Query 025112
Match_columns 257
No_of_seqs 156 out of 1460
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 02:47:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025112hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2191 RNA-binding protein NO 100.0 4E-33 8.7E-38 243.9 21.6 220 17-247 5-237 (402)
2 KOG2192 PolyC-binding hnRNP-K 100.0 6.5E-29 1.4E-33 212.4 12.3 193 10-232 14-207 (390)
3 KOG2193 IGF-II mRNA-binding pr 99.9 9.3E-27 2E-31 209.6 12.1 180 44-240 193-379 (584)
4 KOG2190 PolyC-binding proteins 99.9 7E-25 1.5E-29 206.7 20.6 165 49-221 42-210 (485)
5 KOG1676 K-homology type RNA bi 99.9 6.5E-25 1.4E-29 205.5 15.5 166 47-223 136-304 (600)
6 KOG1676 K-homology type RNA bi 99.9 3.9E-23 8.5E-28 193.6 14.9 165 49-225 229-395 (600)
7 KOG2192 PolyC-binding hnRNP-K 99.8 9E-20 2E-24 156.5 12.8 163 46-220 119-385 (390)
8 KOG2190 PolyC-binding proteins 99.8 1.1E-18 2.3E-23 164.9 17.9 162 49-220 137-410 (485)
9 TIGR03665 arCOG04150 arCOG0415 99.8 5.9E-19 1.3E-23 146.5 10.7 146 54-228 2-160 (172)
10 KOG2193 IGF-II mRNA-binding pr 99.8 2.8E-18 6.1E-23 155.1 12.6 160 48-224 409-569 (584)
11 PRK13763 putative RNA-processi 99.7 1.5E-17 3.2E-22 139.1 12.2 149 50-226 3-164 (180)
12 cd02396 PCBP_like_KH K homolog 99.5 4.8E-14 1.1E-18 98.6 7.6 64 145-214 2-65 (65)
13 cd02396 PCBP_like_KH K homolog 99.5 8.2E-14 1.8E-18 97.4 5.1 63 51-118 1-64 (65)
14 cd02394 vigilin_like_KH K homo 99.4 1.6E-12 3.5E-17 89.8 6.0 61 145-214 2-62 (62)
15 PF00013 KH_1: KH domain syndr 99.3 1.9E-12 4.2E-17 88.8 5.9 60 144-213 1-60 (60)
16 cd02393 PNPase_KH Polynucleoti 99.3 9.2E-12 2E-16 85.9 7.8 57 144-213 3-60 (61)
17 cd00105 KH-I K homology RNA-bi 99.3 1.8E-11 3.9E-16 84.6 8.2 62 145-213 2-63 (64)
18 PF00013 KH_1: KH domain syndr 99.3 3.5E-12 7.7E-17 87.5 3.4 60 51-118 1-60 (60)
19 COG1094 Predicted RNA-binding 99.3 6E-11 1.3E-15 98.7 11.2 156 49-228 7-173 (194)
20 cd02394 vigilin_like_KH K homo 99.3 6.3E-12 1.4E-16 86.8 4.3 60 52-118 2-61 (62)
21 cd00105 KH-I K homology RNA-bi 99.2 2.9E-11 6.2E-16 83.6 6.1 62 52-118 2-63 (64)
22 KOG2191 RNA-binding protein NO 99.2 9.9E-11 2.1E-15 103.7 10.8 79 141-224 37-116 (402)
23 cd02393 PNPase_KH Polynucleoti 99.2 7.8E-11 1.7E-15 81.3 6.0 58 51-118 3-60 (61)
24 PF13014 KH_3: KH domain 99.1 9.6E-11 2.1E-15 75.1 4.8 42 60-101 1-43 (43)
25 PF13014 KH_3: KH domain 99.1 1.8E-10 4E-15 73.7 5.5 43 153-201 1-43 (43)
26 smart00322 KH K homology RNA-b 99.0 2.4E-09 5.1E-14 73.9 9.1 67 143-218 3-69 (69)
27 KOG2113 Predicted RNA binding 98.9 1E-09 2.2E-14 96.6 4.9 151 48-216 24-180 (394)
28 smart00322 KH K homology RNA-b 98.9 7.1E-09 1.5E-13 71.4 7.5 67 49-122 2-68 (69)
29 KOG2279 Kinase anchor protein 98.8 1.1E-08 2.4E-13 96.1 5.8 145 47-219 65-209 (608)
30 cd02395 SF1_like-KH Splicing f 98.6 2E-07 4.4E-12 72.9 8.2 71 151-222 14-98 (120)
31 TIGR03665 arCOG04150 arCOG0415 98.5 1.7E-07 3.6E-12 78.0 5.7 61 147-219 2-65 (172)
32 cd02395 SF1_like-KH Splicing f 98.5 3E-07 6.6E-12 71.8 6.8 72 53-126 3-97 (120)
33 PRK13763 putative RNA-processi 98.5 3.6E-07 7.8E-12 76.5 7.0 64 144-219 4-71 (180)
34 PRK08406 transcription elongat 98.5 5.3E-07 1.1E-11 72.4 7.2 103 50-178 32-134 (140)
35 KOG2208 Vigilin [Lipid transpo 98.4 6.7E-07 1.5E-11 89.5 8.7 146 47-221 344-490 (753)
36 TIGR02696 pppGpp_PNP guanosine 98.3 3.5E-06 7.6E-11 83.3 10.3 94 108-219 548-642 (719)
37 KOG2279 Kinase anchor protein 98.3 1.3E-06 2.9E-11 82.4 6.9 185 45-238 135-393 (608)
38 KOG2208 Vigilin [Lipid transpo 98.2 7.3E-06 1.6E-10 82.2 10.0 164 49-223 200-418 (753)
39 TIGR01952 nusA_arch NusA famil 98.1 1.1E-05 2.4E-10 64.7 7.9 103 51-179 34-136 (141)
40 TIGR03591 polynuc_phos polyrib 98.0 1.7E-05 3.6E-10 79.1 8.3 95 108-219 520-615 (684)
41 TIGR02696 pppGpp_PNP guanosine 97.8 3.7E-05 8E-10 76.2 6.3 66 49-124 577-642 (719)
42 COG0195 NusA Transcription elo 97.8 8.4E-05 1.8E-09 62.5 7.3 103 51-180 77-179 (190)
43 PLN00207 polyribonucleotide nu 97.8 7.5E-05 1.6E-09 75.6 8.0 99 108-223 654-754 (891)
44 KOG0119 Splicing factor 1/bran 97.7 0.00034 7.3E-09 65.7 9.9 78 142-219 137-230 (554)
45 COG1185 Pnp Polyribonucleotide 97.6 0.00015 3.4E-09 70.7 7.8 111 97-225 507-622 (692)
46 KOG0336 ATP-dependent RNA heli 97.6 0.00011 2.4E-09 67.9 6.5 69 141-219 45-113 (629)
47 TIGR03591 polynuc_phos polyrib 97.5 0.00014 3E-09 72.6 5.3 66 49-124 550-615 (684)
48 cd02134 NusA_KH NusA_K homolog 97.4 0.00023 4.9E-09 48.9 4.3 37 49-85 24-60 (61)
49 TIGR01953 NusA transcription t 97.4 9.6E-05 2.1E-09 67.7 2.8 94 60-180 244-338 (341)
50 KOG0119 Splicing factor 1/bran 97.4 0.00027 5.8E-09 66.4 5.6 72 49-124 137-230 (554)
51 KOG1588 RNA-binding protein Sa 97.3 0.00023 5E-09 62.1 4.3 42 46-87 88-135 (259)
52 PRK12328 nusA transcription el 97.3 0.0007 1.5E-08 62.5 7.7 96 60-183 252-348 (374)
53 PRK11824 polynucleotide phosph 97.3 0.00044 9.5E-09 69.2 6.6 95 108-219 523-618 (693)
54 PRK12327 nusA transcription el 97.2 0.00084 1.8E-08 62.0 6.8 105 50-181 231-341 (362)
55 KOG2814 Transcription coactiva 97.2 0.00037 7.9E-09 62.6 4.0 72 49-126 56-127 (345)
56 KOG2814 Transcription coactiva 97.1 0.0008 1.7E-08 60.5 5.3 70 143-221 57-127 (345)
57 KOG2113 Predicted RNA binding 97.1 0.00038 8.3E-09 62.0 2.9 65 141-215 24-88 (394)
58 KOG0336 ATP-dependent RNA heli 97.1 0.00075 1.6E-08 62.6 4.8 55 46-103 43-97 (629)
59 PRK09202 nusA transcription el 97.1 0.0016 3.5E-08 62.2 7.2 104 50-181 231-340 (470)
60 KOG1588 RNA-binding protein Sa 97.0 0.002 4.3E-08 56.3 7.0 86 140-225 89-197 (259)
61 cd02134 NusA_KH NusA_K homolog 97.0 0.0011 2.5E-08 45.4 4.5 36 143-178 25-60 (61)
62 PRK12329 nusA transcription el 97.0 0.00049 1.1E-08 64.6 3.2 94 60-180 278-372 (449)
63 PRK04163 exosome complex RNA-b 96.9 0.0022 4.7E-08 56.0 6.1 68 144-224 146-214 (235)
64 PRK00468 hypothetical protein; 96.9 0.0011 2.3E-08 47.5 3.3 34 46-79 26-59 (75)
65 TIGR03319 YmdA_YtgF conserved 96.9 0.0059 1.3E-07 59.1 9.4 65 143-219 204-270 (514)
66 PRK12704 phosphodiesterase; Pr 96.9 0.006 1.3E-07 59.1 9.4 65 143-219 210-276 (520)
67 PF14611 SLS: Mitochondrial in 96.8 0.074 1.6E-06 45.3 15.1 134 53-225 29-171 (210)
68 PRK00106 hypothetical protein; 96.8 0.007 1.5E-07 58.7 9.6 65 143-219 225-291 (535)
69 PRK02821 hypothetical protein; 96.8 0.0013 2.8E-08 47.3 3.2 35 46-80 27-61 (77)
70 PLN00207 polyribonucleotide nu 96.8 0.0013 2.8E-08 66.9 4.3 67 48-124 683-750 (891)
71 COG1185 Pnp Polyribonucleotide 96.7 0.0033 7E-08 61.7 5.9 67 49-125 551-617 (692)
72 COG1837 Predicted RNA-binding 96.6 0.0023 5.1E-08 45.7 3.4 32 47-78 27-58 (76)
73 KOG3273 Predicted RNA-binding 96.5 0.0059 1.3E-07 51.3 5.9 157 51-226 75-238 (252)
74 PRK01064 hypothetical protein; 96.4 0.004 8.7E-08 44.9 3.4 34 46-79 26-59 (78)
75 PRK12704 phosphodiesterase; Pr 96.4 0.0099 2.1E-07 57.6 7.1 50 49-103 209-259 (520)
76 COG1094 Predicted RNA-binding 96.3 0.0097 2.1E-07 50.0 5.8 54 60-125 112-165 (194)
77 PRK02821 hypothetical protein; 96.3 0.0067 1.4E-07 43.6 4.1 30 143-172 31-60 (77)
78 COG5176 MSL5 Splicing factor ( 96.2 0.015 3.3E-07 49.2 6.3 78 142-219 147-240 (269)
79 TIGR03319 YmdA_YtgF conserved 96.1 0.016 3.5E-07 56.1 7.1 50 48-102 202-252 (514)
80 PRK00468 hypothetical protein; 96.0 0.0076 1.7E-07 43.1 3.4 30 142-171 29-58 (75)
81 COG5176 MSL5 Splicing factor ( 96.0 0.015 3.3E-07 49.2 5.6 42 47-88 145-192 (269)
82 PRK04163 exosome complex RNA-b 96.0 0.012 2.6E-07 51.3 5.1 62 52-123 147-208 (235)
83 PRK00106 hypothetical protein; 96.0 0.021 4.5E-07 55.5 7.1 50 48-102 223-273 (535)
84 KOG1067 Predicted RNA-binding 95.8 0.025 5.4E-07 54.4 6.8 99 108-224 566-665 (760)
85 KOG2874 rRNA processing protei 95.8 0.014 3.1E-07 51.4 4.8 51 155-219 161-211 (356)
86 PRK11824 polynucleotide phosph 95.7 0.0073 1.6E-07 60.5 3.0 65 50-124 554-618 (693)
87 COG1837 Predicted RNA-binding 95.7 0.014 2.9E-07 41.8 3.4 31 141-171 28-58 (76)
88 PRK08406 transcription elongat 95.3 0.017 3.7E-07 46.4 3.1 38 49-86 98-135 (140)
89 PRK12705 hypothetical protein; 95.3 0.05 1.1E-06 52.5 6.9 65 143-219 198-264 (508)
90 PF13083 KH_4: KH domain; PDB: 95.3 0.011 2.5E-07 41.7 1.9 36 47-82 26-61 (73)
91 PRK01064 hypothetical protein; 95.2 0.024 5.3E-07 40.8 3.5 31 141-171 28-58 (78)
92 cd02409 KH-II KH-II (K homolo 95.0 0.041 8.8E-07 37.4 4.1 35 49-83 24-58 (68)
93 PF13184 KH_5: NusA-like KH do 94.8 0.024 5.1E-07 39.9 2.4 38 51-88 4-47 (69)
94 KOG4369 RTK signaling protein 94.0 0.025 5.3E-07 58.5 1.5 73 48-125 1338-1411(2131)
95 PRK12705 hypothetical protein; 93.8 0.11 2.3E-06 50.3 5.3 40 49-88 197-237 (508)
96 KOG4369 RTK signaling protein 93.5 0.04 8.6E-07 57.1 2.0 71 143-219 1340-1410(2131)
97 PF13083 KH_4: KH domain; PDB: 93.1 0.062 1.3E-06 37.9 2.0 32 143-174 29-60 (73)
98 PF07650 KH_2: KH domain syndr 93.1 0.054 1.2E-06 38.6 1.6 35 50-84 25-59 (78)
99 PRK06418 transcription elongat 93.0 0.13 2.9E-06 42.3 4.1 46 42-88 53-98 (166)
100 PF13184 KH_5: NusA-like KH do 92.9 0.11 2.4E-06 36.5 2.9 37 144-180 4-46 (69)
101 cd02409 KH-II KH-II (K homolo 92.6 0.22 4.8E-06 33.7 4.1 34 143-176 25-58 (68)
102 cd02414 jag_KH jag_K homology 92.5 0.13 2.8E-06 36.7 2.9 35 51-85 25-59 (77)
103 COG1097 RRP4 RNA-binding prote 92.3 0.28 6.1E-06 42.6 5.2 66 145-223 148-214 (239)
104 TIGR01952 nusA_arch NusA famil 91.6 0.3 6.4E-06 39.3 4.3 37 144-180 34-70 (141)
105 PF07650 KH_2: KH domain syndr 91.4 0.14 3E-06 36.5 2.0 35 143-177 25-59 (78)
106 COG0195 NusA Transcription elo 91.3 0.2 4.3E-06 42.3 3.1 37 51-87 143-179 (190)
107 COG1855 ATPase (PilT family) [ 91.2 0.15 3.2E-06 48.4 2.5 40 49-88 485-524 (604)
108 cd02410 archeal_CPSF_KH The ar 91.0 1.8 3.9E-05 34.9 8.1 95 65-182 21-115 (145)
109 PRK12328 nusA transcription el 90.8 0.28 6E-06 45.6 3.8 41 48-88 306-346 (374)
110 TIGR01953 NusA transcription t 90.6 0.29 6.4E-06 45.0 3.8 40 48-87 299-338 (341)
111 PF14611 SLS: Mitochondrial in 90.0 2 4.4E-05 36.4 8.4 66 144-221 27-92 (210)
112 PRK13764 ATPase; Provisional 90.0 0.24 5.2E-06 48.9 2.9 41 48-88 479-519 (602)
113 PRK13764 ATPase; Provisional 90.0 0.51 1.1E-05 46.7 5.2 44 142-185 480-523 (602)
114 KOG3273 Predicted RNA-binding 89.8 0.22 4.9E-06 42.0 2.2 56 58-125 177-232 (252)
115 cd02413 40S_S3_KH K homology R 89.8 0.36 7.9E-06 35.0 3.0 37 50-86 30-66 (81)
116 cd02414 jag_KH jag_K homology 89.5 0.42 9.1E-06 34.0 3.2 34 144-177 25-58 (77)
117 COG1855 ATPase (PilT family) [ 89.4 0.3 6.5E-06 46.5 2.9 41 143-183 486-526 (604)
118 PRK12327 nusA transcription el 88.7 0.5 1.1E-05 43.8 3.8 42 47-88 300-341 (362)
119 PRK09202 nusA transcription el 88.4 0.41 8.8E-06 46.0 3.1 39 49-87 301-339 (470)
120 KOG1067 Predicted RNA-binding 87.2 1 2.3E-05 43.7 5.0 68 47-125 594-661 (760)
121 PRK12329 nusA transcription el 87.0 0.58 1.3E-05 44.3 3.2 41 48-88 333-373 (449)
122 PRK06418 transcription elongat 86.7 1.1 2.4E-05 37.0 4.3 36 144-180 62-97 (166)
123 cd02412 30S_S3_KH K homology R 86.3 0.68 1.5E-05 35.4 2.8 30 51-80 62-91 (109)
124 COG1782 Predicted metal-depend 86.2 1.7 3.6E-05 41.9 5.8 98 62-182 41-138 (637)
125 cd02411 archeal_30S_S3_KH K ho 85.9 0.83 1.8E-05 33.2 2.9 28 52-79 40-67 (85)
126 COG1097 RRP4 RNA-binding prote 85.8 2.6 5.7E-05 36.7 6.4 46 53-104 149-194 (239)
127 cd02413 40S_S3_KH K homology R 85.8 1.2 2.7E-05 32.1 3.8 36 143-178 30-65 (81)
128 COG5166 Uncharacterized conser 84.3 1.2 2.5E-05 42.9 3.8 125 63-219 393-524 (657)
129 cd02410 archeal_CPSF_KH The ar 84.1 1.4 3E-05 35.5 3.6 37 53-89 79-115 (145)
130 COG5166 Uncharacterized conser 81.8 1.9 4E-05 41.6 4.1 129 50-180 449-608 (657)
131 COG0092 RpsC Ribosomal protein 81.2 1.4 3E-05 38.3 2.7 31 49-79 50-80 (233)
132 KOG2874 rRNA processing protei 80.9 3.3 7.1E-05 36.9 5.0 25 62-86 161-185 (356)
133 TIGR03675 arCOG00543 arCOG0054 80.5 5.2 0.00011 39.9 7.0 97 63-182 36-132 (630)
134 cd02411 archeal_30S_S3_KH K ho 80.5 2.1 4.7E-05 31.0 3.3 29 144-172 39-67 (85)
135 cd02412 30S_S3_KH K homology R 79.6 2 4.4E-05 32.7 3.0 29 144-172 62-90 (109)
136 COG0092 RpsC Ribosomal protein 76.7 3.9 8.4E-05 35.5 4.2 32 143-174 51-86 (233)
137 PF08067 ROKNT: ROKNT (NUC014) 70.6 1.7 3.8E-05 26.9 0.4 30 13-47 9-38 (43)
138 TIGR00436 era GTP-binding prot 68.2 6.7 0.00014 34.5 3.9 28 143-170 221-249 (270)
139 TIGR00436 era GTP-binding prot 67.1 6.6 0.00014 34.5 3.6 30 50-79 221-251 (270)
140 PRK04191 rps3p 30S ribosomal p 65.3 6.3 0.00014 33.7 3.0 30 52-81 42-71 (207)
141 COG1847 Jag Predicted RNA-bind 64.6 3.7 8.1E-05 35.0 1.4 37 49-85 90-126 (208)
142 PRK15494 era GTPase Era; Provi 63.0 9.3 0.0002 35.0 3.9 36 143-178 273-317 (339)
143 TIGR01008 rpsC_E_A ribosomal p 62.5 7.8 0.00017 32.8 3.0 31 50-80 38-68 (195)
144 CHL00048 rps3 ribosomal protei 62.4 7.6 0.00017 33.4 3.0 31 50-80 66-96 (214)
145 PRK00089 era GTPase Era; Revie 61.6 10 0.00022 33.5 3.8 36 143-178 226-270 (292)
146 COG1159 Era GTPase [General fu 61.0 11 0.00025 33.9 3.9 36 143-178 229-273 (298)
147 PRK15494 era GTPase Era; Provi 60.4 10 0.00022 34.8 3.6 37 50-86 273-318 (339)
148 PTZ00084 40S ribosomal protein 59.9 9 0.00019 33.1 3.0 32 51-82 45-76 (220)
149 PRK00089 era GTPase Era; Revie 58.1 6.5 0.00014 34.8 1.9 37 50-86 226-271 (292)
150 COG1702 PhoH Phosphate starvat 57.6 27 0.00058 32.2 5.7 57 149-219 21-79 (348)
151 COG1782 Predicted metal-depend 57.0 8.7 0.00019 37.2 2.6 38 53-90 102-139 (637)
152 COG1159 Era GTPase [General fu 56.3 14 0.00029 33.4 3.6 30 49-78 228-258 (298)
153 PF02749 QRPTase_N: Quinolinat 55.9 35 0.00075 24.7 5.2 54 161-218 32-85 (88)
154 TIGR03675 arCOG00543 arCOG0054 54.3 14 0.0003 37.0 3.6 39 52-90 95-133 (630)
155 PRK04191 rps3p 30S ribosomal p 54.3 15 0.00032 31.4 3.4 28 145-172 42-69 (207)
156 CHL00048 rps3 ribosomal protei 52.2 18 0.00039 31.1 3.6 30 143-172 66-95 (214)
157 TIGR01008 rpsC_E_A ribosomal p 51.4 18 0.00039 30.6 3.4 28 144-171 39-66 (195)
158 COG1847 Jag Predicted RNA-bind 49.5 14 0.0003 31.6 2.3 35 143-177 91-125 (208)
159 COG2101 SPT15 TATA-box binding 49.1 1.6E+02 0.0034 24.6 10.5 108 96-220 63-182 (185)
160 PTZ00084 40S ribosomal protein 48.7 20 0.00043 31.0 3.3 28 144-171 45-72 (220)
161 TIGR01009 rpsC_bact ribosomal 47.1 19 0.00041 30.9 2.9 28 52-79 64-91 (211)
162 KOG1423 Ras-like GTPase ERA [C 46.9 18 0.0004 33.0 2.9 32 49-80 327-359 (379)
163 PF09869 DUF2096: Uncharacteri 41.3 98 0.0021 25.6 6.0 59 140-218 110-168 (169)
164 TIGR01009 rpsC_bact ribosomal 37.9 36 0.00078 29.1 3.2 28 144-171 63-90 (211)
165 PRK15468 carboxysome structura 37.0 96 0.0021 23.7 5.0 41 170-221 61-101 (111)
166 cd00652 TBP_TLF TATA box bindi 37.0 2.4E+02 0.0052 23.2 10.3 107 96-219 57-174 (174)
167 PRK00310 rpsC 30S ribosomal pr 36.5 33 0.00071 29.9 2.8 29 51-79 63-91 (232)
168 KOG1423 Ras-like GTPase ERA [C 34.4 41 0.00089 30.9 3.1 32 142-173 327-359 (379)
169 COG4010 Uncharacterized protei 34.1 1.5E+02 0.0032 24.0 5.8 44 163-219 126-169 (170)
170 PF10369 ALS_ss_C: Small subun 32.6 1.3E+02 0.0029 21.0 5.0 42 162-214 16-57 (75)
171 PRK04021 hypothetical protein; 30.6 1.4E+02 0.0029 22.1 4.9 39 164-210 51-90 (92)
172 TIGR01334 modD putative molybd 27.5 2.7E+02 0.0058 24.9 7.1 56 160-219 46-101 (277)
173 PRK00310 rpsC 30S ribosomal pr 27.4 65 0.0014 28.0 3.1 29 144-172 63-91 (232)
174 PRK05848 nicotinate-nucleotide 25.4 3E+02 0.0066 24.5 7.1 56 160-219 44-99 (273)
175 PF02080 TrkA_C: TrkA-C domain 25.1 78 0.0017 21.1 2.6 51 162-212 14-69 (71)
176 cd04517 TLF TBP-like factors ( 24.8 4E+02 0.0086 22.0 10.2 107 96-219 57-174 (174)
177 PRK03818 putative transporter; 24.3 6.9E+02 0.015 24.6 10.5 138 51-214 206-360 (552)
178 cd04516 TBP_eukaryotes eukaryo 24.2 4.1E+02 0.0089 21.9 10.6 106 96-219 57-173 (174)
179 KOG3429 Predicted peptidyl-tRN 24.0 59 0.0013 26.7 2.1 61 66-126 51-127 (172)
180 cd07046 BMC_PduU-EutS 1,2-prop 23.4 1.5E+02 0.0032 22.7 4.1 29 194-222 73-101 (110)
181 PF00936 BMC: BMC domain; Int 23.1 1.5E+02 0.0032 20.7 3.8 46 167-220 20-65 (75)
182 TIGR03802 Asp_Ala_antiprt aspa 22.2 4.7E+02 0.01 25.8 8.4 67 144-218 304-381 (562)
183 cd01572 QPRTase Quinolinate ph 21.9 3.5E+02 0.0076 23.9 6.8 55 161-219 43-99 (268)
184 PRK09256 hypothetical protein; 21.3 1.1E+02 0.0023 24.4 3.1 58 66-125 24-98 (138)
185 PRK07428 nicotinate-nucleotide 20.9 4E+02 0.0087 23.9 7.0 56 160-219 56-113 (288)
186 cd01573 modD_like ModD; Quinol 20.9 4.1E+02 0.0089 23.5 7.0 56 160-219 42-97 (272)
187 PRK08385 nicotinate-nucleotide 20.1 4.3E+02 0.0093 23.6 7.0 55 161-219 45-99 (278)
No 1
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=4e-33 Score=243.92 Aligned_cols=220 Identities=25% Similarity=0.386 Sum_probs=170.6
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCcccc-CCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc---ccCC
Q 025112 17 TEPEPRHDVSGKRRREDGEIEGSDPKRR-AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARH 92 (257)
Q Consensus 17 ~~~~~~~~~~~kr~~~~~~~~~~~~~~~-~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~ 92 (257)
++...+...+.||+++...+........ ..+..+++|||||+..+|.||||||++|.+|+++|||+|++++. .|++
T Consensus 5 ~~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGT 84 (402)
T KOG2191|consen 5 VPIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGT 84 (402)
T ss_pred CcccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCc
Confidence 4555667778899998866433222222 22345999999999999999999999999999999999999943 6899
Q ss_pred CccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhh--ccCCCcceEEEEEeecCccceeecCCChhHHHHHH
Q 025112 93 EERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKV--AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRN 170 (257)
Q Consensus 93 ~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~--~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~ 170 (257)
+||+|+|+|+ +..+......|.++|++..........+ .........++++||++.+|.||||+|++||.|++
T Consensus 85 TeRvcli~Gt-----~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~E 159 (402)
T KOG2191|consen 85 TERVCLIQGT-----VEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQE 159 (402)
T ss_pred cceEEEEecc-----HHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHH
Confidence 9999999998 4466777788888887764432211111 01123345689999999999999999999999999
Q ss_pred HhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCCc-c--cC----CCCCCCCCCCCCCCC
Q 025112 171 SSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV-I--SI----SPAYNYSAIRPAQPF 243 (257)
Q Consensus 171 ~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~-~--~~----~p~~~~~~~~~~~~~ 243 (257)
++||+|+|++.. |... ...+|+|++.|.+++..+|+.+|+++|.|+|+..+ + +| .|..|+++ +|+||
T Consensus 160 qsga~iqisPqk--pt~~--sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnP--tGspy 233 (402)
T KOG2191|consen 160 QSGAWIQISPQK--PTGI--SLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNP--TGSPY 233 (402)
T ss_pred hhCcceEecccC--CCCc--cceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCC--CCCCC
Confidence 999999998532 2222 36899999999999999999999999999999866 2 33 58999998 66766
Q ss_pred cCCC
Q 025112 244 VEPT 247 (257)
Q Consensus 244 ~~~~ 247 (257)
.-+.
T Consensus 234 a~~~ 237 (402)
T KOG2191|consen 234 AYQA 237 (402)
T ss_pred CCCC
Confidence 6543
No 2
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=6.5e-29 Score=212.44 Aligned_cols=193 Identities=28% Similarity=0.434 Sum_probs=161.7
Q ss_pred cCCCCCCCCCCCCCCCCCCccCCCCCCCCCCccccCCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccc
Q 025112 10 NPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI 89 (257)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~kr~~~~~~~~~~~~~~~~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~ 89 (257)
++-|..++++.++.+..+||+.+|+.. +++++ ..+.++||+.+..+|+||||+|++||+|+.++++.|.|+++
T Consensus 14 t~q~~~~~~~~e~g~~~gkrp~~d~~~---qa~k~---~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds- 86 (390)
T KOG2192|consen 14 TEQPEETFPNTETGGEFGKRPAEDMEE---QAFKR---SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS- 86 (390)
T ss_pred CCChhhcCCCCcccccccCCcchhhHH---HHhhh---cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-
Confidence 456677899999999999999999973 33333 34899999999999999999999999999999999999988
Q ss_pred cCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHH
Q 025112 90 ARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169 (257)
Q Consensus 90 ~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~ 169 (257)
+.++|+|+|+...+ .+-+-++.|.-.+.+.-. ..+.+.++++|+.++.|.|||++|+.||+|+
T Consensus 87 -~~peri~tisad~~-----ti~~ilk~iip~lee~f~-----------~~~pce~rllihqs~ag~iigrngskikelr 149 (390)
T KOG2192|consen 87 -SGPERILTISADIE-----TIGEILKKIIPTLEEGFQ-----------LPSPCELRLLIHQSLAGGIIGRNGSKIKELR 149 (390)
T ss_pred -CCCceeEEEeccHH-----HHHHHHHHHhhhhhhCCC-----------CCCchhhhhhhhhhhccceecccchhHHHHH
Confidence 58999999999742 344444444444443321 2345789999999999999999999999999
Q ss_pred HHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCCcc-cCCCCC
Q 025112 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVI-SISPAY 232 (257)
Q Consensus 170 ~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~-~~~p~~ 232 (257)
+++.++.+|+. .|| +++++|+|.|.|.+.+|..+++.|++.|.|.|.+++. .|+|.|
T Consensus 150 ekcsarlkift-----~c~-p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~f 207 (390)
T KOG2192|consen 150 EKCSARLKIFT-----ECC-PHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNF 207 (390)
T ss_pred Hhhhhhhhhhh-----ccC-CCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccc
Confidence 99999999984 333 4799999999999999999999999999999999985 776666
No 3
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=9.3e-27 Score=209.56 Aligned_cols=180 Identities=26% Similarity=0.464 Sum_probs=155.7
Q ss_pred cCCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112 44 RAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALI 122 (257)
Q Consensus 44 ~~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i 122 (257)
....-++.+|++||..++|.||||+|+|||.|.+.|.|+|+|.+. ..|..|+.++|-|.++ .+.+||.+|+++|
T Consensus 193 ~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpE-----g~s~Ac~~ILeim 267 (584)
T KOG2193|consen 193 KQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPE-----GTSKACKMILEIM 267 (584)
T ss_pred cccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCcc-----chHHHHHHHHHHH
Confidence 344568999999999999999999999999999999999999854 4578899999999987 5679999999999
Q ss_pred hcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC
Q 025112 123 LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202 (257)
Q Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~ 202 (257)
..+.....-.+ .+.++++..+.+||+||||.|++||+|+++||++|.|.+-.++.. .+.+|.+++.|+
T Consensus 268 qkEA~~~k~~~--------e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~----ynpERTItVkGs 335 (584)
T KOG2193|consen 268 QKEAVDDKVAE--------EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL----YNPERTITVKGS 335 (584)
T ss_pred HHhhhccchhh--------hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc----cCccceEEeccc
Confidence 77654332222 257899999999999999999999999999999999988666655 378999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCcccC------CCCCCCCCCCCC
Q 025112 203 VPAVLNALVEIGNQLRENPPRQVISI------SPAYNYSAIRPA 240 (257)
Q Consensus 203 ~~~v~~A~~~I~~~l~e~~~~~~~~~------~p~~~~~~~~~~ 240 (257)
.++|..|..+|+.+|+|.++++..++ .|++|....+.+
T Consensus 336 iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f 379 (584)
T KOG2193|consen 336 IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLF 379 (584)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCC
Confidence 99999999999999999999987544 588988887665
No 4
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=7e-25 Score=206.68 Aligned_cols=165 Identities=33% Similarity=0.558 Sum_probs=131.2
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC---
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD--- 125 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~--- 125 (257)
+.++|+|++...+|.||||+|..||+||+++.++|+|.+..+++.||+++|+|...+.....+.+|+..+++.+...
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence 34489999999999999999999999999999999999998899999999999211112334455555555555432
Q ss_pred -CCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHH
Q 025112 126 -DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP 204 (257)
Q Consensus 126 -~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~ 204 (257)
+....+.... ......+.+|+||.+++|+||||+|+.||+|+++|||+|.+.+. .+|. .++|.|+|.|.++
T Consensus 122 d~~~~~d~~~~--~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~-----ster~V~IsG~~~ 193 (485)
T KOG2190|consen 122 DDEAAEDNGED--ASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN-----STERAVTISGEPD 193 (485)
T ss_pred cccccccCCcc--ccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc-----ccceeEEEcCchH
Confidence 2221111110 01114689999999999999999999999999999999999754 8887 5788999999999
Q ss_pred HHHHHHHHHHHHHhcCC
Q 025112 205 AVLNALVEIGNQLRENP 221 (257)
Q Consensus 205 ~v~~A~~~I~~~l~e~~ 221 (257)
+|.+|+..|..+|++++
T Consensus 194 av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 194 AVKKALVQISSRLLENP 210 (485)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999999954
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.93 E-value=6.5e-25 Score=205.46 Aligned_cols=166 Identities=23% Similarity=0.383 Sum_probs=137.1
Q ss_pred CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccc--cCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~--~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~ 124 (257)
..+++..|+||.+.+|+||||+|++||+|++++||++.+.... ..+..+.+.|+|.++ .++.|..+|+++|.+
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 4568999999999999999999999999999999999987542 123677899999975 789999999999997
Q ss_pred CCCCCchhh-hhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025112 125 DDDSNSEAS-KVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (257)
Q Consensus 125 ~~~~~~~~~-~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~ 203 (257)
......-.. ....+.....+.++.||++.||.||||+|++||+|+.+||++|+|.+ |+.|. +.+|.+.|.|+.
T Consensus 211 ~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp-Dd~p~-----speR~~~IiG~~ 284 (600)
T KOG1676|consen 211 EDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP-DDDPS-----SPERPAQIIGTV 284 (600)
T ss_pred cccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec-CCCCC-----CccceeeeecCH
Confidence 544332211 11111123348999999999999999999999999999999999865 45554 789999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCC
Q 025112 204 PAVLNALVEIGNQLRENPPR 223 (257)
Q Consensus 204 ~~v~~A~~~I~~~l~e~~~~ 223 (257)
++|++|.++|.++|.+....
T Consensus 285 d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 285 DQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred HHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999997665
No 6
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.90 E-value=3.9e-23 Score=193.59 Aligned_cols=165 Identities=22% Similarity=0.346 Sum_probs=133.6
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEc-ccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCC
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD 127 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~-~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~ 127 (257)
...+++.||.+.||.||||+|++||+|+.+||+||+|- +..+.+.||.+.|.|..+ .+..|-++|.++|.+...
T Consensus 229 ~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d-----~ie~Aa~lI~eii~~~~~ 303 (600)
T KOG1676|consen 229 SATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVD-----QIEHAAELINEIIAEAEA 303 (600)
T ss_pred cceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHH-----HHHHHHHHHHHHHHHHhc
Confidence 35899999999999999999999999999999999997 445578999999999965 677888888888866533
Q ss_pred CCchhhhhccCCC-cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHH
Q 025112 128 SNSEASKVAAGHV-AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206 (257)
Q Consensus 128 ~~~~~~~~~~~~~-~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v 206 (257)
.+.... ..+.. ....+.+.||.+.||.||||+|++||.|..+|||++.+.+. -|.. +..+++|+|.|++.+|
T Consensus 304 ~~~~~~--~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~---~~~ektf~IrG~~~QI 376 (600)
T KOG1676|consen 304 GAGGGM--GGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNG---NPKEKTFVIRGDKRQI 376 (600)
T ss_pred cCCCCc--CCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCC---CccceEEEEecCcccc
Confidence 211000 01111 11278999999999999999999999999999999998754 2221 3689999999999999
Q ss_pred HHHHHHHHHHHhcCCCCCc
Q 025112 207 LNALVEIGNQLRENPPRQV 225 (257)
Q Consensus 207 ~~A~~~I~~~l~e~~~~~~ 225 (257)
+.|..||.+++.+...+..
T Consensus 377 dhAk~LIr~kvg~~~~n~~ 395 (600)
T KOG1676|consen 377 DHAKQLIRDKVGDIAPNTP 395 (600)
T ss_pred hHHHHHHHHHhcccCCCCC
Confidence 9999999999999665543
No 7
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.82 E-value=9e-20 Score=156.45 Aligned_cols=163 Identities=26% Similarity=0.450 Sum_probs=132.4
Q ss_pred CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEc-ccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~-~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~ 124 (257)
......+||||..+.+|.|||++|+.||.||+++.++++|- .-.|++++|+|.+.|.++ .|..+++.|++++.+
T Consensus 119 ~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k-----~v~~~i~~il~~i~e 193 (390)
T KOG2192|consen 119 LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPK-----RVVECIKIILDLISE 193 (390)
T ss_pred CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcc-----hHHHHHHHHHHHhhc
Confidence 34568899999999999999999999999999999999986 456789999999999876 578899999999877
Q ss_pred CCCC-------------Cch------------------------------------------------------------
Q 025112 125 DDDS-------------NSE------------------------------------------------------------ 131 (257)
Q Consensus 125 ~~~~-------------~~~------------------------------------------------------------ 131 (257)
.... ..+
T Consensus 194 ~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~ 273 (390)
T KOG2192|consen 194 SPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWP 273 (390)
T ss_pred CCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCC
Confidence 4220 000
Q ss_pred ----hh-----hh-------------ccC--------CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025112 132 ----AS-----KV-------------AAG--------HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (257)
Q Consensus 132 ----~~-----~~-------------~~~--------~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~ 181 (257)
.+ .. .++ ..-..+.++.||.+.-|.||||+|.+|++|+.++||.|++...
T Consensus 274 saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep 353 (390)
T KOG2192|consen 274 SAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP 353 (390)
T ss_pred CcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc
Confidence 00 00 000 0114578999999999999999999999999999999998532
Q ss_pred CCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112 182 NQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 182 ~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~ 220 (257)
+. ++.+|+++|+|+.++++.|.+++...++..
T Consensus 354 --le-----GsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 354 --LE-----GSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred --CC-----CCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 21 478999999999999999999999999854
No 8
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.81 E-value=1.1e-18 Score=164.92 Aligned_cols=162 Identities=34% Similarity=0.539 Sum_probs=132.8
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC-
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD- 126 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~- 126 (257)
+.++||+||++++|.||||+|+.||+|+++|||+|++... .|.+++|.|+|.|.++ ++.+|+..|...|.+..
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 6899999999999999999999999999999999999865 7899999999999965 89999999999998731
Q ss_pred ---C---------C-------------C-ch---------------------hhhhc-----------------------
Q 025112 127 ---D---------S-------------N-SE---------------------ASKVA----------------------- 136 (257)
Q Consensus 127 ---~---------~-------------~-~~---------------------~~~~~----------------------- 136 (257)
. . . .. ..+..
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 1 0 0 00 00000
Q ss_pred ----cC-----------C-------------------------CcceEEEEEeecCccceeecCCChhHHHHHHHhCCeE
Q 025112 137 ----AG-----------H-------------------------VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATI 176 (257)
Q Consensus 137 ----~~-----------~-------------------------~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I 176 (257)
.. . ...++.+++||++++|+||||+|++|.+||+.|||.|
T Consensus 292 ~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I 371 (485)
T KOG2190|consen 292 GDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASI 371 (485)
T ss_pred ccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCce
Confidence 00 0 1226789999999999999999999999999999999
Q ss_pred EEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112 177 VILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 177 ~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~ 220 (257)
.+...++... ..++.++|+|...+...|.+++...+...
T Consensus 372 ~I~~~~~~~~-----~~e~~~~I~~~~~~~~~~~~~~~~~~~~~ 410 (485)
T KOG2190|consen 372 SILNKEEVSG-----VREALVQITGMLREDLLAQYLIRARLSAP 410 (485)
T ss_pred EEccccccCC-----cceeEEEecchhHHHHhhhhhcccccccC
Confidence 9987765422 68999999999999999999996666553
No 9
>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=99.79 E-value=5.9e-19 Score=146.52 Aligned_cols=146 Identities=21% Similarity=0.275 Sum_probs=110.6
Q ss_pred EEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEe---ccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112 54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIII---SSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (257)
Q Consensus 54 ilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I---~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~ 130 (257)
|.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.| ++. ..++.+|..+|..+.......
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 56899999999999999999999999999999953 356888 333 347888999888877643211
Q ss_pred hhhhhccCCCcceEE-EEEeec---------CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE
Q 025112 131 EASKVAAGHVAANTI-RLLIAG---------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS 200 (257)
Q Consensus 131 ~~~~~~~~~~~~~~~-~l~Vp~---------~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~ 200 (257)
++.+.. + ..+.. -+.|+. ..+|+|||++|++++.|++.|||+|.|. ++.|.|.
T Consensus 70 ~A~~l~-g--d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~--------------~~~v~i~ 132 (172)
T TIGR03665 70 KALKLL-D--DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY--------------GKTVGII 132 (172)
T ss_pred HHHHhc-C--CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc--------------CCEEEEE
Confidence 000000 0 01111 122332 3689999999999999999999999984 2679999
Q ss_pred cCHHHHHHHHHHHHHHHhcCCCCCcccC
Q 025112 201 GDVPAVLNALVEIGNQLRENPPRQVISI 228 (257)
Q Consensus 201 G~~~~v~~A~~~I~~~l~e~~~~~~~~~ 228 (257)
|++++++.|.++|.+++.+.++..+|++
T Consensus 133 G~~~~~~~A~~~i~~li~~~~~~~vy~~ 160 (172)
T TIGR03665 133 GDPEQVQIAREAIEMLIEGAPHGTVYKF 160 (172)
T ss_pred CCHHHHHHHHHHHHHHHcCCCChhHHHH
Confidence 9999999999999999988887765544
No 10
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.77 E-value=2.8e-18 Score=155.07 Aligned_cols=160 Identities=25% Similarity=0.385 Sum_probs=134.7
Q ss_pred CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~ 126 (257)
..-.+++.||...+|+||||+|.+||.|-..+|+.|+|... .+...+|-|+|+|+++ +-.+|-..|..+|.+..
T Consensus 409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppe-----aqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPE-----AQFKAQGRIFGKIKEEN 483 (584)
T ss_pred chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChH-----HHHhhhhhhhhhhhhhc
Confidence 45578999999999999999999999999999999999854 5668899999999975 56788899999998765
Q ss_pred CCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHH
Q 025112 127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206 (257)
Q Consensus 127 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v 206 (257)
......+ ......+.||...+|+||||||.++++|+.-|+|.+.|+. |+-|+ .++.-+|.|.|...++
T Consensus 484 f~~Pkee-------vklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPr-dqtpd----End~vivriiGhfyat 551 (584)
T KOG2193|consen 484 FFLPKEE-------VKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPR-DQTPD----ENDQVIVRIIGHFYAT 551 (584)
T ss_pred cCCchhh-------heeeeeeeccchhhhhhhccccccHHHHhccccceEEccc-cCCCC----ccceeeeeeechhhcc
Confidence 4432221 1246789999999999999999999999999999999864 55554 3667899999999999
Q ss_pred HHHHHHHHHHHhcCCCCC
Q 025112 207 LNALVEIGNQLRENPPRQ 224 (257)
Q Consensus 207 ~~A~~~I~~~l~e~~~~~ 224 (257)
+.|...|.++|.+....+
T Consensus 552 q~aQrki~~iv~qvkq~~ 569 (584)
T KOG2193|consen 552 QNAQRKIAHIVNQVKQSG 569 (584)
T ss_pred hHHHHHHHHHHHHHHHhh
Confidence 999999999999865544
No 11
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.75 E-value=1.5e-17 Score=139.10 Aligned_cols=149 Identities=21% Similarity=0.293 Sum_probs=111.2
Q ss_pred eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEec---cCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS---SKDNDNVVSDAENALQQIAALILKDD 126 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~---G~~~~~~~~~~~~A~~~I~~~i~~~~ 126 (257)
....+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|. +.. ..++.+|..+|..+.....
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 467899999999999999999999999999999999953 4567775 221 3478899999998877432
Q ss_pred CCCchhhhhccCCCcceEEEE-Eee---------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceE
Q 025112 127 DSNSEASKVAAGHVAANTIRL-LIA---------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV 196 (257)
Q Consensus 127 ~~~~~~~~~~~~~~~~~~~~l-~Vp---------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~ 196 (257)
.+ +..+.. + ..+..++ .+. ...+|+|||++|++++.|++.|||+|.|. ++.
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 0011111 111 13689999999999999999999999984 134
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCCCCCcc
Q 025112 197 VQISGDVPAVLNALVEIGNQLRENPPRQVI 226 (257)
Q Consensus 197 V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~ 226 (257)
|.|.|++++++.|...|.++++...+...+
T Consensus 135 v~i~G~~~~~~~A~~~I~~li~g~~~~~~~ 164 (180)
T PRK13763 135 VAIIGDPEQVEIAREAIEMLIEGAPHGTVY 164 (180)
T ss_pred EEEEeCHHHHHHHHHHHHHHHcCCCcHHHH
Confidence 999999999999999999999887766544
No 12
>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=99.52 E-value=4.8e-14 Score=98.56 Aligned_cols=64 Identities=42% Similarity=0.619 Sum_probs=57.2
Q ss_pred EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH
Q 025112 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG 214 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~ 214 (257)
++++||.+.+|+|||++|++|++|+++|||+|.+.+... +. ..+|+|+|+|+++++.+|+.+|.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~~-----~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-PG-----STERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-CC-----CCceEEEEEeCHHHHHHHHHhhC
Confidence 689999999999999999999999999999999975432 22 67899999999999999999873
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=99.46 E-value=8.2e-14 Score=97.40 Aligned_cols=63 Identities=43% Similarity=0.679 Sum_probs=56.1
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEEccccc-CCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA-RHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~-~~~ervv~I~G~~~~~~~~~~~~A~~~I 118 (257)
++||+||.+.+|+|||++|++|++|+++|||+|++.+... +..+|+|+|.|..+ ++.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPS-----AVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHH-----HHHHHHHhh
Confidence 3799999999999999999999999999999999997643 67899999999954 788888776
No 14
>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=99.35 E-value=1.6e-12 Score=89.77 Aligned_cols=61 Identities=26% Similarity=0.332 Sum_probs=54.6
Q ss_pred EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH
Q 025112 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG 214 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~ 214 (257)
.++.||..++|+|||++|++|++|+++|||+|.+++.. +.++.|+|+|++++|.+|..+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~---------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG---------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC---------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999996532 35789999999999999998873
No 15
>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=99.35 E-value=1.9e-12 Score=88.79 Aligned_cols=60 Identities=32% Similarity=0.445 Sum_probs=53.8
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I 213 (257)
|.++.||..++|+|||++|++|++|+++|||+|.+++. +.+..|+|+|++++|++|+++|
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 16
>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=99.31 E-value=9.2e-12 Score=85.93 Aligned_cols=57 Identities=26% Similarity=0.278 Sum_probs=51.8
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC-HHHHHHHHHHH
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEI 213 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~-~~~v~~A~~~I 213 (257)
...+.||.+++|+|||++|++|++|+++|||+|.+. .++.|+|+|+ +++++.|.++|
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 2467999998 89999999887
No 17
>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=99.29 E-value=1.8e-11 Score=84.57 Aligned_cols=62 Identities=34% Similarity=0.500 Sum_probs=55.3
Q ss_pred EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025112 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I 213 (257)
.++.||.+++++|||++|++|++|+++|||+|.|..... ...++.|+|.|+.+++..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-------~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-------GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-------CCCceEEEEEcCHHHHHHHHHHh
Confidence 578999999999999999999999999999999975322 15689999999999999999876
No 18
>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=99.26 E-value=3.5e-12 Score=87.47 Aligned_cols=60 Identities=40% Similarity=0.609 Sum_probs=51.6
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I 118 (257)
|++|.||.+.+|+|||++|++|++|+++|||+|+|++. + .+..|+|+|.++ ++.+|+++|
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-ERDIVTISGSPE-----QVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHH-----HHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHH-----HHHHHHhhC
Confidence 57899999999999999999999999999999999876 2 455899999643 677777665
No 19
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.26 E-value=6e-11 Score=98.70 Aligned_cols=156 Identities=19% Similarity=0.223 Sum_probs=112.9
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCC
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS 128 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~ 128 (257)
.....+.||...++-+||+.|++.+.|++.+++++.++ +.+..|.|.....-.......+|...|..+-..+..+
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 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 34567999999999999999999999999999999999 5567788866531111235566666666654443221
Q ss_pred CchhhhhccCCCcceEEEE------Ee-e----cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEE
Q 025112 129 NSEASKVAAGHVAANTIRL------LI-A----GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV 197 (257)
Q Consensus 129 ~~~~~~~~~~~~~~~~~~l------~V-p----~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V 197 (257)
. +.+.- .+...+.+ .- + ....|+|||++|.+.+.|++.|||.|.|. ...|
T Consensus 82 ~--A~~LL---~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~--------------g~tV 142 (194)
T COG1094 82 K--ALKLL---EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY--------------GKTV 142 (194)
T ss_pred H--HHHHh---cCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe--------------CcEE
Confidence 1 00000 00001110 00 1 22469999999999999999999999985 4679
Q ss_pred EEEcCHHHHHHHHHHHHHHHhcCCCCCcccC
Q 025112 198 QISGDVPAVLNALVEIGNQLRENPPRQVISI 228 (257)
Q Consensus 198 ~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~ 228 (257)
.|.|.+++++.|.+.|.+++...+++.++.|
T Consensus 143 aiiG~~~~v~iAr~AVemli~G~~h~~Vy~f 173 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLINGAPHGKVYKF 173 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcCCCchhHHHH
Confidence 9999999999999999999999998876644
No 20
>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=6.3e-12 Score=86.79 Aligned_cols=60 Identities=30% Similarity=0.450 Sum_probs=52.2
Q ss_pred EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I 118 (257)
.+|.||.++++.|||++|++|++|+++|||+|.|++.. ..++.|+|+|+++ ++..|..+|
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 57899999999999999999999999999999999763 6789999999953 566666654
No 21
>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=99.21 E-value=2.9e-11 Score=83.58 Aligned_cols=62 Identities=44% Similarity=0.669 Sum_probs=53.4
Q ss_pred EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I 118 (257)
.+|.||.++++.|||++|++|++|+++|||+|.|++......++.|.|.|..+ ++..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~-----~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPE-----AVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHH-----HHHHHHHHh
Confidence 68999999999999999999999999999999999765456789999999843 566666554
No 22
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.21 E-value=9.9e-11 Score=103.67 Aligned_cols=79 Identities=30% Similarity=0.479 Sum_probs=71.7
Q ss_pred cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC-CCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
..+.++++||+..+|.||||+|++|.+||.+|||+|++.+..+ .|. .+||+|.|+|+.+++..-.+.|.++|+|
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG-----TTeRvcli~Gt~eai~av~efI~dKire 111 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG-----TTERVCLIQGTVEALNAVHEFIADKIRE 111 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC-----ccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence 3478999999999999999999999999999999999987544 454 8999999999999999999999999999
Q ss_pred CCCCC
Q 025112 220 NPPRQ 224 (257)
Q Consensus 220 ~~~~~ 224 (257)
.++..
T Consensus 112 ~p~~~ 116 (402)
T KOG2191|consen 112 KPQAV 116 (402)
T ss_pred hHHhh
Confidence 87654
No 23
>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=99.16 E-value=7.8e-11 Score=81.29 Aligned_cols=58 Identities=36% Similarity=0.542 Sum_probs=48.3
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHH
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I 118 (257)
...|.||.+.+|+||||+|++|++|+++|||+|++++ ++.|.|+|... .++++|..+|
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~----~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDK----EAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCH----HHHHHHHHHh
Confidence 5678999999999999999999999999999999985 35799999732 2456666554
No 24
>PF13014 KH_3: KH domain
Probab=99.12 E-value=9.6e-11 Score=75.05 Aligned_cols=42 Identities=43% Similarity=0.673 Sum_probs=38.3
Q ss_pred cccceeccCchhHHHHHhhhCceEEEcc-cccCCCccEEEecc
Q 025112 60 QIGKVIGKEGHRIQKIREETKATIKIAD-AIARHEERVIIISS 101 (257)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~tg~~I~i~~-~~~~~~ervv~I~G 101 (257)
+||+|||++|++|++|+++|+|+|+|++ ..++..++.|+|+|
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 45578899999987
No 25
>PF13014 KH_3: KH domain
Probab=99.10 E-value=1.8e-10 Score=73.73 Aligned_cols=43 Identities=37% Similarity=0.652 Sum_probs=37.2
Q ss_pred ccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc
Q 025112 153 QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG 201 (257)
Q Consensus 153 ~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G 201 (257)
+||+|||++|++|++|+++|||+|+|++ +..+ ++.++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~-----~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEP-----GSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccCC-----CCCceEEEEEC
Confidence 5799999999999999999999999976 3333 37899999998
No 26
>smart00322 KH K homology RNA-binding domain.
Probab=99.03 E-value=2.4e-09 Score=73.89 Aligned_cols=67 Identities=33% Similarity=0.457 Sum_probs=59.0
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~ 218 (257)
.+.++.||...+|++||++|++|++|++.||++|.+.... .....|+|.|..+++..|..+|.+.+.
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~---------~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG---------SEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC---------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 4688999999999999999999999999999999985321 246889999999999999999988763
No 27
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.93 E-value=1e-09 Score=96.63 Aligned_cols=151 Identities=21% Similarity=0.315 Sum_probs=112.5
Q ss_pred CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC-
Q 025112 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD- 126 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~- 126 (257)
+.++..+-||+..++.|.|++|.+||.|+.+|..+|+-+.. ..+.++.++|..+ +|..|.++|...-.-..
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 67888999999999999999999999999999999999865 5568899999976 56677666555111100
Q ss_pred --CCCchhhhh-ccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025112 127 --DSNSEASKV-AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (257)
Q Consensus 127 --~~~~~~~~~-~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~ 203 (257)
........+ .+...++.+.+.-+|...+|.|.|..|++|+.|++.++..|..+-+ ..+.++.++|-+
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 000000000 0112456788899999999999999999999999999999987532 367899999999
Q ss_pred HH-HHHHH-HHHHHH
Q 025112 204 PA-VLNAL-VEIGNQ 216 (257)
Q Consensus 204 ~~-v~~A~-~~I~~~ 216 (257)
.+ +++|. +.|...
T Consensus 166 ~nC~kra~s~eie~t 180 (394)
T KOG2113|consen 166 KNCVKRARSCEIEQT 180 (394)
T ss_pred cchhhhccccchhhh
Confidence 88 45554 444443
No 28
>smart00322 KH K homology RNA-binding domain.
Probab=98.90 E-value=7.1e-09 Score=71.44 Aligned_cols=67 Identities=34% Similarity=0.586 Sum_probs=55.9
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHH
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI 122 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i 122 (257)
....++.||...+|.+||++|++|++|++++|++|.+.... .....+.|.|..+ ++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--~~~~~v~i~g~~~-----~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--SEERVVEITGPPE-----NVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--CCccEEEEEcCHH-----HHHHHHHHHHHHh
Confidence 35789999999999999999999999999999999998542 2578899999843 6777777776654
No 29
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.75 E-value=1.1e-08 Score=96.13 Aligned_cols=145 Identities=26% Similarity=0.385 Sum_probs=116.4
Q ss_pred CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~ 126 (257)
..++.++++|+...+-.||||.|++|+.|++.+++||.+.... ..++++.++.|-+. ++..|...+++++....
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~-----~v~~a~a~~~~~~~~~~ 138 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPV-----QVCKAKAAIHQILTENT 138 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCC-----CCChHHHHHHHHHhcCC
Confidence 3678999999999999999999999999999999999998542 25677777776543 45566666677665442
Q ss_pred CCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHH
Q 025112 127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206 (257)
Q Consensus 127 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v 206 (257)
. +...+-+|...+++++|++|.++.+|+.-++++|.+-. + .. ....+...|.|....+
T Consensus 139 p---------------vk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~-n-gr-----~g~~~~~~i~~qqk~~ 196 (608)
T KOG2279|consen 139 P---------------VSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDK-N-GR-----LGLSRLIKISGQQKEV 196 (608)
T ss_pred c---------------ccccccchhhhcccccccchhhhcchhccccccccccc-c-cc-----cccccceecccccchH
Confidence 1 35678899999999999999999999999999999742 2 11 1467888888888888
Q ss_pred HHHHHHHHHHHhc
Q 025112 207 LNALVEIGNQLRE 219 (257)
Q Consensus 207 ~~A~~~I~~~l~e 219 (257)
+.|..++.+.+.+
T Consensus 197 ~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 197 AAAKHLILEKVSE 209 (608)
T ss_pred HHHHhhhhccccc
Confidence 8999999888876
No 30
>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=98.61 E-value=2e-07 Score=72.86 Aligned_cols=71 Identities=21% Similarity=0.289 Sum_probs=53.6
Q ss_pred cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCC-----------cccCCCCCceEEEEEcCH---HHHHHHHHHHHHH
Q 025112 151 GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP-----------LCASAHESDRVVQISGDV---PAVLNALVEIGNQ 216 (257)
Q Consensus 151 ~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p-----------~~~~~~~~~r~V~I~G~~---~~v~~A~~~I~~~ 216 (257)
.+++|.|||++|++||+|+++|||+|.|-.+.... .... .+..-.|.|++.. +++.+|.++|..+
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 46789999999999999999999999986431110 0000 0233679999965 8999999999999
Q ss_pred HhcCCC
Q 025112 217 LRENPP 222 (257)
Q Consensus 217 l~e~~~ 222 (257)
+.+..+
T Consensus 93 l~~~~~ 98 (120)
T cd02395 93 LKPAIE 98 (120)
T ss_pred hccCCC
Confidence 996543
No 31
>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=98.51 E-value=1.7e-07 Score=77.95 Aligned_cols=61 Identities=25% Similarity=0.320 Sum_probs=54.4
Q ss_pred EEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEE---EcCHHHHHHHHHHHHHHHhc
Q 025112 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI---SGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 147 l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I---~G~~~~v~~A~~~I~~~l~e 219 (257)
+.||.+.+|.|||++|++|+.|+++|||+|++.. .+..|.| +++++++.+|..+|..+.+.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~------------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS------------ETGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc------------CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 5689999999999999999999999999999852 2356888 89999999999999998885
No 32
>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=98.51 E-value=3e-07 Score=71.84 Aligned_cols=72 Identities=19% Similarity=0.368 Sum_probs=52.5
Q ss_pred EEEecC------ccccceeccCchhHHHHHhhhCceEEEcccccC-----------------CCccEEEeccCCCCchhh
Q 025112 53 RIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADAIAR-----------------HEERVIIISSKDNDNVVS 109 (257)
Q Consensus 53 rilVP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~-----------------~~ervv~I~G~~~~~~~~ 109 (257)
|+.||. +++|.|||++|.++|+|+++|||+|.|...... ...--|.|++...+ ..
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 455554 468999999999999999999999999954100 12246888887511 13
Q ss_pred HHHHHHHHHHHHHhcCC
Q 025112 110 DAENALQQIAALILKDD 126 (257)
Q Consensus 110 ~~~~A~~~I~~~i~~~~ 126 (257)
++.+|+.+|..++....
T Consensus 81 ~~~~A~~~I~~ll~~~~ 97 (120)
T cd02395 81 ALAKAVEAIEELLKPAI 97 (120)
T ss_pred HHHHHHHHHHHHhccCC
Confidence 67888888888887554
No 33
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.48 E-value=3.6e-07 Score=76.47 Aligned_cols=64 Identities=25% Similarity=0.260 Sum_probs=57.4
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE----cCHHHHHHHHHHHHHHHhc
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS----GDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~----G~~~~v~~A~~~I~~~l~e 219 (257)
...+.||.+.+|.|||++|++|+.|+++|||+|++.. .+..|.|. ++++++++|.++|..++..
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 5788999999999999999999999999999999852 23678885 8999999999999999885
No 34
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.46 E-value=5.3e-07 Score=72.39 Aligned_cols=103 Identities=17% Similarity=0.298 Sum_probs=72.8
Q ss_pred eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCC
Q 025112 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~ 129 (257)
-.+.|+|+...+|+.||++|++|++|++..|-+|++-... + +....|...+.......
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 4688999999999999999999999999999888887541 1 12222333322111000
Q ss_pred chhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEE
Q 025112 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (257)
Q Consensus 130 ~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i 178 (257)
.. . ..........+.|+....|.+|||+|.+++.++.-+|-++.+
T Consensus 90 v~---I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 90 VT---I-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EE---E-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 00 0 000112357788999999999999999999999999998876
No 35
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.43 E-value=6.7e-07 Score=89.52 Aligned_cols=146 Identities=20% Similarity=0.285 Sum_probs=116.0
Q ss_pred CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~ 126 (257)
...+...+-+-...+..++||+|.+|.+|++++.|.+.+... +..+..+.++|..+ ...+|...+...+.+..
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 455888899999999999999999999999999999999985 46778899999865 46777777777776654
Q ss_pred CCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhC-CeEEEeCCCCCCcccCCCCCceEEEEEcCHHH
Q 025112 127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG-ATIVILAPNQLPLCASAHESDRVVQISGDVPA 205 (257)
Q Consensus 127 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~ 205 (257)
.+ .....+.+|...+.++||.+|..|..|..++| .+|++... .+....+++.|....
T Consensus 417 n~-------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~---------~~~~~~~~~~~~~~d 474 (753)
T KOG2208|consen 417 NS-------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN---------NNSSDMVTIRGISKD 474 (753)
T ss_pred cc-------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC---------CcccccceEeccccc
Confidence 32 12467899999999999999999999999999 66665332 134566888888888
Q ss_pred HHHHHHHHHHHHhcCC
Q 025112 206 VLNALVEIGNQLRENP 221 (257)
Q Consensus 206 v~~A~~~I~~~l~e~~ 221 (257)
+..+..+...+..+..
T Consensus 475 v~~~~~~~~~~~~~a~ 490 (753)
T KOG2208|consen 475 VEKSVSLLKALKADAK 490 (753)
T ss_pred cchhHHHHHhhhhhhh
Confidence 8777777766666544
No 36
>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=98.31 E-value=3.5e-06 Score=83.28 Aligned_cols=94 Identities=24% Similarity=0.307 Sum_probs=74.2
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (257)
Q Consensus 108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (257)
+..+.+++..|++.+.+..... ... ....+....+.||.+.+|.|||+||.+||.|+++|||+|.+.
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-DEM----SPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-------- 614 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc-ccc----ccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe--------
Confidence 4566788888888886653322 111 112345788999999999999999999999999999999984
Q ss_pred cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
.+..|.|.+ +.+++++|+.+|..++..
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 357799988 568999999999999995
No 37
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.31 E-value=1.3e-06 Score=82.38 Aligned_cols=185 Identities=18% Similarity=0.194 Sum_probs=124.1
Q ss_pred CCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112 45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 45 ~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~ 124 (257)
..+..+.+.+-+|...+++|+|++|++++.|+.-++++|.+.........+...|.+... ....|..++.+.+.+
T Consensus 135 ~~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk-----~~~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 135 TENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQK-----EVAAAKHLILEKVSE 209 (608)
T ss_pred hcCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccc-----hHHHHHhhhhccccc
Confidence 345678889999999999999999999999999999999999764445677788888654 223444555555543
Q ss_pred CCCCC------------------------------------chhh----hh------------------------ccC--
Q 025112 125 DDDSN------------------------------------SEAS----KV------------------------AAG-- 138 (257)
Q Consensus 125 ~~~~~------------------------------------~~~~----~~------------------------~~~-- 138 (257)
..... .... +. .++
T Consensus 210 deelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~ 289 (608)
T KOG2279|consen 210 DEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSF 289 (608)
T ss_pred hhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccccc
Confidence 21100 0000 00 000
Q ss_pred --CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH--
Q 025112 139 --HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG-- 214 (257)
Q Consensus 139 --~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~-- 214 (257)
........+.+|...+|.+||+.|+.++.+...+++.+.|... |.... -..-.++.+.|+..-+.+|..++.
T Consensus 290 ~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~---pyt~~-v~~~qic~~egkqh~~n~vl~ml~~~ 365 (608)
T KOG2279|consen 290 QKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ---PYTSR-VLQLQICVNEGKQHYENSVLEMLTVH 365 (608)
T ss_pred ccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec---cccch-hhhhhhheecchhHHHHHHHhhhhcc
Confidence 1123456788999999999999999999999999999998642 32000 011256889999999999999988
Q ss_pred ---HHHhcCCCCCc-ccCCCCCCCCCCC
Q 025112 215 ---NQLRENPPRQV-ISISPAYNYSAIR 238 (257)
Q Consensus 215 ---~~l~e~~~~~~-~~~~p~~~~~~~~ 238 (257)
....|-+-.++ ++..|--++..++
T Consensus 366 ~p~~~f~eLnl~~~~~p~lps~al~~L~ 393 (608)
T KOG2279|consen 366 VPDIVFAELNLNGSWYPALPSGALENLN 393 (608)
T ss_pred CCccccccccccCccCcccCcccccccC
Confidence 44444444443 2344444444443
No 38
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.20 E-value=7.3e-06 Score=82.18 Aligned_cols=164 Identities=22% Similarity=0.254 Sum_probs=109.5
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCch--hhHHHHHHHHHHHHH-hc-
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNV--VSDAENALQQIAALI-LK- 124 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~--~~~~~~A~~~I~~~i-~~- 124 (257)
-+..++.+-...++++||++|.+++.+++++.+.++|++..-..+ ...+.|..+.-. ...++.++.++..-. .+
T Consensus 200 ~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~--~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~ 277 (753)
T KOG2208|consen 200 SVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSP--SNKIDGRLNSSSSINVEIQEALTRLESEFDYDE 277 (753)
T ss_pred eEEEEeeccccchhhhccccccccccccccceeEEEcccccccch--hhhhccccccceehhhhhHHHHHHhcChhhhhh
Confidence 388999999999999999999999999999999999996532211 122222111100 011222222221100 00
Q ss_pred ---------------------------CCCCCch------hh-----hhc-------------cCCCcceEEEEEeecCc
Q 025112 125 ---------------------------DDDSNSE------AS-----KVA-------------AGHVAANTIRLLIAGSQ 153 (257)
Q Consensus 125 ---------------------------~~~~~~~------~~-----~~~-------------~~~~~~~~~~l~Vp~~~ 153 (257)
......+ .. +.. .-........+.+....
T Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~ 357 (753)
T KOG2208|consen 278 IIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEE 357 (753)
T ss_pred hhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHh
Confidence 0000000 00 000 00012356778888999
Q ss_pred cceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 025112 154 AGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223 (257)
Q Consensus 154 vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~ 223 (257)
+..++|++|.+|.+|++.+.|.|.+... ++.+..+.++|...++.+|...+...+.+-+.+
T Consensus 358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~---------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~ 418 (753)
T KOG2208|consen 358 LKFVIGKKGANIEKIREESQVKIDLPKQ---------GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS 418 (753)
T ss_pred hhhhcCCCCccHHHHHHhhhhceecccc---------cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc
Confidence 9999999999999999999999998642 256789999999999999999999999997763
No 39
>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=98.14 E-value=1.1e-05 Score=64.69 Aligned_cols=103 Identities=19% Similarity=0.281 Sum_probs=71.6
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~ 130 (257)
-+-|+|....+|+.||++|++|++|++..|-+|++-.. +++. ...|...+.-......
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey---s~D~-------------------~~fI~N~l~PA~V~~V 91 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY---SENL-------------------EEFVANKLAPAEVKNV 91 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc---CCCH-------------------HHHHHHcCCCceEEEE
Confidence 68899999999999999999999999999988888754 1110 1111111111000000
Q ss_pred hhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEe
Q 025112 131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVIL 179 (257)
Q Consensus 131 ~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~ 179 (257)
.. ....+.....+.||.+..+..|||+|.|++...+-+|-++.+.
T Consensus 92 ---~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 92 ---TV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred ---EE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 00 0011224678889999999999999999999999999888763
No 40
>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=98.02 E-value=1.7e-05 Score=79.09 Aligned_cols=95 Identities=22% Similarity=0.199 Sum_probs=69.1
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (257)
Q Consensus 108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (257)
+..+.+++..|++.+.+........ .....+....+.||.+.+|.|||+||++||.|+++|||+|.|.
T Consensus 520 l~~a~~~~~~I~~~m~~~l~~~~~~----~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-------- 587 (684)
T TIGR03591 520 LEQAKEGRLHILGEMNKVISEPRAE----LSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-------- 587 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhcc----ccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe--------
Confidence 3355667777777775532211000 0111234678899999999999999999999999999999984
Q ss_pred cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
.+..|.|.+ ..+.+++|..+|..+..+
T Consensus 588 -----ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 588 -----DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred -----cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 246677777 567899999999988775
No 41
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.80 E-value=3.7e-05 Score=76.15 Aligned_cols=66 Identities=33% Similarity=0.524 Sum_probs=56.7
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~ 124 (257)
.-...|.||.+.+|.|||+||.+||.|+++||++|+|.+ +..|.|.+... ..+++|+.+|..+...
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 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADG----PSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCH----HHHHHHHHHHHHhhCc
Confidence 456788889999999999999999999999999999985 46788988753 3678899999888874
No 42
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.78 E-value=8.4e-05 Score=62.54 Aligned_cols=103 Identities=20% Similarity=0.297 Sum_probs=71.1
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~ 130 (257)
.+-+++-.+.+|..||++|++|+.|+++.|-+|+|-... ++ -...|...+.--.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~d---------~~~fI~nal~Pa~---- 130 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------ED---------PAEFIKNALAPAE---- 130 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------CC---------HHHHHHHhcCcce----
Confidence 566677778899999999999999999999888777541 11 0112222222000
Q ss_pred hhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112 131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 131 ~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
...+.-...+.....+.||.+..+.+|||+|.+++-+.+-||-++.|..
T Consensus 131 -v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 131 -VLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred -EeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0000000001126788899999999999999999999999999999964
No 43
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.77 E-value=7.5e-05 Score=75.56 Aligned_cols=99 Identities=16% Similarity=0.195 Sum_probs=73.1
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCe-EEEeCCCCCCc
Q 025112 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPL 186 (257)
Q Consensus 108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~ 186 (257)
+..+.+++..|++.+.+.....-.. ..........+.||.+.+|.|||.||.+||.|.++||++ |.+.
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~----~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~------- 722 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKR----LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------- 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhh----hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-------
Confidence 4456777777887776543211110 111234578889999999999999999999999999999 8862
Q ss_pred ccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCCCC
Q 025112 187 CASAHESDRVVQISG-DVPAVLNALVEIGNQLRENPPR 223 (257)
Q Consensus 187 ~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~~~~ 223 (257)
.+-.|.|.+ +.+.+++|+++|..++.+....
T Consensus 723 ------ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG 754 (891)
T PLN00207 723 ------DDGTVKITAKDLSSLEKSKAIISSLTMVPTVG 754 (891)
T ss_pred ------CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCC
Confidence 356788888 5689999999999998754333
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.66 E-value=0.00034 Score=65.72 Aligned_cols=78 Identities=21% Similarity=0.249 Sum_probs=57.4
Q ss_pred ceEEEEEee------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCccc---------CCCCCceEEEEEcC-HHH
Q 025112 142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA---------SAHESDRVVQISGD-VPA 205 (257)
Q Consensus 142 ~~~~~l~Vp------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~---------~~~~~~r~V~I~G~-~~~ 205 (257)
....+|.|| .++||.|||..|.+.|+|+++|||+|.|.-+..+-+.. .-...+=-+.|+++ .+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 346678887 46899999999999999999999999997421111000 00123346888886 569
Q ss_pred HHHHHHHHHHHHhc
Q 025112 206 VLNALVEIGNQLRE 219 (257)
Q Consensus 206 v~~A~~~I~~~l~e 219 (257)
|++|++.|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999996
No 45
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.64 E-value=0.00015 Score=70.69 Aligned_cols=111 Identities=22% Similarity=0.223 Sum_probs=81.3
Q ss_pred EEeccCCCC---chhhHHHHHHHHHHHHHhcCCCCC-chhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHh
Q 025112 97 IIISSKDND---NVVSDAENALQQIAALILKDDDSN-SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 97 v~I~G~~~~---~~~~~~~~A~~~I~~~i~~~~~~~-~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
+.|.|-... ..+..++.|..+|+..+.+-.... .+.. ........+.|+...++-+||++|.+|++|.++|
T Consensus 507 iKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els-----~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eet 581 (692)
T COG1185 507 IKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELS-----PYAPRIETIKIDPDKIRDVIGPGGKTIKAITEET 581 (692)
T ss_pred eeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh-----ccCCceEEEccCHHHHhhccCCcccchhhhhhhh
Confidence 455554432 124466777888888886643321 1111 1123467888999999999999999999999999
Q ss_pred CCeEEEeCCCCCCcccCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcCCCCCc
Q 025112 173 GATIVILAPNQLPLCASAHESDRVVQISGDV-PAVLNALVEIGNQLRENPPRQV 225 (257)
Q Consensus 173 ga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~-~~v~~A~~~I~~~l~e~~~~~~ 225 (257)
||+|++. .+..|.|.++. +.+.+|++.|.++.++......
T Consensus 582 g~~Idie-------------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~i 622 (692)
T COG1185 582 GVKIDIE-------------DDGTVKIAASDGESAKKAKERIEAITREVEVGEV 622 (692)
T ss_pred CcEEEec-------------CCCcEEEEecchHHHHHHHHHHHHHHhhcccccE
Confidence 9999984 34668999976 7999999999999988666554
No 46
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.64 E-value=0.00011 Score=67.94 Aligned_cols=69 Identities=20% Similarity=0.250 Sum_probs=56.2
Q ss_pred cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
+...+.+.|-+++||.|||++|++|++||..|+++|++..- +.+..|+|.|...--.+|...|...++.
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~----------~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC----------DLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc----------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 34567788999999999999999999999999999999642 4678899999988666666666554443
No 47
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.49 E-value=0.00014 Score=72.63 Aligned_cols=66 Identities=32% Similarity=0.455 Sum_probs=53.0
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~ 124 (257)
.-...+.||.+.++.|||+||.+||+|+++|||+|+|.+ +..|.|.+... ..+.+|..+|..+..+
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~----~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDG----EAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcH----HHHHHHHHHHHhhhcc
Confidence 456788899999999999999999999999999999985 34577777543 2567777777776543
No 48
>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=97.43 E-value=0.00023 Score=48.90 Aligned_cols=37 Identities=30% Similarity=0.504 Sum_probs=34.4
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEE
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i 85 (257)
+....+.|+.+.+|..|||+|.+|+.+++.++-+|++
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4678999999999999999999999999999988876
No 49
>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=97.40 E-value=9.6e-05 Score=67.72 Aligned_cols=94 Identities=22% Similarity=0.336 Sum_probs=63.7
Q ss_pred cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025112 60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138 (257)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~ 138 (257)
-+|+.||++|++|+.|.++. |=+|+|-.. +++.. ..|...+.-. ....+.-.
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~---s~d~~-------------------~fi~nal~Pa-----~v~~v~i~ 296 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEY---SDDPA-------------------EFIANALSPA-----KVISVEVL 296 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhcCCc-----eEEEEEEE
Confidence 39999999999999999998 888887754 11110 1111111000 00000000
Q ss_pred CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112 139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
........+.||.++.+..|||+|.|++-..+-||.+|.|.+
T Consensus 297 ~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 297 DEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 001136899999999999999999999999999999999975
No 50
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.39 E-value=0.00027 Score=66.38 Aligned_cols=72 Identities=24% Similarity=0.386 Sum_probs=54.9
Q ss_pred CeEEEEEecC------ccccceeccCchhHHHHHhhhCceEEEccc------c---------cCC-CccEEEeccCCCCc
Q 025112 49 DVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA------I---------ARH-EERVIIISSKDNDN 106 (257)
Q Consensus 49 ~~~~rilVP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~------~---------~~~-~ervv~I~G~~~~~ 106 (257)
.++-|+.||. +++|+|||..|.|.|+|+++|||||.|--. . ++. .+--|.|++...
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 6777888886 469999999999999999999999999731 0 111 122377777654
Q ss_pred hhhHHHHHHHHHHHHHhc
Q 025112 107 VVSDAENALQQIAALILK 124 (257)
Q Consensus 107 ~~~~~~~A~~~I~~~i~~ 124 (257)
+.+++|+..|..+|.+
T Consensus 215 --eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 215 --EKIKKAIAVIENLIQS 230 (554)
T ss_pred --HHHHHHHHHHHHHHHh
Confidence 4788999999888875
No 51
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.34 E-value=0.00023 Score=62.05 Aligned_cols=42 Identities=26% Similarity=0.600 Sum_probs=37.5
Q ss_pred CCCCeEEEEEecCc------cccceeccCchhHHHHHhhhCceEEEcc
Q 025112 46 KAQDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIAD 87 (257)
Q Consensus 46 ~~~~~~~rilVP~~------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~ 87 (257)
+.-.++.||+||.. +||+|+|++|.++|+|+++|+|+|-|--
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 44568899999986 6999999999999999999999999983
No 52
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.34 E-value=0.0007 Score=62.45 Aligned_cols=96 Identities=21% Similarity=0.196 Sum_probs=65.3
Q ss_pred cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025112 60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138 (257)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~ 138 (257)
-+|+.||++|.+|+.|.++. |=+|+|-.. +++.. ..|...+.-.. ...+...
T Consensus 252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~~---s~D~~-------------------~fI~Nal~Pa~-----V~~V~i~ 304 (374)
T PRK12328 252 PIGATVGVKGVRINAVSKELNGENIDCIEY---SNVPE-------------------IFIARALAPAI-----ISSVKIE 304 (374)
T ss_pred hHHhhcCCCcchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhCCCce-----eeEEEEc
Confidence 49999999999999999998 788887654 11111 11111111000 0000000
Q ss_pred CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC
Q 025112 139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ 183 (257)
Q Consensus 139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~ 183 (257)
.......+.||..+.+..|||+|.|++-..+-||.+|.|.+-.+
T Consensus 305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 11236789999999999999999999999999999999986443
No 53
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.32 E-value=0.00044 Score=69.18 Aligned_cols=95 Identities=21% Similarity=0.202 Sum_probs=69.7
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (257)
Q Consensus 108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (257)
+..+.+++.+|++.+.+......... .........+.||.+.++.+||+||.+||.|.++||+.|.+.
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 34567778888888876432211111 111223467778999999999999999999999999998862
Q ss_pred cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
.+-.|.|.+ ..+.+++|..+|..+..+
T Consensus 591 -----d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 -----DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred -----CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 246688888 567999999999998875
No 54
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.21 E-value=0.00084 Score=62.01 Aligned_cols=105 Identities=25% Similarity=0.297 Sum_probs=69.1
Q ss_pred eEEEEEecCc-----cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112 50 VLFRIIVPSR-----QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (257)
Q Consensus 50 ~~~rilVP~~-----~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~ 123 (257)
.-.++-|-+. -+|+.||++|.+|+.|.++. |=+|+|-.. +++. ...|...+.
T Consensus 231 ~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~~---s~d~-------------------~~fi~nal~ 288 (362)
T PRK12327 231 DRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIIDW---SEDP-------------------AEFVANALS 288 (362)
T ss_pred ceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhCCCeEEEEEc---CCCH-------------------HHHHHHhCC
Confidence 3445555433 49999999999999999998 888887754 1111 011111111
Q ss_pred cCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025112 124 KDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (257)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~ 181 (257)
-. ....+...........+.||.++.+..|||+|.|++-..+-||.+|.|.+.
T Consensus 289 Pa-----~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 289 PA-----KVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred Cc-----eEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 00 000000000112468999999999999999999999999999999999753
No 55
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.19 E-value=0.00037 Score=62.59 Aligned_cols=72 Identities=33% Similarity=0.370 Sum_probs=58.1
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~ 126 (257)
+....++|+++..|+|||++|.|.++|+++|+++|.++.+. .....+.|+|-. .+.|.+|..+|..+|.+..
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 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN--TNKEEIKIIGIS----RNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC--CCcceEEEeehh----HHHHHHHHHHHHHHHHhhh
Confidence 56778999999999999999999999999999999999873 334446666654 3467888888888886653
No 56
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.11 E-value=0.0008 Score=60.46 Aligned_cols=70 Identities=26% Similarity=0.419 Sum_probs=57.6
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCC
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRENP 221 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~~ 221 (257)
....+.+++...|.|||++|.+.++|+++|+|+|.++.+. .....++|+| +.+.|.+|.+.|..+|.+.-
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 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN---------TNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC---------CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 4567889999999999999999999999999999987642 2334455555 67899999999999988854
No 57
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.08 E-value=0.00038 Score=61.96 Aligned_cols=65 Identities=18% Similarity=0.242 Sum_probs=57.7
Q ss_pred cceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 025112 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGN 215 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 215 (257)
+..+..+.||+.+++-+.|++|.+||.|+.+|.++|+-+... .+.++.++|..+.|..|+..|..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~----------eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG----------EEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC----------CCCcceeccCchhHHHHhhcCcc
Confidence 456889999999999999999999999999999999987542 35789999999999999988865
No 58
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.06 E-value=0.00075 Score=62.61 Aligned_cols=55 Identities=25% Similarity=0.439 Sum_probs=48.2
Q ss_pred CCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCC
Q 025112 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD 103 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~ 103 (257)
..+++.+.|.|-++.||.+||++|++||.||..|+++|++... ..+-.|+|-|..
T Consensus 43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN 97 (629)
T ss_pred CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence 4578999999999999999999999999999999999999864 456678888864
No 59
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.05 E-value=0.0016 Score=62.17 Aligned_cols=104 Identities=25% Similarity=0.330 Sum_probs=68.9
Q ss_pred eEEEEEecCc-----cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112 50 VLFRIIVPSR-----QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (257)
Q Consensus 50 ~~~rilVP~~-----~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~ 123 (257)
.-.++-|-+. -+|+.||++|++|+.|.++. |=+|+|-.. +++.. ..|...+.
T Consensus 231 ~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~---s~d~~-------------------~fi~nal~ 288 (470)
T PRK09202 231 SRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILW---SDDPA-------------------QFIINALS 288 (470)
T ss_pred ceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhCC
Confidence 3445555443 38999999999999999998 888887754 11111 11111111
Q ss_pred cCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025112 124 KDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (257)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~ 181 (257)
-.. ...+... .......+.||..+.+..|||+|.|++-..+-||.+|.|...
T Consensus 289 pa~-----v~~v~~~-~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 289 PAE-----VSSVVVD-EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CCE-----EEEEEEe-CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 000 0000000 001368899999999999999999999999999999999863
No 60
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.05 E-value=0.002 Score=56.34 Aligned_cols=86 Identities=17% Similarity=0.252 Sum_probs=59.3
Q ss_pred CcceEEEEEeec------CccceeecCCChhHHHHHHHhCCeEEEeCCCCC------------Cccc-CCCCCceEEEEE
Q 025112 140 VAANTIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQL------------PLCA-SAHESDRVVQIS 200 (257)
Q Consensus 140 ~~~~~~~l~Vp~------~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~------------p~~~-~~~~~~r~V~I~ 200 (257)
....+.+|+||- ++||+|+|+.|.++|+|+++|||+|-|--+... |..+ ....---.|+..
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 345678888884 589999999999999999999999998632111 1100 000111467777
Q ss_pred cCHHHH----HHHHHHHHHHHhcCCCCCc
Q 025112 201 GDVPAV----LNALVEIGNQLRENPPRQV 225 (257)
Q Consensus 201 G~~~~v----~~A~~~I~~~l~e~~~~~~ 225 (257)
+.+..+ ..|++.|.++|.-+.+...
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~P~~e~~d 197 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLVPDHEDED 197 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCCCch
Confidence 877654 4689999998887666543
No 61
>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=97.05 E-value=0.0011 Score=45.38 Aligned_cols=36 Identities=31% Similarity=0.451 Sum_probs=33.8
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEE
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i 178 (257)
....+.|+....|.+|||+|.+|+.+++.+|-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 478999999999999999999999999999998876
No 62
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.01 E-value=0.00049 Score=64.56 Aligned_cols=94 Identities=23% Similarity=0.292 Sum_probs=63.2
Q ss_pred cccceeccCchhHHHHHhhh-CceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025112 60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138 (257)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~ 138 (257)
-+|+.||++|.+|+.|.++. |=+|+|-.. +++.. ..|...+.-. ....+...
T Consensus 278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~y---s~Dp~-------------------~fI~NaLsPA-----~V~~V~i~ 330 (449)
T PRK12329 278 PVGACIGARGSRIQAVVNELRGEKIDVIRW---SPDPA-------------------TYIANALSPA-----RVDEVRLV 330 (449)
T ss_pred hhhccCCCCcchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhcCCc-----eeeEEEEE
Confidence 39999999999999999998 788887654 11111 1111111000 00000000
Q ss_pred CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112 139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
........+.||.++.+..|||+|.|++-...-||.+|.|.+
T Consensus 331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 001135789999999999999999999999999999999864
No 63
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.90 E-value=0.0022 Score=55.97 Aligned_cols=68 Identities=21% Similarity=0.207 Sum_probs=57.7
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcCCC
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV-PAVLNALVEIGNQLRENPP 222 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~-~~v~~A~~~I~~~l~e~~~ 222 (257)
-+.+.||...++++||++|.+|+.|.+.|+++|.+- .+-.|.|.+.. +++.+|..+|..+-+++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-------------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-------------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-------------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 467889999999999999999999999999999983 24668888865 5889999999888887766
Q ss_pred CC
Q 025112 223 RQ 224 (257)
Q Consensus 223 ~~ 224 (257)
++
T Consensus 213 ~~ 214 (235)
T PRK04163 213 SG 214 (235)
T ss_pred cC
Confidence 65
No 64
>PRK00468 hypothetical protein; Provisional
Probab=96.88 E-value=0.0011 Score=47.52 Aligned_cols=34 Identities=35% Similarity=0.587 Sum_probs=30.1
Q ss_pred CCCCeEEEEEecCccccceeccCchhHHHHHhhh
Q 025112 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t 79 (257)
.+..+.+++.|..+.+|+||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456889999999999999999999999998764
No 65
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.87 E-value=0.0059 Score=59.12 Aligned_cols=65 Identities=22% Similarity=0.344 Sum_probs=54.3
Q ss_pred eEEEEEeec-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
....+.+|+ ++-|+|||+.|.||+.+..-||+.+.|- ++...|+|+| +|-.-+-|...+..+|.+
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid------------dtp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID------------DTPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc------------CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 456677888 5679999999999999999999999982 3456788999 788888888888888876
No 66
>PRK12704 phosphodiesterase; Provisional
Probab=96.87 E-value=0.006 Score=59.12 Aligned_cols=65 Identities=22% Similarity=0.336 Sum_probs=52.5
Q ss_pred eEEEEEeec-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
....+.+|+ ++.|+|||+.|.||+.+..-||+.|.|- ++...|.|+| +|-.-+.|...+..++.+
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid------------dtp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID------------DTPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc------------CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 355677888 5779999999999999999999999982 3456788999 677767777777777765
No 67
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.85 E-value=0.074 Score=45.25 Aligned_cols=134 Identities=14% Similarity=0.106 Sum_probs=87.1
Q ss_pred EEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchh
Q 025112 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA 132 (257)
Q Consensus 53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~ 132 (257)
.+.++....-.+...+|..++.|-...||+|.+.. .+..+.|+|++. .+..+...|.+++..-
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~-----~~~~i~~~i~~~l~~i------- 91 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKS-----TAEYIEASINEILSNI------- 91 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHH-----HHHHHHHHHHHHHhhc-------
Confidence 44445888899999999999999888999999984 356799999864 2233333333333221
Q ss_pred hhhccCCCcceEEEEEeecCccceee----cCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-----CH
Q 025112 133 SKVAAGHVAANTIRLLIAGSQAGCLI----GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-----DV 203 (257)
Q Consensus 133 ~~~~~~~~~~~~~~l~Vp~~~vG~iI----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-----~~ 203 (257)
.+..+-++.-.--..- -.....++.|++.|++.|.... .+..+.|.+ ..
T Consensus 92 ----------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~------------~~~~~~i~~~~~~~~~ 149 (210)
T PF14611_consen 92 ----------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP------------DGNKLKISWLASPENE 149 (210)
T ss_pred ----------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC------------CCCeEEEEEEeecccc
Confidence 1233333322111111 1235679999999999999742 233444554 56
Q ss_pred HHHHHHHHHHHHHHhcCCCCCc
Q 025112 204 PAVLNALVEIGNQLRENPPRQV 225 (257)
Q Consensus 204 ~~v~~A~~~I~~~l~e~~~~~~ 225 (257)
..++.|..++.-.+...++...
T Consensus 150 ~~~~~a~RlL~~a~~~~~~~~~ 171 (210)
T PF14611_consen 150 KRADRAKRLLLWALDYNPHSQE 171 (210)
T ss_pred chHHHHHHHHHHhccCCccccc
Confidence 7889999999999975555543
No 68
>PRK00106 hypothetical protein; Provisional
Probab=96.85 E-value=0.007 Score=58.66 Aligned_cols=65 Identities=23% Similarity=0.387 Sum_probs=54.7
Q ss_pred eEEEEEeec-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
....+.+|+ ++-|+|||+.|.||+.+..-||+.+.|- ++...|+|+| +|-.-+-|...+..++.+
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid------------dtp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID------------DTPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc------------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 456677888 5779999999999999999999999982 3456788999 788888888888888876
No 69
>PRK02821 hypothetical protein; Provisional
Probab=96.80 E-value=0.0013 Score=47.31 Aligned_cols=35 Identities=23% Similarity=0.423 Sum_probs=30.5
Q ss_pred CCCCeEEEEEecCccccceeccCchhHHHHHhhhC
Q 025112 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg 80 (257)
..+...+++.|..+.+|+||||+|.+|+.||.--.
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 34557899999999999999999999999998754
No 70
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.80 E-value=0.0013 Score=66.88 Aligned_cols=67 Identities=25% Similarity=0.413 Sum_probs=55.9
Q ss_pred CCeEEEEEecCccccceeccCchhHHHHHhhhCce-EEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT-IKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~-I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~ 124 (257)
-.-...|.||.+.++.|||.||.+||.|.++||++ |++.+ +..|.|.+... ..+.+|..+|..+..+
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~----~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDL----SSLEKSKAIISSLTMV 750 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCH----HHHHHHHHHHHHHhcC
Confidence 35677889999999999999999999999999999 88875 35688888653 4678888888888764
No 71
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.66 E-value=0.0033 Score=61.70 Aligned_cols=67 Identities=30% Similarity=0.413 Sum_probs=55.0
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~ 125 (257)
.-...+.|+.+.++.+||++|.+|++|.++||++|++.+. ..|.|.+...+ .+.+|+..|..+..+.
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~----~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGE----SAKKAKERIEAITREV 617 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchH----HHHHHHHHHHHHHhhc
Confidence 4456788899999999999999999999999999999843 34778787643 6778888888888554
No 72
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.60 E-value=0.0023 Score=45.75 Aligned_cols=32 Identities=41% Similarity=0.637 Sum_probs=29.3
Q ss_pred CCCeEEEEEecCccccceeccCchhHHHHHhh
Q 025112 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE 78 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~ 78 (257)
+....+++.+..+.+|.+|||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 45678999999999999999999999999876
No 73
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=96.55 E-value=0.0059 Score=51.32 Aligned_cols=157 Identities=17% Similarity=0.174 Sum_probs=99.9
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~ 130 (257)
+-++-||......+=--==....-|-+..+.+|.+. ...|.|.+.-.++-....+.+++...|...+..++....
T Consensus 75 ~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmN-----lK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DA 149 (252)
T KOG3273|consen 75 TRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMN-----LKARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDA 149 (252)
T ss_pred eeeccCCcccCChHHHhhHhhhhHHHHhhhheeEee-----cccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhH
Confidence 446677776655441111111234566677777776 334556665544433356778888888888877654321
Q ss_pred hhh----hhccC---CCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025112 131 EAS----KVAAG---HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (257)
Q Consensus 131 ~~~----~~~~~---~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~ 203 (257)
-.. ..... -.+..+++=.=-+..+|+|+|++|.+--.|++-|.++|.+. +..|.|-|..
T Consensus 150 iALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla--------------d~kIHiLG~~ 215 (252)
T KOG3273|consen 150 IALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA--------------DSKIHILGAF 215 (252)
T ss_pred HHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec--------------CceEEEeecc
Confidence 110 00000 00001122112245689999999999999999999999874 4669999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCcc
Q 025112 204 PAVLNALVEIGNQLRENPPRQVI 226 (257)
Q Consensus 204 ~~v~~A~~~I~~~l~e~~~~~~~ 226 (257)
+++..|...|+.+|-.+|+..+|
T Consensus 216 ~niriAR~avcsLIlGsppgkVy 238 (252)
T KOG3273|consen 216 QNIRIARDAVCSLILGSPPGKVY 238 (252)
T ss_pred hhhHHHHHhhHhhhccCCchhHH
Confidence 99999999999999998887644
No 74
>PRK01064 hypothetical protein; Provisional
Probab=96.36 E-value=0.004 Score=44.88 Aligned_cols=34 Identities=35% Similarity=0.677 Sum_probs=30.2
Q ss_pred CCCCeEEEEEecCccccceeccCchhHHHHHhhh
Q 025112 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t 79 (257)
..+.+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 3466899999999999999999999999998863
No 75
>PRK12704 phosphodiesterase; Provisional
Probab=96.36 E-value=0.0099 Score=57.65 Aligned_cols=50 Identities=26% Similarity=0.482 Sum_probs=40.7
Q ss_pred CeEEEEEecC-ccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCC
Q 025112 49 DVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD 103 (257)
Q Consensus 49 ~~~~rilVP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~ 103 (257)
.++-.+-+|+ +.-|+||||.|.|||.|+.-||+.|-|++. + .+|+|+|..
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~~~ 259 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGFD 259 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC----C-CeEEEecCC
Confidence 4555677788 558999999999999999999999999964 3 357788854
No 76
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.29 E-value=0.0097 Score=49.97 Aligned_cols=54 Identities=26% Similarity=0.311 Sum_probs=43.4
Q ss_pred cccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112 60 QIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~ 125 (257)
..|+|||++|.+.+.|++-|+|+|.|... .|.|-|..+ +++.|...|..++...
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------tVaiiG~~~-----~v~iAr~AVemli~G~ 165 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-------TVAIIGGFE-----QVEIAREAVEMLINGA 165 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-------EEEEecChh-----hhHHHHHHHHHHHcCC
Confidence 47999999999999999999999999944 478888755 5666666666666543
No 77
>PRK02821 hypothetical protein; Provisional
Probab=96.27 E-value=0.0067 Score=43.62 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=27.0
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHh
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
..+.+.+..+.+|+||||+|.+|+.||.--
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 578899999999999999999999998643
No 78
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.16 E-value=0.015 Score=49.17 Aligned_cols=78 Identities=19% Similarity=0.243 Sum_probs=49.2
Q ss_pred ceEEEEEee------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCC-------CCCce--EEEEE-cCHHH
Q 025112 142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASA-------HESDR--VVQIS-GDVPA 205 (257)
Q Consensus 142 ~~~~~l~Vp------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~-------~~~~r--~V~I~-G~~~~ 205 (257)
.++-++.|| .++||.|||+.|++.|++++.|+|+|-|--....-.|-.. .+.+. -+.|. -+.+.
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedk 226 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDK 226 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhh
Confidence 355677777 5689999999999999999999999998532211111100 00111 12222 23456
Q ss_pred HHHHHHHHHHHHhc
Q 025112 206 VLNALVEIGNQLRE 219 (257)
Q Consensus 206 v~~A~~~I~~~l~e 219 (257)
++++++.+...|++
T Consensus 227 i~~~ik~~~n~I~~ 240 (269)
T COG5176 227 ICRLIKSQLNAIRE 240 (269)
T ss_pred HHHHHHHHHHHHHH
Confidence 66777777777776
No 79
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.10 E-value=0.016 Score=56.14 Aligned_cols=50 Identities=26% Similarity=0.484 Sum_probs=40.7
Q ss_pred CCeEEEEEecC-ccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccC
Q 025112 48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK 102 (257)
Q Consensus 48 ~~~~~rilVP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~ 102 (257)
..++-.+-+|+ +.-|+||||.|.|||.++..|||.|-|++. ++ .|+|++-
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt----p~-~v~ls~f 252 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----PE-AVILSGF 252 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC----CC-eEEecCC
Confidence 34556677888 558999999999999999999999999964 33 4668885
No 80
>PRK00468 hypothetical protein; Provisional
Probab=96.02 E-value=0.0076 Score=43.12 Aligned_cols=30 Identities=23% Similarity=0.390 Sum_probs=26.9
Q ss_pred ceEEEEEeecCccceeecCCChhHHHHHHH
Q 025112 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
...+++.+..+.+|+||||+|.+|+.||.-
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 367889999999999999999999999853
No 81
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.01 E-value=0.015 Score=49.21 Aligned_cols=42 Identities=21% Similarity=0.447 Sum_probs=36.2
Q ss_pred CCCeEEEEEecC------ccccceeccCchhHHHHHhhhCceEEEccc
Q 025112 47 AQDVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 47 ~~~~~~rilVP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (257)
+..++-++.||. ++||+|||+.|.|.|+|+..|+|+|-|--.
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 346777888885 569999999999999999999999999743
No 82
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.99 E-value=0.012 Score=51.33 Aligned_cols=62 Identities=27% Similarity=0.393 Sum_probs=47.6
Q ss_pred EEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHh
Q 025112 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (257)
Q Consensus 52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~ 123 (257)
+.+.||.+.++.+||++|.+|+.|.+++++.|.+-. +..|-|.+... ..+.+|..+|..+-.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~----~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDE----EDEEIAIEAIKKIER 208 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCH----HHHHHHHHHHHHHHh
Confidence 457789999999999999999999999999999864 35688888753 234555555554433
No 83
>PRK00106 hypothetical protein; Provisional
Probab=95.97 E-value=0.021 Score=55.45 Aligned_cols=50 Identities=26% Similarity=0.530 Sum_probs=40.9
Q ss_pred CCeEEEEEecC-ccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccC
Q 025112 48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK 102 (257)
Q Consensus 48 ~~~~~rilVP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~ 102 (257)
..++-.+.+|+ +.-|+||||.|.||+.|+.-|||.|-|++. ++ .|+|+|.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt----p~-~v~lS~f 273 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT----PE-VVVLSGF 273 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC----CC-eEEEeCC
Confidence 34566777898 558999999999999999999999999964 34 4668885
No 84
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.82 E-value=0.025 Score=54.43 Aligned_cols=99 Identities=19% Similarity=0.204 Sum_probs=72.7
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025112 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (257)
Q Consensus 108 ~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (257)
+.++..|..+|++.+.+...+.-... .........+-++.+....+||++|-+.|+|..+||+.-.+
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 LQKAREARLQILDIMEKNINSPRGSD----KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV--------- 632 (760)
T ss_pred HHhhhHHHHHHHHHHHhhcCCcccCc----cccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------
Confidence 44667777888888876543321111 11234567888999999999999999999999999943333
Q ss_pred cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCCCCC
Q 025112 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRENPPRQ 224 (257)
Q Consensus 188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~~~~~ 224 (257)
++..++|.- ++...++|.+.|..++......+
T Consensus 633 -----De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~ 665 (760)
T KOG1067|consen 633 -----DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQD 665 (760)
T ss_pred -----cCceEEEEecCHHHHHHHHHHHHHHhcCccccc
Confidence 345677776 57799999999999998866654
No 85
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=95.82 E-value=0.014 Score=51.39 Aligned_cols=51 Identities=16% Similarity=0.249 Sum_probs=45.5
Q ss_pred ceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 155 G~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
-+|||++|++++.|+--|.|.|-|. ...|.+.|....+..+...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq--------------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ--------------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee--------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 4799999999999999999999883 36699999999999999999888875
No 86
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.71 E-value=0.0073 Score=60.54 Aligned_cols=65 Identities=34% Similarity=0.507 Sum_probs=51.0
Q ss_pred eEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhc
Q 025112 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~ 124 (257)
-...+.||.+.++.+||+||.+||.|.++||++|++.+ +..|.|.+... ..+.+|..+|..+..+
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~----~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDG----EAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccH----HHHHHHHHHHHHhccc
Confidence 34566679999999999999999999999999988864 34577777653 3567777777777653
No 87
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.66 E-value=0.014 Score=41.85 Aligned_cols=31 Identities=32% Similarity=0.493 Sum_probs=27.4
Q ss_pred cceEEEEEeecCccceeecCCChhHHHHHHH
Q 025112 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
....+++.+.....|+||||+|.+|+.||.-
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 3457899999999999999999999999853
No 88
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=95.26 E-value=0.017 Score=46.37 Aligned_cols=38 Identities=26% Similarity=0.435 Sum_probs=34.1
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEc
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA 86 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~ 86 (257)
+..+.+.|+.+..|..|||+|.|++.+++-++-+++|.
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 45677889999999999999999999999999888775
No 89
>PRK12705 hypothetical protein; Provisional
Probab=95.26 E-value=0.05 Score=52.49 Aligned_cols=65 Identities=22% Similarity=0.293 Sum_probs=46.5
Q ss_pred eEEEEEeecC-ccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025112 143 NTIRLLIAGS-QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~~-~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
....+.+|++ +-|+|||+.|.||+.+...||+.+.|. + +...|.|.+ +|..-+.|...+..+|.+
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d---------tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---D---------TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---C---------CccchhhcccCccchHHHHHHHHHHHhc
Confidence 3455667874 669999999999999999999999983 2 334466666 444555566666555554
No 90
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=95.26 E-value=0.011 Score=41.70 Aligned_cols=36 Identities=17% Similarity=0.348 Sum_probs=30.4
Q ss_pred CCCeEEEEEecCccccceeccCchhHHHHHhhhCce
Q 025112 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT 82 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~ 82 (257)
.+...+.+.+..+..|.+|||+|.+++.||.-.+.-
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~ 61 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAA 61 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHH
Confidence 456678888899999999999999999999876543
No 91
>PRK01064 hypothetical protein; Provisional
Probab=95.20 E-value=0.024 Score=40.82 Aligned_cols=31 Identities=26% Similarity=0.420 Sum_probs=27.5
Q ss_pred cceEEEEEeecCccceeecCCChhHHHHHHH
Q 025112 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
....+++.+.....|++|||+|.+|+.||.-
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 3467889999999999999999999999864
No 92
>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=95.02 E-value=0.041 Score=37.40 Aligned_cols=35 Identities=29% Similarity=0.462 Sum_probs=29.0
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceE
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI 83 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I 83 (257)
...+.+.+.....|.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45666777776799999999999999999988544
No 93
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=94.77 E-value=0.024 Score=39.91 Aligned_cols=38 Identities=34% Similarity=0.552 Sum_probs=30.7
Q ss_pred EEEEEecCcc-----ccceeccCchhHHHHHhhh-CceEEEccc
Q 025112 51 LFRIIVPSRQ-----IGKVIGKEGHRIQKIREET-KATIKIADA 88 (257)
Q Consensus 51 ~~rilVP~~~-----vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~ 88 (257)
..++.|-+.. +|..||++|..|+.|.++. |-+|++-..
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 3577778877 9999999999999999999 889888754
No 94
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=94.00 E-value=0.025 Score=58.50 Aligned_cols=73 Identities=19% Similarity=0.139 Sum_probs=58.5
Q ss_pred CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc-ccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~ 125 (257)
....-++.+|-..++++||++|.+|+.++.-||+.|.+..- ..+-.||.+.+.|.++ ..+-|-..|...+.+.
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~-----~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPP-----SQRVATSPIGLPIIDP 1411 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCCh-----hhhhhhccccceeecC
Confidence 45667889999999999999999999999999999999974 3345799999999976 4455555565555543
No 95
>PRK12705 hypothetical protein; Provisional
Probab=93.75 E-value=0.11 Score=50.26 Aligned_cols=40 Identities=28% Similarity=0.442 Sum_probs=33.9
Q ss_pred CeEEEEEecCc-cccceeccCchhHHHHHhhhCceEEEccc
Q 025112 49 DVLFRIIVPSR-QIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 49 ~~~~rilVP~~-~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (257)
.++-.+-+|++ .-|+||||.|.|||.++..||+.|.|++.
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 34556667774 58999999999999999999999999964
No 96
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.53 E-value=0.04 Score=57.06 Aligned_cols=71 Identities=23% Similarity=0.205 Sum_probs=59.2
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
..-++.+|-....+|||++|++|+.++..||+.|++..-. +. ...+|.+.+.|.++.+.-|...|.-.+.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~----Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD----NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc----cchhhhcccCCCChhhhhhhccccceeec
Confidence 3566788888899999999999999999999999986411 22 25789999999999999998888766665
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.12 E-value=0.062 Score=37.88 Aligned_cols=32 Identities=38% Similarity=0.547 Sum_probs=27.8
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCC
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGA 174 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga 174 (257)
..+.+.+..+..|.||||.|.+++.||--.+.
T Consensus 29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred eEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 47888899999999999999999999965543
No 98
>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=93.10 E-value=0.054 Score=38.62 Aligned_cols=35 Identities=40% Similarity=0.608 Sum_probs=29.8
Q ss_pred eEEEEEecCccccceeccCchhHHHHHhhhCceEE
Q 025112 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIK 84 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~ 84 (257)
..+.+.+..++.|.+||++|++|++|+++.+-.+.
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 45788899999999999999999999888755543
No 99
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=93.05 E-value=0.13 Score=42.33 Aligned_cols=46 Identities=20% Similarity=0.304 Sum_probs=37.6
Q ss_pred cccCCCCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112 42 KRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 42 ~~~~~~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (257)
..++...+-.+-|+|-... |..|||+|.+|+++++..|-+|.+-+.
T Consensus 53 ~~k~~~~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 53 YKKAYEVDDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEEeCCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 3444444566778888788 999999999999999999999998864
No 100
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=92.89 E-value=0.11 Score=36.53 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=30.7
Q ss_pred EEEEEeecCc-----cceeecCCChhHHHHHHHh-CCeEEEeC
Q 025112 144 TIRLLIAGSQ-----AGCLIGMSGQNIEKLRNSS-GATIVILA 180 (257)
Q Consensus 144 ~~~l~Vp~~~-----vG~iIGk~G~~Ik~I~~~t-ga~I~i~~ 180 (257)
...+.|-+.. +|..||++|++|+.|.++. |-+|++..
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 4567777777 8999999999999999999 99999874
No 101
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=92.58 E-value=0.22 Score=33.66 Aligned_cols=34 Identities=32% Similarity=0.459 Sum_probs=26.8
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeE
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATI 176 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I 176 (257)
....+.+.....|.+||++|.+++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 3455666665689999999999999999887544
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=92.52 E-value=0.13 Score=36.73 Aligned_cols=35 Identities=17% Similarity=0.373 Sum_probs=28.6
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEE
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i 85 (257)
.+.+.+.....|.+|||+|+++..||--.+.-++-
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 45666778899999999999999999887755543
No 103
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=92.32 E-value=0.28 Score=42.60 Aligned_cols=66 Identities=20% Similarity=0.244 Sum_probs=50.5
Q ss_pred EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHH-HHHHHHHHHHHHHhcCCCC
Q 025112 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP-AVLNALVEIGNQLRENPPR 223 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~-~v~~A~~~I~~~l~e~~~~ 223 (257)
.-+.|+...|.++||++|+.++-|.+.++|.|.+-. .-.|-|.|..+ ....|...|..+=+|+...
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-------------NG~IWV~~~~~~~e~~~~~aI~~ie~ea~~~ 214 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-------------NGRIWVDGENESLEELAIEAIRKIEREAHTS 214 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-------------CCEEEecCCCcchHHHHHHHHHHHhhhhhhh
Confidence 457899999999999999999999999999999842 35577777766 4556666666655554433
No 104
>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=91.60 E-value=0.3 Score=39.26 Aligned_cols=37 Identities=22% Similarity=0.536 Sum_probs=33.7
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
..-++|....+|..||++|++|+.|++..|-+|.+..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5678899999999999999999999999999999863
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=91.40 E-value=0.14 Score=36.46 Aligned_cols=35 Identities=34% Similarity=0.564 Sum_probs=29.3
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEE
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIV 177 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~ 177 (257)
....+.+..++-|.+||++|++|++|....+-.+.
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 35788899999999999999999999876655553
No 106
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=91.31 E-value=0.2 Score=42.31 Aligned_cols=37 Identities=27% Similarity=0.416 Sum_probs=35.2
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEEcc
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~ 87 (257)
...+.||.+..+..|||+|.|++.+.+-||-+++|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 7888999999999999999999999999999999984
No 107
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=91.18 E-value=0.15 Score=48.44 Aligned_cols=40 Identities=35% Similarity=0.482 Sum_probs=35.7
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (257)
+-...+.||..+++.+|||+|.+|++|++..|.+|+|...
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 4456788899999999999999999999999999999743
No 108
>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=90.98 E-value=1.8 Score=34.86 Aligned_cols=95 Identities=14% Similarity=0.291 Sum_probs=63.9
Q ss_pred eccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceE
Q 025112 65 IGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANT 144 (257)
Q Consensus 65 IGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~ 144 (257)
+=.+|.-|++|-++..-+|.|-... . +.- +-.+|.+.|.+++-++..-..-.. +..+
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dp-----s---~l~--------~~e~A~~~I~~ivP~ea~i~di~F-------d~~t 77 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDP-----S---VLK--------PPEEAIKIILEIVPEEAGITDIYF-------DDDT 77 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCCh-----h---hcC--------CHHHHHHHHHHhCCCccCceeeEe-------cCCC
Confidence 3456778888888888777775221 0 111 124688888888854422110000 0124
Q ss_pred EEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025112 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~ 182 (257)
-++.|-...-|.+||++|.++++|..+||-.-.+.+..
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 57788888889999999999999999999999987643
No 109
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=90.75 E-value=0.28 Score=45.55 Aligned_cols=41 Identities=24% Similarity=0.244 Sum_probs=37.2
Q ss_pred CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (257)
......+.||.+..+..|||+|.|++-..+-||.+|+|-..
T Consensus 306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 44578899999999999999999999999999999999843
No 110
>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=90.58 E-value=0.29 Score=45.01 Aligned_cols=40 Identities=23% Similarity=0.361 Sum_probs=36.7
Q ss_pred CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcc
Q 025112 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~ 87 (257)
......+.||.+..+..|||+|.|++...+-||.+|+|-.
T Consensus 299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 3467899999999999999999999999999999999974
No 111
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=90.04 E-value=2 Score=36.36 Aligned_cols=66 Identities=18% Similarity=0.234 Sum_probs=55.8
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~ 221 (257)
.+.+.++....-.+...+|..+++|....||+|.+. .....+.|+|+...+..+...|.++++...
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~------------~~~~~i~I~g~k~~~~~i~~~i~~~l~~i~ 92 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS------------RSENRIRITGTKSTAEYIEASINEILSNIR 92 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEe------------cCCcEEEEEccHHHHHHHHHHHHHHHhhcE
Confidence 455666788888999999999999988899999985 346789999999999999999988887643
No 112
>PRK13764 ATPase; Provisional
Probab=90.03 E-value=0.24 Score=48.93 Aligned_cols=41 Identities=37% Similarity=0.528 Sum_probs=36.7
Q ss_pred CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (257)
.+....+.||...++.+|||+|.+|++|++..|.+|+|-..
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 45567788999999999999999999999999999999743
No 113
>PRK13764 ATPase; Provisional
Probab=90.02 E-value=0.51 Score=46.66 Aligned_cols=44 Identities=20% Similarity=0.348 Sum_probs=39.0
Q ss_pred ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCC
Q 025112 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP 185 (257)
Q Consensus 142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p 185 (257)
.....+.||...++.+|||+|.+|++|.++.|.+|.|-+.++.+
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 34688999999999999999999999999999999998765543
No 114
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=89.80 E-value=0.22 Score=42.02 Aligned_cols=56 Identities=32% Similarity=0.440 Sum_probs=47.3
Q ss_pred CccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112 58 SRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 58 ~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~ 125 (257)
+..+|+|+||+|.+--.|+..|..+|.+.+. .+.|-|. +++++-|...|+.+|...
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 4569999999999999999999999999854 3778787 457888888899998765
No 115
>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=89.78 E-value=0.36 Score=34.95 Aligned_cols=37 Identities=19% Similarity=0.412 Sum_probs=30.9
Q ss_pred eEEEEEecCccccceeccCchhHHHHHhhhCceEEEc
Q 025112 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA 86 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~ 86 (257)
..+++.|....-|.+||++|++|++|+++-.-...+.
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 3478888999999999999999999999876555554
No 116
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=89.50 E-value=0.42 Score=34.05 Aligned_cols=34 Identities=26% Similarity=0.509 Sum_probs=27.6
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHhCCeEE
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIV 177 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~ 177 (257)
...+.+.....|.+|||.|.+++.||--.+.-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 4677788889999999999999999976654443
No 117
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=89.37 E-value=0.3 Score=46.48 Aligned_cols=41 Identities=15% Similarity=0.243 Sum_probs=37.0
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCC
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ 183 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~ 183 (257)
....+.||...++.+|||+|.+|++|+++.|.+|.+.+.+.
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 46789999999999999999999999999999999976543
No 118
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=88.69 E-value=0.5 Score=43.85 Aligned_cols=42 Identities=29% Similarity=0.402 Sum_probs=37.8
Q ss_pred CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (257)
+......+.||.+..+..|||+|.|++--.+-||.+|+|...
T Consensus 300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 344678999999999999999999999999999999999854
No 119
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=88.41 E-value=0.41 Score=45.98 Aligned_cols=39 Identities=26% Similarity=0.392 Sum_probs=36.3
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcc
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~ 87 (257)
...+.+.||....+..|||+|.|++...+-||.+|.|-.
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 358899999999999999999999999999999999974
No 120
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=87.19 E-value=1 Score=43.74 Aligned_cols=68 Identities=26% Similarity=0.272 Sum_probs=50.5
Q ss_pred CCCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~ 125 (257)
.......+.|+.+....+||.+|...|+|+.|||+.-.++ |..+.|-.+.. ....+|...|..++...
T Consensus 594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~~----~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPTQ----AAMEEAKEFIDGIIKDD 661 (760)
T ss_pred cCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecCH----HHHHHHHHHHHHHhcCc
Confidence 4567889999999999999999999999999999544444 44566766542 24456666666666543
No 121
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=86.97 E-value=0.58 Score=44.32 Aligned_cols=41 Identities=29% Similarity=0.433 Sum_probs=37.0
Q ss_pred CCeEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc
Q 025112 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (257)
......+.||.+..+..|||+|.|++--.+-||.+|+|.+.
T Consensus 333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 44567899999999999999999999999999999999843
No 122
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=86.71 E-value=1.1 Score=36.96 Aligned_cols=36 Identities=19% Similarity=0.340 Sum_probs=31.5
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
..-++|-... |..||++|.+++++++..|-+|.+..
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 4667777777 99999999999999999999999873
No 123
>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=86.30 E-value=0.68 Score=35.38 Aligned_cols=30 Identities=30% Similarity=0.572 Sum_probs=26.0
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhC
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg 80 (257)
.+++.|-...-|.|||++|++|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 367888888999999999999999988754
No 124
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=86.22 E-value=1.7 Score=41.95 Aligned_cols=98 Identities=16% Similarity=0.296 Sum_probs=68.8
Q ss_pred cceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCc
Q 025112 62 GKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVA 141 (257)
Q Consensus 62 g~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~ 141 (257)
..++=++|.-||+|-++..-+|.|-.... + +.+-.+|.+.|.+++-++..-..-.. .
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPs------v----------l~~~e~A~~~I~eivP~ea~i~~i~F-------d 97 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPS------V----------LKPPEEARKIILEIVPEEAGITDIYF-------D 97 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCch------h----------cCCHHHHHHHHHHhCccccCceeEEe-------c
Confidence 34566788999999999988888763210 0 11335788888888855432111000 0
Q ss_pred ceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025112 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (257)
Q Consensus 142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~ 182 (257)
..+-+++|-...=|.+|||+|++.++|..+||-.-+|.+..
T Consensus 98 ~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 98 DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred CCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 12457888888899999999999999999999988887643
No 125
>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=85.89 E-value=0.83 Score=33.20 Aligned_cols=28 Identities=29% Similarity=0.484 Sum_probs=23.8
Q ss_pred EEEEecCccccceeccCchhHHHHHhhh
Q 025112 52 FRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~t 79 (257)
+++.|....-|.+||++|++|++|++.-
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 5666666899999999999999998774
No 126
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=85.85 E-value=2.6 Score=36.69 Aligned_cols=46 Identities=22% Similarity=0.489 Sum_probs=38.7
Q ss_pred EEEecCccccceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCC
Q 025112 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN 104 (257)
Q Consensus 53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~ 104 (257)
-+.|++..+-++||++|+.++.|.++++|.|-+-. +..+-|.+..+
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~------NG~IWV~~~~~ 194 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ------NGRIWVDGENE 194 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec------CCEEEecCCCc
Confidence 46789999999999999999999999999999863 23467777765
No 127
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.79 E-value=1.2 Score=32.15 Aligned_cols=36 Identities=14% Similarity=0.312 Sum_probs=29.0
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEE
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i 178 (257)
...++.|....-|.+||++|+.|++|++.-.-...+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 357888888899999999999999998766444443
No 128
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=84.27 E-value=1.2 Score=42.87 Aligned_cols=125 Identities=12% Similarity=0.053 Sum_probs=74.7
Q ss_pred ceeccCchhHHHHHhhhCceEEEc--ccccCCCccEEE-eccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCC
Q 025112 63 KVIGKEGHRIQKIREETKATIKIA--DAIARHEERVII-ISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGH 139 (257)
Q Consensus 63 ~IIGk~G~~Ik~I~~~tg~~I~i~--~~~~~~~ervv~-I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 139 (257)
+|=||+--.+.+|++...|-+.+. +. .+.++.+ +.|..- +-++++..+ ..+.
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~---~gs~~~~~~~g~~~-----~F~k~~~~~---~~EF-------------- 447 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSS---TGSIVETNGIGEKM-----SFSKKLSIP---PTEF-------------- 447 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEec---CCcEEEEeccCcch-----hhHHHhcCC---cccC--------------
Confidence 677886666999999999985544 33 2224443 344321 112222111 0111
Q ss_pred CcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCce-EEEEEcCH---HHHHHHHHHHHH
Q 025112 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDR-VVQISGDV---PAVLNALVEIGN 215 (257)
Q Consensus 140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r-~V~I~G~~---~~v~~A~~~I~~ 215 (257)
.-...+.||...|..|||-||..|.+++.+.++.|++...-.++. +.-+ .|.|.-.. +++.-+.--+++
T Consensus 448 --pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q-----s~~~dNV~I~~PrKn~~ni~~~KNd~~~ 520 (657)
T COG5166 448 --PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ-----SQWHDNVLIEAPRKNQDNISGKKNDKLD 520 (657)
T ss_pred --chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch-----hhhhcceEEECCccCccchhcccccHHH
Confidence 124788999999999999999999999999999999764333333 2222 24444432 234444445555
Q ss_pred HHhc
Q 025112 216 QLRE 219 (257)
Q Consensus 216 ~l~e 219 (257)
++++
T Consensus 521 ~V~~ 524 (657)
T COG5166 521 KVKQ 524 (657)
T ss_pred HHhh
Confidence 5553
No 129
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=84.10 E-value=1.4 Score=35.48 Aligned_cols=37 Identities=30% Similarity=0.459 Sum_probs=32.2
Q ss_pred EEEecCccccceeccCchhHHHHHhhhCceEEEcccc
Q 025112 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI 89 (257)
Q Consensus 53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~ 89 (257)
.+.|-...-|.+||++|.++++|..+||-+-.+.+..
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 5666778899999999999999999999888887654
No 130
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=81.79 E-value=1.9 Score=41.58 Aligned_cols=129 Identities=12% Similarity=0.150 Sum_probs=80.8
Q ss_pred eEEEEEecCccccceeccCchhHHHHHhhhCceEEEccc--ccCCCcc-EEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEER-VIIISSKDNDNVVSDAENALQQIAALILKDD 126 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~--~~~~~er-vv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~ 126 (257)
-.+.|.||...|..|||-||..|.+++.+.++.|++... .+.+--+ -|.|..+.++.. .+--+...+.+++.+.+
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~--ni~~~KNd~~~~V~~~c 526 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQD--NISGKKNDKLDKVKQQC 526 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCcc--chhcccccHHHHHhhhc
Confidence 356789999999999999999999999999999998843 1222222 266766555422 22233334444444333
Q ss_pred CCCchh---------------------hhhccC----CCcceEEEEEeecCccceeec---CCChhHHHHHHHhCCeEEE
Q 025112 127 DSNSEA---------------------SKVAAG----HVAANTIRLLIAGSQAGCLIG---MSGQNIEKLRNSSGATIVI 178 (257)
Q Consensus 127 ~~~~~~---------------------~~~~~~----~~~~~~~~l~Vp~~~vG~iIG---k~G~~Ik~I~~~tga~I~i 178 (257)
..+... +.+... ........+.+|+..++..+| -.|++|..+.....-.|..
T Consensus 527 ~f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~ 606 (657)
T COG5166 527 RFNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEF 606 (657)
T ss_pred ccccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhcccee
Confidence 211100 000000 011234556788888999999 6788888888888888876
Q ss_pred eC
Q 025112 179 LA 180 (257)
Q Consensus 179 ~~ 180 (257)
..
T Consensus 607 ~~ 608 (657)
T COG5166 607 ST 608 (657)
T ss_pred ec
Confidence 53
No 131
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=81.17 E-value=1.4 Score=38.28 Aligned_cols=31 Identities=35% Similarity=0.529 Sum_probs=27.0
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhh
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~t 79 (257)
...+++.|....-|.|||++|++|++|++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 4567888999999999999999999987763
No 132
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=80.91 E-value=3.3 Score=36.91 Aligned_cols=25 Identities=20% Similarity=0.385 Sum_probs=23.9
Q ss_pred cceeccCchhHHHHHhhhCceEEEc
Q 025112 62 GKVIGKEGHRIQKIREETKATIKIA 86 (257)
Q Consensus 62 g~IIGk~G~~Ik~I~~~tg~~I~i~ 86 (257)
-++||.+|+|+|.|+=-|+|.|-|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq 185 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ 185 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee
Confidence 5799999999999999999999998
No 133
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=80.54 E-value=5.2 Score=39.94 Aligned_cols=97 Identities=14% Similarity=0.274 Sum_probs=65.7
Q ss_pred ceeccCchhHHHHHhhhCceEEEcccccCCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcc
Q 025112 63 KVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAA 142 (257)
Q Consensus 63 ~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~ 142 (257)
..+=.+|..||+|-++..-+|.|-... . +.- +-.+|.+.|.+++-++..-..-.. +.
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~-----~---~~~--------~~~~~~~~i~~~~~~~~~~~~~~f-------~~ 92 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDP-----S---VLL--------PPEEAIEKIKEIVPEEAGITDIYF-------DD 92 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecCh-----h---hcC--------CHHHHHHHHHHhCCCcCCceeEEe-------cC
Confidence 344567788888888888777775221 0 111 124677888888755422110000 01
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~ 182 (257)
.+-+++|-...-|.|||++|+++++|..+||-.-.+.+..
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 2457888888899999999999999999999999987643
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=80.50 E-value=2.1 Score=31.01 Aligned_cols=29 Identities=28% Similarity=0.469 Sum_probs=23.6
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHh
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
..++.|....-|.+||++|++|++|++.-
T Consensus 39 ~i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 39 GTQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred cEEEEEEECCCCceECCCchhHHHHHHHH
Confidence 36667777888999999999999987543
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=79.61 E-value=2 Score=32.72 Aligned_cols=29 Identities=34% Similarity=0.594 Sum_probs=24.6
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHh
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
..++.|-...-|.|||++|+.|++|++..
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 46788888888999999999999998653
No 136
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=76.71 E-value=3.9 Score=35.51 Aligned_cols=32 Identities=41% Similarity=0.618 Sum_probs=26.8
Q ss_pred eEEEEEeecCccceeecCCChhHHHHH----HHhCC
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLR----NSSGA 174 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~----~~tga 174 (257)
...++.|....=|.|||++|++|++|+ +.+|.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~ 86 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGK 86 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCC
Confidence 467888888999999999999999886 45555
No 137
>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=70.60 E-value=1.7 Score=26.94 Aligned_cols=30 Identities=20% Similarity=0.170 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCCCCccCCCCCCCCCCccccCCC
Q 025112 13 VSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKA 47 (257)
Q Consensus 13 ~~~~~~~~~~~~~~~kr~~~~~~~~~~~~~~~~~~ 47 (257)
+..+|++.+.++ ||+.||+++ ..++++++.
T Consensus 9 ~e~tF~n~etNG---KrpaeDmeE--e~afKRsrN 38 (43)
T PF08067_consen 9 EEETFSNTETNG---KRPAEDMEE--EQAFKRSRN 38 (43)
T ss_pred ccccccccccCC---CCchhhHHH--HHHhccccc
Confidence 567899999998 999999884 445555543
No 138
>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=68.23 E-value=6.7 Score=34.48 Aligned_cols=28 Identities=18% Similarity=0.220 Sum_probs=21.4
Q ss_pred eEEEEEeecC-ccceeecCCChhHHHHHH
Q 025112 143 NTIRLLIAGS-QAGCLIGMSGQNIEKLRN 170 (257)
Q Consensus 143 ~~~~l~Vp~~-~vG~iIGk~G~~Ik~I~~ 170 (257)
+...++|..+ +-+.|||++|+.||+|..
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~ 249 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGI 249 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHH
Confidence 4556667644 569999999999998854
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=67.06 E-value=6.6 Score=34.53 Aligned_cols=30 Identities=27% Similarity=0.284 Sum_probs=23.3
Q ss_pred eEEEEEecCcc-ccceeccCchhHHHHHhhh
Q 025112 50 VLFRIIVPSRQ-IGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 50 ~~~rilVP~~~-vg~IIGk~G~~Ik~I~~~t 79 (257)
+...++|..+. .+-|||++|+.||+|..+.
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 66777787555 6788899999999986553
No 140
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=65.31 E-value=6.3 Score=33.69 Aligned_cols=30 Identities=30% Similarity=0.496 Sum_probs=24.8
Q ss_pred EEEEecCccccceeccCchhHHHHHhhhCc
Q 025112 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (257)
Q Consensus 52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~ 81 (257)
.++.|....-|.+||++|++|++|++...-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 566666688999999999999999887644
No 141
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=64.60 E-value=3.7 Score=35.00 Aligned_cols=37 Identities=14% Similarity=0.299 Sum_probs=30.4
Q ss_pred CeEEEEEecCccccceeccCchhHHHHHhhhCceEEE
Q 025112 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i 85 (257)
.-.+.+-+-.+..+.+||+.|.++..||--+++.++-
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3455666677789999999999999999998877665
No 142
>PRK15494 era GTPase Era; Provisional
Probab=63.00 E-value=9.3 Score=34.98 Aligned_cols=36 Identities=11% Similarity=0.261 Sum_probs=26.2
Q ss_pred eEEEEEeecC-ccceeecCCChhHHHHH--------HHhCCeEEE
Q 025112 143 NTIRLLIAGS-QAGCLIGMSGQNIEKLR--------NSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~~-~vG~iIGk~G~~Ik~I~--------~~tga~I~i 178 (257)
+...++|... +-+.|||++|+.||+|. +-.|++|.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 3455667654 56999999999999875 556666654
No 143
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=62.47 E-value=7.8 Score=32.83 Aligned_cols=31 Identities=29% Similarity=0.552 Sum_probs=26.4
Q ss_pred eEEEEEecCccccceeccCchhHHHHHhhhC
Q 025112 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg 80 (257)
..+++.|....-|.+||++|..|++|+++-.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 3478888888999999999999999987753
No 144
>CHL00048 rps3 ribosomal protein S3
Probab=62.39 E-value=7.6 Score=33.37 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=26.2
Q ss_pred eEEEEEecCccccceeccCchhHHHHHhhhC
Q 025112 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg 80 (257)
..+++.|-...-|.|||++|.+|++|++...
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 3467777888899999999999999988763
No 145
>PRK00089 era GTPase Era; Reviewed
Probab=61.60 E-value=10 Score=33.52 Aligned_cols=36 Identities=22% Similarity=0.422 Sum_probs=25.7
Q ss_pred eEEEEEeec-CccceeecCCChhHHHHH--------HHhCCeEEE
Q 025112 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLR--------NSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~--------~~tga~I~i 178 (257)
+...+.|.. ++-+.|||++|+.||+|. +-+|++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 344556654 456999999999998875 556776664
No 146
>COG1159 Era GTPase [General function prediction only]
Probab=60.96 E-value=11 Score=33.89 Aligned_cols=36 Identities=25% Similarity=0.433 Sum_probs=26.0
Q ss_pred eEEEEEeec-CccceeecCCChhHHHHH--------HHhCCeEEE
Q 025112 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLR--------NSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~--------~~tga~I~i 178 (257)
+...++|+. ++-|.|||++|+.||+|- +-.+++|.+
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 345566775 466999999999998874 556666654
No 147
>PRK15494 era GTPase Era; Provisional
Probab=60.39 E-value=10 Score=34.78 Aligned_cols=37 Identities=19% Similarity=0.333 Sum_probs=26.8
Q ss_pred eEEEEEecCcc-ccceeccCchhHHHHHhh--------hCceEEEc
Q 025112 50 VLFRIIVPSRQ-IGKVIGKEGHRIQKIREE--------TKATIKIA 86 (257)
Q Consensus 50 ~~~rilVP~~~-vg~IIGk~G~~Ik~I~~~--------tg~~I~i~ 86 (257)
+...|+|.... -+.|||++|+.||+|..+ +|++|.+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 55677787655 677889999999998554 45555544
No 148
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=59.91 E-value=9 Score=33.10 Aligned_cols=32 Identities=22% Similarity=0.427 Sum_probs=26.5
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCce
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKAT 82 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~ 82 (257)
.+++.|....-|.|||++|..|++|+++..-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~ 76 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKR 76 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHH
Confidence 46777888889999999999999998876433
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=58.13 E-value=6.5 Score=34.79 Aligned_cols=37 Identities=27% Similarity=0.363 Sum_probs=26.1
Q ss_pred eEEEEEecCcc-ccceeccCchhHHHHHhh--------hCceEEEc
Q 025112 50 VLFRIIVPSRQ-IGKVIGKEGHRIQKIREE--------TKATIKIA 86 (257)
Q Consensus 50 ~~~rilVP~~~-vg~IIGk~G~~Ik~I~~~--------tg~~I~i~ 86 (257)
+...|.|..+. .+.|||++|+.||+|... ++++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 55566666544 678889999999988554 46665554
No 150
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=57.57 E-value=27 Score=32.22 Aligned_cols=57 Identities=26% Similarity=0.261 Sum_probs=45.3
Q ss_pred eecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH--HHHhc
Q 025112 149 IAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG--NQLRE 219 (257)
Q Consensus 149 Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~--~~l~e 219 (257)
-+.+..-.|.|..|.+++.|.+.+|++|.. + .+.++|+|+...+..|...+. .++..
T Consensus 21 ~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~-r-------------G~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 21 SDDNELVALFGPTDTNLSLLEIALGVSIVA-R-------------GEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CCchhhhhhcCCCCccHHHHHHHhCcEEEe-C-------------CceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 335667889999999999999999999984 2 367999999778888877776 44444
No 151
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=57.04 E-value=8.7 Score=37.24 Aligned_cols=38 Identities=32% Similarity=0.474 Sum_probs=33.1
Q ss_pred EEEecCccccceeccCchhHHHHHhhhCceEEEccccc
Q 025112 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA 90 (257)
Q Consensus 53 rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~ 90 (257)
.++|-...-|.+|||+|++.+.|.+++|-.-+|.+..|
T Consensus 102 EViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PP 139 (637)
T COG1782 102 EVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPP 139 (637)
T ss_pred eEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCC
Confidence 56777889999999999999999999998888876544
No 152
>COG1159 Era GTPase [General function prediction only]
Probab=56.32 E-value=14 Score=33.43 Aligned_cols=30 Identities=37% Similarity=0.492 Sum_probs=22.3
Q ss_pred CeEEEEEecCc-cccceeccCchhHHHHHhh
Q 025112 49 DVLFRIIVPSR-QIGKVIGKEGHRIQKIREE 78 (257)
Q Consensus 49 ~~~~rilVP~~-~vg~IIGk~G~~Ik~I~~~ 78 (257)
.+...|+|+.+ +-|-||||+|+.||+|-..
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 35556777754 4788999999999988444
No 153
>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=55.86 E-value=35 Score=24.68 Aligned_cols=54 Identities=20% Similarity=0.212 Sum_probs=41.6
Q ss_pred CChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 025112 161 SGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (257)
Q Consensus 161 ~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~ 218 (257)
|=..+.++-+..|++++..-+|...- ..++.++++.|+..++..|...++.+|+
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 45667888888899999765443221 2468999999999999999999988875
No 154
>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=54.28 E-value=14 Score=37.02 Aligned_cols=39 Identities=31% Similarity=0.406 Sum_probs=33.9
Q ss_pred EEEEecCccccceeccCchhHHHHHhhhCceEEEccccc
Q 025112 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA 90 (257)
Q Consensus 52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~ 90 (257)
=.++|-...-|.+|||+|.++++|.++||-+-.+.+..|
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 356777888999999999999999999999999886644
No 155
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=54.28 E-value=15 Score=31.39 Aligned_cols=28 Identities=32% Similarity=0.536 Sum_probs=23.0
Q ss_pred EEEEeecCccceeecCCChhHHHHHHHh
Q 025112 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
..+.|....-|.+||++|++|+++++.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~L 69 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEIL 69 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHH
Confidence 5666666888999999999999987544
No 156
>CHL00048 rps3 ribosomal protein S3
Probab=52.20 E-value=18 Score=31.05 Aligned_cols=30 Identities=27% Similarity=0.353 Sum_probs=24.7
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHh
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
...++.|-...-|.|||++|.+|++|++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 357777888888999999999999987543
No 157
>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=51.38 E-value=18 Score=30.61 Aligned_cols=28 Identities=25% Similarity=0.534 Sum_probs=23.9
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHH
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
..++.|....-|.+||++|..|++|++.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHH
Confidence 5778888888899999999999988743
No 158
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=49.47 E-value=14 Score=31.62 Aligned_cols=35 Identities=26% Similarity=0.450 Sum_probs=29.9
Q ss_pred eEEEEEeecCccceeecCCChhHHHHHHHhCCeEE
Q 025112 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIV 177 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~ 177 (257)
....+-+..+..+.|||+.|.++..||--++.-.+
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 35777788888999999999999999988876665
No 159
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=49.13 E-value=1.6e+02 Score=24.64 Aligned_cols=108 Identities=17% Similarity=0.244 Sum_probs=58.1
Q ss_pred EEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCe
Q 025112 96 VIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT 175 (257)
Q Consensus 96 vv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~ 175 (257)
.+.++|.+. +.++.+|+..+.+.+.+....-.... .+..+=+|.+...+.-+ ++..|.-..|-.
T Consensus 63 K~VcTGaKs---~ed~~~av~~~~~~L~~~g~~~~~~p--------~i~iQNIVaSadL~~~l-----nL~~iA~~lg~e 126 (185)
T COG2101 63 KVVCTGAKS---VEDVHRAVKKLAKKLKDGGIDIDFEP--------EIKVQNIVASADLGVEL-----NLNAIAIGLGLE 126 (185)
T ss_pred cEEEeccCc---HHHHHHHHHHHHHHHHhcCcCcCCCC--------ceEEEEEEEEeccCccc-----cHHHHHHhcccc
Confidence 367788664 56889999999999987433221111 12233333333222221 334443333332
Q ss_pred -EEEeCCCCCCcccCCCC---------CceEEEEEc--CHHHHHHHHHHHHHHHhcC
Q 025112 176 -IVILAPNQLPLCASAHE---------SDRVVQISG--DVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 176 -I~i~~~~~~p~~~~~~~---------~~r~V~I~G--~~~~v~~A~~~I~~~l~e~ 220 (257)
+. +.+++.|.-..... ....+.||| +++.+++|++.|...|.+.
T Consensus 127 ~~e-YEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ed~~~Av~~i~~~L~el 182 (185)
T COG2101 127 NIE-YEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQSRLEEL 182 (185)
T ss_pred ccc-cccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCHHHHHHHHHHHHHHHHHh
Confidence 22 22333333211111 223467888 5789999999999999873
No 160
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=48.69 E-value=20 Score=30.99 Aligned_cols=28 Identities=18% Similarity=0.401 Sum_probs=23.5
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHH
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
..++.|....-|.|||++|..|++|++.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~ 72 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSL 72 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHH
Confidence 4677888888899999999999988743
No 161
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=47.09 E-value=19 Score=30.87 Aligned_cols=28 Identities=36% Similarity=0.699 Sum_probs=24.4
Q ss_pred EEEEecCccccceeccCchhHHHHHhhh
Q 025112 52 FRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 52 ~rilVP~~~vg~IIGk~G~~Ik~I~~~t 79 (257)
+++.|....-|.|||++|..+++|++..
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 6777888888999999999999998765
No 162
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=46.90 E-value=18 Score=33.05 Aligned_cols=32 Identities=22% Similarity=0.435 Sum_probs=25.3
Q ss_pred CeEEEEEecCcc-ccceeccCchhHHHHHhhhC
Q 025112 49 DVLFRIIVPSRQ-IGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 49 ~~~~rilVP~~~-vg~IIGk~G~~Ik~I~~~tg 80 (257)
-+...+.||... ...||||||..|++|-++.+
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 477889999876 55667999999999866643
No 163
>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=41.27 E-value=98 Score=25.56 Aligned_cols=59 Identities=20% Similarity=0.269 Sum_probs=43.3
Q ss_pred CcceEEEEEeecCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 025112 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (257)
Q Consensus 140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~ 218 (257)
.+..+.++.++...+- ..+.+|.+-.|+-+.+. .+..|.|-|..+.+..|++.+..+-+
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efe-------------e~~~V~I~Gdke~Ik~aLKe~s~~wk 168 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEFE-------------EDDKVVIEGDKERIKKALKEFSSFWK 168 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEec-------------CCcEEEEeccHHHHHHHHHHHHHHhc
Confidence 3445666666665432 46778889999999871 24569999999999999998876543
No 164
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=37.87 E-value=36 Score=29.14 Aligned_cols=28 Identities=43% Similarity=0.707 Sum_probs=23.3
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHH
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
..++.|....-|.|||++|..|++|++.
T Consensus 63 ~i~I~I~~~~pg~vIG~~g~~i~~l~~~ 90 (211)
T TIGR01009 63 KIRVTIHTARPGIVIGKKGSEIEKLRKD 90 (211)
T ss_pred ceEEEEEeCCCcceeCCCchHHHHHHHH
Confidence 3677788888899999999999998743
No 165
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=37.05 E-value=96 Score=23.72 Aligned_cols=41 Identities=24% Similarity=0.169 Sum_probs=32.8
Q ss_pred HHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025112 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (257)
Q Consensus 170 ~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~ 221 (257)
+..++.|-+.++ -...+.|+|+-++|+.|++.+.+.+++..
T Consensus 61 Kaa~V~igF~DR-----------FsGslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 61 KAADVHIGFLDR-----------FSGALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred hccCcEEeeeec-----------cceeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 345788887632 34569999999999999999999999843
No 166
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=37.00 E-value=2.4e+02 Score=23.24 Aligned_cols=107 Identities=17% Similarity=0.170 Sum_probs=58.9
Q ss_pred EEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCe
Q 025112 96 VIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT 175 (257)
Q Consensus 96 vv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~ 175 (257)
.+.++|... ..++..|++.+.+++.+......... ....+-++....+++ .-.++.|....+-+
T Consensus 57 KivitGaks---~~~~~~a~~~~~~~L~~~g~~~~~~~--------~~~v~NIvas~~l~~-----~i~L~~la~~~~~~ 120 (174)
T cd00652 57 KMVITGAKS---EEDAKLAARKYARILQKLGFPVEKFP--------EFKVQNIVASCDLGF-----PIRLEELALKHPEN 120 (174)
T ss_pred EEEEEecCC---HHHHHHHHHHHHHHHHHcCCCccccC--------ceEEEEEEEEEECCC-----cccHHHHHhhhhcc
Confidence 477888543 35788899999998876653321110 123333333333333 23467776655433
Q ss_pred EEEeCCCCCCcccCC---------CCCceEEEEEcC--HHHHHHHHHHHHHHHhc
Q 025112 176 IVILAPNQLPLCASA---------HESDRVVQISGD--VPAVLNALVEIGNQLRE 219 (257)
Q Consensus 176 I~i~~~~~~p~~~~~---------~~~~r~V~I~G~--~~~v~~A~~~I~~~l~e 219 (257)
+.- .++..|..... --....|.|+|. .+.++.|.+.|..+|.+
T Consensus 121 ~~Y-ePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~L~~ 174 (174)
T cd00652 121 ASY-EPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILKE 174 (174)
T ss_pred cEE-CCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHhC
Confidence 332 22222221100 012356888995 57899999999988864
No 167
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=36.52 E-value=33 Score=29.87 Aligned_cols=29 Identities=38% Similarity=0.643 Sum_probs=23.9
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhh
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~t 79 (257)
.+.+.|-...-+.|||++|..|++|++..
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 35666677778999999999999998775
No 168
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=34.38 E-value=41 Score=30.86 Aligned_cols=32 Identities=19% Similarity=0.340 Sum_probs=24.5
Q ss_pred ceEEEEEeecC-ccceeecCCChhHHHHHHHhC
Q 025112 142 ANTIRLLIAGS-QAGCLIGMSGQNIEKLRNSSG 173 (257)
Q Consensus 142 ~~~~~l~Vp~~-~vG~iIGk~G~~Ik~I~~~tg 173 (257)
.+..++.+|.. +...|||+||..|++|-+.-+
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 45677888855 557889999999999876543
No 169
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.06 E-value=1.5e+02 Score=24.02 Aligned_cols=44 Identities=30% Similarity=0.425 Sum_probs=34.9
Q ss_pred hhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 163 ~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
.++..|.+..|+-|.+. ....|.|.|..+.|.+|++.|-..-++
T Consensus 126 eRlqDi~E~hgvIiE~~-------------E~D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFE-------------EYDLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEee-------------eccEEEEeccHHHHHHHHHHHHHHHhc
Confidence 45667778889888873 246799999999999999998776554
No 170
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=32.55 E-value=1.3e+02 Score=21.03 Aligned_cols=42 Identities=14% Similarity=0.168 Sum_probs=30.2
Q ss_pred ChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH
Q 025112 162 GQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG 214 (257)
Q Consensus 162 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~ 214 (257)
-..|.+|-+.++++|.=.. .+.-+++++|+++.+...++++.
T Consensus 16 r~ei~~l~~~f~a~ivd~~-----------~~~~iie~tG~~~kid~fi~~l~ 57 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVS-----------PDSIIIELTGTPEKIDAFIKLLK 57 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEE-----------TTEEEEEEEE-HHHHHHHHHHST
T ss_pred HHHHHHHHHHhCCEEEEEC-----------CCEEEEEEcCCHHHHHHHHHHhh
Confidence 3467888899999997542 34688999999999987665543
No 171
>PRK04021 hypothetical protein; Reviewed
Probab=30.62 E-value=1.4e+02 Score=22.12 Aligned_cols=39 Identities=15% Similarity=0.273 Sum_probs=29.7
Q ss_pred hHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHH
Q 025112 164 NIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNAL 210 (257)
Q Consensus 164 ~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~ 210 (257)
-|+-|.+..|++|.+.+.. .+..+.|.|.| +++.+...+
T Consensus 51 li~~LAk~l~~~I~I~~G~--------~sr~K~v~i~g~~~e~l~~~L 90 (92)
T PRK04021 51 LVKFFSKLLGAEVEIIRGE--------TSREKDLLVKGISLEEVKKKL 90 (92)
T ss_pred HHHHHHHHhCCCEEEEecC--------CcCceEEEEecCCHHHHHHHh
Confidence 4777888999999987532 26789999999 777776554
No 172
>TIGR01334 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.
Probab=27.52 E-value=2.7e+02 Score=24.91 Aligned_cols=56 Identities=14% Similarity=0.097 Sum_probs=43.6
Q ss_pred CCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 160 k~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
-|-....++-+..|+++.+...|.-.- ..++.++++.|+...+..|...++.+|+-
T Consensus 46 ~G~~~~~~i~~~l~~~~~~~~~dG~~v----~~g~~i~~~~G~a~~ll~~eR~alN~l~~ 101 (277)
T TIGR01334 46 SGVSEAAKLLKQLGASIDYAVPSGSRA----LAGTLLLEAKGSAGQLHQGWKSAQSVLEW 101 (277)
T ss_pred ECHHHHHHHHHHcCCEEEEEeCCCCEe----CCCCEEEEEEecHHHHHHHHHHHHHHHHH
Confidence 445677888889999999876543221 25789999999999999998888877764
No 173
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=27.36 E-value=65 Score=28.02 Aligned_cols=29 Identities=38% Similarity=0.637 Sum_probs=23.1
Q ss_pred EEEEEeecCccceeecCCChhHHHHHHHh
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
.+++.|-...-|.|||++|..|++|++.-
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 46677777777999999999999887543
No 174
>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=25.42 E-value=3e+02 Score=24.48 Aligned_cols=56 Identities=18% Similarity=0.226 Sum_probs=42.8
Q ss_pred CCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 160 k~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
-|-....+|-+..|+++.+.-++...- ...+.+++|.|...++..+...++.+|+-
T Consensus 44 ~G~~~a~~i~~~l~~~~~~~~~dG~~v----~~g~~i~~i~G~a~~ll~~Er~~ln~l~~ 99 (273)
T PRK05848 44 SGEKYALELLEMTGIECVFTIKDGERF----KKGDILMEIEGDFSMLLKVERTLLNLLQH 99 (273)
T ss_pred ECHHHHHHHHHHcCCEEEEEcCCCCEe----cCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 445667888888999888765443211 25789999999999999999988888775
No 175
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=25.10 E-value=78 Score=21.12 Aligned_cols=51 Identities=16% Similarity=0.272 Sum_probs=31.4
Q ss_pred ChhHHH--HHHHhCCeEEEeCCCC---CCcccCCCCCceEEEEEcCHHHHHHHHHH
Q 025112 162 GQNIEK--LRNSSGATIVILAPNQ---LPLCASAHESDRVVQISGDVPAVLNALVE 212 (257)
Q Consensus 162 G~~Ik~--I~~~tga~I~i~~~~~---~p~~~~~~~~~r~V~I~G~~~~v~~A~~~ 212 (257)
|.+|++ +++.+|+.|.-..++. .|..-..-.....+.|.|+.+.+.++.++
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~ 69 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFREL 69 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHh
Confidence 457777 7777888887553321 11100001245789999999999887665
No 176
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=24.77 E-value=4e+02 Score=21.95 Aligned_cols=107 Identities=17% Similarity=0.124 Sum_probs=55.8
Q ss_pred EEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCe
Q 025112 96 VIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT 175 (257)
Q Consensus 96 vv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~ 175 (257)
.+.++|... ..++.+|++.+.+.+.+........ .....+-++.....++= -++..|...+.-+
T Consensus 57 KiviTGaks---~~~~~~a~~~~~~~l~~~g~~~~~~--------~~f~v~nIvat~~~~~~-----i~L~~la~~~~~~ 120 (174)
T cd04517 57 KITITGATS---EEEAKQAARRAARLLQKLGFKVVRF--------SNFRVVNVLATCSMPFP-----IRLDELAAKNRSS 120 (174)
T ss_pred eEEEEccCC---HHHHHHHHHHHHHHHHHcCCCcccC--------CceEEEEEEEEEeCCCc-----ccHHHHHHhchhh
Confidence 477888654 3477888888888887654322110 01233333333333222 2355555443222
Q ss_pred EEEeCCCCCCcccCC---------CCCceEEEEEc--CHHHHHHHHHHHHHHHhc
Q 025112 176 IVILAPNQLPLCASA---------HESDRVVQISG--DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 176 I~i~~~~~~p~~~~~---------~~~~r~V~I~G--~~~~v~~A~~~I~~~l~e 219 (257)
+.- .++..|..... --....|+|+| +.+.+.+|.+.|..+|.+
T Consensus 121 ~~Y-ePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~pil~~ 174 (174)
T cd04517 121 ASY-EPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPIVFE 174 (174)
T ss_pred cEe-CCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHhC
Confidence 221 11221211100 01235688899 467999999999988754
No 177
>PRK03818 putative transporter; Validated
Probab=24.32 E-value=6.9e+02 Score=24.58 Aligned_cols=138 Identities=13% Similarity=0.185 Sum_probs=71.1
Q ss_pred EEEEEecCccccceeccCchhHHHHHhhhCceEEEcccc-------c--C---CCccEEEeccCCCCchhhHHHHHHHHH
Q 025112 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI-------A--R---HEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~-------~--~---~~ervv~I~G~~~~~~~~~~~~A~~~I 118 (257)
..++.|+.+. ++ |.+++++.......+.+.+-. + + ....++.|.|..+ ++..+
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e---------~l~~l 270 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPE---------DLHKA 270 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHH---------HHHHH
Confidence 3566666433 34 678999988877666654211 1 1 1234577888743 33333
Q ss_pred HHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHH--HHHhCCeEEEeCCCC--CCccc-CCCCC
Q 025112 119 AALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKL--RNSSGATIVILAPNQ--LPLCA-SAHES 193 (257)
Q Consensus 119 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I--~~~tga~I~i~~~~~--~p~~~-~~~~~ 193 (257)
.+..-.......+ ..........+++|++ .++|+ +++++ ++.+|+.+.=..+.+ ++... ..-..
T Consensus 271 ~~~~Gl~~~~~~~-----~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~ 339 (552)
T PRK03818 271 QLVIGEEVDTSLS-----TRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQF 339 (552)
T ss_pred HHhcCCccCcccc-----ccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEec
Confidence 3333221100000 0001122344455543 66665 77777 577888776444322 21100 00023
Q ss_pred ceEEEEEcCHHHHHHHHHHHH
Q 025112 194 DRVVQISGDVPAVLNALVEIG 214 (257)
Q Consensus 194 ~r~V~I~G~~~~v~~A~~~I~ 214 (257)
...+.+.|++++++++.+.+-
T Consensus 340 GD~LlVvG~~~~i~~l~~~Lg 360 (552)
T PRK03818 340 GDILNLVGRPEAIDAVANVLG 360 (552)
T ss_pred CCEEEEEECHHHHHHHHHHhC
Confidence 467899999999998777533
No 178
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=24.25 E-value=4.1e+02 Score=21.92 Aligned_cols=106 Identities=14% Similarity=0.124 Sum_probs=54.9
Q ss_pred EEEeccCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeecCccceeecCCChhHHHHHHHhCCe
Q 025112 96 VIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT 175 (257)
Q Consensus 96 vv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~ 175 (257)
.+.++|... ..++..|++.+.+++.+........ ....+=++....+++=| ++..|.....-.
T Consensus 57 KiviTGaks---~e~a~~a~~~i~~~L~~~g~~~~~~---------~~~v~Nivat~~l~~~i-----~L~~la~~~~~~ 119 (174)
T cd04516 57 KMVCTGAKS---EDDSKLAARKYARIIQKLGFPAKFT---------DFKIQNIVGSCDVKFPI-----RLEGLAHAHKQF 119 (174)
T ss_pred eEEEEecCC---HHHHHHHHHHHHHHHHHcCCCCCCC---------ceEEEEEEEEEECCCcc-----cHHHHHHhChhc
Confidence 477888544 3467888888888887654322110 12223233333223222 345554322222
Q ss_pred EEEeCCCCCCcccCCC---------CCceEEEEEcC--HHHHHHHHHHHHHHHhc
Q 025112 176 IVILAPNQLPLCASAH---------ESDRVVQISGD--VPAVLNALVEIGNQLRE 219 (257)
Q Consensus 176 I~i~~~~~~p~~~~~~---------~~~r~V~I~G~--~~~v~~A~~~I~~~l~e 219 (257)
+. +.++..|...... -....|.|+|. .+.+++|++.|..+|.+
T Consensus 120 ~~-YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~~a~~~i~p~L~~ 173 (174)
T cd04516 120 SS-YEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEIYQAFENIYPILLQ 173 (174)
T ss_pred cE-eCCccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 22 1222222211000 12346788884 67899999999998875
No 179
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=23.97 E-value=59 Score=26.75 Aligned_cols=61 Identities=16% Similarity=0.408 Sum_probs=36.1
Q ss_pred ccCchhHHHHHhhhCceEEEccc--ccC--------------CCccEEEeccCCCCchhhHHHHHHHHHHHHHhcCC
Q 025112 66 GKEGHRIQKIREETKATIKIADA--IAR--------------HEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (257)
Q Consensus 66 Gk~G~~Ik~I~~~tg~~I~i~~~--~~~--------------~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~~ 126 (257)
|+||.+++++-.+..++..+... .|. .....+.|+...--...-++.+|++.|.++|....
T Consensus 51 GPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~NiaDcleKlr~~I~~~~ 127 (172)
T KOG3429|consen 51 GPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNIADCLEKLRDIIRAAE 127 (172)
T ss_pred CCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccHHHHHHHHHHHHHHHh
Confidence 99999999886555555544321 000 11222666664432223367899999999886643
No 180
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=23.40 E-value=1.5e+02 Score=22.72 Aligned_cols=29 Identities=34% Similarity=0.412 Sum_probs=24.7
Q ss_pred ceEEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 025112 194 DRVVQISGDVPAVLNALVEIGNQLRENPP 222 (257)
Q Consensus 194 ~r~V~I~G~~~~v~~A~~~I~~~l~e~~~ 222 (257)
.-.+.|+|+..+|+.|++...+.+++...
T Consensus 73 ~g~vii~GdvsaV~aAl~a~~~~~~~~~~ 101 (110)
T cd07046 73 SGALVITGDVSEVESALEAVVDYLRETLG 101 (110)
T ss_pred eEEEEEEECHHHHHHHHHHHHHHHhhccC
Confidence 34688999999999999999999988543
No 181
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=23.06 E-value=1.5e+02 Score=20.74 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=32.6
Q ss_pred HHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025112 167 KLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 167 ~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~ 220 (257)
..-+.+++.+.-... .| .+.-.+.|+|+..+|+.|++...+.+.+.
T Consensus 20 ~alKaa~V~l~~~~~----~~----~g~~~~~i~G~vs~V~~Av~a~~~~~~~~ 65 (75)
T PF00936_consen 20 AALKAANVELVEIEL----IC----GGKVTVIITGDVSAVKAAVDAAEEAAGKK 65 (75)
T ss_dssp HHHHHSSEEEEEEEE----ES----TTEEEEEEEESHHHHHHHHHHHHHHHHHT
T ss_pred HHhhcCCEEEEEEEe----cC----CCeEEEEEEECHHHHHHHHHHHHHHHhhc
Confidence 344556666654322 11 34678999999999999999999988874
No 182
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=22.16 E-value=4.7e+02 Score=25.77 Aligned_cols=67 Identities=15% Similarity=0.249 Sum_probs=40.1
Q ss_pred EEEEEeecCccceeecCCChhHHHHH------HHhCCeEEEeCCCCC--Cc---ccCCCCCceEEEEEcCHHHHHHHHHH
Q 025112 144 TIRLLIAGSQAGCLIGMSGQNIEKLR------NSSGATIVILAPNQL--PL---CASAHESDRVVQISGDVPAVLNALVE 212 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~------~~tga~I~i~~~~~~--p~---~~~~~~~~r~V~I~G~~~~v~~A~~~ 212 (257)
...+++|++ .++|| ++++++ +.+|+.|.-..+.+. +. -.. .....+.+.|++++++++.+.
T Consensus 304 ~e~VV~~~S---~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L--~~GD~LlV~G~~~~l~~~~~~ 375 (562)
T TIGR03802 304 TKDVVLTNK---EYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVL--QRGDVVTLVGTPQDVDRAAKQ 375 (562)
T ss_pred EEEEEECCc---ccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEe--cCCCEEEEEeCHHHHHHHHHH
Confidence 344555543 56664 788776 267888875544321 11 000 234688999999999987776
Q ss_pred HHHHHh
Q 025112 213 IGNQLR 218 (257)
Q Consensus 213 I~~~l~ 218 (257)
+-...+
T Consensus 376 lG~~~~ 381 (562)
T TIGR03802 376 LGYAIA 381 (562)
T ss_pred cCCchh
Confidence 443333
No 183
>cd01572 QPRTase Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=21.85 E-value=3.5e+02 Score=23.88 Aligned_cols=55 Identities=15% Similarity=0.099 Sum_probs=41.6
Q ss_pred CChhHHHHHHHh--CCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 161 SGQNIEKLRNSS--GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 161 ~G~~Ik~I~~~t--ga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
|-....+|-+.. |+++...-+|...- ...+.+++|.|+..++..+...++.+|.-
T Consensus 43 G~~~~~~i~~~~~~~l~v~~~~~dG~~v----~~g~~i~~i~G~~~~ll~~Er~~ln~L~~ 99 (268)
T cd01572 43 GLPVAEEVFELLDPGIEVEWLVKDGDRV----EPGQVLATVEGPARSLLTAERTALNFLQR 99 (268)
T ss_pred CHHHHHHHHHHcCCCeEEEEEeCCCCEe----cCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 455678888888 88887654433211 25789999999999999999988888764
No 184
>PRK09256 hypothetical protein; Provisional
Probab=21.33 E-value=1.1e+02 Score=24.44 Aligned_cols=58 Identities=24% Similarity=0.439 Sum_probs=33.9
Q ss_pred ccCchhHHHHHhhhCceEEEccc---cc--------------CCCccEEEeccCCCCchhhHHHHHHHHHHHHHhcC
Q 025112 66 GKEGHRIQKIREETKATIKIADA---IA--------------RHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 66 Gk~G~~Ik~I~~~tg~~I~i~~~---~~--------------~~~ervv~I~G~~~~~~~~~~~~A~~~I~~~i~~~ 125 (257)
|+||.++++.. |.|.+.++-. .| -+.+..++|+....-....+...|+..+.++|.+.
T Consensus 24 GPGGQ~VNKt~--SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~ 98 (138)
T PRK09256 24 GPGGQNVNKVS--TAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALERLVALIREA 98 (138)
T ss_pred CCCcccccccc--eeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHH
Confidence 88888887653 4445544211 00 01234466666554333456788898888888764
No 185
>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=20.92 E-value=4e+02 Score=23.93 Aligned_cols=56 Identities=13% Similarity=0.013 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHhCCeEE--EeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 160 MSGQNIEKLRNSSGATIV--ILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 160 k~G~~Ik~I~~~tga~I~--i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
-|-....+|-+..|++++ +.-++...- ..++.++++.|+..++..|...++.+|.-
T Consensus 56 ~G~~~a~~i~~~~~~~~~~~~~~~dG~~v----~~g~~i~~~~G~a~~ll~~eR~~lN~l~~ 113 (288)
T PRK07428 56 AGLPIAARVFQLLDPQVSFTPLVAEGAAC----ESGQVVAEIEGPLDALLMGERVALNLAMR 113 (288)
T ss_pred ECHHHHHHHHHHcCCcEEEEEEcCCCCEe----cCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 445667888899997776 333332111 25789999999999999999888888764
No 186
>cd01573 modD_like ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.
Probab=20.90 E-value=4.1e+02 Score=23.50 Aligned_cols=56 Identities=9% Similarity=0.060 Sum_probs=41.8
Q ss_pred CCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 160 k~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
-|-....++-+..++++.+.-+|...- ...+.+++|.|+..++..+...++.+|+-
T Consensus 42 aG~~~~~~~~~~~~~~v~~~~~dG~~v----~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 97 (272)
T cd01573 42 CGTEEAARILELLGLEVDLAAASGSRV----AAGAVLLEAEGPAAALHLGWKVAQTLLEW 97 (272)
T ss_pred ECHHHHHHHHHHcCcEEEEEcCCCCEe----cCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 344567788888899988654433211 25789999999999999999888887764
No 187
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=20.14 E-value=4.3e+02 Score=23.61 Aligned_cols=55 Identities=11% Similarity=0.150 Sum_probs=41.5
Q ss_pred CChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025112 161 SGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 161 ~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
|-....++-+..++++...-+|...- ...+.++++.|+..++..|...++.+|+-
T Consensus 45 G~~~a~~i~~~l~~~v~~~~~dG~~v----~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 99 (278)
T PRK08385 45 GLEEAKALFEHFGVKVEVRKRDGEEV----KAGEVILELKGNARAILLVERTALNIIGR 99 (278)
T ss_pred CHHHHHHHHHHcCCEEEEEcCCCCEe----cCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 34556778788899998865443221 25789999999999999998888887764
Done!