Query 006806
Match_columns 630
No_of_seqs 410 out of 1443
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 14:45:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006806.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006806hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1886 BAH domain proteins [T 100.0 4.2E-45 9E-50 392.5 12.1 434 89-591 8-445 (464)
2 TIGR01385 TFSII transcription 100.0 5.2E-38 1.1E-42 327.1 15.6 161 338-542 126-299 (299)
3 KOG1105 Transcription elongati 100.0 1.3E-36 2.8E-41 313.3 12.8 155 345-542 129-296 (296)
4 cd04713 BAH_plant_3 BAH, or Br 100.0 2.5E-34 5.5E-39 271.9 16.2 146 111-257 1-146 (146)
5 cd04716 BAH_plantDCM_I BAH, or 99.9 5E-26 1.1E-30 209.7 13.1 118 128-248 1-121 (122)
6 cd04717 BAH_polybromo BAH, or 99.9 8.6E-26 1.9E-30 206.6 12.1 117 128-247 1-119 (121)
7 cd04715 BAH_Orc1p_like BAH, or 99.9 1.5E-25 3.2E-30 215.1 14.0 138 101-246 5-153 (159)
8 cd04714 BAH_BAHCC1 BAH, or Bro 99.9 1.3E-25 2.8E-30 206.3 10.8 112 128-242 1-117 (121)
9 cd04370 BAH BAH, or Bromo Adja 99.9 1.1E-24 2.4E-29 194.8 12.5 117 128-247 1-122 (123)
10 smart00439 BAH Bromo adjacent 99.9 1.1E-24 2.4E-29 195.3 12.0 116 130-248 1-120 (120)
11 PF01426 BAH: BAH domain; Int 99.9 1.8E-24 4E-29 193.9 10.2 115 129-248 1-119 (119)
12 cd04710 BAH_fungalPHD BAH, or 99.9 4E-24 8.6E-29 200.2 11.3 118 124-246 5-135 (135)
13 cd04721 BAH_plant_1 BAH, or Br 99.9 5.8E-24 1.3E-28 197.9 10.5 120 124-247 1-124 (130)
14 cd04709 BAH_MTA BAH, or Bromo 99.9 2.8E-23 6.2E-28 200.1 11.8 118 128-246 1-138 (164)
15 smart00510 TFS2M Domain in the 99.9 5.2E-23 1.1E-27 184.3 10.3 99 349-489 1-101 (102)
16 cd04712 BAH_DCM_I BAH, or Brom 99.9 7.5E-22 1.6E-26 183.8 13.2 114 127-248 2-129 (130)
17 cd04708 BAH_plantDCM_II BAH, o 99.9 4.7E-22 1E-26 196.6 11.7 124 124-250 1-148 (202)
18 PF07500 TFIIS_M: Transcriptio 99.9 6.3E-23 1.4E-27 186.4 3.9 113 347-501 1-115 (115)
19 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 1.7E-21 3.7E-26 179.7 11.0 112 128-244 1-123 (124)
20 cd04720 BAH_Orc1p_Yeast BAH, o 99.8 3.5E-19 7.6E-24 174.2 11.6 119 127-246 49-176 (179)
21 cd04718 BAH_plant_2 BAH, or Br 99.8 2.8E-20 6E-25 175.7 1.9 98 145-247 50-147 (148)
22 cd04719 BAH_Orc1p_animal BAH, 99.8 5.2E-19 1.1E-23 164.4 9.6 113 129-244 2-125 (128)
23 cd04711 BAH_Dnmt1_II BAH, or B 99.7 2.6E-17 5.6E-22 153.4 7.8 114 134-248 13-136 (137)
24 KOG1827 Chromatin remodeling c 99.5 1.6E-14 3.4E-19 162.1 6.8 120 124-246 184-310 (629)
25 smart00440 ZnF_C2C2 C2C2 Zinc 99.2 1E-11 2.2E-16 93.8 4.1 37 504-541 1-40 (40)
26 PF01096 TFIIS_C: Transcriptio 99.1 2.6E-11 5.6E-16 91.1 3.6 36 504-540 1-39 (39)
27 KOG2906 RNA polymerase III sub 99.1 4.8E-11 1E-15 105.3 2.4 47 494-541 56-105 (105)
28 COG1594 RPB9 DNA-directed RNA 99.0 1.2E-10 2.6E-15 106.6 3.6 39 503-542 72-113 (113)
29 KOG1634 Predicted transcriptio 99.0 8.6E-11 1.9E-15 134.3 3.2 79 408-489 262-343 (778)
30 PHA02998 RNA polymerase subuni 99.0 3E-10 6.4E-15 110.1 4.5 41 502-543 142-185 (195)
31 TIGR01384 TFS_arch transcripti 98.9 8E-10 1.7E-14 98.8 4.2 41 501-542 60-103 (104)
32 KOG3554 Histone deacetylase co 98.6 8.5E-09 1.8E-13 111.6 -0.9 136 129-267 4-184 (693)
33 KOG2907 RNA polymerase I trans 98.4 5.7E-08 1.2E-12 88.1 1.2 41 500-541 71-114 (116)
34 KOG2691 RNA polymerase II subu 98.0 3.5E-06 7.7E-11 76.0 3.4 37 503-540 73-112 (113)
35 PF09855 DUF2082: Nucleic-acid 93.2 0.095 2.1E-06 43.9 3.4 43 504-547 1-53 (64)
36 COG5076 Transcription factor i 92.9 0.014 3E-07 63.5 -2.5 97 122-221 268-364 (371)
37 COG3478 Predicted nucleic-acid 87.2 0.53 1.1E-05 39.6 2.7 44 503-547 4-57 (68)
38 PRK09678 DNA-binding transcrip 85.4 0.85 1.9E-05 39.2 3.2 34 503-540 1-40 (72)
39 COG2051 RPS27A Ribosomal prote 85.0 0.56 1.2E-05 39.6 1.8 29 503-538 19-47 (67)
40 PF08274 PhnA_Zn_Ribbon: PhnA 83.9 0.42 9.1E-06 34.4 0.5 27 505-540 4-30 (30)
41 PF13717 zinc_ribbon_4: zinc-r 83.7 0.68 1.5E-05 34.4 1.6 33 504-540 3-36 (36)
42 TIGR00686 phnA alkylphosphonat 82.7 0.8 1.7E-05 42.1 2.0 29 505-542 4-32 (109)
43 TIGR00244 transcriptional regu 80.6 1.3 2.9E-05 42.9 2.7 44 505-551 2-51 (147)
44 PF04606 Ogr_Delta: Ogr/Delta- 80.3 1.3 2.8E-05 34.7 2.1 33 505-540 1-38 (47)
45 TIGR02098 MJ0042_CXXC MJ0042 f 79.9 1.3 2.7E-05 32.7 1.9 34 504-541 3-37 (38)
46 PRK10220 hypothetical protein; 78.6 1.6 3.4E-05 40.3 2.4 32 502-542 2-33 (111)
47 PF12760 Zn_Tnp_IS1595: Transp 78.2 1.8 3.9E-05 33.5 2.4 30 502-538 17-46 (46)
48 PF13719 zinc_ribbon_5: zinc-r 78.0 1.5 3.2E-05 32.7 1.7 34 504-541 3-37 (37)
49 PRK00415 rps27e 30S ribosomal 77.7 1.6 3.5E-05 36.2 2.0 30 503-539 11-40 (59)
50 PRK00464 nrdR transcriptional 76.1 1.7 3.7E-05 42.3 2.1 36 504-542 1-41 (154)
51 PLN00209 ribosomal protein S27 75.9 2.7 5.9E-05 37.3 3.0 30 503-539 36-65 (86)
52 PTZ00112 origin recognition co 75.0 3 6.4E-05 51.0 4.0 134 119-252 441-615 (1164)
53 PF09926 DUF2158: Uncharacteri 74.5 4.2 9E-05 33.0 3.6 39 131-173 1-39 (53)
54 PTZ00083 40S ribosomal protein 74.2 3.3 7.2E-05 36.7 3.1 30 503-539 35-64 (85)
55 PF04216 FdhE: Protein involve 73.5 2.9 6.2E-05 44.2 3.1 39 503-543 172-211 (290)
56 PF07282 OrfB_Zn_ribbon: Putat 72.8 1.5 3.2E-05 36.3 0.6 40 502-551 27-66 (69)
57 PF08271 TF_Zn_Ribbon: TFIIB z 72.5 2 4.4E-05 32.7 1.3 30 504-540 1-30 (43)
58 COG1327 Predicted transcriptio 70.8 2.7 6E-05 40.9 2.1 59 504-570 1-65 (156)
59 TIGR02443 conserved hypothetic 68.3 8.2 0.00018 32.1 4.0 43 502-548 8-50 (59)
60 PHA00626 hypothetical protein 68.2 3.6 7.7E-05 33.9 1.9 31 505-539 2-33 (59)
61 TIGR01562 FdhE formate dehydro 66.0 3.5 7.5E-05 44.4 1.9 49 503-553 184-243 (305)
62 PF01667 Ribosomal_S27e: Ribos 65.1 2.2 4.9E-05 34.9 0.2 29 503-538 7-35 (55)
63 PRK00398 rpoP DNA-directed RNA 64.8 3.9 8.4E-05 31.6 1.4 32 501-540 1-32 (46)
64 COG4332 Uncharacterized protei 64.5 4.2 9.1E-05 40.8 1.9 36 504-541 18-61 (203)
65 PRK03564 formate dehydrogenase 62.2 6.1 0.00013 42.7 2.9 38 503-543 187-226 (309)
66 PF11792 Baculo_LEF5_C: Baculo 61.2 0.89 1.9E-05 35.4 -2.6 28 508-537 12-42 (43)
67 PF14353 CpXC: CpXC protein 60.4 11 0.00023 35.0 3.8 45 504-552 2-58 (128)
68 PHA02942 putative transposase; 60.4 2.1 4.5E-05 47.3 -1.1 51 502-565 324-374 (383)
69 smart00661 RPOL9 RNA polymeras 58.4 13 0.00028 28.8 3.4 33 505-544 2-35 (52)
70 PF13453 zf-TFIIB: Transcripti 58.4 11 0.00024 28.4 2.9 29 505-540 1-30 (41)
71 PF01873 eIF-5_eIF-2B: Domain 58.0 12 0.00026 35.3 3.7 30 503-538 93-123 (125)
72 PF09538 FYDLN_acid: Protein o 57.9 4.4 9.5E-05 37.4 0.8 32 502-542 8-39 (108)
73 KOG3507 DNA-directed RNA polym 57.7 4.2 9E-05 33.8 0.5 28 503-539 20-47 (62)
74 smart00653 eIF2B_5 domain pres 55.5 11 0.00024 34.8 3.0 30 503-538 80-110 (110)
75 PF09526 DUF2387: Probable met 54.8 14 0.00029 31.8 3.2 38 503-544 8-45 (71)
76 TIGR02300 FYDLN_acid conserved 54.7 5.5 0.00012 37.9 0.8 32 502-542 8-39 (129)
77 TIGR00311 aIF-2beta translatio 54.2 12 0.00026 35.7 3.1 30 503-538 97-127 (133)
78 COG1326 Uncharacterized archae 53.3 4.7 0.0001 40.8 0.2 34 504-540 7-41 (201)
79 TIGR00310 ZPR1_znf ZPR1 zinc f 53.3 18 0.00039 36.5 4.3 74 504-579 1-86 (192)
80 PF14354 Lar_restr_allev: Rest 52.9 16 0.00034 29.5 3.2 33 504-537 4-37 (61)
81 cd05834 HDGF_related The PWWP 52.5 19 0.0004 31.5 3.7 43 130-174 2-44 (83)
82 PRK03988 translation initiatio 51.8 14 0.0003 35.5 3.1 30 503-538 102-132 (138)
83 COG1779 C4-type Zn-finger prot 51.7 14 0.00031 37.6 3.3 40 500-540 11-54 (201)
84 COG2824 PhnA Uncharacterized Z 51.1 13 0.00028 34.4 2.6 30 504-542 4-33 (112)
85 COG1645 Uncharacterized Zn-fin 50.5 13 0.00029 35.5 2.7 33 497-539 22-54 (131)
86 COG0675 Transposase and inacti 50.1 7 0.00015 40.4 0.9 37 501-552 307-343 (364)
87 smart00659 RPOLCX RNA polymera 49.9 10 0.00023 29.5 1.6 28 504-540 3-30 (44)
88 COG4888 Uncharacterized Zn rib 49.4 20 0.00044 32.8 3.6 37 502-541 21-58 (104)
89 PRK12336 translation initiatio 48.6 16 0.00035 37.0 3.1 30 503-538 98-128 (201)
90 TIGR00340 zpr1_rel ZPR1-relate 48.0 20 0.00044 35.3 3.7 74 506-579 1-84 (163)
91 PF11781 RRN7: RNA polymerase 48.0 13 0.00029 27.8 1.8 26 504-538 9-34 (36)
92 PF10080 DUF2318: Predicted me 47.8 12 0.00026 34.2 1.9 28 505-541 37-64 (102)
93 cd06080 MUM1_like Mutated mela 47.1 28 0.00062 30.5 4.0 39 131-174 1-39 (80)
94 COG1996 RPC10 DNA-directed RNA 47.1 7.7 0.00017 31.1 0.5 32 501-540 4-35 (49)
95 PF03367 zf-ZPR1: ZPR1 zinc-fi 46.6 20 0.00044 35.1 3.4 74 505-578 3-87 (161)
96 PRK03976 rpl37ae 50S ribosomal 46.0 19 0.0004 32.4 2.8 39 494-540 27-65 (90)
97 TIGR00280 L37a ribosomal prote 44.5 20 0.00043 32.4 2.6 39 494-540 26-64 (91)
98 COG0777 AccD Acetyl-CoA carbox 44.4 4.9 0.00011 42.7 -1.3 75 504-608 29-104 (294)
99 COG1997 RPL43A Ribosomal prote 43.8 22 0.00048 31.8 2.8 38 495-540 27-64 (89)
100 KOG0909 Peptide:N-glycanase [P 43.1 21 0.00045 40.4 3.1 95 438-543 87-208 (500)
101 PF03604 DNA_RNApol_7kD: DNA d 42.7 15 0.00034 26.8 1.4 26 505-539 2-27 (32)
102 cd05835 Dnmt3b_related The PWW 42.4 28 0.00061 30.5 3.3 40 131-172 1-43 (87)
103 smart00531 TFIIE Transcription 42.2 8.7 0.00019 36.8 0.1 38 502-542 98-136 (147)
104 TIGR03655 anti_R_Lar restricti 41.9 35 0.00076 27.2 3.5 33 504-538 2-35 (53)
105 smart00709 Zpr1 Duplicated dom 41.8 34 0.00074 33.6 4.1 72 505-578 2-86 (160)
106 PRK00432 30S ribosomal protein 41.7 15 0.00032 29.4 1.3 28 504-540 21-48 (50)
107 PF05129 Elf1: Transcription e 41.2 35 0.00076 29.9 3.7 38 502-542 21-59 (81)
108 PF09332 Mcm10: Mcm10 replicat 40.9 5.6 0.00012 43.5 -1.5 11 528-538 284-294 (344)
109 PRK09710 lar restriction allev 40.4 28 0.00061 29.5 2.8 35 504-544 7-42 (64)
110 PTZ00255 60S ribosomal protein 40.4 25 0.00054 31.6 2.7 39 494-540 27-65 (90)
111 PF01780 Ribosomal_L37ae: Ribo 39.8 21 0.00045 32.1 2.1 39 494-540 26-64 (90)
112 KOG1827 Chromatin remodeling c 39.4 17 0.00038 42.7 2.0 89 130-241 375-465 (629)
113 COG4307 Uncharacterized protei 39.3 13 0.00028 39.6 0.8 12 501-512 1-12 (349)
114 PF10383 Clr2: Transcription-s 39.0 1.2E+02 0.0027 28.9 7.3 52 120-171 2-70 (139)
115 smart00834 CxxC_CXXC_SSSS Puta 38.6 18 0.0004 26.5 1.4 31 502-537 4-34 (41)
116 PF02172 KIX: KIX domain; Int 38.6 1.3E+02 0.0029 26.5 6.9 66 349-453 12-77 (81)
117 PRK10708 hypothetical protein; 38.0 69 0.0015 26.7 4.6 42 132-175 2-50 (62)
118 PF11302 DUF3104: Protein of u 37.5 66 0.0014 28.1 4.7 30 130-159 5-39 (75)
119 cd05162 PWWP The PWWP domain, 36.8 44 0.00096 28.8 3.7 40 131-172 1-46 (87)
120 TIGR02605 CxxC_CxxC_SSSS putat 36.3 24 0.00052 27.6 1.8 31 502-537 4-34 (52)
121 PF10571 UPF0547: Uncharacteri 33.7 21 0.00046 24.9 0.9 24 505-540 2-25 (26)
122 PF09723 Zn-ribbon_8: Zinc rib 33.6 32 0.00069 26.3 2.0 31 502-537 4-34 (42)
123 PF05876 Terminase_GpA: Phage 33.4 34 0.00074 39.8 3.1 39 502-541 199-241 (557)
124 PF01921 tRNA-synt_1f: tRNA sy 33.2 27 0.00059 38.6 2.2 66 502-584 173-250 (360)
125 COG2816 NPY1 NTP pyrophosphohy 33.2 38 0.00082 36.3 3.1 42 505-554 113-155 (279)
126 PF10781 DSRB: Dextransucrase 33.0 91 0.002 26.0 4.5 43 132-176 2-51 (62)
127 PF11717 Tudor-knot: RNA bindi 32.1 79 0.0017 25.3 4.2 37 131-170 1-37 (55)
128 PF08940 DUF1918: Domain of un 31.2 60 0.0013 27.1 3.3 40 132-172 4-43 (58)
129 cd05840 SPBC215_ISWI_like The 30.7 49 0.0011 29.6 3.0 39 131-171 1-48 (93)
130 PF06353 DUF1062: Protein of u 30.5 26 0.00056 33.9 1.3 16 525-540 8-24 (142)
131 PRK06266 transcription initiat 29.8 13 0.00027 37.1 -1.0 33 502-541 116-148 (178)
132 PF05180 zf-DNL: DNL zinc fing 29.5 22 0.00048 30.2 0.6 34 503-540 4-40 (66)
133 PRK05978 hypothetical protein; 28.7 28 0.0006 34.0 1.1 31 503-542 33-65 (148)
134 smart00293 PWWP domain with co 28.6 64 0.0014 26.4 3.1 40 131-172 1-47 (63)
135 COG2888 Predicted Zn-ribbon RN 28.3 30 0.00065 29.0 1.1 29 502-537 26-58 (61)
136 KOG1779 40s ribosomal protein 28.2 46 0.001 29.4 2.2 27 503-536 34-60 (84)
137 KOG0343 RNA Helicase [RNA proc 28.0 26 0.00057 40.9 1.0 66 47-112 645-715 (758)
138 COG1594 RPB9 DNA-directed RNA 27.9 58 0.0013 30.2 3.0 47 505-558 4-51 (113)
139 TIGR00373 conserved hypothetic 27.8 14 0.0003 36.1 -1.1 48 483-537 89-136 (158)
140 smart00401 ZnF_GATA zinc finge 27.7 25 0.00053 28.2 0.5 34 504-542 4-38 (52)
141 PF02459 Adeno_terminal: Adeno 27.2 30 0.00065 40.0 1.2 8 65-72 293-300 (548)
142 PRK13251 transcription attenua 26.3 1.4E+02 0.003 25.9 4.7 48 166-216 19-66 (75)
143 PF00855 PWWP: PWWP domain; I 25.8 45 0.00098 28.2 1.8 40 131-172 1-43 (86)
144 KOG2462 C2H2-type Zn-finger pr 25.7 32 0.0007 36.7 1.1 48 501-549 128-180 (279)
145 PF09297 zf-NADH-PPase: NADH p 25.1 47 0.001 23.7 1.5 26 505-538 5-30 (32)
146 COG5475 Uncharacterized small 24.6 1.4E+02 0.0031 24.9 4.3 38 128-175 2-40 (60)
147 PF14311 DUF4379: Domain of un 24.2 46 0.001 26.5 1.5 15 528-542 27-41 (55)
148 COG1571 Predicted DNA-binding 24.0 38 0.00082 38.2 1.3 29 503-540 350-378 (421)
149 PRK14892 putative transcriptio 23.9 53 0.0012 30.0 2.0 41 502-550 20-60 (99)
150 COG2023 RPR2 RNase P subunit R 23.3 52 0.0011 30.5 1.8 37 504-541 57-94 (105)
151 cd00674 LysRS_core_class_I cat 22.7 66 0.0014 35.5 2.8 34 502-540 168-203 (353)
152 PF00467 KOW: KOW motif; Inte 22.6 1.4E+02 0.0031 21.3 3.6 25 133-159 1-25 (32)
153 PRK11823 DNA repair protein Ra 22.5 42 0.00092 37.9 1.3 32 502-546 6-37 (446)
154 COG4640 Predicted membrane pro 22.4 40 0.00086 37.8 1.0 25 504-540 2-26 (465)
155 PRK14890 putative Zn-ribbon RN 22.3 28 0.00062 29.0 -0.1 30 502-538 24-57 (59)
156 PF08792 A2L_zn_ribbon: A2L zi 21.5 97 0.0021 22.8 2.6 28 503-538 3-30 (33)
157 KOG2593 Transcription initiati 21.3 40 0.00087 38.0 0.8 37 501-540 126-164 (436)
158 COG4014 Uncharacterized protei 21.2 1.9E+02 0.0041 26.3 4.7 41 132-178 10-54 (97)
159 TIGR01206 lysW lysine biosynth 21.1 1E+02 0.0023 25.2 2.9 30 503-540 2-33 (54)
160 COG1198 PriA Primosomal protei 20.9 88 0.0019 37.8 3.5 79 466-556 386-491 (730)
161 PRK00241 nudC NADH pyrophospha 20.6 85 0.0018 32.9 3.0 30 504-541 100-129 (256)
162 PRK00420 hypothetical protein; 20.5 59 0.0013 30.4 1.6 34 498-540 18-51 (112)
163 smart00739 KOW KOW (Kyprides, 20.2 1.4E+02 0.003 19.8 3.0 25 131-157 2-26 (28)
164 PF04032 Rpr2: RNAse P Rpr2/Rp 20.0 1.2E+02 0.0026 25.7 3.3 36 502-537 45-85 (85)
No 1
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=100.00 E-value=4.2e-45 Score=392.46 Aligned_cols=434 Identities=35% Similarity=0.542 Sum_probs=364.4
Q ss_pred hhhhhccCCCCCccccccceeecCCCCCcceeeeeEEEcCeEEee-CCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceEE
Q 006806 89 EEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYEL-EDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMMV 166 (630)
Q Consensus 89 ~~~~~~~~~~~~a~~iG~pvk~~gKG~~~r~~Y~sf~~dG~~YkV-GD~VyV~~e~~~~~pyIArI~~I~e~~d-G~~~V 166 (630)
...+.++.+.++|.|+|...++.|+|...++||.+|.+.|..|.. ||+|++.+++++.+||||+|..||.+.. +.+.+
T Consensus 8 ~~~~~~~~~~~~a~~~g~a~~~qGv~~~k~~h~~t~~~~~g~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~ 87 (464)
T KOG1886|consen 8 PKLKSELRPRDEASSMGDANKEQGVGGVKSLHFETFIYRGGRYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKV 87 (464)
T ss_pred ccccccCCccchhhhhhhhhhhccccccccccccceeeccCcccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcce
Confidence 334568999999999999999999999999999999999988888 9999999999999999999999998766 58999
Q ss_pred EEEEEecccccCCCCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCCCCCCCCceEEeeeeecCCcEEee
Q 006806 167 TGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWK 246 (630)
Q Consensus 167 rVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesIigKC~V~~i~ey~qlP~~~~~~~F~Cr~vYD~~~kkl~~ 246 (630)
+|+|||||+|+.....+.|....++|||+|+|+|.+++++|.++|.|+|++.|.++|.+..+++|+|+++||..+.++|.
T Consensus 88 ev~W~YrPee~~~~~~~~~~a~~~relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~ 167 (464)
T KOG1886|consen 88 EVQWFYRPEESEGGGSGKWGAKQPRELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRK 167 (464)
T ss_pred ecccccCCCccCCCCCCCcccCCCccccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccC
Confidence 99999999999988888888889999999999999999999999999999999999988889999999999999999999
Q ss_pred cCCccccccccchhhHHHHHhhhhcCCCCCCCccccccchhhhhhhcccccccCCCCCCcccccccccCCcccccccCCC
Q 006806 247 LTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETP 326 (630)
Q Consensus 247 l~dkDy~~~~q~Evd~ll~kt~~~lG~lpd~~~~e~~~~~~~~~~~~k~~~r~~~~~~~~~~~~~~~~~~~~~~~k~etp 326 (630)
+++.+|....+.++|.++.++..++++++++....+. ..+++++..++++++ .++|.
T Consensus 168 ~~~~~~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~t~-----~~~~~~~~~~~s~~~--~~~r~---------------- 224 (464)
T KOG1886|consen 168 LRDGDFGDGQKLEIDMLVPKTGPRRGTLPDPKKVQTL-----NAAASKRSQQKSEIS--SLSRA---------------- 224 (464)
T ss_pred ccccchhcccccCCccchhhhcccCCCCCCccccccc-----cccccceeccccccc--ccccc----------------
Confidence 9999999999999999999999999999999999833 477888999998887 22222
Q ss_pred CccCCCCcchhhhhccccCCcChhhHHHHHHHHHHHh-hhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccc
Q 006806 327 GSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGL-QYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKG 405 (630)
Q Consensus 327 ~~~~~~~~~~~~~l~~~~~lTgd~~RDK~le~L~~al-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 405 (630)
..+.++.++..|..+||++.|||++..|++.+ +..|.......
T Consensus 225 -----ss~~~~~~~e~~~~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~------------------------------- 268 (464)
T KOG1886|consen 225 -----SSSVDGEILESFDLLTGRSDRDKVLGKLLEVVWQNSCSTSEAKP------------------------------- 268 (464)
T ss_pred -----ccccccccccCCCCCCCcccccccccccchhhccccccccccCC-------------------------------
Confidence 34577888999999999999999999999999 66665432211
Q ss_pred cCCCCCCCChhhHHHHHHHHHHHHHHHcCcChHHHHHHHHHHHHhcccCHHHHHHhhcCC-CCccccccCChhhhcChHh
Q 006806 406 QKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKSTALLARRLLNGE-LEPSKILNMSPNELKEGLT 484 (630)
Q Consensus 406 ~~~~~~~~w~~~v~~~A~~IE~alf~~~~~~~~kYk~KiRSL~fNLKkNp~Lr~rVl~Ge-IsP~~La~Ms~eEMASdel 484 (630)
....++ .||+.++..+.+||.+.|+.++.+..+|..+...|+++||.--.|+.+.++|. +.|+-++.|.+-++-..-.
T Consensus 269 ~~~~~~-~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k~~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~ 347 (464)
T KOG1886|consen 269 AGDQGS-LWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLKGQALLKPEPLNPGETKPEPKQELHPPSFPDGQS 347 (464)
T ss_pred Cccccc-CCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhcchhhhccccCCCcccCchhhhhccCCCCCCCcc
Confidence 111222 78999999999999999999998889999999999999998889999999995 9999999988877766532
Q ss_pred HHHHHhcCCchhhhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccccccceeecCCCCCCCccccc
Q 006806 485 AEEMAKKEPDESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIV 564 (630)
Q Consensus 485 keer~k~~~e~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~s~l~~~~~~~~~~~~~~~ 564 (630)
...-.+....-.....|+...|..|-.--|+-.++|+..+.+-....|..|+.+|...|+++..+++-.+.+++ ++.
T Consensus 348 ~~~~~~~~~d~~~~l~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~~~~~~~~~---~q~ 424 (464)
T KOG1886|consen 348 SPSSMKLNDDDYDGLCVGLELTAGSLYLYCGQEGLICAGHLPCPMLPEVKLSPVAAVHREGLLLAPSSVPKGTP---FQH 424 (464)
T ss_pred CccccccCchhHHHHHHhhhhhccchhhhcccccceeccccCCCCCCCcCcccccccchhhhcccceeccCCCC---ccC
Confidence 11111122222233344556788877777777777766667768889999999999999999999988777633 443
Q ss_pred CccchhhhhhhhhhcCCccccchhhhh
Q 006806 565 PLATAKFDSLEKNLLSPRESEKLANDV 591 (630)
Q Consensus 565 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 591 (630)
| ..-||+|.|||++.++.+.+
T Consensus 425 ~------~~~~k~~~~~ret~~~~ea~ 445 (464)
T KOG1886|consen 425 P------PWPEKRLCSPRETGVNGEAI 445 (464)
T ss_pred C------CChhhcccCccccCCchhcc
Confidence 2 35799999999998665554
No 2
>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=5.2e-38 Score=327.06 Aligned_cols=161 Identities=20% Similarity=0.320 Sum_probs=141.2
Q ss_pred hhhccccCCcChhhHHHHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccccCCCCCCCChhh
Q 006806 338 NILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDT 417 (630)
Q Consensus 338 ~~l~~~~~lTgd~~RDK~le~L~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~ 417 (630)
..++... +|||.+||+|+++||+||....+.... ...
T Consensus 126 ~~~~~~~-~t~d~~Rdk~r~~L~~aL~~~~~~~~~------------------------------------------~~~ 162 (299)
T TIGR01385 126 NDFVPTA-VTNDKVRDKCRELLYDALAKDSDHPPQ------------------------------------------SID 162 (299)
T ss_pred CCCCCCc-cCCcHHHHHHHHHHHHHHhhcCCCCcc------------------------------------------ccC
Confidence 3444444 799999999999999999986542110 123
Q ss_pred HHHHHHHHHHHHHHHcCcChHHHHHHHHHHHHhcc--cCHHHHHHhhcCCCCccccccCChhhhcChHhHHHHHhcCCch
Q 006806 418 AIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKEGLTAEEMAKKEPDE 495 (630)
Q Consensus 418 v~~~A~~IE~alf~~~~~~~~kYk~KiRSL~fNLK--kNp~Lr~rVl~GeIsP~~La~Ms~eEMASdelkeer~k~~~e~ 495 (630)
+..+|.+||.+||..|+.+..+|+++||||+|||| +||+||++||+|+|+|++||.|+++||||+++++++++...+.
T Consensus 163 ~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~ 242 (299)
T TIGR01385 163 PEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKEN 242 (299)
T ss_pred HHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHH
Confidence 44689999999999999888899999999999998 9999999999999999999999999999999999998777788
Q ss_pred hhhccc--------CccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccccc
Q 006806 496 SEQMQM--------TDARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYAS 542 (630)
Q Consensus 496 i~~~~m--------~~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~s 542 (630)
|...++ +.|+|++|++++|+|+|+| |||||| +||+|++|||+|+||
T Consensus 243 l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~Q-trsaDEpmT~f~~C~~Cg~~w~fc 299 (299)
T TIGR01385 243 LFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQ-TRSADEPMTTFVTCEECGNRWKFC 299 (299)
T ss_pred HHHHHhhhhhcCCcccccCCCCCCccceEEEec-ccCCCCCCeEEEEcCCCCCeeeeC
Confidence 877665 3599999999999999999 999999 999999999999986
No 3
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=1.3e-36 Score=313.34 Aligned_cols=155 Identities=24% Similarity=0.387 Sum_probs=141.1
Q ss_pred CCcChhhHHHHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccccCCCCCCCChhhHHHHHHH
Q 006806 345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA 424 (630)
Q Consensus 345 ~lTgd~~RDK~le~L~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~v~~~A~~ 424 (630)
+++.|++|++|++|||.||.....+... +..+..+|.+
T Consensus 129 ~~~~d~~r~k~~e~l~~al~~~~~~~~~------------------------------------------~~~~~~~a~~ 166 (296)
T KOG1105|consen 129 PITNDPVRDKCRELLYAALTTEDDSRVT------------------------------------------GADPLELAVQ 166 (296)
T ss_pred CCCCchHHHHHHHHHHHHhccccccccc------------------------------------------CCCHHHHHHH
Confidence 4678999999999999999844432111 3466789999
Q ss_pred HHHHHHHHcCcChHHHHHHHHHHHHhcc--cCHHHHHHhhcCCCCccccccCChhhhcChHhHHHHHhcCCchhhhccc-
Q 006806 425 LEKASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKEGLTAEEMAKKEPDESEQMQM- 501 (630)
Q Consensus 425 IE~alf~~~~~~~~kYk~KiRSL~fNLK--kNp~Lr~rVl~GeIsP~~La~Ms~eEMASdelkeer~k~~~e~i~~~~m- 501 (630)
||.+||..++.+.++|+++|||++|||+ +||+||++||+|+|+|++|+.|+++||||+++++++++...+.|+.+||
T Consensus 167 iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~k~~keal~~~q~~ 246 (296)
T KOG1105|consen 167 IEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKEERQKLTKEALREHQMA 246 (296)
T ss_pred HHHHHHHHhCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999999999997 9999999999999999999999999999999999998888999999888
Q ss_pred -------CccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccccc
Q 006806 502 -------TDARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYAS 542 (630)
Q Consensus 502 -------~~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~s 542 (630)
..|+|++|++++|+|+|+| |||||| |||.|..|||+||||
T Consensus 247 ~~~gt~td~fkcgkckk~~cty~q~Q-trs~DePmtTfv~C~ecgnrWkfc 296 (296)
T KOG1105|consen 247 KIQGTQTDLFKCGKCKKKNCTYTQLQ-TRSADEPMTTFVTCNECGNRWKFC 296 (296)
T ss_pred ccccccccceeeccccccceeEEeec-cCCCCCCcceeeeecccCCccccC
Confidence 2499999999999999999 999999 999999999999986
No 4
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=100.00 E-value=2.5e-34 Score=271.90 Aligned_cols=146 Identities=64% Similarity=1.163 Sum_probs=134.3
Q ss_pred cCCCCCcceeeeeEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCC
Q 006806 111 SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDT 190 (630)
Q Consensus 111 ~gKG~~~r~~Y~sf~~dG~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~ 190 (630)
.|||.++|+||++|.++|++|+|||+|||.+++ +.+||||+|++||++.+|.++|+|+|||||+||.....+.+..+++
T Consensus 1 ~~~~~~~~~~y~s~~~dg~~y~vgD~Vlv~~~~-~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~ 79 (146)
T cd04713 1 TGKGKKKKCHYTSFEKDGNKYRLEDCVLLVPED-DQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDP 79 (146)
T ss_pred CCCCccceeeeeeEEECCEEEECCCEEEEeCCC-CCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCC
Confidence 489999999999999999999999999999887 4899999999999988899999999999999998755555555679
Q ss_pred CeeEeeCCcccccccccceecEEEEcCccccCCCCCCCCceEEeeeeecCCcEEeecCCcccccccc
Q 006806 191 RELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQ 257 (630)
Q Consensus 191 nELFlS~h~D~~plesIigKC~V~~i~ey~qlP~~~~~~~F~Cr~vYD~~~kkl~~l~dkDy~~~~q 257 (630)
||||+|.|.|.+|+++|+|||+|++++++.++|.....++|||+++||..+++||+|+++||+.+.|
T Consensus 80 ~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~~~~~~~~~~~~~ 146 (146)
T cd04713 80 RELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLWKLTDQDYEDERQ 146 (146)
T ss_pred CeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEeeccccccccccC
Confidence 9999999999999999999999999999999987666789999999999999999999999997654
No 5
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.93 E-value=5e-26 Score=209.67 Aligned_cols=118 Identities=22% Similarity=0.411 Sum_probs=104.6
Q ss_pred CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCccccccccc
Q 006806 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207 (630)
Q Consensus 128 G~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesI 207 (630)
|+.|++||+|||.+++ +.++|||+|++||++.+|..+|+|+|||||+||.+. +....++++|||+|+|+|++|+++|
T Consensus 1 g~~~~lgD~V~v~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~--r~~~~~~~rEvFlS~~~D~~pl~~I 77 (122)
T cd04716 1 GITYNLGDDAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIE--RQATNHDKKRVFYSEIKNDNPLDCL 77 (122)
T ss_pred CcEEEcCCEEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhccc--cccccCCCceEEEecccCccchhhe
Confidence 7889999999999986 599999999999999999999999999999999963 2234679999999999999999999
Q ss_pred ceecEEEEcCccccCC---CCCCCCceEEeeeeecCCcEEeecC
Q 006806 208 MHKCVVHFVPIHKQLP---NRKQHPGFIVQKVYDTVERKLWKLT 248 (630)
Q Consensus 208 igKC~V~~i~ey~qlP---~~~~~~~F~Cr~vYD~~~kkl~~l~ 248 (630)
+|||+|++++++..++ ....+..|||++.|+.....|..|+
T Consensus 78 ~~Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~~~~ 121 (122)
T cd04716 78 ISKVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQTLR 121 (122)
T ss_pred eeeeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheEeCC
Confidence 9999999999998874 2334789999999999888887765
No 6
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.93 E-value=8.6e-26 Score=206.57 Aligned_cols=117 Identities=25% Similarity=0.401 Sum_probs=103.4
Q ss_pred CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCccccccccc
Q 006806 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207 (630)
Q Consensus 128 G~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesI 207 (630)
|..|++||+|||.+++.+.++|||+|.+||++.+|..+|+|+|||||+||.+...+. .++||||+|.+.+++|+++|
T Consensus 1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~---~~~~Evfls~~~d~~~~~~I 77 (121)
T cd04717 1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRK---FYKNEVFKSPLYETVPVEEI 77 (121)
T ss_pred CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccc---cccCceEEcCccccccHHHh
Confidence 678999999999998756889999999999998899999999999999998765544 48999999999999999999
Q ss_pred ceecEEEEcCccccCC-C-CCCCCceEEeeeeecCCcEEeec
Q 006806 208 MHKCVVHFVPIHKQLP-N-RKQHPGFIVQKVYDTVERKLWKL 247 (630)
Q Consensus 208 igKC~V~~i~ey~qlP-~-~~~~~~F~Cr~vYD~~~kkl~~l 247 (630)
+|||.|+++.+|.+.. . ....+.|+|++.||...+.|..|
T Consensus 78 ~~kc~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~~ 119 (121)
T cd04717 78 VGKCAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKI 119 (121)
T ss_pred cCeeEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEecc
Confidence 9999999999998863 2 22458899999999988877654
No 7
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.93 E-value=1.5e-25 Score=215.06 Aligned_cols=138 Identities=25% Similarity=0.401 Sum_probs=114.0
Q ss_pred ccccccceeecCCCCCcceeeeeEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC--CceEEEEEEEecccccC
Q 006806 101 AKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD--GSMMVTGQWFYRPEEAD 178 (630)
Q Consensus 101 a~~iG~pvk~~gKG~~~r~~Y~sf~~dG~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~d--G~~~VrVqWFYRPeEt~ 178 (630)
.+|.|.|.+.-+ ++||+++.++|..|+|||+|||.+++ .+||||+|.+||+..+ |.++|+|+|||||+||.
T Consensus 5 ~~~~g~~~~~~~-----~~~Y~s~~~~g~~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~ 77 (159)
T cd04715 5 GVKRGEGGKKKD-----GQFYRSFTYDGVEYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIR 77 (159)
T ss_pred ceecccccccCC-----ceEEEEEEECCEEEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhc
Confidence 567777777654 57999999999999999999999854 8999999999999865 89999999999999998
Q ss_pred CCCCCCCCCCCCCeeEeeCCc-----ccccccccceecEEEEcCccccCC--CCC--CCCceEEeeeeecCCcEEee
Q 006806 179 RKGGGNWLSRDTRELFYSFHR-----DEVPAESVMHKCVVHFVPIHKQLP--NRK--QHPGFIVQKVYDTVERKLWK 246 (630)
Q Consensus 179 ~~~~g~~~~~~~nELFlS~h~-----D~~plesIigKC~V~~i~ey~qlP--~~~--~~~~F~Cr~vYD~~~kkl~~ 246 (630)
+...+. +.+++||||+|.|. ++||+++|+|||.|+++++|...+ +.. ....|++.+.||...++...
T Consensus 78 ~~~~~~-~~~~~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~~~~s~~~~~~~~~~f~~~f~~~~~~~~~ 153 (159)
T cd04715 78 MELKGE-PKRHINEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRNPQPSDGIPTSADFLFPCNFDVGRCVIVD 153 (159)
T ss_pred cccccC-cccCCCcEEEecCcCccccccCcHHHccceeEEEEehHhhhCCCCcCCccccCcceeeeEEEecCceecc
Confidence 643333 34689999999985 668999999999999999998754 212 33667888889988776643
No 8
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.93 E-value=1.3e-25 Score=206.25 Aligned_cols=112 Identities=27% Similarity=0.439 Sum_probs=99.1
Q ss_pred CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCccccccccc
Q 006806 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207 (630)
Q Consensus 128 G~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesI 207 (630)
|..|++||+|||.+++.+.+||||+|.+||++.+|.++|+|+|||||+||.+... ..+++||||+|+|.|++|+++|
T Consensus 1 ~~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~---~~~~~~EvF~S~~~d~~~~~~I 77 (121)
T cd04714 1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRK---PNHGEKELFASDHQDENSVQTI 77 (121)
T ss_pred CCEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCccc---ccCCCCceEecCCcccccHHHh
Confidence 5789999999999987568899999999999988999999999999999986432 3469999999999999999999
Q ss_pred ceecEEEEcCccccCCC-----CCCCCceEEeeeeecCCc
Q 006806 208 MHKCVVHFVPIHKQLPN-----RKQHPGFIVQKVYDTVER 242 (630)
Q Consensus 208 igKC~V~~i~ey~qlP~-----~~~~~~F~Cr~vYD~~~k 242 (630)
+|||.|+++++|.++.. ....+.|+|+..||+...
T Consensus 78 ~gkc~V~~~~ey~~~~~~~~~~~~~~d~~~Ce~~yn~~~~ 117 (121)
T cd04714 78 EHKCYVLTFAEYERLARVKKKPQDGVDFYYCAGTYNPDTG 117 (121)
T ss_pred CcccEEEehhHheecccccCCCCcCCCEEEEeccCCCCcC
Confidence 99999999999998642 235689999999998654
No 9
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=99.92 E-value=1.1e-24 Score=194.82 Aligned_cols=117 Identities=38% Similarity=0.646 Sum_probs=103.4
Q ss_pred CeEEeeCCeEEEcCCCC--CCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCccccccc
Q 006806 128 GNKYELEDPVLLTPEDT--NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAE 205 (630)
Q Consensus 128 G~~YkVGD~VyV~~e~~--~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~ple 205 (630)
|.+|++||+|||.+++. ..++|||+|.+||++.+|.++|+|+|||||+||.+...+ .+.+||||+|+++++++++
T Consensus 1 g~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~---~~~~~Elf~s~~~~~i~v~ 77 (123)
T cd04370 1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSP---FALRRELFLSDHLDEIPVE 77 (123)
T ss_pred CCEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhcccccc---ccccceeEEecCccccCHH
Confidence 68999999999999874 478999999999999899999999999999999974432 4699999999999999999
Q ss_pred ccceecEEEEcCccccCC---CCCCCCceEEeeeeecCCcEEeec
Q 006806 206 SVMHKCVVHFVPIHKQLP---NRKQHPGFIVQKVYDTVERKLWKL 247 (630)
Q Consensus 206 sIigKC~V~~i~ey~qlP---~~~~~~~F~Cr~vYD~~~kkl~~l 247 (630)
+|+|||.|++..+|.+.. ....++.|||++.||.....|..+
T Consensus 78 ~I~gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~~ 122 (123)
T cd04370 78 SIIGKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKAL 122 (123)
T ss_pred HhccccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEeC
Confidence 999999999999998762 444678999999999988777654
No 10
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.92 E-value=1.1e-24 Score=195.25 Aligned_cols=116 Identities=31% Similarity=0.464 Sum_probs=102.2
Q ss_pred EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCc-eEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCcccccccccc
Q 006806 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS-MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVM 208 (630)
Q Consensus 130 ~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~-~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesIi 208 (630)
.|++||+|||.+++...++|||+|.+||++.+|. ++++|+|||||+||.+...+ .+++||||+|++++++++++|+
T Consensus 1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~---~~~~~Elf~s~~~~~i~~~~I~ 77 (120)
T smart00439 1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAA---LFDKNEVFLSDEYDTVPLSDII 77 (120)
T ss_pred CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccccccc---cCCCcceEEEccCccCChHHee
Confidence 4799999999998766789999999999998888 89999999999999975433 3489999999999999999999
Q ss_pred eecEEEEcCccccCCCCC---CCCceEEeeeeecCCcEEeecC
Q 006806 209 HKCVVHFVPIHKQLPNRK---QHPGFIVQKVYDTVERKLWKLT 248 (630)
Q Consensus 209 gKC~V~~i~ey~qlP~~~---~~~~F~Cr~vYD~~~kkl~~l~ 248 (630)
|||.|++.++|...+... .++.|||++.||...++|++++
T Consensus 78 ~kc~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~~~ 120 (120)
T smart00439 78 GKCNVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKKLP 120 (120)
T ss_pred eEEEEEEcchhcccccccCCCCCCeEEEEEEEccccCcccCCC
Confidence 999999999998865322 4689999999999998887663
No 11
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=99.91 E-value=1.8e-24 Score=193.93 Aligned_cols=115 Identities=37% Similarity=0.613 Sum_probs=100.4
Q ss_pred eEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCc--eEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCcccccccc
Q 006806 129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS--MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAES 206 (630)
Q Consensus 129 ~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~--~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~ples 206 (630)
++|++||+|||.+++...++|||+|.+||++.++. ++|+|+|||||+||.. + ....+||||+|++++++|+++
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~---~--~~~~~~Elf~s~~~~~~~~~~ 75 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSL---G--KTFSPRELFLSDHCDDIPVES 75 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTT---G--GHSCTTEEEEEEEEEEEEGGG
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECcccccc---c--ccCCCCEEEEECcEeEEehhh
Confidence 57999999999999878899999999999988877 9999999999999932 1 123569999999999999999
Q ss_pred cceecEEEEcCccccCCCCC--CCCceEEeeeeecCCcEEeecC
Q 006806 207 VMHKCVVHFVPIHKQLPNRK--QHPGFIVQKVYDTVERKLWKLT 248 (630)
Q Consensus 207 IigKC~V~~i~ey~qlP~~~--~~~~F~Cr~vYD~~~kkl~~l~ 248 (630)
|+|||.|++..++.+..... .++.|||++.||...++|..++
T Consensus 76 I~gkc~V~~~~~~~~~~~~~~~~~~~F~cr~~yd~~~~~f~~~~ 119 (119)
T PF01426_consen 76 IRGKCNVLHLEDYEQARPYGKEEPDTFFCRYAYDPQKKRFKKLP 119 (119)
T ss_dssp EEEEEEEEEHHHHTTGCCHCHHTTTEEEEEEEEETTTTEEEE-S
T ss_pred EEeeeEEEECCccccccccccCCCCEEEEEEEEeCCcCEEeCCC
Confidence 99999999999998865332 6799999999999999998764
No 12
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.91 E-value=4e-24 Score=200.23 Aligned_cols=118 Identities=24% Similarity=0.444 Sum_probs=101.5
Q ss_pred EEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC------------CceEEEEEEEecccccCCCCCCCCCCCCCC
Q 006806 124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD------------GSMMVTGQWFYRPEEADRKGGGNWLSRDTR 191 (630)
Q Consensus 124 f~~dG~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~d------------G~~~VrVqWFYRPeEt~~~~~g~~~~~~~n 191 (630)
+..+|..|++||+|||.+++.+.|+|||+|++|+...+ +..+|+|+|||||+||... . .++.+
T Consensus 5 ~~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~---~--~~d~r 79 (135)
T cd04710 5 VLKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRR---V--VADSR 79 (135)
T ss_pred EccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCc---c--cCCce
Confidence 34689999999999999988788999999999998543 2368999999999998632 1 46999
Q ss_pred eeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEee
Q 006806 192 ELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWK 246 (630)
Q Consensus 192 ELFlS~h~D~~plesIigKC~V~~i~ey~qlP-~~~~~~~F~Cr~vYD~~~kkl~~ 246 (630)
|||+|.|.|++|+++|.|||+|++..++..+. ....++.|||.++||+..+++++
T Consensus 80 elf~S~h~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~~~ 135 (135)
T cd04710 80 LLYASMHSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRYYD 135 (135)
T ss_pred EEEEEeeEeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhccC
Confidence 99999999999999999999999999887764 23357899999999999998863
No 13
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.90 E-value=5.8e-24 Score=197.94 Aligned_cols=120 Identities=22% Similarity=0.329 Sum_probs=103.0
Q ss_pred EEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCccccc
Q 006806 124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVP 203 (630)
Q Consensus 124 f~~dG~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~p 203 (630)
|+.||..|++||||||.+++ .++|||+|.+||++.+|.++|+|+||+||+|+.+...+. .+.+||||+|++.+++|
T Consensus 1 ~~r~~~~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~--~~~~~EvFlS~~~d~i~ 76 (130)
T cd04721 1 FCRNGVTISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPD--SVNPREIFLSPNLQVIS 76 (130)
T ss_pred CccCCEEEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCC--CCCCCeEEEcCCccccc
Confidence 46799999999999999876 788999999999998899999999999999999743332 26999999999999999
Q ss_pred ccccceecEEEEcCccccCCC----CCCCCceEEeeeeecCCcEEeec
Q 006806 204 AESVMHKCVVHFVPIHKQLPN----RKQHPGFIVQKVYDTVERKLWKL 247 (630)
Q Consensus 204 lesIigKC~V~~i~ey~qlP~----~~~~~~F~Cr~vYD~~~kkl~~l 247 (630)
+++|+|||+||+..+|.++.. ......|+|++.||....+-+++
T Consensus 77 ~~~I~gk~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~~~~~fd~ 124 (130)
T cd04721 77 VECIDGLATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNNKVKPFDI 124 (130)
T ss_pred hHHeeeeeEECCHHHHhhhhccccCccccccEEEEEEecCCCCceeee
Confidence 999999999999999988641 12357999999999876644443
No 14
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.89 E-value=2.8e-23 Score=200.13 Aligned_cols=118 Identities=21% Similarity=0.336 Sum_probs=100.9
Q ss_pred CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCC----CCC---------------CCCCC
Q 006806 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK----GGG---------------NWLSR 188 (630)
Q Consensus 128 G~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~----~~g---------------~~~~~ 188 (630)
++.|+|||+|||.++. +.++|||+|++||++.+|.++|+|+|||||+|++.. ..+ ..+..
T Consensus 1 ~~~yrvGD~Vy~~~~~-~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~ 79 (164)
T cd04709 1 ANMYRVGDYVYFESSP-NNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQL 79 (164)
T ss_pred CcEEecCCEEEEECCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhcc
Confidence 3689999999999884 667889999999999999999999999999998641 111 11335
Q ss_pred CCCeeEeeCCcccccccccceecEEEEcCccccCCC-CCCCCceEEeeeeecCCcEEee
Q 006806 189 DTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN-RKQHPGFIVQKVYDTVERKLWK 246 (630)
Q Consensus 189 ~~nELFlS~h~D~~plesIigKC~V~~i~ey~qlP~-~~~~~~F~Cr~vYD~~~kkl~~ 246 (630)
+.+|||+|.|.+.+|+.+|.|||.|+++.+|..+.. ...++.|||+.+||+.+++|..
T Consensus 80 ~~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~~ 138 (164)
T cd04709 80 RHRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLLA 138 (164)
T ss_pred CcceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeecc
Confidence 899999999999999999999999999999988753 2357999999999999999953
No 15
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.89 E-value=5.2e-23 Score=184.25 Aligned_cols=99 Identities=30% Similarity=0.429 Sum_probs=87.9
Q ss_pred hhhHHHHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccccCCCCCCCChhhHHHHHHHHHHH
Q 006806 349 ETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKA 428 (630)
Q Consensus 349 d~~RDK~le~L~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~v~~~A~~IE~a 428 (630)
|.+||+|+++|+++|...+..... ...+..+|.+||.+
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~~------------------------------------------~~~~~~lA~~IE~~ 38 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEEI------------------------------------------ELDPTELAVQIEAE 38 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCcc------------------------------------------cccHHHHHHHHHHH
Confidence 579999999999999988754211 12455799999999
Q ss_pred HHHHcCcChHHHHHHHHHHHHhcc--cCHHHHHHhhcCCCCccccccCChhhhcChHhHHHHH
Q 006806 429 SHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKEGLTAEEMA 489 (630)
Q Consensus 429 lf~~~~~~~~kYk~KiRSL~fNLK--kNp~Lr~rVl~GeIsP~~La~Ms~eEMASdelkeer~ 489 (630)
||..|++...+|++|+|||+|||| +||+||++|++|+|+|++||.||++||||++++++++
T Consensus 39 lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~vl~G~i~p~~lv~Ms~~ElAs~elk~~~e 101 (102)
T smart00510 39 MFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPEKLATMTAEELASAELKEKRE 101 (102)
T ss_pred HHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHh
Confidence 999999888899999999999999 9999999999999999999999999999999998874
No 16
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.87 E-value=7.5e-22 Score=183.82 Aligned_cols=114 Identities=20% Similarity=0.263 Sum_probs=98.8
Q ss_pred cCeEEeeCCeEEEcCCCCC----------CCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEee
Q 006806 127 DGNKYELEDPVLLTPEDTN----------QKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYS 196 (630)
Q Consensus 127 dG~~YkVGD~VyV~~e~~~----------~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS 196 (630)
+|..|+|||+|+|.+++.. .++||++|..||++.+|.+||+|+|||||+||.+.. .+++||||||
T Consensus 2 ~~~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~-----~~~~~ElFLS 76 (130)
T cd04712 2 HGLTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN-----YANERELFLT 76 (130)
T ss_pred CCCEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc-----cCCCceEEEe
Confidence 5789999999999998754 389999999999999999999999999999999743 5799999999
Q ss_pred CCccccccc----ccceecEEEEcCccccCCCCCCCCceEEeeeeecCCcEEeecC
Q 006806 197 FHRDEVPAE----SVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLT 248 (630)
Q Consensus 197 ~h~D~~ple----sIigKC~V~~i~ey~qlP~~~~~~~F~Cr~vYD~~~kkl~~l~ 248 (630)
+||+++++. .|++||.|++...+... ..++.|+|+..|++..+.|..|+
T Consensus 77 d~c~~~~~~~~~~~I~~k~~V~~~~~~~~~---~~~~~F~r~syy~~e~~~F~~l~ 129 (130)
T cd04712 77 NECTCLELDLLSTEIKGVHKVDWSGTPWGK---GLPEFFVRQSYYWPERGAFTSLK 129 (130)
T ss_pred ccccccccccccceeEEEEEEEEecCcCCc---CCCCEEEEEEEECccCCceEcCC
Confidence 999999999 99999999998776531 23466777777777999998775
No 17
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.87 E-value=4.7e-22 Score=196.59 Aligned_cols=124 Identities=27% Similarity=0.382 Sum_probs=104.4
Q ss_pred EEEcCeEEeeCCeEEEcCCC-----------------CCCCCeEEEEeEEeeCCCC------ceEEEEEEEecccccCCC
Q 006806 124 FEFDGNKYELEDPVLLTPED-----------------TNQKPYVAIIKEITQSKDG------SMMVTGQWFYRPEEADRK 180 (630)
Q Consensus 124 f~~dG~~YkVGD~VyV~~e~-----------------~~~~pyIArI~~I~e~~dG------~~~VrVqWFYRPeEt~~~ 180 (630)
|.++|++|++||+|||.|+. ...+++||+|.+|+..+++ ..+|+|+|||||+||..
T Consensus 1 f~~~Gv~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~- 79 (202)
T cd04708 1 FVYDGVTYSVGDFLYVSPDAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSP- 79 (202)
T ss_pred CcCCCEEEecCCeEEECcccccccccccccccccccCCCCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCc-
Confidence 57899999999999999981 1347789999999986554 68999999999999863
Q ss_pred CCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEeecCCc
Q 006806 181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLTDK 250 (630)
Q Consensus 181 ~~g~~~~~~~nELFlS~h~D~~plesIigKC~V~~i~ey~qlP-~~~~~~~F~Cr~vYD~~~kkl~~l~dk 250 (630)
+....++.+|||+|++.+++|+++|.|||.|++..++..+. ....++.|||+..||+.++.|-.||..
T Consensus 80 --~~~y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~~lP~~ 148 (202)
T cd04708 80 --EKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLKQLPPN 148 (202)
T ss_pred --ccceecCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccCCCCch
Confidence 22245699999999999999999999999999999886642 122479999999999999999888775
No 18
>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=99.86 E-value=6.3e-23 Score=186.40 Aligned_cols=113 Identities=35% Similarity=0.511 Sum_probs=97.9
Q ss_pred cChhhHHHHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccccCCCCCCCChhhHHHHHHHHH
Q 006806 347 TGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALE 426 (630)
Q Consensus 347 Tgd~~RDK~le~L~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~v~~~A~~IE 426 (630)
|++.+|++|+++|+.+|...... .. . +..+..+|.+||
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~--------------------------~---------------~~~~~~lA~~IE 38 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QD--------------------------D---------------PEDAKELAKEIE 38 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CC--------------------------C---------------TCCHHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-cc--------------------------c---------------hhHHHHHHHHHH
Confidence 78999999999999999988543 10 0 457789999999
Q ss_pred HHHHHHcCcChHHHHHHHHHHHHhcc--cCHHHHHHhhcCCCCccccccCChhhhcChHhHHHHHhcCCchhhhccc
Q 006806 427 KASHDTLSLDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKEGLTAEEMAKKEPDESEQMQM 501 (630)
Q Consensus 427 ~alf~~~~~~~~kYk~KiRSL~fNLK--kNp~Lr~rVl~GeIsP~~La~Ms~eEMASdelkeer~k~~~e~i~~~~m 501 (630)
.+||..|+++..+|++++|||+|||| +||.|+.+|++|+|+|.+||.||++||||+++++++++...+.+...||
T Consensus 39 ~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~~~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~~~l~~~~~ 115 (115)
T PF07500_consen 39 EALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLRRRILSGEISPEELVTMSPEELASEELKEEREKIRKESLKQSQM 115 (115)
T ss_dssp HHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHHHHHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHHHHHHHTB-
T ss_pred HHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHHHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhC
Confidence 99999998888999999999999999 9999999999999999999999999999999998876555666666554
No 19
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.86 E-value=1.7e-21 Score=179.69 Aligned_cols=112 Identities=22% Similarity=0.326 Sum_probs=95.8
Q ss_pred CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCccccccccc
Q 006806 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207 (630)
Q Consensus 128 G~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesI 207 (630)
|..|.+||+|+|.+++...++|||+|..||++.+|.+||+|+|||||+||.++. .++++|||+|++|++++|.+|
T Consensus 1 g~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~-----~~~~kEvFlsd~c~d~~l~~I 75 (124)
T cd04760 1 GEELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGE-----TSDPLELFLVDECEDMALSSI 75 (124)
T ss_pred CCEEecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCcccccc-----cCCCcEEEeecccCCcchHHh
Confidence 678999999999998778999999999999999999999999999999999643 369999999999999999999
Q ss_pred ceecEEEEcCcccc--------CC---CCCCCCceEEeeeeecCCcEE
Q 006806 208 MHKCVVHFVPIHKQ--------LP---NRKQHPGFIVQKVYDTVERKL 244 (630)
Q Consensus 208 igKC~V~~i~ey~q--------lP---~~~~~~~F~Cr~vYD~~~kkl 244 (630)
.+||+|+..++-.. .+ ....-.+|||++.||+...+|
T Consensus 76 ~~Kv~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf 123 (124)
T cd04760 76 HGKVNVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARF 123 (124)
T ss_pred eeeeEEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhcc
Confidence 99999999876521 12 112337899999999865554
No 20
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.79 E-value=3.5e-19 Score=174.17 Aligned_cols=119 Identities=17% Similarity=0.235 Sum_probs=99.0
Q ss_pred cCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceEEEEEEEecccccCCCCC-CCCC-----CCCCCeeEeeCCc
Q 006806 127 DGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMMVTGQWFYRPEEADRKGG-GNWL-----SRDTRELFYSFHR 199 (630)
Q Consensus 127 dG~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~d-G~~~VrVqWFYRPeEt~~~~~-g~~~-----~~~~nELFlS~h~ 199 (630)
+|..|++||+|+|.++. ..++|||+|.+|+.+.. +.+.+.|+|||||.|+..... +.+. ...+||||+|.|.
T Consensus 49 d~~~~~vGD~Vlik~~~-~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~ 127 (179)
T cd04720 49 DGLELSVGDTILVKDDV-ANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAEL 127 (179)
T ss_pred CCeEEeCCCEEEEeCCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEeccc
Confidence 89999999999999986 58999999999998765 567999999999999964221 1111 2348999999999
Q ss_pred ccccccccceecEEEEcCccccCCC--CCCCCceEEeeeeecCCcEEee
Q 006806 200 DEVPAESVMHKCVVHFVPIHKQLPN--RKQHPGFIVQKVYDTVERKLWK 246 (630)
Q Consensus 200 D~~plesIigKC~V~~i~ey~qlP~--~~~~~~F~Cr~vYD~~~kkl~~ 246 (630)
+.+++.+|++||+||...+|.++.. .....+||||++||+..+.|..
T Consensus 128 d~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~ 176 (179)
T cd04720 128 SEIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVW 176 (179)
T ss_pred ceEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEcc
Confidence 9999999999999999999987642 2346899999999998886654
No 21
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.78 E-value=2.8e-20 Score=175.69 Aligned_cols=98 Identities=18% Similarity=0.340 Sum_probs=86.7
Q ss_pred CCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCcccccccccceecEEEEcCccccCCC
Q 006806 145 NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN 224 (630)
Q Consensus 145 ~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesIigKC~V~~i~ey~qlP~ 224 (630)
...+|||+|.+||++. |..+|+|+|||||+||.+... ..++.+|||+|+|.|++++++|+|||.||++.+|.++..
T Consensus 50 ~~~~~vArIekiW~~~-G~~~~~grWy~rPEET~~gr~---~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~ 125 (148)
T cd04718 50 SGDLWLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQ---PHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASN 125 (148)
T ss_pred cCchHHHHHHHHHhcc-CceEEEEEEEeCchhccCccc---cccccceeeeccccccccHHHHhcccEEcCHHHcccccC
Confidence 3678999999999986 999999999999999997543 456999999999999999999999999999999998653
Q ss_pred CCCCCceEEeeeeecCCcEEeec
Q 006806 225 RKQHPGFIVQKVYDTVERKLWKL 247 (630)
Q Consensus 225 ~~~~~~F~Cr~vYD~~~kkl~~l 247 (630)
. ..++|+|+..||...+.|..+
T Consensus 126 ~-g~Dvy~Ce~~Yd~~~~~Fkr~ 147 (148)
T cd04718 126 D-GDDVFLCEYEYDVHWQSFKRL 147 (148)
T ss_pred C-CCceEEEEEEEhhhcCceeec
Confidence 3 568999999999998887654
No 22
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.78 E-value=5.2e-19 Score=164.39 Aligned_cols=113 Identities=27% Similarity=0.401 Sum_probs=93.2
Q ss_pred eEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCC---ceEEEEEEEecccccCCCC---CCCCCCCCCCeeEeeCCcc--
Q 006806 129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDG---SMMVTGQWFYRPEEADRKG---GGNWLSRDTRELFYSFHRD-- 200 (630)
Q Consensus 129 ~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG---~~~VrVqWFYRPeEt~~~~---~g~~~~~~~nELFlS~h~D-- 200 (630)
.+|+|||||+|.+++. .++|||+|++|+++.+| ...++|||||||+|+++.. .|. ..+.+|||+++|.+
T Consensus 2 ~~i~vGd~VlI~~~d~-~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~--~~~~~EvF~~~~~~~~ 78 (128)
T cd04719 2 LTIEVGDFVLIEGEDA-DGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGR--EPHSQEVFFYSRSSCD 78 (128)
T ss_pred eEEecCCEEEEECCCC-CCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccC--CCCCcEEEEecCcccc
Confidence 4799999999999874 88999999999998765 5699999999999997422 222 34899999999874
Q ss_pred -cccccccceecEEEEcCccccCCC--CCCCCceEEeeeeecCCcEE
Q 006806 201 -EVPAESVMHKCVVHFVPIHKQLPN--RKQHPGFIVQKVYDTVERKL 244 (630)
Q Consensus 201 -~~plesIigKC~V~~i~ey~qlP~--~~~~~~F~Cr~vYD~~~kkl 244 (630)
++++++|.|+|.|+.+.+|..++. ......||+++.|+....+.
T Consensus 79 ~~i~~etI~gkc~V~~~~~y~~l~~~~~~~~~~~F~r~~~~~k~~~~ 125 (128)
T cd04719 79 NDIDAETIIGKVRVEPVEPKTDLPETKKKTGGPLFVKRYWDTKTFRS 125 (128)
T ss_pred CcEeHHHcccEEEEEEcCCccchhhhccccCceEEEEEEeccccccc
Confidence 899999999999999999999883 22346788888888765443
No 23
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.70 E-value=2.6e-17 Score=153.36 Aligned_cols=114 Identities=18% Similarity=0.216 Sum_probs=87.5
Q ss_pred CCeEEEcCCCCCCCCeEEEEeEEeeCCCC-------ceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCcccccccc
Q 006806 134 EDPVLLTPEDTNQKPYVAIIKEITQSKDG-------SMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAES 206 (630)
Q Consensus 134 GD~VyV~~e~~~~~pyIArI~~I~e~~dG-------~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~ples 206 (630)
+|.|-=.+-+.+.+++||||++|...+++ .++|+|+|||||++|..+... ..+.+.||||+|+|.+++|+.+
T Consensus 13 ~~~~~~~~~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~-ayhsDirevy~Sd~~~~~~~~~ 91 (137)
T cd04711 13 SDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKA-TYHADINMLYWSDEEATVDFSA 91 (137)
T ss_pred ccccccccCCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEeccccccccccc-ccccceeeEEeecceeecChhh
Confidence 34444344456788999999999876432 468999999999999953211 1345779999999999999999
Q ss_pred cceecEEEEcCcccc-CC--CCCCCCceEEeeeeecCCcEEeecC
Q 006806 207 VMHKCVVHFVPIHKQ-LP--NRKQHPGFIVQKVYDTVERKLWKLT 248 (630)
Q Consensus 207 IigKC~V~~i~ey~q-lP--~~~~~~~F~Cr~vYD~~~kkl~~l~ 248 (630)
|.|||.|++..+... +. ....++.|||+.+||..++.|.+.|
T Consensus 92 I~GKC~V~~~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~d~p 136 (137)
T cd04711 92 VQGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFEDPP 136 (137)
T ss_pred ccceEEEEeccccchhHHHHhcCCCcceEEhhhhccccCcccCCC
Confidence 999999997655432 22 2346899999999999999887654
No 24
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.51 E-value=1.6e-14 Score=162.07 Aligned_cols=120 Identities=28% Similarity=0.416 Sum_probs=108.7
Q ss_pred EEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCccccc
Q 006806 124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVP 203 (630)
Q Consensus 124 f~~dG~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~p 203 (630)
+.++|..|.+||+|||.+..++.++.|++|.++|+..+|..|+.++|||||++|.|..++.| ..+|||.+..+.+++
T Consensus 184 ~~i~~~~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F---~k~Evfkt~~~~~~~ 260 (629)
T KOG1827|consen 184 VEIDGTKYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKF---YKQEVFKTSLYRDDL 260 (629)
T ss_pred ccccCcccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccccch---hcccceecccccccH
Confidence 78999999999999999988779999999999999999999999999999999999998888 999999999999999
Q ss_pred ccccceecEEEEcCccccCC--CCCCCCceEEeeeeecCC-----cEEee
Q 006806 204 AESVMHKCVVHFVPIHKQLP--NRKQHPGFIVQKVYDTVE-----RKLWK 246 (630)
Q Consensus 204 lesIigKC~V~~i~ey~qlP--~~~~~~~F~Cr~vYD~~~-----kkl~~ 246 (630)
+.-|+|+|.|+++..|.... ....-+.|+|+..|+... ++.|.
T Consensus 261 ~q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K~f~kirsw~ 310 (629)
T KOG1827|consen 261 VQRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLKKFNKIRSWK 310 (629)
T ss_pred HHHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchhhhccccCch
Confidence 99999999999999998753 334568999999998654 55554
No 25
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.21 E-value=1e-11 Score=93.75 Aligned_cols=37 Identities=24% Similarity=0.664 Sum_probs=35.0
Q ss_pred cccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYA 541 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~ 541 (630)
++|++|+++++.|+|+| +||||| .||.|.+|||+|+.
T Consensus 1 ~~Cp~C~~~~a~~~q~Q-~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQ-TRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEc-ccCCCCCCeEEEEeCCCCCEeCC
Confidence 47999999999999999 999999 99999999999984
No 26
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=99.15 E-value=2.6e-11 Score=91.11 Aligned_cols=36 Identities=25% Similarity=0.683 Sum_probs=31.7
Q ss_pred cccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWY 540 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk 540 (630)
+.|++||++++.|+|+| +||||| .||.|.+|||+|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q-~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQ-TRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEES-SSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEee-ccCCCCCCeEEEEeCCCCCeeC
Confidence 57999999999999999 999999 9999999999996
No 27
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=99.07 E-value=4.8e-11 Score=105.32 Aligned_cols=47 Identities=21% Similarity=0.531 Sum_probs=41.5
Q ss_pred chhhhcccCccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCccccc
Q 006806 494 DESEQMQMTDARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYA 541 (630)
Q Consensus 494 e~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~ 541 (630)
+.+...+.+...|++||+.+++|.|+| |||||| +||.|.+|+|+|+.
T Consensus 56 ~a~~nv~~t~~~Cp~Cgh~rayF~qlQ-tRSADEPmT~FYkC~~C~~~Wre 105 (105)
T KOG2906|consen 56 EAWENVDQTEATCPTCGHERAYFMQLQ-TRSADEPMTTFYKCCKCKHRWRE 105 (105)
T ss_pred ccccchhhccCcCCCCCCCceEEEEee-eccCCCcHhHhhhhhcccccccC
Confidence 344445567899999999999999999 999999 99999999999984
No 28
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.04 E-value=1.2e-10 Score=106.56 Aligned_cols=39 Identities=18% Similarity=0.544 Sum_probs=37.1
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYAS 542 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~s 542 (630)
.+.|++||+.++.|+|+| +||||| +||+|..|||+|+++
T Consensus 72 ~~~CpkCg~~ea~y~~~Q-tRsaDEp~T~Fy~C~~Cg~~wre~ 113 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQ-TRSADEPETRFYKCTRCGYRWREY 113 (113)
T ss_pred cccCCCCCCceeEEEeee-hhccCCCceEEEEecccCCEeecC
Confidence 578999999999999999 999999 999999999999975
No 29
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.04 E-value=8.6e-11 Score=134.31 Aligned_cols=79 Identities=32% Similarity=0.410 Sum_probs=71.6
Q ss_pred CCCCCCChhhHHHHHHHHHHHHHHHcC-cChHHHHHHHHHHHHhcc--cCHHHHHHhhcCCCCccccccCChhhhcChHh
Q 006806 408 NGKSFIWPDTAIAAVTALEKASHDTLS-LDFQKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKEGLT 484 (630)
Q Consensus 408 ~~~~~~w~~~v~~~A~~IE~alf~~~~-~~~~kYk~KiRSL~fNLK--kNp~Lr~rVl~GeIsP~~La~Ms~eEMASdel 484 (630)
+.+.+.|+.. ++..||..+|..|+ +.+.+|++|+|||+|||| +||.||.+|+.|+|+|.+|+.|+++|||+.++
T Consensus 262 g~k~~~d~~l---l~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL 338 (778)
T KOG1634|consen 262 GEKQLQDPNL---LLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPEL 338 (778)
T ss_pred ccccccchhh---HhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchH
Confidence 4566777864 44499999999999 788899999999999997 99999999999999999999999999999999
Q ss_pred HHHHH
Q 006806 485 AEEMA 489 (630)
Q Consensus 485 keer~ 489 (630)
.++++
T Consensus 339 ~~~rE 343 (778)
T KOG1634|consen 339 AEWRE 343 (778)
T ss_pred HHHHH
Confidence 98886
No 30
>PHA02998 RNA polymerase subunit; Provisional
Probab=98.99 E-value=3e-10 Score=110.06 Aligned_cols=41 Identities=15% Similarity=0.360 Sum_probs=38.0
Q ss_pred CccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCccccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYASR 543 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~sr 543 (630)
+.++|++|+++++.|+|+| |||||| +||.|..|||+|+..+
T Consensus 142 t~v~CPkCg~~~A~f~qlQ-TRSADEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQ-TRAADEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred cCCCCCCCCCCceEEEEEe-eccCCCCceEEEEcCCCCCccCCcc
Confidence 4689999999999999999 999999 9999999999999643
No 31
>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=98.92 E-value=8e-10 Score=98.85 Aligned_cols=41 Identities=20% Similarity=0.467 Sum_probs=38.2
Q ss_pred cCccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccccc
Q 006806 501 MTDARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYAS 542 (630)
Q Consensus 501 m~~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~s 542 (630)
.+.+.|++||+.++.|+|+| +||||| .||.|.+|||+|+.+
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~Q-~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLLQ-TRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cccCCCCCCCCCeeEEEEec-cCCCCCCcEEEEEeCCCCCeeEeC
Confidence 35789999999999999999 999999 999999999999975
No 32
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=98.57 E-value=8.5e-09 Score=111.61 Aligned_cols=136 Identities=21% Similarity=0.325 Sum_probs=105.7
Q ss_pred eEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCC-------CCC-----------------C
Q 006806 129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK-------GGG-----------------N 184 (630)
Q Consensus 129 ~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~-------~~g-----------------~ 184 (630)
..|.|||+||+.+.. ..++.|-+|+++.++.+|++..+|..|||-.|+... ..+ .
T Consensus 4 n~y~vgd~vYf~~ss-s~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e 82 (693)
T KOG3554|consen 4 NMYRVGDYVYFENSS-SNPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAE 82 (693)
T ss_pred ccceecceEEEecCC-CChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhh
Confidence 379999999999887 456669999999999999999999999999998641 001 1
Q ss_pred C-----------------CCCCCCeeEeeCCcccccccccceecEEEEcCccccCC-CCCCCCceEEeeeeecCCcEEee
Q 006806 185 W-----------------LSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWK 246 (630)
Q Consensus 185 ~-----------------~~~~~nELFlS~h~D~~plesIigKC~V~~i~ey~qlP-~~~~~~~F~Cr~vYD~~~kkl~~ 246 (630)
+ +..-.+|||+|-+....|+..|.|||.|..+-+.+.+- .....+.||...|||+..+.|.
T Consensus 83 ~EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLL- 161 (693)
T KOG3554|consen 83 IEEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLL- 161 (693)
T ss_pred hhhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhh-
Confidence 1 01246899999999999999999999999987765532 2335689999999999998884
Q ss_pred cCCcccc---ccccchhhHHHHHh
Q 006806 247 LTDKDYE---DNKQHEIDLLVQKT 267 (630)
Q Consensus 247 l~dkDy~---~~~q~Evd~ll~kt 267 (630)
.|+..+ +..|.+|+..|...
T Consensus 162 -ADkGeIRVG~kYQA~i~e~l~Eg 184 (693)
T KOG3554|consen 162 -ADKGEIRVGEKYQADIPEWLEEG 184 (693)
T ss_pred -ccCcceeecccccccchHHHHhc
Confidence 566543 44667788877643
No 33
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=98.44 E-value=5.7e-08 Score=88.09 Aligned_cols=41 Identities=12% Similarity=0.405 Sum_probs=37.1
Q ss_pred ccCccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCccccc
Q 006806 500 QMTDARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYA 541 (630)
Q Consensus 500 ~m~~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~ 541 (630)
...+-+|++||+.+..|..+| +||||| +||+|.+|+++...
T Consensus 71 a~I~~kCpkCghe~m~Y~T~Q-lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQ-LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred cchhccCcccCCchhhhhhhh-cccccCCceEEEEcCccceeeec
Confidence 445678999999999999999 999999 99999999998764
No 34
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=98.03 E-value=3.5e-06 Score=76.03 Aligned_cols=37 Identities=24% Similarity=0.663 Sum_probs=34.7
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWY 540 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk 540 (630)
+..|++||+++.-|+|.| +|-||+ -||.|.+|||+|.
T Consensus 73 ~~~C~~C~~~eavffQ~~-~~r~d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 73 DKHCPKCGHREAVFFQAQ-TRRADEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred cccCCccCCcceEEEecc-cccccceEEEEEEecccccccc
Confidence 578999999999999999 899999 8999999999996
No 35
>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=93.18 E-value=0.095 Score=43.93 Aligned_cols=43 Identities=21% Similarity=0.520 Sum_probs=30.4
Q ss_pred cccCCCCCCceEEEEeeeccCC-----Cc-----eEEEcCcCCccccccccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHG-----DR-----YQLECIACGHSWYASRDEAS 547 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsA-----DE-----~Fv~C~~Cg~rWk~srd~~s 547 (630)
..|++|+......-+++.++.. |- +.+.|.+||++ .++....|
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT-E~Y~~~~~ 53 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT-EFYKAKTS 53 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE-EEEeecCc
Confidence 3799999988777777655542 32 67899999998 44554444
No 36
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=92.92 E-value=0.014 Score=63.54 Aligned_cols=97 Identities=11% Similarity=0.001 Sum_probs=83.2
Q ss_pred eeEEEcCeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCccc
Q 006806 122 EAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDE 201 (630)
Q Consensus 122 ~sf~~dG~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~ 201 (630)
.+..+.+....+|+++.+.+......|.++.+..+|.+.++..+.-++|||||.++.+..... ...+++.+....+.
T Consensus 268 ~~~~i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~ 344 (371)
T COG5076 268 ESVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKL---FFDNCVMYNGEVTD 344 (371)
T ss_pred hhhcccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccch---hhhcccccchhhhh
Confidence 344567779999999999998888999999999999988888888999999999888755444 48999999999999
Q ss_pred ccccccceecEEEEcCcccc
Q 006806 202 VPAESVMHKCVVHFVPIHKQ 221 (630)
Q Consensus 202 ~plesIigKC~V~~i~ey~q 221 (630)
+.+....+.|.|.....+..
T Consensus 345 ~~~~~~~~~~~~~~~~~~~~ 364 (371)
T COG5076 345 YYKNANVLEDFVIKKTRLIR 364 (371)
T ss_pred hhhhccchhhhHhhhhhhhh
Confidence 99999999999988766543
No 37
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=87.19 E-value=0.53 Score=39.59 Aligned_cols=44 Identities=23% Similarity=0.566 Sum_probs=26.9
Q ss_pred ccccCCCCCCceEEEEeeeccCC-----Cc-----eEEEcCcCCccccccccccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHG-----DR-----YQLECIACGHSWYASRDEAS 547 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsA-----DE-----~Fv~C~~Cg~rWk~srd~~s 547 (630)
.++|++||.++..--+++.|.-. |- +-++|.+||++=. +.-.+|
T Consensus 4 ~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEf-Y~a~~s 57 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEF-YSAKIS 57 (68)
T ss_pred cccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhh-eecccc
Confidence 36799999886555555533211 21 3369999998753 444444
No 38
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=85.40 E-value=0.85 Score=39.17 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=24.5
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc----eEEEcC--cCCcccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR----YQLECI--ACGHSWY 540 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE----~Fv~C~--~Cg~rWk 540 (630)
++.|+.||... . +...|..++ .++.|. +||++|.
T Consensus 1 mm~CP~Cg~~a-~---irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 1 MFHCPLCQHAA-H---ARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred CccCCCCCCcc-E---EEEChhcChhhheeeeecCCCCCCCEEE
Confidence 36899999875 2 222344444 889999 8999997
No 39
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=85.02 E-value=0.56 Score=39.62 Aligned_cols=29 Identities=21% Similarity=0.646 Sum_probs=26.1
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHS 538 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~r 538 (630)
.++|+.|++..+-|.-.| +-++|..||..
T Consensus 19 ~VkCpdC~N~q~vFshas-------t~V~C~~CG~~ 47 (67)
T COG2051 19 RVKCPDCGNEQVVFSHAS-------TVVTCLICGTT 47 (67)
T ss_pred EEECCCCCCEEEEeccCc-------eEEEecccccE
Confidence 589999999999998888 89999999954
No 40
>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=83.89 E-value=0.42 Score=34.45 Aligned_cols=27 Identities=33% Similarity=0.802 Sum_probs=15.4
Q ss_pred ccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
+|+.|+... +| .|...+.|..|||.|-
T Consensus 4 ~Cp~C~se~-~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 4 KCPLCGSEY-TY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp --TTT------E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCcc-ee--------ccCCEEeCCcccccCC
Confidence 699999875 44 2337899999999993
No 41
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.70 E-value=0.68 Score=34.42 Aligned_cols=33 Identities=21% Similarity=0.634 Sum_probs=21.4
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWY 540 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk 540 (630)
+.|+.|+.. |.+--..-.+. .-+.|..|||.|+
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 679999854 22220111122 7899999999995
No 42
>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=82.75 E-value=0.8 Score=42.15 Aligned_cols=29 Identities=28% Similarity=0.509 Sum_probs=22.6
Q ss_pred ccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYAS 542 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~s 542 (630)
.|++|++.- + |+.+ ..+.|..|||.|-..
T Consensus 4 ~CP~C~sey-t-Y~dg-------~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEY-T-YHDG-------TQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcc-e-EecC-------CeeECcccccccccc
Confidence 699999764 4 3444 689999999999754
No 43
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=80.62 E-value=1.3 Score=42.87 Aligned_cols=44 Identities=20% Similarity=0.445 Sum_probs=31.3
Q ss_pred ccCCCCCCceEEEEeeeccCCCc-----eEEEcCcCCccccc-ccccccceee
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDR-----YQLECIACGHSWYA-SRDEASSLTI 551 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE-----~Fv~C~~Cg~rWk~-srd~~s~l~~ 551 (630)
+||.|++......+ .|++++ .=-.|.+||+||-- -+-+...|.|
T Consensus 2 ~CP~C~~~dtkViD---SR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~V 51 (147)
T TIGR00244 2 HCPFCQHHNTRVLD---SRLVEDGQSIRRRRECLECHERFTTFERAELLPPTV 51 (147)
T ss_pred CCCCCCCCCCEeee---ccccCCCCeeeecccCCccCCccceeeeccccccEE
Confidence 79999998875444 688888 23589999999964 3444444443
No 44
>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=80.35 E-value=1.3 Score=34.65 Aligned_cols=33 Identities=24% Similarity=0.598 Sum_probs=21.8
Q ss_pred ccCCCCCCceEEEEeeeccCCCc---eEEEcCc--CCcccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDR---YQLECIA--CGHSWY 540 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~--Cg~rWk 540 (630)
.|+.||.+-. .+... .-.+. .++.|.+ |||+|.
T Consensus 1 ~CP~Cg~~a~-ir~S~--~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKAR-IRTSR--QLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeE-EEEch--hhCcceEEEEEEECCCcCCCEEE
Confidence 5999998743 22221 11222 8899999 999997
No 45
>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=79.90 E-value=1.3 Score=32.71 Aligned_cols=34 Identities=29% Similarity=0.856 Sum_probs=22.8
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYA 541 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~ 541 (630)
+.|+.|+.. +.+....-++. .-+.|.+||+.|..
T Consensus 3 ~~CP~C~~~----~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 3 IQCPNCKTS----FRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EECCCCCCE----EEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 679999964 33331122233 68999999999973
No 46
>PRK10220 hypothetical protein; Provisional
Probab=78.59 E-value=1.6 Score=40.35 Aligned_cols=32 Identities=22% Similarity=0.536 Sum_probs=24.0
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYAS 542 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~s 542 (630)
+.-.|+.|...- +| +.+ ..+.|..|+|.|...
T Consensus 2 ~lP~CP~C~sey-tY-~d~-------~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 2 SLPHCPKCNSEY-TY-EDN-------GMYICPECAHEWNDA 33 (111)
T ss_pred CCCcCCCCCCcc-eE-cCC-------CeEECCcccCcCCcc
Confidence 345799999764 43 444 579999999999854
No 47
>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=78.23 E-value=1.8 Score=33.53 Aligned_cols=30 Identities=23% Similarity=0.513 Sum_probs=21.9
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHS 538 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~r 538 (630)
..|.|++||..+ ++.+. . ...|.|..|+++
T Consensus 17 ~g~~CP~Cg~~~--~~~~~-~----~~~~~C~~C~~q 46 (46)
T PF12760_consen 17 DGFVCPHCGSTK--HYRLK-T----RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCCee--eEEeC-C----CCeEECCCCCCc
Confidence 458899999874 34443 1 478999999975
No 48
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=78.04 E-value=1.5 Score=32.72 Aligned_cols=34 Identities=18% Similarity=0.473 Sum_probs=22.2
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYA 541 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~ 541 (630)
++|+.|+.. +.+...+-... .-+.|..|+|.|.+
T Consensus 3 i~CP~C~~~----f~v~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 3 ITCPNCQTR----FRVPDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EECCCCCce----EEcCHHHcccCCcEEECCCCCcEeeC
Confidence 579999853 33321111222 78999999999963
No 49
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=77.67 E-value=1.6 Score=36.16 Aligned_cols=30 Identities=20% Similarity=0.651 Sum_probs=26.7
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSW 539 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rW 539 (630)
+++|+.|++..+-|.-.| +-+.|..||..-
T Consensus 11 ~VkCp~C~n~q~vFsha~-------t~V~C~~Cg~~L 40 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHAS-------TVVRCLVCGKTL 40 (59)
T ss_pred EEECCCCCCeEEEEecCC-------cEEECcccCCCc
Confidence 589999999999888888 899999999754
No 50
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=76.09 E-value=1.7 Score=42.35 Aligned_cols=36 Identities=28% Similarity=0.586 Sum_probs=24.0
Q ss_pred cccCCCCCCceEEEEeeeccC-CCc----eEEEcCcCCcccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGH-GDR----YQLECIACGHSWYAS 542 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRs-ADE----~Fv~C~~Cg~rWk~s 542 (630)
.+||-||...+.... .|. ++- .|+.|.+||.++..+
T Consensus 1 m~cp~c~~~~~~~~~---s~~~~~~~~~~~~~~c~~c~~~f~~~ 41 (154)
T PRK00464 1 MRCPFCGHPDTRVID---SRPAEDGNAIRRRRECLACGKRFTTF 41 (154)
T ss_pred CcCCCCCCCCCEeEe---ccccCCCCceeeeeeccccCCcceEe
Confidence 379999998753222 121 221 689999999998743
No 51
>PLN00209 ribosomal protein S27; Provisional
Probab=75.87 E-value=2.7 Score=37.29 Aligned_cols=30 Identities=17% Similarity=0.388 Sum_probs=27.0
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSW 539 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rW 539 (630)
+++|+.|++..+-|...| +-|.|..||..-
T Consensus 36 ~VkCp~C~n~q~VFShA~-------t~V~C~~Cg~~L 65 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQ-------TVVVCGSCQTVL 65 (86)
T ss_pred EEECCCCCCeeEEEecCc-------eEEEccccCCEe
Confidence 689999999999999998 999999999644
No 52
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=74.98 E-value=3 Score=50.96 Aligned_cols=134 Identities=14% Similarity=0.238 Sum_probs=86.5
Q ss_pred eeeeeEEEcCeEEeeCCeEEEcCCCCC-------------------CCCe---EEEEeEEeeCCC-CceEEEEEEEeccc
Q 006806 119 SHYEAFEFDGNKYELEDPVLLTPEDTN-------------------QKPY---VAIIKEITQSKD-GSMMVTGQWFYRPE 175 (630)
Q Consensus 119 ~~Y~sf~~dG~~YkVGD~VyV~~e~~~-------------------~~py---IArI~~I~e~~d-G~~~VrVqWFYRPe 175 (630)
..|.++.++++.|.+||.|+|.....+ ...| =|+|-.|+++.. ..+.+.||.||-..
T Consensus 441 ~iye~~~in~~~ys~g~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~kg~is~fy~~~~~~~~~~e~c~y~d~~ 520 (1164)
T PTZ00112 441 VIYESIQINDVEYSIGDDVLIFCTGNGNTYNGKSGTKKNQNNKNIKENIYQLRKGKISSFYKNTNSNQVEAEVCIYYDQH 520 (1164)
T ss_pred eEEEEEEEcceeeccCCcEEEEEcCCCCccccccCccccccccchhhhhheecccccchhhhcCCCceeeEEEEEEEccc
Confidence 479999999999999999999855421 1112 488889987644 46899999999888
Q ss_pred ccCC---CC----C----CCC---CCCCCCeeEeeC--CcccccccccceecEEEEcCc-cccCC-CCCCCCceEEeeee
Q 006806 176 EADR---KG----G----GNW---LSRDTRELFYSF--HRDEVPAESVMHKCVVHFVPI-HKQLP-NRKQHPGFIVQKVY 237 (630)
Q Consensus 176 Et~~---~~----~----g~~---~~~~~nELFlS~--h~D~~plesIigKC~V~~i~e-y~qlP-~~~~~~~F~Cr~vY 237 (630)
|..- .. . ..| .....++.||-. |+-.+.+.-|..|..|..-.. |..-- ....-+-|.|-+..
T Consensus 521 d~~~i~~~~~~~~~rr~~~~f~~~~d~~~~~~~llgni~f~~~~~~~i~kki~~~ne~~~~~~d~~~~~g~~kflc~~~~ 600 (1164)
T PTZ00112 521 DAQYIKELEEKQKSRRCKADFEVFLDDDTKNFYLLGNIHFKILDAKMILKKIYVYNEKELYDEDKTAKQGKDKFLCTHYL 600 (1164)
T ss_pred cHHHHHHHHHHHHhhhhhhhhhHhcccccceeEEecceeEEEechHhhhhhheeecchhhcccchhhhcccchhhhhHhh
Confidence 7542 10 0 112 123455666555 445567777888888876432 22110 11234789998877
Q ss_pred ecCCcEEeecCCccc
Q 006806 238 DTVERKLWKLTDKDY 252 (630)
Q Consensus 238 D~~~kkl~~l~dkDy 252 (630)
-....++..|+++..
T Consensus 601 k~~~~~~~~~~~~~h 615 (1164)
T PTZ00112 601 KEREERICFIQNSEH 615 (1164)
T ss_pred hcchhheeeccchhh
Confidence 766666766666543
No 53
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=74.47 E-value=4.2 Score=33.00 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=26.6
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEec
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYR 173 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYR 173 (630)
|++||.|.|+++. ...-|..|..- ......++.++||--
T Consensus 1 f~~GDvV~LKSGG--p~MTV~~v~~~--~~~~~~~v~C~WFd~ 39 (53)
T PF09926_consen 1 FKIGDVVQLKSGG--PRMTVTEVGPN--AGASGGWVECQWFDG 39 (53)
T ss_pred CCCCCEEEEccCC--CCeEEEEcccc--ccCCCCeEEEEeCCC
Confidence 5799999999976 44445544332 123457999999963
No 54
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=74.19 E-value=3.3 Score=36.69 Aligned_cols=30 Identities=17% Similarity=0.468 Sum_probs=27.0
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSW 539 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rW 539 (630)
+++|+.|++..+-|...| +-|.|..||..-
T Consensus 35 ~VkCp~C~n~q~VFShA~-------t~V~C~~Cg~~L 64 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQ-------TVVLCGGCSSQL 64 (85)
T ss_pred EEECCCCCCeeEEEecCc-------eEEEccccCCEe
Confidence 689999999999999999 999999999643
No 55
>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=73.49 E-value=2.9 Score=44.23 Aligned_cols=39 Identities=26% Similarity=0.548 Sum_probs=20.1
Q ss_pred ccccCCCCCCceEEEEeeeccCC-CceEEEcCcCCccccccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHG-DRYQLECIACGHSWYASR 543 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsA-DE~Fv~C~~Cg~rWk~sr 543 (630)
.-.|+-||.. .....+. .... -..|..|.-||+.|.+-|
T Consensus 172 ~g~CPvCGs~-P~~s~l~-~~~~~G~R~L~Cs~C~t~W~~~R 211 (290)
T PF04216_consen 172 RGYCPVCGSP-PVLSVLR-GGEREGKRYLHCSLCGTEWRFVR 211 (290)
T ss_dssp -SS-TTT----EEEEEEE-------EEEEEETTT--EEE--T
T ss_pred CCcCCCCCCc-CceEEEe-cCCCCccEEEEcCCCCCeeeecC
Confidence 4689999976 5566664 1221 129999999999999655
No 56
>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=72.77 E-value=1.5 Score=36.32 Aligned_cols=40 Identities=25% Similarity=0.528 Sum_probs=29.6
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccccccceee
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTI 551 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~s~l~~ 551 (630)
|.-.|+.||..... ......+.|.+||.. ..||.++.+.|
T Consensus 27 TSq~C~~CG~~~~~--------~~~~r~~~C~~Cg~~--~~rD~naA~NI 66 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--------RRSGRVFTCPNCGFE--MDRDVNAARNI 66 (69)
T ss_pred CccCccCccccccc--------ccccceEEcCCCCCE--ECcHHHHHHHH
Confidence 56779999987543 111278899999977 47998887766
No 57
>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=72.46 E-value=2 Score=32.73 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=20.1
Q ss_pred cccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
++|+.|+... .+.+-. .-.+.|.+||.-.-
T Consensus 1 m~Cp~Cg~~~-~~~D~~------~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFDPE------RGELVCPNCGLVLE 30 (43)
T ss_dssp ESBTTTSSSE-EEEETT------TTEEEETTT-BBEE
T ss_pred CCCcCCcCCc-eEEcCC------CCeEECCCCCCEee
Confidence 4799999976 444422 16789999996554
No 58
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=70.84 E-value=2.7 Score=40.91 Aligned_cols=59 Identities=20% Similarity=0.429 Sum_probs=40.8
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-----eEEEcCcCCcccc-cccccccceeecCCCCCCCcccccCccchh
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-----YQLECIACGHSWY-ASRDEASSLTIDGPGSAAKSVGIVPLATAK 570 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-----~Fv~C~~Cg~rWk-~srd~~s~l~~~~~~~~~~~~~~~~~~~~~ 570 (630)
.+||-|++..+...+ .|.+++ .=-.|.+||+|+- +-+-++..|.|--.+. ..-|+.-.|
T Consensus 1 M~CPfC~~~~tkViD---SR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~~VvKkdg-----~Re~F~r~K 65 (156)
T COG1327 1 MKCPFCGHEDTKVID---SRPAEEGNAIRRRRECLECGERFTTFERAELRPLIVVKKDG-----RREPFDREK 65 (156)
T ss_pred CCCCCCCCCCCeeee---cccccccchhhhhhcccccccccchhheeeeccceEECcCC-----CcCCCCHHH
Confidence 379999998765444 588888 4469999999996 4677777666654443 345554444
No 59
>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=68.27 E-value=8.2 Score=32.10 Aligned_cols=43 Identities=21% Similarity=0.363 Sum_probs=27.6
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASS 548 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~s~ 548 (630)
....||+|+.-. +...++ -.+--.++|+.|||+-...-..++.
T Consensus 8 AGA~CP~C~~~D-tl~~~~---e~~~e~vECv~Cg~~~~~~~~~~~~ 50 (59)
T TIGR02443 8 AGAVCPACSAQD-TLAMWK---ENNIELVECVECGYQEQQKDQSVSV 50 (59)
T ss_pred ccccCCCCcCcc-EEEEEE---eCCceEEEeccCCCccccCCccccc
Confidence 346899999865 333332 1222679999999987655554443
No 60
>PHA00626 hypothetical protein
Probab=68.23 E-value=3.6 Score=33.91 Aligned_cols=31 Identities=16% Similarity=0.500 Sum_probs=19.6
Q ss_pred ccCCCCCCceEEEEeeeccCCC-ceEEEcCcCCccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGD-RYQLECIACGHSW 539 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsAD-E~Fv~C~~Cg~rW 539 (630)
.||+||+....-.-+- | . ..-|.|..||+++
T Consensus 2 ~CP~CGS~~Ivrcg~c--r--~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--R--GWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeecee--c--ccCcceEcCCCCCee
Confidence 5999998754311110 0 0 1579999999875
No 61
>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=66.04 E-value=3.5 Score=44.44 Aligned_cols=49 Identities=18% Similarity=0.411 Sum_probs=32.4
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc--eEEEcCcCCccccccc---------ccccceeecC
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR--YQLECIACGHSWYASR---------DEASSLTIDG 553 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE--~Fv~C~~Cg~rWk~sr---------d~~s~l~~~~ 553 (630)
.-.|+-||+.- ....++ ....++ +|..|.-|++.|.+-| +.+..++++.
T Consensus 184 ~~~CPvCGs~P-~~s~~~-~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~ 243 (305)
T TIGR01562 184 RTLCPACGSPP-VASMVR-QGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEH 243 (305)
T ss_pred CCcCCCCCChh-hhhhhc-ccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecC
Confidence 35799999864 334443 333344 9999999999998544 3455566654
No 62
>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=65.10 E-value=2.2 Score=34.88 Aligned_cols=29 Identities=21% Similarity=0.657 Sum_probs=20.8
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHS 538 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~r 538 (630)
+++|+.|++..+-|...| +-+.|..||..
T Consensus 7 ~VkCp~C~~~q~vFSha~-------t~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQ-------TVVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEETT-S-------S-EE-SSSTSE
T ss_pred EEECCCCCCeeEEEecCC-------eEEEcccCCCE
Confidence 579999999988888888 89999999964
No 63
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=64.83 E-value=3.9 Score=31.61 Aligned_cols=32 Identities=28% Similarity=0.609 Sum_probs=21.3
Q ss_pred cCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 501 MTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 501 m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
|..++|++||.. ..+.+.. .-++|..||++--
T Consensus 1 ~~~y~C~~CG~~-~~~~~~~-------~~~~Cp~CG~~~~ 32 (46)
T PRK00398 1 MAEYKCARCGRE-VELDEYG-------TGVRCPYCGYRIL 32 (46)
T ss_pred CCEEECCCCCCE-EEECCCC-------CceECCCCCCeEE
Confidence 456899999964 3332221 3689999997653
No 64
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.49 E-value=4.2 Score=40.77 Aligned_cols=36 Identities=19% Similarity=0.462 Sum_probs=24.9
Q ss_pred cccCCCCCCceEEEEe-------eeccCCCc-eEEEcCcCCccccc
Q 006806 504 ARCSRCNECKVGLRDI-------IQAGHGDR-YQLECIACGHSWYA 541 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~-------q~tRsADE-~Fv~C~~Cg~rWk~ 541 (630)
.+|.+||..+ .|+=. | -+--|- -.|.|.+|.++|.+
T Consensus 18 k~C~~Cg~kr-~f~cSg~fRvNAq-~K~LDvWlIYkC~~Cd~tWN~ 61 (203)
T COG4332 18 KRCNSCGVKR-AFTCSGKFRVNAQ-GKVLDVWLIYKCTHCDYTWNI 61 (203)
T ss_pred hhCcccCCcc-eeeecCcEEEcCC-CcEEEEEEEEEeeccCCccch
Confidence 5799999865 33211 2 233444 78999999999983
No 65
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=62.25 E-value=6.1 Score=42.68 Aligned_cols=38 Identities=24% Similarity=0.503 Sum_probs=27.0
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc--eEEEcCcCCccccccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR--YQLECIACGHSWYASR 543 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE--~Fv~C~~Cg~rWk~sr 543 (630)
.-.|+-||..-+ ...+. .+ .++ .|..|.-|++.|.+-|
T Consensus 187 ~~~CPvCGs~P~-~s~v~-~~-~~~G~RyL~CslC~teW~~~R 226 (309)
T PRK03564 187 RQFCPVCGSMPV-SSVVQ-IG-TTQGLRYLHCNLCESEWHVVR 226 (309)
T ss_pred CCCCCCCCCcch-hheee-cc-CCCCceEEEcCCCCCcccccC
Confidence 467999998743 33333 22 234 9999999999999654
No 66
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=61.16 E-value=0.89 Score=35.39 Aligned_cols=28 Identities=25% Similarity=0.469 Sum_probs=19.2
Q ss_pred CCCCCceEEEEeeeccCCCc--eEE-EcCcCCc
Q 006806 508 RCNECKVGLRDIIQAGHGDR--YQL-ECIACGH 537 (630)
Q Consensus 508 ~C~~~k~~y~q~q~tRsADE--~Fv-~C~~Cg~ 537 (630)
.|.+.=. ..+.| +|++|| .|+ .|..||.
T Consensus 12 ~C~H~f~-~~E~Q-~RAGDE~VSfI~~C~~C~~ 42 (43)
T PF11792_consen 12 QCKHKFV-TIEKQ-LRAGDEAVSFIKYCQKCGQ 42 (43)
T ss_pred cceeeee-ehhhh-hcccchHHHHHHHHHHhCC
Confidence 3665433 34455 999999 665 7888884
No 67
>PF14353 CpXC: CpXC protein
Probab=60.41 E-value=11 Score=35.01 Aligned_cols=45 Identities=24% Similarity=0.513 Sum_probs=28.0
Q ss_pred cccCCCCCCc-eEEEEeeeccCCCc-----------eEEEcCcCCcccccccccccceeec
Q 006806 504 ARCSRCNECK-VGLRDIIQAGHGDR-----------YQLECIACGHSWYASRDEASSLTID 552 (630)
Q Consensus 504 ~~C~~C~~~k-~~y~q~q~tRsADE-----------~Fv~C~~Cg~rWk~srd~~s~l~~~ 552 (630)
+.|+.|+..- ..++++. .-+.|. -.++|.+||+.-.. ....|-+|
T Consensus 2 itCP~C~~~~~~~v~~~I-~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~---~~p~lY~D 58 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSI-NADEDPELKEKILDGSLFSFTCPSCGHKFRL---EYPLLYHD 58 (128)
T ss_pred cCCCCCCCeeEEEEEeEE-cCcCCHHHHHHHHcCCcCEEECCCCCCceec---CCCEEEEc
Confidence 5799998753 4445555 333332 45899999988763 33444444
No 68
>PHA02942 putative transposase; Provisional
Probab=60.40 E-value=2.1 Score=47.34 Aligned_cols=51 Identities=20% Similarity=0.513 Sum_probs=34.6
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccccccceeecCCCCCCCcccccC
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIVP 565 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~s~l~~~~~~~~~~~~~~~~ 565 (630)
|.-.|+.||..... -. ...|.|.+||+.+ .||-+..+.|-.- +.-.++|||
T Consensus 324 TSq~Cs~CG~~~~~--------l~-~r~f~C~~CG~~~--drD~nAA~NI~~r--g~~~~~~~~ 374 (383)
T PHA02942 324 SSVSCPKCGHKMVE--------IA-HRYFHCPSCGYEN--DRDVIAIMNLNGR--GSLTLSTAP 374 (383)
T ss_pred CCccCCCCCCccCc--------CC-CCEEECCCCCCEe--CcHHHHHHHHHHH--HHHHhccCc
Confidence 55679999975321 11 1579999999765 8999998888432 234456666
No 69
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=58.38 E-value=13 Score=28.81 Aligned_cols=33 Identities=21% Similarity=0.515 Sum_probs=21.5
Q ss_pred ccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcccccccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYASRD 544 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~srd 544 (630)
-|+.||.-- . .+..+. .++.|..||+.++.+.-
T Consensus 2 FCp~Cg~~l------~-~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNML------I-PKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCcc------c-cccCCCCCEEECCcCCCeEECCCc
Confidence 399999731 1 222222 48899999999886543
No 70
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=58.37 E-value=11 Score=28.45 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=20.5
Q ss_pred ccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWY 540 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk 540 (630)
+||+|+.. .. ....++ ....|.+||.-|-
T Consensus 1 ~CP~C~~~-l~------~~~~~~~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGTE-LE------PVRLGDVEIDVCPSCGGIWF 30 (41)
T ss_pred CcCCCCcc-cc------eEEECCEEEEECCCCCeEEc
Confidence 59999863 22 222255 7789999999996
No 71
>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=57.97 E-value=12 Score=35.32 Aligned_cols=30 Identities=33% Similarity=0.595 Sum_probs=22.7
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHS 538 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~r 538 (630)
-+.|+.|++..+.+..- +. .|..|..||.+
T Consensus 93 yVlC~~C~spdT~l~k~------~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKE------GRLIFLKCKACGAS 123 (125)
T ss_dssp HSSCTSTSSSSEEEEEE------TTCCEEEETTTSCE
T ss_pred EEEcCCCCCCccEEEEc------CCEEEEEecccCCc
Confidence 36799999998654322 34 89999999964
No 72
>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=57.87 E-value=4.4 Score=37.37 Aligned_cols=32 Identities=22% Similarity=0.589 Sum_probs=24.9
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYAS 542 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~s 542 (630)
++..|+.||. .||.+.+ .=++|..||..|-.+
T Consensus 8 tKR~Cp~CG~---kFYDLnk------~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGA---KFYDLNK------DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcc---hhccCCC------CCccCCCCCCccCcc
Confidence 4567999995 5788873 457899999999755
No 73
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=57.74 E-value=4.2 Score=33.78 Aligned_cols=28 Identities=21% Similarity=0.541 Sum_probs=20.4
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSW 539 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rW 539 (630)
-+.|+.|++.+. + .+. .-+.|..||||.
T Consensus 20 iYiCgdC~~en~----l---k~~--D~irCReCG~RI 47 (62)
T KOG3507|consen 20 IYICGDCGQENT----L---KRG--DVIRCRECGYRI 47 (62)
T ss_pred EEEecccccccc----c---cCC--CcEehhhcchHH
Confidence 467999998863 2 222 357899999985
No 74
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=55.52 E-value=11 Score=34.80 Aligned_cols=30 Identities=30% Similarity=0.649 Sum_probs=22.1
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHS 538 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~r 538 (630)
-+.|+.|+++.+.+..- +. .|..|..||.+
T Consensus 80 yVlC~~C~spdT~l~k~------~r~~~l~C~aCGa~ 110 (110)
T smart00653 80 YVLCPECGSPDTELIKE------NRLFFLKCEACGAR 110 (110)
T ss_pred cEECCCCCCCCcEEEEe------CCeEEEEccccCCC
Confidence 47899999998654321 23 78899999964
No 75
>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=54.79 E-value=14 Score=31.80 Aligned_cols=38 Identities=18% Similarity=0.407 Sum_probs=25.8
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRD 544 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd 544 (630)
...||+|+.-. +..-++ -.+--.++|+.|||+-....+
T Consensus 8 Ga~CP~C~~~D-~i~~~~---e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 8 GAVCPKCQAMD-TIMMWR---ENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred CccCCCCcCcc-EEEEEE---eCCceEEEecCCCCeeccCCc
Confidence 46899999876 222222 112278999999999876655
No 76
>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=54.65 E-value=5.5 Score=37.85 Aligned_cols=32 Identities=13% Similarity=0.163 Sum_probs=24.8
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYAS 542 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~s 542 (630)
++..|+.||. .||.+.+ .-+.|..||..|-.+
T Consensus 8 tKr~Cp~cg~---kFYDLnk------~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGS---KFYDLNR------RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCc---cccccCC------CCccCCCcCCccCcc
Confidence 4567999995 4778863 568999999999643
No 77
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=54.17 E-value=12 Score=35.69 Aligned_cols=30 Identities=30% Similarity=0.578 Sum_probs=21.9
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHS 538 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~r 538 (630)
-+.|+.|+++.+.+.- . +. .|..|..||.+
T Consensus 97 yVlC~~C~sPdT~l~k-~-----~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNRPDTRIIK-E-----GRVSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCCCCcEEEE-e-----CCeEEEecccCCCC
Confidence 4679999999865432 1 23 67899999954
No 78
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=53.33 E-value=4.7 Score=40.79 Aligned_cols=34 Identities=24% Similarity=0.599 Sum_probs=24.5
Q ss_pred cccCCCCCCceEEEEeeeccC-CCceEEEcCcCCcccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGH-GDRYQLECIACGHSWY 540 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRs-ADE~Fv~C~~Cg~rWk 540 (630)
..|+.|+..++. .++. +. .++..+.|.+||+-|.
T Consensus 7 ~~Cp~Cg~eev~-hEVi--k~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 7 IECPSCGSEEVS-HEVI--KERGREPLVRCEECGTVHP 41 (201)
T ss_pred EECCCCCcchhh-HHHH--HhcCCceEEEccCCCcEee
Confidence 679999965542 2333 33 5558999999999995
No 79
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=53.25 E-value=18 Score=36.54 Aligned_cols=74 Identities=16% Similarity=0.139 Sum_probs=39.4
Q ss_pred cccCCCCCCceEEEEeeecc---CCCc---eEEEcCcCCcccccc------cccccceeecCCCCCCCcccccCccchhh
Q 006806 504 ARCSRCNECKVGLRDIIQAG---HGDR---YQLECIACGHSWYAS------RDEASSLTIDGPGSAAKSVGIVPLATAKF 571 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tR---sADE---~Fv~C~~Cg~rWk~s------rd~~s~l~~~~~~~~~~~~~~~~~~~~~~ 571 (630)
..|+.|++. .++..+. +. .--+ .-+.|..||++...- .+.-..|.|..+.--.|-|=-..+||-..
T Consensus 1 ~~Cp~C~~~-~~~~~~~-~~~IP~F~evii~sf~C~~CGyr~~ev~~~g~~~p~r~~l~V~~~~DL~r~VvkS~tati~I 78 (192)
T TIGR00310 1 IDCPSCGGE-CETVMKT-VNDIPYFGEVLETSTICEHCGYRSNDVKTLGAKEPKRYILKIDDEADLNRRVVKSESATIRI 78 (192)
T ss_pred CcCCCCCCC-CEEEEEE-EcCCCCcceEEEEEEECCCCCCccceeEECCCCCCEEEEEEECChhcccceEEEcCCcEEEc
Confidence 369999976 3433333 33 2334 457999999987631 11133455554433344444445555555
Q ss_pred hhhhhhhc
Q 006806 572 DSLEKNLL 579 (630)
Q Consensus 572 ~~~~~~~~ 579 (630)
-+++=.|.
T Consensus 79 PEl~lei~ 86 (192)
T TIGR00310 79 PELGLDIE 86 (192)
T ss_pred cceEEEEC
Confidence 44444443
No 80
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=52.92 E-value=16 Score=29.47 Aligned_cols=33 Identities=27% Similarity=0.515 Sum_probs=21.0
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGH 537 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~ 537 (630)
..||-||.....+.+.. ....+. .++.|..||.
T Consensus 4 kPCPFCG~~~~~~~~~~-~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDE-GFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeeccc-CCCCCCEEEEEcCCCCC
Confidence 46999987765444332 122222 7789999997
No 81
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=52.50 E-value=19 Score=31.53 Aligned_cols=43 Identities=14% Similarity=0.099 Sum_probs=34.0
Q ss_pred EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecc
Q 006806 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRP 174 (630)
Q Consensus 130 ~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRP 174 (630)
.|++||.|.-+-. +-++|-|+|.+.-........+.|+||-..
T Consensus 2 ~f~~GdlVwaK~k--Gyp~WPa~I~~~~~~~~~~~~~~V~FfGt~ 44 (83)
T cd05834 2 QFKAGDLVFAKVK--GYPAWPARVDEPEDWKPPGKKYPVYFFGTH 44 (83)
T ss_pred CCCCCCEEEEecC--CCCCCCEEEecccccCCCCCEEEEEEeCCC
Confidence 4789999999874 589999999988754344567899999854
No 82
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=51.80 E-value=14 Score=35.50 Aligned_cols=30 Identities=30% Similarity=0.660 Sum_probs=22.2
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHS 538 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~r 538 (630)
-+.|+.|+++.+.+.. . +. .|..|..||.+
T Consensus 102 yVlC~~C~spdT~l~k-----~-~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSPDTKLIK-----E-GRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCCCcEEEE-----c-CCeEEEEcccCCCC
Confidence 4689999999865432 1 23 78999999964
No 83
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=51.67 E-value=14 Score=37.55 Aligned_cols=40 Identities=15% Similarity=0.138 Sum_probs=26.0
Q ss_pred ccCccccCCCCCCceEEEEeee-ccCCCc---eEEEcCcCCcccc
Q 006806 500 QMTDARCSRCNECKVGLRDIIQ-AGHGDR---YQLECIACGHSWY 540 (630)
Q Consensus 500 ~m~~~~C~~C~~~k~~y~q~q~-tRsADE---~Fv~C~~Cg~rWk 540 (630)
+.+...||-||+ .+.+.+... +-+--+ ..+.|.+||+|..
T Consensus 11 ~~~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 11 FETRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeeeecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 345688999998 454443330 122333 6689999999876
No 84
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=51.09 E-value=13 Score=34.39 Aligned_cols=30 Identities=33% Similarity=0.730 Sum_probs=22.3
Q ss_pred cccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYAS 542 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~s 542 (630)
-.|++|... -+|.+. ..+.|..|+|.|...
T Consensus 4 p~cp~c~sE-ytYed~--------~~~~cpec~~ew~~~ 33 (112)
T COG2824 4 PPCPKCNSE-YTYEDG--------GQLICPECAHEWNEN 33 (112)
T ss_pred CCCCccCCc-eEEecC--------ceEeCchhccccccc
Confidence 469999865 344443 589999999999843
No 85
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=50.50 E-value=13 Score=35.47 Aligned_cols=33 Identities=18% Similarity=0.360 Sum_probs=23.9
Q ss_pred hhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCccc
Q 006806 497 EQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSW 539 (630)
Q Consensus 497 ~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rW 539 (630)
+-+-|...+|+.||-+-. +-+ -=+.|..||++-
T Consensus 22 ~GAkML~~hCp~Cg~PLF---~Kd-------G~v~CPvC~~~~ 54 (131)
T COG1645 22 QGAKMLAKHCPKCGTPLF---RKD-------GEVFCPVCGYRE 54 (131)
T ss_pred hhhHHHHhhCcccCCcce---eeC-------CeEECCCCCceE
Confidence 455688999999997643 333 357799999843
No 86
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.14 E-value=7 Score=40.41 Aligned_cols=37 Identities=27% Similarity=0.508 Sum_probs=28.0
Q ss_pred cCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccccccceeec
Q 006806 501 MTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTID 552 (630)
Q Consensus 501 m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~s~l~~~ 552 (630)
.+.-.|+.||. ... ..+.|..||+.+ .||-+.++.|-
T Consensus 307 ~tS~~C~~cg~------~~~-------r~~~C~~cg~~~--~rD~naa~Ni~ 343 (364)
T COG0675 307 YTSKTCPCCGH------LSG-------RLFKCPRCGFVH--DRDVNAALNIA 343 (364)
T ss_pred CCcccccccCC------ccc-------eeEECCCCCCee--hhhHHHHHHHH
Confidence 46688999998 123 678999999887 57777777664
No 87
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=49.94 E-value=10 Score=29.50 Aligned_cols=28 Identities=18% Similarity=0.424 Sum_probs=18.9
Q ss_pred cccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
+.|++||.. .. ..+ ..-+.|.+|||+--
T Consensus 3 Y~C~~Cg~~-~~------~~~--~~~irC~~CG~rIl 30 (44)
T smart00659 3 YICGECGRE-NE------IKS--KDVVRCRECGYRIL 30 (44)
T ss_pred EECCCCCCE-ee------cCC--CCceECCCCCceEE
Confidence 679999974 22 111 14589999999863
No 88
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=49.44 E-value=20 Score=32.83 Aligned_cols=37 Identities=24% Similarity=0.393 Sum_probs=26.0
Q ss_pred CccccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYA 541 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~ 541 (630)
..|.|+.|++.++.-..+. .-+- .+..|-+||.+...
T Consensus 21 k~FtCp~Cghe~vs~ctvk---k~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVK---KTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred ceEecCccCCeeeeEEEEE---ecCceeEEEcccCcceEEE
Confidence 4699999999876533322 1122 78999999988763
No 89
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=48.58 E-value=16 Score=37.04 Aligned_cols=30 Identities=37% Similarity=0.638 Sum_probs=22.0
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHS 538 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~r 538 (630)
-+.|+.|++..+.+.. . +. .|..|..||.+
T Consensus 98 yV~C~~C~~pdT~l~k-----~-~~~~~l~C~aCGa~ 128 (201)
T PRK12336 98 YVICSECGLPDTRLVK-----E-DRVLMLRCDACGAH 128 (201)
T ss_pred eEECCCCCCCCcEEEE-----c-CCeEEEEcccCCCC
Confidence 4689999999865432 1 23 78899999954
No 90
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=48.04 E-value=20 Score=35.32 Aligned_cols=74 Identities=14% Similarity=0.081 Sum_probs=39.4
Q ss_pred cCCCCCCceEEEEee-eccCCCc---eEEEcCcCCcccccc--c----ccccceeecCCCCCCCcccccCccchhhhhhh
Q 006806 506 CSRCNECKVGLRDII-QAGHGDR---YQLECIACGHSWYAS--R----DEASSLTIDGPGSAAKSVGIVPLATAKFDSLE 575 (630)
Q Consensus 506 C~~C~~~k~~y~q~q-~tRsADE---~Fv~C~~Cg~rWk~s--r----d~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 575 (630)
|+.||.....+.... .+-.--+ .-+.|..||++...- - +.-.+|+|..+.--.|-|=-..+||-..-+++
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~~~~~p~r~~l~V~~~~DL~r~VvkS~ta~i~IPEl~ 80 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTDVYQLEEKEPVRYIIKIENEDDLFTLVYRSRSATIRIPELG 80 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhheeEcCCcCCEEEEEEECChhhccceEEEcCCcEEEcccee
Confidence 899997644442221 1223333 457999999887631 1 12234555544333455555555555555555
Q ss_pred hhhc
Q 006806 576 KNLL 579 (630)
Q Consensus 576 ~~~~ 579 (630)
=.|.
T Consensus 81 lei~ 84 (163)
T TIGR00340 81 IKIE 84 (163)
T ss_pred EEec
Confidence 4444
No 91
>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=48.02 E-value=13 Score=27.76 Aligned_cols=26 Identities=27% Similarity=0.529 Sum_probs=18.4
Q ss_pred cccCCCCCCceEEEEeeeccCCCceEEEcCcCCcc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHS 538 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~r 538 (630)
+.|+.|+.+ . |. . |+=||.|..|||.
T Consensus 9 ~~C~~C~~~-~-~~-~------~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR-W-FY-S------DDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe-E-eE-c------cCCEEEhhhCceE
Confidence 569999987 2 22 2 2268899999985
No 92
>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=47.77 E-value=12 Score=34.23 Aligned_cols=28 Identities=29% Similarity=0.535 Sum_probs=22.8
Q ss_pred ccCCCCCCceEEEEeeeccCCCceEEEcCcCCccccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYA 541 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~ 541 (630)
.|.-|+. ..|+|-- ..+.|.+||.+|..
T Consensus 37 aCeiC~~--~GY~q~g-------~~lvC~~C~~~~~~ 64 (102)
T PF10080_consen 37 ACEICGP--KGYYQEG-------DQLVCKNCGVRFNL 64 (102)
T ss_pred eccccCC--CceEEEC-------CEEEEecCCCEEeh
Confidence 4999954 4788665 79999999999973
No 93
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=47.14 E-value=28 Score=30.50 Aligned_cols=39 Identities=18% Similarity=0.166 Sum_probs=31.3
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecc
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRP 174 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRP 174 (630)
|.+||.|.-.-. +-++|-|+|.++.. +...+.|.||=-.
T Consensus 1 f~~gdlVWaK~~--g~P~WPa~I~~~~~---~~~k~~V~FfG~~ 39 (80)
T cd06080 1 FEKNDLVWAKIQ--GYPWWPAVIKSISR---KKQKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEEeCC--CCCCCCEEEeeecC---CCCEEEEEEeCCC
Confidence 578999998864 48999999999863 3678889988665
No 94
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.14 E-value=7.7 Score=31.13 Aligned_cols=32 Identities=25% Similarity=0.552 Sum_probs=21.4
Q ss_pred cCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 501 MTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 501 m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
|....|.+||.. . ..+|.+ .-+.|..|||+--
T Consensus 4 ~~~Y~C~~Cg~~-~--~~~~~~-----~~irCp~Cg~rIl 35 (49)
T COG1996 4 MMEYKCARCGRE-V--ELDQET-----RGIRCPYCGSRIL 35 (49)
T ss_pred eEEEEhhhcCCe-e--ehhhcc-----CceeCCCCCcEEE
Confidence 455789999964 3 223200 6789999999863
No 95
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=46.63 E-value=20 Score=35.08 Aligned_cols=74 Identities=18% Similarity=0.256 Sum_probs=33.5
Q ss_pred ccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccccc------ccc--ccceeecCCCCCCCcccccCccchhhhh
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWYAS------RDE--ASSLTIDGPGSAAKSVGIVPLATAKFDS 573 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk~s------rd~--~s~l~~~~~~~~~~~~~~~~~~~~~~~~ 573 (630)
.|+.|++...+...+..+-.--+ .-+.|..||++...- .+- ..+|+|+.+.--.|-|=-.+-||-.+-+
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~tl~V~~~~DL~r~VvkS~~ati~IPE 82 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPKGVRITLKVESPEDLNRQVVKSDTATIEIPE 82 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SSEEEEEEEE-SHHHHC-EEEE-TT-EEEEGG
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCCceEEEEEECCHHHhcceEEecCcEEEEEee
Confidence 59999987654333322334444 447999999887631 122 3445554422223334344444445555
Q ss_pred hhhhh
Q 006806 574 LEKNL 578 (630)
Q Consensus 574 ~~~~~ 578 (630)
++=.|
T Consensus 83 l~~ei 87 (161)
T PF03367_consen 83 LGLEI 87 (161)
T ss_dssp GTEEE
T ss_pred cceEE
Confidence 44444
No 96
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=46.05 E-value=19 Score=32.43 Aligned_cols=39 Identities=26% Similarity=0.394 Sum_probs=27.3
Q ss_pred chhhhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 494 DESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 494 e~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
.+|...|-....|+.|++..+. +..- -...|..||..|-
T Consensus 27 ~kie~~q~a~y~CpfCgk~~vk-R~a~-------GIW~C~~C~~~~A 65 (90)
T PRK03976 27 ADIEEKMRAKHVCPVCGRPKVK-RVGT-------GIWECRKCGAKFA 65 (90)
T ss_pred HHHHHHHhcCccCCCCCCCceE-EEEE-------EEEEcCCCCCEEe
Confidence 4555556678899999877653 2221 4679999998874
No 97
>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=44.47 E-value=20 Score=32.36 Aligned_cols=39 Identities=23% Similarity=0.372 Sum_probs=27.0
Q ss_pred chhhhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 494 DESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 494 e~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
.+|...|-....|+.|++..+. +..- -...|..||..|-
T Consensus 26 ~kie~~q~a~y~CpfCgk~~vk-R~a~-------GIW~C~~C~~~~A 64 (91)
T TIGR00280 26 KKIEIQQKAKYVCPFCGKKTVK-RGST-------GIWTCRKCGAKFA 64 (91)
T ss_pred HHHHHHHhcCccCCCCCCCceE-EEee-------EEEEcCCCCCEEe
Confidence 4555556678899999976543 2221 4679999998774
No 98
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=44.42 E-value=4.9 Score=42.74 Aligned_cols=75 Identities=31% Similarity=0.475 Sum_probs=48.3
Q ss_pred cccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccccccceeecCCCCCCCcccccCccchhhhhhhhhhcCCcc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIVPLATAKFDSLEKNLLSPRE 583 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 583 (630)
.+|+.|+.- .+..++.+ .+..|.+|||..+-+-.+---+.+|.- | |+++...|.+
T Consensus 29 ~KCp~c~~~-~y~~eL~~------n~~vcp~c~~h~ri~A~~Ri~~llD~g-s--------------f~el~~~l~~--- 83 (294)
T COG0777 29 TKCPSCGEM-LYRKELES------NLKVCPKCGHHMRISARERLEALLDEG-S--------------FEELDSPLEP--- 83 (294)
T ss_pred eECCCccce-eeHHHHHh------hhhcccccCcccccCHHHHHHHhhCCC-c--------------ceecccCCCc---
Confidence 689999963 33344442 689999999999988777777777832 2 4444333322
Q ss_pred ccchhhhhhccc-cccchhhhHhhhc
Q 006806 584 SEKLANDVLKKS-SEAYMPVLEAQRS 608 (630)
Q Consensus 584 ~~~~~~~~~~~~-~~~~~~~~~~~~~ 608 (630)
.|-|+-. +..|.+.|++++.
T Consensus 84 -----~dPL~F~d~k~Y~~rL~~a~~ 104 (294)
T COG0777 84 -----KDPLKFPDSKKYKDRLEAARK 104 (294)
T ss_pred -----CCcccCCcchhhHHHHHHHHh
Confidence 2223333 6677778877664
No 99
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=43.85 E-value=22 Score=31.83 Aligned_cols=38 Identities=26% Similarity=0.485 Sum_probs=25.7
Q ss_pred hhhhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 495 ESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 495 ~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
+|...+-....|+.|+.+.+ .-+- - -...|..||+.|.
T Consensus 27 ~ie~~~~~~~~Cp~C~~~~V--kR~a-----~-GIW~C~kCg~~fA 64 (89)
T COG1997 27 EIEAQQRAKHVCPFCGRTTV--KRIA-----T-GIWKCRKCGAKFA 64 (89)
T ss_pred HHHHHHhcCCcCCCCCCcce--eeec-----c-CeEEcCCCCCeec
Confidence 44444556788999998743 2222 1 5679999998885
No 100
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=43.14 E-value=21 Score=40.37 Aligned_cols=95 Identities=14% Similarity=0.271 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHhcc--cCHHHHHHhhcCCCCccccccCChhhhcChHhHHHHHhcCCc--hhh-------hccc----C
Q 006806 438 QKYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNELKEGLTAEEMAKKEPD--ESE-------QMQM----T 502 (630)
Q Consensus 438 ~kYk~KiRSL~fNLK--kNp~Lr~rVl~GeIsP~~La~Ms~eEMASdelkeer~k~~~e--~i~-------~~~m----~ 502 (630)
+.+-..+|+-+..+- .||.|....+ -.|+-++|..|..++|+-.+ .. +... .|+ +.+. .
T Consensus 87 ~~Fle~l~~~sqhvlvYEDP~lq~~Al-s~iPvdEL~~kA~ekla~~e---g~--ki~kdy~i~leLL~WFKq~FF~WvN 160 (500)
T KOG0909|consen 87 NAFLEVLRSYSQHVLVYEDPVLQAKAL-STIPVDELKEKASEKLAKAE---GE--KIYKDYLIKLELLNWFKQDFFKWVN 160 (500)
T ss_pred hHHHHHHHHhccCceeecCHHHHHHHH-hcCCHHHHHHHHHHhhcccc---hh--hhhcchHHHHHHHHHHHHhhheecC
Confidence 345555666566664 8898866444 45666888777777777410 11 1111 111 1121 3
Q ss_pred ccccCCCCCCceEEEEeeeccC----CCc--------eEEEcCcCCccccccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGH----GDR--------YQLECIACGHSWYASR 543 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRs----ADE--------~Fv~C~~Cg~rWk~sr 543 (630)
...|.+||.. +. .- +|+ .+| -.|.|..||+.=+|.|
T Consensus 161 ~PpC~~CG~e-t~-~~---l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPR 208 (500)
T KOG0909|consen 161 NPPCNKCGGE-TS-SG---LGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPR 208 (500)
T ss_pred CCCccccccc-cc-cc---ccCCCCchhHhhcCCceEEEEEecCCCCcccCcc
Confidence 4689999976 43 22 333 233 5799999999988876
No 101
>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=42.71 E-value=15 Score=26.83 Aligned_cols=26 Identities=31% Similarity=0.797 Sum_probs=15.5
Q ss_pred ccCCCCCCceEEEEeeeccCCCceEEEcCcCCccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSW 539 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rW 539 (630)
.|++||... . + ...| -+.|..||||-
T Consensus 2 ~C~~Cg~~~-~---~---~~~~--~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEV-E---L---KPGD--PIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE-----B---STSS--TSSBSSSS-SE
T ss_pred CCCcCCCee-E---c---CCCC--cEECCcCCCeE
Confidence 588898652 2 2 2223 36899999874
No 102
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=42.37 E-value=28 Score=30.51 Aligned_cols=40 Identities=18% Similarity=0.097 Sum_probs=30.8
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCC---CCceEEEEEEEe
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSK---DGSMMVTGQWFY 172 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~e~~---dG~~~VrVqWFY 172 (630)
|.+||.|..+-. +-+.|-|+|.+..... ....++.|+||=
T Consensus 1 f~vGDlVWaK~k--g~pwWP~~V~~~~~~~~~~~~~~~~~V~fFG 43 (87)
T cd05835 1 FNVGDLVWGKIK--GFPWWPGRVVSITVTSKRPPVVGMRWVTWFG 43 (87)
T ss_pred CCCCCEEEEecC--CCCCCCeEEechhhcccccCCCCeEEEEEeC
Confidence 578999999874 4889999999986543 124578888886
No 103
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.19 E-value=8.7 Score=36.78 Aligned_cols=38 Identities=16% Similarity=0.304 Sum_probs=24.0
Q ss_pred CccccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYAS 542 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~s 542 (630)
..+.|+.|+.+ .++.+.+ +..|. .-|.|..||..-...
T Consensus 98 ~~Y~Cp~C~~~-y~~~ea~--~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 98 AYYKCPNCQSK-YTFLEAN--QLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred cEEECcCCCCE-eeHHHHH--HhcCCCCcEECCCCCCEEEEc
Confidence 35889999843 4443333 22223 339999999877653
No 104
>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=41.89 E-value=35 Score=27.17 Aligned_cols=33 Identities=33% Similarity=0.497 Sum_probs=19.9
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHS 538 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~r 538 (630)
..|+.||.....+... ..--|. .++.|..||.+
T Consensus 2 kPCPfCGg~~~~~~~~--~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRRG--FDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEec--cCCCCCEEEEECCCCCCC
Confidence 3699999876533211 122233 44589999976
No 105
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=41.84 E-value=34 Score=33.61 Aligned_cols=72 Identities=18% Similarity=0.321 Sum_probs=40.3
Q ss_pred ccCCCCCCceEEEEeeeccC--CCc---eEEEcCcCCcccccc------ccc--ccceeecCCCCCCCcccccCccchhh
Q 006806 505 RCSRCNECKVGLRDIIQAGH--GDR---YQLECIACGHSWYAS------RDE--ASSLTIDGPGSAAKSVGIVPLATAKF 571 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRs--ADE---~Fv~C~~Cg~rWk~s------rd~--~s~l~~~~~~~~~~~~~~~~~~~~~~ 571 (630)
.|+.|++.. .+.... +.- --| .-+.|..||++...- .+. ..+|.|....--.|-|=-.++||-..
T Consensus 2 ~Cp~C~~~~-~~~~~~-~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~p~G~r~~l~V~~~~DL~r~VvkS~ta~i~I 79 (160)
T smart00709 2 DCPSCGGNG-TTRMLL-TSIPYFREVIIMSFECEHCGYRNNEVKSGGAIEPKGTRITLKVESPEDLNRDVVKSETATISI 79 (160)
T ss_pred cCCCCCCCC-EEEEEE-ecCCCcceEEEEEEECCCCCCccceEEECcccCCCceEEEEEECChhhccceEEEcCCcEEEe
Confidence 499999764 433333 332 333 457999999887632 222 44555555433355555555566555
Q ss_pred hhhhhhh
Q 006806 572 DSLEKNL 578 (630)
Q Consensus 572 ~~~~~~~ 578 (630)
-+++=.|
T Consensus 80 PEl~~ei 86 (160)
T smart00709 80 PELDLEI 86 (160)
T ss_pred eeeeEEe
Confidence 5555444
No 106
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=41.65 E-value=15 Score=29.41 Aligned_cols=28 Identities=21% Similarity=0.468 Sum_probs=18.7
Q ss_pred cccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
..|++||.. +.-.. ...+.|..||+++.
T Consensus 21 ~fCP~Cg~~---~m~~~------~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 21 KFCPRCGSG---FMAEH------LDRWHCGKCGYTEF 48 (50)
T ss_pred CcCcCCCcc---hhecc------CCcEECCCcCCEEe
Confidence 469999964 11111 15778999998875
No 107
>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=41.25 E-value=35 Score=29.86 Aligned_cols=38 Identities=26% Similarity=0.383 Sum_probs=18.7
Q ss_pred CccccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYAS 542 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~s 542 (630)
+.|.|+.|++.++---.|. +. .. -.+.|..||..+...
T Consensus 21 ~~F~CPfC~~~~sV~v~id--kk-~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKID--KK-EGIGILSCRVCGESFQTK 59 (81)
T ss_dssp S----TTT--SS-EEEEEE--TT-TTEEEEEESSS--EEEEE
T ss_pred ceEcCCcCCCCCeEEEEEE--cc-CCEEEEEecCCCCeEEEc
Confidence 6799999997665333332 33 22 678999999888643
No 108
>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=40.87 E-value=5.6 Score=43.54 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=7.6
Q ss_pred eEEEcCcCCcc
Q 006806 528 YQLECIACGHS 538 (630)
Q Consensus 528 ~Fv~C~~Cg~r 538 (630)
.||.|.+||+|
T Consensus 284 RFFkC~~C~~R 294 (344)
T PF09332_consen 284 RFFKCKDCGNR 294 (344)
T ss_dssp EEEE-T-TS-E
T ss_pred eeEECCCCCCe
Confidence 89999999988
No 109
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=40.43 E-value=28 Score=29.49 Aligned_cols=35 Identities=17% Similarity=0.319 Sum_probs=24.5
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcccccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYASRD 544 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~srd 544 (630)
..||-||...+... .-+- .++.|..||-+|-.-.+
T Consensus 7 KPCPFCG~~~~~v~------~~~g~~~v~C~~CgA~~~~~~t 42 (64)
T PRK09710 7 KPCPFCGCPSVTVK------AISGYYRAKCNGCESRTGYGGS 42 (64)
T ss_pred cCCCCCCCceeEEE------ecCceEEEEcCCCCcCcccccC
Confidence 46999998866432 2244 56899999988765443
No 110
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=40.41 E-value=25 Score=31.64 Aligned_cols=39 Identities=21% Similarity=0.335 Sum_probs=27.1
Q ss_pred chhhhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 494 DESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 494 e~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
.+|...|-....|+.|++..+. ...- -...|..||..|-
T Consensus 27 ~kie~~q~a~y~CpfCgk~~vk-R~a~-------GIW~C~~C~~~~A 65 (90)
T PTZ00255 27 KKIEISQHAKYFCPFCGKHAVK-RQAV-------GIWRCKGCKKTVA 65 (90)
T ss_pred HHHHHHHhCCccCCCCCCCcee-eeee-------EEEEcCCCCCEEe
Confidence 4555556678899999976653 1111 4679999998763
No 111
>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=39.84 E-value=21 Score=32.13 Aligned_cols=39 Identities=23% Similarity=0.413 Sum_probs=25.5
Q ss_pred chhhhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 494 DESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 494 e~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
.+|...|-....|+.|++..+. ++.- =...|..||..|-
T Consensus 26 kkie~~q~~ky~Cp~Cgk~~vk-R~a~-------GIW~C~~C~~~~A 64 (90)
T PF01780_consen 26 KKIEISQHAKYTCPFCGKTSVK-RVAT-------GIWKCKKCGKKFA 64 (90)
T ss_dssp HHHHHHHHS-BEESSSSSSEEE-EEET-------TEEEETTTTEEEE
T ss_pred HHHHHHHhCCCcCCCCCCceeE-Eeee-------EEeecCCCCCEEe
Confidence 3454555677899999987643 1111 3589999998773
No 112
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=39.36 E-value=17 Score=42.69 Aligned_cols=89 Identities=17% Similarity=0.238 Sum_probs=57.9
Q ss_pred EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEecccccCCCCCCCCCCCCCCeeEeeCCcccccccccce
Q 006806 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMH 209 (630)
Q Consensus 130 ~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesIig 209 (630)
.+..|||+++.+.. .-+-+..+ -.|-..+|..++...|+.++.++.+...+.+ +. .+
T Consensus 375 ~~~~~d~~~~an~~--~~~~~i~~-p~~~~~eg~~~~~t~~~~~~t~t~~s~~~~~---------~~-----------~~ 431 (629)
T KOG1827|consen 375 KLETGDFLLVANSP--LCPRYIIR-PNTPEPEGKNDFSTGWIITSTETTPSEPRKF---------FK-----------YN 431 (629)
T ss_pred cccccceeeecCCC--CCcceeec-cCCCCcccccccccceeccCCCCccCCCccc---------cc-----------cc
Confidence 78899999999843 22223333 3343458999999999999999986332222 22 56
Q ss_pred ecEEEEcCccccCC--CCCCCCceEEeeeeecCC
Q 006806 210 KCVVHFVPIHKQLP--NRKQHPGFIVQKVYDTVE 241 (630)
Q Consensus 210 KC~V~~i~ey~qlP--~~~~~~~F~Cr~vYD~~~ 241 (630)
.|.++....+..-+ .....+.+.|...||...
T Consensus 432 ~~~~~~~~~~~~s~~~~~~~~~~~~~~~~p~~~s 465 (629)
T KOG1827|consen 432 RCSSFVKEAFINSPPHTPLSKPLSPIQQIPDLLS 465 (629)
T ss_pred chHHHHHHHhhcCCCCcccCCCcccccccchHhH
Confidence 67766666555432 112357888999997543
No 113
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.32 E-value=13 Score=39.61 Aligned_cols=12 Identities=33% Similarity=0.861 Sum_probs=9.9
Q ss_pred cCccccCCCCCC
Q 006806 501 MTDARCSRCNEC 512 (630)
Q Consensus 501 m~~~~C~~C~~~ 512 (630)
|..|+|++||++
T Consensus 1 mk~FhC~~CgQ~ 12 (349)
T COG4307 1 MKDFHCPNCGQR 12 (349)
T ss_pred CCcccCCCCCCe
Confidence 457999999986
No 114
>PF10383 Clr2: Transcription-silencing protein Clr2 ; InterPro: IPR018839 Clr2 (cryptic loci regulator) is a chromatin silencing protein, one of a quartet of proteins forming the core of SHREC, a multienzyme effector complex that mediates hetero-chromatic transcriptional gene silencing in fission yeast []. Clr2 does not have any obvious well-conserved domains but, along with the other core proteins, binds to the histone deacetylase Clr3, and on its own might also have a role in chromatin organisation at the cnt domain, the site of kinetochore assembly.
Probab=38.98 E-value=1.2e+02 Score=28.93 Aligned_cols=52 Identities=19% Similarity=0.251 Sum_probs=37.1
Q ss_pred eeeeEEEcCeEEeeCCeEEEcCCC----------CCCCCeEEEEeEEeeCCCC-------ceEEEEEEE
Q 006806 120 HYEAFEFDGNKYELEDPVLLTPED----------TNQKPYVAIIKEITQSKDG-------SMMVTGQWF 171 (630)
Q Consensus 120 ~Y~sf~~dG~~YkVGD~VyV~~e~----------~~~~pyIArI~~I~e~~dG-------~~~VrVqWF 171 (630)
||..+.++.+.+.+||.|=|++.. ......|-.|.+|...... .++|.+.=|
T Consensus 2 ~y~GiflGAE~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~lY 70 (139)
T PF10383_consen 2 YYRGIFLGAEMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGDLY 70 (139)
T ss_pred eECeEEEeeEEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeEec
Confidence 899999999999999999995432 2344578888888754322 356666543
No 115
>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=38.65 E-value=18 Score=26.54 Aligned_cols=31 Identities=23% Similarity=0.517 Sum_probs=19.6
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGH 537 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~ 537 (630)
-.|+|..||.. |..++ ..+|.....|..||.
T Consensus 4 Y~y~C~~Cg~~---fe~~~--~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHT---FEVLQ--KISDDPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCE---EEEEE--ecCCCCCCCCCCCCC
Confidence 35789999863 33333 333345667999986
No 116
>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=38.63 E-value=1.3e+02 Score=26.47 Aligned_cols=66 Identities=15% Similarity=0.239 Sum_probs=45.8
Q ss_pred hhhHHHHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCcccccccccCCccccccCCCCCCCChhhHHHHHHHHHHH
Q 006806 349 ETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKA 428 (630)
Q Consensus 349 d~~RDK~le~L~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~v~~~A~~IE~a 428 (630)
...|...+++|+.+|-...+.... .+.. ...+...|..||..
T Consensus 12 ~~lR~hlV~KLv~aI~P~pdp~a~-----------------------------------~d~r---m~~l~~yarkvE~~ 53 (81)
T PF02172_consen 12 PDLRNHLVHKLVQAIFPTPDPNAM-----------------------------------NDPR---MKNLIEYARKVEKD 53 (81)
T ss_dssp HHHHHHHHHHHHHHHS-SSSCCCC-----------------------------------CSHH---HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCCCCChhhh-----------------------------------hhHH---HHHHHHHHHHHHHH
Confidence 678999999999998665432211 0100 35788999999999
Q ss_pred HHHHcCcChHHHHHHHHHHHHhccc
Q 006806 429 SHDTLSLDFQKYNQKLRQLLFNLKS 453 (630)
Q Consensus 429 lf~~~~~~~~kYk~KiRSL~fNLKk 453 (630)
+|..-. +...|=..+--.+++++|
T Consensus 54 ~fe~A~-sreeYY~llA~kiy~iqK 77 (81)
T PF02172_consen 54 MFETAQ-SREEYYHLLAEKIYKIQK 77 (81)
T ss_dssp HHHC-S-SHHHHHHHHHHHHHHHHH
T ss_pred HHHHhc-cHHHHHHHHHHHHHHHHH
Confidence 998754 455788888877777753
No 117
>PRK10708 hypothetical protein; Provisional
Probab=37.98 E-value=69 Score=26.65 Aligned_cols=42 Identities=17% Similarity=0.487 Sum_probs=31.2
Q ss_pred eeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEE-------EEEEEeccc
Q 006806 132 ELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMV-------TGQWFYRPE 175 (630)
Q Consensus 132 kVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~V-------rVqWFYRPe 175 (630)
++.|.|.|+.+. .+...|.|..+-.=.+|.+|+ .+.||+--.
T Consensus 2 kvnD~VtVKTDG--~~rR~G~iLavE~F~EG~MyLvaL~dYP~GiWFFNE~ 50 (62)
T PRK10708 2 KVNDRVTVKTDG--GPRRPGVVLAVEEFSEGTMYLVSLEDYPLGIWFFNEA 50 (62)
T ss_pred ccccEEEEecCC--CccccceEEEEeeccCcEEEEEEcCcCCCceEEEecc
Confidence 588999999975 777788888886656776654 467887543
No 118
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=37.54 E-value=66 Score=28.11 Aligned_cols=30 Identities=10% Similarity=0.189 Sum_probs=23.3
Q ss_pred EEeeCCeEEEcCCC-----CCCCCeEEEEeEEeeC
Q 006806 130 KYELEDPVLLTPED-----TNQKPYVAIIKEITQS 159 (630)
Q Consensus 130 ~YkVGD~VyV~~e~-----~~~~pyIArI~~I~e~ 159 (630)
-++.||+|.|..+. .....|+|+|+.+-..
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg 39 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG 39 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEecc
Confidence 36899999999765 2356789999988754
No 119
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=36.80 E-value=44 Score=28.76 Aligned_cols=40 Identities=13% Similarity=0.060 Sum_probs=30.4
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCC------CCceEEEEEEEe
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSK------DGSMMVTGQWFY 172 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~e~~------dG~~~VrVqWFY 172 (630)
|++||.|..+-.. -+.|-|+|....... .....+.|++|-
T Consensus 1 f~~GdlVwaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg 46 (87)
T cd05162 1 FRPGDLVWAKMKG--YPWWPALVVDPPKDSKKAKKKAKEGKVLVLFFG 46 (87)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEccccccchhhhccCCCCEEEEEEeC
Confidence 5789999998854 789999999887642 223577788875
No 120
>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=36.32 E-value=24 Score=27.55 Aligned_cols=31 Identities=23% Similarity=0.519 Sum_probs=20.5
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGH 537 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~ 537 (630)
-+++|..||.. |..++ ..+|.....|..||.
T Consensus 4 Yey~C~~Cg~~---fe~~~--~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHR---FEVLQ--KMSDDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCE---eEEEE--ecCCCCCCCCCCCCC
Confidence 36899999953 33343 333445577999997
No 121
>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=33.71 E-value=21 Score=24.92 Aligned_cols=24 Identities=25% Similarity=0.595 Sum_probs=16.1
Q ss_pred ccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
.|+.|+.. +. . .--.|..|||.|.
T Consensus 2 ~CP~C~~~-V~--~---------~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAE-VP--E---------SAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCC-ch--h---------hcCcCCCCCCCCc
Confidence 58888864 21 1 2346999999885
No 122
>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=33.64 E-value=32 Score=26.25 Aligned_cols=31 Identities=19% Similarity=0.551 Sum_probs=20.6
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGH 537 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~ 537 (630)
-+|+|..||.. |..+| ..+|..-..|..||.
T Consensus 4 Yey~C~~Cg~~---fe~~~--~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHE---FEVLQ--SISEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCE---EEEEE--EcCCCCCCcCCCCCC
Confidence 36899999953 33444 333356778999996
No 123
>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=33.36 E-value=34 Score=39.77 Aligned_cols=39 Identities=18% Similarity=0.356 Sum_probs=26.8
Q ss_pred CccccCCCCCCce-EEEEeeeccC--CCc-eEEEcCcCCccccc
Q 006806 502 TDARCSRCNECKV-GLRDIIQAGH--GDR-YQLECIACGHSWYA 541 (630)
Q Consensus 502 ~~~~C~~C~~~k~-~y~q~q~tRs--ADE-~Fv~C~~Cg~rWk~ 541 (630)
..+.|+.||.... .|.+++ --. +.+ ..|.|..||..|..
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~-w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLK-WDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEccCCCCCCCcccccccee-ecCCCCccceEEECCCCcCCCCH
Confidence 3588999998754 333444 211 233 99999999999974
No 124
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=33.20 E-value=27 Score=38.59 Aligned_cols=66 Identities=20% Similarity=0.388 Sum_probs=34.0
Q ss_pred CccccCCCCCCceEEEEeeeccCCCc--eEEEcCcCCcccccccccccceeecCCCCCCCcccccCcc----------ch
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDR--YQLECIACGHSWYASRDEASSLTIDGPGSAAKSVGIVPLA----------TA 569 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE--~Fv~C~~Cg~rWk~srd~~s~l~~~~~~~~~~~~~~~~~~----------~~ 569 (630)
....|.+||. +..+.+. ..-+|. ..|.|..|||+-.. +-. .++ |=-||- --
T Consensus 173 f~piC~~cGr--i~tt~v~-~~d~~~~~v~Y~c~~cG~~g~~----------~i~---~g~-gKL~WkvDW~mRW~~lgV 235 (360)
T PF01921_consen 173 FLPICEKCGR--IDTTEVT-EYDPEGGTVTYRCEECGHEGEV----------DIT---GGN-GKLQWKVDWPMRWAALGV 235 (360)
T ss_dssp EEEEETTTEE----EEEEE-EE--SSSEEEEE--TTS---EE----------ETT---TT--EEE-HHHHHHHHHHHTT-
T ss_pred eeeeccccCC--cccceee-EeecCCCEEEEEecCCCCEEEE----------ecC---CCc-ccccCCCcChhhhhhcCc
Confidence 4567999995 2224444 233333 88999999987651 111 222 555552 12
Q ss_pred hhhhhhhhhcCCccc
Q 006806 570 KFDSLEKNLLSPRES 584 (630)
Q Consensus 570 ~~~~~~~~~~~~~~~ 584 (630)
-||=..|++.+|-.|
T Consensus 236 dfEp~GKDH~~~GGS 250 (360)
T PF01921_consen 236 DFEPFGKDHASPGGS 250 (360)
T ss_dssp SEEEEEHHHHCTTSH
T ss_pred eeccCCCccCCCCCC
Confidence 577778888887777
No 125
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.16 E-value=38 Score=36.29 Aligned_cols=42 Identities=21% Similarity=0.421 Sum_probs=27.6
Q ss_pred ccCCCCCCceEEEEeeeccCCCceEEEcCcCCccccc-ccccccceeecCC
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYA-SRDEASSLTIDGP 554 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~-srd~~s~l~~~~~ 554 (630)
-|++||.+. . -..+++-..|.+|||.-+. -...|-+++++..
T Consensus 113 FCg~CG~~~-~-------~~~~g~~~~C~~cg~~~fPR~dP~vIv~v~~~~ 155 (279)
T COG2816 113 FCGRCGTKT-Y-------PREGGWARVCPKCGHEHFPRIDPCVIVAVIRGD 155 (279)
T ss_pred CCCCCCCcC-c-------cccCceeeeCCCCCCccCCCCCCeEEEEEecCC
Confidence 399999873 2 2233388899999999873 3344555565543
No 126
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=33.05 E-value=91 Score=25.98 Aligned_cols=43 Identities=19% Similarity=0.518 Sum_probs=31.3
Q ss_pred eeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEE-------EEEEEecccc
Q 006806 132 ELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMV-------TGQWFYRPEE 176 (630)
Q Consensus 132 kVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~V-------rVqWFYRPeE 176 (630)
++.|.|+|+.+. .+..-|.|..+-.=.+|.+|+ .+.||+--.+
T Consensus 2 kvnD~VtVKTDG--~~rR~G~ilavE~F~EG~MYLvaL~dYP~GiWFFNE~~ 51 (62)
T PF10781_consen 2 KVNDRVTVKTDG--GPRREGVILAVEPFNEGTMYLVALEDYPAGIWFFNEKD 51 (62)
T ss_pred ccccEEEEecCC--cccccceEEEEeeccCcEEEEEEcCcCCcceEEEecCC
Confidence 688999999875 677778888776655776654 4678876443
No 127
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=32.14 E-value=79 Score=25.28 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=25.7
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEE
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQW 170 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqW 170 (630)
+.+|+.|++.-. ....|-|+|+++... .|...+.|.+
T Consensus 1 ~~vG~~v~~~~~--~~~~y~A~I~~~r~~-~~~~~YyVHY 37 (55)
T PF11717_consen 1 FEVGEKVLCKYK--DGQWYEAKILDIREK-NGEPEYYVHY 37 (55)
T ss_dssp --TTEEEEEEET--TTEEEEEEEEEEEEC-TTCEEEEEEE
T ss_pred CCcCCEEEEEEC--CCcEEEEEEEEEEec-CCCEEEEEEc
Confidence 468999999872 478999999999984 4444444443
No 128
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=31.24 E-value=60 Score=27.06 Aligned_cols=40 Identities=20% Similarity=0.204 Sum_probs=27.1
Q ss_pred eeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEEe
Q 006806 132 ELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFY 172 (630)
Q Consensus 132 kVGD~VyV~~e~~~~~pyIArI~~I~e~~dG~~~VrVqWFY 172 (630)
++||.+.+....-..+...|.|.++.-. +|..=+.|+|--
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g~-dG~PPY~VRw~D 43 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRGP-DGSPPYLVRWDD 43 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S-S-SS-S-EEEEETT
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEECC-CCCCCEEEEecC
Confidence 6899999998776788899999999864 777888899964
No 129
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=30.71 E-value=49 Score=29.56 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=28.8
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEe---------eCCCCceEEEEEEE
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEIT---------QSKDGSMMVTGQWF 171 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~---------e~~dG~~~VrVqWF 171 (630)
|++||.|..+-.. -++|-|+|..-- ....+...+.|+||
T Consensus 1 f~~GDlVwaK~~G--yPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FF 48 (93)
T cd05840 1 FQPGDRVLAKVKG--FPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFF 48 (93)
T ss_pred CCCCCEEEEeCCC--CCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEe
Confidence 5789999998754 899999997621 12234567888888
No 130
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=30.53 E-value=26 Score=33.92 Aligned_cols=16 Identities=25% Similarity=0.603 Sum_probs=13.5
Q ss_pred CCc-eEEEcCcCCcccc
Q 006806 525 GDR-YQLECIACGHSWY 540 (630)
Q Consensus 525 ADE-~Fv~C~~Cg~rWk 540 (630)
-|= -.|.|..|+++|+
T Consensus 8 LDVWLIYrC~~C~~TwN 24 (142)
T PF06353_consen 8 LDVWLIYRCEKCDYTWN 24 (142)
T ss_pred ccEEEEEEcccCcCccc
Confidence 344 6799999999998
No 131
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.81 E-value=13 Score=37.09 Aligned_cols=33 Identities=18% Similarity=0.471 Sum_probs=22.6
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYA 541 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~ 541 (630)
..+.|++|+.+ .++.+.. +..|.|..||..-.+
T Consensus 116 ~~Y~Cp~C~~r-ytf~eA~------~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIR-FTFDEAM------EYGFRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcE-EeHHHHh------hcCCcCCCCCCCCee
Confidence 35889999943 4433322 267999999987664
No 132
>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=29.55 E-value=22 Score=30.22 Aligned_cols=34 Identities=12% Similarity=0.424 Sum_probs=20.3
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc---eEEEcCcCCcccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR---YQLECIACGHSWY 540 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE---~Fv~C~~Cg~rWk 540 (630)
.|.|..|+.+.. ..+ .+.|=+ .++.|.+|.++-.
T Consensus 4 ~FTC~~C~~Rs~--~~~--sk~aY~~GvViv~C~gC~~~Hl 40 (66)
T PF05180_consen 4 TFTCNKCGTRSA--KMF--SKQAYHKGVVIVQCPGCKNRHL 40 (66)
T ss_dssp EEEETTTTEEEE--EEE--EHHHHHTSEEEEE-TTS--EEE
T ss_pred EEEcCCCCCccc--eee--CHHHHhCCeEEEECCCCcceee
Confidence 489999997754 222 133333 8999999986543
No 133
>PRK05978 hypothetical protein; Provisional
Probab=28.67 E-value=28 Score=34.00 Aligned_cols=31 Identities=29% Similarity=0.591 Sum_probs=22.3
Q ss_pred ccccCCCCCCceE--EEEeeeccCCCceEEEcCcCCcccccc
Q 006806 503 DARCSRCNECKVG--LRDIIQAGHGDRYQLECIACGHSWYAS 542 (630)
Q Consensus 503 ~~~C~~C~~~k~~--y~q~q~tRsADE~Fv~C~~Cg~rWk~s 542 (630)
.-+|++||+-+.. |..+ --.|..||..+.+-
T Consensus 33 ~grCP~CG~G~LF~g~Lkv---------~~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKP---------VDHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCCCccccccccc---------CCCccccCCccccC
Confidence 4789999998763 2222 23799999998764
No 134
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=28.61 E-value=64 Score=26.41 Aligned_cols=40 Identities=10% Similarity=0.028 Sum_probs=29.4
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCC-------CCceEEEEEEEe
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSK-------DGSMMVTGQWFY 172 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~e~~-------dG~~~VrVqWFY 172 (630)
|++||.|..+-.. -+.|-|+|..-.... .....+.|++|-
T Consensus 1 f~~GdlVwaK~~G--~p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg 47 (63)
T smart00293 1 FKPGDLVWAKMKG--FPWWPALVVSPKETPDNIRKRKRFENLYPVLFFG 47 (63)
T ss_pred CCCCCEEEEECCC--CCCCCeEEcCcccCChhHhhccCCCCEEEEEEeC
Confidence 5789999998754 789999998876432 224567777774
No 135
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=28.28 E-value=30 Score=28.97 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=19.4
Q ss_pred CccccCCCCCCceEEEEeeeccCCCc----eEEEcCcCCc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDR----YQLECIACGH 537 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE----~Fv~C~~Cg~ 537 (630)
+.|.|++||... + .|.+-= .-|+|.+||.
T Consensus 26 v~F~CPnCGe~~------I-~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVE------I-YRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCcee------e-ehhhhHHHcCCceECCCcCc
Confidence 469999999532 1 233222 6799999995
No 136
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=28.18 E-value=46 Score=29.36 Aligned_cols=27 Identities=19% Similarity=0.506 Sum_probs=24.6
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCC
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACG 536 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg 536 (630)
+++|+.|-+-.+-|.-.| +-+.|.+|+
T Consensus 34 ~VkC~gc~~iT~vfSHaq-------tvVvc~~c~ 60 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFSHAQ-------TVVVCEGCS 60 (84)
T ss_pred EEEcCCceEEEEEeecCc-------eEEEcCCCc
Confidence 689999999888899998 899999997
No 137
>KOG0343 consensus RNA Helicase [RNA processing and modification]
Probab=27.98 E-value=26 Score=40.92 Aligned_cols=66 Identities=20% Similarity=0.280 Sum_probs=28.7
Q ss_pred ccccccccchH-HHHHHhHhhhhccCccccccCCCCCC-CcchhhhhhhccCCCC---CccccccceeecC
Q 006806 47 LQEEEDYEEPE-EERKASKRERRDKGKVREAEKPRNDG-VEDEEEEEEEEEQPQE---DAKPVGELVRFSG 112 (630)
Q Consensus 47 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~---~a~~iG~pvk~~g 112 (630)
|.+++..+++. .+++.+.+++++-...|++|+.++++ +++++++.-..|.-.+ +.-|+++|-++..
T Consensus 645 l~~~D~~DK~~~kek~~ek~r~k~~k~rr~aeea~~~e~e~~e~d~~~~~~~gs~dD~d~s~lPd~dk~~k 715 (758)
T KOG0343|consen 645 LKEEDKEDKKRFKEKRKEKRREKLEKERRRAEEANEEEAEAEEEDGDFVDWSGSEDDPDISWLPDPDKVRK 715 (758)
T ss_pred HhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccccccchhccCchhcccCCcccCCcccCCChhhhhh
Confidence 44444333322 33333333333333346666655544 2222222222333222 4467777777654
No 138
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=27.87 E-value=58 Score=30.23 Aligned_cols=47 Identities=19% Similarity=0.369 Sum_probs=34.3
Q ss_pred ccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcccccccccccceeecCCCCCC
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYASRDEASSLTIDGPGSAA 558 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~srd~~s~l~~~~~~~~~ 558 (630)
-|++||+- |. .+.++. ..+.|..||+.-..+...|..+.+....+..
T Consensus 4 FCp~Cgsl------l~-p~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~ 51 (113)
T COG1594 4 FCPKCGSL------LY-PKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKK 51 (113)
T ss_pred ccCCccCe------eE-EeEcCCCcEEECCCCCcchhccccceeEEEEeeccCCc
Confidence 49999963 22 466656 8999999999999887777777666555533
No 139
>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=27.83 E-value=14 Score=36.07 Aligned_cols=48 Identities=13% Similarity=0.174 Sum_probs=0.0
Q ss_pred HhHHHHHhcCCchhhhcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCc
Q 006806 483 LTAEEMAKKEPDESEQMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGH 537 (630)
Q Consensus 483 elkeer~k~~~e~i~~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~ 537 (630)
.+....++.+.+--.+.+-..+.|++|+.+ .++.+... .-|+|..||.
T Consensus 89 ~~~~~~~~lk~~l~~e~~~~~Y~Cp~c~~r-~tf~eA~~------~~F~Cp~Cg~ 136 (158)
T TIGR00373 89 KLEETAKKLREKLEFETNNMFFICPNMCVR-FTFNEAME------LNFTCPRCGA 136 (158)
T ss_pred HHHHHHHHHHHHHhhccCCCeEECCCCCcE-eeHHHHHH------cCCcCCCCCC
No 140
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=27.71 E-value=25 Score=28.19 Aligned_cols=34 Identities=26% Similarity=0.536 Sum_probs=23.9
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCcccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYAS 542 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~s 542 (630)
..|..|+...+..+ |.... .-+.|+.||-.|+..
T Consensus 4 ~~C~~C~~~~T~~W-----R~g~~g~~~LCnaCgl~~~k~ 38 (52)
T smart00401 4 RSCSNCGTTETPLW-----RRGPSGNKTLCNACGLYYKKH 38 (52)
T ss_pred CCcCCCCCCCCCcc-----ccCCCCCCcEeecccHHHHHc
Confidence 47999997766422 33333 458899999999753
No 141
>PF02459 Adeno_terminal: Adenoviral DNA terminal protein; InterPro: IPR003391 The genome of adenovirus contains a protein covalently bound to the 5' end of each strand of the linear DNA molecule []. Since adenovirus DNA replication is initiated at the termini of the DNA molecule it has been proposed that the terminal protein serves as the primer for initiation of replication. However, the priming function now appears to reside in the precursor form of the terminal protein (pTP) found on the 5' ends of nascent DNA strands replicated in vitro [, ] and as a component of DNA-protein complexes isolated from virions of the protease-deficient adenovirus serotype 2 (Ad2) mutant tsl. The pTP is encoded by the leftward-transcribed strand of the viral genome and comprises part of a transcription unit that also encodes the single-strand DNA binding protein [].; GO: 0003677 DNA binding, 0006260 DNA replication
Probab=27.21 E-value=30 Score=40.00 Aligned_cols=8 Identities=38% Similarity=0.638 Sum_probs=4.5
Q ss_pred hhhhccCc
Q 006806 65 RERRDKGK 72 (630)
Q Consensus 65 ~~~~~~~~ 72 (630)
++||||+.
T Consensus 293 ~rRrRR~p 300 (548)
T PF02459_consen 293 RRRRRRRP 300 (548)
T ss_pred ccccCCCC
Confidence 55555554
No 142
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=26.33 E-value=1.4e+02 Score=25.92 Aligned_cols=48 Identities=13% Similarity=0.049 Sum_probs=37.4
Q ss_pred EEEEEEecccccCCCCCCCCCCCCCCeeEeeCCcccccccccceecEEEEc
Q 006806 166 VTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFV 216 (630)
Q Consensus 166 VrVqWFYRPeEt~~~~~g~~~~~~~nELFlS~h~D~~plesIigKC~V~~i 216 (630)
|.|.=+-|..||.-... +..+..||.+....+-..+-.|.||+.|+..
T Consensus 19 V~vIgltrg~dtkfhht---EkLDkGEVmiaqftehtsaiKirGkA~I~t~ 66 (75)
T PRK13251 19 VNVIGLTRGKDTKFHHT---EKLDKGEVMIAQFTEHTSAIKIRGKAEIQTK 66 (75)
T ss_pred eEEEEEecCCCccchhh---hhcCCCcEEEEEeecceeEEEEeceEEEEee
Confidence 66677778888842222 2248999999999999999999999999864
No 143
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=25.84 E-value=45 Score=28.17 Aligned_cols=40 Identities=15% Similarity=0.061 Sum_probs=27.7
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeC---CCCceEEEEEEEe
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEITQS---KDGSMMVTGQWFY 172 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~e~---~dG~~~VrVqWFY 172 (630)
|.+||.|..+-.. -+.|-|+|...... ......+.|.||-
T Consensus 1 f~~GdlVWaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg 43 (86)
T PF00855_consen 1 FRPGDLVWAKLKG--YPWWPARVCDPDEKSKKKRKDGHVLVRFFG 43 (86)
T ss_dssp -STTEEEEEEETT--SEEEEEEEEECCHCTSCSSSSTEEEEEETT
T ss_pred CCCCCEEEEEeCC--CCCCceEEeecccccccCCCCCEEEEEecC
Confidence 6789999998754 77899999988642 1233556666654
No 144
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=25.73 E-value=32 Score=36.70 Aligned_cols=48 Identities=15% Similarity=0.296 Sum_probs=33.6
Q ss_pred cCccccCCCCCCceEEEEe----eeccCCCc-eEEEcCcCCcccccccccccce
Q 006806 501 MTDARCSRCNECKVGLRDI----IQAGHGDR-YQLECIACGHSWYASRDEASSL 549 (630)
Q Consensus 501 m~~~~C~~C~~~k~~y~q~----q~tRsADE-~Fv~C~~Cg~rWk~srd~~s~l 549 (630)
-..++|++||+.-.++.-+ |..|++|+ .-+.|..||..+- |=.|+.++
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Yv-SmpALkMH 180 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYV-SMPALKMH 180 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceee-ehHHHhhH
Confidence 3568899999887777643 44689999 6677888886553 55555554
No 145
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=25.13 E-value=47 Score=23.75 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=13.5
Q ss_pred ccCCCCCCceEEEEeeeccCCCceEEEcCcCCcc
Q 006806 505 RCSRCNECKVGLRDIIQAGHGDRYQLECIACGHS 538 (630)
Q Consensus 505 ~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~r 538 (630)
-|++||..- ....++.-..|..||+.
T Consensus 5 fC~~CG~~t--------~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPT--------KPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BE--------EE-SSSS-EEESSSS-E
T ss_pred ccCcCCccc--------cCCCCcCEeECCCCcCE
Confidence 499999862 22333477789999975
No 146
>COG5475 Uncharacterized small protein [Function unknown]
Probab=24.62 E-value=1.4e+02 Score=24.85 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=25.2
Q ss_pred CeEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCC-CCceEEEEEEEeccc
Q 006806 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK-DGSMMVTGQWFYRPE 175 (630)
Q Consensus 128 G~~YkVGD~VyV~~e~~~~~pyIArI~~I~e~~-dG~~~VrVqWFYRPe 175 (630)
+..|++||.|.|+.+.+ +|.-+. ...-++.++||-+-.
T Consensus 2 ~~~FstgdvV~lKsGGP----------~Mtvs~~ss~Gmy~C~Wf~g~g 40 (60)
T COG5475 2 EMSFSTGDVVTLKSGGP----------RMTVSGYSSDGMYECRWFDGYG 40 (60)
T ss_pred CceeecCcEEEeecCCc----------eEEEeccccCCeEEEEEecCCC
Confidence 35789999999998762 222111 112588999998765
No 147
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=24.17 E-value=46 Score=26.51 Aligned_cols=15 Identities=47% Similarity=1.026 Sum_probs=12.4
Q ss_pred eEEEcCcCCcccccc
Q 006806 528 YQLECIACGHSWYAS 542 (630)
Q Consensus 528 ~Fv~C~~Cg~rWk~s 542 (630)
....|..|||.|+.+
T Consensus 27 v~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 27 VWWKCPKCGHEWKAS 41 (55)
T ss_pred EEEECCCCCCeeEcc
Confidence 667999999999853
No 148
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.02 E-value=38 Score=38.22 Aligned_cols=29 Identities=24% Similarity=0.581 Sum_probs=23.0
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
.-.|++||.+ +-||-..-|.|..||.+..
T Consensus 350 ~p~Cp~Cg~~---------m~S~G~~g~rC~kCg~~~~ 378 (421)
T COG1571 350 NPVCPRCGGR---------MKSAGRNGFRCKKCGTRAR 378 (421)
T ss_pred CCCCCccCCc---------hhhcCCCCcccccccccCC
Confidence 4579999975 4666666899999998876
No 149
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=23.88 E-value=53 Score=29.99 Aligned_cols=41 Identities=22% Similarity=0.397 Sum_probs=24.3
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCccccccccccccee
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEASSLT 550 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~s~l~ 550 (630)
+.|.|+.|+...+.. .+ .+ ....+.|.+||+.-. + .|..|+
T Consensus 20 t~f~CP~Cge~~v~v-~~--~k--~~~h~~C~~CG~y~~--~-~V~~l~ 60 (99)
T PRK14892 20 KIFECPRCGKVSISV-KI--KK--NIAIITCGNCGLYTE--F-EVPSVY 60 (99)
T ss_pred cEeECCCCCCeEeee-ec--CC--CcceEECCCCCCccC--E-ECCccc
Confidence 569999999532211 11 12 226889999996532 3 355554
No 150
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=23.31 E-value=52 Score=30.47 Aligned_cols=37 Identities=16% Similarity=0.325 Sum_probs=24.3
Q ss_pred cccCCCCCCceEEEEeeeccCCCc-eEEEcCcCCccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDR-YQLECIACGHSWYA 541 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE-~Fv~C~~Cg~rWk~ 541 (630)
.-|.+|...=+.+...- .|.... .-++|..||+--++
T Consensus 57 ~~CkkC~t~Lvpg~n~r-vR~~~~~v~vtC~~CG~~~R~ 94 (105)
T COG2023 57 TICKKCYTPLVPGKNAR-VRLRKGRVVVTCLECGTIRRY 94 (105)
T ss_pred HhccccCcccccCcceE-EEEcCCeEEEEecCCCcEEEe
Confidence 56999997422222222 455555 88999999976654
No 151
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=22.72 E-value=66 Score=35.46 Aligned_cols=34 Identities=21% Similarity=0.412 Sum_probs=21.4
Q ss_pred CccccCCCCCCceEEEEeeeccCCCc--eEEEcCcCCcccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDR--YQLECIACGHSWY 540 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE--~Fv~C~~Cg~rWk 540 (630)
....|++|| + .+ +.+. ...+|. ..|.| .|||.-.
T Consensus 168 ~~p~c~~cg-~-~~-~~v~-~~d~~~~~v~y~c-~cG~~g~ 203 (353)
T cd00674 168 FMPYCEKCG-K-DT-TTVE-AYDAKAGTVTYKC-ECGHEET 203 (353)
T ss_pred eeeecCCcC-c-ce-eEEE-EEeCCCCeEEEEc-CCCCEEE
Confidence 456799999 3 22 3332 244444 77899 5998765
No 152
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=22.64 E-value=1.4e+02 Score=21.26 Aligned_cols=25 Identities=28% Similarity=0.258 Sum_probs=21.1
Q ss_pred eCCeEEEcCCCCCCCCeEEEEeEEeeC
Q 006806 133 LEDPVLLTPEDTNQKPYVAIIKEITQS 159 (630)
Q Consensus 133 VGD~VyV~~e~~~~~pyIArI~~I~e~ 159 (630)
+||.|.|..+. ..-.+|.|.+|...
T Consensus 1 ~Gd~V~V~~G~--~~G~~G~I~~i~~~ 25 (32)
T PF00467_consen 1 VGDTVKVISGP--FKGKIGKIVEIDRS 25 (32)
T ss_dssp TTSEEEESSST--TTTEEEEEEEEETT
T ss_pred CCCEEEEeEcC--CCCceEEEEEEECC
Confidence 59999999875 66799999999865
No 153
>PRK11823 DNA repair protein RadA; Provisional
Probab=22.48 E-value=42 Score=37.86 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=22.0
Q ss_pred CccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccccccccc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYASRDEA 546 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~srd~~ 546 (630)
+.+.|..||..- ..|.. .|..|| .|..-..++
T Consensus 6 ~~y~C~~Cg~~~-~~~~g-----------~Cp~C~-~w~t~~e~~ 37 (446)
T PRK11823 6 TAYVCQECGAES-PKWLG-----------RCPECG-AWNTLVEEV 37 (446)
T ss_pred CeEECCcCCCCC-cccCe-----------eCcCCC-Cccceeeec
Confidence 458999999764 32333 599996 898655543
No 154
>COG4640 Predicted membrane protein [Function unknown]
Probab=22.44 E-value=40 Score=37.79 Aligned_cols=25 Identities=36% Similarity=0.877 Sum_probs=17.5
Q ss_pred cccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
.-|++||+-+. -|+.| |..|||..-
T Consensus 2 ~fC~kcG~qk~----------Ed~~q--C~qCG~~~t 26 (465)
T COG4640 2 KFCPKCGSQKA----------EDDVQ--CTQCGHKFT 26 (465)
T ss_pred Ccccccccccc----------ccccc--ccccCCcCC
Confidence 35999995432 24455 999998875
No 155
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.30 E-value=28 Score=29.00 Aligned_cols=30 Identities=20% Similarity=0.530 Sum_probs=19.2
Q ss_pred CccccCCCCCCceEEEEeeeccCCC--c--eEEEcCcCCcc
Q 006806 502 TDARCSRCNECKVGLRDIIQAGHGD--R--YQLECIACGHS 538 (630)
Q Consensus 502 ~~~~C~~C~~~k~~y~q~q~tRsAD--E--~Fv~C~~Cg~r 538 (630)
+.|.|+.||.... .|.+= + .-|+|.+||..
T Consensus 24 ~~F~CPnCG~~~I-------~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVII-------YRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCeeE-------eechhHHhcCCceECCCCCCc
Confidence 5699999986411 12211 1 67999999953
No 156
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=21.52 E-value=97 Score=22.79 Aligned_cols=28 Identities=29% Similarity=0.551 Sum_probs=20.6
Q ss_pred ccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHS 538 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~r 538 (630)
...|..|+.... |..-+ -.+.|..||..
T Consensus 3 ~~~C~~C~~~~i-~~~~~-------~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGI-VNKED-------DYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeE-EEecC-------CeEEcccCCcE
Confidence 457999998864 33444 68899999964
No 157
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=21.27 E-value=40 Score=38.04 Aligned_cols=37 Identities=16% Similarity=0.460 Sum_probs=25.4
Q ss_pred cCccccCCCCCCceEEEEe--eeccCCCceEEEcCcCCcccc
Q 006806 501 MTDARCSRCNECKVGLRDI--IQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 501 m~~~~C~~C~~~k~~y~q~--q~tRsADE~Fv~C~~Cg~rWk 540 (630)
...+.|+.|.+. |+++ +|.=..++..|.|..||.--.
T Consensus 126 ~~~Y~Cp~C~kk---yt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 126 VAGYVCPNCQKK---YTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccccCCccccc---hhhhHHHHhhcccCceEEEecCCCchh
Confidence 346999999964 4433 324455668899999996544
No 158
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.20 E-value=1.9e+02 Score=26.25 Aligned_cols=41 Identities=22% Similarity=0.412 Sum_probs=29.6
Q ss_pred eeCCeE-EEcCCCCCCCCeEEEEeEEeeCCCCceEEEEE---EEecccccC
Q 006806 132 ELEDPV-LLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQ---WFYRPEEAD 178 (630)
Q Consensus 132 kVGD~V-yV~~e~~~~~pyIArI~~I~e~~dG~~~VrVq---WFYRPeEt~ 178 (630)
.|||.| |+.++ -+++|..|.++.+|..||..- -+||+.=+.
T Consensus 10 ~VG~avrYvnTg------TvgrV~dIkkdEdG~~WV~LdstdLwYre~~le 54 (97)
T COG4014 10 KVGDAVRYVNTG------TVGRVVDIKKDEDGDIWVVLDSTDLWYREHYLE 54 (97)
T ss_pred hhcceEEEeecC------ceeeEEEEEeecCCceEEEEecCCceeccccee
Confidence 388875 44443 489999999999999998763 356665443
No 159
>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=21.15 E-value=1e+02 Score=25.17 Aligned_cols=30 Identities=20% Similarity=0.478 Sum_probs=20.4
Q ss_pred ccccCCCCCCceEEEEeeeccCCCc--eEEEcCcCCcccc
Q 006806 503 DARCSRCNECKVGLRDIIQAGHGDR--YQLECIACGHSWY 540 (630)
Q Consensus 503 ~~~C~~C~~~k~~y~q~q~tRsADE--~Fv~C~~Cg~rWk 540 (630)
.|.|+.||.. ..+ ..+. ..+.|..||....
T Consensus 2 ~~~CP~CG~~-iev-------~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAE-IEL-------ENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCE-Eec-------CCCccCCEEeCCCCCCEEE
Confidence 4799999973 222 1222 6789999996654
No 160
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.92 E-value=88 Score=37.83 Aligned_cols=79 Identities=27% Similarity=0.385 Sum_probs=46.2
Q ss_pred CCccccccCChhhhcCh-----HhHHHHHhcCCchhhhc-c-c---------C---------ccccCCCCCCceEEEEee
Q 006806 466 LEPSKILNMSPNELKEG-----LTAEEMAKKEPDESEQM-Q-M---------T---------DARCSRCNECKVGLRDII 520 (630)
Q Consensus 466 IsP~~La~Ms~eEMASd-----elkeer~k~~~e~i~~~-~-m---------~---------~~~C~~C~~~k~~y~q~q 520 (630)
++.-.++.|..+.+... .+-+.++ +.++.. | + . -++|+.|... .+|.+-.
T Consensus 386 ~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~----~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~-lt~H~~~ 460 (730)
T COG1198 386 LPRVEIIDMRKEPLETGRSLSPALLEAIR----KTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSP-LTLHKAT 460 (730)
T ss_pred CCcceEEeccccccccCccCCHHHHHHHH----HHHhcCCeEEEEEccCCccceeecccCCCcccCCCCCcc-eEEecCC
Confidence 66677899999888873 3322221 122111 1 1 1 2556666644 4566555
Q ss_pred eccCCCceEEEcCcCCcccc--cccccccceeecCCCC
Q 006806 521 QAGHGDRYQLECIACGHSWY--ASRDEASSLTIDGPGS 556 (630)
Q Consensus 521 ~tRsADE~Fv~C~~Cg~rWk--~srd~~s~l~~~~~~~ 556 (630)
....|.-||++=. ..|.+-.+-.+-+-.+
T Consensus 461 -------~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~ 491 (730)
T COG1198 461 -------GQLRCHYCGYQEPIPQSCPECGSEHLRAVGP 491 (730)
T ss_pred -------CeeEeCCCCCCCCCCCCCCCCCCCeeEEecc
Confidence 6789999998843 4666666666665555
No 161
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.55 E-value=85 Score=32.90 Aligned_cols=30 Identities=17% Similarity=0.501 Sum_probs=20.4
Q ss_pred cccCCCCCCceEEEEeeeccCCCceEEEcCcCCccccc
Q 006806 504 ARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWYA 541 (630)
Q Consensus 504 ~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk~ 541 (630)
--|+.||++- .. + .++.-..|..||+..+.
T Consensus 100 ~fC~~CG~~~-~~------~-~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 100 RFCGYCGHPM-HP------S-KTEWAMLCPHCRERYYP 129 (256)
T ss_pred ccccccCCCC-ee------c-CCceeEECCCCCCEECC
Confidence 3499999863 21 1 23356789999988775
No 162
>PRK00420 hypothetical protein; Validated
Probab=20.55 E-value=59 Score=30.38 Aligned_cols=34 Identities=18% Similarity=0.292 Sum_probs=23.1
Q ss_pred hcccCccccCCCCCCceEEEEeeeccCCCceEEEcCcCCcccc
Q 006806 498 QMQMTDARCSRCNECKVGLRDIIQAGHGDRYQLECIACGHSWY 540 (630)
Q Consensus 498 ~~~m~~~~C~~C~~~k~~y~q~q~tRsADE~Fv~C~~Cg~rWk 540 (630)
...|...+|+.||..-..+ -+ .-+.|.+||..-.
T Consensus 18 Ga~ml~~~CP~Cg~pLf~l--k~-------g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 18 GAKMLSKHCPVCGLPLFEL--KD-------GEVVCPVHGKVYI 51 (112)
T ss_pred HHHHccCCCCCCCCcceec--CC-------CceECCCCCCeee
Confidence 3456678999999764322 22 4578999997554
No 163
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=20.18 E-value=1.4e+02 Score=19.80 Aligned_cols=25 Identities=24% Similarity=0.296 Sum_probs=19.7
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEe
Q 006806 131 YELEDPVLLTPEDTNQKPYVAIIKEIT 157 (630)
Q Consensus 131 YkVGD~VyV~~e~~~~~pyIArI~~I~ 157 (630)
+.+||.|.|..+. ..-.+|.|.++.
T Consensus 2 ~~~G~~V~I~~G~--~~g~~g~i~~i~ 26 (28)
T smart00739 2 FEVGDTVRVIAGP--FKGKVGKVLEVD 26 (28)
T ss_pred CCCCCEEEEeECC--CCCcEEEEEEEc
Confidence 5689999999865 566788888875
No 164
>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=20.03 E-value=1.2e+02 Score=25.73 Aligned_cols=36 Identities=19% Similarity=0.545 Sum_probs=17.7
Q ss_pred CccccCCCCC-----CceEEEEeeeccCCCceEEEcCcCCc
Q 006806 502 TDARCSRCNE-----CKVGLRDIIQAGHGDRYQLECIACGH 537 (630)
Q Consensus 502 ~~~~C~~C~~-----~k~~y~q~q~tRsADE~Fv~C~~Cg~ 537 (630)
-..-|.+|+. ..+++.-......+.-..|+|..|||
T Consensus 45 kr~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CCTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred hcccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 4567999997 23333222100122228899999996
Done!