Query 037763
Match_columns 354
No_of_seqs 224 out of 719
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 04:09:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037763.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037763hhsearch_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 1E-62 2.2E-67 474.1 22.8 285 7-345 3-299 (299)
2 KOG1105 Transcription elongati 100.0 3.8E-61 8.2E-66 457.6 21.3 283 7-345 1-296 (296)
3 smart00510 TFS2M Domain in the 100.0 4.3E-29 9.4E-34 206.0 9.8 102 176-287 1-102 (102)
4 PF07500 TFIIS_M: Transcriptio 99.9 1E-26 2.3E-31 195.5 4.2 109 174-292 1-109 (115)
5 smart00509 TFS2N Domain in the 99.6 3.6E-16 7.9E-21 122.2 4.3 69 8-79 1-71 (75)
6 cd00183 TFIIS_I N-terminal dom 99.5 3.8E-14 8.2E-19 111.0 4.3 55 25-79 17-73 (76)
7 KOG1634 Predicted transcriptio 99.4 1.9E-13 4.1E-18 144.1 5.0 81 211-291 267-348 (778)
8 PF08711 Med26: TFIIS helical 99.1 1.2E-11 2.6E-16 90.1 1.0 47 33-79 1-50 (53)
9 smart00440 ZnF_C2C2 C2C2 Zinc 99.0 3.3E-10 7.2E-15 78.2 2.6 30 314-343 1-39 (40)
10 PF01096 TFIIS_C: Transcriptio 98.9 5.7E-10 1.2E-14 76.6 2.1 30 314-343 1-39 (39)
11 COG1594 RPB9 DNA-directed RNA 98.7 7.4E-09 1.6E-13 87.2 2.8 36 310-345 69-113 (113)
12 PHA02998 RNA polymerase subuni 98.5 7.3E-08 1.6E-12 86.0 2.8 33 312-344 142-183 (195)
13 TIGR01384 TFS_arch transcripti 98.4 1.5E-07 3.3E-12 77.6 2.8 33 312-344 61-102 (104)
14 KOG2906 RNA polymerase III sub 98.3 3.1E-07 6.6E-12 74.5 1.5 34 309-343 62-104 (105)
15 KOG2691 RNA polymerase II subu 98.0 2.5E-06 5.4E-11 70.4 2.2 34 310-343 70-112 (113)
16 KOG2907 RNA polymerase I trans 96.9 0.00028 6.1E-09 58.9 0.5 30 314-343 75-113 (116)
17 PF11467 LEDGF: Lens epitheliu 96.1 0.0053 1.2E-07 51.2 3.5 72 2-79 1-77 (106)
18 KOG2821 RNA polymerase II tran 95.9 0.0027 5.8E-08 64.5 1.0 68 4-79 6-75 (433)
19 PF09855 DUF2082: Nucleic-acid 95.6 0.007 1.5E-07 46.0 1.9 28 314-341 1-45 (64)
20 KOG1793 Uncharacterized conser 95.2 0.023 5E-07 57.0 4.6 54 26-79 230-288 (417)
21 COG3478 Predicted nucleic-acid 95.0 0.015 3.3E-07 44.0 1.8 30 312-341 3-49 (68)
22 COG5139 Uncharacterized conser 94.7 0.042 9.1E-07 53.3 4.7 54 26-79 227-284 (397)
23 COG2051 RPS27A Ribosomal prote 94.1 0.032 6.9E-07 42.5 1.8 29 313-341 19-47 (67)
24 PF08271 TF_Zn_Ribbon: TFIIB z 92.9 0.053 1.1E-06 37.6 1.3 29 314-342 1-29 (43)
25 COG4888 Uncharacterized Zn rib 91.9 0.17 3.8E-06 41.7 3.2 40 311-350 20-64 (104)
26 PRK09678 DNA-binding transcrip 91.2 0.13 2.8E-06 40.1 1.8 34 313-346 1-43 (72)
27 PF08274 PhnA_Zn_Ribbon: PhnA 91.1 0.12 2.5E-06 33.6 1.2 26 315-342 4-29 (30)
28 PRK00415 rps27e 30S ribosomal 91.0 0.15 3.3E-06 38.1 1.9 30 313-342 11-40 (59)
29 TIGR02098 MJ0042_CXXC MJ0042 f 90.8 0.2 4.3E-06 33.6 2.2 31 314-344 3-37 (38)
30 PF01667 Ribosomal_S27e: Ribos 90.5 0.12 2.7E-06 38.1 1.1 28 314-341 8-35 (55)
31 PTZ00083 40S ribosomal protein 90.5 0.19 4.2E-06 40.1 2.2 29 313-341 35-63 (85)
32 PLN00209 ribosomal protein S27 90.3 0.2 4.4E-06 40.1 2.2 29 313-341 36-64 (86)
33 PF12760 Zn_Tnp_IS1595: Transp 90.2 0.23 5E-06 34.9 2.2 27 313-341 18-46 (46)
34 TIGR00686 phnA alkylphosphonat 89.2 0.22 4.7E-06 41.6 1.6 30 315-346 4-33 (109)
35 PF03604 DNA_RNApol_7kD: DNA d 89.1 0.17 3.7E-06 33.3 0.8 26 314-341 1-26 (32)
36 PF05180 zf-DNL: DNL zinc fing 88.9 0.22 4.8E-06 38.1 1.4 30 313-342 4-39 (66)
37 PF13717 zinc_ribbon_4: zinc-r 88.5 0.34 7.4E-06 32.5 2.0 26 314-343 3-36 (36)
38 PF04606 Ogr_Delta: Ogr/Delta- 87.9 0.32 7E-06 34.4 1.6 31 315-345 1-40 (47)
39 KOG3507 DNA-directed RNA polym 87.9 0.27 5.8E-06 36.7 1.2 30 308-341 15-46 (62)
40 PF13719 zinc_ribbon_5: zinc-r 86.9 0.53 1.1E-05 31.7 2.1 31 314-344 3-37 (37)
41 smart00659 RPOLCX RNA polymera 86.3 0.55 1.2E-05 33.0 2.1 27 313-342 2-29 (44)
42 PRK10220 hypothetical protein; 86.1 0.44 9.5E-06 39.9 1.7 30 315-346 5-34 (111)
43 PF09526 DUF2387: Probable met 86.0 0.75 1.6E-05 35.7 2.8 33 315-347 10-45 (71)
44 PHA00626 hypothetical protein 84.5 0.6 1.3E-05 34.6 1.6 27 315-342 2-33 (59)
45 PF10080 DUF2318: Predicted me 83.6 0.78 1.7E-05 38.1 2.1 35 310-346 32-66 (102)
46 TIGR02443 conserved hypothetic 83.3 1.5 3.2E-05 32.9 3.2 36 315-350 11-49 (59)
47 COG1996 RPC10 DNA-directed RNA 83.3 0.58 1.3E-05 33.7 1.1 30 310-342 3-34 (49)
48 PF09332 Mcm10: Mcm10 replicat 83.2 0.4 8.6E-06 47.9 0.3 10 332-341 285-294 (344)
49 KOG1886 BAH domain proteins [T 82.8 1 2.2E-05 46.6 3.0 162 172-354 238-414 (464)
50 PF11781 RRN7: RNA polymerase 82.8 0.78 1.7E-05 30.9 1.5 26 313-341 8-34 (36)
51 PRK00398 rpoP DNA-directed RNA 82.0 0.91 2E-05 31.8 1.7 29 313-342 3-31 (46)
52 smart00531 TFIIE Transcription 81.5 1.1 2.4E-05 39.2 2.4 34 310-344 96-135 (147)
53 PF05129 Elf1: Transcription e 78.8 1.8 3.9E-05 34.4 2.6 40 310-349 19-63 (81)
54 PF13453 zf-TFIIB: Transcripti 76.3 2 4.3E-05 29.4 1.9 28 315-343 1-30 (41)
55 TIGR02300 FYDLN_acid conserved 75.4 1.4 3E-05 38.0 1.1 30 313-345 9-39 (129)
56 PF09538 FYDLN_acid: Protein o 74.7 1.3 2.8E-05 37.1 0.8 30 313-345 9-39 (108)
57 TIGR00373 conserved hypothetic 73.3 2.1 4.5E-05 38.1 1.7 34 309-343 105-139 (158)
58 PF01873 eIF-5_eIF-2B: Domain 72.0 3.2 7E-05 35.6 2.6 27 315-341 95-123 (125)
59 PRK09710 lar restriction allev 71.3 3.6 7.9E-05 31.3 2.4 35 314-348 7-43 (64)
60 COG1997 RPL43A Ribosomal prote 70.4 3.4 7.4E-05 33.3 2.2 31 311-343 33-64 (89)
61 PRK14892 putative transcriptio 68.4 3.9 8.5E-05 33.8 2.2 35 310-344 18-54 (99)
62 smart00653 eIF2B_5 domain pres 67.3 5.2 0.00011 33.6 2.8 28 314-341 81-110 (110)
63 KOG3277 Uncharacterized conser 67.0 2.9 6.2E-05 37.2 1.2 35 310-344 76-116 (165)
64 PF14354 Lar_restr_allev: Rest 67.0 4.3 9.3E-05 29.7 2.0 29 312-340 2-37 (61)
65 TIGR00311 aIF-2beta translatio 66.0 5.5 0.00012 34.6 2.8 28 313-341 97-127 (133)
66 PRK03988 translation initiatio 65.8 5.5 0.00012 34.8 2.8 28 314-341 103-132 (138)
67 PRK06266 transcription initiat 65.2 4 8.6E-05 37.1 1.8 34 310-344 114-148 (178)
68 smart00834 CxxC_CXXC_SSSS Puta 64.1 6.7 0.00015 26.1 2.4 25 313-340 5-34 (41)
69 KOG1779 40s ribosomal protein 63.9 4.4 9.5E-05 32.1 1.6 27 314-340 35-61 (84)
70 TIGR01206 lysW lysine biosynth 63.2 5.3 0.00012 29.4 1.8 31 313-344 2-34 (54)
71 PF04032 Rpr2: RNAse P Rpr2/Rp 63.0 6 0.00013 30.7 2.3 28 313-340 46-85 (85)
72 PF11648 RIG-I_C-RD: C-termina 62.1 5.2 0.00011 34.1 1.9 13 332-344 60-72 (123)
73 PF07282 OrfB_Zn_ribbon: Putat 61.0 4.8 0.0001 30.2 1.4 31 310-342 26-56 (69)
74 PF09332 Mcm10: Mcm10 replicat 60.7 3.9 8.3E-05 41.0 1.0 35 308-343 280-315 (344)
75 PRK03564 formate dehydrogenase 58.0 6.9 0.00015 38.7 2.2 36 312-347 186-227 (309)
76 PF04216 FdhE: Protein involve 56.1 7.9 0.00017 37.5 2.2 34 314-347 173-212 (290)
77 PF01780 Ribosomal_L37ae: Ribo 55.1 25 0.00054 28.6 4.6 29 312-342 34-63 (90)
78 COG2023 RPR2 RNase P subunit R 53.7 10 0.00023 31.6 2.2 33 314-346 57-96 (105)
79 PRK12336 translation initiatio 53.5 11 0.00025 34.8 2.7 29 313-341 98-128 (201)
80 TIGR00373 conserved hypothetic 52.5 21 0.00046 31.6 4.2 36 254-291 19-55 (158)
81 KOG4274 Positive cofactor 2 (P 50.8 23 0.0005 37.8 4.7 62 176-254 9-70 (742)
82 PRK05978 hypothetical protein; 50.6 9 0.00019 33.9 1.5 31 314-346 34-66 (148)
83 KOG0704 ADP-ribosylation facto 50.4 15 0.00032 36.9 3.1 30 315-344 21-51 (386)
84 PRK03954 ribonuclease P protei 50.3 12 0.00025 32.1 2.1 31 315-345 66-106 (121)
85 TIGR00280 L37a ribosomal prote 50.0 34 0.00073 27.9 4.6 30 311-342 33-63 (91)
86 PRK12286 rpmF 50S ribosomal pr 49.7 13 0.00028 27.6 2.0 25 309-339 23-47 (57)
87 PRK11827 hypothetical protein; 49.4 14 0.00031 27.7 2.2 39 312-352 7-45 (60)
88 PF07295 DUF1451: Protein of u 49.1 16 0.00034 32.2 2.8 34 307-341 106-139 (146)
89 TIGR03655 anti_R_Lar restricti 48.6 15 0.00033 26.4 2.2 27 315-341 3-35 (53)
90 PRK04338 N(2),N(2)-dimethylgua 48.2 9.6 0.00021 38.6 1.5 34 313-348 244-277 (382)
91 smart00661 RPOL9 RNA polymeras 48.1 11 0.00024 26.5 1.4 29 316-346 3-34 (52)
92 COG2835 Uncharacterized conser 47.8 20 0.00044 27.0 2.7 38 312-352 7-45 (60)
93 PF09723 Zn-ribbon_8: Zinc rib 47.2 16 0.00034 25.1 2.0 25 313-340 5-34 (42)
94 PLN03119 putative ADP-ribosyla 46.7 27 0.00058 37.4 4.4 25 315-339 25-50 (648)
95 PRK00432 30S ribosomal protein 45.6 12 0.00025 27.0 1.2 27 315-343 22-48 (50)
96 PF08792 A2L_zn_ribbon: A2L zi 44.5 23 0.00049 23.4 2.3 29 312-341 2-30 (33)
97 PRK12380 hydrogenase nickel in 44.0 14 0.00031 30.9 1.6 28 309-340 66-94 (113)
98 smart00401 ZnF_GATA zinc finge 43.6 9.5 0.00021 27.6 0.5 31 314-344 4-37 (52)
99 PF14726 RTTN_N: Rotatin, an a 42.8 34 0.00073 28.2 3.6 52 24-75 43-94 (98)
100 smart00647 IBR In Between Ring 42.6 18 0.0004 26.0 1.9 12 332-343 48-59 (64)
101 PRK14714 DNA polymerase II lar 42.2 14 0.0003 42.8 1.7 13 310-322 664-676 (1337)
102 TIGR02605 CxxC_CxxC_SSSS putat 42.0 20 0.00043 25.3 2.0 25 313-340 5-34 (52)
103 COG5347 GTPase-activating prot 41.0 31 0.00068 34.3 3.8 28 314-341 21-49 (319)
104 TIGR01562 FdhE formate dehydro 40.8 13 0.00029 36.7 1.1 34 313-346 184-224 (305)
105 PTZ00255 60S ribosomal protein 40.8 55 0.0012 26.6 4.5 30 311-342 34-64 (90)
106 PRK03976 rpl37ae 50S ribosomal 40.5 60 0.0013 26.4 4.6 30 311-342 34-64 (90)
107 TIGR00100 hypA hydrogenase nic 39.8 19 0.00041 30.2 1.8 29 309-341 66-95 (115)
108 PRK03681 hypA hydrogenase nick 38.9 19 0.0004 30.3 1.6 29 309-341 66-96 (114)
109 PRK00564 hypA hydrogenase nick 38.9 13 0.00029 31.3 0.7 29 309-341 67-97 (117)
110 COG1198 PriA Primosomal protei 38.8 18 0.00039 39.9 1.9 27 263-289 386-418 (730)
111 PRK14715 DNA polymerase II lar 38.6 17 0.00036 42.5 1.6 32 309-347 670-701 (1627)
112 PF14949 ARF7EP_C: ARF7 effect 38.3 14 0.00031 30.7 0.8 24 313-344 74-97 (103)
113 PF07754 DUF1610: Domain of un 37.8 17 0.00037 22.4 0.8 14 308-321 11-24 (24)
114 PF15135 UPF0515: Uncharacteri 37.0 34 0.00073 32.9 3.1 15 332-346 155-169 (278)
115 PF13248 zf-ribbon_3: zinc-rib 36.2 15 0.00033 22.6 0.5 22 315-341 4-25 (26)
116 PRK12495 hypothetical protein; 35.6 16 0.00036 34.3 0.8 33 307-342 36-68 (226)
117 PF01783 Ribosomal_L32p: Ribos 35.5 28 0.0006 25.5 1.9 22 312-339 25-46 (56)
118 PF02172 KIX: KIX domain; Int 35.2 48 0.001 26.4 3.3 68 173-247 9-76 (81)
119 KOG2593 Transcription initiati 34.8 24 0.00051 36.4 1.8 33 309-341 124-162 (436)
120 PLN03114 ADP-ribosylation fact 33.8 38 0.00083 34.3 3.1 26 315-340 24-50 (395)
121 COG0675 Transposase and inacti 33.2 22 0.00049 33.7 1.4 22 315-342 311-332 (364)
122 COG2956 Predicted N-acetylgluc 33.1 25 0.00055 35.3 1.7 31 310-347 351-382 (389)
123 PF00320 GATA: GATA zinc finge 32.9 9.8 0.00021 25.3 -0.8 28 316-343 1-31 (36)
124 TIGR01031 rpmF_bact ribosomal 32.8 34 0.00074 25.1 2.0 24 310-339 23-46 (55)
125 TIGR00515 accD acetyl-CoA carb 32.6 11 0.00024 36.8 -0.9 30 313-344 26-57 (285)
126 PRK11032 hypothetical protein; 32.6 25 0.00055 31.5 1.5 33 308-341 119-151 (160)
127 KOG0706 Predicted GTPase-activ 32.6 30 0.00065 35.8 2.2 27 313-339 23-50 (454)
128 COG3529 Predicted nucleic-acid 31.9 13 0.00027 28.1 -0.5 28 315-342 12-42 (66)
129 PF13408 Zn_ribbon_recom: Reco 31.8 41 0.0009 23.7 2.3 28 311-338 3-32 (58)
130 PF12773 DZR: Double zinc ribb 31.7 20 0.00042 25.1 0.5 32 313-346 12-47 (50)
131 PHA02942 putative transposase; 31.4 25 0.00055 35.6 1.5 29 311-342 324-352 (383)
132 TIGR00354 polC DNA polymerase, 31.2 25 0.00055 39.7 1.5 26 309-341 621-646 (1095)
133 COG2888 Predicted Zn-ribbon RN 30.9 18 0.0004 27.2 0.3 34 307-340 21-58 (61)
134 PRK14890 putative Zn-ribbon RN 30.8 21 0.00044 26.8 0.5 31 310-340 22-56 (59)
135 PLN02976 amine oxidase 30.6 45 0.00097 39.9 3.4 50 30-79 1302-1354(1713)
136 COG2816 NPY1 NTP pyrophosphohy 30.5 27 0.00059 34.1 1.4 31 310-342 109-139 (279)
137 PF05605 zf-Di19: Drought indu 30.3 9.6 0.00021 27.4 -1.3 30 312-342 1-41 (54)
138 PRK03824 hypA hydrogenase nick 29.8 35 0.00076 29.5 1.9 31 310-341 67-116 (135)
139 PF01485 IBR: IBR domain; Int 29.6 27 0.00058 25.1 1.0 12 332-343 48-59 (64)
140 cd00202 ZnF_GATA Zinc finger D 29.5 12 0.00026 27.3 -0.9 29 316-346 2-35 (54)
141 COG2824 PhnA Uncharacterized Z 29.4 37 0.0008 28.5 1.8 28 315-344 5-32 (112)
142 PF05443 ROS_MUCR: ROS/MUCR tr 29.3 24 0.00051 30.7 0.7 13 332-344 72-84 (132)
143 TIGR00308 TRM1 tRNA(guanine-26 29.0 30 0.00065 35.0 1.5 36 313-348 233-268 (374)
144 PF01412 ArfGap: Putative GTPa 28.1 15 0.00031 30.8 -0.8 37 313-349 13-50 (116)
145 PF14319 Zn_Tnp_IS91: Transpos 27.7 71 0.0015 26.6 3.3 23 310-341 39-61 (111)
146 PRK00241 nudC NADH pyrophospha 27.5 36 0.00077 32.6 1.7 32 311-344 98-129 (256)
147 PHA00616 hypothetical protein 27.4 19 0.00041 25.4 -0.2 14 313-326 1-14 (44)
148 PF04216 FdhE: Protein involve 27.2 33 0.00072 33.2 1.4 34 313-346 211-252 (290)
149 PRK00420 hypothetical protein; 26.3 36 0.00078 28.8 1.3 28 314-343 24-51 (112)
150 PLN03131 hypothetical protein; 25.8 87 0.0019 34.0 4.2 27 314-340 24-51 (705)
151 PF05876 Terminase_GpA: Phage 25.6 43 0.00093 35.7 2.0 26 259-284 121-146 (557)
152 smart00531 TFIIE Transcription 25.6 31 0.00068 30.0 0.8 14 332-345 99-112 (147)
153 PRK14873 primosome assembly pr 25.5 36 0.00078 37.2 1.4 17 260-276 327-343 (665)
154 PF14311 DUF4379: Domain of un 24.6 33 0.00071 24.7 0.6 13 332-344 28-40 (55)
155 COG5595 Zn-ribbon-containing, 24.3 41 0.00088 31.4 1.3 31 318-348 195-234 (256)
156 PF00096 zf-C2H2: Zinc finger, 24.1 39 0.00084 19.4 0.8 9 314-322 1-9 (23)
157 PF02005 TRM: N2,N2-dimethylgu 23.7 33 0.00072 34.7 0.7 38 310-348 237-275 (377)
158 PF00684 DnaJ_CXXCXGXG: DnaJ c 23.2 1.1E+02 0.0025 22.7 3.4 34 310-343 12-52 (66)
159 PF10571 UPF0547: Uncharacteri 23.0 38 0.00082 21.1 0.6 24 315-343 2-25 (26)
160 PF14122 YokU: YokU-like prote 22.9 60 0.0013 26.2 1.9 9 332-340 35-43 (87)
161 PRK00085 recO DNA repair prote 22.5 36 0.00079 31.6 0.7 30 310-339 146-177 (247)
162 PF03833 PolC_DP2: DNA polymer 22.3 29 0.00063 38.7 0.0 26 309-341 651-676 (900)
163 PF15135 UPF0515: Uncharacteri 22.2 37 0.00079 32.7 0.6 32 310-341 152-183 (278)
164 COG0333 RpmF Ribosomal protein 22.0 54 0.0012 24.4 1.4 22 312-339 26-47 (57)
165 COG1645 Uncharacterized Zn-fin 22.0 39 0.00084 29.4 0.7 31 310-343 25-55 (131)
166 PRK06266 transcription initiat 21.9 39 0.00085 30.6 0.8 14 332-345 117-130 (178)
167 PF01396 zf-C4_Topoisom: Topoi 21.8 73 0.0016 21.5 1.9 26 315-341 3-33 (39)
168 PRK05654 acetyl-CoA carboxylas 21.8 23 0.00049 34.8 -0.9 32 313-345 27-59 (292)
169 COG4049 Uncharacterized protei 21.8 37 0.00081 25.3 0.5 12 310-321 14-25 (65)
170 KOG0909 Peptide:N-glycanase [P 21.7 90 0.002 32.5 3.3 96 234-346 88-208 (500)
171 TIGR03829 YokU_near_AblA uncha 21.5 59 0.0013 26.4 1.6 12 332-343 35-46 (89)
172 TIGR00595 priA primosomal prot 21.4 1.2E+02 0.0025 31.9 4.3 14 26-39 33-46 (505)
173 PF03966 Trm112p: Trm112p-like 21.4 65 0.0014 24.2 1.8 12 310-321 4-15 (68)
174 COG4957 Predicted transcriptio 21.2 44 0.00095 29.3 0.9 13 332-344 76-88 (148)
175 PF10601 zf-LITAF-like: LITAF- 21.2 1.2E+02 0.0025 23.0 3.2 22 310-331 4-25 (73)
176 COG0068 HypF Hydrogenase matur 20.8 20 0.00042 39.3 -1.7 40 310-353 98-140 (750)
177 PRK04023 DNA polymerase II lar 20.8 54 0.0012 37.4 1.6 26 309-341 622-647 (1121)
178 COG1675 TFA1 Transcription ini 20.5 54 0.0012 29.9 1.3 31 310-341 110-141 (176)
179 PF02701 zf-Dof: Dof domain, z 20.3 20 0.00044 27.1 -1.2 33 312-344 4-42 (63)
180 PF06397 Desulfoferrod_N: Desu 20.3 49 0.0011 22.3 0.8 12 332-343 6-17 (36)
181 KOG2879 Predicted E3 ubiquitin 20.1 62 0.0013 31.6 1.7 35 307-341 233-285 (298)
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=1e-62 Score=474.13 Aligned_cols=285 Identities=28% Similarity=0.419 Sum_probs=207.4
Q ss_pred HHHHHHHHHHHHHhhhcCCccHHHHHHHHHHhhcCCCcHHhhhcccceeeccccccCCCHHHHHHHhhhh--cccchhhh
Q 037763 7 ELYEAAKRAAMAAVWKEGGAEEAQCLDALDQLKNCSITYQLLVSTQVARHLVPMLKHPCEKIQLFAIELI--WTISLKQI 84 (354)
Q Consensus 7 ~l~~~~~~~a~~~~~~~~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~Ak~Li--WK~~l~~~ 84 (354)
|+...++..-+++ . +.+++.||++|++|+.++||+++|++|+||++||+||||++++|+.+|+.|| ||+ +
T Consensus 3 ei~~~~k~L~k~~-~---~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~----~ 74 (299)
T TIGR01385 3 EVASHAKALDKNK-S---SKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKK----V 74 (299)
T ss_pred HHHHHHHHhhhhc-c---CCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHH----H
Confidence 4445555443322 1 4678899999999999999999999999999999999999999999999999 999 8
Q ss_pred hhhhcccccCCCCCCCCCCCCCCCCccccCccCCCCCCcccccccccccccccccccccccccccccccchhhcccccCC
Q 037763 85 YHLLECFRSAGICFPGYNGHEFPVKNEQVIPANHNNGKLDQKKQTKEGRKITSALSADFSKAKVVKNVKVEEVINEYQGN 164 (354)
Q Consensus 85 ~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~e~~~~~~~~~ 164 (354)
|. .+..+......+.....++++ ++...+. +.++ . ..+ .+...++..+. .
T Consensus 75 v~-~~k~~~~~~~~~~~~~~~~~~-----~~~~~~~-----~~~~-~-----~~~-~~~~~~~~~~~------------~ 124 (299)
T TIGR01385 75 VD-KNKSDHPGGNPEDKTTVGESV-----NSVKQEA-----KSQS-D-----KIE-QPKYVSSSPRN------------A 124 (299)
T ss_pred Hh-hhcccCcccccccccccCCCC-----CCCCccc-----cCCc-c-----ccc-CCCCCCCcccc------------c
Confidence 82 221111000000000000000 0000000 0000 0 000 00000000011 1
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHHHhhhhhhcCCCchhhhhhhccCChHHHHHhhHHHHHHHhCCCchhhhhhHhhHHh
Q 037763 165 VPNASNSLKCNDCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKFKYRCLLF 244 (354)
Q Consensus 165 ~~~~~~~~~t~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~~~~lA~~IE~aif~~~~~~~~~Yk~k~Rsl~~ 244 (354)
.+.....+.++|++|++||+|||+||..+..+.+ ..+++..+|.+||.+||..|+.+++.|+++||||+|
T Consensus 125 ~~~~~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~----------~~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~ 194 (299)
T TIGR01385 125 KNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPP----------QSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYS 194 (299)
T ss_pred CCCCCCCccCCcHHHHHHHHHHHHHHhhcCCCCc----------cccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Confidence 1222224579999999999999999997543221 234677899999999999999888999999999999
Q ss_pred hcCCCCCHHHHHHHhcCCCCchhcccCChhhcCCHHHHHHHHHHHHHhcCCcCcccccccC-CCcccccceEeCCCCCcc
Q 037763 245 NINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQLWYENLEKERAGTNGRIFSGIVS-PKKIISGICKCGRCRHTR 323 (354)
Q Consensus 245 NLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmAS~e~k~~re~~~~~~~~~~~~~~~~~~~-~~~~~td~f~C~kC~~~k 323 (354)
||||++||+||++|++|+|+|++||.|+++||||+|+|++++++.++.... ++++ ..++.||+|+|++||+++
T Consensus 195 NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~l~~------~~~~~~~~~~t~~~~C~~C~~~~ 268 (299)
T TIGR01385 195 NLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFE------AQGAKIQKAVTDLFTCGKCKQKK 268 (299)
T ss_pred HccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHHHHH------HHhhhhhcCCcccccCCCCCCcc
Confidence 999999999999999999999999999999999999999999999764332 2333 377899999999999999
Q ss_pred ceEEeeee---------eeeeccCCCccccc
Q 037763 324 MSFISLRR---------HIACLNCNQYWDST 345 (354)
Q Consensus 324 ~ty~q~QT---------Fv~C~~CgnrWk~~ 345 (354)
|+|||+|| ||+|.+|||+|+||
T Consensus 269 ~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~fc 299 (299)
T TIGR01385 269 CTYYQLQTRSADEPMTTFVTCEECGNRWKFC 299 (299)
T ss_pred ceEEEecccCCCCCCeEEEEcCCCCCeeeeC
Confidence 99999998 99999999999998
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=3.8e-61 Score=457.61 Aligned_cols=283 Identities=29% Similarity=0.466 Sum_probs=218.5
Q ss_pred HHHHHHHHHHHHHhhhcCCccHHHHHHHHHHhhcCCCcHHhhhcccceeecc-ccccCCCHHHHHHHhhhh--cccchhh
Q 037763 7 ELYEAAKRAAMAAVWKEGGAEEAQCLDALDQLKNCSITYQLLVSTQVARHLV-PMLKHPCEKIQLFAIELI--WTISLKQ 83 (354)
Q Consensus 7 ~l~~~~~~~a~~~~~~~~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~-~Lrkh~~~~I~~~Ak~Li--WK~~l~~ 83 (354)
++|+.++++|++...+-++++.+.+|++|.+|+++|||+++|++|+||+.|| .|++|+|++|.++|+.|| ||+
T Consensus 1 ~~~e~~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk---- 76 (296)
T KOG1105|consen 1 ELEEEALRAAKALEKDKQSKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKK---- 76 (296)
T ss_pred CccHHHHHHHHHHHhhcccccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH----
Confidence 3688899999997666677899999999999999999999999999999999 556788999999999999 999
Q ss_pred hhhhhcccccCCCCCCCCCCCCCCCCccccCccCCCCCCcccccccccccccccccccccccccccccccchhhcccccC
Q 037763 84 IYHLLECFRSAGICFPGYNGHEFPVKNEQVIPANHNNGKLDQKKQTKEGRKITSALSADFSKAKVVKNVKVEEVINEYQG 163 (354)
Q Consensus 84 ~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~e~~~~~~~~ 163 (354)
++.. .+++.. +.....+.|......++ ++.+ + ..+...+. .+. +..+ .
T Consensus 77 ~~~~-~~~~~k----~~~~~~~~p~~~~~~~~-------s~~~-~---~~ks~~~~---------~~~-~~~~------~ 124 (296)
T KOG1105|consen 77 LVDK-SPGREK----SGDNKSHDPGEASSKSP-------SGAK-Q---PEKSRGDS---------KRD-KHSG------S 124 (296)
T ss_pred Hhhc-cccccc----CccccCCCCCcCCcCCc-------cCCC-C---cccccccc---------ccc-cccC------c
Confidence 8821 111111 11111111111100000 0000 0 00000000 000 1000 0
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHHHHhhhhhhcCCCchhhhhhhccCChHHHHHhhHHHHHHHhCCCchhhhhhHhhHH
Q 037763 164 NVPNASNSLKCNDCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKFKYRCLL 243 (354)
Q Consensus 164 ~~~~~~~~~~t~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~~~~lA~~IE~aif~~~~~~~~~Yk~k~Rsl~ 243 (354)
. +..+.++|.+|++|++|||+||... ++ ....++++..+|.+||.+||..++.++++|+++|||++
T Consensus 125 ~----~~~~~~~d~~r~k~~e~l~~al~~~-----~~-----~~~~~~~~~~~a~~iE~~~~~~~g~~~~kyK~r~RS~~ 190 (296)
T KOG1105|consen 125 K----DPVPITNDPVRDKCRELLYAALTTE-----DD-----SRVTGADPLELAVQIEEAIFEKLGNTDSKYKNRYRSRV 190 (296)
T ss_pred C----CCCCCCCchHHHHHHHHHHHHhccc-----cc-----ccccCCCHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHh
Confidence 0 1134578999999999999999842 11 12346778899999999999999999999999999999
Q ss_pred hhcCCCCCHHHHHHHhcCCCCchhcccCChhhcCCHHHHHHHHHHHHHhcCCcCcccccccC-CCcccccceEeCCCCCc
Q 037763 244 FNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQLWYENLEKERAGTNGRIFSGIVS-PKKIISGICKCGRCRHT 322 (354)
Q Consensus 244 ~NLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmAS~e~k~~re~~~~~~~~~~~~~~~~~~~-~~~~~td~f~C~kC~~~ 322 (354)
|||+|++||+||++||+|+|+|++|+.|+++||||++++++++++.++.... +|++ .++++||+|+||+|+++
T Consensus 191 ~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~k~~keal~~------~q~~~~~gt~td~fkcgkckk~ 264 (296)
T KOG1105|consen 191 SNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKEERQKLTKEALRE------HQMAKIQGTQTDLFKCGKCKKK 264 (296)
T ss_pred hccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHHHHHHHHHHHHHH------Hhhcccccccccceeecccccc
Confidence 9999999999999999999999999999999999999999999999887654 6665 58899999999999999
Q ss_pred cceEEeeee---------eeeeccCCCccccc
Q 037763 323 RMSFISLRR---------HIACLNCNQYWDST 345 (354)
Q Consensus 323 k~ty~q~QT---------Fv~C~~CgnrWk~~ 345 (354)
+|+|||+|| ||+|++||||||||
T Consensus 265 ~cty~q~Qtrs~DePmtTfv~C~ecgnrWkfc 296 (296)
T KOG1105|consen 265 NCTYTQLQTRSADEPMTTFVTCNECGNRWKFC 296 (296)
T ss_pred ceeEEeeccCCCCCCcceeeeecccCCccccC
Confidence 999999998 99999999999999
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.96 E-value=4.3e-29 Score=206.02 Aligned_cols=102 Identities=38% Similarity=0.670 Sum_probs=91.9
Q ss_pred hHHHHHHHHHHHHHHhhhhhhcCCCchhhhhhhccCChHHHHHhhHHHHHHHhCCCchhhhhhHhhHHhhcCCCCCHHHH
Q 037763 176 DCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKFKYRCLLFNINDPTNREFR 255 (354)
Q Consensus 176 d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~~~~lA~~IE~aif~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr 255 (354)
|++|++|+++|+++|..+....+ ...++..+|.+||.++|+.|+.++++|++++|||+|||||++||+||
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~----------~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr 70 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEE----------IELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLR 70 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCc----------ccccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHH
Confidence 67999999999999997654322 12356789999999999999888889999999999999999999999
Q ss_pred HHHhcCCCCchhcccCChhhcCCHHHHHHHHH
Q 037763 256 KKVLLGRVKPEKIVNMTAKEMASDKMQLWYEN 287 (354)
Q Consensus 256 ~~vl~G~isp~~lv~Ms~eEmAS~e~k~~re~ 287 (354)
++|++|+|+|++||.||++||||+|+|+++++
T Consensus 71 ~~vl~G~i~p~~lv~Ms~~ElAs~elk~~~e~ 102 (102)
T smart00510 71 RKVLNGEITPEKLATMTAEELASAELKEKREK 102 (102)
T ss_pred HHHHcCCCCHHHHhcCCHHHcCCHHHHHHHhC
Confidence 99999999999999999999999999999863
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=1e-26 Score=195.46 Aligned_cols=109 Identities=37% Similarity=0.686 Sum_probs=97.7
Q ss_pred CChHHHHHHHHHHHHHHhhhhhhcCCCchhhhhhhccCChHHHHHhhHHHHHHHhCCCchhhhhhHhhHHhhcCCCCCHH
Q 037763 174 CNDCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKFKYRCLLFNINDPTNRE 253 (354)
Q Consensus 174 t~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~~~~lA~~IE~aif~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~ 253 (354)
|++++|++|+++|+++|.....+ .++ ..++..+|.+||.+||..|+.++..|++++|+|+|||||++||+
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~~---------~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~ 70 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QDD---------PEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPD 70 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CCC---------TCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCC
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-ccc---------hhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHH
Confidence 67999999999999999986543 112 34567999999999999998888999999999999999999999
Q ss_pred HHHHHhcCCCCchhcccCChhhcCCHHHHHHHHHHHHHh
Q 037763 254 FRKKVLLGRVKPEKIVNMTAKEMASDKMQLWYENLEKER 292 (354)
Q Consensus 254 Lr~~vl~G~isp~~lv~Ms~eEmAS~e~k~~re~~~~~~ 292 (354)
|+.+|++|+|+|.+||.|+++||||+++|++++++.++.
T Consensus 71 L~~~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~~~ 109 (115)
T PF07500_consen 71 LRRRILSGEISPEELVTMSPEELASEELKEEREKIRKES 109 (115)
T ss_dssp HHHHHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHHHH
T ss_pred HHHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999998888664
No 5
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.61 E-value=3.6e-16 Score=122.23 Aligned_cols=69 Identities=38% Similarity=0.544 Sum_probs=63.4
Q ss_pred HHHHHHHHHHHHhhhcCCccHHHHHHHHHHhhcCCCcHHhhhcccceeeccccccCCCHHHHHHHhhhh--ccc
Q 037763 8 LYEAAKRAAMAAVWKEGGAEEAQCLDALDQLKNCSITYQLLVSTQVARHLVPMLKHPCEKIQLFAIELI--WTI 79 (354)
Q Consensus 8 l~~~~~~~a~~~~~~~~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~Ak~Li--WK~ 79 (354)
||+++++++++++. ++++++|+++|++|+.++||.++|++|+||+.|++||||++++|+.+|+.|| ||+
T Consensus 1 ~~~~~k~~~k~~~~---~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~ 71 (75)
T smart00509 1 LLRAAKKLDKVANN---GKEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKK 71 (75)
T ss_pred ChHHHHHHHHHhcC---CCCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 57888888887722 3678999999999999999999999999999999999999999999999999 999
No 6
>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=99.47 E-value=3.8e-14 Score=111.04 Aligned_cols=55 Identities=33% Similarity=0.503 Sum_probs=53.7
Q ss_pred CccHHHHHHHHHHhhcCCCcHHhhhcccceeeccccccCCCHHHHHHHhhhh--ccc
Q 037763 25 GAEEAQCLDALDQLKNCSITYQLLVSTQVARHLVPMLKHPCEKIQLFAIELI--WTI 79 (354)
Q Consensus 25 ~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~Ak~Li--WK~ 79 (354)
+++.+.|+++|+.|+.+|||.++|++|+||+.|++||||++++|+.+|+.|| ||+
T Consensus 17 ~~~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~ 73 (76)
T cd00183 17 NEEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKK 73 (76)
T ss_pred CCCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999999999999999999999 999
No 7
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.39 E-value=1.9e-13 Score=144.08 Aligned_cols=81 Identities=35% Similarity=0.605 Sum_probs=75.1
Q ss_pred CChHHHHHhhHHHHHHHhC-CCchhhhhhHhhHHhhcCCCCCHHHHHHHhcCCCCchhcccCChhhcCCHHHHHHHHHHH
Q 037763 211 CDPIQVAISVESAIYENWG-RSTGTYKFKYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQLWYENLE 289 (354)
Q Consensus 211 ~~~~~lA~~IE~aif~~~~-~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmAS~e~k~~re~~~ 289 (354)
.++..++..||..+|..|| +.+.+|++|+|+|+|||||++||.||.+|+.|+|+|++|+.|+++|||+.|+.+|+++..
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 3555677899999999998 788999999999999999999999999999999999999999999999999999998876
Q ss_pred HH
Q 037763 290 KE 291 (354)
Q Consensus 290 ~~ 291 (354)
++
T Consensus 347 ee 348 (778)
T KOG1634|consen 347 EE 348 (778)
T ss_pred HH
Confidence 54
No 8
>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=99.13 E-value=1.2e-11 Score=90.11 Aligned_cols=47 Identities=34% Similarity=0.489 Sum_probs=43.6
Q ss_pred HHHHHhhcCCCcHHhhhcccceeeccccccC-CCHHHHHHHhhhh--ccc
Q 037763 33 DALDQLKNCSITYQLLVSTQVARHLVPMLKH-PCEKIQLFAIELI--WTI 79 (354)
Q Consensus 33 ~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh-~~~~I~~~Ak~Li--WK~ 79 (354)
++|+.|..+|||.++|++|+||++|++|+|| .+++|+.+|+.|| ||+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~ 50 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKR 50 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHH
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhH
Confidence 5799999999999999999999999999999 8999999999999 999
No 9
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=98.96 E-value=3.3e-10 Score=78.20 Aligned_cols=30 Identities=23% Similarity=0.824 Sum_probs=28.8
Q ss_pred eEeCCCCCccceEEeeee---------eeeeccCCCccc
Q 037763 314 CKCGRCRHTRMSFISLRR---------HIACLNCNQYWD 343 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QT---------Fv~C~~CgnrWk 343 (354)
|+|++||.+++.|+|+|| |+.|.+|||+|+
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 589999999999999998 999999999997
No 10
>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=98.91 E-value=5.7e-10 Score=76.61 Aligned_cols=30 Identities=30% Similarity=0.899 Sum_probs=25.9
Q ss_pred eEeCCCCCccceEEeeee---------eeeeccCCCccc
Q 037763 314 CKCGRCRHTRMSFISLRR---------HIACLNCNQYWD 343 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QT---------Fv~C~~CgnrWk 343 (354)
|+|++||++++.|+|+|| |+.|.+|||+|+
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 589999999999999998 999999999996
No 11
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=98.70 E-value=7.4e-09 Score=87.16 Aligned_cols=36 Identities=19% Similarity=0.541 Sum_probs=32.8
Q ss_pred cccceEeCCCCCccceEEeeee---------eeeeccCCCccccc
Q 037763 310 ISGICKCGRCRHTRMSFISLRR---------HIACLNCNQYWDST 345 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT---------Fv~C~~CgnrWk~~ 345 (354)
.+..++|++||.+++.|+|+|| |++|..|||+|++.
T Consensus 69 ~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre~ 113 (113)
T COG1594 69 PTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWREY 113 (113)
T ss_pred ccccccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeecC
Confidence 3447999999999999999998 99999999999974
No 12
>PHA02998 RNA polymerase subunit; Provisional
Probab=98.48 E-value=7.3e-08 Score=86.02 Aligned_cols=33 Identities=15% Similarity=0.480 Sum_probs=30.3
Q ss_pred cceEeCCCCCccceEEeeee---------eeeeccCCCcccc
Q 037763 312 GICKCGRCRHTRMSFISLRR---------HIACLNCNQYWDS 344 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QT---------Fv~C~~CgnrWk~ 344 (354)
...+|++||+++++|+|+|| |+.|.+|||+|+=
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 44699999999999999999 9999999999973
No 13
>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=98.41 E-value=1.5e-07 Score=77.57 Aligned_cols=33 Identities=21% Similarity=0.649 Sum_probs=30.5
Q ss_pred cceEeCCCCCccceEEeeee---------eeeeccCCCcccc
Q 037763 312 GICKCGRCRHTRMSFISLRR---------HIACLNCNQYWDS 344 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QT---------Fv~C~~CgnrWk~ 344 (354)
..++|++||+.++.|+|+|| |++|.+|||+|+-
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 35799999999999999998 9999999999983
No 14
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=98.27 E-value=3.1e-07 Score=74.52 Aligned_cols=34 Identities=26% Similarity=0.713 Sum_probs=30.8
Q ss_pred ccccceEeCCCCCccceEEeeee---------eeeeccCCCccc
Q 037763 309 IISGICKCGRCRHTRMSFISLRR---------HIACLNCNQYWD 343 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~QT---------Fv~C~~CgnrWk 343 (354)
.+|+. +|++||+.+..|.|+|| |..|.+|+||||
T Consensus 62 ~~t~~-~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 62 DQTEA-TCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hhccC-cCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 34554 89999999999999999 999999999998
No 15
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=98.03 E-value=2.5e-06 Score=70.36 Aligned_cols=34 Identities=21% Similarity=0.639 Sum_probs=30.9
Q ss_pred cccceEeCCCCCccceEEeeee---------eeeeccCCCccc
Q 037763 310 ISGICKCGRCRHTRMSFISLRR---------HIACLNCNQYWD 343 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT---------Fv~C~~CgnrWk 343 (354)
.|..-.|++||+++..|+|-|| |..|.+|||||.
T Consensus 70 rts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 70 RTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred ccccccCCccCCcceEEEecccccccceEEEEEEecccccccc
Confidence 5566799999999999999998 888999999995
No 16
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=96.90 E-value=0.00028 Score=58.89 Aligned_cols=30 Identities=30% Similarity=0.749 Sum_probs=27.1
Q ss_pred eEeCCCCCccceEEeeee---------eeeeccCCCccc
Q 037763 314 CKCGRCRHTRMSFISLRR---------HIACLNCNQYWD 343 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QT---------Fv~C~~CgnrWk 343 (354)
-+|++||..+.+|.-+|+ |.||.+|+++..
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 389999999999988886 999999999865
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=96.15 E-value=0.0053 Score=51.24 Aligned_cols=72 Identities=24% Similarity=0.358 Sum_probs=53.9
Q ss_pred hhhHHHHHHHHHHHHHHHhhhc-CCccHHHHHHHHHHhhcCCCcHHhhh-cccceeeccccccCC-CHHHHHHHhhhh--
Q 037763 2 KEKMMELYEAAKRAAMAAVWKE-GGAEEAQCLDALDQLKNCSITYQLLV-STQVARHLVPMLKHP-CEKIQLFAIELI-- 76 (354)
Q Consensus 2 ~~~~~~l~~~~~~~a~~~~~~~-~~~~~~~~l~~L~~L~~~~~t~~~L~-~T~iG~~v~~Lrkh~-~~~I~~~Ak~Li-- 76 (354)
|+.|.+|--..+-+ .+ ++++..+||++|++|..++||..+|+ .+.+-.++.+||+.. +..|...|..|+
T Consensus 1 E~~L~~l~~~Ik~~------L~~~~~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnk 74 (106)
T PF11467_consen 1 ERRLQELHSEIKSS------LKVDNPDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNK 74 (106)
T ss_dssp HHHHHHHHHHHHHT------CETTEE-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHH------HcCCCCCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence 45677776666544 43 66899999999999999999997776 556888999999985 899999999999
Q ss_pred ccc
Q 037763 77 WTI 79 (354)
Q Consensus 77 WK~ 79 (354)
.|.
T Consensus 75 fK~ 77 (106)
T PF11467_consen 75 FKS 77 (106)
T ss_dssp HHH
T ss_pred HHH
Confidence 888
No 18
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=95.95 E-value=0.0027 Score=64.45 Aligned_cols=68 Identities=15% Similarity=0.240 Sum_probs=59.0
Q ss_pred hHHHHHHHHHHHHHHHhhhcCCccHHHHHHHHHHhhcCCCcHHhhhcccceeeccccccCCCHHHHHHHhhhh--ccc
Q 037763 4 KMMELYEAAKRAAMAAVWKEGGAEEAQCLDALDQLKNCSITYQLLVSTQVARHLVPMLKHPCEKIQLFAIELI--WTI 79 (354)
Q Consensus 4 ~~~~l~~~~~~~a~~~~~~~~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~Ak~Li--WK~ 79 (354)
-.++.++..+..++.. .++.+.+..|..|.++|++.++|.+|.+|++|+.|++|. .+..+|..|+ ||+
T Consensus 6 t~l~~Vr~lQ~~l~~~------~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~ 75 (433)
T KOG2821|consen 6 TGLGAVRKLQARLENR------IDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKD 75 (433)
T ss_pred chHHHHHHHHHHHHhC------ccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHH
Confidence 3566666666554433 789999999999999999999999999999999999998 7999999999 999
No 19
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=95.64 E-value=0.007 Score=46.04 Aligned_cols=28 Identities=25% Similarity=0.623 Sum_probs=24.0
Q ss_pred eEeCCCCCccceEEeeee-----------------eeeeccCCCc
Q 037763 314 CKCGRCRHTRMSFISLRR-----------------HIACLNCNQY 341 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QT-----------------Fv~C~~Cgnr 341 (354)
++|+|||.+...--|+|. +|+|.+||+.
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 479999999887777775 8999999975
No 20
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.22 E-value=0.023 Score=57.00 Aligned_cols=54 Identities=20% Similarity=0.274 Sum_probs=47.8
Q ss_pred ccHHHHHHHHHHhhcCCCcH-HhhhcccceeeccccccCC--CHHHHHHHhhhh--ccc
Q 037763 26 AEEAQCLDALDQLKNCSITY-QLLVSTQVARHLVPMLKHP--CEKIQLFAIELI--WTI 79 (354)
Q Consensus 26 ~~~~~~l~~L~~L~~~~~t~-~~L~~T~iG~~v~~Lrkh~--~~~I~~~Ak~Li--WK~ 79 (354)
|...-=..+|..|.++||-. +.|...+||++|-.|.||+ ..+++.+|..|| |-.
T Consensus 230 Pal~Ir~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsR 288 (417)
T KOG1793|consen 230 PALNIRKSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSR 288 (417)
T ss_pred cchHHHHHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhc
Confidence 55555567888889999988 9999999999999999997 589999999999 998
No 21
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=94.95 E-value=0.015 Score=44.02 Aligned_cols=30 Identities=27% Similarity=0.545 Sum_probs=23.1
Q ss_pred cceEeCCCCCccceEEeeee-----------------eeeeccCCCc
Q 037763 312 GICKCGRCRHTRMSFISLRR-----------------HIACLNCNQY 341 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QT-----------------Fv~C~~Cgnr 341 (354)
.+|+|+|||.++-.--|+|. -++|.+||..
T Consensus 3 ~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 3 NAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred ccccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 46789999987765555554 6899999964
No 22
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=94.75 E-value=0.042 Score=53.33 Aligned_cols=54 Identities=24% Similarity=0.213 Sum_probs=46.4
Q ss_pred ccHHHHHHHHHHhhcCCCcHHhhhcccceeeccccccC--CCHHHHHHHhhhh--ccc
Q 037763 26 AEEAQCLDALDQLKNCSITYQLLVSTQVARHLVPMLKH--PCEKIQLFAIELI--WTI 79 (354)
Q Consensus 26 ~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh--~~~~I~~~Ak~Li--WK~ 79 (354)
|+..---.+|..|..+||-.++|++.+||+.|.....+ ..++|+.+|+.|| |-.
T Consensus 227 P~~~IqksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtr 284 (397)
T COG5139 227 PNIKIQKSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTR 284 (397)
T ss_pred cchHHHHHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhc
Confidence 45554556788889999999999999999999998765 4799999999999 988
No 23
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=94.07 E-value=0.032 Score=42.54 Aligned_cols=29 Identities=24% Similarity=0.597 Sum_probs=26.4
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
..+|+.|+...+.|.--||-|+|+.||.-
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~~ 47 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGTT 47 (67)
T ss_pred EEECCCCCCEEEEeccCceEEEecccccE
Confidence 35899999999999999999999999953
No 24
>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=92.95 E-value=0.053 Score=37.64 Aligned_cols=29 Identities=28% Similarity=0.622 Sum_probs=20.5
Q ss_pred eEeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 314 CKCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
|+|+.||++...+...+..+.|.+||.-.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 68999999884344344488999999643
No 25
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=91.85 E-value=0.17 Score=41.66 Aligned_cols=40 Identities=23% Similarity=0.581 Sum_probs=30.4
Q ss_pred ccceEeCCCCCccceEEeee-e----eeeeccCCCcccccCCCcc
Q 037763 311 SGICKCGRCRHTRMSFISLR-R----HIACLNCNQYWDSTNPGIE 350 (354)
Q Consensus 311 td~f~C~kC~~~k~ty~q~Q-T----Fv~C~~CgnrWk~~~~~~~ 350 (354)
...|.|++|++-+.+-.-+- | |+.|-+||-+.-|--+.++
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~ 64 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELS 64 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccc
Confidence 46799999999998643332 2 9999999999887665543
No 26
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=91.22 E-value=0.13 Score=40.08 Aligned_cols=34 Identities=21% Similarity=0.435 Sum_probs=24.6
Q ss_pred ceEeCCCCCccceEEe-ee---e---eeeec--cCCCcccccC
Q 037763 313 ICKCGRCRHTRMSFIS-LR---R---HIACL--NCNQYWDSTN 346 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q-~Q---T---Fv~C~--~CgnrWk~~~ 346 (354)
||.|+.||..--...- .. + +..|. +||++|..-.
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence 5899999998743321 11 1 99999 9999998643
No 27
>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=91.07 E-value=0.12 Score=33.59 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=14.6
Q ss_pred EeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 315 KCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
+|+.|++..+- +-+....|-.|||.|
T Consensus 4 ~Cp~C~se~~y--~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTY--EDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----E--E-SSSEEETTTTEEE
T ss_pred CCCCCCCccee--ccCCEEeCCcccccC
Confidence 79999887663 445566699999999
No 28
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=90.97 E-value=0.15 Score=38.12 Aligned_cols=30 Identities=23% Similarity=0.583 Sum_probs=27.2
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
..+|+.|+...+-|.-.||-|.|..||+.-
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 358999999999999999999999999754
No 29
>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=90.80 E-value=0.2 Score=33.59 Aligned_cols=31 Identities=19% Similarity=0.554 Sum_probs=20.5
Q ss_pred eEeCCCCCccce-EEee---eeeeeeccCCCcccc
Q 037763 314 CKCGRCRHTRMS-FISL---RRHIACLNCNQYWDS 344 (354)
Q Consensus 314 f~C~kC~~~k~t-y~q~---QTFv~C~~CgnrWk~ 344 (354)
++|+.|+..-.- -.++ ..-|.|-+||+.|+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 689999875210 0111 127899999999974
No 30
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=90.54 E-value=0.12 Score=38.11 Aligned_cols=28 Identities=21% Similarity=0.596 Sum_probs=21.2
Q ss_pred eEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 314 CKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
.+|+.|+...+-|...||-|.|..||.-
T Consensus 8 VkCp~C~~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 8 VKCPGCYNIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EE-TTT-SEEEEETT-SS-EE-SSSTSE
T ss_pred EECCCCCCeeEEEecCCeEEEcccCCCE
Confidence 4899999999999999999999999964
No 31
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=90.49 E-value=0.19 Score=40.14 Aligned_cols=29 Identities=21% Similarity=0.481 Sum_probs=26.8
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
..+|+.|+...+-|...||-|.|..||.-
T Consensus 35 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQTVVLCGGCSSQ 63 (85)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCE
Confidence 45999999999999999999999999974
No 32
>PLN00209 ribosomal protein S27; Provisional
Probab=90.29 E-value=0.2 Score=40.11 Aligned_cols=29 Identities=21% Similarity=0.466 Sum_probs=26.8
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
..+|+.|+...+-|...||-|.|..||.-
T Consensus 36 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCE
Confidence 35999999999999999999999999974
No 33
>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=90.24 E-value=0.23 Score=34.94 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=21.4
Q ss_pred ceEeCCCCCccceEEeeee--eeeeccCCCc
Q 037763 313 ICKCGRCRHTRMSFISLRR--HIACLNCNQY 341 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT--Fv~C~~Cgnr 341 (354)
.|.|++||.. .||.+.+ ...|..|+++
T Consensus 18 g~~CP~Cg~~--~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 18 GFVCPHCGST--KHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCe--eeEEeCCCCeEECCCCCCc
Confidence 3889999999 5666655 7789999875
No 34
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=89.18 E-value=0.22 Score=41.61 Aligned_cols=30 Identities=17% Similarity=0.561 Sum_probs=23.0
Q ss_pred EeCCCCCccceEEeeeeeeeeccCCCcccccC
Q 037763 315 KCGRCRHTRMSFISLRRHIACLNCNQYWDSTN 346 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~~~ 346 (354)
.|++|.+.-+ |+.+....|-+|||.|--..
T Consensus 4 ~CP~C~seyt--Y~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYT--YHDGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcce--EecCCeeECccccccccccc
Confidence 6999987654 56666667999999996553
No 35
>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=89.07 E-value=0.17 Score=33.26 Aligned_cols=26 Identities=23% Similarity=0.571 Sum_probs=16.7
Q ss_pred eEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 314 CKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
+.|++||...- .....-|.|.+||+|
T Consensus 1 Y~C~~Cg~~~~--~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVE--LKPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE---BSTSSTSSBSSSS-S
T ss_pred CCCCcCCCeeE--cCCCCcEECCcCCCe
Confidence 46999987765 111127889999987
No 36
>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=88.86 E-value=0.22 Score=38.13 Aligned_cols=30 Identities=17% Similarity=0.521 Sum_probs=21.4
Q ss_pred ceEeCCCCCccceEEeeee------eeeeccCCCcc
Q 037763 313 ICKCGRCRHTRMSFISLRR------HIACLNCNQYW 342 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT------Fv~C~~CgnrW 342 (354)
.|+|..|+.|...-.-.|- +|+|-.|.++-
T Consensus 4 ~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp EEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EE
T ss_pred EEEcCCCCCccceeeCHHHHhCCeEEEECCCCccee
Confidence 5999999988876555553 99999999864
No 37
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.51 E-value=0.34 Score=32.51 Aligned_cols=26 Identities=15% Similarity=0.584 Sum_probs=18.7
Q ss_pred eEeCCCCCccceEEeee---e-----eeeeccCCCccc
Q 037763 314 CKCGRCRHTRMSFISLR---R-----HIACLNCNQYWD 343 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~Q---T-----Fv~C~~CgnrWk 343 (354)
+.|++|+.+ |++. . -|.|.+|||.|+
T Consensus 3 i~Cp~C~~~----y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAK----YEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCE----EeCCHHHCCCCCcEEECCCCCCEeC
Confidence 679999753 2222 1 899999999995
No 38
>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=87.92 E-value=0.32 Score=34.45 Aligned_cols=31 Identities=19% Similarity=0.442 Sum_probs=22.4
Q ss_pred EeCCCCCccceEEeee-e------eeeecc--CCCccccc
Q 037763 315 KCGRCRHTRMSFISLR-R------HIACLN--CNQYWDST 345 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~Q-T------Fv~C~~--CgnrWk~~ 345 (354)
+|+.||.+-....-.+ + ++.|.| ||+.|..-
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEE
Confidence 4999998765443222 1 999999 99999753
No 39
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=87.86 E-value=0.27 Score=36.67 Aligned_cols=30 Identities=30% Similarity=0.680 Sum_probs=25.1
Q ss_pred cccccceEeCCCCCccceEEeeee--eeeeccCCCc
Q 037763 308 KIISGICKCGRCRHTRMSFISLRR--HIACLNCNQY 341 (354)
Q Consensus 308 ~~~td~f~C~kC~~~k~ty~q~QT--Fv~C~~Cgnr 341 (354)
++.+-.+-||.||+++. ++. -+.|-+||+|
T Consensus 15 r~~~miYiCgdC~~en~----lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENT----LKRGDVIRCRECGYR 46 (62)
T ss_pred CcccEEEEecccccccc----ccCCCcEehhhcchH
Confidence 45778899999999986 454 7889999998
No 40
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.91 E-value=0.53 Score=31.72 Aligned_cols=31 Identities=16% Similarity=0.455 Sum_probs=20.8
Q ss_pred eEeCCCCCcc-ceEEeeee---eeeeccCCCcccc
Q 037763 314 CKCGRCRHTR-MSFISLRR---HIACLNCNQYWDS 344 (354)
Q Consensus 314 f~C~kC~~~k-~ty~q~QT---Fv~C~~CgnrWk~ 344 (354)
++|+.|+..- ..-.|+.. -|.|-.|||.|.+
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEeeC
Confidence 5899997531 22223322 9999999999975
No 41
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.32 E-value=0.55 Score=33.02 Aligned_cols=27 Identities=22% Similarity=0.557 Sum_probs=18.6
Q ss_pred ceEeCCCCCccceEEeeee-eeeeccCCCcc
Q 037763 313 ICKCGRCRHTRMSFISLRR-HIACLNCNQYW 342 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrW 342 (354)
.|.|++||....- ... -+.|.+||+|=
T Consensus 2 ~Y~C~~Cg~~~~~---~~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEI---KSKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeec---CCCCceECCCCCceE
Confidence 3789999985321 122 78899999873
No 42
>PRK10220 hypothetical protein; Provisional
Probab=86.05 E-value=0.44 Score=39.88 Aligned_cols=30 Identities=17% Similarity=0.584 Sum_probs=22.9
Q ss_pred EeCCCCCccceEEeeeeeeeeccCCCcccccC
Q 037763 315 KCGRCRHTRMSFISLRRHIACLNCNQYWDSTN 346 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~~~ 346 (354)
.|++|.+.-+ |+.+....|.+|+|.|.--.
T Consensus 5 ~CP~C~seyt--Y~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYT--YEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcce--EcCCCeEECCcccCcCCccc
Confidence 6999977654 56666667999999997654
No 43
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=86.00 E-value=0.75 Score=35.71 Aligned_cols=33 Identities=12% Similarity=0.368 Sum_probs=23.5
Q ss_pred EeCCCCCccce--EEeeee-eeeeccCCCcccccCC
Q 037763 315 KCGRCRHTRMS--FISLRR-HIACLNCNQYWDSTNP 347 (354)
Q Consensus 315 ~C~kC~~~k~t--y~q~QT-Fv~C~~CgnrWk~~~~ 347 (354)
.|++|+...+- |++-.. .++|..||++=.....
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 79999998852 223333 9999999997655443
No 44
>PHA00626 hypothetical protein
Probab=84.45 E-value=0.6 Score=34.58 Aligned_cols=27 Identities=15% Similarity=0.319 Sum_probs=16.3
Q ss_pred EeCCCCCccceE-----EeeeeeeeeccCCCcc
Q 037763 315 KCGRCRHTRMSF-----ISLRRHIACLNCNQYW 342 (354)
Q Consensus 315 ~C~kC~~~k~ty-----~q~QTFv~C~~CgnrW 342 (354)
.|++||+....- -|-|.| .|..||.++
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrY-kCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDY-VCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcce-EcCCCCCee
Confidence 488888764432 223334 488998765
No 45
>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=83.62 E-value=0.78 Score=38.09 Aligned_cols=35 Identities=14% Similarity=0.401 Sum_probs=27.7
Q ss_pred cccceEeCCCCCccceEEeeeeeeeeccCCCcccccC
Q 037763 310 ISGICKCGRCRHTRMSFISLRRHIACLNCNQYWDSTN 346 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~~~ 346 (354)
.+..=-|-=| ....|+|---.+.|.+||.||-...
T Consensus 32 ~va~daCeiC--~~~GY~q~g~~lvC~~C~~~~~~~~ 66 (102)
T PF10080_consen 32 RVAFDACEIC--GPKGYYQEGDQLVCKNCGVRFNLPT 66 (102)
T ss_pred EEEEEecccc--CCCceEEECCEEEEecCCCEEehhh
Confidence 4445569999 6778996666999999999997644
No 46
>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=83.33 E-value=1.5 Score=32.89 Aligned_cols=36 Identities=11% Similarity=0.355 Sum_probs=25.2
Q ss_pred EeCCCCCccce--EEeeee-eeeeccCCCcccccCCCcc
Q 037763 315 KCGRCRHTRMS--FISLRR-HIACLNCNQYWDSTNPGIE 350 (354)
Q Consensus 315 ~C~kC~~~k~t--y~q~QT-Fv~C~~CgnrWk~~~~~~~ 350 (354)
.|++|+.-.+- |.+-.. .|+|..||++=......++
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~~~~~ 49 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQEQQKDQSVS 49 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCccccCCcccc
Confidence 79999988763 112122 8999999998766555443
No 47
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=83.32 E-value=0.58 Score=33.75 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=23.5
Q ss_pred cccceEeCCCCCccceEEeeee--eeeeccCCCcc
Q 037763 310 ISGICKCGRCRHTRMSFISLRR--HIACLNCNQYW 342 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT--Fv~C~~CgnrW 342 (354)
.+-.++|.+||..- .++|. -+.|..||+|-
T Consensus 3 ~~~~Y~C~~Cg~~~---~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 3 AMMEYKCARCGREV---ELDQETRGIRCPYCGSRI 34 (49)
T ss_pred ceEEEEhhhcCCee---ehhhccCceeCCCCCcEE
Confidence 34568999999876 55665 99999999984
No 48
>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=83.23 E-value=0.4 Score=47.91 Aligned_cols=10 Identities=20% Similarity=0.763 Sum_probs=5.2
Q ss_pred eeeeccCCCc
Q 037763 332 HIACLNCNQY 341 (354)
Q Consensus 332 Fv~C~~Cgnr 341 (354)
|+.|.+||+|
T Consensus 285 FFkC~~C~~R 294 (344)
T PF09332_consen 285 FFKCKDCGNR 294 (344)
T ss_dssp EEE-T-TS-E
T ss_pred eEECCCCCCe
Confidence 7777777777
No 49
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=82.79 E-value=1 Score=46.55 Aligned_cols=162 Identities=12% Similarity=0.078 Sum_probs=103.3
Q ss_pred CCCChHHHHHHHHHHHHHHhhhhhhcCCCchhhhhh--hccCChHHHHHhhHHHHHHHhCCCchhhhhhHhhHHhhcCCC
Q 037763 172 LKCNDCIREIVREKLYGALSKVSEEAGHDNKEIIDQ--VRACDPIQVAISVESAIYENWGRSTGTYKFKYRCLLFNINDP 249 (354)
Q Consensus 172 ~~t~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~--~~~~~~~~lA~~IE~aif~~~~~~~~~Yk~k~Rsl~~NLKd~ 249 (354)
..+++.-|+|++.-|+..+...+.-...... ..+. ....+.+.....||.+.|+.+..+...|..+.+.+.++|+
T Consensus 238 ~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~-~~~~~~~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k-- 314 (464)
T KOG1886|consen 238 LLTGRSDRDKVLGKLLEVVWQNSCSTSEAKP-AGDQGSLWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLK-- 314 (464)
T ss_pred CCCCcccccccccccchhhccccccccccCC-CcccccCCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhc--
Confidence 4688999999999999998554443322200 0110 1123456788999999999987767899999999999998
Q ss_pred CCHHHHHHHhcC-CCCchhcccCChhhcCCHHH-----HHHHHHHHHHhcCCcCcccccccCCCcccccceEeCCCCCcc
Q 037763 250 TNREFRKKVLLG-RVKPEKIVNMTAKEMASDKM-----QLWYENLEKERAGTNGRIFSGIVSPKKIISGICKCGRCRHTR 323 (354)
Q Consensus 250 kNp~Lr~~vl~G-~isp~~lv~Ms~eEmAS~e~-----k~~re~~~~~~~~~~~~~~~~~~~~~~~~td~f~C~kC~~~k 323 (354)
.---|+.+.++| ++.|+-.+.|-+=++-+... +....... ...-++-.|..|=..-
T Consensus 315 ~~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~~~~~~~~~~d~~~------------------~l~~~~~~~~~~~~~~ 376 (464)
T KOG1886|consen 315 GQALLKPEPLNPGETKPEPKQELHPPSFPDGQSSPSSMKLNDDDYD------------------GLCVGLELTAGSLYLY 376 (464)
T ss_pred chhhhccccCCCcccCchhhhhccCCCCCCCccCccccccCchhHH------------------HHHHhhhhhccchhhh
Confidence 556788888888 48888888876655443321 11100000 0011111233333333
Q ss_pred ceEEeeee-------eeeeccCCCcccccCCCccccCC
Q 037763 324 MSFISLRR-------HIACLNCNQYWDSTNPGIEVLPI 354 (354)
Q Consensus 324 ~ty~q~QT-------Fv~C~~CgnrWk~~~~~~~~~~~ 354 (354)
|+-.|+|- ..-|..|+-+|..-+.+..++|+
T Consensus 377 ~g~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~~ 414 (464)
T KOG1886|consen 377 CGQEGLICAGHLPCPMLPEVKLSPVAAVHREGLLLAPS 414 (464)
T ss_pred cccccceeccccCCCCCCCcCcccccccchhhhcccce
Confidence 33333332 56688899999999998888774
No 50
>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=82.75 E-value=0.78 Score=30.89 Aligned_cols=26 Identities=15% Similarity=0.358 Sum_probs=20.1
Q ss_pred ceEeCCCCCccceEEeeee-eeeeccCCCc
Q 037763 313 ICKCGRCRHTRMSFISLRR-HIACLNCNQY 341 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-Fv~C~~Cgnr 341 (354)
.+.|+-|+.+ ++...- |..|..|||.
T Consensus 8 ~~~C~~C~~~---~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeEccCCEEEhhhCceE
Confidence 3569999998 444444 9999999984
No 51
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.02 E-value=0.91 Score=31.80 Aligned_cols=29 Identities=21% Similarity=0.486 Sum_probs=17.8
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
.|+|++||.. ..|.+.-+-++|..||++-
T Consensus 3 ~y~C~~CG~~-~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGRE-VELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCE-EEECCCCCceECCCCCCeE
Confidence 4788888774 3333332256788888753
No 52
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.49 E-value=1.1 Score=39.22 Aligned_cols=34 Identities=18% Similarity=0.568 Sum_probs=23.1
Q ss_pred cccceEeCCCCCccceEEeeee-e-----eeeccCCCcccc
Q 037763 310 ISGICKCGRCRHTRMSFISLRR-H-----IACLNCNQYWDS 344 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT-F-----v~C~~CgnrWk~ 344 (354)
....|.|+.|+.+ -++...+. . ++|.+||..-..
T Consensus 96 ~~~~Y~Cp~C~~~-y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSK-YTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCE-eeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 5678999999843 33333333 4 889999986544
No 53
>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=78.79 E-value=1.8 Score=34.37 Aligned_cols=40 Identities=13% Similarity=0.495 Sum_probs=20.1
Q ss_pred cccceEeCCCCCccceEEeeee-----eeeeccCCCcccccCCCc
Q 037763 310 ISGICKCGRCRHTRMSFISLRR-----HIACLNCNQYWDSTNPGI 349 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT-----Fv~C~~CgnrWk~~~~~~ 349 (354)
-...|.|+-|+..++----+-. .+.|..||-.|.+--+.+
T Consensus 19 l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L 63 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPL 63 (81)
T ss_dssp -SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS
T ss_pred CCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCcc
Confidence 4578999999977765444422 999999999988764433
No 54
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.30 E-value=2 Score=29.37 Aligned_cols=28 Identities=29% Similarity=0.676 Sum_probs=19.7
Q ss_pred EeCCCCCccceEEeeee--eeeeccCCCccc
Q 037763 315 KCGRCRHTRMSFISLRR--HIACLNCNQYWD 343 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QT--Fv~C~~CgnrWk 343 (354)
+|++|+.. ..-+++.. .-.|..||--|-
T Consensus 1 ~CP~C~~~-l~~~~~~~~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRLGDVEIDVCPSCGGIWF 30 (41)
T ss_pred CcCCCCcc-cceEEECCEEEEECCCCCeEEc
Confidence 59999884 44344444 667999999884
No 55
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=75.36 E-value=1.4 Score=38.00 Aligned_cols=30 Identities=13% Similarity=0.176 Sum_probs=24.6
Q ss_pred ceEeCCCCCccceEEeeee-eeeeccCCCccccc
Q 037763 313 ICKCGRCRHTRMSFISLRR-HIACLNCNQYWDST 345 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk~~ 345 (354)
...|+.||.| ||.|.. -++|..||..|-..
T Consensus 9 Kr~Cp~cg~k---FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSK---FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCcc---ccccCCCCccCCCcCCccCcc
Confidence 3479999865 888876 88999999999654
No 56
>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=74.67 E-value=1.3 Score=37.10 Aligned_cols=30 Identities=23% Similarity=0.606 Sum_probs=24.7
Q ss_pred ceEeCCCCCccceEEeeee-eeeeccCCCccccc
Q 037763 313 ICKCGRCRHTRMSFISLRR-HIACLNCNQYWDST 345 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk~~ 345 (354)
...|+.||.| ||-|.. =++|-.||.-|-.-
T Consensus 9 KR~Cp~CG~k---FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAK---FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcch---hccCCCCCccCCCCCCccCcc
Confidence 3479999865 899888 77899999999765
No 57
>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=73.28 E-value=2.1 Score=38.10 Aligned_cols=34 Identities=18% Similarity=0.361 Sum_probs=22.7
Q ss_pred ccccceEeCCCCCccceEEeeee-eeeeccCCCccc
Q 037763 309 IISGICKCGRCRHTRMSFISLRR-HIACLNCNQYWD 343 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk 343 (354)
.....|.|++|+ .+-|+.+... .++|.+||..-.
T Consensus 105 ~~~~~Y~Cp~c~-~r~tf~eA~~~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMC-VRFTFNEAMELNFTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCC-cEeeHHHHHHcCCcCCCCCCEee
Confidence 366789999998 3333333333 778999997643
No 58
>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=72.04 E-value=3.2 Score=35.61 Aligned_cols=27 Identities=19% Similarity=0.485 Sum_probs=22.1
Q ss_pred EeCCCCCccceEEeee-e-eeeeccCCCc
Q 037763 315 KCGRCRHTRMSFISLR-R-HIACLNCNQY 341 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~Q-T-Fv~C~~Cgnr 341 (354)
.|+.|++..|.+.--. + |..|..||.+
T Consensus 95 lC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 95 LCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 6999999998885432 2 9999999975
No 59
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=71.29 E-value=3.6 Score=31.30 Aligned_cols=35 Identities=11% Similarity=0.277 Sum_probs=28.3
Q ss_pred eEeCCCCCccceEEeeee--eeeeccCCCcccccCCC
Q 037763 314 CKCGRCRHTRMSFISLRR--HIACLNCNQYWDSTNPG 348 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QT--Fv~C~~CgnrWk~~~~~ 348 (354)
-.|+-||....+..+.-. +|.|..||-+|.+....
T Consensus 7 KPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~~~~te 43 (64)
T PRK09710 7 KPCPFCGCPSVTVKAISGYYRAKCNGCESRTGYGGSE 43 (64)
T ss_pred cCCCCCCCceeEEEecCceEEEEcCCCCcCcccccCH
Confidence 369999999988876433 69999999999887654
No 60
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=70.41 E-value=3.4 Score=33.35 Aligned_cols=31 Identities=16% Similarity=0.382 Sum_probs=22.9
Q ss_pred ccceEeCCCCCccceEEeeee-eeeeccCCCccc
Q 037763 311 SGICKCGRCRHTRMSFISLRR-HIACLNCNQYWD 343 (354)
Q Consensus 311 td~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk 343 (354)
-+.+.|+.||.+ +..-+-+ .-.|..||+.|.
T Consensus 33 ~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVCPFCGRT--TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcCCCCCCc--ceeeeccCeEEcCCCCCeec
Confidence 345689999988 5555555 888999997663
No 61
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=68.36 E-value=3.9 Score=33.78 Aligned_cols=35 Identities=29% Similarity=0.548 Sum_probs=22.7
Q ss_pred cccceEeCCCCCccce--EEeeeeeeeeccCCCcccc
Q 037763 310 ISGICKCGRCRHTRMS--FISLRRHIACLNCNQYWDS 344 (354)
Q Consensus 310 ~td~f~C~kC~~~k~t--y~q~QTFv~C~~CgnrWk~ 344 (354)
....|.|+.||..... .......+.|.+||..--.
T Consensus 18 lpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 4579999999954332 1111128999999976443
No 62
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=67.30 E-value=5.2 Score=33.61 Aligned_cols=28 Identities=21% Similarity=0.528 Sum_probs=22.1
Q ss_pred eEeCCCCCccceEEee-ee-eeeeccCCCc
Q 037763 314 CKCGRCRHTRMSFISL-RR-HIACLNCNQY 341 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~-QT-Fv~C~~Cgnr 341 (354)
..|+.|++..|.+.-- .+ |..|..||.+
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 4799999999877432 22 9999999975
No 63
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=67.01 E-value=2.9 Score=37.23 Aligned_cols=35 Identities=17% Similarity=0.306 Sum_probs=25.8
Q ss_pred cccceEeCCCCCccceEEeee-----e-eeeeccCCCcccc
Q 037763 310 ISGICKCGRCRHTRMSFISLR-----R-HIACLNCNQYWDS 344 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~Q-----T-Fv~C~~CgnrWk~ 344 (354)
..=.|+|..|+.|.+.-.-.| | ||+|-.|.|+-..
T Consensus 76 m~l~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~Hli 116 (165)
T KOG3277|consen 76 MQLAYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLI 116 (165)
T ss_pred eEEEEEeeccCCccccccChhhhhCceEEEECCCCccceee
Confidence 345699999999988433333 3 9999999987543
No 64
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=66.98 E-value=4.3 Score=29.73 Aligned_cols=29 Identities=14% Similarity=0.390 Sum_probs=22.2
Q ss_pred cceEeCCCCCccceEEeee-------eeeeeccCCC
Q 037763 312 GICKCGRCRHTRMSFISLR-------RHIACLNCNQ 340 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~Q-------TFv~C~~Cgn 340 (354)
.+..|+-||.....+.+-- .+|.|.+||-
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 3557999988877776643 3799999997
No 65
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=66.04 E-value=5.5 Score=34.58 Aligned_cols=28 Identities=18% Similarity=0.481 Sum_probs=22.4
Q ss_pred ceEeCCCCCccceEEeeee---eeeeccCCCc
Q 037763 313 ICKCGRCRHTRMSFISLRR---HIACLNCNQY 341 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT---Fv~C~~Cgnr 341 (354)
-..|+.|+...|.+. ... |..|..||.+
T Consensus 97 yVlC~~C~sPdT~l~-k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNRPDTRII-KEGRVSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCCCCcEEE-EeCCeEEEecccCCCC
Confidence 347999999998764 433 8999999976
No 66
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=65.77 E-value=5.5 Score=34.80 Aligned_cols=28 Identities=21% Similarity=0.472 Sum_probs=22.4
Q ss_pred eEeCCCCCccceEEe-eee-eeeeccCCCc
Q 037763 314 CKCGRCRHTRMSFIS-LRR-HIACLNCNQY 341 (354)
Q Consensus 314 f~C~kC~~~k~ty~q-~QT-Fv~C~~Cgnr 341 (354)
..|+.||+..|.+.- -++ |..|..||.+
T Consensus 103 VlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 479999999988742 123 9999999986
No 67
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.22 E-value=4 Score=37.07 Aligned_cols=34 Identities=15% Similarity=0.391 Sum_probs=22.6
Q ss_pred cccceEeCCCCCccceEEee-eeeeeeccCCCcccc
Q 037763 310 ISGICKCGRCRHTRMSFISL-RRHIACLNCNQYWDS 344 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~-QTFv~C~~CgnrWk~ 344 (354)
....|.|++|+.+ -|+.+. ...++|..||..-..
T Consensus 114 ~~~~Y~Cp~C~~r-ytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIR-FTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcE-EeHHHHhhcCCcCCCCCCCCee
Confidence 5578999999833 333332 236789999976543
No 68
>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=64.09 E-value=6.7 Score=26.13 Aligned_cols=25 Identities=32% Similarity=0.790 Sum_probs=17.2
Q ss_pred ceEeCCCCCccceEEeeee-----eeeeccCCC
Q 037763 313 ICKCGRCRHTRMSFISLRR-----HIACLNCNQ 340 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-----Fv~C~~Cgn 340 (354)
.|+|..||.. |..++. -+.|-.||.
T Consensus 5 ~y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 5789998873 333332 677888886
No 69
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=63.87 E-value=4.4 Score=32.07 Aligned_cols=27 Identities=22% Similarity=0.573 Sum_probs=24.6
Q ss_pred eEeCCCCCccceEEeeeeeeeeccCCC
Q 037763 314 CKCGRCRHTRMSFISLRRHIACLNCNQ 340 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QTFv~C~~Cgn 340 (354)
.+|+.|-+--|-|.-.||-|.|.+|+-
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~ 61 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCST 61 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCce
Confidence 389999999999999999999999973
No 70
>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=63.16 E-value=5.3 Score=29.36 Aligned_cols=31 Identities=16% Similarity=0.409 Sum_probs=20.3
Q ss_pred ceEeCCCCCccceEEe--eeeeeeeccCCCcccc
Q 037763 313 ICKCGRCRHTRMSFIS--LRRHIACLNCNQYWDS 344 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q--~QTFv~C~~CgnrWk~ 344 (354)
+|+|+.||+.- .+.. .--.|.|-.||-....
T Consensus 2 ~~~CP~CG~~i-ev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAEI-ELENPELGELVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCEE-ecCCCccCCEEeCCCCCCEEEE
Confidence 58999999832 1111 1118999999976554
No 71
>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=63.04 E-value=6 Score=30.73 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=18.0
Q ss_pred ceEeCCCCC-----ccceEEee-----ee--eeeeccCCC
Q 037763 313 ICKCGRCRH-----TRMSFISL-----RR--HIACLNCNQ 340 (354)
Q Consensus 313 ~f~C~kC~~-----~k~ty~q~-----QT--Fv~C~~Cgn 340 (354)
..-|.+||. ..|+..-. +. .++|+.|||
T Consensus 46 r~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 46 RTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred cccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 345999997 45676666 23 999999996
No 72
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=62.13 E-value=5.2 Score=34.10 Aligned_cols=13 Identities=46% Similarity=1.058 Sum_probs=11.2
Q ss_pred eeeeccCCCcccc
Q 037763 332 HIACLNCNQYWDS 344 (354)
Q Consensus 332 Fv~C~~CgnrWk~ 344 (354)
.+.|.+||+.|=+
T Consensus 60 ~I~C~~C~~~wG~ 72 (123)
T PF11648_consen 60 KIHCKNCGQDWGI 72 (123)
T ss_dssp EEEETSTSBEEEE
T ss_pred EEEcCCCChHhhh
Confidence 6889999999954
No 73
>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=60.99 E-value=4.8 Score=30.18 Aligned_cols=31 Identities=26% Similarity=0.501 Sum_probs=22.2
Q ss_pred cccceEeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 310 ISGICKCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
-|.+ .|+.||...-. .--+.-.+|.+||..|
T Consensus 26 ~TSq-~C~~CG~~~~~-~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 26 YTSQ-TCPRCGHRNKK-RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCcc-CccCccccccc-ccccceEEcCCCCCEE
Confidence 3555 69999998887 2222377799999874
No 74
>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=60.71 E-value=3.9 Score=41.01 Aligned_cols=35 Identities=26% Similarity=0.680 Sum_probs=19.1
Q ss_pred cccccceEeCCCCCccceEEeeeeeeeeccCCC-ccc
Q 037763 308 KIISGICKCGRCRHTRMSFISLRRHIACLNCNQ-YWD 343 (354)
Q Consensus 308 ~~~td~f~C~kC~~~k~ty~q~QTFv~C~~Cgn-rWk 343 (354)
.+.--.|+|+.|+.|-++|.-+- -..|.+||. +|.
T Consensus 280 ~a~KRFFkC~~C~~Rt~sl~r~P-~~~C~~Cg~~~we 315 (344)
T PF09332_consen 280 DAVKRFFKCKDCGNRTISLERLP-KKHCSNCGSSKWE 315 (344)
T ss_dssp EEE-EEEE-T-TS-EEEESSSS---S--TTT-S---E
T ss_pred eeeeeeEECCCCCCeeeecccCC-CCCCCcCCcCcee
Confidence 35667899999999999886554 488999994 564
No 75
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=57.98 E-value=6.9 Score=38.68 Aligned_cols=36 Identities=17% Similarity=0.406 Sum_probs=26.4
Q ss_pred cceEeCCCCCccc-eEEeeee-----eeeeccCCCcccccCC
Q 037763 312 GICKCGRCRHTRM-SFISLRR-----HIACLNCNQYWDSTNP 347 (354)
Q Consensus 312 d~f~C~kC~~~k~-ty~q~QT-----Fv~C~~CgnrWk~~~~ 347 (354)
..-.|+-||+.-+ ++-...+ |..|.-|+..|.|-|-
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~ 227 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRV 227 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCc
Confidence 3457999999874 3333322 9999999999998653
No 76
>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=56.12 E-value=7.9 Score=37.51 Aligned_cols=34 Identities=21% Similarity=0.462 Sum_probs=17.4
Q ss_pred eEeCCCCCccc-eEEee-----eeeeeeccCCCcccccCC
Q 037763 314 CKCGRCRHTRM-SFISL-----RRHIACLNCNQYWDSTNP 347 (354)
Q Consensus 314 f~C~kC~~~k~-ty~q~-----QTFv~C~~CgnrWk~~~~ 347 (354)
-.|+-||+.-. ++..- +.|..|.-||..|.|-|-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~ 212 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRI 212 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TT
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCC
Confidence 47999998743 33222 239999999999998663
No 77
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=55.11 E-value=25 Score=28.61 Aligned_cols=29 Identities=17% Similarity=0.450 Sum_probs=19.8
Q ss_pred cceEeCCCCCccceEEeeee-eeeeccCCCcc
Q 037763 312 GICKCGRCRHTRMSFISLRR-HIACLNCNQYW 342 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrW 342 (354)
..+.|+.||+..+ .-.-+ .-.|..||..|
T Consensus 34 ~ky~Cp~Cgk~~v--kR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 34 AKYTCPFCGKTSV--KRVATGIWKCKKCGKKF 63 (90)
T ss_dssp S-BEESSSSSSEE--EEEETTEEEETTTTEEE
T ss_pred CCCcCCCCCCcee--EEeeeEEeecCCCCCEE
Confidence 4578999998773 23333 77899998765
No 78
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=53.69 E-value=10 Score=31.61 Aligned_cols=33 Identities=15% Similarity=0.392 Sum_probs=23.4
Q ss_pred eEeCCCCC-----ccceEEeeee--eeeeccCCCcccccC
Q 037763 314 CKCGRCRH-----TRMSFISLRR--HIACLNCNQYWDSTN 346 (354)
Q Consensus 314 f~C~kC~~-----~k~ty~q~QT--Fv~C~~CgnrWk~~~ 346 (354)
.-|.+|.. .+|.+.-..- -|||++||.--+|..
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p~ 96 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYPY 96 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEecc
Confidence 35999987 4555543332 899999998777653
No 79
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=53.55 E-value=11 Score=34.76 Aligned_cols=29 Identities=17% Similarity=0.445 Sum_probs=22.7
Q ss_pred ceEeCCCCCccceEEe-eee-eeeeccCCCc
Q 037763 313 ICKCGRCRHTRMSFIS-LRR-HIACLNCNQY 341 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q-~QT-Fv~C~~Cgnr 341 (354)
--.|+.|+...|.+.- -++ |..|..||.+
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3479999999988843 133 9999999975
No 80
>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=52.49 E-value=21 Score=31.63 Aligned_cols=36 Identities=11% Similarity=-0.027 Sum_probs=22.6
Q ss_pred HHHHHh-cCCCCchhcccCChhhcCCHHHHHHHHHHHHH
Q 037763 254 FRKKVL-LGRVKPEKIVNMTAKEMASDKMQLWYENLEKE 291 (354)
Q Consensus 254 Lr~~vl-~G~isp~~lv~Ms~eEmAS~e~k~~re~~~~~ 291 (354)
+...|+ .|+++.++|+.+. .|-..++++.-.++...
T Consensus 19 Vl~aL~~~~~~tdEeLa~~L--gi~~~~VRk~L~~L~e~ 55 (158)
T TIGR00373 19 VLFSLGIKGEFTDEEISLEL--GIKLNEVRKALYALYDA 55 (158)
T ss_pred HHHHHhccCCCCHHHHHHHH--CCCHHHHHHHHHHHHHC
Confidence 444555 7888888877666 45556666665555543
No 81
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=50.85 E-value=23 Score=37.76 Aligned_cols=62 Identities=18% Similarity=0.197 Sum_probs=47.5
Q ss_pred hHHHHHHHHHHHHHHhhhhhhcCCCchhhhhhhccCChHHHHHhhHHHHHHHhCCCchhhhhhHhhHHhhcCCCCCHHH
Q 037763 176 DCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKFKYRCLLFNINDPTNREF 254 (354)
Q Consensus 176 d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~~~~lA~~IE~aif~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~L 254 (354)
-+.|.+++.-|.+.|....... -.-|..+|++||.+.+ +..+|-..+--||..++|-.|..-
T Consensus 9 ~kFRq~vIsried~l~~n~q~~----------------~k~a~~mE~hVF~K~~-tkDEYl~lvAkli~h~~d~s~~ks 70 (742)
T KOG4274|consen 9 PKFRQHVISRIEDELRKNGQAH----------------SKSAKDMESHVFLKAK-TKDEYLSLVAKLIIHFRDISNKKS 70 (742)
T ss_pred HHHHHHHHHHhhhhhhhhhhcc----------------CcchHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHhhhhhhh
Confidence 5789999999999998632211 1457899999998875 346899999999999998776533
No 82
>PRK05978 hypothetical protein; Provisional
Probab=50.57 E-value=9 Score=33.93 Aligned_cols=31 Identities=16% Similarity=0.555 Sum_probs=23.2
Q ss_pred eEeCCCCCccc--eEEeeeeeeeeccCCCcccccC
Q 037763 314 CKCGRCRHTRM--SFISLRRHIACLNCNQYWDSTN 346 (354)
Q Consensus 314 f~C~kC~~~k~--ty~q~QTFv~C~~CgnrWk~~~ 346 (354)
-+|++||+-+- +|..+ --.|-.||..+.+-+
T Consensus 34 grCP~CG~G~LF~g~Lkv--~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKP--VDHCAACGEDFTHHR 66 (148)
T ss_pred CcCCCCCCCccccccccc--CCCccccCCccccCC
Confidence 37999999887 33222 567999999988764
No 83
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=50.45 E-value=15 Score=36.95 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=24.3
Q ss_pred EeCCCCCccceEEeeee-eeeeccCCCcccc
Q 037763 315 KCGRCRHTRMSFISLRR-HIACLNCNQYWDS 344 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk~ 344 (354)
+|..|+..+..|--+-. ..+|++|-.+=+-
T Consensus 21 ~CfeC~a~NPQWvSvsyGIfICLECSG~HRg 51 (386)
T KOG0704|consen 21 KCFECGAPNPQWVSVSYGIFICLECSGKHRG 51 (386)
T ss_pred ceeecCCCCCCeEeecccEEEEEecCCcccc
Confidence 79999999997776666 7789999866543
No 84
>PRK03954 ribonuclease P protein component 4; Validated
Probab=50.28 E-value=12 Score=32.12 Aligned_cols=31 Identities=23% Similarity=0.466 Sum_probs=22.0
Q ss_pred EeCCCCCc-----cceEEeee-----eeeeeccCCCccccc
Q 037763 315 KCGRCRHT-----RMSFISLR-----RHIACLNCNQYWDST 345 (354)
Q Consensus 315 ~C~kC~~~-----k~ty~q~Q-----TFv~C~~CgnrWk~~ 345 (354)
-|.+|..- +|++.... ..++|+.||+.=+|.
T Consensus 66 ~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 66 YCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred HhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeec
Confidence 48888665 56655444 288999999987764
No 85
>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=50.04 E-value=34 Score=27.92 Aligned_cols=30 Identities=13% Similarity=0.300 Sum_probs=20.4
Q ss_pred ccceEeCCCCCccceEEeeee-eeeeccCCCcc
Q 037763 311 SGICKCGRCRHTRMSFISLRR-HIACLNCNQYW 342 (354)
Q Consensus 311 td~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrW 342 (354)
-..+.|+.||+.. ..-.-| .-.|..||..|
T Consensus 33 ~a~y~CpfCgk~~--vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 33 KAKYVCPFCGKKT--VKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred hcCccCCCCCCCc--eEEEeeEEEEcCCCCCEE
Confidence 3456899998544 334444 78899998765
No 86
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=49.73 E-value=13 Score=27.57 Aligned_cols=25 Identities=24% Similarity=0.812 Sum_probs=21.1
Q ss_pred ccccceEeCCCCCccceEEeeeeeeeeccCC
Q 037763 309 IISGICKCGRCRHTRMSFISLRRHIACLNCN 339 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~QTFv~C~~Cg 339 (354)
....+..|+.||..+-. ...|.+||
T Consensus 23 ~~~~l~~C~~CG~~~~~------H~vC~~CG 47 (57)
T PRK12286 23 KAPGLVECPNCGEPKLP------HRVCPSCG 47 (57)
T ss_pred cCCcceECCCCCCccCC------eEECCCCC
Confidence 35678899999998876 77899999
No 87
>PRK11827 hypothetical protein; Provisional
Probab=49.38 E-value=14 Score=27.74 Aligned_cols=39 Identities=23% Similarity=0.360 Sum_probs=26.1
Q ss_pred cceEeCCCCCccceEEeeeeeeeeccCCCcccccCCCcccc
Q 037763 312 GICKCGRCRHTRMSFISLRRHIACLNCNQYWDSTNPGIEVL 352 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~~~~~~~~~ 352 (354)
+...|+.||+.= .|.+--.-.+|..||-.+-. +++|-||
T Consensus 7 eILaCP~ckg~L-~~~~~~~~Lic~~~~laYPI-~dgIPVl 45 (60)
T PRK11827 7 EIIACPVCNGKL-WYNQEKQELICKLDNLAFPL-RDGIPVL 45 (60)
T ss_pred hheECCCCCCcC-eEcCCCCeEECCccCeeccc-cCCcccc
Confidence 456899998754 45432224559999877665 6777665
No 88
>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=49.11 E-value=16 Score=32.24 Aligned_cols=34 Identities=21% Similarity=0.449 Sum_probs=26.0
Q ss_pred CcccccceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 307 KKIISGICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 307 ~~~~td~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
+....+.|.|-+||..-. |+.-...--|..||+.
T Consensus 106 E~~g~G~l~C~~Cg~~~~-~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 106 EVVGPGTLVCENCGHEVE-LTHPERLPPCPKCGHT 139 (146)
T ss_pred cEecCceEecccCCCEEE-ecCCCcCCCCCCCCCC
Confidence 445789999999987655 4444448889999986
No 89
>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=48.64 E-value=15 Score=26.43 Aligned_cols=27 Identities=19% Similarity=0.435 Sum_probs=18.8
Q ss_pred EeCCCCCccceEE----eeee--eeeeccCCCc
Q 037763 315 KCGRCRHTRMSFI----SLRR--HIACLNCNQY 341 (354)
Q Consensus 315 ~C~kC~~~k~ty~----q~QT--Fv~C~~Cgnr 341 (354)
.|+-||++...+. ..+. ++.|..||..
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 6999999777543 2222 4489999976
No 90
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=48.22 E-value=9.6 Score=38.61 Aligned_cols=34 Identities=15% Similarity=0.269 Sum_probs=26.2
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCCcccccCCC
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQYWDSTNPG 348 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~~~~~ 348 (354)
.+.|..|+.+...+. +.--.|..||.+|...+|-
T Consensus 244 ~~~C~~c~~~~~~~~--~~~~~C~~c~~~~~~~GPl 277 (382)
T PRK04338 244 VYYCPKCLYREEVEG--LPPEECPVCGGKFGTAGPL 277 (382)
T ss_pred EEECCCCCcEEEecC--CCCCCCCCCCCcceecccc
Confidence 688999998766443 2245799999999998874
No 91
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=48.05 E-value=11 Score=26.48 Aligned_cols=29 Identities=14% Similarity=0.367 Sum_probs=17.5
Q ss_pred eCCCCCccceEEe-e-ee-eeeeccCCCcccccC
Q 037763 316 CGRCRHTRMSFIS-L-RR-HIACLNCNQYWDSTN 346 (354)
Q Consensus 316 C~kC~~~k~ty~q-~-QT-Fv~C~~CgnrWk~~~ 346 (354)
|+.||.-- |.. . +. +..|..||+.|+...
T Consensus 3 Cp~Cg~~l--~~~~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 3 CPKCGNML--IPKEGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCcc--ccccCCCCCEEECCcCCCeEECCC
Confidence 78887732 222 2 22 566888888777643
No 92
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=47.82 E-value=20 Score=26.98 Aligned_cols=38 Identities=24% Similarity=0.529 Sum_probs=28.5
Q ss_pred cceEeCCCCCccceEEe-eeeeeeeccCCCcccccCCCcccc
Q 037763 312 GICKCGRCRHTRMSFIS-LRRHIACLNCNQYWDSTNPGIEVL 352 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q-~QTFv~C~~CgnrWk~~~~~~~~~ 352 (354)
+..-|+-|+++ -.|.| -| -..|..| ++|+=-+++|-+|
T Consensus 7 eiLaCP~~kg~-L~~~~~~~-~L~c~~~-~~aYpI~dGIPvl 45 (60)
T COG2835 7 EILACPVCKGP-LVYDEEKQ-ELICPRC-KLAYPIRDGIPVL 45 (60)
T ss_pred eeeeccCcCCc-ceEeccCC-EEEeccc-CceeecccCcccc
Confidence 56789999999 33332 33 5569999 6899999999876
No 93
>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=47.21 E-value=16 Score=25.11 Aligned_cols=25 Identities=28% Similarity=0.801 Sum_probs=16.1
Q ss_pred ceEeCCCCCccceEEeeee-----eeeeccCCC
Q 037763 313 ICKCGRCRHTRMSFISLRR-----HIACLNCNQ 340 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-----Fv~C~~Cgn 340 (354)
.|+|..||.. |..+|. -+.|-.||.
T Consensus 5 ey~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHE---FEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCE---EEEEEEcCCCCCCcCCCCCC
Confidence 4788888753 233333 777888876
No 94
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=46.68 E-value=27 Score=37.38 Aligned_cols=25 Identities=16% Similarity=0.639 Sum_probs=20.2
Q ss_pred EeCCCCCccceEEeeee-eeeeccCC
Q 037763 315 KCGRCRHTRMSFISLRR-HIACLNCN 339 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QT-Fv~C~~Cg 339 (354)
.|..|+.+..+|-=+-. .+.|+.|.
T Consensus 25 ~CADCgs~~P~WASiNlGIFICi~CS 50 (648)
T PLN03119 25 RCINCNSLGPQYVCTTFWTFVCMACS 50 (648)
T ss_pred ccccCCCCCCCceeeccceEEeccch
Confidence 79999999999866654 44599996
No 95
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.61 E-value=12 Score=27.01 Aligned_cols=27 Identities=19% Similarity=0.245 Sum_probs=16.9
Q ss_pred EeCCCCCccceEEeeeeeeeeccCCCccc
Q 037763 315 KCGRCRHTRMSFISLRRHIACLNCNQYWD 343 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QTFv~C~~CgnrWk 343 (354)
-|++||.. -..+-.....|..||..+.
T Consensus 22 fCP~Cg~~--~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 22 FCPRCGSG--FMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred cCcCCCcc--hheccCCcEECCCcCCEEe
Confidence 59999874 1122223667999987653
No 96
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=44.49 E-value=23 Score=23.35 Aligned_cols=29 Identities=17% Similarity=0.444 Sum_probs=20.4
Q ss_pred cceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 312 GICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
+...|..|+....-+ .-|-...|..||.-
T Consensus 2 ~~~~C~~C~~~~i~~-~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVN-KEDDYEVCIFCGSS 30 (33)
T ss_pred CceEcCCCCCCeEEE-ecCCeEEcccCCcE
Confidence 345899999888533 44447889999853
No 97
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=43.97 E-value=14 Score=30.94 Aligned_cols=28 Identities=14% Similarity=0.497 Sum_probs=20.4
Q ss_pred ccccceEeCCCCCccceEEee-eeeeeeccCCC
Q 037763 309 IISGICKCGRCRHTRMSFISL-RRHIACLNCNQ 340 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~-QTFv~C~~Cgn 340 (354)
.....+.|..|| .++.. +.|..|-.||.
T Consensus 66 ~vp~~~~C~~Cg----~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 66 YKPAQAWCWDCS----QVVEIHQHDAQCPHCHG 94 (113)
T ss_pred eeCcEEEcccCC----CEEecCCcCccCcCCCC
Confidence 466889999999 33333 45667999994
No 98
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=43.60 E-value=9.5 Score=27.56 Aligned_cols=31 Identities=19% Similarity=0.509 Sum_probs=21.8
Q ss_pred eEeCCCCCccceEE-eeee--eeeeccCCCcccc
Q 037763 314 CKCGRCRHTRMSFI-SLRR--HIACLNCNQYWDS 344 (354)
Q Consensus 314 f~C~kC~~~k~ty~-q~QT--Fv~C~~CgnrWk~ 344 (354)
..|..|+...+... .-.. -+.|+.||-+|+-
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k 37 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKK 37 (52)
T ss_pred CCcCCCCCCCCCccccCCCCCCcEeecccHHHHH
Confidence 36999998777432 1111 4789999999974
No 99
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=42.81 E-value=34 Score=28.16 Aligned_cols=52 Identities=17% Similarity=0.090 Sum_probs=42.0
Q ss_pred CCccHHHHHHHHHHhhcCCCcHHhhhcccceeeccccccCCCHHHHHHHhhh
Q 037763 24 GGAEEAQCLDALDQLKNCSITYQLLVSTQVARHLVPMLKHPCEKIQLFAIEL 75 (354)
Q Consensus 24 ~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~Ak~L 75 (354)
..+.+++++++|.+|-+-|....+|+.-+.-.-+++||++-++..+...-.+
T Consensus 43 ~~~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~i 94 (98)
T PF14726_consen 43 PVPMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEI 94 (98)
T ss_pred CCccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHH
Confidence 4478999999999999999999999977755669999988777666554443
No 100
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=42.63 E-value=18 Score=26.00 Aligned_cols=12 Identities=25% Similarity=0.885 Sum_probs=8.3
Q ss_pred eeeeccCCCccc
Q 037763 332 HIACLNCNQYWD 343 (354)
Q Consensus 332 Fv~C~~CgnrWk 343 (354)
+..|..||..|-
T Consensus 48 ~~fC~~C~~~~H 59 (64)
T smart00647 48 FSFCFRCKVPWH 59 (64)
T ss_pred CeECCCCCCcCC
Confidence 555777887774
No 101
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=42.21 E-value=14 Score=42.84 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=9.7
Q ss_pred cccceEeCCCCCc
Q 037763 310 ISGICKCGRCRHT 322 (354)
Q Consensus 310 ~td~f~C~kC~~~ 322 (354)
+-..|+|++||..
T Consensus 664 EV~~rkCPkCG~~ 676 (1337)
T PRK14714 664 EVGRRRCPSCGTE 676 (1337)
T ss_pred EEEEEECCCCCCc
Confidence 3456899999875
No 102
>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=42.01 E-value=20 Score=25.30 Aligned_cols=25 Identities=28% Similarity=0.747 Sum_probs=17.3
Q ss_pred ceEeCCCCCccceEEeeee-----eeeeccCCC
Q 037763 313 ICKCGRCRHTRMSFISLRR-----HIACLNCNQ 340 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-----Fv~C~~Cgn 340 (354)
.|+|.+||.. |..+|- -+.|-.||.
T Consensus 5 ey~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHR---FEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCE---eEEEEecCCCCCCCCCCCCC
Confidence 5889999863 333333 567999997
No 103
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=40.99 E-value=31 Score=34.27 Aligned_cols=28 Identities=21% Similarity=0.591 Sum_probs=23.0
Q ss_pred eEeCCCCCccceEEeeee-eeeeccCCCc
Q 037763 314 CKCGRCRHTRMSFISLRR-HIACLNCNQY 341 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QT-Fv~C~~Cgnr 341 (354)
-+|..||....+|.-+=- +++|++|-.-
T Consensus 21 k~CaDCga~~P~W~S~nlGvfiCi~Cagv 49 (319)
T COG5347 21 KKCADCGAPNPTWASVNLGVFLCIDCAGV 49 (319)
T ss_pred CccccCCCCCCceEecccCeEEEeecchh
Confidence 389999999988776665 8899999743
No 104
>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=40.85 E-value=13 Score=36.66 Aligned_cols=34 Identities=18% Similarity=0.480 Sum_probs=25.2
Q ss_pred ceEeCCCCCccc-eEEee----ee--eeeeccCCCcccccC
Q 037763 313 ICKCGRCRHTRM-SFISL----RR--HIACLNCNQYWDSTN 346 (354)
Q Consensus 313 ~f~C~kC~~~k~-ty~q~----QT--Fv~C~~CgnrWk~~~ 346 (354)
.-.|+-||+.-+ ++... +. |..|.-|+..|.|-|
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R 224 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVR 224 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccC
Confidence 447999999875 23222 22 999999999999865
No 105
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=40.81 E-value=55 Score=26.62 Aligned_cols=30 Identities=13% Similarity=0.234 Sum_probs=19.7
Q ss_pred ccceEeCCCCCccceEEeeee-eeeeccCCCcc
Q 037763 311 SGICKCGRCRHTRMSFISLRR-HIACLNCNQYW 342 (354)
Q Consensus 311 td~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrW 342 (354)
-..+.|+.||+..+ .-.-+ .-.|..||..|
T Consensus 34 ~a~y~CpfCgk~~v--kR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 34 HAKYFCPFCGKHAV--KRQAVGIWRCKGCKKTV 64 (90)
T ss_pred hCCccCCCCCCCce--eeeeeEEEEcCCCCCEE
Confidence 34578999985543 33333 77888888754
No 106
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=40.46 E-value=60 Score=26.43 Aligned_cols=30 Identities=13% Similarity=0.403 Sum_probs=19.9
Q ss_pred ccceEeCCCCCccceEEeeee-eeeeccCCCcc
Q 037763 311 SGICKCGRCRHTRMSFISLRR-HIACLNCNQYW 342 (354)
Q Consensus 311 td~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrW 342 (354)
-..+.|+.|++..+ .-.-| .-.|..||..|
T Consensus 34 ~a~y~CpfCgk~~v--kR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 34 RAKHVCPVCGRPKV--KRVGTGIWECRKCGAKF 64 (90)
T ss_pred hcCccCCCCCCCce--EEEEEEEEEcCCCCCEE
Confidence 34578999975544 33334 78899998765
No 107
>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=39.80 E-value=19 Score=30.24 Aligned_cols=29 Identities=21% Similarity=0.423 Sum_probs=20.8
Q ss_pred ccccceEeCCCCCccceEEee-eeeeeeccCCCc
Q 037763 309 IISGICKCGRCRHTRMSFISL-RRHIACLNCNQY 341 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~-QTFv~C~~Cgnr 341 (354)
.....+.|..|| .++.. +.|..|-.||..
T Consensus 66 ~~p~~~~C~~Cg----~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCS----EEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCC----CEEecCCcCccCcCCcCC
Confidence 466789999999 23333 347889999953
No 108
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.94 E-value=19 Score=30.28 Aligned_cols=29 Identities=21% Similarity=0.608 Sum_probs=21.0
Q ss_pred ccccceEeCCCCCccceEEeee-e-eeeeccCCCc
Q 037763 309 IISGICKCGRCRHTRMSFISLR-R-HIACLNCNQY 341 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~Q-T-Fv~C~~Cgnr 341 (354)
.....+.|..||+ ++... . +..|-.||..
T Consensus 66 ~~p~~~~C~~Cg~----~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQ----YVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCC----eeecCCccCCcCcCcCCC
Confidence 4668899999994 44443 3 4779999953
No 109
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.88 E-value=13 Score=31.30 Aligned_cols=29 Identities=14% Similarity=0.212 Sum_probs=20.2
Q ss_pred ccccceEeCCCCCccceEEee-ee-eeeeccCCCc
Q 037763 309 IISGICKCGRCRHTRMSFISL-RR-HIACLNCNQY 341 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~-QT-Fv~C~~Cgnr 341 (354)
.....|.|..|| .++.+ +. |..|-.||..
T Consensus 67 ~vp~~~~C~~Cg----~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCS----HVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCC----CccccCCccCCcCcCCCCC
Confidence 466789999999 33333 23 5569999964
No 110
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.76 E-value=18 Score=39.85 Aligned_cols=27 Identities=15% Similarity=0.316 Sum_probs=17.6
Q ss_pred CCchhcccCChhhcCC-----HHH-HHHHHHHH
Q 037763 263 VKPEKIVNMTAKEMAS-----DKM-QLWYENLE 289 (354)
Q Consensus 263 isp~~lv~Ms~eEmAS-----~e~-k~~re~~~ 289 (354)
++.-.++.|..+.+.. ..+ ++.++.++
T Consensus 386 ~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~ 418 (730)
T COG1198 386 LPRVEIIDMRKEPLETGRSLSPALLEAIRKTLE 418 (730)
T ss_pred CCcceEEeccccccccCccCCHHHHHHHHHHHh
Confidence 5666788999888877 343 44444554
No 111
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=38.57 E-value=17 Score=42.47 Aligned_cols=32 Identities=19% Similarity=0.365 Sum_probs=25.2
Q ss_pred ccccceEeCCCCCccceEEeeeeeeeeccCCCcccccCC
Q 037763 309 IISGICKCGRCRHTRMSFISLRRHIACLNCNQYWDSTNP 347 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~~~~ 347 (354)
.+-..|+|++||.--- +..|..||-++.....
T Consensus 670 vei~~~~Cp~Cg~~~~-------~~~Cp~CG~~~~~~~~ 701 (1627)
T PRK14715 670 IEIAFFKCPKCGKVGL-------YHVCPFCGTRVELKPY 701 (1627)
T ss_pred EEEEeeeCCCCCCccc-------cccCcccCCcccCCCc
Confidence 4567899999998755 8899999998765544
No 112
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=38.33 E-value=14 Score=30.69 Aligned_cols=24 Identities=25% Similarity=0.737 Sum_probs=17.5
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCCcccc
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQYWDS 344 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~ 344 (354)
-|.|++||+++| =+.| -|+-+|-+
T Consensus 74 ~~PC~~C~S~KC-------G~~C-R~nRkw~y 97 (103)
T PF14949_consen 74 HYPCPKCGSRKC-------GPEC-RCNRKWVY 97 (103)
T ss_pred cccCCCCCCCcc-------Chhh-CcCCceee
Confidence 488999999999 4555 35666653
No 113
>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=37.78 E-value=17 Score=22.41 Aligned_cols=14 Identities=14% Similarity=0.299 Sum_probs=10.7
Q ss_pred cccccceEeCCCCC
Q 037763 308 KIISGICKCGRCRH 321 (354)
Q Consensus 308 ~~~td~f~C~kC~~ 321 (354)
......|.|++||.
T Consensus 11 r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 11 REQAVPFPCPNCGF 24 (24)
T ss_pred cccCceEeCCCCCC
Confidence 33567899999984
No 114
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=37.01 E-value=34 Score=32.94 Aligned_cols=15 Identities=13% Similarity=0.521 Sum_probs=12.8
Q ss_pred eeeeccCCCcccccC
Q 037763 332 HIACLNCNQYWDSTN 346 (354)
Q Consensus 332 Fv~C~~CgnrWk~~~ 346 (354)
++.|.+|+|.|+=+.
T Consensus 155 ef~C~~C~h~F~G~~ 169 (278)
T PF15135_consen 155 EFHCPKCRHNFRGFA 169 (278)
T ss_pred eeecccccccchhhh
Confidence 899999999998553
No 115
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=36.23 E-value=15 Score=22.55 Aligned_cols=22 Identities=23% Similarity=0.415 Sum_probs=12.2
Q ss_pred EeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 315 KCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
.|+.||...- ..+-.|.+||.+
T Consensus 4 ~Cp~Cg~~~~-----~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEID-----PDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcCC-----cccccChhhCCC
Confidence 5777776321 115557777754
No 116
>PRK12495 hypothetical protein; Provisional
Probab=35.63 E-value=16 Score=34.34 Aligned_cols=33 Identities=15% Similarity=0.310 Sum_probs=24.6
Q ss_pred CcccccceEeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 307 KKIISGICKCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 307 ~~~~td~f~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
.+.....|.|..||..=-.| .--+.|..|+...
T Consensus 36 ~gatmsa~hC~~CG~PIpa~---pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 36 QGATMTNAHCDECGDPIFRH---DGQEFCPTCQQPV 68 (226)
T ss_pred hhcccchhhcccccCcccCC---CCeeECCCCCCcc
Confidence 45677788999999887633 4477799998653
No 117
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=35.52 E-value=28 Score=25.52 Aligned_cols=22 Identities=27% Similarity=0.896 Sum_probs=17.9
Q ss_pred cceEeCCCCCccceEEeeeeeeeeccCC
Q 037763 312 GICKCGRCRHTRMSFISLRRHIACLNCN 339 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QTFv~C~~Cg 339 (354)
.+..|+.||.-+-. -..|.+||
T Consensus 25 ~l~~c~~cg~~~~~------H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP------HRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEEST------TSBCTTTB
T ss_pred ceeeeccCCCEecc------cEeeCCCC
Confidence 77899999976554 67799998
No 118
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=35.17 E-value=48 Score=26.37 Aligned_cols=68 Identities=19% Similarity=0.234 Sum_probs=43.4
Q ss_pred CCChHHHHHHHHHHHHHHhhhhhhcCCCchhhhhhhccCChHHHHHhhHHHHHHHhCCCchhhhhhHhhHHhhcC
Q 037763 173 KCNDCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKFKYRCLLFNIN 247 (354)
Q Consensus 173 ~t~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~~~~lA~~IE~aif~~~~~~~~~Yk~k~Rsl~~NLK 247 (354)
.-+..+|+..+.-|..++-.......-.|+ ...+....|..||..+|+.-. +..+|-..+--.+++++
T Consensus 9 ~vt~~lR~hlV~KLv~aI~P~pdp~a~~d~------rm~~l~~yarkvE~~~fe~A~-sreeYY~llA~kiy~iq 76 (81)
T PF02172_consen 9 SVTPDLRNHLVHKLVQAIFPTPDPNAMNDP------RMKNLIEYARKVEKDMFETAQ-SREEYYHLLAEKIYKIQ 76 (81)
T ss_dssp CT-HHHHHHHHHHHHHHHS-SSSCCCCCSH------HHHHHHHHHHHHHHHHHHC-S-SHHHHHHHHHHHHHHHH
T ss_pred HcCHHHHHHHHHHHHHhhCCCCChhhhhhH------HHHHHHHHHHHHHHHHHHHhc-cHHHHHHHHHHHHHHHH
Confidence 345789999999999998753211111111 112346889999999998753 34678888877777774
No 119
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.78 E-value=24 Score=36.39 Aligned_cols=33 Identities=21% Similarity=0.386 Sum_probs=22.2
Q ss_pred ccccceEeCCCCCccceEEeeee------eeeeccCCCc
Q 037763 309 IISGICKCGRCRHTRMSFISLRR------HIACLNCNQY 341 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~QT------Fv~C~~Cgnr 341 (354)
+....|.|+-|+++=+..--+|- ++.|.+||--
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHHHhhcccCceEEEecCCCc
Confidence 36678999999875433322232 7889999853
No 120
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=33.83 E-value=38 Score=34.27 Aligned_cols=26 Identities=19% Similarity=0.584 Sum_probs=21.2
Q ss_pred EeCCCCCccceEEeeee-eeeeccCCC
Q 037763 315 KCGRCRHTRMSFISLRR-HIACLNCNQ 340 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QT-Fv~C~~Cgn 340 (354)
.|..|+.++.+|--+=. .+.|++|..
T Consensus 24 ~CaDCga~nPtWASvn~GIFLCl~CSG 50 (395)
T PLN03114 24 ICFDCNAKNPTWASVTYGIFLCIDCSA 50 (395)
T ss_pred cCccCCCCCCCceeeccceeehhhhhH
Confidence 79999999998877744 566999963
No 121
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.21 E-value=22 Score=33.73 Aligned_cols=22 Identities=27% Similarity=0.597 Sum_probs=16.8
Q ss_pred EeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 315 KCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
.|+.||. .-+..+.|..||+.|
T Consensus 311 ~C~~cg~------~~~r~~~C~~cg~~~ 332 (364)
T COG0675 311 TCPCCGH------LSGRLFKCPRCGFVH 332 (364)
T ss_pred cccccCC------ccceeEECCCCCCee
Confidence 7999999 223367799999865
No 122
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=33.11 E-value=25 Score=35.26 Aligned_cols=31 Identities=19% Similarity=0.658 Sum_probs=24.0
Q ss_pred cccceEeCCCCCccceEEeeee-eeeeccCCCcccccCC
Q 037763 310 ISGICKCGRCRHTRMSFISLRR-HIACLNCNQYWDSTNP 347 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk~~~~ 347 (354)
.+-.++|.+|| |+.++ |-.|..| ++|-..-|
T Consensus 351 ~~~~YRC~~CG------F~a~~l~W~CPsC-~~W~TikP 382 (389)
T COG2956 351 RKPRYRCQNCG------FTAHTLYWHCPSC-RAWETIKP 382 (389)
T ss_pred hcCCceecccC------CcceeeeeeCCCc-ccccccCC
Confidence 56789999998 45556 8889999 78876555
No 123
>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=32.95 E-value=9.8 Score=25.33 Aligned_cols=28 Identities=21% Similarity=0.532 Sum_probs=14.6
Q ss_pred eCCCCCccceE-Eeeee--eeeeccCCCccc
Q 037763 316 CGRCRHTRMSF-ISLRR--HIACLNCNQYWD 343 (354)
Q Consensus 316 C~kC~~~k~ty-~q~QT--Fv~C~~CgnrWk 343 (354)
|..|+-.++.. +..-. ...|+.||-+|+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~k 31 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYK 31 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHH
Confidence 66777766532 22222 448999998886
No 124
>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=32.79 E-value=34 Score=25.10 Aligned_cols=24 Identities=21% Similarity=0.696 Sum_probs=19.6
Q ss_pred cccceEeCCCCCccceEEeeeeeeeeccCC
Q 037763 310 ISGICKCGRCRHTRMSFISLRRHIACLNCN 339 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QTFv~C~~Cg 339 (354)
...+..|+.||+-+-. ...|.+||
T Consensus 23 ~p~l~~C~~cG~~~~~------H~vc~~cG 46 (55)
T TIGR01031 23 APTLVVCPNCGEFKLP------HRVCPSCG 46 (55)
T ss_pred CCcceECCCCCCcccC------eeECCccC
Confidence 4677889999997765 66799999
No 125
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=32.64 E-value=11 Score=36.80 Aligned_cols=30 Identities=23% Similarity=0.566 Sum_probs=21.6
Q ss_pred ceEeCCCCCccceE-Eeeee-eeeeccCCCcccc
Q 037763 313 ICKCGRCRHTRMSF-ISLRR-HIACLNCNQYWDS 344 (354)
Q Consensus 313 ~f~C~kC~~~k~ty-~q~QT-Fv~C~~CgnrWk~ 344 (354)
..+|++|++- -| .++.- |-.|.+|||.++.
T Consensus 26 ~~~c~~c~~~--~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 26 WTKCPKCGQV--LYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred eeECCCCcch--hhHHHHHhhCCCCCCCCCcCcC
Confidence 6799999753 23 23333 7889999999885
No 126
>PRK11032 hypothetical protein; Provisional
Probab=32.61 E-value=25 Score=31.50 Aligned_cols=33 Identities=21% Similarity=0.427 Sum_probs=24.9
Q ss_pred cccccceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 308 KIISGICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 308 ~~~td~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
-...+.+.|-+||..-+ |+.-...--|.+||+.
T Consensus 119 vvg~G~LvC~~Cg~~~~-~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 119 VVGLGNLVCEKCHHHLA-FYTPEVLPLCPKCGHD 151 (160)
T ss_pred eeecceEEecCCCCEEE-ecCCCcCCCCCCCCCC
Confidence 35678999999987654 4444447789999985
No 127
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=32.57 E-value=30 Score=35.75 Aligned_cols=27 Identities=19% Similarity=0.485 Sum_probs=24.1
Q ss_pred ceEeCCCCCccceEEeeee-eeeeccCC
Q 037763 313 ICKCGRCRHTRMSFISLRR-HIACLNCN 339 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-Fv~C~~Cg 339 (354)
.-.|..|+-++.||.-+=. ++.|+.|-
T Consensus 23 NKvCFDCgAknPtWaSVTYGIFLCiDCS 50 (454)
T KOG0706|consen 23 NKVCFDCGAKNPTWASVTYGIFLCIDCS 50 (454)
T ss_pred CceecccCCCCCCceeecceEEEEEecc
Confidence 3389999999999999887 88999997
No 128
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=31.92 E-value=13 Score=28.13 Aligned_cols=28 Identities=14% Similarity=0.458 Sum_probs=18.5
Q ss_pred EeCCCCCccce--EEeeee-eeeeccCCCcc
Q 037763 315 KCGRCRHTRMS--FISLRR-HIACLNCNQYW 342 (354)
Q Consensus 315 ~C~kC~~~k~t--y~q~QT-Fv~C~~CgnrW 342 (354)
.|+-|..-.+- |.+=+. .|+|..||+.-
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 69999765541 111122 99999999864
No 129
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=31.76 E-value=41 Score=23.73 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=18.4
Q ss_pred ccceEeCCCCCccceEEeeee--eeeeccC
Q 037763 311 SGICKCGRCRHTRMSFISLRR--HIACLNC 338 (354)
Q Consensus 311 td~f~C~kC~~~k~ty~q~QT--Fv~C~~C 338 (354)
++++.|+.||.+-...+.-.. +..|.++
T Consensus 3 ~g~l~C~~CG~~m~~~~~~~~~~yy~C~~~ 32 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKRKGKYRYYRCSNR 32 (58)
T ss_pred CCcEEcccCCcEeEEEECCCCceEEEcCCC
Confidence 578899999988665433222 6666554
No 130
>PF12773 DZR: Double zinc ribbon
Probab=31.67 E-value=20 Score=25.08 Aligned_cols=32 Identities=16% Similarity=0.190 Sum_probs=20.3
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCC----cccccC
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQ----YWDSTN 346 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~Cgn----rWk~~~ 346 (354)
.--|+.||..-. .+.+..+.|..||. .|+||.
T Consensus 12 ~~fC~~CG~~l~--~~~~~~~~C~~Cg~~~~~~~~fC~ 47 (50)
T PF12773_consen 12 AKFCPHCGTPLP--PPDQSKKICPNCGAENPPNAKFCP 47 (50)
T ss_pred ccCChhhcCChh--hccCCCCCCcCCcCCCcCCcCccC
Confidence 334888887766 22333777888884 566663
No 131
>PHA02942 putative transposase; Provisional
Probab=31.35 E-value=25 Score=35.63 Aligned_cols=29 Identities=24% Similarity=0.600 Sum_probs=19.6
Q ss_pred ccceEeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 311 SGICKCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 311 td~f~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
|.. .|+.||...-.. -+....|.+||+.+
T Consensus 324 TSq-~Cs~CG~~~~~l--~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSV-SCPKCGHKMVEI--AHRYFHCPSCGYEN 352 (383)
T ss_pred CCc-cCCCCCCccCcC--CCCEEECCCCCCEe
Confidence 444 699999865321 12267799999865
No 132
>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=31.25 E-value=25 Score=39.69 Aligned_cols=26 Identities=23% Similarity=0.643 Sum_probs=21.7
Q ss_pred ccccceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 309 IISGICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
.+..+++|++||..-- +.+|-.||-+
T Consensus 621 vev~~RKCPkCG~yTl-------k~rCP~CG~~ 646 (1095)
T TIGR00354 621 VEIAIRKCPQCGKESF-------WLKCPVCGEL 646 (1095)
T ss_pred EEEEEEECCCCCcccc-------cccCCCCCCc
Confidence 4678999999998744 8889999976
No 133
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.91 E-value=18 Score=27.16 Aligned_cols=34 Identities=15% Similarity=0.257 Sum_probs=20.2
Q ss_pred CcccccceEeCCCCCccceE----EeeeeeeeeccCCC
Q 037763 307 KKIISGICKCGRCRHTRMSF----ISLRRHIACLNCNQ 340 (354)
Q Consensus 307 ~~~~td~f~C~kC~~~k~ty----~q~QTFv~C~~Cgn 340 (354)
....-..|.|+.||.-.-.- +++-+-.+|-+||-
T Consensus 21 p~e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 21 PGETAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred cCCceeEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 34456789999999532211 11222667888884
No 134
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=30.85 E-value=21 Score=26.84 Aligned_cols=31 Identities=16% Similarity=0.290 Sum_probs=20.1
Q ss_pred cccceEeCCCCCc---cceE-EeeeeeeeeccCCC
Q 037763 310 ISGICKCGRCRHT---RMSF-ISLRRHIACLNCNQ 340 (354)
Q Consensus 310 ~td~f~C~kC~~~---k~ty-~q~QTFv~C~~Cgn 340 (354)
.-..|.|+.||+. +|.. +++-.-++|-+||.
T Consensus 22 ~~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 22 KAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred ccCEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence 3578999999975 2322 22222677888884
No 135
>PLN02976 amine oxidase
Probab=30.64 E-value=45 Score=39.89 Aligned_cols=50 Identities=14% Similarity=0.187 Sum_probs=41.2
Q ss_pred HHHHHHHHhhcCCCcHHhhhcccceeeccc-cccCCCHHHHHHHhhhh--ccc
Q 037763 30 QCLDALDQLKNCSITYQLLVSTQVARHLVP-MLKHPCEKIQLFAIELI--WTI 79 (354)
Q Consensus 30 ~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~-Lrkh~~~~I~~~Ak~Li--WK~ 79 (354)
-+...|+-|--++.++..++..+||++|.. +--|.+.+|+.+|+.|+ |-.
T Consensus 1302 l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~ 1354 (1713)
T PLN02976 1302 LLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLE 1354 (1713)
T ss_pred HHHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHH
Confidence 334455556667778888899999999965 78899999999999999 999
No 136
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=30.52 E-value=27 Score=34.07 Aligned_cols=31 Identities=23% Similarity=0.321 Sum_probs=22.2
Q ss_pred cccceEeCCCCCccceEEeeeeeeeeccCCCcc
Q 037763 310 ISGICKCGRCRHTRMSFISLRRHIACLNCNQYW 342 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QTFv~C~~CgnrW 342 (354)
.+-.| ||+||++. .+++=.+=..|.+|||+-
T Consensus 109 ~~~RF-Cg~CG~~~-~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRF-CGRCGTKT-YPREGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcC-CCCCCCcC-ccccCceeeeCCCCCCcc
Confidence 44555 99998864 344445578899999874
No 137
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=30.29 E-value=9.6 Score=27.41 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=22.4
Q ss_pred cceEeCCCCCccceEEeeee-----------eeeeccCCCcc
Q 037763 312 GICKCGRCRHTRMSFISLRR-----------HIACLNCNQYW 342 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QT-----------Fv~C~~CgnrW 342 (354)
+.|+|+=|++ ..++..+.. -|.|--|..++
T Consensus 1 ~~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 1 DSFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRV 41 (54)
T ss_pred CCcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhh
Confidence 4689999999 766666654 67899998753
No 138
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.78 E-value=35 Score=29.49 Aligned_cols=31 Identities=19% Similarity=0.548 Sum_probs=20.2
Q ss_pred cccceEeCCCCCccceEEee-------------------eeeeeeccCCCc
Q 037763 310 ISGICKCGRCRHTRMSFISL-------------------RRHIACLNCNQY 341 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~-------------------QTFv~C~~Cgnr 341 (354)
....+.|..||.. ....+. +.|..|-.||.+
T Consensus 67 ~p~~~~C~~CG~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 67 EEAVLKCRNCGNE-WSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred cceEEECCCCCCE-EecccccccccccccccccccccccccCcCCcCCCCC
Confidence 4578999999933 112211 237889999964
No 139
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=29.64 E-value=27 Score=25.08 Aligned_cols=12 Identities=25% Similarity=0.946 Sum_probs=7.9
Q ss_pred eeeeccCCCccc
Q 037763 332 HIACLNCNQYWD 343 (354)
Q Consensus 332 Fv~C~~CgnrWk 343 (354)
+..|..|+..|-
T Consensus 48 ~~fC~~C~~~~H 59 (64)
T PF01485_consen 48 TEFCFKCGEPWH 59 (64)
T ss_dssp SEECSSSTSESC
T ss_pred CcCccccCcccC
Confidence 445777777774
No 140
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=29.47 E-value=12 Score=27.30 Aligned_cols=29 Identities=31% Similarity=0.808 Sum_probs=20.8
Q ss_pred eCCCCCccceEEeeee-----eeeeccCCCcccccC
Q 037763 316 CGRCRHTRMSFISLRR-----HIACLNCNQYWDSTN 346 (354)
Q Consensus 316 C~kC~~~k~ty~q~QT-----Fv~C~~CgnrWk~~~ 346 (354)
|..|+-.++. |+.. -..|+.||-+|+--+
T Consensus 2 C~~C~~~~Tp--~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 2 CSNCGTTTTP--LWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCc--ccccCCCCcchHHHHHHHHHHhcC
Confidence 7888887763 3332 678999999997543
No 141
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=29.40 E-value=37 Score=28.50 Aligned_cols=28 Identities=18% Similarity=0.670 Sum_probs=19.9
Q ss_pred EeCCCCCccceEEeeeeeeeeccCCCcccc
Q 037763 315 KCGRCRHTRMSFISLRRHIACLNCNQYWDS 344 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~ 344 (354)
.|++|.+.- + |+--+...|-+|+|.|--
T Consensus 5 ~cp~c~sEy-t-Yed~~~~~cpec~~ew~~ 32 (112)
T COG2824 5 PCPKCNSEY-T-YEDGGQLICPECAHEWNE 32 (112)
T ss_pred CCCccCCce-E-EecCceEeCchhcccccc
Confidence 588886542 2 444456679999999973
No 142
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=29.33 E-value=24 Score=30.68 Aligned_cols=13 Identities=31% Similarity=0.879 Sum_probs=6.9
Q ss_pred eeeeccCCCcccc
Q 037763 332 HIACLNCNQYWDS 344 (354)
Q Consensus 332 Fv~C~~CgnrWk~ 344 (354)
+|+|++||..+|.
T Consensus 72 ~i~clecGk~~k~ 84 (132)
T PF05443_consen 72 YIICLECGKKFKT 84 (132)
T ss_dssp -EE-TBT--EESB
T ss_pred eeEEccCCcccch
Confidence 8888888887664
No 143
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=29.05 E-value=30 Score=35.02 Aligned_cols=36 Identities=22% Similarity=0.432 Sum_probs=24.2
Q ss_pred ceEeCCCCCccceEEeeeeeeeeccCCCcccccCCC
Q 037763 313 ICKCGRCRHTRMSFISLRRHIACLNCNQYWDSTNPG 348 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~~~~~ 348 (354)
.+.|..|+.+..--...+.--.|..||.+|...+|-
T Consensus 233 v~~C~~c~~~~~~~~~~~~~~~C~~c~~~~~~~GPl 268 (374)
T TIGR00308 233 TYHCSRCLHNKPVNGISQRKGRCKECGGEYHLAGPL 268 (374)
T ss_pred EEECCCcccccccccccCCCCCCCCCCCcceeecCc
Confidence 678999977654211111145699999999988874
No 144
>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=28.11 E-value=15 Score=30.80 Aligned_cols=37 Identities=24% Similarity=0.412 Sum_probs=23.7
Q ss_pred ceEeCCCCCccceEEeeee-eeeeccCCCcccccCCCc
Q 037763 313 ICKCGRCRHTRMSFISLRR-HIACLNCNQYWDSTNPGI 349 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk~~~~~~ 349 (354)
--.|..||....+|--+-. .+.|..|....+-.+.-|
T Consensus 13 N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~i 50 (116)
T PF01412_consen 13 NKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHI 50 (116)
T ss_dssp CTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT
T ss_pred cCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccc
Confidence 3479999999999988876 556999987766665433
No 145
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=27.71 E-value=71 Score=26.65 Aligned_cols=23 Identities=17% Similarity=0.462 Sum_probs=15.5
Q ss_pred cccceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 310 ISGICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
....+.|..||.... .+..|+||
T Consensus 39 G~~~~~C~~Cg~~~~---------~~~SCk~R 61 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKI---------VYNSCKNR 61 (111)
T ss_pred CcceeecCCCCceEE---------ecCcccCc
Confidence 445678999988753 35556666
No 146
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=27.49 E-value=36 Score=32.58 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=20.6
Q ss_pred ccceEeCCCCCccceEEeeeeeeeeccCCCcccc
Q 037763 311 SGICKCGRCRHTRMSFISLRRHIACLNCNQYWDS 344 (354)
Q Consensus 311 td~f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk~ 344 (354)
+-.| |++||+.- ....-..-..|..||++.+-
T Consensus 98 ~~~f-C~~CG~~~-~~~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 98 SHRF-CGYCGHPM-HPSKTEWAMLCPHCRERYYP 129 (256)
T ss_pred cCcc-ccccCCCC-eecCCceeEECCCCCCEECC
Confidence 3444 99999863 33333345669999976653
No 147
>PHA00616 hypothetical protein
Probab=27.36 E-value=19 Score=25.42 Aligned_cols=14 Identities=21% Similarity=0.375 Sum_probs=9.2
Q ss_pred ceEeCCCCCccceE
Q 037763 313 ICKCGRCRHTRMSF 326 (354)
Q Consensus 313 ~f~C~kC~~~k~ty 326 (354)
+|+|++||..=..+
T Consensus 1 pYqC~~CG~~F~~~ 14 (44)
T PHA00616 1 MYQCLRCGGIFRKK 14 (44)
T ss_pred CCccchhhHHHhhH
Confidence 37888888754433
No 148
>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=27.23 E-value=33 Score=33.17 Aligned_cols=34 Identities=21% Similarity=0.472 Sum_probs=18.9
Q ss_pred ceEeCCCCCccceEEee---ee-----eeeeccCCCcccccC
Q 037763 313 ICKCGRCRHTRMSFISL---RR-----HIACLNCNQYWDSTN 346 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~---QT-----Fv~C~~CgnrWk~~~ 346 (354)
.++|+.||..+-.=+.. .. .-+|..||.-||...
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence 44688888776542221 11 778999999999765
No 149
>PRK00420 hypothetical protein; Validated
Probab=26.32 E-value=36 Score=28.78 Aligned_cols=28 Identities=11% Similarity=0.275 Sum_probs=19.3
Q ss_pred eEeCCCCCccceEEeeeeeeeeccCCCccc
Q 037763 314 CKCGRCRHTRMSFISLRRHIACLNCNQYWD 343 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk 343 (354)
-.|+.||..-..+ -+.-+.|.+||..-.
T Consensus 24 ~~CP~Cg~pLf~l--k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFEL--KDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceec--CCCceECCCCCCeee
Confidence 4799999544433 445777999998543
No 150
>PLN03131 hypothetical protein; Provisional
Probab=25.84 E-value=87 Score=33.99 Aligned_cols=27 Identities=19% Similarity=0.581 Sum_probs=20.7
Q ss_pred eEeCCCCCccceEEeeee-eeeeccCCC
Q 037763 314 CKCGRCRHTRMSFISLRR-HIACLNCNQ 340 (354)
Q Consensus 314 f~C~kC~~~k~ty~q~QT-Fv~C~~Cgn 340 (354)
-.|..|+.+..+|--+-. .+.|+.|..
T Consensus 24 k~CADCga~~P~WASiNlGIFICi~CSG 51 (705)
T PLN03131 24 RRCINCNSLGPQFVCTNFWTFICMTCSG 51 (705)
T ss_pred CccccCCCCCCCeeEeccceEEchhchh
Confidence 379999999998866544 445999963
No 151
>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=25.64 E-value=43 Score=35.70 Aligned_cols=26 Identities=19% Similarity=0.394 Sum_probs=20.1
Q ss_pred hcCCCCchhcccCChhhcCCHHHHHH
Q 037763 259 LLGRVKPEKIVNMTAKEMASDKMQLW 284 (354)
Q Consensus 259 l~G~isp~~lv~Ms~eEmAS~e~k~~ 284 (354)
+.|.=+|..|..++..-+.-||+-+.
T Consensus 121 ~~ga~S~~~l~s~~~r~~~~DEvD~~ 146 (557)
T PF05876_consen 121 LVGANSPSNLRSRPARYLLLDEVDRY 146 (557)
T ss_pred EEeCCCCcccccCCcCEEEEechhhc
Confidence 44566888898888888888887665
No 152
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=25.56 E-value=31 Score=30.03 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=12.7
Q ss_pred eeeeccCCCccccc
Q 037763 332 HIACLNCNQYWDST 345 (354)
Q Consensus 332 Fv~C~~CgnrWk~~ 345 (354)
|+.|.+||.+|.|-
T Consensus 99 ~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 99 YYKCPNCQSKYTFL 112 (147)
T ss_pred EEECcCCCCEeeHH
Confidence 99999999999873
No 153
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.46 E-value=36 Score=37.17 Aligned_cols=17 Identities=6% Similarity=0.071 Sum_probs=10.8
Q ss_pred cCCCCchhcccCChhhc
Q 037763 260 LGRVKPEKIVNMTAKEM 276 (354)
Q Consensus 260 ~G~isp~~lv~Ms~eEm 276 (354)
...++.-+++.|..+++
T Consensus 327 ~~~~P~v~~vd~~~~~~ 343 (665)
T PRK14873 327 RARAPRVRALGDSGLAL 343 (665)
T ss_pred cCCCCeEEEEeCchhhh
Confidence 44556667888876544
No 154
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=24.55 E-value=33 Score=24.70 Aligned_cols=13 Identities=23% Similarity=0.851 Sum_probs=8.4
Q ss_pred eeeeccCCCcccc
Q 037763 332 HIACLNCNQYWDS 344 (354)
Q Consensus 332 Fv~C~~CgnrWk~ 344 (354)
.-.|..|||.|+.
T Consensus 28 ~W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 28 WWKCPKCGHEWKA 40 (55)
T ss_pred EEECCCCCCeeEc
Confidence 4456677777764
No 155
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=24.33 E-value=41 Score=31.35 Aligned_cols=31 Identities=23% Similarity=0.540 Sum_probs=25.6
Q ss_pred CCCCccceEEeeee---------eeeeccCCCcccccCCC
Q 037763 318 RCRHTRMSFISLRR---------HIACLNCNQYWDSTNPG 348 (354)
Q Consensus 318 kC~~~k~ty~q~QT---------Fv~C~~CgnrWk~~~~~ 348 (354)
+|-+..+.||+-.. .--|-.||..|-|-.+.
T Consensus 195 k~t~iptyYylyrVgGnSlAqek~r~CPsC~k~Wqlk~~i 234 (256)
T COG5595 195 KCTGIPTYYYLYRVGGNSLAQEKYRCCPSCGKDWQLKNPI 234 (256)
T ss_pred HHhCCCceEEEEEecCchhhhhccCCCCcccccceeccch
Confidence 68888898888765 77899999999887664
No 156
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=24.15 E-value=39 Score=19.35 Aligned_cols=9 Identities=33% Similarity=0.844 Sum_probs=5.8
Q ss_pred eEeCCCCCc
Q 037763 314 CKCGRCRHT 322 (354)
Q Consensus 314 f~C~kC~~~ 322 (354)
|+|+.|++.
T Consensus 1 y~C~~C~~~ 9 (23)
T PF00096_consen 1 YKCPICGKS 9 (23)
T ss_dssp EEETTTTEE
T ss_pred CCCCCCCCc
Confidence 567777654
No 157
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=23.66 E-value=33 Score=34.74 Aligned_cols=38 Identities=16% Similarity=0.367 Sum_probs=22.2
Q ss_pred cccceEeCCCCCccceEEeeee-eeeeccCCCcccccCCC
Q 037763 310 ISGICKCGRCRHTRMSFISLRR-HIACLNCNQYWDSTNPG 348 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk~~~~~ 348 (354)
.--.+.|..|+.++... .++. -..|..||.+|...+|-
T Consensus 237 ~G~v~~C~~C~~~~~~~-~~~~~~~~c~~cg~~~~~~GPl 275 (377)
T PF02005_consen 237 LGYVYYCPSCGYREEVK-GLQKLKSKCPECGSKLHISGPL 275 (377)
T ss_dssp EEEEEEETTT--EECCT--GCC--CEETTT-SCCCEEEEE
T ss_pred eeEEEECCCcccccccc-CccccCCcCCCCCCccceecCc
Confidence 34568999996432211 1111 27899999999988763
No 158
>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=23.17 E-value=1.1e+02 Score=22.71 Aligned_cols=34 Identities=12% Similarity=0.196 Sum_probs=22.7
Q ss_pred cccceEeCCCCCccceEEeeee-------eeeeccCCCccc
Q 037763 310 ISGICKCGRCRHTRMSFISLRR-------HIACLNCNQYWD 343 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT-------Fv~C~~CgnrWk 343 (354)
....-+|..|+..-......|+ -.+|..|+-.=+
T Consensus 12 ~~~~~~C~~C~G~G~~~~~~~~~~~~~~~~~~C~~C~G~G~ 52 (66)
T PF00684_consen 12 GKKPKTCPQCNGSGQVTRRQQTPGGVFQMQQTCPKCGGTGK 52 (66)
T ss_dssp TTT-EE-TTSSSSSEEEEEEESSSTTEEEEEE-TTTSSSSE
T ss_pred CCCCcCCcCCCCeeEEEEEEeCCCeEEEEEEECCCCcceee
Confidence 4556699999999887766653 778999975433
No 159
>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=23.00 E-value=38 Score=21.09 Aligned_cols=24 Identities=17% Similarity=0.480 Sum_probs=14.9
Q ss_pred EeCCCCCccceEEeeeeeeeeccCCCccc
Q 037763 315 KCGRCRHTRMSFISLRRHIACLNCNQYWD 343 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QTFv~C~~CgnrWk 343 (354)
+|+.|++.=-. .-..|-.||+.|.
T Consensus 2 ~CP~C~~~V~~-----~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPE-----SAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchh-----hcCcCCCCCCCCc
Confidence 47777653211 1456888998874
No 160
>PF14122 YokU: YokU-like protein
Probab=22.86 E-value=60 Score=26.21 Aligned_cols=9 Identities=44% Similarity=0.981 Sum_probs=6.9
Q ss_pred eeeeccCCC
Q 037763 332 HIACLNCNQ 340 (354)
Q Consensus 332 Fv~C~~Cgn 340 (354)
-+.|.+||-
T Consensus 35 ~i~C~~Cgm 43 (87)
T PF14122_consen 35 AIICSNCGM 43 (87)
T ss_pred eeeecCCCc
Confidence 777888884
No 161
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=22.51 E-value=36 Score=31.62 Aligned_cols=30 Identities=17% Similarity=0.429 Sum_probs=23.4
Q ss_pred cccceEeCCCCCccc-eEEeeee-eeeeccCC
Q 037763 310 ISGICKCGRCRHTRM-SFISLRR-HIACLNCN 339 (354)
Q Consensus 310 ~td~f~C~kC~~~k~-ty~q~QT-Fv~C~~Cg 339 (354)
..+...|..||+... .|+..+. .+.|..|+
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 456678999998865 5677777 77899996
No 162
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=22.28 E-value=29 Score=38.71 Aligned_cols=26 Identities=19% Similarity=0.548 Sum_probs=0.0
Q ss_pred ccccceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 309 IISGICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
.+...++|+.||..-- +.+|-.||.+
T Consensus 651 vei~~r~Cp~Cg~~t~-------~~~Cp~CG~~ 676 (900)
T PF03833_consen 651 VEIGRRRCPKCGKETF-------YNRCPECGSH 676 (900)
T ss_dssp ---------------------------------
T ss_pred EeeecccCcccCCcch-------hhcCcccCCc
Confidence 4567889999987643 6777777765
No 163
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=22.16 E-value=37 Score=32.69 Aligned_cols=32 Identities=22% Similarity=0.491 Sum_probs=27.3
Q ss_pred cccceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 310 ISGICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
.-..|.|++|+..=..|-|+-.---|..||+.
T Consensus 152 G~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~ 183 (278)
T PF15135_consen 152 GIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNP 183 (278)
T ss_pred ceeeeecccccccchhhhhcCCCCCccCCCCc
Confidence 45789999999999999888887778888874
No 164
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=22.01 E-value=54 Score=24.41 Aligned_cols=22 Identities=27% Similarity=0.865 Sum_probs=18.5
Q ss_pred cceEeCCCCCccceEEeeeeeeeeccCC
Q 037763 312 GICKCGRCRHTRMSFISLRRHIACLNCN 339 (354)
Q Consensus 312 d~f~C~kC~~~k~ty~q~QTFv~C~~Cg 339 (354)
.+-.|+.||..+-. --.|..||
T Consensus 26 ~~~~c~~cG~~~l~------Hrvc~~cg 47 (57)
T COG0333 26 TLSVCPNCGEYKLP------HRVCLKCG 47 (57)
T ss_pred cceeccCCCCcccC------ceEcCCCC
Confidence 37789999998876 77899998
No 165
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=21.96 E-value=39 Score=29.37 Aligned_cols=31 Identities=13% Similarity=0.180 Sum_probs=21.8
Q ss_pred cccceEeCCCCCccceEEeeeeeeeeccCCCccc
Q 037763 310 ISGICKCGRCRHTRMSFISLRRHIACLNCNQYWD 343 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QTFv~C~~CgnrWk 343 (354)
.--...|++||-.- ++.+--|.|-.||++-.
T Consensus 25 kML~~hCp~Cg~PL---F~KdG~v~CPvC~~~~~ 55 (131)
T COG1645 25 KMLAKHCPKCGTPL---FRKDGEVFCPVCGYREV 55 (131)
T ss_pred HHHHhhCcccCCcc---eeeCCeEECCCCCceEE
Confidence 33345899998654 45555889999998654
No 166
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.85 E-value=39 Score=30.60 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=12.4
Q ss_pred eeeeccCCCccccc
Q 037763 332 HIACLNCNQYWDST 345 (354)
Q Consensus 332 Fv~C~~CgnrWk~~ 345 (354)
|..|.+||.||-|-
T Consensus 117 ~Y~Cp~C~~rytf~ 130 (178)
T PRK06266 117 FFFCPNCHIRFTFD 130 (178)
T ss_pred EEECCCCCcEEeHH
Confidence 99999999999763
No 167
>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=21.80 E-value=73 Score=21.54 Aligned_cols=26 Identities=23% Similarity=0.658 Sum_probs=15.3
Q ss_pred EeCCCCCccceEEeeee--eeeecc---CCCc
Q 037763 315 KCGRCRHTRMSFISLRR--HIACLN---CNQY 341 (354)
Q Consensus 315 ~C~kC~~~k~ty~q~QT--Fv~C~~---Cgnr 341 (354)
.|++||+ .....+-.. |+-|.+ |.+.
T Consensus 3 ~CP~Cg~-~lv~r~~k~g~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 3 KCPKCGG-PLVLRRGKKGKFLGCSNYPECKYT 33 (39)
T ss_pred CCCCCCc-eeEEEECCCCCEEECCCCCCcCCe
Confidence 6999993 222222111 998987 7653
No 168
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=21.77 E-value=23 Score=34.77 Aligned_cols=32 Identities=19% Similarity=0.382 Sum_probs=22.3
Q ss_pred ceEeCCCCCccceEEeeee-eeeeccCCCccccc
Q 037763 313 ICKCGRCRHTRMSFISLRR-HIACLNCNQYWDST 345 (354)
Q Consensus 313 ~f~C~kC~~~k~ty~q~QT-Fv~C~~CgnrWk~~ 345 (354)
..+|++|+.- ..+.++.. +-.|..|||.++..
T Consensus 27 ~~~c~~c~~~-~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQV-LYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccch-hhHHHHHhcCCCCCCCCCCeeCC
Confidence 6799999863 11233433 67899999999864
No 169
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=21.77 E-value=37 Score=25.34 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=9.6
Q ss_pred cccceEeCCCCC
Q 037763 310 ISGICKCGRCRH 321 (354)
Q Consensus 310 ~td~f~C~kC~~ 321 (354)
....|+|++|+.
T Consensus 14 GE~~lrCPRC~~ 25 (65)
T COG4049 14 GEEFLRCPRCGM 25 (65)
T ss_pred CceeeeCCchhH
Confidence 446899999985
No 170
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=21.74 E-value=90 Score=32.46 Aligned_cols=96 Identities=10% Similarity=0.161 Sum_probs=55.8
Q ss_pred hhhhhHhhHHhhcCCCCCHHHHHHHhcCCCCchhcccCChhhcCC-HHHHHHHH-HH----H---HHh--cCCcCccccc
Q 037763 234 TYKFKYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMAS-DKMQLWYE-NL----E---KER--AGTNGRIFSG 302 (354)
Q Consensus 234 ~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmAS-~e~k~~re-~~----~---~~~--~~~~~~~~~~ 302 (354)
.+-..+|+-+..+--=.||.|....+ -.|+.++|..|..++++- +..+..+. .+ . ++. .|.
T Consensus 88 ~Fle~l~~~sqhvlvYEDP~lq~~Al-s~iPvdEL~~kA~ekla~~eg~ki~kdy~i~leLL~WFKq~FF~Wv------- 159 (500)
T KOG0909|consen 88 AFLEVLRSYSQHVLVYEDPVLQAKAL-STIPVDELKEKASEKLAKAEGEKIYKDYLIKLELLNWFKQDFFKWV------- 159 (500)
T ss_pred HHHHHHHHhccCceeecCHHHHHHHH-hcCCHHHHHHHHHHhhcccchhhhhcchHHHHHHHHHHHHhhheec-------
Confidence 34444444444444447887765444 467779999998888885 22222221 11 1 111 232
Q ss_pred ccCCCcccccceEeCCCCCccceEEeeee--------------eeeeccCCCcccccC
Q 037763 303 IVSPKKIISGICKCGRCRHTRMSFISLRR--------------HIACLNCNQYWDSTN 346 (354)
Q Consensus 303 ~~~~~~~~td~f~C~kC~~~k~ty~q~QT--------------Fv~C~~CgnrWk~~~ 346 (354)
+.-.|.+||++--+=.+=|- ...|+.||+.=+|.|
T Consensus 160 ---------N~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPR 208 (500)
T KOG0909|consen 160 ---------NNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPR 208 (500)
T ss_pred ---------CCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCcc
Confidence 22369999987643222221 778999999988875
No 171
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=21.48 E-value=59 Score=26.39 Aligned_cols=12 Identities=25% Similarity=0.797 Sum_probs=9.9
Q ss_pred eeeeccCCCccc
Q 037763 332 HIACLNCNQYWD 343 (354)
Q Consensus 332 Fv~C~~CgnrWk 343 (354)
-..|.+||.-|-
T Consensus 35 a~~C~~CGe~y~ 46 (89)
T TIGR03829 35 SISCSHCGMEYQ 46 (89)
T ss_pred cccccCCCcEee
Confidence 678999998874
No 172
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.44 E-value=1.2e+02 Score=31.95 Aligned_cols=14 Identities=21% Similarity=0.235 Sum_probs=7.1
Q ss_pred ccHHHHHHHHHHhh
Q 037763 26 AEEAQCLDALDQLK 39 (354)
Q Consensus 26 ~~~~~~l~~L~~L~ 39 (354)
|+..-+.++.++|+
T Consensus 33 P~i~L~~Q~~~~l~ 46 (505)
T TIGR00595 33 PEIALTPQMIQRFK 46 (505)
T ss_pred CcHHHHHHHHHHHH
Confidence 44444455555554
No 173
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=21.42 E-value=65 Score=24.21 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=8.1
Q ss_pred cccceEeCCCCC
Q 037763 310 ISGICKCGRCRH 321 (354)
Q Consensus 310 ~td~f~C~kC~~ 321 (354)
.-++..|+.|++
T Consensus 4 llniL~Cp~ck~ 15 (68)
T PF03966_consen 4 LLNILACPVCKG 15 (68)
T ss_dssp GCGTBB-TTTSS
T ss_pred HHhhhcCCCCCC
Confidence 346778888888
No 174
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=21.23 E-value=44 Score=29.28 Aligned_cols=13 Identities=31% Similarity=0.521 Sum_probs=10.5
Q ss_pred eeeeccCCCcccc
Q 037763 332 HIACLNCNQYWDS 344 (354)
Q Consensus 332 Fv~C~~CgnrWk~ 344 (354)
|++|++||.++|.
T Consensus 76 ~IicLEDGkkfKS 88 (148)
T COG4957 76 YIICLEDGKKFKS 88 (148)
T ss_pred eEEEeccCcchHH
Confidence 7888888888774
No 175
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=21.23 E-value=1.2e+02 Score=23.05 Aligned_cols=22 Identities=9% Similarity=0.187 Sum_probs=17.8
Q ss_pred cccceEeCCCCCccceEEeeee
Q 037763 310 ISGICKCGRCRHTRMSFISLRR 331 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT 331 (354)
....+.|+.|++.-.|..+-++
T Consensus 4 ~p~~~~CP~C~~~~~T~v~~~~ 25 (73)
T PF10601_consen 4 EPVRIYCPYCQQQVQTRVEYKS 25 (73)
T ss_pred CceeeECCCCCCEEEEEEEEEe
Confidence 4556799999999998877765
No 176
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.78 E-value=20 Score=39.28 Aligned_cols=40 Identities=30% Similarity=0.497 Sum_probs=23.9
Q ss_pred cccceEeCCCCCccceEEeeee---eeeeccCCCcccccCCCccccC
Q 037763 310 ISGICKCGRCRHTRMSFISLRR---HIACLNCNQYWDSTNPGIEVLP 353 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty~q~QT---Fv~C~~CgnrWk~~~~~~~~~~ 353 (354)
..|.-.|..|-..-.+=..-.. |..|.+||-|+. .|+.||
T Consensus 98 ~pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfT----Ii~alP 140 (750)
T COG0068 98 PPDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFT----IIEALP 140 (750)
T ss_pred CCchhhhHHHHHHhcCCCCcceeccccccCCCCccee----eeccCC
Confidence 5677788888543221111111 888999988875 355555
No 177
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.76 E-value=54 Score=37.43 Aligned_cols=26 Identities=23% Similarity=0.407 Sum_probs=16.1
Q ss_pred ccccceEeCCCCCccceEEeeeeeeeeccCCCc
Q 037763 309 IISGICKCGRCRHTRMSFISLRRHIACLNCNQY 341 (354)
Q Consensus 309 ~~td~f~C~kC~~~k~ty~q~QTFv~C~~Cgnr 341 (354)
.+.+.+.|+.||..- .+..|-+||..
T Consensus 622 VEVg~RfCpsCG~~t-------~~frCP~CG~~ 647 (1121)
T PRK04023 622 VEIGRRKCPSCGKET-------FYRRCPFCGTH 647 (1121)
T ss_pred ecccCccCCCCCCcC-------CcccCCCCCCC
Confidence 345666777777762 25567777753
No 178
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.52 E-value=54 Score=29.88 Aligned_cols=31 Identities=19% Similarity=0.490 Sum_probs=20.5
Q ss_pred cccceEeCCCCCccceE-EeeeeeeeeccCCCc
Q 037763 310 ISGICKCGRCRHTRMSF-ISLRRHIACLNCNQY 341 (354)
Q Consensus 310 ~td~f~C~kC~~~k~ty-~q~QTFv~C~~Cgnr 341 (354)
....|.|+.|+-+ .+| .|++.-++|..||.-
T Consensus 110 ~~~~y~C~~~~~r-~sfdeA~~~~F~Cp~Cg~~ 141 (176)
T COG1675 110 ENNYYVCPNCHVK-YSFDEAMELGFTCPKCGED 141 (176)
T ss_pred cCCceeCCCCCCc-ccHHHHHHhCCCCCCCCch
Confidence 6678899766544 333 555555679999853
No 179
>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=20.35 E-value=20 Score=27.12 Aligned_cols=33 Identities=27% Similarity=0.665 Sum_probs=23.2
Q ss_pred cceEeCCCCCccceE------EeeeeeeeeccCCCcccc
Q 037763 312 GICKCGRCRHTRMSF------ISLRRHIACLNCNQYWDS 344 (354)
Q Consensus 312 d~f~C~kC~~~k~ty------~q~QTFv~C~~CgnrWk~ 344 (354)
...+|++|++.++.| .--|--..|..|...|.-
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~ 42 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTH 42 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHh
Confidence 346899999998754 123444458889888864
No 180
>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=20.34 E-value=49 Score=22.35 Aligned_cols=12 Identities=17% Similarity=0.575 Sum_probs=6.2
Q ss_pred eeeeccCCCccc
Q 037763 332 HIACLNCNQYWD 343 (354)
Q Consensus 332 Fv~C~~CgnrWk 343 (354)
|..|..|||--.
T Consensus 6 ~YkC~~CGniVe 17 (36)
T PF06397_consen 6 FYKCEHCGNIVE 17 (36)
T ss_dssp EEE-TTT--EEE
T ss_pred EEEccCCCCEEE
Confidence 777888887543
No 181
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.12 E-value=62 Score=31.63 Aligned_cols=35 Identities=11% Similarity=0.257 Sum_probs=27.2
Q ss_pred CcccccceEeCCCCCccceEEeeee------------------eeeeccCCCc
Q 037763 307 KKIISGICKCGRCRHTRMSFISLRR------------------HIACLNCNQY 341 (354)
Q Consensus 307 ~~~~td~f~C~kC~~~k~ty~q~QT------------------Fv~C~~Cgnr 341 (354)
..+.|+.-.|+.||..-+-=+++|- ..+|..||..
T Consensus 233 ss~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~ 285 (298)
T KOG2879|consen 233 SSTGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGEN 285 (298)
T ss_pred cccccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCC
Confidence 3456777899999999988888882 3589999864
Done!