Query 007293
Match_columns 609
No_of_seqs 266 out of 1959
Neff 7.1
Searched_HMMs 46136
Date Thu Mar 28 21:36:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007293.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007293hhsearch_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 1.2E-42 2.5E-47 377.8 30.9 367 21-445 39-414 (485)
2 KOG1676 K-homology type RNA bi 100.0 7.3E-43 1.6E-47 373.2 28.3 340 23-444 52-393 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 5.9E-42 1.3E-46 349.8 21.3 370 20-442 194-566 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 8.9E-31 1.9E-35 254.5 24.0 329 22-441 45-385 (390)
5 KOG1676 K-homology type RNA bi 100.0 3.7E-29 8.1E-34 268.3 18.5 245 127-441 52-301 (600)
6 KOG2193 IGF-II mRNA-binding pr 100.0 1.6E-28 3.5E-33 251.5 12.5 239 128-440 198-481 (584)
7 KOG2191 RNA-binding protein NO 99.9 3.5E-26 7.5E-31 228.8 19.9 242 17-312 31-282 (402)
8 KOG2191 RNA-binding protein NO 99.9 2.3E-22 4.9E-27 201.6 18.2 250 128-439 38-314 (402)
9 KOG2190 PolyC-binding proteins 99.8 9.4E-20 2E-24 199.0 22.1 163 275-442 44-210 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.6 2.1E-14 4.5E-19 140.8 14.8 159 270-449 44-202 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.5 1.4E-13 3E-18 132.3 9.3 138 29-201 2-152 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.5 3.5E-13 7.7E-18 129.5 10.7 140 278-441 2-152 (172)
13 PRK13763 putative RNA-processi 99.4 5.4E-13 1.2E-17 129.1 10.9 140 25-201 3-158 (180)
14 PRK13763 putative RNA-processi 99.4 2E-12 4.2E-17 125.2 11.7 145 275-441 4-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.3 3.9E-12 8.5E-17 102.5 6.7 65 367-435 1-65 (65)
16 cd02396 PCBP_like_KH K homolog 99.3 4E-12 8.7E-17 102.4 5.6 64 130-194 1-64 (65)
17 KOG2279 Kinase anchor protein 99.2 6.4E-11 1.4E-15 127.0 13.3 298 126-524 65-432 (608)
18 KOG2279 Kinase anchor protein 99.2 9.3E-11 2E-15 125.8 12.5 276 16-327 59-352 (608)
19 cd02394 vigilin_like_KH K homo 99.2 6.1E-11 1.3E-15 94.5 6.4 61 368-435 2-62 (62)
20 PF00013 KH_1: KH domain syndr 99.1 5E-11 1.1E-15 94.3 4.5 60 367-434 1-60 (60)
21 cd02393 PNPase_KH Polynucleoti 99.1 2.3E-10 5.1E-15 90.9 7.1 59 366-435 2-61 (61)
22 cd00105 KH-I K homology RNA-bi 99.0 4.8E-10 1E-14 89.4 7.1 62 368-434 2-63 (64)
23 cd02394 vigilin_like_KH K homo 99.0 4.4E-10 9.5E-15 89.5 4.7 60 131-194 2-61 (62)
24 PF00013 KH_1: KH domain syndr 99.0 2.2E-10 4.7E-15 90.6 2.4 60 130-194 1-60 (60)
25 KOG2208 Vigilin [Lipid transpo 99.0 2.9E-09 6.3E-14 123.3 11.7 288 23-439 199-487 (753)
26 cd00105 KH-I K homology RNA-bi 98.9 2.2E-09 4.8E-14 85.6 6.0 62 131-194 2-63 (64)
27 cd02393 PNPase_KH Polynucleoti 98.9 2.4E-09 5.3E-14 85.1 6.0 58 129-194 2-60 (61)
28 PF13014 KH_3: KH domain 98.8 8E-09 1.7E-13 76.1 5.3 42 35-76 1-43 (43)
29 KOG2208 Vigilin [Lipid transpo 98.8 3.8E-08 8.3E-13 114.1 12.0 287 25-440 273-562 (753)
30 smart00322 KH K homology RNA-b 98.8 4E-08 8.7E-13 78.4 8.5 67 366-439 3-69 (69)
31 PF13014 KH_3: KH domain 98.7 1.3E-08 2.9E-13 75.0 4.6 43 376-422 1-43 (43)
32 smart00322 KH K homology RNA-b 98.6 1.2E-07 2.7E-12 75.5 7.3 67 128-198 2-68 (69)
33 COG1094 Predicted RNA-binding 98.5 1.9E-07 4.1E-12 89.7 6.8 148 23-201 6-165 (194)
34 COG1094 Predicted RNA-binding 98.5 1.1E-06 2.5E-11 84.4 11.7 142 274-440 8-164 (194)
35 cd02395 SF1_like-KH Splicing f 98.1 6.5E-06 1.4E-10 74.4 6.7 67 375-441 15-96 (120)
36 cd02395 SF1_like-KH Splicing f 98.0 1.1E-05 2.3E-10 73.0 6.1 64 138-201 15-96 (120)
37 KOG2113 Predicted RNA binding 97.9 9.8E-06 2.1E-10 82.1 5.1 150 272-438 24-181 (394)
38 PRK08406 transcription elongat 97.8 2.9E-05 6.3E-10 72.2 5.6 103 26-165 33-135 (140)
39 TIGR02696 pppGpp_PNP guanosine 97.7 0.00016 3.4E-09 82.9 9.7 93 334-440 549-642 (719)
40 TIGR02696 pppGpp_PNP guanosine 97.5 0.00029 6.3E-09 80.9 8.5 94 98-200 548-642 (719)
41 KOG2113 Predicted RNA binding 97.4 0.00035 7.6E-09 71.1 7.4 155 23-198 24-181 (394)
42 PRK08406 transcription elongat 97.4 0.00044 9.6E-09 64.3 7.4 102 274-402 32-135 (140)
43 TIGR01952 nusA_arch NusA famil 97.2 0.00047 1E-08 64.1 5.5 102 26-165 34-136 (141)
44 TIGR03591 polynuc_phos polyrib 97.1 0.0011 2.4E-08 77.0 8.3 92 336-440 523-615 (684)
45 KOG0119 Splicing factor 1/bran 97.1 0.0016 3.4E-08 70.4 8.5 73 128-200 137-230 (554)
46 TIGR03591 polynuc_phos polyrib 97.0 0.00097 2.1E-08 77.5 6.8 94 99-200 521-615 (684)
47 TIGR01952 nusA_arch NusA famil 96.9 0.0025 5.3E-08 59.3 7.1 101 275-402 34-136 (141)
48 KOG0119 Splicing factor 1/bran 96.8 0.007 1.5E-07 65.5 9.9 77 365-441 137-231 (554)
49 COG0195 NusA Transcription elo 96.7 0.0033 7.1E-08 61.4 6.0 102 27-166 78-179 (190)
50 KOG1588 RNA-binding protein Sa 96.6 0.0023 5E-08 64.5 4.7 43 19-61 86-134 (259)
51 PLN00207 polyribonucleotide nu 96.5 0.0045 9.7E-08 72.9 7.1 93 335-440 656-750 (891)
52 COG1185 Pnp Polyribonucleotide 96.5 0.0063 1.4E-07 68.8 7.4 98 334-444 522-620 (692)
53 PLN00207 polyribonucleotide nu 96.5 0.0032 7E-08 74.0 5.3 95 98-200 654-750 (891)
54 COG1185 Pnp Polyribonucleotide 96.3 0.0094 2E-07 67.4 7.6 95 98-200 521-616 (692)
55 KOG0336 ATP-dependent RNA heli 96.3 0.0041 8.8E-08 66.1 4.3 68 364-439 45-112 (629)
56 cd02134 NusA_KH NusA_K homolog 96.2 0.0071 1.5E-07 48.0 4.4 37 24-60 24-60 (61)
57 KOG1588 RNA-binding protein Sa 96.1 0.03 6.4E-07 56.6 9.1 81 363-443 89-190 (259)
58 KOG0336 ATP-dependent RNA heli 96.0 0.0067 1.5E-07 64.5 4.5 72 124-200 42-113 (629)
59 TIGR01953 NusA transcription t 96.0 0.011 2.4E-07 63.0 6.1 95 34-166 243-338 (341)
60 KOG2814 Transcription coactiva 96.0 0.009 2E-07 61.9 5.1 71 365-441 56-126 (345)
61 PRK12327 nusA transcription el 95.9 0.013 2.9E-07 62.8 6.1 96 34-167 245-341 (362)
62 PRK12329 nusA transcription el 95.9 0.011 2.3E-07 64.3 5.2 95 34-166 277-372 (449)
63 KOG2814 Transcription coactiva 95.8 0.0073 1.6E-07 62.6 3.7 71 128-201 56-126 (345)
64 COG0195 NusA Transcription elo 95.8 0.0057 1.2E-07 59.7 2.8 101 275-403 77-179 (190)
65 PRK12328 nusA transcription el 95.8 0.013 2.8E-07 62.6 5.5 95 34-167 251-346 (374)
66 PRK11824 polynucleotide phosph 95.6 0.019 4E-07 67.1 6.3 93 335-440 525-618 (693)
67 cd02134 NusA_KH NusA_K homolog 95.6 0.016 3.4E-07 46.0 3.9 36 366-401 25-60 (61)
68 COG5176 MSL5 Splicing factor ( 95.6 0.033 7.1E-07 54.1 6.6 43 21-63 144-192 (269)
69 PRK11824 polynucleotide phosph 95.4 0.013 2.8E-07 68.4 4.2 94 99-200 524-618 (693)
70 PRK04163 exosome complex RNA-b 95.4 0.03 6.5E-07 56.8 6.1 64 367-441 146-210 (235)
71 PRK00468 hypothetical protein; 95.2 0.022 4.8E-07 47.1 3.6 35 21-55 26-60 (75)
72 PRK09202 nusA transcription el 95.0 0.032 6.9E-07 62.0 5.4 95 34-167 245-340 (470)
73 TIGR01953 NusA transcription t 94.8 0.021 4.6E-07 60.8 3.3 95 283-403 243-338 (341)
74 PRK02821 hypothetical protein; 94.5 0.037 8.1E-07 46.0 3.4 35 22-56 28-62 (77)
75 PRK12704 phosphodiesterase; Pr 94.3 0.11 2.5E-06 58.6 7.6 67 364-440 208-276 (520)
76 PRK12328 nusA transcription el 94.2 0.03 6.4E-07 60.0 2.7 97 283-406 251-348 (374)
77 PRK12327 nusA transcription el 94.2 0.098 2.1E-06 56.2 6.5 96 283-404 245-341 (362)
78 TIGR03319 YmdA_YtgF conserved 94.0 0.14 3E-06 57.8 7.6 66 364-439 202-269 (514)
79 PRK12329 nusA transcription el 93.9 0.12 2.6E-06 56.4 6.6 95 283-403 277-372 (449)
80 COG1837 Predicted RNA-binding 93.8 0.063 1.4E-06 44.4 3.2 32 126-157 27-58 (76)
81 PRK01064 hypothetical protein; 93.8 0.071 1.5E-06 44.5 3.6 34 22-55 27-60 (78)
82 PRK00468 hypothetical protein; 93.7 0.067 1.5E-06 44.3 3.4 33 363-395 27-59 (75)
83 COG1837 Predicted RNA-binding 93.7 0.078 1.7E-06 43.9 3.6 33 22-54 27-59 (76)
84 PRK00106 hypothetical protein; 93.6 0.18 3.8E-06 56.9 7.5 66 364-439 223-290 (535)
85 PF14611 SLS: Mitochondrial in 93.5 1.3 2.9E-05 43.8 12.9 86 104-200 5-90 (210)
86 PRK04163 exosome complex RNA-b 93.4 0.12 2.6E-06 52.4 5.2 63 131-201 147-210 (235)
87 PRK02821 hypothetical protein; 93.4 0.079 1.7E-06 44.1 3.2 34 364-397 29-62 (77)
88 COG5176 MSL5 Splicing factor ( 93.3 0.29 6.2E-06 47.7 7.3 42 363-404 145-192 (269)
89 PF14611 SLS: Mitochondrial in 93.2 0.85 1.9E-05 45.2 11.1 128 276-439 28-164 (210)
90 PRK09202 nusA transcription el 93.2 0.17 3.6E-06 56.4 6.4 96 283-405 245-341 (470)
91 PRK01064 hypothetical protein; 93.1 0.1 2.2E-06 43.6 3.4 33 125-157 26-58 (78)
92 TIGR03319 YmdA_YtgF conserved 93.0 0.25 5.5E-06 55.7 7.7 65 129-200 204-270 (514)
93 PRK00106 hypothetical protein; 92.9 0.3 6.5E-06 55.1 7.9 65 129-200 225-291 (535)
94 PRK12704 phosphodiesterase; Pr 92.9 0.25 5.3E-06 55.9 7.2 63 131-200 212-276 (520)
95 KOG1067 Predicted RNA-binding 92.6 0.53 1.1E-05 52.3 9.0 93 100-201 568-661 (760)
96 KOG4369 RTK signaling protein 90.4 0.12 2.6E-06 61.1 1.4 71 366-440 1340-1410(2131)
97 PF13083 KH_4: KH domain; PDB: 90.1 0.17 3.6E-06 41.5 1.7 35 22-56 26-60 (73)
98 cd02409 KH-II KH-II (K homolo 88.8 0.66 1.4E-05 36.5 4.3 35 24-58 24-58 (68)
99 KOG3273 Predicted RNA-binding 88.4 0.28 6.1E-06 47.5 2.0 54 374-439 177-230 (252)
100 KOG1067 Predicted RNA-binding 87.9 1.3 2.9E-05 49.3 7.0 89 338-440 571-660 (760)
101 PRK12705 hypothetical protein; 86.5 0.85 1.8E-05 51.2 4.8 62 132-200 201-264 (508)
102 PF13184 KH_5: NusA-like KH do 86.4 0.56 1.2E-05 38.2 2.4 35 27-61 5-45 (69)
103 KOG3273 Predicted RNA-binding 86.2 0.7 1.5E-05 44.9 3.3 56 137-201 177-232 (252)
104 PF13083 KH_4: KH domain; PDB: 84.9 0.46 1E-05 38.9 1.3 36 364-399 27-62 (73)
105 cd02409 KH-II KH-II (K homolo 84.2 1.5 3.2E-05 34.4 3.9 34 366-399 25-58 (68)
106 PF13184 KH_5: NusA-like KH do 84.2 1 2.2E-05 36.7 3.0 37 367-403 4-46 (69)
107 KOG4369 RTK signaling protein 84.1 0.29 6.2E-06 58.2 -0.3 69 131-200 1342-1410(2131)
108 PF07650 KH_2: KH domain syndr 80.7 0.97 2.1E-05 37.3 1.7 33 27-59 27-59 (78)
109 PRK12705 hypothetical protein; 78.8 2.9 6.2E-05 47.1 5.1 40 364-403 196-236 (508)
110 cd02414 jag_KH jag_K homology 78.8 2 4.4E-05 35.5 3.0 34 27-60 26-59 (77)
111 KOG2874 rRNA processing protei 78.4 3.6 7.8E-05 42.1 5.1 51 378-440 161-211 (356)
112 KOG2874 rRNA processing protei 77.4 2.4 5.2E-05 43.3 3.5 51 141-200 161-211 (356)
113 PRK13764 ATPase; Provisional 77.2 2.5 5.3E-05 48.7 4.1 45 364-408 479-523 (602)
114 PRK06418 transcription elongat 77.2 2.5 5.5E-05 40.4 3.5 32 29-61 65-96 (166)
115 cd02414 jag_KH jag_K homology 77.1 2.3 4.9E-05 35.2 2.8 34 367-400 25-58 (77)
116 cd02410 archeal_CPSF_KH The ar 76.9 3.4 7.5E-05 38.5 4.2 38 130-167 77-114 (145)
117 cd02413 40S_S3_KH K homology R 76.7 2.7 5.8E-05 35.4 3.1 35 27-61 32-66 (81)
118 COG1855 ATPase (PilT family) [ 75.7 2.1 4.6E-05 46.9 2.8 41 366-406 486-526 (604)
119 COG1855 ATPase (PilT family) [ 75.6 2 4.3E-05 47.2 2.6 38 26-63 487-524 (604)
120 COG1097 RRP4 RNA-binding prote 75.3 4.7 0.0001 40.6 5.0 57 133-197 150-207 (239)
121 PF07650 KH_2: KH domain syndr 75.2 1.4 3E-05 36.4 1.0 35 366-400 25-59 (78)
122 COG5166 Uncharacterized conser 73.5 13 0.00029 41.3 8.1 103 276-431 451-557 (657)
123 PRK13764 ATPase; Provisional 71.2 3.4 7.4E-05 47.5 3.3 38 26-63 482-519 (602)
124 cd02412 30S_S3_KH K homology R 69.2 4.3 9.4E-05 36.0 2.9 31 27-57 63-93 (109)
125 COG1097 RRP4 RNA-binding prote 68.9 9.6 0.00021 38.5 5.5 57 367-434 147-204 (239)
126 PRK06418 transcription elongat 68.2 3.4 7.4E-05 39.6 2.1 35 131-166 63-97 (166)
127 COG1782 Predicted metal-depend 66.4 8.1 0.00017 43.0 4.7 38 130-167 100-137 (637)
128 cd02411 archeal_30S_S3_KH K ho 65.6 6.4 0.00014 33.2 3.1 29 27-55 40-68 (85)
129 cd02413 40S_S3_KH K homology R 62.8 4.8 0.0001 33.8 1.8 35 130-164 31-65 (81)
130 COG0092 RpsC Ribosomal protein 60.7 7.2 0.00016 39.2 2.8 31 26-56 52-82 (233)
131 COG1782 Predicted metal-depend 59.8 12 0.00026 41.7 4.6 96 287-404 42-137 (637)
132 cd02410 archeal_CPSF_KH The ar 59.3 9.6 0.00021 35.6 3.2 94 290-406 22-116 (145)
133 TIGR03675 arCOG00543 arCOG0054 55.2 13 0.00028 43.3 4.2 38 130-167 94-131 (630)
134 TIGR03675 arCOG00543 arCOG0054 50.1 28 0.0006 40.6 5.8 97 288-406 37-133 (630)
135 cd02411 archeal_30S_S3_KH K ho 48.2 11 0.00023 31.9 1.5 27 131-157 40-66 (85)
136 COG5166 Uncharacterized conser 48.1 17 0.00036 40.5 3.3 130 284-440 390-524 (657)
137 cd02412 30S_S3_KH K homology R 47.9 15 0.00032 32.6 2.5 30 367-396 62-91 (109)
138 COG0092 RpsC Ribosomal protein 47.2 11 0.00023 38.1 1.6 30 128-157 50-79 (233)
139 TIGR00436 era GTP-binding prot 40.6 25 0.00054 36.1 3.2 31 365-395 220-251 (270)
140 COG1159 Era GTPase [General fu 35.6 33 0.00071 35.9 3.1 31 365-395 228-259 (298)
141 PRK15494 era GTPase Era; Provi 35.4 33 0.00072 36.7 3.2 30 366-395 273-303 (339)
142 PRK00089 era GTPase Era; Revie 35.1 33 0.00072 35.4 3.1 30 366-395 226-256 (292)
143 TIGR01008 rpsC_E_A ribosomal p 34.7 37 0.00079 33.5 3.1 30 27-56 40-69 (195)
144 cd07053 BMC_PduT_repeat1 1,2-p 34.5 49 0.0011 27.5 3.4 37 414-450 37-73 (76)
145 PRK04191 rps3p 30S ribosomal p 33.9 37 0.00081 33.7 3.1 31 27-57 42-72 (207)
146 PRK15494 era GTPase Era; Provi 33.5 27 0.00058 37.3 2.2 29 129-157 273-302 (339)
147 COG1159 Era GTPase [General fu 33.2 32 0.00069 36.1 2.5 29 128-156 228-257 (298)
148 PF00936 BMC: BMC domain; Int 32.7 49 0.0011 27.2 3.1 36 414-449 38-73 (75)
149 CHL00048 rps3 ribosomal protei 32.6 40 0.00087 33.7 3.1 31 26-56 67-97 (214)
150 PTZ00084 40S ribosomal protein 32.5 41 0.00088 33.8 3.1 32 27-58 46-77 (220)
151 PRK03818 putative transporter; 30.8 2.8E+02 0.0061 31.8 9.9 60 128-193 289-358 (552)
152 TIGR00436 era GTP-binding prot 30.3 55 0.0012 33.5 3.8 30 25-54 221-251 (270)
153 KOG1423 Ras-like GTPase ERA [C 28.2 48 0.001 35.1 2.8 33 364-396 326-359 (379)
154 PRK00089 era GTPase Era; Revie 28.1 24 0.00053 36.5 0.7 29 129-157 226-255 (292)
155 KOG2008 BTK-associated SH3-dom 25.4 2E+02 0.0044 30.3 6.7 24 421-444 210-233 (426)
156 TIGR03802 Asp_Ala_antiprt aspa 25.3 4.1E+02 0.0089 30.6 10.0 58 130-193 304-375 (562)
157 COG1847 Jag Predicted RNA-bind 25.1 94 0.002 30.9 4.1 48 28-78 94-141 (208)
158 cd07045 BMC_CcmK_like Carbon d 24.9 91 0.002 26.3 3.5 36 415-450 38-75 (84)
159 COG1702 PhoH Phosphate starvat 24.4 1.5E+02 0.0033 31.8 5.7 51 373-435 22-72 (348)
160 KOG1423 Ras-like GTPase ERA [C 23.9 58 0.0013 34.5 2.5 54 3-56 302-360 (379)
161 COG1847 Jag Predicted RNA-bind 22.4 69 0.0015 31.8 2.6 70 366-442 91-160 (208)
162 cd07056 BMC_PduK 1,2-propanedi 21.7 1.1E+02 0.0023 25.5 3.2 35 415-449 39-75 (77)
163 TIGR01009 rpsC_bact ribosomal 21.3 85 0.0018 31.3 3.0 29 27-55 64-92 (211)
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=1.2e-42 Score=377.84 Aligned_cols=367 Identities=28% Similarity=0.461 Sum_probs=291.9
Q ss_pred CCCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcch
Q 007293 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSS 100 (609)
Q Consensus 21 ~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~ 100 (609)
++...+||+||+.+.+|.||||+|..|++||++|.++|+|.+..+++.|||++|+|...+ ...++
T Consensus 39 p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~---------------~~~~~ 103 (485)
T KOG2190|consen 39 PDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE---------------LNLSP 103 (485)
T ss_pred CCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc---------------ccCCc
Confidence 344445999999999999999999999999999999999999999999999999997322 14788
Q ss_pred HHHHHHHHHHHHhhhhhccC-----CC-CCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCC
Q 007293 101 TQEAVIRVFERMWEVEAEVE-----GD-GDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAID 174 (609)
Q Consensus 101 A~~Al~~v~~~i~~~~~~~~-----~~-~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~ 174 (609)
+++|++++++.+.....+++ .. .....++++|||||.+++|+||||+|+.||+|+++|||+|+|.++ ..+..+
T Consensus 104 ~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~st 182 (485)
T KOG2190|consen 104 ATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPNST 182 (485)
T ss_pred hHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCccc
Confidence 99999999999987533211 11 112226899999999999999999999999999999999999997 667779
Q ss_pred CceEEEeccHHHHHHHHHHHHHHHhccCCCCCC---CcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcc
Q 007293 175 DQLIQITGATLAVKKALVAVTTCLQHLSTMEKS---PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEF 251 (609)
Q Consensus 175 dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~---~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~ 251 (609)
+|.|+|.|.+++|.+|+..|..+|+++..+.-. ...+|+|.. ..+...+|.......+|++
T Consensus 183 er~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~--------------~~~~~~~~s~~~~~~~~~~-- 246 (485)
T KOG2190|consen 183 ERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSA--------------SQGGPVLPSTAQTSPDAHP-- 246 (485)
T ss_pred ceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcc--------------cccCccccccccCCccccc--
Confidence 999999999999999999999999996533111 112222200 0000111211111100100
Q ss_pred CCCCCCCCCCCCCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccC
Q 007293 252 HSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDT 331 (609)
Q Consensus 252 ~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~ 331 (609)
+.......++.+++.+|...++.|||++|..|+.|+.++|+.|.+.+...+ |.|+++..+.+++
T Consensus 247 -------------~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~~~ 310 (485)
T KOG2190|consen 247 -------------FGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENPED 310 (485)
T ss_pred -------------ccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCccc
Confidence 001223466788999999999999999999999999999999999977544 9999999999999
Q ss_pred CCChHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccC
Q 007293 332 RHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCA 411 (609)
Q Consensus 332 ~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~ 411 (609)
..+++++|+.+++.++.+..... . ...++.+|+||++++||||||+|.+|.+|++.|||.|+|...++. .
T Consensus 311 ~~s~a~~a~~~~~~~~~~~~~~~------~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~---~ 380 (485)
T KOG2190|consen 311 RYSMAQEALLLVQPRISENAGDD------L-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV---S 380 (485)
T ss_pred ccccchhhhhhcccccccccccc------c-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc---C
Confidence 99999999999999886643211 1 467899999999999999999999999999999999999987763 2
Q ss_pred CCCCcEEEEcCCHHHHHHHHHHHHHHhhhcccCc
Q 007293 412 AQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSG 445 (609)
Q Consensus 412 ~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~ 445 (609)
..++++++|+|...+...|+++|..++...-...
T Consensus 381 ~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~ 414 (485)
T KOG2190|consen 381 GVREALVQITGMLREDLLAQYLIRARLSAPKSSM 414 (485)
T ss_pred CcceeEEEecchhHHHHhhhhhcccccccCccCC
Confidence 4679999999999999999999988777654433
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=7.3e-43 Score=373.24 Aligned_cols=340 Identities=22% Similarity=0.302 Sum_probs=266.8
Q ss_pred CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (609)
Q Consensus 23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~ 102 (609)
..++-+.-||..+||.||||+|+.|..|..++||+|.+.....+..+|-|.++|..++++ .|.
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~-----------------~aK 114 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVE-----------------VAK 114 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHH-----------------HHH
Confidence 556778899999999999999999999999999999987776677899999999998853 355
Q ss_pred HHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec
Q 007293 103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182 (609)
Q Consensus 103 ~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G 182 (609)
..+..+..+...... . ........++.+++||++.+|+||||+|++||.|++++||++.+..+.......++.+.|+|
T Consensus 115 ~li~evv~r~~~~~~-~-~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritG 192 (600)
T KOG1676|consen 115 QLIGEVVSRGRPPGG-F-PDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITG 192 (600)
T ss_pred HhhhhhhhccCCCCC-c-cccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecC
Confidence 555555554431100 0 01223457899999999999999999999999999999999999997333445889999999
Q ss_pred cHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCC
Q 007293 183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH 262 (609)
Q Consensus 183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~ 262 (609)
++++|+.|..+|.++|++... .... ....|+.
T Consensus 193 dp~~ve~a~~lV~dil~e~~~---~~~g--------------------------------~~~~~g~------------- 224 (600)
T KOG1676|consen 193 DPDKVEQAKQLVADILREEDD---EVPG--------------------------------SGGHAGV------------- 224 (600)
T ss_pred CHHHHHHHHHHHHHHHHhccc---CCCc--------------------------------cccccCc-------------
Confidence 999999999999999986211 0000 0000110
Q ss_pred CCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecC-CCCCCccEEEEcccccccCCCChHHHHHH
Q 007293 263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPVQNAAV 341 (609)
Q Consensus 263 p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~-~~~s~er~vtIsG~e~p~~~~~~a~~A~~ 341 (609)
......+++|.||...||.||||+|++||+|+.+||++|+|..+ .+.+.||.+.|.|+. ..+..|..
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 01123388999999999999999999999999999999999865 448899999999995 55667777
Q ss_pred HHHhhhhhcccccCCCCCCC-CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEE
Q 007293 342 LVFARSVEVEGQQGFSSGEN-KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI 420 (609)
Q Consensus 342 ~i~~~i~e~~~~~g~~~g~~-~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I 420 (609)
+|.+.|.+.....+...+.. ........+.||+++||.||||+|++||.|.++|||++.+.+. +.+...++++|+|
T Consensus 293 lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~I 369 (600)
T KOG1676|consen 293 LINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVI 369 (600)
T ss_pred HHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEE
Confidence 77777765433322221111 1122378999999999999999999999999999999999875 4446788999999
Q ss_pred cCCHHHHHHHHHHHHHHhhhcccC
Q 007293 421 SGEYKNVQNALSEVVGRLRHNLKS 444 (609)
Q Consensus 421 ~G~~~~V~~A~~~I~~~Lr~~~~~ 444 (609)
+|++.+|+.|+.||..++.+....
T Consensus 370 rG~~~QIdhAk~LIr~kvg~~~~n 393 (600)
T KOG1676|consen 370 RGDKRQIDHAKQLIRDKVGDIAPN 393 (600)
T ss_pred ecCcccchHHHHHHHHHhcccCCC
Confidence 999999999999999999985433
No 3
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=5.9e-42 Score=349.83 Aligned_cols=370 Identities=21% Similarity=0.319 Sum_probs=273.3
Q ss_pred CCCCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcC-CCCCCCceEEEEccCcchhhhhhhccccccccCCCc
Q 007293 20 LPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEV 98 (609)
Q Consensus 20 ~~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~ 98 (609)
....+..+|+|||..++|.||||.|++||.|...|.|+|+|.. ...|..||+|+|.|++|. .
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-----------------~ 256 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-----------------T 256 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-----------------h
Confidence 3457889999999999999999999999999999999999975 456889999999999987 3
Q ss_pred chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCce
Q 007293 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQL 177 (609)
Q Consensus 99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~ 177 (609)
+.|+..++.|..+ ...+. +-..++.+++|..+..||+||||.|++||+|+.+||++|.|++. .......||.
T Consensus 257 s~Ac~~ILeimqk---EA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERT 329 (584)
T KOG2193|consen 257 SKACKMILEIMQK---EAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERT 329 (584)
T ss_pred HHHHHHHHHHHHH---hhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccce
Confidence 4455555544433 22111 22247899999999999999999999999999999999999986 3344567999
Q ss_pred EEEeccHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCC
Q 007293 178 IQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSAD 257 (609)
Q Consensus 178 V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~ 257 (609)
|++.|+.++|.+|..+|+.+|++....+-.......++... ...+.-+++|..+.++ ++.+.|....
T Consensus 330 ItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~----l~~~~l~~f~ssS~~~---------~Ph~~Ps~v~ 396 (584)
T KOG2193|consen 330 ITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPG----LNLPALGLFPSSSAVS---------PPHFPPSPVT 396 (584)
T ss_pred EEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcc----cCccccCCCCcccccC---------CCCCCCCccc
Confidence 99999999999999999999998643331111000000000 0000011111111100 0001111100
Q ss_pred CCCCCCCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecC-CCCCCccEEEEcccccccCCCChH
Q 007293 258 ADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPV 336 (609)
Q Consensus 258 ~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~-~~~s~er~vtIsG~e~p~~~~~~a 336 (609)
....-+.+ ....+...++|+||...+|.|||++|.+||.|.+.+||.|+|..+ .++..+|.|+|+|.. .+.
T Consensus 397 ~a~p~~~~--hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp------eaq 468 (584)
T KOG2193|consen 397 FASPYPLF--HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP------EAQ 468 (584)
T ss_pred cCCCchhh--hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh------HHH
Confidence 00000111 112245578999999999999999999999999999999999865 677889999999983 333
Q ss_pred HHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCc
Q 007293 337 QNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDV 416 (609)
Q Consensus 337 ~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er 416 (609)
-.|.-++|.++.|..+- .....-...+.+.||...+|+||||||.+++++++.|+|.+.|+++. .|. .++..
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 47777888888775321 12234567889999999999999999999999999999999998755 453 56778
Q ss_pred EEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293 417 VIQISGEYKNVQNALSEVVGRLRHNL 442 (609)
Q Consensus 417 ~V~I~G~~~~V~~A~~~I~~~Lr~~~ 442 (609)
+|.|.|..-+.+.|+..|.+++.++-
T Consensus 541 ivriiGhfyatq~aQrki~~iv~qvk 566 (584)
T KOG2193|consen 541 IVRIIGHFYATQNAQRKIAHIVNQVK 566 (584)
T ss_pred eeeeechhhcchHHHHHHHHHHHHHH
Confidence 99999999999999999999998764
No 4
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.98 E-value=8.9e-31 Score=254.53 Aligned_cols=329 Identities=17% Similarity=0.305 Sum_probs=208.0
Q ss_pred CCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchH
Q 007293 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSST 101 (609)
Q Consensus 22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A 101 (609)
-..+.+|||+.++.+|+||||+|++||+|+.++++.|.|.++ ..++||++|+.+.+-+
T Consensus 45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~ti-------------------- 102 (390)
T KOG2192|consen 45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIETI-------------------- 102 (390)
T ss_pred hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHHH--------------------
Confidence 466899999999999999999999999999999999999987 5689999999765431
Q ss_pred HHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEe
Q 007293 102 QEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQIT 181 (609)
Q Consensus 102 ~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~ 181 (609)
-+-|++|+.++-+.- ...++..+||||+.+++|.|||++|++||+|++++.|+++|... -|+.++||+|.|.
T Consensus 103 ~~ilk~iip~lee~f-------~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p~stdrv~l~~ 174 (390)
T KOG2192|consen 103 GEILKKIIPTLEEGF-------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCPHSTDRVVLIG 174 (390)
T ss_pred HHHHHHHhhhhhhCC-------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCCCCcceEEEec
Confidence 223444444432221 12347899999999999999999999999999999999999985 7889999999999
Q ss_pred ccHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCC------CCCCcCCCc-CCCCCCCCCCCCCCCccCCC
Q 007293 182 GATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSD------PHREFFPHL-SLVPPLTGNPSDNASEFHSS 254 (609)
Q Consensus 182 G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~------~~~~~~p~~-~~~P~~~~~~~~Ya~~~~p~ 254 (609)
|.+..|..++..|.+.|.+.+.+... +|+...++..... +..+ -|.. ..+|+.++..
T Consensus 175 g~~k~v~~~i~~il~~i~e~pikgsa-----~py~p~fyd~t~dyggf~M~f~d-~pg~pgpapqrggqg---------- 238 (390)
T KOG2192|consen 175 GKPKRVVECIKIILDLISESPIKGSA-----QPYDPNFYDETYDYGGFTMMFDD-RPGRPGPAPQRGGQG---------- 238 (390)
T ss_pred CCcchHHHHHHHHHHHhhcCCcCCcC-----CcCCccccCcccccCCceeecCC-CCCCCCCCCCCCCCC----------
Confidence 99999999999999999987654432 2332222211100 0000 0000 1111111000
Q ss_pred CCCCCCCCCCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCC
Q 007293 255 SADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHS 334 (609)
Q Consensus 255 ~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~ 334 (609)
+.+-..+.- +.+. . -|+-|..-. -.+.|....... . +.+..+
T Consensus 239 ------------pp~~~~sdl--may~--r----~GrpG~ryd-------g~vdFs~detw~---------s--aidtw~ 280 (390)
T KOG2192|consen 239 ------------PPPPRGSDL--MAYD--R----RGRPGDRYD-------GMVDFSADETWP---------S--AIDTWS 280 (390)
T ss_pred ------------CCCCCcccc--ceec--c----CCCCCcccc-------ccccccccccCC---------C--cCCCcC
Confidence 000000000 0000 0 011111100 001111110000 0 000000
Q ss_pred hHHHHHHHHHhhhhhcc----cccCCCC-CCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccc
Q 007293 335 PVQNAAVLVFARSVEVE----GQQGFSS-GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLG 409 (609)
Q Consensus 335 ~a~~A~~~i~~~i~e~~----~~~g~~~-g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~ 409 (609)
+..=+ +.++--.... ...+..+ |.-....+|+.+.||++.-|.||||+|+.|++|++++||.|+|....+
T Consensus 281 ~Sewq--maYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikideple--- 355 (390)
T KOG2192|consen 281 PSEWQ--MAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLE--- 355 (390)
T ss_pred ccccc--cccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCC---
Confidence 00000 0000000000 0000000 111246789999999999999999999999999999999999976433
Q ss_pred cCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293 410 CAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (609)
Q Consensus 410 ~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (609)
++.+|+++|+|+.++++.|++++...++.+
T Consensus 356 --GsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 356 --GSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred --CCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 678999999999999999999999988854
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.96 E-value=3.7e-29 Score=268.27 Aligned_cols=245 Identities=20% Similarity=0.307 Sum_probs=197.2
Q ss_pred CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCC
Q 007293 127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206 (609)
Q Consensus 127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~ 206 (609)
..++.+.-||..++|+||||+|+.|..|+.+|||+|+|... ......|.|.++|.+++|+.|+.+|.+++....
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 46788899999999999999999999999999999998774 235588999999999999999999999986521
Q ss_pred CCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEecccccc
Q 007293 207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (609)
Q Consensus 207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg 286 (609)
.+. .+++ .....+++.++.||.+++|
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 cccccccchhhhhhhccCeeEEEecC--CCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc---ccCCCCCCC
Q 007293 287 GIIGKRGAIVRSLQNASGALISFAAP--LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG---QQGFSSGEN 361 (609)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tGa~I~i~~~--~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~---~~g~~~g~~ 361 (609)
.||||+|++||.|++.+||++.+..+ ......+.+.|+|.. ..++.|..++++.+.+..- ..+...+..
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 223367889999984 5566777788887764311 111111222
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (609)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (609)
.....+.+|.||...||.||||+|++||+|+.+|||+|+|.+.++ | ...+|.+.|.|+.++|+.|.++|.++|++.
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 345569999999999999999999999999999999999998766 3 477999999999999999999999999864
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=1.6e-28 Score=251.53 Aligned_cols=239 Identities=17% Similarity=0.292 Sum_probs=194.1
Q ss_pred ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCCC
Q 007293 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (609)
Q Consensus 128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~ 207 (609)
+..+|+|||..++|.||||.|++||.|...|-|+|.|... ...+..|+.|+|-|.++...+|+.+|.+++......+
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 4568899999999999999999999999997642111
Q ss_pred CcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeccccccc
Q 007293 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (609)
Q Consensus 208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~ 287 (609)
....++.++++..+.+||+
T Consensus 275 -------------------------------------------------------------k~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 275 -------------------------------------------------------------KVAEEIPLKILAHNNLVGR 293 (584)
T ss_pred -------------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence 1225678899999999999
Q ss_pred ccccccchhhhhhhccCeeEEEecC---CCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhc------------cc
Q 007293 288 IIGKRGAIVRSLQNASGALISFAAP---LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV------------EG 352 (609)
Q Consensus 288 IIGk~G~~Ik~I~~~tGa~I~i~~~---~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~------------~~ 352 (609)
+|||.|.+||+|+++||++|.|... ..-..||.|++.|+- ..+..|-..|..++.+. .+
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 33334444454444322 11
Q ss_pred ccCCC-------------------CC----CC-------CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEec
Q 007293 353 QQGFS-------------------SG----EN-------KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (609)
Q Consensus 353 ~~g~~-------------------~g----~~-------~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~ 402 (609)
.+++. +. +. .......+|.||...+|.|||++|.+||.|.+.+||.|+|.
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 11110 00 00 12445788999999999999999999999999999999998
Q ss_pred CCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293 403 GGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 403 ~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (609)
..+- .+..+|+|+|+|.+++..+|+..|..+|.+
T Consensus 448 ppE~----pdvseRMViItGppeaqfKAQgrifgKikE 481 (584)
T KOG2193|consen 448 PPEI----PDVSERMVIITGPPEAQFKAQGRIFGKIKE 481 (584)
T ss_pred CCCC----CCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence 7653 357899999999999999999999999997
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=3.5e-26 Score=228.82 Aligned_cols=242 Identities=19% Similarity=0.293 Sum_probs=172.3
Q ss_pred CCCCCCCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEc---CCCCCCCceEEEEccCcchhhhhhhccccccc
Q 007293 17 PLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE---GGFPGSDHRVILVVGSGSIDRRIMFCENDVVV 93 (609)
Q Consensus 17 ~~~~~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~---~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~ 93 (609)
.+...++.+++|||||+..+|.||||+|++|.+|+++|||+|+++ +.+|++.||||+|.|+.+++.
T Consensus 31 ~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~----------- 99 (402)
T KOG2191|consen 31 TNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN----------- 99 (402)
T ss_pred ccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH-----------
Confidence 344445569999999999999999999999999999999999996 578999999999999876521
Q ss_pred cCCCcchHHHHHHHHHHHHhhhhhccCC------CCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293 94 EGGEVSSTQEAVIRVFERMWEVEAEVEG------DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (609)
Q Consensus 94 e~~~~~~A~~Al~~v~~~i~~~~~~~~~------~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~ 167 (609)
.-+..|.++|.+.....++ ....++.-.++++||++.+|.||||+|.+||.|++++||.|+|++.
T Consensus 100 ---------av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq 170 (402)
T KOG2191|consen 100 ---------AVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ 170 (402)
T ss_pred ---------HHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc
Confidence 1122333444433222222 1123444669999999999999999999999999999999999954
Q ss_pred -CCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCC
Q 007293 168 -PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSD 246 (609)
Q Consensus 168 -p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~ 246 (609)
|..-...||+|+++|++++..+|+.+|.++|.+++..... .+.++..... ....
T Consensus 171 kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~sc---ln~sya~vsG----------------------pvaN 225 (402)
T KOG2191|consen 171 KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSC---LNISYANVSG----------------------PVAN 225 (402)
T ss_pred CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccce---eccchhcccC----------------------cccc
Confidence 5555678999999999999999999999999997654321 1111111000 0011
Q ss_pred CCCccCCCCCCCCCCCCCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecC
Q 007293 247 NASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP 312 (609)
Q Consensus 247 Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 312 (609)
|++...|+.... .........-.-++....|..-|.+|.++-.|-.-+|+.+.+.+.
T Consensus 226 snPtGspya~~~---------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 226 SNPTGSPYAYQA---------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred cCCCCCCCCCCC---------ccccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence 111111111111 111222233456888899999999999999999999998888753
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=2.3e-22 Score=201.58 Aligned_cols=250 Identities=21% Similarity=0.296 Sum_probs=195.3
Q ss_pred ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCC
Q 007293 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206 (609)
Q Consensus 128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~ 206 (609)
.+.+++|||+..+|.||||+|++|.++|.+|||+|++++. ...|+++||+|.|+|+.+++......|.++|++.+....
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 4899999999999999999999999999999999999987 788999999999999999999999999999998543221
Q ss_pred CCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEecccccc
Q 007293 207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (609)
Q Consensus 207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg 286 (609)
.+....+ | ......-.++++||+..+|
T Consensus 118 k~v~~~~------------------------p-----------------------------qt~~r~kqikivvPNstag 144 (402)
T KOG2191|consen 118 KPVDILQ------------------------P-----------------------------QTPDRIKQIKIVVPNSTAG 144 (402)
T ss_pred CCccccC------------------------C-----------------------------CCccccceeEEeccCCccc
Confidence 1100000 0 0001112478999999999
Q ss_pred cccccccchhhhhhhccCeeEEEecCCC---CCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc---------cc
Q 007293 287 GIIGKRGAIVRSLQNASGALISFAAPLT---KSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG---------QQ 354 (609)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tGa~I~i~~~~~---~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~---------~~ 354 (609)
.||||+|.+||.|++++||+|+|.+.++ .-.+|+||++|.. +....|+.+|++++.++.- ..
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 9999999999999999999999995332 3368999999984 5667899999999876520 00
Q ss_pred ------CCCC-C-------CCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEE
Q 007293 355 ------GFSS-G-------ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI 420 (609)
Q Consensus 355 ------g~~~-g-------~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I 420 (609)
++.+ | ...+...+....|+....|..-|.+|.++-.|...+|+.+.+...-+.- .....+ +-+
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 0111 1 0123446677889999999999999999999999999999998755521 223334 788
Q ss_pred cCCHHHHHHHHHHHHHHhh
Q 007293 421 SGEYKNVQNALSEVVGRLR 439 (609)
Q Consensus 421 ~G~~~~V~~A~~~I~~~Lr 439 (609)
.|....+..|-.+|..+..
T Consensus 296 ~g~~ls~~aa~g~L~~~~~ 314 (402)
T KOG2191|consen 296 LGLGLSILAAEGVLAAKVA 314 (402)
T ss_pred cchhhhhhhhhhHHHHhhc
Confidence 9999999999998887654
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.84 E-value=9.4e-20 Score=199.00 Aligned_cols=163 Identities=28% Similarity=0.407 Sum_probs=138.5
Q ss_pred EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc--
Q 007293 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG-- 352 (609)
Q Consensus 275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~-- 352 (609)
++|++|+...+|.||||+|..||+|+.++.++|+|.+..+++.+|+|+|+|+... ...+++++|+.+.++++.....
T Consensus 44 ~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-~~~~~~~~al~ka~~~iv~~~~~d 122 (485)
T KOG2190|consen 44 TYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-LNLSPATDALFKAFDMIVFKLEED 122 (485)
T ss_pred eEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-ccCCchHHHHHHHHHHHhhccccc
Confidence 4899999999999999999999999999999999999999999999999995322 2567889999999998865311
Q ss_pred -ccCCCCC-CCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHH
Q 007293 353 -QQGFSSG-ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNA 430 (609)
Q Consensus 353 -~~g~~~g-~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A 430 (609)
....+.+ ......++.+|+||.+++|+||||+|+.||+|++.|||+|+|.+. .+|. .++|.|+|.|.+++|.+|
T Consensus 123 ~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~a 198 (485)
T KOG2190|consen 123 DEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKA 198 (485)
T ss_pred ccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHH
Confidence 1111111 122236899999999999999999999999999999999999986 6675 667889999999999999
Q ss_pred HHHHHHHhhhcc
Q 007293 431 LSEVVGRLRHNL 442 (609)
Q Consensus 431 ~~~I~~~Lr~~~ 442 (609)
+..|..+|+++.
T Consensus 199 l~~Is~~L~~~~ 210 (485)
T KOG2190|consen 199 LVQISSRLLENP 210 (485)
T ss_pred HHHHHHHHHhcC
Confidence 999999999975
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.59 E-value=2.1e-14 Score=140.75 Aligned_cols=159 Identities=21% Similarity=0.377 Sum_probs=130.0
Q ss_pred CCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhh
Q 007293 270 RKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVE 349 (609)
Q Consensus 270 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e 349 (609)
....+.+++++..+.+|.||||+|++||.|+.+++|+|+|.++ ...+|+++|+..+ +.+..|++++.-
T Consensus 44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~----------~ti~~ilk~iip 111 (390)
T KOG2192|consen 44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADI----------ETIGEILKKIIP 111 (390)
T ss_pred hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccH----------HHHHHHHHHHhh
Confidence 3456789999999999999999999999999999999999865 3578999999874 455556555532
Q ss_pred cccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHH
Q 007293 350 VEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN 429 (609)
Q Consensus 350 ~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~ 429 (609)
. ++.++ ...+.|..+|+|..+.+|.|||++|+.||++++.+.|+.+|.-. . |...++|+|.|.|.+..|..
T Consensus 112 ~-lee~f----~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c---~p~stdrv~l~~g~~k~v~~ 182 (390)
T KOG2192|consen 112 T-LEEGF----QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-C---CPHSTDRVVLIGGKPKRVVE 182 (390)
T ss_pred h-hhhCC----CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-c---CCCCcceEEEecCCcchHHH
Confidence 1 11112 23467999999999999999999999999999999999999752 2 24688999999999999999
Q ss_pred HHHHHHHHhhhcccCccccC
Q 007293 430 ALSEVVGRLRHNLKSGEILN 449 (609)
Q Consensus 430 A~~~I~~~Lr~~~~~~~~~~ 449 (609)
..+.|+..|.+..+..+..|
T Consensus 183 ~i~~il~~i~e~pikgsa~p 202 (390)
T KOG2192|consen 183 CIKIILDLISESPIKGSAQP 202 (390)
T ss_pred HHHHHHHHhhcCCcCCcCCc
Confidence 99999999998766655443
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=99.47 E-value=1.4e-13 Score=132.27 Aligned_cols=138 Identities=18% Similarity=0.205 Sum_probs=96.0
Q ss_pred EEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEE---ccCcchhhhhhhccccccccCCCcchHHHHH
Q 007293 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILV---VGSGSIDRRIMFCENDVVVEGGEVSSTQEAV 105 (609)
Q Consensus 29 ilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I---~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al 105 (609)
+.||.+++|.|||++|++|++|+++|||+|++.+. +..|.| +++++. +..|.+.+
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-----TGEVKIEEEDEDPLA-----------------VMKAREVV 59 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-----------------HHHHHHHH
Confidence 45799999999999999999999999999999753 245777 343333 22343333
Q ss_pred HHHHHHHhhhhhccCCCCCCCCceEEEE-Eeec---------ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCC
Q 007293 106 IRVFERMWEVEAEVEGDGDGDDVAYCGL-LANT---------TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD 175 (609)
Q Consensus 106 ~~v~~~i~~~~~~~~~~~~~~~~vt~rl-lVP~---------~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~d 175 (609)
..+..- ...+..- .--...+++++ -|+. ..+|+|||++|++++.|++.|||+|.|. +
T Consensus 60 ~~i~~g---f~~e~A~-~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~---------~ 126 (172)
T TIGR03665 60 KAIGRG---FSPEKAL-KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY---------G 126 (172)
T ss_pred HHHHcC---CCHHHHH-HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc---------C
Confidence 332210 0011000 00001222222 2222 3789999999999999999999999993 3
Q ss_pred ceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293 176 QLIQITGATLAVKKALVAVTTCLQHL 201 (609)
Q Consensus 176 R~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (609)
+.|.|.|+++++..|..+|.+++.+.
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
>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=3.5e-13 Score=129.50 Aligned_cols=140 Identities=19% Similarity=0.200 Sum_probs=98.1
Q ss_pred EEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEc--ccccccCCCChHHHHHHHHHhhhhhcccccC
Q 007293 278 MLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS--ALEYLDTRHSPVQNAAVLVFARSVEVEGQQG 355 (609)
Q Consensus 278 i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIs--G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g 355 (609)
+.||.+++|.|||++|++|+.|+++||++|.+.+. +..|.|. +. ++ ..++.|...+........+...
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~-d~----~~i~kA~~~I~~i~~gf~~e~A 71 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDE-DP----LAVMKAREVVKAIGRGFSPEKA 71 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCC-CH----HHHHHHHHHHHHHHcCCCHHHH
Confidence 56899999999999999999999999999999953 2468883 21 11 3344555544432211110000
Q ss_pred CCCCCCCCCceEEEEEecc---------ccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHH
Q 007293 356 FSSGENKGDAVAVSILVGA---------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKN 426 (609)
Q Consensus 356 ~~~g~~~~~~~t~~l~VP~---------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~ 426 (609)
+ ..-.....-.-+.|+. ..+|+|||++|++++.|++.|||+|.|.. +.|.|.|++++
T Consensus 72 ~--~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~ 137 (172)
T TIGR03665 72 L--KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQ 137 (172)
T ss_pred H--HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHH
Confidence 0 0000111122233443 47999999999999999999999999952 67999999999
Q ss_pred HHHHHHHHHHHhhhc
Q 007293 427 VQNALSEVVGRLRHN 441 (609)
Q Consensus 427 V~~A~~~I~~~Lr~~ 441 (609)
++.|+++|...|.+.
T Consensus 138 ~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 138 VQIAREAIEMLIEGA 152 (172)
T ss_pred HHHHHHHHHHHHcCC
Confidence 999999999988643
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.44 E-value=5.4e-13 Score=129.08 Aligned_cols=140 Identities=16% Similarity=0.243 Sum_probs=98.3
Q ss_pred EEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEc----cCcchhhhhhhccccccccCCCcch
Q 007293 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVV----GSGSIDRRIMFCENDVVVEGGEVSS 100 (609)
Q Consensus 25 v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~----G~~e~~~~~~~~~~~~~~e~~~~~~ 100 (609)
+...+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|. ++++. +..
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-----TGEVIIEPTDGEDPLA-----------------VLK 60 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-----------------HHH
Confidence 467788999999999999999999999999999999853 2456665 33333 223
Q ss_pred HHHHHHHHHHHHhhhhh--ccCCCCCCCCceEEEEE-----ee-----cceeeeeeecCcchhhhcccccCcEEEecCCC
Q 007293 101 TQEAVIRVFERMWEVEA--EVEGDGDGDDVAYCGLL-----AN-----TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPP 168 (609)
Q Consensus 101 A~~Al~~v~~~i~~~~~--~~~~~~~~~~~vt~rll-----VP-----~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p 168 (609)
|++.+..+..- .+.+. ..-+ ..+..++. .+ ...+|+|||++|++++.|++.|||+|.|..
T Consensus 61 A~~~I~ai~~g-f~~e~A~~l~g-----d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-- 132 (180)
T PRK13763 61 ARDIVKAIGRG-FSPEKALRLLD-----DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-- 132 (180)
T ss_pred HHHHHHHHhcC-CCHHHHHHHhC-----CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC--
Confidence 43333332210 00000 0000 12222221 11 137899999999999999999999999954
Q ss_pred CCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293 169 ACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (609)
Q Consensus 169 ~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (609)
+.|.|.|+++++..|...|..++++.
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 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.39 E-value=2e-12 Score=125.22 Aligned_cols=145 Identities=18% Similarity=0.217 Sum_probs=99.6
Q ss_pred EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccccc
Q 007293 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ 354 (609)
Q Consensus 275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~ 354 (609)
...+.||.+.+|.|||++|++|+.|+++||++|.+.+. +..|.|.-.... + ...++.|...+...........
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-----TGEVIIEPTDGE-D-PLAVLKARDIVKAIGRGFSPEK 76 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCC-C-HHHHHHHHHHHHHHhcCCCHHH
Confidence 56788999999999999999999999999999999954 256777611100 1 1334455554443332100000
Q ss_pred CCCCCCCCCCceEEE-EEec---------cccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCH
Q 007293 355 GFSSGENKGDAVAVS-ILVG---------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY 424 (609)
Q Consensus 355 g~~~g~~~~~~~t~~-l~VP---------~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~ 424 (609)
.+. . ....+..+ +.|. ...+|+|||++|++++.|++.|||+|.|.. +.|.|.|++
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 00111111 1111 147999999999999999999999999953 349999999
Q ss_pred HHHHHHHHHHHHHhhhc
Q 007293 425 KNVQNALSEVVGRLRHN 441 (609)
Q Consensus 425 ~~V~~A~~~I~~~Lr~~ 441 (609)
++++.|...|...++.+
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=99.31 E-value=3.9e-12 Score=102.50 Aligned_cols=65 Identities=28% Similarity=0.473 Sum_probs=58.8
Q ss_pred EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007293 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (609)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~ 435 (609)
+.+|+||.+.+|+|||++|++|++|+++|||+|++.+..+ ...++|+|+|+|++++|+.|+.+|.
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 2567899999999999999999873
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=99.29 E-value=4e-12 Score=102.44 Aligned_cols=64 Identities=31% Similarity=0.549 Sum_probs=59.0
Q ss_pred EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 007293 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (609)
Q Consensus 130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I 194 (609)
++||+||.+.+|+||||+|++|++|+++|||+|.+.+. ..+...+|+|+|+|++++|.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS-VLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCC-CCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 37899999999999999999999999999999999985 33467899999999999999999987
No 17
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.24 E-value=6.4e-11 Score=127.00 Aligned_cols=298 Identities=16% Similarity=0.149 Sum_probs=200.9
Q ss_pred CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCC
Q 007293 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTME 205 (609)
Q Consensus 126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~ 205 (609)
...+.+++.|+...+.+++||+|++|+.|+..++++|.+..+ ....++...+.|-+.++.+|...++.++.++.
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 447889999999999999999999999999999999999775 22345555666689999999999999996631
Q ss_pred CCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeccccc
Q 007293 206 KSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTA 285 (609)
Q Consensus 206 ~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~v 285 (609)
.+...+.+|...+
T Consensus 139 -------------------------------------------------------------------pvk~~lsvpqr~~ 151 (608)
T KOG2279|consen 139 -------------------------------------------------------------------PVSEQLSVPQRSV 151 (608)
T ss_pred -------------------------------------------------------------------cccccccchhhhc
Confidence 2234466889999
Q ss_pred ccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhc---------------
Q 007293 286 SGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV--------------- 350 (609)
Q Consensus 286 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~--------------- 350 (609)
++|+|++|++++.|+..++|+|.+.......-.+...|.+.. ++...|..++.+++.+.
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 999999999999999999999999977544556777887764 22223333333333211
Q ss_pred -------cc-----------------------ccCCCC-----------------------CC--CCCCceEEEEEeccc
Q 007293 351 -------EG-----------------------QQGFSS-----------------------GE--NKGDAVAVSILVGAD 375 (609)
Q Consensus 351 -------~~-----------------------~~g~~~-----------------------g~--~~~~~~t~~l~VP~~ 375 (609)
.+ ..+.+. +. ......-.+|.||..
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 00 001000 00 011234568899999
Q ss_pred cccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcccCccccCCCCCCC
Q 007293 376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRS 455 (609)
Q Consensus 376 ~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~~~~~~~~~~ 455 (609)
.+|.|||+.|..++.....|++.+.|--....-. --.-.++.+.|+..-+..++.|+..+.-+ ..+..+.-...
T Consensus 306 lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~--v~~~qic~~egkqh~~n~vl~ml~~~~p~----~~f~eLnl~~~ 379 (608)
T KOG2279|consen 306 LSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR--VLQLQICVNEGKQHYENSVLEMLTVHVPD----IVFAELNLNGS 379 (608)
T ss_pred cccchhhhhhhhhhhhhhccCccceEEeccccch--hhhhhhheecchhHHHHHHHhhhhccCCc----cccccccccCc
Confidence 9999999999999999999999998865222000 01125688999999999999998754332 21111111110
Q ss_pred CCCCCCCCCCCCCCCCCCCCcccccccccccccceeeecCCCCccccccCCCCCCCCCCCCCCCccccc
Q 007293 456 PSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEG 524 (609)
Q Consensus 456 ~~~~~g~p~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 524 (609)
-++..-.+++-... .-+.-..||-+-.-.....+-+-+.+.+|+.|--|-|.-
T Consensus 380 ~~p~lps~al~~L~----------------td~~wL~fpd~i~cev~V~s~i~a~hlf~pq~tip~F~a 432 (608)
T KOG2279|consen 380 WYPALPSGALENLN----------------TDLYWLDFPDNIDCEVKVLSAIRADHLFLPQQTIPCFLA 432 (608)
T ss_pred cCcccCcccccccC----------------CcceEEEcCCCceEEeeeehhhcccceeeccccchhhhh
Confidence 01111111121111 112234667777777777778889999999988886544
No 18
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.21 E-value=9.3e-11 Score=125.79 Aligned_cols=276 Identities=21% Similarity=0.254 Sum_probs=173.7
Q ss_pred CCCCCCCCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccC
Q 007293 16 GPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEG 95 (609)
Q Consensus 16 ~~~~~~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~ 95 (609)
+..+...+++.+.+.|++..|-.+|||.|++|+.|+..|++||.+.+...+ ++++.++.|-...
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 345667799999999999999999999999999999999999999765333 4677777765543
Q ss_pred CCcchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCC
Q 007293 96 GEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD 175 (609)
Q Consensus 96 ~~~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~d 175 (609)
+++|..++... +... ..+...+-+|...++.|+|++|.+++.|+.-++|+|.+..+ .-...+
T Consensus 123 --v~~a~a~~~~~---~~~~-----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr~g~~ 184 (608)
T KOG2279|consen 123 --VCKAKAAIHQI---LTEN-----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GRLGLS 184 (608)
T ss_pred --CChHHHHHHHH---HhcC-----------Ccccccccchhhhcccccccchhhhcchhcccccccccccc--cccccc
Confidence 45554444332 2221 25667789999999999999999999999999999999875 234578
Q ss_pred ceEEEeccHHHHHHHHHHHHHHHhccCCCCCC-------CcccCCCccccccCCCCCCCCCcCCCc------CCCCCCCC
Q 007293 176 QLIQITGATLAVKKALVAVTTCLQHLSTMEKS-------PICFNRPIEKVFYSNSSDPHREFFPHL------SLVPPLTG 242 (609)
Q Consensus 176 R~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~-------~~~~~~P~~~~~~~~~~~~~~~~~p~~------~~~P~~~~ 242 (609)
++..|.|...-+..|..++.+.+.++-...+. ......|...+. .....+.....+|. ++.|..++
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 89999999999999999999988764211111 001111111100 00000111111110 22222211
Q ss_pred CCCCCCCccCC-CCCCCCCCCCCCCc-cCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCC---
Q 007293 243 NPSDNASEFHS-SSADADRDHPGLDK-KGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSG--- 317 (609)
Q Consensus 243 ~~~~Ya~~~~p-~~~~~~~~~p~~~~-~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~--- 317 (609)
...+-.. +-- ......-..+..+. ........++|.+|...+|.+||+.|+.++.+...+++++.|......+.
T Consensus 264 ~~~eg~d-m~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~ 342 (608)
T KOG2279|consen 264 VTKEGGD-MAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQ 342 (608)
T ss_pred cccCCCc-ceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhh
Confidence 1100000 000 00000000000000 11223346778899999999999999999999999999999975322222
Q ss_pred ccEEEEcccc
Q 007293 318 ERVVTISALE 327 (609)
Q Consensus 318 er~vtIsG~e 327 (609)
-.++.+.|+.
T Consensus 343 ~qic~~egkq 352 (608)
T KOG2279|consen 343 LQICVNEGKQ 352 (608)
T ss_pred hhhheecchh
Confidence 2567777873
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=99.16 E-value=6.1e-11 Score=94.46 Aligned_cols=61 Identities=20% Similarity=0.330 Sum_probs=55.6
Q ss_pred EEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007293 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (609)
Q Consensus 368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~ 435 (609)
.++.||.+++++|||++|++|++|+++|||+|.|++.. ..++.|+|+|+.++|..|+.+|.
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 45799999999999999999873
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=5e-11 Score=94.31 Aligned_cols=60 Identities=27% Similarity=0.422 Sum_probs=54.8
Q ss_pred EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007293 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (609)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I 434 (609)
|.+|.||.+++|+|||++|++|++|++.|||+|+|++. + +...|+|+|++++|+.|+.+|
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=99.10 E-value=2.3e-10 Score=90.93 Aligned_cols=59 Identities=15% Similarity=0.255 Sum_probs=53.8
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHH
Q 007293 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVV 435 (609)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~-~~~V~~A~~~I~ 435 (609)
.+..+.||.+++|+|||++|++|++|+++|||+|.|.+ ++.|.|+|+ +++++.|+.+|.
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=99.05 E-value=4.8e-10 Score=89.44 Aligned_cols=62 Identities=26% Similarity=0.489 Sum_probs=56.5
Q ss_pred EEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007293 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (609)
Q Consensus 368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I 434 (609)
.++.||.+++++|||++|++|++|++.|||+|.|+.... ...++.|+|.|+.+++..|+.+|
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 589999999999999999999999999999999987433 35689999999999999999887
No 23
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.99 E-value=4.4e-10 Score=89.52 Aligned_cols=60 Identities=27% Similarity=0.354 Sum_probs=55.3
Q ss_pred EEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 007293 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (609)
Q Consensus 131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I 194 (609)
.+|.||..++++|||++|++|++|+++|||+|.+... ...++.|+|+|+.++|.+|+.+|
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 5689999999999999999999999999999999773 26789999999999999999886
No 24
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.98 E-value=2.2e-10 Score=90.63 Aligned_cols=60 Identities=23% Similarity=0.418 Sum_probs=54.7
Q ss_pred EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 007293 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (609)
Q Consensus 130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I 194 (609)
|.+|.||..++|+|||++|++|++|+++|||+|.+... + ....|+|+|+.++|.+|+.+|
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 25
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.96 E-value=2.9e-09 Score=123.28 Aligned_cols=288 Identities=17% Similarity=0.158 Sum_probs=196.3
Q ss_pred CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (609)
Q Consensus 23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~ 102 (609)
..+..++.+-......+||++|.+++.++.++.+.|+|++..... ....|.|..... ..+.
T Consensus 199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~--~~~~i~~~~~~~-----------------~~~~ 259 (753)
T KOG2208|consen 199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSS--PSNKIDGRLNSS-----------------SSIN 259 (753)
T ss_pred eeEEEEeeccccchhhhccccccccccccccceeEEEcccccccc--hhhhhccccccc-----------------eehh
Confidence 447888999999999999999999999999999999998754332 223444433221 0111
Q ss_pred HHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec
Q 007293 103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182 (609)
Q Consensus 103 ~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G 182 (609)
--+...+.++.. .....+.++....-.++|..|..+..|+...--...+.+. +.+.+..+.+.|
T Consensus 260 ~~i~~~~~~le~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~---~~s~~~~~~~~~ 323 (753)
T KOG2208|consen 260 VEIQEALTRLES-------------EFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQN---YPSKDDSIVLSG 323 (753)
T ss_pred hhhHHHHHHhcC-------------hhhhhhhhhccccccccccccchhhHHHhhcchhhhhhcc---ccccceeEeecc
Confidence 111122222111 2233456667777888999999999999887665555553 345667788888
Q ss_pred cHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCC
Q 007293 183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH 262 (609)
Q Consensus 183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~ 262 (609)
....+..+...-...+...
T Consensus 324 ~~~~~~~~~~~~~~~~~~~------------------------------------------------------------- 342 (753)
T KOG2208|consen 324 FEVGAVLAKRDKTLLLKNS------------------------------------------------------------- 342 (753)
T ss_pred cccchhhhhhHHHHHHHHh-------------------------------------------------------------
Confidence 8777766665554444331
Q ss_pred CCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHH
Q 007293 263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVL 342 (609)
Q Consensus 263 p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~ 342 (609)
..+.+.+.+.+-...+..++||+|.+|.+|++++.+.+.+.. .++....+.++|.. ...+.|...
T Consensus 343 -------~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~------~~~~ka~~~ 407 (753)
T KOG2208|consen 343 -------EENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVS------ANDEKAVED 407 (753)
T ss_pred -------hccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccc------cchhHHHHH
Confidence 012235567788999999999999999999999999999986 33456678888874 222333333
Q ss_pred HHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhC-CeEEecCCCcccccCCCCCcEEEEc
Q 007293 343 VFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTG-TDIKLVGGEQVLGCAAQNDVVIQIS 421 (609)
Q Consensus 343 i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TG-a~I~I~~~~~~P~~~~~~er~V~I~ 421 (609)
+.....+.. .+.....+.+|...+.+|||.+|..|++|...+| .+|+.++.. .....+++.
T Consensus 408 v~~~~~ei~-----------n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~ 469 (753)
T KOG2208|consen 408 VEKIIAEIL-----------NSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIR 469 (753)
T ss_pred HHHHHHhhh-----------cccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEe
Confidence 333332210 1145778999999999999999999999999999 667666532 345667788
Q ss_pred CCHHHHHHHHHHHHHHhh
Q 007293 422 GEYKNVQNALSEVVGRLR 439 (609)
Q Consensus 422 G~~~~V~~A~~~I~~~Lr 439 (609)
|....+..+..++.....
T Consensus 470 ~~~~dv~~~~~~~~~~~~ 487 (753)
T KOG2208|consen 470 GISKDVEKSVSLLKALKA 487 (753)
T ss_pred ccccccchhHHHHHhhhh
Confidence 887777776666655443
No 26
>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=98.91 E-value=2.2e-09 Score=85.58 Aligned_cols=62 Identities=31% Similarity=0.532 Sum_probs=56.2
Q ss_pred EEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 007293 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (609)
Q Consensus 131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I 194 (609)
.++.||..++++|||++|++|++|+++|||+|.|... .....++.|.|.|..+++.+|+.+|
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 5799999999999999999999999999999999874 2246789999999999999999876
No 27
>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=98.91 E-value=2.4e-09 Score=85.10 Aligned_cols=58 Identities=26% Similarity=0.343 Sum_probs=52.7
Q ss_pred eEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHH
Q 007293 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAV 194 (609)
Q Consensus 129 vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I 194 (609)
.+..+-||.+++|+||||+|++|++|+++|||+|.|.. ++.|.|+|. .+++.+|+.+|
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 45678899999999999999999999999999999955 367999998 99999999887
No 28
>PF13014 KH_3: KH domain
Probab=98.80 E-value=8e-09 Score=76.13 Aligned_cols=42 Identities=40% Similarity=0.727 Sum_probs=38.6
Q ss_pred cccceecCCChHHHHHHHHhCceEEEcC-CCCCCCceEEEEcc
Q 007293 35 VVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVG 76 (609)
Q Consensus 35 ~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~g~~eRvI~I~G 76 (609)
++|+|||++|++|++|+++|||+|+|++ ..++..+|+|+|+|
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 5899999999999999999999999988 56678899999987
No 29
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.76 E-value=3.8e-08 Score=114.08 Aligned_cols=287 Identities=17% Similarity=0.197 Sum_probs=194.7
Q ss_pred EEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHH
Q 007293 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEA 104 (609)
Q Consensus 25 v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~A 104 (609)
..+-..|+....-.++|..|..+++|+....-...+....+. ...++.++|....+.. ...+.
T Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s-~~~~~~~~~~~~~~~~----------------~~~~~ 335 (753)
T KOG2208|consen 273 FDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPS-KDDSIVLSGFEVGAVL----------------AKRDK 335 (753)
T ss_pred hhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccc-cceeEeecccccchhh----------------hhhHH
Confidence 344566777888889999999999999888544444333233 3456777777655311 11122
Q ss_pred HHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccH
Q 007293 105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGAT 184 (609)
Q Consensus 105 l~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~ 184 (609)
. ..+....+. .+.+.+-+....+..++||+|.+|.+|++++.|.+.+.. .+..+..+.++|..
T Consensus 336 ~-~~~~~~~~n------------n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~----~~~~~~~v~~~~~~ 398 (753)
T KOG2208|consen 336 T-LLLKNSEEN------------NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK----QGSNNKKVVITGVS 398 (753)
T ss_pred H-HHHHHhhcc------------ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc----ccCCCCCeEEeccc
Confidence 2 222221111 366778888999999999999999999999999999966 46788999999999
Q ss_pred HHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCC
Q 007293 185 LAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPG 264 (609)
Q Consensus 185 e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~ 264 (609)
.++.+|...|.....+....
T Consensus 399 ~~~~ka~~~v~~~~~ei~n~------------------------------------------------------------ 418 (753)
T KOG2208|consen 399 ANDEKAVEDVEKIIAEILNS------------------------------------------------------------ 418 (753)
T ss_pred cchhHHHHHHHHHHHhhhcc------------------------------------------------------------
Confidence 99999999999999773210
Q ss_pred CCccCCCcceEEEEEecccccccccccccchhhhhhhccC-eeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHH
Q 007293 265 LDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASG-ALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLV 343 (609)
Q Consensus 265 ~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG-a~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i 343 (609)
.....+.+|..++..+||.+|..|..|..+++ ..|++... .+....+++.|.- ..+.. +..++
T Consensus 419 --------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~--~~~~~~~~~~~~~---~dv~~---~~~~~ 482 (753)
T KOG2208|consen 419 --------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN--NNSSDMVTIRGIS---KDVEK---SVSLL 482 (753)
T ss_pred --------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC--CcccccceEeccc---cccch---hHHHH
Confidence 12334679999999999999999999999999 55555543 3334456676653 11111 11111
Q ss_pred Hh--hhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEc
Q 007293 344 FA--RSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS 421 (609)
Q Consensus 344 ~~--~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~ 421 (609)
.. ...... ..-...+...+.|..+.+..+|+.|..+...++..+..+.. ..++..++|.
T Consensus 483 ~~~~~~a~~~---------~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~----------~~~~~~i~i~ 543 (753)
T KOG2208|consen 483 KALKADAKNL---------KFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNE----------DEDHEKITIE 543 (753)
T ss_pred Hhhhhhhhcc---------hhhhhhhccccchHHhhcccccCceeeeccCCceeeccccc----------ccccceeeec
Confidence 11 111100 01133566777788888888888777666555444444332 2567889999
Q ss_pred CCHHHHHHHHHHHHHHhhh
Q 007293 422 GEYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 422 G~~~~V~~A~~~I~~~Lr~ 440 (609)
|..+.|.+|..++...+..
T Consensus 544 gk~~~v~~a~~~L~~~~~~ 562 (753)
T KOG2208|consen 544 GKLELVLEAPAELKALIEA 562 (753)
T ss_pred ccccchhhhHHHHHhcchh
Confidence 9999999999999886654
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=98.76 E-value=4e-08 Score=78.37 Aligned_cols=67 Identities=30% Similarity=0.528 Sum_probs=60.0
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhh
Q 007293 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439 (609)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr 439 (609)
.+.++.||.++++++||++|++|++|++.||++|.+.... .....|+|.|+.++++.|+.+|...++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999997522 257889999999999999999988763
No 31
>PF13014 KH_3: KH domain
Probab=98.74 E-value=1.3e-08 Score=74.97 Aligned_cols=43 Identities=35% Similarity=0.664 Sum_probs=37.8
Q ss_pred cccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC
Q 007293 376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG 422 (609)
Q Consensus 376 ~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G 422 (609)
+||+|||++|++|++|+++|||+|+|++ +.. ...+++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~---~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENE---PGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccC---CCCCceEEEEEC
Confidence 5899999999999999999999999998 221 357899999998
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.61 E-value=1.2e-07 Score=75.51 Aligned_cols=67 Identities=27% Similarity=0.487 Sum_probs=60.4
Q ss_pred ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 007293 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198 (609)
Q Consensus 128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L 198 (609)
.++.++.||...++.+||++|++|++|++.||++|.+... ......+.|.|..+++..|..+|.+.+
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 226789999999999999999998876
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.51 E-value=1.9e-07 Score=89.67 Aligned_cols=148 Identities=18% Similarity=0.220 Sum_probs=98.9
Q ss_pred CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (609)
Q Consensus 23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~ 102 (609)
....+.+.+|.+..+.+||+.|++.+.|.+.++++|.++ ..+..|.|.......+. .....|.
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp------------~~~~ka~ 68 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDP------------LALLKAR 68 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCCh------------HHHHHHH
Confidence 445677999999999999999999999999999999995 34577888765321110 0111222
Q ss_pred HHHHHHHHHHhhhhhccCCC-CCCCCceEEEE-----Eee------cceeeeeeecCcchhhhcccccCcEEEecCCCCC
Q 007293 103 EAVIRVFERMWEVEAEVEGD-GDGDDVAYCGL-----LAN------TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPAC 170 (609)
Q Consensus 103 ~Al~~v~~~i~~~~~~~~~~-~~~~~~vt~rl-----lVP------~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~ 170 (609)
+-+. .+.+ ++..+.+ .--+..+.+.+ ++. ....|+|||++|.+-+.|++-|||+|.|..
T Consensus 69 d~Vk-AIgr----GF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g---- 139 (194)
T COG1094 69 DVVK-AIGR----GFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG---- 139 (194)
T ss_pred HHHH-HHhc----CCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC----
Confidence 2111 1111 1000000 00000112211 111 124699999999999999999999999954
Q ss_pred CCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293 171 AAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (609)
Q Consensus 171 ~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (609)
..|.|-|.+++|+.|...|..++...
T Consensus 140 -----~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 140 -----KTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred -----cEEEEecChhhhHHHHHHHHHHHcCC
Confidence 57999999999999999999999764
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.50 E-value=1.1e-06 Score=84.38 Aligned_cols=142 Identities=18% Similarity=0.223 Sum_probs=98.9
Q ss_pred eEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccc
Q 007293 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQ 353 (609)
Q Consensus 274 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~ 353 (609)
....+.||.+.++.+||+.|+..+.|.+.+++++.++. .+..|+|..++...++. ..+.|...+. .+.
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~-~~~ka~d~Vk------AIg 75 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPL-ALLKARDVVK------AIG 75 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChH-HHHHHHHHHH------HHh
Confidence 35668899999999999999999999999999999983 34678887763222221 1222221111 112
Q ss_pred cCCCCCC----CCCCceEEEE-E----e------ccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEE
Q 007293 354 QGFSSGE----NKGDAVAVSI-L----V------GADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVI 418 (609)
Q Consensus 354 ~g~~~g~----~~~~~~t~~l-~----V------P~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V 418 (609)
.|+++.- -.. .....+ . + =....|+|||++|.+-+-|++.|||.|.|.. .+|
T Consensus 76 rGF~pe~A~~LL~d-~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tV 142 (194)
T COG1094 76 RGFPPEKALKLLED-DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTV 142 (194)
T ss_pred cCCCHHHHHHHhcC-CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEE
Confidence 2332200 000 111111 1 1 1236799999999999999999999999963 679
Q ss_pred EEcCCHHHHHHHHHHHHHHhhh
Q 007293 419 QISGEYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 419 ~I~G~~~~V~~A~~~I~~~Lr~ 440 (609)
.|-|.+++|+.|++.|..+++.
T Consensus 143 aiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcC
Confidence 9999999999999999998875
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=74.40 Aligned_cols=67 Identities=19% Similarity=0.362 Sum_probs=53.1
Q ss_pred ccccccccCCCchhHHHHHhhCCeEEecCCCcc-----------ccc-CCCCCcEEEEcCCH---HHHHHHHHHHHHHhh
Q 007293 375 DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV-----------LGC-AAQNDVVIQISGEY---KNVQNALSEVVGRLR 439 (609)
Q Consensus 375 ~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~-----------P~~-~~~~er~V~I~G~~---~~V~~A~~~I~~~Lr 439 (609)
+++|.|||++|++||+|+++|||+|.|...... |.+ ...+.-.|.|++.. +++++|+.+|...|.
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 689999999999999999999999999875211 111 12334679999975 899999999999888
Q ss_pred hc
Q 007293 440 HN 441 (609)
Q Consensus 440 ~~ 441 (609)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 43
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=98.00 E-value=1.1e-05 Score=72.98 Aligned_cols=64 Identities=23% Similarity=0.311 Sum_probs=51.7
Q ss_pred ceeeeeeecCcchhhhcccccCcEEEecCCC-CC--------------CCCCCceEEEecc---HHHHHHHHHHHHHHHh
Q 007293 138 TKIGVVVGKGGRNVTRMRIESGAKIVMLPPP-AC--------------AAIDDQLIQITGA---TLAVKKALVAVTTCLQ 199 (609)
Q Consensus 138 ~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p-~~--------------~~~~dR~V~I~G~---~e~V~~A~~~I~~~L~ 199 (609)
+.+|.|||++|++||+|+++|||+|.|..+. .. .....-.|.|++. .+++.+|+.+|..++.
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 5789999999999999999999999998750 00 0122357889996 4999999999999997
Q ss_pred cc
Q 007293 200 HL 201 (609)
Q Consensus 200 e~ 201 (609)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 53
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.94 E-value=9.8e-06 Score=82.15 Aligned_cols=150 Identities=18% Similarity=0.254 Sum_probs=105.2
Q ss_pred cceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHh---hhh
Q 007293 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA---RSV 348 (609)
Q Consensus 272 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~---~i~ 348 (609)
+.++..+.||..+++.|.|++|.+||.|+.+|...|+-+.. ..+-++.++|.. .-+..|...+.. .+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~------edv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRH------EDVRRARREIPSAAEHFG 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCc------hhHHHHhhcCccccceee
Confidence 56677888999999999999999999999999999876632 223578888873 112222211111 110
Q ss_pred hcccccCCC---CCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHH
Q 007293 349 EVEGQQGFS---SGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425 (609)
Q Consensus 349 e~~~~~g~~---~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~ 425 (609)
--...+.+. .+.....+.+..+.+|...+|.|.|..|.+|+.||+.+...|.-+-+ ..+.++-++|.+.
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 12223567888999999999999999999999999999999987653 3478899999999
Q ss_pred H-HHHHH-HHHHHHh
Q 007293 426 N-VQNAL-SEVVGRL 438 (609)
Q Consensus 426 ~-V~~A~-~~I~~~L 438 (609)
+ +++|. ..|+..+
T Consensus 167 nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 167 NCVKRARSCEIEQTA 181 (394)
T ss_pred chhhhccccchhhhh
Confidence 8 77776 5555443
No 38
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.81 E-value=2.9e-05 Score=72.17 Aligned_cols=103 Identities=14% Similarity=0.158 Sum_probs=69.0
Q ss_pred EEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHH
Q 007293 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAV 105 (609)
Q Consensus 26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al 105 (609)
.+.++|+...+|+.||++|++|+.|++..|-+|+|-.... . +.+-+
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~-----------d-----------------------~~~fI 78 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD-----------D-----------------------PEEFI 78 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC-----------C-----------------------HHHHH
Confidence 4567889999999999999999999999998888743211 1 11111
Q ss_pred HHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEec
Q 007293 106 IRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165 (609)
Q Consensus 106 ~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~ 165 (609)
..++....-..... ........+.+.|+....|..|||+|++|+.++.-+|-++.|.
T Consensus 79 ~n~l~Pa~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 79 KNIFAPAAVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred HHHcCCCEEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 11111100000000 0011235667789999999999999999999999998877663
No 39
>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=97.67 E-value=0.00016 Score=82.93 Aligned_cols=93 Identities=13% Similarity=0.195 Sum_probs=72.1
Q ss_pred ChHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCC
Q 007293 334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ 413 (609)
Q Consensus 334 ~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~ 413 (609)
..+.++...|++.+.+..... ...........++.||.+++|.|||+||.+||+|+++|||+|.|.+
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 345566677777665542222 1122345678899999999999999999999999999999999954
Q ss_pred CCcEEEEcCC-HHHHHHHHHHHHHHhhh
Q 007293 414 NDVVIQISGE-YKNVQNALSEVVGRLRH 440 (609)
Q Consensus 414 ~er~V~I~G~-~~~V~~A~~~I~~~Lr~ 440 (609)
+..|.|.+. .+++++|+.+|...++.
T Consensus 616 -~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 -DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred -CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 577888884 78999999999998885
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=97.48 E-value=0.00029 Score=80.85 Aligned_cols=94 Identities=18% Similarity=0.232 Sum_probs=72.5
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCce
Q 007293 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (609)
Q Consensus 98 ~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~ 177 (609)
+..|.++..+++..+.+..... .......+....+-||.+.++.|||+||++||+|.++|||+|.|.. +..
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------~G~ 618 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--------DGT 618 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--------CcE
Confidence 3456666667766555443333 2222333667788899999999999999999999999999999954 477
Q ss_pred EEEecc-HHHHHHHHHHHHHHHhc
Q 007293 178 IQITGA-TLAVKKALVAVTTCLQH 200 (609)
Q Consensus 178 V~I~G~-~e~V~~A~~~I~~~L~e 200 (609)
|.|.+. .+++.+|+.+|..++..
T Consensus 619 V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 619 VYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred EEEEeCCHHHHHHHHHHHHHhhCc
Confidence 888885 99999999999999974
No 41
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.43 E-value=0.00035 Score=71.14 Aligned_cols=155 Identities=19% Similarity=0.197 Sum_probs=107.8
Q ss_pred CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (609)
Q Consensus 23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~ 102 (609)
+.++..+-||..+++.|.|++|-+||.|+.+|.+.|+-+-.. .|=+..++|..+.+++|..++.-. |
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~sa---------a- 90 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPSA---------A- 90 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCccc---------c-
Confidence 888999999999999999999999999999999999864321 235777899998887765544221 1
Q ss_pred HHHHHHHHHHhhhhhccCC-CCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEe
Q 007293 103 EAVIRVFERMWEVEAEVEG-DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQIT 181 (609)
Q Consensus 103 ~Al~~v~~~i~~~~~~~~~-~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~ 181 (609)
+ ++-..+.......+- ........+...-+|-..+|++.|..|.+|+.|++.++..|.-.-. | .+.+..++
T Consensus 91 e---H~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--~---~~~Vf~Vt 162 (394)
T KOG2113|consen 91 E---HFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--C---GEPVFCVT 162 (394)
T ss_pred c---eeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--C---CCceEEEe
Confidence 0 000000000000000 0112345667777899999999999999999999999999887652 3 66788899
Q ss_pred ccHHH-HHHHH-HHHHHHH
Q 007293 182 GATLA-VKKAL-VAVTTCL 198 (609)
Q Consensus 182 G~~e~-V~~A~-~~I~~~L 198 (609)
|-+.+ +++|- ..|..-+
T Consensus 163 g~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 163 GAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred cCCcchhhhccccchhhhh
Confidence 98877 55555 4444433
No 42
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.41 E-value=0.00044 Score=64.31 Aligned_cols=102 Identities=16% Similarity=0.163 Sum_probs=71.2
Q ss_pred eEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhh--hhcc
Q 007293 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS--VEVE 351 (609)
Q Consensus 274 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i--~e~~ 351 (609)
..+.++|+...+|..||++|++|+.|++..|-+|.+-....+ ..+-+..++... .+..
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 111121111111 0000
Q ss_pred cccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEec
Q 007293 352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (609)
Q Consensus 352 ~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~ 402 (609)
.. .........+.|+.+..|..|||+|++|+.++.-+|-++.|.
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 012235677889999999999999999999999999998774
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=97.25 E-value=0.00047 Score=64.05 Aligned_cols=102 Identities=14% Similarity=0.159 Sum_probs=68.0
Q ss_pred EEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcch-hhhhhhccccccccCCCcchHHHH
Q 007293 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQEA 104 (609)
Q Consensus 26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~-~~~~~~~~~~~~~e~~~~~~A~~A 104 (609)
-+-++|....+|..||++|++|+.|++..|-+|+|-.. +.+.+. +.+ .++||.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~~fI~N-------------~l~PA~-- 87 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLEEFVAN-------------KLAPAE-- 87 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHHHHHHH-------------cCCCce--
Confidence 44567888899999999999999999888988887432 111111 000 011110
Q ss_pred HHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEec
Q 007293 105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165 (609)
Q Consensus 105 l~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~ 165 (609)
+..... ...++...+.+.|+..+.+..|||+|.+|+..++-+|-++.|.
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 0011245677889999999999999999999999988877663
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=97.13 E-value=0.0011 Score=77.03 Aligned_cols=92 Identities=14% Similarity=0.228 Sum_probs=66.2
Q ss_pred HHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCC
Q 007293 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND 415 (609)
Q Consensus 336 a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~e 415 (609)
+.++...|++.+.+........ .........++.||.++++.|||+||++||+|+++|||+|.|.+ +
T Consensus 523 a~~~~~~I~~~m~~~l~~~~~~--~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------d 589 (684)
T TIGR03591 523 AKEGRLHILGEMNKVISEPRAE--LSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------D 589 (684)
T ss_pred HHHHHHHHHHHHHHHHhhhhcc--ccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------C
Confidence 4455555665554432111110 12234578899999999999999999999999999999999954 4
Q ss_pred cEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293 416 VVIQISG-EYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 416 r~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (609)
-.|.|.+ ..+.+++|+++|.....+
T Consensus 590 G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 590 GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 5577766 467899999999987654
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.11 E-value=0.0016 Score=70.41 Aligned_cols=73 Identities=19% Similarity=0.259 Sum_probs=58.6
Q ss_pred ceEEEEEeec------ceeeeeeecCcchhhhcccccCcEEEecCC----C--------C--CCCCCCceEEEecc-HHH
Q 007293 128 VAYCGLLANT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPP----P--------A--CAAIDDQLIQITGA-TLA 186 (609)
Q Consensus 128 ~vt~rllVP~------~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~----p--------~--~~~~~dR~V~I~G~-~e~ 186 (609)
.++.++.||- +.||+|||..|.|.|+|+++|||||.|..+ + . .....+=.|.|+++ .++
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 6777888886 579999999999999999999999999873 0 0 11123345778886 899
Q ss_pred HHHHHHHHHHHHhc
Q 007293 187 VKKALVAVTTCLQH 200 (609)
Q Consensus 187 V~~A~~~I~~~L~e 200 (609)
|.+|+..|..+|.+
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=97.05 E-value=0.00097 Score=77.49 Aligned_cols=94 Identities=21% Similarity=0.262 Sum_probs=68.8
Q ss_pred chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceE
Q 007293 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI 178 (609)
Q Consensus 99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V 178 (609)
..|.++..+++..+.+...+.......-.+....+-||.+.++.|||+||++||+|+++|||+|.|.. +..|
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 34555555666554443333222222333667788999999999999999999999999999999954 4567
Q ss_pred EEec-cHHHHHHHHHHHHHHHhc
Q 007293 179 QITG-ATLAVKKALVAVTTCLQH 200 (609)
Q Consensus 179 ~I~G-~~e~V~~A~~~I~~~L~e 200 (609)
.|.+ ..+.+.+|+.+|..+..+
T Consensus 593 ~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 593 KIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred EEEECcHHHHHHHHHHHHhhhcc
Confidence 7776 589999999999888653
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=96.93 E-value=0.0025 Score=59.28 Aligned_cols=101 Identities=14% Similarity=0.124 Sum_probs=69.9
Q ss_pred EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHH--hhhhhccc
Q 007293 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEG 352 (609)
Q Consensus 275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~--~~i~e~~~ 352 (609)
.+-++|....+|..||++|.+|+.|++..|-+|.+-....+.. +-+..++ .++.....
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 5667889999999999999999999988888887754211100 0111100 01110000
Q ss_pred ccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEec
Q 007293 353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (609)
Q Consensus 353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~ 402 (609)
. ..++.....+.||.+..+..|||+|++|+...+-+|-++.|.
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 012335788999999999999999999999999999998774
No 48
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.77 E-value=0.007 Score=65.50 Aligned_cols=77 Identities=17% Similarity=0.326 Sum_probs=58.6
Q ss_pred ceEEEEEecc------ccccccccCCCchhHHHHHhhCCeEEecCCC---------ccccc--CCCCCcEEEEcCC-HHH
Q 007293 365 AVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE---------QVLGC--AAQNDVVIQISGE-YKN 426 (609)
Q Consensus 365 ~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~---------~~P~~--~~~~er~V~I~G~-~~~ 426 (609)
..+.+|.||- +++|.|||..|.|.|+|+++|||+|.|-.+. +.+.+ ..+++--+.|+.+ .|.
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 5677888875 6899999999999999999999999997621 10111 1334455777776 568
Q ss_pred HHHHHHHHHHHhhhc
Q 007293 427 VQNALSEVVGRLRHN 441 (609)
Q Consensus 427 V~~A~~~I~~~Lr~~ 441 (609)
|++|..+|..+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999988863
No 49
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.66 E-value=0.0033 Score=61.35 Aligned_cols=102 Identities=19% Similarity=0.247 Sum_probs=67.4
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHH
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVI 106 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~ 106 (609)
+-..+-.+.+|..||++|++|+.|.++.|-+|+|-...++ +.. -..+|+.
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------~~~-------------------fI~nal~ 127 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------PAE-------------------FIKNALA 127 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------HHH-------------------HHHHhcC
Confidence 3344455778999999999999999999977776332111 110 0111111
Q ss_pred HHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecC
Q 007293 107 RVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (609)
Q Consensus 107 ~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~ 166 (609)
- .++...... ..+.. .+.+.||..+.+..|||+|.+++.+.+-||-++.|..
T Consensus 128 P--a~v~~V~~~-----~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 128 P--AEVLSVNIK-----EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred c--ceEeEEEEE-----eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0 000000000 00112 7788999999999999999999999999999999965
No 50
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.62 E-value=0.0023 Score=64.47 Aligned_cols=43 Identities=19% Similarity=0.434 Sum_probs=37.9
Q ss_pred CCCCCcEEEEEEecCC------cccceecCCChHHHHHHHHhCceEEEc
Q 007293 19 NLPDDVVSFRLVCPTP------VVGGLIGRSGSIISSIRRDTKCRIHCE 61 (609)
Q Consensus 19 ~~~~~~v~~RilvP~~------~vG~IIGk~G~~Ik~IreeTga~I~V~ 61 (609)
...+-.++.||+||.+ +||+|+|.+|.++|+|+++|+|+|-|.
T Consensus 86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 3445567889999997 799999999999999999999999984
No 51
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.54 E-value=0.0045 Score=72.85 Aligned_cols=93 Identities=14% Similarity=0.178 Sum_probs=68.1
Q ss_pred hHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCe-EEecCCCcccccCCC
Q 007293 335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTD-IKLVGGEQVLGCAAQ 413 (609)
Q Consensus 335 ~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~-I~I~~~~~~P~~~~~ 413 (609)
.+.++...|++.+.+..... .. ...........+.||.++++.|||.||.+||+|.++||+. |.+.+
T Consensus 656 ~A~~g~~~Il~~M~~~i~~p-r~-~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------- 723 (891)
T PLN00207 656 QAKDGRKHILAEMSKCSPPP-SK-RLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------- 723 (891)
T ss_pred HHHHHHHHHHHHHHHHHhhh-hh-hhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC----------
Confidence 34455566666665432111 00 1123456788999999999999999999999999999999 87743
Q ss_pred CCcEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293 414 NDVVIQISG-EYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 414 ~er~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (609)
+-.|.|.+ +.+.+++|+.+|.....+
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 56688888 577899999999988764
No 52
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.47 E-value=0.0063 Score=68.78 Aligned_cols=98 Identities=13% Similarity=0.159 Sum_probs=72.6
Q ss_pred ChHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCC
Q 007293 334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ 413 (609)
Q Consensus 334 ~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~ 413 (609)
.++..|.++|+..+.+....+ . ........-..++.|+.+.++-+||++|.+||+|.++|||+|.|..
T Consensus 522 ~QAk~aRlhIL~~M~~ai~~p-r-~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied---------- 589 (692)
T COG1185 522 EQAKGARLHILIVMNEAISEP-R-KELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED---------- 589 (692)
T ss_pred HHHHHHHHHHHHHHHHHHhhh-h-hhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC----------
Confidence 344566666766665431110 0 0011234467888999999999999999999999999999999952
Q ss_pred CCcEEEEcCCH-HHHHHHHHHHHHHhhhcccC
Q 007293 414 NDVVIQISGEY-KNVQNALSEVVGRLRHNLKS 444 (609)
Q Consensus 414 ~er~V~I~G~~-~~V~~A~~~I~~~Lr~~~~~ 444 (609)
+-+|.|.++. +.+++|+..|.++.++.-+.
T Consensus 590 -dGtv~i~~s~~~~~~~ak~~I~~i~~e~evg 620 (692)
T COG1185 590 -DGTVKIAASDGESAKKAKERIEAITREVEVG 620 (692)
T ss_pred -CCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence 4668999987 68999999999999876544
No 53
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.46 E-value=0.0032 Score=74.02 Aligned_cols=95 Identities=14% Similarity=0.199 Sum_probs=71.6
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcE-EEecCCCCCCCCCCc
Q 007293 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAK-IVMLPPPACAAIDDQ 176 (609)
Q Consensus 98 ~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~-I~I~~~p~~~~~~dR 176 (609)
+..|.++...++..+.+.....-.......+....+-||.+.++.|||.||.+||.|.++||++ |.+.. +-
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d--------dg 725 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD--------DG 725 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC--------Ce
Confidence 3456666777766655443322111222336678889999999999999999999999999999 88844 46
Q ss_pred eEEEecc-HHHHHHHHHHHHHHHhc
Q 007293 177 LIQITGA-TLAVKKALVAVTTCLQH 200 (609)
Q Consensus 177 ~V~I~G~-~e~V~~A~~~I~~~L~e 200 (609)
.|.|.+. .+++.+|+.+|..++.+
T Consensus 726 ~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 726 TVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 7888884 99999999999999864
No 54
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.31 E-value=0.0094 Score=67.44 Aligned_cols=95 Identities=20% Similarity=0.240 Sum_probs=70.9
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCce
Q 007293 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (609)
Q Consensus 98 ~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~ 177 (609)
+..|..|-++++..+.+...........-.+-...+-|+...+.-+||++|++|++|.++|||+|.|.. +..
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 455666666776665544322211111222445667889999999999999999999999999999953 467
Q ss_pred EEEecc-HHHHHHHHHHHHHHHhc
Q 007293 178 IQITGA-TLAVKKALVAVTTCLQH 200 (609)
Q Consensus 178 V~I~G~-~e~V~~A~~~I~~~L~e 200 (609)
|.|.++ .+.+.+|+..|..+.++
T Consensus 593 v~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 593 VKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred EEEEecchHHHHHHHHHHHHHHhh
Confidence 889887 69999999999999976
No 55
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.28 E-value=0.0041 Score=66.11 Aligned_cols=68 Identities=18% Similarity=0.288 Sum_probs=56.2
Q ss_pred CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhh
Q 007293 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439 (609)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr 439 (609)
.....-|.|-+++||.+||++|+.|+.||..|.++|+|... ..+..|+|.|...--.+|+..|..-++
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence 34566677889999999999999999999999999999874 347889999998877777777755433
No 56
>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=96.21 E-value=0.0071 Score=48.00 Aligned_cols=37 Identities=22% Similarity=0.261 Sum_probs=34.5
Q ss_pred cEEEEEEecCCcccceecCCChHHHHHHHHhCceEEE
Q 007293 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (609)
Q Consensus 24 ~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V 60 (609)
...+.+.|+.+..|.+|||+|.+|+.+++.++.+|.|
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 57
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.09 E-value=0.03 Score=56.63 Aligned_cols=81 Identities=20% Similarity=0.295 Sum_probs=56.4
Q ss_pred CCceEEEEEecc------ccccccccCCCchhHHHHHhhCCeEEecCCCc------------ccccC---CCCCcEEEEc
Q 007293 363 GDAVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ------------VLGCA---AQNDVVIQIS 421 (609)
Q Consensus 363 ~~~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~------------~P~~~---~~~er~V~I~ 421 (609)
....+.+|+||- ++||+|+|..|.++|+++++|||+|-|-.+.- .|.|. ..-.-+|+..
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 456788899886 49999999999999999999999999976533 13322 1223567788
Q ss_pred CCHHHHHHHHHHHHHHhhhccc
Q 007293 422 GEYKNVQNALSEVVGRLRHNLK 443 (609)
Q Consensus 422 G~~~~V~~A~~~I~~~Lr~~~~ 443 (609)
.++..+..=+..-.+.|+++|+
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcC
Confidence 8877666533344444454443
No 58
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.04 E-value=0.0067 Score=64.51 Aligned_cols=72 Identities=18% Similarity=0.284 Sum_probs=58.7
Q ss_pred CCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293 124 DGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH 200 (609)
Q Consensus 124 ~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e 200 (609)
.+.....+-+-+-+++||.+||++|++|++||..|+++|+|.+. ..+-.|+|-|...--.+|...|-..+..
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~-----~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC-----DLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc-----CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 34556777888999999999999999999999999999999872 3567789999877777777666655543
No 59
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.02 E-value=0.011 Score=63.04 Aligned_cols=95 Identities=21% Similarity=0.296 Sum_probs=63.7
Q ss_pred CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (609)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i 112 (609)
+-+|+.||++|+.|+.|.++. |-+|+|-....+..+ .|. ++ ++||. +
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~---fi~-------na-------------l~Pa~---------v 290 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAE---FIA-------NA-------------LSPAK---------V 290 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------Hh-------------cCCce---------E
Confidence 458999999999999999998 778877432111100 000 00 11110 0
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecC
Q 007293 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (609)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~ 166 (609)
....... .....+.+.||..+.+..|||+|.+++....-||.+|.|..
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 01246889999999999999999999999999999999965
No 60
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.00 E-value=0.009 Score=61.92 Aligned_cols=71 Identities=24% Similarity=0.312 Sum_probs=60.3
Q ss_pred ceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (609)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (609)
.....+.|++.+.|.|||++|.+-++|+++|+++|.++++.+ ..+.++.+-++-++|..|.+.|...|-+.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 356788999999999999999999999999999999987432 55677777778899999999998877654
No 61
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.90 E-value=0.013 Score=62.83 Aligned_cols=96 Identities=19% Similarity=0.274 Sum_probs=64.5
Q ss_pred CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (609)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i 112 (609)
+-+|+.||++|+.|+.|.++. |-+|+|-....+..+ .|. ++ ++||. +.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~---fi~-------na-------------l~Pa~-----v~--- 293 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAE---FVA-------NA-------------LSPAK-----VV--- 293 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------Hh-------------CCCce-----EE---
Confidence 468999999999999999998 778887432211100 000 00 11110 00
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (609)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~ 167 (609)
..... + .....+.+.||..+.+..|||+|.+++....-||.+|.|...
T Consensus 294 -~v~i~-----~-~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 294 -SVEVD-----D-EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred -EEEEE-----c-CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 00000 0 113468899999999999999999999999999999999774
No 62
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.87 E-value=0.011 Score=64.31 Aligned_cols=95 Identities=24% Similarity=0.271 Sum_probs=63.4
Q ss_pred CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (609)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i 112 (609)
+-+|+.||++|+.|+.|.++. |-+|+|-....+.. ..|. ++ +++| ++.
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~---~fI~-------Na-------------LsPA-----~V~--- 325 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA---TYIA-------NA-------------LSPA-----RVD--- 325 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH---HHHH-------Hh-------------cCCc-----eee---
Confidence 468999999999999999999 77887743221100 0000 00 1111 000
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecC
Q 007293 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (609)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~ 166 (609)
...... .....+.+.||..+.+..|||+|.+++....-||.+|.|..
T Consensus 326 -~V~i~~------~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 326 -EVRLVD------PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred -EEEEEc------CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 000000 11245789999999999999999999999999999999966
No 63
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.85 E-value=0.0073 Score=62.61 Aligned_cols=71 Identities=18% Similarity=0.266 Sum_probs=58.6
Q ss_pred ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (609)
Q Consensus 128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (609)
....-++|+....|+|||++|.|-++|+++|+++|.+... ....+.++.+.+..++|.+|...|...|.+.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p---~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP---NTNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC---CCCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 3455689999999999999999999999999999999762 1234455555557999999999999999774
No 64
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=95.84 E-value=0.0057 Score=59.67 Aligned_cols=101 Identities=21% Similarity=0.258 Sum_probs=69.0
Q ss_pred EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHh--hhhhccc
Q 007293 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA--RSVEVEG 352 (609)
Q Consensus 275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~--~i~e~~~ 352 (609)
.+-..+-.+.+|..||++|.+|+.|.++.|-+|.|-.-. + .++ +-+..++. ++....+
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~------d~~-~fI~nal~Pa~v~~V~~ 136 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------E------DPA-EFIKNALAPAEVLSVNI 136 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------C------CHH-HHHHHhcCcceEeEEEE
Confidence 344556678889999999999999999999666554321 1 111 11111111 1111000
Q ss_pred ccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecC
Q 007293 353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (609)
Q Consensus 353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~ 403 (609)
. ......+.+.||.+..+..|||+|.+++.+.+-||-+|.|..
T Consensus 137 ~--------~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 137 K--------EDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred E--------eCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0 001127888999999999999999999999999999999975
No 65
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.80 E-value=0.013 Score=62.63 Aligned_cols=95 Identities=16% Similarity=0.255 Sum_probs=64.2
Q ss_pred CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (609)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i 112 (609)
+-+|+.||++|++|+.|.++. |-+|+|-....+..+ .|. ++ ++||. +..+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~---fI~-------Na-------------l~Pa~--V~~V---- 301 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI---FIA-------RA-------------LAPAI--ISSV---- 301 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------Hh-------------CCCce--eeEE----
Confidence 458999999999999999998 778877432111100 000 00 11110 0000
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (609)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~ 167 (609)
. .+ ...-.+.+.||..+.+..|||+|.+++....-||.+|.|..-
T Consensus 302 ---~--i~-----~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 302 ---K--IE-----EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred ---E--Ec-----CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 0 00 113467889999999999999999999999999999999874
No 66
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.60 E-value=0.019 Score=67.11 Aligned_cols=93 Identities=14% Similarity=0.217 Sum_probs=66.3
Q ss_pred hHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCC
Q 007293 335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN 414 (609)
Q Consensus 335 ~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~ 414 (609)
.+.++...|++.+.+..... .. ...........+.||.+.++.+||.||.+||+|.++||+.|.+.+
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-ELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED----------- 591 (693)
T ss_pred HHHHHHHHHHHHHHHHhcCC-hh-hhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-----------
Confidence 34556666777665432111 00 011223456777889999999999999999999999999887632
Q ss_pred CcEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293 415 DVVIQISG-EYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 415 er~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (609)
+-.|.|.+ ..+.+++|+++|.....+
T Consensus 592 ~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 592 DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 46688888 577899999999987754
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=95.58 E-value=0.016 Score=46.01 Aligned_cols=36 Identities=22% Similarity=0.372 Sum_probs=34.0
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHhhCCeEEe
Q 007293 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKL 401 (609)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I 401 (609)
....+.|+.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 688999999999999999999999999999998876
No 68
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.57 E-value=0.033 Score=54.07 Aligned_cols=43 Identities=26% Similarity=0.425 Sum_probs=36.1
Q ss_pred CCCcEEEEEEecC------CcccceecCCChHHHHHHHHhCceEEEcCC
Q 007293 21 PDDVVSFRLVCPT------PVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (609)
Q Consensus 21 ~~~~v~~RilvP~------~~vG~IIGk~G~~Ik~IreeTga~I~V~~~ 63 (609)
-+-.+.-+++||. ++||.|||.+|+|.|+|++.|+|+|-|.-.
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 3445666788886 489999999999999999999999999643
No 69
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.43 E-value=0.013 Score=68.36 Aligned_cols=94 Identities=20% Similarity=0.245 Sum_probs=67.3
Q ss_pred chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceE
Q 007293 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI 178 (609)
Q Consensus 99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V 178 (609)
..|.++..+|++.+.+.....-.+.....+....+-|+.+.++.+||.||.+||+|.++||++|.+.. +-.|
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 35556666676665544322211111222444566679999999999999999999999999888733 4678
Q ss_pred EEecc-HHHHHHHHHHHHHHHhc
Q 007293 179 QITGA-TLAVKKALVAVTTCLQH 200 (609)
Q Consensus 179 ~I~G~-~e~V~~A~~~I~~~L~e 200 (609)
.|.+. .+.+.+|+.+|..+..+
T Consensus 596 ~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 596 KIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred EEEcccHHHHHHHHHHHHHhccc
Confidence 88884 89999999999888854
No 70
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.36 E-value=0.03 Score=56.76 Aligned_cols=64 Identities=19% Similarity=0.180 Sum_probs=54.6
Q ss_pred EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHH-HHHHHHHHHHHHhhhc
Q 007293 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK-NVQNALSEVVGRLRHN 441 (609)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~-~V~~A~~~I~~~Lr~~ 441 (609)
-..+.||.++++.+||++|.+|+.|.+.+++.|.|-. +-.|-|+++.. .+..|+.+|...-++.
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 4678899999999999999999999999999998843 46688888855 8899999998766654
No 71
>PRK00468 hypothetical protein; Provisional
Probab=95.15 E-value=0.022 Score=47.14 Aligned_cols=35 Identities=29% Similarity=0.442 Sum_probs=30.7
Q ss_pred CCCcEEEEEEecCCcccceecCCChHHHHHHHHhC
Q 007293 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (609)
Q Consensus 21 ~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTg 55 (609)
.++.+.+++-|....+|.||||+|.+|+.||.--.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 44668999999999999999999999999987643
No 72
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.01 E-value=0.032 Score=62.01 Aligned_cols=95 Identities=21% Similarity=0.277 Sum_probs=63.3
Q ss_pred CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (609)
Q Consensus 34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i 112 (609)
+-+|+.||++|+.|+.|.++. |-+|.|-...++- ...|. ++ +++| .+
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~---~~fi~-------na-------------l~pa-----~v---- 292 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDP---AQFII-------NA-------------LSPA-----EV---- 292 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH---HHHHH-------Hh-------------CCCC-----EE----
Confidence 358999999999999999998 7788774321110 00000 00 1111 00
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (609)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~ 167 (609)
..... +. ..-.+.+.||..+.+..|||+|.+|+..++-||.+|.|...
T Consensus 293 ~~v~~--~~-----~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 293 SSVVV--DE-----DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEEE--eC-----CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 00000 00 02367899999999999999999999999999999999763
No 73
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=94.83 E-value=0.021 Score=60.84 Aligned_cols=95 Identities=19% Similarity=0.289 Sum_probs=63.2
Q ss_pred cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (609)
Q Consensus 283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~ 361 (609)
+-+|..||++|.+|+.|.++. |-+|.|-....+..+-+ . ...+|+ ++...... .
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~fi--~-------nal~Pa---------~v~~v~i~-------~ 297 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFI--A-------NALSPA---------KVISVEVL-------D 297 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhcCCc---------eEEEEEEE-------c
Confidence 457999999999999999887 76776653221110000 0 000111 11000000 0
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecC
Q 007293 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (609)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~ 403 (609)
.......+.||.++.+..|||+|.+++...+-||.+|.|.+
T Consensus 298 -~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 298 -EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred -CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 12247899999999999999999999999999999999976
No 74
>PRK02821 hypothetical protein; Provisional
Probab=94.53 E-value=0.037 Score=46.01 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=30.8
Q ss_pred CCcEEEEEEecCCcccceecCCChHHHHHHHHhCc
Q 007293 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (609)
Q Consensus 22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga 56 (609)
++.+.+.|-|....+|.||||+|.+|+.||.--.+
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 45588999999999999999999999999987544
No 75
>PRK12704 phosphodiesterase; Provisional
Probab=94.25 E-value=0.11 Score=58.57 Aligned_cols=67 Identities=13% Similarity=0.229 Sum_probs=51.3
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (609)
..+...|.+|+ ++-|+|||+.|.+|+-+...||+.|.|.+ +...|.|+| .|-.-+.|...+...+.+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC----------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 34566778888 89999999999999999999999999953 346688888 555545666555554443
No 76
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=94.23 E-value=0.03 Score=59.97 Aligned_cols=97 Identities=12% Similarity=0.079 Sum_probs=65.3
Q ss_pred cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (609)
Q Consensus 283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~ 361 (609)
+-+|..||++|.+|+.|.++. |-+|.|-.-.++..+-+ . +..+|+ ++..... .
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~fI--~-------Nal~Pa---------~V~~V~i--------~ 304 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIFI--A-------RALAPA---------IISSVKI--------E 304 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhCCCc---------eeeEEEE--------c
Confidence 457999999999999998887 77776653221110000 0 000111 1100000 0
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCc
Q 007293 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (609)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~ 406 (609)
.......+.||.++.+..|||+|.+++.-.+-||.+|.|.+-+.
T Consensus 305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 12247889999999999999999999999999999999988655
No 77
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.17 E-value=0.098 Score=56.24 Aligned_cols=96 Identities=19% Similarity=0.210 Sum_probs=64.0
Q ss_pred cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (609)
Q Consensus 283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~ 361 (609)
+-+|..||++|.+|+.|.++. |-+|.|-...++..+-+ . +..+|+ ++..... .
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~fi--~-------nal~Pa---------~v~~v~i--------~ 298 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEFV--A-------NALSPA---------KVVSVEV--------D 298 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhCCCc---------eEEEEEE--------E
Confidence 457999999999999998888 77776653221110000 0 000111 1100000 0
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCC
Q 007293 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (609)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~ 404 (609)
........+.||.++.+.-|||+|.+++.-.+-||.+|.|.+.
T Consensus 299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0123478899999999999999999999999999999999764
No 78
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.96 E-value=0.14 Score=57.79 Aligned_cols=66 Identities=14% Similarity=0.241 Sum_probs=50.4
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHhh
Q 007293 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLR 439 (609)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~Lr 439 (609)
..+...|.+|+ ++-|+|||+.|.+|+-+...||+.|.|.+ +...|+|+| .|---+.|...|...+.
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 44667788888 89999999999999999999999999953 345677888 55555555555544443
No 79
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.91 E-value=0.12 Score=56.38 Aligned_cols=95 Identities=21% Similarity=0.232 Sum_probs=62.6
Q ss_pred cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (609)
Q Consensus 283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~ 361 (609)
+-+|..||++|.+|+.|.++. |-+|.|-.-.++..+-+ . +.++|+ ++...... .
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~fI--~-------NaLsPA---------~V~~V~i~-------~ 331 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPATYI--A-------NALSPA---------RVDEVRLV-------D 331 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhcCCc---------eeeEEEEE-------c
Confidence 457999999999999999888 76776653211110000 0 000111 11110000 0
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecC
Q 007293 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (609)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~ 403 (609)
.......+.||.++.+.-|||+|.+++.-.+-||.+|.|.+
T Consensus 332 -~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 332 -PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred -CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 12246789999999999999999999999999999999865
No 80
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.78 E-value=0.063 Score=44.42 Aligned_cols=32 Identities=25% Similarity=0.443 Sum_probs=29.1
Q ss_pred CCceEEEEEeecceeeeeeecCcchhhhcccc
Q 007293 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (609)
Q Consensus 126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~e 157 (609)
+..+.++|-+....+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 55788999999999999999999999999854
No 81
>PRK01064 hypothetical protein; Provisional
Probab=93.78 E-value=0.071 Score=44.46 Aligned_cols=34 Identities=26% Similarity=0.527 Sum_probs=30.6
Q ss_pred CCcEEEEEEecCCcccceecCCChHHHHHHHHhC
Q 007293 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (609)
Q Consensus 22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTg 55 (609)
++.+.+++-|.....|.+|||+|.+|+.||.-..
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 5678999999999999999999999999998643
No 82
>PRK00468 hypothetical protein; Provisional
Probab=93.74 E-value=0.067 Score=44.30 Aligned_cols=33 Identities=15% Similarity=0.275 Sum_probs=29.0
Q ss_pred CCceEEEEEeccccccccccCCCchhHHHHHhh
Q 007293 363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVT 395 (609)
Q Consensus 363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~T 395 (609)
+..+..++.|.++-+|+||||+|.+|+.|+.--
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 355788999999999999999999999998654
No 83
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.67 E-value=0.078 Score=43.87 Aligned_cols=33 Identities=27% Similarity=0.458 Sum_probs=29.8
Q ss_pred CCcEEEEEEecCCcccceecCCChHHHHHHHHh
Q 007293 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDT 54 (609)
Q Consensus 22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeT 54 (609)
+..+.++|-+.....|.||||+|.+|+.||---
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 567889999999999999999999999998753
No 84
>PRK00106 hypothetical protein; Provisional
Probab=93.62 E-value=0.18 Score=56.94 Aligned_cols=66 Identities=15% Similarity=0.283 Sum_probs=50.7
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHhh
Q 007293 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLR 439 (609)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~Lr 439 (609)
..+...|.+|+ ++-|+|||+.|.+|+-+...||+.+.|.+ +...|+|+| .|---+.|...+...+.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 44667788898 89999999999999999999999999953 346688888 56555555555544443
No 85
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.52 E-value=1.3 Score=43.82 Aligned_cols=86 Identities=19% Similarity=0.317 Sum_probs=65.1
Q ss_pred HHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc
Q 007293 104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA 183 (609)
Q Consensus 104 Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~ 183 (609)
.+.+|+..+........- +..-.+.+.++....-+|+..+|..++.|....||+|.+.. .+..|.|+|+
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 455666666655433211 11223444456888899999999999999888999999977 5678999999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 007293 184 TLAVKKALVAVTTCLQH 200 (609)
Q Consensus 184 ~e~V~~A~~~I~~~L~e 200 (609)
...+..+...|.+++..
T Consensus 74 k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 74 KSTAEYIEASINEILSN 90 (210)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 99999999999999965
No 86
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.39 E-value=0.12 Score=52.43 Aligned_cols=63 Identities=21% Similarity=0.260 Sum_probs=53.3
Q ss_pred EEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHhcc
Q 007293 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQHL 201 (609)
Q Consensus 131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I~~~L~e~ 201 (609)
+.+-||...++.+||++|.+|+.|.++++++|.|-. +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~--------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ--------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC--------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 347789999999999999999999999999999944 356889887 668888888888777653
No 87
>PRK02821 hypothetical protein; Provisional
Probab=93.35 E-value=0.079 Score=44.06 Aligned_cols=34 Identities=18% Similarity=0.336 Sum_probs=29.6
Q ss_pred CceEEEEEeccccccccccCCCchhHHHHHhhCC
Q 007293 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGT 397 (609)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa 397 (609)
..+..++.|.++-+|+||||+|.+|+.|+.--.|
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 4478999999999999999999999999876544
No 88
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=93.30 E-value=0.29 Score=47.71 Aligned_cols=42 Identities=24% Similarity=0.460 Sum_probs=35.3
Q ss_pred CCceEEEEEec------cccccccccCCCchhHHHHHhhCCeEEecCC
Q 007293 363 GDAVAVSILVG------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (609)
Q Consensus 363 ~~~~t~~l~VP------~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~ 404 (609)
+...+-++.|| .++||.|||..|.+.|++++.|+|+|-|-..
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 44566677776 3799999999999999999999999999653
No 89
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.24 E-value=0.85 Score=45.18 Aligned_cols=128 Identities=15% Similarity=0.104 Sum_probs=85.9
Q ss_pred EEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccC
Q 007293 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG 355 (609)
Q Consensus 276 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g 355 (609)
+.+.++....-.+...+|..++.|....||+|.+... +..+.|+|++ +.+ +.+......+.
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k------~~~-~~i~~~i~~~l------- 88 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTK------STA-EYIEASINEIL------- 88 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccH------HHH-HHHHHHHHHHH-------
Confidence 3445567778889999999999998889999999843 4579999985 222 22222222221
Q ss_pred CCCCCCCCCceEEEEEecccccccccc----CCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEc-----CCHHH
Q 007293 356 FSSGENKGDAVAVSILVGADFVGCLTG----SGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS-----GEYKN 426 (609)
Q Consensus 356 ~~~g~~~~~~~t~~l~VP~~~vG~IIG----kgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~-----G~~~~ 426 (609)
....+.++.++.-.--.-.+ .....+++|++.|++.|+..+. ...+.|+ -....
T Consensus 89 -------~~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~ 151 (210)
T PF14611_consen 89 -------SNIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKR 151 (210)
T ss_pred -------hhcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccch
Confidence 12356677776532221221 1467899999999999998653 2234444 46778
Q ss_pred HHHHHHHHHHHhh
Q 007293 427 VQNALSEVVGRLR 439 (609)
Q Consensus 427 V~~A~~~I~~~Lr 439 (609)
++.|++++...+.
T Consensus 152 ~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 152 ADRAKRLLLWALD 164 (210)
T ss_pred HHHHHHHHHHhcc
Confidence 9999999998875
No 90
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=93.19 E-value=0.17 Score=56.38 Aligned_cols=96 Identities=20% Similarity=0.242 Sum_probs=63.4
Q ss_pred cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (609)
Q Consensus 283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~ 361 (609)
+-+|..||++|.+|+.|.++. |-+|.|-.-.++... + +..|+.- ..+..... .
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 347999999999999999887 767766532111100 0 0000000 00100000 0
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCC
Q 007293 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE 405 (609)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~ 405 (609)
...-...+.||.++.+.-|||+|.+|+...+.||.+|.|....
T Consensus 299 -~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~~ 341 (470)
T PRK09202 299 -EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTEE 341 (470)
T ss_pred -CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEhh
Confidence 1123788999999999999999999999999999999997643
No 91
>PRK01064 hypothetical protein; Provisional
Probab=93.10 E-value=0.1 Score=43.60 Aligned_cols=33 Identities=27% Similarity=0.503 Sum_probs=29.3
Q ss_pred CCCceEEEEEeecceeeeeeecCcchhhhcccc
Q 007293 125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (609)
Q Consensus 125 ~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~e 157 (609)
....+.+++.|.....|.+|||+|.+|+.||.-
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 92
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.03 E-value=0.25 Score=55.72 Aligned_cols=65 Identities=15% Similarity=0.305 Sum_probs=50.0
Q ss_pred eEEEEEeec-ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec-cHHHHHHHHHHHHHHHhc
Q 007293 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQH 200 (609)
Q Consensus 129 vt~rllVP~-~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G-~~e~V~~A~~~I~~~L~e 200 (609)
.+..+-+|+ .+-|.||||.|.+|+.++.-||+.+.|.. +...|.|+| +|---+-|...+..++.+
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 334455666 78999999999999999999999999966 445688888 466556666666666654
No 93
>PRK00106 hypothetical protein; Provisional
Probab=92.86 E-value=0.3 Score=55.10 Aligned_cols=65 Identities=12% Similarity=0.329 Sum_probs=50.7
Q ss_pred eEEEEEeec-ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec-cHHHHHHHHHHHHHHHhc
Q 007293 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQH 200 (609)
Q Consensus 129 vt~rllVP~-~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G-~~e~V~~A~~~I~~~L~e 200 (609)
.+..+-+|+ .+-|.||||.|.+|+.++.-||+.+.|.. +...|.|+| +|---+-|...+..++.+
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 344456666 78999999999999999999999999966 445688998 466666666666666654
No 94
>PRK12704 phosphodiesterase; Provisional
Probab=92.85 E-value=0.25 Score=55.92 Aligned_cols=63 Identities=16% Similarity=0.308 Sum_probs=48.7
Q ss_pred EEEEeec-ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHhc
Q 007293 131 CGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (609)
Q Consensus 131 ~rllVP~-~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I~~~L~e 200 (609)
..+-+|+ .+-|.||||.|.+|+.++.-||+.|.|.. +...|.|+|. +---+.|...+...+.+
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 3345565 89999999999999999999999999966 4567889994 55545666666666654
No 95
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.63 E-value=0.53 Score=52.31 Aligned_cols=93 Identities=17% Similarity=0.230 Sum_probs=68.3
Q ss_pred hHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEE
Q 007293 100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ 179 (609)
Q Consensus 100 ~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~ 179 (609)
.|.+|-..|++.+..+....-.......++...|-|+.+....+||.+|...|+|..|||+.-++ ++..+.
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 44455555555554433332222334457888899999999999999999999999999966665 456677
Q ss_pred Eecc-HHHHHHHHHHHHHHHhcc
Q 007293 180 ITGA-TLAVKKALVAVTTCLQHL 201 (609)
Q Consensus 180 I~G~-~e~V~~A~~~I~~~L~e~ 201 (609)
|--. ..+..+|...|..++...
T Consensus 639 i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 639 IFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred EEecCHHHHHHHHHHHHHHhcCc
Confidence 7664 889999999999998763
No 96
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.40 E-value=0.12 Score=61.11 Aligned_cols=71 Identities=17% Similarity=-0.032 Sum_probs=60.0
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (609)
....+.+|.....+|||++|.+|+.++..|||.|.|.+-.. ....||.+.+.|.++.++.|...|.-.+.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~----~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP----DNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC----ccchhhhcccCCCChhhhhhhccccceeec
Confidence 34567789989999999999999999999999999977322 135689999999999999999988776654
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=90.10 E-value=0.17 Score=41.47 Aligned_cols=35 Identities=17% Similarity=0.273 Sum_probs=29.5
Q ss_pred CCcEEEEEEecCCcccceecCCChHHHHHHHHhCc
Q 007293 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (609)
Q Consensus 22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga 56 (609)
.+...+.+-|.....|.||||+|.+++.||.-.+.
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 45567777889999999999999999999977654
No 98
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=88.83 E-value=0.66 Score=36.48 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=28.0
Q ss_pred cEEEEEEecCCcccceecCCChHHHHHHHHhCceE
Q 007293 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (609)
Q Consensus 24 ~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I 58 (609)
.....+.+.....|.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35555666666789999999999999999998544
No 99
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=88.38 E-value=0.28 Score=47.52 Aligned_cols=54 Identities=28% Similarity=0.417 Sum_probs=48.6
Q ss_pred cccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhh
Q 007293 374 ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439 (609)
Q Consensus 374 ~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr 439 (609)
+..+|+|+||+|.+---|.+.|.++|.+.+ ..|.|-|..++++.|...|+..|-
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhc
Confidence 468999999999999999999999998853 569999999999999999988664
No 100
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=87.89 E-value=1.3 Score=49.25 Aligned_cols=89 Identities=15% Similarity=0.130 Sum_probs=64.3
Q ss_pred HHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcE
Q 007293 338 NAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVV 417 (609)
Q Consensus 338 ~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~ 417 (609)
+|...|.+.+.+....+-.. ..+...+..++.|+.++...+||.+|...|+|..+||+.-.+ ++.+
T Consensus 571 ~ar~~Il~~m~k~i~~Pr~~--~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t 636 (760)
T KOG1067|consen 571 EARLQILDIMEKNINSPRGS--DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGT 636 (760)
T ss_pred HHHHHHHHHHHhhcCCcccC--ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCce
Confidence 44556666665442211111 123567889999999999999999999999999999955444 2456
Q ss_pred EEEcCC-HHHHHHHHHHHHHHhhh
Q 007293 418 IQISGE-YKNVQNALSEVVGRLRH 440 (609)
Q Consensus 418 V~I~G~-~~~V~~A~~~I~~~Lr~ 440 (609)
+.|.-. +...++|++.|.+.+..
T Consensus 637 ~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 637 FSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred EEEEecCHHHHHHHHHHHHHHhcC
Confidence 666654 67889999999998775
No 101
>PRK12705 hypothetical protein; Provisional
Probab=86.49 E-value=0.85 Score=51.23 Aligned_cols=62 Identities=15% Similarity=0.262 Sum_probs=44.3
Q ss_pred EEEeec-ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHhc
Q 007293 132 GLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (609)
Q Consensus 132 rllVP~-~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I~~~L~e 200 (609)
.+-+|+ .+-|.||||.|.+|+.++..||+.+.|... .+.|.|++. +..-+.|...+..++.+
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 344454 789999999999999999999999999763 344666664 44444555555555543
No 102
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=86.40 E-value=0.56 Score=38.22 Aligned_cols=35 Identities=26% Similarity=0.377 Sum_probs=27.5
Q ss_pred EEEEecCCc-----ccceecCCChHHHHHHHHh-CceEEEc
Q 007293 27 FRLVCPTPV-----VGGLIGRSGSIISSIRRDT-KCRIHCE 61 (609)
Q Consensus 27 ~RilvP~~~-----vG~IIGk~G~~Ik~IreeT-ga~I~V~ 61 (609)
..+.|-+.. +|..||++|+.|+.|.++. |-+|+|=
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 345566666 9999999999999999999 8888874
No 103
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=86.21 E-value=0.7 Score=44.87 Aligned_cols=56 Identities=29% Similarity=0.388 Sum_probs=50.3
Q ss_pred cceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293 137 TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (609)
Q Consensus 137 ~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~ 201 (609)
+..+|.|+||+|.+--.|++-|-++|.+. +..|.|-|..++++-|...|+.++-..
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 45689999999999999999999999994 457999999999999999999999764
No 104
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=84.85 E-value=0.46 Score=38.85 Aligned_cols=36 Identities=11% Similarity=0.255 Sum_probs=30.0
Q ss_pred CceEEEEEeccccccccccCCCchhHHHHHhhCCeE
Q 007293 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI 399 (609)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I 399 (609)
......+.+..+..|.||||+|.+++.||.-..+-+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 346788889999999999999999999997665433
No 105
>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=84.21 E-value=1.5 Score=34.45 Aligned_cols=34 Identities=12% Similarity=0.273 Sum_probs=28.4
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHhhCCeE
Q 007293 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI 399 (609)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I 399 (609)
....+.+.....|.+||++|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5666667766789999999999999999998554
No 106
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=84.19 E-value=1 Score=36.66 Aligned_cols=37 Identities=22% Similarity=0.341 Sum_probs=30.1
Q ss_pred EEEEEecccc-----ccccccCCCchhHHHHHhh-CCeEEecC
Q 007293 367 AVSILVGADF-----VGCLTGSGSSAVSEMEDVT-GTDIKLVG 403 (609)
Q Consensus 367 t~~l~VP~~~-----vG~IIGkgG~~Ik~I~~~T-Ga~I~I~~ 403 (609)
...+.|-+.. +|..||++|+.|+.|+++. |-+|+|-.
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 4566666666 9999999999999999999 99999976
No 107
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=84.15 E-value=0.29 Score=58.15 Aligned_cols=69 Identities=17% Similarity=0.114 Sum_probs=59.0
Q ss_pred EEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH 200 (609)
Q Consensus 131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e 200 (609)
.++-+|-....+|||++|++|..++.-|||.|.+.+- ......||.+.+.|.++.++.|-..|.-.+.+
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm-q~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM-QPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhc-CCccchhhhcccCCCChhhhhhhccccceeec
Confidence 4577888889999999999999999999999999873 11225789999999999999999888777765
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=80.72 E-value=0.97 Score=37.33 Aligned_cols=33 Identities=27% Similarity=0.428 Sum_probs=28.3
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhCceEE
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH 59 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~ 59 (609)
..+.+.....|.|||++|++|++|+++.+-.+.
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 457778999999999999999999998876554
No 109
>PRK12705 hypothetical protein; Provisional
Probab=78.81 E-value=2.9 Score=47.10 Aligned_cols=40 Identities=18% Similarity=0.336 Sum_probs=35.0
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHhhCCeEEecC
Q 007293 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (609)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~ 403 (609)
..+...+.+|+ ++-|+|||+.|.+|+-+...||+.|.|.+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 34566777888 89999999999999999999999999965
No 110
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=78.77 E-value=2 Score=35.50 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=26.9
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhCceEEE
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V 60 (609)
+.+-+.....|.+|||+|+++..||--++.-++-
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 3444567889999999999999999988765443
No 111
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=78.41 E-value=3.6 Score=42.08 Aligned_cols=51 Identities=20% Similarity=0.290 Sum_probs=46.3
Q ss_pred cccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293 378 GCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (609)
Q Consensus 378 G~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (609)
-+|||.+|++++.|+-.|.|.|-|+. .+|.+.|....++.+...+.+++..
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 6799999999999999999888775
No 112
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=77.35 E-value=2.4 Score=43.31 Aligned_cols=51 Identities=14% Similarity=0.331 Sum_probs=46.2
Q ss_pred eeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293 141 GVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH 200 (609)
Q Consensus 141 G~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e 200 (609)
-++||.+|+|++.|+--|.|.|-|.. ..|.+.|....+..+...+.+++..
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 46999999999999999999999966 4789999999999999999999865
No 113
>PRK13764 ATPase; Provisional
Probab=77.24 E-value=2.5 Score=48.66 Aligned_cols=45 Identities=16% Similarity=0.209 Sum_probs=40.3
Q ss_pred CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCccc
Q 007293 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVL 408 (609)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P 408 (609)
......+.||.+.++.+|||+|.+|++|.+..|.+|.|...++.+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 345788999999999999999999999999999999998877654
No 114
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=77.19 E-value=2.5 Score=40.43 Aligned_cols=32 Identities=19% Similarity=0.294 Sum_probs=28.0
Q ss_pred EEecCCcccceecCCChHHHHHHHHhCceEEEc
Q 007293 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE 61 (609)
Q Consensus 29 ilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~ 61 (609)
++|-... |.-|||+|++|++|++..|-+|.|=
T Consensus 65 fvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 65 LLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 4555666 9999999999999999999999984
No 115
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=77.13 E-value=2.3 Score=35.23 Aligned_cols=34 Identities=15% Similarity=0.326 Sum_probs=28.0
Q ss_pred EEEEEeccccccccccCCCchhHHHHHhhCCeEE
Q 007293 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIK 400 (609)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~ 400 (609)
...+.|..+..|.+|||.|++++.||--+..-+.
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 4567777888999999999999999987765553
No 116
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=76.86 E-value=3.4 Score=38.48 Aligned_cols=38 Identities=24% Similarity=0.415 Sum_probs=33.5
Q ss_pred EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (609)
Q Consensus 130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~ 167 (609)
+-++.|-...-|++|||+|.++++|..+||-.-.|...
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 34577778889999999999999999999999988775
No 117
>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=76.66 E-value=2.7 Score=35.36 Aligned_cols=35 Identities=11% Similarity=0.217 Sum_probs=30.1
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhCceEEEc
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE 61 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~ 61 (609)
.++.+....-|.|||++|++|++|+++-.-...+.
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 67788889999999999999999999887666553
No 118
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=75.70 E-value=2.1 Score=46.94 Aligned_cols=41 Identities=20% Similarity=0.306 Sum_probs=37.4
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCc
Q 007293 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (609)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~ 406 (609)
....+.||..+++.+|||+|.+|++|.+..|-+|.|...+.
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 46788999999999999999999999999999999987554
No 119
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=75.59 E-value=2 Score=47.19 Aligned_cols=38 Identities=18% Similarity=0.285 Sum_probs=34.2
Q ss_pred EEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCC
Q 007293 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (609)
Q Consensus 26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~ 63 (609)
...+.||...++.+|||+|.+|++|++..|-+|+|...
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 35577899999999999999999999999999999653
No 120
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=75.27 E-value=4.7 Score=40.64 Aligned_cols=57 Identities=19% Similarity=0.298 Sum_probs=43.9
Q ss_pred EEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHH-HHHHHHHHHHH
Q 007293 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLA-VKKALVAVTTC 197 (609)
Q Consensus 133 llVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~-V~~A~~~I~~~ 197 (609)
+.|+...+..+||++|+.++.|.++++|+|.|-.+ ..|=|.|..+. ..-|...|..+
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N--------G~IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN--------GRIWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC--------CEEEecCCCcchHHHHHHHHHHH
Confidence 67899999999999999999999999999999764 34667776553 44444444443
No 121
>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=75.16 E-value=1.4 Score=36.42 Aligned_cols=35 Identities=14% Similarity=0.304 Sum_probs=29.8
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHhhCCeEE
Q 007293 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIK 400 (609)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~ 400 (609)
....+.+-..+-|.|||++|++|++|.+..+-.++
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 45678888999999999999999999888766553
No 122
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=73.49 E-value=13 Score=41.25 Aligned_cols=103 Identities=12% Similarity=0.132 Sum_probs=71.9
Q ss_pred EEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccC
Q 007293 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG 355 (609)
Q Consensus 276 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g 355 (609)
+.+.||...|..|||.||..|++...+.++.|++..... + |. .+ -++
T Consensus 451 ~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~----~-----~q-----------s~---~~d---------- 497 (657)
T COG5166 451 IAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK----F-----GQ-----------SQ---WHD---------- 497 (657)
T ss_pred eEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhh----c-----ch-----------hh---hhc----------
Confidence 447799999999999999999999999999887763210 0 00 00 001
Q ss_pred CCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhh----CCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHH
Q 007293 356 FSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVT----GTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNAL 431 (609)
Q Consensus 356 ~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~T----Ga~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~ 431 (609)
-.-+.-|.+-.+.|+|++......+++.. ...|++.+ ..-++.++-|-..-+.+-.
T Consensus 498 -----------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~---------~~~sI~~v~~~~~~I~rv~ 557 (657)
T COG5166 498 -----------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP---------QSTSIFTVDIYSDEIERVI 557 (657)
T ss_pred -----------ceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC---------CceEEEEEcccccHHHHHh
Confidence 12455688889999999999888888665 55677654 2235888877766555433
No 123
>PRK13764 ATPase; Provisional
Probab=71.19 E-value=3.4 Score=47.52 Aligned_cols=38 Identities=18% Similarity=0.243 Sum_probs=34.0
Q ss_pred EEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCC
Q 007293 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (609)
Q Consensus 26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~ 63 (609)
..-+.||.+.++.+|||+|.+|++|++..|.+|+|...
T Consensus 482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 44577899999999999999999999999999999643
No 124
>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=69.18 E-value=4.3 Score=36.02 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=26.3
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhCce
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~ 57 (609)
++|.+-...-|.|||++|++|++|++.....
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 5677788889999999999999999886543
No 125
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=68.86 E-value=9.6 Score=38.50 Aligned_cols=57 Identities=18% Similarity=0.235 Sum_probs=43.8
Q ss_pred EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHH-HHHHHHHH
Q 007293 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKN-VQNALSEV 434 (609)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~-V~~A~~~I 434 (609)
-.-+.|++..+.++||++|+.++-+.+.|+|+|-|-. +-.|=|.|..+. ...|...|
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~~~e~~~~~aI 204 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENESLEELAIEAI 204 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCcchHHHHHHHH
Confidence 4567899999999999999999999999999998854 344667777663 33343333
No 126
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=68.23 E-value=3.4 Score=39.56 Aligned_cols=35 Identities=23% Similarity=0.406 Sum_probs=30.7
Q ss_pred EEEEeecceeeeeeecCcchhhhcccccCcEEEecC
Q 007293 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (609)
Q Consensus 131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~ 166 (609)
+-++|-... |.-|||+|++|+++++..|-+|.+..
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 446777777 99999999999999999999999865
No 127
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=66.43 E-value=8.1 Score=43.00 Aligned_cols=38 Identities=24% Similarity=0.439 Sum_probs=34.0
Q ss_pred EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (609)
Q Consensus 130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~ 167 (609)
+-.++|-...-|.+|||+|++.++|..++|-.-.|.+.
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 45688888999999999999999999999988888775
No 128
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=65.60 E-value=6.4 Score=33.24 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=24.0
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhC
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTg 55 (609)
.++.+....-|.+||++|.+|++|++.-.
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 55556668999999999999999988753
No 129
>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=62.76 E-value=4.8 Score=33.83 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=28.5
Q ss_pred EEEEEeecceeeeeeecCcchhhhcccccCcEEEe
Q 007293 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVM 164 (609)
Q Consensus 130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I 164 (609)
.+++.|....-|.|||++|++|++|+++-.-...+
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 47788888899999999999999998876544444
No 130
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=60.70 E-value=7.2 Score=39.23 Aligned_cols=31 Identities=26% Similarity=0.402 Sum_probs=26.5
Q ss_pred EEEEEecCCcccceecCCChHHHHHHHHhCc
Q 007293 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (609)
Q Consensus 26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga 56 (609)
-.+|.+....-|.|||++|++|++|+++..-
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k 82 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEK 82 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHH
Confidence 4567888999999999999999999887643
No 131
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=59.80 E-value=12 Score=41.68 Aligned_cols=96 Identities=20% Similarity=0.241 Sum_probs=66.1
Q ss_pred cccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCCCCCce
Q 007293 287 GIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAV 366 (609)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~ 366 (609)
..+=+.|..||+|.++-.-+|.|-.+.. ...+..+|...|.+.+-+...-.. -.-...
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dPs-----------------vl~~~e~A~~~I~eivP~ea~i~~-----i~Fd~~ 99 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDPS-----------------VLKPPEEARKIILEIVPEEAGITD-----IYFDDD 99 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCch-----------------hcCCHHHHHHHHHHhCccccCcee-----EEecCC
Confidence 3445788999999999888887763311 113344677667666532210000 011234
Q ss_pred EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCC
Q 007293 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (609)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~ 404 (609)
+-++.|-++.-|.+|||+|++.++|.++||-.-+|-+.
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 66888999999999999999999999999999888773
No 132
>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=59.28 E-value=9.6 Score=35.57 Aligned_cols=94 Identities=19% Similarity=0.201 Sum_probs=62.2
Q ss_pred ccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhc-ccccCCCCCCCCCCceEE
Q 007293 290 GKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV-EGQQGFSSGENKGDAVAV 368 (609)
Q Consensus 290 Gk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~-~~~~g~~~g~~~~~~~t~ 368 (609)
=.+|..|+.|..+-.-+|.|-.+. ....+-.+|...|.+.+-+. .+.. -.-...+-
T Consensus 22 ~~~~dli~~lAk~lrKRIvvR~dp-----------------s~l~~~e~A~~~I~~ivP~ea~i~d------i~Fd~~tG 78 (145)
T cd02410 22 AEDGDLVKDLAKDLRKRIVIRPDP-----------------SVLKPPEEAIKIILEIVPEEAGITD------IYFDDDTG 78 (145)
T ss_pred hcccHHHHHHHHHHhceEEEcCCh-----------------hhcCCHHHHHHHHHHhCCCccCcee------eEecCCCc
Confidence 356788899988887776664221 01123345666666555322 0000 01133466
Q ss_pred EEEeccccccccccCCCchhHHHHHhhCCeEEecCCCc
Q 007293 369 SILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (609)
Q Consensus 369 ~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~ 406 (609)
++.|-.+.-|.+||++|.++++|...||-.-+|.+.-.
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 88888899999999999999999999999999987433
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=55.21 E-value=13 Score=43.26 Aligned_cols=38 Identities=24% Similarity=0.434 Sum_probs=34.2
Q ss_pred EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (609)
Q Consensus 130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~ 167 (609)
+-.++|-...-|.+|||+|+++++|..+||-.-.|.+.
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 44578888899999999999999999999999999885
No 134
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=50.05 E-value=28 Score=40.61 Aligned_cols=97 Identities=21% Similarity=0.202 Sum_probs=64.6
Q ss_pred ccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCCCCCceE
Q 007293 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVA 367 (609)
Q Consensus 288 IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t 367 (609)
.+=.+|..|++|.++-.-+|.|-.+.. ...+..+|...|.+.+-+...-.. -.-...+
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~~-----------------~~~~~~~~~~~i~~~~~~~~~~~~-----~~f~~~~ 94 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDPS-----------------VLLPPEEAIEKIKEIVPEEAGITD-----IYFDDVT 94 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecChh-----------------hcCCHHHHHHHHHHhCCCcCCcee-----EEecCCC
Confidence 344678899999888877776652210 012234566666555532200000 0123356
Q ss_pred EEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCc
Q 007293 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (609)
Q Consensus 368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~ 406 (609)
-++.|-.+.-|.+|||+|.++++|.++||-.-+|.+...
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 788899999999999999999999999999999987433
No 135
>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=48.23 E-value=11 Score=31.90 Aligned_cols=27 Identities=22% Similarity=0.527 Sum_probs=22.3
Q ss_pred EEEEeecceeeeeeecCcchhhhcccc
Q 007293 131 CGLLANTTKIGVVVGKGGRNVTRMRIE 157 (609)
Q Consensus 131 ~rllVP~~~vG~IIGkgG~~Ik~I~~e 157 (609)
+++.+....-|.+||++|++|++|++.
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 556666688899999999999998865
No 136
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=48.11 E-value=17 Score=40.51 Aligned_cols=130 Identities=11% Similarity=0.046 Sum_probs=77.9
Q ss_pred ccccccccccchhhhhhhccCeeEEEec-CCCCCCccEEE-EcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293 284 TASGIIGKRGAIVRSLQNASGALISFAA-PLTKSGERVVT-ISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (609)
Q Consensus 284 ~vg~IIGk~G~~Ik~I~~~tGa~I~i~~-~~~~s~er~vt-IsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~ 361 (609)
.-..+-||+.-++.+|.+...|.+++.- ...++ +..+ +.|.. ..-+++. +.+ ...+
T Consensus 390 ~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~gs--~~~~~~~g~~------~~F~k~~----~~~-~~EF--------- 447 (657)
T COG5166 390 NEDFLRGKKNGKATRIMKGVSCSELSSIVSSTGS--IVETNGIGEK------MSFSKKL----SIP-PTEF--------- 447 (657)
T ss_pred hHHHhccccCcchhhhhhhcccceeeEEEecCCc--EEEEeccCcc------hhhHHHh----cCC-cccC---------
Confidence 3347788877779999999988865542 11222 3222 23331 1111111 111 1111
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCH---HHHHHHHHHHHHHh
Q 007293 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY---KNVQNALSEVVGRL 438 (609)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~---~~V~~A~~~I~~~L 438 (609)
.-...+.+|...|..|||.||..|.++...-++.|++...-.+|..... .-|.|.-.. .++.-|+.-+.+++
T Consensus 448 ---pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~--dNV~I~~PrKn~~ni~~~KNd~~~~V 522 (657)
T COG5166 448 ---PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWH--DNVLIEAPRKNQDNISGKKNDKLDKV 522 (657)
T ss_pred ---chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhh--cceEEECCccCccchhcccccHHHHH
Confidence 1356788999999999999999999999999999999876666542222 224444332 34444555555656
Q ss_pred hh
Q 007293 439 RH 440 (609)
Q Consensus 439 r~ 440 (609)
.+
T Consensus 523 ~~ 524 (657)
T COG5166 523 KQ 524 (657)
T ss_pred hh
Confidence 53
No 137
>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=47.92 E-value=15 Score=32.58 Aligned_cols=30 Identities=10% Similarity=0.236 Sum_probs=24.4
Q ss_pred EEEEEeccccccccccCCCchhHHHHHhhC
Q 007293 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTG 396 (609)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TG 396 (609)
..++.|-...-|.|||+.|+.|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 356667777789999999999999987654
No 138
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=47.18 E-value=11 Score=38.05 Aligned_cols=30 Identities=27% Similarity=0.479 Sum_probs=25.7
Q ss_pred ceEEEEEeecceeeeeeecCcchhhhcccc
Q 007293 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (609)
Q Consensus 128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~e 157 (609)
+..+++.|....-|.||||+|++|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 446788899999999999999999988754
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=40.61 E-value=25 Score=36.09 Aligned_cols=31 Identities=13% Similarity=0.118 Sum_probs=25.7
Q ss_pred ceEEEEEecc-ccccccccCCCchhHHHHHhh
Q 007293 365 AVAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (609)
Q Consensus 365 ~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (609)
.+...+.|.. ++-+-|||++|+.||+|...+
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 3677888876 678999999999999987655
No 140
>COG1159 Era GTPase [General function prediction only]
Probab=35.57 E-value=33 Score=35.93 Aligned_cols=31 Identities=13% Similarity=0.304 Sum_probs=25.7
Q ss_pred ceEEEEEecc-ccccccccCCCchhHHHHHhh
Q 007293 365 AVAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (609)
Q Consensus 365 ~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (609)
.+...+.|+. ++-|-||||+|++||+|-..+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 4677788887 788999999999999986554
No 141
>PRK15494 era GTPase Era; Provisional
Probab=35.41 E-value=33 Score=36.67 Aligned_cols=30 Identities=17% Similarity=0.333 Sum_probs=25.0
Q ss_pred eEEEEEecc-ccccccccCCCchhHHHHHhh
Q 007293 366 VAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (609)
Q Consensus 366 ~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (609)
+...+.|.. ++-+-|||++|+.||+|....
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 667888877 678899999999999986554
No 142
>PRK00089 era GTPase Era; Reviewed
Probab=35.07 E-value=33 Score=35.44 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=24.8
Q ss_pred eEEEEEecc-ccccccccCCCchhHHHHHhh
Q 007293 366 VAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (609)
Q Consensus 366 ~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (609)
+...+.|.. ++-+-|||++|++||+|...+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 677788876 677899999999999987655
No 143
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=34.70 E-value=37 Score=33.50 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=26.0
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhCc
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga 56 (609)
.+|.+....-|.|||++|..|++|+++-.-
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 667778888999999999999999988654
No 144
>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=34.53 E-value=49 Score=27.45 Aligned_cols=37 Identities=19% Similarity=0.159 Sum_probs=31.6
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHhhhcccCccccCC
Q 007293 414 NDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNE 450 (609)
Q Consensus 414 ~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~~~~~ 450 (609)
..-.+.|+|.-.+|+.|.+.-.+...+.++...+++.
T Consensus 37 Gk~~vii~GdvsaV~~Av~a~~~~~~~~~v~~~vI~~ 73 (76)
T cd07053 37 GKYIIIVSGDVGAVQAAVDAGKEIGGKYVVDSFVLPN 73 (76)
T ss_pred CEEEEEEEEcHHHHHHHHHHHHHHhCCcEEEEEEeCC
Confidence 3457899999999999999999999988888777743
No 145
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=33.87 E-value=37 Score=33.74 Aligned_cols=31 Identities=23% Similarity=0.269 Sum_probs=25.5
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhCce
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~ 57 (609)
.++.+....-|.+||++|++|++|++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 5555566889999999999999999987654
No 146
>PRK15494 era GTPase Era; Provisional
Probab=33.52 E-value=27 Score=37.35 Aligned_cols=29 Identities=10% Similarity=0.284 Sum_probs=22.8
Q ss_pred eEEEEEeec-ceeeeeeecCcchhhhcccc
Q 007293 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIE 157 (609)
Q Consensus 129 vt~rllVP~-~~vG~IIGkgG~~Ik~I~~e 157 (609)
+.+.++|.. ++-+.||||+|+.||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 556677775 57889999999999987643
No 147
>COG1159 Era GTPase [General function prediction only]
Probab=33.22 E-value=32 Score=36.06 Aligned_cols=29 Identities=14% Similarity=0.414 Sum_probs=22.6
Q ss_pred ceEEEEEeec-ceeeeeeecCcchhhhccc
Q 007293 128 VAYCGLLANT-TKIGVVVGKGGRNVTRMRI 156 (609)
Q Consensus 128 ~vt~rllVP~-~~vG~IIGkgG~~Ik~I~~ 156 (609)
.+...++|+. +|-+.||||+|+.||+|-.
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 3455577775 6889999999999998653
No 148
>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=32.68 E-value=49 Score=27.22 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=30.7
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHhhhcccCccccC
Q 007293 414 NDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILN 449 (609)
Q Consensus 414 ~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~~~~ 449 (609)
..-.+.|+|+..+|+.|.+...+.+++.++...+++
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 356799999999999999999999998877666664
No 149
>CHL00048 rps3 ribosomal protein S3
Probab=32.64 E-value=40 Score=33.71 Aligned_cols=31 Identities=19% Similarity=0.159 Sum_probs=25.7
Q ss_pred EEEEEecCCcccceecCCChHHHHHHHHhCc
Q 007293 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (609)
Q Consensus 26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga 56 (609)
..+|.+-....|.|||++|.+|++|++...-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k 97 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQK 97 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHHH
Confidence 3566677788999999999999999988743
No 150
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=32.52 E-value=41 Score=33.82 Aligned_cols=32 Identities=13% Similarity=0.205 Sum_probs=26.6
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhCceE
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I 58 (609)
.+|.+....-|.|||++|..|++|+++..-.+
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 56777788899999999999999998875443
No 151
>PRK03818 putative transporter; Validated
Probab=30.76 E-value=2.8e+02 Score=31.82 Aligned_cols=60 Identities=15% Similarity=0.225 Sum_probs=36.2
Q ss_pred ceEEEEEeecceeeeeeecCcchhhhc--ccccCcEEEecCC--------CCCCCCCCceEEEeccHHHHHHHHHH
Q 007293 128 VAYCGLLANTTKIGVVVGKGGRNVTRM--RIESGAKIVMLPP--------PACAAIDDQLIQITGATLAVKKALVA 193 (609)
Q Consensus 128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I--~~eSGa~I~I~~~--------p~~~~~~dR~V~I~G~~e~V~~A~~~ 193 (609)
....++++|+ ..++|| +++++ +++.|+.|.-..+ +...-..--.+.+.|++++++++...
T Consensus 289 ~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 289 LRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred eEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECHHHHHHHHHH
Confidence 3445566666 356666 68877 4667776554433 11111222357899999999997664
No 152
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=30.34 E-value=55 Score=33.54 Aligned_cols=30 Identities=20% Similarity=0.285 Sum_probs=23.9
Q ss_pred EEEEEEecC-CcccceecCCChHHHHHHHHh
Q 007293 25 VSFRLVCPT-PVVGGLIGRSGSIISSIRRDT 54 (609)
Q Consensus 25 v~~RilvP~-~~vG~IIGk~G~~Ik~IreeT 54 (609)
+...|+|.. ++-+.|||++|+.||+|..+.
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 566688875 567999999999999886654
No 153
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=28.18 E-value=48 Score=35.06 Aligned_cols=33 Identities=15% Similarity=0.216 Sum_probs=27.2
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHhhC
Q 007293 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTG 396 (609)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TG 396 (609)
-.+..++.+|. ++...||||||..|++|-++-+
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 45788889998 6777899999999999976654
No 154
>PRK00089 era GTPase Era; Reviewed
Probab=28.06 E-value=24 Score=36.46 Aligned_cols=29 Identities=21% Similarity=0.525 Sum_probs=22.3
Q ss_pred eEEEEEeec-ceeeeeeecCcchhhhcccc
Q 007293 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIE 157 (609)
Q Consensus 129 vt~rllVP~-~~vG~IIGkgG~~Ik~I~~e 157 (609)
+.+.++|.. ++-+.||||+|++||+|..+
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 455666664 67799999999999987643
No 155
>KOG2008 consensus BTK-associated SH3-domain binding protein SAB [Signal transduction mechanisms]
Probab=25.38 E-value=2e+02 Score=30.25 Aligned_cols=24 Identities=25% Similarity=0.364 Sum_probs=18.8
Q ss_pred cCCHHHHHHHHHHHHHHhhhcccC
Q 007293 421 SGEYKNVQNALSEVVGRLRHNLKS 444 (609)
Q Consensus 421 ~G~~~~V~~A~~~I~~~Lr~~~~~ 444 (609)
.|...--.+++++|.+.|.+.--.
T Consensus 210 K~~Y~~slrnLE~ISd~IHeeRss 233 (426)
T KOG2008|consen 210 KGEYKMSLRNLEMISDEIHEERSS 233 (426)
T ss_pred hccHHHHHHHHHHHHHHHHHhhhh
Confidence 466777788999999999886443
No 156
>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=25.27 E-value=4.1e+02 Score=30.57 Aligned_cols=58 Identities=14% Similarity=0.230 Sum_probs=36.0
Q ss_pred EEEEEeecceeeeeeecCcchhhhcc------cccCcEEEecCC--------CCCCCCCCceEEEeccHHHHHHHHHH
Q 007293 130 YCGLLANTTKIGVVVGKGGRNVTRMR------IESGAKIVMLPP--------PACAAIDDQLIQITGATLAVKKALVA 193 (609)
Q Consensus 130 t~rllVP~~~vG~IIGkgG~~Ik~I~------~eSGa~I~I~~~--------p~~~~~~dR~V~I~G~~e~V~~A~~~ 193 (609)
..++.+|+ ..++|| ++++++ ++.|+.|.-..+ +...-..--.+.+.|++++++++...
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 44566665 445665 788886 267887665543 11111223457899999999987665
No 157
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=25.15 E-value=94 Score=30.89 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=32.7
Q ss_pred EEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCc
Q 007293 28 RLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSG 78 (609)
Q Consensus 28 RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~ 78 (609)
.+-+-++..+.+||+.|+++..||.-++.-++-. .+..-||++=.|..
T Consensus 94 ~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~---~g~~~~v~ldv~~y 141 (208)
T COG1847 94 VVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKI---GGKFKRVTLDVGDY 141 (208)
T ss_pred EEEecCCchhhhhccCCcchHHHHHHHHHHhhhh---cCcceEEEEEhhhH
Confidence 3444566699999999999999999988765542 23334555444443
No 158
>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=24.87 E-value=91 Score=26.33 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=29.8
Q ss_pred CcEEEEcCCHHHHHHHHHHHHHHhhh--cccCccccCC
Q 007293 415 DVVIQISGEYKNVQNALSEVVGRLRH--NLKSGEILNE 450 (609)
Q Consensus 415 er~V~I~G~~~~V~~A~~~I~~~Lr~--~~~~~~~~~~ 450 (609)
.-++.|+|+..+|+.|.+...+..++ .+++..++|.
T Consensus 38 k~~vii~GdvsaV~~Av~a~~~~~~~~~~~v~~~vI~~ 75 (84)
T cd07045 38 LVTVKITGDVAAVKAAVEAGAAAAERIGELVSSHVIPR 75 (84)
T ss_pred EEEEEEEEcHHHHHHHHHHHHHHHhccCcEEEEEEeCC
Confidence 46799999999999999999998887 4677767643
No 159
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=24.37 E-value=1.5e+02 Score=31.82 Aligned_cols=51 Identities=20% Similarity=0.174 Sum_probs=43.9
Q ss_pred ccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007293 373 GADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (609)
Q Consensus 373 P~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~ 435 (609)
+.+..-.|.|..|.+++.|.+..|+.|... .+.++|+|+...|..|...+.
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 367999999878888888877
No 160
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=23.86 E-value=58 Score=34.46 Aligned_cols=54 Identities=24% Similarity=0.326 Sum_probs=34.7
Q ss_pred CCCCCCCCCCCCC-CCCCCCCC---cEEEEEEecCC-cccceecCCChHHHHHHHHhCc
Q 007293 3 HHSNPYGYSSKRR-GPLNLPDD---VVSFRLVCPTP-VVGGLIGRSGSIISSIRRDTKC 56 (609)
Q Consensus 3 ~~~~~~g~~~~~r-~~~~~~~~---~v~~RilvP~~-~vG~IIGk~G~~Ik~IreeTga 56 (609)
|-|++.-|.-+-| ..|...++ .+...++||.. ..-.|||+||..|++|-++.+-
T Consensus 302 ~~pqEVPY~lq~~i~~w~e~~~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~ 360 (379)
T KOG1423|consen 302 HLPQEVPYNLQVRILSWKERPAGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANE 360 (379)
T ss_pred hCccccCcceEEEEEEeeecCCcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHH
Confidence 3344444443333 23333333 56677999975 5667899999999999877653
No 161
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=22.35 E-value=69 Score=31.81 Aligned_cols=70 Identities=11% Similarity=0.217 Sum_probs=43.6
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL 442 (609)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~ 442 (609)
-+..+.+-.+..+.|||+.|.+++.||--+.+...-.. . ....-+|-+-+=-+.=+..+..+..++.+..
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~--g-----~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV 160 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIG--G-----KFKRVTLDVGDYRERRKETLIKLAERAAERV 160 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhc--C-----cceEEEEEhhhHHHHHHHHHHHHHHHHHHHH
Confidence 46677788888999999999999999988877664421 0 1112223333333444445555555555543
No 162
>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=21.68 E-value=1.1e+02 Score=25.48 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=28.2
Q ss_pred CcEEEEcCCHHHHHHHHHHHHHHhh--hcccCccccC
Q 007293 415 DVVIQISGEYKNVQNALSEVVGRLR--HNLKSGEILN 449 (609)
Q Consensus 415 er~V~I~G~~~~V~~A~~~I~~~Lr--~~~~~~~~~~ 449 (609)
.-++.|+|.-.+|+.|.+...+..+ ..++...++|
T Consensus 39 ~~~viv~GdvsaV~~Av~a~~~~~~~~~~~v~~~vI~ 75 (77)
T cd07056 39 WMTVKISGDVAAVNAAIEAGKQTAGASDGYVASTVIA 75 (77)
T ss_pred EEEEEEEeeHHHHHHHHHHHHHHHhccCCEEEEEEeC
Confidence 4568999999999999999998888 5566665653
No 163
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=21.30 E-value=85 Score=31.34 Aligned_cols=29 Identities=34% Similarity=0.542 Sum_probs=24.8
Q ss_pred EEEEecCCcccceecCCChHHHHHHHHhC
Q 007293 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (609)
Q Consensus 27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTg 55 (609)
++|.+....-|.|||++|..|++|++...
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 56777888889999999999999997764
Done!