Query gi|254780751|ref|YP_003065164.1| ribonuclease E [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 723
No_of_seqs 290 out of 2083
Neff 6.5
Searched_HMMs 39220
Date Sun May 29 19:35:52 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780751.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10811 rne ribonuclease E; R 100.0 0 0 1291.3 46.8 498 2-579 1-500 (1063)
2 PRK11712 ribonuclease G; Provi 100.0 0 0 1157.6 47.5 487 1-566 1-487 (489)
3 TIGR00757 RNaseEG ribonuclease 100.0 0 0 1139.0 31.8 453 14-505 1-464 (464)
4 COG1530 CafA Ribonucleases G a 100.0 0 0 945.0 35.8 485 2-571 1-486 (487)
5 pfam10150 RNase_E_G Ribonuclea 100.0 0 0 652.6 27.6 271 201-473 1-271 (271)
6 cd04453 S1_RNase_E S1_RNase_E: 99.9 3.4E-28 8.6E-33 215.0 6.7 87 34-205 2-88 (88)
7 PRK07252 hypothetical protein; 98.3 8.1E-07 2.1E-11 66.5 5.2 40 38-79 2-41 (120)
8 cd05692 S1_RPS1_repeat_hs4 S1_ 98.2 3.2E-06 8.3E-11 62.3 5.6 38 40-79 1-38 (69)
9 PRK08582 hypothetical protein; 98.2 2.7E-06 6.9E-11 62.8 5.1 40 38-79 4-43 (139)
10 PRK05807 hypothetical protein; 98.1 3.4E-06 8.8E-11 62.1 4.9 39 38-79 4-42 (136)
11 PRK03987 translation initiatio 98.1 1.2E-05 3E-10 58.4 7.3 125 37-277 6-135 (262)
12 cd04452 S1_IF2_alpha S1_IF2_al 98.1 5.8E-06 1.5E-10 60.5 5.3 39 38-78 2-42 (76)
13 cd05686 S1_pNO40 S1_pNO40: pNO 98.0 7.9E-06 2E-10 59.6 5.0 38 38-77 2-40 (73)
14 TIGR03591 polynuc_phos polyrib 98.0 1.1E-05 2.9E-10 58.5 5.1 39 517-555 551-589 (684)
15 PRK08059 general stress protei 98.0 1.1E-05 2.9E-10 58.5 4.9 41 36-78 3-43 (119)
16 cd04472 S1_PNPase S1_PNPase: P 98.0 1.6E-05 4.2E-10 57.4 5.7 37 40-78 1-37 (68)
17 pfam00575 S1 S1 RNA binding do 97.9 1.8E-05 4.7E-10 57.1 5.6 40 37-78 2-41 (74)
18 PRK11824 polynucleotide phosph 97.9 1.8E-05 4.6E-10 57.1 5.0 39 517-555 554-592 (694)
19 cd04473 S1_RecJ_like S1_RecJ_l 97.9 3.2E-05 8.1E-10 55.4 5.6 40 35-76 12-51 (77)
20 COG1098 VacB Predicted RNA bin 97.8 1.6E-05 4.2E-10 57.4 3.8 79 38-213 4-82 (129)
21 PRK13806 rpsA 30S ribosomal pr 97.8 2.9E-05 7.3E-10 55.7 5.0 38 36-75 30-67 (489)
22 COG0539 RpsA Ribosomal protein 97.8 3.4E-05 8.7E-10 55.2 5.3 40 34-75 16-55 (541)
23 smart00316 S1 Ribosomal protei 97.8 4.1E-05 1E-09 54.6 5.4 70 39-198 2-71 (72)
24 cd05708 S1_Rrp5_repeat_sc12 S1 97.7 0.0001 2.6E-09 51.9 5.4 39 38-78 1-40 (77)
25 cd05684 S1_DHX8_helicase S1_DH 97.6 1E-04 2.5E-09 51.9 5.2 36 40-77 1-39 (79)
26 cd04461 S1_Rrp5_repeat_hs8_sc7 97.6 0.00015 3.7E-09 50.8 5.3 40 37-78 12-51 (83)
27 PRK07400 30S ribosomal protein 97.5 0.00015 3.9E-09 50.7 5.1 40 34-75 26-65 (314)
28 cd05685 S1_Tex S1_Tex: The C-t 97.5 0.00022 5.6E-09 49.6 5.3 38 40-79 1-38 (68)
29 PRK00087 4-hydroxy-3-methylbut 97.5 0.00018 4.6E-09 50.1 4.8 10 416-425 362-371 (670)
30 PRK07899 rpsA 30S ribosomal pr 97.5 0.00021 5.2E-09 49.8 4.8 62 12-75 6-69 (484)
31 cd05688 S1_RPS1_repeat_ec3 S1_ 97.4 0.00026 6.6E-09 49.1 4.8 36 39-77 1-36 (68)
32 PRK06299 rpsA 30S ribosomal pr 97.4 0.00029 7.3E-09 48.8 4.8 38 36-75 17-54 (556)
33 PRK06299 rpsA 30S ribosomal pr 97.4 0.00024 6.2E-09 49.2 4.4 37 38-77 190-226 (556)
34 cd05698 S1_Rrp5_repeat_hs6_sc5 97.4 0.00037 9.5E-09 48.0 5.2 37 40-78 1-37 (70)
35 cd05687 S1_RPS1_repeat_ec1_hs1 97.4 0.00043 1.1E-08 47.5 5.4 35 40-76 1-35 (70)
36 COG1185 Pnp Polyribonucleotide 97.4 0.0002 5.1E-09 49.9 3.7 62 248-309 187-255 (692)
37 cd05689 S1_RPS1_repeat_ec4 S1_ 97.3 0.00048 1.2E-08 47.2 5.5 38 38-77 2-39 (72)
38 COG0539 RpsA Ribosomal protein 97.3 0.00049 1.2E-08 47.1 5.2 83 37-210 190-272 (541)
39 PRK06676 rpsA 30S ribosomal pr 97.3 0.00073 1.9E-08 45.9 5.9 39 36-76 14-53 (390)
40 cd05691 S1_RPS1_repeat_ec6 S1_ 97.3 0.00066 1.7E-08 46.3 5.4 37 40-78 1-37 (73)
41 cd05706 S1_Rrp5_repeat_sc10 S1 97.2 0.00095 2.4E-08 45.2 5.9 40 38-79 2-41 (73)
42 cd05690 S1_RPS1_repeat_ec5 S1_ 97.2 0.00097 2.5E-08 45.1 5.5 36 40-77 1-36 (69)
43 PRK07899 rpsA 30S ribosomal pr 97.0 0.001 2.7E-08 44.8 4.8 37 38-77 207-243 (484)
44 PRK07400 30S ribosomal protein 96.9 0.0023 5.8E-08 42.5 5.7 35 38-75 117-151 (314)
45 cd05707 S1_Rrp5_repeat_sc11 S1 96.9 0.0016 4.2E-08 43.5 5.0 38 40-79 1-38 (68)
46 cd00164 S1_like S1_like: Ribos 96.9 0.0016 4.1E-08 43.5 4.7 34 43-78 1-34 (65)
47 PRK13806 rpsA 30S ribosomal pr 96.8 0.0012 3.1E-08 44.4 3.4 39 38-78 200-238 (489)
48 PRK12269 bifunctional cytidyla 96.8 0.0017 4.4E-08 43.3 4.1 13 50-62 54-66 (863)
49 cd04471 S1_RNase_R S1_RNase_R: 96.7 0.0032 8.2E-08 41.5 5.0 40 39-80 1-41 (83)
50 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.7 0.0038 9.7E-08 41.0 5.4 34 40-75 1-34 (69)
51 PRK00087 4-hydroxy-3-methylbut 96.6 0.004 1E-07 40.8 4.9 36 37-74 302-337 (670)
52 PRK12269 bifunctional cytidyla 96.5 0.006 1.5E-07 39.6 5.3 14 450-463 495-508 (863)
53 PRK06676 rpsA 30S ribosomal pr 96.2 0.011 2.9E-07 37.7 5.4 39 37-78 103-141 (390)
54 COG1093 SUI2 Translation initi 95.9 0.029 7.5E-07 34.8 6.4 38 37-76 9-48 (269)
55 cd05704 S1_Rrp5_repeat_hs13 S1 95.6 0.036 9.3E-07 34.1 5.7 41 39-80 3-43 (72)
56 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 95.5 0.051 1.3E-06 33.1 6.2 38 37-76 4-41 (86)
57 cd04460 S1_RpoE S1_RpoE: RpoE, 95.2 0.037 9.4E-07 34.1 4.8 38 41-81 1-38 (99)
58 COG2183 Tex Transcriptional ac 95.2 0.044 1.1E-06 33.6 5.0 15 400-414 441-455 (780)
59 cd04455 S1_NusA S1_NusA: N-uti 95.0 0.086 2.2E-06 31.5 6.1 34 38-74 2-35 (67)
60 TIGR00717 rpsA ribosomal prote 94.8 0.066 1.7E-06 32.3 5.0 35 40-74 20-54 (534)
61 TIGR00717 rpsA ribosomal prote 94.6 0.095 2.4E-06 31.3 5.4 37 38-76 286-322 (534)
62 PTZ00248 eukaryotic translatio 94.2 0.079 2E-06 31.8 4.3 89 36-237 14-104 (324)
63 PRK12327 nusA transcription el 93.9 0.18 4.7E-06 29.3 5.8 34 38-74 133-166 (353)
64 PRK08563 DNA-directed RNA poly 93.8 0.54 1.4E-05 26.0 9.1 65 13-80 55-119 (182)
65 PRK11642 exoribonuclease R; Pr 92.7 0.26 6.5E-06 28.3 4.9 90 313-412 378-476 (813)
66 PRK09202 nusA transcription el 92.4 0.46 1.2E-05 26.5 5.9 52 282-338 246-298 (428)
67 cd05702 S1_Rrp5_repeat_hs11_sc 92.2 0.4 1E-05 26.9 5.5 34 40-75 1-34 (70)
68 PRK00499 rnpA ribonuclease P; 91.9 0.73 1.9E-05 25.1 6.5 62 216-277 42-111 (116)
69 KOG1070 consensus 91.8 0.53 1.3E-05 26.1 5.7 66 12-79 570-637 (1710)
70 COG2996 Predicted RNA-bindinin 91.8 1 2.5E-05 24.2 7.3 54 21-75 45-108 (287)
71 PTZ00162 RNA polymerase II sub 90.8 1.3 3.2E-05 23.5 8.7 63 13-78 55-117 (170)
72 TIGR03147 cyt_nit_nrfF cytochr 90.1 0.8 2E-05 24.8 5.2 58 481-556 40-97 (126)
73 PRK12328 nusA transcription el 89.6 1.1 2.8E-05 23.9 5.6 52 282-338 251-303 (375)
74 pfam03918 CcmH Cytochrome C bi 89.4 0.88 2.2E-05 24.5 5.0 58 481-556 37-94 (145)
75 PRK10144 formate-dependent nit 89.2 1.1 2.7E-05 24.0 5.3 58 481-556 40-97 (126)
76 cd05791 S1_CSL4 S1_CSL4: CSL4, 88.9 1.5 3.8E-05 22.9 5.9 23 37-61 4-26 (92)
77 PRK01732 rnpA ribonuclease P; 87.8 2 5.2E-05 22.0 6.5 61 216-279 48-116 (119)
78 PRK01313 rnpA ribonuclease P; 87.7 1.8 4.6E-05 22.4 5.7 58 215-272 53-119 (133)
79 PRK04163 exosome complex RNA-b 86.7 2.3 5.9E-05 21.6 8.9 38 35-74 58-95 (232)
80 cd05694 S1_Rrp5_repeat_hs2_sc2 86.7 2 5.1E-05 22.0 5.4 35 38-74 3-38 (74)
81 PRK03031 rnpA ribonuclease P; 86.1 1.3 3.4E-05 23.3 4.3 58 216-273 50-116 (122)
82 TIGR02696 pppGpp_PNP guanosine 85.3 0.3 7.7E-06 27.7 0.7 162 405-567 326-528 (725)
83 PRK00396 rnpA ribonuclease P; 84.4 3 7.6E-05 20.9 6.9 62 216-280 49-118 (134)
84 pfam01630 Glyco_hydro_56 Hyalu 84.3 1.6 4E-05 22.8 3.9 33 396-428 79-112 (339)
85 COG1095 RPB7 DNA-directed RNA 84.2 3 7.7E-05 20.8 8.4 65 12-79 54-118 (183)
86 PRK12329 nusA transcription el 84.1 3.1 7.8E-05 20.8 5.8 32 283-314 279-310 (457)
87 PRK00349 uvrA excinuclease ABC 83.7 3.2 8.1E-05 20.7 5.4 42 291-332 526-567 (944)
88 TIGR02063 RNase_R ribonuclease 83.3 3.3 8.4E-05 20.6 5.5 157 313-480 393-565 (755)
89 cd04454 S1_Rrp4_like S1_Rrp4_l 83.2 2.4 6.2E-05 21.5 4.6 36 37-74 4-39 (82)
90 TIGR02349 DnaJ_bact chaperone 82.1 0.58 1.5E-05 25.8 1.1 25 477-501 224-248 (386)
91 COG1096 Predicted RNA-binding 81.3 3.9 9.9E-05 20.1 7.2 55 23-79 47-112 (188)
92 pfam10447 EXOSC1 Exosome compo 81.3 3.9 9.9E-05 20.1 5.4 23 37-61 2-24 (72)
93 TIGR02349 DnaJ_bact chaperone 81.2 0.24 6.1E-06 28.5 -1.2 44 480-529 213-256 (386)
94 pfam07092 DUF1356 Protein of u 79.3 0.62 1.6E-05 25.6 0.4 34 454-496 13-46 (231)
95 cd05696 S1_Rrp5_repeat_hs4 S1_ 76.0 2.5 6.4E-05 21.4 2.7 34 40-74 1-35 (71)
96 cd04465 S1_RPS1_repeat_ec2_hs2 76.0 3.3 8.4E-05 20.6 3.3 33 40-75 1-33 (67)
97 COG1107 Archaea-specific RecJ- 75.2 2.8 7E-05 21.1 2.8 49 25-75 108-156 (715)
98 PRK04820 rnpA ribonuclease P; 75.1 5.8 0.00015 18.8 6.6 60 216-278 51-118 (145)
99 TIGR02642 phage_xxxx uncharact 74.3 1.2 3E-05 23.7 0.7 48 440-498 168-216 (270)
100 COG0484 DnaJ DnaJ-class molecu 73.3 1.8 4.7E-05 22.3 1.5 19 476-494 178-196 (371)
101 TIGR01213 TIGR01213 conserved 72.4 1.1 2.9E-05 23.8 0.3 39 349-387 149-188 (450)
102 COG1568 Predicted methyltransf 72.1 3.1 8E-05 20.7 2.4 12 409-420 193-204 (354)
103 COG2425 Uncharacterized protei 71.0 7.2 0.00018 18.2 4.5 99 362-470 312-418 (437)
104 COG0178 UvrA Excinuclease ATPa 70.9 7.2 0.00018 18.2 6.0 13 480-492 397-409 (935)
105 pfam00825 Ribonuclease_P Ribon 70.8 7.3 0.00018 18.2 5.8 57 215-271 40-105 (107)
106 PRK00635 excinuclease ABC subu 70.7 7.3 0.00019 18.1 6.1 42 291-332 513-554 (1809)
107 pfam03589 Antiterm Antitermina 69.3 2.8 7.2E-05 21.0 1.7 31 477-507 28-58 (95)
108 PRK00588 rnpA ribonuclease P; 69.0 7.9 0.0002 17.9 6.1 58 215-272 45-110 (116)
109 PRK02083 imidazole glycerol ph 69.0 6.6 0.00017 18.4 3.6 16 410-425 158-173 (253)
110 PRK05973 replicative DNA helic 68.8 7.2 0.00018 18.2 3.7 85 405-492 133-232 (237)
111 KOG1067 consensus 68.5 6.7 0.00017 18.4 3.5 34 281-314 270-303 (760)
112 PRK13597 imidazole glycerol ph 68.2 7.1 0.00018 18.2 3.6 16 299-314 90-105 (252)
113 COG3088 CcmH Uncharacterized p 67.9 8.3 0.00021 17.8 4.8 57 481-555 44-100 (153)
114 pfam00684 DnaJ_CXXCXGXG DnaJ c 67.8 3.9 9.8E-05 20.1 2.2 21 475-495 48-68 (79)
115 PRK09521 exosome complex RNA-b 67.5 8.5 0.00022 17.7 7.2 24 36-61 61-84 (187)
116 COG0594 RnpA RNase P protein c 66.8 8.7 0.00022 17.6 5.7 57 216-272 44-108 (117)
117 PRK03220 consensus 66.3 7.9 0.0002 17.9 3.5 19 408-426 162-180 (257)
118 COG1198 PriA Primosomal protei 65.4 5.6 0.00014 18.9 2.6 154 412-566 373-573 (730)
119 KOG1015 consensus 65.1 7.1 0.00018 18.2 3.1 135 305-462 726-860 (1567)
120 PRK01659 consensus 64.7 9.5 0.00024 17.3 3.7 15 410-424 158-172 (252)
121 TIGR02034 CysN sulfate adenyly 64.2 0.82 2.1E-05 24.8 -1.9 69 360-428 328-401 (411)
122 PRK04281 consensus 62.9 10 0.00026 17.1 3.6 18 409-426 158-175 (254)
123 PRK06937 type III secretion sy 61.6 11 0.00027 17.0 5.4 50 515-566 129-178 (204)
124 PRK04390 rnpA ribonuclease P; 61.4 11 0.00028 16.9 5.6 56 216-271 48-111 (121)
125 KOG3409 consensus 61.2 11 0.00028 16.9 8.2 57 6-74 33-94 (193)
126 cd05792 S1_eIF1AD_like S1_eIF1 60.6 4.4 0.00011 19.6 1.4 22 356-377 30-51 (78)
127 PRK02621 consensus 59.8 12 0.00029 16.8 3.8 16 411-426 160-175 (254)
128 PRK05054 exoribonuclease II; P 59.5 12 0.0003 16.7 4.8 92 312-413 308-408 (644)
129 cd01889 SelB_euk SelB subfamil 59.5 12 0.0003 16.7 7.5 70 378-462 95-169 (192)
130 cd05693 S1_Rrp5_repeat_hs1_sc1 59.0 12 0.0003 16.7 6.1 41 38-80 2-42 (100)
131 KOG2228 consensus 59.0 12 0.0003 16.7 7.7 83 400-487 89-173 (408)
132 pfam02108 FliH Flagellar assem 58.2 12 0.00031 16.6 5.3 59 503-567 52-112 (128)
133 COG1317 FliH Flagellar biosynt 57.4 13 0.00032 16.5 4.5 48 516-567 157-204 (234)
134 cd00881 GTP_translation_factor 56.9 13 0.00033 16.4 8.5 59 377-450 88-146 (189)
135 PRK11032 hypothetical protein; 56.9 6.4 0.00016 18.5 1.7 53 443-496 104-157 (160)
136 TIGR02716 C20_methyl_CrtF C-20 56.4 9.2 0.00023 17.5 2.4 33 342-374 217-253 (306)
137 smart00333 TUDOR Tudor domain. 56.0 11 0.00028 16.9 2.7 34 39-74 15-50 (57)
138 PRK08903 hypothetical protein; 55.8 13 0.00034 16.3 6.3 109 420-545 91-199 (227)
139 PRK02747 consensus 55.7 13 0.00034 16.3 3.7 19 408-426 159-177 (257)
140 cd05705 S1_Rrp5_repeat_hs14 S1 55.3 13 0.00034 16.3 3.1 38 39-79 3-40 (74)
141 TIGR00393 kpsF sugar isomerase 53.4 14 0.00036 16.1 3.0 41 437-477 151-193 (272)
142 cd04508 TUDOR Tudor domains ar 53.3 13 0.00033 16.4 2.7 34 39-74 11-46 (48)
143 PRK03459 rnpA ribonuclease P; 52.7 15 0.00038 16.0 5.8 60 215-274 57-124 (129)
144 TIGR02390 RNA_pol_rpoA1 DNA-di 51.7 16 0.0004 15.9 3.5 231 166-449 425-699 (901)
145 KOG0546 consensus 51.3 7.9 0.0002 17.9 1.4 37 478-514 126-162 (372)
146 TIGR01953 NusA transcription t 50.3 16 0.00042 15.7 5.9 161 36-338 142-318 (366)
147 TIGR00137 gid gid protein; Int 49.9 11 0.00029 16.8 2.0 37 44-80 298-336 (444)
148 PRK00694 4-hydroxy-3-methylbut 49.6 7.2 0.00018 18.2 1.0 61 403-490 459-519 (606)
149 PRK06328 type III secretion sy 48.7 17 0.00044 15.6 4.8 50 515-566 130-179 (223)
150 cd02394 vigilin_like_KH K homo 46.5 17 0.00044 15.5 2.5 35 519-553 2-36 (62)
151 cd04731 HisF The cyclase subun 46.4 19 0.00047 15.3 3.6 22 230-251 61-82 (243)
152 cd05703 S1_Rrp5_repeat_hs12_sc 46.2 19 0.00048 15.3 5.1 35 40-76 1-35 (73)
153 COG1278 CspC Cold shock protei 46.1 19 0.00048 15.3 4.5 34 44-77 3-37 (67)
154 PTZ00037 DnaJ_C chaperone prot 45.3 10 0.00027 17.1 1.2 49 210-273 7-55 (422)
155 cd01890 LepA LepA subfamily. 45.2 19 0.00049 15.2 6.0 66 378-461 94-159 (179)
156 KOG2002 consensus 43.8 20 0.00052 15.1 3.6 15 401-415 659-673 (1018)
157 PHA02114 hypothetical protein 43.7 20 0.00052 15.0 3.0 23 245-267 1-23 (127)
158 KOG0712 consensus 43.4 9.3 0.00024 17.4 0.7 33 465-497 154-186 (337)
159 TIGR01544 HAD-SF-IE HAD-superf 42.9 20 0.00051 15.1 2.4 45 437-490 12-56 (287)
160 PRK06669 fliH flagellar assemb 42.9 21 0.00053 15.0 6.3 49 516-566 197-245 (268)
161 TIGR00459 aspS_bact aspartyl-t 42.4 6.7 0.00017 18.4 -0.1 56 212-277 222-278 (653)
162 pfam07013 DUF1314 Protein of u 42.2 21 0.00053 15.0 2.4 37 354-394 4-40 (177)
163 pfam02691 VacA Vacuolating cyo 41.9 21 0.00055 14.9 2.4 32 354-385 578-617 (1002)
164 cd00765 Pyrophosphate_PFK Phos 40.9 22 0.00057 14.8 5.3 44 218-264 143-187 (550)
165 cd02396 PCBP_like_KH K homolog 40.9 22 0.00057 14.8 2.6 44 519-562 2-45 (65)
166 PRK02145 consensus 40.8 23 0.00057 14.7 3.5 14 411-424 163-176 (257)
167 pfam06635 NolV Nodulation prot 40.7 23 0.00058 14.7 3.5 49 514-566 128-177 (207)
168 COG2895 CysN GTPases - Sulfate 39.7 4.9 0.00012 19.4 -1.2 31 360-390 330-361 (431)
169 pfam04025 DUF370 Domain of unk 39.5 24 0.0006 14.6 3.2 27 4-30 37-64 (73)
170 pfam04606 Ogr_Delta Ogr/Delta- 39.4 15 0.00039 15.9 1.3 19 483-501 1-19 (47)
171 TIGR02836 spore_IV_A stage IV 39.3 13 0.00033 16.4 1.0 37 27-74 3-40 (492)
172 TIGR02533 type_II_gspE general 39.1 8 0.0002 17.9 -0.1 80 400-493 346-433 (495)
173 TIGR00630 uvra excinuclease AB 38.8 13 0.00033 16.4 0.9 78 419-498 229-312 (956)
174 TIGR00340 zpr1_rel zinc finger 38.3 11 0.00028 16.9 0.4 14 484-497 1-14 (168)
175 PRK06032 fliH flagellar assemb 38.0 25 0.00063 14.5 6.1 63 503-567 112-175 (208)
176 pfam00013 KH_1 KH domain. KH m 38.0 16 0.00041 15.7 1.3 34 519-552 2-35 (57)
177 pfam07295 DUF1451 Protein of u 37.9 15 0.00037 16.1 1.0 44 453-496 103-147 (148)
178 PRK00964 tetrahydromethanopter 37.6 24 0.00062 14.5 2.1 56 385-451 101-156 (243)
179 TIGR02405 trehalos_R_Ecol treh 36.7 8.2 0.00021 17.8 -0.4 90 407-501 104-198 (311)
180 pfam05262 Borrelia_P83 Borreli 36.7 11 0.00029 16.8 0.3 11 53-63 8-18 (489)
181 PRK12366 replication factor A; 35.8 12 0.0003 16.7 0.3 54 512-565 570-629 (649)
182 cd01129 PulE-GspE PulE/GspE Th 35.7 9.2 0.00023 17.5 -0.3 62 195-261 33-96 (264)
183 TIGR01037 pyrD_sub1_fam dihydr 35.4 27 0.00069 14.2 2.5 46 482-531 129-176 (308)
184 cd04702 ASRGL1_like ASRGL1_lik 35.3 27 0.00069 14.2 2.7 17 397-415 186-202 (261)
185 pfam00567 TUDOR Tudor domain. 34.8 28 0.00071 14.1 3.2 24 40-63 63-88 (118)
186 cd01883 EF1_alpha Eukaryotic e 34.1 28 0.00073 14.0 8.8 94 377-489 103-205 (219)
187 COG2052 Uncharacterized protei 34.0 29 0.00073 14.0 2.6 19 4-22 41-59 (89)
188 PRK01172 ski2-like helicase; P 33.8 29 0.00073 14.0 3.6 13 215-227 171-183 (674)
189 pfam00009 GTP_EFTU Elongation 33.3 29 0.00074 14.0 7.1 70 378-462 94-167 (185)
190 pfam01153 Glypican Glypican. 33.2 21 0.00054 14.9 1.2 26 481-506 247-272 (559)
191 PRK10476 multidrug resistance 33.1 29 0.00075 13.9 3.8 11 547-557 264-274 (348)
192 PRK10954 periplasmic protein d 32.5 11 0.00029 16.8 -0.2 13 346-358 144-156 (207)
193 TIGR02738 TrbB type-F conjugat 32.5 15 0.00037 16.0 0.3 34 366-400 133-168 (176)
194 PRK07726 DNA topoisomerase III 32.4 30 0.00076 13.9 1.9 27 233-260 306-332 (716)
195 LOAD_cold consensus 32.2 30 0.00077 13.8 4.6 33 43-75 2-35 (67)
196 TIGR02949 anti_SigH_actin anti 31.9 25 0.00065 14.4 1.5 51 312-362 7-60 (85)
197 PRK04323 hypothetical protein; 31.8 31 0.00079 13.8 3.2 16 5-20 42-57 (91)
198 cd01888 eIF2_gamma eIF2-gamma 31.5 31 0.0008 13.8 8.1 72 378-462 110-182 (203)
199 smart00778 Prim_Zn_Ribbon Zinc 31.3 19 0.00048 15.3 0.7 15 481-495 3-17 (37)
200 PRK02362 ski2-like helicase; P 31.0 32 0.00081 13.7 3.1 15 195-209 338-352 (736)
201 COG1097 RRP4 RNA-binding prote 30.4 32 0.00083 13.6 8.1 39 34-74 59-97 (239)
202 TIGR03655 anti_R_Lar restricti 30.4 19 0.00049 15.2 0.6 11 482-492 2-12 (53)
203 COG1411 Uncharacterized protei 30.3 33 0.00083 13.6 4.3 48 377-434 119-166 (229)
204 COG3634 AhpF Alkyl hydroperoxi 30.3 18 0.00047 15.4 0.5 125 299-449 140-278 (520)
205 PRK07399 DNA polymerase III su 30.2 33 0.00084 13.6 4.9 42 404-445 106-150 (314)
206 cd04171 SelB SelB subfamily. 30.0 33 0.00084 13.6 8.4 70 378-462 78-149 (164)
207 cd00105 KH-I K homology RNA-bi 29.9 33 0.00085 13.6 2.4 39 519-557 2-40 (64)
208 PRK05783 hypothetical protein; 29.8 33 0.00085 13.6 2.1 17 402-418 55-71 (84)
209 COG0557 VacB Exoribonuclease R 29.7 33 0.00085 13.6 5.2 91 313-415 366-464 (706)
210 KOG3013 consensus 29.4 34 0.00086 13.5 7.6 152 23-229 69-220 (301)
211 KOG0950 consensus 28.5 35 0.00089 13.4 2.2 44 418-461 340-385 (1008)
212 COG1352 CheR Methylase of chem 28.2 31 0.0008 13.7 1.4 32 349-380 215-246 (268)
213 KOG3558 consensus 28.2 35 0.0009 13.4 1.8 16 366-382 344-359 (768)
214 pfam08206 OB_RNB Ribonuclease 27.9 32 0.00083 13.7 1.5 15 176-190 34-48 (58)
215 PRK01033 imidazole glycerol ph 27.8 36 0.00092 13.3 3.3 19 408-426 155-173 (253)
216 PRK09098 type III secretion sy 27.8 36 0.00092 13.3 5.6 66 497-566 133-198 (229)
217 TIGR02499 HrpE_YscL_not type I 27.7 36 0.00092 13.3 3.9 65 496-566 105-174 (183)
218 pfam08273 Prim_Zn_Ribbon Zinc- 27.1 23 0.00058 14.7 0.6 14 481-494 3-16 (39)
219 TIGR01111 mtrA tetrahydrometha 26.8 31 0.0008 13.7 1.2 43 401-454 121-164 (246)
220 pfam08800 VirE_N VirE N-termin 26.8 37 0.00095 13.2 5.3 49 416-469 27-76 (136)
221 cd01887 IF2_eIF5B IF2/eIF5B (i 26.8 37 0.00095 13.2 7.0 69 378-462 77-149 (168)
222 PRK07085 diphosphate--fructose 26.5 38 0.00096 13.2 5.4 31 218-251 143-174 (557)
223 KOG0458 consensus 26.5 38 0.00097 13.2 6.4 83 377-468 281-374 (603)
224 PRK12564 carbamoyl phosphate s 26.4 38 0.00097 13.2 2.4 84 198-305 44-128 (355)
225 TIGR01523 ATPase-IID_K-Na pota 26.0 29 0.00073 14.0 0.9 56 474-529 517-580 (1001)
226 COG3585 MopI Molybdopterin-bin 25.9 39 0.00099 13.1 2.1 26 39-64 5-30 (69)
227 TIGR03598 GTPase_YsxC ribosome 25.6 39 0.001 13.1 6.1 55 408-462 119-173 (179)
228 smart00322 KH K homology RNA-b 25.6 31 0.00078 13.8 1.0 40 518-557 4-43 (69)
229 COG2260 Predicted Zn-ribbon RN 25.5 24 0.00062 14.5 0.5 19 479-497 15-33 (59)
230 TIGR01520 FruBisAldo_II_A fruc 25.4 17 0.00043 15.6 -0.4 79 285-369 267-345 (365)
231 COG1867 TRM1 N2,N2-dimethylgua 25.4 38 0.00098 13.1 1.5 58 441-498 193-274 (380)
232 PRK06921 hypothetical protein; 25.3 35 0.00089 13.4 1.2 22 493-514 193-214 (265)
233 PRK13586 1-(5-phosphoribosyl)- 25.1 40 0.001 13.0 4.7 19 408-426 148-166 (231)
234 pfam04208 MtrA Tetrahydrometha 25.1 40 0.001 13.0 2.6 56 387-453 99-154 (176)
235 pfam05772 NinB NinB protein. T 25.1 34 0.00087 13.5 1.1 35 225-259 4-38 (127)
236 PRK10611 chemotaxis methyltran 24.9 29 0.00074 14.0 0.8 21 363-383 250-270 (287)
237 COG0173 AspS Aspartyl-tRNA syn 24.8 39 0.00099 13.1 1.4 61 407-471 375-440 (585)
238 pfam03602 Cons_hypoth95 Conser 24.6 41 0.001 13.0 2.8 34 344-378 121-154 (181)
239 COG1329 Transcriptional regula 24.4 41 0.0011 12.9 1.9 35 293-327 104-139 (166)
240 COG5525 Bacteriophage tail ass 24.2 25 0.00065 14.4 0.4 33 349-387 420-452 (611)
241 pfam00313 CSD 'Cold-shock' DNA 23.6 43 0.0011 12.8 5.4 32 44-75 2-34 (66)
242 PRK02048 4-hydroxy-3-methylbut 23.6 12 0.00031 16.6 -1.4 27 460-490 501-527 (613)
243 pfam06075 DUF936 Plant protein 23.4 43 0.0011 12.8 4.3 44 44-90 27-72 (557)
244 COG5615 Predicted integral mem 23.1 43 0.0011 12.8 4.7 51 418-468 20-79 (161)
245 KOG0955 consensus 23.1 43 0.0011 12.8 1.5 38 348-389 598-635 (1051)
246 PRK06443 chorismate mutase; Va 22.8 44 0.0011 12.7 1.6 33 354-391 118-151 (177)
247 pfam11314 DUF3117 Protein of u 22.7 44 0.0011 12.7 1.4 13 362-374 22-34 (51)
248 KOG2268 consensus 22.7 15 0.00038 16.0 -1.1 65 352-450 205-279 (465)
249 TIGR01054 rgy reverse gyrase; 22.4 34 0.00088 13.5 0.7 86 379-470 321-410 (1843)
250 cd00453 FTBP_aldolase_II Fruct 22.3 39 0.00099 13.1 1.0 16 399-414 178-193 (340)
251 COG2804 PulE Type II secretory 22.3 23 0.00059 14.7 -0.2 66 192-262 208-275 (500)
252 PRK10767 chaperone protein Dna 22.2 16 0.0004 15.9 -1.1 43 479-527 178-220 (376)
253 COG4311 SoxD Sarcosine oxidase 21.9 32 0.00082 13.7 0.5 11 479-489 1-11 (97)
254 TIGR01275 ACC_deam_rel pyridox 21.7 46 0.0012 12.6 2.4 21 404-424 163-187 (339)
255 cd04617 CBS_pair_4 The CBS dom 21.6 46 0.0012 12.6 2.5 19 408-426 13-31 (118)
256 pfam01762 Galactosyl_T Galacto 21.3 47 0.0012 12.5 1.3 16 484-499 145-160 (196)
257 KOG3821 consensus 21.2 46 0.0012 12.6 1.2 26 481-506 253-278 (563)
258 PRK08084 DNA replication initi 21.1 48 0.0012 12.5 5.3 109 421-546 99-210 (235)
259 TIGR03572 WbuZ glycosyl amidat 21.0 48 0.0012 12.5 3.5 23 229-251 63-85 (232)
260 PRK01492 rnpA ribonuclease P; 21.0 48 0.0012 12.5 4.9 68 199-271 37-116 (118)
261 PRK06835 DNA replication prote 20.8 30 0.00077 13.9 0.2 20 259-278 68-87 (330)
262 cd01721 Sm_D3 The eukaryotic S 20.8 48 0.0012 12.4 2.3 24 38-61 18-41 (70)
263 pfam01440 Gemini_AL2 Geminivir 20.7 49 0.0012 12.4 1.4 14 360-373 30-43 (134)
264 TIGR02477 PFKA_PPi diphosphate 20.6 49 0.0012 12.4 5.8 193 343-558 318-549 (566)
265 TIGR01214 rmlD dTDP-4-dehydror 20.2 50 0.0013 12.4 2.6 13 241-253 153-165 (317)
No 1
>PRK10811 rne ribonuclease E; Reviewed
Probab=100.00 E-value=0 Score=1291.31 Aligned_cols=498 Identities=44% Similarity=0.690 Sum_probs=479.8
Q ss_pred CCEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCC
Q ss_conf 85268965289607999998998999996073346042878798997836388231353278977130222137121028
Q gi|254780751|r 2 ANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQI 81 (723)
Q Consensus 2 ~k~~lI~~~~~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~i 81 (723)
.|+||||++|++|+||||++||+|.|||||+.++.+.+||||+|+|+||+|||||||||||.+|||||||+||+++||.-
T Consensus 1 mKrmLInat~~EE~RVAlvdg~~L~dldIE~~~~~q~kgNIYKGkV~rVePgLqAAFVDiG~eR~GFLp~kEI~~ey~~~ 80 (1063)
T PRK10811 1 MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPA 80 (1063)
T ss_pred CCEEEECCCCCCCEEEEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCCCCCCCHHHCCHHHCCC
T ss_conf 96267468884404799974999889862357765340542689997856886057772389755421688828654265
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 98899999998886311111000000011122334443344542222334455433222234321122111211000012
Q gi|254780751|r 82 PFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVP 161 (723)
Q Consensus 82 p~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (723)
.
T Consensus 81 -------------------------------------------------------------------------------~ 81 (1063)
T PRK10811 81 -------------------------------------------------------------------------------N 81 (1063)
T ss_pred -------------------------------------------------------------------------------C
T ss_conf -------------------------------------------------------------------------------5
Q ss_pred CCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHC
Q ss_conf 23444421331068885799984033323456410123345765234422788751242046886899999999986300
Q gi|254780751|r 162 KKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEV 241 (723)
Q Consensus 162 ~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~ 241 (723)
....++++|+++|++||+|||||+|||+|+|||+|||+||||||||||||++++++||||||.+ ++|.+|+.++..+.+
T Consensus 82 ~~~~grp~I~dvLkeGQeILVQV~KEp~GtKGArLTT~ISLaGRYLVLMPn~~~~gGISRKIe~-eER~rLkeiL~~L~~ 160 (1063)
T PRK10811 82 YSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEG-DDRTELKEALASLEL 160 (1063)
T ss_pred CCCCCCCCHHHHCCCCCEEEEEEEECCCCCCCCCEEEEEEECCEEEEECCCCCCCCCEECCCCC-HHHHHHHHHHHHCCC
T ss_conf 3435687878836799989999966787897836642154342018982489877615147890-789999999971357
Q ss_pred CCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHH
Q ss_conf 25871699850455757999999999999999877642014322123456458888887523766311110353203667
Q gi|254780751|r 242 PAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREA 321 (723)
Q Consensus 242 ~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~ 321 (723)
|+|||+||||+|.|++.++|.+|+.+|+++|+.|++.+....+|+|||++.+++.++||||++.++++|+||+.+.|+.+
T Consensus 161 Peg~GlIVRTAa~g~s~eeL~~Dl~~Ll~~W~~I~k~~~~~~AP~LIyqE~~li~R~iRD~l~~di~eIiVDd~e~ye~a 240 (1063)
T PRK10811 161 PEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELA 240 (1063)
T ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHCCCCCCEEEEECHHHHHHH
T ss_conf 88826999757689999999999999999999999997358998687537548999999862177788999699999999
Q ss_pred HHHHHHH-HHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHH
Q ss_conf 8889876-310121122013442035677699999998422214367864998328806999823755444555114799
Q gi|254780751|r 322 KDFMKLL-MPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTAL 400 (723)
Q Consensus 322 ~~~~~~~-~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l 400 (723)
++|+..+ +|++..+|++|.+..|||++|+||.||+.+|+++||||||||||||+|||||+||||||+|++++|+|+|+|
T Consensus 241 k~~i~~l~~P~~~~kVklY~~~~PLF~~Y~IE~QIe~a~~rkV~LpSGGyIVID~TEALtaIDVNSGk~t~g~niEETal 320 (1063)
T PRK10811 241 RQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAF 320 (1063)
T ss_pred HHHHHHHCCCCCCCCEEEECCCCCHHHHHCHHHHHHHHHCCCEECCCCCEEEEECCCCEEEEEECCCCCCCCCCHHHHHH
T ss_conf 99999744733337458857998857770999999998459176798867998456040788616998888989999999
Q ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHH
Q ss_conf 99999999999987310368638960334798888999999999973127872899860486148985156663011210
Q gi|254780751|r 401 QTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLEST 480 (723)
Q Consensus 401 ~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~ 480 (723)
+||||||+||||||||||||||||||||||...+|++.|+++|+++|+.||+|+||+.||.||||||||||+|+||.+++
T Consensus 321 kTNLEAA~EIARQLRLRDLGGIIVIDFIDM~~~~nqr~Ve~~lr~alk~DRARiqig~IS~FGLlEMSRQRlrpSL~es~ 400 (1063)
T PRK10811 321 NTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESS 400 (1063)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCEEEEHHHCCHHHHHHC
T ss_conf 99999999999999860268829997235896566999999999998637201033343676430323321014457542
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHH-CCEEEEEECCCCC
Q ss_conf 023675465378606114689988788999730364310135769999987302379999999984-8879998478778
Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARF-GVSINVVIGIELA 559 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~-~~~I~i~~d~~l~ 559 (723)
++.||+|+|+|.|++.+|+++.|||.|++++.+.++..+.+.+|++||.||||+||..|..||.++ ++.|.|+++++|.
T Consensus 401 ~~~CP~C~G~G~ir~~es~al~ilR~ieeea~k~~t~~v~~~vpv~va~yllNeKR~~i~~ie~r~~~v~~~~~pn~~~~ 480 (1063)
T PRK10811 401 HHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQME 480 (1063)
T ss_pred CCCCCCCCCCCEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
T ss_conf 77488887700225728889999999999987557553999954999999876658999999975268339994898888
Q ss_pred CCCEEEEECCCCCCCCCCCC
Q ss_conf 86338971554433333211
Q gi|254780751|r 560 DKLFYIEKGSPVQALVNTGH 579 (723)
Q Consensus 560 ~~~f~Ier~~~~~~~~~~~~ 579 (723)
+|||.+.|.+.++.....+|
T Consensus 481 tp~~~~~r~r~~~~~~~~sy 500 (1063)
T PRK10811 481 TPHYSVLRVRKGEETPTLSY 500 (1063)
T ss_pred CCCCEEEEECCCCCCCCCHH
T ss_conf 99826898307763441001
No 2
>PRK11712 ribonuclease G; Provisional
Probab=100.00 E-value=0 Score=1157.64 Aligned_cols=487 Identities=32% Similarity=0.521 Sum_probs=467.5
Q ss_pred CCCEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf 98526896528960799999899899999607334604287879899783638823135327897713022213712102
Q gi|254780751|r 1 MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ 80 (723)
Q Consensus 1 M~k~~lI~~~~~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ 80 (723)
|+++||||++ |+|||||+++||+|+||++|+..+.+++||||+|+|+||+|||||||||||.+|+||||++|++|.+..
T Consensus 1 M~~eilIn~~-~~E~RvAlle~g~L~el~iE~~~~~~~vGnIY~G~V~~V~pgl~AAFVdiG~~k~gFL~~~di~~~~~~ 79 (489)
T PRK11712 1 MTAELLVNVT-PSETRVALIEGGILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTEC 79 (489)
T ss_pred CCCEEEEECC-CCEEEEEEEECCEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEHHHCCCCHHC
T ss_conf 9856999789-983699999999999999855888776676699999430688776999847987428785543852111
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 89889999999888631111100000001112233444334454222233445543322223432112211121100001
Q gi|254780751|r 81 IPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDV 160 (723)
Q Consensus 81 ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (723)
.. ..
T Consensus 80 ~~----------------------------------------------------------------------------~~ 83 (489)
T PRK11712 80 VA----------------------------------------------------------------------------GE 83 (489)
T ss_pred CC----------------------------------------------------------------------------CC
T ss_conf 33----------------------------------------------------------------------------32
Q ss_pred CCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf 22344442133106888579998403332345641012334576523442278875124204688689999999998630
Q gi|254780751|r 161 PKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLE 240 (723)
Q Consensus 161 ~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~ 240 (723)
........+|+++|++||.|||||+|||+|+|||+||++|||||||+||||+. .++||||||.++++|.+|+.++..+
T Consensus 84 ~~~~~~~~~I~~~l~~Gq~ilVQV~Ke~~~~KGa~lT~~isl~GRylVl~P~~-~~igiSrkI~~~~eR~rLk~i~~~~- 161 (489)
T PRK11712 84 EQKQFVVRDISELVRQGQDIMVQVVKDPLGTKGARLTTDITLPSRYLVFMPGA-SHVGVSQRIESEEERERLKKIVAPY- 161 (489)
T ss_pred CCCCCCCCCHHHHCCCCCEEEEEEEECCCCCCCCCEEEEEEECCEEEEEECCC-CCCCCCCCCCCHHHHHHHHHHHHHC-
T ss_conf 23566646767746799989999962687898876751255453269995389-9876431679878999999988853-
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHH
Q ss_conf 02587169985045575799999999999999987764201432212345645888888752376631111035320366
Q gi|254780751|r 241 VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYRE 320 (723)
Q Consensus 241 ~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~ 320 (723)
.|+++|+|+||+|++++.++|.+|+.+|.++|+.|.+++...++|+|||++++++.+++||+++.++++|+||+.+.|..
T Consensus 162 ~~~~~G~IiRT~a~~~~~e~l~~d~~~L~~~W~~I~~~~~~~~~p~ll~~e~~~~~r~lRD~~~~~~~~I~vD~~~~~~~ 241 (489)
T PRK11712 162 CDEQGGFIIRTAAEGVGEEELAQDAAFLKRVWTKVMERKKRPQTRYQLYGELALAQRVLRDFVGAELDRIRVDSRLTYEE 241 (489)
T ss_pred CCCCCCEEEECHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCHHHHHHHHHHCCCCCCEEEECCHHHHHH
T ss_conf 88888669841320299999999999999999999999854999614642723899999984477652788578899999
Q ss_pred HHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHH
Q ss_conf 78889876310121122013442035677699999998422214367864998328806999823755444555114799
Q gi|254780751|r 321 AKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTAL 400 (723)
Q Consensus 321 ~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l 400 (723)
+++|+..++|++..++++|.+..|||+.|+|+.||+++|+++||||||||||||+|||||+||||||+|+|++++|+|+|
T Consensus 242 ~~~~~~~~~p~~~~~v~~y~~~~plF~~y~ie~~I~~~l~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~g~~~~eet~~ 321 (489)
T PRK11712 242 LKEFTSEYIPELTDKLEHYSGRQPIFDLYDVENEIQRALERKVELKSGGYLIIDQTEAMTTVDINTGAFVGHRNLEETIF 321 (489)
T ss_pred HHHHHHHHCCCCCCEEEECCCCCHHHHHCCHHHHHHHHHCCEEECCCCCEEEEECCCCEEEEECCCCCCCCCCCHHHHHH
T ss_conf 99999875941001134326862177642899999997168077389878999426100798505765457777678899
Q ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHH
Q ss_conf 99999999999987310368638960334798888999999999973127872899860486148985156663011210
Q gi|254780751|r 401 QTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLEST 480 (723)
Q Consensus 401 ~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~ 480 (723)
+||||||+||||||||||||||||||||||++++|+++|+++|+++|++|+++++|++||+||||||||||+|+||.+++
T Consensus 322 ~tNlEAA~EIaRQLRLRnigGiIvIDFIDM~~~~~~~~V~~~l~~~l~~Dr~k~~v~~is~lGLvEmTRkR~r~sl~~~~ 401 (489)
T PRK11712 322 NTNIEATQAIARQLRLRNLGGIIIIDFIDMNNEDHRRRVLHSLEQALSKDRVKTNINGFSQLGLVEMTRKRTRESLEHVL 401 (489)
T ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCEEEEEEHHCCCCHHHHC
T ss_conf 98999999999998635578869998447998688999999999997468987078564777207996221033757770
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCC
Q ss_conf 02367546537860611468998878899973036431013576999998730237999999998488799984787788
Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELAD 560 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~ 560 (723)
+++||+|+|+|+|+|.+|+|++|+|+|.+.+...+.+.+.+.+||+|+.||+|+++..|.+||.+++.+|.|.+||+++.
T Consensus 402 ~~~Cp~C~G~G~v~s~et~~~~i~R~i~~~~~~~~~~~i~v~~~~~v~~~l~~~~~~~l~~lE~~~~~~i~i~~d~~~~~ 481 (489)
T PRK11712 402 CGECPTCHGRGTVKTVETVCYEIMREIVRVHHAYDSDRFLVYASPAVAEALKGEESHALAELEVFIGKQVKVQIEPLYNQ 481 (489)
T ss_pred CCCCCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHCCCHHHHHHHHHHHCCCEEEEECCCCCC
T ss_conf 78699889872655899999999999999986578873999988999999871578999999998599389995899886
Q ss_pred CCEEEE
Q ss_conf 633897
Q gi|254780751|r 561 KLFYIE 566 (723)
Q Consensus 561 ~~f~Ie 566 (723)
++|.|-
T Consensus 482 e~~~iv 487 (489)
T PRK11712 482 EQFDVV 487 (489)
T ss_pred CCEEEE
T ss_conf 763899
No 3
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659 The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are: Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO Associated components: The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP. Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2] In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , . Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too. RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=100.00 E-value=0 Score=1139.00 Aligned_cols=453 Identities=43% Similarity=0.680 Sum_probs=412.3
Q ss_pred EEEEEEEE-CCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf 07999998-99899999607334604287879899783638823135327897713022213712102898899999998
Q gi|254780751|r 14 ETRVVVLR-DNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKE 92 (723)
Q Consensus 14 e~Rvav~e-~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~ 92 (723)
|+|||+|+ +|.|.||+||+....+.+||||||+|+||+|||||||||||..||||||++||+++|+..+.....
T Consensus 1 e~r~Al~~~~~~l~el~ier~~~~~~~GnIY~G~V~~vlPsl~AAFvdiG~~~~GFLh~sdi~~~~~~~~~~~~~----- 75 (464)
T TIGR00757 1 ETRVALVELGGQLQELIIERPKSRQLVGNIYKGRVTRVLPSLQAAFVDIGLEKNGFLHASDIGENSEKLEQLVDT----- 75 (464)
T ss_pred CEEEEEEEECCEEEEEEEECCHHHCCHHHHHHCEEEEECCCCCEEEEECCCCCCCCCCHHHCCCCHHHHHHHHHC-----
T ss_conf 958999961877999998431110110023202020220376447742068835563033203324568888620-----
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf 88631111100000001112233444334454222233445543322223432112211121100001223444421331
Q gi|254780751|r 93 SNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQE 172 (723)
Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 172 (723)
... .+..+..... .............-+.+...........++|++
T Consensus 76 d~~-----------------------NA~~~a~~~~-----------~~~~~~~~kp~~~~QS~~~~~~~~~~~~~~I~e 121 (464)
T TIGR00757 76 DDD-----------------------NAEAEAAPAE-----------AKREAGQEKPEEIIQSSGDELERRQSKTASISE 121 (464)
T ss_pred CCC-----------------------CCCCCCCHHH-----------HHHHHHCCCCHHHHCCCHHHHHHHHCCCCCHHH
T ss_conf 212-----------------------5767788233-----------220100136213202530245543135435266
Q ss_pred CCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC--CEEEEE
Q ss_conf 068885799984033323456410123345765234422788751242046886899999999986300258--716998
Q gi|254780751|r 173 VIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAG--MGVILR 250 (723)
Q Consensus 173 ~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~--~G~IiR 250 (723)
+|++||.|||||+|||+|+|||+|||+||||||||||||++++.+||||||.+.++|.+||+++.+...|.+ ||+|||
T Consensus 122 ~L~~gq~vlVQV~Kep~G~KGArLTt~ISlpGrYlVlmP~~~~~~g~SRri~~~~eR~rLK~~~~~~~~p~~nt~G~IiR 201 (464)
T TIGR00757 122 LLRPGQSVLVQVVKEPRGNKGARLTTDISLPGRYLVLMPNTSHQVGVSRRIESEEERERLKKLLRSEVLPEGNTMGLIIR 201 (464)
T ss_pred HHCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEEEEEE
T ss_conf 61288858999885267898873546622462107855788943203441288245899999999853888770468998
Q ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCHHHHHHHHHCCCCCCEEECCC----CCHHHHHHHHH
Q ss_conf 5045575799999999999999987764201432212-345645888888752376631111035----32036678889
Q gi|254780751|r 251 TAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHL-VYEEGNLIKRAIRDLYCKDISEIIVSG----EKGYREAKDFM 325 (723)
Q Consensus 251 T~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~l-i~~~~~~~~~~ird~~~~~~~~i~vd~----~~~~~~~~~~~ 325 (723)
|||+++++++|.+|+++|++.|+.|++++....+|++ ||+|++++.++|||+++.++.+|+||+ ..+|..+.+|+
T Consensus 202 Taa~g~~~~~l~~D~~~L~~~W~~i~~~~~~~~~p~l~l~~E~~~i~r~~rD~~~~~~~~i~id~PaG~~~~y~~~~~~~ 281 (464)
T TIGR00757 202 TAAEGASEEELKKDLEELLRKWEKIKEKAQKRSAPILELYEEDDIIKRVLRDYLDTDVKEIVIDSPAGMKEIYEEIKEFI 281 (464)
T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHH
T ss_conf 40379998999999999999899999985047854101124504789999985101257789728610799999999985
Q ss_pred H-HHHHCCCCHHHHCCCCCH-HHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCC-CHHHHHHH
Q ss_conf 8-763101211220134420-35677699999998422214367864998328806999823755444555-11479999
Q gi|254780751|r 326 K-LLMPSYARIVRQYEDPHP-IFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHC-IEDTALQT 402 (723)
Q Consensus 326 ~-~~~p~~~~~v~~~~~~~~-lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~-~e~t~l~t 402 (723)
. .++|+...++.+|.+..| ||+.|+||.+|++||+|+||||||||||||+|||||+||||||+||+.++ +|||+|+|
T Consensus 282 ~~~~~Pe~~~Kl~~y~~~~p~~F~~f~ie~~i~~a~~r~V~L~SGGyivId~TEAlt~IDVNSG~~t~~~~n~EET~~~t 361 (464)
T TIGR00757 282 QDLVAPELVSKLKLYEGSLPPLFEGFQIEKQIEKALSRKVWLPSGGYIVIDQTEALTVIDVNSGRFTGKRNNLEETALNT 361 (464)
T ss_pred HCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCEEECCCCCEEEECCCCCEEEEEECCCHHHCCCCCCHHHHHHH
T ss_conf 00147314541443037788766533368999998388575588878876587403787604503112578723568888
Q ss_pred HHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCC
Q ss_conf 99999999998731036863896033479888899999999997312787289986048614898515666301121002
Q gi|254780751|r 403 NLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTK 482 (723)
Q Consensus 403 NleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~ 482 (723)
|||||+||||||||||||||||||||||.+.+||+.|++.|+++|+.||+|++|.+||.||||||||||.|+||.|.+++
T Consensus 362 NLEAA~EiArQLrLRnlGGiiiiDFIDM~~~k~~~~vl~~l~~~l~~DraR~~i~~~s~lGLvEmTRkR~r~SL~e~~~~ 441 (464)
T TIGR00757 362 NLEAAKEIARQLRLRNLGGIIIIDFIDMKSEKNRRRVLERLKEALSRDRARIQILGISELGLVEMTRKRLRESLMEVLGE 441 (464)
T ss_pred HHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHCCCCHHHHHCC
T ss_conf 89999999877521015847999510698866689999999999861663100110130103333042326743655247
Q ss_pred CCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 36754653786061146899887
Q gi|254780751|r 483 VCTYCKGAGYIRSQSSVALSILR 505 (723)
Q Consensus 483 ~c~~c~g~g~~~~~~~~~~~~~r 505 (723)
.||+|+|+|+|++.+++++.|+|
T Consensus 442 ~CP~C~G~G~v~~~e~~~~~i~R 464 (464)
T TIGR00757 442 TCPHCSGRGIVKTSETVLLEIER 464 (464)
T ss_pred CCCCCCCEEEEECCCCHHHHCCC
T ss_conf 88874741278326500021029
No 4
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=944.98 Aligned_cols=485 Identities=47% Similarity=0.717 Sum_probs=471.1
Q ss_pred CCEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCC
Q ss_conf 85268965289607999998998999996073346042878798997836388231353278977130222137121028
Q gi|254780751|r 2 ANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQI 81 (723)
Q Consensus 2 ~k~~lI~~~~~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~i 81 (723)
.|+||||+++ +|||||++++|.|.||+||+..+.+++||||+|+|+||+|||||||||||.+||||||++||++ ||+.
T Consensus 1 ~k~~~i~~~~-~e~rva~v~~~~l~el~ie~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~ 78 (487)
T COG1530 1 MKKMLINATQ-EETRVAVVDGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRA 78 (487)
T ss_pred CCEEEEECCC-CEEEEEEEECCEEEEEEEECCCCEEEECCCEEEEECCCCCCCHHHEEECCCCCCCEEEECCCCH-HHHH
T ss_conf 9507985265-4169999968877999980477376306716888623176632220551687660688410553-4420
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 98899999998886311111000000011122334443344542222334455433222234321122111211000012
Q gi|254780751|r 82 PFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVP 161 (723)
Q Consensus 82 p~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (723)
+.++
T Consensus 79 ~~~~---------------------------------------------------------------------------- 82 (487)
T COG1530 79 VLEE---------------------------------------------------------------------------- 82 (487)
T ss_pred CCCC----------------------------------------------------------------------------
T ss_conf 0023----------------------------------------------------------------------------
Q ss_pred CCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHC
Q ss_conf 23444421331068885799984033323456410123345765234422788751242046886899999999986300
Q gi|254780751|r 162 KKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEV 241 (723)
Q Consensus 162 ~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~ 241 (723)
+|+++++.||.++|||+|+|+|+|||+||++||++|||+||||+.+..+++|++|.+..+|.+|+.++..+..
T Consensus 83 -------~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~~Is~~grylVl~p~~~~~g~is~ri~~~~er~~Lk~~~~~l~~ 155 (487)
T COG1530 83 -------KIKVRLRGGQATLVQVVKEPRGTKGARLTTDISLAGRYLVLMPNAPDVGGISRRIEGEIERERLKEIVRELVD 155 (487)
T ss_pred -------CCEEEECCCCEEEEEEEEECCCCCCCCCEEEEEECEEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHHCCC
T ss_conf -------5005541786289999862576603421247860315899758987636421282887887767999860327
Q ss_pred CCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHH
Q ss_conf 25871699850455757999999999999999877642014322123456458888887523766311110353203667
Q gi|254780751|r 242 PAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREA 321 (723)
Q Consensus 242 ~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~ 321 (723)
|.+||+|+||++++++.++|.+|+++|...|+.|+..+....+|++||++.+++.+++||+++.++.+|+||+...|..+
T Consensus 156 ~~~~g~iiRTa~~g~~~eel~~d~~~l~~~w~~i~~~~~~~~ap~ll~~e~~~v~r~~rd~~~~~~~~I~Vd~~~~~~~~ 235 (487)
T COG1530 156 PGGMGLIIRTAGEGASEEELRRDLDYLRRLWEAILERAKKRPAPGLLYEETSLVVRVIRDYVGKDITEIVVDGKEAYLEA 235 (487)
T ss_pred CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEEEECCCCCCCCEEEECCCHHHHHH
T ss_conf 67842899640368468999999999998888998876237998699744761478752014676665998370588999
Q ss_pred HHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHHH
Q ss_conf 88898763101211220134420356776999999984222143678649983288069998237554445551147999
Q gi|254780751|r 322 KDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQ 401 (723)
Q Consensus 322 ~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~ 401 (723)
+.|+..++|+...++++|.+..|+|+.|+++.||..+++|+||||||||||||+|||||+||||||++++.+++++|+++
T Consensus 236 ~~~~~~~~~~~~~~l~~~~~~~~~f~~~~ie~~i~~al~r~V~L~sGG~~vId~tEAlt~IDVnsg~~~~~~~~eeta~~ 315 (487)
T COG1530 236 KEFILEIMPELRSKLKLYRGTTPLFALFGIEEQIARALERKVQLPSGGYLVIDPTEALTVIDVNSGRFTGAGDLEETAVN 315 (487)
T ss_pred HHHHHHCCHHHHHHEEECCCCCCCCCHHHHHHHHHHHHHHEEECCCCCCEEEECCCEEEEEECCCCCCCCCCCHHHHHHH
T ss_conf 99887537122110476468873012356999999765406736889824673130138997157642366746776666
Q ss_pred HHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHC
Q ss_conf 99999999999873103686389603347988889999999999731278728998604861489851566630112100
Q gi|254780751|r 402 TNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTT 481 (723)
Q Consensus 402 tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~ 481 (723)
||||||.|||||||||||||||+||||||...++++.|+.+|+++|+.|++++++++||+|||+||||||.++||.+.++
T Consensus 316 tNleAa~eiarqlrlR~lgGiIiIDfIdm~~~~~~~~v~~~l~~~l~~dr~r~~i~~~s~~Gl~emtR~R~~~sl~~~~~ 395 (487)
T COG1530 316 TNLEAAEEIARQLRLRNLGGIIIIDFIDMTEESHQRLVLERLRRALKRDRARIQIGRISELGLLEMTRKRTRESLLEVLS 395 (487)
T ss_pred HHHHHHHHHHHHHHHCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEECCCCCCEEEE
T ss_conf 20788999998872325577599983304125555889999999861588621124542267438998814777744566
Q ss_pred CCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHC-CEEEEEECCCCCC
Q ss_conf 236754653786061146899887889997303643101357699999873023799999999848-8799984787788
Q gi|254780751|r 482 KVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFG-VSINVVIGIELAD 560 (723)
Q Consensus 482 ~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~-~~I~i~~d~~l~~ 560 (723)
++||+|.|+|++++.+++++.++|.|+.++.......+.+.+++.++.|++|+++..+..+|...+ ..+.+..++.+++
T Consensus 396 ~~cp~c~G~g~v~~~~~~~~~i~R~i~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~e~~~~~~~i~~~~~~~~~~ 475 (487)
T COG1530 396 ERCPGCKGTGHVRSTESELLHILRYIEEEADINKTPEVGVEVPPAVAKYLLNEERGAIAELELFKGYLRVRLRVDDRVEQ 475 (487)
T ss_pred EECCCCEEEEEEECCCHHHHHHHCCCHHHHCCCCCCCCEEEECHHHHHHHCCCCCCHHHHHHHHCCCEEEEEEECHHHCC
T ss_conf 38898501589943814412332002454401467500489506665554156430256787630552489740212155
Q ss_pred CCEEEEECCCC
Q ss_conf 63389715544
Q gi|254780751|r 561 KLFYIEKGSPV 571 (723)
Q Consensus 561 ~~f~Ier~~~~ 571 (723)
++|.+.+....
T Consensus 476 ~~~~~~~~~~~ 486 (487)
T COG1530 476 EQYEVVRLREG 486 (487)
T ss_pred CCEEEEEECCC
T ss_conf 55057642147
No 5
>pfam10150 RNase_E_G Ribonuclease E/G family. Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs.
Probab=100.00 E-value=0 Score=652.56 Aligned_cols=271 Identities=51% Similarity=0.800 Sum_probs=266.3
Q ss_pred CCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 45765234422788751242046886899999999986300258716998504557579999999999999998776420
Q gi|254780751|r 201 SLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELAL 280 (723)
Q Consensus 201 sl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~ 280 (723)
||||||+||||+. .++||||||.+.++|.+|+.++..+ .|+++|+|+||+|++++.++|.+|+.+|.++|+.|.+.+.
T Consensus 1 sL~GRylVl~P~~-~~igiSrKI~d~~eR~rLk~i~~~~-~~~~~GiIiRT~A~~~~~e~l~~e~~~L~~~w~~i~~~~~ 78 (271)
T pfam10150 1 SLPGRYLVLMPNS-PGIGISRKIEDEEERKRLKEILESL-KPEGMGLIIRTAAEGASEEELAADLEYLLKLWEEILKKAK 78 (271)
T ss_pred CCCCCEEEEECCC-CCEEECCCCCCHHHHHHHHHHHHHH-CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9886049995599-9707607889869999999999973-8898229997765689999999999999999999999984
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 14322123456458888887523766311110353203667888987631012112201344203567769999999842
Q gi|254780751|r 281 NSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQ 360 (723)
Q Consensus 281 ~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~ 360 (723)
..++|+|||++++++.+++||+++.++++|+||+.+.|+.+++|+..++|....++.+|.+..|||+.|+|+.||+.||+
T Consensus 79 ~~~~p~ll~~~~~~~~~~lrD~~~~~~~~IivDd~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lF~~~~ie~~i~~~~~ 158 (271)
T pfam10150 79 SAKAPSLLYEELDLVLRALRDLLNPDVDEIIVDDREAYEKLKEFLKEFAPELAKKVELYEGERPLFDLYGIEEQIEKALS 158 (271)
T ss_pred CCCCCEEEEECCCHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHCCHHHHHHHHHC
T ss_conf 59998598838858999999726533509995688999999999998681111121021478886764585999999844
Q ss_pred CCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf 22143678649983288069998237554445551147999999999999998731036863896033479888899999
Q gi|254780751|r 361 TEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVE 440 (723)
Q Consensus 361 ~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~ 440 (723)
++||||||||||||+||||||||||||+++++++.++|+|+||||||+||||||||||||||||||||||++.+++++|+
T Consensus 159 ~~V~L~sGG~lvIe~TEAlt~IDVNSG~~~~~~~~e~t~l~~NleAa~EIarQlrLRni~GiIvIDFIdm~~~~~~~~v~ 238 (271)
T pfam10150 159 RKVWLKSGGYLVIEQTEALTAIDVNSGKFTGKRNLEETALKTNLEAAKEIARQLRLRNLGGIIVIDFIDMEDEEHRRQVL 238 (271)
T ss_pred CCEEECCCCEEEEECCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHH
T ss_conf 85891899779994251478985046655566777888999999999999999985688883999778889878899999
Q ss_pred HHHHHHHHHCCCCEEEEEECCCCEEEEECCCCC
Q ss_conf 999997312787289986048614898515666
Q gi|254780751|r 441 KKLKESLKKDRARVQVGAISNFGLLEMSRQRIR 473 (723)
Q Consensus 441 ~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r 473 (723)
+.|+++|++|+++++|++||+||||||||||+|
T Consensus 239 ~~l~~~~~~D~~~~~i~~~T~lGL~E~tRkR~r 271 (271)
T pfam10150 239 RALKEALKRDRAKTQILGITELGLVEMTRKRTR 271 (271)
T ss_pred HHHHHHHHHCCCCCEEECCCCCEEEEEEECCCC
T ss_conf 999999850999867936788714899750469
No 6
>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=99.95 E-value=3.4e-28 Score=215.02 Aligned_cols=87 Identities=46% Similarity=0.785 Sum_probs=79.1
Q ss_pred CCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 34604287879899783638823135327897713022213712102898899999998886311111000000011122
Q gi|254780751|r 34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVT 113 (723)
Q Consensus 34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 113 (723)
++.+++||||+|+|+||+|||||||||||.+++||||++|+.+.||.
T Consensus 2 ~~~~~vGnIY~GkV~~v~p~i~AAFVdiG~~k~gfL~~~d~~~~~~~--------------------------------- 48 (88)
T cd04453 2 NREPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFK--------------------------------- 48 (88)
T ss_pred CCCCCCCCEEEEEEEEECCCCCEEEEECCCCCCEEEECHHCCHHHHC---------------------------------
T ss_conf 87561124899999886668748999658986899990345723513---------------------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCC
Q ss_conf 33444334454222233445543322223432112211121100001223444421331068885799984033323456
Q gi|254780751|r 114 IPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKG 193 (723)
Q Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kg 193 (723)
+..+|.+.|++||.|||||+|||+++||
T Consensus 49 ----------------------------------------------------~~~~~~~~l~~G~~ilVQV~Ke~~~~Kg 76 (88)
T cd04453 49 ----------------------------------------------------KHKKIAKLLKEGQEILVQVVKEPIGTKG 76 (88)
T ss_pred ----------------------------------------------------CCCCHHHHCCCCCEEEEEEEECCCCCCC
T ss_conf ----------------------------------------------------5788778377999999999766879978
Q ss_pred CCCCCCCCCCCC
Q ss_conf 410123345765
Q gi|254780751|r 194 AAVTTYLSLAGR 205 (723)
Q Consensus 194 a~lT~~isl~Gr 205 (723)
|+||++|||+||
T Consensus 77 p~lT~~isl~Gr 88 (88)
T cd04453 77 PRLTTNISLPGR 88 (88)
T ss_pred CEEEEEEECCCC
T ss_conf 608845872889
No 7
>PRK07252 hypothetical protein; Provisional
Probab=98.34 E-value=8.1e-07 Score=66.46 Aligned_cols=40 Identities=23% Similarity=0.419 Sum_probs=36.5
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 428787989978363882313532789771302221371210
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
.+|.+|.|+|++|.|- +|||+++.+..||+|.|||.+.|.
T Consensus 2 kvGdiv~G~V~~I~~f--GaFV~l~~gv~GLiHISEis~~~v 41 (120)
T PRK07252 2 KIGDKLKGTITGIKPY--GAFVALENGTTGLIHISEIKTGFI 41 (120)
T ss_pred CCCCEEEEEEEEEECC--EEEEEECCCCEEEEEHHHHCCCCC
T ss_conf 8888999999999754--579995799578888666010200
No 8
>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=98.19 E-value=3.2e-06 Score=62.28 Aligned_cols=38 Identities=32% Similarity=0.549 Sum_probs=34.6
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 8787989978363882313532789771302221371210
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
|.||.|+|++|.| -.|||+++.+..||||.|||.++|.
T Consensus 1 G~vv~G~V~~I~~--fGaFV~l~~g~~GL~HiSeis~~~v 38 (69)
T cd05692 1 GSVVEGTVTRLKP--FGAFVELGGGISGLVHISQIAHKRV 38 (69)
T ss_pred CCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHHCCCCC
T ss_conf 9999999999985--3899996899889999698345655
No 9
>PRK08582 hypothetical protein; Provisional
Probab=98.19 E-value=2.7e-06 Score=62.85 Aligned_cols=40 Identities=25% Similarity=0.385 Sum_probs=36.1
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 428787989978363882313532789771302221371210
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
-+|+||.|+|++|.|- .|||+|+.+..||+|.+||..+|-
T Consensus 4 evG~iv~G~V~~I~~f--GaFV~l~~g~~GLvHISeis~~~V 43 (139)
T PRK08582 4 EVGSKLQGKVTGITNF--GAFVELPEGKTGLVHISEVADNYV 43 (139)
T ss_pred CCCCEEEEEEEEEECC--EEEEEECCCCEEEEEHHHHCCCCC
T ss_conf 4787999999899641--789995699667887366256656
No 10
>PRK05807 hypothetical protein; Provisional
Probab=98.14 E-value=3.4e-06 Score=62.11 Aligned_cols=39 Identities=23% Similarity=0.396 Sum_probs=34.7
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 428787989978363882313532789771302221371210
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
.+|+||.|+|++|.|= .|||+++ ++.||+|++||...|-
T Consensus 4 evG~iv~G~V~~I~~f--GaFV~l~-g~~GLvHISEis~~~V 42 (136)
T PRK05807 4 EAGSILEGTVVNITNF--GAFVEVE-GKTGLVHISEVADTYV 42 (136)
T ss_pred CCCCEEEEEEEEEECC--EEEEEEC-CEEEEEEHHHHCCCCC
T ss_conf 5788999999999724--4799978-9276898567077643
No 11
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.12 E-value=1.2e-05 Score=58.37 Aligned_cols=125 Identities=18% Similarity=0.298 Sum_probs=82.8
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEEC--CCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 04287879899783638823135327--8977130222137121028988999999988863111110000000111223
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYG--GNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTI 114 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG--~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (723)
.-.|.|+.|+|++|.+ .+|||++. .+..||+|+|||.+.+.
T Consensus 6 Pe~g~~v~~~V~~i~~--~Ga~v~l~ey~~~eG~i~isEis~~~v----------------------------------- 48 (262)
T PRK03987 6 PEEGELVVGTVKEVKD--FGAFVTLDEYPGKEGFIHISEVASGWV----------------------------------- 48 (262)
T ss_pred CCCCCEEEEEEEEEEC--CEEEEEECCCCCCCEEEEHHHCCHHHH-----------------------------------
T ss_conf 9999889999999956--679999356599316788798346775-----------------------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCC
Q ss_conf 34443344542222334455433222234321122111211000012234444213310688857999840333234564
Q gi|254780751|r 115 PNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGA 194 (723)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga 194 (723)
.+|.+++++||.+.|+|.+=-
T Consensus 49 -----------------------------------------------------~~i~d~~k~G~~v~~kVi~vd------ 69 (262)
T PRK03987 49 -----------------------------------------------------KNIRDYVKEGQKVVCKVIRVD------ 69 (262)
T ss_pred -----------------------------------------------------HCHHHHCCCCCEEEEEEEEEC------
T ss_conf -----------------------------------------------------199985158988999999883------
Q ss_pred CCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCC--CCHHHHHHHHHH-HHHH
Q ss_conf 1012334576523442278875124204688689999999998630025871699850455--757999999999-9999
Q gi|254780751|r 195 AVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGAS--RTKIEIKRDFEY-LMRL 271 (723)
Q Consensus 195 ~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~--~~~~~l~~d~~~-L~~~ 271 (723)
|..+ .+.+|.|-.++++++...+...... -..-|+|.+|.. .+.+++...+.. |.+.
T Consensus 70 ----------------~~kg-~IdLS~k~Vs~~e~~~~~~~~k~~k---~a~~il~~va~~~~~~~ee~~~~i~~~l~~~ 129 (262)
T PRK03987 70 ----------------PKKG-HIDLSLKRVNEHQRREKIQEWKNEQ---KAEKLLELAAEKLGKDLEEAWEEVGYKLEEE 129 (262)
T ss_pred ----------------CCCC-EEEEECCCCCHHHHHHHHHHHHHHH---HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf ----------------8788-7871104499899999999999999---9999999999982989899999999999998
Q ss_pred HHHHHH
Q ss_conf 998776
Q gi|254780751|r 272 WDNVRE 277 (723)
Q Consensus 272 w~~i~~ 277 (723)
|.....
T Consensus 130 yg~~y~ 135 (262)
T PRK03987 130 FGDLYD 135 (262)
T ss_pred HCCHHH
T ss_conf 560989
No 12
>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=98.10 E-value=5.8e-06 Score=60.55 Aligned_cols=39 Identities=21% Similarity=0.361 Sum_probs=34.7
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEEC--CCCCCCCCHHHCCCCC
Q ss_conf 4287879899783638823135327--8977130222137121
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYG--GNRHGFLPFLEIHPDY 78 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG--~~k~gFL~~~ei~~~y 78 (723)
..|+||.|+|++|.| -+|||+++ .+..||+|.+||.+.+
T Consensus 2 e~G~iv~G~V~~i~~--~GafV~l~e~~g~eGlihiSEis~~~ 42 (76)
T cd04452 2 EEGELVVVTVKSIAD--MGAYVSLLEYGNIEGMILLSELSRRR 42 (76)
T ss_pred CCCCEEEEEEEEEEC--CEEEEEECCCCCCEEEEEHHHCCCCC
T ss_conf 889999999999973--46999973369919999979968451
No 13
>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=98.04 E-value=7.9e-06 Score=59.59 Aligned_cols=38 Identities=21% Similarity=0.290 Sum_probs=33.3
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCCC
Q ss_conf 428787989978363882313532-7897713022213712
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHPD 77 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~~ 77 (723)
.+|.||.|+|++|.|= .|||+| |.++.|++|.|||.+.
T Consensus 2 evg~i~~G~V~~i~~f--GAFV~i~g~~~~GLvHiSeis~~ 40 (73)
T cd05686 2 ALYQIFKGEVASVTEY--GAFVKIPGCRKQGLVHKSHMSSC 40 (73)
T ss_pred CCCCEEEEEEEEEEEC--CEEEEECCCCCCEEEEEECCCCC
T ss_conf 7886999999899753--23999089884355995605412
No 14
>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=97.99 E-value=1.1e-05 Score=58.54 Aligned_cols=39 Identities=13% Similarity=0.140 Sum_probs=34.2
Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEEC
Q ss_conf 310135769999987302379999999984887999847
Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIG 555 (723)
Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d 555 (723)
.-.++.++|+-..-+.+..-..|..|.+++|++|.|..|
T Consensus 551 ~i~~~~i~~~ki~~vIG~gGk~Ik~i~~~tg~~I~i~dd 589 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD 589 (684)
T ss_pred EEEEEEECHHHHHHEECCCCHHHHHHHHHHCCEEEEECC
T ss_conf 579999787886650787528898999988988998589
No 15
>PRK08059 general stress protein 13; Validated
Probab=97.98 E-value=1.1e-05 Score=58.54 Aligned_cols=41 Identities=24% Similarity=0.370 Sum_probs=36.1
Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 6042878798997836388231353278977130222137121
Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
..-+|.||.|+|++|.| -+|||+++.+-.||||++||...+
T Consensus 3 k~kvGdiv~G~V~~I~~--fG~FV~l~~gv~GLihiSEls~~~ 43 (119)
T PRK08059 3 QYEVGVVVTGKVTGIQD--YGAFVALDEETQGLVHISEITHGF 43 (119)
T ss_pred CCCCCCEEEEEEEEEEC--EEEEEEEECCCEEEEEHHHHCCCC
T ss_conf 78999999999999974--048999943953788878824566
No 16
>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=97.97 E-value=1.6e-05 Score=57.38 Aligned_cols=37 Identities=27% Similarity=0.493 Sum_probs=33.6
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 878798997836388231353278977130222137121
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
|.||.|+|++|.| =.|||+++.+..||+|.|||.+++
T Consensus 1 G~iv~G~V~~i~~--fG~FV~l~~g~~GLiHiSeis~~~ 37 (68)
T cd04472 1 GKIYEGKVVKIKD--FGAFVEILPGKDGLVHISELSDER 37 (68)
T ss_pred CCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHHCCCC
T ss_conf 9999999999973--299999579962488868934565
No 17
>pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Probab=97.95 E-value=1.8e-05 Score=57.06 Aligned_cols=40 Identities=40% Similarity=0.635 Sum_probs=36.0
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 042878798997836388231353278977130222137121
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
..+|.|+.|+|.+|.+ .+|||++|.+-.||+|.+++++++
T Consensus 2 ~~~G~iv~G~V~~i~~--~G~fV~l~~~~~g~v~~s~ls~~~ 41 (74)
T pfam00575 2 PEEGDVVKGTVTRVTK--GGAFVDLGNGVEGFIPISEISDDR 41 (74)
T ss_pred CCCCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCCCCC
T ss_conf 8899999999999987--759999789979999844613655
No 18
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.91 E-value=1.8e-05 Score=57.09 Aligned_cols=39 Identities=15% Similarity=0.154 Sum_probs=33.8
Q ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEEC
Q ss_conf 310135769999987302379999999984887999847
Q gi|254780751|r 517 HNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIG 555 (723)
Q Consensus 517 ~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d 555 (723)
+-..+.++|+-..-+.+..-..|..|.+.+|++|.|..|
T Consensus 554 ~i~~~~i~~~ki~~vIG~gGk~Ik~i~e~tg~~Idi~dd 592 (694)
T PRK11824 554 RIETIKIDPDKIRDVIGPGGKTIREITEETGAKIDIEDD 592 (694)
T ss_pred EEEEEEECHHHHHHEECCCHHHHHHHHHHHCCEEEEECC
T ss_conf 799999787986650686338899999988988999689
No 19
>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=97.87 E-value=3.2e-05 Score=55.39 Aligned_cols=40 Identities=23% Similarity=0.345 Sum_probs=34.8
Q ss_pred CCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf 460428787989978363882313532789771302221371
Q gi|254780751|r 35 KKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP 76 (723)
Q Consensus 35 ~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~ 76 (723)
+.--+|.||.|+|++|.+ =.|||+++.+..|.+|.|++..
T Consensus 12 ~dlevG~~y~G~V~~v~~--fGaFV~l~~~~~GLiHiS~l~~ 51 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAK--YGVFVDLNDHVRGLIHRSNLLR 51 (77)
T ss_pred CCCCCCCEEEEEEEEEEE--CCEEEECCCCCEEEEEEHHCCC
T ss_conf 035239999999988966--2889992699879689316668
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=97.84 E-value=1.6e-05 Score=57.38 Aligned_cols=79 Identities=24% Similarity=0.348 Sum_probs=63.4
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 42878798997836388231353278977130222137121028988999999988863111110000000111223344
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPND 117 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (723)
-+|+++.|+|+.|-|= .|||++-.+..|+.|+|||.-.|-.
T Consensus 4 kvG~~l~GkItgI~~y--GAFV~l~~g~tGLVHISEIa~~fVk------------------------------------- 44 (129)
T COG1098 4 KVGSKLKGKITGITPY--GAFVELEGGKTGLVHISEIADGFVK------------------------------------- 44 (129)
T ss_pred CCCCEEEEEEEEEEEC--CEEEEECCCCCCEEEEHHHHHHHHH-------------------------------------
T ss_conf 3464678889756743--3489823997314883575443677-------------------------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCC
Q ss_conf 43344542222334455433222234321122111211000012234444213310688857999840333234564101
Q gi|254780751|r 118 HSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVT 197 (723)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT 197 (723)
.|.+.|++||+|.|||.-=.. .
T Consensus 45 ---------------------------------------------------dI~d~L~vG~eV~vKVl~ide-------~ 66 (129)
T COG1098 45 ---------------------------------------------------DIHDHLKVGQEVKVKVLDIDE-------N 66 (129)
T ss_pred ---------------------------------------------------HHHHHHCCCCEEEEEEEEECC-------C
T ss_conf ---------------------------------------------------399884278879999972146-------8
Q ss_pred CCCCCCCCCEEECCCC
Q ss_conf 2334576523442278
Q gi|254780751|r 198 TYLSLAGRYSVLMPNT 213 (723)
Q Consensus 198 ~~isl~Gry~Vl~P~~ 213 (723)
..|||.=|-+...|..
T Consensus 67 GKisLSIr~~~e~pe~ 82 (129)
T COG1098 67 GKISLSIRKLEEEPEK 82 (129)
T ss_pred CCCCEEHHHHHHCCCC
T ss_conf 9703356876647443
No 21
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.84 E-value=2.9e-05 Score=55.70 Aligned_cols=38 Identities=18% Similarity=0.281 Sum_probs=33.4
Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 6042878798997836388231353278977130222137
Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
.-..|.|..|+|..|.. ..+|||+|.--.||+|..|+.
T Consensus 30 ~i~~G~iV~G~Vv~I~~--d~v~VDiG~KsEG~Ip~~E~~ 67 (489)
T PRK13806 30 NVRVGDRIKAAIVAIGE--DSVFVATGSKVDGVIDRRELE 67 (489)
T ss_pred CCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHC
T ss_conf 77799889999999979--989999689828995899925
No 22
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.83 E-value=3.4e-05 Score=55.20 Aligned_cols=40 Identities=25% Similarity=0.465 Sum_probs=31.5
Q ss_pred CCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 346042878798997836388231353278977130222137
Q gi|254780751|r 34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
......|.|..|.|+.|.+.. ||||+|.--.||+|.+|+.
T Consensus 16 ~~~~~~G~vV~G~Vv~i~~~~--v~Vdig~Kseg~ip~~E~~ 55 (541)
T COG0539 16 DEEFEPGDVVKGTVVSIEKDG--VLVDIGGKSEGVIPISEFS 55 (541)
T ss_pred HHCCCCCCEEEEEEEEEECCE--EEEEECCCCCCEEEHHHCC
T ss_conf 311688878999999993884--9998367615576889805
No 23
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.81 E-value=4.1e-05 Score=54.64 Aligned_cols=70 Identities=23% Similarity=0.367 Sum_probs=58.8
Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 28787989978363882313532789771302221371210289889999999888631111100000001112233444
Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDH 118 (723)
Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (723)
.|.||.|+|+++.+ ..+||++|.+-.||||++++.+.|.
T Consensus 2 ~G~iv~g~V~~v~~--~g~~v~i~~~~~g~l~~~~l~~~~~--------------------------------------- 40 (72)
T smart00316 2 VGDVVEGTVTEITP--FGAFVDLGNGVEGLIPISELSDKRV--------------------------------------- 40 (72)
T ss_pred CCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCCCCCC---------------------------------------
T ss_conf 99899999999978--7399997699899998075055554---------------------------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCC
Q ss_conf 33445422223344554332222343211221112110000122344442133106888579998403332345641012
Q gi|254780751|r 119 SLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTT 198 (723)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~ 198 (723)
..+.+.++.||.|-++|.+-...++...||.
T Consensus 41 -------------------------------------------------~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~ 71 (72)
T smart00316 41 -------------------------------------------------KDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71 (72)
T ss_pred -------------------------------------------------CCHHHEECCCCEEEEEEEEEECCCCEEEEEE
T ss_conf -------------------------------------------------7846836389899999999999999999985
No 24
>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=97.65 E-value=0.0001 Score=51.93 Aligned_cols=39 Identities=31% Similarity=0.337 Sum_probs=34.1
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCCCC
Q ss_conf 428787989978363882313532-78977130222137121
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~~y 78 (723)
.+|.+|.|+|++|.| =+|||++ |.+-.||+|.+|+.+++
T Consensus 1 kVG~~v~G~V~~i~~--fG~FV~l~g~~i~GLvHiSels~~~ 40 (77)
T cd05708 1 KVGQKIDGTVRRVED--YGVFIDIDGTNVSGLCHKSEISDNR 40 (77)
T ss_pred CCCCEEEEEEEEEEC--EEEEEEECCCCEEEEEEHHHHCCCC
T ss_conf 998999999999964--1789996789807998878817565
No 25
>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=97.63 E-value=1e-04 Score=51.95 Aligned_cols=36 Identities=28% Similarity=0.530 Sum_probs=31.4
Q ss_pred CCEEEEEEEEECCCCCEEEEEEC---CCCCCCCCHHHCCCC
Q ss_conf 87879899783638823135327---897713022213712
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYG---GNRHGFLPFLEIHPD 77 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG---~~k~gFL~~~ei~~~ 77 (723)
|+||.|+|++|.| -+|||++. .+..|++|.|||.++
T Consensus 1 G~i~~G~V~~i~~--fGaFV~l~~~~~~~~GLvHiSeis~~ 39 (79)
T cd05684 1 GKIYKGKVTSIMD--FGCFVQLEGLKGRKEGLVHISQLSFE 39 (79)
T ss_pred CCEEEEEEEEEEE--EEEEEEEECCCCCCEEEEEHHHCCCC
T ss_conf 9999999989975--33999996788980678995681575
No 26
>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=97.58 E-value=0.00015 Score=50.81 Aligned_cols=40 Identities=23% Similarity=0.399 Sum_probs=35.5
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 042878798997836388231353278977130222137121
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
-.+|.|+.|+|++|.| -++||+++.+-.||+|.+++...+
T Consensus 12 lk~G~iv~G~V~~i~~--~G~FV~l~~~v~Glv~~s~ls~~~ 51 (83)
T cd04461 12 LKPGMVVHGYVRNITP--YGVFVEFLGGLTGLAPKSYISDEF 51 (83)
T ss_pred CCCCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCCCCC
T ss_conf 7999999999999927--819999569948998999968642
No 27
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.55 E-value=0.00015 Score=50.68 Aligned_cols=40 Identities=28% Similarity=0.513 Sum_probs=34.8
Q ss_pred CCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 346042878798997836388231353278977130222137
Q gi|254780751|r 34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
......|.|..|+|..|.+ ..+|||||....||||.+|+.
T Consensus 26 ~~~~k~GdiVeG~V~~I~~--~~v~VdiG~k~eG~i~~~E~s 65 (314)
T PRK07400 26 DYHFKPGDIVNGTVFSLEP--KGALIDIGAKTAAFMPLQEMS 65 (314)
T ss_pred HCCCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEHHHHC
T ss_conf 2369999989999999979--989999779807999999936
No 28
>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=97.49 E-value=0.00022 Score=49.59 Aligned_cols=38 Identities=26% Similarity=0.423 Sum_probs=34.0
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 8787989978363882313532789771302221371210
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
|.||.|+|++|.| -.|||++|.+-.||+|.+++...|.
T Consensus 1 G~iv~G~V~~i~~--fG~FV~l~~~~~GLvhisels~~~~ 38 (68)
T cd05685 1 GMVLEGVVTNVTD--FGAFVDIGVKQDGLIHISKMADRFV 38 (68)
T ss_pred CCEEEEEEEEEEC--EEEEEEECCCCEEEEECHHHCCCCC
T ss_conf 9999999999965--2899991499789998189767876
No 29
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.48 E-value=0.00018 Score=50.15 Aligned_cols=10 Identities=30% Similarity=0.614 Sum_probs=3.6
Q ss_pred HHCCCCEEEE
Q ss_conf 1036863896
Q gi|254780751|r 416 LRDLAGLIVV 425 (723)
Q Consensus 416 LRnlgGiIvI 425 (723)
+.|=.|.|+.
T Consensus 362 ~ed~~G~i~L 371 (670)
T PRK00087 362 LENEDGYVVL 371 (670)
T ss_pred EECCCCCEEE
T ss_conf 8689982998
No 30
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.46 E-value=0.00021 Score=49.76 Aligned_cols=62 Identities=23% Similarity=0.315 Sum_probs=48.7
Q ss_pred CCEEEEEEEECCEEEEEE--ECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 960799999899899999--6073346042878798997836388231353278977130222137
Q gi|254780751|r 12 VEETRVVVLRDNRVEELD--FESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 12 ~~e~Rvav~e~g~l~e~~--~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
+.-.+||+-+-|--.||. +|..-+.-..|.|..|+|..|.+. .+|||||.--.||+|.+|+.
T Consensus 6 ~~~~~~~~~~~~S~edf~~~le~s~k~~~eGdIV~GtVv~I~~d--~VlVDIG~KsEGiIP~~E~s 69 (484)
T PRK07899 6 VTSPQVAVNDIGSAEDFLAAIDKTIKYFNDGDIVEGTVVKVDRD--EVLLDIGYKTEGVIPSRELS 69 (484)
T ss_pred CCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEEEEEEECC--EEEEEECCCEEEEEEHHHHC
T ss_conf 88760676589999999998887873588998899999999789--89998268704787999946
No 31
>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=97.40 E-value=0.00026 Score=49.05 Aligned_cols=36 Identities=25% Similarity=0.434 Sum_probs=32.1
Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf 287879899783638823135327897713022213712
Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD 77 (723)
Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~ 77 (723)
.|.||.|+|++|.| -+|||+++ +-.||+|.+|+++.
T Consensus 1 eG~iv~g~V~~i~~--fG~FV~l~-gi~Glihisels~~ 36 (68)
T cd05688 1 EGDVVEGTVKSITD--FGAFVDLG-GVDGLLHISDMSWG 36 (68)
T ss_pred CCCEEEEEEEEEEC--CEEEEEEC-CEEEEEECHHHCCC
T ss_conf 99999999999956--38899979-98999984364666
No 32
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.38 E-value=0.00029 Score=48.76 Aligned_cols=38 Identities=24% Similarity=0.392 Sum_probs=33.8
Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 6042878798997836388231353278977130222137
Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
..-.|.|..|+|.+|.+ +.+|||+|.--.|++|..|+.
T Consensus 17 ~~~~G~iV~G~Vv~i~~--~~v~VdiG~K~eG~I~~~E~~ 54 (556)
T PRK06299 17 ELREGSIVKGTVVAIDK--DYVLVDVGLKSEGRIPLEEFK 54 (556)
T ss_pred CCCCCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHHC
T ss_conf 78899989999999979--999999688835787999934
No 33
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.37 E-value=0.00024 Score=49.24 Aligned_cols=37 Identities=27% Similarity=0.405 Sum_probs=22.1
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf 4287879899783638823135327897713022213712
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD 77 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~ 77 (723)
..|.++.|+|++|.+ -+||||+| +-.||||.+||.+.
T Consensus 190 ~~G~vv~G~V~~i~~--~GaFVdlg-gvdGllhiseiSw~ 226 (556)
T PRK06299 190 EEGQVVEGVVKNITD--YGAFVDLG-GVDGLLHITDISWK 226 (556)
T ss_pred CCCCEEEEEEEEEEC--CCEEEEEC-CEEEEEEHHHCCCC
T ss_conf 479727899999705--75899958-95899985671556
No 34
>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=97.36 E-value=0.00037 Score=47.99 Aligned_cols=37 Identities=27% Similarity=0.517 Sum_probs=33.5
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 878798997836388231353278977130222137121
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
|.|+.|.|++|.|. .|||++..+-.||+|.+||..+|
T Consensus 1 G~vv~G~V~~i~~~--G~fV~~~~~i~Glvp~seis~~~ 37 (70)
T cd05698 1 GLKTHGTIVKVKPN--GCIVSFYNNVKGFLPKSELSEAF 37 (70)
T ss_pred CCEEEEEEEEEECC--CEEEEECCCCEEEEEHHHHCCCC
T ss_conf 99999999999817--18999489969998989928320
No 35
>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=97.35 E-value=0.00043 Score=47.53 Aligned_cols=35 Identities=29% Similarity=0.509 Sum_probs=31.8
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf 8787989978363882313532789771302221371
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP 76 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~ 76 (723)
|.|..|+|..|.+ ..||||||..-.||||.+|+..
T Consensus 1 G~iV~G~V~~i~~--~gv~Vdig~k~eG~ip~~E~s~ 35 (70)
T cd05687 1 GDIVKGTVVSVDD--DEVLVDIGYKSEGIIPISEFSD 35 (70)
T ss_pred CCEEEEEEEEEEC--CEEEEEECCCCCEEEEHHHHCC
T ss_conf 9989999999978--8699996898502689999453
No 36
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.35 E-value=0.0002 Score=49.87 Aligned_cols=62 Identities=10% Similarity=0.012 Sum_probs=28.1
Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHH-------HHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCE
Q ss_conf 9985045575799999999999999987-------7642014322123456458888887523766311
Q gi|254780751|r 248 ILRTAGASRTKIEIKRDFEYLMRLWDNV-------RELALNSVAPHLVYEEGNLIKRAIRDLYCKDISE 309 (723)
Q Consensus 248 IiRT~a~~~~~~~l~~d~~~L~~~w~~i-------~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~ 309 (723)
-|-..|...+++.+..-+.+-+...+.+ ........-+........-+...+++.+..++.+
T Consensus 187 MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~~~~~~~l~~~i~~~~~~~l~~ 255 (692)
T COG1185 187 MVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDEELEAKVRDLAEDELKE 255 (692)
T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 043466668889999999988898999999999999973765532335686489999999986788999
No 37
>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=97.33 E-value=0.00048 Score=47.19 Aligned_cols=38 Identities=21% Similarity=0.305 Sum_probs=34.4
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf 4287879899783638823135327897713022213712
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD 77 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~ 77 (723)
-.|.+|.|+|++|.+ -+|||+|+.+-.|++|.||+.+.
T Consensus 2 ~~G~~v~G~V~~It~--fG~FV~i~~g~eGLvHiSelsw~ 39 (72)
T cd05689 2 PEGTRLFGKVTNLTD--YGCFVELEEGVEGLVHVSEMDWT 39 (72)
T ss_pred CCCCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCCCC
T ss_conf 889999999989947--62399966993899997663165
No 38
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.29 E-value=0.00049 Score=47.15 Aligned_cols=83 Identities=19% Similarity=0.214 Sum_probs=67.0
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 04287879899783638823135327897713022213712102898899999998886311111000000011122334
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPN 116 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (723)
-..|.+..|+|+++-| ..||||||. =.|+||.+||.+.+-.
T Consensus 190 l~~G~vV~G~V~~It~--~GafVdigG-vdGLlHiseiS~~rv~------------------------------------ 230 (541)
T COG0539 190 LEVGEVVEGVVKNITD--YGAFVDIGG-VDGLLHISEISWKRVD------------------------------------ 230 (541)
T ss_pred CCCCCEEEEEEEEEEC--CCEEEEECC-EEEEEEHHHCCCCCCC------------------------------------
T ss_conf 7887669999998615--747999257-1668864760655558------------------------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCC
Q ss_conf 44334454222233445543322223432112211121100001223444421331068885799984033323456410
Q gi|254780751|r 117 DHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAV 196 (723)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~l 196 (723)
.-.++++.||+|-|+|.+--..++--.|
T Consensus 231 ----------------------------------------------------~P~~vvkvGd~VkvkVi~~D~e~~RVsL 258 (541)
T COG0539 231 ----------------------------------------------------HPSEVVKVGDEVKVKVISLDEERGRVSL 258 (541)
T ss_pred ----------------------------------------------------CHHHHCCCCCEEEEEEEEECCCCCEEEE
T ss_conf ----------------------------------------------------9899535698899999997267886999
Q ss_pred CCCCCCCCCCEEEC
Q ss_conf 12334576523442
Q gi|254780751|r 197 TTYLSLAGRYSVLM 210 (723)
Q Consensus 197 T~~isl~Gry~Vl~ 210 (723)
|..-++++.|.-+-
T Consensus 259 SlK~l~~dPw~~i~ 272 (541)
T COG0539 259 SLKQLEEDPWEGIE 272 (541)
T ss_pred EEHHCCCCCHHHHH
T ss_conf 94650469477776
No 39
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.28 E-value=0.00073 Score=45.93 Aligned_cols=39 Identities=26% Similarity=0.463 Sum_probs=33.6
Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEE-CCCCCCCCCHHHCCC
Q ss_conf 60428787989978363882313532-789771302221371
Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDY-GGNRHGFLPFLEIHP 76 (723)
Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdi-G~~k~gFL~~~ei~~ 76 (723)
.-.+|.|..|+|.+|.+ ..+|||+ |..-.||+|.+|+..
T Consensus 14 ~i~~G~iV~G~V~~I~~--~~v~Vdi~G~k~eG~I~~~E~s~ 53 (390)
T PRK06676 14 EVEVGDVVTGEVLKVED--KQVFVNIEGYKVEGVIPISELSN 53 (390)
T ss_pred CCCCCCEEEEEEEEEEC--CEEEEEECCCEEEEEEEHHHHCC
T ss_conf 68999989999999989--98999933863589999999456
No 40
>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=97.25 E-value=0.00066 Score=46.26 Aligned_cols=37 Identities=38% Similarity=0.515 Sum_probs=33.6
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 878798997836388231353278977130222137121
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
|.|+.|+|++|.|. .|||++|.+-.||+|.+|+.+++
T Consensus 1 G~iV~G~V~~i~~~--G~fV~l~~~v~G~ih~sels~~~ 37 (73)
T cd05691 1 GSIVTGKVTEVDAK--GATVKLGDGVEGFLRAAELSRDR 37 (73)
T ss_pred CCEEEEEEEEEECC--CEEEEECCCCEEEEEHHHCCCCH
T ss_conf 99999999999778--68999289969999989978211
No 41
>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=97.21 E-value=0.00095 Score=45.16 Aligned_cols=40 Identities=25% Similarity=0.319 Sum_probs=36.2
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 428787989978363882313532789771302221371210
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
.+|.|+-|+|++|-|. .|||++|.+-.|+.|.+|+..+|-
T Consensus 2 kvG~~l~G~Vt~V~~~--g~fV~L~~~~~Glvhisel~dd~~ 41 (73)
T cd05706 2 KVGDILPGRVTKVNDR--YVLVQLGNKVTGPSFITDALDDYS 41 (73)
T ss_pred CCCCEEEEEEEEECCC--EEEEEECCCCEEEEEHHHHCCCCC
T ss_conf 8898999999998888--799990899479999899304601
No 42
>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=97.17 E-value=0.00097 Score=45.10 Aligned_cols=36 Identities=19% Similarity=0.355 Sum_probs=32.9
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf 87879899783638823135327897713022213712
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD 77 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~ 77 (723)
|.+|.|+|++|.+- .|||++..+-.||+|.+|+.++
T Consensus 1 G~~v~G~V~~i~~f--G~FV~l~~gieGLvHiselsw~ 36 (69)
T cd05690 1 GTVVSGKIKSITDF--GIFVGLDGGIDGLVHISDISWT 36 (69)
T ss_pred CCEEEEEEEEECCC--EEEEEECCCCEEEEEHHHHCCC
T ss_conf 99999999999131--8999976996599994882456
No 43
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.04 E-value=0.001 Score=44.85 Aligned_cols=37 Identities=27% Similarity=0.372 Sum_probs=23.8
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCC
Q ss_conf 4287879899783638823135327897713022213712
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPD 77 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~ 77 (723)
..|.|+.|+|+++.+= .||||+| +-.||||++||.+.
T Consensus 207 ~~G~vveG~Vk~It~f--GAFVDLG-GVDGLvHiSEiSW~ 243 (484)
T PRK07899 207 QKGQVRKGVVSSIVNF--GAFVDLG-GVDGLVHVSELSWK 243 (484)
T ss_pred CCCCEEEEEEEEECCC--EEEEEEC-CEEEEEEHHHCCCC
T ss_conf 7898799999982164--6899955-72378981340356
No 44
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=96.94 E-value=0.0023 Score=42.51 Aligned_cols=35 Identities=20% Similarity=0.235 Sum_probs=19.6
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 42878798997836388231353278977130222137
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
..|.+..|+|..+.+| .+||+++ +-.||||+|++.
T Consensus 117 ~~~~~V~gkV~~~~kg--G~~V~i~-gl~gFiP~Sqls 151 (314)
T PRK07400 117 KEDATVRSEVFATNRG--GALVRIE-GLRGFIPGSHIS 151 (314)
T ss_pred HCCCEEEEEEEEEECC--CEEEEEC-CEEEEEEHHHCC
T ss_conf 2598799999999638--4899976-865685524516
No 45
>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=96.94 E-value=0.0016 Score=43.48 Aligned_cols=38 Identities=18% Similarity=0.334 Sum_probs=34.0
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 8787989978363882313532789771302221371210
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
|.|-.|.|++|.+ -+|||++|.+-.|+.|++++...|-
T Consensus 1 G~~v~G~V~~i~~--~G~FV~l~~~~~glVhiselsd~fV 38 (68)
T cd05707 1 GDVVRGFVKNIAN--NGVFVTLGRGVDARVRVSELSDSYL 38 (68)
T ss_pred CCEEEEEEEEECC--CCEEEEECCCCEEEEEHHHHCHHHH
T ss_conf 9998999998036--4079991799679999599172356
No 46
>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=96.90 E-value=0.0016 Score=43.54 Aligned_cols=34 Identities=18% Similarity=0.346 Sum_probs=29.8
Q ss_pred EEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 798997836388231353278977130222137121
Q gi|254780751|r 43 YLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 43 Y~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
+.|+|+++.+. .|||+++.+..||+|.+++.+.+
T Consensus 1 v~G~V~~i~~~--G~fV~~~~~~~gli~~s~~s~~~ 34 (65)
T cd00164 1 VTGKVVSITKF--GVFVELEDGVEGLVHISELSDKF 34 (65)
T ss_pred CEEEEEEEECC--EEEEEECCCEEEEEEHHHHCCCC
T ss_conf 98999999784--59999898717889888916765
No 47
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.79 E-value=0.0012 Score=44.39 Aligned_cols=39 Identities=26% Similarity=0.402 Sum_probs=31.0
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 42878798997836388231353278977130222137121
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
.+|.++.|+|+++.| -.||||+|.+-.||||.+||.+..
T Consensus 200 ~~G~vv~G~V~~i~~--~GaFVdl~~GvdGllHiSeiSw~r 238 (489)
T PRK13806 200 KEGDVLEGTVTRLAP--FGAFVEIAPGVEGMVHISELSWSR 238 (489)
T ss_pred CCCCEECEEEEEECC--CEEEEEECCCCEEEEEHHHCCCCC
T ss_conf 148800429999757--538999379807999835558656
No 48
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.78 E-value=0.0017 Score=43.32 Aligned_cols=13 Identities=23% Similarity=0.388 Sum_probs=6.6
Q ss_pred ECCCCCEEEEEEC
Q ss_conf 3638823135327
Q gi|254780751|r 50 VEPSLQAAFVDYG 62 (723)
Q Consensus 50 V~p~lqAAFVdiG 62 (723)
|-..|+-.|+|=|
T Consensus 54 lA~~LG~~yLDTG 66 (863)
T PRK12269 54 LASRLGAQCLNTG 66 (863)
T ss_pred HHHHHCCEEECCC
T ss_conf 9998299588748
No 49
>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=96.71 E-value=0.0032 Score=41.48 Aligned_cols=40 Identities=20% Similarity=0.371 Sum_probs=35.7
Q ss_pred CCCEEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCCCCCCC
Q ss_conf 287879899783638823135327-897713022213712102
Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIHPDYYQ 80 (723)
Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~~~y~~ 80 (723)
+|++|.|+|+.|.|. ++||++. ..-.||+|++++..|||.
T Consensus 1 IG~~f~g~I~~v~~~--GiFV~l~~~~ieGli~~~~l~~d~y~ 41 (83)
T cd04471 1 VGEEFDGVISGVTSF--GLFVELDNLTVEGLVHVSTLGDDYYE 41 (83)
T ss_pred CCCEEEEEEEEEEEE--EEEEEEECCCEEEEEECCCCCCCCEE
T ss_conf 999999999989830--69999828873999982214567224
No 50
>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=96.71 E-value=0.0038 Score=40.96 Aligned_cols=34 Identities=21% Similarity=0.543 Sum_probs=31.9
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 878798997836388231353278977130222137
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
|.|..|+|++|.|- +|||+++.+-.||.|.+++.
T Consensus 1 G~iv~G~V~~i~~f--G~fV~l~~~i~Glv~~s~ls 34 (69)
T cd05697 1 GQVVKGTIRKLRPS--GIFVKLSDHIKGLVPPMHLA 34 (69)
T ss_pred CCEEEEEEEEECCC--EEEEEECCCEEEEEEHHHHC
T ss_conf 99999999997384--27999579906998789908
No 51
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.60 E-value=0.004 Score=40.81 Aligned_cols=36 Identities=31% Similarity=0.528 Sum_probs=17.7
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 04287879899783638823135327897713022213
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
-..|+|-.|+|..|... .+|||||.--.||+|.+|+
T Consensus 302 ~~~G~iV~G~Vv~v~~~--~v~VDiG~KseG~Ip~~E~ 337 (670)
T PRK00087 302 IRRGDIVKGTVVSVNEN--EVFVDVGYKSEGVIPLEEL 337 (670)
T ss_pred CCCCCEEEEEEEEEECC--EEEEEECCCCCEEEEHHHH
T ss_conf 77898799999999389--8999836784368889993
No 52
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.50 E-value=0.006 Score=39.59 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=5.3
Q ss_pred CCCCEEEEEECCCC
Q ss_conf 78728998604861
Q gi|254780751|r 450 DRARVQVGAISNFG 463 (723)
Q Consensus 450 D~~~~~v~~it~lG 463 (723)
|-..-.|-.||.||
T Consensus 495 ~vv~G~VKnitdyG 508 (863)
T PRK12269 495 DSVSGVVKSFTSFG 508 (863)
T ss_pred CEEEEEEEECCCCE
T ss_conf 77889998315640
No 53
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.24 E-value=0.011 Score=37.68 Aligned_cols=39 Identities=31% Similarity=0.437 Sum_probs=33.5
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 042878798997836388231353278977130222137121
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
...|.++.|+|+++.+| ++||+++ +-.||||.+++...|
T Consensus 103 ~~~g~~v~g~V~~~~kg--G~~V~~~-gv~gFlP~S~ls~~~ 141 (390)
T PRK06676 103 FEEGEVVEVKVTEVVKG--GLVVDVG-GVRGFIPASLISTRF 141 (390)
T ss_pred HHCCCEEEEEEEEEECC--CEEEEEC-CCEEEEEHHHCCCCC
T ss_conf 53797799999999558--5999976-816877548725644
No 54
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.94 E-value=0.029 Score=34.80 Aligned_cols=38 Identities=24% Similarity=0.472 Sum_probs=32.1
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEEC--CCCCCCCCHHHCCC
Q ss_conf 04287879899783638823135327--89771302221371
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYG--GNRHGFLPFLEIHP 76 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG--~~k~gFL~~~ei~~ 76 (723)
.-.|.|-.|+|++|.. -+|||.+- .|+.||+|+||+..
T Consensus 9 PeeGEiVv~tV~~V~~--~GA~v~L~EY~g~Eg~ihiSEvas 48 (269)
T COG1093 9 PEEGEIVVGTVKQVAD--YGAYVELDEYPGKEGFIHISEVAS 48 (269)
T ss_pred CCCCCEEEEEEEEEEC--CCCEEEEECCCCEEEEEEHHHHHH
T ss_conf 9888689999998604--642798420599622677899877
No 55
>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=95.57 E-value=0.036 Score=34.14 Aligned_cols=41 Identities=22% Similarity=0.391 Sum_probs=37.3
Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf 287879899783638823135327897713022213712102
Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ 80 (723)
Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ 80 (723)
.|.|-.|+|++|.|+. .+||.++.++.|..|+.|+.-+|-.
T Consensus 3 ~G~i~~G~V~kV~p~~-Gl~Vqlp~g~~G~V~itdl~D~y~~ 43 (72)
T cd05704 3 EGAVTLGMVTKVIPHS-GLTVQLPFGKTGLVSIFHLSDSYTE 43 (72)
T ss_pred CCCEEEEEEEEECCCC-CEEEECCCCCEEEEEEEEECCCCCC
T ss_conf 8747403999972898-5699848996668999971474544
No 56
>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=95.49 E-value=0.051 Score=33.11 Aligned_cols=38 Identities=24% Similarity=0.295 Sum_probs=33.7
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf 0428787989978363882313532789771302221371
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP 76 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~ 76 (723)
..+|++..|+|+.|.+. .-|||||..-+|+||++|++.
T Consensus 4 P~~GD~ViG~V~~i~~~--~w~vdi~s~~~a~L~ls~v~~ 41 (86)
T cd05789 4 PEVGDVVIGRVTEVGFK--RWKVDINSPYDAVLPLSEVNL 41 (86)
T ss_pred CCCCCEEEEEEEEEECC--CEEEECCCCEEEEEEHHHCCC
T ss_conf 98899999999998088--189974996077987454467
No 57
>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=95.24 E-value=0.037 Score=34.10 Aligned_cols=38 Identities=29% Similarity=0.393 Sum_probs=32.6
Q ss_pred CEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCC
Q ss_conf 78798997836388231353278977130222137121028
Q gi|254780751|r 41 NIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQI 81 (723)
Q Consensus 41 nIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~i 81 (723)
.+|-|.|+.|..- .|||++|. -.|++|++++..|||..
T Consensus 1 Ev~eG~Vs~Vt~f--G~FV~L~~-ieGLvHiS~l~dD~~~f 38 (99)
T cd04460 1 EVVEGEVVEVVDF--GAFVRIGP-VDGLLHISQIMDDYISY 38 (99)
T ss_pred CEEEEEEEEEEEC--CEEEEECC-CEEEEEHHHCCCCEEEE
T ss_conf 9799999958825--66999328-10689936757843998
No 58
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=95.18 E-value=0.044 Score=33.57 Aligned_cols=15 Identities=47% Similarity=0.623 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999987
Q gi|254780751|r 400 LQTNLEAAEEIARQL 414 (723)
Q Consensus 400 l~tNleAA~EIaRQl 414 (723)
|.+-+.-|..|||-|
T Consensus 441 L~v~~r~aVSIaRrl 455 (780)
T COG2183 441 LDVSLRGAVSIARRL 455 (780)
T ss_pred CCHHHHHHHHHHHHH
T ss_conf 966677687798862
No 59
>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=94.98 E-value=0.086 Score=31.54 Aligned_cols=34 Identities=32% Similarity=0.421 Sum_probs=29.7
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 4287879899783638823135327897713022213
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
..|.|.-|.|+++.+ ...|||+| .-.|+||-+|.
T Consensus 2 k~geiv~G~V~r~~~--~~v~vdlg-~~eailp~~eq 35 (67)
T cd04455 2 REGEIVTGIVKRVDR--GNVIVDLG-KVEAILPKKEQ 35 (67)
T ss_pred CCCCEEEEEEEEEEC--CCEEEEEC-CCEEECCHHHC
T ss_conf 878889999999808--97999989-94897378995
No 60
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=94.76 E-value=0.066 Score=32.33 Aligned_cols=35 Identities=29% Similarity=0.475 Sum_probs=15.7
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 87879899783638823135327897713022213
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
|.|-.|+|..|-.+=.-+|||+|+=--|-+|.+|+
T Consensus 20 G~i~~G~VV~i~~ndd~v~VDvG~KsEg~ip~~Ef 54 (534)
T TIGR00717 20 GSIVKGTVVKINKNDDTVFVDVGLKSEGRIPVEEF 54 (534)
T ss_pred CCEEEEEEEEEECCCCEEEEEEECCCCCCCCHHHC
T ss_conf 85553278998168889999831563123417682
No 61
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=94.57 E-value=0.095 Score=31.25 Aligned_cols=37 Identities=22% Similarity=0.252 Sum_probs=18.9
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf 428787989978363882313532789771302221371
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP 76 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~ 76 (723)
-.|.--.|||+++.| =.|||||..|=-||+|.|||.|
T Consensus 286 ~~G~~~~G~Vt~~~d--yGvFvEi~eGiEGlvH~SE~sW 322 (534)
T TIGR00717 286 PVGDKIKGRVTNLTD--YGVFVEIEEGIEGLVHVSEISW 322 (534)
T ss_pred CCCCEEEEEEEEECC--CEEEEEECCCCEEEECCEEEEC
T ss_conf 899788999998837--7079992389423423144405
No 62
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional
Probab=94.18 E-value=0.079 Score=31.82 Aligned_cols=89 Identities=17% Similarity=0.269 Sum_probs=65.8
Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEEC--CCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 604287879899783638823135327--897713022213712102898899999998886311111000000011122
Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDYG--GNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVT 113 (723)
Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdiG--~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 113 (723)
-.-.|.|-.++|++|.. .+|||.+- .+..||+|+|||.+-
T Consensus 14 ~Pe~~e~V~~~V~~i~~--~gayV~LlEY~~~egmI~~sEls~r------------------------------------ 55 (324)
T PTZ00248 14 YPEENDLVMVKVNRIEE--MGVYVSLLEYDDIEGMILLSELSKR------------------------------------ 55 (324)
T ss_pred CCCCCCEEEEEEEEEEC--CEEEEEEEEECCCCCEEEHHHHHHH------------------------------------
T ss_conf 99988889999999802--5689998400882221468886378------------------------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCC
Q ss_conf 33444334454222233445543322223432112211121100001223444421331068885799984033323456
Q gi|254780751|r 114 IPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKG 193 (723)
Q Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kg 193 (723)
+-.+|+.+|+.|+.+.|+|.+=-
T Consensus 56 ----------------------------------------------------rir~I~k~ikvG~~~v~~VlRVD----- 78 (324)
T PTZ00248 56 ----------------------------------------------------RIRSINKLVKVGRHEVVLVLRVD----- 78 (324)
T ss_pred ----------------------------------------------------HHHHHHHHHCCCCEEEEEEEEEC-----
T ss_conf ----------------------------------------------------88637887106877899999985-----
Q ss_pred CCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 41012334576523442278875124204688689999999998
Q gi|254780751|r 194 AAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIAR 237 (723)
Q Consensus 194 a~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~ 237 (723)
+..++ +-+|+|-...++...-.+-..
T Consensus 79 -----------------~~KGy-IDLS~rrVs~ed~~kCeery~ 104 (324)
T PTZ00248 79 -----------------KDKGY-IDLSKRRVTPEDIIKCEEKFS 104 (324)
T ss_pred -----------------CCCCC-EECHHHCCCHHHHHHHHHHHH
T ss_conf -----------------87782-444150299889999999998
No 63
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=93.94 E-value=0.18 Score=29.27 Aligned_cols=34 Identities=26% Similarity=0.369 Sum_probs=28.8
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 4287879899783638823135327897713022213
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
.+|.|..|.|.|+.++ ..|||+|. -.|+||.+|.
T Consensus 133 r~GeiV~G~V~r~~~~--~~~Vdlg~-~ea~LP~~eq 166 (353)
T PRK12327 133 REGDIVTGTVQRDDNR--FVYVNLGK-IEAVLPPAEQ 166 (353)
T ss_pred HCCCEEEEEEEEECCC--CEEEEECC-EEEECCHHHC
T ss_conf 4396699999997588--58999788-2464687986
No 64
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=93.78 E-value=0.54 Score=25.98 Aligned_cols=65 Identities=25% Similarity=0.294 Sum_probs=50.4
Q ss_pred CEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf 60799999899899999607334604287879899783638823135327897713022213712102
Q gi|254780751|r 13 EETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ 80 (723)
Q Consensus 13 ~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ 80 (723)
.|-+|.-=++....+.-+.---=+..+|-|..|+|+.+.. ..|||.+|. -.+|+|.+.+.+||+.
T Consensus 55 ~eG~I~~gdG~~~~~V~F~~ivfrPf~~EVv~g~V~~~~~--~G~fv~~Gp-~d~~vh~sqi~dd~~~ 119 (182)
T PRK08563 55 GEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEVVE--FGAFVRIGP-VDGLLHISQIMDDYIS 119 (182)
T ss_pred CCCEEEECCCCEEEEEEEEEEEEECCCCCEEEEEEEEEEC--CEEEEEEEC-CCEEEEHHHCCCCCCE
T ss_conf 4998991999899999978999941368489999999966--769999846-6117609994777623
No 65
>PRK11642 exoribonuclease R; Provisional
Probab=92.68 E-value=0.26 Score=28.27 Aligned_cols=90 Identities=16% Similarity=0.172 Sum_probs=45.8
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCC---
Q ss_conf 35320366788898763101211220134-42035677699999998422214367864998328806999823755---
Q gi|254780751|r 313 SGEKGYREAKDFMKLLMPSYARIVRQYED-PHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGR--- 388 (723)
Q Consensus 313 d~~~~~~~~~~~~~~~~p~~~~~v~~~~~-~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~--- 388 (723)
...-.|..+..++..- +... ..|.. ...|...+.+-..+..... .-|.|-+|..|+-...|-+..-
T Consensus 378 ~arLTY~~v~~il~g~-~~~~---~~~~~~~~~L~~L~~l~~~L~~~R~------~rGai~fd~~E~~~~ld~~g~i~~i 447 (813)
T PRK11642 378 HARLTYTKVWHILQGD-QDLR---EQYAPLVKHLEELHNLYKVLDKARE------ERGGISFESEEAKFIFNAERRIERI 447 (813)
T ss_pred CCEECHHHHHHHHHCC-HHHH---HHHHHHHHHHHHHHHHHHHHHHHHH------HCCCCCCCCCCCEEEECCCCCCCCE
T ss_conf 8362399999998188-5444---4556799999999999999999999------7789665677644897788873424
Q ss_pred -----CCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf -----444555114799999999999999
Q gi|254780751|r 389 -----STREHCIEDTALQTNLEAAEEIAR 412 (723)
Q Consensus 389 -----~~~~~~~e~t~l~tNleAA~EIaR 412 (723)
.....=+|+..+.+|..||+-+..
T Consensus 448 ~~~~r~~ah~LIEE~Ml~AN~~vA~~l~~ 476 (813)
T PRK11642 448 EQTQRNDAHKLIEECMILANISAARFVEK 476 (813)
T ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 76223505678999999999999999997
No 66
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=92.37 E-value=0.46 Score=26.47 Aligned_cols=52 Identities=19% Similarity=0.206 Sum_probs=34.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHH-HHHHHHCCCCHHHH
Q ss_conf 4322123456458888887523766311110353203667888-98763101211220
Q gi|254780751|r 282 SVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDF-MKLLMPSYARIVRQ 338 (723)
Q Consensus 282 ~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~-~~~~~p~~~~~v~~ 338 (723)
-+..+|+..-..-+..+++.+-+..++-|..+++. ..| ...+.|.....|..
T Consensus 246 DpVGAcVG~rGsRI~~I~~EL~gEkIDIi~~s~d~-----~~fi~nAlsPA~v~~V~i 298 (428)
T PRK09202 246 DPVGACVGMRGSRIQAISNELNGEKIDIILWSDDP-----AQFIINALSPAEVSSIVV 298 (428)
T ss_pred CCCEEEECCCCCCHHHHHHHHCCCEEEEEECCCCH-----HHHHHHHCCCCCCEEEEE
T ss_conf 85137777886429999987467768999678888-----999998179421218997
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=92.24 E-value=0.4 Score=26.88 Aligned_cols=34 Identities=32% Similarity=0.466 Sum_probs=31.6
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 878798997836388231353278977130222137
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
|.+-.|+|+.|-| -.+||.++.+-+|+.|++||.
T Consensus 1 G~vv~g~V~sik~--~~l~V~L~d~~~GrVhiSei~ 34 (70)
T cd05702 1 GDLVKAKVKSVKP--TQLNVQLADNVHGRIHVSEVF 34 (70)
T ss_pred CCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHCC
T ss_conf 9779999999946--708999689957789845521
No 68
>PRK00499 rnpA ribonuclease P; Reviewed
Probab=91.88 E-value=0.73 Score=25.08 Aligned_cols=62 Identities=24% Similarity=0.238 Sum_probs=45.0
Q ss_pred CCEEEECCCCHHHHHHHHHHHHHHH--------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5124204688689999999998630--------0258716998504557579999999999999998776
Q gi|254780751|r 216 GETISRKITNPVDRKNLKEIARGLE--------VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRE 277 (723)
Q Consensus 216 ~~~iSrki~~~~~r~~l~~~~~~~~--------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~ 277 (723)
|+.+|+|+.+.-.|.+++..+.++. .+.++=+|.|..+.+++..+|..|+..|+..-.-+.+
T Consensus 42 G~~vsKKvg~AV~RNriKR~lRe~~R~~~~~l~~g~DiViiar~~~~~~~~~~l~~~l~~ll~Ka~ll~~ 111 (116)
T PRK00499 42 GISVSKKIGNAVVRNRVKRLIRESFRELKDEIKKGYDFVVIARKPAEDLDYEEIKKSLIHVLKKAKLYNK 111 (116)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 9998044675237889999999999974650588975999968654549999999999999998264000
No 69
>KOG1070 consensus
Probab=91.84 E-value=0.53 Score=26.07 Aligned_cols=66 Identities=21% Similarity=0.411 Sum_probs=52.6
Q ss_pred CCEEEEEEEECCEEEEEEECCCC--CCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 96079999989989999960733--460428787989978363882313532789771302221371210
Q gi|254780751|r 12 VEETRVVVLRDNRVEELDFESEH--KKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 12 ~~e~Rvav~e~g~l~e~~~e~~~--~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
..+-|||+.-.+.|++....-+. ...+.|-||+|.|.++-+ +.|||.+=.+-.||+|.+++.-+|-
T Consensus 570 ~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~--~g~~V~F~g~lsGf~p~s~~sd~~v 637 (1710)
T KOG1070 570 RDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKE--NGAFVTFTGGLSGFAPVSEMSDDFV 637 (1710)
T ss_pred CCCCEEEEEECHHHHCCCCCCCCCHHHCCCCCEEEEEEEEECC--CCEEEEECCCCCCCCCHHHHHHHHH
T ss_conf 3687258882233431468886425335878368987765426--8728995676565664454310121
No 70
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=91.82 E-value=1 Score=24.16 Aligned_cols=54 Identities=20% Similarity=0.247 Sum_probs=40.4
Q ss_pred ECCEEEEEEECCCCCC----------CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 8998999996073346----------042878798997836388231353278977130222137
Q gi|254780751|r 21 RDNRVEELDFESEHKK----------QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 21 e~g~l~e~~~e~~~~~----------~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
+-|.-+++|+-..... ..+|.-=.++|+.|-+.|. ||||.|..|.-|+|.+|..
T Consensus 45 evGdev~vFiY~D~~~rl~aTt~~p~~tvg~~g~~~Vv~v~~~lG-aFlD~Gl~KDl~vp~~elp 108 (287)
T COG2996 45 EVGDEVTVFIYVDSEDRLIATTREPKATVGEYGWLKVVEVNKDLG-AFLDWGLPKDLLVPLDELP 108 (287)
T ss_pred CCCCEEEEEEEECCCCCEEHEEECCEEEECCEEEEEEEEECCCCC-EEEECCCCCCEEEEHHHCC
T ss_conf 137689999998887763010104137405323799998737751-5896598700361625364
No 71
>PTZ00162 RNA polymerase II subunit 7; Provisional
Probab=90.75 E-value=1.3 Score=23.45 Aligned_cols=63 Identities=24% Similarity=0.230 Sum_probs=49.2
Q ss_pred CEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 607999998998999996073346042878798997836388231353278977130222137121
Q gi|254780751|r 13 EETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 13 ~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
.|-+|---++......-++-.-=+..+|-|.-|.|++|.+ .+|||++|.=. +|+|.+-|.+||
T Consensus 55 ~~G~I~~gdG~v~~~V~f~aivfkP~~~EVvdg~V~~v~~--~G~fv~~GPl~-~fv~~s~i~~d~ 117 (170)
T PTZ00162 55 EPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNK--LGFFAQAGPLK-IFVSRTAIPPNF 117 (170)
T ss_pred CCCEEEECCCCEEEEEEEEEEEEECCCCCEEEEEEEEEEC--CEEEEEECCEE-EEEEHHHCCCCC
T ss_conf 5797995898699999999999933679899999999964--07999912808-998989999864
No 72
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=90.07 E-value=0.8 Score=24.84 Aligned_cols=58 Identities=19% Similarity=0.247 Sum_probs=46.5
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECC
Q ss_conf 0236754653786061146899887889997303643101357699999873023799999999848879998478
Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGI 556 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~ 556 (723)
.-.||.|+|.-.--|...+|..+-+.|++....+.+ +.+-+..+.++||-.|...|.-
T Consensus 40 ~lRCpvCq~qsi~~S~a~~A~dmR~~I~~~i~~G~s------------------d~eI~~~l~~RYG~~Il~~Pp~ 97 (126)
T TIGR03147 40 SLRCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGKS------------------NQQIIDFMTARFGDFVLYNPPF 97 (126)
T ss_pred HCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHCCCEEEECCCC
T ss_conf 168877799774007619999999999999985999------------------8999999999708828753999
No 73
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=89.61 E-value=1.1 Score=23.91 Aligned_cols=52 Identities=21% Similarity=0.181 Sum_probs=35.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHH-HHHHHCCCCHHHH
Q ss_conf 43221234564588888875237663111103532036678889-8763101211220
Q gi|254780751|r 282 SVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFM-KLLMPSYARIVRQ 338 (723)
Q Consensus 282 ~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~-~~~~p~~~~~v~~ 338 (723)
-+..+|+..-..-+..+++.+-+..++-|..+++. ..|+ ..+.|.....|..
T Consensus 251 DpVGAcVG~kG~RI~~I~~EL~gEkIDii~~s~d~-----~~fi~nALsPA~V~~V~i 303 (375)
T PRK12328 251 DPVGATVGVKGVRINAVSKELNGENIDCIEYSNIP-----EIFIARALAPAIILSVKI 303 (375)
T ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCH-----HHHHHHCCCCCCCEEEEE
T ss_conf 74047888886309999998579627899778888-----999986378553018999
No 74
>pfam03918 CcmH Cytochrome C biogenesis protein. Members of this family include NrfF, CcmH, CycL, Ccl2.
Probab=89.38 E-value=0.88 Score=24.54 Aligned_cols=58 Identities=19% Similarity=0.238 Sum_probs=46.1
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECC
Q ss_conf 0236754653786061146899887889997303643101357699999873023799999999848879998478
Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGI 556 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~ 556 (723)
.-.||.|+|.-.--|...+|..+-+.|++....+.+ +.+-+..+-++||-.|...+--
T Consensus 37 ~lRCpvCq~qsi~dS~a~iA~dmR~~i~~~i~~G~s------------------d~eI~~~~~~rYG~~Vl~~Pp~ 94 (145)
T pfam03918 37 ELRCPVCQNQSIADSNAPLARDLRLEVREMLVEGKS------------------DEEIIDYMVARYGDFVLYKPPL 94 (145)
T ss_pred HCCCCCCCCCCHHCCCHHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHCCCCEEECCCC
T ss_conf 278888799765007779999999999999985999------------------9999999998638615555999
No 75
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=89.24 E-value=1.1 Score=23.99 Aligned_cols=58 Identities=17% Similarity=0.244 Sum_probs=45.9
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECC
Q ss_conf 0236754653786061146899887889997303643101357699999873023799999999848879998478
Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGI 556 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~ 556 (723)
.-.||.|.|.-.--|...+|..+-..|++....+.+ ..+-+..+.++||-.|...+.-
T Consensus 40 elRCpvCq~qsi~~S~s~iA~dmR~~Ir~~i~~G~s------------------d~eI~~~l~~rYG~~Il~~Pp~ 97 (126)
T PRK10144 40 QLRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKS------------------EVEIIGWMTERYGDFVRYNPPL 97 (126)
T ss_pred HCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHCCCEEEEECCC
T ss_conf 278877899884115779999999999999986999------------------9999999998648849861899
No 76
>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=88.94 E-value=1.5 Score=22.95 Aligned_cols=23 Identities=43% Similarity=0.612 Sum_probs=19.9
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 0428787989978363882313532
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDY 61 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdi 61 (723)
..+|+|-.|||++|-| +.|+|+|
T Consensus 4 P~vGdiV~~rVtrv~~--~~a~v~I 26 (92)
T cd05791 4 PKVGSIVIARVTRINP--RFAKVDI 26 (92)
T ss_pred CCCCCEEEEEEEEECC--CEEEEEE
T ss_conf 8899999999999711--3789999
No 77
>PRK01732 rnpA ribonuclease P; Reviewed
Probab=87.75 E-value=2 Score=21.99 Aligned_cols=61 Identities=21% Similarity=0.342 Sum_probs=45.8
Q ss_pred CCEEEEC-CCCHHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5124204-688689999999998630-------025871699850455757999999999999999877642
Q gi|254780751|r 216 GETISRK-ITNPVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELA 279 (723)
Q Consensus 216 ~~~iSrk-i~~~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~ 279 (723)
|+.||+| +...-.|.++|.++.+.- .+.++=+|+|..+.+.+..+|..++..| |..+...+
T Consensus 48 Gl~VsKK~v~~AV~RNRiKR~iRE~fR~~~~~l~~~DiVviar~~~~~~~~~~l~~~L~~l---~~kl~r~~ 116 (119)
T PRK01732 48 GLTVAKKNVKRAHERNRIKRLTRESFRLRQHELPAMDFVVVAKKGVADLDNRALSEALEKL---WRRHCRLA 116 (119)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHH---HHHHHHHH
T ss_conf 9999765563267888999999999984802289860999956875538999999999999---99998750
No 78
>PRK01313 rnpA ribonuclease P; Reviewed
Probab=87.68 E-value=1.8 Score=22.35 Aligned_cols=58 Identities=12% Similarity=0.179 Sum_probs=43.5
Q ss_pred CCCEEEECCCCHHHHHHHHHHHHHH---------HCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 7512420468868999999999863---------002587169985045575799999999999999
Q gi|254780751|r 215 KGETISRKITNPVDRKNLKEIARGL---------EVPAGMGVILRTAGASRTKIEIKRDFEYLMRLW 272 (723)
Q Consensus 215 ~~~~iSrki~~~~~r~~l~~~~~~~---------~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w 272 (723)
-|..+|+|+-+.-.|.+.+..+.++ ..+.++-+|.|..+.+++.++|..|+...++..
T Consensus 53 vG~tvsKKvGnAV~RNRiKRrlRe~~r~~~~~~~~~g~D~ViiaR~~a~~~~f~~L~~dL~~alk~~ 119 (133)
T PRK01313 53 VGFTVTKKNGNAVERNRIRRRLKEAVRVHAGRDMAPGTDYVIVARRDALNAPFSQLTEELSRRIEAK 119 (133)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCHHCCCCHHHHHHHHHHHHHHH
T ss_conf 8899841235167788999999999998605306899708999371110299999999999999983
No 79
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=86.74 E-value=2.3 Score=21.61 Aligned_cols=38 Identities=32% Similarity=0.328 Sum_probs=32.5
Q ss_pred CCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 4604287879899783638823135327897713022213
Q gi|254780751|r 35 KKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 35 ~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
-...+|++-.|+|+.|-++ .=+||||.--+||||+++.
T Consensus 58 Y~P~~GD~VIG~V~~v~~~--~W~VDI~s~~~a~L~~s~~ 95 (232)
T PRK04163 58 YIPKKGDLVIGKVTDVGFS--GWEVDINSPYKAILPVSEV 95 (232)
T ss_pred CCCCCCCEEEEEEEEECCC--EEEEECCCCCEEEECHHHC
T ss_conf 0587699899999983187--1799869960558524445
No 80
>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=86.66 E-value=2 Score=22.05 Aligned_cols=35 Identities=29% Similarity=0.489 Sum_probs=28.5
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEEC-CCCCCCCCHHHC
Q ss_conf 4287879899783638823135327-897713022213
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEI 74 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei 74 (723)
..|.+.-|-|+-|+- ...-+|+| .+-.||||.+|+
T Consensus 3 ~~g~~l~a~V~SvED--HGyild~Gi~~~~gFl~~k~~ 38 (74)
T cd05694 3 VEGMVLSGCVSSVED--HGYILDIGIPGTTGFLPKKDA 38 (74)
T ss_pred CCCCEEEEEEEEEEC--CEEEEECCCCCCEEEEEHHHC
T ss_conf 678299999856714--418998477772667301334
No 81
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=86.14 E-value=1.3 Score=23.32 Aligned_cols=58 Identities=19% Similarity=0.306 Sum_probs=37.9
Q ss_pred CCEEEECCC-CHHHH----HHHHHHHHHH----HCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 512420468-86899----9999999863----0025871699850455757999999999999999
Q gi|254780751|r 216 GETISRKIT-NPVDR----KNLKEIARGL----EVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWD 273 (723)
Q Consensus 216 ~~~iSrki~-~~~~r----~~l~~~~~~~----~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~ 273 (723)
|+.+|+|+. +.-.| +++++++... ..+.++=+|.|..+.+.+.++|..|+..|+..-.
T Consensus 50 G~~VsKKvgk~AV~RNriKR~lRe~~r~~~~~l~~g~diViiar~~~~~~~~~~l~~el~~lL~kA~ 116 (122)
T PRK03031 50 GISISQKVSKKAVVRNRLKRQIRAAIRQLLPRIAPGWDLVIIVKPGASECNYEQFLQELEQLLIQAE 116 (122)
T ss_pred EEEEEEECCCCCEEECCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 9999620054402204122008999998676238896699997887565999999999999999847
No 82
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase; InterPro: IPR014069 The of the characterization of two proteins from Streptomyces coelicolor ahs been presented . The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. It has also been shown that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase ..
Probab=85.27 E-value=0.3 Score=27.75 Aligned_cols=162 Identities=16% Similarity=0.189 Sum_probs=77.9
Q ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCC--CCHHHH---
Q ss_conf 999999998731036863896033479888899999999997312787289986048614898515666--301121---
Q gi|254780751|r 405 EAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIR--SSVLES--- 479 (723)
Q Consensus 405 eAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r--~sl~e~--- 479 (723)
.-.+.|.|+.-|.+---|=-=-.-|++.-...-.+.-+..-..--.|..|||.|+|-|.+|.|..+=-. |....-
T Consensus 326 ~~~~~~~r~~~~~~~~r~dGrG~~dir~l~~ev~~~Pr~hGsa~f~rGetq~lGv~tl~ml~m~q~~d~l~P~~~~ry~h 405 (725)
T TIGR02696 326 AVTKKLVRERVLKEGVRIDGRGLTDIRSLSAEVEVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPVTSKRYLH 405 (725)
T ss_pred HHHHHHHHHHHHHCCCEECCCCHHHHHHHHCCEEEECCCCCHHHHHCCCEEEEHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999888623620136764455521000024133101023205760354034778888876553116202300110
Q ss_pred HCCCCCCCCC-EEEEECCH----------------------HHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCC-H
Q ss_conf 0023675465-37860611----------------------4689988788999730364310135769999987302-3
Q gi|254780751|r 480 TTKVCTYCKG-AGYIRSQS----------------------SVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQ-K 535 (723)
Q Consensus 480 ~~~~c~~c~g-~g~~~~~~----------------------~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~-k 535 (723)
.+.-.|+..| +|+|-|+. ..-+ ..|.+.+....+....+--.|...++.+-.+- .
T Consensus 406 ~yn~PPys~Ge~GrvG~PkrreiGhG~laeral~PvlP~~e~fPy-air~vseal~snGstsmGsvCastl~l~~aGvPl 484 (725)
T TIGR02696 406 HYNFPPYSTGETGRVGSPKRREIGHGALAERALVPVLPSREEFPY-AIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPL 484 (725)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCH-HHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 037887566764566887532025650221100034467665636-8999988741577630357899999998648862
Q ss_pred HHHHH-----------HHHHHHCCEEEEE-ECCCCCCCCEEEEE
Q ss_conf 79999-----------9999848879998-47877886338971
Q gi|254780751|r 536 RATIV-----------EYEARFGVSINVV-IGIELADKLFYIEK 567 (723)
Q Consensus 536 r~~l~-----------~lE~~~~~~I~i~-~d~~l~~~~f~Ier 567 (723)
+..++ +-+.+|-.--.|. +++.+...+|++.-
T Consensus 485 ~~~vaGiamGl~~~~~~~~~~y~~ltdi~Gaeda~GdmdfkvaG 528 (725)
T TIGR02696 485 KAPVAGIAMGLISDEVDGETRYVALTDILGAEDALGDMDFKVAG 528 (725)
T ss_pred CCCHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCEEECC
T ss_conf 00020122222222003542567642011320102553212214
No 83
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=84.39 E-value=3 Score=20.86 Aligned_cols=62 Identities=21% Similarity=0.314 Sum_probs=45.3
Q ss_pred CCEEEEC-CCCHHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 5124204-688689999999998630-------0258716998504557579999999999999998776420
Q gi|254780751|r 216 GETISRK-ITNPVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELAL 280 (723)
Q Consensus 216 ~~~iSrk-i~~~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~ 280 (723)
|+.|||| +...-.|.++|.++.+.- .+.++=+|.|..+...+-.+|..++.. +|..+.....
T Consensus 49 Gl~VsKK~vk~AV~RNriKR~iRE~FR~~~~~L~~~DiVViar~~~~~l~n~el~~~L~~---lw~rL~r~~~ 118 (134)
T PRK00396 49 GLVIGKKSVKLAVQRNRLKRLMRESFRLNQDSLAGWDIVIVARKGLGELENPELHQQFGK---LWKRLARSRP 118 (134)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHCCHHHHHHHHHH---HHHHHHHCCC
T ss_conf 899866555057778889999999999573007998989993777002499999999999---9999985579
No 84
>pfam01630 Glyco_hydro_56 Hyaluronidase.
Probab=84.26 E-value=1.6 Score=22.82 Aligned_cols=33 Identities=27% Similarity=0.421 Sum_probs=16.3
Q ss_pred HHHHHHHHHH-HHHHHHHHHHHHCCCCEEEEECC
Q ss_conf 1479999999-99999998731036863896033
Q gi|254780751|r 396 EDTALQTNLE-AAEEIARQLRLRDLAGLIVVDFI 428 (723)
Q Consensus 396 e~t~l~tNle-AA~EIaRQlRLRnlgGiIvIDFI 428 (723)
....|...|+ |.+.|...|.-+|-+||-||||=
T Consensus 79 Q~g~L~~HL~ka~~dI~~~ip~~~f~GLaVIDwE 112 (339)
T pfam01630 79 QLGSLTAHLAKAKKDIEHYIPDPDFNGLAVIDWE 112 (339)
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEECC
T ss_conf 8577999999999989985789999841898754
No 85
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=84.17 E-value=3 Score=20.80 Aligned_cols=65 Identities=25% Similarity=0.335 Sum_probs=51.8
Q ss_pred CCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 96079999989989999960733460428787989978363882313532789771302221371210
Q gi|254780751|r 12 VEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 12 ~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
-+|-+|..-+++.-.+.-++-.-=....|.|--|.|..+.. -.|||.+| --.||+|.+.|..||+
T Consensus 54 igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~--~G~fV~ig-p~dglvh~sqi~dd~~ 118 (183)
T COG1095 54 IGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVE--FGAFVRIG-PLDGLVHVSQIMDDYI 118 (183)
T ss_pred EECCEEECCCCCEEEEEEEEEEEEEECCCCEEEEEEEEEEE--CCEEEEEC-CCCCCCCHHHCCCCCC
T ss_conf 20457862999679999999999970356389999999961--44699963-6222113866657532
No 86
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=84.10 E-value=3.1 Score=20.78 Aligned_cols=32 Identities=19% Similarity=0.174 Sum_probs=23.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHCCCCCCEEECCC
Q ss_conf 32212345645888888752376631111035
Q gi|254780751|r 283 VAPHLVYEEGNLIKRAIRDLYCKDISEIIVSG 314 (723)
Q Consensus 283 ~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~ 314 (723)
...+|+..-..-+..+++.+-+..++-|..+.
T Consensus 279 PVGaCVG~rG~RIq~I~~EL~gEkIDii~ws~ 310 (457)
T PRK12329 279 PVGACIGARGSRIQQVVNELRGEKIDVIRWSP 310 (457)
T ss_pred CEEEEECCCCCCHHHHHHHHCCCEEEEEECCC
T ss_conf 31478889974299999885796389997578
No 87
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=83.66 E-value=3.2 Score=20.66 Aligned_cols=42 Identities=14% Similarity=0.208 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCC
Q ss_conf 645888888752376631111035320366788898763101
Q gi|254780751|r 291 EGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSY 332 (723)
Q Consensus 291 ~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~ 332 (723)
+..-+..+|+.+-+..-.-|+|+.+...-..-+|+-.+.|.-
T Consensus 526 D~~rLi~~L~~Lrd~GNTVlVVEHD~~~i~~AD~iIDlGPgA 567 (944)
T PRK00349 526 DNDRLIETLKRLRDLGNTLIVVEHDEDTIRAADYIVDIGPGA 567 (944)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHCCEEEEECCCC
T ss_conf 999999999999857985999835687775287789717877
No 88
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=83.29 E-value=3.3 Score=20.55 Aligned_cols=157 Identities=15% Similarity=0.123 Sum_probs=70.7
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCH---HHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCC--
Q ss_conf 35320366788898763101211---2201344203567769999999842221436786499832880699982375--
Q gi|254780751|r 313 SGEKGYREAKDFMKLLMPSYARI---VRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSG-- 387 (723)
Q Consensus 313 d~~~~~~~~~~~~~~~~p~~~~~---v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG-- 387 (723)
...-+|.++.+++..-....... -.+...=.+++..|.|=..-. ..=|+|=+|-.||=+.+|=|-=
T Consensus 393 ~~R~TY~~Vn~~~~g~~~~~~~~~Gy~~~~~~l~~~~~L~~~L~~~R---------~~rG~IdFd~~E~k~ilDe~G~~~ 463 (755)
T TIGR02063 393 KARLTYTQVNDILEGKDALEDKEYGYAPLKEMLKNLEELYKILRKKR---------KKRGAIDFDSKEAKIILDENGKPI 463 (755)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH---------HHCCCCCCCCCCCEEEECCCCEEE
T ss_conf 64457789999764985699963587115777998999999999877---------651881237764179987884289
Q ss_pred ------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHHHHHHHHHCCC----CEEE
Q ss_conf ------5444555114799999999999999873103686389603347-9888899999999997312787----2899
Q gi|254780751|r 388 ------RSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDM-EEKKNNRSVEKKLKESLKKDRA----RVQV 456 (723)
Q Consensus 388 ------~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM-~~~~~~~~v~~~l~~~l~~D~~----~~~v 456 (723)
+....+=+|+--+..|--||.-.-+.+..-+.+ +=.|==|.= .+.+.-..+.+.| ..|.-.-. -.++
T Consensus 464 ~I~~~~R~~A~klIEefM~~ANe~vA~~~~~~~~~~~~~-~P~~YRvH~~P~~~kl~~l~~fl-~~lG~~~~~~G~~~~~ 541 (755)
T TIGR02063 464 DIVPRERGDAHKLIEEFMIVANETVAEFLEKKLKKNKAK-LPFIYRVHEKPSEEKLQNLREFL-KELGLTLKGGGTSDKI 541 (755)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCEEEEECCCCCHHHHHHHHHHH-HHCCCEECCCCCCCCC
T ss_conf 989841333222368889999999999999888875489-95167647899889999999999-8718154488888875
Q ss_pred EEECCCCEEEEECCCCCCCHHHHH
Q ss_conf 860486148985156663011210
Q gi|254780751|r 457 GAISNFGLLEMSRQRIRSSVLEST 480 (723)
Q Consensus 457 ~~it~lGLlEltRkR~r~sl~e~~ 480 (723)
.+-+==-|||..+.|--..|.+++
T Consensus 542 ~P~~~~~~le~~~~~P~~~l~~~~ 565 (755)
T TIGR02063 542 QPKDLQKLLEKVKGRPEEELINTV 565 (755)
T ss_pred CHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 869999999984088438999999
No 89
>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=83.18 E-value=2.4 Score=21.48 Aligned_cols=36 Identities=22% Similarity=0.047 Sum_probs=30.7
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 04287879899783638823135327897713022213
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
..+|+|-.|+|+.|-+. -++|||+.--.+.|+.+.+
T Consensus 4 P~vGDvVigrV~~v~~~--~w~vdI~~~~~a~l~~~~~ 39 (82)
T cd04454 4 PDVGDIVIGIVTEVNSR--FWKVDILSRGTARLEDSSA 39 (82)
T ss_pred CCCCCEEEEEEEEECCC--EEEEEECCCEEEEEEEHHC
T ss_conf 98999999999997078--1899968632889730216
No 90
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately. This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=82.09 E-value=0.58 Score=25.78 Aligned_cols=25 Identities=20% Similarity=0.611 Sum_probs=11.8
Q ss_pred HHHHCCCCCCCCCEEEEECCHHHHH
Q ss_conf 1210023675465378606114689
Q gi|254780751|r 477 LESTTKVCTYCKGAGYIRSQSSVAL 501 (723)
Q Consensus 477 ~e~~~~~c~~c~g~g~~~~~~~~~~ 501 (723)
-....++|+.|+|.|+++...++.+
T Consensus 224 G~ii~~~C~~C~G~G~~~~~~~~~v 248 (386)
T TIGR02349 224 GKIIKEPCSTCKGKGRVKERKTISV 248 (386)
T ss_pred EEEEECCCCCCCCCEEEEEEEEEEE
T ss_conf 3896336899887406988889999
No 91
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=81.32 E-value=3.9 Score=20.07 Aligned_cols=55 Identities=24% Similarity=0.261 Sum_probs=33.1
Q ss_pred CEEEEEEECCC-CCCCCCCCEEEEEEEEECCCCCEEEEEE----C------CCCCCCCCHHHCCCCCC
Q ss_conf 98999996073-3460428787989978363882313532----7------89771302221371210
Q gi|254780751|r 23 NRVEELDFESE-HKKQIKGNIYLAKVTRVEPSLQAAFVDY----G------GNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 23 g~l~e~~~e~~-~~~~~~GnIY~G~V~~V~p~lqAAFVdi----G------~~k~gFL~~~ei~~~y~ 79 (723)
+++.-+.-... ......|.|-+|+|++| ..|+|-|.| | ....|-+|++.+...|+
T Consensus 47 n~~~~V~p~~~~~~~~K~GdiV~grV~~v--~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~ 112 (188)
T COG1096 47 NRVISVKPGKKTPPLPKGGDIVYGRVTDV--REQRALVRIVGVEGKERELATSGAADIHVSQVRDGYV 112 (188)
T ss_pred CEEEEECCCCCCCCCCCCCCEEEEEEEEC--CCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCC
T ss_conf 44999524777777689887999999532--6608999999994333367887402589782023111
No 92
>pfam10447 EXOSC1 Exosome component EXOSC1/CSL4. This family of proteins are components of the exosome 3'-5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions.
Probab=81.30 E-value=3.9 Score=20.06 Aligned_cols=23 Identities=43% Similarity=0.712 Sum_probs=19.1
Q ss_pred CCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 0428787989978363882313532
Q gi|254780751|r 37 QIKGNIYLAKVTRVEPSLQAAFVDY 61 (723)
Q Consensus 37 ~~~GnIY~G~V~~V~p~lqAAFVdi 61 (723)
..+|+|-++||+||-+ +-|+++|
T Consensus 2 P~vGdiV~arVtrv~~--~~a~~~I 24 (72)
T pfam10447 2 PKVGDIVLARVTRVTP--RQAYCEI 24 (72)
T ss_pred CCCCCEEEEEEEEECH--HEEEEEE
T ss_conf 9899999999999750--1579999
No 93
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately. This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=81.18 E-value=0.24 Score=28.45 Aligned_cols=44 Identities=18% Similarity=0.227 Sum_probs=28.6
Q ss_pred HCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 00236754653786061146899887889997303643101357699999
Q gi|254780751|r 480 TTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVL 529 (723)
Q Consensus 480 ~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~ 529 (723)
+..+||.|+|+|.|-+.. +..=.=.......+.|.|.+|+-|.+
T Consensus 213 ~~~tC~~C~G~G~ii~~~------C~~C~G~G~~~~~~~~~v~IPaGV~~ 256 (386)
T TIGR02349 213 QQQTCPTCGGEGKIIKEP------CSTCKGKGRVKERKTISVKIPAGVDT 256 (386)
T ss_pred EEEECCCCCCEEEEEECC------CCCCCCCEEEEEEEEEEEECCCCCCC
T ss_conf 858778858423896336------89988740698888999961799888
No 94
>pfam07092 DUF1356 Protein of unknown function (DUF1356). This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=79.34 E-value=0.62 Score=25.58 Aligned_cols=34 Identities=26% Similarity=0.614 Sum_probs=26.1
Q ss_pred EEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCEEEEECC
Q ss_conf 8998604861489851566630112100236754653786061
Q gi|254780751|r 454 VQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQ 496 (723)
Q Consensus 454 ~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~g~~~~~ 496 (723)
-+-+.|+.|--+|.|-+ -+-.||.|+|+|+|...
T Consensus 13 ~~~~~~~~fpyveftg~---------~~vtCPTCqGtGrIp~e 46 (231)
T pfam07092 13 NREGDIAQFPYVEFTGR---------DSITCPTCQGTGRIPRE 46 (231)
T ss_pred CCCCCHHHCCEEEECCC---------CCEECCCCCCCCCCCCC
T ss_conf 54676210856665178---------85046877677616823
No 95
>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=76.01 E-value=2.5 Score=21.38 Aligned_cols=34 Identities=32% Similarity=0.504 Sum_probs=28.3
Q ss_pred CCEEE-EEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 87879-899783638823135327897713022213
Q gi|254780751|r 40 GNIYL-AKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 40 GnIY~-G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
|.|+. .+|++|.|++. +|+++|.+-.||.|++.+
T Consensus 1 G~i~~~~~V~~v~~~~G-~~~~l~~g~~gfvhiS~l 35 (71)
T cd05696 1 GAVVDSVKVTKVEPDLG-AVFELKDGLLGFVHISHL 35 (71)
T ss_pred CCCCCEEEEEEECCCCC-EEEEECCCCEEEEEEHHC
T ss_conf 96233405999858853-799969996899996012
No 96
>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=75.95 E-value=3.3 Score=20.56 Aligned_cols=33 Identities=30% Similarity=0.401 Sum_probs=28.7
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 878798997836388231353278977130222137
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
|.+-.|+|+....| +.+|+++ +-.||||.|.+.
T Consensus 1 g~~v~g~I~~~~kG--G~~v~~~-gv~~FiP~Sq~~ 33 (67)
T cd04465 1 GEIVEGKVTEKVKG--GLIVDIE-GVRAFLPASQVD 33 (67)
T ss_pred CCEEEEEEEEEECC--CEEEEEC-CEEEEEECHHCC
T ss_conf 99999999999857--1999999-999998802525
No 97
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=75.25 E-value=2.8 Score=21.09 Aligned_cols=49 Identities=24% Similarity=0.333 Sum_probs=35.4
Q ss_pred EEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCC
Q ss_conf 999996073346042878798997836388231353278977130222137
Q gi|254780751|r 25 VEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIH 75 (723)
Q Consensus 25 l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~ 75 (723)
+.-|+.--.-...-.|-+|+|.|.+|+. =.|||++...--|.+|-++..
T Consensus 108 vy~l~~~c~~~Dve~g~~Y~g~v~~v~~--~GvFv~Ln~~v~GL~~~~d~~ 156 (715)
T COG1107 108 VYVLDNSCTMEDVEAGKYYKGIVSRVEK--YGVFVELNSHVRGLIHRRDLG 156 (715)
T ss_pred EEEECCCCCHHHCCCCEEEECCCCCHHH--HCCEEECCHHHHCCCCCCCCC
T ss_conf 6996355662003464054031021434--065243373543344401247
No 98
>PRK04820 rnpA ribonuclease P; Reviewed
Probab=75.14 E-value=5.8 Score=18.85 Aligned_cols=60 Identities=27% Similarity=0.431 Sum_probs=42.4
Q ss_pred CCEEEECCC-CHHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 512420468-8689999999998630-------02587169985045575799999999999999987764
Q gi|254780751|r 216 GETISRKIT-NPVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVREL 278 (723)
Q Consensus 216 ~~~iSrki~-~~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~ 278 (723)
|..||||.. ..-.|.++|.++.+.- .+.++=+|.|-.+...+-.+|..- |.++|..+-..
T Consensus 51 GL~VsKK~~k~AV~RNRIKR~iREsFRl~Q~~Lp~~DiVVlaR~g~~~l~N~el~~~---l~kLw~r~~~~ 118 (145)
T PRK04820 51 GMAVSRKVDTRAVGRNRIKRVLRDAMRHLLPELAGGDYVIVARSAAAKATNPQIRDA---FLRLLRRAGAL 118 (145)
T ss_pred EEEEECHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHCCHHHHHHH---HHHHHHHHCCC
T ss_conf 789751224566788889999999999731138888889993677344051999999---99999980468
No 99
>TIGR02642 phage_xxxx uncharacterized phage protein; InterPro: IPR013464 This uncharacterised protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus (strain YJ016), Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to the phage lambda antitermination protein Q..
Probab=74.26 E-value=1.2 Score=23.70 Aligned_cols=48 Identities=13% Similarity=0.203 Sum_probs=28.5
Q ss_pred HHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHC-CCCCCCCCEEEEECCHH
Q ss_conf 999999731278728998604861489851566630112100-23675465378606114
Q gi|254780751|r 440 EKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTT-KVCTYCKGAGYIRSQSS 498 (723)
Q Consensus 440 ~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~-~~c~~c~g~g~~~~~~~ 498 (723)
...|++.+...-+..+..|= =.+.++..--. ..|++|+|+|.+....-
T Consensus 168 ~~~Lrd~a~~~a~~~~~CP~-----------C~Gtg~~~~~~P~~C~~C~G~G~~~~~~e 216 (270)
T TIGR02642 168 RRALRDYAVAKAAESRKCPR-----------CRGTGLRLRRQPEECDKCAGTGRLLPTVE 216 (270)
T ss_pred HHHHHHHHHHHHHHCCCCCC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCHH
T ss_conf 88899999998741488798-----------65667888977887777786433030089
No 100
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=73.32 E-value=1.8 Score=22.32 Aligned_cols=19 Identities=32% Similarity=0.555 Sum_probs=12.3
Q ss_pred HHHHHCCCCCCCCCEEEEE
Q ss_conf 1121002367546537860
Q gi|254780751|r 476 VLESTTKVCTYCKGAGYIR 494 (723)
Q Consensus 476 l~e~~~~~c~~c~g~g~~~ 494 (723)
...++..+||.|+|+|.+.
T Consensus 178 g~~~~~~~C~~C~G~G~~i 196 (371)
T COG0484 178 GFFSFQQTCPTCNGTGKII 196 (371)
T ss_pred EEEEEEEECCCCCCCEEEC
T ss_conf 5899999899976612389
No 101
>TIGR01213 TIGR01213 conserved hypothetical protein TIGR01213; InterPro: IPR005912 The members of this family of conserved hypothetical proteins show a low level of similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs. .
Probab=72.42 E-value=1.1 Score=23.75 Aligned_cols=39 Identities=8% Similarity=0.114 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEE-CCC
Q ss_conf 769999999842221436786499832880699982-375
Q gi|254780751|r 349 SGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDV-NSG 387 (723)
Q Consensus 349 y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDV-NSG 387 (723)
-.|..++.+=|.+.+--..|-..=.|.=++++.||+ -+.
T Consensus 149 EsiK~E~nRE~GK~~~~rtG~~~d~e~PD~v~~v~~r~~~ 188 (450)
T TIGR01213 149 ESIKREFNRELGKLLAKRTGKEVDFERPDIVVMVEFREAE 188 (450)
T ss_pred CCHHHHHCCCHHEEEEEECCCCCCCCCCCEEEEEECCCCC
T ss_conf 8624551610100231002724447888379998247776
No 102
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=72.07 E-value=3.1 Score=20.71 Aligned_cols=12 Identities=17% Similarity=0.476 Sum_probs=5.1
Q ss_pred HHHHHHHHHCCC
Q ss_conf 999987310368
Q gi|254780751|r 409 EIARQLRLRDLA 420 (723)
Q Consensus 409 EIaRQlRLRnlg 420 (723)
.+|-|+-+-|+-
T Consensus 193 k~aee~g~~~ie 204 (354)
T COG1568 193 KVAEELGYNNIE 204 (354)
T ss_pred HHHHHHCCCCHH
T ss_conf 999984833155
No 103
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=70.97 E-value=7.2 Score=18.19 Aligned_cols=99 Identities=23% Similarity=0.187 Sum_probs=64.5
Q ss_pred CCCCCCCCEEEEECCCEEE----EEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEE-EECCCCCCHHHH
Q ss_conf 2143678649983288069----99823755444555114799999999999999873103686389-603347988889
Q gi|254780751|r 362 EVTLPSRGYVIINQTEALV----SIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIV-VDFIDMEEKKNN 436 (723)
Q Consensus 362 ~V~L~sGG~lvIe~TEALt----~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIv-IDFIdM~~~~~~ 436 (723)
.|||-+-..+-++-++--+ .||.=|.-+-|+.| +.+-+.+|-+.+.+-.+.+ +-||+ -||||+..
T Consensus 312 ~~~lF~s~~~~~el~~k~~~~~e~i~fL~~~f~GGTD-----~~~~l~~al~~~k~~~~~~-adiv~ITDg~~~~~---- 381 (437)
T COG2425 312 YVILFDSEVIEYELYEKKIDIEELIEFLSYVFGGGTD-----ITKALRSALEDLKSRELFK-ADIVVITDGEDERL---- 381 (437)
T ss_pred EEEEECCCCEEEEECCCCCCHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHHCCCCCC-CCEEEEECCHHHHH----
T ss_conf 8999525202555057745799999999650689888-----5899999999864366567-77899804376654----
Q ss_pred HHHHHHHHHHHHHCCCCEEEEEECCCC---EEEEECC
Q ss_conf 999999999731278728998604861---4898515
Q gi|254780751|r 437 RSVEKKLKESLKKDRARVQVGAISNFG---LLEMSRQ 470 (723)
Q Consensus 437 ~~v~~~l~~~l~~D~~~~~v~~it~lG---LlEltRk 470 (723)
..++....+..+...++..-+=|+..| |+.|+..
T Consensus 382 ~~~~~~v~e~~k~~~~rl~aV~I~~~~~~~l~~Isd~ 418 (437)
T COG2425 382 DDFLRKVKELKKRRNARLHAVLIGGYGKPGLMRISDH 418 (437)
T ss_pred HHHHHHHHHHHHHHHCEEEEEEECCCCCCCCCEECEE
T ss_conf 6789999999887543489999647898660001114
No 104
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=70.90 E-value=7.2 Score=18.18 Aligned_cols=13 Identities=38% Similarity=0.856 Sum_probs=7.0
Q ss_pred HCCCCCCCCCEEE
Q ss_conf 0023675465378
Q gi|254780751|r 480 TTKVCTYCKGAGY 492 (723)
Q Consensus 480 ~~~~c~~c~g~g~ 492 (723)
+..+||.|+|+..
T Consensus 397 s~~~C~~C~G~RL 409 (935)
T COG0178 397 SEKPCPSCKGTRL 409 (935)
T ss_pred CCCCCCCCCCCCC
T ss_conf 4274887888605
No 105
>pfam00825 Ribonuclease_P Ribonuclease P.
Probab=70.83 E-value=7.3 Score=18.17 Aligned_cols=57 Identities=23% Similarity=0.358 Sum_probs=38.4
Q ss_pred CCCEEEECCCC-HHHHHHHHHHHHHH----H--C--CCCCEEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf 75124204688-68999999999863----0--0--258716998504557579999999999999
Q gi|254780751|r 215 KGETISRKITN-PVDRKNLKEIARGL----E--V--PAGMGVILRTAGASRTKIEIKRDFEYLMRL 271 (723)
Q Consensus 215 ~~~~iSrki~~-~~~r~~l~~~~~~~----~--~--~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~ 271 (723)
-|+.+|+|+-+ .-.|.+++..+.+. . . +.++=+|+|..+.+.+..+|..|+..|+..
T Consensus 40 ~G~~vsKK~g~~AV~RNriKR~lRe~~r~~~~~l~~~~d~Vvi~r~~~~~~~~~~l~~~l~~ll~k 105 (107)
T pfam00825 40 LGISVSKKVGKRAVVRNRIKRLLREAFRLNKDRLPPGLDIVVIARKGALEADFAELLKELEKLLKK 105 (107)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf 899995513636889889999999999973510588977999978754549999999999999997
No 106
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=70.66 E-value=7.3 Score=18.14 Aligned_cols=42 Identities=12% Similarity=0.139 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCC
Q ss_conf 645888888752376631111035320366788898763101
Q gi|254780751|r 291 EGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSY 332 (723)
Q Consensus 291 ~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~ 332 (723)
+..-+..+|+.+-+..-.-|+|+.++..-..-+|+-.+.|.-
T Consensus 513 D~~rLi~~L~~Lrd~GNTViVVEHD~~~i~~AD~iIDiGPgA 554 (1809)
T PRK00635 513 DTHKLIQVIKKLRDQGNTVLLVEHDEQMISLADRIIDIGPGA 554 (1809)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHCCEEEECCCCC
T ss_conf 899999999999856997999966899996277789617887
No 107
>pfam03589 Antiterm Antitermination protein.
Probab=69.28 E-value=2.8 Score=21.03 Aligned_cols=31 Identities=32% Similarity=0.478 Sum_probs=24.9
Q ss_pred HHHHCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 1210023675465378606114689988788
Q gi|254780751|r 477 LESTTKVCTYCKGAGYIRSQSSVALSILRSV 507 (723)
Q Consensus 477 ~e~~~~~c~~c~g~g~~~~~~~~~~~~~r~i 507 (723)
.-..+..|+.|+|.|+-+-+.+.|++.+..+
T Consensus 28 G~pvfk~c~rc~g~G~sr~~~~~a~~ai~~~ 58 (95)
T pfam03589 28 GVPVFKTCERCGGRGYSRLDSTEAIEALCKY 58 (95)
T ss_pred CCCEEEECCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 9751434777789785989709999999987
No 108
>PRK00588 rnpA ribonuclease P; Reviewed
Probab=69.04 E-value=7.9 Score=17.91 Aligned_cols=58 Identities=17% Similarity=0.353 Sum_probs=39.9
Q ss_pred CCCEEEECCCCHHHHHHH----HHHHHHH--HCCCCCEEEEE--EECCCCCHHHHHHHHHHHHHHH
Q ss_conf 751242046886899999----9999863--00258716998--5045575799999999999999
Q gi|254780751|r 215 KGETISRKITNPVDRKNL----KEIARGL--EVPAGMGVILR--TAGASRTKIEIKRDFEYLMRLW 272 (723)
Q Consensus 215 ~~~~iSrki~~~~~r~~l----~~~~~~~--~~~~~~G~IiR--T~a~~~~~~~l~~d~~~L~~~w 272 (723)
-|..+||++-+.-.|.+. +.++... ..|.|.-++|| ..|+.++..+|..|++..+..-
T Consensus 45 vG~vVSK~VGnAV~RnrVkRrLR~~~r~~l~~lp~g~~vVvrAlp~aa~as~~eL~~~l~~~l~ra 110 (116)
T PRK00588 45 VGLIIAKSVGSAVERHRVARRLRHVARPMLKELHPSDRVVIRALPSSRHVSSARLEQQLRCGLRRA 110 (116)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 899982310004678899999999999987407998879999588747489999999999999999
No 109
>PRK02083 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=68.95 E-value=6.6 Score=18.43 Aligned_cols=16 Identities=6% Similarity=0.196 Sum_probs=6.0
Q ss_pred HHHHHHHHCCCCEEEE
Q ss_conf 9998731036863896
Q gi|254780751|r 410 IARQLRLRDLAGLIVV 425 (723)
Q Consensus 410 IaRQlRLRnlgGiIvI 425 (723)
.+.++.=.++|.|++.
T Consensus 158 ~i~~~~~~g~geil~t 173 (253)
T PRK02083 158 WAKEVQELGAGEILLT 173 (253)
T ss_pred HHHHHHHCCCCEEEEE
T ss_conf 9999875698789999
No 110
>PRK05973 replicative DNA helicase; Provisional
Probab=68.83 E-value=7.2 Score=18.18 Aligned_cols=85 Identities=18% Similarity=0.251 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHH----HHHHHHHHHHHHCCCCEEEEEECCCC-EEEEECCCCCCCHHH-
Q ss_conf 999999998731036863896033479888899----99999999731278728998604861-489851566630112-
Q gi|254780751|r 405 EAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNR----SVEKKLKESLKKDRARVQVGAISNFG-LLEMSRQRIRSSVLE- 478 (723)
Q Consensus 405 eAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~----~v~~~l~~~l~~D~~~~~v~~it~lG-LlEltRkR~r~sl~e- 478 (723)
..+.+|+|+|+=-.=+|+||||++-..+.+++. .+.+.||...+.= .+-|+-+|+|. =+| +|...||-+.+
T Consensus 133 i~~~~i~rrl~~~~~~~LIVIDYLQLM~~~r~~~eiseisRsLK~lAkEl--~vPVvaLSQLnRs~E-~R~dKrP~lSDL 209 (237)
T PRK05973 133 ICADYIIARLASAPRGTLVVIDYLQLLDQRREKPDLSVQVRALKSFARKR--GVILVFISQIDRSFD-PASKPLPDIRDV 209 (237)
T ss_pred HHHHHHHHHHHHCCCCCEEEEECHHHHCCCCCCCCHHHHHHHHHHHHHHH--CCCEEEEECCCCCCC-CCCCCCCCCCCC
T ss_conf 33999999985278996899976775266778866899999999999986--993999400364322-356789974013
Q ss_pred ---------HHCCCCCCCCCEEE
Q ss_conf ---------10023675465378
Q gi|254780751|r 479 ---------STTKVCTYCKGAGY 492 (723)
Q Consensus 479 ---------~~~~~c~~c~g~g~ 492 (723)
.|...|-.-+|.-.
T Consensus 210 Rlpnp~dl~lf~k~~fl~~g~~~ 232 (237)
T PRK05973 210 RLPNPLDLSLFDKACFLNNGEIR 232 (237)
T ss_pred CCCCCCHHHHHCHHEEECCCEEE
T ss_conf 69982104230321031277378
No 111
>KOG1067 consensus
Probab=68.49 E-value=6.7 Score=18.41 Aligned_cols=34 Identities=6% Similarity=0.159 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCC
Q ss_conf 1432212345645888888752376631111035
Q gi|254780751|r 281 NSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSG 314 (723)
Q Consensus 281 ~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~ 314 (723)
..+.|.+++..++-+...++++....+..+..|.
T Consensus 270 ~Kr~~~~~~~p~pel~K~v~~la~erl~~vftd~ 303 (760)
T KOG1067 270 QKREPQKLFLPDPELVKHVHKLAMERLYAVFTDY 303 (760)
T ss_pred CCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 6243244428987899999999999999985253
No 112
>PRK13597 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=68.15 E-value=7.1 Score=18.23 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=7.3
Q ss_pred HHHHCCCCCCEEECCC
Q ss_conf 8752376631111035
Q gi|254780751|r 299 IRDLYCKDISEIIVSG 314 (723)
Q Consensus 299 ird~~~~~~~~i~vd~ 314 (723)
+..++...++.|++..
T Consensus 90 ~~~ll~~GadkViigS 105 (252)
T PRK13597 90 ARKLLLSGADKVSVNS 105 (252)
T ss_pred HHHHHHCCCCEEEECH
T ss_conf 9999856987798326
No 113
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=67.94 E-value=8.3 Score=17.76 Aligned_cols=57 Identities=19% Similarity=0.220 Sum_probs=40.7
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEEC
Q ss_conf 023675465378606114689988788999730364310135769999987302379999999984887999847
Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIG 555 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d 555 (723)
.-.||.|.+.-..-|...+|..+-..+.+....+++ +.+.+..+-.+||-.|...+-
T Consensus 44 ~LRCp~CQNqsIadSnA~IA~DlR~~V~e~l~eGkS------------------~~qIid~mVaRYG~FVly~Pp 100 (153)
T COG3088 44 ELRCPQCQNQSIADSNAPIARDLRHQVYELLQEGKS------------------DQQIIDYMVARYGEFVLYKPP 100 (153)
T ss_pred HCCCCCCCCCCHHHHCCHHHHHHHHHHHHHHHCCCC------------------HHHHHHHHHHHHCCEEEECCC
T ss_conf 638875789773320667899999999999985786------------------899999999853463432699
No 114
>pfam00684 DnaJ_CXXCXGXG DnaJ central domain (4 repeats). The central cysteine-rich (CR) domain of DnaJ proteins contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DNAJ cysteine rich domain and various hydrophobic peptides has been found.
Probab=67.82 E-value=3.9 Score=20.07 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=14.7
Q ss_pred CHHHHHCCCCCCCCCEEEEEC
Q ss_conf 011210023675465378606
Q gi|254780751|r 475 SVLESTTKVCTYCKGAGYIRS 495 (723)
Q Consensus 475 sl~e~~~~~c~~c~g~g~~~~ 495 (723)
.+.-.+..+|+.|+|+|++..
T Consensus 48 ~~~~~~~~~C~~C~G~G~~i~ 68 (79)
T pfam00684 48 GGVFQFQQTCPACGGTGKIIE 68 (79)
T ss_pred CEEEEEEEECCCCCCEEEEEC
T ss_conf 835886889966886461889
No 115
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=67.45 E-value=8.5 Score=17.70 Aligned_cols=24 Identities=29% Similarity=0.339 Sum_probs=19.8
Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 60428787989978363882313532
Q gi|254780751|r 36 KQIKGNIYLAKVTRVEPSLQAAFVDY 61 (723)
Q Consensus 36 ~~~~GnIY~G~V~~V~p~lqAAFVdi 61 (723)
-..+|+|-.|+|++|-+.+ |+|+|
T Consensus 61 ~p~vGdiVig~V~~v~~~~--a~v~I 84 (187)
T PRK09521 61 LLKKGDIVYGRVVDVKEQR--ALVRI 84 (187)
T ss_pred CCCCCCEEEEEEEEECCCE--EEEEE
T ss_conf 8898999999999954767--99999
No 116
>COG0594 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]
Probab=66.77 E-value=8.7 Score=17.61 Aligned_cols=57 Identities=23% Similarity=0.307 Sum_probs=41.4
Q ss_pred CCEEEE-CCCCHHHHHHHHHHHHHH-------HCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 512420-468868999999999863-------002587169985045575799999999999999
Q gi|254780751|r 216 GETISR-KITNPVDRKNLKEIARGL-------EVPAGMGVILRTAGASRTKIEIKRDFEYLMRLW 272 (723)
Q Consensus 216 ~~~iSr-ki~~~~~r~~l~~~~~~~-------~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w 272 (723)
|+.||+ ++...-.|.+.+..+.+. ..+.++=+|+|..+.+.+-.++.+++.+++..-
T Consensus 44 GlsVsKkk~~~AV~RNRiKR~iRe~~r~~~~~~~~~d~Viiar~~~~~~~~~~l~~~L~~~l~~~ 108 (117)
T COG0594 44 GLTVSKKKVGNAVERNRIKRLIREAFRLLQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKRA 108 (117)
T ss_pred EEEEECHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 99998600241246789999999999962531898609999778867779899999999999861
No 117
>PRK03220 consensus
Probab=66.32 E-value=7.9 Score=17.91 Aligned_cols=19 Identities=11% Similarity=0.011 Sum_probs=9.1
Q ss_pred HHHHHHHHHHCCCCEEEEE
Q ss_conf 9999987310368638960
Q gi|254780751|r 408 EEIARQLRLRDLAGLIVVD 426 (723)
Q Consensus 408 ~EIaRQlRLRnlgGiIvID 426 (723)
.+.+.++.=.++|.||+-|
T Consensus 162 ~~~i~~~~~~g~geil~td 180 (257)
T PRK03220 162 VEWAARGAELGVGEILLNS 180 (257)
T ss_pred HHHHHHHHHCCCCEEEEEE
T ss_conf 9999998626988899998
No 118
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.43 E-value=5.6 Score=18.95 Aligned_cols=154 Identities=14% Similarity=0.181 Sum_probs=82.7
Q ss_pred HHHHHHCCCC---EEEEECCCCCCHHHH------HHHHHHHHHHHHHCCCCEEEEE---ECCCCEE--------------
Q ss_conf 9873103686---389603347988889------9999999997312787289986---0486148--------------
Q gi|254780751|r 412 RQLRLRDLAG---LIVVDFIDMEEKKNN------RSVEKKLKESLKKDRARVQVGA---ISNFGLL-------------- 465 (723)
Q Consensus 412 RQlRLRnlgG---iIvIDFIdM~~~~~~------~~v~~~l~~~l~~D~~~~~v~~---it~lGLl-------------- 465 (723)
+.++|-+=.| +--|..|||+...-. ..+++.+++.|.++..-.-+.. ++.+=+.
T Consensus 373 ~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~ 452 (730)
T COG1198 373 KLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDS 452 (730)
T ss_pred EEEECCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCEEECCCCCCCCCCCCCCC
T ss_conf 89970354555678762587356665546775799999999999842986899971677654004256898024899995
Q ss_pred EEECCCCCCCH-------HHHHCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCC------CCCHHHHHHHH
Q ss_conf 98515666301-------121002367546537860611468998878899973036431013------57699999873
Q gi|254780751|r 466 EMSRQRIRSSV-------LESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIV------HTHSDVVLYLL 532 (723)
Q Consensus 466 EltRkR~r~sl-------~e~~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v------~~~~~va~~ll 532 (723)
=||=-+-+..| .+.....||.|++. +++..-+=...+..++....-..+.-.+-. ..+-....-+.
T Consensus 453 ~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~-~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~ 531 (730)
T COG1198 453 PLTLHKATGQLRCHYCGYQEPIPQSCPECGSE-HLRAVGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFA 531 (730)
T ss_pred CEEEECCCCEEEECCCCCCCCCCCCCCCCCCC-EEEEECCCHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 12786479806707799989988779899997-36996461999999999878999479984666664356899999975
Q ss_pred CCHHHHHHHHH--------HHHCCEEEEEECCCCCCCCEEEE
Q ss_conf 02379999999--------98488799984787788633897
Q gi|254780751|r 533 NQKRATIVEYE--------ARFGVSINVVIGIELADKLFYIE 566 (723)
Q Consensus 533 n~kr~~l~~lE--------~~~~~~I~i~~d~~l~~~~f~Ie 566 (723)
+.+-+-|.... -.++.-..+.+|..|..|+|+-.
T Consensus 532 ~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRAs 573 (730)
T COG1198 532 NGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRAS 573 (730)
T ss_pred CCCCCEEECCHHHHCCCCCCCCEEEEEEECHHHHCCCCCCHH
T ss_conf 799886634166642788666318999963143158884357
No 119
>KOG1015 consensus
Probab=65.10 E-value=7.1 Score=18.23 Aligned_cols=135 Identities=13% Similarity=0.101 Sum_probs=65.6
Q ss_pred CCCCEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEE
Q ss_conf 66311110353203667888987631012112201344203567769999999842221436786499832880699982
Q gi|254780751|r 305 KDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDV 384 (723)
Q Consensus 305 ~~~~~i~vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDV 384 (723)
..+..++|-.+ .+.+..++..+...+.. + ...+...+|..-.+-.-=++.+--.-|-.+||-.+|-.+=- -|=
T Consensus 726 lg~ktaLvV~P--lNt~~NW~~EFekWm~~-~-e~~~~leV~eL~~vkr~e~R~~~L~~W~~~ggVmIiGYdmy--RnL- 798 (1567)
T KOG1015 726 LGFKTALVVCP--LNTALNWMNEFEKWMEG-L-EDDEKLEVSELATVKRPEERSYMLQRWQEDGGVMIIGYDMY--RNL- 798 (1567)
T ss_pred CCCCEEEEECC--HHHHHHHHHHHHHHCCC-C-CCCCCCEEEHHHHCCCHHHHHHHHHHHHHCCCEEEEEHHHH--HHH-
T ss_conf 47856899723--59988999999986124-2-22466212021202674889999999975297799736888--877-
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf 375544455511479999999999999987310368638960334798888999999999973127872899860486
Q gi|254780751|r 385 NSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNF 462 (723)
Q Consensus 385 NSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~l 462 (723)
--|+..+.. | ++|+.++--+++=--|+|.|=-..- +...-.|-++|....-+ .|+-+.| |+|
T Consensus 799 a~gr~vk~r---------k---~ke~f~k~lvdpGPD~vVCDE~HiL-KNeksa~Skam~~irtk--RRI~LTG-TPL 860 (1567)
T KOG1015 799 AQGRNVKSR---------K---LKEIFNKALVDPGPDFVVCDEGHIL-KNEKSAVSKAMNSIRTK--RRIILTG-TPL 860 (1567)
T ss_pred HCCCCHHHH---------H---HHHHHHHHCCCCCCCEEEECCHHHH-CCCHHHHHHHHHHHHHH--EEEEEEC-CCH
T ss_conf 514560356---------7---9999998605789976872421221-35247899999987764--0477526-711
No 120
>PRK01659 consensus
Probab=64.74 E-value=9.5 Score=17.35 Aligned_cols=15 Identities=7% Similarity=0.078 Sum_probs=5.3
Q ss_pred HHHHHHHHCCCCEEE
Q ss_conf 999873103686389
Q gi|254780751|r 410 IARQLRLRDLAGLIV 424 (723)
Q Consensus 410 IaRQlRLRnlgGiIv 424 (723)
.+.++.-.+.|.||+
T Consensus 158 ~i~~~~~~g~geil~ 172 (252)
T PRK01659 158 WAKEAVRLGAGEILL 172 (252)
T ss_pred HHHHHHHCCCCEEEE
T ss_conf 999999769977999
No 121
>TIGR02034 CysN sulfate adenylyltransferase, large subunit; InterPro: IPR011779 Metabolic assimilation of sulphur from inorganic sulphate, requires sulphate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulphates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulphation of sulphate with ATP by sulphate adenylyltransferase (ATP sulphurylase) to produce 5'-phosphosulphate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulphate (PAPS) . In Escherichia coli, ATP sulphurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulphur-containing amino acids . Homologous to this E. coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulphurase and APS kinase activity, yet are involved in Nod factor sulphation, and sulphation of other macromolecules . With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulphurase) and cysC (APS kinase) , .; GO: 0016772 transferase activity transferring phosphorus-containing groups.
Probab=64.24 E-value=0.82 Score=24.76 Aligned_cols=69 Identities=20% Similarity=0.142 Sum_probs=47.5
Q ss_pred CCCCCCCCCCEEEEECCCEEE-EEEECCCCCCCCCCCH-H-HHHHHHHHHHHHHHH--HHHHHCCCCEEEEECC
Q ss_conf 222143678649983288069-9982375544455511-4-799999999999999--8731036863896033
Q gi|254780751|r 360 QTEVTLPSRGYVIINQTEALV-SIDVNSGRSTREHCIE-D-TALQTNLEAAEEIAR--QLRLRDLAGLIVVDFI 428 (723)
Q Consensus 360 ~~~V~L~sGG~lvIe~TEALt-~IDVNSG~~~~~~~~e-~-t~l~tNleAA~EIaR--QlRLRnlgGiIvIDFI 428 (723)
.+..||+.|+..|==.-.++. .+|||+.+....+.++ = .+=.+||.-+++|+= ==.=|-+||+|+||=.
T Consensus 328 G~~Y~lk~g~~~v~a~v~~I~~~vdvn~~~~~~A~~L~GLN~iG~v~l~~~~~~~fd~Y~~nR~tG~FILIDr~ 401 (411)
T TIGR02034 328 GRSYLLKLGTRKVRASVTAIKHKVDVNTLEKNAAKELEGLNEIGLVNLSLDEPIAFDAYAENRTTGAFILIDRL 401 (411)
T ss_pred CCEEEEEECCEEEEEEEEEEEEEECCCCCCHHHHHHHHCCCCEEEEEEEECCCCCCCCHHHCCCCEEEEEEECC
T ss_conf 95378873242775899877799724643102212310687057999830661013542218841027999846
No 122
>PRK04281 consensus
Probab=62.86 E-value=10 Score=17.12 Aligned_cols=18 Identities=17% Similarity=0.315 Sum_probs=7.9
Q ss_pred HHHHHHHHHCCCCEEEEE
Q ss_conf 999987310368638960
Q gi|254780751|r 409 EIARQLRLRDLAGLIVVD 426 (723)
Q Consensus 409 EIaRQlRLRnlgGiIvID 426 (723)
|.+.++.=.++|.+|+-|
T Consensus 158 ~~~~~~~~~g~geil~td 175 (254)
T PRK04281 158 EWAVEMQKRGAGEILLTG 175 (254)
T ss_pred HHHHHHHHCCCCEEEEEE
T ss_conf 999998752998999988
No 123
>PRK06937 type III secretion system protein; Reviewed
Probab=61.62 E-value=11 Score=16.97 Aligned_cols=50 Identities=14% Similarity=0.149 Sum_probs=38.0
Q ss_pred CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE
Q ss_conf 6431013576999998730237999999998488799984787788633897
Q gi|254780751|r 515 TAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE 566 (723)
Q Consensus 515 ~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie 566 (723)
..+.++++|||+-...+............. -..|.|.+|+.|.+..+.++
T Consensus 129 ~~~~v~I~V~P~d~~~v~~~~~~~~~~~~~--~~~l~I~~D~~L~~g~CvlE 178 (204)
T PRK06937 129 NQKQVVVRVAPDQAGAVREQIAKVLKDFPG--VGYLEVVADARLDQGGCILE 178 (204)
T ss_pred CCCEEEEEECHHHHHHHHHHHHHHHHHCCC--CCEEEEEECCCCCCCCEEEE
T ss_conf 597399999946699999999999972888--85079852898899975995
No 124
>PRK04390 rnpA ribonuclease P; Reviewed
Probab=61.39 E-value=11 Score=16.94 Aligned_cols=56 Identities=18% Similarity=0.210 Sum_probs=43.8
Q ss_pred CCEEEECCCC-HHHHHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf 5124204688-689999999998630-------0258716998504557579999999999999
Q gi|254780751|r 216 GETISRKITN-PVDRKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFEYLMRL 271 (723)
Q Consensus 216 ~~~iSrki~~-~~~r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~ 271 (723)
|+.||||... .-.|.++|.++.+.- .+.++=+++|..+...+-.+|..+++.|.-.
T Consensus 48 GlvVsKK~~~~AV~RNriKR~iRE~FR~~q~~L~~~DiVV~ar~~~~~~dn~~l~~~L~~L~~~ 111 (121)
T PRK04390 48 GLVVGKKTAKRANERNYMKRVIRDWFRLNKNRLPPQDFVVRVHRKFDRATAKQARAELAQLMFG 111 (121)
T ss_pred EEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf 7998631213477777899999999986611189978999945444526999999999999843
No 125
>KOG3409 consensus
Probab=61.23 E-value=11 Score=16.92 Aligned_cols=57 Identities=26% Similarity=0.243 Sum_probs=33.1
Q ss_pred EEECCCCCEEEEEEEE--CCEEEEEEECCCCC---CCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 8965289607999998--99899999607334---604287879899783638823135327897713022213
Q gi|254780751|r 6 LIDASHVEETRVVVLR--DNRVEELDFESEHK---KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 6 lI~~~~~~e~Rvav~e--~g~l~e~~~e~~~~---~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
.|.|+... ++ +.+ .+++.=..++...- -..+|.|-++||.++ +++-|=||| |++.|.
T Consensus 33 yI~aS~ag-~~--~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i--~~rfAkv~I-------~~V~d~ 94 (193)
T KOG3409 33 YIFASVAG-VN--FRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRI--NLRFAKVDI-------LSVGDK 94 (193)
T ss_pred EEEECCCC-CE--EECCCCCCEEEEEECCCCHHHCCCCCCCEEEEEEEEE--CCCEEEEEE-------EEECCE
T ss_conf 69851466-16--5437765224665226514330776576799998762--441356789-------998679
No 126
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.
Probab=60.63 E-value=4.4 Score=19.64 Aligned_cols=22 Identities=9% Similarity=0.303 Sum_probs=14.6
Q ss_pred HHHHCCCCCCCCCCEEEEECCC
Q ss_conf 9984222143678649983288
Q gi|254780751|r 356 DSLHQTEVTLPSRGYVIINQTE 377 (723)
Q Consensus 356 ~~~~~~~V~L~sGG~lvIe~TE 377 (723)
-.=|.+.+|.+-|+|+++|+.|
T Consensus 30 P~KFRk~iWiKRG~fVlvd~~~ 51 (78)
T cd05792 30 PTKFRKNIWIKRGDFVLVEPIE 51 (78)
T ss_pred CHHHHCCEEEECCCEEEEEECC
T ss_conf 1334316899718999997604
No 127
>PRK02621 consensus
Probab=59.83 E-value=12 Score=16.76 Aligned_cols=16 Identities=13% Similarity=0.295 Sum_probs=6.7
Q ss_pred HHHHHHHCCCCEEEEE
Q ss_conf 9987310368638960
Q gi|254780751|r 411 ARQLRLRDLAGLIVVD 426 (723)
Q Consensus 411 aRQlRLRnlgGiIvID 426 (723)
+..+-=.++|.||+.|
T Consensus 160 ~~~~~~~g~geil~td 175 (254)
T PRK02621 160 AEEVAERGAGEILLTS 175 (254)
T ss_pred HHHHHHHCCCEEEEEE
T ss_conf 9887762889699988
No 128
>PRK05054 exoribonuclease II; Provisional
Probab=59.53 E-value=12 Score=16.73 Aligned_cols=92 Identities=11% Similarity=0.113 Sum_probs=46.9
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCC-
Q ss_conf 0353203667888987631012112201344203567769999999842221436786499832880699982375544-
Q gi|254780751|r 312 VSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRST- 390 (723)
Q Consensus 312 vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~- 390 (723)
+...-.|.++.+++........ ....+-.....-.++..++ +-|=..+|.|.++..|+-...|-| |..+
T Consensus 308 S~~rLtY~~V~~~l~~~~~~~~-------~~~~l~~~l~~L~~la~~l--~~~R~~~g~~~~d~pe~~~~ld~~-g~~~~ 377 (644)
T PRK05054 308 SKAKLAYDNVSDWLENGGNWQP-------ESEAIAQQIRLLHQFCLAR--SEWRKNHALVFKDRPDYRFELGEK-GEVLD 377 (644)
T ss_pred ECCEECHHHHHHHHHCCCCCCC-------CCHHHHHHHHHHHHHHHHH--HHHHHHCCCCCCCCCCEEEEECCC-CCEEE
T ss_conf 4872539999999845876675-------4088999999999999999--976752876324686359998899-98735
Q ss_pred --------CCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf --------45551147999999999999998
Q gi|254780751|r 391 --------REHCIEDTALQTNLEAAEEIARQ 413 (723)
Q Consensus 391 --------~~~~~e~t~l~tNleAA~EIaRQ 413 (723)
...=+|+-.+.+|..+|+-+..+
T Consensus 378 i~~~~r~~ah~LIEE~MllAN~~vA~~l~~~ 408 (644)
T PRK05054 378 IVAEPRRIANRIVEESMIAANICAARVLRDK 408 (644)
T ss_pred EEEEECCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 8985332788899999999999999999861
No 129
>cd01889 SelB_euk SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and euk
Probab=59.49 E-value=12 Score=16.72 Aligned_cols=70 Identities=19% Similarity=0.182 Sum_probs=39.0
Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHH----HH-CCC
Q ss_conf 0699982375544455511479999999999999987310368638960334798888999999999973----12-787
Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESL----KK-DRA 452 (723)
Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l----~~-D~~ 452 (723)
|+.+||.+.|-. .+| +|..+.+++.++-.||+|-=||+-+....+..++.+++.+ .. ...
T Consensus 95 ailvVda~~G~~------~QT---------~eh~~~~~~~~~~~iv~iNK~D~v~~~~~~~~~~~i~~~l~~~l~~~~~~ 159 (192)
T cd01889 95 MLLVVDATKGIQ------TQT---------AECLVIGEILCKKLIVVLNKIDLIPEEERERKIEKMKKKLQKTLEKTRFK 159 (192)
T ss_pred CEEEEECCCCCC------HHH---------HHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 279998788887------899---------99999999858997999974127881577999999999999998653899
Q ss_pred CEEEEEECCC
Q ss_conf 2899860486
Q gi|254780751|r 453 RVQVGAISNF 462 (723)
Q Consensus 453 ~~~v~~it~l 462 (723)
...+.++|.+
T Consensus 160 ~~~iipiSA~ 169 (192)
T cd01889 160 NSPIIPVSAK 169 (192)
T ss_pred CCEEEEEECC
T ss_conf 9849995789
No 130
>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=58.95 E-value=12 Score=16.66 Aligned_cols=41 Identities=17% Similarity=0.385 Sum_probs=35.3
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf 4287879899783638823135327897713022213712102
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ 80 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ 80 (723)
..|-+-+|.|+.|-+ ...+|-+..+-.||.++.+|...|-+
T Consensus 2 ~~G~lvLG~V~~I~~--~~l~isLP~~L~G~V~it~ISd~~t~ 42 (100)
T cd05693 2 SEGMLVLGQVKEITK--LDLVISLPNGLTGYVPITNISDAYTE 42 (100)
T ss_pred CCCCEEEEEEEEECC--CCEEEECCCCCEEEEEHHHHHHHHHH
T ss_conf 889899999989846--63899858985899887885299999
No 131
>KOG2228 consensus
Probab=58.95 E-value=12 Score=16.66 Aligned_cols=83 Identities=23% Similarity=0.220 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCC-CEEEEECCCCCCCHHH
Q ss_conf 999999999999987310368638960334798888999999999973127872899860486-1489851566630112
Q gi|254780751|r 400 LQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNF-GLLEMSRQRIRSSVLE 478 (723)
Q Consensus 400 l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~l-GLlEltRkR~r~sl~e 478 (723)
+.|.--|.++|+|||-+++-.+ ++-| |.-.++-.+++..|+..-..-..+ .|.=+-.| +.+.++||-+=-.|.+
T Consensus 89 ~~~dk~al~~I~rql~~e~~~~--~k~~--gsfte~l~~lL~~L~~~~~~t~~~-ViFIldEfDlf~~h~rQtllYnlfD 163 (408)
T KOG2228 89 LQTDKIALKGITRQLALELNRI--VKSF--GSFTENLSKLLEALKKGDETTSGK-VIFILDEFDLFAPHSRQTLLYNLFD 163 (408)
T ss_pred CHHHHHHHHHHHHHHHHHHHHH--HEEE--CCCCHHHHHHHHHHHCCCCCCCCE-EEEEEEHHHCCCCCHHHHHHHHHHH
T ss_conf 0155899999999999997532--1242--253346999999873378778851-9998310002464035678999988
Q ss_pred HHC-CCCCCC
Q ss_conf 100-236754
Q gi|254780751|r 479 STT-KVCTYC 487 (723)
Q Consensus 479 ~~~-~~c~~c 487 (723)
... -..|+|
T Consensus 164 isqs~r~Pic 173 (408)
T KOG2228 164 ISQSARAPIC 173 (408)
T ss_pred HHHHCCCCEE
T ss_conf 8762479869
No 132
>pfam02108 FliH Flagellar assembly protein FliH.
Probab=58.17 E-value=12 Score=16.57 Aligned_cols=59 Identities=17% Similarity=0.099 Sum_probs=41.2
Q ss_pred HHHHHHHHHHC--CCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEEE
Q ss_conf 88788999730--364310135769999987302379999999984887999847877886338971
Q gi|254780751|r 503 ILRSVEEYLLQ--YTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEK 567 (723)
Q Consensus 503 ~~r~i~~~~~~--~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ier 567 (723)
++..+++.... .....+.+++||+-..++.....+. .. ...+.|.+|+++..-.+.|+-
T Consensus 52 i~~~v~~al~~l~~~~~~v~I~v~P~D~~~l~~~~~~~----~~--~~~~~l~~D~~l~~Ggc~iet 112 (128)
T pfam02108 52 ILALVREALAALPVLSGKVTLRLNPDDLALVEEHLGDE----LK--ARGWRLVADPSLSRGGCRIES 112 (128)
T ss_pred HHHHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHHHHH----HC--CCCEEEEECCCCCCCCEEEEE
T ss_conf 99999999997134478749998899999999988642----22--277489868987899889997
No 133
>COG1317 FliH Flagellar biosynthesis/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=57.40 E-value=13 Score=16.49 Aligned_cols=48 Identities=19% Similarity=0.143 Sum_probs=38.8
Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEEE
Q ss_conf 4310135769999987302379999999984887999847877886338971
Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEK 567 (723)
Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ier 567 (723)
...+.++|||+-..++...+-.++...... +.|.+|+++..-.+.|+-
T Consensus 157 ~~~i~l~VnP~d~e~i~~~~~~~~~~~~~~----l~l~~D~~l~~GgC~IeT 204 (234)
T COG1317 157 AAAITLRVNPDDLEIIRQQLDEELSLLGWR----LELVADPALSPGGCIIET 204 (234)
T ss_pred CCCEEEEECHHHHHHHHHHHHHHHHHCCCE----EEECCCCCCCCCCEEEEE
T ss_conf 667389988888999999988887424520----243258887899649983
No 134
>cd00881 GTP_translation_factor GTP translation factor family. This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.
Probab=56.93 E-value=13 Score=16.44 Aligned_cols=59 Identities=24% Similarity=0.275 Sum_probs=46.9
Q ss_pred CEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 80699982375544455511479999999999999987310368638960334798888999999999973127
Q gi|254780751|r 377 EALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKD 450 (723)
Q Consensus 377 EALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D 450 (723)
=|+.+||.+.|-. .-..|+.+.++..++.-+|+|-=||+..+++..++++.+++.|...
T Consensus 88 ~ailvVda~~G~~---------------~qt~~~~~~~~~~~~p~iv~iNKiD~~~~~~~~~~~~ei~~~l~~~ 146 (189)
T cd00881 88 GAILVVDANEGVQ---------------PQTREHLRIAREGGLPIIVAINKIDRVGEEDLEEVLREIKELLGLI 146 (189)
T ss_pred EEEEEEECCCCCC---------------HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 5699998798998---------------7899999999976998799998971877562999999999998753
No 135
>PRK11032 hypothetical protein; Provisional
Probab=56.87 E-value=6.4 Score=18.55 Aligned_cols=53 Identities=13% Similarity=0.275 Sum_probs=36.2
Q ss_pred HHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHH-HCCCCCCCCCEEEEECC
Q ss_conf 9997312787289986048614898515666301121-00236754653786061
Q gi|254780751|r 443 LKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLES-TTKVCTYCKGAGYIRSQ 496 (723)
Q Consensus 443 l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~-~~~~c~~c~g~g~~~~~ 496 (723)
|.+-|+.. ..-+.+.|+.+|-|-=..=--...+... ...+||.|+|+.+.|-+
T Consensus 104 l~~dl~h~-g~Y~sGEivg~G~LvC~~Cg~~~~~~~~~~ippCp~Cg~~~F~R~p 157 (160)
T PRK11032 104 VFQDLNHH-GVYHSGEVVGLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQRRP 157 (160)
T ss_pred HHHHHCCC-CEEECCEEEECCEEEHHHCCCEEEEECCCCCCCCCCCCCCEEEECC
T ss_conf 99984357-7243560532556657428987787468779888779997674089
No 136
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU; InterPro: IPR014088 Members of this protein family include S-adenosylmethionine-dependent C-20 methyltransferase (BchU), part of the pathway of bacteriochlorophyll c production in photosynthetic green sulphur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produce bacteriochlorophyll d..
Probab=56.39 E-value=9.2 Score=17.46 Aligned_cols=33 Identities=24% Similarity=0.277 Sum_probs=27.9
Q ss_pred CCHHHHH--HHHHHHHHHHHCCCCC--CCCCCEEEEE
Q ss_conf 4203567--7699999998422214--3678649983
Q gi|254780751|r 342 PHPIFFR--SGIEVQLDSLHQTEVT--LPSRGYVIIN 374 (723)
Q Consensus 342 ~~~lf~~--y~ie~~i~~~~~~~V~--L~sGG~lvIe 374 (723)
+.-||.+ |..++|+..++-+|-+ |+|||-|.|=
T Consensus 217 DAVLF~RILY~~N~Ql~T~l~~KAyDAl~SGGR~LIL 253 (306)
T TIGR02716 217 DAVLFSRILYSANEQLSTILLKKAYDALRSGGRLLIL 253 (306)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf 1656778876446789999999887522578807865
No 137
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=55.99 E-value=11 Score=16.92 Aligned_cols=34 Identities=26% Similarity=0.650 Sum_probs=24.3
Q ss_pred CCCEEEEEEEEECCC--CCEEEEEECCCCCCCCCHHHC
Q ss_conf 287879899783638--823135327897713022213
Q gi|254780751|r 39 KGNIYLAKVTRVEPS--LQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 39 ~GnIY~G~V~~V~p~--lqAAFVdiG~~k~gFL~~~ei 74 (723)
=|.-|.|+|+.+.+. ..--|||||... .++.++|
T Consensus 15 D~~wYRa~I~~~~~~~~~~V~fvDyGn~e--~V~~~~l 50 (57)
T smart00333 15 DGEWYRARIIKVDGEQLYEVFFIDYGNEE--VVPPSDL 50 (57)
T ss_pred CCCEEEEEEEEECCCCEEEEEEECCCCEE--EECHHHH
T ss_conf 89899999999999997999997689849--9859990
No 138
>PRK08903 hypothetical protein; Validated
Probab=55.77 E-value=13 Score=16.31 Aligned_cols=109 Identities=12% Similarity=0.039 Sum_probs=59.8
Q ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCEEEEECCHHH
Q ss_conf 86389603347988889999999999731278728998604861489851566630112100236754653786061146
Q gi|254780751|r 420 AGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSV 499 (723)
Q Consensus 420 gGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~g~~~~~~~~ 499 (723)
..+|+||-|+--....+..+...+..+....+...-+..-..--.+.+. .+++.-|.-.+ +......
T Consensus 91 ~d~l~iDDi~~i~~~~q~~lF~l~N~~~~~~~~~ll~s~~~~p~~l~~~-~DL~SRl~~gl------------~~~i~~p 157 (227)
T PRK08903 91 AELYAVDDVERLDDAQQIALFNLFNRVRAHGKTALLVAGPAAPLALDVR-EDLRTRLGWGL------------VYEVKPL 157 (227)
T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHCCCC-HHHHHHHHCCC------------EEEEECC
T ss_conf 8989996411489569999999999999729948997189971201200-89999993897------------3899797
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHH
Q ss_conf 8998878899973036431013576999998730237999999998
Q gi|254780751|r 500 ALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEAR 545 (723)
Q Consensus 500 ~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~ 545 (723)
-.+..+.|-...... -.+.++.+|+.||+..-...+..|+.-
T Consensus 158 dde~~~~iL~~~a~~----rgl~l~~~v~~yl~~r~~R~~~~L~~~ 199 (227)
T PRK08903 158 SDEDKIAALKAAAAE----RGLQLADEVPDYLLTHFRRDMPSLMAL 199 (227)
T ss_pred CHHHHHHHHHHHHHH----CCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf 999999999999996----299998899999999834789999999
No 139
>PRK02747 consensus
Probab=55.66 E-value=13 Score=16.30 Aligned_cols=19 Identities=11% Similarity=0.179 Sum_probs=8.9
Q ss_pred HHHHHHHHHHCCCCEEEEE
Q ss_conf 9999987310368638960
Q gi|254780751|r 408 EEIARQLRLRDLAGLIVVD 426 (723)
Q Consensus 408 ~EIaRQlRLRnlgGiIvID 426 (723)
.+.+.++-=.++|.|++-|
T Consensus 159 ~~~~~~~~~~G~geil~td 177 (257)
T PRK02747 159 VEFAQKVVSLGAGEILLTS 177 (257)
T ss_pred HHHHHHHHHCCCCEEEEEE
T ss_conf 9999999970998899998
No 140
>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=55.31 E-value=13 Score=16.31 Aligned_cols=38 Identities=21% Similarity=0.419 Sum_probs=33.2
Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCC
Q ss_conf 28787989978363882313532789771302221371210
Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 (723)
Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~ 79 (723)
-|.|..|-|++|-| +.+||.+|..-.|...++.+. +||
T Consensus 3 eGq~vRGyVk~v~~--~GvFv~Ls~~v~grv~~~nls-~~~ 40 (74)
T cd05705 3 EGQLLRGYVSSVTK--QGVFFRLSSSIVGRVLFQNVT-KYF 40 (74)
T ss_pred CCCEEEEEEEECCC--CCEEEEECCCEEEEEEEECCC-HHH
T ss_conf 88798999998268--739999568748999970036-212
No 141
>TIGR00393 kpsF sugar isomerase, KpsF/GutQ family; InterPro: IPR004800 This is a family of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. The group includes GutQ, a protein of the glucitol operon and KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of Escherichia coli.; GO: 0016853 isomerase activity, 0005975 carbohydrate metabolic process.
Probab=53.39 E-value=14 Score=16.12 Aligned_cols=41 Identities=34% Similarity=0.507 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHCCCCEEEEEECCC--CEEEEECCCCCCCHH
Q ss_conf 99999999973127872899860486--148985156663011
Q gi|254780751|r 437 RSVEKKLKESLKKDRARVQVGAISNF--GLLEMSRQRIRSSVL 477 (723)
Q Consensus 437 ~~v~~~l~~~l~~D~~~~~v~~it~l--GLlEltRkR~r~sl~ 477 (723)
++++-+.++.++.+..=.+|.+=|.| -|+||||+|++-.+.
T Consensus 151 ~kLL~kV~dlm~t~d~lP~v~~tas~~DAL~e~~~~~LG~~~v 193 (272)
T TIGR00393 151 RKLLVKVKDLMQTDDELPLVAPTASFKDALLEMSRKRLGLAVV 193 (272)
T ss_pred HHHHHHHHHHHCCCCCCCCEECCCCCEEEEEEEECCCCCEEEE
T ss_conf 7888876776406656782223677202102331378617999
No 142
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=53.35 E-value=13 Score=16.43 Aligned_cols=34 Identities=32% Similarity=0.651 Sum_probs=24.7
Q ss_pred CCCEEEEEEEEEC--CCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 2878798997836--38823135327897713022213
Q gi|254780751|r 39 KGNIYLAKVTRVE--PSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 39 ~GnIY~G~V~~V~--p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
-|.-|.|+|..+. ....--|||||.... +++++|
T Consensus 11 d~~wyRa~I~~i~~~~~~~V~f~DyG~~~~--v~~~~l 46 (48)
T cd04508 11 DGKWYRAKITSILSDGKVEVFFVDYGNTEV--VPLSDL 46 (48)
T ss_pred CCCEEEEEEEEECCCCEEEEEEECCCCEEE--EEHHHC
T ss_conf 997999999998899969999988996699--889997
No 143
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=52.66 E-value=15 Score=15.98 Aligned_cols=60 Identities=20% Similarity=0.283 Sum_probs=40.7
Q ss_pred CCCEEEECCCCHHHHHHH----HHHHHHH--HCCCCCEE--EEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 751242046886899999----9999863--00258716--998504557579999999999999998
Q gi|254780751|r 215 KGETISRKITNPVDRKNL----KEIARGL--EVPAGMGV--ILRTAGASRTKIEIKRDFEYLMRLWDN 274 (723)
Q Consensus 215 ~~~~iSrki~~~~~r~~l----~~~~~~~--~~~~~~G~--IiRT~a~~~~~~~l~~d~~~L~~~w~~ 274 (723)
-|..+||++-+.-.|.+. +.++... ..|.|.-+ +.+..|+.++..+|..|++.++.....
T Consensus 57 vG~vVSK~VGnAVvRnrVkRrLR~~~~~~~~~lp~g~~vVVrA~p~aa~as~~eL~~~l~~~L~r~~~ 124 (129)
T PRK03459 57 FGLVVSKAVGNAVVRHRVSRRLRHICASIVDKSPETHHVVIRALPGAATASSAELERDIRAGLGKLSR 124 (129)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 79997032211567889999999999987741899965999948870307999999999999999864
No 144
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription.
Probab=51.68 E-value=16 Score=15.87 Aligned_cols=231 Identities=17% Similarity=0.233 Sum_probs=116.3
Q ss_pred CCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC-
Q ss_conf 4421331068885799984033323456410123345765234422788751242046886899999999986300258-
Q gi|254780751|r 166 RQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAG- 244 (723)
Q Consensus 166 ~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~- 244 (723)
--|-++..|..||.||- |--|-| -.+|+.|.-+..||+...=.+.- ...|.+
T Consensus 425 pGw~VERHL~dGDiVLF--------NRQPSL-HRmSmMgH~VkVLPgkTFRLNLa------------------VCPPYNA 477 (901)
T TIGR02390 425 PGWVVERHLIDGDIVLF--------NRQPSL-HRMSMMGHKVKVLPGKTFRLNLA------------------VCPPYNA 477 (901)
T ss_pred CCCEEEEEECCCCEEEE--------CCCCCH-HHHHHCCCEEEECCCCCCCCCCC------------------CCCCCCC
T ss_conf 99789987126888766--------588642-02101144546788885213667------------------7728887
Q ss_pred ------CEE-EEEEECCCCCHHHHHHHHHHHHHHHHHHHHH-----------------HCCC-CCCCCCCCCCCHHHHHH
Q ss_conf ------716-9985045575799999999999999987764-----------------2014-32212345645888888
Q gi|254780751|r 245 ------MGV-ILRTAGASRTKIEIKRDFEYLMRLWDNVREL-----------------ALNS-VAPHLVYEEGNLIKRAI 299 (723)
Q Consensus 245 ------~G~-IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~-----------------~~~~-~~p~li~~~~~~~~~~i 299 (723)
|-+ +++ .||=.+|...|+..-+.|..- +.-+ +...+-.++.-.++...
T Consensus 478 DFDGDEMNlHV~Q-------~EEarAEA~~lM~V~~hI~tPRyGGPIIGg~~D~IsGaYLLT~k~~~~t~~ev~~iL~~~ 550 (901)
T TIGR02390 478 DFDGDEMNLHVPQ-------TEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTVKSTLFTKEEVVTILKKA 550 (901)
T ss_pred CCCCCCCCCCCCC-------CHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHC
T ss_conf 8887603764025-------733589999985411101468876401102567888888865047776889999999860
Q ss_pred HHHCCCCCCEE-ECCCCCH----HHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHH---HHCCCCCCCCCCEE
Q ss_conf 75237663111-1035320----3667888987631012112201344203567769999999---84222143678649
Q gi|254780751|r 300 RDLYCKDISEI-IVSGEKG----YREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDS---LHQTEVTLPSRGYV 371 (723)
Q Consensus 300 rd~~~~~~~~i-~vd~~~~----~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~---~~~~~V~L~sGG~l 371 (723)
-+..+..+- .|+...- |-.=++.+..+.|+..+ +..-.++.+ .....-.=|+-.|+
T Consensus 551 --~~~~~~~~~~~ie~~~~eGrdywTGK~ifS~~LP~dLn--------------~~~~a~~~~G~c~~C~~e~Cp~D~Yv 614 (901)
T TIGR02390 551 --GLKGEPEEPKAIEKPKEEGRDYWTGKQIFSAFLPEDLN--------------FEFRAKVCSGKCEACKKEECPHDAYV 614 (901)
T ss_pred --CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCC--------------EEEECCCCCCCCCCCCCCCCCCCCEE
T ss_conf --76778766663317786675322103555420788777--------------21401367885001003679986578
Q ss_pred EEECCCEEE-EEEECCCCCCCC-CCCHHHHHHHHHHHH--------HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf 983288069-998237554445-551147999999999--------9999987310368638960334798888999999
Q gi|254780751|r 372 IINQTEALV-SIDVNSGRSTRE-HCIEDTALQTNLEAA--------EEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEK 441 (723)
Q Consensus 372 vIe~TEALt-~IDVNSG~~~~~-~~~e~t~l~tNleAA--------~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~ 441 (723)
||.-=.=|- |||=++=..-.+ +=+..-+.+-=-|+| +=-.|-|-||.++ +=||=||. .++..+++.+
T Consensus 615 VI~NG~Ll~GViDk~a~G~e~g~~il~~i~~~yG~e~ar~~lD~~trL~i~~i~~~GfT--~g~~D~dI-P~eA~~~I~~ 691 (901)
T TIGR02390 615 VIKNGKLLKGVIDKKAIGAEKGDKILDRIVREYGPEAARRFLDSVTRLAIRFIELRGFT--TGIDDIDI-PKEAKEEIEE 691 (901)
T ss_pred EEECCEEEEEECCHHHCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCC-CHHHHHHHHH
T ss_conf 98668043203020112746637899999876074689999999999999987551660--13360104-6789999999
Q ss_pred HHHHHHHH
Q ss_conf 99997312
Q gi|254780751|r 442 KLKESLKK 449 (723)
Q Consensus 442 ~l~~~l~~ 449 (723)
.++.|.++
T Consensus 692 ~i~~A~~~ 699 (901)
T TIGR02390 692 LIEKAEKR 699 (901)
T ss_pred HHHHHHHH
T ss_conf 99999999
No 145
>KOG0546 consensus
Probab=51.26 E-value=7.9 Score=17.92 Aligned_cols=37 Identities=16% Similarity=0.043 Sum_probs=21.1
Q ss_pred HHHCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCC
Q ss_conf 2100236754653786061146899887889997303
Q gi|254780751|r 478 ESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQY 514 (723)
Q Consensus 478 e~~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~ 514 (723)
-+++.+||||+|.-.|...-.-...+.|.|+......
T Consensus 126 FITT~p~PHLdGkHVVFGqVI~G~~VVr~IEn~~~d~ 162 (372)
T KOG0546 126 FITTVPTPHLDGKHVVFGQVIKGKEVVREIENLETDE 162 (372)
T ss_pred EEECCCCCCCCCCEEEEEEEEECHHHHHHHHCCCCCC
T ss_conf 8967777776882468866764535899975455566
No 146
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213 This entry describes NusA, or N utilisation 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 Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (IPR003029 from INTERPRO) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.; GO: 0003723 RNA binding, 0030528 transcription regulator activity.
Probab=50.29 E-value=16 Score=15.73 Aligned_cols=161 Identities=25% Similarity=0.287 Sum_probs=92.9
Q ss_pred CCCCCCEEEEEEEE--ECCCCC--EEEEEE-CCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 60428787989978--363882--313532-7897713022213712102898899999998886311111000000011
Q gi|254780751|r 36 KQIKGNIYLAKVTR--VEPSLQ--AAFVDY-GGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHG 110 (723)
Q Consensus 36 ~~~~GnIY~G~V~~--V~p~lq--AAFVdi-G~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~ 110 (723)
+..+|.|--|+|.| +..+=+ ..|||+ |.. .||||=+|.-|.
T Consensus 142 ~~~~g~~i~g~V~r~d~~~~~~~~g~~v~l~g~~-e~~lp~~e~iP~--------------------------------- 187 (366)
T TIGR01953 142 KSKVGEIISGTVKRVDVNKEGNETGLIVELAGKT-EAILPKKEQIPG--------------------------------- 187 (366)
T ss_pred HHHHCEEEEEEEEEEEECCCCCCCEEEEEECCCE-EEECCHHHCCCC---------------------------------
T ss_conf 3331808999999975257875210799985750-252135337888---------------------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCE---EEEEEECC
Q ss_conf 122334443344542222334455433222234321122111211000012234444213310688857---99984033
Q gi|254780751|r 111 DVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQI---LLVQIVKE 187 (723)
Q Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~---ilVQV~ke 187 (723)
+-++.|+. ++..|.+.
T Consensus 188 -------------------------------------------------------------E~~~~Gd~i~~~~~eV~~~ 206 (366)
T TIGR01953 188 -------------------------------------------------------------EKFRIGDRIKAYVYEVRKT 206 (366)
T ss_pred -------------------------------------------------------------CCCCCCCEEEEEEEEEEEC
T ss_conf -------------------------------------------------------------7523588899999999986
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCC--CC----EEEEEEECCCCCHHHH
Q ss_conf 32345641012334576523442278875124204688689999999998630025--87----1699850455757999
Q gi|254780751|r 188 ERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPA--GM----GVILRTAGASRTKIEI 261 (723)
Q Consensus 188 ~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~--~~----G~IiRT~a~~~~~~~l 261 (723)
+.|. - + -+-+||. +. ..++.++. +.+|+ +. --|.|-+|.-+--..-
T Consensus 207 ~~g~-~--------------------~-~i~lSRt--~p---~fl~~Ll~-~EvPEI~dG~veIk~iAR~pG~R~KiAV~ 258 (366)
T TIGR01953 207 AKGG-L--------------------P-QIILSRT--HP---EFLKELLK-LEVPEIADGIVEIKKIAREPGSRTKIAVE 258 (366)
T ss_pred CCCC-E--------------------E-EEEEECC--CH---HHHHHHHH-CCCCEEECCEEEEEEEECCCCCCCEEEEE
T ss_conf 8896-6--------------------8-9999708--97---99999986-16965417819999998178876135788
Q ss_pred H-HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHH-HHHHCCCCHHHH
Q ss_conf 9-9999999999987764201432212345645888888752376631111035320366788898-763101211220
Q gi|254780751|r 262 K-RDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMK-LLMPSYARIVRQ 338 (723)
Q Consensus 262 ~-~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~-~~~p~~~~~v~~ 338 (723)
. .| ..--+-.+|+-.-..-+.-+++.|-+..++-|..+.+. ..|+. .+.|.....|..
T Consensus 259 SH~d--------------~~iDPvGAcvG~~G~Ri~~i~~EL~gEkIDii~y~~d~-----~~Fi~nAL~PA~V~~v~i 318 (366)
T TIGR01953 259 SHND--------------ENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP-----AEFIANALSPAEVISVEI 318 (366)
T ss_pred EECC--------------CCCCEEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCH-----HHHHHHHCCCCEECEEEE
T ss_conf 5078--------------99870465888988654333887478717898368887-----999997418631211489
No 147
>TIGR00137 gid gid protein; InterPro: IPR004417 The gid proteins are present in relatively few bacteria but very tightly conserved where they occur. The function of these proteins is unknown. They are closely related to gidA (glucose-inhibited division protein A), which appears to be present in all complete eubacterial genomes so far and in Saccharomyces cerevisiae..
Probab=49.92 E-value=11 Score=16.81 Aligned_cols=37 Identities=30% Similarity=0.420 Sum_probs=29.7
Q ss_pred EEEEEEECCCC-CEEEEEEC-CCCCCCCCHHHCCCCCCC
Q ss_conf 98997836388-23135327-897713022213712102
Q gi|254780751|r 44 LAKVTRVEPSL-QAAFVDYG-GNRHGFLPFLEIHPDYYQ 80 (723)
Q Consensus 44 ~G~V~~V~p~l-qAAFVdiG-~~k~gFL~~~ei~~~y~~ 80 (723)
-++|-|..|+| ||-||=+| ..||-|..-..+--.||+
T Consensus 298 QkrVfrLIPgLeNaefVR~GvMHRNTFInSp~lL~~~l~ 336 (444)
T TIGR00137 298 QKRVFRLIPGLENAEFVRLGVMHRNTFINSPKLLTASLQ 336 (444)
T ss_pred CCEEEECCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHC
T ss_conf 551444057843147885074311111276356557530
No 148
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=49.59 E-value=7.2 Score=18.20 Aligned_cols=61 Identities=20% Similarity=0.351 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCC
Q ss_conf 99999999998731036863896033479888899999999997312787289986048614898515666301121002
Q gi|254780751|r 403 NLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTK 482 (723)
Q Consensus 403 NleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~ 482 (723)
-+.||..+ =-|-+=+||-.|.|++-++.....+. +.||+||=+|-|+ ..+=+-
T Consensus 459 ~i~aa~d~-GsLL~DGlGDGI~i~~~~~~~~~~~~----------------------laF~ILQAaR~R~----sKTEYI 511 (606)
T PRK00694 459 AISIATEF-GALLLDGLGEAVLLDLPNIPLSDVRT----------------------IAFGTLQSAGVRL----VKTEYI 511 (606)
T ss_pred HHHHHHHH-HHHHHCCCCCEEEEECCCCCHHHHHH----------------------HHHHHHHHHCCCC----CCCCEE
T ss_conf 99999874-05664577655898479886778888----------------------8888888757443----356166
Q ss_pred CCCCCCCE
Q ss_conf 36754653
Q gi|254780751|r 483 VCTYCKGA 490 (723)
Q Consensus 483 ~c~~c~g~ 490 (723)
+||-|+=|
T Consensus 512 SCPSCGRT 519 (606)
T PRK00694 512 SCPGCGRT 519 (606)
T ss_pred ECCCCCCC
T ss_conf 58987752
No 149
>PRK06328 type III secretion system protein; Validated
Probab=48.67 E-value=17 Score=15.56 Aligned_cols=50 Identities=12% Similarity=0.119 Sum_probs=37.5
Q ss_pred CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE
Q ss_conf 6431013576999998730237999999998488799984787788633897
Q gi|254780751|r 515 TAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE 566 (723)
Q Consensus 515 ~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie 566 (723)
..+.++++|||+-..++...+......+ .....+.|.+|+.+..-.+.|+
T Consensus 130 ~~~~V~IrV~P~d~~~V~~~~~~L~~~~--~~~~~L~i~~D~~l~~GgCiIE 179 (223)
T PRK06328 130 QNKHIIIHVNPKDLAIVEQNRPELKKIV--EYADSLILSPKADVTPGGCIIE 179 (223)
T ss_pred HCCEEEEEECHHHHHHHHHHHHHHHHHC--CCCCCEEEEECCCCCCCCEEEE
T ss_conf 1881799988876999999899999746--7777626730898799986995
No 150
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=46.46 E-value=17 Score=15.54 Aligned_cols=35 Identities=17% Similarity=0.218 Sum_probs=31.0
Q ss_pred CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEE
Q ss_conf 01357699999873023799999999848879998
Q gi|254780751|r 519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVV 553 (723)
Q Consensus 519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~ 553 (723)
..+.+|+....||.+.+-..|.+|++.+++.|.|-
T Consensus 2 ~~i~vp~~~h~~iIG~~G~~i~~i~~~~~~~I~~P 36 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFP 36 (62)
T ss_pred CEEEECHHHCCCEECCCCCCHHHHHHHHCCEEEEC
T ss_conf 48998978819758899973999999859799958
No 151
>cd04731 HisF The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.
Probab=46.41 E-value=19 Score=15.33 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHCCCCCEEEEEE
Q ss_conf 9999999863002587169985
Q gi|254780751|r 230 KNLKEIARGLEVPAGMGVILRT 251 (723)
Q Consensus 230 ~~l~~~~~~~~~~~~~G~IiRT 251 (723)
..++++...+.+|-.+|==|||
T Consensus 61 ~~i~~i~~~~~~pi~vGGGIrs 82 (243)
T cd04731 61 DVVERVAEEVFIPLTVGGGIRS 82 (243)
T ss_pred HHHHHHHHHCCCCEEEEEEEEE
T ss_conf 9999999867986899850664
No 152
>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=46.18 E-value=19 Score=15.30 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=30.6
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCC
Q ss_conf 8787989978363882313532789771302221371
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHP 76 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~ 76 (723)
|..+.|-|.++ +-...||.+..+-.|.+++.|+.-
T Consensus 1 G~~v~gfV~n~--~~~~~wv~iSp~V~gri~~l~lSd 35 (73)
T cd05703 1 GQEVTGFVNNV--SKEFVWLTISPDVKGRIPLLDLSD 35 (73)
T ss_pred CCEEEEEEEEC--CCCEEEEEECCCEEEEEEHHHHCC
T ss_conf 98799999972--598499998888189997054268
No 153
>COG1278 CspC Cold shock proteins [Transcription]
Probab=46.14 E-value=19 Score=15.30 Aligned_cols=34 Identities=12% Similarity=0.161 Sum_probs=27.2
Q ss_pred EEEEEEECCCCCEEEEEECCC-CCCCCCHHHCCCC
Q ss_conf 989978363882313532789-7713022213712
Q gi|254780751|r 44 LAKVTRVEPSLQAAFVDYGGN-RHGFLPFLEIHPD 77 (723)
Q Consensus 44 ~G~V~~V~p~lqAAFVdiG~~-k~gFL~~~ei~~~ 77 (723)
-|.|+-.-+.....||-=..+ +.-|.|++.|...
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~ 37 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRA 37 (67)
T ss_pred CCEEEEEECCCCCEEECCCCCCCCEEEEEEEECCC
T ss_conf 61688850898633707899985779980125127
No 154
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=45.26 E-value=10 Score=17.05 Aligned_cols=49 Identities=16% Similarity=0.152 Sum_probs=28.3
Q ss_pred CCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 2278875124204688689999999998630025871699850455757999999999999999
Q gi|254780751|r 210 MPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWD 273 (723)
Q Consensus 210 ~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~ 273 (723)
+|+.+.+++-||+...-.+.+... +| | ...+|+.++|++-+..|...|.
T Consensus 7 ~~~~~~~~~~~~~~~~v~~t~yY~-iL---------G-----V~~~As~~EIKKAYRKLA~KyH 55 (422)
T PTZ00037 7 FPFDGMPGGHARRKREVDNEKLYE-VL---------N-----LSKDCTESEIKKAYRKLAIKHH 55 (422)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCHH-HH---------C-----CCCCCCHHHHHHHHHHHHHHHC
T ss_conf 887778776777888787676568-65---------9-----8999899999999999999849
No 155
>cd01890 LepA LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont. Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.
Probab=45.17 E-value=19 Score=15.20 Aligned_cols=66 Identities=18% Similarity=0.214 Sum_probs=44.7
Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf 06999823755444555114799999999999999873103686389603347988889999999999731278728998
Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG 457 (723)
Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~ 457 (723)
|+.+||.++|=. .+ .++..++.+.+++.-|++|-=||.. ..+..++.+.|++.+.-|... +.
T Consensus 94 allVVda~~Gv~------~q---------T~~~~~~a~~~~~p~ivviNKiD~~-~ad~~~v~~~i~~~~g~~~~~--~v 155 (179)
T cd01890 94 ALLLVDATQGVE------AQ---------TLANFYLALENNLEIIPVINKIDLP-SADPERVKQQIEDVLGLDPSE--AI 155 (179)
T ss_pred EEEEEECCCCCC------HH---------HHHHHHHHHHCCCCEEEEEECCCCC-CCCHHHHHHHHHHHHCCCCCC--EE
T ss_conf 789986477873------74---------8999999987699889998655567-789999999999986889767--48
Q ss_pred EECC
Q ss_conf 6048
Q gi|254780751|r 458 AISN 461 (723)
Q Consensus 458 ~it~ 461 (723)
++|.
T Consensus 156 ~vSA 159 (179)
T cd01890 156 LVSA 159 (179)
T ss_pred EEEC
T ss_conf 8437
No 156
>KOG2002 consensus
Probab=43.84 E-value=20 Score=15.06 Aligned_cols=15 Identities=27% Similarity=0.426 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999873
Q gi|254780751|r 401 QTNLEAAEEIARQLR 415 (723)
Q Consensus 401 ~tNleAA~EIaRQlR 415 (723)
+-|+..|..|.+|+|
T Consensus 659 kg~~~~A~dIFsqVr 673 (1018)
T KOG2002 659 KGRFSEARDIFSQVR 673 (1018)
T ss_pred CCCCHHHHHHHHHHH
T ss_conf 368138999999999
No 157
>PHA02114 hypothetical protein
Probab=43.70 E-value=20 Score=15.05 Aligned_cols=23 Identities=52% Similarity=0.651 Sum_probs=19.9
Q ss_pred CEEEEEEECCCCCHHHHHHHHHH
Q ss_conf 71699850455757999999999
Q gi|254780751|r 245 MGVILRTAGASRTKIEIKRDFEY 267 (723)
Q Consensus 245 ~G~IiRT~a~~~~~~~l~~d~~~ 267 (723)
|-+|+||+++|.+.+.|+..+..
T Consensus 1 mklilrta~~gkt~eaiksa~~a 23 (127)
T PHA02114 1 MKLILRTANAGKTQEAIKSAFEA 23 (127)
T ss_pred CEEEEEECCCCCCHHHHHHHHHH
T ss_conf 92576506786408999999987
No 158
>KOG0712 consensus
Probab=43.40 E-value=9.3 Score=17.43 Aligned_cols=33 Identities=21% Similarity=0.483 Sum_probs=22.0
Q ss_pred EEEECCCCCCCHHHHHCCCCCCCCCEEEEECCH
Q ss_conf 898515666301121002367546537860611
Q gi|254780751|r 465 LEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQS 497 (723)
Q Consensus 465 lEltRkR~r~sl~e~~~~~c~~c~g~g~~~~~~ 497 (723)
+....+++.|.+.+++...|.-|+|+|...+..
T Consensus 154 v~~~~~~~gPg~~qs~q~~C~~C~G~G~~~~~k 186 (337)
T KOG0712 154 VQTRTRQMGPGMVQSPQLVCDSCNGSGETISLK 186 (337)
T ss_pred CEEEEEECCCCCCCCCEEEECCCCCCCCCCCCC
T ss_conf 114776425653002245740678851031366
No 159
>TIGR01544 HAD-SF-IE HAD-superfamily (subfamily IE) hydrolase, TIGR01544; InterPro: IPR006434 This family is a small group of metazoan sequences with one sequence from Arabidopsis thaliana. The sequences from mouse are annotated as pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the human homolog. However, no such annotation can currently be found for this gene. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB..
Probab=42.91 E-value=20 Score=15.08 Aligned_cols=45 Identities=22% Similarity=0.349 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCE
Q ss_conf 999999999731278728998604861489851566630112100236754653
Q gi|254780751|r 437 RSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGA 490 (723)
Q Consensus 437 ~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~ 490 (723)
..|++.+++....-.+|+|| ||.|- +-|||++... .+.||.|+|-
T Consensus 12 t~Ve~ii~~~v~GGa~k~~i--isDFD-yTlsrf~~e~------G~r~pt~hgi 56 (287)
T TIGR01544 12 TEVEEIIRELVVGGAEKLQI--ISDFD-YTLSRFATED------GERVPTSHGI 56 (287)
T ss_pred HHHHHHHHHHEECCCCCEEE--EEECC-CCHHHHHHHC------CCCCCCCCCC
T ss_conf 89999987431068765689--85236-4122323115------8605520010
No 160
>PRK06669 fliH flagellar assembly protein H; Validated
Probab=42.90 E-value=21 Score=14.97 Aligned_cols=49 Identities=16% Similarity=0.206 Sum_probs=37.9
Q ss_pred CCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE
Q ss_conf 431013576999998730237999999998488799984787788633897
Q gi|254780751|r 516 AHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE 566 (723)
Q Consensus 516 ~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie 566 (723)
...|.++|||+=..|+..++......+.. ...|.|.+|+.+..-.+.|+
T Consensus 197 ~~~I~I~Vnp~Dye~v~e~k~el~~~l~~--~~~i~I~~D~~l~~GgciIe 245 (268)
T PRK06669 197 ATDITIRVNPEDYEYVKEQKDELISLLDS--EAHLKIYEDEAISKGGCIIE 245 (268)
T ss_pred CCEEEEEECHHHHHHHHHHHHHHHHHHCC--CCCEEEEECCCCCCCCEEEE
T ss_conf 78189998888899999848999987457--77769976788899987996
No 161
>TIGR00459 aspS_bact aspartyl-tRNA synthetase; InterPro: IPR004524 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module . This family represents aspartyl-tRNA synthetases from the bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=42.42 E-value=6.7 Score=18.43 Aligned_cols=56 Identities=14% Similarity=0.159 Sum_probs=24.6
Q ss_pred CCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHH-HHHHHHHH
Q ss_conf 7887512420468868999999999863002587169985045575799999999999-99998776
Q gi|254780751|r 212 NTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLM-RLWDNVRE 277 (723)
Q Consensus 212 ~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~-~~w~~i~~ 277 (723)
+..+..-|.|.--|++-|....=....+. -.|.| .+.+++..-++.|+ ..|..+..
T Consensus 222 G~drYyQIArCFRDEDLRADRQPEFTQiD--~E~SF--------~~~~~vm~l~E~l~~~vf~~v~~ 278 (653)
T TIGR00459 222 GVDRYYQIARCFRDEDLRADRQPEFTQID--MEMSF--------MTQEDVMDLIEKLVSGVFKEVKG 278 (653)
T ss_pred CCCCCEEEEEEECCCCCCCCCCCCCCHHH--HHHHC--------CCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 55531357889766256665778732442--63112--------89356899999999999999707
No 162
>pfam07013 DUF1314 Protein of unknown function (DUF1314). This family consists of several Alphaherpesvirus proteins of around 200 residues in length. The function of this family is unknown.
Probab=42.17 E-value=21 Score=14.96 Aligned_cols=37 Identities=27% Similarity=0.296 Sum_probs=27.4
Q ss_pred HHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCC
Q ss_conf 99998422214367864998328806999823755444555
Q gi|254780751|r 354 QLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHC 394 (723)
Q Consensus 354 ~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~ 394 (723)
-++.+-.+.|.||.||++.|-.+-.- +|+|+|+..+.
T Consensus 4 Ll~~L~GR~vDLPgG~el~I~~~~g~----~~~~~f~~~g~ 40 (177)
T pfam07013 4 LLRSLRGRTVDLPGGGELFIFCNAGR----PVTGKFRRPGS 40 (177)
T ss_pred HHHHHCCCEEECCCCCEEEEECCCCC----CEEEEECCCCC
T ss_conf 65344386164699986998558897----12788716986
No 163
>pfam02691 VacA Vacuolating cyotoxin. This family consists of Vacuolating cyotoxin proteins form Proteobacteria. These proteins are an important virulence determinate in H. pylori and induce cytoplasmic vacuolation in a variety of mammalian cell lines.
Probab=41.86 E-value=21 Score=14.90 Aligned_cols=32 Identities=16% Similarity=0.133 Sum_probs=20.8
Q ss_pred HHHHHHCCCCCCCCCCEEEEECC--------CEEEEEEEC
Q ss_conf 99998422214367864998328--------806999823
Q gi|254780751|r 354 QLDSLHQTEVTLPSRGYVIINQT--------EALVSIDVN 385 (723)
Q Consensus 354 ~i~~~~~~~V~L~sGG~lvIe~T--------EALt~IDVN 385 (723)
--..+|+--|..+||--|||+.- .|.-+-||-
T Consensus 578 GtrsiysGGVkFK~GeKLVIde~Y~aPWNYFdarni~~VE 617 (1002)
T pfam02691 578 GTRPAFSGGVKFKGGEKLVIDEFYHAPWNYFDARNIKDVE 617 (1002)
T ss_pred CCCCCCCCCEEECCCCEEEEEEHHCCCCHHCCCCCCCEEE
T ss_conf 7533301760653786577600111861010335652257
No 164
>cd00765 Pyrophosphate_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include pyrophosphate-dependent phosphofructokinases. These are found in bacteria as well as plants. These may be dimeric nonallosteric enzymes as in bacteria or allosteric heterotetramers as in plants.
Probab=40.90 E-value=22 Score=14.76 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=23.5
Q ss_pred EEEE-CCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHH
Q ss_conf 2420-4688689999999998630025871699850455757999999
Q gi|254780751|r 218 TISR-KITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRD 264 (723)
Q Consensus 218 ~iSr-ki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d 264 (723)
|.+| ||..++....-.+....+... |++|=-....-+...+..+
T Consensus 143 ~sgr~ki~t~eq~~~~~~~~~~l~Ld---gLVIiGGddSnTnaa~LAE 187 (550)
T cd00765 143 CSGRTKIETEDQFKQAEETAKKLDLD---ALVVIGGDDSNTNAALLAE 187 (550)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCC---EEEEECCCCCHHHHHHHHH
T ss_conf 68856248999999999999985998---7999689873487999999
No 165
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=40.87 E-value=22 Score=14.76 Aligned_cols=44 Identities=16% Similarity=0.117 Sum_probs=36.7
Q ss_pred CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCC
Q ss_conf 01357699999873023799999999848879998478778863
Q gi|254780751|r 519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKL 562 (723)
Q Consensus 519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~ 562 (723)
+.+.+|...+..+.+..-..+.+|.+.+|.+|.|..++....++
T Consensus 2 ~rilvP~~~vG~vIGk~G~~I~~i~~~sga~I~i~~~~~~~~~e 45 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTE 45 (65)
T ss_pred EEEEEEHHHEEEEECCCCHHHHHHHHHHCCEEEECCCCCCCCCC
T ss_conf 89998746722899799878999999849889999889999994
No 166
>PRK02145 consensus
Probab=40.76 E-value=23 Score=14.75 Aligned_cols=14 Identities=14% Similarity=0.283 Sum_probs=5.1
Q ss_pred HHHHHHHCCCCEEE
Q ss_conf 99873103686389
Q gi|254780751|r 411 ARQLRLRDLAGLIV 424 (723)
Q Consensus 411 aRQlRLRnlgGiIv 424 (723)
+.++-=.++|.|++
T Consensus 163 ~~~~~~~G~geil~ 176 (257)
T PRK02145 163 ARKMAELGAGEILL 176 (257)
T ss_pred HHHHHHCCCCEEEE
T ss_conf 56887618786899
No 167
>pfam06635 NolV Nodulation protein NolV. This family consists of several nodulation protein NolV sequences from different Rhizobium species. The function of this family is unclear.
Probab=40.73 E-value=23 Score=14.74 Aligned_cols=49 Identities=8% Similarity=0.124 Sum_probs=33.9
Q ss_pred CCCCCCCCCCCHHHHHHHHCCHHHHHHHHHH-HHCCEEEEEECCCCCCCCEEEE
Q ss_conf 3643101357699999873023799999999-8488799984787788633897
Q gi|254780751|r 514 YTAHNIIVHTHSDVVLYLLNQKRATIVEYEA-RFGVSINVVIGIELADKLFYIE 566 (723)
Q Consensus 514 ~~~~~i~v~~~~~va~~lln~kr~~l~~lE~-~~~~~I~i~~d~~l~~~~f~Ie 566 (723)
.+.++++++|||.-+..|... +.++.. .-.-+|.|.+||.|....+..+
T Consensus 128 ~~~keV~LhV~P~~ae~la~~----~ad~~~~~~~~~l~I~~Dp~L~~~~cvLe 177 (207)
T pfam06635 128 YKGAEVCLHVSPLKADLLARE----FADWDGLDGRPKLRIEADPALSADQCVLW 177 (207)
T ss_pred HCCCEEEEEECHHHHHHHHHH----HHCCCCCCCCCEEEEEECCCCCCCCEEEE
T ss_conf 338728999888889999999----73310447886068721876687762664
No 168
>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]
Probab=39.72 E-value=4.9 Score=19.36 Aligned_cols=31 Identities=16% Similarity=0.164 Sum_probs=14.1
Q ss_pred CCCCCCCCCCEEEEECCCEEE-EEEECCCCCC
Q ss_conf 222143678649983288069-9982375544
Q gi|254780751|r 360 QTEVTLPSRGYVIINQTEALV-SIDVNSGRST 390 (723)
Q Consensus 360 ~~~V~L~sGG~lvIe~TEALt-~IDVNSG~~~ 390 (723)
.++.||+.|+--|--.-+++- .+|||+....
T Consensus 330 Gr~Y~lK~~t~~v~a~V~~i~~~ldvntl~~~ 361 (431)
T COG2895 330 GRSYDLKIATRTVRARVEEIKHQLDVNTLEQE 361 (431)
T ss_pred CCEEEEEECCEEEEEEEEEEEEEEECCCCCCC
T ss_conf 84688884124778986112789843500100
No 169
>pfam04025 DUF370 Domain of unknown function (DUF370). Bacterial domain of unknown function.
Probab=39.53 E-value=24 Score=14.62 Aligned_cols=27 Identities=30% Similarity=0.316 Sum_probs=18.4
Q ss_pred EEEEECCCCCEEEEEEE-ECCEEEEEEE
Q ss_conf 26896528960799999-8998999996
Q gi|254780751|r 4 KMLIDASHVEETRVVVL-RDNRVEELDF 30 (723)
Q Consensus 4 ~~lI~~~~~~e~Rvav~-e~g~l~e~~~ 30 (723)
-.|||+|++..||.+++ +.|.++=.-+
T Consensus 37 g~lIDaT~GrkTRavii~DS~HviLSai 64 (73)
T pfam04025 37 GKLIDATYGRKTRAVIITDSGHVILSAL 64 (73)
T ss_pred CCEEECCCCCEEEEEEEECCCCEEEEEC
T ss_conf 9089865696067999970893899705
No 170
>pfam04606 Ogr_Delta Ogr/Delta-like zinc finger. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This family also includes zinc fingers in recombinase proteins.
Probab=39.37 E-value=15 Score=15.89 Aligned_cols=19 Identities=21% Similarity=0.497 Sum_probs=15.6
Q ss_pred CCCCCCCEEEEECCHHHHH
Q ss_conf 3675465378606114689
Q gi|254780751|r 483 VCTYCKGAGYIRSQSSVAL 501 (723)
Q Consensus 483 ~c~~c~g~g~~~~~~~~~~ 501 (723)
.||+|+..+++++...+..
T Consensus 1 ~CP~Cg~~a~irts~~~s~ 19 (47)
T pfam04606 1 RCPHCGAKARIRTSRRLSA 19 (47)
T ss_pred CCCCCCCCEEEEEHHHCCH
T ss_conf 9598898389968356297
No 171
>TIGR02836 spore_IV_A stage IV sporulation protein A; InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. .
Probab=39.32 E-value=13 Score=16.40 Aligned_cols=37 Identities=24% Similarity=0.571 Sum_probs=22.9
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCC-CHHHC
Q ss_conf 9996073346042878798997836388231353278977130-22213
Q gi|254780751|r 27 ELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFL-PFLEI 74 (723)
Q Consensus 27 e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL-~~~ei 74 (723)
.||+=+.=....-||||+|.|=-|- .||.-|. -|-|+
T Consensus 3 ~~DiykDIAeRT~GdIYiGvVGpVR-----------TGKSTfIKkFMeL 40 (492)
T TIGR02836 3 KVDIYKDIAERTQGDIYIGVVGPVR-----------TGKSTFIKKFMEL 40 (492)
T ss_pred CCCCEEEHHHCCCCCEEEEEECCCC-----------CCCCCHHHHEEHE
T ss_conf 8740210230168967898662742-----------7852111110010
No 172
>TIGR02533 type_II_gspE general secretory pathway protein E; InterPro: IPR013369 GspE, the E protein of the type II secretion system, is also referred to as the main terminal branch of the general secretion pathway. ; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=39.06 E-value=8 Score=17.86 Aligned_cols=80 Identities=26% Similarity=0.419 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHH-----HHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCC
Q ss_conf 99999999999998731036863896033479888-----8999999999973127872899860486148985156663
Q gi|254780751|r 400 LQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKK-----NNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRS 474 (723)
Q Consensus 400 l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~-----~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~ 474 (723)
|+||= ||--+. ||+|+| |=+| |-... .|+.| ++|...||.-...+. ..+-++-++++-...
T Consensus 346 LHTND-AAgAvt---RL~DMG---vEPF--L~aSsl~GVLAQRLV-RrlCp~Cke~y~a~~----~~~~~~G~~~~~~~~ 411 (495)
T TIGR02533 346 LHTND-AAGAVT---RLIDMG---VEPF--LLASSLLGVLAQRLV-RRLCPHCKEPYEATD----EELALLGISKKEPKK 411 (495)
T ss_pred HHHHH-HHHHHH---HHHHCC---CCHH--HHHHHHHHHHHHHHH-HHCCCCCCCCCCCCH----HHHHHCCCCHHHHCC
T ss_conf 55401-544665---553258---6404--899999999986334-331514688899897----999854884021035
Q ss_pred C---HHHHHCCCCCCCCCEEEE
Q ss_conf 0---112100236754653786
Q gi|254780751|r 475 S---VLESTTKVCTYCKGAGYI 493 (723)
Q Consensus 475 s---l~e~~~~~c~~c~g~g~~ 493 (723)
. ..=+=-.-||+|.++|+-
T Consensus 412 ~nGv~~lyr~~GC~~C~~~GY~ 433 (495)
T TIGR02533 412 DNGVIILYRPVGCPACNHTGYR 433 (495)
T ss_pred CCCEEEEECCCCCHHHCCCCCC
T ss_conf 7764899778764212788883
No 173
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=38.83 E-value=13 Score=16.41 Aligned_cols=78 Identities=14% Similarity=0.204 Sum_probs=39.2
Q ss_pred CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHC----CCCEEEEEECCCCEEEEECCCCCCCHHHHH--CCCCCCCCCEEE
Q ss_conf 68638960334798888999999999973127----872899860486148985156663011210--023675465378
Q gi|254780751|r 419 LAGLIVVDFIDMEEKKNNRSVEKKLKESLKKD----RARVQVGAISNFGLLEMSRQRIRSSVLEST--TKVCTYCKGAGY 492 (723)
Q Consensus 419 lgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D----~~~~~v~~it~lGLlEltRkR~r~sl~e~~--~~~c~~c~g~g~ 492 (723)
=.|.+.+-|-|-......++- .+.|.+..+ ....-...-...-...+|=.-+-|-|.... +-.||.|.|.|.
T Consensus 229 ~~G~~~v~~~~~~~~~~~~~~--~~SE~~acp~~L~~~~~~f~~~~~c~~~~~s~~eLePRlFSFNSP~GaCp~C~GLG~ 306 (956)
T TIGR00630 229 SEGLLEVEIEDDESPAEGKEE--LYSEKFACPARLEKSELLFSKNAACPECGFSLEELEPRLFSFNSPYGACPECSGLGI 306 (956)
T ss_pred CCCEEEEEECCCCCCCCCHHH--HHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf 587489997367765410222--220210585122246666555337420462210036210332675777787455521
Q ss_pred EECCHH
Q ss_conf 606114
Q gi|254780751|r 493 IRSQSS 498 (723)
Q Consensus 493 ~~~~~~ 498 (723)
-.+.+.
T Consensus 307 ~~~~D~ 312 (956)
T TIGR00630 307 KLEFDP 312 (956)
T ss_pred EEEECH
T ss_conf 575061
No 174
>TIGR00340 zpr1_rel zinc finger protein ZPR1 homolog; InterPro: IPR004470 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates , , , , . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents ZPR1-type zinc finger domains. ZPR1 was shown experimentally to bind approximately two moles of zinc, and has two copies of a domain homologous to this protein, each containing a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by this family by analogy may be suggested to play a role in signal transduction as proven for other Z-finger binding proteins. Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) . ZPR1 interacts with complexes formed by SMN , and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding.
Probab=38.34 E-value=11 Score=16.94 Aligned_cols=14 Identities=21% Similarity=0.733 Sum_probs=6.3
Q ss_pred CCCCCCEEEEECCH
Q ss_conf 67546537860611
Q gi|254780751|r 484 CTYCKGAGYIRSQS 497 (723)
Q Consensus 484 c~~c~g~g~~~~~~ 497 (723)
||.|+|.+..+.+.
T Consensus 1 CPVCGg~~~L~Av~ 14 (168)
T TIGR00340 1 CPVCGGKRTLKAVT 14 (168)
T ss_pred CCCCCCCCEEEEEE
T ss_conf 98638744157665
No 175
>PRK06032 fliH flagellar assembly protein H; Validated
Probab=38.03 E-value=25 Score=14.46 Aligned_cols=63 Identities=17% Similarity=0.166 Sum_probs=41.9
Q ss_pred HHHHHHHHHHCC-CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEEE
Q ss_conf 887889997303-64310135769999987302379999999984887999847877886338971
Q gi|254780751|r 503 ILRSVEEYLLQY-TAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEK 567 (723)
Q Consensus 503 ~~r~i~~~~~~~-~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ier 567 (723)
+...+++....- ....|.|.+++..+.-+...-.. ..-+.-|...|.|.+||.|..-+|+|+=
T Consensus 112 v~a~v~e~l~~l~~~P~LvIrV~~~l~e~l~~~le~--~a~~~Gf~Grl~i~~Dp~l~~GDcrieW 175 (208)
T PRK06032 112 ITALVRDCLRHLVATPHLVVRVNDALVEAARERLER--LARESGFEGRLVVLADPDIAPGDCRIEW 175 (208)
T ss_pred HHHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHH--HHHHCCCCCEEEEEECCCCCCCCEEEEE
T ss_conf 999999999987449728999787657999999999--9996698823898308998988658886
No 176
>pfam00013 KH_1 KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;
Probab=37.95 E-value=16 Score=15.75 Aligned_cols=34 Identities=18% Similarity=0.206 Sum_probs=31.2
Q ss_pred CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEE
Q ss_conf 0135769999987302379999999984887999
Q gi|254780751|r 519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINV 552 (723)
Q Consensus 519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i 552 (723)
..+.+|+....++.+.+-..+..|++.+++.|.|
T Consensus 2 ~~v~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i 35 (57)
T pfam00013 2 EEILIPSSLVGRIIGKGGSNIKEIREETGAKIRI 35 (57)
T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEE
T ss_conf 8999875542068998964769999973999996
No 177
>pfam07295 DUF1451 Protein of unknown function (DUF1451). This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=37.86 E-value=15 Score=16.05 Aligned_cols=44 Identities=18% Similarity=0.268 Sum_probs=29.5
Q ss_pred CEEEEEECCCCEEEEECCCCCCCHHHH-HCCCCCCCCCEEEEECC
Q ss_conf 289986048614898515666301121-00236754653786061
Q gi|254780751|r 453 RVQVGAISNFGLLEMSRQRIRSSVLES-TTKVCTYCKGAGYIRSQ 496 (723)
Q Consensus 453 ~~~v~~it~lGLlEltRkR~r~sl~e~-~~~~c~~c~g~g~~~~~ 496 (723)
.-+.+.|..+|-|-=..=--...+... ...+||.|+|+.+.|-+
T Consensus 103 ~Y~sGEvvg~G~LvC~~Cg~~~~~~~p~~ip~Cp~Cg~~~F~R~~ 147 (148)
T pfam07295 103 VYQSGEIVGLGTLVCENCGHMLTFYHPSVIPPCPKCGHTEFTRQP 147 (148)
T ss_pred EEECCCEEECCEEEECCCCCEEEEECCCCCCCCCCCCCCEEECCC
T ss_conf 242460541645772368987887468768898779998253288
No 178
>PRK00964 tetrahydromethanopterin S-methyltransferase subunit A; Provisional
Probab=37.63 E-value=24 Score=14.54 Aligned_cols=56 Identities=25% Similarity=0.336 Sum_probs=38.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 3755444555114799999999999999873103686389603347988889999999999731278
Q gi|254780751|r 385 NSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDR 451 (723)
Q Consensus 385 NSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~ 451 (723)
+.|+-+|....--..-.++.+|.+..-+|+- +||.||+ +|-..+..+.++|..+|+
T Consensus 101 ~~grIiGa~GaiPfieNi~~~av~rFq~qVe--------~vdlI~~---eD~~~I~a~I~ec~~kdP 156 (243)
T PRK00964 101 DGGRIIGAKGAIPFIENLPDEAVERFQQQVE--------IVDLIDT---EDPGAIAAAIKECIAKDP 156 (243)
T ss_pred CCCCEECCCCCCCHHHHCCHHHHHHHHHHEE--------EEEEECC---CCHHHHHHHHHHHHCCCC
T ss_conf 8997825888863454099899999987457--------8863167---787999999999853899
No 179
>TIGR02405 trehalos_R_Ecol trehalose operon repressor; InterPro: IPR012771 Trehalose is a non-reducing disaccharide which can be used as both a carbon source and an osmoprotectant in bacteria. Trehalose uptake into the cytoplasm occurs via a trehalose-specific phosphotransferase system which phosphorylates trehalase to trehalose-6-phosphate (Tre6P) during transport into the cytoplasm, and a hydrolase which hydrolyses Tre6P to glucose and glucose-6-phophate. This entry represents LacI-type TreR, a transcriptional repressor of trehalose uptake found mainly within the gamma-proteobacteria. It does not include the GntR-type TreR's such as those found in Bacillus species. It is capable of binding both the inducer Tre6P and trehalose. Binding of trehalose does not affect the repressor's affinity for its DNA binding site, while binding Tre6P substantially reduces its affinity. The repression activity of TreR is therefore regulated by the ratio of trehalose to Tre6P within the cell . The protein is composed of two domains, an N-terminal DNA-binding helix-turn-helix domain, and a C-terminal effector-binding domain which is homologous to that of LacI. The effector-binding domain is composed of two subdomains, both of which form an alpha-beta-alpha sandwhich, with the effector binding site located at the interface of these subdomains . Tre6P and trehalose bind competitively to this site, with the affinty for trehalose substantially lower than that for Tre6P.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0005991 trehalose metabolic process, 0016481 negative regulation of transcription.
Probab=36.68 E-value=8.2 Score=17.81 Aligned_cols=90 Identities=16% Similarity=0.290 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHH---HHHHCCCCEEEEEECCCCEEEEECCCC-CCCHHHHHCC
Q ss_conf 999999873103686389603347988889999999999---731278728998604861489851566-6301121002
Q gi|254780751|r 407 AEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKE---SLKKDRARVQVGAISNFGLLEMSRQRI-RSSVLESTTK 482 (723)
Q Consensus 407 A~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~---~l~~D~~~~~v~~it~lGLlEltRkR~-r~sl~e~~~~ 482 (723)
..|=-+||.+||+=|+|+-=|=-+.. +++..++. .|.+|..+..=++.=..|.++|--+++ +++-.+.++-
T Consensus 104 ~~EHL~vL~~Rn~DGviLFGFtG~~e-----e~l~~w~~k~Vv~Ard~~gfsSVcYDd~Gai~llM~~ly~qG~r~ISfl 178 (311)
T TIGR02405 104 VNEHLSVLKKRNVDGVILFGFTGLDE-----EILESWRDKLVVLARDAKGFSSVCYDDIGAIKLLMAELYQQGHREISFL 178 (311)
T ss_pred HHHHHHHHHHCCCCEEEECCCCCCCH-----HHHHHHCCCEEEEEEECCCEEEEEECHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 99999886550678479847657767-----8864420675899860675134521646799999999976277302251
Q ss_pred CCCCCCC-EEEEECCHHHHH
Q ss_conf 3675465-378606114689
Q gi|254780751|r 483 VCTYCKG-AGYIRSQSSVAL 501 (723)
Q Consensus 483 ~c~~c~g-~g~~~~~~~~~~ 501 (723)
-.|+|+- ||..|+.-.+++
T Consensus 179 GVd~sD~TTG~~Rh~aYla~ 198 (311)
T TIGR02405 179 GVDDSDKTTGLLRHEAYLAY 198 (311)
T ss_pred CCCCCCCCCCHHHHHHHHHH
T ss_conf 26988754241478999999
No 180
>pfam05262 Borrelia_P83 Borrelia P83/100 protein. This family consists of several Borrelia P83/P100 antigen proteins.
Probab=36.67 E-value=11 Score=16.84 Aligned_cols=11 Identities=36% Similarity=0.860 Sum_probs=7.8
Q ss_pred CCCEEEEEECC
Q ss_conf 88231353278
Q gi|254780751|r 53 SLQAAFVDYGG 63 (723)
Q Consensus 53 ~lqAAFVdiG~ 63 (723)
+|.--||+|-+
T Consensus 8 N~~lEFvNy~G 18 (489)
T pfam05262 8 NMTLEFVNYKG 18 (489)
T ss_pred CCCEEEEECCC
T ss_conf 38626874258
No 181
>PRK12366 replication factor A; Reviewed
Probab=35.79 E-value=12 Score=16.72 Aligned_cols=54 Identities=9% Similarity=0.018 Sum_probs=42.9
Q ss_pred HCCCCCCCCCCCCHHHHHHHHCCHHHHHHH------HHHHHCCEEEEEECCCCCCCCEEE
Q ss_conf 303643101357699999873023799999------999848879998478778863389
Q gi|254780751|r 512 LQYTAHNIIVHTHSDVVLYLLNQKRATIVE------YEARFGVSINVVIGIELADKLFYI 565 (723)
Q Consensus 512 ~~~~~~~i~v~~~~~va~~lln~kr~~l~~------lE~~~~~~I~i~~d~~l~~~~f~I 565 (723)
....++.+.+.+--.-|.-|++-.++.|.. |+.-.|..+.|.+++++...++.+
T Consensus 570 LDDgTg~i~~~~y~~~vEeLl~m~~eElk~~~~~~~l~~~lG~e~~~~gn~~~~n~dl~~ 629 (649)
T PRK12366 570 LDDGTGVINCRFYGNNVEKLTEMSKEELKNLNLDARLDDILGKEVVFYGNPSFRNDDLEF 629 (649)
T ss_pred EECCCCEEEEEEECCCHHHHHCCCHHHHHHCCHHHHHHHHCCCEEEEEECCCCCCCCEEE
T ss_conf 977997599999336689885779899751212333566428559999524446751388
No 182
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=35.73 E-value=9.2 Score=17.46 Aligned_cols=62 Identities=19% Similarity=0.178 Sum_probs=27.4
Q ss_pred CCCCCCCCCCCCEEECCCCCC--CCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHH
Q ss_conf 101233457652344227887--5124204688689999999998630025871699850455757999
Q gi|254780751|r 195 AVTTYLSLAGRYSVLMPNTSK--GETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEI 261 (723)
Q Consensus 195 ~lT~~isl~Gry~Vl~P~~~~--~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l 261 (723)
++++..+.-|.++|+-=-... ...+..=--.++....++.++. ...|+|+=|..-|..+...
T Consensus 33 Rvst~p~~~Ge~vvlRll~~~~~~~~L~~LG~~~~~~~~l~~~~~-----~~~GlilitGptGSGKtTt 96 (264)
T cd01129 33 RVSTLPTIYGESVVLRILDKKNQILDLEKLGLKPENLEIFRKLLE-----KPHGIILVTGPTGSGKTTT 96 (264)
T ss_pred EEEECCCCCCCEEEEEEECCCCCCCCHHHHCCCHHHHHHHHHHHH-----CCCCEEEEECCCCCCHHHH
T ss_conf 999475799976999975776665798795799999999999970-----8998899978999977999
No 183
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase family protein; InterPro: IPR005720 Dihydroorotate dehydrogenase (1.3.3.1 from EC) (DHOdehase) catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria . This describes dihydroorotate dehydrogenases subfamily 1 that includes a number of uncharacterised proteins and a domain of dihydropyrimidine dehydrogenase.; GO: 0004158 dihydroorotate oxidase activity, 0006207 'de novo' pyrimidine base biosynthetic process, 0005737 cytoplasm.
Probab=35.36 E-value=27 Score=14.18 Aligned_cols=46 Identities=15% Similarity=0.240 Sum_probs=20.8
Q ss_pred CCCCCCCC-EEEEECCHH-HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 23675465-378606114-689988788999730364310135769999987
Q gi|254780751|r 482 KVCTYCKG-AGYIRSQSS-VALSILRSVEEYLLQYTAHNIIVHTHSDVVLYL 531 (723)
Q Consensus 482 ~~c~~c~g-~g~~~~~~~-~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~l 531 (723)
-+|||-.| .|.-.-.+. +++.+...+ ...-...+.+++.|.|.+++
T Consensus 129 ~SCPhvK~G~G~~iG~dP~l~~~vv~av----K~~~d~Pv~aKLsPNV~Di~ 176 (308)
T TIGR01037 129 VSCPHVKGGGGIEIGQDPELSADVVKAV----KDKVDVPVFAKLSPNVTDIT 176 (308)
T ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHH----HCCCCCCEEEECCCCHHHHH
T ss_conf 7774434234655477877999999998----30007865786486566899
No 184
>cd04702 ASRGL1_like ASRGL1_like domains, a subfamily of the L-Asparaginase type 2-like enzymes. The wider family includes Glycosylasparaginase, Taspase 1 and L-Asparaginase type 2 enzymes. The proenzymes undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue. ASRGL1, or asparaginase-like 1, has been cloned from mammalian testis cDNA libraries. It has been identified as a sperm antigen that may induce the production of autoantibodies following obstruction of the male reproductive tract, e.g. vasectomy.
Probab=35.28 E-value=27 Score=14.17 Aligned_cols=17 Identities=18% Similarity=0.323 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 4799999999999999873
Q gi|254780751|r 397 DTALQTNLEAAEEIARQLR 415 (723)
Q Consensus 397 ~t~l~tNleAA~EIaRQlR 415 (723)
|.+++.++ |.+|+.+|+
T Consensus 186 E~iir~~~--A~~v~~~~~ 202 (261)
T cd04702 186 ESIMKVVL--ARLILDHME 202 (261)
T ss_pred HHHHHHHH--HHHHHHHHH
T ss_conf 99998869--999999998
No 185
>pfam00567 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. copies in the Drosophila Tudor protein.
Probab=34.76 E-value=28 Score=14.12 Aligned_cols=24 Identities=33% Similarity=0.605 Sum_probs=9.2
Q ss_pred CCEEEEEEEEECCC--CCEEEEEECC
Q ss_conf 87879899783638--8231353278
Q gi|254780751|r 40 GNIYLAKVTRVEPS--LQAAFVDYGG 63 (723)
Q Consensus 40 GnIY~G~V~~V~p~--lqAAFVdiG~ 63 (723)
|.-|.|+|..+.++ ..--|||||.
T Consensus 63 ~~wyRa~I~~~~~~~~~~V~fvDyG~ 88 (118)
T pfam00567 63 GKWYRAKILVSLDDGLVEVFFIDYGN 88 (118)
T ss_pred CCEEEEEEEEECCCCEEEEEEEECCC
T ss_conf 94999999996699989999994697
No 186
>cd01883 EF1_alpha Eukaryotic elongation factor 1 (EF1) alpha subfamily. EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis. EF-Tu can have no such role in bacteria. In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene. This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in
Probab=34.07 E-value=28 Score=14.04 Aligned_cols=94 Identities=23% Similarity=0.244 Sum_probs=55.1
Q ss_pred CEEEEEEECCCCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHCCCCEEE-EECCCCC----CHHHHHHHHHHHHHHHHHC
Q ss_conf 8069998237554445551-14799999999999999873103686389-6033479----8888999999999973127
Q gi|254780751|r 377 EALVSIDVNSGRSTREHCI-EDTALQTNLEAAEEIARQLRLRDLAGLIV-VDFIDME----EKKNNRSVEKKLKESLKKD 450 (723)
Q Consensus 377 EALt~IDVNSG~~~~~~~~-e~t~l~tNleAA~EIaRQlRLRnlgGiIv-IDFIdM~----~~~~~~~v~~~l~~~l~~D 450 (723)
=|+.+||.+.|-|..+-.. .+ .+|-++-+++-++.-||| |-=+|.. +++-...+.+.++..|++-
T Consensus 103 ~ailvvda~~g~~e~g~~~~~Q---------TreH~~l~~~lGik~iIVavNKMD~v~~~y~~~rf~~i~~~~~~~l~~~ 173 (219)
T cd01883 103 VAVLVVDARKGEFEAGFEKGGQ---------TREHALLARTLGVKQLIVAVNKMDDVTVNWSEERYDEIKKELSPFLKKV 173 (219)
T ss_pred EEEEEEECCCCCCCCCCCCCCH---------HHHHHHHHHHCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 6899998576751036677765---------9999999998499748999987536886525999999999999999982
Q ss_pred ---CCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCC
Q ss_conf ---872899860486148985156663011210023675465
Q gi|254780751|r 451 ---RARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKG 489 (723)
Q Consensus 451 ---~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g 489 (723)
...+.+.++|.|.= .++.+ -++.||...|
T Consensus 174 g~~~~~~~~IPiSa~~G---------dNi~~-~s~~m~WY~G 205 (219)
T cd01883 174 GYNPKDVPFIPISGLTG---------DNLIE-KSENMPWYKG 205 (219)
T ss_pred CCCCCCCEEEEEECCCC---------CCCCC-CCCCCCCCCC
T ss_conf 99956615999336766---------30466-7889989878
No 187
>COG2052 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.98 E-value=29 Score=14.03 Aligned_cols=19 Identities=47% Similarity=0.635 Sum_probs=9.3
Q ss_pred EEEEECCCCCEEEEEEEEC
Q ss_conf 2689652896079999989
Q gi|254780751|r 4 KMLIDASHVEETRVVVLRD 22 (723)
Q Consensus 4 ~~lI~~~~~~e~Rvav~e~ 22 (723)
-||||||++.-||..++-|
T Consensus 41 ~~LIDATYGRrTRavii~D 59 (89)
T COG2052 41 GMLIDATYGRRTRAVIITD 59 (89)
T ss_pred CCEEECCCCCEEEEEEEEC
T ss_conf 8277702485255799963
No 188
>PRK01172 ski2-like helicase; Provisional
Probab=33.78 E-value=29 Score=14.01 Aligned_cols=13 Identities=15% Similarity=0.181 Sum_probs=5.3
Q ss_pred CCCEEEECCCCHH
Q ss_conf 7512420468868
Q gi|254780751|r 215 KGETISRKITNPV 227 (723)
Q Consensus 215 ~~~~iSrki~~~~ 227 (723)
+.+|.|--|.|.+
T Consensus 171 qiIgLSATi~N~~ 183 (674)
T PRK01172 171 RILALSATVSNAN 183 (674)
T ss_pred EEEEECCCCCCHH
T ss_conf 7997157868999
No 189
>pfam00009 GTP_EFTU Elongation factor Tu GTP binding domain. This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.
Probab=33.35 E-value=29 Score=13.97 Aligned_cols=70 Identities=13% Similarity=0.154 Sum_probs=44.5
Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHH----CCCC
Q ss_conf 069998237554445551147999999999999998731036863896033479888899999999997312----7872
Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKK----DRAR 453 (723)
Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~----D~~~ 453 (723)
|+.+||.+.|-.. . .+++.++++..++.-||+|-=||+-+.++..++.+.+.+.+-. ....
T Consensus 94 ~vlVvda~~G~~~------q---------t~~~~~~~~~~~~p~iv~vNKiD~v~~~~~~~~~~e~~~~ll~~~~~~~~~ 158 (185)
T pfam00009 94 AILVVDAVEGVMP------Q---------TREHLLLAKQLGVPIIVFINKMDRVDDAELDEVVEEISRELLEKYGFGGET 158 (185)
T ss_pred CEEEEECCCCCCC------C---------CHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 4299986768532------3---------099999999828987999977327776769999999999988873248998
Q ss_pred EEEEEECCC
Q ss_conf 899860486
Q gi|254780751|r 454 VQVGAISNF 462 (723)
Q Consensus 454 ~~v~~it~l 462 (723)
+.|+++|.+
T Consensus 159 ~pivpiSA~ 167 (185)
T pfam00009 159 IPVIPGSAL 167 (185)
T ss_pred CEEEEEECC
T ss_conf 869996789
No 190
>pfam01153 Glypican Glypican.
Probab=33.18 E-value=21 Score=14.94 Aligned_cols=26 Identities=19% Similarity=0.524 Sum_probs=19.0
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf 02367546537860611468998878
Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRS 506 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~ 506 (723)
..-||||.|...++--..+++.++|-
T Consensus 247 M~YCp~C~G~~~~kPC~gyC~NVmrG 272 (559)
T pfam01153 247 MWYCPHCRGLSEVKPCRGYCLNVMRG 272 (559)
T ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 23585345878788836778998877
No 191
>PRK10476 multidrug resistance protein MdtN; Provisional
Probab=33.11 E-value=29 Score=13.94 Aligned_cols=11 Identities=27% Similarity=0.220 Sum_probs=5.1
Q ss_pred CCEEEEEECCC
Q ss_conf 88799984787
Q gi|254780751|r 547 GVSINVVIGIE 557 (723)
Q Consensus 547 ~~~I~i~~d~~ 557 (723)
|-++.|..|..
T Consensus 264 Gq~v~I~~Da~ 274 (348)
T PRK10476 264 GDCATVYSMID 274 (348)
T ss_pred CCEEEEEEECC
T ss_conf 89899999768
No 192
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=32.53 E-value=11 Score=16.81 Aligned_cols=13 Identities=0% Similarity=-0.100 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 5677699999998
Q gi|254780751|r 346 FFRSGIEVQLDSL 358 (723)
Q Consensus 346 f~~y~ie~~i~~~ 358 (723)
|..+.|...+.++
T Consensus 144 ~~Sf~V~~~v~~a 156 (207)
T PRK10954 144 WNSFVVKSLVAQQ 156 (207)
T ss_pred HHCHHHHHHHHHH
T ss_conf 8588999999999
No 193
>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB; InterPro: IPR014109 This entry includes thiol-disulphide isomerase (TrbB), a protein that is involved in conjugative transfer of plasmid DNA, specifically in the F-type system. TrbB has been predicted to contain a thioredoxin fold, it also contains a conserved pair of cysteines and has been shown to function as a thiol disulphide isomerase by complementation of Escherichia coli DsbA mutants . TtbB is believed to be involved in pilin assembly . TrbB is closely related to TraF (IPR014110 from INTERPRO) though somewhat longer lacking the cysteine motif and is apparently not functional as a disulphide bond isomerase..
Probab=32.52 E-value=15 Score=16.04 Aligned_cols=34 Identities=24% Similarity=0.430 Sum_probs=14.8
Q ss_pred CCCCEEEEECCCEEEEEEECCCCCC--CCCCCHHHHH
Q ss_conf 6786499832880699982375544--4555114799
Q gi|254780751|r 366 PSRGYVIINQTEALVSIDVNSGRST--REHCIEDTAL 400 (723)
Q Consensus 366 ~sGG~lvIe~TEALt~IDVNSG~~~--~~~~~e~t~l 400 (723)
+||-|..|- |=||-.|=|||-++. ..+..++.-|
T Consensus 133 ~~~ey~~~~-~PalFLvNvnt~~~~~v~~G~~~~~~L 168 (176)
T TIGR02738 133 PNGEYRPVV-TPALFLVNVNTRKAYPVLQGAVDEAEL 168 (176)
T ss_pred CCCCCCEEC-CCEEEEECCCHHHHHHHHCCCCCHHHH
T ss_conf 889703010-232233315378887643387678999
No 194
>PRK07726 DNA topoisomerase III; Provisional
Probab=32.41 E-value=30 Score=13.90 Aligned_cols=27 Identities=22% Similarity=0.150 Sum_probs=13.6
Q ss_pred HHHHHHHHCCCCCEEEEEEECCCCCHHH
Q ss_conf 9999863002587169985045575799
Q gi|254780751|r 233 KEIARGLEVPAGMGVILRTAGASRTKIE 260 (723)
Q Consensus 233 ~~~~~~~~~~~~~G~IiRT~a~~~~~~~ 260 (723)
..+++.|.. .|+=---||.+.-.+.+.
T Consensus 306 l~iAQ~LYE-~glITYPRTDS~~ls~~~ 332 (716)
T PRK07726 306 LDITQKLYQ-KGIVSYPRSDSNYVTQGE 332 (716)
T ss_pred HHHHHHHHH-CCCEEECCCCCCCCCHHH
T ss_conf 999999985-696200687776479899
No 195
>LOAD_cold consensus
Probab=32.23 E-value=30 Score=13.84 Aligned_cols=33 Identities=12% Similarity=0.064 Sum_probs=26.3
Q ss_pred EEEEEEEECCCCCEEEEEECC-CCCCCCCHHHCC
Q ss_conf 798997836388231353278-977130222137
Q gi|254780751|r 43 YLAKVTRVEPSLQAAFVDYGG-NRHGFLPFLEIH 75 (723)
Q Consensus 43 Y~G~V~~V~p~lqAAFVdiG~-~k~gFL~~~ei~ 75 (723)
+.|+|+.--+.=.=-||.--. ++.-|+|+++|.
T Consensus 2 ~~G~VK~f~~~kGfGFI~~~~g~~DvFvH~s~l~ 35 (67)
T LOAD_cold 2 VKGTVKWFNVKKGFGFITPEDGGEDVFVHQSAIQ 35 (67)
T ss_pred CCEEEEEEECCCCCEEEEECCCCCEEEEEHHHHC
T ss_conf 9869999989999478875799821899947814
No 196
>TIGR02949 anti_SigH_actin anti-sigma factor, TIGR02949 family; InterPro: IPR014295 This is a group of anti-sigma factors that are associated in an apparent operon with sigma factors belonging to the sigma-70 family (IPR014293 from INTERPRO). They appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family, which is restricted to the Actinobacteria..
Probab=31.91 E-value=25 Score=14.38 Aligned_cols=51 Identities=14% Similarity=0.107 Sum_probs=36.2
Q ss_pred CCCCCH-HHHHHHHHHHHHH-CCCCHHHHCCCCCH-HHHHHHHHHHHHHHHCCC
Q ss_conf 035320-3667888987631-01211220134420-356776999999984222
Q gi|254780751|r 312 VSGEKG-YREAKDFMKLLMP-SYARIVRQYEDPHP-IFFRSGIEVQLDSLHQTE 362 (723)
Q Consensus 312 vd~~~~-~~~~~~~~~~~~p-~~~~~v~~~~~~~~-lf~~y~ie~~i~~~~~~~ 362 (723)
+|..++ ...+.+|+-.-++ +...+++.|-+.-| -|..|++|.+|..++.+.
T Consensus 7 ~dC~evr~~~l~e~LDge~~~~~~~~l~~H~~~C~~Cl~~~dlE~~vr~~lk~~ 60 (85)
T TIGR02949 7 TDCAEVRLDHLYEFLDGEMTEDDAERLRRHLEACPECLEEYDLEQAVRKLLKRC 60 (85)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCHHHHHHHCHHHHHHHHHHHH
T ss_conf 784899999999985688988569999999863756688506889999999853
No 197
>PRK04323 hypothetical protein; Provisional
Probab=31.84 E-value=31 Score=13.80 Aligned_cols=16 Identities=44% Similarity=0.582 Sum_probs=8.1
Q ss_pred EEEECCCCCEEEEEEE
Q ss_conf 6896528960799999
Q gi|254780751|r 5 MLIDASHVEETRVVVL 20 (723)
Q Consensus 5 ~lI~~~~~~e~Rvav~ 20 (723)
.|||+|++.-||.+++
T Consensus 42 ~lIDaT~GRkTRaVii 57 (91)
T PRK04323 42 KLIDATYGRKTRAVII 57 (91)
T ss_pred CEEECCCCCEEEEEEE
T ss_conf 4787357960568999
No 198
>cd01888 eIF2_gamma eIF2-gamma (gamma subunit of initiation factor 2). eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the sel
Probab=31.52 E-value=31 Score=13.76 Aligned_cols=72 Identities=21% Similarity=0.234 Sum_probs=37.9
Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHH-CCCCEEE
Q ss_conf 069998237554445551147999999999999998731036863896033479888899999999997312-7872899
Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKK-DRARVQV 456 (723)
Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~-D~~~~~v 456 (723)
|+-+||.+-|-.. .+| +-++ .+++.|-+.+| ||+|-=||.-+.+...+.++.++..++. ....+.+
T Consensus 110 aiLvVdA~eG~~~-----~QT--~eH~----~l~~~lgv~~i--IV~vNKmDlv~~~~~~~~~~ei~~~l~~~~~~~~~i 176 (203)
T cd01888 110 ALLLIAANEPCPQ-----PQT--SEHL----AALEIMGLKHI--IIVQNKIDLVKEEQALENYEQIKKFVKGTIAENAPI 176 (203)
T ss_pred EEEEEECCCCCCH-----HHH--HHHH----HHHHHCCCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf 6898643667750-----779--9999----99998499863--677507777886789999999999855216899859
Q ss_pred EEECCC
Q ss_conf 860486
Q gi|254780751|r 457 GAISNF 462 (723)
Q Consensus 457 ~~it~l 462 (723)
.++|.+
T Consensus 177 IPiSA~ 182 (203)
T cd01888 177 IPISAQ 182 (203)
T ss_pred EEEECC
T ss_conf 991478
No 199
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=31.29 E-value=19 Score=15.26 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=11.5
Q ss_pred CCCCCCCCCEEEEEC
Q ss_conf 023675465378606
Q gi|254780751|r 481 TKVCTYCKGAGYIRS 495 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~ 495 (723)
..+||.|+|+.+.+=
T Consensus 3 h~pCP~CGG~Drfrf 17 (37)
T smart00778 3 HGPCPNCGGSDRFRF 17 (37)
T ss_pred CCCCCCCCCCCCEEE
T ss_conf 667886778655367
No 200
>PRK02362 ski2-like helicase; Provisional
Probab=31.05 E-value=32 Score=13.71 Aligned_cols=15 Identities=20% Similarity=0.381 Sum_probs=6.2
Q ss_pred CCCCCCCCCCCCEEE
Q ss_conf 101233457652344
Q gi|254780751|r 195 AVTTYLSLAGRYSVL 209 (723)
Q Consensus 195 ~lT~~isl~Gry~Vl 209 (723)
.|..-|.||-|-+|+
T Consensus 338 TLA~GVNLPAr~VIi 352 (736)
T PRK02362 338 TLAAGLNLPARRVII 352 (736)
T ss_pred HHHCCCCCCEEEEEE
T ss_conf 665055785269998
No 201
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=30.45 E-value=32 Score=13.64 Aligned_cols=39 Identities=23% Similarity=0.294 Sum_probs=34.0
Q ss_pred CCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf 34604287879899783638823135327897713022213
Q gi|254780751|r 34 HKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 (723)
Q Consensus 34 ~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei 74 (723)
.-..-+|++-.|+|.-|.+++ =+||||.--+|+||++++
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~--W~VDI~sp~~A~L~ls~~ 97 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSG--WKVDIGSPYPALLSLSDF 97 (239)
T ss_pred CCCCCCCCEEEEEEEEECCCC--EEEECCCCCCEEEEHHHH
T ss_conf 524888999999999971563--389728953237426662
No 202
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=30.36 E-value=19 Score=15.24 Aligned_cols=11 Identities=45% Similarity=1.105 Sum_probs=6.5
Q ss_pred CCCCCCCCEEE
Q ss_conf 23675465378
Q gi|254780751|r 482 KVCTYCKGAGY 492 (723)
Q Consensus 482 ~~c~~c~g~g~ 492 (723)
.+||.|+|.-.
T Consensus 2 kpCPFCG~~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCCHH
T ss_conf 88887897531
No 203
>COG1411 Uncharacterized protein related to proFAR isomerase (HisA) [General function prediction only]
Probab=30.33 E-value=33 Score=13.63 Aligned_cols=48 Identities=33% Similarity=0.392 Sum_probs=36.5
Q ss_pred CEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHH
Q ss_conf 8069998237554445551147999999999999998731036863896033479888
Q gi|254780751|r 377 EALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKK 434 (723)
Q Consensus 377 EALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~ 434 (723)
.+-+++|||-|+--+. ++|---|+.|-|--|..-|+||+|.=-.-..+
T Consensus 119 r~vvslD~k~~~Ll~~----------~~ed~le~Vk~l~~~~~~~lIvLDi~aVGt~~ 166 (229)
T COG1411 119 RIVVSLDVKGGELLGP----------WLEDFLETVKDLNYRRDPGLIVLDIGAVGTKS 166 (229)
T ss_pred CEEEEEECCCCEECCC----------CCHHHHHHHHHHHCCCCCCEEEEECCCCCCCC
T ss_conf 6699996478842377----------71048999998752578884999755433466
No 204
>COG3634 AhpF Alkyl hydroperoxide reductase, large subunit [Posttranslational modification, protein turnover, chaperones]
Probab=30.31 E-value=18 Score=15.37 Aligned_cols=125 Identities=18% Similarity=0.196 Sum_probs=54.0
Q ss_pred HHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEE----EEE
Q ss_conf 8752376631111035320366788898763101211220134420356776999999984222143678649----983
Q gi|254780751|r 299 IRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYV----IIN 374 (723)
Q Consensus 299 ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~l----vIe 374 (723)
+....+..+.-.-+|+.--..++..---+..|.....-+.+. --+..|++-+.++- +|+-- -+.
T Consensus 140 ~msvlNp~I~H~~IdGa~Fq~Evear~IMaVPtvflnGe~fg-----~GRmtleeilaki~-------~gaa~~~ae~~~ 207 (520)
T COG3634 140 LMSVLNPRIKHTAIDGALFQDEVEARNIMAVPTVFLNGEEFG-----QGRMTLEEILAKID-------TGAAKRDAEEFN 207 (520)
T ss_pred HHHHCCCCCEEEEECCHHHHHHHHHCCCEECCEEEECCHHHC-----CCCEEHHHHHHHHC-------CCCCCCCHHHHH
T ss_conf 887608873367752166676787545100444888511214-----65105999999743-------776644667751
Q ss_pred CCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHH-----HHHHCCCCEEE-----EECCCCCCHHHHHHHHHHHH
Q ss_conf 288069998237554445551147999999999999998-----73103686389-----60334798888999999999
Q gi|254780751|r 375 QTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQ-----LRLRDLAGLIV-----VDFIDMEEKKNNRSVEKKLK 444 (723)
Q Consensus 375 ~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQ-----lRLRnlgGiIv-----IDFIdM~~~~~~~~v~~~l~ 444 (723)
--+|.-+.=|-.|-.-. .||.-.||- |----.||.++ =.||....-+.. ++...|.
T Consensus 208 ~k~~yDVLvVGgGPAga-------------aAAIYaARKGiRTGl~aerfGGQvldT~~IENfIsv~~teGp-kl~~ale 273 (520)
T COG3634 208 AKDAYDVLVVGGGPAGA-------------AAAIYAARKGIRTGLVAERFGGQVLDTMGIENFISVPETEGP-KLAAALE 273 (520)
T ss_pred CCCCCEEEEECCCCCHH-------------HHHHHHHHHCCHHHHHHHHHCCEECCCCCHHHEECCCCCCCH-HHHHHHH
T ss_conf 56883499986886316-------------789999861211100156518820000033330056545466-8999999
Q ss_pred HHHHH
Q ss_conf 97312
Q gi|254780751|r 445 ESLKK 449 (723)
Q Consensus 445 ~~l~~ 449 (723)
+.++.
T Consensus 274 ~Hv~~ 278 (520)
T COG3634 274 AHVKQ 278 (520)
T ss_pred HHHHH
T ss_conf 98764
No 205
>PRK07399 DNA polymerase III subunit delta'; Validated
Probab=30.19 E-value=33 Score=13.61 Aligned_cols=42 Identities=26% Similarity=0.345 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHCCCC---EEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf 999999999873103686---389603347988889999999999
Q gi|254780751|r 404 LEAAEEIARQLRLRDLAG---LIVVDFIDMEEKKNNRSVEKKLKE 445 (723)
Q Consensus 404 leAA~EIaRQlRLRnlgG---iIvIDFIdM~~~~~~~~v~~~l~~ 445 (723)
++-.+++.+-+-++-..| ++|||-+|+........+++.|.|
T Consensus 106 idqIR~l~~~l~~~p~~~~~kVvII~~ae~m~~~AaNaLLKtLEE 150 (314)
T PRK07399 106 LEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEE 150 (314)
T ss_pred HHHHHHHHHHHCCCCCCCCCEEEEECCHHHCCHHHHHHHHHHHCC
T ss_conf 999999999973188568847999889787199999999986147
No 206
>cd04171 SelB SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo
Probab=30.04 E-value=33 Score=13.60 Aligned_cols=70 Identities=23% Similarity=0.293 Sum_probs=43.0
Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC-CEEEEECCCCCCHHHHHHHHHHHHHHHHHCC-CCEE
Q ss_conf 0699982375544455511479999999999999987310368-6389603347988889999999999731278-7289
Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLA-GLIVVDFIDMEEKKNNRSVEKKLKESLKKDR-ARVQ 455 (723)
Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlg-GiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~-~~~~ 455 (723)
||.+||.+.|-. ++| .|+..-+++.++- .++|+-=+|+-+++....+.+.+++.++... ....
T Consensus 78 ~llVvda~~g~~------~q~---------~e~~~~~~~~~i~~~ivvlNK~D~v~~~~~~~~~~~i~~~l~~~~~~~~p 142 (164)
T cd04171 78 VLLVVAADEGIM------PQT---------REHLEILELLGIKRGLVVLTKADLVDEDWLELVEEEIRELLAGTFLADAP 142 (164)
T ss_pred EEEEEECCCCCC------HHH---------HHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf 589986177888------889---------99999998738872787346342579789999999999999743999982
Q ss_pred EEEECCC
Q ss_conf 9860486
Q gi|254780751|r 456 VGAISNF 462 (723)
Q Consensus 456 v~~it~l 462 (723)
+.++|.+
T Consensus 143 ii~iSA~ 149 (164)
T cd04171 143 IFPVSAV 149 (164)
T ss_pred EEEEECC
T ss_conf 9994698
No 207
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=29.86 E-value=33 Score=13.58 Aligned_cols=39 Identities=21% Similarity=0.130 Sum_probs=34.5
Q ss_pred CCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC
Q ss_conf 013576999998730237999999998488799984787
Q gi|254780751|r 519 IIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723)
Q Consensus 519 i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723)
..+.+|.....++.+.+-..|.+|++.+++.|.|.....
T Consensus 2 ~~i~ip~~~~g~vIG~~G~~I~~I~~~~~~~I~i~~~~~ 40 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS 40 (64)
T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEECCCCC
T ss_conf 899973665426799898134799997598999888899
No 208
>PRK05783 hypothetical protein; Provisional
Probab=29.79 E-value=33 Score=13.57 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHC
Q ss_conf 99999999999873103
Q gi|254780751|r 402 TNLEAAEEIARQLRLRD 418 (723)
Q Consensus 402 tNleAA~EIaRQlRLRn 418 (723)
.-.+.+.+||.+|||=|
T Consensus 55 eA~~~v~~ic~~lrL~N 71 (84)
T PRK05783 55 EAQELALKLAKEMRLGN 71 (84)
T ss_pred HHHHHHHHHHHHHHCCC
T ss_conf 99999999998620349
No 209
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=29.65 E-value=33 Score=13.55 Aligned_cols=91 Identities=19% Similarity=0.156 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEEC-------
Q ss_conf 3532036678889876310121122013442035677699999998422214367864998328806999823-------
Q gi|254780751|r 313 SGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVN------- 385 (723)
Q Consensus 313 d~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVN------- 385 (723)
...-.|.++...+....+... -.+...-.+++..|.+-.+.. .+=|.|-|+-.|+-...|=+
T Consensus 366 ~~rltY~~v~~~l~~~~~~~~--~~l~~~l~~~~~l~~~l~~~R---------~~rg~i~~~~~E~ki~~d~~~~~~~i~ 434 (706)
T COG0557 366 AARLTYEEVQAILDGKEDDKY--APLLDSLLELLELAKILKKKR---------LSRGAIDFDTPEAKIVLDEEGRPVEIE 434 (706)
T ss_pred HHHCCHHHHHHHHHCCCCCCC--CCCHHHHHHHHHHHHHHHHHH---------HHCCCCCCCCCCEEEEECCCCCCEEEE
T ss_conf 564479999998614553223--320588999999999999999---------868883557863158767888740688
Q ss_pred CC-CCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 75-5444555114799999999999999873
Q gi|254780751|r 386 SG-RSTREHCIEDTALQTNLEAAEEIARQLR 415 (723)
Q Consensus 386 SG-~~~~~~~~e~t~l~tNleAA~EIaRQlR 415 (723)
-- +....+-+|+-.+..|..+|.- ..+..
T Consensus 435 ~~~r~~a~~lIee~Ml~AN~~vA~~-l~~~~ 464 (706)
T COG0557 435 IRERLDAEKLIEEFMLLANETVAEH-LEKHK 464 (706)
T ss_pred EECCCHHHHHHHHHHHHHHHHHHHH-HHHCC
T ss_conf 7305648989999999987999999-99708
No 210
>KOG3013 consensus
Probab=29.40 E-value=34 Score=13.53 Aligned_cols=152 Identities=14% Similarity=0.165 Sum_probs=77.7
Q ss_pred CEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 98999996073346042878798997836388231353278977130222137121028988999999988863111110
Q gi|254780751|r 23 NRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEA 102 (723)
Q Consensus 23 g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~ 102 (723)
++|+-+.-=...-..-+|+|-.|||.-|-+- -==||++...++.|.++-|+ +|+..-- +..+.+...
T Consensus 69 NkLi~V~plk~rY~pEvGDvVVgRV~eVq~K--RWkvd~nsk~d~vL~LsSvN-----LPGg~~R------Rk~~~DEl~ 135 (301)
T KOG3013 69 NKLISVKPLKSRYAPEVGDVVVGRVIEVQQK--RWKVDLNSKQDAVLMLSSVN-----LPGGIQR------RKSEEDELQ 135 (301)
T ss_pred CCEEEEEEHHHHCCCCCCCEEEEEEEEEECC--EEEEECCCCCCEEEEEECCC-----CCCHHHH------CCCHHHHHH
T ss_conf 4237886433203775577788876444023--35775166543378753024-----8861433------022356899
Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEE
Q ss_conf 00000011122334443344542222334455433222234321122111211000012234444213310688857999
Q gi|254780751|r 103 VADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLV 182 (723)
Q Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilV 182 (723)
..+-...||.....+-..- .++.-. ...+. ...=|-||-+||
T Consensus 136 MR~fl~egDLi~AEVQ~v~---------------------~dGs~s--------------LhTRS---~KYGKL~~G~lv 177 (301)
T KOG3013 136 MRSFLKEGDLIVAEVQNVF---------------------HDGSLS--------------LHTRS---LKYGKLGQGILV 177 (301)
T ss_pred HHHHHHCCCEEHHHHHHHC---------------------CCCEEE--------------EEECC---HHCCCCCCCEEE
T ss_conf 9977550675317788761---------------------277378--------------77210---110651686599
Q ss_pred EEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHH
Q ss_conf 84033323456410123345765234422788751242046886899
Q gi|254780751|r 183 QIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDR 229 (723)
Q Consensus 183 QV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r 229 (723)
||----.. ..=|.+.+|||---|+.-.+++ +-+++.|++.++-
T Consensus 178 kVpp~Lvk---r~K~hfh~lp~g~~vIlG~NGy-IWv~~s~~~~~ee 220 (301)
T KOG3013 178 KVPPALVK---RSKTHFHNLPGGVDVILGCNGY-IWVGPSIKDQEEE 220 (301)
T ss_pred EECHHHHH---HHHHHHCCCCCCEEEEEECCCE-EEECCCCCCCHHH
T ss_conf 71889962---5555530588870799824766-9950788860022
No 211
>KOG0950 consensus
Probab=28.54 E-value=35 Score=13.43 Aligned_cols=44 Identities=25% Similarity=0.355 Sum_probs=30.5
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHHHHHHHH--HHCCCCEEEEEECC
Q ss_conf 368638960334798888999999999973--12787289986048
Q gi|254780751|r 418 DLAGLIVVDFIDMEEKKNNRSVEKKLKESL--KKDRARVQVGAISN 461 (723)
Q Consensus 418 nlgGiIvIDFIdM~~~~~~~~v~~~l~~~l--~~D~~~~~v~~it~ 461 (723)
+.=|+||||=..|-.++++...++.|-..+ ..-.+-+|+.|||.
T Consensus 340 ~~~g~vvVdElhmi~d~~rg~~lE~~l~k~~y~~~~~~~~iIGMSA 385 (1008)
T KOG0950 340 DFLGMVVVDELHMIGDKGRGAILELLLAKILYENLETSVQIIGMSA 385 (1008)
T ss_pred CCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf 3047289752246403563558999999999963256346765524
No 212
>COG1352 CheR Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]
Probab=28.24 E-value=31 Score=13.74 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHCCCCCCCCCCEEEEECCCEEE
Q ss_conf 76999999984222143678649983288069
Q gi|254780751|r 349 SGIEVQLDSLHQTEVTLPSRGYVIINQTEALV 380 (723)
Q Consensus 349 y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt 380 (723)
+.-+.|..-+-.=.=.|+.||+|+|-++|.+-
T Consensus 215 Fd~~~q~~il~~f~~~L~~gG~LflG~sE~~~ 246 (268)
T COG1352 215 FDEETQERILRRFADSLKPGGLLFLGHSETIP 246 (268)
T ss_pred ECHHHHHHHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf 37899999999999974899789982676667
No 213
>KOG3558 consensus
Probab=28.16 E-value=35 Score=13.38 Aligned_cols=16 Identities=38% Similarity=0.522 Sum_probs=11.9
Q ss_pred CCCCEEEEECCCEEEEE
Q ss_conf 67864998328806999
Q gi|254780751|r 366 PSRGYVIINQTEALVSI 382 (723)
Q Consensus 366 ~sGG~lvIe~TEALt~I 382 (723)
++|||+||+ |+|-|++
T Consensus 344 k~GGyvWlQ-TqATVi~ 359 (768)
T KOG3558 344 KNGGYVWLQ-TQATVIY 359 (768)
T ss_pred HCCCEEEEE-EEEEEEE
T ss_conf 449769998-6547985
No 214
>pfam08206 OB_RNB Ribonuclease B OB domain. This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
Probab=27.94 E-value=32 Score=13.65 Aligned_cols=15 Identities=33% Similarity=0.494 Sum_probs=10.8
Q ss_pred CCCEEEEEEECCCCC
Q ss_conf 885799984033323
Q gi|254780751|r 176 NRQILLVQIVKEERG 190 (723)
Q Consensus 176 ~gq~ilVQV~ke~~~ 190 (723)
-|+.|+|+|.+...+
T Consensus 34 ~GD~V~v~v~~~~~~ 48 (58)
T pfam08206 34 HGDRVLVRITKGDRR 48 (58)
T ss_pred CCCEEEEEEECCCCC
T ss_conf 999999999538889
No 215
>PRK01033 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=27.78 E-value=36 Score=13.34 Aligned_cols=19 Identities=16% Similarity=0.165 Sum_probs=9.4
Q ss_pred HHHHHHHHHHCCCCEEEEE
Q ss_conf 9999987310368638960
Q gi|254780751|r 408 EEIARQLRLRDLAGLIVVD 426 (723)
Q Consensus 408 ~EIaRQlRLRnlgGiIvID 426 (723)
.+.++++.=.++|.||+-|
T Consensus 155 ~~~~~~~~~~g~geil~Td 173 (253)
T PRK01033 155 VEFAKQAEELGAGEIVLNS 173 (253)
T ss_pred HHHHHHHHHCCCCEEEEEE
T ss_conf 9999998746977999987
No 216
>PRK09098 type III secretion system protein HrpB; Validated
Probab=27.77 E-value=36 Score=13.34 Aligned_cols=66 Identities=20% Similarity=0.082 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCCCCCCCEEEE
Q ss_conf 1468998878899973036431013576999998730237999999998488799984787788633897
Q gi|254780751|r 497 SSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE 566 (723)
Q Consensus 497 ~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~l~~~~f~Ie 566 (723)
..+...+...++... .....++|.|||+-.....+..-..... ......|.|.+|+.|....+.++
T Consensus 133 ~aL~~ra~~~l~~~v--~~~~~l~VRVhPdD~d~ar~a~~~l~~~--~~~~~~i~Vv~D~~L~~G~CI~E 198 (229)
T PRK09098 133 AALFARAAQTLEGVL--DGASYLTVRVHPADLDAARRAFGALAAE--GGRNVPVEVVGDPRLAPGACVCE 198 (229)
T ss_pred HHHHHHHHHHHHHHH--CCCCEEEEEECHHHHHHHHHHHHHHHHC--CCCCCCEEEECCCCCCCCCEEEE
T ss_conf 889999999999986--2466289998887799999989999864--69872137622787899986883
No 217
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family; InterPro: IPR012842 This entry is related to IPR009335 from INTERPRO, but is broader. IPR009335 from INTERPRO describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This entry also includes the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This entry excludes the related protein FliH of the bacterial flagellar apparatus (see IPR000563 from INTERPRO)..
Probab=27.75 E-value=36 Score=13.33 Aligned_cols=65 Identities=14% Similarity=0.083 Sum_probs=44.0
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHH-----CCEEEEEECCCCCCCCEEEE
Q ss_conf 114689988788999730364310135769999987302379999999984-----88799984787788633897
Q gi|254780751|r 496 QSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARF-----GVSINVVIGIELADKLFYIE 566 (723)
Q Consensus 496 ~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~-----~~~I~i~~d~~l~~~~f~Ie 566 (723)
...+...++|.+-. .......++++|||+-..-+. .+|....... ...+.|.+|+.+.+..+.++
T Consensus 105 ~~~~~~~~lr~~~~--~~~~~~~~~l~vhP~~~~~~~----~~l~~~~~~~~~~~~~~~~~l~~D~~l~~g~~~l~ 174 (183)
T TIGR02499 105 ESERLVRLLRQLLA--AVANQERLTLRVHPEQLDEVR----EALAELLALAPEFGLVGKWELEPDASLAPGACVLE 174 (183)
T ss_pred HHHHHHHHHHHHHH--HHHCCCCCEEEECHHHHHHHH----HHHHHHHHHHCCCCCCCHHCCCCCHHHCCCCEEEE
T ss_conf 88999999999999--874457634676746799999----99998884202467421010276021078870675
No 218
>pfam08273 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase.
Probab=27.14 E-value=23 Score=14.72 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=11.1
Q ss_pred CCCCCCCCCEEEEE
Q ss_conf 02367546537860
Q gi|254780751|r 481 TKVCTYCKGAGYIR 494 (723)
Q Consensus 481 ~~~c~~c~g~g~~~ 494 (723)
..+||.|+|+.+.+
T Consensus 3 h~pCP~CGg~Drfr 16 (39)
T pfam08273 3 HGPCPNCGGSDRFR 16 (39)
T ss_pred CCCCCCCCCCCCCE
T ss_conf 66777777857525
No 219
>TIGR01111 mtrA tetrahydromethanopterin S-methyltransferase, subunit A; InterPro: IPR005778 This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit A in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. 5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0006814 sodium ion transport, 0005737 cytoplasm, 0012506 vesicle membrane.
Probab=26.84 E-value=31 Score=13.74 Aligned_cols=43 Identities=33% Similarity=0.518 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHH-HHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf 99999999999987-3103686389603347988889999999999731278728
Q gi|254780751|r 401 QTNLEAAEEIARQL-RLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARV 454 (723)
Q Consensus 401 ~tNleAA~EIaRQl-RLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~ 454 (723)
.+|-||.+=-=+|| - |||.||. +|-.++.++.|+|+.||+-=.
T Consensus 121 N~n~eAveRF~~Q~Ve--------vV~LiD~---ED~g~I~~~vkEc~~KDPGAf 164 (246)
T TIGR01111 121 NINEEAVERFRKQIVE--------VVNLIDV---EDVGAITSKVKECVSKDPGAF 164 (246)
T ss_pred CCCHHHHHHHHHHHHH--------HHCCCCC---CCHHHHHHHHHHHHCCCCCCC
T ss_conf 6876788998641310--------1111463---676789999885322786874
No 220
>pfam08800 VirE_N VirE N-terminal domain. This presumed domain is found at the N-terminus of VirE proteins.
Probab=26.78 E-value=37 Score=13.22 Aligned_cols=49 Identities=14% Similarity=0.180 Sum_probs=29.3
Q ss_pred HHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCC-CEEEEEECCCCEEEEEC
Q ss_conf 1036863896033479888899999999997312787-28998604861489851
Q gi|254780751|r 416 LRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRA-RVQVGAISNFGLLEMSR 469 (723)
Q Consensus 416 LRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~-~~~v~~it~lGLlEltR 469 (723)
|..-+|+|+|||=.+.. + + +..++..+..|+. ...+...|.-||==+-|
T Consensus 27 l~~~sgli~lDiD~l~~-e---e-~~~~r~~l~~dp~t~~~FvSpSG~GvKi~V~ 76 (136)
T pfam08800 27 MKAYNGLVCLDVDHLAK-E---E-LERVKQKAAALPYTVLAFISSSGRGVKIWVR 76 (136)
T ss_pred HHHCCCEEEEEECCCCH-H---H-HHHHHHHHHCCCCEEEEEECCCCCEEEEEEE
T ss_conf 76368808998289998-9---9-9999999846994899998579987999999
No 221
>cd01887 IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.
Probab=26.76 E-value=37 Score=13.22 Aligned_cols=69 Identities=17% Similarity=0.197 Sum_probs=39.9
Q ss_pred EEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHH----HCCCC
Q ss_conf 06999823755444555114799999999999999873103686389603347988889999999999731----27872
Q gi|254780751|r 378 ALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLK----KDRAR 453 (723)
Q Consensus 378 ALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~----~D~~~ 453 (723)
|+.+||...|- .....|+..+++..++--++++--||..+ .+..++...+.+... .....
T Consensus 77 ~ilvvda~~g~---------------~~~~~~~~~~l~~~~~p~ivviNKiD~~~-~~~~~v~~~l~~~~~~~~~~~~~~ 140 (168)
T cd01887 77 AILVVAADDGV---------------MPQTIEAIKLAKAANVPFIVALNKIDKPN-ANPERVKNELSELGLQGEDEWGGD 140 (168)
T ss_pred EEEEEECCCCC---------------CHHHHHHHHHHHHCCCCEEEEEECCCCCC-CCHHHHHHHHHHHHCCCHHHCCCC
T ss_conf 99998646675---------------45899999999876997899998930898-798999999999754524552898
Q ss_pred EEEEEECCC
Q ss_conf 899860486
Q gi|254780751|r 454 VQVGAISNF 462 (723)
Q Consensus 454 ~~v~~it~l 462 (723)
..+.++|.+
T Consensus 141 ~~iIpvSA~ 149 (168)
T cd01887 141 VQIVPTSAK 149 (168)
T ss_pred CEEEEEECC
T ss_conf 759999899
No 222
>PRK07085 diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional
Probab=26.55 E-value=38 Score=13.19 Aligned_cols=31 Identities=16% Similarity=0.305 Sum_probs=16.8
Q ss_pred EEEE-CCCCHHHHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf 2420-468868999999999863002587169985
Q gi|254780751|r 218 TISR-KITNPVDRKNLKEIARGLEVPAGMGVILRT 251 (723)
Q Consensus 218 ~iSr-ki~~~~~r~~l~~~~~~~~~~~~~G~IiRT 251 (723)
|.+| +|..++......+....+.+. |++|=-
T Consensus 143 gs~r~ki~t~e~~~~~~~t~~~l~Ld---gLviiG 174 (557)
T PRK07085 143 GSGRTKIETEEQKEACLQTVKKLKLD---GLVIIG 174 (557)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCC---EEEEEC
T ss_conf 06865458999999999999985998---799979
No 223
>KOG0458 consensus
Probab=26.46 E-value=38 Score=13.18 Aligned_cols=83 Identities=22% Similarity=0.251 Sum_probs=52.0
Q ss_pred CEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE----ECCCCCCHHHHHHHHHHHHHHH----H
Q ss_conf 8069998237554445551147999999999999998731036863896----0334798888999999999973----1
Q gi|254780751|r 377 EALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVV----DFIDMEEKKNNRSVEKKLKESL----K 448 (723)
Q Consensus 377 EALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvI----DFIdM~~~~~~~~v~~~l~~~l----~ 448 (723)
-|.-+||-|+|.|..+-. +..-.+|+|+-||.-|+.-+||. |-|+-.. .--.++-..|...| .
T Consensus 281 ~avLvvd~s~~~FE~gfd--------~~gQtrEha~llr~Lgi~qlivaiNKmD~V~Wsq-~RF~eIk~~l~~fL~~~~g 351 (603)
T KOG0458 281 VAVLVVDASTGEFESGFD--------PGGQTREHALLLRSLGISQLIVAINKMDLVSWSQ-DRFEEIKNKLSSFLKESCG 351 (603)
T ss_pred EEEEEEECCCCHHHHCCC--------CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCH-HHHHHHHHHHHHHHHHHCC
T ss_conf 689999877543331348--------7986589999998749525888863010127538-8999999989999998528
Q ss_pred HCCCCEEEEEECC---CCEEEEE
Q ss_conf 2787289986048---6148985
Q gi|254780751|r 449 KDRARVQVGAISN---FGLLEMS 468 (723)
Q Consensus 449 ~D~~~~~v~~it~---lGLlElt 468 (723)
==..-+++.++|. -+|....
T Consensus 352 f~es~v~FIPiSGl~GeNL~k~~ 374 (603)
T KOG0458 352 FKESSVKFIPISGLSGENLIKIE 374 (603)
T ss_pred CCCCCCCEEECCCCCCCCCCCCC
T ss_conf 50477656955465677621233
No 224
>PRK12564 carbamoyl phosphate synthase small subunit; Reviewed
Probab=26.37 E-value=38 Score=13.17 Aligned_cols=84 Identities=15% Similarity=0.182 Sum_probs=52.5
Q ss_pred CCCCCCCCCEEEC-CCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 2334576523442-278875124204688689999999998630025871699850455757999999999999999877
Q gi|254780751|r 198 TYLSLAGRYSVLM-PNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVR 276 (723)
Q Consensus 198 ~~isl~Gry~Vl~-P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~ 276 (723)
|..|+.|.-+|++ |.-+. .|+.. ++ .. ...+.--|+|+|..+...+--.-...+...++
T Consensus 44 TDPSY~gQIl~fTyP~IGN-yGv~~-----~d-------~E-S~~~~~~G~Iv~e~~~~~s~~~s~~sL~~~L~------ 103 (355)
T PRK12564 44 TDPSYAGQIVTFTYPLIGN-YGVNR-----ED-------FE-SDRIHAKGLIVRELSRIPSNWRSEMSLDDYLK------ 103 (355)
T ss_pred CCCCCCCHHHEECCCCCCC-CCCCH-----HH-------HC-CCCCCEEEEEECCCCCCCCCCCCCCCHHHHHH------
T ss_conf 2877667300007767515-38894-----57-------15-56755106884146778884011069999999------
Q ss_pred HHHCCCCCCCCCCCCCCHHHHHHHHHCCC
Q ss_conf 64201432212345645888888752376
Q gi|254780751|r 277 ELALNSVAPHLVYEEGNLIKRAIRDLYCK 305 (723)
Q Consensus 277 ~~~~~~~~p~li~~~~~~~~~~ird~~~~ 305 (723)
....|++-.-+--.+.+.||+.-.-
T Consensus 104 ----~~~IpgI~gVDTRaLtr~iR~~G~m 128 (355)
T PRK12564 104 ----EHGIPGISGIDTRALTRKLREKGAM 128 (355)
T ss_pred ----HCCCCEEECCCHHHHHHHHHHCCCE
T ss_conf ----7798428525389999999865980
No 225
>TIGR01523 ATPase-IID_K-Na potassium/sodium efflux P-type ATPase, fungal-type; InterPro: IPR006414 Initially described as a calcium efflux ATPase , more recent work has shown that the Schizosaccharomyces pombe CTA3 gene is in fact a potassium ion efflux pump . These sequences form the clade which represents the fungal P-type ATPases which are responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies. This group of ATPases has been classified by phylogentic analysis as type IID . ; GO: 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0006812 cation transport, 0016021 integral to membrane.
Probab=26.03 E-value=29 Score=14.03 Aligned_cols=56 Identities=18% Similarity=0.207 Sum_probs=32.4
Q ss_pred CCHHHHHCCCCCCCCCEEE--------EECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 3011210023675465378--------6061146899887889997303643101357699999
Q gi|254780751|r 474 SSVLESTTKVCTYCKGAGY--------IRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVL 529 (723)
Q Consensus 474 ~sl~e~~~~~c~~c~g~g~--------~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~ 529 (723)
.+-.|...+.|....|+-. ++..+|++.+-||-|--....-.........|-++|.
T Consensus 517 KGA~E~I~~~CS~~~G~~L~~~D~E~I~~~~~~L~~EGLRVL~lA~K~~~K~~~~~T~~R~~AE 580 (1001)
T TIGR01523 517 KGAVERILERCSSSYGSTLEDPDVELIIKNVESLAAEGLRVLALASKVIDKDDVNITLNRDVAE 580 (1001)
T ss_pred CCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCHHH
T ss_conf 4057888865056788867654289999998886631255455664200021202356530100
No 226
>COG3585 MopI Molybdopterin-binding protein [Coenzyme metabolism]
Probab=25.91 E-value=39 Score=13.11 Aligned_cols=26 Identities=15% Similarity=-0.022 Sum_probs=21.4
Q ss_pred CCCEEEEEEEEECCCCCEEEEEECCC
Q ss_conf 28787989978363882313532789
Q gi|254780751|r 39 KGNIYLAKVTRVEPSLQAAFVDYGGN 64 (723)
Q Consensus 39 ~GnIY~G~V~~V~p~lqAAFVdiG~~ 64 (723)
.-|+++|+|+.|++|+=-+-|++-.+
T Consensus 5 aRN~lKG~Vk~iv~G~Vnsev~iei~ 30 (69)
T COG3585 5 ARNQLKGKVKEIVKGSVNSEVTIEIG 30 (69)
T ss_pred HHHEECCEEEEEEECCCCEEEEEEEC
T ss_conf 24203518999998341018999808
No 227
>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB. Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.
Probab=25.58 E-value=39 Score=13.07 Aligned_cols=55 Identities=31% Similarity=0.311 Sum_probs=43.3
Q ss_pred HHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf 9999987310368638960334798888999999999973127872899860486
Q gi|254780751|r 408 EEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNF 462 (723)
Q Consensus 408 ~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~l 462 (723)
.+|+..|+-.+..=+||+-=+|.-+++.+.++++.+++.|..-.--..|..+|.+
T Consensus 119 ~~i~~~l~~~~kp~iivlNK~Dll~~~~~~~~~~~i~~~l~~~~~~~~v~~ISA~ 173 (179)
T TIGR03598 119 LEMLEWLDERGIPVLIVLTKADKLKKSERNKQLKKIKKALKKDADDPSVQLFSSL 173 (179)
T ss_pred HHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECC
T ss_conf 9999999975998899997813069899999999999997336688948999799
No 228
>smart00322 KH K homology RNA-binding domain.
Probab=25.57 E-value=31 Score=13.82 Aligned_cols=40 Identities=25% Similarity=0.243 Sum_probs=34.7
Q ss_pred CCCCCCCHHHHHHHHCCHHHHHHHHHHHHCCEEEEEECCC
Q ss_conf 1013576999998730237999999998488799984787
Q gi|254780751|r 518 NIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIE 557 (723)
Q Consensus 518 ~i~v~~~~~va~~lln~kr~~l~~lE~~~~~~I~i~~d~~ 557 (723)
.+.+.+|.+...++.+.+-..+..|+..+++.|.+.....
T Consensus 4 ~~~i~vp~~~~g~iIG~~G~~i~~i~~~~~~~I~i~~~~~ 43 (69)
T smart00322 4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS 43 (69)
T ss_pred EEEEEECHHHCCEEECCCCCCHHHHHHHHCCEEEECCCCC
T ss_conf 9999989787685499998457999997288899779999
No 229
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=25.48 E-value=24 Score=14.51 Aligned_cols=19 Identities=16% Similarity=0.457 Sum_probs=13.7
Q ss_pred HHCCCCCCCCCEEEEECCH
Q ss_conf 1002367546537860611
Q gi|254780751|r 479 STTKVCTYCKGAGYIRSQS 497 (723)
Q Consensus 479 ~~~~~c~~c~g~g~~~~~~ 497 (723)
++.+.||.|+|.-.+-.+.
T Consensus 15 TLke~Cp~CG~~t~~~~Pp 33 (59)
T COG2260 15 TLKEKCPVCGGDTKVPHPP 33 (59)
T ss_pred EECCCCCCCCCCCCCCCCC
T ss_conf 6113377888745467899
No 230
>TIGR01520 FruBisAldo_II_A fructose-bisphosphate aldolase, class II; InterPro: IPR006411 Members of this family are class II examples of the glycolytic enzyme fructose-bisphosphate aldolase (FBA). They represent one of two deeply split, architecturally distinct clades of the family that includes class II fructose-bisphosphate aldolases, tagatose-bisphosphate aldolases, and related uncharacterised proteins. This family is well-conserved and includes characterised FBA from Saccharomyces cerevisiae, Escherichia coli, and Corynebacterium glutamicum.; GO: 0004332 fructose-bisphosphate aldolase activity, 0006096 glycolysis.
Probab=25.44 E-value=17 Score=15.64 Aligned_cols=79 Identities=9% Similarity=0.053 Sum_probs=53.8
Q ss_pred CCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 21234564588888875237663111103532036678889876310121122013442035677699999998422214
Q gi|254780751|r 285 PHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVT 364 (723)
Q Consensus 285 p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~~~~~~~~~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~ 364 (723)
-...|..++....-+++-....|.++-||.+--|..+.-.+..+ -.....|.--.+ .--+.|.=-.+.|+||||
T Consensus 267 ~fVFHGGSGSt~~Ei~ea~~yGVVKmN~DTDtQwA~~~Gi~~Y~-~~N~dyl~~~~G-----nP~g~~~PnKK~YDPRVW 340 (365)
T TIGR01520 267 FFVFHGGSGSTKQEIEEALSYGVVKMNVDTDTQWAYLEGILDYY-LNNEDYLQSQVG-----NPKGPEKPNKKFYDPRVW 340 (365)
T ss_pred CEEEECCCCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHH-HHHHHHHCCCCC-----CCCCCCCCCCEEECCHHH
T ss_conf 41653775772899976533684788614311167764277665-310222026588-----888888898500376167
Q ss_pred CCCCC
Q ss_conf 36786
Q gi|254780751|r 365 LPSRG 369 (723)
Q Consensus 365 L~sGG 369 (723)
|+-|=
T Consensus 341 lR~gE 345 (365)
T TIGR01520 341 LREGE 345 (365)
T ss_pred HHHHH
T ss_conf 67642
No 231
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=25.43 E-value=38 Score=13.13 Aligned_cols=58 Identities=14% Similarity=0.157 Sum_probs=28.8
Q ss_pred HHHHHHHHHCCCCEEEEEE-----------------------CCCCEEEEECCCC-CCCHHHHHCCCCCCCCCEEEEECC
Q ss_conf 9999973127872899860-----------------------4861489851566-630112100236754653786061
Q gi|254780751|r 441 KKLKESLKKDRARVQVGAI-----------------------SNFGLLEMSRQRI-RSSVLESTTKVCTYCKGAGYIRSQ 496 (723)
Q Consensus 441 ~~l~~~l~~D~~~~~v~~i-----------------------t~lGLlEltRkR~-r~sl~e~~~~~c~~c~g~g~~~~~ 496 (723)
-..+.|.+-|++-.-+.-+ .++|.+-.-++-. -.....-+.+.||+|+|.-++-.+
T Consensus 193 ~vaR~AAkyd~~i~Plls~~~dhY~Rvfv~v~rga~~ad~~~e~~g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~~GP 272 (380)
T COG1867 193 YVARTAAKYDKAIEPLLSLSIDHYVRVFVEVRRGARRADKLLENLGYIYHCSRCGEIVGSFREVDEKCPHCGGKVHLAGP 272 (380)
T ss_pred HHHHHHHHHCCCCEEEEEEEECEEEEEEEEECCCCHHHHHHHHHCCCEEECCCCCCEECCCCCCCCCCCCCCCCCEECCC
T ss_conf 99999986356613677735331899999981473057789975470788266410003555444557766652002257
Q ss_pred HH
Q ss_conf 14
Q gi|254780751|r 497 SS 498 (723)
Q Consensus 497 ~~ 498 (723)
-+
T Consensus 273 lW 274 (380)
T COG1867 273 LW 274 (380)
T ss_pred CC
T ss_conf 41
No 232
>PRK06921 hypothetical protein; Provisional
Probab=25.27 E-value=35 Score=13.44 Aligned_cols=22 Identities=14% Similarity=-0.063 Sum_probs=9.1
Q ss_pred EECCHHHHHHHHHHHHHHHHCC
Q ss_conf 6061146899887889997303
Q gi|254780751|r 493 IRSQSSVALSILRSVEEYLLQY 514 (723)
Q Consensus 493 ~~~~~~~~~~~~r~i~~~~~~~ 514 (723)
-+..++..-+++.-|..-....
T Consensus 193 e~~te~~~~~lf~iIN~Ry~~~ 214 (265)
T PRK06921 193 PRATEWQIEQTYSVVNYRYLNH 214 (265)
T ss_pred CCCCHHHHHHHHHHHHHHHHCC
T ss_conf 7898899999999999999769
No 233
>PRK13586 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=25.13 E-value=40 Score=13.02 Aligned_cols=19 Identities=16% Similarity=0.223 Sum_probs=10.9
Q ss_pred HHHHHHHHHHCCCCEEEEE
Q ss_conf 9999987310368638960
Q gi|254780751|r 408 EEIARQLRLRDLAGLIVVD 426 (723)
Q Consensus 408 ~EIaRQlRLRnlgGiIvID 426 (723)
.+.+.++.-.+++++|+-|
T Consensus 148 ~~~i~~~~~~g~~~ii~Td 166 (231)
T PRK13586 148 EDAISHVNSLESLGVIFTY 166 (231)
T ss_pred HHHHHHHHHCCCCEEEEEE
T ss_conf 9999999975998899976
No 234
>pfam04208 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump.
Probab=25.07 E-value=40 Score=13.01 Aligned_cols=56 Identities=27% Similarity=0.334 Sum_probs=34.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 5544455511479999999999999987310368638960334798888999999999973127872
Q gi|254780751|r 387 GRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRAR 453 (723)
Q Consensus 387 G~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~ 453 (723)
|+-+|....--..-.++.+|.+.--+|+- +||.|+ .+|-..+..+.++|..+|+.-
T Consensus 99 ~rIiGa~GaiPfieNi~~~aV~rFq~qVe--------~vd~i~---~eD~~~I~a~I~ec~~kdPGa 154 (176)
T pfam04208 99 GRIIGAEGAIPYIENIPEEAVERFQQQVE--------LVDLID---VEDLDEITKKVRECVSKDPGA 154 (176)
T ss_pred CCEECCCCCCCHHHHCCHHHHHHHHHHEE--------EEEEEC---CCCHHHHHHHHHHHHHCCCCC
T ss_conf 97816888863555099999999986467--------876426---778899999999998449987
No 235
>pfam05772 NinB NinB protein. The ninR region of phage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage lambda.
Probab=25.05 E-value=34 Score=13.49 Aligned_cols=35 Identities=14% Similarity=0.127 Sum_probs=20.9
Q ss_pred CHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHH
Q ss_conf 86899999999986300258716998504557579
Q gi|254780751|r 225 NPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKI 259 (723)
Q Consensus 225 ~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~ 259 (723)
++..|.+....+..+.+....+++|+---..++.+
T Consensus 4 ~~~~r~~ai~~I~~lP~d~~kp~vV~i~~~~Rtl~ 38 (127)
T pfam05772 4 SPQIKQNAIQAILQLPVDPKKPLVVTIKERTRSLD 38 (127)
T ss_pred CHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHH
T ss_conf 88999999999993899899974899518988877
No 236
>PRK10611 chemotaxis methyltransferase CheR; Provisional
Probab=24.87 E-value=29 Score=13.98 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=14.4
Q ss_pred CCCCCCCEEEEECCCEEEEEE
Q ss_conf 143678649983288069998
Q gi|254780751|r 363 VTLPSRGYVIINQTEALVSID 383 (723)
Q Consensus 363 V~L~sGG~lvIe~TEALt~ID 383 (723)
-.|.-||||++-++|.|.-++
T Consensus 250 ~~L~pgG~L~lG~sEsl~~~~ 270 (287)
T PRK10611 250 PLLKPDGLLFAGHSENFSQLS 270 (287)
T ss_pred HHHCCCCEEEEECCCCCCCCC
T ss_conf 986899289983887778877
No 237
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.77 E-value=39 Score=13.11 Aligned_cols=61 Identities=25% Similarity=0.352 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHH-----CCCCEEEEEECCCCEEEEECCC
Q ss_conf 9999998731036863896033479888899999999997312-----7872899860486148985156
Q gi|254780751|r 407 AEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKK-----DRARVQVGAISNFGLLEMSRQR 471 (723)
Q Consensus 407 A~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~-----D~~~~~v~~it~lGLlEltRkR 471 (723)
..+|..++-+-+ |++|. |.-- +.+---..+-+|+-.+.+ |+-.-.++.++.|-|.|-.-.-
T Consensus 375 ~~~l~~~~~~~~-gD~if--f~A~-~~~~~~~~lGalR~~l~~~l~li~~~~~~f~WVvDFPlfE~~ee~ 440 (585)
T COG0173 375 LEELIERLGAED-GDIIF--FVAD-KKKVVNKALGALRLKLGKELGLIDKDQFKFLWVVDFPLFEWDEEE 440 (585)
T ss_pred HHHHHHHHCCCC-CCEEE--EECC-CHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCC
T ss_conf 999999828777-88899--9669-488999988999999888738778343248999706766775345
No 238
>pfam03602 Cons_hypoth95 Conserved hypothetical protein 95.
Probab=24.63 E-value=41 Score=12.95 Aligned_cols=34 Identities=18% Similarity=0.280 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCE
Q ss_conf 03567769999999842221436786499832880
Q gi|254780751|r 344 PIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEA 378 (723)
Q Consensus 344 ~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEA 378 (723)
|.|....++.-++.+. ..=||..||.||||.--.
T Consensus 121 PPY~~~~~~~~l~~l~-~~~~l~~~~iiiiE~~~~ 154 (181)
T pfam03602 121 PPYAKGLIEEALELLA-EKGWLNPNALIVVETESD 154 (181)
T ss_pred CCCCCHHHHHHHHHHH-HCCCCCCCEEEEEEECCC
T ss_conf 9754206999999999-666657980999996687
No 239
>COG1329 Transcriptional regulators, similar to M. xanthus CarD [Transcription]
Probab=24.35 E-value=41 Score=12.92 Aligned_cols=35 Identities=23% Similarity=0.260 Sum_probs=20.1
Q ss_pred CHHHHHHHHHCCCCCCE-EECCCCCHHHHHHHHHHH
Q ss_conf 58888887523766311-110353203667888987
Q gi|254780751|r 293 NLIKRAIRDLYCKDISE-IIVSGEKGYREAKDFMKL 327 (723)
Q Consensus 293 ~~~~~~ird~~~~~~~~-i~vd~~~~~~~~~~~~~~ 327 (723)
.-+-.++||++..+-.. .-......|+.+..++..
T Consensus 104 ~~~AevvrdL~r~~~qr~l~~~Er~ll~~A~~~l~~ 139 (166)
T COG1329 104 IDIAEVVRDLYRRDKQRELSYSERRLLEKALQILAG 139 (166)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 789999999998640558996899999999999999
No 240
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=24.15 E-value=25 Score=14.38 Aligned_cols=33 Identities=15% Similarity=0.191 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCC
Q ss_conf 769999999842221436786499832880699982375
Q gi|254780751|r 349 SGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSG 387 (723)
Q Consensus 349 y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG 387 (723)
-.....++.+|+++=.+-||.-+ -+-++=|+||
T Consensus 420 ed~~~~ld~~l~ktw~~asg~~M------~i~a~a~DtG 452 (611)
T COG5525 420 EDWLLRLDAYLNKTWPHASGIDM------PISAVAVDTG 452 (611)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCC------EEEEEEEECC
T ss_conf 57899999998520656788723------1578898348
No 241
>pfam00313 CSD 'Cold-shock' DNA-binding domain.
Probab=23.64 E-value=43 Score=12.83 Aligned_cols=32 Identities=19% Similarity=0.317 Sum_probs=25.5
Q ss_pred EEEEEEECCCCCEEEEEEC-CCCCCCCCHHHCC
Q ss_conf 9899783638823135327-8977130222137
Q gi|254780751|r 44 LAKVTRVEPSLQAAFVDYG-GNRHGFLPFLEIH 75 (723)
Q Consensus 44 ~G~V~~V~p~lqAAFVdiG-~~k~gFL~~~ei~ 75 (723)
.|+|+-.-+.-.=-||.-. .+..-|+|.++|.
T Consensus 2 tG~VK~f~~~kGfGFI~~~~~~~DiFvH~s~l~ 34 (66)
T pfam00313 2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQ 34 (66)
T ss_pred CEEEEEEECCCCEEEEEECCCCCEEEEEHHHHC
T ss_conf 489999959999699997899846999926812
No 242
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=23.58 E-value=12 Score=16.61 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=19.4
Q ss_pred CCCCEEEEECCCCCCCHHHHHCCCCCCCCCE
Q ss_conf 4861489851566630112100236754653
Q gi|254780751|r 460 SNFGLLEMSRQRIRSSVLESTTKVCTYCKGA 490 (723)
Q Consensus 460 t~lGLlEltRkR~r~sl~e~~~~~c~~c~g~ 490 (723)
+.||+||=+|-|+. .+=+-+||-|+-|
T Consensus 501 l~f~iLQa~r~R~~----kTeyIsCPsCGRT 527 (613)
T PRK02048 501 TAFGILQAGRIRTS----KTEYISCPGCGRT 527 (613)
T ss_pred HHHHHHHHHCCCCC----CCCEEECCCCCCC
T ss_conf 88888887574433----5627758987652
No 243
>pfam06075 DUF936 Plant protein of unknown function (DUF936). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=23.41 E-value=43 Score=12.80 Aligned_cols=44 Identities=34% Similarity=0.555 Sum_probs=25.2
Q ss_pred EEEEEEECCCCCEEEEEECCCCCCC-CCHHHC-CCCCCCCCHHHHHHHH
Q ss_conf 9899783638823135327897713-022213-7121028988999999
Q gi|254780751|r 44 LAKVTRVEPSLQAAFVDYGGNRHGF-LPFLEI-HPDYYQIPFSDRQALL 90 (723)
Q Consensus 44 ~G~V~~V~p~lqAAFVdiG~~k~gF-L~~~ei-~~~y~~ip~~d~~~l~ 90 (723)
|=.|+.|+|.|-+. |+=.+ ||| |-++|- |.-|-.+|.+|-+-+|
T Consensus 27 LLQV~sIVPALag~--dLwpn-~GFylKVSDSsHStYVSLp~e~~DLIL 72 (557)
T pfam06075 27 LLQVTSIVPALAGS--DLWPN-HGFFLKVSDSSHSTYVSLSDEDDDLIL 72 (557)
T ss_pred CEEEEEEEECCCCC--CCCCC-CCEEEEECCCCCCEEEECCHHHCHHHH
T ss_conf 23665442124568--86777-845898526665346756622110322
No 244
>COG5615 Predicted integral membrane protein [Function unknown]
Probab=23.15 E-value=43 Score=12.76 Aligned_cols=51 Identities=18% Similarity=0.178 Sum_probs=36.9
Q ss_pred CCCCEEEEECC-------CCCCHHHHHHHHHHHHHHHH-HCCCCEEEEEECCCCE-EEEE
Q ss_conf 36863896033-------47988889999999999731-2787289986048614-8985
Q gi|254780751|r 418 DLAGLIVVDFI-------DMEEKKNNRSVEKKLKESLK-KDRARVQVGAISNFGL-LEMS 468 (723)
Q Consensus 418 nlgGiIvIDFI-------dM~~~~~~~~v~~~l~~~l~-~D~~~~~v~~it~lGL-lElt 468 (723)
=+||.+++||| -|.++..+.+.+...-..|. ---+-+-+..+|.-++ .||.
T Consensus 20 wIGGs~f~w~IlrPas~ka~~~~s~~~~~lg~I~rrF~~wvwatV~il~vsGv~~g~~~~ 79 (161)
T COG5615 20 WIGGSFFIWFILRPASYKALEDESRRTKILGIIGRRFGWWVWATVAILPVSGVYLGYEYI 79 (161)
T ss_pred HCCCEEEEEEEECHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCEEEEEEE
T ss_conf 706412576775576666440879888899999988676784631157702432556773
No 245
>KOG0955 consensus
Probab=23.13 E-value=43 Score=12.76 Aligned_cols=38 Identities=24% Similarity=0.176 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCC
Q ss_conf 776999999984222143678649983288069998237554
Q gi|254780751|r 348 RSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRS 389 (723)
Q Consensus 348 ~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~ 389 (723)
.+.|-..-..++.=+-.|.||+|-++|+-|+ |||...+
T Consensus 598 y~~iik~pm~~~tm~~k~~s~~y~tle~iee----d~~l~~~ 635 (1051)
T KOG0955 598 YIDIIKKPMDFFTMRLKLESGAYSTLEPIEE----DVNLIVS 635 (1051)
T ss_pred HHHHHCCCCCHHHHHHHHHCCHHHHHHHHHH----HHHHHHH
T ss_conf 8887257542455422100200222667777----6656666
No 246
>PRK06443 chorismate mutase; Validated
Probab=22.78 E-value=44 Score=12.72 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=22.3
Q ss_pred HHHHHHCCCCCCCCCCEEEEECCC-EEEEEEECCCCCCC
Q ss_conf 999984222143678649983288-06999823755444
Q gi|254780751|r 354 QLDSLHQTEVTLPSRGYVIINQTE-ALVSIDVNSGRSTR 391 (723)
Q Consensus 354 ~i~~~~~~~V~L~sGG~lvIe~TE-ALt~IDVNSG~~~~ 391 (723)
-++..++ .+||.+||---- --++||+|||--++
T Consensus 118 s~e~gcs-----~~ggh~v~g~~~~~d~ivdi~sg~~~k 151 (177)
T PRK06443 118 SIEEGCS-----KAGGHVVIGLPDKDDHIVDINSGFPVK 151 (177)
T ss_pred HHHHHHH-----HCCCEEECCCCCCCCEEEECCCCCEEE
T ss_conf 8997640-----348708427999887278638996344
No 247
>pfam11314 DUF3117 Protein of unknown function (DUF3117). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=22.67 E-value=44 Score=12.70 Aligned_cols=13 Identities=23% Similarity=0.526 Sum_probs=6.6
Q ss_pred CCCCCCCCEEEEE
Q ss_conf 2143678649983
Q gi|254780751|r 362 EVTLPSRGYVIIN 374 (723)
Q Consensus 362 ~V~L~sGG~lvIe 374 (723)
+|+|..||.||+|
T Consensus 22 RvPleGGGRLVvE 34 (51)
T pfam11314 22 RVPLEGGGRLVVE 34 (51)
T ss_pred EEECCCCCEEEEE
T ss_conf 9751788379999
No 248
>KOG2268 consensus
Probab=22.67 E-value=15 Score=15.99 Aligned_cols=65 Identities=17% Similarity=0.256 Sum_probs=39.2
Q ss_pred HHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf 99999984222143678649983288069998237554445551147999999999999998731036863896033479
Q gi|254780751|r 352 EVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDME 431 (723)
Q Consensus 352 e~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~ 431 (723)
..-.+.+..-.|.|-.-|+|--|--|==. -+++=++|+||||--|.
T Consensus 205 ~~ly~~lm~~Iv~la~~GlIHgDFNEFNi----------------------------------mv~dd~~i~vIDFPQmv 250 (465)
T KOG2268 205 PTLYDDLMGLIVRLANHGLIHGDFNEFNI----------------------------------MVKDDDKIVVIDFPQMV 250 (465)
T ss_pred HHHHHHHHHHHHHHHHCCCEECCCCHHEE----------------------------------EEECCCCEEEEECHHHH
T ss_conf 89999999999999875933225305416----------------------------------87148977996345750
Q ss_pred CHHHHH----------HHHHHHHHHHHHC
Q ss_conf 888899----------9999999973127
Q gi|254780751|r 432 EKKNNR----------SVEKKLKESLKKD 450 (723)
Q Consensus 432 ~~~~~~----------~v~~~l~~~l~~D 450 (723)
+-.|.. -|...|+.-+.-.
T Consensus 251 S~sh~nA~~YFdRDv~Ci~~fFrKkf~YE 279 (465)
T KOG2268 251 STSHPNAEYYFDRDVECIRAFFRKKFGYE 279 (465)
T ss_pred CCCCCCCCEEECCCHHHHHHHHHHHCCCC
T ss_conf 46788631000144899999999961888
No 249
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=22.35 E-value=34 Score=13.46 Aligned_cols=86 Identities=20% Similarity=0.205 Sum_probs=47.3
Q ss_pred EEEEEECCCCCCCCCCCHHHHHH-HH--HHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf 69998237554445551147999-99--9999999998731036863896033479888899999999997312787289
Q gi|254780751|r 379 LVSIDVNSGRSTREHCIEDTALQ-TN--LEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQ 455 (723)
Q Consensus 379 Lt~IDVNSG~~~~~~~~e~t~l~-tN--leAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~ 455 (723)
|==-||-+|..+|=+|+.+++-. .+ -|+..|-+--++.=+=||||=+= +||-. + .-+.+++.|+.-..+..
T Consensus 321 LL~FevG~~~~~GLRnvvD~y~~~~d~v~E~~~~sve~v~~LG~GGlVyvs-~~yG~-e----~a~ei~~~L~~~Gv~A~ 394 (1843)
T TIGR01054 321 LLGFEVGKGSDTGLRNVVDVYEEDEDGVKEKLLESVELVKKLGKGGLVYVS-IDYGK-E----KAEEIKEFLREHGVKAV 394 (1843)
T ss_pred HCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEE-CCCCH-H----HHHHHHHHHHHCCCEEE
T ss_conf 527100576422332138851148884468899999999984794399971-22255-8----99999999985794799
Q ss_pred EEEE-CCCCEEEEECC
Q ss_conf 9860-48614898515
Q gi|254780751|r 456 VGAI-SNFGLLEMSRQ 470 (723)
Q Consensus 456 v~~i-t~lGLlEltRk 470 (723)
.+-- ++.++++.=++
T Consensus 395 ~~~~~k~~~~~~~F~~ 410 (1843)
T TIGR01054 395 AYHAKKPKEDLEKFAE 410 (1843)
T ss_pred EEEECCCCCCHHHHHC
T ss_conf 9840377320346634
No 250
>cd00453 FTBP_aldolase_II Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to yield fructose-1,6-bisphosphate. TBP-aldolase is tetrameric and produces tagarose-1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. Although structurally similar, the class I aldolases use a different mechanism and are believed to have an independent evolutionary origin.
Probab=22.34 E-value=39 Score=13.10 Aligned_cols=16 Identities=31% Similarity=0.241 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999987
Q gi|254780751|r 399 ALQTNLEAAEEIARQL 414 (723)
Q Consensus 399 ~l~tNleAA~EIaRQl 414 (723)
.+-|+-|-|.+.+.++
T Consensus 178 ~~yTdPeea~~fv~~t 193 (340)
T cd00453 178 ALYTQPEDVDYAYTEL 193 (340)
T ss_pred CCCCCHHHHHHHHHHH
T ss_conf 4558989999999986
No 251
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.29 E-value=23 Score=14.69 Aligned_cols=66 Identities=20% Similarity=0.170 Sum_probs=35.0
Q ss_pred CCCCCCCCCCCCCCCEEEC--CCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHH
Q ss_conf 5641012334576523442--2788751242046886899999999986300258716998504557579999
Q gi|254780751|r 192 KGAAVTTYLSLAGRYSVLM--PNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIK 262 (723)
Q Consensus 192 Kga~lT~~isl~Gry~Vl~--P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~~G~IiRT~a~~~~~~~l~ 262 (723)
-.-||+|-.++-|.-+|+- +.......+.+-.........+..++ ..| .|+|+-|-.-|..+....
T Consensus 208 vd~RvStlP~~~GEkvVlRil~~~~~~l~l~~Lg~~~~~~~~~~~~~---~~p--~GliLvTGPTGSGKTTTL 275 (500)
T COG2804 208 VDFRVSTLPTFYGEKVVLRILDKDQVILDLEKLGMSPFQLARLLRLL---NRP--QGLILVTGPTGSGKTTTL 275 (500)
T ss_pred EEEEEECCCCCCCCEEEEEEECCCCCCCCHHHHCCCHHHHHHHHHHH---HCC--CEEEEEECCCCCCHHHHH
T ss_conf 88999557887785789998333124688878389988999999997---289--708999689999889999
No 252
>PRK10767 chaperone protein DnaJ; Provisional
Probab=22.21 E-value=16 Score=15.87 Aligned_cols=43 Identities=14% Similarity=0.259 Sum_probs=20.2
Q ss_pred HHCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf 1002367546537860611468998878899973036431013576999
Q gi|254780751|r 479 STTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDV 527 (723)
Q Consensus 479 ~~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~v 527 (723)
.+..+|+.|+|+|.+.... +..-.-.......+.|.|.+|+-+
T Consensus 178 ~~~~~C~~C~G~G~~i~~~------C~~C~G~g~v~~~k~l~V~Ip~G~ 220 (376)
T PRK10767 178 AVQQTCPHCQGRGTLIKDP------CNKCHGHGRVEKSKTLSVKIPAGV 220 (376)
T ss_pred EEEEECCCCCCCCEEECCC------CCCCCCCEEEEEEEEEEEEECCCC
T ss_conf 8887368766575693266------664478537865447998737987
No 253
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=21.86 E-value=32 Score=13.66 Aligned_cols=11 Identities=27% Similarity=0.640 Sum_probs=7.4
Q ss_pred HHCCCCCCCCC
Q ss_conf 10023675465
Q gi|254780751|r 479 STTKVCTYCKG 489 (723)
Q Consensus 479 ~~~~~c~~c~g 489 (723)
++..+||+|+-
T Consensus 1 mlLI~CP~Cg~ 11 (97)
T COG4311 1 MLLIPCPYCGE 11 (97)
T ss_pred CCEECCCCCCC
T ss_conf 95001898887
No 254
>TIGR01275 ACC_deam_rel pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family; InterPro: IPR005966 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy . PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic . This entry represents a family of pyridoxal phosphate-dependent enzymes closely related to (and often designated as) 1-aminocyclopropane-1-carboxylate deaminase. However, the members of this family are less well conserved.; GO: 0003824 catalytic activity, 0030170 pyridoxal phosphate binding.
Probab=21.70 E-value=46 Score=12.57 Aligned_cols=21 Identities=43% Similarity=0.616 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHC----CCCEEE
Q ss_conf 999999999873103----686389
Q gi|254780751|r 404 LEAAEEIARQLRLRD----LAGLIV 424 (723)
Q Consensus 404 leAA~EIaRQlRLRn----lgGiIv 424 (723)
.+||.||+.||-++. +.-|+|
T Consensus 163 v~A~~Ei~~QLN~~~d~vkfd~iVv 187 (339)
T TIGR01275 163 VEAVLEIAEQLNLESDEVKFDSIVV 187 (339)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCEEE
T ss_conf 9999999986078866420152689
No 255
>cd04617 CBS_pair_4 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=21.62 E-value=46 Score=12.56 Aligned_cols=19 Identities=37% Similarity=0.448 Sum_probs=14.0
Q ss_pred HHHHHHHHHHCCCCEEEEE
Q ss_conf 9999987310368638960
Q gi|254780751|r 408 EEIARQLRLRDLAGLIVVD 426 (723)
Q Consensus 408 ~EIaRQlRLRnlgGiIvID 426 (723)
.|.++++.-+|+|++.|+|
T Consensus 13 ~eA~~~M~~~~ig~l~VVD 31 (118)
T cd04617 13 YDAIVTLFLEDVGSLFVVD 31 (118)
T ss_pred HHHHHHHHHHCCCEEEEEC
T ss_conf 9999999983998799984
No 256
>pfam01762 Galactosyl_T Galactosyltransferase. This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2.
Probab=21.33 E-value=47 Score=12.52 Aligned_cols=16 Identities=25% Similarity=0.436 Sum_probs=13.3
Q ss_pred CCCCCCEEEEECCHHH
Q ss_conf 6754653786061146
Q gi|254780751|r 484 CTYCKGAGYIRSQSSV 499 (723)
Q Consensus 484 c~~c~g~g~~~~~~~~ 499 (723)
=|+|.|.|+|.|.+.+
T Consensus 145 P~Y~~G~~YvlS~d~v 160 (196)
T pfam01762 145 PPYASGPFYLLSRDAA 160 (196)
T ss_pred CCCCCCCEEEECHHHH
T ss_conf 8789888888669999
No 257
>KOG3821 consensus
Probab=21.23 E-value=46 Score=12.56 Aligned_cols=26 Identities=19% Similarity=0.489 Sum_probs=20.1
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf 02367546537860611468998878
Q gi|254780751|r 481 TKVCTYCKGAGYIRSQSSVALSILRS 506 (723)
Q Consensus 481 ~~~c~~c~g~g~~~~~~~~~~~~~r~ 506 (723)
..-||+|.|.-.++----.+..++|-
T Consensus 253 M~yCp~CqGl~~~kPC~gYC~NVmrG 278 (563)
T KOG3821 253 MIYCPHCQGLPSVKPCYGYCLNVMRG 278 (563)
T ss_pred HHCCHHCCCCCCCCCCHHHHHHHHHH
T ss_conf 84363105877668707899999988
No 258
>PRK08084 DNA replication initiation factor; Provisional
Probab=21.12 E-value=48 Score=12.49 Aligned_cols=109 Identities=13% Similarity=0.069 Sum_probs=58.3
Q ss_pred CEEEEECCCCCC--HHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCCCCEEEEEC-CH
Q ss_conf 638960334798--888999999999973127872899860486148985156663011210023675465378606-11
Q gi|254780751|r 421 GLIVVDFIDMEE--KKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRS-QS 497 (723)
Q Consensus 421 GiIvIDFIdM~~--~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c~g~g~~~~-~~ 497 (723)
.+|+||=||.-. .+-+..+...+-.+....+.++-+..=..-.-+.+.-.+++.-|.-.+. -.+.. .+
T Consensus 99 dll~iDDi~~i~g~~~~ee~lF~l~N~~~~~g~~~ll~ts~~~P~~l~~~l~DL~SRl~~g~~---------~~i~~~dd 169 (235)
T PRK08084 99 SLVCIDNIECIAGDELWEMAIFDLYNRILESGKTRLLITGDRPPRQLNLGLPDLASRLDWGQI---------YKLQPLSD 169 (235)
T ss_pred CEEEEECHHHHCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHCCCCCHHHHHHHHCCCE---------EEECCCCH
T ss_conf 989982745546997899999999999998489669996798824302312889999956972---------78559998
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 4689988788999730364310135769999987302379999999984
Q gi|254780751|r 498 SVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARF 546 (723)
Q Consensus 498 ~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~~ 546 (723)
..-..+++. . +..--+.++.+|+.||++.-...+..++.-.
T Consensus 170 e~~~~iL~~---~-----a~~rgl~l~~~V~~yl~~~~~R~~~~L~~~l 210 (235)
T PRK08084 170 EEKLQALQL---R-----ARLRGFELPEDVGRFLLKRLDREMRTLFMTL 210 (235)
T ss_pred HHHHHHHHH---H-----HHHCCCCCCHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 999999999---9-----9973999998999999986158899999999
No 259
>TIGR03572 WbuZ glycosyl amidation-associated protein WbuZ. This clade of sequences is highly similar to the HisF protein, but generally represents the second HisF homolog in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. WbuZ genes are invariably observed in the presence of a homolog of the HisH protein (designated WbuY) and a proposed N-acetyl sugar amidotransferase designated in WbuX in E. coli, IfnA in P. aeriginosa and PseA in C. jejuni. Similarly, this trio of genes is invariably found in the context of saccharide biosynthesis loci. It has been shown that the WbuYZ homologs are not essential components of the activity expressed by WbuX, leading to the proposal that these to pr
Probab=21.05 E-value=48 Score=12.48 Aligned_cols=23 Identities=17% Similarity=0.212 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf 99999999863002587169985
Q gi|254780751|r 229 RKNLKEIARGLEVPAGMGVILRT 251 (723)
Q Consensus 229 r~~l~~~~~~~~~~~~~G~IiRT 251 (723)
...++++...+.+|-.+|==|||
T Consensus 63 ~~~I~~i~~~~~ipi~vGGGIrs 85 (232)
T TIGR03572 63 FELISNLAEECFMPLTVGGGIRS 85 (232)
T ss_pred HHHHHHHHHHCCCCEEEEECEEE
T ss_conf 99999999972985899713303
No 260
>PRK01492 rnpA ribonuclease P; Reviewed
Probab=20.99 E-value=48 Score=12.47 Aligned_cols=68 Identities=15% Similarity=0.274 Sum_probs=41.7
Q ss_pred CCCCCCCCEEECCCCCCCCEEEECCCCHHH-----HHHHHHHHHHHH-------CCCCCEEEEEEECCCCCHHHHHHHHH
Q ss_conf 334576523442278875124204688689-----999999998630-------02587169985045575799999999
Q gi|254780751|r 199 YLSLAGRYSVLMPNTSKGETISRKITNPVD-----RKNLKEIARGLE-------VPAGMGVILRTAGASRTKIEIKRDFE 266 (723)
Q Consensus 199 ~isl~Gry~Vl~P~~~~~~~iSrki~~~~~-----r~~l~~~~~~~~-------~~~~~G~IiRT~a~~~~~~~l~~d~~ 266 (723)
.+-++++|-.++ |+.||||+....- .++.+.++..+. ....|=+|.|-.+....-+.+..|+.
T Consensus 37 ~i~~~Sk~~~fl-----GikvSkKvsKKAvvRNkIKRrIRhliR~il~~~~l~a~k~a~Iiiprkgf~e~~f~hl~~Elk 111 (118)
T PRK01492 37 KIFLESKYNTFL-----GIKVSRKLNKKAVVRNKIKRRIRHLIRIIVSDSSLKAIKFAMIIIPRKGFEEINFSHLNYELS 111 (118)
T ss_pred CCCCCCCCCCEE-----EEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHH
T ss_conf 666765577334-----467415433789999999999999999984553146664489999638832312999999999
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780751|r 267 YLMRL 271 (723)
Q Consensus 267 ~L~~~ 271 (723)
.++..
T Consensus 112 ~~l~~ 116 (118)
T PRK01492 112 KIILR 116 (118)
T ss_pred HHHHH
T ss_conf 99864
No 261
>PRK06835 DNA replication protein DnaC; Validated
Probab=20.82 E-value=30 Score=13.87 Aligned_cols=20 Identities=10% Similarity=-0.094 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999987764
Q gi|254780751|r 259 IEIKRDFEYLMRLWDNVREL 278 (723)
Q Consensus 259 ~~l~~d~~~L~~~w~~i~~~ 278 (723)
+.|..++..|...-..+...
T Consensus 68 ~~lk~~i~~L~~~k~~LL~~ 87 (330)
T PRK06835 68 ESLKEKITDLRVKKSELLVS 87 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999998
No 262
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=20.77 E-value=48 Score=12.44 Aligned_cols=24 Identities=21% Similarity=0.433 Sum_probs=20.2
Q ss_pred CCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 428787989978363882313532
Q gi|254780751|r 38 IKGNIYLAKVTRVEPSLQAAFVDY 61 (723)
Q Consensus 38 ~~GnIY~G~V~~V~p~lqAAFVdi 61 (723)
.-|.+|.|++..+++.|+.-.-|.
T Consensus 18 KnG~~y~G~L~~~d~~MN~~L~~v 41 (70)
T cd01721 18 KTGEVYRGKLIEAEDNMNCQLKDV 41 (70)
T ss_pred CCCEEEEEEEEEEECCCCCEEEEE
T ss_conf 899499999988702367499899
No 263
>pfam01440 Gemini_AL2 Geminivirus AL2 protein. Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL2 gene product transactivates expression of TGMV coat protein gene, and BR1 movement protein.
Probab=20.69 E-value=49 Score=12.43 Aligned_cols=14 Identities=21% Similarity=0.330 Sum_probs=5.8
Q ss_pred CCCCCCCCCCEEEE
Q ss_conf 22214367864998
Q gi|254780751|r 360 QTEVTLPSRGYVII 373 (723)
Q Consensus 360 ~~~V~L~sGG~lvI 373 (723)
.|+|+|++|-++.|
T Consensus 30 RRRIDL~CGCS~yi 43 (134)
T pfam01440 30 RRRIDLPCGCSYYI 43 (134)
T ss_pred CCCCCCCCCCEEEE
T ss_conf 54233057886987
No 264
>TIGR02477 PFKA_PPi diphosphate--fructose-6-phosphate 1-phosphotransferase; InterPro: IPR011183 Diphosphate--fructose-6-phosphate 1-phosphotransferase catalyses the addition of phosphate from diphosphate (PPi) to fructose 6-phosphate to give fructose 1,6-bisphosphate (2.7.1.90 from EC). The enzyme is also known as pyrophosphate-dependent phosphofructokinase. The usage of PPi-dependent enzymes in glycolysis presumably frees up ATP for other processes . IPR012828 from INTERPRO represents the ATP-dependent 6-phosphofructokinase enzyme contained within Phosphofructokinase. This entry contains primarily bacterial, plant alpha, and plant beta sequences. These may be dimeric nonallosteric enzymes (bacteria) or allosteric heterotetramers (plants) . For additional information please see , , , .; GO: 0005524 ATP binding, 0047334 diphosphate-fructose-6-phosphate 1-phosphotransferase activity, 0006096 glycolysis, 0005945 6-phosphofructokinase complex.
Probab=20.64 E-value=49 Score=12.43 Aligned_cols=193 Identities=20% Similarity=0.197 Sum_probs=108.9
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCC-CCCCCCCCHHHHHHHHHHHHHHHHHHHH--H-HC
Q ss_conf 203567769999999842221436786499832880699982375-5444555114799999999999999873--1-03
Q gi|254780751|r 343 HPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSG-RSTREHCIEDTALQTNLEAAEEIARQLR--L-RD 418 (723)
Q Consensus 343 ~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG-~~~~~~~~e~t~l~tNleAA~EIaRQlR--L-Rn 418 (723)
+-+++.+.+=.+|+.+|...+.==| -|+ -.+ +..=...+...+.+|=.--=..|..||- | ||
T Consensus 318 EFIPEv~~L~~ELn~~L~~~~~~F~-------------~i~-~~~~~~~~~~kLS~~~~~~f~~LP~~I~~QLLnil~RD 383 (566)
T TIGR02477 318 EFIPEVQALIKELNNLLAQNVEEFS-------------KIK-FEGRKDLVKSKLSPESKALFESLPETIRKQLLNILDRD 383 (566)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHC-------------CCC-HHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCC
T ss_conf 2026688999999865404762001-------------467-78899999862688899997407867999998752679
Q ss_pred CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EEEECCC-CEEEEECCCCCCCHHHHHCCCCCCCCCEEE----
Q ss_conf 6863896033479888899999999997312787289-9860486-148985156663011210023675465378----
Q gi|254780751|r 419 LAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQ-VGAISNF-GLLEMSRQRIRSSVLESTTKVCTYCKGAGY---- 492 (723)
Q Consensus 419 lgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~-v~~it~l-GLlEltRkR~r~sl~e~~~~~c~~c~g~g~---- 492 (723)
=-|-|=|==|.-. +==-..|..+|.+..++-.-|.. +.++++| |= | -|-++-. .-.|.||.+.|+
T Consensus 384 pHGNv~VS~IeTE-KLLi~lV~~~l~~~~~~g~yK~~~F~a~~HFFGY-E-----GRca~PS--nFDs~YcY~LGy~A~~ 454 (566)
T TIGR02477 384 PHGNVQVSQIETE-KLLIELVQTELAKRKKEGEYKGKKFSAVSHFFGY-E-----GRCAFPS--NFDSDYCYALGYTAAI 454 (566)
T ss_pred CCCCEEEEEECHH-HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC-C-----HHCCCCC--CCCHHHHHHHHHHHHH
T ss_conf 9885374211278-9999999999999986366467777754666553-0-----1126775--3210343578999999
Q ss_pred ---------EECCHHHH----------------HHHHHHHHH----HHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHH
Q ss_conf ---------60611468----------------998878899----9730364310135769999987302379999999
Q gi|254780751|r 493 ---------IRSQSSVA----------------LSILRSVEE----YLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYE 543 (723)
Q Consensus 493 ---------~~~~~~~~----------------~~~~r~i~~----~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE 543 (723)
+-++..+. |.+.|+--. ...+.-.++-.|.++...-.++.++.-.|..+=-
T Consensus 455 Ll~~g~TGYm~~i~NL~~p~~eW~~gg~PLt~mMn~E~R~G~PGass~~~PVIkKa~Vdl~G~pFk~f~~~R~~WA~~~~ 534 (566)
T TIGR02477 455 LLANGLTGYMSTIKNLTNPAEEWIAGGVPLTMMMNMERRHGEPGASSIMKPVIKKALVDLEGKPFKKFASNRDKWALEDL 534 (566)
T ss_pred HHHCCCCEEEEEECCCCCCHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf 99716760455500115761240147622444412565457987521366655665547875457899999999988605
Q ss_pred HHHCCEEEEEECCCC
Q ss_conf 984887999847877
Q gi|254780751|r 544 ARFGVSINVVIGIEL 558 (723)
Q Consensus 544 ~~~~~~I~i~~d~~l 558 (723)
-+|-..|++.....+
T Consensus 535 Y~fPGPiQy~Gp~~v 549 (566)
T TIGR02477 535 YVFPGPIQYFGPEEV 549 (566)
T ss_pred CCCCCCEEECCCCCC
T ss_conf 779886663275322
No 265
>TIGR01214 rmlD dTDP-4-dehydrorhamnose reductase; InterPro: IPR005913 dTDP-4-dehydrorhamnose reductase (1.1.1.133 from EC) catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS molecules such as core antigen and O-antigen. dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + NADPH ; GO: 0008831 dTDP-4-dehydrorhamnose reductase activity, 0045226 extracellular polysaccharide biosynthetic process.
Probab=20.24 E-value=50 Score=12.37 Aligned_cols=13 Identities=31% Similarity=0.345 Sum_probs=8.3
Q ss_pred CCCCCEEEEEEEC
Q ss_conf 0258716998504
Q gi|254780751|r 241 VPAGMGVILRTAG 253 (723)
Q Consensus 241 ~~~~~G~IiRT~a 253 (723)
.++.-.+||||+-
T Consensus 153 ~~~e~~lIvRTsW 165 (317)
T TIGR01214 153 GPDENALIVRTSW 165 (317)
T ss_pred CCCCCEEEEEEEE
T ss_conf 7998578898521
Done!