Query psy11929
Match_columns 433
No_of_seqs 297 out of 1871
Neff 8.0
Searched_HMMs 46136
Date Fri Aug 16 22:34:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11929.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11929hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2193|consensus 100.0 5.1E-53 1.1E-57 404.3 16.6 329 12-428 196-536 (584)
2 KOG2192|consensus 100.0 1.4E-42 3E-47 315.5 23.6 307 12-360 45-388 (390)
3 KOG1676|consensus 100.0 7.6E-40 1.6E-44 328.4 23.4 297 12-423 51-356 (600)
4 KOG2190|consensus 100.0 6.6E-39 1.4E-43 326.6 24.7 321 11-419 39-372 (485)
5 KOG1676|consensus 100.0 3.1E-35 6.7E-40 295.2 22.5 248 12-361 136-394 (600)
6 KOG2193|consensus 100.0 3.6E-31 7.8E-36 254.3 12.5 244 8-359 273-567 (584)
7 KOG2191|consensus 100.0 6.5E-29 1.4E-33 232.6 20.9 268 12-360 36-319 (402)
8 KOG2191|consensus 99.9 1.7E-24 3.7E-29 203.0 19.7 212 121-405 36-263 (402)
9 KOG2190|consensus 99.9 8.5E-25 1.8E-29 223.4 18.8 237 14-361 137-414 (485)
10 KOG2192|consensus 99.8 3.6E-18 7.8E-23 156.3 12.3 158 10-194 118-384 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.7 3.3E-16 7.2E-21 140.7 11.2 136 20-194 3-151 (172)
12 PRK13763 putative RNA-processi 99.6 1.8E-15 3.9E-20 136.9 12.9 141 15-194 3-157 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.6 1.3E-15 2.8E-20 136.9 11.8 138 128-356 2-151 (172)
14 PRK13763 putative RNA-processi 99.6 1.1E-14 2.4E-19 131.7 13.5 151 124-356 3-157 (180)
15 cd02396 PCBP_like_KH K homolog 99.5 1.1E-13 2.4E-18 104.2 6.7 63 289-351 1-65 (65)
16 KOG2279|consensus 99.4 9.8E-13 2.1E-17 131.9 12.1 291 13-354 66-366 (608)
17 cd02396 PCBP_like_KH K homolog 99.4 6.9E-13 1.5E-17 99.8 7.3 64 125-188 1-64 (65)
18 cd02394 vigilin_like_KH K homo 99.3 2.8E-12 6.1E-17 95.5 6.4 60 290-350 2-61 (62)
19 PF00013 KH_1: KH domain syndr 99.3 2.5E-12 5.3E-17 95.2 5.1 60 289-350 1-60 (60)
20 cd00105 KH-I K homology RNA-bi 99.2 2E-11 4.4E-16 91.3 7.2 61 290-350 2-63 (64)
21 PF00013 KH_1: KH domain syndr 99.2 7.9E-12 1.7E-16 92.5 4.4 60 16-102 1-60 (60)
22 cd02393 PNPase_KH Polynucleoti 99.2 3.5E-11 7.7E-16 89.2 7.4 58 289-351 3-61 (61)
23 cd02394 vigilin_like_KH K homo 99.2 1.7E-11 3.6E-16 91.4 5.0 61 17-103 2-62 (62)
24 cd02393 PNPase_KH Polynucleoti 99.1 3.5E-10 7.5E-15 83.8 7.6 58 124-188 2-60 (61)
25 cd00105 KH-I K homology RNA-bi 99.1 6.7E-10 1.5E-14 82.9 7.7 62 126-188 2-63 (64)
26 PF13014 KH_3: KH domain 99.0 4.9E-10 1.1E-14 77.0 5.1 40 29-68 1-43 (43)
27 smart00322 KH K homology RNA-b 99.0 4.2E-09 9.2E-14 79.0 8.7 67 287-354 2-68 (69)
28 PF13014 KH_3: KH domain 98.9 1.6E-09 3.4E-14 74.4 5.2 43 134-176 1-43 (43)
29 KOG2208|consensus 98.9 6.2E-09 1.3E-13 113.0 10.3 247 14-412 200-448 (753)
30 smart00322 KH K homology RNA-b 98.9 1.2E-08 2.5E-13 76.6 7.9 67 14-106 2-68 (69)
31 KOG2208|consensus 98.8 8.7E-09 1.9E-13 111.9 9.4 216 15-357 347-563 (753)
32 COG1094 Predicted RNA-binding 98.8 2.4E-08 5.3E-13 89.3 9.5 148 13-194 6-164 (194)
33 KOG2279|consensus 98.7 1.3E-08 2.7E-13 102.8 4.4 146 120-357 64-210 (608)
34 COG1094 Predicted RNA-binding 98.5 6.1E-07 1.3E-11 80.5 9.3 148 123-356 7-164 (194)
35 cd02395 SF1_like-KH Splicing f 98.4 8.4E-07 1.8E-11 74.7 6.9 64 27-109 14-96 (120)
36 cd02395 SF1_like-KH Splicing f 98.3 1.5E-06 3.2E-11 73.2 7.0 60 297-356 15-95 (120)
37 KOG2113|consensus 98.3 1.4E-06 2.9E-11 82.6 5.9 149 122-347 24-173 (394)
38 KOG2113|consensus 98.1 5E-06 1.1E-10 78.8 6.5 151 10-191 21-180 (394)
39 PRK08406 transcription elongat 98.1 9.2E-06 2E-10 70.4 6.6 104 15-160 32-135 (140)
40 PRK08406 transcription elongat 98.0 1.6E-05 3.4E-10 69.0 7.7 38 124-161 32-69 (140)
41 TIGR02696 pppGpp_PNP guanosine 98.0 4.1E-05 8.9E-10 82.1 10.5 98 88-194 544-642 (719)
42 TIGR02696 pppGpp_PNP guanosine 97.8 0.00012 2.7E-09 78.6 10.6 64 288-356 578-642 (719)
43 TIGR01952 nusA_arch NusA famil 97.6 0.00039 8.5E-09 60.2 8.9 103 16-160 34-136 (141)
44 TIGR03591 polynuc_phos polyrib 97.5 0.00034 7.4E-09 76.1 9.0 97 90-194 518-615 (684)
45 TIGR03591 polynuc_phos polyrib 97.5 0.00041 8.9E-09 75.5 9.4 64 288-356 551-615 (684)
46 KOG0119|consensus 97.5 0.00094 2E-08 67.5 10.8 73 123-195 137-231 (554)
47 KOG0336|consensus 97.5 0.00016 3.6E-09 71.6 5.4 72 284-357 43-114 (629)
48 KOG1588|consensus 97.4 0.00029 6.3E-09 66.1 5.9 50 9-58 86-137 (259)
49 TIGR01952 nusA_arch NusA famil 97.3 0.00081 1.7E-08 58.2 7.1 39 287-325 99-137 (141)
50 KOG0119|consensus 97.2 0.00077 1.7E-08 68.1 6.4 87 14-108 137-230 (554)
51 KOG2814|consensus 97.1 0.00033 7.1E-09 67.6 3.1 71 13-109 55-126 (345)
52 COG0195 NusA Transcription elo 97.1 0.0018 3.9E-08 58.9 7.5 96 27-161 84-179 (190)
53 PLN00207 polyribonucleotide nu 97.1 0.0013 2.7E-08 72.5 7.4 99 88-194 650-750 (891)
54 PLN00207 polyribonucleotide nu 97.0 0.0018 3.9E-08 71.3 8.0 64 288-356 685-750 (891)
55 COG1185 Pnp Polyribonucleotide 96.9 0.0035 7.7E-08 66.3 8.7 64 289-357 553-617 (692)
56 COG1185 Pnp Polyribonucleotide 96.9 0.0028 6E-08 67.1 7.5 99 88-194 517-616 (692)
57 KOG2814|consensus 96.8 0.0018 3.9E-08 62.6 5.4 74 286-359 55-128 (345)
58 cd02134 NusA_KH NusA_K homolog 96.8 0.0023 5.1E-08 47.2 4.5 37 14-54 24-60 (61)
59 KOG0336|consensus 96.7 0.002 4.4E-08 64.0 4.9 73 118-194 41-113 (629)
60 cd02134 NusA_KH NusA_K homolog 96.7 0.0023 5E-08 47.2 4.0 37 287-323 24-60 (61)
61 PF14611 SLS: Mitochondrial in 96.5 0.079 1.7E-06 49.2 14.0 64 125-194 27-90 (210)
62 PRK00106 hypothetical protein; 96.3 0.02 4.4E-07 60.2 9.4 66 123-194 224-291 (535)
63 PRK00468 hypothetical protein; 96.2 0.0053 1.1E-07 47.2 3.7 33 12-48 27-59 (75)
64 TIGR03319 YmdA_YtgF conserved 96.2 0.02 4.4E-07 60.3 9.2 65 123-193 203-269 (514)
65 PRK11824 polynucleotide phosph 96.2 0.0087 1.9E-07 65.4 6.2 97 90-194 521-618 (693)
66 COG0195 NusA Transcription elo 96.1 0.022 4.7E-07 51.9 7.7 39 289-327 143-181 (190)
67 TIGR03319 YmdA_YtgF conserved 96.1 0.016 3.4E-07 61.2 7.6 66 286-355 202-269 (514)
68 PRK12704 phosphodiesterase; Pr 96.1 0.026 5.5E-07 59.7 9.0 64 125-194 211-276 (520)
69 PRK12328 nusA transcription el 96.1 0.02 4.3E-07 57.3 7.7 96 26-161 249-345 (374)
70 PRK11824 polynucleotide phosph 96.0 0.014 3.1E-07 63.7 7.1 63 289-356 555-618 (693)
71 TIGR01953 NusA transcription t 96.0 0.029 6.3E-07 55.9 8.7 96 27-161 242-338 (341)
72 PRK00106 hypothetical protein; 96.0 0.019 4.1E-07 60.4 7.6 66 286-355 223-290 (535)
73 PRK12327 nusA transcription el 96.0 0.032 6.8E-07 56.1 8.7 96 27-161 244-340 (362)
74 PRK12704 phosphodiesterase; Pr 95.9 0.019 4.2E-07 60.6 7.4 67 286-356 208-276 (520)
75 KOG1588|consensus 95.9 0.0092 2E-07 56.2 4.4 41 286-326 90-136 (259)
76 PRK02821 hypothetical protein; 95.8 0.0094 2E-07 46.0 3.4 33 13-49 29-61 (77)
77 PRK04163 exosome complex RNA-b 95.8 0.025 5.4E-07 53.6 6.9 62 290-356 147-209 (235)
78 PRK12329 nusA transcription el 95.8 0.028 6.2E-07 57.2 7.5 96 27-161 276-372 (449)
79 COG1837 Predicted RNA-binding 95.8 0.011 2.5E-07 45.3 3.6 32 12-47 27-58 (76)
80 PRK12328 nusA transcription el 95.7 0.031 6.8E-07 55.9 7.3 41 288-328 308-348 (374)
81 PF14611 SLS: Mitochondrial in 95.6 0.28 6.1E-06 45.4 13.2 121 28-193 35-164 (210)
82 PRK09202 nusA transcription el 95.5 0.035 7.6E-07 57.7 7.4 95 27-161 244-339 (470)
83 COG5176 MSL5 Splicing factor ( 95.4 0.022 4.9E-07 51.5 4.6 46 13-58 146-193 (269)
84 TIGR01953 NusA transcription t 95.4 0.06 1.3E-06 53.7 8.1 39 288-326 301-339 (341)
85 PRK01064 hypothetical protein; 95.3 0.022 4.8E-07 44.1 3.8 33 12-48 27-59 (78)
86 PRK02821 hypothetical protein; 95.3 0.026 5.5E-07 43.6 4.1 33 121-153 28-60 (77)
87 PRK12327 nusA transcription el 95.3 0.061 1.3E-06 54.0 7.8 41 287-327 302-342 (362)
88 PRK00468 hypothetical protein; 95.3 0.027 5.8E-07 43.3 4.1 32 121-152 27-58 (75)
89 PRK09202 nusA transcription el 95.1 0.06 1.3E-06 56.0 7.5 40 288-327 302-341 (470)
90 COG1837 Predicted RNA-binding 95.0 0.033 7.2E-07 42.7 3.8 32 121-152 27-58 (76)
91 PRK04163 exosome complex RNA-b 95.0 0.059 1.3E-06 51.0 6.4 62 126-194 147-209 (235)
92 PRK12329 nusA transcription el 94.6 0.094 2E-06 53.5 7.1 40 288-327 335-374 (449)
93 COG5176 MSL5 Splicing factor ( 94.5 0.042 9E-07 49.8 3.9 40 288-327 148-193 (269)
94 KOG4369|consensus 94.2 0.017 3.7E-07 63.9 0.8 70 287-356 1339-1410(2131)
95 PRK12705 hypothetical protein; 94.0 0.12 2.7E-06 54.1 6.8 37 125-161 199-236 (508)
96 PRK01064 hypothetical protein; 94.0 0.081 1.8E-06 41.0 4.0 32 121-152 27-58 (78)
97 KOG1067|consensus 93.6 0.14 3E-06 53.1 6.0 95 91-194 565-660 (760)
98 PRK12705 hypothetical protein; 93.4 0.11 2.4E-06 54.5 5.0 65 286-354 196-262 (508)
99 KOG4369|consensus 92.0 0.064 1.4E-06 59.6 1.1 52 16-71 1341-1395(2131)
100 PF13083 KH_4: KH domain; PDB: 92.0 0.068 1.5E-06 40.8 1.0 33 14-50 28-60 (73)
101 cd02409 KH-II KH-II (K homolo 91.5 0.32 6.9E-06 35.8 4.2 34 15-52 25-58 (68)
102 PF13184 KH_5: NusA-like KH do 91.0 0.25 5.5E-06 37.3 3.2 38 289-326 4-47 (69)
103 PF13184 KH_5: NusA-like KH do 90.3 0.2 4.4E-06 37.8 2.1 27 30-56 19-46 (69)
104 KOG1067|consensus 89.9 0.89 1.9E-05 47.4 6.9 64 288-357 597-661 (760)
105 KOG3273|consensus 89.4 0.25 5.5E-06 44.6 2.3 55 132-194 177-231 (252)
106 PF13083 KH_4: KH domain; PDB: 89.3 0.24 5.2E-06 37.7 1.9 34 121-154 26-59 (73)
107 cd02409 KH-II KH-II (K homolo 89.3 0.6 1.3E-05 34.2 4.0 35 287-321 24-58 (68)
108 PF07650 KH_2: KH domain syndr 88.2 0.26 5.7E-06 37.9 1.5 34 16-53 26-59 (78)
109 COG1855 ATPase (PilT family) [ 87.4 0.47 1E-05 48.5 3.0 41 288-328 486-526 (604)
110 cd02414 jag_KH jag_K homology 87.2 0.62 1.3E-05 35.9 3.0 33 17-53 26-58 (77)
111 KOG3273|consensus 86.9 0.42 9.1E-06 43.2 2.1 53 297-355 178-230 (252)
112 COG1097 RRP4 RNA-binding prote 86.5 1.6 3.5E-05 40.9 5.8 45 19-71 150-194 (239)
113 cd02413 40S_S3_KH K homology R 85.9 0.89 1.9E-05 35.5 3.3 36 16-55 31-66 (81)
114 cd02410 archeal_CPSF_KH The ar 85.4 4 8.6E-05 35.4 7.3 94 33-161 20-113 (145)
115 COG5166 Uncharacterized conser 84.5 1.4 3E-05 45.5 4.7 125 32-194 393-524 (657)
116 cd02410 archeal_CPSF_KH The ar 84.0 5 0.00011 34.8 7.3 39 289-327 77-115 (145)
117 PRK13764 ATPase; Provisional 83.8 0.94 2E-05 48.7 3.4 42 287-328 480-521 (602)
118 cd02414 jag_KH jag_K homology 83.4 1.2 2.6E-05 34.2 3.0 35 288-322 24-58 (77)
119 PF07650 KH_2: KH domain syndr 82.6 0.89 1.9E-05 34.9 2.0 34 124-157 25-58 (78)
120 COG1855 ATPase (PilT family) [ 82.4 0.89 1.9E-05 46.6 2.4 38 16-57 487-524 (604)
121 COG1097 RRP4 RNA-binding prote 81.6 3.3 7.1E-05 38.9 5.6 57 126-189 148-205 (239)
122 PRK06418 transcription elongat 80.8 2.1 4.5E-05 38.2 3.9 35 17-56 63-97 (166)
123 KOG2874|consensus 80.8 3.1 6.6E-05 39.8 5.1 51 300-356 161-211 (356)
124 KOG2874|consensus 79.9 3.6 7.7E-05 39.3 5.2 51 136-194 161-211 (356)
125 cd02412 30S_S3_KH K homology R 79.0 1.8 3.9E-05 35.8 2.7 30 17-50 63-92 (109)
126 PRK06418 transcription elongat 78.9 2.8 6E-05 37.4 4.0 38 289-327 62-99 (166)
127 cd02411 archeal_30S_S3_KH K ho 77.7 2.5 5.3E-05 33.2 3.1 28 17-48 40-67 (85)
128 PRK13764 ATPase; Provisional 77.5 1.7 3.7E-05 46.7 2.8 38 15-56 481-518 (602)
129 COG0092 RpsC Ribosomal protein 74.9 2.6 5.7E-05 39.4 2.9 31 14-48 50-80 (233)
130 cd02413 40S_S3_KH K homology R 73.0 4.1 8.8E-05 31.8 3.1 36 124-159 30-65 (81)
131 COG1782 Predicted metal-depend 72.1 10 0.00022 39.5 6.5 39 289-327 100-138 (637)
132 TIGR00436 era GTP-binding prot 65.4 7.7 0.00017 37.3 4.0 35 13-50 219-253 (270)
133 cd02412 30S_S3_KH K homology R 64.2 6.6 0.00014 32.4 2.8 30 125-154 62-91 (109)
134 COG5166 Uncharacterized conser 61.7 8.6 0.00019 40.0 3.6 123 16-161 450-608 (657)
135 COG1782 Predicted metal-depend 61.4 15 0.00034 38.3 5.4 96 31-161 41-136 (637)
136 TIGR03675 arCOG00543 arCOG0054 61.4 27 0.00058 38.1 7.6 40 289-328 94-133 (630)
137 cd02411 archeal_30S_S3_KH K ho 61.1 9.3 0.0002 29.9 3.1 28 126-153 40-67 (85)
138 TIGR03675 arCOG00543 arCOG0054 61.1 23 0.00051 38.5 7.1 96 31-161 35-130 (630)
139 PTZ00084 40S ribosomal protein 60.5 11 0.00024 35.2 3.9 33 16-52 45-77 (220)
140 PRK15494 era GTPase Era; Provi 58.3 12 0.00026 37.4 4.0 39 13-54 271-317 (339)
141 CHL00048 rps3 ribosomal protei 56.6 15 0.00033 34.1 4.2 31 15-49 66-96 (214)
142 PRK00089 era GTPase Era; Revie 56.4 15 0.00032 35.6 4.3 39 14-55 225-271 (292)
143 TIGR00436 era GTP-binding prot 56.4 11 0.00024 36.2 3.3 31 287-317 220-251 (270)
144 COG0092 RpsC Ribosomal protein 54.6 12 0.00025 35.2 2.9 30 123-152 50-79 (233)
145 TIGR01008 rpsC_E_A ribosomal p 52.3 15 0.00032 33.7 3.2 31 16-50 39-69 (195)
146 PRK15494 era GTPase Era; Provi 51.4 14 0.00031 36.8 3.3 29 287-315 272-301 (339)
147 PRK04191 rps3p 30S ribosomal p 50.0 16 0.00036 33.8 3.2 31 17-51 42-72 (207)
148 PRK00089 era GTPase Era; Revie 47.5 18 0.00038 35.1 3.2 29 287-315 225-254 (292)
149 COG1159 Era GTPase [General fu 46.0 30 0.00064 33.8 4.3 35 10-47 224-258 (298)
150 COG1159 Era GTPase [General fu 45.5 20 0.00043 35.0 3.1 30 287-316 228-258 (298)
151 PF02749 QRPTase_N: Quinolinat 43.5 96 0.0021 24.2 6.3 66 287-356 17-86 (88)
152 COG1702 PhoH Phosphate starvat 42.6 66 0.0014 32.1 6.2 57 294-356 21-79 (348)
153 KOG1423|consensus 42.3 26 0.00057 34.5 3.3 34 13-49 326-359 (379)
154 KOG1423|consensus 41.5 25 0.00053 34.7 3.0 34 285-318 325-359 (379)
155 PF09869 DUF2096: Uncharacteri 37.1 94 0.002 27.6 5.7 59 121-193 110-168 (169)
156 COG1847 Jag Predicted RNA-bind 36.9 25 0.00053 32.5 2.1 35 16-54 92-126 (208)
157 COG1847 Jag Predicted RNA-bind 34.6 31 0.00067 31.8 2.4 37 122-158 89-125 (208)
158 TIGR01009 rpsC_bact ribosomal 33.8 39 0.00084 31.4 3.0 29 17-49 64-92 (211)
159 TIGR01008 rpsC_E_A ribosomal p 30.5 51 0.0011 30.3 3.1 29 124-152 38-66 (195)
160 PRK03818 putative transporter; 29.4 4.6E+02 0.01 28.1 10.6 116 38-187 218-358 (552)
161 PRK04191 rps3p 30S ribosomal p 28.8 55 0.0012 30.3 3.1 28 126-153 42-69 (207)
162 PTZ00084 40S ribosomal protein 28.3 57 0.0012 30.5 3.1 29 125-153 45-73 (220)
163 CHL00048 rps3 ribosomal protei 28.0 57 0.0012 30.4 3.1 30 124-153 66-95 (214)
164 COG1702 PhoH Phosphate starvat 28.0 1.5E+02 0.0033 29.6 6.1 53 129-189 20-72 (348)
165 cd00652 TBP_TLF TATA box bindi 24.6 5.1E+02 0.011 23.1 12.3 90 94-193 68-173 (174)
166 PRK00310 rpsC 30S ribosomal pr 24.0 67 0.0015 30.3 2.8 29 17-49 64-92 (232)
167 PRK04021 hypothetical protein; 23.2 1.6E+02 0.0035 23.5 4.4 40 308-347 50-90 (92)
168 COG4010 Uncharacterized protei 23.1 2.4E+02 0.0053 24.5 5.6 44 144-194 126-169 (170)
169 cd04517 TLF TBP-like factors ( 22.4 5.6E+02 0.012 22.9 12.4 90 94-193 68-173 (174)
170 TIGR03802 Asp_Ala_antiprt aspa 21.9 8.8E+02 0.019 26.1 11.1 117 38-189 232-377 (562)
171 PF10369 ALS_ss_C: Small subun 21.2 2.2E+02 0.0047 21.6 4.6 41 307-351 16-57 (75)
172 PF03958 Secretin_N: Bacterial 20.9 2.3E+02 0.0051 21.1 4.9 34 316-353 43-76 (82)
No 1
>KOG2193|consensus
Probab=100.00 E-value=5.1e-53 Score=404.28 Aligned_cols=329 Identities=20% Similarity=0.309 Sum_probs=257.6
Q ss_pred CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC---CCCCcceEEEecccCCCCCCccccCCCCCccc
Q psy11929 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD---GACPDRIVTVSGSVDNSSTSSVETGYPGHTLW 88 (433)
Q Consensus 12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~ 88 (433)
..++++|+|||. .+||.||||.|.|||.|...|.|+|+|.. .|..||+|+|.|+++
T Consensus 196 ~~D~PlR~lVpt----qyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpE----------------- 254 (584)
T KOG2193|consen 196 LKDWPLRLLVPT----QYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPE----------------- 254 (584)
T ss_pred ccCcceeeeecc----ceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCcc-----------------
Confidence 357999999999 99999999999999999999999999986 378999999999999
Q ss_pred cchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc--CCCCC
Q psy11929 89 VTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPM 166 (433)
Q Consensus 89 ~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~--~~~~~ 166 (433)
...+|+++|++++...... +.-...+.++++.++.+||+||||.|++||+|+.+||++|.|++ +....
T Consensus 255 -----g~s~Ac~~ILeimqkEA~~-----~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y 324 (584)
T KOG2193|consen 255 -----GTSKACKMILEIMQKEAVD-----DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY 324 (584)
T ss_pred -----chHHHHHHHHHHHHHhhhc-----cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc
Confidence 8999999999998764321 12246788999999999999999999999999999999999986 43335
Q ss_pred CCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCC
Q psy11929 167 STERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHP 246 (433)
Q Consensus 167 ~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p 246 (433)
..||+|++.|+.++|.+|..+|+.+|++|++++... ..++.+.. |.+.. ..+ |.+ |.
T Consensus 325 npERTItVkGsiEac~~AE~eImkKlre~yEnDl~a--~s~q~~l~---P~l~~--~~l---~~f--~s----------- 381 (584)
T KOG2193|consen 325 NPERTITVKGSIEACVQAEAEIMKKLRECYENDLAA--MSLQCHLP---PGLNL--PAL---GLF--PS----------- 381 (584)
T ss_pred CccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHH--hhccCCCC---cccCc--ccc---CCC--Cc-----------
Confidence 679999999999999999999999999999866432 11111100 00000 000 000 00
Q ss_pred CccccccCcCCCCCCCC---CccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEE
Q psy11929 247 LAGLAVLGIEGIGSTSL---TPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI 323 (433)
Q Consensus 247 ~~~~~~~~~~~~~~p~~---~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I 323 (433)
..++.+++||-. ..++|+ ......+...++|+||...||+||||+|.+||+|.+++||+|+|
T Consensus 382 -----sS~~~~Ph~~Ps~v~~a~p~~----------~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKI 446 (584)
T KOG2193|consen 382 -----SSAVSPPHFPPSPVTFASPYP----------LFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKI 446 (584)
T ss_pred -----ccccCCCCCCCCccccCCCch----------hhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeee
Confidence 001111111100 000111 01123367788999999999999999999999999999999999
Q ss_pred ccCCC--CCceEEEEEeCHHHHHHHHHHHHHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCccee
Q psy11929 324 HTGTE--SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMV 401 (433)
Q Consensus 324 ~~~~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~ii 401 (433)
.+++. ..+|+|+|+|.+++..+|+..|+.+|.++..-. . .+.++++. ++.||++.+||||
T Consensus 447 appE~pdvseRMViItGppeaqfKAQgrifgKikEenf~~--P---keevklet-------------hirVPs~~aGRvI 508 (584)
T KOG2193|consen 447 APPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFL--P---KEEVKLET-------------HIRVPSSAAGRVI 508 (584)
T ss_pred cCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCC--c---hhhheeee-------------eeeccchhhhhhh
Confidence 98876 889999999999999999999999999874322 2 24566664 4669999999999
Q ss_pred cccc--HHHHHHhhhccccccceeecccc
Q psy11929 402 TLGG--LSELLANIAASNVKSTVQTTGAY 428 (433)
Q Consensus 402 GkgG--~~e~~~~~~~~~~~~~~~~~~~~ 428 (433)
|||| ++|| ||||+|+|++|++-|+-.
T Consensus 509 GKGGktVnEL-Qnlt~AeV~vPrdqtpdE 536 (584)
T KOG2193|consen 509 GKGGKTVNEL-QNLTSAEVVVPRDQTPDE 536 (584)
T ss_pred ccccccHHHH-hccccceEEccccCCCCc
Confidence 9999 7999 999999999999987643
No 2
>KOG2192|consensus
Probab=100.00 E-value=1.4e-42 Score=315.47 Aligned_cols=307 Identities=27% Similarity=0.498 Sum_probs=235.4
Q ss_pred CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS 91 (433)
Q Consensus 12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a 91 (433)
...+.+|||+.+ +.+|+||||+|++||.|+.+++|+|+|++.+.++|+++|+...+
T Consensus 45 ~~r~e~ril~~s----k~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~-------------------- 100 (390)
T KOG2192|consen 45 RSRVELRILLQS----KNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIE-------------------- 100 (390)
T ss_pred hcceeEEEEEec----ccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHH--------------------
Confidence 356999999999 99999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccE
Q psy11929 92 VDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERI 171 (433)
Q Consensus 92 ~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~ 171 (433)
.+...++.|+..|++... ...++.++|||+.+++|.|||++|++||+|++++.|+.+|..+++|++++|+
T Consensus 101 --ti~~ilk~iip~lee~f~--------~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv 170 (390)
T KOG2192|consen 101 --TIGEILKKIIPTLEEGFQ--------LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRV 170 (390)
T ss_pred --HHHHHHHHHhhhhhhCCC--------CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceE
Confidence 889988888888776321 2567899999999999999999999999999999999999999999999999
Q ss_pred EEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCC------CCccccCCcccccCCCCCCCcccccCCCCCC
Q psy11929 172 VTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNA------GPVILSGGQAYTLHGEYAVPVQEVAGKKQPH 245 (433)
Q Consensus 172 v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~------~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~ 245 (433)
|.|.|.+.+|..+++.|++.|.| .|.|+.+.||.|.+++. ++++|.+..+.+ | +.|.... .+.+++
T Consensus 171 ~l~~g~~k~v~~~i~~il~~i~e---~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~p--g--papqrgg-qgpp~~ 242 (390)
T KOG2192|consen 171 VLIGGKPKRVVECIKIILDLISE---SPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRP--G--PAPQRGG-QGPPPP 242 (390)
T ss_pred EEecCCcchHHHHHHHHHHHhhc---CCcCCcCCcCCccccCcccccCCceeecCCCCCCC--C--CCCCCCC-CCCCCC
Confidence 99999999999999999999999 99999999999988763 333443322111 0 0010000 000000
Q ss_pred C---CccccccCcCCCC-CCCC-------CccccccccCCCcc---------------c---C-CCCCCCCceEEEEEeC
Q psy11929 246 P---LAGLAVLGIEGIG-STSL-------TPAALAALSGSRVK---------------S---G-GKDTGDDFVETEIVLT 295 (433)
Q Consensus 246 p---~~~~~~~~~~~~~-~p~~-------~~~~~~~~~~~~~~---------------~---~-~~~~~~~~~t~~i~VP 295 (433)
+ ++.....+..+.. +.+. .+.++..|+.+.|. . + -.+......|.++.||
T Consensus 243 ~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip 322 (390)
T KOG2192|consen 243 RGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIP 322 (390)
T ss_pred CccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecc
Confidence 0 1111111100000 0000 01111112111110 0 0 1123456788999999
Q ss_pred cccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhcccc
Q psy11929 296 DDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQKNN 360 (433)
Q Consensus 296 ~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~ 360 (433)
.++-|.||||+|++|++|++++||+|+|+++.+ +.+|+++|+||.+|++.||+|+++++.+-+++
T Consensus 323 ~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~rer 388 (390)
T KOG2192|consen 323 KDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRER 388 (390)
T ss_pred cccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhcc
Confidence 999999999999999999999999999999888 99999999999999999999999999865443
No 3
>KOG1676|consensus
Probab=100.00 E-value=7.6e-40 Score=328.38 Aligned_cols=297 Identities=23% Similarity=0.368 Sum_probs=237.7
Q ss_pred CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC--CCCcceEEEecccCCCCCCccccCCCCCcccc
Q psy11929 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG--ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWV 89 (433)
Q Consensus 12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~--~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~ 89 (433)
+..++.+.-||. ..||.||||+|+.|..|..++||+|++... +..+|-|.+.|.++
T Consensus 51 ~~~~~~~~~VPd----~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe------------------ 108 (600)
T KOG1676|consen 51 DTVQTERYKVPD----EAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPE------------------ 108 (600)
T ss_pred ccccccccCCCc----hhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcc------------------
Confidence 356788899999 999999999999999999999999998653 67899999999999
Q ss_pred chHHHHHHHHHHHHhhhhhhc--ccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCC-CC
Q psy11929 90 TSVDNVCTAYNFMCRSLEDYH--INRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDML-PM 166 (433)
Q Consensus 90 ~a~~~v~~A~~~I~~~~~~~~--~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~-~~ 166 (433)
.+..|+.||.+++.... ..+. .......++.+++||++.+|.||||+|++||.|++.+||++.+..|.. ..
T Consensus 109 ----~v~~aK~li~evv~r~~~~~~~~--~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~ 182 (600)
T KOG1676|consen 109 ----NVEVAKQLIGEVVSRGRPPGGFP--DNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT 182 (600)
T ss_pred ----cHHHHHHhhhhhhhccCCCCCcc--ccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC
Confidence 99999999998876642 1111 112245688999999999999999999999999999999998887543 33
Q ss_pred CCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCC
Q psy11929 167 STERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHP 246 (433)
Q Consensus 167 ~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p 246 (433)
..++.+.|+|+++.|+.|+.+|.++|++...... +..+.+
T Consensus 183 ~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~-------------------------g~~~~~--------------- 222 (600)
T KOG1676|consen 183 GADKPLRITGDPDKVEQAKQLVADILREEDDEVP-------------------------GSGGHA--------------- 222 (600)
T ss_pred CCCCceeecCCHHHHHHHHHHHHHHHHhcccCCC-------------------------cccccc---------------
Confidence 4889999999999999999999999997321000 000000
Q ss_pred CccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929 247 LAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTG 326 (433)
Q Consensus 247 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~ 326 (433)
+.. .....+.+|.||...||.||||+|++||.|+.+|||+|+|.++
T Consensus 223 ---------------------------------g~~-~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpD 268 (600)
T KOG1676|consen 223 ---------------------------------GVR-GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPD 268 (600)
T ss_pred ---------------------------------CcC-ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecC
Confidence 000 0123378999999999999999999999999999999999988
Q ss_pred CC--CCceEEEEEeCHHHHHHHHHHHHHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCcceeccc
Q psy11929 327 TE--SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLG 404 (433)
Q Consensus 327 ~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~iiGkg 404 (433)
.+ +.||.+.|.|+.++|+.|..||.++|+...+...+..+.-.+.-. ..++++||+++||.|||||
T Consensus 269 d~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~------------~~fy~~VPa~KcGLvIGrG 336 (600)
T KOG1676|consen 269 DDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLV------------AQFYMKVPADKCGLVIGRG 336 (600)
T ss_pred CCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCCcCCCCccce------------eeEEEeccccccccccCCC
Confidence 87 899999999999999999999999999876654332211111110 1367999999999999999
Q ss_pred c--HHHHHHhhhcccccccee
Q psy11929 405 G--LSELLANIAASNVKSTVQ 423 (433)
Q Consensus 405 G--~~e~~~~~~~~~~~~~~~ 423 (433)
| ++.| ..-++|.+-.+++
T Consensus 337 GEtIK~i-n~qSGA~~el~r~ 356 (600)
T KOG1676|consen 337 GETIKQI-NQQSGARCELSRQ 356 (600)
T ss_pred ccchhhh-cccCCccccccCC
Confidence 9 7877 6678886666666
No 4
>KOG2190|consensus
Probab=100.00 E-value=6.6e-39 Score=326.63 Aligned_cols=321 Identities=30% Similarity=0.498 Sum_probs=242.9
Q ss_pred CCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC--CCCCcceEEEecccCCCCCCccccCCCCCccc
Q psy11929 11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDNSSTSSVETGYPGHTLW 88 (433)
Q Consensus 11 ~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~--~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~ 88 (433)
.+.+.++|||||. +.+|.||||+|.+||+||.+|.++|+|.+ +++.+|+++|+|... +..+
T Consensus 39 p~~t~~~RlL~~~----kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~-------------~~~~ 101 (485)
T KOG2190|consen 39 PDETLTYRLLCHV----KEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRV-------------ELNL 101 (485)
T ss_pred CCCcceEEEEecc----ccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccc-------------cccC
Confidence 3445569999999 99999999999999999999999999977 489999999999733 1267
Q ss_pred cchHHHHHHHHHHHHhhhhhhccccc-CCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCC
Q psy11929 89 VTSVDNVCTAYNFMCRSLEDYHINRN-RMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS 167 (433)
Q Consensus 89 ~~a~~~v~~A~~~I~~~~~~~~~~~~-~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~ 167 (433)
+++++++++|+.+|...+++...... ...+....+++++|+||.+++|+||||+|+.||+|+++|||+|++.++.+|.+
T Consensus 102 ~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~s 181 (485)
T KOG2190|consen 102 SPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNS 181 (485)
T ss_pred CchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcc
Confidence 88999999999999998764322221 11122233689999999999999999999999999999999999999999999
Q ss_pred CccEEEEEccHHHHHHHHHHHHHHHHhhc--cccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCC
Q psy11929 168 TERIVTVHGNPDTISQAIYQICLVLIECT--LQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPH 245 (433)
Q Consensus 168 ~er~v~I~G~~~~v~~A~~~I~~~l~e~~--~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~ 245 (433)
++|.|+|.|.+++|.+|+..|..+|+++. ..+.+..+++|.|......+.+...++...
T Consensus 182 ter~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~------------------- 242 (485)
T KOG2190|consen 182 TERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSP------------------- 242 (485)
T ss_pred cceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCc-------------------
Confidence 99999999999999999999999999942 133355667777622221121111111000
Q ss_pred CCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEcc
Q psy11929 246 PLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHT 325 (433)
Q Consensus 246 p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~ 325 (433)
.+.+ .+......+...++.+|...++.|||++|..|+.|+.++|+.|.+..
T Consensus 243 ---------------------~~~~--------~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~ 293 (485)
T KOG2190|consen 243 ---------------------DAHP--------FGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGD 293 (485)
T ss_pred ---------------------cccc--------ccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEecc
Confidence 0000 01112345677889999999999999999999999999999999999
Q ss_pred CCCCCceEEEEEeCH--H----HHHHHHHHHHHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCcc
Q psy11929 326 GTESHKKMFHIQGCQ--E----AVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGS 399 (433)
Q Consensus 326 ~~~~~er~V~IsGt~--e----~v~~A~~lI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~ 399 (433)
+. .+ |.|+++... + ..+.|..+++..+.+..... .... .++.|.||++.+||
T Consensus 294 ~~-~~-~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~-----------~~~~---------v~~~l~vps~~igc 351 (485)
T KOG2190|consen 294 SR-TD-RIVTISARENPEDRYSMAQEALLLVQPRISENAGDD-----------LTQT---------VTQRLLVPSDLIGC 351 (485)
T ss_pred cc-Cc-ceeeeccccCcccccccchhhhhhcccccccccccc-----------ccce---------eeeeeccCccccce
Confidence 87 33 899998875 3 34667777777665432100 0111 23668899999999
Q ss_pred eecccc--HHHHHHhhhccccc
Q psy11929 400 MVTLGG--LSELLANIAASNVK 419 (433)
Q Consensus 400 iiGkgG--~~e~~~~~~~~~~~ 419 (433)
+|||+| ++|||| .|+|.+.
T Consensus 352 iiGk~G~~iseir~-~tgA~I~ 372 (485)
T KOG2190|consen 352 IIGKGGAKISEIRQ-RTGASIS 372 (485)
T ss_pred eecccccchHHHHH-hcCCceE
Confidence 999999 799955 5777544
No 5
>KOG1676|consensus
Probab=100.00 E-value=3.1e-35 Score=295.24 Aligned_cols=248 Identities=26% Similarity=0.380 Sum_probs=206.1
Q ss_pred CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCC----CCcceEEEecccCCCCCCccccCCCCCcc
Q psy11929 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA----CPDRIVTVSGSVDNSSTSSVETGYPGHTL 87 (433)
Q Consensus 12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~----~~eRvv~I~G~~~~~~~~~v~~~~~~~~~ 87 (433)
...++..|+||. +++|.||||+|++||+|++++||++.+-.++ ...+-+.|+|.++
T Consensus 136 ~~~ttqeI~IPa----~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~---------------- 195 (600)
T KOG1676|consen 136 SVETTQEILIPA----NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPD---------------- 195 (600)
T ss_pred ccceeeeeccCc----cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHH----------------
Confidence 567899999999 9999999999999999999999999987653 2678999999999
Q ss_pred ccchHHHHHHHHHHHHhhhhhhcccccCC----CCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCC
Q psy11929 88 WVTSVDNVCTAYNFMCRSLEDYHINRNRM----ENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM 163 (433)
Q Consensus 88 ~~~a~~~v~~A~~~I~~~~~~~~~~~~~~----~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~ 163 (433)
.|..|..++.++|.+...+.... ........++++.||...||.||||+|++||+|+.+||++|+|.+|.
T Consensus 196 ------~ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd 269 (600)
T KOG1676|consen 196 ------KVEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD 269 (600)
T ss_pred ------HHHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCC
Confidence 99999999999998633221111 11223344899999999999999999999999999999999999988
Q ss_pred CCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCC
Q psy11929 164 LPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQ 243 (433)
Q Consensus 164 ~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~ 243 (433)
.|.+.||.+.|.|+.+.|+.|.++|.++|.+..+.. ++ +
T Consensus 270 ~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~---------------------~~---~----------------- 308 (600)
T KOG1676|consen 270 DPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGA---------------------GG---G----------------- 308 (600)
T ss_pred CCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccC---------------------CC---C-----------------
Confidence 888999999999999999999999999999832100 00 0
Q ss_pred CCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEE
Q psy11929 244 PHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI 323 (433)
Q Consensus 244 ~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I 323 (433)
++. +. +. ....++|.||.+++|.||||+|++||+|.++|||++.+
T Consensus 309 ---------~~~------------------------G~-P~-~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el 353 (600)
T KOG1676|consen 309 ---------MGG------------------------GA-PG-LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCEL 353 (600)
T ss_pred ---------cCC------------------------CC-cc-ceeeEEEeccccccccccCCCccchhhhcccCCccccc
Confidence 000 00 00 11278999999999999999999999999999999999
Q ss_pred ccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhccccC
Q psy11929 324 HTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNT 361 (433)
Q Consensus 324 ~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~ 361 (433)
.+..+ ..|++|+|+|++.+|+.|+.||..++..-..+.
T Consensus 354 ~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n~ 394 (600)
T KOG1676|consen 354 SRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPNT 394 (600)
T ss_pred cCCCCCCCccceEEEEecCcccchHHHHHHHHHhcccCCCC
Confidence 98733 889999999999999999999999998754333
No 6
>KOG2193|consensus
Probab=99.97 E-value=3.6e-31 Score=254.32 Aligned_cols=244 Identities=27% Similarity=0.410 Sum_probs=206.6
Q ss_pred CCCCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC-----CCCcceEEEecccCCCCCCccccCC
Q psy11929 8 KIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG-----ACPDRIVTVSGSVDNSSTSSVETGY 82 (433)
Q Consensus 8 ~~~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-----~~~eRvv~I~G~~~~~~~~~v~~~~ 82 (433)
+|+...++++|||.++ ..+|++|||.|.+||+|+++||++|.|+.- -.+||.|+|.|+.+
T Consensus 273 ~~k~~~e~pLk~lAHN----~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiE----------- 337 (584)
T KOG2193|consen 273 DDKVAEEIPLKILAHN----NLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIE----------- 337 (584)
T ss_pred ccchhhhcchhhhhhc----chhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHH-----------
Confidence 4566789999999999 999999999999999999999999999872 36899999999999
Q ss_pred CCCccccchHHHHHHHHHHHHhhhhhhccc--------------c--------cCCC---------------------CC
Q psy11929 83 PGHTLWVTSVDNVCTAYNFMCRSLEDYHIN--------------R--------NRME---------------------NC 119 (433)
Q Consensus 83 ~~~~~~~~a~~~v~~A~~~I~~~~~~~~~~--------------~--------~~~~---------------------~~ 119 (433)
+|.+|..+|+.++.+..++ + .... ..
T Consensus 338 -----------ac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq 406 (584)
T KOG2193|consen 338 -----------ACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQ 406 (584)
T ss_pred -----------HHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhc
Confidence 9999999999988762110 0 0000 00
Q ss_pred CCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhcccc
Q psy11929 120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQV 199 (433)
Q Consensus 120 ~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~ 199 (433)
......++|.||...+|.||||+|.+||.|.+.+||.|+|.+...|+..+|.|+|+|++++..+|...|..+|.|...
T Consensus 407 ~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf-- 484 (584)
T KOG2193|consen 407 NPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF-- 484 (584)
T ss_pred CcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc--
Confidence 123456899999999999999999999999999999999998778889999999999999999999999999998210
Q ss_pred CCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccC
Q psy11929 200 VKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSG 279 (433)
Q Consensus 200 ~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 279 (433)
+. |.
T Consensus 485 -------~~-------------------------Pk-------------------------------------------- 488 (584)
T KOG2193|consen 485 -------FL-------------------------PK-------------------------------------------- 488 (584)
T ss_pred -------CC-------------------------ch--------------------------------------------
Confidence 11 10
Q ss_pred CCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929 280 GKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIEL 356 (433)
Q Consensus 280 ~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~ 356 (433)
........+.||...+|+||||||.++++|++.|+|.|.|+++.. .+.-+|.|.|..-+.+.|++.|.+++.+
T Consensus 489 ----eevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~q 564 (584)
T KOG2193|consen 489 ----EEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQ 564 (584)
T ss_pred ----hhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHH
Confidence 123556789999999999999999999999999999999998776 6667889999999999999999999987
Q ss_pred ccc
Q psy11929 357 QKN 359 (433)
Q Consensus 357 ~~~ 359 (433)
-+.
T Consensus 565 vkq 567 (584)
T KOG2193|consen 565 VKQ 567 (584)
T ss_pred HHH
Confidence 643
No 7
>KOG2191|consensus
Probab=99.97 E-value=6.5e-29 Score=232.60 Aligned_cols=268 Identities=23% Similarity=0.343 Sum_probs=204.8
Q ss_pred CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC-----CCCcceEEEecccCCCCCCccccCCCCCc
Q psy11929 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG-----ACPDRIVTVSGSVDNSSTSSVETGYPGHT 86 (433)
Q Consensus 12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-----~~~eRvv~I~G~~~~~~~~~v~~~~~~~~ 86 (433)
+..+.+|+|||+ ..+|.||||+|++|.+|+++|||+|++++. ++.||||.|+|+.+
T Consensus 36 ~~~y~ikvLips----~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~e--------------- 96 (402)
T KOG2191|consen 36 DGQYFLKVLIPS----YAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVE--------------- 96 (402)
T ss_pred CCceEEEEEeec----ccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHH---------------
Confidence 344999999999 999999999999999999999999999983 89999999999999
Q ss_pred cccchHHHHHHHHHHHHhhhhhhcccccCC-C----CCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 87 LWVTSVDNVCTAYNFMCRSLEDYHINRNRM-E----NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 87 ~~~~a~~~v~~A~~~I~~~~~~~~~~~~~~-~----~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
++..++++|.+++++........ + ...+....+++++|++.+|.||||+|.+||.|++++||.|+|++
T Consensus 97 -------ai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP 169 (402)
T KOG2191|consen 97 -------ALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP 169 (402)
T ss_pred -------HHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc
Confidence 99999999999999865443321 1 11223345899999999999999999999999999999999984
Q ss_pred --CCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCccccc
Q psy11929 162 --DMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVA 239 (433)
Q Consensus 162 --~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~ 239 (433)
+....-.+|+|++.|++++..+|..+|+++|.+ +|..+..+. .+.....+|+..+
T Consensus 170 qkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~e---Dpqs~scln-~sya~vsGpvaNs------------------- 226 (402)
T KOG2191|consen 170 QKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQE---DPQSGSCLN-ISYANVSGPVANS------------------- 226 (402)
T ss_pred cCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhc---CCcccceec-cchhcccCccccc-------------------
Confidence 223345899999999999999999999999999 665443222 0000000000000
Q ss_pred CCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCC
Q psy11929 240 GKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGA 319 (433)
Q Consensus 240 ~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA 319 (433)
. | .+.+-.+ ..+...........++...+|..-|.+|.++-.|-..+|+
T Consensus 227 -----------n-----P----tGspya~-----------~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~ 275 (402)
T KOG2191|consen 227 -----------N-----P----TGSPYAY-----------QAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGA 275 (402)
T ss_pred -----------C-----C----CCCCCCC-----------CCccccccchhhccccccccccccccccccceeeeccccc
Confidence 0 0 0000000 1112223344567789999999999999999999999999
Q ss_pred eEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHHHhcccc
Q psy11929 320 QINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCIELQKNN 360 (433)
Q Consensus 320 ~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~ 360 (433)
.+.+++..+ ...+ .-+.|.+-++..|..+|..++.....+
T Consensus 276 l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~a~t~ 319 (402)
T KOG2191|consen 276 LIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVASANTA 319 (402)
T ss_pred ceeeccccccccccccc-ccccchhhhhhhhhhHHHHhhcccCcc
Confidence 999998766 4444 888999999999999999888776443
No 8
>KOG2191|consensus
Probab=99.93 E-value=1.7e-24 Score=203.02 Aligned_cols=212 Identities=26% Similarity=0.364 Sum_probs=158.3
Q ss_pred CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc--CCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccc
Q psy11929 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQ 198 (433)
Q Consensus 121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~--~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~ 198 (433)
.....+++|||+..+|.||||+|++|.+++++|||+|++++ |.+|+.+||++-|+|+.+++......|.++|++.
T Consensus 36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~--- 112 (402)
T KOG2191|consen 36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREK--- 112 (402)
T ss_pred CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHh---
Confidence 34489999999999999999999999999999999999985 8899999999999999999999999999999992
Q ss_pred cCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCccc
Q psy11929 199 VVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKS 278 (433)
Q Consensus 199 ~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~ 278 (433)
+... . .|+ + .+.++
T Consensus 113 p~~~----------~-k~v------------~-~~~pq------------------------------------------ 126 (402)
T KOG2191|consen 113 PQAV----------A-KPV------------D-ILQPQ------------------------------------------ 126 (402)
T ss_pred HHhh----------c-CCc------------c-ccCCC------------------------------------------
Confidence 2100 0 000 0 00000
Q ss_pred CCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929 279 GGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCI 354 (433)
Q Consensus 279 ~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i 354 (433)
........++.||+.-+|.||||+|.+||.|++++||.|+|.+..+ -.+|+|+++|++|+..+|..||.++|
T Consensus 127 ----t~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki 202 (402)
T KOG2191|consen 127 ----TPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKI 202 (402)
T ss_pred ----CccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHh
Confidence 0012334799999999999999999999999999999999995443 67999999999999999999999999
Q ss_pred HhccccCCC---CC----C---CCCccccccccccchhccccccccccCCCCCcceecccc
Q psy11929 355 ELQKNNTTN---TS----D---NPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGG 405 (433)
Q Consensus 355 ~~~~~~~~~---~~----~---~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~iiGkgG 405 (433)
.+....... .| + ++.|..-.-.+..-.....++.+.+||+..+|-.-|.||
T Consensus 203 ~eDpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~ 263 (402)
T KOG2191|consen 203 QEDPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGG 263 (402)
T ss_pred hcCCcccceeccchhcccCcccccCCCCCCCCCCCccccccchhhcccccccccccccccc
Confidence 887542211 00 0 000110000011100111146778899999999888887
No 9
>KOG2190|consensus
Probab=99.93 E-value=8.5e-25 Score=223.36 Aligned_cols=237 Identities=33% Similarity=0.520 Sum_probs=180.1
Q ss_pred eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC---CCCcceEEEecccCCCCCCccccCCCCCccccc
Q psy11929 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG---ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVT 90 (433)
Q Consensus 14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~ 90 (433)
.+++|||||. +++|+||||+|+.||+|+++|||+|+|..+ .+.+|.|+|.|.++
T Consensus 137 ~v~~RLlVp~----sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~------------------- 193 (485)
T KOG2190|consen 137 EVTCRLLVPS----SQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPD------------------- 193 (485)
T ss_pred ceEEEEEech----hheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchH-------------------
Confidence 6999999999 999999999999999999999999999874 78999999999999
Q ss_pred hHHHHHHHHHHHHhhhhhhc----cccc-----CC-----------C------------CCCCCCeEEEEEeccCcccce
Q psy11929 91 SVDNVCTAYNFMCRSLEDYH----INRN-----RM-----------E------------NCSPQPLQLKLVIPATHCGSL 138 (433)
Q Consensus 91 a~~~v~~A~~~I~~~~~~~~----~~~~-----~~-----------~------------~~~~~~~~~~l~ip~~~vg~i 138 (433)
++.+|...|...|.+.. .... .+ . .........+++.|...++.+
T Consensus 194 ---av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v 270 (485)
T KOG2190|consen 194 ---AVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSV 270 (485)
T ss_pred ---HHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceee
Confidence 99999999988877632 1000 00 0 011223446788999999999
Q ss_pred ecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccH--HHH-HHHHHHHHHHHHhhccccCCCcccccCCCCCCCC
Q psy11929 139 IGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNP--DTI-SQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAG 215 (433)
Q Consensus 139 IGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~--~~v-~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~ 215 (433)
+|++|..|+.|+.++++.|.+.... ++++++++... +.. ..|...+......
T Consensus 271 ~g~~~~~i~~l~~~~~~~i~v~~~~----~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~--------------------- 325 (485)
T KOG2190|consen 271 IGKGGLVIRALRNETGASISVGDSR----TDRIVTISARENPEDRYSMAQEALLLVQPR--------------------- 325 (485)
T ss_pred ecCCCccchhhhhhcCCceEecccc----CcceeeeccccCcccccccchhhhhhcccc---------------------
Confidence 9999999999999999999997421 12666666521 000 0000000000000
Q ss_pred CccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeC
Q psy11929 216 PVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLT 295 (433)
Q Consensus 216 p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP 295 (433)
.... ...+. ...++.++.||
T Consensus 326 ----------------------------------------------------~~~~-------~~~~~-~~~v~~~l~vp 345 (485)
T KOG2190|consen 326 ----------------------------------------------------ISEN-------AGDDL-TQTVTQRLLVP 345 (485)
T ss_pred ----------------------------------------------------cccc-------ccccc-cceeeeeeccC
Confidence 0000 01111 35788999999
Q ss_pred cccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhccccC
Q psy11929 296 DDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNT 361 (433)
Q Consensus 296 ~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~ 361 (433)
.+++||||||+|.+|.+||+.|||.|+|.+... ..++.++|+|...+...|++++..++...+...
T Consensus 346 s~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~ 414 (485)
T KOG2190|consen 346 SDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSAPKSSM 414 (485)
T ss_pred ccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccccCccCC
Confidence 999999999999999999999999999998875 789999999999999999999999998876644
No 10
>KOG2192|consensus
Probab=99.76 E-value=3.6e-18 Score=156.32 Aligned_cols=158 Identities=27% Similarity=0.407 Sum_probs=131.2
Q ss_pred CCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC---CCCCcceEEEecccCCCCCCccccCCCCCc
Q psy11929 10 DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD---GACPDRIVTVSGSVDNSSTSSVETGYPGHT 86 (433)
Q Consensus 10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~ 86 (433)
.+.....+||||+. +.+|.|||++|+.||.||+++.|+++|-. +++.+|+|.|.|.+.
T Consensus 118 ~~~~pce~rllihq----s~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k--------------- 178 (390)
T KOG2192|consen 118 QLPSPCELRLLIHQ----SLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPK--------------- 178 (390)
T ss_pred CCCCchhhhhhhhh----hhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcc---------------
Confidence 34556789999999 99999999999999999999999999976 478999999999999
Q ss_pred cccchHHHHHHHHHHHHhhhhhhc---------cccc--------------C------C---------------------
Q psy11929 87 LWVTSVDNVCTAYNFMCRSLEDYH---------INRN--------------R------M--------------------- 116 (433)
Q Consensus 87 ~~~~a~~~v~~A~~~I~~~~~~~~---------~~~~--------------~------~--------------------- 116 (433)
.|..+++.|++.+.+.. .+|- + .
T Consensus 179 -------~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~ 251 (390)
T KOG2192|consen 179 -------RVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYD 251 (390)
T ss_pred -------hHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceec
Confidence 77777777776665410 0000 0 0
Q ss_pred --------------------------------------------------------CCCCCCCeEEEEEeccCcccceec
Q psy11929 117 --------------------------------------------------------ENCSPQPLQLKLVIPATHCGSLIG 140 (433)
Q Consensus 117 --------------------------------------------------------~~~~~~~~~~~l~ip~~~vg~iIG 140 (433)
.+......+..+.||..+-|.|||
T Consensus 252 r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiig 331 (390)
T KOG2192|consen 252 RRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIG 331 (390)
T ss_pred cCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceec
Confidence 012344578899999999999999
Q ss_pred CCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 141 k~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
|+|+.|++|+.++||.|++.. .+.++.||+++|+|+.+++..|..++...++.
T Consensus 332 kggqri~~ir~esGA~Ikide-pleGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 332 KGGQRIKQIRHESGASIKIDE-PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred ccchhhhhhhhccCceEEecC-cCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 999999999999999999973 56789999999999999999999999888875
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=3.3e-16 Score=140.72 Aligned_cols=136 Identities=20% Similarity=0.312 Sum_probs=104.6
Q ss_pred EeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEE---ecccCCCCCCccccCCCCCccccchHHHHH
Q psy11929 20 LFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTV---SGSVDNSSTSSVETGYPGHTLWVTSVDNVC 96 (433)
Q Consensus 20 lvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I---~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~ 96 (433)
.||. +.+|.|||++|++||.|+++|||+|++.+. +..|.| .+.++ ++.
T Consensus 3 ~Ip~----~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---~g~V~I~~~t~d~~----------------------~i~ 53 (172)
T TIGR03665 3 KIPK----DRIGVLIGKGGETKKEIEERTGVKLDIDSE---TGEVKIEEEDEDPL----------------------AVM 53 (172)
T ss_pred cCCH----HHhhhHhCCchhHHHHHHHHhCcEEEEEcC---CceEEEecCCCCHH----------------------HHH
Confidence 4566 999999999999999999999999999973 356888 44444 999
Q ss_pred HHHHHHHhhhhhhcccccCCCCCCCCCeEEE-EEecc---------CcccceecCCchhHHHHHHhhCceEEeccCCCCC
Q psy11929 97 TAYNFMCRSLEDYHINRNRMENCSPQPLQLK-LVIPA---------THCGSLIGKGGCKIKDIRDLSGANVQVASDMLPM 166 (433)
Q Consensus 97 ~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~-l~ip~---------~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~ 166 (433)
+|.++|..+...+.... ........+..+ +.|+. ..+|+|||++|++++.|++.|||+|.+.
T Consensus 54 kA~~~I~~i~~gf~~e~--A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------ 125 (172)
T TIGR03665 54 KAREVVKAIGRGFSPEK--ALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------ 125 (172)
T ss_pred HHHHHHHHHHcCCCHHH--HHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------
Confidence 99999988665422110 000001222222 23433 3689999999999999999999999996
Q ss_pred CCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 167 STERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 167 ~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
++.|.|.|++++++.|..+|.+++.+
T Consensus 126 --~~~v~i~G~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 126 --GKTVGIIGDPEQVQIAREAIEMLIEG 151 (172)
T ss_pred --CCEEEEECCHHHHHHHHHHHHHHHcC
Confidence 36899999999999999999999965
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.64 E-value=1.8e-15 Score=136.87 Aligned_cols=141 Identities=18% Similarity=0.286 Sum_probs=108.2
Q ss_pred EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEe----cccCCCCCCccccCCCCCccccc
Q psy11929 15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVS----GSVDNSSTSSVETGYPGHTLWVT 90 (433)
Q Consensus 15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~----G~~~~~~~~~v~~~~~~~~~~~~ 90 (433)
+...+.||. +.+|.|||++|++||.|+++|||+|++.+. +..|.|. +.++
T Consensus 3 ~~~~i~IP~----~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---~g~V~I~~~~~~d~~------------------- 56 (180)
T PRK13763 3 MMEYVKIPK----DRIGVLIGKKGETKKEIEERTGVKLEIDSE---TGEVIIEPTDGEDPL------------------- 56 (180)
T ss_pred ceEEEEcCH----HHhhhHhccchhHHHHHHHHHCcEEEEECC---CCeEEEEeCCCCCHH-------------------
Confidence 567788898 999999999999999999999999999973 3567785 4555
Q ss_pred hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEE-Eec---------cCcccceecCCchhHHHHHHhhCceEEec
Q psy11929 91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKL-VIP---------ATHCGSLIGKGGCKIKDIRDLSGANVQVA 160 (433)
Q Consensus 91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l-~ip---------~~~vg~iIGk~G~~Ik~I~~~sga~I~i~ 160 (433)
++.+|.++|..+...+..... .......+..++ .+. ...+|+|||++|++++.|++.|||+|.|.
T Consensus 57 ---~i~kA~~~I~ai~~gf~~e~A--~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~ 131 (180)
T PRK13763 57 ---AVLKARDIVKAIGRGFSPEKA--LRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY 131 (180)
T ss_pred ---HHHHHHHHHHHHhcCCCHHHH--HHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc
Confidence 899999999887664211100 000011222222 111 13689999999999999999999999997
Q ss_pred cCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 161 SDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 161 ~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
. +.|.|.|++++++.|...|..+++.
T Consensus 132 ~--------~~v~i~G~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 132 G--------KTVAIIGDPEQVEIAREAIEMLIEG 157 (180)
T ss_pred C--------CEEEEEeCHHHHHHHHHHHHHHHcC
Confidence 3 4599999999999999999999865
No 13
>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=1.3e-15 Score=136.94 Aligned_cols=138 Identities=28% Similarity=0.389 Sum_probs=106.6
Q ss_pred EEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEE---EccHHHHHHHHHHHHHHHHhhccccCCCcc
Q psy11929 128 LVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTV---HGNPDTISQAIYQICLVLIECTLQVVKGAV 204 (433)
Q Consensus 128 l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I---~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~ 204 (433)
+.||.+.+|.|||++|++|+.|+++||++|.+..+ +..|.| +++++++.+|..+|..+.+. ..+..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g---f~~e~-- 70 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE------TGEVKIEEEDEDPLAVMKAREVVKAIGRG---FSPEK-- 70 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC------CceEEEecCCCCHHHHHHHHHHHHHHHcC---CCHHH--
Confidence 56899999999999999999999999999999853 357888 78999999999999987764 11100
Q ss_pred cccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCC
Q psy11929 205 IPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTG 284 (433)
Q Consensus 205 ~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 284 (433)
++...+.
T Consensus 71 -------------------A~~l~gd------------------------------------------------------ 77 (172)
T TIGR03665 71 -------------------ALKLLDD------------------------------------------------------ 77 (172)
T ss_pred -------------------HHHhcCC------------------------------------------------------
Confidence 0000000
Q ss_pred CCceEEEEEeC---------cccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Q psy11929 285 DDFVETEIVLT---------DDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIE 355 (433)
Q Consensus 285 ~~~~t~~i~VP---------~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~ 355 (433)
...-.-+.|+ ...+|+|||++|++++.|+..|||+|.|++ ..|.|+|++++++.|+.+|.++++
T Consensus 78 -~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------~~v~i~G~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 78 -DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------KTVGIIGDPEQVQIAREAIEMLIE 150 (172)
T ss_pred -cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------CEEEEECCHHHHHHHHHHHHHHHc
Confidence 0000001111 137899999999999999999999999986 569999999999999999999995
Q ss_pred h
Q psy11929 356 L 356 (433)
Q Consensus 356 ~ 356 (433)
.
T Consensus 151 ~ 151 (172)
T TIGR03665 151 G 151 (172)
T ss_pred C
Confidence 4
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.60 E-value=1.1e-14 Score=131.71 Aligned_cols=151 Identities=25% Similarity=0.295 Sum_probs=109.4
Q ss_pred eEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEE----ccHHHHHHHHHHHHHHHHhhcccc
Q psy11929 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVH----GNPDTISQAIYQICLVLIECTLQV 199 (433)
Q Consensus 124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~----G~~~~v~~A~~~I~~~l~e~~~~~ 199 (433)
....+.||.+.+|.|||++|++|+.|+++||++|.+..+ +..|.|. ++++++.+|+.+|..+++. +.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g---f~ 73 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE------TGEVIIEPTDGEDPLAVLKARDIVKAIGRG---FS 73 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC---CC
Confidence 456889999999999999999999999999999999853 3678885 8999999999999998774 11
Q ss_pred CCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccC
Q psy11929 200 VKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSG 279 (433)
Q Consensus 200 ~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 279 (433)
+..+ +...+....-. +..+...+
T Consensus 74 ~e~A---------------------~~l~gd~y~~~-----------Vi~i~~~~------------------------- 96 (180)
T PRK13763 74 PEKA---------------------LRLLDDDYVLE-----------VIDLSDYG------------------------- 96 (180)
T ss_pred HHHH---------------------HHHhCCCceEE-----------EEEhhhcc-------------------------
Confidence 1000 00000000000 00000000
Q ss_pred CCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929 280 GKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIEL 356 (433)
Q Consensus 280 ~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~ 356 (433)
. . . ......+|+|||++|++++.|+..|||+|.|.+. .|.|.|++++++.|+..|..+++.
T Consensus 97 ~---~------~-~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~------~v~i~G~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 97 D---S------P-NALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK------TVAIIGDPEQVEIAREAIEMLIEG 157 (180)
T ss_pred C---C------h-hHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC------EEEEEeCHHHHHHHHHHHHHHHcC
Confidence 0 0 0 0112379999999999999999999999999863 499999999999999999998854
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=99.47 E-value=1.1e-13 Score=104.20 Aligned_cols=63 Identities=33% Similarity=0.496 Sum_probs=58.9
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC--CCceEEEEEeCHHHHHHHHHHHH
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE--SHKKMFHIQGCQEAVSLAQYLIN 351 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~--~~er~V~IsGt~e~v~~A~~lI~ 351 (433)
+.+|.||..++|+|||++|.+|++|+++|||+|++.+... ..+|.|+|+|+++++++|+.+|+
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 3689999999999999999999999999999999998775 78999999999999999999873
No 16
>KOG2279|consensus
Probab=99.43 E-value=9.8e-13 Score=131.93 Aligned_cols=291 Identities=20% Similarity=0.284 Sum_probs=186.5
Q ss_pred ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCC-CCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929 13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA-CPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS 91 (433)
Q Consensus 13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~-~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a 91 (433)
.++.+.++++. ..|-++|||+|++||.|+..|++||.+.+.. .++++.++.|.+.
T Consensus 66 k~v~~e~Vv~~----e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~-------------------- 121 (608)
T KOG2279|consen 66 KDIEIEMVVPQ----EAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPV-------------------- 121 (608)
T ss_pred hheeeeEeecc----cceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCC--------------------
Confidence 56888999999 9999999999999999999999999998864 4566666666777
Q ss_pred HHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccE
Q psy11929 92 VDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERI 171 (433)
Q Consensus 92 ~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~ 171 (433)
++..|...++.++.+ ..++...+-+|...+++|+|++|++++.|+.-++++|.+..+ .-..-.+.
T Consensus 122 --~v~~a~a~~~~~~~~------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n-gr~g~~~~ 186 (608)
T KOG2279|consen 122 --QVCKAKAAIHQILTE------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN-GRLGLSRL 186 (608)
T ss_pred --CCChHHHHHHHHHhc------------CCcccccccchhhhcccccccchhhhcchhcccccccccccc-cccccccc
Confidence 677777787777655 467788899999999999999999999999999999999864 22345678
Q ss_pred EEEEccHHHHHHHHHHHHHHHHhhccccCCC--cccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCcc
Q psy11929 172 VTVHGNPDTISQAIYQICLVLIECTLQVVKG--AVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAG 249 (433)
Q Consensus 172 v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~--~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~ 249 (433)
..|.|....+..|..++.+.+.+..+.-.+. ....-.|... |....+...+. ++....|+.......+..|-.+
T Consensus 187 ~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~---p~n~~~~~m~~-~~~s~~~h~~~~t~~s~spg~~ 262 (608)
T KOG2279|consen 187 IKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQ---PINVRREDMTE-PGGAGEPHLWKNTSSSMSPGAP 262 (608)
T ss_pred eecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCC---Cccccchhhcc-cccCCccccCccchhccCCCCC
Confidence 8888888888899999988877643211100 0000011110 00000000010 0000011110000000000000
Q ss_pred ccccCcCCCCCCCCCccccccccCCCccc---CCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929 250 LAVLGIEGIGSTSLTPAALAALSGSRVKS---GGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTG 326 (433)
Q Consensus 250 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~~---~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~ 326 (433)
... +.+ -+| ...---+.++.. +...........+|.+|...+|.+||+.|..++.+...|++.+.|.-.
T Consensus 263 ~~~--~eg--~dm----~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~ 334 (608)
T KOG2279|consen 263 LVT--KEG--GDM----AVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ 334 (608)
T ss_pred Ccc--cCC--Ccc----eeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec
Confidence 000 000 000 000000000100 001112334567999999999999999999999999999999888765
Q ss_pred CC----CCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929 327 TE----SHKKMFHIQGCQEAVSLAQYLINMCI 354 (433)
Q Consensus 327 ~~----~~er~V~IsGt~e~v~~A~~lI~~~i 354 (433)
.- -.-.++.+.|+..-+..+..++...+
T Consensus 335 pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 335 PYTSRVLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred cccchhhhhhhheecchhHHHHHHHhhhhccC
Confidence 43 22367889999999999999997433
No 17
>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=99.41 E-value=6.9e-13 Score=99.82 Aligned_cols=64 Identities=45% Similarity=0.879 Sum_probs=59.6
Q ss_pred EEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHH
Q psy11929 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI 188 (433)
Q Consensus 125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I 188 (433)
+++|+||.+.+|+|||++|++|++|+++|||+|.+.++..+...+|+|+|.|+++++.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999997655678899999999999999999887
No 18
>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=99.33 E-value=2.8e-12 Score=95.51 Aligned_cols=60 Identities=27% Similarity=0.381 Sum_probs=56.7
Q ss_pred EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHH
Q psy11929 290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLI 350 (433)
Q Consensus 290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI 350 (433)
.++.||.+++|+|||++|++|++|+++|||+|.|++.. ..++.|+|+|+++++..|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999999977 6789999999999999999887
No 19
>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=99.31 E-value=2.5e-12 Score=95.18 Aligned_cols=60 Identities=30% Similarity=0.534 Sum_probs=55.4
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHH
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLI 350 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI 350 (433)
|.+|.||.+++|+|||++|++|++|++.|||+|+|++. + .+..|+|+|+++++++|+.+|
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 57899999999999999999999999999999999887 2 456999999999999999886
No 20
>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=99.25 E-value=2e-11 Score=91.26 Aligned_cols=61 Identities=36% Similarity=0.591 Sum_probs=57.4
Q ss_pred EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHH
Q psy11929 290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLI 350 (433)
Q Consensus 290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI 350 (433)
.+|.||..++|+|||++|++|++|++.|||+|.|++... ..++.|+|+|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 589999999999999999999999999999999998765 6789999999999999999887
No 21
>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=99.24 E-value=7.9e-12 Score=92.45 Aligned_cols=60 Identities=33% Similarity=0.479 Sum_probs=55.2
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHH
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNV 95 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v 95 (433)
|++|+||. +++|+|||++|++|++|+++|||+|+|++.+ .+..|+|+|+++ ++
T Consensus 1 T~~i~vp~----~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~-~~~~v~I~G~~~----------------------~v 53 (60)
T PF00013_consen 1 TERIEVPS----SLVGRIIGKKGSNIKEIEEETGVKIQIPDDD-ERDIVTISGSPE----------------------QV 53 (60)
T ss_dssp EEEEEEEH----HHHHHHHTGGGHHHHHHHHHHTSEEEEESTT-EEEEEEEEESHH----------------------HH
T ss_pred CEEEEECH----HHcCEEECCCCCcHHHhhhhcCeEEEEcCCC-CcEEEEEEeCHH----------------------HH
Confidence 68999999 9999999999999999999999999999874 455999999888 99
Q ss_pred HHHHHHH
Q psy11929 96 CTAYNFM 102 (433)
Q Consensus 96 ~~A~~~I 102 (433)
.+|+++|
T Consensus 54 ~~A~~~I 60 (60)
T PF00013_consen 54 EKAKKMI 60 (60)
T ss_dssp HHHHHHH
T ss_pred HHHHhhC
Confidence 9999876
No 22
>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=99.22 E-value=3.5e-11 Score=89.15 Aligned_cols=58 Identities=24% Similarity=0.328 Sum_probs=53.4
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHH
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLIN 351 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~ 351 (433)
+..+.||.+++|+||||+|++|++|+++|||+|.|++. +.|.|+|+ +++++.|+.+|.
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~-----g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD-----GTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCC-----CEEEEEeCCHHHHHHHHHHhC
Confidence 56899999999999999999999999999999999872 67999999 999999998873
No 23
>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=99.21 E-value=1.7e-11 Score=91.36 Aligned_cols=61 Identities=23% Similarity=0.341 Sum_probs=56.7
Q ss_pred EEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHH
Q psy11929 17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVC 96 (433)
Q Consensus 17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~ 96 (433)
.+|.||. .++++|||++|++|++|+++|||+|.|++...+++.|+|+|+.+ ++.
T Consensus 2 ~~i~Vp~----~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~----------------------~v~ 55 (62)
T cd02394 2 EEVEIPK----KLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKE----------------------NVE 55 (62)
T ss_pred eEEEeCH----HHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHH----------------------HHH
Confidence 5788999 99999999999999999999999999999778899999999999 999
Q ss_pred HHHHHHH
Q psy11929 97 TAYNFMC 103 (433)
Q Consensus 97 ~A~~~I~ 103 (433)
.|..+|.
T Consensus 56 ~A~~~i~ 62 (62)
T cd02394 56 KAKEEIL 62 (62)
T ss_pred HHHHHhC
Confidence 9988863
No 24
>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=99.10 E-value=3.5e-10 Score=83.85 Aligned_cols=58 Identities=22% Similarity=0.371 Sum_probs=53.0
Q ss_pred eEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEcc-HHHHHHHHHHH
Q psy11929 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGN-PDTISQAIYQI 188 (433)
Q Consensus 124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~-~~~v~~A~~~I 188 (433)
....+.||.+++|+|||++|++|++|+++|||+|.+++ ++.|.|+|+ .++++.|+.+|
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 45678999999999999999999999999999999975 468999998 99999999886
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=6.7e-10 Score=82.93 Aligned_cols=62 Identities=37% Similarity=0.696 Sum_probs=55.9
Q ss_pred EEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHH
Q psy11929 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI 188 (433)
Q Consensus 126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I 188 (433)
.++.||..++++|||++|++|++|+++|||+|.|+... ....++.|.|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~-~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-SGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCC-CCCCceEEEEEcCHHHHHHHHHHh
Confidence 58999999999999999999999999999999998632 246789999999999999998876
No 26
>PF13014 KH_3: KH domain
Probab=99.01 E-value=4.9e-10 Score=76.96 Aligned_cols=40 Identities=38% Similarity=0.737 Sum_probs=37.6
Q ss_pred ccceeeecCchHHHHHHHHhCCeEEEeC---CCCCcceEEEec
Q psy11929 29 EISCLIGPGGCIVRRLRKESGAKISITD---GACPDRIVTVSG 68 (433)
Q Consensus 29 ~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~eRvv~I~G 68 (433)
++|+||||+|++|++|+++|||+|+|++ ++..+|+|+|+|
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 5899999999999999999999999999 578999999987
No 27
>smart00322 KH K homology RNA-binding domain.
Probab=98.95 E-value=4.2e-09 Score=78.96 Aligned_cols=67 Identities=31% Similarity=0.457 Sum_probs=60.8
Q ss_pred ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929 287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCI 354 (433)
Q Consensus 287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i 354 (433)
..+.++.||..++|.+||++|.+|++|++.||++|.+.... .....|.|.|+++++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 35679999999999999999999999999999999998765 36688999999999999999998776
No 28
>PF13014 KH_3: KH domain
Probab=98.94 E-value=1.6e-09 Score=74.43 Aligned_cols=43 Identities=47% Similarity=0.828 Sum_probs=40.3
Q ss_pred cccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc
Q psy11929 134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG 176 (433)
Q Consensus 134 ~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G 176 (433)
++|+|||++|++|++|+++|||+|.|+++..+...++.|+|+|
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 5899999999999999999999999998777888999999998
No 29
>KOG2208|consensus
Probab=98.89 E-value=6.2e-09 Score=113.03 Aligned_cols=247 Identities=17% Similarity=0.172 Sum_probs=180.0
Q ss_pred eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHH
Q psy11929 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVD 93 (433)
Q Consensus 14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~ 93 (433)
.+..++.+.. ..++++||++|.+++.+++++.+.|+++..+.......|.|......- +.-
T Consensus 200 ~~~~k~~v~~----~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~---------------~~~ 260 (753)
T KOG2208|consen 200 SVFEKMNVGI----TLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSS---------------INV 260 (753)
T ss_pred eEEEEeeccc----cchhhhccccccccccccccceeEEEcccccccchhhhhcccccccee---------------hhh
Confidence 3778888888 999999999999999999999999999986544444555554441100 000
Q ss_pred HHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEE
Q psy11929 94 NVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVT 173 (433)
Q Consensus 94 ~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~ 173 (433)
.+..+..++ ..+..+.+.++..+.-.++|..|..+..++...--...+.++ +.+.+..+.
T Consensus 261 ~i~~~~~~l------------------e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~--~~s~~~~~~ 320 (753)
T KOG2208|consen 261 EIQEALTRL------------------ESEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQN--YPSKDDSIV 320 (753)
T ss_pred hhHHHHHHh------------------cChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhcc--ccccceeEe
Confidence 233333222 234455667788888899999999999998876544333322 235566788
Q ss_pred EEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCcccccc
Q psy11929 174 VHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVL 253 (433)
Q Consensus 174 I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~ 253 (433)
+.|....+..+......++....
T Consensus 321 ~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------------------- 343 (753)
T KOG2208|consen 321 LSGFEVGAVLAKRDKTLLLKNSE--------------------------------------------------------- 343 (753)
T ss_pred ecccccchhhhhhHHHHHHHHhh---------------------------------------------------------
Confidence 88887777666555554444310
Q ss_pred CcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceE
Q psy11929 254 GIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKM 333 (433)
Q Consensus 254 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~ 333 (433)
.+.....+.+-++.+..++||+|.+|.+|++++.+.|.+.... +++..
T Consensus 344 -------------------------------~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~-~~~~~ 391 (753)
T KOG2208|consen 344 -------------------------------ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG-SNNKK 391 (753)
T ss_pred -------------------------------ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc-CCCCC
Confidence 0123457788889999999999999999999999999999955 67889
Q ss_pred EEEEeCHHHHHHHHHHHHHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCcceecccc--HHHHHH
Q psy11929 334 FHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGG--LSELLA 411 (433)
Q Consensus 334 V~IsGt~e~v~~A~~lI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~iiGkgG--~~e~~~ 411 (433)
++++|....+++|...++..+.+....- ..-++.+|+....+++|.|| ++++..
T Consensus 392 v~~~~~~~~~~ka~~~v~~~~~ei~n~~------------------------~~~~~~iP~k~~~~iig~~g~~i~~I~~ 447 (753)
T KOG2208|consen 392 VVITGVSANDEKAVEDVEKIIAEILNSI------------------------VKEEVQIPTKSHKRIIGTKGALINYIMG 447 (753)
T ss_pred eEEeccccchhHHHHHHHHHHHhhhccc------------------------ccceeecCccchhhhhccccccHHHHHh
Confidence 9999999999999999988887754310 01235699999999999999 677754
Q ss_pred h
Q psy11929 412 N 412 (433)
Q Consensus 412 ~ 412 (433)
.
T Consensus 448 k 448 (753)
T KOG2208|consen 448 K 448 (753)
T ss_pred h
Confidence 4
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=98.85 E-value=1.2e-08 Score=76.57 Aligned_cols=67 Identities=27% Similarity=0.592 Sum_probs=60.6
Q ss_pred eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHH
Q psy11929 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVD 93 (433)
Q Consensus 14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~ 93 (433)
.++.++.||. .++|.+||++|.+|++|+++|||+|.+.......+++.|.|..+
T Consensus 2 ~~~~~i~i~~----~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~---------------------- 55 (69)
T smart00322 2 PVTIEVLIPA----DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPE---------------------- 55 (69)
T ss_pred ceEEEEEEcc----hhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHH----------------------
Confidence 4678999999 99999999999999999999999999988665789999999988
Q ss_pred HHHHHHHHHHhhh
Q psy11929 94 NVCTAYNFMCRSL 106 (433)
Q Consensus 94 ~v~~A~~~I~~~~ 106 (433)
++..|..+|.+.+
T Consensus 56 ~v~~a~~~i~~~~ 68 (69)
T smart00322 56 NVEKAAELILEIL 68 (69)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999987754
No 31
>KOG2208|consensus
Probab=98.84 E-value=8.7e-09 Score=111.89 Aligned_cols=216 Identities=19% Similarity=0.259 Sum_probs=164.3
Q ss_pred EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHH
Q psy11929 15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDN 94 (433)
Q Consensus 15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~ 94 (433)
+...+-+.. ..+..|+||+|.+|.+|++++.|+|.++..+..+..+.++|... +
T Consensus 347 ~~i~~~i~~----~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~----------------------~ 400 (753)
T KOG2208|consen 347 ENIKREIFP----EELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSA----------------------N 400 (753)
T ss_pred eeeEEeecH----HhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEecccc----------------------c
Confidence 555666666 88999999999999999999999999999888999999999999 8
Q ss_pred HHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhC-ceEEeccCCCCCCCccEEE
Q psy11929 95 VCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSG-ANVQVASDMLPMSTERIVT 173 (433)
Q Consensus 95 v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sg-a~I~i~~~~~~~~~er~v~ 173 (433)
+.+|.+.+.....++.. ......+.+|...+.++||.+|..|.+|..+++ ..|.+..+ .+....++
T Consensus 401 ~~ka~~~v~~~~~ei~n----------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~---~~~~~~~~ 467 (753)
T KOG2208|consen 401 DEKAVEDVEKIIAEILN----------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN---NNSSDMVT 467 (753)
T ss_pred hhHHHHHHHHHHHhhhc----------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC---Ccccccce
Confidence 88999998888777532 145667899999999999999999999999999 66766642 34455678
Q ss_pred EEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCcccccc
Q psy11929 174 VHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVL 253 (433)
Q Consensus 174 I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~ 253 (433)
+.|....+..+..+...+.....+ ..
T Consensus 468 ~~~~~~dv~~~~~~~~~~~~~a~~-~~----------------------------------------------------- 493 (753)
T KOG2208|consen 468 IRGISKDVEKSVSLLKALKADAKN-LK----------------------------------------------------- 493 (753)
T ss_pred EeccccccchhHHHHHhhhhhhhc-ch-----------------------------------------------------
Confidence 888888887776666555443110 00
Q ss_pred CcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceE
Q psy11929 254 GIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKM 333 (433)
Q Consensus 254 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~ 333 (433)
.....+.+...|..+.+..+|+.|..+ +..+....++...+.++..
T Consensus 494 ------------------------------~~~~~~~d~~~~~~~~~~~~g~~~~i~----d~~~~~~i~~~~~~~~~~~ 539 (753)
T KOG2208|consen 494 ------------------------------FRDVVTKDKLLPVKYIGKEIGKNGTIR----DSLGDKSIFPPNEDEDHEK 539 (753)
T ss_pred ------------------------------hhhhhhccccchHHhhcccccCceeee----ccCCceeecccccccccce
Confidence 001122345567777777777776654 4555555666554456789
Q ss_pred EEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929 334 FHIQGCQEAVSLAQYLINMCIELQ 357 (433)
Q Consensus 334 V~IsGt~e~v~~A~~lI~~~i~~~ 357 (433)
++|.|..+.+..|+..+...+...
T Consensus 540 i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 540 ITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred eeecccccchhhhHHHHHhcchhh
Confidence 999999999999999888877654
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.81 E-value=2.4e-08 Score=89.33 Aligned_cols=148 Identities=16% Similarity=0.223 Sum_probs=107.2
Q ss_pred ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchH
Q psy11929 13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV 92 (433)
Q Consensus 13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~ 92 (433)
......+.||. ..++.+||+.|++.+.|.+.++++|.+.. .+..|.|..+..-. ++
T Consensus 6 ~~~~~~v~iPk----~R~~~lig~~g~v~k~ie~~~~~~~~iD~---~~~~V~i~~~~~t~------Dp----------- 61 (194)
T COG1094 6 EKSSEAVKIPK----DRIGVLIGKWGEVKKAIEEKTGVKLRIDS---KTGSVTIRTTRKTE------DP----------- 61 (194)
T ss_pred ccceeeeecCc----hhheeeecccccchHHHHhhcCeEEEEEC---CCCeEEEEecCCCC------Ch-----------
Confidence 34566789999 99999999999999999999999999987 55678887773200 00
Q ss_pred HHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEE-EE----ec------cCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 93 DNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLK-LV----IP------ATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 93 ~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~-l~----ip------~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
..+.+|.+.|..+-..+..... -....+...+. +. +- ....|+|||++|.+-+-|++-|+|.|.+.
T Consensus 62 ~~~~ka~d~VkAIgrGF~pe~A--~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~- 138 (194)
T COG1094 62 LALLKARDVVKAIGRGFPPEKA--LKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY- 138 (194)
T ss_pred HHHHHHHHHHHHHhcCCCHHHH--HHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-
Confidence 0677777777665443321100 00001111221 11 11 12459999999999999999999999997
Q ss_pred CCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 162 DMLPMSTERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 162 ~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
...|.|.|.++++..|...|..++..
T Consensus 139 -------g~tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 139 -------GKTVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred -------CcEEEEecChhhhHHHHHHHHHHHcC
Confidence 46899999999999999999999976
No 33
>KOG2279|consensus
Probab=98.69 E-value=1.3e-08 Score=102.83 Aligned_cols=146 Identities=24% Similarity=0.439 Sum_probs=123.3
Q ss_pred CCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhcccc
Q psy11929 120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQV 199 (433)
Q Consensus 120 ~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~ 199 (433)
....+.+++.++...+-+++|+.|++|+.|+..++++|.+..+.. ..++...+.|-+.++..|...++.++.+ +.
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~--g~e~~~~~~~~p~~v~~a~a~~~~~~~~---~~ 138 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV--GDERVLLISGFPVQVCKAKAAIHQILTE---NT 138 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC--CcccchhhccCCCCCChHHHHHHHHHhc---CC
Confidence 356788999999999999999999999999999999999986532 2455666677899999999999998876 11
Q ss_pred CCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccC
Q psy11929 200 VKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSG 279 (433)
Q Consensus 200 ~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 279 (433)
T Consensus 139 -------------------------------------------------------------------------------- 138 (608)
T KOG2279|consen 139 -------------------------------------------------------------------------------- 138 (608)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929 280 GKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ 357 (433)
Q Consensus 280 ~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~ 357 (433)
.+..++.+|...+++|+|++|.++..|+..++|+|.+..... .-.+.+.|.|...-+..|+.++.+++++.
T Consensus 139 -------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~ed 210 (608)
T KOG2279|consen 139 -------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSED 210 (608)
T ss_pred -------cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccch
Confidence 223355678899999999999999999999999999998866 66788889999888889999998888664
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.50 E-value=6.1e-07 Score=80.47 Aligned_cols=148 Identities=24% Similarity=0.302 Sum_probs=106.2
Q ss_pred CeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-----cHHHHHHHHHHHHHHHHhhcc
Q psy11929 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-----NPDTISQAIYQICLVLIECTL 197 (433)
Q Consensus 123 ~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-----~~~~v~~A~~~I~~~l~e~~~ 197 (433)
.....+.||...++.+||+.|+.-+.|.+.+++++.+..+ +..|.|.. +|-.+.+|...|..+=+.
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG--- 77 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK------TGSVTIRTTRKTEDPLALLKARDVVKAIGRG--- 77 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC------CCeEEEEecCCCCChHHHHHHHHHHHHHhcC---
Confidence 3455689999999999999999999999999999999743 45666643 578889998888776554
Q ss_pred ccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcc
Q psy11929 198 QVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVK 277 (433)
Q Consensus 198 ~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~ 277 (433)
+++..+-. +......+- .-. +
T Consensus 78 F~pe~A~~------------LL~d~~~le--------------------vId------------------i--------- 98 (194)
T COG1094 78 FPPEKALK------------LLEDDYYLE--------------------VID------------------L--------- 98 (194)
T ss_pred CCHHHHHH------------HhcCCcEEE--------------------EEE------------------H---------
Confidence 22111000 000000000 000 0
Q ss_pred cCCCCCCCCceEEEEEe-----CcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHH
Q psy11929 278 SGGKDTGDDFVETEIVL-----TDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINM 352 (433)
Q Consensus 278 ~~~~~~~~~~~t~~i~V-----P~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~ 352 (433)
..+.- =....|+|||++|.+-+.|+..|||.|-|.... |-|-|.+++++.|+..|..
T Consensus 99 ------------~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~t------VaiiG~~~~v~iAr~AVem 160 (194)
T COG1094 99 ------------KDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGKT------VAIIGGFEQVEIAREAVEM 160 (194)
T ss_pred ------------HHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCcE------EEEecChhhhHHHHHHHHH
Confidence 00000 112569999999999999999999999999865 9999999999999999999
Q ss_pred HHHh
Q psy11929 353 CIEL 356 (433)
Q Consensus 353 ~i~~ 356 (433)
+++.
T Consensus 161 li~G 164 (194)
T COG1094 161 LING 164 (194)
T ss_pred HHcC
Confidence 9975
No 35
>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=98.39 E-value=8.4e-07 Score=74.72 Aligned_cols=64 Identities=25% Similarity=0.353 Sum_probs=48.5
Q ss_pred ccccceeeecCchHHHHHHHHhCCeEEEeCCCCC-------------------cceEEEecccCCCCCCccccCCCCCcc
Q psy11929 27 VNEISCLIGPGGCIVRRLRKESGAKISITDGACP-------------------DRIVTVSGSVDNSSTSSVETGYPGHTL 87 (433)
Q Consensus 27 ~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~-------------------eRvv~I~G~~~~~~~~~v~~~~~~~~~ 87 (433)
++++|.|||++|.+||+|+++|||+|.|...++. .-.|.|++..
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~----------------- 76 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAET----------------- 76 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCC-----------------
Confidence 5889999999999999999999999999875311 1234444443
Q ss_pred ccchHHHHHHHHHHHHhhhhhh
Q psy11929 88 WVTSVDNVCTAYNFMCRSLEDY 109 (433)
Q Consensus 88 ~~~a~~~v~~A~~~I~~~~~~~ 109 (433)
++.+++.+|..+|..++...
T Consensus 77 --~~~e~~~~A~~~I~~ll~~~ 96 (120)
T cd02395 77 --PPEEALAKAVEAIEELLKPA 96 (120)
T ss_pred --cHHHHHHHHHHHHHHHhccC
Confidence 12458999999998887653
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=98.33 E-value=1.5e-06 Score=73.22 Aligned_cols=60 Identities=22% Similarity=0.306 Sum_probs=51.4
Q ss_pred ccccccccCCCchHHHHHhHhCCeEEEccCCC------------------CCceEEEEEeCH---HHHHHHHHHHHHHHH
Q psy11929 297 DIAGCVIGKAGSRLLEIRQISGAQINIHTGTE------------------SHKKMFHIQGCQ---EAVSLAQYLINMCIE 355 (433)
Q Consensus 297 ~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~------------------~~er~V~IsGt~---e~v~~A~~lI~~~i~ 355 (433)
+++|.|||.+|++||+|+++|||+|.|..... .++-.|.|++.. +++++|..+|..++.
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 57899999999999999999999999997632 233678899964 899999999999987
Q ss_pred h
Q psy11929 356 L 356 (433)
Q Consensus 356 ~ 356 (433)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 37
>KOG2113|consensus
Probab=98.26 E-value=1.4e-06 Score=82.57 Aligned_cols=149 Identities=21% Similarity=0.358 Sum_probs=110.1
Q ss_pred CCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCC
Q psy11929 122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVK 201 (433)
Q Consensus 122 ~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~ 201 (433)
..++..+.+|..+++.++|++|.+||.|+.+|...|.-+.. ..+.++.++|..+.|+.|+..|...-+. ..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr----~eePiF~vTg~~edv~~aRrei~saaeH---~~-- 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR----GEEPIFPVTGRHEDVRRARREIPSAAEH---FG-- 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC----CCCCcceeccCchhHHHHhhcCccccce---ee--
Confidence 67888899999999999999999999999999999998742 2457899999999999998876543221 00
Q ss_pred CcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCC
Q psy11929 202 GAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGK 281 (433)
Q Consensus 202 ~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~ 281 (433)
-+.|.+... | ..+ .+
T Consensus 95 --l~~~s~s~S--------g-------------------------------------g~~-----~~------------- 109 (394)
T KOG2113|consen 95 --LIRASRSFS--------G-------------------------------------GTN-----GA------------- 109 (394)
T ss_pred --eeeeccccc--------C-------------------------------------CCc-----cc-------------
Confidence 000100000 0 000 00
Q ss_pred CCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHH-HHHHH
Q psy11929 282 DTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEA-VSLAQ 347 (433)
Q Consensus 282 ~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~-v~~A~ 347 (433)
....+.+.+..+|-..+|.|.|.+|.+|+.|++.+...|.-.-+. .+.++.++|.+.. +++|.
T Consensus 110 -s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--~~~Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 110 -SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--GEPVFCVTGAPKNCVKRAR 173 (394)
T ss_pred -cccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--CCceEEEecCCcchhhhcc
Confidence 012355678889999999999999999999999999999877665 6778888998876 55555
No 38
>KOG2113|consensus
Probab=98.12 E-value=5e-06 Score=78.79 Aligned_cols=151 Identities=18% Similarity=0.284 Sum_probs=115.0
Q ss_pred CCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCcccc
Q psy11929 10 DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWV 89 (433)
Q Consensus 10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~ 89 (433)
+-...++..+-+|. .+++.|.|++|.+||.|+.+|...|.-+..+ .+-+..++|..+
T Consensus 21 ~~p~nvt~sv~vps----~~v~~ivg~qg~kikalr~KTqtyi~tPsr~-eePiF~vTg~~e------------------ 77 (394)
T KOG2113|consen 21 SIGQNVTESVEVPS----EHVAEIVGRQGCKIKALRAKTQTYIKTPSRG-EEPIFPVTGRHE------------------ 77 (394)
T ss_pred CCCCccceeeecCc----ccceeecccCccccchhhhhhcceeccCCCC-CCCcceeccCch------------------
Confidence 34467888889998 9999999999999999999999999887655 347889999999
Q ss_pred chHHHHHHHHHHHHhhhhhhc-----ccccCCC--CCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccC
Q psy11929 90 TSVDNVCTAYNFMCRSLEDYH-----INRNRME--NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD 162 (433)
Q Consensus 90 ~a~~~v~~A~~~I~~~~~~~~-----~~~~~~~--~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~ 162 (433)
.|.+|++.|....+.+. ..+.+.. .......+...-+|-..+|.+.|..|.+|+.|++.++..|.-.-
T Consensus 78 ----dv~~aRrei~saaeH~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v- 152 (394)
T KOG2113|consen 78 ----DVRRARREIPSAAEHFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV- 152 (394)
T ss_pred ----hHHHHhhcCccccceeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeec-
Confidence 89999988876433321 1111111 11234455667889999999999999999999999999887753
Q ss_pred CCCCCCccEEEEEccHHH-HHHHH-HHHHHH
Q psy11929 163 MLPMSTERIVTVHGNPDT-ISQAI-YQICLV 191 (433)
Q Consensus 163 ~~~~~~er~v~I~G~~~~-v~~A~-~~I~~~ 191 (433)
.+.+.++.++|.+.+ +++|. +.|...
T Consensus 153 ---~~~~~Vf~Vtg~~~nC~kra~s~eie~t 180 (394)
T KOG2113|consen 153 ---RCGEPVFCVTGAPKNCVKRARSCEIEQT 180 (394)
T ss_pred ---cCCCceEEEecCCcchhhhccccchhhh
Confidence 345778999998888 56665 555543
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.06 E-value=9.2e-06 Score=70.43 Aligned_cols=104 Identities=18% Similarity=0.272 Sum_probs=71.1
Q ss_pred EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHH
Q psy11929 15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDN 94 (433)
Q Consensus 15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~ 94 (433)
=.+.++|+. ..+|..||++|++|+.|++..|-+|.|-.-. +
T Consensus 32 ~~vi~vV~~----~~vG~~IG~~G~rI~~i~e~lgekIdVve~s------------~----------------------- 72 (140)
T PRK08406 32 DRIIFVVKE----GDMGLAIGKGGENVKRLEEKLGKDIELVEYS------------D----------------------- 72 (140)
T ss_pred CEEEEEEeC----CCccccCCcCchHHHHHHHHhCCceEEEEcC------------C-----------------------
Confidence 356788888 9999999999999999999999888876410 1
Q ss_pred HHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEec
Q psy11929 95 VCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVA 160 (433)
Q Consensus 95 v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~ 160 (433)
.+..+|...+......--. -........+.+.|+....|.+|||+|.+++.++.-++-.+.+.
T Consensus 73 --d~~~fI~n~l~Pa~V~~v~-I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 73 --DPEEFIKNIFAPAAVRSVT-IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred --CHHHHHHHHcCCCEEEEEE-EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 1122222222211000000 00012235667789999999999999999999999998877663
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.05 E-value=1.6e-05 Score=69.00 Aligned_cols=38 Identities=24% Similarity=0.489 Sum_probs=34.3
Q ss_pred eEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
-.+.++|+...+|..||++|++|+.|++..|-+|.+-.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 46778999999999999999999999999999988863
No 41
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.96 E-value=4.1e-05 Score=82.13 Aligned_cols=98 Identities=17% Similarity=0.210 Sum_probs=77.1
Q ss_pred ccchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCC
Q psy11929 88 WVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS 167 (433)
Q Consensus 88 ~~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~ 167 (433)
+..|++.+.+++..|.+.+++.-... .......+....+.||.+++|.|||+||.+||.|+++||++|.+..
T Consensus 544 l~~aL~~A~~g~~~Il~~m~~al~~p--~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------ 615 (719)
T TIGR02696 544 LASALKQARDARLAILDVMAEAIDTP--DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------ 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCc--cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------
Confidence 44466777777778877776632222 1223345677889999999999999999999999999999999974
Q ss_pred CccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929 168 TERIVTVHG-NPDTISQAIYQICLVLIE 194 (433)
Q Consensus 168 ~er~v~I~G-~~~~v~~A~~~I~~~l~e 194 (433)
+..|.|.+ +.+.+++|+.+|..++..
T Consensus 616 -~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 -DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred -CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 57788888 788999999999988873
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=97.79 E-value=0.00012 Score=78.56 Aligned_cols=64 Identities=23% Similarity=0.280 Sum_probs=57.4
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL 356 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~ 356 (433)
...++.||.+++|.|||.||.+||.|+++|||+|.|.++ ..|.|.+. .++.++|+.+|...+..
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~-----G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD-----GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC-----cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 356899999999999999999999999999999999984 57888885 68999999999998874
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=97.59 E-value=0.00039 Score=60.18 Aligned_cols=103 Identities=20% Similarity=0.311 Sum_probs=68.7
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHH
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNV 95 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v 95 (433)
.+-+++.. ..+|..||++|++|+.|++..|=+|.|-.=. + ..
T Consensus 34 riifvV~~----g~vG~~IG~~G~rIk~i~el~gekIdVVeys------------~----------------------D~ 75 (141)
T TIGR01952 34 RVVFVVKE----GEMGAAIGKGGENVKRLEELIGKSIELIEYS------------E----------------------NL 75 (141)
T ss_pred EEEEEEcC----CCccccCCCCchHHHHHHHhcCCeeEEEEcC------------C----------------------CH
Confidence 56677777 8999999999999999998889888876411 0 00
Q ss_pred HHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEec
Q psy11929 96 CTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVA 160 (433)
Q Consensus 96 ~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~ 160 (433)
. .+|...+....-..- .....+....+.+.||.+..+..|||+|.+++...+-++-++.+.
T Consensus 76 ~---~fI~N~l~PA~V~~V-~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 76 E---EFVANKLAPAEVKNV-TVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred H---HHHHHcCCCceEEEE-EEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 1 111111111000000 000012345677889999999999999999999999998877664
No 44
>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=97.50 E-value=0.00034 Score=76.08 Aligned_cols=97 Identities=16% Similarity=0.234 Sum_probs=70.1
Q ss_pred chHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCc
Q psy11929 90 TSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTE 169 (433)
Q Consensus 90 ~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~e 169 (433)
.|++...+++..|.+.+++.-.... .......+....+.||.+.++.|||++|++||+|+++|||+|.|.. +
T Consensus 518 ~al~~a~~~~~~I~~~m~~~l~~~~-~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-------d 589 (684)
T TIGR03591 518 QALEQAKEGRLHILGEMNKVISEPR-AELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-------D 589 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhh-ccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-------C
Confidence 3445555666666665555221110 1122345667788999999999999999999999999999999974 4
Q ss_pred cEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929 170 RIVTVHG-NPDTISQAIYQICLVLIE 194 (433)
Q Consensus 170 r~v~I~G-~~~~v~~A~~~I~~~l~e 194 (433)
..|.|.+ +.+.+.+|...|..+..+
T Consensus 590 G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 590 GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 5677766 678889999998887653
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=0.00041 Score=75.45 Aligned_cols=64 Identities=27% Similarity=0.270 Sum_probs=55.2
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL 356 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~ 356 (433)
...++.||.+++|.|||+||++||.|+++|||+|.|.++ -.|.|.+. .+.+++|..+|..+...
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd-----G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD-----GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC-----eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 356899999999999999999999999999999999875 45667664 68899999999888653
No 46
>KOG0119|consensus
Probab=97.46 E-value=0.00094 Score=67.48 Aligned_cols=73 Identities=23% Similarity=0.362 Sum_probs=56.3
Q ss_pred CeEEEEEecc------CcccceecCCchhHHHHHHhhCceEEecc-----CC---------CCCCCc-cEEEEEc-cHHH
Q psy11929 123 PLQLKLVIPA------THCGSLIGKGGCKIKDIRDLSGANVQVAS-----DM---------LPMSTE-RIVTVHG-NPDT 180 (433)
Q Consensus 123 ~~~~~l~ip~------~~vg~iIGk~G~~Ik~I~~~sga~I~i~~-----~~---------~~~~~e-r~v~I~G-~~~~ 180 (433)
..+-++.||- +++|+|||..|.|.|+|+++|||+|.|-. +. .+...| =-+.|++ +.+.
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 6677888883 58999999999999999999999999963 11 112222 3456777 5678
Q ss_pred HHHHHHHHHHHHHhh
Q psy11929 181 ISQAIYQICLVLIEC 195 (433)
Q Consensus 181 v~~A~~~I~~~l~e~ 195 (433)
|++|++.|..+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 899999999998863
No 47
>KOG0336|consensus
Probab=97.46 E-value=0.00016 Score=71.58 Aligned_cols=72 Identities=19% Similarity=0.245 Sum_probs=61.3
Q ss_pred CCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929 284 GDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ 357 (433)
Q Consensus 284 ~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~ 357 (433)
+..+...-+.|-.++||.|||++|++|++||..|+++|+|.+.+ -+..|+|-|...--.+|+..|...+..+
T Consensus 43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~--~e~kv~ifg~~~m~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD--LEVKVTIFGINHMRKKAKASIDRGQDKD 114 (629)
T ss_pred CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC--ceeEEEEechHHHHHHHHhhHhhhhhhh
Confidence 34566778889999999999999999999999999999999876 6788999999988888888776665443
No 48
>KOG1588|consensus
Probab=97.39 E-value=0.00029 Score=66.13 Aligned_cols=50 Identities=26% Similarity=0.422 Sum_probs=41.6
Q ss_pred CCCCceEEEEEEeccC--CcccccceeeecCchHHHHHHHHhCCeEEEeCCC
Q psy11929 9 IDEDTLITMRCLFHSS--VNVNEISCLIGPGGCIVRRLRKESGAKISITDGA 58 (433)
Q Consensus 9 ~~~~~~~~~rilvp~~--~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~ 58 (433)
......++.|++||.+ ...++||.|+|++|.++|+|+++|||+|.|-..+
T Consensus 86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg 137 (259)
T KOG1588|consen 86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG 137 (259)
T ss_pred cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence 3455678899999874 3456899999999999999999999999987643
No 49
>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=97.29 E-value=0.00081 Score=58.24 Aligned_cols=39 Identities=15% Similarity=0.234 Sum_probs=34.2
Q ss_pred ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEcc
Q psy11929 287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHT 325 (433)
Q Consensus 287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~ 325 (433)
.....+.||.+..+..|||+|+||+...+.+|-++.|.+
T Consensus 99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~~ 137 (141)
T TIGR01952 99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDD 137 (141)
T ss_pred CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCeE
Confidence 356788999999999999999999999999998887653
No 50
>KOG0119|consensus
Probab=97.16 E-value=0.00077 Score=68.07 Aligned_cols=87 Identities=21% Similarity=0.322 Sum_probs=53.9
Q ss_pred eEEEEEEeccC--CcccccceeeecCchHHHHHHHHhCCeEEEeCCCC-CcceEEEecccCCCCCCccccCCCCCcccc-
Q psy11929 14 LITMRCLFHSS--VNVNEISCLIGPGGCIVRRLRKESGAKISITDGAC-PDRIVTVSGSVDNSSTSSVETGYPGHTLWV- 89 (433)
Q Consensus 14 ~~~~rilvp~~--~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~-~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~- 89 (433)
.++-|+.||.+ =.+++||+|||.+|.|.|+|++||||||.|-..++ .|.. |..+.-. .....++..+|
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk----~~~~d~~----~~~~~~epLH~~ 208 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK----GRSDDLS----YIPKENEPLHCL 208 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc----cCCcccc----cccccccceeEE
Confidence 55667777641 12368999999999999999999999999976421 2211 1111000 00011112222
Q ss_pred ---chHHHHHHHHHHHHhhhhh
Q psy11929 90 ---TSVDNVCTAYNFMCRSLED 108 (433)
Q Consensus 90 ---~a~~~v~~A~~~I~~~~~~ 108 (433)
..+|.|.+|++.|..++.+
T Consensus 209 Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 209 ISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred EecchHHHHHHHHHHHHHHHHh
Confidence 2467899999998888775
No 51
>KOG2814|consensus
Probab=97.11 E-value=0.00033 Score=67.60 Aligned_cols=71 Identities=20% Similarity=0.253 Sum_probs=59.2
Q ss_pred ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEec-ccCCCCCCccccCCCCCccccch
Q psy11929 13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSG-SVDNSSTSSVETGYPGHTLWVTS 91 (433)
Q Consensus 13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G-~~~~~~~~~v~~~~~~~~~~~~a 91 (433)
.+...-++++. ...|.|||++|.|-++|++||+++|.++.++...-.|+|.| ..+
T Consensus 55 ~~~~~si~v~s----~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~-------------------- 110 (345)
T KOG2814|consen 55 KDFSSSILVRS----SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRN-------------------- 110 (345)
T ss_pred ccchhhhhhhH----HHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHH--------------------
Confidence 35777888998 99999999999999999999999999999875554555554 445
Q ss_pred HHHHHHHHHHHHhhhhhh
Q psy11929 92 VDNVCTAYNFMCRSLEDY 109 (433)
Q Consensus 92 ~~~v~~A~~~I~~~~~~~ 109 (433)
+|.+|.++|.-.+.+.
T Consensus 111 --~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 111 --CVIQALERIAKLIDSD 126 (345)
T ss_pred --HHHHHHHHHHHHHHhh
Confidence 8999999998887764
No 52
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.09 E-value=0.0018 Score=58.92 Aligned_cols=96 Identities=22% Similarity=0.346 Sum_probs=64.9
Q ss_pred ccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhh
Q psy11929 27 VNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSL 106 (433)
Q Consensus 27 ~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~ 106 (433)
...+|..||++|++|+.|.++.|=+|.|-.-+ ++ -..-+..++. -.
T Consensus 84 ~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-----------~d----------------------~~~fI~nal~-Pa 129 (190)
T COG0195 84 IDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-----------ED----------------------PAEFIKNALA-PA 129 (190)
T ss_pred cCchhhhccCCChHHHHHHHHhCCceEEEEeC-----------CC----------------------HHHHHHHhcC-cc
Confidence 48899999999999999999999777775411 11 1111111111 00
Q ss_pred hhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 107 EDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
+-..-... ..+.. ...+.||.+..+..|||+|.+++-+.+-||-++.|..
T Consensus 130 ~v~~V~~~----~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 130 EVLSVNIK----EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred eEeEEEEE----eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 00000000 00112 7788999999999999999999999999999998864
No 53
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.06 E-value=0.0013 Score=72.54 Aligned_cols=99 Identities=12% Similarity=0.187 Sum_probs=73.8
Q ss_pred ccchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCce-EEeccCCCCC
Q psy11929 88 WVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGAN-VQVASDMLPM 166 (433)
Q Consensus 88 ~~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~-I~i~~~~~~~ 166 (433)
+..|++.+.+++..|++.+++.-... ........+....+.||.++++.|||.||.+||.|.++||++ |.+..
T Consensus 650 l~eAL~~A~~g~~~Il~~M~~~i~~p-r~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d----- 723 (891)
T PLN00207 650 MERALLQAKDGRKHILAEMSKCSPPP-SKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD----- 723 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh-hhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----
Confidence 33455666666677776666532111 111223456778899999999999999999999999999999 88864
Q ss_pred CCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929 167 STERIVTVHG-NPDTISQAIYQICLVLIE 194 (433)
Q Consensus 167 ~~er~v~I~G-~~~~v~~A~~~I~~~l~e 194 (433)
+-.|.|.+ +.+.+++|+.+|..++.+
T Consensus 724 --dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 724 --DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred --CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 45788877 788999999999888764
No 54
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.01 E-value=0.0018 Score=71.32 Aligned_cols=64 Identities=13% Similarity=0.231 Sum_probs=56.1
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCe-EEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQ-INIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL 356 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~-I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~ 356 (433)
....|.||.+++|.|||.||.+||.|.++||+. |.|.+. -.|.|.+. .+.+++|+.+|.+.+..
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd-----g~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD-----GTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC-----eeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 356899999999999999999999999999999 988875 46777775 78999999999988863
No 55
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.90 E-value=0.0035 Score=66.30 Aligned_cols=64 Identities=22% Similarity=0.252 Sum_probs=57.1
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCH-HHHHHHHHHHHHHHHhc
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQ-EAVSLAQYLINMCIELQ 357 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~-e~v~~A~~lI~~~i~~~ 357 (433)
..++.|+.+.++.+||++|.+|++|..+|||+|.|.++. .|.|.++. +.+.+|+.+|.++.++.
T Consensus 553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG-----tv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG-----TVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC-----cEEEEecchHHHHHHHHHHHHHHhhc
Confidence 468899999999999999999999999999999999544 68888886 78999999999999664
No 56
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.85 E-value=0.0028 Score=67.10 Aligned_cols=99 Identities=17% Similarity=0.220 Sum_probs=73.7
Q ss_pred ccchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCC
Q psy11929 88 WVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS 167 (433)
Q Consensus 88 ~~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~ 167 (433)
+..|..+...|.-.|+..+.+.-... ........+....+-|+...+.-+||++|.+|++|.++||++|.+..
T Consensus 517 m~~AL~QAk~aRlhIL~~M~~ai~~p-r~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------ 589 (692)
T COG1185 517 MKKALEQAKGARLHILIVMNEAISEP-RKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------ 589 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh-hhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------
Confidence 44455666667667776665522111 01122244556778899999999999999999999999999999973
Q ss_pred CccEEEEEccH-HHHHHHHHHHHHHHHh
Q psy11929 168 TERIVTVHGNP-DTISQAIYQICLVLIE 194 (433)
Q Consensus 168 ~er~v~I~G~~-~~v~~A~~~I~~~l~e 194 (433)
+..|.|.++. +.+.+|+..|..+.++
T Consensus 590 -dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 590 -DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred -CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 5678888854 7889999999999987
No 57
>KOG2814|consensus
Probab=96.83 E-value=0.0018 Score=62.56 Aligned_cols=74 Identities=16% Similarity=0.201 Sum_probs=63.8
Q ss_pred CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929 286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKN 359 (433)
Q Consensus 286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~ 359 (433)
......+.++..+.|.|||++|.+-+.|+.+|+++|.++.+.+..+.++.+-+..++|.+|...|.-.|...+.
T Consensus 55 ~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~ 128 (345)
T KOG2814|consen 55 KDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDRK 128 (345)
T ss_pred ccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhhh
Confidence 35667889999999999999999999999999999999998855555555566689999999999999988763
No 58
>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=96.76 E-value=0.0023 Score=47.18 Aligned_cols=37 Identities=32% Similarity=0.395 Sum_probs=34.3
Q ss_pred eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEE
Q psy11929 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISI 54 (433)
Q Consensus 14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v 54 (433)
...+++.|+. ...|..|||+|.+|+.+++.+|-+|.|
T Consensus 24 ~~~~~v~V~~----~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPD----DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECc----ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999 999999999999999999999998876
No 59
>KOG0336|consensus
Probab=96.70 E-value=0.002 Score=64.03 Aligned_cols=73 Identities=25% Similarity=0.276 Sum_probs=59.8
Q ss_pred CCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 118 NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 118 ~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
..+.....+.|-|-++++|.+||++|++|+.||..|+++|++.+. ..+-.|+|.|...--.+|+..|......
T Consensus 41 aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~----~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 41 AAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC----DLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred ccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc----CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 345667788899999999999999999999999999999999863 2367899999887777777766655443
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=96.69 E-value=0.0023 Score=47.24 Aligned_cols=37 Identities=30% Similarity=0.482 Sum_probs=34.4
Q ss_pred ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEE
Q psy11929 287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI 323 (433)
Q Consensus 287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I 323 (433)
.....+.||.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3678999999999999999999999999999988876
No 61
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.50 E-value=0.079 Score=49.16 Aligned_cols=64 Identities=17% Similarity=0.251 Sum_probs=55.6
Q ss_pred EEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
.+.+.++....-.|...+|..++.|....||+|.+..+ +..+.|+|+...+..+...|.+.+..
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~------~~~i~I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS------ENRIRITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC------CcEEEEEccHHHHHHHHHHHHHHHhh
Confidence 44556668888999999999999998889999999754 56899999999999999999998876
No 62
>PRK00106 hypothetical protein; Provisional
Probab=96.27 E-value=0.02 Score=60.19 Aligned_cols=66 Identities=21% Similarity=0.399 Sum_probs=48.9
Q ss_pred CeEEEEEecc-CcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929 123 PLQLKLVIPA-THCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLIE 194 (433)
Q Consensus 123 ~~~~~l~ip~-~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~e 194 (433)
..+-.+.+|+ ++-|+|||+.|.+|+-++..||+.+.|.. +...|+|+| +|-.-+-|...+..++.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3444567887 78899999999999999999999999974 245677888 665555555555554443
No 63
>PRK00468 hypothetical protein; Provisional
Probab=96.25 E-value=0.0053 Score=47.20 Aligned_cols=33 Identities=15% Similarity=0.327 Sum_probs=29.4
Q ss_pred CceEEEEEEeccCCcccccceeeecCchHHHHHHHHh
Q psy11929 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKES 48 (433)
Q Consensus 12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~t 48 (433)
+..+.+++-|.. ..+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~----~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 27 EQSVILELKVAP----EDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCeEEEEEEECh----hhCcceecCCChhHHHHHHHH
Confidence 345889999999 999999999999999999753
No 64
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.22 E-value=0.02 Score=60.28 Aligned_cols=65 Identities=20% Similarity=0.352 Sum_probs=47.8
Q ss_pred CeEEEEEecc-CcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHH
Q psy11929 123 PLQLKLVIPA-THCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLI 193 (433)
Q Consensus 123 ~~~~~l~ip~-~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~ 193 (433)
..+-.+.+|+ ++-|+|||+.|.+|+-++..||+.+.|.. +...|+|+| +|-.-+-|...+..++.
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd------tp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD------TPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 3344567887 78899999999999999999999999974 245677888 56444455555544443
No 65
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.15 E-value=0.0087 Score=65.42 Aligned_cols=97 Identities=18% Similarity=0.273 Sum_probs=68.8
Q ss_pred chHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCc
Q psy11929 90 TSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTE 169 (433)
Q Consensus 90 ~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~e 169 (433)
.|++...+++..|.+.+.+.-... ........+....+.||.+.++.+||.||.+||+|.++||++|.+.. +
T Consensus 521 ~al~~a~~g~~~I~~~M~~aI~~~-r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d-------~ 592 (693)
T PRK11824 521 EALEQAKEGRLHILGKMNEAISEP-RAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-------D 592 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-hhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-------C
Confidence 345556666667776665532111 01111233455567789999999999999999999999999888753 4
Q ss_pred cEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929 170 RIVTVHG-NPDTISQAIYQICLVLIE 194 (433)
Q Consensus 170 r~v~I~G-~~~~v~~A~~~I~~~l~e 194 (433)
-.|.|.+ +.+.+.+|...|..+..+
T Consensus 593 G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 593 GTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred ceEEEEcccHHHHHHHHHHHHHhccc
Confidence 5688887 778899999999887754
No 66
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.13 E-value=0.022 Score=51.93 Aligned_cols=39 Identities=28% Similarity=0.371 Sum_probs=36.0
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT 327 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~ 327 (433)
...+.||.+..+..|||+|.|++-+.+.||-+|.|....
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~~ 181 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETIS 181 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEehh
Confidence 678899999999999999999999999999999987643
No 67
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.10 E-value=0.016 Score=61.18 Aligned_cols=66 Identities=17% Similarity=0.371 Sum_probs=50.1
Q ss_pred CceEEEEEeCcc-cccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHH
Q psy11929 286 DFVETEIVLTDD-IAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIE 355 (433)
Q Consensus 286 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~ 355 (433)
...+..+.+|++ +-|+||||.|.||+-+...||++|.|++.+ ..|+|||- |---+.|+.-|...|.
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp----~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP----EAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC----CeEEecCCchHHHHHHHHHHHHHHH
Confidence 455667889995 559999999999999999999999999876 67888883 5333445544444443
No 68
>PRK12704 phosphodiesterase; Provisional
Probab=96.06 E-value=0.026 Score=59.65 Aligned_cols=64 Identities=20% Similarity=0.368 Sum_probs=48.2
Q ss_pred EEEEEecc-CcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929 125 QLKLVIPA-THCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLIE 194 (433)
Q Consensus 125 ~~~l~ip~-~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~e 194 (433)
+-.+.+|+ ++-|+|||+.|.+|+-++..||+.|.|.. +...|.|+| ++-.-+.|...+..++.+
T Consensus 211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 34466887 78899999999999999999999999974 245778888 555545565555555544
No 69
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.06 E-value=0.02 Score=57.28 Aligned_cols=96 Identities=20% Similarity=0.299 Sum_probs=64.8
Q ss_pred cccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHh
Q psy11929 26 NVNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCR 104 (433)
Q Consensus 26 ~~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~ 104 (433)
.++-+|+.||++|.+|+.|.++- |=+|.|-.=+ .+ . ..+|..
T Consensus 249 ~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s-----------~D-----------------------~---~~fI~N 291 (374)
T PRK12328 249 NIDPIGATVGVKGVRINAVSKELNGENIDCIEYS-----------NV-----------------------P---EIFIAR 291 (374)
T ss_pred CCChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC-----------CC-----------------------H---HHHHHH
Confidence 35779999999999999999998 7788875411 01 0 011111
Q ss_pred hhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 105 SLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
.|.-.... .-. .........+.||..+.+..|||+|.+++-..+-||.+|.|..
T Consensus 292 al~Pa~V~--~V~-i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 292 ALAPAIIS--SVK-IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred hCCCceee--EEE-EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 11110000 000 0012246788999999999999999999999999999999964
No 70
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.02 E-value=0.014 Score=63.75 Aligned_cols=63 Identities=27% Similarity=0.277 Sum_probs=53.5
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL 356 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~ 356 (433)
...+.||.+.++.+||.||.+|++|.++||+.|.+.++ -.|.|.+. .+.+++|+.+|......
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~-----G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD-----GTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC-----ceEEEEcccHHHHHHHHHHHHHhccc
Confidence 34677799999999999999999999999998888654 46778775 68899999999888753
No 71
>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=96.02 E-value=0.029 Score=55.90 Aligned_cols=96 Identities=25% Similarity=0.456 Sum_probs=64.5
Q ss_pred ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929 27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS 105 (433)
Q Consensus 27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~ 105 (433)
++-+|+.||++|++|+.|.++- |=+|.|-.=+. + .. .+|...
T Consensus 242 iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~-----------d-----------------------~~---~fi~na 284 (341)
T TIGR01953 242 IDPVGACVGPKGSRIQAISKELNGEKIDIIEYSD-----------D-----------------------PA---EFIANA 284 (341)
T ss_pred CCcceeeECCCCchHHHHHHHhCCCeEEEEEcCC-----------C-----------------------HH---HHHHHh
Confidence 5679999999999999999998 78888754110 0 00 011111
Q ss_pred hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
+.-.... .-.-.......+.+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 285 l~Pa~v~--~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 285 LSPAKVI--SVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cCCceEE--EEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 1100000 00000012246788999999999999999999999999999999864
No 72
>PRK00106 hypothetical protein; Provisional
Probab=95.99 E-value=0.019 Score=60.40 Aligned_cols=66 Identities=20% Similarity=0.384 Sum_probs=50.1
Q ss_pred CceEEEEEeCcc-cccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEe-CHHHHHHHHHHHHHHHH
Q psy11929 286 DFVETEIVLTDD-IAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQG-CQEAVSLAQYLINMCIE 355 (433)
Q Consensus 286 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsG-t~e~v~~A~~lI~~~i~ 355 (433)
...+..+.+|++ +-|+||||-|.||+-+...||++|.|++.+ ..|+||| .|---+.|+..+...|.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp----~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP----EVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC----CeEEEeCCChHHHHHHHHHHHHHHH
Confidence 456678889994 559999999999999999999999999976 6788888 35333444444444443
No 73
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.95 E-value=0.032 Score=56.06 Aligned_cols=96 Identities=25% Similarity=0.358 Sum_probs=65.0
Q ss_pred ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929 27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS 105 (433)
Q Consensus 27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~ 105 (433)
++-+|+.||++|.+|+.|.++. |=+|.|-.=+. + . ..+|...
T Consensus 244 iDpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~-----------d-----------------------~---~~fi~na 286 (362)
T PRK12327 244 VDAKGACVGPKGQRVQNIVSELKGEKIDIIDWSE-----------D-----------------------P---AEFVANA 286 (362)
T ss_pred CCchheeECCCChhHHHHHHHhCCCeEEEEEcCC-----------C-----------------------H---HHHHHHh
Confidence 5679999999999999999998 78888754110 0 0 0111111
Q ss_pred hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
|.-.... .-.........+.+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 287 l~Pa~v~--~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 287 LSPAKVV--SVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CCCceEE--EEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 1110000 00000012346788999999999999999999999999999999875
No 74
>PRK12704 phosphodiesterase; Provisional
Probab=95.94 E-value=0.019 Score=60.56 Aligned_cols=67 Identities=15% Similarity=0.339 Sum_probs=52.2
Q ss_pred CceEEEEEeCcc-cccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929 286 DFVETEIVLTDD-IAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL 356 (433)
Q Consensus 286 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~ 356 (433)
...+..+.+|++ +-|+||||.|.||+-+...||++|.|++.+ ..|+|||. |---+.|+..+...+..
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp----~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP----EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC----CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 455667889985 559999999999999999999999999976 67889984 54444566666555543
No 75
>KOG1588|consensus
Probab=95.92 E-value=0.0092 Score=56.23 Aligned_cols=41 Identities=17% Similarity=0.359 Sum_probs=36.6
Q ss_pred CceEEEEEeCcc------cccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929 286 DFVETEIVLTDD------IAGCVIGKAGSRLLEIRQISGAQINIHTG 326 (433)
Q Consensus 286 ~~~t~~i~VP~~------~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~ 326 (433)
...+.+|+||.. +||+|+|.+|.++|+|+++|||+|-|-..
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 467788899875 89999999999999999999999999754
No 76
>PRK02821 hypothetical protein; Provisional
Probab=95.84 E-value=0.0094 Score=46.00 Aligned_cols=33 Identities=24% Similarity=0.364 Sum_probs=28.9
Q ss_pred ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhC
Q psy11929 13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESG 49 (433)
Q Consensus 13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tg 49 (433)
..+.+.+.|.. ..+|.||||+|.+|+.||.--.
T Consensus 29 ~~~~i~l~v~~----~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 29 RGRTLEVRVHP----DDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcEEEEEEECh----hhCcceeCCCCchHHHHHHHHH
Confidence 34778899998 9999999999999999998754
No 77
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.80 E-value=0.025 Score=53.60 Aligned_cols=62 Identities=23% Similarity=0.216 Sum_probs=53.1
Q ss_pred EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929 290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL 356 (433)
Q Consensus 290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~ 356 (433)
+.+.||..+++.+||++|.+|+.|.+.+++.|.|.... .|-|+++ .+.+.+|..+|+..-++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG-----~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQNG-----RIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCCc-----EEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 57889999999999999999999999999999998754 6788777 45888898888766544
No 78
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.79 E-value=0.028 Score=57.16 Aligned_cols=96 Identities=20% Similarity=0.403 Sum_probs=64.0
Q ss_pred ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929 27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS 105 (433)
Q Consensus 27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~ 105 (433)
++-+|+.||++|.+|+.|.++. |=+|.|-.=+ .+ . ..+|...
T Consensus 276 VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-----------~D-----------------------p---~~fI~Na 318 (449)
T PRK12329 276 VDPVGACIGARGSRIQAVVNELRGEKIDVIRWS-----------PD-----------------------P---ATYIANA 318 (449)
T ss_pred CChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-----------CC-----------------------H---HHHHHHh
Confidence 5679999999999999999998 7888875411 01 0 0111111
Q ss_pred hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
|.-.....-.-.+ .....+.+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 319 LsPA~V~~V~i~~--~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 319 LSPARVDEVRLVD--PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cCCceeeEEEEEc--CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 1100000000000 11235688999999999999999999999999999999864
No 79
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.79 E-value=0.011 Score=45.26 Aligned_cols=32 Identities=16% Similarity=0.346 Sum_probs=29.5
Q ss_pred CceEEEEEEeccCCcccccceeeecCchHHHHHHHH
Q psy11929 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKE 47 (433)
Q Consensus 12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~ 47 (433)
+..+.+++-+.. ..+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~----~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAP----EDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECc----ccccceecCCChhHHHHHHH
Confidence 567889999999 99999999999999999975
No 80
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.68 E-value=0.031 Score=55.88 Aligned_cols=41 Identities=20% Similarity=0.262 Sum_probs=37.4
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE 328 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~ 328 (433)
....+.||.+..+..|||+|+|++-.++.||.+|.|..-.+
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 46789999999999999999999999999999999986553
No 81
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.63 E-value=0.28 Score=45.44 Aligned_cols=121 Identities=14% Similarity=0.162 Sum_probs=86.9
Q ss_pred cccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhh
Q psy11929 28 NEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLE 107 (433)
Q Consensus 28 ~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~ 107 (433)
...-.+...+|..++.|-...||+|.+.. .+..|.|+|+.. .+..+...|.+.+.
T Consensus 35 ~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---~~~~i~I~g~k~----------------------~~~~i~~~i~~~l~ 89 (210)
T PF14611_consen 35 DEFFLLLTGNGRILENLAARNGAKIEVSR---SENRIRITGTKS----------------------TAEYIEASINEILS 89 (210)
T ss_pred hheeeeecCCchHHHHHHHhcCceEEEec---CCcEEEEEccHH----------------------HHHHHHHHHHHHHh
Confidence 78889999999999999888899999987 566899999999 77777777777664
Q ss_pred hhcccccCCCCCCCCCeEEEEEeccCccccee----cCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEE-----ccH
Q psy11929 108 DYHINRNRMENCSPQPLQLKLVIPATHCGSLI----GKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVH-----GNP 178 (433)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iI----Gk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~-----G~~ 178 (433)
. ..+..+.++.-.--.-. -.....++.|++.|++.|....+ +..+.|. -..
T Consensus 90 ~--------------i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~------~~~~~i~~~~~~~~~ 149 (210)
T PF14611_consen 90 N--------------IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD------GNKLKISWLASPENE 149 (210)
T ss_pred h--------------cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC------CCeEEEEEEeecccc
Confidence 4 33444444422111111 12356799999999999998753 2234444 456
Q ss_pred HHHHHHHHHHHHHHH
Q psy11929 179 DTISQAIYQICLVLI 193 (433)
Q Consensus 179 ~~v~~A~~~I~~~l~ 193 (433)
..+..|+.++...+.
T Consensus 150 ~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 150 KRADRAKRLLLWALD 164 (210)
T ss_pred chHHHHHHHHHHhcc
Confidence 788888888877764
No 82
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.54 E-value=0.035 Score=57.69 Aligned_cols=95 Identities=19% Similarity=0.348 Sum_probs=64.3
Q ss_pred ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929 27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS 105 (433)
Q Consensus 27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~ 105 (433)
++-+|+.||++|++|+.|.++- |=+|.|-.=+ .+ . ..+|...
T Consensus 244 iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-----------~d-----------------------~---~~fi~na 286 (470)
T PRK09202 244 IDPVGACVGMRGSRIQAISNELGGEKIDIILWS-----------DD-----------------------P---AQFIINA 286 (470)
T ss_pred CChhHccCCCCCchHHHHHHHhCCCeEEEEEcC-----------CC-----------------------H---HHHHHHh
Confidence 4668999999999999999998 7888875411 01 0 0111111
Q ss_pred hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
+....... - ......-.+.+.||..+.+..|||+|.+++-..+-||.+|.|..
T Consensus 287 l~pa~v~~--v-~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 287 LSPAEVSS--V-VVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCCCEEEE--E-EEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 11100000 0 00011237789999999999999999999999999999999864
No 83
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.39 E-value=0.022 Score=51.48 Aligned_cols=46 Identities=26% Similarity=0.375 Sum_probs=36.2
Q ss_pred ceEEEEEEeccC--CcccccceeeecCchHHHHHHHHhCCeEEEeCCC
Q psy11929 13 TLITMRCLFHSS--VNVNEISCLIGPGGCIVRRLRKESGAKISITDGA 58 (433)
Q Consensus 13 ~~~~~rilvp~~--~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~ 58 (433)
..++-++.||.. -.+++||.|||+.|.|+|+|+..|+|+|-|-..+
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 445566776631 1237899999999999999999999999998754
No 84
>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=95.38 E-value=0.06 Score=53.71 Aligned_cols=39 Identities=28% Similarity=0.466 Sum_probs=36.3
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTG 326 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~ 326 (433)
....+.||.+..+..|||+|.|++-.++.||.+|.|...
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 468999999999999999999999999999999998754
No 85
>PRK01064 hypothetical protein; Provisional
Probab=95.33 E-value=0.022 Score=44.10 Aligned_cols=33 Identities=18% Similarity=0.261 Sum_probs=29.6
Q ss_pred CceEEEEEEeccCCcccccceeeecCchHHHHHHHHh
Q psy11929 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKES 48 (433)
Q Consensus 12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~t 48 (433)
+..+.+++.|.. ...|.+|||+|.+|+.||.-.
T Consensus 27 ~~~~~~~l~v~~----~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAK----PDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECc----ccceEEECCCCccHHHHHHHH
Confidence 456889999999 999999999999999999853
No 86
>PRK02821 hypothetical protein; Provisional
Probab=95.30 E-value=0.026 Score=43.61 Aligned_cols=33 Identities=21% Similarity=0.437 Sum_probs=28.7
Q ss_pred CCCeEEEEEeccCcccceecCCchhHHHHHHhh
Q psy11929 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLS 153 (433)
Q Consensus 121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~s 153 (433)
.....+++.+..+-+|+||||+|.+|+.|+.--
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 345778999999999999999999999998754
No 87
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.26 E-value=0.061 Score=54.05 Aligned_cols=41 Identities=22% Similarity=0.312 Sum_probs=37.3
Q ss_pred ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929 287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT 327 (433)
Q Consensus 287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~ 327 (433)
.....+.||.+..+..|||+|.|++-..+.||.+|.|....
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 34689999999999999999999999999999999998754
No 88
>PRK00468 hypothetical protein; Provisional
Probab=95.25 E-value=0.027 Score=43.31 Aligned_cols=32 Identities=34% Similarity=0.514 Sum_probs=28.6
Q ss_pred CCCeEEEEEeccCcccceecCCchhHHHHHHh
Q psy11929 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDL 152 (433)
Q Consensus 121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~ 152 (433)
...+.+++.+..+-+|+||||+|.+|+.|+.-
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 45588899999999999999999999999864
No 89
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.11 E-value=0.06 Score=55.99 Aligned_cols=40 Identities=28% Similarity=0.438 Sum_probs=36.9
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT 327 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~ 327 (433)
....+.||.+..+.-|||+|+|++..++.||.+|.|-...
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~~ 341 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTEE 341 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEhh
Confidence 4789999999999999999999999999999999997644
No 90
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.99 E-value=0.033 Score=42.73 Aligned_cols=32 Identities=31% Similarity=0.581 Sum_probs=29.2
Q ss_pred CCCeEEEEEeccCcccceecCCchhHHHHHHh
Q psy11929 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDL 152 (433)
Q Consensus 121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~ 152 (433)
.....+++.+...-+|++|||+|.+|+.|+.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 56788999999999999999999999999864
No 91
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.97 E-value=0.059 Score=51.05 Aligned_cols=62 Identities=21% Similarity=0.290 Sum_probs=52.5
Q ss_pred EEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLIE 194 (433)
Q Consensus 126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~e 194 (433)
+.+.||..+++++||++|.+|+.|.++++++|.+-. +-.|.|.+ +.+++.+|..+|..+-++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-------NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-------NGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-------CcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 557899999999999999999999999999999964 35677777 556888888888877666
No 92
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.61 E-value=0.094 Score=53.47 Aligned_cols=40 Identities=20% Similarity=0.372 Sum_probs=36.6
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT 327 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~ 327 (433)
....+.||.+..+.-|||+|.|++-..+.||.+|.|....
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~~ 374 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDSA 374 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccHH
Confidence 4578999999999999999999999999999999998654
No 93
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.53 E-value=0.042 Score=49.79 Aligned_cols=40 Identities=30% Similarity=0.507 Sum_probs=33.4
Q ss_pred eEEEEEeC------cccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929 288 VETEIVLT------DDIAGCVIGKAGSRLLEIRQISGAQINIHTGT 327 (433)
Q Consensus 288 ~t~~i~VP------~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~ 327 (433)
.+-+++|| .++||.+||..|++.++|++.|+|+|-|-...
T Consensus 148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 34456665 46899999999999999999999999997654
No 94
>KOG4369|consensus
Probab=94.21 E-value=0.017 Score=63.93 Aligned_cols=70 Identities=19% Similarity=0.061 Sum_probs=60.5
Q ss_pred ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC--CCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929 287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE--SHKKMFHIQGCQEAVSLAQYLINMCIEL 356 (433)
Q Consensus 287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~ 356 (433)
....++.+|-....+|||++|++|+.++.-|||.|+|.+-.. ..||.+.+.|.++.+..|..+|.-.|-.
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeec
Confidence 344577899999999999999999999999999999998443 7899999999999999999888665543
No 95
>PRK12705 hypothetical protein; Provisional
Probab=94.04 E-value=0.12 Score=54.06 Aligned_cols=37 Identities=24% Similarity=0.508 Sum_probs=32.0
Q ss_pred EEEEEecc-CcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 125 QLKLVIPA-THCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 125 ~~~l~ip~-~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
.-.+.+|+ ++-|+|||+.|.+|+.++..||+.+.|..
T Consensus 199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred eeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 33456776 67899999999999999999999999974
No 96
>PRK01064 hypothetical protein; Provisional
Probab=94.01 E-value=0.081 Score=40.98 Aligned_cols=32 Identities=34% Similarity=0.589 Sum_probs=28.8
Q ss_pred CCCeEEEEEeccCcccceecCCchhHHHHHHh
Q psy11929 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDL 152 (433)
Q Consensus 121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~ 152 (433)
...+.+++.+..+-.|++|||+|.+|+.|+.-
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 56688999999999999999999999999864
No 97
>KOG1067|consensus
Probab=93.60 E-value=0.14 Score=53.12 Aligned_cols=95 Identities=20% Similarity=0.194 Sum_probs=68.2
Q ss_pred hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCcc
Q psy11929 91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTER 170 (433)
Q Consensus 91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er 170 (433)
|..+...|...|++.+++.-. .+........++...+-++++....+||.+|...|+|+.+||+.-.+. +.
T Consensus 565 al~~a~~ar~~Il~~m~k~i~-~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD--------e~ 635 (760)
T KOG1067|consen 565 ALQKAREARLQILDIMEKNIN-SPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD--------EG 635 (760)
T ss_pred HHHhhhHHHHHHHHHHHhhcC-CcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec--------Cc
Confidence 334444555566666554221 111223345677888999999999999999999999999999555553 56
Q ss_pred EEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929 171 IVTVHG-NPDTISQAIYQICLVLIE 194 (433)
Q Consensus 171 ~v~I~G-~~~~v~~A~~~I~~~l~e 194 (433)
.++|.. ++.+.++|++.|..++..
T Consensus 636 t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 636 TFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eEEEEecCHHHHHHHHHHHHHHhcC
Confidence 777776 678889999999988765
No 98
>PRK12705 hypothetical protein; Provisional
Probab=93.39 E-value=0.11 Score=54.48 Aligned_cols=65 Identities=15% Similarity=0.315 Sum_probs=47.0
Q ss_pred CceEEEEEeCcccc-cccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHH
Q psy11929 286 DFVETEIVLTDDIA-GCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCI 354 (433)
Q Consensus 286 ~~~t~~i~VP~~~v-G~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i 354 (433)
...+..+.+|++-+ |+||||-|.||+.+...||+.|.|++.. ..|+|++- |.--+.|...+...|
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp----~~V~ls~fdp~rreia~~~l~~Li 262 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP----EAVVISSFNPIRREIARLTLEKLL 262 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc----cchhhcccCccchHHHHHHHHHHH
Confidence 45566778888655 9999999999999999999999999876 45666654 333333444444443
No 99
>KOG4369|consensus
Probab=92.00 E-value=0.064 Score=59.64 Aligned_cols=52 Identities=23% Similarity=0.180 Sum_probs=45.7
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC---CCCCcceEEEecccC
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD---GACPDRIVTVSGSVD 71 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~eRvv~I~G~~~ 71 (433)
.-+.-+|. ...++|||++|.+|..+|.-||+.|.+.+ .+..||.+.+.|.++
T Consensus 1341 ~~k~~~P~----~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~ 1395 (2131)
T KOG4369|consen 1341 QGKGDGPL----YASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPP 1395 (2131)
T ss_pred ccccccch----hhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCCh
Confidence 34556666 89999999999999999999999999977 356899999999999
No 100
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=91.97 E-value=0.068 Score=40.76 Aligned_cols=33 Identities=21% Similarity=0.147 Sum_probs=27.2
Q ss_pred eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCC
Q psy11929 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGA 50 (433)
Q Consensus 14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga 50 (433)
...+.+-|.. ...|.||||+|.+++.||.-.+.
T Consensus 28 ~~~i~v~i~~----ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 28 GDTIVVNIDG----EDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTEEEEEEES----CCCHHHCTTHHHHHHHHHHHHHH
T ss_pred ceEEEEEECC----CccceEECCCCeeHHHHHHHHHH
Confidence 4466777788 99999999999999999976543
No 101
>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=91.49 E-value=0.32 Score=35.75 Aligned_cols=34 Identities=21% Similarity=0.243 Sum_probs=27.2
Q ss_pred EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeE
Q psy11929 15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKI 52 (433)
Q Consensus 15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I 52 (433)
....+.+.. ...|.+||++|.+|+.|+..++-.+
T Consensus 25 ~~~~i~~~~----~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVAR----GQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECC----CCCceEECCCCccHHHHHHHHHHHc
Confidence 455566655 5689999999999999999998544
No 102
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.95 E-value=0.25 Score=37.30 Aligned_cols=38 Identities=29% Similarity=0.464 Sum_probs=29.3
Q ss_pred EEEEEeCccc-----ccccccCCCchHHHHHhHh-CCeEEEccC
Q psy11929 289 ETEIVLTDDI-----AGCVIGKAGSRLLEIRQIS-GAQINIHTG 326 (433)
Q Consensus 289 t~~i~VP~~~-----vG~IIGkgG~~Ik~I~~~s-GA~I~I~~~ 326 (433)
...+.|-... +|..||++|++|+.|.++. |-+|.|-.-
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 3466666666 9999999999999999999 888887653
No 103
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.27 E-value=0.2 Score=37.81 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=23.3
Q ss_pred cceeeecCchHHHHHHHHh-CCeEEEeC
Q psy11929 30 ISCLIGPGGCIVRRLRKES-GAKISITD 56 (433)
Q Consensus 30 vg~IIGk~G~~Ik~I~~~t-ga~I~v~~ 56 (433)
+|..||++|..||.|.++. |-+|+|-.
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred ceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 9999999999999999999 89988864
No 104
>KOG1067|consensus
Probab=89.92 E-value=0.89 Score=47.43 Aligned_cols=64 Identities=22% Similarity=0.213 Sum_probs=53.6
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHhc
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIELQ 357 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~~ 357 (433)
...++.|+.+....+||.+|.+.|.|..+|||.-.+++ -.+.|-.. +.+.++|+.+|..++...
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe------~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE------GTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeeecC------ceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 45688999999999999999999999999996666655 34777665 678999999999988664
No 105
>KOG3273|consensus
Probab=89.36 E-value=0.25 Score=44.61 Aligned_cols=55 Identities=20% Similarity=0.388 Sum_probs=49.9
Q ss_pred cCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 132 ATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 132 ~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
...+|+|.||+|.+--.|++.|.++|.+. +..|.|-|..++++-|...|+.++..
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla--------d~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA--------DSKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec--------CceEEEeecchhhHHHHHhhHhhhcc
Confidence 55789999999999889999999999996 45799999999999999999999887
No 106
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=89.33 E-value=0.24 Score=37.71 Aligned_cols=34 Identities=24% Similarity=0.345 Sum_probs=28.6
Q ss_pred CCCeEEEEEeccCcccceecCCchhHHHHHHhhC
Q psy11929 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSG 154 (433)
Q Consensus 121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sg 154 (433)
.....+.+.+..+..|+||||+|.+++.||--.+
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 4556778888999999999999999999986543
No 107
>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=89.30 E-value=0.6 Score=34.24 Aligned_cols=35 Identities=26% Similarity=0.421 Sum_probs=28.4
Q ss_pred ceEEEEEeCcccccccccCCCchHHHHHhHhCCeE
Q psy11929 287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQI 321 (433)
Q Consensus 287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I 321 (433)
.....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556677766789999999999999999988554
No 108
>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=88.25 E-value=0.26 Score=37.95 Aligned_cols=34 Identities=15% Similarity=0.383 Sum_probs=28.4
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEE
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKIS 53 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~ 53 (433)
...+.+.. .+.|.|||++|++|++|+++.+-.+.
T Consensus 26 ~~~i~i~~----~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 26 QIIIVIKA----SQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEEE----SSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred eEEEEEeC----CCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 45677788 99999999999999999988765553
No 109
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.38 E-value=0.47 Score=48.51 Aligned_cols=41 Identities=27% Similarity=0.391 Sum_probs=37.3
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE 328 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~ 328 (433)
....+.||..+++.+|||+|.+|++|.+..|-+|.|.....
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 34678999999999999999999999999999999988764
No 110
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=87.25 E-value=0.62 Score=35.89 Aligned_cols=33 Identities=18% Similarity=0.284 Sum_probs=26.0
Q ss_pred EEEEeccCCcccccceeeecCchHHHHHHHHhCCeEE
Q psy11929 17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKIS 53 (433)
Q Consensus 17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~ 53 (433)
+.+-+.. ...|.+|||+|+++..||--++.-++
T Consensus 26 i~i~i~~----~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 26 VEVNISG----DDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEec----CCCCeEECCCCccHHHHHHHHHHHHh
Confidence 4455566 88899999999999999987664443
No 111
>KOG3273|consensus
Probab=86.88 E-value=0.42 Score=43.22 Aligned_cols=53 Identities=21% Similarity=0.360 Sum_probs=48.5
Q ss_pred ccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Q psy11929 297 DIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIE 355 (433)
Q Consensus 297 ~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~ 355 (433)
..+|+|+||+|.+--.|...|.++|-+.+.. |-|-|+.+++..|+..|...|-
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad~k------IHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLADSK------IHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecCce------EEEeecchhhHHHHHhhHhhhc
Confidence 4789999999999999999999999998854 9999999999999999988774
No 112
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=86.50 E-value=1.6 Score=40.93 Aligned_cols=45 Identities=18% Similarity=0.410 Sum_probs=38.8
Q ss_pred EEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccC
Q psy11929 19 CLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVD 71 (433)
Q Consensus 19 ilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~ 71 (433)
+.+|. ..|.++|||+|+.++.|.++|+|+|-|..+| .|-|.+..+
T Consensus 150 v~i~p----~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG----~IWV~~~~~ 194 (239)
T COG1097 150 VKIPP----SKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG----RIWVDGENE 194 (239)
T ss_pred EEEch----hhcceEecCCCcHHHHhhhhcCeEEEEecCC----EEEecCCCc
Confidence 56777 9999999999999999999999999998765 367777766
No 113
>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=85.87 E-value=0.89 Score=35.48 Aligned_cols=36 Identities=11% Similarity=0.251 Sum_probs=29.6
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEe
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISIT 55 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~ 55 (433)
.+++.+.. ..-|.|||++|+.|++|+++-.-...+.
T Consensus 31 ~i~I~I~t----arPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 31 RTEIIIRA----TRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred eEEEEEEe----CCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 36777777 8899999999999999999876655553
No 114
>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=85.44 E-value=4 Score=35.39 Aligned_cols=94 Identities=20% Similarity=0.241 Sum_probs=61.1
Q ss_pred eeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhhhhccc
Q psy11929 33 LIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHIN 112 (433)
Q Consensus 33 IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~~~~~~ 112 (433)
.+=.+|+.|+.|-++-.-+|.|-.+ +.. ...=.+|.+.|.+.+-+...
T Consensus 20 ~~~~~~dli~~lAk~lrKRIvvR~d------------ps~-------------------l~~~e~A~~~I~~ivP~ea~- 67 (145)
T cd02410 20 LFAEDGDLVKDLAKDLRKRIVIRPD------------PSV-------------------LKPPEEAIKIILEIVPEEAG- 67 (145)
T ss_pred HHhcccHHHHHHHHHHhceEEEcCC------------hhh-------------------cCCHHHHHHHHHHhCCCccC-
Confidence 4445688999999998888877542 110 00124677777776633100
Q ss_pred ccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 113 RNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 113 ~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
. .+-.=+..+-++.|-...-|.+||++|.++++|..+||-.-.+..
T Consensus 68 i---~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 68 I---TDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred c---eeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 0 000011224466777888899999999999999999998877764
No 115
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=84.54 E-value=1.4 Score=45.55 Aligned_cols=125 Identities=14% Similarity=0.084 Sum_probs=82.5
Q ss_pred eeeecCchHHHHHHHHhCCeEEEeCC-CCCcceE-EEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhhhh
Q psy11929 32 CLIGPGGCIVRRLRKESGAKISITDG-ACPDRIV-TVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDY 109 (433)
Q Consensus 32 ~IIGk~G~~Ik~I~~~tga~I~v~~~-~~~eRvv-~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~~~ 109 (433)
.|-||+--.+.+|++...|.+.+.=. ..+.++. .+.|... +-.++++.+. .+
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~gs~~~~~~~g~~~----------------------~F~k~~~~~~---~E- 446 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSSTGSIVETNGIGEKM----------------------SFSKKLSIPP---TE- 446 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEecCCcEEEEeccCcch----------------------hhHHHhcCCc---cc-
Confidence 56777666699999999888544321 1122332 2344444 4444444332 22
Q ss_pred cccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc-CCCCCCCccE-EEEEcc---HHHHHHH
Q psy11929 110 HINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS-DMLPMSTERI-VTVHGN---PDTISQA 184 (433)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~-~~~~~~~er~-v~I~G~---~~~v~~A 184 (433)
-+..+.+.||...+-.|||.||..|++++.+-++.|++.. -.++.+..+- |.|.-+ .+++.-+
T Consensus 447 ------------Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~ 514 (657)
T COG5166 447 ------------FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGK 514 (657)
T ss_pred ------------CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcc
Confidence 2445678999999999999999999999999999999874 2334444443 666654 4566667
Q ss_pred HHHHHHHHHh
Q psy11929 185 IYQICLVLIE 194 (433)
Q Consensus 185 ~~~I~~~l~e 194 (433)
+.-+++++.+
T Consensus 515 KNd~~~~V~~ 524 (657)
T COG5166 515 KNDKLDKVKQ 524 (657)
T ss_pred cccHHHHHhh
Confidence 7777777775
No 116
>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=84.04 E-value=5 Score=34.78 Aligned_cols=39 Identities=31% Similarity=0.460 Sum_probs=33.8
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT 327 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~ 327 (433)
+-++.|-.+.-|.+||++|.++++|...||-.-+|-...
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 347888889999999999999999999999887776554
No 117
>PRK13764 ATPase; Provisional
Probab=83.84 E-value=0.94 Score=48.68 Aligned_cols=42 Identities=24% Similarity=0.318 Sum_probs=38.0
Q ss_pred ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929 287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE 328 (433)
Q Consensus 287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~ 328 (433)
.....+.||..+++.+|||+|.+|++|.+..|.+|.|....+
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 455688999999999999999999999999999999987664
No 118
>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=83.36 E-value=1.2 Score=34.24 Aligned_cols=35 Identities=26% Similarity=0.414 Sum_probs=28.6
Q ss_pred eEEEEEeCcccccccccCCCchHHHHHhHhCCeEE
Q psy11929 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQIN 322 (433)
Q Consensus 288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~ 322 (433)
....+.+..+..|.+|||+|++++.||-.+...+.
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 34667777888999999999999999988765544
No 119
>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=82.60 E-value=0.89 Score=34.93 Aligned_cols=34 Identities=38% Similarity=0.523 Sum_probs=28.6
Q ss_pred eEEEEEeccCcccceecCCchhHHHHHHhhCceE
Q psy11929 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANV 157 (433)
Q Consensus 124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I 157 (433)
..+.+.+...+-|.+||++|++|++|.+...-.+
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 4567889999999999999999999987765444
No 120
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=82.45 E-value=0.89 Score=46.58 Aligned_cols=38 Identities=24% Similarity=0.326 Sum_probs=34.6
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG 57 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~ 57 (433)
...+.+|. .+++.+|||+|.+|++|++..|-+|.|...
T Consensus 487 ~avv~vpe----~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 487 RAVVKVPE----KYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred eEEEEeCH----HHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 36678888 999999999999999999999999999764
No 121
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=81.57 E-value=3.3 Score=38.94 Aligned_cols=57 Identities=23% Similarity=0.376 Sum_probs=42.1
Q ss_pred EEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHH-HHHHHHHHH
Q psy11929 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDT-ISQAIYQIC 189 (433)
Q Consensus 126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~-v~~A~~~I~ 189 (433)
.-+.|+...+-++||++|+.++-+.++++|+|.+-.+ -.|=|.+..+. ...|...|.
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-------G~IWV~~~~~~~e~~~~~aI~ 205 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-------GRIWVDGENESLEELAIEAIR 205 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-------CEEEecCCCcchHHHHHHHHH
Confidence 3468999999999999999999999999999999753 34555555442 333444443
No 122
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=80.83 E-value=2.1 Score=38.18 Aligned_cols=35 Identities=29% Similarity=0.480 Sum_probs=29.8
Q ss_pred EEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC
Q psy11929 17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD 56 (433)
Q Consensus 17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 56 (433)
+-++|-. .. |.-|||+|++|+++++..|-+|.+-+
T Consensus 63 vIfvV~~----gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 63 VILLVTS----GP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEeC----CC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 3455655 66 99999999999999999999999865
No 123
>KOG2874|consensus
Probab=80.79 E-value=3.1 Score=39.76 Aligned_cols=51 Identities=18% Similarity=0.298 Sum_probs=45.8
Q ss_pred cccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929 300 GCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIEL 356 (433)
Q Consensus 300 G~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~ 356 (433)
-++||.+|++++.|+-.|.|-|-|.... |.+.|....+..+...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~T------VsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGNT------VSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCcE------EEeecCcchHHHHHHHHHHHHhc
Confidence 5789999999999999999999999855 99999999999998888887764
No 124
>KOG2874|consensus
Probab=79.89 E-value=3.6 Score=39.31 Aligned_cols=51 Identities=18% Similarity=0.229 Sum_probs=45.8
Q ss_pred cceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 136 GSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 136 g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
-+|||.+|.+++.|+-.|.|.|-+.. .+|.+.|....+..+...+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG--------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG--------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC--------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 57999999999999999999999963 4799999999999999988888775
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=78.96 E-value=1.8 Score=35.78 Aligned_cols=30 Identities=27% Similarity=0.429 Sum_probs=25.4
Q ss_pred EEEEeccCCcccccceeeecCchHHHHHHHHhCC
Q psy11929 17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGA 50 (433)
Q Consensus 17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga 50 (433)
+++.+.. ..-|.|||++|++|++|++....
T Consensus 63 i~I~I~t----~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHT----ARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEe----CCCCcccCCchHHHHHHHHHHHH
Confidence 5677777 88999999999999999987543
No 126
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.89 E-value=2.8 Score=37.39 Aligned_cols=38 Identities=18% Similarity=0.232 Sum_probs=32.1
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT 327 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~ 327 (433)
..-+.|-... |.-|||+|.+|+.+++..|-+|.+-...
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s 99 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT 99 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence 4566776666 9999999999999999999999887644
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=77.68 E-value=2.5 Score=33.23 Aligned_cols=28 Identities=21% Similarity=0.288 Sum_probs=23.9
Q ss_pred EEEEeccCCcccccceeeecCchHHHHHHHHh
Q psy11929 17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKES 48 (433)
Q Consensus 17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~t 48 (433)
+++.+.. ..-|.+||++|.+|++|++.-
T Consensus 40 i~V~I~t----~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYA----ERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEE----CCCCceECCCchhHHHHHHHH
Confidence 5666766 888999999999999998874
No 128
>PRK13764 ATPase; Provisional
Probab=77.50 E-value=1.7 Score=46.71 Aligned_cols=38 Identities=21% Similarity=0.402 Sum_probs=34.5
Q ss_pred EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC
Q psy11929 15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD 56 (433)
Q Consensus 15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 56 (433)
-...+.||. ..++.+|||+|.+|++|++..|.+|.|..
T Consensus 481 ~~~~v~~~~----~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 481 NKAVVYVPE----KDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred CeEEEEECh----hhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 356678888 99999999999999999999999999976
No 129
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=74.89 E-value=2.6 Score=39.40 Aligned_cols=31 Identities=29% Similarity=0.388 Sum_probs=26.6
Q ss_pred eEEEEEEeccCCcccccceeeecCchHHHHHHHHh
Q psy11929 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKES 48 (433)
Q Consensus 14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~t 48 (433)
....++.++. ..-|.||||+|+.|++|+++-
T Consensus 50 ~~~~~V~I~a----arPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 50 PKGTRVTIHA----ARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCceEEEEEe----CCCcceEcCCCccHHHHHHHH
Confidence 3467888888 999999999999999998864
No 130
>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=72.99 E-value=4.1 Score=31.78 Aligned_cols=36 Identities=19% Similarity=0.443 Sum_probs=28.5
Q ss_pred eEEEEEeccCcccceecCCchhHHHHHHhhCceEEe
Q psy11929 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQV 159 (433)
Q Consensus 124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i 159 (433)
..+++.|....-|.+||++|+.|++|++.-.-...+
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 347788888899999999999999998875443333
No 131
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=72.05 E-value=10 Score=39.48 Aligned_cols=39 Identities=33% Similarity=0.434 Sum_probs=33.4
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT 327 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~ 327 (433)
+-++.|-.+.=|.+|||+|++.++|.++||-.=+|-...
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 348888899999999999999999999999876666544
No 132
>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=65.45 E-value=7.7 Score=37.27 Aligned_cols=35 Identities=11% Similarity=0.204 Sum_probs=29.0
Q ss_pred ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCC
Q psy11929 13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGA 50 (433)
Q Consensus 13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga 50 (433)
..+...|+|... ++-+.|||++|+.||+|..+..-
T Consensus 219 ~~i~~~i~v~~~---s~k~iiig~~g~~ik~i~~~ar~ 253 (270)
T TIGR00436 219 LKIHALISVERE---SQKKIIIGKNGSMIKAIGIAARK 253 (270)
T ss_pred EEEEEEEEECcC---CceeEEEcCCcHHHHHHHHHHHH
Confidence 357788888873 77899999999999999987643
No 133
>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=64.18 E-value=6.6 Score=32.39 Aligned_cols=30 Identities=27% Similarity=0.468 Sum_probs=24.9
Q ss_pred EEEEEeccCcccceecCCchhHHHHHHhhC
Q psy11929 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSG 154 (433)
Q Consensus 125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sg 154 (433)
.+++.|....-|.|||++|+.|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 366777888889999999999999887643
No 134
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=61.69 E-value=8.6 Score=39.97 Aligned_cols=123 Identities=13% Similarity=0.151 Sum_probs=77.3
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC-----CCCcceEEEecccCCCCCCccccCCCCCccccc
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG-----ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVT 90 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-----~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~ 90 (433)
.+-+.||. ..+-.|||.||..|.+++..-++-|++... +.-..-|.|..+..+..
T Consensus 450 e~~f~i~e----~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~---------------- 509 (657)
T COG5166 450 EIAFIIME----SGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQD---------------- 509 (657)
T ss_pred heEEEeec----ccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCcc----------------
Confidence 45688999 999999999999999999999999999763 21223377777766332
Q ss_pred hHHHHHHHHHHHHhhhhhhcc-------ccc---------------------CCCCCCCCCeEEEEEeccCcccceec--
Q psy11929 91 SVDNVCTAYNFMCRSLEDYHI-------NRN---------------------RMENCSPQPLQLKLVIPATHCGSLIG-- 140 (433)
Q Consensus 91 a~~~v~~A~~~I~~~~~~~~~-------~~~---------------------~~~~~~~~~~~~~l~ip~~~vg~iIG-- 140 (433)
++.-++.-.++++.+.+. ++. +......-+....+.+|.+.++..+|
T Consensus 510 ---ni~~~KNd~~~~V~~~c~f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gen 586 (657)
T COG5166 510 ---NISGKKNDKLDKVKQQCRFNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGEN 586 (657)
T ss_pred ---chhcccccHHHHHhhhcccccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcc
Confidence 222222222222221110 000 00001122344456778888899999
Q ss_pred -CCchhHHHHHHhhCceEEecc
Q psy11929 141 -KGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 141 -k~G~~Ik~I~~~sga~I~i~~ 161 (433)
-.|++|..+..-+.-.|....
T Consensus 587 a~R~~ni~~~t~~y~~~ie~~~ 608 (657)
T COG5166 587 AFRGENIQRVTKLYNSYIEFST 608 (657)
T ss_pred cccccchhhhhhhhhccceeec
Confidence 778888888888777777654
No 135
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=61.41 E-value=15 Score=38.26 Aligned_cols=96 Identities=18% Similarity=0.228 Sum_probs=65.4
Q ss_pred ceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhhhhc
Q psy11929 31 SCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYH 110 (433)
Q Consensus 31 g~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~~~~ 110 (433)
..++=+.|+.||+|-++-.-+|.+-...+ + . . .-.+|.+.|.+++-+..
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPs---v---l---~----------------------~~e~A~~~I~eivP~ea 89 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPS---V---L---K----------------------PPEEARKIILEIVPEEA 89 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCch---h---c---C----------------------CHHHHHHHHHHhCcccc
Confidence 45677889999999999998888854210 0 0 0 33577777777764321
Q ss_pred ccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 111 INRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 111 ~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
.- .+-.=...+-+++|-...-|.+|||+|++.++|..++|-.-.+.+
T Consensus 90 ~i----~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 90 GI----TDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred Cc----eeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 00 000012234567888889999999999999999999998766654
No 136
>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=61.35 E-value=27 Score=38.08 Aligned_cols=40 Identities=30% Similarity=0.432 Sum_probs=34.8
Q ss_pred EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE 328 (433)
Q Consensus 289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~ 328 (433)
+-++.|-.++-|.||||+|.++++|.++||-.-+|-....
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 4488888999999999999999999999999888766553
No 137
>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=61.14 E-value=9.3 Score=29.91 Aligned_cols=28 Identities=29% Similarity=0.603 Sum_probs=22.9
Q ss_pred EEEEeccCcccceecCCchhHHHHHHhh
Q psy11929 126 LKLVIPATHCGSLIGKGGCKIKDIRDLS 153 (433)
Q Consensus 126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~s 153 (433)
+++.|....-|.+||++|++|+++++.-
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 5566666888999999999999988653
No 138
>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=61.11 E-value=23 Score=38.54 Aligned_cols=96 Identities=20% Similarity=0.200 Sum_probs=62.7
Q ss_pred ceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhhhhc
Q psy11929 31 SCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYH 110 (433)
Q Consensus 31 g~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~~~~ 110 (433)
...+=..|+.||.|-++-.-+|.|-...+ +.- .=.+|.+.|.+++-+..
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~------~~~-------------------------~~~~~~~~i~~~~~~~~ 83 (630)
T TIGR03675 35 PELFAKDDDLVKELAKKLRKRIVIRPDPS------VLL-------------------------PPEEAIEKIKEIVPEEA 83 (630)
T ss_pred HHHhccchHHHHHHHHHhhceEEEecChh------hcC-------------------------CHHHHHHHHHHhCCCcC
Confidence 34555678889999988888877754210 000 12466777776653311
Q ss_pred ccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929 111 INRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS 161 (433)
Q Consensus 111 ~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~ 161 (433)
. . .+-.=...+-++.|-...-|.+|||+|.++++|.+++|-.-.+.+
T Consensus 84 ~-~---~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 84 G-I---TDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred C-c---eeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 0 0 000012234567788888999999999999999999998887764
No 139
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=60.45 E-value=11 Score=35.21 Aligned_cols=33 Identities=12% Similarity=0.224 Sum_probs=26.6
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeE
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKI 52 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I 52 (433)
.+++.+.. ..-|.|||++|..|++|+++-.-.+
T Consensus 45 ~i~V~I~t----arPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 45 RTEIIIRA----TRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred cEEEEEEE----CCCccEEcCCchHHHHHHHHHHHHh
Confidence 35667777 8889999999999999998865443
No 140
>PRK15494 era GTPase Era; Provisional
Probab=58.27 E-value=12 Score=37.40 Aligned_cols=39 Identities=10% Similarity=0.245 Sum_probs=30.2
Q ss_pred ceEEEEEEeccCCcccccceeeecCchHHHHHHHH--------hCCeEEE
Q psy11929 13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKE--------SGAKISI 54 (433)
Q Consensus 13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~--------tga~I~v 54 (433)
-.+...|+|... ++-+.|||++|+.||+|..+ .|++|.+
T Consensus 271 ~~i~~~i~v~~~---sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 271 VKINQVIVVSRE---SYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEEEECCC---CceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 346788889874 78999999999999987654 4666555
No 141
>CHL00048 rps3 ribosomal protein S3
Probab=56.63 E-value=15 Score=34.15 Aligned_cols=31 Identities=13% Similarity=0.053 Sum_probs=26.0
Q ss_pred EEEEEEeccCCcccccceeeecCchHHHHHHHHhC
Q psy11929 15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESG 49 (433)
Q Consensus 15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tg 49 (433)
..+++.+.. ..-|.|||++|.+|++|++.-.
T Consensus 66 ~~~~I~I~~----~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 66 DLIQVIIYT----GFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CeEEEEEEE----CCCceEECCCcHhHHHHHHHHH
Confidence 346777777 8889999999999999998764
No 142
>PRK00089 era GTPase Era; Reviewed
Probab=56.39 E-value=15 Score=35.58 Aligned_cols=39 Identities=21% Similarity=0.448 Sum_probs=29.3
Q ss_pred eEEEEEEeccCCcccccceeeecCchHHHHHHHH--------hCCeEEEe
Q psy11929 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKE--------SGAKISIT 55 (433)
Q Consensus 14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~--------tga~I~v~ 55 (433)
.+...|+|... ++-+.||||+|+.||+|..+ .+++|.+.
T Consensus 225 ~i~~~i~v~~~---~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 225 RIEATIYVERD---SQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEEccC---CceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 46677788763 77899999999999987654 46665553
No 143
>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=56.37 E-value=11 Score=36.22 Aligned_cols=31 Identities=23% Similarity=0.289 Sum_probs=25.5
Q ss_pred ceEEEEEeCcccc-cccccCCCchHHHHHhHh
Q psy11929 287 FVETEIVLTDDIA-GCVIGKAGSRLLEIRQIS 317 (433)
Q Consensus 287 ~~t~~i~VP~~~v-G~IIGkgG~~Ik~I~~~s 317 (433)
.+...+.|..+.. +-||||+|+.||+|...+
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 4677888988777 999999999999986543
No 144
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=54.58 E-value=12 Score=35.20 Aligned_cols=30 Identities=33% Similarity=0.540 Sum_probs=25.7
Q ss_pred CeEEEEEeccCcccceecCCchhHHHHHHh
Q psy11929 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDL 152 (433)
Q Consensus 123 ~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~ 152 (433)
+..+++.|....-|.+||++|+.|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 556788888999999999999999987754
No 145
>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=52.31 E-value=15 Score=33.73 Aligned_cols=31 Identities=19% Similarity=0.371 Sum_probs=26.2
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCC
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGA 50 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga 50 (433)
.+++.+.. ..-|.|||++|..|++|+++-.-
T Consensus 39 ~~~I~I~~----~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFA----ERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEE----CCCceEECCCchHHHHHHHHHHH
Confidence 46777777 88999999999999999987544
No 146
>PRK15494 era GTPase Era; Provisional
Probab=51.40 E-value=14 Score=36.85 Aligned_cols=29 Identities=28% Similarity=0.457 Sum_probs=24.5
Q ss_pred ceEEEEEeCcccc-cccccCCCchHHHHHh
Q psy11929 287 FVETEIVLTDDIA-GCVIGKAGSRLLEIRQ 315 (433)
Q Consensus 287 ~~t~~i~VP~~~v-G~IIGkgG~~Ik~I~~ 315 (433)
.+...+.|..+-. +-||||+|+.||+|..
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~ 301 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGA 301 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHH
Confidence 3667889998877 9999999999999854
No 147
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=49.96 E-value=16 Score=33.77 Aligned_cols=31 Identities=26% Similarity=0.317 Sum_probs=25.9
Q ss_pred EEEEeccCCcccccceeeecCchHHHHHHHHhCCe
Q psy11929 17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAK 51 (433)
Q Consensus 17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~ 51 (433)
.++.+.. ..-|.+||++|.+|+++++.-.-.
T Consensus 42 i~I~I~t----a~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYA----ERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEE----CCCCeEECCCchhHHHHHHHHHHH
Confidence 6666766 888999999999999999986544
No 148
>PRK00089 era GTPase Era; Reviewed
Probab=47.54 E-value=18 Score=35.08 Aligned_cols=29 Identities=34% Similarity=0.530 Sum_probs=23.8
Q ss_pred ceEEEEEeCcccc-cccccCCCchHHHHHh
Q psy11929 287 FVETEIVLTDDIA-GCVIGKAGSRLLEIRQ 315 (433)
Q Consensus 287 ~~t~~i~VP~~~v-G~IIGkgG~~Ik~I~~ 315 (433)
.+...+.|..+.. +-||||+|++|++|..
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~ 254 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGT 254 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHH
Confidence 3667788887776 9999999999999854
No 149
>COG1159 Era GTPase [General function prediction only]
Probab=45.99 E-value=30 Score=33.82 Aligned_cols=35 Identities=11% Similarity=0.264 Sum_probs=26.7
Q ss_pred CCCceEEEEEEeccCCcccccceeeecCchHHHHHHHH
Q psy11929 10 DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKE 47 (433)
Q Consensus 10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~ 47 (433)
+..-.+...|+|+.. ++-|.||||+|+.||+|-..
T Consensus 224 ~~~~~I~a~I~Ver~---sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 224 KGLLKIHATIYVERE---SQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred CCeEEEEEEEEEecC---CccceEECCCcHHHHHHHHH
Confidence 334456677888873 78899999999999987544
No 150
>COG1159 Era GTPase [General function prediction only]
Probab=45.47 E-value=20 Score=34.97 Aligned_cols=30 Identities=23% Similarity=0.422 Sum_probs=24.4
Q ss_pred ceEEEEEeCcccc-cccccCCCchHHHHHhH
Q psy11929 287 FVETEIVLTDDIA-GCVIGKAGSRLLEIRQI 316 (433)
Q Consensus 287 ~~t~~i~VP~~~v-G~IIGkgG~~Ik~I~~~ 316 (433)
.+...++|+.+.. |-||||+|++||+|-..
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 4556788888776 99999999999998543
No 151
>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=43.55 E-value=96 Score=24.23 Aligned_cols=66 Identities=14% Similarity=0.074 Sum_probs=48.8
Q ss_pred ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929 287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCIEL 356 (433)
Q Consensus 287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i~~ 356 (433)
..+.++..-.+.+ += |=.-+.++-+..|+.++..-.+. .++.+++|+|+..++..|...+..+|..
T Consensus 17 ~~~a~i~are~gV--~a--G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 17 TGTATIIAREDGV--LA--GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp EEEEEEEESSSEE--E---SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred EEEEEEEeCCCEE--EE--CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 4455555555533 22 44567788888899998875554 8899999999999999999999888753
No 152
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=42.57 E-value=66 Score=32.11 Aligned_cols=57 Identities=16% Similarity=0.171 Sum_probs=47.6
Q ss_pred eCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHH--HHHHh
Q psy11929 294 LTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLIN--MCIEL 356 (433)
Q Consensus 294 VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~--~~i~~ 356 (433)
-+....-.+.|..+.+++.|.+..|++|.... +.++|+|+...++.|...+. +.+..
T Consensus 21 ~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG------~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 21 SDDNELVALFGPTDTNLSLLEIALGVSIVARG------EAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CCchhhhhhcCCCCccHHHHHHHhCcEEEeCC------ceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 34667789999999999999999999888766 45999999889999988887 55544
No 153
>KOG1423|consensus
Probab=42.32 E-value=26 Score=34.48 Aligned_cols=34 Identities=18% Similarity=0.366 Sum_probs=28.0
Q ss_pred ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhC
Q psy11929 13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESG 49 (433)
Q Consensus 13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tg 49 (433)
-.+...++||.. ++...||||||..|++|-++.+
T Consensus 326 l~I~~~v~~pK~---s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 326 LFIQVEVVCPKN---SQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEcCCC---cceeEEEcCCCccHHHHHHHHH
Confidence 356778999983 6788999999999999987754
No 154
>KOG1423|consensus
Probab=41.48 E-value=25 Score=34.69 Aligned_cols=34 Identities=24% Similarity=0.410 Sum_probs=27.8
Q ss_pred CCceEEEEEeCcccc-cccccCCCchHHHHHhHhC
Q psy11929 285 DDFVETEIVLTDDIA-GCVIGKAGSRLLEIRQISG 318 (433)
Q Consensus 285 ~~~~t~~i~VP~~~v-G~IIGkgG~~Ik~I~~~sG 318 (433)
.-.+..++.||.... -.||||||..|++|.++.+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 346788999999877 5679999999999977654
No 155
>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=37.11 E-value=94 Score=27.63 Aligned_cols=59 Identities=12% Similarity=0.254 Sum_probs=44.3
Q ss_pred CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHH
Q psy11929 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLI 193 (433)
Q Consensus 121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~ 193 (433)
....++|+-++...+- +.+++|.+-.|+-+.+. .+..|.|.|+.+.|..|++.+.....
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efe-------e~~~V~I~Gdke~Ik~aLKe~s~~wk 168 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEFE-------EDDKVVIEGDKERIKKALKEFSSFWK 168 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEec-------CCcEEEEeccHHHHHHHHHHHHHHhc
Confidence 4455667766665542 45788889999888883 25679999999999999998876543
No 156
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=36.90 E-value=25 Score=32.45 Aligned_cols=35 Identities=14% Similarity=0.166 Sum_probs=27.3
Q ss_pred EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEE
Q psy11929 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISI 54 (433)
Q Consensus 16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v 54 (433)
.+.+-+.. +..+.|||+.|+++..||--+++-++-
T Consensus 92 ~v~~~i~~----~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEG----EDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecC----CchhhhhccCCcchHHHHHHHHHHhhh
Confidence 34455556 779999999999999999887765544
No 157
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=34.62 E-value=31 Score=31.82 Aligned_cols=37 Identities=22% Similarity=0.377 Sum_probs=28.6
Q ss_pred CCeEEEEEeccCcccceecCCchhHHHHHHhhCceEE
Q psy11929 122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQ 158 (433)
Q Consensus 122 ~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~ 158 (433)
..-.+.+-+..+..++|||+.|.++..||--+.+-+.
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 3445666777777999999999999999977655443
No 158
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=33.81 E-value=39 Score=31.42 Aligned_cols=29 Identities=28% Similarity=0.502 Sum_probs=24.4
Q ss_pred EEEEeccCCcccccceeeecCchHHHHHHHHhC
Q psy11929 17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESG 49 (433)
Q Consensus 17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tg 49 (433)
+++.+.. ..-|.|||++|..|++|++.-.
T Consensus 64 i~I~I~~----~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHT----ARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEe----CCCcceeCCCchHHHHHHHHHH
Confidence 5677777 8889999999999999997653
No 159
>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=30.47 E-value=51 Score=30.25 Aligned_cols=29 Identities=34% Similarity=0.641 Sum_probs=24.4
Q ss_pred eEEEEEeccCcccceecCCchhHHHHHHh
Q psy11929 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDL 152 (433)
Q Consensus 124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~ 152 (433)
..+++.|....-|.+||++|..|++|++.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHH
Confidence 34777888888899999999999998765
No 160
>PRK03818 putative transporter; Validated
Probab=29.42 E-value=4.6e+02 Score=28.15 Aligned_cols=116 Identities=15% Similarity=0.288 Sum_probs=65.8
Q ss_pred chHHHHHHHHhCCeEEEeC---CC-----------CCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHH
Q psy11929 38 GCIVRRLRKESGAKISITD---GA-----------CPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMC 103 (433)
Q Consensus 38 G~~Ik~I~~~tga~I~v~~---~~-----------~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~ 103 (433)
|++++++.......+.|.. .+ ....++.|.|..+ ++.++...+-
T Consensus 218 GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e----------------------~l~~l~~~~G 275 (552)
T PRK03818 218 GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPE----------------------DLHKAQLVIG 275 (552)
T ss_pred CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHH----------------------HHHHHHHhcC
Confidence 5789999999887776643 11 1234567777777 7766655543
Q ss_pred hhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHH--HHhhCceEE-eccC--CC-CC-----CCccEE
Q psy11929 104 RSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDI--RDLSGANVQ-VASD--ML-PM-----STERIV 172 (433)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I--~~~sga~I~-i~~~--~~-~~-----~~er~v 172 (433)
..... .. ...........+++|+ ..++|| +++++ ++++|+.|. +.+. .. +. ..-..+
T Consensus 276 l~~~~---~~---~~~~~~~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~L 343 (552)
T PRK03818 276 EEVDT---SL---STRGTDLRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDIL 343 (552)
T ss_pred CccCc---cc---cccCcceEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEE
Confidence 32110 00 0011223333444554 366666 67777 466777653 3321 11 11 122578
Q ss_pred EEEccHHHHHHHHHH
Q psy11929 173 TVHGNPDTISQAIYQ 187 (433)
Q Consensus 173 ~I~G~~~~v~~A~~~ 187 (433)
.+.|+++++++..+.
T Consensus 344 lVvG~~~~i~~l~~~ 358 (552)
T PRK03818 344 NLVGRPEAIDAVANV 358 (552)
T ss_pred EEEECHHHHHHHHHH
Confidence 899999999987664
No 161
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=28.78 E-value=55 Score=30.32 Aligned_cols=28 Identities=29% Similarity=0.617 Sum_probs=23.0
Q ss_pred EEEEeccCcccceecCCchhHHHHHHhh
Q psy11929 126 LKLVIPATHCGSLIGKGGCKIKDIRDLS 153 (433)
Q Consensus 126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~s 153 (433)
+++.|....-|.+||++|++|+++++..
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 5566666888999999999999988764
No 162
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=28.30 E-value=57 Score=30.55 Aligned_cols=29 Identities=24% Similarity=0.538 Sum_probs=24.1
Q ss_pred EEEEEeccCcccceecCCchhHHHHHHhh
Q psy11929 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLS 153 (433)
Q Consensus 125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~s 153 (433)
.+++.|....-|.+||++|..|++|++.-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 46777778888999999999999987653
No 163
>CHL00048 rps3 ribosomal protein S3
Probab=28.05 E-value=57 Score=30.37 Aligned_cols=30 Identities=17% Similarity=0.146 Sum_probs=24.6
Q ss_pred eEEEEEeccCcccceecCCchhHHHHHHhh
Q psy11929 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLS 153 (433)
Q Consensus 124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~s 153 (433)
..+++.|....-|.+||++|..|++|++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 346777777888999999999999988754
No 164
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=27.96 E-value=1.5e+02 Score=29.60 Aligned_cols=53 Identities=11% Similarity=0.125 Sum_probs=45.0
Q ss_pred EeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHH
Q psy11929 129 VIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQIC 189 (433)
Q Consensus 129 ~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~ 189 (433)
+-++...-.+.|..+.+++.|++.+|+.|.... +.++|+|+...+..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG--------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVARG--------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeCC--------ceEEEEechHHHHHHHHHHh
Confidence 344677888999999999999999999988863 57899999778888888877
No 165
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=24.60 E-value=5.1e+02 Score=23.14 Aligned_cols=90 Identities=12% Similarity=0.180 Sum_probs=53.5
Q ss_pred HHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCC------
Q psy11929 94 NVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS------ 167 (433)
Q Consensus 94 ~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~------ 167 (433)
.+.+|.+.+.+.++++.-.. .....+.++-.+-...++. .-.++.|....+-.+...++..|+.
T Consensus 68 ~~~~a~~~~~~~L~~~g~~~-----~~~~~~~v~NIvas~~l~~-----~i~L~~la~~~~~~~~YePe~fpgli~r~~~ 137 (174)
T cd00652 68 DAKLAARKYARILQKLGFPV-----EKFPEFKVQNIVASCDLGF-----PIRLEELALKHPENASYEPELFPGLIYRMDE 137 (174)
T ss_pred HHHHHHHHHHHHHHHcCCCc-----cccCceEEEEEEEEEECCC-----cccHHHHHhhhhcccEECCccCceEEEEecC
Confidence 78888888888887753111 0123344443333322222 1247777776665566655544431
Q ss_pred --------CccEEEEEc--cHHHHHHHHHHHHHHHH
Q psy11929 168 --------TERIVTVHG--NPDTISQAIYQICLVLI 193 (433)
Q Consensus 168 --------~er~v~I~G--~~~~v~~A~~~I~~~l~ 193 (433)
..-.|.|+| +.+.+.+|...|..+|.
T Consensus 138 pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~L~ 173 (174)
T cd00652 138 PKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILK 173 (174)
T ss_pred CcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 235677888 46889999999988875
No 166
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=24.03 E-value=67 Score=30.32 Aligned_cols=29 Identities=31% Similarity=0.509 Sum_probs=23.7
Q ss_pred EEEEeccCCcccccceeeecCchHHHHHHHHhC
Q psy11929 17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESG 49 (433)
Q Consensus 17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tg 49 (433)
+++.+.. ..-+.|||++|..|++|++.-.
T Consensus 64 i~I~I~~----~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 64 VRVTIHT----ARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred EEEEEEE----CCCccccCCCcHHHHHHHHHHH
Confidence 5566666 7789999999999999998764
No 167
>PRK04021 hypothetical protein; Reviewed
Probab=23.21 E-value=1.6e+02 Score=23.48 Aligned_cols=40 Identities=23% Similarity=0.306 Sum_probs=31.4
Q ss_pred chHHHHHhHhCCeEEEccCCCCCceEEEEEe-CHHHHHHHH
Q psy11929 308 SRLLEIRQISGAQINIHTGTESHKKMFHIQG-CQEAVSLAQ 347 (433)
Q Consensus 308 ~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsG-t~e~v~~A~ 347 (433)
.-|+-|.+..|.+|.|-....+....|.|.| +++++....
T Consensus 50 ali~~LAk~l~~~I~I~~G~~sr~K~v~i~g~~~e~l~~~L 90 (92)
T PRK04021 50 ELVKFFSKLLGAEVEIIRGETSREKDLLVKGISLEEVKKKL 90 (92)
T ss_pred HHHHHHHHHhCCCEEEEecCCcCceEEEEecCCHHHHHHHh
Confidence 4567788999999999876558889999999 677776553
No 168
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.10 E-value=2.4e+02 Score=24.49 Aligned_cols=44 Identities=20% Similarity=0.388 Sum_probs=34.4
Q ss_pred hhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929 144 CKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE 194 (433)
Q Consensus 144 ~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e 194 (433)
+.++.|.+-.|+-|.+.. -..|.|.|+.+.|.+|++.|....++
T Consensus 126 eRlqDi~E~hgvIiE~~E-------~D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE-------YDLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEeee-------ccEEEEeccHHHHHHHHHHHHHHHhc
Confidence 356667777777777752 45899999999999999999877654
No 169
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=22.45 E-value=5.6e+02 Score=22.88 Aligned_cols=90 Identities=12% Similarity=0.166 Sum_probs=51.9
Q ss_pred HHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCC------
Q psy11929 94 NVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS------ 167 (433)
Q Consensus 94 ~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~------ 167 (433)
.+.+|.+.+.+.++++.-.. .....+.+.-.+-.-.++.= -.+.+|...+.-.+...++..|+-
T Consensus 68 ~~~~a~~~~~~~l~~~g~~~-----~~~~~f~v~nIvat~~~~~~-----i~L~~la~~~~~~~~YePE~fPgliyr~~~ 137 (174)
T cd04517 68 EAKQAARRAARLLQKLGFKV-----VRFSNFRVVNVLATCSMPFP-----IRLDELAAKNRSSASYEPELHPGVVYRITG 137 (174)
T ss_pred HHHHHHHHHHHHHHHcCCCc-----ccCCceEEEEEEEEEeCCCc-----ccHHHHHHhchhhcEeCCccCCEEEEEECC
Confidence 78888888888887642111 01233444433333323221 136777665544555555544421
Q ss_pred --------CccEEEEEc--cHHHHHHHHHHHHHHHH
Q psy11929 168 --------TERIVTVHG--NPDTISQAIYQICLVLI 193 (433)
Q Consensus 168 --------~er~v~I~G--~~~~v~~A~~~I~~~l~ 193 (433)
..-.|.|+| +.+.+.+|.+.|..+|.
T Consensus 138 p~~t~lIF~sGkivitGaks~~~~~~a~~~i~pil~ 173 (174)
T cd04517 138 PRATLSIFSTGSVTVTGARSMEDVREAVEKIYPIVF 173 (174)
T ss_pred CcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 234677888 56899999999888775
No 170
>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=21.87 E-value=8.8e+02 Score=26.08 Aligned_cols=117 Identities=21% Similarity=0.273 Sum_probs=63.7
Q ss_pred chHHHHHHHHhCCeEEEeC---CC-----------CCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHH
Q psy11929 38 GCIVRRLRKESGAKISITD---GA-----------CPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMC 103 (433)
Q Consensus 38 G~~Ik~I~~~tga~I~v~~---~~-----------~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~ 103 (433)
|.+|+++.......+.+.. .+ ....++.+.|+++ ++.++.+.+-
T Consensus 232 GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e----------------------~L~~l~~~~G 289 (562)
T TIGR03802 232 GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRD----------------------AVVQFGAEIG 289 (562)
T ss_pred CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHH----------------------HHHHHHHhcC
Confidence 4678888887765555532 11 1224566777777 7766665543
Q ss_pred hhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHH------HhhCceEE-eccC--CCCC------CC
Q psy11929 104 RSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIR------DLSGANVQ-VASD--MLPM------ST 168 (433)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~------~~sga~I~-i~~~--~~~~------~~ 168 (433)
..+.+.. ..+ ......++.+|+ ..++|| +|+++. +.+|+.|. +.+. ..+. ..
T Consensus 290 ~~~~~~~-----~~~--~~~~~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~ 356 (562)
T TIGR03802 290 EEVQEVE-----GLD--VPMETKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQR 356 (562)
T ss_pred CccCCcc-----ccC--CceEEEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecC
Confidence 3221110 000 111233344443 455666 788886 26787754 3321 1111 12
Q ss_pred ccEEEEEccHHHHHHHHHHHH
Q psy11929 169 ERIVTVHGNPDTISQAIYQIC 189 (433)
Q Consensus 169 er~v~I~G~~~~v~~A~~~I~ 189 (433)
-..+.+.|++++++++.+.+-
T Consensus 357 GD~LlV~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 357 GDVVTLVGTPQDVDRAAKQLG 377 (562)
T ss_pred CCEEEEEeCHHHHHHHHHHcC
Confidence 357889999999998766543
No 171
>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=21.20 E-value=2.2e+02 Score=21.61 Aligned_cols=41 Identities=20% Similarity=0.378 Sum_probs=29.3
Q ss_pred CchHHHHHhHhCCeE-EEccCCCCCceEEEEEeCHHHHHHHHHHHH
Q psy11929 307 GSRLLEIRQISGAQI-NIHTGTESHKKMFHIQGCQEAVSLAQYLIN 351 (433)
Q Consensus 307 G~~Ik~I~~~sGA~I-~I~~~~~~~er~V~IsGt~e~v~~A~~lI~ 351 (433)
-..|.+|-+..+|+| .+.+.. -+|.++|+++.++....++.
T Consensus 16 r~ei~~l~~~f~a~ivd~~~~~----~iie~tG~~~kid~fi~~l~ 57 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVSPDS----IIIELTGTPEKIDAFIKLLK 57 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEETTE----EEEEEEE-HHHHHHHHHHST
T ss_pred HHHHHHHHHHhCCEEEEECCCE----EEEEEcCCHHHHHHHHHHhh
Confidence 356788889999985 555543 88999999999987766653
No 172
>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=20.89 E-value=2.3e+02 Score=21.15 Aligned_cols=34 Identities=21% Similarity=0.230 Sum_probs=25.7
Q ss_pred HhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHH
Q psy11929 316 ISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMC 353 (433)
Q Consensus 316 ~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~ 353 (433)
..+.+|..++.. ..+.|+|+++.++..+.+|.++
T Consensus 43 ~~~~~i~~d~~t----Nsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 43 SSSGRIVADERT----NSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp HTTTEEEEECTT----TEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCCeEEEEECCC----CEEEEEeCHHHHHHHHHHHHHH
Confidence 344566666655 6788999999999999988653
Done!