Query 039337
Match_columns 1344
No_of_seqs 567 out of 2906
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 08:43:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039337.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039337hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1856 Transcription elongati 100.0 2E-228 4E-233 2041.9 73.0 1090 9-1157 179-1292(1299)
2 COG2183 Tex Transcriptional ac 100.0 3E-142 6E-147 1282.2 64.0 750 58-989 20-780 (780)
3 PF14633 SH2_2: SH2 domain; PD 100.0 1.1E-68 2.4E-73 576.8 18.1 216 932-1153 3-220 (220)
4 PF09371 Tex_N: Tex-like prote 100.0 2E-36 4.4E-41 322.4 17.3 184 56-317 5-190 (193)
5 PF14639 YqgF: Holliday-juncti 100.0 2.7E-33 5.8E-38 288.4 12.1 147 456-614 2-150 (150)
6 PF14635 HHH_7: Helix-hairpin- 100.0 9.5E-32 2.1E-36 256.0 4.4 103 618-720 1-104 (104)
7 PF14878 DLD: Death-like domai 100.0 4.2E-30 9.1E-35 248.3 3.2 110 732-843 1-115 (115)
8 KOG1857 Transcription accessor 99.9 2.2E-24 4.8E-29 245.1 2.2 511 341-915 57-618 (623)
9 PF14641 HTH_44: Helix-turn-he 99.8 4.7E-22 1E-26 196.4 4.6 110 13-146 4-113 (121)
10 KOG1857 Transcription accessor 99.6 5.9E-16 1.3E-20 177.1 1.7 397 349-880 198-609 (623)
11 COG1098 VacB Predicted RNA bin 99.5 4.1E-14 9E-19 136.5 5.7 78 843-922 2-79 (129)
12 TIGR01259 comE comEA protein. 99.4 1.2E-13 2.7E-18 137.9 7.2 120 572-719 1-120 (120)
13 COG0539 RpsA Ribosomal protein 99.4 2.1E-12 4.6E-17 155.7 12.0 184 841-1041 272-495 (541)
14 COG0539 RpsA Ribosomal protein 99.3 2.4E-12 5.1E-17 155.3 9.8 168 840-1019 186-393 (541)
15 cd05705 S1_Rrp5_repeat_hs14 S1 99.3 4.9E-12 1.1E-16 115.9 9.0 71 844-915 1-74 (74)
16 cd05706 S1_Rrp5_repeat_sc10 S1 99.3 2.3E-11 5.1E-16 111.0 10.3 73 844-917 1-73 (73)
17 cd05704 S1_Rrp5_repeat_hs13 S1 99.2 2.4E-11 5.3E-16 110.8 8.6 71 844-917 1-72 (72)
18 cd04461 S1_Rrp5_repeat_hs8_sc7 99.2 2.2E-11 4.8E-16 114.2 8.5 76 840-916 8-83 (83)
19 PF12836 HHH_3: Helix-hairpin- 99.2 7.9E-12 1.7E-16 111.5 4.1 65 649-718 1-65 (65)
20 cd05703 S1_Rrp5_repeat_hs12_sc 99.2 6.1E-11 1.3E-15 108.4 9.2 71 847-917 1-72 (73)
21 cd05698 S1_Rrp5_repeat_hs6_sc5 99.2 5.8E-11 1.3E-15 107.4 8.8 70 847-917 1-70 (70)
22 PF00575 S1: S1 RNA binding do 99.2 8.5E-11 1.8E-15 107.5 9.7 73 844-917 2-74 (74)
23 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.2 9E-11 2E-15 106.0 8.9 69 847-916 1-69 (69)
24 COG1555 ComEA DNA uptake prote 99.2 1.7E-11 3.7E-16 126.8 4.6 63 652-719 87-149 (149)
25 cd05694 S1_Rrp5_repeat_hs2_sc2 99.2 1.7E-10 3.7E-15 105.7 10.2 70 843-919 1-71 (74)
26 PRK08582 hypothetical protein; 99.1 1.6E-10 3.4E-15 118.6 10.4 75 843-919 2-76 (139)
27 cd05693 S1_Rrp5_repeat_hs1_sc1 99.1 7.8E-11 1.7E-15 114.2 7.2 77 844-921 1-99 (100)
28 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.1 2E-10 4.3E-15 104.5 8.9 69 847-916 1-71 (71)
29 PRK07252 hypothetical protein; 99.1 4.5E-10 9.8E-15 112.3 11.2 76 845-921 2-77 (120)
30 cd05690 S1_RPS1_repeat_ec5 S1_ 99.1 2.3E-10 4.9E-15 103.1 8.2 69 847-915 1-69 (69)
31 cd04452 S1_IF2_alpha S1_IF2_al 99.1 4.8E-10 1E-14 103.0 9.9 73 845-918 2-76 (76)
32 cd05686 S1_pNO40 S1_pNO40: pNO 99.1 4E-10 8.7E-15 103.0 9.1 70 845-916 2-72 (73)
33 PTZ00248 eukaryotic translatio 99.1 2.9E-10 6.3E-15 130.0 9.5 78 841-919 11-91 (319)
34 cd05707 S1_Rrp5_repeat_sc11 S1 99.1 3.6E-10 7.8E-15 101.8 8.2 68 847-915 1-68 (68)
35 cd05691 S1_RPS1_repeat_ec6 S1_ 99.1 6.1E-10 1.3E-14 101.4 9.7 71 847-918 1-71 (73)
36 cd05708 S1_Rrp5_repeat_sc12 S1 99.1 6.6E-10 1.4E-14 102.2 9.9 74 845-919 1-75 (77)
37 PLN00207 polyribonucleotide nu 99.1 6.1E-10 1.3E-14 141.5 12.0 119 798-919 699-825 (891)
38 PRK07899 rpsA 30S ribosomal pr 99.0 1.3E-09 2.9E-14 132.8 13.7 76 842-919 204-279 (486)
39 cd05689 S1_RPS1_repeat_ec4 S1_ 99.0 1.2E-09 2.7E-14 99.4 9.3 72 844-915 1-72 (72)
40 PRK05807 hypothetical protein; 99.0 1.3E-09 2.8E-14 111.6 10.1 74 844-920 3-76 (136)
41 PRK13806 rpsA 30S ribosomal pr 99.0 2.4E-09 5.3E-14 132.1 13.7 79 841-919 287-365 (491)
42 cd05692 S1_RPS1_repeat_hs4 S1_ 99.0 1.5E-09 3.3E-14 97.2 8.7 69 847-917 1-69 (69)
43 PRK11824 polynucleotide phosph 99.0 2.9E-09 6.4E-14 135.8 14.7 125 788-918 560-691 (693)
44 PRK08059 general stress protei 99.0 1.9E-09 4.2E-14 108.7 10.3 79 842-921 3-81 (123)
45 PRK12269 bifunctional cytidyla 99.0 3E-09 6.5E-14 137.2 13.4 78 842-919 574-651 (863)
46 cd05687 S1_RPS1_repeat_ec1_hs1 99.0 2.7E-09 5.8E-14 96.6 9.4 70 847-917 1-70 (70)
47 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.9 3.9E-09 8.4E-14 94.6 8.7 66 847-915 1-66 (66)
48 cd05684 S1_DHX8_helicase S1_DH 98.9 4.8E-09 1E-13 97.4 9.7 70 847-919 1-74 (79)
49 PHA02945 interferon resistance 98.9 4.9E-09 1.1E-13 96.3 8.8 70 845-918 10-83 (88)
50 cd05685 S1_Tex S1_Tex: The C-t 98.9 3.9E-09 8.6E-14 94.3 8.1 68 847-915 1-68 (68)
51 PRK12269 bifunctional cytidyla 98.9 7.4E-09 1.6E-13 133.6 13.6 77 842-918 661-737 (863)
52 PRK13806 rpsA 30S ribosomal pr 98.9 1.3E-08 2.8E-13 125.7 13.0 76 843-919 199-278 (491)
53 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.8 9.1E-09 2E-13 97.1 8.2 76 844-920 4-82 (86)
54 KOG0921 Dosage compensation co 98.8 1.7E-08 3.6E-13 124.0 12.1 26 1068-1093 1002-1027(1282)
55 smart00316 S1 Ribosomal protei 98.8 1.7E-08 3.7E-13 90.5 9.3 72 845-917 1-72 (72)
56 PRK07400 30S ribosomal protein 98.8 2.1E-08 4.6E-13 116.9 11.3 78 841-920 191-268 (318)
57 PRK06299 rpsA 30S ribosomal pr 98.8 3.3E-08 7.1E-13 124.9 13.9 76 842-919 197-272 (565)
58 cd04472 S1_PNPase S1_PNPase: P 98.8 1.8E-08 3.8E-13 90.3 8.2 68 847-916 1-68 (68)
59 cd04465 S1_RPS1_repeat_ec2_hs2 98.8 2.5E-08 5.4E-13 89.6 9.0 67 847-917 1-67 (67)
60 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 2E-08 4.3E-13 89.9 8.4 68 846-915 1-68 (68)
61 COG1093 SUI2 Translation initi 98.8 5.1E-09 1.1E-13 114.3 5.2 74 845-919 10-85 (269)
62 cd04471 S1_RNase_R S1_RNase_R: 98.8 2.8E-08 6.1E-13 92.8 9.6 71 846-916 1-82 (83)
63 cd04454 S1_Rrp4_like S1_Rrp4_l 98.7 3.7E-08 8.1E-13 92.1 8.6 75 844-920 4-78 (82)
64 cd04453 S1_RNase_E S1_RNase_E: 98.7 3.9E-08 8.4E-13 93.3 8.7 75 843-917 4-82 (88)
65 KOG0921 Dosage compensation co 98.7 4.3E-08 9.2E-13 120.5 11.2 21 511-531 384-404 (1282)
66 TIGR02696 pppGpp_PNP guanosine 98.7 2.2E-08 4.7E-13 125.2 9.0 72 843-915 644-718 (719)
67 cd05702 S1_Rrp5_repeat_hs11_sc 98.7 3.4E-08 7.5E-13 89.5 8.0 63 847-909 1-64 (70)
68 PRK07899 rpsA 30S ribosomal pr 98.7 2.9E-08 6.3E-13 121.2 9.8 76 843-919 290-365 (486)
69 PRK03987 translation initiatio 98.7 3.8E-08 8.2E-13 111.3 9.8 75 844-919 6-82 (262)
70 PRK06299 rpsA 30S ribosomal pr 98.7 8.4E-08 1.8E-12 121.3 13.2 77 842-919 369-446 (565)
71 cd04473 S1_RecJ_like S1_RecJ_l 98.7 1.1E-07 2.4E-12 87.9 9.7 67 840-916 10-76 (77)
72 TIGR00717 rpsA ribosomal prote 98.7 1.4E-07 3.1E-12 118.0 13.5 78 842-919 355-432 (516)
73 TIGR00426 competence protein C 98.7 2.4E-08 5.1E-13 90.4 4.7 63 652-719 6-69 (69)
74 PRK06676 rpsA 30S ribosomal pr 98.6 1.4E-07 3E-12 113.9 10.2 79 841-920 272-350 (390)
75 PRK07400 30S ribosomal protein 98.6 1.9E-07 4E-12 109.1 10.1 79 840-919 25-103 (318)
76 cd00164 S1_like S1_like: Ribos 98.6 1.6E-07 3.4E-12 82.5 7.1 65 850-915 1-65 (65)
77 PRK02515 psbU photosystem II c 98.5 7.2E-08 1.6E-12 95.4 5.1 63 652-723 51-116 (132)
78 PRK00087 4-hydroxy-3-methylbut 98.5 6.1E-07 1.3E-11 114.7 13.7 77 841-919 472-548 (647)
79 TIGR00717 rpsA ribosomal prote 98.5 2.7E-07 5.9E-12 115.5 9.9 75 842-917 442-516 (516)
80 KOG3973 Uncharacterized conser 98.5 1.1E-06 2.4E-11 98.1 13.2 20 806-825 76-100 (465)
81 PRK06676 rpsA 30S ribosomal pr 98.4 4.5E-07 9.8E-12 109.5 9.5 76 842-919 188-263 (390)
82 cd04460 S1_RpoE S1_RpoE: RpoE, 98.4 8.4E-07 1.8E-11 86.2 9.1 73 848-921 1-88 (99)
83 smart00252 SH2 Src homology 2 98.4 1E-06 2.2E-11 82.6 9.4 80 968-1059 1-81 (84)
84 PRK00087 4-hydroxy-3-methylbut 98.4 7.1E-07 1.5E-11 114.1 10.3 78 842-920 558-635 (647)
85 KOG3973 Uncharacterized conser 98.4 2.4E-06 5.3E-11 95.5 12.7 23 1254-1276 402-424 (465)
86 PRK09521 exosome complex RNA-b 98.3 9.2E-07 2E-11 96.1 8.0 76 842-921 60-145 (189)
87 TIGR03591 polynuc_phos polyrib 98.3 1E-06 2.2E-11 112.7 7.8 70 843-914 615-684 (684)
88 PRK04163 exosome complex RNA-b 98.3 2.6E-06 5.5E-11 95.6 9.0 77 842-920 59-139 (235)
89 COG1185 Pnp Polyribonucleotide 98.2 1.3E-06 2.9E-11 107.0 6.6 75 842-918 615-689 (692)
90 PRK11642 exoribonuclease R; Pr 98.1 6.5E-06 1.4E-10 106.9 10.2 74 845-918 642-726 (813)
91 TIGR00448 rpoE DNA-directed RN 98.1 1.1E-05 2.4E-10 86.9 9.3 77 844-921 79-170 (179)
92 cd04455 S1_NusA S1_NusA: N-uti 98.1 2.3E-05 4.9E-10 70.6 9.1 63 845-915 2-66 (67)
93 TIGR02063 RNase_R ribonuclease 98.0 1.3E-05 2.7E-10 104.0 10.2 72 845-916 626-708 (709)
94 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.0 1.8E-05 3.8E-10 75.9 7.8 76 844-921 4-89 (92)
95 cd00173 SH2 Src homology 2 dom 98.0 3.6E-05 7.8E-10 73.5 10.0 77 972-1060 5-81 (94)
96 TIGR00358 3_prime_RNase VacB a 98.0 2.1E-05 4.6E-10 100.8 10.2 71 846-916 572-653 (654)
97 smart00732 YqgFc Likely ribonu 97.8 0.00012 2.6E-09 70.6 10.6 93 460-577 2-99 (99)
98 COG1095 RPB7 DNA-directed RNA 97.8 4.8E-05 1E-09 80.2 8.1 76 845-921 80-170 (183)
99 PF00017 SH2: SH2 domain; Int 97.7 0.00011 2.3E-09 67.8 8.1 74 971-1056 3-77 (77)
100 KOG1070 rRNA processing protei 97.7 2.9E-05 6.4E-10 100.2 5.0 79 841-920 594-672 (1710)
101 PRK08563 DNA-directed RNA poly 97.7 0.00014 3E-09 79.1 9.5 77 844-921 79-170 (187)
102 KOG1070 rRNA processing protei 97.7 0.00011 2.4E-09 95.2 9.4 83 840-923 1156-1238(1710)
103 PRK09202 nusA transcription el 97.5 0.00023 5E-09 87.1 9.0 68 846-921 134-203 (470)
104 KOG0790 Protein tyrosine phosp 97.5 0.00098 2.1E-08 77.7 12.9 165 971-1153 8-200 (600)
105 KOG1067 Predicted RNA-binding 97.3 0.00021 4.5E-09 85.1 5.2 76 840-917 662-737 (760)
106 COG1096 Predicted RNA-binding 97.2 0.001 2.2E-08 70.4 8.6 78 840-921 58-145 (188)
107 PRK05054 exoribonuclease II; P 97.1 0.0013 2.8E-08 84.3 9.5 70 847-916 562-643 (644)
108 PHA02858 EIF2a-like PKR inhibi 97.1 0.0011 2.3E-08 61.0 6.1 69 845-916 15-85 (86)
109 PF10447 EXOSC1: Exosome compo 97.0 0.0016 3.4E-08 60.9 6.6 61 845-905 3-82 (82)
110 cd04462 S1_RNAPII_Rpb7 S1_RNAP 96.9 0.0044 9.6E-08 58.9 8.9 62 846-909 1-73 (88)
111 TIGR02062 RNase_B exoribonucle 96.8 0.0025 5.4E-08 81.5 8.6 69 847-915 558-638 (639)
112 TIGR01953 NusA transcription t 96.8 0.0037 7.9E-08 73.8 9.3 69 845-921 130-201 (341)
113 cd05699 S1_Rrp5_repeat_hs7 S1_ 96.8 0.0043 9.3E-08 56.2 7.1 68 847-917 1-72 (72)
114 cd05790 S1_Rrp40 S1_Rrp40: Rrp 96.8 0.0061 1.3E-07 57.6 8.4 73 844-919 4-76 (86)
115 PRK12327 nusA transcription el 96.7 0.0053 1.2E-07 72.9 9.1 68 845-920 133-202 (362)
116 COG0557 VacB Exoribonuclease R 96.5 0.0053 1.1E-07 79.8 8.6 74 845-918 621-705 (706)
117 COG2996 Predicted RNA-bindinin 96.4 0.0083 1.8E-07 66.9 7.6 64 846-919 155-218 (287)
118 cd00173 SH2 Src homology 2 dom 96.3 0.015 3.3E-07 55.3 8.2 73 1077-1154 8-82 (94)
119 COG1097 RRP4 RNA-binding prote 96.3 0.013 2.8E-07 64.7 8.4 77 843-920 61-140 (239)
120 PTZ00162 DNA-directed RNA poly 96.2 0.016 3.6E-07 62.2 8.5 74 844-919 79-166 (176)
121 TIGR00757 RNaseEG ribonuclease 96.1 0.013 2.8E-07 71.1 8.0 64 843-906 22-98 (414)
122 PRK00109 Holliday junction res 96.1 0.046 1E-06 56.5 10.8 96 460-578 5-105 (138)
123 KOG2916 Translation initiation 96.0 0.0037 8E-08 68.8 2.6 74 844-918 14-89 (304)
124 smart00252 SH2 Src homology 2 96.0 0.029 6.3E-07 52.5 8.4 72 1077-1153 9-82 (84)
125 COG1107 Archaea-specific RecJ- 95.9 0.0063 1.4E-07 73.6 4.1 73 839-918 115-187 (715)
126 KOG1999 RNA polymerase II tran 95.8 0.33 7.1E-06 62.6 18.4 55 844-900 408-468 (1024)
127 COG5164 SPT5 Transcription elo 95.7 0.14 3E-06 60.6 13.7 49 1124-1177 390-440 (607)
128 TIGR00250 RNAse_H_YqgF RNAse H 95.5 0.13 2.8E-06 52.8 11.2 94 462-578 1-99 (130)
129 PF00017 SH2: SH2 domain; Int 95.4 0.047 1E-06 50.2 7.1 69 1077-1149 7-77 (77)
130 PRK12328 nusA transcription el 95.0 0.077 1.7E-06 62.9 8.6 68 845-920 137-208 (374)
131 PF03652 UPF0081: Uncharacteri 94.5 0.22 4.7E-06 51.4 9.7 95 460-577 2-102 (135)
132 KOG3409 Exosomal 3'-5' exoribo 94.5 0.13 2.8E-06 53.7 7.8 77 844-921 66-151 (193)
133 KOG2044 5'-3' exonuclease HKE1 94.4 0.5 1.1E-05 59.7 14.0 22 274-295 168-189 (931)
134 PRK12329 nusA transcription el 93.8 0.19 4.2E-06 60.6 8.7 69 845-920 151-227 (449)
135 PF14579 HHH_6: Helix-hairpin- 93.6 0.11 2.5E-06 49.6 5.2 47 667-714 27-74 (90)
136 KOG1999 RNA polymerase II tran 93.6 1.7 3.6E-05 56.5 16.6 9 76-84 64-72 (1024)
137 PF13509 S1_2: S1 domain; PDB: 93.3 0.35 7.6E-06 42.8 7.3 61 846-917 1-61 (61)
138 COG0816 Predicted endonuclease 93.1 0.76 1.7E-05 47.6 10.6 103 460-583 3-109 (141)
139 PRK00039 ruvC Holliday junctio 92.8 0.38 8.3E-06 51.3 8.3 65 460-527 3-67 (164)
140 cd00529 RuvC_resolvase Hollida 92.0 0.55 1.2E-05 49.5 8.1 66 460-528 1-66 (154)
141 PRK10811 rne ribonuclease E; R 91.8 0.34 7.4E-06 63.0 7.4 64 845-908 37-110 (1068)
142 KOG1264 Phospholipase C [Lipid 91.7 0.6 1.3E-05 58.8 8.9 89 1065-1153 528-625 (1267)
143 PF00633 HHH: Helix-hairpin-he 91.5 0.13 2.9E-06 38.8 2.1 20 667-686 11-30 (30)
144 PF14520 HHH_5: Helix-hairpin- 91.5 0.1 2.2E-06 45.9 1.6 44 667-715 5-56 (60)
145 PF02075 RuvC: Crossover junct 90.7 0.56 1.2E-05 49.2 6.6 64 461-527 1-64 (149)
146 PRK11712 ribonuclease G; Provi 89.9 0.65 1.4E-05 57.7 7.2 65 843-907 35-112 (489)
147 COG0322 UvrC Nuclease subunit 89.9 3.7 7.9E-05 52.2 13.8 48 665-713 528-577 (581)
148 KOG1264 Phospholipase C [Lipid 89.8 3.2 7E-05 52.7 12.8 163 977-1154 545-728 (1267)
149 KOG2044 5'-3' exonuclease HKE1 89.4 2.6 5.6E-05 53.6 11.7 36 563-605 296-331 (931)
150 PRK14666 uvrC excinuclease ABC 88.5 2.5 5.5E-05 54.3 11.0 52 666-717 636-689 (694)
151 TIGR00228 ruvC crossover junct 88.4 1.4 3E-05 46.6 7.3 63 461-527 1-63 (156)
152 KOG4792 Crk family adapters [S 88.0 1.6 3.4E-05 47.8 7.4 82 1072-1158 14-103 (293)
153 PRK14670 uvrC excinuclease ABC 87.8 6.8 0.00015 49.9 14.3 54 665-718 512-567 (574)
154 PRK14605 ruvA Holliday junctio 87.6 0.31 6.8E-06 53.4 2.1 48 665-712 71-123 (194)
155 PRK00116 ruvA Holliday junctio 87.5 0.19 4.2E-06 55.0 0.4 55 666-720 72-131 (192)
156 PF06514 PsbU: Photosystem II 86.7 0.46 9.9E-06 45.1 2.3 62 652-722 13-77 (93)
157 PRK13901 ruvA Holliday junctio 86.7 0.49 1.1E-05 51.7 2.9 51 665-715 70-125 (196)
158 KOG4637 Adaptor for phosphoino 86.6 0.89 1.9E-05 52.8 5.0 58 966-1025 331-388 (464)
159 TIGR00084 ruvA Holliday juncti 86.3 0.23 4.9E-06 54.3 0.1 50 665-714 70-124 (191)
160 KOG4226 Adaptor protein NCK/Do 85.9 2.2 4.7E-05 47.8 7.3 81 964-1058 277-359 (379)
161 PRK14672 uvrC excinuclease ABC 85.9 7.4 0.00016 50.0 13.0 49 666-714 607-657 (691)
162 KOG3298 DNA-directed RNA polym 85.6 4.4 9.4E-05 42.5 8.8 61 846-908 81-152 (170)
163 KOG0790 Protein tyrosine phosp 85.5 2.5 5.4E-05 50.4 7.9 81 970-1062 112-203 (600)
164 PRK14601 ruvA Holliday junctio 84.8 0.37 8E-06 52.2 0.9 50 665-714 71-125 (183)
165 PF03934 T2SK: Type II secreti 84.6 0.47 1E-05 55.0 1.7 66 650-721 181-248 (280)
166 PRK14603 ruvA Holliday junctio 84.5 0.7 1.5E-05 50.8 2.8 50 665-714 70-124 (197)
167 PRK00558 uvrC excinuclease ABC 84.3 12 0.00026 48.1 14.2 52 666-717 542-595 (598)
168 PF14633 SH2_2: SH2 domain; PD 83.4 4.8 0.0001 45.0 8.8 84 1062-1150 30-122 (220)
169 PF12826 HHH_2: Helix-hairpin- 83.0 0.41 9E-06 42.8 0.3 47 672-718 8-56 (64)
170 PF06682 DUF1183: Protein of u 82.5 9 0.0002 45.0 10.9 16 994-1009 68-83 (318)
171 PRK14606 ruvA Holliday junctio 82.3 0.52 1.1E-05 51.4 0.8 53 665-717 71-128 (188)
172 PRK14602 ruvA Holliday junctio 82.3 0.63 1.4E-05 51.4 1.4 50 665-714 72-126 (203)
173 COG0632 RuvA Holliday junction 82.3 0.78 1.7E-05 50.4 2.1 55 665-719 71-130 (201)
174 KOG4661 Hsp27-ERE-TATA-binding 82.2 9.2 0.0002 46.8 10.9 42 671-723 409-458 (940)
175 KOG4792 Crk family adapters [S 82.0 4.6 0.0001 44.3 7.6 81 968-1054 12-92 (293)
176 PRK14604 ruvA Holliday junctio 81.9 0.55 1.2E-05 51.5 0.8 53 665-717 71-128 (195)
177 PF02371 Transposase_20: Trans 79.9 1.1 2.3E-05 42.7 1.9 44 667-710 2-45 (87)
178 PF04919 DUF655: Protein of un 79.8 2.8 6.1E-05 44.9 5.1 38 667-705 116-154 (181)
179 KOG4307 RNA binding protein RB 78.9 18 0.0004 45.6 12.1 27 972-999 529-555 (944)
180 PRK06958 single-stranded DNA-b 78.8 4.6 9.9E-05 43.8 6.4 7 1122-1128 51-57 (182)
181 PRK14600 ruvA Holliday junctio 78.6 0.68 1.5E-05 50.4 0.1 50 665-715 71-125 (186)
182 PRK12766 50S ribosomal protein 78.4 1.3 2.9E-05 49.2 2.3 52 667-718 3-57 (232)
183 cd00141 NT_POLXc Nucleotidyltr 77.6 1.9 4.1E-05 50.8 3.4 52 667-720 45-107 (307)
184 COG0817 RuvC Holliday junction 77.6 5.4 0.00012 41.9 6.3 63 462-527 1-63 (160)
185 smart00278 HhH1 Helix-hairpin- 77.5 2 4.3E-05 31.3 2.2 20 668-687 2-21 (26)
186 PRK14669 uvrC excinuclease ABC 76.9 23 0.00051 45.6 13.0 51 667-719 552-604 (624)
187 PF05918 API5: Apoptosis inhib 76.6 0.81 1.8E-05 57.3 0.0 32 270-304 53-85 (556)
188 PRK14668 uvrC excinuclease ABC 75.5 38 0.00083 43.4 14.3 50 667-716 525-576 (577)
189 PF00633 HHH: Helix-hairpin-he 75.5 1.7 3.8E-05 32.9 1.5 24 693-716 7-30 (30)
190 PF08292 RNA_pol_Rbc25: RNA po 73.7 13 0.00027 37.9 7.6 62 846-907 3-76 (122)
191 PRK07772 single-stranded DNA-b 73.6 7.4 0.00016 42.4 6.4 7 1315-1321 165-171 (186)
192 TIGR01405 polC_Gram_pos DNA po 73.4 5.4 0.00012 55.0 6.5 65 649-714 1126-1196(1213)
193 COG1512 Beta-propeller domains 73.3 3.6 7.7E-05 47.4 4.1 34 957-990 60-94 (271)
194 COG4907 Predicted membrane pro 72.7 2.7 5.9E-05 50.3 3.0 26 893-918 332-357 (595)
195 PRK12442 translation initiatio 70.5 22 0.00047 33.8 7.7 66 848-918 7-73 (87)
196 PF05918 API5: Apoptosis inhib 69.9 1.5 3.2E-05 55.1 0.0 8 1110-1117 457-464 (556)
197 PRK14667 uvrC excinuclease ABC 68.4 3.1 6.7E-05 52.8 2.4 51 666-717 513-565 (567)
198 COG1948 MUS81 ERCC4-type nucle 67.4 3.4 7.4E-05 46.8 2.2 56 667-722 182-239 (254)
199 PRK07373 DNA polymerase III su 67.1 11 0.00023 46.9 6.5 63 652-714 94-164 (449)
200 COG4907 Predicted membrane pro 66.4 4.5 9.7E-05 48.6 3.0 12 1146-1157 488-499 (595)
201 COG1031 Uncharacterized Fe-S o 66.4 3.6 7.9E-05 49.6 2.3 43 652-703 506-548 (560)
202 KOG4661 Hsp27-ERE-TATA-binding 66.1 59 0.0013 40.3 12.0 31 670-700 450-483 (940)
203 KOG1930 Focal adhesion protein 66.0 7.2 0.00016 46.5 4.5 176 960-1155 205-411 (483)
204 PF07355 GRDB: Glycine/sarcosi 65.9 18 0.00039 42.9 7.8 52 477-535 43-95 (349)
205 cd02069 methionine_synthase_B1 65.5 56 0.0012 36.5 11.3 82 511-603 129-212 (213)
206 PF10246 MRP-S35: Mitochondria 64.9 23 0.00049 34.7 6.8 55 845-907 22-76 (104)
207 PRK08609 hypothetical protein; 64.4 6.9 0.00015 50.1 4.4 43 668-714 89-140 (570)
208 KOG4307 RNA binding protein RB 64.1 92 0.002 39.8 13.4 21 1056-1077 607-627 (944)
209 COG0177 Nth Predicted EndoIII- 63.0 8.8 0.00019 42.6 4.3 45 672-716 78-128 (211)
210 PRK07772 single-stranded DNA-b 62.4 15 0.00032 40.1 5.9 6 1109-1114 30-35 (186)
211 COG1530 CafA Ribonucleases G a 61.6 12 0.00026 46.9 5.7 73 843-916 34-112 (487)
212 KOG1924 RhoA GTPase effector D 61.1 27 0.00059 44.8 8.3 22 593-614 237-258 (1102)
213 TIGR00008 infA translation ini 61.0 37 0.0008 31.0 7.1 60 849-913 6-66 (68)
214 PRK00448 polC DNA polymerase I 60.9 13 0.00027 52.4 6.1 65 649-714 1349-1419(1437)
215 TIGR01917 gly_red_sel_B glycin 59.7 27 0.00059 42.4 7.9 96 477-588 39-135 (431)
216 TIGR01918 various_sel_PB selen 59.5 31 0.00067 42.0 8.3 87 477-578 39-126 (431)
217 PRK11634 ATP-dependent RNA hel 59.4 17 0.00036 47.2 6.7 19 1132-1150 528-546 (629)
218 COG4277 Predicted DNA-binding 59.3 5.7 0.00012 45.5 2.1 59 651-720 319-377 (404)
219 smart00483 POLXc DNA polymeras 59.3 7.9 0.00017 46.2 3.4 52 668-721 49-112 (334)
220 PF07318 DUF1464: Protein of u 59.1 19 0.00041 42.8 6.3 54 467-531 3-57 (343)
221 PF14520 HHH_5: Helix-hairpin- 56.7 7.6 0.00016 34.1 2.0 22 667-688 38-59 (60)
222 KOG4817 Unnamed protein [Funct 56.6 1.4E+02 0.0031 35.5 12.5 11 1185-1195 83-93 (468)
223 KOG0116 RasGAP SH3 binding pro 56.6 17 0.00038 44.4 5.7 14 1141-1154 301-314 (419)
224 COG2176 PolC DNA polymerase II 55.8 12 0.00025 50.3 4.3 147 569-716 1252-1429(1444)
225 PF11215 DUF3010: Protein of u 54.9 30 0.00065 35.8 6.1 64 460-527 2-67 (138)
226 KOG2996 Rho guanine nucleotide 54.6 25 0.00054 43.6 6.4 77 964-1054 681-759 (865)
227 cd02070 corrinoid_protein_B12- 54.2 1.3E+02 0.0027 33.2 11.6 54 511-573 123-176 (201)
228 KOG2841 Structure-specific end 53.8 8.3 0.00018 42.9 2.2 23 667-689 227-249 (254)
229 KOG4226 Adaptor protein NCK/Do 53.7 50 0.0011 37.4 8.1 73 1075-1151 287-359 (379)
230 PRK13910 DNA glycosylase MutY; 53.5 13 0.00028 43.4 3.8 50 667-716 35-91 (289)
231 COG2433 Uncharacterized conser 53.5 78 0.0017 40.1 10.4 101 460-588 3-108 (652)
232 COG1491 Predicted RNA-binding 53.5 13 0.00029 39.8 3.5 34 667-701 130-163 (202)
233 COG0361 InfA Translation initi 53.2 69 0.0015 29.8 7.6 66 847-917 6-72 (75)
234 PF12826 HHH_2: Helix-hairpin- 52.6 9.6 0.00021 34.1 2.0 23 667-689 35-57 (64)
235 KOG0194 Protein tyrosine kinas 51.8 40 0.00087 42.1 7.8 77 968-1059 49-132 (474)
236 PHA01623 hypothetical protein 51.6 34 0.00073 29.9 5.1 45 350-407 7-51 (56)
237 PF02762 Cbl_N3: CBL proto-onc 50.7 44 0.00096 30.9 5.8 51 967-1017 1-55 (86)
238 cd05700 S1_Rrp5_repeat_hs9 S1_ 50.5 58 0.0013 28.8 6.2 64 847-916 1-65 (65)
239 PRK06826 dnaE DNA polymerase I 50.2 27 0.00059 48.2 6.6 66 649-714 801-874 (1151)
240 PF04312 DUF460: Protein of un 50.1 24 0.00051 36.5 4.6 54 458-529 31-84 (138)
241 PRK05673 dnaE DNA polymerase I 50.0 28 0.0006 48.2 6.6 66 649-714 797-870 (1135)
242 PRK14671 uvrC excinuclease ABC 49.9 7.7 0.00017 50.0 1.3 50 666-717 568-619 (621)
243 PF00313 CSD: 'Cold-shock' DNA 49.9 1.3E+02 0.0027 26.8 8.8 49 850-904 1-53 (66)
244 PRK15464 cold shock-like prote 49.3 65 0.0014 29.5 6.8 51 850-906 5-59 (70)
245 PRK08609 hypothetical protein; 49.2 15 0.00033 47.1 3.8 51 668-719 49-110 (570)
246 PF10391 DNA_pol_lambd_f: Fing 48.9 14 0.0003 31.8 2.3 30 667-701 2-31 (52)
247 TIGR00594 polc DNA-directed DN 48.6 30 0.00064 47.4 6.6 66 649-714 801-874 (1022)
248 COG5164 SPT5 Transcription elo 48.3 3.3E+02 0.0071 33.6 13.9 8 1183-1190 454-461 (607)
249 PRK10943 cold shock-like prote 47.9 80 0.0017 28.7 7.2 52 849-906 3-58 (69)
250 PRK09937 stationary phase/star 47.3 93 0.002 28.8 7.6 58 851-914 3-64 (74)
251 KOG0194 Protein tyrosine kinas 46.9 74 0.0016 39.8 9.0 80 1071-1157 49-137 (474)
252 PRK07374 dnaE DNA polymerase I 46.4 33 0.00071 47.5 6.5 66 649-714 812-885 (1170)
253 PTZ00473 Plasmodium Vir superf 46.4 64 0.0014 38.8 7.9 10 1079-1088 202-211 (420)
254 PRK10308 3-methyl-adenine DNA 46.0 20 0.00044 41.7 3.9 44 673-716 172-226 (283)
255 PRK11634 ATP-dependent RNA hel 46.0 38 0.00082 44.1 6.7 7 564-570 151-157 (629)
256 PF00370 FGGY_N: FGGY family o 46.0 54 0.0012 36.9 7.3 27 461-489 2-28 (245)
257 PRK10590 ATP-dependent RNA hel 45.8 38 0.00082 42.2 6.5 6 523-528 40-45 (456)
258 PRK07135 dnaE DNA polymerase I 45.5 36 0.00077 46.2 6.5 65 650-714 731-803 (973)
259 PF06682 DUF1183: Protein of u 45.3 1.7E+02 0.0038 34.6 11.3 6 1032-1037 90-95 (318)
260 COG1512 Beta-propeller domains 45.2 23 0.00049 40.9 4.0 10 991-1000 68-77 (271)
261 KOG1924 RhoA GTPase effector D 44.8 60 0.0013 41.9 7.7 9 1049-1057 456-464 (1102)
262 COG2996 Predicted RNA-bindinin 44.6 72 0.0016 36.6 7.7 72 844-925 3-75 (287)
263 KOG1856 Transcription elongati 44.4 43 0.00094 45.0 6.7 83 1061-1149 1099-1191(1299)
264 COG1796 POL4 DNA polymerase IV 44.3 22 0.00048 41.5 3.8 50 669-719 55-115 (326)
265 PF03934 T2SK: Type II secreti 43.8 26 0.00055 40.7 4.3 67 654-721 76-180 (280)
266 PRK10702 endonuclease III; Pro 43.0 26 0.00057 39.0 4.1 49 668-716 72-128 (211)
267 PRK09507 cspE cold shock prote 42.3 89 0.0019 28.5 6.6 52 849-906 3-58 (69)
268 PRK01229 N-glycosylase/DNA lya 42.3 18 0.00038 40.3 2.5 36 674-709 84-131 (208)
269 TIGR03252 uncharacterized HhH- 41.3 37 0.00079 36.8 4.6 50 674-723 75-145 (177)
270 smart00279 HhH2 Helix-hairpin- 41.1 19 0.00041 28.6 1.8 17 670-686 19-35 (36)
271 PRK15463 cold shock-like prote 41.1 1E+02 0.0022 28.2 6.8 51 850-906 5-59 (70)
272 PRK10354 RNA chaperone/anti-te 40.9 1.5E+02 0.0032 27.1 7.9 51 850-906 5-59 (70)
273 COG2433 Uncharacterized conser 40.5 43 0.00094 42.2 5.6 55 459-531 244-298 (652)
274 cd05793 S1_IF1A S1_IF1A: Trans 38.9 1E+02 0.0022 28.8 6.5 63 850-918 2-65 (77)
275 COG1796 POL4 DNA polymerase IV 38.8 22 0.00047 41.6 2.6 73 667-757 93-176 (326)
276 PRK09890 cold shock protein Cs 38.7 1.8E+02 0.004 26.5 8.1 51 850-906 5-59 (70)
277 PRK06958 single-stranded DNA-b 38.5 65 0.0014 35.1 6.0 10 1133-1142 53-62 (182)
278 TIGR02370 pyl_corrinoid methyl 38.5 1.2E+02 0.0025 33.5 8.1 38 510-550 124-161 (197)
279 smart00478 ENDO3c endonuclease 37.4 36 0.00077 35.4 3.8 41 673-713 42-88 (149)
280 PRK14998 cold shock-like prote 36.9 1.6E+02 0.0034 27.3 7.4 57 851-913 3-63 (73)
281 PRK05672 dnaE2 error-prone DNA 36.9 36 0.00079 46.7 4.7 63 651-714 790-862 (1046)
282 COG4278 Uncharacterized conser 36.8 55 0.0012 36.5 5.1 7 964-970 48-54 (269)
283 KOG1004 Exosomal 3'-5' exoribo 36.5 1.4E+02 0.003 33.1 8.0 75 843-920 62-136 (230)
284 PTZ00294 glycerol kinase-like 36.4 1.1E+02 0.0024 38.7 8.6 70 460-531 3-81 (504)
285 PF00464 SHMT: Serine hydroxym 35.5 12 0.00026 45.6 -0.1 35 509-543 157-191 (399)
286 KOG2841 Structure-specific end 35.0 19 0.00041 40.2 1.3 53 667-719 195-249 (254)
287 PRK13913 3-methyladenine DNA g 34.9 41 0.00089 37.7 3.9 83 673-757 87-179 (218)
288 KOG0116 RasGAP SH3 binding pro 34.6 55 0.0012 40.2 5.2 8 843-850 87-94 (419)
289 PRK04012 translation initiatio 34.3 1.6E+02 0.0035 29.0 7.4 64 848-917 21-85 (100)
290 TIGR01314 gntK_FGGY gluconate 33.6 1.1E+02 0.0024 38.7 8.0 69 461-531 2-76 (505)
291 TIGR02628 fuculo_kin_coli L-fu 33.3 1.1E+02 0.0024 38.2 7.9 27 461-489 3-29 (465)
292 TIGR00575 dnlj DNA ligase, NAD 33.0 22 0.00048 46.3 1.6 57 654-715 458-516 (652)
293 TIGR01083 nth endonuclease III 32.6 52 0.0011 36.0 4.3 44 673-716 76-125 (191)
294 PRK06920 dnaE DNA polymerase I 32.3 74 0.0016 43.9 6.4 65 649-714 779-851 (1107)
295 PRK15027 xylulokinase; Provisi 32.1 1.3E+02 0.0028 37.8 8.2 69 461-531 2-75 (484)
296 PF11731 Cdd1: Pathogenicity l 31.7 31 0.00068 33.4 2.0 29 667-700 12-40 (93)
297 COG1545 Predicted nucleic-acid 31.5 2.1E+02 0.0046 29.8 8.2 63 842-912 59-130 (140)
298 TIGR01315 5C_CHO_kinase FGGY-f 31.4 1.4E+02 0.003 38.2 8.4 69 461-531 2-77 (541)
299 COG1940 NagC Transcriptional r 31.3 1.6E+02 0.0034 34.5 8.4 65 460-530 7-73 (314)
300 KOG4278 Protein tyrosine kinas 31.2 1.1E+02 0.0025 38.8 7.0 81 964-1056 148-229 (1157)
301 PRK00047 glpK glycerol kinase; 31.1 1.4E+02 0.003 37.7 8.3 70 460-531 6-82 (498)
302 PRK10331 L-fuculokinase; Provi 31.0 1.5E+02 0.0031 37.2 8.4 28 460-489 3-30 (470)
303 PRK13766 Hef nuclease; Provisi 30.2 27 0.00058 46.6 1.8 51 668-718 716-768 (773)
304 PRK13318 pantothenate kinase; 29.7 2.9E+02 0.0063 31.6 9.9 58 461-529 2-64 (258)
305 smart00483 POLXc DNA polymeras 29.6 44 0.00095 40.0 3.3 33 665-702 87-119 (334)
306 PF11149 DUF2924: Protein of u 29.1 44 0.00095 34.6 2.7 24 1124-1147 97-120 (136)
307 PRK13482 DNA integrity scannin 28.9 29 0.00062 41.4 1.5 51 662-712 282-334 (352)
308 TIGR00638 Mop molybdenum-pteri 28.8 1.6E+02 0.0036 25.9 6.2 49 849-905 8-62 (69)
309 PRK14601 ruvA Holliday junctio 28.7 32 0.00069 37.5 1.7 21 667-687 108-128 (183)
310 PRK13901 ruvA Holliday junctio 28.6 32 0.00069 37.9 1.7 21 667-687 107-127 (196)
311 cd00080 HhH2_motif Helix-hairp 28.6 36 0.00077 31.5 1.8 19 668-686 23-41 (75)
312 PRK00254 ski2-like helicase; P 28.2 27 0.00058 46.2 1.3 51 668-718 646-699 (720)
313 PRK14603 ruvA Holliday junctio 27.9 33 0.00072 37.9 1.7 21 667-687 107-127 (197)
314 COG0112 GlyA Glycine/serine hy 27.7 1.5E+02 0.0032 36.0 7.0 75 460-543 114-188 (413)
315 TIGR01448 recD_rel helicase, p 27.7 36 0.00078 45.0 2.3 49 668-716 118-166 (720)
316 PLN02295 glycerol kinase 27.3 1.8E+02 0.004 36.8 8.4 25 461-487 2-26 (512)
317 PF14716 HHH_8: Helix-hairpin- 27.1 25 0.00055 31.7 0.6 19 669-687 49-67 (68)
318 cd04458 CSP_CDS Cold-Shock Pro 26.8 2.6E+02 0.0056 24.7 7.0 50 851-906 2-55 (65)
319 COG0554 GlpK Glycerol kinase [ 26.8 1.3E+02 0.0027 37.5 6.4 59 460-520 6-68 (499)
320 PRK14351 ligA NAD-dependent DN 26.8 33 0.00072 44.9 1.7 46 667-713 496-544 (689)
321 TIGR01311 glycerol_kin glycero 26.6 1.9E+02 0.0042 36.3 8.5 28 460-489 2-29 (493)
322 PRK07956 ligA NAD-dependent DN 26.5 33 0.00071 44.8 1.6 55 654-714 471-528 (665)
323 PF05642 Sporozoite_P67: Sporo 26.4 2.7E+02 0.0058 35.2 8.9 10 1142-1151 56-65 (727)
324 TIGR00064 ftsY signal recognit 26.3 8.3E+02 0.018 28.3 12.9 22 509-530 115-136 (272)
325 PRK10939 autoinducer-2 (AI-2) 26.3 1.8E+02 0.0039 36.9 8.2 27 460-488 4-30 (520)
326 TIGR02381 cspD cold shock doma 26.0 2.3E+02 0.005 25.6 6.5 50 851-906 3-56 (68)
327 cd00141 NT_POLXc Nucleotidyltr 25.7 46 0.001 39.3 2.5 32 667-703 85-116 (307)
328 PRK14606 ruvA Holliday junctio 25.4 39 0.00085 37.0 1.7 22 667-688 108-129 (188)
329 PRK05898 dnaE DNA polymerase I 25.4 1.2E+02 0.0027 41.1 6.5 64 650-714 728-801 (971)
330 PRK14602 ruvA Holliday junctio 25.4 38 0.00083 37.5 1.7 22 667-688 109-130 (203)
331 PF05268 GP38: Phage tail fibr 25.3 2.9E+02 0.0064 30.8 8.1 98 1232-1329 115-237 (260)
332 PRK14604 ruvA Holliday junctio 25.2 40 0.00086 37.2 1.7 22 667-688 108-129 (195)
333 PF01548 DEDD_Tnp_IS110: Trans 25.0 1.5E+02 0.0033 30.3 6.0 106 461-605 1-108 (144)
334 KOG2534 DNA polymerase IV (fam 24.7 79 0.0017 37.0 3.9 42 667-709 56-109 (353)
335 PRK09698 D-allose kinase; Prov 24.4 2.5E+02 0.0055 32.6 8.4 64 460-530 5-68 (302)
336 KOG2391 Vacuolar sorting prote 23.9 6.8E+02 0.015 29.9 11.2 65 1092-1158 66-140 (365)
337 PF03459 TOBE: TOBE domain; I 23.8 1.7E+02 0.0037 25.5 5.3 47 849-903 6-58 (64)
338 COG1070 XylB Sugar (pentulose 23.7 2.2E+02 0.0047 36.1 8.1 59 460-520 5-68 (502)
339 PRK14667 uvrC excinuclease ABC 23.7 1.3E+03 0.028 29.9 14.8 27 655-687 539-565 (567)
340 PLN02271 serine hydroxymethylt 23.3 2.1E+02 0.0045 36.8 7.5 65 460-533 240-310 (586)
341 TIGR01234 L-ribulokinase L-rib 22.9 2.2E+02 0.0049 36.2 8.1 27 460-488 2-29 (536)
342 PF03276 Gag_spuma: Spumavirus 22.8 1.7E+03 0.036 28.5 14.7 23 465-487 39-63 (582)
343 KOG3279 Uncharacterized conser 22.8 1.5E+02 0.0033 32.5 5.4 109 306-444 126-248 (283)
344 PRK10880 adenine DNA glycosyla 22.2 70 0.0015 38.5 3.2 50 667-716 72-128 (350)
345 KOG4637 Adaptor for phosphoino 21.8 2.4E+02 0.0051 33.8 7.0 75 1072-1151 26-101 (464)
346 PF04959 ARS2: Arsenite-resist 21.7 40 0.00086 37.7 0.9 13 1145-1157 111-123 (214)
347 PF01869 BcrAD_BadFG: BadF/Bad 21.5 2.1E+02 0.0045 32.9 6.8 28 462-491 1-28 (271)
348 TIGR03286 methan_mark_15 putat 21.5 3.9E+02 0.0084 32.9 9.1 49 460-521 145-193 (404)
349 smart00652 eIF1a eukaryotic tr 21.1 3.3E+02 0.0072 25.8 6.8 65 849-919 6-71 (83)
350 cd04456 S1_IF1A_like S1_IF1A_l 21.1 3.8E+02 0.0083 25.2 7.0 64 850-919 2-67 (78)
351 PRK14605 ruvA Holliday junctio 20.9 55 0.0012 36.1 1.7 21 667-687 108-128 (194)
352 KOG3013 Exosomal 3'-5' exoribo 20.6 97 0.0021 35.2 3.5 73 845-918 84-165 (301)
353 KOG4211 Splicing factor hnRNP- 20.6 2.7E+02 0.0059 34.6 7.5 76 1189-1264 353-429 (510)
354 PRK10116 universal stress prot 20.4 2.6E+02 0.0057 28.1 6.6 50 511-572 92-141 (142)
355 PRK01002 nickel responsive reg 20.3 1.8E+02 0.0039 30.4 5.3 42 354-407 2-43 (141)
356 cd05701 S1_Rrp5_repeat_hs10 S1 20.1 1.3E+02 0.0027 27.2 3.4 56 849-906 3-60 (69)
No 1
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=100.00 E-value=1.8e-228 Score=2041.91 Aligned_cols=1090 Identities=37% Similarity=0.594 Sum_probs=996.5
Q ss_pred ccccCCCCCCCchhHHHHHHHHHHHHhcCcCcccccCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCccceeeecchhhh
Q 039337 9 LRKALAGPPTDGESIVDESTWIYNQLLSGTLPLFGQRGAGSPKEGHDLSISRDDIMRFLDLLHLQKLDIPFIAMYRKEEC 88 (1344)
Q Consensus 9 ~~~~~~~~~~~~~el~~ea~WI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~vL~l~~~~~~eVPFIarYRKE~~ 88 (1344)
.+.++ .+++++||++||.|||..+..+- .+.+. ....+.+.++|++||+||+.+++||||||+|||||+
T Consensus 179 ~~~~v--~~~~~de~e~Ea~WI~~~~~~~q------~~~d~---~~~~~s~~e~I~~vl~f~r~q~levpFI~~yRkEyi 247 (1299)
T KOG1856|consen 179 RRAPV--TDVSEDELEEEANWIYEKTLSNQ------EDFDK---MRLGPSFKEAIKKVLEFIRRQHLEVPFIAFYRKEYI 247 (1299)
T ss_pred hhccC--CCCCchHHHHHHHHHHHHHhhhh------hhhhh---hccCchHHHHHHHHHHHHHhhcccccHHHHHHHHHh
Confidence 34444 56678999999999999888752 22221 123467999999999999999999999999999999
Q ss_pred cccccccccccccCCCCCCccCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhhhhhhhhhH
Q 039337 89 LSLLKDLEQNEVNNDNNDDFERTPTLKWHKVLWAIHDLDKKWLLLQKRKSALQSYYKKRYEEESRRIYDETRLALNQQLF 168 (1344)
Q Consensus 89 ~~l~~~~~~~e~~~~~~~~~~~~~~l~~~~dLw~I~~ld~k~~~L~~RK~~l~~~~~k~~~~~~~~~~~~~~l~~~~~l~ 168 (1344)
.+++.+.+ +-......+.|+|.|..|.+++..++..+..++..+.. +...+.+.
T Consensus 248 ~~~l~~~d------------ld~~~~~~~~dk~~i~~L~~km~~~q~~~~~~~~~~~~--------------~~~~d~~~ 301 (1299)
T KOG1856|consen 248 RSLLEESD------------LDEKWCLLSIDKWDITSLFEKMWSLQEEKRYVLELYPH--------------LDAEDAIV 301 (1299)
T ss_pred hhhhcccc------------ccccchhhhhhhhhHHHHHHHHHHHHHHHHHHhhhCCc--------------ccchhccc
Confidence 99986521 11122222359999999999999999999888776642 11122222
Q ss_pred HHHHHHHHhhhhhhhHhhhhcccccCCCCCCCCCCc---------------cCccCCCCcchHHHHHHcChHHHHHHhcc
Q 039337 169 DSISKSLEAAETEREVDDVDLKFNLHFPPGEVGVDE---------------GQYKRPKRSTKYSSCSKAGLWEVASKFGY 233 (1344)
Q Consensus 169 ~~~~~~l~~a~t~eel~Di~~~~~l~y~~~~~~~~~---------------~~~kr~~r~t~y~~a~~~GL~~la~~fgl 233 (1344)
.+..+ ...+|++|.|||.+|.|.|+.++.+|.. .++|++.|+|.|++|+++||+.||+.||+
T Consensus 302 t~~~e---~~~sl~~l~Dl~~~~~~~y~~~i~~m~~~k~~r~~~~e~~~~~~e~kq~~r~s~y~~~~~sgi~~~a~~fGl 378 (1299)
T KOG1856|consen 302 TKYFE---RLSSLDELKDLNKYFELAYSNEIPRMESEKFNRHFGGECETDEAELKQGSRYSIYEKFRKSGIYELAKEFGL 378 (1299)
T ss_pred ccccc---hhhhhHHHHHHHHHHHHHHHhhhHHHHHHHhhhhcccccccchhhhcccccccHHHHHHhccHHHHHHHcCC
Confidence 22222 3348999999999999999988776522 24689999999999999999999999999
Q ss_pred ChHHHhhhhhhcccCCCCCCCCCCHHHHHHhhhhhcCCCHHHHHHHHHHHHHHHhcCChhHHHHHHHHhhceEEEEEEeC
Q 039337 234 SSEQLGLQLSLEKMGDELEDPKETPEEMASNFKCAMFNSSQAVLQGARHMAAVEISCEPCVRKYVRSIFMDNAVVSTCPT 313 (1344)
Q Consensus 234 s~~~f~~nl~~~~~~~~~~~~~~~p~~~A~~~i~~~~~t~e~vl~ga~~ilA~eis~dp~vR~~vR~~~~~~a~Ist~~T 313 (1344)
||+||++||++.+++|++++++..|+++|.+|+|+.|.|++.||+||++|+|.+||++|.||+.+|..|+++|+++++||
T Consensus 379 saeq~~enl~~~~~~~~ve~~~~~P~E~a~~yv~~~f~~~~~vl~~ak~~lA~eis~ep~iRk~vR~~f~~~a~~~i~pT 458 (1299)
T KOG1856|consen 379 SAEQFGENLRDFKQRHEVEQRSRYPEELALQYVCAVFSSSEAVLSGAKKMLAKEISREPQLRKSVRQCFNERAKVNIHPT 458 (1299)
T ss_pred CHHHHHHHHHhhhccchhhccccCHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhheeeeecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcccccccccccccccccccCcCCCchHHHHHHhhhccccEEEEEecChhhhhhHHHHHHhhhccCCCcchhhhHHH
Q 039337 314 PDGDSAIDSFHQFAGVKWLREKPLRKFEDAQWLLIQKAEEEKLLQVTIKLPEDSLNKLFSDCKEHYLSDGVSKSAQLWND 393 (1344)
Q Consensus 314 ~kg~~~id~~h~y~~~Kyl~~kpv~~l~~~q~L~i~raE~egll~v~i~~~~~~~~~~~~~l~~~~~~d~~s~~~~~wn~ 393 (1344)
++|.+.||..||||.||||++|||++|...|||.+..||+|||+.|+|.++.+..++++++|.++|++|++|+.+++||.
T Consensus 459 kkG~~~Id~~h~~y~~Kyl~~kPv~~f~~d~~l~l~~aeeEkl~lv~~~~~~e~~~~y~e~l~~~y~sd~~Se~a~eWN~ 538 (1299)
T KOG1856|consen 459 KKGRKLIDSAHPYYDIKYLKNKPVRSFRLDQFLFLHMAEEEKLLLVTFKLEMEGPNDYIEELKEFYLSDNFSENAQEWNR 538 (1299)
T ss_pred CCcceeccccChHHHHHHHHhCChhhhcccHHHHHHHhhhhhccceeeehhhcchhhHHHHHHHHHHhhhhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999988888999999999999999999999999
Q ss_pred HHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCCCCCCCCCCc-eEeEeecCCCC-C
Q 039337 394 QRELILKDALDNFLLPSMVKEARSLMSGRAKSWLLMEYGKALWNKVSVGPYQRKDNDITPDEEAAP-RVLACCWGPGK-P 471 (1344)
Q Consensus 394 ~r~~~l~~a~~~~L~P~~~revr~~L~~~Ae~~~i~~~~~nL~~~L~~~P~~~~~~~~~~~~~~~~-rVlai~~dpg~-~ 471 (1344)
+|++||++|+.++++|.|.+|+|+.|+.+|++.+++.|+..|+++|++|||.|. +.+.++...| |||+|||+++. .
T Consensus 539 ~R~~~v~~A~~k~~~~~m~~elr~~L~~rak~~v~k~c~~kl~~~ls~apy~p~--~~~~~d~~~p~rvl~~~~~~~~~~ 616 (1299)
T KOG1856|consen 539 QRKEIVNSAVQKFFKPDMVKELRSTLTSRAKKRVAKVCRVKLYSKLSQAPYRPD--DDTFEDEKIPKRVLAVCGGTERSD 616 (1299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCcCCC--CCCcccccccceEEEeccCCCCCc
Confidence 999999999999999999999999999999999999999999999999999996 2233344444 89999999988 5
Q ss_pred ceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCCcchhhhHHHHHHHHHHHHhh
Q 039337 472 ETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVNLSCTSLKDDIYEIIFKMVEE 551 (1344)
Q Consensus 472 g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~~~~~v~~~~~~ 551 (1344)
.+++|+||..|+++|++++..+..+.+.+..+.++++.+..|.+||++++||||+|++.+.-.+.++..|.++|.++.-
T Consensus 617 a~f~v~vn~~Gd~vD~lrl~~~~kr~~~~n~~~r~~k~~d~f~kFI~~~kP~vi~v~g~~r~~q~~~~~I~~~v~el~~- 695 (1299)
T KOG1856|consen 617 AIFCVLVNFEGDLVDYLRLVDITKRKTLVNDEERKKKFQDLFKKFIEKKKPHVIGVSGENRLKQKIYEAIRQLVHELLI- 695 (1299)
T ss_pred eEEEEEEcCCCceeeeeeccchhhhhhccchhhhhhhHHHHHHHHHHhcCCCEEEeeCCCchhHHHHHHHHHHHHhccc-
Confidence 6788899999999999999999988776667778888899999999999999999999987777777776666655421
Q ss_pred CCCCcCCCCCcceEEEecCCCchHHhhhHHhhhcCCCCchhhHHHHHhhhhhcccceehhcccCCCcccccccccCcccc
Q 039337 552 HPRDVGHEMDELSIVYGDESLPRLYENSRISSDQLPGQKGNVKRAVALGRYLQNPLAMVATLCGPGREILSWKLCPLENF 631 (1344)
Q Consensus 552 ~~~~~~~~~~~i~v~~v~~~~a~vy~~s~~a~~e~p~~~~~~R~avslaR~lqdPl~e~~~l~~~~~~~~~i~~~~~Q~~ 631 (1344)
.++..+|+|++|++++|+||++|++|..|||++|+++++|||||||+||||.||+.||++++|++|+++||+|+.
T Consensus 696 -----~~~~~~ipv~~vd~ela~lY~nS~~a~~efpd~pp~~k~avsLAR~iq~PL~EYa~l~~~dedi~sls~hp~Q~~ 770 (1299)
T KOG1856|consen 696 -----SDQGHPIPVIYVDNELARLYQNSRRAEAEFPDYPPTLKQAVSLARYIQDPLIEYAQLCSPDEDILSLSLHPLQEL 770 (1299)
T ss_pred -----cccCCCcceeecccHHHHHHHhhhhhHhhcccCChHHHHHHHHHHHhcCcHHHHHHhcCcccceeeeeechhhhc
Confidence 123568999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChhhhhhhhhhhhhcccccccccccccccccccccchhhccCCCHHHHHHHHHHHHh-cCCCCCHHHHhhccCCCHHHH
Q 039337 632 LTPDEKYGMIEQVMVDVTNQVGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVR-AGAIFTRKDFVTAHGLGKKVF 710 (1344)
Q Consensus 632 ~~~~~l~~~l~~~~~~~vn~vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~-~g~~~sr~~L~~v~~iG~kvf 710 (1344)
||+++|.++|+.+|+++||.||||||.|+.|||++++||||||||||||..+++.+.+ ++++.+|+||++.|.||||||
T Consensus 771 l~~eql~e~Le~~~Vd~vn~VGVDIN~a~~n~~~~~lLqyI~GlGpRKa~~lLKsl~~~~~~i~~R~qLit~c~lg~kVF 850 (1299)
T KOG1856|consen 771 LPREQLLEALETAFVDIVNEVGVDINKAANNPYYANLLQYICGLGPRKATSLLKSLKRNNRRIENRSQLITHCILGPKVF 850 (1299)
T ss_pred CCHHHHHHHHHHHHHHhHhhhhhhHHHHhcChhhhhhHHHhcCCCcccHHHHHHHHHHcCchhhhHHHHHHhcccCceeE
Confidence 9999999999999999999999999999999999999999999999999999999988 559999999999999999999
Q ss_pred HhccCcEEEecCCCCCCccccCCcCcCCCCCCCCHHHHHHHHHHHcCCCcCCCCCChhHHHHHHHHHHhcChhhhhccCh
Q 039337 711 VNAVGFLRVRRSGQAASSSQFIDLLDDTRIHPESYGLAQELAKEVYNRDIEGDLNDDEDALEMAIEHVRDRPDLLKTYLL 790 (1344)
Q Consensus 711 ~n~a~FlrI~~~~~~~~~~~~~d~LD~TrIHPEsY~~A~kma~dal~~d~~~d~~~~~~~~~~~v~~i~~~~~kl~~ldl 790 (1344)
.||||||+|+++.++++++.++|+||+||||||+|+||||||.||+++|+. ++++.+++++++|+++|++|++|+|
T Consensus 851 mNcagFikI~~~~l~~std~~~evLD~TRVHPEtYelArKmA~Dale~D~~----~E~~~~~~ale~i~E~p~rLkdL~L 926 (1299)
T KOG1856|consen 851 MNCAGFIKIDTSELSDSTDSYIEVLDGTRVHPETYELARKMAVDALEYDED----EEDGTPEGALEEILEEPARLKDLDL 926 (1299)
T ss_pred eecceeEEEchhhccccchhhhhhccCCcCCccchHHHHHHHHHHHhcCcc----ccccChHHHHHHHHhChHHHHHhhh
Confidence 999999999999999999999999999999999999999999999999852 2456788999999999999999999
Q ss_pred HHH---HHHhhccCccchHHHHHHHHhcCccCccCCCCCCCchhhhhhhccCCcccccCCeEEEEEEEEEeccc---EEE
Q 039337 791 DRH---IKEKKRENKRETLYLIRRELIHGFQDWRNQYKEPSQDEEFYMISGETEDTLAEGRVVQATVRRVQGQR---AIC 864 (1344)
Q Consensus 791 ~~~---~e~~~~~~~~~tL~~I~~EL~~p~~D~R~~~~~p~~~e~f~~lTget~~~l~~G~iV~g~V~~V~~~g---~fV 864 (1344)
++| ++++++++|..||++|+.||.++|.|+|.+|+.|+.+++|.||||||+++|.+|.+|+|+|++|+... +-|
T Consensus 927 daya~eLerq~~~~K~~tl~dI~~ELsdgykd~R~~f~~l~~eeiF~mLTget~et~~~g~iV~~~V~~vt~rr~~Cv~v 1006 (1299)
T KOG1856|consen 927 DAYADELERQGFGRKKNTLYDIRLELSDGYKDLRNPFHELTGEEIFDMLTGETPETFYEGAIVPVTVTKVTHRRGICVRV 1006 (1299)
T ss_pred HHHHHHHhhcccccccchHHHHHHHhhcchhhhccccCCCCHHHHHHHHhCCChhHhccCceEEEeeeEEEecccceeEE
Confidence 999 56788899999999999999999999999999999999999999999999999999999999999988 455
Q ss_pred EeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccccccccccCCCCCCCCcccccccch
Q 039337 865 VLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESEMRNNRYQHCQNLDPYYHEERSSRQ 944 (1344)
Q Consensus 865 ~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~dl~~~~~~~~~~~D~y~~~~~~~~~ 944 (1344)
+++||+.|+|+.+++|+. .+.+|...+++||+|.|||++||+++|.+.|||+.+|+++....+....|.|||..+.+-+
T Consensus 1007 ~ld~G~~g~i~~~~~Sd~-~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~sdlk~~n~~~~~~~d~y~d~~~e~~d 1085 (1299)
T KOG1856|consen 1007 RLDCGVTGFILAKNLSDR-DVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTSDLKDQNNEDLSLRDTYWDEVQESAD 1085 (1299)
T ss_pred EecCCCceeeeccccChh-hccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhHHhhhccccccccCchHHHHHHhhhh
Confidence 999999999999999997 7889999999999999999999999999999999999998666777788999998877667
Q ss_pred HHHHHHHHHHHHhhhccccccccCCCcccCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCC
Q 039337 945 SEQEKARKEKELAKKHFKERLIVHPCFQNVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGK 1024 (1344)
Q Consensus 945 ~e~~~~~k~~~~~~~~~~~RvI~HP~F~n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K 1024 (1344)
.++++..+ ++++++.+++|||.||+|+|+|++||++||+++++||+||||||||.|||+|||||+|||||||+|+|+.|
T Consensus 1086 ~E~~k~~~-~~~~r~~r~~RvI~HP~F~n~n~eQAe~yL~~~d~ge~iiRpSSrgddhLvvtwKVsD~iYqhidV~E~eK 1164 (1299)
T KOG1856|consen 1086 AEQEKDEK-KAEQRKQRVSRVIAHPLFKNLNAEQAEAYLSDMDQGELIIRPSSRGDDHLVVTWKVSDGIYQHIDVQELEK 1164 (1299)
T ss_pred HHhhhhhh-HHHHHHhhhhhhhcCccccCCCHHHHHHHHHhcccccEEeccccCCCCceEEEEEecCchhhhhhhhhhhc
Confidence 66665554 56778899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcCcccccccCceeeeCCccccchHHHHHHHHhhhHHHHHHHhhCcccccCCHHHHHHHHHHHHHhCCCcceEEEEeCC
Q 039337 1025 DHKDIKSLVGIGKTLKIGEDTFEDLDEVVDRYIDPLVSHLKAMLSYRKFRKGSKAEVDELLRIEKAEFPTRIVYGFGISH 1104 (1344)
Q Consensus 1025 ~~~~~~~~~sLG~~L~i~~~~y~DLDEii~~~V~pm~~~v~~i~~h~kf~~g~~~e~e~~L~~~~~~np~~i~Y~f~~~~ 1104 (1344)
+| .||||++|+|++++|+||||||+|||+||++++++|++|+||+.||++++|+||+.||+.||++|||+||+||
T Consensus 1165 En-----~fslg~~l~i~~e~feDLDEiI~r~vqpm~~~~~em~nhkyf~~Gt~~~~ek~L~~~k~~np~~~~Y~F~~s~ 1239 (1299)
T KOG1856|consen 1165 EN-----YFSLGKTLWIGGEEFEDLDEIIARYVQPMATNLREMTNHKYFFTGTKKEVEKLLRDYKKVNPKKSVYFFCASH 1239 (1299)
T ss_pred cc-----cccccceEEECCcccccHHHHHHHHHHHHHHHHHHHHhhhHhhcCCHHHHHHHHHHHhccCCCeeeEEEEecc
Confidence 99 5999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcEEEEEEecCCCCceeeEEEecCceEEcccccccHHHHHHHHHhhcCCCC
Q 039337 1105 EHPGTFILTYIRSTNPHHEYIGLYPKGFKFRKRMFEDIDRLVAYFQRHIDDPQ 1157 (1344)
Q Consensus 1105 ~~PG~f~L~~~~~~~~~~e~i~v~p~gf~~~~~~~~~~~~L~~~fK~~~~d~~ 1157 (1344)
+|||+|+|+|+|+++++||||+|+|+||+|++++|+||++||+|||.|++++.
T Consensus 1240 ~~PG~F~L~y~~~~k~~heyv~v~p~g~~~rg~~f~tld~L~~~FK~h~~~~~ 1292 (1299)
T KOG1856|consen 1240 EHPGKFCLSYKPSSKPRHEYVKVVPEGFRFRGQNFGTLDELCRWFKRHYKDPT 1292 (1299)
T ss_pred cCCceEEEEeccCCCccceeEEEcccceEEecccchhHHHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999999999999999976
No 2
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=100.00 E-value=2.7e-142 Score=1282.18 Aligned_cols=750 Identities=22% Similarity=0.306 Sum_probs=666.0
Q ss_pred CCHHHHHHHHHHhhhCCCccceeeecchhhhcccccccccccccCCCCCCccCcccchhhHHHHHHHHHHHHHHHHHHHH
Q 039337 58 ISRDDIMRFLDLLHLQKLDIPFIAMYRKEECLSLLKDLEQNEVNNDNNDDFERTPTLKWHKVLWAIHDLDKKWLLLQKRK 137 (1344)
Q Consensus 58 ~~~~~I~~vL~l~~~~~~eVPFIarYRKE~~~~l~~~~~~~e~~~~~~~~~~~~~~l~~~~dLw~I~~ld~k~~~L~~RK 137 (1344)
....+|.+|++|+++ |+|||||||||||.|++|++. +||.|.++++++++|++||
T Consensus 20 ~~~~qv~av~~ll~e-g~tVPFIarYRke~tg~Lde~------------------------qlr~i~~~~~yl~~L~~Rk 74 (780)
T COG2183 20 FKPAQVEAVIELLDE-GNTVPFIARYRKEITGGLDEV------------------------QLRDLEERLEYLRELEERK 74 (780)
T ss_pred CcHHHHHHHHHHHhc-CCceeehhhhccccCCCCCHH------------------------HHHHHHHHHHHHHHHHHHH
Confidence 577899999999987 899999999999999999732 8999999999999999999
Q ss_pred HHHHHHHHHHhHHHHhhhhhhhhhhhhhhhHHHHHHHHHhhhhhhhHhhhhcccccCCCCCCCCCCccCccCCCCcchHH
Q 039337 138 SALQSYYKKRYEEESRRIYDETRLALNQQLFDSISKSLEAAETEREVDDVDLKFNLHFPPGEVGVDEGQYKRPKRSTKYS 217 (1344)
Q Consensus 138 ~~l~~~~~k~~~~~~~~~~~~~~l~~~~~l~~~~~~~l~~a~t~eel~Di~~~~~l~y~~~~~~~~~~~~kr~~r~t~y~ 217 (1344)
+.|+++|++ ++.||+++.+.+..|+++.+|+|||.|| |+||||+|+
T Consensus 75 e~Ilk~Iee-----------------qGklTd~L~~~I~~a~~l~eleDLYlpy-----------------K~KrRtra~ 120 (780)
T COG2183 75 ESILKSIEE-----------------QGKLTDELKEQIEAAEELTELEDLYLPY-----------------KEKRRTRAT 120 (780)
T ss_pred HHHHHHHHH-----------------hccchHHHHHHHHHhhhhhhHHHhcccc-----------------hHHHHHHHH
Confidence 999999984 5778889999999999999999999987 899999999
Q ss_pred HHHHcChHHHHHHhccChHHHhhhhhhcccCCCCCCCCCCHH-HHHHhhhh--hcCCCHHHHHHHHHHHHHHHhcCChhH
Q 039337 218 SCSKAGLWEVASKFGYSSEQLGLQLSLEKMGDELEDPKETPE-EMASNFKC--AMFNSSQAVLQGARHMAAVEISCEPCV 294 (1344)
Q Consensus 218 ~a~~~GL~~la~~fgls~~~f~~nl~~~~~~~~~~~~~~~p~-~~A~~~i~--~~~~t~e~vl~ga~~ilA~eis~dp~v 294 (1344)
+|+++||+|||..+. .++..+|+ +.|++|++ .+++|+++||+||++|+|++||+||.+
T Consensus 121 ia~e~GlepLa~~~~-------------------~~~~~~~~~~~A~~fi~~~~~v~s~~~Al~gA~dilae~is~da~l 181 (780)
T COG2183 121 IAREKGLEPLADLIL-------------------SKPSLDPLLESAADFISIEEGVSSSKLALDGARDILAERISEDAEL 181 (780)
T ss_pred HhHhhccHHHHHHHH-------------------hccccCcHHHHHHHHhhcccCcCCHHHHHHHHHHHHHHHHhhCHHH
Confidence 999999999999987 44455565 88999999 789999999999999999999999999
Q ss_pred HHHHHHHhhceEEEEEEeCCCCCc--ccccccccccccccccccCcCCCchHHHHHHhhhccccEEEEEecChhhh--hh
Q 039337 295 RKYVRSIFMDNAVVSTCPTPDGDS--AIDSFHQFAGVKWLREKPLRKFEDAQWLLIQKAEEEKLLQVTIKLPEDSL--NK 370 (1344)
Q Consensus 295 R~~vR~~~~~~a~Ist~~T~kg~~--~id~~h~y~~~Kyl~~kpv~~l~~~q~L~i~raE~egll~v~i~~~~~~~--~~ 370 (1344)
|.++|+.|+++|+++++. .+|.. +.+.|..||++ .+|++++++|++|+|+|||+||+|.|+|++++... ..
T Consensus 182 r~~lr~~~~~~g~~~~~~-~~~~~~~e~~~f~~Y~d~----~e~i~~~~~hr~Lam~Rge~E~iL~v~l~~~~~~~~~~~ 256 (780)
T COG2183 182 REKLRDYLRKHGVLTSKV-VKGKEDDEGAKFEDYYDH----SEPIDNLPSHRALAMNRGEKEGILSLKLEFDDLEAKRRE 256 (780)
T ss_pred HHHHHHHHHhccEEEEec-cCCcccccccceehhhhh----hhHhhhhhHHHHHHHhhhcccCceEEEEeeccccccchH
Confidence 999999999999999998 44443 56667777666 59999999999999999999999999999865311 11
Q ss_pred HH-HHHHhhhccCCCcchhhhHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCC
Q 039337 371 LF-SDCKEHYLSDGVSKSAQLWNDQRELILKDALDNFLLPSMVKEARSLMSGRAKSWLLMEYGKALWNKVSVGPYQRKDN 449 (1344)
Q Consensus 371 ~~-~~l~~~~~~d~~s~~~~~wn~~r~~~l~~a~~~~L~P~~~revr~~L~~~Ae~~~i~~~~~nL~~~L~~~P~~~~~~ 449 (1344)
++ ..+...|...+ .. .|+.++++++.++|+++|.|++++|+|..|+++||+.+|.+|++||+++|+|||++++
T Consensus 257 ~~e~~~~~~~~~~~---~~-~~~~~~~~~i~~~~~k~i~~~~e~el~~~Ltekae~~ai~vF~~nL~~lLl~aP~~~~-- 330 (780)
T COG2183 257 FLEQIIAEVFGSND---IK-PADNWLKEAVEDTWKKKISPSIERELRDELTEKAEEEAINVFAENLKDLLLAAPAKPK-- 330 (780)
T ss_pred HHHHHHHHHhcccc---Cc-cHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCc--
Confidence 22 22233343332 23 6888999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCCCCceEeEeecCCCC-CceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEc
Q 039337 450 DITPDEEAAPRVLACCWGPGK-PETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLG 528 (1344)
Q Consensus 450 ~~~~~~~~~~rVlai~~dpg~-~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG 528 (1344)
.|||+ |||+ +|||+|++|.+|+++++ ..+|++ .++.........|.+++.+|++++|+||
T Consensus 331 ----------~~lgl--DPg~rtG~k~Avvd~tGk~l~~---~~Iyp~----~p~~~~~~~~~~l~~l~~~~~Ve~iaIG 391 (780)
T COG2183 331 ----------ATLGL--DPGFRTGCKVAVVDDTGKLLDT---ATIYPH----PPVNQSDKAEATLKDLIRKYKVELIAIG 391 (780)
T ss_pred ----------ceeec--CCccccccEEEEEcCCCceece---eEEEcC----CCccchHHHHHHHHHHHHHhCceEEEEe
Confidence 79998 9999 89999999999999986 445555 2334456778889999999999999999
Q ss_pred CCCcchhhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhhhHHhhhcCCCCchhhHHHHHhhhhhcccce
Q 039337 529 AVNLSCTSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYENSRISSDQLPGQKGNVKRAVALGRYLQNPLA 608 (1344)
Q Consensus 529 ~~t~s~~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~s~~a~~e~p~~~~~~R~avslaR~lqdPl~ 608 (1344)
|||+|+ +++.||.+++++.+ ...+.++||+++||++||+|++|.+|||++++++|+||||||||||||+
T Consensus 392 ngTaSr-----ete~fv~~vl~~~~------~~~~~~viVsEagAsvYsaSe~A~~EFPdL~v~~r~aVSIaRrlqdPLa 460 (780)
T COG2183 392 NGTASR-----ETEKFVADVLKELP------KEKVLKVIVSEAGASVYSASERAAEEFPDLDVSLRGAVSIARRLQDPLA 460 (780)
T ss_pred cCCcch-----hHHHHHHHHHHhcc------CCCCcEEEEcccccchhcccHHHHHHCCCCchhHHhHHHHHHhhcchHh
Confidence 999998 78899999998742 2468999999999999999999999999999999999999999999999
Q ss_pred ehhcccCCCcccccccccCccccCChhhhhhhhhhhhhcccccccccccccccccccccchhhccCCCHHHHHHHHHHHH
Q 039337 609 MVATLCGPGREILSWKLCPLENFLTPDEKYGMIEQVMVDVTNQVGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLV 688 (1344)
Q Consensus 609 e~~~l~~~~~~~~~i~~~~~Q~~~~~~~l~~~l~~~~~~~vn~vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~ 688 (1344)
|||+| ||+|||+|||||++++++|.++|+.++++|||+||||+|+|+. ++|++|+|||+++|++|++||+
T Consensus 461 ElvkI-----dpKSiGVgqyQHdv~q~~L~~~Ld~vved~VN~VGVdvNtAsa-----~lL~~VsGL~kt~A~nIv~~r~ 530 (780)
T COG2183 461 ELVKI-----DPKSIGVGQYQHDVSQKKLAESLDAVVEDCVNAVGVDVNTASA-----SLLSYVSGLNKTLAKNIVAYRD 530 (780)
T ss_pred HHhhc-----CccccccccccccCCHHHHHHHHHHHHHHHhcccccccccCCH-----HHHHHHhhhchhHHHHHHHHHh
Confidence 99999 9999999999999999999999999999999999999999997 8999999999999999999999
Q ss_pred hcCCCCCHHHHhhccCCCHHHHHhccCcEEEecCCCCCCccccCCcCcCCCCCCCCHHHHHHHHHHHcCCCcCCCCCChh
Q 039337 689 RAGAIFTRKDFVTAHGLGKKVFVNAVGFLRVRRSGQAASSSQFIDLLDDTRIHPESYGLAQELAKEVYNRDIEGDLNDDE 768 (1344)
Q Consensus 689 ~~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI~~~~~~~~~~~~~d~LD~TrIHPEsY~~A~kma~dal~~d~~~d~~~~~ 768 (1344)
++|.|.||+||++|+.||+|+|+||||||||+.++ ||||+|+||||+|.+|++|+.++...++
T Consensus 531 ~~g~f~~Rk~L~kv~rlg~k~Feq~aGFLrI~~g~---------~pLD~t~VHPE~Y~v~~~i~~~~~~~~~-------- 593 (780)
T COG2183 531 ENGAFDNRKQLKKVPRLGPKAFEQCAGFLRIPNGD---------NPLDATAVHPEAYKVVKKILADLGEADP-------- 593 (780)
T ss_pred hcCCcccHHHHhcCCCcChhhhhhcceeeEecCCC---------CCccccccCccchHHHHHHHHHhccccH--------
Confidence 99999999999999999999999999999999998 9999999999999999999999986331
Q ss_pred HHHHHHHHHHhcC--hhhhhccChHHHHHHhhccCccchHHHHHHHHhcCccCccCCCCCCCchhhhhhhccCCcccccC
Q 039337 769 DALEMAIEHVRDR--PDLLKTYLLDRHIKEKKRENKRETLYLIRRELIHGFQDWRNQYKEPSQDEEFYMISGETEDTLAE 846 (1344)
Q Consensus 769 ~~~~~~v~~i~~~--~~kl~~ldl~~~~e~~~~~~~~~tL~~I~~EL~~p~~D~R~~~~~p~~~e~f~~lTget~~~l~~ 846 (1344)
+++.+ ..+|+.|++++|++. ...+.+||.||+.||++|++|+|..|++|.+++.|. ++++|++
T Consensus 594 --------~~i~~~e~~~l~~L~~~~~a~~--~~~gl~Tl~dIi~eL~kp~rdpR~~f~~~~~~~~v~-----~i~dLk~ 658 (780)
T COG2183 594 --------DLIGNRERAKLKSLNLEEFADE--LDFGLPTLEDIILELEKPGRDPRDEFHTPTLDEGVE-----SITDLKP 658 (780)
T ss_pred --------HHhhhhhHHHHHhcCHHHHHHH--HhcCCchHHHHHHHhhcCCCCCcccccccchhhhhh-----hHhhccC
Confidence 12222 568999999999886 456899999999999999999999999999999996 5559999
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccccccccc
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESEMRNNRY 926 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~dl~~~~~ 926 (1344)
||+++|+|+||++||+||+|+++.+|+||+|.+|++ ++.+|.+++++||+|+|+|++||..+++|.|||+..+.....+
T Consensus 659 Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~-fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~~~~~ 737 (780)
T COG2183 659 GMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDK-FVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEEEGKLN 737 (780)
T ss_pred CCEEEEEEEEeeeccceEEeccccceeeeHHHhhhh-hcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCCcccCC
Confidence 999999999999999999999999999999999999 9999999999999999999999999999999999876554311
Q ss_pred cCCCCCCCCcccccccchHHHHHHHHHHHHhhhccccccccCCCcccCCHHHHHHHhhcCCCC
Q 039337 927 QHCQNLDPYYHEERSSRQSEQEKARKEKELAKKHFKERLIVHPCFQNVTADEAMKLLSAKEPG 989 (1344)
Q Consensus 927 ~~~~~~D~y~~~~~~~~~~e~~~~~k~~~~~~~~~~~RvI~HP~F~n~~~~qAe~~L~~~~~G 989 (1344)
+.+ +. .++ +. ..+.+..+++.||.|...|..+|++|++.+..|
T Consensus 738 ~~~---~~-----------~~~-----~~-~~~~r~~~~~~~~~~~~~n~a~~~af~~~~k~~ 780 (780)
T COG2183 738 SGR---GF-----------CRE-----RG-LCRPRRAPVIEHPVYPGRNGAMADAFARAMKSG 780 (780)
T ss_pred CCC---Cc-----------ccc-----cc-ccCcccCccccCCCCCCcchHHHHHHHHHhccC
Confidence 111 00 000 01 112267899999999999999999999987654
No 3
>PF14633 SH2_2: SH2 domain; PDB: 3GXX_A 3GXW_B 3PJP_B 2XP1_A.
Probab=100.00 E-value=1.1e-68 Score=576.76 Aligned_cols=216 Identities=45% Similarity=0.809 Sum_probs=171.7
Q ss_pred CCCCcccccccchHHHHHHHHHHHHhhhccccccccCCCcccCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeC
Q 039337 932 LDPYYHEERSSRQSEQEKARKEKELAKKHFKERLIVHPCFQNVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYD 1011 (1344)
Q Consensus 932 ~D~y~~~~~~~~~~e~~~~~k~~~~~~~~~~~RvI~HP~F~n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d 1011 (1344)
.|.|||.+++.-+.++++++ ++.++++.+++|+|+||+|||||+.||++||+++++|||||||||||.|||+|||||+|
T Consensus 3 ~d~~~d~~~e~~d~~~~~~~-~~~~~r~~~~~R~I~HP~F~n~~~~qAe~~L~~~~~Ge~iIRPSSkG~dhL~vTwKv~d 81 (220)
T PF14633_consen 3 RDPYYDFDQEEEDKEKEKAK-KKKQQRKKFVKRVIKHPLFKNFNYKQAEEYLADQDVGEVIIRPSSKGPDHLTVTWKVAD 81 (220)
T ss_dssp -------------------------------HHHHCSTTEESS-HHHHHHHHCCS-TT-EEEEE-TTTTTEEEEEEEEET
T ss_pred CCcccchhhhhhhHHHHHHH-HHHhhhcccccccccCCCccCCCHHHHHHHHhcCCCCCEEEeeCCCCCCeEEEEEEEcC
Confidence 57889887654443332222 22344557899999999999999999999999999999999999999999999999999
Q ss_pred ceeeEEEEeecCCCCcCcccccccCceeeeCCccccchHHHHHHHHhhhHHHHHHHhhCcccccCCHHHHHHHHHHHHHh
Q 039337 1012 GVYAHKDIIEGGKDHKDIKSLVGIGKTLKIGEDTFEDLDEVVDRYIDPLVSHLKAMLSYRKFRKGSKAEVDELLRIEKAE 1091 (1344)
Q Consensus 1012 ~v~~HidV~E~~K~~~~~~~~~sLG~~L~i~~~~y~DLDEii~~~V~pm~~~v~~i~~h~kf~~g~~~e~e~~L~~~~~~ 1091 (1344)
|+||||||+|.+|+| .++||++|+|++++|+||||||+|||+||+++|++|++|+||++|++++++++|++|+++
T Consensus 82 ~vyqHidV~E~~K~n-----~~slG~~L~i~~~~yeDLDEii~r~V~pm~~~v~~~~~h~kf~~g~~~e~e~~L~~~k~~ 156 (220)
T PF14633_consen 82 GVYQHIDVKEEDKEN-----EFSLGKTLKIGGEEYEDLDEIIARHVEPMARNVEEMMNHRKFKDGTKEEVEEWLKEEKKA 156 (220)
T ss_dssp TEEEEEEEEEECSSS-----TTS-SSEEEETTEEESSHHHHHHHCHHHHHHHHHHHHCSTTEESS-CCCCHHHHHCHHHH
T ss_pred CcEEEEEEEECCCcC-----ccccCcEEEECCeEECCHHHHHHHHHHHHHHHHHHHHhCccccCCCHHHHHHHHHHHHHh
Confidence 999999999999999 499999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcceEEEEeCCCCCcEEEEEEecCCCCc--eeeEEEecCceEEcccccccHHHHHHHHHhhc
Q 039337 1092 FPTRIVYGFGISHEHPGTFILTYIRSTNPH--HEYIGLYPKGFKFRKRMFEDIDRLVAYFQRHI 1153 (1344)
Q Consensus 1092 np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~--~e~i~v~p~gf~~~~~~~~~~~~L~~~fK~~~ 1153 (1344)
||++|||+||++++|||+|+|+|+|+++++ +|||+|+|+||+||+++|++|++||||||+||
T Consensus 157 nP~~i~Y~f~~~~~~PG~F~L~y~~~~~~~~~~~~v~V~p~Gf~~r~~~f~~~~~L~~~FK~~~ 220 (220)
T PF14633_consen 157 NPKRIPYAFCISKEHPGYFILSYKPNKNPRHEYWPVKVTPDGFRFRKQVFPSLDRLINWFKKHY 220 (220)
T ss_dssp STTS-EEEEEE-TTSTTEEEEEEESSTTS-EEEEEEEE-SSSEEETTEEESSHHHHHHHHHHH-
T ss_pred CCCCceEEEEECCCCCCEEEEEEEcCCCCceEEeeEEEecCcEEEecccCCCHHHHHHHHhhcC
Confidence 999999999999999999999999998876 45699999999999999999999999999997
No 4
>PF09371 Tex_N: Tex-like protein N-terminal domain; InterPro: IPR018974 This presumed domain is found at the N terminus of Q45388 from SWISSPROT. This protein defines a novel family of prokaryotic transcriptional accessory factors []. ; PDB: 2OCE_A 3BZK_A 3BZC_A.
Probab=100.00 E-value=2e-36 Score=322.39 Aligned_cols=184 Identities=29% Similarity=0.403 Sum_probs=147.8
Q ss_pred CCCCHHHHHHHHHHhhhCCCccceeeecchhhhcccccccccccccCCCCCCccCcccchhhHHHHHHHHHHHHHHHHHH
Q 039337 56 LSISRDDIMRFLDLLHLQKLDIPFIAMYRKEECLSLLKDLEQNEVNNDNNDDFERTPTLKWHKVLWAIHDLDKKWLLLQK 135 (1344)
Q Consensus 56 ~~~~~~~I~~vL~l~~~~~~eVPFIarYRKE~~~~l~~~~~~~e~~~~~~~~~~~~~~l~~~~dLw~I~~ld~k~~~L~~ 135 (1344)
+++...+|+++|.||++ |+|||||||||||.|++|+++ +||.|.+.+.++++|++
T Consensus 5 l~i~~~~v~~~i~Ll~e-G~TvPFIARYRKe~TG~Lde~------------------------~lR~i~~~~~~~~~L~~ 59 (193)
T PF09371_consen 5 LNIKPKQVENVIKLLDE-GNTVPFIARYRKEMTGGLDEV------------------------QLREIQDRYEYLRELEK 59 (193)
T ss_dssp ----HHHHHHHHHHHHT-T--HHHHHHH-HHHHTS--HH------------------------HHHHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHhC-CCCcchhhhhhhhhhCCCCHH------------------------HHHHHHHHHHHHHHHHH
Confidence 35788999999999986 899999999999999999853 89999999999999999
Q ss_pred HHHHHHHHHHHHhHHHHhhhhhhhhhhhhhhhHHHHHHHHHhhhhhhhHhhhhcccccCCCCCCCCCCccCccCCCCcch
Q 039337 136 RKSALQSYYKKRYEEESRRIYDETRLALNQQLFDSISKSLEAAETEREVDDVDLKFNLHFPPGEVGVDEGQYKRPKRSTK 215 (1344)
Q Consensus 136 RK~~l~~~~~k~~~~~~~~~~~~~~l~~~~~l~~~~~~~l~~a~t~eel~Di~~~~~l~y~~~~~~~~~~~~kr~~r~t~ 215 (1344)
||+.|++++++ ++.|++++...|..|.|+++|+|||.|| ||||+|+
T Consensus 60 Rk~~il~~i~e-----------------qgkLt~eL~~~I~~a~tl~elEdlY~Py-----------------K~kr~T~ 105 (193)
T PF09371_consen 60 RKESILKSIEE-----------------QGKLTPELKQAIENATTLQELEDLYLPY-----------------KPKRKTR 105 (193)
T ss_dssp HHHHHHHHHHH-----------------TT---HHHHHHHHH--SHHHHHHHHGGG-----------------S---S-H
T ss_pred HHHHHHHHHHH-----------------cccCCHHHHHHHHhcCCHHHHHHHHhhh-----------------ccCcCCH
Confidence 99999999875 5778899999999999999999999998 7899999
Q ss_pred HHHHHHcChHHHHHHhccChHHHhhhhhhcccCCCCCCCCCCHHHHHHhhhhhc--CCCHHHHHHHHHHHHHHHhcCChh
Q 039337 216 YSSCSKAGLWEVASKFGYSSEQLGLQLSLEKMGDELEDPKETPEEMASNFKCAM--FNSSQAVLQGARHMAAVEISCEPC 293 (1344)
Q Consensus 216 y~~a~~~GL~~la~~fgls~~~f~~nl~~~~~~~~~~~~~~~p~~~A~~~i~~~--~~t~e~vl~ga~~ilA~eis~dp~ 293 (1344)
|++||++||+|||+.++ ..+..+|+..|..|++++ ++|+++||+||+||+|++||+||.
T Consensus 106 A~~Are~GLeplA~~il-------------------~~~~~~~~~~a~~~v~~~~gv~s~e~al~Ga~dIiAE~is~d~~ 166 (193)
T PF09371_consen 106 ATIAREAGLEPLADKIL-------------------EQPESDPEVEAKKFVNEEKGVPSVEEALAGAQDIIAERISEDPE 166 (193)
T ss_dssp HHHHHHTTTHHHHHHHH-------------------H-TTS-HHHHHHTT-BGGGTB-SHHHHHHHHHHHHHHHHTT-HH
T ss_pred HHHHHHcCCHHHHHHHH-------------------cCCccchHHHHHHHhCcccCCCCHHHHHHhHHHHHHHHHHcCHH
Confidence 99999999999999998 223337889999999987 999999999999999999999999
Q ss_pred HHHHHHHHhhceEEEEEEeCCCCC
Q 039337 294 VRKYVRSIFMDNAVVSTCPTPDGD 317 (1344)
Q Consensus 294 vR~~vR~~~~~~a~Ist~~T~kg~ 317 (1344)
+|+++|+.++++|+|+|+.++...
T Consensus 167 ~r~~lr~~~~~~g~i~s~~~k~~~ 190 (193)
T PF09371_consen 167 LREKLRKLLWKNGVIESKVKKGKE 190 (193)
T ss_dssp HHHHHHHHHHHH-EEEEEE-TTHC
T ss_pred HHHHHHHHHHhccEEEEEeeCccc
Confidence 999999999999999999887543
No 5
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=100.00 E-value=2.7e-33 Score=288.37 Aligned_cols=147 Identities=38% Similarity=0.652 Sum_probs=105.5
Q ss_pred CCCceEeEeecCCCC--CceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCCcc
Q 039337 456 EAAPRVLACCWGPGK--PETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVNLS 533 (1344)
Q Consensus 456 ~~~~rVlai~~dpg~--~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t~s 533 (1344)
|++||||||||++|. .++++|+||++|+++|++++.. +..+++++++++++|.+||.+|+|||||||+.+++
T Consensus 2 g~~~rVla~~~g~g~~~~~~~~v~ld~~G~v~d~~~~~~------~~~~~~~~~~~~~~l~~~i~~~kP~vI~v~g~~~~ 75 (150)
T PF14639_consen 2 GTGPRVLALSWGSGDGDDAVFCVVLDENGEVLDHLKLVY------NERDRERKEEDMERLKKFIEKHKPDVIAVGGNSRE 75 (150)
T ss_dssp -----EEEEE-TT--TTS-EEEEEE-TTS-EEEEEEE-S-------TT-SS-SHHHHHHHHHHHHHH--SEEEE--SSTH
T ss_pred CCCCEEEEEEcCCCCCCCCEEEEEECCCCcEEEEEEEcC------CccchHHHHHHHHHHHHHHHHcCCeEEEEcCCChh
Confidence 678999999999998 6899999999999999988711 11245567889999999999999999999999999
Q ss_pred hhhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhhhHHhhhcCCCCchhhHHHHHhhhhhcccceehhcc
Q 039337 534 CTSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYENSRISSDQLPGQKGNVKRAVALGRYLQNPLAMVATL 613 (1344)
Q Consensus 534 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~s~~a~~e~p~~~~~~R~avslaR~lqdPl~e~~~l 613 (1344)
+++|+++++++|.++-. ++...+|+|+||++++||||++|++|.+|||++|+++|+||||||||||||+||++|
T Consensus 76 s~~l~~~v~~~v~~~~~------~~~~~~i~V~~v~~~~A~lY~~S~rA~~EFP~~p~~~R~AIslAR~lQdPL~E~a~L 149 (150)
T PF14639_consen 76 SRKLYDDVRDIVEELDE------DEQMPPIPVVIVDDEVARLYSNSKRAAEEFPDYPPLLRYAISLARYLQDPLAEYAAL 149 (150)
T ss_dssp HHHHHHHHHHHHHHTTB-------TTS-B--EEE---TTHHHHHTSHHHHHHSTT--HHHHHHHHHHHHHH-HHHHHHCS
T ss_pred HHHHHHHHHHHHHHhhh------cccCCCceEEEECcHHHHHHhcCHHHHHHCCCCCHHHHHHHHHHHHhhChHHHHHhc
Confidence 99999988888865431 234567999999999999999999999999999999999999999999999999999
Q ss_pred c
Q 039337 614 C 614 (1344)
Q Consensus 614 ~ 614 (1344)
|
T Consensus 150 c 150 (150)
T PF14639_consen 150 C 150 (150)
T ss_dssp -
T ss_pred C
Confidence 7
No 6
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=99.97 E-value=9.5e-32 Score=255.98 Aligned_cols=103 Identities=45% Similarity=0.715 Sum_probs=84.8
Q ss_pred cccccccccCccccCChhhhhhhhhhhhhcccccccccccccccccccccchhhccCCCHHHHHHHHHHHHh-cCCCCCH
Q 039337 618 REILSWKLCPLENFLTPDEKYGMIEQVMVDVTNQVGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVR-AGAIFTR 696 (1344)
Q Consensus 618 ~~~~~i~~~~~Q~~~~~~~l~~~l~~~~~~~vn~vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~-~g~~~sr 696 (1344)
+|++||++||+|+.+|+++|+++||++|+++||+||||||.|..|||++++||||||||||||.+|++.+++ +|.+.||
T Consensus 1 ~dilsl~lHplQ~~l~~d~L~~~le~~~vd~vN~vGVDIN~a~~~~~~~~~LqfV~GLGPRKA~~Ll~~l~~~g~~l~~R 80 (104)
T PF14635_consen 1 EDILSLKLHPLQDLLPKDKLLEALERAFVDVVNQVGVDINRAVSHPHLANLLQFVCGLGPRKAQALLKALKQNGGRLENR 80 (104)
T ss_dssp HHHHTS---TTGGGS-HHHHHHHHHHHHHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHHHHC-S----T
T ss_pred CceeeeecCcchhhCCHHHHHHHHHHHHHHHHHhhCccHHHHhcChHHHhhHhHhcCCChHHHHHHHHHHHHcCCccccH
Confidence 378999999999999999999999999999999999999999999999999999999999999999999987 5699999
Q ss_pred HHHhhccCCCHHHHHhccCcEEEe
Q 039337 697 KDFVTAHGLGKKVFVNAVGFLRVR 720 (1344)
Q Consensus 697 ~~L~~v~~iG~kvf~n~a~FlrI~ 720 (1344)
++|++.+.+|++||.||||||||+
T Consensus 81 ~~Lv~~~~~g~~Vf~NcagFlrI~ 104 (104)
T PF14635_consen 81 SQLVTKCLMGPKVFINCAGFLRID 104 (104)
T ss_dssp THHHHTTSS-HHHHHHHCCCEE--
T ss_pred HHHHhcCCCCCeEEEeccEeEeeC
Confidence 999999999999999999999995
No 7
>PF14878 DLD: Death-like domain of SPT6; PDB: 3PSI_A 3PSF_A.
Probab=99.96 E-value=4.2e-30 Score=248.31 Aligned_cols=110 Identities=45% Similarity=0.740 Sum_probs=76.7
Q ss_pred CCcCcCCCCCCCCHHHHHHHHHHHcCCCcCCCCCChhHHHHHHHHHHhc--ChhhhhccChHHH---HHHhhccCccchH
Q 039337 732 IDLLDDTRIHPESYGLAQELAKEVYNRDIEGDLNDDEDALEMAIEHVRD--RPDLLKTYLLDRH---IKEKKRENKRETL 806 (1344)
Q Consensus 732 ~d~LD~TrIHPEsY~~A~kma~dal~~d~~~d~~~~~~~~~~~v~~i~~--~~~kl~~ldl~~~---~e~~~~~~~~~tL 806 (1344)
+||||+||||||+|+||||||+||+++|++ +.+ ++..+..+|+++++ .|++|++|||++| ++++++++|+.||
T Consensus 1 iD~LD~TRIHPE~Y~lArkmA~DAle~dee-d~~-~~~~~~~av~~~~~~~~p~kL~~LdLd~yA~~Le~~~~~~K~~TL 78 (115)
T PF14878_consen 1 IDPLDDTRIHPEDYDLARKMAADALEYDEE-DIA-EDEDPSGAVEEIMEDDRPEKLNDLDLDEYAEELERQGGGNKRATL 78 (115)
T ss_dssp --GGGGSS--GGGHHHHHHHHHHHTT--HH-HHH-HHHH-HT-TTHHHHTTHHHHHTTS-HHHHHHHHHHHHS---HHHH
T ss_pred CCccccCCcCCcchHHHHHHHHHHHhcChh-hhc-chhhHHHHHHHHHccccHHHHhhcCHHHHHHHHHHhcCCcHHHHH
Confidence 489999999999999999999999998853 221 23455668899987 8999999999999 5668889999999
Q ss_pred HHHHHHHhcCccCccCCCCCCCchhhhhhhccCCccc
Q 039337 807 YLIRRELIHGFQDWRNQYKEPSQDEEFYMISGETEDT 843 (1344)
Q Consensus 807 ~~I~~EL~~p~~D~R~~~~~p~~~e~f~~lTget~~~ 843 (1344)
++|+.||++||.|+|.+|..|+.+++|+||||||.+|
T Consensus 79 ~~Ir~EL~~pf~d~R~~f~~pt~de~F~mlTGET~~T 115 (115)
T PF14878_consen 79 YDIRSELQHPFEDLRKPFREPTPDEIFTMLTGETEET 115 (115)
T ss_dssp HHHHHHHHSTT---SB----B-HHHHHHHHC---TTT
T ss_pred HHHHHHHhCcccccccCCCCCCHHHhhhHhhcCCCCC
Confidence 9999999999999999999999999999999999875
No 8
>KOG1857 consensus Transcription accessory protein TEX, contains S1 domain [Transcription]
Probab=99.89 E-value=2.2e-24 Score=245.13 Aligned_cols=511 Identities=19% Similarity=0.251 Sum_probs=347.6
Q ss_pred CchHHHHHHhhhccccEEEEEecChhhhhhHHHH--HHhhh-ccCCCcchhhhHHHHHHHHHHHHHHHhHHhHHHHHHHH
Q 039337 341 EDAQWLLIQKAEEEKLLQVTIKLPEDSLNKLFSD--CKEHY-LSDGVSKSAQLWNDQRELILKDALDNFLLPSMVKEARS 417 (1344)
Q Consensus 341 ~~~q~L~i~raE~egll~v~i~~~~~~~~~~~~~--l~~~~-~~d~~s~~~~~wn~~r~~~l~~a~~~~L~P~~~revr~ 417 (1344)
..|+.|++++||++++++|+=.+-+... +|+-- ....+ ...+.. ..-.++..--+-+..+++++|.+.+++|.
T Consensus 57 ~~~~~la~~~G~~~k~~~v~R~i~d~~k-EY~~G~K~~~~~A~~sG~~---p~~~~il~~~~~ds~k~l~~~Hl~~~Lr~ 132 (623)
T KOG1857|consen 57 HHHQILAINRGENLKVLTVKRNISDGVK-EYFCGWKIQNRWAPRSGAR---PELMKILYNSLNDSFKRLIYPHLCRELRA 132 (623)
T ss_pred hhHhHHhhcCCCceeEEEEEeechhhhh-hhhcchhhhhhhhhhccCC---chhHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 4579999999999999999987544322 11100 00011 111211 11223444456788899999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCCCCCCCCCCceEeEeecCCCC-CceEEEEECCCCCEE--EEEEecccc
Q 039337 418 LMSGRAKSWLLMEYGKALWNKVSVGPYQRKDNDITPDEEAAPRVLACCWGPGK-PETTFVMLDSSGEVV--DVLFTGCLT 494 (1344)
Q Consensus 418 ~L~~~Ae~~~i~~~~~nL~~~L~~~P~~~~~~~~~~~~~~~~rVlai~~dpg~-~g~~~a~vd~~G~vl--d~~~~~~~~ 494 (1344)
.|+.++|-+-+..+..+|++.+.+.-.... ..+. .+|++ .||+==+....|+.+ |+++.|...
T Consensus 133 ~l~~d~e~~~v~~~~~~l~~~~~~sA~p~r------------~~~~--~~~~~kRG~~EK~~~~~~~~~~~d~~R~H~~f 198 (623)
T KOG1857|consen 133 KLTSDAEKESVMMFGRNLRQLLLTSAVPGR------------TLMG--VDPGYKRGCKEKIISPTSQILHTDVVRLHCGF 198 (623)
T ss_pred HhhhhhhhHHHHhhcchhhhHHhccCCchh------------hhhc--cCchhhcchHHHhhccccchhhhhHHHHhCcc
Confidence 999999999999999999999887655544 1223 48998 798777888888876 344433321
Q ss_pred ccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCCcchhhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCch
Q 039337 495 LRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVNLSCTSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPR 574 (1344)
Q Consensus 495 ~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~ 574 (1344)
+--++..++..+...++-...+++=+++|+ ..+.....+|-... ..+.+.-+..+.++++.
T Consensus 199 ----------~gf~e~~~~~~I~~~FnD~~~~~~F~~~Sr-----~~ea~~~~~i~~~~----~~~~~~~~~~~~~~~~~ 259 (623)
T KOG1857|consen 199 ----------QGFREAEKIKTILLNFNDSTVVIGFGTASR-----ETEAYFADLIMKNY----FAPLDVVYCIVSEAGAS 259 (623)
T ss_pred ----------cchHHHHHhhhhhhccccceEEeecccccc-----chhHhhcccchhcc----cCCCCcceeeecccCcc
Confidence 112334455555666666677777777776 22233333332211 11334567889999999
Q ss_pred HHhhhHHhhhcCCCCchhhHHHHHhhhhhcccceehhcccCCCcccccccccCccccCChhhhhhhhhhhhhcccccccc
Q 039337 575 LYENSRISSDQLPGQKGNVKRAVALGRYLQNPLAMVATLCGPGREILSWKLCPLENFLTPDEKYGMIEQVMVDVTNQVGL 654 (1344)
Q Consensus 575 vy~~s~~a~~e~p~~~~~~R~avslaR~lqdPl~e~~~l~~~~~~~~~i~~~~~Q~~~~~~~l~~~l~~~~~~~vn~vGV 654 (1344)
+|+.+..--.-.|..++..+.|++.+|++|||++|++.| .+.+|+=+.|||..++-.+.-.+.++++++|..+||
T Consensus 260 L~~~~p~Q~~S~~g~~~~F~~a~~~GR~~~~p~~eVv~~-----~~~~i~G~~~~~~~~~~l~k~~~~T~~e~~V~~igv 334 (623)
T KOG1857|consen 260 LYSVSPEQNKSMPGLDPNFRSAVSIGRRVQDPLAEVVKI-----EPKHIGGGMYQHDVSQTLLKATLDTVVEECVSFVGV 334 (623)
T ss_pred cCCCCHHHhccCCCcchhhhhccCCCcccccchhhheec-----cceeecceeeccCCcHHHHHHHHHHHHHHHHHHHcc
Confidence 999998777778889999999999999999999999999 889999999999999988888889999999999999
Q ss_pred cccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhccCcEEEecCCCCC-------C
Q 039337 655 DINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAVGFLRVRRSGQAA-------S 727 (1344)
Q Consensus 655 diN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI~~~~~~~-------~ 727 (1344)
++|.++. .++.++.||+.-.+.+|++++..+|.++++.++..+.++|++.|..|++|++|....+.+ .
T Consensus 335 ~~n~~~e-----~l~~~~~~lN~~~~~ni~~w~~~~G~~K~~~~~k~~~~lg~~A~~~~~~~~~i~~~~ir~~~Sq~~~~ 409 (623)
T KOG1857|consen 335 DINICSE-----VLLRHIAGLNANRAKNIIEWREKNGPFKNREQLKKVKGLGPKAFQQCAGFIRINQDYIRTFCSQQTET 409 (623)
T ss_pred cchhhHH-----HHHHHHHhcCCCCCcceeEEcCCCCcchhhcccchhhhhCcccchhhhhhhhhhhhhhhhhhcccccc
Confidence 9998888 899999999999999999999999999999999999999999999999999996433211 0
Q ss_pred c-----------------------c---------ccCCcCcCCCCCCCCHHHHHHHHHHHcCCCcCCCCCChhHHHHHHH
Q 039337 728 S-----------------------S---------QFIDLLDDTRIHPESYGLAQELAKEVYNRDIEGDLNDDEDALEMAI 775 (1344)
Q Consensus 728 ~-----------------------~---------~~~d~LD~TrIHPEsY~~A~kma~dal~~d~~~d~~~~~~~~~~~v 775 (1344)
+ + --.=+||.|.+||+.|+.+..++.-+....++.. ..+. .+
T Consensus 410 s~~G~G~~v~P~~~~e~~~V~~~~S~~~t~vN~~lk~L~l~~~~~~~~N~~~~~RL~~~~~~g~lT~~-----g~~~-~~ 483 (623)
T KOG1857|consen 410 SGQGQGVAVTPPADVEVTNVKQGKSKSKTAVNVLLKPLPLDQTCIHPENYDIAMRLFLSSIGGTLTEV-----GKPE-MQ 483 (623)
T ss_pred ccCCcceecCChhhccceeecccccccchhhhhhhcccccccccCCccccchHHHHHHhhccceeeec-----cCcc-eE
Confidence 0 0 0123789999999999999998876643221100 0000 00
Q ss_pred HHHhcChhhhhccChHHH-HHHhhccCccchHHHHHHHHhcCcc-CccCCCCCCCchhhhhhhccCCcccccCCeEEEEE
Q 039337 776 EHVRDRPDLLKTYLLDRH-IKEKKRENKRETLYLIRRELIHGFQ-DWRNQYKEPSQDEEFYMISGETEDTLAEGRVVQAT 853 (1344)
Q Consensus 776 ~~i~~~~~kl~~ldl~~~-~e~~~~~~~~~tL~~I~~EL~~p~~-D~R~~~~~p~~~e~f~~lTget~~~l~~G~iV~g~ 853 (1344)
+..++. ..-|=.+| +++ .+.-..|+.-|..-+.+|-. +-|.++..|-...-|.+ ...-.++-+|.+.
T Consensus 484 --~~~~~~--~~~Dg~~k~~~r--K~~t~h~~~~~~~T~~~p~~~~~~~S~D~~~~~KS~~~-----~~~T~~~AvV~~~ 552 (623)
T KOG1857|consen 484 --QKINSF--LEKDGMEKIAER--KQTTVHTLQVIIDTLSQPESFDFRTSFDKPDFKKSIVC-----LEDTQIGAVVTGK 552 (623)
T ss_pred --EeccCC--cCcccchHHHHh--hhccceeccceeccccCCCCCCccccccccchhhheee-----eehhhhhHHHhcc
Confidence 001110 00011111 111 12235667777777777632 55666766665555532 1122346666777
Q ss_pred EEEEecccEEEEeCCC-eEEEEeceecCCCcccc---CcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 854 VRRVQGQRAICVLESG-LAGMLMKEDYSDDWRDS---ELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 854 V~~V~~~g~fV~L~~g-i~GlIh~s~lsd~~~~~---~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
.+|.+=++.|+..+.+ ..+++.+..+......+ ...--+.+||.+.|-|..++.-+.+|.|-
T Consensus 553 L~N~tl~~~~~~~gV~~~~~l~~~~~~Te~~~sKtD~~r~~~~g~ger~eA~I~H~~~~~s~i~~d 618 (623)
T KOG1857|consen 553 LENATLFGIFVDIGVVGKSGLIPIRNVTEAKLSKTDKRRSLGLGPGERVEAQILHIDIPRSRITLD 618 (623)
T ss_pred ccccccccccccCCcccccccchhhhhccccccccccccccCcccchhhhhhhcccccCcceeEee
Confidence 7777777777766543 46777776665531111 11223567778888887777666665554
No 9
>PF14641 HTH_44: Helix-turn-helix DNA-binding domain of SPT6; PDB: 3PSI_A 3PSF_A.
Probab=99.85 E-value=4.7e-22 Score=196.41 Aligned_cols=110 Identities=30% Similarity=0.499 Sum_probs=76.0
Q ss_pred CCCCCCCchhHHHHHHHHHHHHhcCcCcccccCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCccceeeecchhhhcccc
Q 039337 13 LAGPPTDGESIVDESTWIYNQLLSGTLPLFGQRGAGSPKEGHDLSISRDDIMRFLDLLHLQKLDIPFIAMYRKEECLSLL 92 (1344)
Q Consensus 13 ~~~~~~~~~el~~ea~WI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~vL~l~~~~~~eVPFIarYRKE~~~~l~ 92 (1344)
++..+++++||++||+||+++||.+.+.++ +. ....++..+|++||+||.++++||||||+|||||+.+..
T Consensus 4 ~~~~~~~~~El~~EA~WI~~~~~~~k~~~~-~~--------~~~~~f~~aI~~vL~Fi~~d~~EVPFI~~yRkdy~~~~~ 74 (121)
T PF14641_consen 4 IPVTEAEDEELEEEAEWIYKRLFPEKNFSL-QE--------DLREPFKEAIGKVLEFIRNDNLEVPFIWFYRKDYLSSRE 74 (121)
T ss_dssp TT---HHHHHHHHH--HHHHHHHHHH---S-S------------HHHHHHHHHHHHHHHTS---HHHHHHH-GGGSB-SS
T ss_pred CCCCCCCHHHHHHHHHHHHHHHhcCCCCCc-cH--------HHhHHHHHHHHHHHHHHhhCCCcCCcHHHHHHHhhcccc
Confidence 567788999999999999999998753221 11 123467899999999999999999999999999992211
Q ss_pred cccccccccCCCCCCccCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039337 93 KDLEQNEVNNDNNDDFERTPTLKWHKVLWAIHDLDKKWLLLQKRKSALQSYYKK 146 (1344)
Q Consensus 93 ~~~~~~e~~~~~~~~~~~~~~l~~~~dLw~I~~ld~k~~~L~~RK~~l~~~~~k 146 (1344)
. ....|+|+ ++|||+|++||+||++|.+||++|.++|++
T Consensus 75 ~--------------~~~~~lL~-~~DLWrI~~lD~k~~~L~~kk~~l~~~~~~ 113 (121)
T PF14641_consen 75 K--------------DGFEPLLN-EDDLWRIYDLDIKWRSLLEKKNNLEKLYEK 113 (121)
T ss_dssp T--------------TS---B---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred c--------------cchhhhcc-HHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 0 12346777 469999999999999999999999999985
No 10
>KOG1857 consensus Transcription accessory protein TEX, contains S1 domain [Transcription]
Probab=99.56 E-value=5.9e-16 Score=177.13 Aligned_cols=397 Identities=12% Similarity=0.025 Sum_probs=260.0
Q ss_pred HhhhccccEEEEEecChhhhhhHHHHHHhhhccCCCcchhhhHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHH
Q 039337 349 QKAEEEKLLQVTIKLPEDSLNKLFSDCKEHYLSDGVSKSAQLWNDQRELILKDALDNFLLPSMVKEARSLMSGRAKSWLL 428 (1344)
Q Consensus 349 ~raE~egll~v~i~~~~~~~~~~~~~l~~~~~~d~~s~~~~~wn~~r~~~l~~a~~~~L~P~~~revr~~L~~~Ae~~~i 428 (1344)
+++-+|+++..+|.+.... ...-..|+.-+. -..|+-.-++|-.++-.-+-+...+++.-+
T Consensus 198 f~gf~e~~~~~~I~~~FnD----------~~~~~~F~~~Sr---------~~ea~~~~~i~~~~~~~~~~~~~~~~~~~~ 258 (623)
T KOG1857|consen 198 FQGFREAEKIKTILLNFND----------STVVIGFGTASR---------ETEAYFADLIMKNYFAPLDVVYCIVSEAGA 258 (623)
T ss_pred ccchHHHHHhhhhhhcccc----------ceEEeecccccc---------chhHhhcccchhcccCCCCcceeeecccCc
Confidence 6777888777777654321 111122332111 223443447777777777888999999999
Q ss_pred HHHHHHHHHHHccCCCCCCCCCCCCCCCCCceEeEeecCCCCCceEEEEECCCCCEEEEEEecccccccc--chhhhhhh
Q 039337 429 MEYGKALWNKVSVGPYQRKDNDITPDEEAAPRVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQ--NVRDQQSK 506 (1344)
Q Consensus 429 ~~~~~nL~~~L~~~P~~~~~~~~~~~~~~~~rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~--~~~~~~~~ 506 (1344)
..|..+-.++++++|..++ -+.|+ +||.+ |+|+.|+|++.-- -+++-... ...+ -.+
T Consensus 259 ~L~~~~p~Q~~S~~g~~~~------------F~~a~--~~GR~-----~~~p~~eVv~~~~-~~i~G~~~~~~~~~-~l~ 317 (623)
T KOG1857|consen 259 SLYSVSPEQNKSMPGLDPN------------FRSAV--SIGRR-----VQDPLAEVVKIEP-KHIGGGMYQHDVSQ-TLL 317 (623)
T ss_pred ccCCCCHHHhccCCCcchh------------hhhcc--CCCcc-----cccchhhheeccc-eeecceeeccCCcH-HHH
Confidence 9999999999999999998 45676 88876 8999999997311 12221110 0011 112
Q ss_pred HHHHHHHHHHHHHhCCeEEEEcCCCcchhhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhhhHHhhhcC
Q 039337 507 KNDQERLLKFMMDHQPHVVVLGAVNLSCTSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYENSRISSDQL 586 (1344)
Q Consensus 507 ~~~~~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~s~~a~~e~ 586 (1344)
+-...++++=+ |-+||+++.-| .+.++..++.-+. .-.+..++|+.+.||.-|.....+.++|
T Consensus 318 k~~~~T~~e~~------V~~igv~~n~~------~e~l~~~~~~lN~-----~~~~ni~~w~~~~G~~K~~~~~k~~~~l 380 (623)
T KOG1857|consen 318 KATLDTVVEEC------VSFVGVDINIC------SEVLLRHIAGLNA-----NRAKNIIEWREKNGPFKNREQLKKVKGL 380 (623)
T ss_pred HHHHHHHHHHH------HHHHcccchhh------HHHHHHHHHhcCC-----CCCcceeEEcCCCCcchhhcccchhhhh
Confidence 22222222221 22455555332 3344555555432 1124678999999999999998888887
Q ss_pred CC-CchhhHHHHHhhhhhccc-ceehhcccCCCcccccccccCccccCChhhhhhhhhhhhhcccccccccccccccccc
Q 039337 587 PG-QKGNVKRAVALGRYLQNP-LAMVATLCGPGREILSWKLCPLENFLTPDEKYGMIEQVMVDVTNQVGLDINLAIHREW 664 (1344)
Q Consensus 587 p~-~~~~~R~avslaR~lqdP-l~e~~~l~~~~~~~~~i~~~~~Q~~~~~~~l~~~l~~~~~~~vn~vGVdiN~A~~~~~ 664 (1344)
.. +-..--.+|+++|++.+| +.++++.-+ .|-| ..+.+..+.+.+ ++-+.++..|+++|+++.
T Consensus 381 g~~A~~~~~~~~~i~~~~ir~~~Sq~~~~s~-------~G~G---~~v~P~~~~e~~--~V~~~~S~~~t~vN~~lk--- 445 (623)
T KOG1857|consen 381 GPKAFQQCAGFIRINQDYIRTFCSQQTETSG-------QGQG---VAVTPPADVEVT--NVKQGKSKSKTAVNVLLK--- 445 (623)
T ss_pred Ccccchhhhhhhhhhhhhhhhhhcccccccc-------CCcc---eecCChhhccce--eecccccccchhhhhhhc---
Confidence 64 555667899999999999 899998732 1111 345667777666 667788999999999999
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhccCcEEEecCCCCC-----------CccccCC
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAVGFLRVRRSGQAA-----------SSSQFID 733 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI~~~~~~~-----------~~~~~~d 733 (1344)
+|++-..|+.| +|+.|.+| |..+.++|.-+|.+|++||.+....+.. ++...++
T Consensus 446 --~L~l~~~~~~~-----------~N~~~~~R--L~~~~~~g~lT~~g~~~~~~~~~~~~~~Dg~~k~~~rK~~t~h~~~ 510 (623)
T KOG1857|consen 446 --PLPLDQTCIHP-----------ENYDIAMR--LFLSSIGGTLTEVGKPEMQQKINSFLEKDGMEKIAERKQTTVHTLQ 510 (623)
T ss_pred --ccccccccCCc-----------cccchHHH--HHHhhccceeeeccCcceEEeccCCcCcccchHHHHhhhccceecc
Confidence 89999999999 89999999 9889999999999999999987655432 1234589
Q ss_pred cCcCCCCCCCCHHHHHHHHHHHcCCCcCCCCCChhHHHHHHHHHHhcChhhhhccChHHHHHHhhccCccchHHHHHHHH
Q 039337 734 LLDDTRIHPESYGLAQELAKEVYNRDIEGDLNDDEDALEMAIEHVRDRPDLLKTYLLDRHIKEKKRENKRETLYLIRREL 813 (1344)
Q Consensus 734 ~LD~TrIHPEsY~~A~kma~dal~~d~~~d~~~~~~~~~~~v~~i~~~~~kl~~ldl~~~~e~~~~~~~~~tL~~I~~EL 813 (1344)
+.|.|-||||+|..-+- + | ++...+.+..-.+.... --++.-|
T Consensus 511 ~~~~T~~~p~~~~~~~S-----~--D---------------------~~~~~KS~~~~~~T~~~---------AvV~~~L 553 (623)
T KOG1857|consen 511 VIIDTLSQPESFDFRTS-----F--D---------------------KPDFKKSIVCLEDTQIG---------AVVTGKL 553 (623)
T ss_pred ceeccccCCCCCCcccc-----c--c---------------------ccchhhheeeeehhhhh---------HHHhccc
Confidence 99999999999976432 1 1 11111112111110000 0111122
Q ss_pred hcCccCccCCCCCCCchhhhhhhccCCcccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecC
Q 039337 814 IHGFQDWRNQYKEPSQDEEFYMISGETEDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYS 880 (1344)
Q Consensus 814 ~~p~~D~R~~~~~p~~~e~f~~lTget~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~ls 880 (1344)
++|. +-..|..|. + -....|-+++.|++++.+-+|++.|..+..|.++.-||+++.
T Consensus 554 ~N~t--l~~~~~~~g----V-----~~~~~l~~~~~~Te~~~sKtD~~r~~~~g~ger~eA~I~H~~ 609 (623)
T KOG1857|consen 554 ENAT--LFGIFVDIG----V-----VGKSGLIPIRNVTEAKLSKTDKRRSLGLGPGERVEAQILHID 609 (623)
T ss_pred cccc--cccccccCC----c-----ccccccchhhhhccccccccccccccCcccchhhhhhhcccc
Confidence 3331 111222222 1 155678899999999999999999999999999988888753
No 11
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.47 E-value=4.1e-14 Score=136.55 Aligned_cols=78 Identities=19% Similarity=0.311 Sum_probs=73.7
Q ss_pred cccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccccc
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESEMR 922 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~dl~ 922 (1344)
++++|.+|+|+|++|++|||||.|+.|-.||||||++++. |++|..+.+++||.|+|+|++||. +.+|+||+|...-.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~-fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e~ 79 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADG-FVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEEE 79 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhh-hHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhhC
Confidence 5789999999999999999999999999999999999999 999999999999999999999998 89999999975543
No 12
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=99.44 E-value=1.2e-13 Score=137.87 Aligned_cols=120 Identities=20% Similarity=0.261 Sum_probs=100.5
Q ss_pred CchHHhhhHHhhhcCCCCchhhHHHHHhhhhhcccceehhcccCCCcccccccccCccccCChhhhhhhhhhhhhccccc
Q 039337 572 LPRLYENSRISSDQLPGQKGNVKRAVALGRYLQNPLAMVATLCGPGREILSWKLCPLENFLTPDEKYGMIEQVMVDVTNQ 651 (1344)
Q Consensus 572 ~a~vy~~s~~a~~e~p~~~~~~R~avslaR~lqdPl~e~~~l~~~~~~~~~i~~~~~Q~~~~~~~l~~~l~~~~~~~vn~ 651 (1344)
++||+++.+.|+..++++|.. +||||..|.|-+..|++..++.. ... + . .-......
T Consensus 1 ~~rv~d~i~~agg~~~~ad~~---~inla~~l~d~~~i~vp~~~e~~--~~~-----~-~------------~~~~~~~~ 57 (120)
T TIGR01259 1 GLRVWDAIEKAGGFTEQADGL---SVNLAGKLMDEMFVYVPMKGEEA--VSQ-----Q-G------------TQSSAGKL 57 (120)
T ss_pred CChHHHHHHHccCCCcccchh---cccccccccCCCEEEECCCCCcc--ccC-----c-C------------cccccCCC
Confidence 589999999999888988875 99999999999999998855321 111 0 0 00112334
Q ss_pred ccccccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhccCcEEE
Q 039337 652 VGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAVGFLRV 719 (1344)
Q Consensus 652 vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI 719 (1344)
..||||+|+. ..|+.|||||+.+|++||+||+++|.|.|.+||.+|+|||+++|+++..||.|
T Consensus 58 ~~iniNtA~~-----~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~V~GIg~k~~~~i~~~l~v 120 (120)
T TIGR01259 58 AAVNINAASL-----EELQALPGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDYATV 120 (120)
T ss_pred CCEeCCcCCH-----HHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHcCCCCCHHHHHHHHhceEC
Confidence 5799999999 79999999999999999999999999999999999999999999999999875
No 13
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.36 E-value=2.1e-12 Score=155.69 Aligned_cols=184 Identities=16% Similarity=0.151 Sum_probs=144.8
Q ss_pred cccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 841 EDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 841 ~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
.+.+.+|+.+.|+|+++++|||||++..|++||+|+|+||+. +...|.+.+++||.|.|+|++||++++||+|+||+..
T Consensus 272 ~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~-~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~ 350 (541)
T COG0539 272 EKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWT-KKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLK 350 (541)
T ss_pred hhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhccc-ccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhh
Confidence 346789999999999999999999999999999999999998 5555999999999999999999999999999999753
Q ss_pred ccccc-----c-------------------cCC-CCCCCCcccccccchHHHHHH--HH-------------HHHHhhhc
Q 039337 921 MRNNR-----Y-------------------QHC-QNLDPYYHEERSSRQSEQEKA--RK-------------EKELAKKH 960 (1344)
Q Consensus 921 l~~~~-----~-------------------~~~-~~~D~y~~~~~~~~~~e~~~~--~k-------------~~~~~~~~ 960 (1344)
-++-. + ... ...|.+.+.+..+|+..-+.. .| .++++.+.
T Consensus 351 ~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isL 430 (541)
T COG0539 351 ENPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISL 430 (541)
T ss_pred cChhhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEEEEEEEEEecccceeee
Confidence 22100 0 011 126666666667777532222 12 12345567
Q ss_pred cccccccCCCcccCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceee
Q 039337 961 FKERLIVHPCFQNVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLK 1040 (1344)
Q Consensus 961 ~~~RvI~HP~F~n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~ 1040 (1344)
.+++.-..|+ +++....+.|++|--....-.+. .+.+.+.+++-..++..+..++. |++|+.+.
T Consensus 431 giKql~~~p~---------~~~~~~~~~~~~v~~~v~~i~~~-G~~v~l~~~v~G~i~~~~~~~~~------~~~gd~v~ 494 (541)
T COG0539 431 GIKQLEESPW---------EEFSEKYKKGSVVKGKVKSVKDK-GAFVELGGGVEGLIRLSELSRDV------LKVGDEVE 494 (541)
T ss_pred ehhhhccCch---------hhhHhhccCCCeEEEEEEEEccC-ceEEEecCceeeeeecchhhhhh------ccCCCEEE
Confidence 8888888899 88899999999999988886666 89999999998889998888763 77777665
Q ss_pred e
Q 039337 1041 I 1041 (1344)
Q Consensus 1041 i 1041 (1344)
.
T Consensus 495 a 495 (541)
T COG0539 495 A 495 (541)
T ss_pred E
Confidence 4
No 14
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.33 E-value=2.4e-12 Score=155.31 Aligned_cols=168 Identities=17% Similarity=0.197 Sum_probs=129.0
Q ss_pred CcccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 840 TEDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 840 t~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
..++|++|++|.|+|++|++|||||+|+ |++||+|+++||+. ++.+|++.|++||.|+|+|+++|.++.+|+||+|..
T Consensus 186 ~~~~l~~G~vV~G~V~~It~~GafVdig-GvdGLlHiseiS~~-rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l 263 (541)
T COG0539 186 LLNKLEVGEVVEGVVKNITDYGAFVDIG-GVDGLLHISEISWK-RVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQL 263 (541)
T ss_pred HHhcCCCCceEEEEEEEeecCcEEEEec-CeeeEEehhhcccc-ccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhc
Confidence 3568999999999999999999999998 59999999999999 899999999999999999999999999999999975
Q ss_pred ccccc-----ccc--------------------CCCCCCCCcccccccchHHHHHHH--H-------------HHHHhhh
Q 039337 920 EMRNN-----RYQ--------------------HCQNLDPYYHEERSSRQSEQEKAR--K-------------EKELAKK 959 (1344)
Q Consensus 920 dl~~~-----~~~--------------------~~~~~D~y~~~~~~~~~~e~~~~~--k-------------~~~~~~~ 959 (1344)
.-.+- .+. -.+....+.+.+..+|........ + ..+++.+
T Consensus 264 ~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIs 343 (541)
T COG0539 264 EEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRIS 343 (541)
T ss_pred ccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEE
Confidence 32110 000 123455556666667775321000 1 1234556
Q ss_pred ccccccccCCCcccCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEE
Q 039337 960 HFKERLIVHPCFQNVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDI 1019 (1344)
Q Consensus 960 ~~~~RvI~HP~F~n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV 1019 (1344)
..+++....|| +.+....++|++|-....+-.+. .+.+.+.+++-..+..
T Consensus 344 L~iKq~~~~pw---------~~~~~~~~~g~~v~g~v~~~t~~-g~fv~le~gidG~vh~ 393 (541)
T COG0539 344 LGLKQLKENPW---------EEFADKHPVGDVVEGKVKSITDF-GAFVELEGGIDGLVHL 393 (541)
T ss_pred eeehhhhcChh---------hhhhhhcCCCCeEEEEEeeeccc-ceEEccCCCccceEEH
Confidence 78899999999 88888899999887777776666 8888888876544433
No 15
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.32 E-value=4.9e-12 Score=115.88 Aligned_cols=71 Identities=25% Similarity=0.347 Sum_probs=65.7
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCc---ccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSEL---SDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~---~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
|++|++|.|+|++|++||+||+|+.+++|+||++++|+. ++.+| .+.|++||.|+|+|+++|.++.+|.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~-~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKY-FVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCc-cccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 579999999999999999999999999999999999998 65554 589999999999999999999999886
No 16
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.27 E-value=2.3e-11 Score=110.99 Aligned_cols=73 Identities=22% Similarity=0.312 Sum_probs=68.6
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
|++|++|.|+|++|+++|+||+|+++++|+||+++++++ +..++.+.|++||.|+|+|+++|.+++++.||++
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~-~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD-YSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc-cccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 578999999999999999999999999999999999998 6667888999999999999999999999999975
No 17
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.24 E-value=2.4e-11 Score=110.75 Aligned_cols=71 Identities=25% Similarity=0.276 Sum_probs=66.2
Q ss_pred ccCCeEEEEEEEEEec-ccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 844 LAEGRVVQATVRRVQG-QRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~-~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
|++|++|.|+|++|.+ ||+||+|..+.+|++|+++++++ ++.+|.+.|++||.|+|+|+++|. .++.||++
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~-~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDS-YTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCc-ccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 5799999999999986 89999999999999999999998 788898999999999999999985 79999975
No 18
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.24 E-value=2.2e-11 Score=114.17 Aligned_cols=76 Identities=24% Similarity=0.316 Sum_probs=71.8
Q ss_pred CcccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 840 TEDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 840 t~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
+..++++|++|+|+|++|.++|+||+|.++++|+||+++++++ +..++.+.|++||.|+|+|+++|.++.+|.|||
T Consensus 8 ~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~-~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDE-FVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred hHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcc-cccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 4667999999999999999999999999999999999999998 777899999999999999999999999999986
No 19
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=99.21 E-value=7.9e-12 Score=111.53 Aligned_cols=65 Identities=26% Similarity=0.456 Sum_probs=55.6
Q ss_pred cccccccccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhccCcEE
Q 039337 649 TNQVGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAVGFLR 718 (1344)
Q Consensus 649 vn~vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a~Flr 718 (1344)
||...||||+|+. ..|+.+||||+..|++||+||+++|+|.|.+||..++||++++++++..||+
T Consensus 1 v~~~~idiN~as~-----~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~~l~ 65 (65)
T PF12836_consen 1 VNEQKIDINTASA-----EELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKPYLT 65 (65)
T ss_dssp HHHHSEETTTS-H-----HHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCCCEE
T ss_pred CCCCCccCccCCH-----HHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHhhcC
Confidence 5778899999999 8999999999999999999999999999999999999999999999999986
No 20
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.20 E-value=6.1e-11 Score=108.43 Aligned_cols=71 Identities=23% Similarity=0.239 Sum_probs=66.1
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCC-ccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDD-WRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~-~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
|++|+|+|+++.++|+||.|+.+++|+||.+++++. ....++.+.|++||.|+|+|+++|.++.+|.||++
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 789999999999999999999999999999999976 13668899999999999999999999999999986
No 21
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.19 E-value=5.8e-11 Score=107.43 Aligned_cols=70 Identities=19% Similarity=0.376 Sum_probs=66.6
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
|++|+|+|++|.++|+||+|..+++||||+++++++ +..++.+.|++||.|+|+|+++|.++.++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~-~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEA-FIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChh-hcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 789999999999999999999899999999999988 6778999999999999999999999999999985
No 22
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.19 E-value=8.5e-11 Score=107.50 Aligned_cols=73 Identities=25% Similarity=0.402 Sum_probs=69.8
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
+++|++|.|+|++|.++|+||+|+.+++|+||.+++++. +..++...+++||.|+|+|+++|.++.++.||+|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~-~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD-RIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS-EESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc-cccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 689999999999999999999999999999999999998 7778999999999999999999999999999985
No 23
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.17 E-value=9e-11 Score=105.98 Aligned_cols=69 Identities=22% Similarity=0.401 Sum_probs=65.1
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
|++|.|+|++|.++|+||+|+.+++|+||++++++. +..++.+.|++||.|+|+|+++|.++.+|.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~-~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV-RLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCc-cccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999999999999999999998 666788899999999999999999999999985
No 24
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=99.17 E-value=1.7e-11 Score=126.81 Aligned_cols=63 Identities=25% Similarity=0.435 Sum_probs=59.7
Q ss_pred ccccccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhccCcEEE
Q 039337 652 VGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAVGFLRV 719 (1344)
Q Consensus 652 vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI 719 (1344)
--||||+|+. +.|+.||||||.||++||+||+++|+|+|.+||.+|+|||++++++..++|++
T Consensus 87 ~~vNiNtAs~-----eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~~~i~~ 149 (149)
T COG1555 87 KKVNINTASA-----EELQALPGIGPKKAQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLKDYITV 149 (149)
T ss_pred ccccccccCH-----HHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHhccCCCHHHHHHHHhhccC
Confidence 4599999999 79999999999999999999999999999999999999999999999998764
No 25
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.16 E-value=1.7e-10 Score=105.70 Aligned_cols=70 Identities=29% Similarity=0.425 Sum_probs=64.8
Q ss_pred cccCCeEEEEEEEEEecccEEEEeC-CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLE-SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~-~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
+|++|++|.|+|++|+++|+||+++ .|++||||.+++++. +.+++||.|.|+|+++|.++.++.||+|..
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~-------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~ 71 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPS 71 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc-------cccCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence 5789999999999999999999997 589999999999874 578999999999999999999999999864
No 26
>PRK08582 hypothetical protein; Provisional
Probab=99.15 E-value=1.6e-10 Score=118.61 Aligned_cols=75 Identities=19% Similarity=0.345 Sum_probs=70.1
Q ss_pred cccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.+++|++|.|+|++|++||+||+|+.+++||||++++++. ++.++.+.|++||.|+|+|++||.+ .+|.||++..
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~-~v~~~~~~l~vGD~VkvkV~~id~~-gkI~LSlk~~ 76 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN-YVKDINDHLKVGDEVEVKVLNVEDD-GKIGLSIKKA 76 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcc-cccccccccCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 3789999999999999999999999999999999999998 7788889999999999999999974 8999999875
No 27
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.14 E-value=7.8e-11 Score=114.22 Aligned_cols=77 Identities=25% Similarity=0.413 Sum_probs=70.2
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCcc-------------------ccCcccccCCCCEEEEEEEE
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWR-------------------DSELSDKLHEGDILTCKIKS 904 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~-------------------~~~~~~~~~vGq~V~vkVi~ 904 (1344)
|++|++|.|+|++|.++|+||.|..|++|+||++++++. + ..++.+.|++||.|+|+|++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~ 79 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDA-YTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS 79 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHH-HHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence 579999999999999999999999999999999999985 3 23477889999999999999
Q ss_pred EeCC---CcEEEEEEecccc
Q 039337 905 IQKN---RYQVFLVCRESEM 921 (1344)
Q Consensus 905 iD~~---~~~I~LSlk~~dl 921 (1344)
+|.+ +.+|.||+|++++
T Consensus 80 ~d~~~~~~~~i~LSlr~~~v 99 (100)
T cd05693 80 LDKSKSGKKRIELSLEPELV 99 (100)
T ss_pred ccCCcCCCcEEEEEecHHHC
Confidence 9997 7999999999875
No 28
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.13 E-value=2e-10 Score=104.49 Aligned_cols=69 Identities=23% Similarity=0.284 Sum_probs=64.4
Q ss_pred CeEEE-EEEEEE-ecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 847 GRVVQ-ATVRRV-QGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 847 G~iV~-g~V~~V-~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
|.+|+ |+|++| .++|+||+|..|++||||+|++++. +..++.+.|++||.|.|+|+++|..+.+|.|||
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~-~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDD-KVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcc-hhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78899 999999 6999999999899999999999987 677788899999999999999999999999986
No 29
>PRK07252 hypothetical protein; Provisional
Probab=99.10 E-value=4.5e-10 Score=112.28 Aligned_cols=76 Identities=16% Similarity=0.221 Sum_probs=70.9
Q ss_pred cCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecccc
Q 039337 845 AEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESEM 921 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~dl 921 (1344)
++|++|.|+|++|+++|+||+|..+++|+||+++++++ +..++.+.|++||.|+|+|+++|.++.++.||++....
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~-~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~ 77 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTG-FIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEE 77 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCc-cccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence 58999999999999999999999999999999999998 67788889999999999999999999999999997653
No 30
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.10 E-value=2.3e-10 Score=103.12 Aligned_cols=69 Identities=20% Similarity=0.285 Sum_probs=63.1
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
|++|+|+|++|++||+||+|+++++||||++++++.....++.+.|++||.|+|+|+++|.++.+|.|+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 789999999999999999999999999999999853256678889999999999999999999999875
No 31
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=99.09 E-value=4.8e-10 Score=103.00 Aligned_cols=73 Identities=21% Similarity=0.288 Sum_probs=67.7
Q ss_pred cCCeEEEEEEEEEecccEEEEeCC--CeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 845 AEGRVVQATVRRVQGQRAICVLES--GLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~--gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
++|++|.|+|++|.++|+||+|.. +++|+||+++++++ +..++.+.|++||.|+|+|+++|.++.++.||++.
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~-~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRR-RIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCc-ccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 589999999999999999999963 69999999999998 77789999999999999999999999999999873
No 32
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=99.08 E-value=4e-10 Score=103.04 Aligned_cols=70 Identities=17% Similarity=0.168 Sum_probs=63.8
Q ss_pred cCCeEEEEEEEEEecccEEEEeCC-CeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVLES-GLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~-gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
..|+++.|+|++|++||+||+|+. +.+||||++++++. +..++.+.|++||.|+|+|+++|.++ ++.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~-~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC-RVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCC-cccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 479999999999999999999942 37999999999998 67789999999999999999999987 999986
No 33
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.07 E-value=2.9e-10 Score=130.04 Aligned_cols=78 Identities=18% Similarity=0.248 Sum_probs=72.2
Q ss_pred ccccc-CCeEEEEEEEEEecccEEEEeC--CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 841 EDTLA-EGRVVQATVRRVQGQRAICVLE--SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 841 ~~~l~-~G~iV~g~V~~V~~~g~fV~L~--~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
.+.|. +|++|.|+|++|.+||+||.|+ .|++||||+|+||+. ++.++.+.+++||.|.|+|++||.++.+|.||+|
T Consensus 11 ~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~-ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K 89 (319)
T PTZ00248 11 EQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKR-RIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKK 89 (319)
T ss_pred hhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhccc-ccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEee
Confidence 34555 7999999999999999999996 689999999999998 8899999999999999999999999999999998
Q ss_pred cc
Q 039337 918 ES 919 (1344)
Q Consensus 918 ~~ 919 (1344)
..
T Consensus 90 ~v 91 (319)
T PTZ00248 90 RV 91 (319)
T ss_pred ec
Confidence 63
No 34
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.07 E-value=3.6e-10 Score=101.77 Aligned_cols=68 Identities=19% Similarity=0.327 Sum_probs=64.3
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
|++|.|+|++|.++|+||+|..+++|+||+++++++ +..++.+.|++||.|+|+|+++|.++.+|.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~-~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDS-YLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCch-hhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999999999999999999988 67788999999999999999999999999875
No 35
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.07 E-value=6.1e-10 Score=101.37 Aligned_cols=71 Identities=24% Similarity=0.454 Sum_probs=67.4
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
|++|.|+|++|.++|+||+|..+++|+||+++++++ +..++.+.|++||.|+|+|+++|.++.++.||++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~-~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~ 71 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRD-RVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCc-cccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEE
Confidence 789999999999999999999999999999999998 67788899999999999999999999999999985
No 36
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.07 E-value=6.6e-10 Score=102.19 Aligned_cols=74 Identities=24% Similarity=0.398 Sum_probs=68.7
Q ss_pred cCCeEEEEEEEEEecccEEEEeC-CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 845 AEGRVVQATVRRVQGQRAICVLE-SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~-~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
++|++|.|+|++|+++|+||+|. .+.+|++|+++++++ +..++.+.|++||.|+|+|+++|.++.++.||+|.+
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~-~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN-RVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCC-ccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 46999999999999999999998 489999999999998 677888999999999999999999999999999875
No 37
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.05 E-value=6.1e-10 Score=141.53 Aligned_cols=119 Identities=15% Similarity=0.124 Sum_probs=99.3
Q ss_pred hccCccchHHHHHHHHhcCccCccCCCCCCCc-------hhhhhhhccCCcccccCCeEEE-EEEEEEecccEEEEeCCC
Q 039337 798 KRENKRETLYLIRRELIHGFQDWRNQYKEPSQ-------DEEFYMISGETEDTLAEGRVVQ-ATVRRVQGQRAICVLESG 869 (1344)
Q Consensus 798 ~~~~~~~tL~~I~~EL~~p~~D~R~~~~~p~~-------~e~f~~lTget~~~l~~G~iV~-g~V~~V~~~g~fV~L~~g 869 (1344)
..+.+-.|+++|.+|+..+..|++.......+ +....++...+. ..++|+++. |+|++|++||+||+|..|
T Consensus 699 vIG~GGktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~~-~~~vG~iy~~g~V~~I~~FGaFVeL~~g 777 (891)
T PLN00207 699 IIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLTM-VPTVGDIYRNCEIKSIAPYGAFVEIAPG 777 (891)
T ss_pred HhcCCchhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHhc-CcCCCcEEECcEEEEEeccEEEEEeCCC
Confidence 35677899999999999998899998765432 222233333333 468999995 699999999999999999
Q ss_pred eEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 870 LAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 870 i~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
++||||+|+|+++ ++.++.+.|++||.|+|+|++||. +.+|.||+|..
T Consensus 778 ~EGLVHISeLs~~-rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l 825 (891)
T PLN00207 778 REGLCHISELSSN-WLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRAL 825 (891)
T ss_pred CEEEEEhhhcCCc-cccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEecc
Confidence 9999999999998 778899999999999999999997 78999999873
No 38
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.04 E-value=1.3e-09 Score=132.80 Aligned_cols=76 Identities=20% Similarity=0.290 Sum_probs=71.5
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
..|++|++|+|+|++|++||+||+|+ |++||||+|+|++. ++.+|.+.|++||.|+|+|+++|.++.+|.||+|..
T Consensus 204 ~~lk~G~iv~G~V~~i~~~G~FVdlg-gv~Glv~~Sels~~-~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~ 279 (486)
T PRK07899 204 NQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWK-HIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKAT 279 (486)
T ss_pred HhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHCCCc-ccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence 46889999999999999999999996 79999999999998 778999999999999999999999999999999864
No 39
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.02 E-value=1.2e-09 Score=99.37 Aligned_cols=72 Identities=18% Similarity=0.247 Sum_probs=63.9
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
+.+|+++.|+|++|++||+||+|+.+++||+|++++++.....++.+.|++||.|+|+|+++|.++.+|.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 468999999999999999999999999999999999853234467788999999999999999999998774
No 40
>PRK05807 hypothetical protein; Provisional
Probab=99.01 E-value=1.3e-09 Score=111.57 Aligned_cols=74 Identities=20% Similarity=0.345 Sum_probs=68.9
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
+++|++|+|+|+.|+++|+||.| .+..||||++++++. ++.++.+.|++||.|+|+|++||. ..+|+||++...
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~-~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADT-YVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccc-cccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 67999999999999999999999 578999999999998 888899999999999999999998 689999999743
No 41
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.99 E-value=2.4e-09 Score=132.11 Aligned_cols=79 Identities=25% Similarity=0.347 Sum_probs=72.9
Q ss_pred cccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 841 EDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 841 ~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.+.+++|++|.|+|++|++||+||+|..|++||||+|+|++..++.+|.+.+++||.|+|+|+++|.++.+|.||+|..
T Consensus 287 ~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~ 365 (491)
T PRK13806 287 GDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDA 365 (491)
T ss_pred hccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeec
Confidence 4578899999999999999999999999999999999999843567889999999999999999999999999999864
No 42
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.99 E-value=1.5e-09 Score=97.19 Aligned_cols=69 Identities=30% Similarity=0.467 Sum_probs=64.9
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
|++|.|+|++++++|+||+|+.+.+|+||.++++++ +..++.+.|++||.|+|+|+++|. +.++.||+|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~-~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK-RVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCc-ccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 789999999999999999999999999999999988 677888899999999999999998 789999985
No 43
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.99 E-value=2.9e-09 Score=135.83 Aligned_cols=125 Identities=20% Similarity=0.174 Sum_probs=101.0
Q ss_pred cChHHHHHHhhccCccchHHHHHHHHhcCccCccCCCCCCCch-------hhhhhhccCCcccccCCeEEEEEEEEEecc
Q 039337 788 YLLDRHIKEKKRENKRETLYLIRRELIHGFQDWRNQYKEPSQD-------EEFYMISGETEDTLAEGRVVQATVRRVQGQ 860 (1344)
Q Consensus 788 ldl~~~~e~~~~~~~~~tL~~I~~EL~~p~~D~R~~~~~p~~~-------e~f~~lTget~~~l~~G~iV~g~V~~V~~~ 860 (1344)
++.+...+- .+.+-.|+++|++|+.. -.|++......... ....++...+ .++++|++|.|+|++|.+|
T Consensus 560 I~~~kI~~v--IG~gg~~ik~I~~~~~~-~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~-~~~~vG~v~~G~V~~I~~f 635 (693)
T PRK11824 560 IPPDKIRDV--IGPGGKTIREITEETGA-KIDIEDDGTVKIAATDGEAAEAAKERIEGIT-AEPEVGEIYEGKVVRIVDF 635 (693)
T ss_pred CCHHHHHHH--hcCCchhHHHHHHHHCC-ccccCCCceEEEEcccHHHHHHHHHHHHHhc-ccCcCCeEEEEEEEEEECC
Confidence 344444333 56788999999999988 67888876543321 2222333222 4689999999999999999
Q ss_pred cEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 861 RAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 861 g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
|+||+|..+.+||||+|+++++ ++.++.+.|++||.|+|+|+++|.+ .+|.||+|.
T Consensus 636 GafVei~~~~~GllhiSels~~-~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~ 691 (693)
T PRK11824 636 GAFVEILPGKDGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKA 691 (693)
T ss_pred eEEEEECCCCEEEEEeeeccCc-cccCccceeCCCCEEEEEEEEECCC-CcEEEEEEe
Confidence 9999999999999999999998 7889999999999999999999987 899999975
No 44
>PRK08059 general stress protein 13; Validated
Probab=98.99 E-value=1.9e-09 Score=108.69 Aligned_cols=79 Identities=22% Similarity=0.305 Sum_probs=73.4
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecccc
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESEM 921 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~dl 921 (1344)
+++++|++|.|+|++|+++|+||+|+.+++|+||+++++++ +..++.+.|++||.|.|+|+++|.++.++.||++....
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~-~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~ 81 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG-FVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE 81 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc-cccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence 45889999999999999999999999999999999999988 77788889999999999999999999999999997643
No 45
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.96 E-value=3e-09 Score=137.16 Aligned_cols=78 Identities=22% Similarity=0.279 Sum_probs=72.2
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
+.|++|++|+|+|++|++||+||+|..|++||||+|++++.....+|.+.|++||.|+|+|+++|.++.+|+||+|..
T Consensus 574 ~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l 651 (863)
T PRK12269 574 NKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQV 651 (863)
T ss_pred ccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhc
Confidence 468899999999999999999999999999999999999843677899999999999999999999999999999863
No 46
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.96 E-value=2.7e-09 Score=96.58 Aligned_cols=70 Identities=21% Similarity=0.322 Sum_probs=65.9
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
|++|+|+|.+|.++|+||+|+.+.+|++|.+++++. +..++.+.|++||.|+|+|+++|.++.+|.||++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~-~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD-PIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc-ccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 789999999999999999999899999999999987 7778999999999999999999988889999975
No 47
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.92 E-value=3.9e-09 Score=94.64 Aligned_cols=66 Identities=21% Similarity=0.256 Sum_probs=59.8
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
|++|+|+|++|.++|+||.|..+++|+||.+++++. ... .+.|++||.|+|+|+++|+++.+|.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~-~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPE-KSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCc-cCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999998789999999999865 332 678999999999999999999999886
No 48
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.92 E-value=4.8e-09 Score=97.37 Aligned_cols=70 Identities=20% Similarity=0.290 Sum_probs=64.0
Q ss_pred CeEEEEEEEEEecccEEEEeC---CCeEEEEeceecCCCccc-cCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 847 GRVVQATVRRVQGQRAICVLE---SGLAGMLMKEDYSDDWRD-SELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~---~gi~GlIh~s~lsd~~~~-~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
|+++.|+|++|.+||+||+|+ .+++||+|++++++. +. .++.+.|++||.|+|+|+++| +.++.||+|..
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~-~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~ 74 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFE-GRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDV 74 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCC-CCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEec
Confidence 789999999999999999998 579999999999988 44 788889999999999999999 78999999863
No 49
>PHA02945 interferon resistance protein; Provisional
Probab=98.91 E-value=4.9e-09 Score=96.33 Aligned_cols=70 Identities=16% Similarity=0.129 Sum_probs=64.7
Q ss_pred cCCeEEEEEEEEEecccEEEEeC--CCeEEEEeceec--CCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 845 AEGRVVQATVRRVQGQRAICVLE--SGLAGMLMKEDY--SDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~--~gi~GlIh~s~l--sd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
.+|++|.|+|.. .+||+||.|+ .|++||||+|++ ++. ++++ ++.+ .||+|.|+|+.+|+.+..|+||+|.
T Consensus 10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~-wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~ 83 (88)
T PHA02945 10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNR-YFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR 83 (88)
T ss_pred CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccc-eEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence 589999999999 9999999996 389999999955 888 7888 8888 9999999999999999999999986
No 50
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.90 E-value=3.9e-09 Score=94.26 Aligned_cols=68 Identities=26% Similarity=0.315 Sum_probs=63.3
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
|+++.|+|++|+++|+||+|..+.+|++|.+++++. +..++.+.|++||.|+|+|+++|.++.++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~-~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADR-FVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCc-cccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 689999999999999999999999999999999987 66688888999999999999999988999875
No 51
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.90 E-value=7.4e-09 Score=133.61 Aligned_cols=77 Identities=18% Similarity=0.264 Sum_probs=69.7
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
+.+++|++|+|+|++|++||+||+|..|++||||++++|+.....++.+.|++||.|+|+|++||.++.+|.||+|.
T Consensus 661 ~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~ 737 (863)
T PRK12269 661 ARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQ 737 (863)
T ss_pred HhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecc
Confidence 45889999999999999999999999999999999999986233456678999999999999999999999999985
No 52
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.85 E-value=1.3e-08 Score=125.70 Aligned_cols=76 Identities=26% Similarity=0.418 Sum_probs=70.6
Q ss_pred cccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCC----cEEEEEEec
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNR----YQVFLVCRE 918 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~----~~I~LSlk~ 918 (1344)
.+++|++|+|+|++|.++|+||+|+.|++||||++++++. ++.+|.+.|++||.|+|+|+++|.++ .+|.||+|.
T Consensus 199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~-~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~ 277 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWS-RVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQ 277 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCc-cccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehh
Confidence 5789999999999999999999998899999999999998 78899999999999999999999876 479999886
Q ss_pred c
Q 039337 919 S 919 (1344)
Q Consensus 919 ~ 919 (1344)
.
T Consensus 278 ~ 278 (491)
T PRK13806 278 A 278 (491)
T ss_pred h
Confidence 4
No 53
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.83 E-value=9.1e-09 Score=97.10 Aligned_cols=76 Identities=21% Similarity=0.218 Sum_probs=67.0
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCC---ccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDD---WRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~---~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
+++|++|.|+|+.|.++|++|+|+.+.+|+||+++++.. ....++.+.+++||.|.|+|+++|.+ .++.||++...
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~~~ 82 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRSLK 82 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCccc
Confidence 579999999999999999999999999999999999852 13456677899999999999999876 89999998754
No 54
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=98.82 E-value=1.7e-08 Score=123.96 Aligned_cols=26 Identities=12% Similarity=0.096 Sum_probs=13.1
Q ss_pred hhCcccccCCHHHHHHHHHHHHHhCC
Q 039337 1068 LSYRKFRKGSKAEVDELLRIEKAEFP 1093 (1344)
Q Consensus 1068 ~~h~kf~~g~~~e~e~~L~~~~~~np 1093 (1344)
+-|+|=|.-+.++-..+|..++..+|
T Consensus 1002 ~y~ekrkvLtTe~~~alihk~Svncp 1027 (1282)
T KOG0921|consen 1002 YYVEKRKVLTTEQSSALIHKYSVNCP 1027 (1282)
T ss_pred eeccceeEEeecchhhhhhhhcccCC
Confidence 33444433344555566655555555
No 55
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.82 E-value=1.7e-08 Score=90.52 Aligned_cols=72 Identities=25% Similarity=0.400 Sum_probs=66.6
Q ss_pred cCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 845 AEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
++|++|.|+|.+++++|+||++++++.|++|.+++++. +..++.+.|++||.|.|+|++++.++.++.||++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~-~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc-ccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 36999999999999999999999999999999999987 5667778899999999999999999999999975
No 56
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.79 E-value=2.1e-08 Score=116.94 Aligned_cols=78 Identities=22% Similarity=0.297 Sum_probs=72.5
Q ss_pred cccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 841 EDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 841 ~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
..++++|++|.|+|++|++||+||++. |++||||+++++++ ++.++.+.|++||.|+|+|+++|.++.+|.||+|...
T Consensus 191 ~~~~k~G~vv~G~V~~I~~~G~fV~i~-gv~Gllhisels~~-~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~ 268 (318)
T PRK07400 191 MNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHE-HIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLE 268 (318)
T ss_pred hccCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcccc-cccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccc
Confidence 346889999999999999999999995 89999999999998 7788999999999999999999999999999999754
No 57
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.79 E-value=3.3e-08 Score=124.91 Aligned_cols=76 Identities=28% Similarity=0.388 Sum_probs=71.7
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.+|++|++|+|+|++|+++|+||+++ |++|+||++++++. ++.+|.+.|++||.|.|+|+++|.++.+|.||+|..
T Consensus 197 ~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~-~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~ 272 (565)
T PRK06299 197 ENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWK-RVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQL 272 (565)
T ss_pred hcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhccc-ccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEec
Confidence 46889999999999999999999998 99999999999998 778999999999999999999999999999999863
No 58
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.79 E-value=1.8e-08 Score=90.29 Aligned_cols=68 Identities=22% Similarity=0.388 Sum_probs=63.0
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
|+++.|+|++|.++|+||+|..+.+|++|+++++++ +..++.+.|++||.|.|+|+++|. +.++.||+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~-~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDE-RVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCc-cccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 679999999999999999999899999999999987 666788899999999999999998 88998874
No 59
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.78 E-value=2.5e-08 Score=89.58 Aligned_cols=67 Identities=22% Similarity=0.299 Sum_probs=60.2
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
|++|+|+|+++.++|++|++ .|++||||.++++.. +..++.+ .+||.+.|+|+++|.++.+|.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~-~~~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLR-PVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCc-ccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 689999999999977 5556655 3899999999999999999999975
No 60
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.78 E-value=2e-08 Score=89.87 Aligned_cols=68 Identities=32% Similarity=0.411 Sum_probs=62.7
Q ss_pred CCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 846 EGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
+|++|.|+|+++.++|+||+|+ +.+|++|.+++++. +..++.+.|++||.|+|+|+++|.++.++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~-~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWG-RVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCc-cccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 4899999999999999999997 69999999999976 66778889999999999999999999999875
No 61
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.78 E-value=5.1e-09 Score=114.25 Aligned_cols=74 Identities=22% Similarity=0.348 Sum_probs=69.8
Q ss_pred cCCeEEEEEEEEEecccEEEEeC--CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 845 AEGRVVQATVRRVQGQRAICVLE--SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~--~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.+|++|-|||+.|.+||+||.|+ .|++||||+|+++.. ++++.++.+++||.|-|+|+.||+.+..|+||||..
T Consensus 10 eeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~-wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV 85 (269)
T COG1093 10 EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASG-WVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRV 85 (269)
T ss_pred CCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHH-HHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhC
Confidence 48999999999999999999997 479999999999998 888999999999999999999999999999999863
No 62
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=98.78 E-value=2.8e-08 Score=92.79 Aligned_cols=71 Identities=13% Similarity=0.247 Sum_probs=62.2
Q ss_pred CCeEEEEEEEEEecccEEEEeCC-CeEEEEeceecCCCcccc----------CcccccCCCCEEEEEEEEEeCCCcEEEE
Q 039337 846 EGRVVQATVRRVQGQRAICVLES-GLAGMLMKEDYSDDWRDS----------ELSDKLHEGDILTCKIKSIQKNRYQVFL 914 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~~-gi~GlIh~s~lsd~~~~~----------~~~~~~~vGq~V~vkVi~iD~~~~~I~L 914 (1344)
+|+++.|+|++|+++|+||+|.. +++|+||.++++++++.. ++...|++||.|+|+|+++|.++.++.|
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~ 80 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence 48899999999999999999987 899999999998763332 2346899999999999999999999999
Q ss_pred EE
Q 039337 915 VC 916 (1344)
Q Consensus 915 Sl 916 (1344)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 85
No 63
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.73 E-value=3.7e-08 Score=92.13 Aligned_cols=75 Identities=20% Similarity=0.272 Sum_probs=68.8
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
.++|++|.|+|+.|.+.+++|++..+.+|+||.++++.. ...++.+.|++||.|.|+|+++|.+ .++.||++..+
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~-~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~~ 78 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK-DKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADNE 78 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc-chHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCCC
Confidence 468999999999999999999999999999999999887 5667788899999999999999987 89999998754
No 64
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=98.73 E-value=3.9e-08 Score=93.28 Aligned_cols=75 Identities=15% Similarity=0.195 Sum_probs=64.7
Q ss_pred cccCCeEEEEEEEEEecc--cEEEEeCCCeEEEEeceecCCCc--cccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 843 TLAEGRVVQATVRRVQGQ--RAICVLESGLAGMLMKEDYSDDW--RDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~--g~fV~L~~gi~GlIh~s~lsd~~--~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
.+.+|+++.|+|++|.++ ||||+|+.|.+||+|+|++|+.. .+.++.+.+++||.|.|+|++......-..||..
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~ 82 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence 467999999999999996 99999999999999999998821 4567888999999999999998877766666654
No 65
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=98.72 E-value=4.3e-08 Score=120.52 Aligned_cols=21 Identities=5% Similarity=0.064 Sum_probs=10.8
Q ss_pred HHHHHHHHHhCCeEEEEcCCC
Q 039337 511 ERLLKFMMDHQPHVVVLGAVN 531 (1344)
Q Consensus 511 ~~l~~~i~~~~p~vIaIG~~t 531 (1344)
+.+.+.+..+.+.+|-.-.++
T Consensus 384 ~~i~q~v~dn~v~~I~getgc 404 (1282)
T KOG0921|consen 384 SEILQAVAENRVVIIKGETGC 404 (1282)
T ss_pred HHHHHHHhcCceeeEeecccc
Confidence 445666666655544443343
No 66
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.72 E-value=2.2e-08 Score=125.20 Aligned_cols=72 Identities=24% Similarity=0.257 Sum_probs=65.3
Q ss_pred cccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecC---CCccccCcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYS---DDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~ls---d~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
.+++|++|+|+|++|++||+||+|..|++||||+|+|+ +..++.++.+.|++||.|+|+|++||. +.+|+|+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 47899999999999999999999999999999999997 333778999999999999999999995 6788885
No 67
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.72 E-value=3.4e-08 Score=89.51 Aligned_cols=63 Identities=17% Similarity=0.342 Sum_probs=57.7
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCc-cccCcccccCCCCEEEEEEEEEeCCC
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDW-RDSELSDKLHEGDILTCKIKSIQKNR 909 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~-~~~~~~~~~~vGq~V~vkVi~iD~~~ 909 (1344)
|++|+|+|++|.++|+||.|+++++|+||++++++++ ...++.+.|++||.|+|+|+++|.++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 7899999999999999999999999999999999873 25678889999999999999999764
No 68
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.72 E-value=2.9e-08 Score=121.19 Aligned_cols=76 Identities=20% Similarity=0.306 Sum_probs=71.3
Q ss_pred cccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.+++|++|+|+|++|++||+||+|..|++||||+++|+++ +..++.+.|++||.|+|+|++||.++.+|.||+|..
T Consensus 290 ~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~-~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~ 365 (486)
T PRK07899 290 THAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAER-HVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQA 365 (486)
T ss_pred hcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcc-cccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEc
Confidence 4678999999999999999999999999999999999987 667888999999999999999999999999999954
No 69
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.71 E-value=3.8e-08 Score=111.29 Aligned_cols=75 Identities=21% Similarity=0.391 Sum_probs=69.7
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCC--CeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLES--GLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~--gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.++|++|.|+|++|.++|+||+|+. |++||||+|+++++ +..++.+.|++||.|.|+|+++|.++.+|.||++..
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~-~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v 82 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASG-WVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV 82 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcc-cccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence 4689999999999999999999974 89999999999988 777888999999999999999999999999999863
No 70
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.69 E-value=8.4e-08 Score=121.25 Aligned_cols=77 Identities=21% Similarity=0.338 Sum_probs=71.4
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccc-cCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRD-SELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~-~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
..+++|++|.|+|++|+++|+||+|+.+++|+||++++++. +. .++.+.|++||.|+|+|+++|.++.+|.||+|..
T Consensus 369 ~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~-~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~ 446 (565)
T PRK06299 369 EKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWD-KKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQL 446 (565)
T ss_pred HhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCcc-ccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehh
Confidence 45789999999999999999999999899999999999987 54 6888999999999999999999999999999864
No 71
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.67 E-value=1.1e-07 Score=87.87 Aligned_cols=67 Identities=16% Similarity=0.272 Sum_probs=60.5
Q ss_pred CcccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 840 TEDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 840 t~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
...++++|+++.|+|++++++|+||+++.+.+|++|.+++. +.+++||.|+|+|+++ .++.++.|++
T Consensus 10 ~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~---------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL---------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred chhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc---------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 45568999999999999999999999999999999999864 3489999999999999 8889999985
No 72
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=98.66 E-value=1.4e-07 Score=118.02 Aligned_cols=78 Identities=19% Similarity=0.317 Sum_probs=70.6
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
+.+.+|++|+|+|++++++|+||+|+.+++|+||.+++++.....++...|++||.|.|+|+++|.++.+|.||+|..
T Consensus 355 ~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~ 432 (516)
T TIGR00717 355 EKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQL 432 (516)
T ss_pred HhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccc
Confidence 357899999999999999999999999999999999999873344677889999999999999999999999999863
No 73
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=98.65 E-value=2.4e-08 Score=90.39 Aligned_cols=63 Identities=22% Similarity=0.355 Sum_probs=58.1
Q ss_pred ccccccccccccccccchhh-ccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhccCcEEE
Q 039337 652 VGLDINLAIHREWQFAPLQF-ISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAVGFLRV 719 (1344)
Q Consensus 652 vGVdiN~A~~~~~~~~~Lq~-v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI 719 (1344)
..||||+|.. ..|.. ++|||+.+|++||++|..+|.|.+.+||..++|||+++++....||.+
T Consensus 6 ~~invNta~~-----~~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v~gi~~~~~~~i~~~~~~ 69 (69)
T TIGR00426 6 TRVNINTATA-----EELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAVITL 69 (69)
T ss_pred CeeECcCCCH-----HHHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcCCCCCHHHHHHHHhhccC
Confidence 3599999998 68877 999999999999999999999999999999999999999999988753
No 74
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.58 E-value=1.4e-07 Score=113.94 Aligned_cols=79 Identities=24% Similarity=0.387 Sum_probs=73.2
Q ss_pred cccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 841 EDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 841 ~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
.+++++|++|+|+|+++.++|+||++++|++|++|++++++. +..++.+.|++||.|+|+|+++|.++.+|.||++...
T Consensus 272 ~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~-~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~ 350 (390)
T PRK06676 272 EEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHK-HIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALE 350 (390)
T ss_pred hhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCcc-ccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEecc
Confidence 347899999999999999999999999999999999999987 6678888999999999999999999999999998754
No 75
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.56 E-value=1.9e-07 Score=109.13 Aligned_cols=79 Identities=18% Similarity=0.150 Sum_probs=73.4
Q ss_pred CcccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 840 TEDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 840 t~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
....+++|++|+|+|.+|.++|+||+|+.+.+|+||.+++++. ++.++.+.|++||+|.|+|++++.++.++.||+|..
T Consensus 25 ~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~-~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~ 103 (318)
T PRK07400 25 YDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSIN-RVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRI 103 (318)
T ss_pred hHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc-cccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhh
Confidence 3345899999999999999999999998889999999999998 888999999999999999999999999999999974
No 76
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.56 E-value=1.6e-07 Score=82.52 Aligned_cols=65 Identities=20% Similarity=0.300 Sum_probs=59.5
Q ss_pred EEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 850 VQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 850 V~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
|.|+|+++.++|+||+++.+.+|++|.+++++. +..++.+.|++||.|+|+|+++|.++.++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~-~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCc-cccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 479999999999999999999999999999987 55677888999999999999999988888875
No 77
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=98.55 E-value=7.2e-08 Score=95.36 Aligned_cols=63 Identities=14% Similarity=0.237 Sum_probs=57.4
Q ss_pred ccccccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCH---HHHHhccCcEEEecCC
Q 039337 652 VGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGK---KVFVNAVGFLRVRRSG 723 (1344)
Q Consensus 652 vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~---kvf~n~a~FlrI~~~~ 723 (1344)
..||||+|+. ..|+.+||+||.+|++|| +||+|+|.+||++|+|||+ ++|+.-.+.+.+.+..
T Consensus 51 ~kIdiN~A~~-----~el~~lpGigP~~A~~IV----~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ftV~~p~ 116 (132)
T PRK02515 51 EKIDLNNSSV-----RAFRQFPGMYPTLAGKIV----KNAPYDSVEDVLNLPGLSERQKELLEANLDNFTVTEPE 116 (132)
T ss_pred CcccCCccCH-----HHHHHCCCCCHHHHHHHH----HCCCCCCHHHHHcCCCCCHHHHHHHHHhhcceeeCCch
Confidence 4699999999 789999999999999999 4999999999999999997 5899999999987654
No 78
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.51 E-value=6.1e-07 Score=114.69 Aligned_cols=77 Identities=29% Similarity=0.367 Sum_probs=71.3
Q ss_pred cccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 841 EDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 841 ~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.+.+++|++|.|+|+++.++|+||+| .+++|+||++++++. +..++.+.|++||.|+|+|+++|.++.+|.||+|..
T Consensus 472 ~~~l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~-~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~ 548 (647)
T PRK00087 472 WNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWG-RVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKL 548 (647)
T ss_pred HHhCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCcc-ccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeecc
Confidence 34578999999999999999999999 799999999999987 777899999999999999999999999999999863
No 79
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=98.50 E-value=2.7e-07 Score=115.48 Aligned_cols=75 Identities=25% Similarity=0.458 Sum_probs=71.3
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
+.+++|++|.|+|++++++|+||.|+.+++||||.++++++ ++.++.+.|++||.|+|+|+++|.++.+|.||+|
T Consensus 442 ~~~~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~-~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~k 516 (516)
T TIGR00717 442 AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSEN-RDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516 (516)
T ss_pred hccCcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCcc-ccccccccCCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 56889999999999999999999999999999999999998 7778999999999999999999999999999986
No 80
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=98.50 E-value=1.1e-06 Score=98.13 Aligned_cols=20 Identities=25% Similarity=0.404 Sum_probs=13.7
Q ss_pred HHHHHHHHhcCcc-----CccCCCC
Q 039337 806 LYLIRRELIHGFQ-----DWRNQYK 825 (1344)
Q Consensus 806 L~~I~~EL~~p~~-----D~R~~~~ 825 (1344)
|..+.-||.|||+ |+|..|.
T Consensus 76 lS~lL~El~CPy~eLt~Gdi~~Rf~ 100 (465)
T KOG3973|consen 76 LSTLLLELECPYEELTCGDIRTRFQ 100 (465)
T ss_pred HHHHHHHcCCchHhhccccHHHHHH
Confidence 4556789999987 4555554
No 81
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.44 E-value=4.5e-07 Score=109.52 Aligned_cols=76 Identities=25% Similarity=0.377 Sum_probs=70.8
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
..+++|++|+|+|+++.++|+||+++ +++|+||++++++. ++.++.+.|++||.|+|+|+++|.++.+|.||+|..
T Consensus 188 ~~~~~G~~v~g~V~~v~~~G~fV~l~-~v~g~v~~sels~~-~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~ 263 (390)
T PRK06676 188 SSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHE-RVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDT 263 (390)
T ss_pred hhCCCCCEEEEEEEEEecceEEEEeC-CeEEEEEHHHcCcc-ccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 45789999999999999999999995 79999999999997 778899999999999999999999999999999864
No 82
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.43 E-value=8.4e-07 Score=86.15 Aligned_cols=73 Identities=21% Similarity=0.312 Sum_probs=61.6
Q ss_pred eEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccC----------cccccCCCCEEEEEEEEEeCCC-----cEE
Q 039337 848 RVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSE----------LSDKLHEGDILTCKIKSIQKNR-----YQV 912 (1344)
Q Consensus 848 ~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~----------~~~~~~vGq~V~vkVi~iD~~~-----~~I 912 (1344)
++|.|+|+.|.++|+||+|+ +++|+||+++++++++..+ +...|++||.|+|+|.++|.+. .+|
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 47899999999999999998 5999999999988733322 3478999999999999999864 589
Q ss_pred EEEEecccc
Q 039337 913 FLVCRESEM 921 (1344)
Q Consensus 913 ~LSlk~~dl 921 (1344)
.||++...+
T Consensus 80 ~ls~k~~~~ 88 (99)
T cd04460 80 GLTMRQPGL 88 (99)
T ss_pred EEEEecCCC
Confidence 999987654
No 83
>smart00252 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
Probab=98.42 E-value=1e-06 Score=82.61 Aligned_cols=80 Identities=25% Similarity=0.397 Sum_probs=66.9
Q ss_pred CCCcc-cCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeeeCCccc
Q 039337 968 HPCFQ-NVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKIGEDTF 1046 (1344)
Q Consensus 968 HP~F~-n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i~~~~y 1046 (1344)
+|||+ +++-.+|+++|.+.+.|+++||+|+..++.++|+|++. +...|+.|...+. + .|.|+. ...|
T Consensus 1 ~~w~~g~i~r~~Ae~lL~~~~~G~FLvR~s~~~~~~~~Lsv~~~-~~~~h~~I~~~~~-~-----~~~l~~-----~~~F 68 (84)
T smart00252 1 QPWYHGFISREEAEKLLKNEGDGDFLVRDSESEPGDYVLSVRVK-GKVKHYRIRRNED-G-----KFYLDG-----GRKF 68 (84)
T ss_pred CCeecccCCHHHHHHHHhcCCCcEEEEEcCCCCCCCEEEEEEEC-CEEEEEEEEECCC-C-----cEEECC-----CCcc
Confidence 58888 89999999999999999999999999889999999987 6677998877553 2 244432 4899
Q ss_pred cchHHHHHHHHhh
Q 039337 1047 EDLDEVVDRYIDP 1059 (1344)
Q Consensus 1047 ~DLDEii~~~V~p 1059 (1344)
.+|.|||..|.++
T Consensus 69 ~sl~eLI~~y~~~ 81 (84)
T smart00252 69 PSLVELVEHYQKN 81 (84)
T ss_pred CCHHHHHHHHhhC
Confidence 9999999998764
No 84
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.40 E-value=7.1e-07 Score=114.14 Aligned_cols=78 Identities=26% Similarity=0.344 Sum_probs=72.8
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
+.+++|++|.|+|++|++||+||+|..+++||+|++++++. +..++.+.|++||.|+|+|+++|.++.++.||+|...
T Consensus 558 ~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~-~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~ 635 (647)
T PRK00087 558 EKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWK-RIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVE 635 (647)
T ss_pred hhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcc-ccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 45789999999999999999999999999999999999998 7778889999999999999999999999999998743
No 85
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=98.40 E-value=2.4e-06 Score=95.47 Aligned_cols=23 Identities=22% Similarity=0.518 Sum_probs=12.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC
Q 039337 1254 RQDSSYDTPKWDSANKSGDDSWG 1276 (1344)
Q Consensus 1254 ~g~gg~~~~~w~~~~~~g~~~~g 1276 (1344)
++++++..+.|-+|++=-|+||.
T Consensus 402 ~~~~~~~~qq~~sgsg~qg~g~~ 424 (465)
T KOG3973|consen 402 RDRSDRNDQQWISGSGVQGTGWN 424 (465)
T ss_pred CCcCCccccceeecccccCCccC
Confidence 44455555666665554466664
No 86
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.35 E-value=9.2e-07 Score=96.06 Aligned_cols=76 Identities=24% Similarity=0.312 Sum_probs=67.3
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeC----------CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcE
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLE----------SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQ 911 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~----------~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~ 911 (1344)
..+++|++|.|+|++|.++++||+|. .+++|+||++++++. ...++.+.|++||.|.|+|++++ .+
T Consensus 60 ~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~-~~~~~~~~~~~GD~V~akV~~i~---~~ 135 (189)
T PRK09521 60 PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDG-YVESLTDAFKIGDIVRAKVISYT---DP 135 (189)
T ss_pred CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChh-hhhhHHhccCCCCEEEEEEEecC---Cc
Confidence 45679999999999999999999984 368999999999987 56678889999999999999998 58
Q ss_pred EEEEEecccc
Q 039337 912 VFLVCRESEM 921 (1344)
Q Consensus 912 I~LSlk~~dl 921 (1344)
+.||+++..+
T Consensus 136 i~LS~k~~~l 145 (189)
T PRK09521 136 LQLSTKGKDL 145 (189)
T ss_pred EEEEEecCCc
Confidence 9999998654
No 87
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.29 E-value=1e-06 Score=112.65 Aligned_cols=70 Identities=23% Similarity=0.374 Sum_probs=64.4
Q ss_pred cccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEE
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFL 914 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~L 914 (1344)
.+++|++|.|+|++|.+||+||+|..+++||||+|++++. ++.++.+.|++||.|+|+|+++|. +.+|+|
T Consensus 615 ~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~-~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANE-RVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred ccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCC-cccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 4679999999999999999999999999999999999998 788899999999999999999997 566654
No 88
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.25 E-value=2.6e-06 Score=95.57 Aligned_cols=77 Identities=19% Similarity=0.195 Sum_probs=68.2
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccc----cCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRD----SELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~----~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
-..++|++|.|+|++|+++++||+|....+|+||++++++. ++ .++.+.|++||.|.|+|++++.++ .+.|||+
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~-~~~~d~~~~~~~~~~GDlV~akV~~i~~~~-~~~LS~k 136 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGR-PVNVEGTDLRKYLDIGDYIIAKVKDVDRTR-DVVLTLK 136 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCC-ccccchhhhHhhCCCCCEEEEEEEEECCCC-cEEEEEc
Confidence 34579999999999999999999999999999999999987 54 577888999999999999999764 5999998
Q ss_pred ccc
Q 039337 918 ESE 920 (1344)
Q Consensus 918 ~~d 920 (1344)
...
T Consensus 137 ~~~ 139 (235)
T PRK04163 137 GKG 139 (235)
T ss_pred CCC
Confidence 754
No 89
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.23 E-value=1.3e-06 Score=106.96 Aligned_cols=75 Identities=25% Similarity=0.362 Sum_probs=69.8
Q ss_pred ccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 842 DTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
..+++|+++.|+|++|.+||+||.|-.|.+|++|+|++++. ++....+.+++||.|.|||++||. +++|.||++.
T Consensus 615 ~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~-rv~kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~ 689 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKE-RVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKA 689 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhh-hhhcccceeecCceEEEEEeeecc-cCCccceehh
Confidence 45789999999999999999999999999999999999998 777888999999999999999995 5899999875
No 90
>PRK11642 exoribonuclease R; Provisional
Probab=98.13 E-value=6.5e-06 Score=106.87 Aligned_cols=74 Identities=12% Similarity=0.256 Sum_probs=65.6
Q ss_pred cCCeEEEEEEEEEecccEEEEeCCC-eEEEEeceecCCCccccCc----------ccccCCCCEEEEEEEEEeCCCcEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVLESG-LAGMLMKEDYSDDWRDSEL----------SDKLHEGDILTCKIKSIQKNRYQVF 913 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~g-i~GlIh~s~lsd~~~~~~~----------~~~~~vGq~V~vkVi~iD~~~~~I~ 913 (1344)
++|++++|+|++|++||+||+|+.+ ++|+||++++.+++|..+. ...|++||.|+|+|+++|.++.+|.
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~ 721 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID 721 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEE
Confidence 5799999999999999999999864 9999999999987555442 4679999999999999999999999
Q ss_pred EEEec
Q 039337 914 LVCRE 918 (1344)
Q Consensus 914 LSlk~ 918 (1344)
|++..
T Consensus 722 f~l~~ 726 (813)
T PRK11642 722 FSLIS 726 (813)
T ss_pred EEEec
Confidence 99863
No 91
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.09 E-value=1.1e-05 Score=86.89 Aligned_cols=77 Identities=19% Similarity=0.286 Sum_probs=64.3
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCc----------ccccCCCCEEEEEEEEEe-----CC
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSEL----------SDKLHEGDILTCKIKSIQ-----KN 908 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~----------~~~~~vGq~V~vkVi~iD-----~~ 908 (1344)
-.+|+++.|+|++++++|+||+|+ .++|++|.+++.++....++ ...+++||.|+++|++++ ++
T Consensus 79 p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~ 157 (179)
T TIGR00448 79 PELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE 157 (179)
T ss_pred ccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence 347999999999999999999995 49999999999876332233 367999999999999999 45
Q ss_pred CcEEEEEEecccc
Q 039337 909 RYQVFLVCRESEM 921 (1344)
Q Consensus 909 ~~~I~LSlk~~dl 921 (1344)
..+|.||+|+.-|
T Consensus 158 ~~~I~lt~k~~~L 170 (179)
T TIGR00448 158 GSKIGLTMRQPLL 170 (179)
T ss_pred cceEEEEeccCcC
Confidence 6789999998654
No 92
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.05 E-value=2.3e-05 Score=70.55 Aligned_cols=63 Identities=24% Similarity=0.382 Sum_probs=53.9
Q ss_pred cCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCC--cEEEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNR--YQVFLV 915 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~--~~I~LS 915 (1344)
++|++|+|+|.++.++++||+++ +.+|++|.++++. .+.+++||.|+|.|++++.++ .+|.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~~-------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQIP-------GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCCC-------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 47999999999999999999996 4999999999864 346899999999999999654 457666
No 93
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.04 E-value=1.3e-05 Score=104.02 Aligned_cols=72 Identities=13% Similarity=0.170 Sum_probs=63.2
Q ss_pred cCCeEEEEEEEEEecccEEEEeCC-CeEEEEeceecCCCcccc----------CcccccCCCCEEEEEEEEEeCCCcEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVLES-GLAGMLMKEDYSDDWRDS----------ELSDKLHEGDILTCKIKSIQKNRYQVF 913 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~-gi~GlIh~s~lsd~~~~~----------~~~~~~~vGq~V~vkVi~iD~~~~~I~ 913 (1344)
++|++++|+|++|++||+||+|+. +++|+||+++++++++.. +....|++||.|+|+|++||..+.+|.
T Consensus 626 ~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~ 705 (709)
T TIGR02063 626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKID 705 (709)
T ss_pred cCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeEE
Confidence 479999999999999999999987 899999999999764322 234679999999999999999999999
Q ss_pred EEE
Q 039337 914 LVC 916 (1344)
Q Consensus 914 LSl 916 (1344)
|++
T Consensus 706 ~~l 708 (709)
T TIGR02063 706 FEL 708 (709)
T ss_pred EEE
Confidence 986
No 94
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.00 E-value=1.8e-05 Score=75.87 Aligned_cols=76 Identities=25% Similarity=0.381 Sum_probs=64.0
Q ss_pred ccCCeEEEEEEEEEecccEEEEe--------CCCeEEEEeceecCCCcccc--CcccccCCCCEEEEEEEEEeCCCcEEE
Q 039337 844 LAEGRVVQATVRRVQGQRAICVL--------ESGLAGMLMKEDYSDDWRDS--ELSDKLHEGDILTCKIKSIQKNRYQVF 913 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L--------~~gi~GlIh~s~lsd~~~~~--~~~~~~~vGq~V~vkVi~iD~~~~~I~ 913 (1344)
.++|++|.|+|++|+...+.|+| .....|++|++++... +.. ++.+.|++||.|+|+|++++.. ..+.
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~-~~d~~~~~~~f~~GDiV~AkVis~~~~-~~~~ 81 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRAT-EKDKVEMYKCFRPGDIVRAKVISLGDA-SSYY 81 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHcccc-ccchHHHHhhcCCCCEEEEEEEEcCCC-CCcE
Confidence 47999999999999999999999 6677999999998875 333 5678899999999999999753 4588
Q ss_pred EEEecccc
Q 039337 914 LVCRESEM 921 (1344)
Q Consensus 914 LSlk~~dl 921 (1344)
||+++.++
T Consensus 82 Lst~~~~l 89 (92)
T cd05791 82 LSTAENEL 89 (92)
T ss_pred EEecCCCC
Confidence 99887654
No 95
>cd00173 SH2 Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
Probab=97.99 E-value=3.6e-05 Score=73.51 Aligned_cols=77 Identities=23% Similarity=0.306 Sum_probs=63.7
Q ss_pred ccCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeeeCCccccchHH
Q 039337 972 QNVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKIGEDTFEDLDE 1051 (1344)
Q Consensus 972 ~n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i~~~~y~DLDE 1051 (1344)
-+++-.+|+++|.+.+.|+++||+|+...+.++++++..+ ...|+.|...+... . +...+..|.+|.|
T Consensus 5 g~i~r~~Ae~~L~~~~~G~FLiR~s~~~~~~~~Lsv~~~~-~v~H~~I~~~~~~~-------~----~~~~~~~f~sl~e 72 (94)
T cd00173 5 GPISREEAEELLKKKPDGTFLVRDSESSPGDYVLSVRVKG-KVKHYRIERTDDGY-------Y----LLGEGRSFPSLPE 72 (94)
T ss_pred cCCCHHHHHHHHhcCCCceEEEEecCCCCCCEEEEEEECC-EEEEEEEEECCCCe-------E----EecCCCccCCHHH
Confidence 3789999999999999999999999988899999999987 66799987765432 1 1224689999999
Q ss_pred HHHHHHhhh
Q 039337 1052 VVDRYIDPL 1060 (1344)
Q Consensus 1052 ii~~~V~pm 1060 (1344)
||..|...-
T Consensus 73 Lv~~y~~~~ 81 (94)
T cd00173 73 LIEHYQKNP 81 (94)
T ss_pred HHHHHhhCc
Confidence 999987754
No 96
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=97.97 E-value=2.1e-05 Score=100.77 Aligned_cols=71 Identities=14% Similarity=0.257 Sum_probs=63.1
Q ss_pred CCeEEEEEEEEEecccEEEEeC-CCeEEEEeceecCCCccccC----------cccccCCCCEEEEEEEEEeCCCcEEEE
Q 039337 846 EGRVVQATVRRVQGQRAICVLE-SGLAGMLMKEDYSDDWRDSE----------LSDKLHEGDILTCKIKSIQKNRYQVFL 914 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~-~gi~GlIh~s~lsd~~~~~~----------~~~~~~vGq~V~vkVi~iD~~~~~I~L 914 (1344)
+|++++|+|++|++||+||+|+ .+++|+||++++.++++..+ ....|++||.|+|+|++||.++.+|.+
T Consensus 572 iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f 651 (654)
T TIGR00358 572 VGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSIIF 651 (654)
T ss_pred CCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEEE
Confidence 6999999999999999999997 88999999999998744332 236799999999999999999999999
Q ss_pred EE
Q 039337 915 VC 916 (1344)
Q Consensus 915 Sl 916 (1344)
++
T Consensus 652 ~l 653 (654)
T TIGR00358 652 EL 653 (654)
T ss_pred EE
Confidence 85
No 97
>smart00732 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.
Probab=97.83 E-value=0.00012 Score=70.58 Aligned_cols=93 Identities=28% Similarity=0.413 Sum_probs=65.5
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEc-----CCCcch
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLG-----AVNLSC 534 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG-----~~t~s~ 534 (1344)
+|||| |+|.+.++++++|++|++++..+.... . +..+..+.|.+++.+++|+.|+|| ++....
T Consensus 2 ~ilgi--D~Ggt~i~~a~~d~~g~~~~~~~~~~~--~--------~~~~~~~~l~~~i~~~~~~~i~Ig~pg~v~g~~~~ 69 (99)
T smart00732 2 RVLGL--DPGRKGIGVAVVDETGKLADPLEVIPR--T--------NKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASR 69 (99)
T ss_pred cEEEE--ccCCCeEEEEEECCCCCEecCEEEEEe--c--------CcchHHHHHHHHHHHhCCCEEEEeCCcCCCCCcCH
Confidence 58888 999999999999999999986553221 0 123457889999999999999999 554321
Q ss_pred hhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHh
Q 039337 535 TSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYE 577 (1344)
Q Consensus 535 ~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~ 577 (1344)
... . -+.+.+++. ..++|.++||+.++.|+
T Consensus 70 -~~~---~-~l~~~l~~~--------~~~pv~~~nDa~st~~a 99 (99)
T smart00732 70 -ETE---E-AFAELLKER--------FNLPVVLVDERLATVYA 99 (99)
T ss_pred -HHH---H-HHHHHHHHh--------hCCcEEEEeCCcccccC
Confidence 111 1 222333321 25899999999999875
No 98
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.83 E-value=4.8e-05 Score=80.21 Aligned_cols=76 Identities=22% Similarity=0.302 Sum_probs=62.5
Q ss_pred cCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCc----------ccccCCCCEEEEEEEEEeCCC-----
Q 039337 845 AEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSEL----------SDKLHEGDILTCKIKSIQKNR----- 909 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~----------~~~~~vGq~V~vkVi~iD~~~----- 909 (1344)
..|.+|.|.|+.+..||+||.|+ -++||||++++.|+.+..++ ...+++||.|++||+.+....
T Consensus 80 ~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~ 158 (183)
T COG1095 80 FRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRE 158 (183)
T ss_pred ccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcccc
Confidence 36999999999999999999998 58999999999998332222 236999999999999988765
Q ss_pred cEEEEEEecccc
Q 039337 910 YQVFLVCRESEM 921 (1344)
Q Consensus 910 ~~I~LSlk~~dl 921 (1344)
-+|.|||++.-|
T Consensus 159 ~~I~lTmrq~~L 170 (183)
T COG1095 159 SKIGLTMRQPGL 170 (183)
T ss_pred ceEEEEeccccC
Confidence 578888887543
No 99
>PF00017 SH2: SH2 domain; InterPro: IPR000980 The Src homology 2 (SH2) domain is a protein domain of about 100 amino-acid residues first identified as a conserved sequence region between the oncoproteins Src and Fps []. Similar sequences were later found in many other intracellular signal-transducing proteins []. SH2 domains function as regulatory modules of intracellular signalling cascades by interacting with high affinity to phosphotyrosine-containing target peptides in a sequence-specific, SH2 domains recognise between 3-6 residues C-terminal to the phosphorylated tyrosine in a fashion that differs from one SH2 domain to another, and strictly phosphorylation-dependent manner [, , , ]. They are found in a wide variety of protein contexts e.g., in association with catalytic domains of phospholipase Cy (PLCy) and the non-receptor protein tyrosine kinases; within structural proteins such as fodrin and tensin; and in a group of small adaptor molecules, i.e Crk and Nck. The domains are frequently found as repeats in a single protein sequence and will then often bind both mono- and di-phosphorylated substrates. The structure of the SH2 domain belongs to the alpha+beta class, its overall shape forming a compact flattened hemisphere. The core structural elements comprise a central hydrophobic anti-parallel beta-sheet, flanked by 2 short alpha-helices. The loop between strands 2 and 3 provides many of the binding interactions with the phosphate group of its phosphopeptide ligand, and is hence designated the phosphate binding loop, the phosphorylated ligand binds perpendicular to the beta-sheet and typically interacts with the phosphate binding loop and a hydrophobic binding pocket that interacts with a pY+3 side chain. The N- and C-termini of the domain are close together in space and on the opposite face from the phosphopeptide binding surface and it has been speculated that this has facilitated their integration into surface-exposed regions of host proteins [].; GO: 0005515 protein binding; PDB: 1M27_A 1KA6_A 1D4W_B 1D4T_A 1D1Z_B 1KA7_A 1UUR_A 1UUS_A 1BLJ_A 1BLK_A ....
Probab=97.74 E-value=0.00011 Score=67.78 Aligned_cols=74 Identities=24% Similarity=0.329 Sum_probs=60.9
Q ss_pred cccCCHHHHHHHhhc-CCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeeeCCccccch
Q 039337 971 FQNVTADEAMKLLSA-KEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKIGEDTFEDL 1049 (1344)
Q Consensus 971 F~n~~~~qAe~~L~~-~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i~~~~y~DL 1049 (1344)
+-+++-.+|+++|.. .+.|.++||||+..+..++++|+..+ -..|+.|...+... +- ..++..|.+|
T Consensus 3 ~g~isr~~Ae~~L~~~~~~G~FLvR~s~~~~~~~~Lsv~~~~-~v~h~~I~~~~~~~------~~-----~~~~~~F~sl 70 (77)
T PF00017_consen 3 HGFISRQEAERLLMQGKPDGTFLVRPSSSKPGKYVLSVRFDG-KVKHFRINRTENGG------YF-----LSDGKKFPSL 70 (77)
T ss_dssp EESSHHHHHHHHHHTTSSTTEEEEEEESSSTTSEEEEEEETT-EEEEEEEEEETTSE------EE-----SSTSSEBSSH
T ss_pred CCCCCHHHHHHHHHhcCCCCeEEEEecccccccccccccccc-ccEEEEEEecCCce------EE-----ccCCCcCCCH
Confidence 456788899999999 99999999999988889999999998 66799998876541 22 2345789999
Q ss_pred HHHHHHH
Q 039337 1050 DEVVDRY 1056 (1344)
Q Consensus 1050 DEii~~~ 1056 (1344)
.|||.-|
T Consensus 71 ~~LV~~y 77 (77)
T PF00017_consen 71 SDLVEHY 77 (77)
T ss_dssp HHHHHHH
T ss_pred HHHHHhC
Confidence 9999765
No 100
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=97.70 E-value=2.9e-05 Score=100.19 Aligned_cols=79 Identities=20% Similarity=0.297 Sum_probs=74.4
Q ss_pred cccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 841 EDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 841 ~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
.+...+|+++.|+|.++.++|+||...+|++||.+.+.++|+ ++.++++-|.+||+|.|+|.++|.++.+|-|+|+.+.
T Consensus 594 ~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~-~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~ 672 (1710)
T KOG1070|consen 594 FEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDD-FVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASS 672 (1710)
T ss_pred hhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhh-hhcChhhhcccccEEEEEEEecCchhceeehhhhhhh
Confidence 345669999999999999999999999999999999999999 9999999999999999999999999999999999764
No 101
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.70 E-value=0.00014 Score=79.08 Aligned_cols=77 Identities=21% Similarity=0.267 Sum_probs=63.6
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCcccc----------CcccccCCCCEEEEEEEEEeCCC----
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDS----------ELSDKLHEGDILTCKIKSIQKNR---- 909 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~----------~~~~~~~vGq~V~vkVi~iD~~~---- 909 (1344)
..+|++|.|+|+++.++|+||+|+ .++|++|.+++++++... +....+++||.|+++|++++.+.
T Consensus 79 P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~ 157 (187)
T PRK08563 79 PELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPR 157 (187)
T ss_pred ccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence 458999999999999999999998 499999999998762222 23457899999999999999764
Q ss_pred -cEEEEEEecccc
Q 039337 910 -YQVFLVCRESEM 921 (1344)
Q Consensus 910 -~~I~LSlk~~dl 921 (1344)
.+|.||++..-|
T Consensus 158 ~~~I~ls~~~~~L 170 (187)
T PRK08563 158 GSKIGLTMRQPGL 170 (187)
T ss_pred CCEEEEEecCCCC
Confidence 489999987543
No 102
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=97.67 E-value=0.00011 Score=95.17 Aligned_cols=83 Identities=18% Similarity=0.336 Sum_probs=79.0
Q ss_pred CcccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 840 TEDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 840 t~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
+.++|++|++|.|.|.+|.+.|+|+.|..+++++++++++++. +.+.++..|.+|+.|.++|.+++....++.|+++.+
T Consensus 1156 s~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds-~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s 1234 (1710)
T KOG1070|consen 1156 SIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDS-FEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNS 1234 (1710)
T ss_pred chhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccc-hhhhhhccCCccceeeeEEEEeeccCceEEEEEecc
Confidence 4789999999999999999999999999999999999999999 888999999999999999999999999999999998
Q ss_pred cccc
Q 039337 920 EMRN 923 (1344)
Q Consensus 920 dl~~ 923 (1344)
++.+
T Consensus 1235 ~~~d 1238 (1710)
T KOG1070|consen 1235 DIKD 1238 (1710)
T ss_pred ccCC
Confidence 8765
No 103
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.52 E-value=0.00023 Score=87.06 Aligned_cols=68 Identities=19% Similarity=0.334 Sum_probs=61.5
Q ss_pred CCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCc--EEEEEEecccc
Q 039337 846 EGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRY--QVFLVCRESEM 921 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~--~I~LSlk~~dl 921 (1344)
+|++|+|+|.++.++|+||+|+ |++|++|.++++ |.+.|++||.|+|.|++|+.++. +|.||.+..++
T Consensus 134 ~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~i-------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p~~ 203 (470)
T PRK09202 134 VGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQI-------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEF 203 (470)
T ss_pred cCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHcC-------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcHHH
Confidence 8999999999999999999995 899999999874 56789999999999999999877 99999887643
No 104
>KOG0790 consensus Protein tyrosine phosphatase Corkscrew and related SH2 domain enzymes [Signal transduction mechanisms]
Probab=97.49 E-value=0.00098 Score=77.68 Aligned_cols=165 Identities=24% Similarity=0.383 Sum_probs=116.5
Q ss_pred cccCCHHHHHHHhhcC-CCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeeeCCccccch
Q 039337 971 FQNVTADEAMKLLSAK-EPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKIGEDTFEDL 1049 (1344)
Q Consensus 971 F~n~~~~qAe~~L~~~-~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i~~~~y~DL 1049 (1344)
+.+++-.+||++|..+ --|+++.|||.+.+...++..+..|.+- ||.|...+.. |+| .+++.|..|
T Consensus 8 h~~~~g~~ae~Ll~~~g~dgsfl~r~s~sNp~~fsl~~r~~~~v~-hikiq~~~~~-------~~l-----~~gekfat~ 74 (600)
T KOG0790|consen 8 HPDLSGVEAETLLKERGVDGSFLARPSESNPGDFSLSVRRGDKVT-HIKIQNSGDF-------YDL-----YGGEKFATL 74 (600)
T ss_pred CCCccchhHHHHHHHhccccchhhccccCCCcceeEEEEeCCceE-EEEEeecCcc-------ccc-----cCCccccch
Confidence 3468999999999988 4799999999999999899888888775 9998875532 333 368999999
Q ss_pred HHHHHHHHhhhHHHHHH---HhhC------------cccccC--CHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEE
Q 039337 1050 DEVVDRYIDPLVSHLKA---MLSY------------RKFRKG--SKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFIL 1112 (1344)
Q Consensus 1050 DEii~~~V~pm~~~v~~---i~~h------------~kf~~g--~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L 1112 (1344)
-||+.-|.+-- ..+++ ..-+ +.|.+| +-.+.|++| .++-+|. .|-.--|..|||-|+|
T Consensus 75 ~ELvqyyme~~-~~lkekng~~ielK~pl~cAdptserWfHG~LsgkeAekLl-~ekgk~g---sfLvReSqs~PGdfVl 149 (600)
T KOG0790|consen 75 AELVQYYMEHH-GQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLL-QEKGKHG---SFLVRESQSHPGDFVL 149 (600)
T ss_pred HHHHHHHHhhh-HHHHhcCCCEEEecCCCccCCchhhhhhccCCCchhHHHHH-HhcCCCc---cEEEeccccCCCceEE
Confidence 99987665533 11121 1112 223344 347888888 4444443 3666668899999999
Q ss_pred EEecCC-------CCceeeEEEecCceEEc---ccccccHHHHHHHHHhhc
Q 039337 1113 TYIRST-------NPHHEYIGLYPKGFKFR---KRMFEDIDRLVAYFQRHI 1153 (1344)
Q Consensus 1113 ~~~~~~-------~~~~e~i~v~p~gf~~~---~~~~~~~~~L~~~fK~~~ 1153 (1344)
+..... +...-+|++.-++-+|. +..|.++.+|++.||++.
T Consensus 150 SvrTdd~~~~~~~~~kVtHvmI~~q~~kydVGgge~F~sltdLidhykknp 200 (600)
T KOG0790|consen 150 SVRTDDKKESNDSKLKVTHVMIRCQEGKYDVGGGERFDSLTDLVEHYKKNP 200 (600)
T ss_pred EEEcCCcccCCCCccceEEEEEEecccccccCCccccchHHHHHHHhccCc
Confidence 999642 12333444544445554 789999999999999875
No 105
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.33 E-value=0.00021 Score=85.11 Aligned_cols=76 Identities=20% Similarity=0.253 Sum_probs=67.3
Q ss_pred CcccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 840 TEDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 840 t~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
...+|..|-+++|+|+.+.++|+||.|-.+..||+|.|+++.. .+.+|++.+.+||.|+|+.++.|... .+-|+.|
T Consensus 662 ~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e-~iakpsd~levGq~I~vk~ie~d~~g-~~~ls~r 737 (760)
T KOG1067|consen 662 QVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQE-KIAKPSDLLEVGQEIQVKYIERDPRG-GIMLSSR 737 (760)
T ss_pred cccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccc-cccChHHHHhhcceeEEEEEeecCcc-ceeehhh
Confidence 4557889999999999999999999999999999999999998 78899999999999999999999754 4444443
No 106
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.25 E-value=0.001 Score=70.43 Aligned_cols=78 Identities=23% Similarity=0.279 Sum_probs=67.2
Q ss_pred CcccccCCeEEEEEEEEEecccEEEEe----CC------CeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCC
Q 039337 840 TEDTLAEGRVVQATVRRVQGQRAICVL----ES------GLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNR 909 (1344)
Q Consensus 840 t~~~l~~G~iV~g~V~~V~~~g~fV~L----~~------gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~ 909 (1344)
++..+++|++|-|.|+++....+.|++ +. -..|-||+|++++. +..+.++.|++||+|+|+|++.-
T Consensus 58 ~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~-~~~~~~d~f~~GDivrA~Vis~~--- 133 (188)
T COG1096 58 TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDG-YVEKLSDAFRIGDIVRARVISTG--- 133 (188)
T ss_pred CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccc-cccccccccccccEEEEEEEecC---
Confidence 477899999999999999999988876 21 14789999999998 88889999999999999999985
Q ss_pred cEEEEEEecccc
Q 039337 910 YQVFLVCRESEM 921 (1344)
Q Consensus 910 ~~I~LSlk~~dl 921 (1344)
..+.||.+..|+
T Consensus 134 ~~~~Lst~~~dl 145 (188)
T COG1096 134 DPIQLSTKGNDL 145 (188)
T ss_pred CCeEEEecCCcc
Confidence 578899988764
No 107
>PRK05054 exoribonuclease II; Provisional
Probab=97.12 E-value=0.0013 Score=84.30 Aligned_cols=70 Identities=10% Similarity=0.071 Sum_probs=58.4
Q ss_pred CeEEEEEEEEEecccEEEEe-CCCeEEEEeceecCCCc--ccc--Cc-------ccccCCCCEEEEEEEEEeCCCcEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVL-ESGLAGMLMKEDYSDDW--RDS--EL-------SDKLHEGDILTCKIKSIQKNRYQVFL 914 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L-~~gi~GlIh~s~lsd~~--~~~--~~-------~~~~~vGq~V~vkVi~iD~~~~~I~L 914 (1344)
|..+.|+|++|++||+||+| +.+++|+||++.|.+++ +.. +. ...|++||.|+|+|.+||..+.+|.+
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~ 641 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIA 641 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEE
Confidence 45999999999999999999 46799999999998742 211 11 24799999999999999999999988
Q ss_pred EE
Q 039337 915 VC 916 (1344)
Q Consensus 915 Sl 916 (1344)
++
T Consensus 642 ~~ 643 (644)
T PRK05054 642 RP 643 (644)
T ss_pred EE
Confidence 75
No 108
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.10 E-value=0.0011 Score=60.98 Aligned_cols=69 Identities=17% Similarity=0.224 Sum_probs=61.1
Q ss_pred cCCeEEEEEEEEEecccEEEEe-CCCeEEEEe-ceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVL-ESGLAGMLM-KEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L-~~gi~GlIh-~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
.+|+++. .|+.|.+.|++|.| +-+++|+|. .++++-+ +.....+.+ +|-++.|+|+.+|++++.|+||.
T Consensus 15 ~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~-rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 15 NINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNAD-RAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred CCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHH-HHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 4789998 89999999999987 557999998 8899887 666777888 99999999999999999999984
No 109
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=97.02 E-value=0.0016 Score=60.85 Aligned_cols=61 Identities=26% Similarity=0.413 Sum_probs=41.6
Q ss_pred cCCeEEEEEEEEEecccEEEEeC-C-----------------CeEEEEeceecCCCcccc-CcccccCCCCEEEEEEEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVLE-S-----------------GLAGMLMKEDYSDDWRDS-ELSDKLHEGDILTCKIKSI 905 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~-~-----------------gi~GlIh~s~lsd~~~~~-~~~~~~~vGq~V~vkVi~i 905 (1344)
++|++|.|+|++|+...|.|.|- . ...|+||++++.....++ .+.+.|++||+|+|+|+++
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence 58999999999999999998762 1 247999999987642222 5678899999999999974
No 110
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=96.92 E-value=0.0044 Score=58.95 Aligned_cols=62 Identities=16% Similarity=0.158 Sum_probs=51.6
Q ss_pred CCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCc-----------ccccCCCCEEEEEEEEEeCCC
Q 039337 846 EGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSEL-----------SDKLHEGDILTCKIKSIQKNR 909 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~-----------~~~~~vGq~V~vkVi~iD~~~ 909 (1344)
+|++|.|+|+++..+|+||.++ .+++|+|.+.++++ +..+| ...+.+|+.|++||+.+..+.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~-~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 73 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSD-MEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDA 73 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCcc-ceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEcc
Confidence 4899999999999999999986 58899999999876 44443 234899999999999987654
No 111
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=96.84 E-value=0.0025 Score=81.55 Aligned_cols=69 Identities=9% Similarity=0.087 Sum_probs=57.1
Q ss_pred CeEEEEEEEEEecccEEEEe-CCCeEEEEeceecCC--CccccCc---------ccccCCCCEEEEEEEEEeCCCcEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVL-ESGLAGMLMKEDYSD--DWRDSEL---------SDKLHEGDILTCKIKSIQKNRYQVFL 914 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L-~~gi~GlIh~s~lsd--~~~~~~~---------~~~~~vGq~V~vkVi~iD~~~~~I~L 914 (1344)
|..+.|+|+.|+.||+||+| ++|++|+||++.+.+ +.+..+. ...|++||.|+|+|.+||.++.+|.+
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~ 637 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA 637 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence 45899999999999999999 678999999999977 3232221 12699999999999999999998876
Q ss_pred E
Q 039337 915 V 915 (1344)
Q Consensus 915 S 915 (1344)
.
T Consensus 638 ~ 638 (639)
T TIGR02062 638 R 638 (639)
T ss_pred e
Confidence 4
No 112
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.84 E-value=0.0037 Score=73.80 Aligned_cols=69 Identities=25% Similarity=0.379 Sum_probs=58.9
Q ss_pred cCCeEEEEEEEEEeccc-EEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCC--CcEEEEEEecccc
Q 039337 845 AEGRVVQATVRRVQGQR-AICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKN--RYQVFLVCRESEM 921 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g-~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~--~~~I~LSlk~~dl 921 (1344)
++|++|+|+|.++.+.| ++|+|+ +++|++|.++++ |.+.|++||.|+|.|++|+.+ ...|.||.+..++
T Consensus 130 k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i-------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~~~ 201 (341)
T TIGR01953 130 KEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI-------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEF 201 (341)
T ss_pred hcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC-------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcHHH
Confidence 58999999999999988 699995 899999998875 345699999999999999955 4679999887654
No 113
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.78 E-value=0.0043 Score=56.23 Aligned_cols=68 Identities=18% Similarity=0.175 Sum_probs=58.2
Q ss_pred CeEEEEEEEEEecccEEEEeC-CCeEEEEeceecCCCccccCc--ccccCCCCEE-EEEEEEEeCCCcEEEEEEe
Q 039337 847 GRVVQATVRRVQGQRAICVLE-SGLAGMLMKEDYSDDWRDSEL--SDKLHEGDIL-TCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~-~gi~GlIh~s~lsd~~~~~~~--~~~~~vGq~V-~vkVi~iD~~~~~I~LSlk 917 (1344)
|++|+|+|..-++.+++|+|. .++.|+|+..++||. ...++ -..+++||++ .+.|+ +..++.|.||.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~-~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDH-VSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCc-hhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 789999999999999999995 489999999999994 55543 3569999999 89999 878888888865
No 114
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.77 E-value=0.0061 Score=57.56 Aligned_cols=73 Identities=16% Similarity=0.195 Sum_probs=61.3
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
-++|++|-|+|+.+.....+|+|.+-..|++|...+... .+..+..+++||.|.|+|.++|.. ..+.|||..+
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga--tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~~ 76 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA--TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVDS 76 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc--cccccccCCCCCEEEEEEEecCCC-CCeEEEEeCC
Confidence 358999999999999999999999888999999877543 223455799999999999999976 5689999864
No 115
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.67 E-value=0.0053 Score=72.88 Aligned_cols=68 Identities=18% Similarity=0.283 Sum_probs=57.9
Q ss_pred cCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCC--cEEEEEEeccc
Q 039337 845 AEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNR--YQVFLVCRESE 920 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~--~~I~LSlk~~d 920 (1344)
++|++|+|+|.++.++++||+|+ +++|++|.+++. |.+.|++||.|+|.|++|+.+. -.|.||....+
T Consensus 133 k~GeiV~G~V~~~~~~~~~Vdlg-~vEa~LP~~E~i-------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~p~ 202 (362)
T PRK12327 133 REGDIVTGVVQRRDNRFVYVNLG-KIEAVLPPAEQI-------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTHPG 202 (362)
T ss_pred hcCCEEEEEEEEEeCCcEEEEeC-CeEEEecHHHcC-------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCCHH
Confidence 79999999999999999999996 599999987664 4567999999999999999654 46888877554
No 116
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=96.54 E-value=0.0053 Score=79.82 Aligned_cols=74 Identities=19% Similarity=0.249 Sum_probs=63.2
Q ss_pred cCCeEEEEEEEEEecccEEEEeCC-CeEEEEeceecCCCccccCc----------ccccCCCCEEEEEEEEEeCCCcEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVLES-GLAGMLMKEDYSDDWRDSEL----------SDKLHEGDILTCKIKSIQKNRYQVF 913 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~-gi~GlIh~s~lsd~~~~~~~----------~~~~~vGq~V~vkVi~iD~~~~~I~ 913 (1344)
++|+.+.|+|++|+.||+||.|.. +++|+||++.+.++++..++ ...+++||.|+|+|.+++....+|.
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~ 700 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKID 700 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccceE
Confidence 478999999999999999999965 59999999999986444433 2369999999999999999999999
Q ss_pred EEEec
Q 039337 914 LVCRE 918 (1344)
Q Consensus 914 LSlk~ 918 (1344)
+++..
T Consensus 701 ~~~v~ 705 (706)
T COG0557 701 FELVE 705 (706)
T ss_pred EEecC
Confidence 88643
No 117
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=96.38 E-value=0.0083 Score=66.89 Aligned_cols=64 Identities=22% Similarity=0.321 Sum_probs=57.4
Q ss_pred CCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 846 EGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.++.|+|+|-++...|.||-++++.-||||.|+.-. ..++|+.|+++|+.+.. ..++.||+++.
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~---------~prlG~~l~~rVi~~re-Dg~lnLSl~p~ 218 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSERFA---------EPRLGERLTARVIGVRE-DGKLNLSLRPR 218 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhcc---------cccCCceEEEEEEEEcc-CCeeecccccc
Confidence 489999999999999999999999999999887533 36889999999999987 78999999975
No 118
>cd00173 SH2 Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
Probab=96.30 E-value=0.015 Score=55.34 Aligned_cols=73 Identities=22% Similarity=0.306 Sum_probs=62.0
Q ss_pred CHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEEEEecCCCCceeeEEEecCceEEc--ccccccHHHHHHHHHhhcC
Q 039337 1077 SKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFILTYIRSTNPHHEYIGLYPKGFKFR--KRMFEDIDRLVAYFQRHID 1154 (1344)
Q Consensus 1077 ~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~~e~i~v~p~gf~~~--~~~~~~~~~L~~~fK~~~~ 1154 (1344)
++++++++|.. . .--.|.+=.+...|+.|.|++.-+..+.|-.|...++||.+. ...|+||.+||++++.+.-
T Consensus 8 ~r~~Ae~~L~~----~-~~G~FLiR~s~~~~~~~~Lsv~~~~~v~H~~I~~~~~~~~~~~~~~~f~sl~eLv~~y~~~~~ 82 (94)
T cd00173 8 SREEAEELLKK----K-PDGTFLVRDSESSPGDYVLSVRVKGKVKHYRIERTDDGYYLLGEGRSFPSLPELIEHYQKNPL 82 (94)
T ss_pred CHHHHHHHHhc----C-CCceEEEEecCCCCCCEEEEEEECCEEEEEEEEECCCCeEEecCCCccCCHHHHHHHHhhCcc
Confidence 68999999965 2 223566666777899999999998888999999999999999 8999999999999997764
No 119
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.29 E-value=0.013 Score=64.73 Aligned_cols=77 Identities=18% Similarity=0.211 Sum_probs=65.8
Q ss_pred cccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCcc---ccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWR---DSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~---~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.-++|++|-|.|..|...+..|+|.+-..+++|.|++....+ ..+++..|++||.|.|+|..+|.+ ..+.|+||..
T Consensus 61 iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~-~~~~L~~k~~ 139 (239)
T COG1097 61 IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRD-GEVELTLKDE 139 (239)
T ss_pred cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCC-CceEEEeecC
Confidence 456899999999999999999999999999999999854422 246778899999999999999975 6899999764
Q ss_pred c
Q 039337 920 E 920 (1344)
Q Consensus 920 d 920 (1344)
.
T Consensus 140 ~ 140 (239)
T COG1097 140 G 140 (239)
T ss_pred C
Confidence 4
No 120
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.19 E-value=0.016 Score=62.24 Aligned_cols=74 Identities=8% Similarity=0.078 Sum_probs=57.1
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCc------------ccccCCCCEEEEEEEEEeCCC--
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSEL------------SDKLHEGDILTCKIKSIQKNR-- 909 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~------------~~~~~vGq~V~vkVi~iD~~~-- 909 (1344)
...|++|.|+|++++++|+||.++. ++++||.++|.++ ...++ ...++.|+.|++||+.+..+.
T Consensus 79 Pf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~-~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~ 156 (176)
T PTZ00162 79 PFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPD-FVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN 156 (176)
T ss_pred cCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCc-cEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence 3479999999999999999999963 5699999999865 22221 346899999999999886543
Q ss_pred cEEEEEEecc
Q 039337 910 YQVFLVCRES 919 (1344)
Q Consensus 910 ~~I~LSlk~~ 919 (1344)
..+-.|||+.
T Consensus 157 ~~~i~T~~~~ 166 (176)
T PTZ00162 157 LFAIATINSD 166 (176)
T ss_pred cEEEEEecCC
Confidence 4455677654
No 121
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=96.09 E-value=0.013 Score=71.08 Aligned_cols=64 Identities=16% Similarity=0.264 Sum_probs=52.9
Q ss_pred cccCCeEEEEEEEEEecc--cEEEEeCCCeEEEEeceecCCCc-----------cccCcccccCCCCEEEEEEEEEe
Q 039337 843 TLAEGRVVQATVRRVQGQ--RAICVLESGLAGMLMKEDYSDDW-----------RDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~--g~fV~L~~gi~GlIh~s~lsd~~-----------~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
...+|.|+.|+|++|.++ +|||+|+.+..||+|.+++.... ...++.+.+++||.|.|.|++--
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~ 98 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEP 98 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCC
Confidence 345899999999999998 99999999999999999986420 12244567999999999999843
No 122
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=96.07 E-value=0.046 Score=56.54 Aligned_cols=96 Identities=20% Similarity=0.242 Sum_probs=67.0
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEc-----CCCcch
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLG-----AVNLSC 534 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG-----~~t~s~ 534 (1344)
++||| |+|..-|=+|+-|..|.+.--+ ..+... ......+.|.+++.+++|+.|||| +|+.+.
T Consensus 5 ~iLal--D~G~kriGvAv~d~~~~~a~pl--~~i~~~--------~~~~~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~ 72 (138)
T PRK00109 5 RILGL--DVGTKRIGVAVSDPLGGTAQPL--ETIKRN--------NGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGP 72 (138)
T ss_pred cEEEE--EeCCCEEEEEEecCCCCEEcCE--EEEEcC--------CCchHHHHHHHHHHHhCCCEEEEeccCCCCCCcCH
Confidence 79998 8888666678899988775321 111111 112347889999999999999999 887664
Q ss_pred hhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhh
Q 039337 535 TSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYEN 578 (1344)
Q Consensus 535 ~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~ 578 (1344)
..+.+..|+.++.+. .+++|+++||...+.-+.
T Consensus 73 --~~~~v~~f~~~L~~~---------~~~~v~~~DEr~TT~~A~ 105 (138)
T PRK00109 73 --RTERARKFANRLEGR---------FGLPVVLVDERLSTVEAE 105 (138)
T ss_pred --HHHHHHHHHHHHHHH---------hCCCEEEEcCCcCHHHHH
Confidence 344566777666532 158999999998864443
No 123
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.03 E-value=0.0037 Score=68.78 Aligned_cols=74 Identities=18% Similarity=0.211 Sum_probs=67.5
Q ss_pred ccCCeEEEEEEEEEecccEEEEeC--CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLE--SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~--~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
-.++++|.+.|+.|.+-|++|.|- +.++|+|-.|++|.. ++...+..+++|-.=-|.|+.||++++.|+||.+.
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrR-RIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrr 89 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRR-RIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRR 89 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHH-HHHHHHHHHhcCCcceEEEEEEcCCCCceechhcc
Confidence 348999999999999999999983 568999999999988 78888899999999999999999999999999774
No 124
>smart00252 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
Probab=96.03 E-value=0.029 Score=52.47 Aligned_cols=72 Identities=22% Similarity=0.265 Sum_probs=59.0
Q ss_pred CHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEEEEecCCCCceeeEEEec-CceEEcc-cccccHHHHHHHHHhhc
Q 039337 1077 SKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFILTYIRSTNPHHEYIGLYP-KGFKFRK-RMFEDIDRLVAYFQRHI 1153 (1344)
Q Consensus 1077 ~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~~e~i~v~p-~gf~~~~-~~~~~~~~L~~~fK~~~ 1153 (1344)
++++++++|.. .| --.|.+=.+...||.|.|+++-+..+.|-.|.-++ .+|.+.+ ..|+||.+||++|+++.
T Consensus 9 ~r~~Ae~lL~~----~~-~G~FLvR~s~~~~~~~~Lsv~~~~~~~h~~I~~~~~~~~~l~~~~~F~sl~eLI~~y~~~~ 82 (84)
T smart00252 9 SREEAEKLLKN----EG-DGDFLVRDSESEPGDYVLSVRVKGKVKHYRIRRNEDGKFYLDGGRKFPSLVELVEHYQKNS 82 (84)
T ss_pred CHHHHHHHHhc----CC-CcEEEEEcCCCCCCCEEEEEEECCEEEEEEEEECCCCcEEECCCCccCCHHHHHHHHhhCC
Confidence 68999999954 33 33566666777799999999998778888888777 6799996 99999999999998753
No 125
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=95.92 E-value=0.0063 Score=73.61 Aligned_cols=73 Identities=16% Similarity=0.280 Sum_probs=65.0
Q ss_pred CCcccccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 839 ETEDTLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 839 et~~~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
.+.++++.|.++.|+|++|..+|+||+|+..+.||+|.++++.. ..+.+|+.|-|.|..|-.++..|+|....
T Consensus 115 c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~-------~~~~vgdeiiV~v~~vr~~~geidf~~~~ 187 (715)
T COG1107 115 CTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD-------PDYAVGDEIIVQVSDVRPEKGEIDFEPVG 187 (715)
T ss_pred cchhhcccceeeeccccchhhhcceeecChhhhccccccccCCC-------CCCCCCCeEEEEeeccCCCCCccceeecC
Confidence 47889999999999999999999999999999999999999874 14789999999999999887888776554
No 126
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=95.80 E-value=0.33 Score=62.56 Aligned_cols=55 Identities=20% Similarity=0.369 Sum_probs=28.6
Q ss_pred ccCCeEEEEEEEEEecccEEE-EeCCCeEEEEece--ecCCCcccc---CcccccCCCCEEEE
Q 039337 844 LAEGRVVQATVRRVQGQRAIC-VLESGLAGMLMKE--DYSDDWRDS---ELSDKLHEGDILTC 900 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV-~L~~gi~GlIh~s--~lsd~~~~~---~~~~~~~vGq~V~v 900 (1344)
|.+|+.|..++-........| .++ |-.-+|..+ .+.+. +.. .+.+.|++||.|+|
T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~vd-g~~vti~~~~e~l~~p-l~~~~~eLrKyF~~GDhVKV 468 (1024)
T KOG1999|consen 408 FSPGDAVEVIVGELKGLKGKVESVD-GTIVTIMSKHEDLKGP-LEVPASELRKYFEPGDHVKV 468 (1024)
T ss_pred cCCCCeEEEeeeeeccceeEEEecc-CceEEEeeccccCCCc-cccchHhhhhhccCCCeEEE
Confidence 778888877665555433333 233 222222211 22221 222 34567999999887
No 127
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=95.73 E-value=0.14 Score=60.58 Aligned_cols=49 Identities=10% Similarity=-0.054 Sum_probs=23.1
Q ss_pred eEEEecCceEEccc--ccccHHHHHHHHHhhcCCCCCCCCCCcccccCcCCCCCCC
Q 039337 1124 YIGLYPKGFKFRKR--MFEDIDRLVAYFQRHIDDPQGDSAPSIRSVAAMVPMRSPA 1177 (1344)
Q Consensus 1124 ~i~v~p~gf~~~~~--~~~~~~~L~~~fK~~~~d~~P~a~p~~~~v~~~~~~r~p~ 1177 (1344)
+|+|.-.-.-|-++ .--+.++|+|-- -..|+.+.+++..++++.+.++.
T Consensus 390 ~VTI~K~~l~y~~reGe~ity~e~vnr~-----~~~~p~r~s~a~gs~~pn~atgg 440 (607)
T COG5164 390 FVTIEKSRLAYLGREGEGITYDELVNRR-----GLSKPLRYSEAIGSKTPNYATGG 440 (607)
T ss_pred eEEeehhheEEecccccccchhhhhhhh-----cCCCcccccccccCCCCCccccc
Confidence 45554443333322 344566777642 22333444555555555554443
No 128
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=95.51 E-value=0.13 Score=52.75 Aligned_cols=94 Identities=15% Similarity=0.194 Sum_probs=63.8
Q ss_pred eEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEc-----CCCcchhh
Q 039337 462 LACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLG-----AVNLSCTS 536 (1344)
Q Consensus 462 lai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG-----~~t~s~~~ 536 (1344)
||| |+|..-|=+|+-|..|.+.--+. .+..+ ......+.|.+++++++|+.|||| +|+.+.
T Consensus 1 lai--D~G~kriGvA~~d~~~~~a~pl~--~i~~~--------~~~~~~~~l~~~i~~~~~~~iVvGlP~~~dG~~~~-- 66 (130)
T TIGR00250 1 LGL--DFGTKSIGVAGQDITGWTAQGIP--TIKAQ--------DGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGP-- 66 (130)
T ss_pred CeE--ccCCCeEEEEEECCCCCEEeceE--EEEec--------CCcHHHHHHHHHHHHcCCCEEEEeccCCCCcCcCH--
Confidence 455 88876566788899887752111 11111 113456889999999999999999 888765
Q ss_pred hHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhh
Q 039337 537 LKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYEN 578 (1344)
Q Consensus 537 l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~ 578 (1344)
..+.+.+|+.++.+. . .++|.++||...++-+.
T Consensus 67 ~a~~v~~f~~~L~~~--------~-~~~v~~~DEr~TT~~A~ 99 (130)
T TIGR00250 67 LTERAQKFANRLEGR--------F-GVPVVLWDERLSTVEAE 99 (130)
T ss_pred HHHHHHHHHHHHHHH--------h-CCCEEEEcCCcCHHHHH
Confidence 344566777666432 1 58999999998875443
No 129
>PF00017 SH2: SH2 domain; InterPro: IPR000980 The Src homology 2 (SH2) domain is a protein domain of about 100 amino-acid residues first identified as a conserved sequence region between the oncoproteins Src and Fps []. Similar sequences were later found in many other intracellular signal-transducing proteins []. SH2 domains function as regulatory modules of intracellular signalling cascades by interacting with high affinity to phosphotyrosine-containing target peptides in a sequence-specific, SH2 domains recognise between 3-6 residues C-terminal to the phosphorylated tyrosine in a fashion that differs from one SH2 domain to another, and strictly phosphorylation-dependent manner [, , , ]. They are found in a wide variety of protein contexts e.g., in association with catalytic domains of phospholipase Cy (PLCy) and the non-receptor protein tyrosine kinases; within structural proteins such as fodrin and tensin; and in a group of small adaptor molecules, i.e Crk and Nck. The domains are frequently found as repeats in a single protein sequence and will then often bind both mono- and di-phosphorylated substrates. The structure of the SH2 domain belongs to the alpha+beta class, its overall shape forming a compact flattened hemisphere. The core structural elements comprise a central hydrophobic anti-parallel beta-sheet, flanked by 2 short alpha-helices. The loop between strands 2 and 3 provides many of the binding interactions with the phosphate group of its phosphopeptide ligand, and is hence designated the phosphate binding loop, the phosphorylated ligand binds perpendicular to the beta-sheet and typically interacts with the phosphate binding loop and a hydrophobic binding pocket that interacts with a pY+3 side chain. The N- and C-termini of the domain are close together in space and on the opposite face from the phosphopeptide binding surface and it has been speculated that this has facilitated their integration into surface-exposed regions of host proteins [].; GO: 0005515 protein binding; PDB: 1M27_A 1KA6_A 1D4W_B 1D4T_A 1D1Z_B 1KA7_A 1UUR_A 1UUS_A 1BLJ_A 1BLK_A ....
Probab=95.44 E-value=0.047 Score=50.24 Aligned_cols=69 Identities=20% Similarity=0.298 Sum_probs=55.9
Q ss_pred CHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEEEEecCCCCceeeEEEecCc-eEEc-ccccccHHHHHHHH
Q 039337 1077 SKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFILTYIRSTNPHHEYIGLYPKG-FKFR-KRMFEDIDRLVAYF 1149 (1344)
Q Consensus 1077 ~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~~e~i~v~p~g-f~~~-~~~~~~~~~L~~~f 1149 (1344)
++++++++|.. . ..--.|.+=.+...||.|.|++..+.+++|-.|..+++| |.+. +..|+||.+||++|
T Consensus 7 sr~~Ae~~L~~-~---~~~G~FLvR~s~~~~~~~~Lsv~~~~~v~h~~I~~~~~~~~~~~~~~~F~sl~~LV~~y 77 (77)
T PF00017_consen 7 SRQEAERLLMQ-G---KPDGTFLVRPSSSKPGKYVLSVRFDGKVKHFRINRTENGGYFLSDGKKFPSLSDLVEHY 77 (77)
T ss_dssp HHHHHHHHHHT-T---SSTTEEEEEEESSSTTSEEEEEEETTEEEEEEEEEETTSEEESSTSSEBSSHHHHHHHH
T ss_pred CHHHHHHHHHh-c---CCCCeEEEEeccccccccccccccccccEEEEEEecCCceEEccCCCcCCCHHHHHHhC
Confidence 67899999964 1 222346565677799999999999988999999999999 5554 58899999999986
No 130
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=94.96 E-value=0.077 Score=62.92 Aligned_cols=68 Identities=18% Similarity=0.325 Sum_probs=57.3
Q ss_pred cCCeEEEEEEEEEecc-cEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCc---EEEEEEeccc
Q 039337 845 AEGRVVQATVRRVQGQ-RAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRY---QVFLVCRESE 920 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~-g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~---~I~LSlk~~d 920 (1344)
++|++|+|+|.++... .++|+|+ +.+|+++.++.. |.+.|++||.|+|.|.+|+.... .|-||....+
T Consensus 137 ~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqi-------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p~ 208 (374)
T PRK12328 137 KVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRI-------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSRTSPK 208 (374)
T ss_pred hcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcC-------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcCCHH
Confidence 5899999999999864 5899997 799999977643 56789999999999999998765 7888877654
No 131
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=94.51 E-value=0.22 Score=51.39 Aligned_cols=95 Identities=17% Similarity=0.215 Sum_probs=62.7
Q ss_pred eEeEeecCCCCCceEEEEECCCCCE---EEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCCc---c
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEV---VDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVNL---S 533 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~v---ld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t~---s 533 (1344)
|+||| |.|..-|=+|+-|..+.+ +.++.... .....+.|.+++++++|+.||||.-.. +
T Consensus 2 riL~l--D~G~kriGiAvsd~~~~~a~pl~~i~~~~-------------~~~~~~~l~~li~~~~i~~iVvGlP~~~~G~ 66 (135)
T PF03652_consen 2 RILGL--DYGTKRIGIAVSDPLGIIASPLETIPRRN-------------REKDIEELKKLIEEYQIDGIVVGLPLNMDGS 66 (135)
T ss_dssp EEEEE--EECSSEEEEEEEETTTSSEEEEEEEEECC-------------CCCCHHHHHHHHHHCCECEEEEEEEBBCTSS
T ss_pred eEEEE--EeCCCeEEEEEecCCCCeEeeeEEEECCC-------------CchHHHHHHHHHHHhCCCEEEEeCCcccCCC
Confidence 78998 888755667888998875 23332111 123567899999999999999997321 1
Q ss_pred hhhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHh
Q 039337 534 CTSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYE 577 (1344)
Q Consensus 534 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~ 577 (1344)
-....+.+.+|+.++.+. .++++|.++||...+.-+
T Consensus 67 ~~~~~~~v~~f~~~L~~~--------~~~ipV~~~DEr~TT~~A 102 (135)
T PF03652_consen 67 ESEQARRVRKFAEELKKR--------FPGIPVILVDERLTTKEA 102 (135)
T ss_dssp C-CCHHHHHHHHHHHHHH--------H-TSEEEEEECSCSHHCC
T ss_pred ccHHHHHHHHHHHHHHHh--------cCCCcEEEECCChhHHHH
Confidence 111234566677666543 136899999999875433
No 132
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=94.50 E-value=0.13 Score=53.75 Aligned_cols=77 Identities=22% Similarity=0.305 Sum_probs=58.5
Q ss_pred ccCCeEEEEEEEEEecccEEEEeC--------CCeEEEEeceecCCCcc-ccCcccccCCCCEEEEEEEEEeCCCcEEEE
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLE--------SGLAGMLMKEDYSDDWR-DSELSDKLHEGDILTCKIKSIQKNRYQVFL 914 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~--------~gi~GlIh~s~lsd~~~-~~~~~~~~~vGq~V~vkVi~iD~~~~~I~L 914 (1344)
-.+|.||.++|..|....|-|+|- .-..|+||..++-.... -.++-+.|++||+|.|+|++.+. ....-|
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y~L 144 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNYLL 144 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcEEE
Confidence 458999999999999998888762 23589999988755311 12456779999999999999654 346677
Q ss_pred EEecccc
Q 039337 915 VCRESEM 921 (1344)
Q Consensus 915 Slk~~dl 921 (1344)
|..+.||
T Consensus 145 TtAeneL 151 (193)
T KOG3409|consen 145 TTAENEL 151 (193)
T ss_pred EEecccc
Confidence 8777765
No 133
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=94.42 E-value=0.5 Score=59.69 Aligned_cols=22 Identities=9% Similarity=0.185 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHhcCChhHH
Q 039337 274 QAVLQGARHMAAVEISCEPCVR 295 (1344)
Q Consensus 274 e~vl~ga~~ilA~eis~dp~vR 295 (1344)
+..-.+.++.++..+.+||..+
T Consensus 168 ~~La~aLrYyI~~rLn~DPgWk 189 (931)
T KOG2044|consen 168 DRLAKALRYYIHDRLNSDPGWK 189 (931)
T ss_pred HHHHHHHHHHHHHhhcCCcccc
Confidence 4444677889999999998754
No 134
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.83 E-value=0.19 Score=60.56 Aligned_cols=69 Identities=22% Similarity=0.283 Sum_probs=56.4
Q ss_pred cCCeEEEEEEEEEecccEEEEeCC--C---eEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCC---cEEEEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVLES--G---LAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNR---YQVFLVC 916 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~--g---i~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~---~~I~LSl 916 (1344)
++|++|+|+|.++...+++|+|+. | ++|+++.++.. |.+.|++||.|+|.|.+|.... -+|.||.
T Consensus 151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi-------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR 223 (449)
T PRK12329 151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL-------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 223 (449)
T ss_pred hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC-------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence 489999999999999999999842 3 79999877642 5678999999999999998753 4688887
Q ss_pred eccc
Q 039337 917 RESE 920 (1344)
Q Consensus 917 k~~d 920 (1344)
....
T Consensus 224 t~p~ 227 (449)
T PRK12329 224 ANAG 227 (449)
T ss_pred CCHH
Confidence 6543
No 135
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=93.62 E-value=0.11 Score=49.58 Aligned_cols=47 Identities=21% Similarity=0.315 Sum_probs=38.6
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhcc-CCCHHHHHhcc
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAH-GLGKKVFVNAV 714 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~-~iG~kvf~n~a 714 (1344)
--|..|.|||+..|+.|++.|+ +|+|+|.+|+..-. ++...+++.++
T Consensus 27 ~gl~~Ikglg~~~a~~I~~~R~-~g~f~s~~df~~R~~~i~~~~le~Li 74 (90)
T PF14579_consen 27 LGLSAIKGLGEEVAEKIVEERE-NGPFKSLEDFIQRLPKINKRQLEALI 74 (90)
T ss_dssp -BGGGSTTS-HHHHHHHHHHHH-CSS-SSHHHHHHHS-TS-HHHHHHHH
T ss_pred ehHhhcCCCCHHHHHHHHHhHh-cCCCCCHHHHHHHHhcCCHHHHHHHH
Confidence 4689999999999999999998 99999999998766 88888888764
No 136
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=93.57 E-value=1.7 Score=56.47 Aligned_cols=9 Identities=22% Similarity=-0.009 Sum_probs=3.5
Q ss_pred ccceeeecc
Q 039337 76 DIPFIAMYR 84 (1344)
Q Consensus 76 eVPFIarYR 84 (1344)
..=||.+=+
T Consensus 64 ~~gf~~~e~ 72 (1024)
T KOG1999|consen 64 GGGFIDREA 72 (1024)
T ss_pred ccccccccc
Confidence 333443333
No 137
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=93.27 E-value=0.35 Score=42.79 Aligned_cols=61 Identities=15% Similarity=0.143 Sum_probs=33.8
Q ss_pred CCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 846 EGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
+|++.+.+|..+.++|+|++.+.+.+=++|.+++.. .+++||.|.|-|- .|.+. ++..|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~---------~~~~Gd~v~VFvY-~D~~~-rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPE---------PLKVGDEVEVFVY-LDKEG-RLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG---------------TTSEEEEEEE-E-TTS--EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCC---------CCCCCCEEEEEEE-ECCCC-CEEEecC
Confidence 588999999999999999988777889999887653 3789999999765 45443 5556553
No 138
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]
Probab=93.12 E-value=0.76 Score=47.63 Aligned_cols=103 Identities=19% Similarity=0.214 Sum_probs=66.5
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhH-HHHHHHHHHHHHhCCeEEEEcCCC-c--chh
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKK-NDQERLLKFMMDHQPHVVVLGAVN-L--SCT 535 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~i~~~~p~vIaIG~~t-~--s~~ 535 (1344)
++||+ |-|.--|=+|+-|..|.+.-= +.++.. +... .+.+.|.+++++++|+.||||--. + +..
T Consensus 3 ~ilal--D~G~KrIGvA~sd~~~~~A~p--l~~i~~--------~~~~~~~~~~l~~li~~~~~~~vVVGlP~~m~g~~~ 70 (141)
T COG0816 3 RILAL--DVGTKRIGVAVSDILGSLASP--LETIKR--------KNGKPQDFNALLKLVKEYQVDTVVVGLPLNMDGTEG 70 (141)
T ss_pred eEEEE--ecCCceEEEEEecCCCccccc--hhhhee--------ccccHhhHHHHHHHHHHhCCCEEEEecCcCCCCCcc
Confidence 78998 777655667788887744311 011111 1112 478899999999999999999522 2 222
Q ss_pred hhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhhhHHhh
Q 039337 536 SLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYENSRISS 583 (1344)
Q Consensus 536 ~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~s~~a~ 583 (1344)
...+.++.|...+.+. -+++|+++||....+........
T Consensus 71 ~~~~~~~~f~~~L~~r---------~~lpv~l~DERltTv~A~~~L~~ 109 (141)
T COG0816 71 PRAELARKFAERLKKR---------FNLPVVLWDERLSTVEAERMLIE 109 (141)
T ss_pred hhHHHHHHHHHHHHHh---------cCCCEEEEcCccCHHHHHHHHHH
Confidence 2334566676655443 25899999999998887664433
No 139
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=92.83 E-value=0.38 Score=51.28 Aligned_cols=65 Identities=20% Similarity=0.319 Sum_probs=45.0
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEE
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVL 527 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaI 527 (1344)
+|||| |||-+.|=+++|+.+|+-+..+..+.+...+.. ....|-..--+.|.++|.+|+||+|+|
T Consensus 3 ~iLGI--DPgl~~tG~avi~~~~~~~~~~~~G~i~t~~~~-~~~~Rl~~I~~~l~~~i~~~~Pd~vai 67 (164)
T PRK00039 3 RILGI--DPGLRRTGYGVIEVEGRRLSYVASGVIRTPSDL-DLPERLKQIYDGLSELIDEYQPDEVAI 67 (164)
T ss_pred EEEEE--ccccCceeEEEEEecCCeEEEEEeeEEECCCCC-CHHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 89999 999877778899888875444444444322111 112344444578999999999999998
No 140
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=91.98 E-value=0.55 Score=49.54 Aligned_cols=66 Identities=23% Similarity=0.340 Sum_probs=45.4
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEc
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLG 528 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG 528 (1344)
||||| |||-..+=+++++..+.-+..+....+...+.. ....+...-.+.|.++|..|+||+|+|=
T Consensus 1 rILGI--DPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~~-~~~~rl~~I~~~l~~~i~~~~Pd~vaiE 66 (154)
T cd00529 1 RILGI--DPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDA-PLPSRLKTIYDGLNEVIDQFQPDVVAIE 66 (154)
T ss_pred CEEEE--ccCcCceEEEEEEeeCCeEEEEEeeEEECCCCC-CHHHHHHHHHHHHHHHHHHhCCCEEEEE
Confidence 69999 999977778888866655555444554332111 1233445566789999999999999983
No 141
>PRK10811 rne ribonuclease E; Reviewed
Probab=91.83 E-value=0.34 Score=62.96 Aligned_cols=64 Identities=14% Similarity=0.311 Sum_probs=50.7
Q ss_pred cCCeEEEEEEEEEec--ccEEEEeCCCeEEEEeceecCCCcccc--------CcccccCCCCEEEEEEEEEeCC
Q 039337 845 AEGRVVQATVRRVQG--QRAICVLESGLAGMLMKEDYSDDWRDS--------ELSDKLHEGDILTCKIKSIQKN 908 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~--~g~fV~L~~gi~GlIh~s~lsd~~~~~--------~~~~~~~vGq~V~vkVi~iD~~ 908 (1344)
.+|.|+.|+|.+|.+ .++||+|+.|..||+|++++....+.. +....+++||.|-|.|.+--..
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~g 110 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG 110 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccC
Confidence 489999999999987 579999999999999999885431111 1245689999999999975544
No 142
>KOG1264 consensus Phospholipase C [Lipid transport and metabolism]
Probab=91.67 E-value=0.6 Score=58.79 Aligned_cols=89 Identities=18% Similarity=0.243 Sum_probs=69.5
Q ss_pred HHHhhCcccccCC---HHHHHHHHHHH-HHhCCCcceEEEEeCCCCCcEEEEEEecCCCCceeeEEEecCc----eEEc-
Q 039337 1065 KAMLSYRKFRKGS---KAEVDELLRIE-KAEFPTRIVYGFGISHEHPGTFILTYIRSTNPHHEYIGLYPKG----FKFR- 1135 (1344)
Q Consensus 1065 ~~i~~h~kf~~g~---~~e~e~~L~~~-~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~~e~i~v~p~g----f~~~- 1135 (1344)
.||-..+||.+|. +.+.+++|.+| +....+--.+-.--+.-.+|-|.|+|..+.+++|--|+.+-+| |+|-
T Consensus 528 ~ElH~~E~WFHgkle~R~eAekll~eycke~G~~dGtFlVReS~tFvgDytLSfwr~grv~HcRIrsk~e~gt~Kyyl~d 607 (1267)
T KOG1264|consen 528 TELHFGEKWFHGKLEGRTEAEKLLQEYCKETGGKDGTFLVRESETFVGDYTLSFWRSGRVQHCRIRSKMEGGTLKYYLTD 607 (1267)
T ss_pred hhhccchhhhhcccccchHHHHHHHHHHHHhCCCCccEEEeeccccccceeeeeeECCceeeEEEEeeecCCceeEEEec
Confidence 5666677777663 67999999999 5444333444444577899999999999999999999887665 5555
Q ss_pred ccccccHHHHHHHHHhhc
Q 039337 1136 KRMFEDIDRLVAYFQRHI 1153 (1344)
Q Consensus 1136 ~~~~~~~~~L~~~fK~~~ 1153 (1344)
+.+|.|+=+||.|+.+++
T Consensus 608 N~vfdslY~LI~~Y~~~~ 625 (1267)
T KOG1264|consen 608 NLVFDSLYALIQHYRETH 625 (1267)
T ss_pred chhHHHHHHHHHHHHhcc
Confidence 889999999999988765
No 143
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=91.54 E-value=0.13 Score=38.82 Aligned_cols=20 Identities=25% Similarity=0.504 Sum_probs=17.4
Q ss_pred cchhhccCCCHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRS 686 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~ 686 (1344)
..|..||||||.+|..|+.+
T Consensus 11 eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 11 EELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HHHHTSTT-SHHHHHHHHHH
T ss_pred HHHHhCCCcCHHHHHHHHhC
Confidence 79999999999999999875
No 144
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=91.45 E-value=0.1 Score=45.94 Aligned_cols=44 Identities=32% Similarity=0.534 Sum_probs=34.8
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHH--------HhhccCCCHHHHHhccC
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKD--------FVTAHGLGKKVFVNAVG 715 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~--------L~~v~~iG~kvf~n~a~ 715 (1344)
..|..|+||||+.|+.|+++ | |.|.++ |..++|||++.-++...
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~----G-~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEA----G-IKTLEDLANADPEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHT----T-CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHhc----C-CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHH
Confidence 46888999999999999876 3 666655 46689999998877653
No 145
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=90.70 E-value=0.56 Score=49.23 Aligned_cols=64 Identities=19% Similarity=0.354 Sum_probs=40.3
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEE
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVL 527 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaI 527 (1344)
|||| |||-..|=+++|+.+|.-+..+..+.+...+.. ...+|-..-.+.|.++|++|+|+.|||
T Consensus 1 ILGI--DPgl~~tG~avi~~~~~~~~~i~~G~I~t~~~~-~~~~Rl~~I~~~l~~li~~~~P~~vai 64 (149)
T PF02075_consen 1 ILGI--DPGLSNTGYAVIEEDGGKLRLIDYGTIKTSSKD-SLPERLKEIYEELEELIEEYNPDEVAI 64 (149)
T ss_dssp EEEE--E--SSEEEEEEEEEETTEEEEEEEEEEE---S---HHHHHHHHHHHHHHHHHHH--SEEEE
T ss_pred CEEE--CCCCCCeeEEEEEeeCCEEEEEEeCeEECCCCC-CHHHHHHHHHHHHHHHHHhhCCCEEEe
Confidence 7898 999977889999988876655554555433211 112344444567999999999999999
No 146
>PRK11712 ribonuclease G; Provisional
Probab=89.89 E-value=0.65 Score=57.71 Aligned_cols=65 Identities=17% Similarity=0.146 Sum_probs=50.1
Q ss_pred cccCCeEEEEEEEEEec--ccEEEEeCCCeEEEEeceecCCCc-c----------ccCcccccCCCCEEEEEEEEEeC
Q 039337 843 TLAEGRVVQATVRRVQG--QRAICVLESGLAGMLMKEDYSDDW-R----------DSELSDKLHEGDILTCKIKSIQK 907 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~--~g~fV~L~~gi~GlIh~s~lsd~~-~----------~~~~~~~~~vGq~V~vkVi~iD~ 907 (1344)
...+|.|+.|+|.+|.+ ..|||+|+.+..||+|.+++.... + ..+..+.+++||.|-|.|++--.
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~ 112 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPL 112 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCc
Confidence 34589999999999988 579999999999999999873210 0 11224569999999999997543
No 147
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=89.89 E-value=3.7 Score=52.17 Aligned_cols=48 Identities=19% Similarity=0.306 Sum_probs=39.0
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhc--CCCCCHHHHhhccCCCHHHHHhc
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRA--GAIFTRKDFVTAHGLGKKVFVNA 713 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~--g~~~sr~~L~~v~~iG~kvf~n~ 713 (1344)
+++.|--|+||||.+.++|+++...- =.-.|.+||.+| ||++++-+..
T Consensus 528 ~~s~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~v-gi~~~~a~~i 577 (581)
T COG0322 528 LQSSLDDIPGIGPKRRKALLKHFGSLKGIKSASVEELAKV-GISKKLAEKI 577 (581)
T ss_pred hcCccccCCCcCHHHHHHHHHHhhCHHHHHhcCHHHHHHc-CCCHHHHHHH
Confidence 45789999999999999999998642 245778999999 9998765544
No 148
>KOG1264 consensus Phospholipase C [Lipid transport and metabolism]
Probab=89.82 E-value=3.2 Score=52.66 Aligned_cols=163 Identities=21% Similarity=0.287 Sum_probs=114.0
Q ss_pred HHHHHHhhcC------CCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeeeCCccccchH
Q 039337 977 DEAMKLLSAK------EPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKIGEDTFEDLD 1050 (1344)
Q Consensus 977 ~qAe~~L~~~------~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i~~~~y~DLD 1050 (1344)
.+|++.|..+ +-|.+++|-|-.=..-.++.+ ..+|--||.-|.-.- +++ ++ +-+..+|..|+.|=
T Consensus 545 ~eAekll~eycke~G~~dGtFlVReS~tFvgDytLSf-wr~grv~HcRIrsk~-e~g------t~-Kyyl~dN~vfdslY 615 (1267)
T KOG1264|consen 545 TEAEKLLQEYCKETGGKDGTFLVRESETFVGDYTLSF-WRSGRVQHCRIRSKM-EGG------TL-KYYLTDNLVFDSLY 615 (1267)
T ss_pred hHHHHHHHHHHHHhCCCCccEEEeeccccccceeeee-eECCceeeEEEEeee-cCC------ce-eEEEecchhHHHHH
Confidence 3566666554 468999999987655546654 246666887775432 121 11 34556889999999
Q ss_pred HHHHHHHhhhHHHHH-HH-h-----------hCcccc-cCCHHHHHHHHHHHHHhCCCcceEEEEe-CCCCCcEEEEEEe
Q 039337 1051 EVVDRYIDPLVSHLK-AM-L-----------SYRKFR-KGSKAEVDELLRIEKAEFPTRIVYGFGI-SHEHPGTFILTYI 1115 (1344)
Q Consensus 1051 Eii~~~V~pm~~~v~-~i-~-----------~h~kf~-~g~~~e~e~~L~~~~~~np~~i~Y~f~~-~~~~PG~f~L~~~ 1115 (1344)
+||.-|-+.+.+-.+ +| + +-+-|. .-++++.|++|. .-|--- +|-+ +.+-|-.|.|+|.
T Consensus 616 ~LI~~Y~~~~Lr~aeF~m~LtePvPqp~~He~k~W~~as~treqAE~mL~----rvp~DG--aFLiR~~~~~nsy~iSfr 689 (1267)
T KOG1264|consen 616 ALIQHYRETHLRCAEFEMRLTEPVPQPNPHESKPWYHASLTREQAEDMLM----RVPRDG--AFLIRKREGSNSYAISFR 689 (1267)
T ss_pred HHHHHHHhccccccceEEEecCCCCCCCcccCCccccccccHHHHHHHHh----hCccCc--ceEEEeccCCceEEEEEE
Confidence 999999988876443 11 1 112232 237899999993 222212 3333 7889999999999
Q ss_pred cCCCCceeeEEEecCceEEcccccccHHHHHHHHHhhcC
Q 039337 1116 RSTNPHHEYIGLYPKGFKFRKRMFEDIDRLVAYFQRHID 1154 (1344)
Q Consensus 1116 ~~~~~~~e~i~v~p~gf~~~~~~~~~~~~L~~~fK~~~~ 1154 (1344)
.+.++.|.-|.-...-|.+....|.|+.+|++|+-+|.-
T Consensus 690 ~~gkikHcRi~rdGr~fvl~t~~FesLv~lv~yY~k~~l 728 (1267)
T KOG1264|consen 690 ARGKIKHCRINRDGRHFVLGTSAFESLVELVSYYEKHPL 728 (1267)
T ss_pred EcCcEeEEEEccCceEEEeccHHHHHHHHHHHHHhcChh
Confidence 998888888887777899999999999999999987753
No 149
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=89.37 E-value=2.6 Score=53.64 Aligned_cols=36 Identities=17% Similarity=0.298 Sum_probs=21.9
Q ss_pred ceEEEecCCCchHHhhhHHhhhcCCCCchhhHHHHHhhhhhcc
Q 039337 563 LSIVYGDESLPRLYENSRISSDQLPGQKGNVKRAVALGRYLQN 605 (1344)
Q Consensus 563 i~v~~v~~~~a~vy~~s~~a~~e~p~~~~~~R~avslaR~lqd 605 (1344)
-+++|++-.+-|=|---+. ..|++|- -++|-|-+-|
T Consensus 296 k~fifl~I~vLREYLe~El---~~p~lPf----~fd~ER~iDD 331 (931)
T KOG2044|consen 296 KPFIFLNISVLREYLEREL---RMPNLPF----TFDLERAIDD 331 (931)
T ss_pred cceEEEEHHHHHHHHHHHh---cCCCCCc----cccHHhhhcc
Confidence 4677777777777764433 4565553 3556666656
No 150
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=88.47 E-value=2.5 Score=54.25 Aligned_cols=52 Identities=23% Similarity=0.247 Sum_probs=41.5
Q ss_pred ccchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcE
Q 039337 666 FAPLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFL 717 (1344)
Q Consensus 666 ~~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~Fl 717 (1344)
.+.|..|+||||+++++|+++... +=.-.+.++|.+|+|||++..++...+|
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L 689 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHL 689 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHH
Confidence 379999999999999999998632 1122478889999999999988876654
No 151
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=88.43 E-value=1.4 Score=46.56 Aligned_cols=63 Identities=17% Similarity=0.316 Sum_probs=43.7
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEE
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVL 527 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaI 527 (1344)
|||| |||-..|=+++|+..|.-+..+....+...+. .-.+|-..=-+.|.++|.+|+|++++|
T Consensus 1 ILGI--DPGl~~tG~gvi~~~~~~~~~v~~G~I~t~~~--~~~~RL~~I~~~l~~~i~~y~P~~~ai 63 (156)
T TIGR00228 1 ILGI--DPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVD--DLPSRLKLIYAGVTEIITQFQPNYFAI 63 (156)
T ss_pred CEeE--CcccccccEEEEEecCCeEEEEEeeEEECCCC--CHHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 6898 99987777899987777655555555543321 112333444567999999999999998
No 152
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=87.97 E-value=1.6 Score=47.77 Aligned_cols=82 Identities=21% Similarity=0.316 Sum_probs=58.1
Q ss_pred ccccCCHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEEEEecCCCCceeeEEE--------ecCceEEcccccccHH
Q 039337 1072 KFRKGSKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFILTYIRSTNPHHEYIGL--------YPKGFKFRKRMFEDID 1143 (1344)
Q Consensus 1072 kf~~g~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~~e~i~v--------~p~gf~~~~~~~~~~~ 1143 (1344)
||-.-++.|..++|. ++-.-++-.-=+..-||-+.||.--++++-|--|.- .|-+|+...+.|++|.
T Consensus 14 Yfg~mSRqeA~~lL~-----~~r~G~FLvRDSst~pGdYvLsV~E~srVshYiIn~~~p~~~~~~~~~~rIgdQ~Fd~lP 88 (293)
T KOG4792|consen 14 YFGPMSRQEAVALLQ-----GQRHGVFLVRDSSTSPGDYVLSVSENSRVSHYIINSSPPSPAQPPPSRLRIGDQEFDSLP 88 (293)
T ss_pred ecCcccHHHHHHHhc-----CcceeeEEEecCCCCCCceEEEEecCcceeeeeecCCCCCccCCCcceeeeccccccchH
Confidence 444457899999993 444333333335556999999988776544432221 1458899999999999
Q ss_pred HHHHHHHhhcCCCCC
Q 039337 1144 RLVAYFQRHIDDPQG 1158 (1344)
Q Consensus 1144 ~L~~~fK~~~~d~~P 1158 (1344)
+|+++||-|+-|-.+
T Consensus 89 aLL~fykihyLdttt 103 (293)
T KOG4792|consen 89 ALLEFYKIHYLDTTT 103 (293)
T ss_pred HHHhheeEeeecccc
Confidence 999999999988554
No 153
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=87.81 E-value=6.8 Score=49.85 Aligned_cols=54 Identities=17% Similarity=0.187 Sum_probs=45.2
Q ss_pred cccchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcEE
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFLR 718 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~Flr 718 (1344)
+.+.|..|+||||.+.++|+++... +=.-.|.+||.+|+||++++-++...+|+
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAE 567 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4479999999999999999999853 33557889999999999999888877763
No 154
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.63 E-value=0.31 Score=53.37 Aligned_cols=48 Identities=25% Similarity=0.342 Sum_probs=38.0
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhcC---C--CCCHHHHhhccCCCHHHHHh
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRAG---A--IFTRKDFVTAHGLGKKVFVN 712 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~g---~--~~sr~~L~~v~~iG~kvf~n 712 (1344)
++.+|..|+|+||+.|.+|+......- . -.+.+.|.+++|||+|+-++
T Consensus 71 lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAer 123 (194)
T PRK14605 71 LFETLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASR 123 (194)
T ss_pred HHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHH
Confidence 447899999999999999999753211 1 24567788999999999998
No 155
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=87.54 E-value=0.19 Score=54.96 Aligned_cols=55 Identities=29% Similarity=0.320 Sum_probs=42.6
Q ss_pred ccchhhccCCCHHHHHHHHHHHHhcC-----CCCCHHHHhhccCCCHHHHHhccCcEEEe
Q 039337 666 FAPLQFISGLGPRKAASLQRSLVRAG-----AIFTRKDFVTAHGLGKKVFVNAVGFLRVR 720 (1344)
Q Consensus 666 ~~~Lq~v~GlGprkA~~ii~~r~~~g-----~~~sr~~L~~v~~iG~kvf~n~a~FlrI~ 720 (1344)
...|..|+||||++|.+|+++....- .-.+.++|.+++|||+|+-+.....|+-.
T Consensus 72 f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~ 131 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDK 131 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 36888899999999999998753210 12367889999999999998888776543
No 156
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=86.72 E-value=0.46 Score=45.13 Aligned_cols=62 Identities=16% Similarity=0.203 Sum_probs=44.5
Q ss_pred ccccccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCH---HHHHhccCcEEEecC
Q 039337 652 VGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGK---KVFVNAVGFLRVRRS 722 (1344)
Q Consensus 652 vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~---kvf~n~a~FlrI~~~ 722 (1344)
..||||.|.. ...+..||+=|..|..|++ ||++.|.+|+++++||.+ .+|+.-.+...+.+.
T Consensus 13 ~KIDlNNa~v-----r~f~~~pGmYPtlA~kIv~----naPY~sveDvl~ipgLse~qK~~lk~~~~~Ftv~~p 77 (93)
T PF06514_consen 13 QKIDLNNANV-----RAFRQFPGMYPTLAGKIVS----NAPYKSVEDVLNIPGLSERQKALLKKYEDNFTVTPP 77 (93)
T ss_dssp TCEETTSS-G-----GGGCCSTTTTCCHHHHHHH----S---SSGGGGCCSTT--HHHHHHHHHHGGGEE----
T ss_pred CceecccHhH-----HHHHHCCCCCHHHHHHHHh----CCCCCCHHHHHhccCCCHHHHHHHHHHhccceecCc
Confidence 3599999998 6888999999999999986 789999999999999976 667766666666543
No 157
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.71 E-value=0.49 Score=51.69 Aligned_cols=51 Identities=22% Similarity=0.225 Sum_probs=37.8
Q ss_pred cccchhhccCCCHHHHHHHHHHHH-----hcCCCCCHHHHhhccCCCHHHHHhccC
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLV-----RAGAIFTRKDFVTAHGLGKKVFVNAVG 715 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~-----~~g~~~sr~~L~~v~~iG~kvf~n~a~ 715 (1344)
++.+|..|+|+||+.|-+|+.... .-=.-.+.+.|.++||||+|+-++..-
T Consensus 70 lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 70 VFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 346899999999999999996431 101224556688899999999888763
No 158
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=86.56 E-value=0.89 Score=52.81 Aligned_cols=58 Identities=29% Similarity=0.339 Sum_probs=49.3
Q ss_pred ccCCCcccCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCC
Q 039337 966 IVHPCFQNVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKD 1025 (1344)
Q Consensus 966 I~HP~F~n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~ 1025 (1344)
..|.+++.++-.+||++|..++-|-++||-||+| +++++.+ |+++.-+|-.|.+-...
T Consensus 331 e~~w~~~~a~r~kAe~llrg~~dGtFLIR~ss~~-g~yalSV-~~~~~V~HClIy~tatG 388 (464)
T KOG4637|consen 331 EKTWRVRDANRDKAEELLRGKPDGTFLIRESSKG-GCYALSV-VHDGEVKHCLIYQTATG 388 (464)
T ss_pred hhHhHHhhhhHHHHHHHhcCCCCCeEEEeeccCC-CceEEEE-EECCceeeeEEeecccc
Confidence 4577888899999999999999999999999996 7878887 67788889888875543
No 159
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=86.31 E-value=0.23 Score=54.32 Aligned_cols=50 Identities=28% Similarity=0.379 Sum_probs=37.2
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhc---CCC--CCHHHHhhccCCCHHHHHhcc
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRA---GAI--FTRKDFVTAHGLGKKVFVNAV 714 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~---g~~--~sr~~L~~v~~iG~kvf~n~a 714 (1344)
++.+|..|+||||++|.+|+....-. -.+ .+...|.+++|||+|+-++..
T Consensus 70 lF~~L~~V~GIGpK~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 70 LFKELIKVNGVGPKLALAILSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHhCCCCCCHHHHHHHHhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 34688999999999999997753111 011 244567889999999999987
No 160
>KOG4226 consensus Adaptor protein NCK/Dock, contains SH2 and SH3 domains [Signal transduction mechanisms]
Probab=85.91 E-value=2.2 Score=47.78 Aligned_cols=81 Identities=26% Similarity=0.413 Sum_probs=61.6
Q ss_pred ccccCCC-cccCCHHHHHHHh-hcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeee
Q 039337 964 RLIVHPC-FQNVTADEAMKLL-SAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKI 1041 (1344)
Q Consensus 964 RvI~HP~-F~n~~~~qAe~~L-~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i 1041 (1344)
|+.-.|| |-+|+-.|||..| ..-.-||++||-|-..+.-+.|..|-... -.|+.|.-.+ + .+-|
T Consensus 277 ~~ag~~WYyG~itR~qae~~Ln~hG~eGdFLiRDSEsnpgD~SvSlka~gr-NKHFkVq~~d--~-----------~ycI 342 (379)
T KOG4226|consen 277 RFAGRPWYYGNITRHQAECALNEHGHEGDFLIRDSESNPGDFSVSLKASGR-NKHFKVQLVD--N-----------VYCI 342 (379)
T ss_pred cccCCcceeccccHHHHHHHHhccCccCceEEecCCCCCcceeEEeeccCC-CcceEEEEec--c-----------eEEe
Confidence 4555555 5799999999999 44578999999999889888999986543 3577665432 2 3567
Q ss_pred CCccccchHHHHHHHHh
Q 039337 1042 GEDTFEDLDEVVDRYID 1058 (1344)
Q Consensus 1042 ~~~~y~DLDEii~~~V~ 1058 (1344)
|..+|.++|||+..|-+
T Consensus 343 GqRkF~tmd~Lv~HY~k 359 (379)
T KOG4226|consen 343 GQRKFHTMDELVEHYKK 359 (379)
T ss_pred ccceeccHHHHHHhhhc
Confidence 78899999999877643
No 161
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=85.88 E-value=7.4 Score=50.04 Aligned_cols=49 Identities=14% Similarity=0.064 Sum_probs=40.4
Q ss_pred ccchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhcc
Q 039337 666 FAPLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAV 714 (1344)
Q Consensus 666 ~~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a 714 (1344)
.+.|..|+||||.++++|+++... +=.-.|.+||.+|+||++++.++..
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~ 657 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTIL 657 (691)
T ss_pred ccccccCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 378999999999999999999853 2345678999999999998877653
No 162
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=85.59 E-value=4.4 Score=42.49 Aligned_cols=61 Identities=16% Similarity=0.170 Sum_probs=41.6
Q ss_pred CCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCc-----------ccccCCCCEEEEEEEEEeCC
Q 039337 846 EGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSEL-----------SDKLHEGDILTCKIKSIQKN 908 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~-----------~~~~~vGq~V~vkVi~iD~~ 908 (1344)
.|++|.|+|+.|...|+|++++. ++-++..-.+..+ +..+| ..++++|..|+++|+.+..+
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd-~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~ 152 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPD-YEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVD 152 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCC-cccCCCCCCCcccccccceeeeCcEEEEEEEEEEEe
Confidence 69999999999999999998753 3333332222222 21111 23689999999999977554
No 163
>KOG0790 consensus Protein tyrosine phosphatase Corkscrew and related SH2 domain enzymes [Signal transduction mechanisms]
Probab=85.45 E-value=2.5 Score=50.44 Aligned_cols=81 Identities=27% Similarity=0.467 Sum_probs=65.4
Q ss_pred Ccc-cCCHHHHHHHh-hcCCCCcEEEecCCCCCCceEEEEEEeC--------ceeeEEEEeecCCCCcCcccccccCcee
Q 039337 970 CFQ-NVTADEAMKLL-SAKEPGESIIRPSSRGPSYLTLTLKVYD--------GVYAHKDIIEGGKDHKDIKSLVGIGKTL 1039 (1344)
Q Consensus 970 ~F~-n~~~~qAe~~L-~~~~~Gd~viRPSSkG~d~L~vTwKv~d--------~v~~HidV~E~~K~~~~~~~~~sLG~~L 1039 (1344)
||| |++-++||++| +.-+-|.+++|-|-..+.-+.+.++.+| .--.|+-|.-.++ .|.+|
T Consensus 112 WfHG~LsgkeAekLl~ekgk~gsfLvReSqs~PGdfVlSvrTdd~~~~~~~~~kVtHvmI~~q~~-------kydVG--- 181 (600)
T KOG0790|consen 112 WFHGHLSGKEAEKLLQEKGKHGSFLVRESQSHPGDFVLSVRTDDKKESNDSKLKVTHVMIRCQEG-------KYDVG--- 181 (600)
T ss_pred hhccCCCchhHHHHHHhcCCCccEEEeccccCCCceEEEEEcCCcccCCCCccceEEEEEEeccc-------ccccC---
Confidence 666 79999999999 6668999999999999999999999966 3667988887664 25555
Q ss_pred eeCCccccchHHHHHHHH-hhhHH
Q 039337 1040 KIGEDTFEDLDEVVDRYI-DPLVS 1062 (1344)
Q Consensus 1040 ~i~~~~y~DLDEii~~~V-~pm~~ 1062 (1344)
|++.|..|-+||..|= .||+.
T Consensus 182 --gge~F~sltdLidhykknpmvE 203 (600)
T KOG0790|consen 182 --GGERFDSLTDLVEHYKKNPMVE 203 (600)
T ss_pred --CccccchHHHHHHHhccCchhh
Confidence 6799999999998753 35543
No 164
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.85 E-value=0.37 Score=52.24 Aligned_cols=50 Identities=20% Similarity=0.250 Sum_probs=37.5
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhc---C--CCCCHHHHhhccCCCHHHHHhcc
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRA---G--AIFTRKDFVTAHGLGKKVFVNAV 714 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~---g--~~~sr~~L~~v~~iG~kvf~n~a 714 (1344)
++.+|..|+|+||+.|-+|+....-. . .=.+.+-|.++||||+|+-++..
T Consensus 71 lF~~Li~VsGIGpK~Al~ILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 71 MFEMLLKVNGIGANTAMAVCSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 34789999999999999998754211 1 12345667889999999988875
No 165
>PF03934 T2SK: Type II secretion system (T2SS), protein K; InterPro: IPR005628 Members of this family are involved in the general secretion pathway. The family includes proteins such as ExeK, PulK, OutX and XcpX.; GO: 0009306 protein secretion, 0016021 integral to membrane; PDB: 3CI0_K.
Probab=84.60 E-value=0.47 Score=55.02 Aligned_cols=66 Identities=18% Similarity=0.155 Sum_probs=39.1
Q ss_pred ccccccccccccccccccchhhccC-CCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCH-HHHHhccCcEEEec
Q 039337 650 NQVGLDINLAIHREWQFAPLQFISG-LGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGK-KVFVNAVGFLRVRR 721 (1344)
Q Consensus 650 n~vGVdiN~A~~~~~~~~~Lq~v~G-lGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~-kvf~n~a~FlrI~~ 721 (1344)
....||||+|.. .+|+-+.+ |.+..|+.||.+|..+ .|.+.+++...+.|+. .++......|.+..
T Consensus 181 ~~~~iNiNta~~-----~vL~Al~~~l~~~~a~~ii~~R~~~-~~~~~~d~~~~~~l~~~~~~~~~~~~l~v~S 248 (280)
T PF03934_consen 181 GGTKININTAPA-----EVLAALLPGLSESQAQAIIAARPEN-GFKSVDDFWAAPALSGSDQSAAIKPLLTVKS 248 (280)
T ss_dssp SS--EETTT-GT-----HHHHHHT---------HHHHT--TT---S-HHHHHTSGGGSS-HHHHHHHHHEES--
T ss_pred CCCccChhhCCH-----HHHHHhccCCCHHHHHHHHHhcccc-CCCCHHHHHhhhhccCcchhhhhcceeeecc
Confidence 467899999977 78886655 9999999999999544 7999999998877765 77777777777764
No 166
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.48 E-value=0.7 Score=50.79 Aligned_cols=50 Identities=30% Similarity=0.337 Sum_probs=36.9
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhc---C--CCCCHHHHhhccCCCHHHHHhcc
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRA---G--AIFTRKDFVTAHGLGKKVFVNAV 714 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~---g--~~~sr~~L~~v~~iG~kvf~n~a 714 (1344)
++.+|..|+||||+.|-+|+....-. - .=.+..-|.+++|+|+|+-++..
T Consensus 70 lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 70 LFELLLGVSGVGPKLALALLSALPPALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 45788999999999999998853110 0 12345567789999999988865
No 167
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=84.34 E-value=12 Score=48.11 Aligned_cols=52 Identities=19% Similarity=0.296 Sum_probs=42.5
Q ss_pred ccchhhccCCCHHHHHHHHHHHHhcC--CCCCHHHHhhccCCCHHHHHhccCcE
Q 039337 666 FAPLQFISGLGPRKAASLQRSLVRAG--AIFTRKDFVTAHGLGKKVFVNAVGFL 717 (1344)
Q Consensus 666 ~~~Lq~v~GlGprkA~~ii~~r~~~g--~~~sr~~L~~v~~iG~kvf~n~a~Fl 717 (1344)
...|..|+|||+++++.|+++...-. .-.+.++|..++|||+++-.++..|+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l 595 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEAL 595 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHh
Confidence 36899999999999999999874311 22578899999999999998887775
No 168
>PF14633 SH2_2: SH2 domain; PDB: 3GXX_A 3GXW_B 3PJP_B 2XP1_A.
Probab=83.40 E-value=4.8 Score=44.95 Aligned_cols=84 Identities=15% Similarity=0.143 Sum_probs=60.9
Q ss_pred HHHHHHhhCcccccCCHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEEEEecCCCCc-eeeEEEec--Cc------e
Q 039337 1062 SHLKAMLSYRKFRKGSKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFILTYIRSTNPH-HEYIGLYP--KG------F 1132 (1344)
Q Consensus 1062 ~~v~~i~~h~kf~~g~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~-~e~i~v~p--~g------f 1132 (1344)
..+..++.|+.|++-+-.+++++| ++-..-=+.+.+|.+.+.+..+.++....+. |.-|.=.. .+ +
T Consensus 30 ~~~~R~I~HP~F~n~~~~qAe~~L-----~~~~~Ge~iIRPSSkG~dhL~vTwKv~d~vyqHidV~E~~K~n~~slG~~L 104 (220)
T PF14633_consen 30 KFVKRVIKHPLFKNFNYKQAEEYL-----ADQDVGEVIIRPSSKGPDHLTVTWKVADGVYQHIDVKEEDKENEFSLGKTL 104 (220)
T ss_dssp ---HHHHCSTTEESS-HHHHHHHH-----CCS-TT-EEEEE-TTTTTEEEEEEEEETTEEEEEEEEEECSSSTTS-SSEE
T ss_pred ccccccccCCCccCCCHHHHHHHH-----hcCCCCCEEEeeCCCCCCeEEEEEEEcCCcEEEEEEEECCCcCccccCcEE
Confidence 357899999999999999999999 4445677999999999999999999875543 43333322 22 4
Q ss_pred EEcccccccHHHHHHHHH
Q 039337 1133 KFRKRMFEDIDRLVAYFQ 1150 (1344)
Q Consensus 1133 ~~~~~~~~~~~~L~~~fK 1150 (1344)
+..+..|.|||+||.-|=
T Consensus 105 ~i~~~~yeDLDEii~r~V 122 (220)
T PF14633_consen 105 KIGGEEYEDLDEIIARHV 122 (220)
T ss_dssp EETTEEESSHHHHHHHCH
T ss_pred EECCeEECCHHHHHHHHH
Confidence 567889999999987664
No 169
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=82.98 E-value=0.41 Score=42.77 Aligned_cols=47 Identities=21% Similarity=0.344 Sum_probs=29.5
Q ss_pred ccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcEE
Q 039337 672 ISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFLR 718 (1344)
Q Consensus 672 v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~Flr 718 (1344)
|+|+|++.|+.|.++... +=.=.+.++|..++|||+++-++...|+.
T Consensus 8 I~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp STT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHC
Confidence 788999999998875421 11224677888899999998888777654
No 170
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=82.55 E-value=9 Score=45.04 Aligned_cols=16 Identities=6% Similarity=0.040 Sum_probs=8.5
Q ss_pred ecCCCCCCceEEEEEE
Q 039337 994 RPSSRGPSYLTLTLKV 1009 (1344)
Q Consensus 994 RPSSkG~d~L~vTwKv 1009 (1344)
|=-.+|.|...|-|+=
T Consensus 68 qC~N~G~dg~dvqW~C 83 (318)
T PF06682_consen 68 QCTNQGYDGEDVQWEC 83 (318)
T ss_pred EEEecCCCCcccceEE
Confidence 3334556655666653
No 171
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.35 E-value=0.52 Score=51.37 Aligned_cols=53 Identities=25% Similarity=0.214 Sum_probs=38.3
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhc---C--CCCCHHHHhhccCCCHHHHHhccCcE
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRA---G--AIFTRKDFVTAHGLGKKVFVNAVGFL 717 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~---g--~~~sr~~L~~v~~iG~kvf~n~a~Fl 717 (1344)
++.+|..|+|+||+.|-+|+....-. . .-.+.+-|.++||||+|+-++..-=|
T Consensus 71 lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 71 LFLSLTKVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred HHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 34689999999999999999653210 0 12345567789999999988876333
No 172
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.31 E-value=0.63 Score=51.37 Aligned_cols=50 Identities=22% Similarity=0.238 Sum_probs=37.7
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhc---C--CCCCHHHHhhccCCCHHHHHhcc
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRA---G--AIFTRKDFVTAHGLGKKVFVNAV 714 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~---g--~~~sr~~L~~v~~iG~kvf~n~a 714 (1344)
++.+|..|+|+||+.|-+|+....-. . .=.+.+.|.+++|||+|+-++..
T Consensus 72 lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 72 TFIVLISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 34688999999999999999864210 1 12356678889999999988765
No 173
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=82.30 E-value=0.78 Score=50.36 Aligned_cols=55 Identities=27% Similarity=0.256 Sum_probs=41.6
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhc-----CCCCCHHHHhhccCCCHHHHHhccCcEEE
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRA-----GAIFTRKDFVTAHGLGKKVFVNAVGFLRV 719 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~-----g~~~sr~~L~~v~~iG~kvf~n~a~FlrI 719 (1344)
++..|+.|+||||+.|-+|+....-+ =.-.+.+-|.++||+|+|+-++..-=|+=
T Consensus 71 lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~ 130 (201)
T COG0632 71 LFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKG 130 (201)
T ss_pred HHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhh
Confidence 45789999999999999998874211 12345667889999999999887655543
No 174
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=82.21 E-value=9.2 Score=46.82 Aligned_cols=42 Identities=31% Similarity=0.567 Sum_probs=23.9
Q ss_pred hccCCCHH-HHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHh-------ccCcEEEecCC
Q 039337 671 FISGLGPR-KAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVN-------AVGFLRVRRSG 723 (1344)
Q Consensus 671 ~v~GlGpr-kA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n-------~a~FlrI~~~~ 723 (1344)
.|+||... .|..|-....+-|. -+|.||..| |-||+....+.
T Consensus 409 WVSGLSstTRAtDLKnlFSKyGK-----------VvGAKVVTNaRsPGaRCYGfVTMSts~ 458 (940)
T KOG4661|consen 409 WVSGLSSTTRATDLKNLFSKYGK-----------VVGAKVVTNARSPGARCYGFVTMSTSA 458 (940)
T ss_pred eeeccccchhhhHHHHHHHHhcc-----------eeceeeeecCCCCCcceeEEEEecchH
Confidence 46777654 34444444444442 356666655 67788877553
No 175
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=81.98 E-value=4.6 Score=44.27 Aligned_cols=81 Identities=23% Similarity=0.342 Sum_probs=58.9
Q ss_pred CCCcccCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeeeCCcccc
Q 039337 968 HPCFQNVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKIGEDTFE 1047 (1344)
Q Consensus 968 HP~F~n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i~~~~y~ 1047 (1344)
...|-.++-.+|.+.|..+..|-+++|=||..+.--.+++.=.+.|. |.-| +..-++.+ ...-..|+|++++|.
T Consensus 12 swYfg~mSRqeA~~lL~~~r~G~FLvRDSst~pGdYvLsV~E~srVs-hYiI-n~~~p~~~----~~~~~~~rIgdQ~Fd 85 (293)
T KOG4792|consen 12 SWYFGPMSRQEAVALLQGQRHGVFLVRDSSTSPGDYVLSVSENSRVS-HYII-NSSPPSPA----QPPPSRLRIGDQEFD 85 (293)
T ss_pred ceecCcccHHHHHHHhcCcceeeEEEecCCCCCCceEEEEecCccee-eeee-cCCCCCcc----CCCcceeeecccccc
Confidence 35677889999999999999999999999997666678877666643 4433 33223211 122237999999999
Q ss_pred chHHHHH
Q 039337 1048 DLDEVVD 1054 (1344)
Q Consensus 1048 DLDEii~ 1054 (1344)
+|--|+.
T Consensus 86 ~lPaLL~ 92 (293)
T KOG4792|consen 86 SLPALLE 92 (293)
T ss_pred chHHHHh
Confidence 9887764
No 176
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.87 E-value=0.55 Score=51.45 Aligned_cols=53 Identities=30% Similarity=0.227 Sum_probs=38.8
Q ss_pred cccchhhccCCCHHHHHHHHHHHH--h-cC--CCCCHHHHhhccCCCHHHHHhccCcE
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLV--R-AG--AIFTRKDFVTAHGLGKKVFVNAVGFL 717 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~--~-~g--~~~sr~~L~~v~~iG~kvf~n~a~Fl 717 (1344)
++.+|..|+||||+.|-+|+.... + .. .=.+.+-|.+++|||+|+-++..-=|
T Consensus 71 lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 71 LFELLIGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 346889999999999999988541 1 11 12345667889999999988876433
No 177
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=79.92 E-value=1.1 Score=42.66 Aligned_cols=44 Identities=25% Similarity=0.387 Sum_probs=38.3
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVF 710 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf 710 (1344)
++|..|||||+..|..|+..+-.-.+|.|.++|..-.|+.|..+
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~~~~l~~~~Gl~P~~~ 45 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKSAKQLASYAGLAPRPY 45 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcccchhhhhccccccccc
Confidence 68999999999999999999944568999999998888877664
No 178
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=79.76 E-value=2.8 Score=44.91 Aligned_cols=38 Identities=16% Similarity=0.323 Sum_probs=27.3
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh-ccCC
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT-AHGL 705 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~-v~~i 705 (1344)
+.|.-+||||.+...+||+-|++. +|.|-+||.+ |+|+
T Consensus 116 H~LeLLPGIGKK~m~~ILeERkkk-pFeSFeDi~~Rv~gl 154 (181)
T PF04919_consen 116 HSLELLPGIGKKTMWKILEERKKK-PFESFEDIEERVKGL 154 (181)
T ss_dssp BGGGGSTT--HHHHHHHHHHHHHS----SHHHHHHHSTT-
T ss_pred HHHhhcccccHHHHHHHHHHHccC-CCCCHHHHHHHhccC
Confidence 589999999999999999999655 9999999965 4444
No 179
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=78.86 E-value=18 Score=45.62 Aligned_cols=27 Identities=19% Similarity=0.153 Sum_probs=15.5
Q ss_pred ccCCHHHHHHHhhcCCCCcEEEecCCCC
Q 039337 972 QNVTADEAMKLLSAKEPGESIIRPSSRG 999 (1344)
Q Consensus 972 ~n~~~~qAe~~L~~~~~Gd~viRPSSkG 999 (1344)
++.++.|-|+.|.. +++++=--|+..-
T Consensus 529 q~~~~dqre~~l~~-p~~~v~~~~~~~~ 555 (944)
T KOG4307|consen 529 QQSDKDQRETALDG-PIPSVSMVPSKEQ 555 (944)
T ss_pred hhhhhHHHHHhhcC-Cccchhhhhhhhh
Confidence 35566666666666 5555555555443
No 180
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=78.83 E-value=4.6 Score=43.78 Aligned_cols=7 Identities=14% Similarity=0.183 Sum_probs=3.7
Q ss_pred eeeEEEe
Q 039337 1122 HEYIGLY 1128 (1344)
Q Consensus 1122 ~e~i~v~ 1128 (1344)
++|+.|+
T Consensus 51 T~w~~V~ 57 (182)
T PRK06958 51 TEWHRVA 57 (182)
T ss_pred ceEEEEE
Confidence 4556653
No 181
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.65 E-value=0.68 Score=50.37 Aligned_cols=50 Identities=20% Similarity=0.280 Sum_probs=36.5
Q ss_pred cccchhhccCCCHHHHHHHHHHHH--h-cCC--CCCHHHHhhccCCCHHHHHhccC
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLV--R-AGA--IFTRKDFVTAHGLGKKVFVNAVG 715 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~--~-~g~--~~sr~~L~~v~~iG~kvf~n~a~ 715 (1344)
++.+|..|+|+||+.|-+|+.... + ... =.+.+-| ++||||+|+-++..-
T Consensus 71 lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 71 CLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred HHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHH
Confidence 347899999999999999988531 1 011 1334567 899999999888763
No 182
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=78.41 E-value=1.3 Score=49.18 Aligned_cols=52 Identities=21% Similarity=0.341 Sum_probs=41.7
Q ss_pred cchhhccCCCHHHHHHHHHH-HHh--cCCCCCHHHHhhccCCCHHHHHhccCcEE
Q 039337 667 APLQFISGLGPRKAASLQRS-LVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFLR 718 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~-r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~Flr 718 (1344)
..|.-|+|||+.+|+.|+++ ... .=.-.|.++|..|+|||+++-++...+|.
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 46888999999999999887 321 12345678889999999999999888876
No 183
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=77.64 E-value=1.9 Score=50.81 Aligned_cols=52 Identities=19% Similarity=0.335 Sum_probs=40.4
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHH-----------hhccCCCHHHHHhccCcEEEe
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDF-----------VTAHGLGKKVFVNAVGFLRVR 720 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L-----------~~v~~iG~kvf~n~a~FlrI~ 720 (1344)
..+..|||||++.|+.|.+++++ |.+...++| .+|+||||++....- -+-|.
T Consensus 45 ~~~~~ipgiG~~ia~kI~E~~~t-G~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~-~lGi~ 107 (307)
T cd00141 45 EEAKKLPGIGKKIAEKIEEILET-GKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY-ELGIR 107 (307)
T ss_pred HHhcCCCCccHHHHHHHHHHHHc-CCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH-HcCCC
Confidence 35689999999999999999964 777776655 468999999877665 44443
No 184
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=77.61 E-value=5.4 Score=41.95 Aligned_cols=63 Identities=21% Similarity=0.316 Sum_probs=43.1
Q ss_pred eEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEE
Q 039337 462 LACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVL 527 (1344)
Q Consensus 462 lai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaI 527 (1344)
||| |||-.-|=+.+|+..|.-+.++..+.+...+ +.+-..|-..--+.|.++|.+|+||.+||
T Consensus 1 lGI--DPGl~~~G~gvI~~~~~~l~~v~~G~I~t~~-~~~l~~RL~~l~~~l~~vl~~~~P~~~AI 63 (160)
T COG0817 1 LGI--DPGLRRTGYGVIEVEGRQLSYLASGVIRTSS-DAPLAERLKQLYDGLSEVLDEYQPDEVAI 63 (160)
T ss_pred CCc--CCCccccceEEEEccCCeEEEEeeeEEecCC-CccHHHHHHHHHHHHHHHHHHhCCCeeeh
Confidence 466 8988767789999999866655545543221 11223344445567889999999999998
No 185
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=77.52 E-value=2 Score=31.29 Aligned_cols=20 Identities=25% Similarity=0.556 Sum_probs=17.6
Q ss_pred chhhccCCCHHHHHHHHHHH
Q 039337 668 PLQFISGLGPRKAASLQRSL 687 (1344)
Q Consensus 668 ~Lq~v~GlGprkA~~ii~~r 687 (1344)
.|..|+|+|+++|++|+++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57889999999999999865
No 186
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=76.89 E-value=23 Score=45.63 Aligned_cols=51 Identities=14% Similarity=0.228 Sum_probs=42.5
Q ss_pred cchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcEEE
Q 039337 667 APLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFLRV 719 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI 719 (1344)
+.|.-|+||||+++++|+++... +=.-.|.++|.+| ||+++-++...||.-
T Consensus 552 S~L~~IpGIG~kr~~~LL~~FgSi~~I~~As~eeL~~v--i~~k~A~~I~~~l~~ 604 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHFGSLERVRAATETQLAAV--VGRAAAEAIIAHFTT 604 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhcC
Confidence 78999999999999999998743 2345678889877 999999999888863
No 187
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=76.57 E-value=0.81 Score=57.31 Aligned_cols=32 Identities=9% Similarity=0.137 Sum_probs=15.8
Q ss_pred CCC-HHHHHHHHHHHHHHHhcCChhHHHHHHHHhhc
Q 039337 270 FNS-SQAVLQGARHMAAVEISCEPCVRKYVRSIFMD 304 (1344)
Q Consensus 270 ~~t-~e~vl~ga~~ilA~eis~dp~vR~~vR~~~~~ 304 (1344)
||+ .++|+++..+.+= -.|..||...-+.+..
T Consensus 53 FP~l~~~Ai~a~~DLcE---Ded~~iR~~aik~lp~ 85 (556)
T PF05918_consen 53 FPDLQEEAINAQLDLCE---DEDVQIRKQAIKGLPQ 85 (556)
T ss_dssp -GGGHHHHHHHHHHHHT----SSHHHHHHHHHHGGG
T ss_pred ChhhHHHHHHHHHHHHh---cccHHHHHHHHHhHHH
Confidence 444 3456665555542 3456666655554444
No 188
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=75.52 E-value=38 Score=43.44 Aligned_cols=50 Identities=20% Similarity=0.234 Sum_probs=40.0
Q ss_pred cchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCc
Q 039337 667 APLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
..|..|+|||++++++|+++... +=.-.|.++|..++|+|+++-..+..|
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~~~ 576 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETIRER 576 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHh
Confidence 68999999999999999998732 112367889999999999987766544
No 189
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=75.51 E-value=1.7 Score=32.89 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=18.9
Q ss_pred CCCHHHHhhccCCCHHHHHhccCc
Q 039337 693 IFTRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 693 ~~sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
-.|++||++++|||+++-..+..|
T Consensus 7 pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 7 PASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCHHHHHhCCCcCHHHHHHHHhC
Confidence 578999999999999987765543
No 190
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=73.65 E-value=13 Score=37.89 Aligned_cols=62 Identities=11% Similarity=0.020 Sum_probs=43.6
Q ss_pred CCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCC-ccc-----------cCcccccCCCCEEEEEEEEEeC
Q 039337 846 EGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDD-WRD-----------SELSDKLHEGDILTCKIKSIQK 907 (1344)
Q Consensus 846 ~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~-~~~-----------~~~~~~~~vGq~V~vkVi~iD~ 907 (1344)
+|.++.|+|++.+..|+.|.|+---+=+|+.+.|.+. .|. .+-.-.+..|+.|+.||.++..
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 7999999999999999999997656778888877643 111 0111236889999999998865
No 191
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=73.64 E-value=7.4 Score=42.39 Aligned_cols=7 Identities=14% Similarity=0.772 Sum_probs=3.3
Q ss_pred CCCCCCC
Q 039337 1315 NGGWGHS 1321 (1344)
Q Consensus 1315 ~~g~g~~ 1321 (1344)
.-.|++.
T Consensus 165 ~~~w~~~ 171 (186)
T PRK07772 165 DDPWSSA 171 (186)
T ss_pred CCccccC
Confidence 3445544
No 192
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=73.43 E-value=5.4 Score=54.97 Aligned_cols=65 Identities=17% Similarity=0.241 Sum_probs=53.4
Q ss_pred cccccccccccccccc------cccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhcc
Q 039337 649 TNQVGLDINLAIHREW------QFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAV 714 (1344)
Q Consensus 649 vn~vGVdiN~A~~~~~------~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a 714 (1344)
+....+|||......+ +.--|..|.|||..-|++|++.|++ |+|.|.+||..-.++++++++.++
T Consensus 1126 i~vlppdin~S~~~~f~i~~~~I~~~l~aI~glg~~~a~~Iv~~R~~-g~F~s~~Df~~R~~v~k~~le~L~ 1196 (1213)
T TIGR01405 1126 FKFQPIDLYKSQATEFLIEGNTLIPPFNAIPGLGENVANSIVEARNE-KPFLSKEDLKKRTKISKTHIEKLD 1196 (1213)
T ss_pred CeEeCCcccccCCceeEeeCCEEEeehhhcCCCCHHHHHHHHHHHhh-CCCCCHHHHHHHhCCCHHHHHHHH
Confidence 4456789998765322 3446889999999999999999975 899999999988889999988764
No 193
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=73.33 E-value=3.6 Score=47.35 Aligned_cols=34 Identities=18% Similarity=0.168 Sum_probs=21.4
Q ss_pred hhhccccccccCCCcccCCHHHHHHHhhcC-CCCc
Q 039337 957 AKKHFKERLIVHPCFQNVTADEAMKLLSAK-EPGE 990 (1344)
Q Consensus 957 ~~~~~~~RvI~HP~F~n~~~~qAe~~L~~~-~~Gd 990 (1344)
++....-+|+.=|.=..-+.++....|-+. .+|+
T Consensus 60 ~kt~~QiaVv~vpSt~g~~IE~ya~rlfd~W~lG~ 94 (271)
T COG1512 60 QKTGAQIAVVTVPSTGGETIEQYATRLFDKWKLGD 94 (271)
T ss_pred hccCCeEEEEEecCCCCCCHHHHHHHHHHhcCCCc
Confidence 344555677777776677777766666555 5554
No 194
>COG4907 Predicted membrane protein [Function unknown]
Probab=72.72 E-value=2.7 Score=50.28 Aligned_cols=26 Identities=8% Similarity=0.124 Sum_probs=15.9
Q ss_pred CCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 893 HEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 893 ~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
++-+.++-+|++.+.+...+..|...
T Consensus 332 ~i~~~~~~~vlk~e~ed~~~~~td~~ 357 (595)
T COG4907 332 TIVDLIRKKVLKLETEDKKTIITDTG 357 (595)
T ss_pred EEeecceeeeeecccccceeEEeccc
Confidence 33444556777777777666666443
No 195
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=70.48 E-value=22 Score=33.84 Aligned_cols=66 Identities=12% Similarity=0.141 Sum_probs=49.9
Q ss_pred eEEEEEEEEEecccEE-EEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 848 RVVQATVRRVQGQRAI-CVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 848 ~iV~g~V~~V~~~g~f-V~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
-.++|+|+.+...+.| |.|++|..=+.|++ .+ . ..-.-.+.+||.|.|.+-..|..+.+|....+.
T Consensus 7 ie~~G~V~e~Lp~~~frV~LenG~~vla~is---GK-m-R~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLENGVEVGAYAS---GR-M-RKHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCCCCEEEEEec---cc-e-eeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 3579999999887766 58899987777754 22 1 111225789999999999999999999888764
No 196
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=69.85 E-value=1.5 Score=55.09 Aligned_cols=8 Identities=13% Similarity=0.393 Sum_probs=1.5
Q ss_pred EEEEEecC
Q 039337 1110 FILTYIRS 1117 (1344)
Q Consensus 1110 f~L~~~~~ 1117 (1344)
..|||++.
T Consensus 457 itlSWk~~ 464 (556)
T PF05918_consen 457 ITLSWKEA 464 (556)
T ss_dssp ---TTS--
T ss_pred cceeeeec
Confidence 34455544
No 197
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=68.44 E-value=3.1 Score=52.84 Aligned_cols=51 Identities=18% Similarity=0.170 Sum_probs=42.6
Q ss_pred ccchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcE
Q 039337 666 FAPLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFL 717 (1344)
Q Consensus 666 ~~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~Fl 717 (1344)
.+.|..|+||||++.++|+++... +=.-.|.+||.+| ||++++-++...+|
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l 565 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYL 565 (567)
T ss_pred cCccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHh
Confidence 379999999999999999998853 3345788999999 99999988876655
No 198
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=67.44 E-value=3.4 Score=46.80 Aligned_cols=56 Identities=23% Similarity=0.370 Sum_probs=49.0
Q ss_pred cchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcEEEecC
Q 039337 667 APLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFLRVRRS 722 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI~~~ 722 (1344)
.+|.-+||+|+..|.+++++... +....|-++|.+|.|||++.-.-...|++=+..
T Consensus 182 ~il~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~~~ 239 (254)
T COG1948 182 YILESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTEYK 239 (254)
T ss_pred HHHHcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhchhh
Confidence 68999999999999999999964 456677899999999999999999999887654
No 199
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=67.06 E-value=11 Score=46.90 Aligned_cols=63 Identities=17% Similarity=0.192 Sum_probs=48.4
Q ss_pred ccccccccccc-----cccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh---ccCCCHHHHHhcc
Q 039337 652 VGLDINLAIHR-----EWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT---AHGLGKKVFVNAV 714 (1344)
Q Consensus 652 vGVdiN~A~~~-----~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~---v~~iG~kvf~n~a 714 (1344)
.+-|||....+ ....-=|..|-|+|..-+++|++.|+++|+|+|..|+.. .+.+.++++++++
T Consensus 94 lpPdIN~S~~~Ftv~~~~IrfGL~aIKGVG~~~i~~Iv~eR~~~g~F~sl~DF~~Rvd~~~vnkr~lE~LI 164 (449)
T PRK07373 94 EPPDINRSGKDFTPVGEKILFGLSAVRNLGEGAIESILKAREEGGEFKSLADFCDRVDLRVVNRRALETLI 164 (449)
T ss_pred eCCceeccCCccEEECCEEEEcchhcCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHhCcccCCHHHHHHHH
Confidence 34466655432 112246889999999999999999988999999999954 4568999999874
No 200
>COG4907 Predicted membrane protein [Function unknown]
Probab=66.42 E-value=4.5 Score=48.57 Aligned_cols=12 Identities=17% Similarity=0.246 Sum_probs=7.6
Q ss_pred HHHHHhhcCCCC
Q 039337 1146 VAYFQRHIDDPQ 1157 (1344)
Q Consensus 1146 ~~~fK~~~~d~~ 1157 (1344)
-+.||+.+.|..
T Consensus 488 W~aFKnfLsd~s 499 (595)
T COG4907 488 WQAFKNFLSDYS 499 (595)
T ss_pred HHHHHHHHHhHH
Confidence 456887776643
No 201
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=66.36 E-value=3.6 Score=49.61 Aligned_cols=43 Identities=23% Similarity=0.358 Sum_probs=38.8
Q ss_pred ccccccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhcc
Q 039337 652 VGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAH 703 (1344)
Q Consensus 652 vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~ 703 (1344)
+-+|+|+|+. ..|..|||||.++|..|+..| +|+|.+++++.-
T Consensus 506 ~pl~vn~~s~-----~vl~~ipgig~~~~~~I~~~R----p~~s~e~~l~~v 548 (560)
T COG1031 506 VPLDVNSASK-----DVLRAIPGIGKKTLRKILAER----PFKSSEEFLKLV 548 (560)
T ss_pred cccccccccH-----HHHHhcccchhhhHHHHHhcC----CccchHHHHhcc
Confidence 4589999998 799999999999999999988 999999998543
No 202
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=66.09 E-value=59 Score=40.28 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=14.8
Q ss_pred hhccCCCHHHHHHHHHHHHh---cCCCCCHHHHh
Q 039337 670 QFISGLGPRKAASLQRSLVR---AGAIFTRKDFV 700 (1344)
Q Consensus 670 q~v~GlGprkA~~ii~~r~~---~g~~~sr~~L~ 700 (1344)
-||.=-...-|...|.++.. +|++.|.+.-+
T Consensus 450 GfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK 483 (940)
T KOG4661|consen 450 GFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK 483 (940)
T ss_pred EEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence 33333344445555555532 55555555444
No 203
>KOG1930 consensus Focal adhesion protein Tensin, contains PTB domain [Signal transduction mechanisms; Cytoskeleton]
Probab=65.96 E-value=7.2 Score=46.47 Aligned_cols=176 Identities=20% Similarity=0.210 Sum_probs=111.8
Q ss_pred ccccccccCCCcccCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeC--------------ceeeEEEEeecCCC
Q 039337 960 HFKERLIVHPCFQNVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYD--------------GVYAHKDIIEGGKD 1025 (1344)
Q Consensus 960 ~~~~RvI~HP~F~n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d--------------~v~~HidV~E~~K~ 1025 (1344)
.|++=..+..+=-||+-+||.++|++++.|-+|||=|+.=.+-..+-.||.. .+.-|+.|.-..|.
T Consensus 205 kFV~DTSKyWYKP~isREQAIalLrdkePGtFvvRDS~SfrGayGLAlKVstPPPs~~~~~g~~~neLVRHFLIE~spkG 284 (483)
T KOG1930|consen 205 LFVKDTSKYWYKPNISREQAIALLRDKEPGTFVVRDSHSFRGAYGLALKVSTPPPSVQPGDGSDSNELVRHFLIEPSPKG 284 (483)
T ss_pred eeeecccccccCCCCCHHHHHHHhhcCCCCeEEEecCCcCCCccceEEEeccCCCcccCCCCCchhhhhhhheeccCCCc
Confidence 3444444554445899999999999999999999999988888888899864 24456665443332
Q ss_pred CcCcccccccCceeee-CCc-cccchHHHHHHH-HhhhHHHHHHHhhCccccc--C---CHHHHHHHHHHHHHhCCCcce
Q 039337 1026 HKDIKSLVGIGKTLKI-GED-TFEDLDEVVDRY-IDPLVSHLKAMLSYRKFRK--G---SKAEVDELLRIEKAEFPTRIV 1097 (1344)
Q Consensus 1026 ~~~~~~~~sLG~~L~i-~~~-~y~DLDEii~~~-V~pm~~~v~~i~~h~kf~~--g---~~~e~e~~L~~~~~~np~~i~ 1097 (1344)
- +|+- ++| .|..|--|+.+| |-|++.=++-++=.+---+ . ......++|+ +.++ -...
T Consensus 285 V-----------kLKGC~nEP~FGSLSALV~QHSIt~LALPckL~iP~rDp~ee~~~~~~~~a~a~LLk-qGAA--CnVl 350 (483)
T KOG1930|consen 285 V-----------KLKGCDNEPVFGSLSALVYQHSITALALPCKLVIPDRDPLEEAPVPEHTSATAALLK-QGAA--CNVL 350 (483)
T ss_pred e-----------eccCCCCCCccchhHHHHhhccchhhhcceeEeccCCCcccCCCCCCCchhHHHHHh-hCcc--ceEE
Confidence 1 2221 234 899999999995 7787766654443333321 1 2233455553 3332 2456
Q ss_pred EEEEeCCC---------CCcEEEEEEecCCCCceeeEEEecCceEEcccccccHHHHHHHHHhhcCC
Q 039337 1098 YGFGISHE---------HPGTFILTYIRSTNPHHEYIGLYPKGFKFRKRMFEDIDRLVAYFQRHIDD 1155 (1344)
Q Consensus 1098 Y~f~~~~~---------~PG~f~L~~~~~~~~~~e~i~v~p~gf~~~~~~~~~~~~L~~~fK~~~~d 1155 (1344)
|.-+++-+ +.=.+.|.-.|.-.+..-+++|.-.|..|-..+-. -+|.+||..
T Consensus 351 yl~SVd~ESLTG~~av~kAt~~~~~~~p~p~~tvVHFKVSsQGITLTDNqRK------~FFRRHypv 411 (483)
T KOG1930|consen 351 YLGSVDVESLTGNEAVQKATSSQRAINPTPRATVVHFKVSSQGITLTDNQRK------VFFRRHYPV 411 (483)
T ss_pred EEeeeeccccccHHHHHHHHHHHhhcCCCCCceEEEEEEeccceeeeccchh------hheeccccc
Confidence 76666553 23334444444333445689999999999865433 478888854
No 204
>PF07355 GRDB: Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); InterPro: IPR022787 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. ; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=65.86 E-value=18 Score=42.88 Aligned_cols=52 Identities=23% Similarity=0.409 Sum_probs=42.7
Q ss_pred EECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEc-CCCcchh
Q 039337 477 MLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLG-AVNLSCT 535 (1344)
Q Consensus 477 ~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG-~~t~s~~ 535 (1344)
++.++++|+.++++...|.. +..++..+++.+++++++||+++-| ++++-+.
T Consensus 43 ~l~~~~eIv~TiiCGDnyf~-------en~eea~~~i~~mv~~~~pD~viaGPaFnagrY 95 (349)
T PF07355_consen 43 ALKDDAEIVATIICGDNYFN-------ENKEEALKKILEMVKKLKPDVVIAGPAFNAGRY 95 (349)
T ss_pred HhcCCCEEEEEEEECcchhh-------hCHHHHHHHHHHHHHhcCCCEEEEcCCcCCchH
Confidence 55668999999999987765 2346788999999999999999999 6776653
No 205
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=65.53 E-value=56 Score=36.49 Aligned_cols=82 Identities=17% Similarity=0.295 Sum_probs=46.7
Q ss_pred HHHHHHHHHhCCeEEEEcCCCcchhhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhhhHHhhhc-CCC-
Q 039337 511 ERLLKFMMDHQPHVVVLGAVNLSCTSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYENSRISSDQ-LPG- 588 (1344)
Q Consensus 511 ~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~s~~a~~e-~p~- 588 (1344)
+.|.+.+.+++||+|+++...... ...+++++..+.+. . ..+++++.=-....-|........+ -.|
T Consensus 129 e~~v~~~~~~~~~~V~lS~~~~~~---~~~~~~~i~~L~~~-~-------~~~~i~vGG~~~~~~~~~~~~~~~~~gad~ 197 (213)
T cd02069 129 EKILEAAKEHKADIIGLSGLLVPS---LDEMVEVAEEMNRR-G-------IKIPLLIGGAATSRKHTAVKIAPEYDGPVV 197 (213)
T ss_pred HHHHHHHHHcCCCEEEEccchhcc---HHHHHHHHHHHHhc-C-------CCCeEEEEChhcCHHHHhhhhccccCCCce
Confidence 578899999999999999876554 23455666655432 1 2467776554444444332100001 111
Q ss_pred CchhhHHHHHhhhhh
Q 039337 589 QKGNVKRAVALGRYL 603 (1344)
Q Consensus 589 ~~~~~R~avslaR~l 603 (1344)
+-.....||.+|+++
T Consensus 198 y~~da~~~v~~~~~~ 212 (213)
T cd02069 198 YVKDASRALGVANKL 212 (213)
T ss_pred EecCHHHHHHHHHHh
Confidence 233445677777764
No 206
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 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 is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=64.86 E-value=23 Score=34.67 Aligned_cols=55 Identities=13% Similarity=0.223 Sum_probs=44.6
Q ss_pred cCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeC
Q 039337 845 AEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQK 907 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~ 907 (1344)
.+|.+|.|+|..|.+.-+|++++....+++....... +.|..|..|.+++.+.+.
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~--------~~y~~G~rV~lrLkdlEL 76 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG--------EKYVRGSRVRLRLKDLEL 76 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc--------cccccCCEEEEEECCHhh
Confidence 3799999999999999999999888899987554322 358889999998886653
No 207
>PRK08609 hypothetical protein; Provisional
Probab=64.37 E-value=6.9 Score=50.09 Aligned_cols=43 Identities=30% Similarity=0.519 Sum_probs=35.8
Q ss_pred chhhccCCCHHHHHHHHHHHHhcCCCCCHHHHh---------hccCCCHHHHHhcc
Q 039337 668 PLQFISGLGPRKAASLQRSLVRAGAIFTRKDFV---------TAHGLGKKVFVNAV 714 (1344)
Q Consensus 668 ~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~---------~v~~iG~kvf~n~a 714 (1344)
.|..|+||||++|..|-+.+ .++|.+||. .++|+|+|+.+++.
T Consensus 89 ~l~~i~GiGpk~a~~l~~~l----Gi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il 140 (570)
T PRK08609 89 PLLKLPGLGGKKIAKLYKEL----GVVDKESLKEACENGKVQALAGFGKKTEEKIL 140 (570)
T ss_pred HHhcCCCCCHHHHHHHHHHh----CCCCHHHHHHHHHhCChhhccCcchhHHHHHH
Confidence 45579999999999998776 688888885 46899999988863
No 208
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=64.15 E-value=92 Score=39.82 Aligned_cols=21 Identities=10% Similarity=-0.015 Sum_probs=11.8
Q ss_pred HHhhhHHHHHHHhhCcccccCC
Q 039337 1056 YIDPLVSHLKAMLSYRKFRKGS 1077 (1344)
Q Consensus 1056 ~V~pm~~~v~~i~~h~kf~~g~ 1077 (1344)
|-++..++...+-+.+ |+..+
T Consensus 607 ~r~~~~~~~~~vnn~p-F~m~~ 627 (944)
T KOG4307|consen 607 RREEHTRWCVQVNNVP-FRMKD 627 (944)
T ss_pred ccchhhhhhhcccCcc-eeecc
Confidence 4455555555665555 77544
No 209
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=63.03 E-value=8.8 Score=42.60 Aligned_cols=45 Identities=24% Similarity=0.359 Sum_probs=34.6
Q ss_pred ccCCCHHHHHHHHHHHH----h-cC-CCCCHHHHhhccCCCHHHHHhccCc
Q 039337 672 ISGLGPRKAASLQRSLV----R-AG-AIFTRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 672 v~GlGprkA~~ii~~r~----~-~g-~~~sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
=.||-.+||++|++.-+ + +| ...+|++|++++|+|+|+-.=.-++
T Consensus 78 ~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 78 SIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred hcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcchHHHHHHHHh
Confidence 46899999999987653 3 34 5788999999999999885444333
No 210
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=62.42 E-value=15 Score=40.08 Aligned_cols=6 Identities=17% Similarity=0.412 Sum_probs=2.6
Q ss_pred EEEEEE
Q 039337 1109 TFILTY 1114 (1344)
Q Consensus 1109 ~f~L~~ 1114 (1344)
.|.|..
T Consensus 30 ~FrVAv 35 (186)
T PRK07772 30 NFTVAS 35 (186)
T ss_pred EEEEEe
Confidence 344443
No 211
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=61.58 E-value=12 Score=46.90 Aligned_cols=73 Identities=14% Similarity=0.127 Sum_probs=56.9
Q ss_pred cccCCeEEEEEEEEEecc--cEEEEeCCCeEEEEeceecCCCcccc----CcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 843 TLAEGRVVQATVRRVQGQ--RAICVLESGLAGMLMKEDYSDDWRDS----ELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~--g~fV~L~~gi~GlIh~s~lsd~~~~~----~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
.-.+|.|+.|+|++|.+. .+||+++..-.||+|.+++.+. +.. +....++.||.+-|.|+.-.....-..||.
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~-~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~ 112 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPY-FRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLTT 112 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccCCccceEEecccchh-hhhcccccceeeecCCceEEEEEEeecCcccccccee
Confidence 345799999999999885 5899999999999999999872 222 124589999999999998776655455553
No 212
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=61.11 E-value=27 Score=44.81 Aligned_cols=22 Identities=27% Similarity=0.102 Sum_probs=12.4
Q ss_pred hHHHHHhhhhhcccceehhccc
Q 039337 593 VKRAVALGRYLQNPLAMVATLC 614 (1344)
Q Consensus 593 ~R~avslaR~lqdPl~e~~~l~ 614 (1344)
+..|-+|-++-+|=+.+.|++|
T Consensus 237 llla~aldpr~pnmm~dvvkll 258 (1102)
T KOG1924|consen 237 LLLARALDPREPNMMTDVVKLL 258 (1102)
T ss_pred HHHHHhcCccCccHHHHHHHHH
Confidence 3345555555666566666664
No 213
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=60.95 E-value=37 Score=30.97 Aligned_cols=60 Identities=12% Similarity=0.089 Sum_probs=44.4
Q ss_pred EEEEEEEEEecccEE-EEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEE
Q 039337 849 VVQATVRRVQGQRAI-CVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVF 913 (1344)
Q Consensus 849 iV~g~V~~V~~~g~f-V~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~ 913 (1344)
.+.|+|+...+.+.| |.|++|..=+.|++ .+ ...-.-.+.+||.|.|.+-..|..+.+|.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~---GK--mr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHIS---GK--IRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEec---Cc--chhccEEECCCCEEEEEECcccCCcEeEE
Confidence 578999999888766 58899988777765 22 11112357899999999988888877764
No 214
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=60.86 E-value=13 Score=52.36 Aligned_cols=65 Identities=15% Similarity=0.232 Sum_probs=52.8
Q ss_pred cccccccccccccc------cccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhcc
Q 039337 649 TNQVGLDINLAIHR------EWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAV 714 (1344)
Q Consensus 649 vn~vGVdiN~A~~~------~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a 714 (1344)
+....+|||..... .-+.--|..|.|||..-|++|++.|+ +|+|.|.+||..-.++++++.+.+.
T Consensus 1349 i~~lp~din~S~~~~f~i~~~~i~~pl~~I~glG~~~a~~Iv~~R~-~g~F~s~~Df~~R~~v~k~~ie~L~ 1419 (1437)
T PRK00448 1349 FKFQKVDLYKSDATEFIIEGDSLIPPFNALPGLGENVAKSIVEARE-EGEFLSKEDLRKRTKVSKTLIEKLD 1419 (1437)
T ss_pred CeEeCCcccccCCcceEeeCCEEEecchhcCCCCHHHHHHHHHHHh-cCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34466899987653 23445788999999999999999996 6999999999988889998887754
No 215
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=59.69 E-value=27 Score=42.42 Aligned_cols=96 Identities=13% Similarity=0.299 Sum_probs=61.6
Q ss_pred EECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEc-CCCcchhhhHHHHHHHHHHHHhhCCCC
Q 039337 477 MLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLG-AVNLSCTSLKDDIYEIIFKMVEEHPRD 555 (1344)
Q Consensus 477 ~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG-~~t~s~~~l~~~~~~~v~~~~~~~~~~ 555 (1344)
++-.+++++.++++...|.. +..++..+++.+++++++|||++-| ++++-+.-.+ ..-|.+.+++..
T Consensus 39 ~~~~~~eVvaTiiCGDnYf~-------en~eea~~~i~~mv~k~~pDv~iaGPaFNagrYG~a---cg~va~aV~e~~-- 106 (431)
T TIGR01917 39 LIEEDAEIVATVVCGDSFFG-------ENLEEAKAKVLEMIKGANPDIFIAGPAFNAGRYGMA---AGAITKAVQDEL-- 106 (431)
T ss_pred HhcCCCEEEEEEEECchhhh-------hCHHHHHHHHHHHHHhcCCCEEEEcCccCCccHHHH---HHHHHHHHHHhh--
Confidence 56678999999999988765 2346778999999999999999999 6777663332 233444444321
Q ss_pred cCCCCCcceEEEecCCCchHHhhhHHhhhcCCC
Q 039337 556 VGHEMDELSIVYGDESLPRLYENSRISSDQLPG 588 (1344)
Q Consensus 556 ~~~~~~~i~v~~v~~~~a~vy~~s~~a~~e~p~ 588 (1344)
..+.+.-++..+.+..+|-.. .---+.|+
T Consensus 107 ---~IP~vtaMy~ENpgvd~yk~~-vyIv~t~~ 135 (431)
T TIGR01917 107 ---GIKAFTAMYEENPGADMFKKE-VYVIPTAD 135 (431)
T ss_pred ---CCCeEEEecccChHHHHHhhC-cEEEECCC
Confidence 122334445555677777642 22235554
No 216
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=59.48 E-value=31 Score=41.99 Aligned_cols=87 Identities=18% Similarity=0.366 Sum_probs=57.5
Q ss_pred EECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEc-CCCcchhhhHHHHHHHHHHHHhhCCCC
Q 039337 477 MLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLG-AVNLSCTSLKDDIYEIIFKMVEEHPRD 555 (1344)
Q Consensus 477 ~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG-~~t~s~~~l~~~~~~~v~~~~~~~~~~ 555 (1344)
++-.+++++.++++...|.. +..++..+++.+++++++|||++-| ++++-+.-.+ ..-|.+.+++..
T Consensus 39 ~l~~~~eVvaTiiCGDnYf~-------en~eea~~~i~~mv~k~~pDv~iaGPaFNagrYG~a---cg~va~aV~e~~-- 106 (431)
T TIGR01918 39 LLEEDAEVVHTVVCGDSFFG-------ENLEEAVARVLEMLKDKEPDIFIAGPAFNAGRYGVA---CGEICKVVQDKL-- 106 (431)
T ss_pred HhccCCEEEEEEEECchhhh-------hCHHHHHHHHHHHHHhcCCCEEEEcCccCCccHHHH---HHHHHHHHHHhh--
Confidence 34478999999999988765 2346778999999999999999999 6777663332 233444444321
Q ss_pred cCCCCCcceEEEecCCCchHHhh
Q 039337 556 VGHEMDELSIVYGDESLPRLYEN 578 (1344)
Q Consensus 556 ~~~~~~~i~v~~v~~~~a~vy~~ 578 (1344)
..+.+.-++..+.+..+|-.
T Consensus 107 ---~IP~vt~My~ENpgvd~yk~ 126 (431)
T TIGR01918 107 ---NVPAVTSMYVENPGVDMFKK 126 (431)
T ss_pred ---CCCeEEEecccChHHHHHhh
Confidence 12233444555567666654
No 217
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=59.42 E-value=17 Score=47.23 Aligned_cols=19 Identities=5% Similarity=-0.155 Sum_probs=8.9
Q ss_pred eEEcccccccHHHHHHHHH
Q 039337 1132 FKFRKRMFEDIDRLVAYFQ 1150 (1344)
Q Consensus 1132 f~~~~~~~~~~~~L~~~fK 1150 (1344)
|.|-.-.....++++..++
T Consensus 528 ~s~v~~~~~~~~~~~~~~~ 546 (629)
T PRK11634 528 HSTIELPKGMPGEVLQHFT 546 (629)
T ss_pred ceEEEcChhhHHHHHHHhc
Confidence 3333333344555555554
No 218
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=59.31 E-value=5.7 Score=45.48 Aligned_cols=59 Identities=24% Similarity=0.316 Sum_probs=42.9
Q ss_pred cccccccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhccCcEEEe
Q 039337 651 QVGLDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAVGFLRVR 720 (1344)
Q Consensus 651 ~vGVdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI~ 720 (1344)
.--||||.|.. .+|-.|||||++-|+.||..|... =-+-++|+++ | .+..++..||...
T Consensus 319 ~FPVdvn~A~~-----~~llRVPGiG~ksa~rIv~~Rr~~--rl~~e~Lkk~---G-vvlkRak~Fi~~~ 377 (404)
T COG4277 319 RFPVDVNKAPY-----KELLRVPGIGVKSARRIVMTRRRT--RLTLEDLKKL---G-VVLKRAKPFITLD 377 (404)
T ss_pred cccccccccCH-----HHhcccCCCChHHHHHHHHHhhhc--ccCHHHHhhh---c-eeeeccceeEEec
Confidence 35799999999 689999999999999999998421 1235667643 3 2445666666665
No 219
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=59.29 E-value=7.9 Score=46.19 Aligned_cols=52 Identities=19% Similarity=0.291 Sum_probs=40.2
Q ss_pred chhhccCCCHHHHHHHHHHHHhcCCCC------------CHHHHhhccCCCHHHHHhccCcEEEec
Q 039337 668 PLQFISGLGPRKAASLQRSLVRAGAIF------------TRKDFVTAHGLGKKVFVNAVGFLRVRR 721 (1344)
Q Consensus 668 ~Lq~v~GlGprkA~~ii~~r~~~g~~~------------sr~~L~~v~~iG~kvf~n~a~FlrI~~ 721 (1344)
.|+.|||||++.|+.|.++++ .|.+. ...+|.+|+|||||+-...-. +-|.+
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~-tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~-lGi~t 112 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIE-TGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR-KGIRT 112 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHH-hCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH-hCCCC
Confidence 578899999999999999986 45554 234457799999998777766 66654
No 220
>PF07318 DUF1464: Protein of unknown function (DUF1464); InterPro: IPR009927 This family consists of several hypothetical archaeal proteins of around 350 residues in length. The function of this family is unknown.
Probab=59.06 E-value=19 Score=42.80 Aligned_cols=54 Identities=11% Similarity=0.145 Sum_probs=40.1
Q ss_pred CCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHh-CCeEEEEcCCC
Q 039337 467 GPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDH-QPHVVVLGAVN 531 (1344)
Q Consensus 467 dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~-~p~vIaIG~~t 531 (1344)
|||.....++++|++|+|+.....+. ....++-..++++|.++ +||+||.-.+-
T Consensus 3 DpGT~s~dv~~~dd~g~v~~~~~ipt-----------~~v~~~p~~iv~~l~~~~~~dlIa~psGy 57 (343)
T PF07318_consen 3 DPGTKSFDVCGLDDDGKVIFYFSIPT-----------EEVAKNPSIIVEELEEFGDIDLIAGPSGY 57 (343)
T ss_pred CCCCCcEEEEEEccCCcEEEEeeccH-----------HHhhhCHHHHHHHHHhccCCCEEEeCCcC
Confidence 88887788899999999987644322 12233456689999998 99999996654
No 221
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=56.73 E-value=7.6 Score=34.10 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=19.7
Q ss_pred cchhhccCCCHHHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSLV 688 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~ 688 (1344)
..|.-|+|+|+++|++|+++.+
T Consensus 38 ~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 38 EELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHTSTTSSHHHHHHHHHHHH
T ss_pred HHHhcCCCCCHHHHHHHHHHHh
Confidence 5788899999999999999875
No 222
>KOG4817 consensus Unnamed protein [Function unknown]
Probab=56.60 E-value=1.4e+02 Score=35.45 Aligned_cols=11 Identities=45% Similarity=1.241 Sum_probs=6.6
Q ss_pred CCCCCCCCCCC
Q 039337 1185 AGSGWGGSTNE 1195 (1344)
Q Consensus 1185 ~~~~~gg~~~~ 1195 (1344)
.|.||+++.++
T Consensus 83 ~GTgw~~~~~~ 93 (468)
T KOG4817|consen 83 EGTGWGGAGAG 93 (468)
T ss_pred CCcccccCCCC
Confidence 55667765554
No 223
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=56.58 E-value=17 Score=44.39 Aligned_cols=14 Identities=14% Similarity=0.078 Sum_probs=7.9
Q ss_pred cHHHHHHHHHhhcC
Q 039337 1141 DIDRLVAYFQRHID 1154 (1344)
Q Consensus 1141 ~~~~L~~~fK~~~~ 1154 (1344)
+.+.|-+.||+...
T Consensus 301 ~~~~l~~~Fk~FG~ 314 (419)
T KOG0116|consen 301 TPAELEEVFKQFGP 314 (419)
T ss_pred CHHHHHHHHhhccc
Confidence 45556666665543
No 224
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=55.80 E-value=12 Score=50.25 Aligned_cols=147 Identities=17% Similarity=0.205 Sum_probs=89.5
Q ss_pred cCCCchHHhhhHH-hhhcCCCCc--hhhHHHHHhhh-hhcccceehhcccCCC---cccccc---------ccc---C-c
Q 039337 569 DESLPRLYENSRI-SSDQLPGQK--GNVKRAVALGR-YLQNPLAMVATLCGPG---REILSW---------KLC---P-L 628 (1344)
Q Consensus 569 ~~~~a~vy~~s~~-a~~e~p~~~--~~~R~avslaR-~lqdPl~e~~~l~~~~---~~~~~i---------~~~---~-~ 628 (1344)
...++-.|=.|-. =.=.||.+. ..+-.|+-+|- .+--||.-||..+... =|+... ++- . -
T Consensus 1252 e~~Vp~WyIeSC~KIkYMFPKAHAaAYVlMA~RIAyFKVhhPl~YYAayfSira~~FDi~~m~~Gke~ik~k~~Ei~~~~ 1331 (1444)
T COG2176 1252 ENKVPEWYIESCLKIKYMFPKAHAAAYVLMAWRIAYFKVHHPLEYYAAYFSIRADDFDIETMSKGKEAIKAKMEEINKRK 1331 (1444)
T ss_pred HcCCcHHHHHHhhhhhhhCchHHHHHHHHHHHHHHHHHhcchHHHHHHHheeehhhcCHHHHhccHHHHHHHHHHHhhcc
Confidence 3456666655422 222789864 34677888886 4788999999876421 011111 011 1 1
Q ss_pred cccCC--hhhhhhhhhhhhhcc---cccccccccccccccc------cccchhhccCCCHHHHHHHHHHHHhcCCCCCHH
Q 039337 629 ENFLT--PDEKYGMIEQVMVDV---TNQVGLDINLAIHREW------QFAPLQFISGLGPRKAASLQRSLVRAGAIFTRK 697 (1344)
Q Consensus 629 Q~~~~--~~~l~~~l~~~~~~~---vn~vGVdiN~A~~~~~------~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~ 697 (1344)
+..++ ++.|+..||-+++-+ .+...|||-...+..+ +-..+-.|+|||..-|++||+.| ..|+|.|.+
T Consensus 1332 ~~~~~~kEk~l~t~lEi~~EM~aRGf~f~~idly~S~At~Fvid~~~LipPFi~i~GlGe~vA~~IV~AR-~Ek~FlS~e 1410 (1444)
T COG2176 1332 GNKASPKEKNLLTVLEIVLEMLARGFKFQKIDLYKSDATEFVIDGDTLIPPFIAIPGLGENVAKSIVEAR-EEKEFLSKE 1410 (1444)
T ss_pred cccCChhhhhhHhHHHHHHHHHHccCcccCceeeeccCeEEEEeCCeecCceeccCChhHHHHHHHHHHh-hcCCcCCHH
Confidence 22222 233445555443322 2233455543333221 23466789999999999999999 679999999
Q ss_pred HHhhccCCCHHHHHhccCc
Q 039337 698 DFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 698 ~L~~v~~iG~kvf~n~a~F 716 (1344)
||++--+|+.+..++.-.+
T Consensus 1411 DlkkRtkis~t~ie~~~~~ 1429 (1444)
T COG2176 1411 DLKKRTKISKTHIEKLDEM 1429 (1444)
T ss_pred HHHHhcCccHHHHHHHHhc
Confidence 9999999999988876543
No 225
>PF11215 DUF3010: Protein of unknown function (DUF3010); InterPro: IPR021378 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=54.88 E-value=30 Score=35.79 Aligned_cols=64 Identities=17% Similarity=0.180 Sum_probs=39.3
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEE--eccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEE
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLF--TGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVL 527 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaI 527 (1344)
+|+||-. .| +-+-+|+|+.++.+.+..- ...+.+. +...++...+-...+.+|+..|++|.|||
T Consensus 2 ~vCGVEL-kg-neaii~ll~~~~~~~~~pdcr~~k~~l~--~~~~~~~vr~Fq~~f~kl~~dy~Vd~VvI 67 (138)
T PF11215_consen 2 KVCGVEL-KG-NEAIICLLSLDDGLFQLPDCRVRKFSLS--DDNSTEEVRKFQFTFAKLMEDYKVDKVVI 67 (138)
T ss_pred eEEEEEE-ec-CeEEEEEEecCCCceECCccceeEEEcC--CCccHHHHHHHHHHHHHHHHHcCCCEEEE
Confidence 6778722 22 2366777877777665311 1222222 11233344566778999999999999999
No 226
>KOG2996 consensus Rho guanine nucleotide exchange factor VAV3 [Signal transduction mechanisms]
Probab=54.60 E-value=25 Score=43.63 Aligned_cols=77 Identities=19% Similarity=0.349 Sum_probs=61.5
Q ss_pred ccccCCCcc-cCCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeee-
Q 039337 964 RLIVHPCFQ-NVTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKI- 1041 (1344)
Q Consensus 964 RvI~HP~F~-n~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i- 1041 (1344)
-...||||- ++.-.|||..|++.+-|.+++|-+.|-....++.+|..+.|- ||.|.+. ++ .+.|
T Consensus 681 d~s~~~WyaG~MERaqaes~Lk~~~ngT~LVR~r~kea~e~AISikynnevK-HikI~~~--dg-----------~~~i~ 746 (865)
T KOG2996|consen 681 DYSEFPWYAGEMERAQAESTLKNRPNGTYLVRYRTKEAKEFAISIKYNNEVK-HIKIETN--DG-----------KVHIT 746 (865)
T ss_pred chhhhhhhcchHhhhhhhhHhhcCCCceEEEEecccchhheeEEEEeccccc-eEEEEec--CC-----------eEEec
Confidence 346788885 678889999999999999999999999899999999998875 8888775 22 1223
Q ss_pred CCccccchHHHHH
Q 039337 1042 GEDTFEDLDEVVD 1054 (1344)
Q Consensus 1042 ~~~~y~DLDEii~ 1054 (1344)
.+..|..|=||+.
T Consensus 747 E~k~F~sl~ELVe 759 (865)
T KOG2996|consen 747 EDKKFNSLVELVE 759 (865)
T ss_pred hhhhhhhHHHHHH
Confidence 3468888887753
No 227
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=54.20 E-value=1.3e+02 Score=33.21 Aligned_cols=54 Identities=19% Similarity=0.359 Sum_probs=34.5
Q ss_pred HHHHHHHHHhCCeEEEEcCCCcchhhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCc
Q 039337 511 ERLLKFMMDHQPHVVVLGAVNLSCTSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLP 573 (1344)
Q Consensus 511 ~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a 573 (1344)
+.|.+.+.+++|++|+++....... ..+.+++..+-+..+ ...+++++.=....
T Consensus 123 ~~l~~~~~~~~~d~v~lS~~~~~~~---~~~~~~i~~lr~~~~------~~~~~i~vGG~~~~ 176 (201)
T cd02070 123 EEFVEAVKEHKPDILGLSALMTTTM---GGMKEVIEALKEAGL------RDKVKVMVGGAPVN 176 (201)
T ss_pred HHHHHHHHHcCCCEEEEeccccccH---HHHHHHHHHHHHCCC------CcCCeEEEECCcCC
Confidence 5788889999999999998655542 345566655543321 12467776544443
No 228
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=53.77 E-value=8.3 Score=42.88 Aligned_cols=23 Identities=39% Similarity=0.583 Sum_probs=20.6
Q ss_pred cchhhccCCCHHHHHHHHHHHHh
Q 039337 667 APLQFISGLGPRKAASLQRSLVR 689 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~ 689 (1344)
..|..++||||+||+.|.+++.+
T Consensus 227 ~ele~~~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 227 GELEQCPGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred hHHHhCcCcCHHHHHHHHHHHhc
Confidence 68999999999999999999843
No 229
>KOG4226 consensus Adaptor protein NCK/Dock, contains SH2 and SH3 domains [Signal transduction mechanisms]
Probab=53.68 E-value=50 Score=37.45 Aligned_cols=73 Identities=18% Similarity=0.240 Sum_probs=54.7
Q ss_pred cCCHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEEEEecCCCCceeeEEEecCceEEcccccccHHHHHHHHHh
Q 039337 1075 KGSKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFILTYIRSTNPHHEYIGLYPKGFKFRKRMFEDIDRLVAYFQR 1151 (1344)
Q Consensus 1075 ~g~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~~e~i~v~p~gf~~~~~~~~~~~~L~~~fK~ 1151 (1344)
.-++...|..|..--. .. -+-+-=+...||-|..+-+...+..|--|.+...=|...++.|-+|++|++.+|+
T Consensus 287 ~itR~qae~~Ln~hG~-eG---dFLiRDSEsnpgD~SvSlka~grNKHFkVq~~d~~ycIGqRkF~tmd~Lv~HY~k 359 (379)
T KOG4226|consen 287 NITRHQAECALNEHGH-EG---DFLIRDSESNPGDFSVSLKASGRNKHFKVQLVDNVYCIGQRKFHTMDELVEHYKK 359 (379)
T ss_pred cccHHHHHHHHhccCc-cC---ceEEecCCCCCcceeEEeeccCCCcceEEEEecceEEeccceeccHHHHHHhhhc
Confidence 3467777777722111 11 1223336679999999999987777777888888999999999999999999885
No 230
>PRK13910 DNA glycosylase MutY; Provisional
Probab=53.53 E-value=13 Score=43.45 Aligned_cols=50 Identities=20% Similarity=0.291 Sum_probs=38.5
Q ss_pred cchhhccCCC-HHHHHHHHHHHH----h-cCCC-CCHHHHhhccCCCHHHHHhccCc
Q 039337 667 APLQFISGLG-PRKAASLQRSLV----R-AGAI-FTRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 667 ~~Lq~v~GlG-prkA~~ii~~r~----~-~g~~-~sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
.++..+.|+| -+||++|.+.-+ + +|.| .++++|++++|||++|-.-...|
T Consensus 35 el~~~~~glGyy~RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 35 EVLLLWRGLGYYSRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred HHHHHHHcCCcHHHHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHHHH
Confidence 6788888888 678999977654 2 4544 68999999999999986655554
No 231
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=53.52 E-value=78 Score=40.06 Aligned_cols=101 Identities=22% Similarity=0.392 Sum_probs=61.2
Q ss_pred eEeEeecCCCCCceE-----EEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCCcch
Q 039337 460 RVLACCWGPGKPETT-----FVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVNLSC 534 (1344)
Q Consensus 460 rVlai~~dpg~~g~~-----~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t~s~ 534 (1344)
.||||-.-.|.+.-+ +|++ ++|+++.. . +-...+|..||.+++||+|||-|-.
T Consensus 3 ~I~GVDI~~g~p~~~~p~yAvv~~-~dg~~~~k---~---------------~~s~~rllrli~~~kpDIvAvDnvy--- 60 (652)
T COG2433 3 VIMGVDIVSGSPRGKAPLYAVVIL-EDGEIVEK---G---------------EVSLRRLLRLIWSYKPDIVAVDNVY--- 60 (652)
T ss_pred eEEEEeeecCCCCCcCcceeEEEE-ecCcEEee---h---------------hhhHHHHHHHHHhcCCCEEEeccHH---
Confidence 477775443433222 3444 99998754 1 1235689999999999999998743
Q ss_pred hhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhhhHHhhhcCCC
Q 039337 535 TSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYENSRISSDQLPG 588 (1344)
Q Consensus 535 ~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~s~~a~~e~p~ 588 (1344)
.|.++=.+++ .+++..| +...-|+|..-+..-.++.+.+++=+-.+++
T Consensus 61 -EL~~~~~~li-~il~~lP----~~tkLVQVTg~~g~~~sL~~lArr~G~~~~~ 108 (652)
T COG2433 61 -ELGADKRDLI-RILKRLP----EGTKLVQVTGRPGEQESLWELARRHGIRVNG 108 (652)
T ss_pred -HHhcChhHHH-HHHHhCC----CCceEEEEeCCCCCcchHHHHHHHhCCCCCC
Confidence 2222212232 2333333 2223366776667778888888877767764
No 232
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=53.47 E-value=13 Score=39.79 Aligned_cols=34 Identities=12% Similarity=0.256 Sum_probs=30.7
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT 701 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~ 701 (1344)
+.|.-+||||.+...+||+-|++. +|+|-+|+.+
T Consensus 130 H~LELLpGiGkK~m~~ILeERkkk-pFeSFeDi~~ 163 (202)
T COG1491 130 HQLELLPGIGKKTMWAILEERKKK-PFESFEDIKE 163 (202)
T ss_pred HHHHhcccccHHHHHHHHHHHhcC-CCcCHHHHHH
Confidence 489999999999999999999654 9999999975
No 233
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=53.17 E-value=69 Score=29.81 Aligned_cols=66 Identities=11% Similarity=0.117 Sum_probs=46.6
Q ss_pred CeEEEEEEEEEecccE-EEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 847 GRVVQATVRRVQGQRA-ICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~-fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
.-.+.|+|..+-..+- .|.+++|..=+-|++ .+ .-. -.-.+.+||+|.|..-..|.++.+|.-..+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~---GK-mr~-~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHIS---GK-MRK-NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEcc---Cc-chh-eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 3457899999887664 477888877666654 33 111 122578999999999999988888866544
No 234
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=52.56 E-value=9.6 Score=34.08 Aligned_cols=23 Identities=30% Similarity=0.483 Sum_probs=18.7
Q ss_pred cchhhccCCCHHHHHHHHHHHHh
Q 039337 667 APLQFISGLGPRKAASLQRSLVR 689 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~ 689 (1344)
..|..|+||||..|++|.+|.+.
T Consensus 35 e~L~~i~gIG~~~A~si~~ff~~ 57 (64)
T PF12826_consen 35 EELSAIPGIGPKIAQSIYEFFQD 57 (64)
T ss_dssp HHHCTSTT--HHHHHHHHHHHH-
T ss_pred HHHhccCCcCHHHHHHHHHHHCC
Confidence 68999999999999999999863
No 235
>KOG0194 consensus Protein tyrosine kinase [Signal transduction mechanisms]
Probab=51.82 E-value=40 Score=42.07 Aligned_cols=77 Identities=25% Similarity=0.374 Sum_probs=55.8
Q ss_pred CCCcccCCHHH-HHHHhhcCCCCcEEEecCCCCCC------ceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceee
Q 039337 968 HPCFQNVTADE-AMKLLSAKEPGESIIRPSSRGPS------YLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLK 1040 (1344)
Q Consensus 968 HP~F~n~~~~q-Ae~~L~~~~~Gd~viRPSSkG~d------~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~ 1040 (1344)
-|+||-+=..+ |+..|.+ .||++||-|--... -|.|-|.+..+++ |+.|...+. ..+.
T Consensus 49 ~~~yHG~l~red~~~lL~~--~GDfLvR~s~~~~~~~~~~~vlSv~~~~~~~~~-h~vi~~~~~------------~~~~ 113 (474)
T KOG0194|consen 49 LPYYHGLLPREDAEKLLKN--DGDFLVRASEPKEGEKREFVVLSVKWSVFKKIK-HYVIKRNGN------------LFFF 113 (474)
T ss_pred CccccccccHhHHHHHhCC--CCceEEEeecccCCcceeEEEEEEEeecCCcee-EEEEEEcCC------------eeEE
Confidence 59999887665 8888887 89999998876433 4455554446666 888877553 2344
Q ss_pred eCCccccchHHHHHHHHhh
Q 039337 1041 IGEDTFEDLDEVVDRYIDP 1059 (1344)
Q Consensus 1041 i~~~~y~DLDEii~~~V~p 1059 (1344)
.+...|..+.+++..|..-
T Consensus 114 ~~~~~F~si~~li~~~~~~ 132 (474)
T KOG0194|consen 114 EGLRKFPTISELVNYYKFS 132 (474)
T ss_pred eccccCCcHHHHHHHHHhc
Confidence 5568999999999988653
No 236
>PHA01623 hypothetical protein
Probab=51.62 E-value=34 Score=29.95 Aligned_cols=45 Identities=20% Similarity=0.252 Sum_probs=32.3
Q ss_pred hhhccccEEEEEecChhhhhhHHHHHHhhhccCCCcchhhhHHHHHHHHHHHHHHHhH
Q 039337 350 KAEEEKLLQVTIKLPEDSLNKLFSDCKEHYLSDGVSKSAQLWNDQRELILKDALDNFL 407 (1344)
Q Consensus 350 raE~egll~v~i~~~~~~~~~~~~~l~~~~~~d~~s~~~~~wn~~r~~~l~~a~~~~L 407 (1344)
..|+|+-+.++|.+|++....+...+. ..+--|.++|++|++.+|
T Consensus 7 ~~~~~k~~r~sVrldeel~~~Ld~y~~-------------~~g~~rSe~IreAI~~yL 51 (56)
T PHA01623 7 STEKKQKAVFGIYMDKDLKTRLKVYCA-------------KNNLQLTQAIEEAIKEYL 51 (56)
T ss_pred chhhccceeEEEEeCHHHHHHHHHHHH-------------HcCCCHHHHHHHHHHHHH
Confidence 568999999999999987655433322 122237889999998865
No 237
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=50.65 E-value=44 Score=30.93 Aligned_cols=51 Identities=25% Similarity=0.329 Sum_probs=37.6
Q ss_pred cCCCcccC-CHHHHHHHhhcC--CCCcEEEecCCCCCCceEEEEEEeCc-eeeEE
Q 039337 967 VHPCFQNV-TADEAMKLLSAK--EPGESIIRPSSRGPSYLTLTLKVYDG-VYAHK 1017 (1344)
Q Consensus 967 ~HP~F~n~-~~~qAe~~L~~~--~~Gd~viRPSSkG~d~L~vTwKv~d~-v~~Hi 1017 (1344)
.||-|..| ++.|..+-|+.. ..|..|+|+|..-...-++-.-..|+ |+|-|
T Consensus 1 tHpgY~AFlTYdevk~~L~~~~~kpGsYiFRlSCTrLGQWAIGyV~~dg~I~QTI 55 (86)
T PF02762_consen 1 THPGYMAFLTYDEVKARLQHYRDKPGSYIFRLSCTRLGQWAIGYVTQDGKILQTI 55 (86)
T ss_dssp S-TTBETT--HHHHHHHHGGGTTSTTEEEEEEESSSTTSEEEEEEETTSEEEEE-
T ss_pred CCCceeEEEeHHHHHHHHHHHhCCcccEEEeeccccccceeEEEEcCCCcEEEec
Confidence 48888774 889999999875 58999999999988887776666665 44433
No 238
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=50.47 E-value=58 Score=28.79 Aligned_cols=64 Identities=16% Similarity=0.238 Sum_probs=40.1
Q ss_pred CeEEEEEEEEEecccEEEEeCCCeEEE-EeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEE
Q 039337 847 GRVVQATVRRVQGQRAICVLESGLAGM-LMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVC 916 (1344)
Q Consensus 847 G~iV~g~V~~V~~~g~fV~L~~gi~Gl-Ih~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSl 916 (1344)
|+.++-+|..++..|-......-+.|+ +..+...- -...+-+||.+++.|+.||.-+..|.+|+
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~AtryH~------~g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHK------EGVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEEEEEEe------cceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 566777888887766433223234444 22232211 12357899999999999998777776663
No 239
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=50.19 E-value=27 Score=48.21 Aligned_cols=66 Identities=15% Similarity=0.185 Sum_probs=50.9
Q ss_pred cccccccccccccc-----cccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh---ccCCCHHHHHhcc
Q 039337 649 TNQVGLDINLAIHR-----EWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT---AHGLGKKVFVNAV 714 (1344)
Q Consensus 649 vn~vGVdiN~A~~~-----~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~---v~~iG~kvf~n~a 714 (1344)
+.-...|||....+ ....--|..|-|||..-|++|++.|+++|+|+|..|+.. .+.+..+++++++
T Consensus 801 i~vlpPdIN~S~~~f~v~~~~Ir~gL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~Li 874 (1151)
T PRK06826 801 IEVLPPDINESYSKFTVEGDKIRFGLAAVKNVGENAIDSIVEEREKKGKFKSLVDFCERVDTSQINKRAVESLI 874 (1151)
T ss_pred CEEeCCceecCCCCcEEECCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHH
Confidence 34455788886542 223346888999999999999999988999999999964 3458888888764
No 240
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=50.12 E-value=24 Score=36.46 Aligned_cols=54 Identities=20% Similarity=0.393 Sum_probs=35.9
Q ss_pred CceEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcC
Q 039337 458 APRVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGA 529 (1344)
Q Consensus 458 ~~rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~ 529 (1344)
.+-|+|| |||-+ +-+|+||-+|++++..-. | .-+...+.++|.++.--||+-.-
T Consensus 31 ~~lIVGi--DPG~t-tgiAildL~G~~l~l~S~-----R----------~~~~~evi~~I~~~G~PviVAtD 84 (138)
T PF04312_consen 31 RYLIVGI--DPGTT-TGIAILDLDGELLDLKSS-----R----------NMSRSEVIEWISEYGKPVIVATD 84 (138)
T ss_pred CCEEEEE--CCCce-eEEEEEecCCcEEEEEee-----c----------CCCHHHHHHHHHHcCCEEEEEec
Confidence 4568898 99973 347899999999975211 1 12345678888888555554443
No 241
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=49.97 E-value=28 Score=48.19 Aligned_cols=66 Identities=17% Similarity=0.180 Sum_probs=51.0
Q ss_pred cccccccccccccc-----cccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhc---cCCCHHHHHhcc
Q 039337 649 TNQVGLDINLAIHR-----EWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTA---HGLGKKVFVNAV 714 (1344)
Q Consensus 649 vn~vGVdiN~A~~~-----~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v---~~iG~kvf~n~a 714 (1344)
+.-...|||..... .-..--|..|.|||...|++|++.|+++|+|+|..|+..- ..+.++++++++
T Consensus 797 i~vl~pdin~S~~~f~~~~~~I~~gL~~Ikgvg~~~~~~I~~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li 870 (1135)
T PRK05673 797 IKVLPPDVNESLYDFTVVDGDIRYGLGAIKGVGEGAVEAIVEAREEGGPFKDLFDFCARVDLKKVNKRVLESLI 870 (1135)
T ss_pred CeEeCCceeccCCccEEECCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccCCCCHHHHHHHH
Confidence 33455688876531 1233468899999999999999999999999999999652 568888888764
No 242
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=49.89 E-value=7.7 Score=50.02 Aligned_cols=50 Identities=18% Similarity=0.207 Sum_probs=40.0
Q ss_pred ccchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcE
Q 039337 666 FAPLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFL 717 (1344)
Q Consensus 666 ~~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~Fl 717 (1344)
.+.|.-|+||||++|..|+++... +=.-.+.++|.++ ||+++-++...|+
T Consensus 568 ~s~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~As~eeL~~v--ig~k~A~~I~~~~ 619 (621)
T PRK14671 568 QTELTDIAGIGEKTAEKLLEHFGSVEKVAKASLEELAAV--AGPKTAETIYRYY 619 (621)
T ss_pred hhhhhcCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCHHHHHHHHHHh
Confidence 479999999999999999998732 1122478888877 9999998887775
No 243
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=49.87 E-value=1.3e+02 Score=26.77 Aligned_cols=49 Identities=18% Similarity=0.252 Sum_probs=36.0
Q ss_pred EEEEEEEEec---ccEEEEeCCC-eEEEEeceecCCCccccCcccccCCCCEEEEEEEE
Q 039337 850 VQATVRRVQG---QRAICVLESG-LAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKS 904 (1344)
Q Consensus 850 V~g~V~~V~~---~g~fV~L~~g-i~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~ 904 (1344)
++|+|+...+ || |+.-+.+ .+=++|++++... . -..++.|+.|+..|..
T Consensus 1 ~~G~V~~~~~~kgyG-FI~~~~~~~diFfh~s~~~~~-~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYG-FITSDDGGEDIFFHISDLSGN-G----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEE-EEEETTSSSEEEEEGGGBCSS-S----STS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCce-EEEEcccceeEEecccccccc-c----cccCCCCCEEEEEEEE
Confidence 4799998875 55 5555554 4899999999876 1 3468999999999887
No 244
>PRK15464 cold shock-like protein CspH; Provisional
Probab=49.28 E-value=65 Score=29.52 Aligned_cols=51 Identities=6% Similarity=-0.036 Sum_probs=36.9
Q ss_pred EEEEEEEEec---ccEEEEeC-CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 850 VQATVRRVQG---QRAICVLE-SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 850 V~g~V~~V~~---~g~fV~L~-~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
++|+|+...+ || |+..+ .+-+-|+|++.|... -...+.+||.|...|..-.
T Consensus 5 ~~G~Vk~fn~~KGfG-FI~~~~g~~DvFvH~s~l~~~-----g~~~l~~G~~V~f~v~~~~ 59 (70)
T PRK15464 5 MTGIVKTFDRKSGKG-FIIPSDGRKEVQVHISAFTPR-----DAEVLIPGLRVEFCRVNGL 59 (70)
T ss_pred ceEEEEEEECCCCeE-EEccCCCCccEEEEehhehhc-----CCCCCCCCCEEEEEEEECC
Confidence 4799998864 55 56554 457999999998644 1235899999999887643
No 245
>PRK08609 hypothetical protein; Provisional
Probab=49.23 E-value=15 Score=47.06 Aligned_cols=51 Identities=22% Similarity=0.227 Sum_probs=37.2
Q ss_pred chhhccCCCHHHHHHHHHHHHhcCCCCCH-----------HHHhhccCCCHHHHHhccCcEEE
Q 039337 668 PLQFISGLGPRKAASLQRSLVRAGAIFTR-----------KDFVTAHGLGKKVFVNAVGFLRV 719 (1344)
Q Consensus 668 ~Lq~v~GlGprkA~~ii~~r~~~g~~~sr-----------~~L~~v~~iG~kvf~n~a~FlrI 719 (1344)
.|+.|||||++.|+.|.++++ .|.+.-. .+|.+|+|||||+-.+.-.-+-|
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~-tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~~lGi 110 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRE-TGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYKELGV 110 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHH-hCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHHHhCC
Confidence 578999999999999999985 4455433 34567889999876665444444
No 246
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=48.95 E-value=14 Score=31.82 Aligned_cols=30 Identities=27% Similarity=0.299 Sum_probs=21.6
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT 701 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~ 701 (1344)
.++..|-|+||++|+..++. -++|.+||.+
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~-----G~rtl~Dl~~ 31 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAK-----GIRTLEDLRK 31 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHT-----T--SHHHHHH
T ss_pred cchhhcccccHHHHHHHHHh-----CCCCHHHHhh
Confidence 36889999999999999872 5899999964
No 247
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=48.60 E-value=30 Score=47.43 Aligned_cols=66 Identities=23% Similarity=0.204 Sum_probs=50.6
Q ss_pred ccccccccccccc-----ccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh---ccCCCHHHHHhcc
Q 039337 649 TNQVGLDINLAIH-----REWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT---AHGLGKKVFVNAV 714 (1344)
Q Consensus 649 vn~vGVdiN~A~~-----~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~---v~~iG~kvf~n~a 714 (1344)
+.-...|||.... .....--|..|.|||...|++|++.|+++|+|+|..|+.. .+++..+++++++
T Consensus 801 i~v~ppdin~S~~~f~~~~~~i~~gl~~Ikgig~~~~~~Iv~~R~~~~~f~s~~Df~~R~~~~~~~~~~le~Li 874 (1022)
T TIGR00594 801 IEVLPPDINESGQDFAVEDKGIRYGLGAIKGVGESVVKSIIEERNKNGPFKSLFDFINRVDFKKLNKKVLEALI 874 (1022)
T ss_pred CEEECCcccccCCCcEEECCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHH
Confidence 3344568887543 1123447889999999999999999988999999999964 3468888888765
No 248
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=48.30 E-value=3.3e+02 Score=33.56 Aligned_cols=8 Identities=25% Similarity=0.709 Sum_probs=3.6
Q ss_pred CCCCCCCC
Q 039337 1183 ASAGSGWG 1190 (1344)
Q Consensus 1183 ~~~~~~~g 1190 (1344)
|...+||.
T Consensus 454 g~rTPgw~ 461 (607)
T COG5164 454 GYRTPGWK 461 (607)
T ss_pred CCcCcCcc
Confidence 33445554
No 249
>PRK10943 cold shock-like protein CspC; Provisional
Probab=47.92 E-value=80 Score=28.74 Aligned_cols=52 Identities=12% Similarity=0.075 Sum_probs=37.8
Q ss_pred EEEEEEEEEec---ccEEEEe-CCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 849 VVQATVRRVQG---QRAICVL-ESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 849 iV~g~V~~V~~---~g~fV~L-~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
.++|+|+...+ || |+.- +.+-+=|+|+|.+... -...+.+||.|...|..-+
T Consensus 3 ~~~G~Vk~f~~~kGfG-FI~~~~g~~dvFvH~s~l~~~-----g~~~l~~G~~V~f~~~~~~ 58 (69)
T PRK10943 3 KIKGQVKWFNESKGFG-FITPADGSKDVFVHFSAIQGN-----GFKTLAEGQNVEFEIQDGQ 58 (69)
T ss_pred ccceEEEEEeCCCCcE-EEecCCCCeeEEEEhhHcccc-----CCCCCCCCCEEEEEEEECC
Confidence 46899998754 56 5555 4467999999998754 1235789999999877644
No 250
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=47.27 E-value=93 Score=28.84 Aligned_cols=58 Identities=12% Similarity=0.057 Sum_probs=39.7
Q ss_pred EEEEEEEec---ccEEEEe-CCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEE
Q 039337 851 QATVRRVQG---QRAICVL-ESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFL 914 (1344)
Q Consensus 851 ~g~V~~V~~---~g~fV~L-~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~L 914 (1344)
+|+|+-..+ || |+.. +.+.+-|+|+|.|.... ...+..||.|...|..-.....-+.+
T Consensus 3 ~G~Vkwfn~~KGfG-FI~~~~gg~dVFvH~s~i~~~g-----~~~l~~G~~V~f~~~~~~~G~~A~~V 64 (74)
T PRK09937 3 KGTVKWFNNAKGFG-FICPEGGGEDIFAHYSTIQMDG-----YRTLKAGQSVQFDVHQGPKGNHASVI 64 (74)
T ss_pred CeEEEEEeCCCCeE-EEeeCCCCccEEEEEeeccccC-----CCCCCCCCEEEEEEEECCCCceeeEE
Confidence 478887654 55 5544 45689999999987541 23579999999998876554433333
No 251
>KOG0194 consensus Protein tyrosine kinase [Signal transduction mechanisms]
Probab=46.91 E-value=74 Score=39.79 Aligned_cols=80 Identities=23% Similarity=0.289 Sum_probs=58.6
Q ss_pred cccccC--CHHHHHHHHHHHHHhCCCcceEEEEeCCCCCc---EE-EEEEecC--CCCceeeEEEecCceEEcc-ccccc
Q 039337 1071 RKFRKG--SKAEVDELLRIEKAEFPTRIVYGFGISHEHPG---TF-ILTYIRS--TNPHHEYIGLYPKGFKFRK-RMFED 1141 (1344)
Q Consensus 1071 ~kf~~g--~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG---~f-~L~~~~~--~~~~~e~i~v~p~gf~~~~-~~~~~ 1141 (1344)
-.|.+| .+++++.+|+. +. =|.+-.+.-.+| .| +|+.+.+ .+++|.-|.-..+.|.+-. ..|++
T Consensus 49 ~~~yHG~l~red~~~lL~~----~G---DfLvR~s~~~~~~~~~~~vlSv~~~~~~~~~h~vi~~~~~~~~~~~~~~F~s 121 (474)
T KOG0194|consen 49 LPYYHGLLPREDAEKLLKN----DG---DFLVRASEPKEGEKREFVVLSVKWSVFKKIKHYVIKRNGNLFFFEGLRKFPT 121 (474)
T ss_pred CccccccccHhHHHHHhCC----CC---ceEEEeecccCCcceeEEEEEEEeecCCceeEEEEEEcCCeeEEeccccCCc
Confidence 445566 68999999953 22 266666665554 45 8888875 5677777887787777774 89999
Q ss_pred HHHHHHHHHhhcCCCC
Q 039337 1142 IDRLVAYFQRHIDDPQ 1157 (1344)
Q Consensus 1142 ~~~L~~~fK~~~~d~~ 1157 (1344)
+.+|++|++.+.....
T Consensus 122 i~~li~~~~~~~~~~~ 137 (474)
T KOG0194|consen 122 ISELVNYYKFSKLEIT 137 (474)
T ss_pred HHHHHHHHHhccccee
Confidence 9999999998876544
No 252
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=46.38 E-value=33 Score=47.51 Aligned_cols=66 Identities=14% Similarity=0.136 Sum_probs=50.6
Q ss_pred cccccccccccccc-----cccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh---ccCCCHHHHHhcc
Q 039337 649 TNQVGLDINLAIHR-----EWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT---AHGLGKKVFVNAV 714 (1344)
Q Consensus 649 vn~vGVdiN~A~~~-----~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~---v~~iG~kvf~n~a 714 (1344)
+.-...|||....+ ....--|..|-|||...|++|++.|+++|+|+|..|+.. .+.+.++++++++
T Consensus 812 I~vlpPdIN~S~~~f~~~~~~Ir~GL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~LI 885 (1170)
T PRK07374 812 IEVMPPDINRSGIDFTPKGNRILFGLSAVKNLGDGAIRNIIAARDSDGPFKSLADLCDRLPSNVLNRRSLESLI 885 (1170)
T ss_pred CEEeCCceecCCCCcEEECCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccccCCHHHHHHHH
Confidence 34456788886432 123346888999999999999999998999999999964 2458888888764
No 253
>PTZ00473 Plasmodium Vir superfamily; Provisional
Probab=46.37 E-value=64 Score=38.79 Aligned_cols=10 Identities=10% Similarity=0.238 Sum_probs=4.1
Q ss_pred HHHHHHHHHH
Q 039337 1079 AEVDELLRIE 1088 (1344)
Q Consensus 1079 ~e~e~~L~~~ 1088 (1344)
.|++.+...|
T Consensus 202 ~EL~~F~D~Y 211 (420)
T PTZ00473 202 NELNNFFDKY 211 (420)
T ss_pred HHHHHHHHHH
Confidence 3444444333
No 254
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=46.01 E-value=20 Score=41.74 Aligned_cols=44 Identities=18% Similarity=0.126 Sum_probs=34.5
Q ss_pred cCCCHHHHHHHHHHHHh--cCCCC---------CHHHHhhccCCCHHHHHhccCc
Q 039337 673 SGLGPRKAASLQRSLVR--AGAIF---------TRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 673 ~GlGprkA~~ii~~r~~--~g~~~---------sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
+|++.+||+.|++.-+. +|.+. .+++|+.++|||++|-.-.+-|
T Consensus 172 ~Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr 226 (283)
T PRK10308 172 LGMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALR 226 (283)
T ss_pred CCCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHH
Confidence 69999999999887754 56553 3788999999999987655444
No 255
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=46.01 E-value=38 Score=44.06 Aligned_cols=7 Identities=43% Similarity=0.112 Sum_probs=2.6
Q ss_pred eEEEecC
Q 039337 564 SIVYGDE 570 (1344)
Q Consensus 564 ~v~~v~~ 570 (1344)
.++++||
T Consensus 151 ~~lVlDE 157 (629)
T PRK11634 151 SGLVLDE 157 (629)
T ss_pred eEEEecc
Confidence 3333333
No 256
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR018484 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3G25_D 3GE1_D 2NLX_A 2ITM_A 2ZF5_Y 3L0Q_B 3GG4_B 3I8B_A 3H3O_C 3FLC_X ....
Probab=45.96 E-value=54 Score=36.95 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=23.2
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEE
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLF 489 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~ 489 (1344)
+||| |=|.+++|++++|++|+++..-+
T Consensus 2 ~lgi--DiGTts~K~~l~d~~g~iv~~~~ 28 (245)
T PF00370_consen 2 YLGI--DIGTTSVKAVLFDEDGKIVASAS 28 (245)
T ss_dssp EEEE--EECSSEEEEEEEETTSCEEEEEE
T ss_pred EEEE--EEcccceEEEEEeCCCCEEEEEE
Confidence 6777 88889999999999999997544
No 257
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=45.79 E-value=38 Score=42.18 Aligned_cols=6 Identities=0% Similarity=0.130 Sum_probs=2.7
Q ss_pred eEEEEc
Q 039337 523 HVVVLG 528 (1344)
Q Consensus 523 ~vIaIG 528 (1344)
|+|+++
T Consensus 40 dvlv~a 45 (456)
T PRK10590 40 DLMASA 45 (456)
T ss_pred CEEEEC
Confidence 444443
No 258
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=45.50 E-value=36 Score=46.17 Aligned_cols=65 Identities=23% Similarity=0.334 Sum_probs=50.2
Q ss_pred ccccccccccccc-----cccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhc---cCCCHHHHHhcc
Q 039337 650 NQVGLDINLAIHR-----EWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTA---HGLGKKVFVNAV 714 (1344)
Q Consensus 650 n~vGVdiN~A~~~-----~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v---~~iG~kvf~n~a 714 (1344)
.-...|||..... ....--|..|.|||...|++|++.|+++|+|+|..|+..- +.+..+++++++
T Consensus 731 ~vlpPdin~S~~~~~~~~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li 803 (973)
T PRK07135 731 KVYSPDINFSTENAVFDNGKIFLPLIMIKGLGSVAIKKIIDERNKNGKYKNFFDFILRLKFIGISKSIIEKLI 803 (973)
T ss_pred EEeCCceeccCCcceeECCEEEECccccCCcCHHHHHHHHHHHHhCCCCCCHHHHHHhccccCCCHHHHHHHH
Confidence 3345688876542 2233468889999999999999999989999999999652 468888888764
No 259
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=45.34 E-value=1.7e+02 Score=34.65 Aligned_cols=6 Identities=17% Similarity=0.252 Sum_probs=2.9
Q ss_pred ccccCc
Q 039337 1032 LVGIGK 1037 (1344)
Q Consensus 1032 ~~sLG~ 1037 (1344)
.+.||+
T Consensus 90 ~~klG~ 95 (318)
T PF06682_consen 90 EYKLGS 95 (318)
T ss_pred ceeecc
Confidence 455554
No 260
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=45.22 E-value=23 Score=40.94 Aligned_cols=10 Identities=30% Similarity=0.531 Sum_probs=6.6
Q ss_pred EEEecCCCCC
Q 039337 991 SIIRPSSRGP 1000 (1344)
Q Consensus 991 ~viRPSSkG~ 1000 (1344)
||+-||+.|.
T Consensus 68 Vv~vpSt~g~ 77 (271)
T COG1512 68 VVTVPSTGGE 77 (271)
T ss_pred EEEecCCCCC
Confidence 5667777754
No 261
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=44.76 E-value=60 Score=41.93 Aligned_cols=9 Identities=33% Similarity=0.844 Sum_probs=4.4
Q ss_pred hHHHHHHHH
Q 039337 1049 LDEVVDRYI 1057 (1344)
Q Consensus 1049 LDEii~~~V 1057 (1344)
+.+||...|
T Consensus 456 ~~~liD~~v 464 (1102)
T KOG1924|consen 456 LTELIDKMV 464 (1102)
T ss_pred HHHHHHHHH
Confidence 445555544
No 262
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=44.58 E-value=72 Score=36.61 Aligned_cols=72 Identities=17% Similarity=0.157 Sum_probs=48.8
Q ss_pred ccCCeEEEEEEEEEecccEEEEeCCCe-EEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccccc
Q 039337 844 LAEGRVVQATVRRVQGQRAICVLESGL-AGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESEMR 922 (1344)
Q Consensus 844 l~~G~iV~g~V~~V~~~g~fV~L~~gi-~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~dl~ 922 (1344)
.++|++....|.+.++||+|+.=+.+- .=++|.++..+ +.+.+||.|+|=| .+|.+ .++-++++...+.
T Consensus 3 ~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~--------~e~evGdev~vFi-Y~D~~-~rl~aTt~~p~~t 72 (287)
T COG2996 3 IKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEE--------DELEVGDEVTVFI-YVDSE-DRLIATTREPKAT 72 (287)
T ss_pred ccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcC--------CccccCcEEEEEE-EECCC-CceeheeecceEe
Confidence 578999999999999999999765543 34555554322 2478899999854 46654 3566666655544
Q ss_pred ccc
Q 039337 923 NNR 925 (1344)
Q Consensus 923 ~~~ 925 (1344)
.+.
T Consensus 73 vg~ 75 (287)
T COG2996 73 VGE 75 (287)
T ss_pred ecc
Confidence 333
No 263
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=44.36 E-value=43 Score=45.01 Aligned_cols=83 Identities=16% Similarity=0.199 Sum_probs=58.5
Q ss_pred HHHHHHHhhCcccccCCHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEEEEecCCCCc---------ee-eEEEecC
Q 039337 1061 VSHLKAMLSYRKFRKGSKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFILTYIRSTNPH---------HE-YIGLYPK 1130 (1344)
Q Consensus 1061 ~~~v~~i~~h~kf~~g~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~---------~e-~i~v~p~ 1130 (1344)
+..+..+++|+.|++-+-++++++|.. -+..--.+=+|.+--.+..+.++.+..+. +| +++ ...
T Consensus 1099 ~~r~~RvI~HP~F~n~n~eQAe~yL~~-----~d~ge~iiRpSSrgddhLvvtwKVsD~iYqhidV~E~eKEn~fs-lg~ 1172 (1299)
T KOG1856|consen 1099 KQRVSRVIAHPLFKNLNAEQAEAYLSD-----MDQGELIIRPSSRGDDHLVVTWKVSDGIYQHIDVQELEKENYFS-LGK 1172 (1299)
T ss_pred HhhhhhhhcCccccCCCHHHHHHHHHh-----cccccEEeccccCCCCceEEEEEecCchhhhhhhhhhhcccccc-ccc
Confidence 456789999999999999999999943 23444445556677778888998875421 34 333 333
Q ss_pred ceEEcccccccHHHHHHHH
Q 039337 1131 GFKFRKRMFEDIDRLVAYF 1149 (1344)
Q Consensus 1131 gf~~~~~~~~~~~~L~~~f 1149 (1344)
-+.-.+..|.+||++|.-|
T Consensus 1173 ~l~i~~e~feDLDEiI~r~ 1191 (1299)
T KOG1856|consen 1173 TLWIGGEEFEDLDEIIARY 1191 (1299)
T ss_pred eEEECCcccccHHHHHHHH
Confidence 3444588999999998754
No 264
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=44.27 E-value=22 Score=41.54 Aligned_cols=50 Identities=24% Similarity=0.343 Sum_probs=36.9
Q ss_pred hhhccCCCHHHHHHHHHHHHhcCCCCCH-----------HHHhhccCCCHHHHHhccCcEEE
Q 039337 669 LQFISGLGPRKAASLQRSLVRAGAIFTR-----------KDFVTAHGLGKKVFVNAVGFLRV 719 (1344)
Q Consensus 669 Lq~v~GlGprkA~~ii~~r~~~g~~~sr-----------~~L~~v~~iG~kvf~n~a~FlrI 719 (1344)
|..++|||+..|..|..|++ .|.+.-- .+|++++|+|||.+...---|-|
T Consensus 55 ~t~l~gIGk~ia~~I~e~l~-tG~~~~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi 115 (326)
T COG1796 55 LTELPGIGKGIAEKISEYLD-TGEVKKLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELGI 115 (326)
T ss_pred cCCCCCccHHHHHHHHHHHH-cCccHHHHHHHHhCCcchHHHhhCCCCCcHHHHHHHHHHCc
Confidence 77899999999999999985 4555444 44567899999877665444433
No 265
>PF03934 T2SK: Type II secretion system (T2SS), protein K; InterPro: IPR005628 Members of this family are involved in the general secretion pathway. The family includes proteins such as ExeK, PulK, OutX and XcpX.; GO: 0009306 protein secretion, 0016021 integral to membrane; PDB: 3CI0_K.
Probab=43.82 E-value=26 Score=40.69 Aligned_cols=67 Identities=12% Similarity=0.127 Sum_probs=43.5
Q ss_pred ccccccccc---------cccccchhhccCCC----HHHHHHHHHHHHhc-------------------------CCCCC
Q 039337 654 LDINLAIHR---------EWQFAPLQFISGLG----PRKAASLQRSLVRA-------------------------GAIFT 695 (1344)
Q Consensus 654 VdiN~A~~~---------~~~~~~Lq~v~GlG----prkA~~ii~~r~~~-------------------------g~~~s 695 (1344)
+|||.+... ..+..|| -..|+. ...|.+|++++... ++|.+
T Consensus 76 fNLN~L~~~~~~~~~~~~~~~~rLl-~~lg~~~~~a~~la~~i~Dw~D~d~~~~~~~GaE~~~Y~~~~~py~~~n~~~~~ 154 (280)
T PF03934_consen 76 FNLNNLVDNDGQIDPEAQAQFQRLL-EALGLDEQEAERLADAIVDWIDADSNPTRPGGAEDSYYQSLDPPYRPANRPFAS 154 (280)
T ss_dssp EEGGGGGS---SSS-HHHHHHHHHH-HTTT--HHHHHHHHHHHHHHHSSSSS--SSS---HHHHHTSSS-B----S--SS
T ss_pred eeHHHhcccccccchHHHHHHHHHH-HHcCCchhHHHHHHHHHHHHHhccCcccCCCCccccchhhcCCCCCCcCCCCCC
Confidence 788887432 1122333 357788 67777778877543 56899
Q ss_pred HHHHhhccCCCHHHHHhccCcEEEec
Q 039337 696 RKDFVTAHGLGKKVFVNAVGFLRVRR 721 (1344)
Q Consensus 696 r~~L~~v~~iG~kvf~n~a~FlrI~~ 721 (1344)
.+||..|+|+.+..|.....||.+.+
T Consensus 155 ~~EL~~v~G~~~~~~~~l~p~vtv~p 180 (280)
T PF03934_consen 155 VSELRLVPGMDPELYERLRPYVTVLP 180 (280)
T ss_dssp GGGGGGSTT--HHHHHHHTTTEE--S
T ss_pred HHHHHhhhhcCHHHHHhhcCcEEEec
Confidence 99999999999999999999999986
No 266
>PRK10702 endonuclease III; Provisional
Probab=42.97 E-value=26 Score=39.01 Aligned_cols=49 Identities=18% Similarity=0.232 Sum_probs=34.3
Q ss_pred chhhccCCC--HHHHHHHHHHHHh-----cC-CCCCHHHHhhccCCCHHHHHhccCc
Q 039337 668 PLQFISGLG--PRKAASLQRSLVR-----AG-AIFTRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 668 ~Lq~v~GlG--prkA~~ii~~r~~-----~g-~~~sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
+.+.|.++| .+||+.|++..+. +| ...+|++|++++|+|+||-.-...|
T Consensus 72 l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~~~p~~~~~Ll~lpGVG~ktA~~ill~ 128 (211)
T PRK10702 72 VKTYIKTIGLYNSKAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNT 128 (211)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCCchHHHHhcCCcccHHHHHHHHHH
Confidence 444444444 7899988766532 45 4578999999999999986655444
No 267
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=42.31 E-value=89 Score=28.46 Aligned_cols=52 Identities=12% Similarity=0.061 Sum_probs=37.2
Q ss_pred EEEEEEEEEec---ccEEEEeC-CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 849 VVQATVRRVQG---QRAICVLE-SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 849 iV~g~V~~V~~---~g~fV~L~-~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
.++|+|+...+ || |+..+ .+-+=|+|++.+... -...+.+||.|...|..-+
T Consensus 3 ~~~G~Vk~f~~~kGyG-FI~~~~g~~dvfvH~s~l~~~-----g~~~l~~G~~V~f~~~~~~ 58 (69)
T PRK09507 3 KIKGNVKWFNESKGFG-FITPEDGSKDVFVHFSAIQTN-----GFKTLAEGQRVEFEITNGA 58 (69)
T ss_pred ccceEEEEEeCCCCcE-EEecCCCCeeEEEEeeccccc-----CCCCCCCCCEEEEEEEECC
Confidence 35788988754 56 56554 456999999998654 1245789999999777644
No 268
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=42.28 E-value=18 Score=40.28 Aligned_cols=36 Identities=17% Similarity=0.160 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHHh----------cC-CCCCHHHHh-hccCCCHHH
Q 039337 674 GLGPRKAASLQRSLVR----------AG-AIFTRKDFV-TAHGLGKKV 709 (1344)
Q Consensus 674 GlGprkA~~ii~~r~~----------~g-~~~sr~~L~-~v~~iG~kv 709 (1344)
|+-..||+.|++..+. ++ ....|++|+ +++|||+|+
T Consensus 84 gf~~~KAk~I~~~~~~~~~l~~~~~~~~~~~~~R~~Ll~~lpGIG~KT 131 (208)
T PRK01229 84 RFYNKRAEYIVEARKLYGKLKEIIKADKDQFEAREFLVKNIKGIGYKE 131 (208)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhccCCchHHHHHHHHcCCCCcHHH
Confidence 5889999998776642 33 368899999 999999986
No 269
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=41.29 E-value=37 Score=36.79 Aligned_cols=50 Identities=18% Similarity=0.112 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHH----h-cCCC---------CC---HHHHhhccCCCHHH----HHhccCcEEEecCC
Q 039337 674 GLGPRKAASLQRSLV----R-AGAI---------FT---RKDFVTAHGLGKKV----FVNAVGFLRVRRSG 723 (1344)
Q Consensus 674 GlGprkA~~ii~~r~----~-~g~~---------~s---r~~L~~v~~iG~kv----f~n~a~FlrI~~~~ 723 (1344)
|+-..||+.|.+.-+ + +|.+ .+ |++|+.++|||+|+ ...|+..+.|.+..
T Consensus 75 Gfy~~KAk~Lk~~a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~~~~~~~ 145 (177)
T TIGR03252 75 RFPGSMAKRVQALAQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQLGVTPEG 145 (177)
T ss_pred CchHHHHHHHHHHHHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHhCCCCcc
Confidence 888999999976543 2 5653 44 78999999999976 44677777777543
No 270
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=41.15 E-value=19 Score=28.57 Aligned_cols=17 Identities=35% Similarity=0.644 Sum_probs=14.9
Q ss_pred hhccCCCHHHHHHHHHH
Q 039337 670 QFISGLGPRKAASLQRS 686 (1344)
Q Consensus 670 q~v~GlGprkA~~ii~~ 686 (1344)
.-|+|+|+++|..||+.
T Consensus 19 ~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 19 PGVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCCcccHHHHHHHHHh
Confidence 56899999999999874
No 271
>PRK15463 cold shock-like protein CspF; Provisional
Probab=41.15 E-value=1e+02 Score=28.20 Aligned_cols=51 Identities=8% Similarity=0.001 Sum_probs=36.6
Q ss_pred EEEEEEEEec---ccEEEEeCC-CeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 850 VQATVRRVQG---QRAICVLES-GLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 850 V~g~V~~V~~---~g~fV~L~~-gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
+.|+|+...+ || |+..+. +-+-|+|++.+... - ...+++||.|...|..-+
T Consensus 5 ~~G~Vk~fn~~kGfG-FI~~~~g~~DvFvH~sal~~~-g----~~~l~~G~~V~f~v~~~~ 59 (70)
T PRK15463 5 MTGIVKTFDGKSGKG-LITPSDGRKDVQVHISALNLR-D----AEELTTGLRVEFCRINGL 59 (70)
T ss_pred ceEEEEEEeCCCceE-EEecCCCCccEEEEehhhhhc-C----CCCCCCCCEEEEEEEECC
Confidence 3799998865 55 565544 57999999998754 1 235789999999876543
No 272
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=40.93 E-value=1.5e+02 Score=27.06 Aligned_cols=51 Identities=16% Similarity=0.154 Sum_probs=36.6
Q ss_pred EEEEEEEEe---cccEEEEeC-CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 850 VQATVRRVQ---GQRAICVLE-SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 850 V~g~V~~V~---~~g~fV~L~-~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
+.|+|+... .|| |+.-+ .+-+=++|++.+... ....+.+||.|...+..-+
T Consensus 5 ~~G~Vk~f~~~kGfG-FI~~~~g~~dvfvH~s~l~~~-----g~~~l~~G~~V~f~~~~~~ 59 (70)
T PRK10354 5 MTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAIQND-----GYKSLDEGQKVSFTIESGA 59 (70)
T ss_pred ceEEEEEEeCCCCcE-EEecCCCCccEEEEEeecccc-----CCCCCCCCCEEEEEEEECC
Confidence 379998874 366 55554 457999999998754 1245799999998776543
No 273
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=40.53 E-value=43 Score=42.20 Aligned_cols=55 Identities=27% Similarity=0.427 Sum_probs=36.4
Q ss_pred ceEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCC
Q 039337 459 PRVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVN 531 (1344)
Q Consensus 459 ~rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t 531 (1344)
+-++|| |||-+ +-+|+||-+|++++..-. +.-+...+.+||..+.--+||-.--|
T Consensus 244 ~lIVGI--DPGiT-tgiAvldldGevl~~~S~---------------r~~~~~eVve~I~~lG~PvvVAtDVt 298 (652)
T COG2433 244 SLIVGI--DPGIT-TGIAVLDLDGEVLDLESR---------------RGIDRSEVVEFISELGKPVVVATDVT 298 (652)
T ss_pred ceEEEe--CCCce-eeEEEEecCCcEEeeecc---------------ccCCHHHHHHHHHHcCCceEEEccCC
Confidence 357788 99973 347899999999986211 12234678999999954444443333
No 274
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=38.91 E-value=1e+02 Score=28.84 Aligned_cols=63 Identities=13% Similarity=0.132 Sum_probs=44.0
Q ss_pred EEEEEEEEecccEE-EEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEec
Q 039337 850 VQATVRRVQGQRAI-CVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRE 918 (1344)
Q Consensus 850 V~g~V~~V~~~g~f-V~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~ 918 (1344)
+.|+|+.....+.| |.+++|..-++|++ .+ +-. .-.++.||.|.|....-|..+.+|.-.+..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~---gK-~rk--~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIR---GK-MRK--RVWINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEc---hh-hcc--cEEEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 56889998877765 57788887777754 32 221 346899999999988777766666555443
No 275
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=38.82 E-value=22 Score=41.61 Aligned_cols=73 Identities=26% Similarity=0.391 Sum_probs=52.6
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh---------ccCCCHHHHHhccCcEEEecCCCCCCccccCCcCcC
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT---------AHGLGKKVFVNAVGFLRVRRSGQAASSSQFIDLLDD 737 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~---------v~~iG~kvf~n~a~FlrI~~~~~~~~~~~~~d~LD~ 737 (1344)
..|.-|+||||+|=..+-+.+ .+++.++|.+ ++|+|+|.=.+..-++..-. +.
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~el----gi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~--------------~~ 154 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKEL----GIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAE--------------ES 154 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHH----CcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHh--------------hh
Confidence 578889999999988887777 4888888854 57888887777776665543 23
Q ss_pred CCCCC--CCHHHHHHHHHHHcC
Q 039337 738 TRIHP--ESYGLAQELAKEVYN 757 (1344)
Q Consensus 738 TrIHP--EsY~~A~kma~dal~ 757 (1344)
++-|| +.|.+|..+...+.+
T Consensus 155 ~~R~~l~~~l~ia~ei~~yl~~ 176 (326)
T COG1796 155 PERIPLSFTLPIAQEIEGYLEE 176 (326)
T ss_pred hhhcchHHHHHHHHHHHHHHHh
Confidence 45566 456777777665543
No 276
>PRK09890 cold shock protein CspG; Provisional
Probab=38.74 E-value=1.8e+02 Score=26.50 Aligned_cols=51 Identities=10% Similarity=0.041 Sum_probs=36.5
Q ss_pred EEEEEEEEec---ccEEEEeCC-CeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 850 VQATVRRVQG---QRAICVLES-GLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 850 V~g~V~~V~~---~g~fV~L~~-gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
++|+|+...+ || |+.-+. +-+=++|+|.+... -...+.+||.|...+..-+
T Consensus 5 ~~G~Vk~f~~~kGfG-FI~~~~g~~dvFvH~s~l~~~-----~~~~l~~G~~V~f~~~~~~ 59 (70)
T PRK09890 5 MTGLVKWFNADKGFG-FITPDDGSKDVFVHFTAIQSN-----EFRTLNENQKVEFSIEQGQ 59 (70)
T ss_pred ceEEEEEEECCCCcE-EEecCCCCceEEEEEeeeccC-----CCCCCCCCCEEEEEEEECC
Confidence 4799988754 56 565554 47999999998754 1235789999999776543
No 277
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=38.47 E-value=65 Score=35.09 Aligned_cols=10 Identities=20% Similarity=0.305 Sum_probs=4.6
Q ss_pred EEcccccccH
Q 039337 1133 KFRKRMFEDI 1142 (1344)
Q Consensus 1133 ~~~~~~~~~~ 1142 (1344)
.++=..|..+
T Consensus 53 w~~V~~fGk~ 62 (182)
T PRK06958 53 WHRVAFFGRL 62 (182)
T ss_pred EEEEEEehHH
Confidence 3444455543
No 278
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=38.46 E-value=1.2e+02 Score=33.51 Aligned_cols=38 Identities=13% Similarity=0.103 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhCCeEEEEcCCCcchhhhHHHHHHHHHHHHh
Q 039337 510 QERLLKFMMDHQPHVVVLGAVNLSCTSLKDDIYEIIFKMVE 550 (1344)
Q Consensus 510 ~~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~~~~~v~~~~~ 550 (1344)
.+.|.+.+.+++||+|+|+....... ..+.+++..+-+
T Consensus 124 ~e~~v~~~~~~~pd~v~lS~~~~~~~---~~~~~~i~~l~~ 161 (197)
T TIGR02370 124 IDTVVEKVKKEKPLMLTGSALMTTTM---YGQKDINDKLKE 161 (197)
T ss_pred HHHHHHHHHHcCCCEEEEccccccCH---HHHHHHHHHHHH
Confidence 36789999999999999998665542 234555554443
No 279
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=37.41 E-value=36 Score=35.37 Aligned_cols=41 Identities=24% Similarity=0.253 Sum_probs=30.3
Q ss_pred cCCCHHHHHHHHHHHHh-----cC-CCCCHHHHhhccCCCHHHHHhc
Q 039337 673 SGLGPRKAASLQRSLVR-----AG-AIFTRKDFVTAHGLGKKVFVNA 713 (1344)
Q Consensus 673 ~GlGprkA~~ii~~r~~-----~g-~~~sr~~L~~v~~iG~kvf~n~ 713 (1344)
+|+..+||+.|++..+. +| .-..++.|++++|||+++-.-.
T Consensus 42 ~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~ 88 (149)
T smart00478 42 LGFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAV 88 (149)
T ss_pred cCChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHH
Confidence 58888999999766532 33 3346888999999999985443
No 280
>PRK14998 cold shock-like protein CspD; Provisional
Probab=36.92 E-value=1.6e+02 Score=27.29 Aligned_cols=57 Identities=12% Similarity=0.029 Sum_probs=39.3
Q ss_pred EEEEEEEec---ccEEEEe-CCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEE
Q 039337 851 QATVRRVQG---QRAICVL-ESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVF 913 (1344)
Q Consensus 851 ~g~V~~V~~---~g~fV~L-~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~ 913 (1344)
+|+|+-..+ || |+.. +.+-+-|+|+|.|... -...+..||.|...|..-+.....+.
T Consensus 3 ~G~Vkwfn~~kGfG-FI~~~~g~~dVFvH~s~l~~~-----g~~~l~~G~~V~f~~~~~~~G~~A~~ 63 (73)
T PRK14998 3 TGTVKWFNNAKGFG-FICPEGGGEDIFAHYSTIQMD-----GYRTLKAGQSVRFDVHQGPKGNHASV 63 (73)
T ss_pred CeEEEEEeCCCceE-EEecCCCCccEEEEeeeeccc-----CCCCCCCCCEEEEEEEECCCCceeEE
Confidence 478887654 56 5544 4567999999998654 12467999999999887655443333
No 281
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=36.87 E-value=36 Score=46.67 Aligned_cols=63 Identities=17% Similarity=0.259 Sum_probs=50.1
Q ss_pred ccccccccccccc----------ccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhcc
Q 039337 651 QVGLDINLAIHRE----------WQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAV 714 (1344)
Q Consensus 651 ~vGVdiN~A~~~~----------~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a 714 (1344)
-...|||.....- -..--|..|.|||...|+.|++.|+ +|+|+|..|+..-.++.+++++++.
T Consensus 790 vlpPdin~S~~~~~~~~~~~~~~~I~~gl~~Ikgvg~~~~~~Iv~~R~-~g~f~s~~Df~~R~~~~~~~le~Li 862 (1046)
T PRK05672 790 VLPVDVNASGWDATLEPLPDGGPAVRLGLRLVRGLGEEAAERIVAARA-RGPFTSVEDLARRAGLDRRQLEALA 862 (1046)
T ss_pred EcCCeeecCCCCceEeeccCCCCcEEechhhcCCCCHHHHHHHHHHhh-cCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3456888865321 2334688999999999999999996 7999999999877678898888765
No 282
>COG4278 Uncharacterized conserved protein [Function unknown]
Probab=36.84 E-value=55 Score=36.49 Aligned_cols=7 Identities=29% Similarity=0.045 Sum_probs=2.8
Q ss_pred ccccCCC
Q 039337 964 RLIVHPC 970 (1344)
Q Consensus 964 RvI~HP~ 970 (1344)
+.|+||-
T Consensus 48 ~~~ry~g 54 (269)
T COG4278 48 IKIRYPG 54 (269)
T ss_pred HHhhCCC
Confidence 3344443
No 283
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=36.53 E-value=1.4e+02 Score=33.09 Aligned_cols=75 Identities=17% Similarity=0.205 Sum_probs=51.6
Q ss_pred cccCCeEEEEEEEEEecccEEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEeccc
Q 039337 843 TLAEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRESE 920 (1344)
Q Consensus 843 ~l~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~d 920 (1344)
--.+|+.|-|.|+.-......|+|+.-..+.++.-.+... .+.-.-.+++||.|.|+|...+++ ..-.|+|-.+.
T Consensus 62 iP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~A--tkrNrPnl~vGdliyakv~~a~~~-~Epel~Cids~ 136 (230)
T KOG1004|consen 62 IPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGA--TKRNRPNLQVGDLIYAKVVDANKD-MEPELTCIDST 136 (230)
T ss_pred cCCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCc--cccCCCccccccEEEEEEEecCCC-cCcceEEEccc
Confidence 3468999999999988877788887644555543333221 111223589999999999988754 56677777654
No 284
>PTZ00294 glycerol kinase-like protein; Provisional
Probab=36.38 E-value=1.1e+02 Score=38.67 Aligned_cols=70 Identities=16% Similarity=0.219 Sum_probs=41.5
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEecc--cccccc--chhhhhhhHHHHHHHHHHHHHhC--C---eEEEEcCC
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGC--LTLRSQ--NVRDQQSKKNDQERLLKFMMDHQ--P---HVVVLGAV 530 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~--~~~~~~--~~~~~~~~~~~~~~l~~~i~~~~--p---~vIaIG~~ 530 (1344)
-+||| |=|-+.||++++|.+|+++..-+... ..+... ...+..-.+...+.|.+++.+.. + +|.+||-.
T Consensus 3 ~~lgi--DiGTts~Ka~l~d~~G~~v~~~~~~~~~~~~~~g~~eqd~~~~~~~~~~~l~~~~~~~~~~~~~~~I~aIgis 80 (504)
T PTZ00294 3 YIGSI--DQGTTSTRFIIFDEKGNVVSSHQIPHEQITPHPGWLEHDPEEILRNVYKCMNEAIKKLREKGPSFKIKAIGIT 80 (504)
T ss_pred EEEEE--ecCCCceEEEEECCCCCEEEEEEEeecccCCCCCeEeeCHHHHHHHHHHHHHHHHHHcCCCCccCceEEEEee
Confidence 47887 88889999999999999997533222 111111 00111223333445666666543 3 57777765
Q ss_pred C
Q 039337 531 N 531 (1344)
Q Consensus 531 t 531 (1344)
+
T Consensus 81 ~ 81 (504)
T PTZ00294 81 N 81 (504)
T ss_pred c
Confidence 5
No 285
>PF00464 SHMT: Serine hydroxymethyltransferase; InterPro: IPR001085 Synonym(s): Serine hydroxymethyltransferase, Serine aldolase, Threonine aldolase Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) dependent enzyme and belongs to the aspartate aminotransferase superfamily (fold type I) []. The pyridoxal-P group is attached to a lysine residue around which the sequence is highly conserved in all forms of the enzyme []. The enzyme carries out interconversion of serine and glycine using PLP as the cofactor. SHMT catalyses the transfer of a hydroxymethyl group from N5, N10- methylene tetrahydrofolate to glycine, resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers and the mammalian enzyme forms a homotetramer [, ]. PLP dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalysed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), D-amino acid superfamily (fold type IV) and glycogen phophorylase family (fold type V) [, ]. In vertebrates, glycine hydroxymethyltransferase exists in a cytoplasmic and a mitochondrial form whereas only one form is found in prokaryotes.; GO: 0004372 glycine hydroxymethyltransferase activity, 0006544 glycine metabolic process, 0006563 L-serine metabolic process; PDB: 3GBX_B 3H7F_A 1YJS_A 2VMW_A 2W7H_A 2W7E_A 2VMY_B 2W7L_A 2VMZ_A 2VMS_A ....
Probab=35.47 E-value=12 Score=45.60 Aligned_cols=35 Identities=23% Similarity=0.348 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHhCCeEEEEcCCCcchhhhHHHHHH
Q 039337 509 DQERLLKFMMDHQPHVVVLGAVNLSCTSLKDDIYE 543 (1344)
Q Consensus 509 ~~~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~~~~ 543 (1344)
|.+.|.+++++++|.+|++|...-.+..=++.+.+
T Consensus 157 D~d~l~~~a~~~kPklIi~G~S~y~~~~d~~~~re 191 (399)
T PF00464_consen 157 DYDELEKLAKEHKPKLIICGASSYPRPIDFKRFRE 191 (399)
T ss_dssp -HHHHHHHHHHH--SEEEEE-SSTSS---HHHHHH
T ss_pred CHHHHHHHHhhcCCCEEEECchhccCccCHHHHHH
Confidence 56789999999999999999988776433333333
No 286
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=34.99 E-value=19 Score=40.23 Aligned_cols=53 Identities=19% Similarity=0.159 Sum_probs=43.3
Q ss_pred cchhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcEEE
Q 039337 667 APLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFLRV 719 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~FlrI 719 (1344)
..|+.|+|+++.+|+.|+...-. .=.-.|+++|-.++|+||.+-++.-.|+.-
T Consensus 195 ~~Lt~i~~VnKtda~~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 195 GFLTTIPGVNKTDAQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHHhCCCCCcccHHHHHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhc
Confidence 68999999999999999887632 223467899999999999999988877643
No 287
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=34.92 E-value=41 Score=37.73 Aligned_cols=83 Identities=19% Similarity=0.161 Sum_probs=48.3
Q ss_pred cCCCHHHHHHHHHHHH----hcCC------CCCHHHHhhccCCCHHHHHhccCcEEEecCCCCCCccccCCcCcCCCCCC
Q 039337 673 SGLGPRKAASLQRSLV----RAGA------IFTRKDFVTAHGLGKKVFVNAVGFLRVRRSGQAASSSQFIDLLDDTRIHP 742 (1344)
Q Consensus 673 ~GlGprkA~~ii~~r~----~~g~------~~sr~~L~~v~~iG~kvf~n~a~FlrI~~~~~~~~~~~~~d~LD~TrIHP 742 (1344)
+|+-.+||+.|.+..+ ..|. -..|++|++++|||++|-.-..-|--=.+.-..| ....=++-.-.+-+
T Consensus 87 ~Gf~~~KA~~Lk~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVD--ty~~Rv~~RlG~~~ 164 (218)
T PRK13913 87 SGFYNQKAKRLIDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVCAKEVMVVD--KYSYLFLKKLGIEI 164 (218)
T ss_pred cCCHHHHHHHHHHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHcCCCccccc--hhHHHHHHHcCCCC
Confidence 7899999999876543 2233 3578999999999999866555442111110000 00001111122335
Q ss_pred CCHHHHHHHHHHHcC
Q 039337 743 ESYGLAQELAKEVYN 757 (1344)
Q Consensus 743 EsY~~A~kma~dal~ 757 (1344)
++|+-.+++....+.
T Consensus 165 ~~y~~~~~~~~~~l~ 179 (218)
T PRK13913 165 EDYDELQHFFEKGVQ 179 (218)
T ss_pred CCHHHHHHHHHHhhh
Confidence 678888888877663
No 288
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=34.63 E-value=55 Score=40.23 Aligned_cols=8 Identities=38% Similarity=0.742 Sum_probs=3.4
Q ss_pred cccCCeEE
Q 039337 843 TLAEGRVV 850 (1344)
Q Consensus 843 ~l~~G~iV 850 (1344)
++.-|.+|
T Consensus 87 S~~~GvvI 94 (419)
T KOG0116|consen 87 SLEKGVVI 94 (419)
T ss_pred hccCCeEE
Confidence 44444443
No 289
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=34.30 E-value=1.6e+02 Score=28.99 Aligned_cols=64 Identities=14% Similarity=0.145 Sum_probs=45.0
Q ss_pred eEEEEEEEEEecccEE-EEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEe
Q 039337 848 RVVQATVRRVQGQRAI-CVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCR 917 (1344)
Q Consensus 848 ~iV~g~V~~V~~~g~f-V~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk 917 (1344)
..+.|+|+.....+.| |.+++|..-++|++ .+ +-. .-.++.||.|.|.+...|..+.+|...+.
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~---GK-~Rk--~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 85 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMDGVERMGRIP---GK-MKK--RMWIREGDVVIVAPWDFQDEKADIIWRYT 85 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCCCEEEEEEc---hh-hcc--cEEecCCCEEEEEecccCCCEEEEEEEcC
Confidence 3477999998887765 57788888777754 22 221 34589999999998888876666655443
No 290
>TIGR01314 gntK_FGGY gluconate kinase, FGGY type. Gluconate is derived from glucose in two steps. This model describes one form of gluconate kinase, belonging to the FGGY family of carbohydrate kinases. Gluconate kinase phosphoryates gluconate for entry into the Entner-Douderoff pathway.
Probab=33.55 E-value=1.1e+02 Score=38.66 Aligned_cols=69 Identities=12% Similarity=0.160 Sum_probs=40.2
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEEecc--ccccccc--hhhhhhhHHHHHHHHHHHHHhCC--eEEEEcCCC
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLFTGC--LTLRSQN--VRDQQSKKNDQERLLKFMMDHQP--HVVVLGAVN 531 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~~~~--~~~~~~~--~~~~~~~~~~~~~l~~~i~~~~p--~vIaIG~~t 531 (1344)
+||| |=|.+.+|++++|.+|+++...+... .+++... ..+..-.+.-.+.+.+++.+... ++.+||-++
T Consensus 2 ~lgi--DiGtt~~K~~l~d~~g~i~~~~~~~~~~~~~~~g~~e~d~~~~~~~~~~~i~~~~~~~~~~~~I~~Igis~ 76 (505)
T TIGR01314 2 MIGV--DIGTTSTKAVLFEENGKIVAKSSIGYPLYTPASGMAEENPEEIFEAVLVTIREVSINLEDEDEILFVSFST 76 (505)
T ss_pred EEEE--eccccceEEEEEcCCCCEEEEEEeecccccCCCCCeeeCHHHHHHHHHHHHHHHHHhCCCcCceEEEEEec
Confidence 6787 88989999999999999997644321 1222110 01111223334456666665542 466676654
No 291
>TIGR02628 fuculo_kin_coli L-fuculokinase. Members of this family are L-fuculokinase, from the clade that includes the L-fuculokinase of Escherichia coli. This enzyme catalyzes the second step in fucose catabolism. This family belongs to FGGY family of carbohydrate kinases (pfam02782, pfam00370). It is encoded by the kinase (K) gene of the fucose (fuc) operon.
Probab=33.32 E-value=1.1e+02 Score=38.21 Aligned_cols=27 Identities=15% Similarity=0.279 Sum_probs=23.6
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEE
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLF 489 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~ 489 (1344)
|||| |=|.++||++++|.+|+++....
T Consensus 3 ilgi--D~GTss~K~~l~d~~g~~va~~~ 29 (465)
T TIGR02628 3 ILVL--DCGATNLRAIAINRQGKIVASAS 29 (465)
T ss_pred EEEE--ecCCCcEEEEEEcCCCCEEEEEe
Confidence 7787 88989999999999999997544
No 292
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=32.96 E-value=22 Score=46.28 Aligned_cols=57 Identities=14% Similarity=0.142 Sum_probs=37.0
Q ss_pred ccccccccccccccchhhccCCCHHHHHHHHHHHHhcC--CCCCHHHHhhccCCCHHHHHhccC
Q 039337 654 LDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAG--AIFTRKDFVTAHGLGKKVFVNAVG 715 (1344)
Q Consensus 654 VdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g--~~~sr~~L~~v~~iG~kvf~n~a~ 715 (1344)
.||-.+.. ..|..++|+|+++|++|++.++... +|...-..+.++++|+++-...+.
T Consensus 458 ~Dl~~L~~-----~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~ 516 (652)
T TIGR00575 458 ADLYALKK-----EDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAK 516 (652)
T ss_pred HHHHhcCH-----HHHhhccCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHH
Confidence 34554443 5777889999999999999987532 222222224578889886655554
No 293
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=32.59 E-value=52 Score=35.96 Aligned_cols=44 Identities=23% Similarity=0.241 Sum_probs=32.0
Q ss_pred cCCCHHHHHHHHHHHHh-----cCC-CCCHHHHhhccCCCHHHHHhccCc
Q 039337 673 SGLGPRKAASLQRSLVR-----AGA-IFTRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 673 ~GlGprkA~~ii~~r~~-----~g~-~~sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
+|+-.+||+.|.+.-+. +|. -..+++|++++|||+++-.-+.-|
T Consensus 76 ~G~~~~Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill~ 125 (191)
T TIGR01083 76 IGLYRNKAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNV 125 (191)
T ss_pred cCChHHHHHHHHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHHH
Confidence 36767899998766432 343 357899999999999987665544
No 294
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=32.32 E-value=74 Score=43.92 Aligned_cols=65 Identities=9% Similarity=-0.035 Sum_probs=49.2
Q ss_pred ccccccccccccc-----ccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhh---ccCCCHHHHHhcc
Q 039337 649 TNQVGLDINLAIH-----REWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVT---AHGLGKKVFVNAV 714 (1344)
Q Consensus 649 vn~vGVdiN~A~~-----~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~---v~~iG~kvf~n~a 714 (1344)
+.-...|||.... +....--|..|.|||...|++|++.|++ |+|+|..|+.. ...+.++++++++
T Consensus 779 i~vlpPdin~S~~~f~~~~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~-g~f~s~~Df~~R~~~~~~nk~~le~Li 851 (1107)
T PRK06920 779 FHVLPPSLQRSGYNFQIEGNAIRYSLLSIRNIGMATVTALYEEREK-KMFEDLFEFCLRMPSKFVTERNLEAFV 851 (1107)
T ss_pred CEEeCCeeecCCCCcEEECCeeEechhhcCCCCHHHHHHHHHHhhc-CCCCCHHHHHHHHhccCCCHHHHHHHH
Confidence 3334568887643 1123346889999999999999999976 99999999854 4468899988874
No 295
>PRK15027 xylulokinase; Provisional
Probab=32.14 E-value=1.3e+02 Score=37.80 Aligned_cols=69 Identities=16% Similarity=0.161 Sum_probs=39.3
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEEecc--cccccc--chhhhhhhHHHHHHHHHHHHHhCC-eEEEEcCCC
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLFTGC--LTLRSQ--NVRDQQSKKNDQERLLKFMMDHQP-HVVVLGAVN 531 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~~~~--~~~~~~--~~~~~~~~~~~~~~l~~~i~~~~p-~vIaIG~~t 531 (1344)
+||| |=|.+.+|++++|.+|+++..-...+ .++... ...+..-.+.-.+.+.+++.+..+ +|.+||-.+
T Consensus 2 ~lgI--D~GTts~Ka~l~d~~G~vva~~~~~~~~~~~~~g~~eqd~~~~w~~~~~~~~~l~~~~~~~~I~aI~is~ 75 (484)
T PRK15027 2 YIGI--DLGTSGVKVILLNEQGEVVASQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHSLQDVKALGIAG 75 (484)
T ss_pred EEEE--EecccceEEEEEcCCCCEEEEEeecccccCCCCCccccCHHHHHHHHHHHHHHHHHhCCccceeEEEEec
Confidence 6787 88888999999999999997533222 111111 001111223334456666666533 466676543
No 296
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=31.69 E-value=31 Score=33.37 Aligned_cols=29 Identities=28% Similarity=0.343 Sum_probs=25.7
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHh
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDFV 700 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~ 700 (1344)
+.|+.||||||+.|+.|+. + -+.+.+||+
T Consensus 12 ~~L~~iP~IG~a~a~DL~~-L----Gi~s~~~L~ 40 (93)
T PF11731_consen 12 SDLTDIPNIGKATAEDLRL-L----GIRSPADLK 40 (93)
T ss_pred HHHhcCCCccHHHHHHHHH-c----CCCCHHHHh
Confidence 6899999999999999985 3 599999997
No 297
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=31.46 E-value=2.1e+02 Score=29.84 Aligned_cols=63 Identities=22% Similarity=0.148 Sum_probs=45.5
Q ss_pred ccccCCeEEEEEEEEEeccc---------EEEEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEE
Q 039337 842 DTLAEGRVVQATVRRVQGQR---------AICVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQV 912 (1344)
Q Consensus 842 ~~l~~G~iV~g~V~~V~~~g---------~fV~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I 912 (1344)
+--..|.+++-||..+...| +.|+|+.+...+.|+.. . +| +.+++|+.|++++..+......+
T Consensus 59 els~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~--~-----~p-~~v~iGm~V~~v~~~~~~~~~~~ 130 (140)
T COG1545 59 ELSGEGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVD--V-----DP-DDVEIGMKVEAVFRKREEDGGRG 130 (140)
T ss_pred EeCCCeEEEEEEEEeeCCCCcccCCCEEEEEEEeCCCCceEEEEEe--c-----Cc-ccccCCCEEEEEEEEccccCCce
Confidence 33457999999999998764 57788766667777665 1 12 25799999999999876554443
No 298
>TIGR01315 5C_CHO_kinase FGGY-family pentulose kinase. This model represents a subfamily of the FGGY family of carbohydrate kinases. This subfamily is closely related to a set of ribulose kinases, and many members are designated ribitol kinase. However, the member from Klebsiella pneumoniae, from a ribitol catabolism operon, accepts D-ribulose and to a lesser extent D-arabinitol and ribitol (PubMed:9639934 and JW Lengeler, personal communication); its annotation in GenBank as ribitol kinase is imprecise and may have affected public annotation of related proteins.
Probab=31.39 E-value=1.4e+02 Score=38.20 Aligned_cols=69 Identities=12% Similarity=0.086 Sum_probs=39.4
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEEe--ccccccccc--hhhhhhhHHHHHHHHHHHHHhCC---eEEEEcCCC
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLFT--GCLTLRSQN--VRDQQSKKNDQERLLKFMMDHQP---HVVVLGAVN 531 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~~--~~~~~~~~~--~~~~~~~~~~~~~l~~~i~~~~p---~vIaIG~~t 531 (1344)
+||| |-|.+.||++++|.+|+++..... ...++.... ..+..-...-.+.+.+++.+.+. ++.+||-.+
T Consensus 2 ~lgI--D~GTts~Ka~l~d~~G~i~~~~~~~~~~~~~~~g~~eqdp~~~~~~~~~~i~~~~~~~~~~~~~I~~Igis~ 77 (541)
T TIGR01315 2 YIGV--DVGTGSARACIIDSTGDILALAAQNIKTWTPSSGLEGQSSVYIWQAICNCVKQVLAESKVDPNSVKGIGFDA 77 (541)
T ss_pred EEEE--EecCcCEEEEEEcCCCCEEEEEEeeeeeccCCCCcccCCHHHHHHHHHHHHHHHHHHcCCChhheEEEEecc
Confidence 6787 889899999999999999975332 222222111 01112223334556666766532 255555444
No 299
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=31.31 E-value=1.6e+02 Score=34.54 Aligned_cols=65 Identities=12% Similarity=0.120 Sum_probs=40.3
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHh--CCeEEEEcCC
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDH--QPHVVVLGAV 530 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~--~p~vIaIG~~ 530 (1344)
.++|| |=|.+.++++++|.+|+++...+....... .+..-.+.-.+.+.+++..+ ...+|.||-.
T Consensus 7 ~~lgi--dIggt~i~~~l~d~~g~~l~~~~~~~~~~~----~~~~~~~~i~~~i~~~~~~~~~~~~~iGIgi~ 73 (314)
T COG1940 7 TVLGI--DIGGTKIKVALVDLDGEILLRERIPTPTPD----PEEAILEAILALVAELLKQAQGRVAIIGIGIP 73 (314)
T ss_pred EEEEE--EecCCEEEEEEECCCCcEEEEEEEecCCCC----chhHHHHHHHHHHHHHHHhcCCcCceEEEEec
Confidence 67887 777788999999999999875443321111 01011223344456666665 6778888764
No 300
>KOG4278 consensus Protein tyrosine kinase [Signal transduction mechanisms]
Probab=31.17 E-value=1.1e+02 Score=38.84 Aligned_cols=81 Identities=27% Similarity=0.397 Sum_probs=61.8
Q ss_pred ccccCCCccc-CCHHHHHHHhhcCCCCcEEEecCCCCCCceEEEEEEeCceeeEEEEeecCCCCcCcccccccCceeeeC
Q 039337 964 RLIVHPCFQN-VTADEAMKLLSAKEPGESIIRPSSRGPSYLTLTLKVYDGVYAHKDIIEGGKDHKDIKSLVGIGKTLKIG 1042 (1344)
Q Consensus 964 RvI~HP~F~n-~~~~qAe~~L~~~~~Gd~viRPSSkG~d~L~vTwKv~d~v~~HidV~E~~K~~~~~~~~~sLG~~L~i~ 1042 (1344)
-+-+|-|||- ++-..||-.|.+-=.|.+++|-|-..+..++|.+.-...|| |..|--.+. |+.+.-.
T Consensus 148 SLeKhsWYHGpvSRsaaEy~LsSgInGSFLVRESEsSpgQ~sISlRyeGRVy-HYRINt~~d-----------gK~yvt~ 215 (1157)
T KOG4278|consen 148 SLEKHSWYHGPVSRSAAEYILSSGINGSFLVRESESSPGQYSISLRYEGRVY-HYRINTDND-----------GKMYVTQ 215 (1157)
T ss_pred chhhcccccCccccchhhhhhhcCcccceEEeeccCCCcceeEEEEecceEE-EEEeeccCC-----------ccEEEee
Confidence 3457889985 56666777788888999999999999999999999888888 777643222 3333334
Q ss_pred CccccchHHHHHHH
Q 039337 1043 EDTFEDLDEVVDRY 1056 (1344)
Q Consensus 1043 ~~~y~DLDEii~~~ 1056 (1344)
...|..|-||+..|
T Consensus 216 EsrF~TLaELVHHH 229 (1157)
T KOG4278|consen 216 ESRFRTLAELVHHH 229 (1157)
T ss_pred hhhhhHHHHHHhhc
Confidence 56999999998776
No 301
>PRK00047 glpK glycerol kinase; Provisional
Probab=31.11 E-value=1.4e+02 Score=37.69 Aligned_cols=70 Identities=13% Similarity=0.217 Sum_probs=40.2
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEecc--cccccc--chhhhhhhHHHHHHHHHHHHHhCC---eEEEEcCCC
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGC--LTLRSQ--NVRDQQSKKNDQERLLKFMMDHQP---HVVVLGAVN 531 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~--~~~~~~--~~~~~~~~~~~~~~l~~~i~~~~p---~vIaIG~~t 531 (1344)
.+||| |=|.+.||++++|.+|+++....-.. .+++.. ...+..-.+.-.+.+.+++.+... +|.+||-.+
T Consensus 6 ~~lgi--D~GTts~Ka~l~d~~g~~~~~~~~~~~~~~~~~g~~e~d~~~~~~~~~~~~~~~~~~~~~~~~~I~~Igis~ 82 (498)
T PRK00047 6 YILAL--DQGTTSSRAIIFDHDGNIVSVAQKEFTQIFPQPGWVEHDPNEIWASQLSVIAEALAKAGISPDQIAAIGITN 82 (498)
T ss_pred EEEEE--ecCCCceEEEEECCCCCEEEEEeeeccccCCCCCeEeeCHHHHHHHHHHHHHHHHHHcCCChhHeeEEEEec
Confidence 47888 88989999999999999997633111 112211 001112233344456666655432 366666544
No 302
>PRK10331 L-fuculokinase; Provisional
Probab=31.02 E-value=1.5e+02 Score=37.19 Aligned_cols=28 Identities=18% Similarity=0.267 Sum_probs=24.1
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEE
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLF 489 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~ 489 (1344)
.+||| |=|-++||++++|.+|+++..-.
T Consensus 3 ~~lgI--D~GTt~~Ka~l~d~~G~~~~~~~ 30 (470)
T PRK10331 3 VILVL--DCGATNVRAIAVDRQGKIVARAS 30 (470)
T ss_pred eEEEE--ecCCCceEEEEEcCCCcEEEEEe
Confidence 47888 88989999999999999997543
No 303
>PRK13766 Hef nuclease; Provisional
Probab=30.23 E-value=27 Score=46.56 Aligned_cols=51 Identities=16% Similarity=0.245 Sum_probs=39.6
Q ss_pred chhhccCCCHHHHHHHHHHHHh--cCCCCCHHHHhhccCCCHHHHHhccCcEE
Q 039337 668 PLQFISGLGPRKAASLQRSLVR--AGAIFTRKDFVTAHGLGKKVFVNAVGFLR 718 (1344)
Q Consensus 668 ~Lq~v~GlGprkA~~ii~~r~~--~g~~~sr~~L~~v~~iG~kvf~n~a~Flr 718 (1344)
+|..|+|+|+.+|..|+++... .=.-.+.++|..++|+|++.-..+..|+.
T Consensus 716 ~L~~ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence 6899999999999999987521 11224677898899999998888766654
No 304
>PRK13318 pantothenate kinase; Reviewed
Probab=29.69 E-value=2.9e+02 Score=31.58 Aligned_cols=58 Identities=16% Similarity=0.180 Sum_probs=36.1
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhC-----CeEEEEcC
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQ-----PHVVVLGA 529 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~-----p~vIaIG~ 529 (1344)
+|+| |=|.+.+|++++| +|++++..+...-... ....-...+.+++..++ ++-|+||.
T Consensus 2 iL~I--DIGnT~iK~al~d-~g~i~~~~~~~t~~~~--------~~~~~~~~l~~l~~~~~~~~~~i~~I~iss 64 (258)
T PRK13318 2 LLAI--DVGNTNTVFGLYE-GGKLVAHWRISTDSRR--------TADEYGVWLKQLLGLSGLDPEDITGIIISS 64 (258)
T ss_pred EEEE--EECCCcEEEEEEE-CCEEEEEEEEeCCCCC--------CHHHHHHHHHHHHHHcCCCcccCceEEEEE
Confidence 4566 8888999999999 5898876443221100 01223456677777765 55677765
No 305
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=29.61 E-value=44 Score=39.99 Aligned_cols=33 Identities=24% Similarity=0.353 Sum_probs=28.1
Q ss_pred cccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhc
Q 039337 665 QFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTA 702 (1344)
Q Consensus 665 ~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v 702 (1344)
.-..|..|+||||+||+.+.+ + .++|.+||...
T Consensus 87 ~l~~l~~i~GiGpk~a~~l~~-l----Gi~tl~eL~~a 119 (334)
T smart00483 87 SLKLFTNVFGVGPKTAAKWYR-K----GIRTLEELKKN 119 (334)
T ss_pred HHHHHHccCCcCHHHHHHHHH-h----CCCCHHHHHhc
Confidence 335888999999999999987 5 69999999753
No 306
>PF11149 DUF2924: Protein of unknown function (DUF2924); InterPro: IPR021322 This entry is represented by Bacteriophage WO, Gp30. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This bacterial family of proteins has no known function.
Probab=29.07 E-value=44 Score=34.61 Aligned_cols=24 Identities=13% Similarity=0.504 Sum_probs=21.5
Q ss_pred eEEEecCceEEcccccccHHHHHH
Q 039337 1124 YIGLYPKGFKFRKRMFEDIDRLVA 1147 (1344)
Q Consensus 1124 ~i~v~p~gf~~~~~~~~~~~~L~~ 1147 (1344)
-|+|+.+||.|.++.|.||...-.
T Consensus 97 ~V~V~~dGfey~Gr~y~SLSaIAr 120 (136)
T PF11149_consen 97 EVTVLEDGFEYQGRRYKSLSAIAR 120 (136)
T ss_pred EEEEeCCCEEECCccccCHHHHHH
Confidence 499999999999999999987644
No 307
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=28.91 E-value=29 Score=41.45 Aligned_cols=51 Identities=16% Similarity=0.136 Sum_probs=39.4
Q ss_pred ccccccchhhccCCCHHHHHHHHHHHHh-cC-CCCCHHHHhhccCCCHHHHHh
Q 039337 662 REWQFAPLQFISGLGPRKAASLQRSLVR-AG-AIFTRKDFVTAHGLGKKVFVN 712 (1344)
Q Consensus 662 ~~~~~~~Lq~v~GlGprkA~~ii~~r~~-~g-~~~sr~~L~~v~~iG~kvf~n 712 (1344)
.|.---+|..||+|++.-|++|++.... .+ .=.+.++|.+|+|||++.-..
T Consensus 282 ~prGyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 282 SPRGYRLLSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARA 334 (352)
T ss_pred CCcHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHH
Confidence 3555679999999999999999997632 11 124688999999999987554
No 308
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=28.78 E-value=1.6e+02 Score=25.93 Aligned_cols=49 Identities=16% Similarity=0.211 Sum_probs=29.9
Q ss_pred EEEEEEEEEecccEEEEeC----CC--eEEEEeceecCCCccccCcccccCCCCEEEEEEEEE
Q 039337 849 VVQATVRRVQGQRAICVLE----SG--LAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSI 905 (1344)
Q Consensus 849 iV~g~V~~V~~~g~fV~L~----~g--i~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~i 905 (1344)
.++|+|.+|...|.++++. .+ +...|+.+.+ ..-.+++|+.|.+.|...
T Consensus 8 ~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~--------~~l~l~~G~~v~~~ik~~ 62 (69)
T TIGR00638 8 QLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESV--------AELGLKPGKEVYAVIKAP 62 (69)
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHH--------hhCCCCCCCEEEEEEECc
Confidence 5789999998877655442 22 2233332221 122478999999887643
No 309
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.65 E-value=32 Score=37.53 Aligned_cols=21 Identities=29% Similarity=0.599 Sum_probs=18.8
Q ss_pred cchhhccCCCHHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSL 687 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r 687 (1344)
..|+.|||||++.|+.|+=-+
T Consensus 108 ~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 589999999999999998655
No 310
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.65 E-value=32 Score=37.90 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=18.9
Q ss_pred cchhhccCCCHHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSL 687 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r 687 (1344)
..|+.|||||++.|+.||--+
T Consensus 107 ~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 589999999999999998665
No 311
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=28.60 E-value=36 Score=31.50 Aligned_cols=19 Identities=26% Similarity=0.580 Sum_probs=16.6
Q ss_pred chhhccCCCHHHHHHHHHH
Q 039337 668 PLQFISGLGPRKAASLQRS 686 (1344)
Q Consensus 668 ~Lq~v~GlGprkA~~ii~~ 686 (1344)
-++-|+||||++|..||+.
T Consensus 23 ~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 23 NIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred cCCCCCcccHHHHHHHHHH
Confidence 4567999999999999975
No 312
>PRK00254 ski2-like helicase; Provisional
Probab=28.21 E-value=27 Score=46.22 Aligned_cols=51 Identities=16% Similarity=0.268 Sum_probs=38.4
Q ss_pred chhhccCCCHHHHHHHHHH-HHhcC--CCCCHHHHhhccCCCHHHHHhccCcEE
Q 039337 668 PLQFISGLGPRKAASLQRS-LVRAG--AIFTRKDFVTAHGLGKKVFVNAVGFLR 718 (1344)
Q Consensus 668 ~Lq~v~GlGprkA~~ii~~-r~~~g--~~~sr~~L~~v~~iG~kvf~n~a~Flr 718 (1344)
.|..|||+|+.+|+.+.++ ...-. .-.+.++|..++|||+++-++...+|+
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 4567999999999999876 22110 124456677799999999999988877
No 313
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.91 E-value=33 Score=37.85 Aligned_cols=21 Identities=29% Similarity=0.343 Sum_probs=18.8
Q ss_pred cchhhccCCCHHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSL 687 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r 687 (1344)
..|+.|||||++.|+.|+--+
T Consensus 107 ~~L~kvpGIGkKtAerIilEL 127 (197)
T PRK14603 107 RLLTSASGVGKKLAERIALEL 127 (197)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 589999999999999998655
No 314
>COG0112 GlyA Glycine/serine hydroxymethyltransferase [Amino acid transport and metabolism]
Probab=27.70 E-value=1.5e+02 Score=36.01 Aligned_cols=75 Identities=16% Similarity=0.178 Sum_probs=46.3
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCCcchhhhHH
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVNLSCTSLKD 539 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t~s~~~l~~ 539 (1344)
+||++...-|..-++.+=++-.|....++..+. . .+...=|.+.+.++++.++|.+|+.|.+.-++.-=.+
T Consensus 114 timgm~l~~GGHltHg~~v~~sG~~~~~v~Y~v---d------~et~~IDyD~~~k~a~e~kPK~ii~G~SaY~r~id~~ 184 (413)
T COG0112 114 TIMGLDLSHGGHLTHGSPVNFSGKLFNVVSYGV---D------PETGLIDYDEVEKLAKEVKPKLIIAGGSAYSRPIDFK 184 (413)
T ss_pred eEecccCCCCCcccCCCCCCccceeEEeEeccc---c------cccCccCHHHHHHHHHHhCCCEEEECccccccccCHH
Confidence 788886666664444455666777755422121 1 0111235678899999999999999987766533333
Q ss_pred HHHH
Q 039337 540 DIYE 543 (1344)
Q Consensus 540 ~~~~ 543 (1344)
.+++
T Consensus 185 ~~re 188 (413)
T COG0112 185 RFRE 188 (413)
T ss_pred HHHH
Confidence 3333
No 315
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=27.67 E-value=36 Score=44.97 Aligned_cols=49 Identities=14% Similarity=0.138 Sum_probs=25.7
Q ss_pred chhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhccCCCHHHHHhccCc
Q 039337 668 PLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 668 ~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
.|..|+|||+++|+.|++..+++......-..+.-.||+++.-.+...+
T Consensus 118 ~L~~v~gi~~~~~~~i~~~~~~~~~~~~~~~~L~~~gi~~~~a~ki~~~ 166 (720)
T TIGR01448 118 KLLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLGIGIKLAQRIYKF 166 (720)
T ss_pred HHhcCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4556666666666666666654433222223344455665554444443
No 316
>PLN02295 glycerol kinase
Probab=27.26 E-value=1.8e+02 Score=36.78 Aligned_cols=25 Identities=28% Similarity=0.379 Sum_probs=22.5
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEE
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDV 487 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~ 487 (1344)
|||| |-|-+++|.+++|.+|+++..
T Consensus 2 vlgI--D~GTts~Ka~l~d~~G~~~~~ 26 (512)
T PLN02295 2 VGAI--DQGTTSTRFIIYDRDARPVAS 26 (512)
T ss_pred EEEE--ecCCCceEEEEECCCCCEEEE
Confidence 6787 889899999999999999964
No 317
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=27.12 E-value=25 Score=31.71 Aligned_cols=19 Identities=26% Similarity=0.473 Sum_probs=11.7
Q ss_pred hhhccCCCHHHHHHHHHHH
Q 039337 669 LQFISGLGPRKAASLQRSL 687 (1344)
Q Consensus 669 Lq~v~GlGprkA~~ii~~r 687 (1344)
|+.|+|||++.|..|.+++
T Consensus 49 ~~~l~gIG~~ia~kI~E~l 67 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKIDEIL 67 (68)
T ss_dssp HCTSTTTTHHHHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHHHHH
Confidence 5666666666666665554
No 318
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=26.83 E-value=2.6e+02 Score=24.67 Aligned_cols=50 Identities=16% Similarity=0.156 Sum_probs=36.8
Q ss_pred EEEEEEEec---ccEEEEeCC-CeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 851 QATVRRVQG---QRAICVLES-GLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 851 ~g~V~~V~~---~g~fV~L~~-gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
.|+|+...+ || |+..+. +-+=++|.+.+... -...+++||.|...+..-+
T Consensus 2 ~G~Vk~~~~~kGfG-FI~~~~~g~diffh~~~~~~~-----~~~~~~~G~~V~f~~~~~~ 55 (65)
T cd04458 2 TGTVKWFDDEKGFG-FITPDDGGEDVFVHISALEGD-----GFRSLEEGDRVEFELEEGD 55 (65)
T ss_pred cEEEEEEECCCCeE-EEecCCCCcCEEEEhhHhhcc-----CCCcCCCCCEEEEEEEECC
Confidence 578877754 55 565554 78999999998764 1346899999999887653
No 319
>COG0554 GlpK Glycerol kinase [Energy production and conversion]
Probab=26.81 E-value=1.3e+02 Score=37.52 Aligned_cols=59 Identities=14% Similarity=0.130 Sum_probs=38.6
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEE--EEeccccccccch--hhhhhhHHHHHHHHHHHHHh
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDV--LFTGCLTLRSQNV--RDQQSKKNDQERLLKFMMDH 520 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~--~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~i~~~ 520 (1344)
.|||| |.|-+.+++.+.|.+|+++.. ..+..+||.+.=. .+.+-.......|.+.+.+.
T Consensus 6 yIlAi--DqGTTssRaivfd~~g~iva~~q~e~~Q~yP~~GWVEhDp~eIw~~~~~~l~~a~~~~ 68 (499)
T COG0554 6 YILAI--DQGTTSSRAIVFDEDGNIVAIAQREFTQIYPQPGWVEHDPLEIWASVRSVLKEALAKA 68 (499)
T ss_pred EEEEE--ecCCcceeEEEECCCCCchhhhhhhhhhhCCCCCccccCHHHHHHHHHHHHHHHHHHc
Confidence 68998 999999999999999999963 2234556553211 12333444555666666654
No 320
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.76 E-value=33 Score=44.89 Aligned_cols=46 Identities=24% Similarity=0.221 Sum_probs=27.6
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHH---hhccCCCHHHHHhc
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDF---VTAHGLGKKVFVNA 713 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L---~~v~~iG~kvf~n~ 713 (1344)
..|..++|+|+++|++|++.+++.. =.+-..+ +.++++|+++-...
T Consensus 496 ~~L~~l~g~g~Ksa~~Ll~~Ie~sk-~~~l~r~l~ALgIpgIG~~~ak~L 544 (689)
T PRK14351 496 ADLAELEGWGETSAENLLAELEASR-EPPLADFLVALGIPEVGPTTARNL 544 (689)
T ss_pred HHHhcCcCcchhHHHHHHHHHHHHc-cCCHHHHHHHcCCCCcCHHHHHHH
Confidence 3566778888888888888876421 1222223 34777887554333
No 321
>TIGR01311 glycerol_kin glycerol kinase. This model describes glycerol kinase, a member of the FGGY family of carbohydrate kinases.
Probab=26.60 E-value=1.9e+02 Score=36.31 Aligned_cols=28 Identities=21% Similarity=0.439 Sum_probs=24.0
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEE
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLF 489 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~ 489 (1344)
.|||| |=|.+.+|++++|.+|+++....
T Consensus 2 ~~lgi--DiGtt~iKa~l~d~~g~~l~~~~ 29 (493)
T TIGR01311 2 YILAI--DQGTTSSRAIVFDKDGNIVAIHQ 29 (493)
T ss_pred eEEEE--ecCCCceEEEEECCCCCEEEEEe
Confidence 47888 88889999999999999997533
No 322
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=26.55 E-value=33 Score=44.81 Aligned_cols=55 Identities=16% Similarity=0.226 Sum_probs=34.6
Q ss_pred ccccccccccccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHH---hhccCCCHHHHHhcc
Q 039337 654 LDINLAIHREWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDF---VTAHGLGKKVFVNAV 714 (1344)
Q Consensus 654 VdiN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L---~~v~~iG~kvf~n~a 714 (1344)
.||-.+.. ..|..++|+|+++|++|++.++..... +-+.+ +.++++|+++-...+
T Consensus 471 ~DL~~L~~-----~~L~~l~gfG~Ksa~~ll~~Ie~sk~~-~l~R~l~algi~~IG~~~ak~L~ 528 (665)
T PRK07956 471 ADLFKLTA-----EDLLGLEGFGEKSAQNLLDAIEKSKET-SLARFLYALGIRHVGEKAAKALA 528 (665)
T ss_pred HHHHhcCH-----HHHhcCcCcchHHHHHHHHHHHHhhcC-CHHHhhHhhhccCcCHHHHHHHH
Confidence 34554444 467778899999999998888753211 11122 357888887655544
No 323
>PF05642 Sporozoite_P67: Sporozoite P67 surface antigen; InterPro: IPR008845 This family consists of several Theileria P67 surface antigens. A stage specific surface antigen of Theileria parva, p67, is the basis for the development of an anti-sporozoite vaccine for the control of East Coast fever (ECF) in Bos taurus. The antigen has been shown to contain five distinct linear peptide sequences recognised by sporozoite-neutralising murine monoclonal antibodies [].
Probab=26.41 E-value=2.7e+02 Score=35.17 Aligned_cols=10 Identities=0% Similarity=0.282 Sum_probs=5.0
Q ss_pred HHHHHHHHHh
Q 039337 1142 IDRLVAYFQR 1151 (1344)
Q Consensus 1142 ~~~L~~~fK~ 1151 (1344)
|.+.-|-||-
T Consensus 56 lska~~vwks 65 (727)
T PF05642_consen 56 LSKAANVWKS 65 (727)
T ss_pred HHHHHHHHHh
Confidence 4444555663
No 324
>TIGR00064 ftsY signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
Probab=26.33 E-value=8.3e+02 Score=28.31 Aligned_cols=22 Identities=14% Similarity=0.018 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHhCCeEEEEcCC
Q 039337 509 DQERLLKFMMDHQPHVVVLGAV 530 (1344)
Q Consensus 509 ~~~~l~~~i~~~~p~vIaIG~~ 530 (1344)
+.++|..+..+....++..+..
T Consensus 115 a~~ql~~~~~~~~i~~~~~~~~ 136 (272)
T TIGR00064 115 AIEQLEEWAKRLGVDVIKQKEG 136 (272)
T ss_pred HHHHHHHHHHhCCeEEEeCCCC
Confidence 4567777888888777765543
No 325
>PRK10939 autoinducer-2 (AI-2) kinase; Provisional
Probab=26.26 E-value=1.8e+02 Score=36.88 Aligned_cols=27 Identities=22% Similarity=0.316 Sum_probs=23.9
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEE
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVL 488 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~ 488 (1344)
-|||| |-|.+++|++++|.+|+++..-
T Consensus 4 ~~lgI--D~GTts~Ka~l~d~~G~~l~~~ 30 (520)
T PRK10939 4 YLMAL--DAGTGSIRAVIFDLNGNQIAVG 30 (520)
T ss_pred EEEEE--ecCCCceEEEEECCCCCEEEEE
Confidence 48888 8899999999999999999754
No 326
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=26.02 E-value=2.3e+02 Score=25.65 Aligned_cols=50 Identities=12% Similarity=-0.005 Sum_probs=35.2
Q ss_pred EEEEEEEe---cccEEEEeC-CCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 851 QATVRRVQ---GQRAICVLE-SGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 851 ~g~V~~V~---~~g~fV~L~-~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
+|+|+-.. .|| |+..+ .+-+-++|+|.+.... ...+..||.|...+..-+
T Consensus 3 ~G~Vk~f~~~kGfG-FI~~~~g~~dvfvH~s~~~~~g-----~~~l~~G~~V~f~~~~~~ 56 (68)
T TIGR02381 3 IGIVKWFNNAKGFG-FICPEGVDGDIFAHYSTIQMDG-----YRTLKAGQKVQFEVVQGP 56 (68)
T ss_pred CeEEEEEeCCCCeE-EEecCCCCccEEEEHHHhhhcC-----CCCCCCCCEEEEEEEECC
Confidence 47888764 356 55554 4689999999987541 235789999999776544
No 327
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=25.74 E-value=46 Score=39.29 Aligned_cols=32 Identities=34% Similarity=0.441 Sum_probs=27.2
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHhhcc
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDFVTAH 703 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~~v~ 703 (1344)
..|..|+||||++|+.+. .. .+.|.+||...+
T Consensus 85 ~~l~~i~GiGpk~a~~l~-~l----Gi~sl~dL~~a~ 116 (307)
T cd00141 85 LLLLRVPGVGPKTARKLY-EL----GIRTLEDLRKAA 116 (307)
T ss_pred HHHHcCCCCCHHHHHHHH-Hc----CCCCHHHHHHHh
Confidence 477889999999999998 44 699999998755
No 328
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.44 E-value=39 Score=37.00 Aligned_cols=22 Identities=18% Similarity=0.286 Sum_probs=19.2
Q ss_pred cchhhccCCCHHHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSLV 688 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~ 688 (1344)
..|..|||||++.|+.|+--++
T Consensus 108 ~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred HHHhhCCCCCHHHHHHHHHHHH
Confidence 5899999999999999986653
No 329
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=25.39 E-value=1.2e+02 Score=41.15 Aligned_cols=64 Identities=11% Similarity=0.104 Sum_probs=47.6
Q ss_pred ccccccccccccc-------cccccchhhccCCCHHHHHHHHHHHHhcCCCCCHHHHh---hccCCCHHHHHhcc
Q 039337 650 NQVGLDINLAIHR-------EWQFAPLQFISGLGPRKAASLQRSLVRAGAIFTRKDFV---TAHGLGKKVFVNAV 714 (1344)
Q Consensus 650 n~vGVdiN~A~~~-------~~~~~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L~---~v~~iG~kvf~n~a 714 (1344)
.-...|||..... .-..--|..|.|||...|++|++.|+ +|+|+|-.|+. ...++..++.++++
T Consensus 728 ~vlpPdIN~S~~~f~~~~~~~~Ir~gL~~Ikgig~~~~~~I~~~R~-~g~f~~~~df~~r~~~~~i~k~~le~LI 801 (971)
T PRK05898 728 SIKKPDINYSSNSFVLDTQKQIIRFGFNTIKGFGDELLKKIKSALQ-NKTFSDFISYIDALKKNNVSLSNIEILI 801 (971)
T ss_pred eEeCCceeccCCCeEEecCCCeEEecchhcCCcCHHHHHHHHHHHh-cCCCCCHHHHHHHhhhcCCCHHHHHHHH
Confidence 3345677775421 11334688999999999999999995 79999988874 35678899888875
No 330
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.37 E-value=38 Score=37.52 Aligned_cols=22 Identities=32% Similarity=0.448 Sum_probs=19.3
Q ss_pred cchhhccCCCHHHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSLV 688 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~ 688 (1344)
..|+.|||||+++|+.|+--++
T Consensus 109 ~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred HHHhcCCCcCHHHHHHHHHHHH
Confidence 5899999999999999986653
No 331
>PF05268 GP38: Phage tail fibre adhesin Gp38; InterPro: IPR007932 This entry is represented by Bacteriophage T2, Gp38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains several Gp38 proteins from T-even-like phages. Gp38, together with a second phage protein, Gp57, catalyses the organisation of Gp37 but is absent from the phage particle. Gp37 is responsible for receptor recognition [].
Probab=25.35 E-value=2.9e+02 Score=30.76 Aligned_cols=98 Identities=18% Similarity=0.284 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCC--------------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCC
Q 039337 1232 YGGRGRGRGSNNSNRGNS--------------------SNSERQDSSYDTPKWDSANKSGDDSWGNF--PGAKAQNPAGR 1289 (1344)
Q Consensus 1232 ~gg~g~g~g~~~~~gG~G--------------------~g~g~g~gg~~~~~w~~~~~~g~~~~g~~--~~~~~~~~~g~ 1289 (1344)
||..|.|.++...+.-.| +|+|+|++.+....|.....-|+++-..| +++....+++.
T Consensus 115 yGRGGnGs~~~~~g~~GG~~I~N~iG~rLRI~N~GaIAgGGGGGgg~~~~~~~~~~~~~GGGGGRPfG~gG~~~~~~~ga 194 (260)
T PF05268_consen 115 YGRGGNGSGSNSAGAAGGHAIQNDIGGRLRINNNGAIAGGGGGGGGASYQNSWQGNLTFGGGGGRPFGAGGSGSNMSGGA 194 (260)
T ss_pred EecCCCCCCCCCCccccceeeecCCcceEEEecCCEEecCCCCccccccCCCcccceeecCCCCCccCCCCCcCcCCCcc
Q ss_pred CCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 039337 1290 EAFPGGWGSSGGG---GSSGWGGASDGDNGGWGHSSGGADKDS 1329 (1344)
Q Consensus 1290 g~~~gG~g~~g~g---gg~g~gg~~~g~~~g~g~~~~~~~~~~ 1329 (1344)
.+..+-+++.+.+ .+|.+|.-+.-|+..|+.......+++
T Consensus 195 as~~~pG~G~~~~~~y~gG~GGnvG~~Gg~~~~~~g~~~~gGa 237 (260)
T PF05268_consen 195 ASLTAPGGGSGSGSQYYGGNGGNVGAAGGRCNGGNGTEYAGGA 237 (260)
T ss_pred ceeccCCCcccccceeecCCCccccCcccccccCcccccCCCc
No 332
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.21 E-value=40 Score=37.18 Aligned_cols=22 Identities=27% Similarity=0.419 Sum_probs=19.3
Q ss_pred cchhhccCCCHHHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSLV 688 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~ 688 (1344)
..|..|||+|++.|+.|+--++
T Consensus 108 ~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHHH
Confidence 5899999999999999986663
No 333
>PF01548 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 Transposase proteins are necessary for efficient DNA transposition. This entry represents the N-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=24.97 E-value=1.5e+02 Score=30.30 Aligned_cols=106 Identities=19% Similarity=0.269 Sum_probs=60.8
Q ss_pred EeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCCcchhhhHHH
Q 039337 461 VLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVNLSCTSLKDD 540 (1344)
Q Consensus 461 Vlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~ 540 (1344)
++|| |-+..-+.++++|..|.++....+.+ .......|.+.+.++.+.+|++=+...-...|.+
T Consensus 1 ~vGi--Dv~k~~~~v~v~~~~~~~~~~~~~~~-------------~~~~~~~l~~~l~~~~~~~v~~E~tg~y~~~l~~- 64 (144)
T PF01548_consen 1 FVGI--DVSKDTHDVCVIDPNGEKLRRFKFEN-------------DPAGLEKLLDWLASLGPVLVVMEATGGYWRPLAD- 64 (144)
T ss_pred eEEE--EcccCeEEEEEEcCCCcEEEEEEEec-------------cccchhHHhhhhccccccccccccccccchhhhh-
Confidence 4677 55555567789999997776644433 1234567888888887666666443321112221
Q ss_pred HHHHHHHHHhhCCCCcCCCCCcceEEEecCCCchHHhhh--HHhhhcCCCCchhhHHHHHhhhhhcc
Q 039337 541 IYEIIFKMVEEHPRDVGHEMDELSIVYGDESLPRLYENS--RISSDQLPGQKGNVKRAVALGRYLQN 605 (1344)
Q Consensus 541 ~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~a~vy~~s--~~a~~e~p~~~~~~R~avslaR~lqd 605 (1344)
.+.+ ..++|.+|+....+-+..+ ..+. -|. .-|-.||+++..
T Consensus 65 -------~L~~---------~g~~v~~vnp~~~~~~~~~~~~~~K-----tD~--~DA~~ia~~~~~ 108 (144)
T PF01548_consen 65 -------FLQD---------AGIEVVVVNPLQVKRFRKSLGRRAK-----TDK--IDARAIARLLRR 108 (144)
T ss_pred -------heec---------ccccccccccccccccccccccccc-----ccc--cchHHHHHHHhc
Confidence 1211 1467888888766655433 1111 121 247778887776
No 334
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=24.66 E-value=79 Score=37.04 Aligned_cols=42 Identities=24% Similarity=0.430 Sum_probs=30.4
Q ss_pred cchhhccCCCHHHHHHHHHHHHhcCCCCCHHHH------------hhccCCCHHH
Q 039337 667 APLQFISGLGPRKAASLQRSLVRAGAIFTRKDF------------VTAHGLGKKV 709 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r~~~g~~~sr~~L------------~~v~~iG~kv 709 (1344)
+.++.+||+||+.|..|.+.++ .|.+.-.++. .++-|+|.++
T Consensus 56 ~ea~~lP~iG~kia~ki~Eile-tG~l~ele~v~~de~~~~lklFtnifGvG~kt 109 (353)
T KOG2534|consen 56 EEAEKLPGIGPKIAEKIQEILE-TGVLRELEAVRNDERSQSLKLFTNIFGVGLKT 109 (353)
T ss_pred HHhcCCCCCCHHHHHHHHHHHH-cCCchhHHHHhcchhHHHHHHHHHHhccCHHH
Confidence 6788999999999999999884 5555444443 2456666655
No 335
>PRK09698 D-allose kinase; Provisional
Probab=24.36 E-value=2.5e+02 Score=32.62 Aligned_cols=64 Identities=13% Similarity=0.101 Sum_probs=38.3
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCC
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAV 530 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~ 530 (1344)
.++|| |=|.+.++++++|.+|+++.......- . .. .+. ..+.-.+.+.+++.+++.++..||-+
T Consensus 5 ~~lgi--dig~t~i~~~l~d~~g~i~~~~~~~~~--~-~~-~~~-~~~~l~~~i~~~~~~~~~~i~gigia 68 (302)
T PRK09698 5 VVLGI--DMGGTHIRFCLVDAEGEILHCEKKRTA--E-VI-APD-LVSGLGEMIDEYLRRFNARCHGIVMG 68 (302)
T ss_pred EEEEE--EcCCcEEEEEEEcCCCCEEEEEEeCCc--c-cc-chH-HHHHHHHHHHHHHHHcCCCeeEEEEe
Confidence 57887 667777899999999999976443221 1 10 111 12334455677777765455555433
No 336
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=23.91 E-value=6.8e+02 Score=29.90 Aligned_cols=65 Identities=14% Similarity=0.100 Sum_probs=36.7
Q ss_pred CCCcceEEEEeCCCCCcEEEEEEecCCC----CceeeEEEecCceEE----ccccccc--HHHHHHHHHhhcCCCCC
Q 039337 1092 FPTRIVYGFGISHEHPGTFILTYIRSTN----PHHEYIGLYPKGFKF----RKRMFED--IDRLVAYFQRHIDDPQG 1158 (1344)
Q Consensus 1092 np~~i~Y~f~~~~~~PG~f~L~~~~~~~----~~~e~i~v~p~gf~~----~~~~~~~--~~~L~~~fK~~~~d~~P 1158 (1344)
|+=.||=+|.+---||-+==.||+-.++ ..|+| |+++|..| +.=.|++ |-.||.-.=-.|.+.+|
T Consensus 66 ~tYnIPV~iWlldtyP~~pP~c~VnPT~~M~ik~~~h--Vd~nG~V~LPYLh~W~~pssdLv~Liq~l~a~f~~~pP 140 (365)
T KOG2391|consen 66 VTYNIPVIIWLLDTYPYYPPICYVNPTSTMIIKVHEH--VDPNGKVYLPYLHNWDPPSSDLVGLIQELIAAFSEDPP 140 (365)
T ss_pred CcccceEEEEecccCCCCCCeEEecCCchhhhHHhhc--cCCCCeEechhhccCCCccchHHHHHHHHHHHhcCCCc
Confidence 5666777777766677776677775543 22566 78888754 4445554 33444333333444443
No 337
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=23.84 E-value=1.7e+02 Score=25.49 Aligned_cols=47 Identities=23% Similarity=0.266 Sum_probs=27.7
Q ss_pred EEEEEEEEEeccc----EEEEeCCC--eEEEEeceecCCCccccCcccccCCCCEEEEEEE
Q 039337 849 VVQATVRRVQGQR----AICVLESG--LAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIK 903 (1344)
Q Consensus 849 iV~g~V~~V~~~g----~fV~L~~g--i~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi 903 (1344)
.++|+|..|.+.| +.++++.+ +.+.|...... .-.+++||.|.+.|.
T Consensus 6 ~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~--------~L~L~~G~~V~~~ik 58 (64)
T PF03459_consen 6 QLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAE--------ELGLKPGDEVYASIK 58 (64)
T ss_dssp EEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHH--------HCT-STT-EEEEEE-
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHH--------HcCCCCCCEEEEEEe
Confidence 5789999999988 34444544 34454433221 113789999988764
No 338
>COG1070 XylB Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]
Probab=23.72 E-value=2.2e+02 Score=36.08 Aligned_cols=59 Identities=20% Similarity=0.160 Sum_probs=37.7
Q ss_pred eEeEeecCCCCCceEEEEECCC-CCEEEEEEeccccccccc----hhhhhhhHHHHHHHHHHHHHh
Q 039337 460 RVLACCWGPGKPETTFVMLDSS-GEVVDVLFTGCLTLRSQN----VRDQQSKKNDQERLLKFMMDH 520 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~-G~vld~~~~~~~~~~~~~----~~~~~~~~~~~~~l~~~i~~~ 520 (1344)
.+||| |=|.+++|.+++|.+ |+++..-+..+...+..+ ..+..-...-.+.+.+++.+.
T Consensus 5 ~~lgI--DiGTt~~Kavl~d~~~~~~~~~~~~~~~~~~~~~g~~e~d~~~~w~~~~~ai~~l~~~~ 68 (502)
T COG1070 5 YVLGI--DIGTTSVKAVLFDEDGGEVVATARFENPVSTPQPGWAEQDPDELWQAILEALRQLLEES 68 (502)
T ss_pred EEEEE--EcCCCcEEEEEEeCCCCeEEEEeeccccccCCCCCCcccCHHHHHHHHHHHHHHHHHhc
Confidence 58888 888899999999999 899987554443322111 112223344455677777765
No 339
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=23.68 E-value=1.3e+03 Score=29.86 Aligned_cols=27 Identities=22% Similarity=0.314 Sum_probs=23.2
Q ss_pred cccccccccccccchhhccCCCHHHHHHHHHHH
Q 039337 655 DINLAIHREWQFAPLQFISGLGPRKAASLQRSL 687 (1344)
Q Consensus 655 diN~A~~~~~~~~~Lq~v~GlGprkA~~ii~~r 687 (1344)
+|=.|+. +.|..| ||+++.|+.|.+++
T Consensus 539 ~ik~As~-----eeL~~v-gi~~~~A~~I~~~l 565 (567)
T PRK14667 539 DFLKADD-----EELKKL-GIPPSVKQEVKKYL 565 (567)
T ss_pred HHHhCCH-----HHHHHc-CCCHHHHHHHHHHh
Confidence 4567777 789999 99999999999886
No 340
>PLN02271 serine hydroxymethyltransferase
Probab=23.28 E-value=2.1e+02 Score=36.76 Aligned_cols=65 Identities=14% Similarity=0.156 Sum_probs=37.2
Q ss_pred eEeEeecCCCCCceEE------EEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEcCCCcc
Q 039337 460 RVLACCWGPGKPETTF------VMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQPHVVVLGAVNLS 533 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~------a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~p~vIaIG~~t~s 533 (1344)
+||++....|..-+.. ..+...|...+++..... + ....-+.+.|.+++..++|.+|++|+..-.
T Consensus 240 ~IL~ldl~~GGHlshg~~~~~g~~vs~sG~~~~~vpY~~d--------~-~~g~IDyd~lek~a~~~rPKLII~g~Sayp 310 (586)
T PLN02271 240 RIMGLDSPSGGHMSHGYYTPGGKKVSGASIFFESLPYKVN--------P-QTGYIDYDKLEEKALDFRPKILICGGSSYP 310 (586)
T ss_pred EEEEecCCCCCchhcccccccccccccccceEEEEEcccc--------c-ccCccCHHHHHHHhhhcCCeEEEECchhcc
Confidence 7888744445432222 234556766555332110 0 001124567777788999999999886655
No 341
>TIGR01234 L-ribulokinase L-ribulokinase. This enzyme catalyzes the second step in arabinose catabolism. The most closely related protein subfamily outside the scope of this model includes ribitol kinase from E. coli.
Probab=22.88 E-value=2.2e+02 Score=36.22 Aligned_cols=27 Identities=15% Similarity=0.236 Sum_probs=23.5
Q ss_pred eEeEeecCCCCCceEEEEEC-CCCCEEEEE
Q 039337 460 RVLACCWGPGKPETTFVMLD-SSGEVVDVL 488 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd-~~G~vld~~ 488 (1344)
.|||| |-|-++||++++| .+|+++..-
T Consensus 2 ~~lgi--D~GTss~Ka~l~d~~~G~~~a~~ 29 (536)
T TIGR01234 2 YAIGV--DFGTLSGRALAVDVATGEEIATA 29 (536)
T ss_pred eEEEE--ecCCCceEEEEEECCCCcEeeee
Confidence 37888 9999999999999 999999643
No 342
>PF03276 Gag_spuma: Spumavirus gag protein; InterPro: IPR004957 The Spumavirus gag protein is a core viral polyprotein that undergoes specific enzymatic cleavages in vivo to yield the mature protein.; GO: 0019028 viral capsid
Probab=22.85 E-value=1.7e+03 Score=28.50 Aligned_cols=23 Identities=30% Similarity=0.749 Sum_probs=17.2
Q ss_pred ecCCCC--CceEEEEECCCCCEEEE
Q 039337 465 CWGPGK--PETTFVMLDSSGEVVDV 487 (1344)
Q Consensus 465 ~~dpg~--~g~~~a~vd~~G~vld~ 487 (1344)
-||++. .-+.+++.|++|+.|-.
T Consensus 39 wWG~~~Ry~~vri~LQD~~GqPLqq 63 (582)
T PF03276_consen 39 WWGPGDRYQLVRIILQDDSGQPLQQ 63 (582)
T ss_pred cCCCccceeEEEEEEECCCCCcCCC
Confidence 356665 35778889999999865
No 343
>KOG3279 consensus Uncharacterized conserved protein (melanoma antigen P15) [Function unknown]
Probab=22.84 E-value=1.5e+02 Score=32.47 Aligned_cols=109 Identities=18% Similarity=0.119 Sum_probs=58.4
Q ss_pred EEEEEEeCCCCCccccccc--ccccccccccccCcCCCchHHHHHHhhhccccEEEEEecChhhhhhHHHHHHhhhccCC
Q 039337 306 AVVSTCPTPDGDSAIDSFH--QFAGVKWLREKPLRKFEDAQWLLIQKAEEEKLLQVTIKLPEDSLNKLFSDCKEHYLSDG 383 (1344)
Q Consensus 306 a~Ist~~T~kg~~~id~~h--~y~~~Kyl~~kpv~~l~~~q~L~i~raE~egll~v~i~~~~~~~~~~~~~l~~~~~~d~ 383 (1344)
+.|++..|+....-||+.| +||..| + |- +++......++.++|.-.+.. +
T Consensus 126 ~y~~v~vteRtl~LIDE~~GLD~YILk---~-~~-----------------------~DL~SKFa~~LKReMLL~L~~-~ 177 (283)
T KOG3279|consen 126 CYMSVVVTERTLELIDECHGLDHYILK---N-RA-----------------------CDLRSKFALKLKREMLLALQN-G 177 (283)
T ss_pred hhheeeehHHHHHHHHHhcCcceeeec---C-cc-----------------------hhHHHHHHHHHHHHHHHHHhc-C
Confidence 4577888888888999987 444332 2 21 122232223333333211111 1
Q ss_pred CcchhhhHHHHHHHHHHHHHHHhHHhHHHHHH-HHHHHHHHHH-----------HHHHHHHHHHHHHHccCCC
Q 039337 384 VSKSAQLWNDQRELILKDALDNFLLPSMVKEA-RSLMSGRAKS-----------WLLMEYGKALWNKVSVGPY 444 (1344)
Q Consensus 384 ~s~~~~~wn~~r~~~l~~a~~~~L~P~~~rev-r~~L~~~Ae~-----------~~i~~~~~nL~~~L~~~P~ 444 (1344)
.. .-.=|.+|+..|.+-|++|++|.=+.|. =-.|.+.++. -+-..|...|-+.|.|+-.
T Consensus 178 ~p--~~~E~pEr~A~I~~KY~~F~IPEeEAEW~GLtL~EAirKQ~~lEe~~~PvPLk~~f~~~LieqLrq~~~ 248 (283)
T KOG3279|consen 178 VP--ALAEEPERQAEILKKYRRFLIPEEEAEWYGLTLLEAIRKQKQLEEAEKPVPLKLEFRGKLIEQLRQAGI 248 (283)
T ss_pred CC--cccCChHHHHHHHHHHHHhcCCHHHhhHhhhHHHHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhhhh
Confidence 10 1122567888888888888888776553 2233333222 2344677777777777544
No 344
>PRK10880 adenine DNA glycosylase; Provisional
Probab=22.21 E-value=70 Score=38.48 Aligned_cols=50 Identities=20% Similarity=0.306 Sum_probs=36.8
Q ss_pred cchhhccCCCH-HHHHHHHHHHH----h-cCC-CCCHHHHhhccCCCHHHHHhccCc
Q 039337 667 APLQFISGLGP-RKAASLQRSLV----R-AGA-IFTRKDFVTAHGLGKKVFVNAVGF 716 (1344)
Q Consensus 667 ~~Lq~v~GlGp-rkA~~ii~~r~----~-~g~-~~sr~~L~~v~~iG~kvf~n~a~F 716 (1344)
.++..+.|+|= +||++|.+.-+ + +|. ..++++|++++|||++|-.-...|
T Consensus 72 el~~~~~glGyy~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 72 EVLHLWTGLGYYARARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred HHHHHHHcCChHHHHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHH
Confidence 67777877775 67888876543 2 454 477999999999999986655544
No 345
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=21.81 E-value=2.4e+02 Score=33.79 Aligned_cols=75 Identities=20% Similarity=0.235 Sum_probs=54.4
Q ss_pred ccccCCHHHHHHHHHHHHHhCCCcceEEEEeCCCCCcEEEEEEecCCCCceeeEEEecCceEEc-ccccccHHHHHHHHH
Q 039337 1072 KFRKGSKAEVDELLRIEKAEFPTRIVYGFGISHEHPGTFILTYIRSTNPHHEYIGLYPKGFKFR-KRMFEDIDRLVAYFQ 1150 (1344)
Q Consensus 1072 kf~~g~~~e~e~~L~~~~~~np~~i~Y~f~~~~~~PG~f~L~~~~~~~~~~e~i~v~p~gf~~~-~~~~~~~~~L~~~fK 1150 (1344)
||-+-+++||.+.|. -.|+.+.-.=-++. -||-+.|+-+-..+..-=-|-+...-|=|- .-+|.|+-+|||+++
T Consensus 26 YWgdisReev~~~L~----d~PDGsFlVRdAst-m~GdYTLtl~k~g~~KLikI~h~DgKyGF~d~ltf~SVVelIn~yr 100 (464)
T KOG4637|consen 26 YWGDISREEVNKKLR----DQPDGSFLVRDAST-MQGDYTLTLRKGGNNKLIKIVHRDGKYGFSDPLTFNSVVELINHYR 100 (464)
T ss_pred cccccCHHHHHHHhc----CCCCCcEEeecccc-CCCceEEEEecCCccceeeeEEecCccCCCCchhhHHHHHHHHHHh
Confidence 455678999999995 57887754444444 799999999887655443444444444444 779999999999999
Q ss_pred h
Q 039337 1151 R 1151 (1344)
Q Consensus 1151 ~ 1151 (1344)
.
T Consensus 101 ~ 101 (464)
T KOG4637|consen 101 N 101 (464)
T ss_pred h
Confidence 4
No 346
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=21.69 E-value=40 Score=37.66 Aligned_cols=13 Identities=38% Similarity=0.687 Sum_probs=5.7
Q ss_pred HHHHHHhhcCCCC
Q 039337 1145 LVAYFQRHIDDPQ 1157 (1344)
Q Consensus 1145 L~~~fK~~~~d~~ 1157 (1344)
=+.||..++.|+.
T Consensus 111 ev~~fnnY~~Dp~ 123 (214)
T PF04959_consen 111 EVEYFNNYLLDPK 123 (214)
T ss_dssp HHHHHHHH-----
T ss_pred HHHHHHHHhcCcc
Confidence 3568888888865
No 347
>PF01869 BcrAD_BadFG: BadF/BadG/BcrA/BcrD ATPase family; InterPro: IPR002731 This domain is found in the BadF (O07462 from SWISSPROT) and BadG (O07463 from SWISSPROT) proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase (P11568 from SWISSPROT). The hypothetical protein AQ_278 from Aquifex aeolicus O66634 from SWISSPROT contains two copies of this region suggesting that the family may structurally dimerise.; PDB: 2E2N_B 2E2Q_A 2E2P_B 2E2O_A 1ZBS_A 2CH6_A 2CH5_D 1ZC6_A 1HUX_A.
Probab=21.54 E-value=2.1e+02 Score=32.85 Aligned_cols=28 Identities=25% Similarity=0.372 Sum_probs=22.9
Q ss_pred eEeecCCCCCceEEEEECCCCCEEEEEEec
Q 039337 462 LACCWGPGKPETTFVMLDSSGEVVDVLFTG 491 (1344)
Q Consensus 462 lai~~dpg~~g~~~a~vd~~G~vld~~~~~ 491 (1344)
||| |-|.|.|+++++|.+|+++...+..
T Consensus 1 lGI--DgGgTkt~~vl~d~~g~il~~~~~~ 28 (271)
T PF01869_consen 1 LGI--DGGGTKTKAVLVDENGNILGRGKGG 28 (271)
T ss_dssp EEE--EECSSEEEEEEEETTSEEEEEEEES
T ss_pred CEE--eeChheeeeEEEeCCCCEEEEEEeC
Confidence 566 7788999999999999998765543
No 348
>TIGR03286 methan_mark_15 putative methanogenesis marker protein 15. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. Related proteins include the BadF/BadG/BcrA/BcrD ATPase family (pfam01869), which includes an activator for (R)-2-hydroxyglutaryl-CoA dehydratase.
Probab=21.50 E-value=3.9e+02 Score=32.90 Aligned_cols=49 Identities=14% Similarity=0.198 Sum_probs=32.5
Q ss_pred eEeEeecCCCCCceEEEEECCCCCEEEEEEeccccccccchhhhhhhHHHHHHHHHHHHHhC
Q 039337 460 RVLACCWGPGKPETTFVMLDSSGEVVDVLFTGCLTLRSQNVRDQQSKKNDQERLLKFMMDHQ 521 (1344)
Q Consensus 460 rVlai~~dpg~~g~~~a~vd~~G~vld~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~ 521 (1344)
.++|| |-|.+-+|+|++| +++++.+.+..+.. + .+...+.|.+++++..
T Consensus 145 ~~lGI--DiGSTttK~Vl~d-d~~Ii~~~~~~t~~-------~---~~~a~~~l~~~l~~~G 193 (404)
T TIGR03286 145 LTLGI--DSGSTTTKAVVME-DNEVIGTGWVPTTK-------V---IESAEEAVERALEEAG 193 (404)
T ss_pred EEEEE--EcChhheeeEEEc-CCeEEEEEEeeccc-------H---HHHHHHHHHHHHHHcC
Confidence 47898 9999899999998 57888765543210 1 2334555667776543
No 349
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=21.11 E-value=3.3e+02 Score=25.84 Aligned_cols=65 Identities=12% Similarity=0.129 Sum_probs=43.8
Q ss_pred EEEEEEEEEecccEE-EEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEEeCCCcEEEEEEecc
Q 039337 849 VVQATVRRVQGQRAI-CVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSIQKNRYQVFLVCRES 919 (1344)
Q Consensus 849 iV~g~V~~V~~~g~f-V~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD~~~~~I~LSlk~~ 919 (1344)
.+.|+|+.....+.| |.+.+|..=++|++ .+ +-+ .-.++.||.|.|.....+..+..|...+...
T Consensus 6 q~~g~V~~~lG~~~~~V~~~dG~~~la~ip---gK-~Rk--~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 6 QEIAQVVKMLGNGRLEVMCADGKERLARIP---GK-MRK--KVWIRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEEc---hh-hcc--cEEEcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 367888888777765 57788887777754 32 221 3358999999998877666555665554443
No 350
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=21.10 E-value=3.8e+02 Score=25.16 Aligned_cols=64 Identities=13% Similarity=0.121 Sum_probs=42.6
Q ss_pred EEEEEEEEecccEE-EEeCCCeEEEEeceecCCCccccCcccccCCCCEEEEEEEEE-eCCCcEEEEEEecc
Q 039337 850 VQATVRRVQGQRAI-CVLESGLAGMLMKEDYSDDWRDSELSDKLHEGDILTCKIKSI-QKNRYQVFLVCRES 919 (1344)
Q Consensus 850 V~g~V~~V~~~g~f-V~L~~gi~GlIh~s~lsd~~~~~~~~~~~~vGq~V~vkVi~i-D~~~~~I~LSlk~~ 919 (1344)
+-|+|+.....+.| |.+++|..-++|++ .+ +-.+ -.++.||.|.|..... |..+..|...+..+
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~---gK-~Rk~--iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIP---GK-LRKN--IWIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEc---hh-hccC--EEEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 34788888777765 57788888777754 32 2222 3589999999988776 56666665554443
No 351
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.90 E-value=55 Score=36.06 Aligned_cols=21 Identities=29% Similarity=0.460 Sum_probs=18.4
Q ss_pred cchhhccCCCHHHHHHHHHHH
Q 039337 667 APLQFISGLGPRKAASLQRSL 687 (1344)
Q Consensus 667 ~~Lq~v~GlGprkA~~ii~~r 687 (1344)
..|..|||||+++|+.|+--+
T Consensus 108 ~~L~~vpGIGkKtAerIilEL 128 (194)
T PRK14605 108 ELLSTIPGIGKKTASRIVLEL 128 (194)
T ss_pred HHHHhCCCCCHHHHHHHHHHH
Confidence 578999999999999997655
No 352
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=20.61 E-value=97 Score=35.18 Aligned_cols=73 Identities=25% Similarity=0.297 Sum_probs=56.2
Q ss_pred cCCeEEEEEEEEEecccEEEEeCCCeEEEEeceec--CCC-cccc------CcccccCCCCEEEEEEEEEeCCCcEEEEE
Q 039337 845 AEGRVVQATVRRVQGQRAICVLESGLAGMLMKEDY--SDD-WRDS------ELSDKLHEGDILTCKIKSIQKNRYQVFLV 915 (1344)
Q Consensus 845 ~~G~iV~g~V~~V~~~g~fV~L~~gi~GlIh~s~l--sd~-~~~~------~~~~~~~vGq~V~vkVi~iD~~~~~I~LS 915 (1344)
.+|++|-|+|..|.....-|++.+..++++..|.+ +.. .+-+ ..++.|+.||.|-+.|..+-. ...++|-
T Consensus 84 EvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~-dGs~sLh 162 (301)
T KOG3013|consen 84 EVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFH-DGSLSLH 162 (301)
T ss_pred ccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhcc-CCeEEEE
Confidence 48999999999999999999999999998888754 221 0111 235679999999999998865 4677776
Q ss_pred Eec
Q 039337 916 CRE 918 (1344)
Q Consensus 916 lk~ 918 (1344)
.+.
T Consensus 163 TRS 165 (301)
T KOG3013|consen 163 TRS 165 (301)
T ss_pred ecc
Confidence 554
No 353
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=20.59 E-value=2.7e+02 Score=34.56 Aligned_cols=76 Identities=16% Similarity=0.171 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCC
Q 039337 1189 WGGSTNEGGWNRDRSSTPGSRTGRNDYRNGGGRDGHPSGLPRPYGGRGRGRGSNNSNRGNSSNSE-RQDSSYDTPKW 1264 (1344)
Q Consensus 1189 ~gg~~~~~g~gg~~~~~~~~~~g~~~~~~gg~~~g~~~g~~~~~gg~g~g~g~~~~~gG~G~g~g-~g~gg~~~~~w 1264 (1344)
+..+..+...++..++.++.+..+...++|+.-.++..+++.++++++...|....+.+...++| .+..+++...|
T Consensus 353 Fln~~~ga~g~~~~s~~~g~~~~~~~~~~Gg~a~g~~~gG~~g~~~~~~~~G~~~~~~~~~~~~Gy~g~~~~~~~~~ 429 (510)
T KOG4211|consen 353 FLNGAPGASGGGGPSGPGGVGSSGDRNGGGGYASGSYGGGGNGGGGRGSPYGRPSDGYSSPGGGGYSGPRGYGRGPQ 429 (510)
T ss_pred cccCCcccccCccCCCCCCccccccccCCCCccccccccCCCCCccccCCCCCCcccccCCCCCCCcCcccCCCCcc
No 354
>PRK10116 universal stress protein UspC; Provisional
Probab=20.37 E-value=2.6e+02 Score=28.10 Aligned_cols=50 Identities=16% Similarity=0.191 Sum_probs=33.5
Q ss_pred HHHHHHHHHhCCeEEEEcCCCcchhhhHHHHHHHHHHHHhhCCCCcCCCCCcceEEEecCCC
Q 039337 511 ERLLKFMMDHQPHVVVLGAVNLSCTSLKDDIYEIIFKMVEEHPRDVGHEMDELSIVYGDESL 572 (1344)
Q Consensus 511 ~~l~~~i~~~~p~vIaIG~~t~s~~~l~~~~~~~v~~~~~~~~~~~~~~~~~i~v~~v~~~~ 572 (1344)
+.+.++++++++|+|++|.-..+. +.+.+ ....+++.. .+++|.+|..++
T Consensus 92 ~~I~~~a~~~~~DLiV~g~~~~~~--~~~~~-s~a~~v~~~---------~~~pVLvv~~~~ 141 (142)
T PRK10116 92 EHILEVCRKHHFDLVICGNHNHSF--FSRAS-CSAKRVIAS---------SEVDVLLVPLTG 141 (142)
T ss_pred HHHHHHHHHhCCCEEEEcCCcchH--HHHHH-HHHHHHHhc---------CCCCEEEEeCCC
Confidence 577889999999999999876543 33322 223345543 358888887654
No 355
>PRK01002 nickel responsive regulator; Provisional
Probab=20.28 E-value=1.8e+02 Score=30.37 Aligned_cols=42 Identities=21% Similarity=0.500 Sum_probs=26.6
Q ss_pred cccEEEEEecChhhhhhHHHHHHhhhccCCCcchhhhHHHHHHHHHHHHHHHhH
Q 039337 354 EKLLQVTIKLPEDSLNKLFSDCKEHYLSDGVSKSAQLWNDQRELILKDALDNFL 407 (1344)
Q Consensus 354 egll~v~i~~~~~~~~~~~~~l~~~~~~d~~s~~~~~wn~~r~~~l~~a~~~~L 407 (1344)
+++.+++|.+|++.++.|-+.+.+. +++. |.++|++|+..+|
T Consensus 2 ~~~~risislp~~ll~~lD~~~~~~----g~~s--------RSe~Ir~air~~l 43 (141)
T PRK01002 2 TEMMRISISLPDKLLGEFDEIIEER----GYAS--------RSEGIRDAIRDYI 43 (141)
T ss_pred CCcEEEEEEeCHHHHHHHHHHHHHc----CCCC--------HHHHHHHHHHHHH
Confidence 3578999999998765543333322 2211 6678888887753
No 356
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.15 E-value=1.3e+02 Score=27.16 Aligned_cols=56 Identities=23% Similarity=0.202 Sum_probs=38.0
Q ss_pred EEEEEEEEEecccEEEEeC-CCeEEEEec-eecCCCccccCcccccCCCCEEEEEEEEEe
Q 039337 849 VVQATVRRVQGQRAICVLE-SGLAGMLMK-EDYSDDWRDSELSDKLHEGDILTCKIKSIQ 906 (1344)
Q Consensus 849 iV~g~V~~V~~~g~fV~L~-~gi~GlIh~-s~lsd~~~~~~~~~~~~vGq~V~vkVi~iD 906 (1344)
..+++|.-+....+.|.|. .+.-..++. |++.+. +.. -++.+++||.|.|.++..+
T Consensus 3 ~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdt-frf-~seklkvG~~l~v~lk~~~ 60 (69)
T cd05701 3 RHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDT-FRF-DSEKLSVGQCLDVTLKDPN 60 (69)
T ss_pred ccchhhhhhhhceEEEEeeccccEEEEEchhhcccc-ccc-cceeeeccceEEEEEecCc
Confidence 3467788888778888874 344444444 566654 332 2467999999999988764
Done!