Query 007844
Match_columns 587
No_of_seqs 252 out of 1980
Neff 7.3
Searched_HMMs 46136
Date Thu Mar 28 16:06:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007844.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007844hhsearch_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 9E-43 2E-47 375.7 33.7 370 19-446 37-415 (485)
2 KOG2193 IGF-II mRNA-binding pr 100.0 2.2E-42 4.7E-47 350.0 21.6 369 21-443 195-567 (584)
3 KOG1676 K-homology type RNA bi 100.0 6E-41 1.3E-45 355.6 31.2 341 23-445 52-394 (600)
4 KOG2192 PolyC-binding hnRNP-K 100.0 1.5E-32 3.2E-37 264.5 23.0 336 20-441 43-385 (390)
5 KOG1676 K-homology type RNA bi 100.0 3.8E-28 8.2E-33 258.4 19.2 246 127-442 52-302 (600)
6 KOG2193 IGF-II mRNA-binding pr 100.0 6.4E-29 1.4E-33 252.3 12.6 239 128-440 198-481 (584)
7 KOG2191 RNA-binding protein NO 99.9 2.6E-26 5.7E-31 227.6 20.7 241 18-312 32-282 (402)
8 KOG2191 RNA-binding protein NO 99.9 5.7E-24 1.2E-28 211.1 18.9 250 128-439 38-314 (402)
9 KOG2190 PolyC-binding proteins 99.8 8.5E-20 1.8E-24 197.8 22.6 164 274-442 43-210 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.6 3.3E-15 7.1E-20 144.9 10.8 149 128-352 47-196 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.5 1.8E-13 4E-18 130.4 10.8 138 29-201 2-152 (172)
12 PRK13763 putative RNA-processi 99.5 4.6E-13 9.9E-18 128.6 12.3 142 25-201 3-158 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.4 4.1E-13 8.9E-18 128.0 10.9 140 278-440 2-151 (172)
14 PRK13763 putative RNA-processi 99.4 2E-12 4.4E-17 124.1 12.3 145 275-441 4-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.3 3.7E-12 8E-17 101.7 7.4 65 130-195 1-65 (65)
16 cd02396 PCBP_like_KH K homolog 99.3 3.3E-12 7.1E-17 102.0 6.7 65 367-435 1-65 (65)
17 KOG2279 Kinase anchor protein 99.2 5.1E-11 1.1E-15 126.7 12.3 275 16-327 59-352 (608)
18 KOG2279 Kinase anchor protein 99.2 5.5E-11 1.2E-15 126.4 10.2 230 126-436 65-364 (608)
19 cd02394 vigilin_like_KH K homo 99.2 4.2E-11 9.2E-16 94.6 6.4 61 368-435 2-62 (62)
20 PF00013 KH_1: KH domain syndr 99.1 3.8E-11 8.2E-16 94.2 4.1 60 367-434 1-60 (60)
21 cd02393 PNPase_KH Polynucleoti 99.1 1.8E-10 4E-15 90.7 7.1 59 366-435 2-61 (61)
22 cd00105 KH-I K homology RNA-bi 99.1 4E-10 8.7E-15 89.2 7.2 62 368-434 2-63 (64)
23 PF00013 KH_1: KH domain syndr 99.0 2E-10 4.3E-15 90.1 4.4 60 130-194 1-60 (60)
24 cd02394 vigilin_like_KH K homo 99.0 4E-10 8.7E-15 89.0 5.8 60 131-194 2-61 (62)
25 KOG2208 Vigilin [Lipid transpo 99.0 2.2E-09 4.8E-14 123.3 12.0 288 23-439 199-487 (753)
26 cd02393 PNPase_KH Polynucleoti 99.0 2.2E-09 4.7E-14 84.6 7.9 58 129-194 2-60 (61)
27 cd00105 KH-I K homology RNA-bi 99.0 1.9E-09 4.2E-14 85.2 7.7 62 131-194 2-63 (64)
28 KOG2208 Vigilin [Lipid transpo 98.9 3.4E-09 7.4E-14 121.8 9.1 301 25-454 347-652 (753)
29 PF13014 KH_3: KH domain 98.8 5.9E-09 1.3E-13 76.1 5.2 42 35-76 1-43 (43)
30 PF13014 KH_3: KH domain 98.8 7E-09 1.5E-13 75.7 4.6 43 376-422 1-43 (43)
31 smart00322 KH K homology RNA-b 98.8 3.7E-08 8.1E-13 78.0 8.5 68 365-439 2-69 (69)
32 smart00322 KH K homology RNA-b 98.7 1.2E-07 2.7E-12 75.0 8.9 67 128-198 2-68 (69)
33 COG1094 Predicted RNA-binding 98.6 2.8E-07 6E-12 87.7 10.4 141 23-201 6-165 (194)
34 COG1094 Predicted RNA-binding 98.5 1.1E-06 2.3E-11 83.8 10.9 143 274-440 8-164 (194)
35 cd02395 SF1_like-KH Splicing f 98.1 6.5E-06 1.4E-10 73.7 6.7 68 375-442 15-97 (120)
36 cd02395 SF1_like-KH Splicing f 98.1 1.7E-05 3.6E-10 71.1 8.4 64 138-201 15-96 (120)
37 PRK08406 transcription elongat 97.9 2.6E-05 5.5E-10 71.9 7.3 102 26-165 33-135 (140)
38 KOG2113 Predicted RNA binding 97.9 1.2E-05 2.7E-10 80.7 5.0 149 272-437 24-180 (394)
39 KOG2113 Predicted RNA binding 97.7 8.3E-05 1.8E-09 74.9 6.5 154 16-191 18-173 (394)
40 TIGR02696 pppGpp_PNP guanosine 97.7 0.00017 3.6E-09 82.1 9.6 93 334-440 549-642 (719)
41 TIGR02696 pppGpp_PNP guanosine 97.6 0.00025 5.5E-09 80.7 10.3 93 99-200 549-642 (719)
42 PRK08406 transcription elongat 97.6 0.00026 5.7E-09 65.2 8.3 102 274-402 32-135 (140)
43 TIGR01952 nusA_arch NusA famil 97.4 0.00045 9.7E-09 63.6 7.3 102 26-165 34-136 (141)
44 TIGR03591 polynuc_phos polyrib 97.3 0.00076 1.6E-08 77.8 8.8 94 99-200 521-615 (684)
45 KOG0119 Splicing factor 1/bran 97.2 0.0017 3.6E-08 69.6 9.5 73 128-200 137-230 (554)
46 TIGR03591 polynuc_phos polyrib 97.1 0.0011 2.3E-08 76.6 8.1 67 363-440 548-615 (684)
47 TIGR01952 nusA_arch NusA famil 97.0 0.0014 3.1E-08 60.3 6.4 101 275-402 34-136 (141)
48 COG0195 NusA Transcription elo 96.8 0.0044 9.5E-08 59.9 7.7 101 28-166 79-179 (190)
49 PLN00207 polyribonucleotide nu 96.7 0.0027 5.9E-08 74.0 6.9 94 99-200 655-750 (891)
50 COG1185 Pnp Polyribonucleotide 96.7 0.004 8.8E-08 69.7 7.4 99 334-445 522-621 (692)
51 KOG0336 ATP-dependent RNA heli 96.6 0.0024 5.2E-08 67.2 4.9 67 365-439 46-112 (629)
52 KOG0119 Splicing factor 1/bran 96.6 0.0049 1.1E-07 66.1 6.9 76 365-440 137-230 (554)
53 PLN00207 polyribonucleotide nu 96.5 0.0045 9.7E-08 72.3 7.0 92 336-440 657-750 (891)
54 KOG0336 ATP-dependent RNA heli 96.5 0.0017 3.6E-08 68.4 3.0 67 17-86 39-105 (629)
55 KOG1588 RNA-binding protein Sa 96.5 0.012 2.7E-07 58.8 8.9 81 363-443 89-190 (259)
56 KOG1588 RNA-binding protein Sa 96.5 0.0028 6E-08 63.3 4.3 40 22-61 89-134 (259)
57 COG1185 Pnp Polyribonucleotide 96.4 0.011 2.4E-07 66.4 8.9 95 98-200 521-616 (692)
58 cd02134 NusA_KH NusA_K homolog 96.4 0.0044 9.6E-08 48.7 4.2 37 24-60 24-60 (61)
59 KOG2814 Transcription coactiva 96.4 0.004 8.8E-08 63.9 4.9 70 129-201 57-126 (345)
60 TIGR01953 NusA transcription t 96.2 0.013 2.8E-07 62.0 7.7 95 34-166 243-338 (341)
61 COG0195 NusA Transcription elo 96.2 0.0038 8.3E-08 60.3 3.4 101 276-404 78-180 (190)
62 PRK12327 nusA transcription el 96.1 0.016 3.4E-07 61.8 7.9 96 34-167 245-341 (362)
63 PRK12329 nusA transcription el 96.1 0.012 2.6E-07 63.3 7.0 95 34-166 277-372 (449)
64 PRK12328 nusA transcription el 96.1 0.015 3.3E-07 61.6 7.2 95 34-167 251-346 (374)
65 KOG2814 Transcription coactiva 95.9 0.012 2.5E-07 60.6 5.1 70 365-440 56-125 (345)
66 PRK11824 polynucleotide phosph 95.7 0.013 2.8E-07 67.9 5.6 94 99-200 524-618 (693)
67 cd02134 NusA_KH NusA_K homolog 95.6 0.015 3.3E-07 45.6 3.9 37 365-401 24-60 (61)
68 PRK11824 polynucleotide phosph 95.6 0.018 3.8E-07 66.8 6.1 93 335-440 525-618 (693)
69 PRK04163 exosome complex RNA-b 95.6 0.024 5.2E-07 57.0 6.1 65 367-442 146-211 (235)
70 PRK00468 hypothetical protein; 95.5 0.014 3.1E-07 47.8 3.4 35 21-55 26-60 (75)
71 TIGR01953 NusA transcription t 95.3 0.046 9.9E-07 57.9 7.5 96 283-404 243-339 (341)
72 PRK09202 nusA transcription el 95.3 0.039 8.4E-07 60.9 7.0 94 34-166 245-339 (470)
73 PRK02821 hypothetical protein; 94.9 0.025 5.4E-07 46.6 3.2 36 21-56 27-62 (77)
74 PRK12327 nusA transcription el 94.8 0.076 1.7E-06 56.6 7.4 97 283-405 245-342 (362)
75 COG5176 MSL5 Splicing factor ( 94.8 0.077 1.7E-06 51.1 6.5 42 22-63 145-192 (269)
76 PRK12328 nusA transcription el 94.6 0.14 3E-06 54.5 8.6 98 283-407 251-349 (374)
77 PRK00468 hypothetical protein; 94.6 0.041 8.8E-07 45.1 3.6 33 125-157 26-58 (75)
78 PRK12329 nusA transcription el 94.5 0.094 2E-06 56.7 7.3 95 283-403 277-372 (449)
79 PRK12704 phosphodiesterase; Pr 94.4 0.11 2.3E-06 58.3 7.7 63 364-436 208-272 (520)
80 PRK01064 hypothetical protein; 94.3 0.048 1E-06 45.0 3.6 34 22-55 27-60 (78)
81 COG1837 Predicted RNA-binding 94.3 0.058 1.2E-06 44.2 4.0 32 126-157 27-58 (76)
82 COG1837 Predicted RNA-binding 94.3 0.048 1E-06 44.6 3.4 33 22-54 27-59 (76)
83 PF14611 SLS: Mitochondrial in 94.1 1.8 3.9E-05 42.5 15.1 86 104-200 5-90 (210)
84 TIGR03319 YmdA_YtgF conserved 94.1 0.13 2.9E-06 57.5 7.6 61 364-434 202-264 (514)
85 PRK02821 hypothetical protein; 94.0 0.089 1.9E-06 43.3 4.5 32 126-157 28-59 (77)
86 PRK04163 exosome complex RNA-b 93.8 0.12 2.5E-06 52.1 6.0 62 132-201 148-210 (235)
87 PRK00106 hypothetical protein; 93.8 0.16 3.5E-06 56.8 7.5 61 364-434 223-285 (535)
88 PRK09202 nusA transcription el 93.7 0.04 8.8E-07 60.7 2.6 96 283-405 245-341 (470)
89 PRK01064 hypothetical protein; 93.6 0.096 2.1E-06 43.2 4.0 33 125-157 26-58 (78)
90 PRK12704 phosphodiesterase; Pr 93.4 0.3 6.6E-06 54.7 8.9 63 131-200 212-276 (520)
91 TIGR03319 YmdA_YtgF conserved 93.3 0.33 7.1E-06 54.4 9.1 65 129-200 204-270 (514)
92 PF14611 SLS: Mitochondrial in 93.2 0.96 2.1E-05 44.5 11.3 127 277-439 29-164 (210)
93 PRK00106 hypothetical protein; 93.2 0.4 8.6E-06 53.7 9.3 66 128-200 224-291 (535)
94 KOG4369 RTK signaling protein 92.2 0.085 1.8E-06 61.9 2.4 64 24-87 1339-1403(2131)
95 KOG1067 Predicted RNA-binding 92.0 0.46 1E-05 52.3 7.6 93 100-201 568-661 (760)
96 COG5176 MSL5 Splicing factor ( 91.9 0.24 5.2E-06 47.8 4.7 43 125-167 144-192 (269)
97 KOG4369 RTK signaling protein 91.3 0.13 2.9E-06 60.3 2.8 72 365-440 1339-1410(2131)
98 PF13083 KH_4: KH domain; PDB: 90.7 0.13 2.8E-06 41.7 1.5 35 22-56 26-60 (73)
99 cd02409 KH-II KH-II (K homolo 89.4 0.56 1.2E-05 36.6 4.2 35 24-58 24-58 (68)
100 PF13184 KH_5: NusA-like KH do 88.4 0.4 8.7E-06 38.6 2.7 36 27-62 5-46 (69)
101 KOG3273 Predicted RNA-binding 88.1 0.3 6.5E-06 46.9 2.0 56 373-440 176-231 (252)
102 PRK12705 hypothetical protein; 87.6 0.9 1.9E-05 50.6 5.7 62 132-200 201-264 (508)
103 KOG1067 Predicted RNA-binding 87.1 1.5 3.3E-05 48.4 6.9 90 337-440 570-660 (760)
104 KOG3273 Predicted RNA-binding 86.0 0.5 1.1E-05 45.4 2.2 56 137-201 177-232 (252)
105 PF13184 KH_5: NusA-like KH do 85.6 0.81 1.8E-05 36.9 3.0 39 367-405 4-48 (69)
106 cd02409 KH-II KH-II (K homolo 85.1 1.3 2.8E-05 34.5 4.0 35 365-399 24-58 (68)
107 PF13083 KH_4: KH domain; PDB: 84.9 0.59 1.3E-05 37.9 1.9 34 272-305 27-60 (73)
108 PF07650 KH_2: KH domain syndr 83.3 0.73 1.6E-05 37.7 1.9 33 27-59 27-59 (78)
109 cd02410 archeal_CPSF_KH The ar 81.1 3.2 6.8E-05 38.3 5.2 38 130-167 77-114 (145)
110 PRK12705 hypothetical protein; 80.6 2.3 5E-05 47.5 5.1 40 364-403 196-236 (508)
111 cd02414 jag_KH jag_K homology 80.5 1.6 3.5E-05 35.7 3.0 34 27-60 26-59 (77)
112 KOG2874 rRNA processing protei 79.9 2.8 6.1E-05 42.4 4.8 51 141-200 161-211 (356)
113 PF07650 KH_2: KH domain syndr 79.8 0.79 1.7E-05 37.5 0.9 34 130-163 26-59 (78)
114 cd02413 40S_S3_KH K homology R 79.4 2 4.3E-05 35.7 3.1 35 27-61 32-66 (81)
115 KOG2874 rRNA processing protei 79.1 3.4 7.4E-05 41.8 5.1 51 378-440 161-211 (356)
116 PRK13764 ATPase; Provisional 79.0 2.1 4.5E-05 48.9 4.1 45 364-408 479-523 (602)
117 PRK06418 transcription elongat 78.9 2.1 4.5E-05 40.6 3.4 33 29-62 65-97 (166)
118 COG5166 Uncharacterized conser 78.7 9.4 0.0002 42.0 8.6 153 128-402 448-607 (657)
119 COG1097 RRP4 RNA-binding prote 78.5 4 8.7E-05 40.7 5.5 56 133-196 150-206 (239)
120 cd02414 jag_KH jag_K homology 78.0 2.1 4.5E-05 35.1 2.8 34 367-400 25-58 (77)
121 COG1855 ATPase (PilT family) [ 77.9 1.7 3.7E-05 47.2 2.8 41 366-406 486-526 (604)
122 COG1782 Predicted metal-depend 77.1 4.3 9.3E-05 44.6 5.6 39 130-168 100-138 (637)
123 COG1855 ATPase (PilT family) [ 76.9 2.2 4.7E-05 46.4 3.3 39 129-167 486-524 (604)
124 PRK13764 ATPase; Provisional 72.7 2.6 5.6E-05 48.1 2.8 38 26-63 482-519 (602)
125 cd02412 30S_S3_KH K homology R 72.5 3.4 7.4E-05 36.3 2.9 31 27-57 63-93 (109)
126 PRK06418 transcription elongat 72.1 4.3 9.4E-05 38.5 3.7 35 131-166 63-97 (166)
127 cd02413 40S_S3_KH K homology R 71.6 4.3 9.3E-05 33.8 3.1 35 130-164 31-65 (81)
128 cd02410 archeal_CPSF_KH The ar 70.9 12 0.00027 34.5 6.2 96 288-406 20-116 (145)
129 COG1097 RRP4 RNA-binding prote 70.7 9.8 0.00021 38.1 5.9 48 367-425 147-194 (239)
130 cd02411 archeal_30S_S3_KH K ho 68.7 5 0.00011 33.6 3.0 29 27-55 40-68 (85)
131 COG0092 RpsC Ribosomal protein 66.1 4.9 0.00011 40.0 2.8 33 26-58 52-84 (233)
132 COG1782 Predicted metal-depend 64.7 10 0.00022 41.8 5.0 97 286-405 41-138 (637)
133 TIGR03675 arCOG00543 arCOG0054 60.8 11 0.00024 43.4 4.9 38 130-167 94-131 (630)
134 cd02411 archeal_30S_S3_KH K ho 59.6 9.1 0.0002 32.0 2.9 27 131-157 40-66 (85)
135 cd02412 30S_S3_KH K homology R 57.8 8.4 0.00018 33.8 2.5 28 131-158 63-90 (109)
136 COG5166 Uncharacterized conser 57.4 8.8 0.00019 42.2 3.0 130 285-440 391-524 (657)
137 COG0092 RpsC Ribosomal protein 55.1 10 0.00022 37.9 2.8 30 128-157 50-79 (233)
138 TIGR03675 arCOG00543 arCOG0054 52.6 27 0.00058 40.4 6.1 97 287-406 36-133 (630)
139 TIGR00436 era GTP-binding prot 47.0 21 0.00046 36.3 3.9 30 129-158 221-251 (270)
140 PRK15494 era GTPase Era; Provi 42.5 27 0.00059 37.0 3.9 29 129-157 273-302 (339)
141 PRK00089 era GTPase Era; Revie 41.4 30 0.00065 35.5 4.0 29 129-157 226-255 (292)
142 TIGR00436 era GTP-binding prot 40.8 25 0.00055 35.8 3.3 31 365-395 220-251 (270)
143 COG1159 Era GTPase [General fu 40.1 31 0.00067 35.8 3.7 29 128-156 228-257 (298)
144 TIGR01008 rpsC_E_A ribosomal p 38.1 30 0.00066 33.7 3.1 31 27-57 40-70 (195)
145 PRK04191 rps3p 30S ribosomal p 37.4 30 0.00066 34.1 3.1 32 27-58 42-73 (207)
146 CHL00048 rps3 ribosomal protei 36.3 33 0.00071 34.0 3.1 32 26-57 67-98 (214)
147 PRK00089 era GTPase Era; Revie 36.1 32 0.00069 35.3 3.2 31 365-395 225-256 (292)
148 PRK15494 era GTPase Era; Provi 36.0 33 0.00071 36.4 3.3 30 366-395 273-303 (339)
149 PTZ00084 40S ribosomal protein 35.6 33 0.00072 34.1 3.0 32 27-58 46-77 (220)
150 COG1159 Era GTPase [General fu 35.6 33 0.00072 35.6 3.1 32 364-395 227-259 (298)
151 cd07053 BMC_PduT_repeat1 1,2-p 34.8 49 0.0011 27.1 3.4 37 414-450 37-73 (76)
152 PF00936 BMC: BMC domain; Int 32.8 45 0.00098 27.1 2.9 36 414-449 38-73 (75)
153 KOG1423 Ras-like GTPase ERA [C 30.6 42 0.00092 35.1 2.9 34 363-396 325-359 (379)
154 TIGR01008 rpsC_E_A ribosomal p 27.7 57 0.0012 31.9 3.1 28 130-157 39-66 (195)
155 PRK03818 putative transporter; 27.7 3.3E+02 0.0072 31.0 9.7 131 26-193 206-358 (552)
156 PRK04191 rps3p 30S ribosomal p 27.4 56 0.0012 32.2 3.1 29 131-159 42-70 (207)
157 CHL00048 rps3 ribosomal protei 26.5 60 0.0013 32.2 3.1 29 130-158 67-95 (214)
158 KOG1423 Ras-like GTPase ERA [C 26.2 58 0.0013 34.1 3.0 33 24-56 327-360 (379)
159 PTZ00084 40S ribosomal protein 25.8 61 0.0013 32.3 3.0 28 131-158 46-73 (220)
160 COG1847 Jag Predicted RNA-bind 24.5 53 0.0011 32.3 2.2 34 27-60 93-126 (208)
161 TIGR03802 Asp_Ala_antiprt aspa 24.0 4E+02 0.0087 30.4 9.5 58 130-193 304-375 (562)
162 cd07045 BMC_CcmK_like Carbon d 23.7 92 0.002 26.0 3.3 36 415-450 38-75 (84)
163 TIGR01009 rpsC_bact ribosomal 23.6 71 0.0015 31.6 3.0 30 27-56 64-93 (211)
164 COG1847 Jag Predicted RNA-bind 23.4 64 0.0014 31.7 2.6 37 365-401 90-126 (208)
165 COG1702 PhoH Phosphate starvat 23.4 1.7E+02 0.0036 31.2 5.7 51 373-435 22-72 (348)
166 cd07056 BMC_PduK 1,2-propanedi 22.2 1.1E+02 0.0023 25.2 3.3 36 414-449 38-75 (77)
167 PRK15468 carboxysome structura 22.2 1.8E+02 0.0038 25.6 4.7 40 393-441 61-100 (111)
168 COG1702 PhoH Phosphate starvat 20.1 1.8E+02 0.0039 30.9 5.2 53 134-195 20-72 (348)
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=9e-43 Score=375.74 Aligned_cols=370 Identities=28% Similarity=0.453 Sum_probs=293.1
Q ss_pred CCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCc
Q 007844 19 NLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEV 98 (587)
Q Consensus 19 ~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~ 98 (587)
..++...+|||||+.+.+|.||||+|.+||+||++|.++|+|.+..++++|||++|+|...+ ...
T Consensus 37 ~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~---------------~~~ 101 (485)
T KOG2190|consen 37 TGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE---------------LNL 101 (485)
T ss_pred CCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc---------------ccC
Confidence 33344445999999999999999999999999999999999999999999999999997322 247
Q ss_pred cHHHHHHHHHHHHHHhhhhccCC-----C-CCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCC
Q 007844 99 SSTQEAVIRVFERMWEVEAEVEG-----D-GDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAA 172 (587)
Q Consensus 99 ~~A~~Al~~i~~~i~~~~~~~~~-----~-~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~ 172 (587)
+++++|++++++.|.....+++. . .....++++|||||.+++|+||||+|+.||+|+++|||+|+|.++ ..+.
T Consensus 102 ~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~ 180 (485)
T KOG2190|consen 102 SPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN 180 (485)
T ss_pred CchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc
Confidence 88999999999999875332211 1 111226899999999999999999999999999999999999996 5566
Q ss_pred CCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCC---CCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 007844 173 IDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK---SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNAS 249 (587)
Q Consensus 173 ~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~---~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~ 249 (587)
.++|.|+|.|.+++|.+|+..|..+|++++.+.- ....+|+|... .+...+|........|+
T Consensus 181 ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~--------------~~~~~~~s~~~~~~~~~- 245 (485)
T KOG2190|consen 181 STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSAS--------------QGGPVLPSTAQTSPDAH- 245 (485)
T ss_pred ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCccc--------------ccCccccccccCCcccc-
Confidence 6999999999999999999999999999653311 11223333100 00011111111100000
Q ss_pred ccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCc
Q 007844 250 EFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYL 329 (587)
Q Consensus 250 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p 329 (587)
. +.......+..+++.+|.+.++.|||++|..|+.++.++++.|.+.....+ ++|+++..+.+
T Consensus 246 --------~------~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~ 308 (485)
T KOG2190|consen 246 --------P------FGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENP 308 (485)
T ss_pred --------c------ccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCc
Confidence 0 000223456788999999999999999999999999999999999977554 89999999999
Q ss_pred CCCCChHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccc
Q 007844 330 DTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLG 409 (587)
Q Consensus 330 ~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~ 409 (587)
++..+++++|+.+++.++.+..... . ...++.+|+||++++||||||+|++|.+|++.|||.|+|...++.
T Consensus 309 ~~~~s~a~~a~~~~~~~~~~~~~~~------~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~-- 379 (485)
T KOG2190|consen 309 EDRYSMAQEALLLVQPRISENAGDD------L-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV-- 379 (485)
T ss_pred ccccccchhhhhhcccccccccccc------c-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc--
Confidence 9999999999999999987653211 1 467899999999999999999999999999999999999998773
Q ss_pred cCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcccCcc
Q 007844 410 CAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGE 446 (587)
Q Consensus 410 ~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~ 446 (587)
...+++.++|+|...+...|+++|..++........
T Consensus 380 -~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~ 415 (485)
T KOG2190|consen 380 -SGVREALVQITGMLREDLLAQYLIRARLSAPKSSMG 415 (485)
T ss_pred -CCcceeEEEecchhHHHHhhhhhcccccccCccCCC
Confidence 257899999999999999999999888776554443
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=2.2e-42 Score=349.98 Aligned_cols=369 Identities=21% Similarity=0.338 Sum_probs=272.2
Q ss_pred CCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeC-CCCCCCceEEEEecCCchhhhhhhccccccccCCCcc
Q 007844 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVS 99 (587)
Q Consensus 21 ~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~ 99 (587)
...+..+|+|||..++|+||||.|+|||.|...|.|+|+|.. ...|..||+|+|.+++|. .+
T Consensus 195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-----------------~s 257 (584)
T KOG2193|consen 195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-----------------TS 257 (584)
T ss_pred cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-----------------hH
Confidence 356789999999999999999999999999999999999975 456889999999999987 34
Q ss_pred HHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEE
Q 007844 100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLI 178 (587)
Q Consensus 100 ~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V 178 (587)
.|+..++.|..+ ...+. .-..++.+++|.++.+||+||||.|++||+|+++||++|.|++. .....+.||+|
T Consensus 258 ~Ac~~ILeimqk---EA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTI 330 (584)
T KOG2193|consen 258 KACKMILEIMQK---EAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTI 330 (584)
T ss_pred HHHHHHHHHHHH---hhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceE
Confidence 455555544433 22221 12247899999999999999999999999999999999999986 44445679999
Q ss_pred EEeecHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcC-CCCCCCCCCCCCCCccCCCCCC
Q 007844 179 QITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLS-LVPPLTGNPSDNASEFHSSSAD 257 (587)
Q Consensus 179 ~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~-~~P~~~~~~~~y~~~~~p~~~~ 257 (587)
+++|+.|+|.+|..+|..+|++....+-..+...-++.... ..+.-..+|..+ +.|| .+.|....
T Consensus 331 tVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l----~~~~l~~f~ssS~~~~P----------h~~Ps~v~ 396 (584)
T KOG2193|consen 331 TVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGL----NLPALGLFPSSSAVSPP----------HFPPSPVT 396 (584)
T ss_pred EecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCccc----CccccCCCCcccccCCC----------CCCCCccc
Confidence 99999999999999999999986544421111000000000 000000111111 1111 00111100
Q ss_pred CCCCCCCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC-CCCCCccEEEEEecCCcCCCCChH
Q 007844 258 ADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPV 336 (587)
Q Consensus 258 ~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~er~V~IsG~~~p~~~~~~a 336 (587)
+...-+.+ ....+...++|+||...+|.|||++|.+||.|.+.+||.|+|.++ .++..+|.|+|+|. |+ +.
T Consensus 397 ~a~p~~~~--hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGp--pe----aq 468 (584)
T KOG2193|consen 397 FASPYPLF--HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGP--PE----AQ 468 (584)
T ss_pred cCCCchhh--hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCC--hH----HH
Confidence 00000000 112244578999999999999999999999999999999999975 67789999999998 33 23
Q ss_pred HHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCc
Q 007844 337 QNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDV 416 (587)
Q Consensus 337 ~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r 416 (587)
-+|.-+||.++.|..+- .+...-...+.+.||...+|+||||||.+++++|+.|+|.+.|+.+. .|. .++..
T Consensus 469 fKAQgrifgKikEenf~-----~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdq-tpd--End~v 540 (584)
T KOG2193|consen 469 FKAQGRIFGKIKEENFF-----LPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQ-TPD--ENDQV 540 (584)
T ss_pred HhhhhhhhhhhhhhccC-----CchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccC-CCC--cccee
Confidence 37777888888664321 11234567888999999999999999999999999999999998754 553 56778
Q ss_pred EEEEcCCHHHHHHHHHHHHHHHhhccc
Q 007844 417 VIQISGEYKNVQNALSEVVGRLRHNLK 443 (587)
Q Consensus 417 ~V~I~G~~~~V~~A~~~I~~~Lr~~~~ 443 (587)
+|.|.|.+.+.+.|+..|.+.+.++.-
T Consensus 541 ivriiGhfyatq~aQrki~~iv~qvkq 567 (584)
T KOG2193|consen 541 IVRIIGHFYATQNAQRKIAHIVNQVKQ 567 (584)
T ss_pred eeeeechhhcchHHHHHHHHHHHHHHH
Confidence 999999999999999999998887553
No 3
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=6e-41 Score=355.64 Aligned_cols=341 Identities=22% Similarity=0.293 Sum_probs=262.7
Q ss_pred CcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHH
Q 007844 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (587)
Q Consensus 23 ~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~ 102 (587)
..++-+.-||..++|.||||+|+.|..|+.++||+|.+.....+..+|-+.++|..++++. |.
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~-----------------aK 114 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEV-----------------AK 114 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHH-----------------HH
Confidence 4567788899999999999999999999999999999877666778999999999998654 33
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEee
Q 007844 103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182 (587)
Q Consensus 103 ~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G 182 (587)
..+-.+..+......-. .......++.+|+||.+.+|.||||+|++||.|++++||++.+.++-......++.+.|+|
T Consensus 115 ~li~evv~r~~~~~~~~--~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritG 192 (600)
T KOG1676|consen 115 QLIGEVVSRGRPPGGFP--DNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITG 192 (600)
T ss_pred HhhhhhhhccCCCCCcc--ccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecC
Confidence 33334444432110000 1122457899999999999999999999999999999999999987333344889999999
Q ss_pred cHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCC
Q 007844 183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH 262 (587)
Q Consensus 183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~ 262 (587)
+++.|+.|..+|.++|++... ... . ....|+.
T Consensus 193 dp~~ve~a~~lV~dil~e~~~---~~~-----g---------------------------~~~~~g~------------- 224 (600)
T KOG1676|consen 193 DPDKVEQAKQLVADILREEDD---EVP-----G---------------------------SGGHAGV------------- 224 (600)
T ss_pred CHHHHHHHHHHHHHHHHhccc---CCC-----c---------------------------cccccCc-------------
Confidence 999999999999999986210 000 0 0000000
Q ss_pred CCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC-CCCCCccEEEEEecCCcCCCCChHHHHHH
Q 007844 263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPVQNAAV 341 (587)
Q Consensus 263 ~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~er~V~IsG~~~p~~~~~~a~~Av~ 341 (587)
......+++|.||...||.||||+|++||+|+.+||++|+|.+. .+.+.||.+.|.|+. ..+..|..
T Consensus 225 ------~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~------d~ie~Aa~ 292 (600)
T KOG1676|consen 225 ------RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTV------DQIEHAAE 292 (600)
T ss_pred ------CccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCH------HHHHHHHH
Confidence 00123388999999999999999999999999999999999876 448899999999994 55567777
Q ss_pred HHHhhhhcccccCCCCCCCC-CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEE
Q 007844 342 LVFARSVEVEGQQGFSSGEN-KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI 420 (587)
Q Consensus 342 ~i~~~v~e~~~~~g~~~g~~-~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I 420 (587)
+|.+.+.+.....+...+.. ........+.||.+.||.||||+|++||.|.++|||++.+.+. .| ..+..+++++|
T Consensus 293 lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p-~~~~~ektf~I 369 (600)
T KOG1676|consen 293 LINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PP-NGNPKEKTFVI 369 (600)
T ss_pred HHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CC-CCCccceEEEE
Confidence 77666655433222211100 0112278899999999999999999999999999999999886 23 36778999999
Q ss_pred cCCHHHHHHHHHHHHHHHhhcccCc
Q 007844 421 SGEYKNVQNALSEVVGRLRHNLKSG 445 (587)
Q Consensus 421 ~G~~~~V~~A~~~I~~~Lr~~~~~~ 445 (587)
+|+..+|+.|+.||..++-.....-
T Consensus 370 rG~~~QIdhAk~LIr~kvg~~~~n~ 394 (600)
T KOG1676|consen 370 RGDKRQIDHAKQLIRDKVGDIAPNT 394 (600)
T ss_pred ecCcccchHHHHHHHHHhcccCCCC
Confidence 9999999999999999998754433
No 4
>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=1.5e-32 Score=264.50 Aligned_cols=336 Identities=17% Similarity=0.284 Sum_probs=210.7
Q ss_pred CCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCcc
Q 007844 20 LPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVS 99 (587)
Q Consensus 20 ~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~ 99 (587)
..-..+.+|||+.++.+|+||||+|+|||+|+.+.+|.|.|.|+ ..+|||++|+...+.+
T Consensus 43 ~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~ti------------------ 102 (390)
T KOG2192|consen 43 FKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIETI------------------ 102 (390)
T ss_pred hhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHHH------------------
Confidence 34457999999999999999999999999999999999999887 5689999999866442
Q ss_pred HHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEE
Q 007844 100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ 179 (587)
Q Consensus 100 ~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~ 179 (587)
-+.|.+|+.++.+.-. ..+++.+||||+.+++|.|||++|++||+|++++.|+++|... .|+.++||+|.
T Consensus 103 --~~ilk~iip~lee~f~-------~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p~stdrv~l 172 (390)
T KOG2192|consen 103 --GEILKKIIPTLEEGFQ-------LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCPHSTDRVVL 172 (390)
T ss_pred --HHHHHHHhhhhhhCCC-------CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCCCCcceEEE
Confidence 2334445544433221 2347899999999999999999999999999999999999995 88999999999
Q ss_pred EeecHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCC-----CCc-CCCCCCCCCCCCCCCccCC
Q 007844 180 ITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFF-----PHL-SLVPPLTGNPSDNASEFHS 253 (587)
Q Consensus 180 I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~-----p~~-~~~P~~~~~~~~y~~~~~p 253 (587)
|.|.+.+|..++..|.+.|.+.+.+... +|+...++.....-....+ |.. ..+|+.++...
T Consensus 173 ~~g~~k~v~~~i~~il~~i~e~pikgsa-----~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgp-------- 239 (390)
T KOG2192|consen 173 IGGKPKRVVECIKIILDLISESPIKGSA-----QPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGP-------- 239 (390)
T ss_pred ecCCcchHHHHHHHHHHHhhcCCcCCcC-----CcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCC--------
Confidence 9999999999999999999997765543 2222112211100000000 000 11111111000
Q ss_pred CCCCCCCCCCCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCC
Q 007844 254 SSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRH 333 (587)
Q Consensus 254 ~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~ 333 (587)
.......- +.+. . -|+-|..-. --+.|........ .|-+-. +..+
T Consensus 240 --------------p~~~~sdl--may~--r----~GrpG~ryd-------g~vdFs~detw~s----aidtw~-~Sew- 284 (390)
T KOG2192|consen 240 --------------PPPRGSDL--MAYD--R----RGRPGDRYD-------GMVDFSADETWPS----AIDTWS-PSEW- 284 (390)
T ss_pred --------------CCCCcccc--ceec--c----CCCCCcccc-------ccccccccccCCC----cCCCcC-cccc-
Confidence 00000000 0000 0 011111000 0011111000000 000000 0000
Q ss_pred ChHHHHHHHHHhhhhcccccCCCCC-CCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCC
Q 007844 334 SPVQNAAVLVFARSVEVEGQQGFSS-GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAA 412 (587)
Q Consensus 334 ~~a~~Av~~i~~~v~e~~~~~g~~~-g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~ 412 (587)
.+ |-.--...--+.....+... |.-.....|.+|.||++.-|.||||+|+.|++|++++||.|++....+ +
T Consensus 285 qm---aYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikideple-----G 356 (390)
T KOG2192|consen 285 QM---AYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLE-----G 356 (390)
T ss_pred cc---ccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCC-----C
Confidence 00 00000000000000000000 111246789999999999999999999999999999999999976443 7
Q ss_pred CCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844 413 QNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (587)
Q Consensus 413 ~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (587)
+.+|+++|+|+.++++.|++++...++.+
T Consensus 357 sedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 357 SEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred CCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 88999999999999999999999988853
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.96 E-value=3.8e-28 Score=258.41 Aligned_cols=246 Identities=20% Similarity=0.299 Sum_probs=194.5
Q ss_pred CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCC
Q 007844 127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206 (587)
Q Consensus 127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~ 206 (587)
..++.+.-||..++|.||||+|+.|..|+.+|||+|+|... ......|.|.++|.+++|+.|+.+|.+++....
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~--~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~---- 125 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAAD--PSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR---- 125 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCC--CCCcccccccccCCcccHHHHHHhhhhhhhccC----
Confidence 46778899999999999999999999999999999998774 234578999999999999999999999986521
Q ss_pred CCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeeccccc
Q 007844 207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (587)
Q Consensus 207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG 286 (587)
.+. .+++ .....+++.+|.||.+++|
T Consensus 126 ~~~--------------------~~~~----------------------------------~q~~~~ttqeI~IPa~k~G 151 (600)
T KOG1676|consen 126 PPG--------------------GFPD----------------------------------NQGSVETTQEILIPANKCG 151 (600)
T ss_pred CCC--------------------Cccc----------------------------------cCCccceeeeeccCcccee
Confidence 000 0000 1113567999999999999
Q ss_pred ccccccchhhHhhhhhcCceEEeeCC--CCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccc---ccCCCCCCCC
Q 007844 287 GIIGKRGAIVRSLQNASGALISFAAP--LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE---GQQGFSSGEN 361 (587)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tga~I~i~~~--~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~---~~~g~~~g~~ 361 (587)
.||||+|++||.|++.+||++.+..+ ......+.+.|+|.. ..+..|-.++++.+.+.. +..+...+..
T Consensus 152 lIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp------~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~ 225 (600)
T KOG1676|consen 152 LIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDP------DKVEQAKQLVADILREEDDEVPGSGGHAGVR 225 (600)
T ss_pred eEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCH------HHHHHHHHHHHHHHHhcccCCCccccccCcC
Confidence 99999999999999999999887643 223367789999983 445566666666665321 1111111222
Q ss_pred CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (587)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (587)
.....+.+|.||...||.||||+|++||+|+.+|||+|+|.++++ | ...+|.+.|.|+.++|+.|.++|.+.|++.
T Consensus 226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~~~IiG~~d~ie~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERPAQIIGTVDQIEHAAELINEIIAEA 301 (600)
T ss_pred ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccceeeeecCHHHHHHHHHHHHHHHHHH
Confidence 234569999999999999999999999999999999999988766 3 578999999999999999999999999864
Q ss_pred c
Q 007844 442 L 442 (587)
Q Consensus 442 ~ 442 (587)
.
T Consensus 302 ~ 302 (600)
T KOG1676|consen 302 E 302 (600)
T ss_pred h
Confidence 3
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=6.4e-29 Score=252.32 Aligned_cols=239 Identities=17% Similarity=0.291 Sum_probs=195.0
Q ss_pred ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCCC
Q 007844 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (587)
Q Consensus 128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~ 207 (587)
+..+|+|||..++|.||||.|++||.|...|-|+|.|... ...+..|+.|+|.|++|...+|+.+|.+++......+
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrk-en~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~-- 274 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRK-ENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDD-- 274 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeec-ccCCcccCceEEecCccchHHHHHHHHHHHHHhhhcc--
Confidence 4679999999999999999999999999999999999986 5568899999999999999999999999997632211
Q ss_pred CcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccc
Q 007844 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (587)
Q Consensus 208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~ 287 (587)
....++.++|+..+.+||+
T Consensus 275 -------------------------------------------------------------k~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 275 -------------------------------------------------------------KVAEEIPLKILAHNNLVGR 293 (584)
T ss_pred -------------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence 1235678899999999999
Q ss_pred cccccchhhHhhhhhcCceEEeeCC---CCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcc------------cc
Q 007844 288 IIGKRGAIVRSLQNASGALISFAAP---LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV------------EG 352 (587)
Q Consensus 288 IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~------------~~ 352 (587)
+|||.|.+||+|..+||++|.|... ..-..||+|++.|+- .....|..+|.+++.+. .+
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsi------Eac~~AE~eImkKlre~yEnDl~a~s~q~~l 367 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSI------EACVQAEAEIMKKLRECYENDLAAMSLQCHL 367 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccH------HHHHHHHHHHHHHHHHHHhhhHHHhhccCCC
Confidence 9999999999999999999999863 334569999999973 33345555555554322 11
Q ss_pred cCCC-------------------CCC----C-------CCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEc
Q 007844 353 QQGF-------------------SSG----E-------NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (587)
Q Consensus 353 ~~g~-------------------~~g----~-------~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~ 402 (587)
.+++ ++. . .......++|.||...+|.|||++|.+||.|.+.+||.|+|.
T Consensus 368 ~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIa 447 (584)
T KOG2193|consen 368 PPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIA 447 (584)
T ss_pred CcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeec
Confidence 1110 010 0 012556789999999999999999999999999999999998
Q ss_pred CCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844 403 GGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 403 ~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (587)
+.+- .+..+|+|+|+|.+++..+|+..|..+|.+
T Consensus 448 ppE~----pdvseRMViItGppeaqfKAQgrifgKikE 481 (584)
T KOG2193|consen 448 PPEI----PDVSERMVIITGPPEAQFKAQGRIFGKIKE 481 (584)
T ss_pred CCCC----CCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence 8653 357899999999999999999999999995
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=2.6e-26 Score=227.62 Aligned_cols=241 Identities=20% Similarity=0.294 Sum_probs=171.4
Q ss_pred CCCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEe---CCCCCCCceEEEEecCCchhhhhhhcccccccc
Q 007844 18 LNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE---GGFPGSDHRVILVVGSGSIDRRIMFCENDVVVE 94 (587)
Q Consensus 18 ~~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~---~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e 94 (587)
+...++.+++|||||+..+|.||||+|++|.+|+++|||+|+++ |.+|++.||||.|.|+.+++.
T Consensus 32 n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~------------ 99 (402)
T KOG2191|consen 32 NTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN------------ 99 (402)
T ss_pred cCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH------------
Confidence 34445569999999999999999999999999999999999996 578999999999999876521
Q ss_pred CCCccHHHHHHHHHHHHHHhhhhccCC------CCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-
Q 007844 95 GGEVSSTQEAVIRVFERMWEVEAEVEG------DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP- 167 (587)
Q Consensus 95 ~~~~~~A~~Al~~i~~~i~~~~~~~~~------~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~- 167 (587)
.-+..|.++|.+.....+. ....++.-.++++||++.+|.||||+|.+||.|++++||.|+|++.
T Consensus 100 --------av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk 171 (402)
T KOG2191|consen 100 --------AVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK 171 (402)
T ss_pred --------HHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC
Confidence 1122333344333222221 1123445679999999999999999999999999999999999954
Q ss_pred CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCC
Q 007844 168 PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDN 247 (587)
Q Consensus 168 p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y 247 (587)
|..-...||+|++.|++++..+|+.+|.++|.+++....... .++.... +....|
T Consensus 172 pt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln---~sya~vs----------------------GpvaNs 226 (402)
T KOG2191|consen 172 PTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLN---ISYANVS----------------------GPVANS 226 (402)
T ss_pred CCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceec---cchhccc----------------------Cccccc
Confidence 555667899999999999999999999999999765443211 0110000 001111
Q ss_pred CCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC
Q 007844 248 ASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP 312 (587)
Q Consensus 248 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~ 312 (587)
++...|+.... .......+.-.-|+....|..-|.+|.++-.|-.-+|+.+.+.+.
T Consensus 227 nPtGspya~~~---------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 227 NPTGSPYAYQA---------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred CCCCCCCCCCC---------ccccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence 11111111000 011122233355888999999999999999999999998888753
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.92 E-value=5.7e-24 Score=211.10 Aligned_cols=250 Identities=21% Similarity=0.290 Sum_probs=197.2
Q ss_pred ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCC
Q 007844 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206 (587)
Q Consensus 128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~ 206 (587)
.+.+|+|||+..+|.||||+|++|.+|+.+|||+|++++. .++++++||+|.|+|+.+++......|.++|++.+....
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 4899999999999999999999999999999999999988 889999999999999999999999999999998543211
Q ss_pred CCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeeccccc
Q 007844 207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (587)
Q Consensus 207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG 286 (587)
.+.... ++........++++||+..+|
T Consensus 118 k~v~~~-----------------------------------------------------~pqt~~r~kqikivvPNstag 144 (402)
T KOG2191|consen 118 KPVDIL-----------------------------------------------------QPQTPDRIKQIKIVVPNSTAG 144 (402)
T ss_pred CCcccc-----------------------------------------------------CCCCccccceeEEeccCCccc
Confidence 100000 000111223588999999999
Q ss_pred ccccccchhhHhhhhhcCceEEeeCCCC---CCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccc-------cC--
Q 007844 287 GIIGKRGAIVRSLQNASGALISFAAPLT---KSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG-------QQ-- 354 (587)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tga~I~i~~~~~---~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~-------~~-- 354 (587)
.||||+|.+||.|++++||+|+|.+.++ .-.+|+||++|.. ....+|+.+|++++.|++- ..
T Consensus 145 ~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~------e~~~~A~~~IL~Ki~eDpqs~scln~sya~ 218 (402)
T KOG2191|consen 145 MIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEP------EQNMKAVSLILQKIQEDPQSGSCLNISYAN 218 (402)
T ss_pred ceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCH------HHHHHHHHHHHHHhhcCCcccceeccchhc
Confidence 9999999999999999999999995433 3468999999984 5566899999999987521 00
Q ss_pred --C----CCC-C-------CCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEE
Q 007844 355 --G----FSS-G-------ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI 420 (587)
Q Consensus 355 --g----~~~-g-------~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I 420 (587)
| +.+ | ...+...+....|+....|..-|.+|.++-.+...+|+.+.+...-+.- .+...+ +.+
T Consensus 219 vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m--~g~gy~-~n~ 295 (402)
T KOG2191|consen 219 VSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTM--AGYGYN-TNI 295 (402)
T ss_pred ccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeeccccccc--cccccc-ccc
Confidence 0 001 0 0123456677889999999999999999999999999999998866622 233344 889
Q ss_pred cCCHHHHHHHHHHHHHHHh
Q 007844 421 SGEYKNVQNALSEVVGRLR 439 (587)
Q Consensus 421 ~G~~~~V~~A~~~I~~~Lr 439 (587)
.|...++..|-.+|..+..
T Consensus 296 ~g~~ls~~aa~g~L~~~~~ 314 (402)
T KOG2191|consen 296 LGLGLSILAAEGVLAAKVA 314 (402)
T ss_pred cchhhhhhhhhhHHHHhhc
Confidence 9999999999998877554
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.85 E-value=8.5e-20 Score=197.76 Aligned_cols=164 Identities=27% Similarity=0.408 Sum_probs=138.6
Q ss_pred eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccc-
Q 007844 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG- 352 (587)
Q Consensus 274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~- 352 (587)
.++||+|+...+|.||||+|..||+|+.++.++|+|.+...++.+|+|+|+|+... ...+++++|+.+.++.+.....
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-LNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-ccCCchHHHHHHHHHHHhhcccc
Confidence 35999999999999999999999999999999999999999999999999995322 2567889999999988865311
Q ss_pred --cCCCCCC-CCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHH
Q 007844 353 --QQGFSSG-ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN 429 (587)
Q Consensus 353 --~~g~~~g-~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~ 429 (587)
....+.+ ......++.+|+||.+++|+||||+|+.||+|++.|||+|+|.+. .+|. .++|.|+|.|.+++|.+
T Consensus 122 d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~ 197 (485)
T KOG2190|consen 122 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKK 197 (485)
T ss_pred cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHH
Confidence 1111111 122236899999999999999999999999999999999999986 6665 67788999999999999
Q ss_pred HHHHHHHHHhhcc
Q 007844 430 ALSEVVGRLRHNL 442 (587)
Q Consensus 430 A~~~I~~~Lr~~~ 442 (587)
|+..|..+|+++.
T Consensus 198 al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 198 ALVQISSRLLENP 210 (485)
T ss_pred HHHHHHHHHHhcC
Confidence 9999999999965
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.60 E-value=3.3e-15 Score=144.94 Aligned_cols=149 Identities=21% Similarity=0.313 Sum_probs=126.5
Q ss_pred ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCCC
Q 007844 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (587)
Q Consensus 128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~ 207 (587)
.+.++||+.++.+|.||||+|++||+|+.+++|.|+|.. ....+|+|+|+-+.+-|-.-++.|...|++..
T Consensus 47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd----s~~peri~tisad~~ti~~ilk~iip~lee~f----- 117 (390)
T KOG2192|consen 47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD----SSGPERILTISADIETIGEILKKIIPTLEEGF----- 117 (390)
T ss_pred ceeEEEEEecccccceeccccccHHHHhhhccceeeccC----CCCCceeEEEeccHHHHHHHHHHHhhhhhhCC-----
Confidence 689999999999999999999999999999999999976 35579999999999999999999999998731
Q ss_pred CcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccc
Q 007844 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (587)
Q Consensus 208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~ 287 (587)
.+...+.++|+|..+++|.
T Consensus 118 -------------------------------------------------------------~~~~pce~rllihqs~ag~ 136 (390)
T KOG2192|consen 118 -------------------------------------------------------------QLPSPCELRLLIHQSLAGG 136 (390)
T ss_pred -------------------------------------------------------------CCCCchhhhhhhhhhhccc
Confidence 1123467899999999999
Q ss_pred cccccchhhHhhhhhcCceEEeeC-CCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccc
Q 007844 288 IIGKRGAIVRSLQNASGALISFAA-PLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG 352 (587)
Q Consensus 288 IIGk~G~~Ik~I~~~tga~I~i~~-~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~ 352 (587)
|||++|++||++++++.|+.+|.. -.+.+++|+|.|.|.. ..+...+..+.+.+.|..+
T Consensus 137 iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~------k~v~~~i~~il~~i~e~pi 196 (390)
T KOG2192|consen 137 IIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKP------KRVVECIKIILDLISESPI 196 (390)
T ss_pred eecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCc------chHHHHHHHHHHHhhcCCc
Confidence 999999999999999999999885 4788999999999873 3445555566666666543
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=99.48 E-value=1.8e-13 Score=130.37 Aligned_cols=138 Identities=17% Similarity=0.190 Sum_probs=95.5
Q ss_pred EEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEE---ecCCchhhhhhhccccccccCCCccHHHHHH
Q 007844 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILV---VGSGSIDRRIMFCENDVVVEGGEVSSTQEAV 105 (587)
Q Consensus 29 iLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I---~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al 105 (587)
+.||.+++|.|||++|++|+.|+++|||+|++.+. +..|.| +++++.+ ..|++.+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i-----------------~kA~~~I 59 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAV-----------------MKAREVV 59 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHH-----------------HHHHHHH
Confidence 45799999999999999999999999999999763 245777 3333332 2233333
Q ss_pred HHHHHHHHhhhhccCCCCCCCCceEEEE-Eeec---------ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCC
Q 007844 106 IRVFERMWEVEAEVEGDGDGDDVAYCGL-LANT---------TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD 175 (587)
Q Consensus 106 ~~i~~~i~~~~~~~~~~~~~~~~vt~rl-lVp~---------~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~d 175 (587)
..+.. ....+..- .--...+++++ -|+. ..+|.|||++|++++.|++.|||+|.|. +
T Consensus 60 ~~i~~---gf~~e~A~-~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~---------~ 126 (172)
T TIGR03665 60 KAIGR---GFSPEKAL-KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY---------G 126 (172)
T ss_pred HHHHc---CCCHHHHH-HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc---------C
Confidence 22211 00000000 00001223332 2222 3689999999999999999999999994 3
Q ss_pred cEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844 176 QLIQITGATLAVKKALVAVTTCLQHL 201 (587)
Q Consensus 176 r~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (587)
+.|.|.|++++++.|..+|.+++.+.
T Consensus 127 ~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 127 KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 67999999999999999999999653
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.46 E-value=4.6e-13 Score=128.56 Aligned_cols=142 Identities=16% Similarity=0.199 Sum_probs=98.0
Q ss_pred EEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEe----cCCchhhhhhhccccccccCCCccH
Q 007844 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVV----GSGSIDRRIMFCENDVVVEGGEVSS 100 (587)
Q Consensus 25 v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~----G~~e~~~~a~~~~~~~~~e~~~~~~ 100 (587)
+...+-||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|. ++++.. ..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i-----------------~k 60 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAV-----------------LK 60 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHH-----------------HH
Confidence 567889999999999999999999999999999999863 2556675 333332 22
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEE-----ee-----cceeeeeeecCchHHHHHHhhhCCeEEecCCCCC
Q 007844 101 TQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLL-----AN-----TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPAC 170 (587)
Q Consensus 101 A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rll-----Vp-----~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~ 170 (587)
|++.+..+.. .-..+... ..-.+.+.+++. .+ ...+|.|||++|++++.|++.|||+|.|..
T Consensus 61 A~~~I~ai~~---gf~~e~A~-~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~---- 132 (180)
T PRK13763 61 ARDIVKAIGR---GFSPEKAL-RLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG---- 132 (180)
T ss_pred HHHHHHHHhc---CCCHHHHH-HHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----
Confidence 3333222211 00001000 000012222221 11 136899999999999999999999999954
Q ss_pred CCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844 171 AAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (587)
Q Consensus 171 ~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (587)
+.|.|.|+++++..|...|..++++.
T Consensus 133 -----~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 133 -----KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred -----CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 45899999999999999999999663
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=99.45 E-value=4.1e-13 Score=127.98 Aligned_cols=140 Identities=19% Similarity=0.207 Sum_probs=98.2
Q ss_pred EEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEe-cCCcCCCCChHHHHHHHHHhhhhcccccCCC
Q 007844 278 MLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISA-LEYLDTRHSPVQNAAVLVFARSVEVEGQQGF 356 (587)
Q Consensus 278 i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG-~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~ 356 (587)
+.||.+.+|.|||++|++|+.|+++||++|.+++. +..|.|.. +.+| ..++.|...|........+...+
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~ 72 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDP----LAVMKAREVVKAIGRGFSPEKAL 72 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCH----HHHHHHHHHHHHHHcCCCHHHHH
Confidence 56899999999999999999999999999999953 24688841 1111 34455555554432210100000
Q ss_pred CCCCCCCCceEEEEEeCc---------ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHH
Q 007844 357 SSGENKGDAVAVSILVGA---------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV 427 (587)
Q Consensus 357 ~~g~~~~~~~t~~l~VP~---------~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V 427 (587)
..-.....-.-+.|+. ..+|+|||++|++++.|++.|||+|.|.. ..|.|.|+++++
T Consensus 73 --~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~~ 138 (172)
T TIGR03665 73 --KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQV 138 (172)
T ss_pred --HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHHH
Confidence 0000111122234444 47999999999999999999999999952 679999999999
Q ss_pred HHHHHHHHHHHhh
Q 007844 428 QNALSEVVGRLRH 440 (587)
Q Consensus 428 ~~A~~~I~~~Lr~ 440 (587)
+.|.++|...|..
T Consensus 139 ~~A~~~i~~li~~ 151 (172)
T TIGR03665 139 QIAREAIEMLIEG 151 (172)
T ss_pred HHHHHHHHHHHcC
Confidence 9999999997754
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.40 E-value=2e-12 Score=124.10 Aligned_cols=145 Identities=19% Similarity=0.228 Sum_probs=99.7
Q ss_pred EEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccC
Q 007844 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ 354 (587)
Q Consensus 275 ~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~ 354 (587)
...+.||.+.+|.|||++|.+|+.|+++||++|++.+. +..|.|.-...++ ...+..|...+..-......+.
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d--~~~i~kA~~~I~ai~~gf~~e~ 76 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGED--PLAVLKARDIVKAIGRGFSPEK 76 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCC--HHHHHHHHHHHHHHhcCCCHHH
Confidence 56788999999999999999999999999999999954 2567776211001 1334455555443332100000
Q ss_pred CCCCCCCCCCceEEE-EEeC---------cccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCH
Q 007844 355 GFSSGENKGDAVAVS-ILVG---------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY 424 (587)
Q Consensus 355 g~~~g~~~~~~~t~~-l~VP---------~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~ 424 (587)
.+- . .......+ +.|. ...+|+|||++|++++.|++.|||+|.|.. ..|.|.|++
T Consensus 77 A~~--l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~ 141 (180)
T PRK13763 77 ALR--L-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDP 141 (180)
T ss_pred HHH--H-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCH
Confidence 000 0 01111111 1221 147999999999999999999999999953 349999999
Q ss_pred HHHHHHHHHHHHHHhhc
Q 007844 425 KNVQNALSEVVGRLRHN 441 (587)
Q Consensus 425 ~~V~~A~~~I~~~Lr~~ 441 (587)
++++.|...|...++.+
T Consensus 142 ~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 142 EQVEIAREAIEMLIEGA 158 (180)
T ss_pred HHHHHHHHHHHHHHcCC
Confidence 99999999999988654
No 15
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.32 E-value=3.7e-12 Score=101.71 Aligned_cols=65 Identities=31% Similarity=0.534 Sum_probs=59.3
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHH
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVT 195 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~ 195 (587)
++||+||.+.+|+||||+|++|++|+++|||+|.+.+. ......+|+|+|+|++++|.+|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS-VLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCC-CCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 37899999999999999999999999999999999985 334678999999999999999999873
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.32 E-value=3.3e-12 Score=102.04 Aligned_cols=65 Identities=28% Similarity=0.473 Sum_probs=59.0
Q ss_pred EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007844 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (587)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~ 435 (587)
+.+|+||.+.+|+|||++|++|++|+++|||+|++.+..+ ....+|.|+|+|+++++++|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhhC
Confidence 3689999999999999999999999999999999987554 2577899999999999999999983
No 17
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.24 E-value=5.1e-11 Score=126.69 Aligned_cols=275 Identities=20% Similarity=0.226 Sum_probs=172.9
Q ss_pred CCCCCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccC
Q 007844 16 GPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEG 95 (587)
Q Consensus 16 ~~~~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~ 95 (587)
+..+...+++.+.+.|++..+-.+|||.|++|+.|++.|+++|.+.+...+ ++++.++.|-+..
T Consensus 59 ~~e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~--------------- 122 (608)
T KOG2279|consen 59 TEEQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQ--------------- 122 (608)
T ss_pred ceecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCC---------------
Confidence 345667789999999999999999999999999999999999999765333 5677777665433
Q ss_pred CCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCC
Q 007844 96 GEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD 175 (587)
Q Consensus 96 ~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~d 175 (587)
+++|..++.. .+.. +..+...+-+|...++.|+|++|.+++.|+.-++|+|.+..+ .-...+
T Consensus 123 --v~~a~a~~~~---~~~~-----------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr~g~~ 184 (608)
T KOG2279|consen 123 --VCKAKAAIHQ---ILTE-----------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GRLGLS 184 (608)
T ss_pred --CChHHHHHHH---HHhc-----------CCcccccccchhhhcccccccchhhhcchhcccccccccccc--cccccc
Confidence 4555444332 2221 126667789999999999999999999999999999999874 334578
Q ss_pred cEEEEeecHHHHHHHHHHHHHHHhcCCCCCC-C------CcccCCCccccccCCCCCCCCCCCCC------cCCCCCCCC
Q 007844 176 QLIQITGATLAVKKALVAVTTCLQHLSTMEK-S------PICFNRPIEKVFYSNSSDPHREFFPH------LSLVPPLTG 242 (587)
Q Consensus 176 r~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~-~------~~~~~~P~~~~~~~~~~~~~~~~~p~------~~~~P~~~~ 242 (587)
+...|.|...-++.|..++.+.+.+.-..-+ . ..+...|...+. .....+.....+| .++.|..++
T Consensus 185 ~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~-~~m~~~~~s~~~h~~~~t~~s~spg~~~ 263 (608)
T KOG2279|consen 185 RLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRR-EDMTEPGGAGEPHLWKNTSSSMSPGAPL 263 (608)
T ss_pred cceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccc-hhhcccccCCccccCccchhccCCCCCC
Confidence 9999999999999999999998876421111 0 111111111110 0000000000011 012222111
Q ss_pred CCCCCCCccCCCCCCCCC--CCCCCC-ccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCC--
Q 007844 243 NPSDNASEFHSSSADADR--DHPGLD-KKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSG-- 317 (587)
Q Consensus 243 ~~~~y~~~~~p~~~~~~~--~~~~~~-~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~-- 317 (587)
... .++.........+ ..+..+ .........++|-+|...+|.+||+.|++++.+...+++.+.|........
T Consensus 264 ~~~--eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~ 341 (608)
T KOG2279|consen 264 VTK--EGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVL 341 (608)
T ss_pred ccc--CCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhh
Confidence 110 0000000000000 000000 011223346778899999999999999999999999999999875322221
Q ss_pred -ccEEEEEecC
Q 007844 318 -ERVVTISALE 327 (587)
Q Consensus 318 -er~V~IsG~~ 327 (587)
-.++.+.|+.
T Consensus 342 ~~qic~~egkq 352 (608)
T KOG2279|consen 342 QLQICVNEGKQ 352 (608)
T ss_pred hhhhheecchh
Confidence 2567777773
No 18
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.20 E-value=5.5e-11 Score=126.43 Aligned_cols=230 Identities=18% Similarity=0.216 Sum_probs=168.0
Q ss_pred CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCC
Q 007844 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTME 205 (587)
Q Consensus 126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~ 205 (587)
...+.+++.|+...+.+++||.|++|+.|+..++++|.+..+ ....+++..+.|-+.++.+|...+..++.++.
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e---d~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~--- 138 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE---DVGDERVLLISGFPVQVCKAKAAIHQILTENT--- 138 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc---cCCcccchhhccCCCCCChHHHHHHHHHhcCC---
Confidence 346889999999999999999999999999999999999774 22345556666689999999999999996631
Q ss_pred CCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccc
Q 007844 206 KSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTA 285 (587)
Q Consensus 206 ~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~v 285 (587)
.+...+.+|...+
T Consensus 139 -------------------------------------------------------------------pvk~~lsvpqr~~ 151 (608)
T KOG2279|consen 139 -------------------------------------------------------------------PVSEQLSVPQRSV 151 (608)
T ss_pred -------------------------------------------------------------------cccccccchhhhc
Confidence 1234456889999
Q ss_pred cccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccc--------------
Q 007844 286 SGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE-------------- 351 (587)
Q Consensus 286 G~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~-------------- 351 (587)
++|+|++|.+++.|+.-++|+|.+..+......+...|.+.. +....|-..+.+++.++.
T Consensus 152 ~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qq------k~~~~a~~~~~~~~~edeelv~~~~e~~q~rv 225 (608)
T KOG2279|consen 152 GRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQ------KEVAAAKHLILEKVSEDEELVKRIAESAQTRV 225 (608)
T ss_pred ccccccchhhhcchhcccccccccccccccccccceeccccc------chHHHHHhhhhccccchhHHhhhchhhcccCC
Confidence 999999999999999999999999977444456777777764 222223333333332210
Q ss_pred -------------------------------ccCCCCC-----------------------CC--CCCCceEEEEEeCcc
Q 007844 352 -------------------------------GQQGFSS-----------------------GE--NKGDAVAVSILVGAD 375 (587)
Q Consensus 352 -------------------------------~~~g~~~-----------------------g~--~~~~~~t~~l~VP~~ 375 (587)
...+.+. +. ......-.+|.||..
T Consensus 226 prk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~ 305 (608)
T KOG2279|consen 226 PRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEI 305 (608)
T ss_pred CCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcc
Confidence 0011000 00 012335567899999
Q ss_pred cccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHH
Q 007844 376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVG 436 (587)
Q Consensus 376 ~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~ 436 (587)
.+|.|||..|+.++.....|++.+.|--...... --.-.++.+.|+..-+..++.|+..
T Consensus 306 lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~--v~~~qic~~egkqh~~n~vl~ml~~ 364 (608)
T KOG2279|consen 306 LSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR--VLQLQICVNEGKQHYENSVLEMLTV 364 (608)
T ss_pred cccchhhhhhhhhhhhhhccCccceEEeccccch--hhhhhhheecchhHHHHHHHhhhhc
Confidence 9999999999999999999999999875322100 0011568899999999999999884
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=99.18 E-value=4.2e-11 Score=94.56 Aligned_cols=61 Identities=20% Similarity=0.330 Sum_probs=55.9
Q ss_pred EEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007844 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (587)
Q Consensus 368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~ 435 (587)
.+|.||.+++++|||++|++|++|++.|||+|.|++.. ..++.|+|+|+.++|..|+.+|.
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 57899999999999999999999999999999998743 46799999999999999999873
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=99.13 E-value=3.8e-11 Score=94.20 Aligned_cols=60 Identities=27% Similarity=0.422 Sum_probs=54.9
Q ss_pred EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007844 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (587)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I 434 (587)
|.+|.||.+++++|||++|++|++|+++|||+|+|++. + ++..|+|+|++++|++|+.+|
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 67899999999999999999999999999999999763 2 356999999999999999987
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.11 E-value=1.8e-10 Score=90.65 Aligned_cols=59 Identities=15% Similarity=0.255 Sum_probs=53.7
Q ss_pred eEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHH
Q 007844 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVV 435 (587)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~V~~A~~~I~ 435 (587)
.+..+.||.+++|+|||++|++|++|+++|||+|.|.+ ++.|.|+|+ .++++.|+.+|.
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHhC
Confidence 46789999999999999999999999999999999964 467999999 999999999873
No 22
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.06 E-value=4e-10 Score=89.20 Aligned_cols=62 Identities=26% Similarity=0.489 Sum_probs=56.6
Q ss_pred EEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007844 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (587)
Q Consensus 368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I 434 (587)
.+|.||.+++++|||++|++|++|++.|||+|.|+.... ...++.|+|.|+.+++..|+.+|
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 579999999999999999999999999999999987543 35789999999999999999887
No 23
>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=99.04 E-value=2e-10 Score=90.07 Aligned_cols=60 Identities=23% Similarity=0.418 Sum_probs=54.7
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I 194 (587)
|.+|.||.+++++|||++|++|++|+++|||+|.|... + .+..|+|+|+.++|.+|+.+|
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 67899999999999999999999999999999999762 2 445999999999999999886
No 24
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.03 E-value=4e-10 Score=88.96 Aligned_cols=60 Identities=27% Similarity=0.354 Sum_probs=55.2
Q ss_pred EEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007844 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (587)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I 194 (587)
.+|.||..++++|||++|++|++|+++|||+|.|... ...++.|+|+|+.++|.+|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~----~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP----GSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC----CCCCCEEEEEcCHHHHHHHHHHh
Confidence 4689999999999999999999999999999999773 25789999999999999999886
No 25
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.99 E-value=2.2e-09 Score=123.33 Aligned_cols=288 Identities=17% Similarity=0.154 Sum_probs=196.1
Q ss_pred CcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHH
Q 007844 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (587)
Q Consensus 23 ~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~ 102 (587)
..+..++.+-......+||++|.+++.++.++.+.|++++..... ....|.|...... .+.
T Consensus 199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~--~~~~i~~~~~~~~-----------------~~~ 259 (753)
T KOG2208|consen 199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSS--PSNKIDGRLNSSS-----------------SIN 259 (753)
T ss_pred eeEEEEeeccccchhhhccccccccccccccceeEEEcccccccc--hhhhhccccccce-----------------ehh
Confidence 357888999999999999999999999999999999998753322 2233444332210 011
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEee
Q 007844 103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182 (587)
Q Consensus 103 ~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G 182 (587)
--+...+.++. .+....+.++....-.++|..|..+..|+...--...+.+. +.+.+..+.+.|
T Consensus 260 ~~i~~~~~~le-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~---~~s~~~~~~~~~ 323 (753)
T KOG2208|consen 260 VEIQEALTRLE-------------SEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQN---YPSKDDSIVLSG 323 (753)
T ss_pred hhhHHHHHHhc-------------ChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhcc---ccccceeEeecc
Confidence 11111222221 12333466777777889999999999999887655555542 344667788888
Q ss_pred cHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCC
Q 007844 183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH 262 (587)
Q Consensus 183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~ 262 (587)
....+..+...-...+....
T Consensus 324 ~~~~~~~~~~~~~~~~~~~~------------------------------------------------------------ 343 (753)
T KOG2208|consen 324 FEVGAVLAKRDKTLLLKNSE------------------------------------------------------------ 343 (753)
T ss_pred cccchhhhhhHHHHHHHHhh------------------------------------------------------------
Confidence 87777766655444443310
Q ss_pred CCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHH
Q 007844 263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVL 342 (587)
Q Consensus 263 ~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~ 342 (587)
.......+.+-...+..|+||+|.+|.+|++++.+.+.+.. .++....++++|.. .....|...
T Consensus 344 --------~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~------~~~~ka~~~ 407 (753)
T KOG2208|consen 344 --------ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVS------ANDEKAVED 407 (753)
T ss_pred --------ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccc------cchhHHHHH
Confidence 11235556788899999999999999999999999999986 23456678888874 222334433
Q ss_pred HHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhC-CeEEEcCCCcccccCCCCCcEEEEc
Q 007844 343 VFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTG-TDIKLVGGEQVLGCAAQNDVVIQIS 421 (587)
Q Consensus 343 i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TG-a~I~i~~~~~~p~~~~~~~r~V~I~ 421 (587)
+.....+-. .......+.+|...+.+|||.+|..|++|...+| .+|+.+.. ......+++.
T Consensus 408 v~~~~~ei~-----------n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-------~~~~~~~~~~ 469 (753)
T KOG2208|consen 408 VEKIIAEIL-----------NSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-------NNSSDMVTIR 469 (753)
T ss_pred HHHHHHhhh-----------cccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-------CcccccceEe
Confidence 333332210 1145677999999999999999999999999999 66666553 2345667888
Q ss_pred CCHHHHHHHHHHHHHHHh
Q 007844 422 GEYKNVQNALSEVVGRLR 439 (587)
Q Consensus 422 G~~~~V~~A~~~I~~~Lr 439 (587)
|....+..++.+......
T Consensus 470 ~~~~dv~~~~~~~~~~~~ 487 (753)
T KOG2208|consen 470 GISKDVEKSVSLLKALKA 487 (753)
T ss_pred ccccccchhHHHHHhhhh
Confidence 887777776666654443
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=98.97 E-value=2.2e-09 Score=84.57 Aligned_cols=58 Identities=26% Similarity=0.343 Sum_probs=52.8
Q ss_pred eEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHH
Q 007844 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAV 194 (587)
Q Consensus 129 vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I 194 (587)
.+..+-||.+++|+||||+|++|++|+++|||+|.|.. ++.|.|+|+ .+++.+|+.+|
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 45678899999999999999999999999999999965 467999999 99999999886
No 27
>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=98.97 E-value=1.9e-09 Score=85.23 Aligned_cols=62 Identities=31% Similarity=0.532 Sum_probs=56.2
Q ss_pred EEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007844 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (587)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I 194 (587)
.++.||..++++|||++|++|++|+++|||+|.|... .....++.|.|.|..+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~--~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDS--GSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCC--CCCCCceEEEEEcCHHHHHHHHHHh
Confidence 5799999999999999999999999999999999873 2246789999999999999999876
No 28
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.89 E-value=3.4e-09 Score=121.79 Aligned_cols=301 Identities=16% Similarity=0.165 Sum_probs=196.9
Q ss_pred EEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHH
Q 007844 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEA 104 (587)
Q Consensus 25 v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~A 104 (587)
....+-+-......|+||+|.+|.+|+++++|.|.+... +..+..+.+++..+++ ..|.+.
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~-----------------~ka~~~ 407 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND-----------------EKAVED 407 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch-----------------hHHHHH
Confidence 445556677889999999999999999999999999874 4566789999888763 445566
Q ss_pred HHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhC-CeEEecCCCCCCCCCCcEEEEeec
Q 007844 105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESG-AKIVMLPPPACAAIDDQLIQITGA 183 (587)
Q Consensus 105 l~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etG-a~I~I~~~p~~~~~~dr~V~I~G~ 183 (587)
+..++..+... .+.-.+++|...+..|||.+|..|..|..++| ..|.... .......+++.|.
T Consensus 408 v~~~~~ei~n~------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~----~~~~~~~~~~~~~ 471 (753)
T KOG2208|consen 408 VEKIIAEILNS------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQN----NNNSSDMVTIRGI 471 (753)
T ss_pred HHHHHHhhhcc------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCC----CCcccccceEecc
Confidence 66655554331 34455899999999999999999999999999 5555544 2345556788888
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCC
Q 007844 184 TLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHP 263 (587)
Q Consensus 184 ~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~ 263 (587)
...+..+..+...+........
T Consensus 472 ~~dv~~~~~~~~~~~~~a~~~~---------------------------------------------------------- 493 (753)
T KOG2208|consen 472 SKDVEKSVSLLKALKADAKNLK---------------------------------------------------------- 493 (753)
T ss_pred ccccchhHHHHHhhhhhhhcch----------------------------------------------------------
Confidence 8888887766665554321100
Q ss_pred CCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHH
Q 007844 264 GLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLV 343 (587)
Q Consensus 264 ~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i 343 (587)
.....+.+...|..+.+..+|+.|..+....++....+..+ ..+..++|.|... .+.+|...+
T Consensus 494 ------~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~-----~~~~~i~i~gk~~------~v~~a~~~L 556 (753)
T KOG2208|consen 494 ------FRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNED-----EDHEKITIEGKLE------LVLEAPAEL 556 (753)
T ss_pred ------hhhhhhccccchHHhhcccccCceeeeccCCceeecccccc-----cccceeeeccccc------chhhhHHHH
Confidence 01122334556777777777777776666665555433322 3456788888752 222333333
Q ss_pred HhhhhcccccCCCCCCCCCCCceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC
Q 007844 344 FARSVEVEGQQGFSSGENKGDAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG 422 (587)
Q Consensus 344 ~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G 422 (587)
...+... .......+.+|. .+.-++++++....+..+...|+.+.+++. ....+.++|.|
T Consensus 557 ~~~~~~~------------~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~-------~~~~~e~~i~g 617 (753)
T KOG2208|consen 557 KALIEAL------------IKATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRS-------PTSSDEVSIKG 617 (753)
T ss_pred Hhcchhh------------hhhhhhhccCcchheeeeeeccccccccceeecCcccccCCCC-------CCchhhhccch
Confidence 3333111 112233444454 455566666666666666666678877763 34566899999
Q ss_pred CHHHHHHHHHHHHHHHh---hcccCccccccCCCC
Q 007844 423 EYKNVQNALSEVVGRLR---HNLKSGEILNEARPR 454 (587)
Q Consensus 423 ~~~~V~~A~~~I~~~Lr---~~~~~~~~~~~~~~~ 454 (587)
....++.|...+..... .+...+-+++....+
T Consensus 618 ~~~~v~aa~~~~~~i~~~~~~~~~~~~~i~~~~~~ 652 (753)
T KOG2208|consen 618 AKDEVKAAKGRLEEIVEYLSAYATTNTKIPDKFHR 652 (753)
T ss_pred hHHHHHHhhccchhhhhhcccccceeeecccccce
Confidence 99999999988877555 344444344333333
No 29
>PF13014 KH_3: KH domain
Probab=98.83 E-value=5.9e-09 Score=76.07 Aligned_cols=42 Identities=40% Similarity=0.727 Sum_probs=38.5
Q ss_pred ccceeccCCChHHHHHHhHhCceEEEeC-CCCCCCceEEEEec
Q 007844 35 VVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVG 76 (587)
Q Consensus 35 ~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~~~~eRvI~I~G 76 (587)
++|+|||++|++|++|+++|||+|+|++ ..++..+|+|+|+|
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 4799999999999999999999999988 55678899999987
No 30
>PF13014 KH_3: KH domain
Probab=98.79 E-value=7e-09 Score=75.68 Aligned_cols=43 Identities=33% Similarity=0.630 Sum_probs=37.9
Q ss_pred cccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC
Q 007844 376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG 422 (587)
Q Consensus 376 ~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G 422 (587)
+||+|||++|++|++|+++|||+|+|++. .. ....++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~-~~---~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPE-NE---PGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCc-cC---CCCCceEEEEEC
Confidence 58999999999999999999999999982 21 357899999998
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.76 E-value=3.7e-08 Score=78.02 Aligned_cols=68 Identities=29% Similarity=0.521 Sum_probs=60.4
Q ss_pred ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHh
Q 007844 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439 (587)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr 439 (587)
..+.++.||.++++++||++|++|++|++.||++|.+.... .....|+|.|+.++++.|+.+|...++
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 35789999999999999999999999999999999997532 257899999999999999999988763
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.67 E-value=1.2e-07 Score=74.97 Aligned_cols=67 Identities=27% Similarity=0.487 Sum_probs=60.3
Q ss_pred ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007844 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198 (587)
Q Consensus 128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L 198 (587)
.++.++.||...++.+||++|++|++|++++|++|.+... .....++.|.|+.+++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~----~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED----GSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC----CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 4678899999999999999999999999999999999763 225789999999999999999998876
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.60 E-value=2.8e-07 Score=87.71 Aligned_cols=141 Identities=16% Similarity=0.208 Sum_probs=98.6
Q ss_pred CcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCc---hhh--hhh---hcccccccc
Q 007844 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGS---IDR--RIM---FCENDVVVE 94 (587)
Q Consensus 23 ~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e---~~~--~a~---~~~~~~~~e 94 (587)
....+.+.+|.+..+.+||+.|++.+.|.+.++++|.++. .+..|.|..... ... +|. ..++..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG--- 77 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRG--- 77 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcC---
Confidence 4456779999999999999999999999999999999953 456788876532 111 000 001111
Q ss_pred CCCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEE-----ee------cceeeeeeecCchHHHHHHhhhCCeEE
Q 007844 95 GGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLL-----AN------TTKIGVVVGKGGRNVTRMRIESGAKIV 163 (587)
Q Consensus 95 ~~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rll-----Vp------~~~vG~IIGkgG~~Ik~I~~etGa~I~ 163 (587)
+++- +|+.. ++. .+.|.+. +. ....|+|||++|.+-+.|++-|||+|.
T Consensus 78 ---F~pe-~A~~L-L~d----------------~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~ 136 (194)
T COG1094 78 ---FPPE-KALKL-LED----------------DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYIS 136 (194)
T ss_pred ---CCHH-HHHHH-hcC----------------CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEE
Confidence 1111 11111 100 2222211 11 124599999999999999999999999
Q ss_pred ecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844 164 MLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (587)
Q Consensus 164 I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (587)
|. +..|.|-|.+++|+.|...|..++...
T Consensus 137 V~---------g~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 137 VY---------GKTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred Ee---------CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence 94 468999999999999999999999764
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.48 E-value=1.1e-06 Score=83.76 Aligned_cols=143 Identities=19% Similarity=0.226 Sum_probs=98.6
Q ss_pred eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccccc
Q 007844 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQ 353 (587)
Q Consensus 274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~ 353 (587)
....+.||.+..+.+||+.|...+.|.+.+++++.++.. +..|+|..++.-.++ ...+.|...+.. +.
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp-~~~~ka~d~VkA------Ig 75 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDP-LALLKARDVVKA------IG 75 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCCh-HHHHHHHHHHHH------Hh
Confidence 356688999999999999999999999999999999833 456888776311111 122233222211 12
Q ss_pred CCCCCC----CCCCCceEEEEEe------C----cccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEE
Q 007844 354 QGFSSG----ENKGDAVAVSILV------G----ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQ 419 (587)
Q Consensus 354 ~g~~~g----~~~~~~~t~~l~V------P----~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~ 419 (587)
.|+++. +-.....-..+.+ + ....|+|||++|.+.+-|++.|||.|-|.. .+|.
T Consensus 76 rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tVa 143 (194)
T COG1094 76 RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTVA 143 (194)
T ss_pred cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEEE
Confidence 233320 0001111111111 1 236799999999999999999999999963 6799
Q ss_pred EcCCHHHHHHHHHHHHHHHhh
Q 007844 420 ISGEYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 420 I~G~~~~V~~A~~~I~~~Lr~ 440 (587)
|-|.+++|+.|.+.|...+..
T Consensus 144 iiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 144 IIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred EecChhhhHHHHHHHHHHHcC
Confidence 999999999999999998775
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=98.11 E-value=6.5e-06 Score=73.71 Aligned_cols=68 Identities=19% Similarity=0.370 Sum_probs=53.7
Q ss_pred ccccccccCCCchhHHHHHhhCCeEEEcCCCcc-----------ccc-CCCCCcEEEEcCCH---HHHHHHHHHHHHHHh
Q 007844 375 DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV-----------LGC-AAQNDVVIQISGEY---KNVQNALSEVVGRLR 439 (587)
Q Consensus 375 ~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~-----------p~~-~~~~~r~V~I~G~~---~~V~~A~~~I~~~Lr 439 (587)
+++|.|||++|++||+|+++|||+|.|..+... |.+ ..++.-.|.|++.. +++++|+.+|...|.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 689999999999999999999999999875210 111 12344789999975 899999999999888
Q ss_pred hcc
Q 007844 440 HNL 442 (587)
Q Consensus 440 ~~~ 442 (587)
...
T Consensus 95 ~~~ 97 (120)
T cd02395 95 PAI 97 (120)
T ss_pred cCC
Confidence 543
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=98.06 E-value=1.7e-05 Score=71.07 Aligned_cols=64 Identities=25% Similarity=0.352 Sum_probs=51.7
Q ss_pred ceeeeeeecCchHHHHHHhhhCCeEEecCC-CC--------------CCCCCCcEEEEeecH---HHHHHHHHHHHHHHh
Q 007844 138 TKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PA--------------CAAIDDQLIQITGAT---LAVKKALVAVTTCLQ 199 (587)
Q Consensus 138 ~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~--------------~~~~~dr~V~I~G~~---e~V~~A~~~I~~~L~ 199 (587)
+.+|.|||++|++||+|+++|||+|.|..+ .. .....+-.|.|++.. +++.+|+.+|..++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 578999999999999999999999999864 00 001223578899975 999999999999997
Q ss_pred cC
Q 007844 200 HL 201 (587)
Q Consensus 200 e~ 201 (587)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 53
No 37
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.93 E-value=2.6e-05 Score=71.87 Aligned_cols=102 Identities=13% Similarity=0.122 Sum_probs=69.1
Q ss_pred EEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHH
Q 007844 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAV 105 (587)
Q Consensus 26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al 105 (587)
.+.++|+...+|+.||++|++|+.|++..|-+|+|-....+ ++
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d-----------~~-------------------------- 75 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD-----------PE-------------------------- 75 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC-----------HH--------------------------
Confidence 45678899999999999999999999999988887442111 00
Q ss_pred HHHHHHHHhhhhccCC-CCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEec
Q 007844 106 IRVFERMWEVEAEVEG-DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165 (587)
Q Consensus 106 ~~i~~~i~~~~~~~~~-~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~ 165 (587)
..+..+.....-.+- -...+....+.+.|+....|.+|||+|++|+.++.-++-++.|.
T Consensus 76 -~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 76 -EFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred -HHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 011111110000000 00011235667789999999999999999999999999887763
No 38
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.90 E-value=1.2e-05 Score=80.72 Aligned_cols=149 Identities=18% Similarity=0.253 Sum_probs=104.7
Q ss_pred cceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHh---hhh
Q 007844 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA---RSV 348 (587)
Q Consensus 272 ~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~---~v~ 348 (587)
+.++..+.||..+++.|.|++|.+||.|+.+|...|+-+... .+-++.++|.. + -+..|-..|.. .+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~--e----dv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRH--E----DVRRARREIPSAAEHFG 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCc--h----hHHHHhhcCccccceee
Confidence 566777889999999999999999999999999998766331 23567888873 1 11122221111 000
Q ss_pred cccccCCCC---CCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHH
Q 007844 349 EVEGQQGFS---SGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425 (587)
Q Consensus 349 e~~~~~g~~---~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~ 425 (587)
--...+.+. .+...+.+.+..+.+|-+.+|.+.|..|.+|+.||+.+...|.-+-+ ..+.++-++|.+.
T Consensus 95 l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~~ 166 (394)
T KOG2113|consen 95 LIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPK 166 (394)
T ss_pred eeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCc
Confidence 000001111 12233567888999999999999999999999999999999987653 4578899999999
Q ss_pred H-HHHHH-HHHHHH
Q 007844 426 N-VQNAL-SEVVGR 437 (587)
Q Consensus 426 ~-V~~A~-~~I~~~ 437 (587)
+ +++|. ..|...
T Consensus 167 nC~kra~s~eie~t 180 (394)
T KOG2113|consen 167 NCVKRARSCEIEQT 180 (394)
T ss_pred chhhhccccchhhh
Confidence 8 77776 555543
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.66 E-value=8.3e-05 Score=74.87 Aligned_cols=154 Identities=18% Similarity=0.185 Sum_probs=109.0
Q ss_pred CCCCCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccC
Q 007844 16 GPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEG 95 (587)
Q Consensus 16 ~~~~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~ 95 (587)
.+...+ +.++..+-||...++.|.|++|-+||.|+.+|...|+-+-. -.|-+..++|..+.+++|..++.-.
T Consensus 18 ~~~~~p-~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv~~aRrei~sa---- 89 (394)
T KOG2113|consen 18 YRTSIG-QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDVRRARREIPSA---- 89 (394)
T ss_pred cCCCCC-CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhHHHHhhcCccc----
Confidence 333444 88899999999999999999999999999999999986432 1346788899999988887765321
Q ss_pred CCccHHHHHHHHHHHHHHhhhhccCC-CCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCC
Q 007844 96 GEVSSTQEAVIRVFERMWEVEAEVEG-DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAID 174 (587)
Q Consensus 96 ~~~~~A~~Al~~i~~~i~~~~~~~~~-~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~ 174 (587)
| .++-..+.......+- ........+...-+|-..+|.|.|..|.+|++|++.++..|.-.- .| .
T Consensus 90 -----a----eH~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v--~~---~ 155 (394)
T KOG2113|consen 90 -----A----EHFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV--RC---G 155 (394)
T ss_pred -----c----ceeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeec--cC---C
Confidence 1 0100000000000000 011234566777889999999999999999999999999988766 23 6
Q ss_pred CcEEEEeecHHH-HHHHH
Q 007844 175 DQLIQITGATLA-VKKAL 191 (587)
Q Consensus 175 dr~V~I~G~~e~-V~~A~ 191 (587)
+-+..++|-+.+ +.+|.
T Consensus 156 ~~Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 156 EPVFCVTGAPKNCVKRAR 173 (394)
T ss_pred CceEEEecCCcchhhhcc
Confidence 678889999888 44444
No 40
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.65 E-value=0.00017 Score=82.11 Aligned_cols=93 Identities=13% Similarity=0.205 Sum_probs=71.1
Q ss_pred ChHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCC
Q 007844 334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ 413 (587)
Q Consensus 334 ~~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~ 413 (587)
..+.++...|++.+.+....+ ...........++.||.+++|.|||+||.+||+|+++|||+|.|.+
T Consensus 549 ~~A~~g~~~Il~~m~~al~~p---~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------- 615 (719)
T TIGR02696 549 KQARDARLAILDVMAEAIDTP---DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHhCc---cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----------
Confidence 344566666766665432222 1122345678889999999999999999999999999999999853
Q ss_pred CCcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844 414 NDVVIQISG-EYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 414 ~~r~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (587)
+..|.|.+ +.+.+++|+.+|...++.
T Consensus 616 -~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 -DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred -CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 57788887 567899999999998884
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=97.62 E-value=0.00025 Score=80.69 Aligned_cols=93 Identities=18% Similarity=0.228 Sum_probs=73.0
Q ss_pred cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI 178 (587)
Q Consensus 99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V 178 (587)
..|.++..+++..+.+..... .+-....+....+.||.+.++.|||+||.+||.|.++|||+|.|.. +..|
T Consensus 549 ~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------~G~V 619 (719)
T TIGR02696 549 KQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--------DGTV 619 (719)
T ss_pred HHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--------CcEE
Confidence 456667777766655443333 2222334667788999999999999999999999999999999954 5778
Q ss_pred EEeec-HHHHHHHHHHHHHHHhc
Q 007844 179 QITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 179 ~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
.|.+. .+++.+|+.+|..++..
T Consensus 620 ~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 620 YIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred EEEeCCHHHHHHHHHHHHHhhCc
Confidence 88886 99999999999999974
No 42
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.59 E-value=0.00026 Score=65.21 Aligned_cols=102 Identities=16% Similarity=0.163 Sum_probs=71.2
Q ss_pred eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhh--hccc
Q 007844 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS--VEVE 351 (587)
Q Consensus 274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v--~e~~ 351 (587)
..+.++|+...+|..||++|++|+.|++..|-+|.+-.-..+ ..+-+..++..+ .+..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d--------------------~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD--------------------PEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC--------------------HHHHHHHHcCCCEEEEEE
Confidence 366788999999999999999999999999988877642111 011111111111 0000
Q ss_pred ccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEc
Q 007844 352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (587)
Q Consensus 352 ~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~ 402 (587)
.. .........+.|+.+..|..|||+|++|+.++..+|-++.|.
T Consensus 92 I~-------~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 92 IK-------KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EE-------ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 00 012345677889999999999999999999999999998774
No 43
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.41 E-value=0.00045 Score=63.57 Aligned_cols=102 Identities=14% Similarity=0.152 Sum_probs=68.5
Q ss_pred EEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCch-hhhhhhccccccccCCCccHHHHH
Q 007844 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQEA 104 (587)
Q Consensus 26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~-~~~a~~~~~~~~~e~~~~~~A~~A 104 (587)
-+=++|....+|+.||++|++|+.|++..|-+|+|-+...+ ++. +.+ .++||.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D-----------~~~fI~N-------------~l~PA~-- 87 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-----------LEEFVAN-------------KLAPAE-- 87 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-----------HHHHHHH-------------cCCCce--
Confidence 44467788899999999999999999988988887442111 111 000 011110
Q ss_pred HHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEec
Q 007844 105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165 (587)
Q Consensus 105 l~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~ 165 (587)
+..... ...++.....+.|+..+.+..|||+|++|+..++-++-++.|.
T Consensus 88 -------V~~V~i-----~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 88 -------VKNVTV-----SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred -------EEEEEE-----EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 000000 0011245677889999999999999999999999999887763
No 44
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.27 E-value=0.00076 Score=77.76 Aligned_cols=94 Identities=21% Similarity=0.267 Sum_probs=69.6
Q ss_pred cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI 178 (587)
Q Consensus 99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V 178 (587)
..|.++..++++.+.....+...+...-.+....+-||.+.++.|||+||++||+|.++|||+|.|.. +..|
T Consensus 521 ~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------dG~V 592 (684)
T TIGR03591 521 EQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------DGTV 592 (684)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec--------CeEE
Confidence 34555666666655544333222222334667788999999999999999999999999999999954 4667
Q ss_pred EEeec-HHHHHHHHHHHHHHHhc
Q 007844 179 QITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 179 ~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
.|.+. .+.+.+|..+|..+..+
T Consensus 593 ~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 593 KIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred EEEECcHHHHHHHHHHHHhhhcc
Confidence 77765 88999999999988653
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.18 E-value=0.0017 Score=69.59 Aligned_cols=73 Identities=19% Similarity=0.259 Sum_probs=59.0
Q ss_pred ceEEEEEeec------ceeeeeeecCchHHHHHHhhhCCeEEecCC----C--------C--CCCCCCcEEEEeec-HHH
Q 007844 128 VAYCGLLANT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPP----P--------A--CAAIDDQLIQITGA-TLA 186 (587)
Q Consensus 128 ~vt~rllVp~------~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~----p--------~--~~~~~dr~V~I~G~-~e~ 186 (587)
.++.|+.||. +.+|+|||.+|.|.|+|+++|||+|.|..+ + . -....+=-|.|+++ .|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 6778888886 489999999999999999999999999863 0 0 11123345788888 889
Q ss_pred HHHHHHHHHHHHhc
Q 007844 187 VKKALVAVTTCLQH 200 (587)
Q Consensus 187 V~~A~~~I~~~L~e 200 (587)
|.+|+..|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
No 46
>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=97.13 E-value=0.0011 Score=76.62 Aligned_cols=67 Identities=18% Similarity=0.298 Sum_probs=56.6
Q ss_pred CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844 363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (587)
......++.||.+.++.|||+||++||+|+++|||+|.|.+ +-.|.|.+ ..+.+++|..+|......
T Consensus 548 ~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 548 YAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred cCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 35678889999999999999999999999999999999954 35566665 566899999999887664
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=97.03 E-value=0.0014 Score=60.28 Aligned_cols=101 Identities=14% Similarity=0.124 Sum_probs=69.4
Q ss_pred EEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHH--hhhhcccc
Q 007844 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEG 352 (587)
Q Consensus 275 ~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~--~~v~e~~~ 352 (587)
.+-++|....+|..||++|.+|+.|++..|-+|.+-.-..+.. +-+..++ .++.....
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~~--------------------~fI~N~l~PA~V~~V~i 93 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENLE--------------------EFVANKLAPAEVKNVTV 93 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCCHH--------------------HHHHHcCCCceEEEEEE
Confidence 5557789999999999999999999988898887764211100 0000000 00000000
Q ss_pred cCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEc
Q 007844 353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (587)
Q Consensus 353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~ 402 (587)
. .........+.||.+..+..|||+|++|+...+.+|-++.|.
T Consensus 94 ~-------~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 94 S-------EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred E-------cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 0 012345678999999999999999999999999999988764
No 48
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.78 E-value=0.0044 Score=59.90 Aligned_cols=101 Identities=19% Similarity=0.250 Sum_probs=66.8
Q ss_pred EEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHH
Q 007844 28 RLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIR 107 (587)
Q Consensus 28 riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~ 107 (587)
-..+-.+.+|..||++|++|+.|+++.|-+|+|-...++ ++. ...+||.-
T Consensus 79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------~~~-------------------fI~nal~P 128 (190)
T COG0195 79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------PAE-------------------FIKNALAP 128 (190)
T ss_pred EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------HHH-------------------HHHHhcCc
Confidence 334445778999999999999999999977877433211 100 01111110
Q ss_pred HHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844 108 VFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (587)
Q Consensus 108 i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~ 166 (587)
+ ++...... ..+.. ...+.||.++.+..|||+|.+++.+.+-||-++.|..
T Consensus 129 a--~v~~V~~~-----~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 129 A--EVLSVNIK-----EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred c--eEeEEEEE-----eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0 00000000 00112 7788899999999999999999999999999999965
No 49
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.72 E-value=0.0027 Score=74.03 Aligned_cols=94 Identities=14% Similarity=0.195 Sum_probs=71.5
Q ss_pred cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCe-EEecCCCCCCCCCCcE
Q 007844 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAK-IVMLPPPACAAIDDQL 177 (587)
Q Consensus 99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~-I~I~~~p~~~~~~dr~ 177 (587)
..|.++..+++..+.+.....-.+-....+....|-||.+.++.|||.||.+||.|.++||++ |.+.. +-.
T Consensus 655 ~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d--------dg~ 726 (891)
T PLN00207 655 LQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD--------DGT 726 (891)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC--------Cee
Confidence 456667777766655443222111222346778899999999999999999999999999999 88854 467
Q ss_pred EEEeec-HHHHHHHHHHHHHHHhc
Q 007844 178 IQITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 178 V~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
|.|.+. .+.+.+|+.+|..++.+
T Consensus 727 V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 727 VKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred EEEEeCCHHHHHHHHHHHHHHhcC
Confidence 888885 99999999999999864
No 50
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.66 E-value=0.004 Score=69.73 Aligned_cols=99 Identities=13% Similarity=0.161 Sum_probs=74.4
Q ss_pred ChHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCC
Q 007844 334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ 413 (587)
Q Consensus 334 ~~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~ 413 (587)
.++..|.++|+..+.+....+ . ...........++.|+.+.++-+||++|.+|++|.++|||+|.|.
T Consensus 522 ~QAk~aRlhIL~~M~~ai~~p-r-~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------- 588 (692)
T COG1185 522 EQAKGARLHILIVMNEAISEP-R-KELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------- 588 (692)
T ss_pred HHHHHHHHHHHHHHHHHHhhh-h-hhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------
Confidence 445566667777775432111 0 001123456778899999999999999999999999999999995
Q ss_pred CCcEEEEcCCH-HHHHHHHHHHHHHHhhcccCc
Q 007844 414 NDVVIQISGEY-KNVQNALSEVVGRLRHNLKSG 445 (587)
Q Consensus 414 ~~r~V~I~G~~-~~V~~A~~~I~~~Lr~~~~~~ 445 (587)
++-+|.|.++. +.+++|+..|.+.+++..+..
T Consensus 589 ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~ 621 (692)
T COG1185 589 DDGTVKIAASDGESAKKAKERIEAITREVEVGE 621 (692)
T ss_pred CCCcEEEEecchHHHHHHHHHHHHHHhhccccc
Confidence 25678888888 679999999999999877654
No 51
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.61 E-value=0.0024 Score=67.20 Aligned_cols=67 Identities=18% Similarity=0.292 Sum_probs=55.8
Q ss_pred ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHh
Q 007844 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439 (587)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr 439 (587)
....-+.|-+++||.+||++|+.|+.||..|.++|+|.+. +.+..|+|.|...--.+|+..|..-++
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence 3445567888999999999999999999999999999874 348899999999988888777755443
No 52
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.57 E-value=0.0049 Score=66.09 Aligned_cols=76 Identities=17% Similarity=0.335 Sum_probs=57.6
Q ss_pred ceEEEEEeCc------ccccccccCCCchhHHHHHhhCCeEEEcCC---------Cccccc--CCCCCcEEEEcCCH-HH
Q 007844 365 AVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGG---------EQVLGC--AAQNDVVIQISGEY-KN 426 (587)
Q Consensus 365 ~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~---------~~~p~~--~~~~~r~V~I~G~~-~~ 426 (587)
..+.+|.||- ++||.|||..|.|.|+|+++|||+|.|-.+ .+.+.+ ..+++--+.|+.+. ++
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 5677777774 689999999999999999999999999761 111111 13445567777765 47
Q ss_pred HHHHHHHHHHHHhh
Q 007844 427 VQNALSEVVGRLRH 440 (587)
Q Consensus 427 V~~A~~~I~~~Lr~ 440 (587)
|++|..+|...|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999888885
No 53
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.54 E-value=0.0045 Score=72.28 Aligned_cols=92 Identities=14% Similarity=0.181 Sum_probs=66.9
Q ss_pred HHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCe-EEEcCCCcccccCCCC
Q 007844 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTD-IKLVGGEQVLGCAAQN 414 (587)
Q Consensus 336 a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~-I~i~~~~~~p~~~~~~ 414 (587)
+.++...|++.|.+....+ .. ...........+.||.++++.|||.||.+||+|+++||++ |.+.+
T Consensus 657 A~~g~~~Il~~M~~~i~~p-r~-~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d----------- 723 (891)
T PLN00207 657 AKDGRKHILAEMSKCSPPP-SK-RLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD----------- 723 (891)
T ss_pred HHHHHHHHHHHHHHHHhhh-hh-hhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----------
Confidence 4455555666654432111 00 1123456788899999999999999999999999999999 86643
Q ss_pred CcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844 415 DVVIQISG-EYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 415 ~r~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (587)
+-.|.|.+ +.+.+++|+.+|.....+
T Consensus 724 dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 724 DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 56788877 667899999999988764
No 54
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.51 E-value=0.0017 Score=68.38 Aligned_cols=67 Identities=21% Similarity=0.281 Sum_probs=54.2
Q ss_pred CCCCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhh
Q 007844 17 PLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMF 86 (587)
Q Consensus 17 ~~~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~ 86 (587)
+-....+++.+++-+-+.+||.|||++|++|+.||..|+++|++... ..|-.|+|.|..+-..+|+.
T Consensus 39 ~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m~~kaka 105 (629)
T KOG0336|consen 39 SAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHMRKKAKA 105 (629)
T ss_pred ccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHHHHHHHh
Confidence 44566678999999999999999999999999999999999999653 34567888887654444433
No 55
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.49 E-value=0.012 Score=58.76 Aligned_cols=81 Identities=20% Similarity=0.292 Sum_probs=58.2
Q ss_pred CCceEEEEEeCc------ccccccccCCCchhHHHHHhhCCeEEEcCCCc------------ccccCC---CCCcEEEEc
Q 007844 363 GDAVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ------------VLGCAA---QNDVVIQIS 421 (587)
Q Consensus 363 ~~~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~------------~p~~~~---~~~r~V~I~ 421 (587)
....+.+|+||- ++||+|+|+.|.++|+++++|||+|-|-.+.- .|+|.. .--.+|+..
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 456888899886 49999999999999999999999999976432 233322 123677888
Q ss_pred CCHHHHHHHHHHHHHHHhhccc
Q 007844 422 GEYKNVQNALSEVVGRLRHNLK 443 (587)
Q Consensus 422 G~~~~V~~A~~~I~~~Lr~~~~ 443 (587)
.++..+..=+..-.+.|+++++
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcC
Confidence 8887766644444555555553
No 56
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.49 E-value=0.0028 Score=63.34 Aligned_cols=40 Identities=20% Similarity=0.500 Sum_probs=36.1
Q ss_pred CCcEEEEEEeccC------ccceeccCCChHHHHHHhHhCceEEEe
Q 007844 22 DDVVSFRLVCPTP------VVGGLIGRSGSIISSIRRDTKCRIHCE 61 (587)
Q Consensus 22 ~~~v~~riLvP~~------~vG~IIGk~G~~Ik~IreeTga~I~V~ 61 (587)
+-.++.||+||.+ +||+|+|.+|.++|+|+++|+|+|.|-
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 3466889999996 799999999999999999999999995
No 57
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.43 E-value=0.011 Score=66.39 Aligned_cols=95 Identities=20% Similarity=0.240 Sum_probs=71.5
Q ss_pred ccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcE
Q 007844 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (587)
Q Consensus 98 ~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~ 177 (587)
+..|..|-++++..+.+.-.+...+...-.+-...+-|+...+.-+||++|.+|++|.++|||+|.|.. |..
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied--------dGt 592 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED--------DGT 592 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC--------CCc
Confidence 345667777777666544332211111222445667889999999999999999999999999999953 567
Q ss_pred EEEeec-HHHHHHHHHHHHHHHhc
Q 007844 178 IQITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 178 V~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
|.|.+. .+.+.+|+..|..+.++
T Consensus 593 v~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 593 VKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred EEEEecchHHHHHHHHHHHHHHhh
Confidence 889888 69999999999999976
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=96.42 E-value=0.0044 Score=48.66 Aligned_cols=37 Identities=22% Similarity=0.261 Sum_probs=34.5
Q ss_pred cEEEEEEeccCccceeccCCChHHHHHHhHhCceEEE
Q 007844 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (587)
Q Consensus 24 ~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V 60 (587)
...+.+.|+.+..|.+|||+|.+|+.+++.++.+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999998876
No 59
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.39 E-value=0.004 Score=63.86 Aligned_cols=70 Identities=19% Similarity=0.284 Sum_probs=58.0
Q ss_pred eEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (587)
Q Consensus 129 vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (587)
...-++|+....++|||++|.|-++|+++|+++|.++.. . ...+.++.+.+..++|.+|...|...|.+.
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-~--~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-N--TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-C--CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 445589999999999999999999999999999999772 1 234555555556999999999999999774
No 60
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.22 E-value=0.013 Score=62.01 Aligned_cols=95 Identities=21% Similarity=0.269 Sum_probs=63.9
Q ss_pred CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (587)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (587)
+-+|+.||++|++|+.|.++. |-+|+|-....+..+ . +.+| ++||. +
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~---f-------i~na-------------l~Pa~---------v 290 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAE---F-------IANA-------------LSPAK---------V 290 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------cCCce---------E
Confidence 558999999999999999999 778887433211100 0 0000 11110 0
Q ss_pred HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (587)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~ 166 (587)
....... ...-.+.+.||..+.+..|||+|.+++....-||.+|.|..
T Consensus 291 ~~v~i~~------~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 291 ISVEVLD------EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEEc------CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 0000000 01246789999999999999999999999999999999965
No 61
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.20 E-value=0.0038 Score=60.30 Aligned_cols=101 Identities=20% Similarity=0.230 Sum_probs=68.8
Q ss_pred EEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHh--hhhccccc
Q 007844 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA--RSVEVEGQ 353 (587)
Q Consensus 276 ~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~--~v~e~~~~ 353 (587)
+-..+-.+.+|..||++|.+|+.|.++.|-+|.|-.-.+ .++ +-+..++. ++....+.
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~-------------------d~~-~fI~nal~Pa~v~~V~~~ 137 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE-------------------DPA-EFIKNALAPAEVLSVNIK 137 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC-------------------CHH-HHHHHhcCcceEeEEEEE
Confidence 344566788999999999999999999997666543211 111 11111111 11100000
Q ss_pred CCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCC
Q 007844 354 QGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (587)
Q Consensus 354 ~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~ 404 (587)
..+...+.+.||.++.+..|||+|.+++-+.+-||-+|.|...
T Consensus 138 --------~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 138 --------EDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred --------eCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 0012278899999999999999999999999999999999763
No 62
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.14 E-value=0.016 Score=61.78 Aligned_cols=96 Identities=17% Similarity=0.252 Sum_probs=64.7
Q ss_pred CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (587)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (587)
+-+|+.||++|+.|+.|.++. |-+|+|-....+..+ . +.+| ++||. +..+
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~---f-------i~na-------------l~Pa~--v~~v---- 295 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAE---F-------VANA-------------LSPAK--VVSV---- 295 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------CCCce--EEEE----
Confidence 568999999999999999999 778887433211100 0 0000 11110 0000
Q ss_pred HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (587)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~ 167 (587)
... + ...-.+.+.||..+.+..|||+|.+++....-||.+|.|...
T Consensus 296 ---~i~-~-----~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 296 ---EVD-D-----EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred ---EEE-c-----CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 000 0 113467899999999999999999999999999999999763
No 63
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.13 E-value=0.012 Score=63.34 Aligned_cols=95 Identities=23% Similarity=0.232 Sum_probs=63.6
Q ss_pred CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (587)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (587)
+-+|+.||++|++|+.|.++. |-+|+|-....+..+ . +.+| ++||. +
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~---f-------I~Na-------------LsPA~-----V---- 324 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPAT---Y-------IANA-------------LSPAR-----V---- 324 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------cCCce-----e----
Confidence 558999999999999999999 778887433211100 0 0000 11110 0
Q ss_pred HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (587)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~ 166 (587)
....... ...-.+.+.||..+.+..|||+|.+++....-||.+|.|..
T Consensus 325 ~~V~i~~------~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 325 DEVRLVD------PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred eEEEEEc------CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0000000 01235689999999999999999999999999999999966
No 64
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.05 E-value=0.015 Score=61.62 Aligned_cols=95 Identities=16% Similarity=0.214 Sum_probs=64.4
Q ss_pred CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (587)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (587)
+-+|+.||++|++|+.|.++. |-+|+|-....+..+ . +.+| ++||. +..+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~---f-------I~Na-------------l~Pa~--V~~V---- 301 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI---F-------IARA-------------LAPAI--ISSV---- 301 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------CCCce--eeEE----
Confidence 558999999999999999999 777877433211100 0 0000 11110 0000
Q ss_pred HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (587)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~ 167 (587)
.. + +..-.+.+.||..+.+..|||+|.+++....-||.+|.|..-
T Consensus 302 ---~i--~-----~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 302 ---KI--E-----EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred ---EE--c-----CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 00 0 113467889999999999999999999999999999999864
No 65
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.85 E-value=0.012 Score=60.61 Aligned_cols=70 Identities=24% Similarity=0.306 Sum_probs=58.6
Q ss_pred ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (587)
.....+.|++.+.+.|||++|.+.+.|+++|+++|.++.+.+ ..+.++.+-+.-++|.+|.+.|.-.|-.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 356678999999999999999999999999999999988432 4566666777888999999999776654
No 66
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.74 E-value=0.013 Score=67.94 Aligned_cols=94 Identities=20% Similarity=0.245 Sum_probs=67.8
Q ss_pred cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI 178 (587)
Q Consensus 99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V 178 (587)
..|.++..++++.+.+.....-.+-....+....+.|+.+.++.+||.||.+||+|.++||++|.+.. +-.|
T Consensus 524 ~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d--------~G~v 595 (693)
T PRK11824 524 EQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED--------DGTV 595 (693)
T ss_pred HHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC--------CceE
Confidence 35666667777666554322211111222445566779999999999999999999999999888743 5678
Q ss_pred EEeec-HHHHHHHHHHHHHHHhc
Q 007844 179 QITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 179 ~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
.|.+. .+.+.+|..+|..+..+
T Consensus 596 ~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 596 KIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred EEEcccHHHHHHHHHHHHHhccc
Confidence 88885 89999999999888754
No 67
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.64 E-value=0.015 Score=45.65 Aligned_cols=37 Identities=22% Similarity=0.362 Sum_probs=34.4
Q ss_pred ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEE
Q 007844 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKL 401 (587)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i 401 (587)
.....+.|+.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999998876
No 68
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.62 E-value=0.018 Score=66.83 Aligned_cols=93 Identities=14% Similarity=0.224 Sum_probs=65.6
Q ss_pred hHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCC
Q 007844 335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN 414 (587)
Q Consensus 335 ~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~ 414 (587)
.+.++...|++.|.+..... .. ...........+.||.+.++.+||.||.+||+|+++||+.|.+. +
T Consensus 525 ~a~~g~~~I~~~M~~aI~~~-r~-~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d 591 (693)
T PRK11824 525 QAKEGRLHILGKMNEAISEP-RA-ELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------D 591 (693)
T ss_pred HHHHHHHHHHHHHHHHhcCC-hh-hhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------C
Confidence 34455566666665432111 00 01122445667788999999999999999999999999988663 2
Q ss_pred CcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844 415 DVVIQISG-EYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 415 ~r~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (587)
+-.|.|.+ ..+.+++|+++|.....+
T Consensus 592 ~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 592 DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 56688887 567899999999987764
No 69
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.57 E-value=0.024 Score=57.01 Aligned_cols=65 Identities=18% Similarity=0.168 Sum_probs=55.1
Q ss_pred EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHH-HHHHHHHHHHHHHhhcc
Q 007844 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK-NVQNALSEVVGRLRHNL 442 (587)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~-~V~~A~~~I~~~Lr~~~ 442 (587)
-..+.||.++++.+||++|.+|+.|.+.+++.|.|-. +-.|.|++... ++.+|+.+|...-++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 3568899999999999999999999999999998843 56788888876 78899999987666543
No 70
>PRK00468 hypothetical protein; Provisional
Probab=95.50 E-value=0.014 Score=47.80 Aligned_cols=35 Identities=29% Similarity=0.442 Sum_probs=31.1
Q ss_pred CCCcEEEEEEeccCccceeccCCChHHHHHHhHhC
Q 007844 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (587)
Q Consensus 21 ~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTg 55 (587)
.++.+.+++-|..+.+|.||||+|.+|+.||.--.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 45668999999999999999999999999997654
No 71
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.33 E-value=0.046 Score=57.85 Aligned_cols=96 Identities=20% Similarity=0.273 Sum_probs=63.9
Q ss_pred ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (587)
Q Consensus 283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~ 361 (587)
+-+|..||++|.+|+.|.++. |-+|.|-.-..+..+- +..|+.- .++...... .
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~f----------------i~nal~P--a~v~~v~i~-------~ 297 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEF----------------IANALSP--AKVISVEVL-------D 297 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHH----------------HHHhcCC--ceEEEEEEE-------c
Confidence 458999999999999999998 7777665322111000 0011000 000000000 0
Q ss_pred CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCC
Q 007844 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (587)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~ 404 (587)
.......+.||.++.+..|||+|.+++...+.||.+|.|...
T Consensus 298 -~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 298 -EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred -CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 122578899999999999999999999999999999999763
No 72
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.28 E-value=0.039 Score=60.86 Aligned_cols=94 Identities=21% Similarity=0.298 Sum_probs=63.1
Q ss_pred CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (587)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (587)
+-+|+.||++|++|+.|.++. |-+|+|-....+.. ..|. +| ++||. +
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~---~fi~-------na-------------l~pa~-----v---- 292 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPA---QFII-------NA-------------LSPAE-----V---- 292 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHH---HHHH-------Hh-------------CCCCE-----E----
Confidence 448999999999999999999 77887743321100 0000 00 11110 0
Q ss_pred HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (587)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~ 166 (587)
..... + ...-.+.+.||..+.+..|||+|.+|+..++-||.+|.|..
T Consensus 293 ~~v~~--~-----~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 293 SSVVV--D-----EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EEEEE--e-----CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 00000 0 00236779999999999999999999999999999999976
No 73
>PRK02821 hypothetical protein; Provisional
Probab=94.93 E-value=0.025 Score=46.56 Aligned_cols=36 Identities=17% Similarity=0.272 Sum_probs=31.5
Q ss_pred CCCcEEEEEEeccCccceeccCCChHHHHHHhHhCc
Q 007844 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (587)
Q Consensus 21 ~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga 56 (587)
.++.+.+.|-|..+.+|.||||+|.+|+.||.--.+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 345688999999999999999999999999987654
No 74
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.79 E-value=0.076 Score=56.60 Aligned_cols=97 Identities=20% Similarity=0.198 Sum_probs=64.7
Q ss_pred ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (587)
Q Consensus 283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~ 361 (587)
+-+|..||++|.+|+.|.++. |-+|.|-.-..+..+- +..|+.- .++..... .
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~f----------------i~nal~P--a~v~~v~i--------~ 298 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEF----------------VANALSP--AKVVSVEV--------D 298 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHHH----------------HHHhCCC--ceEEEEEE--------E
Confidence 568999999999999999998 7777665322111000 0001000 00000000 0
Q ss_pred CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCC
Q 007844 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE 405 (587)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~ 405 (587)
........+.||.++.+.-|||+|.+++.-.+.||.+|.|...+
T Consensus 299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 02235788999999999999999999999999999999997643
No 75
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.77 E-value=0.077 Score=51.06 Aligned_cols=42 Identities=26% Similarity=0.442 Sum_probs=35.4
Q ss_pred CCcEEEEEEecc------CccceeccCCChHHHHHHhHhCceEEEeCC
Q 007844 22 DDVVSFRLVCPT------PVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (587)
Q Consensus 22 ~~~v~~riLvP~------~~vG~IIGk~G~~Ik~IreeTga~I~V~~~ 63 (587)
+-.+.-++.||. ++||.|||..|+|.|+|++.|+|+|-|...
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 335566788875 689999999999999999999999999654
No 76
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=94.58 E-value=0.14 Score=54.49 Aligned_cols=98 Identities=13% Similarity=0.059 Sum_probs=66.1
Q ss_pred ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (587)
Q Consensus 283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~ 361 (587)
+-+|..||++|.+|+.|.++. |-+|.|-.-..+..+- +..|+.- .++..... .
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~f----------------I~Nal~P--a~V~~V~i--------~ 304 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIF----------------IARALAP--AIISSVKI--------E 304 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHHH----------------HHHhCCC--ceeeEEEE--------c
Confidence 568999999999999999998 7777665321111000 0011000 00000000 0
Q ss_pred CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcc
Q 007844 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV 407 (587)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~ 407 (587)
.......+.||.++.+..|||+|.+++-..+.||.+|.|..-+..
T Consensus 305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~ 349 (374)
T PRK12328 305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSK 349 (374)
T ss_pred -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCC
Confidence 123477899999999999999999999999999999999886653
No 77
>PRK00468 hypothetical protein; Provisional
Probab=94.57 E-value=0.041 Score=45.11 Aligned_cols=33 Identities=27% Similarity=0.446 Sum_probs=29.2
Q ss_pred CCCceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844 125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 125 ~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e 157 (587)
.+..+.++|.+..+.+|.||||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 345688999999999999999999999999864
No 78
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.54 E-value=0.094 Score=56.70 Aligned_cols=95 Identities=22% Similarity=0.213 Sum_probs=62.9
Q ss_pred ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (587)
Q Consensus 283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~ 361 (587)
+-+|..||++|.+|+.|.++. |-+|.|-.-..+...- +..|+.- .++..... .
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~f----------------I~NaLsP--A~V~~V~i--------~ 330 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPATY----------------IANALSP--ARVDEVRL--------V 330 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHHH----------------HHHhcCC--ceeeEEEE--------E
Confidence 568999999999999999998 7677665321110000 0011000 00100000 0
Q ss_pred CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcC
Q 007844 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (587)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~ 403 (587)
........+.||.++.+.-|||+|.+++--.+.||.+|.|.+
T Consensus 331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 012246789999999999999999999999999999999865
No 79
>PRK12704 phosphodiesterase; Provisional
Probab=94.39 E-value=0.11 Score=58.32 Aligned_cols=63 Identities=14% Similarity=0.235 Sum_probs=48.2
Q ss_pred CceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHH
Q 007844 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVG 436 (587)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I~~ 436 (587)
......|.+|+ ++-|+||||.|.+|+-+...||+.|.|.+ +...|.|+| +|---+.|...+..
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~~~~~rre~a~~~l~~ 272 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPIRREIARLALEK 272 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC----------CCCeEEEecCChhhHHHHHHHHHH
Confidence 34566688898 89999999999999999999999999953 346777888 55544445444433
No 80
>PRK01064 hypothetical protein; Provisional
Probab=94.34 E-value=0.048 Score=45.02 Aligned_cols=34 Identities=26% Similarity=0.527 Sum_probs=30.8
Q ss_pred CCcEEEEEEeccCccceeccCCChHHHHHHhHhC
Q 007844 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (587)
Q Consensus 22 ~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTg 55 (587)
++.+.+++-|.....|.+|||+|.+|+.||.-..
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 5678999999999999999999999999998653
No 81
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.32 E-value=0.058 Score=44.16 Aligned_cols=32 Identities=25% Similarity=0.443 Sum_probs=29.2
Q ss_pred CCceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e 157 (587)
+..+.++|-+.....|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 55788999999999999999999999999964
No 82
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.30 E-value=0.048 Score=44.64 Aligned_cols=33 Identities=27% Similarity=0.458 Sum_probs=30.1
Q ss_pred CCcEEEEEEeccCccceeccCCChHHHHHHhHh
Q 007844 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDT 54 (587)
Q Consensus 22 ~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeT 54 (587)
+..+.++|-+.....|.||||+|.+|+.||---
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 667889999999999999999999999998754
No 83
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.14 E-value=1.8 Score=42.54 Aligned_cols=86 Identities=19% Similarity=0.317 Sum_probs=64.8
Q ss_pred HHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec
Q 007844 104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA 183 (587)
Q Consensus 104 Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~ 183 (587)
.+.+|++.+........- +..-.+.+.++....-.|+..+|..++.|....||+|.+.. .+..|.|+|+
T Consensus 5 l~~~Il~d~W~l~v~e~v----~~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-------~~~~i~I~g~ 73 (210)
T PF14611_consen 5 LAERILRDCWNLEVSEEV----DELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-------SENRIRITGT 73 (210)
T ss_pred HHHHHHHHhcCCccccee----eccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-------CCcEEEEEcc
Confidence 345666666655432211 11223444556888899999999999999888999999977 5678999999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 007844 184 TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 184 ~e~V~~A~~~I~~~L~e 200 (587)
...+..+...|.+++..
T Consensus 74 k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 74 KSTAEYIEASINEILSN 90 (210)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 99999999999999965
No 84
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.09 E-value=0.13 Score=57.53 Aligned_cols=61 Identities=15% Similarity=0.265 Sum_probs=47.0
Q ss_pred CceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHH
Q 007844 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEV 434 (587)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I 434 (587)
......|.+|+ ++-|+||||.|.+|+-+...||+.|.|.+ +...|+|+| +|---+.|...+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l 264 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMAL 264 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHH
Confidence 44566788999 89999999999999999999999999953 346677888 554444444433
No 85
>PRK02821 hypothetical protein; Provisional
Probab=93.98 E-value=0.089 Score=43.30 Aligned_cols=32 Identities=25% Similarity=0.435 Sum_probs=28.5
Q ss_pred CCceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e 157 (587)
+..+.+.|.|....+|.||||+|.+|+.||.-
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtl 59 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTV 59 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHH
Confidence 34578899999999999999999999999975
No 86
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.83 E-value=0.12 Score=52.07 Aligned_cols=62 Identities=21% Similarity=0.267 Sum_probs=53.0
Q ss_pred EEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhcC
Q 007844 132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQHL 201 (587)
Q Consensus 132 rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e~ 201 (587)
.+-||..+++.+||++|.+|+.|.++++++|.|-. +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus 148 ~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~--------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 148 IVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ--------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC--------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 36789999999999999999999999999999954 356888888 668888888888777663
No 87
>PRK00106 hypothetical protein; Provisional
Probab=93.78 E-value=0.16 Score=56.78 Aligned_cols=61 Identities=16% Similarity=0.296 Sum_probs=47.4
Q ss_pred CceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHH
Q 007844 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEV 434 (587)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I 434 (587)
......|.+|+ ++-|+||||.|.+|+-+...||+.+.|.+ +...|+|+| +|---+.|...+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~l 285 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTL 285 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHH
Confidence 44566788999 89999999999999999999999999953 446777888 554444444433
No 88
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=93.69 E-value=0.04 Score=60.70 Aligned_cols=96 Identities=20% Similarity=0.242 Sum_probs=63.9
Q ss_pred ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (587)
Q Consensus 283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~ 361 (587)
+-+|..||++|.+|+.|.++. |-+|.|-.-..+... + +..|+.- .++..... .
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~--f--------------i~nal~p--a~v~~v~~--------~ 298 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQ--F--------------IINALSP--AEVSSVVV--------D 298 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHHH--H--------------HHHhCCC--CEEEEEEE--------e
Confidence 457999999999999999998 777766532111000 0 0011000 00000000 0
Q ss_pred CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCC
Q 007844 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE 405 (587)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~ 405 (587)
.......+.||..+.+.-|||+|.+++...+.||.+|.|...+
T Consensus 299 -~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~~ 341 (470)
T PRK09202 299 -EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTEE 341 (470)
T ss_pred -CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEhh
Confidence 1224788999999999999999999999999999999997643
No 89
>PRK01064 hypothetical protein; Provisional
Probab=93.58 E-value=0.096 Score=43.23 Aligned_cols=33 Identities=27% Similarity=0.503 Sum_probs=29.3
Q ss_pred CCCceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844 125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 125 ~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e 157 (587)
.+..+.+++.|.....|.+|||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 345788999999999999999999999999864
No 90
>PRK12704 phosphodiesterase; Provisional
Probab=93.38 E-value=0.3 Score=54.75 Aligned_cols=63 Identities=16% Similarity=0.308 Sum_probs=48.8
Q ss_pred EEEEeec-ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844 131 CGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 131 ~rllVp~-~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
..+-+|+ .+-|.||||.|.+|+.+..-||++|.|.. +..+|.|+|. +---+.|...+...+.+
T Consensus 212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3455566 88999999999999999999999999966 4567889984 54445666666666654
No 91
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.33 E-value=0.33 Score=54.40 Aligned_cols=65 Identities=15% Similarity=0.295 Sum_probs=49.6
Q ss_pred eEEEEEeec-ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 129 vt~rllVp~-~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
.+..+-+|+ .+-|.||||.|.+|+.+..-||+++-|.. +...|+|+|. +---+-|...+..++.+
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 344456666 78999999999999999999999999976 4466788884 55555566666666654
No 92
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.24 E-value=0.96 Score=44.46 Aligned_cols=127 Identities=13% Similarity=0.086 Sum_probs=85.4
Q ss_pred EEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCC
Q 007844 277 RMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGF 356 (587)
Q Consensus 277 ~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~ 356 (587)
.+.++....-.+...+|..++.|....||+|.+... +..+.|+|++ .+.+.+......+.
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k-------~~~~~i~~~i~~~l-------- 88 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTK-------STAEYIEASINEIL-------- 88 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccH-------HHHHHHHHHHHHHH--------
Confidence 344557777888999999999998889999999843 4579999984 22233333333322
Q ss_pred CCCCCCCCceEEEEEeCccccccccc----CCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEc-----CCHHHH
Q 007844 357 SSGENKGDAVAVSILVGADFVGCLTG----SGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS-----GEYKNV 427 (587)
Q Consensus 357 ~~g~~~~~~~t~~l~VP~~~vG~IIG----kgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~-----G~~~~V 427 (587)
....+.+|.++.-..-.-.+ .....+++|++.|++.|+..+.+ ..+.|+ -....+
T Consensus 89 ------~~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~----------~~~~i~~~~~~~~~~~~ 152 (210)
T PF14611_consen 89 ------SNIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG----------NKLKISWLASPENEKRA 152 (210)
T ss_pred ------hhcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC----------CeEEEEEEeeccccchH
Confidence 13356666666432211111 13667999999999999886532 234444 466789
Q ss_pred HHHHHHHHHHHh
Q 007844 428 QNALSEVVGRLR 439 (587)
Q Consensus 428 ~~A~~~I~~~Lr 439 (587)
+.|++++...+.
T Consensus 153 ~~a~RlL~~a~~ 164 (210)
T PF14611_consen 153 DRAKRLLLWALD 164 (210)
T ss_pred HHHHHHHHHhcc
Confidence 999999998775
No 93
>PRK00106 hypothetical protein; Provisional
Probab=93.15 E-value=0.4 Score=53.71 Aligned_cols=66 Identities=12% Similarity=0.306 Sum_probs=50.6
Q ss_pred ceEEEEEeec-ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844 128 VAYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 128 ~vt~rllVp~-~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
..+..+-+|+ .+-|.||||.|.+|+.+..-||+++-|.. +...|.|+|. +---+-|...+..++.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3444566677 78999999999999999999999999976 4466789984 65555566666666654
No 94
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=92.20 E-value=0.085 Score=61.87 Aligned_cols=64 Identities=19% Similarity=0.056 Sum_probs=52.9
Q ss_pred cEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeC-CCCCCCceEEEEecCCchhhhhhhc
Q 007844 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFC 87 (587)
Q Consensus 24 ~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~~~~eRvI~I~G~~e~~~~a~~~ 87 (587)
....++-+|...+.+|||++|+||+.+|.-||+.|+|.. -..+..||-+++.|.++.++-+..-
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~ 1403 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSP 1403 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcc
Confidence 345567789999999999999999999999999999986 3344679999999999877655544
No 95
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.02 E-value=0.46 Score=52.27 Aligned_cols=93 Identities=17% Similarity=0.230 Sum_probs=67.6
Q ss_pred HHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEE
Q 007844 100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ 179 (587)
Q Consensus 100 ~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~ 179 (587)
.|.+|-..|++.+...-...-.......++...|-|+.+....+||.+|...|+|..|||+.-++ ++..+.
T Consensus 568 ~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------De~t~~ 638 (760)
T KOG1067|consen 568 KAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------DEGTFS 638 (760)
T ss_pred hhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------cCceEE
Confidence 34455555555544333222222233457888899999999999999999999999999966665 456677
Q ss_pred Eeec-HHHHHHHHHHHHHHHhcC
Q 007844 180 ITGA-TLAVKKALVAVTTCLQHL 201 (587)
Q Consensus 180 I~G~-~e~V~~A~~~I~~~L~e~ 201 (587)
|--. ..+.++|...|..++...
T Consensus 639 i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 639 IFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred EEecCHHHHHHHHHHHHHHhcCc
Confidence 7666 889999999999998763
No 96
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=91.88 E-value=0.24 Score=47.79 Aligned_cols=43 Identities=16% Similarity=0.222 Sum_probs=36.8
Q ss_pred CCCceEEEEEeec------ceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844 125 GDDVAYCGLLANT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (587)
Q Consensus 125 ~~~~vt~rllVp~------~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~ 167 (587)
.....+-++.||- +.||.|||..|+|+|+|++.|+|+|.|-..
T Consensus 144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 3446777888885 589999999999999999999999999763
No 97
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=91.30 E-value=0.13 Score=60.31 Aligned_cols=72 Identities=18% Similarity=-0.021 Sum_probs=60.7
Q ss_pred ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (587)
....++.+|-....+|||++|.+|+.++.-|||.|.|.+-.. ....||.+.+.|.++.+..|...|.-.+.+
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~----~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP----DNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC----ccchhhhcccCCCChhhhhhhccccceeec
Confidence 345567899999999999999999999999999999987332 135689999999999999999888765553
No 98
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=90.70 E-value=0.13 Score=41.75 Aligned_cols=35 Identities=17% Similarity=0.273 Sum_probs=29.9
Q ss_pred CCcEEEEEEeccCccceeccCCChHHHHHHhHhCc
Q 007844 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (587)
Q Consensus 22 ~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga 56 (587)
.+...+.+-|..+..|.||||+|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 45567788889999999999999999999987654
No 99
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=89.43 E-value=0.56 Score=36.61 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=28.0
Q ss_pred cEEEEEEeccCccceeccCCChHHHHHHhHhCceE
Q 007844 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (587)
Q Consensus 24 ~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I 58 (587)
.....+.+.....|.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35555666666789999999999999999998554
No 100
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.42 E-value=0.4 Score=38.63 Aligned_cols=36 Identities=25% Similarity=0.360 Sum_probs=28.3
Q ss_pred EEEEeccCc-----cceeccCCChHHHHHHhHh-CceEEEeC
Q 007844 27 FRLVCPTPV-----VGGLIGRSGSIISSIRRDT-KCRIHCEG 62 (587)
Q Consensus 27 ~riLvP~~~-----vG~IIGk~G~~Ik~IreeT-ga~I~V~~ 62 (587)
..+.|-+.. +|..||++|+.|+.|.++. |-+|+|-.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 345666666 9999999999999999999 88888743
No 101
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=88.07 E-value=0.3 Score=46.87 Aligned_cols=56 Identities=27% Similarity=0.367 Sum_probs=49.1
Q ss_pred CcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844 373 GADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 373 P~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (587)
-+..+|+|+||+|.+---|.+.|.++|.+.+ ..|.|-|..+++..|...|+..|-.
T Consensus 176 lsRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 176 LSRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhcc
Confidence 3468999999999999999999999998863 6799999999999999998876543
No 102
>PRK12705 hypothetical protein; Provisional
Probab=87.65 E-value=0.9 Score=50.64 Aligned_cols=62 Identities=15% Similarity=0.262 Sum_probs=43.9
Q ss_pred EEEeec-ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844 132 GLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (587)
Q Consensus 132 rllVp~-~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e 200 (587)
.+-+|+ ++-|.||||.|.+|+.+...||+.+.|..- .+.|.|++. +.--+.|...+..++.+
T Consensus 201 ~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-------p~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 201 VVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT-------PEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeecCChHhhccccCccchhHHHHHHhhCCceEecCC-------ccchhhcccCccchHHHHHHHHHHHhc
Confidence 344555 789999999999999999999999999763 344556665 44444455555555543
No 103
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=87.14 E-value=1.5 Score=48.40 Aligned_cols=90 Identities=14% Similarity=0.136 Sum_probs=63.5
Q ss_pred HHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCc
Q 007844 337 QNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDV 416 (587)
Q Consensus 337 ~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r 416 (587)
.+|-..|++.|......+-.. ..+...+..++.|+.+....+||.+|...|.|..+||+.-.+ ++.
T Consensus 570 ~~ar~~Il~~m~k~i~~Pr~~--~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~ 635 (760)
T KOG1067|consen 570 REARLQILDIMEKNINSPRGS--DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEG 635 (760)
T ss_pred hHHHHHHHHHHHhhcCCcccC--ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCc
Confidence 344556666665432211111 123467888999999999999999999999999999955444 245
Q ss_pred EEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844 417 VIQISG-EYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 417 ~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (587)
+++|.- ++.+.++|+++|.+.+..
T Consensus 636 t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 636 TFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eEEEEecCHHHHHHHHHHHHHHhcC
Confidence 566554 566789999999987764
No 104
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=85.99 E-value=0.5 Score=45.39 Aligned_cols=56 Identities=29% Similarity=0.388 Sum_probs=50.2
Q ss_pred cceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844 137 TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (587)
Q Consensus 137 ~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (587)
+..+|.|+||+|.+--.|++-|-++|.+. +..|.|-|..++++-|...|+.+|...
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla---------d~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA---------DSKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec---------CceEEEeecchhhHHHHHhhHhhhccC
Confidence 45679999999999999999999999994 467999999999999999999999764
No 105
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.58 E-value=0.81 Score=36.86 Aligned_cols=39 Identities=21% Similarity=0.291 Sum_probs=30.5
Q ss_pred EEEEEeCccc-----ccccccCCCchhHHHHHhh-CCeEEEcCCC
Q 007844 367 AVSILVGADF-----VGCLTGSGSSAVSEMEDVT-GTDIKLVGGE 405 (587)
Q Consensus 367 t~~l~VP~~~-----vG~IIGkgG~~Ik~I~~~T-Ga~I~i~~~~ 405 (587)
...+.|-+.. +|..||++|+.|+.|+++. |-+|+|-.-+
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s 48 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS 48 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence 4566777777 9999999999999999999 9999997643
No 106
>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=85.14 E-value=1.3 Score=34.46 Aligned_cols=35 Identities=11% Similarity=0.260 Sum_probs=29.1
Q ss_pred ceEEEEEeCcccccccccCCCchhHHHHHhhCCeE
Q 007844 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI 399 (587)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I 399 (587)
.....+.+.....|.+||++|++|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35666777776789999999999999999998655
No 107
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=84.95 E-value=0.59 Score=37.86 Aligned_cols=34 Identities=26% Similarity=0.342 Sum_probs=28.7
Q ss_pred cceEEEEEeecccccccccccchhhHhhhhhcCc
Q 007844 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGA 305 (587)
Q Consensus 272 ~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga 305 (587)
....+.+.+..+..|.||||+|.+++.||.-.+.
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 3457778899999999999999999999876554
No 108
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=83.30 E-value=0.73 Score=37.71 Aligned_cols=33 Identities=27% Similarity=0.428 Sum_probs=28.6
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCceEE
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH 59 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~ 59 (587)
..+.+.....|.|||++|++|++|+++.+-.+.
T Consensus 27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 27 IIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 467889999999999999999999998876553
No 109
>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=81.13 E-value=3.2 Score=38.34 Aligned_cols=38 Identities=24% Similarity=0.415 Sum_probs=33.6
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~ 167 (587)
+-.+.|-...-|.+|||+|.++++|..+||=.-.|.+.
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 34577888889999999999999999999999888875
No 110
>PRK12705 hypothetical protein; Provisional
Probab=80.64 E-value=2.3 Score=47.45 Aligned_cols=40 Identities=18% Similarity=0.336 Sum_probs=35.2
Q ss_pred CceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcC
Q 007844 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (587)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~ 403 (587)
......+.+|+ ++-|+||||.|.+|+-+...||+.|.|.+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 34556678888 89999999999999999999999999975
No 111
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.54 E-value=1.6 Score=35.73 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=27.0
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCceEEE
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V 60 (587)
+.+-+..+..|.+|||+|++++.||--++.-++-
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 3455567889999999999999999888765443
No 112
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=79.87 E-value=2.8 Score=42.41 Aligned_cols=51 Identities=14% Similarity=0.331 Sum_probs=45.9
Q ss_pred eeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844 141 GVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH 200 (587)
Q Consensus 141 G~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e 200 (587)
-+|||.+|+|++.|+--|.|.|-|.. .+|.+.|....+..+...|.+++..
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 46999999999999999999999965 4789999999999999999999865
No 113
>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=79.80 E-value=0.79 Score=37.52 Aligned_cols=34 Identities=24% Similarity=0.452 Sum_probs=28.9
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhhhCCeEE
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIV 163 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~ 163 (587)
...+.+..++.+.|||++|++|++|+....-.+.
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 4568899999999999999999999987765553
No 114
>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=79.39 E-value=2 Score=35.74 Aligned_cols=35 Identities=11% Similarity=0.217 Sum_probs=30.6
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCceEEEe
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE 61 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~ 61 (587)
.++.+....-|.|||++|++|++|+++-.-...+.
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 77888999999999999999999999987666553
No 115
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=79.14 E-value=3.4 Score=41.84 Aligned_cols=51 Identities=20% Similarity=0.290 Sum_probs=46.0
Q ss_pred cccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844 378 GCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (587)
Q Consensus 378 G~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (587)
-+|||.+|+|++.|+-.|.|.|-|.. .+|.+.|....+..+...+..++..
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 47999999999999999999999964 6799999999999999999887775
No 116
>PRK13764 ATPase; Provisional
Probab=78.98 E-value=2.1 Score=48.89 Aligned_cols=45 Identities=16% Similarity=0.209 Sum_probs=40.7
Q ss_pred CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCccc
Q 007844 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVL 408 (587)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p 408 (587)
......+.||.+.++.+|||+|.+|++|.+..|.+|.|-..++.+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 446788999999999999999999999999999999998877754
No 117
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.94 E-value=2.1 Score=40.62 Aligned_cols=33 Identities=18% Similarity=0.277 Sum_probs=28.3
Q ss_pred EEeccCccceeccCCChHHHHHHhHhCceEEEeC
Q 007844 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG 62 (587)
Q Consensus 29 iLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~ 62 (587)
++|-... |.-|||+|++|+++++..|-+|.|-+
T Consensus 65 fvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 65 LLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 4555566 99999999999999999999999843
No 118
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=78.69 E-value=9.4 Score=42.01 Aligned_cols=153 Identities=12% Similarity=0.133 Sum_probs=100.5
Q ss_pred ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCCC
Q 007844 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (587)
Q Consensus 128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~ 207 (587)
+-.+-+.++...+..|||.||..|++++.+.++.|++... +- +.+
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~--------~~--------------------~~q------- 492 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNF--------YK--------------------FGQ------- 492 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhh--------hh--------------------cch-------
Confidence 3456689999999999999999999999999988888542 00 000
Q ss_pred CcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccc
Q 007844 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (587)
Q Consensus 208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~ 287 (587)
..+.+.+. +-+|.+-.+.
T Consensus 493 ------------------------------------------------------------s~~~dNV~--I~~PrKn~~n 510 (657)
T COG5166 493 ------------------------------------------------------------SQWHDNVL--IEAPRKNQDN 510 (657)
T ss_pred ------------------------------------------------------------hhhhcceE--EECCccCccc
Confidence 00112233 4489999999
Q ss_pred cccccchhhHhhhhhcCc----eEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCCCC
Q 007844 288 IIGKRGAIVRSLQNASGA----LISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKG 363 (587)
Q Consensus 288 IIGk~G~~Ik~I~~~tga----~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~~~ 363 (587)
|+|++......+++.... .|.+.+ ++ -++.++-+.. .-+.++... +... ..
T Consensus 511 i~~~KNd~~~~V~~~c~f~~Kgdirf~~---~~-~sI~~v~~~~----------~~I~rv~kn--e~v~---------~~ 565 (657)
T COG5166 511 ISGKKNDKLDKVKQQCRFNLKGDIRFCP---QS-TSIFTVDIYS----------DEIERVIKN--ETVL---------LE 565 (657)
T ss_pred hhcccccHHHHHhhhcccccccceEEcC---Cc-eEEEEEcccc----------cHHHHHhhc--cceE---------Ee
Confidence 999999988888866533 344442 22 3477777763 122232221 1100 01
Q ss_pred CceEEEEEeCccccccccc---CCCchhHHHHHhhCCeEEEc
Q 007844 364 DAVAVSILVGADFVGCLTG---SGSSAVSEMEDVTGTDIKLV 402 (587)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIG---kgG~~Ik~I~~~TGa~I~i~ 402 (587)
-.....+.+|++.++..+| -.|++|..+.....-.|...
T Consensus 566 ~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~ 607 (657)
T COG5166 566 FPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFS 607 (657)
T ss_pred cccccccccchhhhhccCCcccccccchhhhhhhhhccceee
Confidence 2345678899999999999 67888887777766666554
No 119
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=78.51 E-value=4 Score=40.74 Aligned_cols=56 Identities=20% Similarity=0.310 Sum_probs=43.0
Q ss_pred EEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHH-HHHHHHHHHH
Q 007844 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLA-VKKALVAVTT 196 (587)
Q Consensus 133 llVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~-V~~A~~~I~~ 196 (587)
+.|+...+..+||++|+.++-|.++++|+|-+-.+ -.|-|.|..+. ..-|...|..
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N--------G~IWV~~~~~~~e~~~~~aI~~ 206 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN--------GRIWVDGENESLEELAIEAIRK 206 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC--------CEEEecCCCcchHHHHHHHHHH
Confidence 66899999999999999999999999999999774 34566666553 3444444443
No 120
>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=78.05 E-value=2.1 Score=35.12 Aligned_cols=34 Identities=15% Similarity=0.326 Sum_probs=28.5
Q ss_pred EEEEEeCcccccccccCCCchhHHHHHhhCCeEE
Q 007844 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIK 400 (587)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~ 400 (587)
...+.|..+..|.||||.|++++.||--+..-++
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 4567777888999999999999999988776554
No 121
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=77.91 E-value=1.7 Score=47.21 Aligned_cols=41 Identities=20% Similarity=0.306 Sum_probs=37.6
Q ss_pred eEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCc
Q 007844 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (587)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~ 406 (587)
....+.||..+++.+|||+|.+|++|.+..|-+|.|...++
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 46788999999999999999999999999999999987655
No 122
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=77.15 E-value=4.3 Score=44.63 Aligned_cols=39 Identities=26% Similarity=0.492 Sum_probs=34.2
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCC
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPP 168 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p 168 (587)
+-.++|-...-|.+|||+|++.++|..++|-.-.|.+.|
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 456888889999999999999999999999888887753
No 123
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=76.93 E-value=2.2 Score=46.43 Aligned_cols=39 Identities=26% Similarity=0.380 Sum_probs=35.4
Q ss_pred eEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (587)
Q Consensus 129 vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~ 167 (587)
-.+.+.||...++.+|||+|.+|++|+++.|-+|.|...
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 346688999999999999999999999999999999764
No 124
>PRK13764 ATPase; Provisional
Probab=72.75 E-value=2.6 Score=48.09 Aligned_cols=38 Identities=18% Similarity=0.243 Sum_probs=34.0
Q ss_pred EEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCC
Q 007844 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (587)
Q Consensus 26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~ 63 (587)
..-+.||.+.++.+|||+|.+|++|++..|.+|+|...
T Consensus 482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 34577899999999999999999999999999999643
No 125
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=72.48 E-value=3.4 Score=36.35 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=26.9
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCce
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~ 57 (587)
++|.+....-|.|||++|++|++|++.....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 5678888899999999999999999887543
No 126
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=72.07 E-value=4.3 Score=38.47 Aligned_cols=35 Identities=23% Similarity=0.406 Sum_probs=30.6
Q ss_pred EEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (587)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~ 166 (587)
+-++|.... |.-|||+|.+|+++++..|-+|.+..
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 446677777 99999999999999999999999965
No 127
>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=71.60 E-value=4.3 Score=33.78 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=28.6
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEe
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVM 164 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I 164 (587)
.+++.|....-|.|||++|+.|++|+++-.....+
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 47788888899999999999999999876544444
No 128
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=70.89 E-value=12 Score=34.53 Aligned_cols=96 Identities=19% Similarity=0.210 Sum_probs=63.9
Q ss_pred cccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcc-cccCCCCCCCCCCCce
Q 007844 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV-EGQQGFSSGENKGDAV 366 (587)
Q Consensus 288 IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~-~~~~g~~~g~~~~~~~ 366 (587)
.+-.+|..|++|.++..-+|.|-.... ...+-.+|...|.+.+-+. .+.. -.-...
T Consensus 20 ~~~~~~dli~~lAk~lrKRIvvR~dps-----------------~l~~~e~A~~~I~~ivP~ea~i~d------i~Fd~~ 76 (145)
T cd02410 20 LFAEDGDLVKDLAKDLRKRIVIRPDPS-----------------VLKPPEEAIKIILEIVPEEAGITD------IYFDDD 76 (145)
T ss_pred HHhcccHHHHHHHHHHhceEEEcCChh-----------------hcCCHHHHHHHHHHhCCCccCcee------eEecCC
Confidence 444678899999999888877753210 0122335665665555321 1100 012344
Q ss_pred EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCc
Q 007844 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (587)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~ 406 (587)
+-++.|-...-|.+||++|.++++|..+||-.-+|.....
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 6678888889999999999999999999999999976443
No 129
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=70.68 E-value=9.8 Score=38.06 Aligned_cols=48 Identities=19% Similarity=0.236 Sum_probs=40.6
Q ss_pred EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHH
Q 007844 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425 (587)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~ 425 (587)
-.-+.|+...+.++||++|+.++-+.+.|+|+|-|-. +-.|=|.|..+
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~ 194 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENE 194 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCc
Confidence 3567899999999999999999999999999999854 44566777666
No 130
>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=68.75 E-value=5 Score=33.56 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=24.5
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhC
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTg 55 (587)
.++.+....-|.+||++|.+|++|++.-.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~ 68 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEILE 68 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHHH
Confidence 55666668999999999999999998763
No 131
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=66.11 E-value=4.9 Score=40.00 Aligned_cols=33 Identities=24% Similarity=0.366 Sum_probs=27.9
Q ss_pred EEEEEeccCccceeccCCChHHHHHHhHhCceE
Q 007844 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (587)
Q Consensus 26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I 58 (587)
-.+|.+....-|.|||++|++|++|+++..-..
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~ 84 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEKLF 84 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHHHh
Confidence 467888999999999999999999998765433
No 132
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=64.72 E-value=10 Score=41.85 Aligned_cols=97 Identities=19% Similarity=0.209 Sum_probs=67.1
Q ss_pred cccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccc-ccCCCCCCCCCCC
Q 007844 286 SGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE-GQQGFSSGENKGD 364 (587)
Q Consensus 286 G~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~-~~~g~~~g~~~~~ 364 (587)
..++-+.|..||+|.++..-+|.|-.... ...+...|...|.+.+-+.. +.. -.-.
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPs-----------------vl~~~e~A~~~I~eivP~ea~i~~------i~Fd 97 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPS-----------------VLKPPEEARKIILEIVPEEAGITD------IYFD 97 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCch-----------------hcCCHHHHHHHHHHhCccccCcee------EEec
Confidence 34566889999999999998887764311 01333466666665553210 000 0113
Q ss_pred ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCC
Q 007844 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE 405 (587)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~ 405 (587)
..+-++.|-++.=|.+|||+|++.++|.++||-.-+|.+..
T Consensus 98 ~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 98 DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred CCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 35667888899999999999999999999999988887643
No 133
>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=60.78 E-value=11 Score=43.44 Aligned_cols=38 Identities=24% Similarity=0.434 Sum_probs=34.2
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~ 167 (587)
+-.++|-...-|.+|||+|.++++|..+||-.-.|.+.
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 44588888899999999999999999999999999875
No 134
>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=59.56 E-value=9.1 Score=31.97 Aligned_cols=27 Identities=22% Similarity=0.527 Sum_probs=22.9
Q ss_pred EEEEeecceeeeeeecCchHHHHHHhh
Q 007844 131 CGLLANTTKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~e 157 (587)
+++.|....-|.+||++|++|++|++.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~ 66 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEI 66 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHH
Confidence 566667788899999999999998865
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=57.76 E-value=8.4 Score=33.85 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=24.2
Q ss_pred EEEEeecceeeeeeecCchHHHHHHhhh
Q 007844 131 CGLLANTTKIGVVVGKGGRNVTRMRIES 158 (587)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~et 158 (587)
+++.|....-|.|||++|++|++|++..
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 6677888888999999999999998763
No 136
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=57.36 E-value=8.8 Score=42.21 Aligned_cols=130 Identities=8% Similarity=0.089 Sum_probs=77.8
Q ss_pred ccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChH-HHHHHHHHhhhhcccccCCCCCCCCCC
Q 007844 285 ASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPV-QNAAVLVFARSVEVEGQQGFSSGENKG 363 (587)
Q Consensus 285 vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a-~~Av~~i~~~v~e~~~~~g~~~g~~~~ 363 (587)
-..+-||+.-++.+|.+...|.+.+.-... .+.+ +.--|.. + .++ +++. +.+ .. +
T Consensus 391 EdFl~gkkngK~TrIm~~v~c~~~~~i~~~-~gs~-~~~~~~g----~-~~~F~k~~----~~~-~~------------E 446 (657)
T COG5166 391 EDFLRGKKNGKATRIMKGVSCSELSSIVSS-TGSI-VETNGIG----E-KMSFSKKL----SIP-PT------------E 446 (657)
T ss_pred HHHhccccCcchhhhhhhcccceeeEEEec-CCcE-EEEeccC----c-chhhHHHh----cCC-cc------------c
Confidence 347888888889999999888855442111 1112 3222221 0 111 1111 111 11 1
Q ss_pred CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCH---HHHHHHHHHHHHHHhh
Q 007844 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY---KNVQNALSEVVGRLRH 440 (587)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~---~~V~~A~~~I~~~Lr~ 440 (587)
=.....+.+|...|..|||.||..|.++++..++.|++...-++|.....++ |.|.-.. .++.-|+.-+.+++.+
T Consensus 447 Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dN--V~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 447 FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDN--VLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcc--eEEECCccCccchhcccccHHHHHhh
Confidence 1235578899999999999999999999999999999988766665222222 3343332 3455566666666663
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=55.14 E-value=10 Score=37.87 Aligned_cols=30 Identities=27% Similarity=0.479 Sum_probs=25.9
Q ss_pred ceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e 157 (587)
+..+++.|....-|.||||+|+.|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 446788899999999999999999998854
No 138
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=52.55 E-value=27 Score=40.42 Aligned_cols=97 Identities=20% Similarity=0.167 Sum_probs=65.7
Q ss_pred ccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcc-cccCCCCCCCCCCCc
Q 007844 287 GIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV-EGQQGFSSGENKGDA 365 (587)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~-~~~~g~~~g~~~~~~ 365 (587)
..+-.+|..|++|.++..-+|.|-.... ...+-.+|...|.+.+-+. .+.. -.-..
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~~-----------------~~~~~~~~~~~i~~~~~~~~~~~~------~~f~~ 92 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDPS-----------------VLLPPEEAIEKIKEIVPEEAGITD------IYFDD 92 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecChh-----------------hcCCHHHHHHHHHHhCCCcCCcee------EEecC
Confidence 3455788999999999888877753211 0122235665555555321 1000 01234
Q ss_pred eEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCc
Q 007844 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (587)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~ 406 (587)
.+-++.|-.+.-|.+|||+|.++++|.++||-.-+|.+...
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 56788888999999999999999999999999999977443
No 139
>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=47.04 E-value=21 Score=36.31 Aligned_cols=30 Identities=13% Similarity=0.305 Sum_probs=23.5
Q ss_pred eEEEEEeec-ceeeeeeecCchHHHHHHhhh
Q 007844 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIES 158 (587)
Q Consensus 129 vt~rllVp~-~~vG~IIGkgG~~Ik~I~~et 158 (587)
+.+.++|.. ++-+.||||+|+.||+|..++
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 556677775 678999999999999987543
No 140
>PRK15494 era GTPase Era; Provisional
Probab=42.49 E-value=27 Score=37.01 Aligned_cols=29 Identities=10% Similarity=0.284 Sum_probs=22.9
Q ss_pred eEEEEEeec-ceeeeeeecCchHHHHHHhh
Q 007844 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 129 vt~rllVp~-~~vG~IIGkgG~~Ik~I~~e 157 (587)
+.+.++|.. ++-+.||||+|+.||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 456677776 67889999999999987643
No 141
>PRK00089 era GTPase Era; Reviewed
Probab=41.44 E-value=30 Score=35.51 Aligned_cols=29 Identities=21% Similarity=0.525 Sum_probs=22.3
Q ss_pred eEEEEEeec-ceeeeeeecCchHHHHHHhh
Q 007844 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 129 vt~rllVp~-~~vG~IIGkgG~~Ik~I~~e 157 (587)
+.+.++|.. ++-+.||||+|++||+|..+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 455566664 67799999999999988644
No 142
>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=40.82 E-value=25 Score=35.78 Aligned_cols=31 Identities=13% Similarity=0.118 Sum_probs=25.7
Q ss_pred ceEEEEEeCc-ccccccccCCCchhHHHHHhh
Q 007844 365 AVAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (587)
Q Consensus 365 ~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (587)
.+...+.|.. ++-+.|||++|+.||+|....
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 3677888887 788999999999999987654
No 143
>COG1159 Era GTPase [General function prediction only]
Probab=40.09 E-value=31 Score=35.78 Aligned_cols=29 Identities=14% Similarity=0.414 Sum_probs=22.6
Q ss_pred ceEEEEEeec-ceeeeeeecCchHHHHHHh
Q 007844 128 VAYCGLLANT-TKIGVVVGKGGRNVTRMRI 156 (587)
Q Consensus 128 ~vt~rllVp~-~~vG~IIGkgG~~Ik~I~~ 156 (587)
.+...++|+. ++-+.||||+|++||+|-.
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHH
Confidence 3455577776 6889999999999998753
No 144
>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=38.07 E-value=30 Score=33.75 Aligned_cols=31 Identities=19% Similarity=0.304 Sum_probs=26.9
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCce
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~ 57 (587)
.+|.+....-|.|||++|.+|++|+++-.-.
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~ 70 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKLQKK 70 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHHHHH
Confidence 6788888899999999999999999887543
No 145
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=37.43 E-value=30 Score=34.05 Aligned_cols=32 Identities=22% Similarity=0.271 Sum_probs=26.4
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCceE
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I 58 (587)
.++.+....-|.+||++|++|++|++.-.-..
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~ 73 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKKF 73 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHHh
Confidence 55666668899999999999999999876543
No 146
>CHL00048 rps3 ribosomal protein S3
Probab=36.32 E-value=33 Score=34.04 Aligned_cols=32 Identities=19% Similarity=0.158 Sum_probs=26.7
Q ss_pred EEEEEeccCccceeccCCChHHHHHHhHhCce
Q 007844 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (587)
Q Consensus 26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~ 57 (587)
..+|.+-...-|.|||++|.+|++|++.-.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k~ 98 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQKE 98 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHHHH
Confidence 36677778889999999999999999887433
No 147
>PRK00089 era GTPase Era; Reviewed
Probab=36.09 E-value=32 Score=35.31 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=25.2
Q ss_pred ceEEEEEeCc-ccccccccCCCchhHHHHHhh
Q 007844 365 AVAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (587)
Q Consensus 365 ~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (587)
.+...+.|.. ++-+.|||++|++||+|....
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 3677788887 678999999999999886554
No 148
>PRK15494 era GTPase Era; Provisional
Probab=36.01 E-value=33 Score=36.41 Aligned_cols=30 Identities=17% Similarity=0.333 Sum_probs=25.1
Q ss_pred eEEEEEeCc-ccccccccCCCchhHHHHHhh
Q 007844 366 VAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (587)
Q Consensus 366 ~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (587)
+...+.|.. ++-+.|||++|+.||+|....
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 667788887 788999999999999886554
No 149
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=35.62 E-value=33 Score=34.12 Aligned_cols=32 Identities=13% Similarity=0.205 Sum_probs=27.4
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCceE
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I 58 (587)
.+|.+....-|.|||++|..|++|+++-.-.+
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 67778888899999999999999998876544
No 150
>COG1159 Era GTPase [General function prediction only]
Probab=35.57 E-value=33 Score=35.56 Aligned_cols=32 Identities=13% Similarity=0.253 Sum_probs=26.2
Q ss_pred CceEEEEEeCc-ccccccccCCCchhHHHHHhh
Q 007844 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (587)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (587)
-.+...+.|+. ++-+-|||++|++||+|-..+
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 35677788887 788999999999999886554
No 151
>cd07053 BMC_PduT_repeat1 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.
Probab=34.76 E-value=49 Score=27.12 Aligned_cols=37 Identities=19% Similarity=0.159 Sum_probs=31.8
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHHhhcccCcccccc
Q 007844 414 NDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNE 450 (587)
Q Consensus 414 ~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~~~~~ 450 (587)
..-.+.|+|+-.+|+.|++.-.+...+.+++..+++.
T Consensus 37 Gk~~vii~GdvsaV~~Av~a~~~~~~~~~v~~~vI~~ 73 (76)
T cd07053 37 GKYIIIVSGDVGAVQAAVDAGKEIGGKYVVDSFVLPN 73 (76)
T ss_pred CEEEEEEEEcHHHHHHHHHHHHHHhCCcEEEEEEeCC
Confidence 3567999999999999999999999988888877753
No 152
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=32.83 E-value=45 Score=27.12 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=30.9
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHHhhcccCccccc
Q 007844 414 NDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILN 449 (587)
Q Consensus 414 ~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~~~~ 449 (587)
..-.+.|+|+..+|+.|++...+.+.+.++...+++
T Consensus 38 g~~~~~i~G~vs~V~~Av~a~~~~~~~~~v~~~vI~ 73 (75)
T PF00936_consen 38 GKVTVIITGDVSAVKAAVDAAEEAAGKKLVSSTVIP 73 (75)
T ss_dssp TEEEEEEEESHHHHHHHHHHHHHHHHHTEEEEEEES
T ss_pred CeEEEEEEECHHHHHHHHHHHHHHHhhceeeEEEeC
Confidence 357899999999999999999999998877766664
No 153
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=30.55 E-value=42 Score=35.11 Aligned_cols=34 Identities=15% Similarity=0.177 Sum_probs=28.0
Q ss_pred CCceEEEEEeCc-ccccccccCCCchhHHHHHhhC
Q 007844 363 GDAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTG 396 (587)
Q Consensus 363 ~~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TG 396 (587)
.-.+..++.+|. ++...|||+||..|++|-++-+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 346788899998 6778899999999999976654
No 154
>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=27.68 E-value=57 Score=31.86 Aligned_cols=28 Identities=21% Similarity=0.507 Sum_probs=24.1
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhh
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~e 157 (587)
.+++.|....-|.|||++|..|++|+++
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHH
Confidence 4677888888899999999999998865
No 155
>PRK03818 putative transporter; Validated
Probab=27.67 E-value=3.3e+02 Score=31.02 Aligned_cols=131 Identities=15% Similarity=0.202 Sum_probs=68.2
Q ss_pred EEEEEeccCccceeccCCChHHHHHHhHhCceEEEeC---------CCCC---CCceEEEEecCCchhhhhhhccccccc
Q 007844 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG---------GFPG---SDHRVILVVGSGSIDRRIMFCENDVVV 93 (587)
Q Consensus 26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~---------~~~~---~~eRvI~I~G~~e~~~~a~~~~~~~~~ 93 (587)
..++.|+++. ++ |++++++.......+.|.. +.++ ....++.|.|..+..+++....+.+
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~-- 277 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEE-- 277 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCc--
Confidence 3556666443 34 6689999998877666521 1111 1235677777766543332221111
Q ss_pred cCCCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHH--hhhCCeEEecCC----
Q 007844 94 EGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMR--IESGAKIVMLPP---- 167 (587)
Q Consensus 94 e~~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~--~etGa~I~I~~~---- 167 (587)
.+.+.+...+.....++++|++ .++|| ++++++ ++.|+.+.-..+
T Consensus 278 -----------------------~~~~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~ 328 (552)
T PRK03818 278 -----------------------VDTSLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVE 328 (552)
T ss_pred -----------------------cCccccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCee
Confidence 0000000112233444555553 56666 788874 667776544432
Q ss_pred ----CCCCCCCCcEEEEeecHHHHHHHHHH
Q 007844 168 ----PACAAIDDQLIQITGATLAVKKALVA 193 (587)
Q Consensus 168 ----p~~~~~~dr~V~I~G~~e~V~~A~~~ 193 (587)
+...-..-.++.+.|++++++++.+.
T Consensus 329 l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 329 LVASPDLSLQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred cCCCCCCEEecCCEEEEEECHHHHHHHHHH
Confidence 11111222457799999999997664
No 156
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=27.35 E-value=56 Score=32.18 Aligned_cols=29 Identities=21% Similarity=0.457 Sum_probs=23.8
Q ss_pred EEEEeecceeeeeeecCchHHHHHHhhhC
Q 007844 131 CGLLANTTKIGVVVGKGGRNVTRMRIESG 159 (587)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~etG 159 (587)
.++.|....-|.+||++|++|+++++.-.
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 55666668889999999999999887643
No 157
>CHL00048 rps3 ribosomal protein S3
Probab=26.52 E-value=60 Score=32.16 Aligned_cols=29 Identities=14% Similarity=0.282 Sum_probs=24.6
Q ss_pred EEEEEeecceeeeeeecCchHHHHHHhhh
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMRIES 158 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~~et 158 (587)
.+++.|....-|.|||++|.+|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46677788888999999999999998764
No 158
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=26.24 E-value=58 Score=34.14 Aligned_cols=33 Identities=30% Similarity=0.502 Sum_probs=26.8
Q ss_pred cEEEEEEecc-CccceeccCCChHHHHHHhHhCc
Q 007844 24 VVSFRLVCPT-PVVGGLIGRSGSIISSIRRDTKC 56 (587)
Q Consensus 24 ~v~~riLvP~-~~vG~IIGk~G~~Ik~IreeTga 56 (587)
.+...++||. +....||||+|..|++|-++.+-
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~ 360 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANE 360 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHH
Confidence 5677899997 45667899999999999887654
No 159
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=25.81 E-value=61 Score=32.30 Aligned_cols=28 Identities=18% Similarity=0.336 Sum_probs=23.7
Q ss_pred EEEEeecceeeeeeecCchHHHHHHhhh
Q 007844 131 CGLLANTTKIGVVVGKGGRNVTRMRIES 158 (587)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~et 158 (587)
+++.|....-|.|||++|..|++|+++-
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 6677777888999999999999988654
No 160
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=24.50 E-value=53 Score=32.28 Aligned_cols=34 Identities=15% Similarity=0.236 Sum_probs=27.0
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCceEEE
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V 60 (587)
+.+-+-++.++.+||+.|+++..||--+++-++-
T Consensus 93 v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 93 VVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3444456669999999999999999998876554
No 161
>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=23.96 E-value=4e+02 Score=30.43 Aligned_cols=58 Identities=14% Similarity=0.230 Sum_probs=35.2
Q ss_pred EEEEEeecceeeeeeecCchHHHHHH------hhhCCeEEecCC--------CCCCCCCCcEEEEeecHHHHHHHHHH
Q 007844 130 YCGLLANTTKIGVVVGKGGRNVTRMR------IESGAKIVMLPP--------PACAAIDDQLIQITGATLAVKKALVA 193 (587)
Q Consensus 130 t~rllVp~~~vG~IIGkgG~~Ik~I~------~etGa~I~I~~~--------p~~~~~~dr~V~I~G~~e~V~~A~~~ 193 (587)
..++.+|+ ..++|| +|++++ ++.|+.|.-..+ +...-..-.++.+.|++++++++...
T Consensus 304 ~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~ 375 (562)
T TIGR03802 304 TKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQ 375 (562)
T ss_pred EEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHH
Confidence 34455554 445665 788886 267777655443 11111223457799999999987765
No 162
>cd07045 BMC_CcmK_like Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). Potential functional differences between the two types are not yet fully understood. In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carbox
Probab=23.66 E-value=92 Score=25.99 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=30.1
Q ss_pred CcEEEEcCCHHHHHHHHHHHHHHHhh--cccCcccccc
Q 007844 415 DVVIQISGEYKNVQNALSEVVGRLRH--NLKSGEILNE 450 (587)
Q Consensus 415 ~r~V~I~G~~~~V~~A~~~I~~~Lr~--~~~~~~~~~~ 450 (587)
.-.+.|+|+..+|+.|.+...+..++ .++++.+++.
T Consensus 38 k~~vii~GdvsaV~~Av~a~~~~~~~~~~~v~~~vI~~ 75 (84)
T cd07045 38 LVTVKITGDVAAVKAAVEAGAAAAERIGELVSSHVIPR 75 (84)
T ss_pred EEEEEEEEcHHHHHHHHHHHHHHHhccCcEEEEEEeCC
Confidence 57899999999999999999998887 4677767653
No 163
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=23.61 E-value=71 Score=31.57 Aligned_cols=30 Identities=33% Similarity=0.493 Sum_probs=25.8
Q ss_pred EEEEeccCccceeccCCChHHHHHHhHhCc
Q 007844 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (587)
Q Consensus 27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga 56 (587)
++|.+....-+.|||++|.+|++|++.-.-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~~ 93 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQK 93 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHHH
Confidence 668888888899999999999999977643
No 164
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=23.43 E-value=64 Score=31.69 Aligned_cols=37 Identities=11% Similarity=0.189 Sum_probs=31.2
Q ss_pred ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEE
Q 007844 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKL 401 (587)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i 401 (587)
.-+..+.+-.+..+.|||+.|.+++.||-.+.+.+.-
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3466777888889999999999999999988877644
No 165
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=23.38 E-value=1.7e+02 Score=31.20 Aligned_cols=51 Identities=20% Similarity=0.174 Sum_probs=43.7
Q ss_pred CcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007844 373 GADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (587)
Q Consensus 373 P~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~ 435 (587)
+.+..-.|.|..+.+++.|.+..|+.|... .+.++|+|+...|..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 357788999999999999999999999663 367999999878888887776
No 166
>cd07056 BMC_PduK 1,2-propanediol utilization protein K (PduK), Bacterial Micro-Compartment (BMC) domain repeat 1l. PduK proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduK might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view.
Probab=22.24 E-value=1.1e+02 Score=25.19 Aligned_cols=36 Identities=14% Similarity=0.206 Sum_probs=28.9
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHHh--hcccCccccc
Q 007844 414 NDVVIQISGEYKNVQNALSEVVGRLR--HNLKSGEILN 449 (587)
Q Consensus 414 ~~r~V~I~G~~~~V~~A~~~I~~~Lr--~~~~~~~~~~ 449 (587)
..-.+.|+|+-.+|+.|.+...+..+ ..++++.++|
T Consensus 38 G~~~viv~GdvsaV~~Av~a~~~~~~~~~~~v~~~vI~ 75 (77)
T cd07056 38 GWMTVKISGDVAAVNAAIEAGKQTAGASDGYVASTVIA 75 (77)
T ss_pred eEEEEEEEeeHHHHHHHHHHHHHHHhccCCEEEEEEeC
Confidence 34668999999999999999998888 5566665654
No 167
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=22.21 E-value=1.8e+02 Score=25.60 Aligned_cols=40 Identities=23% Similarity=0.244 Sum_probs=31.9
Q ss_pred HhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844 393 DVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (587)
Q Consensus 393 ~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (587)
+..++.|-+.++ -.-.+.|+|+-.+|+.|++.|...+++.
T Consensus 61 Kaa~V~igF~DR---------FsGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 61 KAADVHIGFLDR---------FSGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred hccCcEEeeeec---------cceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 455667777642 3467899999999999999999999873
No 168
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=20.10 E-value=1.8e+02 Score=30.94 Aligned_cols=53 Identities=23% Similarity=0.320 Sum_probs=44.7
Q ss_pred EeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHH
Q 007844 134 LANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVT 195 (587)
Q Consensus 134 lVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~ 195 (587)
+-+...+-.|.|..+.+++.|.+..|+.|.... +.++|+|+...|..|...+.
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 444677788999999999999999999888843 67899999878888888777
Done!