Query 014452
Match_columns 424
No_of_seqs 208 out of 2101
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 05:15:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014452.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014452hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2192 PolyC-binding hnRNP-K 100.0 7.2E-40 1.6E-44 297.9 28.5 330 41-421 39-385 (390)
2 KOG1676 K-homology type RNA bi 100.0 4.7E-34 1E-38 286.6 21.3 239 47-420 136-389 (600)
3 KOG1676 K-homology type RNA bi 100.0 9.6E-33 2.1E-37 277.2 21.8 258 34-420 35-300 (600)
4 KOG2190 PolyC-binding proteins 100.0 3.4E-31 7.5E-36 269.9 26.4 352 48-422 41-411 (485)
5 KOG2193 IGF-II mRNA-binding pr 100.0 2.5E-30 5.4E-35 248.5 16.2 285 46-422 195-483 (584)
6 KOG2193 IGF-II mRNA-binding pr 100.0 1.1E-28 2.3E-33 237.4 12.1 243 43-420 273-564 (584)
7 KOG2191 RNA-binding protein NO 99.9 4.8E-26 1.1E-30 213.4 24.3 268 42-421 31-316 (402)
8 KOG2191 RNA-binding protein NO 99.9 3.5E-22 7.6E-27 187.5 18.2 166 132-421 37-205 (402)
9 KOG2190 PolyC-binding proteins 99.8 7.1E-18 1.5E-22 172.5 16.5 159 131-420 40-208 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.7 9.2E-17 2E-21 147.2 11.6 151 48-209 121-385 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.7 3.9E-16 8.6E-21 140.1 12.1 61 138-208 2-65 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.6 1.4E-15 3E-20 136.6 11.2 129 54-209 2-152 (172)
13 PRK13763 putative RNA-processi 99.6 6.1E-15 1.3E-19 133.3 14.5 65 134-208 3-71 (180)
14 PRK13763 putative RNA-processi 99.6 1E-14 2.2E-19 131.8 13.3 133 50-209 3-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.5 4.6E-14 9.9E-19 106.2 6.9 63 353-415 2-65 (65)
16 KOG2279 Kinase anchor protein 99.4 1.8E-12 3.8E-17 130.1 12.8 294 44-416 62-364 (608)
17 cd02394 vigilin_like_KH K homo 99.4 6.9E-13 1.5E-17 98.8 6.0 61 353-415 2-62 (62)
18 PF00013 KH_1: KH domain syndr 99.4 5.3E-13 1.1E-17 98.7 5.2 60 352-414 1-60 (60)
19 cd00105 KH-I K homology RNA-bi 99.3 2.7E-12 5.8E-17 96.0 7.4 63 353-415 2-64 (64)
20 cd02393 PNPase_KH Polynucleoti 99.3 2.7E-12 5.8E-17 95.2 7.1 59 351-415 2-61 (61)
21 cd02396 PCBP_like_KH K homolog 99.3 4.9E-12 1.1E-16 95.1 7.2 65 135-203 1-65 (65)
22 cd02394 vigilin_like_KH K homo 99.2 2.8E-11 6.1E-16 90.0 5.6 61 136-203 2-62 (62)
23 cd02393 PNPase_KH Polynucleoti 99.1 2.4E-10 5.1E-15 84.7 7.7 58 134-202 2-60 (61)
24 PF00013 KH_1: KH domain syndr 99.1 6E-11 1.3E-15 87.7 4.3 60 135-202 1-60 (60)
25 cd00105 KH-I K homology RNA-bi 99.1 5.8E-10 1.3E-14 83.2 7.7 62 136-202 2-63 (64)
26 COG1094 Predicted RNA-binding 99.1 3.4E-09 7.4E-14 94.8 13.5 140 48-209 6-165 (194)
27 smart00322 KH K homology RNA-b 99.0 1.3E-09 2.9E-14 81.6 8.9 67 351-419 3-69 (69)
28 PF13014 KH_3: KH domain 99.0 6.4E-10 1.4E-14 76.4 5.2 42 361-402 1-43 (43)
29 PF13014 KH_3: KH domain 99.0 8.1E-10 1.8E-14 75.9 5.2 42 60-101 1-43 (43)
30 KOG2208 Vigilin [Lipid transpo 99.0 2.3E-09 4.9E-14 116.2 10.6 224 48-418 199-486 (753)
31 KOG2279 Kinase anchor protein 98.8 2.9E-09 6.2E-14 107.3 4.3 145 131-420 65-209 (608)
32 smart00322 KH K homology RNA-b 98.8 3.2E-08 6.9E-13 74.0 8.7 66 134-206 3-68 (69)
33 KOG2208 Vigilin [Lipid transpo 98.7 2.1E-08 4.6E-13 108.7 8.6 146 46-209 343-489 (753)
34 COG1094 Predicted RNA-binding 98.6 5.8E-07 1.3E-11 80.6 12.3 53 361-420 112-164 (194)
35 KOG2113 Predicted RNA binding 98.6 5.5E-08 1.2E-12 91.8 5.8 149 132-411 24-173 (394)
36 cd02395 SF1_like-KH Splicing f 98.5 2.9E-07 6.3E-12 77.5 7.2 61 360-420 15-95 (120)
37 KOG2113 Predicted RNA binding 98.5 1.3E-07 2.9E-12 89.3 4.0 151 45-206 21-181 (394)
38 cd02395 SF1_like-KH Splicing f 98.3 1.9E-06 4E-11 72.6 7.6 73 137-209 3-96 (120)
39 PRK08406 transcription elongat 98.2 3.9E-06 8.5E-11 72.7 6.7 100 51-170 33-135 (140)
40 TIGR02696 pppGpp_PNP guanosine 98.0 3.2E-05 7E-10 82.8 11.0 63 351-419 578-641 (719)
41 PRK08406 transcription elongat 97.7 6.1E-05 1.3E-09 65.3 5.7 39 134-172 32-70 (140)
42 TIGR02696 pppGpp_PNP guanosine 97.7 0.00015 3.3E-09 77.8 9.4 65 133-208 577-642 (719)
43 TIGR01952 nusA_arch NusA famil 97.7 0.00014 3.1E-09 62.8 7.3 100 51-170 34-136 (141)
44 KOG0119 Splicing factor 1/bran 97.5 0.00067 1.4E-08 68.5 10.6 76 133-208 137-230 (554)
45 TIGR03591 polynuc_phos polyrib 97.5 0.00016 3.4E-09 78.5 6.3 65 349-419 549-614 (684)
46 KOG0119 Splicing factor 1/bran 97.3 0.00057 1.2E-08 68.9 7.2 63 360-422 153-232 (554)
47 KOG0336 ATP-dependent RNA heli 97.2 0.00027 5.9E-09 70.1 4.1 80 18-103 16-97 (629)
48 TIGR03591 polynuc_phos polyrib 97.2 0.00093 2E-08 72.6 8.6 65 133-208 550-615 (684)
49 TIGR03319 YmdA_YtgF conserved 97.2 0.00095 2.1E-08 70.1 7.7 69 349-422 202-272 (514)
50 PRK00106 hypothetical protein; 97.1 0.0012 2.6E-08 69.1 7.9 69 349-422 223-293 (535)
51 KOG0336 ATP-dependent RNA heli 97.0 0.00073 1.6E-08 67.1 4.7 70 131-208 44-113 (629)
52 KOG2814 Transcription coactiva 97.0 0.00084 1.8E-08 64.8 5.0 69 350-420 56-125 (345)
53 PRK04163 exosome complex RNA-b 97.0 0.0015 3.3E-08 61.8 6.6 65 353-423 147-212 (235)
54 TIGR01952 nusA_arch NusA famil 97.0 0.0015 3.3E-08 56.5 5.9 37 351-387 100-136 (141)
55 PLN00207 polyribonucleotide nu 97.0 0.00071 1.5E-08 74.3 4.7 64 350-419 684-749 (891)
56 KOG1588 RNA-binding protein Sa 97.0 0.00098 2.1E-08 62.6 4.8 41 46-86 88-134 (259)
57 COG0195 NusA Transcription elo 96.9 0.0017 3.6E-08 59.1 5.7 98 53-171 79-179 (190)
58 PRK12704 phosphodiesterase; Pr 96.9 0.0025 5.5E-08 67.0 7.8 68 350-422 209-278 (520)
59 COG1185 Pnp Polyribonucleotide 96.9 0.0016 3.5E-08 68.7 6.0 65 349-419 550-615 (692)
60 cd02134 NusA_KH NusA_K homolog 96.9 0.0017 3.8E-08 47.9 4.5 37 49-85 24-60 (61)
61 PF14611 SLS: Mitochondrial in 96.8 0.042 9.2E-07 50.9 14.3 64 136-209 28-91 (210)
62 KOG1588 RNA-binding protein Sa 96.8 0.0043 9.4E-08 58.3 7.4 39 349-387 90-134 (259)
63 COG1185 Pnp Polyribonucleotide 96.8 0.0027 5.8E-08 67.1 6.6 66 133-209 551-617 (692)
64 PLN00207 polyribonucleotide nu 96.7 0.0025 5.3E-08 70.2 6.2 65 133-208 684-750 (891)
65 cd02134 NusA_KH NusA_K homolog 96.6 0.0031 6.7E-08 46.5 4.2 36 351-386 25-60 (61)
66 TIGR01953 NusA transcription t 96.4 0.0054 1.2E-07 61.0 5.7 93 59-172 243-339 (341)
67 KOG2814 Transcription coactiva 96.4 0.0044 9.6E-08 59.9 4.6 65 49-124 56-120 (345)
68 PRK12328 nusA transcription el 96.2 0.017 3.7E-07 57.7 8.2 94 59-173 251-347 (374)
69 PRK00468 hypothetical protein; 96.2 0.0057 1.2E-07 47.0 3.5 34 46-79 26-59 (75)
70 PRK12705 hypothetical protein; 96.0 0.0081 1.8E-07 62.7 5.0 68 350-422 197-266 (508)
71 PRK12327 nusA transcription el 96.0 0.011 2.4E-07 59.3 5.8 94 59-172 245-341 (362)
72 KOG4369 RTK signaling protein 96.0 0.0025 5.4E-08 70.1 1.1 70 349-418 1338-1408(2131)
73 PRK11824 polynucleotide phosph 96.0 0.006 1.3E-07 66.5 3.9 63 351-419 554-617 (693)
74 PRK02821 hypothetical protein; 95.9 0.0078 1.7E-07 46.5 3.2 34 48-81 29-62 (77)
75 COG0195 NusA Transcription elo 95.9 0.019 4.1E-07 52.2 6.2 37 352-388 143-179 (190)
76 PRK04163 exosome complex RNA-b 95.9 0.019 4E-07 54.4 6.2 63 136-209 147-210 (235)
77 PRK12329 nusA transcription el 95.8 0.0093 2E-07 60.6 4.3 92 59-171 277-372 (449)
78 COG1837 Predicted RNA-binding 95.8 0.011 2.3E-07 45.4 3.4 32 47-78 27-58 (76)
79 PRK11824 polynucleotide phosph 95.7 0.015 3.2E-07 63.6 5.6 64 134-208 554-618 (693)
80 PRK09202 nusA transcription el 95.6 0.024 5.1E-07 58.9 6.5 93 59-172 245-340 (470)
81 COG5176 MSL5 Splicing factor ( 95.4 0.016 3.5E-07 52.4 3.8 40 48-87 146-191 (269)
82 COG5176 MSL5 Splicing factor ( 95.3 0.021 4.5E-07 51.7 4.1 37 351-387 148-190 (269)
83 PRK01064 hypothetical protein; 95.2 0.024 5.2E-07 43.9 3.6 33 47-79 27-59 (78)
84 PRK00468 hypothetical protein; 95.1 0.023 5E-07 43.7 3.3 31 350-380 29-59 (75)
85 PRK02821 hypothetical protein; 95.1 0.023 5E-07 43.9 3.2 32 350-381 30-61 (77)
86 TIGR01953 NusA transcription t 95.0 0.056 1.2E-06 53.9 6.5 37 351-387 301-337 (341)
87 TIGR03319 YmdA_YtgF conserved 94.9 0.065 1.4E-06 56.5 7.2 65 134-208 204-270 (514)
88 PRK00106 hypothetical protein; 94.9 0.072 1.6E-06 56.1 7.4 65 134-208 225-291 (535)
89 PRK12704 phosphodiesterase; Pr 94.9 0.072 1.6E-06 56.2 7.4 66 134-209 210-277 (520)
90 PRK12328 nusA transcription el 94.7 0.049 1.1E-06 54.5 5.3 37 351-387 308-344 (374)
91 PF14611 SLS: Mitochondrial in 94.7 0.52 1.1E-05 43.6 11.8 127 53-207 29-164 (210)
92 PRK12327 nusA transcription el 94.5 0.08 1.7E-06 53.2 6.4 37 351-387 303-339 (362)
93 COG1837 Predicted RNA-binding 94.2 0.052 1.1E-06 41.7 3.3 32 349-380 28-59 (76)
94 PRK09202 nusA transcription el 94.1 0.1 2.2E-06 54.3 6.3 38 351-388 302-339 (470)
95 PRK12329 nusA transcription el 93.7 0.1 2.2E-06 53.2 5.3 37 351-387 335-371 (449)
96 PRK01064 hypothetical protein; 93.7 0.074 1.6E-06 41.2 3.3 32 349-380 28-59 (78)
97 PF13083 KH_4: KH domain; PDB: 93.2 0.042 9E-07 41.9 1.3 36 48-83 27-62 (73)
98 KOG1067 Predicted RNA-binding 93.1 0.34 7.3E-06 50.4 7.8 63 351-420 597-660 (760)
99 KOG3273 Predicted RNA-binding 92.7 0.23 5.1E-06 44.8 5.4 137 51-209 75-232 (252)
100 cd02409 KH-II KH-II (K homolo 92.1 0.24 5.1E-06 36.4 4.1 35 49-83 24-58 (68)
101 KOG4369 RTK signaling protein 91.9 0.19 4E-06 56.1 4.4 56 51-106 1341-1397(2131)
102 KOG2874 rRNA processing protei 90.9 0.48 1E-05 45.0 5.5 53 363-422 161-213 (356)
103 COG1097 RRP4 RNA-binding prote 90.5 0.51 1.1E-05 44.2 5.3 47 53-105 149-195 (239)
104 PF13184 KH_5: NusA-like KH do 90.4 0.19 4.2E-06 37.9 2.1 34 53-86 6-45 (69)
105 COG1097 RRP4 RNA-binding prote 90.3 0.56 1.2E-05 43.9 5.4 47 353-405 148-194 (239)
106 PF13083 KH_4: KH domain; PDB: 89.6 0.19 4.1E-06 38.3 1.5 33 350-382 28-60 (73)
107 KOG2874 rRNA processing protei 89.6 0.55 1.2E-05 44.6 4.7 52 146-209 161-212 (356)
108 PRK12705 hypothetical protein; 89.2 0.64 1.4E-05 48.8 5.5 35 136-170 200-235 (508)
109 KOG1067 Predicted RNA-binding 88.6 1.5 3.2E-05 45.8 7.4 66 132-209 595-661 (760)
110 PF07650 KH_2: KH domain syndr 88.6 0.28 6.1E-06 37.7 1.8 34 51-84 26-59 (78)
111 cd02414 jag_KH jag_K homology 88.5 0.44 9.6E-06 36.7 2.9 35 51-85 25-59 (77)
112 cd02409 KH-II KH-II (K homolo 88.4 0.82 1.8E-05 33.4 4.3 34 351-384 25-58 (68)
113 PF13184 KH_5: NusA-like KH do 87.4 0.57 1.2E-05 35.4 2.8 36 353-388 5-46 (69)
114 KOG3273 Predicted RNA-binding 87.2 0.32 6.9E-06 44.0 1.5 53 360-419 178-230 (252)
115 PF07650 KH_2: KH domain syndr 86.0 0.49 1.1E-05 36.4 1.9 34 351-384 25-58 (78)
116 COG1855 ATPase (PilT family) [ 85.1 0.61 1.3E-05 47.7 2.4 36 52-87 488-523 (604)
117 PRK13764 ATPase; Provisional 84.5 2.3 5E-05 45.7 6.7 42 134-175 481-522 (602)
118 cd02413 40S_S3_KH K homology R 84.4 1.1 2.4E-05 34.9 3.2 35 51-85 31-65 (81)
119 COG5166 Uncharacterized conser 83.7 1.6 3.5E-05 45.0 4.8 120 51-170 450-607 (657)
120 PRK06418 transcription elongat 82.7 1.6 3.5E-05 38.8 3.9 44 42-87 54-97 (166)
121 PRK13764 ATPase; Provisional 81.9 1 2.2E-05 48.3 2.8 37 51-87 482-518 (602)
122 cd02414 jag_KH jag_K homology 81.4 1.8 3.9E-05 33.2 3.3 33 135-167 25-57 (77)
123 cd02410 archeal_CPSF_KH The ar 80.8 2.8 6E-05 36.3 4.5 87 66-172 22-114 (145)
124 COG1855 ATPase (PilT family) [ 80.6 1.2 2.6E-05 45.6 2.6 37 351-387 486-522 (604)
125 cd02412 30S_S3_KH K homology R 79.7 1.7 3.6E-05 35.9 2.8 31 52-82 63-93 (109)
126 cd02413 40S_S3_KH K homology R 77.3 2.9 6.3E-05 32.6 3.3 36 351-386 30-65 (81)
127 cd02411 archeal_30S_S3_KH K ho 76.4 2.8 6.1E-05 32.9 3.0 28 52-79 40-67 (85)
128 cd02410 archeal_CPSF_KH The ar 74.9 3.9 8.4E-05 35.4 3.7 39 350-388 75-113 (145)
129 PRK06418 transcription elongat 72.8 4.6 0.0001 36.0 3.8 36 136-172 63-98 (166)
130 COG0092 RpsC Ribosomal protein 70.7 3.7 8E-05 38.4 2.8 30 51-80 52-81 (233)
131 cd02412 30S_S3_KH K homology R 66.7 5.3 0.00011 32.9 2.7 28 353-380 63-90 (109)
132 cd02411 archeal_30S_S3_KH K ho 65.4 6.7 0.00014 30.7 2.9 28 353-380 40-67 (85)
133 COG1782 Predicted metal-depend 64.3 21 0.00047 37.2 6.9 39 351-389 99-137 (637)
134 COG0092 RpsC Ribosomal protein 63.9 6.3 0.00014 36.9 2.9 36 351-386 51-91 (233)
135 COG5166 Uncharacterized conser 61.9 6.3 0.00014 40.9 2.7 128 63-209 393-525 (657)
136 COG1782 Predicted metal-depend 61.5 17 0.00036 38.0 5.6 90 63-172 42-137 (637)
137 PRK03818 putative transporter; 55.2 1.8E+02 0.0038 31.2 12.4 129 51-201 206-358 (552)
138 COG1702 PhoH Phosphate starvat 52.2 37 0.00081 33.8 6.2 50 359-415 23-72 (348)
139 TIGR03802 Asp_Ala_antiprt aspa 50.6 3.5E+02 0.0076 29.1 15.9 131 50-201 218-375 (562)
140 TIGR01008 rpsC_E_A ribosomal p 49.1 18 0.00038 33.2 3.2 31 51-81 39-69 (195)
141 TIGR00436 era GTP-binding prot 48.8 19 0.00041 34.5 3.6 31 350-380 220-251 (270)
142 PRK04191 rps3p 30S ribosomal p 48.3 18 0.00039 33.5 3.2 31 52-82 42-72 (207)
143 CHL00048 rps3 ribosomal protei 48.0 18 0.0004 33.6 3.2 30 51-80 67-96 (214)
144 TIGR03675 arCOG00543 arCOG0054 46.9 25 0.00054 38.3 4.5 38 135-172 94-131 (630)
145 TIGR00436 era GTP-binding prot 45.5 26 0.00055 33.6 3.9 29 50-78 221-250 (270)
146 TIGR03675 arCOG00543 arCOG0054 45.4 16 0.00035 39.7 2.8 40 350-389 92-131 (630)
147 PTZ00084 40S ribosomal protein 44.2 40 0.00087 31.5 4.8 32 52-83 46-77 (220)
148 COG1847 Jag Predicted RNA-bind 43.8 13 0.00027 34.3 1.4 35 51-85 92-126 (208)
149 KOG1423 Ras-like GTPase ERA [C 43.7 23 0.0005 34.9 3.2 32 349-380 326-358 (379)
150 PF09869 DUF2096: Uncharacteri 42.9 1.2E+02 0.0026 27.0 7.2 57 131-205 110-166 (169)
151 PRK15494 era GTPase Era; Provi 42.6 26 0.00057 34.9 3.6 37 351-387 273-318 (339)
152 PRK00089 era GTPase Era; Revie 41.6 28 0.00061 33.6 3.6 37 351-387 226-271 (292)
153 PRK15494 era GTPase Era; Provi 38.4 37 0.0008 33.8 3.9 36 50-85 273-317 (339)
154 COG1159 Era GTPase [General fu 38.1 35 0.00076 33.3 3.5 37 351-387 229-274 (298)
155 PF02749 QRPTase_N: Quinolinat 36.0 1.1E+02 0.0023 23.9 5.5 55 152-208 32-86 (88)
156 PRK00089 era GTPase Era; Revie 34.7 28 0.00061 33.6 2.4 36 50-85 226-270 (292)
157 COG1847 Jag Predicted RNA-bind 34.6 72 0.0016 29.5 4.7 69 351-422 91-165 (208)
158 PRK04972 putative transporter; 34.1 6.2E+02 0.013 27.2 12.9 133 51-202 215-371 (558)
159 PRK04191 rps3p 30S ribosomal p 34.1 38 0.00082 31.4 3.0 28 353-380 42-69 (207)
160 TIGR01008 rpsC_E_A ribosomal p 34.1 40 0.00088 30.9 3.1 29 352-380 39-67 (195)
161 PF02749 QRPTase_N: Quinolinat 33.7 1.5E+02 0.0034 23.0 6.1 51 369-419 32-85 (88)
162 TIGR01009 rpsC_bact ribosomal 33.3 40 0.00087 31.3 3.0 29 52-80 64-92 (211)
163 COG1159 Era GTPase [General fu 33.2 54 0.0012 32.0 3.9 36 50-85 229-273 (298)
164 PTZ00084 40S ribosomal protein 31.8 43 0.00093 31.3 2.9 28 353-380 46-73 (220)
165 CHL00048 rps3 ribosomal protei 31.8 47 0.001 30.9 3.2 29 352-380 67-95 (214)
166 KOG1423 Ras-like GTPase ERA [C 30.1 54 0.0012 32.4 3.3 33 134-166 328-361 (379)
167 COG1702 PhoH Phosphate starvat 29.4 1.2E+02 0.0026 30.3 5.7 51 141-203 22-72 (348)
168 PF03958 Secretin_N: Bacterial 29.1 1.5E+02 0.0032 22.3 5.2 33 380-417 44-76 (82)
169 PRK15468 carboxysome structura 26.8 1.8E+02 0.0038 24.0 5.2 44 158-210 57-101 (111)
170 COG4010 Uncharacterized protei 26.7 1.7E+02 0.0037 25.4 5.4 42 154-206 126-167 (170)
171 COG3140 Uncharacterized protei 25.5 91 0.002 22.3 2.9 22 403-424 9-30 (60)
172 PRK00310 rpsC 30S ribosomal pr 24.4 67 0.0014 30.3 2.8 29 52-80 64-92 (232)
173 COG0331 FabD (acyl-carrier-pro 22.0 1.7E+02 0.0038 28.8 5.3 54 361-417 132-187 (310)
174 TIGR01009 rpsC_bact ribosomal 21.7 83 0.0018 29.2 2.9 28 353-380 64-91 (211)
175 PF02080 TrkA_C: TrkA-C domain 21.1 1.1E+02 0.0024 22.2 3.0 49 153-201 14-69 (71)
176 PF10369 ALS_ss_C: Small subun 20.8 1.8E+02 0.004 22.0 4.2 43 370-416 16-58 (75)
No 1
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=7.2e-40 Score=297.87 Aligned_cols=330 Identities=24% Similarity=0.394 Sum_probs=229.5
Q ss_pred CCCcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHH
Q 014452 41 RNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVH 120 (424)
Q Consensus 41 ~~~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~ 120 (424)
..+.+....+.++||+.++.+|+||||+|++||.|+.+++|.|+|++. +.++|+++|+...+ .+..++
T Consensus 39 ~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~----------ti~~il 106 (390)
T KOG2192|consen 39 EEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIE----------TIGEIL 106 (390)
T ss_pred HHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHH----------HHHHHH
Confidence 455666678999999999999999999999999999999999999988 58999999998843 444444
Q ss_pred HHHH---hhcCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHH
Q 014452 121 SRIA---EIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQD 197 (424)
Q Consensus 121 ~~i~---e~~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~ 197 (424)
..+. |.++.....|+++|+|..+++|.|||++|+.||+|++++.|+++|+.. .|+.+++|+|.|.|.+++|..
T Consensus 107 k~iip~lee~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~----c~p~stdrv~l~~g~~k~v~~ 182 (390)
T KOG2192|consen 107 KKIIPTLEEGFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE----CCPHSTDRVVLIGGKPKRVVE 182 (390)
T ss_pred HHHhhhhhhCCCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc----cCCCCcceEEEecCCcchHHH
Confidence 4432 456777788999999999999999999999999999999999999864 477799999999999999999
Q ss_pred HHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCC
Q 014452 198 ALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHG 277 (424)
Q Consensus 198 A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g 277 (424)
+++.|+++|.+. |.+...+||.|.|++... ..+.|..+.+...+ ...|+.++. |
T Consensus 183 ~i~~il~~i~e~------pikgsa~py~p~fyd~t~----------dyggf~M~f~d~pg------~pgpapqrg----g 236 (390)
T KOG2192|consen 183 CIKIILDLISES------PIKGSAQPYDPNFYDETY----------DYGGFTMMFDDRPG------RPGPAPQRG----G 236 (390)
T ss_pred HHHHHHHHhhcC------CcCCcCCcCCccccCccc----------ccCCceeecCCCCC------CCCCCCCCC----C
Confidence 999999999987 677888999999877431 11222211111100 001111110 0
Q ss_pred CCCCCCCCCCCCCCCCCC------CCCCCCCCCC------CCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCC-CCCCC
Q 014452 278 MDPMVPPNSDRIPFPYGS------ERPGHGPTFD------RPPSPRSWTPQGVG-GGDPRGFDASSGFTPRNRP-VESGN 343 (424)
Q Consensus 278 ~~~~~~~~~~~~~~~~g~------~~~g~~~~~~------~~~~p~~~~~~~~~-~g~~~g~~~~~~~~~r~~~-~~~g~ 343 (424)
.++-++.......+..++ ..-+....+. ..-.|..|....-- +|..+.+ ...+ .++..
T Consensus 237 qgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydy--------syAG~~GsYG 308 (390)
T KOG2192|consen 237 QGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDY--------SYAGGYGSYG 308 (390)
T ss_pred CCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCc--------cccccccccC
Confidence 000000000000000000 0000000000 01133334322211 1111111 1111 11100
Q ss_pred ccccCcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452 344 HAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG 421 (424)
Q Consensus 344 ~~~~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~ 421 (424)
... ..-+|.+|+||.++-|.||||+|.+|++|++++||.|+|+++.+++.+|+|+|+||.+|++.||+|++++|.++
T Consensus 309 dlG-GPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 309 DLG-GPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred CCC-CceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 101 23578999999999999999999999999999999999999999999999999999999999999999999865
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=4.7e-34 Score=286.58 Aligned_cols=239 Identities=23% Similarity=0.363 Sum_probs=192.2
Q ss_pred CccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccC-C-CCCcccEEEeecccccccccChhHHHHHHHHHHHH
Q 014452 47 EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI-L-PDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA 124 (424)
Q Consensus 47 ~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-~-~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~ 124 (424)
+.+++..|+||.+.+|+||||+|++||+|++++||++.+-+. . .....+.+.|+|.+..++. +...+++.|.
T Consensus 136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~------a~~lV~dil~ 209 (600)
T KOG1676|consen 136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQ------AKQLVADILR 209 (600)
T ss_pred ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHH------HHHHHHHHHH
Confidence 677899999999999999999999999999999999887633 2 2337789999999987765 3344444444
Q ss_pred hhcC-----------CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHH
Q 014452 125 EIGF-----------EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 193 (424)
Q Consensus 125 e~~~-----------~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~ 193 (424)
|... ......++++.||...||.||||+|++||+|+.+||++|+|.++++ | .+.||.+.|.|+.+
T Consensus 210 e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~~~IiG~~d 285 (600)
T KOG1676|consen 210 EEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERPAQIIGTVD 285 (600)
T ss_pred hcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccceeeeecCHH
Confidence 3211 1223558999999999999999999999999999999999987543 3 47899999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 014452 194 SVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAA 273 (424)
Q Consensus 194 ~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~ 273 (424)
+|+.|.++|.++|++.....
T Consensus 286 ~ie~Aa~lI~eii~~~~~~~------------------------------------------------------------ 305 (600)
T KOG1676|consen 286 QIEHAAELINEIIAEAEAGA------------------------------------------------------------ 305 (600)
T ss_pred HHHHHHHHHHHHHHHHhccC------------------------------------------------------------
Confidence 99999999999999872100
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEE
Q 014452 274 FSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTI 353 (424)
Q Consensus 274 ~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~ 353 (424)
+. .| ++|.. .....+
T Consensus 306 ---~~---------------------------------~~-----~~G~P------------------------~~~~~f 320 (600)
T KOG1676|consen 306 ---GG---------------------------------GM-----GGGAP------------------------GLVAQF 320 (600)
T ss_pred ---CC---------------------------------Cc-----CCCCc------------------------cceeeE
Confidence 00 00 00000 011278
Q ss_pred EEEeccCcccceeccccchHHHHHHHhCCEEEEeCC--CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452 354 EVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP--KPGATEGVVMVSGTSDQMRAAQSLIHAFILC 420 (424)
Q Consensus 354 ~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~--~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~ 420 (424)
+|.||...+|+||||+|++||.|..+|||++.+... .....+++|+|+|++.+|+.|+.||+++|..
T Consensus 321 y~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~ 389 (600)
T KOG1676|consen 321 YMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD 389 (600)
T ss_pred EEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence 999999999999999999999999999999999843 3456799999999999999999999999864
No 3
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=9.6e-33 Score=277.18 Aligned_cols=258 Identities=20% Similarity=0.260 Sum_probs=198.4
Q ss_pred CCCCCCCCCCc--CCC-ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccC
Q 014452 34 GHETVGGRNRM--FYE-EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHS 110 (424)
Q Consensus 34 ~~~~~~~~~~~--~~~-~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~ 110 (424)
+-+....++++ ... ..++.+..||.+.||.||||+|+.|..|..++||+|++........+|.|.++|.++.+..++
T Consensus 35 ~~~~~~~~l~p~~~~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK 114 (600)
T KOG1676|consen 35 KGPSEDTDLDPDMDPSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAK 114 (600)
T ss_pred cCCCCccccCcccCCcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHH
Confidence 33344445552 233 445789999999999999999999999999999999988665577899999999998876522
Q ss_pred hhHHHHHHHHHHHHh-hcC---CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEE
Q 014452 111 PAQDAVMRVHSRIAE-IGF---EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV 186 (424)
Q Consensus 111 ~a~~av~~~~~~i~e-~~~---~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v 186 (424)
.-+..+.++.+. ..+ ....+++.+++||.+.+|+||||+|++||.|++++||++.+..+.+.. ...++.+
T Consensus 115 ---~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~---~~~~Kpl 188 (600)
T KOG1676|consen 115 ---QLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA---TGADKPL 188 (600)
T ss_pred ---HhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC---CCCCCce
Confidence 222222222221 111 123568899999999999999999999999999999999888765432 2478899
Q ss_pred EEEeCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452 187 QVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQ 266 (424)
Q Consensus 187 ~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 266 (424)
.|+|+++.|+.|+.||.++|++.... .|+.. +
T Consensus 189 ritGdp~~ve~a~~lV~dil~e~~~~----------------------~~g~~------~-------------------- 220 (600)
T KOG1676|consen 189 RITGDPDKVEQAKQLVADILREEDDE----------------------VPGSG------G-------------------- 220 (600)
T ss_pred eecCCHHHHHHHHHHHHHHHHhcccC----------------------CCccc------c--------------------
Confidence 99999999999999999999986110 00000 0
Q ss_pred CCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 014452 267 PFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA 346 (424)
Q Consensus 267 ~~~~q~~~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~ 346 (424)
.+| ..
T Consensus 221 -------------------------~~g---------------------------~~----------------------- 225 (600)
T KOG1676|consen 221 -------------------------HAG---------------------------VR----------------------- 225 (600)
T ss_pred -------------------------ccC---------------------------cC-----------------------
Confidence 000 00
Q ss_pred cCcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC-CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452 347 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILC 420 (424)
Q Consensus 347 ~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~-~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~ 420 (424)
.....+.+|.||...||.||||+|++||+|+.+||++|+|-.+ .+.+.||.+.|.|++++|++|.+||.++|++
T Consensus 226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~ 300 (600)
T KOG1676|consen 226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAE 300 (600)
T ss_pred ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence 0113589999999999999999999999999999999999733 3357899999999999999999999999985
No 4
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=3.4e-31 Score=269.85 Aligned_cols=352 Identities=27% Similarity=0.382 Sum_probs=217.4
Q ss_pred ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhc
Q 014452 48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIG 127 (424)
Q Consensus 48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~ 127 (424)
...++||||+.+.+|.||||+|.+||+|+.+|.++|+|.+..+++.+|+|+|+|..... ..+++.+++.++++++....
T Consensus 41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKL 119 (485)
T ss_pred CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhcc
Confidence 33348999999999999999999999999999999999999999999999999952222 55567899999999876521
Q ss_pred ------C------CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHH
Q 014452 128 ------F------EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSV 195 (424)
Q Consensus 128 ------~------~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v 195 (424)
. ....+++++|+||..++|+||||+|+.||+|+++|||+|+|.++ .+|. .++|.|+|.|.+++|
T Consensus 120 ~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av 195 (485)
T KOG2190|consen 120 EEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAV 195 (485)
T ss_pred cccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHH
Confidence 1 11225889999999999999999999999999999999999865 7777 588999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCccc
Q 014452 196 QDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPS--QPFDHQAA 273 (424)
Q Consensus 196 ~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--~~~~~q~~ 273 (424)
.+|+..|..+|.+..-. ..+......+|.|+.+...+....-.+... .+. +.+. ....+..... .|.+. ..
T Consensus 196 ~~al~~Is~~L~~~~~~-~~~~~~st~~y~P~~~~~~~~~~s~~~~~~---~~~-~~~~-~~~~~e~~~~~~~p~~~-~~ 268 (485)
T KOG2190|consen 196 KKALVQISSRLLENPPR-SPPPLVSTIPYRPSASQGGPVLPSTAQTSP---DAH-PFGG-IVPEEELVFKLICPSDK-VG 268 (485)
T ss_pred HHHHHHHHHHHHhcCCc-CCCCCCCcccCCCcccccCccccccccCCc---ccc-cccc-cccchhhhhhhcCchhh-ce
Confidence 99999999999996321 223334455665521111111111000000 000 0000 0000000000 00000 00
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCccccCcc
Q 014452 274 FSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGV---GGGDPRGFDASSGFTPRNRPVESGNHAAILTS 350 (424)
Q Consensus 274 ~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~---~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~ 350 (424)
...|.+...-...... .+..-.+..+.....-+.++. ...-.+..++......+-.+ .....+ ...
T Consensus 269 ~v~g~~~~~i~~l~~~--------~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~--~~~~~~-~~~ 337 (485)
T KOG2190|consen 269 SVIGKGGLVIRALRNE--------TGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISE--NAGDDL-TQT 337 (485)
T ss_pred eeecCCCccchhhhhh--------cCCceEeccccCcceeeeccccCcccccccchhhhhhccccccc--cccccc-cce
Confidence 0000000000000000 000000000000000000000 00000000000000000000 000111 346
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCC--CCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP--GATEGVVMVSGTSDQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~--~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~ 422 (424)
++.++.||.+++|+||||+|++|.+||+.|||.|.|.+..+ ...++.++|+|+..+...|+++|..++....
T Consensus 338 v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~ 411 (485)
T KOG2190|consen 338 VTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSAPK 411 (485)
T ss_pred eeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccccCc
Confidence 88999999999999999999999999999999999997655 6789999999999999999999988877543
No 5
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=2.5e-30 Score=248.50 Aligned_cols=285 Identities=19% Similarity=0.294 Sum_probs=203.5
Q ss_pred CCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEecc-CCCCCcccEEEeecccccccccChhHHHHHHHHHHHH
Q 014452 46 YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD-ILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA 124 (424)
Q Consensus 46 ~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~-~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~ 124 (424)
...++.+|++||...||.||||.|+|||.|-..|.|+|.|.. ...+..|+.++|-++++...+ |+..+++.+.
T Consensus 195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~------Ac~~ILeimq 268 (584)
T KOG2193|consen 195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSK------ACKMILEIMQ 268 (584)
T ss_pred cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHH------HHHHHHHHHH
Confidence 357788999999999999999999999999999999999983 334788999999999887544 5666665554
Q ss_pred hhc--CCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 014452 125 EIG--FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI 202 (424)
Q Consensus 125 e~~--~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 202 (424)
... .+...++.++++-.+.+||++|||.|.+||+|+.+||++|.|.+--++-. -..||.+++.|+.|+|..|..+|
T Consensus 269 kEA~~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERTItVkGsiEac~~AE~eI 346 (584)
T KOG2193|consen 269 KEAVDDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERTITVKGSIEACVQAEAEI 346 (584)
T ss_pred HhhhccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccceEEecccHHHHHHHHHHH
Confidence 332 22346677889999999999999999999999999999999987544422 25699999999999999999999
Q ss_pred HHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCC
Q 014452 203 TSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMV 282 (424)
Q Consensus 203 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~ 282 (424)
..+|++...++-.. .+...+++| +.+..-.|.|.+......|+.+-.+
T Consensus 347 mkKlre~yEnDl~a-~s~q~~l~P-------------------~l~~~~l~~f~ssS~~~~Ph~~Ps~------------ 394 (584)
T KOG2193|consen 347 MKKLRECYENDLAA-MSLQCHLPP-------------------GLNLPALGLFPSSSAVSPPHFPPSP------------ 394 (584)
T ss_pred HHHHHHHHhhhHHH-hhccCCCCc-------------------ccCccccCCCCcccccCCCCCCCCc------------
Confidence 99999874332110 011111111 0000000111000000000000000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcc
Q 014452 283 PPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYM 362 (424)
Q Consensus 283 ~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~ 362 (424)
.+ |. ++.|... ...+.....+.||...+
T Consensus 395 ----------------v~---~a-~p~~~~h--------------------------------q~pe~e~V~~fiP~~~v 422 (584)
T KOG2193|consen 395 ----------------VT---FA-SPYPLFH--------------------------------QNPEQEQVRMFIPAQAV 422 (584)
T ss_pred ----------------cc---cC-CCchhhh--------------------------------cCcchhheeeeccHHHH
Confidence 00 00 0000000 01235678999999999
Q ss_pred cceeccccchHHHHHHHhCCEEEEeCC-CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452 363 AHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 363 g~IIGk~G~~Ik~Ir~~SGa~I~i~~~-~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~ 422 (424)
|.|||+.|.+||+|.+.+||.|+|..+ -++..+|+|+|+|.+++.-+|+..|..+|+++-
T Consensus 423 GAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 423 GAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred HHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence 999999999999999999999999754 355789999999999999999999999998764
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=1.1e-28 Score=237.36 Aligned_cols=243 Identities=22% Similarity=0.372 Sum_probs=190.2
Q ss_pred CcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEec---cCCCCCcccEEEeecccccccccChh-HHHHHH
Q 014452 43 RMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENSEMRHSPA-QDAVMR 118 (424)
Q Consensus 43 ~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~---~~~~~~~er~v~I~G~~~~~~~~~~a-~~av~~ 118 (424)
+....+++.++++-++.+||++|||.|++||+|+++||++|.|+ +-..-++||.|+|.|..++|..+... +..+.+
T Consensus 273 ~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre 352 (584)
T KOG2193|consen 273 DDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRE 352 (584)
T ss_pred ccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHH
Confidence 34455889999999999999999999999999999999999998 33345679999999987776542111 111222
Q ss_pred HHHH-HHhh---------------c-CC-----------C---------------CcceEEEEEecCCCcceeeccCCch
Q 014452 119 VHSR-IAEI---------------G-FE-----------P---------------GQAVVARLLVHSQQIGCLLGRGGHI 155 (424)
Q Consensus 119 ~~~~-i~e~---------------~-~~-----------~---------------~~~~t~~l~IP~~~vg~IIGkgG~~ 155 (424)
+++. +... + +. + .....++|.||...+|.|||++|..
T Consensus 353 ~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~h 432 (584)
T KOG2193|consen 353 CYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQH 432 (584)
T ss_pred HHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchh
Confidence 2221 0000 0 00 0 1234578999999999999999999
Q ss_pred HHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452 156 VSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPP 235 (424)
Q Consensus 156 Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (424)
||.|.+.+||.|+|.+.+ . +...+|.|+|+|++++..+|...|+.+|.|+.+- .|
T Consensus 433 IKql~RfagASiKIappE-~---pdvseRMViItGppeaqfKAQgrifgKikEenf~------------~P--------- 487 (584)
T KOG2193|consen 433 IKQLSRFAGASIKIAPPE-I---PDVSERMVIITGPPEAQFKAQGRIFGKIKEENFF------------LP--------- 487 (584)
T ss_pred HHHHHHhccceeeecCCC-C---CCcceeEEEecCChHHHHhhhhhhhhhhhhhccC------------Cc---------
Confidence 999999999999998753 3 3478999999999999999999999999998210 00
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452 236 FRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTP 315 (424)
Q Consensus 236 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~ 315 (424)
.
T Consensus 488 ---------------------------------------------------------------------------k---- 488 (584)
T KOG2193|consen 488 ---------------------------------------------------------------------------K---- 488 (584)
T ss_pred ---------------------------------------------------------------------------h----
Confidence 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC--CCCC
Q 014452 316 QGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP--KPGA 393 (424)
Q Consensus 316 ~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~--~~~~ 393 (424)
..-....+|.||...+|+||||||.++++|+..|+|.|.|+.+ .++.
T Consensus 489 -------------------------------eevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEn 537 (584)
T KOG2193|consen 489 -------------------------------EEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDEN 537 (584)
T ss_pred -------------------------------hhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCcc
Confidence 0124678999999999999999999999999999999999843 2334
Q ss_pred CCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452 394 TEGVVMVSGTSDQMRAAQSLIHAFILC 420 (424)
Q Consensus 394 ~~r~i~I~Gt~e~v~~A~~lI~~~i~~ 420 (424)
+.-+|.|+|...+.+.|++.|.++|.+
T Consensus 538 d~vivriiGhfyatq~aQrki~~iv~q 564 (584)
T KOG2193|consen 538 DQVIVRIIGHFYATQNAQRKIAHIVNQ 564 (584)
T ss_pred ceeeeeeechhhcchHHHHHHHHHHHH
Confidence 556888999999999999999998864
No 7
>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=4.8e-26 Score=213.37 Aligned_cols=268 Identities=21% Similarity=0.333 Sum_probs=189.9
Q ss_pred CCcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEec---cCCCCCcccEEEeecccccccccChhHHHHHH
Q 014452 42 NRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA---DILPDSEERIVVISARENSEMRHSPAQDAVMR 118 (424)
Q Consensus 42 ~~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~---~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~ 118 (424)
+.-..+..+++|||||+..+|+||||+|++|.+|+++|||+|+++ +..|++.||+|.|+|+.+++. ..+..
T Consensus 31 ~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~------av~ef 104 (402)
T KOG2191|consen 31 TNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN------AVHEF 104 (402)
T ss_pred ccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH------HHHHH
Confidence 334444559999999999999999999999999999999999998 678999999999999954421 12233
Q ss_pred HHHHHHhhc---------CC---CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEE
Q 014452 119 VHSRIAEIG---------FE---PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV 186 (424)
Q Consensus 119 ~~~~i~e~~---------~~---~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v 186 (424)
+.++|+|.- ++ ++..-.+++.||++.+|.||||+|.+||.|+|+++|.|+|.+.. |..-.-.+|+|
T Consensus 105 I~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqervv 182 (402)
T KOG2191|consen 105 IADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERVV 182 (402)
T ss_pred HHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEEE
Confidence 344444321 11 12224589999999999999999999999999999999998532 23334679999
Q ss_pred EEEeCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452 187 QVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQ 266 (424)
Q Consensus 187 ~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 266 (424)
++.|++++..+|+.+|+.+|.+.. .+..+ +..+| ..
T Consensus 183 t~sge~e~~~~A~~~IL~Ki~eDp------qs~sc--ln~sy--------------------a~---------------- 218 (402)
T KOG2191|consen 183 TVSGEPEQNMKAVSLILQKIQEDP------QSGSC--LNISY--------------------AN---------------- 218 (402)
T ss_pred EecCCHHHHHHHHHHHHHHhhcCC------cccce--eccch--------------------hc----------------
Confidence 999999999999999999999871 11000 00000 00
Q ss_pred CCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 014452 267 PFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAA 346 (424)
Q Consensus 267 ~~~~q~~~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~ 346 (424)
..++ .-+ ++ +.+ ++|++.. ..
T Consensus 219 ----------vsGp--vaN------------------sn-----------PtG--spya~~~----------------~~ 239 (402)
T KOG2191|consen 219 ----------VSGP--VAN------------------SN-----------PTG--SPYAYQA----------------HV 239 (402)
T ss_pred ----------ccCc--ccc------------------cC-----------CCC--CCCCCCC----------------cc
Confidence 0000 000 00 000 0000000 00
Q ss_pred cCcceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCC---CCCCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452 347 ILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK---PGATEGVVMVSGTSDQMRAAQSLIHAFILCG 421 (424)
Q Consensus 347 ~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~---~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~ 421 (424)
..+..+..+-++....|..-|.+|.++-.|-..+|+.+.+.+.. .+..++ .-+.|.+-.+..|-.+|...+.+-
T Consensus 240 ~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~a 316 (402)
T KOG2191|consen 240 LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVASA 316 (402)
T ss_pred ccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhhhhhhhhhHHHHhhccc
Confidence 12234566778899999999999999999999999999997532 334455 788899999999999998887654
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=3.5e-22 Score=187.52 Aligned_cols=166 Identities=23% Similarity=0.362 Sum_probs=134.6
Q ss_pred cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcC
Q 014452 132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF 211 (424)
Q Consensus 132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~ 211 (424)
....++++||...+|.||||+|++|.+++.+|||+|+++...+ .+++.+||+|.|+|+.+++....+.|.++|++...
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~d--fyPGTTeRvcli~Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKD--FYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccc--cCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence 3488999999999999999999999999999999999986544 35569999999999999999999999999999732
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCC
Q 014452 212 PMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPF 291 (424)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~ 291 (424)
....+ ...+ .+|
T Consensus 115 ~~~k~----------------v~~~--------------------------------~pq-------------------- 126 (402)
T KOG2191|consen 115 AVAKP----------------VDIL--------------------------------QPQ-------------------- 126 (402)
T ss_pred hhcCC----------------cccc--------------------------------CCC--------------------
Confidence 11000 0000 000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccc
Q 014452 292 PYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNS 371 (424)
Q Consensus 292 ~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~ 371 (424)
. + .....+++.||...+|.||||+|.
T Consensus 127 -------------------------t---------------~--------------~r~kqikivvPNstag~iigkggA 152 (402)
T KOG2191|consen 127 -------------------------T---------------P--------------DRIKQIKIVVPNSTAGMIIGKGGA 152 (402)
T ss_pred -------------------------C---------------c--------------cccceeEEeccCCcccceecCCcc
Confidence 0 0 011348899999999999999999
Q ss_pred hHHHHHHHhCCEEEEeCCCCC---CCCcEEEEEcCHHHHHHHHHHHHHHHHcC
Q 014452 372 NLSHIRQISGANVVVNDPKPG---ATEGVVMVSGTSDQMRAAQSLIHAFILCG 421 (424)
Q Consensus 372 ~Ik~Ir~~SGa~I~i~~~~~~---~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~ 421 (424)
+||.|+|++||+|+|...++. -.+|+||++|++|+..+|..||.++|.+.
T Consensus 153 tiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eD 205 (402)
T KOG2191|consen 153 TIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQED 205 (402)
T ss_pred hHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcC
Confidence 999999999999999843322 24799999999999999999999999865
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.77 E-value=7.1e-18 Score=172.52 Aligned_cols=159 Identities=27% Similarity=0.424 Sum_probs=131.6
Q ss_pred CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe---------CHHHHHHHHHH
Q 014452 131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG---------NYHSVQDALFH 201 (424)
Q Consensus 131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G---------~~~~v~~A~~~ 201 (424)
+...+++++++...+|.||||+|..||+|+.++.++|+|... .+ +..+|+|+|+| ..+++.+|..+
T Consensus 40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~--~~---~c~eRIiti~g~~~~~~~~~~~~al~ka~~~ 114 (485)
T KOG2190|consen 40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES--LP---GCPERIITITGNRVELNLSPATDALFKAFDM 114 (485)
T ss_pred CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC--CC---CCCcceEEEecccccccCCchHHHHHHHHHH
Confidence 344558999999999999999999999999999999999643 33 35899999999 99999999999
Q ss_pred HHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCC
Q 014452 202 ITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPM 281 (424)
Q Consensus 202 I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~ 281 (424)
|...+++..... . +
T Consensus 115 iv~~~~~d~~~~------------~---d--------------------------------------------------- 128 (485)
T KOG2190|consen 115 IVFKLEEDDEAA------------E---D--------------------------------------------------- 128 (485)
T ss_pred Hhhccccccccc------------c---c---------------------------------------------------
Confidence 998877431100 0 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCc
Q 014452 282 VPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLY 361 (424)
Q Consensus 282 ~~~~~~~~~~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~ 361 (424)
. +.+. ....+++.+.||...
T Consensus 129 -----------~-------------------------------~~~~------------------~~~~v~~RLlVp~sq 148 (485)
T KOG2190|consen 129 -----------N-------------------------------GEDA------------------SGPEVTCRLLVPSSQ 148 (485)
T ss_pred -----------C-------------------------------Cccc------------------cCCceEEEEEechhh
Confidence 0 0000 011478999999999
Q ss_pred ccceeccccchHHHHHHHhCCEEEEeCC-CCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452 362 MAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILC 420 (424)
Q Consensus 362 ~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~-~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~ 420 (424)
+|+||||+|++||+||++|||+|.|... .+.+++|.|+|+|++++|.+|...|..+|.+
T Consensus 149 ~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 149 VGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLE 208 (485)
T ss_pred eeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999854 6789999999999999999999999999986
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.70 E-value=9.2e-17 Score=147.18 Aligned_cols=151 Identities=24% Similarity=0.487 Sum_probs=123.9
Q ss_pred ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEec-cCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhh
Q 014452 48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIA-DILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEI 126 (424)
Q Consensus 48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~-~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~ 126 (424)
+.-.+||||+.+++|.|||++|+.||.|++++.|+++|- +..|.+.+|+|.|.|.+.++.. .+..+++.+.|.
T Consensus 121 ~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~------~i~~il~~i~e~ 194 (390)
T KOG2192|consen 121 SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVE------CIKIILDLISES 194 (390)
T ss_pred CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHH------HHHHHHHHhhcC
Confidence 445789999999999999999999999999999999987 7778899999999999866432 333333333221
Q ss_pred c----------------------------------------------------------------------C--------
Q 014452 127 G----------------------------------------------------------------------F-------- 128 (424)
Q Consensus 127 ~----------------------------------------------------------------------~-------- 128 (424)
. |
T Consensus 195 pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~s 274 (390)
T KOG2192|consen 195 PIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPS 274 (390)
T ss_pred CcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCC
Confidence 0 0
Q ss_pred --------------C---------------------CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCC
Q 014452 129 --------------E---------------------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD 173 (424)
Q Consensus 129 --------------~---------------------~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~ 173 (424)
+ .....|.++.||.++-|.||||+|++|++|+.++||.|++...
T Consensus 275 aidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep- 353 (390)
T KOG2192|consen 275 AIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP- 353 (390)
T ss_pred cCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc-
Confidence 0 0124678999999999999999999999999999999999642
Q ss_pred CCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452 174 QAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 209 (424)
Q Consensus 174 ~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 209 (424)
..++.+|+++|+|+.++++.|..++...++.+
T Consensus 354 ----leGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 354 ----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred ----CCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 33588999999999999999999999999865
No 11
>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=99.67 E-value=3.9e-16 Score=140.11 Aligned_cols=61 Identities=21% Similarity=0.315 Sum_probs=53.9
Q ss_pred EEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEE---EeCHHHHHHHHHHHHHHHHh
Q 014452 138 LLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV---IGNYHSVQDALFHITSRLRE 208 (424)
Q Consensus 138 l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I---~G~~~~v~~A~~~I~~~l~~ 208 (424)
+.||.+.+|.|||++|++|+.|+++|||+|++..+ +..|.| +++++++.+|+.+|..+...
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~----------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE----------TGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC----------CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 57899999999999999999999999999999643 245888 78999999999999987664
No 12
>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=99.64 E-value=1.4e-15 Score=136.62 Aligned_cols=129 Identities=29% Similarity=0.445 Sum_probs=96.9
Q ss_pred EEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEee---cccccccccChhHHHHHHHHHHHHhh--cC
Q 014452 54 LLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS---ARENSEMRHSPAQDAVMRVHSRIAEI--GF 128 (424)
Q Consensus 54 i~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~---G~~~~~~~~~~a~~av~~~~~~i~e~--~~ 128 (424)
|.||.+.+|.|||++|++|+.|+++|||+|++.+ ++..|.|+ +.+. ++.++.+.+... ++
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~----------~i~kA~~~I~~i~~gf 66 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL----------AVMKAREVVKAIGRGF 66 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH----------HHHHHHHHHHHHHcCC
Confidence 5689999999999999999999999999999953 34678883 3332 344444433321 11
Q ss_pred CC-------CcceEEE-EEecC---------CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC
Q 014452 129 EP-------GQAVVAR-LLVHS---------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN 191 (424)
Q Consensus 129 ~~-------~~~~t~~-l~IP~---------~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~ 191 (424)
++ .+.++.+ +.|+. ..+|+|||++|++++.|++.|||+|.|.. +.|.|.|+
T Consensus 67 ~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~ 134 (172)
T TIGR03665 67 SPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGD 134 (172)
T ss_pred CHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECC
Confidence 11 2233333 33443 36899999999999999999999998852 46999999
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 014452 192 YHSVQDALFHITSRLRET 209 (424)
Q Consensus 192 ~~~v~~A~~~I~~~l~~~ 209 (424)
+++++.|+.+|.++++..
T Consensus 135 ~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 135 PEQVQIAREAIEMLIEGA 152 (172)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 999999999999999554
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.63 E-value=6.1e-15 Score=133.29 Aligned_cols=65 Identities=18% Similarity=0.248 Sum_probs=57.2
Q ss_pred eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE----eCHHHHHHHHHHHHHHHHh
Q 014452 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI----GNYHSVQDALFHITSRLRE 208 (424)
Q Consensus 134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~----G~~~~v~~A~~~I~~~l~~ 208 (424)
+...+.||.+.++.|||++|++|+.|+++|||+|++..+ +..|.|. ++++++.+|+.+|..++..
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE----------TGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC----------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 356899999999999999999999999999999999643 2468885 8999999999999988774
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.60 E-value=1e-14 Score=131.83 Aligned_cols=133 Identities=25% Similarity=0.385 Sum_probs=98.0
Q ss_pred EEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEee----cccccccccChhHHHHHHHHHHHHh
Q 014452 50 VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVIS----ARENSEMRHSPAQDAVMRVHSRIAE 125 (424)
Q Consensus 50 ~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~----G~~~~~~~~~~a~~av~~~~~~i~e 125 (424)
+...+.||.+.+|.|||++|++|+.|+++|||+|++.+ ++..|.|. +.++ ++.++.+.+..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~----------~i~kA~~~I~a 67 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPL----------AVLKARDIVKA 67 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHH----------HHHHHHHHHHH
Confidence 45689999999999999999999999999999999953 34678886 3433 33333333322
Q ss_pred hc--CC-------CCcceEEEE-Eec---------CCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEE
Q 014452 126 IG--FE-------PGQAVVARL-LVH---------SQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIV 186 (424)
Q Consensus 126 ~~--~~-------~~~~~t~~l-~IP---------~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v 186 (424)
.. ++ ..+.+..++ .|. ...+|+|||++|++++.|++.|||+|.|.. +.|
T Consensus 68 i~~gf~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v 135 (180)
T PRK13763 68 IGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTV 135 (180)
T ss_pred HhcCCCHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEE
Confidence 11 11 112222221 121 137899999999999999999999999852 239
Q ss_pred EEEeCHHHHHHHHHHHHHHHHhh
Q 014452 187 QVIGNYHSVQDALFHITSRLRET 209 (424)
Q Consensus 187 ~I~G~~~~v~~A~~~I~~~l~~~ 209 (424)
.|.|++++++.|+..|.++++..
T Consensus 136 ~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 136 AIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred EEEeCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999998554
No 15
>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=99.50 E-value=4.6e-14 Score=106.21 Aligned_cols=63 Identities=29% Similarity=0.482 Sum_probs=58.5
Q ss_pred EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCC-CCCCcEEEEEcCHHHHHHHHHHHH
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP-GATEGVVMVSGTSDQMRAAQSLIH 415 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~-~~~~r~i~I~Gt~e~v~~A~~lI~ 415 (424)
.+|.||.+.+|+|||++|++|++|+++|||+|.+.+... ...+|+|+|+|++++|+.|+.||.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 689999999999999999999999999999999986544 678899999999999999999984
No 16
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.41 E-value=1.8e-12 Score=130.05 Aligned_cols=294 Identities=17% Similarity=0.240 Sum_probs=181.2
Q ss_pred cCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHH
Q 014452 44 MFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRI 123 (424)
Q Consensus 44 ~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i 123 (424)
....+++.++++|+...|-.+|||.|++|+.|+..++++|.+.+.. -.+++...+.|.+..+.. +.+++.+ .+
T Consensus 62 ~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~v~~---a~a~~~~---~~ 134 (608)
T KOG2279|consen 62 QKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQVCK---AKAAIHQ---IL 134 (608)
T ss_pred cCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCCCCh---HHHHHHH---HH
Confidence 3445889999999999999999999999999999999999997442 245566666665544332 3333322 22
Q ss_pred HhhcCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014452 124 AEIGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT 203 (424)
Q Consensus 124 ~e~~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~ 203 (424)
.+ +..+...+.+|...+++|+|++|.+++.|+..++|+|.+..... ..-.+...|.+...-+..|+.++.
T Consensus 135 ~~-----~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr-----~g~~~~~~i~~qqk~~~~a~~~~~ 204 (608)
T KOG2279|consen 135 TE-----NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR-----LGLSRLIKISGQQKEVAAAKHLIL 204 (608)
T ss_pred hc-----CCcccccccchhhhcccccccchhhhcchhcccccccccccccc-----cccccceecccccchHHHHHhhhh
Confidence 21 34567789999999999999999999999999999998754311 145778888888888889999999
Q ss_pred HHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCC
Q 014452 204 SRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVP 283 (424)
Q Consensus 204 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~ 283 (424)
+.+.+.....+.......... | .. .+...++. ++..+
T Consensus 205 ~~~~edeelv~~~~e~~q~rv-p-rk-~p~n~~~~--~m~~~-------------------------------------- 241 (608)
T KOG2279|consen 205 EKVSEDEELVKRIAESAQTRV-P-RK-QPINVRRE--DMTEP-------------------------------------- 241 (608)
T ss_pred ccccchhHHhhhchhhcccCC-C-CC-CCccccch--hhccc--------------------------------------
Confidence 988764222111111110000 0 00 00000000 00000
Q ss_pred CCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCccccCcceEEEEEe
Q 014452 284 PNSDRIPFPYGSERPGHGPTF----DRPPSPRSWTPQGVGGGDPRGFDAS--SGFTPRNRPVESGNHAAILTSTTIEVVI 357 (424)
Q Consensus 284 ~~~~~~~~~~g~~~~g~~~~~----~~~~~p~~~~~~~~~~g~~~g~~~~--~~~~~r~~~~~~g~~~~~~~~~t~~v~I 357 (424)
+...++|.... +.|..|.. ..+|..+..... ..|. +..-|+..........+|.+
T Consensus 242 ----------~~s~~~h~~~~t~~s~spg~~~~-----~~eg~dm~v~vsk~~s~~----~~~d~s~~k~~~l~i~e~e~ 302 (608)
T KOG2279|consen 242 ----------GGAGEPHLWKNTSSSMSPGAPLV-----TKEGGDMAVVVSKEGSWE----KPSDDSFQKSEALAIPEMEM 302 (608)
T ss_pred ----------ccCCccccCccchhccCCCCCCc-----ccCCCcceeEEecccccC----Cccccccccccccccceeec
Confidence 00000000000 00000000 000111110000 0000 01112223334567789999
Q ss_pred ccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCC---CcEEEEEcCHHHHHHHHHHHHH
Q 014452 358 PQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGAT---EGVVMVSGTSDQMRAAQSLIHA 416 (424)
Q Consensus 358 P~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~---~r~i~I~Gt~e~v~~A~~lI~~ 416 (424)
|...+|.+||+.|++++.+...|++.+.|........ -.++.+.|+..-+..|..||..
T Consensus 303 p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n~vl~ml~~ 364 (608)
T KOG2279|consen 303 PEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHYENSVLEMLTV 364 (608)
T ss_pred CcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHHHHHHHhhhhc
Confidence 9999999999999999999999999999974322211 2578899999999999999974
No 17
>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=99.38 E-value=6.9e-13 Score=98.77 Aligned_cols=61 Identities=23% Similarity=0.425 Sum_probs=56.3
Q ss_pred EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHH
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 415 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~ 415 (424)
.+|.||.+++++|||++|++|++|+++|||+|.|++.. ..++.|+|+|++++|+.|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence 67999999999999999999999999999999997543 67899999999999999999884
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=99.38 E-value=5.3e-13 Score=98.71 Aligned_cols=60 Identities=23% Similarity=0.511 Sum_probs=55.4
Q ss_pred EEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHH
Q 014452 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLI 414 (424)
Q Consensus 352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI 414 (424)
|.+|.||.+++|+|||++|++|++|+++|||+|.|++. + .+..|+|+|++++|+.|+.+|
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 67899999999999999999999999999999999865 2 455999999999999999987
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=99.35 E-value=2.7e-12 Score=95.96 Aligned_cols=63 Identities=27% Similarity=0.545 Sum_probs=58.3
Q ss_pred EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHH
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 415 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~ 415 (424)
.+|.||.+++++|||++|++|++|+++|||+|.|++..+...++.|+|+|+.++++.|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 679999999999999999999999999999999987655567899999999999999999874
No 20
>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=99.35 E-value=2.7e-12 Score=95.16 Aligned_cols=59 Identities=19% Similarity=0.385 Sum_probs=54.0
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcC-HHHHHHHHHHHH
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIH 415 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt-~e~v~~A~~lI~ 415 (424)
.+..|.||.+++|+|||++|++|++|+++|||+|.|++ ++.|+|+|+ +++++.|+.+|+
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 35789999999999999999999999999999999964 468999998 999999999984
No 21
>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=99.32 E-value=4.9e-12 Score=95.11 Aligned_cols=65 Identities=38% Similarity=0.581 Sum_probs=57.9
Q ss_pred EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014452 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT 203 (424)
Q Consensus 135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~ 203 (424)
+++|.||.+.+|.|||++|++|++|+++|||+|.+.+... ....+|+|+|+|+++++.+|+.+|.
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 3689999999999999999999999999999999976432 2467999999999999999999873
No 22
>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=99.19 E-value=2.8e-11 Score=90.04 Aligned_cols=61 Identities=16% Similarity=0.288 Sum_probs=55.2
Q ss_pred EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014452 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT 203 (424)
Q Consensus 136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~ 203 (424)
.++.||.+++++|||++|++|++|+++|||+|.+++.+ +.++.|+|+|+.++|..|+.+|.
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999997542 56789999999999999998873
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=99.12 E-value=2.4e-10 Score=84.72 Aligned_cols=58 Identities=19% Similarity=0.324 Sum_probs=52.3
Q ss_pred eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHH
Q 014452 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHI 202 (424)
Q Consensus 134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I 202 (424)
....+.||.+++++|||++|++|++|+++|||+|.+.. ++.|.|+|+ .++++.|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence 35678999999999999999999999999999999852 346999998 99999999887
No 24
>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=99.12 E-value=6e-11 Score=87.65 Aligned_cols=60 Identities=27% Similarity=0.433 Sum_probs=54.1
Q ss_pred EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 014452 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI 202 (424)
Q Consensus 135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 202 (424)
|.+|.||.+++++|||++|++|++|+++|||+|+++++ ..+..|+|+|+.++|++|+++|
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--------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999643 2345899999999999999886
No 25
>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=99.06 E-value=5.8e-10 Score=83.19 Aligned_cols=62 Identities=32% Similarity=0.559 Sum_probs=55.7
Q ss_pred EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 014452 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI 202 (424)
Q Consensus 136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 202 (424)
.++.||.++++.|||++|++|++|+++|||+|.|.+... ...++.|.|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence 579999999999999999999999999999999975432 35789999999999999999876
No 26
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.06 E-value=3.4e-09 Score=94.76 Aligned_cols=140 Identities=24% Similarity=0.395 Sum_probs=104.9
Q ss_pred ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHh--
Q 014452 48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAE-- 125 (424)
Q Consensus 48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e-- 125 (424)
......+.||.+.++.+||+.|++.+.|++.++++|.+ +..+..|.|.......+ ..+++++.+.+..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~i-----D~~~~~V~i~~~~~t~D-----p~~~~ka~d~VkAIg 75 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRI-----DSKTGSVTIRTTRKTED-----PLALLKARDVVKAIG 75 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEE-----ECCCCeEEEEecCCCCC-----hHHHHHHHHHHHHHh
Confidence 34456799999999999999999999999999999999 67888999987732111 2234555444332
Q ss_pred hcCCCC-------cceEEE-EEe------cC----CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEE
Q 014452 126 IGFEPG-------QAVVAR-LLV------HS----QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQ 187 (424)
Q Consensus 126 ~~~~~~-------~~~t~~-l~I------P~----~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~ 187 (424)
.+|+++ +.+.+. +.+ +. ...|+|||++|.+.+.|++.|+|.|.|..+ .|.
T Consensus 76 rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~------------tVa 143 (194)
T COG1094 76 RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK------------TVA 143 (194)
T ss_pred cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc------------EEE
Confidence 244321 122222 222 11 245999999999999999999999988643 499
Q ss_pred EEeCHHHHHHHHHHHHHHHHhh
Q 014452 188 VIGNYHSVQDALFHITSRLRET 209 (424)
Q Consensus 188 I~G~~~~v~~A~~~I~~~l~~~ 209 (424)
|.|.+++|+.|+..|++++...
T Consensus 144 iiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 144 IIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred EecChhhhHHHHHHHHHHHcCC
Confidence 9999999999999999999765
No 27
>smart00322 KH K homology RNA-binding domain.
Probab=99.04 E-value=1.3e-09 Score=81.60 Aligned_cols=67 Identities=25% Similarity=0.440 Sum_probs=60.3
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHH
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL 419 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~ 419 (424)
.+.+|.||...++++||++|++|++|++.|||+|.+.... .....|+|.|+.++++.|+.+|.+.++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--SEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999996432 256899999999999999999998763
No 28
>PF13014 KH_3: KH domain
Probab=99.00 E-value=6.4e-10 Score=76.38 Aligned_cols=42 Identities=29% Similarity=0.659 Sum_probs=38.2
Q ss_pred cccceeccccchHHHHHHHhCCEEEEeC-CCCCCCCcEEEEEc
Q 014452 361 YMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSG 402 (424)
Q Consensus 361 ~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~-~~~~~~~r~i~I~G 402 (424)
++|+|||++|++|++|+++|||+|+|++ ..++..+++|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5799999999999999999999999986 45667899999998
No 29
>PF13014 KH_3: KH domain
Probab=98.98 E-value=8.1e-10 Score=75.86 Aligned_cols=42 Identities=48% Similarity=0.772 Sum_probs=38.7
Q ss_pred ccceeeccCchHHHHHHHHhCceEEecc-CCCCCcccEEEeec
Q 014452 60 KVGSLIGKGGSIVRTFQNETGASIKIAD-ILPDSEERIVVISA 101 (424)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~tga~I~v~~-~~~~~~er~v~I~G 101 (424)
+||+|||++|++|++|+++|+|+|+|++ ..++..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 4899999999999999999999999997 56688999999987
No 30
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.97 E-value=2.3e-09 Score=116.22 Aligned_cols=224 Identities=19% Similarity=0.281 Sum_probs=156.7
Q ss_pred ccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccc-cChhHHH-----------
Q 014452 48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMR-HSPAQDA----------- 115 (424)
Q Consensus 48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~-~~~a~~a----------- 115 (424)
.-+..++.+....+.+|||++|.+++.+++++.+.|.|++.. .......|.+....... ....+++
T Consensus 199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~ 276 (753)
T KOG2208|consen 199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYD 276 (753)
T ss_pred eeEEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhccccccceehhhhhHHHHHHhcChhhhh
Confidence 346778999999999999999999999999999999998542 22222223332111100 0000001
Q ss_pred ------------------HHHHHHHHHhh-----c------------CC-----------------CCcceEEEEEecCC
Q 014452 116 ------------------VMRVHSRIAEI-----G------------FE-----------------PGQAVVARLLVHSQ 143 (424)
Q Consensus 116 ------------------v~~~~~~i~e~-----~------------~~-----------------~~~~~t~~l~IP~~ 143 (424)
+..+.+...+. . .+ ....+.+.+.|-..
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~ 356 (753)
T KOG2208|consen 277 EIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPE 356 (753)
T ss_pred hhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHH
Confidence 01110000000 0 00 01246677888889
Q ss_pred CcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCC
Q 014452 144 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHS 223 (424)
Q Consensus 144 ~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~ 223 (424)
.+..|+||+|.+|.+|++++.|.|.+... ++.+..+.++|...++.+|...++....+...
T Consensus 357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------------ 417 (753)
T KOG2208|consen 357 ELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN------------ 417 (753)
T ss_pred hhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc------------
Confidence 99999999999999999999999988642 25678899999999999999999998888721
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 014452 224 YLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPT 303 (424)
Q Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~~~g~~~~g~~~~ 303 (424)
T Consensus 418 -------------------------------------------------------------------------------- 417 (753)
T KOG2208|consen 418 -------------------------------------------------------------------------------- 417 (753)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccchHHHHHHHhCCE
Q 014452 304 FDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN 383 (424)
Q Consensus 304 ~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~ 383 (424)
.....++.||..++.++||.+|..|+.|...+++
T Consensus 418 ---------------------------------------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~- 451 (753)
T KOG2208|consen 418 ---------------------------------------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGG- 451 (753)
T ss_pred ---------------------------------------------ccccceeecCccchhhhhccccccHHHHHhhcCc-
Confidence 0134678999999999999999999999999995
Q ss_pred EEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452 384 VVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI 418 (424)
Q Consensus 384 I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i 418 (424)
+.|..+........+++.|....+..++.++..+.
T Consensus 452 v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~ 486 (753)
T KOG2208|consen 452 VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALK 486 (753)
T ss_pred EEEecCCCCcccccceEeccccccchhHHHHHhhh
Confidence 44443444455567888887777777666655443
No 31
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.81 E-value=2.9e-09 Score=107.34 Aligned_cols=145 Identities=20% Similarity=0.321 Sum_probs=121.4
Q ss_pred CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhc
Q 014452 131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI 210 (424)
Q Consensus 131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 210 (424)
.+.+.+++.|+...+-+++|+.|++|+.|+..++++|.+.+++ . ..++.-.+.|-+.++..|..+++.++.+.-
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~ 138 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-----GDERVLLISGFPVQVCKAKAAIHQILTENT 138 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-----CcccchhhccCCCCCChHHHHHHHHHhcCC
Confidence 3567889999999999999999999999999999999886543 1 355666677789999999999998887650
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 014452 211 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP 290 (424)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~ 290 (424)
T Consensus 139 -------------------------------------------------------------------------------- 138 (608)
T KOG2279|consen 139 -------------------------------------------------------------------------------- 138 (608)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceecccc
Q 014452 291 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENN 370 (424)
Q Consensus 291 ~~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G 370 (424)
.+..+..+|...+++|+||+|
T Consensus 139 -----------------------------------------------------------pvk~~lsvpqr~~~~i~grgg 159 (608)
T KOG2279|consen 139 -----------------------------------------------------------PVSEQLSVPQRSVGRIIGRGG 159 (608)
T ss_pred -----------------------------------------------------------cccccccchhhhcccccccch
Confidence 133556778889999999999
Q ss_pred chHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452 371 SNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC 420 (424)
Q Consensus 371 ~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~ 420 (424)
.++..|+..|+|+|.++..--....+.+.|.+...-++.|+.++.++++.
T Consensus 160 et~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 160 ETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSE 209 (608)
T ss_pred hhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccc
Confidence 99999999999999998653334568899999999999999999998875
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.80 E-value=3.2e-08 Score=74.00 Aligned_cols=66 Identities=23% Similarity=0.475 Sum_probs=58.9
Q ss_pred eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 014452 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL 206 (424)
Q Consensus 134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 206 (424)
.+.++.||...++.+||++|++|++|++.++++|.+.... .....|.|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 5678999999999999999999999999999999986432 25678999999999999999998876
No 33
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.74 E-value=2.1e-08 Score=108.72 Aligned_cols=146 Identities=16% Similarity=0.272 Sum_probs=112.8
Q ss_pred CCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHh
Q 014452 46 YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAE 125 (424)
Q Consensus 46 ~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e 125 (424)
.+..+...+.+-...+..|+||+|.+|.+|++++.|.|.++.. +..+..+++++...++.+ +.+.+.++...+.+
T Consensus 343 ~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~~k---a~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 343 EENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSANDEK---AVEDVEKIIAEILN 417 (753)
T ss_pred hccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccchhH---HHHHHHHHHHhhhc
Confidence 3444677888999999999999999999999999999999874 577788999998766554 34444444433322
Q ss_pred hcCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcC-ceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHH
Q 014452 126 IGFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATG-ASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITS 204 (424)
Q Consensus 126 ~~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tg-a~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~ 204 (424)
......+.||...+..|||.+|..|++|.++++ .+|+..... .....+++.|....+..++.++..
T Consensus 418 ------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~dv~~~~~~~~~ 484 (753)
T KOG2208|consen 418 ------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISKDVEKSVSLLKA 484 (753)
T ss_pred ------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEeccccccchhHHHHHh
Confidence 145567999999999999999999999999999 666664332 445668999999888887777666
Q ss_pred HHHhh
Q 014452 205 RLRET 209 (424)
Q Consensus 205 ~l~~~ 209 (424)
+....
T Consensus 485 ~~~~a 489 (753)
T KOG2208|consen 485 LKADA 489 (753)
T ss_pred hhhhh
Confidence 55543
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.61 E-value=5.8e-07 Score=80.57 Aligned_cols=53 Identities=17% Similarity=0.290 Sum_probs=48.6
Q ss_pred cccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHc
Q 014452 361 YMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC 420 (424)
Q Consensus 361 ~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~ 420 (424)
.-|+|||++|.+.+.|++.|||+|.|.. .+|.|.|.+++|+.|+..|..+|..
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChhhhHHHHHHHHHHHcC
Confidence 4599999999999999999999999963 4799999999999999999999864
No 35
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.61 E-value=5.5e-08 Score=91.81 Aligned_cols=149 Identities=23% Similarity=0.288 Sum_probs=112.3
Q ss_pred cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhcC
Q 014452 132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF 211 (424)
Q Consensus 132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~ 211 (424)
+.++..+.||..+++.|+|++|.+||.|+.+|...|+-+.+. .+-++.++|..+.|+.|+..|...-++.-.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~--------eePiF~vTg~~edv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG--------EEPIFPVTGRHEDVRRARREIPSAAEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC--------CCCcceeccCchhHHHHhhcCccccceeee
Confidence 678889999999999999999999999999999999776553 446799999999999999877655444310
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCC
Q 014452 212 PMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPF 291 (424)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~q~~~~~g~~~~~~~~~~~~~~ 291 (424)
. .|.+++ +.|.
T Consensus 96 ~----------~~s~s~----------------------------------------------Sgg~------------- 106 (394)
T KOG2113|consen 96 I----------RASRSF----------------------------------------------SGGT------------- 106 (394)
T ss_pred e----------eecccc----------------------------------------------cCCC-------------
Confidence 0 000000 0000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccCcccceeccccc
Q 014452 292 PYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNS 371 (424)
Q Consensus 292 ~~g~~~~g~~~~~~~~~~p~~~~~~~~~~g~~~g~~~~~~~~~r~~~~~~g~~~~~~~~~t~~v~IP~~~~g~IIGk~G~ 371 (424)
+ ++. ...+.+.++.+|.+.+|.|.|..|.
T Consensus 107 ----------~----------------------~~s-------------------~s~qt~sy~svP~rvvglvv~~~~~ 135 (394)
T KOG2113|consen 107 ----------N----------------------GAS-------------------ASGQTTSYVSVPLRVVGLVVGPKGA 135 (394)
T ss_pred ----------c----------------------ccc-------------------ccCCCceeeeccceeeeeccccccC
Confidence 0 000 0125678899999999999999999
Q ss_pred hHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHH-HHHHH
Q 014452 372 NLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQ-MRAAQ 411 (424)
Q Consensus 372 ~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~-v~~A~ 411 (424)
+|+.|++.+...|...-+ ..+.++.++|-+++ +++|+
T Consensus 136 ti~~iqq~tnt~I~T~v~---~~~~Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 136 TIKRIQQFTNTYIATPVR---CGEPVFCVTGAPKNCVKRAR 173 (394)
T ss_pred ccchheecccceEeeecc---CCCceEEEecCCcchhhhcc
Confidence 999999999999988533 46789999998877 77776
No 36
>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=98.51 E-value=2.9e-07 Score=77.47 Aligned_cols=61 Identities=13% Similarity=0.258 Sum_probs=50.8
Q ss_pred CcccceeccccchHHHHHHHhCCEEEEeCCCC-----------------CCCCcEEEEEc-C--HHHHHHHHHHHHHHHH
Q 014452 360 LYMAHVYGENNSNLSHIRQISGANVVVNDPKP-----------------GATEGVVMVSG-T--SDQMRAAQSLIHAFIL 419 (424)
Q Consensus 360 ~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~-----------------~~~~r~i~I~G-t--~e~v~~A~~lI~~~i~ 419 (424)
+++|.|||++|++||+|+++|||+|.|...-. ..+.-.|.|++ + .+++++|..+|++++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 78899999999999999999999999974311 11235789999 4 6999999999999887
Q ss_pred c
Q 014452 420 C 420 (424)
Q Consensus 420 ~ 420 (424)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.45 E-value=1.3e-07 Score=89.25 Aligned_cols=151 Identities=17% Similarity=0.219 Sum_probs=108.5
Q ss_pred CCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHH
Q 014452 45 FYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA 124 (424)
Q Consensus 45 ~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~ 124 (424)
.-++.++..+.+|..+|+.|.|++|.+||.|+.+|.++|+-+.. ..+-++.++|..+++..++...++...-+..+.
T Consensus 21 ~~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv~~aRrei~saaeH~~l~~ 97 (394)
T KOG2113|consen 21 SIGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDVRRARREIPSAAEHFGLIR 97 (394)
T ss_pred CCCCccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhHHHHhhcCccccceeeeee
Confidence 33477888999999999999999999999999999999998744 344778899997765542222221111111111
Q ss_pred hh--------cCCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHH-H
Q 014452 125 EI--------GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHS-V 195 (424)
Q Consensus 125 e~--------~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~-v 195 (424)
.. .+......+...-+|...+|.|.|..|.+|+.|++.++..|.-.-+ ..+.++.++|.+++ +
T Consensus 98 ~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~~nC~ 169 (394)
T KOG2113|consen 98 ASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPKNCV 169 (394)
T ss_pred ecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCcchh
Confidence 00 1112345677888999999999999999999999999999966543 35778999999888 5
Q ss_pred HHHH-HHHHHHH
Q 014452 196 QDAL-FHITSRL 206 (424)
Q Consensus 196 ~~A~-~~I~~~l 206 (424)
++|. ..|+..+
T Consensus 170 kra~s~eie~ta 181 (394)
T KOG2113|consen 170 KRARSCEIEQTA 181 (394)
T ss_pred hhccccchhhhh
Confidence 5565 4554443
No 38
>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=98.33 E-value=1.9e-06 Score=72.62 Aligned_cols=73 Identities=18% Similarity=0.298 Sum_probs=54.6
Q ss_pred EEEecCC------CcceeeccCCchHHHHHhhcCceEEEecCCCCC-----------C-CCCCCCcEEEEEeC---HHHH
Q 014452 137 RLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAP-----------R-CGSPHDEIVQVIGN---YHSV 195 (424)
Q Consensus 137 ~l~IP~~------~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p-----------~-~~~~~~r~v~I~G~---~~~v 195 (424)
++.||.+ ++|.|||++|++||+|+++|||+|.|..+.... . ......-.|.|++. .+++
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 4555554 789999999999999999999999997542110 0 00122356899996 4999
Q ss_pred HHHHHHHHHHHHhh
Q 014452 196 QDALFHITSRLRET 209 (424)
Q Consensus 196 ~~A~~~I~~~l~~~ 209 (424)
.+|+.+|..++...
T Consensus 83 ~~A~~~I~~ll~~~ 96 (120)
T cd02395 83 AKAVEAIEELLKPA 96 (120)
T ss_pred HHHHHHHHHHhccC
Confidence 99999999998854
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.18 E-value=3.9e-06 Score=72.67 Aligned_cols=100 Identities=17% Similarity=0.324 Sum_probs=70.3
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHH--hhcC
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA--EIGF 128 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~--e~~~ 128 (424)
.+.++|+...+|+.||++|++|+.|++..|-+|.|-+- +-.+ .+-+..++..+. +...
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s~d~---------~~fI~n~l~Pa~V~~v~I 92 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------SDDP---------EEFIKNIFAPAAVRSVTI 92 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------CCCH---------HHHHHHHcCCCEEEEEEE
Confidence 45788899999999999999999999999988888322 1111 111111111110 0001
Q ss_pred -CCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEe
Q 014452 129 -EPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF 170 (424)
Q Consensus 129 -~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~ 170 (424)
+......+.+.|+.+..|..|||+|++++.++.-++-++.|.
T Consensus 93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 122334567789999999999999999999999999888763
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=98.02 E-value=3.2e-05 Score=82.81 Aligned_cols=63 Identities=25% Similarity=0.435 Sum_probs=57.6
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL 419 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~ 419 (424)
....+.||.+.++.|||.||.+||.|.++|||+|.|++ +.+|.|.+ +.+.+++|+.+|+..+.
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 35789999999999999999999999999999999964 47899988 88999999999999876
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.71 E-value=6.1e-05 Score=65.26 Aligned_cols=39 Identities=21% Similarity=0.388 Sum_probs=34.6
Q ss_pred eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172 (424)
Q Consensus 134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~ 172 (424)
-.+.+.|+...+|..||++|++|+.|++..|-+|.+..-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~ 70 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY 70 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc
Confidence 356788899999999999999999999999999988753
No 42
>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=97.69 E-value=0.00015 Score=77.81 Aligned_cols=65 Identities=20% Similarity=0.292 Sum_probs=57.3
Q ss_pred ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452 133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE 208 (424)
Q Consensus 133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 208 (424)
.....+.||.+.++.|||+||.+||.|+++|||+|.+.. +..|.|.+ ..+.+++|+.+|..++..
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 455789999999999999999999999999999999953 34699988 588999999999988875
No 43
>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=97.67 E-value=0.00014 Score=62.81 Aligned_cols=100 Identities=21% Similarity=0.307 Sum_probs=70.2
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhh-c
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEI-G 127 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~-~ 127 (424)
-+-++|....+|+.||++|++|+.|++..|=+|.|- .-+..+. +-+..++. .+... .
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV-----------eys~D~~---------~fI~N~l~PA~V~~V~i 93 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI-----------EYSENLE---------EFVANKLAPAEVKNVTV 93 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE-----------EcCCCHH---------HHHHHcCCCceEEEEEE
Confidence 567888999999999999999999999899888883 2222210 01111110 00110 0
Q ss_pred CCCCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEe
Q 014452 128 FEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF 170 (424)
Q Consensus 128 ~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~ 170 (424)
.+.++.....+.|+.+..+..|||+|++++..++-++-++.|.
T Consensus 94 ~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 94 SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 1223345677889999999999999999999999999888663
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.52 E-value=0.00067 Score=68.48 Aligned_cols=76 Identities=14% Similarity=0.244 Sum_probs=57.3
Q ss_pred ceEEEEEecCC------CcceeeccCCchHHHHHhhcCceEEEecCCC----------CCCCCCCC-CcEEEEEe-CHHH
Q 014452 133 AVVARLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQ----------APRCGSPH-DEIVQVIG-NYHS 194 (424)
Q Consensus 133 ~~t~~l~IP~~------~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~----------~p~~~~~~-~r~v~I~G-~~~~ 194 (424)
..+.++.||.+ +||+|||..|.|.|+|+++|||+|.|..+.. +....... +=-|.|++ +.|.
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 55667888765 8899999999999999999999999976321 11111122 23477888 4779
Q ss_pred HHHHHHHHHHHHHh
Q 014452 195 VQDALFHITSRLRE 208 (424)
Q Consensus 195 v~~A~~~I~~~l~~ 208 (424)
|++|+++|..+|++
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
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=97.49 E-value=0.00016 Score=78.50 Aligned_cols=65 Identities=18% Similarity=0.309 Sum_probs=56.9
Q ss_pred cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL 419 (424)
Q Consensus 349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~ 419 (424)
......+.||.+.++.|||++|++||.|.++|||+|.|.+ +..|.|.+ +.+.+++|+.+|+....
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence 3456889999999999999999999999999999999963 35677776 78999999999998765
No 46
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.31 E-value=0.00057 Score=68.94 Aligned_cols=63 Identities=16% Similarity=0.340 Sum_probs=50.5
Q ss_pred CcccceeccccchHHHHHHHhCCEEEEeC------C---------CCCC-CCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452 360 LYMAHVYGENNSNLSHIRQISGANVVVND------P---------KPGA-TEGVVMVSG-TSDQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 360 ~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~------~---------~~~~-~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~ 422 (424)
+|+|+|||..|.+.|+|+++|||+|.|-- - .+.. .+=-+.|+. |.|.|++|..+|+.+|.+..
T Consensus 153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av 232 (554)
T KOG0119|consen 153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAV 232 (554)
T ss_pred ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhc
Confidence 78999999999999999999999999942 0 0111 122477888 88999999999999998643
No 47
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.25 E-value=0.00027 Score=70.06 Aligned_cols=80 Identities=26% Similarity=0.351 Sum_probs=57.7
Q ss_pred CCCCCCCCCC--CCCCCCCCCCCCCCCCcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCccc
Q 014452 18 RGYAPGYHSR--GYSSGPGHETVGGRNRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEER 95 (424)
Q Consensus 18 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er 95 (424)
+.|+..++.+ .||.+.-.+ ........+++.+.+-|-+++||.|||++|++||+|+..|+++|++-+. ..+-
T Consensus 16 rd~g~g~~v~rg~~w~g~~~~---~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~ 89 (629)
T KOG0336|consen 16 RDYGGGRRVNRGNYWAGHRDS---RDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEV 89 (629)
T ss_pred ccCCcceecCCCCCccCCCCC---CcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---Ccee
Confidence 4444444444 245433322 2334455678888999999999999999999999999999999999755 3456
Q ss_pred EEEeeccc
Q 014452 96 IVVISARE 103 (424)
Q Consensus 96 ~v~I~G~~ 103 (424)
.|+|-|..
T Consensus 90 kv~ifg~~ 97 (629)
T KOG0336|consen 90 KVTIFGIN 97 (629)
T ss_pred EEEEechH
Confidence 67787764
No 48
>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=97.24 E-value=0.00093 Score=72.62 Aligned_cols=65 Identities=22% Similarity=0.388 Sum_probs=55.2
Q ss_pred ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452 133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE 208 (424)
Q Consensus 133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 208 (424)
.....+.||.+.++.|||++|++||.|+++|||+|.|.. +..|.|.+ ..+.+.+|+.+|..+..+
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 456789999999999999999999999999999999953 33577777 578899999999888654
No 49
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.18 E-value=0.00095 Score=70.09 Aligned_cols=69 Identities=20% Similarity=0.392 Sum_probs=59.8
Q ss_pred cceEEEEEeccCcc-cceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452 349 TSTTIEVVIPQLYM-AHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 349 ~~~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~ 422 (424)
..++..|.+|.+-+ |+||||.|.||+.+...||++|.|++. ...|+||+ +|--=+.|+.-|+.+|..|-
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~fdp~rreia~~~l~~li~dgr 272 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPVRREIARMALEKLIQDGR 272 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC-----CCeEEecCCchHHHHHHHHHHHHHHHcCC
Confidence 35677899999554 999999999999999999999999854 35788999 99999999999999998763
No 50
>PRK00106 hypothetical protein; Provisional
Probab=97.14 E-value=0.0012 Score=69.13 Aligned_cols=69 Identities=22% Similarity=0.395 Sum_probs=60.0
Q ss_pred cceEEEEEeccCc-ccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452 349 TSTTIEVVIPQLY-MAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 349 ~~~t~~v~IP~~~-~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~ 422 (424)
..++..|.+|.+- -|+||||.|.||+.+...||++|.|++.+ ..|+||| +|--=+.|+.-|..+|..|-
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~dgr 293 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIKDGR 293 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHHcCC
Confidence 3567789999954 59999999999999999999999998533 5688999 99999999999999998773
No 51
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.03 E-value=0.00073 Score=67.11 Aligned_cols=70 Identities=20% Similarity=0.327 Sum_probs=58.6
Q ss_pred CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452 131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208 (424)
Q Consensus 131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 208 (424)
..+..+.|.|-+++||.|||++|++|+.||..|+++|++... ..+-.|+|-|..+--.+|+..|...++.
T Consensus 44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 346678899999999999999999999999999999999753 3577899999988777777777665543
No 52
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.03 E-value=0.00084 Score=64.81 Aligned_cols=69 Identities=10% Similarity=0.251 Sum_probs=58.2
Q ss_pred ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHc
Q 014452 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC 420 (424)
Q Consensus 350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~ 420 (424)
.+...+.|+..+.|.|||+.|.+.+.|+++|+|+|.++.+ .+....|+|+| .-++|.+|...|.-+|.+
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 4667789999999999999999999999999999999654 33444556655 889999999999888865
No 53
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.02 E-value=0.0015 Score=61.76 Aligned_cols=65 Identities=18% Similarity=0.312 Sum_probs=56.5
Q ss_pred EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCcC
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGVT 423 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~~ 423 (424)
..+.||..+++.+||++|.+|+.|.+.++++|.|.. +-.|.|.+ +.+.+++|+.+|++.-++-++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 668999999999999999999999999999999953 36789988 677999999999987665543
No 54
>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=97.00 E-value=0.0015 Score=56.53 Aligned_cols=37 Identities=8% Similarity=0.135 Sum_probs=33.9
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~ 387 (424)
....+.||.+..++.|||+|.|++..++.++-++.|.
T Consensus 100 ~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 100 KVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 5678999999999999999999999999999998874
No 55
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.99 E-value=0.00071 Score=74.35 Aligned_cols=64 Identities=11% Similarity=0.273 Sum_probs=57.3
Q ss_pred ceEEEEEeccCcccceeccccchHHHHHHHhCCE-EEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN-VVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL 419 (424)
Q Consensus 350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~-I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~ 419 (424)
.....+.||.+.++.|||.||.+||.|.++||+. |.|.+ +-.|.|.+ +.+.+++|+.+|++.+.
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 4568899999999999999999999999999999 99853 46788888 88999999999998865
No 56
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.97 E-value=0.00098 Score=62.60 Aligned_cols=41 Identities=27% Similarity=0.455 Sum_probs=36.4
Q ss_pred CCccEEEEEEeccc------ccceeeccCchHHHHHHHHhCceEEec
Q 014452 46 YEEEVVFKLLCHLD------KVGSLIGKGGSIVRTFQNETGASIKIA 86 (424)
Q Consensus 46 ~~~~~~~ri~ip~~------~vg~IIGk~G~~Ik~I~~~tga~I~v~ 86 (424)
.+-.++.+|+||.+ +||+|+|.+|.++|+|+++|+|+|.|.
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 34566889999986 699999999999999999999999985
No 57
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.92 E-value=0.0017 Score=59.10 Aligned_cols=98 Identities=26% Similarity=0.397 Sum_probs=67.0
Q ss_pred EEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHH--HHhhcC-C
Q 014452 53 KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSR--IAEIGF-E 129 (424)
Q Consensus 53 ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~--i~e~~~-~ 129 (424)
-+.+-.+.+|..||++|++|+.|+++.|=+|.|-+- +-.+ ..-+..++.- +..... +
T Consensus 79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s~d~---------~~fI~nal~Pa~v~~V~~~~ 138 (190)
T COG0195 79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------SEDP---------AEFIKNALAPAEVLSVNIKE 138 (190)
T ss_pred EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------CCCH---------HHHHHHhcCcceEeEEEEEe
Confidence 444555778999999999999999999977777322 2111 1111111110 000001 1
Q ss_pred CCcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEec
Q 014452 130 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP 171 (424)
Q Consensus 130 ~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~ 171 (424)
.+.. ...+.||.+..+..|||+|.+++-+.+-||-++.|..
T Consensus 139 ~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 139 DDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred CCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 1122 6778899999999999999999999999999999964
No 58
>PRK12704 phosphodiesterase; Provisional
Probab=96.91 E-value=0.0025 Score=67.05 Aligned_cols=68 Identities=18% Similarity=0.358 Sum_probs=57.9
Q ss_pred ceEEEEEeccCc-ccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452 350 STTIEVVIPQLY-MAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 350 ~~t~~v~IP~~~-~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~ 422 (424)
.++..|.+|.+- -|+||||.|.||+.+...||++|.|++. ..+|+||| +|--=+.|+.-|...+..|.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~~~~~rre~a~~~l~~l~~dg~ 278 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPIRREIARLALEKLVQDGR 278 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEecCChhhHHHHHHHHHHHHhcCC
Confidence 567788999954 4999999999999999999999999853 35789999 88887889998888887664
No 59
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.88 E-value=0.0016 Score=68.73 Aligned_cols=65 Identities=15% Similarity=0.280 Sum_probs=57.4
Q ss_pred cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL 419 (424)
Q Consensus 349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~ 419 (424)
.....++.|+.+.+..|||++|++|++|.++|||+|.|. ++-+|.|.+ +.+.+++|+.+|.+..+
T Consensus 550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie------ddGtv~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------DDGTVKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec------CCCcEEEEecchHHHHHHHHHHHHHHh
Confidence 445689999999999999999999999999999999995 335789988 45999999999999875
No 60
>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=96.86 E-value=0.0017 Score=47.87 Aligned_cols=37 Identities=35% Similarity=0.461 Sum_probs=34.2
Q ss_pred cEEEEEEecccccceeeccCchHHHHHHHHhCceEEe
Q 014452 49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKI 85 (424)
Q Consensus 49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v 85 (424)
...+.+.|+.+.+|.+|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3577999999999999999999999999999988876
No 61
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.79 E-value=0.042 Score=50.91 Aligned_cols=64 Identities=17% Similarity=0.255 Sum_probs=53.6
Q ss_pred EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 209 (424)
Q Consensus 136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 209 (424)
+.+.++....-.+...+|..++.|....||+|.+.. .+..+.|+|+...+..+...|.+++...
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~----------~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR----------SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEec----------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 345556778889999999999999888999999964 3457999999999999998888888765
No 62
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.78 E-value=0.0043 Score=58.35 Aligned_cols=39 Identities=15% Similarity=0.472 Sum_probs=34.6
Q ss_pred cceEEEEEecc------CcccceeccccchHHHHHHHhCCEEEEe
Q 014452 349 TSTTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVN 387 (424)
Q Consensus 349 ~~~t~~v~IP~------~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~ 387 (424)
...+.+|.||. ++||+|+|..|.++|+|+++|||+|.|-
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 35678888885 5999999999999999999999999994
No 63
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.77 E-value=0.0027 Score=67.14 Aligned_cols=66 Identities=21% Similarity=0.351 Sum_probs=57.0
Q ss_pred ceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHhh
Q 014452 133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRET 209 (424)
Q Consensus 133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~ 209 (424)
.-..++.|+.+.+..+||++|.+|++|.++|||+|++. + +..|.|.++ .+.+.+|+..|..++++.
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-d----------dGtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-D----------DGTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-C----------CCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 34567889999999999999999999999999999995 2 234899886 488999999999999776
No 64
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.73 E-value=0.0025 Score=70.21 Aligned_cols=65 Identities=20% Similarity=0.335 Sum_probs=55.9
Q ss_pred ceEEEEEecCCCcceeeccCCchHHHHHhhcCce-EEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452 133 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS-IRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE 208 (424)
Q Consensus 133 ~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~-I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 208 (424)
.....|.||.+.++.|||.||.+||.|.++||++ |.+.+ +-.|.|.+ ..+.+++|+.+|..++.+
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-----------dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-----------DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 4567899999999999999999999999999999 87742 34588888 588999999999888763
No 65
>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=96.60 E-value=0.0031 Score=46.51 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=33.8
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEE
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV 386 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i 386 (424)
....+.|+.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578899999999999999999999999999988876
No 66
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.39 E-value=0.0054 Score=61.01 Aligned_cols=93 Identities=24% Similarity=0.397 Sum_probs=63.8
Q ss_pred cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhh-cCCCCcce
Q 014452 59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEI-GFEPGQAV 134 (424)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~-~~~~~~~~ 134 (424)
+-+|+.||++|++|+.|.++. |=+|.|-.-. -.+ ..-+..++. .+... ..+. ...
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-----------~d~---------~~fi~nal~Pa~v~~v~i~~~-~~~ 301 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS-----------DDP---------AEFIANALSPAKVISVEVLDE-DKH 301 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcC-----------CCH---------HHHHHHhcCCceEEEEEEEcC-CCc
Confidence 458999999999999999998 8888884321 111 000111000 00000 0011 224
Q ss_pred EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172 (424)
Q Consensus 135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~ 172 (424)
...+.||..+.+..|||+|.+++-...-||.+|.|...
T Consensus 302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred EEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 67899999999999999999999999999999999753
No 67
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.35 E-value=0.0044 Score=59.93 Aligned_cols=65 Identities=23% Similarity=0.362 Sum_probs=50.7
Q ss_pred cEEEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHH
Q 014452 49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA 124 (424)
Q Consensus 49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~ 124 (424)
+...-+++++...+.|||++|.|.++|+++|+|+|.++.+ ++....|+|+|-. ++++.++.++|.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~---------~~~V~~a~~Ri~ 120 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGIS---------RNCVIQALERIA 120 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehh---------HHHHHHHHHHHH
Confidence 4556788999999999999999999999999999999866 4455667777652 445555555554
No 68
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.25 E-value=0.017 Score=57.73 Aligned_cols=94 Identities=20% Similarity=0.244 Sum_probs=64.2
Q ss_pred cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhhcCCCCcceE
Q 014452 59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEIGFEPGQAVV 135 (424)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~~~~~~~~~t 135 (424)
+-+|+.||++|++|+.|.++. |=+|.|-.-..+..+ -+..++. .+...... .....
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~--------------------fI~Nal~Pa~V~~V~i~-~~~~~ 309 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI--------------------FIARALAPAIISSVKIE-EEEKK 309 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH--------------------HHHHhCCCceeeEEEEc-CCCcE
Confidence 458999999999999999998 888887432111100 0000000 00000001 12246
Q ss_pred EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCC
Q 014452 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKD 173 (424)
Q Consensus 136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~ 173 (424)
..+.||..+.+..|||+|.+++-..+-||.+|+|..-.
T Consensus 310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 78899999999999999999999999999999998644
No 69
>PRK00468 hypothetical protein; Provisional
Probab=96.17 E-value=0.0057 Score=47.01 Aligned_cols=34 Identities=26% Similarity=0.501 Sum_probs=30.0
Q ss_pred CCccEEEEEEecccccceeeccCchHHHHHHHHh
Q 014452 46 YEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNET 79 (424)
Q Consensus 46 ~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~t 79 (424)
.++.+.++|.+..+.+|+||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456789999999999999999999999999864
No 70
>PRK12705 hypothetical protein; Provisional
Probab=96.04 E-value=0.0081 Score=62.66 Aligned_cols=68 Identities=18% Similarity=0.331 Sum_probs=57.0
Q ss_pred ceEEEEEeccCcc-cceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 014452 350 STTIEVVIPQLYM-AHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 350 ~~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~~~ 422 (424)
.++..|.+|.+-+ |+||||.|.||+.+...||+.|.|++.+ ..|+|++ +|.-=+.|+.-+...|..|.
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~fdp~rreia~~~l~~Li~dgr 266 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSFNPIRREIARLTLEKLLADGR 266 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhcccCccchHHHHHHHHHHHhcCC
Confidence 5667788998555 9999999999999999999999998543 4577888 88888888888888887664
No 71
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.03 E-value=0.011 Score=59.26 Aligned_cols=94 Identities=24% Similarity=0.357 Sum_probs=64.0
Q ss_pred cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHH--HHhhcCCCCcceE
Q 014452 59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSR--IAEIGFEPGQAVV 135 (424)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~--i~e~~~~~~~~~t 135 (424)
+-+|+.||++|++|+.|.++. |=+|.|-.-..+.. .-+..++.- +............
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~--------------------~fi~nal~Pa~v~~v~i~~~~~~~ 304 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPA--------------------EFVANALSPAKVVSVEVDDEEEKA 304 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHH--------------------HHHHHhCCCceEEEEEEEcCCCcE
Confidence 459999999999999999998 88888843211100 001110000 0000000022345
Q ss_pred EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172 (424)
Q Consensus 136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~ 172 (424)
..+.||..+.+..|||+|.+++--..-||.+|.|...
T Consensus 305 ~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 305 ARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 7889999999999999999999999999999999754
No 72
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=96.00 E-value=0.0025 Score=70.07 Aligned_cols=70 Identities=21% Similarity=0.159 Sum_probs=60.9
Q ss_pred cceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC-CCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 014452 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAAQSLIHAFI 418 (424)
Q Consensus 349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~-~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i 418 (424)
......+.+|.....+|||++|++|+.+|..|||.|+|.+ ......||.+++.|+++.+..|..+|.-.|
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcccccee
Confidence 4456788999999999999999999999999999999986 334468999999999999999998886544
No 73
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.96 E-value=0.006 Score=66.55 Aligned_cols=63 Identities=19% Similarity=0.340 Sum_probs=54.9
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHH
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL 419 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~ 419 (424)
....+.||.+.++.+||.||.+||.|.++||+.|.+. ++-.|.|.+ ..+.+++|+.+|+..+.
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~------d~G~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC------CCceEEEEcccHHHHHHHHHHHHHhcc
Confidence 3467888999999999999999999999999988874 246788888 88999999999998765
No 74
>PRK02821 hypothetical protein; Provisional
Probab=95.92 E-value=0.0078 Score=46.46 Aligned_cols=34 Identities=24% Similarity=0.499 Sum_probs=29.9
Q ss_pred ccEEEEEEecccccceeeccCchHHHHHHHHhCc
Q 014452 48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGA 81 (424)
Q Consensus 48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga 81 (424)
+.+.++|.+..+.+|+||||+|.+|+.||.--.+
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 4577899999999999999999999999987544
No 75
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=95.90 E-value=0.019 Score=52.24 Aligned_cols=37 Identities=19% Similarity=0.325 Sum_probs=34.8
Q ss_pred EEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC
Q 014452 352 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 388 (424)
Q Consensus 352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~ 388 (424)
...+.||.+..+.+|||+|.+++-+.+.||-+|.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6889999999999999999999999999999999963
No 76
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.85 E-value=0.019 Score=54.35 Aligned_cols=63 Identities=17% Similarity=0.259 Sum_probs=53.1
Q ss_pred EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHhh
Q 014452 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHITSRLRET 209 (424)
Q Consensus 136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~ 209 (424)
+.+.||.+.++++||++|.+|+.|.+.++++|.+-. +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 458899999999999999999999999999998842 346899986 558888998888777665
No 77
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.84 E-value=0.0093 Score=60.55 Aligned_cols=92 Identities=28% Similarity=0.382 Sum_probs=62.7
Q ss_pred cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHH--HHHhh-cCCCCcce
Q 014452 59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHS--RIAEI-GFEPGQAV 134 (424)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~--~i~e~-~~~~~~~~ 134 (424)
+-+|+.||++|++|+.|.++. |=+|.|-.- +-.+ ..-+..++. .+... ..+ ....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~y-----------s~Dp---------~~fI~NaLsPA~V~~V~i~~-~~~k 335 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRW-----------SPDP---------ATYIANALSPARVDEVRLVD-PEGR 335 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEc-----------CCCH---------HHHHHHhcCCceeeEEEEEc-CCCc
Confidence 459999999999999999998 888887422 1111 000111100 00000 001 1223
Q ss_pred EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEec
Q 014452 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP 171 (424)
Q Consensus 135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~ 171 (424)
...+.||..+.+..|||+|.+++--..-||.+|.|..
T Consensus 336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 5688999999999999999999999999999998853
No 78
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.78 E-value=0.011 Score=45.44 Aligned_cols=32 Identities=25% Similarity=0.483 Sum_probs=29.4
Q ss_pred CccEEEEEEecccccceeeccCchHHHHHHHH
Q 014452 47 EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNE 78 (424)
Q Consensus 47 ~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~ 78 (424)
+..+.++|.+..+.+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 56678999999999999999999999999975
No 79
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.72 E-value=0.015 Score=63.58 Aligned_cols=64 Identities=22% Similarity=0.343 Sum_probs=53.3
Q ss_pred eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE 208 (424)
Q Consensus 134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 208 (424)
....+.||.+.++.+||.||.+||+|.++||++|.+.. +-.|.|.+ ..+.+.+|+.+|..+..+
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d-----------~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-----------DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-----------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 34567789999999999999999999999999887732 34588888 588999999999887754
No 80
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.63 E-value=0.024 Score=58.88 Aligned_cols=93 Identities=23% Similarity=0.358 Sum_probs=63.4
Q ss_pred cccceeeccCchHHHHHHHHh-CceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHH--HHhhcCCCCcceE
Q 014452 59 DKVGSLIGKGGSIVRTFQNET-GASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSR--IAEIGFEPGQAVV 135 (424)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~--i~e~~~~~~~~~t 135 (424)
+-+|+.||++|++|+.|.++. |=+|.|-.-. -.+ ..-+..++.- +.....+ ...-.
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-----------~d~---------~~fi~nal~pa~v~~v~~~-~~~~~ 303 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS-----------DDP---------AQFIINALSPAEVSSVVVD-EDEHS 303 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC-----------CCH---------HHHHHHhCCCCEEEEEEEe-CCCCE
Confidence 348999999999999999998 8888884221 111 0000000000 0000001 11236
Q ss_pred EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172 (424)
Q Consensus 136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~ 172 (424)
+.+.||..+.+..|||+|.+++-.++.||.+|.|...
T Consensus 304 ~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 304 ADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 7899999999999999999999999999999999764
No 81
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.43 E-value=0.016 Score=52.37 Aligned_cols=40 Identities=28% Similarity=0.378 Sum_probs=33.7
Q ss_pred ccEEEEEEecc------cccceeeccCchHHHHHHHHhCceEEecc
Q 014452 48 EEVVFKLLCHL------DKVGSLIGKGGSIVRTFQNETGASIKIAD 87 (424)
Q Consensus 48 ~~~~~ri~ip~------~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 87 (424)
..++-++.||. ++||+|||+.|+|+|+|++.|+|+|-|..
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 34455677774 67999999999999999999999999973
No 82
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.32 E-value=0.021 Score=51.72 Aligned_cols=37 Identities=22% Similarity=0.420 Sum_probs=31.3
Q ss_pred eEEEEEecc------CcccceeccccchHHHHHHHhCCEEEEe
Q 014452 351 TTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~------~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~ 387 (424)
.+.++.||- +++|+|||..|+++|++++.|+|+|-|-
T Consensus 148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR 190 (269)
T COG5176 148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR 190 (269)
T ss_pred ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence 344555553 7899999999999999999999999995
No 83
>PRK01064 hypothetical protein; Provisional
Probab=95.17 E-value=0.024 Score=43.91 Aligned_cols=33 Identities=18% Similarity=0.496 Sum_probs=29.8
Q ss_pred CccEEEEEEecccccceeeccCchHHHHHHHHh
Q 014452 47 EEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNET 79 (424)
Q Consensus 47 ~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~t 79 (424)
.+.+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 466789999999999999999999999999854
No 84
>PRK00468 hypothetical protein; Provisional
Probab=95.10 E-value=0.023 Score=43.68 Aligned_cols=31 Identities=23% Similarity=0.309 Sum_probs=28.4
Q ss_pred ceEEEEEeccCcccceeccccchHHHHHHHh
Q 014452 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
...+++.+..+-+|+||||+|.+|+.||..-
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 4789999999999999999999999999864
No 85
>PRK02821 hypothetical protein; Provisional
Probab=95.07 E-value=0.023 Score=43.86 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=29.0
Q ss_pred ceEEEEEeccCcccceeccccchHHHHHHHhC
Q 014452 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISG 381 (424)
Q Consensus 350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SG 381 (424)
...+++.|.++-+|+||||+|.+|+.||..-.
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 47799999999999999999999999998743
No 86
>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=94.96 E-value=0.056 Score=53.87 Aligned_cols=37 Identities=24% Similarity=0.419 Sum_probs=35.1
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~ 387 (424)
....+.||.+..+..|||+|.|++-.++.||.+|.|.
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence 4688999999999999999999999999999999995
No 87
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.93 E-value=0.065 Score=56.47 Aligned_cols=65 Identities=17% Similarity=0.260 Sum_probs=49.2
Q ss_pred eEEEEEecC-CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452 134 VVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE 208 (424)
Q Consensus 134 ~t~~l~IP~-~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 208 (424)
.+-.+.+|+ ++-|+|||+.|.||+.++..||++|-|.+ +...|+|++ .|---+.|+..|..++.+
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 344567888 58899999999999999999999997742 233577888 566666677766666653
No 88
>PRK00106 hypothetical protein; Provisional
Probab=94.92 E-value=0.072 Score=56.09 Aligned_cols=65 Identities=17% Similarity=0.300 Sum_probs=49.5
Q ss_pred eEEEEEecC-CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 014452 134 VVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRE 208 (424)
Q Consensus 134 ~t~~l~IP~-~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 208 (424)
.+-.+.+|+ ++-|+||||.|.||+.++..||+++-|.+ +...|+|++ .|---+.|+..+..++.+
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 344577888 58899999999999999999999997742 233588888 666666677666666653
No 89
>PRK12704 phosphodiesterase; Provisional
Probab=94.88 E-value=0.072 Score=56.21 Aligned_cols=66 Identities=17% Similarity=0.255 Sum_probs=49.4
Q ss_pred eEEEEEecC-CCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHhh
Q 014452 134 VVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRET 209 (424)
Q Consensus 134 ~t~~l~IP~-~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~ 209 (424)
.+-.+.+|+ ++-|+||||.|.||+.++..||++|-|. + +...|.|+| .+-.-+.|+..+..++.+.
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 334567787 5889999999999999999999999774 2 233588888 5655556776666666543
No 90
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=94.70 E-value=0.049 Score=54.47 Aligned_cols=37 Identities=16% Similarity=0.217 Sum_probs=34.9
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~ 387 (424)
....+.||.+..+..|||+|.|++-.++.||.+|.|.
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 4678999999999999999999999999999999996
No 91
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.67 E-value=0.52 Score=43.61 Aligned_cols=127 Identities=13% Similarity=0.133 Sum_probs=83.5
Q ss_pred EEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHhhcCCCCc
Q 014452 53 KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQ 132 (424)
Q Consensus 53 ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e~~~~~~~ 132 (424)
.+.++....-.+...+|..++.|-...||+|.+ ..++..+.|+|+...+.. +......+.. .
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~-----~~~~~~i~I~g~k~~~~~-------i~~~i~~~l~------~ 90 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEV-----SRSENRIRITGTKSTAEY-------IEASINEILS------N 90 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEE-----ecCCcEEEEEccHHHHHH-------HHHHHHHHHh------h
Confidence 344468889999999999999998889999999 456678999999655332 2222222221 1
Q ss_pred ceEEEEEecCCCcceee----ccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE-----eCHHHHHHHHHHHH
Q 014452 133 AVVARLLVHSQQIGCLL----GRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI-----GNYHSVQDALFHIT 203 (424)
Q Consensus 133 ~~t~~l~IP~~~vg~II----GkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~-----G~~~~v~~A~~~I~ 203 (424)
..+.++.++.-.--... -.....++.|++.|++.|...+++ ..+.|. -....+..|+.++.
T Consensus 91 i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~----------~~~~i~~~~~~~~~~~~~~a~RlL~ 160 (210)
T PF14611_consen 91 IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG----------NKLKISWLASPENEKRADRAKRLLL 160 (210)
T ss_pred cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC----------CeEEEEEEeeccccchHHHHHHHHH
Confidence 23445555532111111 113567899999999999886432 224444 45778888998888
Q ss_pred HHHH
Q 014452 204 SRLR 207 (424)
Q Consensus 204 ~~l~ 207 (424)
..+.
T Consensus 161 ~a~~ 164 (210)
T PF14611_consen 161 WALD 164 (210)
T ss_pred Hhcc
Confidence 8774
No 92
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.53 E-value=0.08 Score=53.15 Aligned_cols=37 Identities=16% Similarity=0.366 Sum_probs=35.0
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~ 387 (424)
....+.||.+..+..|||+|.|++--++.||.+|.|-
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~ 339 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK 339 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence 4688999999999999999999999999999999996
No 93
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.22 E-value=0.052 Score=41.67 Aligned_cols=32 Identities=25% Similarity=0.397 Sum_probs=28.9
Q ss_pred cceEEEEEeccCcccceeccccchHHHHHHHh
Q 014452 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
.....++.+.+.-+|+||||+|.+|+.||..-
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 35789999999999999999999999999863
No 94
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.13 E-value=0.1 Score=54.31 Aligned_cols=38 Identities=18% Similarity=0.375 Sum_probs=35.4
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 388 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~ 388 (424)
....+.||....+..|||+|.|++..++.||.+|.|-.
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 46889999999999999999999999999999999963
No 95
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.74 E-value=0.1 Score=53.20 Aligned_cols=37 Identities=14% Similarity=0.322 Sum_probs=34.7
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~ 387 (424)
....+.||.+..+..|||+|.|++--.+.||.+|.|.
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence 3578999999999999999999999999999999996
No 96
>PRK01064 hypothetical protein; Provisional
Probab=93.67 E-value=0.074 Score=41.19 Aligned_cols=32 Identities=13% Similarity=0.328 Sum_probs=28.8
Q ss_pred cceEEEEEeccCcccceeccccchHHHHHHHh
Q 014452 349 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 349 ~~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
..+.+++.|..+-.|.+|||+|.+|+.||...
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 35789999999999999999999999999863
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.23 E-value=0.042 Score=41.91 Aligned_cols=36 Identities=22% Similarity=0.284 Sum_probs=30.1
Q ss_pred ccEEEEEEecccccceeeccCchHHHHHHHHhCceE
Q 014452 48 EEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASI 83 (424)
Q Consensus 48 ~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I 83 (424)
+...+.+.+..+..|.||||+|.+++.||.-.+.-+
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 455678888999999999999999999998765543
No 98
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.09 E-value=0.34 Score=50.38 Aligned_cols=63 Identities=21% Similarity=0.195 Sum_probs=54.8
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHHc
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC 420 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~G-t~e~v~~A~~lI~~~i~~ 420 (424)
....+.|+.+..-.+||.+|-+.|+|..+||+.-.++ +.+++|-- ++++.+.|+.+|.+.+.-
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 5678999999999999999999999999999666663 35688877 899999999999998765
No 99
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=92.74 E-value=0.23 Score=44.81 Aligned_cols=137 Identities=15% Similarity=0.229 Sum_probs=84.9
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHh--hcC
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAE--IGF 128 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e--~~~ 128 (424)
+-++.||....-.+--.==....-|-+..+..|.+ +-..|.|.+.-..+..+ ..++.+..+.+.. .+|
T Consensus 75 ~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRm-----NlK~r~VelRt~~~t~D-----~s~Lqk~adfv~Af~lGF 144 (252)
T KOG3273|consen 75 TRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRM-----NLKARSVELRTCKDTED-----PSALQKGADFVRAFILGF 144 (252)
T ss_pred eeeccCCcccCChHHHhhHhhhhHHHHhhhheeEe-----ecccceeEeecCCCCCC-----hHHHHHHHHHHHHHHhCC
Confidence 44777888776655222122233456667777877 45667787765443222 1122222222211 111
Q ss_pred CC---------CcceEEEEEe----------cCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEE
Q 014452 129 EP---------GQAVVARLLV----------HSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 189 (424)
Q Consensus 129 ~~---------~~~~t~~l~I----------P~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~ 189 (424)
+- ++-+-..|.| -+..+|+|+||+|.+--.|++.|.++|.+.. ..+.|-
T Consensus 145 ~i~DAiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiL 212 (252)
T KOG3273|consen 145 DIDDAIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHIL 212 (252)
T ss_pred cchhHHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEe
Confidence 11 1111112222 2347799999999999999999999997742 359999
Q ss_pred eCHHHHHHHHHHHHHHHHhh
Q 014452 190 GNYHSVQDALFHITSRLRET 209 (424)
Q Consensus 190 G~~~~v~~A~~~I~~~l~~~ 209 (424)
|..+++..|+..|+.++...
T Consensus 213 G~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 213 GAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred ecchhhHHHHHhhHhhhccC
Confidence 99999999999999998765
No 100
>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=92.06 E-value=0.24 Score=36.40 Aligned_cols=35 Identities=20% Similarity=0.325 Sum_probs=28.2
Q ss_pred cEEEEEEecccccceeeccCchHHHHHHHHhCceE
Q 014452 49 EVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASI 83 (424)
Q Consensus 49 ~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I 83 (424)
.....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556666666799999999999999999988544
No 101
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=91.87 E-value=0.19 Score=56.14 Aligned_cols=56 Identities=29% Similarity=0.245 Sum_probs=48.5
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEeccCC-CCCcccEEEeecccccc
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADIL-PDSEERIVVISARENSE 106 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~-~~~~er~v~I~G~~~~~ 106 (424)
..++.+|.....+|||++|.+|..++.-||+.|.+.... .+..||.+.+.|.++..
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQ 1397 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhh
Confidence 447889999999999999999999999999999999743 35678999999998553
No 102
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=90.93 E-value=0.48 Score=45.04 Aligned_cols=53 Identities=13% Similarity=0.259 Sum_probs=48.1
Q ss_pred cceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 014452 363 AHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 363 g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~~~~ 422 (424)
-++||.+|++++.|+-.|.|+|-|.. .+|.+.|.-..++.++..+.++|.+-|
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~NiH 213 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKNIH 213 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhccc
Confidence 57999999999999999999999952 469999999999999999999998754
No 103
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=90.47 E-value=0.51 Score=44.22 Aligned_cols=47 Identities=23% Similarity=0.389 Sum_probs=40.5
Q ss_pred EEEecccccceeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeeccccc
Q 014452 53 KLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENS 105 (424)
Q Consensus 53 ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~ 105 (424)
-+.|+...|.++||++|+.++.|.++|+|+|-| ...-.|.|.+..+.
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~V------G~NG~IWV~~~~~~ 195 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIV------GQNGRIWVDGENES 195 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEE------ecCCEEEecCCCcc
Confidence 467899999999999999999999999999999 34456888888663
No 104
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.38 E-value=0.19 Score=37.94 Aligned_cols=34 Identities=32% Similarity=0.558 Sum_probs=27.8
Q ss_pred EEEecccc-----cceeeccCchHHHHHHHHh-CceEEec
Q 014452 53 KLLCHLDK-----VGSLIGKGGSIVRTFQNET-GASIKIA 86 (424)
Q Consensus 53 ri~ip~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~v~ 86 (424)
++.|-+.. +|..||++|++|+.|+++. |-+|.|-
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 56666666 9999999999999999999 8888884
No 105
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=90.27 E-value=0.56 Score=43.93 Aligned_cols=47 Identities=26% Similarity=0.479 Sum_probs=38.4
Q ss_pred EEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHH
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSD 405 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e 405 (424)
.-+.|+...+-++||++|+.++.|.+.++|+|.|..+ -.|=|.+..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc
Confidence 5589999999999999999999999999999999632 3455555444
No 106
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=89.61 E-value=0.19 Score=38.26 Aligned_cols=33 Identities=21% Similarity=0.261 Sum_probs=29.1
Q ss_pred ceEEEEEeccCcccceeccccchHHHHHHHhCC
Q 014452 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGA 382 (424)
Q Consensus 350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa 382 (424)
.....+.|..+..|.||||.|.+++.||.....
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 467889999999999999999999999987643
No 107
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=89.56 E-value=0.55 Score=44.64 Aligned_cols=52 Identities=17% Similarity=0.289 Sum_probs=45.8
Q ss_pred ceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhh
Q 014452 146 GCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 209 (424)
Q Consensus 146 g~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 209 (424)
-++||.+|.+++.|+-.|.|.|-|... .|.+.|....+..+...+.+++...
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~Ni 212 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKNI 212 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhcc
Confidence 579999999999999999999988532 4999999999999999999988753
No 108
>PRK12705 hypothetical protein; Provisional
Probab=89.25 E-value=0.64 Score=48.77 Aligned_cols=35 Identities=20% Similarity=0.342 Sum_probs=30.3
Q ss_pred EEEEecC-CCcceeeccCCchHHHHHhhcCceEEEe
Q 014452 136 ARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVF 170 (424)
Q Consensus 136 ~~l~IP~-~~vg~IIGkgG~~Ik~I~~~tga~I~v~ 170 (424)
-.+.+|+ ++-|+|||+.|.+|+.++..||+.+-|.
T Consensus 200 s~v~lp~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred eeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence 3456777 4779999999999999999999999784
No 109
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=88.60 E-value=1.5 Score=45.82 Aligned_cols=66 Identities=20% Similarity=0.322 Sum_probs=53.4
Q ss_pred cceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHhh
Q 014452 132 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-NYHSVQDALFHITSRLRET 209 (424)
Q Consensus 132 ~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~ 209 (424)
..+...+.++.+....+||.+|...|+|..+||+.-++. +..++|.. +..+.++|++.|..++...
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD------------e~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD------------EGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred CceeeEEeecchhhheeecCccceeeeEeeeccceeeec------------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 356778999999999999999999999999999555442 23477766 5778889999998888663
No 110
>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=88.55 E-value=0.28 Score=37.74 Aligned_cols=34 Identities=21% Similarity=0.395 Sum_probs=29.6
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEE
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIK 84 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~ 84 (424)
...+.+.....|.|||++|++|++|++...-.+.
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 3578889999999999999999999998777664
No 111
>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=88.53 E-value=0.44 Score=36.68 Aligned_cols=35 Identities=23% Similarity=0.313 Sum_probs=28.4
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEe
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKI 85 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v 85 (424)
.+.+.|..+..|.+|||+|++++.||--+..-++-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 34566778899999999999999999887765553
No 112
>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=88.42 E-value=0.82 Score=33.43 Aligned_cols=34 Identities=15% Similarity=0.232 Sum_probs=27.1
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEE
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV 384 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I 384 (424)
....+.+...-.|.+||++|.+|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666665689999999999999999987544
No 113
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.38 E-value=0.57 Score=35.38 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=28.3
Q ss_pred EEEEeccCc-----ccceeccccchHHHHHHHh-CCEEEEeC
Q 014452 353 IEVVIPQLY-----MAHVYGENNSNLSHIRQIS-GANVVVND 388 (424)
Q Consensus 353 ~~v~IP~~~-----~g~IIGk~G~~Ik~Ir~~S-Ga~I~i~~ 388 (424)
..+.|-... +|..||++|++|+.|.++. |-+|.|-+
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 455665655 8999999999999999999 99998853
No 114
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=87.16 E-value=0.32 Score=43.98 Aligned_cols=53 Identities=17% Similarity=0.353 Sum_probs=47.8
Q ss_pred CcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHH
Q 014452 360 LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL 419 (424)
Q Consensus 360 ~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~i~ 419 (424)
..+|+|+||+|.+--.|...|.++|.+.+ ..|-|-|+-++++.|+..|-.+|.
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhc
Confidence 57899999999999999999999999954 469999999999999998887775
No 115
>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=85.99 E-value=0.49 Score=36.36 Aligned_cols=34 Identities=26% Similarity=0.307 Sum_probs=28.5
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEE
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV 384 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I 384 (424)
....+.+-...-|.|||++|++|++|++..+-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4577888889999999999999999988765444
No 116
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=85.07 E-value=0.61 Score=47.72 Aligned_cols=36 Identities=19% Similarity=0.370 Sum_probs=33.5
Q ss_pred EEEEecccccceeeccCchHHHHHHHHhCceEEecc
Q 014452 52 FKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD 87 (424)
Q Consensus 52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 87 (424)
..+.||.+..+.+|||+|.+|++|+++.|-+|.|..
T Consensus 488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 567889999999999999999999999999999973
No 117
>PRK13764 ATPase; Provisional
Probab=84.54 E-value=2.3 Score=45.66 Aligned_cols=42 Identities=26% Similarity=0.465 Sum_probs=37.6
Q ss_pred eEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCC
Q 014452 134 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA 175 (424)
Q Consensus 134 ~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~ 175 (424)
-...+.||...++.+|||+|.+|++|.++.|.+|.|-+.++.
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~ 522 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEE 522 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcccc
Confidence 356788999999999999999999999999999999887654
No 118
>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=84.44 E-value=1.1 Score=34.92 Aligned_cols=35 Identities=9% Similarity=0.266 Sum_probs=30.5
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEe
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKI 85 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v 85 (424)
.+++.|....-|.|||++|+.|++|+++-.-...+
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 36888899999999999999999999987766655
No 119
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=83.65 E-value=1.6 Score=45.01 Aligned_cols=120 Identities=13% Similarity=0.135 Sum_probs=78.3
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEeccC---CCCCcccEEEeecccccccccChhHHHHHHHHHH---HH
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI---LPDSEERIVVISARENSEMRHSPAQDAVMRVHSR---IA 124 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~---i~ 124 (424)
.+.+.||...+-.|||.+|..|.+++.+.++.|++... ....-...|.|..+..+....+-+...++.+... +.
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~ 529 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFN 529 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhhhcccc
Confidence 46688999999999999999999999999999999732 1122334588888876655444444433333221 10
Q ss_pred hhc---C----------C----------CCc------ceEEEEEecCCCcceeec---cCCchHHHHHhhcCceEEEe
Q 014452 125 EIG---F----------E----------PGQ------AVVARLLVHSQQIGCLLG---RGGHIVSEMRRATGASIRVF 170 (424)
Q Consensus 125 e~~---~----------~----------~~~------~~t~~l~IP~~~vg~IIG---kgG~~Ik~I~~~tga~I~v~ 170 (424)
-.+ + + ... +....+-+|.+.++..+| -.|++|..+.....-.|...
T Consensus 530 ~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~ 607 (657)
T COG5166 530 LKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFS 607 (657)
T ss_pred cccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccceee
Confidence 000 0 0 011 122335567777788888 77888888888877777654
No 120
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=82.70 E-value=1.6 Score=38.84 Aligned_cols=44 Identities=23% Similarity=0.506 Sum_probs=32.6
Q ss_pred CCcCCCccEEEEEEecccccceeeccCchHHHHHHHHhCceEEecc
Q 014452 42 NRMFYEEEVVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD 87 (424)
Q Consensus 42 ~~~~~~~~~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 87 (424)
++....+... -++|-... |.-|||+|++|++|++..|-+|.+-+
T Consensus 54 ~k~~~~ddrv-IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 54 KKAYEVDDLV-ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEeCCEE-EEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 3333333333 45555566 99999999999999999999999843
No 121
>PRK13764 ATPase; Provisional
Probab=81.91 E-value=1 Score=48.30 Aligned_cols=37 Identities=19% Similarity=0.390 Sum_probs=34.0
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEecc
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD 87 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 87 (424)
...+.||.+.++.+|||+|.+|++|+++.|.+|.|..
T Consensus 482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 4567899999999999999999999999999999973
No 122
>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=81.44 E-value=1.8 Score=33.23 Aligned_cols=33 Identities=15% Similarity=0.409 Sum_probs=26.9
Q ss_pred EEEEEecCCCcceeeccCCchHHHHHhhcCceE
Q 014452 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 167 (424)
Q Consensus 135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I 167 (424)
.+.+.|..+..|.+|||.|++++.||--.+.-+
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 356677778899999999999999997766544
No 123
>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=80.81 E-value=2.8 Score=36.35 Aligned_cols=87 Identities=18% Similarity=0.373 Sum_probs=52.9
Q ss_pred ccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHH------hhcCCCCcceEEEEE
Q 014452 66 GKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIA------EIGFEPGQAVVARLL 139 (424)
Q Consensus 66 Gk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~------e~~~~~~~~~t~~l~ 139 (424)
=..|..|++|-++..-+|.|... +..... ..+|...+.+.+- +.-|+. .+-++.
T Consensus 22 ~~~~dli~~lAk~lrKRIvvR~d--------------ps~l~~---~e~A~~~I~~ivP~ea~i~di~Fd~---~tGEV~ 81 (145)
T cd02410 22 AEDGDLVKDLAKDLRKRIVIRPD--------------PSVLKP---PEEAIKIILEIVPEEAGITDIYFDD---DTGEVI 81 (145)
T ss_pred hcccHHHHHHHHHHhceEEEcCC--------------hhhcCC---HHHHHHHHHHhCCCccCceeeEecC---CCcEEE
Confidence 34577888888888777777421 111100 1223333333221 112222 233455
Q ss_pred ecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452 140 VHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172 (424)
Q Consensus 140 IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~ 172 (424)
|-.+.-|.+||++|.++++|..+||-.-.|...
T Consensus 82 IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 82 IEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred EEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 556677999999999999999999999888654
No 124
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=80.63 E-value=1.2 Score=45.64 Aligned_cols=37 Identities=22% Similarity=0.424 Sum_probs=34.3
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEe
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~ 387 (424)
....+.||..+++.||||+|.+|++|++..|-+|.|-
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 4567899999999999999999999999999999996
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=79.74 E-value=1.7 Score=35.94 Aligned_cols=31 Identities=23% Similarity=0.391 Sum_probs=26.6
Q ss_pred EEEEecccccceeeccCchHHHHHHHHhCce
Q 014452 52 FKLLCHLDKVGSLIGKGGSIVRTFQNETGAS 82 (424)
Q Consensus 52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~ 82 (424)
++|.|....-|.|||++|++|++|++.....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 6788888999999999999999999875443
No 126
>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=77.26 E-value=2.9 Score=32.57 Aligned_cols=36 Identities=17% Similarity=0.289 Sum_probs=28.6
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEE
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV 386 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i 386 (424)
...+|.|-...-|.|||++|+.|++|++.---...+
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 347778878888999999999999998876544444
No 127
>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=76.42 E-value=2.8 Score=32.89 Aligned_cols=28 Identities=21% Similarity=0.445 Sum_probs=23.8
Q ss_pred EEEEecccccceeeccCchHHHHHHHHh
Q 014452 52 FKLLCHLDKVGSLIGKGGSIVRTFQNET 79 (424)
Q Consensus 52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~t 79 (424)
+++.|....-|.+||++|.+|++|++.-
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 4666667899999999999999998874
No 128
>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=74.91 E-value=3.9 Score=35.44 Aligned_cols=39 Identities=28% Similarity=0.221 Sum_probs=34.6
Q ss_pred ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeC
Q 014452 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 388 (424)
Q Consensus 350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~ 388 (424)
..+-+|.|-.+.-|.|||++|.++++|..+||-.-.|-.
T Consensus 75 ~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 75 DDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred CCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 356788888899999999999999999999999888864
No 129
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=72.80 E-value=4.6 Score=35.97 Aligned_cols=36 Identities=36% Similarity=0.569 Sum_probs=30.9
Q ss_pred EEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452 136 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172 (424)
Q Consensus 136 ~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~ 172 (424)
+-++|-... |.-|||+|.+|+.+++..|-+|.+...
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 456676667 999999999999999999999998743
No 130
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=70.68 E-value=3.7 Score=38.42 Aligned_cols=30 Identities=27% Similarity=0.406 Sum_probs=26.0
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhC
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETG 80 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tg 80 (424)
..+|.|....-|.|||++|+.|++|++...
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 467888999999999999999999887643
No 131
>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=66.65 E-value=5.3 Score=32.94 Aligned_cols=28 Identities=18% Similarity=0.318 Sum_probs=23.7
Q ss_pred EEEEeccCcccceeccccchHHHHHHHh
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
++|.|-...-|.|||+.|+.|++|++..
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 5667777778999999999999998774
No 132
>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=65.39 E-value=6.7 Score=30.73 Aligned_cols=28 Identities=18% Similarity=0.248 Sum_probs=22.1
Q ss_pred EEEEeccCcccceeccccchHHHHHHHh
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
.++.|-...-|.+||++|.+|++|++.-
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 4455555777999999999999988763
No 133
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=64.25 E-value=21 Score=37.23 Aligned_cols=39 Identities=26% Similarity=0.206 Sum_probs=33.5
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP 389 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~ 389 (424)
.+.+|.|-.+.-|.||||+|++.++|.++||-.-+|...
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 356788888899999999999999999999988777643
No 134
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=63.89 E-value=6.3 Score=36.91 Aligned_cols=36 Identities=28% Similarity=0.352 Sum_probs=27.8
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHH----hCC-EEEE
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQI----SGA-NVVV 386 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~----SGa-~I~i 386 (424)
....|+|-...-|.|||++|++|++|++. +|. .++|
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I 91 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI 91 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence 34678888888899999999999988764 565 3444
No 135
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=61.95 E-value=6.3 Score=40.90 Aligned_cols=128 Identities=9% Similarity=0.010 Sum_probs=79.6
Q ss_pred eeeccCchHHHHHHHHhCceEEec-cCCCCCcccEEE-eecccccccccChhHHHHHHHHHHHHhhcCCCCcceEEEEEe
Q 014452 63 SLIGKGGSIVRTFQNETGASIKIA-DILPDSEERIVV-ISARENSEMRHSPAQDAVMRVHSRIAEIGFEPGQAVVARLLV 140 (424)
Q Consensus 63 ~IIGk~G~~Ik~I~~~tga~I~v~-~~~~~~~er~v~-I~G~~~~~~~~~~a~~av~~~~~~i~e~~~~~~~~~t~~l~I 140 (424)
.|-||+--.+.+|++...|.+.+. ....++ ++.+ +.|... +..+.+..+. .+=...+.+.|
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~gs--~~~~~~~g~~~----------~F~k~~~~~~-----~EFpae~~f~i 455 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSSTGS--IVETNGIGEKM----------SFSKKLSIPP-----TEFPAEIAFII 455 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEecCCc--EEEEeccCcch----------hhHHHhcCCc-----ccCchheEEEe
Confidence 677888777999999999986654 221122 3333 233321 1112121110 01122467899
Q ss_pred cCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHH---HHHHHHHHHHHHHHhh
Q 014452 141 HSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH---SVQDALFHITSRLRET 209 (424)
Q Consensus 141 P~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~---~v~~A~~~I~~~l~~~ 209 (424)
|...|..|||.||..|++++.+.++.|++...-+++.. .--..|.|.-+.+ ++--++--+.+++.++
T Consensus 456 ~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs--~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~ 525 (657)
T COG5166 456 MESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQS--QWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQ 525 (657)
T ss_pred ecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchh--hhhcceEEECCccCccchhcccccHHHHHhhh
Confidence 99999999999999999999999999988764444321 1112377776654 3444666667777765
No 136
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=61.49 E-value=17 Score=38.03 Aligned_cols=90 Identities=19% Similarity=0.375 Sum_probs=58.4
Q ss_pred eeeccCchHHHHHHHHhCceEEeccCCCCCcccEEEeecccccccccChhHHHHHHHHHHHHh------hcCCCCcceEE
Q 014452 63 SLIGKGGSIVRTFQNETGASIKIADILPDSEERIVVISARENSEMRHSPAQDAVMRVHSRIAE------IGFEPGQAVVA 136 (424)
Q Consensus 63 ~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~v~I~G~~~~~~~~~~a~~av~~~~~~i~e------~~~~~~~~~t~ 136 (424)
.++=+.|..||+|-++..-+|.|.... .+ .. + ..+|...+.+.+-+ ..|+ ..+-
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP------sv-l~-~---------~e~A~~~I~eivP~ea~i~~i~Fd---~~tG 101 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP------SV-LK-P---------PEEARKIILEIVPEEAGITDIYFD---DDTG 101 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc------hh-cC-C---------HHHHHHHHHHhCccccCceeEEec---CCCc
Confidence 456678899999999988888884221 01 01 1 12333333333321 1121 2234
Q ss_pred EEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452 137 RLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172 (424)
Q Consensus 137 ~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~ 172 (424)
++.|-.+.-|.+|||+|++.++|..++|-.-+|...
T Consensus 102 EViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 102 EVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred eEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 667777788999999999999999999988877654
No 137
>PRK03818 putative transporter; Validated
Probab=55.16 E-value=1.8e+02 Score=31.23 Aligned_cols=129 Identities=12% Similarity=0.227 Sum_probs=70.4
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEeccC---------CCC---CcccEEEeecccccccccChhHHHHHH
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI---------LPD---SEERIVVISARENSEMRHSPAQDAVMR 118 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---------~~~---~~er~v~I~G~~~~~~~~~~a~~av~~ 118 (424)
..++.|+++. ++ |.++++++......+.|..- .++ ...+++.|.|..++ +.+
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~----------l~~ 269 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPED----------LHK 269 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHH----------HHH
Confidence 3566666443 34 67999999988877766411 111 13466778887543 333
Q ss_pred HHHHHHhh---cCC--CCcceEEEEEecCCCcceeeccCCchHHHH--HhhcCceE-EEecCCC-CCCCCC---CCCcEE
Q 014452 119 VHSRIAEI---GFE--PGQAVVARLLVHSQQIGCLLGRGGHIVSEM--RRATGASI-RVFPKDQ-APRCGS---PHDEIV 186 (424)
Q Consensus 119 ~~~~i~e~---~~~--~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I--~~~tga~I-~v~~~~~-~p~~~~---~~~r~v 186 (424)
+.+.+-.. ..+ ........+.+|.+ .++|| +++++ ++++|+.| .|.+.+. .+...+ ..-..+
T Consensus 270 l~~~~Gl~~~~~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~L 343 (552)
T PRK03818 270 AQLVIGEEVDTSLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDIL 343 (552)
T ss_pred HHHhcCCccCccccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEE
Confidence 33222111 011 12233444555653 55554 68887 57788886 3333221 111110 122578
Q ss_pred EEEeCHHHHHHHHHH
Q 014452 187 QVIGNYHSVQDALFH 201 (424)
Q Consensus 187 ~I~G~~~~v~~A~~~ 201 (424)
.+.|++++++++.+.
T Consensus 344 lVvG~~~~i~~l~~~ 358 (552)
T PRK03818 344 NLVGRPEAIDAVANV 358 (552)
T ss_pred EEEECHHHHHHHHHH
Confidence 999999999987664
No 138
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=52.18 E-value=37 Score=33.80 Aligned_cols=50 Identities=18% Similarity=0.321 Sum_probs=44.0
Q ss_pred cCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHH
Q 014452 359 QLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 415 (424)
Q Consensus 359 ~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~ 415 (424)
.+..-.+.|..+.+++.|.+..|+.|... .+.++|+|+...|+.|...++
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~r-------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVAR-------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeC-------CceEEEEechHHHHHHHHHHh
Confidence 56778899999999999999999988873 256999999889999999888
No 139
>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=50.56 E-value=3.5e+02 Score=29.06 Aligned_cols=131 Identities=19% Similarity=0.263 Sum_probs=67.9
Q ss_pred EEEEEEecccccceeeccCchHHHHHHHHhCceEEecc---------CCCC---CcccEEEeecccccccccChhHHHHH
Q 014452 50 VVFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIAD---------ILPD---SEERIVVISARENSEMRHSPAQDAVM 117 (424)
Q Consensus 50 ~~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~---------~~~~---~~er~v~I~G~~~~~~~~~~a~~av~ 117 (424)
....+.|+.+ ..++ |.+|+++.......+.|.. ..++ ....++.+.|..++ +.
T Consensus 218 ~~r~~~V~~~--s~li---GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~----------L~ 282 (562)
T TIGR03802 218 VGRAYRVNRA--SSLI---GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDA----------VV 282 (562)
T ss_pred eeEEEEECCC--cccC---CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHH----------HH
Confidence 3445555554 2234 6678888887765555531 1111 12356777887543 33
Q ss_pred HHHHHHHhh----cCCCCcceEEEEEecCCCcceeeccCCchHHHHH------hhcCceEEEecCCCC--CCCC---CCC
Q 014452 118 RVHSRIAEI----GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMR------RATGASIRVFPKDQA--PRCG---SPH 182 (424)
Q Consensus 118 ~~~~~i~e~----~~~~~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~------~~tga~I~v~~~~~~--p~~~---~~~ 182 (424)
++.+.+-.. ..........++.+|++ .++ |++++++. +++|+.|.-..+.+. +... -..
T Consensus 283 ~l~~~~G~~~~~~~~~~~~~~~e~VV~~~S---~li---GkTL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~ 356 (562)
T TIGR03802 283 QFGAEIGEEVQEVEGLDVPMETKDVVLTNK---EYN---GKTVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQR 356 (562)
T ss_pred HHHHhcCCccCCccccCCceEEEEEEECCc---ccC---CccHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecC
Confidence 332221110 00011122344555653 455 45788887 378888744333321 1110 112
Q ss_pred CcEEEEEeCHHHHHHHHHH
Q 014452 183 DEIVQVIGNYHSVQDALFH 201 (424)
Q Consensus 183 ~r~v~I~G~~~~v~~A~~~ 201 (424)
-..+.+.|++++++++.+.
T Consensus 357 GD~LlV~G~~~~l~~~~~~ 375 (562)
T TIGR03802 357 GDVVTLVGTPQDVDRAAKQ 375 (562)
T ss_pred CCEEEEEeCHHHHHHHHHH
Confidence 3578999999999887665
No 140
>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=49.10 E-value=18 Score=33.21 Aligned_cols=31 Identities=23% Similarity=0.461 Sum_probs=26.6
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCc
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGA 81 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga 81 (424)
..+|.|....-|.|||++|..|++|+++-.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 3678888889999999999999999887544
No 141
>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=48.78 E-value=19 Score=34.46 Aligned_cols=31 Identities=13% Similarity=0.125 Sum_probs=24.2
Q ss_pred ceEEEEEeccCcc-cceeccccchHHHHHHHh
Q 014452 350 STTIEVVIPQLYM-AHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 350 ~~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir~~S 380 (424)
.+...|.|..+.+ +-|||++|+.||+|..+.
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 3667788887555 999999999999876543
No 142
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=48.33 E-value=18 Score=33.51 Aligned_cols=31 Identities=19% Similarity=0.403 Sum_probs=25.6
Q ss_pred EEEEecccccceeeccCchHHHHHHHHhCce
Q 014452 52 FKLLCHLDKVGSLIGKGGSIVRTFQNETGAS 82 (424)
Q Consensus 52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~ 82 (424)
.++.|....-|.+||++|++|++|++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 4566666889999999999999999886554
No 143
>CHL00048 rps3 ribosomal protein S3
Probab=47.96 E-value=18 Score=33.61 Aligned_cols=30 Identities=13% Similarity=0.121 Sum_probs=25.8
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhC
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETG 80 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tg 80 (424)
..+|.|-...-|.|||++|++|++|++...
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 357777888899999999999999998764
No 144
>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=46.90 E-value=25 Score=38.29 Aligned_cols=38 Identities=21% Similarity=0.517 Sum_probs=32.1
Q ss_pred EEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecC
Q 014452 135 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 172 (424)
Q Consensus 135 t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~ 172 (424)
+-++.|-.+.-|.||||+|.++++|..+||-.-.|...
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 34566667777999999999999999999999888754
No 145
>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=45.47 E-value=26 Score=33.57 Aligned_cols=29 Identities=17% Similarity=0.288 Sum_probs=22.6
Q ss_pred EEEEEEecc-cccceeeccCchHHHHHHHH
Q 014452 50 VVFKLLCHL-DKVGSLIGKGGSIVRTFQNE 78 (424)
Q Consensus 50 ~~~ri~ip~-~~vg~IIGk~G~~Ik~I~~~ 78 (424)
+...|+|.. ++-+-|||++|+.||+|..+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 556677775 55788999999999987554
No 146
>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=45.35 E-value=16 Score=39.69 Aligned_cols=40 Identities=28% Similarity=0.208 Sum_probs=35.4
Q ss_pred ceEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCC
Q 014452 350 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP 389 (424)
Q Consensus 350 ~~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~ 389 (424)
..+-+|.|-.+.-|.||||+|+++++|.++||-.-+|-..
T Consensus 92 ~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 92 DVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 4568889999999999999999999999999998888643
No 147
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=44.18 E-value=40 Score=31.50 Aligned_cols=32 Identities=9% Similarity=0.265 Sum_probs=27.2
Q ss_pred EEEEecccccceeeccCchHHHHHHHHhCceE
Q 014452 52 FKLLCHLDKVGSLIGKGGSIVRTFQNETGASI 83 (424)
Q Consensus 52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I 83 (424)
.++.|....-|.|||++|..|++|+++..-.+
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 57778888899999999999999998865544
No 148
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=43.77 E-value=13 Score=34.31 Aligned_cols=35 Identities=20% Similarity=0.242 Sum_probs=29.3
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEe
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKI 85 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v 85 (424)
.+.+-+..+..+.|||+.|+++..||--+.+-++-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 45666777889999999999999999988876655
No 149
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=43.67 E-value=23 Score=34.87 Aligned_cols=32 Identities=22% Similarity=0.284 Sum_probs=26.1
Q ss_pred cceEEEEEeccCcc-cceeccccchHHHHHHHh
Q 014452 349 TSTTIEVVIPQLYM-AHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 349 ~~~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir~~S 380 (424)
-.+..++.||.... ..||||+|.+|++|-++-
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 35788999999655 778999999999986653
No 150
>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=42.89 E-value=1.2e+02 Score=26.95 Aligned_cols=57 Identities=16% Similarity=0.145 Sum_probs=43.8
Q ss_pred CcceEEEEEecCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHH
Q 014452 131 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSR 205 (424)
Q Consensus 131 ~~~~t~~l~IP~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~ 205 (424)
.+..++++.++...+- .++.+|.+-.|+-+.+. .+..|.|-|..+.|.+|+..+...
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efe-----------e~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEFE-----------EDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEec-----------CCcEEEEeccHHHHHHHHHHHHHH
Confidence 3445677777776553 57889999999999882 234699999999999999887654
No 151
>PRK15494 era GTPase Era; Provisional
Probab=42.65 E-value=26 Score=34.89 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=28.2
Q ss_pred eEEEEEeccCcc-cceeccccchHHHHHH--------HhCCEEEEe
Q 014452 351 TTIEVVIPQLYM-AHVYGENNSNLSHIRQ--------ISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir~--------~SGa~I~i~ 387 (424)
+...|.|..+.+ +-|||++|+.||+|.. ..|++|.+.
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 557788888655 8999999999987754 467776664
No 152
>PRK00089 era GTPase Era; Reviewed
Probab=41.64 E-value=28 Score=33.57 Aligned_cols=37 Identities=14% Similarity=0.262 Sum_probs=27.6
Q ss_pred eEEEEEeccCcc-cceeccccchHHHHH--------HHhCCEEEEe
Q 014452 351 TTIEVVIPQLYM-AHVYGENNSNLSHIR--------QISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir--------~~SGa~I~i~ 387 (424)
+...|.|..+.. +-|||++|++|++|. +..+++|.+.
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 556677777554 899999999998765 4467777664
No 153
>PRK15494 era GTPase Era; Provisional
Probab=38.40 E-value=37 Score=33.84 Aligned_cols=36 Identities=14% Similarity=0.239 Sum_probs=26.5
Q ss_pred EEEEEEecc-cccceeeccCchHHHHHHH--------HhCceEEe
Q 014452 50 VVFKLLCHL-DKVGSLIGKGGSIVRTFQN--------ETGASIKI 85 (424)
Q Consensus 50 ~~~ri~ip~-~~vg~IIGk~G~~Ik~I~~--------~tga~I~v 85 (424)
+...|+|.. ++-+-|||++|+.||+|.. -.+++|.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 456677776 5678899999999998754 45666655
No 154
>COG1159 Era GTPase [General function prediction only]
Probab=38.08 E-value=35 Score=33.28 Aligned_cols=37 Identities=14% Similarity=0.288 Sum_probs=27.1
Q ss_pred eEEEEEeccCcc-cceeccccchHHHHH--------HHhCCEEEEe
Q 014452 351 TTIEVVIPQLYM-AHVYGENNSNLSHIR--------QISGANVVVN 387 (424)
Q Consensus 351 ~t~~v~IP~~~~-g~IIGk~G~~Ik~Ir--------~~SGa~I~i~ 387 (424)
+-..|.|+.+.. +-||||+|++||+|- +..+++|.+.
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 445677887555 999999999998764 4456666663
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=36.03 E-value=1.1e+02 Score=23.91 Aligned_cols=55 Identities=20% Similarity=0.190 Sum_probs=42.0
Q ss_pred CCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 014452 152 GGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 208 (424)
Q Consensus 152 gG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 208 (424)
|=..+.++-+..+++++..-++... ....+.++++.|+..++..|-+.++.+|+.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~--v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDR--VEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-E--EETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCC--ccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 3446788888889999877554321 225678999999999999999999988865
No 156
>PRK00089 era GTPase Era; Reviewed
Probab=34.74 E-value=28 Score=33.58 Aligned_cols=36 Identities=19% Similarity=0.449 Sum_probs=25.5
Q ss_pred EEEEEEecc-cccceeeccCchHHHHHHH--------HhCceEEe
Q 014452 50 VVFKLLCHL-DKVGSLIGKGGSIVRTFQN--------ETGASIKI 85 (424)
Q Consensus 50 ~~~ri~ip~-~~vg~IIGk~G~~Ik~I~~--------~tga~I~v 85 (424)
+...|.|.. ++-+-|||++|++||+|.. -.+++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 445566654 5578899999999998754 45666655
No 157
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=34.63 E-value=72 Score=29.46 Aligned_cols=69 Identities=13% Similarity=0.163 Sum_probs=44.0
Q ss_pred eEEEEEeccCcccceeccccchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCH------HHHHHHHHHHHHHHHcCc
Q 014452 351 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS------DQMRAAQSLIHAFILCGV 422 (424)
Q Consensus 351 ~t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~------e~v~~A~~lI~~~i~~~~ 422 (424)
.+..+.|-.+..+.+||+.|.+++.|+-.+.+.+.- ..+...+++.=.|.. .=+..|..+-...+++|.
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~---~~g~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV~~tg~ 165 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK---IGGKFKRVTLDVGDYRERRKETLIKLAERAAERVLETGR 165 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh---hcCcceEEEEEhhhHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 357778888889999999999999999988554443 222222322223332 345556666666666554
No 158
>PRK04972 putative transporter; Provisional
Probab=34.13 E-value=6.2e+02 Score=27.17 Aligned_cols=133 Identities=14% Similarity=0.168 Sum_probs=67.1
Q ss_pred EEEEEecccccceeeccCchHHHHHHHHhCceEEeccC---------CCC---CcccEEEeecccccccccChhHHHHHH
Q 014452 51 VFKLLCHLDKVGSLIGKGGSIVRTFQNETGASIKIADI---------LPD---SEERIVVISARENSEMRHSPAQDAVMR 118 (424)
Q Consensus 51 ~~ri~ip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---------~~~---~~er~v~I~G~~~~~~~~~~a~~av~~ 118 (424)
...+.|.+..+..++ |++|+++.......+.|..- .++ ....++.|.|.++. +.+
T Consensus 215 ~r~~~V~~~~~~~~~---Gktl~el~~~~~~~v~I~~I~R~g~~~~p~~dt~L~~GDiL~V~G~~e~----------l~~ 281 (558)
T PRK04972 215 IRAYRVGPELVAWTD---GKNLRELGIYRQTGCYIERIRRNGILANPDGDAVLQMGDEIALVGYPDA----------HAR 281 (558)
T ss_pred eeEEEECCccccCcC---CCCHHHHHhhcCCCEEEEEEEECCEEecCCCCCEeCCCCEEEEEECHHH----------HHH
Confidence 445555554333323 77899998888666555411 111 12356777777543 222
Q ss_pred HHHHH--HhhcCC-C--Ccc-eEEEEEecCCCcceeeccCCchHHHHH-hhcCceEEEecCC--CCCCCCC---CCCcEE
Q 014452 119 VHSRI--AEIGFE-P--GQA-VVARLLVHSQQIGCLLGRGGHIVSEMR-RATGASIRVFPKD--QAPRCGS---PHDEIV 186 (424)
Q Consensus 119 ~~~~i--~e~~~~-~--~~~-~t~~l~IP~~~vg~IIGkgG~~Ik~I~-~~tga~I~v~~~~--~~p~~~~---~~~r~v 186 (424)
+.+.. .+...+ . +.. ....+.+|+ ..++| ++++++. +++|+.|.-..+. +.+...+ ..-..+
T Consensus 282 l~~~~~lg~e~~~~~~~~~~~~~E~vVv~~---s~liG---kTL~eL~~r~~gv~Vl~I~R~g~~~~~~~~~~L~~GD~L 355 (558)
T PRK04972 282 LDPSFRNGKEVFDRDLLDMRIVTEEIVVKN---HNAVG---KRLSQLKLTDHGCFLNRVIRSQIEMPIDDNVVLNKGDVL 355 (558)
T ss_pred HHHhhcCCCcccCccccCcceEEEEEEEcC---cccCC---CCHHHhCCccCCeEEEEEecCCcccCCCCCCEecCCCEE
Confidence 22221 010001 1 111 334455555 34554 4688774 2388887433332 2211110 123578
Q ss_pred EEEeCHHHHHHHHHHH
Q 014452 187 QVIGNYHSVQDALFHI 202 (424)
Q Consensus 187 ~I~G~~~~v~~A~~~I 202 (424)
.+.|+++++++..+.+
T Consensus 356 lVvG~~~~i~~l~~~l 371 (558)
T PRK04972 356 QVSGDARRVKTIADRI 371 (558)
T ss_pred EEEECHHHHHHHHHHh
Confidence 9999999998865544
No 159
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=34.11 E-value=38 Score=31.36 Aligned_cols=28 Identities=18% Similarity=0.233 Sum_probs=22.2
Q ss_pred EEEEeccCcccceeccccchHHHHHHHh
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
.++.|-...-|.+||++|++|+++++.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~L 69 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEIL 69 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHH
Confidence 4455555778999999999999988775
No 160
>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=34.09 E-value=40 Score=30.87 Aligned_cols=29 Identities=14% Similarity=0.132 Sum_probs=23.9
Q ss_pred EEEEEeccCcccceeccccchHHHHHHHh
Q 014452 352 TIEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
..+|.|-...-|.|||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46677777778999999999999987763
No 161
>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=33.73 E-value=1.5e+02 Score=23.01 Aligned_cols=51 Identities=12% Similarity=0.100 Sum_probs=40.2
Q ss_pred ccchHHHHHHHhCCEEEEeCCCCC---CCCcEEEEEcCHHHHHHHHHHHHHHHH
Q 014452 369 NNSNLSHIRQISGANVVVNDPKPG---ATEGVVMVSGTSDQMRAAQSLIHAFIL 419 (424)
Q Consensus 369 ~G~~Ik~Ir~~SGa~I~i~~~~~~---~~~r~i~I~Gt~e~v~~A~~lI~~~i~ 419 (424)
|=..+.+|=+..+++++..-.... ..+.+++|+|+..++-.|.+.++++|.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 445778888888999888633222 357899999999999999999999875
No 162
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=33.31 E-value=40 Score=31.29 Aligned_cols=29 Identities=24% Similarity=0.485 Sum_probs=25.0
Q ss_pred EEEEecccccceeeccCchHHHHHHHHhC
Q 014452 52 FKLLCHLDKVGSLIGKGGSIVRTFQNETG 80 (424)
Q Consensus 52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tg 80 (424)
++|.|....-+.|||++|..|++|++...
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 57888888889999999999999987653
No 163
>COG1159 Era GTPase [General function prediction only]
Probab=33.17 E-value=54 Score=32.03 Aligned_cols=36 Identities=17% Similarity=0.425 Sum_probs=25.4
Q ss_pred EEEEEEecc-cccceeeccCchHHHHHH--------HHhCceEEe
Q 014452 50 VVFKLLCHL-DKVGSLIGKGGSIVRTFQ--------NETGASIKI 85 (424)
Q Consensus 50 ~~~ri~ip~-~~vg~IIGk~G~~Ik~I~--------~~tga~I~v 85 (424)
+...|+|+. ++-+-||||+|+.||+|- +-.+++|.+
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 344566665 567889999999999764 445666555
No 164
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=31.82 E-value=43 Score=31.30 Aligned_cols=28 Identities=14% Similarity=0.343 Sum_probs=23.1
Q ss_pred EEEEeccCcccceeccccchHHHHHHHh
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
.+|.|-...-|.|||++|..|++|++.-
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 6667767778999999999999987664
No 165
>CHL00048 rps3 ribosomal protein S3
Probab=31.78 E-value=47 Score=30.92 Aligned_cols=29 Identities=10% Similarity=0.126 Sum_probs=23.9
Q ss_pred EEEEEeccCcccceeccccchHHHHHHHh
Q 014452 352 TIEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 352 t~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
..+|.|-...-|.|||++|.+|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46666667778999999999999998764
No 166
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=30.14 E-value=54 Score=32.38 Aligned_cols=33 Identities=18% Similarity=0.409 Sum_probs=25.6
Q ss_pred eEEEEEecCC-CcceeeccCCchHHHHHhhcCce
Q 014452 134 VVARLLVHSQ-QIGCLLGRGGHIVSEMRRATGAS 166 (424)
Q Consensus 134 ~t~~l~IP~~-~vg~IIGkgG~~Ik~I~~~tga~ 166 (424)
+..++.+|.. +...||||+|..|++|-++.+-+
T Consensus 328 I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~d 361 (379)
T KOG1423|consen 328 IQVEVVCPKNSQKKLLIGKGGKKISQIGTRANED 361 (379)
T ss_pred EEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHH
Confidence 5567788876 55678999999999998766544
No 167
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=29.38 E-value=1.2e+02 Score=30.31 Aligned_cols=51 Identities=25% Similarity=0.242 Sum_probs=42.1
Q ss_pred cCCCcceeeccCCchHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014452 141 HSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT 203 (424)
Q Consensus 141 P~~~vg~IIGkgG~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~ 203 (424)
+...+-.+.|..+.+++.|++.+|+.|... .+.++|+|+...+..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 355667899999999999999999999552 224999999878888888877
No 168
>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=29.06 E-value=1.5e+02 Score=22.26 Aligned_cols=33 Identities=21% Similarity=0.495 Sum_probs=25.1
Q ss_pred hCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHH
Q 014452 380 SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAF 417 (424)
Q Consensus 380 SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~ 417 (424)
...+|..++ ....+.|+|+++.++..+.||.++
T Consensus 44 ~~~~i~~d~-----~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 44 SSGRIVADE-----RTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEEC-----TTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEC-----CCCEEEEEeCHHHHHHHHHHHHHH
Confidence 344676653 235788999999999999999864
No 169
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=26.85 E-value=1.8e+02 Score=23.99 Aligned_cols=44 Identities=18% Similarity=0.293 Sum_probs=33.2
Q ss_pred HHHh-hcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhhc
Q 014452 158 EMRR-ATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI 210 (424)
Q Consensus 158 ~I~~-~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 210 (424)
+|.. ..++.|-+.++ ...-+.|+|.-.+|+.|+..+.+.+++.+
T Consensus 57 DIA~Kaa~V~igF~DR---------FsGslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 57 DLALKAADVHIGFLDR---------FSGALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred HhhhhccCcEEeeeec---------cceeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 4443 34667777643 23359999999999999999999999864
No 170
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.69 E-value=1.7e+02 Score=25.41 Aligned_cols=42 Identities=21% Similarity=0.286 Sum_probs=34.2
Q ss_pred chHHHHHhhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 014452 154 HIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL 206 (424)
Q Consensus 154 ~~Ik~I~~~tga~I~v~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 206 (424)
.++.+|.+..|+-|.+.. -.+|.|.|..+.|.+|+..|-..-
T Consensus 126 eRlqDi~E~hgvIiE~~E-----------~D~V~i~Gd~drVk~aLke~~~~w 167 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE-----------YDLVAIYGDSDRVKKALKEIGSFW 167 (170)
T ss_pred HHHHHHHHhhheeEEeee-----------ccEEEEeccHHHHHHHHHHHHHHH
Confidence 467888899999888752 336999999999999999887653
No 171
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.50 E-value=91 Score=22.30 Aligned_cols=22 Identities=27% Similarity=0.366 Sum_probs=19.2
Q ss_pred CHHHHHHHHHHHHHHHHcCcCC
Q 014452 403 TSDQMRAAQSLIHAFILCGVTS 424 (424)
Q Consensus 403 t~e~v~~A~~lI~~~i~~~~~~ 424 (424)
|-++-+.|...|++++.+|-+|
T Consensus 9 tHeqQQ~AVE~Iq~lMaeGmSs 30 (60)
T COG3140 9 THEQQQKAVERIQELMAEGMSS 30 (60)
T ss_pred cHHHHHHHHHHHHHHHHccccc
Confidence 6788899999999999998764
No 172
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=24.41 E-value=67 Score=30.31 Aligned_cols=29 Identities=24% Similarity=0.475 Sum_probs=24.3
Q ss_pred EEEEecccccceeeccCchHHHHHHHHhC
Q 014452 52 FKLLCHLDKVGSLIGKGGSIVRTFQNETG 80 (424)
Q Consensus 52 ~ri~ip~~~vg~IIGk~G~~Ik~I~~~tg 80 (424)
++|.|-...-+.|||++|..|++|++...
T Consensus 64 i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 64 VRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred EEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 56666777789999999999999988754
No 173
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=21.99 E-value=1.7e+02 Score=28.79 Aligned_cols=54 Identities=19% Similarity=0.330 Sum_probs=41.5
Q ss_pred cccceeccccchHHHHHHHhCC--EEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHHH
Q 014452 361 YMAHVYGENNSNLSHIRQISGA--NVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAF 417 (424)
Q Consensus 361 ~~g~IIGk~G~~Ik~Ir~~SGa--~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~~ 417 (424)
....|+|-.-+.|.++-++..- .|.+.+.. .++-|+|+|+++++++|...+++.
T Consensus 132 ~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~N---~~~QiVIsG~~~ale~a~~~~~~~ 187 (310)
T COG0331 132 GMAAVLGLDDEQVEKACEEAAQGTVVEIANYN---SPGQIVISGTKEALEKAAEILKEA 187 (310)
T ss_pred cHHHHcCCCHHHHHHHHHHhccCCeEEEeeeC---CCCcEEEECCHHHHHHHHHHHHHh
Confidence 4466788888899999888764 36665332 337899999999999999998875
No 174
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=21.70 E-value=83 Score=29.20 Aligned_cols=28 Identities=25% Similarity=0.300 Sum_probs=22.8
Q ss_pred EEEEeccCcccceeccccchHHHHHHHh
Q 014452 353 IEVVIPQLYMAHVYGENNSNLSHIRQIS 380 (424)
Q Consensus 353 ~~v~IP~~~~g~IIGk~G~~Ik~Ir~~S 380 (424)
++|.|-...-|.|||+.|..|++|++.-
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 5566767777999999999999998553
No 175
>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=21.11 E-value=1.1e+02 Score=22.18 Aligned_cols=49 Identities=16% Similarity=0.249 Sum_probs=31.4
Q ss_pred CchHHH--HHhhcCceEEEecCCC---CCC--CCCCCCcEEEEEeCHHHHHHHHHH
Q 014452 153 GHIVSE--MRRATGASIRVFPKDQ---APR--CGSPHDEIVQVIGNYHSVQDALFH 201 (424)
Q Consensus 153 G~~Ik~--I~~~tga~I~v~~~~~---~p~--~~~~~~r~v~I~G~~~~v~~A~~~ 201 (424)
|.+|++ +.+.+++.|--..+++ .|. ..-.....+.+.|+.++++++..+
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~ 69 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFREL 69 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHh
Confidence 567888 8888899874433332 111 111234679999999999887765
No 176
>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=20.76 E-value=1.8e+02 Score=21.97 Aligned_cols=43 Identities=19% Similarity=0.307 Sum_probs=31.2
Q ss_pred cchHHHHHHHhCCEEEEeCCCCCCCCcEEEEEcCHHHHHHHHHHHHH
Q 014452 370 NSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHA 416 (424)
Q Consensus 370 G~~Ik~Ir~~SGa~I~i~~~~~~~~~r~i~I~Gt~e~v~~A~~lI~~ 416 (424)
-..|.+|-+.++|+|.=-. .+.-+|.++|+++.++....++..
T Consensus 16 r~ei~~l~~~f~a~ivd~~----~~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVS----PDSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEE----TTEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHHhCCEEEEEC----CCEEEEEEcCCHHHHHHHHHHhhh
Confidence 3567888899999865432 345789999999999988877654
Done!