Query 022746
Match_columns 292
No_of_seqs 211 out of 1761
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 05:50:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022746.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022746hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1676 K-homology type RNA bi 100.0 2.8E-32 6.2E-37 258.1 18.5 217 47-289 136-355 (600)
2 KOG2192 PolyC-binding hnRNP-K 100.0 5.3E-32 1.2E-36 233.7 17.1 248 11-289 15-352 (390)
3 KOG2191 RNA-binding protein NO 100.0 5.3E-31 1.1E-35 233.3 21.0 261 18-290 6-282 (402)
4 KOG2193 IGF-II mRNA-binding pr 100.0 3.8E-29 8.3E-34 227.5 13.2 225 45-287 194-446 (584)
5 KOG1676 K-homology type RNA bi 100.0 2.9E-28 6.4E-33 230.9 18.2 216 48-290 52-268 (600)
6 KOG2190 PolyC-binding proteins 100.0 1.1E-27 2.3E-32 229.3 21.2 257 17-287 14-291 (485)
7 KOG2193 IGF-II mRNA-binding pr 100.0 9.7E-30 2.1E-34 231.4 5.1 231 21-287 254-528 (584)
8 KOG2190 PolyC-binding proteins 99.9 7.8E-22 1.7E-26 189.1 14.8 204 49-290 137-376 (485)
9 KOG2192 PolyC-binding hnRNP-K 99.8 5.2E-19 1.1E-23 153.4 12.3 161 48-220 121-385 (390)
10 KOG2191 RNA-binding protein NO 99.8 5.6E-19 1.2E-23 157.1 12.8 135 139-290 35-171 (402)
11 TIGR03665 arCOG04150 arCOG0415 99.7 2E-16 4.4E-21 133.3 10.7 140 54-221 2-153 (172)
12 PRK13763 putative RNA-processi 99.6 2.3E-15 4.9E-20 127.8 13.1 143 50-220 3-158 (180)
13 cd02396 PCBP_like_KH K homolog 99.4 5.6E-13 1.2E-17 94.4 7.5 64 144-213 1-64 (65)
14 cd02396 PCBP_like_KH K homolog 99.4 3.1E-13 6.6E-18 95.8 5.9 63 51-118 1-64 (65)
15 TIGR03665 arCOG04150 arCOG0415 99.4 4.4E-13 9.6E-18 113.1 6.9 112 147-288 2-125 (172)
16 PRK13763 putative RNA-processi 99.4 1.4E-12 3E-17 110.8 9.1 117 144-290 4-133 (180)
17 KOG2279 Kinase anchor protein 99.3 6.7E-12 1.5E-16 118.9 9.5 217 45-290 63-334 (608)
18 cd02394 vigilin_like_KH K homo 99.3 1.5E-11 3.2E-16 86.1 6.3 60 145-213 2-61 (62)
19 cd02393 PNPase_KH Polynucleoti 99.2 5.3E-11 1.2E-15 83.1 7.9 57 144-213 3-60 (61)
20 PF00013 KH_1: KH domain syndr 99.2 2.3E-11 5E-16 84.6 5.1 60 144-213 1-60 (60)
21 PF00013 KH_1: KH domain syndr 99.2 9.1E-12 2E-16 86.6 2.7 60 51-118 1-60 (60)
22 cd02394 vigilin_like_KH K homo 99.2 1.7E-11 3.7E-16 85.8 4.1 60 52-118 2-61 (62)
23 cd00105 KH-I K homology RNA-bi 99.2 1.5E-10 3.2E-15 81.2 8.0 62 145-213 2-63 (64)
24 cd00105 KH-I K homology RNA-bi 99.2 7.8E-11 1.7E-15 82.6 6.1 62 52-118 2-63 (64)
25 cd02393 PNPase_KH Polynucleoti 99.1 2.1E-10 4.5E-15 80.1 6.4 59 50-118 2-60 (61)
26 PF13014 KH_3: KH domain 99.1 2.2E-10 4.9E-15 74.2 4.8 42 60-101 1-43 (43)
27 PF13014 KH_3: KH domain 99.0 1.2E-09 2.6E-14 70.8 5.4 43 153-201 1-43 (43)
28 COG1094 Predicted RNA-binding 98.9 1.3E-08 2.7E-13 85.9 12.0 149 49-221 7-166 (194)
29 smart00322 KH K homology RNA-b 98.9 1.3E-08 2.8E-13 71.4 9.0 66 143-217 3-68 (69)
30 smart00322 KH K homology RNA-b 98.8 1.6E-08 3.5E-13 70.9 7.3 67 49-122 2-68 (69)
31 KOG2208 Vigilin [Lipid transpo 98.7 3.2E-08 6.9E-13 100.6 8.7 196 50-283 201-451 (753)
32 KOG2208 Vigilin [Lipid transpo 98.6 1E-07 2.2E-12 97.0 6.4 145 47-220 344-489 (753)
33 KOG2113 Predicted RNA binding 98.5 1.3E-07 2.8E-12 84.5 6.2 149 48-214 24-178 (394)
34 KOG2279 Kinase anchor protein 98.5 5.4E-08 1.2E-12 92.8 3.1 110 141-287 66-175 (608)
35 cd02395 SF1_like-KH Splicing f 98.5 4.6E-07 9.9E-12 71.8 7.0 72 53-126 3-97 (120)
36 cd02395 SF1_like-KH Splicing f 98.5 9.1E-07 2E-11 70.1 8.5 69 151-220 14-96 (120)
37 PRK08406 transcription elongat 98.2 2.7E-06 5.9E-11 69.3 5.9 103 50-178 32-134 (140)
38 TIGR02696 pppGpp_PNP guanosine 98.1 1.9E-05 4E-10 79.5 9.8 94 108-219 548-642 (719)
39 PRK08406 transcription elongat 98.1 1.8E-05 4E-10 64.4 7.9 102 144-287 33-134 (140)
40 KOG2113 Predicted RNA binding 98.0 7.5E-06 1.6E-10 73.4 4.4 122 141-282 24-145 (394)
41 COG1094 Predicted RNA-binding 97.9 0.00012 2.6E-09 62.0 9.6 115 144-288 9-138 (194)
42 TIGR03591 polynuc_phos polyrib 97.7 8E-05 1.7E-09 75.6 7.9 95 108-219 520-615 (684)
43 TIGR01952 nusA_arch NusA famil 97.7 0.00017 3.7E-09 58.7 7.8 102 51-178 34-135 (141)
44 TIGR02696 pppGpp_PNP guanosine 97.6 9.3E-05 2E-09 74.5 6.3 66 49-124 577-642 (719)
45 KOG0119 Splicing factor 1/bran 97.6 0.00025 5.4E-09 67.5 8.3 78 142-220 137-231 (554)
46 TIGR01952 nusA_arch NusA famil 97.4 0.00053 1.2E-08 55.8 7.3 102 144-287 34-135 (141)
47 KOG1588 RNA-binding protein Sa 97.4 0.00054 1.2E-08 60.6 7.8 42 45-86 87-134 (259)
48 PLN00207 polyribonucleotide nu 97.4 0.00033 7.1E-09 72.2 6.9 95 108-219 654-750 (891)
49 COG1185 Pnp Polyribonucleotide 97.3 0.0006 1.3E-08 67.6 7.5 107 97-220 507-617 (692)
50 TIGR03591 polynuc_phos polyrib 97.3 0.00027 5.9E-09 71.8 5.3 65 49-123 550-614 (684)
51 KOG0119 Splicing factor 1/bran 97.2 0.00053 1.2E-08 65.3 5.6 73 49-125 137-231 (554)
52 COG0195 NusA Transcription elo 97.2 0.0018 3.9E-08 55.3 7.8 103 51-180 77-179 (190)
53 KOG0336 ATP-dependent RNA heli 97.1 0.00047 1E-08 64.7 3.8 74 44-122 41-114 (629)
54 cd02134 NusA_KH NusA_K homolog 97.1 0.00067 1.4E-08 47.1 3.6 36 50-85 25-60 (61)
55 KOG2814 Transcription coactiva 97.0 0.0007 1.5E-08 61.6 4.2 72 49-126 56-127 (345)
56 KOG1588 RNA-binding protein Sa 96.9 0.0023 5.1E-08 56.6 6.7 81 140-220 89-192 (259)
57 PRK11824 polynucleotide phosph 96.9 0.0017 3.8E-08 66.1 6.2 95 108-219 523-618 (693)
58 TIGR01953 NusA transcription t 96.8 0.0058 1.3E-07 57.0 8.5 95 59-180 243-338 (341)
59 PRK12328 nusA transcription el 96.7 0.006 1.3E-07 57.2 7.6 97 59-183 251-348 (374)
60 KOG2814 Transcription coactiva 96.7 0.003 6.4E-08 57.6 5.2 71 143-221 57-127 (345)
61 KOG0336 ATP-dependent RNA heli 96.6 0.0025 5.5E-08 59.9 4.8 68 142-219 46-113 (629)
62 cd02134 NusA_KH NusA_K homolog 96.6 0.0041 8.9E-08 43.1 4.6 36 143-178 25-60 (61)
63 PRK00468 hypothetical protein; 96.6 0.0023 4.9E-08 46.4 3.1 34 46-79 26-59 (75)
64 PRK12327 nusA transcription el 96.5 0.0095 2.1E-07 56.0 8.0 96 59-181 245-341 (362)
65 COG1185 Pnp Polyribonucleotide 96.5 0.006 1.3E-07 60.8 6.4 65 51-125 553-617 (692)
66 PLN00207 polyribonucleotide nu 96.4 0.0028 6E-08 65.6 4.1 66 49-124 684-750 (891)
67 PRK02821 hypothetical protein; 96.4 0.0032 6.8E-08 45.8 3.1 35 47-81 28-62 (77)
68 PRK12329 nusA transcription el 96.4 0.0096 2.1E-07 56.9 7.0 95 59-180 277-372 (449)
69 COG0195 NusA Transcription elo 96.3 0.0082 1.8E-07 51.3 5.4 100 145-287 78-177 (190)
70 PRK09202 nusA transcription el 96.3 0.013 2.7E-07 57.1 7.2 95 59-181 245-340 (470)
71 COG1837 Predicted RNA-binding 96.2 0.0049 1.1E-07 44.6 3.1 32 47-78 27-58 (76)
72 PRK00468 hypothetical protein; 96.2 0.0065 1.4E-07 44.0 3.6 31 249-280 28-58 (75)
73 PRK04163 exosome complex RNA-b 96.2 0.011 2.4E-07 52.3 5.9 65 144-221 146-211 (235)
74 COG5176 MSL5 Splicing factor ( 96.1 0.014 3E-07 49.9 5.8 39 142-180 147-191 (269)
75 PRK04163 exosome complex RNA-b 96.0 0.011 2.3E-07 52.4 5.1 60 52-121 147-206 (235)
76 PRK01064 hypothetical protein; 96.0 0.008 1.7E-07 43.8 3.3 33 47-79 27-59 (78)
77 PRK02821 hypothetical protein; 95.9 0.0075 1.6E-07 43.9 2.9 33 250-283 30-62 (77)
78 TIGR03319 YmdA_YtgF conserved 95.8 0.029 6.3E-07 55.3 7.4 67 142-220 203-271 (514)
79 COG5176 MSL5 Splicing factor ( 95.7 0.011 2.3E-07 50.7 3.6 41 47-87 145-191 (269)
80 PRK00106 hypothetical protein; 95.7 0.034 7.3E-07 54.9 7.7 67 142-220 224-292 (535)
81 PRK12704 phosphodiesterase; Pr 95.7 0.036 7.8E-07 54.7 7.6 67 142-220 209-277 (520)
82 PRK12327 nusA transcription el 95.5 0.029 6.3E-07 52.8 5.8 94 152-288 245-339 (362)
83 PRK01064 hypothetical protein; 95.4 0.025 5.4E-07 41.3 4.1 31 249-280 28-58 (78)
84 PRK12704 phosphodiesterase; Pr 95.4 0.035 7.6E-07 54.8 6.3 49 50-103 210-259 (520)
85 TIGR01953 NusA transcription t 95.3 0.031 6.7E-07 52.2 5.3 94 152-288 243-337 (341)
86 COG1837 Predicted RNA-binding 95.2 0.026 5.6E-07 40.8 3.6 31 249-280 28-58 (76)
87 TIGR03319 YmdA_YtgF conserved 95.2 0.037 8E-07 54.6 5.8 49 49-102 203-252 (514)
88 PRK00106 hypothetical protein; 95.1 0.042 9.1E-07 54.2 5.9 50 49-103 224-274 (535)
89 PRK11824 polynucleotide phosph 95.1 0.016 3.4E-07 59.3 3.0 63 51-123 555-617 (693)
90 PRK12329 nusA transcription el 95.1 0.043 9.3E-07 52.5 5.6 94 152-288 277-371 (449)
91 PF14611 SLS: Mitochondrial in 95.0 1.2 2.6E-05 38.5 14.3 131 52-221 28-167 (210)
92 PRK09202 nusA transcription el 95.0 0.028 6.1E-07 54.7 4.5 92 153-288 246-338 (470)
93 PRK12328 nusA transcription el 94.8 0.033 7.3E-07 52.3 4.1 93 152-288 251-344 (374)
94 KOG1067 Predicted RNA-binding 94.5 0.12 2.5E-06 50.6 7.1 96 108-221 566-662 (760)
95 PF13083 KH_4: KH domain; PDB: 94.4 0.017 3.8E-07 41.4 1.0 35 47-81 26-60 (73)
96 cd02409 KH-II KH-II (K homolo 94.2 0.076 1.7E-06 36.6 3.9 35 49-83 24-58 (68)
97 PF13184 KH_5: NusA-like KH do 93.8 0.048 1E-06 38.8 2.2 37 52-88 5-47 (69)
98 cd02410 archeal_CPSF_KH The ar 93.8 0.16 3.5E-06 41.3 5.5 85 160-286 23-110 (145)
99 KOG4369 RTK signaling protein 93.3 0.034 7.3E-07 58.3 1.2 72 50-126 1340-1412(2131)
100 PF14611 SLS: Mitochondrial in 93.0 1.1 2.5E-05 38.6 10.2 65 144-220 27-91 (210)
101 PRK12705 hypothetical protein; 92.9 0.26 5.7E-06 48.4 6.6 66 143-220 198-265 (508)
102 cd02414 jag_KH jag_K homology 92.2 0.15 3.4E-06 36.9 3.0 35 51-85 25-59 (77)
103 PF13083 KH_4: KH domain; PDB: 92.0 0.055 1.2E-06 38.7 0.4 31 250-281 28-58 (73)
104 PRK12705 hypothetical protein; 91.3 0.28 6.1E-06 48.2 4.6 46 52-102 200-246 (508)
105 PF07650 KH_2: KH domain syndr 91.2 0.083 1.8E-06 38.2 0.7 35 50-84 25-59 (78)
106 KOG3273 Predicted RNA-binding 90.9 0.16 3.5E-06 43.3 2.2 56 58-125 177-232 (252)
107 PF13184 KH_5: NusA-like KH do 90.6 0.21 4.5E-06 35.5 2.3 37 144-180 4-46 (69)
108 KOG3273 Predicted RNA-binding 89.7 0.2 4.2E-06 42.8 1.8 129 74-221 98-233 (252)
109 COG1097 RRP4 RNA-binding prote 89.6 1.1 2.3E-05 39.6 6.4 45 54-104 150-194 (239)
110 cd02414 jag_KH jag_K homology 89.4 0.45 9.7E-06 34.4 3.3 30 252-282 25-54 (77)
111 cd02413 40S_S3_KH K homology R 89.1 0.41 8.9E-06 35.1 2.9 36 51-86 31-66 (81)
112 COG1097 RRP4 RNA-binding prote 88.9 1 2.3E-05 39.7 5.7 62 145-219 148-210 (239)
113 cd02409 KH-II KH-II (K homolo 88.8 0.62 1.3E-05 31.9 3.6 32 251-283 25-56 (68)
114 PF07650 KH_2: KH domain syndr 88.5 0.2 4.4E-06 36.1 1.0 31 252-283 26-56 (78)
115 PRK06418 transcription elongat 88.2 0.56 1.2E-05 39.2 3.4 38 50-88 61-98 (166)
116 PRK13764 ATPase; Provisional 88.1 0.79 1.7E-05 46.1 5.1 44 142-185 480-523 (602)
117 COG1855 ATPase (PilT family) [ 87.7 0.31 6.8E-06 47.0 1.9 36 52-87 488-523 (604)
118 COG1855 ATPase (PilT family) [ 87.6 0.42 9.2E-06 46.1 2.6 41 142-182 485-525 (604)
119 cd02410 archeal_CPSF_KH The ar 87.3 2.4 5.3E-05 34.5 6.6 93 66-181 22-114 (145)
120 KOG2874 rRNA processing protei 87.0 1.3 2.8E-05 39.8 5.2 52 155-220 161-212 (356)
121 KOG1067 Predicted RNA-binding 86.4 1.6 3.4E-05 43.1 5.8 66 48-124 595-660 (760)
122 PRK13764 ATPase; Provisional 86.4 0.47 1E-05 47.7 2.4 38 50-87 481-518 (602)
123 cd02413 40S_S3_KH K homology R 85.2 1 2.2E-05 33.0 3.1 28 252-280 31-58 (81)
124 cd02412 30S_S3_KH K homology R 84.9 0.76 1.6E-05 35.6 2.5 30 52-81 63-92 (109)
125 KOG2874 rRNA processing protei 84.6 1.7 3.6E-05 39.2 4.7 50 62-123 161-210 (356)
126 COG5166 Uncharacterized conser 84.0 2.6 5.5E-05 41.2 5.9 143 51-280 450-599 (657)
127 cd02411 archeal_30S_S3_KH K ho 83.7 1.1 2.3E-05 33.1 2.7 28 52-79 40-67 (85)
128 COG1782 Predicted metal-depend 83.6 2.5 5.4E-05 41.3 5.7 91 156-285 42-132 (637)
129 KOG4369 RTK signaling protein 83.0 0.39 8.4E-06 50.8 0.1 74 141-220 1338-1411(2131)
130 COG0092 RpsC Ribosomal protein 80.7 1.4 3E-05 38.7 2.7 31 49-79 50-80 (233)
131 TIGR03675 arCOG00543 arCOG0054 80.7 3.2 6.9E-05 42.2 5.6 92 157-287 37-128 (630)
132 PRK06418 transcription elongat 80.4 2.4 5.2E-05 35.5 3.9 36 144-180 62-97 (166)
133 COG1782 Predicted metal-depend 79.6 4.9 0.00011 39.4 6.1 96 63-181 42-137 (637)
134 cd02411 archeal_30S_S3_KH K ho 79.4 2.1 4.5E-05 31.5 2.9 27 253-280 40-66 (85)
135 cd02412 30S_S3_KH K homology R 78.7 1.8 3.8E-05 33.6 2.5 29 252-281 62-90 (109)
136 COG0092 RpsC Ribosomal protein 71.7 3.8 8.3E-05 36.0 3.0 28 252-280 52-79 (233)
137 TIGR03675 arCOG00543 arCOG0054 65.7 18 0.00038 36.9 6.7 96 64-182 37-132 (630)
138 PF08067 ROKNT: ROKNT (NUC014) 63.7 3.1 6.8E-05 26.0 0.6 31 13-48 9-39 (43)
139 TIGR00436 era GTP-binding prot 63.2 9 0.00019 34.3 3.8 32 250-282 220-252 (270)
140 COG1847 Jag Predicted RNA-bind 61.7 24 0.00052 30.6 5.8 29 251-280 91-119 (208)
141 COG1847 Jag Predicted RNA-bind 61.0 6.4 0.00014 34.0 2.2 36 50-85 91-126 (208)
142 TIGR01008 rpsC_E_A ribosomal p 60.1 8.4 0.00018 33.1 2.8 31 51-81 39-69 (195)
143 PRK04191 rps3p 30S ribosomal p 59.8 8.4 0.00018 33.4 2.8 31 52-82 42-72 (207)
144 TIGR00436 era GTP-binding prot 59.3 9.2 0.0002 34.2 3.1 30 50-79 221-251 (270)
145 PRK15494 era GTPase Era; Provi 58.9 11 0.00025 35.0 3.8 32 250-282 272-304 (339)
146 COG5166 Uncharacterized conser 58.7 12 0.00027 36.7 3.9 127 63-220 393-525 (657)
147 CHL00048 rps3 ribosomal protei 58.4 9.1 0.0002 33.4 2.8 31 50-80 66-96 (214)
148 PTZ00084 40S ribosomal protein 57.6 9.2 0.0002 33.5 2.7 32 52-83 46-77 (220)
149 PRK00089 era GTPase Era; Revie 57.5 13 0.00028 33.5 3.8 32 250-282 225-257 (292)
150 COG1159 Era GTPase [General fu 55.2 15 0.00032 33.7 3.6 32 250-282 228-260 (298)
151 PRK15494 era GTPase Era; Provi 53.9 12 0.00027 34.8 3.1 30 50-79 273-303 (339)
152 COG1159 Era GTPase [General fu 53.6 14 0.00029 33.9 3.1 31 49-79 228-259 (298)
153 PRK00089 era GTPase Era; Revie 50.4 15 0.00033 33.1 3.0 30 50-79 226-256 (292)
154 PRK04191 rps3p 30S ribosomal p 50.0 17 0.00036 31.6 3.0 28 253-281 42-69 (207)
155 TIGR01008 rpsC_E_A ribosomal p 48.4 18 0.0004 31.1 3.0 28 252-280 39-66 (195)
156 PTZ00084 40S ribosomal protein 46.7 19 0.0004 31.6 2.8 28 252-280 45-72 (220)
157 CHL00048 rps3 ribosomal protei 46.1 20 0.00044 31.2 3.0 29 252-281 67-95 (214)
158 PF09869 DUF2096: Uncharacteri 44.8 76 0.0016 26.5 5.9 58 140-217 110-167 (169)
159 COG1702 PhoH Phosphate starvat 43.9 62 0.0013 30.4 5.9 55 151-219 23-79 (348)
160 TIGR01009 rpsC_bact ribosomal 42.9 21 0.00046 31.0 2.6 29 52-80 64-92 (211)
161 KOG1423 Ras-like GTPase ERA [C 41.7 23 0.00051 32.8 2.8 32 49-80 327-359 (379)
162 KOG1423 Ras-like GTPase ERA [C 40.7 33 0.0007 31.9 3.5 32 250-282 327-359 (379)
163 PF00472 RF-1: RF-1 domain; I 33.8 1.3E+02 0.0028 23.3 5.5 62 48-125 12-73 (113)
164 PRK09256 hypothetical protein; 33.0 71 0.0015 25.8 4.0 59 66-126 24-99 (138)
165 PRK00310 rpsC 30S ribosomal pr 32.6 37 0.00079 30.0 2.5 29 52-80 64-92 (232)
166 TIGR01009 rpsC_bact ribosomal 32.5 41 0.00089 29.3 2.7 27 253-280 64-90 (211)
167 PF02749 QRPTase_N: Quinolinat 30.2 1.6E+02 0.0035 21.4 5.3 54 161-218 32-85 (88)
168 COG4010 Uncharacterized protei 27.5 2.1E+02 0.0046 23.4 5.7 43 163-218 126-168 (170)
169 PF02044 Bombesin: Bombesin-li 25.1 17 0.00036 17.4 -0.5 12 57-68 2-13 (14)
170 KOG3429 Predicted peptidyl-tRN 23.6 76 0.0016 26.5 2.6 72 49-127 41-128 (172)
171 PRK00310 rpsC 30S ribosomal pr 22.0 75 0.0016 28.1 2.5 29 252-281 63-91 (232)
172 PRK15468 carboxysome structura 20.2 1.6E+02 0.0034 22.8 3.6 27 194-220 74-100 (111)
173 KOG2675 Adenylate cyclase-asso 20.1 87 0.0019 30.3 2.6 12 168-179 415-426 (480)
No 1
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=2.8e-32 Score=258.09 Aligned_cols=217 Identities=20% Similarity=0.274 Sum_probs=173.9
Q ss_pred CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC--CCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (292)
Q Consensus 47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~--~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~ 124 (292)
...++..|+||.+.+|+||||+|++||+|++++||++.+-.+. ..+..+.+.|+|.++ .++.|..+|+++|.+
T Consensus 136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~-----~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPD-----KVEQAKQLVADILRE 210 (600)
T ss_pred ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHH-----HHHHHHHHHHHHHHh
Confidence 4568999999999999999999999999999999999887542 223678899999986 688999999999997
Q ss_pred CCCCCcch-hhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 022746 125 DDDSNSEA-SKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (292)
Q Consensus 125 ~~~~~~~~-~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~ 203 (292)
........ ...+.+.....+.+|.||+..||.||||+|++||+|+.+||++|+|.++ +.|. +.+|.+.|.|+.
T Consensus 211 ~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpD-d~p~-----speR~~~IiG~~ 284 (600)
T KOG1676|consen 211 EDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPD-DDPS-----SPERPAQIIGTV 284 (600)
T ss_pred cccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecC-CCCC-----CccceeeeecCH
Confidence 54432211 1111122344589999999999999999999999999999999998764 4453 789999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746 204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL 283 (292)
Q Consensus 204 ~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~ 283 (292)
+.|.+|.++|.++|........ +++ . .+.......|+|.||+..||.|||| ||+|||.|.+.|||
T Consensus 285 d~ie~Aa~lI~eii~~~~~~~~---------~~~----~-~G~P~~~~~fy~~VPa~KcGLvIGr-GGEtIK~in~qSGA 349 (600)
T KOG1676|consen 285 DQIEHAAELINEIIAEAEAGAG---------GGM----G-GGAPGLVAQFYMKVPADKCGLVIGR-GGETIKQINQQSGA 349 (600)
T ss_pred HHHHHHHHHHHHHHHHHhccCC---------CCc----C-CCCccceeeEEEeccccccccccCC-CccchhhhcccCCc
Confidence 9999999999999988732210 000 0 0111112389999999999999999 99999999999999
Q ss_pred CCcccc
Q 022746 284 GQPLLQ 289 (292)
Q Consensus 284 ~~~~~~ 289 (292)
.++|-+
T Consensus 350 ~~el~r 355 (600)
T KOG1676|consen 350 RCELSR 355 (600)
T ss_pred cccccC
Confidence 998854
No 2
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=5.3e-32 Score=233.69 Aligned_cols=248 Identities=25% Similarity=0.357 Sum_probs=193.5
Q ss_pred CCCCCCCCCCCCCCCCCCccCCCCccCCCCccccCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCC
Q 022746 11 PTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA 90 (292)
Q Consensus 11 ~~~~~~~~~~~~~~~~~kr~~~~~~~e~~~~~~~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~ 90 (292)
+-|..++++.++.+.++||+.+|+. .++.+. ..+.++||+.+..+|+||||+|++||.|+.+++|.|+|++.
T Consensus 15 ~q~~~~~~~~e~g~~~gkrp~~d~~---~qa~k~---~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-- 86 (390)
T KOG2192|consen 15 EQPEETFPNTETGGEFGKRPAEDME---EQAFKR---SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-- 86 (390)
T ss_pred CChhhcCCCCcccccccCCcchhhH---HHHhhh---cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--
Confidence 3456779999999999999999993 333333 34999999999999999999999999999999999999986
Q ss_pred CCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHH
Q 022746 91 RHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRN 170 (292)
Q Consensus 91 ~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~ 170 (292)
++++|+++|+...+ -+.+-+..|.-.+.+... ....+.++++|..+++|.|||++|+.||+|++
T Consensus 87 ~~peri~tisad~~-----ti~~ilk~iip~lee~f~-----------~~~pce~rllihqs~ag~iigrngskikelre 150 (390)
T KOG2192|consen 87 SGPERILTISADIE-----TIGEILKKIIPTLEEGFQ-----------LPSPCELRLLIHQSLAGGIIGRNGSKIKELRE 150 (390)
T ss_pred CCCceeEEEeccHH-----HHHHHHHHHhhhhhhCCC-----------CCCchhhhhhhhhhhccceecccchhHHHHHH
Confidence 57899999999732 344444444444443322 23467899999999999999999999999999
Q ss_pred hhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCC-CCCCCC-----CCCCC-------
Q 022746 171 SSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVI-SISPAY-----NYSAI------- 237 (292)
Q Consensus 171 ~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~-~~~p~~-----n~~~~------- 237 (292)
++.|+++++. .|+. ++++|+|.+.|.+..|..+++.|++.|.+.+.+++. .|.|.+ .|.+.
T Consensus 151 kcsarlkift-----~c~p-~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~ 224 (390)
T KOG2192|consen 151 KCSARLKIFT-----ECCP-HSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDR 224 (390)
T ss_pred hhhhhhhhhh-----ccCC-CCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCC
Confidence 9999999974 2332 489999999999999999999999999999887753 222221 11100
Q ss_pred ------------------------------CCC---------C--------------------------CCCC-------
Q 022746 238 ------------------------------RPA---------Q--------------------------PFVE------- 245 (292)
Q Consensus 238 ------------------------------~~~---------~--------------------------~~~~------- 245 (292)
+++ + .+++
T Consensus 225 pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~ 304 (390)
T KOG2192|consen 225 PGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGY 304 (390)
T ss_pred CCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccc
Confidence 000 0 0000
Q ss_pred -----CCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcccc
Q 022746 246 -----PTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQ 289 (292)
Q Consensus 246 -----~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~ 289 (292)
-.+...+..|.||.++-|.|||| ||+.|++|+..|||.+.|-|
T Consensus 305 GsYGdlGGPitTaQvtip~dlggsiigk-ggqri~~ir~esGA~Ikide 352 (390)
T KOG2192|consen 305 GSYGDLGGPITTAQVTIPKDLGGSIIGK-GGQRIKQIRHESGASIKIDE 352 (390)
T ss_pred cccCCCCCceeeeeEecccccCcceecc-cchhhhhhhhccCceEEecC
Confidence 01124788999999999999999 99999999999999998876
No 3
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.98 E-value=5.3e-31 Score=233.27 Aligned_cols=261 Identities=22% Similarity=0.293 Sum_probs=192.0
Q ss_pred CCCCCCCCCCCccCCCCccCCCCccccCCC-CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEcc---CCCCCC
Q 022746 18 EPEPRHDVSGKRRREDGEIEGSDPKRRAKA-QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD---AIARHE 93 (292)
Q Consensus 18 ~~~~~~~~~~kr~~~~~~~e~~~~~~~~~~-~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~---~~~~~~ 93 (292)
+.+.+.-.|.||+++.-+.-.......... ..+++|||||+..+|.||||+|++|.+||.+|||+|+++. ..|+++
T Consensus 6 ~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTT 85 (402)
T KOG2191|consen 6 PIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTT 85 (402)
T ss_pred cccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCcc
Confidence 344445557888888775211222222222 2499999999999999999999999999999999999994 368999
Q ss_pred ceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhc--ccCCCcccEEEEEeccCcceeeecCCChhHHHHHHh
Q 022746 94 ERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKV--AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (292)
Q Consensus 94 ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~--~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~ 171 (292)
||+|.|+|+ +.++...+..|+++|.+........... +........++++||+..+|.||||+|++||.++++
T Consensus 86 eRvcli~Gt-----~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq 160 (402)
T KOG2191|consen 86 ERVCLIQGT-----VEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160 (402)
T ss_pred ceEEEEecc-----HHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence 999999998 4567777888888888765432211100 011223346899999999999999999999999999
Q ss_pred hCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCC---CCC----CCCCCCCCCCCCCCCC
Q 022746 172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV---ISI----SPAYNYSAIRPAQPFV 244 (292)
Q Consensus 172 tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~---~~~----~p~~n~~~~~~~~~~~ 244 (292)
+||+|+++|.. |..-+ ..+|+|++.|++++..+|+.+|+++|.+++.... .+| .|..|+++. +.+|.
T Consensus 161 sga~iqisPqk--pt~~s--Lqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnPt--Gspya 234 (402)
T KOG2191|consen 161 SGAWIQISPQK--PTGIS--LQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNPT--GSPYA 234 (402)
T ss_pred hCcceEecccC--CCCcc--ceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCCC--CCCCC
Confidence 99999998632 22211 5799999999999999999999999999987653 111 123333322 22222
Q ss_pred CCC---CceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746 245 EPT---SGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL 290 (292)
Q Consensus 245 ~~~---~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~ 290 (292)
... .........++....|..-|. ||.++-.|...+|+.+-+-|.
T Consensus 235 ~~~~~~~astas~~sva~~~iG~a~ga-G~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 235 YQAHVLPASTASTISVAAGLIGGANGA-GGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred CCCccccccchhhcccccccccccccc-ccccceeeecccccceeeccc
Confidence 211 124556677999999999999 999999999999987777664
No 4
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=3.8e-29 Score=227.47 Aligned_cols=225 Identities=24% Similarity=0.385 Sum_probs=183.5
Q ss_pred CCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC-CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746 45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (292)
Q Consensus 45 ~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~ 123 (292)
....++++|+|||..+||.||||.|++||.|...|.|+|+|... ..+..|+.++|-|+++ .+-+|+.+|+++|.
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpE-----g~s~Ac~~ILeimq 268 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPE-----GTSKACKMILEIMQ 268 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCcc-----chHHHHHHHHHHHH
Confidence 34567899999999999999999999999999999999999854 3577899999999987 57899999999998
Q ss_pred cCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 022746 124 KDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (292)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~ 203 (292)
++.....-. ..+.++++..+.+||++|||.|.+||+|.++||++|.|.+-.++... +.+|.+++.|+-
T Consensus 269 kEA~~~k~~--------~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y----npERTItVkGsi 336 (584)
T KOG2193|consen 269 KEAVDDKVA--------EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY----NPERTITVKGSI 336 (584)
T ss_pred Hhhhccchh--------hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc----CccceEEecccH
Confidence 765432111 24468899999999999999999999999999999999876555443 579999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCC------CCCCCCCCCCCCCCCCC---------------CCCC------CCceeEEEEE
Q 022746 204 PAVLNALVEIGNQLRENPPRQV------ISISPAYNYSAIRPAQP---------------FVEP------TSGYSMFLMQ 256 (292)
Q Consensus 204 ~~v~~A~~~I~~~l~~~~~~~~------~~~~p~~n~~~~~~~~~---------------~~~~------~~~~~~~~v~ 256 (292)
++|..|..+|+.+|+++++.+. ..+.|..|++.++++.+ |.++ +.+...++|.
T Consensus 337 Eac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~f 416 (584)
T KOG2193|consen 337 EACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMF 416 (584)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeee
Confidence 9999999999999999987664 23455555544432211 1111 1235778999
Q ss_pred eccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746 257 NTRYFVTAIFAVLSSFNIFFLITTSSLGQPL 287 (292)
Q Consensus 257 iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~ 287 (292)
||+.++|+|||| .|.+||.|.+..||-+-|
T Consensus 417 iP~~~vGAiIGk-kG~hIKql~RfagASiKI 446 (584)
T KOG2193|consen 417 IPAQAVGAIIGK-KGQHIKQLSRFAGASIKI 446 (584)
T ss_pred ccHHHHHHHHhh-cchhHHHHHHhccceeee
Confidence 999999999999 999999999999998765
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.96 E-value=2.9e-28 Score=230.91 Aligned_cols=216 Identities=21% Similarity=0.250 Sum_probs=171.9
Q ss_pred CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD 127 (292)
Q Consensus 48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~ 127 (292)
..++.+..||..+||+||||+|+.|..|+.++||+|++.....+..+|.+.++|.++ .+..|..++-+.+.....
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe-----~v~~aK~li~evv~r~~~ 126 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPE-----NVEVAKQLIGEVVSRGRP 126 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcc-----cHHHHHHhhhhhhhccCC
Confidence 567789999999999999999999999999999999988665566899999999987 577887777777655431
Q ss_pred CCcchhhcc-cCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 022746 128 SNSEASKVA-AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206 (292)
Q Consensus 128 ~~~~~~~~~-~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v 206 (292)
..... +.....++.++.||.+.+|+||||+|++||.|++++||++.+..+..... ..++.+.|+|++++|
T Consensus 127 ----~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~-----~~~KplritGdp~~v 197 (600)
T KOG1676|consen 127 ----PGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT-----GADKPLRITGDPDKV 197 (600)
T ss_pred ----CCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC-----CCCCceeecCCHHHH
Confidence 01111 11134568999999999999999999999999999999999876544332 467899999999999
Q ss_pred HHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCc
Q 022746 207 LNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQP 286 (292)
Q Consensus 207 ~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~ 286 (292)
+.|..++.++|++........ ..-+........+++|.||...||.|||| +|++||.|+-.||++++
T Consensus 198 e~a~~lV~dil~e~~~~~~g~------------~~~~g~~~g~~~~~~V~VPr~~VG~IIGk-gGE~IKklq~etG~KIQ 264 (600)
T KOG1676|consen 198 EQAKQLVADILREEDDEVPGS------------GGHAGVRGGGSATREVKVPRSKVGIIIGK-GGEMIKKLQNETGAKIQ 264 (600)
T ss_pred HHHHHHHHHHHHhcccCCCcc------------ccccCcCccccceeEEeccccceeeEEec-CchHHHHHhhccCceeE
Confidence 999999999999753221100 01111222334589999999999999999 99999999999999999
Q ss_pred cccc
Q 022746 287 LLQL 290 (292)
Q Consensus 287 ~~~~ 290 (292)
++..
T Consensus 265 fkpD 268 (600)
T KOG1676|consen 265 FKPD 268 (600)
T ss_pred eecC
Confidence 8754
No 6
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=1.1e-27 Score=229.28 Aligned_cols=257 Identities=28% Similarity=0.409 Sum_probs=181.1
Q ss_pred CCCCCCCCC-CCCccCCCCccCCCCccccCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCce
Q 022746 17 TEPEPRHDV-SGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEER 95 (292)
Q Consensus 17 ~~~~~~~~~-~~kr~~~~~~~e~~~~~~~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er 95 (292)
..+....+. +.+|+...+. ......+...++||||+...+|.||||+|..|++|+.+|.++|+|.+..+++.+|
T Consensus 14 ~~~~~~~~~~~~~~~~~~~~-----~~~~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eR 88 (485)
T KOG2190|consen 14 STTSNVGDNGSIKRPSLGDP-----VISTGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPER 88 (485)
T ss_pred CCcccccCCCcccccCCCCC-----cccCCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcc
Confidence 444444444 4566666553 1112233445599999999999999999999999999999999999989999999
Q ss_pred EEEEecCCCCcchhHHHHHHHHHHHHHhcC----CCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHh
Q 022746 96 VIIISSKDNDNVVSDAENALQQIAALILKD----DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (292)
Q Consensus 96 vv~I~G~~~~~~v~~v~~A~~~I~~~i~~~----~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~ 171 (292)
+++|+|...+.....+.+|+..+.+++... .....+... ......++++|+||..++|+||||+|+.||+|+++
T Consensus 89 Iiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~--~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~ 166 (485)
T KOG2190|consen 89 IITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEAAEDNGE--DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREE 166 (485)
T ss_pred eEEEecccccccCCchHHHHHHHHHHHhhcccccccccccCCc--cccCCceEEEEEechhheeeeeccCcHHHHHHHHh
Confidence 999999222112333445555555554432 211111110 11112578999999999999999999999999999
Q ss_pred hCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCC------CCCCCC-CCCCCCCC--CCC-
Q 022746 172 SGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQ------VISISP-AYNYSAIR--PAQ- 241 (292)
Q Consensus 172 tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~------~~~~~p-~~n~~~~~--~~~- 241 (292)
|||+|++.+. .+|. +++|.|+|.|.+++|.+|+..|..+|.+..... ...|.| ..-..... .+.
T Consensus 167 TgA~I~v~~~-~lP~-----ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~ 240 (485)
T KOG2190|consen 167 TGAKIRVSSD-MLPN-----STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQT 240 (485)
T ss_pred cCceEEecCC-CCCc-----ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccC
Confidence 9999999764 8888 578999999999999999999999999964221 122223 11000000 000
Q ss_pred -----CCC-CCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746 242 -----PFV-EPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL 287 (292)
Q Consensus 242 -----~~~-~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~ 287 (292)
++. ...+.+..+.+.+|...++.|||+ +|..|+.|+..+++-+.+
T Consensus 241 ~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~-~~~~i~~l~~~~~~~i~v 291 (485)
T KOG2190|consen 241 SPDAHPFGGIVPEEELVFKLICPSDKVGSVIGK-GGLVIRALRNETGASISV 291 (485)
T ss_pred CcccccccccccchhhhhhhcCchhhceeeecC-CCccchhhhhhcCCceEe
Confidence 111 112235667889999999999999 999999999999987654
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=9.7e-30 Score=231.35 Aligned_cols=231 Identities=22% Similarity=0.293 Sum_probs=184.3
Q ss_pred CCCCCCCCccCCCCccCCCCccccCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC---CCCCCceEE
Q 022746 21 PRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVI 97 (292)
Q Consensus 21 ~~~~~~~kr~~~~~~~e~~~~~~~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~ervv 97 (292)
+.-+..+||.+|-+..| +....-..++++|++..+.++|++|||.|.+||+|+++||++|.|+.. .-.++||.|
T Consensus 254 Eg~s~Ac~~ILeimqkE---A~~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTI 330 (584)
T KOG2193|consen 254 EGTSKACKMILEIMQKE---AVDDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTI 330 (584)
T ss_pred cchHHHHHHHHHHHHHh---hhccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceE
Confidence 33445678888877432 233344478999999999999999999999999999999999999853 234579999
Q ss_pred EEecCCCCcchhHHHHHHHHHHHHHhcCCCCCc--------------------------c-hh-----hcc-c-------
Q 022746 98 IISSKDNDNVVSDAENALQQIAALILKDDDSNS--------------------------E-AS-----KVA-A------- 137 (292)
Q Consensus 98 ~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~--------------------------~-~~-----~~~-~------- 137 (292)
++.|+ ++++..|-.+|..++.+...... . ++ .+. +
T Consensus 331 tVkGs-----iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~h 405 (584)
T KOG2193|consen 331 TVKGS-----IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFH 405 (584)
T ss_pred Eeccc-----HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhh
Confidence 99997 66788888889888877432110 0 00 000 0
Q ss_pred CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217 (292)
Q Consensus 138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 217 (292)
.......+++.||...+|.|||++|.+||.|...+||.|+|.+.+ .|+ ..+|.|+|+|++++..+|...|..+|
T Consensus 406 q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE-~pd-----vseRMViItGppeaqfKAQgrifgKi 479 (584)
T KOG2193|consen 406 QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE-IPD-----VSERMVIITGPPEAQFKAQGRIFGKI 479 (584)
T ss_pred cCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC-CCC-----cceeEEEecCChHHHHhhhhhhhhhh
Confidence 023456789999999999999999999999999999999998754 454 67999999999999999999999999
Q ss_pred hcCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746 218 RENPPRQVISISPAYNYSAIRPAQPFVEPT-SGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL 287 (292)
Q Consensus 218 ~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~-~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~ 287 (292)
.+. +|..|+ .-.....+.||...+|+|||| ||.|+++|+..++|.|.+
T Consensus 480 kEe---------------------nf~~PkeevklethirVPs~~aGRvIGK-GGktVnELQnlt~AeV~v 528 (584)
T KOG2193|consen 480 KEE---------------------NFFLPKEEVKLETHIRVPSSAAGRVIGK-GGKTVNELQNLTSAEVVV 528 (584)
T ss_pred hhh---------------------ccCCchhhheeeeeeeccchhhhhhhcc-ccccHHHHhccccceEEc
Confidence 987 222232 236788899999999999999 999999999999999865
No 8
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.87 E-value=7.8e-22 Score=189.06 Aligned_cols=204 Identities=25% Similarity=0.378 Sum_probs=156.8
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC-CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD 127 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~ 127 (292)
++++||+||++++|.||||+|+.||+|+++|||+|++... .|.+.+|.|+|.|.++ ++.+|+..|...|.+...
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~-----av~~al~~Is~~L~~~~~ 211 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPD-----AVKKALVQISSRLLENPP 211 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchH-----HHHHHHHHHHHHHHhcCC
Confidence 7999999999999999999999999999999999999855 7999999999999864 799999999999988431
Q ss_pred CC---cch-----h-hccc-------C-------------CCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEE
Q 022746 128 SN---SEA-----S-KVAA-------G-------------HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (292)
Q Consensus 128 ~~---~~~-----~-~~~~-------~-------------~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i 178 (292)
.. ... + .... + ......+++..|...++.|+|++|..|+.|+.++|+.|.+
T Consensus 212 ~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v 291 (485)
T KOG2190|consen 212 RSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISV 291 (485)
T ss_pred cCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEe
Confidence 10 000 0 0000 0 0123346788999999999999999999999999999998
Q ss_pred eCCCCCCcccCCCCCCcEEEEEcCH--H----HHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeE
Q 022746 179 LAPNQLPLCASAHESDRVVQISGDV--P----AVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSM 252 (292)
Q Consensus 179 ~~~~~~p~~~~~~~~~r~v~I~G~~--~----~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~ 252 (292)
... .+++.|+++... + .-..|+.++...+.+... .+. ...++
T Consensus 292 ~~~----------~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~---------------------~~~-~~~v~ 339 (485)
T KOG2190|consen 292 GDS----------RTDRIVTISARENPEDRYSMAQEALLLVQPRISENAG---------------------DDL-TQTVT 339 (485)
T ss_pred ccc----------cCcceeeeccccCcccccccchhhhhhcccccccccc---------------------ccc-cceee
Confidence 532 234788887753 2 123344444444333311 111 34688
Q ss_pred EEEEeccCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746 253 FLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL 290 (292)
Q Consensus 253 ~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~ 290 (292)
.++.||.+++|+|||| +|.+|.+|++.|||.+.|.+.
T Consensus 340 ~~l~vps~~igciiGk-~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 340 QRLLVPSDLIGCIIGK-GGAKISEIRQRTGASISILNK 376 (485)
T ss_pred eeeccCccccceeecc-cccchHHHHHhcCCceEEccc
Confidence 9999999999999999 999999999999999988764
No 9
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.80 E-value=5.2e-19 Score=153.37 Aligned_cols=161 Identities=27% Similarity=0.444 Sum_probs=131.5
Q ss_pred CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC-CCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (292)
Q Consensus 48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~ 126 (292)
..-.+||||+.+++|.|||++|+.||+|++++.|+++|-.. -|.+++|+|.|.|.++ +|..++..|++++.+..
T Consensus 121 ~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k-----~v~~~i~~il~~i~e~p 195 (390)
T KOG2192|consen 121 SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPK-----RVVECIKIILDLISESP 195 (390)
T ss_pred CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcc-----hHHHHHHHHHHHhhcCC
Confidence 35678999999999999999999999999999999999743 5788999999999876 58899999999987743
Q ss_pred CCCc-------------ch-------------------------------------------------------------
Q 022746 127 DSNS-------------EA------------------------------------------------------------- 132 (292)
Q Consensus 127 ~~~~-------------~~------------------------------------------------------------- 132 (292)
.... |.
T Consensus 196 ikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~sa 275 (390)
T KOG2192|consen 196 IKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSA 275 (390)
T ss_pred cCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCc
Confidence 2100 00
Q ss_pred ------h--hc-------------cc--------CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCC
Q 022746 133 ------S--KV-------------AA--------GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ 183 (292)
Q Consensus 133 ------~--~~-------------~~--------~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~ 183 (292)
. .+ ++ ..-..++.++.||.++-|.||||+|+.|++|++++||.|.+...
T Consensus 276 idtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep-- 353 (390)
T KOG2192|consen 276 IDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP-- 353 (390)
T ss_pred CCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc--
Confidence 0 00 00 01235688999999999999999999999999999999998532
Q ss_pred CCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746 184 LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (292)
Q Consensus 184 ~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 220 (292)
+. ++.+|+++|+|+.++++.|..++...++..
T Consensus 354 le-----GsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 354 LE-----GSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred CC-----CCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 22 378999999999999999999999998865
No 10
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.80 E-value=5.6e-19 Score=157.08 Aligned_cols=135 Identities=22% Similarity=0.255 Sum_probs=111.1
Q ss_pred CCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC-CCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746 139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP-NQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217 (292)
Q Consensus 139 ~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 217 (292)
......++|+||+..+|.||||+|++|.+|+.+|||+|+++.. |.+|. +++|+|.|+|+.+++....+.|.++|
T Consensus 35 e~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG-----TTeRvcli~Gt~eai~av~efI~dKi 109 (402)
T KOG2191|consen 35 EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG-----TTERVCLIQGTVEALNAVHEFIADKI 109 (402)
T ss_pred CCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC-----ccceEEEEeccHHHHHHHHHHHHHHH
Confidence 3455799999999999999999999999999999999999864 45676 89999999999999999999999999
Q ss_pred hcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc-cc
Q 022746 218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL-QL 290 (292)
Q Consensus 218 ~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~-~~ 290 (292)
++.+...... .+. +++.. .+....+++.||+.-+|.|||| ||.+||.|+++|||.|+|- |+
T Consensus 110 re~p~~~~k~----v~~-----~~pqt--~~r~kqikivvPNstag~iigk-ggAtiK~~~Eqsga~iqisPqk 171 (402)
T KOG2191|consen 110 REKPQAVAKP----VDI-----LQPQT--PDRIKQIKIVVPNSTAGMIIGK-GGATIKAIQEQSGAWIQISPQK 171 (402)
T ss_pred HHhHHhhcCC----ccc-----cCCCC--ccccceeEEeccCCcccceecC-CcchHHHHHHhhCcceEecccC
Confidence 9987543210 000 00000 1123458999999999999999 9999999999999999997 64
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=99.68 E-value=2e-16 Score=133.35 Aligned_cols=140 Identities=21% Similarity=0.263 Sum_probs=105.2
Q ss_pred EEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEE---ecCCCCcchhHHHHHHHHHHHHHhcCCCCCc
Q 022746 54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIII---SSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (292)
Q Consensus 54 ilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I---~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~ 130 (292)
|.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.| +++ ..++.+|..+|..+.......
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d-----~~~i~kA~~~I~~i~~gf~~e-- 69 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDED-----PLAVMKAREVVKAIGRGFSPE-- 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCC-----HHHHHHHHHHHHHHHcCCCHH--
Confidence 57899999999999999999999999999999963 256888 333 347889999888876642211
Q ss_pred chhhcccCCCcccEEEEEecc---------CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc
Q 022746 131 EASKVAAGHVAANTIRLLIAG---------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG 201 (292)
Q Consensus 131 ~~~~~~~~~~~~~~~~i~IP~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G 201 (292)
++.... +. .....-+.|+. ..+|+|||++|++++.|++.|||+|.+. +..|.|.|
T Consensus 70 ~A~~l~-gd-~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~--------------~~~v~i~G 133 (172)
T TIGR03665 70 KALKLL-DD-DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY--------------GKTVGIIG 133 (172)
T ss_pred HHHHhc-CC-cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc--------------CCEEEEEC
Confidence 000000 00 00011122332 3689999999999999999999999983 26899999
Q ss_pred CHHHHHHHHHHHHHHHhcCC
Q 022746 202 DVPAVLNALVEIGNQLRENP 221 (292)
Q Consensus 202 ~~~~v~~A~~~I~~~l~~~~ 221 (292)
++++++.|..+|.+++...+
T Consensus 134 ~~~~~~~A~~~i~~li~~~~ 153 (172)
T TIGR03665 134 DPEQVQIAREAIEMLIEGAP 153 (172)
T ss_pred CHHHHHHHHHHHHHHHcCCC
Confidence 99999999999999996663
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.65 E-value=2.3e-15 Score=127.84 Aligned_cols=143 Identities=21% Similarity=0.283 Sum_probs=107.0
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEe---cCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS---SKDNDNVVSDAENALQQIAALILKDD 126 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~---G~~~~~~v~~v~~A~~~I~~~i~~~~ 126 (292)
+...+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|. +.. ..++.+|..+|..+.....
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d----~~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGED----PLAVLKARDIVKAIGRGFS 73 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCC----HHHHHHHHHHHHHHhcCCC
Confidence 467899999999999999999999999999999999964 3567775 222 3578899999988876422
Q ss_pred CCCcchhhcccCCCcccEEEE-Ee----c-----cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcE
Q 022746 127 DSNSEASKVAAGHVAANTIRL-LI----A-----GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV 196 (292)
Q Consensus 127 ~~~~~~~~~~~~~~~~~~~~i-~I----P-----~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~ 196 (292)
.. +..... + .....++ .+ + ...+|+|||++|++++.|++.|||+|.|. +..
T Consensus 74 ~e--~A~~l~-g--d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~--------------~~~ 134 (180)
T PRK13763 74 PE--KALRLL-D--DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY--------------GKT 134 (180)
T ss_pred HH--HHHHHh-C--CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc--------------CCE
Confidence 11 000000 0 0001111 11 1 13689999999999999999999999984 234
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcC
Q 022746 197 VQISGDVPAVLNALVEIGNQLREN 220 (292)
Q Consensus 197 v~I~G~~~~v~~A~~~I~~~l~~~ 220 (292)
|.|.|+++++..|...|..++...
T Consensus 135 v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 135 VAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred EEEEeCHHHHHHHHHHHHHHHcCC
Confidence 889999999999999999999665
No 13
>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=99.42 E-value=5.6e-13 Score=94.42 Aligned_cols=64 Identities=44% Similarity=0.655 Sum_probs=57.1
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I 213 (292)
+++|+||...+|+|||++|.+|++|+++|||+|.+.+... +. ..+|.|+|.|+++++.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~~-----~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-PG-----STERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-CC-----CCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999975432 22 5789999999999999999987
No 14
>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=99.42 E-value=3.1e-13 Score=95.79 Aligned_cols=63 Identities=44% Similarity=0.685 Sum_probs=56.4
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCC-CCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA-RHEERVIIISSKDNDNVVSDAENALQQI 118 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~~~ervv~I~G~~~~~~v~~v~~A~~~I 118 (292)
+++|+||.+.+|+|||++|++|++|+++|||+|++.+... +..+|+|+|+|+. +++.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKP-----SAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCH-----HHHHHHHHhh
Confidence 4799999999999999999999999999999999997643 6789999999985 4788888776
No 15
>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=99.40 E-value=4.4e-13 Score=113.05 Aligned_cols=112 Identities=16% Similarity=0.211 Sum_probs=85.1
Q ss_pred EEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEE---EcCHHHHHHHHHHHHHHHhcCCCC
Q 022746 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI---SGDVPAVLNALVEIGNQLRENPPR 223 (292)
Q Consensus 147 i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I---~G~~~~v~~A~~~I~~~l~~~~~~ 223 (292)
+.||.+.+|.|||++|++|+.|+++||++|++.+ .+..|.| +++++++.+|..+|..+.......
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~------------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e 69 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS------------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc------------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH
Confidence 5689999999999999999999999999999953 2356888 899999999999999987753111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecc---------CccceeeecCCCccHHHHHHhhCCCCccc
Q 022746 224 QVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTR---------YFVTAIFAVLSSFNIFFLITTSSLGQPLL 288 (292)
Q Consensus 224 ~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~---------~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~ 288 (292)
.+.. . -...+....+.|+. ...|+|||+ +|++++.|++.|||.+.+-
T Consensus 70 ~A~~------l-----------~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~-~G~t~~~ie~~t~~~i~i~ 125 (172)
T TIGR03665 70 KALK------L-----------LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGE-GGKTRRIIEELTGVSISVY 125 (172)
T ss_pred HHHH------h-----------cCCcceEEEEEhhhccCCHHHHHHHHhhhcCC-CcHHHHHHHHHHCCeEEEc
Confidence 0000 0 00122233344544 479999999 9999999999999998764
No 16
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.39 E-value=1.4e-12 Score=110.76 Aligned_cols=117 Identities=17% Similarity=0.187 Sum_probs=87.2
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEE----cCHHHHHHHHHHHHHHHhc
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS----GDVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~----G~~~~v~~A~~~I~~~l~~ 219 (292)
...+.||.+.+|.|||++|++|+.|+++|||+|++.. .+..|.|. ++++++.+|..+|..++..
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~------------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS------------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC------------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 5789999999999999999999999999999999952 23678885 8999999999999998874
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEec---------cCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746 220 NPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNT---------RYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL 290 (292)
Q Consensus 220 ~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP---------~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~ 290 (292)
.....+.. .. ...+....+.+. ...+|+|||+ +|++++.|++.|||.+.+...
T Consensus 72 f~~e~A~~---l~--------------gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~-~G~~~k~ie~~t~~~i~i~~~ 133 (180)
T PRK13763 72 FSPEKALR---LL--------------DDDYVLEVIDLSDYGDSPNALRRIKGRIIGE-GGKTRRIIEELTGVDISVYGK 133 (180)
T ss_pred CCHHHHHH---Hh--------------CCCceEEEEEhhhccCChhHHHHHhhheeCC-CcHHHHHHHHHHCcEEEEcCC
Confidence 21000000 00 011111222222 1479999999 999999999999999887543
No 17
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.31 E-value=6.7e-12 Score=118.85 Aligned_cols=217 Identities=21% Similarity=0.325 Sum_probs=155.3
Q ss_pred CCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746 45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (292)
Q Consensus 45 ~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~ 124 (292)
....++.++++|+...|-.++||.|++|+.|+..++++|.+.... ..++++..+.|.+. ++..|...+..++..
T Consensus 63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~-----~v~~a~a~~~~~~~~ 136 (608)
T KOG2279|consen 63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPV-----QVCKAKAAIHQILTE 136 (608)
T ss_pred CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCC-----CCChHHHHHHHHHhc
Confidence 344678999999999999999999999999999999999998542 23566666776553 355566666666554
Q ss_pred CCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHH
Q 022746 125 DDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP 204 (292)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~ 204 (292)
.. .+...+.+|...+++|+|++|.+++.++..++|+|.+... . .+ -..+...|.|...
T Consensus 137 ~~---------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n-g--r~----g~~~~~~i~~qqk 194 (608)
T KOG2279|consen 137 NT---------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN-G--RL----GLSRLIKISGQQK 194 (608)
T ss_pred CC---------------cccccccchhhhcccccccchhhhcchhcccccccccccc-c--cc----ccccceecccccc
Confidence 33 2356788999999999999999999999999999998532 1 21 3467888888888
Q ss_pred HHHHHHHHHHHHHhcCCC---------------CCCCCC------------CCCC--CC-CCCCCC--------------
Q 022746 205 AVLNALVEIGNQLRENPP---------------RQVISI------------SPAY--NY-SAIRPA-------------- 240 (292)
Q Consensus 205 ~v~~A~~~I~~~l~~~~~---------------~~~~~~------------~p~~--n~-~~~~~~-------------- 240 (292)
.+..|..++.+.+.+... ++..+. .+.. ++ .+..++
T Consensus 195 ~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~ 274 (608)
T KOG2279|consen 195 EVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVV 274 (608)
T ss_pred hHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeE
Confidence 888999999888766521 111000 0000 00 000000
Q ss_pred ----CCCCCCC-------CceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccccc
Q 022746 241 ----QPFVEPT-------SGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLLQL 290 (292)
Q Consensus 241 ----~~~~~~~-------~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~~~ 290 (292)
..|..+. ......+|.||.-.+|.+||+ .|+.|+.+...|++..-|.|.
T Consensus 275 vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~-~gey~s~yssasn~~~hi~t~ 334 (608)
T KOG2279|consen 275 VSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGH-AGEYLSVYSSASNHPNHIWTQ 334 (608)
T ss_pred EecccccCCccccccccccccccceeecCcccccchhhh-hhhhhhhhhhccCccceEEec
Confidence 0011111 123567999999999999999 999999999999998777654
No 18
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.25 E-value=1.5e-11 Score=86.13 Aligned_cols=60 Identities=27% Similarity=0.362 Sum_probs=54.2
Q ss_pred EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 022746 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (292)
Q Consensus 145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I 213 (292)
.++.||..++++|||++|++|++|+++|||+|.+++.+ +.++.|+|+|+.++|..|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~---------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG---------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC---------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999986432 3578999999999999999887
No 19
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.22 E-value=5.3e-11 Score=83.15 Aligned_cols=57 Identities=26% Similarity=0.278 Sum_probs=52.0
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHH
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEI 213 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I 213 (292)
...+.||.+++|+|||++|++|++|+++|||+|.+. .++.|.|+|+ +++++.|..+|
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~-------------~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIE-------------DDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeC-------------CCCEEEEEeCCHHHHHHHHHHh
Confidence 568899999999999999999999999999999984 2468999998 89999999887
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=99.20 E-value=2.3e-11 Score=84.58 Aligned_cols=60 Identities=32% Similarity=0.445 Sum_probs=53.7
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I 213 (292)
|.+|.||..++++|||++|++|++|+++|||+|.+.+. .....|+|+|++++|.+|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~----------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD----------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST----------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC----------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999643 1245999999999999999886
No 21
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.19 E-value=9.1e-12 Score=86.64 Aligned_cols=60 Identities=40% Similarity=0.606 Sum_probs=51.9
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I 118 (292)
|.+|.||.+++|+|||++|++|++|+++|||.|+|++. + ....|+|+|++ .++.+|..+|
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-ERDIVTISGSP-----EQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESH-----HHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCH-----HHHHHHHhhC
Confidence 67899999999999999999999999999999999876 3 45599999964 4677777654
No 22
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.19 E-value=1.7e-11 Score=85.81 Aligned_cols=60 Identities=30% Similarity=0.450 Sum_probs=52.2
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I 118 (292)
.+|.||.+++|+|||++|++|++|+++|||+|.+++.. .+++.|+|+|+++ ++..|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~-----~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKE-----NVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHH-----HHHHHHHHh
Confidence 67999999999999999999999999999999999763 5678999999853 567776654
No 23
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.17 E-value=1.5e-10 Score=81.21 Aligned_cols=62 Identities=34% Similarity=0.484 Sum_probs=55.2
Q ss_pred EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 022746 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (292)
Q Consensus 145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I 213 (292)
.++.||.+++++|||++|++|++|+++|||+|.+.+... . ..++.|.|.|+.+++..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~--~-----~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS--G-----SEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC--C-----CCceEEEEEcCHHHHHHHHHHh
Confidence 589999999999999999999999999999999965332 1 4689999999999999999876
No 24
>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=99.15 E-value=7.8e-11 Score=82.64 Aligned_cols=62 Identities=44% Similarity=0.665 Sum_probs=53.6
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I 118 (292)
.+|.||..++++|||++|++|++|+++|||+|.|+....+..++.|.|.|.. .++..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~-----~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTP-----EAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCH-----HHHHHHHHHh
Confidence 6899999999999999999999999999999999976545678999999984 3577776654
No 25
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.11 E-value=2.1e-10 Score=80.14 Aligned_cols=59 Identities=36% Similarity=0.522 Sum_probs=49.2
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHH
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I 118 (292)
.+..|.||.+++|+||||+|++|+.|+++|||+|.+++ ++.|.|+|... .++.+|..+|
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------DGTVYIAASDK----EAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCH----HHHHHHHHHh
Confidence 35678999999999999999999999999999999986 35799999732 3566666554
No 26
>PF13014 KH_3: KH domain
Probab=99.07 E-value=2.2e-10 Score=74.21 Aligned_cols=42 Identities=43% Similarity=0.673 Sum_probs=38.4
Q ss_pred ccceeecCCCchhhhhhhhcCcEEEEcc-CCCCCCceEEEEec
Q 022746 60 QIGKVIGKEGHRIQKIREETKATIKIAD-AIARHEERVIIISS 101 (292)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~tga~I~i~~-~~~~~~ervv~I~G 101 (292)
+||+|||++|++|++|+++|||+|+|++ ..++..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999998 45677899999987
No 27
>PF13014 KH_3: KH domain
Probab=98.98 E-value=1.2e-09 Score=70.79 Aligned_cols=43 Identities=37% Similarity=0.629 Sum_probs=37.1
Q ss_pred cceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc
Q 022746 153 QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG 201 (292)
Q Consensus 153 ~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G 201 (292)
+||+|||++|++|++|+++|||+|+|++ +..+. +.++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~~-----~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEPG-----SNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccCCC-----CCceEEEEEC
Confidence 5799999999999999999999999976 33333 6899999998
No 28
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.94 E-value=1.3e-08 Score=85.95 Aligned_cols=149 Identities=19% Similarity=0.224 Sum_probs=110.2
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCC
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS 128 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~ 128 (292)
.....+.||...++.+||+.|+..+.|.+.+++++.+... +..|.|.......+....++|...|..+-......
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe 81 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 3456799999999999999999999999999999999853 46788876643223456788888777775544321
Q ss_pred CcchhhcccCCCcccEEEE------Ee-----ccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEE
Q 022746 129 NSEASKVAAGHVAANTIRL------LI-----AGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV 197 (292)
Q Consensus 129 ~~~~~~~~~~~~~~~~~~i------~I-----P~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v 197 (292)
. +.+.-.. ...+.+ .- -....|+|||++|.+-+-|++-|||.|.|. ...|
T Consensus 82 ~--A~~LL~d---~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~--------------g~tV 142 (194)
T COG1094 82 K--ALKLLED---DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY--------------GKTV 142 (194)
T ss_pred H--HHHHhcC---CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe--------------CcEE
Confidence 1 1110000 001110 01 123469999999999999999999999985 4689
Q ss_pred EEEcCHHHHHHHHHHHHHHHhcCC
Q 022746 198 QISGDVPAVLNALVEIGNQLRENP 221 (292)
Q Consensus 198 ~I~G~~~~v~~A~~~I~~~l~~~~ 221 (292)
.|-|.+++|..|...|..++...+
T Consensus 143 aiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcCCC
Confidence 999999999999999999998874
No 29
>smart00322 KH K homology RNA-binding domain.
Probab=98.90 E-value=1.3e-08 Score=71.41 Aligned_cols=66 Identities=33% Similarity=0.462 Sum_probs=58.5
Q ss_pred cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217 (292)
Q Consensus 143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 217 (292)
.+.++.||..+++.+||++|++|++|++.||++|.+.... .....+.|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~---------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG---------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC---------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 4688999999999999999999999999999999985321 24689999999999999999998876
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=98.82 E-value=1.6e-08 Score=70.88 Aligned_cols=67 Identities=34% Similarity=0.582 Sum_probs=56.1
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI 122 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i 122 (292)
.++.++.||...+|.+||++|++|++|++.||++|.+.... .....+.|.|.. .++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--~~~~~v~i~g~~-----~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--SEERVVEITGPP-----ENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--CCccEEEEEcCH-----HHHHHHHHHHHHHh
Confidence 46789999999999999999999999999999999998642 256889999985 36777777776654
No 31
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.73 E-value=3.2e-08 Score=100.59 Aligned_cols=196 Identities=19% Similarity=0.169 Sum_probs=138.0
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcc--hhHHHHHHHHHHHHHh-c--
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNV--VSDAENALQQIAALIL-K-- 124 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~--v~~v~~A~~~I~~~i~-~-- 124 (292)
+..++.+....+.++||++|.+++.++.++.+.++++..... .....|.|..+... ...++.++.++..-.. +
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~--~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~ 278 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKS--SPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEI 278 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEccccccc--chhhhhccccccceehhhhhHHHHHHhcChhhhhhh
Confidence 678999999999999999999999999999999999954211 11222222211100 1122333322211000 0
Q ss_pred ------CCC--CC------------------cc------hhhcc------------------cCCCcccEEEEEeccCcc
Q 022746 125 ------DDD--SN------------------SE------ASKVA------------------AGHVAANTIRLLIAGSQA 154 (292)
Q Consensus 125 ------~~~--~~------------------~~------~~~~~------------------~~~~~~~~~~i~IP~~~v 154 (292)
... .. .. ..... .-......+.+.+-..++
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~ 358 (753)
T KOG2208|consen 279 IYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEEL 358 (753)
T ss_pred hhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhh
Confidence 000 00 00 00000 001234667888889999
Q ss_pred eeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q 022746 155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNY 234 (292)
Q Consensus 155 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~ 234 (292)
..++||+|.+|.+|++++.+.|.+... ++.+..+.++|...++.+|...+...+.+....
T Consensus 359 ~~v~GK~~~ni~ki~e~~~~~i~~~~~---------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~----------- 418 (753)
T KOG2208|consen 359 KFVIGKKGANIEKIREESQVKIDLPKQ---------GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS----------- 418 (753)
T ss_pred hhhcCCCCccHHHHHHhhhhceecccc---------cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc-----------
Confidence 999999999999999999999998531 157889999999999999999999999888421
Q ss_pred CCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746 235 SAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL 283 (292)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~ 283 (292)
.....+.+|...+.++||. +|..|+.|...+++
T Consensus 419 ---------------~~~~~~~iP~k~~~~iig~-~g~~i~~I~~k~~~ 451 (753)
T KOG2208|consen 419 ---------------IVKEEVQIPTKSHKRIIGT-KGALINYIMGKHGG 451 (753)
T ss_pred ---------------cccceeecCccchhhhhcc-ccccHHHHHhhcCc
Confidence 2456788999999999999 99999999999995
No 32
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.55 E-value=1e-07 Score=96.97 Aligned_cols=145 Identities=21% Similarity=0.298 Sum_probs=113.2
Q ss_pred CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (292)
Q Consensus 47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~ 126 (292)
.+.+.+.+-+-...+..++||+|.+|.+|++++.|.+.+... +.++..+.++|... ++.+|...+.....+..
T Consensus 344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~-----~~~ka~~~v~~~~~ei~ 416 (753)
T KOG2208|consen 344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSA-----NDEKAVEDVEKIIAEIL 416 (753)
T ss_pred ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEecccc-----chhHHHHHHHHHHHhhh
Confidence 345788888999999999999999999999999999999974 35667788888754 46777777777766654
Q ss_pred CCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhC-CeEEEeCCCCCCcccCCCCCCcEEEEEcCHHH
Q 022746 127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG-ATIVILAPNQLPLCASAHESDRVVQISGDVPA 205 (292)
Q Consensus 127 ~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~ 205 (292)
.. .....+.+|...+.++||.+|..|..|.+++| .+|+... +. +....+++.|....
T Consensus 417 n~-------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~-~~--------~~~~~~~~~~~~~d 474 (753)
T KOG2208|consen 417 NS-------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQN-NN--------NSSDMVTIRGISKD 474 (753)
T ss_pred cc-------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCC-CC--------cccccceEeccccc
Confidence 32 12467999999999999999999999999999 5666432 21 34567888888887
Q ss_pred HHHHHHHHHHHHhcC
Q 022746 206 VLNALVEIGNQLREN 220 (292)
Q Consensus 206 v~~A~~~I~~~l~~~ 220 (292)
+..+..++..+..+.
T Consensus 475 v~~~~~~~~~~~~~a 489 (753)
T KOG2208|consen 475 VEKSVSLLKALKADA 489 (753)
T ss_pred cchhHHHHHhhhhhh
Confidence 777766666665544
No 33
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.55 E-value=1.3e-07 Score=84.53 Aligned_cols=149 Identities=21% Similarity=0.302 Sum_probs=109.4
Q ss_pred CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCC
Q 022746 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD 127 (292)
Q Consensus 48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~ 127 (292)
+.++..+-||..+++.|.|++|.+||.|+.+|..+|+-+.. ..+-++.++|..+ .|..|.+.|...-.....
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~e-----dv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHE-----DVRRARREIPSAAEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCch-----hHHHHhhcCccccceeee
Confidence 68899999999999999999999999999999999988754 2457888999876 577777666543211111
Q ss_pred CCcchhh---c-ccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 022746 128 SNSEASK---V-AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (292)
Q Consensus 128 ~~~~~~~---~-~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~ 203 (292)
....... . .+....+.+..+.+|...+|.+.|..|++|+.+++.++..|.-.-. -.+.++.++|-+
T Consensus 96 ~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~----------~~~~Vf~Vtg~~ 165 (394)
T KOG2113|consen 96 IRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR----------CGEPVFCVTGAP 165 (394)
T ss_pred eeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc----------CCCceEEEecCC
Confidence 0000000 0 0112456788899999999999999999999999999999886422 346788899988
Q ss_pred HH-HHHHH-HHHH
Q 022746 204 PA-VLNAL-VEIG 214 (292)
Q Consensus 204 ~~-v~~A~-~~I~ 214 (292)
.+ +++|. +.|.
T Consensus 166 ~nC~kra~s~eie 178 (394)
T KOG2113|consen 166 KNCVKRARSCEIE 178 (394)
T ss_pred cchhhhccccchh
Confidence 87 55555 4443
No 34
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.51 E-value=5.4e-08 Score=92.76 Aligned_cols=110 Identities=24% Similarity=0.233 Sum_probs=94.5
Q ss_pred cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (292)
Q Consensus 141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 220 (292)
..+..++.|+..++-+++|++|.+|+.|+..++++|.+.+. +. ..++.-.+.|-+.++..|+..+..++.+.
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~-------g~e~~~~~~~~p~~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DV-------GDERVLLISGFPVQVCKAKAAIHQILTEN 137 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cC-------CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence 45678999999999999999999999999999999998543 32 34677777889999999999999999887
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746 221 PPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL 287 (292)
Q Consensus 221 ~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~ 287 (292)
. .+.....+|...+++|+|| +|++++.|...|+|+..+
T Consensus 138 ~----------------------------pvk~~lsvpqr~~~~i~gr-gget~~si~~ss~aki~~ 175 (608)
T KOG2279|consen 138 T----------------------------PVSEQLSVPQRSVGRIIGR-GGETIRSICKSSGAKITC 175 (608)
T ss_pred C----------------------------cccccccchhhhccccccc-chhhhcchhccccccccc
Confidence 3 2455677999999999999 999999999999998753
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=98.48 E-value=4.6e-07 Score=71.82 Aligned_cols=72 Identities=19% Similarity=0.368 Sum_probs=53.2
Q ss_pred EEEeeC------CccceeecCCCchhhhhhhhcCcEEEEccCCCC-----------------CCceEEEEecCCCCcchh
Q 022746 53 RIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADAIAR-----------------HEERVIIISSKDNDNVVS 109 (292)
Q Consensus 53 rilvp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-----------------~~ervv~I~G~~~~~~v~ 109 (292)
|+.||. .++|.|||++|++||+|+++|||+|.|...... .+.-.|.|++.... -.
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~--~e 80 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPP--EE 80 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcH--HH
Confidence 455555 568999999999999999999999999954111 12256889987610 13
Q ss_pred HHHHHHHHHHHHHhcCC
Q 022746 110 DAENALQQIAALILKDD 126 (292)
Q Consensus 110 ~v~~A~~~I~~~i~~~~ 126 (292)
++.+|+.+|..++....
T Consensus 81 ~~~~A~~~I~~ll~~~~ 97 (120)
T cd02395 81 ALAKAVEAIEELLKPAI 97 (120)
T ss_pred HHHHHHHHHHHHhccCC
Confidence 67888888888887544
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=98.47 E-value=9.1e-07 Score=70.09 Aligned_cols=69 Identities=22% Similarity=0.312 Sum_probs=52.7
Q ss_pred cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCC-----------cccCCCCCCcEEEEEcCH---HHHHHHHHHHHHH
Q 022746 151 GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP-----------LCASAHESDRVVQISGDV---PAVLNALVEIGNQ 216 (292)
Q Consensus 151 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p-----------~~~~~~~~~r~v~I~G~~---~~v~~A~~~I~~~ 216 (292)
.+++|.|||++|.+||+|+++|||+|.|....... .... ....-.|.|++.. +++.+|..+|..+
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~-~~eplhV~I~a~~~~~e~~~~A~~~I~~l 92 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAH-LNEPLHVLITAETPPEEALAKAVEAIEEL 92 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCccccc-CCCCcEEEEEeCCcHHHHHHHHHHHHHHH
Confidence 46889999999999999999999999996431110 0000 0234678999965 8999999999999
Q ss_pred HhcC
Q 022746 217 LREN 220 (292)
Q Consensus 217 l~~~ 220 (292)
+...
T Consensus 93 l~~~ 96 (120)
T cd02395 93 LKPA 96 (120)
T ss_pred hccC
Confidence 9865
No 37
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.21 E-value=2.7e-06 Score=69.26 Aligned_cols=103 Identities=17% Similarity=0.297 Sum_probs=71.9
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCC
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~ 129 (292)
-.+.|+|+...+|+.||++|++|+.|++..|-+|.+-+.. + ++...|.+.+.......
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s--------------~--------d~~~fI~n~l~Pa~V~~ 89 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS--------------D--------DPEEFIKNIFAPAAVRS 89 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC--------------C--------CHHHHHHHHcCCCEEEE
Confidence 3578999999999999999999999999998777765421 1 12233344433221110
Q ss_pred cchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEE
Q 022746 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (292)
Q Consensus 130 ~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i 178 (292)
- .. ..........+.|+....|..|||+|++++.++.-++-.+.+
T Consensus 90 v---~I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 90 V---TI-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred E---EE-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 0 00 000112357788999999999999999999999999888776
No 38
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.07 E-value=1.9e-05 Score=79.47 Aligned_cols=94 Identities=24% Similarity=0.306 Sum_probs=73.6
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (292)
Q Consensus 108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (292)
+..+.+++..|.+.|.+..... .... ...+....+.||.+.++.|||+||.+||.|+++||++|.+.
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p-~~~s----~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-------- 614 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTP-DEMS----PYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-------- 614 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc-cccc----cCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe--------
Confidence 4556777778888877654333 1111 12345788999999999999999999999999999999984
Q ss_pred cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 219 (292)
++..|.|.+ +.+.+.+|+.+|..++..
T Consensus 615 -----d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 615 -----DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred -----cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 357888888 468999999999999885
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.06 E-value=1.8e-05 Score=64.39 Aligned_cols=102 Identities=17% Similarity=0.154 Sum_probs=73.3
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~ 223 (292)
.+.++|+...+|..||++|++|+.|++..|-+|.+..- +.+ +...|.+.|.-..-.
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~----------s~d--------------~~~fI~n~l~Pa~V~ 88 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY----------SDD--------------PEEFIKNIFAPAAVR 88 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc----------CCC--------------HHHHHHHHcCCCEEE
Confidence 68889999999999999999999999999999998742 122 344555544333111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746 224 QVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL 287 (292)
Q Consensus 224 ~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~ 287 (292)
... . ....+.....+.|+.+..|..||| +|+||+.++...+-...+
T Consensus 89 ~v~-------I----------~~~~~~~~~~V~V~~~d~g~aIGK-~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 89 SVT-------I----------KKKNGDKVAYVEVAPEDKGIAIGK-NGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEE-------E----------EecCCcEEEEEEECccccchhhCC-CCHHHHHHHHHhCCccCC
Confidence 000 0 000113466788999999999999 999999999988876544
No 40
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.98 E-value=7.5e-06 Score=73.40 Aligned_cols=122 Identities=14% Similarity=0.103 Sum_probs=89.1
Q ss_pred cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (292)
Q Consensus 141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 220 (292)
...+..+.||..+++.+.|++|..||.|+.+|...|.-+.. ..+.++.++|..+.|..|+..|..--+..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr----------~eePiF~vTg~~edv~~aRrei~saaeH~ 93 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR----------GEEPIFPVTGRHEDVRRARREIPSAAEHF 93 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC----------CCCCcceeccCchhHHHHhhcCcccccee
Confidence 56788999999999999999999999999999999986432 24578999999999999998886522111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhC
Q 022746 221 PPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSS 282 (292)
Q Consensus 221 ~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~ 282 (292)
-.. .+.+.+ ..+.+.+. .....+.++.+|...+|.|.|. .|.+|+.|++...
T Consensus 94 ~l~---~~s~s~-----Sgg~~~~s-~s~qt~sy~svP~rvvglvv~~-~~~ti~~iqq~tn 145 (394)
T KOG2113|consen 94 GLI---RASRSF-----SGGTNGAS-ASGQTTSYVSVPLRVVGLVVGP-KGATIKRIQQFTN 145 (394)
T ss_pred eee---eecccc-----cCCCcccc-ccCCCceeeeccceeeeecccc-ccCccchheeccc
Confidence 000 000000 00111111 1235677888999999999999 9999999998764
No 41
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.86 E-value=0.00012 Score=62.02 Aligned_cols=115 Identities=17% Similarity=0.192 Sum_probs=82.0
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-----CHHHHHHHHHHHHHHHh
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-----DVPAVLNALVEIGNQLR 218 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-----~~~~v~~A~~~I~~~l~ 218 (292)
...+.||...++.+||+.|...+.|.+.+++++.+. +.+..|+|.. +|..+.+|...|..+-.
T Consensus 9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD------------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr 76 (194)
T COG1094 9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID------------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGR 76 (194)
T ss_pred eeeeecCchhheeeecccccchHHHHhhcCeEEEEE------------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence 466899999999999999999999999999999985 3456677654 47789999998877654
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEec----------cCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746 219 ENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNT----------RYFVTAIFAVLSSFNIFFLITTSSLGQPLL 288 (292)
Q Consensus 219 ~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP----------~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~ 288 (292)
..+...+..+ . ..++.-..|.+- ...-|+|||+ +|.|-+-|++.|+|.+.+.
T Consensus 77 GF~pe~A~~L---L--------------~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~-~GkTr~~IE~lt~~~I~V~ 138 (194)
T COG1094 77 GFPPEKALKL---L--------------EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGR-EGKTRRAIEELTGVYISVY 138 (194)
T ss_pred CCCHHHHHHH---h--------------cCCcEEEEEEHHHhccCchhhhhHhhceeeCC-CchHHHHHHHHhCCeEEEe
Confidence 4321111000 0 001112222211 2457999999 9999999999999998764
No 42
>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=97.74 E-value=8e-05 Score=75.60 Aligned_cols=95 Identities=22% Similarity=0.196 Sum_probs=68.1
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (292)
Q Consensus 108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (292)
+..+.++...|.+.|.+......... ....+....+.||.+.++.|||+||++||.|+++|||+|.+.
T Consensus 520 l~~a~~~~~~I~~~m~~~l~~~~~~~----~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-------- 587 (684)
T TIGR03591 520 LEQAKEGRLHILGEMNKVISEPRAEL----SPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-------- 587 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhccc----cccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe--------
Confidence 34455666677777655432211100 111345678999999999999999999999999999999984
Q ss_pred cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 219 (292)
++..|.|.+ ..+.+.+|...|..+..+
T Consensus 588 -----ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 588 -----DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred -----cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 345677766 567888899998888664
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=97.70 E-value=0.00017 Score=58.69 Aligned_cols=102 Identities=19% Similarity=0.274 Sum_probs=69.3
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCc
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~ 130 (292)
-+-|+|....+|..||++|++|+.|++..|-+|.+-+.. ..+ ...|.+.+.......-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys-----------~D~-----------~~fI~N~l~PA~V~~V 91 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS-----------ENL-----------EEFVANKLAPAEVKNV 91 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC-----------CCH-----------HHHHHHcCCCceEEEE
Confidence 577899999999999999999999998888777765421 111 1122222221110000
Q ss_pred chhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEE
Q 022746 131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (292)
Q Consensus 131 ~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i 178 (292)
.. ....+.....+.||.+..+..|||+|.+++....-++-++.+
T Consensus 92 ---~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 92 ---TV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred ---EE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 00 000123467888999999999999999999999988887766
No 44
>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=97.63 E-value=9.3e-05 Score=74.55 Aligned_cols=66 Identities=33% Similarity=0.509 Sum_probs=57.1
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~ 124 (292)
.-...|.||.+.+|.|||+||.+||.|+++|||+|++.+. ..|.|.+... ..+.+|+.+|..+...
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~------G~V~I~a~d~----~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD------GTVYIGAADG----PSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC------cEEEEEeCCH----HHHHHHHHHHHHhhCc
Confidence 5567888999999999999999999999999999999963 6799999764 4688888888888764
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.60 E-value=0.00025 Score=67.46 Aligned_cols=78 Identities=21% Similarity=0.278 Sum_probs=58.3
Q ss_pred ccEEEEEec------cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCC----------CcccCCCCCCcEEEEEcCH-H
Q 022746 142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQL----------PLCASAHESDRVVQISGDV-P 204 (292)
Q Consensus 142 ~~~~~i~IP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~----------p~~~~~~~~~r~v~I~G~~-~ 204 (292)
....++.|| .+|||+|||..|.+.|+|+.+|||+|.|.-+... ..... ...+--+.|+++. +
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~-~~epLH~~Isadt~e 215 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPK-ENEPLHCLISADTQE 215 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccc-cccceeEEEecchHH
Confidence 446788888 4699999999999999999999999999752111 11000 1234557788865 7
Q ss_pred HHHHHHHHHHHHHhcC
Q 022746 205 AVLNALVEIGNQLREN 220 (292)
Q Consensus 205 ~v~~A~~~I~~~l~~~ 220 (292)
.|++|++.|..+|.+.
T Consensus 216 ki~~Ai~vienli~~a 231 (554)
T KOG0119|consen 216 KIKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999999873
No 46
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.44 E-value=0.00053 Score=55.80 Aligned_cols=102 Identities=15% Similarity=0.189 Sum_probs=69.1
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~ 223 (292)
.+-|+|....+|..||++|++|+.|++..|-+|.+..- +.+ + ...|.+.|.=..-.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey----------s~D--------~------~~fI~N~l~PA~V~ 89 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY----------SEN--------L------EEFVANKLAPAEVK 89 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc----------CCC--------H------HHHHHHcCCCceEE
Confidence 57788999999999999999999999999999988642 112 1 12222211111000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746 224 QVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL 287 (292)
Q Consensus 224 ~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~ 287 (292)
.. + ... .++.....+.||.+..|..||| +|+||+-..+.++-...+
T Consensus 90 ~V-------~---------i~~-~~~~~~a~V~V~~~d~~~AIGk-~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 90 NV-------T---------VSE-FNGKKVAYVEVHPRDKGIAIGK-GGKNIERAKELAKRHHDI 135 (141)
T ss_pred EE-------E---------EEc-CCCCEEEEEEEChhhhhhhhCC-CchhHHHHHHHhcCccCC
Confidence 00 0 000 0123567788999999999999 999999999988765543
No 47
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.44 E-value=0.00054 Score=60.57 Aligned_cols=42 Identities=26% Similarity=0.604 Sum_probs=37.4
Q ss_pred CCCCCeEEEEEeeCC------ccceeecCCCchhhhhhhhcCcEEEEc
Q 022746 45 AKAQDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIA 86 (292)
Q Consensus 45 ~~~~~~~~rilvp~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~ 86 (292)
.+.-.++.|++||.. +||.|+|++|.++|+|+++|||+|-|.
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 344567889999985 799999999999999999999999998
No 48
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.40 E-value=0.00033 Score=72.19 Aligned_cols=95 Identities=17% Similarity=0.212 Sum_probs=70.9
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCe-EEEeCCCCCCc
Q 022746 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPL 186 (292)
Q Consensus 108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~ 186 (292)
+..+.+++..|++.|.+......... .........+.||.+.++.|||.||.+||.|.++||++ |.+.
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~~----s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~------- 722 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKRL----SKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------- 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhh----cccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-------
Confidence 44556677777777766543221111 11234578899999999999999999999999999999 8862
Q ss_pred ccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746 187 CASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 187 ~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 219 (292)
++-.|.|.+ +.+.+.+|+.+|..++.+
T Consensus 723 ------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 723 ------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred ------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 356788877 568999999999988764
No 49
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.33 E-value=0.0006 Score=67.65 Aligned_cols=107 Identities=20% Similarity=0.212 Sum_probs=78.3
Q ss_pred EEEecCCCC---cchhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhC
Q 022746 97 IIISSKDND---NVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG 173 (292)
Q Consensus 97 v~I~G~~~~---~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tg 173 (292)
+.|.|-+.. ..+..+..|...|+..|.+........ ..........+.|+...++-+||++|++|+.|.++||
T Consensus 507 iKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~e----ls~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg 582 (692)
T COG1185 507 IKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKE----LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETG 582 (692)
T ss_pred eeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh----hhccCCceEEEccCHHHHhhccCCcccchhhhhhhhC
Confidence 455665442 114456677778888887654322111 1112344678899999999999999999999999999
Q ss_pred CeEEEeCCCCCCcccCCCCCCcEEEEEcCH-HHHHHHHHHHHHHHhcC
Q 022746 174 ATIVILAPNQLPLCASAHESDRVVQISGDV-PAVLNALVEIGNQLREN 220 (292)
Q Consensus 174 a~I~i~~~~~~p~~~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~l~~~ 220 (292)
++|++. ++..|.|.++. +.+.+|+.+|..+.++.
T Consensus 583 ~~Idie-------------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 583 VKIDIE-------------DDGTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred cEEEec-------------CCCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 999983 45688898887 78899999999998665
No 50
>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=97.32 E-value=0.00027 Score=71.79 Aligned_cols=65 Identities=32% Similarity=0.441 Sum_probs=53.3
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~ 123 (292)
.-...+.||.+.+|.|||++|++||+|+++|||+|.|.+. ..|.|.+... ..+.+|..+|..+..
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~----~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDG----EAAEAAIKMIEGITA 614 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcH----HHHHHHHHHHHhhhc
Confidence 4567888999999999999999999999999999999863 5688887653 356777777776644
No 51
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.22 E-value=0.00053 Score=65.26 Aligned_cols=73 Identities=23% Similarity=0.380 Sum_probs=57.0
Q ss_pred CeEEEEEeeC------CccceeecCCCchhhhhhhhcCcEEEEccC------C---------CCC-CceEEEEecCCCCc
Q 022746 49 DVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA------I---------ARH-EERVIIISSKDNDN 106 (292)
Q Consensus 49 ~~~~rilvp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~------~---------~~~-~ervv~I~G~~~~~ 106 (292)
.++-|+.||. ++||+|||.+|.|.|+|+++|||+|.|--. . ++. ++--+.|++...
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~-- 214 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ-- 214 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH--
Confidence 5667888886 579999999999999999999999999731 0 111 233478888765
Q ss_pred chhHHHHHHHHHHHHHhcC
Q 022746 107 VVSDAENALQQIAALILKD 125 (292)
Q Consensus 107 ~v~~v~~A~~~I~~~i~~~ 125 (292)
+.+.+|+..|..+|.+.
T Consensus 215 --eki~~Ai~vienli~~a 231 (554)
T KOG0119|consen 215 --EKIKKAIAVIENLIQSA 231 (554)
T ss_pred --HHHHHHHHHHHHHHHhh
Confidence 57899999999998763
No 52
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.16 E-value=0.0018 Score=55.31 Aligned_cols=103 Identities=20% Similarity=0.288 Sum_probs=69.6
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCc
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~ 130 (292)
.+-+.+-...+|..||++|++|+.|+++.|=+|.|-+-. ++ -...|.+.+......
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~d---------~~~fI~nal~Pa~v~-- 132 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------ED---------PAEFIKNALAPAEVL-- 132 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------CC---------HHHHHHHhcCcceEe--
Confidence 455566667899999999999999999999666665431 11 112233333311100
Q ss_pred chhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746 131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (292)
Q Consensus 131 ~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 180 (292)
...-.........+.||.+..+..|||+|.+++-..+-||-++.+..
T Consensus 133 ---~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 133 ---SVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred ---EEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 00000001116888999999999999999999999999999999864
No 53
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.09 E-value=0.00047 Score=64.70 Aligned_cols=74 Identities=22% Similarity=0.315 Sum_probs=55.8
Q ss_pred cCCCCCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHH
Q 022746 44 RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI 122 (292)
Q Consensus 44 ~~~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i 122 (292)
.....++++.|.|-+++||.+||++|++|+.||..|+++|++-.. ..+-.|+|-|.... ...+.+++....+..
T Consensus 41 aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m--~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 41 AAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHM--RKKAKASIDRGQDKD 114 (629)
T ss_pred ccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHH--HHHHHhhHhhhhhhh
Confidence 345568889999999999999999999999999999999999864 34567888887542 123344444444443
No 54
>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=97.08 E-value=0.00067 Score=47.15 Aligned_cols=36 Identities=31% Similarity=0.493 Sum_probs=33.6
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEE
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i 85 (292)
....+.|+.+..|..|||+|.+|+.+++.+|-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578999999999999999999999999999988876
No 55
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.03 E-value=0.0007 Score=61.59 Aligned_cols=72 Identities=33% Similarity=0.385 Sum_probs=59.2
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~ 126 (292)
.+...+.+++...|+|||++|.+-++|+++|+++|.++.+ +.....+.|+|-. ...|..|..+|..+|.+..
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~----~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGIS----RNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehh----HHHHHHHHHHHHHHHHhhh
Confidence 5667889999999999999999999999999999999976 3344457777754 4578899999988886644
No 56
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.94 E-value=0.0023 Score=56.62 Aligned_cols=81 Identities=17% Similarity=0.257 Sum_probs=54.9
Q ss_pred CcccEEEEEecc------CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCC------------cccCCC-CCCcEEEEE
Q 022746 140 VAANTIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP------------LCASAH-ESDRVVQIS 200 (292)
Q Consensus 140 ~~~~~~~i~IP~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p------------~~~~~~-~~~r~v~I~ 200 (292)
....+.+|+||. ++||+|+|..|.++|+|+++|||+|.|--....- ..+... .--..|...
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 345678889984 4999999999999999999999999996432111 111000 011446667
Q ss_pred cCHH----HHHHHHHHHHHHHhcC
Q 022746 201 GDVP----AVLNALVEIGNQLREN 220 (292)
Q Consensus 201 G~~~----~v~~A~~~I~~~l~~~ 220 (292)
+++. .+..|++.|..+|.-.
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~P~ 192 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLVPD 192 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCC
Confidence 7765 3446888888877544
No 57
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.88 E-value=0.0017 Score=66.13 Aligned_cols=95 Identities=21% Similarity=0.202 Sum_probs=68.8
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (292)
Q Consensus 108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (292)
+..+.+++..|.+.|.+......... .........+.||.+.++.+||.||.+||+|.++||+.|.+.
T Consensus 523 l~~a~~g~~~I~~~M~~aI~~~r~~~----~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-------- 590 (693)
T PRK11824 523 LEQAKEGRLHILGKMNEAISEPRAEL----SPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-------- 590 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhcCChhhh----cccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC--------
Confidence 44556777778888776543221111 111233567778999999999999999999999999988862
Q ss_pred cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 219 (292)
++..|.|.+ ..+.+.+|...|..+..+
T Consensus 591 -----d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 -----DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred -----CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 356788887 567888999999888764
No 58
>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=96.80 E-value=0.0058 Score=57.02 Aligned_cols=95 Identities=23% Similarity=0.320 Sum_probs=63.5
Q ss_pred CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (292)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~ 137 (292)
+-+|+.||++|++|+.|.++. |=+|.|-... ++ -...|.+.+....... +.-
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-------------~d---------~~~fi~nal~Pa~v~~-----v~i 295 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS-------------DD---------PAEFIANALSPAKVIS-----VEV 295 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhcCCceEEE-----EEE
Confidence 459999999999999999998 6666665321 00 0111222221111000 000
Q ss_pred CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (292)
Q Consensus 138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 180 (292)
.........+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 296 ~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 296 LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 0001236899999999999999999999999999999999964
No 59
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.69 E-value=0.006 Score=57.23 Aligned_cols=97 Identities=21% Similarity=0.185 Sum_probs=65.3
Q ss_pred CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (292)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~ 137 (292)
+-+|+.||++|++|+.|.++. |=+|.|-.-. ++ -...|.+.+....... +..
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s-------------~D---------~~~fI~Nal~Pa~V~~-----V~i 303 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS-------------NV---------PEIFIARALAPAIISS-----VKI 303 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhCCCceeeE-----EEE
Confidence 459999999999999999998 6666665321 10 1112222222111000 000
Q ss_pred CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCC
Q 022746 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ 183 (292)
Q Consensus 138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~ 183 (292)
. .......+.||..+.+..|||+|.+++-...-||.+|.|.+-..
T Consensus 304 ~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 304 E-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred c-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 0 11236889999999999999999999999999999999987543
No 60
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.65 E-value=0.003 Score=57.62 Aligned_cols=71 Identities=24% Similarity=0.368 Sum_probs=57.3
Q ss_pred cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (292)
Q Consensus 143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 221 (292)
....+.++..+.++|||++|.+-++|+++|+++|.++.+.. ..+.++.+.+..++|.+|...|...+.+..
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~--------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT--------NKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC--------CcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 35678899999999999999999999999999999865431 233344445567899999999999988774
No 61
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.65 E-value=0.0025 Score=59.94 Aligned_cols=68 Identities=21% Similarity=0.251 Sum_probs=55.2
Q ss_pred ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhc
Q 022746 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 219 (292)
.....|.|-+++||.+||++|+.|++||..|+++|++..- ..+..|+|-|...--.+|...|...+..
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~----------~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC----------DLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc----------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 4467788999999999999999999999999999999642 3578999999987666666666555443
No 62
>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=96.61 E-value=0.0041 Score=43.14 Aligned_cols=36 Identities=31% Similarity=0.451 Sum_probs=33.6
Q ss_pred cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEE
Q 022746 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (292)
Q Consensus 143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i 178 (292)
....+.|+...+|..|||+|.+|+.+++.+|-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 478999999999999999999999999999988876
No 63
>PRK00468 hypothetical protein; Provisional
Probab=96.56 E-value=0.0023 Score=46.37 Aligned_cols=34 Identities=35% Similarity=0.587 Sum_probs=29.8
Q ss_pred CCCCeEEEEEeeCCccceeecCCCchhhhhhhhc
Q 022746 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (292)
Q Consensus 46 ~~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~t 79 (292)
.+..+.+++.|..+.+|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3446789999999999999999999999999763
No 64
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.54 E-value=0.0095 Score=55.99 Aligned_cols=96 Identities=23% Similarity=0.294 Sum_probs=64.3
Q ss_pred CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (292)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~ 137 (292)
+-+|+.||++|++|+.|.++. |-+|.|-... ++ ....|.+.+....... +..
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s-------------~d---------~~~fi~nal~Pa~v~~-----v~i 297 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS-------------ED---------PAEFVANALSPAKVVS-----VEV 297 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhCCCceEEE-----EEE
Confidence 459999999999999999998 7666665321 00 1112222222111000 000
Q ss_pred CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC
Q 022746 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (292)
Q Consensus 138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 181 (292)
.........+.||..+.+..|||+|.+++--..-||.+|.+.+.
T Consensus 298 ~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 298 DDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 00112368999999999999999999999999999999999753
No 65
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.47 E-value=0.006 Score=60.75 Aligned_cols=65 Identities=31% Similarity=0.440 Sum_probs=54.2
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~ 125 (292)
...+.++.+.++-+||++|.+|++|.++|||+|++.+. ..|.|.++..+ .+.+|+..|..+..+.
T Consensus 553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~----~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGE----SAKKAKERIEAITREV 617 (692)
T ss_pred eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchH----HHHHHHHHHHHHHhhc
Confidence 45677899999999999999999999999999999954 45888887653 6778888888887543
No 66
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.44 E-value=0.0028 Score=65.56 Aligned_cols=66 Identities=26% Similarity=0.405 Sum_probs=56.1
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcE-EEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT-IKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~ 124 (292)
.....|.||.+.++.|||.||.+||.|.++||+. |++.+. -.|.|.+... ..+.+|+.+|..+..+
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------g~V~I~a~d~----~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------GTVKITAKDL----SSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------eeEEEEeCCH----HHHHHHHHHHHHHhcC
Confidence 5667889999999999999999999999999999 998863 5688988764 5788888888888753
No 67
>PRK02821 hypothetical protein; Provisional
Probab=96.41 E-value=0.0032 Score=45.83 Aligned_cols=35 Identities=26% Similarity=0.438 Sum_probs=30.3
Q ss_pred CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCc
Q 022746 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (292)
Q Consensus 47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga 81 (292)
.....+++.|..+.+|.||||+|.+|+.||.--.+
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 34577899999999999999999999999987544
No 68
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.39 E-value=0.0096 Score=56.86 Aligned_cols=95 Identities=23% Similarity=0.265 Sum_probs=63.0
Q ss_pred CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (292)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~ 137 (292)
+-+|+.||++|++|+.|.++. |=+|.|-.-. ++ -...|.+.+....... +..
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-------------~D---------p~~fI~NaLsPA~V~~-----V~i 329 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS-------------PD---------PATYIANALSPARVDE-----VRL 329 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhcCCceeeE-----EEE
Confidence 459999999999999999998 6666665321 10 1112222222111000 000
Q ss_pred CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (292)
Q Consensus 138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 180 (292)
.........+.||..+.+..|||+|.+++--..-||.+|.|..
T Consensus 330 ~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 330 VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0001235789999999999999999999999999999999853
No 69
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.28 E-value=0.0082 Score=51.34 Aligned_cols=100 Identities=15% Similarity=0.178 Sum_probs=67.3
Q ss_pred EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCC
Q 022746 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQ 224 (292)
Q Consensus 145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~ 224 (292)
..+.+-.+.+|..||++|.+|+.|+++.|-+|.+... +.+ -...|.+.|. |..
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~----------s~d--------------~~~fI~nal~--Pa~- 130 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW----------SED--------------PAEFIKNALA--PAE- 130 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe----------CCC--------------HHHHHHHhcC--cce-
Confidence 4455556788999999999999999999988887632 111 1233333333 110
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746 225 VISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL 287 (292)
Q Consensus 225 ~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~ 287 (292)
... .+.. ..+.....+.||.+.-+..||| +|.|++-+.+-+|-.+.+
T Consensus 131 v~~----V~~~-----------~~d~~~~~v~V~~~~~~~aIGk-~G~Nvrla~~Ltg~~i~I 177 (190)
T COG0195 131 VLS----VNIK-----------EDDGHVAIVVVPPDQLSLAIGK-GGQNVRLASQLTGWEIDI 177 (190)
T ss_pred EeE----EEEE-----------eCCCcEEEEEECHHHHhhccCc-ccHHHHHHHHHhCCEEEE
Confidence 000 0000 0011267888999999999999 999999999999987655
No 70
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.26 E-value=0.013 Score=57.08 Aligned_cols=95 Identities=25% Similarity=0.332 Sum_probs=64.0
Q ss_pred CccceeecCCCchhhhhhhhc-CcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhccc
Q 022746 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (292)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~ 137 (292)
+-+|+.||++|++|+.|.++. |=+|.|-.-. ++ -...|.+.+....... +-.
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-------------~d---------~~~fi~nal~pa~v~~-----v~~ 297 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS-------------DD---------PAQFIINALSPAEVSS-----VVV 297 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhCCCCEEEE-----EEE
Confidence 348999999999999999998 6666665321 10 0112222222111000 000
Q ss_pred CCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC
Q 022746 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (292)
Q Consensus 138 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 181 (292)
. .....+.+.||..+.+..|||+|.+++-...-||.+|.|...
T Consensus 298 ~-~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 298 D-EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred e-CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 0 012378999999999999999999999999999999999763
No 71
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.20 E-value=0.0049 Score=44.60 Aligned_cols=32 Identities=41% Similarity=0.637 Sum_probs=29.3
Q ss_pred CCCeEEEEEeeCCccceeecCCCchhhhhhhh
Q 022746 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE 78 (292)
Q Consensus 47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~ 78 (292)
+..+.++|-+..+.+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 45678999999999999999999999999975
No 72
>PRK00468 hypothetical protein; Provisional
Probab=96.16 E-value=0.0065 Score=43.99 Aligned_cols=31 Identities=3% Similarity=-0.142 Sum_probs=28.5
Q ss_pred ceeEEEEEeccCccceeeecCCCccHHHHHHh
Q 022746 249 GYSMFLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 249 ~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
....+++.+..+-+|+|||| +|.+|+.||..
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk-~Gr~i~AIRtv 58 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGK-QGRIAKAIRTV 58 (75)
T ss_pred CeEEEEEEEChhhCcceecC-CChhHHHHHHH
Confidence 45788999999999999999 99999999986
No 73
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.16 E-value=0.011 Score=52.33 Aligned_cols=65 Identities=22% Similarity=0.222 Sum_probs=54.1
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH-HHHHHHHHHHHHHHhcCC
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV-PAVLNALVEIGNQLRENP 221 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~l~~~~ 221 (292)
-+.+.||..+++.+||++|.+|+.|.+++++.|.+- .+..|.|.|.. +.+.+|...|..+-++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-------------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-------------QNGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-------------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 467899999999999999999999999999999982 34678888865 588888888877766663
No 74
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.09 E-value=0.014 Score=49.92 Aligned_cols=39 Identities=28% Similarity=0.402 Sum_probs=34.0
Q ss_pred ccEEEEEec------cCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746 142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (292)
Q Consensus 142 ~~~~~i~IP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 180 (292)
..+-+++|| .++||.|||..|.+.|+|+..|+|+|.|--
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 445677777 679999999999999999999999999864
No 75
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.03 E-value=0.011 Score=52.44 Aligned_cols=60 Identities=28% Similarity=0.427 Sum_probs=48.6
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHH
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL 121 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~ 121 (292)
+.+.||.+.++.+||++|.+|+.|.+++++.|.+..+ ..|.|.+... ..+.+|..+|..+
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~----~~~~~a~~~I~~~ 206 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDE----EDEEIAIEAIKKI 206 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCH----HHHHHHHHHHHHH
Confidence 4578899999999999999999999999999999864 5689999764 3455666655555
No 76
>PRK01064 hypothetical protein; Provisional
Probab=95.96 E-value=0.008 Score=43.84 Aligned_cols=33 Identities=36% Similarity=0.708 Sum_probs=29.6
Q ss_pred CCCeEEEEEeeCCccceeecCCCchhhhhhhhc
Q 022746 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (292)
Q Consensus 47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~t 79 (292)
.+.+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 456889999999999999999999999999854
No 77
>PRK02821 hypothetical protein; Provisional
Probab=95.89 E-value=0.0075 Score=43.86 Aligned_cols=33 Identities=6% Similarity=-0.144 Sum_probs=29.2
Q ss_pred eeEEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746 250 YSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL 283 (292)
Q Consensus 250 ~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~ 283 (292)
...+++.+..+-+|+|||| +|.+|+.||..-++
T Consensus 30 ~~~i~l~v~~~D~GrVIGk-~Gr~i~AIRtlv~a 62 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGR-GGRTATALRTVVAA 62 (77)
T ss_pred cEEEEEEEChhhCcceeCC-CCchHHHHHHHHHH
Confidence 4678999999999999999 99999999987443
No 78
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.77 E-value=0.029 Score=55.32 Aligned_cols=67 Identities=21% Similarity=0.330 Sum_probs=51.9
Q ss_pred ccEEEEEecc-CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746 142 ANTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 142 ~~~~~i~IP~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 219 (292)
.+...+.+|+ +.-|+|||+.|.+|+-|..-||+.+-|. + +...|+|+| +|-.-.-|...|..++.+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d---------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D---------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C---------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3456678888 4669999999999999999999999983 2 345788888 555556677777777766
Q ss_pred C
Q 022746 220 N 220 (292)
Q Consensus 220 ~ 220 (292)
-
T Consensus 271 g 271 (514)
T TIGR03319 271 G 271 (514)
T ss_pred C
Confidence 4
No 79
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.75 E-value=0.011 Score=50.66 Aligned_cols=41 Identities=22% Similarity=0.449 Sum_probs=35.1
Q ss_pred CCCeEEEEEeeC------CccceeecCCCchhhhhhhhcCcEEEEcc
Q 022746 47 AQDVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIAD 87 (292)
Q Consensus 47 ~~~~~~rilvp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 87 (292)
...++-++.||- .+||+|||++|+++|+|+..|+|+|-|..
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 345666777774 67999999999999999999999999974
No 80
>PRK00106 hypothetical protein; Provisional
Probab=95.74 E-value=0.034 Score=54.88 Aligned_cols=67 Identities=22% Similarity=0.368 Sum_probs=52.6
Q ss_pred ccEEEEEecc-CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746 142 ANTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 142 ~~~~~i~IP~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 219 (292)
.+...+.+|+ +.-|+|||+.|.+|+-|..-||+.+-|. + +...|+|+| +|-.-.-|...+..++.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d---------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---D---------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---C---------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3456678888 4669999999999999999999999983 2 345788998 566666677777777766
Q ss_pred C
Q 022746 220 N 220 (292)
Q Consensus 220 ~ 220 (292)
-
T Consensus 292 g 292 (535)
T PRK00106 292 G 292 (535)
T ss_pred C
Confidence 4
No 81
>PRK12704 phosphodiesterase; Provisional
Probab=95.67 E-value=0.036 Score=54.74 Aligned_cols=67 Identities=21% Similarity=0.322 Sum_probs=51.0
Q ss_pred ccEEEEEecc-CcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhc
Q 022746 142 ANTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (292)
Q Consensus 142 ~~~~~i~IP~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 219 (292)
.+...+.+|+ +.-|+|||+.|.+|+-|..-||+.|-|. + +...|.++| ++-.-.-|...+..++.+
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d---------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D---------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C---------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3456677887 5669999999999999999999999983 2 345888999 455545667777666665
Q ss_pred C
Q 022746 220 N 220 (292)
Q Consensus 220 ~ 220 (292)
-
T Consensus 277 g 277 (520)
T PRK12704 277 G 277 (520)
T ss_pred C
Confidence 5
No 82
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.45 E-value=0.029 Score=52.76 Aligned_cols=94 Identities=15% Similarity=0.125 Sum_probs=63.5
Q ss_pred CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746 152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP 230 (292)
Q Consensus 152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p 230 (292)
+-+|.+||++|.+|+.|.++. |-+|.+..-+ .+ ....|.+.|.=..-...
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s----------~d--------------~~~fi~nal~Pa~v~~v----- 295 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS----------ED--------------PAEFVANALSPAKVVSV----- 295 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcC----------CC--------------HHHHHHHhCCCceEEEE-----
Confidence 357999999999999999888 8899987532 22 12222222211100000
Q ss_pred CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746 231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL 288 (292)
Q Consensus 231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~ 288 (292)
.. ...+...+.+.||.+..+.-||| +|.||+-....+|..+.|+
T Consensus 296 ------------~i-~~~~~~~~~v~V~~~~~~~AIGk-~G~Nv~la~~L~~~~idi~ 339 (362)
T PRK12327 296 ------------EV-DDEEEKAARVVVPDYQLSLAIGK-EGQNARLAARLTGWKIDIK 339 (362)
T ss_pred ------------EE-EcCCCcEEEEEEChhhcchhhcC-CChhHHHHHHHHCCeeeEE
Confidence 00 00112468899999999999999 9999999999999887654
No 83
>PRK01064 hypothetical protein; Provisional
Probab=95.41 E-value=0.025 Score=41.26 Aligned_cols=31 Identities=10% Similarity=-0.005 Sum_probs=28.4
Q ss_pred ceeEEEEEeccCccceeeecCCCccHHHHHHh
Q 022746 249 GYSMFLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 249 ~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
....+++.+..+-.|.+||| +|.+|+.|+..
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk-~G~~i~air~l 58 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGK-EGRTIKAIRTL 58 (78)
T ss_pred CEEEEEEEECcccceEEECC-CCccHHHHHHH
Confidence 46788999999999999999 99999999985
No 84
>PRK12704 phosphodiesterase; Provisional
Probab=95.36 E-value=0.035 Score=54.81 Aligned_cols=49 Identities=27% Similarity=0.492 Sum_probs=40.3
Q ss_pred eEEEEEeeC-CccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCC
Q 022746 50 VLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD 103 (292)
Q Consensus 50 ~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~ 103 (292)
.+-.+-+|+ ++-|+||||.|.||+.|+.-||+.|-|.+. + .+|+++|..
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~~~ 259 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGFD 259 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC----C-CeEEEecCC
Confidence 344566777 679999999999999999999999999974 2 457899854
No 85
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.27 E-value=0.031 Score=52.23 Aligned_cols=94 Identities=16% Similarity=0.176 Sum_probs=63.2
Q ss_pred CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746 152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP 230 (292)
Q Consensus 152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p 230 (292)
+-+|.+||++|.+|+.|.++. |-+|.+..-+ .+. ...|.+.|.=.. ...+
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s----------~d~--------------~~fi~nal~Pa~---v~~v-- 293 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS----------DDP--------------AEFIANALSPAK---VISV-- 293 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcC----------CCH--------------HHHHHHhcCCce---EEEE--
Confidence 457999999999999999988 8899987532 220 111212111000 0000
Q ss_pred CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746 231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL 288 (292)
Q Consensus 231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~ 288 (292)
. ... .+.....+.||.+..+..||| +|.|++-....+|..+.|.
T Consensus 294 --~---------i~~--~~~~~~~v~V~~~~~~~aIGk-~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 294 --E---------VLD--EDKHSAEVVVPDDQLSLAIGK-GGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred --E---------EEc--CCCcEEEEEEChHHcchhhcC-CChhHHHHHHHhCCEEEEE
Confidence 0 000 012478899999999999999 9999999999999987664
No 86
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.20 E-value=0.026 Score=40.85 Aligned_cols=31 Identities=6% Similarity=-0.107 Sum_probs=28.4
Q ss_pred ceeEEEEEeccCccceeeecCCCccHHHHHHh
Q 022746 249 GYSMFLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 249 ~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
...++++.+...-.|.|||| +|.+|+.||..
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk-~GRti~AIRTl 58 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGK-QGRTIQAIRTL 58 (76)
T ss_pred CeEEEEEEECcccccceecC-CChhHHHHHHH
Confidence 36788999999999999999 99999999986
No 87
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.17 E-value=0.037 Score=54.60 Aligned_cols=49 Identities=24% Similarity=0.460 Sum_probs=40.3
Q ss_pred CeEEEEEeeC-CccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecC
Q 022746 49 DVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK 102 (292)
Q Consensus 49 ~~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~ 102 (292)
..+-.+.+|+ ++-|+||||.|.||+.++.-||+.|-|.+. + ..|+|++.
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~f 252 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGF 252 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC----C-CeEEecCC
Confidence 3444567788 679999999999999999999999999974 3 45778885
No 88
>PRK00106 hypothetical protein; Provisional
Probab=95.09 E-value=0.042 Score=54.21 Aligned_cols=50 Identities=26% Similarity=0.529 Sum_probs=40.7
Q ss_pred CeEEEEEeeC-CccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCC
Q 022746 49 DVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD 103 (292)
Q Consensus 49 ~~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~ 103 (292)
..+-.+.+|+ ++-|+||||.|.||+.++.-||+.+-|.+. + ..|+++|.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt----p-~~v~lS~fd 274 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT----P-EVVVLSGFD 274 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC----C-CeEEEeCCC
Confidence 3445677788 679999999999999999999999999974 3 347788853
No 89
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.08 E-value=0.016 Score=59.28 Aligned_cols=63 Identities=35% Similarity=0.511 Sum_probs=50.4
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~ 123 (292)
...+.||.+.++.+||+||.+||.|.++||++|++.+. ..|.|.+... ..+.+|..+|..+..
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~------G~v~i~~~~~----~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD------GTVKIAATDG----EAAEAAKERIEGITA 617 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC------ceEEEEcccH----HHHHHHHHHHHHhcc
Confidence 34566699999999999999999999999999988753 5588888653 467777777777654
No 90
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.05 E-value=0.043 Score=52.51 Aligned_cols=94 Identities=16% Similarity=0.145 Sum_probs=62.4
Q ss_pred CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746 152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP 230 (292)
Q Consensus 152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p 230 (292)
+-+|.+||++|.+|+.|.++. |-+|.|..-+ .+ -...|.+.|.=..-....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys----------~D--------------p~~fI~NaLsPA~V~~V~---- 328 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS----------PD--------------PATYIANALSPARVDEVR---- 328 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC----------CC--------------HHHHHHHhcCCceeeEEE----
Confidence 457999999999999999988 8899987532 22 111222211111000000
Q ss_pred CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746 231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL 288 (292)
Q Consensus 231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~ 288 (292)
... .+.....+.||.+..+.-||| +|.||+-....+|..+.|.
T Consensus 329 ------------i~~--~~~k~a~V~V~~~qlslAIGK-~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 329 ------------LVD--PEGRHAHVLVPPDQLSLAIGK-EGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred ------------EEc--CCCcEEEEEEChHhcchhhcC-CChhHHHHHHHHCCEeccc
Confidence 000 112367899999999999999 9999999999998877653
No 91
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.03 E-value=1.2 Score=38.49 Aligned_cols=131 Identities=14% Similarity=0.122 Sum_probs=84.8
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcc
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSE 131 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~ 131 (292)
+.+.++....-+|...+|..++.|-...||+|.+... +..+.|+|++. .+..+...|.+++..-
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~-----~~~~i~~~i~~~l~~i------ 91 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKS-----TAEYIEASINEILSNI------ 91 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHH-----HHHHHHHHHHHHHhhc------
Confidence 3344458888999999999999998889999999853 45799999864 3333334444443321
Q ss_pred hhhcccCCCcccEEEEEeccCcceeee----cCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEE-----cC
Q 022746 132 ASKVAAGHVAANTIRLLIAGSQAGCLI----GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GD 202 (292)
Q Consensus 132 ~~~~~~~~~~~~~~~i~IP~~~vg~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~-----G~ 202 (292)
.+..+.++.-.-..-- -.....++.|++.|++.|...+. +..+.|+ -.
T Consensus 92 -----------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~------------~~~~~i~~~~~~~~ 148 (210)
T PF14611_consen 92 -----------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD------------GNKLKISWLASPEN 148 (210)
T ss_pred -----------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC------------CCeEEEEEEeeccc
Confidence 1334444422111111 11356789999999999997432 2234444 45
Q ss_pred HHHHHHHHHHHHHHHhcCC
Q 022746 203 VPAVLNALVEIGNQLRENP 221 (292)
Q Consensus 203 ~~~v~~A~~~I~~~l~~~~ 221 (292)
...+..|..+|..-+...+
T Consensus 149 ~~~~~~a~RlL~~a~~~~~ 167 (210)
T PF14611_consen 149 EKRADRAKRLLLWALDYNP 167 (210)
T ss_pred cchHHHHHHHHHHhccCCc
Confidence 6788889999988886443
No 92
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.02 E-value=0.028 Score=54.67 Aligned_cols=92 Identities=17% Similarity=0.148 Sum_probs=62.8
Q ss_pred cceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q 022746 153 QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA 231 (292)
Q Consensus 153 ~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~ 231 (292)
-+|.+||++|++|+.|.++. |-+|.|..-+ .+. ...|.+.|.-..-...
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s----------~d~--------------~~fi~nal~pa~v~~v------ 295 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWS----------DDP--------------AQFIINALSPAEVSSV------ 295 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcC----------CCH--------------HHHHHHhCCCCEEEEE------
Confidence 57999999999999999887 8899987532 221 1222222211100000
Q ss_pred CCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746 232 YNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL 288 (292)
Q Consensus 232 ~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~ 288 (292)
.. ......+.+.||....+.-||| +|.||+-..+.+|..+.|.
T Consensus 296 -----------~~--~~~~~~~~v~V~~~~~~~AIGk-~G~Nvrla~~l~g~~idi~ 338 (470)
T PRK09202 296 -----------VV--DEDEHSADVVVPDDQLSLAIGK-NGQNVRLASKLTGWKIDIM 338 (470)
T ss_pred -----------EE--eCCCCEEEEEECcchHHHhhCC-CCeeHHHHHHHHCCeEEEE
Confidence 00 0012377899999999999999 9999999999999887653
No 93
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=94.78 E-value=0.033 Score=52.29 Aligned_cols=93 Identities=13% Similarity=0.122 Sum_probs=63.1
Q ss_pred CcceeeecCCChhHHHHHHhh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 022746 152 SQAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISP 230 (292)
Q Consensus 152 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p 230 (292)
+-+|.+||++|.+|+.|.++. |-+|.+..-+ .+ -...|.+.|.=.. ...+.
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s----------~D--------------~~~fI~Nal~Pa~---V~~V~- 302 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS----------NV--------------PEIFIARALAPAI---ISSVK- 302 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC----------CC--------------HHHHHHHhCCCce---eeEEE-
Confidence 467999999999999999887 8899987532 22 1112222211100 00000
Q ss_pred CCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCccc
Q 022746 231 AYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPLL 288 (292)
Q Consensus 231 ~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~~ 288 (292)
. ..+.....+.||.+..+..||| +|.|++-..+.+|..+-|.
T Consensus 303 -------------i--~~~~~~~~V~V~~~qlslAIGk-~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 303 -------------I--EEEEKKAIVTLLSDQKSKAIGK-NGINIRLASMLTGYEIELN 344 (374)
T ss_pred -------------E--cCCCcEEEEEEChHHhhhhhcC-CChhHHHHHHHhCCEEEEE
Confidence 0 0112477889999999999999 9999999999999887654
No 94
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.51 E-value=0.12 Score=50.65 Aligned_cols=96 Identities=20% Similarity=0.205 Sum_probs=71.2
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcc
Q 022746 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (292)
Q Consensus 108 v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (292)
+.++.+|...|++.|.+........ ..........+.++.+....+||.+|...|+|..+||+.-.+
T Consensus 566 l~~a~~ar~~Il~~m~k~i~~Pr~~----~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v--------- 632 (760)
T KOG1067|consen 566 LQKAREARLQILDIMEKNINSPRGS----DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV--------- 632 (760)
T ss_pred HHhhhHHHHHHHHHHHhhcCCcccC----ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------
Confidence 4556677788888887765432211 122345577889999999999999999999999999954443
Q ss_pred cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhcCC
Q 022746 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRENP 221 (292)
Q Consensus 188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~~ 221 (292)
++..++|-. ++.+..+|++.|..++.+..
T Consensus 633 -----De~t~~i~A~~~~am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 633 -----DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred -----cCceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence 355777765 56788999999999987753
No 95
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=94.41 E-value=0.017 Score=41.36 Aligned_cols=35 Identities=17% Similarity=0.352 Sum_probs=29.8
Q ss_pred CCCeEEEEEeeCCccceeecCCCchhhhhhhhcCc
Q 022746 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (292)
Q Consensus 47 ~~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga 81 (292)
.+...+.+-+..+..|.||||+|.+++.||.-.+.
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 44567888889999999999999999999986654
No 96
>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=94.18 E-value=0.076 Score=36.63 Aligned_cols=35 Identities=29% Similarity=0.462 Sum_probs=28.8
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEE
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI 83 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I 83 (292)
...+.+.+.....|.+||++|.++++|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45566777766799999999999999999988554
No 97
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=93.78 E-value=0.048 Score=38.83 Aligned_cols=37 Identities=35% Similarity=0.587 Sum_probs=29.5
Q ss_pred EEEEeeCCc-----cceeecCCCchhhhhhhhc-CcEEEEccC
Q 022746 52 FRIIVPSRQ-----IGKVIGKEGHRIQKIREET-KATIKIADA 88 (292)
Q Consensus 52 ~rilvp~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~ 88 (292)
.++.|-+.. +|..||++|++|+.|.++. |-+|++-+.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 567777777 9999999999999999999 888877643
No 98
>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=93.78 E-value=0.16 Score=41.32 Aligned_cols=85 Identities=12% Similarity=0.029 Sum_probs=56.8
Q ss_pred CCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH---HHHHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 022746 160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV---LNALVEIGNQLRENPPRQVISISPAYNYSA 236 (292)
Q Consensus 160 k~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v---~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~ 236 (292)
.+|..|++|..+---+|.+-+ +++.. ..|.+.|.+++-+...-...
T Consensus 23 ~~~dli~~lAk~lrKRIvvR~---------------------dps~l~~~e~A~~~I~~ivP~ea~i~di---------- 71 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIRP---------------------DPSVLKPPEEAIKIILEIVPEEAGITDI---------- 71 (145)
T ss_pred cccHHHHHHHHHHhceEEEcC---------------------ChhhcCCHHHHHHHHHHhCCCccCceee----------
Confidence 456788888777766666633 22222 45888888888655211100
Q ss_pred CCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCc
Q 022746 237 IRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQP 286 (292)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~ 286 (292)
+++ ..+-++.|-++.-|.+||| +|.++++|...+|-.-.
T Consensus 72 ------~Fd----~~tGEV~IeaeKPG~ViGk-~g~~~reI~~~tgW~p~ 110 (145)
T cd02410 72 ------YFD----DDTGEVIIEAEKPGLVIGK-GGSTLREITRETGWAPK 110 (145)
T ss_pred ------Eec----CCCcEEEEEEcCCeEEEec-CchhHHHHHHHhCCeeE
Confidence 011 1244677888999999999 99999999999986543
No 99
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.34 E-value=0.034 Score=58.30 Aligned_cols=72 Identities=21% Similarity=0.168 Sum_probs=57.5
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCC-CCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI-ARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~-~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~ 126 (292)
..-++.+|.....+|||++|.+|..++.-||+.|.+.... .+..||.+++.|.++ ..+-|...|.-.+.+.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~-----~~r~a~~~I~~~i~Dpd 1412 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPP-----SQRVATSPIGLPIIDPD 1412 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCCh-----hhhhhhccccceeecCC
Confidence 4557889999999999999999999999999999999743 345799999999986 35556665655555443
No 100
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.01 E-value=1.1 Score=38.60 Aligned_cols=65 Identities=18% Similarity=0.237 Sum_probs=56.3
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 220 (292)
...+.++....-.+...+|..++.|....||+|.+.. ....+.|+|+...+..+...|.+++...
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~------------~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR------------SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec------------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 4566667888889999999999999888999999863 4679999999999999999999998776
No 101
>PRK12705 hypothetical protein; Provisional
Probab=92.95 E-value=0.26 Score=48.39 Aligned_cols=66 Identities=23% Similarity=0.285 Sum_probs=44.2
Q ss_pred cEEEEEeccC-cceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhcC
Q 022746 143 NTIRLLIAGS-QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLREN 220 (292)
Q Consensus 143 ~~~~i~IP~~-~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~ 220 (292)
+...+.+|++ .-|+|||+.|.+|+.+...||+.+-|. +.| ..|++++- +..-+.|...+..++.+.
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---dtp---------~~V~ls~fdp~rreia~~~l~~Li~dg 265 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---DTP---------EAVVISSFNPIRREIARLTLEKLLADG 265 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---CCc---------cchhhcccCccchHHHHHHHHHHHhcC
Confidence 3456778875 559999999999999999999999984 322 34555553 233333455555554443
No 102
>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=92.19 E-value=0.15 Score=36.85 Aligned_cols=35 Identities=17% Similarity=0.373 Sum_probs=28.4
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEE
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i 85 (292)
.+.+-+..+..|.+|||+|+++..||--++.-++-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 35566678899999999999999999887755543
No 103
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=91.96 E-value=0.055 Score=38.73 Aligned_cols=31 Identities=3% Similarity=-0.172 Sum_probs=27.2
Q ss_pred eeEEEEEeccCccceeeecCCCccHHHHHHhh
Q 022746 250 YSMFLMQNTRYFVTAIFAVLSSFNIFFLITTS 281 (292)
Q Consensus 250 ~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S 281 (292)
...+.+.+..+..|.|||| .|.+++.||.-.
T Consensus 28 ~~~i~v~i~~ed~g~lIGk-~G~tl~ALq~l~ 58 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGK-HGKTLNALQYLV 58 (73)
T ss_dssp TTEEEEEEESCCCHHHCTT-HHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECC-CCeeHHHHHHHH
Confidence 4577888999999999999 999999998653
No 104
>PRK12705 hypothetical protein; Provisional
Probab=91.30 E-value=0.28 Score=48.21 Aligned_cols=46 Identities=30% Similarity=0.472 Sum_probs=36.3
Q ss_pred EEEEeeC-CccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecC
Q 022746 52 FRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK 102 (292)
Q Consensus 52 ~rilvp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~ 102 (292)
-.+-+|+ ++-|+||||.|.||+.++..||+.|-|.+.. ..|++++.
T Consensus 200 s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~f 246 (508)
T PRK12705 200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSF 246 (508)
T ss_pred eeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhccc
Confidence 3455566 6799999999999999999999999999742 33556654
No 105
>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=91.19 E-value=0.083 Score=38.22 Aligned_cols=35 Identities=40% Similarity=0.608 Sum_probs=29.9
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEE
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIK 84 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~ 84 (292)
..+.+.+..+..|.|||++|++|++|.+..+-.+.
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 45778899999999999999999999988765553
No 106
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=90.86 E-value=0.16 Score=43.31 Aligned_cols=56 Identities=32% Similarity=0.440 Sum_probs=47.7
Q ss_pred CCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746 58 SRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (292)
Q Consensus 58 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~ 125 (292)
+..+|+|+||+|.+--.|+.-|.++|.+.+. .|.|-|. ++++.-|...|+.++...
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~-------kIHiLG~-----~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS-------KIHILGA-----FQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecCc-------eEEEeec-----chhhHHHHHhhHhhhccC
Confidence 4579999999999999999999999999864 4899998 457888888888888654
No 107
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.62 E-value=0.21 Score=35.52 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=30.2
Q ss_pred EEEEEeccCc-----ceeeecCCChhHHHHHHhh-CCeEEEeC
Q 022746 144 TIRLLIAGSQ-----AGCLIGMSGQNIEKLRNSS-GATIVILA 180 (292)
Q Consensus 144 ~~~i~IP~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~ 180 (292)
...+.|-... +|.+||++|.+|+.|.++. |-+|++..
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 4566777777 8999999999999999999 99999874
No 108
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=89.74 E-value=0.2 Score=42.83 Aligned_cols=129 Identities=18% Similarity=0.184 Sum_probs=85.1
Q ss_pred hhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchh-h---cccC---CCcccEEE
Q 022746 74 KIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEAS-K---VAAG---HVAANTIR 146 (292)
Q Consensus 74 ~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~-~---~~~~---~~~~~~~~ 146 (292)
-|-+..+.+|.+.- ..|.|.+.-..+..+.++.+++...|...+...+....-.. + ++.. -..-.+.+
T Consensus 98 Pive~lklqiRmNl-----K~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALlrlddlflesFEi~dVKtL~ 172 (252)
T KOG3273|consen 98 PIVEHLKLQIRMNL-----KARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALLRLDDLFLESFEIKDVKTLK 172 (252)
T ss_pred HHHHhhhheeEeec-----ccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHHhhhhhhheeeeeccccccc
Confidence 34455566666652 23566666555555577888888888888876654321100 0 0000 00000111
Q ss_pred EEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 022746 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (292)
Q Consensus 147 i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 221 (292)
=.=-+..+|+|+||+|.+--.|.+.|-++|.+. +..+.|-|..+++.-|...|+.++-..+
T Consensus 173 GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla--------------d~kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 173 GDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA--------------DSKIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred chhHHHHHHHhhcCCCcceeeeeccceeEEEec--------------CceEEEeecchhhHHHHHhhHhhhccCC
Confidence 111245679999999999989999999999874 4689999999999999999999988774
No 109
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=89.65 E-value=1.1 Score=39.57 Aligned_cols=45 Identities=22% Similarity=0.508 Sum_probs=39.7
Q ss_pred EEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCC
Q 022746 54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN 104 (292)
Q Consensus 54 ilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~ 104 (292)
+.|++..|.++||++|+.++.|.++|+|.|-+-.+ ..|-|.+..+
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~ 194 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE 194 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc
Confidence 67899999999999999999999999999999865 3477888765
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=89.45 E-value=0.45 Score=34.41 Aligned_cols=30 Identities=3% Similarity=-0.140 Sum_probs=24.8
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHhhC
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITTSS 282 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~ 282 (292)
.+.+.+..+..|.+||| .|++++.||--.+
T Consensus 25 ~i~i~i~~~~~g~LIGk-~G~tL~AlQ~L~~ 54 (77)
T cd02414 25 TVEVNISGDDIGLLIGK-RGKTLDALQYLAN 54 (77)
T ss_pred EEEEEEecCCCCeEECC-CCccHHHHHHHHH
Confidence 45677778889999999 9999999986543
No 111
>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=89.11 E-value=0.41 Score=35.14 Aligned_cols=36 Identities=19% Similarity=0.423 Sum_probs=30.6
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEc
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA 86 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 86 (292)
.+++.|....-|.|||++|++|++|+++..-...+.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 378888999999999999999999999876655554
No 112
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=88.91 E-value=1 Score=39.66 Aligned_cols=62 Identities=21% Similarity=0.282 Sum_probs=46.6
Q ss_pred EEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHH-HHHHHHHHHHHHhc
Q 022746 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPA-VLNALVEIGNQLRE 219 (292)
Q Consensus 145 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~-v~~A~~~I~~~l~~ 219 (292)
.-+.|+...+.++||++|+.++.|.+.|+|+|.+- .+..|-|.|..+. ...|...|..+=.+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG-------------~NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG-------------QNGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe-------------cCCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 55788889999999999999999999999999984 3456777777663 44455555444333
No 113
>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=88.84 E-value=0.62 Score=31.91 Aligned_cols=32 Identities=13% Similarity=-0.066 Sum_probs=25.3
Q ss_pred eEEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746 251 SMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL 283 (292)
Q Consensus 251 ~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~ 283 (292)
....+.+.....|.+||| +|++|+.|+...+.
T Consensus 25 ~~~~i~~~~~~~g~lIGk-~G~~l~~l~~l~~~ 56 (68)
T cd02409 25 IEIIIVVARGQPGLVIGK-KGQNIRALQKLLQK 56 (68)
T ss_pred EEEEEEECCCCCceEECC-CCccHHHHHHHHHH
Confidence 445555665568999999 99999999988763
No 114
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=88.53 E-value=0.2 Score=36.13 Aligned_cols=31 Identities=6% Similarity=-0.106 Sum_probs=27.0
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHhhCC
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITTSSL 283 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~ 283 (292)
...+.+....-|.|||+ +|++|++|.+...-
T Consensus 26 ~~~i~i~~~~~~ivIGk-~G~~ik~i~~~~~k 56 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGK-KGSNIKKIREELRK 56 (78)
T ss_dssp EEEEEEEESSHHHHHTG-GGHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHh-hhHHHHHHHHHHHH
Confidence 56777889999999999 99999999987653
No 115
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=88.15 E-value=0.56 Score=39.22 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=31.9
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 88 (292)
--+-|+|-... |.-|||+|++|++|++..|-+|.+-+.
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 34567787777 999999999999999999988877653
No 116
>PRK13764 ATPase; Provisional
Probab=88.11 E-value=0.79 Score=46.10 Aligned_cols=44 Identities=20% Similarity=0.348 Sum_probs=39.3
Q ss_pred ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCC
Q 022746 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP 185 (292)
Q Consensus 142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p 185 (292)
.....+.||...++.+|||+|.+|++|.++.|.+|.|.+.+..+
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 45788999999999999999999999999999999998766543
No 117
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.72 E-value=0.31 Score=46.96 Aligned_cols=36 Identities=36% Similarity=0.553 Sum_probs=33.3
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcCcEEEEcc
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 87 (292)
..+.||...++.+|||+|.+|++|++..|.+|.+..
T Consensus 488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 567789999999999999999999999999999974
No 118
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.56 E-value=0.42 Score=46.08 Aligned_cols=41 Identities=15% Similarity=0.227 Sum_probs=37.2
Q ss_pred ccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCC
Q 022746 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (292)
Q Consensus 142 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 182 (292)
.....+.||...++.+|||+|.+|++|.++.|.+|.+.+.+
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 34688999999999999999999999999999999998654
No 119
>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=87.34 E-value=2.4 Score=34.51 Aligned_cols=93 Identities=14% Similarity=0.300 Sum_probs=60.8
Q ss_pred cCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcccEE
Q 022746 66 GKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTI 145 (292)
Q Consensus 66 Gk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~ 145 (292)
=.+|.-|+.|-++..-+|.|-.+ +.. +..-.+|...|.+++-++..-..-.+ ...+-
T Consensus 22 ~~~~dli~~lAk~lrKRIvvR~d--------------ps~--l~~~e~A~~~I~~ivP~ea~i~di~F-------d~~tG 78 (145)
T cd02410 22 AEDGDLVKDLAKDLRKRIVIRPD--------------PSV--LKPPEEAIKIILEIVPEEAGITDIYF-------DDDTG 78 (145)
T ss_pred hcccHHHHHHHHHHhceEEEcCC--------------hhh--cCCHHHHHHHHHHhCCCccCceeeEe-------cCCCc
Confidence 35567788888877766666432 110 11124677788887754422111001 01245
Q ss_pred EEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC
Q 022746 146 RLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (292)
Q Consensus 146 ~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 181 (292)
++.|-...-|.+||++|.++++|..+||-.-.+...
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 777888888999999999999999999998888653
No 120
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=87.00 E-value=1.3 Score=39.85 Aligned_cols=52 Identities=15% Similarity=0.226 Sum_probs=46.2
Q ss_pred eeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746 155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (292)
Q Consensus 155 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 220 (292)
-++||.+|+++|.|+--|.|.|-|. ...|.+.|....+..+...+.+++...
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq--------------G~TVsaiGpfkGlkevr~IV~DcM~Ni 212 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ--------------GNTVSAIGPFKGLKEVRKIVEDCMKNI 212 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee--------------CcEEEeecCcchHHHHHHHHHHHHhcc
Confidence 4799999999999999999999983 358999999999999999998888774
No 121
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=86.41 E-value=1.6 Score=43.11 Aligned_cols=66 Identities=24% Similarity=0.263 Sum_probs=49.6
Q ss_pred CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhc
Q 022746 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (292)
Q Consensus 48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~ 124 (292)
..+...+.++.+....+||.+|-..|+|+.+||+.-.+.+ ..+.|-.... .+..+|...|..++..
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe-------~t~~i~A~~~----~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE-------GTFSIFAPTQ----AAMEEAKEFIDGIIKD 660 (760)
T ss_pred CceeeEEeecchhhheeecCccceeeeEeeeccceeeecC-------ceEEEEecCH----HHHHHHHHHHHHHhcC
Confidence 4677889999999999999999999999999996555544 4577777542 3455666666655543
No 122
>PRK13764 ATPase; Provisional
Probab=86.41 E-value=0.47 Score=47.66 Aligned_cols=38 Identities=37% Similarity=0.537 Sum_probs=34.5
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEcc
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 87 (292)
-...+.||...++.+|||+|.+|++|++..|.+|.|..
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 34567889999999999999999999999999999974
No 123
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.16 E-value=1 Score=32.99 Aligned_cols=28 Identities=7% Similarity=-0.155 Sum_probs=24.8
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHh
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
.+++.|-...-|.|||+ +|++|++|++.
T Consensus 31 ~i~I~I~tarPg~vIG~-~G~~i~~L~~~ 58 (81)
T cd02413 31 RTEIIIRATRTQNVLGE-KGRRIRELTSL 58 (81)
T ss_pred eEEEEEEeCCCceEECC-CchhHHHHHHH
Confidence 46788888899999999 99999999875
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=84.90 E-value=0.76 Score=35.63 Aligned_cols=30 Identities=30% Similarity=0.592 Sum_probs=26.1
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcCc
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga 81 (292)
+++.|-...-|.|||++|++|++|++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 678888888999999999999999987543
No 125
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=84.64 E-value=1.7 Score=39.17 Aligned_cols=50 Identities=10% Similarity=0.155 Sum_probs=35.6
Q ss_pred ceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 022746 62 GKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (292)
Q Consensus 62 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~ 123 (292)
-++||.+|++++.|+--|.|.|-|+.. .|.+-|.- ..+.++...+.+.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~-------TVsaiGpf-----kGlkevr~IV~DcM~ 210 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN-------TVSAIGPF-----KGLKEVRKIVEDCMK 210 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc-------EEEeecCc-----chHHHHHHHHHHHHh
Confidence 469999999999999999999999864 35555653 244444444444443
No 126
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=83.96 E-value=2.6 Score=41.18 Aligned_cols=143 Identities=12% Similarity=0.093 Sum_probs=92.2
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCc
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~ 130 (292)
.+.|.||...+-.|||.||..|.+.....++.|++.... ++ |. +++ . +
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~----~~-----~q-------s~~----------~--d---- 497 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFY----KF-----GQ-------SQW----------H--D---- 497 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhh----hc-----ch-------hhh----------h--c----
Confidence 467999999999999999999999999999888877431 00 00 000 0 0
Q ss_pred chhhcccCCCcccEEEEEeccCcceeeecCCChhHHHHHHhh----CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 022746 131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS----GATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206 (292)
Q Consensus 131 ~~~~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~t----ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v 206 (292)
.+-+..|.+-.+.|+|++......+++.+ ...|++.+ ..-+++++.|-...+
T Consensus 498 -------------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~-----------~~~sI~~v~~~~~~I 553 (657)
T COG5166 498 -------------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP-----------QSTSIFTVDIYSDEI 553 (657)
T ss_pred -------------ceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC-----------CceEEEEEcccccHH
Confidence 24566777777889999988888888655 45666643 234588888876655
Q ss_pred HHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEeccCccceeee---cCCCccHHHHHHh
Q 022746 207 LNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFA---VLSSFNIFFLITT 280 (292)
Q Consensus 207 ~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIG---k~gG~~Ik~I~~~ 280 (292)
.+-.. -...+...+ ....+.+|.+.++.-+| - .|++|-.+...
T Consensus 554 ~rv~k-ne~v~~~~p-----------------------------~~~~~y~~se~h~~g~gena~-R~~ni~~~t~~ 599 (657)
T COG5166 554 ERVIK-NETVLLEFP-----------------------------AEMHFYVPSEIHKKGIGENAF-RGENIQRVTKL 599 (657)
T ss_pred HHHhh-ccceEEecc-----------------------------cccccccchhhhhccCCcccc-cccchhhhhhh
Confidence 43332 111122211 23345577788888888 4 56776665443
No 127
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=83.72 E-value=1.1 Score=33.10 Aligned_cols=28 Identities=29% Similarity=0.484 Sum_probs=23.7
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhc
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREET 79 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~t 79 (292)
+++.+....-|.+||++|++|++|++..
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5666666889999999999999998874
No 128
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=83.58 E-value=2.5 Score=41.32 Aligned_cols=91 Identities=11% Similarity=-0.020 Sum_probs=62.8
Q ss_pred eeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 022746 156 CLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYS 235 (292)
Q Consensus 156 ~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~ 235 (292)
.++-+.|..|++|..+.--+|.+-++... . ..-+.|...|.+++-++..-.... |
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dPsv---------------l---~~~e~A~~~I~eivP~ea~i~~i~------F- 96 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDPSV---------------L---KPPEEARKIILEIVPEEAGITDIY------F- 96 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCchh---------------c---CCHHHHHHHHHHhCccccCceeEE------e-
Confidence 45567889999999999888887542110 0 112468888888886552111000 0
Q ss_pred CCCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCC
Q 022746 236 AIRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQ 285 (292)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~ 285 (292)
+..+-++.|-++.-|.+||| +|++.++|.+.+|-.-
T Consensus 97 -------------d~~tGEViIea~KPGlvigk-~g~~~reI~~~tgW~p 132 (637)
T COG1782 97 -------------DDDTGEVIIEAKKPGLVIGK-GGSTLREITAETGWAP 132 (637)
T ss_pred -------------cCCCceEEEEecCCceEEec-CchHHHHHHHHhCCcc
Confidence 11345778889999999999 9999999999988653
No 129
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=82.97 E-value=0.39 Score=50.84 Aligned_cols=74 Identities=23% Similarity=0.195 Sum_probs=60.2
Q ss_pred cccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (292)
Q Consensus 141 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 220 (292)
...+-++.+|-....++||++|.+|..++.-||+.|.+..- -+. ...+|.+.+.|.++.++.|...|.-.+.|-
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~----Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPD----NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCc----cchhhhcccCCCChhhhhhhccccceeecC
Confidence 34456788999899999999999999999999999998541 111 146899999999999999988887666554
No 130
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=80.74 E-value=1.4 Score=38.74 Aligned_cols=31 Identities=35% Similarity=0.529 Sum_probs=26.8
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhc
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~t 79 (292)
...+++.|....-|.|||++|++|++|++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 3457888999999999999999999888764
No 131
>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=80.72 E-value=3.2 Score=42.20 Aligned_cols=92 Identities=10% Similarity=-0.030 Sum_probs=60.9
Q ss_pred eecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q 022746 157 LIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSA 236 (292)
Q Consensus 157 IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~p~~n~~~ 236 (292)
.+-..|..|++|..+---+|.|-++.. +.-++ .+|.+.|.+++-++..-....
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~~---------------~~~~~---~~~~~~i~~~~~~~~~~~~~~--------- 89 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDPS---------------VLLPP---EEAIEKIKEIVPEEAGITDIY--------- 89 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecChh---------------hcCCH---HHHHHHHHHhCCCcCCceeEE---------
Confidence 344667889999888877777743211 11111 358888888886652111000
Q ss_pred CCCCCCCCCCCCceeEEEEEeccCccceeeecCCCccHHHHHHhhCCCCcc
Q 022746 237 IRPAQPFVEPTSGYSMFLMQNTRYFVTAIFAVLSSFNIFFLITTSSLGQPL 287 (292)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S~~~~~~ 287 (292)
. +..+-+|.|-++.-|.|||| +|.++++|.+.+|-.-.+
T Consensus 90 -------f----~~~~~~v~i~~~~p~~~~~~-~~~~~~~i~~~~~w~~~~ 128 (630)
T TIGR03675 90 -------F----DDVTGEVIIEAEKPGLVIGK-GGSTLREITAETGWTPKV 128 (630)
T ss_pred -------e----cCCCceEEEEEcCCeEEEec-CcchHHHHHHHhCCeeeE
Confidence 0 12345778889999999999 999999999999865443
No 132
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=80.45 E-value=2.4 Score=35.49 Aligned_cols=36 Identities=19% Similarity=0.340 Sum_probs=31.5
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeC
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 180 (292)
.+-++|-... |.-|||+|.+++.+++..|-+|.+.-
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 5667776667 99999999999999999999999874
No 133
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=79.61 E-value=4.9 Score=39.42 Aligned_cols=96 Identities=17% Similarity=0.304 Sum_probs=67.9
Q ss_pred eeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCcc
Q 022746 63 KVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAA 142 (292)
Q Consensus 63 ~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~ 142 (292)
.++-+.|.-|++|-++..-+|.+..+. .+ +..-.+|...|.+++-++..-....+ ..
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP------sv----------l~~~e~A~~~I~eivP~ea~i~~i~F-------d~ 98 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP------SV----------LKPPEEARKIILEIVPEEAGITDIYF-------DD 98 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc------hh----------cCCHHHHHHHHHHhCccccCceeEEe-------cC
Confidence 456688999999999988888876431 01 12235788888888755433221111 12
Q ss_pred cEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCC
Q 022746 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (292)
Q Consensus 143 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 181 (292)
.+-++.|-.+.-|.+|||+|++.++|..+||-.-++...
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 245788888899999999999999999999987777643
No 134
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.38 E-value=2.1 Score=31.54 Aligned_cols=27 Identities=11% Similarity=-0.153 Sum_probs=22.5
Q ss_pred EEEEeccCccceeeecCCCccHHHHHHh
Q 022746 253 FLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 253 ~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
.++.|-...-|.+||+ +|++|++|++.
T Consensus 40 i~V~I~t~~pg~iIGk-~G~~I~~l~~~ 66 (85)
T cd02411 40 TQITIYAERPGMVIGR-GGKNIRELTEI 66 (85)
T ss_pred EEEEEEECCCCceECC-CchhHHHHHHH
Confidence 4555666888999999 99999999876
No 135
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=78.67 E-value=1.8 Score=33.57 Aligned_cols=29 Identities=10% Similarity=-0.187 Sum_probs=24.7
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHhh
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITTS 281 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S 281 (292)
.++|.|-...-|.|||+ .|++|++|++.-
T Consensus 62 ~i~I~I~t~rPg~vIG~-~G~~i~~L~~~l 90 (109)
T cd02412 62 RVEVTIHTARPGIIIGK-KGAGIEKLRKEL 90 (109)
T ss_pred CEEEEEEeCCCCcccCC-chHHHHHHHHHH
Confidence 36777778889999999 999999998763
No 136
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=71.67 E-value=3.8 Score=36.03 Aligned_cols=28 Identities=11% Similarity=-0.196 Sum_probs=24.4
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHh
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
.+.|.|-...-|.|||| +|++|+.|++.
T Consensus 52 ~~~V~I~aarPg~VIGk-~G~~I~~L~~~ 79 (233)
T COG0092 52 GTRVTIHAARPGLVIGK-KGSNIEKLRKE 79 (233)
T ss_pred ceEEEEEeCCCcceEcC-CCccHHHHHHH
Confidence 56777888899999999 99999998764
No 137
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=65.73 E-value=18 Score=36.91 Aligned_cols=96 Identities=15% Similarity=0.276 Sum_probs=62.5
Q ss_pred eecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhcccCCCccc
Q 022746 64 VIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAAN 143 (292)
Q Consensus 64 IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~ 143 (292)
.+=.+|..|++|-++..-+|.|... +.. +..-.+|...|.+++-++..-..-.+ ...
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~--------------~~~--~~~~~~~~~~i~~~~~~~~~~~~~~f-------~~~ 93 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPD--------------PSV--LLPPEEAIEKIKEIVPEEAGITDIYF-------DDV 93 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecC--------------hhh--cCCHHHHHHHHHHhCCCcCCceeEEe-------cCC
Confidence 3446677778887777766666532 110 11124677777777654432111001 122
Q ss_pred EEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCC
Q 022746 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (292)
Q Consensus 144 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 182 (292)
+-++.|-...-|.+|||+|.++++|..+||-.-.+....
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 457888888999999999999999999999988886543
No 138
>PF08067 ROKNT: ROKNT (NUC014) domain; InterPro: IPR012987 This presumed domain is found at the N terminus of RNP K-like proteins that also contain KH domains IPR004088 from INTERPRO [].
Probab=63.70 E-value=3.1 Score=26.04 Aligned_cols=31 Identities=23% Similarity=0.254 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCCCCccCCCCccCCCCccccCCCC
Q 022746 13 VSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQ 48 (292)
Q Consensus 13 ~~~~~~~~~~~~~~~kr~~~~~~~e~~~~~~~~~~~ 48 (292)
+...+++.+.+ +||+.+|++ +.++.+.+++.
T Consensus 9 ~e~tF~n~etN---GKrpaeDme--Ee~afKRsrNt 39 (43)
T PF08067_consen 9 EEETFSNTETN---GKRPAEDME--EEQAFKRSRNT 39 (43)
T ss_pred ccccccccccC---CCCchhhHH--HHHHhcccccc
Confidence 56678888776 599999995 66666666553
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=63.17 E-value=9 Score=34.30 Aligned_cols=32 Identities=13% Similarity=-0.076 Sum_probs=25.8
Q ss_pred eeEEEEEecc-CccceeeecCCCccHHHHHHhhC
Q 022746 250 YSMFLMQNTR-YFVTAIFAVLSSFNIFFLITTSS 282 (292)
Q Consensus 250 ~~~~~v~iP~-~~vG~IIGk~gG~~Ik~I~~~S~ 282 (292)
.+...+.|.. ++-+-|||| +|++||+|...+.
T Consensus 220 ~i~~~i~v~~~s~k~iiig~-~g~~ik~i~~~ar 252 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGK-NGSMIKAIGIAAR 252 (270)
T ss_pred EEEEEEEECcCCceeEEEcC-CcHHHHHHHHHHH
Confidence 4667788886 555999999 9999999987654
No 140
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=61.72 E-value=24 Score=30.55 Aligned_cols=29 Identities=3% Similarity=-0.181 Sum_probs=24.4
Q ss_pred eEEEEEeccCccceeeecCCCccHHHHHHh
Q 022746 251 SMFLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 251 ~~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
..+.+.+-.+..|.+||+ .|.+++.||--
T Consensus 91 ~~v~~~i~~~~~~~LIG~-~Gk~LdALQ~L 119 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGK-HGKTLDALQYL 119 (208)
T ss_pred cEEEEEecCCchhhhhcc-CCcchHHHHHH
Confidence 356677777889999999 99999999854
No 141
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=61.02 E-value=6.4 Score=34.04 Aligned_cols=36 Identities=14% Similarity=0.306 Sum_probs=29.5
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEE
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i 85 (292)
-.+.+-+..+..+.|||+.|+++..||--+.+.++-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 345566677779999999999999999998876655
No 142
>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=60.12 E-value=8.4 Score=33.13 Aligned_cols=31 Identities=29% Similarity=0.529 Sum_probs=26.5
Q ss_pred EEEEEeeCCccceeecCCCchhhhhhhhcCc
Q 022746 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (292)
Q Consensus 51 ~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga 81 (292)
.+++.|....-|.|||++|+.|++|++...-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 4778888889999999999999999887543
No 143
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=59.82 E-value=8.4 Score=33.43 Aligned_cols=31 Identities=29% Similarity=0.482 Sum_probs=25.4
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcCcE
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKAT 82 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~ 82 (292)
+.+.|....-|.+||++|++|++|++...-.
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 5566666889999999999999999886543
No 144
>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=59.29 E-value=9.2 Score=34.24 Aligned_cols=30 Identities=30% Similarity=0.305 Sum_probs=23.6
Q ss_pred eEEEEEeeC-CccceeecCCCchhhhhhhhc
Q 022746 50 VLFRIIVPS-RQIGKVIGKEGHRIQKIREET 79 (292)
Q Consensus 50 ~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~t 79 (292)
+...++|.. ++-+.|||++|+.||+|..+.
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 566778876 457889999999999876654
No 145
>PRK15494 era GTPase Era; Provisional
Probab=58.94 E-value=11 Score=35.02 Aligned_cols=32 Identities=16% Similarity=0.036 Sum_probs=25.5
Q ss_pred eeEEEEEecc-CccceeeecCCCccHHHHHHhhC
Q 022746 250 YSMFLMQNTR-YFVTAIFAVLSSFNIFFLITTSS 282 (292)
Q Consensus 250 ~~~~~v~iP~-~~vG~IIGk~gG~~Ik~I~~~S~ 282 (292)
.+...+.|.. ++-+-|||| +|++||+|...+.
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~-~g~~ik~i~~~ar 304 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGK-NGSKIKEIGAKSR 304 (339)
T ss_pred EEEEEEEECCCCceeEEEcC-CcHHHHHHHHHHH
Confidence 3567788886 555899999 9999999987654
No 146
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=58.68 E-value=12 Score=36.66 Aligned_cols=127 Identities=12% Similarity=0.081 Sum_probs=77.8
Q ss_pred eeecCCCchhhhhhhhcCcEEEEc--cCCCCCCceEEEE-ecCCCCcchhHHHHHHHHHHHHHhcCCCCCcchhhcccCC
Q 022746 63 KVIGKEGHRIQKIREETKATIKIA--DAIARHEERVIII-SSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGH 139 (292)
Q Consensus 63 ~IIGk~G~~Ik~I~~~tga~I~i~--~~~~~~~ervv~I-~G~~~~~~v~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 139 (292)
+|=||+--.+.+|++...|.+.+. +. .+.++.+. .|..- +-.+++. .+..+.
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~---~gs~~~~~~~g~~~-----~F~k~~~----~~~~EF------------- 447 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSS---TGSIVETNGIGEKM-----SFSKKLS----IPPTEF------------- 447 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEec---CCcEEEEeccCcch-----hhHHHhc----CCcccC-------------
Confidence 677876555999999999985554 32 12233332 33211 1112221 111111
Q ss_pred CcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH---HHHHHHHHHHHHH
Q 022746 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV---PAVLNALVEIGNQ 216 (292)
Q Consensus 140 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~---~~v~~A~~~I~~~ 216 (292)
.....+.||...|..|||.||..|++.+...++.|++...-.++..+ --..|.|..+. +++.-+..-++++
T Consensus 448 --pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~----~~dNV~I~~PrKn~~ni~~~KNd~~~~ 521 (657)
T COG5166 448 --PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQ----WHDNVLIEAPRKNQDNISGKKNDKLDK 521 (657)
T ss_pred --chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhh----hhcceEEECCccCccchhcccccHHHH
Confidence 12578999999999999999999999999999999976543444321 11235666543 3555566667777
Q ss_pred HhcC
Q 022746 217 LREN 220 (292)
Q Consensus 217 l~~~ 220 (292)
+.+.
T Consensus 522 V~~~ 525 (657)
T COG5166 522 VKQQ 525 (657)
T ss_pred Hhhh
Confidence 7754
No 147
>CHL00048 rps3 ribosomal protein S3
Probab=58.40 E-value=9.1 Score=33.43 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=26.2
Q ss_pred eEEEEEeeCCccceeecCCCchhhhhhhhcC
Q 022746 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (292)
Q Consensus 50 ~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tg 80 (292)
..+++.|-...-|.|||++|++|++|++...
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 3467777788899999999999999998764
No 148
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=57.60 E-value=9.2 Score=33.52 Aligned_cols=32 Identities=22% Similarity=0.460 Sum_probs=26.8
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcCcEE
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATI 83 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I 83 (292)
+++.|....-|.|||++|+.|++|++...-.+
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 67778888899999999999999998765443
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=57.51 E-value=13 Score=33.50 Aligned_cols=32 Identities=9% Similarity=-0.166 Sum_probs=25.1
Q ss_pred eeEEEEEecc-CccceeeecCCCccHHHHHHhhC
Q 022746 250 YSMFLMQNTR-YFVTAIFAVLSSFNIFFLITTSS 282 (292)
Q Consensus 250 ~~~~~v~iP~-~~vG~IIGk~gG~~Ik~I~~~S~ 282 (292)
.+...+.|.. ++-+-|||| +|++||+|...+.
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~-~g~~i~~i~~~ar 257 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGK-GGAMLKKIGTEAR 257 (292)
T ss_pred EEEEEEEEccCCceeEEEeC-CcHHHHHHHHHHH
Confidence 3666777775 555899999 9999999987654
No 150
>COG1159 Era GTPase [General function prediction only]
Probab=55.16 E-value=15 Score=33.72 Aligned_cols=32 Identities=13% Similarity=-0.137 Sum_probs=25.5
Q ss_pred eeEEEEEecc-CccceeeecCCCccHHHHHHhhC
Q 022746 250 YSMFLMQNTR-YFVTAIFAVLSSFNIFFLITTSS 282 (292)
Q Consensus 250 ~~~~~v~iP~-~~vG~IIGk~gG~~Ik~I~~~S~ 282 (292)
.+...+.|+. ++=|-|||| +|++||+|-..+.
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk-~G~~iK~IG~~AR 260 (298)
T COG1159 228 KIHATIYVERESQKGIIIGK-NGAMIKKIGTAAR 260 (298)
T ss_pred EEEEEEEEecCCccceEECC-CcHHHHHHHHHHH
Confidence 4566778886 555999999 9999999987664
No 151
>PRK15494 era GTPase Era; Provisional
Probab=53.92 E-value=12 Score=34.78 Aligned_cols=30 Identities=23% Similarity=0.413 Sum_probs=23.4
Q ss_pred eEEEEEeeC-CccceeecCCCchhhhhhhhc
Q 022746 50 VLFRIIVPS-RQIGKVIGKEGHRIQKIREET 79 (292)
Q Consensus 50 ~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~t 79 (292)
+...|+|.. ++-+.|||++|+.||+|..+.
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 556788877 457889999999999876543
No 152
>COG1159 Era GTPase [General function prediction only]
Probab=53.59 E-value=14 Score=33.92 Aligned_cols=31 Identities=35% Similarity=0.476 Sum_probs=23.5
Q ss_pred CeEEEEEeeC-CccceeecCCCchhhhhhhhc
Q 022746 49 DVLFRIIVPS-RQIGKVIGKEGHRIQKIREET 79 (292)
Q Consensus 49 ~~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~t 79 (292)
.+...|+|+. ++=|-||||+|+.||+|-...
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 4455677776 458899999999999876543
No 153
>PRK00089 era GTPase Era; Reviewed
Probab=50.40 E-value=15 Score=33.09 Aligned_cols=30 Identities=37% Similarity=0.484 Sum_probs=22.6
Q ss_pred eEEEEEeeC-CccceeecCCCchhhhhhhhc
Q 022746 50 VLFRIIVPS-RQIGKVIGKEGHRIQKIREET 79 (292)
Q Consensus 50 ~~~rilvp~-~~vg~IIGk~G~~Ik~I~~~t 79 (292)
+...|.|.. ++-+.|||++|+.||+|....
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 455677765 457889999999999876543
No 154
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=49.96 E-value=17 Score=31.60 Aligned_cols=28 Identities=11% Similarity=-0.179 Sum_probs=22.9
Q ss_pred EEEEeccCccceeeecCCCccHHHHHHhh
Q 022746 253 FLMQNTRYFVTAIFAVLSSFNIFFLITTS 281 (292)
Q Consensus 253 ~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S 281 (292)
..+.|-...-|.+||+ +|++|+++++.-
T Consensus 42 i~I~I~ta~PGivIGk-~G~~I~klk~~L 69 (207)
T PRK04191 42 TRITIYAERPGMVIGR-GGKNIRELTEIL 69 (207)
T ss_pred EEEEEEECCCCeEECC-CchhHHHHHHHH
Confidence 4555556888999999 999999998763
No 155
>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=48.38 E-value=18 Score=31.06 Aligned_cols=28 Identities=7% Similarity=-0.269 Sum_probs=24.1
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHh
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
.+++.|-...-|.|||+ +|.+|++|++.
T Consensus 39 ~~~I~I~~~rPg~vIG~-~g~~i~~l~~~ 66 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGR-GGRRIRELTEK 66 (195)
T ss_pred cEEEEEEECCCceEECC-CchHHHHHHHH
Confidence 46777778888999999 99999999875
No 156
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=46.69 E-value=19 Score=31.63 Aligned_cols=28 Identities=7% Similarity=-0.166 Sum_probs=23.9
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHh
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
.++|.|-...-|.|||+ +|..|++|++.
T Consensus 45 ~i~V~I~tarPg~vIG~-~G~~i~~l~~~ 72 (220)
T PTZ00084 45 RTEIIIRATRTREVLGD-KGRRIRELTSL 72 (220)
T ss_pred cEEEEEEECCCccEEcC-CchHHHHHHHH
Confidence 36677777888999999 99999999875
No 157
>CHL00048 rps3 ribosomal protein S3
Probab=46.07 E-value=20 Score=31.23 Aligned_cols=29 Identities=10% Similarity=-0.081 Sum_probs=23.9
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHhh
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITTS 281 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S 281 (292)
..++.|-...-|.|||+ +|.+|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~-~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIER-KGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECC-CcHhHHHHHHHH
Confidence 45666777788999999 999999998763
No 158
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=44.80 E-value=76 Score=26.54 Aligned_cols=58 Identities=22% Similarity=0.295 Sum_probs=44.4
Q ss_pred CcccEEEEEeccCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 022746 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217 (292)
Q Consensus 140 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 217 (292)
.+..++|+.++...+- ..+.+|.+..|+=+.+ .++..|.|.|..+.|..|+..+...-
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Ef-------------ee~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEF-------------EEDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEe-------------cCCcEEEEeccHHHHHHHHHHHHHHh
Confidence 4455777777776542 4667899999998886 13567999999999999999887653
No 159
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=43.86 E-value=62 Score=30.36 Aligned_cols=55 Identities=27% Similarity=0.286 Sum_probs=45.1
Q ss_pred cCcceeeecCCChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHH--HHHhc
Q 022746 151 GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG--NQLRE 219 (292)
Q Consensus 151 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~--~~l~~ 219 (292)
....-.+.|..+.+++.|.+.+|++|.. ..+.++|.|+...+..|...+. ..+..
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~--------------rG~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVA--------------RGEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEe--------------CCceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 5566789999999999999999999985 2468999999878888888877 44444
No 160
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=42.94 E-value=21 Score=31.03 Aligned_cols=29 Identities=34% Similarity=0.692 Sum_probs=25.0
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcC
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tg 80 (292)
+++.|....-|.|||++|..|++|++...
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 66788888889999999999999987653
No 161
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=41.73 E-value=23 Score=32.81 Aligned_cols=32 Identities=22% Similarity=0.435 Sum_probs=26.1
Q ss_pred CeEEEEEeeCCc-cceeecCCCchhhhhhhhcC
Q 022746 49 DVLFRIIVPSRQ-IGKVIGKEGHRIQKIREETK 80 (292)
Q Consensus 49 ~~~~rilvp~~~-vg~IIGk~G~~Ik~I~~~tg 80 (292)
.+..+++||... ...||||+|..|++|-++-+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 567789999855 67799999999999877654
No 162
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=40.67 E-value=33 Score=31.91 Aligned_cols=32 Identities=6% Similarity=-0.044 Sum_probs=26.6
Q ss_pred eeEEEEEecc-CccceeeecCCCccHHHHHHhhC
Q 022746 250 YSMFLMQNTR-YFVTAIFAVLSSFNIFFLITTSS 282 (292)
Q Consensus 250 ~~~~~v~iP~-~~vG~IIGk~gG~~Ik~I~~~S~ 282 (292)
++..++.||. .....|||| ||..|++|-+.-+
T Consensus 327 ~I~~~v~~pK~s~~klliGk-gG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGK-GGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcC-CCccHHHHHHHHH
Confidence 6888999996 566778999 9999999977644
No 163
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=33.78 E-value=1.3e+02 Score=23.30 Aligned_cols=62 Identities=16% Similarity=0.329 Sum_probs=40.8
Q ss_pred CCeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccCCCCCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcC
Q 022746 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (292)
Q Consensus 48 ~~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~ 125 (292)
..+.+.+.=.+ |+||.++++.. |.|.|..... . ++|..........+-..|+..+.++|...
T Consensus 12 ~dl~~~~~Rss-------GpGGQ~VNk~~--s~V~l~h~pt---g----i~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~ 73 (113)
T PF00472_consen 12 KDLEISFSRSS-------GPGGQNVNKTN--SKVRLRHIPT---G----IVVKCQESRSQHQNREDALEKLREKLDEA 73 (113)
T ss_dssp GGEEEEEEESS-------SSSSCHHHSSS--EEEEEEETTT---T----EEEEEESSSSHHHHHHHHHHHHHHHHHHH
T ss_pred HHeEEEEEecC-------CCCCCcccccC--CEEEEEEecc---c----EEEEEcccCCHHHHHHHHHHHHHHHHHHH
Confidence 35556655544 89999998643 4455554421 1 77776666666778888998888887653
No 164
>PRK09256 hypothetical protein; Provisional
Probab=32.99 E-value=71 Score=25.83 Aligned_cols=59 Identities=24% Similarity=0.409 Sum_probs=39.8
Q ss_pred cCCCchhhhhhhhcCcEEEEccC---CC--------------CCCceEEEEecCCCCcchhHHHHHHHHHHHHHhcCC
Q 022746 66 GKEGHRIQKIREETKATIKIADA---IA--------------RHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (292)
Q Consensus 66 Gk~G~~Ik~I~~~tga~I~i~~~---~~--------------~~~ervv~I~G~~~~~~v~~v~~A~~~I~~~i~~~~ 126 (292)
|+||.++++.. |.|.+.++-. .| -+.+..+.|+.........+...|+..+.++|....
T Consensus 24 GPGGQ~VNKt~--SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~~ 99 (138)
T PRK09256 24 GPGGQNVNKVS--TAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALERLVALIREAL 99 (138)
T ss_pred CCCcccccccc--eeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHh
Confidence 89999998764 4555554311 11 012345778877777778888999999999987643
No 165
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=32.62 E-value=37 Score=30.04 Aligned_cols=29 Identities=38% Similarity=0.682 Sum_probs=24.0
Q ss_pred EEEEeeCCccceeecCCCchhhhhhhhcC
Q 022746 52 FRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (292)
Q Consensus 52 ~rilvp~~~vg~IIGk~G~~Ik~I~~~tg 80 (292)
+.+.|-...-|.|||++|..|++|++...
T Consensus 64 i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 64 VRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred EEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 56666677789999999999999988754
No 166
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=32.46 E-value=41 Score=29.27 Aligned_cols=27 Identities=7% Similarity=-0.145 Sum_probs=23.0
Q ss_pred EEEEeccCccceeeecCCCccHHHHHHh
Q 022746 253 FLMQNTRYFVTAIFAVLSSFNIFFLITT 280 (292)
Q Consensus 253 ~~v~iP~~~vG~IIGk~gG~~Ik~I~~~ 280 (292)
++|.|-...-|.|||+ +|.+|++|++.
T Consensus 64 i~I~I~~~~pg~vIG~-~g~~i~~l~~~ 90 (211)
T TIGR01009 64 IRVTIHTARPGIVIGK-KGSEIEKLRKD 90 (211)
T ss_pred eEEEEEeCCCcceeCC-CchHHHHHHHH
Confidence 5677777788999999 99999999865
No 167
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=30.15 E-value=1.6e+02 Score=21.39 Aligned_cols=54 Identities=20% Similarity=0.212 Sum_probs=40.7
Q ss_pred CChhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHh
Q 022746 161 SGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (292)
Q Consensus 161 ~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 218 (292)
|=..+.++-+..|+++...-.|.-.- ...+.++++.|+..++..|.+.+++.|.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v----~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRV----EPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EE----ETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCc----cCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 44566778888899998765444221 1468999999999999999999988875
No 168
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.54 E-value=2.1e+02 Score=23.44 Aligned_cols=43 Identities=28% Similarity=0.407 Sum_probs=33.8
Q ss_pred hhHHHHHHhhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHh
Q 022746 163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (292)
Q Consensus 163 ~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 218 (292)
..+..|.+..|+-|.+. ....|.|.|+.+.|.+|+..|-..-.
T Consensus 126 eRlqDi~E~hgvIiE~~-------------E~D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFE-------------EYDLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEee-------------eccEEEEeccHHHHHHHHHHHHHHHh
Confidence 45567777888888863 35689999999999999999876643
No 169
>PF02044 Bombesin: Bombesin-like peptide; InterPro: IPR000874 Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells. The amphibian peptides which belong to this family are currently classified into three subfamilies [, ]; the Bombesin group, which includes bombesin and alytesin; the Ranatensin group, which includes ranatensins, litorin, and Rohdei litorin; and the Phyllolitorin group, which includes Leu(8)- and Phe(8)-phyllolitorins. In mammals and birds two categories of bombesin-like peptides are known [, ], gastrin-releasing peptide (GRP), which stimulates the release of gastrin as well as other gastrointestinal hormones, and neuromedin B (NMB), a neuropeptide whose function is not yet clear. Bombesin-like peptides, like many other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. The final peptides are eight to fourteen residues long.; GO: 0007218 neuropeptide signaling pathway; PDB: 1C9A_A 1C98_A.
Probab=25.11 E-value=17 Score=17.36 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=5.7
Q ss_pred eCCccceeecCC
Q 022746 57 PSRQIGKVIGKE 68 (292)
Q Consensus 57 p~~~vg~IIGk~ 68 (292)
|...+|++.||+
T Consensus 2 ~~WAvGh~Mgkk 13 (14)
T PF02044_consen 2 PQWAVGHFMGKK 13 (14)
T ss_dssp -TCHHHCT----
T ss_pred CccceeeeeccC
Confidence 567788998875
No 170
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=23.58 E-value=76 Score=26.46 Aligned_cols=72 Identities=15% Similarity=0.332 Sum_probs=46.6
Q ss_pred CeEEEEEeeCCccceeecCCCchhhhhhhhcCcEEEEccC--CC--------------CCCceEEEEecCCCCcchhHHH
Q 022746 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IA--------------RHEERVIIISSKDNDNVVSDAE 112 (292)
Q Consensus 49 ~~~~rilvp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~--~~--------------~~~ervv~I~G~~~~~~v~~v~ 112 (292)
.+++++--++ |+||.++.++-.+.-++.+++.. .| .....-+.|.........-++.
T Consensus 41 ~~~i~y~RSS-------GPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~Nia 113 (172)
T KOG3429|consen 41 QLEISYSRSS-------GPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNIA 113 (172)
T ss_pred heEEEEeecC-------CCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccHH
Confidence 3445554444 99999999997776666665532 11 1112227787765555566788
Q ss_pred HHHHHHHHHHhcCCC
Q 022746 113 NALQQIAALILKDDD 127 (292)
Q Consensus 113 ~A~~~I~~~i~~~~~ 127 (292)
+|+..+.++|.....
T Consensus 114 DcleKlr~~I~~~~~ 128 (172)
T KOG3429|consen 114 DCLEKLRDIIRAAEQ 128 (172)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999876543
No 171
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=22.00 E-value=75 Score=28.06 Aligned_cols=29 Identities=7% Similarity=-0.184 Sum_probs=23.0
Q ss_pred EEEEEeccCccceeeecCCCccHHHHHHhh
Q 022746 252 MFLMQNTRYFVTAIFAVLSSFNIFFLITTS 281 (292)
Q Consensus 252 ~~~v~iP~~~vG~IIGk~gG~~Ik~I~~~S 281 (292)
.++|.|-...-|.|||+ +|.+|++|++.-
T Consensus 63 ~i~I~I~~~rP~~iiG~-~g~~i~~l~~~L 91 (232)
T PRK00310 63 RVRVTIHTARPGIVIGK-KGAEIEKLRKEL 91 (232)
T ss_pred eEEEEEEECCCccccCC-CcHHHHHHHHHH
Confidence 35566666778999999 999999998763
No 172
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=20.17 E-value=1.6e+02 Score=22.82 Aligned_cols=27 Identities=30% Similarity=0.228 Sum_probs=24.7
Q ss_pred CcEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022746 194 DRVVQISGDVPAVLNALVEIGNQLREN 220 (292)
Q Consensus 194 ~r~v~I~G~~~~v~~A~~~I~~~l~~~ 220 (292)
...+.|+|+-.+|+.|+..+.+.+++.
T Consensus 74 sGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 74 SGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred ceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 457889999999999999999999986
No 173
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=20.12 E-value=87 Score=30.27 Aligned_cols=12 Identities=17% Similarity=0.437 Sum_probs=7.6
Q ss_pred HHHhhCCeEEEe
Q 022746 168 LRNSSGATIVIL 179 (292)
Q Consensus 168 I~~~tga~I~i~ 179 (292)
|....||+|-++
T Consensus 415 I~ktdGc~iYLS 426 (480)
T KOG2675|consen 415 IDKTDGCHIYLS 426 (480)
T ss_pred EecCCCeeEEec
Confidence 445667777764
Done!