Query 003933
Match_columns 785
No_of_seqs 391 out of 2034
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 14:34:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003933.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003933hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1676 K-homology type RNA bi 100.0 2.4E-41 5.3E-46 376.7 29.1 351 1-375 1-394 (600)
2 KOG1676 K-homology type RNA bi 100.0 5.1E-30 1.1E-34 286.5 32.9 206 160-374 97-304 (600)
3 KOG2191 RNA-binding protein NO 99.9 8.3E-27 1.8E-31 244.2 20.8 172 196-373 35-207 (402)
4 KOG2193 IGF-II mRNA-binding pr 99.9 1.1E-21 2.3E-26 210.8 9.5 207 158-371 241-482 (584)
5 KOG2190 PolyC-binding proteins 99.8 6.4E-21 1.4E-25 216.3 15.7 159 200-372 43-210 (485)
6 KOG2192 PolyC-binding hnRNP-K 99.8 9.7E-20 2.1E-24 186.5 12.8 202 159-370 85-384 (390)
7 KOG2193 IGF-II mRNA-binding pr 99.8 4.2E-20 9E-25 198.7 8.6 161 197-374 196-356 (584)
8 KOG2192 PolyC-binding hnRNP-K 99.8 3.7E-18 8E-23 175.0 18.7 149 198-371 46-194 (390)
9 KOG2190 PolyC-binding proteins 99.8 1.3E-17 2.8E-22 189.5 17.6 202 169-375 104-414 (485)
10 TIGR03665 arCOG04150 arCOG0415 99.7 6.9E-18 1.5E-22 168.8 10.9 139 204-371 2-152 (172)
11 PRK13763 putative RNA-processi 99.7 8.3E-18 1.8E-22 169.3 9.2 145 200-371 3-158 (180)
12 KOG2191 RNA-binding protein NO 99.4 1E-12 2.2E-17 139.0 9.6 202 166-370 91-315 (402)
13 cd02396 PCBP_like_KH K homolog 99.3 4.4E-12 9.5E-17 107.1 7.6 63 298-364 2-64 (65)
14 cd02396 PCBP_like_KH K homolog 99.3 5.3E-12 1.2E-16 106.5 7.1 65 201-267 1-65 (65)
15 COG1094 Predicted RNA-binding 99.3 5.4E-11 1.2E-15 119.5 14.5 141 199-372 7-166 (194)
16 cd02394 vigilin_like_KH K homo 99.1 6E-11 1.3E-15 98.8 6.0 61 298-365 2-62 (62)
17 cd02393 PNPase_KH Polynucleoti 99.1 1.8E-10 3.9E-15 96.3 7.5 59 296-365 2-61 (61)
18 PF00013 KH_1: KH domain syndr 99.1 6.3E-11 1.4E-15 98.0 4.6 60 297-364 1-60 (60)
19 cd00105 KH-I K homology RNA-bi 99.1 3.9E-10 8.4E-15 93.7 7.7 63 298-365 2-64 (64)
20 PF00013 KH_1: KH domain syndr 99.0 1.5E-10 3.3E-15 95.7 3.7 60 201-266 1-60 (60)
21 cd02394 vigilin_like_KH K homo 99.0 2.8E-10 6.2E-15 94.7 5.3 62 201-267 1-62 (62)
22 cd00105 KH-I K homology RNA-bi 99.0 8.1E-10 1.7E-14 91.8 7.5 63 202-267 2-64 (64)
23 cd02393 PNPase_KH Polynucleoti 99.0 7E-10 1.5E-14 92.7 6.9 59 200-267 2-61 (61)
24 smart00322 KH K homology RNA-b 98.9 6.9E-09 1.5E-13 85.8 9.4 67 296-369 3-69 (69)
25 KOG2279 Kinase anchor protein 98.9 6.8E-10 1.5E-14 124.6 4.0 144 198-370 66-209 (608)
26 KOG2279 Kinase anchor protein 98.8 6.5E-09 1.4E-13 116.8 7.4 183 168-366 118-364 (608)
27 smart00322 KH K homology RNA-b 98.8 2.3E-08 4.9E-13 82.7 8.6 67 199-270 2-68 (69)
28 KOG2113 Predicted RNA binding 98.8 4.6E-09 1E-13 110.9 4.7 153 198-366 24-179 (394)
29 PF13014 KH_3: KH domain 98.7 3E-08 6.5E-13 77.0 5.6 43 306-352 1-43 (43)
30 cd02395 SF1_like-KH Splicing f 98.7 7.7E-08 1.7E-12 91.2 8.5 67 305-372 15-97 (120)
31 PF13014 KH_3: KH domain 98.6 4.1E-08 8.8E-13 76.2 5.1 43 210-254 1-43 (43)
32 cd02395 SF1_like-KH Splicing f 98.6 7.5E-08 1.6E-12 91.2 7.6 71 203-273 3-96 (120)
33 KOG0119 Splicing factor 1/bran 98.6 1.5E-07 3.1E-12 105.1 9.0 75 199-273 137-231 (554)
34 KOG2208 Vigilin [Lipid transpo 98.4 4.2E-07 9.1E-12 109.6 8.9 139 200-367 347-485 (753)
35 TIGR03665 arCOG04150 arCOG0415 98.4 4.7E-07 1E-11 91.0 7.0 97 167-273 46-152 (172)
36 KOG0119 Splicing factor 1/bran 98.4 1.4E-06 3.1E-11 97.3 10.3 76 295-370 137-230 (554)
37 PRK13763 putative RNA-processi 98.3 7.3E-07 1.6E-11 90.3 6.6 65 296-370 3-71 (180)
38 KOG2208 Vigilin [Lipid transpo 98.3 1.3E-06 2.7E-11 105.6 9.3 192 164-370 173-414 (753)
39 PRK08406 transcription elongat 98.3 1.9E-06 4E-11 83.9 7.5 103 200-331 32-134 (140)
40 TIGR02696 pppGpp_PNP guanosine 98.2 5.2E-06 1.1E-10 98.8 11.3 66 294-370 576-642 (719)
41 TIGR02696 pppGpp_PNP guanosine 98.1 3.3E-06 7.1E-11 100.4 6.5 85 179-272 557-642 (719)
42 TIGR03591 polynuc_phos polyrib 98.0 2.3E-05 4.9E-10 94.3 10.1 65 295-370 550-615 (684)
43 COG1185 Pnp Polyribonucleotide 98.0 4.8E-06 1E-10 97.2 3.8 121 145-274 496-618 (692)
44 TIGR01952 nusA_arch NusA famil 97.9 3.6E-05 7.8E-10 75.0 8.6 102 201-331 34-135 (141)
45 TIGR03591 polynuc_phos polyrib 97.9 1.2E-05 2.6E-10 96.5 5.4 69 196-273 547-616 (684)
46 KOG1588 RNA-binding protein Sa 97.8 2.5E-05 5.4E-10 82.2 6.3 46 195-240 87-138 (259)
47 KOG1588 RNA-binding protein Sa 97.8 9.3E-05 2E-09 78.0 10.1 77 294-370 90-191 (259)
48 COG1185 Pnp Polyribonucleotide 97.7 9.5E-05 2.1E-09 86.7 9.5 68 295-373 551-619 (692)
49 KOG3273 Predicted RNA-binding 97.7 2.9E-05 6.2E-10 78.3 3.6 157 199-370 73-231 (252)
50 PLN00207 polyribonucleotide nu 97.7 9.3E-05 2E-09 90.1 8.6 68 294-372 683-752 (891)
51 PF14611 SLS: Mitochondrial in 97.6 0.0008 1.7E-08 69.5 13.8 128 202-369 28-164 (210)
52 COG0195 NusA Transcription elo 97.6 0.00023 5E-09 72.7 8.3 102 201-332 77-178 (190)
53 PLN00207 polyribonucleotide nu 97.5 4.9E-05 1.1E-09 92.5 3.0 70 195-273 680-751 (891)
54 KOG0336 ATP-dependent RNA heli 97.5 8.3E-05 1.8E-09 82.2 4.4 72 294-373 45-116 (629)
55 COG5176 MSL5 Splicing factor ( 97.4 0.0003 6.5E-09 71.4 6.4 42 197-238 145-192 (269)
56 KOG0336 ATP-dependent RNA heli 97.4 0.0002 4.4E-09 79.3 5.5 74 195-274 42-115 (629)
57 PRK11824 polynucleotide phosph 97.3 0.00043 9.3E-09 83.6 7.4 65 295-370 553-618 (693)
58 PRK12328 nusA transcription el 97.2 0.0013 2.7E-08 73.5 8.8 93 209-332 251-344 (374)
59 TIGR01953 NusA transcription t 97.1 0.0013 2.8E-08 73.0 8.7 93 210-332 244-337 (341)
60 PRK00106 hypothetical protein; 97.1 0.0023 5.1E-08 74.7 10.4 64 297-370 226-291 (535)
61 TIGR03319 YmdA_YtgF conserved 97.1 0.0022 4.7E-08 75.0 10.1 64 297-370 205-270 (514)
62 COG5176 MSL5 Splicing factor ( 97.0 0.0022 4.7E-08 65.3 8.2 79 296-374 148-244 (269)
63 PRK12327 nusA transcription el 97.0 0.002 4.3E-08 72.1 8.5 93 210-332 246-339 (362)
64 PRK11824 polynucleotide phosph 97.0 0.00039 8.4E-09 84.0 2.6 69 196-273 550-619 (693)
65 KOG2814 Transcription coactiva 96.9 0.0008 1.7E-08 73.0 4.5 70 200-273 57-126 (345)
66 PRK12704 phosphodiesterase; Pr 96.9 0.0035 7.6E-08 73.4 10.2 64 297-370 211-276 (520)
67 PRK12329 nusA transcription el 96.9 0.0017 3.7E-08 73.5 7.2 92 210-331 278-370 (449)
68 PRK09202 nusA transcription el 96.8 0.0022 4.7E-08 74.1 7.3 93 210-333 246-339 (470)
69 KOG2113 Predicted RNA binding 96.7 0.0014 2.9E-08 70.4 4.1 67 294-368 24-90 (394)
70 COG1094 Predicted RNA-binding 96.6 0.0032 7E-08 64.1 6.0 54 210-273 112-165 (194)
71 KOG2814 Transcription coactiva 96.6 0.0024 5.2E-08 69.3 5.0 70 296-372 57-127 (345)
72 TIGR03319 YmdA_YtgF conserved 96.6 0.0044 9.5E-08 72.5 7.3 91 169-271 177-269 (514)
73 PRK00106 hypothetical protein; 96.6 0.0047 1E-07 72.3 7.3 91 169-271 198-290 (535)
74 PRK04163 exosome complex RNA-b 96.5 0.0041 9E-08 65.7 6.3 64 297-371 146-210 (235)
75 KOG1067 Predicted RNA-binding 96.5 0.0046 9.9E-08 71.0 6.7 66 295-372 596-662 (760)
76 cd02134 NusA_KH NusA_K homolog 96.4 0.0046 9.9E-08 51.8 4.7 37 295-331 24-60 (61)
77 PRK04163 exosome complex RNA-b 96.4 0.0048 1E-07 65.3 6.0 65 201-274 146-211 (235)
78 PRK12704 phosphodiesterase; Pr 96.4 0.006 1.3E-07 71.5 6.9 92 169-272 183-276 (520)
79 PRK12705 hypothetical protein; 96.1 0.01 2.2E-07 69.1 7.1 64 297-370 199-264 (508)
80 KOG1960 Predicted RNA-binding 95.9 0.014 2.9E-07 64.7 6.4 164 218-384 112-307 (531)
81 cd02134 NusA_KH NusA_K homolog 95.9 0.012 2.6E-07 49.3 4.6 36 200-235 25-60 (61)
82 COG1782 Predicted metal-depend 95.9 0.019 4E-07 65.7 7.2 95 212-332 41-135 (637)
83 cd02410 archeal_CPSF_KH The ar 95.5 0.054 1.2E-06 53.0 7.9 92 215-332 21-112 (145)
84 PRK12705 hypothetical protein; 95.2 0.016 3.4E-07 67.6 3.8 65 170-238 172-237 (508)
85 PRK00468 hypothetical protein; 94.9 0.025 5.4E-07 49.6 3.4 34 196-229 26-59 (75)
86 KOG1067 Predicted RNA-binding 94.8 0.029 6.2E-07 64.7 4.5 88 176-273 572-661 (760)
87 PRK00468 hypothetical protein; 94.6 0.033 7.2E-07 48.8 3.4 32 294-325 28-59 (75)
88 PRK02821 hypothetical protein; 94.6 0.031 6.8E-07 49.2 3.1 36 196-231 27-62 (77)
89 PRK02821 hypothetical protein; 94.5 0.035 7.6E-07 48.9 3.3 32 294-325 29-60 (77)
90 KOG1960 Predicted RNA-binding 94.2 0.059 1.3E-06 59.9 5.0 134 212-370 227-375 (531)
91 COG1837 Predicted RNA-binding 93.9 0.058 1.3E-06 47.3 3.5 32 294-325 28-59 (76)
92 KOG4369 RTK signaling protein 93.9 0.016 3.6E-07 70.8 0.1 70 297-370 1341-1410(2131)
93 COG1837 Predicted RNA-binding 93.9 0.062 1.3E-06 47.2 3.6 33 196-228 26-58 (76)
94 KOG4369 RTK signaling protein 93.8 0.021 4.6E-07 69.9 0.7 75 198-274 1338-1412(2131)
95 PRK01064 hypothetical protein; 93.6 0.072 1.6E-06 47.1 3.6 34 196-229 26-59 (78)
96 PF14611 SLS: Mitochondrial in 93.4 0.53 1.1E-05 48.7 10.2 66 296-371 26-91 (210)
97 PRK01064 hypothetical protein; 93.4 0.088 1.9E-06 46.5 3.7 32 294-325 28-59 (78)
98 KOG3273 Predicted RNA-binding 93.2 0.038 8.3E-07 56.3 1.3 54 209-272 178-231 (252)
99 TIGR03675 arCOG00543 arCOG0054 93.1 0.22 4.8E-06 59.9 7.7 94 213-332 36-129 (630)
100 PRK06418 transcription elongat 92.2 0.7 1.5E-05 46.6 8.6 103 200-331 61-163 (166)
101 PRK08406 transcription elongat 91.7 0.21 4.6E-06 48.9 4.3 36 296-331 32-67 (140)
102 cd02410 archeal_CPSF_KH The ar 91.6 0.24 5.3E-06 48.6 4.6 73 162-238 37-114 (145)
103 KOG2874 rRNA processing protei 91.4 0.31 6.7E-06 52.2 5.3 52 307-370 160-211 (356)
104 PF13083 KH_4: KH domain; PDB: 91.3 0.12 2.5E-06 44.7 1.8 36 294-329 27-62 (73)
105 COG1097 RRP4 RNA-binding prote 91.2 0.43 9.4E-06 50.4 6.3 38 201-238 147-184 (239)
106 PF13083 KH_4: KH domain; PDB: 90.2 0.17 3.7E-06 43.6 1.8 35 197-231 26-60 (73)
107 cd02413 40S_S3_KH K homology R 90.1 0.51 1.1E-05 42.0 4.8 36 295-330 29-64 (81)
108 COG1855 ATPase (PilT family) [ 89.5 0.67 1.4E-05 53.2 6.3 65 258-332 458-522 (604)
109 PF13184 KH_5: NusA-like KH do 89.1 0.31 6.8E-06 42.0 2.6 37 296-332 3-45 (69)
110 cd02409 KH-II KH-II (K homolo 89.0 0.62 1.3E-05 38.4 4.3 34 296-329 25-58 (68)
111 cd02409 KH-II KH-II (K homolo 88.8 0.67 1.4E-05 38.2 4.4 34 200-233 25-58 (68)
112 PF13184 KH_5: NusA-like KH do 88.3 0.33 7.2E-06 41.9 2.2 39 201-239 4-48 (69)
113 PRK13764 ATPase; Provisional 88.2 0.92 2E-05 54.4 6.6 65 258-332 453-517 (602)
114 COG1097 RRP4 RNA-binding prote 88.0 0.98 2.1E-05 47.8 5.9 34 298-331 148-181 (239)
115 cd02414 jag_KH jag_K homology 87.5 0.58 1.3E-05 40.9 3.3 36 295-330 23-58 (77)
116 TIGR03802 Asp_Ala_antiprt aspa 87.5 4.7 0.0001 48.2 11.9 143 199-368 217-380 (562)
117 cd02414 jag_KH jag_K homology 87.3 0.42 9.1E-06 41.8 2.3 33 201-233 25-57 (77)
118 COG0092 RpsC Ribosomal protein 86.4 1.8 4E-05 45.7 6.8 37 295-331 50-91 (233)
119 COG1855 ATPase (PilT family) [ 86.2 0.35 7.6E-06 55.3 1.6 40 199-238 485-524 (604)
120 TIGR03675 arCOG00543 arCOG0054 85.5 0.98 2.1E-05 54.6 5.0 63 174-238 69-131 (630)
121 PRK03818 putative transporter; 85.1 6.3 0.00014 47.0 11.3 139 200-365 205-360 (552)
122 TIGR01952 nusA_arch NusA famil 85.0 1.2 2.5E-05 43.8 4.4 35 297-331 34-68 (141)
123 PF07650 KH_2: KH domain syndr 84.9 0.49 1.1E-05 41.1 1.5 35 296-330 25-59 (78)
124 PRK13764 ATPase; Provisional 84.1 0.63 1.4E-05 55.7 2.5 42 198-239 479-520 (602)
125 cd02412 30S_S3_KH K homology R 83.7 1.2 2.6E-05 41.6 3.7 32 296-327 61-92 (109)
126 KOG2874 rRNA processing protei 83.6 1.6 3.5E-05 47.0 4.9 51 212-272 161-211 (356)
127 PRK06418 transcription elongat 82.5 1.7 3.8E-05 43.8 4.5 38 294-332 59-96 (166)
128 COG1782 Predicted metal-depend 81.6 1.7 3.7E-05 50.4 4.4 65 172-238 73-137 (637)
129 cd02411 archeal_30S_S3_KH K ho 79.0 3.2 7E-05 37.0 4.6 30 296-325 38-67 (85)
130 COG5166 Uncharacterized conser 78.8 1.6 3.5E-05 50.4 3.2 72 296-370 449-524 (657)
131 PF07650 KH_2: KH domain syndr 78.5 1.2 2.7E-05 38.6 1.7 35 200-234 25-59 (78)
132 TIGR01008 rpsC_E_A ribosomal p 77.4 7.5 0.00016 40.3 7.2 32 295-326 37-68 (195)
133 COG1847 Jag Predicted RNA-bind 76.5 8.7 0.00019 40.1 7.4 37 294-330 89-125 (208)
134 COG5166 Uncharacterized conser 75.1 2.6 5.5E-05 48.9 3.4 131 199-330 448-605 (657)
135 cd02413 40S_S3_KH K homology R 74.3 3.9 8.5E-05 36.4 3.7 36 200-235 30-65 (81)
136 PTZ00084 40S ribosomal protein 73.4 5.3 0.00012 42.1 5.0 32 295-326 43-74 (220)
137 COG1159 Era GTPase [General fu 73.3 4.5 9.7E-05 44.4 4.6 30 297-326 230-260 (298)
138 PRK11895 ilvH acetolactate syn 72.8 53 0.0012 33.1 11.8 144 200-373 3-148 (161)
139 TIGR01953 NusA transcription t 72.5 4.1 8.9E-05 45.7 4.2 40 199-238 300-339 (341)
140 PRK12328 nusA transcription el 72.4 4.9 0.00011 45.5 4.8 40 199-238 307-346 (374)
141 KOG1924 RhoA GTPase effector D 72.0 16 0.00034 44.7 8.9 19 350-368 377-395 (1102)
142 PRK04191 rps3p 30S ribosomal p 71.5 7.7 0.00017 40.5 5.7 32 296-327 40-71 (207)
143 PRK15494 era GTPase Era; Provi 70.3 9.2 0.0002 42.7 6.4 29 297-325 274-303 (339)
144 KOG2416 Acinus (induces apopto 70.3 3.7 8.1E-05 48.3 3.3 64 210-273 460-538 (718)
145 KOG2236 Uncharacterized conser 70.1 2.2E+02 0.0048 33.3 20.1 14 260-273 244-257 (483)
146 COG0092 RpsC Ribosomal protein 69.5 6.4 0.00014 41.7 4.6 33 199-231 50-86 (233)
147 TIGR00119 acolac_sm acetolacta 69.0 76 0.0016 31.8 11.9 137 201-367 3-140 (157)
148 PRK00089 era GTPase Era; Revie 68.6 10 0.00022 40.8 6.2 30 296-325 226-256 (292)
149 TIGR00436 era GTP-binding prot 68.1 9.5 0.00021 40.9 5.8 35 296-330 221-256 (270)
150 cd01572 QPRTase Quinolinate ph 67.2 44 0.00096 36.2 10.6 69 298-370 29-99 (268)
151 COG0195 NusA Transcription elo 66.7 5.2 0.00011 41.3 3.2 38 201-238 143-180 (190)
152 cd02412 30S_S3_KH K homology R 66.7 4.9 0.00011 37.6 2.8 30 201-230 62-91 (109)
153 COG5271 MDN1 AAA ATPase contai 66.7 5 0.00011 52.8 3.5 7 74-80 3989-3995(4600)
154 PRK05848 nicotinate-nucleotide 66.5 55 0.0012 35.7 11.1 70 297-370 30-99 (273)
155 PF02749 QRPTase_N: Quinolinat 65.2 25 0.00053 31.5 6.9 70 296-369 16-85 (88)
156 COG1847 Jag Predicted RNA-bind 64.9 5.5 0.00012 41.5 3.0 38 198-235 89-126 (208)
157 KOG1423 Ras-like GTPase ERA [C 64.3 8.3 0.00018 42.7 4.3 34 296-329 328-362 (379)
158 COG0490 Putative regulatory, l 64.3 5.7 0.00012 39.8 2.9 56 305-365 97-158 (162)
159 TIGR01334 modD putative molybd 63.8 63 0.0014 35.4 11.0 68 299-370 34-101 (277)
160 cd01568 QPRTase_NadC Quinolina 63.2 58 0.0012 35.3 10.6 70 297-370 28-98 (269)
161 TIGR01009 rpsC_bact ribosomal 63.0 25 0.00055 36.8 7.5 30 296-325 62-91 (211)
162 PRK12327 nusA transcription el 62.7 7.9 0.00017 43.8 4.0 41 198-238 301-341 (362)
163 PRK09202 nusA transcription el 62.1 6.7 0.00015 45.9 3.4 40 199-238 301-340 (470)
164 COG1702 PhoH Phosphate starvat 61.7 17 0.00037 40.7 6.3 57 207-273 22-80 (348)
165 cd01573 modD_like ModD; Quinol 61.3 72 0.0016 34.7 10.9 68 299-370 30-97 (272)
166 PRK07428 nicotinate-nucleotide 60.7 76 0.0016 34.9 11.0 70 297-370 42-113 (288)
167 PRK12329 nusA transcription el 60.7 7.5 0.00016 44.9 3.4 39 199-237 334-372 (449)
168 CHL00048 rps3 ribosomal protei 60.6 14 0.00031 38.8 5.2 31 295-325 65-95 (214)
169 KOG0943 Predicted ubiquitin-pr 60.4 13 0.00028 47.2 5.3 32 43-78 1668-1699(3015)
170 cd02411 archeal_30S_S3_KH K ho 59.6 9.2 0.0002 34.1 3.1 28 202-229 40-67 (85)
171 TIGR00078 nadC nicotinate-nucl 59.2 58 0.0013 35.3 9.7 69 298-370 27-95 (265)
172 PRK00310 rpsC 30S ribosomal pr 59.1 31 0.00067 36.8 7.4 30 296-325 62-91 (232)
173 COG4010 Uncharacterized protei 58.3 20 0.00043 35.4 5.3 44 220-272 126-169 (170)
174 KOG1924 RhoA GTPase effector D 58.2 58 0.0012 40.2 10.0 16 251-266 262-277 (1102)
175 PF02749 QRPTase_N: Quinolinat 57.9 36 0.00077 30.5 6.6 55 218-272 32-86 (88)
176 PRK08385 nicotinate-nucleotide 57.2 94 0.002 34.1 10.9 68 299-370 32-99 (278)
177 PRK15405 ethanolamine utilizat 57.0 1.3E+02 0.0028 31.9 11.2 144 222-372 51-211 (217)
178 PLN02716 nicotinate-nucleotide 53.8 1.2E+02 0.0025 33.9 10.9 68 299-370 50-119 (308)
179 PRK06096 molybdenum transport 53.7 1.3E+02 0.0027 33.2 11.2 68 299-370 35-102 (284)
180 CHL00048 rps3 ribosomal protei 52.7 34 0.00074 36.0 6.4 30 200-229 66-95 (214)
181 cd00652 TBP_TLF TATA box bindi 52.4 1.7E+02 0.0037 29.7 11.2 36 230-274 47-84 (174)
182 COG1159 Era GTPase [General fu 52.4 31 0.00067 38.0 6.2 39 198-236 227-274 (298)
183 KOG1999 RNA polymerase II tran 51.9 30 0.00065 43.3 6.6 70 195-266 148-230 (1024)
184 KOG4264 Nucleo-cytoplasmic pro 51.8 17 0.00036 42.5 4.2 19 575-593 503-521 (694)
185 KOG0262 RNA polymerase I, larg 51.4 13 0.00028 47.4 3.5 15 197-211 1440-1454(1640)
186 COG1702 PhoH Phosphate starvat 51.0 31 0.00068 38.7 6.0 56 303-370 22-79 (348)
187 TIGR00436 era GTP-binding prot 50.2 23 0.00049 38.0 4.8 36 200-235 221-265 (270)
188 PRK08072 nicotinate-nucleotide 48.5 62 0.0013 35.4 7.8 53 316-370 51-105 (277)
189 PRK09016 quinolinate phosphori 48.3 1.6E+02 0.0034 32.7 10.9 69 298-370 56-126 (296)
190 PRK06978 nicotinate-nucleotide 48.3 1.7E+02 0.0038 32.3 11.2 69 298-370 53-123 (294)
191 PRK04972 putative transporter; 47.5 1.4E+02 0.003 35.9 11.2 145 200-368 214-375 (558)
192 PRK00089 era GTPase Era; Revie 47.4 28 0.00061 37.5 5.1 37 200-236 226-271 (292)
193 PRK06543 nicotinate-nucleotide 45.3 2.1E+02 0.0045 31.5 11.2 55 314-370 50-106 (281)
194 PRK06559 nicotinate-nucleotide 44.5 2E+02 0.0044 31.8 11.0 68 299-370 43-114 (290)
195 PF04147 Nop14: Nop14-like fam 44.0 22 0.00047 44.7 4.0 13 15-27 278-290 (840)
196 PRK15494 era GTPase Era; Provi 44.0 31 0.00067 38.5 4.8 37 200-236 273-318 (339)
197 PRK06106 nicotinate-nucleotide 44.0 2.1E+02 0.0045 31.5 11.0 54 315-370 56-111 (281)
198 COG2101 SPT15 TATA-box binding 43.9 40 0.00087 34.4 5.0 107 249-370 63-181 (185)
199 PTZ00084 40S ribosomal protein 42.8 56 0.0012 34.6 6.2 29 201-229 45-73 (220)
200 TIGR01008 rpsC_E_A ribosomal p 42.8 46 0.00099 34.6 5.4 30 200-229 38-67 (195)
201 cd04517 TLF TBP-like factors ( 42.7 2.6E+02 0.0057 28.4 10.8 35 230-273 47-83 (174)
202 PF09869 DUF2096: Uncharacteri 42.4 48 0.001 33.5 5.3 57 200-272 113-169 (169)
203 PRK07896 nicotinate-nucleotide 40.1 3.3E+02 0.0071 30.1 11.8 69 298-370 45-117 (289)
204 COG0014 ProA Gamma-glutamyl ph 39.6 1.1E+02 0.0025 35.1 8.3 112 196-330 103-221 (417)
205 COG0331 FabD (acyl-carrier-pro 38.9 1.5E+02 0.0033 33.0 9.1 57 305-369 131-189 (310)
206 PRK05742 nicotinate-nucleotide 37.4 3.3E+02 0.0072 29.8 11.3 69 298-370 37-107 (277)
207 KOG0391 SNF2 family DNA-depend 37.2 10 0.00022 48.3 -0.3 15 196-210 598-612 (1958)
208 PLN00062 TATA-box-binding prot 35.9 3E+02 0.0065 28.2 10.0 27 346-372 147-175 (179)
209 KOG4264 Nucleo-cytoplasmic pro 35.5 23 0.00049 41.5 2.0 11 493-503 433-443 (694)
210 CHL00100 ilvH acetohydroxyacid 34.3 3.3E+02 0.0072 27.8 10.0 52 314-374 97-149 (174)
211 COG2061 ACT-domain-containing 34.0 4.5E+02 0.0097 26.6 10.3 64 306-370 92-157 (170)
212 PRK04191 rps3p 30S ribosomal p 33.7 38 0.00083 35.4 3.3 29 202-230 42-70 (207)
213 PRK00394 transcription factor; 33.6 4.7E+02 0.01 26.8 11.0 34 231-273 47-82 (179)
214 KOG3181 40S ribosomal protein 33.5 56 0.0012 33.8 4.2 37 200-236 44-80 (244)
215 cd04516 TBP_eukaryotes eukaryo 33.0 3.7E+02 0.008 27.4 10.1 25 249-273 57-83 (174)
216 PRK03818 putative transporter; 31.8 72 0.0016 38.2 5.5 97 161-267 255-360 (552)
217 PRK09616 pheT phenylalanyl-tRN 31.7 65 0.0014 38.5 5.2 114 245-369 222-338 (552)
218 PRK06703 flavodoxin; Provision 31.2 2.2E+02 0.0047 27.5 7.9 40 317-370 104-146 (151)
219 PRK05848 nicotinate-nucleotide 31.1 2.5E+02 0.0054 30.7 9.1 146 218-365 45-224 (273)
220 COG2985 Predicted permease [Ge 31.0 1E+02 0.0022 36.3 6.2 97 248-366 254-357 (544)
221 COG5014 Predicted Fe-S oxidore 30.1 95 0.0021 31.9 5.1 58 307-370 126-184 (228)
222 TIGR01009 rpsC_bact ribosomal 29.8 1.2E+02 0.0025 32.0 6.0 28 202-229 64-91 (211)
223 cd04518 TBP_archaea archaeal T 29.6 4E+02 0.0086 27.2 9.7 26 249-274 57-84 (174)
224 PF04461 DUF520: Protein of un 29.1 5.4E+02 0.012 26.1 10.2 41 317-367 107-148 (160)
225 PF03958 Secretin_N: Bacterial 29.0 1.5E+02 0.0032 25.4 5.7 24 344-367 53-76 (82)
226 TIGR03802 Asp_Ala_antiprt aspa 28.4 1.2E+02 0.0026 36.5 6.6 101 161-272 269-382 (562)
227 KOG1060 Vesicle coat complex A 28.2 1.1E+02 0.0024 38.0 6.1 18 200-217 802-819 (968)
228 PF03958 Secretin_N: Bacterial 28.0 1.6E+02 0.0034 25.2 5.7 33 229-269 44-76 (82)
229 cd01572 QPRTase Quinolinate ph 27.5 3E+02 0.0065 29.9 8.9 56 218-273 43-100 (268)
230 PRK05412 putative nucleotide-b 27.1 6.8E+02 0.015 25.4 10.7 41 317-367 107-148 (161)
231 COG4010 Uncharacterized protei 26.0 3.3E+02 0.0071 27.2 7.8 43 316-369 126-168 (170)
232 PF02080 TrkA_C: TrkA-C domain 25.9 49 0.0011 27.5 2.1 49 315-364 14-70 (71)
233 PRK06039 ileS isoleucyl-tRNA s 25.2 3.8E+02 0.0083 34.5 10.6 25 348-373 920-944 (975)
234 TIGR01334 modD putative molybd 25.2 2.9E+02 0.0063 30.3 8.3 148 218-365 47-230 (277)
235 PTZ00415 transmission-blocking 24.9 2.1E+02 0.0047 38.6 7.9 8 297-304 361-368 (2849)
236 PRK15468 carboxysome structura 24.9 1.3E+02 0.0029 28.4 4.7 40 323-371 61-100 (111)
237 PRK04021 hypothetical protein; 24.3 1.4E+02 0.003 27.4 4.7 40 316-361 50-90 (92)
238 KOG2333 Uncharacterized conser 24.1 2.5E+02 0.0053 33.3 7.6 65 201-271 265-346 (614)
239 KOG0262 RNA polymerase I, larg 23.7 59 0.0013 42.0 2.9 14 258-271 1530-1543(1640)
240 COG5014 Predicted Fe-S oxidore 23.5 60 0.0013 33.3 2.4 59 210-272 125-184 (228)
241 PF10369 ALS_ss_C: Small subun 23.4 1.4E+02 0.0031 26.0 4.5 42 316-366 17-58 (75)
242 cd02191 FtsZ FtsZ is a GTPase 23.2 1.1E+02 0.0023 33.9 4.6 132 220-370 138-277 (303)
243 PRK04021 hypothetical protein; 23.2 1.2E+02 0.0026 27.8 4.1 42 219-264 49-91 (92)
244 COG0072 PheT Phenylalanyl-tRNA 23.0 1.4E+02 0.003 36.6 5.9 109 247-369 217-328 (650)
245 COG1570 XseA Exonuclease VII, 22.9 1.8E+02 0.0039 34.0 6.4 53 300-366 129-190 (440)
246 COG5624 TAF61 Transcription in 22.7 33 0.00073 39.0 0.5 48 16-71 384-435 (505)
247 PF09383 NIL: NIL domain; Int 21.8 3E+02 0.0065 23.5 6.2 63 200-268 3-68 (76)
248 KOG2199 Signal transducing ada 21.8 3.7E+02 0.008 31.1 8.3 19 250-268 160-178 (462)
249 PF06183 DinI: DinI-like famil 21.6 2.6E+02 0.0056 24.0 5.6 46 220-272 12-59 (65)
250 cd01573 modD_like ModD; Quinol 21.3 3.7E+02 0.0081 29.3 8.2 55 219-273 44-98 (272)
251 TIGR02516 type_III_yscC type I 20.8 1E+03 0.023 27.7 12.3 25 344-368 206-230 (462)
252 TIGR00078 nadC nicotinate-nucl 20.7 3.7E+02 0.0081 29.2 8.0 54 220-273 43-96 (265)
253 PF00352 TBP: Transcription fa 20.7 1.5E+02 0.0031 26.4 4.1 35 230-273 49-85 (86)
254 KOG0968 DNA polymerase zeta, c 20.7 70 0.0015 41.0 2.7 62 301-371 1096-1166(1488)
255 COG1135 AbcC ABC-type metal io 20.6 1E+03 0.022 26.9 11.3 66 296-367 264-330 (339)
256 CHL00100 ilvH acetohydroxyacid 20.6 2.8E+02 0.0061 28.3 6.6 45 218-269 97-141 (174)
257 TIGR00119 acolac_sm acetolacta 20.4 2.8E+02 0.006 27.9 6.4 45 218-269 96-140 (157)
258 PRK11895 ilvH acetolactate syn 20.3 2.7E+02 0.0059 28.1 6.4 91 164-269 48-141 (161)
259 TIGR02517 type_II_gspD general 20.2 7.5E+02 0.016 29.7 11.3 158 158-367 129-325 (594)
260 PF03460 NIR_SIR_ferr: Nitrite 20.2 2.1E+02 0.0045 23.9 4.8 58 199-268 9-68 (69)
261 PRK08385 nicotinate-nucleotide 20.1 3.9E+02 0.0085 29.3 8.1 55 219-273 46-100 (278)
No 1
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=2.4e-41 Score=376.74 Aligned_cols=351 Identities=29% Similarity=0.434 Sum_probs=237.8
Q ss_pred CCcCceecc-cccchhhHHhhhcCCCchHHHHhhcCCcchhhccchhhhhccccccccCCccccCCCcCcCCCCCCCCCc
Q 003933 1 MAEEEVLAP-ASAAAADLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDGPV 79 (785)
Q Consensus 1 maee~~~~~-~~~~~~d~krkl~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~kr~~~dd~~~~~~d~l~ 79 (785)
|+||.++++ ......++||+|+.+|.|.-+.-. +.++++-+.+++..-+|++-.+|.+|.|+.. +|.
T Consensus 1 m~~~~q~~~~~~~~~~~~~r~~~~~ele~~~~p~--------~~~~~~~~l~p~~~~s~~~~~~~~~VPd~~V----glv 68 (600)
T KOG1676|consen 1 MNEERQIAIKIYPIDGKYKRKLQSRELEDGPQPF--------KGPSEDTDLDPDMDPSDTVQTERYKVPDEAV----GLV 68 (600)
T ss_pred CCccceeeeeccCcccccccccCCccccccCccc--------cCCCCccccCcccCCcccccccccCCCchhc----eeE
Confidence 899999999 555556799999998888211111 2333342233334668899999999999984 443
Q ss_pred c-ccCccC-----CCCcc-------cc------ccccccccccchhhhhhhhccccC-------CChh----hhh----h
Q 003933 80 N-VNGLKE-----EKPDE-------VV------DAEQLTEDTTKEEELESAEVKTEQ-------HSSV----EEQ----A 125 (785)
Q Consensus 80 ~-~~~~~~-----~k~~e-------~~------~e~~~~e~v~~~s~d~See~~~~~-------~~~e----~~~----~ 125 (785)
+ +++-.. +.... .. +.+...|.|++.+. -..+..+.. .... +.+ +
T Consensus 69 IGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~-li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa 147 (600)
T KOG1676|consen 69 IGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQ-LIGEVVSRGRPPGGFPDNQGSVETTQEILIPA 147 (600)
T ss_pred eeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHH-hhhhhhhccCCCCCccccCCccceeeeeccCc
Confidence 2 111110 00000 00 11111111110000 000000000 0000 000 0
Q ss_pred ccccccccccchhhhhcc-cchhhhhccccccccc-cccccccccchhhhhhhcccchhhhccCCCCCC------CCCCC
Q 003933 126 SVDNQQISVKEETKEVLF-STEEAFIDVKEETKEV-TVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP------SSTDD 197 (785)
Q Consensus 126 ~~~~ke~~~~ee~k~~~~-s~~~~~~~~~e~~~~d-s~k~~~i~g~~esVE~A~~lI~~ii~~~~~~~p------~~~~~ 197 (785)
..+..=|.+..|+..... -++|.+.++.+....+ ..|++.|+++.+.||.|+.|+.++|.++....+ .....
T Consensus 148 ~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g 227 (600)
T KOG1676|consen 148 NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGGHAGVRGG 227 (600)
T ss_pred cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccccccCcCcc
Confidence 011111333344444443 2346667777766666 689999999999999999999999974322221 22334
Q ss_pred CCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCC
Q 003933 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGG 277 (785)
Q Consensus 198 ~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg 277 (785)
...+++|.||++.||.||||+|+|||+|+.+||+||+|..|++ +.+.+|++.|.|+++.|.+|.+||++||++...+.
T Consensus 228 ~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~--p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 228 GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD--PSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred ccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC--CCCccceeeeecCHHHHHHHHHHHHHHHHHHhccC
Confidence 5569999999999999999999999999999999999998754 57889999999999999999999999999876431
Q ss_pred CCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHH
Q 003933 278 SPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQI 357 (785)
Q Consensus 278 ~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqV 357 (785)
... ...|.. .....+.|.||.+|||+||||+|+|||.|.++|||||+ |+.+ ++..+.++|+|+|+|+..+|
T Consensus 306 ~~~-~~~G~P-----~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~e-l~r~--~p~~~~~ektf~IrG~~~QI 376 (600)
T KOG1676|consen 306 GGG-MGGGAP-----GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCE-LSRQ--PPNGNPKEKTFVIRGDKRQI 376 (600)
T ss_pred CCC-cCCCCc-----cceeeEEEeccccccccccCCCccchhhhcccCCcccc-ccCC--CCCCCccceEEEEecCcccc
Confidence 111 111111 12237899999999999999999999999999999999 5655 57788999999999999999
Q ss_pred HHHHHHHHHHHhcccCCC
Q 003933 358 EIAQEMIKEVLSQTVRPS 375 (785)
Q Consensus 358 e~Ak~lI~~ll~~~~r~~ 375 (785)
++|++||+++|.....+.
T Consensus 377 dhAk~LIr~kvg~~~~n~ 394 (600)
T KOG1676|consen 377 DHAKQLIRDKVGDIAPNT 394 (600)
T ss_pred hHHHHHHHHHhcccCCCC
Confidence 999999999998765554
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.98 E-value=5.1e-30 Score=286.50 Aligned_cols=206 Identities=33% Similarity=0.555 Sum_probs=169.2
Q ss_pred cccccccccchhhhhhhcccchhhhccCCCCC--CCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 003933 160 TVKEEETVKEEESVEPSNVVPQQVVDNSKSDD--PSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITR 237 (785)
Q Consensus 160 s~k~~~i~g~~esVE~A~~lI~~ii~~~~~~~--p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k 237 (785)
......+++..++|+.||.||..++++..... +.......++.+|+||.+++|+||||+|+|||.|+++|||+|.+..
T Consensus 97 ~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iq 176 (600)
T KOG1676|consen 97 GYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQ 176 (600)
T ss_pred ccccccccCCcccHHHHHHhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEe
Confidence 34556778999999999999999997664221 1222346789999999999999999999999999999999999998
Q ss_pred CCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchH
Q 003933 238 DADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET 317 (785)
Q Consensus 238 ~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGet 317 (785)
++....+ .++.|+|+|+.+.|+.|+.||.++|+|++..........+.. .....+++|.||+++||.||||+|+|
T Consensus 177 d~~~~~~-~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~----~g~~~~~~V~VPr~~VG~IIGkgGE~ 251 (600)
T KOG1676|consen 177 DGSIATG-ADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGGHAGVR----GGGSATREVKVPRSKVGIIIGKGGEM 251 (600)
T ss_pred cCCcCCC-CCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccccccCcC----ccccceeEEeccccceeeEEecCchH
Confidence 8765544 789999999999999999999999998654322221111111 12345899999999999999999999
Q ss_pred HHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcccCC
Q 003933 318 IKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRP 374 (785)
Q Consensus 318 IK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~~~r~ 374 (785)
||+|+.+||+||+ |++++.+ .+.||++.|.|+.++|++|.+||.+||++..+.
T Consensus 252 IKklq~etG~KIQ-fkpDd~p---~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 252 IKKLQNETGAKIQ-FKPDDDP---SSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred HHHHhhccCceeE-eecCCCC---CCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999999 5776654 778999999999999999999999999876543
No 3
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=8.3e-27 Score=244.20 Aligned_cols=172 Identities=34% Similarity=0.528 Sum_probs=146.5
Q ss_pred CCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhcc
Q 003933 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA 275 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~ 275 (785)
.+..+.+|||||+..+|.||||+|+||..|+++|||+|+++|..|+.|+.++|+|.|.|+.++|...+++|.++|+|...
T Consensus 35 e~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 35 EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred CCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence 34448999999999999999999999999999999999999999999999999999999999999999999999998743
Q ss_pred CCCC-cccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCH
Q 003933 276 GGSP-SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDM 354 (785)
Q Consensus 276 gg~p-~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~ 354 (785)
.-.. ..+ +.. +..++..+++|.||+..+|.||||+|.|||.|++++||.|+| .+.. +...+..+|+|+|+|++
T Consensus 115 ~~~k~v~~---~~p-qt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqi-sPqk-pt~~sLqervvt~sge~ 188 (402)
T KOG2191|consen 115 AVAKPVDI---LQP-QTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQI-SPQK-PTGISLQERVVTVSGEP 188 (402)
T ss_pred hhcCCccc---cCC-CCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEe-cccC-CCCccceeEEEEecCCH
Confidence 1111 111 111 123455678999999999999999999999999999999995 4433 46678899999999999
Q ss_pred HHHHHHHHHHHHHHhcccC
Q 003933 355 RQIEIAQEMIKEVLSQTVR 373 (785)
Q Consensus 355 eqVe~Ak~lI~~ll~~~~r 373 (785)
+++.+|..||.++|.++..
T Consensus 189 e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 189 EQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred HHHHHHHHHHHHHhhcCCc
Confidence 9999999999998877543
No 4
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.85 E-value=1.1e-21 Score=210.80 Aligned_cols=207 Identities=27% Similarity=0.342 Sum_probs=164.8
Q ss_pred cccccccccccchhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 003933 158 EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITR 237 (785)
Q Consensus 158 ~ds~k~~~i~g~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k 237 (785)
-...+.+.+.+..|....|.++|.+++..+..+... ...+.++|+.-+.+||+||||.|++||+|+.+||++|+|++
T Consensus 241 Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k~---~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~ 317 (584)
T KOG2193|consen 241 GAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDKV---AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK 317 (584)
T ss_pred CcccCceEEecCccchHHHHHHHHHHHHHhhhccch---hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee
Confidence 334566677788888889999999999755543332 36789999999999999999999999999999999999998
Q ss_pred CCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCC----------Cccc--ccccch-----------------
Q 003933 238 DADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGS----------PSLV--ARGLAT----------------- 288 (785)
Q Consensus 238 ~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~----------p~~~--~~g~~~----------------- 288 (785)
--+..--+.+|.|+|.|+.|+|.+|..+|+++|++.-...+ +.+. .-+++.
T Consensus 318 lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~ 397 (584)
T KOG2193|consen 318 LQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTF 397 (584)
T ss_pred hhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCcccc
Confidence 77665667799999999999999999999999997532111 0000 000000
Q ss_pred ------hhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHH
Q 003933 289 ------AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQE 362 (785)
Q Consensus 289 ------~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~ 362 (785)
.......+.++|.||...||.||||+|.+||.|.+.+||.|+|.- ++..+..+|+|+|+|++++.-+|.-
T Consensus 398 a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIap----pE~pdvseRMViItGppeaqfKAQg 473 (584)
T KOG2193|consen 398 ASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAP----PEIPDVSERMVIITGPPEAQFKAQG 473 (584)
T ss_pred CCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecC----CCCCCcceeEEEecCChHHHHhhhh
Confidence 011124567899999999999999999999999999999999643 2445788999999999999999999
Q ss_pred HHHHHHhcc
Q 003933 363 MIKEVLSQT 371 (785)
Q Consensus 363 lI~~ll~~~ 371 (785)
.|..+|.+.
T Consensus 474 rifgKikEe 482 (584)
T KOG2193|consen 474 RIFGKIKEE 482 (584)
T ss_pred hhhhhhhhh
Confidence 999988763
No 5
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.85 E-value=6.4e-21 Score=216.28 Aligned_cols=159 Identities=29% Similarity=0.472 Sum_probs=133.5
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc---------cHHHHHHHHHHHHHHH
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG---------TLSNIDKAEKLINAVI 270 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G---------t~e~V~kA~~lI~elI 270 (785)
.++|||++...||.||||+|.+||+||++|.++|.|.. ..+++.+|+|+|+| ..++|.+|.++|...+
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~---~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNE---SLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKL 119 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeec---CCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcc
Confidence 34899999999999999999999999999999999984 36789999999999 9999999999999987
Q ss_pred HhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEE
Q 003933 271 AEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRV 350 (785)
Q Consensus 271 ~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtI 350 (785)
.+++.. ..+.+.. .....+++||+||.++||.||||+|+.||+|+++|||+|+| ..+.+| .+++|.|+|
T Consensus 120 ~~d~~~----~~d~~~~---~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v-~~~~lP---~ster~V~I 188 (485)
T KOG2190|consen 120 EEDDEA----AEDNGED---ASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRV-SSDMLP---NSTERAVTI 188 (485)
T ss_pred cccccc----cccCCcc---ccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEe-cCCCCC---cccceeEEE
Confidence 744211 0011100 00114689999999999999999999999999999999997 455777 667999999
Q ss_pred EcCHHHHHHHHHHHHHHHhccc
Q 003933 351 TGDMRQIEIAQEMIKEVLSQTV 372 (785)
Q Consensus 351 sG~~eqVe~Ak~lI~~ll~~~~ 372 (785)
.|+.+.|.+|+..|..+|.++.
T Consensus 189 sG~~~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 189 SGEPDAVKKALVQISSRLLENP 210 (485)
T ss_pred cCchHHHHHHHHHHHHHHHhcC
Confidence 9999999999999998887643
No 6
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.81 E-value=9.7e-20 Score=186.50 Aligned_cols=202 Identities=25% Similarity=0.423 Sum_probs=148.1
Q ss_pred ccccccccccchhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 159 VTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 159 ds~k~~~i~g~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
|++..+.|..-..+++...+++.++|...+.. -.....|.+||||..+++|.||||+|+.||+||+++.|+++|..
T Consensus 85 ds~~peri~tisad~~ti~~ilk~iip~lee~---f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift- 160 (390)
T KOG2192|consen 85 DSSGPERILTISADIETIGEILKKIIPTLEEG---FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT- 160 (390)
T ss_pred CCCCCceeEEEeccHHHHHHHHHHHhhhhhhC---CCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh-
Confidence 34444444333344444445555555321111 01234589999999999999999999999999999999999985
Q ss_pred CCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCC------------------Cc--------------------
Q 003933 239 ADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGS------------------PS-------------------- 280 (785)
Q Consensus 239 ~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~------------------p~-------------------- 280 (785)
+.++.+++|+|.|.|...+|..|++.|+++|+|....++ +.
T Consensus 161 -~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgp 239 (390)
T KOG2192|consen 161 -ECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGP 239 (390)
T ss_pred -ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCC
Confidence 478899999999999999999999999999998541111 00
Q ss_pred -------cc---ccc-----------cchh--------------------------------------hcc-CCccEEEE
Q 003933 281 -------LV---ARG-----------LATA--------------------------------------QAS-GAAEQVEI 300 (785)
Q Consensus 281 -------~~---~~g-----------~~~~--------------------------------------~~~-~~~~~~~i 300 (785)
++ .++ |+.. -.. .-..+..+
T Consensus 240 p~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQv 319 (390)
T KOG2192|consen 240 PPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQV 319 (390)
T ss_pred CCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeE
Confidence 00 000 0000 000 12346788
Q ss_pred EecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 301 KVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 301 ~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
.||.++-|.||||+|+.||+|+.++||.|+| ++ +.+.+.+|+++|+|+.++|+.|..|+...+++
T Consensus 320 tip~dlggsiigkggqri~~ir~esGA~Iki--de---pleGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 320 TIPKDLGGSIIGKGGQRIKQIRHESGASIKI--DE---PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred ecccccCcceecccchhhhhhhhccCceEEe--cC---cCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 9999999999999999999999999999994 33 34577899999999999999999999887763
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.81 E-value=4.2e-20 Score=198.69 Aligned_cols=161 Identities=24% Similarity=0.363 Sum_probs=135.7
Q ss_pred CCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccC
Q 003933 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG 276 (785)
Q Consensus 197 ~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~g 276 (785)
....-+|++||..+||.||||.|.|||.|-+.|.|+|+|.+... .+..+|+|+|.++.|...+|+++|+++|..+-.
T Consensus 196 ~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken--~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~- 272 (584)
T KOG2193|consen 196 LKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN--AGAAEKIITVHSTPEGTSKACKMILEIMQKEAV- 272 (584)
T ss_pred ccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc--CCcccCceEEecCccchHHHHHHHHHHHHHhhh-
Confidence 34678999999999999999999999999999999999987643 467899999999999999999999999987521
Q ss_pred CCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHH
Q 003933 277 GSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQ 356 (785)
Q Consensus 277 g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eq 356 (785)
+..+ .....++|+-.+++||+||||.|.+||+|+++||++|.|..-.++ .....||+|+|.|+.|.
T Consensus 273 ------~~k~------~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqel--s~ynpERTItVkGsiEa 338 (584)
T KOG2193|consen 273 ------DDKV------AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQEL--SLYNPERTITVKGSIEA 338 (584)
T ss_pred ------ccch------hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhh--cccCccceEEecccHHH
Confidence 1111 134567888999999999999999999999999999997433332 23456999999999999
Q ss_pred HHHHHHHHHHHHhcccCC
Q 003933 357 IEIAQEMIKEVLSQTVRP 374 (785)
Q Consensus 357 Ve~Ak~lI~~ll~~~~r~ 374 (785)
|..|..+|..+|+++-..
T Consensus 339 c~~AE~eImkKlre~yEn 356 (584)
T KOG2193|consen 339 CVQAEAEIMKKLRECYEN 356 (584)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 999999999999886444
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.79 E-value=3.7e-18 Score=174.99 Aligned_cols=149 Identities=23% Similarity=0.421 Sum_probs=130.2
Q ss_pred CCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCC
Q 003933 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGG 277 (785)
Q Consensus 198 ~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg 277 (785)
..+.++|||-++.+|.||||+|++||.|+.+++|.|.|... +.++|+|+|+.+.+.|...++.|.-.|++.
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-----~~peri~tisad~~ti~~ilk~iip~lee~---- 116 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-----SGPERILTISADIETIGEILKKIIPTLEEG---- 116 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-----CCCceeEEEeccHHHHHHHHHHHhhhhhhC----
Confidence 34789999999999999999999999999999999999854 467999999999999998888888877763
Q ss_pred CCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHH
Q 003933 278 SPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQI 357 (785)
Q Consensus 278 ~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqV 357 (785)
|. ....+.+||+|..+++|.||||+|..||+|++++.||++|| -...| .+++|+|.|.|.+..|
T Consensus 117 --------f~----~~~pce~rllihqs~ag~iigrngskikelrekcsarlkif-t~c~p---~stdrv~l~~g~~k~v 180 (390)
T KOG2192|consen 117 --------FQ----LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIF-TECCP---HSTDRVVLIGGKPKRV 180 (390)
T ss_pred --------CC----CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhh-hccCC---CCcceEEEecCCcchH
Confidence 11 12457889999999999999999999999999999999975 34433 7789999999999999
Q ss_pred HHHHHHHHHHHhcc
Q 003933 358 EIAQEMIKEVLSQT 371 (785)
Q Consensus 358 e~Ak~lI~~ll~~~ 371 (785)
..+++.|+++|++.
T Consensus 181 ~~~i~~il~~i~e~ 194 (390)
T KOG2192|consen 181 VECIKIILDLISES 194 (390)
T ss_pred HHHHHHHHHHhhcC
Confidence 99999999999874
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.75 E-value=1.3e-17 Score=189.53 Aligned_cols=202 Identities=26% Similarity=0.434 Sum_probs=150.2
Q ss_pred chhhhhhhcccchhhhccC-CCCCCC--CCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCC
Q 003933 169 EEESVEPSNVVPQQVVDNS-KSDDPS--STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHA 245 (785)
Q Consensus 169 ~~esVE~A~~lI~~ii~~~-~~~~p~--~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s 245 (785)
..+++.+|..+|...++.. ...... ......+++||+||.+++|.||||+|++||+|+++|||+|.|.++ ..|.+
T Consensus 104 ~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~s 181 (485)
T KOG2190|consen 104 ATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNS 181 (485)
T ss_pred hHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcc
Confidence 6677777776666654311 111111 112225899999999999999999999999999999999999986 68999
Q ss_pred CCcceEecccHHHHHHHHHHHHHHHHhhc----c-CC---------------CCccc-----------------------
Q 003933 246 ATRPVEIIGTLSNIDKAEKLINAVIAEAD----A-GG---------------SPSLV----------------------- 282 (785)
Q Consensus 246 ~eRiV~I~Gt~e~V~kA~~lI~elI~e~~----~-gg---------------~p~~~----------------------- 282 (785)
.+|.|+|.|+.+.|.+|+..|..+|.+.. . .. ++...
T Consensus 182 ter~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~ 261 (485)
T KOG2190|consen 182 TERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLI 261 (485)
T ss_pred cceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhc
Confidence 99999999999999999999999998831 0 00 00000
Q ss_pred ----------ccc--------------------cc------hhhc--c-------------------------CCccEEE
Q 003933 283 ----------ARG--------------------LA------TAQA--S-------------------------GAAEQVE 299 (785)
Q Consensus 283 ----------~~g--------------------~~------~~~~--~-------------------------~~~~~~~ 299 (785)
+.+ +. +... . ....+.+
T Consensus 262 ~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~ 341 (485)
T KOG2190|consen 262 CPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQR 341 (485)
T ss_pred CchhhceeeecCCCccchhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeee
Confidence 000 00 0000 0 1125679
Q ss_pred EEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcccCCC
Q 003933 300 IKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS 375 (785)
Q Consensus 300 i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~~~r~~ 375 (785)
|+||++++|+||||+|.+|.+|++.|||.|+|+..++. ....+++|+|+|...+...+..+|...+....+..
T Consensus 342 l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~ 414 (485)
T KOG2190|consen 342 LLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLSAPKSSM 414 (485)
T ss_pred eccCccccceeecccccchHHHHHhcCCceEEcccccc---CCcceeEEEecchhHHHHhhhhhcccccccCccCC
Confidence 99999999999999999999999999999997644331 25689999999999999999999977776655443
No 10
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.74 E-value=6.9e-18 Score=168.78 Aligned_cols=139 Identities=27% Similarity=0.441 Sum_probs=107.9
Q ss_pred EEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEe---cccHHHHHHHHHHHHHHHHhhccCCCCc
Q 003933 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEI---IGTLSNIDKAEKLINAVIAEADAGGSPS 280 (785)
Q Consensus 204 IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I---~Gt~e~V~kA~~lI~elI~e~~~gg~p~ 280 (785)
|.||.+++|.|||++|++||.|+++|||+|.|..+ +..|.| .++.+.+.+|+++|..+++.+.......
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~--------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~ 73 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALK 73 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 67899999999999999999999999999999853 346777 6799999999999999877421000000
Q ss_pred ccccccchhhccCCccEEEEEecC---------CccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEE
Q 003933 281 LVARGLATAQASGAAEQVEIKVPN---------EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVT 351 (785)
Q Consensus 281 ~~~~g~~~~~~~~~~~~~~i~VP~---------~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIs 351 (785)
++... ..-..+.|.. ..+|+||||+|+|||.|++.|||+|.| . +++|+|.
T Consensus 74 l~gd~---------y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i-~-----------~~~v~i~ 132 (172)
T TIGR03665 74 LLDDD---------YMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISV-Y-----------GKTVGII 132 (172)
T ss_pred hcCCc---------ceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEE-c-----------CCEEEEE
Confidence 01111 1111223332 368999999999999999999999995 1 3689999
Q ss_pred cCHHHHHHHHHHHHHHHhcc
Q 003933 352 GDMRQIEIAQEMIKEVLSQT 371 (785)
Q Consensus 352 G~~eqVe~Ak~lI~~ll~~~ 371 (785)
|+.++|+.|+++|++||+..
T Consensus 133 G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 133 GDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred CCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999653
No 11
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.73 E-value=8.3e-18 Score=169.33 Aligned_cols=145 Identities=28% Similarity=0.444 Sum_probs=110.3
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEec----ccHHHHHHHHHHHHHHHHhhcc
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEII----GTLSNIDKAEKLINAVIAEADA 275 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~----Gt~e~V~kA~~lI~elI~e~~~ 275 (785)
+...|.||.+++|.|||++|++||.|+++|||+|+|..+ +..|.|. ++.+.+.+|+++|.+++..++.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~ 74 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSP 74 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCH
Confidence 567999999999999999999999999999999999853 3577775 7999999999999999873210
Q ss_pred CCCCcccccccchhhccCCccEEEEE--ecC-----CccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEE
Q 003933 276 GGSPSLVARGLATAQASGAAEQVEIK--VPN-----EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIV 348 (785)
Q Consensus 276 gg~p~~~~~g~~~~~~~~~~~~~~i~--VP~-----~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~V 348 (785)
.....++...+. .+.++|. ..+ ..+|+||||+|++||.|++.|||+|.| . ++.|
T Consensus 75 e~A~~l~gd~y~-------~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i-~-----------~~~v 135 (180)
T PRK13763 75 EKALRLLDDDYV-------LEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISV-Y-----------GKTV 135 (180)
T ss_pred HHHHHHhCCCce-------EEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEE-c-----------CCEE
Confidence 000000111110 0111110 111 368999999999999999999999995 2 3469
Q ss_pred EEEcCHHHHHHHHHHHHHHHhcc
Q 003933 349 RVTGDMRQIEIAQEMIKEVLSQT 371 (785)
Q Consensus 349 tIsG~~eqVe~Ak~lI~~ll~~~ 371 (785)
+|.|++++|+.|+++|+.|++..
T Consensus 136 ~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 136 AIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred EEEeCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999654
No 12
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.38 E-value=1e-12 Score=139.04 Aligned_cols=202 Identities=26% Similarity=0.253 Sum_probs=142.9
Q ss_pred cccchhhhhhhcccchhhhccCCCCCC--CC-----CCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 166 TVKEEESVEPSNVVPQQVVDNSKSDDP--SS-----TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 166 i~g~~esVE~A~~lI~~ii~~~~~~~p--~~-----~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
|.++-+.|....+.|.++|........ .. ..+....++|+||+...|.||||+|.|||.|+|+++|-|+|...
T Consensus 91 i~Gt~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq 170 (402)
T KOG2191|consen 91 IQGTVEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ 170 (402)
T ss_pred EeccHHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc
Confidence 456666666666777777752221111 10 12233458999999999999999999999999999999999954
Q ss_pred CCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCccccc----c-----------c-chhhccCCccEEEEEe
Q 003933 239 ADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVAR----G-----------L-ATAQASGAAEQVEIKV 302 (785)
Q Consensus 239 ~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~----g-----------~-~~~~~~~~~~~~~i~V 302 (785)
..+.-+..+|+|+|+|+.|++.+|+++|+++|.|+...+.--.+.. | . .............+-|
T Consensus 171 kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sv 250 (402)
T KOG2191|consen 171 KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISV 250 (402)
T ss_pred CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCCCCCCCCCCCccccccchhhccc
Confidence 4555567799999999999999999999999998763211000000 0 0 0001112233456778
Q ss_pred cCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 303 PNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 303 P~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
+..++|.+-|.+|.++-.|-..+|++|.| .+.+........+ +.|.|..-.+..|..||..++..
T Consensus 251 a~~~iG~a~gaG~~~~a~l~~~~G~l~~i--tq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~ 315 (402)
T KOG2191|consen 251 AAGLIGGANGAGGAFGAALSGFTGALIAI--TQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVAS 315 (402)
T ss_pred cccccccccccccccceeeecccccceee--ccccccccccccc-ccccchhhhhhhhhhHHHHhhcc
Confidence 99999999999999999999999998884 3333223344455 78888888899898888876653
No 13
>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=99.31 E-value=4.4e-12 Score=107.05 Aligned_cols=63 Identities=37% Similarity=0.625 Sum_probs=56.2
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 364 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI 364 (785)
++|+||.+++|+||||+|++||+|+++|||+|.| .+.. .....+|+|+|.|+.++|++|+.||
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i-~~~~---~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRV-SKSV---LPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEE-cCCC---CCCCCceEEEEEeCHHHHHHHHHhh
Confidence 6899999999999999999999999999999995 3322 1357799999999999999999998
No 14
>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=99.30 E-value=5.3e-12 Score=106.53 Aligned_cols=65 Identities=35% Similarity=0.567 Sum_probs=59.1
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHH
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~ 267 (785)
+++|+||.+.+|+||||+|++|++|+++|||+|+|.+..+ ....+|+|+|.|+.++|.+|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhhC
Confidence 4799999999999999999999999999999999987543 4567999999999999999999983
No 15
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.28 E-value=5.4e-11 Score=119.49 Aligned_cols=141 Identities=27% Similarity=0.440 Sum_probs=107.7
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc-----cHHHHHHHHHHHHHHHHhh
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-----TLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G-----t~e~V~kA~~lI~elI~e~ 273 (785)
..++.+.||...++.|||++|++.+.|.+.++++|.|+.+ +..|.|.. ++-.+.+|+++|..+=.
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr-- 76 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIGR-- 76 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHhc--
Confidence 3567899999999999999999999999999999999743 45666654 46688888888777533
Q ss_pred ccCCCCcccccccchhhcc---CCccE-EEEEe-----cC-----CccceeecCCchHHHHHHHHhCCeEEEecCCCCCC
Q 003933 274 DAGGSPSLVARGLATAQAS---GAAEQ-VEIKV-----PN-----EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPE 339 (785)
Q Consensus 274 ~~gg~p~~~~~g~~~~~~~---~~~~~-~~i~V-----P~-----~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~ 339 (785)
||....+. ..... ..|.| .+ ...|+|||++|.|.+.|++.|+|+|.|.
T Consensus 77 -----------GF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~------- 138 (194)
T COG1094 77 -----------GFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY------- 138 (194)
T ss_pred -----------CCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-------
Confidence 33322211 01111 11211 11 3469999999999999999999999963
Q ss_pred CCCCCccEEEEEcCHHHHHHHHHHHHHHHhccc
Q 003933 340 GDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTV 372 (785)
Q Consensus 340 ~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~~~ 372 (785)
..+|+|.|..++|+.|++.|+.+|+...
T Consensus 139 -----g~tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 139 -----GKTVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred -----CcEEEEecChhhhHHHHHHHHHHHcCCC
Confidence 5689999999999999999999998644
No 16
>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=99.15 E-value=6e-11 Score=98.78 Aligned_cols=61 Identities=30% Similarity=0.536 Sum_probs=54.0
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK 365 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~ 365 (785)
.+|.||.+++++|||++|++||+|+++|||+|.| . +. ...++.|+|+|+.++|+.|+++|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i-~-~~-----~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRF-P-DP-----GSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEc-C-CC-----CCCCCEEEEEcCHHHHHHHHHHhC
Confidence 5799999999999999999999999999999994 2 21 256899999999999999999874
No 17
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.11 E-value=1.8e-10 Score=96.30 Aligned_cols=59 Identities=29% Similarity=0.518 Sum_probs=52.6
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHH
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIK 365 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~ 365 (785)
....|.||.+++|+||||+|++||.|+++|||+|.| . + ++.|.|+|+ .+.|+.|+++|+
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i-~-~---------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDI-E-D---------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEe-C-C---------CCEEEEEeCCHHHHHHHHHHhC
Confidence 356799999999999999999999999999999994 2 1 468999998 999999999984
No 18
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.11 E-value=6.3e-11 Score=98.01 Aligned_cols=60 Identities=37% Similarity=0.637 Sum_probs=53.3
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 003933 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 364 (785)
Q Consensus 297 ~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI 364 (785)
+.+|.||.+++++||||+|++||+|+++|||+|.| . ++ + ....|+|+|+.++|+.|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i-~-~~-----~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQI-P-DD-----D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEE-E-ST-----T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEE-c-CC-----C-CcEEEEEEeCHHHHHHHHhhC
Confidence 56899999999999999999999999999999994 2 21 2 456999999999999999987
No 19
>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=99.07 E-value=3.9e-10 Score=93.72 Aligned_cols=63 Identities=43% Similarity=0.696 Sum_probs=55.2
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK 365 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~ 365 (785)
.+|.||.+++++|||++|++|++|+++|||+|.| .... .+..+++|+|.|+.++|+.|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i-~~~~----~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKI-PDSG----SGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEE-cCCC----CCCCceEEEEEcCHHHHHHHHHHhC
Confidence 5899999999999999999999999999999994 3221 2467899999999999999999873
No 20
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.03 E-value=1.5e-10 Score=95.73 Aligned_cols=60 Identities=40% Similarity=0.668 Sum_probs=54.7
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHH
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI 266 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI 266 (785)
|.+|+||.+++|+|||++|++||+|+++|||+|.|.++ . ....|+|+|+.++|++|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-----~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-----D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----C-CcEEEEEEeCHHHHHHHHhhC
Confidence 57999999999999999999999999999999999854 1 345999999999999999987
No 21
>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=99.03 E-value=2.8e-10 Score=94.72 Aligned_cols=62 Identities=27% Similarity=0.506 Sum_probs=56.2
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHH
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~ 267 (785)
+.+|.||..++++|||++|++|++|+++|||+|.|.+.. ..++.|+|+|+.++|.+|+.+|+
T Consensus 1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-----~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-----CCCCEEEEEcCHHHHHHHHHHhC
Confidence 368999999999999999999999999999999998643 45789999999999999999874
No 22
>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=99.02 E-value=8.1e-10 Score=91.82 Aligned_cols=63 Identities=38% Similarity=0.602 Sum_probs=56.8
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHH
Q 003933 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (785)
Q Consensus 202 ~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~ 267 (785)
.+|.||.+++++|||++|++|++|+++|+|+|.|....+ ...++.|+|.|+.++|.+|+.+|.
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHhC
Confidence 689999999999999999999999999999999986532 456889999999999999999873
No 23
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.01 E-value=7e-10 Score=92.75 Aligned_cols=59 Identities=29% Similarity=0.470 Sum_probs=53.7
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEeccc-HHHHHHHHHHHH
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDKAEKLIN 267 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt-~e~V~kA~~lI~ 267 (785)
.+..|.||.+++|+||||+|++||+|+++|||+|.|.+ ++.|.|+|+ .++|++|+++|+
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeCCHHHHHHHHHHhC
Confidence 46789999999999999999999999999999999974 357999997 999999999874
No 24
>smart00322 KH K homology RNA-binding domain.
Probab=98.92 E-value=6.9e-09 Score=85.76 Aligned_cols=67 Identities=43% Similarity=0.787 Sum_probs=58.6
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 369 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~ 369 (785)
.+.+|.||.+++++|||++|++|++|++.|+|+|.| ... ....++|+|.|+.++|+.|+.+|.++++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~-~~~------~~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI-PED------GSEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEE-CCC------CCCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 467899999999999999999999999999999995 221 1257899999999999999999998763
No 25
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.91 E-value=6.8e-10 Score=124.58 Aligned_cols=144 Identities=30% Similarity=0.543 Sum_probs=121.6
Q ss_pred CCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCC
Q 003933 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGG 277 (785)
Q Consensus 198 ~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg 277 (785)
..+.+++.|+...|-+||||.|.+||.|++.|++||.+..+. ...+++..+.|....+.+|..+|+.++.+.
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed----~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~---- 137 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED----VGDERVLLISGFPVQVCKAKAAIHQILTEN---- 137 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCccc----CCcccchhhccCCCCCChHHHHHHHHHhcC----
Confidence 457889999999999999999999999999999999998542 233566666678999999999999988764
Q ss_pred CCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHH
Q 003933 278 SPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQI 357 (785)
Q Consensus 278 ~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqV 357 (785)
....+.+.||...+++||||+|++|+.|+..++++|.| +. ++.....+.+.|.+....+
T Consensus 138 ----------------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~--d~---ngr~g~~~~~~i~~qqk~~ 196 (608)
T KOG2279|consen 138 ----------------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITC--DK---NGRLGLSRLIKISGQQKEV 196 (608)
T ss_pred ----------------Ccccccccchhhhcccccccchhhhcchhccccccccc--cc---ccccccccceecccccchH
Confidence 23566788999999999999999999999999999994 22 2456668889999998899
Q ss_pred HHHHHHHHHHHhc
Q 003933 358 EIAQEMIKEVLSQ 370 (785)
Q Consensus 358 e~Ak~lI~~ll~~ 370 (785)
+.|+.||.+.|++
T Consensus 197 ~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 197 AAAKHLILEKVSE 209 (608)
T ss_pred HHHHhhhhccccc
Confidence 9999999887765
No 26
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.81 E-value=6.5e-09 Score=116.85 Aligned_cols=183 Identities=25% Similarity=0.357 Sum_probs=131.9
Q ss_pred cchhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCC
Q 003933 168 KEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAAT 247 (785)
Q Consensus 168 g~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~e 247 (785)
+...+|..|+.++..++. .+..+...+-+|...+++||||+|++|+.|+.-++++|.+.+.. -+...
T Consensus 118 ~~p~~v~~a~a~~~~~~~----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~g~~ 184 (608)
T KOG2279|consen 118 GFPVQVCKAKAAIHQILT----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RLGLS 184 (608)
T ss_pred cCCCCCChHHHHHHHHHh----------cCCcccccccchhhhcccccccchhhhcchhccccccccccccc---ccccc
Confidence 356677778877777662 34567788899999999999999999999999999999998652 23457
Q ss_pred cceEecccHHHHHHHHHHHHHHHHhhcc--C-----------------------------CCCcc-------cccc----
Q 003933 248 RPVEIIGTLSNIDKAEKLINAVIAEADA--G-----------------------------GSPSL-------VARG---- 285 (785)
Q Consensus 248 RiV~I~Gt~e~V~kA~~lI~elI~e~~~--g-----------------------------g~p~~-------~~~g---- 285 (785)
++..|.+....++.|..+|.+.+.+... . +.+.+ ...+
T Consensus 185 ~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~ 264 (608)
T KOG2279|consen 185 RLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLV 264 (608)
T ss_pred cceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCc
Confidence 8889999999999999999887765320 0 00000 0000
Q ss_pred ----------c-----ch------hhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCC-CC
Q 003933 286 ----------L-----AT------AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGD-GS 343 (785)
Q Consensus 286 ----------~-----~~------~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~-~s 343 (785)
+ +. ..........+|.||+.++|+|||+.|++|+.+...|++++.|..- +... ..
T Consensus 265 ~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~---pyt~~v~ 341 (608)
T KOG2279|consen 265 TKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ---PYTSRVL 341 (608)
T ss_pred ccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec---cccchhh
Confidence 0 00 0011122345789999999999999999999999999999996431 1111 12
Q ss_pred CccEEEEEcCHHHHHHHHHHHHH
Q 003933 344 KERIVRVTGDMRQIEIAQEMIKE 366 (785)
Q Consensus 344 ~er~VtIsG~~eqVe~Ak~lI~~ 366 (785)
...+|+|.|+...+.++.+||..
T Consensus 342 ~~qic~~egkqh~~n~vl~ml~~ 364 (608)
T KOG2279|consen 342 QLQICVNEGKQHYENSVLEMLTV 364 (608)
T ss_pred hhhhheecchhHHHHHHHhhhhc
Confidence 23678999999999999999873
No 27
>smart00322 KH K homology RNA-binding domain.
Probab=98.80 E-value=2.3e-08 Score=82.66 Aligned_cols=67 Identities=37% Similarity=0.674 Sum_probs=60.0
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHH
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI 270 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI 270 (785)
..+.+|.|+..++++|||++|++|++|+++|+++|.+..... ..+.|+|.|+.+++..|+.+|.+++
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-----~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-----EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC-----CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 357899999999999999999999999999999999975421 4678999999999999999999876
No 28
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.78 E-value=4.6e-09 Score=110.91 Aligned_cols=153 Identities=22% Similarity=0.344 Sum_probs=112.9
Q ss_pred CCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhcc-C
Q 003933 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA-G 276 (785)
Q Consensus 198 ~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~-g 276 (785)
..+++.+.||..+|+.|+|++|.+||.|+.+|.+.|+.....+ +-++.++|..+.|++|++.|...-+.... .
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e------ePiF~vTg~~edv~~aRrei~saaeH~~l~~ 97 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE------EPIFPVTGRHEDVRRARREIPSAAEHFGLIR 97 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC------CCcceeccCchhHHHHhhcCccccceeeeee
Confidence 5678899999999999999999999999999999998875533 56899999999999999998773322210 0
Q ss_pred CCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHH-
Q 003933 277 GSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMR- 355 (785)
Q Consensus 277 g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~e- 355 (785)
.++... .+... .......+....||...+|+|+|..|++||.|++.++..|.-.. ...+.+|.|+|-.+
T Consensus 98 ~s~s~S-gg~~~-~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v--------~~~~~Vf~Vtg~~~n 167 (394)
T KOG2113|consen 98 ASRSFS-GGTNG-ASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV--------RCGEPVFCVTGAPKN 167 (394)
T ss_pred eccccc-CCCcc-ccccCCCceeeeccceeeeeccccccCccchheecccceEeeec--------cCCCceEEEecCCcc
Confidence 000000 00000 01123455677889999999999999999999999999998332 23578999999755
Q ss_pred HHHHHH-HHHHH
Q 003933 356 QIEIAQ-EMIKE 366 (785)
Q Consensus 356 qVe~Ak-~lI~~ 366 (785)
+|++|+ ..|+.
T Consensus 168 C~kra~s~eie~ 179 (394)
T KOG2113|consen 168 CVKRARSCEIEQ 179 (394)
T ss_pred hhhhccccchhh
Confidence 488887 45554
No 29
>PF13014 KH_3: KH domain
Probab=98.69 E-value=3e-08 Score=76.96 Aligned_cols=43 Identities=51% Similarity=0.885 Sum_probs=36.8
Q ss_pred ccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEc
Q 003933 306 KVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTG 352 (785)
Q Consensus 306 ~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG 352 (785)
++|+||||+|++||+|+++|||+|+| .++ ......+|+|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i-~~~---~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQI-PPE---NEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEE-CCc---cCCCCCceEEEEEC
Confidence 58999999999999999999999995 332 34567899999998
No 30
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. 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=98.66 E-value=7.7e-08 Score=91.16 Aligned_cols=67 Identities=28% Similarity=0.399 Sum_probs=52.4
Q ss_pred CccceeecCCchHHHHHHHHhCCeEEEecCCCCC-------------CCCCCCccEEEEEcCH---HHHHHHHHHHHHHH
Q 003933 305 EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLP-------------EGDGSKERIVRVTGDM---RQIEIAQEMIKEVL 368 (785)
Q Consensus 305 ~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP-------------~~~~s~er~VtIsG~~---eqVe~Ak~lI~~ll 368 (785)
|++|+|||.+|.|||+|+++|||+|.|. .+..- ....++.-.|.|++.. +.+++|+++|+.+|
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Ir-g~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIR-GKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEe-cCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 8999999999999999999999999963 33110 1112334679999964 89999999999999
Q ss_pred hccc
Q 003933 369 SQTV 372 (785)
Q Consensus 369 ~~~~ 372 (785)
....
T Consensus 94 ~~~~ 97 (120)
T cd02395 94 KPAI 97 (120)
T ss_pred ccCC
Confidence 8543
No 31
>PF13014 KH_3: KH domain
Probab=98.64 E-value=4.1e-08 Score=76.23 Aligned_cols=43 Identities=44% Similarity=0.696 Sum_probs=38.4
Q ss_pred ccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc
Q 003933 210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG 254 (785)
Q Consensus 210 ~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G 254 (785)
+||+||||+|++|++|+++|+|+|+|.+ +..+...+|+|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~--~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP--ENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC--ccCCCCCceEEEEEC
Confidence 5899999999999999999999999997 345667899999987
No 32
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. 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=98.63 E-value=7.5e-08 Score=91.23 Aligned_cols=71 Identities=30% Similarity=0.436 Sum_probs=55.8
Q ss_pred EEEecC------CccceeecCCchHHHHHHHHhCCeEEEccCCCCCCC--------------CCCcceEecc-c--HHHH
Q 003933 203 KIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPH--------------AATRPVEIIG-T--LSNI 259 (785)
Q Consensus 203 ~IlVP~------~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~--------------s~eRiV~I~G-t--~e~V 259 (785)
+|+||. +++|+|||.+|+|||+|+++|||+|.|..+...... .....|.|++ + .+.+
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~ 82 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL 82 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence 566655 579999999999999999999999999975321111 1225688888 5 6999
Q ss_pred HHHHHHHHHHHHhh
Q 003933 260 DKAEKLINAVIAEA 273 (785)
Q Consensus 260 ~kA~~lI~elI~e~ 273 (785)
++|+++|..||...
T Consensus 83 ~~A~~~I~~ll~~~ 96 (120)
T cd02395 83 AKAVEAIEELLKPA 96 (120)
T ss_pred HHHHHHHHHHhccC
Confidence 99999999999864
No 33
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.58 E-value=1.5e-07 Score=105.10 Aligned_cols=75 Identities=32% Similarity=0.436 Sum_probs=60.2
Q ss_pred CeEEEEEecC------CccceeecCCchHHHHHHHHhCCeEEEccCCC------------CCC-CCCCcceEecc-cHHH
Q 003933 199 TMSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDAD------------ADP-HAATRPVEIIG-TLSN 258 (785)
Q Consensus 199 ~~t~~IlVP~------~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d------------~~p-~s~eRiV~I~G-t~e~ 258 (785)
.+..+|.||. ++||+|||..|.|+|+|+++|||||.|+.+.. ..+ ...+..|.|++ |.|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 6778888886 57999999999999999999999999986211 111 12245677777 8899
Q ss_pred HHHHHHHHHHHHHhh
Q 003933 259 IDKAEKLINAVIAEA 273 (785)
Q Consensus 259 V~kA~~lI~elI~e~ 273 (785)
|++|+++|+.||.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999974
No 34
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.44 E-value=4.2e-07 Score=109.58 Aligned_cols=139 Identities=22% Similarity=0.374 Sum_probs=110.8
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCC
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP 279 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p 279 (785)
....+.|-..++..||||+|.+|.+|++++.|+|.+.+.. ..+..|+|.+...++.+|.+.|+.++.+...
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~-----~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n---- 417 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG-----SNNKKVVITGVSANDEKAVEDVEKIIAEILN---- 417 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc-----CCCCCeEEeccccchhHHHHHHHHHHHhhhc----
Confidence 6778888889999999999999999999999999998742 3477899999999999999999999998631
Q ss_pred cccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHH
Q 003933 280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEI 359 (785)
Q Consensus 280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~ 359 (785)
......+.||...+.+|||.+|.+|..|..+++| |+|...++ .+....++|.|....|..
T Consensus 418 --------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-v~i~f~~~-----~~~~~~~~~~~~~~dv~~ 477 (753)
T KOG2208|consen 418 --------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGG-VHIKFQNN-----NNSSDMVTIRGISKDVEK 477 (753)
T ss_pred --------------ccccceeecCccchhhhhccccccHHHHHhhcCc-EEEecCCC-----CcccccceEeccccccch
Confidence 1235578999999999999999999999999996 55434333 334556777777665655
Q ss_pred HHHHHHHH
Q 003933 360 AQEMIKEV 367 (785)
Q Consensus 360 Ak~lI~~l 367 (785)
++.++..+
T Consensus 478 ~~~~~~~~ 485 (753)
T KOG2208|consen 478 SVSLLKAL 485 (753)
T ss_pred hHHHHHhh
Confidence 55555443
No 35
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.41 E-value=4.7e-07 Score=91.04 Aligned_cols=97 Identities=23% Similarity=0.315 Sum_probs=73.4
Q ss_pred ccchhhhhhhcccchhhhccCCCCCCCC-CCCCCeEEEEEecC---------CccceeecCCchHHHHHHHHhCCeEEEc
Q 003933 167 VKEEESVEPSNVVPQQVVDNSKSDDPSS-TDDSTMSRKIEVPN---------NKVGVLIGKAGDTIRYLQYNSGAKIQIT 236 (785)
Q Consensus 167 ~g~~esVE~A~~lI~~ii~~~~~~~p~~-~~~~~~t~~IlVP~---------~~VG~IIGk~G~tIK~IqeeTGAkI~I~ 236 (785)
+.+.+++..|+.+|..+..++....... -.+..+..-|.|.. ..+|+|||++|+||+.|++.|||+|.|.
T Consensus 46 t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~ 125 (172)
T TIGR03665 46 DEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY 125 (172)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc
Confidence 6888999999999998876533221000 01222333344443 3689999999999999999999999997
Q ss_pred cCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhh
Q 003933 237 RDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 237 k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~ 273 (785)
. +.|+|.|+.++|+.|.++|.+||+..
T Consensus 126 ~----------~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 126 G----------KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred C----------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 2 57999999999999999999999643
No 36
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.37 E-value=1.4e-06 Score=97.34 Aligned_cols=76 Identities=25% Similarity=0.338 Sum_probs=56.7
Q ss_pred ccEEEEEecC------CccceeecCCchHHHHHHHHhCCeEEEecCCC----------CCCC-CCCCccEEEEEcC-HHH
Q 003933 295 AEQVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQVLIPQH----------LPEG-DGSKERIVRVTGD-MRQ 356 (785)
Q Consensus 295 ~~~~~i~VP~------~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~----------lP~~-~~s~er~VtIsG~-~eq 356 (785)
..+.+|.||- ++||+|||.+|.|+|+|+++|||||.|+-... +... ...++-.|.|+.+ .|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 4456676665 89999999999999999999999999853211 1111 1222334778886 789
Q ss_pred HHHHHHHHHHHHhc
Q 003933 357 IEIAQEMIKEVLSQ 370 (785)
Q Consensus 357 Ve~Ak~lI~~ll~~ 370 (785)
|++|+++|+.||..
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
No 37
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.34 E-value=7.3e-07 Score=90.25 Aligned_cols=65 Identities=23% Similarity=0.467 Sum_probs=56.6
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEE----cCHHHHHHHHHHHHHHHhc
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVT----GDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIs----G~~eqVe~Ak~lI~~ll~~ 370 (785)
....|.||.+++|.|||++|++||.|+++|||+|+| .. ++..|.|. ++++.+++|+++|+.++..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i-~~---------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEI-DS---------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEE-EC---------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 356899999999999999999999999999999995 21 24688886 7899999999999998873
No 38
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.33 E-value=1.3e-06 Score=105.56 Aligned_cols=192 Identities=20% Similarity=0.282 Sum_probs=127.5
Q ss_pred cccccchhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCC
Q 003933 164 EETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADP 243 (785)
Q Consensus 164 ~~i~g~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p 243 (785)
....+.-++|+.|++.+..++... ...-+..++.|-...+..|||++|.+|+.++.++.+.|+|....+..+
T Consensus 173 i~~~G~~e~V~~a~~~~~~~~~~~--------~~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~ 244 (753)
T KOG2208|consen 173 IKLQGVVESVERAREPILNLIDRK--------NERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSP 244 (753)
T ss_pred eeeecchhhhhhhhhhhhhhhhcc--------cceeEEEEeeccccchhhhccccccccccccccceeEEEcccccccch
Confidence 445688889999999988888322 334478899999999999999999999999999999999985433211
Q ss_pred C--CCCcceEecccHHHHHHHHHHHHH-H-HHhhc-------------------------------c--CCCCccccccc
Q 003933 244 H--AATRPVEIIGTLSNIDKAEKLINA-V-IAEAD-------------------------------A--GGSPSLVARGL 286 (785)
Q Consensus 244 ~--s~eRiV~I~Gt~e~V~kA~~lI~e-l-I~e~~-------------------------------~--gg~p~~~~~g~ 286 (785)
. ...+...+....-.+..++.++.. + +.+.- . .....++.+++
T Consensus 245 ~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~ 324 (753)
T KOG2208|consen 245 SNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGF 324 (753)
T ss_pred hhhhccccccceehhhhhHHHHHHhcChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeeccc
Confidence 1 112223333333344444444322 1 00000 0 00001111111
Q ss_pred chh-------------hccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC
Q 003933 287 ATA-------------QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD 353 (785)
Q Consensus 287 ~~~-------------~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~ 353 (785)
... ........+.+.|-..++..||||+|.+|.+|++++.|+|. +- ...++++.|.|.|.
T Consensus 325 ~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~-~~------~~~~~~~~v~~~~~ 397 (753)
T KOG2208|consen 325 EVGAVLAKRDKTLLLKNSEENNENIKREIFPEELKFVIGKKGANIEKIREESQVKID-LP------KQGSNNKKVVITGV 397 (753)
T ss_pred ccchhhhhhHHHHHHHHhhccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhcee-cc------cccCCCCCeEEecc
Confidence 100 11123456778889999999999999999999999999999 32 23567888999999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 003933 354 MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 354 ~eqVe~Ak~lI~~ll~~ 370 (785)
...+++|+++|+.++.+
T Consensus 398 ~~~~~ka~~~v~~~~~e 414 (753)
T KOG2208|consen 398 SANDEKAVEDVEKIIAE 414 (753)
T ss_pred ccchhHHHHHHHHHHHh
Confidence 99999999999876654
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.28 E-value=1.9e-06 Score=83.95 Aligned_cols=103 Identities=21% Similarity=0.380 Sum_probs=75.5
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCC
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP 279 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p 279 (785)
-...|+|....+|..||++|++|+.|++..|-+|.|...++ .+.++|..+|.-..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------------d~~~fI~n~l~Pa~----- 86 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------------DPEEFIKNIFAPAA----- 86 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC--------------------CHHHHHHHHcCCCE-----
Confidence 46788899999999999999999999999999999886432 23344555444221
Q ss_pred cccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331 (785)
Q Consensus 280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI 331 (785)
+..-.- ........+.+.|+.+.+|++|||+|.|||.++.-++-++.|
T Consensus 87 --V~~v~I--~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 87 --VRSVTI--KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred --EEEEEE--EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 000000 001123456778999999999999999999999999999874
No 40
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.23 E-value=5.2e-06 Score=98.75 Aligned_cols=66 Identities=27% Similarity=0.479 Sum_probs=58.5
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~ 370 (785)
......|.|+.++++.|||.||++||.|+++|||+|.| . ++.+|.|.+. .+.+++|+++|+.++..
T Consensus 576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi-~----------d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISI-E----------DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEE-e----------cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 35577899999999999999999999999999999995 2 2578999996 88999999999999883
No 41
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.12 E-value=3.3e-06 Score=100.40 Aligned_cols=85 Identities=22% Similarity=0.305 Sum_probs=67.8
Q ss_pred cchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc-cHH
Q 003933 179 VPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLS 257 (785)
Q Consensus 179 lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G-t~e 257 (785)
.|.+++...................|.|+.++++.|||.+|.+||.|+++|||+|.|.. +..|.|.+ +.+
T Consensus 557 ~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~I~a~d~~ 627 (719)
T TIGR02696 557 AILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVYIGAADGP 627 (719)
T ss_pred HHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEEEEeCCHH
Confidence 34444443322223233556889999999999999999999999999999999999985 34788887 889
Q ss_pred HHHHHHHHHHHHHHh
Q 003933 258 NIDKAEKLINAVIAE 272 (785)
Q Consensus 258 ~V~kA~~lI~elI~e 272 (785)
.+++|+++|+.++..
T Consensus 628 ~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 628 SAEAARAMINAIANP 642 (719)
T ss_pred HHHHHHHHHHHhhCc
Confidence 999999999999884
No 42
>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=97.98 E-value=2.3e-05 Score=94.29 Aligned_cols=65 Identities=25% Similarity=0.463 Sum_probs=56.4
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~ 370 (785)
....+|.|+.++++.|||+||++||.|+++|||+|.| . ++-.|.|.+. .+.+++|+++|+.++..
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i-~----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDI-E----------DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEE-e----------cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 4567899999999999999999999999999999995 2 1457888875 78999999999988765
No 43
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.96 E-value=4.8e-06 Score=97.15 Aligned_cols=121 Identities=21% Similarity=0.290 Sum_probs=91.6
Q ss_pred chhhhhccccccccccccccccccchhhhhhhcccchhhhccCCCCCC-CCCCCCCeEEEEEecCCccceeecCCchHHH
Q 003933 145 TEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP-SSTDDSTMSRKIEVPNNKVGVLIGKAGDTIR 223 (785)
Q Consensus 145 ~~~~~~~~~e~~~~ds~k~~~i~g~~esVE~A~~lI~~ii~~~~~~~p-~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK 223 (785)
++..++..+.+.++...+.....-...+...|+..|..++........ ...........|.|+..++..|||++|++||
T Consensus 496 T~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~ 575 (692)
T COG1185 496 TDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIK 575 (692)
T ss_pred CCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchh
Confidence 456677777777777776666655555555566566666654333332 2234566788999999999999999999999
Q ss_pred HHHHHhCCeEEEccCCCCCCCCCCcceEecc-cHHHHHHHHHHHHHHHHhhc
Q 003933 224 YLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD 274 (785)
Q Consensus 224 ~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G-t~e~V~kA~~lI~elI~e~~ 274 (785)
.|.++|||+|.|..+ -.|.|.+ +.+.+.+|+++|..+.++..
T Consensus 576 ~I~eetg~~Idiedd---------Gtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 576 AITEETGVKIDIEDD---------GTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred hhhhhhCcEEEecCC---------CcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 999999999999843 3778887 56899999999999998764
No 44
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.93 E-value=3.6e-05 Score=75.01 Aligned_cols=102 Identities=19% Similarity=0.336 Sum_probs=74.0
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCc
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS 280 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~ 280 (785)
.+-|.|....+|..||++|++|+.|++..|-+|.|...++ + +.++|+... .|.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~--------------D----------~~~fI~N~l---~PA 86 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSE--------------N----------LEEFVANKL---APA 86 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCC--------------C----------HHHHHHHcC---CCc
Confidence 7788999999999999999999999999999998875432 1 333344321 121
Q ss_pred ccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 281 LVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331 (785)
Q Consensus 281 ~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI 331 (785)
.+..-.. ....+.....+.|+.+..+++|||+|.|||...+-++-++.|
T Consensus 87 ~V~~V~i--~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 87 EVKNVTV--SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred eEEEEEE--EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 1111000 011233556788999999999999999999999999999874
No 45
>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=97.88 E-value=1.2e-05 Score=96.54 Aligned_cols=69 Identities=29% Similarity=0.404 Sum_probs=60.1
Q ss_pred CCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc-cHHHHHHHHHHHHHHHHhh
Q 003933 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G-t~e~V~kA~~lI~elI~e~ 273 (785)
........|.|+.++++.|||++|++||.|+++|||+|.|..+ -.|.|.+ +.+.+++|+++|..++.+.
T Consensus 547 ~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd---------G~V~i~~~~~~~~~~a~~~I~~~~~~~ 616 (684)
T TIGR03591 547 PYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD---------GTVKIAASDGEAAEAAIKMIEGITAEP 616 (684)
T ss_pred ccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC---------eEEEEEECcHHHHHHHHHHHHhhhccc
Confidence 4567889999999999999999999999999999999999853 3666665 8899999999999987653
No 46
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.84 E-value=2.5e-05 Score=82.23 Aligned_cols=46 Identities=26% Similarity=0.490 Sum_probs=40.2
Q ss_pred CCCCCeEEEEEecCC------ccceeecCCchHHHHHHHHhCCeEEEccCCC
Q 003933 195 TDDSTMSRKIEVPNN------KVGVLIGKAGDTIRYLQYNSGAKIQITRDAD 240 (785)
Q Consensus 195 ~~~~~~t~~IlVP~~------~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d 240 (785)
....+.+.+|+||.. +||+|||.+|.++|+|+++|+|+|.|..+..
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgS 138 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGS 138 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCc
Confidence 355678999999975 7999999999999999999999999986543
No 47
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.82 E-value=9.3e-05 Score=78.00 Aligned_cols=77 Identities=23% Similarity=0.345 Sum_probs=51.3
Q ss_pred CccEEEEEecC------CccceeecCCchHHHHHHHHhCCeEEEecCC---------CC---CCCCCCC---ccEEEEEc
Q 003933 294 AAEQVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQVLIPQ---------HL---PEGDGSK---ERIVRVTG 352 (785)
Q Consensus 294 ~~~~~~i~VP~------~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~---------~l---P~~~~s~---er~VtIsG 352 (785)
...+.+|+||- |+||+|||.+|.++|+|+++|||||-|.-.- .+ +..+..+ .-.|++..
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence 34556777765 7999999999999999999999999973220 01 1111111 12355666
Q ss_pred CHH----HHHHHHHHHHHHHhc
Q 003933 353 DMR----QIEIAQEMIKEVLSQ 370 (785)
Q Consensus 353 ~~e----qVe~Ak~lI~~ll~~ 370 (785)
+.. .|..|++.|+.+|.-
T Consensus 170 p~~ea~~rl~~AleeI~klL~P 191 (259)
T KOG1588|consen 170 PPAEAYARLAYALEEIKKLLVP 191 (259)
T ss_pred CHHHHHHHHHHHHHHHHHhcCC
Confidence 644 345688888887754
No 48
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.74 E-value=9.5e-05 Score=86.65 Aligned_cols=68 Identities=24% Similarity=0.415 Sum_probs=59.3
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhcccC
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTVR 373 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~~~r 373 (785)
.....+.|+.+++..|||++|++||.|.++|||+|.| . ++-+|.|.++ .+.+.+|+++|++++++...
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idi-e----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDI-E----------DDGTVKIAASDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEe-c----------CCCcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence 4567889999999999999999999999999999995 2 2568999998 58999999999999987543
No 49
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=97.68 E-value=2.9e-05 Score=78.27 Aligned_cols=157 Identities=17% Similarity=0.230 Sum_probs=103.0
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCC
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGS 278 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~ 278 (785)
..+.+|.||.+...-|--.+-....-|-+..+..|.+.-+.. ....|.|.-+-+..++.++...|..++.-++....
T Consensus 73 ~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r---~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DA 149 (252)
T KOG3273|consen 73 IETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKAR---SVELRTCKDTEDPSALQKGADFVRAFILGFDIDDA 149 (252)
T ss_pred cceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccc---eeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhH
Confidence 456789999998877765555666777888888887753321 12234454455778999999999998875432111
Q ss_pred Ccccc-cccchh-hccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHH
Q 003933 279 PSLVA-RGLATA-QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQ 356 (785)
Q Consensus 279 p~~~~-~g~~~~-~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eq 356 (785)
..|.. ..++-. -+.....+++=.-=...+|+|+||+|.|--.|++.|.+||.|. +..|+|-|...+
T Consensus 150 iALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~n 217 (252)
T KOG3273|consen 150 IALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQN 217 (252)
T ss_pred HHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchh
Confidence 11110 000000 0000001111111124679999999999999999999999942 458999999999
Q ss_pred HHHHHHHHHHHHhc
Q 003933 357 IEIAQEMIKEVLSQ 370 (785)
Q Consensus 357 Ve~Ak~lI~~ll~~ 370 (785)
|..|+..|..||-.
T Consensus 218 iriAR~avcsLIlG 231 (252)
T KOG3273|consen 218 IRIARDAVCSLILG 231 (252)
T ss_pred hHHHHHhhHhhhcc
Confidence 99999999998854
No 50
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.68 E-value=9.3e-05 Score=90.09 Aligned_cols=68 Identities=26% Similarity=0.456 Sum_probs=58.1
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHhCCe-EEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhcc
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGAR-IQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQT 371 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGAr-IqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~~ 371 (785)
......|.|+.++++.|||.||.|||.|+++||++ |.| . ++-.|.|.+. .+.+++|+++|++++.+.
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi--~---------ddg~V~I~a~d~~~i~~A~~~I~~l~~~~ 751 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDT--Q---------DDGTVKITAKDLSSLEKSKAIISSLTMVP 751 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCc--C---------CCeeEEEEeCCHHHHHHHHHHHHHHhcCc
Confidence 35577899999999999999999999999999999 873 1 2467889986 889999999999987654
Q ss_pred c
Q 003933 372 V 372 (785)
Q Consensus 372 ~ 372 (785)
.
T Consensus 752 ~ 752 (891)
T PLN00207 752 T 752 (891)
T ss_pred C
Confidence 3
No 51
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=97.64 E-value=0.0008 Score=69.49 Aligned_cols=128 Identities=17% Similarity=0.239 Sum_probs=95.1
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcc
Q 003933 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSL 281 (785)
Q Consensus 202 ~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~ 281 (785)
+.|.+.....-+|+..+|..++.|-...||+|.|..+ +..|+|+|++..|+.++..|.+++...
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~--------~~~i~I~g~k~~~~~i~~~i~~~l~~i-------- 91 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS--------ENRIRITGTKSTAEYIEASINEILSNI-------- 91 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC--------CcEEEEEccHHHHHHHHHHHHHHHhhc--------
Confidence 4455557788899999999999998889999999854 568999999999999999999999864
Q ss_pred cccccchhhccCCccEEEEEecCCccceee----cCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEc-----
Q 003933 282 VARGLATAQASGAAEQVEIKVPNEKVGLII----GRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTG----- 352 (785)
Q Consensus 282 ~~~g~~~~~~~~~~~~~~i~VP~~~vG~VI----GKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG----- 352 (785)
.+.+|.++.-+.-... -.....|+.|++.|++.|+. ..+ ...+.|..
T Consensus 92 --------------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~-~~~---------~~~~~i~~~~~~~ 147 (210)
T PF14611_consen 92 --------------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEK-NPD---------GNKLKISWLASPE 147 (210)
T ss_pred --------------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEE-CCC---------CCeEEEEEEeecc
Confidence 2334444432111111 11367899999999999993 321 33455554
Q ss_pred CHHHHHHHHHHHHHHHh
Q 003933 353 DMRQIEIAQEMIKEVLS 369 (785)
Q Consensus 353 ~~eqVe~Ak~lI~~ll~ 369 (785)
..+.++.|++||.-.+.
T Consensus 148 ~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 148 NEKRADRAKRLLLWALD 164 (210)
T ss_pred ccchHHHHHHHHHHhcc
Confidence 47899999999998886
No 52
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.56 E-value=0.00023 Score=72.67 Aligned_cols=102 Identities=22% Similarity=0.341 Sum_probs=71.3
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCc
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS 280 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~ 280 (785)
.+-+.+-.+.+|.+||++|.+|+.|.++.|-+|.|...++ .-..+|..+|.- .
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------------d~~~fI~nal~P-------a 129 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------------DPAEFIKNALAP-------A 129 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------------CHHHHHHHhcCc-------c
Confidence 4455556678999999999999999999998888875432 112233333331 1
Q ss_pred ccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 281 LVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 281 ~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
.+..-.. .. .......+.|+.+..+++|||+|.||+.+.+-||-+|.|.
T Consensus 130 ~v~~V~~--~~-~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 130 EVLSVNI--KE-DDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred eEeEEEE--Ee-CCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 1100000 00 0122678889999999999999999999999999999963
No 53
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.51 E-value=4.9e-05 Score=92.47 Aligned_cols=70 Identities=21% Similarity=0.431 Sum_probs=61.6
Q ss_pred CCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCe-EEEccCCCCCCCCCCcceEecc-cHHHHHHHHHHHHHHHHh
Q 003933 195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAK-IQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 195 ~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAk-I~I~k~~d~~p~s~eRiV~I~G-t~e~V~kA~~lI~elI~e 272 (785)
.........|.|+.++++.|||.+|.|||.|.++||++ |.|..+ -.|.|.+ +.+.+++|+++|..++.+
T Consensus 680 s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd---------g~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 680 SKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD---------GTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred cccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC---------eeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 35567899999999999999999999999999999999 988743 4677777 889999999999999875
Q ss_pred h
Q 003933 273 A 273 (785)
Q Consensus 273 ~ 273 (785)
.
T Consensus 751 ~ 751 (891)
T PLN00207 751 P 751 (891)
T ss_pred c
Confidence 4
No 54
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.50 E-value=8.3e-05 Score=82.24 Aligned_cols=72 Identities=29% Similarity=0.361 Sum_probs=60.4
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcccC
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVR 373 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~~~r 373 (785)
+...+.|.|-+++||.|||++|.+||+||..|.++|+| +... .+-.|+|.|..+.-.+|+..|...+++..+
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqi-i~~~-------~e~kv~ifg~~~m~~kaka~id~~~~k~e~ 116 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQI-IKCD-------LEVKVTIFGINHMRKKAKASIDRGQDKDER 116 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEE-eccC-------ceeEEEEechHHHHHHHHhhHhhhhhhhhh
Confidence 34456788999999999999999999999999999996 4322 367899999999999999999887776544
No 55
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.39 E-value=0.0003 Score=71.44 Aligned_cols=42 Identities=43% Similarity=0.548 Sum_probs=36.6
Q ss_pred CCCeEEEEEecC------CccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 197 DSTMSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 197 ~~~~t~~IlVP~------~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
...+..+|.||. ++||+|||..|.|+|+|++.|+|+|.|...
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 345777888875 579999999999999999999999999864
No 56
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.39 E-value=0.0002 Score=79.27 Aligned_cols=74 Identities=22% Similarity=0.317 Sum_probs=63.9
Q ss_pred CCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhc
Q 003933 195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD 274 (785)
Q Consensus 195 ~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~ 274 (785)
.+...+.+.|.|-++.||+|||++|++||.|+..|+++|+|.+.. .+-.|+|.|...--.+|...|...++...
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~------~e~kv~ifg~~~m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD------LEVKVTIFGINHMRKKAKASIDRGQDKDE 115 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC------ceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence 456778899999999999999999999999999999999998642 35678999999988889988888887654
No 57
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.29 E-value=0.00043 Score=83.62 Aligned_cols=65 Identities=28% Similarity=0.516 Sum_probs=55.4
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~ 370 (785)
.....+.|+.++++.|||.||.|||.|+++||++|.| . ++-.|.|.+. .+.+++|+++|+.++.+
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi-~----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI-E----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCcccc-C----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 3455778899999999999999999999999999883 1 2467888886 78999999999998865
No 58
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.17 E-value=0.0013 Score=73.47 Aligned_cols=93 Identities=17% Similarity=0.279 Sum_probs=67.1
Q ss_pred CccceeecCCchHHHHHHHHh-CCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccc
Q 003933 209 NKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLA 287 (785)
Q Consensus 209 ~~VG~IIGk~G~tIK~IqeeT-GAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~ 287 (785)
+-+|..||++|.+|+.|.++. |-+|.|...++. +.++|+... +|..+.+-.-
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D------------------------~~~fI~Nal---~Pa~V~~V~i 303 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV------------------------PEIFIARAL---APAIISSVKI 303 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhC---CCceeeEEEE
Confidence 348999999999999999998 888988765331 233333321 1221111100
Q ss_pred hhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 288 TAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 288 ~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
........+.|+.+..++.|||+|.|||-..+-||.+|.|.
T Consensus 304 ----~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 304 ----EEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred ----cCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 02235678899999999999999999999999999999974
No 59
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.15 E-value=0.0013 Score=73.02 Aligned_cols=93 Identities=29% Similarity=0.432 Sum_probs=66.7
Q ss_pred ccceeecCCchHHHHHHHHh-CCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccch
Q 003933 210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288 (785)
Q Consensus 210 ~VG~IIGk~G~tIK~IqeeT-GAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~ 288 (785)
-+|..||++|.+|+.|.++. |-+|.|...++. +..+|+... +|..+..-.-.
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------------~~~fi~nal---~Pa~v~~v~i~ 296 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDD------------------------PAEFIANAL---SPAKVISVEVL 296 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhc---CCceEEEEEEE
Confidence 48999999999999999998 888988765331 223333321 12211111000
Q ss_pred hhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 289 ~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
........+.|+.+..++.|||+|.|||....-||++|.|.
T Consensus 297 ---~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 297 ---DEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred ---cCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence 01235678999999999999999999999999999999974
No 60
>PRK00106 hypothetical protein; Provisional
Probab=97.09 E-value=0.0023 Score=74.74 Aligned_cols=64 Identities=23% Similarity=0.449 Sum_probs=54.1
Q ss_pred EEEEEecC-CccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003933 297 QVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 297 ~~~i~VP~-~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~ 370 (785)
...+.+|+ ++.|+||||.|.|||.|...|||.|.| + ++...|+|++. +-.-+.|+..++.||..
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdlii--d--------dtp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVII--D--------DTPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEE--c--------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 44678898 788999999999999999999999984 2 24568889995 88889999999888865
No 61
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.08 E-value=0.0022 Score=75.04 Aligned_cols=64 Identities=28% Similarity=0.462 Sum_probs=53.7
Q ss_pred EEEEEecC-CccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003933 297 QVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 297 ~~~i~VP~-~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~ 370 (785)
...+.+|+ ++.|+||||.|.|||.+...||+.|.| + ++..+|+|++. +-.-+.|+..|+.||..
T Consensus 205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~ii--d--------dtp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII--D--------DTPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEE--c--------CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 44678888 788999999999999999999999984 2 23567889995 77889999999888864
No 62
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.03 E-value=0.0022 Score=65.35 Aligned_cols=79 Identities=25% Similarity=0.281 Sum_probs=50.1
Q ss_pred cEEEEEecC------CccceeecCCchHHHHHHHHhCCeEEEecC---------CCCCCCCCCCccE---EEEEcCHHHH
Q 003933 296 EQVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQVLIP---------QHLPEGDGSKERI---VRVTGDMRQI 357 (785)
Q Consensus 296 ~~~~i~VP~------~~vG~VIGKgGetIK~Iq~~TGArIqI~i~---------~~lP~~~~s~er~---VtIsG~~eqV 357 (785)
.+.+|-||- ++||+|||..|.|+|.|++.|+|+|-|.-. .++++.....+.+ +.+.-..+.|
T Consensus 148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki 227 (269)
T COG5176 148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKI 227 (269)
T ss_pred ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhH
Confidence 445666654 899999999999999999999999997321 1111111111111 2233335667
Q ss_pred HHHHHHHHHHHhcccCC
Q 003933 358 EIAQEMIKEVLSQTVRP 374 (785)
Q Consensus 358 e~Ak~lI~~ll~~~~r~ 374 (785)
.+++.+|..+|.+.++.
T Consensus 228 ~~~ik~~~n~I~~a~~~ 244 (269)
T COG5176 228 CRLIKSQLNAIREARRN 244 (269)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 77777777777665544
No 63
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.01 E-value=0.002 Score=72.12 Aligned_cols=93 Identities=22% Similarity=0.333 Sum_probs=67.0
Q ss_pred ccceeecCCchHHHHHHHHh-CCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccch
Q 003933 210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288 (785)
Q Consensus 210 ~VG~IIGk~G~tIK~IqeeT-GAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~ 288 (785)
-+|..||++|.+|+.|.++. |-+|.|...++. +.++|+... +|..+.+-.-
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d------------------------~~~fi~nal---~Pa~v~~v~i- 297 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSED------------------------PAEFVANAL---SPAKVVSVEV- 297 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhC---CCceEEEEEE-
Confidence 48999999999999999998 888988764331 223333321 1222111100
Q ss_pred hhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 289 ~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
.........+.|+.+..++.|||+|.|||....-||++|.|.
T Consensus 298 --~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~ 339 (362)
T PRK12327 298 --DDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK 339 (362)
T ss_pred --EcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence 002235678999999999999999999999999999999974
No 64
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.96 E-value=0.00039 Score=84.02 Aligned_cols=69 Identities=30% Similarity=0.442 Sum_probs=58.9
Q ss_pred CCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc-cHHHHHHHHHHHHHHHHhh
Q 003933 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G-t~e~V~kA~~lI~elI~e~ 273 (785)
........+.|+.++++.|||.+|.|||.|.++||++|.|..+ -.|.|.+ +.+.+++|+++|..++.+.
T Consensus 550 ~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~---------G~v~i~~~~~~~~~~a~~~I~~~~~~~ 619 (693)
T PRK11824 550 PYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD---------GTVKIAATDGEAAEAAKERIEGITAEP 619 (693)
T ss_pred ccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC---------ceEEEEcccHHHHHHHHHHHHHhcccC
Confidence 3456677888899999999999999999999999999998643 3677777 8899999999999988653
No 65
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.94 E-value=0.0008 Score=72.96 Aligned_cols=70 Identities=24% Similarity=0.222 Sum_probs=57.9
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhh
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~ 273 (785)
....++|...+++.|||++|.|.|+|+++|+++|.+.+..+ ..+.++.+....++|-+|++.|..+|.+.
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~----n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT----NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC----CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 45578899999999999999999999999999999986532 23444444459999999999999999875
No 66
>PRK12704 phosphodiesterase; Provisional
Probab=96.94 E-value=0.0035 Score=73.44 Aligned_cols=64 Identities=28% Similarity=0.450 Sum_probs=51.8
Q ss_pred EEEEEecC-CccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003933 297 QVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 297 ~~~i~VP~-~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~ 370 (785)
...+.+|+ ++.|+||||.|.|||.+...||+.|.| + ++..+|.|+|. +-.-+.|+..|+.+|..
T Consensus 211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~ii--d--------dtp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII--D--------DTPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEE--c--------CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 34677888 788999999999999999999999984 2 23568889995 66667888888877754
No 67
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.93 E-value=0.0017 Score=73.53 Aligned_cols=92 Identities=26% Similarity=0.387 Sum_probs=65.7
Q ss_pred ccceeecCCchHHHHHHHHh-CCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccch
Q 003933 210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288 (785)
Q Consensus 210 ~VG~IIGk~G~tIK~IqeeT-GAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~ 288 (785)
-||..||++|.+|+.|.++. |-+|.|..-++. +..+|+... +|..+..-.-.
T Consensus 278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D------------------------p~~fI~NaL---sPA~V~~V~i~ 330 (449)
T PRK12329 278 PVGACIGARGSRIQAVVNELRGEKIDVIRWSPD------------------------PATYIANAL---SPARVDEVRLV 330 (449)
T ss_pred hhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhc---CCceeeEEEEE
Confidence 48999999999999999998 888888754321 223333321 12222111000
Q ss_pred hhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331 (785)
Q Consensus 289 ~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI 331 (785)
........+.|+.+..++.|||+|.|||-...-||.+|.|
T Consensus 331 ---~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI 370 (449)
T PRK12329 331 ---DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDI 370 (449)
T ss_pred ---cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecc
Confidence 0123467899999999999999999999999999999996
No 68
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.85 E-value=0.0022 Score=74.14 Aligned_cols=93 Identities=25% Similarity=0.426 Sum_probs=66.8
Q ss_pred ccceeecCCchHHHHHHHHh-CCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccch
Q 003933 210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288 (785)
Q Consensus 210 ~VG~IIGk~G~tIK~IqeeT-GAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~ 288 (785)
-||..||++|.+|+.|.++. |-+|.|..-++ + +..+|+... ++..+.+-.
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~------d------------------~~~fi~nal---~pa~v~~v~-- 296 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD------D------------------PAQFIINAL---SPAEVSSVV-- 296 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC------C------------------HHHHHHHhC---CCCEEEEEE--
Confidence 38999999999999999998 88888875432 1 223333321 122111110
Q ss_pred hhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEec
Q 003933 289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLI 333 (785)
Q Consensus 289 ~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i 333 (785)
.......+.+.|+.+..++.|||+|.|||...+.||.+|.|+.
T Consensus 297 --~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 297 --VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred --EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 0012347889999999999999999999999999999999754
No 69
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=96.72 E-value=0.0014 Score=70.39 Aligned_cols=67 Identities=28% Similarity=0.416 Sum_probs=57.5
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVL 368 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll 368 (785)
...++.+.||.++|+.|+|++|.+||+|+.+|..+|. .-.+ .++-+|.++|..+.|++||+.|...-
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~-tPsr-------~eePiF~vTg~~edv~~aRrei~saa 90 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIK-TPSR-------GEEPIFPVTGRHEDVRRARREIPSAA 90 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceec-cCCC-------CCCCcceeccCchhHHHHhhcCcccc
Confidence 5567788999999999999999999999999999998 2222 24589999999999999999998743
No 70
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.65 E-value=0.0032 Score=64.09 Aligned_cols=54 Identities=28% Similarity=0.466 Sum_probs=49.4
Q ss_pred ccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhh
Q 003933 210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 210 ~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~ 273 (785)
..|+|||++|.|-+-|++-|+|+|.|-. ..|.|.|..++|..|.+.|+.+|.-.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHHHHHHcCC
Confidence 4699999999999999999999999984 38999999999999999999998753
No 71
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.60 E-value=0.0024 Score=69.33 Aligned_cols=70 Identities=21% Similarity=0.350 Sum_probs=56.0
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEc-CHHHHHHHHHHHHHHHhccc
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQEMIKEVLSQTV 372 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG-~~eqVe~Ak~lI~~ll~~~~ 372 (785)
....|+|+..+.+.|||+.|.|.|+|+++|+|+|.+ ++ ...+...|+|+| ..++|..|.+.|..+|...+
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~l--p~-----p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFL--PR-----PNTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEc--cC-----CCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 345688999999999999999999999999999984 22 122344566665 58999999999999887654
No 72
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.56 E-value=0.0044 Score=72.54 Aligned_cols=91 Identities=21% Similarity=0.326 Sum_probs=60.8
Q ss_pred chhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCC-ccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCC
Q 003933 169 EEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAAT 247 (785)
Q Consensus 169 ~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~-~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~e 247 (785)
..++-..|+++|...+.....+ .....++..|.+|++ .-|+||||.|.|||.|+.-||++|.|+...
T Consensus 177 ~~~a~~~a~~i~~~aiqr~a~~----~~~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-------- 244 (514)
T TIGR03319 177 KEEADKKAKEILATAIQRYAGD----HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-------- 244 (514)
T ss_pred HHHHHHHHHHHHHHHHHhccch----hhhhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC--------
Confidence 3344555666666666543322 233567778899985 679999999999999999999999998432
Q ss_pred cceEecc-cHHHHHHHHHHHHHHHH
Q 003933 248 RPVEIIG-TLSNIDKAEKLINAVIA 271 (785)
Q Consensus 248 RiV~I~G-t~e~V~kA~~lI~elI~ 271 (785)
..|+|++ ++-.-+.|...|..||.
T Consensus 245 ~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 245 EAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred CeEEecCCchHHHHHHHHHHHHHHH
Confidence 3666777 44444444444444443
No 73
>PRK00106 hypothetical protein; Provisional
Probab=96.55 E-value=0.0047 Score=72.29 Aligned_cols=91 Identities=18% Similarity=0.271 Sum_probs=62.2
Q ss_pred chhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCC-ccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCC
Q 003933 169 EEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAAT 247 (785)
Q Consensus 169 ~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~-~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~e 247 (785)
..++-..|+++|...+.....+. ....++..|.+|++ .-|+||||.|.+||.|+.-||++|.|+...
T Consensus 198 ~~~a~~~a~~ii~~aiqr~a~~~----~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-------- 265 (535)
T PRK00106 198 KDRSDKMAKDLLAQAMQRLAGEY----VTEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-------- 265 (535)
T ss_pred HHHHHHHHHHHHHHHHHHhcchh----hhhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC--------
Confidence 33445566777766665433222 33467788899985 679999999999999999999999998432
Q ss_pred cceEecc-cHHHHHHHHHHHHHHHH
Q 003933 248 RPVEIIG-TLSNIDKAEKLINAVIA 271 (785)
Q Consensus 248 RiV~I~G-t~e~V~kA~~lI~elI~ 271 (785)
..|+|++ ++-.-+.|...|..||.
T Consensus 266 ~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 266 EVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred CeEEEeCCChHHHHHHHHHHHHHHH
Confidence 3666777 54444445554444444
No 74
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.54 E-value=0.0041 Score=65.74 Aligned_cols=64 Identities=28% Similarity=0.367 Sum_probs=54.7
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhcc
Q 003933 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQT 371 (785)
Q Consensus 297 ~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~~ 371 (785)
-+.|.||.+++++|||++|.+||.|.++++|+|.| . . +-.|.|.+. .+.+++|+++|+.+-++.
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~i-g-~---------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIV-G-Q---------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEE-c-C---------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 35789999999999999999999999999999984 2 1 357899997 779999999998876654
No 75
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.51 E-value=0.0046 Score=70.98 Aligned_cols=66 Identities=26% Similarity=0.340 Sum_probs=56.2
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhccc
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTV 372 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~~~ 372 (785)
.....|.|+.+++..+||.+|.++|+|+.+||+...| ++.+|+|.-. ...++.|+++|..++..+.
T Consensus 596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred ceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence 4567889999999999999999999999999976663 2567888886 7899999999999887643
No 76
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.44 E-value=0.0046 Score=51.83 Aligned_cols=37 Identities=27% Similarity=0.683 Sum_probs=34.4
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI 331 (785)
.....+.|+.+.+|.+|||+|.|||.|++.++.+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3678899999999999999999999999999999985
No 77
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.44 E-value=0.0048 Score=65.27 Aligned_cols=65 Identities=26% Similarity=0.344 Sum_probs=55.8
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc-cHHHHHHHHHHHHHHHHhhc
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD 274 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G-t~e~V~kA~~lI~elI~e~~ 274 (785)
-+.|.||..++++|||++|.+|+.|.++|+++|.|-.+ -.|.|++ +.+.+.+|+.+|+.+-++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N---------G~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN---------GRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC---------cEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 35788999999999999999999999999999999743 3677777 77799999999998877764
No 78
>PRK12704 phosphodiesterase; Provisional
Probab=96.38 E-value=0.006 Score=71.54 Aligned_cols=92 Identities=21% Similarity=0.345 Sum_probs=63.1
Q ss_pred chhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCC-ccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCC
Q 003933 169 EEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAAT 247 (785)
Q Consensus 169 ~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~-~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~e 247 (785)
..++-..|+++|...+.....+. ....++..|.+|++ .-|+||||.|.|||.|+.-||++|.|+.. .
T Consensus 183 ~~~a~~~a~~i~~~a~qr~a~~~----~~e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt--------p 250 (520)
T PRK12704 183 KEEADKKAKEILAQAIQRCAADH----VAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--------P 250 (520)
T ss_pred HHHHHHHHHHHHHHHHHhhcchh----hhhhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC--------C
Confidence 33445566777766665433221 33456778889985 67999999999999999999999999843 2
Q ss_pred cceEecc-cHHHHHHHHHHHHHHHHh
Q 003933 248 RPVEIIG-TLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 248 RiV~I~G-t~e~V~kA~~lI~elI~e 272 (785)
.+|+|++ +.-.-+.|+..|..+|.+
T Consensus 251 ~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 251 EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3667777 444444555555555543
No 79
>PRK12705 hypothetical protein; Provisional
Probab=96.13 E-value=0.01 Score=69.07 Aligned_cols=64 Identities=22% Similarity=0.382 Sum_probs=48.2
Q ss_pred EEEEEecC-CccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003933 297 QVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 297 ~~~i~VP~-~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~ 370 (785)
...+.+|+ ++.|+||||.|.|||.++..||+.|.| ++ +.+.|.|++. +..-+.|+..++.||..
T Consensus 199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdlii--dd--------tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLII--DD--------TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeeeecCChHhhccccCccchhHHHHHHhhCCceEe--cC--------CccchhhcccCccchHHHHHHHHHHHhc
Confidence 34567888 788999999999999999999999984 22 2455777775 55666677666666544
No 80
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=95.94 E-value=0.014 Score=64.72 Aligned_cols=164 Identities=14% Similarity=-0.027 Sum_probs=98.5
Q ss_pred CchHHHHHHHHhCCeEEEccCCCC------CCCCCCcceEecc-cHHHHHHHHHHHHHHHHhhccCCCCcccc--cccch
Q 003933 218 AGDTIRYLQYNSGAKIQITRDADA------DPHAATRPVEIIG-TLSNIDKAEKLINAVIAEADAGGSPSLVA--RGLAT 288 (785)
Q Consensus 218 ~G~tIK~IqeeTGAkI~I~k~~d~------~p~s~eRiV~I~G-t~e~V~kA~~lI~elI~e~~~gg~p~~~~--~g~~~ 288 (785)
+|.+..+|.+.||+.|.++..-.. .++..-.+.+|.+ |.|-+++|+..|.-+++.+....+...|. ....+
T Consensus 112 Rg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~i~~~~sP 191 (531)
T KOG1960|consen 112 RGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVYILVRASP 191 (531)
T ss_pred cchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEEEeecCCc
Confidence 678899999999999988753221 1222335678888 89999999999987766542111100000 00000
Q ss_pred hhc----------cCC-----ccEEEEEecC-CccceeecCCchHHHHHHHHhCCeEEEecCCC---CC---CCCCCCcc
Q 003933 289 AQA----------SGA-----AEQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQVLIPQH---LP---EGDGSKER 346 (785)
Q Consensus 289 ~~~----------~~~-----~~~~~i~VP~-~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~---lP---~~~~s~er 346 (785)
... ..+ ...+.+.+|. ...+.+=+++-.++.+|+.+|++++-| ..+. .. -.+..+-+
T Consensus 192 ~~~i~~~V~~~~f~~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~-~Gr~SG~iEP~~G~EsnEPM 270 (531)
T KOG1960|consen 192 LSEIENKVGVQLFSKGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLI-DGRRSGRREPNEGNESNEPM 270 (531)
T ss_pred hhhhccccccccccccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhh-ccccccccCcccccccCCce
Confidence 000 001 1112223344 345667778888999999999998763 1111 11 12334455
Q ss_pred EEEEEcC-HHHHHHHHHHHHHHHhcccCCCCCCCCCCCC
Q 003933 347 IVRVTGD-MRQIEIAQEMIKEVLSQTVRPSTLSGGFNQQ 384 (785)
Q Consensus 347 ~VtIsG~-~eqVe~Ak~lI~~ll~~~~r~~~~~g~~~~q 384 (785)
.|.|++. .+.+.+|+++|.+|++.+.... +++|+++
T Consensus 271 YI~i~h~~~~g~~~A~r~~~nl~~~v~~~~--sr~~~~~ 307 (531)
T KOG1960|consen 271 YIFSTHGNGNGENGAPRRKWNLEEKVYINL--SRGFHRQ 307 (531)
T ss_pred eEEeecCCchhhccchhHHHhHHHHHHHHh--hhhhhhc
Confidence 6777775 8999999999999987654432 4666544
No 81
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.91 E-value=0.012 Score=49.29 Aligned_cols=36 Identities=33% Similarity=0.632 Sum_probs=34.0
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI 235 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I 235 (785)
....|.|+.+.+|.+|||+|.+|+.+++.++.+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678999999999999999999999999999998876
No 82
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=95.86 E-value=0.019 Score=65.72 Aligned_cols=95 Identities=24% Similarity=0.423 Sum_probs=69.7
Q ss_pred ceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhc
Q 003933 212 GVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQA 291 (785)
Q Consensus 212 G~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~ 291 (785)
-.+|=+.|+.||+|-++...+|.|+.+... . ..-+.|++.|++++-++.. ..... |
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsv---------l-----~~~e~A~~~I~eivP~ea~--i~~i~---F----- 96 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSV---------L-----KPPEEARKIILEIVPEEAG--ITDIY---F----- 96 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCchh---------c-----CCHHHHHHHHHHhCccccC--ceeEE---e-----
Confidence 345668899999999999999999865321 0 1245788889998866521 11111 1
Q ss_pred cCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 292 SGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 292 ~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
...+-++.|-..+=|+||||+|++++.|..+||-+-+|+
T Consensus 97 --d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 97 --DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred --cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 123457888899999999999999999999999988853
No 83
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=95.48 E-value=0.054 Score=53.04 Aligned_cols=92 Identities=25% Similarity=0.473 Sum_probs=65.9
Q ss_pred ecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhccCC
Q 003933 215 IGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGA 294 (785)
Q Consensus 215 IGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~ 294 (785)
+=.++..|++|-++..-+|.|..+.+ +.- .=+.|.++|.+++-++ ++...+. | .
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dps-----------~l~---~~e~A~~~I~~ivP~e--a~i~di~---F-------d 74 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDPS-----------VLK---PPEEAIKIILEIVPEE--AGITDIY---F-------D 74 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCChh-----------hcC---CHHHHHHHHHHhCCCc--cCceeeE---e-------c
Confidence 44567899999999999998875421 111 1245888999988654 1111111 1 1
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
..+-++.|-.++-|+||||+|.++++|..+||-+..|+
T Consensus 75 ~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 75 DDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred CCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 23457888899999999999999999999999999863
No 84
>PRK12705 hypothetical protein; Provisional
Probab=95.19 E-value=0.016 Score=67.63 Aligned_cols=65 Identities=18% Similarity=0.313 Sum_probs=48.1
Q ss_pred hhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCC-ccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 170 EESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 170 ~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~-~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
.++-..|+.+|...+.....+. ....++..|.+|++ .-|+||||.|.+||.|+..||++|.|+..
T Consensus 172 ~~a~~~A~~ii~~aiqr~a~~~----~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 172 LEAERKAQNILAQAMQRIASET----ASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred HHHHHHHHHHHHHHHHHhccch----hhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 3444556777766665433222 33456778888886 57999999999999999999999999854
No 85
>PRK00468 hypothetical protein; Provisional
Probab=94.90 E-value=0.025 Score=49.56 Aligned_cols=34 Identities=18% Similarity=0.374 Sum_probs=29.5
Q ss_pred CCCCeEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeT 229 (785)
.+..+.++|.|..+.+|+||||+|.+|+.||.-.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 4455889999999999999999999999998643
No 86
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.82 E-value=0.029 Score=64.71 Aligned_cols=88 Identities=18% Similarity=0.329 Sum_probs=67.9
Q ss_pred hcccchhhhccCCCCC-CCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc
Q 003933 176 SNVVPQQVVDNSKSDD-PSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG 254 (785)
Q Consensus 176 A~~lI~~ii~~~~~~~-p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G 254 (785)
|+..|.+++....... ........+...|.|+.+++..+||.+|-++|+|..+||+.-.|+ +..+.|..
T Consensus 572 ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----------e~t~~i~A 641 (760)
T KOG1067|consen 572 ARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----------EGTFSIFA 641 (760)
T ss_pred HHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------CceEEEEe
Confidence 4445666664333322 233455788999999999999999999999999999999655554 34677776
Q ss_pred -cHHHHHHHHHHHHHHHHhh
Q 003933 255 -TLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 255 -t~e~V~kA~~lI~elI~e~ 273 (785)
+...+++|+++|..++.+.
T Consensus 642 ~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 642 PTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred cCHHHHHHHHHHHHHHhcCc
Confidence 8899999999999999875
No 87
>PRK00468 hypothetical protein; Provisional
Probab=94.62 E-value=0.033 Score=48.81 Aligned_cols=32 Identities=31% Similarity=0.522 Sum_probs=27.6
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T 325 (785)
....++|.|..+-+|+||||+|.+|+.|+.--
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 34567889999999999999999999998654
No 88
>PRK02821 hypothetical protein; Provisional
Probab=94.57 E-value=0.031 Score=49.21 Aligned_cols=36 Identities=22% Similarity=0.355 Sum_probs=30.4
Q ss_pred CCCCeEEEEEecCCccceeecCCchHHHHHHHHhCC
Q 003933 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA 231 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGA 231 (785)
....+.++|.|....+|+||||+|.+|+.||.--.+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 344578999999999999999999999999875443
No 89
>PRK02821 hypothetical protein; Provisional
Probab=94.50 E-value=0.035 Score=48.91 Aligned_cols=32 Identities=34% Similarity=0.643 Sum_probs=27.8
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T 325 (785)
....++|.|..+-+|+||||+|.+|+.|+.--
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 34678889999999999999999999998654
No 90
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=94.22 E-value=0.059 Score=59.87 Aligned_cols=134 Identities=14% Similarity=0.149 Sum_probs=87.3
Q ss_pred ceeecCCchHHHHHHHHhCCeEEEccCCC--C------CCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccc
Q 003933 212 GVLIGKAGDTIRYLQYNSGAKIQITRDAD--A------DPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVA 283 (785)
Q Consensus 212 G~IIGk~G~tIK~IqeeTGAkI~I~k~~d--~------~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~ 283 (785)
+.+-+++-.++..|+.++++++.++.+.. . ..+.+..|.++.++.+.+.+|.++|.+|++..... ..
T Consensus 227 ~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~-----~s 301 (531)
T KOG1960|consen 227 IVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYIN-----LS 301 (531)
T ss_pred hhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHH-----hh
Confidence 44556677788999999999987743221 1 12223456677779999999999999988764211 11
Q ss_pred cccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCC------CCCC-CCCCccEEEEEcCHHH
Q 003933 284 RGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQH------LPEG-DGSKERIVRVTGDMRQ 356 (785)
Q Consensus 284 ~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~------lP~~-~~s~er~VtIsG~~eq 356 (785)
|+|. + -.|+|.-|.++|+|+..+-.+++| .... .+.. .+..--++.|.-....
T Consensus 302 r~~~---------~----------~~~~~p~~~y~~~~~~~~~~~~~~-~g~~s~~i~p~~~~~~~~p~~~~~~~~~~~~ 361 (531)
T KOG1960|consen 302 RGFH---------R----------QAIVGPQGAYVKHIQQETRTRVQI-KGQGSAFIEPSTNRESDEPIHLCIMSHDPNA 361 (531)
T ss_pred hhhh---------h----------cccccCCcccccccCCCCCcceec-cCccceeecCCCCCCCCCCcccccccCChhh
Confidence 1111 1 134566788999999999999985 2211 0111 1222345677777889
Q ss_pred HHHHHHHHHHHHhc
Q 003933 357 IEIAQEMIKEVLSQ 370 (785)
Q Consensus 357 Ve~Ak~lI~~ll~~ 370 (785)
|+.|+-||.++|..
T Consensus 362 ~~~~~~~~~~~i~~ 375 (531)
T KOG1960|consen 362 IQRAKVLCEDLIAS 375 (531)
T ss_pred hhhhhhcccccCCc
Confidence 99999999888864
No 91
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.94 E-value=0.058 Score=47.34 Aligned_cols=32 Identities=31% Similarity=0.593 Sum_probs=27.6
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T 325 (785)
....++|.|..+-+|+||||+|.+|+.|+.--
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 45567889999999999999999999998643
No 92
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.93 E-value=0.016 Score=70.81 Aligned_cols=70 Identities=21% Similarity=0.213 Sum_probs=58.4
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 297 ~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
.-++.||...+.+|||++|.||+.|+..||+.|+| . ... .++-.||.+.|.|.++.+..|..+|.-+|..
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~iel-e-kmq--~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIEL-E-KMQ--PDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEeh-h-hcC--CccchhhhcccCCCChhhhhhhccccceeec
Confidence 44678999999999999999999999999999994 2 221 2346799999999999999999999876654
No 93
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.91 E-value=0.062 Score=47.18 Aligned_cols=33 Identities=27% Similarity=0.487 Sum_probs=29.3
Q ss_pred CCCCeEEEEEecCCccceeecCCchHHHHHHHH
Q 003933 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN 228 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~VG~IIGk~G~tIK~Iqee 228 (785)
.+....++|.|-...+|+||||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 356678999999999999999999999999864
No 94
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.79 E-value=0.021 Score=69.90 Aligned_cols=75 Identities=20% Similarity=0.224 Sum_probs=64.6
Q ss_pred CCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhc
Q 003933 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD 274 (785)
Q Consensus 198 ~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~ 274 (785)
.....++.||...+.+|||++|.+|+.|+.-||+.|.|.+- ...+-.+|.+.+.|+.+.++.|...|..+|.+.+
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpd 1412 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPD 1412 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCccchhhhcccCCCChhhhhhhccccceeecCC
Confidence 34567888998899999999999999999999999999862 1234568999999999999999999999988754
No 95
>PRK01064 hypothetical protein; Provisional
Probab=93.64 E-value=0.072 Score=47.07 Aligned_cols=34 Identities=26% Similarity=0.437 Sum_probs=29.6
Q ss_pred CCCCeEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeT 229 (785)
....+.++|.|....+|+||||+|+||+.||.-.
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 3456889999999999999999999999998743
No 96
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.43 E-value=0.53 Score=48.67 Aligned_cols=66 Identities=26% Similarity=0.446 Sum_probs=55.7
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT 371 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~~ 371 (785)
..+.+.+.....-+|+..+|..++.|....||+|.+.. .+..|.|+|+...|+.+...|.+++.+.
T Consensus 26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~----------~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR----------SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEec----------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 45566667888899999999999999888899999532 3568999999999999999999988763
No 97
>PRK01064 hypothetical protein; Provisional
Probab=93.40 E-value=0.088 Score=46.51 Aligned_cols=32 Identities=34% Similarity=0.510 Sum_probs=27.6
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T 325 (785)
....++|.|..+.+|+||||+|+||+.|+.-.
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 45667889999999999999999999998753
No 98
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=93.22 E-value=0.038 Score=56.28 Aligned_cols=54 Identities=22% Similarity=0.404 Sum_probs=49.0
Q ss_pred CccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHh
Q 003933 209 NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 209 ~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e 272 (785)
..+|+|+||+|.|--.|++.|.++|.|. +..|+|.|+.++|..|...|+.||--
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVla----------d~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLA----------DSKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEec----------CceEEEeecchhhHHHHHhhHhhhcc
Confidence 4589999999999999999999999997 34789999999999999999999864
No 99
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=93.06 E-value=0.22 Score=59.93 Aligned_cols=94 Identities=24% Similarity=0.413 Sum_probs=68.2
Q ss_pred eeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhcc
Q 003933 213 VLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQAS 292 (785)
Q Consensus 213 ~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~ 292 (785)
.++=.++..||+|-++..-+|.|+.+.. +.- .-++|+++|.+++-++. +...+. |
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~~-----------~~~---~~~~~~~~i~~~~~~~~--~~~~~~---f------ 90 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDPS-----------VLL---PPEEAIEKIKEIVPEEA--GITDIY---F------ 90 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecChh-----------hcC---CHHHHHHHHHHhCCCcC--CceeEE---e------
Confidence 3455778999999999999999985421 111 12458888988886541 111111 1
Q ss_pred CCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 293 ~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
...+-++.|-..+-|+||||+|.++++|..+||-+..|+
T Consensus 91 -~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 91 -DDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred -cCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEE
Confidence 223457888899999999999999999999999999864
No 100
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=92.15 E-value=0.7 Score=46.55 Aligned_cols=103 Identities=17% Similarity=0.175 Sum_probs=63.1
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCC
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP 279 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p 279 (785)
-.+-|+|-... |..|||+|.+||+|++..|-+|.|...++. +.++|++.- .|
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s~d------------------------~~~fl~Nl~---~P 112 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKTND------------------------IKKLAVQLL---SP 112 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcCCC------------------------HHHHHHhcC---CC
Confidence 35677777777 999999999999999999999999865431 333344321 12
Q ss_pred cccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331 (785)
Q Consensus 280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI 331 (785)
..+..-... ...++...+++.|......+|-.|--..-+-+.+-||..|.|
T Consensus 113 A~V~gV~i~-~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk~v~~ 163 (166)
T PRK06418 113 ARVLGVNTV-WLPDGTVQYVIRVSRRDRRRLPAKPELLESILSKITGTEVKI 163 (166)
T ss_pred cEEEEEEEE-EeCCCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCCcEEE
Confidence 211110000 011233444577777666666555554455557888888874
No 101
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=91.70 E-value=0.21 Score=48.86 Aligned_cols=36 Identities=33% Similarity=0.687 Sum_probs=34.1
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI 331 (785)
.++.|.|....+|..||++|++||.|++..|-+|.|
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdV 67 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIEL 67 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEE
Confidence 678889999999999999999999999999999997
No 102
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=91.63 E-value=0.24 Score=48.56 Aligned_cols=73 Identities=19% Similarity=0.267 Sum_probs=50.6
Q ss_pred cccccccchhhh---hhhcccchhhhccCC--CCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEc
Q 003933 162 KEEETVKEEESV---EPSNVVPQQVVDNSK--SDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT 236 (785)
Q Consensus 162 k~~~i~g~~esV---E~A~~lI~~ii~~~~--~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~ 236 (785)
|...+..+.+.. ++|+++|.+++-.+. .+.-+ ...+-+|.|-..+-|.||||+|.++++|..+||-+..|.
T Consensus 37 KRIvvR~dps~l~~~e~A~~~I~~ivP~ea~i~di~F----d~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 37 KRIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYF----DDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred ceEEEcCChhhcCCHHHHHHHHHHhCCCccCceeeEe----cCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 334444444444 678888888884221 11111 123457777788899999999999999999999999887
Q ss_pred cC
Q 003933 237 RD 238 (785)
Q Consensus 237 k~ 238 (785)
+.
T Consensus 113 Rt 114 (145)
T cd02410 113 RT 114 (145)
T ss_pred ec
Confidence 54
No 103
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=91.36 E-value=0.31 Score=52.17 Aligned_cols=52 Identities=19% Similarity=0.376 Sum_probs=46.7
Q ss_pred cceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 307 VGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 307 vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
+-+|||.+|.|+|.|+--|.|.|-|- -.+|.+.|....++.++.+|.+.|.+
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVq------------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQ------------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEee------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 46799999999999999999999852 46899999999999999999998876
No 104
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=91.30 E-value=0.12 Score=44.66 Aligned_cols=36 Identities=25% Similarity=0.478 Sum_probs=30.6
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHhCCeE
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARI 329 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArI 329 (785)
....+.+.|..+..|+||||+|+||+.||.-...-+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 456788999999999999999999999997665544
No 105
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=91.24 E-value=0.43 Score=50.43 Aligned_cols=38 Identities=26% Similarity=0.559 Sum_probs=34.1
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
-.-|.|+..+|-++|||+|++|++|+++|+|+|.|-.+
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N 184 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN 184 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC
Confidence 35788899999999999999999999999999998643
No 106
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=90.16 E-value=0.17 Score=43.61 Aligned_cols=35 Identities=31% Similarity=0.479 Sum_probs=29.4
Q ss_pred CCCeEEEEEecCCccceeecCCchHHHHHHHHhCC
Q 003933 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA 231 (785)
Q Consensus 197 ~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGA 231 (785)
.....+.|.|.....|+||||+|+||+.|+.-...
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 34568889999999999999999999999875544
No 107
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=90.09 E-value=0.51 Score=41.96 Aligned_cols=36 Identities=19% Similarity=0.367 Sum_probs=30.6
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhCCeEE
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ 330 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIq 330 (785)
...+++.|-..+-|.|||++|++|++|++...-+..
T Consensus 29 ~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~ 64 (81)
T cd02413 29 PTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFN 64 (81)
T ss_pred CCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhC
Confidence 456889999999999999999999999887655554
No 108
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=89.53 E-value=0.67 Score=53.16 Aligned_cols=65 Identities=26% Similarity=0.385 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 258 ~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
....|..+|.+.|+....+ +.. ....+.....+.||...++.||||+|.+|++|.++.|.+|.|.
T Consensus 458 ~~~~a~~~i~~~i~r~~p~--~~e--------Ve~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 458 ALKLAEEEIEREIKRYLPG--DVE--------VEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred hhHHHHHHHHHHHHHhCCC--Cce--------EEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 3566777787777775321 110 1112345678899999999999999999999999999999963
No 109
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=89.10 E-value=0.31 Score=42.04 Aligned_cols=37 Identities=30% Similarity=0.582 Sum_probs=29.8
Q ss_pred cEEEEEecCCc-----cceeecCCchHHHHHHHHh-CCeEEEe
Q 003933 296 EQVEIKVPNEK-----VGLIIGRGGETIKGLQTRS-GARIQVL 332 (785)
Q Consensus 296 ~~~~i~VP~~~-----vG~VIGKgGetIK~Iq~~T-GArIqI~ 332 (785)
.+..+.|-... +|..||++|.+||.|.++. |-+|.|+
T Consensus 3 ~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 3 NRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp TEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred ceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 35567777766 9999999999999999999 9999964
No 110
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=88.96 E-value=0.62 Score=38.39 Aligned_cols=34 Identities=29% Similarity=0.473 Sum_probs=26.7
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeE
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARI 329 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArI 329 (785)
..+.+.+.....|.||||+|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4445555555689999999999999999988544
No 111
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=88.84 E-value=0.67 Score=38.17 Aligned_cols=34 Identities=32% Similarity=0.406 Sum_probs=27.5
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeE
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKI 233 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI 233 (785)
....+.+.....|.+|||+|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666655789999999999999999988654
No 112
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.29 E-value=0.33 Score=41.89 Aligned_cols=39 Identities=31% Similarity=0.509 Sum_probs=30.2
Q ss_pred EEEEEecCCc-----cceeecCCchHHHHHHHHh-CCeEEEccCC
Q 003933 201 SRKIEVPNNK-----VGVLIGKAGDTIRYLQYNS-GAKIQITRDA 239 (785)
Q Consensus 201 t~~IlVP~~~-----VG~IIGk~G~tIK~IqeeT-GAkI~I~k~~ 239 (785)
..+|.|-... +|.+||++|.+||.|.++. |-+|.|...+
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s 48 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS 48 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence 4566666666 9999999999999999999 9999998653
No 113
>PRK13764 ATPase; Provisional
Probab=88.20 E-value=0.92 Score=54.35 Aligned_cols=65 Identities=26% Similarity=0.355 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 258 ~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
....|.+.|.+.|+....+ .-. ..........+.|+...++.||||+|.+|++|.++.|.+|.|.
T Consensus 453 ~~~~~~~~~~~~~~~~~~~-~~~---------~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~ 517 (602)
T PRK13764 453 VWRLAEKEIEREIKRYLPG-PVE---------VEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVR 517 (602)
T ss_pred HHHHHHHHHHHHHHHhcCC-ceE---------EEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEE
Confidence 3455777788877775311 000 1112445778899999999999999999999999999999974
No 114
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=88.01 E-value=0.98 Score=47.82 Aligned_cols=34 Identities=32% Similarity=0.580 Sum_probs=31.4
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI 331 (785)
.-+.|+..+|-+||||+|.+||.|.+.|+|+|.|
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~V 181 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIV 181 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEE
Confidence 3578999999999999999999999999999985
No 115
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=87.46 E-value=0.58 Score=40.90 Aligned_cols=36 Identities=28% Similarity=0.635 Sum_probs=29.6
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhCCeEE
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ 330 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIq 330 (785)
...+.+.|..+..|+||||+|++|+.||--+..-+.
T Consensus 23 ~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 23 GDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 345678888899999999999999999977665554
No 116
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=87.45 E-value=4.7 Score=48.19 Aligned_cols=143 Identities=21% Similarity=0.311 Sum_probs=78.2
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEc---cCCCC-CCCC-----CCcceEecccHHHHHHHHHHHHHH
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT---RDADA-DPHA-----ATRPVEIIGTLSNIDKAEKLINAV 269 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~---k~~d~-~p~s-----~eRiV~I~Gt~e~V~kA~~lI~el 269 (785)
...+.+.|+.. ..+| |.+|++|...+..+|+|. ++.+. .+.. ..-++.|.|+.++|++..+.+...
T Consensus 217 ~~~r~~~V~~~--s~li---GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~ 291 (562)
T TIGR03802 217 LVGRAYRVNRA--SSLI---GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEE 291 (562)
T ss_pred eeeEEEEECCC--cccC---CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCc
Confidence 34566666654 2244 557888887665544443 22111 1111 124678999999998877665433
Q ss_pred HHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHH-H-----HhCCeEEEecCCC---C---
Q 003933 270 IAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ-T-----RSGARIQVLIPQH---L--- 337 (785)
Q Consensus 270 I~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq-~-----~TGArIqI~i~~~---l--- 337 (785)
+.+.. ... ...+..++.+++ ..+||| +|++|. + +.|+.|.- +.|. +
T Consensus 292 ~~~~~----------~~~-----~~~~~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~-I~R~g~~i~~~ 349 (562)
T TIGR03802 292 VQEVE----------GLD-----VPMETKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEK-IKRDDQPLPIL 349 (562)
T ss_pred cCCcc----------ccC-----CceEEEEEEECC---cccCCc---cHHHHhccccccccCCeEEEE-EeeCCccccCC
Confidence 22110 000 011233455554 345654 888886 2 67888773 3332 1
Q ss_pred CCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 003933 338 PEGDGSKERIVRVTGDMRQIEIAQEMIKEVL 368 (785)
Q Consensus 338 P~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll 368 (785)
++..-..-.+|.|.|+.+.++++++.+-+..
T Consensus 350 ~d~~L~~GD~LlV~G~~~~l~~~~~~lG~~~ 380 (562)
T TIGR03802 350 PETVLQRGDVVTLVGTPQDVDRAAKQLGYAI 380 (562)
T ss_pred CCCEecCCCEEEEEeCHHHHHHHHHHcCCch
Confidence 1111123346999999999999888755433
No 117
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=87.26 E-value=0.42 Score=41.78 Aligned_cols=33 Identities=30% Similarity=0.635 Sum_probs=26.6
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeE
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKI 233 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI 233 (785)
.+.|.|.....|.||||+|+||+.|+.-+..-+
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 456777788999999999999999987655433
No 118
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=86.39 E-value=1.8 Score=45.66 Aligned_cols=37 Identities=24% Similarity=0.541 Sum_probs=29.8
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHH----HHhCC-eEEE
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQ----TRSGA-RIQV 331 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq----~~TGA-rIqI 331 (785)
...++|.|....-|.||||+|++|+.|+ +.+|. .|+|
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I 91 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI 91 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence 4567889999999999999999999876 45666 4554
No 119
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=86.23 E-value=0.35 Score=55.31 Aligned_cols=40 Identities=25% Similarity=0.410 Sum_probs=36.3
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
.....|.||...++.||||+|.+|++|+++.|.+|.|...
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 3457889999999999999999999999999999999854
No 120
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=85.55 E-value=0.98 Score=54.56 Aligned_cols=63 Identities=19% Similarity=0.278 Sum_probs=45.9
Q ss_pred hhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 174 EPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 174 E~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
++|+++|.+++-.+..-... .-...+-+|+|-..+-|.||||+|.++++|.++||-+..|.+.
T Consensus 69 ~~~~~~i~~~~~~~~~~~~~--~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 69 EEAIEKIKEIVPEEAGITDI--YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred HHHHHHHHHhCCCcCCceeE--EecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 66778888877422111100 1123456788888999999999999999999999999988864
No 121
>PRK03818 putative transporter; Validated
Probab=85.06 E-value=6.3 Score=47.02 Aligned_cols=139 Identities=19% Similarity=0.305 Sum_probs=78.1
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEcc---CCCC-CC--C---CCCcceEecccHHHHHHHHHHHHHHH
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITR---DADA-DP--H---AATRPVEIIGTLSNIDKAEKLINAVI 270 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k---~~d~-~p--~---s~eRiV~I~Gt~e~V~kA~~lI~elI 270 (785)
...++.|+++. +| |++|+++......+|.|.+ +... .+ + ...-++.|.|+.+.++++.+.+...+
T Consensus 205 ~~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~ 278 (552)
T PRK03818 205 QTINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEV 278 (552)
T ss_pred eeEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence 34677776443 34 6689999988877666532 2111 01 1 12246789999999887776654322
Q ss_pred HhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHH--HHHhCCeEEEecCCC---CCC---CCC
Q 003933 271 AEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGL--QTRSGARIQVLIPQH---LPE---GDG 342 (785)
Q Consensus 271 ~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~I--q~~TGArIqI~i~~~---lP~---~~~ 342 (785)
.+. .. .........++.++++ .++|| +|++| +++.|+.|.- +.|. ++. ..-
T Consensus 279 ~~~------------~~--~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~Vla-I~R~g~~l~~~~d~~L 337 (552)
T PRK03818 279 DTS------------LS--TRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISR-LNRAGVELVASPDLSL 337 (552)
T ss_pred Ccc------------cc--ccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEE-EeECCeecCCCCCCEE
Confidence 100 00 0001223444555553 56655 88887 4777877663 3331 111 011
Q ss_pred CCccEEEEEcCHHHHHHHHHHHH
Q 003933 343 SKERIVRVTGDMRQIEIAQEMIK 365 (785)
Q Consensus 343 s~er~VtIsG~~eqVe~Ak~lI~ 365 (785)
..-.+|.|.|+.+++++.++.+.
T Consensus 338 q~GD~LlVvG~~~~i~~l~~~Lg 360 (552)
T PRK03818 338 QFGDILNLVGRPEAIDAVANVLG 360 (552)
T ss_pred ecCCEEEEEECHHHHHHHHHHhC
Confidence 22345999999999999887644
No 122
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=85.01 E-value=1.2 Score=43.83 Aligned_cols=35 Identities=34% Similarity=0.606 Sum_probs=32.9
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331 (785)
Q Consensus 297 ~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI 331 (785)
++-|.|-...+|..||++|.+||.|++..|-+|.|
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV 68 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL 68 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE
Confidence 67788999999999999999999999999999997
No 123
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=84.87 E-value=0.49 Score=41.12 Aligned_cols=35 Identities=23% Similarity=0.518 Sum_probs=30.3
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEE
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ 330 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIq 330 (785)
..+.+.|-..+.+.||||+|++||.|...+.-++.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 56788899999999999999999999987766664
No 124
>PRK13764 ATPase; Provisional
Probab=84.13 E-value=0.63 Score=55.69 Aligned_cols=42 Identities=24% Similarity=0.389 Sum_probs=38.0
Q ss_pred CCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCC
Q 003933 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA 239 (785)
Q Consensus 198 ~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~ 239 (785)
......|.|+...++.+|||+|.+|++|.++.|.+|.|....
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 456778999999999999999999999999999999998654
No 125
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=83.71 E-value=1.2 Score=41.65 Aligned_cols=32 Identities=28% Similarity=0.579 Sum_probs=27.0
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCC
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGA 327 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGA 327 (785)
..++|.|-..+-|.||||+|++|++|++....
T Consensus 61 ~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 61 DRVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CCEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 45788899999999999999999999866443
No 126
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=83.55 E-value=1.6 Score=46.95 Aligned_cols=51 Identities=22% Similarity=0.440 Sum_probs=42.8
Q ss_pred ceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHh
Q 003933 212 GVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 212 G~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e 272 (785)
-+|||.+|.|+|.|+--|.|-|-|... .|.+.|....|..+.+.+.+.|+.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~----------TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN----------TVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc----------EEEeecCcchHHHHHHHHHHHHhc
Confidence 579999999999999999999999843 678888888887777777777664
No 127
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=82.53 E-value=1.7 Score=43.77 Aligned_cols=38 Identities=26% Similarity=0.508 Sum_probs=33.0
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEe
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL 332 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~ 332 (785)
...++-|.|-... |..|||+|.+||.+++..|-+|.|+
T Consensus 59 ~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 59 VDDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred eCCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 3456778887777 9999999999999999999999973
No 128
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=81.55 E-value=1.7 Score=50.44 Aligned_cols=65 Identities=20% Similarity=0.266 Sum_probs=45.4
Q ss_pred hhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 172 SVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 172 sVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
+-+.|+++|.+++-.+..-... .-...+-+|+|-..+=|.||||.|+++++|..+||-+-.|.+.
T Consensus 73 ~~e~A~~~I~eivP~ea~i~~i--~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 73 PPEEARKIILEIVPEEAGITDI--YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CHHHHHHHHHHhCccccCceeE--EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 3566777777777322111110 1122345788888999999999999999999999988887753
No 129
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=78.99 E-value=3.2 Score=37.00 Aligned_cols=30 Identities=33% Similarity=0.603 Sum_probs=25.1
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T 325 (785)
..+++.|-...-|.|||++|++|++|++..
T Consensus 38 ~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 38 LGTQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred CcEEEEEEECCCCceECCCchhHHHHHHHH
Confidence 346777777899999999999999988654
No 130
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=78.79 E-value=1.6 Score=50.42 Aligned_cols=72 Identities=15% Similarity=0.122 Sum_probs=50.1
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccE-EEEEcC---HHHHHHHHHHHHHHHhc
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERI-VRVTGD---MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~-VtIsG~---~eqVe~Ak~lI~~ll~~ 370 (785)
..+.|.|+...+..|||-||..|.+++...++.|+..+..+++ -+-.+- |.|.-+ .+.|..+|.-+.+++.+
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~---qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFG---QSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcc---hhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 4568999999999999999999999999999999832222222 112222 666665 34556666666666654
No 131
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=78.53 E-value=1.2 Score=38.65 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=28.9
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEE
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQ 234 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~ 234 (785)
....|.|-....|.|||++|++|++|+....-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 45678888899999999999999999877665553
No 132
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=77.37 E-value=7.5 Score=40.31 Aligned_cols=32 Identities=31% Similarity=0.563 Sum_probs=27.0
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhC
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG 326 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TG 326 (785)
...++|.|-...-|.|||++|.+|++|++...
T Consensus 37 ~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 37 PLGTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred CCcEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 34678899999999999999999999876543
No 133
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=76.50 E-value=8.7 Score=40.05 Aligned_cols=37 Identities=24% Similarity=0.470 Sum_probs=31.6
Q ss_pred CccEEEEEecCCccceeecCCchHHHHHHHHhCCeEE
Q 003933 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ 330 (785)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIq 330 (785)
....+.+.|-.+..++||||.|++++.||--+.+.+.
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 3456778888888999999999999999988877766
No 134
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=75.05 E-value=2.6 Score=48.90 Aligned_cols=131 Identities=14% Similarity=0.041 Sum_probs=84.9
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcc-eEecc---cHHHHHHHHHHHHHHHHhhc
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP-VEIIG---TLSNIDKAEKLINAVIAEAD 274 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRi-V~I~G---t~e~V~kA~~lI~elI~e~~ 274 (785)
...+.|.|+...+-.|||-+|..|.++..+.++.|.+...-+ .+.+..+- |.|.. ..++|.-++.-+++++++.+
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~-~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c 526 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK-FGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQC 526 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhh-cchhhhhcceEEECCccCccchhcccccHHHHHhhhc
Confidence 346789999999999999999999999999999998874322 22233333 66665 44567777777888888654
Q ss_pred cCCCCcc--cc---------cccc----hhhcc-----CCccEEEEEecCCccceeec---CCchHHHHHHHHhCCeEE
Q 003933 275 AGGSPSL--VA---------RGLA----TAQAS-----GAAEQVEIKVPNEKVGLIIG---RGGETIKGLQTRSGARIQ 330 (785)
Q Consensus 275 ~gg~p~~--~~---------~g~~----~~~~~-----~~~~~~~i~VP~~~vG~VIG---KgGetIK~Iq~~TGArIq 330 (785)
.-.+..+ .. .+.. +..-. +-.....+.++.+.++..|| -+|++|-.+..-..-.|.
T Consensus 527 ~f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie 605 (657)
T COG5166 527 RFNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIE 605 (657)
T ss_pred ccccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccce
Confidence 1101000 00 0000 00000 01122345677788899999 789999999888777777
No 135
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=74.29 E-value=3.9 Score=36.38 Aligned_cols=36 Identities=17% Similarity=0.276 Sum_probs=28.9
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI 235 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I 235 (785)
...+|.|-..+-|.|||++|++|++|+++....+.+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 347888888899999999999999998876554433
No 136
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=73.38 E-value=5.3 Score=42.12 Aligned_cols=32 Identities=19% Similarity=0.307 Sum_probs=26.9
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHhC
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG 326 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TG 326 (785)
...++|.|-..+-|.|||++|..|++|++...
T Consensus 43 ~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 43 PIRTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred CCcEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 34578889999999999999999999886654
No 137
>COG1159 Era GTPase [General function prediction only]
Probab=73.27 E-value=4.5 Score=44.36 Aligned_cols=30 Identities=33% Similarity=0.548 Sum_probs=23.5
Q ss_pred EEEEEecC-CccceeecCCchHHHHHHHHhC
Q 003933 297 QVEIKVPN-EKVGLIIGRGGETIKGLQTRSG 326 (785)
Q Consensus 297 ~~~i~VP~-~~vG~VIGKgGetIK~Iq~~TG 326 (785)
...|.|.. ++-+.||||+|++||+|-.++.
T Consensus 230 ~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR 260 (298)
T COG1159 230 HATIYVERESQKGIIIGKNGAMIKKIGTAAR 260 (298)
T ss_pred EEEEEEecCCccceEECCCcHHHHHHHHHHH
Confidence 44567777 6789999999999999865443
No 138
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=72.82 E-value=53 Score=33.07 Aligned_cols=144 Identities=22% Similarity=0.253 Sum_probs=80.5
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEE-EccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCC
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQ-ITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGS 278 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~-I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~ 278 (785)
.++.|++. +..|.| +.|-.|-.+.|.+|. +.-......+-..-.+++.|+.+.|++..+.|++++.-.....
T Consensus 3 ~~IsV~ve-N~pGvL-----~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~~~~~i~qi~kQl~KLidV~~V~~- 75 (161)
T PRK11895 3 HTLSVLVE-NEPGVL-----SRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSGDEQVIEQITKQLNKLIDVLKVVD- 75 (161)
T ss_pred EEEEEEEc-CCCcHH-----HHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEECCHHHHHHHHHHHhccccEEEEEe-
Confidence 35666665 345555 556666667777663 2211000011112235666888888888888888776332100
Q ss_pred CcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHH
Q 003933 279 PSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358 (785)
Q Consensus 279 p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe 358 (785)
+.... .-..+-.-+.|..+.. .-..|.+|.+..+|+|.- . +.+.-+|+|+|+.+.|+
T Consensus 76 -------~~~~~-~v~rEl~LiKv~~~~~------~r~~i~~i~~~f~a~ivd-v--------~~~~~~iE~tG~~~ki~ 132 (161)
T PRK11895 76 -------LTEEA-HVERELALVKVRASGE------NRAEILRLADIFRAKIVD-V--------TPESLTIEVTGDSDKID 132 (161)
T ss_pred -------cCCcc-hhheEEEEEEEECCcc------cHHHHHHHHHHhCCEEEE-e--------cCCEEEEEEeCCHHHHH
Confidence 00000 0011122223332211 235788999999999872 2 23467899999999999
Q ss_pred HHHHHHHHH-HhcccC
Q 003933 359 IAQEMIKEV-LSQTVR 373 (785)
Q Consensus 359 ~Ak~lI~~l-l~~~~r 373 (785)
.-.++++.. |.+..|
T Consensus 133 ~~~~~l~~~gi~e~~R 148 (161)
T PRK11895 133 AFIDLLRPYGIKEIVR 148 (161)
T ss_pred HHHHHhhhcCCEEEEc
Confidence 988888764 334344
No 139
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=72.47 E-value=4.1 Score=45.68 Aligned_cols=40 Identities=25% Similarity=0.521 Sum_probs=36.5
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
.....+.|+....+..|||+|.+||...+-||.+|.|...
T Consensus 300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 3578899999999999999999999999999999999753
No 140
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=72.37 E-value=4.9 Score=45.51 Aligned_cols=40 Identities=20% Similarity=0.275 Sum_probs=36.7
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
.....|.|+....++.|||+|.+|+...+-||.+|.|..-
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 4577899999999999999999999999999999999864
No 141
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=71.99 E-value=16 Score=44.68 Aligned_cols=19 Identities=11% Similarity=0.307 Sum_probs=7.8
Q ss_pred EEcCHHHHHHHHHHHHHHH
Q 003933 350 VTGDMRQIEIAQEMIKEVL 368 (785)
Q Consensus 350 IsG~~eqVe~Ak~lI~~ll 368 (785)
|++..+....+-+|+...+
T Consensus 377 ir~emDd~~~~f~lL~n~v 395 (1102)
T KOG1924|consen 377 IRAEMDDANEVFELLANTV 395 (1102)
T ss_pred hhhhhccHHHHHHHHHHhh
Confidence 4444333344444444433
No 142
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=71.51 E-value=7.7 Score=40.52 Aligned_cols=32 Identities=31% Similarity=0.539 Sum_probs=26.3
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCC
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGA 327 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGA 327 (785)
..+++.|-...-|.||||+|++|++|++...-
T Consensus 40 ~~i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 40 LGTRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred CcEEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 34677777789999999999999999876544
No 143
>PRK15494 era GTPase Era; Provisional
Probab=70.34 E-value=9.2 Score=42.66 Aligned_cols=29 Identities=28% Similarity=0.448 Sum_probs=22.8
Q ss_pred EEEEEecC-CccceeecCCchHHHHHHHHh
Q 003933 297 QVEIKVPN-EKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 297 ~~~i~VP~-~~vG~VIGKgGetIK~Iq~~T 325 (785)
...|.|.. ++.+.||||+|++||+|..+.
T Consensus 274 ~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 274 NQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 34567777 678999999999999976543
No 144
>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]
Probab=70.29 E-value=3.7 Score=48.30 Aligned_cols=64 Identities=16% Similarity=0.262 Sum_probs=45.0
Q ss_pred ccceeecCCchHHHHH---HHHhCCeEEEccCCCC------------CCCCCCcceEecccHHHHHHHHHHHHHHHHhh
Q 003933 210 KVGVLIGKAGDTIRYL---QYNSGAKIQITRDADA------------DPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 210 ~VG~IIGk~G~tIK~I---qeeTGAkI~I~k~~d~------------~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~ 273 (785)
.+-.||||.|.+|..+ +=+|.|.|......++ .++++.++|..+++.+.|++++..+.+++.+.
T Consensus 460 QLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~deld~hr~~led~~ae~ 538 (718)
T KOG2416|consen 460 QLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRADELDKHRNGLEDLEAEL 538 (718)
T ss_pred HHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecchhHHHHHhccchhccccc
Confidence 3556899887776443 3356666666532221 34566788888999999999999998888765
No 145
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.12 E-value=2.2e+02 Score=33.25 Aligned_cols=14 Identities=14% Similarity=0.045 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHhh
Q 003933 260 DKAEKLINAVIAEA 273 (785)
Q Consensus 260 ~kA~~lI~elI~e~ 273 (785)
+.|+-+|.++|--.
T Consensus 244 R~~lG~I~EiFGpV 257 (483)
T KOG2236|consen 244 RTALGQIFEIFGPV 257 (483)
T ss_pred cccchhhhhhhccc
Confidence 66788888877543
No 146
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=69.48 E-value=6.4 Score=41.73 Aligned_cols=33 Identities=24% Similarity=0.447 Sum_probs=26.9
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHH----HhCC
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQY----NSGA 231 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~Iqe----eTGA 231 (785)
....+|.|-...=|.||||+|+.|++|++ .+|.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~ 86 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGK 86 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCC
Confidence 45678888888999999999999988765 5555
No 147
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=69.03 E-value=76 Score=31.83 Aligned_cols=137 Identities=21% Similarity=0.270 Sum_probs=74.1
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCC-CCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCC
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADAD-PHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP 279 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~-p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p 279 (785)
++.|++.+ ..|.| +.|-.|-.+-|.+|.-.--.... .+-..-.+++.++.+.++...+.|++++.-....
T Consensus 3 ~isI~ven-~pGvL-----~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~d~~~i~qi~kQl~Kli~V~~V~--- 73 (157)
T TIGR00119 3 ILSVLVEN-EPGVL-----SRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVGDDKVLEQITKQLNKLVDVIKVS--- 73 (157)
T ss_pred EEEEEEcC-CCcHH-----HHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEECCHHHHHHHHHHHhcCccEEEEE---
Confidence 55666653 44555 45666666777766321111111 1111123455676666666666666665432110
Q ss_pred cccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHH
Q 003933 280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEI 359 (785)
Q Consensus 280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~ 359 (785)
.+.. ...-..+-+-|.|..+. ..-..|.+|.+..+|+|.-+ ..+.-+|+++|+.+.|+.
T Consensus 74 -----~~~~-~~~v~rEl~LiKv~~~~------~~r~~i~~i~~~f~a~ivdv---------~~~~~~ie~tG~~~ki~~ 132 (157)
T TIGR00119 74 -----DLTE-SAIVERELCLVKVSAPG------EGRDEIIRLTNIFRGRIVDV---------SPDSYTVEVTGDSDKIDA 132 (157)
T ss_pred -----ecCC-CcceeeEEEEEEEECCc------cCHHHHHHHHHHhCCEEEEe---------cCCEEEEEEcCCHHHHHH
Confidence 0000 00001122223333322 23456889999999999722 234678999999999999
Q ss_pred HHHHHHHH
Q 003933 360 AQEMIKEV 367 (785)
Q Consensus 360 Ak~lI~~l 367 (785)
-.++++..
T Consensus 133 ~~~~l~~~ 140 (157)
T TIGR00119 133 FLELLRPF 140 (157)
T ss_pred HHHHhhhc
Confidence 88888763
No 148
>PRK00089 era GTPase Era; Reviewed
Probab=68.56 E-value=10 Score=40.84 Aligned_cols=30 Identities=33% Similarity=0.602 Sum_probs=23.0
Q ss_pred cEEEEEecC-CccceeecCCchHHHHHHHHh
Q 003933 296 EQVEIKVPN-EKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 296 ~~~~i~VP~-~~vG~VIGKgGetIK~Iq~~T 325 (785)
....|.|.. ++.+.||||+|++||+|..++
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 344566766 677999999999999976543
No 149
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=68.05 E-value=9.5 Score=40.86 Aligned_cols=35 Identities=26% Similarity=0.371 Sum_probs=25.8
Q ss_pred cEEEEEecC-CccceeecCCchHHHHHHHHhCCeEE
Q 003933 296 EQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQ 330 (785)
Q Consensus 296 ~~~~i~VP~-~~vG~VIGKgGetIK~Iq~~TGArIq 330 (785)
....|.|.. ++.+.||||+|++||+|..++.-.|+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~ 256 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAARKDIL 256 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHH
Confidence 345667776 67899999999999998765544433
No 150
>cd01572 QPRTase Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=67.24 E-value=44 Score=36.24 Aligned_cols=69 Identities=14% Similarity=0.225 Sum_probs=49.6
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHh--CCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRS--GARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~T--GArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
.++.|-...-+.|- |=+.+++|-+.. +++|+.+..+. ..-...+.+++|.|....+.++.+.+..+|+.
T Consensus 29 ~~~~~~ar~~~v~~--G~~~~~~i~~~~~~~l~v~~~~~dG--~~v~~g~~i~~i~G~~~~ll~~Er~~ln~L~~ 99 (268)
T cd01572 29 AEARLIAKEEGVLA--GLPVAEEVFELLDPGIEVEWLVKDG--DRVEPGQVLATVEGPARSLLTAERTALNFLQR 99 (268)
T ss_pred EEEEEEEcCCEEEE--CHHHHHHHHHHcCCCeEEEEEeCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 34444443334444 357788999998 99997666554 22345789999999999999999999888754
No 151
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=66.71 E-value=5.2 Score=41.31 Aligned_cols=38 Identities=26% Similarity=0.431 Sum_probs=35.5
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
...+.|+.+..+++|||+|.+|+.+.+-||-+|.|...
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 78899999999999999999999999999999999743
No 152
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=66.70 E-value=4.9 Score=37.59 Aligned_cols=30 Identities=23% Similarity=0.442 Sum_probs=24.9
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhC
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSG 230 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTG 230 (785)
.++|.|-..+-|.|||++|++|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 367777778899999999999999887543
No 153
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=66.68 E-value=5 Score=52.83 Aligned_cols=7 Identities=14% Similarity=0.064 Sum_probs=3.9
Q ss_pred CCCCCcc
Q 003933 74 KPDGPVN 80 (785)
Q Consensus 74 ~~d~l~~ 80 (785)
||.+|..
T Consensus 3989 lpedl~l 3995 (4600)
T COG5271 3989 LPEDLKL 3995 (4600)
T ss_pred CchhcCC
Confidence 5666643
No 154
>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=66.47 E-value=55 Score=35.74 Aligned_cols=70 Identities=14% Similarity=0.211 Sum_probs=51.1
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 297 ~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
..++.|-...-+.|- |-+.+++|-+..+|+|.++..+. ..-...+.+++|.|....+..+.+.+..+|..
T Consensus 30 ~~~a~i~ar~~~v~~--G~~~a~~i~~~l~~~~~~~~~dG--~~v~~g~~i~~i~G~a~~ll~~Er~~ln~l~~ 99 (273)
T PRK05848 30 KATAKIIAKSEGVFS--GEKYALELLEMTGIECVFTIKDG--ERFKKGDILMEIEGDFSMLLKVERTLLNLLQH 99 (273)
T ss_pred eEEEEEEEcCCEEEE--CHHHHHHHHHHcCCEEEEEcCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 344554444445554 34678899999999999766654 22346789999999999999999998887753
No 155
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=65.23 E-value=25 Score=31.50 Aligned_cols=70 Identities=14% Similarity=0.235 Sum_probs=49.4
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 369 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~ 369 (785)
...++.|=...-|.|- |=+.+++|-+..+++|+.+..+. ..-...+.+++|.|+...|..|.+.+..+|.
T Consensus 16 ~~~~a~i~are~gV~a--G~~~~~~i~~~l~~~v~~~~~dG--~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 16 KTGTATIIAREDGVLA--GLEEAEEIFEKLGLEVEWLVKDG--DRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SEEEEEEEESSSEEE---SHHHHHHHHHHCTEEEEESS-TT---EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CEEEEEEEeCCCEEEE--CHHHHHHHHhhccEEEEEEeCCC--CCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 3444444444444454 44778999999999999655544 2234567899999999999999999998875
No 156
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=64.92 E-value=5.5 Score=41.49 Aligned_cols=38 Identities=26% Similarity=0.386 Sum_probs=30.6
Q ss_pred CCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEE
Q 003933 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI 235 (785)
Q Consensus 198 ~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I 235 (785)
...++.+.|-.+..++|||++|.++..|+.-+.+-++-
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 45567777888889999999999999999877665544
No 157
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=64.35 E-value=8.3 Score=42.67 Aligned_cols=34 Identities=35% Similarity=0.651 Sum_probs=26.5
Q ss_pred cEEEEEecC-CccceeecCCchHHHHHHHHhCCeE
Q 003933 296 EQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARI 329 (785)
Q Consensus 296 ~~~~i~VP~-~~vG~VIGKgGetIK~Iq~~TGArI 329 (785)
...++.+|. +...+||||||..|+.|-++.+-.+
T Consensus 328 I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL 362 (379)
T KOG1423|consen 328 IQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDL 362 (379)
T ss_pred EEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHH
Confidence 456788888 5678899999999999976655443
No 158
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=64.26 E-value=5.7 Score=39.84 Aligned_cols=56 Identities=16% Similarity=0.247 Sum_probs=36.3
Q ss_pred CccceeecCCchHHHHHHHHhCCeEEEecCCC------CCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 003933 305 EKVGLIIGRGGETIKGLQTRSGARIQVLIPQH------LPEGDGSKERIVRVTGDMRQIEIAQEMIK 365 (785)
Q Consensus 305 ~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~------lP~~~~s~er~VtIsG~~eqVe~Ak~lI~ 365 (785)
.++|+=||- -+|+++|||.|.=++.+. -|...-....+|.|.|+...+.+++.++.
T Consensus 97 ~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 97 PFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred cccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 455555542 358899999987322211 12223345568999999999999988764
No 159
>TIGR01334 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.
Probab=63.77 E-value=63 Score=35.37 Aligned_cols=68 Identities=18% Similarity=0.238 Sum_probs=49.8
Q ss_pred EEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 299 ~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
++.|-...-|.|= |-+.+++|-+..+|+|+++..+. ......+.+++|+|+...+..|.+.+..+|+.
T Consensus 34 ~~~~~are~gv~~--G~~~~~~i~~~l~~~~~~~~~dG--~~v~~g~~i~~~~G~a~~ll~~eR~alN~l~~ 101 (277)
T TIGR01334 34 HITFTARDEGIVS--GVSEAAKLLKQLGASIDYAVPSG--SRALAGTLLLEAKGSAGQLHQGWKSAQSVLEW 101 (277)
T ss_pred EEEEEEcCCEEEE--CHHHHHHHHHHcCCEEEEEeCCC--CEeCCCCEEEEEEecHHHHHHHHHHHHHHHHH
Confidence 4444444444443 34778999999999999776655 33456788999999999999999888877753
No 160
>cd01568 QPRTase_NadC Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=63.24 E-value=58 Score=35.33 Aligned_cols=70 Identities=14% Similarity=0.243 Sum_probs=50.1
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHh-CCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRS-GARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 297 ~~~i~VP~~~vG~VIGKgGetIK~Iq~~T-GArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
..++.|-...-+.|-| =+.+++|-+.. ++.|+.+.++. ..-...+.+++|.|+...+..+.+.+..+|..
T Consensus 28 ~~~~~i~~r~~~v~~G--~~~~~~i~~~~~~~~v~~~~~dG--~~v~~g~~i~~i~G~~~~l~~~Er~~ln~L~~ 98 (269)
T cd01568 28 PATATLIAKEEGVLAG--LEVAEEVFELLDGIEVEWLVKDG--DRVEAGQVLLEVEGPARSLLTAERVALNLLQR 98 (269)
T ss_pred eEEEEEEecCCEEEEC--HHHHHHHHHHhCCeEEEEEeCCC--CEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 3444444444455544 46788888888 88887565554 23346789999999999999999998887754
No 161
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=62.99 E-value=25 Score=36.84 Aligned_cols=30 Identities=20% Similarity=0.589 Sum_probs=25.5
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T 325 (785)
..++|.|-..+-+.|||++|++|++|++..
T Consensus 62 ~~i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 62 DKIRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred CceEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 347788889999999999999999987544
No 162
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=62.67 E-value=7.9 Score=43.83 Aligned_cols=41 Identities=27% Similarity=0.472 Sum_probs=37.0
Q ss_pred CCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 198 ~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
......+.|+....++.|||+|.+|+...+-||.+|.|...
T Consensus 301 ~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 301 EEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred CCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 34678899999999999999999999999999999999854
No 163
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=62.08 E-value=6.7 Score=45.85 Aligned_cols=40 Identities=30% Similarity=0.528 Sum_probs=36.6
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~ 238 (785)
.....|.|+....+..|||+|.+||...+-||.+|.|...
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 3588899999999999999999999999999999999854
No 164
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=61.74 E-value=17 Score=40.71 Aligned_cols=57 Identities=25% Similarity=0.399 Sum_probs=47.9
Q ss_pred cCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHH--HHHHhh
Q 003933 207 PNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN--AVIAEA 273 (785)
Q Consensus 207 P~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~--elI~e~ 273 (785)
+...+-.|.|..+.+++.|++.+|+.|.... +.++|.|+...|+.|.+.|. +++...
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----------~~~~i~g~~~~v~~A~~~l~~l~~~~~~ 80 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG----------EAVRIIGARPLVDVATRVLLTLELLAEV 80 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC----------ceEEEEechHHHHHHHHHHhHHHHHHHH
Confidence 3567888999999999999999999998873 47899999889999998888 555543
No 165
>cd01573 modD_like ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.
Probab=61.26 E-value=72 Score=34.71 Aligned_cols=68 Identities=10% Similarity=0.200 Sum_probs=48.2
Q ss_pred EEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 299 ~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
++.|-...-|.|=| -+.+++|-+..+|+|+++.++. ..-...+.+++|.|+...+..+.+.+..+|..
T Consensus 30 ~~~~~ak~~gv~aG--~~~~~~~~~~~~~~v~~~~~dG--~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 97 (272)
T cd01573 30 KITFRARDPGVLCG--TEEAARILELLGLEVDLAAASG--SRVAAGAVLLEAEGPAAALHLGWKVAQTLLEW 97 (272)
T ss_pred EEEEEECCCEEEEC--HHHHHHHHHHcCcEEEEEcCCC--CEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 33333333344432 3678889899999998666554 22345789999999999999999988877753
No 166
>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=60.71 E-value=76 Score=34.94 Aligned_cols=70 Identities=10% Similarity=0.148 Sum_probs=49.3
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEE--EecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ--VLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 297 ~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIq--I~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
..++.|-...-|.|- |-+.+.+|-+..+++|+ ++..+. ......+.+++|.|+...+..+.+.+..+|+.
T Consensus 42 ~~~~~i~ar~~gv~~--G~~~a~~i~~~~~~~~~~~~~~~dG--~~v~~g~~i~~~~G~a~~ll~~eR~~lN~l~~ 113 (288)
T PRK07428 42 TGQAKWIAKESGVIA--GLPIAARVFQLLDPQVSFTPLVAEG--AACESGQVVAEIEGPLDALLMGERVALNLAMR 113 (288)
T ss_pred EEEEEEEecCCeEEE--CHHHHHHHHHHcCCcEEEEEEcCCC--CEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 344554444445554 34678899999998877 444443 22345788999999999999999988877753
No 167
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=60.70 E-value=7.5 Score=44.89 Aligned_cols=39 Identities=28% Similarity=0.460 Sum_probs=35.6
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITR 237 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k 237 (785)
.....|.|+....++.|||+|.+||...+-||.+|.|..
T Consensus 334 ~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 334 GRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 356789999999999999999999999999999999974
No 168
>CHL00048 rps3 ribosomal protein S3
Probab=60.59 E-value=14 Score=38.75 Aligned_cols=31 Identities=23% Similarity=0.300 Sum_probs=26.7
Q ss_pred ccEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T 325 (785)
...++|.|-...-|.|||++|++|++|++..
T Consensus 65 ~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 65 IDLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CCeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 4467888888999999999999999988665
No 169
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=60.38 E-value=13 Score=47.21 Aligned_cols=32 Identities=28% Similarity=0.200 Sum_probs=22.0
Q ss_pred cchhhhhccccccccCCccccCCCcCcCCCCCCCCC
Q 003933 43 NSDEVEKNVDGFAEAHGSEVKRPRLDDDKTEKPDGP 78 (785)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~e~kr~~~dd~~~~~~d~l 78 (785)
++-|+|+++.| -++.-.+..|.|-||+.. |.+
T Consensus 1668 eSmedeRnagd-Rase~qesl~iR~ddeaq---d~i 1699 (3015)
T KOG0943|consen 1668 ESMEDERNAGD-RASEIQESLPIRGDDEAQ---DDI 1699 (3015)
T ss_pred hhhhhhcChhh-hhhhhhhcccccCCcccc---ccC
Confidence 55566666555 456667888888888876 555
No 170
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. 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=59.59 E-value=9.2 Score=34.07 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=22.5
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHh
Q 003933 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (785)
Q Consensus 202 ~~IlVP~~~VG~IIGk~G~tIK~IqeeT 229 (785)
.++.|-...-|.|||++|++|++|++..
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5555556888999999999998887653
No 171
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating)
Probab=59.20 E-value=58 Score=35.29 Aligned_cols=69 Identities=14% Similarity=0.241 Sum_probs=49.0
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
.++.|-...-+.|-| -+.+.+|-+..++.|+.+..+. ..-...+.+++|.|....+..+.+.+..+|..
T Consensus 27 ~~~~~~ar~~~v~~G--~~~~~~i~~~~~~~v~~~~~dG--~~v~~g~~i~~i~G~~~~il~~Er~~ln~l~~ 95 (265)
T TIGR00078 27 ATASLVAKEDGVLAG--LPVARRVFEQLGVQVEWLVKDG--DRVEPGEVVAEVEGPARSLLTAERTALNFLGR 95 (265)
T ss_pred EEEEEEecCCEEEEC--HHHHHHHHHHcCeEEEEEeCCC--CEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 344444444444543 4678889899999987666554 22345789999999999999999999888754
No 172
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=59.10 E-value=31 Score=36.76 Aligned_cols=30 Identities=23% Similarity=0.582 Sum_probs=25.3
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T 325 (785)
..++|.|-...-+.|||++|++|++|++..
T Consensus 62 ~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 62 KRVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred CeEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 457788888889999999999999987654
No 173
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.32 E-value=20 Score=35.38 Aligned_cols=44 Identities=23% Similarity=0.276 Sum_probs=37.2
Q ss_pred hHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHh
Q 003933 220 DTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 220 ~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e 272 (785)
+.+..|.+-.|+-|.+... -+|.|.|+.+.|.+|++.|..++++
T Consensus 126 eRlqDi~E~hgvIiE~~E~---------D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFEEY---------DLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEeeec---------cEEEEeccHHHHHHHHHHHHHHHhc
Confidence 5677888888988888743 3889999999999999999999876
No 174
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=58.19 E-value=58 Score=40.15 Aligned_cols=16 Identities=25% Similarity=0.399 Sum_probs=6.4
Q ss_pred EecccHHHHHHHHHHH
Q 003933 251 EIIGTLSNIDKAEKLI 266 (785)
Q Consensus 251 ~I~Gt~e~V~kA~~lI 266 (785)
.|.+.....++.+..|
T Consensus 262 ciV~ee~~~ekvl~ai 277 (1102)
T KOG1924|consen 262 CIVGEENGLEKVLEAI 277 (1102)
T ss_pred heeehhhHHHHHHHHH
Confidence 3444443333333333
No 175
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=57.87 E-value=36 Score=30.46 Aligned_cols=55 Identities=11% Similarity=0.061 Sum_probs=43.3
Q ss_pred CchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHh
Q 003933 218 AGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 218 ~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e 272 (785)
+=..+++|-+..+++|.+...+...-...+.+++|+|+...|..|.+.++.+|..
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 4467888999999999987543333344578999999999999999999998875
No 176
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=57.24 E-value=94 Score=34.08 Aligned_cols=68 Identities=21% Similarity=0.304 Sum_probs=48.4
Q ss_pred EEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 299 ~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
++.|-...-|.|-| -+.+.+|-+..+|+|+++..+. ......+.+++|.|....+..+.+.+..+|..
T Consensus 32 ~~~~~ar~~gi~aG--~~~a~~i~~~l~~~v~~~~~dG--~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 99 (278)
T PRK08385 32 RAVIIAKQDGVIAG--LEEAKALFEHFGVKVEVRKRDG--EEVKAGEVILELKGNARAILLVERTALNIIGR 99 (278)
T ss_pred EEEEEecCCeEEeC--HHHHHHHHHHcCCEEEEEcCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 33333333344432 3667888889999999766554 23346789999999999999999988877753
No 177
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=57.04 E-value=1.3e+02 Score=31.85 Aligned_cols=144 Identities=13% Similarity=0.161 Sum_probs=78.1
Q ss_pred HHHHHHHhCCeEEEccCCCC------CCCCCCcceEecc-cHHHHHHHHHHHHHHHHhhcc------CCCCcccccccch
Q 003933 222 IRYLQYNSGAKIQITRDADA------DPHAATRPVEIIG-TLSNIDKAEKLINAVIAEADA------GGSPSLVARGLAT 288 (785)
Q Consensus 222 IK~IqeeTGAkI~I~k~~d~------~p~s~eRiV~I~G-t~e~V~kA~~lI~elI~e~~~------gg~p~~~~~g~~~ 288 (785)
+...-+.+.++|.+.++... .+.+.+.++.|.| +...|+.|++...+.|++... .+...+...-..+
T Consensus 51 aDeA~KAAnVevv~a~~~~gGaghg~~~~~G~viiIi~G~dvsdVrsAveaa~~~i~~~~~f~~~n~~g~~~~~a~~~aR 130 (217)
T PRK15405 51 LDEATKQAMVEVVYARSFYAGAAHASTPLAGEVIGILAGPNPAEVRAGLDAMVAFIENGAAFQSANDDDSTAFFAHVVSR 130 (217)
T ss_pred HHHHHhhcceEEEEEEeeccccccCCCCCCccEEEEEeCCCHHHHHHHHHHHHHHHHhhhceEeeCCCCCEEEEEEEccc
Confidence 35556778888887764310 1123345678889 999999999999999887521 0000000000000
Q ss_pred hhccCCccEEEEEecC-CccceeecCCchHHHHH---HHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 003933 289 AQASGAAEQVEIKVPN-EKVGLIIGRGGETIKGL---QTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 364 (785)
Q Consensus 289 ~~~~~~~~~~~i~VP~-~~vG~VIGKgGetIK~I---q~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI 364 (785)
. ..-....+-+|. +-.|.|||.=++-+--+ .+...++|..+. .|+.+.+-.. +.|+|+...|+.|.+.-
T Consensus 131 a---g~~l~k~~g~~~G~a~~~li~~P~~~~~~~D~AlKaA~V~~~~~~---~P~~~t~f~~-~~ltG~~~A~r~A~~a~ 203 (217)
T PRK15405 131 T---GSYLSKTAGIAEGEPLAYLIAPPLEAMYGIDAALKAADVQLVTFV---GPPSETNFGG-ALLTGSQSACKAACNAF 203 (217)
T ss_pred H---HHHHHHHcCCCCCceeEEEecCcHHHHHHHHHHHhhcCceEEEEe---CCCCCceecC-eeEEeCHHHHHHHHHHH
Confidence 0 000011223444 45678887765554443 344455554332 2222222222 99999988888877776
Q ss_pred HHHHhccc
Q 003933 365 KEVLSQTV 372 (785)
Q Consensus 365 ~~ll~~~~ 372 (785)
++.++...
T Consensus 204 ~e~v~~~a 211 (217)
T PRK15405 204 TDAVLEVA 211 (217)
T ss_pred HHHHHHHH
Confidence 66665543
No 178
>PLN02716 nicotinate-nucleotide diphosphorylase (carboxylating)
Probab=53.76 E-value=1.2e+02 Score=33.89 Aligned_cols=68 Identities=12% Similarity=0.121 Sum_probs=47.6
Q ss_pred EEEecCCccceeecCCchHHHHHHHHhC--CeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 299 EIKVPNEKVGLIIGRGGETIKGLQTRSG--ARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 299 ~i~VP~~~vG~VIGKgGetIK~Iq~~TG--ArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
++.|-...-|.|-| -+.+++|-+..+ |+|+++..+. ......+.+++|+|+...|..|.+.+..+|..
T Consensus 50 ~a~i~ake~gvlaG--~~~a~~vf~~l~~~~~v~~~~~dG--~~v~~G~~i~~v~G~a~~il~~ER~aLN~L~~ 119 (308)
T PLN02716 50 EATFLAKADGVLAG--IALADMVFEEVDPSLKVEWAAIDG--DFVHKGLKFGKVTGPAHSILVAERVVLNFMQR 119 (308)
T ss_pred EEEEEeCCCEEEEC--HHHHHHHHHHcCCCeEEEEEeCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 34443334444443 367788888888 7877665554 22345789999999999999999999887753
No 179
>PRK06096 molybdenum transport protein ModD; Provisional
Probab=53.73 E-value=1.3e+02 Score=33.23 Aligned_cols=68 Identities=15% Similarity=0.207 Sum_probs=48.8
Q ss_pred EEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 299 ~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
++.|-...-|.|= |-+.+++|-+..+++|+++..+. ......+.+++|.|+...+..+.+.+..+|..
T Consensus 35 ~~~~~ake~gv~a--G~~~a~~if~~l~~~v~~~~~dG--~~v~~G~~i~~~~G~a~~ll~~eR~alN~l~~ 102 (284)
T PRK06096 35 YIEFFHRQGGCVS--GISVACKMLTTLGLTIDDAVSDG--SQANAGQRLISAQGNAAALHQGWKAVQNVLEW 102 (284)
T ss_pred EEEEEEcCCEEEE--CHHHHHHHHHHcCCEEEEEeCCC--CEeCCCCEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 3333333334443 34678889899999999776654 33456788999999999999999988877753
No 180
>CHL00048 rps3 ribosomal protein S3
Probab=52.65 E-value=34 Score=35.97 Aligned_cols=30 Identities=23% Similarity=0.169 Sum_probs=24.2
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeT 229 (785)
...+|.|=....|.|||++|.+|++|+++.
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 346677777788999999999999887654
No 181
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=52.43 E-value=1.7e+02 Score=29.72 Aligned_cols=36 Identities=11% Similarity=0.139 Sum_probs=27.1
Q ss_pred CCeEEEccCCCCCCCCCCcceEecc--cHHHHHHHHHHHHHHHHhhc
Q 003933 230 GAKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEAD 274 (785)
Q Consensus 230 GAkI~I~k~~d~~p~s~eRiV~I~G--t~e~V~kA~~lI~elI~e~~ 274 (785)
.+.+.|.... .|.|+| +.+.+.+|++.|.++|++..
T Consensus 47 ~~t~lIf~sG---------KivitGaks~~~~~~a~~~~~~~L~~~g 84 (174)
T cd00652 47 KTTALIFSSG---------KMVITGAKSEEDAKLAARKYARILQKLG 84 (174)
T ss_pred cEEEEEECCC---------EEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence 4556666432 567777 78999999999999998763
No 182
>COG1159 Era GTPase [General function prediction only]
Probab=52.37 E-value=31 Score=38.05 Aligned_cols=39 Identities=26% Similarity=0.454 Sum_probs=27.9
Q ss_pred CCeEEEEEecCC-ccceeecCCchHHHHH--------HHHhCCeEEEc
Q 003933 198 STMSRKIEVPNN-KVGVLIGKAGDTIRYL--------QYNSGAKIQIT 236 (785)
Q Consensus 198 ~~~t~~IlVP~~-~VG~IIGk~G~tIK~I--------qeeTGAkI~I~ 236 (785)
-.+...|.|... .-+-||||+|++||+| ++-.+++|.+.
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 344455677654 6789999999999887 45567777663
No 183
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=51.87 E-value=30 Score=43.34 Aligned_cols=70 Identities=16% Similarity=0.179 Sum_probs=40.5
Q ss_pred CCCCCeEEEEEecCCc------cceeecCCchHHHHHHHH------hCCeEEEccCCCCCCCCCCcceEecccHH-HHHH
Q 003933 195 TDDSTMSRKIEVPNNK------VGVLIGKAGDTIRYLQYN------SGAKIQITRDADADPHAATRPVEIIGTLS-NIDK 261 (785)
Q Consensus 195 ~~~~~~t~~IlVP~~~------VG~IIGk~G~tIK~Iqee------TGAkI~I~k~~d~~p~s~eRiV~I~Gt~e-~V~k 261 (785)
+....+..+.|+|..+ |-+-||+.-+++..|+++ |++.++|..- .....-.-.|-|...++ -|..
T Consensus 148 ~~~d~I~Q~~LLPsvkDP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~plqI~Sv--~a~D~lkGyIYIEA~KqshV~~ 225 (1024)
T KOG1999|consen 148 EDSDDIPQQALLPSVKDPNLWIVKCKIGREREVAFCLMRKFIELDKTDTPLQIKSV--FAKDHLKGYIYIEADKQSHVKE 225 (1024)
T ss_pred hcccchhHHhhCCCCCCCCeeEEEeccccHHHHHHHHHHHHHhhcccCCCceEEEE--EeccccceeEEEEechhHHHHH
Confidence 3455677788888765 778899999888777654 3444444321 00111123556666544 4555
Q ss_pred HHHHH
Q 003933 262 AEKLI 266 (785)
Q Consensus 262 A~~lI 266 (785)
|++-+
T Consensus 226 Ai~gv 230 (1024)
T KOG1999|consen 226 AIEGV 230 (1024)
T ss_pred HHhhh
Confidence 65543
No 184
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=51.78 E-value=17 Score=42.50 Aligned_cols=19 Identities=42% Similarity=0.391 Sum_probs=10.8
Q ss_pred CCCCCCCCCCCCCCCCCCC
Q 003933 575 AQGTQPQSYGPPRPGQPGD 593 (785)
Q Consensus 575 ~~~~~~~~yg~~~~~~~g~ 593 (785)
-|+...+.|+.+++++-..
T Consensus 503 ~q~~~aq~~~~Qrg~p~~~ 521 (694)
T KOG4264|consen 503 RQDTSAQSEGYQRGGPGTD 521 (694)
T ss_pred hhhhhhhhhhhhcCCCCCC
Confidence 4555666776666444444
No 185
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=51.41 E-value=13 Score=47.40 Aligned_cols=15 Identities=13% Similarity=0.204 Sum_probs=10.8
Q ss_pred CCCeEEEEEecCCcc
Q 003933 197 DSTMSRKIEVPNNKV 211 (785)
Q Consensus 197 ~~~~t~~IlVP~~~V 211 (785)
..-++++|.+|....
T Consensus 1440 ~~wcev~~~lp~~~~ 1454 (1640)
T KOG0262|consen 1440 GKWCEVELKLPLDKE 1454 (1640)
T ss_pred CcEEEEEEEecCCCc
Confidence 456788888887753
No 186
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=50.99 E-value=31 Score=38.73 Aligned_cols=56 Identities=18% Similarity=0.352 Sum_probs=46.4
Q ss_pred cCCccceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH--HHHhc
Q 003933 303 PNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK--EVLSQ 370 (785)
Q Consensus 303 P~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~--~ll~~ 370 (785)
+++.+-.|.|..+++++.|.+..|+.|. . ..+.++|.|+...|+.|..++. .++..
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~-~-----------rG~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIV-A-----------RGEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEE-e-----------CCceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 3577888999999999999999999998 2 2468999999779999988887 55443
No 187
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=50.20 E-value=23 Score=37.97 Aligned_cols=36 Identities=19% Similarity=0.341 Sum_probs=26.1
Q ss_pred eEEEEEecCC-ccceeecCCchHHHHHHH--------HhCCeEEE
Q 003933 200 MSRKIEVPNN-KVGVLIGKAGDTIRYLQY--------NSGAKIQI 235 (785)
Q Consensus 200 ~t~~IlVP~~-~VG~IIGk~G~tIK~Iqe--------eTGAkI~I 235 (785)
+...|+|..+ .-+-||||+|++||+|.. -++++|.+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l 265 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 5566677654 678999999999998754 45566554
No 188
>PRK08072 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=48.53 E-value=62 Score=35.41 Aligned_cols=53 Identities=13% Similarity=0.123 Sum_probs=38.8
Q ss_pred hHHHHHHHHhCCe--EEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 316 ETIKGLQTRSGAR--IQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 316 etIK~Iq~~TGAr--IqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
+.+++|-+..+++ |+++..+. ......+.+++|.|....+.++.+.+..+|..
T Consensus 51 ~~a~~i~~~~~~~~~v~~~~~dG--~~v~~g~~i~~~~G~~~~ll~~er~~ln~l~~ 105 (277)
T PRK08072 51 LVIEEGYKLLDERIEVELHKKDG--DLVKKGEIIATVQGPVASLLTGERVILNLIQR 105 (277)
T ss_pred HHHHHHHHHcCCceEEEEEeCCC--CEEcCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 4567888877755 66554443 22345688999999999999999998887753
No 189
>PRK09016 quinolinate phosphoribosyltransferase; Validated
Probab=48.32 E-value=1.6e+02 Score=32.66 Aligned_cols=69 Identities=10% Similarity=0.172 Sum_probs=46.5
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCe--EEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGAR--IQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~TGAr--IqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
.++.|-...-|.|-| -+.+++|-+..++. |+++..+. ......+.+++|.|....|..+.+.+..+|..
T Consensus 56 ~~~~i~ake~gi~aG--~~~a~~vf~~l~~~~~v~~~~~dG--~~v~~G~~i~~i~G~a~~ll~~ER~~LN~L~~ 126 (296)
T PRK09016 56 SHATIITREDGVFCG--KRWVEEVFIQLGDDVTIEWHVDDG--DVITANQTLFELTGPARVLLTGERTALNFVQT 126 (296)
T ss_pred EEEEEEEcCCEEEEC--HHHHHHHHHHcCCCeEEEEEcCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 344444433444433 35688888999866 55455443 22345689999999999999999988877753
No 190
>PRK06978 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=48.25 E-value=1.7e+02 Score=32.32 Aligned_cols=69 Identities=9% Similarity=0.085 Sum_probs=47.1
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCC--eEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGA--RIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~TGA--rIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
.++.|-...-|.|= |-+.+++|-+..++ +|+++..+. ......+.+++|+|....+..+.+.+..+|..
T Consensus 53 ~~a~i~are~gvla--G~~~a~~if~~l~~~~~v~~~~~dG--~~v~~G~~i~~~~G~a~~lL~~ER~aLN~l~~ 123 (294)
T PRK06978 53 RRARVIVREEAVLC--GVPWFDAVMRAVDPSIEVTWRYREG--DRMTADSTVCELEGPARALLTAERNALNFLQL 123 (294)
T ss_pred EEEEEEEcCCEEEE--CHHHHHHHHHHhCCCeEEEEEcCCC--CEeCCCCEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 34444444444443 34678889998887 555444443 22345788999999999999999988877753
No 191
>PRK04972 putative transporter; Provisional
Probab=47.47 E-value=1.4e+02 Score=35.89 Aligned_cols=145 Identities=18% Similarity=0.243 Sum_probs=75.2
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEc---cCCCC-CCCC-----CCcceEecccHHHHHHHHHHHHHHH
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT---RDADA-DPHA-----ATRPVEIIGTLSNIDKAEKLINAVI 270 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~---k~~d~-~p~s-----~eRiV~I~Gt~e~V~kA~~lI~elI 270 (785)
+.+.+.|.+..+..++ |++|++|......+|.|. ++.+. .+.. ..-++.|.|+.+.+.++.+.+. +
T Consensus 214 ~~r~~~V~~~~~~~~~---Gktl~el~~~~~~~v~I~~I~R~g~~~~p~~dt~L~~GDiL~V~G~~e~l~~l~~~~~--l 288 (558)
T PRK04972 214 VIRAYRVGPELVAWTD---GKNLRELGIYRQTGCYIERIRRNGILANPDGDAVLQMGDEIALVGYPDAHARLDPSFR--N 288 (558)
T ss_pred eeeEEEECCccccCcC---CCCHHHHHhhcCCCEEEEEEEECCEEecCCCCCEeCCCCEEEEEECHHHHHHHHHhhc--C
Confidence 3667777665332223 678999988775555443 22111 1111 1235788999998766654420 1
Q ss_pred HhhccCCCCcccccccchhhccCC-ccEEEEEecCCccceeecCCchHHHHHH-HHhCCeEEEecCC-C--CCCC---CC
Q 003933 271 AEADAGGSPSLVARGLATAQASGA-AEQVEIKVPNEKVGLIIGRGGETIKGLQ-TRSGARIQVLIPQ-H--LPEG---DG 342 (785)
Q Consensus 271 ~e~~~gg~p~~~~~g~~~~~~~~~-~~~~~i~VP~~~vG~VIGKgGetIK~Iq-~~TGArIqI~i~~-~--lP~~---~~ 342 (785)
.++ ..++ ...+. ....++.+++ ..+||| +|++|. ++.|+.|. .+.| . .+.. .-
T Consensus 289 g~e-------~~~~-----~~~~~~~~~E~vVv~~---s~liGk---TL~eL~~r~~gv~Vl-~I~R~g~~~~~~~~~~L 349 (558)
T PRK04972 289 GKE-------VFDR-----DLLDMRIVTEEIVVKN---HNAVGK---RLSQLKLTDHGCFLN-RVIRSQIEMPIDDNVVL 349 (558)
T ss_pred CCc-------ccCc-----cccCcceEEEEEEEcC---cccCCC---CHHHhCCccCCeEEE-EEecCCcccCCCCCCEe
Confidence 111 0000 00011 1233444554 346654 777774 23788776 3444 1 1111 11
Q ss_pred CCccEEEEEcCHHHHHHHHHHHHHHH
Q 003933 343 SKERIVRVTGDMRQIEIAQEMIKEVL 368 (785)
Q Consensus 343 s~er~VtIsG~~eqVe~Ak~lI~~ll 368 (785)
..-.+|.|.|+.+.+++..+.+-.++
T Consensus 350 ~~GD~LlVvG~~~~i~~l~~~lG~~~ 375 (558)
T PRK04972 350 NKGDVLQVSGDARRVKTIADRIGFIS 375 (558)
T ss_pred cCCCEEEEEECHHHHHHHHHHhCCcc
Confidence 23346999999999999877665433
No 192
>PRK00089 era GTPase Era; Reviewed
Probab=47.38 E-value=28 Score=37.48 Aligned_cols=37 Identities=24% Similarity=0.468 Sum_probs=26.3
Q ss_pred eEEEEEecCC-ccceeecCCchHHHHHH--------HHhCCeEEEc
Q 003933 200 MSRKIEVPNN-KVGVLIGKAGDTIRYLQ--------YNSGAKIQIT 236 (785)
Q Consensus 200 ~t~~IlVP~~-~VG~IIGk~G~tIK~Iq--------eeTGAkI~I~ 236 (785)
+...|.|... .-+-||||+|++||+|. +-++++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 4455566543 56889999999998874 4567777664
No 193
>PRK06543 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=45.33 E-value=2.1e+02 Score=31.52 Aligned_cols=55 Identities=13% Similarity=0.166 Sum_probs=41.5
Q ss_pred CchHHHHHHHHhCC--eEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 314 GGETIKGLQTRSGA--RIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 314 gGetIK~Iq~~TGA--rIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
|-+.+++|-+..++ +|+++..+. ......+.+++|.|+...+..|.+.+..+|..
T Consensus 50 G~~~a~~if~~~~~~~~v~~~~~dG--~~v~~G~~i~~~~G~a~~ll~~eR~alN~l~~ 106 (281)
T PRK06543 50 GIDVFAAAFRLVDPAITVTLAVADG--ERFEAGDILATVTGPARSVLTAERIALNFTQR 106 (281)
T ss_pred CHHHHHHHHHHhCCCeEEEEEeCCC--CEecCCCEEEEEEecHHHHHHHHHHHHHHHHH
Confidence 34778899898987 555454443 23346789999999999999999988877753
No 194
>PRK06559 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=44.52 E-value=2e+02 Score=31.76 Aligned_cols=68 Identities=12% Similarity=0.229 Sum_probs=46.6
Q ss_pred EEEecCCccceeecCCchHHHHHHHHhCCeEEEe----cCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVL----IPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 299 ~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~----i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
++.|-...-|.|- |-+.+++|-+..++.|.+. ..+. ......+.+++|.|+...|..+.+.+..+|..
T Consensus 43 ~~~~~are~gvla--G~~~a~~if~~l~~~~~~~~~~~~~dG--~~v~~G~~i~~v~G~a~~ll~~ER~alN~l~~ 114 (290)
T PRK06559 43 KVSLFAKEAGVLA--GLTVFQRVFTLFDAEVTFQNPHQFKDG--DRLTSGDLVLEIIGSVRSLLTCERVALNFLQH 114 (290)
T ss_pred EEEEEecCCeEEE--CHHHHHHHHHHhCCcEEEEEeecCCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 3333333334443 3467889999999988853 1333 22345789999999999999999888877653
No 195
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=44.03 E-value=22 Score=44.70 Aligned_cols=13 Identities=31% Similarity=0.585 Sum_probs=10.3
Q ss_pred hhHHhhhcCCCch
Q 003933 15 ADLKRKLDDLEPD 27 (785)
Q Consensus 15 ~d~krkl~~le~~ 27 (785)
-..|+||+.||.+
T Consensus 278 ~ee~erLeklE~~ 290 (840)
T PF04147_consen 278 KEEKERLEKLEEE 290 (840)
T ss_pred HHHHHHHHHHHHH
Confidence 4568889999888
No 196
>PRK15494 era GTPase Era; Provisional
Probab=44.00 E-value=31 Score=38.52 Aligned_cols=37 Identities=19% Similarity=0.339 Sum_probs=27.1
Q ss_pred eEEEEEecCC-ccceeecCCchHHHHHH--------HHhCCeEEEc
Q 003933 200 MSRKIEVPNN-KVGVLIGKAGDTIRYLQ--------YNSGAKIQIT 236 (785)
Q Consensus 200 ~t~~IlVP~~-~VG~IIGk~G~tIK~Iq--------eeTGAkI~I~ 236 (785)
+...|.|... +-+-|||++|++||+|. +-++++|.+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 4456667654 67889999999998874 4567777664
No 197
>PRK06106 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=43.97 E-value=2.1e+02 Score=31.51 Aligned_cols=54 Identities=11% Similarity=0.127 Sum_probs=40.7
Q ss_pred chHHHHHHHHhCCe--EEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 315 GETIKGLQTRSGAR--IQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 315 GetIK~Iq~~TGAr--IqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
-+.+++|-+..++. |+++..+. ..-...+.+++|.|....+..|.+.+..+|..
T Consensus 56 ~~~a~~vf~~~~~~~~~~~~~~dG--~~v~~g~~i~~i~G~a~~ll~~ER~~LN~L~~ 111 (281)
T PRK06106 56 LDLARLAFRLVDPEIEMRRHLPDG--AAVAPGDVIATISGPARGLLTAERTALNFLCH 111 (281)
T ss_pred HHHHHHHHHHhCCceEEEEEeCCC--CEEcCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 46678999999866 55444443 22345788999999999999999998887753
No 198
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=43.90 E-value=40 Score=34.39 Aligned_cols=107 Identities=19% Similarity=0.237 Sum_probs=55.9
Q ss_pred ceEecc--cHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHHHHh-
Q 003933 249 PVEIIG--TLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS- 325 (785)
Q Consensus 249 iV~I~G--t~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~T- 325 (785)
.+.++| +.+.+++|++.+.++|++... .......+ .-.....+..|.++-++-+..||-+.+++-.==+..
T Consensus 63 K~VcTGaKs~ed~~~av~~~~~~L~~~g~---~~~~~p~i---~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFP 136 (185)
T COG2101 63 KVVCTGAKSVEDVHRAVKKLAKKLKDGGI---DIDFEPEI---KVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFP 136 (185)
T ss_pred cEEEeccCcHHHHHHHHHHHHHHHHhcCc---CcCCCCce---EEEEEEEEeccCccccHHHHHHhccccccccccccCC
Confidence 345555 788999999999999997421 00000000 000011122334444555555555555432211111
Q ss_pred C-------CeEEEecCCCCCCCCCCCccEEEEEcC--HHHHHHHHHHHHHHHhc
Q 003933 326 G-------ARIQVLIPQHLPEGDGSKERIVRVTGD--MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 326 G-------ArIqI~i~~~lP~~~~s~er~VtIsG~--~eqVe~Ak~lI~~ll~~ 370 (785)
| -||.+++ =..-.+.|+|- .+.++.|.+.|.+.|++
T Consensus 137 GLVYRl~~P~VV~Li---------F~SGK~ViTGaK~~ed~~~Av~~i~~~L~e 181 (185)
T COG2101 137 GLVYRLDEPRVVLLL---------FGSGKLVITGAKSEEDAEQAVEKIQSRLEE 181 (185)
T ss_pred eeEEEcCCCCEEEEE---------ecCCcEEEecCCCHHHHHHHHHHHHHHHHH
Confidence 1 1221111 01234778885 78999999999998875
No 199
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=42.85 E-value=56 Score=34.61 Aligned_cols=29 Identities=21% Similarity=0.285 Sum_probs=23.9
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeT 229 (785)
..+|.|-..+-|.|||++|..|++|+++.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 46777777888999999999998887654
No 200
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=42.76 E-value=46 Score=34.60 Aligned_cols=30 Identities=27% Similarity=0.484 Sum_probs=24.4
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHh
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeT 229 (785)
...+|.|-...-|.|||++|..|++|+++.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 346777777889999999999998887643
No 201
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=42.67 E-value=2.6e+02 Score=28.44 Aligned_cols=35 Identities=11% Similarity=0.195 Sum_probs=26.1
Q ss_pred CCeEEEccCCCCCCCCCCcceEecc--cHHHHHHHHHHHHHHHHhh
Q 003933 230 GAKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 230 GAkI~I~k~~d~~p~s~eRiV~I~G--t~e~V~kA~~lI~elI~e~ 273 (785)
.|.+.|.... .|.|+| +.+.+.+|+++|.++|++.
T Consensus 47 k~t~lIF~sG---------KiviTGaks~~~~~~a~~~~~~~l~~~ 83 (174)
T cd04517 47 RATASVWSSG---------KITITGATSEEEAKQAARRAARLLQKL 83 (174)
T ss_pred cEEEEEECCC---------eEEEEccCCHHHHHHHHHHHHHHHHHc
Confidence 4556666432 567777 6889999999999999875
No 202
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=42.41 E-value=48 Score=33.52 Aligned_cols=57 Identities=16% Similarity=0.172 Sum_probs=43.3
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHh
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e 272 (785)
.+.||.++.... =+.+..|.+-.|+-|.+.. +..|.|.|..+.|.+|++.|..+++|
T Consensus 113 ~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efee---------~~~V~I~Gdke~Ik~aLKe~s~~wke 169 (169)
T PF09869_consen 113 ETIRVKLKKPIQ-------EERLQEISEWHGVIFEFEE---------DDKVVIEGDKERIKKALKEFSSFWKE 169 (169)
T ss_pred eeEEEecCccch-------HHHHHHHHHHhceeEEecC---------CcEEEEeccHHHHHHHHHHHHHHhcC
Confidence 455666654432 2678899999999888832 33799999999999999999887764
No 203
>PRK07896 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=40.06 E-value=3.3e+02 Score=30.11 Aligned_cols=69 Identities=13% Similarity=0.165 Sum_probs=45.0
Q ss_pred EEEEecCCccceeecCCchHHHHHHH-HhCC---eEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQT-RSGA---RIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~-~TGA---rIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
.++.|-...-|.|- |-+.+.+|-+ ..++ +|+++..+. ..-...+.+++|.|....+..+.+.+..+|..
T Consensus 45 ~~a~i~are~gila--G~~~a~~if~~~~~~~~~~v~~~~~dG--~~v~~g~~i~~i~G~a~~ll~~ER~aLN~L~~ 117 (289)
T PRK07896 45 ATASVVSREAGVVA--GLDVALLVLDEVLGTDGYEVLDRVEDG--ARVPPGQALLTVTAPTRGLLTAERTMLNLLCH 117 (289)
T ss_pred EEEEEEecCCEEEE--CHHHHHHHHHHhcCCCceEEEEEcCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 34444444444443 3466777774 5566 666554443 22345689999999999999999988877753
No 204
>COG0014 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=39.63 E-value=1.1e+02 Score=35.06 Aligned_cols=112 Identities=19% Similarity=0.309 Sum_probs=60.2
Q ss_pred CCCCeEEEEEecCCccceeecCCchH---HHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHH---HHHH
Q 003933 196 DDSTMSRKIEVPNNKVGVLIGKAGDT---IRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL---INAV 269 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~VG~IIGk~G~t---IK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~l---I~el 269 (785)
.+.....++.||-..+|.|.=..=+. +-.|+-+||-.| +++|..|.++-...+ |.+-
T Consensus 103 ~nGL~i~~~rvPLGVigvIYEsRPnVtvdaaaLclKsGNAv-----------------ILRGGsea~~Sn~ai~~~i~~a 165 (417)
T COG0014 103 PNGLQIYRVRVPLGVIGVIYESRPNVTVDAAALCLKSGNAV-----------------ILRGGSEAIHSNAAIVEVIQEA 165 (417)
T ss_pred CCCCEEEEEEccceEEEEEEecCCccHHHHHHHHHhcCCEE-----------------EEeCcHHHhhhHHHHHHHHHHH
Confidence 45667899999999999998554332 345566666554 444555554443332 2222
Q ss_pred HHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchH-HHHHHHHhCCeEE
Q 003933 270 IAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET-IKGLQTRSGARIQ 330 (785)
Q Consensus 270 I~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGet-IK~Iq~~TGArIq 330 (785)
|++. +++.....-+ ....+....+|+=-...+-.||=|||+. |+.|++++.+-|.
T Consensus 166 L~~~---~lP~~aVqli---~~~~R~~v~~ll~l~~yiD~iIPRGg~~Li~~v~~~a~vPVi 221 (417)
T COG0014 166 LEKA---GLPADAVQLI---EDTDREEVLELLRLDGYIDLVIPRGGAGLIRRVVENATVPVI 221 (417)
T ss_pred HHHc---CCCHHHhhhc---cCCCHHHHHHHHhhcCceeEEEcCCcHHHHHHHHhCCcCCEE
Confidence 3332 2222110000 0000111112222456777788899976 7888888877665
No 205
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=38.91 E-value=1.5e+02 Score=32.97 Aligned_cols=57 Identities=14% Similarity=0.268 Sum_probs=43.8
Q ss_pred CccceeecCCchHHHHHHHHhCCe--EEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 003933 305 EKVGLIIGRGGETIKGLQTRSGAR--IQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 369 (785)
Q Consensus 305 ~~vG~VIGKgGetIK~Iq~~TGAr--IqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~ 369 (785)
..+..|+|-.-+.|+++.++..-. |.|. ..+ ..+.|.|+|+.+.|++|.+.++++=.
T Consensus 131 g~Maav~gl~~e~v~~~~~~~~~~~~v~ia-N~N-------~~~QiVIsG~~~ale~a~~~~~~~g~ 189 (310)
T COG0331 131 GGMAAVLGLDDEQVEKACEEAAQGTVVEIA-NYN-------SPGQIVISGTKEALEKAAEILKEAGA 189 (310)
T ss_pred ccHHHHcCCCHHHHHHHHHHhccCCeEEEe-eeC-------CCCcEEEECCHHHHHHHHHHHHHhhh
Confidence 455677787889999999988764 5542 222 34899999999999999999987653
No 206
>PRK05742 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=37.44 E-value=3.3e+02 Score=29.83 Aligned_cols=69 Identities=12% Similarity=0.195 Sum_probs=46.3
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhCCe--EEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhc
Q 003933 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGAR--IQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 298 ~~i~VP~~~vG~VIGKgGetIK~Iq~~TGAr--IqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~ 370 (785)
.++.|-...-|.|= |-+.+++|-+..+++ |+++..+. ......+.+++|.|....+..+.+.+..+|..
T Consensus 37 ~~~~i~ar~~gi~~--G~~~~~~i~~~~~~~~~~~~~~~dG--~~v~~g~~i~~i~G~~~~ll~~ER~~ln~l~~ 107 (277)
T PRK05742 37 AKATVITREAAVIA--GTAWVDAVFRQLDPRVAVHWQVADG--ERVSANQVLFHLEGPARSLLTGERSALNFLQL 107 (277)
T ss_pred EEEEEEECCCEEEE--CHHHHHHHHHHcCCceEEEEEeCCC--CEEcCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 34444443334443 346788888899866 55444443 22345789999999999999999988877753
No 207
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=37.23 E-value=10 Score=48.27 Aligned_cols=15 Identities=27% Similarity=0.091 Sum_probs=8.5
Q ss_pred CCCCeEEEEEecCCc
Q 003933 196 DDSTMSRKIEVPNNK 210 (785)
Q Consensus 196 ~~~~~t~~IlVP~~~ 210 (785)
....+.+++.||.-+
T Consensus 598 tl~tTqVktpvPsLL 612 (1958)
T KOG0391|consen 598 TLVTTQVKTPVPSLL 612 (1958)
T ss_pred eeeeeeeccCchHHH
Confidence 344566666776533
No 208
>PLN00062 TATA-box-binding protein; Provisional
Probab=35.91 E-value=3e+02 Score=28.23 Aligned_cols=27 Identities=30% Similarity=0.249 Sum_probs=22.2
Q ss_pred cEEEEEcC--HHHHHHHHHHHHHHHhccc
Q 003933 346 RIVRVTGD--MRQIEIAQEMIKEVLSQTV 372 (785)
Q Consensus 346 r~VtIsG~--~eqVe~Ak~lI~~ll~~~~ 372 (785)
-.|.|+|. .+.++.|.+.|..+|.+..
T Consensus 147 GkvvitGaks~~~~~~ai~~i~p~L~~~~ 175 (179)
T PLN00062 147 GKIVITGAKVREEIYTAFENIYPVLTEFR 175 (179)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHHhc
Confidence 46888986 7899999999999887644
No 209
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=35.48 E-value=23 Score=41.48 Aligned_cols=11 Identities=36% Similarity=0.682 Sum_probs=4.7
Q ss_pred CCCCCCCCCCC
Q 003933 493 GGPPPSQANYN 503 (785)
Q Consensus 493 p~ppp~~g~Yn 503 (785)
+.+|+.++.-|
T Consensus 433 p~pP~~~~~r~ 443 (694)
T KOG4264|consen 433 PPPPPSSSSRR 443 (694)
T ss_pred CCCCCcccccc
Confidence 34444444433
No 210
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=34.33 E-value=3.3e+02 Score=27.84 Aligned_cols=52 Identities=19% Similarity=0.277 Sum_probs=38.8
Q ss_pred CchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHH-HhcccCC
Q 003933 314 GGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEV-LSQTVRP 374 (785)
Q Consensus 314 gGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~l-l~~~~r~ 374 (785)
.-..|.+|.+..+|+|.-+ ..+.-+|+|+|+.+.|+.-.++++.. |.+..|.
T Consensus 97 ~r~ei~~~~~~f~a~ivdv---------~~~~~~ie~tG~~~ki~a~~~~l~~~gi~e~~Rt 149 (174)
T CHL00100 97 TRPEILEIAQIFRAKVVDL---------SEESLILEVTGDPGKIVAIEQLLEKFGIIEIART 149 (174)
T ss_pred CHHHHHHHHHHhCCEEEEe---------cCCEEEEEEcCCHHHHHHHHHHhhhcCCEEEEcc
Confidence 3456889999999999832 22457899999999999999998764 3344443
No 211
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=34.03 E-value=4.5e+02 Score=26.60 Aligned_cols=64 Identities=20% Similarity=0.308 Sum_probs=41.9
Q ss_pred ccceeecCC-chHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEc-CHHHHHHHHHHHHHHHhc
Q 003933 306 KVGLIIGRG-GETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 306 ~vG~VIGKg-GetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG-~~eqVe~Ak~lI~~ll~~ 370 (785)
++|.|+-.+ -+||-+|...-||.|.=+.-.+ |.-+....-.|+|.- ..+.++.|.++|+++-.+
T Consensus 92 LIGhiv~tdiqDTId~In~ig~A~vvDl~L~M-p~~e~~SsA~iti~a~~~e~l~ea~~~l~ev~~e 157 (170)
T COG2061 92 LIGHIVHTDIQDTIDRINSIGGAEVVDLSLSM-PGIEGESSARITIIAVGKEKLDEALRRLKEVAME 157 (170)
T ss_pred EEEeeecCcHHHHHHHhhccCCEEEEEEEeec-CCCCCCcceeEEEEEcChhHHHHHHHHHHHHHhh
Confidence 345555333 3788899888888876332222 323344455677777 578999999999887654
No 212
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=33.72 E-value=38 Score=35.40 Aligned_cols=29 Identities=28% Similarity=0.471 Sum_probs=22.9
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHhC
Q 003933 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSG 230 (785)
Q Consensus 202 ~~IlVP~~~VG~IIGk~G~tIK~IqeeTG 230 (785)
.+|.|-...-|.|||++|++|++|++...
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 45555558899999999999998876543
No 213
>PRK00394 transcription factor; Reviewed
Probab=33.63 E-value=4.7e+02 Score=26.78 Aligned_cols=34 Identities=24% Similarity=0.298 Sum_probs=26.0
Q ss_pred CeEEEccCCCCCCCCCCcceEecc--cHHHHHHHHHHHHHHHHhh
Q 003933 231 AKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 231 AkI~I~k~~d~~p~s~eRiV~I~G--t~e~V~kA~~lI~elI~e~ 273 (785)
+.+.|.... .+.|+| +.+.+.+|+++|.++|++.
T Consensus 47 ~t~lIf~sG---------Kiv~tGa~S~~~a~~a~~~~~~~l~~~ 82 (179)
T PRK00394 47 IAALIFRSG---------KVVCTGAKSVEDLHEAVKIIIKKLKEL 82 (179)
T ss_pred eEEEEEcCC---------cEEEEccCCHHHHHHHHHHHHHHHHHc
Confidence 556666432 567777 7889999999999999875
No 214
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=33.52 E-value=56 Score=33.80 Aligned_cols=37 Identities=16% Similarity=0.276 Sum_probs=25.7
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEc
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT 236 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~ 236 (785)
+..+|.|-..+--.+||-+|..|++|..-..-+..+.
T Consensus 44 tr~eiIi~atrtq~vlGEkgrRirelt~lvqkRf~f~ 80 (244)
T KOG3181|consen 44 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFP 80 (244)
T ss_pred cceeEEEEecchhhhhhhcchhHHHHHHHHHHhcCCC
Confidence 4456666666677899999999999876544444443
No 215
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=33.02 E-value=3.7e+02 Score=27.41 Aligned_cols=25 Identities=12% Similarity=0.139 Sum_probs=20.9
Q ss_pred ceEecc--cHHHHHHHHHHHHHHHHhh
Q 003933 249 PVEIIG--TLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 249 iV~I~G--t~e~V~kA~~lI~elI~e~ 273 (785)
.|.|+| +.+.+.+|++.|.++|++.
T Consensus 57 KiviTGaks~e~a~~a~~~i~~~L~~~ 83 (174)
T cd04516 57 KMVCTGAKSEDDSKLAARKYARIIQKL 83 (174)
T ss_pred eEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 567777 7789999999999999875
No 216
>PRK03818 putative transporter; Validated
Probab=31.77 E-value=72 Score=38.23 Aligned_cols=97 Identities=20% Similarity=0.247 Sum_probs=53.3
Q ss_pred ccccccccchhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHH--HHHhCCeEEEccC
Q 003933 161 VKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYL--QYNSGAKIQITRD 238 (785)
Q Consensus 161 ~k~~~i~g~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~I--qeeTGAkI~I~k~ 238 (785)
.+.+.+.++.++++++.+.+...+.. +. ..+......++|.++++ .++|| +|++| +++.|+.|.-.++
T Consensus 255 GDiLlV~G~~e~l~~l~~~~Gl~~~~---~~-~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R 324 (552)
T PRK03818 255 GDLLHLVGQPEDLHKAQLVIGEEVDT---SL-STRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNR 324 (552)
T ss_pred CCEEEEEECHHHHHHHHHhcCCccCc---cc-cccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeE
Confidence 34455667777777766554433211 01 11123345666777664 45554 77777 5667776543322
Q ss_pred CCC-C-CCCC-----CcceEecccHHHHHHHHHHHH
Q 003933 239 ADA-D-PHAA-----TRPVEIIGTLSNIDKAEKLIN 267 (785)
Q Consensus 239 ~d~-~-p~s~-----eRiV~I~Gt~e~V~kA~~lI~ 267 (785)
.+. . .... --++.+.|+++.+++..+.+.
T Consensus 325 ~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~Lg 360 (552)
T PRK03818 325 AGVELVASPDLSLQFGDILNLVGRPEAIDAVANVLG 360 (552)
T ss_pred CCeecCCCCCCEEecCCEEEEEECHHHHHHHHHHhC
Confidence 221 1 1111 125788999999999777544
No 217
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=31.70 E-value=65 Score=38.54 Aligned_cols=114 Identities=18% Similarity=0.128 Sum_probs=70.7
Q ss_pred CCCcceEecc-cHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCC--chHHHHH
Q 003933 245 AATRPVEIIG-TLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRG--GETIKGL 321 (785)
Q Consensus 245 s~eRiV~I~G-t~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKg--GetIK~I 321 (785)
+++-++.+.| +.+.+..|++++..+|.+.. +.......................|.+..+.+.+|+|.. -+.|++|
T Consensus 222 Tkni~lE~ag~d~~~~~~al~~~~~ll~~~~-g~v~~~~~~~~~~~~~~~~~~~~~i~l~~~~i~~~lG~~i~~~~i~~i 300 (552)
T PRK09616 222 TRNLFIDVTGTDLEAVLLALNIIATALAERG-GTIESVKVIYPDGELTTPDLTPRTREVSVEYINKLLGIDLSAEEIIEL 300 (552)
T ss_pred CcEEEEEeccCCHHHHHHHHHHHHHHHHHhC-CEEEEEEEEeCCCCEeCCCCCceEEEecHHHHHHHhCCCCCHHHHHHH
Confidence 3455666777 67788899999999998762 111111110000000000123456888889999999865 3679999
Q ss_pred HHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 003933 322 QTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 369 (785)
Q Consensus 322 q~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~ 369 (785)
-++.|+.|.. .. +.-.|+|=--...|.+...+|+++++
T Consensus 301 L~~Lgf~~~~-~~---------~~~~v~vP~~R~DI~~~~DliEEiaR 338 (552)
T PRK09616 301 LERMRYDAEI-GD---------DKVKVTVPPYRVDILHEVDVIEDVAI 338 (552)
T ss_pred HHHcCCCcEe-cC---------CeEEEEeCCCcccccccchHHHHHHH
Confidence 9999999862 11 12235555546678888888888775
No 218
>PRK06703 flavodoxin; Provisional
Probab=31.19 E-value=2.2e+02 Score=27.53 Aligned_cols=40 Identities=8% Similarity=0.108 Sum_probs=28.6
Q ss_pred HHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCH---HHHHHHHHHHHHHHhc
Q 003933 317 TIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDM---RQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 317 tIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~---eqVe~Ak~lI~~ll~~ 370 (785)
.|+++.++.|+++. .+.|.|.+.+ +.++++++++.++++.
T Consensus 104 ~l~~~l~~~G~~~~--------------~~~~~~~~~p~~~~~~~~~~~~~~~~~~~ 146 (151)
T PRK06703 104 IFEERLVERGAELV--------------QEGLKIELAPETDEDVEKCSNFAIAFAEK 146 (151)
T ss_pred HHHHHHHHCCCEEc--------------ccCeEEecCCCchhHHHHHHHHHHHHHHH
Confidence 37778888899876 2356676653 6888888888887653
No 219
>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=31.06 E-value=2.5e+02 Score=30.71 Aligned_cols=146 Identities=14% Similarity=0.077 Sum_probs=83.6
Q ss_pred CchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhc------------cCCCC-cccc-
Q 003933 218 AGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD------------AGGSP-SLVA- 283 (785)
Q Consensus 218 ~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~------------~gg~p-~~~~- 283 (785)
+-..+.+|-+..+++|.+...+...-...+.+++|+|....|.++.+.++.+|.... ..+.. .+.+
T Consensus 45 G~~~a~~i~~~l~~~~~~~~~dG~~v~~g~~i~~i~G~a~~ll~~Er~~ln~l~~~SGIAT~t~~~v~~~~~~~~~i~~T 124 (273)
T PRK05848 45 GEKYALELLEMTGIECVFTIKDGERFKKGDILMEIEGDFSMLLKVERTLLNLLQHSSGIATLTSRYVEALESHKVKLLDT 124 (273)
T ss_pred CHHHHHHHHHHcCCEEEEEcCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEEEec
Confidence 345678888889998887654443344568899999999999999999888887542 11111 1111
Q ss_pred cccchh--------------hccCCccEEEEEecCCccceeecCCchHHHHHHHHhC--CeEEEecCCCCC---CCCCCC
Q 003933 284 RGLATA--------------QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG--ARIQVLIPQHLP---EGDGSK 344 (785)
Q Consensus 284 ~g~~~~--------------~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TG--ArIqI~i~~~lP---~~~~s~ 344 (785)
|...+. ..........++|-.|++... |.=-+.|++|+++.. .+|.|..+ .+. ......
T Consensus 125 RKt~Pg~r~~~k~Av~~GGg~~HR~gL~d~vlikdnHi~~~-g~i~~~v~~~k~~~p~~~~I~VEv~-tleea~~A~~~G 202 (273)
T PRK05848 125 RKTRPLLRIFEKYSVRNGGASNHRLGLDDCLMLKDTHLKHI-KDLKEFIQHARKNIPFTAKIEIECE-SLEEAKNAMNAG 202 (273)
T ss_pred CCCCcchhHHHHHHHHhCCCccccCCchhhhCcCHHHHHHH-CcHHHHHHHHHHhCCCCceEEEEeC-CHHHHHHHHHcC
Confidence 111110 000111223456767765544 333467899988876 45665222 110 001122
Q ss_pred ccEEEEEcC-HHHHHHHHHHHH
Q 003933 345 ERIVRVTGD-MRQIEIAQEMIK 365 (785)
Q Consensus 345 er~VtIsG~-~eqVe~Ak~lI~ 365 (785)
-.+|.+... .+.++++.+++.
T Consensus 203 aDiI~LDn~~~e~l~~~v~~~~ 224 (273)
T PRK05848 203 ADIVMCDNMSVEEIKEVVAYRN 224 (273)
T ss_pred CCEEEECCCCHHHHHHHHHHhh
Confidence 335666664 778888877653
No 220
>COG2985 Predicted permease [General function prediction only]
Probab=30.98 E-value=1e+02 Score=36.34 Aligned_cols=97 Identities=18% Similarity=0.299 Sum_probs=59.3
Q ss_pred cceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecCCchHHHHHH-HHhC
Q 003933 248 RPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ-TRSG 326 (785)
Q Consensus 248 RiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGKgGetIK~Iq-~~TG 326 (785)
.++++.|..+.++++...|-+.+.... -......+.|+.|-++.| . |++|++|. .+.|
T Consensus 254 d~l~lVG~~~~l~r~~~~~G~evd~~~---------------~~~~~l~~~rivVtn~~v---l---Gk~l~~L~~~~~g 312 (544)
T COG2985 254 DELHLVGYPDALARLDLRIGKEVDDRL---------------LLDTRLRTERVVVTNENV---L---GKRLRDLNLTEYG 312 (544)
T ss_pred cEEEecCChHHHHHHHHhccccccccc---------------ccccceeeEEEEeechhh---h---ccchhhcCccccc
Confidence 367899999999999865554443321 011234567888888764 3 44566665 3477
Q ss_pred CeEEEecCCC---CCCC---CCCCccEEEEEcCHHHHHHHHHHHHH
Q 003933 327 ARIQVLIPQH---LPEG---DGSKERIVRVTGDMRQIEIAQEMIKE 366 (785)
Q Consensus 327 ArIqI~i~~~---lP~~---~~s~er~VtIsG~~eqVe~Ak~lI~~ 366 (785)
|-|.. +.|. +... ....-.++++.|.++.|+.+...+-+
T Consensus 313 ~~I~R-i~Ra~iElv~~~d~~lq~gDvl~vvg~~~~v~~~~~~lG~ 357 (544)
T COG2985 313 VFINR-INRADIELVASDDVVLQKGDVLQVVGRARRVKAVADVLGN 357 (544)
T ss_pred eeeee-hhhcCccccCCcchhhhhcceeeeccchHHHHHHHHHhcc
Confidence 77763 2221 1111 12234568999999999887777643
No 221
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=30.08 E-value=95 Score=31.90 Aligned_cols=58 Identities=16% Similarity=0.253 Sum_probs=39.1
Q ss_pred cceeecCCchHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003933 307 VGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 307 vG~VIGKgGetIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~ll~~ 370 (785)
-|.+||-.-..++.+-...++.|.|.++- -+.+..+.|+|. ++-...-.+.++-++.+
T Consensus 126 NG~~~g~drslv~el~nr~nv~vRVsvKG------~dpesF~kIT~asp~~F~~QL~aLr~L~~~ 184 (228)
T COG5014 126 NGLMFGFDRSLVDELVNRLNVLVRVSVKG------WDPESFEKITGASPEYFRYQLKALRHLHGK 184 (228)
T ss_pred CCeEEecCHHHHHHHhcCCceEEEEEecC------CCHHHHHHHhcCChHHHHHHHHHHHHHHhc
Confidence 48899999999999999999998875432 234667888874 55444444444444443
No 222
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=29.84 E-value=1.2e+02 Score=32.02 Aligned_cols=28 Identities=25% Similarity=0.526 Sum_probs=23.1
Q ss_pred EEEEecCCccceeecCCchHHHHHHHHh
Q 003933 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (785)
Q Consensus 202 ~~IlVP~~~VG~IIGk~G~tIK~IqeeT 229 (785)
++|.|-...-+.|||++|..|++|++..
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5677777788999999999999887543
No 223
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=29.62 E-value=4e+02 Score=27.20 Aligned_cols=26 Identities=15% Similarity=0.240 Sum_probs=21.3
Q ss_pred ceEecc--cHHHHHHHHHHHHHHHHhhc
Q 003933 249 PVEIIG--TLSNIDKAEKLINAVIAEAD 274 (785)
Q Consensus 249 iV~I~G--t~e~V~kA~~lI~elI~e~~ 274 (785)
.+.|+| +.+.+..|++.|.++|++..
T Consensus 57 Kiv~tGaks~~~a~~a~~~~~~~L~~~g 84 (174)
T cd04518 57 KMVCTGAKSVEDLHRAVKEIIKKLKDYG 84 (174)
T ss_pred eEEEEccCCHHHHHHHHHHHHHHHHhcC
Confidence 567776 78899999999999998763
No 224
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=29.14 E-value=5.4e+02 Score=26.08 Aligned_cols=41 Identities=29% Similarity=0.341 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHH
Q 003933 317 TIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEV 367 (785)
Q Consensus 317 tIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~l 367 (785)
.|-++.+.++-+|+..|. ...|.|+|. .+.++.++.||.+.
T Consensus 107 kIvK~IKd~klKVqa~IQ----------gd~vRVtgKkrDDLQ~viallk~~ 148 (160)
T PF04461_consen 107 KIVKLIKDSKLKVQAQIQ----------GDQVRVTGKKRDDLQEVIALLKEQ 148 (160)
T ss_dssp HHHHHHHHH--SEEEEEE----------TTEEEEEES-HHHHHHHHHHHHHS
T ss_pred HHHHHHHhcCCceeEEec----------CcEEEEecCCHHHHHHHHHHHHcc
Confidence 344445777777775432 457999998 78899998888753
No 225
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=29.00 E-value=1.5e+02 Score=25.41 Aligned_cols=24 Identities=25% Similarity=0.439 Sum_probs=21.1
Q ss_pred CccEEEEEcCHHHHHHHHHHHHHH
Q 003933 344 KERIVRVTGDMRQIEIAQEMIKEV 367 (785)
Q Consensus 344 ~er~VtIsG~~eqVe~Ak~lI~~l 367 (785)
..+.|.|+|+.+.++..++||+.|
T Consensus 53 ~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 53 RTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCCEEEEEeCHHHHHHHHHHHHHH
Confidence 357899999999999999999875
No 226
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=28.42 E-value=1.2e+02 Score=36.51 Aligned_cols=101 Identities=17% Similarity=0.204 Sum_probs=55.9
Q ss_pred ccccccccchhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHH------HHhCCeEE
Q 003933 161 VKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQ------YNSGAKIQ 234 (785)
Q Consensus 161 ~k~~~i~g~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~Iq------eeTGAkI~ 234 (785)
.+.+.+.++.+++++..+.+...+.... ..+. ....++|.++++. +| |+||++|+ ++.|+.|.
T Consensus 269 GD~L~V~G~~e~L~~l~~~~G~~~~~~~----~~~~-~~~~e~VV~~~S~---li---GkTL~eL~~r~~~~~~~Gv~Vl 337 (562)
T TIGR03802 269 GDVVLVVGRRDAVVQFGAEIGEEVQEVE----GLDV-PMETKDVVLTNKE---YN---GKTVAEILKNAQQFMRHGVYVE 337 (562)
T ss_pred CCEEEEEECHHHHHHHHHhcCCccCCcc----ccCC-ceEEEEEEECCcc---cC---CccHHHHhccccccccCCeEEE
Confidence 3445566777777776655444332111 1111 1236666666544 44 45788886 26677665
Q ss_pred EccCCCC-CCCCC------CcceEecccHHHHHHHHHHHHHHHHh
Q 003933 235 ITRDADA-DPHAA------TRPVEIIGTLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 235 I~k~~d~-~p~s~------eRiV~I~Gt~e~V~kA~~lI~elI~e 272 (785)
-.++.+. ..... --+++|.|+.+.++++.+.+....++
T Consensus 338 ~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~lG~~~~~ 382 (562)
T TIGR03802 338 KIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQLGYAIAP 382 (562)
T ss_pred EEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHcCCchhh
Confidence 4333221 11111 13578899999999988876555443
No 227
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.17 E-value=1.1e+02 Score=37.95 Aligned_cols=18 Identities=22% Similarity=0.218 Sum_probs=11.7
Q ss_pred eEEEEEecCCccceeecC
Q 003933 200 MSRKIEVPNNKVGVLIGK 217 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk 217 (785)
+.+++.+-++.+..|.|.
T Consensus 802 ~~i~~~~~n~~~~~~~~~ 819 (968)
T KOG1060|consen 802 VSISLHFTNKSDLELLGI 819 (968)
T ss_pred eeEEEecccCCCcccccc
Confidence 666777766666666554
No 228
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=28.04 E-value=1.6e+02 Score=25.24 Aligned_cols=33 Identities=21% Similarity=0.385 Sum_probs=23.9
Q ss_pred hCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHH
Q 003933 229 SGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAV 269 (785)
Q Consensus 229 TGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~el 269 (785)
...+|..... ...|.|+|+.+.+++..++|.+|
T Consensus 44 ~~~~i~~d~~--------tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 44 SSGRIVADER--------TNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEECT--------TTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEECC--------CCEEEEEeCHHHHHHHHHHHHHH
Confidence 3446666533 45788889999999888877765
No 229
>cd01572 QPRTase Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=27.52 E-value=3e+02 Score=29.91 Aligned_cols=56 Identities=7% Similarity=-0.022 Sum_probs=42.8
Q ss_pred CchHHHHHHHHh--CCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhh
Q 003933 218 AGDTIRYLQYNS--GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 218 ~G~tIK~IqeeT--GAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~ 273 (785)
+-+.+.+|-+.. +++|.+...+...-...+.+++|+|....|..+.+.++.+|...
T Consensus 43 G~~~~~~i~~~~~~~l~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~L~~~ 100 (268)
T cd01572 43 GLPVAEEVFELLDPGIEVEWLVKDGDRVEPGQVLATVEGPARSLLTAERTALNFLQRL 100 (268)
T ss_pred CHHHHHHHHHHcCCCeEEEEEeCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHHH
Confidence 336678888888 88886654433333456889999999999999999998888753
No 230
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=27.13 E-value=6.8e+02 Score=25.44 Aligned_cols=41 Identities=24% Similarity=0.346 Sum_probs=29.5
Q ss_pred HHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHH
Q 003933 317 TIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEV 367 (785)
Q Consensus 317 tIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~-~eqVe~Ak~lI~~l 367 (785)
.|-++.++++-+|+..|. ...|.|+|. .+.++.++.||.+.
T Consensus 107 kIvK~IKd~klKVqa~IQ----------Gd~vRVtgKkrDDLQ~viallk~~ 148 (161)
T PRK05412 107 KIVKLIKDSKLKVQAQIQ----------GDQVRVTGKKRDDLQAVIALLRKA 148 (161)
T ss_pred HHHHHHHhcCCceeEEec----------CcEEEEecCCHhHHHHHHHHHHhc
Confidence 444556778888875432 457999996 68899988888753
No 231
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.01 E-value=3.3e+02 Score=27.21 Aligned_cols=43 Identities=19% Similarity=0.312 Sum_probs=33.3
Q ss_pred hHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 003933 316 ETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 369 (785)
Q Consensus 316 etIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~ 369 (785)
+.+..|.+-.|+-|. +. .-.+|.|.|..+.|.+|++.|..+-+
T Consensus 126 eRlqDi~E~hgvIiE-~~----------E~D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIE-FE----------EYDLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEE-ee----------eccEEEEeccHHHHHHHHHHHHHHHh
Confidence 456677777787777 42 24589999999999999999887644
No 232
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=25.88 E-value=49 Score=27.46 Aligned_cols=49 Identities=35% Similarity=0.489 Sum_probs=32.0
Q ss_pred chHHHH--HHHHhCCeEEEecCCC----CC--CCCCCCccEEEEEcCHHHHHHHHHHH
Q 003933 315 GETIKG--LQTRSGARIQVLIPQH----LP--EGDGSKERIVRVTGDMRQIEIAQEMI 364 (785)
Q Consensus 315 GetIK~--Iq~~TGArIqI~i~~~----lP--~~~~s~er~VtIsG~~eqVe~Ak~lI 364 (785)
|.+|++ +.+.++|+|.- +.++ .| ...-....+|.|.|..+.|+++++++
T Consensus 14 gk~l~el~l~~~~~~~i~~-i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~~ 70 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVA-IKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFRELF 70 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEE-EEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHHT
T ss_pred CCCHHHCCCCccCCEEEEE-EEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHhh
Confidence 557888 77778998873 3322 11 11223455699999999999888764
No 233
>PRK06039 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=25.24 E-value=3.8e+02 Score=34.50 Aligned_cols=25 Identities=12% Similarity=0.195 Sum_probs=17.0
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcccC
Q 003933 348 VRVTGDMRQIEIAQEMIKEVLSQTVR 373 (785)
Q Consensus 348 VtIsG~~eqVe~Ak~lI~~ll~~~~r 373 (785)
|.|.+. +.|..|++...+.|.+..+
T Consensus 920 ~~~~~~-~~~~~~~~~~~~~i~~~~~ 944 (975)
T PRK06039 920 VYISAP-EEVAEAVEKHEDYIKEETL 944 (975)
T ss_pred EEEeCc-HHHHHHHHHHHHHHHHhhC
Confidence 666666 6777777777777765444
No 234
>TIGR01334 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.
Probab=25.16 E-value=2.9e+02 Score=30.31 Aligned_cols=148 Identities=14% Similarity=0.078 Sum_probs=83.8
Q ss_pred CchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhc-------------cC--CCCccc
Q 003933 218 AGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD-------------AG--GSPSLV 282 (785)
Q Consensus 218 ~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~-------------~g--g~p~~~ 282 (785)
+-..+++|-+..+++|.+...+...-...+.+++++|....|..+.+.++.+|.... .. ..-.++
T Consensus 47 G~~~~~~i~~~l~~~~~~~~~dG~~v~~g~~i~~~~G~a~~ll~~eR~alN~l~~~SGIAT~T~~~V~~~~~~~~~~~I~ 126 (277)
T TIGR01334 47 GVSEAAKLLKQLGASIDYAVPSGSRALAGTLLLEAKGSAGQLHQGWKSAQSVLEWSCGVATYTHKMVTLAKKISPMAVVA 126 (277)
T ss_pred CHHHHHHHHHHcCCEEEEEeCCCCEeCCCCEEEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCEEE
Confidence 346788999999999998865544445668899999999999999998888876532 00 001111
Q ss_pred ccc-cchh------hc--cCC------ccEEEEEecCCccceeecC--CchHHHHHHHHh-CCeEEEecCC--CCCCCCC
Q 003933 283 ARG-LATA------QA--SGA------AEQVEIKVPNEKVGLIIGR--GGETIKGLQTRS-GARIQVLIPQ--HLPEGDG 342 (785)
Q Consensus 283 ~~g-~~~~------~~--~~~------~~~~~i~VP~~~vG~VIGK--gGetIK~Iq~~T-GArIqI~i~~--~lP~~~~ 342 (785)
+.+ ..+. .+ ..+ .-...++|-.|++..+=+. =.+.|+.+++.. ..+|.|-... .+-....
T Consensus 127 ~TRKT~Pg~R~l~k~Av~~GGg~~HR~gLsd~ilikdnHi~~~g~~~~i~~av~~~r~~~~~~kIeVEv~tleea~ea~~ 206 (277)
T TIGR01334 127 CTRKAIPLTRPLAVKAVLAAGGVIHRIGLSETLLVFANHRTFLNDNFDWGGAIGRLKQTAPERKITVEADTIEQALTVLQ 206 (277)
T ss_pred ecCCCCCChhHHHHHHHHhCCCcCeecCCchhheehHHHHHHhCCcccHHHHHHHHHHhCCCCCEEEECCCHHHHHHHHH
Confidence 111 0000 00 011 1133457777777655211 235677777654 3556642210 0001112
Q ss_pred CCccEEEEEcC-HHHHHHHHHHHH
Q 003933 343 SKERIVRVTGD-MRQIEIAQEMIK 365 (785)
Q Consensus 343 s~er~VtIsG~-~eqVe~Ak~lI~ 365 (785)
..-.+|.+..- ++.+..+.++|.
T Consensus 207 ~GaDiI~lDn~~~e~l~~~v~~l~ 230 (277)
T TIGR01334 207 ASPDILQLDKFTPQQLHHLHERLK 230 (277)
T ss_pred cCcCEEEECCCCHHHHHHHHHHHh
Confidence 23445666653 788888887774
No 235
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=24.87 E-value=2.1e+02 Score=38.62 Aligned_cols=8 Identities=25% Similarity=0.617 Sum_probs=4.3
Q ss_pred EEEEEecC
Q 003933 297 QVEIKVPN 304 (785)
Q Consensus 297 ~~~i~VP~ 304 (785)
.++|.+|.
T Consensus 361 ~i~f~lpp 368 (2849)
T PTZ00415 361 VIEFTLPP 368 (2849)
T ss_pred eEEEecCC
Confidence 45555554
No 236
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=24.86 E-value=1.3e+02 Score=28.43 Aligned_cols=40 Identities=13% Similarity=0.169 Sum_probs=31.2
Q ss_pred HHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003933 323 TRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT 371 (785)
Q Consensus 323 ~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~~~ 371 (785)
+..++.|- |.++. .-.|.|+|+..+|+.|++.|.+.+++.
T Consensus 61 Kaa~V~ig-F~DRF--------sGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 61 KAADVHIG-FLDRF--------SGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred hccCcEEe-eeecc--------ceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 33456666 66655 457999999999999999999988763
No 237
>PRK04021 hypothetical protein; Reviewed
Probab=24.33 E-value=1.4e+02 Score=27.44 Aligned_cols=40 Identities=23% Similarity=0.441 Sum_probs=29.4
Q ss_pred hHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEc-CHHHHHHHH
Q 003933 316 ETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQ 361 (785)
Q Consensus 316 etIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG-~~eqVe~Ak 361 (785)
+-|+-|.+..|+.|.|+ .+..+..++|.|.| +.+.+....
T Consensus 50 ali~~LAk~l~~~I~I~------~G~~sr~K~v~i~g~~~e~l~~~L 90 (92)
T PRK04021 50 ELVKFFSKLLGAEVEII------RGETSREKDLLVKGISLEEVKKKL 90 (92)
T ss_pred HHHHHHHHHhCCCEEEE------ecCCcCceEEEEecCCHHHHHHHh
Confidence 34777888999999965 34467789999999 466665543
No 238
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=24.09 E-value=2.5e+02 Score=33.31 Aligned_cols=65 Identities=26% Similarity=0.298 Sum_probs=42.6
Q ss_pred EEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCC------------C--CCCCCCcc--eEecc-cHHHHHHHH
Q 003933 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDAD------------A--DPHAATRP--VEIIG-TLSNIDKAE 263 (785)
Q Consensus 201 t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d------------~--~p~s~eRi--V~I~G-t~e~V~kA~ 263 (785)
-..+|-|-..||.| -+++|+++.||+|+...=.- . .-...+.+ |.|.| ..+.+.+|.
T Consensus 265 ~K~~LaPLTTvGNL------PFRRlCk~lGADvTcgEMA~~tpLlqG~~sEWALlkRH~sEdiFGVQlag~~pdt~~kaa 338 (614)
T KOG2333|consen 265 DKKYLAPLTTVGNL------PFRRLCKKLGADVTCGEMAMATPLLQGTASEWALLKRHQSEDIFGVQLAGSKPDTAAKAA 338 (614)
T ss_pred cceeeccccccCCc------cHHHHHHHhCCccchhHHHHHHHHhcccchhhhhhhhcCcccceeeEeccCChHHHHHHH
Confidence 44777888888877 58999999999998753000 0 00011112 45555 778899998
Q ss_pred HHHHHHHH
Q 003933 264 KLINAVIA 271 (785)
Q Consensus 264 ~lI~elI~ 271 (785)
++|.+-..
T Consensus 339 q~i~e~~~ 346 (614)
T KOG2333|consen 339 QVIAETCD 346 (614)
T ss_pred HHHHhhcc
Confidence 88877544
No 239
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=23.68 E-value=59 Score=42.00 Aligned_cols=14 Identities=14% Similarity=0.254 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHH
Q 003933 258 NIDKAEKLINAVIA 271 (785)
Q Consensus 258 ~V~kA~~lI~elI~ 271 (785)
.|++|.+.|..-|.
T Consensus 1530 GVEAar~~Iv~Ev~ 1543 (1640)
T KOG0262|consen 1530 GVEAARNAIVNEVN 1543 (1640)
T ss_pred hHHHHHHHHHHHHH
Confidence 45555554444333
No 240
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=23.47 E-value=60 Score=33.31 Aligned_cols=59 Identities=10% Similarity=0.096 Sum_probs=43.5
Q ss_pred ccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc-cHHHHHHHHHHHHHHHHh
Q 003933 210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAE 272 (785)
Q Consensus 210 ~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G-t~e~V~kA~~lI~elI~e 272 (785)
.-|.|||-.-+.++.|-+.-.+.|.|.-+.. .++..++|+| +.+-...-++.+.-++.+
T Consensus 125 TNG~~~g~drslv~el~nr~nv~vRVsvKG~----dpesF~kIT~asp~~F~~QL~aLr~L~~~ 184 (228)
T COG5014 125 TNGLMFGFDRSLVDELVNRLNVLVRVSVKGW----DPESFEKITGASPEYFRYQLKALRHLHGK 184 (228)
T ss_pred eCCeEEecCHHHHHHHhcCCceEEEEEecCC----CHHHHHHHhcCChHHHHHHHHHHHHHHhc
Confidence 4589999999999999998888888875432 3366788886 777666656655555554
No 241
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=23.43 E-value=1.4e+02 Score=26.01 Aligned_cols=42 Identities=24% Similarity=0.281 Sum_probs=31.9
Q ss_pred hHHHHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHH
Q 003933 316 ETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKE 366 (785)
Q Consensus 316 etIK~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ 366 (785)
..|.+|.+..+|+|.-+ +.+.-+|.++|+.+.|+...+++..
T Consensus 17 ~ei~~l~~~f~a~ivd~---------~~~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 17 SEILQLAEIFRARIVDV---------SPDSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHTT-EEEEE---------ETTEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHhCCEEEEE---------CCCEEEEEEcCCHHHHHHHHHHhhh
Confidence 56888999999998832 2246789999999999998888765
No 242
>cd02191 FtsZ FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
Probab=23.20 E-value=1.1e+02 Score=33.92 Aligned_cols=132 Identities=13% Similarity=0.168 Sum_probs=62.1
Q ss_pred hHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEE
Q 003933 220 DTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVE 299 (785)
Q Consensus 220 ~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~ 299 (785)
..|++|++.+.+-|.|..+ ++..+... -.+..|.+.++++|.+...+-...+...+.-.. ....++
T Consensus 138 ~~l~~L~~~~D~~iv~dN~---------~L~~~~~~-~~~~~af~~~N~~ia~~i~~it~~i~~~g~inv----D~~dv~ 203 (303)
T cd02191 138 EGFQTLVREVDNLMVIPNE---------KLRQIGEK-ASLEGAFDHADEVLVRAVGGLFGAIEIEGEINV----DFADVK 203 (303)
T ss_pred HHHHHHHHhCCEEEEEehH---------HHHHHhhc-CChHHHHHHHHHHHHHHHHHHHHhhccCCcccC----CHHHHH
Confidence 4789999999998888642 23323222 234457777777776543211100000010000 000000
Q ss_pred EEecCCc---cceeecCCchHH-HHHHHHhCCeEEEecCCCCCCCCCCCccEEEEEcC----HHHHHHHHHHHHHHHhc
Q 003933 300 IKVPNEK---VGLIIGRGGETI-KGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGD----MRQIEIAQEMIKEVLSQ 370 (785)
Q Consensus 300 i~VP~~~---vG~VIGKgGetI-K~Iq~~TGArIqI~i~~~lP~~~~s~er~VtIsG~----~eqVe~Ak~lI~~ll~~ 370 (785)
-.+-+.- +|.=.+++-..+ +.+++.....+- .... -.....-+|.|+|. .+.|..+.++|.+.+.+
T Consensus 204 ~~l~~~G~a~ig~g~~~g~~~~~~a~~~Al~~pll--~~~~---~~~A~~~Lv~i~g~~~l~~~e~~~~~~~i~~~~~~ 277 (303)
T cd02191 204 NVMDGGGVAMVGYGSEDVTNRATEAVRKAALGPLL--LPCE---IEGAEGALLVMAGPPDLNLKEIERVRKWLEEQTGE 277 (303)
T ss_pred HHhccCCeEEEEEEEecCchHHHHHHHHHHhCCCC--CCCC---cccCCEEEEEEECCCCCCHHHHHHHHHHHHHHcCC
Confidence 0111111 121123333333 344555555543 1111 12334567999995 55888888888877653
No 243
>PRK04021 hypothetical protein; Reviewed
Probab=23.16 E-value=1.2e+02 Score=27.80 Aligned_cols=42 Identities=19% Similarity=0.410 Sum_probs=32.7
Q ss_pred chHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecc-cHHHHHHHHH
Q 003933 219 GDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEK 264 (785)
Q Consensus 219 G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~G-t~e~V~kA~~ 264 (785)
-+.|+.|.+.++++|.|.+.. .+..++|.|.| +.+.+.+.+.
T Consensus 49 ~ali~~LAk~l~~~I~I~~G~----~sr~K~v~i~g~~~e~l~~~L~ 91 (92)
T PRK04021 49 KELVKFFSKLLGAEVEIIRGE----TSREKDLLVKGISLEEVKKKLK 91 (92)
T ss_pred HHHHHHHHHHhCCCEEEEecC----CcCceEEEEecCCHHHHHHHhc
Confidence 456889999999999998643 35678999988 8888776654
No 244
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=22.98 E-value=1.4e+02 Score=36.62 Aligned_cols=109 Identities=22% Similarity=0.231 Sum_probs=69.8
Q ss_pred CcceEecc-cHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEEEEecCCccceeecC--CchHHHHHHH
Q 003933 247 TRPVEIIG-TLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGR--GGETIKGLQT 323 (785)
Q Consensus 247 eRiV~I~G-t~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGK--gGetIK~Iq~ 323 (785)
...+.++| +...+..|+..+..+|.+...+............ .......|.+..+.+.+|+|. .-+.|++|-+
T Consensus 217 ~~~r~~rGvD~~~v~~al~~~~~ll~e~~gg~v~~~~~~~~~~----~~~~~~~i~~~~~~i~~llG~~ls~eei~~iL~ 292 (650)
T COG0072 217 ASFRFERGVDPELVEKALNRATTLLAEICGGEVSSVVIVGGDE----KLTPPRKIELRLERINRLLGLELSAEEIEKILK 292 (650)
T ss_pred eeEEeecCCCHHHHHHHHHHHHHHHHHhcCCeeeeEEEecCCc----CCCCCceEEecHHHHHHHhCCCCCHHHHHHHHH
Confidence 45667778 7789999999999999987421111111000000 000034677777888888884 4788999999
Q ss_pred HhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 003933 324 RSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 369 (785)
Q Consensus 324 ~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~ll~ 369 (785)
+.|+.+.. ..+ .-.|+|=--.-.|.+...+|++++.
T Consensus 293 rLg~~~~~-~~~---------~~~V~vPs~R~DI~~e~DliEEv~r 328 (650)
T COG0072 293 RLGFKVEV-KGD---------GLTVTVPSYRVDILIEADLIEEVAR 328 (650)
T ss_pred HcCCeeEe-cCC---------cEEEeCCCCcccccchhHHHHHHHH
Confidence 99999983 211 1234444446677888888888775
No 245
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=22.91 E-value=1.8e+02 Score=33.95 Aligned_cols=53 Identities=21% Similarity=0.322 Sum_probs=36.7
Q ss_pred EEecC--CccceeecCCchHHHHHHHHhC-----CeEEEecCCCCCCCCCCCccEEEEEcC--HHHHHHHHHHHHH
Q 003933 300 IKVPN--EKVGLIIGRGGETIKGLQTRSG-----ARIQVLIPQHLPEGDGSKERIVRVTGD--MRQIEIAQEMIKE 366 (785)
Q Consensus 300 i~VP~--~~vG~VIGKgGetIK~Iq~~TG-----ArIqI~i~~~lP~~~~s~er~VtIsG~--~eqVe~Ak~lI~~ 366 (785)
..+|. .+||.|..+.|+.|+.|..... |+|.|+ -+.|.|. ..+|-+|++..+.
T Consensus 129 kpLP~~p~~IGVITS~tgAairDIl~~~~rR~P~~~viv~--------------pt~VQG~~A~~eIv~aI~~an~ 190 (440)
T COG1570 129 KPLPFFPKKIGVITSPTGAALRDILHTLSRRFPSVEVIVY--------------PTLVQGEGAAEEIVEAIERANQ 190 (440)
T ss_pred CCCCCCCCeEEEEcCCchHHHHHHHHHHHhhCCCCeEEEE--------------eccccCCCcHHHHHHHHHHhhc
Confidence 34444 8999999999999999875543 555542 3567776 5566666666654
No 246
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=22.66 E-value=33 Score=39.00 Aligned_cols=48 Identities=31% Similarity=0.423 Sum_probs=26.8
Q ss_pred hHHhhhcCCCchHHHHhhcCCcchhhccchhhhh----ccccccccCCccccCCCcCcCC
Q 003933 16 DLKRKLDDLEPDEALEHAEGMRDDEAKNSDEVEK----NVDGFAEAHGSEVKRPRLDDDK 71 (785)
Q Consensus 16 d~krkl~~le~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~e~kr~~~dd~~ 71 (785)
|-|||||+|.-- . ++..|- +.-|||+ -+|||+++-..=.=||+.+.++
T Consensus 384 ~skrkL~el~~~------~-vd~eek-ie~eveelll~~ad~fve~vt~FsCrlakhrkS 435 (505)
T COG5624 384 DSKRKLEELQHG------G-VDEEEK-IENEVEELLLSRADGFVEPVTEFSCRLAKHRKS 435 (505)
T ss_pred hhhhhHHHHHhh------c-cCccee-ccchHHHHHHhhhcccccccchheeEeeccCCC
Confidence 568999876543 3 332222 2223432 3566666666666667666665
No 247
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=21.78 E-value=3e+02 Score=23.49 Aligned_cols=63 Identities=16% Similarity=0.117 Sum_probs=39.4
Q ss_pred eEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCC-CCCC--CCCcceEecccHHHHHHHHHHHHH
Q 003933 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDAD-ADPH--AATRPVEIIGTLSNIDKAEKLINA 268 (785)
Q Consensus 200 ~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d-~~p~--s~eRiV~I~Gt~e~V~kA~~lI~e 268 (785)
..++|.+..+.+ ..-.|.+|.+++++.++|....- ...+ --.-+|.|.|+.+.+++|++.+.+
T Consensus 3 ~l~~l~f~g~~~------~~piis~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~g~~~~~~~a~~~L~~ 68 (76)
T PF09383_consen 3 RLVRLTFTGNSA------QEPIISQLIREFGVDVNILHGNIEEIQGTPFGILILELPGDDEEIEKAIAYLRE 68 (76)
T ss_dssp EEEEEEEESCSS------SSCHHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHH
T ss_pred eEEEEEEcCCCc------CchHHHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEECCHHHHHHHHHHHHH
Confidence 345666655443 44568999999999999874210 0000 113467888999999998887665
No 248
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=21.77 E-value=3.7e+02 Score=31.07 Aligned_cols=19 Identities=26% Similarity=0.087 Sum_probs=11.6
Q ss_pred eEecccHHHHHHHHHHHHH
Q 003933 250 VEIIGTLSNIDKAEKLINA 268 (785)
Q Consensus 250 V~I~Gt~e~V~kA~~lI~e 268 (785)
|...-..|.|.+|++|-+.
T Consensus 160 v~~k~EeEdiaKAi~lSL~ 178 (462)
T KOG2199|consen 160 VSSKQEEEDIAKAIELSLK 178 (462)
T ss_pred ccccccHHHHHHHHHhhHH
Confidence 3344466778888776543
No 249
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=21.64 E-value=2.6e+02 Score=23.99 Aligned_cols=46 Identities=9% Similarity=0.290 Sum_probs=23.3
Q ss_pred hHHHHHHHHh-CCeEEEccCCCCCCCCCCcceEecccHHH-HHHHHHHHHHHHHh
Q 003933 220 DTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSN-IDKAEKLINAVIAE 272 (785)
Q Consensus 220 ~tIK~IqeeT-GAkI~I~k~~d~~p~s~eRiV~I~Gt~e~-V~kA~~lI~elI~e 272 (785)
+..|+|.+.+ .+.|+|...+ .--|.|.|+.+. -.+..++|.+++.+
T Consensus 12 EL~kRl~~~yPd~~v~Vr~~s-------~~~l~v~g~~~~~k~~i~~iLqe~we~ 59 (65)
T PF06183_consen 12 ELTKRLHRQYPDAEVRVRPGS-------ANGLSVSGGKKDDKERIEEILQEMWED 59 (65)
T ss_dssp HHHHHHHHH-SS-EEEEEEES-------S-EEEEES--HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHCCCceEeeeecc-------cCccccCCcCchHHHHHHHHHHHHHhc
Confidence 4567777766 4667776432 347788886644 33344444444443
No 250
>cd01573 modD_like ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.
Probab=21.31 E-value=3.7e+02 Score=29.26 Aligned_cols=55 Identities=11% Similarity=0.106 Sum_probs=42.2
Q ss_pred chHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhh
Q 003933 219 GDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 219 G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~ 273 (785)
-..+.+|-+..+++|.+...+...-...+.+++|.|....|..+.+.++.+|...
T Consensus 44 ~~~~~~~~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~~ 98 (272)
T cd01573 44 TEEAARILELLGLEVDLAAASGSRVAAGAVLLEAEGPAAALHLGWKVAQTLLEWA 98 (272)
T ss_pred HHHHHHHHHHcCcEEEEEcCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHHH
Confidence 3567888888899998654333333456889999999999999999988887653
No 251
>TIGR02516 type_III_yscC type III secretion outer membrane pore, YscC/HrcC family. A number of proteins homologous to the type IV pilus secretin PilQ (TIGR02515) are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also called the main terminal branch of the general secretion pathway). The clade described by this model contains the outer membrane pore proteins of bacterial type III secretion systems, typified by YscC for animal pathogens and HrcC for plant pathogens.
Probab=20.85 E-value=1e+03 Score=27.65 Aligned_cols=25 Identities=12% Similarity=0.282 Sum_probs=21.1
Q ss_pred CccEEEEEcCHHHHHHHHHHHHHHH
Q 003933 344 KERIVRVTGDMRQIEIAQEMIKEVL 368 (785)
Q Consensus 344 ~er~VtIsG~~eqVe~Ak~lI~~ll 368 (785)
....|.|+|+++.+++.+++|..+-
T Consensus 206 ~tNsliv~~~~~~~~~i~~lI~~LD 230 (462)
T TIGR02516 206 RTNAVLIRDRPERMAIYEQLIQQLD 230 (462)
T ss_pred CCCEEEEEeCHHHHHHHHHHHHHhC
Confidence 3567999999999999999998653
No 252
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating)
Probab=20.73 E-value=3.7e+02 Score=29.17 Aligned_cols=54 Identities=11% Similarity=0.093 Sum_probs=41.5
Q ss_pred hHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhh
Q 003933 220 DTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 220 ~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~ 273 (785)
..+.+|-+..+++|.+...+...-...+.+++|+|....|..+.+.++.+|...
T Consensus 43 ~~~~~i~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~il~~Er~~ln~l~~~ 96 (265)
T TIGR00078 43 PVARRVFEQLGVQVEWLVKDGDRVEPGEVVAEVEGPARSLLTAERTALNFLGRL 96 (265)
T ss_pred HHHHHHHHHcCeEEEEEeCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHHH
Confidence 567888888898875554333333456889999999999999999998888754
No 253
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.72 E-value=1.5e+02 Score=26.40 Aligned_cols=35 Identities=20% Similarity=0.222 Sum_probs=26.8
Q ss_pred CCeEEEccCCCCCCCCCCcceEecc--cHHHHHHHHHHHHHHHHhh
Q 003933 230 GAKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 230 GAkI~I~k~~d~~p~s~eRiV~I~G--t~e~V~kA~~lI~elI~e~ 273 (785)
.+.+.|... -.|+|+| +.+.+.+|++.|..+|++.
T Consensus 49 ~~t~~IF~s---------Gki~itGaks~~~~~~a~~~i~~~L~~~ 85 (86)
T PF00352_consen 49 KATVLIFSS---------GKIVITGAKSEEEAKKAIEKILPILQKL 85 (86)
T ss_dssp TEEEEEETT---------SEEEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred cEEEEEEcC---------CEEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 456666643 2567777 7899999999999999874
No 254
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=20.70 E-value=70 Score=41.04 Aligned_cols=62 Identities=24% Similarity=0.381 Sum_probs=44.5
Q ss_pred EecC-CccceeecCCchHHHH----HH--HHhCCeEEEecCCCCCCCCCCCccEEEEEcC--HHHHHHHHHHHHHHHhcc
Q 003933 301 KVPN-EKVGLIIGRGGETIKG----LQ--TRSGARIQVLIPQHLPEGDGSKERIVRVTGD--MRQIEIAQEMIKEVLSQT 371 (785)
Q Consensus 301 ~VP~-~~vG~VIGKgGetIK~----Iq--~~TGArIqI~i~~~lP~~~~s~er~VtIsG~--~eqVe~Ak~lI~~ll~~~ 371 (785)
.+|. +++-.|+++|-+|+.+ |+ +..||||. .- +.+.++|.+.|. .++.+...++.+++.+.+
T Consensus 1096 RMPCaElADsIV~~GRETLEraIe~Vn~~d~w~AkVV-YG--------DTDSmFVlL~GaT~eeAF~IGq~iAe~VT~~N 1166 (1488)
T KOG0968|consen 1096 RMPCAELADSIVQKGRETLERAIEMVNRGDYWGAKVV-YG--------DTDSMFVLLPGATVEEAFEIGQEIAEAVTNSN 1166 (1488)
T ss_pred CCchHHHHHHHHHhhHHHHHHHHHHHhcCCcCCeEEE-Ec--------CCCceEEEecCccHHHHHHHHHHHHHHHHhcC
Confidence 3566 6677899999988654 32 45688887 32 335789999996 567788888888877653
No 255
>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=20.64 E-value=1e+03 Score=26.90 Aligned_cols=66 Identities=18% Similarity=0.255 Sum_probs=43.2
Q ss_pred cEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEecCCC-CCCCCCCCccEEEEEcCHHHHHHHHHHHHHH
Q 003933 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQH-LPEGDGSKERIVRVTGDMRQIEIAQEMIKEV 367 (785)
Q Consensus 296 ~~~~i~VP~~~vG~VIGKgGetIK~Iq~~TGArIqI~i~~~-lP~~~~s~er~VtIsG~~eqVe~Ak~lI~~l 367 (785)
..++|....+.+- .--|.++-+++++.+.|+...- .-.+..-...+|.|.|..+.+++|++.+.+.
T Consensus 264 ~~~rl~f~g~~~~------~plis~~~~~~~v~~nIl~G~I~~~~~~~~G~L~v~l~g~~~~~~~a~~~l~~~ 330 (339)
T COG1135 264 PLLRLTFTGESAD------QPLLSEVARRFGVDVNILSGNIDEIQGQPFGSLVVELEGDDEEIAAAIEYLNEH 330 (339)
T ss_pred eEEEEEecCcccc------chHHHHHHHHhCCceEEEecchhhhCCCcceEEEEEecCchhhHHHHHHHHHHc
Confidence 4455555544332 2347889999999999753211 0022234566799999999999999988764
No 256
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=20.60 E-value=2.8e+02 Score=28.32 Aligned_cols=45 Identities=18% Similarity=0.145 Sum_probs=34.3
Q ss_pred CchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHH
Q 003933 218 AGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAV 269 (785)
Q Consensus 218 ~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~el 269 (785)
...-|.+|.+.++++|.-... ..-+|.++|+.+.|+..++++..+
T Consensus 97 ~r~ei~~~~~~f~a~ivdv~~-------~~~~ie~tG~~~ki~a~~~~l~~~ 141 (174)
T CHL00100 97 TRPEILEIAQIFRAKVVDLSE-------ESLILEVTGDPGKIVAIEQLLEKF 141 (174)
T ss_pred CHHHHHHHHHHhCCEEEEecC-------CEEEEEEcCCHHHHHHHHHHhhhc
Confidence 456688999999999855432 246899999999999887776553
No 257
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=20.41 E-value=2.8e+02 Score=27.87 Aligned_cols=45 Identities=22% Similarity=0.206 Sum_probs=33.6
Q ss_pred CchHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHH
Q 003933 218 AGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAV 269 (785)
Q Consensus 218 ~G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~el 269 (785)
....|.+|.+.++++|.=... ..-++.++|+.+.|+.-++++...
T Consensus 96 ~r~~i~~i~~~f~a~ivdv~~-------~~~~ie~tG~~~ki~~~~~~l~~~ 140 (157)
T TIGR00119 96 GRDEIIRLTNIFRGRIVDVSP-------DSYTVEVTGDSDKIDAFLELLRPF 140 (157)
T ss_pred CHHHHHHHHHHhCCEEEEecC-------CEEEEEEcCCHHHHHHHHHHhhhc
Confidence 446788999999999854322 256899999999998877766553
No 258
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=20.29 E-value=2.7e+02 Score=28.07 Aligned_cols=91 Identities=18% Similarity=0.152 Sum_probs=52.6
Q ss_pred cccccchhhhhhhcccchhhhccCCC---CCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhCCeEEEccCCC
Q 003933 164 EETVKEEESVEPSNVVPQQVVDNSKS---DDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDAD 240 (785)
Q Consensus 164 ~~i~g~~esVE~A~~lI~~ii~~~~~---~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTGAkI~I~k~~d 240 (785)
+.+.++...++...+.+.++++-... +.......+-.-++|.+... ....|.+|.+.++++|.=...
T Consensus 48 i~V~~~~~~i~qi~kQl~KLidV~~V~~~~~~~~v~rEl~LiKv~~~~~--------~r~~i~~i~~~f~a~ivdv~~-- 117 (161)
T PRK11895 48 IVTSGDEQVIEQITKQLNKLIDVLKVVDLTEEAHVERELALVKVRASGE--------NRAEILRLADIFRAKIVDVTP-- 117 (161)
T ss_pred EEEECCHHHHHHHHHHHhccccEEEEEecCCcchhheEEEEEEEECCcc--------cHHHHHHHHHHhCCEEEEecC--
Confidence 34446677788777777766641111 00011011122223333221 345788999999999854322
Q ss_pred CCCCCCCcceEecccHHHHHHHHHHHHHH
Q 003933 241 ADPHAATRPVEIIGTLSNIDKAEKLINAV 269 (785)
Q Consensus 241 ~~p~s~eRiV~I~Gt~e~V~kA~~lI~el 269 (785)
..-++.++|+.+.|+.-++++..+
T Consensus 118 -----~~~~iE~tG~~~ki~~~~~~l~~~ 141 (161)
T PRK11895 118 -----ESLTIEVTGDSDKIDAFIDLLRPY 141 (161)
T ss_pred -----CEEEEEEeCCHHHHHHHHHHhhhc
Confidence 256899999999988777766543
No 259
>TIGR02517 type_II_gspD general secretion pathway protein D. In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion, also called the main terminal branch of the general secretion pathway. Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II secretion system specifically associated with virulence (See PubMed:12654803). This family is closely homologous to the type IV pilus outer membrane secretin PilQ (TIGR02515) and to the type III secretion system pore YscC/HrcC (TIGR02516).
Probab=20.19 E-value=7.5e+02 Score=29.74 Aligned_cols=158 Identities=14% Similarity=0.131 Sum_probs=0.0
Q ss_pred cccccccccccchhhhhhhcccchhhhccCCCCCCCCCCCCCeEEEEEecCCccceeecCCchHHHHHHHHhC-------
Q 003933 158 EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG------- 230 (785)
Q Consensus 158 ~ds~k~~~i~g~~esVE~A~~lI~~ii~~~~~~~p~~~~~~~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTG------- 230 (785)
.+....+.+.+..+.+++.+++|..+. .... ..+.-|.+-...+..|. ..|+.|-...+
T Consensus 129 d~~~N~liv~~~~~~l~~i~~li~~lD--------~p~~--~~~~v~~Lk~a~a~ev~----~~L~~l~~~~~~~~~~~~ 194 (594)
T TIGR02517 129 YPPTNTIVVTDYASNINRVARIIQQLD--------VDGA--GSVEVIPLKNASAVDIA----DVLNKLLGEGGKTDGGGK 194 (594)
T ss_pred cCCCCEEEEEcCHHHHHHHHHHHHHhc--------ccCC--CceEEEEeecCCHHHHH----HHHHHHhcccccccccCc
Q ss_pred -CeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhhccCCCCcccccccchhhccCCccEEEEEecCCccce
Q 003933 231 -AKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGL 309 (785)
Q Consensus 231 -AkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~~~gg~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~ 309 (785)
..|.+.+. ..++.|.++.+.++++.++|.++=..... .....-+.|-+..+..
T Consensus 195 ~~~i~~~~~--------~n~Lvv~~~~~~~~~i~~~I~~LD~~~~~------------------~~~~~v~~l~~~~a~~ 248 (594)
T TIGR02517 195 LSVIAPDRR--------NNILIRAGSPEALERIKKLISQLDVPASE------------------GGNVRVYYLRNADAEE 248 (594)
T ss_pred eeEEecCCC--------CceEEEcCCHHHHHHHHHHHHHhCccccc------------------CCceEEEEEecCCHHH
Q ss_pred eecCCchHHHHHHH-------------------------------HhCCeEEEecCCCCCCCCCCCccEEEEEcCHHHHH
Q 003933 310 IIGRGGETIKGLQT-------------------------------RSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358 (785)
Q Consensus 310 VIGKgGetIK~Iq~-------------------------------~TGArIqI~i~~~lP~~~~s~er~VtIsG~~eqVe 358 (785)
|. ..|+.|-. .+...+.|..+.. ...|.|.++++.++
T Consensus 249 la----~~L~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~d~~--------~n~liv~~~~~~~~ 316 (594)
T TIGR02517 249 LA----KTLQGVFGGGGNEPGSSSSPGLGGAVNPGGSQSAQAASSASGGSVSGSADKA--------TNSLIITASPQDYK 316 (594)
T ss_pred HH----HHHHHhhccCCCCCCCcccccccccccccCcccCccccccCCCCeeEEEcCC--------ccEEEEEcCHHHHH
Q ss_pred HHHHHHHHH
Q 003933 359 IAQEMIKEV 367 (785)
Q Consensus 359 ~Ak~lI~~l 367 (785)
+.+++|+.+
T Consensus 317 ~i~~~i~~l 325 (594)
T TIGR02517 317 NIRAVIKQL 325 (594)
T ss_pred HHHHHHHHh
No 260
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=20.16 E-value=2.1e+02 Score=23.90 Aligned_cols=58 Identities=14% Similarity=0.253 Sum_probs=39.5
Q ss_pred CeEEEEEecCCccceeecCCchHHHHHHHHhC-CeEEEccCCCCCCCCCCcceEecc-cHHHHHHHHHHHHH
Q 003933 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG-AKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINA 268 (785)
Q Consensus 199 ~~t~~IlVP~~~VG~IIGk~G~tIK~IqeeTG-AkI~I~k~~d~~p~s~eRiV~I~G-t~e~V~kA~~lI~e 268 (785)
.+.++|.+|. |.|=...=..|..|-++.| ..|.+... ..|.|.+ ..++|....+.|.+
T Consensus 9 ~~~v~~~~~~---G~i~~~~l~~la~ia~~yg~~~irlT~~---------Q~l~l~~v~~~~~~~i~~~L~~ 68 (69)
T PF03460_consen 9 FYMVRIRIPG---GRISAEQLRALAEIAEKYGDGEIRLTTR---------QNLQLRGVPEENLPAIFEELKE 68 (69)
T ss_dssp EEEEEEB-GG---GEEEHHHHHHHHHHHHHHSTSEEEEETT---------SCEEEEEEEGGGHHHHHHHHHH
T ss_pred EEEEEEeCCC---EEECHHHHHHHHHHHHHhCCCeEEECCC---------CeEEEeCCCHHHHHHHHHHHHc
Confidence 3578888875 6666566677888888888 78888743 3467776 66777776666554
No 261
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=20.13 E-value=3.9e+02 Score=29.33 Aligned_cols=55 Identities=16% Similarity=0.197 Sum_probs=42.3
Q ss_pred chHHHHHHHHhCCeEEEccCCCCCCCCCCcceEecccHHHHHHHHHHHHHHHHhh
Q 003933 219 GDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (785)
Q Consensus 219 G~tIK~IqeeTGAkI~I~k~~d~~p~s~eRiV~I~Gt~e~V~kA~~lI~elI~e~ 273 (785)
-..+.+|-+..+++|.+...+...-...+.+++|.|....|..+.+.++.+|...
T Consensus 46 ~~~a~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~~ 100 (278)
T PRK08385 46 LEEAKALFEHFGVKVEVRKRDGEEVKAGEVILELKGNARAILLVERTALNIIGRM 100 (278)
T ss_pred HHHHHHHHHHcCCEEEEEcCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHHH
Confidence 3556888888899998854433333456889999999999999999988887653
Done!