confidence 469999999999996544 35899999974
No 51
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.45 E-value=1.2 Score=39.20 Aligned_cols=76 Identities=17% Similarity=0.200 Sum_probs=43.5
Q ss_pred cCCCChhhhhcCChhhcCcHHHHHHHHHHHHhhhhhhccccccCCCccceecCCCCCCceEEEee---------------
Q 035641 226 IGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQM--------------- 290 (314)
Q Consensus 226 ~G~i~p~~lv~Ms~eEmas~e~k~~~~~~~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~--------------- 290 (314)
.|.++.++|+... .|...++++.-.++.++.|-..... +.+. .++-.+||.+
T Consensus 34 ~g~~tdeeLA~~L--gi~~~~VRk~L~~L~e~gLv~~~r~----------r~~~-~Gr~~y~w~l~~~~i~d~ik~~~~~ 100 (178)
T PRK06266 34 KGEVTDEEIAEQT--GIKLNTVRKILYKLYDARLADYKRE----------KDEE-TNWYTYTWKPELEKLPEIIKKKKME 100 (178)
T ss_pred cCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEeee----------eccC-CCcEEEEEEeCHHHHHHHHHHHHHH
Confidence 3888888887755 4555667766666666555322111 1100 1234444554
Q ss_pred -----eccCCCCCCeEEEEcCCCCCcccC
Q 035641 291 -----QTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 291 -----q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
..+-..+.-..||+|.+|+.+|.|
T Consensus 101 ~~~klk~~l~~e~~~~~Y~Cp~C~~rytf 129 (178)
T PRK06266 101 ELKKLKEQLEEEENNMFFFCPNCHIRFTF 129 (178)
T ss_pred HHHHHHHHhhhccCCCEEECCCCCcEEeH
Confidence 112233444589999999999975
No 52
>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=84.49 E-value=0.63 Score=33.15 Aligned_cols=29 Identities=31% Similarity=0.702 Sum_probs=19.7
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
+.+||.|++...+|-..|+ -+.|..||..
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 4699999999999966654 5899999863
No 53
>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=83.77 E-value=0.53 Score=38.18 Aligned_cols=29 Identities=21% Similarity=0.893 Sum_probs=22.0
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
...||.||.+ ||.+.. .| .+|..||..|.
T Consensus 9 KR~Cp~CG~k---FYDLnk----~P----ivCP~CG~~~~ 37 (108)
T PF09538_consen 9 KRTCPSCGAK---FYDLNK----DP----IVCPKCGTEFP 37 (108)
T ss_pred cccCCCCcch---hccCCC----CC----ccCCCCCCccC
Confidence 4679999875 777753 34 67999999884
No 54
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=83.66 E-value=0.73 Score=32.13 Aligned_cols=28 Identities=18% Similarity=0.373 Sum_probs=18.9
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
..-||+||+. ....- . ..+.|..||+.+
T Consensus 20 ~~fCP~Cg~~--~m~~~------~---~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSG--FMAEH------L---DRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcc--hhecc------C---CcEECCCcCCEE
Confidence 3479999985 22111 1 368899999875
No 55
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.99 E-value=1.2 Score=30.18 Aligned_cols=28 Identities=39% Similarity=0.767 Sum_probs=16.7
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.+.|++||..-. | ++.++ -+.|..||++
T Consensus 3 ~y~C~~CG~~~~-~--------~~~~~-~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVE-L--------DEYGT-GVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEE-E--------CCCCC-ceECCCCCCe
Confidence 477888887322 1 22222 5688888875
No 56
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=82.94 E-value=1.2 Score=37.76 Aligned_cols=32 Identities=19% Similarity=0.429 Sum_probs=25.5
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
-..|+.||+.++.+- . +.-..|..|..||++-
T Consensus 102 yVlC~~C~spdT~l~-k------~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 102 YVICPECGSPDTKLI-K------EGRIWVLKCEACGAET 133 (138)
T ss_pred cEECCCCCCCCcEEE-E------cCCeEEEEcccCCCCC
Confidence 478999999998773 2 2448899999999863
No 57
>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=82.64 E-value=0.93 Score=33.14 Aligned_cols=29 Identities=24% Similarity=0.543 Sum_probs=21.8
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.-.||.||...-. ..-...+.|..||+.|
T Consensus 28 Sq~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc----------ccccceEEcCCCCCEE
Confidence 4579999987664 2234579999999875
No 58
>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=82.58 E-value=0.67 Score=27.90 Aligned_cols=24 Identities=21% Similarity=0.634 Sum_probs=16.5
Q ss_pred ecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 276 KCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 276 ~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.||.|+..=. ..--.|..|||.|.
T Consensus 2 ~CP~C~~~V~--------------~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVP--------------ESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCch--------------hhcCcCCCCCCCCc
Confidence 5888876431 23457999999884
No 59
>PLN02976 amine oxidase
Probab=82.24 E-value=1.3 Score=50.50 Aligned_cols=59 Identities=17% Similarity=0.329 Sum_probs=49.6
Q ss_pred HHHHHHHHHhcCCCCCHHhhhcCcceeec-ccccCCCCHHHHHHHHHHHHHHHHhhhccccc
Q 035641 30 QRCADALKHLQAFPVTYDLLVSTQVGKSL-RHLKKHPCEKVQNAASELLHIWKQKIVLGKET 90 (314)
Q Consensus 30 ~~~~~~L~~L~~~~~t~~~L~~T~iG~~V-~~Lrkh~~~~i~~~Ak~Li~~WK~~~v~~~~~ 90 (314)
+-+..+|+-|--++.++..|+..+||++| +++--|..++|+.+|+.|+..|.. ++. .++
T Consensus 1301 ~l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~-~~~-~~~ 1360 (1713)
T PLN02976 1301 QLLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLE-VFR-REK 1360 (1713)
T ss_pred HHHHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHH-HHH-Hhh
Confidence 34455666666788888999999999999 679999999999999999999999 876 443
No 60
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=81.61 E-value=2.2 Score=31.29 Aligned_cols=33 Identities=18% Similarity=0.362 Sum_probs=25.1
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
..+||-||.......+. .-..+++|..||-+|-
T Consensus 6 lKPCPFCG~~~~~v~~~-------~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI-------SGYYRAKCNGCESRTG 38 (64)
T ss_pred ccCCCCCCCceeEEEec-------CceEEEEcCCCCcCcc
Confidence 46899999998887642 2255799999997763
No 61
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=81.42 E-value=1.5 Score=35.00 Aligned_cols=34 Identities=26% Similarity=0.579 Sum_probs=22.4
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.+.|.||.||......- + |. .....+|..||+..
T Consensus 19 pt~f~CP~Cge~~v~v~----~--~k-~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISVK----I--KK-NIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeeee----c--CC-CcceEECCCCCCcc
Confidence 46799999995322111 0 11 57899999999864
No 62
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=81.18 E-value=1.3 Score=31.87 Aligned_cols=32 Identities=28% Similarity=0.692 Sum_probs=23.2
Q ss_pred CCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 269 KGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 269 ~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
...+--+.|+.||.+... + . +--+.|..||||
T Consensus 15 r~~~miYiCgdC~~en~l----k---~----~D~irCReCG~R 46 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTL----K---R----GDVIRCRECGYR 46 (62)
T ss_pred CcccEEEEeccccccccc----c---C----CCcEehhhcchH
Confidence 345666899999998762 2 1 224889999997
No 63
>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=81.12 E-value=1.6 Score=28.31 Aligned_cols=33 Identities=15% Similarity=0.377 Sum_probs=22.5
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAEC 308 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C 308 (314)
+..+.||.|++.+.+|---+..+ =..-|.|..|
T Consensus 3 ~i~v~CP~C~s~~~v~k~G~~~~----G~qryrC~~C 35 (36)
T PF03811_consen 3 KIDVHCPRCQSTEGVKKNGKSPS----GHQRYRCKDC 35 (36)
T ss_pred cEeeeCCCCCCCCcceeCCCCCC----CCEeEecCcC
Confidence 56789999999997774333222 1345888888
No 64
>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=80.69 E-value=1.8 Score=35.97 Aligned_cols=31 Identities=16% Similarity=0.532 Sum_probs=24.7
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-..|+.|++.++.+.-- .-..|..|..||++
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 46899999999887533 23689999999975
No 65
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.59 E-value=0.88 Score=32.84 Aligned_cols=36 Identities=22% Similarity=0.542 Sum_probs=21.9
Q ss_pred CCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 270 GTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 270 ~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
..-..|.||+||....+ .-..-|. ...-|+|.+||.
T Consensus 23 e~~v~F~CPnCGe~~I~-Rc~~CRk----~g~~Y~Cp~CGF 58 (61)
T COG2888 23 ETAVKFPCPNCGEVEIY-RCAKCRK----LGNPYRCPKCGF 58 (61)
T ss_pred CceeEeeCCCCCceeee-hhhhHHH----cCCceECCCcCc
Confidence 34567999999964332 1111122 234599999985
No 66
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=80.47 E-value=2.2 Score=35.93 Aligned_cols=32 Identities=16% Similarity=0.468 Sum_probs=24.8
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
-..|+.||+.++.+. . ++-..|..|..||++-
T Consensus 97 yVlC~~C~sPdT~l~-k------~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 97 YVICRECNRPDTRII-K------EGRVSLLKCEACGAKA 128 (133)
T ss_pred eEECCCCCCCCcEEE-E------eCCeEEEecccCCCCC
Confidence 578999999998864 2 2345688999999863
No 67
>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=79.38 E-value=3 Score=29.50 Aligned_cols=32 Identities=22% Similarity=0.305 Sum_probs=24.3
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
-...|++|....-.+. ..++..+-|+|..||+
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 3468999998777654 3556667999999986
No 68
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=79.08 E-value=1.8 Score=35.22 Aligned_cols=31 Identities=19% Similarity=0.579 Sum_probs=24.3
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-..|+.|++.++.+--- .=+.|..|..||.+
T Consensus 80 yVlC~~C~spdT~l~k~-------~r~~~l~C~aCGa~ 110 (110)
T smart00653 80 YVLCPECGSPDTELIKE-------NRLFFLKCEACGAR 110 (110)
T ss_pred cEECCCCCCCCcEEEEe-------CCeEEEEccccCCC
Confidence 47899999999876422 23789999999974
No 69
>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=78.79 E-value=1.4 Score=42.26 Aligned_cols=39 Identities=18% Similarity=0.619 Sum_probs=26.7
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcccC
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
...||-||+.-. .-.++....+++ -.|..|.-|++.|.|
T Consensus 184 ~~~CPvCGs~P~-~s~~~~~~~~~G-~RyL~CslC~teW~~ 222 (305)
T TIGR01562 184 RTLCPACGSPPV-ASMVRQGGKETG-LRYLSCSLCATEWHY 222 (305)
T ss_pred CCcCCCCCChhh-hhhhcccCCCCC-ceEEEcCCCCCcccc
Confidence 458999998763 222332223444 678999999999986
No 70
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.62 E-value=1.5 Score=37.73 Aligned_cols=35 Identities=20% Similarity=0.449 Sum_probs=28.2
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.|+|..|+.+...-+-. .|-+.-|+|+.|+.|.+.
T Consensus 79 ~yTCkvCntRs~ktisk---~AY~~GvVivqC~gC~~~ 113 (165)
T KOG3277|consen 79 AYTCKVCNTRSTKTISK---QAYEKGVVIVQCPGCKNH 113 (165)
T ss_pred EEEeeccCCccccccCh---hhhhCceEEEECCCCccc
Confidence 48999999988865543 377788999999999753
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=77.16 E-value=2 Score=29.08 Aligned_cols=27 Identities=33% Similarity=0.837 Sum_probs=17.0
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.+.|+.||..-. +. ...-+.|.+|||+
T Consensus 2 ~Y~C~~Cg~~~~----~~-------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENE----IK-------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEee----cC-------CCCceECCCCCce
Confidence 377889987422 11 1223788899886
No 72
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=77.09 E-value=3.7 Score=26.07 Aligned_cols=30 Identities=27% Similarity=0.617 Sum_probs=22.0
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
+...|..||+...++ +- .-+++|..||..+
T Consensus 2 ~~~~C~~C~~~~i~~-~~---------~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVN-KE---------DDYEVCIFCGSSF 31 (33)
T ss_pred CceEcCCCCCCeEEE-ec---------CCeEEcccCCcEe
Confidence 356899999988654 21 2379999999764
No 73
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=76.28 E-value=2.1 Score=41.03 Aligned_cols=39 Identities=23% Similarity=0.586 Sum_probs=26.7
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcccC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
....||-||+.-..- .++. ..+++ -.|..|.-|++.|.|
T Consensus 186 ~~~~CPvCGs~P~~s-~v~~-~~~~G-~RyL~CslC~teW~~ 224 (309)
T PRK03564 186 QRQFCPVCGSMPVSS-VVQI-GTTQG-LRYLHCNLCESEWHV 224 (309)
T ss_pred CCCCCCCCCCcchhh-eeec-cCCCC-ceEEEcCCCCCcccc
Confidence 457899999876422 2222 12333 478999999999986
No 74
>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=75.87 E-value=3.5 Score=27.44 Aligned_cols=31 Identities=29% Similarity=0.688 Sum_probs=19.4
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
=.|.|..||+.--+ +|.-+. ..-..|..||.
T Consensus 4 Yey~C~~Cg~~fe~---~~~~~~----~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEV---LQSISE----DDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEE---EEEcCC----CCCCcCCCCCC
Confidence 35899999974433 333333 22467999987
No 75
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=75.68 E-value=2.5 Score=37.91 Aligned_cols=31 Identities=23% Similarity=0.551 Sum_probs=24.9
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-..|+.|++.++.+.- +.-+.|..|..||..
T Consensus 98 yV~C~~C~~pdT~l~k-------~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 98 YVICSECGLPDTRLVK-------EDRVLMLRCDACGAH 128 (201)
T ss_pred eEECCCCCCCCcEEEE-------cCCeEEEEcccCCCC
Confidence 5789999999988742 135788999999975
No 76
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=75.54 E-value=2.6 Score=30.40 Aligned_cols=35 Identities=26% Similarity=0.600 Sum_probs=22.1
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-..|.||.||.. ..|.=..=|. ...-|+|.+||..
T Consensus 23 ~~~F~CPnCG~~-~I~RC~~CRk----~~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEV-IIYRCEKCRK----QSNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCe-eEeechhHHh----cCCceECCCCCCc
Confidence 567999999873 2333222232 2356999999863
No 77
>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=75.26 E-value=3.9 Score=26.82 Aligned_cols=29 Identities=21% Similarity=0.591 Sum_probs=18.7
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCC---CCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAE---CNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~---C~~~ 311 (314)
..||.||+ ..+ +.++|. + .|+.|.+ |.+.
T Consensus 2 ~~CP~Cg~-~lv--~r~~k~---g--~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 2 EKCPKCGG-PLV--LRRGKK---G--KFLGCSNYPECKYT 33 (39)
T ss_pred cCCCCCCc-eeE--EEECCC---C--CEEECCCCCCcCCe
Confidence 47999993 332 233333 2 8999986 8775
No 78
>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=75.16 E-value=1.6 Score=27.58 Aligned_cols=26 Identities=31% Similarity=0.990 Sum_probs=14.4
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
+.|++||...- +. ..++ +.|..|||+
T Consensus 1 Y~C~~Cg~~~~----~~---~~~~----irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVE----LK---PGDP----IRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-----BS---TSST----SSBSSSS-S
T ss_pred CCCCcCCCeeE----cC---CCCc----EECCcCCCe
Confidence 35888887544 11 1222 478888886
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.43 E-value=5.1 Score=33.98 Aligned_cols=22 Identities=23% Similarity=0.694 Sum_probs=17.6
Q ss_pred cCCCCCCeEEEEcCCCCCcccC
Q 035641 293 RSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 293 rsade~mt~f~~C~~C~~~w~~ 314 (314)
+-..+....||.|.+||.+|.|
T Consensus 90 ~l~~e~~~~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 90 KLEDETNNAYYKCPNCQSKYTF 111 (147)
T ss_pred HHhcccCCcEEECcCCCCEeeH
Confidence 4456666789999999999975
No 80
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.91 E-value=3.1 Score=32.40 Aligned_cols=32 Identities=22% Similarity=0.589 Sum_probs=23.0
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
...+.||.||.... - |. -+-+..|..||+.|.
T Consensus 33 ~~~~~Cp~C~~~~V-k-----R~----a~GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVCPFCGRTTV-K-----RI----ATGIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcCCCCCCcce-e-----ee----ccCeEEcCCCCCeec
Confidence 34688999999833 1 21 355899999999873
No 81
>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=73.45 E-value=4.3 Score=26.24 Aligned_cols=31 Identities=29% Similarity=0.742 Sum_probs=18.8
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
=.|.|+.||+.-- ..+.. .+ .....|..||.
T Consensus 4 Y~y~C~~Cg~~fe---~~~~~-~~---~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFE---VLQKI-SD---DPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEE---EEEec-CC---CCCCCCCCCCC
Confidence 3589999998332 22322 22 23467999986
No 82
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=72.60 E-value=1.5 Score=36.74 Aligned_cols=32 Identities=22% Similarity=0.385 Sum_probs=22.0
Q ss_pred CCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 269 KGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 269 ~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
++.....+||.||-.- |+.+. -+.|..|||+.
T Consensus 23 GAkML~~hCp~Cg~PL---F~KdG---------~v~CPvC~~~~ 54 (131)
T COG1645 23 GAKMLAKHCPKCGTPL---FRKDG---------EVFCPVCGYRE 54 (131)
T ss_pred hhHHHHhhCcccCCcc---eeeCC---------eEECCCCCceE
Confidence 3456678999998653 44322 37899999875
No 83
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=70.87 E-value=2.4 Score=29.45 Aligned_cols=30 Identities=30% Similarity=0.670 Sum_probs=19.9
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
+..+.|.+||..- -+.| -+.-+.|..|||+
T Consensus 4 ~~~Y~C~~Cg~~~---~~~~-------~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREV---ELDQ-------ETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCee---ehhh-------ccCceeCCCCCcE
Confidence 3457899998753 1122 3556889999986
No 84
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=69.65 E-value=2 Score=30.05 Aligned_cols=34 Identities=24% Similarity=0.525 Sum_probs=24.8
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
...|..|+-.++..+ |....+. -+.|..||-.|+
T Consensus 3 ~~~C~~C~~~~T~~W----R~g~~g~--~~LCnaCgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPLW----RRGPSGN--KTLCNACGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCcc----ccCCCCC--CcEeecccHHHH
Confidence 357999998888654 5555554 478999998885
No 85
>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=69.49 E-value=3.6 Score=29.19 Aligned_cols=31 Identities=29% Similarity=0.746 Sum_probs=19.9
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
+|.||.||..=. + .+...--.+.|..||...
T Consensus 2 ~~~CP~CG~~ie----v----~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIE----L----ENPELGELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEe----c----CCCccCCEEeCCCCCCEE
Confidence 579999998322 1 111123478999999764
No 86
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=68.28 E-value=4 Score=26.16 Aligned_cols=29 Identities=21% Similarity=0.493 Sum_probs=13.4
Q ss_pred cCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 277 CSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 277 C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
||.||+.- .+ +-.+..-..=++|..||..
T Consensus 3 C~~CG~~l-~~-----~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPL-ER-----RIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B--EE-----E--TT-SS-EEEETTTTEE
T ss_pred cccccChh-hh-----hcCCCCCccceECCCCCCE
Confidence 99999972 22 2222223345789999864
No 87
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=67.62 E-value=7.7 Score=36.14 Aligned_cols=26 Identities=19% Similarity=0.539 Sum_probs=19.5
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.+...|+.||+ . -...+.|..||+.|
T Consensus 307 ~tS~~C~~cg~-------~--------~~r~~~C~~cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH-------L--------SGRLFKCPRCGFVH 332 (364)
T ss_pred CCcccccccCC-------c--------cceeEECCCCCCee
Confidence 44578999999 1 13468999999865
No 88
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=67.33 E-value=3.2 Score=24.14 Aligned_cols=7 Identities=29% Similarity=1.132 Sum_probs=5.2
Q ss_pred cCCCCCc
Q 035641 305 CAECNKR 311 (314)
Q Consensus 305 C~~C~~~ 311 (314)
|.+||+.
T Consensus 16 C~~CG~~ 22 (23)
T PF13240_consen 16 CPNCGTP 22 (23)
T ss_pred hhhhCCc
Confidence 7888764
No 89
>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=66.07 E-value=4.2 Score=38.37 Aligned_cols=39 Identities=23% Similarity=0.503 Sum_probs=20.1
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.+.||.||+.+..-+..= ...+++--..++|..|++-+|
T Consensus 211 R~~Cp~Cg~~~~~~l~~~-~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYF-TVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TTS-TTT---SS-EEE---------SEEEEEETTTTEEEE
T ss_pred CCCCcCCCCCCCcceeeE-ecCCCCcEEEEECCcccchHH
Confidence 358999998776543321 135666778899999998775
No 90
>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=65.85 E-value=0.4 Score=32.33 Aligned_cols=30 Identities=23% Similarity=0.479 Sum_probs=24.2
Q ss_pred CCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 280 CGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 280 C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
|.|.-. .-..|+|++||..+.+-.|..||.
T Consensus 13 C~H~f~-~~E~Q~RAGDE~VSfI~~C~~C~~ 42 (43)
T PF11792_consen 13 CKHKFV-TIEKQLRAGDEAVSFIKYCQKCGQ 42 (43)
T ss_pred ceeeee-ehhhhhcccchHHHHHHHHHHhCC
Confidence 766554 345799999999999999999985
No 91
>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=65.10 E-value=4.9 Score=39.32 Aligned_cols=35 Identities=23% Similarity=0.434 Sum_probs=19.4
Q ss_pred ceecCCCCC-CceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGK-SNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~-~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.--|++||. ..+..... -.+.-++.|.|..|||.-
T Consensus 174 ~piC~~cGri~tt~v~~~----d~~~~~v~Y~c~~cG~~g 209 (360)
T PF01921_consen 174 LPICEKCGRIDTTEVTEY----DPEGGTVTYRCEECGHEG 209 (360)
T ss_dssp EEEETTTEE--EEEEEEE------SSSEEEEE--TTS---
T ss_pred eeeccccCCcccceeeEe----ecCCCEEEEEecCCCCEE
Confidence 457999998 44443322 224568999999999963
No 92
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=64.57 E-value=9.7 Score=38.08 Aligned_cols=94 Identities=20% Similarity=0.351 Sum_probs=52.7
Q ss_pred CChhhhhhhhcCCCChhhhhcCChhhcCc-HHHHHHHH-HHHHhhh--hhhccccccCCCccceecCCCCCCceEEEeee
Q 035641 216 KNPDLRRRVLIGEVTPERLATMTPEELAS-DERRQENE-EIKAKFM--FKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQ 291 (314)
Q Consensus 216 ~Np~Lr~~vl~G~i~p~~lv~Ms~eEmas-~e~k~~~~-~~~~~~l--~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q 291 (314)
.||.|....+ .-|+.++|..|..++++- +..+..+. -+.-+-| ++-+ --.=-+..+|++||+..-.-.+.|
T Consensus 104 EDP~lq~~Al-s~iPvdEL~~kA~ekla~~eg~ki~kdy~i~leLL~WFKq~----FF~WvN~PpC~~CG~et~~~l~~~ 178 (500)
T KOG0909|consen 104 EDPVLQAKAL-STIPVDELKEKASEKLAKAEGEKIYKDYLIKLELLNWFKQD----FFKWVNNPPCNKCGGETSSGLGNQ 178 (500)
T ss_pred cCHHHHHHHH-hcCCHHHHHHHHHHhhcccchhhhhcchHHHHHHHHHHHHh----hheecCCCCcccccccccccccCC
Confidence 6887766544 356779999988888884 11111111 1110111 2211 011134578999999776433333
Q ss_pred ccCCCC---C--CeEEEEcCCCCCcccC
Q 035641 292 TRSADE---P--MTTYVTCAECNKRWKC 314 (314)
Q Consensus 292 ~rsade---~--mt~f~~C~~C~~~w~~ 314 (314)
.-..+| + -.-.|.|..||+.=||
T Consensus 179 ~p~eeE~~~Ga~rVEiy~C~~C~~~~RF 206 (500)
T KOG0909|consen 179 PPNEEEKKFGAGRVEIYKCNRCGTETRF 206 (500)
T ss_pred CCchhHhhcCCceEEEEEecCCCCcccC
Confidence 333444 2 3468999999997655
No 93
>PRK05978 hypothetical protein; Provisional
Probab=64.07 E-value=3.4 Score=35.38 Aligned_cols=31 Identities=19% Similarity=0.550 Sum_probs=22.0
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.-+||+||..+..- ...+.--.|..||..+.
T Consensus 33 ~grCP~CG~G~LF~---------g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 33 RGRCPACGEGKLFR---------AFLKPVDHCAACGEDFT 63 (148)
T ss_pred cCcCCCCCCCcccc---------cccccCCCccccCCccc
Confidence 35899999887741 12445567999998764
No 94
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=63.96 E-value=7 Score=32.64 Aligned_cols=38 Identities=18% Similarity=0.434 Sum_probs=25.4
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
...+..||.|+... ++---..+.. -.-|.|..|+..|.
T Consensus 27 ~~~~~~cP~C~s~~-~~k~g~~~~~----~qRyrC~~C~~tf~ 64 (129)
T COG3677 27 QITKVNCPRCKSSN-VVKIGGIRRG----HQRYKCKSCGSTFT 64 (129)
T ss_pred hcccCcCCCCCccc-eeeECCcccc----ccccccCCcCccee
Confidence 35568899999887 4432332322 23599999998875
No 95
>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=63.69 E-value=3.8 Score=37.83 Aligned_cols=33 Identities=24% Similarity=0.729 Sum_probs=11.9
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.+-||.||+..-.-|.- --|.-- |.|.+|++.|
T Consensus 31 n~yCP~Cg~~~L~~f~N-----N~PVaD-F~C~~C~eey 63 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFEN-----NRPVAD-FYCPNCNEEY 63 (254)
T ss_dssp H---TTT--SS-EE-------------E-EE-TTT--EE
T ss_pred CCcCCCCCChhHhhccC-----CCccce-eECCCCchHH
Confidence 46799999986655533 223333 5599999876
No 96
>PRK12495 hypothetical protein; Provisional
Probab=62.81 E-value=8.1 Score=35.17 Aligned_cols=31 Identities=19% Similarity=0.440 Sum_probs=21.3
Q ss_pred CCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 270 GTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 270 ~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.....+.|+.||..=. .+.-.+.|+.|+...
T Consensus 38 atmsa~hC~~CG~PIp------------a~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 38 ATMTNAHCDECGDPIF------------RHDGQEFCPTCQQPV 68 (226)
T ss_pred cccchhhcccccCccc------------CCCCeeECCCCCCcc
Confidence 3466789999998654 123357789998653
No 97
>PHA02942 putative transposase; Provisional
Probab=62.59 E-value=5 Score=39.56 Aligned_cols=28 Identities=21% Similarity=0.661 Sum_probs=19.3
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.-.||.||+.... . -...|.|.+||+.+
T Consensus 325 Sq~Cs~CG~~~~~---l--------~~r~f~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCPKCGHKMVE---I--------AHRYFHCPSCGYEN 352 (383)
T ss_pred CccCCCCCCccCc---C--------CCCEEECCCCCCEe
Confidence 3679999986421 0 11379999999864
No 98
>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=62.52 E-value=5.2 Score=23.63 Aligned_cols=10 Identities=40% Similarity=1.142 Sum_probs=7.0
Q ss_pred ccceecCCCC
Q 035641 272 TDQFKCSGCG 281 (314)
Q Consensus 272 t~~~~C~~C~ 281 (314)
...|.||+||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 4567777777
No 99
>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=60.75 E-value=12 Score=28.21 Aligned_cols=36 Identities=25% Similarity=0.562 Sum_probs=19.3
Q ss_pred cceecCCCCC-----CceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGK-----SNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~-----~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
...-|.+||. ..+.+... +..-..-.+.|+|..|||
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 3567999994 44444333 222223468999999997
No 100
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=60.53 E-value=11 Score=28.71 Aligned_cols=57 Identities=25% Similarity=0.448 Sum_probs=35.0
Q ss_pred hhcCcHHHHHHHHHHHHhhhhhhccccccCCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 240 EELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 240 eEmas~e~k~~~~~~~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
.||+-+..+++..+...+.|- +.+..---..+||.|-+-.++|.-.|+ -++|.+|+.
T Consensus 5 ~dllhPs~e~e~r~hK~krLv-----q~~nsyFm~VkC~gc~~iT~vfSHaqt---------vVvc~~c~~ 61 (84)
T KOG1779|consen 5 KDLLHPSPEKEKRKHKLKRLV-----QSPNSYFMDVKCPGCFKITTVFSHAQT---------VVVCEGCST 61 (84)
T ss_pred hhhcCCCHHHHhhhhhhhhhe-----eCCCceEEEEEcCCceEEEEEeecCce---------EEEcCCCce
Confidence 355555555554444444442 122222234699999999999977664 578888863
No 101
>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=59.58 E-value=4.2 Score=35.05 Aligned_cols=19 Identities=16% Similarity=0.307 Sum_probs=15.5
Q ss_pred CCCCeEEEEcCCCCCcccC
Q 035641 296 DEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 296 de~mt~f~~C~~C~~~w~~ 314 (314)
.+.-..||+|.+|+.+|.|
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf 121 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTF 121 (158)
T ss_pred hccCCCeEECCCCCcEeeH
Confidence 4445689999999999975
No 102
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=59.06 E-value=9 Score=27.41 Aligned_cols=25 Identities=20% Similarity=0.660 Sum_probs=18.7
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
......||.||+..- ...+|.+||+
T Consensus 24 ~~~l~~C~~CG~~~~---------------~H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKL---------------PHRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccC---------------CeEECCCCCc
Confidence 355678999998543 3788999985
No 103
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=58.43 E-value=16 Score=37.74 Aligned_cols=60 Identities=15% Similarity=0.211 Sum_probs=44.4
Q ss_pred cHHHHHHHHHHHHHHHhhhccccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCChhhHhHHHhHHhhcCCCCCh
Q 035641 143 DSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNP 218 (314)
Q Consensus 143 d~~R~k~~~~L~~aL~~~~~~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~~~yk~k~Rsl~~NLkd~~Np 218 (314)
-++|.+++.-|.+.|.........+ |..+|++||.+... .++|-.-+--|+.+++|-.|.
T Consensus 9 ~kFRq~vIsried~l~~n~q~~~k~---------------a~~mE~hVF~K~~t-kDEYl~lvAkli~h~~d~s~~ 68 (742)
T KOG4274|consen 9 PKFRQHVISRIEDELRKNGQAHSKS---------------AKDMESHVFLKAKT-KDEYLSLVAKLIIHFRDISNK 68 (742)
T ss_pred HHHHHHHHHHhhhhhhhhhhccCcc---------------hHHHHHHHHHhhhh-HHHHHHHHHHHHHHHHhhhhh
Confidence 5899999999999998775433322 57999999987754 467866666678888876654
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=58.23 E-value=7.8 Score=25.31 Aligned_cols=31 Identities=23% Similarity=0.408 Sum_probs=20.1
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
..+||.||.+.-.-| .|-..+--+.|..|+.
T Consensus 3 ~~pCP~CGG~DrFr~------~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRF------DDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCcccccc------ccCCCCcCEEeCCCCC
Confidence 358999999777543 2223344567888864
No 105
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=58.23 E-value=9.1 Score=26.74 Aligned_cols=16 Identities=25% Similarity=0.889 Sum_probs=10.5
Q ss_pred CCeEEEEcCCCCCccc
Q 035641 298 PMTTYVTCAECNKRWK 313 (314)
Q Consensus 298 ~mt~f~~C~~C~~~w~ 313 (314)
....+..|..|||.|+
T Consensus 24 ~~~v~W~C~~Cgh~w~ 39 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWK 39 (55)
T ss_pred CCEEEEECCCCCCeeE
Confidence 3455667777777774
No 106
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=57.56 E-value=4.1 Score=35.89 Aligned_cols=32 Identities=25% Similarity=0.590 Sum_probs=23.6
Q ss_pred CCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 270 GTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 270 ~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
.+...|.||.|+-+-. =||.|..-|+|..||.
T Consensus 109 ~~~~~y~C~~~~~r~s---------fdeA~~~~F~Cp~Cg~ 140 (176)
T COG1675 109 TENNYYVCPNCHVKYS---------FDEAMELGFTCPKCGE 140 (176)
T ss_pred ccCCceeCCCCCCccc---------HHHHHHhCCCCCCCCc
Confidence 4566799987765433 4666777799999985
No 107
>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=56.71 E-value=12 Score=30.07 Aligned_cols=34 Identities=18% Similarity=0.445 Sum_probs=20.3
Q ss_pred eecCCCCCCceEE--EeeeccCCCCCCeEEEEcCCCC
Q 035641 275 FKCSGCGKSNCSY--HQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 275 ~~C~~C~~~~~~~--~q~q~rsade~mt~f~~C~~C~ 309 (314)
..||-||..-..- -++-.++.++. ..+|+|..|+
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~-~~~y~C~~C~ 38 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDG-PYLYVCTPCD 38 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCC-ceeEECCCCC
Confidence 5799999743221 12233444443 2559999996
No 108
>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=55.78 E-value=13 Score=36.35 Aligned_cols=33 Identities=27% Similarity=0.542 Sum_probs=19.9
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.-.|++||.-.+... .... +.-|+.|.| .|||.
T Consensus 169 ~p~c~~cg~~~~~v~---~~d~-~~~~v~y~c-~cG~~ 201 (353)
T cd00674 169 MPYCEKCGKDTTTVE---AYDA-KAGTVTYKC-ECGHE 201 (353)
T ss_pred eeecCCcCcceeEEE---EEeC-CCCeEEEEc-CCCCE
Confidence 457999993222221 1222 345888899 59985
No 109
>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=55.72 E-value=28 Score=27.36 Aligned_cols=30 Identities=27% Similarity=0.665 Sum_probs=21.8
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
..+.||.||.... -.+ -+-+..|..||..|
T Consensus 34 a~y~CpfCgk~~v-kR~---------a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 34 AKYVCPFCGKKTV-KRG---------STGIWTCRKCGAKF 63 (91)
T ss_pred cCccCCCCCCCce-EEE---------eeEEEEcCCCCCEE
Confidence 3689999996553 221 35689999999876
No 110
>PRK00420 hypothetical protein; Validated
Probab=54.71 E-value=8.2 Score=31.54 Aligned_cols=28 Identities=21% Similarity=0.409 Sum_probs=18.0
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
..+||.||..-..+.+ .-+.|+.||...
T Consensus 23 ~~~CP~Cg~pLf~lk~-----------g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFELKD-----------GEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcceecCC-----------CceECCCCCCee
Confidence 4789999954432211 137899999743
No 111
>PRK11032 hypothetical protein; Provisional
Probab=54.67 E-value=6.2 Score=34.25 Aligned_cols=30 Identities=17% Similarity=0.475 Sum_probs=23.1
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.+.+.|-+||+.-..|+ -+..--|.+|||.
T Consensus 122 ~G~LvC~~Cg~~~~~~~----------p~~i~pCp~C~~~ 151 (160)
T PRK11032 122 LGNLVCEKCHHHLAFYT----------PEVLPLCPKCGHD 151 (160)
T ss_pred cceEEecCCCCEEEecC----------CCcCCCCCCCCCC
Confidence 56789999999887764 2345679999985
No 112
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=54.21 E-value=5.4 Score=23.69 Aligned_cols=23 Identities=22% Similarity=0.629 Sum_probs=14.3
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
..||.||..-. ..+-.|.+||+.
T Consensus 3 ~~Cp~Cg~~~~--------------~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEID--------------PDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCC--------------cccccChhhCCC
Confidence 46899987321 114568888864
No 113
>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=53.86 E-value=12 Score=38.55 Aligned_cols=32 Identities=19% Similarity=0.613 Sum_probs=21.4
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.-.|++||.-..... ...++. |+.|.| .|||.
T Consensus 168 ~pic~~cGrv~~~~~---~~~~~~--~v~Y~c-~cG~~ 199 (515)
T TIGR00467 168 SVFCENCGRDTTTVN---NYDNEY--SIEYSC-ECGNQ 199 (515)
T ss_pred eeecCCcCccCceEE---EecCCc--eEEEEc-CCCCE
Confidence 467999998644332 233434 789999 49984
No 114
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=53.80 E-value=9.3 Score=35.44 Aligned_cols=13 Identities=15% Similarity=0.761 Sum_probs=11.9
Q ss_pred EEEEcCCCCCccc
Q 035641 301 TYVTCAECNKRWK 313 (314)
Q Consensus 301 ~f~~C~~C~~~w~ 313 (314)
-+|.|.+|+|.|+
T Consensus 154 aef~C~~C~h~F~ 166 (278)
T PF15135_consen 154 AEFHCPKCRHNFR 166 (278)
T ss_pred eeeecccccccch
Confidence 6899999999996
No 115
>PF06290 PsiB: Plasmid SOS inhibition protein (PsiB); InterPro: IPR009385 This family consists of several plasmid SOS inhibition protein (PsiB) sequences [].; PDB: 3NCT_B.
Probab=53.73 E-value=16 Score=30.86 Aligned_cols=76 Identities=17% Similarity=0.210 Sum_probs=39.3
Q ss_pred CCCChhhhhcCChhhcCcHHHHHHHHHHHHhhhhhhccccccCCCccceecCCCCCCceEEEeeecc-CCCCCCeEEEEc
Q 035641 227 GEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTR-SADEPMTTYVTC 305 (314)
Q Consensus 227 G~i~p~~lv~Ms~eEmas~e~k~~~~~~~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q~r-sade~mt~f~~C 305 (314)
..|+++.|-+|+++|+ ++.+..-+..+.+--..... +-..+.....|..|+..=+.||=+|-| +++.+-+..++|
T Consensus 3 ~~ltl~~L~tm~a~el--E~~R~~Ged~RR~L~~aVm~--~L~~P~gW~~n~Ey~~EFgGffPVq~Rftp~~~~~~l~vC 78 (143)
T PF06290_consen 3 TELTLEVLKTMSAQEL--EDYRAAGEDFRRELTHAVMR--ELTLPEGWRVNAEYRSEFGGFFPVQCRFTPSHERFHLAVC 78 (143)
T ss_dssp ----HHHHHH--HHHH--HHHHHH-HHHHHHHHHHHHH--T----TTEEEEE-SSSTT-S-SSSEEEEEETT-SEEEEEE
T ss_pred ceehHHHHhhcCHHHH--HHHHHhhHHHHHHhHHHHHH--hccCCccceeeceeccccccEeeEEEEecCCCCcEEEEEc
Confidence 4688999999999999 67776655555532222221 122344566778888888888877776 333466666777
Q ss_pred C
Q 035641 306 A 306 (314)
Q Consensus 306 ~ 306 (314)
.
T Consensus 79 S 79 (143)
T PF06290_consen 79 S 79 (143)
T ss_dssp -
T ss_pred C
Confidence 4
No 116
>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=53.44 E-value=12 Score=26.60 Aligned_cols=24 Identities=21% Similarity=0.566 Sum_probs=17.9
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
.....|+.||.. +....+|..||+
T Consensus 24 p~l~~C~~cG~~---------------~~~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEF---------------KLPHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCc---------------ccCeeECCccCe
Confidence 456789999973 344788999984
No 117
>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=52.95 E-value=5.7 Score=28.93 Aligned_cols=38 Identities=18% Similarity=0.646 Sum_probs=23.0
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
....||+|++.++-|-=.---+...| -|.|..|...|+
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QP---R~~Ck~C~rywT 41 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQP---RYFCKSCRRYWT 41 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCc---chhhHHHHHHHH
Confidence 35789999988877621101111111 377888888885
No 118
>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=52.77 E-value=10 Score=24.29 Aligned_cols=28 Identities=21% Similarity=0.540 Sum_probs=15.4
Q ss_pred ecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 276 KCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 276 ~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
-||.||+-=.. + .|...+. .|..||+..
T Consensus 3 FCp~C~nlL~p------~-~~~~~~~--~C~~C~Y~~ 30 (35)
T PF02150_consen 3 FCPECGNLLYP------K-EDKEKRV--ACRTCGYEE 30 (35)
T ss_dssp BETTTTSBEEE------E-EETTTTE--EESSSS-EE
T ss_pred eCCCCCccceE------c-CCCccCc--CCCCCCCcc
Confidence 49999974321 1 1112222 999999864
No 119
>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=52.76 E-value=8.6 Score=26.34 Aligned_cols=30 Identities=30% Similarity=0.813 Sum_probs=17.4
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
.|.|.+||+.--.+ +. ..++ ....|..||.
T Consensus 5 ey~C~~Cg~~fe~~---~~-~~~~---~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVL---QK-MSDD---PLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEE---Ee-cCCC---CCCCCCCCCC
Confidence 57899998633322 21 1222 2356889987
No 120
>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=52.70 E-value=17 Score=34.77 Aligned_cols=40 Identities=28% Similarity=0.543 Sum_probs=26.1
Q ss_pred cceecCCCCCCceE-EEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 273 DQFKCSGCGKSNCS-YHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 273 ~~~~C~~C~~~~~~-~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
....|+.||+.+-. |+.+-. ..+++-....+|..|+.-+|
T Consensus 223 ~R~~C~~Cg~~~~l~y~~~e~-~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 223 VRVKCSHCEESKHLAYLSLEH-DAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred cCccCCCCCCCCceeeEeecC-CCCCcceEEeeccccccchh
Confidence 35689999987643 444421 11345567789999987665
No 121
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=52.37 E-value=9 Score=30.91 Aligned_cols=37 Identities=22% Similarity=0.424 Sum_probs=22.0
Q ss_pred ceecCCCCCCceEEE--eeeccCCCCCCeEEEEcCCCCCcccC
Q 035641 274 QFKCSGCGKSNCSYH--QMQTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~--q~q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
...|++|...=.... -+..+++. +-++|..||+.-+|
T Consensus 56 R~~CkkC~t~Lvpg~n~rvR~~~~~----v~vtC~~CG~~~R~ 94 (105)
T COG2023 56 RTICKKCYTPLVPGKNARVRLRKGR----VVVTCLECGTIRRY 94 (105)
T ss_pred HHhccccCcccccCcceEEEEcCCe----EEEEecCCCcEEEe
Confidence 357999986322221 12222222 88999999987554
No 122
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.03 E-value=8.2 Score=34.15 Aligned_cols=16 Identities=19% Similarity=0.686 Sum_probs=13.7
Q ss_pred CeEEEEcCCCCCcccC
Q 035641 299 MTTYVTCAECNKRWKC 314 (314)
Q Consensus 299 mt~f~~C~~C~~~w~~ 314 (314)
.=.+|.|++|.++|.+
T Consensus 46 vWlIYkC~~Cd~tWN~ 61 (203)
T COG4332 46 VWLIYKCTHCDYTWNI 61 (203)
T ss_pred EEEEEEeeccCCccch
Confidence 3578999999999975
No 123
>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=51.61 E-value=13 Score=29.15 Aligned_cols=30 Identities=27% Similarity=0.747 Sum_probs=21.1
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
..+.||.||..... .+ -+-+..|..||+.|
T Consensus 34 ~ky~Cp~Cgk~~vk-R~---------a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK-RV---------ATGIWKCKKCGKKF 63 (90)
T ss_dssp S-BEESSSSSSEEE-EE---------ETTEEEETTTTEEE
T ss_pred CCCcCCCCCCceeE-Ee---------eeEEeecCCCCCEE
Confidence 36899999997742 22 23368999999876
No 124
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=51.35 E-value=36 Score=26.70 Aligned_cols=31 Identities=26% Similarity=0.529 Sum_probs=21.8
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
...+.||.||.... -.+ -+-+..|..||..|
T Consensus 34 ~a~y~CpfCgk~~v-kR~---------a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 34 HAKYFCPFCGKHAV-KRQ---------AVGIWRCKGCKKTV 64 (90)
T ss_pred hCCccCCCCCCCce-eee---------eeEEEEcCCCCCEE
Confidence 34689999996553 211 34688999999875
No 125
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=50.96 E-value=14 Score=29.34 Aligned_cols=52 Identities=19% Similarity=0.214 Sum_probs=44.2
Q ss_pred ccHHHHHHHHHHhcCCCCCHHhhhcCcceeecccccCCCCHHHHHHHHHHHH
Q 035641 27 PEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLH 78 (314)
Q Consensus 27 ~~~~~~~~~L~~L~~~~~t~~~L~~T~iG~~V~~Lrkh~~~~i~~~Ak~Li~ 78 (314)
+..++++++|.+|-+.|....+|..-+.-..+++||++-++..+...-.|++
T Consensus 45 ~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 45 PMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred ccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 5789999999999999999999998776666899999988887777766654
No 126
>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=50.51 E-value=14 Score=32.00 Aligned_cols=35 Identities=26% Similarity=0.459 Sum_probs=24.6
Q ss_pred ceecCCCCCCceEEEeeec------cCC-------CCCCeEEEEcC-CC
Q 035641 274 QFKCSGCGKSNCSYHQMQT------RSA-------DEPMTTYVTCA-EC 308 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~------rsa-------de~mt~f~~C~-~C 308 (314)
--+|+.||+.++.=||+.. ... |=+....|+|. +|
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 3579999999998899832 112 22335899997 48
No 127
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=50.47 E-value=37 Score=26.64 Aligned_cols=30 Identities=20% Similarity=0.566 Sum_probs=21.6
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
..+.||.||.....- .-+-+..|..||+.|
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 35 AKHVCPVCGRPKVKR----------VGTGIWECRKCGAKF 64 (90)
T ss_pred cCccCCCCCCCceEE----------EEEEEEEcCCCCCEE
Confidence 468999997655421 135688999999876
No 128
>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=50.34 E-value=5.9 Score=38.57 Aligned_cols=13 Identities=23% Similarity=0.974 Sum_probs=7.1
Q ss_pred CeEEEEcCCCCCc
Q 035641 299 MTTYVTCAECNKR 311 (314)
Q Consensus 299 mt~f~~C~~C~~~ 311 (314)
+..||.|.+||+|
T Consensus 282 ~KRFFkC~~C~~R 294 (344)
T PF09332_consen 282 VKRFFKCKDCGNR 294 (344)
T ss_dssp E-EEEE-T-TS-E
T ss_pred eeeeEECCCCCCe
Confidence 4578888888876
No 129
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=50.24 E-value=6.8 Score=34.10 Aligned_cols=40 Identities=13% Similarity=0.375 Sum_probs=22.7
Q ss_pred CccceecCCCCCCceEE------EeeeccCCCCCCeEEEEcCCCCCc
Q 035641 271 TTDQFKCSGCGKSNCSY------HQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~------~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
....-.||.|+..=.-. -++..+ -...-..|++|.+||..
T Consensus 94 ~~e~~RCp~CN~~L~~vs~eev~~~Vp~~-~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 94 FPEFSRCPECNGELEKVSREEVKEKVPEK-VYRNYEEFYRCPKCGKI 139 (165)
T ss_pred ccccccCcccCCEeccCcHHHHhhccchh-hhhcccceeECCCCccc
Confidence 34456899999643321 011100 11224579999999875
No 130
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=50.17 E-value=8.1 Score=38.94 Aligned_cols=103 Identities=13% Similarity=0.107 Sum_probs=73.2
Q ss_pred CCCCcHHHHHHHHHHHHHHHhhhccccchhHHHhh--hhcCChHHHHHHHHHHHHHhhcCCChhhHhHHHhHHhhcCCCC
Q 035641 139 DQAKDSMRDKIRKDLEKALSRVASEAADDEEITDR--VKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEK 216 (314)
Q Consensus 139 ~~~~d~~R~k~~~~L~~aL~~~~~~~~~~~~~~~~--~~~~d~~~lA~~IE~alf~~~~~~~~~yk~k~Rsl~~NLkd~~ 216 (314)
+.+++.-|++++.-++..+..++.........-+. .-..+......+||.+.|+.+......|..++..|.++|+ .
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 57889999999999999986555332221000000 0011245667899999999998877889999999999997 4
Q ss_pred ChhhhhhhhcCC-CChhhhhcCChhhcC
Q 035641 217 NPDLRRRVLIGE-VTPERLATMTPEELA 243 (314)
Q Consensus 217 Np~Lr~~vl~G~-i~p~~lv~Ms~eEma 243 (314)
---|+.+.+.|. +.|+-.+.|-+-++-
T Consensus 316 ~~~l~~~~ln~~~~~~e~~~~l~~p~~p 343 (464)
T KOG1886|consen 316 QALLKPEPLNPGETKPEPKQELHPPSFP 343 (464)
T ss_pred hhhhccccCCCcccCchhhhhccCCCCC
Confidence 456788888884 888888888655444
No 131
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=49.55 E-value=3.4 Score=39.38 Aligned_cols=31 Identities=19% Similarity=0.458 Sum_probs=20.7
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
..+||.|+.- .| ..+ =-..+++|.+|||-++
T Consensus 38 w~kc~~C~~~--~~-~~~------l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 38 WVQCENCYGL--NY-KKF------LKSKMNICEQCGYHLK 68 (296)
T ss_pred eeECCCccch--hh-HHH------HHHcCCCCCCCCCCcC
Confidence 6799999862 22 111 1235799999999765
No 132
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=49.17 E-value=6.7 Score=38.09 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=25.1
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
..||.|+++++.++-.- .-|+-+-|..||.+-
T Consensus 97 VlC~~C~NPETel~itk------~q~i~~~CkACG~r~ 128 (400)
T KOG2767|consen 97 VLCPSCENPETELIITK------KQTISLKCKACGFRS 128 (400)
T ss_pred eeCcCCCCCceeEEecc------cchhhhHHHHcCCcc
Confidence 57999999999886532 246678999999874
No 133
>PRK13701 psiB plasmid SOS inhibition protein B; Provisional
Probab=47.72 E-value=59 Score=27.53 Aligned_cols=29 Identities=24% Similarity=0.375 Sum_probs=23.0
Q ss_pred CCCChhhhhcCChhhcCcHHHHHHHHHHHHh
Q 035641 227 GEVTPERLATMTPEELASDERRQENEEIKAK 257 (314)
Q Consensus 227 G~i~p~~lv~Ms~eEmas~e~k~~~~~~~~~ 257 (314)
-+++++.|-.|+++|| ++.|..-+.++.+
T Consensus 3 ~~ltl~~l~tM~a~El--Ed~R~~G~d~RR~ 31 (144)
T PRK13701 3 TELTLNVLQTMSAQEY--EDIRAAGSDERRE 31 (144)
T ss_pred cEEcHHHHhccCHHHH--HHHHHHhHHHHHH
Confidence 4689999999999999 7777776666554
No 134
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=47.22 E-value=11 Score=35.57 Aligned_cols=39 Identities=36% Similarity=0.693 Sum_probs=24.3
Q ss_pred ccceecCCCCCCceEEEe----eec-cCCCCCCeEEEEcCCCCCcc
Q 035641 272 TDQFKCSGCGKSNCSYHQ----MQT-RSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q----~q~-rsade~mt~f~~C~~C~~~w 312 (314)
...+.|+.||..-+++.= .|+ |++|++ .-+.|..||..|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~--ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSK--KAFSCKYCGKVY 171 (279)
T ss_pred CCceeccccccccccccccchhhccccccccc--ccccCCCCCcee
Confidence 456788888887777741 133 566663 345667776654
No 135
>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=47.11 E-value=20 Score=30.65 Aligned_cols=31 Identities=23% Similarity=0.625 Sum_probs=23.1
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-.+.+.|-+||+.-..++ | +..--|..|||.
T Consensus 109 g~G~l~C~~Cg~~~~~~~---------~-~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTH---------P-ERLPPCPKCGHT 139 (146)
T ss_pred cCceEecccCCCEEEecC---------C-CcCCCCCCCCCC
Confidence 356799999999777653 1 236679999985
No 136
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.48 E-value=9.6 Score=30.98 Aligned_cols=28 Identities=18% Similarity=0.409 Sum_probs=18.1
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
....+.|+.||+.-. . ...++.|..||-
T Consensus 67 vp~~~~C~~Cg~~~~----~--------~~~~~~CP~Cgs 94 (113)
T PRK12380 67 KPAQAWCWDCSQVVE----I--------HQHDAQCPHCHG 94 (113)
T ss_pred eCcEEEcccCCCEEe----c--------CCcCccCcCCCC
Confidence 355689999993222 1 124667999984
No 137
>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=46.33 E-value=11 Score=30.63 Aligned_cols=28 Identities=14% Similarity=0.483 Sum_probs=17.9
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
....+.|+.||..-. . ...++.|..||-
T Consensus 67 ~p~~~~C~~Cg~~~~----~--------~~~~~~CP~Cgs 94 (115)
T TIGR00100 67 EPVECECEDCSEEVS----P--------EIDLYRCPKCHG 94 (115)
T ss_pred eCcEEEcccCCCEEe----c--------CCcCccCcCCcC
Confidence 455689999993222 1 112678999984
No 138
>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=45.32 E-value=17 Score=30.71 Aligned_cols=40 Identities=15% Similarity=0.340 Sum_probs=21.4
Q ss_pred ccceecCCCCCCceEEEeeeccC-----CCCCCeEEEEcCCCCCc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRS-----ADEPMTTYVTCAECNKR 311 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rs-----ade~mt~f~~C~~C~~~ 311 (314)
.....|+.|++.=...---+.+. .-+....|+.|..||.-
T Consensus 89 ~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 89 PIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 33568999998322110000000 11123459999999875
No 139
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.62 E-value=8.2 Score=31.92 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=8.7
Q ss_pred eecCCCCCCce
Q 035641 275 FKCSGCGKSNC 285 (314)
Q Consensus 275 ~~C~~C~~~~~ 285 (314)
-.||+||.-+-
T Consensus 22 grCP~CGeGrL 32 (126)
T COG5349 22 GRCPRCGEGRL 32 (126)
T ss_pred CCCCCCCCchh
Confidence 58999997665
No 140
>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=44.42 E-value=50 Score=23.85 Aligned_cols=36 Identities=19% Similarity=0.413 Sum_probs=24.9
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~ 309 (314)
.....|+.|+..-.+....| ...-.+....+|..|+
T Consensus 13 ~~~~~C~~C~G~G~~~~~~~--~~~~~~~~~~~C~~C~ 48 (66)
T PF00684_consen 13 KKPKTCPQCNGSGQVTRRQQ--TPGGVFQMQQTCPKCG 48 (66)
T ss_dssp TT-EE-TTSSSSSEEEEEEE--SSSTTEEEEEE-TTTS
T ss_pred CCCcCCcCCCCeeEEEEEEe--CCCeEEEEEEECCCCc
Confidence 44579999999998887765 3444566788899985
No 141
>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=44.19 E-value=24 Score=23.00 Aligned_cols=10 Identities=20% Similarity=1.095 Sum_probs=7.3
Q ss_pred EEcCCCCCcc
Q 035641 303 VTCAECNKRW 312 (314)
Q Consensus 303 ~~C~~C~~~w 312 (314)
+.|..||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3588898764
No 142
>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=44.08 E-value=14 Score=31.60 Aligned_cols=36 Identities=14% Similarity=0.504 Sum_probs=23.8
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
...||+||+..+... .+- +..+=.-.|.|..|..-|
T Consensus 105 ~~~cp~c~s~~t~~~-s~f--g~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT-SIF--GPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee-cCC--CChhhHHHhhhhhhCCcH
Confidence 379999999888642 111 222334678899998754
No 143
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=43.71 E-value=19 Score=25.60 Aligned_cols=34 Identities=18% Similarity=0.473 Sum_probs=19.3
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
..+.||-||++.- .+.|.--+--..-+-|..|.+
T Consensus 3 ~Wi~CP~CgnKTR----~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 3 EWILCPICGNKTR----LKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred eEEECCCCCCccc----eeeecCceeccccccCCCCCc
Confidence 3567888887653 244432222334466788865
No 144
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=43.51 E-value=46 Score=34.92 Aligned_cols=15 Identities=7% Similarity=0.071 Sum_probs=12.5
Q ss_pred hhhhcCCCChhhhhc
Q 035641 222 RRVLIGEVTPERLAT 236 (314)
Q Consensus 222 ~~vl~G~i~p~~lv~ 236 (314)
..|..|+.++++|+.
T Consensus 535 ~~I~~G~~~~~~~l~ 549 (610)
T TIGR01051 535 DEIAEGKAEWKPVLK 549 (610)
T ss_pred HHHHcCCCCHHHHHH
Confidence 568889999998876
No 145
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.15 E-value=12 Score=37.37 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=20.9
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
..-.||.||.+- .|+... -|.|..||.+.+
T Consensus 349 ~~p~Cp~Cg~~m--------~S~G~~---g~rC~kCg~~~~ 378 (421)
T COG1571 349 VNPVCPRCGGRM--------KSAGRN---GFRCKKCGTRAR 378 (421)
T ss_pred cCCCCCccCCch--------hhcCCC---CcccccccccCC
Confidence 334799999853 344443 799999998753
No 146
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=43.10 E-value=12 Score=33.84 Aligned_cols=34 Identities=29% Similarity=0.689 Sum_probs=24.1
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
+.-.+.||.|.+..--| |-+.-|.. -|+|..|+|
T Consensus 189 ~~~alIC~~C~hhngl~-----~~~ek~~~-efiC~~Cn~ 222 (251)
T COG5415 189 PFKALICPQCHHHNGLY-----RLAEKPII-EFICPHCNH 222 (251)
T ss_pred chhhhcccccccccccc-----ccccccch-heecccchh
Confidence 34457899999887766 33444544 688999976
No 147
>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=42.88 E-value=18 Score=22.32 Aligned_cols=26 Identities=19% Similarity=0.487 Sum_probs=12.5
Q ss_pred ecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 276 KCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 276 ~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-|++||..-... .. -.-.+|..||+.
T Consensus 5 fC~~CG~~t~~~-------~~---g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPA-------PG---GWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE--------SS---SS-EEESSSS-E
T ss_pred ccCcCCccccCC-------CC---cCEeECCCCcCE
Confidence 399999865421 11 134678999875
No 148
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized 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.
Probab=42.69 E-value=13 Score=40.74 Aligned_cols=23 Identities=30% Similarity=0.784 Sum_probs=17.9
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
....||+||. .|.+.+|..||-+
T Consensus 624 ~~RKCPkCG~----------------yTlk~rCP~CG~~ 646 (1095)
T TIGR00354 624 AIRKCPQCGK----------------ESFWLKCPVCGEL 646 (1095)
T ss_pred EEEECCCCCc----------------ccccccCCCCCCc
Confidence 4568999987 4778899999854
No 149
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=42.66 E-value=5.5 Score=27.74 Aligned_cols=36 Identities=31% Similarity=0.635 Sum_probs=20.5
Q ss_pred ceecCCCCCCceEEEee----eccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQM----QTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~----q~rsade~mt~f~~C~~C~~~w 312 (314)
.|+||-||. +...-.+ +....+++. -|+|.-|..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~--~v~CPiC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESK--NVVCPICSSRV 41 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCC--CccCCCchhhh
Confidence 588999988 5333222 222333333 48888887543
No 150
>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=42.55 E-value=20 Score=28.73 Aligned_cols=28 Identities=25% Similarity=0.567 Sum_probs=20.2
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
-.|--| ....|+|-- -.++|.+||.+|.
T Consensus 36 daCeiC--~~~GY~q~g---------~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 36 DACEIC--GPKGYYQEG---------DQLVCKNCGVRFN 63 (102)
T ss_pred Eecccc--CCCceEEEC---------CEEEEecCCCEEe
Confidence 379999 445566531 2689999999995
No 151
>PRK08173 DNA topoisomerase III; Validated
Probab=42.10 E-value=45 Score=36.54 Aligned_cols=15 Identities=7% Similarity=0.286 Sum_probs=12.0
Q ss_pred hhhhcCCCChhhhhc
Q 035641 222 RRVLIGEVTPERLAT 236 (314)
Q Consensus 222 ~~vl~G~i~p~~lv~ 236 (314)
..|-.|++++++|..
T Consensus 581 ~~I~~G~~~~~~f~~ 595 (862)
T PRK08173 581 SQIERGKLSRDAFMQ 595 (862)
T ss_pred HHHHcCCCCHHHHHH
Confidence 567889998888865
No 152
>PRK03954 ribonuclease P protein component 4; Validated
Probab=41.78 E-value=27 Score=28.87 Aligned_cols=37 Identities=24% Similarity=0.500 Sum_probs=22.3
Q ss_pred ceecCCCCCC-----ceEEEeeeccCCCCCCeEEEEcCCCCCcccC
Q 035641 274 QFKCSGCGKS-----NCSYHQMQTRSADEPMTTYVTCAECNKRWKC 314 (314)
Q Consensus 274 ~~~C~~C~~~-----~~~~~q~q~rsade~mt~f~~C~~C~~~w~~ 314 (314)
..-|.+|..- .+.+.. +....+ .+.++|..||+.-+|
T Consensus 64 R~~CK~C~t~LiPG~n~~vRi---~~~~~~-~vvitCl~CG~~kR~ 105 (121)
T PRK03954 64 RRYCKRCHSFLVPGVNARVRL---RQKRMP-HVVITCLECGHIMRY 105 (121)
T ss_pred HHHhhcCCCeeecCCceEEEE---ecCCcc-eEEEECccCCCEEee
Confidence 3569999743 444332 222112 478899999997554
No 153
>PRK07219 DNA topoisomerase I; Validated
Probab=40.82 E-value=45 Score=36.29 Aligned_cols=18 Identities=11% Similarity=0.121 Sum_probs=14.1
Q ss_pred hhhhhcCCCChhhhhcCC
Q 035641 221 RRRVLIGEVTPERLATMT 238 (314)
Q Consensus 221 r~~vl~G~i~p~~lv~Ms 238 (314)
...|-.|++++++|+.-.
T Consensus 549 L~~I~~G~~~~~~~l~~~ 566 (822)
T PRK07219 549 MQAIEDGKKKKEDVTEES 566 (822)
T ss_pred HHHHHcCCCCHHHHHHHH
Confidence 357889999999987743
No 154
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=40.45 E-value=38 Score=23.15 Aligned_cols=30 Identities=20% Similarity=0.553 Sum_probs=19.6
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAEC 308 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C 308 (314)
+..+.|+.||+.-.. +.+. .-..+|.|.++
T Consensus 3 ~g~l~C~~CG~~m~~----~~~~---~~~~yy~C~~~ 32 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTR----RKRK---GKYRYYRCSNR 32 (58)
T ss_pred CCcEEcccCCcEeEE----EECC---CCceEEEcCCC
Confidence 456889999987444 2232 22378999765
No 155
>KOG3286 consensus Selenoprotein T [General function prediction only]
Probab=40.25 E-value=17 Score=32.73 Aligned_cols=33 Identities=21% Similarity=0.252 Sum_probs=27.2
Q ss_pred CCCCceEEEeeeccCCCC------CCeEEEEcCCCCCcc
Q 035641 280 CGKSNCSYHQMQTRSADE------PMTTYVTCAECNKRW 312 (314)
Q Consensus 280 C~~~~~~~~q~q~rsade------~mt~f~~C~~C~~~w 312 (314)
|.-.+..|+|-|.-+.-+ |..+|..|..||++-
T Consensus 46 ~~~~e~~~~~g~ke~gv~~~~~~~ptl~i~fCvSCgYk~ 84 (226)
T KOG3286|consen 46 DEIDETSFAQGQKESGVGKHIKYGPTLEINFCVSCGYKQ 84 (226)
T ss_pred cccchhcccCcccccCcccccccCCcEEEEEEEecCcHH
Confidence 888899999988766554 777999999999873
No 156
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=40.16 E-value=33 Score=32.95 Aligned_cols=38 Identities=24% Similarity=0.603 Sum_probs=25.2
Q ss_pred cceecCCCCCCce-EEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 273 DQFKCSGCGKSNC-SYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 273 ~~~~C~~C~~~~~-~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
....|+.||+.+- .|+.+- .+++-....+|..|+.-+|
T Consensus 225 ~R~~C~~Cg~~~~l~y~~~~---~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 225 VRVKCSNCEQSGKLHYWSLD---SEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred cCccCCCCCCCCceeeeeec---CCCcceEeeecccccccce
Confidence 3568999997643 344441 2334467799999987665
No 157
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.79 E-value=7.5 Score=28.19 Aligned_cols=32 Identities=19% Similarity=0.506 Sum_probs=19.7
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
...||.|..-.. +|-+. |.-.-.+.|+.|||.
T Consensus 10 GA~CP~C~~~Dt----l~mW~--En~ve~vECV~CG~~ 41 (66)
T COG3529 10 GAVCPACQAQDT----LAMWR--ENNVEIVECVKCGHH 41 (66)
T ss_pred cCCCcccchhhH----HHHHH--hcCCceEehhhcchH
Confidence 357888876554 23222 233457889999874
No 158
>PF14122 YokU: YokU-like protein
Probab=39.66 E-value=21 Score=27.70 Aligned_cols=37 Identities=24% Similarity=0.641 Sum_probs=24.3
Q ss_pred ecCCCCCC------ceEEEeeec--cCCCCCCeEEEEcCCCCCcc
Q 035641 276 KCSGCGKS------NCSYHQMQT--RSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 276 ~C~~C~~~------~~~~~q~q~--rsade~mt~f~~C~~C~~~w 312 (314)
+|.-||.. ..+|+.+.. |.-.=.+|.-++|.+||-.+
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 47788865 456776632 33334567789999998643
No 159
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=37.57 E-value=23 Score=33.52 Aligned_cols=31 Identities=19% Similarity=0.576 Sum_probs=20.5
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.+..| ||+||++.-.. + --.-+.|.+|||..
T Consensus 109 ~~~RF-Cg~CG~~~~~~--------~--~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRF-CGRCGTKTYPR--------E--GGWARVCPKCGHEH 139 (279)
T ss_pred hhCcC-CCCCCCcCccc--------c--CceeeeCCCCCCcc
Confidence 45556 99999865421 1 12357899999864
No 160
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=37.26 E-value=14 Score=36.90 Aligned_cols=38 Identities=16% Similarity=0.399 Sum_probs=25.0
Q ss_pred CCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 270 GTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 270 ~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
++...|.||.|...-. ++-.-+-=+.++..|.|..||-
T Consensus 124 t~~~~Y~Cp~C~kkyt---~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYT---SLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchh---hhHHHHhhcccCceEEEecCCC
Confidence 3456799999987533 3311122345678999999974
No 161
>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=37.23 E-value=9 Score=37.31 Aligned_cols=30 Identities=30% Similarity=0.912 Sum_probs=14.3
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC-cc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK-RW 312 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~-~w 312 (314)
--|.|+.||++-.+|..+. ...|.+||. .|
T Consensus 284 RFFkC~~C~~Rt~sl~r~P----------~~~C~~Cg~~~w 314 (344)
T PF09332_consen 284 RFFKCKDCGNRTISLERLP----------KKHCSNCGSSKW 314 (344)
T ss_dssp EEEE-T-TS-EEEESSSS------------S--TTT-S---
T ss_pred eeEECCCCCCeeeecccCC----------CCCCCcCCcCce
Confidence 3489999999977664332 247999985 36
No 162
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=36.36 E-value=23 Score=25.28 Aligned_cols=9 Identities=44% Similarity=0.936 Sum_probs=4.7
Q ss_pred ceecCCCCC
Q 035641 274 QFKCSGCGK 282 (314)
Q Consensus 274 ~~~C~~C~~ 282 (314)
+-.|++||-
T Consensus 5 mr~C~~Cgv 13 (56)
T PRK13130 5 IRKCPKCGV 13 (56)
T ss_pred ceECCCCCC
Confidence 345665553
No 163
>PF15616 TerY-C: TerY-C metal binding domain
Probab=36.21 E-value=23 Score=29.73 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=8.2
Q ss_pred eecCCCCCCce
Q 035641 275 FKCSGCGKSNC 285 (314)
Q Consensus 275 ~~C~~C~~~~~ 285 (314)
-.||.||+.-+
T Consensus 78 PgCP~CGn~~~ 88 (131)
T PF15616_consen 78 PGCPHCGNQYA 88 (131)
T ss_pred CCCCCCcChhc
Confidence 47999998644
No 164
>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=36.18 E-value=20 Score=22.72 Aligned_cols=11 Identities=18% Similarity=0.389 Sum_probs=7.6
Q ss_pred EEEcCCCCCcc
Q 035641 302 YVTCAECNKRW 312 (314)
Q Consensus 302 f~~C~~C~~~w 312 (314)
+|+|..||+..
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 57777777754
No 165
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.86 E-value=22 Score=39.24 Aligned_cols=14 Identities=21% Similarity=0.316 Sum_probs=10.2
Q ss_pred CHHHHHHHHHHHHH
Q 035641 66 CEKVQNAASELLHI 79 (314)
Q Consensus 66 ~~~i~~~Ak~Li~~ 79 (314)
.+.|...|+.|++.
T Consensus 246 aEGi~~KA~Ki~k~ 259 (1121)
T PRK04023 246 AEGIALKAPKILKY 259 (1121)
T ss_pred hhHHHhhhHHHHHH
Confidence 46678888887765
No 166
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.82 E-value=22 Score=33.51 Aligned_cols=21 Identities=24% Similarity=0.474 Sum_probs=17.4
Q ss_pred CccceecCCCCCCceEEEeee
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQ 291 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q 291 (314)
.|....||.||..-+.-++++
T Consensus 236 ~t~~~~C~~Cg~~PtiP~~~~ 256 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIPHVIG 256 (298)
T ss_pred ccCCceeeccCCCCCCCeeec
Confidence 467789999999888878876
No 167
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=35.52 E-value=18 Score=29.48 Aligned_cols=29 Identities=17% Similarity=0.548 Sum_probs=17.8
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
....+.|+.||. +|... ...++.|..||-
T Consensus 67 ~p~~~~C~~Cg~----~~~~~-------~~~~~~CP~Cgs 95 (114)
T PRK03681 67 QEAECWCETCQQ----YVTLL-------TQRVRRCPQCHG 95 (114)
T ss_pred eCcEEEcccCCC----eeecC-------CccCCcCcCcCC
Confidence 355689999995 22221 112367999984
No 168
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=34.97 E-value=20 Score=19.85 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=5.9
Q ss_pred EEcCCCCCcc
Q 035641 303 VTCAECNKRW 312 (314)
Q Consensus 303 ~~C~~C~~~w 312 (314)
|.|..||..+
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 4566666554
No 169
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=34.47 E-value=21 Score=40.54 Aligned_cols=23 Identities=43% Similarity=0.966 Sum_probs=16.6
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.+.||+||. .+.+..|..||.++
T Consensus 674 ~~~Cp~Cg~----------------~~~~~~Cp~CG~~~ 696 (1627)
T PRK14715 674 FFKCPKCGK----------------VGLYHVCPFCGTRV 696 (1627)
T ss_pred eeeCCCCCC----------------ccccccCcccCCcc
Confidence 468888886 45677888888653
No 170
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.21 E-value=15 Score=30.05 Aligned_cols=28 Identities=18% Similarity=0.545 Sum_probs=16.3
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
...+.|..||+.-. .. ...|+.|..||.
T Consensus 69 p~~~~C~~Cg~~~~----~~-------~~~~~~CP~Cgs 96 (117)
T PRK00564 69 KVELECKDCSHVFK----PN-------ALDYGVCEKCHS 96 (117)
T ss_pred CCEEEhhhCCCccc----cC-------CccCCcCcCCCC
Confidence 45678999983221 11 113445999985
No 171
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=34.21 E-value=25 Score=22.04 Aligned_cols=12 Identities=17% Similarity=0.434 Sum_probs=9.5
Q ss_pred eEEEEcCCCCCc
Q 035641 300 TTYVTCAECNKR 311 (314)
Q Consensus 300 t~f~~C~~C~~~ 311 (314)
..||.|..||+.
T Consensus 2 ~~~ykC~~CGni 13 (34)
T cd00974 2 LEVYKCEICGNI 13 (34)
T ss_pred CcEEEcCCCCcE
Confidence 358999999875
No 172
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=34.09 E-value=34 Score=27.69 Aligned_cols=38 Identities=16% Similarity=0.391 Sum_probs=18.4
Q ss_pred ceecCCCCCCceEEEeeeccCCCCC---CeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEP---MTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~---mt~f~~C~~C~~~ 311 (314)
-.-|..|++++-+-.+-.+-..+++ .|.--+|.+|+|.
T Consensus 27 ~~~Ca~C~krdfv~i~nk~~~eedgeEivTY~HvC~nC~Hv 67 (112)
T PF06573_consen 27 FVGCASCQKRDFVLISNKSIEEEDGEEIVTYDHVCKNCHHV 67 (112)
T ss_dssp B---SSS--SS-EEEEEEEEEEETTEEEEEEEEEETTT--E
T ss_pred chhhhccCCCCcEEEecccccccCCcEEEEeeeccCccceE
Confidence 3479999999866644433332222 4666789999873
No 173
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=33.98 E-value=41 Score=34.52 Aligned_cols=35 Identities=23% Similarity=0.298 Sum_probs=21.7
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.-.|++||.-..+-.-. . -.+.-|+.|.|. |||..
T Consensus 175 ~pic~~cg~~~~~~~~~--~-d~~~~~v~y~~~-cG~~~ 209 (510)
T PRK00750 175 LPICPKCGKVLTTPVIS--Y-DAEAGTVTYDCE-CGHEG 209 (510)
T ss_pred eeeCCCCCccceEEEEE--E-eCCCCEEEEEcC-CCCEE
Confidence 45799999876544311 1 223347778774 99863
No 174
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=33.75 E-value=19 Score=38.73 Aligned_cols=25 Identities=32% Similarity=0.679 Sum_probs=17.4
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-.||.||. ...|| |+ +++|.+||+.
T Consensus 725 ~~Cp~Cg~--~l~~~-------~G---C~~C~~CG~s 749 (752)
T PRK08665 725 GACPECGS--ILEHE-------EG---CVVCHSCGYS 749 (752)
T ss_pred CCCCCCCc--ccEEC-------CC---CCcCCCCCCC
Confidence 36999984 33333 23 7899999985
No 175
>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=33.68 E-value=20 Score=25.29 Aligned_cols=33 Identities=21% Similarity=0.616 Sum_probs=18.8
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
=.++| +||.. |.+...-..++ ...+.|..|...
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 34799 99998 33321111122 678999999753
No 176
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=33.48 E-value=26 Score=28.65 Aligned_cols=24 Identities=17% Similarity=0.400 Sum_probs=18.0
Q ss_pred ccccccCCCccceecCCCCCCceE
Q 035641 263 EVPEKKKGTTDQFKCSGCGKSNCS 286 (314)
Q Consensus 263 ~~~~~~~~~t~~~~C~~C~~~~~~ 286 (314)
|+-....++|.-++|++|+.+...
T Consensus 91 QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 91 QLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hcccccCCceEEEEcCccceeeec
Confidence 344455678999999999987654
No 177
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=33.28 E-value=27 Score=21.85 Aligned_cols=12 Identities=17% Similarity=0.465 Sum_probs=9.6
Q ss_pred eEEEEcCCCCCc
Q 035641 300 TTYVTCAECNKR 311 (314)
Q Consensus 300 t~f~~C~~C~~~ 311 (314)
..||.|..||+.
T Consensus 5 ~~~ykC~~Cgni 16 (34)
T TIGR00319 5 GQVYKCEVCGNI 16 (34)
T ss_pred CcEEEcCCCCcE
Confidence 349999999975
No 178
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=33.24 E-value=26 Score=22.74 Aligned_cols=13 Identities=15% Similarity=0.608 Sum_probs=7.8
Q ss_pred CeEEEEcCCCCCc
Q 035641 299 MTTYVTCAECNKR 311 (314)
Q Consensus 299 mt~f~~C~~C~~~ 311 (314)
+..||.|..||+.
T Consensus 3 ~~~~YkC~~CGni 15 (36)
T PF06397_consen 3 KGEFYKCEHCGNI 15 (36)
T ss_dssp TTEEEE-TTT--E
T ss_pred cccEEEccCCCCE
Confidence 4568999999975
No 179
>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=32.62 E-value=13 Score=29.44 Aligned_cols=36 Identities=19% Similarity=0.505 Sum_probs=27.5
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-.|.+|+++.++.-..|++ +-=+|..|-+|..||.+
T Consensus 6 ~~c~~c~g~g~al~~~~s~-~~~G~pvfk~c~rcgg~ 41 (95)
T PF03589_consen 6 DSCRRCAGDGAALDMKQSK-AQFGVPVFKDCERCGGR 41 (95)
T ss_pred CCcCccCCcceeccHHHhH-hccCCchhhhhhhhcCC
Confidence 4688999999887766765 33378899999999754
No 180
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.41 E-value=28 Score=39.38 Aligned_cols=14 Identities=14% Similarity=0.183 Sum_probs=10.2
Q ss_pred CHHHHHHHHHHHHH
Q 035641 66 CEKVQNAASELLHI 79 (314)
Q Consensus 66 ~~~i~~~Ak~Li~~ 79 (314)
.+.|...|+.|++.
T Consensus 248 aEGi~~Ka~Ki~k~ 261 (1337)
T PRK14714 248 AEGIALKAPKIQKY 261 (1337)
T ss_pred hhhHhhhcHHHHHH
Confidence 46678888887765
No 181
>PRK05582 DNA topoisomerase I; Validated
Probab=32.36 E-value=98 Score=32.71 Aligned_cols=16 Identities=6% Similarity=0.005 Sum_probs=12.8
Q ss_pred hhhhcCCCChhhhhcC
Q 035641 222 RRVLIGEVTPERLATM 237 (314)
Q Consensus 222 ~~vl~G~i~p~~lv~M 237 (314)
..|..|+.++++|+..
T Consensus 529 ~~I~~G~~~~~~~l~~ 544 (650)
T PRK05582 529 DEIEEGKEDWKKVLDD 544 (650)
T ss_pred HHHHcCCCCHHHHHHH
Confidence 4578899999988764
No 182
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=32.31 E-value=21 Score=28.79 Aligned_cols=13 Identities=31% Similarity=1.209 Sum_probs=11.2
Q ss_pred ceecCCCCCCceE
Q 035641 274 QFKCSGCGKSNCS 286 (314)
Q Consensus 274 ~~~C~~C~~~~~~ 286 (314)
.|+||+||+++|.
T Consensus 74 ~~PC~~C~S~KCG 86 (103)
T PF14949_consen 74 HYPCPKCGSRKCG 86 (103)
T ss_pred cccCCCCCCCccC
Confidence 4799999999984
No 183
>PRK06599 DNA topoisomerase I; Validated
Probab=32.15 E-value=88 Score=33.23 Aligned_cols=15 Identities=7% Similarity=0.027 Sum_probs=12.8
Q ss_pred hhhhcCCCChhhhhc
Q 035641 222 RRVLIGEVTPERLAT 236 (314)
Q Consensus 222 ~~vl~G~i~p~~lv~ 236 (314)
..|..|+.++++|+.
T Consensus 543 ~~I~~G~~~~~~~l~ 557 (675)
T PRK06599 543 DEIAEGKKDWKPVLR 557 (675)
T ss_pred HHHHcCCCCHHHHHH
Confidence 568899999999977
No 184
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=31.53 E-value=35 Score=24.86 Aligned_cols=17 Identities=24% Similarity=0.663 Sum_probs=12.4
Q ss_pred CCCeEEEEcCCCCCccc
Q 035641 297 EPMTTYVTCAECNKRWK 313 (314)
Q Consensus 297 e~mt~f~~C~~C~~~w~ 313 (314)
+.+.--.+|.+||+.|-
T Consensus 48 ~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 48 EIVEGELICPECGREYP 64 (68)
T ss_dssp ETTTTEEEETTTTEEEE
T ss_pred cccCCEEEcCCCCCEEe
Confidence 34555789999988763
No 185
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=31.52 E-value=35 Score=26.03 Aligned_cols=26 Identities=27% Similarity=0.654 Sum_probs=16.6
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCC
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~ 309 (314)
++||=||..-- .+.+--+|.+|..|+
T Consensus 2 ~~CPCCg~~Tl---------~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 2 YPCPCCGYYTL---------EERGEGTYDICPVCF 27 (78)
T ss_pred ccCCCCCcEEe---------ccCCCcCceECCCCC
Confidence 68999986322 222333489999995
No 186
>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=30.46 E-value=1.9e+02 Score=22.23 Aligned_cols=66 Identities=15% Similarity=0.188 Sum_probs=37.6
Q ss_pred CCcHHHHHHHHHHHHHHHhhhccccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCChhhHhHHHhHHhhc
Q 035641 141 AKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNM 212 (314)
Q Consensus 141 ~~d~~R~k~~~~L~~aL~~~~~~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~~~yk~k~Rsl~~NL 212 (314)
.+..+|+..++-|..++-.......-.+.-... ...-|..||..+|+.-.+ -..|=.-+-..++.+
T Consensus 10 vt~~lR~hlV~KLv~aI~P~pdp~a~~d~rm~~-----l~~yarkvE~~~fe~A~s-reeYY~llA~kiy~i 75 (81)
T PF02172_consen 10 VTPDLRNHLVHKLVQAIFPTPDPNAMNDPRMKN-----LIEYARKVEKDMFETAQS-REEYYHLLAEKIYKI 75 (81)
T ss_dssp T-HHHHHHHHHHHHHHHS-SSSCCCCCSHHHHH-----HHHHHHHHHHHHHHC-SS-HHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhCCCCChhhhhhHHHHH-----HHHHHHHHHHHHHHHhcc-HHHHHHHHHHHHHHH
Confidence 357899999999999987553221111111211 246789999999987654 245644443344444
No 187
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=30.06 E-value=30 Score=18.72 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=4.6
Q ss_pred EEcCCCCCcc
Q 035641 303 VTCAECNKRW 312 (314)
Q Consensus 303 ~~C~~C~~~w 312 (314)
|.|..||..+
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 4566666554
No 188
>PRK07726 DNA topoisomerase III; Provisional
Probab=30.00 E-value=1.1e+02 Score=32.39 Aligned_cols=15 Identities=7% Similarity=0.239 Sum_probs=11.4
Q ss_pred hhhhcCCCChhhhhc
Q 035641 222 RRVLIGEVTPERLAT 236 (314)
Q Consensus 222 ~~vl~G~i~p~~lv~ 236 (314)
..|-.|+.++++|+.
T Consensus 569 ~~I~~G~~~~~~fl~ 583 (658)
T PRK07726 569 DQISEGQLSYQDFMQ 583 (658)
T ss_pred HHHHcCCCCHHHHHH
Confidence 467788888888765
No 189
>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=29.76 E-value=11 Score=26.66 Aligned_cols=23 Identities=26% Similarity=0.769 Sum_probs=15.8
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
+...||.||.-. ....+|.+||+
T Consensus 25 ~l~~c~~cg~~~---------------~~H~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------------LPHRVCPSCGY 47 (56)
T ss_dssp SEEESSSSSSEE---------------STTSBCTTTBB
T ss_pred ceeeeccCCCEe---------------cccEeeCCCCe
Confidence 668999999522 12477888874
No 190
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=29.64 E-value=67 Score=35.20 Aligned_cols=19 Identities=5% Similarity=-0.317 Sum_probs=12.5
Q ss_pred hhhhhcCCCChhhhhcCCh
Q 035641 221 RRRVLIGEVTPERLATMTP 239 (314)
Q Consensus 221 r~~vl~G~i~p~~lv~Ms~ 239 (314)
...|..|+++..+|+..--
T Consensus 552 Ld~I~~G~~~~~~~l~~f~ 570 (860)
T PRK06319 552 LELIADNKKPWKLLLQEFW 570 (860)
T ss_pred HHHHHcCCccHHHHHHHHH
Confidence 3567778887777766433
No 191
>PHA02540 61 DNA primase; Provisional
Probab=29.60 E-value=53 Score=31.96 Aligned_cols=34 Identities=18% Similarity=0.516 Sum_probs=24.5
Q ss_pred cceecCCCCC-----CceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 273 DQFKCSGCGK-----SNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 273 ~~~~C~~C~~-----~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
=.+.||=|+. +++.|+-...+. -.||-|-+||..
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~-----~~~yhCFgCGa~ 64 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEKKD-----GGVFKCHNCGYH 64 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEeccCC-----ceEEEecCCCCC
Confidence 4789999997 346676654331 569999999963
No 192
>PRK14973 DNA topoisomerase I; Provisional
Probab=29.58 E-value=33 Score=37.93 Aligned_cols=32 Identities=16% Similarity=0.282 Sum_probs=21.1
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
...||.||..-. +..|.+.-|+ |+-|..|.|.
T Consensus 635 ~~~Cp~CG~p~~----~~~r~Gr~g~--fl~CP~C~~~ 666 (936)
T PRK14973 635 DEVCPIHHLNHV----RLIRKGARPW--DIGCPLCSHI 666 (936)
T ss_pred CCCCCCCCCCce----EEeecCCCcc--cccCccccch
Confidence 357999998622 2224444555 8889999884
No 193
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.14 E-value=46 Score=24.24 Aligned_cols=16 Identities=38% Similarity=0.854 Sum_probs=12.9
Q ss_pred CCCCCeEEEEcCCCCCccc
Q 035641 295 ADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 295 ade~mt~f~~C~~C~~~w~ 313 (314)
++++ +++|..||.+|+
T Consensus 44 g~~g---ev~CPYC~t~y~ 59 (62)
T COG4391 44 GDEG---EVVCPYCSTRYR 59 (62)
T ss_pred CCCC---cEecCccccEEE
Confidence 4554 899999999886
No 194
>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=29.05 E-value=61 Score=19.53 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=14.4
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
.+|++|++.-...-+. -...|.|..|-+
T Consensus 2 ~~C~rC~~~~~~~~~~--------~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGIN--------GRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEET--------TEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEec--------CCCCeECcCCcC
Confidence 4799999875544332 233577888864
No 195
>PRK04023 DNA polymerase II large subunit; Validated
Probab=29.04 E-value=30 Score=38.26 Aligned_cols=11 Identities=27% Similarity=0.546 Sum_probs=5.8
Q ss_pred cceecCCCCCC
Q 035641 273 DQFKCSGCGKS 283 (314)
Q Consensus 273 ~~~~C~~C~~~ 283 (314)
..+.||.||..
T Consensus 637 ~~frCP~CG~~ 647 (1121)
T PRK04023 637 FYRRCPFCGTH 647 (1121)
T ss_pred CcccCCCCCCC
Confidence 44556666543
No 196
>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=28.93 E-value=38 Score=29.26 Aligned_cols=10 Identities=30% Similarity=0.660 Sum_probs=7.9
Q ss_pred EEEcCCCCCc
Q 035641 302 YVTCAECNKR 311 (314)
Q Consensus 302 f~~C~~C~~~ 311 (314)
=.-|.+||+.
T Consensus 68 PsYC~~CGkp 77 (158)
T PF10083_consen 68 PSYCHNCGKP 77 (158)
T ss_pred ChhHHhCCCC
Confidence 3569999986
No 197
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=28.93 E-value=59 Score=33.38 Aligned_cols=33 Identities=21% Similarity=0.390 Sum_probs=21.9
Q ss_pred cceecCCCCC-CceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 273 DQFKCSGCGK-SNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 273 ~~~~C~~C~~-~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
-+-.|++||. ..+..... |.+-|+-|.|. |||.
T Consensus 170 ~~piC~kcGri~~t~v~~~-----d~~~~v~Y~Ce-~Gh~ 203 (521)
T COG1384 170 FMPICEKCGRILTTPVIEW-----DGEGTVEYRCE-CGHE 203 (521)
T ss_pred ccccccccCCcceeEEEEe-----cCCceEEEEec-CCcc
Confidence 3567999998 55544332 33368889997 8873
No 198
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=28.46 E-value=33 Score=33.13 Aligned_cols=41 Identities=29% Similarity=0.554 Sum_probs=28.2
Q ss_pred cceecCCCCCCceEEEee------------ec---cCCCCCCeEE------EEcCCCCCccc
Q 035641 273 DQFKCSGCGKSNCSYHQM------------QT---RSADEPMTTY------VTCAECNKRWK 313 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~------------q~---rsade~mt~f------~~C~~C~~~w~ 313 (314)
.-|+||-=|..+++-.|. |. --+.++|..| |+|..|++||+
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYK 409 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYK 409 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhc
Confidence 348999655555544333 11 2377889988 99999999986
No 199
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=28.23 E-value=5.9 Score=25.45 Aligned_cols=31 Identities=26% Similarity=0.641 Sum_probs=15.9
Q ss_pred cCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 277 CSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 277 C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
|..|+-.+...+ |.+..+ ...+|..||-.|+
T Consensus 1 C~~C~tt~t~~W----R~~~~g--~~~LCn~Cg~~~k 31 (36)
T PF00320_consen 1 CSNCGTTETPQW----RRGPNG--NRTLCNACGLYYK 31 (36)
T ss_dssp -TTT--ST-SSE----EEETTS--EE-EEHHHHHHHH
T ss_pred CcCCcCCCCchh----hcCCCC--CCHHHHHHHHHHH
Confidence 677887775443 333322 2238999998775
No 200
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=27.75 E-value=68 Score=22.52 Aligned_cols=34 Identities=15% Similarity=0.311 Sum_probs=21.5
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
+.||.||..-...-.. ..++-..+--|-.|-+-+
T Consensus 1 i~CPyCge~~~~~iD~----s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDP----SAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEEEEec----CCCCeeEEeehhhcCCcc
Confidence 4699999877665443 222456666777776554
No 201
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=27.53 E-value=19 Score=27.72 Aligned_cols=47 Identities=23% Similarity=0.396 Sum_probs=21.5
Q ss_pred hhcCChhhcCcHHHHHHHHHHHHhhhhhhcccccc-CCCccceecCCCCCCce
Q 035641 234 LATMTPEELASDERRQENEEIKAKFMFKCEVPEKK-KGTTDQFKCSGCGKSNC 285 (314)
Q Consensus 234 lv~Ms~eEmas~e~k~~~~~~~~~~l~~~~~~~~~-~~~t~~~~C~~C~~~~~ 285 (314)
++-=+|++++....++.-.-.++-++ +.-. -.+...|.||.||+.--
T Consensus 29 ivVTTPq~la~~dv~r~~~~~~~~~v-----pilGvVENMs~~~Cp~Cg~~~~ 76 (81)
T PF10609_consen 29 IVVTTPQELALADVRRAIDMFRKLNV-----PILGVVENMSYFVCPHCGERIY 76 (81)
T ss_dssp EEEE-CCC--HHHHHHHHHHHHCTT------EEEEEEECT-EEE-TTT--EEE
T ss_pred EEEeCCHHHHHHHHHHHHHHHHhcCC-----CcEEEEECCCccCCCCCCCeec
Confidence 44457888888877765543333222 1111 12467799999998644
No 202
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=27.42 E-value=42 Score=26.89 Aligned_cols=38 Identities=16% Similarity=0.446 Sum_probs=27.4
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.+.|.||-|.|.+.+---+- -.-|.-|.-|.-|+..|.
T Consensus 21 dt~FnClfcnHek~v~~~~D----k~~~iG~~sC~iC~esFq 58 (109)
T KOG3214|consen 21 DTQFNCLFCNHEKSVSCTLD----KKHNIGKASCRICEESFQ 58 (109)
T ss_pred heeeccCccccccceeeeeh----hhcCcceeeeeehhhhhc
Confidence 45699999999886554331 223778999999987764
No 203
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=27.20 E-value=74 Score=25.69 Aligned_cols=30 Identities=23% Similarity=0.867 Sum_probs=21.9
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
...+.|+.||+...+|+-=-.| -|..||+.
T Consensus 40 ~~~~~C~~Cg~~~~~~~SCk~R----------~CP~C~~~ 69 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIVYNSCKNR----------HCPSCQAK 69 (111)
T ss_pred cceeecCCCCceEEecCcccCc----------CCCCCCCh
Confidence 4468999999998877655433 47888874
No 204
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=26.97 E-value=45 Score=35.83 Aligned_cols=16 Identities=19% Similarity=0.285 Sum_probs=11.2
Q ss_pred CChhhhhcCChhhcCc
Q 035641 229 VTPERLATMTPEELAS 244 (314)
Q Consensus 229 i~p~~lv~Ms~eEmas 244 (314)
+..-.+++|..+.+..
T Consensus 386 ~p~v~iiDmr~e~~~~ 401 (730)
T COG1198 386 LPRVEIIDMRKEPLET 401 (730)
T ss_pred CCcceEEecccccccc
Confidence 4455678888877766
No 205
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=26.84 E-value=17 Score=34.23 Aligned_cols=35 Identities=34% Similarity=0.717 Sum_probs=23.5
Q ss_pred ceecCCCCCCceEEE----eeeccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYH----QMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~----q~q~rsade~mt~f~~C~~C~~~w 312 (314)
-|.|+.|+..=+--- -+||-|.+.+ |.|..||.+|
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 388999986433221 2377776664 8999998876
No 206
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=26.81 E-value=19 Score=38.38 Aligned_cols=35 Identities=37% Similarity=0.930 Sum_probs=0.0
Q ss_pred ceecCCCCCCceEEEee----eccCCCCCCeEEEEcCCCCCcc
Q 035641 274 QFKCSGCGKSNCSYHQM----QTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~----q~rsade~mt~f~~C~~C~~~w 312 (314)
.|+|+.||+.=-+=+-+ ..-|+.-| |.|.+|++||
T Consensus 281 KFKCtECgKAFKfKHHLKEHlRIHSGEKP----feCpnCkKRF 319 (1007)
T KOG3623|consen 281 KFKCTECGKAFKFKHHLKEHLRIHSGEKP----FECPNCKKRF 319 (1007)
T ss_pred cccccccchhhhhHHHHHhhheeecCCCC----cCCccccccc
No 207
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=26.74 E-value=32 Score=26.93 Aligned_cols=11 Identities=18% Similarity=0.929 Sum_probs=8.9
Q ss_pred EEEcCCCCCcc
Q 035641 302 YVTCAECNKRW 312 (314)
Q Consensus 302 f~~C~~C~~~w 312 (314)
-.+|.+||-.|
T Consensus 35 a~~C~~CGe~y 45 (89)
T TIGR03829 35 SISCSHCGMEY 45 (89)
T ss_pred cccccCCCcEe
Confidence 56799999876
No 208
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=26.74 E-value=46 Score=32.45 Aligned_cols=27 Identities=30% Similarity=0.972 Sum_probs=19.5
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
..-.++|.+||..- -+.|.-|+.|. .|
T Consensus 351 ~~~~YRC~~CGF~a--------------~~l~W~CPsC~-~W 377 (389)
T COG2956 351 RKPRYRCQNCGFTA--------------HTLYWHCPSCR-AW 377 (389)
T ss_pred hcCCceecccCCcc--------------eeeeeeCCCcc-cc
Confidence 35579999999632 25678899994 45
No 209
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=26.29 E-value=56 Score=26.54 Aligned_cols=61 Identities=20% Similarity=0.256 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHHhhcCC----ChhhHhHHHhHHhhcCCCCChhhhhhhhcCCCChhhhhcCChhhc
Q 035641 180 KQVAASVERVMFEKLRPM----GVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEEL 242 (314)
Q Consensus 180 ~~lA~~IE~alf~~~~~~----~~~yk~k~Rsl~~NLkd~~Np~Lr~~vl~G~i~p~~lv~Ms~eEm 242 (314)
..++..++..|.++|.+. ....=+-+|.|.-| ++..|.|...-..--|+.++|..+=|.||
T Consensus 28 ~~F~~~L~~~L~~~y~~HWyP~~P~kGqayRCIrIn--~~~Dp~l~~Aa~~sGl~~~~l~~~LP~el 92 (108)
T smart00099 28 EIFAEKLTRLLKEKYKNHWYPEKPYKGSGFRCIRIN--QKVDPVIEQACKESGLDIDDLGGNLPKEL 92 (108)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCCCcceEEEEEC--CcCCHHHHHHHHHhCCCHHHHHHhCCccc
Confidence 478999999999998752 22335678888888 66889888887777788888877766665
No 210
>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=26.21 E-value=22 Score=38.49 Aligned_cols=37 Identities=19% Similarity=0.568 Sum_probs=0.0
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCc
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKR 311 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~ 311 (314)
.....||.||..-- |+.- ..-....+..|.|..||+.
T Consensus 653 i~~r~Cp~Cg~~t~-~~~C--p~CG~~T~~~~~Cp~C~~~ 689 (900)
T PF03833_consen 653 IGRRRCPKCGKETF-YNRC--PECGSHTEPVYVCPDCGIE 689 (900)
T ss_dssp ----------------------------------------
T ss_pred eecccCcccCCcch-hhcC--cccCCccccceeccccccc
Confidence 34568999986421 1111 1122334567788888764
No 211
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=26.04 E-value=62 Score=22.48 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=10.2
Q ss_pred ceecCCCCCCceE
Q 035641 274 QFKCSGCGKSNCS 286 (314)
Q Consensus 274 ~~~C~~C~~~~~~ 286 (314)
--.||.||+.+..
T Consensus 13 Y~~Cp~CGN~~vG 25 (49)
T PF12677_consen 13 YCKCPKCGNDKVG 25 (49)
T ss_pred hccCcccCCcEee
Confidence 3579999988763
No 212
>PF08256 Antimicrobial20: Aurein-like antibiotic peptide; InterPro: IPR013157 This family of antibacterial peptides are secreted from the granular dorsal glands of Litoria aurea (Green and golden bell frog), Litoria raniformis (Southern bell frog), Litoria citropa (Australian blue mountains tree frog) and frogs from genus Uperoleia. They are a part of the FSAP peptide family. Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6 []; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides [].; GO: 0006952 defense response
Probab=25.97 E-value=56 Score=16.46 Aligned_cols=9 Identities=56% Similarity=0.715 Sum_probs=7.0
Q ss_pred HHHHHHHHH
Q 035641 8 LFGAAKKAA 16 (314)
Q Consensus 8 l~~~a~k~~ 16 (314)
||+++||-+
T Consensus 2 l~Di~Kkv~ 10 (13)
T PF08256_consen 2 LFDIAKKVV 10 (13)
T ss_pred HHHHHHHHh
Confidence 688888765
No 213
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=25.94 E-value=48 Score=32.96 Aligned_cols=14 Identities=36% Similarity=0.933 Sum_probs=11.1
Q ss_pred ceecCCCCCCceEE
Q 035641 274 QFKCSGCGKSNCSY 287 (314)
Q Consensus 274 ~~~C~~C~~~~~~~ 287 (314)
.|.||+||++.+-+
T Consensus 68 SF~CpHCG~kN~ei 81 (460)
T KOG2703|consen 68 SFECPHCGHKNNEI 81 (460)
T ss_pred EeecCccCCccccc
Confidence 47888888888865
No 214
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=25.91 E-value=28 Score=21.78 Aligned_cols=16 Identities=19% Similarity=0.652 Sum_probs=11.9
Q ss_pred cceecCCCCCCceEEE
Q 035641 273 DQFKCSGCGKSNCSYH 288 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~ 288 (314)
....||.||..+..|.
T Consensus 16 ~~~~CP~Cg~~~~~F~ 31 (33)
T cd00350 16 APWVCPVCGAPKDKFE 31 (33)
T ss_pred CCCcCcCCCCcHHHcE
Confidence 4568999998776654
No 215
>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=25.16 E-value=65 Score=21.34 Aligned_cols=29 Identities=21% Similarity=0.400 Sum_probs=14.1
Q ss_pred eecCCCCCCceEE-EeeeccCCCCCCeEEEEcCCCC
Q 035641 275 FKCSGCGKSNCSY-HQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 275 ~~C~~C~~~~~~~-~q~q~rsade~mt~f~~C~~C~ 309 (314)
.+||.||.+...- |. |..-+--+.|..|+
T Consensus 4 ~pCP~CGG~DrFri~~------d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFD------DKDGRGTWICRQCG 33 (40)
T ss_dssp E--TTTT-TTTEEEET------T----S-EEETTTT
T ss_pred CCCCCCcCccccccCc------CcccCCCEECCCCC
Confidence 5899999877643 32 21222357788884
No 216
>PRK07220 DNA topoisomerase I; Validated
Probab=24.33 E-value=73 Score=34.27 Aligned_cols=32 Identities=19% Similarity=0.405 Sum_probs=18.9
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
....||.||....... +....+ .|+.|.+|.+
T Consensus 634 ~~~~Cp~Cg~~~~k~~----~~g~~~--~~~~Cp~C~~ 665 (740)
T PRK07220 634 TDKVCEAHGLNHIRII----NGGKRP--WDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCCCceEEEE----ecCCcc--ceeeCCCCCC
Confidence 3467999986533221 212222 2889999986
No 217
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=24.06 E-value=81 Score=26.83 Aligned_cols=33 Identities=27% Similarity=0.597 Sum_probs=22.9
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
.-.+|+.|++..-+|..- + ++...|..|..|+.
T Consensus 109 rfv~C~~C~Gs~k~~~~~----~-~~~~~~~rC~~Cne 141 (147)
T cd03031 109 RFVPCSECNGSCKVFAEN----A-TAAGGFLRCPECNE 141 (147)
T ss_pred CeEECCCCCCcceEEecc----C-cccccEEECCCCCc
Confidence 346888888877776432 1 14567999999974
No 218
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=24.05 E-value=40 Score=19.73 Aligned_cols=7 Identities=57% Similarity=1.630 Sum_probs=3.9
Q ss_pred eecCCCC
Q 035641 275 FKCSGCG 281 (314)
Q Consensus 275 ~~C~~C~ 281 (314)
+.|+.|+
T Consensus 15 ~~C~~C~ 21 (26)
T PF13465_consen 15 YKCPYCG 21 (26)
T ss_dssp EEESSSS
T ss_pred CCCCCCc
Confidence 5555554
No 219
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=23.96 E-value=77 Score=31.25 Aligned_cols=34 Identities=29% Similarity=0.458 Sum_probs=23.5
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~ 309 (314)
+...+|+.|+..-.+..+.++ --+....+|..|+
T Consensus 157 t~~~tC~tC~G~G~v~~~~~~----g~~~~~~~C~~C~ 190 (371)
T COG0484 157 TDPKTCPTCNGSGQVRTVQRT----GFFSFQQTCPTCN 190 (371)
T ss_pred CCCCcCCCCCCcCeEEEEEee----eEEEEEEECCCCc
Confidence 466799999988876644333 2355677888885
No 220
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=23.59 E-value=53 Score=31.13 Aligned_cols=22 Identities=27% Similarity=0.991 Sum_probs=16.6
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCC
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~ 309 (314)
.+.|..||..-..| ++.|.+||
T Consensus 354 ~~~c~~cg~~~~~~--------------~~~c~~c~ 375 (389)
T PRK11788 354 RYRCRNCGFTARTL--------------YWHCPSCK 375 (389)
T ss_pred CEECCCCCCCCccc--------------eeECcCCC
Confidence 37799999865543 78899996
No 221
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=23.52 E-value=74 Score=29.73 Aligned_cols=29 Identities=28% Similarity=0.552 Sum_probs=17.9
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
..+||+||..=....+ -.| .-|-|..|..
T Consensus 245 g~pC~~Cg~~I~~~~~-~gR-------~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQ-GGR-------STFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEE-CCC-------CcEECcCCCC
Confidence 3589999965332222 223 3577999975
No 222
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=23.34 E-value=1.1e+02 Score=21.94 Aligned_cols=14 Identities=14% Similarity=0.567 Sum_probs=11.0
Q ss_pred CCeEEEEcCCCCCc
Q 035641 298 PMTTYVTCAECNKR 311 (314)
Q Consensus 298 ~mt~f~~C~~C~~~ 311 (314)
+|-.-+.|..|||.
T Consensus 27 GaDikikC~gCg~~ 40 (57)
T PF06107_consen 27 GADIKIKCLGCGRQ 40 (57)
T ss_pred cCcEEEEECCCCCE
Confidence 46677889999985
No 223
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.30 E-value=43 Score=28.00 Aligned_cols=11 Identities=18% Similarity=0.978 Sum_probs=8.9
Q ss_pred eEEEEcCCCCC
Q 035641 300 TTYVTCAECNK 310 (314)
Q Consensus 300 t~f~~C~~C~~ 310 (314)
..|+.|..||.
T Consensus 105 ~~~~~CP~Cgs 115 (135)
T PRK03824 105 HAFLKCPKCGS 115 (135)
T ss_pred ccCcCCcCCCC
Confidence 46788999985
No 224
>PRK11827 hypothetical protein; Provisional
Probab=23.05 E-value=71 Score=23.13 Aligned_cols=30 Identities=20% Similarity=0.406 Sum_probs=19.3
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
-..||.|++.=. |.. + ..-++|..||..|-
T Consensus 8 ILaCP~ckg~L~-~~~------~---~~~Lic~~~~laYP 37 (60)
T PRK11827 8 IIACPVCNGKLW-YNQ------E---KQELICKLDNLAFP 37 (60)
T ss_pred heECCCCCCcCe-EcC------C---CCeEECCccCeecc
Confidence 368999987543 321 1 12577999997763
No 225
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=22.64 E-value=66 Score=29.87 Aligned_cols=33 Identities=21% Similarity=0.570 Sum_probs=19.9
Q ss_pred CCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 269 KGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 269 ~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
+..+..| ||+||+.-.. .++. .-..|..||+..
T Consensus 95 w~~~~~f-C~~CG~~~~~--------~~~~--~~~~C~~c~~~~ 127 (256)
T PRK00241 95 FYRSHRF-CGYCGHPMHP--------SKTE--WAMLCPHCRERY 127 (256)
T ss_pred HhhcCcc-ccccCCCCee--------cCCc--eeEECCCCCCEE
Confidence 3334445 9999986432 1222 236799999764
No 226
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.51 E-value=16 Score=27.85 Aligned_cols=36 Identities=36% Similarity=0.752 Sum_probs=22.9
Q ss_pred CCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 270 GTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 270 ~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.++-.+.|-.||++..+. |. -.|.|.| +|..||-+.
T Consensus 8 MPtY~Y~c~~cg~~~dvv---q~-~~ddplt---~ce~c~a~~ 43 (82)
T COG2331 8 MPTYSYECTECGNRFDVV---QA-MTDDPLT---TCEECGARL 43 (82)
T ss_pred ccceEEeecccchHHHHH---Hh-cccCccc---cChhhChHH
Confidence 456678899998876643 32 2566644 577777543
No 227
>PRK14284 chaperone protein DnaJ; Provisional
Probab=22.46 E-value=83 Score=31.03 Aligned_cols=31 Identities=23% Similarity=0.386 Sum_probs=21.0
Q ss_pred cceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCC
Q 035641 273 DQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 273 ~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~ 309 (314)
....|+.|+....+..+. -.+....+|..|+
T Consensus 174 ~~~~C~~C~G~G~v~~~~------G~~~~~~~C~~C~ 204 (391)
T PRK14284 174 GIKVCDRCKGSGQVVQSR------GFFSMASTCPECG 204 (391)
T ss_pred CCeecCccCCeeEEEEEe------ceEEEEEECCCCC
Confidence 346799999887765432 1355667888885
No 228
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.38 E-value=36 Score=28.07 Aligned_cols=31 Identities=23% Similarity=0.551 Sum_probs=17.1
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeE--EEEcCCCC
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTT--YVTCAECN 309 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~--f~~C~~C~ 309 (314)
....+.| .||.. |... ..+.+.. ++.|..||
T Consensus 67 vp~~~~C-~Cg~~----~~~~---~~~~~~~~~~~~CP~Cg 99 (124)
T PRK00762 67 IPVEIEC-ECGYE----GVVD---EDEIDHYAAVIECPVCG 99 (124)
T ss_pred cCeeEEe-eCcCc----cccc---ccchhccccCCcCcCCC
Confidence 3556899 99943 1111 0111222 47899998
No 229
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=22.33 E-value=43 Score=32.33 Aligned_cols=33 Identities=27% Similarity=0.461 Sum_probs=22.1
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
.-...|+.|.+..--+ | ..|---+-|.|..|+|
T Consensus 218 ryALIC~~C~~HNGla-----~-~ee~~yi~F~C~~Cn~ 250 (328)
T KOG2846|consen 218 RYALICSQCHHHNGLA-----R-KEEYEYITFRCPHCNA 250 (328)
T ss_pred hhhhcchhhccccCcC-----C-hhhcCceEEECccccc
Confidence 4457899999766543 2 2333345577999987
No 230
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=21.95 E-value=1.7e+02 Score=31.61 Aligned_cols=33 Identities=24% Similarity=0.645 Sum_probs=20.3
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCe--EEEEcCCCCCc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMT--TYVTCAECNKR 311 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt--~f~~C~~C~~~ 311 (314)
...|+.|..+=.+.- +...|+| +|..|..|.|+
T Consensus 1131 ~~~c~ec~~kfP~Ci-----asG~pIt~~~fWlC~~CkH~ 1165 (1189)
T KOG2041|consen 1131 DLQCSECQTKFPVCI-----ASGRPITDNIFWLCPRCKHR 1165 (1189)
T ss_pred CCCChhhcCcCceee-----ccCCccccceEEEccccccc
Confidence 345666655444332 2344555 69999999885
No 231
>PRK07220 DNA topoisomerase I; Validated
Probab=21.95 E-value=1.8e+02 Score=31.38 Aligned_cols=18 Identities=6% Similarity=0.233 Sum_probs=13.8
Q ss_pred hhhhhcCCCChhhhhcCC
Q 035641 221 RRRVLIGEVTPERLATMT 238 (314)
Q Consensus 221 r~~vl~G~i~p~~lv~Ms 238 (314)
...|-.|+++.++|+.-.
T Consensus 540 Ld~I~~G~~~~~~~l~~~ 557 (740)
T PRK07220 540 MDKIAEGKIKEDAVLEES 557 (740)
T ss_pred HHHHHcCCCCHHHHHHHH
Confidence 356889999999987633
No 232
>PF14353 CpXC: CpXC protein
Probab=21.83 E-value=52 Score=26.82 Aligned_cols=11 Identities=36% Similarity=1.026 Sum_probs=8.5
Q ss_pred cceecCCCCCC
Q 035641 273 DQFKCSGCGKS 283 (314)
Q Consensus 273 ~~~~C~~C~~~ 283 (314)
..++||.||+.
T Consensus 37 ~~~~CP~Cg~~ 47 (128)
T PF14353_consen 37 FSFTCPSCGHK 47 (128)
T ss_pred CEEECCCCCCc
Confidence 36889999874
No 233
>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=21.78 E-value=30 Score=37.50 Aligned_cols=15 Identities=27% Similarity=0.541 Sum_probs=0.0
Q ss_pred CCccceecCCCCCCc
Q 035641 270 GTTDQFKCSGCGKSN 284 (314)
Q Consensus 270 ~~t~~~~C~~C~~~~ 284 (314)
..|-...||.||.+.
T Consensus 663 ~~t~~~~Cp~CG~~T 677 (900)
T PF03833_consen 663 KETFYNRCPECGSHT 677 (900)
T ss_dssp ---------------
T ss_pred CcchhhcCcccCCcc
Confidence 356678899998763
No 234
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=21.65 E-value=21 Score=25.11 Aligned_cols=32 Identities=28% Similarity=0.699 Sum_probs=20.4
Q ss_pred ecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 276 KCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 276 ~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.|..|+-.+...+ |... ...-..|..||-.|+
T Consensus 1 ~C~~C~~~~Tp~W----R~g~--~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLW----RRGP--SGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCccc----ccCC--CCcchHHHHHHHHHH
Confidence 3888988777433 3333 122458999998875
No 235
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=21.63 E-value=43 Score=26.93 Aligned_cols=17 Identities=24% Similarity=0.452 Sum_probs=13.0
Q ss_pred ceecCCCCCCceEEEee
Q 035641 274 QFKCSGCGKSNCSYHQM 290 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~ 290 (314)
.--||+||.++-.|.-.
T Consensus 20 l~GCp~CG~nkF~yv~~ 36 (112)
T COG3364 20 LSGCPKCGCNKFLYVPE 36 (112)
T ss_pred HccCccccchheEeccc
Confidence 34699999998887543
No 236
>PRK04860 hypothetical protein; Provisional
Probab=21.45 E-value=29 Score=30.08 Aligned_cols=14 Identities=14% Similarity=0.475 Sum_probs=11.2
Q ss_pred eEEEEcCCCCCccc
Q 035641 300 TTYVTCAECNKRWK 313 (314)
Q Consensus 300 t~f~~C~~C~~~w~ 313 (314)
...|.|..|+..+.
T Consensus 141 ~~~YrC~~C~~~l~ 154 (160)
T PRK04860 141 EAVYRCRRCGETLV 154 (160)
T ss_pred CccEECCCCCceeE
Confidence 35699999998765
No 237
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=21.16 E-value=42 Score=30.23 Aligned_cols=35 Identities=26% Similarity=0.612 Sum_probs=22.1
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCC--eEEEEcCCCC----CcccC
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPM--TTYVTCAECN----KRWKC 314 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~m--t~f~~C~~C~----~~w~~ 314 (314)
....-.||.||+.=. -++|+ +.+|.|..|. -.|.|
T Consensus 215 qek~r~CPsC~k~Wq---------lk~~i~d~fhfkcd~crlvsnlsw~~ 255 (256)
T COG5595 215 QEKYRCCPSCGKDWQ---------LKNPIFDTFHFKCDTCRLVSNLSWNF 255 (256)
T ss_pred hhccCCCCcccccce---------eccchhhheeeecccceeeccccccc
Confidence 445568999987522 34453 5778888883 45653
No 238
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=21.12 E-value=43 Score=33.02 Aligned_cols=29 Identities=14% Similarity=0.323 Sum_probs=19.6
Q ss_pred ceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 274 QFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 274 ~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
.+.|+.|+.+..... . .--.|..||.+|.
T Consensus 244 ~~~C~~c~~~~~~~~--------~---~~~~C~~c~~~~~ 272 (382)
T PRK04338 244 VYYCPKCLYREEVEG--------L---PPEECPVCGGKFG 272 (382)
T ss_pred EEECCCCCcEEEecC--------C---CCCCCCCCCCcce
Confidence 468999998776432 1 1236999988764
No 239
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=20.83 E-value=43 Score=27.05 Aligned_cols=30 Identities=23% Similarity=0.624 Sum_probs=17.4
Q ss_pred ccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCC
Q 035641 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~ 309 (314)
..+-.|..||.....|--+.. -.|+|..|.
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~--------GiflC~~Ca 40 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNY--------GIFLCLECA 40 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTT--------TEEE-HHHH
T ss_pred cCcCcCCCCCCCCCCEEEeec--------ChhhhHHHH
Confidence 445789999999998855422 268888884
No 240
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=20.75 E-value=1.2e+02 Score=24.62 Aligned_cols=30 Identities=17% Similarity=0.334 Sum_probs=18.8
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCC
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECN 309 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~ 309 (314)
.+|+.|+++.....+. .. .+.....|..|+
T Consensus 53 ~~C~~C~G~G~v~~~~---~g--~~q~~~~C~~C~ 82 (111)
T PLN03165 53 QVCRFCVGSGNVTVEL---GG--GEKEVSKCINCD 82 (111)
T ss_pred cCCCCCcCcCeEEEEe---CC--cEEEEEECCCCC
Confidence 4899999988765432 11 245566666663
No 241
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.65 E-value=24 Score=32.59 Aligned_cols=36 Identities=28% Similarity=0.468 Sum_probs=26.5
Q ss_pred CccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCC
Q 035641 271 TTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNK 310 (314)
Q Consensus 271 ~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~ 310 (314)
+..+-.|+.|+-.=..-+....|..|+. +.|..||-
T Consensus 194 pl~g~~C~GC~m~l~~~~~~~V~~~d~i----v~CP~CgR 229 (239)
T COG1579 194 PLEGRVCGGCHMKLPSQTLSKVRKKDEI----VFCPYCGR 229 (239)
T ss_pred eecCCcccCCeeeecHHHHHHHhcCCCC----ccCCccch
Confidence 4566789999876665566666765554 88999995
No 242
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=20.62 E-value=46 Score=22.81 Aligned_cols=16 Identities=25% Similarity=0.850 Sum_probs=9.9
Q ss_pred ccceecCCCCCCceEE
Q 035641 272 TDQFKCSGCGKSNCSY 287 (314)
Q Consensus 272 t~~~~C~~C~~~~~~~ 287 (314)
...+.||.|+..+..|
T Consensus 32 p~~w~CP~C~a~K~~F 47 (47)
T PF00301_consen 32 PDDWVCPVCGAPKSDF 47 (47)
T ss_dssp -TT-B-TTTSSBGGGE
T ss_pred CCCCcCcCCCCccccC
Confidence 4568999999877543
No 243
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=20.54 E-value=1.1e+02 Score=25.04 Aligned_cols=63 Identities=21% Similarity=0.319 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHhhcCC----ChhhHhHHHhHHhhcCCCCChhhhhhhhcCCCChhhhhcCChhhc
Q 035641 180 KQVAASVERVMFEKLRPM----GVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEEL 242 (314)
Q Consensus 180 ~~lA~~IE~alf~~~~~~----~~~yk~k~Rsl~~NLkd~~Np~Lr~~vl~G~i~p~~lv~Ms~eEm 242 (314)
..++..++..|.++|.+. +...=+-+|.|..|-...-.|.|...-..--|+.++|...=|.||
T Consensus 28 ~~F~~~L~~~L~~ry~~HW~P~~P~kGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~~~LP~el 94 (118)
T PF07742_consen 28 DRFAEELENLLCERYKGHWYPENPSKGSAYRCIRINPGHKMDPVLEQAAKESGLSYEDLRSLLPREL 94 (118)
T ss_dssp HHHHHHHHHHHHHHHTTS--TTSTTTTHHHH-EEES--SSB-HHHHHHHHHTT--HHHHHHHS-TTE
T ss_pred HHHHHHHHHHHHHHHhCCCCCCCCCCCCceEEEEEcCCCCCCHHHHHHHHHhCCCHHHHHHhcchhc
Confidence 478899999999999763 222346688898885556778888876666666666654444443
No 244
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.51 E-value=93 Score=23.88 Aligned_cols=30 Identities=30% Similarity=0.676 Sum_probs=18.6
Q ss_pred eecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcc
Q 035641 275 FKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRW 312 (314)
Q Consensus 275 ~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w 312 (314)
.-||.|+-.- ++-.||. .-|-.|..|+--|
T Consensus 2 llCP~C~v~l----~~~~rs~----vEiD~CPrCrGVW 31 (88)
T COG3809 2 LLCPICGVEL----VMSVRSG----VEIDYCPRCRGVW 31 (88)
T ss_pred cccCcCCcee----eeeeecC----ceeeeCCccccEe
Confidence 4588887532 2333442 3467788998877
No 245
>PRK14724 DNA topoisomerase III; Provisional
Probab=20.48 E-value=1.9e+02 Score=32.39 Aligned_cols=15 Identities=13% Similarity=0.282 Sum_probs=11.6
Q ss_pred hhhhcCCCChhhhhc
Q 035641 222 RRVLIGEVTPERLAT 236 (314)
Q Consensus 222 ~~vl~G~i~p~~lv~ 236 (314)
..|-.|++++++|..
T Consensus 600 ~~I~~G~~~~~~fl~ 614 (987)
T PRK14724 600 AQMEKGQLSREAFMQ 614 (987)
T ss_pred HHHHhCCCCHHHHHH
Confidence 567888888888864
No 246
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=20.45 E-value=85 Score=27.00 Aligned_cols=31 Identities=26% Similarity=0.738 Sum_probs=19.0
Q ss_pred eecCCCCCCc--eEEEeeeccCCCCCCeEEEEcCCCCCccc
Q 035641 275 FKCSGCGKSN--CSYHQMQTRSADEPMTTYVTCAECNKRWK 313 (314)
Q Consensus 275 ~~C~~C~~~~--~~~~q~q~rsade~mt~f~~C~~C~~~w~ 313 (314)
+-| -|+..+ +.||-++ .+|+ ..|+.|||-|+
T Consensus 112 VGC-~c~eD~~~V~Wmwl~---Kge~----~rc~eCG~~fk 144 (153)
T KOG3352|consen 112 VGC-GCEEDSHAVVWMWLE---KGET----QRCPECGHYFK 144 (153)
T ss_pred Eee-cccCCCcceEEEEEE---cCCc----ccCCcccceEE
Confidence 357 566443 3455554 4444 45999999876
Done!