Query 017145
Match_columns 376
No_of_seqs 286 out of 1111
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 06:00:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017145.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017145hhsearch_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 3.5E-70 7.6E-75 527.6 28.1 298 6-376 2-299 (299)
2 KOG1105 Transcription elongati 100.0 1.7E-63 3.6E-68 474.2 24.9 292 6-376 4-296 (296)
3 smart00510 TFS2M Domain in the 99.9 1.6E-27 3.6E-32 196.8 10.1 101 206-313 1-101 (102)
4 PF07500 TFIIS_M: Transcriptio 99.9 8.5E-27 1.8E-31 196.8 5.2 114 204-324 1-114 (115)
5 smart00440 ZnF_C2C2 C2C2 Zinc 99.8 3.9E-19 8.5E-24 122.3 4.3 39 336-374 1-39 (40)
6 PF01096 TFIIS_C: Transcriptio 99.7 9.2E-19 2E-23 119.8 3.9 39 336-374 1-39 (39)
7 smart00509 TFS2N Domain in the 99.7 3.6E-18 7.8E-23 133.6 5.7 74 8-87 1-74 (75)
8 KOG2906 RNA polymerase III sub 99.7 9.2E-18 2E-22 134.2 1.9 44 331-374 61-104 (105)
9 COG1594 RPB9 DNA-directed RNA 99.7 4.1E-17 8.9E-22 137.2 4.5 48 329-376 66-113 (113)
10 TIGR01384 TFS_arch transcripti 99.6 2.6E-16 5.6E-21 130.5 4.9 46 329-374 56-101 (104)
11 PHA02998 RNA polymerase subuni 99.6 3.1E-16 6.6E-21 138.5 4.9 44 331-374 138-182 (195)
12 cd00183 TFIIS_I N-terminal dom 99.6 1.4E-15 3.1E-20 119.3 6.0 74 7-87 3-76 (76)
13 KOG2691 RNA polymerase II subu 99.5 3.2E-14 6.9E-19 115.8 4.9 51 324-374 61-112 (113)
14 PF08711 Med26: TFIIS helical 99.4 1.9E-13 4.1E-18 99.8 2.3 52 36-87 1-53 (53)
15 KOG1634 Predicted transcriptio 99.3 1.1E-12 2.4E-17 138.6 4.8 82 238-319 267-349 (778)
16 KOG2907 RNA polymerase I trans 99.2 6.2E-12 1.3E-16 103.5 1.9 44 331-374 70-113 (116)
17 PF11467 LEDGF: Lens epitheliu 96.8 0.0023 4.9E-08 53.4 5.0 78 2-87 1-80 (106)
18 KOG2821 RNA polymerase II tran 96.3 0.0019 4.2E-08 65.5 2.0 58 29-88 22-79 (433)
19 KOG1793 Uncharacterized conser 95.9 0.0091 2E-07 59.8 4.4 53 36-88 237-292 (417)
20 COG5139 Uncharacterized conser 94.9 0.032 6.9E-07 54.0 4.3 53 36-88 234-288 (397)
21 PF08274 PhnA_Zn_Ribbon: PhnA 94.7 0.0076 1.6E-07 38.8 -0.3 27 337-374 4-30 (30)
22 PF09855 DUF2082: Nucleic-acid 94.4 0.045 9.9E-07 41.5 3.4 37 336-372 1-45 (64)
23 PF13717 zinc_ribbon_4: zinc-r 93.7 0.041 8.9E-07 36.8 1.7 32 335-374 2-36 (36)
24 PRK09678 DNA-binding transcrip 93.5 0.065 1.4E-06 41.6 2.8 37 335-374 1-40 (72)
25 TIGR02098 MJ0042_CXXC MJ0042 f 93.2 0.074 1.6E-06 35.6 2.3 35 335-375 2-37 (38)
26 PF13719 zinc_ribbon_5: zinc-r 93.0 0.056 1.2E-06 36.3 1.6 32 336-375 3-37 (37)
27 PF12760 Zn_Tnp_IS1595: Transp 92.8 0.093 2E-06 36.9 2.4 30 334-372 17-46 (46)
28 PF04606 Ogr_Delta: Ogr/Delta- 92.4 0.12 2.6E-06 36.6 2.6 36 337-374 1-38 (47)
29 COG3478 Predicted nucleic-acid 91.1 0.18 3.9E-06 38.0 2.4 38 335-372 4-49 (68)
30 PF08271 TF_Zn_Ribbon: TFIIB z 90.8 0.21 4.5E-06 34.6 2.3 28 336-372 1-28 (43)
31 PHA00626 hypothetical protein 90.3 0.18 4E-06 37.0 1.8 33 337-374 2-34 (59)
32 COG4888 Uncharacterized Zn rib 89.6 0.43 9.3E-06 39.2 3.6 37 334-374 21-57 (104)
33 PF14354 Lar_restr_allev: Rest 89.4 0.44 9.5E-06 35.2 3.4 36 334-371 2-37 (61)
34 PLN02976 amine oxidase 89.0 0.48 1E-05 55.5 4.8 60 34-93 1303-1363(1713)
35 PF11781 RRN7: RNA polymerase 87.1 0.46 9.9E-06 31.8 1.9 27 335-372 8-34 (36)
36 TIGR03655 anti_R_Lar restricti 87.1 1 2.2E-05 32.6 3.9 34 336-372 2-35 (53)
37 COG2051 RPS27A Ribosomal prote 86.3 0.49 1.1E-05 36.0 1.9 29 335-372 19-47 (67)
38 PF05876 Terminase_GpA: Phage 85.9 0.59 1.3E-05 49.9 3.0 39 335-374 200-240 (557)
39 TIGR00373 conserved hypothetic 85.8 0.84 1.8E-05 40.7 3.5 30 334-372 108-137 (158)
40 TIGR02443 conserved hypothetic 85.4 1.3 2.9E-05 32.9 3.7 33 335-373 9-41 (59)
41 PRK09710 lar restriction allev 85.4 1.2 2.6E-05 33.7 3.5 34 335-375 6-39 (64)
42 PF04216 FdhE: Protein involve 85.2 0.62 1.3E-05 45.4 2.6 38 335-375 172-209 (290)
43 PF05129 Elf1: Transcription e 84.9 1.1 2.4E-05 35.5 3.4 38 334-375 21-58 (81)
44 smart00531 TFIIE Transcription 84.8 0.55 1.2E-05 41.2 1.8 37 332-372 96-132 (147)
45 PF09526 DUF2387: Probable met 84.4 0.95 2.1E-05 35.0 2.8 32 335-372 8-39 (71)
46 PRK06266 transcription initiat 83.7 1.1 2.4E-05 40.8 3.3 31 288-320 35-65 (178)
47 smart00661 RPOL9 RNA polymeras 83.1 1.1 2.4E-05 31.7 2.5 30 337-374 2-31 (52)
48 PF10571 UPF0547: Uncharacteri 82.4 0.62 1.3E-05 29.0 0.8 24 337-374 2-25 (26)
49 PRK06266 transcription initiat 81.1 0.94 2E-05 41.2 1.9 32 332-372 114-145 (178)
50 TIGR01562 FdhE formate dehydro 80.9 0.92 2E-05 44.8 1.9 39 335-375 184-222 (305)
51 PF01873 eIF-5_eIF-2B: Domain 80.7 1.7 3.7E-05 37.3 3.2 32 334-372 92-123 (125)
52 PRK00398 rpoP DNA-directed RNA 79.8 1.3 2.9E-05 30.9 1.9 28 335-372 3-30 (46)
53 PF13453 zf-TFIIB: Transcripti 79.7 2.3 5E-05 29.0 3.0 29 337-373 1-29 (41)
54 PF05180 zf-DNL: DNL zinc fing 79.6 0.67 1.5E-05 35.4 0.3 36 335-373 4-39 (66)
55 PF10058 DUF2296: Predicted in 79.5 2.9 6.3E-05 30.6 3.7 44 322-371 7-52 (54)
56 PLN00209 ribosomal protein S27 79.3 1.6 3.5E-05 34.9 2.4 29 335-372 36-64 (86)
57 smart00653 eIF2B_5 domain pres 79.3 2.2 4.8E-05 35.8 3.4 32 334-372 79-110 (110)
58 PF07282 OrfB_Zn_ribbon: Putat 79.0 2.7 5.9E-05 31.6 3.6 30 334-373 27-56 (69)
59 TIGR00311 aIF-2beta translatio 78.9 2.2 4.9E-05 37.0 3.4 32 334-372 96-127 (133)
60 PRK00415 rps27e 30S ribosomal 78.8 1.7 3.8E-05 32.4 2.3 29 335-372 11-39 (59)
61 PRK03988 translation initiatio 78.8 2.2 4.9E-05 37.2 3.4 32 334-372 101-132 (138)
62 PRK03564 formate dehydrogenase 78.4 1.6 3.4E-05 43.2 2.6 39 334-375 186-224 (309)
63 PTZ00083 40S ribosomal protein 78.0 1.8 3.9E-05 34.5 2.3 29 335-372 35-63 (85)
64 COG1997 RPL43A Ribosomal prote 77.5 2.1 4.6E-05 34.3 2.6 32 333-374 33-64 (89)
65 PRK14892 putative transcriptio 75.9 2.3 4.9E-05 35.1 2.4 33 334-373 20-52 (99)
66 TIGR00373 conserved hypothetic 75.8 1.4 3E-05 39.2 1.3 12 334-345 127-138 (158)
67 smart00531 TFIIE Transcription 75.4 3.8 8.3E-05 35.9 3.9 77 287-375 13-111 (147)
68 PF01667 Ribosomal_S27e: Ribos 73.0 1.6 3.4E-05 32.1 0.8 29 335-372 7-35 (55)
69 PF03604 DNA_RNApol_7kD: DNA d 72.8 2.1 4.5E-05 28.0 1.2 26 336-372 1-26 (32)
70 KOG3507 DNA-directed RNA polym 71.9 2.6 5.6E-05 31.3 1.6 31 331-372 16-46 (62)
71 COG1996 RPC10 DNA-directed RNA 71.8 1.9 4.1E-05 31.0 0.9 30 333-372 4-33 (49)
72 smart00659 RPOLCX RNA polymera 71.3 2.8 6.1E-05 29.3 1.7 27 335-372 2-28 (44)
73 PF01396 zf-C4_Topoisom: Topoi 70.4 6 0.00013 26.8 3.1 29 336-372 2-33 (39)
74 PRK12336 translation initiatio 69.3 5 0.00011 37.2 3.4 32 334-372 97-128 (201)
75 KOG3277 Uncharacterized conser 69.1 2.6 5.5E-05 37.4 1.3 36 335-373 79-114 (165)
76 PF09538 FYDLN_acid: Protein o 68.5 2.4 5.3E-05 35.5 1.0 29 335-374 9-37 (108)
77 PF11792 Baculo_LEF5_C: Baculo 67.3 0.36 7.8E-06 33.6 -3.4 30 341-371 13-42 (43)
78 COG2888 Predicted Zn-ribbon RN 66.8 2.2 4.7E-05 31.8 0.4 34 334-372 26-59 (61)
79 KOG0909 Peptide:N-glycanase [P 66.3 7.3 0.00016 40.1 4.1 94 277-375 104-206 (500)
80 TIGR00280 L37a ribosomal prote 65.1 13 0.00028 30.2 4.5 31 333-373 33-63 (91)
81 PRK03976 rpl37ae 50S ribosomal 64.1 14 0.00031 29.9 4.6 31 333-373 34-64 (90)
82 PRK00432 30S ribosomal protein 63.6 3.6 7.9E-05 29.6 1.0 30 334-374 19-48 (50)
83 smart00401 ZnF_GATA zinc finge 63.3 3.3 7.2E-05 29.9 0.8 34 335-374 3-36 (52)
84 COG2023 RPR2 RNase P subunit R 63.0 4.8 0.0001 33.5 1.8 39 335-375 56-94 (105)
85 PRK03954 ribonuclease P protei 62.9 7.8 0.00017 33.1 3.1 37 335-375 64-105 (121)
86 PF01780 Ribosomal_L37ae: Ribo 61.5 9.5 0.00021 30.9 3.2 31 333-373 33-63 (90)
87 smart00834 CxxC_CXXC_SSSS Puta 61.3 6.7 0.00015 26.1 2.0 34 332-372 2-35 (41)
88 PF12773 DZR: Double zinc ribb 60.5 4 8.7E-05 28.7 0.8 33 333-376 10-46 (50)
89 PTZ00255 60S ribosomal protein 59.9 18 0.0004 29.3 4.5 31 333-373 34-64 (90)
90 COG0675 Transposase and inacti 59.7 10 0.00022 36.5 3.8 26 333-373 307-332 (364)
91 PF13240 zinc_ribbon_2: zinc-r 58.6 4.9 0.00011 24.1 0.8 8 338-345 2-9 (23)
92 PF04216 FdhE: Protein involve 56.7 7.8 0.00017 37.7 2.4 39 335-374 211-249 (290)
93 PF08792 A2L_zn_ribbon: A2L zi 56.0 12 0.00027 24.4 2.5 30 334-373 2-31 (33)
94 PF14726 RTTN_N: Rotatin, an a 55.3 21 0.00045 29.3 4.3 55 26-80 42-96 (98)
95 PF14311 DUF4379: Domain of un 54.9 11 0.00024 27.2 2.3 16 359-374 24-39 (55)
96 PF04032 Rpr2: RNAse P Rpr2/Rp 54.8 44 0.00095 25.9 6.0 35 335-371 46-85 (85)
97 PRK14890 putative Zn-ribbon RN 54.0 7.3 0.00016 29.1 1.2 35 333-372 23-57 (59)
98 PRK14714 DNA polymerase II lar 53.3 9.1 0.0002 44.3 2.4 36 334-372 666-701 (1337)
99 PF06044 DRP: Dam-replacing fa 53.3 6.7 0.00015 37.4 1.2 34 334-373 30-63 (254)
100 PF13248 zf-ribbon_3: zinc-rib 51.7 6.4 0.00014 24.2 0.5 23 336-372 3-25 (26)
101 PF07754 DUF1610: Domain of un 51.4 8.4 0.00018 23.5 1.0 11 333-343 14-24 (24)
102 PF01921 tRNA-synt_1f: tRNA sy 51.0 13 0.00028 37.6 2.9 35 335-373 174-209 (360)
103 PRK05978 hypothetical protein; 50.9 7.2 0.00016 34.5 0.9 32 335-375 33-64 (148)
104 PF14803 Nudix_N_2: Nudix N-te 50.7 13 0.00029 24.5 2.0 29 338-372 3-31 (34)
105 TIGR01206 lysW lysine biosynth 50.2 15 0.00032 27.0 2.3 32 335-374 2-33 (54)
106 PRK12495 hypothetical protein; 49.7 19 0.00041 33.9 3.5 29 332-372 39-67 (226)
107 PF09332 Mcm10: Mcm10 replicat 48.8 4.8 0.0001 40.4 -0.5 13 360-372 282-294 (344)
108 TIGR00467 lysS_arch lysyl-tRNA 48.2 32 0.00069 36.5 5.4 33 334-372 167-199 (515)
109 KOG1886 BAH domain proteins [T 48.1 13 0.00029 38.6 2.5 99 202-302 238-341 (464)
110 PF06290 PsiB: Plasmid SOS inh 47.8 17 0.00037 31.7 2.7 75 289-367 4-79 (143)
111 KOG2462 C2H2-type Zn-finger pr 47.0 9.8 0.00021 36.9 1.3 41 331-373 126-171 (279)
112 PHA02942 putative transposase; 45.9 13 0.00028 37.9 2.0 28 335-373 325-352 (383)
113 PRK13701 psiB plasmid SOS inhi 45.7 65 0.0014 28.2 5.9 76 288-367 3-79 (144)
114 TIGR02605 CxxC_CxxC_SSSS putat 45.3 13 0.00028 26.3 1.4 33 332-371 2-34 (52)
115 TIGR02159 PA_CoA_Oxy4 phenylac 44.5 16 0.00035 32.2 2.1 37 335-374 105-141 (146)
116 PRK08173 DNA topoisomerase III 44.4 38 0.00083 38.2 5.6 28 335-374 624-652 (862)
117 cd00674 LysRS_core_class_I cat 43.9 25 0.00054 35.5 3.7 34 334-372 168-201 (353)
118 PF02701 zf-Dof: Dof domain, z 43.2 10 0.00022 28.6 0.5 38 334-374 4-41 (63)
119 COG4332 Uncharacterized protei 43.1 13 0.00029 33.9 1.4 16 360-375 46-61 (203)
120 COG1656 Uncharacterized conser 42.7 12 0.00026 33.6 1.1 44 331-374 93-142 (165)
121 TIGR01562 FdhE formate dehydro 42.7 30 0.00065 34.2 3.9 40 334-374 223-263 (305)
122 PF15135 UPF0515: Uncharacteri 42.0 14 0.0003 35.4 1.4 14 361-374 153-166 (278)
123 PRK04023 DNA polymerase II lar 40.6 17 0.00037 41.3 2.0 13 69-81 247-259 (1121)
124 PRK12286 rpmF 50S ribosomal pr 40.4 21 0.00046 26.4 1.9 24 333-371 25-48 (57)
125 PF00684 DnaJ_CXXCXGXG: DnaJ c 39.8 56 0.0012 24.4 4.2 36 334-371 14-49 (66)
126 smart00778 Prim_Zn_Ribbon Zinc 39.7 21 0.00046 24.0 1.7 31 335-371 3-33 (37)
127 COG3677 Transposase and inacti 39.7 28 0.00061 29.9 2.9 39 331-374 26-64 (129)
128 KOG4274 Positive cofactor 2 (P 39.3 47 0.001 35.5 4.8 60 206-279 9-68 (742)
129 PF13408 Zn_ribbon_recom: Reco 38.6 33 0.00072 24.3 2.7 31 333-370 3-33 (58)
130 PF09723 Zn-ribbon_8: Zinc rib 38.2 16 0.00035 25.0 0.9 33 332-371 2-34 (42)
131 PF01927 Mut7-C: Mut7-C RNAse 37.9 25 0.00053 30.7 2.3 38 335-372 91-133 (147)
132 PF07295 DUF1451: Protein of u 37.7 25 0.00053 31.1 2.2 31 332-372 109-139 (146)
133 CHL00174 accD acetyl-CoA carbo 37.2 7.5 0.00016 38.2 -1.2 41 325-374 27-68 (296)
134 PF10080 DUF2318: Predicted me 36.8 24 0.00052 29.3 1.9 29 335-374 35-63 (102)
135 COG1675 TFA1 Transcription ini 36.8 13 0.00029 33.8 0.4 33 331-372 109-141 (176)
136 PF04194 PDCD2_C: Programmed c 36.2 35 0.00076 30.4 3.0 35 335-369 97-145 (164)
137 PF03811 Zn_Tnp_IS1: InsA N-te 35.9 43 0.00094 22.4 2.7 33 333-369 3-35 (36)
138 PRK03564 formate dehydrogenase 35.7 42 0.00091 33.3 3.7 38 334-374 225-263 (309)
139 PRK12380 hydrogenase nickel in 35.6 16 0.00034 30.7 0.6 28 332-371 67-94 (113)
140 cd00974 DSRD Desulforedoxin (D 34.9 23 0.0005 23.0 1.2 13 361-373 2-14 (34)
141 PF04502 DUF572: Family of unk 34.9 41 0.00089 33.4 3.6 41 335-375 40-89 (324)
142 PF06397 Desulfoferrod_N: Desu 34.8 23 0.0005 23.8 1.2 14 360-373 3-16 (36)
143 KOG2041 WD40 repeat protein [G 34.6 50 0.0011 36.4 4.3 33 335-372 1131-1165(1189)
144 PF14122 YokU: YokU-like prote 33.8 31 0.00068 27.7 2.0 37 337-373 1-45 (87)
145 KOG1779 40s ribosomal protein 33.4 46 0.00099 26.3 2.8 56 302-371 6-61 (84)
146 PRK11032 hypothetical protein; 32.9 36 0.00078 30.5 2.5 30 333-372 122-151 (160)
147 TIGR00100 hypA hydrogenase nic 32.9 20 0.00042 30.2 0.8 28 332-371 67-94 (115)
148 TIGR00319 desulf_FeS4 desulfof 32.9 27 0.00058 22.6 1.3 13 361-373 5-17 (34)
149 COG0777 AccD Acetyl-CoA carbox 32.7 13 0.00028 36.2 -0.3 33 334-375 27-59 (294)
150 TIGR03831 YgiT_finger YgiT-typ 32.7 49 0.0011 22.2 2.7 9 365-373 34-42 (46)
151 COG1571 Predicted DNA-binding 32.1 22 0.00048 36.6 1.2 31 333-374 348-378 (421)
152 KOG2593 Transcription initiati 32.0 15 0.00033 37.7 -0.0 38 331-371 124-161 (436)
153 KOG2767 Translation initiation 31.2 18 0.0004 36.3 0.4 33 335-373 96-128 (400)
154 COG2816 NPY1 NTP pyrophosphohy 31.1 28 0.00061 34.0 1.6 28 336-373 112-139 (279)
155 PF09332 Mcm10: Mcm10 replicat 29.2 15 0.00032 37.0 -0.7 31 334-374 284-315 (344)
156 PF14206 Cys_rich_CPCC: Cystei 29.0 41 0.00089 26.5 1.9 26 336-370 2-27 (78)
157 PF06827 zf-FPG_IleRS: Zinc fi 28.6 70 0.0015 19.9 2.7 28 336-371 2-29 (30)
158 COG1645 Uncharacterized Zn-fin 28.4 26 0.00057 30.3 0.9 30 332-373 25-54 (131)
159 PHA02540 61 DNA primase; Provi 27.9 55 0.0012 32.9 3.1 34 334-372 26-64 (337)
160 PRK05582 DNA topoisomerase I; 27.3 1.7E+02 0.0038 31.9 7.1 15 283-297 529-543 (650)
161 PF06573 Churchill: Churchill 27.0 56 0.0012 27.3 2.5 37 336-372 28-67 (112)
162 KOG2879 Predicted E3 ubiquitin 26.8 32 0.0007 33.5 1.2 24 329-352 233-256 (298)
163 PRK14810 formamidopyrimidine-D 26.7 1.8E+02 0.0038 28.1 6.4 29 334-370 243-271 (272)
164 PRK00420 hypothetical protein; 26.7 36 0.00077 28.7 1.3 27 335-372 23-49 (112)
165 TIGR01051 topA_bact DNA topois 26.3 1.4E+02 0.0031 32.2 6.2 15 283-297 535-549 (610)
166 COG2956 Predicted N-acetylgluc 26.3 43 0.00092 33.7 2.0 25 333-371 352-376 (389)
167 PRK07219 DNA topoisomerase I; 26.2 90 0.002 35.1 4.8 15 283-297 550-564 (822)
168 PRK04023 DNA polymerase II lar 25.9 39 0.00085 38.5 1.8 15 24-38 192-206 (1121)
169 PF10609 ParA: ParA/MinD ATPas 25.9 18 0.00038 28.8 -0.6 47 295-345 29-75 (81)
170 TIGR01031 rpmF_bact ribosomal 25.8 49 0.0011 24.2 1.8 24 333-371 24-47 (55)
171 cd00729 rubredoxin_SM Rubredox 25.8 37 0.0008 22.2 1.0 11 363-373 2-12 (34)
172 PF09297 zf-NADH-PPase: NADH p 25.7 34 0.00073 21.8 0.8 27 337-373 5-31 (32)
173 PF11672 DUF3268: Protein of u 25.1 73 0.0016 26.4 2.8 35 336-371 3-39 (102)
174 PF10083 DUF2321: Uncharacteri 24.2 52 0.0011 29.3 1.9 11 362-372 67-77 (158)
175 PF03589 Antiterm: Antitermina 24.0 20 0.00043 29.3 -0.7 36 336-372 6-41 (95)
176 PRK03681 hypA hydrogenase nick 23.4 36 0.00078 28.6 0.8 29 332-371 67-95 (114)
177 COG2331 Uncharacterized protei 22.7 14 0.0003 29.1 -1.7 38 330-374 7-44 (82)
178 TIGR00354 polC DNA polymerase, 22.6 41 0.00089 38.1 1.2 25 332-372 622-646 (1095)
179 COG0484 DnaJ DnaJ-class molecu 22.4 89 0.0019 31.8 3.4 35 333-371 157-191 (371)
180 PF14205 Cys_rich_KTR: Cystein 22.2 60 0.0013 23.9 1.6 33 335-371 4-36 (55)
181 KOG2907 RNA polymerase I trans 22.1 51 0.0011 27.8 1.4 26 322-347 89-114 (116)
182 COG3058 FdhE Uncharacterized p 22.0 32 0.00069 33.6 0.2 38 335-374 185-222 (308)
183 PF14949 ARF7EP_C: ARF7 effect 21.7 40 0.00087 28.0 0.7 13 335-347 74-86 (103)
184 PF01412 ArfGap: Putative GTPa 21.6 37 0.00081 28.4 0.5 32 333-372 11-42 (116)
185 PRK00750 lysK lysyl-tRNA synth 21.6 2E+02 0.0043 30.5 6.0 36 334-373 174-209 (510)
186 PF05207 zf-CSL: CSL zinc fing 21.2 48 0.001 24.2 0.9 33 334-372 17-49 (55)
187 PF00320 GATA: GATA zinc finge 20.9 7.7 0.00017 25.7 -3.1 31 338-374 1-31 (36)
188 PRK07726 DNA topoisomerase III 20.7 2.1E+02 0.0045 31.4 6.1 26 335-368 610-635 (658)
189 PRK03824 hypA hydrogenase nick 20.4 53 0.0011 28.4 1.2 12 361-372 105-116 (135)
190 PRK10445 endonuclease VIII; Pr 20.2 2.6E+02 0.0056 26.9 6.0 28 335-370 235-262 (263)
191 PRK14724 DNA topoisomerase III 20.0 1.7E+02 0.0036 33.8 5.3 14 283-296 600-613 (987)
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=3.5e-70 Score=527.60 Aligned_cols=298 Identities=42% Similarity=0.678 Sum_probs=233.7
Q ss_pred HHHHHHHHHHHhHhhhcCCCCCCCCHHHHHHHHHHhcCCCCCHHhhhcCccceecccccCCCCHHHHHHHHHHHHHHHHH
Q 017145 6 VELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKI 85 (376)
Q Consensus 6 ~el~~~a~k~a~~~~~~~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~ 85 (376)
.|+..+++.+.+++. +.+++.||++|++|+.++||.++|++|+||++||+||||++++|+.+|+.||++||++
T Consensus 2 ~ei~~~~k~L~k~~~-------~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~ 74 (299)
T TIGR01385 2 AEVASHAKALDKNKS-------SKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKV 74 (299)
T ss_pred hHHHHHHHHhhhhcc-------CCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence 477888888777663 2467899999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhccCCCCCCCCCCCcccCccCCCCCCccccccccchhhcccccchhhhhhccCCCCCchhhhhhhcccCCCcccC
Q 017145 86 VIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNGDSVMD 165 (376)
Q Consensus 86 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (376)
|..++.++....+. ..+ . .+.+.+ ..+. +.+.
T Consensus 75 v~~~k~~~~~~~~~-~~~-~-----~~~~~~---~~~~----------------~~~~---------------------- 106 (299)
T TIGR01385 75 VDKNKSDHPGGNPE-DKT-T-----VGESVN---SVKQ----------------EAKS---------------------- 106 (299)
T ss_pred HhhhcccCcccccc-ccc-c-----cCCCCC---CCCc----------------cccC----------------------
Confidence 98762221100000 000 0 000000 0000 0000
Q ss_pred CCcchhhhHHHhhhhcCCCCCCCCCCCCCCCcccccccCCchhHHHHHHHHHHHHhhhhccChhhhhhhhcccChHHHHH
Q 017145 166 RGEAVKVEKIIEEEKQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAV 245 (376)
Q Consensus 166 ~~~~~~~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~lA~ 245 (376)
++.+.++ + .. .++......++..+++.++|++|++||++||+||.....+.. ..+++..+|.
T Consensus 107 --~~~~~~~------~--~~-~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~-------~~~~~~~lA~ 168 (299)
T TIGR01385 107 --QSDKIEQ------P--KY-VSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPP-------QSIDPEAKAI 168 (299)
T ss_pred --CcccccC------C--CC-CCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhhcCCCCc-------cccCHHHHHH
Confidence 0000000 0 00 000011122334445679999999999999999996443221 2346678999
Q ss_pred HHHHHHHHHhCCCchhhhHHHHHHHhhccCCCChhhhhchhcCCCChhhhccCChhhcCcHHHHHHHHHHHHHHHHHhhh
Q 017145 246 SVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQR 325 (376)
Q Consensus 246 ~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~l~~Ms~eEmas~e~k~~~~~~~ee~l~~~~~ 325 (376)
+||.+||..|+.+++.|+++||+|+|||||++||+||++||+|+|+|++||.|+++||||++++++++++.+++|+++++
T Consensus 169 ~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~l~~~~~ 248 (299)
T TIGR01385 169 QIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQG 248 (299)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccccC
Q 017145 326 GGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC 376 (376)
Q Consensus 326 ~~~~~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkfc 376 (376)
+.....+++.|+|++||+++|+|||+|||+||||||+||+|.+|||+|+||
T Consensus 249 ~~~~~~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~fc 299 (299)
T TIGR01385 249 AKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKFC 299 (299)
T ss_pred hhhhcCCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeeeC
Confidence 988888999999999999999999999999999999999999999999999
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=1.7e-63 Score=474.18 Aligned_cols=292 Identities=40% Similarity=0.667 Sum_probs=227.7
Q ss_pred HHHHHHHHHHHhHhhhcCCCCCCCCHHHHHHHHHHhcCCCCCHHhhhcCccceecc-cccCCCCHHHHHHHHHHHHHHHH
Q 017145 6 VELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLR-PLTKHPREKIQIVASNLLDIWKK 84 (376)
Q Consensus 6 ~el~~~a~k~a~~~~~~~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~iG~~V~-~Lrkh~~~~I~~~Ak~Lv~~WK~ 84 (376)
.|.+++|+++.+++. +++.+.+||+|.+|++++||+++|++|+||+.|| .|++|+|++|+++|+.||+.||+
T Consensus 4 e~~~r~ak~l~~~~~-------~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk 76 (296)
T KOG1105|consen 4 EEALRAAKALEKDKQ-------SKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKK 76 (296)
T ss_pred HHHHHHHHHHHhhcc-------cccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 456666666555552 2689999999999999999999999999999999 77889999999999999999999
Q ss_pred HHHhhhhccCCCCCCCCCCCcccCccCCCCCCccccccccchhhcccccchhhhhhccCCCCCchhhhhhhcccCCCccc
Q 017145 85 IVIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNGDSVM 164 (376)
Q Consensus 85 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (376)
+|.......+ +.. . +.+.+ ...+... .+ ..+ .+.+...+.
T Consensus 77 ~~~~~~~~~k--~~~-~----------~~~~p----~~~~~~~----~s--------------~~~-~~~ks~~~~---- 116 (296)
T KOG1105|consen 77 LVDKSPGREK--SGD-N----------KSHDP----GEASSKS----PS--------------GAK-QPEKSRGDS---- 116 (296)
T ss_pred Hhhccccccc--Ccc-c----------cCCCC----CcCCcCC----cc--------------CCC-Ccccccccc----
Confidence 9986411111 110 0 00000 0000000 00 000 000000000
Q ss_pred CCCcchhhhHHHhhhhcCCCCCCCCCCCCCCCcccccccCCchhHHHHHHHHHHHHhhhhccChhhhhhhhcccChHHHH
Q 017145 165 DRGEAVKVEKIIEEEKQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVA 244 (376)
Q Consensus 165 ~~~~~~~~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~lA 244 (376)
. ..+..+++ ...+.++|.+|++|++|||+||.. ... +....+++..+|
T Consensus 117 ------~------------~~~~~~~~-------~~~~~~~d~~r~k~~e~l~~al~~-----~~~--~~~~~~~~~~~a 164 (296)
T KOG1105|consen 117 ------K------------RDKHSGSK-------DPVPITNDPVRDKCRELLYAALTT-----EDD--SRVTGADPLELA 164 (296)
T ss_pred ------c------------cccccCcC-------CCCCCCCchHHHHHHHHHHHHhcc-----ccc--ccccCCCHHHHH
Confidence 0 00000000 112346899999999999999982 111 123456778999
Q ss_pred HHHHHHHHHHhCCCchhhhHHHHHHHhhccCCCChhhhhchhcCCCChhhhccCChhhcCcHHHHHHHHHHHHHHHHHhh
Q 017145 245 VSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQ 324 (376)
Q Consensus 245 ~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~l~~Ms~eEmas~e~k~~~~~~~ee~l~~~~ 324 (376)
.+||.+||..++.++++||++|||++|||+|++||+||++||.|+|+|++|+.|+++||||++++++++++.+++|+.+|
T Consensus 165 ~~iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~k~~keal~~~q 244 (296)
T KOG1105|consen 165 VQIEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKEERQKLTKEALREHQ 244 (296)
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccccC
Q 017145 325 RGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC 376 (376)
Q Consensus 325 ~~~~~~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkfc 376 (376)
.+....++|+.|.|++|++++|+|+|+||||+||||||||+|..||||||||
T Consensus 245 ~~~~~gt~td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnrWkfc 296 (296)
T KOG1105|consen 245 MAKIQGTQTDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNRWKFC 296 (296)
T ss_pred hcccccccccceeeccccccceeEEeeccCCCCCCcceeeeecccCCccccC
Confidence 9988889999999999999999999999999999999999999999999999
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.95 E-value=1.6e-27 Score=196.81 Aligned_cols=101 Identities=47% Similarity=0.747 Sum_probs=91.1
Q ss_pred chhHHHHHHHHHHHHhhhhccChhhhhhhhcccChHHHHHHHHHHHHHHhCCCchhhhHHHHHHHhhccCCCChhhhhch
Q 017145 206 DSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRV 285 (376)
Q Consensus 206 d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~v 285 (376)
|.+|++|+++|+++|........ ...++..+|.+||.+||..|+...+.|++++|||+|||||++||+||++|
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~-------~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~v 73 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEE-------IELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKV 73 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCc-------ccccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 67999999999999997554332 12356789999999999999988889999999999999999999999999
Q ss_pred hcCCCChhhhccCChhhcCcHHHHHHHH
Q 017145 286 LLGEVTPERLVTMSPEEMASDERQRQIE 313 (376)
Q Consensus 286 l~G~i~p~~l~~Ms~eEmas~e~k~~~~ 313 (376)
|+|+|+|++||.||++||||+++|++++
T Consensus 74 l~G~i~p~~lv~Ms~~ElAs~elk~~~e 101 (102)
T smart00510 74 LNGEITPEKLATMTAEELASAELKEKRE 101 (102)
T ss_pred HcCCCCHHHHhcCCHHHcCCHHHHHHHh
Confidence 9999999999999999999999999876
No 4
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=99.93 E-value=8.5e-27 Score=196.81 Aligned_cols=114 Identities=46% Similarity=0.756 Sum_probs=103.4
Q ss_pred CCchhHHHHHHHHHHHHhhhhccChhhhhhhhcccChHHHHHHHHHHHHHHhCCCchhhhHHHHHHHhhccCCCChhhhh
Q 017145 204 CNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRK 283 (376)
Q Consensus 204 ~~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~ 283 (376)
|++++|++|+++|+++|.....+ .+ ...++..+|.+||.+||..|+.....|++++|+|+|||||++||+|+.
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~------~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~~ 73 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QD------DPEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLRR 73 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CC------CTCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHHH
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-cc------chhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHHH
Confidence 56899999999999999986554 11 234567999999999999998888999999999999999999999999
Q ss_pred chhcCCCChhhhccCChhhcCcHHHHHHHHHHHHHHHHHhh
Q 017145 284 RVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQ 324 (376)
Q Consensus 284 ~vl~G~i~p~~l~~Ms~eEmas~e~k~~~~~~~ee~l~~~~ 324 (376)
+||+|+|+|.+||.|+++||||++++++++++.++++++++
T Consensus 74 ~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~~~l~~~~ 114 (115)
T PF07500_consen 74 RILSGEISPEELVTMSPEELASEELKEEREKIRKESLKQSQ 114 (115)
T ss_dssp HHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHHHHHHHTB
T ss_pred HHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999998876
No 5
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.76 E-value=3.9e-19 Score=122.27 Aligned_cols=39 Identities=51% Similarity=1.218 Sum_probs=37.9
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
++||+||+++++|+|+|+||||||||+||+|.+|||+|+
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=99.75 E-value=9.2e-19 Score=119.82 Aligned_cols=39 Identities=51% Similarity=1.236 Sum_probs=35.2
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
++||+||+++++|+|+|+|+||||||+||+|.+|||+|+
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 579999999999999999999999999999999999997
No 7
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.73 E-value=3.6e-18 Score=133.59 Aligned_cols=74 Identities=47% Similarity=0.762 Sum_probs=68.6
Q ss_pred HHHHHHHHHhHhhhcCCCCCCCCHHHHHHHHHHhcCCCCCHHhhhcCccceecccccCCCCHHHHHHHHHHHHHHHHHHH
Q 017145 8 LFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIVI 87 (376)
Q Consensus 8 l~~~a~k~a~~~~~~~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~ 87 (376)
||+++++++++++. +++++.|+++|++|+.++||.++|++|+||++|++||+|+|++|+.+|+.||+.||++|+
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------GKEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred ChHHHHHHHHHhcC------CCCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 57899999998842 356889999999999999999999999999999999999999999999999999999985
No 8
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=99.68 E-value=9.2e-18 Score=134.16 Aligned_cols=44 Identities=43% Similarity=1.004 Sum_probs=41.3
Q ss_pred cccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 331 ATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 331 ~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.+.+...||+||+.+++|+|+||||||||||+||.|.+|+|+||
T Consensus 61 v~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 61 VDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 34567899999999999999999999999999999999999998
No 9
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.67 E-value=4.1e-17 Score=137.16 Aligned_cols=48 Identities=44% Similarity=0.908 Sum_probs=43.9
Q ss_pred CccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccccC
Q 017145 329 ATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC 376 (376)
Q Consensus 329 ~~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkfc 376 (376)
++.++..+.||+||++++.|+|+|+||||||||+||+|..|||+|+|+
T Consensus 66 ~~~~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre~ 113 (113)
T COG1594 66 KTLPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWREY 113 (113)
T ss_pred cccccccccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeecC
Confidence 344555899999999999999999999999999999999999999984
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=99.62 E-value=2.6e-16 Score=130.46 Aligned_cols=46 Identities=37% Similarity=0.910 Sum_probs=43.5
Q ss_pred CccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 329 ATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 329 ~~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
++++++.+.||+||+.+++|+|+|+||||||||+||+|.+|||+|+
T Consensus 56 ~~~~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 56 ETLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 4567778999999999999999999999999999999999999997
No 11
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.62 E-value=3.1e-16 Score=138.45 Aligned_cols=44 Identities=32% Similarity=0.581 Sum_probs=41.3
Q ss_pred ccc-ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 331 ATT-DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 331 ~~t-~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
+++ ...+||+||+++++|+|+||||||||||+||.|.+|||+|+
T Consensus 138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 344 67899999999999999999999999999999999999998
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=99.59 E-value=1.4e-15 Score=119.27 Aligned_cols=74 Identities=42% Similarity=0.657 Sum_probs=64.0
Q ss_pred HHHHHHHHHHhHhhhcCCCCCCCCHHHHHHHHHHhcCCCCCHHhhhcCccceecccccCCCCHHHHHHHHHHHHHHHHHH
Q 017145 7 ELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIV 86 (376)
Q Consensus 7 el~~~a~k~a~~~~~~~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v 86 (376)
|+.++.+++.... + .++.+.|+++|+.|+.++||.++|++|+||+.||+||+|++++|+.+|+.||++||++|
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------S-NEEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLV 75 (76)
T ss_pred HHHHHHHHhhccc------c-CCCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhc
Confidence 4555555555443 1 25789999999999999999999999999999999999999999999999999999987
Q ss_pred H
Q 017145 87 I 87 (376)
Q Consensus 87 ~ 87 (376)
+
T Consensus 76 ~ 76 (76)
T cd00183 76 D 76 (76)
T ss_pred C
Confidence 3
No 13
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=99.48 E-value=3.2e-14 Score=115.81 Aligned_cols=51 Identities=33% Similarity=0.826 Sum_probs=48.4
Q ss_pred hhcCCCcccc-ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 324 QRGGEATATT-DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 324 ~~~~~~~~~t-~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.++.||++++ ....||+||+++++|||.|+|.+|+.|++||+|++|||+|.
T Consensus 61 Dl~~DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 61 DLASDPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred hhccCCCcCccccccCCccCCcceEEEecccccccceEEEEEEecccccccc
Confidence 4688999999 58999999999999999999999999999999999999995
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=99.37 E-value=1.9e-13 Score=99.75 Aligned_cols=52 Identities=38% Similarity=0.653 Sum_probs=47.5
Q ss_pred HHHHHhcCCCCCHHhhhcCccceecccccCC-CCHHHHHHHHHHHHHHHHHHH
Q 017145 36 DALKRLKSFPVTYDVLVSTQVGKRLRPLTKH-PREKIQIVASNLLDIWKKIVI 87 (376)
Q Consensus 36 ~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh-~~~~I~~~Ak~Lv~~WK~~v~ 87 (376)
++|+.|..+|||.++|++|+||++|+.|++| .+++|+.+|+.||++||++|+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 5899999999999999999999999999999 899999999999999999874
No 15
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.31 E-value=1.1e-12 Score=138.59 Aligned_cols=82 Identities=40% Similarity=0.578 Sum_probs=75.1
Q ss_pred cChHHHHHHHHHHHHHHhC-CCchhhhHHHHHHHhhccCCCChhhhhchhcCCCChhhhccCChhhcCcHHHHHHHHHHH
Q 017145 238 CDPIRVAVSVESVMFEKLG-RSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIK 316 (376)
Q Consensus 238 ~~~~~lA~~IE~alf~~~~-~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~l~~Ms~eEmas~e~k~~~~~~~ 316 (376)
.++..++..||..||..|+ +.+.+|+.++|+|+|||||++||.||.+|+.|+|+|++|+.|+++|||+.++.+.+++..
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 3455677899999999999 778999999999999999999999999999999999999999999999999999988766
Q ss_pred HHH
Q 017145 317 EKA 319 (376)
Q Consensus 317 ee~ 319 (376)
++.
T Consensus 347 ee~ 349 (778)
T KOG1634|consen 347 EEM 349 (778)
T ss_pred HHH
Confidence 654
No 16
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=99.19 E-value=6.2e-12 Score=103.49 Aligned_cols=44 Identities=34% Similarity=0.744 Sum_probs=41.2
Q ss_pred cccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 331 ATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 331 ~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.++..-+||+||+.+..|..+|+|||||+.|+||+|.+|+++++
T Consensus 70 ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 70 GAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred ccchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 46778899999999999999999999999999999999999874
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=96.78 E-value=0.0023 Score=53.37 Aligned_cols=78 Identities=28% Similarity=0.463 Sum_probs=57.5
Q ss_pred hhHHHHHHHHHHHHHhHhhhcCCCCCCCCHHHHHHHHHHhcCCCCCHHhhh-cCccceecccccCCC-CHHHHHHHHHHH
Q 017145 2 EQELVELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLV-STQVGKRLRPLTKHP-REKIQIVASNLL 79 (376)
Q Consensus 2 e~e~~el~~~a~k~a~~~~~~~~~~~~~~~~~~l~~L~~L~~~~it~~~L~-~T~iG~~V~~Lrkh~-~~~I~~~Ak~Lv 79 (376)
|+.|.+|-.--+-+-. -+++++.+|+++|.+|..++||.-+|+ .+.+-.++++||+.. |..|+..|..|+
T Consensus 1 E~~L~~l~~~Ik~~L~--------~~~~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lY 72 (106)
T PF11467_consen 1 ERRLQELHSEIKSSLK--------VDNPDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELY 72 (106)
T ss_dssp HHHHHHHHHHHHHTCE--------TTEE-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHHHc--------CCCCCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence 4556666655544332 234789999999999999999998666 556888899999984 799999999999
Q ss_pred HHHHHHHH
Q 017145 80 DIWKKIVI 87 (376)
Q Consensus 80 ~~WK~~v~ 87 (376)
.+.|.++.
T Consensus 73 nkfK~~f~ 80 (106)
T PF11467_consen 73 NKFKSLFL 80 (106)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhC
Confidence 99999996
No 18
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=96.31 E-value=0.0019 Score=65.54 Aligned_cols=58 Identities=26% Similarity=0.507 Sum_probs=54.7
Q ss_pred CCHHHHHHHHHHhcCCCCCHHhhhcCccceecccccCCCCHHHHHHHHHHHHHHHHHHHh
Q 017145 29 PEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIVIE 88 (376)
Q Consensus 29 ~~~~~~l~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~~ 88 (376)
.++.+++..|..|..+|+++++|.+|+||+.|+.|++|. .|..+|..|+..||++|..
T Consensus 22 ~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~~ 79 (433)
T KOG2821|consen 22 IDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVLV 79 (433)
T ss_pred ccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhccc
Confidence 578999999999999999999999999999999999998 6999999999999999953
No 19
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.89 E-value=0.0091 Score=59.81 Aligned_cols=53 Identities=23% Similarity=0.463 Sum_probs=47.0
Q ss_pred HHHHHhcCCCCCH-HhhhcCccceecccccCCC--CHHHHHHHHHHHHHHHHHHHh
Q 017145 36 DALKRLKSFPVTY-DVLVSTQVGKRLRPLTKHP--REKIQIVASNLLDIWKKIVIE 88 (376)
Q Consensus 36 ~~L~~L~~~~it~-~~L~~T~iG~~V~~Lrkh~--~~~I~~~Ak~Lv~~WK~~v~~ 88 (376)
.+|..|..+||-. +.|...+||++|=.|.||+ ...++.+|..||..|-.-|..
T Consensus 237 ~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI~~ 292 (417)
T KOG1793|consen 237 SLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPIFK 292 (417)
T ss_pred HHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccccC
Confidence 4667777888888 9999999999999999997 488999999999999988864
No 20
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=94.88 E-value=0.032 Score=53.97 Aligned_cols=53 Identities=25% Similarity=0.434 Sum_probs=45.2
Q ss_pred HHHHHhcCCCCCHHhhhcCccceecccccCC--CCHHHHHHHHHHHHHHHHHHHh
Q 017145 36 DALKRLKSFPVTYDVLVSTQVGKRLRPLTKH--PREKIQIVASNLLDIWKKIVIE 88 (376)
Q Consensus 36 ~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh--~~~~I~~~Ak~Lv~~WK~~v~~ 88 (376)
.+|..|..+||-.++|.+.+||+.|=+.... ..++|+.+|+.||..|-.-|..
T Consensus 234 sL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpIik 288 (397)
T COG5139 234 SLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPIIK 288 (397)
T ss_pred HHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhccccC
Confidence 3556677889999999999999999887654 5799999999999999887753
No 21
>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=94.67 E-value=0.0076 Score=38.80 Aligned_cols=27 Identities=26% Similarity=0.780 Sum_probs=15.1
Q ss_pred cccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 337 KCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 337 ~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
+|+.|+...++ . ....++|..|+|.|.
T Consensus 4 ~Cp~C~se~~y--------~---D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 4 KCPLCGSEYTY--------E---DGELLVCPECGHEWN 30 (30)
T ss_dssp --TTT-----E--------E----SSSEEETTTTEEE-
T ss_pred CCCCCCCccee--------c---cCCEEeCCcccccCC
Confidence 69999998886 2 245789999999994
No 22
>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=94.44 E-value=0.045 Score=41.49 Aligned_cols=37 Identities=27% Similarity=0.652 Sum_probs=25.8
Q ss_pred ccccccCCcceEEEEEeccCC------CCC--CeEEEEcCCCCCc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSA------DEP--MTTYVTCVNCSKR 372 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsa------DEp--mt~f~~C~~C~~~ 372 (376)
+.|||||+++...-++|.-.+ |-. .=+.++|.+||+.
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 479999999888777765321 322 2356679999986
No 23
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.72 E-value=0.041 Score=36.84 Aligned_cols=32 Identities=25% Similarity=0.559 Sum_probs=23.2
Q ss_pred cccccccCCcceEEEEEeccCCCC---CCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADE---PMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDE---pmt~f~~C~~C~~~Wk 374 (376)
.+.||+|+..-. -.|+ +-..-+.|.+|||.|+
T Consensus 2 ~i~Cp~C~~~y~--------i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 2 IITCPNCQAKYE--------IDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EEECCCCCCEEe--------CCHHHCCCCCcEEECCCCCCEeC
Confidence 367999986433 2444 4557899999999995
No 24
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=93.54 E-value=0.065 Score=41.60 Aligned_cols=37 Identities=24% Similarity=0.571 Sum_probs=25.7
Q ss_pred cccccccCCcceEEEEEeccCCCC-CCeEEEEcC--CCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADE-PMTTYVTCV--NCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDE-pmt~f~~C~--~C~~~Wk 374 (376)
++.||.||..-.+ .. +|..++ -.-.|+.|. +|||+|.
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 4789999998732 22 223333 344899998 7999996
No 25
>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=93.16 E-value=0.074 Score=35.64 Aligned_cols=35 Identities=17% Similarity=0.590 Sum_probs=22.8
Q ss_pred cccccccCCcceEEEEEeccC-CCCCCeEEEEcCCCCCcccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRS-ADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrs-aDEpmt~f~~C~~C~~~Wkf 375 (376)
.+.||.|+.. |.++... .+.+ ..+.|.+||+.|+.
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 3689999975 3333221 2222 37899999999974
No 26
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.05 E-value=0.056 Score=36.35 Aligned_cols=32 Identities=22% Similarity=0.587 Sum_probs=22.4
Q ss_pred ccccccCCcceEEEEEeccCCCC---CCeEEEEcCCCCCcccc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADE---PMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDE---pmt~f~~C~~C~~~Wkf 375 (376)
+.||.|+..-- + .|+ +-..-+.|..|+|.|.|
T Consensus 3 i~CP~C~~~f~----v----~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 3 ITCPNCQTRFR----V----PDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EECCCCCceEE----c----CHHHcccCCcEEECCCCCcEeeC
Confidence 57999985322 2 222 23468999999999975
No 27
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=92.76 E-value=0.093 Score=36.91 Aligned_cols=30 Identities=33% Similarity=0.699 Sum_probs=22.1
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
+.+.||+||+.+.+... + ...|.|..|+++
T Consensus 17 ~g~~CP~Cg~~~~~~~~--~-------~~~~~C~~C~~q 46 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLK--T-------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCCeeeEEeC--C-------CCeEECCCCCCc
Confidence 34889999999443332 2 568999999985
No 28
>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=92.43 E-value=0.12 Score=36.59 Aligned_cols=36 Identities=22% Similarity=0.566 Sum_probs=23.9
Q ss_pred cccccCCcceEEEEEeccCCCCCCeEEEEcCC--CCCccc
Q 017145 337 KCSRCGQRKCTYYQMQTRSADEPMTTYVTCVN--CSKRWK 374 (376)
Q Consensus 337 ~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~--C~~~Wk 374 (376)
.||.||.+-....-.+. .+.--..|+.|.| |||.|.
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 59999987654432211 2222348999998 999996
No 29
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=91.09 E-value=0.18 Score=38.04 Aligned_cols=38 Identities=26% Similarity=0.667 Sum_probs=23.2
Q ss_pred cccccccCCcceEEEEEeccC------CCCCCeEE--EEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRS------ADEPMTTY--VTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrs------aDEpmt~f--~~C~~C~~~ 372 (376)
.++||+||.++..--+++... -|-.-..| ++|.+||+.
T Consensus 4 ~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred cccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 467999999876555554321 01112233 459999975
No 30
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=90.78 E-value=0.21 Score=34.58 Aligned_cols=28 Identities=29% Similarity=0.812 Sum_probs=20.6
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
+.||.||... .++. +++-.++|.+||.-
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 45668899999964
No 31
>PHA00626 hypothetical protein
Probab=90.35 E-value=0.18 Score=36.98 Aligned_cols=33 Identities=18% Similarity=0.445 Sum_probs=21.2
Q ss_pred cccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 337 KCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 337 ~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.||+||+.+.+-- -.-| ....-|.|..||+++.
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 1134689999999864
No 32
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=89.58 E-value=0.43 Score=39.21 Aligned_cols=37 Identities=24% Similarity=0.615 Sum_probs=28.2
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
..|.||.||+...+-..+-. -.+.-+..|-+||.++.
T Consensus 21 k~FtCp~Cghe~vs~ctvkk----~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKK----TVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ceEecCccCCeeeeEEEEEe----cCceeEEEcccCcceEE
Confidence 47999999999987544321 14678899999998865
No 33
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=89.45 E-value=0.44 Score=35.15 Aligned_cols=36 Identities=28% Similarity=0.528 Sum_probs=24.5
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
...+||-||.....+.+.- ..+..+..|+.|.+||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~--~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDE--GFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeeccc--CCCCCCEEEEEcCCCCC
Confidence 3578999987777666532 22333447788999997
No 34
>PLN02976 amine oxidase
Probab=89.04 E-value=0.48 Score=55.48 Aligned_cols=60 Identities=18% Similarity=0.336 Sum_probs=49.9
Q ss_pred HHHHHHHhcCCCCCHHhhhcCccceec-ccccCCCCHHHHHHHHHHHHHHHHHHHhhhhcc
Q 017145 34 CVDALKRLKSFPVTYDVLVSTQVGKRL-RPLTKHPREKIQIVASNLLDIWKKIVIEETTRN 93 (376)
Q Consensus 34 ~l~~L~~L~~~~it~~~L~~T~iG~~V-~~Lrkh~~~~I~~~Ak~Lv~~WK~~v~~~~~~~ 93 (376)
+..+|+-|--++..+..|+..+||++| +++.-|.+++|+.+|..|+..|.+++..++..+
T Consensus 1303 ~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~~~ 1363 (1713)
T PLN02976 1303 LRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKASN 1363 (1713)
T ss_pred HHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 344555555567777788999999999 889999999999999999999999998776533
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=87.11 E-value=0.46 Score=31.84 Aligned_cols=27 Identities=26% Similarity=0.814 Sum_probs=20.1
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.+.|+.|+.. ++.. +++ ||.|..|||.
T Consensus 8 ~~~C~~C~~~---~~~~-----~dG---~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYS-----DDG---FYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeEc-----cCC---EEEhhhCceE
Confidence 4679999998 4443 233 9999999985
No 36
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=87.10 E-value=1 Score=32.55 Aligned_cols=34 Identities=18% Similarity=0.446 Sum_probs=22.6
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.+||.||.....+.- +..|-.-..++.|..||..
T Consensus 2 kPCPfCGg~~~~~~~---~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR---GFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe---ccCCCCCEEEEECCCCCCC
Confidence 579999997765531 1223334556689999975
No 37
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=86.26 E-value=0.49 Score=35.95 Aligned_cols=29 Identities=31% Similarity=0.811 Sum_probs=23.8
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
..+||.|++..+.|--.| +.++|..||..
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 459999999999987654 47899999963
No 38
>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=85.90 E-value=0.59 Score=49.87 Aligned_cols=39 Identities=18% Similarity=0.451 Sum_probs=28.9
Q ss_pred cccccccCCcceEE-EEEeccCCC-CCCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTY-YQMQTRSAD-EPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~-~q~qtrsaD-Epmt~f~~C~~C~~~Wk 374 (376)
..+||.||.....- -+++- ..+ .|.+.+|+|..||..|.
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w-~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKW-DKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EccCCCCCCCccccccceee-cCCCCccceEEECCCCcCCCC
Confidence 46999999876644 34443 223 68899999999999884
No 39
>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=85.75 E-value=0.84 Score=40.69 Aligned_cols=30 Identities=27% Similarity=0.420 Sum_probs=17.7
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
..|.||+|+.+- +-+|.|..-|+|..||..
T Consensus 108 ~~Y~Cp~c~~r~---------tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRF---------TFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEe---------eHHHHHHcCCcCCCCCCE
Confidence 456677776322 245566666777777653
No 40
>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=85.41 E-value=1.3 Score=32.95 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=22.5
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
...||+|+.-.....- + |.-.-++.|..|||+=
T Consensus 9 GA~CP~C~~~Dtl~~~-~-----e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 9 GAVCPACSAQDTLAMW-K-----ENNIELVECVECGYQE 41 (59)
T ss_pred cccCCCCcCccEEEEE-E-----eCCceEEEeccCCCcc
Confidence 5689999987765321 1 1224689999999973
No 41
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=85.36 E-value=1.2 Score=33.72 Aligned_cols=34 Identities=21% Similarity=0.374 Sum_probs=26.4
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
..+||-||.......+. .-..++.|..|+-.|-|
T Consensus 6 lKPCPFCG~~~~~v~~~-------~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI-------SGYYRAKCNGCESRTGY 39 (64)
T ss_pred ccCCCCCCCceeEEEec-------CceEEEEcCCCCcCccc
Confidence 56899999999988753 12556899999988753
No 42
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=85.24 E-value=0.62 Score=45.41 Aligned_cols=38 Identities=24% Similarity=0.641 Sum_probs=17.8
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
.-.||-||..-..- .+..... ++ -.|..|.-||+.|+|
T Consensus 172 ~g~CPvCGs~P~~s-~l~~~~~-~G-~R~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 172 RGYCPVCGSPPVLS-VLRGGER-EG-KRYLHCSLCGTEWRF 209 (290)
T ss_dssp -SS-TTT---EEEE-EEE--------EEEEEETTT--EEE-
T ss_pred CCcCCCCCCcCceE-EEecCCC-Cc-cEEEEcCCCCCeeee
Confidence 46899999864432 2221111 24 489999999999996
No 43
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=84.93 E-value=1.1 Score=35.50 Aligned_cols=38 Identities=16% Similarity=0.498 Sum_probs=21.3
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
..|.||.|++.++.--.+-.. .++-.+.|..||..|.+
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk----~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKK----EGIGILSCRVCGESFQT 58 (81)
T ss_dssp S----TTT--SS-EEEEEETT----TTEEEEEESSS--EEEE
T ss_pred ceEcCCcCCCCCeEEEEEEcc----CCEEEEEecCCCCeEEE
Confidence 689999999888776655322 56888999999988764
No 44
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.82 E-value=0.55 Score=41.23 Aligned_cols=37 Identities=22% Similarity=0.608 Sum_probs=21.8
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
....|.||.||.+-. |...+ +-.| ++..|+|.+||..
T Consensus 96 ~~~~Y~Cp~C~~~y~-~~ea~-~~~d--~~~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCPNCQSKYT-FLEAN-QLLD--MDGTFTCPRCGEE 132 (147)
T ss_pred CCcEEECcCCCCEee-HHHHH-HhcC--CCCcEECCCCCCE
Confidence 346899999983322 22211 1112 2445999999975
No 45
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=84.41 E-value=0.95 Score=35.04 Aligned_cols=32 Identities=22% Similarity=0.520 Sum_probs=22.2
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
+..||+|+.-....+=. -+ . .-++.|..|||+
T Consensus 8 Ga~CP~C~~~D~i~~~~----e~-~-ve~vECV~CGy~ 39 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWR----EN-G-VEYVECVECGYT 39 (71)
T ss_pred CccCCCCcCccEEEEEE----eC-C-ceEEEecCCCCe
Confidence 56899999877533211 11 1 668999999996
No 46
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=83.73 E-value=1.1 Score=40.78 Aligned_cols=31 Identities=19% Similarity=0.341 Sum_probs=17.0
Q ss_pred CCCChhhhccCChhhcCcHHHHHHHHHHHHHHH
Q 017145 288 GEVTPERLVTMSPEEMASDERQRQIENIKEKAL 320 (376)
Q Consensus 288 G~i~p~~l~~Ms~eEmas~e~k~~~~~~~ee~l 320 (376)
|.++.++|+... .|...++++.-.++.++.|
T Consensus 35 g~~tdeeLA~~L--gi~~~~VRk~L~~L~e~gL 65 (178)
T PRK06266 35 GEVTDEEIAEQT--GIKLNTVRKILYKLYDARL 65 (178)
T ss_pred CCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCC
Confidence 666666665443 3445556655555555444
No 47
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.11 E-value=1.1 Score=31.75 Aligned_cols=30 Identities=17% Similarity=0.449 Sum_probs=18.3
Q ss_pred cccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 337 KCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 337 ~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
-||.||.-- ..+ .++ ...++.|..||+.|+
T Consensus 2 FCp~Cg~~l------~~~-~~~-~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNML------IPK-EGK-EKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCcc------ccc-cCC-CCCEEECCcCCCeEE
Confidence 399998822 111 121 123778999998875
No 48
>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=82.36 E-value=0.62 Score=28.95 Aligned_cols=24 Identities=21% Similarity=0.645 Sum_probs=16.9
Q ss_pred cccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 337 KCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 337 ~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.||.|+..-. ..-..|.+|||.|.
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 5888876542 34557999999874
No 49
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.09 E-value=0.94 Score=41.21 Aligned_cols=32 Identities=28% Similarity=0.487 Sum_probs=24.7
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
....|.||.|+.+-. .+|.|...|+|..||..
T Consensus 114 ~~~~Y~Cp~C~~ryt---------f~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 114 NNMFFFCPNCHIRFT---------FDEAMEYGFRCPQCGEM 145 (178)
T ss_pred CCCEEECCCCCcEEe---------HHHHhhcCCcCCCCCCC
Confidence 346789999994432 56678889999999975
No 50
>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=80.93 E-value=0.92 Score=44.77 Aligned_cols=39 Identities=18% Similarity=0.628 Sum_probs=27.1
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
.-.||-||..-+ .-.++.+..+++ -.|..|.-|++.|+|
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 448999998763 222333223344 689999999999996
No 51
>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=80.73 E-value=1.7 Score=37.30 Aligned_cols=32 Identities=19% Similarity=0.593 Sum_probs=25.5
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.-+.|+.|+++++.+.-- .| ..|..|..||.+
T Consensus 92 ~yVlC~~C~spdT~l~k~-~r------~~~l~C~aCGa~ 123 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIKE-GR------LIFLKCKACGAS 123 (125)
T ss_dssp HHSSCTSTSSSSEEEEEE-TT------CCEEEETTTSCE
T ss_pred HEEEcCCCCCCccEEEEc-CC------EEEEEecccCCc
Confidence 346799999999877654 34 689999999975
No 52
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.84 E-value=1.3 Score=30.88 Aligned_cols=28 Identities=43% Similarity=0.803 Sum_probs=17.9
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.|.|++||..-.. |+.++ -+.|..||++
T Consensus 3 ~y~C~~CG~~~~~---------~~~~~-~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVEL---------DEYGT-GVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEE---------CCCCC-ceECCCCCCe
Confidence 4788888874331 22223 6788888875
No 53
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=79.69 E-value=2.3 Score=28.97 Aligned_cols=29 Identities=28% Similarity=0.709 Sum_probs=19.8
Q ss_pred cccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 337 KCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 337 ~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
+||+|+.. ..-..+ +-.....|..|+-.|
T Consensus 1 ~CP~C~~~-l~~~~~-------~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRL-------GDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcc-cceEEE-------CCEEEEECCCCCeEE
Confidence 59999873 322222 226778899999888
No 54
>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=79.59 E-value=0.67 Score=35.36 Aligned_cols=36 Identities=28% Similarity=0.697 Sum_probs=25.2
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
.|+|..|+.+....+-.|. =+--++++.|.+|.++-
T Consensus 4 ~FTC~~C~~Rs~~~~sk~a---Y~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQA---YHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp EEEETTTTEEEEEEEEHHH---HHTSEEEEE-TTS--EE
T ss_pred EEEcCCCCCccceeeCHHH---HhCCeEEEECCCCccee
Confidence 5899999999887766553 23348999999999763
No 55
>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=79.52 E-value=2.9 Score=30.57 Aligned_cols=44 Identities=18% Similarity=0.362 Sum_probs=30.4
Q ss_pred HhhhcCCCccccc--cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 322 ECQRGGEATATTD--QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 322 ~~~~~~~~~~~t~--~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
+.-+|.+++.+.. .+-|++|....-.+. ..|+..+-|+|..||+
T Consensus 7 d~L~G~d~~~~~~r~aLIC~~C~~hNGla~------~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 7 DVLLGDDPTSPSNRYALICSKCFSHNGLAP------KEEFEEIQYRCPYCGA 52 (54)
T ss_pred HHHhCCCCccccCceeEECcccchhhcccc------cccCCceEEEcCCCCC
Confidence 3345666644443 568999998777554 3456667999999996
No 56
>PLN00209 ribosomal protein S27; Provisional
Probab=79.30 E-value=1.6 Score=34.91 Aligned_cols=29 Identities=28% Similarity=0.558 Sum_probs=24.6
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
..+|+.|++..+.|-..| +-|.|..||..
T Consensus 36 ~VkCp~C~n~q~VFShA~---------t~V~C~~Cg~~ 64 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQ---------TVVVCGSCQTV 64 (86)
T ss_pred EEECCCCCCeeEEEecCc---------eEEEccccCCE
Confidence 679999999999998765 47889999864
No 57
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=79.28 E-value=2.2 Score=35.79 Aligned_cols=32 Identities=22% Similarity=0.642 Sum_probs=25.0
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.-..|+.|+++++.+.-- .| +.|..|..||.+
T Consensus 79 ~yVlC~~C~spdT~l~k~-~r------~~~l~C~aCGa~ 110 (110)
T smart00653 79 EYVLCPECGSPDTELIKE-NR------LFFLKCEACGAR 110 (110)
T ss_pred hcEECCCCCCCCcEEEEe-CC------eEEEEccccCCC
Confidence 356799999999876543 33 788899999974
No 58
>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=79.01 E-value=2.7 Score=31.62 Aligned_cols=30 Identities=30% Similarity=0.625 Sum_probs=22.6
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
+-..|+.||...-. ......+.|.+||+.|
T Consensus 27 TSq~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCccccccc----------ccccceEEcCCCCCEE
Confidence 34569999988774 2345689999999875
No 59
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=78.92 E-value=2.2 Score=37.00 Aligned_cols=32 Identities=13% Similarity=0.457 Sum_probs=24.7
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.-..|+.|+++++.+. ... -..|..|..||.+
T Consensus 96 ~yVlC~~C~sPdT~l~-k~~------r~~~l~C~ACGa~ 127 (133)
T TIGR00311 96 KYVICRECNRPDTRII-KEG------RVSLLKCEACGAK 127 (133)
T ss_pred heEECCCCCCCCcEEE-EeC------CeEEEecccCCCC
Confidence 4568999999998765 332 3668899999986
No 60
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=78.80 E-value=1.7 Score=32.36 Aligned_cols=29 Identities=31% Similarity=0.823 Sum_probs=24.2
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
..+|+.|++..+.|--.| +-+.|..||+.
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 569999999999987654 46889999975
No 61
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=78.80 E-value=2.2 Score=37.24 Aligned_cols=32 Identities=16% Similarity=0.484 Sum_probs=25.2
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.-..|+.||++++.+.- .. -+.|..|..||.+
T Consensus 101 ~yVlC~~C~spdT~l~k-~~------r~~~l~C~ACGa~ 132 (138)
T PRK03988 101 EYVICPECGSPDTKLIK-EG------RIWVLKCEACGAE 132 (138)
T ss_pred hcEECCCCCCCCcEEEE-cC------CeEEEEcccCCCC
Confidence 35679999999987753 33 3889999999986
No 62
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=78.38 E-value=1.6 Score=43.22 Aligned_cols=39 Identities=21% Similarity=0.557 Sum_probs=26.8
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
..-.||-||..-+.- ++..+ .+++ -.|..|.-|++.|+|
T Consensus 186 ~~~~CPvCGs~P~~s-~v~~~-~~~G-~RyL~CslC~teW~~ 224 (309)
T PRK03564 186 QRQFCPVCGSMPVSS-VVQIG-TTQG-LRYLHCNLCESEWHV 224 (309)
T ss_pred CCCCCCCCCCcchhh-eeecc-CCCC-ceEEEcCCCCCcccc
Confidence 356899999876422 22221 2333 589999999999996
No 63
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=78.04 E-value=1.8 Score=34.54 Aligned_cols=29 Identities=34% Similarity=0.698 Sum_probs=24.7
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
+.+|+.|++..+.|-..| +-|.|..||..
T Consensus 35 ~VkCp~C~n~q~VFShA~---------t~V~C~~Cg~~ 63 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQ---------TVVLCGGCSSQ 63 (85)
T ss_pred EEECCCCCCeeEEEecCc---------eEEEccccCCE
Confidence 679999999999998875 46889999864
No 64
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=77.50 E-value=2.1 Score=34.32 Aligned_cols=32 Identities=19% Similarity=0.568 Sum_probs=23.9
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.....||.|+.+.+ ..+ .+-...|..||+.|-
T Consensus 33 ~~~~~Cp~C~~~~V--kR~--------a~GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVCPFCGRTTV--KRI--------ATGIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcCCCCCCcce--eee--------ccCeEEcCCCCCeec
Confidence 45778999999833 222 366999999999874
No 65
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=75.92 E-value=2.3 Score=35.12 Aligned_cols=33 Identities=27% Similarity=0.590 Sum_probs=22.4
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
..|.||.||.......- .| ....++|.+||+..
T Consensus 20 t~f~CP~Cge~~v~v~~--~k-----~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKVSISVKI--KK-----NIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCeEeeeec--CC-----CcceEECCCCCCcc
Confidence 58999999953332111 11 47899999999764
No 66
>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=75.84 E-value=1.4 Score=39.25 Aligned_cols=12 Identities=42% Similarity=0.958 Sum_probs=9.5
Q ss_pred ccccccccCCcc
Q 017145 334 DQFKCSRCGQRK 345 (376)
Q Consensus 334 ~~~~C~~C~~~~ 345 (376)
..|.||.||..=
T Consensus 127 ~~F~Cp~Cg~~L 138 (158)
T TIGR00373 127 LNFTCPRCGAML 138 (158)
T ss_pred cCCcCCCCCCEe
Confidence 479999998763
No 67
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.37 E-value=3.8 Score=35.90 Aligned_cols=77 Identities=19% Similarity=0.397 Sum_probs=44.9
Q ss_pred cCCCChhhhccCChhhcCcHHHHHHHHHHHHHHHHHh--hhcCCCccccccccccccCCcceEEEEE-------------
Q 017145 287 LGEVTPERLVTMSPEEMASDERQRQIENIKEKALFEC--QRGGEATATTDQFKCSRCGQRKCTYYQM------------- 351 (376)
Q Consensus 287 ~G~i~p~~l~~Ms~eEmas~e~k~~~~~~~ee~l~~~--~~~~~~~~~t~~~~C~~C~~~~~~~~q~------------- 351 (376)
.|.++-++|+.+. .|-..++++.-.++.++.+... ....++.. |..-.+||-+
T Consensus 13 ~~~~~dedLa~~l--~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~----------~~~~~~yw~i~y~~~~~vik~r~ 80 (147)
T smart00531 13 NGCVTEEDLAELL--GIKQKQLRKILYLLYDEKLIKIDYKREKDPET----------KTWYRYYWYINYDTLLDVVKYKL 80 (147)
T ss_pred cCCcCHHHHHHHh--CCCHHHHHHHHHHHHhhhcchhheeeeeCCCC----------ceEEEEEEEecHHHHHHHHHHHH
Confidence 4667777776555 3556677777777777544211 11111110 1134445544
Q ss_pred -------eccCCCCCCeEEEEcCCCCCcccc
Q 017145 352 -------QTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 352 -------qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
+.+-..|....||.|.+||.+|.|
T Consensus 81 ~~~~~~L~~~l~~e~~~~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 81 DKMRKRLEDKLEDETNNAYYKCPNCQSKYTF 111 (147)
T ss_pred HHHHHHHHHHHhcccCCcEEECcCCCCEeeH
Confidence 334456666789999999999976
No 68
>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=72.99 E-value=1.6 Score=32.14 Aligned_cols=29 Identities=31% Similarity=0.643 Sum_probs=19.7
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
+.+|+.|++..+.|-..|+ -+.|..||..
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 5699999999999877654 6889999864
No 69
>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=72.81 E-value=2.1 Score=27.97 Aligned_cols=26 Identities=27% Similarity=0.971 Sum_probs=14.3
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
+.|++||...- + . ..++ +.|.+||||
T Consensus 1 Y~C~~Cg~~~~----~--~-~~~~----irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVE----L--K-PGDP----IRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-----B--S-TSST----SSBSSSS-S
T ss_pred CCCCcCCCeeE----c--C-CCCc----EECCcCCCe
Confidence 35888876644 1 1 1222 478888887
No 70
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=71.92 E-value=2.6 Score=31.33 Aligned_cols=31 Identities=26% Similarity=0.668 Sum_probs=22.8
Q ss_pred cccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 331 ATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 331 ~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.++-.+.|+.||.++.. + +. --+.|-.||||
T Consensus 16 ~~~miYiCgdC~~en~l----k--~~-----D~irCReCG~R 46 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTL----K--RG-----DVIRCRECGYR 46 (62)
T ss_pred cccEEEEeccccccccc----c--CC-----CcEehhhcchH
Confidence 35557899999998762 2 22 25789999998
No 71
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=71.79 E-value=1.9 Score=30.96 Aligned_cols=30 Identities=30% Similarity=0.653 Sum_probs=21.4
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
+..+.|.+||..- .+. .-+..+.|..|||+
T Consensus 4 ~~~Y~C~~Cg~~~---~~~-------~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREV---ELD-------QETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCee---ehh-------hccCceeCCCCCcE
Confidence 3468899998765 111 24678889999987
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=71.31 E-value=2.8 Score=29.32 Aligned_cols=27 Identities=26% Similarity=0.740 Sum_probs=17.1
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.+.|++||..-- + + ..--+.|.+|||+
T Consensus 2 ~Y~C~~Cg~~~~----~-----~--~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENE----I-----K--SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEee----c-----C--CCCceECCCCCce
Confidence 367888987432 1 1 1223788899987
No 73
>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=70.42 E-value=6 Score=26.81 Aligned_cols=29 Identities=24% Similarity=0.689 Sum_probs=19.7
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCC---CCCc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVN---CSKR 372 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~---C~~~ 372 (376)
..||.||+ ...+.++|.. .|+-|.+ |.+.
T Consensus 2 ~~CP~Cg~---~lv~r~~k~g-----~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 2 EKCPKCGG---PLVLRRGKKG-----KFLGCSNYPECKYT 33 (39)
T ss_pred cCCCCCCc---eeEEEECCCC-----CEEECCCCCCcCCe
Confidence 47999993 2334444444 7999987 8875
No 74
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=69.25 E-value=5 Score=37.20 Aligned_cols=32 Identities=19% Similarity=0.508 Sum_probs=25.2
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.-..|+.|+++++.+.- . .-+.|..|..||.+
T Consensus 97 ~yV~C~~C~~pdT~l~k-~------~~~~~l~C~aCGa~ 128 (201)
T PRK12336 97 EYVICSECGLPDTRLVK-E------DRVLMLRCDACGAH 128 (201)
T ss_pred heEECCCCCCCCcEEEE-c------CCeEEEEcccCCCC
Confidence 45689999999987753 2 24788899999975
No 75
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.09 E-value=2.6 Score=37.41 Aligned_cols=36 Identities=25% Similarity=0.500 Sum_probs=28.5
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
.|.|..|+.+...-+-.| |=+.-|+|+.|..|.+.-
T Consensus 79 ~yTCkvCntRs~ktisk~---AY~~GvVivqC~gC~~~H 114 (165)
T KOG3277|consen 79 AYTCKVCNTRSTKTISKQ---AYEKGVVIVQCPGCKNHH 114 (165)
T ss_pred EEEeeccCCccccccChh---hhhCceEEEECCCCccce
Confidence 689999999888555443 556679999999998763
No 76
>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=68.54 E-value=2.4 Score=35.48 Aligned_cols=29 Identities=24% Similarity=0.969 Sum_probs=21.0
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
...|+.||.+ ||-+..+ | .+|..||..|.
T Consensus 9 KR~Cp~CG~k---FYDLnk~----P----ivCP~CG~~~~ 37 (108)
T PF09538_consen 9 KRTCPSCGAK---FYDLNKD----P----IVCPKCGTEFP 37 (108)
T ss_pred cccCCCCcch---hccCCCC----C----ccCCCCCCccC
Confidence 5579999864 6776532 4 46999999885
No 77
>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=67.34 E-value=0.36 Score=33.58 Aligned_cols=30 Identities=23% Similarity=0.510 Sum_probs=23.1
Q ss_pred cCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 341 CGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 341 C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
|.+.-. ....|+|++||-...+-.|..||.
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 665554 456899999998777777999985
No 78
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=66.75 E-value=2.2 Score=31.83 Aligned_cols=34 Identities=21% Similarity=0.493 Sum_probs=20.6
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
..|.||+||.....--+. -| -.-.-|+|.+||..
T Consensus 26 v~F~CPnCGe~~I~Rc~~-CR----k~g~~Y~Cp~CGF~ 59 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAK-CR----KLGNPYRCPKCGFE 59 (61)
T ss_pred eEeeCCCCCceeeehhhh-HH----HcCCceECCCcCcc
Confidence 479999999644321111 11 13456899999863
No 79
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=66.34 E-value=7.3 Score=40.10 Aligned_cols=94 Identities=18% Similarity=0.315 Sum_probs=55.3
Q ss_pred CChhhhhchhcCCCChhhhccCChhhcCcHHHHHHHH--HH--HHHHHHHhhhcCCCccccccccccccCCcceEEEEEe
Q 017145 277 KNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIE--NI--KEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQ 352 (376)
Q Consensus 277 kN~~Lr~~vl~G~i~p~~l~~Ms~eEmas~e~k~~~~--~~--~ee~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q 352 (376)
.||.|....+. -|+.++|..|..++++-.+=+++.+ -+ +--..|..+.- .=-+.-.|++||+..-.-.+.|
T Consensus 104 EDP~lq~~Als-~iPvdEL~~kA~ekla~~eg~ki~kdy~i~leLL~WFKq~FF----~WvN~PpC~~CG~et~~~l~~~ 178 (500)
T KOG0909|consen 104 EDPVLQAKALS-TIPVDELKEKASEKLAKAEGEKIYKDYLIKLELLNWFKQDFF----KWVNNPPCNKCGGETSSGLGNQ 178 (500)
T ss_pred cCHHHHHHHHh-cCCHHHHHHHHHHhhcccchhhhhcchHHHHHHHHHHHHhhh----eecCCCCcccccccccccccCC
Confidence 68888766663 4677999988888888522112221 12 12223333311 1124567999999876333333
Q ss_pred ccCCCC-----CCeEEEEcCCCCCcccc
Q 017145 353 TRSADE-----PMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 353 trsaDE-----pmt~f~~C~~C~~~Wkf 375 (376)
.-..+| .-.-.|.|..||+.=||
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 23568889999998777
No 80
>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=65.14 E-value=13 Score=30.22 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=22.8
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
...+.||.||+..+. .+ -+-...|..|+..|
T Consensus 33 ~a~y~CpfCgk~~vk-R~---------a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 33 KAKYVCPFCGKKTVK-RG---------STGIWTCRKCGAKF 63 (91)
T ss_pred hcCccCCCCCCCceE-EE---------eeEEEEcCCCCCEE
Confidence 457889999976542 11 36789999999876
No 81
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=64.12 E-value=14 Score=29.89 Aligned_cols=31 Identities=23% Similarity=0.547 Sum_probs=22.7
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
...+.||.||+..+.-. -+-...|..|+..|
T Consensus 34 ~a~y~CpfCgk~~vkR~----------a~GIW~C~~C~~~~ 64 (90)
T PRK03976 34 RAKHVCPVCGRPKVKRV----------GTGIWECRKCGAKF 64 (90)
T ss_pred hcCccCCCCCCCceEEE----------EEEEEEcCCCCCEE
Confidence 45788999986655211 36789999999876
No 82
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=63.58 E-value=3.6 Score=29.57 Aligned_cols=30 Identities=20% Similarity=0.324 Sum_probs=19.9
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
....||+||+. ...... ..+.|..||..+.
T Consensus 19 ~~~fCP~Cg~~--~m~~~~---------~r~~C~~Cgyt~~ 48 (50)
T PRK00432 19 KNKFCPRCGSG--FMAEHL---------DRWHCGKCGYTEF 48 (50)
T ss_pred ccCcCcCCCcc--hheccC---------CcEECCCcCCEEe
Confidence 44579999985 222211 4778999998763
No 83
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=63.29 E-value=3.3 Score=29.88 Aligned_cols=34 Identities=24% Similarity=0.533 Sum_probs=24.3
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
...|..|+-.+...+ |...... -+.|+.||-.|+
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 457999998877555 4443333 478999999886
No 84
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=62.99 E-value=4.8 Score=33.47 Aligned_cols=39 Identities=18% Similarity=0.404 Sum_probs=23.4
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
-.-|.+|...=....-...|....- +-++|..||+.-+|
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 4569999984222221122211111 88999999998776
No 85
>PRK03954 ribonuclease P protein component 4; Validated
Probab=62.90 E-value=7.8 Score=33.14 Aligned_cols=37 Identities=19% Similarity=0.495 Sum_probs=23.8
Q ss_pred cccccccCCc-----ceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 335 QFKCSRCGQR-----KCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 335 ~~~C~~C~~~-----~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
..-|.+|+.. .+++... ....+ .+.++|..||+.-+|
T Consensus 64 R~~CK~C~t~LiPG~n~~vRi~---~~~~~-~vvitCl~CG~~kR~ 105 (121)
T PRK03954 64 RRYCKRCHSFLVPGVNARVRLR---QKRMP-HVVITCLECGHIMRY 105 (121)
T ss_pred HHHhhcCCCeeecCCceEEEEe---cCCcc-eEEEECccCCCEEee
Confidence 4569999865 4444332 22122 468889999998765
No 86
>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=61.47 E-value=9.5 Score=30.91 Aligned_cols=31 Identities=23% Similarity=0.652 Sum_probs=22.0
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
...+.||.||+..+. .+ .+-+..|..||+.|
T Consensus 33 ~~ky~Cp~Cgk~~vk-R~---------a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVK-RV---------ATGIWKCKKCGKKF 63 (90)
T ss_dssp HS-BEESSSSSSEEE-EE---------ETTEEEETTTTEEE
T ss_pred hCCCcCCCCCCceeE-Ee---------eeEEeecCCCCCEE
Confidence 357889999998842 22 14479999999876
No 87
>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=61.32 E-value=6.7 Score=26.13 Aligned_cols=34 Identities=24% Similarity=0.690 Sum_probs=20.5
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
+.-.|.|+.||+. |...+.. .+ .....|..||..
T Consensus 2 p~Y~y~C~~Cg~~---fe~~~~~-~~---~~~~~CP~Cg~~ 35 (41)
T smart00834 2 PIYEYRCEDCGHT---FEVLQKI-SD---DPLATCPECGGD 35 (41)
T ss_pred CCEEEEcCCCCCE---EEEEEec-CC---CCCCCCCCCCCc
Confidence 3457899999983 3333322 22 334569999863
No 88
>PF12773 DZR: Double zinc ribbon
Probab=60.54 E-value=4 Score=28.68 Aligned_cols=33 Identities=33% Similarity=0.678 Sum_probs=21.7
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc----cccC
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR----WKFC 376 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~----Wkfc 376 (376)
.+...|+.||..-. .+....+.|..||.. |+||
T Consensus 10 ~~~~fC~~CG~~l~-----------~~~~~~~~C~~Cg~~~~~~~~fC 46 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP-----------PPDQSKKICPNCGAENPPNAKFC 46 (50)
T ss_pred ccccCChhhcCChh-----------hccCCCCCCcCCcCCCcCCcCcc
Confidence 34556888887665 222446778888864 7776
No 89
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=59.86 E-value=18 Score=29.29 Aligned_cols=31 Identities=23% Similarity=0.529 Sum_probs=22.6
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
...+.||.||+..+. .+ -+-...|..|+..|
T Consensus 34 ~a~y~CpfCgk~~vk-R~---------a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 34 HAKYFCPFCGKHAVK-RQ---------AVGIWRCKGCKKTV 64 (90)
T ss_pred hCCccCCCCCCCcee-ee---------eeEEEEcCCCCCEE
Confidence 467889999976542 11 25789999999875
No 90
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=59.67 E-value=10 Score=36.48 Aligned_cols=26 Identities=19% Similarity=0.451 Sum_probs=19.9
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
.+-..|+.||. .-...+.|..||+.|
T Consensus 307 ~tS~~C~~cg~---------------~~~r~~~C~~cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH---------------LSGRLFKCPRCGFVH 332 (364)
T ss_pred CCcccccccCC---------------ccceeEECCCCCCee
Confidence 34567999999 124578999999875
No 91
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=58.59 E-value=4.9 Score=24.12 Aligned_cols=8 Identities=38% Similarity=1.182 Sum_probs=5.1
Q ss_pred ccccCCcc
Q 017145 338 CSRCGQRK 345 (376)
Q Consensus 338 C~~C~~~~ 345 (376)
|++||..-
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 77777643
No 92
>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=56.68 E-value=7.8 Score=37.71 Aligned_cols=39 Identities=23% Similarity=0.495 Sum_probs=20.5
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
...|+.||+.+..-+..= ...+++.-...+|..|+.-||
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 457999998766533321 135667788999999999887
No 93
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=55.99 E-value=12 Score=24.45 Aligned_cols=30 Identities=27% Similarity=0.700 Sum_probs=21.7
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
+...|..|++....+ .. .-+++|..||..+
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 356899999998754 21 2378899999754
No 94
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=55.34 E-value=21 Score=29.35 Aligned_cols=55 Identities=20% Similarity=0.205 Sum_probs=45.9
Q ss_pred CCCCCHHHHHHHHHHhcCCCCCHHhhhcCccceecccccCCCCHHHHHHHHHHHH
Q 017145 26 SGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLD 80 (376)
Q Consensus 26 ~~~~~~~~~l~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~I~~~Ak~Lv~ 80 (376)
...+.+++++++|.+|-+.+....+|+.-+.-..+++||++-++..+...-.|++
T Consensus 42 ~~~~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 42 PPVPMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred CCCccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 3445789999999999999999999999887777999999988877776666654
No 95
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=54.86 E-value=11 Score=27.17 Aligned_cols=16 Identities=25% Similarity=0.837 Sum_probs=11.7
Q ss_pred CCeEEEEcCCCCCccc
Q 017145 359 PMTTYVTCVNCSKRWK 374 (376)
Q Consensus 359 pmt~f~~C~~C~~~Wk 374 (376)
....+..|..|||.|+
T Consensus 24 ~~~v~W~C~~Cgh~w~ 39 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWK 39 (55)
T ss_pred CCEEEEECCCCCCeeE
Confidence 3456778888888886
No 96
>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=54.81 E-value=44 Score=25.86 Aligned_cols=35 Identities=23% Similarity=0.599 Sum_probs=18.6
Q ss_pred cccccccCC-----cceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 335 QFKCSRCGQ-----RKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 335 ~~~C~~C~~-----~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
..-|.+||. ..+.+... +..-..-.+.++|..|||
T Consensus 46 r~~Ck~C~~~liPG~~~~vri~--~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 46 RTICKKCGSLLIPGVNCSVRIR--KKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CTB-TTT--B--CTTTEEEEEE-----SSS-EEEEEETTTTE
T ss_pred cccccCCCCEEeCCCccEEEEE--ecCCCCCEEEEEccccCC
Confidence 567999997 34444333 212223468889999997
No 97
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.02 E-value=7.3 Score=29.05 Aligned_cols=35 Identities=26% Similarity=0.542 Sum_probs=21.4
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
-..|.||.||... .|+=..=| ..-.-|+|.+||..
T Consensus 23 ~~~F~CPnCG~~~-I~RC~~CR----k~~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEVI-IYRCEKCR----KQSNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCee-EeechhHH----hcCCceECCCCCCc
Confidence 3589999998742 23222222 12457899999863
No 98
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.33 E-value=9.1 Score=44.32 Aligned_cols=36 Identities=14% Similarity=0.460 Sum_probs=17.6
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
..++||+||..... ..=..-..+++.-|.|..||..
T Consensus 666 ~~rkCPkCG~~t~~---~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 666 GRRRCPSCGTETYE---NRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EEEECCCCCCcccc---ccCcccCCcCCCceeCccCCCc
Confidence 46788888864211 1101122233334577777764
No 99
>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=53.33 E-value=6.7 Score=37.39 Aligned_cols=34 Identities=21% Similarity=0.647 Sum_probs=12.6
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
...-||.||+..-.-|..=...| =|.|.+|++.+
T Consensus 30 ~n~yCP~Cg~~~L~~f~NN~PVa------DF~C~~C~eey 63 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKFENNRPVA------DFYCPNCNEEY 63 (254)
T ss_dssp HH---TTT--SS-EE--------------EEE-TTT--EE
T ss_pred HCCcCCCCCChhHhhccCCCccc------eeECCCCchHH
Confidence 35569999999766554433333 36799999875
No 100
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.70 E-value=6.4 Score=24.16 Aligned_cols=23 Identities=26% Similarity=0.655 Sum_probs=13.7
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
..|++||.... ..+-.|.+||++
T Consensus 3 ~~Cp~Cg~~~~--------------~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEID--------------PDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCC--------------cccccChhhCCC
Confidence 45888887321 124567777764
No 101
>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=51.36 E-value=8.4 Score=23.52 Aligned_cols=11 Identities=36% Similarity=0.957 Sum_probs=8.4
Q ss_pred cccccccccCC
Q 017145 333 TDQFKCSRCGQ 343 (376)
Q Consensus 333 t~~~~C~~C~~ 343 (376)
...|.||+||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45788999984
No 102
>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=50.99 E-value=13 Score=37.62 Aligned_cols=35 Identities=20% Similarity=0.403 Sum_probs=19.2
Q ss_pred cccccccCC-cceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 335 QFKCSRCGQ-RKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 335 ~~~C~~C~~-~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
.--|++||. -.+..... .. +.-++.|.|..|||.-
T Consensus 174 ~piC~~cGri~tt~v~~~---d~-~~~~v~Y~c~~cG~~g 209 (360)
T PF01921_consen 174 LPICEKCGRIDTTEVTEY---DP-EGGTVTYRCEECGHEG 209 (360)
T ss_dssp EEEETTTEE--EEEEEEE------SSSEEEEE--TTS---
T ss_pred eeeccccCCcccceeeEe---ec-CCCEEEEEecCCCCEE
Confidence 557999998 44433332 22 3458999999999964
No 103
>PRK05978 hypothetical protein; Provisional
Probab=50.89 E-value=7.2 Score=34.53 Aligned_cols=32 Identities=19% Similarity=0.515 Sum_probs=22.0
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
.-+||+||+-+..- --...--.|..||..+.+
T Consensus 33 ~grCP~CG~G~LF~---------g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 33 RGRCPACGEGKLFR---------AFLKPVDHCAACGEDFTH 64 (148)
T ss_pred cCcCCCCCCCcccc---------cccccCCCccccCCcccc
Confidence 45899999887742 123444569999988753
No 104
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=50.72 E-value=13 Score=24.50 Aligned_cols=29 Identities=21% Similarity=0.472 Sum_probs=13.4
Q ss_pred ccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 338 CSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 338 C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
|+.||..-. .+-.+..-..=.+|..||.-
T Consensus 3 C~~CG~~l~------~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLE------RRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-E------EE--TT-SS-EEEETTTTEE
T ss_pred cccccChhh------hhcCCCCCccceECCCCCCE
Confidence 999998832 22232223445678999864
No 105
>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=50.23 E-value=15 Score=26.95 Aligned_cols=32 Identities=28% Similarity=0.704 Sum_probs=20.4
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.|.||.||..-. + ..+. .--.+.|..||....
T Consensus 2 ~~~CP~CG~~ie----v---~~~~-~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIE----L---ENPE-LGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEe----c---CCCc-cCCEEeCCCCCCEEE
Confidence 579999998332 1 1111 234779999997643
No 106
>PRK12495 hypothetical protein; Provisional
Probab=49.72 E-value=19 Score=33.90 Aligned_cols=29 Identities=21% Similarity=0.482 Sum_probs=20.7
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
....+.|+.||..-. -+.-.++|..|+..
T Consensus 39 tmsa~hC~~CG~PIp------------a~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 39 TMTNAHCDECGDPIF------------RHDGQEFCPTCQQP 67 (226)
T ss_pred ccchhhcccccCccc------------CCCCeeECCCCCCc
Confidence 456789999998755 12345678889865
No 107
>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=48.83 E-value=4.8 Score=40.40 Aligned_cols=13 Identities=23% Similarity=0.928 Sum_probs=7.1
Q ss_pred CeEEEEcCCCCCc
Q 017145 360 MTTYVTCVNCSKR 372 (376)
Q Consensus 360 mt~f~~C~~C~~~ 372 (376)
.-.||.|.+||+|
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 4578888888886
No 108
>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=48.23 E-value=32 Score=36.54 Aligned_cols=33 Identities=18% Similarity=0.488 Sum_probs=22.3
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
-.--|++||.-..+.. ...++. |+.|.| .|||.
T Consensus 167 ~~pic~~cGrv~~~~~---~~~~~~--~v~Y~c-~cG~~ 199 (515)
T TIGR00467 167 ISVFCENCGRDTTTVN---NYDNEY--SIEYSC-ECGNQ 199 (515)
T ss_pred eeeecCCcCccCceEE---EecCCc--eEEEEc-CCCCE
Confidence 3557999998754332 344444 788899 59985
No 109
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=48.07 E-value=13 Score=38.57 Aligned_cols=99 Identities=14% Similarity=0.141 Sum_probs=71.4
Q ss_pred ccCCchhHHHHHHHHHHHHhhhhccChhh--hhhh--hcccChHHHHHHHHHHHHHHhCCCchhhhHHHHHHHhhccCCC
Q 017145 202 IKCNDSSRDKIRELLANALSKVTSEADEE--IIDE--VNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEK 277 (376)
Q Consensus 202 ~~~~d~vR~k~r~~L~~aL~~~~~~~~~~--~~~~--~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~k 277 (376)
..+++.-|+|++.-+++++...+.-.... .-++ ....+.......||.+.|+.+..+...|-.+.+.|.++|+ .
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 35789999999999999986544322211 0000 0112245677899999999998777889999999999998 4
Q ss_pred ChhhhhchhcCC-CChhhhccCChhh
Q 017145 278 NPDLRKRVLLGE-VTPERLVTMSPEE 302 (376)
Q Consensus 278 N~~Lr~~vl~G~-i~p~~l~~Ms~eE 302 (376)
---|+.+.++|. +.|+-.+.|.+=+
T Consensus 316 ~~~l~~~~ln~~~~~~e~~~~l~~p~ 341 (464)
T KOG1886|consen 316 QALLKPEPLNPGETKPEPKQELHPPS 341 (464)
T ss_pred hhhhccccCCCcccCchhhhhccCCC
Confidence 567888888884 8888888885443
No 110
>PF06290 PsiB: Plasmid SOS inhibition protein (PsiB); InterPro: IPR009385 This family consists of several plasmid SOS inhibition protein (PsiB) sequences [].; PDB: 3NCT_B.
Probab=47.81 E-value=17 Score=31.75 Aligned_cols=75 Identities=20% Similarity=0.244 Sum_probs=36.0
Q ss_pred CCChhhhccCChhhcCcHHHHHHHHHHHHHHHHHhhhcCCCccccccccccccCCcceEEEEEecc-CCCCCCeEEEEcC
Q 017145 289 EVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTR-SADEPMTTYVTCV 367 (376)
Q Consensus 289 ~i~p~~l~~Ms~eEmas~e~k~~~~~~~ee~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~qtr-saDEpmt~f~~C~ 367 (376)
.|+++.|-+|+++|+ ++.+..-+..+.+--+...+ +-..|.....|+.|+..=+-||=+|.| +++.+-+..++|.
T Consensus 4 ~ltl~~L~tm~a~el--E~~R~~Ged~RR~L~~aVm~--~L~~P~gW~~n~Ey~~EFgGffPVq~Rftp~~~~~~l~vCS 79 (143)
T PF06290_consen 4 ELTLEVLKTMSAQEL--EDYRAAGEDFRRELTHAVMR--ELTLPEGWRVNAEYRSEFGGFFPVQCRFTPSHERFHLAVCS 79 (143)
T ss_dssp ---HHHHHH--HHHH--HHHHHH-HHHHHHHHHHHHH--T----TTEEEEE-SSSTT-S-SSSEEEEEETT-SEEEEEE-
T ss_pred eehHHHHhhcCHHHH--HHHHHhhHHHHHHhHHHHHH--hccCCccceeeceeccccccEeeEEEEecCCCCcEEEEEcC
Confidence 578889999999887 33444333344332222222 233556666677777777777766766 4444667777774
No 111
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=47.01 E-value=9.8 Score=36.88 Aligned_cols=41 Identities=34% Similarity=0.645 Sum_probs=28.8
Q ss_pred cccccccccccCCcceEEEE----Eec-cCCCCCCeEEEEcCCCCCcc
Q 017145 331 ATTDQFKCSRCGQRKCTYYQ----MQT-RSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 331 ~~t~~~~C~~C~~~~~~~~q----~qt-rsaDEpmt~f~~C~~C~~~W 373 (376)
.....++|+.||+...++.= .|| |++|++ .-+.|..||..+
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~--ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSK--KAFSCKYCGKVY 171 (279)
T ss_pred ccCCceeccccccccccccccchhhccccccccc--ccccCCCCCcee
Confidence 34567889999998888862 255 788873 446677887664
No 112
>PHA02942 putative transposase; Provisional
Probab=45.87 E-value=13 Score=37.86 Aligned_cols=28 Identities=21% Similarity=0.673 Sum_probs=19.6
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
--.|+.||+.... .-...|.|.+||+.+
T Consensus 325 Sq~Cs~CG~~~~~-----------l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCPKCGHKMVE-----------IAHRYFHCPSCGYEN 352 (383)
T ss_pred CccCCCCCCccCc-----------CCCCEEECCCCCCEe
Confidence 4679999986531 112379999999865
No 113
>PRK13701 psiB plasmid SOS inhibition protein B; Provisional
Probab=45.66 E-value=65 Score=28.15 Aligned_cols=76 Identities=18% Similarity=0.213 Sum_probs=38.2
Q ss_pred CCCChhhhccCChhhcCcHHHHHHHHHHHHHHHHHhhhcCCCccccccccccccCCcceEEEEEecc-CCCCCCeEEEEc
Q 017145 288 GEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTR-SADEPMTTYVTC 366 (376)
Q Consensus 288 G~i~p~~l~~Ms~eEmas~e~k~~~~~~~ee~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~qtr-saDEpmt~f~~C 366 (376)
-.|+++.|-.|+++|| ++.|..-+.++.+--+...+ +-+.|.+...|+.=+..=+-||=+|-| +++..-+-.+.|
T Consensus 3 ~~ltl~~l~tM~a~El--Ed~R~~G~d~RR~Lt~aVm~--~L~~P~gW~~naEy~sEFgGffPVq~Rfsp~~~~~~l~vC 78 (144)
T PRK13701 3 TELTLNVLQTMSAQEY--EDIRAAGSDERRELTHAVMR--ELDAPDGWTMNGEYGSEFGGFFPVQVRFTPAHERFHLALC 78 (144)
T ss_pred cEEcHHHHhccCHHHH--HHHHHHhHHHHHHhHHHHHh--ccCCCccceeehhhhccccCeeeEEEEecCCCCCeEEEEe
Confidence 3578999999999987 34444444444432222222 223444443344333333334545555 333334555555
Q ss_pred C
Q 017145 367 V 367 (376)
Q Consensus 367 ~ 367 (376)
.
T Consensus 79 S 79 (144)
T PRK13701 79 S 79 (144)
T ss_pred C
Confidence 3
No 114
>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=45.34 E-value=13 Score=26.29 Aligned_cols=33 Identities=27% Similarity=0.723 Sum_probs=19.6
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
+.-.|+|.+||..-- .+|. ..|+ ....|..||.
T Consensus 2 P~Yey~C~~Cg~~fe---~~~~-~~~~---~~~~CP~Cg~ 34 (52)
T TIGR02605 2 PIYEYRCTACGHRFE---VLQK-MSDD---PLATCPECGG 34 (52)
T ss_pred CCEEEEeCCCCCEeE---EEEe-cCCC---CCCCCCCCCC
Confidence 345789999996322 2222 2232 3356999997
No 115
>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=44.51 E-value=16 Score=32.17 Aligned_cols=37 Identities=19% Similarity=0.482 Sum_probs=24.7
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
...||+||+.++... .|-. --.=.-.|.|..|...|-
T Consensus 105 ~~~cp~c~s~~t~~~-s~fg--~t~cka~~~c~~c~epf~ 141 (146)
T TIGR02159 105 SVQCPRCGSADTTIT-SIFG--PTACKALYRCRACKEPFE 141 (146)
T ss_pred CCcCCCCCCCCcEee-cCCC--ChhhHHHhhhhhhCCcHh
Confidence 479999999988543 2222 112235788999998764
No 116
>PRK08173 DNA topoisomerase III; Validated
Probab=44.40 E-value=38 Score=38.24 Aligned_cols=28 Identities=25% Similarity=0.520 Sum_probs=18.5
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc-cc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR-WK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~-Wk 374 (376)
...||+||+.- .. + ..+|.|.+|+.. |+
T Consensus 624 ~~~CP~Cg~~~-----~~-~------~~~~~Cs~C~f~~~~ 652 (862)
T PRK08173 624 QTPCPNCGGVV-----KE-N------YRRFACTKCDFSISK 652 (862)
T ss_pred cccCCcccccc-----cc-c------CceeEcCCCCcccch
Confidence 46799999741 11 1 235899999965 75
No 117
>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=43.94 E-value=25 Score=35.49 Aligned_cols=34 Identities=24% Similarity=0.434 Sum_probs=20.4
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
-.-.|++||.-.+... ....|. -|+.|.| .|||.
T Consensus 168 ~~p~c~~cg~~~~~v~---~~d~~~-~~v~y~c-~cG~~ 201 (353)
T cd00674 168 FMPYCEKCGKDTTTVE---AYDAKA-GTVTYKC-ECGHE 201 (353)
T ss_pred eeeecCCcCcceeEEE---EEeCCC-CeEEEEc-CCCCE
Confidence 3557999993222221 223333 4788899 59986
No 118
>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=43.17 E-value=10 Score=28.58 Aligned_cols=38 Identities=18% Similarity=0.653 Sum_probs=23.2
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
....||+|++.++.|-=--.-+...| -+.|..|...|.
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 45789999998876632211122222 256888888885
No 119
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.13 E-value=13 Score=33.87 Aligned_cols=16 Identities=19% Similarity=0.698 Sum_probs=14.1
Q ss_pred CeEEEEcCCCCCcccc
Q 017145 360 MTTYVTCVNCSKRWKF 375 (376)
Q Consensus 360 mt~f~~C~~C~~~Wkf 375 (376)
.=..|.|.+|.+.|.|
T Consensus 46 vWlIYkC~~Cd~tWN~ 61 (203)
T COG4332 46 VWLIYKCTHCDYTWNI 61 (203)
T ss_pred EEEEEEeeccCCccch
Confidence 4578999999999986
No 120
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=42.66 E-value=12 Score=33.63 Aligned_cols=44 Identities=16% Similarity=0.434 Sum_probs=24.9
Q ss_pred cccccccccccCCcceEEEEEecc-----CCCCCCeEEEEcCCCCCc-cc
Q 017145 331 ATTDQFKCSRCGQRKCTYYQMQTR-----SADEPMTTYVTCVNCSKR-WK 374 (376)
Q Consensus 331 ~~t~~~~C~~C~~~~~~~~q~qtr-----saDEpmt~f~~C~~C~~~-Wk 374 (376)
+....-.||.|+..=.-..---.+ .-...-..|++|.+||.. |+
T Consensus 93 ~~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 93 LFPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred cccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence 344566899999854322100000 011234679999999976 53
No 121
>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=42.65 E-value=30 Score=34.23 Aligned_cols=40 Identities=28% Similarity=0.582 Sum_probs=26.6
Q ss_pred ccccccccCCcce-EEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 334 DQFKCSRCGQRKC-TYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 334 ~~~~C~~C~~~~~-~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
....|+.||+.+- .|+.+-. ..+++-....+|..|+.-+|
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 4568999997653 3554422 11345677788999998877
No 122
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=42.03 E-value=14 Score=35.42 Aligned_cols=14 Identities=14% Similarity=0.622 Sum_probs=12.5
Q ss_pred eEEEEcCCCCCccc
Q 017145 361 TTYVTCVNCSKRWK 374 (376)
Q Consensus 361 t~f~~C~~C~~~Wk 374 (376)
--+|.|.+|+|.|+
T Consensus 153 ~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 153 IAEFHCPKCRHNFR 166 (278)
T ss_pred eeeeecccccccch
Confidence 36899999999998
No 123
>PRK04023 DNA polymerase II large subunit; Validated
Probab=40.62 E-value=17 Score=41.30 Aligned_cols=13 Identities=31% Similarity=0.452 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHH
Q 017145 69 EKIQIVASNLLDI 81 (376)
Q Consensus 69 ~~I~~~Ak~Lv~~ 81 (376)
+-|...|+.|++.
T Consensus 247 EGi~~KA~Ki~k~ 259 (1121)
T PRK04023 247 EGIALKAPKILKY 259 (1121)
T ss_pred hHHHhhhHHHHHH
Confidence 4566667666654
No 124
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=40.44 E-value=21 Score=26.35 Aligned_cols=24 Identities=25% Similarity=0.681 Sum_probs=18.3
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
.....|+.||...- -..+|.+||.
T Consensus 25 ~~l~~C~~CG~~~~---------------~H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPKL---------------PHRVCPSCGY 48 (57)
T ss_pred CcceECCCCCCccC---------------CeEECCCCCc
Confidence 45678999997654 3788999985
No 125
>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=39.78 E-value=56 Score=24.41 Aligned_cols=36 Identities=17% Similarity=0.354 Sum_probs=24.8
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
....|+.|+.......+.| ...-.+....+|..|+=
T Consensus 14 ~~~~C~~C~G~G~~~~~~~--~~~~~~~~~~~C~~C~G 49 (66)
T PF00684_consen 14 KPKTCPQCNGSGQVTRRQQ--TPGGVFQMQQTCPKCGG 49 (66)
T ss_dssp T-EE-TTSSSSSEEEEEEE--SSSTTEEEEEE-TTTSS
T ss_pred CCcCCcCCCCeeEEEEEEe--CCCeEEEEEEECCCCcc
Confidence 4568999999999888776 34445667777999963
No 126
>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=39.67 E-value=21 Score=24.03 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=20.1
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
..+||.||.+.-.-| .|-..+--+.|..|+.
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 357999999776542 2333455677777864
No 127
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.66 E-value=28 Score=29.95 Aligned_cols=39 Identities=15% Similarity=0.394 Sum_probs=26.2
Q ss_pred cccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 331 ATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 331 ~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
....+..||.|+... .+.--..+ +. ---|.|..|+..|.
T Consensus 26 ~~~~~~~cP~C~s~~-~~k~g~~~-~~---~qRyrC~~C~~tf~ 64 (129)
T COG3677 26 MQITKVNCPRCKSSN-VVKIGGIR-RG---HQRYKCKSCGSTFT 64 (129)
T ss_pred hhcccCcCCCCCccc-eeeECCcc-cc---ccccccCCcCccee
Confidence 345678899999988 33333333 22 34688999998875
No 128
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=39.27 E-value=47 Score=35.51 Aligned_cols=60 Identities=18% Similarity=0.182 Sum_probs=44.1
Q ss_pred chhHHHHHHHHHHHHhhhhccChhhhhhhhcccChHHHHHHHHHHHHHHhCCCchhhhHHHHHHHhhccCCCCh
Q 017145 206 DSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNP 279 (376)
Q Consensus 206 d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~lA~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~ 279 (376)
.++|.+++.-|.+.|.+..... ..-|..+|+++|.+.. +..+|-..+--|+..++|-.|.
T Consensus 9 ~kFRq~vIsried~l~~n~q~~-------------~k~a~~mE~hVF~K~~-tkDEYl~lvAkli~h~~d~s~~ 68 (742)
T KOG4274|consen 9 PKFRQHVISRIEDELRKNGQAH-------------SKSAKDMESHVFLKAK-TKDEYLSLVAKLIIHFRDISNK 68 (742)
T ss_pred HHHHHHHHHHhhhhhhhhhhcc-------------CcchHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHhhhhh
Confidence 5799999999999988533221 1457789999998775 4568877777778888876653
No 129
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=38.56 E-value=33 Score=24.29 Aligned_cols=31 Identities=23% Similarity=0.600 Sum_probs=20.2
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCC
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCS 370 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~ 370 (376)
++.+.|+.||..-.. +++. .-..+|.|.++.
T Consensus 3 ~g~l~C~~CG~~m~~----~~~~---~~~~yy~C~~~~ 33 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTR----RKRK---GKYRYYRCSNRR 33 (58)
T ss_pred CCcEEcccCCcEeEE----EECC---CCceEEEcCCCc
Confidence 457889999987554 2232 223889997653
No 130
>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=38.24 E-value=16 Score=25.01 Aligned_cols=33 Identities=24% Similarity=0.610 Sum_probs=20.4
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
++-.|.|.+||+.- ..+|.-+. ..-..|..||.
T Consensus 2 P~Yey~C~~Cg~~f---e~~~~~~~----~~~~~CP~Cg~ 34 (42)
T PF09723_consen 2 PIYEYRCEECGHEF---EVLQSISE----DDPVPCPECGS 34 (42)
T ss_pred CCEEEEeCCCCCEE---EEEEEcCC----CCCCcCCCCCC
Confidence 34578999999643 33343322 22457999987
No 131
>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=37.93 E-value=25 Score=30.73 Aligned_cols=38 Identities=16% Similarity=0.374 Sum_probs=21.6
Q ss_pred cccccccCCcceEEEEEecc-----CCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTR-----SADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtr-----saDEpmt~f~~C~~C~~~ 372 (376)
.-.|+.|++.-....-.+.+ ..-+....|+.|..||.-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 56899999833222111111 011223469999999975
No 132
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=37.74 E-value=25 Score=31.05 Aligned_cols=31 Identities=16% Similarity=0.448 Sum_probs=22.8
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
-.+.+.|-+||+.-..+.- +..--|..||+.
T Consensus 109 g~G~l~C~~Cg~~~~~~~~----------~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTHP----------ERLPPCPKCGHT 139 (146)
T ss_pred cCceEecccCCCEEEecCC----------CcCCCCCCCCCC
Confidence 3468999999998775431 335569999986
No 133
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=37.17 E-value=7.5 Score=38.25 Aligned_cols=41 Identities=12% Similarity=0.208 Sum_probs=25.7
Q ss_pred hcCCCccccc-cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 325 RGGEATATTD-QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 325 ~~~~~~~~t~-~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
..+.+..+.. ..+|+.|+.--- ..+ =-..+++|.+|||-++
T Consensus 27 ~~~~~~~p~~lw~kc~~C~~~~~---~~~------l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 27 YSWNTQKYKHLWVQCENCYGLNY---KKF------LKSKMNICEQCGYHLK 68 (296)
T ss_pred cccCCCCCCCCeeECCCccchhh---HHH------HHHcCCCCCCCCCCcC
Confidence 3444445554 679999986322 111 1145789999999876
No 134
>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=36.85 E-value=24 Score=29.25 Aligned_cols=29 Identities=31% Similarity=0.644 Sum_probs=20.6
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.-.|--| ....|+|. --.++|.+||.+|.
T Consensus 35 ~daCeiC--~~~GY~q~---------g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 35 FDACEIC--GPKGYYQE---------GDQLVCKNCGVRFN 63 (102)
T ss_pred EEecccc--CCCceEEE---------CCEEEEecCCCEEe
Confidence 3479999 34455553 22789999999995
No 135
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.83 E-value=13 Score=33.80 Aligned_cols=33 Identities=27% Similarity=0.602 Sum_probs=23.9
Q ss_pred cccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 331 ATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 331 ~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.+...|.||.|+-+- |=||.|..-|+|..||.-
T Consensus 109 ~~~~~y~C~~~~~r~---------sfdeA~~~~F~Cp~Cg~~ 141 (176)
T COG1675 109 TENNYYVCPNCHVKY---------SFDEAMELGFTCPKCGED 141 (176)
T ss_pred ccCCceeCCCCCCcc---------cHHHHHHhCCCCCCCCch
Confidence 345689998776543 356777778999999964
No 136
>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=36.19 E-value=35 Score=30.43 Aligned_cols=35 Identities=26% Similarity=0.496 Sum_probs=24.6
Q ss_pred cccccccCCcceEEEEEec------cC-------CCCCCeEEEEcCC-C
Q 017145 335 QFKCSRCGQRKCTYYQMQT------RS-------ADEPMTTYVTCVN-C 369 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qt------rs-------aDEpmt~f~~C~~-C 369 (376)
.-.|+.||+.++.=+|+.- .- -|=+....|+|.+ |
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 4479999999998888833 11 1223457889974 8
No 137
>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=35.91 E-value=43 Score=22.35 Aligned_cols=33 Identities=18% Similarity=0.386 Sum_probs=21.6
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCC
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNC 369 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C 369 (376)
+..+.||.|++.+.+|.-=++.+ -..-|.|..|
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 45789999999986554332211 2356788877
No 138
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.71 E-value=42 Score=33.28 Aligned_cols=38 Identities=26% Similarity=0.628 Sum_probs=26.1
Q ss_pred ccccccccCCc-ceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 334 DQFKCSRCGQR-KCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 334 ~~~~C~~C~~~-~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
....|+.||+. +-.|+.+ ..+++-....+|..|+.-+|
T Consensus 225 ~R~~C~~Cg~~~~l~y~~~---~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 225 VRVKCSNCEQSGKLHYWSL---DSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred cCccCCCCCCCCceeeeee---cCCCcceEeeecccccccce
Confidence 46689999975 3445444 22335567888999998877
No 139
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=35.60 E-value=16 Score=30.72 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=18.0
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
....+.|+.||..-. . ...++.|..||-
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 345789999993322 1 124667999994
No 140
>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=34.92 E-value=23 Score=22.97 Aligned_cols=13 Identities=15% Similarity=0.284 Sum_probs=10.3
Q ss_pred eEEEEcCCCCCcc
Q 017145 361 TTYVTCVNCSKRW 373 (376)
Q Consensus 361 t~f~~C~~C~~~W 373 (376)
..||.|..||+.-
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4599999999853
No 141
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=34.88 E-value=41 Score=33.42 Aligned_cols=41 Identities=22% Similarity=0.695 Sum_probs=24.4
Q ss_pred cccccccCC---cceEEEEEeccCCCC-----CCeEEEE-cCCCCCcccc
Q 017145 335 QFKCSRCGQ---RKCTYYQMQTRSADE-----PMTTYVT-CVNCSKRWKF 375 (376)
Q Consensus 335 ~~~C~~C~~---~~~~~~q~qtrsaDE-----pmt~f~~-C~~C~~~Wkf 375 (376)
.+.|..||. ..+.|.-.-.+-.+| |+-.||. |..|++.+.|
T Consensus 40 ~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~ 89 (324)
T PF04502_consen 40 NIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIEF 89 (324)
T ss_pred cCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEee
Confidence 457999996 344443322222332 3344555 9999998765
No 142
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=34.77 E-value=23 Score=23.79 Aligned_cols=14 Identities=14% Similarity=0.477 Sum_probs=8.4
Q ss_pred CeEEEEcCCCCCcc
Q 017145 360 MTTYVTCVNCSKRW 373 (376)
Q Consensus 360 mt~f~~C~~C~~~W 373 (376)
+..||.|..|||.-
T Consensus 3 ~~~~YkC~~CGniV 16 (36)
T PF06397_consen 3 KGEFYKCEHCGNIV 16 (36)
T ss_dssp TTEEEE-TTT--EE
T ss_pred cccEEEccCCCCEE
Confidence 45799999999853
No 143
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=34.60 E-value=50 Score=36.43 Aligned_cols=33 Identities=24% Similarity=0.676 Sum_probs=19.4
Q ss_pred cccccccCCcceEEEEEeccCCCCCCe--EEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMT--TYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt--~f~~C~~C~~~ 372 (376)
...|+.|..+-.+.. +..-|+| +|..|..|.|+
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 445555654433322 2333544 69999999986
No 144
>PF14122 YokU: YokU-like protein
Probab=33.80 E-value=31 Score=27.68 Aligned_cols=37 Identities=24% Similarity=0.671 Sum_probs=24.7
Q ss_pred cccccCCc------ceEEEEEeccC--CCCCCeEEEEcCCCCCcc
Q 017145 337 KCSRCGQR------KCTYYQMQTRS--ADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 337 ~C~~C~~~------~~~~~q~qtrs--aDEpmt~f~~C~~C~~~W 373 (376)
+|.-||.. ..+|+.+..+. -.=++|--++|.+||-.+
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 48888875 45677664432 223677888999999643
No 145
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=33.43 E-value=46 Score=26.32 Aligned_cols=56 Identities=21% Similarity=0.385 Sum_probs=33.8
Q ss_pred hcCcHHHHHHHHHHHHHHHHHhhhcCCCccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 302 EMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 302 Emas~e~k~~~~~~~ee~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
||+-...+++..+.+.+.|.++ +..---..+|+.|-+-.+.|.-.|| -++|.+|+.
T Consensus 6 dllhPs~e~e~r~hK~krLvq~-----~nsyFm~VkC~gc~~iT~vfSHaqt---------vVvc~~c~~ 61 (84)
T KOG1779|consen 6 DLLHPSPEKEKRKHKLKRLVQS-----PNSYFMDVKCPGCFKITTVFSHAQT---------VVVCEGCST 61 (84)
T ss_pred hhcCCCHHHHhhhhhhhhheeC-----CCceEEEEEcCCceEEEEEeecCce---------EEEcCCCce
Confidence 4444444455555555555322 1111125699999999999887764 577888863
No 146
>PRK11032 hypothetical protein; Provisional
Probab=32.89 E-value=36 Score=30.53 Aligned_cols=30 Identities=17% Similarity=0.528 Sum_probs=22.7
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
.+.+.|-+||+..+.|+- +..--|.+|||.
T Consensus 122 ~G~LvC~~Cg~~~~~~~p----------~~i~pCp~C~~~ 151 (160)
T PRK11032 122 LGNLVCEKCHHHLAFYTP----------EVLPLCPKCGHD 151 (160)
T ss_pred cceEEecCCCCEEEecCC----------CcCCCCCCCCCC
Confidence 357899999998876543 345569999985
No 147
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=32.88 E-value=20 Score=30.19 Aligned_cols=28 Identities=14% Similarity=0.502 Sum_probs=17.7
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
....+.|+.||..-. . + ..++.|..||.
T Consensus 67 ~p~~~~C~~Cg~~~~----~-----~---~~~~~CP~Cgs 94 (115)
T TIGR00100 67 EPVECECEDCSEEVS----P-----E---IDLYRCPKCHG 94 (115)
T ss_pred eCcEEEcccCCCEEe----c-----C---CcCccCcCCcC
Confidence 345788999993322 1 1 12678999985
No 148
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=32.85 E-value=27 Score=22.62 Aligned_cols=13 Identities=15% Similarity=0.307 Sum_probs=10.3
Q ss_pred eEEEEcCCCCCcc
Q 017145 361 TTYVTCVNCSKRW 373 (376)
Q Consensus 361 t~f~~C~~C~~~W 373 (376)
..||.|..||+.-
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 3599999999853
No 149
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=32.73 E-value=13 Score=36.17 Aligned_cols=33 Identities=24% Similarity=0.570 Sum_probs=23.2
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcccc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkf 375 (376)
-..+||.|+.- .| ..|=+..+.+|.+|+|-.+.
T Consensus 27 lw~KCp~c~~~--~y-------~~eL~~n~~vcp~c~~h~ri 59 (294)
T COG0777 27 LWTKCPSCGEM--LY-------RKELESNLKVCPKCGHHMRI 59 (294)
T ss_pred ceeECCCccce--ee-------HHHHHhhhhcccccCccccc
Confidence 36799999853 22 12335679999999997763
No 150
>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=32.68 E-value=49 Score=22.23 Aligned_cols=9 Identities=22% Similarity=1.036 Sum_probs=7.0
Q ss_pred EcCCCCCcc
Q 017145 365 TCVNCSKRW 373 (376)
Q Consensus 365 ~C~~C~~~W 373 (376)
.|.+||..+
T Consensus 34 ~C~~CGE~~ 42 (46)
T TIGR03831 34 VCPQCGEEY 42 (46)
T ss_pred ccccCCCEe
Confidence 589998765
No 151
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.13 E-value=22 Score=36.64 Aligned_cols=31 Identities=32% Similarity=0.583 Sum_probs=21.5
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
...-.||.||.+-- |+.- . .|.|..||.+.+
T Consensus 348 ~~~p~Cp~Cg~~m~--------S~G~--~-g~rC~kCg~~~~ 378 (421)
T COG1571 348 RVNPVCPRCGGRMK--------SAGR--N-GFRCKKCGTRAR 378 (421)
T ss_pred EcCCCCCccCCchh--------hcCC--C-CcccccccccCC
Confidence 34557999997644 4443 3 889999998754
No 152
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=32.03 E-value=15 Score=37.74 Aligned_cols=38 Identities=18% Similarity=0.429 Sum_probs=25.7
Q ss_pred cccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 331 ATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 331 ~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
.....|.||.|.+.-...--.|. =..++..|.|.+||-
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHHh---hcccCceEEEecCCC
Confidence 44568999999886443322222 235678999999984
No 153
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=31.24 E-value=18 Score=36.27 Aligned_cols=33 Identities=18% Similarity=0.368 Sum_probs=25.3
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
-+.|+.|+++++.++-.- ..|+-+-|..||.+-
T Consensus 96 FVlC~~C~NPETel~itk------~q~i~~~CkACG~r~ 128 (400)
T KOG2767|consen 96 FVLCPSCENPETELIITK------KQTISLKCKACGFRS 128 (400)
T ss_pred heeCcCCCCCceeEEecc------cchhhhHHHHcCCcc
Confidence 357999999999887532 246778899999874
No 154
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.11 E-value=28 Score=33.98 Aligned_cols=28 Identities=21% Similarity=0.498 Sum_probs=18.7
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
--|++||++.-.. + --.-..|.+|||..
T Consensus 112 RFCg~CG~~~~~~--------~--~g~~~~C~~cg~~~ 139 (279)
T COG2816 112 RFCGRCGTKTYPR--------E--GGWARVCPKCGHEH 139 (279)
T ss_pred cCCCCCCCcCccc--------c--CceeeeCCCCCCcc
Confidence 3499999876521 1 12456799999875
No 155
>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=29.17 E-value=15 Score=37.02 Aligned_cols=31 Identities=35% Similarity=0.958 Sum_probs=14.7
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc-cc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR-WK 374 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~-Wk 374 (376)
.-|+|+.|+++-++|..+ | ...|.+||.. |.
T Consensus 284 RFFkC~~C~~Rt~sl~r~-------P---~~~C~~Cg~~~we 315 (344)
T PF09332_consen 284 RFFKCKDCGNRTISLERL-------P---KKHCSNCGSSKWE 315 (344)
T ss_dssp EEEE-T-TS-EEEESSSS------------S--TTT-S---E
T ss_pred eeEECCCCCCeeeecccC-------C---CCCCCcCCcCcee
Confidence 468999999997766332 2 2479999964 64
No 156
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=28.99 E-value=41 Score=26.54 Aligned_cols=26 Identities=27% Similarity=0.626 Sum_probs=17.3
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCC
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCS 370 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~ 370 (376)
++||=||...- .+.+--+|.+|..|+
T Consensus 2 ~~CPCCg~~Tl---------~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 2 YPCPCCGYYTL---------EERGEGTYDICPVCF 27 (78)
T ss_pred ccCCCCCcEEe---------ccCCCcCceECCCCC
Confidence 68999986543 122333499999996
No 157
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=28.60 E-value=70 Score=19.95 Aligned_cols=28 Identities=25% Similarity=0.350 Sum_probs=14.8
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
.+|++|+..-....+.+ ...+.|..|-+
T Consensus 2 ~~C~rC~~~~~~~~~~~--------r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGING--------RSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETT--------EEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecC--------CCCeECcCCcC
Confidence 47999998755443322 44677888864
No 158
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=28.40 E-value=26 Score=30.33 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=20.4
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
.....+||+||-+- |+. +--+.|..||++.
T Consensus 25 kML~~hCp~Cg~PL---F~K---------dG~v~CPvC~~~~ 54 (131)
T COG1645 25 KMLAKHCPKCGTPL---FRK---------DGEVFCPVCGYRE 54 (131)
T ss_pred HHHHhhCcccCCcc---eee---------CCeEECCCCCceE
Confidence 34577899998654 332 2247799999864
No 159
>PHA02540 61 DNA primase; Provisional
Probab=27.90 E-value=55 Score=32.90 Aligned_cols=34 Identities=24% Similarity=0.623 Sum_probs=25.1
Q ss_pred ccccccccCC-----cceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQ-----RKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~-----~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
-.+.||-|+. ++..|+....+. -.||-|-+||..
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 446777764331 469999999964
No 160
>PRK05582 DNA topoisomerase I; Validated
Probab=27.32 E-value=1.7e+02 Score=31.88 Aligned_cols=15 Identities=7% Similarity=0.153 Sum_probs=11.0
Q ss_pred hchhcCCCChhhhcc
Q 017145 283 KRVLLGEVTPERLVT 297 (376)
Q Consensus 283 ~~vl~G~i~p~~l~~ 297 (376)
..|..|++++++|+.
T Consensus 529 ~~I~~G~~~~~~~l~ 543 (650)
T PRK05582 529 DEIEEGKEDWKKVLD 543 (650)
T ss_pred HHHHcCCCCHHHHHH
Confidence 356778888888863
No 161
>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=27.00 E-value=56 Score=27.31 Aligned_cols=37 Identities=22% Similarity=0.456 Sum_probs=17.2
Q ss_pred ccccccCCcceEEEEEeccCC---CCCCeEEEEcCCCCCc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSA---DEPMTTYVTCVNCSKR 372 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsa---DEpmt~f~~C~~C~~~ 372 (376)
.-|..|+++.-...+-.+..- +|-.|.--+|.+|+|.
T Consensus 28 ~~Ca~C~krdfv~i~nk~~~eedgeEivTY~HvC~nC~Hv 67 (112)
T PF06573_consen 28 VGCASCQKRDFVLISNKSIEEEDGEEIVTYDHVCKNCHHV 67 (112)
T ss_dssp ---SSS--SS-EEEEEEEEEEETTEEEEEEEEEETTT--E
T ss_pred hhhhccCCCCcEEEecccccccCCcEEEEeeeccCccceE
Confidence 479999999966554443322 2224444569999974
No 162
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.79 E-value=32 Score=33.47 Aligned_cols=24 Identities=17% Similarity=0.373 Sum_probs=19.0
Q ss_pred CccccccccccccCCcceEEEEEe
Q 017145 329 ATATTDQFKCSRCGQRKCTYYQMQ 352 (376)
Q Consensus 329 ~~~~t~~~~C~~C~~~~~~~~q~q 352 (376)
..+.|....|+.||..-+.-++++
T Consensus 233 ss~~t~~~~C~~Cg~~PtiP~~~~ 256 (298)
T KOG2879|consen 233 SSTGTSDTECPVCGEPPTIPHVIG 256 (298)
T ss_pred cccccCCceeeccCCCCCCCeeec
Confidence 345566889999999888878876
No 163
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.70 E-value=1.8e+02 Score=28.11 Aligned_cols=29 Identities=14% Similarity=0.253 Sum_probs=18.3
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCC
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCS 370 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~ 370 (376)
....|++||..=....+.+ ..-|.|..|.
T Consensus 243 ~g~pCprCG~~I~~~~~~g--------R~t~~CP~CQ 271 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVAG--------RSSHYCPHCQ 271 (272)
T ss_pred CCCcCCCCCCeeEEEEECC--------CccEECcCCc
Confidence 3569999996443322221 4567799996
No 164
>PRK00420 hypothetical protein; Validated
Probab=26.65 E-value=36 Score=28.75 Aligned_cols=27 Identities=22% Similarity=0.314 Sum_probs=17.7
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
...||.||.+-..+. ..-+.|.+||..
T Consensus 23 ~~~CP~Cg~pLf~lk-----------~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFELK-----------DGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceecC-----------CCceECCCCCCe
Confidence 368999996544221 224679999874
No 165
>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=26.30 E-value=1.4e+02 Score=32.25 Aligned_cols=15 Identities=7% Similarity=0.153 Sum_probs=11.5
Q ss_pred hchhcCCCChhhhcc
Q 017145 283 KRVLLGEVTPERLVT 297 (376)
Q Consensus 283 ~~vl~G~i~p~~l~~ 297 (376)
..|..|+.+++.|+.
T Consensus 535 ~~I~~G~~~~~~~l~ 549 (610)
T TIGR01051 535 DEIAEGKAEWKPVLK 549 (610)
T ss_pred HHHHcCCCCHHHHHH
Confidence 467789999988863
No 166
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=26.29 E-value=43 Score=33.69 Aligned_cols=25 Identities=28% Similarity=0.825 Sum_probs=19.7
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
.-.++|.+||..-- +.|..|..|.+
T Consensus 352 ~~~YRC~~CGF~a~--------------~l~W~CPsC~~ 376 (389)
T COG2956 352 KPRYRCQNCGFTAH--------------TLYWHCPSCRA 376 (389)
T ss_pred cCCceecccCCcce--------------eeeeeCCCccc
Confidence 34899999997543 77889999964
No 167
>PRK07219 DNA topoisomerase I; Validated
Probab=26.24 E-value=90 Score=35.10 Aligned_cols=15 Identities=13% Similarity=0.175 Sum_probs=11.2
Q ss_pred hchhcCCCChhhhcc
Q 017145 283 KRVLLGEVTPERLVT 297 (376)
Q Consensus 283 ~~vl~G~i~p~~l~~ 297 (376)
..|-.|++++++|+.
T Consensus 550 ~~I~~G~~~~~~~l~ 564 (822)
T PRK07219 550 QAIEDGKKKKEDVTE 564 (822)
T ss_pred HHHHcCCCCHHHHHH
Confidence 466778888888864
No 168
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.95 E-value=39 Score=38.53 Aligned_cols=15 Identities=7% Similarity=-0.155 Sum_probs=7.2
Q ss_pred CCCCCCCHHHHHHHH
Q 017145 24 VSSGGPEVSRCVDAL 38 (376)
Q Consensus 24 ~~~~~~~~~~~l~~L 38 (376)
.++=.|+++.+--++
T Consensus 192 ~lQY~P~~~Eir~iv 206 (1121)
T PRK04023 192 SLQYSPSDEEIRLIV 206 (1121)
T ss_pred cCCcCCCHHHHHHHH
Confidence 344445555554444
No 169
>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=25.87 E-value=18 Score=28.79 Aligned_cols=47 Identities=26% Similarity=0.510 Sum_probs=21.4
Q ss_pred hccCChhhcCcHHHHHHHHHHHHHHHHHhhhcCCCccccccccccccCCcc
Q 017145 295 LVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRK 345 (376)
Q Consensus 295 l~~Ms~eEmas~e~k~~~~~~~ee~l~~~~~~~~~~~~t~~~~C~~C~~~~ 345 (376)
++-=|++++|....++...-+++..+.- .+- -.....|.|+.||++-
T Consensus 29 ivVTTPq~la~~dv~r~~~~~~~~~vpi--lGv--VENMs~~~Cp~Cg~~~ 75 (81)
T PF10609_consen 29 IVVTTPQELALADVRRAIDMFRKLNVPI--LGV--VENMSYFVCPHCGERI 75 (81)
T ss_dssp EEEE-CCC--HHHHHHHHHHHHCTT-EE--EEE--EECT-EEE-TTT--EE
T ss_pred EEEeCCHHHHHHHHHHHHHHHHhcCCCc--EEE--EECCCccCCCCCCCee
Confidence 3445778888887776655554433211 110 0134578999998764
No 170
>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=25.85 E-value=49 Score=24.20 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=17.1
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
.....|+.||... .-..+|..||+
T Consensus 24 p~l~~C~~cG~~~---------------~~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFK---------------LPHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCcc---------------cCeeECCccCe
Confidence 3466799998643 34778888884
No 171
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=25.79 E-value=37 Score=22.23 Aligned_cols=11 Identities=18% Similarity=0.317 Sum_probs=8.0
Q ss_pred EEEcCCCCCcc
Q 017145 363 YVTCVNCSKRW 373 (376)
Q Consensus 363 f~~C~~C~~~W 373 (376)
+++|..||+..
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 57788888754
No 172
>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=25.66 E-value=34 Score=21.84 Aligned_cols=27 Identities=26% Similarity=0.523 Sum_probs=12.8
Q ss_pred cccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 337 KCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 337 ~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
-|++||..-.. .+. -.-..|..||+..
T Consensus 5 fC~~CG~~t~~--------~~~--g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 5 FCGRCGAPTKP--------APG--GWARRCPSCGHEH 31 (32)
T ss_dssp B-TTT--BEEE---------SS--SS-EEESSSS-EE
T ss_pred ccCcCCccccC--------CCC--cCEeECCCCcCEe
Confidence 49999987652 111 2345688888753
No 173
>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=25.05 E-value=73 Score=26.44 Aligned_cols=35 Identities=17% Similarity=0.371 Sum_probs=21.5
Q ss_pred ccccccCCcceEEE--EEeccCCCCCCeEEEEcCCCCC
Q 017145 336 FKCSRCGQRKCTYY--QMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 336 ~~C~~C~~~~~~~~--q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
..|+-||..-.... ++-.+..|+.. .+|+|..|+-
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~-~~y~C~~C~A 39 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGP-YLYVCTPCDA 39 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCc-eeEECCCCCc
Confidence 46999998544321 33334554432 4599999974
No 174
>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=24.21 E-value=52 Score=29.34 Aligned_cols=11 Identities=36% Similarity=0.670 Sum_probs=8.3
Q ss_pred EEEEcCCCCCc
Q 017145 362 TYVTCVNCSKR 372 (376)
Q Consensus 362 ~f~~C~~C~~~ 372 (376)
.=..|.+||+.
T Consensus 67 ~PsYC~~CGkp 77 (158)
T PF10083_consen 67 APSYCHNCGKP 77 (158)
T ss_pred CChhHHhCCCC
Confidence 33459999987
No 175
>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=24.05 E-value=20 Score=29.26 Aligned_cols=36 Identities=22% Similarity=0.485 Sum_probs=27.1
Q ss_pred ccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 336 FKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 336 ~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
-.|.+|+.+....-..|++ +.=+|.+|-+|..||.+
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 4688899988877777765 33368888899988864
No 176
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.44 E-value=36 Score=28.56 Aligned_cols=29 Identities=21% Similarity=0.531 Sum_probs=17.7
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
....+.|+.||. ++... ...++.|..||-
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 345788999995 22211 122367999994
No 177
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.71 E-value=14 Score=29.06 Aligned_cols=38 Identities=37% Similarity=0.796 Sum_probs=24.7
Q ss_pred ccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 330 TATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 330 ~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
-.|+-.+.|-.||++.-+ +|. -.|.|.| +|..||-+.|
T Consensus 7 lMPtY~Y~c~~cg~~~dv---vq~-~~ddplt---~ce~c~a~~k 44 (82)
T COG2331 7 LMPTYSYECTECGNRFDV---VQA-MTDDPLT---TCEECGARLK 44 (82)
T ss_pred cccceEEeecccchHHHH---HHh-cccCccc---cChhhChHHH
Confidence 356778899999987543 232 2566744 6788877654
No 178
>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=22.62 E-value=41 Score=38.14 Aligned_cols=25 Identities=24% Similarity=0.723 Sum_probs=18.4
Q ss_pred ccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 332 TTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 332 ~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
....++||+||.. |.+.+|..||-+
T Consensus 622 ev~~RKCPkCG~y----------------Tlk~rCP~CG~~ 646 (1095)
T TIGR00354 622 EIAIRKCPQCGKE----------------SFWLKCPVCGEL 646 (1095)
T ss_pred EEEEEECCCCCcc----------------cccccCCCCCCc
Confidence 3346788888863 668889999865
No 179
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=22.42 E-value=89 Score=31.83 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=25.0
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
+....|+.|+....+..+.++ --+....+|..|+=
T Consensus 157 t~~~tC~tC~G~G~v~~~~~~----g~~~~~~~C~~C~G 191 (371)
T COG0484 157 TDPKTCPTCNGSGQVRTVQRT----GFFSFQQTCPTCNG 191 (371)
T ss_pred CCCCcCCCCCCcCeEEEEEee----eEEEEEEECCCCcc
Confidence 357799999998887665544 23556677988873
No 180
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=22.21 E-value=60 Score=23.86 Aligned_cols=33 Identities=18% Similarity=0.471 Sum_probs=15.5
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCC
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~ 371 (376)
.+.||-||++.- .|.|.--+=-..-+.|..|.+
T Consensus 4 Wi~CP~CgnKTR----~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 4 WILCPICGNKTR----LKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred EEECCCCCCccc----eeeecCceeccccccCCCCCc
Confidence 456777775542 233321111222344677754
No 181
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=22.07 E-value=51 Score=27.85 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=18.7
Q ss_pred HhhhcCCCccccccccccccCCcceE
Q 017145 322 ECQRGGEATATTDQFKCSRCGQRKCT 347 (376)
Q Consensus 322 ~~~~~~~~~~~t~~~~C~~C~~~~~~ 347 (376)
..|..++...+|.-|.|++|+.+...
T Consensus 89 T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 89 TLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hhhcccccCCceEEEEcCccceeeec
Confidence 34444555568889999999987653
No 182
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=22.01 E-value=32 Score=33.61 Aligned_cols=38 Identities=21% Similarity=0.510 Sum_probs=25.7
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
.-.||.||+.-+.-+-.++ - ++.--.|..|.-|-.-|.
T Consensus 185 ~~~CPvCGS~PvaSmV~~g-~-~~~GlRYL~CslC~teW~ 222 (308)
T COG3058 185 RQYCPVCGSMPVASMVQIG-E-TEQGLRYLHCSLCETEWH 222 (308)
T ss_pred cccCCCcCCCCcceeeeec-C-ccccchhhhhhhHHHHHH
Confidence 4479999998776555443 2 333356888888877775
No 183
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=21.71 E-value=40 Score=28.01 Aligned_cols=13 Identities=46% Similarity=1.456 Sum_probs=11.4
Q ss_pred cccccccCCcceE
Q 017145 335 QFKCSRCGQRKCT 347 (376)
Q Consensus 335 ~~~C~~C~~~~~~ 347 (376)
.|+|++||+++|.
T Consensus 74 ~~PC~~C~S~KCG 86 (103)
T PF14949_consen 74 HYPCPKCGSRKCG 86 (103)
T ss_pred cccCCCCCCCccC
Confidence 6899999999983
No 184
>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=21.62 E-value=37 Score=28.35 Aligned_cols=32 Identities=19% Similarity=0.516 Sum_probs=19.4
Q ss_pred cccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 333 t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
..+..|..||....+|--+... .|+|..|.-.
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~G--------iflC~~Cag~ 42 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYG--------IFLCLECAGI 42 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTT--------EEE-HHHHHH
T ss_pred cCcCcCCCCCCCCCCEEEeecC--------hhhhHHHHHH
Confidence 4567899999999988765433 7788888643
No 185
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=21.58 E-value=2e+02 Score=30.51 Aligned_cols=36 Identities=22% Similarity=0.316 Sum_probs=22.3
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCcc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRW 373 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~W 373 (376)
-.--|++||+-..+..-. ...+ .-|+.|.| .|||..
T Consensus 174 ~~pic~~cg~~~~~~~~~--~d~~-~~~v~y~~-~cG~~~ 209 (510)
T PRK00750 174 FLPICPKCGKVLTTPVIS--YDAE-AGTVTYDC-ECGHEG 209 (510)
T ss_pred eeeeCCCCCccceEEEEE--EeCC-CCEEEEEc-CCCCEE
Confidence 355799999876544321 2233 33777777 499864
No 186
>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=21.16 E-value=48 Score=24.16 Aligned_cols=33 Identities=27% Similarity=0.722 Sum_probs=18.8
Q ss_pred ccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCc
Q 017145 334 DQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKR 372 (376)
Q Consensus 334 ~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~ 372 (376)
-.+.| +||.. |.+.-.-..+. ...+.|..|+..
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 35789 89988 33221111112 678889999864
No 187
>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=20.85 E-value=7.7 Score=25.74 Aligned_cols=31 Identities=26% Similarity=0.622 Sum_probs=15.1
Q ss_pred ccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccc
Q 017145 338 CSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374 (376)
Q Consensus 338 C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wk 374 (376)
|..|+-.+...+ |.+. .-....|+.||-.|+
T Consensus 1 C~~C~tt~t~~W----R~~~--~g~~~LCn~Cg~~~k 31 (36)
T PF00320_consen 1 CSNCGTTETPQW----RRGP--NGNRTLCNACGLYYK 31 (36)
T ss_dssp -TTT--ST-SSE----EEET--TSEE-EEHHHHHHHH
T ss_pred CcCCcCCCCchh----hcCC--CCCCHHHHHHHHHHH
Confidence 667776665433 2222 122238999998886
No 188
>PRK07726 DNA topoisomerase III; Provisional
Probab=20.66 E-value=2.1e+02 Score=31.39 Aligned_cols=26 Identities=19% Similarity=0.549 Sum_probs=15.3
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCC
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVN 368 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~ 368 (376)
...||+||+. ..+ ...+. ..||-|.+
T Consensus 610 ~~~CP~C~~~-~~~--~~~~~-----~~f~~Cs~ 635 (658)
T PRK07726 610 GPKCPDCGKP-MLK--VKGKN-----GKMLVCQD 635 (658)
T ss_pred cccccccCcc-cee--ecccC-----CeeEecCC
Confidence 4679999975 211 11221 35888887
No 189
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.41 E-value=53 Score=28.42 Aligned_cols=12 Identities=25% Similarity=0.958 Sum_probs=9.2
Q ss_pred eEEEEcCCCCCc
Q 017145 361 TTYVTCVNCSKR 372 (376)
Q Consensus 361 t~f~~C~~C~~~ 372 (376)
..|+.|..||..
T Consensus 105 ~~~~~CP~Cgs~ 116 (135)
T PRK03824 105 HAFLKCPKCGSR 116 (135)
T ss_pred ccCcCCcCCCCC
Confidence 367789999953
No 190
>PRK10445 endonuclease VIII; Provisional
Probab=20.21 E-value=2.6e+02 Score=26.85 Aligned_cols=28 Identities=21% Similarity=0.450 Sum_probs=17.9
Q ss_pred cccccccCCcceEEEEEeccCCCCCCeEEEEcCCCC
Q 017145 335 QFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCS 370 (376)
Q Consensus 335 ~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~ 370 (376)
...||+||..=....+. . ..-|.|.+|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~-g-------R~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLS-S-------RPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEEC-C-------CCcEECCCCc
Confidence 56899999664333332 2 4456799996
No 191
>PRK14724 DNA topoisomerase III; Provisional
Probab=20.01 E-value=1.7e+02 Score=33.84 Aligned_cols=14 Identities=14% Similarity=0.361 Sum_probs=9.6
Q ss_pred hchhcCCCChhhhc
Q 017145 283 KRVLLGEVTPERLV 296 (376)
Q Consensus 283 ~~vl~G~i~p~~l~ 296 (376)
..|-.|++++++|.
T Consensus 600 ~~I~~G~~~~~~fl 613 (987)
T PRK14724 600 AQMEKGQLSREAFM 613 (987)
T ss_pred HHHHhCCCCHHHHH
Confidence 35666888877774
Done!