Query 006943
Match_columns 624
No_of_seqs 293 out of 2499
Neff 8.7
Searched_HMMs 46136
Date Thu Mar 28 16:42:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006943.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006943hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2190 PolyC-binding proteins 100.0 8.1E-42 1.8E-46 361.8 36.9 361 32-460 38-407 (485)
2 KOG2193 IGF-II mRNA-binding pr 100.0 6.3E-43 1.4E-47 344.3 20.9 366 29-463 191-565 (584)
3 KOG1676 K-homology type RNA bi 100.0 1E-41 2.2E-46 353.2 26.0 325 138-622 52-388 (600)
4 KOG1676 K-homology type RNA bi 100.0 1.4E-38 3E-43 330.0 34.2 333 33-463 50-390 (600)
5 KOG2193 IGF-II mRNA-binding pr 100.0 5.9E-39 1.3E-43 316.3 16.0 312 139-622 198-563 (584)
6 KOG2192 PolyC-binding hnRNP-K 100.0 5E-37 1.1E-41 286.0 25.6 317 297-622 37-383 (390)
7 KOG2192 PolyC-binding hnRNP-K 100.0 1.3E-35 2.9E-40 276.5 23.2 307 7-361 20-368 (390)
8 KOG2190 PolyC-binding proteins 100.0 1.9E-29 4E-34 267.8 25.5 313 306-622 41-408 (485)
9 KOG2191 RNA-binding protein NO 99.9 9.8E-26 2.1E-30 217.1 20.4 233 36-346 38-282 (402)
10 KOG2191 RNA-binding protein NO 99.9 3.9E-24 8.4E-29 206.2 21.9 262 307-622 38-314 (402)
11 TIGR03665 arCOG04150 arCOG0415 99.6 2.3E-15 5.1E-20 140.5 11.2 137 393-622 2-150 (172)
12 PRK13763 putative RNA-processi 99.6 2.9E-14 6.2E-19 134.1 12.9 139 389-622 3-156 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.5 6.7E-14 1.5E-18 130.7 10.8 136 41-218 2-152 (172)
14 PRK13763 putative RNA-processi 99.5 1.4E-13 3.1E-18 129.4 11.4 141 37-219 3-159 (180)
15 KOG2208 Vigilin [Lipid transpo 99.5 1.1E-13 2.4E-18 156.2 11.1 363 34-623 198-562 (753)
16 KOG2208 Vigilin [Lipid transpo 99.5 2.8E-13 6.1E-18 152.9 13.2 396 37-592 347-747 (753)
17 cd02396 PCBP_like_KH K homolog 99.4 2.1E-13 4.6E-18 106.1 7.1 63 556-618 2-65 (65)
18 KOG2279 Kinase anchor protein 99.3 1.3E-11 2.9E-16 127.9 14.1 286 303-619 63-364 (608)
19 cd02394 vigilin_like_KH K homo 99.3 2.8E-12 6.1E-17 99.0 6.2 61 556-618 2-62 (62)
20 PF00013 KH_1: KH domain syndr 99.3 2.5E-12 5.4E-17 98.5 5.2 60 555-617 1-60 (60)
21 cd02396 PCBP_like_KH K homolog 99.3 6.4E-12 1.4E-16 97.8 7.4 64 141-211 1-64 (65)
22 cd02393 PNPase_KH Polynucleoti 99.3 1.2E-11 2.5E-16 94.6 7.1 58 555-618 3-61 (61)
23 cd00105 KH-I K homology RNA-bi 99.3 1.5E-11 3.3E-16 95.6 7.6 63 556-618 2-64 (64)
24 KOG2279 Kinase anchor protein 99.2 3.1E-11 6.8E-16 125.2 8.8 225 136-457 64-363 (608)
25 cd02394 vigilin_like_KH K homo 99.1 1.1E-10 2.4E-15 90.0 5.7 60 142-211 2-61 (62)
26 cd02393 PNPase_KH Polynucleoti 99.0 8E-10 1.7E-14 84.4 7.9 58 389-456 2-60 (61)
27 PF00013 KH_1: KH domain syndr 99.0 1.5E-10 3.2E-15 88.7 3.2 60 141-211 1-60 (60)
28 cd00105 KH-I K homology RNA-bi 99.0 1.7E-09 3.7E-14 84.0 7.6 62 391-456 2-63 (64)
29 PF13014 KH_3: KH domain 98.9 1.5E-09 3.2E-14 76.8 5.4 42 564-605 1-43 (43)
30 PF13014 KH_3: KH domain 98.9 2.2E-09 4.8E-14 75.9 5.2 42 47-88 1-43 (43)
31 smart00322 KH K homology RNA-b 98.9 8.1E-09 1.7E-13 81.0 8.9 66 554-621 3-68 (69)
32 smart00322 KH K homology RNA-b 98.7 7.8E-08 1.7E-12 75.3 8.7 67 139-215 2-68 (69)
33 COG1094 Predicted RNA-binding 98.6 5.5E-07 1.2E-11 83.2 13.5 145 35-217 6-164 (194)
34 COG1094 Predicted RNA-binding 98.6 9E-07 2E-11 81.9 13.5 139 308-462 8-164 (194)
35 cd02395 SF1_like-KH Splicing f 98.4 7.1E-07 1.5E-11 77.7 7.5 61 562-622 14-94 (120)
36 cd02395 SF1_like-KH Splicing f 98.1 9.1E-06 2E-10 70.8 8.0 72 148-219 14-97 (120)
37 KOG2113 Predicted RNA binding 98.1 6.3E-06 1.4E-10 80.4 7.3 155 387-620 24-180 (394)
38 TIGR02696 pppGpp_PNP guanosine 97.9 4.3E-05 9.4E-10 85.3 10.8 62 555-622 579-641 (719)
39 PRK08406 transcription elongat 97.9 2.6E-05 5.6E-10 70.1 7.0 101 37-176 32-135 (140)
40 PRK08406 transcription elongat 97.9 3.1E-05 6.8E-10 69.5 6.3 101 309-425 33-135 (140)
41 TIGR02696 pppGpp_PNP guanosine 97.8 9.2E-05 2E-09 82.7 10.2 94 108-217 548-642 (719)
42 KOG2113 Predicted RNA binding 97.7 5.3E-05 1.1E-09 74.1 6.1 141 138-360 24-164 (394)
43 TIGR03591 polynuc_phos polyrib 97.5 0.00032 6.9E-09 79.8 9.4 62 555-622 552-614 (684)
44 KOG0119 Splicing factor 1/bran 97.4 0.0015 3.2E-08 68.3 11.3 79 139-217 137-230 (554)
45 TIGR03591 polynuc_phos polyrib 97.3 0.00057 1.2E-08 77.8 8.3 93 109-216 521-614 (684)
46 TIGR01952 nusA_arch NusA famil 97.3 0.0009 1.9E-08 60.0 7.2 100 309-425 34-136 (141)
47 TIGR01952 nusA_arch NusA famil 97.3 0.00063 1.4E-08 60.9 6.2 100 38-176 34-136 (141)
48 KOG0336 ATP-dependent RNA heli 97.2 0.00081 1.8E-08 68.8 6.7 64 555-621 48-111 (629)
49 PLN00207 polyribonucleotide nu 97.1 0.00097 2.1E-08 76.4 7.6 62 555-622 686-749 (891)
50 KOG0336 ATP-dependent RNA heli 97.0 0.0013 2.7E-08 67.4 6.2 57 32-91 42-98 (629)
51 KOG0119 Splicing factor 1/bran 97.0 0.0017 3.7E-08 67.8 7.2 62 562-623 152-230 (554)
52 KOG1588 RNA-binding protein Sa 97.0 0.0036 7.9E-08 60.9 8.8 77 305-381 89-189 (259)
53 COG0195 NusA Transcription elo 96.9 0.0017 3.6E-08 61.3 6.0 101 309-426 77-179 (190)
54 COG1185 Pnp Polyribonucleotide 96.9 0.0031 6.7E-08 69.2 8.2 62 555-622 553-615 (692)
55 KOG1588 RNA-binding protein Sa 96.9 0.0038 8.3E-08 60.7 7.9 81 139-219 91-193 (259)
56 COG0195 NusA Transcription elo 96.7 0.0039 8.4E-08 58.8 6.8 100 38-177 77-179 (190)
57 PLN00207 polyribonucleotide nu 96.7 0.0026 5.7E-08 73.0 6.6 94 108-216 654-749 (891)
58 cd02134 NusA_KH NusA_K homolog 96.6 0.0031 6.8E-08 48.0 4.2 36 554-589 25-60 (61)
59 COG1185 Pnp Polyribonucleotide 96.5 0.0065 1.4E-07 66.8 7.6 98 108-220 521-619 (692)
60 KOG2814 Transcription coactiva 96.4 0.0042 9.1E-08 62.1 4.9 68 554-623 57-125 (345)
61 KOG2814 Transcription coactiva 96.4 0.0042 9.1E-08 62.1 4.6 72 139-219 56-127 (345)
62 PRK00106 hypothetical protein; 96.4 0.0094 2E-07 65.3 7.8 65 553-622 224-290 (535)
63 TIGR03319 YmdA_YtgF conserved 96.3 0.0086 1.9E-07 65.9 7.4 65 553-622 203-269 (514)
64 cd02134 NusA_KH NusA_K homolog 96.3 0.0054 1.2E-07 46.7 4.2 37 36-72 24-60 (61)
65 PRK04163 exosome complex RNA-b 96.3 0.0085 1.8E-07 59.2 6.4 60 555-620 146-206 (235)
66 PRK12704 phosphodiesterase; Pr 96.3 0.011 2.3E-07 65.2 7.7 65 553-622 209-275 (520)
67 PRK11824 polynucleotide phosph 96.3 0.0074 1.6E-07 69.1 6.7 62 555-622 555-617 (693)
68 PF14611 SLS: Mitochondrial in 96.2 0.25 5.4E-06 48.0 16.0 63 391-462 28-90 (210)
69 PRK11824 polynucleotide phosph 95.9 0.012 2.6E-07 67.4 5.9 95 108-217 523-618 (693)
70 PRK12328 nusA transcription el 95.8 0.017 3.7E-07 59.9 6.4 94 46-178 251-346 (374)
71 KOG4369 RTK signaling protein 95.7 0.0073 1.6E-07 68.9 3.2 70 552-621 1338-1408(2131)
72 TIGR01953 NusA transcription t 95.7 0.024 5.2E-07 58.9 6.7 93 46-177 243-338 (341)
73 TIGR01953 NusA transcription t 95.5 0.047 1E-06 56.8 8.2 92 317-426 243-338 (341)
74 PRK02821 hypothetical protein; 95.4 0.027 5.9E-07 44.7 4.6 33 386-418 28-60 (77)
75 PRK00106 hypothetical protein; 95.4 0.068 1.5E-06 58.7 9.2 57 388-453 224-282 (535)
76 TIGR03319 YmdA_YtgF conserved 95.4 0.062 1.3E-06 59.3 8.9 56 389-453 204-261 (514)
77 PRK12327 nusA transcription el 95.3 0.035 7.5E-07 58.1 6.6 94 46-178 245-341 (362)
78 PRK12329 nusA transcription el 95.3 0.027 5.8E-07 59.5 5.7 93 46-177 277-372 (449)
79 PRK02821 hypothetical protein; 95.3 0.032 6.9E-07 44.4 4.7 53 117-169 4-60 (77)
80 PRK12704 phosphodiesterase; Pr 95.3 0.063 1.4E-06 59.3 8.8 56 389-453 210-267 (520)
81 PRK12328 nusA transcription el 95.3 0.011 2.4E-07 61.4 2.7 94 317-428 251-347 (374)
82 PRK00468 hypothetical protein; 95.3 0.029 6.2E-07 44.5 4.4 32 136-167 26-57 (75)
83 PRK12327 nusA transcription el 95.3 0.055 1.2E-06 56.6 7.8 92 317-426 245-340 (362)
84 PRK00468 hypothetical protein; 95.2 0.021 4.6E-07 45.2 3.5 34 33-66 26-59 (75)
85 COG5176 MSL5 Splicing factor ( 95.1 0.039 8.4E-07 51.3 5.3 39 554-592 148-192 (269)
86 PRK12329 nusA transcription el 95.0 0.052 1.1E-06 57.4 6.6 92 317-426 277-372 (449)
87 COG5176 MSL5 Splicing factor ( 94.9 0.04 8.7E-07 51.2 4.8 41 139-179 147-193 (269)
88 PRK09202 nusA transcription el 94.9 0.033 7.1E-07 60.4 4.9 92 317-426 245-339 (470)
89 PRK04163 exosome complex RNA-b 94.8 0.049 1.1E-06 53.8 5.7 63 143-219 148-211 (235)
90 PRK09202 nusA transcription el 94.7 0.065 1.4E-06 58.1 6.7 94 46-178 245-340 (470)
91 COG1837 Predicted RNA-binding 94.7 0.065 1.4E-06 42.3 4.8 31 137-167 27-57 (76)
92 COG1837 Predicted RNA-binding 94.4 0.044 9.5E-07 43.2 3.4 34 33-66 26-59 (76)
93 PRK01064 hypothetical protein; 94.4 0.092 2E-06 41.9 5.1 32 137-168 27-58 (78)
94 PRK12705 hypothetical protein; 94.2 0.054 1.2E-06 59.1 4.8 64 554-622 198-263 (508)
95 PF14611 SLS: Mitochondrial in 94.0 1 2.2E-05 43.7 12.9 126 311-460 29-163 (210)
96 PRK01064 hypothetical protein; 94.0 0.062 1.4E-06 42.9 3.5 34 33-66 26-59 (78)
97 PRK12705 hypothetical protein; 91.9 0.33 7.1E-06 53.1 6.5 38 389-426 198-236 (508)
98 COG5166 Uncharacterized conser 91.4 1.1 2.3E-05 47.8 9.2 103 311-427 500-609 (657)
99 KOG1067 Predicted RNA-binding 91.0 0.42 9E-06 51.4 5.8 65 138-217 595-660 (760)
100 KOG3273 Predicted RNA-binding 90.7 0.12 2.6E-06 47.9 1.4 54 562-622 177-230 (252)
101 KOG2874 rRNA processing protei 90.6 0.39 8.4E-06 47.0 4.8 53 152-219 161-213 (356)
102 KOG1067 Predicted RNA-binding 89.9 0.62 1.3E-05 50.2 6.0 67 385-462 593-660 (760)
103 PF13083 KH_4: KH domain; PDB: 89.9 0.13 2.9E-06 40.6 0.9 34 137-170 26-59 (73)
104 PF13083 KH_4: KH domain; PDB: 88.5 0.24 5.2E-06 39.1 1.5 33 35-67 27-59 (73)
105 PF13184 KH_5: NusA-like KH do 87.2 0.59 1.3E-05 36.5 2.8 38 555-592 4-47 (69)
106 COG1855 ATPase (PilT family) [ 87.1 1.4 3E-05 46.8 6.2 40 140-179 486-525 (604)
107 cd02409 KH-II KH-II (K homolo 87.0 0.84 1.8E-05 34.9 3.7 34 37-70 25-58 (68)
108 cd02409 KH-II KH-II (K homolo 86.9 1 2.2E-05 34.5 4.2 33 555-587 26-58 (68)
109 COG1855 ATPase (PilT family) [ 86.7 0.54 1.2E-05 49.7 3.1 39 555-593 487-525 (604)
110 PF13184 KH_5: NusA-like KH do 85.7 0.58 1.3E-05 36.5 2.1 35 40-74 6-46 (69)
111 COG1097 RRP4 RNA-binding prote 84.4 2.4 5.3E-05 41.2 6.1 48 555-608 147-194 (239)
112 PF07650 KH_2: KH domain syndr 84.4 0.59 1.3E-05 37.4 1.7 34 38-71 26-59 (78)
113 cd02413 40S_S3_KH K homology R 84.2 1 2.2E-05 36.4 2.9 35 39-73 32-66 (81)
114 COG1097 RRP4 RNA-binding prote 83.7 2.3 5E-05 41.4 5.6 59 143-215 149-208 (239)
115 KOG2874 rRNA processing protei 83.4 2.1 4.6E-05 42.0 5.2 51 566-623 161-211 (356)
116 cd02414 jag_KH jag_K homology 83.2 1.2 2.6E-05 35.6 3.0 33 141-173 25-57 (77)
117 PRK13764 ATPase; Provisional 83.2 1.1 2.4E-05 50.2 3.8 41 553-593 480-520 (602)
118 KOG3273 Predicted RNA-binding 82.6 0.69 1.5E-05 43.0 1.5 56 147-217 176-231 (252)
119 PF07650 KH_2: KH domain syndr 81.5 0.97 2.1E-05 36.1 1.9 34 554-587 25-58 (78)
120 cd02410 archeal_CPSF_KH The ar 81.3 9 0.0002 34.4 8.0 38 140-177 76-113 (145)
121 PRK13764 ATPase; Provisional 81.2 3.7 8.1E-05 46.1 7.0 41 139-179 480-520 (602)
122 cd02414 jag_KH jag_K homology 80.6 1.8 3.9E-05 34.5 3.2 34 309-342 25-58 (77)
123 cd02410 archeal_CPSF_KH The ar 79.9 3.6 7.9E-05 36.8 5.1 93 323-426 21-113 (145)
124 PRK06418 transcription elongat 78.7 2.6 5.5E-05 39.0 3.9 36 38-74 62-97 (166)
125 KOG4369 RTK signaling protein 77.9 0.65 1.4E-05 53.9 -0.3 66 390-458 1341-1406(2131)
126 COG5166 Uncharacterized conser 77.5 1.8 4E-05 46.2 2.9 127 320-462 392-524 (657)
127 cd02412 30S_S3_KH K homology R 76.1 2.4 5.1E-05 36.5 2.8 30 39-68 63-92 (109)
128 cd02411 archeal_30S_S3_KH K ho 75.1 2.7 5.9E-05 34.2 2.8 28 39-66 40-67 (85)
129 COG0092 RpsC Ribosomal protein 73.7 2.5 5.5E-05 40.9 2.5 31 37-67 51-81 (233)
130 cd02413 40S_S3_KH K homology R 73.2 4.2 9.2E-05 32.8 3.4 35 141-175 31-65 (81)
131 COG1782 Predicted metal-depend 72.5 7.1 0.00015 42.0 5.7 96 49-177 41-136 (637)
132 PRK06418 transcription elongat 70.1 5.4 0.00012 36.8 3.8 35 142-177 63-97 (166)
133 COG1782 Predicted metal-depend 68.1 8.9 0.00019 41.3 5.3 94 322-426 43-136 (637)
134 TIGR03675 arCOG00543 arCOG0054 63.9 17 0.00037 41.4 7.0 95 322-427 37-131 (630)
135 cd02412 30S_S3_KH K homology R 61.7 6.8 0.00015 33.6 2.5 30 141-170 62-91 (109)
136 cd02411 archeal_30S_S3_KH K ho 59.8 9.9 0.00021 30.9 3.1 28 142-169 40-67 (85)
137 TIGR03675 arCOG00543 arCOG0054 55.1 40 0.00087 38.5 7.9 38 140-177 93-130 (630)
138 COG0092 RpsC Ribosomal protein 54.8 17 0.00037 35.4 4.2 30 139-168 50-79 (233)
139 COG1702 PhoH Phosphate starvat 51.4 33 0.00072 35.5 5.9 51 561-618 22-72 (348)
140 COG1847 Jag Predicted RNA-bind 49.0 27 0.00058 33.4 4.4 59 365-423 62-125 (208)
141 TIGR01008 rpsC_E_A ribosomal p 43.9 21 0.00045 34.1 2.9 31 38-68 39-69 (195)
142 CHL00048 rps3 ribosomal protei 43.8 20 0.00044 34.7 2.9 30 38-67 67-96 (214)
143 TIGR00436 era GTP-binding prot 43.6 22 0.00049 35.8 3.4 30 554-583 221-251 (270)
144 PRK04191 rps3p 30S ribosomal p 43.4 21 0.00045 34.5 2.9 31 39-69 42-72 (207)
145 cd00652 TBP_TLF TATA box bindi 42.8 1.7E+02 0.0037 27.3 8.9 102 355-461 58-173 (174)
146 PF02749 QRPTase_N: Quinolinat 42.4 90 0.002 25.4 6.2 51 572-622 32-85 (88)
147 PTZ00084 40S ribosomal protein 42.3 22 0.00047 34.6 2.8 32 39-70 46-77 (220)
148 COG1159 Era GTPase [General fu 38.8 30 0.00065 35.1 3.3 37 554-590 229-274 (298)
149 PRK15494 era GTPase Era; Provi 38.7 29 0.00063 36.3 3.4 37 554-590 273-318 (339)
150 COG1847 Jag Predicted RNA-bind 38.3 41 0.00089 32.2 3.9 35 140-174 91-125 (208)
151 PRK00089 era GTPase Era; Revie 37.6 31 0.00066 35.1 3.3 37 554-590 226-271 (292)
152 TIGR00436 era GTP-binding prot 37.5 24 0.00051 35.6 2.4 29 140-168 221-250 (270)
153 cd04517 TLF TBP-like factors ( 36.8 2.3E+02 0.0049 26.5 8.7 102 355-461 58-173 (174)
154 COG1159 Era GTPase [General fu 36.6 22 0.00049 36.0 2.0 33 143-175 232-273 (298)
155 PRK00089 era GTPase Era; Revie 34.8 28 0.00061 35.4 2.5 28 141-168 227-255 (292)
156 PRK15494 era GTPase Era; Provi 31.4 35 0.00077 35.7 2.6 27 141-167 274-301 (339)
157 TIGR03802 Asp_Ala_antiprt aspa 29.6 4.5E+02 0.0098 29.7 11.1 57 555-617 304-376 (562)
158 TIGR01008 rpsC_E_A ribosomal p 29.2 58 0.0013 31.1 3.4 29 141-169 39-67 (195)
159 KOG1423 Ras-like GTPase ERA [C 29.0 53 0.0012 33.5 3.2 36 32-67 323-359 (379)
160 CHL00048 rps3 ribosomal protei 28.2 60 0.0013 31.5 3.4 29 141-169 67-95 (214)
161 TIGR01009 rpsC_bact ribosomal 28.0 51 0.0011 31.9 2.8 29 39-67 64-92 (211)
162 PRK04191 rps3p 30S ribosomal p 27.3 63 0.0014 31.2 3.3 29 142-170 42-70 (207)
163 KOG1960 Predicted RNA-binding 26.9 3.4E+02 0.0074 28.7 8.5 57 158-215 112-171 (531)
164 PTZ00084 40S ribosomal protein 26.8 62 0.0013 31.5 3.2 30 141-170 45-74 (220)
165 COG1702 PhoH Phosphate starvat 26.7 96 0.0021 32.2 4.6 53 145-212 20-72 (348)
166 KOG1423 Ras-like GTPase ERA [C 26.4 58 0.0013 33.3 2.9 31 554-584 328-359 (379)
167 PRK03818 putative transporter; 25.7 4.1E+02 0.0089 29.9 9.9 66 140-210 289-358 (552)
168 cd04516 TBP_eukaryotes eukaryo 25.1 5.4E+02 0.012 24.0 9.0 103 355-462 58-173 (174)
169 PRK15468 carboxysome structura 24.6 1.9E+02 0.0041 24.6 5.1 27 440-466 77-103 (111)
170 PF09869 DUF2096: Uncharacteri 24.5 2.1E+02 0.0045 26.4 5.8 58 136-214 109-166 (169)
171 PRK03818 putative transporter; 23.9 7.3E+02 0.016 27.9 11.4 127 310-454 207-357 (552)
172 TIGR03802 Asp_Ala_antiprt aspa 23.0 9E+02 0.02 27.3 12.0 60 390-455 304-375 (562)
173 PLN00062 TATA-box-binding prot 20.9 5.8E+02 0.013 24.0 8.4 24 440-463 149-174 (179)
174 PF10369 ALS_ss_C: Small subun 20.3 1.7E+02 0.0036 23.1 3.9 41 574-619 17-58 (75)
175 PRK00310 rpsC 30S ribosomal pr 20.1 86 0.0019 30.9 2.7 29 39-67 64-92 (232)
No 1
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=8.1e-42 Score=361.80 Aligned_cols=361 Identities=38% Similarity=0.627 Sum_probs=281.8
Q ss_pred CCCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHH
Q 006943 32 GNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAA 111 (624)
Q Consensus 32 ~~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a 111 (624)
..+...++||||+.+.+|.||||+|..|++||++|.++|+|.+..++++||+++|+|.... ..+|++
T Consensus 38 ~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-------------~~~~~~ 104 (485)
T KOG2190|consen 38 GPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-------------LNLSPA 104 (485)
T ss_pred CCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-------------ccCCch
Confidence 3344555999999999999999999999999999999999999999999999999997222 147899
Q ss_pred HHHHHHHHHHHHHhhhccC----CCcccCC-CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCc
Q 006943 112 QDALLKVHAAIANAVANAT----DNDKKRK-EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHS 186 (624)
Q Consensus 112 ~~ai~~v~~~i~~~~~~~~----~~~~~~~-~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~ 186 (624)
++|++++++.+...++... |...... ..++||||||++++|.||||+|++||+|+++|||+|+|.++.
T Consensus 105 ~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~------- 177 (485)
T KOG2190|consen 105 TDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDM------- 177 (485)
T ss_pred HHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCC-------
Confidence 9999999999998755321 1111112 258999999999999999999999999999999999999862
Q ss_pred ccccCCceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943 187 CAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPS 266 (624)
Q Consensus 187 ~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ 266 (624)
.|.+++|.|+|.|.+++|.+|+.+|..+|++.......+..... ++.| ..+...++
T Consensus 178 lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~-------------~y~P---~~~~~~~~-------- 233 (485)
T KOG2190|consen 178 LPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTI-------------PYRP---SASQGGPV-------- 233 (485)
T ss_pred CCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcc-------------cCCC---cccccCcc--------
Confidence 24478999999999999999999999999886543111111110 0000 00000000
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCC
Q 006943 267 ILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDT 346 (624)
Q Consensus 267 ~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~ 346 (624)
.+......+.++.+.....+.++.+++.+|...++.|||++|..|+.|+.++++.|.+.+.
T Consensus 234 -------------------~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~ 294 (485)
T KOG2190|consen 234 -------------------LPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDS 294 (485)
T ss_pred -------------------ccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccc
Confidence 0001111111222223455677889999999999999999999999999999999999876
Q ss_pred CCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCCC----cEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceE
Q 006943 347 KDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDD----TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADV 422 (624)
Q Consensus 347 ~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~----~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I 422 (624)
... |+|+++..+..++..+++++++.+.+..+.+...+ .++.+|+||.+++++||||+|.+|.+|++.|||.|
T Consensus 295 ~~~---~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I 371 (485)
T KOG2190|consen 295 RTD---RIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASI 371 (485)
T ss_pred cCc---ceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCce
Confidence 553 89999998888888999999999988887654433 48899999999999999999999999999999999
Q ss_pred EEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHH
Q 006943 423 RISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRL 460 (624)
Q Consensus 423 ~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 460 (624)
+|.....- ....++.++|+|...+...+...+...+
T Consensus 372 ~I~~~~~~--~~~~e~~~~I~~~~~~~~~~~~~~~~~~ 407 (485)
T KOG2190|consen 372 SILNKEEV--SGVREALVQITGMLREDLLAQYLIRARL 407 (485)
T ss_pred EEcccccc--CCcceeEEEecchhHHHHhhhhhccccc
Confidence 99875431 1367999999999999998877765444
No 2
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=6.3e-43 Score=344.31 Aligned_cols=366 Identities=23% Similarity=0.383 Sum_probs=270.6
Q ss_pred CCCCCCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeC-CCCCCCceEEEEEccCCcccccccccccCCCCc
Q 006943 29 DEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD-PFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEP 107 (624)
Q Consensus 29 ~~~~~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~-~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~ 107 (624)
-++......++|+|||..++|+||||.|++||.|.+.|.|||+|+. ...|..||+|||.+.+|.+
T Consensus 191 ~~~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~-------------- 256 (584)
T KOG2193|consen 191 HHKQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGT-------------- 256 (584)
T ss_pred cccccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccch--------------
Confidence 3445577899999999999999999999999999999999999986 5679999999999999984
Q ss_pred ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943 108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC 187 (624)
Q Consensus 108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~ 187 (624)
+.|+..|+.++..-+. +.+....+.++++.++.++|+||||.|.+||+|+.+||++|.|.+.-.. .
T Consensus 257 -s~Ac~~ILeimqkEA~--------~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqel-----s 322 (584)
T KOG2193|consen 257 -SKACKMILEIMQKEAV--------DDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQEL-----S 322 (584)
T ss_pred -HHHHHHHHHHHHHhhh--------ccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhh-----c
Confidence 3344444444433211 1223457899999999999999999999999999999999999874221 1
Q ss_pred cccCCceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 006943 188 AMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSI 267 (624)
Q Consensus 188 ~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~ 267 (624)
-...||+|+|+|+.++|..|..+|...|+++.+.+. ..-...++.||-+. ++.-|.++..+.+.|+...|+.
T Consensus 323 ~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl-~a~s~q~~l~P~l~-------~~~l~~f~ssS~~~~Ph~~Ps~ 394 (584)
T KOG2193|consen 323 LYNPERTITVKGSIEACVQAEAEIMKKLRECYENDL-AAMSLQCHLPPGLN-------LPALGLFPSSSAVSPPHFPPSP 394 (584)
T ss_pred ccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhH-HHhhccCCCCcccC-------ccccCCCCcccccCCCCCCCCc
Confidence 224599999999999999999999999999887652 11112222222221 1222333333333333222221
Q ss_pred c-CCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCC
Q 006943 268 L-GAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDT 346 (624)
Q Consensus 268 ~-g~~~~p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~ 346 (624)
. ++.+.|..+. ..+...+++.||...+|.||||+|.+||+|...+||.|+|..+
T Consensus 395 v~~a~p~~~~hq-------------------------~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIapp 449 (584)
T KOG2193|consen 395 VTFASPYPLFHQ-------------------------NPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPP 449 (584)
T ss_pred cccCCCchhhhc-------------------------CcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCC
Confidence 1 1111111111 1144578899999999999999999999999999999999865
Q ss_pred C-CCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCC------CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcC
Q 006943 347 K-DNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDE------DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTK 419 (624)
Q Consensus 347 ~-~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~------~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tg 419 (624)
+ ++..+|.|+|+|+. .+ ..+|.-+++.++.++ ....+..++.||...+|+||||||.++++|+.-|+
T Consensus 450 E~pdvseRMViItGpp---ea---qfKAQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~ 523 (584)
T KOG2193|consen 450 EIPDVSERMVIITGPP---EA---QFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTS 523 (584)
T ss_pred CCCCcceeEEEecCCh---HH---HHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhcccc
Confidence 4 45689999999972 23 245555666666553 23445667999999999999999999999999999
Q ss_pred ceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhc
Q 006943 420 ADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDD 463 (624)
Q Consensus 420 a~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~ 463 (624)
|-|.|+++..|. .++.-+|.|.|..-+.+.|...|...+.+.
T Consensus 524 AeV~vPrdqtpd--End~vivriiGhfyatq~aQrki~~iv~qv 565 (584)
T KOG2193|consen 524 AEVVVPRDQTPD--ENDQVIVRIIGHFYATQNAQRKIAHIVNQV 565 (584)
T ss_pred ceEEccccCCCC--ccceeeeeeechhhcchHHHHHHHHHHHHH
Confidence 999999988663 234456999999999999988887777664
No 3
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1e-41 Score=353.19 Aligned_cols=325 Identities=23% Similarity=0.375 Sum_probs=257.5
Q ss_pred CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943 138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK 217 (624)
Q Consensus 138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~ 217 (624)
..++.+.-||...+|+||||+|+.|..|+.+|||+|++...... ...|.+.++|.+++|+.|+.+|.+++..
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~--------~~~r~~~~~G~pe~v~~aK~li~evv~r 123 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSG--------IGYRSVDLTGSPENVEVAKQLIGEVVSR 123 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCC--------cccccccccCCcccHHHHHHhhhhhhhc
Confidence 45778899999999999999999999999999999998765432 3689999999999999999999888742
Q ss_pred cCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q 006943 218 FSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVS 297 (624)
Q Consensus 218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~ 297 (624)
... .++ |.
T Consensus 124 ~~~---------------------------~~~----------------------------~~----------------- 131 (600)
T KOG1676|consen 124 GRP---------------------------PGG----------------------------FP----------------- 131 (600)
T ss_pred cCC---------------------------CCC----------------------------cc-----------------
Confidence 110 000 00
Q ss_pred CCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCC--CCCceEEEEeec-CCchhHHHHHHHHH
Q 006943 298 GLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD--NRDECVITVTAI-ESPDDIKSMAVEAV 374 (624)
Q Consensus 298 ~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~--~~~er~i~I~G~-~~~~~a~~~~~~~i 374 (624)
.+-.+..++..++||...+|+||||+|++||+|++++||++.+-.... ....+-+.|+|. .+++.|+.++.++|
T Consensus 132 ---~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil 208 (600)
T KOG1676|consen 132 ---DNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADIL 208 (600)
T ss_pred ---ccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHH
Confidence 001135678999999999999999999999999999999988764322 225667888885 67888888888887
Q ss_pred HHHhhccCCC-------CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehH
Q 006943 375 LLLQTKINDE-------DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVG 447 (624)
Q Consensus 375 ~~~~~~~~~~-------~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~ 447 (624)
..-.+..... .....+.+|.||++.||.||||+|++||+|+.+||++|+|.+++.| .+.+|.+.|.|+.+
T Consensus 209 ~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p---~speR~~~IiG~~d 285 (600)
T KOG1676|consen 209 REEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDP---SSPERPAQIIGTVD 285 (600)
T ss_pred HhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCC---CCccceeeeecCHH
Confidence 6432222111 1233489999999999999999999999999999999999999988 47799999999999
Q ss_pred HHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943 448 SVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYG 527 (624)
Q Consensus 448 ~v~~A~~~I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~ 527 (624)
+|+.|.++|.+.|.+..... +.+
T Consensus 286 ~ie~Aa~lI~eii~~~~~~~----------------------------------------------~~~----------- 308 (600)
T KOG1676|consen 286 QIEHAAELINEIIAEAEAGA----------------------------------------------GGG----------- 308 (600)
T ss_pred HHHHHHHHHHHHHHHHhccC----------------------------------------------CCC-----------
Confidence 99999988888776642110 000
Q ss_pred CCCCCCCCCCCCCCcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC--CCCCCeEEEEEc
Q 006943 528 SLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK--SSRGDRVALISG 605 (624)
Q Consensus 528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~--~~~~~r~v~I~G 605 (624)
...|.+. ....+++.||.++||+||||||+|||.|.++|||++.+.+.. .+.++++|+|+|
T Consensus 309 ------~~~G~P~-----------~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG 371 (600)
T KOG1676|consen 309 ------MGGGAPG-----------LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRG 371 (600)
T ss_pred ------cCCCCcc-----------ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEec
Confidence 0000000 011789999999999999999999999999999999999873 345789999999
Q ss_pred CHHHHHHHHHHHHHHHh
Q 006943 606 TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 606 t~e~v~~A~~lI~~~i~ 622 (624)
++.||+.|+.||.+.+.
T Consensus 372 ~~~QIdhAk~LIr~kvg 388 (600)
T KOG1676|consen 372 DKRQIDHAKQLIRDKVG 388 (600)
T ss_pred CcccchHHHHHHHHHhc
Confidence 99999999999998874
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1.4e-38 Score=330.03 Aligned_cols=333 Identities=21% Similarity=0.325 Sum_probs=257.1
Q ss_pred CCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHH
Q 006943 33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQ 112 (624)
Q Consensus 33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~ 112 (624)
.+..++.+..||.+.+|+||||+|+-|..|..++||+|.+.....+...|.+.++|.++++++ |
T Consensus 50 s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~---------------a- 113 (600)
T KOG1676|consen 50 SDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEV---------------A- 113 (600)
T ss_pred cccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHH---------------H-
Confidence 446788899999999999999999999999999999999877767889999999999999764 2
Q ss_pred HHHHHHHHHHHHhhh-ccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccC
Q 006943 113 DALLKVHAAIANAVA-NATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEF 191 (624)
Q Consensus 113 ~ai~~v~~~i~~~~~-~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~ 191 (624)
.+++..+.+... ..+-........++..|+||.+.+|.||||+|++||.|++.|||++.+..+.... ...
T Consensus 114 ---K~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~------~~~ 184 (600)
T KOG1676|consen 114 ---KQLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA------TGA 184 (600)
T ss_pred ---HHhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC------CCC
Confidence 233333433221 1111112225568999999999999999999999999999999999998865322 136
Q ss_pred CceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 006943 192 DNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAA 271 (624)
Q Consensus 192 ~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~ 271 (624)
++.+.|+|.+++|+.|+.+|.++|++.... .+-.
T Consensus 185 ~KplritGdp~~ve~a~~lV~dil~e~~~~--~~g~-------------------------------------------- 218 (600)
T KOG1676|consen 185 DKPLRITGDPDKVEQAKQLVADILREEDDE--VPGS-------------------------------------------- 218 (600)
T ss_pred CCceeecCCHHHHHHHHHHHHHHHHhcccC--CCcc--------------------------------------------
Confidence 788999999999999999999999863221 0000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCC-CC
Q 006943 272 RVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD-NR 350 (624)
Q Consensus 272 ~~p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~-~~ 350 (624)
...+ +.......+++|.||...||.||||+|++||+|+.+||++|+|...+. ..
T Consensus 219 ----~~~~---------------------g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~s 273 (600)
T KOG1676|consen 219 ----GGHA---------------------GVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSS 273 (600)
T ss_pred ----cccc---------------------CcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCC
Confidence 0000 001112237899999999999999999999999999999999975544 77
Q ss_pred CceEEEEeec-CCchhHHHHHHHHHHHHhhccCCC---CCCcE--EEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEE
Q 006943 351 DECVITVTAI-ESPDDIKSMAVEAVLLLQTKINDE---DDDTV--TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRI 424 (624)
Q Consensus 351 ~er~i~I~G~-~~~~~a~~~~~~~i~~~~~~~~~~---~~~~~--~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i 424 (624)
.||.+.|.|+ +.++.|.+.+.++|......-... ..... .+.|.||.+.||.||||+|++||.|..+|||+|.+
T Consensus 274 peR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el 353 (600)
T KOG1676|consen 274 PERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCEL 353 (600)
T ss_pred ccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccc
Confidence 9999999997 445555555555555444321100 11112 67899999999999999999999999999999999
Q ss_pred eCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhc
Q 006943 425 SKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDD 463 (624)
Q Consensus 425 ~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~ 463 (624)
+++ +...+..+++++|+|+..+|..|..+|-.++-+.
T Consensus 354 ~r~--~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~ 390 (600)
T KOG1676|consen 354 SRQ--PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI 390 (600)
T ss_pred cCC--CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence 987 3344688999999999999999999998887663
No 5
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=5.9e-39 Score=316.30 Aligned_cols=312 Identities=24% Similarity=0.404 Sum_probs=255.3
Q ss_pred ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943 139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF 218 (624)
Q Consensus 139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~ 218 (624)
...+|+|||..++|.||||.|.+||.|...|-|+|.|..+... ...|+.|+|.|+++...+|+++|+++|.+.
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~-------Gaaek~itvh~tpEg~s~Ac~~ILeimqkE 270 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENA-------GAAEKIITVHSTPEGTSKACKMILEIMQKE 270 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccC-------CcccCceEEecCccchHHHHHHHHHHHHHh
Confidence 3578999999999999999999999999999999999876432 357999999999999999999999999764
Q ss_pred CCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCccccC
Q 006943 219 SPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSG 298 (624)
Q Consensus 219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~~ 298 (624)
..+..
T Consensus 271 A~~~k--------------------------------------------------------------------------- 275 (584)
T KOG2193|consen 271 AVDDK--------------------------------------------------------------------------- 275 (584)
T ss_pred hhccc---------------------------------------------------------------------------
Confidence 43211
Q ss_pred CCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCC---CCCCceEEEEeecCCchhHHHHHHHHHH
Q 006943 299 LVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTK---DNRDECVITVTAIESPDDIKSMAVEAVL 375 (624)
Q Consensus 299 ~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~---~~~~er~i~I~G~~~~~~a~~~~~~~i~ 375 (624)
...+++++++-.+.++|++|||.|.+||+|+++||++|.|..-. .-..||.|++.|+ +|.++.+-.+++.
T Consensus 276 -----~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGs--iEac~~AE~eImk 348 (584)
T KOG2193|consen 276 -----VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGS--IEACVQAEAEIMK 348 (584)
T ss_pred -----hhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEeccc--HHHHHHHHHHHHH
Confidence 12467889999999999999999999999999999999998532 2347999999995 5555444344444
Q ss_pred HHhhccCCC-------------------------------------------------CCCcEEEEEEecCCeeeEEEcC
Q 006943 376 LLQTKINDE-------------------------------------------------DDDTVTIRLLVSSKVIGCIIGK 406 (624)
Q Consensus 376 ~~~~~~~~~-------------------------------------------------~~~~~~~~l~vp~~~~g~iIGk 406 (624)
.+.+.+..+ ....-.++|.||...+|.|||+
T Consensus 349 Klre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGk 428 (584)
T KOG2193|consen 349 KLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGK 428 (584)
T ss_pred HHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhh
Confidence 333221110 0122357899999999999999
Q ss_pred CCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCC
Q 006943 407 SGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGT 486 (624)
Q Consensus 407 ~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~ 486 (624)
+|..||.|.+.+||.|+|.+...| +..+|+|+|+|++++..+|...|..+|.|.-+..
T Consensus 429 kG~hIKql~RfagASiKIappE~p---dvseRMViItGppeaqfKAQgrifgKikEenf~~------------------- 486 (584)
T KOG2193|consen 429 KGQHIKQLSRFAGASIKIAPPEIP---DVSERMVIITGPPEAQFKAQGRIFGKIKEENFFL------------------- 486 (584)
T ss_pred cchhHHHHHHhccceeeecCCCCC---CcceeEEEecCChHHHHhhhhhhhhhhhhhccCC-------------------
Confidence 999999999999999999986666 5789999999999999999999999998853211
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCcEEEEEecccccc
Q 006943 487 GISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVG 566 (624)
Q Consensus 487 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg 566 (624)
|.- ......+|.||...+|
T Consensus 487 ----Pke---------------------------------------------------------evklethirVPs~~aG 505 (584)
T KOG2193|consen 487 ----PKE---------------------------------------------------------EVKLETHIRVPSSAAG 505 (584)
T ss_pred ----chh---------------------------------------------------------hheeeeeeeccchhhh
Confidence 000 1134788999999999
Q ss_pred ceeccCCchHHHHHHHhCCEEEEeCCCCC--CCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943 567 KVIGKAGSNLANIRKISGATIEMSDSKSS--RGDRVALISGTPEQKRAAENLIQAFIM 622 (624)
Q Consensus 567 ~IIGkgG~~I~~I~~~sGa~I~i~~~~~~--~~~r~v~I~Gt~e~v~~A~~lI~~~i~ 622 (624)
+||||||.++++|++.|+|.|.|+++..+ .+.-+|.|.|...+++.|+..|.++++
T Consensus 506 RvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~ 563 (584)
T KOG2193|consen 506 RVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVN 563 (584)
T ss_pred hhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHH
Confidence 99999999999999999999999988633 344678899999999999999998875
No 6
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=5e-37 Score=286.03 Aligned_cols=317 Identities=28% Similarity=0.433 Sum_probs=228.0
Q ss_pred cCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH
Q 006943 297 SGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL 376 (624)
Q Consensus 297 ~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~ 376 (624)
.++..+.....+.+++++.++.+|+||||+|++||.|+.++++.|+|+++.. ++|+++|+.. .+.....+++++-.
T Consensus 37 d~~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~--peri~tisad--~~ti~~ilk~iip~ 112 (390)
T KOG2192|consen 37 DMEEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG--PERILTISAD--IETIGEILKKIIPT 112 (390)
T ss_pred hhHHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCC--CceeEEEecc--HHHHHHHHHHHhhh
Confidence 3344455667799999999999999999999999999999999999987654 7999999986 23333334444444
Q ss_pred HhhccCCCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHH
Q 006943 377 LQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQI 456 (624)
Q Consensus 377 ~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I 456 (624)
+.+... ..+++.++|+|..++.|.|||++|+.||+|++++.|+++|.. .+|..++||+|.|.|.+..|..+++.|
T Consensus 113 lee~f~--~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift---~c~p~stdrv~l~~g~~k~v~~~i~~i 187 (390)
T KOG2192|consen 113 LEEGFQ--LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT---ECCPHSTDRVVLIGGKPKRVVECIKII 187 (390)
T ss_pred hhhCCC--CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh---ccCCCCcceEEEecCCcchHHHHHHHH
Confidence 444332 457899999999999999999999999999999999999876 455679999999999999999999999
Q ss_pred HHHHhhccccCCCCCCCCCCCCCCC-CCCCC-------CCCCCCCCCCC--CCCC----CCCCCCCCCCC-CCCCC--CC
Q 006943 457 ILRLRDDALKDRDGSRNPPVGADHI-YSSGT-------GISMPPLLPSI--PPVG----PLGYDQRADSG-SGIGM--LS 519 (624)
Q Consensus 457 ~~~l~e~~~~~~~~~~~p~~~~~~~-~~~~~-------~~~~p~~~~~~--~~~~----~~~~~~~~~~~-~~~g~--~~ 519 (624)
++.|.|...+....+|.|.++.+.+ |+|+. +...|...... |+.+ -+.|++.+..+ ...+| .+
T Consensus 188 l~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs 267 (390)
T KOG2192|consen 188 LDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFS 267 (390)
T ss_pred HHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccccccccc
Confidence 9999999999999999988755433 33321 11111100000 1111 12344433221 11111 11
Q ss_pred C-------CCCCCCCCCCCCCCCC-CCCCCcccc----cCCCC-CCCcEEEEEeccccccceeccCCchHHHHHHHhCCE
Q 006943 520 S-------SSLYGYGSLSMGDSPY-GSMSSYSSK----LYGGL-PPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGAT 586 (624)
Q Consensus 520 ~-------~~~~~~~~~~~~~~~~-~~~~~~~~~----~~~~~-~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~ 586 (624)
. -..|.++.|.++-.+- |.-..+... .+|.+ .+.+|..|+||.+.-|.||||||+.|++|++++||.
T Consensus 268 ~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~ 347 (390)
T KOG2192|consen 268 ADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGAS 347 (390)
T ss_pred ccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCce
Confidence 1 1112222232221110 100011100 12221 345789999999999999999999999999999999
Q ss_pred EEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943 587 IEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM 622 (624)
Q Consensus 587 I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~ 622 (624)
|+|..+..++.+|+++|+||.+|++.|++|+++++.
T Consensus 348 IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vk 383 (390)
T KOG2192|consen 348 IKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVK 383 (390)
T ss_pred EEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHH
Confidence 999999989999999999999999999999999874
No 7
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1.3e-35 Score=276.55 Aligned_cols=307 Identities=25% Similarity=0.383 Sum_probs=216.5
Q ss_pred CCCCCCcCCCCCCccccccCCC-CCCCCCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEE
Q 006943 7 RYRSQRDNDRDGKNQKRRINEK-DEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVT 85 (624)
Q Consensus 7 r~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~ 85 (624)
|.++.++.++-+ +|+..+. .+......+.+|||+.++.+|+||||+|+|||.|+.++++.|.|++. ..++|+++
T Consensus 20 ~~~~~e~g~~~g---krp~~d~~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~t 94 (390)
T KOG2192|consen 20 TFPNTETGGEFG---KRPAEDMEEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILT 94 (390)
T ss_pred cCCCCccccccc---CCcchhhHHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEE
Confidence 444455555444 3443332 22234567999999999999999999999999999999999999986 67999999
Q ss_pred EEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHH
Q 006943 86 IYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRL 165 (624)
Q Consensus 86 I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I 165 (624)
|+...+ .+..+++.+.-.+++. ....+.+++||||+.+++|.|||++|++||+|
T Consensus 95 isad~~----------------------ti~~ilk~iip~lee~----f~~~~pce~rllihqs~ag~iigrngskikel 148 (390)
T KOG2192|consen 95 ISADIE----------------------TIGEILKKIIPTLEEG----FQLPSPCELRLLIHQSLAGGIIGRNGSKIKEL 148 (390)
T ss_pred EeccHH----------------------HHHHHHHHHhhhhhhC----CCCCCchhhhhhhhhhhccceecccchhHHHH
Confidence 987754 4555666665555542 22345699999999999999999999999999
Q ss_pred HHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCC
Q 006943 166 RSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPI 245 (624)
Q Consensus 166 ~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (624)
++++.|+++|+. .+||+++||+|.|.|.+.+|..+++.|.++|.+. |+....+++.|+|++++
T Consensus 149 rekcsarlkift-------~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~------pikgsa~py~p~fyd~t---- 211 (390)
T KOG2192|consen 149 REKCSARLKIFT-------ECCPHSTDRVVLIGGKPKRVVECIKIILDLISES------PIKGSAQPYDPNFYDET---- 211 (390)
T ss_pred HHhhhhhhhhhh-------ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcC------CcCCcCCcCCccccCcc----
Confidence 999999999985 6899999999999999999999999999999654 56666677777887765
Q ss_pred CCCCCCCCCCCC--CCCCCC-CCCccCCC-------------CCCCCC-----CCCC---CCCCCCCCC-----CCCcc-
Q 006943 246 YPPGGLYPNADP--ILPSRS-VPSILGAA-------------RVPDLQ-----GYAD---TGNTWPVYS-----TGLSL- 295 (624)
Q Consensus 246 ~~~~g~~~~~~~--~~~~~~-~~~~~g~~-------------~~p~~~-----~~~~---~~~~~~~~~-----~~~p~- 295 (624)
|..|||.+.++. ..|-++ .+...|.. .-|+.. .+.. -.+..+.|+ ...+.
T Consensus 212 ~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQ 291 (390)
T KOG2192|consen 212 YDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQ 291 (390)
T ss_pred cccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCC
Confidence 566666433221 111111 01111110 001100 0000 000011111 11111
Q ss_pred --------ccCC---CCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecC
Q 006943 296 --------VSGL---VGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIE 361 (624)
Q Consensus 296 --------~~~~---~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~ 361 (624)
.++. .+....--.+..+.||.+.-|.||||+|+.|++|+.++||.|++.++..+.++|+++|+|++
T Consensus 292 gGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTq 368 (390)
T KOG2192|consen 292 GGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 368 (390)
T ss_pred CCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccH
Confidence 1110 01122223577889999999999999999999999999999999999999999999999984
No 8
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=1.9e-29 Score=267.78 Aligned_cols=313 Identities=28% Similarity=0.356 Sum_probs=203.9
Q ss_pred ccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeec------CCchhHHHHHHHHHHHHhh
Q 006943 306 EELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI------ESPDDIKSMAVEAVLLLQT 379 (624)
Q Consensus 306 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~------~~~~~a~~~~~~~i~~~~~ 379 (624)
...++|++|+.+.+|.||||+|.+|++|+.++.++|+|.+...+|.+|+++|+|+ ....+|+..+.+++....+
T Consensus 41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~ 120 (485)
T KOG2190|consen 41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLE 120 (485)
T ss_pred CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccc
Confidence 3445999999999999999999999999999999999999999999999999992 0113344444444433211
Q ss_pred -ccC---C----CCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHH
Q 006943 380 -KIN---D----EDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRD 451 (624)
Q Consensus 380 -~~~---~----~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~ 451 (624)
... + ....+++++|+||.+++|+||||+|+.||+|+++|||+|++.++.+|. .++|.|+|.|.+++|.+
T Consensus 121 ~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~---ster~V~IsG~~~av~~ 197 (485)
T KOG2190|consen 121 EDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPN---STERAVTISGEPDAVKK 197 (485)
T ss_pred ccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCc---ccceeEEEcCchHHHHH
Confidence 110 0 122358999999999999999999999999999999999999998886 56888999999999999
Q ss_pred HHHHHHHHHhhccc-----cCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCC--CCCC-CCCCCCCCCCCCCCCCCCC
Q 006943 452 ALVQIILRLRDDAL-----KDRDGSRNPPVGADHIYSSGTGISMP----PLLPS--IPPV-GPLGYDQRADSGSGIGMLS 519 (624)
Q Consensus 452 A~~~I~~~l~e~~~-----~~~~~~~~p~~~~~~~~~~~~~~~~p----~~~~~--~~~~-~~~~~~~~~~~~~~~g~~~ 519 (624)
|+..|+..|.++.. ......|.|.......+....+...+ ..... .+.. .............+.++..
T Consensus 198 al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~ 277 (485)
T KOG2190|consen 198 ALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLV 277 (485)
T ss_pred HHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCcc
Confidence 99999999998542 22233455511111111000000000 00000 0000 0000000000000000000
Q ss_pred CC--------CCCCCCCCCC---CCCCCCCCC---Cc-------------ccccCCCCCCCcEEEEEeccccccceeccC
Q 006943 520 SS--------SLYGYGSLSM---GDSPYGSMS---SY-------------SSKLYGGLPPPLTLEVLVPANAVGKVIGKA 572 (624)
Q Consensus 520 ~~--------~~~~~~~~~~---~~~~~~~~~---~~-------------~~~~~~~~~~~~~~~i~VP~~~vg~IIGkg 572 (624)
.. ...-..++.. ......... +. ......+ ...++.++.||++++|+||||+
T Consensus 278 i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~ 356 (485)
T KOG2190|consen 278 IRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKG 356 (485)
T ss_pred chhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeeccc
Confidence 00 0000000000 000000000 00 0000111 3457899999999999999999
Q ss_pred CchHHHHHHHhCCEEEEeCCCC--CCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943 573 GSNLANIRKISGATIEMSDSKS--SRGDRVALISGTPEQKRAAENLIQAFIM 622 (624)
Q Consensus 573 G~~I~~I~~~sGa~I~i~~~~~--~~~~r~v~I~Gt~e~v~~A~~lI~~~i~ 622 (624)
|.+|.+||+.|||.|+|.+... ...+++++|+|+..+...|+++|...+.
T Consensus 357 G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~ 408 (485)
T KOG2190|consen 357 GAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLS 408 (485)
T ss_pred ccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccc
Confidence 9999999999999999999876 6789999999999999999999977654
No 9
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=9.8e-26 Score=217.13 Aligned_cols=233 Identities=27% Similarity=0.370 Sum_probs=169.6
Q ss_pred eEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeC---CCCCCCceEEEEEccCCcccccccccccCCCCcccHHH
Q 006943 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD---PFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQ 112 (624)
Q Consensus 36 ~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~---~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~ 112 (624)
.+.++||||+..+|.||||+|++|.+|+++|||+|++++ .+||+.||+|.|.|..+
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~e--------------------- 96 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVE--------------------- 96 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHH---------------------
Confidence 499999999999999999999999999999999999964 68999999999999954
Q ss_pred HHHHHHHHHHHHhhhccCCCc---------ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCC
Q 006943 113 DALLKVHAAIANAVANATDND---------KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP 183 (624)
Q Consensus 113 ~ai~~v~~~i~~~~~~~~~~~---------~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~ 183 (624)
+|+.+++.|.+.+.+..+.. ...+..-.++|+||++.+|.||||+|.+||.|+|++||.|+|.+....
T Consensus 97 -ai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt-- 173 (402)
T KOG2191|consen 97 -ALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPT-- 173 (402)
T ss_pred -HHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCC--
Confidence 67888888888776643211 112333568999999999999999999999999999999999963211
Q ss_pred CCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943 184 THSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRS 263 (624)
Q Consensus 184 ~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 263 (624)
.-.-.||+|++.|++++..+|+.+|++.|.+.+....+-.... ..... +...+
T Consensus 174 ---~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sy-----------a~vsG-pvaNs------------ 226 (402)
T KOG2191|consen 174 ---GISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISY-----------ANVSG-PVANS------------ 226 (402)
T ss_pred ---CccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccch-----------hcccC-ccccc------------
Confidence 1124689999999999999999999999977654432210000 00000 00000
Q ss_pred CCCccCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEE
Q 006943 264 VPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV 343 (624)
Q Consensus 264 ~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v 343 (624)
-|...+|...+.. .+.......-++....|..-|.+|.+.-.|-.-+|..+.+
T Consensus 227 ---------nPtGspya~~~~~------------------~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~i 279 (402)
T KOG2191|consen 227 ---------NPTGSPYAYQAHV------------------LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAI 279 (402)
T ss_pred ---------CCCCCCCCCCCcc------------------ccccchhhccccccccccccccccccceeeecccccceee
Confidence 0111111111111 1112233456788899999999999999999999998888
Q ss_pred cCC
Q 006943 344 DDT 346 (624)
Q Consensus 344 ~~~ 346 (624)
.+.
T Consensus 280 tq~ 282 (402)
T KOG2191|consen 280 TQA 282 (402)
T ss_pred ccc
Confidence 753
No 10
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=3.9e-24 Score=206.17 Aligned_cols=262 Identities=26% Similarity=0.368 Sum_probs=187.9
Q ss_pred cEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCC---CCCCceEEEEeec-CCchhHHHHHHHHHHHHhh---
Q 006943 307 ELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTK---DNRDECVITVTAI-ESPDDIKSMAVEAVLLLQT--- 379 (624)
Q Consensus 307 ~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~---~~~~er~i~I~G~-~~~~~a~~~~~~~i~~~~~--- 379 (624)
.+.++|+||+..+|.||||+|++|.+|+++|||+|++++.. +++.||++.|.|+ +++......+.+-|...-.
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~ 117 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA 117 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence 38999999999999999999999999999999999998654 4679999999997 2222222223332221111
Q ss_pred ccCCC-----CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHH
Q 006943 380 KINDE-----DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALV 454 (624)
Q Consensus 380 ~~~~~-----~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~ 454 (624)
+..+- .+....+++.||++.+|.||||+|.+||.|++++||.|+|++. .|....-.+|+|++.|++++..+|+.
T Consensus 118 k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq-kpt~~sLqervvt~sge~e~~~~A~~ 196 (402)
T KOG2191|consen 118 KPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ-KPTGISLQERVVTVSGEPEQNMKAVS 196 (402)
T ss_pred CCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc-CCCCccceeEEEEecCCHHHHHHHHH
Confidence 11110 1112348899999999999999999999999999999999963 35555678999999999999999999
Q ss_pred HHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943 455 QIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDS 534 (624)
Q Consensus 455 ~I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~ 534 (624)
+|+++|.|+.....+... .|+...+ |- .++.....
T Consensus 197 ~IL~Ki~eDpqs~scln~--------sya~vsG---pv----------------------------------aNsnPtGs 231 (402)
T KOG2191|consen 197 LILQKIQEDPQSGSCLNI--------SYANVSG---PV----------------------------------ANSNPTGS 231 (402)
T ss_pred HHHHHhhcCCcccceecc--------chhcccC---cc----------------------------------cccCCCCC
Confidence 999999998654433210 0100000 00 00000000
Q ss_pred CCCCCCCcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC---CCCCeEEEEEcCHHHHH
Q 006943 535 PYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS---SRGDRVALISGTPEQKR 611 (624)
Q Consensus 535 ~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~---~~~~r~v~I~Gt~e~v~ 611 (624)
+|+.. .+.++...+..+.++...+|..-|.+|.++..|...+|+.|.+++.-+ +...+ .-+.|.+-+++
T Consensus 232 pya~~-------~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~ 303 (402)
T KOG2191|consen 232 PYAYQ-------AHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGLSIL 303 (402)
T ss_pred CCCCC-------Cccccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhhhhh
Confidence 11100 112334456778899999999999999999999999999999987643 33445 77889999999
Q ss_pred HHHHHHHHHHh
Q 006943 612 AAENLIQAFIM 622 (624)
Q Consensus 612 ~A~~lI~~~i~ 622 (624)
.|.-+|...+.
T Consensus 304 aa~g~L~~~~~ 314 (402)
T KOG2191|consen 304 AAEGVLAAKVA 314 (402)
T ss_pred hhhhHHHHhhc
Confidence 99988887664
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=99.62 E-value=2.3e-15 Score=140.50 Aligned_cols=137 Identities=22% Similarity=0.301 Sum_probs=103.5
Q ss_pred EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEE---EeehHHHHHHHHHHHHHHhhccccCCC
Q 006943 393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEV---VGEVGSVRDALVQIILRLRDDALKDRD 469 (624)
Q Consensus 393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I---~G~~~~v~~A~~~I~~~l~e~~~~~~~ 469 (624)
+.||.+.+|.|||++|++|++|+++|||+|++..+ +..|.| +++++++.+|...|..........+ +
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~-A 71 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE---------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEK-A 71 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC---------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHH-H
Confidence 56899999999999999999999999999999742 345788 7899999999988866443210000 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCC
Q 006943 470 GSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGG 549 (624)
Q Consensus 470 ~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 549 (624)
+.+ .+.
T Consensus 72 ------------------~~l--------------------------------------------------------~gd 77 (172)
T TIGR03665 72 ------------------LKL--------------------------------------------------------LDD 77 (172)
T ss_pred ------------------HHh--------------------------------------------------------cCC
Confidence 000 000
Q ss_pred CCCCcEEEEEecc---------ccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHH
Q 006943 550 LPPPLTLEVLVPA---------NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAF 620 (624)
Q Consensus 550 ~~~~~~~~i~VP~---------~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~ 620 (624)
.-....+.|++ ..+|+|||++|++++.|+..|||+|.|++ ..|.|.|++++++.|+.+|+.+
T Consensus 78 --~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~l 148 (172)
T TIGR03665 78 --DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEML 148 (172)
T ss_pred --cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHH
Confidence 00011122222 46899999999999999999999999984 5699999999999999999998
Q ss_pred Hh
Q 006943 621 IM 622 (624)
Q Consensus 621 i~ 622 (624)
|.
T Consensus 149 i~ 150 (172)
T TIGR03665 149 IE 150 (172)
T ss_pred Hc
Confidence 84
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.56 E-value=2.9e-14 Score=134.08 Aligned_cols=139 Identities=22% Similarity=0.246 Sum_probs=105.7
Q ss_pred EEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEE----eehHHHHHHHHHHHHHHhhcc
Q 006943 389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVV----GEVGSVRDALVQIILRLRDDA 464 (624)
Q Consensus 389 ~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~l~e~~ 464 (624)
....+.||.+.++.|||++|++|+.|+++|||+|++..+ +..|.|. ++++++.+|..+|.+.+....
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS 73 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC---------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC
Confidence 457899999999999999999999999999999999742 3567885 899999999988876554210
Q ss_pred ccCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 006943 465 LKDR--DGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSY 542 (624)
Q Consensus 465 ~~~~--~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 (624)
..+. ..+ +.++
T Consensus 74 ~e~A~~l~g-------d~y~------------------------------------------------------------ 86 (180)
T PRK13763 74 PEKALRLLD-------DDYV------------------------------------------------------------ 86 (180)
T ss_pred HHHHHHHhC-------CCce------------------------------------------------------------
Confidence 0000 000 0000
Q ss_pred ccccCCCCCCCcEEEEE---------eccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHH
Q 006943 543 SSKLYGGLPPPLTLEVL---------VPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAA 613 (624)
Q Consensus 543 ~~~~~~~~~~~~~~~i~---------VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A 613 (624)
...+. .....+|+|||++|++++.|++.|||+|.|.+ ..|.|.|++++++.|
T Consensus 87 ------------~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A 147 (180)
T PRK13763 87 ------------LEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQVEIA 147 (180)
T ss_pred ------------EEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHHHHHH
Confidence 00000 11247899999999999999999999999984 339999999999999
Q ss_pred HHHHHHHHh
Q 006943 614 ENLIQAFIM 622 (624)
Q Consensus 614 ~~lI~~~i~ 622 (624)
+..|+.++.
T Consensus 148 ~~~I~~li~ 156 (180)
T PRK13763 148 REAIEMLIE 156 (180)
T ss_pred HHHHHHHHc
Confidence 999999874
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=99.51 E-value=6.7e-14 Score=130.70 Aligned_cols=136 Identities=24% Similarity=0.262 Sum_probs=95.9
Q ss_pred EEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEE---ccCCcccccccccccCCCCcccHHHHHHHH
Q 006943 41 ILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIY---SHVKDKEDVEVDDEFNDKEPLCAAQDALLK 117 (624)
Q Consensus 41 ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~---G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~ 117 (624)
|.||.+.+|.|||++|++|++|+++|||+|.+.+ .+..|.|. ++++ ++.+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~----------------------~i~k 54 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL----------------------AVMK 54 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH----------------------HHHH
Confidence 5689999999999999999999999999999975 23568884 2222 3333
Q ss_pred HHHHHHHhhhccC-C-CcccCCCceeEE-EEEec---------cceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCC
Q 006943 118 VHAAIANAVANAT-D-NDKKRKEKEECQ-ILVPS---------SQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTH 185 (624)
Q Consensus 118 v~~~i~~~~~~~~-~-~~~~~~~~~~~~-llvp~---------~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~ 185 (624)
+.+.|..-..... + ...-..+.++++ +-|+. ...|+|||++|++++.|++.|||+|.|..
T Consensus 55 A~~~I~~i~~gf~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~-------- 126 (172)
T TIGR03665 55 AREVVKAIGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG-------- 126 (172)
T ss_pred HHHHHHHHHcCCCHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC--------
Confidence 3333322111100 0 000011223333 23333 37999999999999999999999999852
Q ss_pred cccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943 186 SCAMEFDNFVLISGESEAVKKALFAISAIMYKF 218 (624)
Q Consensus 186 ~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~ 218 (624)
..|.|.|.+++|..|..+|.+++...
T Consensus 127 -------~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 127 -------KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred -------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 56999999999999999999998543
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.50 E-value=1.4e-13 Score=129.38 Aligned_cols=141 Identities=21% Similarity=0.251 Sum_probs=98.0
Q ss_pred EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEE----ccCCcccccccccccCCCCcccHHH
Q 006943 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIY----SHVKDKEDVEVDDEFNDKEPLCAAQ 112 (624)
Q Consensus 37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~----G~~~~~~~~~~~~~~~~~~~~~~a~ 112 (624)
+...+.||.+.++.|||++|++|+.|+++|||+|.+.+. +..|.|. +.++
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~--------------------- 56 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPL--------------------- 56 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHH---------------------
Confidence 567899999999999999999999999999999999762 3567776 2222
Q ss_pred HHHHHHHHHHHHhhhccC-CC-cccCCCceeEEE-EEe---------ccceeEEEeCCchHHHHHHHhcCCeEEEccCCC
Q 006943 113 DALLKVHAAIANAVANAT-DN-DKKRKEKEECQI-LVP---------SSQSANIIGKAGATIKRLRSKTRTSIKVTPKDA 180 (624)
Q Consensus 113 ~ai~~v~~~i~~~~~~~~-~~-~~~~~~~~~~~l-lvp---------~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~ 180 (624)
++.++.+.|.+-..... +. ..-..+.+.+++ -+. ...+|+|||++|++++.|++.|||+|.|..
T Consensus 57 -~i~kA~~~I~ai~~gf~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~--- 132 (180)
T PRK13763 57 -AVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG--- 132 (180)
T ss_pred -HHHHHHHHHHHHhcCCCHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC---
Confidence 22222222221111100 00 000111223222 111 137999999999999999999999999863
Q ss_pred CCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcC
Q 006943 181 SEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFS 219 (624)
Q Consensus 181 ~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~ 219 (624)
+.|.|.|.++++..|...|..+++...
T Consensus 133 ------------~~v~i~G~~~~~~~A~~~I~~li~g~~ 159 (180)
T PRK13763 133 ------------KTVAIIGDPEQVEIAREAIEMLIEGAP 159 (180)
T ss_pred ------------CEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence 348999999999999999999996543
No 15
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.48 E-value=1.1e-13 Score=156.19 Aligned_cols=363 Identities=18% Similarity=0.222 Sum_probs=245.4
Q ss_pred CceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHH
Q 006943 34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQD 113 (624)
Q Consensus 34 ~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ 113 (624)
.-.+..++.+....+..+||++|.++..++.++.+.|+|++.. .....+.+.|....+.. +.-
T Consensus 198 ~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~---------------~~~ 260 (753)
T KOG2208|consen 198 ERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSS---------------INV 260 (753)
T ss_pred ceeEEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhcccccccee---------------hhh
Confidence 3358889999999999999999999999999999999998753 23344455454333210 111
Q ss_pred HHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCc
Q 006943 114 ALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN 193 (624)
Q Consensus 114 ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r 193 (624)
-+...+..+ +....+.+.++..++-+++|..|+.+..|+...-=...+.+. +.+.+.
T Consensus 261 ~i~~~~~~l--------------e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~---------~~s~~~ 317 (753)
T KOG2208|consen 261 EIQEALTRL--------------ESEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQN---------YPSKDD 317 (753)
T ss_pred hhHHHHHHh--------------cChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhcc---------ccccce
Confidence 112222221 223445567788888999999999999998865544433332 125677
Q ss_pred eEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCC
Q 006943 194 FVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARV 273 (624)
Q Consensus 194 ~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~ 273 (624)
.+.+.|....+..+......++..+..
T Consensus 318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------------------------- 344 (753)
T KOG2208|consen 318 SIVLSGFEVGAVLAKRDKTLLLKNSEE----------------------------------------------------- 344 (753)
T ss_pred eEeecccccchhhhhhHHHHHHHHhhc-----------------------------------------------------
Confidence 888999988777666655444432111
Q ss_pred CCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCce
Q 006943 274 PDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDEC 353 (624)
Q Consensus 274 p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er 353 (624)
+.....+.+...++..|+||+|.+|.+|+++++|.+.++... ....
T Consensus 345 --------------------------------nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~--~~~~ 390 (753)
T KOG2208|consen 345 --------------------------------NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG--SNNK 390 (753)
T ss_pred --------------------------------cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc--CCCC
Confidence 124556778889999999999999999999999999998733 3455
Q ss_pred EEEEeec-CCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcC-ceEEEeCCCCCC
Q 006943 354 VITVTAI-ESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTK-ADVRISKGDKPK 431 (624)
Q Consensus 354 ~i~I~G~-~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tg-a~I~i~~~~~p~ 431 (624)
.+.+++. .+.+.+...+.+.+..+. +..+...+.+|...+.++||.+|..|++|..+++ .+|++....
T Consensus 391 ~v~~~~~~~~~~ka~~~v~~~~~ei~-------n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~--- 460 (753)
T KOG2208|consen 391 KVVITGVSANDEKAVEDVEKIIAEIL-------NSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN--- 460 (753)
T ss_pred CeEEeccccchhHHHHHHHHHHHhhh-------cccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC---
Confidence 6777775 344445444444333322 1245667999999999999999999999999999 667776533
Q ss_pred CCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943 432 CADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADS 511 (624)
Q Consensus 432 ~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~ 511 (624)
+....+++.|....+..+..+......+..... .
T Consensus 461 ---~~~~~~~~~~~~~dv~~~~~~~~~~~~~a~~~~-~------------------------------------------ 494 (753)
T KOG2208|consen 461 ---NSSDMVTIRGISKDVEKSVSLLKALKADAKNLK-F------------------------------------------ 494 (753)
T ss_pred ---cccccceEeccccccchhHHHHHhhhhhhhcch-h------------------------------------------
Confidence 234457788888888877655543332210000 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeC
Q 006943 512 GSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD 591 (624)
Q Consensus 512 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~ 591 (624)
....+.....|..+.+..+|+.|..+... +....++.
T Consensus 495 ---------------------------------------~~~~~~d~~~~~~~~~~~~g~~~~i~d~~----~~~~i~~~ 531 (753)
T KOG2208|consen 495 ---------------------------------------RDVVTKDKLLPVKYIGKEIGKNGTIRDSL----GDKSIFPP 531 (753)
T ss_pred ---------------------------------------hhhhhccccchHHhhcccccCceeeeccC----Cceeeccc
Confidence 00124566678888888888887766554 44555554
Q ss_pred CCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943 592 SKSSRGDRVALISGTPEQKRAAENLIQAFIMA 623 (624)
Q Consensus 592 ~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~ 623 (624)
... .....++|.|-.+.|..|+..+..++.+
T Consensus 532 ~~~-~~~~~i~i~gk~~~v~~a~~~L~~~~~~ 562 (753)
T KOG2208|consen 532 NED-EDHEKITIEGKLELVLEAPAELKALIEA 562 (753)
T ss_pred ccc-cccceeeecccccchhhhHHHHHhcchh
Confidence 422 3456799999999999999999887654
No 16
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.47 E-value=2.8e-13 Score=152.87 Aligned_cols=396 Identities=20% Similarity=0.189 Sum_probs=230.1
Q ss_pred EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHH
Q 006943 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALL 116 (624)
Q Consensus 37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~ 116 (624)
+...+-+-+.++.+|+||+|.+|.+|+++++|.|.+++ .+..+..+.++|...+++ .|.+.+.
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~~---------------ka~~~v~ 409 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSANDE---------------KAVEDVE 409 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccchh---------------HHHHHHH
Confidence 67778888999999999999999999999999999987 367888999999988743 3555555
Q ss_pred HHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcC-CeEEEccCCCCCCCCcccccCCceE
Q 006943 117 KVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTR-TSIKVTPKDASEPTHSCAMEFDNFV 195 (624)
Q Consensus 117 ~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sg-a~I~i~~~~~~~~~~~~~~~~~r~V 195 (624)
.++..+.. +.+.-.+.+|...+.+|||.+|..|..|++++| ..|...... .....+
T Consensus 410 ~~~~ei~n-------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~----------~~~~~~ 466 (753)
T KOG2208|consen 410 KIIAEILN-------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN----------NSSDMV 466 (753)
T ss_pred HHHHhhhc-------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC----------cccccc
Confidence 55555432 134556899999999999999999999999999 455444322 234557
Q ss_pred EEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCC
Q 006943 196 LISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPD 275 (624)
Q Consensus 196 ~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~ 275 (624)
++.|....|..++..+..+.......
T Consensus 467 ~~~~~~~dv~~~~~~~~~~~~~a~~~------------------------------------------------------ 492 (753)
T KOG2208|consen 467 TIRGISKDVEKSVSLLKALKADAKNL------------------------------------------------------ 492 (753)
T ss_pred eEeccccccchhHHHHHhhhhhhhcc------------------------------------------------------
Confidence 88898888888777666555321110
Q ss_pred CCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEE
Q 006943 276 LQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVI 355 (624)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i 355 (624)
......+...+.|..+.+..+|+.|..+....++....+..+. .+..+
T Consensus 493 ---------------------------~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~-----~~~~i 540 (753)
T KOG2208|consen 493 ---------------------------KFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDE-----DHEKI 540 (753)
T ss_pred ---------------------------hhhhhhhccccchHHhhcccccCceeeeccCCceeeccccccc-----cccee
Confidence 0001123345567777777777776655555544444433322 34468
Q ss_pred EEeec-CCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecCCee-eEEEcCCCchHHHHHHhcCceEEEeCCCCCCCC
Q 006943 356 TVTAI-ESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVI-GCIIGKSGSIINEIRKRTKADVRISKGDKPKCA 433 (624)
Q Consensus 356 ~I~G~-~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~-g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~ 433 (624)
+|.|. +.+. ++.+.+...+.... ......+.+|..++ -++++++....+..+...|+.+.+++...
T Consensus 541 ~i~gk~~~v~-------~a~~~L~~~~~~~~-~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~~---- 608 (753)
T KOG2208|consen 541 TIEGKLELVL-------EAPAELKALIEALI-KATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSPT---- 608 (753)
T ss_pred eecccccchh-------hhHHHHHhcchhhh-hhhhhhccCcchheeeeeeccccccccceeecCcccccCCCCCC----
Confidence 88885 2232 23333322221111 12234455666665 45555555566666666667888876433
Q ss_pred CCCCcEEEEEeehHHHHHHHHHHHHHHhhccccCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943 434 DANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGS-RNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSG 512 (624)
Q Consensus 434 ~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~-~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 512 (624)
+.+-+.|.|....++.|...+.+..... ....... .-|... .....+..+...+... +..
T Consensus 609 --~~~e~~i~g~~~~v~aa~~~~~~i~~~~-~~~~~~~~~i~~~~-~~~~~~~~g~~~~~~t----------~~~----- 669 (753)
T KOG2208|consen 609 --SSDEVSIKGAKDEVKAAKGRLEEIVEYL-SAYATTNTKIPDKF-HRSIVGYRGHIIEEIT----------SKF----- 669 (753)
T ss_pred --chhhhccchhHHHHHHhhccchhhhhhc-ccccceeeeccccc-ceeeecCCCcccccce----------eec-----
Confidence 2334789999999999977665444322 1111000 000000 0000000111111000 000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCC-CcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeC
Q 006943 513 SGIGMLSSSSLYGYGSLSMGDSPYGSMS-SYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD 591 (624)
Q Consensus 513 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~ 591 (624)
.+.|..+.... .++... ....+... .......-.....++.++.+|.++++.+||++|.+++++..++++.+.+++
T Consensus 670 ~~~~~~~~~~~--~~s~~~-~~~~~~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 670 GVGGYFGDAPT--EGSVNT-IHVSGEKMQSEIAKIALEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred CccceeCCCCC--ccccCc-chhhhhhhhhhhcccccccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 00000000000 000000 00000000 000111111223579999999999999999999999999999999999987
Q ss_pred C
Q 006943 592 S 592 (624)
Q Consensus 592 ~ 592 (624)
+
T Consensus 747 ~ 747 (753)
T KOG2208|consen 747 P 747 (753)
T ss_pred c
Confidence 3
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=99.45 E-value=2.1e-13 Score=106.11 Aligned_cols=63 Identities=41% Similarity=0.616 Sum_probs=59.0
Q ss_pred EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC-CCCCeEEEEEcCHHHHHHHHHHHH
Q 006943 556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS-SRGDRVALISGTPEQKRAAENLIQ 618 (624)
Q Consensus 556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~-~~~~r~v~I~Gt~e~v~~A~~lI~ 618 (624)
.++.||.+.+|+|||++|++|++|+++|||+|++.+... +..+|.|+|+|++++++.|..||+
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 689999999999999999999999999999999998765 578899999999999999999984
No 18
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.34 E-value=1.3e-11 Score=127.94 Aligned_cols=286 Identities=20% Similarity=0.262 Sum_probs=176.4
Q ss_pred CCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeec-CCchhHHHHHHHHHHHHhhcc
Q 006943 303 SQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI-ESPDDIKSMAVEAVLLLQTKI 381 (624)
Q Consensus 303 ~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~-~~~~~a~~~~~~~i~~~~~~~ 381 (624)
..++++..++.|+..++.+++|+.|++|+.|+..++++|.+....-+ +++..++.|- ..+-.+.....+.+ .
T Consensus 63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~v~~a~a~~~~~~---~--- 135 (608)
T KOG2279|consen 63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQVCKAKAAIHQIL---T--- 135 (608)
T ss_pred CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCCCChHHHHHHHHH---h---
Confidence 44577889999999999999999999999999999999999754433 4566666653 22222222221111 1
Q ss_pred CCCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHh
Q 006943 382 NDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLR 461 (624)
Q Consensus 382 ~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~ 461 (624)
.+.++...+.+|...+++|+|++|.+++.|+.-++|+|.+..... ....+...|.|...-++.|..++.+++.
T Consensus 136 ---~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr----~g~~~~~~i~~qqk~~~~a~~~~~~~~~ 208 (608)
T KOG2279|consen 136 ---ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR----LGLSRLIKISGQQKEVAAAKHLILEKVS 208 (608)
T ss_pred ---cCCcccccccchhhhcccccccchhhhcchhcccccccccccccc----cccccceecccccchHHHHHhhhhcccc
Confidence 345788889999999999999999999999999999999976521 3457778888888888889888888886
Q ss_pred hccccCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-
Q 006943 462 DDALKDRDGS-----RNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSP- 535 (624)
Q Consensus 462 e~~~~~~~~~-----~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~- 535 (624)
++-..-+... ..|.....+.+ +.++.-|.. ...+...+....+...|.+...+...+
T Consensus 209 edeelv~~~~e~~q~rvprk~p~n~~--~~~m~~~~~---------------s~~~h~~~~t~~s~spg~~~~~~eg~dm 271 (608)
T KOG2279|consen 209 EDEELVKRIAESAQTRVPRKQPINVR--REDMTEPGG---------------AGEPHLWKNTSSSMSPGAPLVTKEGGDM 271 (608)
T ss_pred chhHHhhhchhhcccCCCCCCCcccc--chhhccccc---------------CCccccCccchhccCCCCCCcccCCCcc
Confidence 6432221110 11110000000 000000000 000000000000000000000000000
Q ss_pred ------CCCCCCcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCC---CeEEEEEcC
Q 006943 536 ------YGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG---DRVALISGT 606 (624)
Q Consensus 536 ------~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~---~r~v~I~Gt 606 (624)
.+......-...-........+|.+|...+|.+||+.|+.++.+...|++.+.|.-..-... -.++.+.|+
T Consensus 272 ~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egk 351 (608)
T KOG2279|consen 272 AVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGK 351 (608)
T ss_pred eeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecch
Confidence 00000000000000112357899999999999999999999999999999999986543222 267889999
Q ss_pred HHHHHHHHHHHHH
Q 006943 607 PEQKRAAENLIQA 619 (624)
Q Consensus 607 ~e~v~~A~~lI~~ 619 (624)
..-++.+-.||..
T Consensus 352 qh~~n~vl~ml~~ 364 (608)
T KOG2279|consen 352 QHYENSVLEMLTV 364 (608)
T ss_pred hHHHHHHHhhhhc
Confidence 9999999999873
No 19
>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=99.32 E-value=2.8e-12 Score=98.96 Aligned_cols=61 Identities=30% Similarity=0.393 Sum_probs=56.5
Q ss_pred EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 006943 556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQ 618 (624)
Q Consensus 556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~ 618 (624)
.++.||.+++|+|||++|++|++|+++|||+|.|++.. ..++.|+|+|++++++.|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999999875 46788999999999999999874
No 20
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.31 E-value=2.5e-12 Score=98.53 Aligned_cols=60 Identities=38% Similarity=0.673 Sum_probs=55.5
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHH
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLI 617 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI 617 (624)
|.+|.||.+++|+|||++|++|++|+++|||+|.|++. + ....|+|+|++++|+.|+.+|
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 57899999999999999999999999999999999977 2 445899999999999999987
No 21
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.30 E-value=6.4e-12 Score=97.77 Aligned_cols=64 Identities=44% Similarity=0.614 Sum_probs=57.8
Q ss_pred eEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHH
Q 006943 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAI 211 (624)
Q Consensus 141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I 211 (624)
+++|+||.+.+|.|||++|++|++|+++|||+|.+.+... +..++|+|+|.|++++|.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-------PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-------CCCCceEEEEEeCHHHHHHHHHhh
Confidence 4789999999999999999999999999999999987532 236789999999999999999887
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=99.27 E-value=1.2e-11 Score=94.60 Aligned_cols=58 Identities=22% Similarity=0.462 Sum_probs=53.8
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC-HHHHHHHHHHHH
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT-PEQKRAAENLIQ 618 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt-~e~v~~A~~lI~ 618 (624)
+..+.||.+++|+|||++|++|++|+++|||+|.|+++ +.|+|+|+ +++++.|+.+|+
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 67899999999999999999999999999999999862 56999998 999999999984
No 23
>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=99.26 E-value=1.5e-11 Score=95.61 Aligned_cols=63 Identities=44% Similarity=0.724 Sum_probs=58.7
Q ss_pred EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 006943 556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQ 618 (624)
Q Consensus 556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~ 618 (624)
.++.||.+++++|||++|++|++|++.|||+|.|++...+..++.|+|+|+.++++.|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 579999999999999999999999999999999998766667899999999999999999874
No 24
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.21 E-value=3.1e-11 Score=125.22 Aligned_cols=225 Identities=24% Similarity=0.308 Sum_probs=167.0
Q ss_pred CCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943 136 RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM 215 (624)
Q Consensus 136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l 215 (624)
..+.+.++++|+...+..++|+.|.+|+.|+..++++|.+..++. ..+++..+.|.+.+|..|..++...+
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~---------g~e~~~~~~~~p~~v~~a~a~~~~~~ 134 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV---------GDERVLLISGFPVQVCKAKAAIHQIL 134 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC---------CcccchhhccCCCCCChHHHHHHHHH
Confidence 345688899999999999999999999999999999999988764 34666777779999999999988877
Q ss_pred hhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 006943 216 YKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSL 295 (624)
Q Consensus 216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~ 295 (624)
...
T Consensus 135 ~~~----------------------------------------------------------------------------- 137 (608)
T KOG2279|consen 135 TEN----------------------------------------------------------------------------- 137 (608)
T ss_pred hcC-----------------------------------------------------------------------------
Confidence 431
Q ss_pred ccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCch-hHHHHHHHHH
Q 006943 296 VSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPD-DIKSMAVEAV 374 (624)
Q Consensus 296 ~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~-~a~~~~~~~i 374 (624)
..+.....+|...+++|+|++|++++.|+.-++++|.+..+......+.+.|.+..+.. .+..+.-+-+
T Consensus 138 ----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~ 207 (608)
T KOG2279|consen 138 ----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKV 207 (608)
T ss_pred ----------CcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccc
Confidence 12344566899999999999999999999999999999877555567788888865443 2332222222
Q ss_pred HHHh---hccC--------------------------C---------------------C--------------------
Q 006943 375 LLLQ---TKIN--------------------------D---------------------E-------------------- 384 (624)
Q Consensus 375 ~~~~---~~~~--------------------------~---------------------~-------------------- 384 (624)
+.-. +.+. . +
T Consensus 208 ~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~ 287 (608)
T KOG2279|consen 208 SEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDD 287 (608)
T ss_pred cchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccc
Confidence 1100 0000 0 0
Q ss_pred ----CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHH
Q 006943 385 ----DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQII 457 (624)
Q Consensus 385 ----~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~ 457 (624)
.......+|.+|...+|.|||+.|++++.+...+++.++|........ --.-.++.+.|...-+..+..++-
T Consensus 288 s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~-v~~~qic~~egkqh~~n~vl~ml~ 363 (608)
T KOG2279|consen 288 SFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR-VLQLQICVNEGKQHYENSVLEMLT 363 (608)
T ss_pred ccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccch-hhhhhhheecchhHHHHHHHhhhh
Confidence 012234678999999999999999999999999999999875432100 011256889999999988876654
No 25
>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=99.11 E-value=1.1e-10 Score=90.02 Aligned_cols=60 Identities=27% Similarity=0.399 Sum_probs=54.7
Q ss_pred EEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHH
Q 006943 142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAI 211 (624)
Q Consensus 142 ~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I 211 (624)
.+|.||..++++|||++|++|++|+++|||+|.|+... +.++.|+|+|+.++|..|+.+|
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 57899999999999999999999999999999998643 4578999999999999999876
No 26
>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=99.05 E-value=8e-10 Score=84.43 Aligned_cols=58 Identities=21% Similarity=0.257 Sum_probs=52.1
Q ss_pred EEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEee-hHHHHHHHHHH
Q 006943 389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGE-VGSVRDALVQI 456 (624)
Q Consensus 389 ~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~-~~~v~~A~~~I 456 (624)
....+.||..++++|||++|++|++|+++|||+|.++. ++.|.|+|+ .++++.|+.+|
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 56789999999999999999999999999999999964 456999998 89999998765
No 27
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.03 E-value=1.5e-10 Score=88.65 Aligned_cols=60 Identities=38% Similarity=0.500 Sum_probs=53.9
Q ss_pred eEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHH
Q 006943 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAI 211 (624)
Q Consensus 141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I 211 (624)
|.+|.||.+++++|||++|++|++|+++|||+|.|+.. ..+..|+|+|+.++|.+|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-----------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-----------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999752 1245899999999999999876
No 28
>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=98.98 E-value=1.7e-09 Score=83.97 Aligned_cols=62 Identities=37% Similarity=0.583 Sum_probs=55.3
Q ss_pred EEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHH
Q 006943 391 IRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQI 456 (624)
Q Consensus 391 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I 456 (624)
.++.||..++++|||++|++|++|+++|||+|.|++... ...++.|.|.|+.+++..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~----~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS----GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC----CCCceEEEEEcCHHHHHHHHHHh
Confidence 579999999999999999999999999999999986433 35688999999999999998665
No 29
>PF13014 KH_3: KH domain
Probab=98.94 E-value=1.5e-09 Score=76.78 Aligned_cols=42 Identities=38% Similarity=0.722 Sum_probs=37.9
Q ss_pred cccceeccCCchHHHHHHHhCCEEEEeC-CCCCCCCeEEEEEc
Q 006943 564 AVGKVIGKAGSNLANIRKISGATIEMSD-SKSSRGDRVALISG 605 (624)
Q Consensus 564 ~vg~IIGkgG~~I~~I~~~sGa~I~i~~-~~~~~~~r~v~I~G 605 (624)
+||+|||++|++|++|+++|||+|+|++ ..++..++.|+|+|
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 34456789999998
No 30
>PF13014 KH_3: KH domain
Probab=98.91 E-value=2.2e-09 Score=75.92 Aligned_cols=42 Identities=43% Similarity=0.753 Sum_probs=39.0
Q ss_pred ccceeccCCchHHHHHHHhcCCeEEeeC-CCCCCCceEEEEEc
Q 006943 47 VIGSVIGKSGKVINSIRQETRARVKVVD-PFPGAKDRVVTIYS 88 (624)
Q Consensus 47 ~~g~vIGk~G~~I~~i~~etg~~I~v~~-~~~~~~er~i~I~G 88 (624)
++|+||||+|++|++|+++|+|+|.|++ ..++..+|.|+|+|
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 5899999999999999999999999998 56788999999987
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.90 E-value=8.1e-09 Score=81.00 Aligned_cols=66 Identities=39% Similarity=0.703 Sum_probs=60.2
Q ss_pred cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943 554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI 621 (624)
Q Consensus 554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i 621 (624)
.+.++.||.+++|.+||++|.+|++|++.||++|.+..... ....++|.|++++++.|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 47899999999999999999999999999999999986643 5678999999999999999999876
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.71 E-value=7.8e-08 Score=75.32 Aligned_cols=67 Identities=31% Similarity=0.477 Sum_probs=59.5
Q ss_pred ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943 139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM 215 (624)
Q Consensus 139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l 215 (624)
.++.++.||..++++|||++|++|++|++.|||+|.+.... .....|.|.|+.+++..|..+|.+.+
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 36788999999999999999999999999999999997532 24688999999999999999998775
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.65 E-value=5.5e-07 Score=83.24 Aligned_cols=145 Identities=28% Similarity=0.333 Sum_probs=99.7
Q ss_pred ceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHH
Q 006943 35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDA 114 (624)
Q Consensus 35 ~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~a 114 (624)
....+.+.||.+..+.+||+.|+..+.|.+.+++++.+. ..+..|+|...... .+ | -+
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t-~D-----------p-----~~ 63 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKT-ED-----------P-----LA 63 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCC-CC-----------h-----HH
Confidence 345677999999999999999999999999999999995 35677888877321 10 0 12
Q ss_pred HHHHHHH---HHHhhhccCCCcccCCCceeEEE-----EEe------ccceeEEEeCCchHHHHHHHhcCCeEEEccCCC
Q 006943 115 LLKVHAA---IANAVANATDNDKKRKEKEECQI-----LVP------SSQSANIIGKAGATIKRLRSKTRTSIKVTPKDA 180 (624)
Q Consensus 115 i~~v~~~---i~~~~~~~~~~~~~~~~~~~~~l-----lvp------~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~ 180 (624)
++++.+. |.-.+... +...-..+.+.|.+ ++. ....|+|||++|.+-+.|++-|||.|.|..
T Consensus 64 ~~ka~d~VkAIgrGF~pe-~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g--- 139 (194)
T COG1094 64 LLKARDVVKAIGRGFPPE-KALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG--- 139 (194)
T ss_pred HHHHHHHHHHHhcCCCHH-HHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC---
Confidence 2222222 11111110 00000111222211 111 234699999999999999999999999864
Q ss_pred CCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943 181 SEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK 217 (624)
Q Consensus 181 ~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~ 217 (624)
..|.|-|..++|..|..+|..++.-
T Consensus 140 ------------~tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 140 ------------KTVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred ------------cEEEEecChhhhHHHHHHHHHHHcC
Confidence 5699999999999999999999954
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.60 E-value=9e-07 Score=81.85 Aligned_cols=139 Identities=22% Similarity=0.312 Sum_probs=97.9
Q ss_pred EEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchh--HHHHHHHHHHHHhhccCCC-
Q 006943 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDD--IKSMAVEAVLLLQTKINDE- 384 (624)
Q Consensus 308 ~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~--a~~~~~~~i~~~~~~~~~~- 384 (624)
....+.||.+..+.+||+.|++.+.|.+.+++++.++.. +..|.|..++...+ +...+.+.+..+-..++.+
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~ 82 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEK 82 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHH
Confidence 356789999999999999999999999999999999643 34577776532222 2223344444332222110
Q ss_pred ----CCCcEEEE-EEe------c----CCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHH
Q 006943 385 ----DDDTVTIR-LLV------S----SKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449 (624)
Q Consensus 385 ----~~~~~~~~-l~v------p----~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v 449 (624)
.++.+.+. +.+ + ....|+|||++|.+.+.|++-|||.|.+.. ..|.|-|.+++|
T Consensus 83 A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-----------~tVaiiG~~~~v 151 (194)
T COG1094 83 ALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG-----------KTVAIIGGFEQV 151 (194)
T ss_pred HHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC-----------cEEEEecChhhh
Confidence 01122222 211 1 234699999999999999999999999973 458999999999
Q ss_pred HHHHHHHHHHHhh
Q 006943 450 RDALVQIILRLRD 462 (624)
Q Consensus 450 ~~A~~~I~~~l~e 462 (624)
..|...|...+..
T Consensus 152 ~iAr~AVemli~G 164 (194)
T COG1094 152 EIAREAVEMLING 164 (194)
T ss_pred HHHHHHHHHHHcC
Confidence 9999888877754
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=98.42 E-value=7.1e-07 Score=77.70 Aligned_cols=61 Identities=26% Similarity=0.358 Sum_probs=50.6
Q ss_pred cccccceeccCCchHHHHHHHhCCEEEEeCCCCC-----------------CCCeEEEEEcC---HHHHHHHHHHHHHHH
Q 006943 562 ANAVGKVIGKAGSNLANIRKISGATIEMSDSKSS-----------------RGDRVALISGT---PEQKRAAENLIQAFI 621 (624)
Q Consensus 562 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~-----------------~~~r~v~I~Gt---~e~v~~A~~lI~~~i 621 (624)
-+++|.|||++|.+||+|+++|||+|.|...... ...-.|.|++. .++++.|..+|+.++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 3788999999999999999999999999976311 11246889985 599999999999987
Q ss_pred h
Q 006943 622 M 622 (624)
Q Consensus 622 ~ 622 (624)
.
T Consensus 94 ~ 94 (120)
T cd02395 94 K 94 (120)
T ss_pred c
Confidence 5
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=98.14 E-value=9.1e-06 Score=70.82 Aligned_cols=72 Identities=28% Similarity=0.320 Sum_probs=53.9
Q ss_pred ccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCC--------Cccc-ccCCceEEEecCH---HHHHHHHHHHHHHH
Q 006943 148 SSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPT--------HSCA-MEFDNFVLISGES---EAVKKALFAISAIM 215 (624)
Q Consensus 148 ~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~--------~~~~-~~~~r~V~I~G~~---~~V~~A~~~I~~~l 215 (624)
.+++|.|||++|++||+|+++|||+|.|..+...... +... ....-.|.|++.. +++.+|+.+|..++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 4678999999999999999999999999976321100 0011 1233578899965 99999999999999
Q ss_pred hhcC
Q 006943 216 YKFS 219 (624)
Q Consensus 216 ~~~~ 219 (624)
....
T Consensus 94 ~~~~ 97 (120)
T cd02395 94 KPAI 97 (120)
T ss_pred ccCC
Confidence 7543
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.12 E-value=6.3e-06 Score=80.38 Aligned_cols=155 Identities=24% Similarity=0.306 Sum_probs=109.8
Q ss_pred CcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhcccc
Q 006943 387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALK 466 (624)
Q Consensus 387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~ 466 (624)
+.++..+.||..+++.+.|++|++||.|+.+|...|.-+.. ..+-++.++|..+.|..|+..|... .+++-.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr-------~eePiF~vTg~~edv~~aRrei~sa-aeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR-------GEEPIFPVTGRHEDVRRARREIPSA-AEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC-------CCCCcceeccCchhHHHHhhcCccc-cceeee
Confidence 56888899999999999999999999999999999887643 2346788999999999998655321 011000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccc
Q 006943 467 DRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKL 546 (624)
Q Consensus 467 ~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 546 (624)
..|.+ ++..+.+.+.
T Consensus 96 -------------~~~s~-------------------------------------------s~Sgg~~~~s--------- 110 (394)
T KOG2113|consen 96 -------------IRASR-------------------------------------------SFSGGTNGAS--------- 110 (394)
T ss_pred -------------eeecc-------------------------------------------cccCCCcccc---------
Confidence 00000 0000000000
Q ss_pred CCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHH-HHHHH-HHHHHH
Q 006943 547 YGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQ-KRAAE-NLIQAF 620 (624)
Q Consensus 547 ~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~-v~~A~-~lI~~~ 620 (624)
.+.+.+.++.+|-..+|.|.|..|.+|+.|++.+...|.-+-+. .+-++-++|.+.. +++|. ..|++.
T Consensus 111 ---~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg~~~nC~kra~s~eie~t 180 (394)
T KOG2113|consen 111 ---ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTGAPKNCVKRARSCEIEQT 180 (394)
T ss_pred ---ccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC---CCceEEEecCCcchhhhccccchhhh
Confidence 11234778899999999999999999999999999999777553 4567889998888 56666 455443
No 38
>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=97.95 E-value=4.3e-05 Score=85.30 Aligned_cols=62 Identities=27% Similarity=0.476 Sum_probs=56.8
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~ 622 (624)
..++.||.+++|.|||+||.+|+.|.++|||+|.|.++ ..|.|.+ +.+++++|+.+|+.++.
T Consensus 579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~------G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD------GTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC------cEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 77899999999999999999999999999999999963 5588888 68999999999998875
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.92 E-value=2.6e-05 Score=70.08 Aligned_cols=101 Identities=21% Similarity=0.318 Sum_probs=70.3
Q ss_pred EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHH
Q 006943 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALL 116 (624)
Q Consensus 37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~ 116 (624)
-.+.++++...+|+.||++|++|+.|++..|-+|.|-+- + ++ ..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s---~d----------------------~~ 75 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------S---DD----------------------PE 75 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------C---CC----------------------HH
Confidence 456788899999999999999999999999988887441 1 11 01
Q ss_pred HHHHHHHHhhhccC--CC-cccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEc
Q 006943 117 KVHAAIANAVANAT--DN-DKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVT 176 (624)
Q Consensus 117 ~v~~~i~~~~~~~~--~~-~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~ 176 (624)
.. +.+.+.... +- ..+..+...+.+.|+...+|.+|||+|.+++.++.-++-.+.|.
T Consensus 76 ~f---I~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 76 EF---IKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred HH---HHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 11 111111110 00 00112234566789999999999999999999999999888664
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.85 E-value=3.1e-05 Score=69.53 Aligned_cols=101 Identities=21% Similarity=0.323 Sum_probs=71.6
Q ss_pred EEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhc-c-CCCCC
Q 006943 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTK-I-NDEDD 386 (624)
Q Consensus 309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~-~-~~~~~ 386 (624)
.+.|.|+...+|..||++|++|+.|++..|-+|.+-.- . ++....+..++.-..-. + -...+
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~------------s----~d~~~fI~n~l~Pa~V~~v~I~~~~ 96 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY------------S----DDPEEFIKNIFAPAAVRSVTIKKKN 96 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc------------C----CCHHHHHHHHcCCCEEEEEEEEecC
Confidence 56788899999999999999999999999888887321 1 12223333333211100 0 00122
Q ss_pred CcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEe
Q 006943 387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRIS 425 (624)
Q Consensus 387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~ 425 (624)
....+.+.|+....|.+|||+|.+++.++.-+|-++.+.
T Consensus 97 ~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 97 GDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 335677889999999999999999999999999877653
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=97.80 E-value=9.2e-05 Score=82.74 Aligned_cols=94 Identities=23% Similarity=0.341 Sum_probs=73.8
Q ss_pred ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943 108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC 187 (624)
Q Consensus 108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~ 187 (624)
+..|++++.++++.+.+.+... . .....-.....+.||.+..+.|||++|++||.|.++|||+|.|..
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p-~-~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------- 615 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTP-D-EMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc-c-ccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----------
Confidence 5567778888877776666654 2 112222345668999999999999999999999999999999853
Q ss_pred cccCCceEEEecC-HHHHHHHHHHHHHHHhh
Q 006943 188 AMEFDNFVLISGE-SEAVKKALFAISAIMYK 217 (624)
Q Consensus 188 ~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~~ 217 (624)
+..|.|.+. .+++.+|+.+|..++..
T Consensus 616 ----~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 ----DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ----CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 567899886 79999999999988853
No 42
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.73 E-value=5.3e-05 Score=74.09 Aligned_cols=141 Identities=30% Similarity=0.372 Sum_probs=100.9
Q ss_pred CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943 138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK 217 (624)
Q Consensus 138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~ 217 (624)
..++..+.||..+++.+.|++|.+||.|+.+|...|.-+.+. .+-+..++|..+.|..|++.|...-+-
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~-----------eePiF~vTg~~edv~~aRrei~saaeH 92 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG-----------EEPIFPVTGRHEDVRRARREIPSAAEH 92 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC-----------CCCcceeccCchhHHHHhhcCccccce
Confidence 678999999999999999999999999999999999765432 345788999999999999877442211
Q ss_pred cCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q 006943 218 FSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVS 297 (624)
Q Consensus 218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~ 297 (624)
+.- . .+. ++ ...+..+|
T Consensus 93 ~~l------~----~~s------------------------------~s-----~Sgg~~~~------------------ 109 (394)
T KOG2113|consen 93 FGL------I----RAS------------------------------RS-----FSGGTNGA------------------ 109 (394)
T ss_pred eee------e----eec------------------------------cc-----ccCCCccc------------------
Confidence 000 0 000 00 00000000
Q ss_pred CCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeec
Q 006943 298 GLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI 360 (624)
Q Consensus 298 ~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~ 360 (624)
..+.+.+....+|...+|.|.|.+|.+|+.|++.++..|.-.-. +.+.++.++|-
T Consensus 110 -----s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~---~~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 110 -----SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR---CGEPVFCVTGA 164 (394)
T ss_pred -----cccCCCceeeeccceeeeeccccccCccchheecccceEeeecc---CCCceEEEecC
Confidence 11223455677899999999999999999999999999886532 35678899984
No 43
>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=97.51 E-value=0.00032 Score=79.83 Aligned_cols=62 Identities=23% Similarity=0.374 Sum_probs=54.4
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~ 622 (624)
..++.||.+.+|.|||+||.+|+.|.++|||+|.|.++ ..|.|.+ ..+.++.|+.+|+.+..
T Consensus 552 ~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 552 IETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred EEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcHHHHHHHHHHHHhhhc
Confidence 77899999999999999999999999999999999863 4466666 67889999999988753
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.38 E-value=0.0015 Score=68.29 Aligned_cols=79 Identities=28% Similarity=0.360 Sum_probs=58.3
Q ss_pred ceeEEEEEec------cceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCC-------CCcccccCCc-eEEEecC-HHH
Q 006943 139 KEECQILVPS------SQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP-------THSCAMEFDN-FVLISGE-SEA 203 (624)
Q Consensus 139 ~~~~~llvp~------~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~-------~~~~~~~~~r-~V~I~G~-~~~ 203 (624)
.++-+|.||. +++|+|||..|.|+|+|+++|||+|.|..+..... +...+...|. -+.|+++ -++
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 5666777774 68999999999999999999999999998432110 1112222222 4667776 589
Q ss_pred HHHHHHHHHHHHhh
Q 006943 204 VKKALFAISAIMYK 217 (624)
Q Consensus 204 V~~A~~~I~~~l~~ 217 (624)
|.+|++.|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999975
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=97.31 E-value=0.00057 Score=77.80 Aligned_cols=93 Identities=18% Similarity=0.269 Sum_probs=68.1
Q ss_pred cHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCccc
Q 006943 109 CAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCA 188 (624)
Q Consensus 109 ~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~ 188 (624)
..|.++..++++.+.+.+....... ...-.....+.||.+.++.|||++|++||+|+++|||+|.|..
T Consensus 521 ~~a~~~~~~I~~~m~~~l~~~~~~~-~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d----------- 588 (684)
T TIGR03591 521 EQAKEGRLHILGEMNKVISEPRAEL-SPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED----------- 588 (684)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccc-cccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------
Confidence 3455666666666665555432111 1112345668999999999999999999999999999999953
Q ss_pred ccCCceEEEecC-HHHHHHHHHHHHHHHh
Q 006943 189 MEFDNFVLISGE-SEAVKKALFAISAIMY 216 (624)
Q Consensus 189 ~~~~r~V~I~G~-~~~V~~A~~~I~~~l~ 216 (624)
+..|.|.+. .+.+.+|+.+|..+..
T Consensus 589 ---dG~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 589 ---DGTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred ---CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence 456778775 6888999999888764
No 46
>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=97.26 E-value=0.0009 Score=59.95 Aligned_cols=100 Identities=18% Similarity=0.343 Sum_probs=70.0
Q ss_pred EEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--Hhh-ccCCCC
Q 006943 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQT-KINDED 385 (624)
Q Consensus 309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~-~~~~~~ 385 (624)
.+-|.|....+|..||++|++|+.|++..|=+|.+-.-.. +-...+..++.- +.. .+.+ .
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~----------------D~~~fI~N~l~PA~V~~V~i~~-~ 96 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSE----------------NLEEFVANKLAPAEVKNVTVSE-F 96 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCC----------------CHHHHHHHcCCCceEEEEEEEc-C
Confidence 6668899999999999999999999988888888732111 111112222210 111 0111 2
Q ss_pred CCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEe
Q 006943 386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRIS 425 (624)
Q Consensus 386 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~ 425 (624)
++.....+.||....+..|||+|.+++...+-+|-++.+.
T Consensus 97 ~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 97 NGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 3346677899999999999999999999999998876653
No 47
>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=97.25 E-value=0.00063 Score=60.93 Aligned_cols=100 Identities=18% Similarity=0.321 Sum_probs=69.6
Q ss_pred EEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHH
Q 006943 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLK 117 (624)
Q Consensus 38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~ 117 (624)
-+-+++....+|+.||++|++|+.|++..|=+|.|-+- +..++
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~-------------------------- 76 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLE-------------------------- 76 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHH--------------------------
Confidence 66778999999999999999999998888988887441 11110
Q ss_pred HHHHHHHhhhccC--C-CcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEc
Q 006943 118 VHAAIANAVANAT--D-NDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVT 176 (624)
Q Consensus 118 v~~~i~~~~~~~~--~-~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~ 176 (624)
+.+...+.... . ...+..+.....+.|+..+.+..|||+|.+++...+-++-++.|.
T Consensus 77 --~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 77 --EFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred --HHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 11111111110 0 000112345567889999999999999999999999999888664
No 48
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.17 E-value=0.00081 Score=68.82 Aligned_cols=64 Identities=23% Similarity=0.316 Sum_probs=56.5
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI 621 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i 621 (624)
..-+.|-+++||.|||++|++|++||..|.++|+|.+.+ .+..|+|-|..+--.+|+.-|..++
T Consensus 48 plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 48 PLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---LEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred chhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---ceeEEEEechHHHHHHHHhhHhhhh
Confidence 556778999999999999999999999999999999874 4678999999988888888887665
No 49
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.13 E-value=0.00097 Score=76.43 Aligned_cols=62 Identities=19% Similarity=0.318 Sum_probs=55.5
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCE-EEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGAT-IEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~-I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~ 622 (624)
...+.||.++++.|||.||.+|+.|.++||+. |.|.++ -.|.|.+ +.+.++.|+.+|+++..
T Consensus 686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------g~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------GTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------eeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 78899999999999999999999999999999 988863 4577877 68899999999998864
No 50
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.00 E-value=0.0013 Score=67.44 Aligned_cols=57 Identities=21% Similarity=0.377 Sum_probs=50.2
Q ss_pred CCCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCC
Q 006943 32 GNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVK 91 (624)
Q Consensus 32 ~~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~ 91 (624)
.+.++.++.|.+-+.++|.|||++|++|+.|+..|+++|.+-. ...+-.|+|.|...
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~---~~~e~kv~ifg~~~ 98 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---CDLEVKVTIFGINH 98 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec---cCceeEEEEechHH
Confidence 4667899999999999999999999999999999999999976 45677899988754
No 51
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.99 E-value=0.0017 Score=67.85 Aligned_cols=62 Identities=29% Similarity=0.405 Sum_probs=49.5
Q ss_pred cccccceeccCCchHHHHHHHhCCEEEEeCCCC---------------CC-CCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 006943 562 ANAVGKVIGKAGSNLANIRKISGATIEMSDSKS---------------SR-GDRVALISG-TPEQKRAAENLIQAFIMA 623 (624)
Q Consensus 562 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~---------------~~-~~r~v~I~G-t~e~v~~A~~lI~~~i~~ 623 (624)
-++||+|||..|.+.|+|.++|||+|.|--... .. .+=-+.|++ |.|.|++|..+|+.+|.+
T Consensus 152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 478999999999999999999999999975210 11 112356777 788899999999999974
No 52
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.97 E-value=0.0036 Score=60.87 Aligned_cols=77 Identities=17% Similarity=0.346 Sum_probs=54.2
Q ss_pred CccEEEEEEecCC------ccceeeccCcchHHHHHhHhCCeEEEcCCCC------------------CCCceEEEEeec
Q 006943 305 SEELVIRVLCPFN------KIGRVIGKGGGTIKSIRQASGAQIDVDDTKD------------------NRDECVITVTAI 360 (624)
Q Consensus 305 ~~~~~~~i~vp~~------~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~------------------~~~er~i~I~G~ 360 (624)
...++.+|+||.+ +||+|+|.+|.++|+|+++|||+|-|--... -+..-.|.|...
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~ 168 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE 168 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence 4567888999864 8999999999999999999999999942100 012223444443
Q ss_pred CCchhHHHHHHHHHHHHhhcc
Q 006943 361 ESPDDIKSMAVEAVLLLQTKI 381 (624)
Q Consensus 361 ~~~~~a~~~~~~~i~~~~~~~ 381 (624)
.....|...+..|++.|...+
T Consensus 169 ~p~~ea~~rl~~AleeI~klL 189 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLL 189 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhc
Confidence 334567677778888777544
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.93 E-value=0.0017 Score=61.29 Aligned_cols=101 Identities=24% Similarity=0.355 Sum_probs=70.4
Q ss_pred EEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--HhhccCCCCC
Q 006943 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQTKINDEDD 386 (624)
Q Consensus 309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~~~~~~~~ 386 (624)
.+.+.+-.+.+|..||++|++|+.|+++.|=+|.|-. .+ + +....+..++.- +..-.....+
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe------------~s-~---d~~~fI~nal~Pa~v~~V~~~~~d 140 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE------------WS-E---DPAEFIKNALAPAEVLSVNIKEDD 140 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE------------eC-C---CHHHHHHHhcCcceEeEEEEEeCC
Confidence 4455667788899999999999999999996676622 11 1 112223344331 1100001112
Q ss_pred CcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943 387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISK 426 (624)
Q Consensus 387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~ 426 (624)
+. ...+.||....+.+|||+|.+++-+.+-||-++.|..
T Consensus 141 ~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 141 GH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred Cc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 22 6778899999999999999999999999999999864
No 54
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.87 E-value=0.0031 Score=69.23 Aligned_cols=62 Identities=21% Similarity=0.384 Sum_probs=54.9
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCH-HHHHHHHHHHHHHHh
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTP-EQKRAAENLIQAFIM 622 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~-e~v~~A~~lI~~~i~ 622 (624)
..++.|+.+.++-|||++|.+|++|.++|||+|.|.++ -.|.|.++. +.+..|+.+|.++..
T Consensus 553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchHHHHHHHHHHHHHHh
Confidence 67899999999999999999999999999999999943 338888865 778999999998764
No 55
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.86 E-value=0.0038 Score=60.72 Aligned_cols=81 Identities=19% Similarity=0.238 Sum_probs=56.1
Q ss_pred ceeEEEEEecc------ceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCC---------CCcccccCCc---eEEEecC
Q 006943 139 KEECQILVPSS------QSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP---------THSCAMEFDN---FVLISGE 200 (624)
Q Consensus 139 ~~~~~llvp~~------~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~---------~~~~~~~~~r---~V~I~G~ 200 (624)
..+.+++||-. ++|.|+|++|.++|+|+++|||+|.|..+..-.. -+.+++-++. .|+..++
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p 170 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP 170 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC
Confidence 46678899875 8999999999999999999999999998643211 1122222222 3556666
Q ss_pred HHH----HHHHHHHHHHHHhhcC
Q 006943 201 SEA----VKKALFAISAIMYKFS 219 (624)
Q Consensus 201 ~~~----V~~A~~~I~~~l~~~~ 219 (624)
+.- +..|+..|..+|.-..
T Consensus 171 ~~ea~~rl~~AleeI~klL~P~~ 193 (259)
T KOG1588|consen 171 PAEAYARLAYALEEIKKLLVPDH 193 (259)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCC
Confidence 543 3468888888875433
No 56
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.73 E-value=0.0039 Score=58.80 Aligned_cols=100 Identities=26% Similarity=0.364 Sum_probs=69.0
Q ss_pred EEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHH
Q 006943 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLK 117 (624)
Q Consensus 38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~ 117 (624)
.+-+.+-.+.+|..||++|++|+.|.++.|=+|.|-+- + ++ ++
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s---~d-----------------~~------ 119 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------S---ED-----------------PA------ 119 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------C---CC-----------------HH------
Confidence 45556666789999999999999999999988877432 1 11 00
Q ss_pred HHHHHHHhhhccC--C-CcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943 118 VHAAIANAVANAT--D-NDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP 177 (624)
Q Consensus 118 v~~~i~~~~~~~~--~-~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~ 177 (624)
+.+.+.+.... . .....++. ...+.||+++.+..|||+|.+++-+.+-||-++.|..
T Consensus 120 --~fI~nal~Pa~v~~V~~~~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 120 --EFIKNALAPAEVLSVNIKEDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred --HHHHHhcCcceEeEEEEEeCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 11111111100 0 00001122 6778899999999999999999999999999999975
No 57
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.71 E-value=0.0026 Score=72.98 Aligned_cols=94 Identities=19% Similarity=0.220 Sum_probs=68.5
Q ss_pred ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCe-EEEccCCCCCCCCc
Q 006943 108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTS-IKVTPKDASEPTHS 186 (624)
Q Consensus 108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~-I~i~~~~~~~~~~~ 186 (624)
+..|.+++..+++.+.+.+...-.. ....-.....+.||.+.++.|||++|.+||.|.++||++ |.+.
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~-~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~---------- 722 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKR-LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ---------- 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhh-hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC----------
Confidence 3455666666666655544432111 111223556789999999999999999999999999999 8764
Q ss_pred ccccCCceEEEecC-HHHHHHHHHHHHHHHh
Q 006943 187 CAMEFDNFVLISGE-SEAVKKALFAISAIMY 216 (624)
Q Consensus 187 ~~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~ 216 (624)
++-.|.|.+. .+++.+|+.+|..+..
T Consensus 723 ----ddg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 723 ----DDGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred ----CCeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 3566888885 7999999999988874
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=96.58 E-value=0.0031 Score=48.02 Aligned_cols=36 Identities=33% Similarity=0.585 Sum_probs=33.8
Q ss_pred cEEEEEeccccccceeccCCchHHHHHHHhCCEEEE
Q 006943 554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEM 589 (624)
Q Consensus 554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i 589 (624)
....+.||++..|.+|||+|.||+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 488999999999999999999999999999988876
No 59
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.51 E-value=0.0065 Score=66.79 Aligned_cols=98 Identities=24% Similarity=0.283 Sum_probs=73.2
Q ss_pred ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943 108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC 187 (624)
Q Consensus 108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~ 187 (624)
+.+|.+|-++++..+.+.+...- .+......-...+-|+.....-+||++|.+|++|.++|||+|.+.
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr-~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------- 588 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPR-KELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------- 588 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhh-hhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------
Confidence 45666777777776666655431 111122233456789999999999999999999999999999996
Q ss_pred cccCCceEEEecCH-HHHHHHHHHHHHHHhhcCC
Q 006943 188 AMEFDNFVLISGES-EAVKKALFAISAIMYKFSP 220 (624)
Q Consensus 188 ~~~~~r~V~I~G~~-~~V~~A~~~I~~~l~~~~~ 220 (624)
++..|.|.+.. +.+.+|+..|..+.++...
T Consensus 589 ---ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 589 ---DDGTVKIAASDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred ---CCCcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence 25669999986 8889999999999976543
No 60
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.40 E-value=0.0042 Score=62.09 Aligned_cols=68 Identities=19% Similarity=0.263 Sum_probs=57.6
Q ss_pred cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 006943 554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIMA 623 (624)
Q Consensus 554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~~ 623 (624)
....+.|++.++|.|||+.|.+.+.|+++|+++|.++.+.+. ...|+|+| ..++|.+|...|.-+|.+
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n--~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN--KEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC--cceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 467789999999999999999999999999999999988533 33455555 789999999999888764
No 61
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.36 E-value=0.0042 Score=62.12 Aligned_cols=72 Identities=28% Similarity=0.289 Sum_probs=57.3
Q ss_pred ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943 139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF 218 (624)
Q Consensus 139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~ 218 (624)
.....++|+++..++|||++|.|.++|+++|+|+|.++.... ..+.++.+.+..++|.+|...|..+|.++
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~---------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT---------NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC---------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 355678999999999999999999999999999998875321 23344444455799999999999888654
Q ss_pred C
Q 006943 219 S 219 (624)
Q Consensus 219 ~ 219 (624)
.
T Consensus 127 r 127 (345)
T KOG2814|consen 127 R 127 (345)
T ss_pred h
Confidence 4
No 62
>PRK00106 hypothetical protein; Provisional
Probab=96.36 E-value=0.0094 Score=65.28 Aligned_cols=65 Identities=25% Similarity=0.539 Sum_probs=55.8
Q ss_pred CcEEEEEecc-ccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943 553 PLTLEVLVPA-NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 553 ~~~~~i~VP~-~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~ 622 (624)
.++..|.+|+ ++-|+||||.|.||+.+...||++|.|++.+ ..|+||| .|---+.|+.-++.+|.
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHH
Confidence 3477889999 5559999999999999999999999999753 4588999 88888999988888775
No 63
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.33 E-value=0.0086 Score=65.92 Aligned_cols=65 Identities=22% Similarity=0.503 Sum_probs=55.5
Q ss_pred CcEEEEEeccc-cccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943 553 PLTLEVLVPAN-AVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 553 ~~~~~i~VP~~-~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~ 622 (624)
.++..|.+|++ +-|+||||.|.||+.+...||++|.|++.+ ..|+||| .|---+.|+.-|+.+|.
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHH
Confidence 35778899994 559999999999999999999999999753 4588999 78888999988888775
No 64
>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=96.33 E-value=0.0054 Score=46.71 Aligned_cols=37 Identities=22% Similarity=0.434 Sum_probs=34.2
Q ss_pred eEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEe
Q 006943 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKV 72 (624)
Q Consensus 36 ~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v 72 (624)
...+.+.||.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999988876
No 65
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.28 E-value=0.0085 Score=59.17 Aligned_cols=60 Identities=25% Similarity=0.325 Sum_probs=52.3
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHH
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT-PEQKRAAENLIQAF 620 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt-~e~v~~A~~lI~~~ 620 (624)
-+.+.||.++++.+||++|.+|+.|.+.+++.|.|... -.|.|+++ .+++++|+.+|+.+
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~~~~~~a~~~I~~~ 206 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDEEDEEIAIEAIKKI 206 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCHHHHHHHHHHHHHH
Confidence 36789999999999999999999999999999999854 44888885 66889999999865
No 66
>PRK12704 phosphodiesterase; Provisional
Probab=96.27 E-value=0.011 Score=65.25 Aligned_cols=65 Identities=20% Similarity=0.483 Sum_probs=53.6
Q ss_pred CcEEEEEecc-ccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943 553 PLTLEVLVPA-NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 553 ~~~~~i~VP~-~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~ 622 (624)
.++..|.+|+ ++-|+||||.|.||+.+...||++|.|++.+ ..|+||| .|---+.|+.-++.++.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHh
Confidence 3467788998 4559999999999999999999999999753 4588999 77777788877777654
No 67
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.26 E-value=0.0074 Score=69.06 Aligned_cols=62 Identities=24% Similarity=0.429 Sum_probs=53.2
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~ 622 (624)
...+.||.+.++.+||.||.+|+.|.++||+.|.+.++ -.|.|.+ ..+.++.|+.+|+.+..
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~------G~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD------GTVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC------ceEEEEcccHHHHHHHHHHHHHhcc
Confidence 56778899999999999999999999999998887542 4488888 68889999999998753
No 68
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.16 E-value=0.25 Score=48.02 Aligned_cols=63 Identities=13% Similarity=0.269 Sum_probs=50.6
Q ss_pred EEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhh
Q 006943 391 IRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRD 462 (624)
Q Consensus 391 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e 462 (624)
+.+.++....-.++..+|..+++|....||+|.+.. .+..+.|+|+...+..+...|.+.+..
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---------~~~~i~I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR---------SENRIRITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEec---------CCcEEEEEccHHHHHHHHHHHHHHHhh
Confidence 445566888899999999999999888999999975 245688999998888887766655543
No 69
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.86 E-value=0.012 Score=67.39 Aligned_cols=95 Identities=22% Similarity=0.294 Sum_probs=67.7
Q ss_pred ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943 108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC 187 (624)
Q Consensus 108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~ 187 (624)
+..|.++..++++.+.+.+...-.... ........+.|+.+.++.+||++|.+||+|.++||++|.+.
T Consensus 523 l~~a~~g~~~I~~~M~~aI~~~r~~~~-~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------- 590 (693)
T PRK11824 523 LEQAKEGRLHILGKMNEAISEPRAELS-PYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------- 590 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhcCChhhhc-ccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------
Confidence 335667777777776665543211111 11123345667999999999999999999999999988763
Q ss_pred cccCCceEEEecC-HHHHHHHHHHHHHHHhh
Q 006943 188 AMEFDNFVLISGE-SEAVKKALFAISAIMYK 217 (624)
Q Consensus 188 ~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~~ 217 (624)
++..|.|.+. .+++.+|+.+|..+..+
T Consensus 591 ---d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 ---DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred ---CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 3566888885 78999999999887743
No 70
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.84 E-value=0.017 Score=59.92 Aligned_cols=94 Identities=24% Similarity=0.300 Sum_probs=64.8
Q ss_pred cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943 46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN 124 (624)
Q Consensus 46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~ 124 (624)
+-+|+.||++|.+|+.|.++. |=+|.|-+-.. + ..+.+..
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~--------------D-------------------------~~~fI~N 291 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSN--------------V-------------------------PEIFIAR 291 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC--------------C-------------------------HHHHHHH
Confidence 458999999999999999998 78888743210 0 0011222
Q ss_pred hhhccC-CCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccC
Q 006943 125 AVANAT-DNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK 178 (624)
Q Consensus 125 ~~~~~~-~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~ 178 (624)
++.... ..-.-..+.....+.||..+.+..|||+|.+++-...-||.+|.|..-
T Consensus 292 al~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 292 ALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred hCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 221110 000000123466789999999999999999999999999999999874
No 71
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=95.69 E-value=0.0073 Score=68.86 Aligned_cols=70 Identities=30% Similarity=0.359 Sum_probs=61.5
Q ss_pred CCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeC-CCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943 552 PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD-SKSSRGDRVALISGTPEQKRAAENLIQAFI 621 (624)
Q Consensus 552 ~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~-~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i 621 (624)
+.....+.+|.....+|||+||.||+.+|.-|||.|.|.+ ..+...+|.+.+.|+++.+..|..+|.-.|
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcccccee
Confidence 4456788999999999999999999999999999999998 444567999999999999999998886544
No 72
>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=95.66 E-value=0.024 Score=58.86 Aligned_cols=93 Identities=25% Similarity=0.374 Sum_probs=64.2
Q ss_pred cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943 46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN 124 (624)
Q Consensus 46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~ 124 (624)
+-+|+.||++|++|+.|.++. |=+|.|-+-.. + ..+.+..
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d-------------------------~~~fi~n 283 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSD--------------D-------------------------PAEFIAN 283 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCC--------------C-------------------------HHHHHHH
Confidence 458999999999999999998 78888743210 0 0011112
Q ss_pred hhhccC-CCc-ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943 125 AVANAT-DND-KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP 177 (624)
Q Consensus 125 ~~~~~~-~~~-~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~ 177 (624)
++.... ..- -...+.....+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 284 al~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 284 ALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred hcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 111110 000 00012246788999999999999999999999999999999975
No 73
>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=95.53 E-value=0.047 Score=56.75 Aligned_cols=92 Identities=23% Similarity=0.410 Sum_probs=64.5
Q ss_pred CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--Hhhc-cCCCCCCcEEEE
Q 006943 317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQTK-INDEDDDTVTIR 392 (624)
Q Consensus 317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~~-~~~~~~~~~~~~ 392 (624)
+-+|..||++|++|+.|.++. |=+|.|-.-... + ...+..|+.- +..- +.+. ......
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-------------~---~~fi~nal~Pa~v~~v~i~~~--~~~~~~ 304 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDD-------------P---AEFIANALSPAKVISVEVLDE--DKHSAE 304 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCC-------------H---HHHHHHhcCCceEEEEEEEcC--CCcEEE
Confidence 567999999999999999999 777776321111 1 1112222221 1110 1111 224688
Q ss_pred EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943 393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISK 426 (624)
Q Consensus 393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~ 426 (624)
+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 305 v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 305 VVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 9999999999999999999999999999999864
No 74
>PRK02821 hypothetical protein; Provisional
Probab=95.40 E-value=0.027 Score=44.74 Aligned_cols=33 Identities=21% Similarity=0.378 Sum_probs=28.3
Q ss_pred CCcEEEEEEecCCeeeEEEcCCCchHHHHHHhc
Q 006943 386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRT 418 (624)
Q Consensus 386 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~t 418 (624)
+..+.+++.+.+..+|+||||+|.+|+.|+.--
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 445778999999999999999999999887643
No 75
>PRK00106 hypothetical protein; Provisional
Probab=95.37 E-value=0.068 Score=58.70 Aligned_cols=57 Identities=25% Similarity=0.286 Sum_probs=43.2
Q ss_pred cEEEEEEecC-CeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEe-ehHHHHHHH
Q 006943 388 TVTIRLLVSS-KVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG-EVGSVRDAL 453 (624)
Q Consensus 388 ~~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~ 453 (624)
.+.-.+.+|+ .+-|+|||+.|.+||-++.-||+.+-|.. +...|.|+| +|---+-|.
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---------tp~~v~lS~fdpvRReiAr 282 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD---------TPEVVVLSGFDPIRREIAR 282 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC---------CCCeEEEeCCChHHHHHHH
Confidence 3445578888 67799999999999999999999999964 344577888 554444443
No 76
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.35 E-value=0.062 Score=59.27 Aligned_cols=56 Identities=23% Similarity=0.256 Sum_probs=42.4
Q ss_pred EEEEEEecC-CeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEe-ehHHHHHHH
Q 006943 389 VTIRLLVSS-KVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG-EVGSVRDAL 453 (624)
Q Consensus 389 ~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~ 453 (624)
+.-.+.+|+ .+-|+|||+.|.+||-++..||+.+-|.. +...|.|+| +|---+-|.
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd---------tp~~v~ls~fdp~rreia~ 261 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---------TPEAVILSGFDPVRREIAR 261 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC---------CCCeEEecCCchHHHHHHH
Confidence 444578887 57799999999999999999999999964 344577887 454334443
No 77
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.35 E-value=0.035 Score=58.08 Aligned_cols=94 Identities=22% Similarity=0.332 Sum_probs=64.9
Q ss_pred cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943 46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN 124 (624)
Q Consensus 46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~ 124 (624)
+-+|+.||++|.+|+.|.++. |=+|.|-+-.. + ..+.+..
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~--------------d-------------------------~~~fi~n 285 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSE--------------D-------------------------PAEFVAN 285 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCC--------------C-------------------------HHHHHHH
Confidence 458999999999999999998 78888743210 0 0011122
Q ss_pred hhhccC-CCc-ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccC
Q 006943 125 AVANAT-DND-KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK 178 (624)
Q Consensus 125 ~~~~~~-~~~-~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~ 178 (624)
++.... ..- -...+...+.+.||..+.+..|||+|.+++--..-||.+|.|...
T Consensus 286 al~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 286 ALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred hCCCceEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 221110 000 000123467899999999999999999999999999999999864
No 78
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.33 E-value=0.027 Score=59.50 Aligned_cols=93 Identities=28% Similarity=0.387 Sum_probs=63.6
Q ss_pred cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943 46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN 124 (624)
Q Consensus 46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~ 124 (624)
+-+|+.||++|.+|+.|.++. |=+|.|-.-.. + ....|..
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~--------------D-------------------------p~~fI~N 317 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSP--------------D-------------------------PATYIAN 317 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCC--------------C-------------------------HHHHHHH
Confidence 558999999999999999998 78888743210 0 0011111
Q ss_pred hhhccC-CCc-ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943 125 AVANAT-DND-KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP 177 (624)
Q Consensus 125 ~~~~~~-~~~-~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~ 177 (624)
++.... ..- ....+.....+.||..+.+..|||+|.+++--..-||.+|.|..
T Consensus 318 aLsPA~V~~V~i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 318 ALSPARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred hcCCceeeEEEEEcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 111110 000 00011235679999999999999999999999999999998864
No 79
>PRK02821 hypothetical protein; Provisional
Probab=95.32 E-value=0.032 Score=44.39 Aligned_cols=53 Identities=15% Similarity=0.322 Sum_probs=36.5
Q ss_pred HHHHHHHHhhhccCCCc----ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhc
Q 006943 117 KVHAAIANAVANATDND----KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKT 169 (624)
Q Consensus 117 ~v~~~i~~~~~~~~~~~----~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~s 169 (624)
.+++.++..+-..++.- ....+.+.+.|.+...-+|.||||+|.+|+.|+.--
T Consensus 4 ~lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 4 DAVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred HHHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 34455555554433211 123345778899999999999999999999998743
No 80
>PRK12704 phosphodiesterase; Provisional
Probab=95.31 E-value=0.063 Score=59.27 Aligned_cols=56 Identities=23% Similarity=0.249 Sum_probs=42.7
Q ss_pred EEEEEEecC-CeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEe-ehHHHHHHH
Q 006943 389 VTIRLLVSS-KVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG-EVGSVRDAL 453 (624)
Q Consensus 389 ~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~ 453 (624)
+.-.+.+|+ .+-|+|||+.|.+||-++.-||+.|-|.. +...|.|+| ++-.-+.|.
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd---------tp~~v~ls~~~~~rre~a~ 267 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---------TPEAVILSGFDPIRREIAR 267 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC---------CCCeEEEecCChhhHHHHH
Confidence 334577887 67799999999999999999999999964 345677898 454433443
No 81
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.31 E-value=0.011 Score=61.38 Aligned_cols=94 Identities=17% Similarity=0.207 Sum_probs=65.0
Q ss_pred CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--HhhccCCCCCCcEEEEE
Q 006943 317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQTKINDEDDDTVTIRL 393 (624)
Q Consensus 317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~~~~~~~~~~~~~~l 393 (624)
+-+|..||++|++|+.|.++. |=+|.|-.-.. +....+..++.- +..-..+ ++.....+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~----------------D~~~fI~Nal~Pa~V~~V~i~--~~~~~~~V 312 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSN----------------VPEIFIARALAPAIISSVKIE--EEEKKAIV 312 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhCCCceeeEEEEc--CCCcEEEE
Confidence 567999999999999999999 77777632111 111112222210 0010001 22346788
Q ss_pred EecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCC
Q 006943 394 LVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGD 428 (624)
Q Consensus 394 ~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~ 428 (624)
.||..+.+..|||+|.+++-..+-||.+|.|..-.
T Consensus 313 ~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 313 TLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred EEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 99999999999999999999999999999997543
No 82
>PRK00468 hypothetical protein; Provisional
Probab=95.30 E-value=0.029 Score=44.49 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=28.6
Q ss_pred CCCceeEEEEEeccceeEEEeCCchHHHHHHH
Q 006943 136 RKEKEECQILVPSSQSANIIGKAGATIKRLRS 167 (624)
Q Consensus 136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~ 167 (624)
..+.+.++|.+..+-+|.||||+|.+|+.|+.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 34568889999999999999999999999986
No 83
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.28 E-value=0.055 Score=56.61 Aligned_cols=92 Identities=21% Similarity=0.344 Sum_probs=64.5
Q ss_pred CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--Hhh-ccCCCCCCcEEEE
Q 006943 317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQT-KINDEDDDTVTIR 392 (624)
Q Consensus 317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~-~~~~~~~~~~~~~ 392 (624)
+-+|..||++|.+|+.|.++. |=+|.|-.-.. +....+..++.- +.. .+.+ +......
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~----------------d~~~fi~nal~Pa~v~~v~i~~--~~~~~~~ 306 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSE----------------DPAEFVANALSPAKVVSVEVDD--EEEKAAR 306 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhCCCceEEEEEEEc--CCCcEEE
Confidence 568999999999999999999 77777632111 111112222220 111 0111 2234678
Q ss_pred EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943 393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISK 426 (624)
Q Consensus 393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~ 426 (624)
+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 307 v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 307 VVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred EEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 9999999999999999999999999999999865
No 84
>PRK00468 hypothetical protein; Provisional
Probab=95.22 E-value=0.021 Score=45.22 Aligned_cols=34 Identities=35% Similarity=0.581 Sum_probs=30.4
Q ss_pred CCceEEEEEEecCcccceeccCCchHHHHHHHhc
Q 006943 33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQET 66 (624)
Q Consensus 33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~et 66 (624)
.+..+.+++.|...-.|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 4456899999999999999999999999999764
No 85
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.10 E-value=0.039 Score=51.33 Aligned_cols=39 Identities=36% Similarity=0.594 Sum_probs=33.2
Q ss_pred cEEEEEec------cccccceeccCCchHHHHHHHhCCEEEEeCC
Q 006943 554 LTLEVLVP------ANAVGKVIGKAGSNLANIRKISGATIEMSDS 592 (624)
Q Consensus 554 ~~~~i~VP------~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~ 592 (624)
++-++.|| .++||.+||..|.+++++++.|+|+|.|-..
T Consensus 148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 34556665 4789999999999999999999999999755
No 86
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.99 E-value=0.052 Score=57.37 Aligned_cols=92 Identities=22% Similarity=0.335 Sum_probs=63.8
Q ss_pred CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHH--HHhhc-cCCCCCCcEEEE
Q 006943 317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVL--LLQTK-INDEDDDTVTIR 392 (624)
Q Consensus 317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~--~~~~~-~~~~~~~~~~~~ 392 (624)
+-+|..||++|..|+.|.++. |=+|.|-.-.. ++ ...+..++. .+..- +.+ .......
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~-------------Dp---~~fI~NaLsPA~V~~V~i~~--~~~k~a~ 338 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSP-------------DP---ATYIANALSPARVDEVRLVD--PEGRHAH 338 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCC-------------CH---HHHHHHhcCCceeeEEEEEc--CCCcEEE
Confidence 568999999999999999999 77777632111 11 111222221 11110 111 1224578
Q ss_pred EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943 393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISK 426 (624)
Q Consensus 393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~ 426 (624)
+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 339 V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 339 VLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 9999999999999999999999999999998864
No 87
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.91 E-value=0.04 Score=51.25 Aligned_cols=41 Identities=29% Similarity=0.469 Sum_probs=34.4
Q ss_pred ceeEEEEEe------ccceeEEEeCCchHHHHHHHhcCCeEEEccCC
Q 006943 139 KEECQILVP------SSQSANIIGKAGATIKRLRSKTRTSIKVTPKD 179 (624)
Q Consensus 139 ~~~~~llvp------~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~ 179 (624)
..+-++.|| .+++|.|||+.|.++|+|++.|+|+|-|-...
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 345566666 57899999999999999999999999998753
No 88
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.88 E-value=0.033 Score=60.43 Aligned_cols=92 Identities=24% Similarity=0.378 Sum_probs=63.9
Q ss_pred CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHH--HHhhccCCCCCCcEEEEE
Q 006943 317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVL--LLQTKINDEDDDTVTIRL 393 (624)
Q Consensus 317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~--~~~~~~~~~~~~~~~~~l 393 (624)
+-+|..||++|++|+.|.++. |=+|.|-.-.. ++ ...+..++. .+...+.+.. .-.+.+
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~-------------d~---~~fi~nal~pa~v~~v~~~~~--~~~~~v 306 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSD-------------DP---AQFIINALSPAEVSSVVVDED--EHSADV 306 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCC-------------CH---HHHHHHhCCCCEEEEEEEeCC--CCEEEE
Confidence 467999999999999999999 77777632111 11 111222221 0111111111 236789
Q ss_pred EecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943 394 LVSSKVIGCIIGKSGSIINEIRKRTKADVRISK 426 (624)
Q Consensus 394 ~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~ 426 (624)
.||..+.+..|||+|.+++-..+-||.+|.|..
T Consensus 307 ~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 307 VVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 999999999999999999999999999999965
No 89
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.84 E-value=0.049 Score=53.83 Aligned_cols=63 Identities=25% Similarity=0.324 Sum_probs=53.3
Q ss_pred EEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCH-HHHHHHHHHHHHHHhhcC
Q 006943 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGES-EAVKKALFAISAIMYKFS 219 (624)
Q Consensus 143 ~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~-~~V~~A~~~I~~~l~~~~ 219 (624)
.+.||..+++.|||++|..|+.|.++++++|.+-. +-.|.|.+.. +++.+|..+|..+-++..
T Consensus 148 ~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~--------------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 148 IVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ--------------NGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred EEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC--------------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 58899999999999999999999999999998843 4568899984 588899998887765543
No 90
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.72 E-value=0.065 Score=58.14 Aligned_cols=94 Identities=21% Similarity=0.327 Sum_probs=64.5
Q ss_pred cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943 46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN 124 (624)
Q Consensus 46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~ 124 (624)
+-+|+.||++|++|+.|.++. |=+|.|-.-. ++ ....+..
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s--------------~d-------------------------~~~fi~n 285 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS--------------DD-------------------------PAQFIIN 285 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC--------------CC-------------------------HHHHHHH
Confidence 348999999999999999998 7888874321 00 0011222
Q ss_pred hhhccC-CCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccC
Q 006943 125 AVANAT-DNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK 178 (624)
Q Consensus 125 ~~~~~~-~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~ 178 (624)
++.... ..-.-......+.+.||..+.+.-|||+|.+++-..+-||.+|.|...
T Consensus 286 al~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 286 ALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred hCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 222110 000000112367789999999999999999999999999999999763
No 91
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.67 E-value=0.065 Score=42.31 Aligned_cols=31 Identities=26% Similarity=0.495 Sum_probs=28.7
Q ss_pred CCceeEEEEEeccceeEEEeCCchHHHHHHH
Q 006943 137 KEKEECQILVPSSQSANIIGKAGATIKRLRS 167 (624)
Q Consensus 137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~ 167 (624)
.....++|.++..-+|.+|||+|.+|+.|+.
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHH
Confidence 5678899999999999999999999999986
No 92
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.43 E-value=0.044 Score=43.24 Aligned_cols=34 Identities=32% Similarity=0.511 Sum_probs=30.8
Q ss_pred CCceEEEEEEecCcccceeccCCchHHHHHHHhc
Q 006943 33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQET 66 (624)
Q Consensus 33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~et 66 (624)
.+..+.+++-+.+...|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 3678999999999999999999999999999763
No 93
>PRK01064 hypothetical protein; Provisional
Probab=94.35 E-value=0.092 Score=41.92 Aligned_cols=32 Identities=31% Similarity=0.442 Sum_probs=28.8
Q ss_pred CCceeEEEEEeccceeEEEeCCchHHHHHHHh
Q 006943 137 KEKEECQILVPSSQSANIIGKAGATIKRLRSK 168 (624)
Q Consensus 137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~ 168 (624)
.+.+.+++.+...-.|.+|||+|.+|+.|+.-
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 45688899999999999999999999999874
No 94
>PRK12705 hypothetical protein; Provisional
Probab=94.24 E-value=0.054 Score=59.07 Aligned_cols=64 Identities=22% Similarity=0.499 Sum_probs=50.2
Q ss_pred cEEEEEeccccc-cceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943 554 LTLEVLVPANAV-GKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM 622 (624)
Q Consensus 554 ~~~~i~VP~~~v-g~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~ 622 (624)
+...|.+|++-. |+||||.|.||+.+...||+.|.|++.+ ..|+|++ .|.--+.|..-+..+|.
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhcccCccchHHHHHHHHHHHh
Confidence 466788888555 9999999999999999999999999764 3367777 56666777766666653
No 95
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.00 E-value=1 Score=43.65 Aligned_cols=126 Identities=14% Similarity=0.156 Sum_probs=82.2
Q ss_pred EEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCCCcEE
Q 006943 311 RVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVT 390 (624)
Q Consensus 311 ~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~ 390 (624)
.+.++....-.+...+|..++.|....||+|.+... +..|.|+|++ .++..+...+..+...+ .+
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k---~~~~~i~~~i~~~l~~i-------~~ 93 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTK---STAEYIEASINEILSNI-------RT 93 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccH---HHHHHHHHHHHHHHhhc-------EE
Confidence 445567888899999999999998889999999753 3479999973 33333444444444333 44
Q ss_pred EEEEecCCeeeEEE-c---CCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEE-----eehHHHHHHHHHHHHHH
Q 006943 391 IRLLVSSKVIGCII-G---KSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVV-----GEVGSVRDALVQIILRL 460 (624)
Q Consensus 391 ~~l~vp~~~~g~iI-G---k~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~l 460 (624)
.++.++.-..-.-. + .....++.|++.|++.|...++. ..+.|. -....+..|...+...+
T Consensus 94 ~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~---------~~~~i~~~~~~~~~~~~~~a~RlL~~a~ 163 (210)
T PF14611_consen 94 EEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG---------NKLKISWLASPENEKRADRAKRLLLWAL 163 (210)
T ss_pred EEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC---------CeEEEEEEeeccccchHHHHHHHHHHhc
Confidence 55555532211111 1 13557999999999999987532 224444 35677778877766555
No 96
>PRK01064 hypothetical protein; Provisional
Probab=94.00 E-value=0.062 Score=42.87 Aligned_cols=34 Identities=32% Similarity=0.617 Sum_probs=30.4
Q ss_pred CCceEEEEEEecCcccceeccCCchHHHHHHHhc
Q 006943 33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQET 66 (624)
Q Consensus 33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~et 66 (624)
.+..+.+++.|.+...|.+|||+|.+|+.||.-.
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 3567999999999999999999999999999753
No 97
>PRK12705 hypothetical protein; Provisional
Probab=91.90 E-value=0.33 Score=53.10 Aligned_cols=38 Identities=26% Similarity=0.335 Sum_probs=32.0
Q ss_pred EEEEEEecC-CeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943 389 VTIRLLVSS-KVIGCIIGKSGSIINEIRKRTKADVRISK 426 (624)
Q Consensus 389 ~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~ 426 (624)
+.-.+.+|+ .+-|+|||+.|.+||.++..||+.+-|..
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 334467776 56799999999999999999999999975
No 98
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=91.39 E-value=1.1 Score=47.83 Aligned_cols=103 Identities=15% Similarity=0.159 Sum_probs=69.3
Q ss_pred EEEecCCccceeeccCcchHHHHHhHh----CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCC
Q 006943 311 RVLCPFNKIGRVIGKGGGTIKSIRQAS----GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDD 386 (624)
Q Consensus 311 ~i~vp~~~vg~IIGk~G~~Ik~I~~~t----ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~ 386 (624)
-+.+|.+..+.|+|++......+++.. ...|.|... ..++.++.+... .+.++...-+--..
T Consensus 500 ~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~~----~~sI~~v~~~~~----------~I~rv~kne~v~~~ 565 (657)
T COG5166 500 LIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCPQ----STSIFTVDIYSD----------EIERVIKNETVLLE 565 (657)
T ss_pred EEECCccCccchhcccccHHHHHhhhcccccccceEEcCC----ceEEEEEccccc----------HHHHHhhccceEEe
Confidence 366999999999999999999998665 345666432 456888887532 22222211111123
Q ss_pred CcEEEEEEecCCeeeEEEc---CCCchHHHHHHhcCceEEEeCC
Q 006943 387 DTVTIRLLVSSKVIGCIIG---KSGSIINEIRKRTKADVRISKG 427 (624)
Q Consensus 387 ~~~~~~l~vp~~~~g~iIG---k~G~~Ik~I~~~tga~I~i~~~ 427 (624)
-++...+.+|...|+..+| -.|++|..+..-..-.|.+...
T Consensus 566 ~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~~t 609 (657)
T COG5166 566 FPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFSTT 609 (657)
T ss_pred cccccccccchhhhhccCCcccccccchhhhhhhhhccceeecC
Confidence 3456678889999999999 6788888877776666666543
No 99
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=90.96 E-value=0.42 Score=51.41 Aligned_cols=65 Identities=22% Similarity=0.200 Sum_probs=53.0
Q ss_pred CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecC-HHHHHHHHHHHHHHHh
Q 006943 138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE-SEAVKKALFAISAIMY 216 (624)
Q Consensus 138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~ 216 (624)
..+...|.|+.+....+||++|...|+|+.+||+.-.+ ++..+.|-.+ ..+.++|+..|..++.
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------------De~t~~i~A~~~~am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------------DEGTFSIFAPTQAAMEEAKEFIDGIIK 659 (760)
T ss_pred CceeeEEeecchhhheeecCccceeeeEeeeccceeee---------------cCceEEEEecCHHHHHHHHHHHHHHhc
Confidence 45667789999999999999999999999999955444 3566777776 5667899999988875
Q ss_pred h
Q 006943 217 K 217 (624)
Q Consensus 217 ~ 217 (624)
+
T Consensus 660 ~ 660 (760)
T KOG1067|consen 660 D 660 (760)
T ss_pred C
Confidence 4
No 100
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=90.65 E-value=0.12 Score=47.87 Aligned_cols=54 Identities=26% Similarity=0.451 Sum_probs=49.4
Q ss_pred cccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943 562 ANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM 622 (624)
Q Consensus 562 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~ 622 (624)
+..+|+|+||+|.+--.|.+.|.++|-+.+. .|-|-|+.+.+..|+.-|+.+|+
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~-------kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS-------KIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecCc-------eEEEeecchhhHHHHHhhHhhhc
Confidence 5678999999999999999999999999864 49999999999999999999886
No 101
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=90.60 E-value=0.39 Score=46.97 Aligned_cols=53 Identities=26% Similarity=0.275 Sum_probs=47.0
Q ss_pred eEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcC
Q 006943 152 ANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFS 219 (624)
Q Consensus 152 g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~ 219 (624)
-+|||++|.+++.|+--|.|.|-|.. .+|.+.|...++..+...+.++++...
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG---------------~TVsaiGpfkGlkevr~IV~DcM~NiH 213 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG---------------NTVSAIGPFKGLKEVRKIVEDCMKNIH 213 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC---------------cEEEeecCcchHHHHHHHHHHHHhccc
Confidence 46999999999999999999998875 458999999999999999999997543
No 102
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=89.92 E-value=0.62 Score=50.15 Aligned_cols=67 Identities=19% Similarity=0.206 Sum_probs=52.6
Q ss_pred CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEe-ehHHHHHHHHHHHHHHhh
Q 006943 385 DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG-EVGSVRDALVQIILRLRD 462 (624)
Q Consensus 385 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~e 462 (624)
...++...|.|+.+....+||.+|...|+|+.+||+.-++. +..+.|.- ++.+.++|...|...+..
T Consensus 593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------EGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred ccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 45678899999999999999999999999999999644443 44566666 677788898777655543
No 103
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=89.90 E-value=0.13 Score=40.60 Aligned_cols=34 Identities=18% Similarity=0.374 Sum_probs=28.8
Q ss_pred CCceeEEEEEeccceeEEEeCCchHHHHHHHhcC
Q 006943 137 KEKEECQILVPSSQSANIIGKAGATIKRLRSKTR 170 (624)
Q Consensus 137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sg 170 (624)
.+...+.+-+.....|.||||+|.+++.|+--.+
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 3456778889999999999999999999987544
No 104
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=88.53 E-value=0.24 Score=39.13 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=28.0
Q ss_pred ceEEEEEEecCcccceeccCCchHHHHHHHhcC
Q 006943 35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETR 67 (624)
Q Consensus 35 ~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg 67 (624)
+...+.+-|..+..|.||||+|.+++.||.-.+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 345677888999999999999999999997654
No 105
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.18 E-value=0.59 Score=36.46 Aligned_cols=38 Identities=32% Similarity=0.484 Sum_probs=30.4
Q ss_pred EEEEEecccc-----ccceeccCCchHHHHHHHh-CCEEEEeCC
Q 006943 555 TLEVLVPANA-----VGKVIGKAGSNLANIRKIS-GATIEMSDS 592 (624)
Q Consensus 555 ~~~i~VP~~~-----vg~IIGkgG~~I~~I~~~s-Ga~I~i~~~ 592 (624)
...+.|-... +|..||++|.+|+.|+++. |-+|.|-.-
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 5667777777 8999999999999999999 899987654
No 106
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.07 E-value=1.4 Score=46.78 Aligned_cols=40 Identities=30% Similarity=0.496 Sum_probs=36.3
Q ss_pred eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCC
Q 006943 140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKD 179 (624)
Q Consensus 140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~ 179 (624)
-...+.||..+++.+|||+|.+|++|+++.|-+|.|.+.+
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 3467899999999999999999999999999999998754
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=86.95 E-value=0.84 Score=34.94 Aligned_cols=34 Identities=26% Similarity=0.404 Sum_probs=27.0
Q ss_pred EEEEEEecCcccceeccCCchHHHHHHHhcCCeE
Q 006943 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARV 70 (624)
Q Consensus 37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I 70 (624)
....+.+.....|.+|||+|.+++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666665789999999999999999987443
No 108
>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=86.93 E-value=1 Score=34.45 Aligned_cols=33 Identities=27% Similarity=0.491 Sum_probs=27.2
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEE
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATI 587 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I 587 (624)
...+.+.....|.+||++|++|+.|+..++-.+
T Consensus 26 ~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 26 EIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 556666665689999999999999999998554
No 109
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=86.65 E-value=0.54 Score=49.69 Aligned_cols=39 Identities=33% Similarity=0.483 Sum_probs=36.4
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK 593 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~ 593 (624)
...+.||+.+++.||||+|.+|++|.+..|-+|.|....
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 678999999999999999999999999999999998664
No 110
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.65 E-value=0.58 Score=36.49 Aligned_cols=35 Identities=31% Similarity=0.630 Sum_probs=27.3
Q ss_pred EEEecCcc-----cceeccCCchHHHHHHHhc-CCeEEeeC
Q 006943 40 RILCPDGV-----IGSVIGKSGKVINSIRQET-RARVKVVD 74 (624)
Q Consensus 40 ~ilvp~~~-----~g~vIGk~G~~I~~i~~et-g~~I~v~~ 74 (624)
.+.+-+.. +|..||++|+.|+.|.++. |-+|.|-+
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 45555555 8999999999999999999 88988743
No 111
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=84.45 E-value=2.4 Score=41.18 Aligned_cols=48 Identities=31% Similarity=0.486 Sum_probs=40.7
Q ss_pred EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHH
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPE 608 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e 608 (624)
-+-+.|+...|.++||++|++++.|.+.++|+|-+.... + |-|.|..+
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG-----~-IWV~~~~~ 194 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG-----R-IWVDGENE 194 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC-----E-EEecCCCc
Confidence 357899999999999999999999999999999998652 3 66666555
No 112
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=84.40 E-value=0.59 Score=37.37 Aligned_cols=34 Identities=35% Similarity=0.462 Sum_probs=28.8
Q ss_pred EEEEEecCcccceeccCCchHHHHHHHhcCCeEE
Q 006943 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVK 71 (624)
Q Consensus 38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~ 71 (624)
...+.+.....|.|||++|++|++|+++.+-.+.
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 4577888999999999999999999988765553
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=84.15 E-value=1 Score=36.39 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=30.4
Q ss_pred EEEEecCcccceeccCCchHHHHHHHhcCCeEEee
Q 006943 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV 73 (624)
Q Consensus 39 ~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~ 73 (624)
+++.+.....|.|||++|++|++|+++-.-...+.
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 78889999999999999999999999876666553
No 114
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=83.73 E-value=2.3 Score=41.38 Aligned_cols=59 Identities=31% Similarity=0.455 Sum_probs=46.9
Q ss_pred EEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHH-HHHHHHHHHHHH
Q 006943 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEA-VKKALFAISAIM 215 (624)
Q Consensus 143 ~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~-V~~A~~~I~~~l 215 (624)
-+.|++..+.++||++|+.++-|.+.++|+|-|-.+ ..|-|.|+.+. ...|..+|..+=
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N--------------G~IWV~~~~~~~e~~~~~aI~~ie 208 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN--------------GRIWVDGENESLEELAIEAIRKIE 208 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC--------------CEEEecCCCcchHHHHHHHHHHHh
Confidence 478999999999999999999999999999988653 45778888763 555665555443
No 115
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=83.43 E-value=2.1 Score=42.05 Aligned_cols=51 Identities=14% Similarity=0.272 Sum_probs=46.7
Q ss_pred cceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943 566 GKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA 623 (624)
Q Consensus 566 g~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~ 623 (624)
-++||.+|.+++.|+-.|.|-|-|.. .+|.+.|....++.++..+.+++.+
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 58999999999999999999999984 3489999999999999999999876
No 116
>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=83.23 E-value=1.2 Score=35.59 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=26.9
Q ss_pred eEEEEEeccceeEEEeCCchHHHHHHHhcCCeE
Q 006943 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSI 173 (624)
Q Consensus 141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I 173 (624)
.+.+-+.....|.||||.|++++.||--...-+
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 456777888999999999999999987655443
No 117
>PRK13764 ATPase; Provisional
Probab=83.23 E-value=1.1 Score=50.21 Aligned_cols=41 Identities=32% Similarity=0.455 Sum_probs=37.7
Q ss_pred CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC
Q 006943 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK 593 (624)
Q Consensus 553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~ 593 (624)
.....|.||+..++.+|||+|.+|++|.+..|.+|.|....
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 45788999999999999999999999999999999998654
No 118
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=82.58 E-value=0.69 Score=43.04 Aligned_cols=56 Identities=27% Similarity=0.312 Sum_probs=49.2
Q ss_pred eccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943 147 PSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK 217 (624)
Q Consensus 147 p~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~ 217 (624)
-+..+|+|+||+|.+--.|++-|-++|.+. +-.|.|-|..+++.-|...|+.+|--
T Consensus 176 lsRAIGRiaGk~GkTkfaIEn~trtrIVla---------------d~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 176 LSRAIGRIAGKGGKTKFAIENVTRTRIVLA---------------DSKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHHhhcCCCcceeeeeccceeEEEec---------------CceEEEeecchhhHHHHHhhHhhhcc
Confidence 356789999999999999999999999875 34589999999999999999999843
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=81.51 E-value=0.97 Score=36.13 Aligned_cols=34 Identities=32% Similarity=0.474 Sum_probs=29.0
Q ss_pred cEEEEEeccccccceeccCCchHHHHHHHhCCEE
Q 006943 554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATI 587 (624)
Q Consensus 554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I 587 (624)
....+.+-...-|.|||++|++|++|++..+-.+
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 3678888999999999999999999988775544
No 120
>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=81.33 E-value=9 Score=34.36 Aligned_cols=38 Identities=21% Similarity=0.447 Sum_probs=33.1
Q ss_pred eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943 140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP 177 (624)
Q Consensus 140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~ 177 (624)
.+-.+.|-...-|.+||++|.++++|..+||-+-.|..
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 34567777888899999999999999999999988875
No 121
>PRK13764 ATPase; Provisional
Probab=81.24 E-value=3.7 Score=46.14 Aligned_cols=41 Identities=32% Similarity=0.582 Sum_probs=37.0
Q ss_pred ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCC
Q 006943 139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKD 179 (624)
Q Consensus 139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~ 179 (624)
.-...+.||...++.+|||+|.+|++|+++.|.+|.|.+.+
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 34567899999999999999999999999999999998754
No 122
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.65 E-value=1.8 Score=34.51 Aligned_cols=34 Identities=24% Similarity=0.406 Sum_probs=27.3
Q ss_pred EEEEEecCCccceeeccCcchHHHHHhHhCCeEE
Q 006943 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQID 342 (624)
Q Consensus 309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~ 342 (624)
.+.+.+..+..|.+|||+|+++..|+--.+.-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 4556677888999999999999999977665444
No 123
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.93 E-value=3.6 Score=36.83 Aligned_cols=93 Identities=22% Similarity=0.314 Sum_probs=56.5
Q ss_pred eccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecCCeeeE
Q 006943 323 IGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGC 402 (624)
Q Consensus 323 IGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~g~ 402 (624)
+=.+|..|++|-++..-+|.|-.... +.-+ .++|...+.+++-. ...+.+-.=+..+-++.|-...-|.
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dps--------~l~~--~e~A~~~I~~ivP~-ea~i~di~Fd~~tGEV~IeaeKPG~ 89 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDPS--------VLKP--PEEAIKIILEIVPE-EAGITDIYFDDDTGEVIIEAEKPGL 89 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCChh--------hcCC--HHHHHHHHHHhCCC-ccCceeeEecCCCcEEEEEEcCCeE
Confidence 33567889999999988888843211 1111 23343333332200 0011110112234556677788899
Q ss_pred EEcCCCchHHHHHHhcCceEEEeC
Q 006943 403 IIGKSGSIINEIRKRTKADVRISK 426 (624)
Q Consensus 403 iIGk~G~~Ik~I~~~tga~I~i~~ 426 (624)
+||++|.++++|..+||-.-.+.+
T Consensus 90 ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 90 VIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EEecCchhHHHHHHHhCCeeEEEe
Confidence 999999999999999999887765
No 124
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.71 E-value=2.6 Score=38.97 Aligned_cols=36 Identities=28% Similarity=0.519 Sum_probs=30.6
Q ss_pred EEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeC
Q 006943 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD 74 (624)
Q Consensus 38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~ 74 (624)
.+-++|.... |.-|||+|++|++|++..|-+|.|-+
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 3446676677 99999999999999999999998855
No 125
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=77.91 E-value=0.65 Score=53.92 Aligned_cols=66 Identities=24% Similarity=0.151 Sum_probs=53.7
Q ss_pred EEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHH
Q 006943 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIIL 458 (624)
Q Consensus 390 ~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 458 (624)
..++.+|-....+|||++|++|+.++..|||.|++.+-. |. ...||.+.+.|.++.+..|...|..
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq-~~--Nqaers~~~kg~p~~~r~a~~~I~~ 1406 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ-PD--NQAERSKAPKGRPPSQRVATSPIGL 1406 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC-Cc--cchhhhcccCCCChhhhhhhccccc
Confidence 345778888899999999999999999999999997622 11 1458899999999999999765543
No 126
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=77.49 E-value=1.8 Score=46.16 Aligned_cols=127 Identities=13% Similarity=0.063 Sum_probs=76.4
Q ss_pred ceeeccCcchHHHHHhHhCCeEEEc--CCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecC
Q 006943 320 GRVIGKGGGTIKSIRQASGAQIDVD--DTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSS 397 (624)
Q Consensus 320 g~IIGk~G~~Ik~I~~~tga~I~v~--~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~ 397 (624)
-++-||+.-.+.+|++...|.+.+. ... + .++.+...-+.. + -++++..+. .+=+-.+.+.+|.
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~-g--s~~~~~~~g~~~--~---F~k~~~~~~------~EFpae~~f~i~e 457 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSST-G--SIVETNGIGEKM--S---FSKKLSIPP------TEFPAEIAFIIME 457 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEecC-C--cEEEEeccCcch--h---hHHHhcCCc------ccCchheEEEeec
Confidence 4788888888999999999985543 322 2 233333221111 1 123332221 1223456799999
Q ss_pred CeeeEEEcCCCchHHHHHHhcCceEEEeCCC-CCCCCCCCCcEEEEEeeh---HHHHHHHHHHHHHHhh
Q 006943 398 KVIGCIIGKSGSIINEIRKRTKADVRISKGD-KPKCADANDELVEVVGEV---GSVRDALVQIILRLRD 462 (624)
Q Consensus 398 ~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~-~p~~~~~~~~~v~I~G~~---~~v~~A~~~I~~~l~e 462 (624)
..|..|||-||..|++++.+.++.|++.... .|.. .-..-|.|.-+. +++.-++--+++++.+
T Consensus 458 ~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs--~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 458 SGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQS--QWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred ccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchh--hhhcceEEECCccCccchhcccccHHHHHhh
Confidence 9999999999999999999999999986432 2221 111124466543 3344444445555554
No 127
>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=76.12 E-value=2.4 Score=36.45 Aligned_cols=30 Identities=27% Similarity=0.411 Sum_probs=26.1
Q ss_pred EEEEecCcccceeccCCchHHHHHHHhcCC
Q 006943 39 YRILCPDGVIGSVIGKSGKVINSIRQETRA 68 (624)
Q Consensus 39 ~~ilvp~~~~g~vIGk~G~~I~~i~~etg~ 68 (624)
+++.+.....|.|||++|++|++|++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 678888889999999999999999987543
No 128
>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=75.12 E-value=2.7 Score=34.24 Aligned_cols=28 Identities=29% Similarity=0.324 Sum_probs=23.8
Q ss_pred EEEEecCcccceeccCCchHHHHHHHhc
Q 006943 39 YRILCPDGVIGSVIGKSGKVINSIRQET 66 (624)
Q Consensus 39 ~~ilvp~~~~g~vIGk~G~~I~~i~~et 66 (624)
+++.+.....|.+||++|.+|++|++..
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 5566666889999999999999999875
No 129
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=73.66 E-value=2.5 Score=40.92 Aligned_cols=31 Identities=32% Similarity=0.376 Sum_probs=26.8
Q ss_pred EEEEEEecCcccceeccCCchHHHHHHHhcC
Q 006943 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETR 67 (624)
Q Consensus 37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg 67 (624)
...++.|....-|.||||+|++|++|+++..
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 3467888899999999999999999998754
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=73.18 E-value=4.2 Score=32.80 Aligned_cols=35 Identities=20% Similarity=0.508 Sum_probs=28.8
Q ss_pred eEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEE
Q 006943 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKV 175 (624)
Q Consensus 141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i 175 (624)
.+++.|....-|.|||++|+.|++|++.-.-...+
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 47788999999999999999999999875544433
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=72.51 E-value=7.1 Score=42.04 Aligned_cols=96 Identities=15% Similarity=0.290 Sum_probs=63.1
Q ss_pred ceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHHhhhc
Q 006943 49 GSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVAN 128 (624)
Q Consensus 49 g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~~~~~ 128 (624)
...+-+.|+.|++|.++..-||.|-.. +.. +.+..+|...+.+-+-+
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~d--------------Psv---------------l~~~e~A~~~I~eivP~---- 87 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPD--------------PSV---------------LKPPEEARKIILEIVPE---- 87 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccC--------------chh---------------cCCHHHHHHHHHHhCcc----
Confidence 345567889999999999888888432 111 12223455444443321
Q ss_pred cCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943 129 ATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP 177 (624)
Q Consensus 129 ~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~ 177 (624)
...-..-.-+..+..++|-...-|.+|||+|++.++|..+||-.-+|..
T Consensus 88 ea~i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 88 EAGITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred ccCceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 1100111122345678888999999999999999999999998877765
No 132
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=70.13 E-value=5.4 Score=36.84 Aligned_cols=35 Identities=31% Similarity=0.381 Sum_probs=30.7
Q ss_pred EEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943 142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP 177 (624)
Q Consensus 142 ~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~ 177 (624)
+-++|.... |.-|||+|.+++++++..|-+|.+-.
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 456777777 99999999999999999999998865
No 133
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=68.12 E-value=8.9 Score=41.33 Aligned_cols=94 Identities=24% Similarity=0.336 Sum_probs=59.9
Q ss_pred eeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecCCeee
Q 006943 322 VIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIG 401 (624)
Q Consensus 322 IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~g 401 (624)
.+=+.|.-|++|.++..-+|.+..... .... .+.|...+.+++-.- ..+.+-.=+..+-++.|-...-|
T Consensus 43 ~~~~~~dlik~lAk~lrKRI~iR~dPs-------vl~~---~e~A~~~I~eivP~e-a~i~~i~Fd~~tGEViIea~KPG 111 (637)
T COG1782 43 LFAKDGDLIKDLAKDLRKRIIIRPDPS-------VLKP---PEEARKIILEIVPEE-AGITDIYFDDDTGEVIIEAKKPG 111 (637)
T ss_pred HhccchhHHHHHHHHHhhceEeccCch-------hcCC---HHHHHHHHHHhCccc-cCceeEEecCCCceEEEEecCCc
Confidence 455788999999999999988853211 1111 244433333333100 01111111223456778888999
Q ss_pred EEEcCCCchHHHHHHhcCceEEEeC
Q 006943 402 CIIGKSGSIINEIRKRTKADVRISK 426 (624)
Q Consensus 402 ~iIGk~G~~Ik~I~~~tga~I~i~~ 426 (624)
.+|||+|++.++|..+||-.-++.+
T Consensus 112 lvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 112 LVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred eEEecCchHHHHHHHHhCCcceeee
Confidence 9999999999999999998877765
No 134
>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=63.85 E-value=17 Score=41.43 Aligned_cols=95 Identities=22% Similarity=0.261 Sum_probs=59.3
Q ss_pred eeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecCCeee
Q 006943 322 VIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIG 401 (624)
Q Consensus 322 IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~g 401 (624)
.+=.+|..|++|.++..-+|.|..... +.-+ .++|...+.+++-.- ..+.+-.=+..+-++.|-...-|
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~~--------~~~~--~~~~~~~i~~~~~~~-~~~~~~~f~~~~~~v~i~~~~p~ 105 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDPS--------VLLP--PEEAIEKIKEIVPEE-AGITDIYFDDVTGEVIIEAEKPG 105 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecChh--------hcCC--HHHHHHHHHHhCCCc-CCceeEEecCCCceEEEEEcCCe
Confidence 345678999999999988888853211 1111 233333333222100 01111111234456778888899
Q ss_pred EEEcCCCchHHHHHHhcCceEEEeCC
Q 006943 402 CIIGKSGSIINEIRKRTKADVRISKG 427 (624)
Q Consensus 402 ~iIGk~G~~Ik~I~~~tga~I~i~~~ 427 (624)
.+|||+|.++++|..+||-+-++.+.
T Consensus 106 ~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 106 LVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred EEEecCcchHHHHHHHhCCeeeEEec
Confidence 99999999999999999999888653
No 135
>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=61.71 E-value=6.8 Score=33.62 Aligned_cols=30 Identities=30% Similarity=0.573 Sum_probs=25.6
Q ss_pred eEEEEEeccceeEEEeCCchHHHHHHHhcC
Q 006943 141 ECQILVPSSQSANIIGKAGATIKRLRSKTR 170 (624)
Q Consensus 141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sg 170 (624)
.+++.|....-|.|||++|+.|++|++...
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 367888888899999999999999987644
No 136
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=59.80 E-value=9.9 Score=30.93 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=23.8
Q ss_pred EEEEEeccceeEEEeCCchHHHHHHHhc
Q 006943 142 CQILVPSSQSANIIGKAGATIKRLRSKT 169 (624)
Q Consensus 142 ~~llvp~~~~g~iIGk~G~~Ik~I~~~s 169 (624)
+++.|....-|.+||++|..|++|++.-
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 6677777889999999999999988753
No 137
>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=55.07 E-value=40 Score=38.53 Aligned_cols=38 Identities=21% Similarity=0.421 Sum_probs=33.8
Q ss_pred eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943 140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP 177 (624)
Q Consensus 140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~ 177 (624)
.+-.++|-...-|.+|||+|.++++|..+||-+-+|..
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 45567888888899999999999999999999988876
No 138
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=54.78 E-value=17 Score=35.38 Aligned_cols=30 Identities=23% Similarity=0.543 Sum_probs=25.7
Q ss_pred ceeEEEEEeccceeEEEeCCchHHHHHHHh
Q 006943 139 KEECQILVPSSQSANIIGKAGATIKRLRSK 168 (624)
Q Consensus 139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~ 168 (624)
...+++.|....-|.|||++|+.|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 346788999999999999999999988764
No 139
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=51.45 E-value=33 Score=35.49 Aligned_cols=51 Identities=18% Similarity=0.224 Sum_probs=44.4
Q ss_pred ccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 006943 561 PANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQ 618 (624)
Q Consensus 561 P~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~ 618 (624)
+++..-.+.|..|.+++.|.+..|+.|.... +.++|+|+.+.++.|...++
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG-------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG-------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC-------ceEEEEechHHHHHHHHHHh
Confidence 3667789999999999999999999887663 44899999889999999888
No 140
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=48.95 E-value=27 Score=33.38 Aligned_cols=59 Identities=15% Similarity=0.226 Sum_probs=38.7
Q ss_pred hHHHHHHHHHHHHhhccCCC-----CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEE
Q 006943 365 DIKSMAVEAVLLLQTKINDE-----DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVR 423 (624)
Q Consensus 365 ~a~~~~~~~i~~~~~~~~~~-----~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~ 423 (624)
+....+.+-+..+.+.+.-. ....-.+.+.+..+..+.|||+.|.++..||--+.+.+.
T Consensus 62 ~~~~~~~~~L~ell~~m~~~~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 62 KIAQEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred HHHHHHHHHHHHHHHHhCCceEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 34444555555555544321 123345667777788999999999999999887765443
No 141
>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=43.94 E-value=21 Score=34.08 Aligned_cols=31 Identities=19% Similarity=0.327 Sum_probs=26.6
Q ss_pred EEEEEecCcccceeccCCchHHHHHHHhcCC
Q 006943 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRA 68 (624)
Q Consensus 38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~ 68 (624)
..++.+.....|.|||++|..|++|+++-.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 3778888888999999999999999988643
No 142
>CHL00048 rps3 ribosomal protein S3
Probab=43.81 E-value=20 Score=34.73 Aligned_cols=30 Identities=13% Similarity=0.319 Sum_probs=25.6
Q ss_pred EEEEEecCcccceeccCCchHHHHHHHhcC
Q 006943 38 IYRILCPDGVIGSVIGKSGKVINSIRQETR 67 (624)
Q Consensus 38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg 67 (624)
..++.|-....|.|||++|++|++|++...
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 366777788889999999999999998864
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=43.61 E-value=22 Score=35.76 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=24.2
Q ss_pred cEEEEEeccccc-cceeccCCchHHHHHHHh
Q 006943 554 LTLEVLVPANAV-GKVIGKAGSNLANIRKIS 583 (624)
Q Consensus 554 ~~~~i~VP~~~v-g~IIGkgG~~I~~I~~~s 583 (624)
....|.|..+.. +-|||++|+.|++|...+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 467888887766 999999999999776543
No 144
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=43.43 E-value=21 Score=34.52 Aligned_cols=31 Identities=29% Similarity=0.356 Sum_probs=25.7
Q ss_pred EEEEecCcccceeccCCchHHHHHHHhcCCe
Q 006943 39 YRILCPDGVIGSVIGKSGKVINSIRQETRAR 69 (624)
Q Consensus 39 ~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~ 69 (624)
.++.+.....|.+||++|++|++|++...-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 5666666889999999999999999886543
No 145
>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=42.83 E-value=1.7e+02 Score=27.35 Aligned_cols=102 Identities=16% Similarity=0.111 Sum_probs=55.6
Q ss_pred EEEeecCCchhHHHHHHHHHHHHhhccCCC-CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCC
Q 006943 355 ITVTAIESPDDIKSMAVEAVLLLQTKINDE-DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCA 433 (624)
Q Consensus 355 i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~-~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~ 433 (624)
++++|..+.++++..+.+.+..++..-... ....++++-.|-....++ .-.++.|....+-.+...++..|...
T Consensus 58 ivitGaks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v~NIvas~~l~~-----~i~L~~la~~~~~~~~YePe~fpgli 132 (174)
T cd00652 58 MVITGAKSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCDLGF-----PIRLEELALKHPENASYEPELFPGLI 132 (174)
T ss_pred EEEEecCCHHHHHHHHHHHHHHHHHcCCCccccCceEEEEEEEEEECCC-----cccHHHHHhhhhcccEECCccCceEE
Confidence 788887778888777766666554332221 222333333332222221 22577777766544555444322110
Q ss_pred -----------CCCCcEEEEEe--ehHHHHHHHHHHHHHHh
Q 006943 434 -----------DANDELVEVVG--EVGSVRDALVQIILRLR 461 (624)
Q Consensus 434 -----------~~~~~~v~I~G--~~~~v~~A~~~I~~~l~ 461 (624)
--....|.|+| +.+.+.+|...|...|.
T Consensus 133 ~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~L~ 173 (174)
T cd00652 133 YRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILK 173 (174)
T ss_pred EEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 00122367999 56889999888877664
No 146
>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=42.37 E-value=90 Score=25.40 Aligned_cols=51 Identities=20% Similarity=0.188 Sum_probs=41.6
Q ss_pred CCchHHHHHHHhCCEEEEeCCCCC---CCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943 572 AGSNLANIRKISGATIEMSDSKSS---RGDRVALISGTPEQKRAAENLIQAFIM 622 (624)
Q Consensus 572 gG~~I~~I~~~sGa~I~i~~~~~~---~~~r~v~I~Gt~e~v~~A~~lI~~~i~ 622 (624)
|=.-+.+|=+..|++++...++.. ..+.+++|+|+..++..|.+.++.+|.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 445788888888999988866543 467899999999999999999999885
No 147
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=42.32 E-value=22 Score=34.60 Aligned_cols=32 Identities=19% Similarity=0.296 Sum_probs=27.1
Q ss_pred EEEEecCcccceeccCCchHHHHHHHhcCCeE
Q 006943 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARV 70 (624)
Q Consensus 39 ~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I 70 (624)
.++.+.....|.|||++|..|++|+++..-.+
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 67778888899999999999999998865444
No 148
>COG1159 Era GTPase [General function prediction only]
Probab=38.78 E-value=30 Score=35.09 Aligned_cols=37 Identities=22% Similarity=0.463 Sum_probs=27.4
Q ss_pred cEEEEEeccccc-cceeccCCchHHHHHH--------HhCCEEEEe
Q 006943 554 LTLEVLVPANAV-GKVIGKAGSNLANIRK--------ISGATIEMS 590 (624)
Q Consensus 554 ~~~~i~VP~~~v-g~IIGkgG~~I~~I~~--------~sGa~I~i~ 590 (624)
....|.|+.+.. |-||||+|++||+|-. ..+++|.+.
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 466788887666 9999999999997644 456666543
No 149
>PRK15494 era GTPase Era; Provisional
Probab=38.71 E-value=29 Score=36.35 Aligned_cols=37 Identities=19% Similarity=0.413 Sum_probs=28.2
Q ss_pred cEEEEEeccccc-cceeccCCchHHHHH--------HHhCCEEEEe
Q 006943 554 LTLEVLVPANAV-GKVIGKAGSNLANIR--------KISGATIEMS 590 (624)
Q Consensus 554 ~~~~i~VP~~~v-g~IIGkgG~~I~~I~--------~~sGa~I~i~ 590 (624)
....|.|..+.. +-|||++|+.||+|. +..|++|.+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 457888887777 899999999999765 4456666554
No 150
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=38.27 E-value=41 Score=32.18 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=28.7
Q ss_pred eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEE
Q 006943 140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIK 174 (624)
Q Consensus 140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~ 174 (624)
-.+.+-+..+..+.|||+.|++++.||--+.+-++
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 34567777888999999999999999987776554
No 151
>PRK00089 era GTPase Era; Reviewed
Probab=37.63 E-value=31 Score=35.13 Aligned_cols=37 Identities=27% Similarity=0.504 Sum_probs=27.6
Q ss_pred cEEEEEeccccc-cceeccCCchHHHHH--------HHhCCEEEEe
Q 006943 554 LTLEVLVPANAV-GKVIGKAGSNLANIR--------KISGATIEMS 590 (624)
Q Consensus 554 ~~~~i~VP~~~v-g~IIGkgG~~I~~I~--------~~sGa~I~i~ 590 (624)
....|.|..+.. +-|||++|++|++|. +..|++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 467778876666 899999999999765 4556666554
No 152
>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=37.51 E-value=24 Score=35.60 Aligned_cols=29 Identities=38% Similarity=0.394 Sum_probs=21.6
Q ss_pred eeEEEEEe-ccceeEEEeCCchHHHHHHHh
Q 006943 140 EECQILVP-SSQSANIIGKAGATIKRLRSK 168 (624)
Q Consensus 140 ~~~~llvp-~~~~g~iIGk~G~~Ik~I~~~ 168 (624)
+...+.|. .+|-+.||||+|++||+|...
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 34456666 566788999999999987653
No 153
>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=36.85 E-value=2.3e+02 Score=26.54 Aligned_cols=102 Identities=19% Similarity=0.165 Sum_probs=52.4
Q ss_pred EEEeecCCchhHHHHHHHHHHHHhhccCCC-CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCC
Q 006943 355 ITVTAIESPDDIKSMAVEAVLLLQTKINDE-DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCA 433 (624)
Q Consensus 355 i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~-~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~ 433 (624)
+.++|..+.++++..+...+..++..-... ....+++.-.|.....++ .-.+.+|...+.-.+...++..|...
T Consensus 58 iviTGaks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~~~~-----~i~L~~la~~~~~~~~YePE~fPgli 132 (174)
T cd04517 58 ITITGATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCSMPF-----PIRLDELAAKNRSSASYEPELHPGVV 132 (174)
T ss_pred EEEEccCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEeCCC-----cccHHHHHHhchhhcEeCCccCCEEE
Confidence 788887777777766655555444322111 122333333222222221 22467776555444444443322110
Q ss_pred -----------CCCCcEEEEEe--ehHHHHHHHHHHHHHHh
Q 006943 434 -----------DANDELVEVVG--EVGSVRDALVQIILRLR 461 (624)
Q Consensus 434 -----------~~~~~~v~I~G--~~~~v~~A~~~I~~~l~ 461 (624)
--....|.|+| +.+.+.+|+..|...|.
T Consensus 133 yr~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~pil~ 173 (174)
T cd04517 133 YRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPIVF 173 (174)
T ss_pred EEECCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 00122367899 57899999888877664
No 154
>COG1159 Era GTPase [General function prediction only]
Probab=36.62 E-value=22 Score=35.97 Aligned_cols=33 Identities=36% Similarity=0.461 Sum_probs=23.8
Q ss_pred EEEEe-ccceeEEEeCCchHHHHHH--------HhcCCeEEE
Q 006943 143 QILVP-SSQSANIIGKAGATIKRLR--------SKTRTSIKV 175 (624)
Q Consensus 143 ~llvp-~~~~g~iIGk~G~~Ik~I~--------~~sga~I~i 175 (624)
.+.|+ .+|-+.||||+|++||+|- +-.+++|.+
T Consensus 232 ~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 232 TIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 45665 4678899999999998864 445566554
No 155
>PRK00089 era GTPase Era; Reviewed
Probab=34.84 E-value=28 Score=35.38 Aligned_cols=28 Identities=43% Similarity=0.644 Sum_probs=20.5
Q ss_pred eEEEEEe-ccceeEEEeCCchHHHHHHHh
Q 006943 141 ECQILVP-SSQSANIIGKAGATIKRLRSK 168 (624)
Q Consensus 141 ~~~llvp-~~~~g~iIGk~G~~Ik~I~~~ 168 (624)
...|.|. .++.+.||||+|++||+|..+
T Consensus 227 ~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 227 EATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 3345555 566789999999999887553
No 156
>PRK15494 era GTPase Era; Provisional
Probab=31.43 E-value=35 Score=35.69 Aligned_cols=27 Identities=33% Similarity=0.487 Sum_probs=20.3
Q ss_pred eEEEEEec-cceeEEEeCCchHHHHHHH
Q 006943 141 ECQILVPS-SQSANIIGKAGATIKRLRS 167 (624)
Q Consensus 141 ~~~llvp~-~~~g~iIGk~G~~Ik~I~~ 167 (624)
...|.|.. ++-+.||||+|++||+|..
T Consensus 274 ~~~i~v~~~sqk~iiiG~~g~~ik~i~~ 301 (339)
T PRK15494 274 NQVIVVSRESYKTIILGKNGSKIKEIGA 301 (339)
T ss_pred EEEEEECCCCceeEEEcCCcHHHHHHHH
Confidence 34566654 5678899999999998754
No 157
>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=29.59 E-value=4.5e+02 Score=29.65 Aligned_cols=57 Identities=21% Similarity=0.351 Sum_probs=35.6
Q ss_pred EEEEEeccccccceeccCCchHHHHH-H-----HhCCEE-EEeCCCC------C---CCCeEEEEEcCHHHHHHHHHHH
Q 006943 555 TLEVLVPANAVGKVIGKAGSNLANIR-K-----ISGATI-EMSDSKS------S---RGDRVALISGTPEQKRAAENLI 617 (624)
Q Consensus 555 ~~~i~VP~~~vg~IIGkgG~~I~~I~-~-----~sGa~I-~i~~~~~------~---~~~r~v~I~Gt~e~v~~A~~lI 617 (624)
...+.+|+ ..++|| +|++++ + ..|+.| .|.+... + .....+++.|++++++.+.+.+
T Consensus 304 ~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~l 376 (562)
T TIGR03802 304 TKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQL 376 (562)
T ss_pred EEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHc
Confidence 34455554 456666 688886 2 567777 4444321 1 1224699999999999887654
No 158
>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=29.15 E-value=58 Score=31.09 Aligned_cols=29 Identities=21% Similarity=0.481 Sum_probs=24.8
Q ss_pred eEEEEEeccceeEEEeCCchHHHHHHHhc
Q 006943 141 ECQILVPSSQSANIIGKAGATIKRLRSKT 169 (624)
Q Consensus 141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~s 169 (624)
.+++.|....-|.+||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46788888889999999999999887753
No 159
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=29.04 E-value=53 Score=33.55 Aligned_cols=36 Identities=25% Similarity=0.422 Sum_probs=29.3
Q ss_pred CCCceEEEEEEecCc-ccceeccCCchHHHHHHHhcC
Q 006943 32 GNEESVIYRILCPDG-VIGSVIGKSGKVINSIRQETR 67 (624)
Q Consensus 32 ~~~~~~~~~ilvp~~-~~g~vIGk~G~~I~~i~~etg 67 (624)
++.-++..+++||-. ....||||+|..|++|-++.+
T Consensus 323 ~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 323 AGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred CcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 445678889999974 477899999999999987754
No 160
>CHL00048 rps3 ribosomal protein S3
Probab=28.19 E-value=60 Score=31.51 Aligned_cols=29 Identities=17% Similarity=0.266 Sum_probs=24.7
Q ss_pred eEEEEEeccceeEEEeCCchHHHHHHHhc
Q 006943 141 ECQILVPSSQSANIIGKAGATIKRLRSKT 169 (624)
Q Consensus 141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~s 169 (624)
.+++.|....-|.|||++|..|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46778888888999999999999998754
No 161
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=27.96 E-value=51 Score=31.92 Aligned_cols=29 Identities=31% Similarity=0.499 Sum_probs=25.1
Q ss_pred EEEEecCcccceeccCCchHHHHHHHhcC
Q 006943 39 YRILCPDGVIGSVIGKSGKVINSIRQETR 67 (624)
Q Consensus 39 ~~ilvp~~~~g~vIGk~G~~I~~i~~etg 67 (624)
+++.+.....+.|||++|.+|++|++.-.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 66788888889999999999999997753
No 162
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=27.29 E-value=63 Score=31.22 Aligned_cols=29 Identities=21% Similarity=0.425 Sum_probs=24.3
Q ss_pred EEEEEeccceeEEEeCCchHHHHHHHhcC
Q 006943 142 CQILVPSSQSANIIGKAGATIKRLRSKTR 170 (624)
Q Consensus 142 ~~llvp~~~~g~iIGk~G~~Ik~I~~~sg 170 (624)
+.+.|....-|.+||++|++|+++++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 56777778899999999999999887654
No 163
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=26.88 E-value=3.4e+02 Score=28.66 Aligned_cols=57 Identities=14% Similarity=0.106 Sum_probs=39.3
Q ss_pred CchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCc--eEEEecC-HHHHHHHHHHHHHHH
Q 006943 158 AGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN--FVLISGE-SEAVKKALFAISAIM 215 (624)
Q Consensus 158 ~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r--~V~I~G~-~~~V~~A~~~I~~~l 215 (624)
.|.+...|++.+|+.|-....-....+. ...++++ +..|.|. +|=+.+|+..|..++
T Consensus 112 Rg~~~d~Ie~~~G~~~~~RGs~~~~El~-~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~ 171 (531)
T KOG1960|consen 112 RGTSYDHIEGITGTTSASRGSAPAPELP-PVGSSEGPLVDHIPPSTAEITSKAIERIKGVF 171 (531)
T ss_pred cchhHHhhhhhccceeeccCCCCCccCC-CCCCCCCcceeecCCccHHHHHHHHhhCccce
Confidence 5788999999999999876654333222 2445555 5678887 577788888776443
No 164
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=26.85 E-value=62 Score=31.50 Aligned_cols=30 Identities=20% Similarity=0.513 Sum_probs=24.9
Q ss_pred eEEEEEeccceeEEEeCCchHHHHHHHhcC
Q 006943 141 ECQILVPSSQSANIIGKAGATIKRLRSKTR 170 (624)
Q Consensus 141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sg 170 (624)
.+++.|....-|.|||++|..|++|++.-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 367788888889999999999999887543
No 165
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=26.75 E-value=96 Score=32.23 Aligned_cols=53 Identities=19% Similarity=0.164 Sum_probs=44.7
Q ss_pred EEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHH
Q 006943 145 LVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAIS 212 (624)
Q Consensus 145 lvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~ 212 (624)
+-+....-.|.|..+..++.|++..|+.|.... +.++|.|....|..|...+.
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 445677788999999999999999999987543 55899999888988888877
No 166
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=26.42 E-value=58 Score=33.27 Aligned_cols=31 Identities=29% Similarity=0.551 Sum_probs=25.5
Q ss_pred cEEEEEeccccc-cceeccCCchHHHHHHHhC
Q 006943 554 LTLEVLVPANAV-GKVIGKAGSNLANIRKISG 584 (624)
Q Consensus 554 ~~~~i~VP~~~v-g~IIGkgG~~I~~I~~~sG 584 (624)
+..++.||.... -.||||||..|++|-++-+
T Consensus 328 I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 328 IQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 578999998877 5789999999999876543
No 167
>PRK03818 putative transporter; Validated
Probab=25.71 E-value=4.1e+02 Score=29.90 Aligned_cols=66 Identities=17% Similarity=0.320 Sum_probs=36.7
Q ss_pred eeEEEEEeccceeEEEeCCchHHHHH--HHhcCCeEEEccCCCCCC--CCcccccCCceEEEecCHHHHHHHHHH
Q 006943 140 EECQILVPSSQSANIIGKAGATIKRL--RSKTRTSIKVTPKDASEP--THSCAMEFDNFVLISGESEAVKKALFA 210 (624)
Q Consensus 140 ~~~~llvp~~~~g~iIGk~G~~Ik~I--~~~sga~I~i~~~~~~~~--~~~~~~~~~r~V~I~G~~~~V~~A~~~ 210 (624)
...+.+++.+ ..++|| +++++ +++.|+.|.=-.+..... .+.-.-..-.++.+.|+++++++..+.
T Consensus 289 ~~~E~Vvv~~--S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 289 LRSERVVVTN--EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred eEEEEEEEcC--hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECHHHHHHHHHH
Confidence 3344444443 467887 68877 577777754333321110 110111223467899999999987663
No 168
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=25.06 E-value=5.4e+02 Score=24.02 Aligned_cols=103 Identities=16% Similarity=0.022 Sum_probs=50.3
Q ss_pred EEEeecCCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCC-
Q 006943 355 ITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCA- 433 (624)
Q Consensus 355 i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~- 433 (624)
++++|..+.++++..+.+....+++.--......++++=.|-.... |. .-.+..|.....-.+.-.++..|...
T Consensus 58 iviTGaks~e~a~~a~~~i~~~L~~~g~~~~~~~~~v~Nivat~~l----~~-~i~L~~la~~~~~~~~YePE~fPgliy 132 (174)
T cd04516 58 MVCTGAKSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCDV----KF-PIRLEGLAHAHKQFSSYEPELFPGLIY 132 (174)
T ss_pred EEEEecCCHHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEEEEEEC----CC-cccHHHHHHhChhccEeCCccCceEEE
Confidence 7888877777777666665555443221111122222222211111 11 22355665433333333333222110
Q ss_pred ----------CCCCcEEEEEe--ehHHHHHHHHHHHHHHhh
Q 006943 434 ----------DANDELVEVVG--EVGSVRDALVQIILRLRD 462 (624)
Q Consensus 434 ----------~~~~~~v~I~G--~~~~v~~A~~~I~~~l~e 462 (624)
--....|.|+| +.+.+++|+..|...|.+
T Consensus 133 r~~~pk~~~liF~sGkvvitGaks~~~~~~a~~~i~p~L~~ 173 (174)
T cd04516 133 RMVKPKIVLLIFVSGKIVLTGAKSREEIYQAFENIYPILLQ 173 (174)
T ss_pred EecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 00112366898 578899999988887754
No 169
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=24.58 E-value=1.9e+02 Score=24.59 Aligned_cols=27 Identities=30% Similarity=0.325 Sum_probs=23.6
Q ss_pred EEEEeehHHHHHHHHHHHHHHhhcccc
Q 006943 440 VEVVGEVGSVRDALVQIILRLRDDALK 466 (624)
Q Consensus 440 v~I~G~~~~v~~A~~~I~~~l~e~~~~ 466 (624)
+.|+|+..+|+.|+..+++.+++.+..
T Consensus 77 lvitGdvs~Ve~Al~~V~~~l~~~L~F 103 (111)
T PRK15468 77 LVIYGSVGAVEEALSQTVSGLGRLLNY 103 (111)
T ss_pred EEEEccHHHHHHHHHHHHHHHHhhcCc
Confidence 679999999999999999999886543
No 170
>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=24.49 E-value=2.1e+02 Score=26.43 Aligned_cols=58 Identities=19% Similarity=0.236 Sum_probs=44.4
Q ss_pred CCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHH
Q 006943 136 RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAI 214 (624)
Q Consensus 136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~ 214 (624)
+.+..++|+-++...+ =+.+.+|.+-.|+-+.+. ++..|.|.|..+.|..|++.+..+
T Consensus 109 p~~~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efe--------------e~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 109 PPGFETIRVKLKKPIQ-------EERLQEISEWHGVIFEFE--------------EDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred CCCceeEEEecCccch-------HHHHHHHHHHhceeEEec--------------CCcEEEEeccHHHHHHHHHHHHHH
Confidence 4455667777766654 257888999999888772 356799999999999999988765
No 171
>PRK03818 putative transporter; Validated
Probab=23.86 E-value=7.3e+02 Score=27.94 Aligned_cols=127 Identities=12% Similarity=0.219 Sum_probs=63.7
Q ss_pred EEEEecCCccceeeccCcchHHHHHhHhCCeEEEcC---C------CC---CCCceEEEEeecCCchhHHHHHHHHHHHH
Q 006943 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD---T------KD---NRDECVITVTAIESPDDIKSMAVEAVLLL 377 (624)
Q Consensus 310 ~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~------~~---~~~er~i~I~G~~~~~~a~~~~~~~i~~~ 377 (624)
.++.|+... ++ |.+++++.......+.+.. . .. -....++.+.|.. ++. .++....
T Consensus 207 r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~---e~l---~~l~~~~ 274 (552)
T PRK03818 207 INIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQP---EDL---HKAQLVI 274 (552)
T ss_pred EEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECH---HHH---HHHHHhc
Confidence 455566332 23 6799999998876655521 1 01 1123356777751 111 1222111
Q ss_pred hhc----cCCCCCCcEEEEEEecCCeeeEEEcCCCchHHHH--HHhcCceEE-EeCCCCCCCCC-----CCCcEEEEEee
Q 006943 378 QTK----INDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEI--RKRTKADVR-ISKGDKPKCAD-----ANDELVEVVGE 445 (624)
Q Consensus 378 ~~~----~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I--~~~tga~I~-i~~~~~p~~~~-----~~~~~v~I~G~ 445 (624)
-.. .....+......+.+|++ .++|| +++++ ++++|+.|. +.+.+...... ..-.++.+.|+
T Consensus 275 Gl~~~~~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~ 348 (552)
T PRK03818 275 GEEVDTSLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGR 348 (552)
T ss_pred CCccCccccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEEC
Confidence 111 111112223344555553 45655 78887 577888744 44432211011 11234779999
Q ss_pred hHHHHHHHH
Q 006943 446 VGSVRDALV 454 (624)
Q Consensus 446 ~~~v~~A~~ 454 (624)
++++++..+
T Consensus 349 ~~~i~~l~~ 357 (552)
T PRK03818 349 PEAIDAVAN 357 (552)
T ss_pred HHHHHHHHH
Confidence 999998755
No 172
>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=23.01 E-value=9e+02 Score=27.27 Aligned_cols=60 Identities=27% Similarity=0.307 Sum_probs=34.5
Q ss_pred EEEEEecCCeeeEEEcCCCchHHHHH------HhcCceEE-EeCCCCCCCCC-----CCCcEEEEEeehHHHHHHHHH
Q 006943 390 TIRLLVSSKVIGCIIGKSGSIINEIR------KRTKADVR-ISKGDKPKCAD-----ANDELVEVVGEVGSVRDALVQ 455 (624)
Q Consensus 390 ~~~l~vp~~~~g~iIGk~G~~Ik~I~------~~tga~I~-i~~~~~p~~~~-----~~~~~v~I~G~~~~v~~A~~~ 455 (624)
..++.+|++ .++| ++++++. +++|+.|. +.+.+...... ..-.++.+.|++++++++.+.
T Consensus 304 ~e~VV~~~S---~liG---kTL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~ 375 (562)
T TIGR03802 304 TKDVVLTNK---EYNG---KTVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQ 375 (562)
T ss_pred EEEEEECCc---ccCC---ccHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHH
Confidence 334555543 3455 4888886 26788755 44433211111 122347799999999987653
No 173
>PLN00062 TATA-box-binding protein; Provisional
Probab=20.85 E-value=5.8e+02 Score=23.95 Aligned_cols=24 Identities=17% Similarity=0.167 Sum_probs=20.0
Q ss_pred EEEEe--ehHHHHHHHHHHHHHHhhc
Q 006943 440 VEVVG--EVGSVRDALVQIILRLRDD 463 (624)
Q Consensus 440 v~I~G--~~~~v~~A~~~I~~~l~e~ 463 (624)
|.|+| +.+.+.+|+..|...|.+.
T Consensus 149 vvitGaks~~~~~~ai~~i~p~L~~~ 174 (179)
T PLN00062 149 IVITGAKVREEIYTAFENIYPVLTEF 174 (179)
T ss_pred EEEEecCCHHHHHHHHHHHHHHHHHh
Confidence 67898 5788999999999888764
No 174
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=20.34 E-value=1.7e+02 Score=23.13 Aligned_cols=41 Identities=27% Similarity=0.401 Sum_probs=29.7
Q ss_pred chHHHHHHHhCCEE-EEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHH
Q 006943 574 SNLANIRKISGATI-EMSDSKSSRGDRVALISGTPEQKRAAENLIQA 619 (624)
Q Consensus 574 ~~I~~I~~~sGa~I-~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~ 619 (624)
..|.+|-+..+|+| .+.+ +.-+|.++|+++.++....++..
T Consensus 17 ~ei~~l~~~f~a~ivd~~~-----~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 17 SEILQLAEIFRARIVDVSP-----DSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHTT-EEEEEET-----TEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHhCCEEEEECC-----CEEEEEEcCCHHHHHHHHHHhhh
Confidence 46778888899988 4443 24778999999999988877654
No 175
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=20.07 E-value=86 Score=30.87 Aligned_cols=29 Identities=34% Similarity=0.486 Sum_probs=24.0
Q ss_pred EEEEecCcccceeccCCchHHHHHHHhcC
Q 006943 39 YRILCPDGVIGSVIGKSGKVINSIRQETR 67 (624)
Q Consensus 39 ~~ilvp~~~~g~vIGk~G~~I~~i~~etg 67 (624)
+.+.|.....+.|||++|.+|++|++...
T Consensus 64 i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 64 VRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred EEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 55666667789999999999999998764
Done!