Query 003989
Match_columns 781
No_of_seqs 247 out of 786
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 15:34:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003989.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003989hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0119 Splicing factor 1/bran 100.0 1E-57 2.2E-62 494.1 38.1 275 66-370 13-323 (554)
2 COG5176 MSL5 Splicing factor ( 100.0 4.1E-39 8.9E-44 321.5 11.0 178 83-264 58-243 (269)
3 cd02395 SF1_like-KH Splicing f 99.9 4E-28 8.6E-33 226.0 10.1 109 169-277 1-117 (120)
4 KOG1588 RNA-binding protein Sa 99.9 8.7E-28 1.9E-32 247.1 12.0 145 135-279 53-212 (259)
5 TIGR02696 pppGpp_PNP guanosine 99.3 1.3E-11 2.9E-16 142.9 11.8 95 136-261 548-642 (719)
6 PLN00207 polyribonucleotide nu 99.2 1.9E-11 4.1E-16 144.3 8.2 101 136-267 654-756 (891)
7 TIGR03591 polynuc_phos polyrib 99.2 5.1E-11 1.1E-15 138.2 9.9 98 137-265 521-619 (684)
8 cd02393 PNPase_KH Polynucleoti 99.1 1E-10 2.3E-15 97.2 7.5 59 169-256 3-61 (61)
9 COG1185 Pnp Polyribonucleotide 99.1 2.9E-10 6.3E-15 130.3 8.6 100 137-267 522-622 (692)
10 PRK11824 polynucleotide phosph 99.0 6.7E-10 1.4E-14 129.2 7.6 99 136-265 523-622 (693)
11 PF00013 KH_1: KH domain syndr 98.8 7.5E-09 1.6E-13 84.2 4.4 59 170-255 2-60 (60)
12 cd00105 KH-I K homology RNA-bi 98.7 3.7E-08 8E-13 79.8 7.8 63 170-256 2-64 (64)
13 cd02394 vigilin_like_KH K homo 98.7 2.3E-08 5E-13 81.8 5.8 61 170-256 2-62 (62)
14 smart00322 KH K homology RNA-b 98.6 2.4E-07 5.3E-12 73.5 8.5 66 169-260 4-69 (69)
15 PRK13763 putative RNA-processi 98.5 1.3E-07 2.8E-12 94.0 6.7 66 169-263 4-73 (180)
16 cd02396 PCBP_like_KH K homolog 98.5 3.9E-07 8.4E-12 76.1 7.9 63 170-255 2-64 (65)
17 TIGR03665 arCOG04150 arCOG0415 98.4 2.4E-07 5.3E-12 91.4 5.5 63 172-263 2-67 (172)
18 KOG1960 Predicted RNA-binding 98.4 8.3E-06 1.8E-10 89.8 16.6 91 170-268 212-302 (531)
19 KOG1067 Predicted RNA-binding 98.4 7E-07 1.5E-11 101.2 7.6 98 136-265 566-664 (760)
20 TIGR03665 arCOG04150 arCOG0415 98.2 1.9E-06 4.2E-11 85.1 6.2 55 184-263 99-153 (172)
21 KOG1676 K-homology type RNA bi 98.2 9E-06 2E-10 92.9 12.0 109 125-263 102-212 (600)
22 KOG1676 K-homology type RNA bi 98.2 6.7E-06 1.5E-10 93.9 10.8 75 169-266 231-305 (600)
23 PF13014 KH_3: KH domain 98.2 2.9E-06 6.3E-11 65.8 5.5 28 184-211 1-28 (43)
24 PRK13763 putative RNA-processi 98.1 4.1E-06 9E-11 83.4 6.8 55 184-263 105-159 (180)
25 KOG2191 RNA-binding protein NO 97.8 0.0001 2.3E-09 79.9 11.2 125 136-281 95-225 (402)
26 PRK04163 exosome complex RNA-b 97.8 2.5E-05 5.4E-10 80.7 6.3 66 170-264 147-212 (235)
27 COG1094 Predicted RNA-binding 97.5 0.00016 3.5E-09 73.6 6.6 56 184-264 112-167 (194)
28 KOG0119 Splicing factor 1/bran 97.3 0.0076 1.7E-07 68.6 17.0 71 8-93 30-102 (554)
29 KOG2193 IGF-II mRNA-binding pr 97.1 0.00071 1.5E-08 75.5 6.4 97 174-285 280-378 (584)
30 KOG2191 RNA-binding protein NO 97.0 0.0024 5.3E-08 69.7 8.2 78 169-267 40-117 (402)
31 KOG2814 Transcription coactiva 96.9 0.0012 2.7E-08 71.8 5.3 62 183-263 66-127 (345)
32 KOG2190 PolyC-binding proteins 96.7 0.0066 1.4E-07 69.4 9.7 101 135-261 104-208 (485)
33 PRK12704 phosphodiesterase; Pr 96.6 0.007 1.5E-07 69.6 9.3 68 168-262 210-277 (520)
34 TIGR03319 YmdA_YtgF conserved 96.6 0.008 1.7E-07 69.0 9.2 74 162-262 198-271 (514)
35 PRK00106 hypothetical protein; 96.5 0.01 2.3E-07 68.5 9.5 71 168-265 225-295 (535)
36 KOG2193 IGF-II mRNA-binding pr 96.4 0.0028 6.1E-08 70.9 3.8 74 170-266 201-274 (584)
37 KOG1960 Predicted RNA-binding 95.2 0.02 4.3E-07 64.1 4.3 63 191-261 111-173 (531)
38 PRK12705 hypothetical protein; 94.7 0.067 1.4E-06 61.8 7.0 41 168-213 198-238 (508)
39 COG1094 Predicted RNA-binding 93.4 0.23 5E-06 51.3 7.2 65 169-261 9-77 (194)
40 cd02134 NusA_KH NusA_K homolog 92.8 0.18 3.8E-06 42.5 4.5 37 168-210 25-61 (61)
41 KOG2192 PolyC-binding hnRNP-K 92.4 0.35 7.5E-06 52.3 7.1 70 169-262 316-385 (390)
42 KOG2874 rRNA processing protei 92.2 0.2 4.4E-06 54.3 5.1 27 186-212 161-187 (356)
43 COG1097 RRP4 RNA-binding prote 92.0 0.29 6.2E-06 52.0 5.8 38 170-213 148-185 (239)
44 KOG2190 PolyC-binding proteins 90.7 0.56 1.2E-05 54.2 6.9 68 170-261 45-121 (485)
45 KOG2192 PolyC-binding hnRNP-K 90.3 0.98 2.1E-05 49.0 7.9 38 169-212 49-86 (390)
46 COG1855 ATPase (PilT family) [ 89.8 0.48 1E-05 54.7 5.4 62 145-214 465-526 (604)
47 KOG0336 ATP-dependent RNA heli 88.8 0.52 1.1E-05 53.8 4.7 61 183-264 56-116 (629)
48 PF13184 KH_5: NusA-like KH do 86.9 0.33 7.2E-06 42.3 1.4 41 171-212 6-47 (69)
49 PRK13764 ATPase; Provisional 83.6 1.2 2.7E-05 52.7 4.5 39 169-213 482-520 (602)
50 COG1702 PhoH Phosphate starvat 79.0 3.4 7.3E-05 46.3 5.5 58 183-265 24-83 (348)
51 cd02409 KH-II KH-II (K homolo 78.3 1.8 3.9E-05 34.9 2.4 24 184-207 35-58 (68)
52 PRK08406 transcription elongat 75.9 3.3 7E-05 40.6 3.9 30 183-212 41-70 (140)
53 PF09981 DUF2218: Uncharacteri 74.3 5.5 0.00012 36.3 4.7 67 193-263 11-79 (89)
54 KOG0633 Histidinol phosphate a 73.5 7.2 0.00016 42.9 6.1 100 125-258 272-374 (375)
55 KOG3273 Predicted RNA-binding 68.8 3 6.6E-05 43.8 2.0 62 183-277 178-239 (252)
56 PF14611 SLS: Mitochondrial in 66.0 16 0.00036 36.9 6.6 59 184-265 36-94 (210)
57 COG0195 NusA Transcription elo 64.0 5.5 0.00012 41.2 2.7 33 181-213 83-115 (190)
58 KOG2279 Kinase anchor protein 62.3 5 0.00011 47.3 2.3 40 169-214 69-108 (608)
59 cd02414 jag_KH jag_K homology 61.6 10 0.00022 33.2 3.6 27 184-210 34-60 (77)
60 KOG2208 Vigilin [Lipid transpo 61.5 10 0.00022 46.3 4.8 61 184-260 357-417 (753)
61 PF13083 KH_4: KH domain; PDB: 60.4 3.7 8E-05 35.2 0.7 30 169-204 30-59 (73)
62 PRK09986 DNA-binding transcrip 58.9 14 0.00031 37.7 4.7 21 193-213 39-59 (294)
63 TIGR01952 nusA_arch NusA famil 58.9 8 0.00017 38.2 2.8 30 183-212 42-71 (141)
64 KOG2113 Predicted RNA binding 58.0 6.1 0.00013 44.0 1.9 32 182-213 34-65 (394)
65 PRK12327 nusA transcription el 57.2 10 0.00022 42.7 3.5 42 170-212 233-275 (362)
66 PRK00089 era GTPase Era; Revie 56.2 27 0.00059 36.7 6.3 69 138-211 191-272 (292)
67 TIGR01953 NusA transcription t 55.7 11 0.00024 42.0 3.5 42 170-212 231-273 (341)
68 PRK08406 transcription elongat 55.5 9.3 0.0002 37.5 2.6 36 169-210 100-135 (140)
69 PRK15494 era GTPase Era; Provi 52.2 41 0.00089 36.9 7.1 69 138-211 236-319 (339)
70 KOG0334 RNA helicase [RNA proc 49.7 7.6 0.00017 48.5 1.2 85 173-269 901-985 (997)
71 KOG4849 mRNA cleavage factor I 49.1 3.9E+02 0.0084 30.9 13.8 15 762-776 353-367 (498)
72 PRK12328 nusA transcription el 48.9 13 0.00027 42.3 2.6 42 170-212 239-281 (374)
73 PRK06418 transcription elongat 47.8 14 0.00031 37.6 2.6 30 183-213 70-99 (166)
74 PRK12329 nusA transcription el 47.5 11 0.00024 43.6 2.0 43 169-212 264-307 (449)
75 TIGR01825 gly_Cac_T_rel pyrido 46.4 1.7E+02 0.0036 31.5 10.5 62 183-261 314-381 (385)
76 TIGR00436 era GTP-binding prot 46.1 55 0.0012 34.3 6.7 68 138-210 184-266 (270)
77 PRK11242 DNA-binding transcrip 46.0 32 0.0007 35.2 4.9 19 194-212 34-52 (296)
78 KOG2113 Predicted RNA binding 45.9 11 0.00025 42.0 1.7 31 182-212 123-153 (394)
79 PRK11716 DNA-binding transcrip 45.7 30 0.00065 34.5 4.5 19 194-212 10-28 (269)
80 cd02410 archeal_CPSF_KH The ar 45.7 24 0.00052 35.4 3.7 29 183-211 85-113 (145)
81 PRK00468 hypothetical protein; 44.4 13 0.00027 33.3 1.4 18 184-201 40-57 (75)
82 PRK10837 putative DNA-binding 44.3 33 0.00071 35.0 4.6 20 194-213 36-55 (290)
83 PRK02821 hypothetical protein; 44.2 12 0.00027 33.6 1.4 22 183-204 40-61 (77)
84 PRK09906 DNA-binding transcrip 44.2 33 0.0007 35.3 4.6 21 193-213 33-53 (296)
85 PRK15421 DNA-binding transcrip 41.9 36 0.00078 36.2 4.6 19 194-212 35-53 (317)
86 PRK03601 transcriptional regul 41.7 36 0.00078 35.1 4.5 19 194-212 34-52 (275)
87 PRK13392 5-aminolevulinate syn 40.9 2.3E+02 0.0049 31.3 10.7 25 237-261 370-397 (410)
88 PRK09202 nusA transcription el 40.9 22 0.00047 41.4 3.0 42 170-212 233-275 (470)
89 TIGR01169 rplA_bact ribosomal 40.8 35 0.00075 36.1 4.2 77 171-266 111-202 (227)
90 TIGR00707 argD acetylornithine 40.3 2.2E+02 0.0047 30.6 10.2 23 237-259 354-379 (379)
91 PRK11013 DNA-binding transcrip 39.3 30 0.00064 36.3 3.5 20 194-213 37-56 (309)
92 KOG2208 Vigilin [Lipid transpo 38.7 20 0.00044 43.9 2.4 37 169-211 710-746 (753)
93 COG0026 PurK Phosphoribosylami 38.4 50 0.0011 37.7 5.2 51 195-259 318-368 (375)
94 PRK09791 putative DNA-binding 38.1 50 0.0011 34.2 4.9 20 194-213 38-57 (302)
95 PRK01064 hypothetical protein; 37.8 20 0.00043 32.4 1.6 21 184-204 40-60 (78)
96 PRK10094 DNA-binding transcrip 37.7 46 0.00099 35.1 4.6 20 194-213 35-54 (308)
97 COG1837 Predicted RNA-binding 37.4 19 0.00041 32.6 1.4 18 184-201 40-57 (76)
98 PRK12328 nusA transcription el 37.1 39 0.00084 38.5 4.1 41 168-214 308-348 (374)
99 PRK01170 phosphopantetheine ad 36.4 2.3E+02 0.0049 31.9 9.7 80 184-267 86-187 (322)
100 PRK11151 DNA-binding transcrip 36.0 49 0.0011 34.4 4.4 19 194-212 34-52 (305)
101 PRK11074 putative DNA-binding 35.4 57 0.0012 33.9 4.8 19 194-212 35-53 (300)
102 PLN02397 aspartate transaminas 35.4 2.6E+02 0.0057 31.4 10.2 42 194-260 379-420 (423)
103 KOG1423 Ras-like GTPase ERA [C 35.2 1.2E+02 0.0026 34.5 7.3 65 135-204 288-359 (379)
104 TIGR03418 chol_sulf_TF putativ 34.9 32 0.00069 35.3 2.8 19 194-212 34-52 (291)
105 PRK12680 transcriptional regul 34.8 47 0.001 35.6 4.2 21 194-214 35-55 (327)
106 COG1159 Era GTPase [General fu 34.5 90 0.0019 34.8 6.2 69 137-210 191-274 (298)
107 cd04517 TLF TBP-like factors ( 34.2 1.8E+02 0.0038 29.7 7.9 62 92-154 17-84 (174)
108 COG0014 ProA Gamma-glutamyl ph 34.1 63 0.0014 37.3 5.1 55 183-260 195-250 (417)
109 KOG4369 RTK signaling protein 33.5 62 0.0013 41.9 5.3 79 170-272 1342-1421(2131)
110 TIGR02424 TF_pcaQ pca operon t 33.3 52 0.0011 33.9 4.1 20 194-213 36-55 (300)
111 COG1847 Jag Predicted RNA-bind 33.3 96 0.0021 33.0 6.0 26 185-210 102-127 (208)
112 PF09692 Arb1: Argonaute siRNA 32.7 1.5E+02 0.0034 34.1 7.9 21 240-260 139-159 (396)
113 cd00652 TBP_TLF TATA box bindi 32.7 2E+02 0.0043 29.3 8.0 63 92-154 16-84 (174)
114 TIGR02036 dsdC D-serine deamin 32.5 58 0.0013 34.1 4.3 20 194-213 41-60 (302)
115 COG0081 RplA Ribosomal protein 32.3 57 0.0012 35.0 4.2 77 169-264 112-203 (228)
116 TIGR01953 NusA transcription t 32.2 45 0.00098 37.3 3.6 39 168-212 301-339 (341)
117 PRK10341 DNA-binding transcrip 30.7 68 0.0015 33.7 4.5 21 193-213 39-59 (312)
118 PRK15092 DNA-binding transcrip 30.5 61 0.0013 34.5 4.2 21 193-213 43-63 (310)
119 PF03420 Peptidase_U9: Prohead 30.4 59 0.0013 34.6 3.9 76 136-217 59-147 (213)
120 PF08303 tRNA_lig_kinase: tRNA 30.3 2.2E+02 0.0048 29.5 7.8 55 139-212 66-120 (168)
121 PRK11139 DNA-binding transcrip 29.8 59 0.0013 33.7 3.8 20 194-213 39-58 (297)
122 TIGR03675 arCOG00543 arCOG0054 29.8 46 0.001 40.0 3.4 29 183-211 102-130 (630)
123 PRK10086 DNA-binding transcrip 29.6 57 0.0012 34.3 3.7 21 193-213 46-66 (311)
124 KOG2279 Kinase anchor protein 29.2 28 0.00061 41.4 1.5 31 183-213 149-179 (608)
125 PF00126 HTH_1: Bacterial regu 29.0 41 0.0009 27.7 2.1 20 194-213 32-51 (60)
126 PF00408 PGM_PMM_IV: Phosphogl 28.7 95 0.0021 26.6 4.3 26 235-260 48-73 (73)
127 PRK09801 transcriptional activ 28.7 59 0.0013 34.4 3.7 20 194-213 39-58 (310)
128 PRK06107 aspartate aminotransf 28.5 4.5E+02 0.0098 29.0 10.5 26 237-262 375-401 (402)
129 COG3967 DltE Short-chain dehyd 28.4 44 0.00096 36.0 2.6 57 201-265 2-59 (245)
130 PRK10082 cell density-dependen 28.4 58 0.0013 34.0 3.5 20 194-213 44-63 (303)
131 cd04518 TBP_archaea archaeal T 28.2 2.2E+02 0.0047 29.2 7.4 63 92-154 16-84 (174)
132 TIGR03812 tyr_de_CO2_Arch tyro 28.1 3.5E+02 0.0076 28.9 9.3 23 236-258 350-373 (373)
133 TIGR03339 phn_lysR aminoethylp 28.0 96 0.0021 31.2 4.9 19 194-212 30-48 (279)
134 PRK11482 putative DNA-binding 27.9 53 0.0011 34.9 3.2 20 194-213 62-81 (317)
135 PRK14997 LysR family transcrip 27.4 83 0.0018 32.6 4.4 20 194-213 35-54 (301)
136 PLN00062 TATA-box-binding prot 26.7 3.2E+02 0.0069 28.2 8.3 140 91-263 15-175 (179)
137 PRK08175 aminotransferase; Val 26.4 4.1E+02 0.0089 29.2 9.7 25 237-261 364-389 (395)
138 PRK06019 phosphoribosylaminoim 26.4 1.5E+02 0.0033 32.7 6.4 48 196-257 319-366 (372)
139 COG0583 LysR Transcriptional r 26.4 76 0.0016 31.8 3.8 21 193-213 33-53 (297)
140 KOG4165 Gamma-glutamyl phospha 26.1 74 0.0016 36.3 3.9 66 183-272 190-257 (433)
141 PRK05387 histidinol-phosphate 25.6 6E+02 0.013 27.0 10.5 24 237-260 329-352 (353)
142 PRK11062 nhaR transcriptional 25.5 78 0.0017 33.0 3.8 20 194-213 37-56 (296)
143 PRK02936 argD acetylornithine 25.2 4.5E+02 0.0097 28.5 9.6 23 237-259 352-377 (377)
144 PRK13348 chromosome replicatio 25.1 70 0.0015 33.0 3.4 21 194-214 35-55 (294)
145 CHL00180 rbcR LysR transcripti 24.8 1E+02 0.0022 32.2 4.5 19 194-212 38-56 (305)
146 PRK12682 transcriptional regul 24.8 82 0.0018 33.0 3.8 19 194-212 35-53 (309)
147 PRK05424 rplA 50S ribosomal pr 24.3 1.4E+02 0.003 31.8 5.4 78 170-266 111-203 (230)
148 PF15188 CCDC-167: Coiled-coil 24.1 1.3E+02 0.0027 28.0 4.4 42 86-151 12-53 (85)
149 PRK13520 L-tyrosine decarboxyl 24.0 5.1E+02 0.011 27.6 9.6 18 243-260 353-370 (371)
150 PF00381 PTS-HPr: PTS HPr comp 23.9 1E+02 0.0022 27.2 3.7 60 196-260 22-82 (84)
151 KOG2335 tRNA-dihydrouridine sy 23.5 87 0.0019 35.7 3.9 70 196-267 34-107 (358)
152 PF07650 KH_2: KH domain syndr 23.5 27 0.00058 30.2 -0.0 25 183-207 34-58 (78)
153 PRK10632 transcriptional regul 23.2 93 0.002 32.7 3.9 20 194-213 35-54 (309)
154 PRK09064 5-aminolevulinate syn 23.2 6.6E+02 0.014 27.6 10.5 27 237-263 370-399 (407)
155 PRK12683 transcriptional regul 22.8 85 0.0018 33.1 3.5 20 194-213 35-55 (309)
156 PRK02047 hypothetical protein; 22.6 2.5E+02 0.0055 25.8 6.1 59 183-257 16-83 (91)
157 PRK12327 nusA transcription el 22.6 86 0.0019 35.5 3.7 39 168-212 303-341 (362)
158 TIGR03298 argP transcriptional 22.6 69 0.0015 33.0 2.8 20 194-213 34-53 (292)
159 PRK12681 cysB transcriptional 22.3 92 0.002 33.3 3.7 19 194-212 35-53 (324)
160 cd04516 TBP_eukaryotes eukaryo 22.3 3.8E+02 0.0083 27.4 7.9 137 92-261 16-173 (174)
161 PF04795 PAPA-1: PAPA-1-like c 22.2 1.1E+02 0.0023 28.2 3.6 60 137-196 19-80 (89)
162 PRK00394 transcription factor; 22.1 2.8E+02 0.006 28.5 6.9 65 92-156 15-85 (179)
163 PRK07179 hypothetical protein; 22.0 8E+02 0.017 27.1 10.9 27 237-263 371-400 (407)
164 PRK13393 5-aminolevulinate syn 22.0 8.3E+02 0.018 27.0 11.0 26 237-262 369-397 (406)
165 PF00639 Rotamase: PPIC-type P 21.7 43 0.00093 29.8 0.9 41 237-277 1-42 (95)
166 KOG1478 3-keto sterol reductas 21.7 1E+02 0.0022 34.4 3.8 32 229-260 26-57 (341)
167 PRK07682 hypothetical protein; 21.5 6.6E+02 0.014 27.2 10.0 26 237-262 351-377 (378)
168 PF00352 TBP: Transcription fa 21.4 1.3E+02 0.0029 26.7 4.0 37 202-261 47-84 (86)
169 COG0079 HisC Histidinol-phosph 21.0 6.6E+02 0.014 28.2 10.1 86 136-261 265-354 (356)
170 PRK09202 nusA transcription el 21.0 84 0.0018 36.8 3.3 38 169-212 303-340 (470)
171 CHL00129 rpl1 ribosomal protei 20.8 1.2E+02 0.0025 32.4 4.0 79 170-267 111-204 (229)
172 PRK06939 2-amino-3-ketobutyrat 20.7 8.8E+02 0.019 26.0 10.6 20 243-262 375-394 (397)
173 PRK03635 chromosome replicatio 20.6 89 0.0019 32.4 3.1 21 194-214 35-55 (294)
174 PRK07324 transaminase; Validat 20.6 4.9E+02 0.011 28.5 8.9 25 237-261 345-370 (373)
175 COG0436 Aspartate/tyrosine/aro 20.6 1E+03 0.022 26.9 11.5 26 236-261 365-391 (393)
176 PTZ00225 60S ribosomal protein 20.6 1.6E+02 0.0034 31.1 4.8 28 185-212 117-157 (214)
177 TIGR03538 DapC_gpp succinyldia 20.3 5.9E+02 0.013 27.9 9.4 23 237-259 370-393 (393)
No 1
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=1e-57 Score=494.10 Aligned_cols=275 Identities=26% Similarity=0.378 Sum_probs=210.9
Q ss_pred cccccCCCCCCCCcch-------------------hhhhhhHHHHHHHHHHHHHHHhcCCCcccCCCCCCCCCCCCCCCC
Q 003989 66 KVVRKTKWGPDLSLDA-------------------SVKRGRALAYQTRVDQIVQQLESGSLEAEENQVPEVAAQNADQKS 126 (781)
Q Consensus 66 ~rkRkSRWg~dl~~d~-------------------~v~~~ra~a~Q~RieEItrkL~sg~le~~~~e~s~SPpP~p~yds 126 (781)
.|+|+|||..|..... ..++.++|++++|||||++||+++|+.++...+.+||+++++||.
T Consensus 13 p~~~rS~w~~~~~es~~~~s~~~~~~lp~~m~~~lt~eq~~~y~l~~~iee~t~kLrt~d~~~p~~~e~rSPsp~p~yda 92 (554)
T KOG0119|consen 13 PRRNRSRWDRDTVESDVVNSMTSTSALPSSMPGGLTEEQKESYSLNLRIEEITRKLRTGDVGVPPPRELRSPSPEPVYDA 92 (554)
T ss_pred cchhhccCCCCccccccccCcccccccccccccccchhhhhhhhHHHHHHHhhhhhccccCCCCCCccccCCCcchhhhh
Confidence 4566999998753210 124668999999999999999999998888877899999999999
Q ss_pred CCCccchH---HHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCC-ccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHH
Q 003989 127 PNPQVDRE---KLECLELEKQEVIGEILKLNPSYRTPPDYKPL-LKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKE 202 (781)
Q Consensus 127 ~GkRiNTR---~rekLEeER~~IIe~mlkliP~frPPsDYkP~-~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeE 202 (781)
.|+|+||| +|++||+||++||++|+|+||.||+|.|||++ ++.+|||||+|||||||||||||||||+|+|+||+|
T Consensus 93 ~g~R~ntRe~R~r~~Le~er~e~I~~~lk~nP~fkpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~e 172 (554)
T KOG0119|consen 93 KGKRLNTREQRARKKLEDERHEIIEEILKLNPGFKPPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERE 172 (554)
T ss_pred hccchhhHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCcccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHH
Confidence 99999995 57899999999999999999999999999999 578999999999999999999999999999999999
Q ss_pred hCCeEEEeCCccCCCcchhcccCCCC-ccCCCCceEEEEEecCHHHHHHHHHHHHhhccc---cccchh-----hhcccc
Q 003989 203 TRTVIKVYGTKADTGEKVEISTSDAN-VQSTYEEFHISISADSYEKVDAATDLIELLVTS---VSGSLA-----AISTST 273 (781)
Q Consensus 203 TGAKI~IRGkGS~k~~K~E~~~~Dg~-~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~p---ve~g~~-----a~~~~~ 273 (781)
|||||.||||||+||+|. ...|.. ...++|+|||+|+||++|+|++|+++||+||.+ +.++.. .+++++
T Consensus 173 tgAKI~IRGkgSvkEgk~--~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela 250 (554)
T KOG0119|consen 173 TGAKIAIRGKGSVKEGKG--RSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELA 250 (554)
T ss_pred hCCeEEEecccccccccc--CCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhccCccccccccHHHHHHHH
Confidence 999999999999999882 334466 778999999999999999999999999999995 334433 344445
Q ss_pred cccc---ccccccccccCCCcccccccccccCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCC-CCCCCCCCCCCC
Q 003989 274 LVSG---ENVSALNQSQGDGAQFLVPNTFVNQGVPQPEVGPLQTPLHGQFQSQTPWFPSGPSQNPMH-PLNTSSPILSNP 349 (781)
Q Consensus 274 ~v~g---~~~~~~~~~~~~~a~~~~~~t~vn~~~~~~~~g~~~t~q~g~~qy~~~w~~~~~~~~p~~-~~~ss~p~~nn~ 349 (781)
+.+| +.-|++-.+|++ .-+-++.-++. |.........| ++-+.+--+++.
T Consensus 251 ~lNgt~r~~d~~~c~~cg~-------------------------~~H~q~~cp~r-~~~~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 251 RLNGTLRDDDNRACRNCGS-------------------------TGHKQYDCPGR-IPNTTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred HhCCCCCccccccccccCC-------------------------CccccccCCcc-cccccccccccCCcccccccCCCc
Confidence 6555 222233444442 22333333343 33333333433 222222223333
Q ss_pred CCCCCCCCCCCCCCCCCCCCC
Q 003989 350 VNMPARFPSTFKTPSLVPPSS 370 (781)
Q Consensus 350 ~~~~~~~~~~~~m~s~~g~~p 370 (781)
-|..+.+.++|.-.|+..-
T Consensus 305 --~q~~~~~~~~~d~ey~~lm 323 (554)
T KOG0119|consen 305 --DQQMPMSSANFDREYASLM 323 (554)
T ss_pred --ccccchhhhccCHHHHhhh
Confidence 5555577888877776654
No 2
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=100.00 E-value=4.1e-39 Score=321.46 Aligned_cols=178 Identities=24% Similarity=0.315 Sum_probs=157.8
Q ss_pred hhhhhHHHHHH--HHHHHHHHHhcCCCcccCCCCCCCCCCCCCCCCCCCccchH---HHHHHHHHHHHHHHHHHHhCCCC
Q 003989 83 VKRGRALAYQT--RVDQIVQQLESGSLEAEENQVPEVAAQNADQKSPNPQVDRE---KLECLELEKQEVIGEILKLNPSY 157 (781)
Q Consensus 83 v~~~ra~a~Q~--RieEItrkL~sg~le~~~~e~s~SPpP~p~yds~GkRiNTR---~rekLEeER~~IIe~mlkliP~f 157 (781)
+.+++.|.||+ |++||+.||+++|.+....+ .+||+|.+.||..|+|+||| |++|||+||+.|++..+|++|.|
T Consensus 58 lt~eqi~~y~~~~r~~eit~Klrt~d~Vp~~re-~Rspsppp~yd~~GrRlntre~ry~kkLeder~~l~era~k~lp~f 136 (269)
T COG5176 58 LTREQIYSYQVMMRPFEITEKLRTPDGVPSKRE-LRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKERAQKILPRF 136 (269)
T ss_pred hhHHHHHHHHHhccHhhhhhhhcCCCCCCchhh-ccCCCCCcchhHHhhhhhHHHHHHhhhhhHHHHHHHHHHHHhcCcc
Confidence 45778899998 99999999999999877654 35566668889999999995 68999999999999999999999
Q ss_pred CCCCCCCCCc-cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCC--ccCCCC
Q 003989 158 RTPPDYKPLL-KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDAN--VQSTYE 234 (781)
Q Consensus 158 rPPsDYkP~~-K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~--~~~~~E 234 (781)
++|.||+... .++|||||+++||+.|||||||||||.|+|+||+.|+|||.|||+||+|++|.. .|.. .....+
T Consensus 137 v~p~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~s---sd~p~~~~N~e~ 213 (269)
T COG5176 137 VLPNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKIS---SDTPESLKNAEA 213 (269)
T ss_pred cCCccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCccc---ccCchhhhhhHH
Confidence 9999998776 479999999999999999999999999999999999999999999999988753 4432 456788
Q ss_pred ceEEEEEecCHHHHHHHHHHHHhhcccccc
Q 003989 235 EFHISISADSYEKVDAATDLIELLVTSVSG 264 (781)
Q Consensus 235 pLHVlIsAdteEkVdkAvelIE~LL~pve~ 264 (781)
+|||+|++|.++++.++++.|.++|.+..-
T Consensus 214 ~lhcLI~adsedki~~~ik~~~n~I~~a~~ 243 (269)
T COG5176 214 VLHCLIEADSEDKICRLIKSQLNAIREARR 243 (269)
T ss_pred hHHHHhhcchhhhHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999876443
No 3
>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=99.95 E-value=4e-28 Score=225.99 Aligned_cols=109 Identities=34% Similarity=0.501 Sum_probs=96.2
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecC--HH
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADS--YE 246 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdt--eE 246 (781)
++|||||+|+||+|||||+||||||+|+|+||+||||||.|||+||++++++|....+..+++++|+|||+|+|++ .+
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e 80 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEE 80 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHH
Confidence 3799999999999999999999999999999999999999999999999988876555448999999999999999 99
Q ss_pred HHHHHHHHHHhhccccccc------hhhhcccccccc
Q 003989 247 KVDAATDLIELLVTSVSGS------LAAISTSTLVSG 277 (781)
Q Consensus 247 kVdkAvelIE~LL~pve~g------~~a~~~~~~v~g 277 (781)
++++|+++|++||.++.++ ...+.+++.++|
T Consensus 81 ~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nG 117 (120)
T cd02395 81 ALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNG 117 (120)
T ss_pred HHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcc
Confidence 9999999999999998766 224444466655
No 4
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=99.95 E-value=8.7e-28 Score=247.11 Aligned_cols=145 Identities=26% Similarity=0.355 Sum_probs=115.1
Q ss_pred HHHHHHHHHHHHHHHHHHh---CCCCCCC-CCC--CCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEE
Q 003989 135 KLECLELEKQEVIGEILKL---NPSYRTP-PDY--KPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIK 208 (781)
Q Consensus 135 ~rekLEeER~~IIe~mlkl---iP~frPP-sDY--kP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~ 208 (781)
..+.|.+|+.++...+.+. .+.-..- ..| ++.+..+||+||+++||+|||||+||||||+|+|+||+||||||.
T Consensus 53 ~~rLL~~Ei~rv~~~~~~~~~~~~~~~~~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~ 132 (259)
T KOG1588|consen 53 AERLLDEEIERVQTSGRQHGSKEPEELPYADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIM 132 (259)
T ss_pred HHHHHHHHHHHHHhhhhhccCCCchhcccccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEE
Confidence 3466677776666665543 2222220 122 234457999999999999999999999999999999999999999
Q ss_pred EeCCccCCCcchhcc-cCCCCccCCCCceEEEEEecCH-----HHHHHHHHHHHhhccccccchh---hhcccccccccc
Q 003989 209 VYGTKADTGEKVEIS-TSDANVQSTYEEFHISISADSY-----EKVDAATDLIELLVTSVSGSLA---AISTSTLVSGEN 279 (781)
Q Consensus 209 IRGkGS~k~~K~E~~-~~Dg~~~~~~EpLHVlIsAdte-----EkVdkAvelIE~LL~pve~g~~---a~~~~~~v~g~~ 279 (781)
||||||+|+.++|++ +.|..|+|++|||||+|++... .+|.+|++.|++||.++.++.. .+.+++..+|..
T Consensus 133 IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~dk~~QL~ELa~lngt~ 212 (259)
T KOG1588|consen 133 IRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDEDKREQLRELAILNGTY 212 (259)
T ss_pred EecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHhhcCCcc
Confidence 999999999888875 5677799999999999998763 4889999999999999999876 444457777753
No 5
>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=99.28 E-value=1.3e-11 Score=142.89 Aligned_cols=95 Identities=19% Similarity=0.279 Sum_probs=86.8
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccC
Q 003989 136 LECLELEKQEVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKAD 215 (781)
Q Consensus 136 rekLEeER~~IIe~mlkliP~frPPsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~ 215 (781)
.+...++|.+|++.|.+.+..+...++|.|. +.++.|+.+ +||.||||+|+|||.|++||||||.|.++|
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p~~~s~~aP~--~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G-- 617 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTPDEMSPYAPR--IITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIEDDG-- 617 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCccccccCCCe--eEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEecCc--
Confidence 3556789999999999999888337888887 999999994 999999999999999999999999999987
Q ss_pred CCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccc
Q 003989 216 TGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 216 k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~p 261 (781)
+|.|.|.+.+++++|+++|+.|+..
T Consensus 618 ---------------------~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 618 ---------------------TVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ---------------------EEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 8999999999999999999999994
No 6
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.21 E-value=1.9e-11 Score=144.25 Aligned_cols=101 Identities=17% Similarity=0.251 Sum_probs=92.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCe-EEEeCCc
Q 003989 136 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTV-IKVYGTK 213 (781)
Q Consensus 136 rekLEeER~~IIe~mlkliP~frP-PsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAK-I~IRGkG 213 (781)
.+...++|.+|+++|.+.++.+|. .++|.|. +.++.|+. ++||.||||+|+|||.|++|||++ |.|+++|
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~--i~~~~i~~------~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg 725 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPL--IHIMKVKP------EKVNMIIGSGGKKVKSIIEETGVEAIDTQDDG 725 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCe--eEEEEcCH------HHHHHHhcCCchhHHHHHHHHCCCccCcCCCe
Confidence 356678999999999999999998 8899987 99999999 499999999999999999999999 9999987
Q ss_pred cCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccccchh
Q 003989 214 ADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSLA 267 (781)
Q Consensus 214 S~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve~g~~ 267 (781)
+|.|.+.|.+++++|+++|+.|+..+++|..
T Consensus 726 -----------------------~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~i 756 (891)
T PLN00207 726 -----------------------TVKITAKDLSSLEKSKAIISSLTMVPTVGDI 756 (891)
T ss_pred -----------------------eEEEEeCCHHHHHHHHHHHHHHhcCcCCCcE
Confidence 7999999999999999999999987776643
No 7
>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=99.18 E-value=5.1e-11 Score=138.15 Aligned_cols=98 Identities=20% Similarity=0.280 Sum_probs=89.7
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccC
Q 003989 137 ECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKAD 215 (781)
Q Consensus 137 ekLEeER~~IIe~mlkliP~frP-PsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~ 215 (781)
+...++|.+|++.|.+.+..++. .++|.|. ++++.||.+ +||.||||+|+|||+|++||||+|.|.++|
T Consensus 521 ~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~--~~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG-- 590 (684)
T TIGR03591 521 EQAKEGRLHILGEMNKVISEPRAELSPYAPR--IETIKINPD------KIRDVIGPGGKVIREITEETGAKIDIEDDG-- 590 (684)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccccccCCe--EEEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEEEEecCe--
Confidence 45668899999999999999987 8899987 999999994 999999999999999999999999999886
Q ss_pred CCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccccc
Q 003989 216 TGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGS 265 (781)
Q Consensus 216 k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve~g 265 (781)
+|.|.+.+.+.+++|+++|+.|....++|
T Consensus 591 ---------------------~V~i~~~~~~~~~~a~~~I~~~~~~~~~G 619 (684)
T TIGR03591 591 ---------------------TVKIAASDGEAAEAAIKMIEGITAEPEVG 619 (684)
T ss_pred ---------------------EEEEEECcHHHHHHHHHHHHhhhcccccC
Confidence 89999999999999999999998865554
No 8
>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=99.15 E-value=1e-10 Score=97.24 Aligned_cols=59 Identities=25% Similarity=0.374 Sum_probs=53.9
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 248 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkV 248 (781)
.+.|.||. +++|+|||++|.|+|+|+++|||+|.|..+| .|.|+|++.+++
T Consensus 3 ~~~i~Ip~------~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g-----------------------~v~I~G~~~~~v 53 (61)
T cd02393 3 IETMKIPP------DKIRDVIGPGGKTIKKIIEETGVKIDIEDDG-----------------------TVYIAASDKEAA 53 (61)
T ss_pred EEEEEeCh------hheeeeECCCchHHHHHHHHHCCEEEeCCCC-----------------------EEEEEeCCHHHH
Confidence 67899999 4999999999999999999999999997643 599999999999
Q ss_pred HHHHHHHH
Q 003989 249 DAATDLIE 256 (781)
Q Consensus 249 dkAvelIE 256 (781)
++|+++|+
T Consensus 54 ~~A~~~I~ 61 (61)
T cd02393 54 EKAKKMIE 61 (61)
T ss_pred HHHHHHhC
Confidence 99999985
No 9
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.06 E-value=2.9e-10 Score=130.35 Aligned_cols=100 Identities=19% Similarity=0.198 Sum_probs=91.9
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccC
Q 003989 137 ECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKAD 215 (781)
Q Consensus 137 ekLEeER~~IIe~mlkliP~frP-PsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~ 215 (781)
..+.+.|.+||+.|.+.+...|. .+.|+|. ++.+.|+++ +|+.+|||+|+|+|.|.+||||||.|.++|
T Consensus 522 ~QAk~aRlhIL~~M~~ai~~pr~els~~aPr--i~t~~i~~d------KI~dvIG~gGk~I~~I~eetg~~IdieddG-- 591 (692)
T COG1185 522 EQAKGARLHILIVMNEAISEPRKELSPYAPR--IETIKIDPD------KIRDVIGPGGKTIKAITEETGVKIDIEDDG-- 591 (692)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhccCCc--eEEEccCHH------HHhhccCCcccchhhhhhhhCcEEEecCCC--
Confidence 34668899999999999999996 8889887 899999995 999999999999999999999999999887
Q ss_pred CCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccccchh
Q 003989 216 TGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSLA 267 (781)
Q Consensus 216 k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve~g~~ 267 (781)
.|.|.+.+.+++++|+++|+.|+.++++|.-
T Consensus 592 ---------------------tv~i~~s~~~~~~~ak~~I~~i~~e~evg~i 622 (692)
T COG1185 592 ---------------------TVKIAASDGESAKKAKERIEAITREVEVGEV 622 (692)
T ss_pred ---------------------cEEEEecchHHHHHHHHHHHHHHhhcccccE
Confidence 5889999999999999999999999998843
No 10
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.98 E-value=6.7e-10 Score=129.15 Aligned_cols=99 Identities=21% Similarity=0.300 Sum_probs=88.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCcc
Q 003989 136 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 214 (781)
Q Consensus 136 rekLEeER~~IIe~mlkliP~frP-PsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS 214 (781)
.+...++|.+|+++|.+.+..+|. .++|.|. +..+.|+. ++||.|||++|+|||.|++|||++|.|+++|
T Consensus 523 l~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~--~~~~~I~~------~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G- 593 (693)
T PRK11824 523 LEQAKEGRLHILGKMNEAISEPRAELSPYAPR--IETIKIPP------DKIRDVIGPGGKTIREITEETGAKIDIEDDG- 593 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhcCChhhhcccCch--heeecCCH------HHHHHHhcCCchhHHHHHHHHCCccccCCCc-
Confidence 345678999999999999999998 7888876 77777776 5999999999999999999999999999887
Q ss_pred CCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccccc
Q 003989 215 DTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGS 265 (781)
Q Consensus 215 ~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve~g 265 (781)
+|.|++.+.+++++|+++|+.|+.+.++|
T Consensus 594 ----------------------~v~i~~~~~~~~~~a~~~I~~~~~~~~vG 622 (693)
T PRK11824 594 ----------------------TVKIAATDGEAAEAAKERIEGITAEPEVG 622 (693)
T ss_pred ----------------------eEEEEcccHHHHHHHHHHHHHhcccCcCC
Confidence 79999999999999999999999876654
No 11
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.76 E-value=7.5e-09 Score=84.19 Aligned_cols=59 Identities=29% Similarity=0.445 Sum_probs=51.6
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 249 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVd 249 (781)
++|.||. +++|+|||.+|.++|+|+++|||+|.|..++ +.-.|.|+| +.+.|+
T Consensus 2 ~~i~vp~------~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~--------------------~~~~v~I~G-~~~~v~ 54 (60)
T PF00013_consen 2 ERIEVPS------SLVGRIIGKKGSNIKEIEEETGVKIQIPDDD--------------------ERDIVTISG-SPEQVE 54 (60)
T ss_dssp EEEEEEH------HHHHHHHTGGGHHHHHHHHHHTSEEEEESTT--------------------EEEEEEEEE-SHHHHH
T ss_pred EEEEECH------HHcCEEECCCCCcHHHhhhhcCeEEEEcCCC--------------------CcEEEEEEe-CHHHHH
Confidence 5788887 5999999999999999999999999997762 112799999 999999
Q ss_pred HHHHHH
Q 003989 250 AATDLI 255 (781)
Q Consensus 250 kAvelI 255 (781)
+|+++|
T Consensus 55 ~A~~~I 60 (60)
T PF00013_consen 55 KAKKMI 60 (60)
T ss_dssp HHHHHH
T ss_pred HHHhhC
Confidence 999987
No 12
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.74 E-value=3.7e-08 Score=79.77 Aligned_cols=63 Identities=30% Similarity=0.410 Sum_probs=53.0
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 249 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVd 249 (781)
.+|+||. +++|+|||++|+++|+|+++|||+|.|...+. ..++..|.|.|. .+.++
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----------------~~~~~~v~i~G~-~~~v~ 57 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----------------GSEERIVTITGT-PEAVE 57 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----------------CCCceEEEEEcC-HHHHH
Confidence 5788998 59999999999999999999999999998742 123447899997 78999
Q ss_pred HHHHHHH
Q 003989 250 AATDLIE 256 (781)
Q Consensus 250 kAvelIE 256 (781)
+|..+|+
T Consensus 58 ~a~~~i~ 64 (64)
T cd00105 58 KAKELIL 64 (64)
T ss_pred HHHHHhC
Confidence 9988874
No 13
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.71 E-value=2.3e-08 Score=81.83 Aligned_cols=61 Identities=23% Similarity=0.311 Sum_probs=51.8
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 249 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVd 249 (781)
++|.||. .++|.|||++|.++|+|+++|||+|.|..... ++-.|.|+|. .|+|+
T Consensus 2 ~~i~Vp~------~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~-------------------~~~~v~I~G~-~~~v~ 55 (62)
T cd02394 2 EEVEIPK------KLHRFIIGKKGSNIRKIMEETGVKIRFPDPGS-------------------KSDTITITGP-KENVE 55 (62)
T ss_pred eEEEeCH------HHhhhccCCCCCcHHHHHHHhCCEEEcCCCCC-------------------CCCEEEEEcC-HHHHH
Confidence 5788888 49999999999999999999999999998741 1127999998 78999
Q ss_pred HHHHHHH
Q 003989 250 AATDLIE 256 (781)
Q Consensus 250 kAvelIE 256 (781)
+|+++|+
T Consensus 56 ~A~~~i~ 62 (62)
T cd02394 56 KAKEEIL 62 (62)
T ss_pred HHHHHhC
Confidence 9998873
No 14
>smart00322 KH K homology RNA-binding domain.
Probab=98.60 E-value=2.4e-07 Score=73.50 Aligned_cols=66 Identities=32% Similarity=0.431 Sum_probs=56.4
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 248 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkV 248 (781)
..+|+||. +++|+|||.+|+++|+|+++|||+|.|.+.+. +.-.|.|.|+ .+.+
T Consensus 4 ~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-------------------~~~~v~i~g~-~~~v 57 (69)
T smart00322 4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-------------------EERVVEITGP-PENV 57 (69)
T ss_pred EEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC-------------------CccEEEEEcC-HHHH
Confidence 56888888 59999999999999999999999999987642 1237899998 8999
Q ss_pred HHHHHHHHhhcc
Q 003989 249 DAATDLIELLVT 260 (781)
Q Consensus 249 dkAvelIE~LL~ 260 (781)
+.|.++|++++.
T Consensus 58 ~~a~~~i~~~~~ 69 (69)
T smart00322 58 EKAAELILEILE 69 (69)
T ss_pred HHHHHHHHHHhC
Confidence 999999988763
No 15
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.54 E-value=1.3e-07 Score=93.96 Aligned_cols=66 Identities=21% Similarity=0.346 Sum_probs=59.3
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCC-ccCCCcchhcccCCCCccCCCCceEEEEE---ecC
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT-KADTGEKVEISTSDANVQSTYEEFHISIS---ADS 244 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk-GS~k~~K~E~~~~Dg~~~~~~EpLHVlIs---Adt 244 (781)
+..+.||. +.||+|||++|+|+|.|+++|||+|.|..+ | .|.|. +.|
T Consensus 4 ~~~i~IP~------~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g-----------------------~V~I~~~~~~d 54 (180)
T PRK13763 4 MEYVKIPK------DRIGVLIGKKGETKKEIEERTGVKLEIDSETG-----------------------EVIIEPTDGED 54 (180)
T ss_pred eEEEEcCH------HHhhhHhccchhHHHHHHHHHCcEEEEECCCC-----------------------eEEEEeCCCCC
Confidence 46788988 599999999999999999999999999987 3 68888 889
Q ss_pred HHHHHHHHHHHHhhccccc
Q 003989 245 YEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 245 eEkVdkAvelIE~LL~pve 263 (781)
.+++++|+++|+.|+..++
T Consensus 55 ~~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 55 PLAVLKARDIVKAIGRGFS 73 (180)
T ss_pred HHHHHHHHHHHHHHhcCCC
Confidence 9999999999999998533
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=98.52 E-value=3.9e-07 Score=76.11 Aligned_cols=63 Identities=27% Similarity=0.274 Sum_probs=51.2
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 249 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVd 249 (781)
.++.||. +.+|+|||.+|.++|+|+++|||+|.|..... ..+.+--|.|+|+ .|.++
T Consensus 2 ~r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----------------~~~~~r~v~I~G~-~~~v~ 58 (65)
T cd02396 2 LRLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----------------PGSTERVVTISGK-PSAVQ 58 (65)
T ss_pred EEEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----------------CCCCceEEEEEeC-HHHHH
Confidence 4788998 59999999999999999999999999976531 0122335888885 88999
Q ss_pred HHHHHH
Q 003989 250 AATDLI 255 (781)
Q Consensus 250 kAvelI 255 (781)
+|+++|
T Consensus 59 ~A~~~I 64 (65)
T cd02396 59 KALLLI 64 (65)
T ss_pred HHHHhh
Confidence 999887
No 17
>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=98.43 E-value=2.4e-07 Score=91.35 Aligned_cols=63 Identities=21% Similarity=0.375 Sum_probs=55.2
Q ss_pred EEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCC-ccCCCcchhcccCCCCccCCCCceEEEE--EecCHHHH
Q 003989 172 VPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT-KADTGEKVEISTSDANVQSTYEEFHISI--SADSYEKV 248 (781)
Q Consensus 172 IyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk-GS~k~~K~E~~~~Dg~~~~~~EpLHVlI--sAdteEkV 248 (781)
|+||. +.||+|||++|+|+|+|+++|||+|.|..+ | .|.| .+.|.+++
T Consensus 2 i~Ip~------~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g-----------------------~V~I~~~t~d~~~i 52 (172)
T TIGR03665 2 VKIPK------DRIGVLIGKGGETKKEIEERTGVKLDIDSETG-----------------------EVKIEEEDEDPLAV 52 (172)
T ss_pred ccCCH------HHhhhHhCCchhHHHHHHHHhCcEEEEEcCCc-----------------------eEEEecCCCCHHHH
Confidence 45666 599999999999999999999999999976 3 5788 78899999
Q ss_pred HHHHHHHHhhccccc
Q 003989 249 DAATDLIELLVTSVS 263 (781)
Q Consensus 249 dkAvelIE~LL~pve 263 (781)
++|+++|+.|+..+.
T Consensus 53 ~kA~~~I~~i~~gf~ 67 (172)
T TIGR03665 53 MKAREVVKAIGRGFS 67 (172)
T ss_pred HHHHHHHHHHHcCCC
Confidence 999999999988533
No 18
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.40 E-value=8.3e-06 Score=89.77 Aligned_cols=91 Identities=15% Similarity=-0.037 Sum_probs=80.6
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 249 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVd 249 (781)
.|++|++| .|.+|.-+..=|+|..+|..+|.|+++++.||||+|+.-+-++ .++.+|+++|+|++.+.+.+.
T Consensus 212 ~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~-------G~EsnEPMYI~i~h~~~~g~~ 283 (531)
T KOG1960|consen 212 NKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNE-------GNESNEPMYIFSTHGNGNGEN 283 (531)
T ss_pred hheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCccc-------ccccCCceeEEeecCCchhhc
Confidence 48899987 7889999999999999999999999999999999986432221 577999999999999999999
Q ss_pred HHHHHHHhhccccccchhh
Q 003989 250 AATDLIELLVTSVSGSLAA 268 (781)
Q Consensus 250 kAvelIE~LL~pve~g~~a 268 (781)
+|+++|++|++.+..++--
T Consensus 284 ~A~r~~~nl~~~v~~~~sr 302 (531)
T KOG1960|consen 284 GAPRRKWNLEEKVYINLSR 302 (531)
T ss_pred cchhHHHhHHHHHHHHhhh
Confidence 9999999999999988653
No 19
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.36 E-value=7e-07 Score=101.22 Aligned_cols=98 Identities=18% Similarity=0.241 Sum_probs=83.8
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCcc
Q 003989 136 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 214 (781)
Q Consensus 136 rekLEeER~~IIe~mlkliP~frP-PsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS 214 (781)
-+++.+.|.+||++|.|.++.+|. .++|.|. .+++.++. .....||||+|...|+|+.|||+ |.--+.|
T Consensus 566 l~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~--~~tlkv~~------sk~~~lIGp~G~~~kki~~EtGa-i~~vDe~- 635 (760)
T KOG1067|consen 566 LQKAREARLQILDIMEKNINSPRGSDKEYSPV--LETLKVSP------SKRATLIGPGGVLKKKIEVETGA-ISQVDEG- 635 (760)
T ss_pred HHhhhHHHHHHHHHHHhhcCCcccCccccCce--eeEEeecc------hhhheeecCccceeeeEeeeccc-eeeecCc-
Confidence 456778999999999999999999 8889998 66666666 37889999999999999999994 4333333
Q ss_pred CCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccccc
Q 003989 215 DTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGS 265 (781)
Q Consensus 215 ~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve~g 265 (781)
|+.|.|.+...+++|.+.|+.|+....++
T Consensus 636 ----------------------t~~i~A~~~~am~~Ak~~I~~i~~~~~~~ 664 (760)
T KOG1067|consen 636 ----------------------TFSIFAPTQAAMEEAKEFIDGIIKDDQVQ 664 (760)
T ss_pred ----------------------eEEEEecCHHHHHHHHHHHHHHhcCcccc
Confidence 89999999999999999999999987664
No 20
>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=98.22 E-value=1.9e-06 Score=85.10 Aligned_cols=55 Identities=31% Similarity=0.494 Sum_probs=50.3
Q ss_pred ccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccc
Q 003989 184 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve 263 (781)
.+|+|||++|+|+|.||+.|||+|.|.|+ .|.|.| +.+.++.|.++|+.||..-.
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~------------------------~v~i~G-~~~~~~~A~~~i~~li~~~~ 153 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGK------------------------TVGIIG-DPEQVQIAREAIEMLIEGAP 153 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCC------------------------EEEEEC-CHHHHHHHHHHHHHHHcCCC
Confidence 69999999999999999999999999863 689999 99999999999999996543
No 21
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.21 E-value=9e-06 Score=92.86 Aligned_cols=109 Identities=19% Similarity=0.260 Sum_probs=73.8
Q ss_pred CCCCCccchHHHHHHHHHHHHHHHHHHHhCC-CCCCCCCCCCC-ccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHH
Q 003989 125 KSPNPQVDREKLECLELEKQEVIGEILKLNP-SYRTPPDYKPL-LKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKE 202 (781)
Q Consensus 125 ds~GkRiNTR~rekLEeER~~IIe~mlkliP-~frPPsDYkP~-~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeE 202 (781)
+-+|..+|-.+-| +||+++..-+- ... ..+.... ....+|.||. |++|+|||-+|.|||.|+++
T Consensus 102 ~~~G~pe~v~~aK-------~li~evv~r~~~~~~-~~~~q~~~~ttqeI~IPa------~k~GlIIGKgGETikqlqe~ 167 (600)
T KOG1676|consen 102 DLTGSPENVEVAK-------QLIGEVVSRGRPPGG-FPDNQGSVETTQEILIPA------NKCGLIIGKGGETIKQLQEQ 167 (600)
T ss_pred cccCCcccHHHHH-------HhhhhhhhccCCCCC-ccccCCccceeeeeccCc------cceeeEeccCccHHHHHHhh
Confidence 6667777653322 34444433331 111 1233332 2467889998 79999999999999999999
Q ss_pred hCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccc
Q 003989 203 TRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 203 TGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve 263 (781)
+|||+.+--+|+...+ .+. -+.|++ |.++|+.|++||.+||.+-.
T Consensus 168 sg~k~i~iqd~~~~~~-------------~~K--plritG-dp~~ve~a~~lV~dil~e~~ 212 (600)
T KOG1676|consen 168 SGVKMILVQDGSIATG-------------ADK--PLRITG-DPDKVEQAKQLVADILREED 212 (600)
T ss_pred cCCceEEEecCCcCCC-------------CCC--ceeecC-CHHHHHHHHHHHHHHHHhcc
Confidence 9999988877753211 122 345777 57899999999999999633
No 22
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.20 E-value=6.7e-06 Score=93.87 Aligned_cols=75 Identities=20% Similarity=0.341 Sum_probs=59.9
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 248 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkV 248 (781)
...|.||- +.||.|||-+|+|||+|+.|||+||.++-+.- - ...+--+.|.| +.++|
T Consensus 231 ~~~V~VPr------~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~---p-------------~speR~~~IiG-~~d~i 287 (600)
T KOG1676|consen 231 TREVKVPR------SKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD---P-------------SSPERPAQIIG-TVDQI 287 (600)
T ss_pred eeEEeccc------cceeeEEecCchHHHHHhhccCceeEeecCCC---C-------------CCccceeeeec-CHHHH
Confidence 34566665 69999999999999999999999999986621 0 11223566777 78999
Q ss_pred HHHHHHHHhhccccccch
Q 003989 249 DAATDLIELLVTSVSGSL 266 (781)
Q Consensus 249 dkAvelIE~LL~pve~g~ 266 (781)
++|.+||++||...+.+-
T Consensus 288 e~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 288 EHAAELINEIIAEAEAGA 305 (600)
T ss_pred HHHHHHHHHHHHHHhccC
Confidence 999999999999999884
No 23
>PF13014 KH_3: KH domain
Probab=98.19 E-value=2.9e-06 Score=65.76 Aligned_cols=28 Identities=32% Similarity=0.502 Sum_probs=27.2
Q ss_pred ccceeeCCCchhHHHHHHHhCCeEEEeC
Q 003989 184 FLGLIFGPASDTQKRLEKETRTVIKVYG 211 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETGAKI~IRG 211 (781)
|+|+|||++|.|||+|++||||+|.|..
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC
Confidence 6899999999999999999999999998
No 24
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.14 E-value=4.1e-06 Score=83.39 Aligned_cols=55 Identities=31% Similarity=0.497 Sum_probs=49.4
Q ss_pred ccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccc
Q 003989 184 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve 263 (781)
.+|+|||++|+|+|.||+.|||+|.|.++ .|.|.| +.+.++.|.+.|+.|+..-.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~------------------------~v~i~G-~~~~~~~A~~~I~~li~g~~ 159 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK------------------------TVAIIG-DPEQVEIAREAIEMLIEGAP 159 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC------------------------EEEEEe-CHHHHHHHHHHHHHHHcCCC
Confidence 69999999999999999999999999765 477887 89999999999999996543
No 25
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.85 E-value=0.0001 Score=79.93 Aligned_cols=125 Identities=18% Similarity=0.275 Sum_probs=78.3
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCC-CCCc----cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEe
Q 003989 136 LECLELEKQEVIGEILKLNPSYRTPPDY-KPLL----KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVY 210 (781)
Q Consensus 136 rekLEeER~~IIe~mlkliP~frPPsDY-kP~~----K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IR 210 (781)
.|.|+.-...|.|++.+.--.--.|.|. .|.. |+.||.+|-. --|.|||.+|.|||.++||+||-|.|.
T Consensus 95 ~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqis 168 (402)
T KOG2191|consen 95 VEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQIS 168 (402)
T ss_pred HHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCC------cccceecCCcchHHHHHHhhCcceEec
Confidence 4566666666666666643333224443 3433 5789999974 679999999999999999999999998
Q ss_pred CCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccccchhhhccc-ccccccccc
Q 003989 211 GTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSLAAISTS-TLVSGENVS 281 (781)
Q Consensus 211 GkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve~g~~a~~~~-~~v~g~~~~ 281 (781)
-.. ..+ -..++.-|.|+++-++.++++-.++++|.++++-+.. +... +.|+|-+.|
T Consensus 169 Pqk---pt~-----------~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~sc-ln~sya~vsGpvaN 225 (402)
T KOG2191|consen 169 PQK---PTG-----------ISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSC-LNISYANVSGPVAN 225 (402)
T ss_pred ccC---CCC-----------ccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccce-eccchhcccCcccc
Confidence 421 111 1223345556665555555555555666666665544 2333 777775544
No 26
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.84 E-value=2.5e-05 Score=80.74 Aligned_cols=66 Identities=20% Similarity=0.148 Sum_probs=58.9
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 249 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVd 249 (781)
..+.||. ++|++|||++|.++|.|.++|+|+|.|-..| +|+|+|.+.+.++
T Consensus 147 ~~~~V~~------~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG-----------------------~VwI~~~~~~~~~ 197 (235)
T PRK04163 147 TIVEIKP------VKVPRVIGKKGSMINMLKEETGCDIIVGQNG-----------------------RIWIKGPDEEDEE 197 (235)
T ss_pred EEEEECH------HHHHhhcCCCChhHhhhhhhhCcEEEEcCCc-----------------------EEEEeeCCHHHHH
Confidence 4677777 5999999999999999999999999997665 8999999999999
Q ss_pred HHHHHHHhhcccccc
Q 003989 250 AATDLIELLVTSVSG 264 (781)
Q Consensus 250 kAvelIE~LL~pve~ 264 (781)
+|+++|++|-+..+.
T Consensus 198 ~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 198 IAIEAIKKIEREAHT 212 (235)
T ss_pred HHHHHHHHHHhhhhc
Confidence 999999998776543
No 27
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.54 E-value=0.00016 Score=73.65 Aligned_cols=56 Identities=29% Similarity=0.542 Sum_probs=51.3
Q ss_pred ccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccc
Q 003989 184 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve 263 (781)
..|+|||.+|+|.+.||+-|||.|.|.|+ +|.|.| +.+.|+.|.+.|+.|+.-.+
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~------------------------tVaiiG-~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK------------------------TVAIIG-GFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc------------------------EEEEec-ChhhhHHHHHHHHHHHcCCC
Confidence 57999999999999999999999999999 788888 68899999999999998665
Q ss_pred c
Q 003989 264 G 264 (781)
Q Consensus 264 ~ 264 (781)
.
T Consensus 167 h 167 (194)
T COG1094 167 H 167 (194)
T ss_pred c
Confidence 4
No 28
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.33 E-value=0.0076 Score=68.61 Aligned_cols=71 Identities=17% Similarity=-0.015 Sum_probs=46.4
Q ss_pred CCCcccCCCCceeeecccccceecCCCCCCcccceeccCCCC--cccchhhhcCCCCCCCcccccCCCCCCCCcchhhhh
Q 003989 8 TPSTVSNAGPKISKFAAKSGFVIPKNKLSGSLVPVFKGAKKN--DAINEEEKASSNDDGKKVVRKTKWGPDLSLDASVKR 85 (781)
Q Consensus 8 ~~~~~~~~~~kiS~F~AKsGFvIPknkl~Gslvp~fr~~k~~--~a~~~e~~~~~~~~g~~rkRkSRWg~dl~~d~~v~~ 85 (781)
+-|..++..-|++|| ||+|.+||++++|..+|.-.++. .+.-+ -..-|+. |++++..+-+++.
T Consensus 30 ~~s~~~~~~lp~~m~----~~lt~eq~~~y~l~~~iee~t~kLrt~d~~----------~p~~~e~-rSPsp~p~yda~g 94 (554)
T KOG0119|consen 30 VNSMTSTSALPSSMP----GGLTEEQKESYSLNLRIEEITRKLRTGDVG----------VPPPREL-RSPSPEPVYDAKG 94 (554)
T ss_pred ccCcccccccccccc----cccchhhhhhhhHHHHHHHhhhhhccccCC----------CCCCccc-cCCCcchhhhhhc
Confidence 344667788999999 99999999999999987654441 11111 1112222 9999887766655
Q ss_pred hhHHHHHH
Q 003989 86 GRALAYQT 93 (781)
Q Consensus 86 ~ra~a~Q~ 93 (781)
.|..+++.
T Consensus 95 ~R~ntRe~ 102 (554)
T KOG0119|consen 95 KRLNTREQ 102 (554)
T ss_pred cchhhHHH
Confidence 55444444
No 29
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.13 E-value=0.00071 Score=75.48 Aligned_cols=97 Identities=29% Similarity=0.334 Sum_probs=67.5
Q ss_pred cCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHH
Q 003989 174 IPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATD 253 (781)
Q Consensus 174 IPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAve 253 (781)
||.+-.--.||+|+|||-.|.+||+||.+||+||.|---- | ....+.+-.+.|.| +-|.+..|.+
T Consensus 280 ~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lq-------e-------ls~ynpERTItVkG-siEac~~AE~ 344 (584)
T KOG2193|consen 280 IPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQ-------E-------LSLYNPERTITVKG-SIEACVQAEA 344 (584)
T ss_pred cchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehh-------h-------hcccCccceEEecc-cHHHHHHHHH
Confidence 4444445579999999999999999999999999996431 1 11234456888889 5555555555
Q ss_pred HHH-hhccccccchhhhccc-ccccccccccccc
Q 003989 254 LIE-LLVTSVSGSLAAISTS-TLVSGENVSALNQ 285 (781)
Q Consensus 254 lIE-~LL~pve~g~~a~~~~-~~v~g~~~~~~~~ 285 (781)
+|- +|-+-.|.++.|.+.. -...|.|+++|+-
T Consensus 345 eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~ 378 (584)
T KOG2193|consen 345 EIMKKLRECYENDLAAMSLQCHLPPGLNLPALGL 378 (584)
T ss_pred HHHHHHHHHHhhhHHHhhccCCCCcccCccccCC
Confidence 554 4555566667776666 5677777776643
No 30
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.96 E-value=0.0024 Score=69.69 Aligned_cols=78 Identities=26% Similarity=0.216 Sum_probs=54.6
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 248 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkV 248 (781)
..||.||- +-.|-|||-+|.||.+||+||||+|.+--..-- +. -.-+.-|+|.+ +.|.|
T Consensus 40 ~ikvLips------~AaGsIIGKGG~ti~~lqk~tgariklSks~df-------------yP-GTTeRvcli~G-t~eai 98 (402)
T KOG2191|consen 40 FLKVLIPS------YAAGSIIGKGGQTIVQLQKETGARIKLSKSKDF-------------YP-GTTERVCLIQG-TVEAL 98 (402)
T ss_pred EEEEEeec------ccccceeccchHHHHHHHhccCcEEEecccccc-------------CC-CccceEEEEec-cHHHH
Confidence 78999998 589999999999999999999999998622100 11 11234788888 45566
Q ss_pred HHHHHHHHhhccccccchh
Q 003989 249 DAATDLIELLVTSVSGSLA 267 (781)
Q Consensus 249 dkAvelIE~LL~pve~g~~ 267 (781)
.+.++.|.+-|.+......
T Consensus 99 ~av~efI~dKire~p~~~~ 117 (402)
T KOG2191|consen 99 NAVHEFIADKIREKPQAVA 117 (402)
T ss_pred HHHHHHHHHHHHHhHHhhc
Confidence 6666666555555444433
No 31
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.88 E-value=0.0012 Score=71.80 Aligned_cols=62 Identities=31% Similarity=0.340 Sum_probs=54.2
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhcccc
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSV 262 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pv 262 (781)
-|||-|||-+|+|.|+||+||+|+|.|=-.+..+ -|+.|++-..++|-+|.++|..||+++
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~-------------------~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK-------------------EEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCCCCc-------------------ceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 4999999999999999999999999987664211 189999999999999999999999876
Q ss_pred c
Q 003989 263 S 263 (781)
Q Consensus 263 e 263 (781)
-
T Consensus 127 r 127 (345)
T KOG2814|consen 127 R 127 (345)
T ss_pred h
Confidence 5
No 32
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.71 E-value=0.0066 Score=69.42 Aligned_cols=101 Identities=16% Similarity=0.126 Sum_probs=68.9
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCCCCCCC---C-ccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEe
Q 003989 135 KLECLELEKQEVIGEILKLNPSYRTPPDYKP---L-LKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVY 210 (781)
Q Consensus 135 ~rekLEeER~~IIe~mlkliP~frPPsDYkP---~-~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IR 210 (781)
..+.|.+.-..|+.+..+-+-.+. |.-- . ....++.||- +-+|-|||-+|+.||+|.++|||||.|-
T Consensus 104 ~~~al~ka~~~iv~~~~~d~~~~~---d~~~~~~~~~v~~RLlVp~------sq~GslIGK~G~~Ik~Ire~TgA~I~v~ 174 (485)
T KOG2190|consen 104 ATDALFKAFDMIVFKLEEDDEAAE---DNGEDASGPEVTCRLLVPS------SQVGSLIGKGGSLIKEIREETGAKIRVS 174 (485)
T ss_pred hHHHHHHHHHHHhhcccccccccc---cCCccccCCceEEEEEech------hheeeeeccCcHHHHHHHHhcCceEEec
Confidence 345566655556665442222222 2211 1 1357888998 6999999999999999999999999999
Q ss_pred CCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccc
Q 003989 211 GTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 211 GkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~p 261 (781)
++ . . ....|-. |.|.| ..++|.+|+..|-.+|.+
T Consensus 175 ~~-~--l------------P~ster~-V~IsG-~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 175 SD-M--L------------PNSTERA-VTISG-EPDAVKKALVQISSRLLE 208 (485)
T ss_pred CC-C--C------------Cccccee-EEEcC-chHHHHHHHHHHHHHHHh
Confidence 88 1 1 1111222 77777 678999999999888876
No 33
>PRK12704 phosphodiesterase; Provisional
Probab=96.64 E-value=0.007 Score=69.57 Aligned_cols=68 Identities=22% Similarity=0.205 Sum_probs=54.7
Q ss_pred cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHH
Q 003989 168 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEK 247 (781)
Q Consensus 168 K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEk 247 (781)
.+..|.||-| ++-|+|||-.|.+||.||.-|||.|.|.+.-. -|+|++-|...
T Consensus 210 ~~~~v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iiddtp~----------------------~v~ls~~~~~r 262 (520)
T PRK12704 210 TVSVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDDTPE----------------------AVILSGFDPIR 262 (520)
T ss_pred ceeeeecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEcCCCC----------------------eEEEecCChhh
Confidence 4678888887 68899999999999999999999999998831 57788877766
Q ss_pred HHHHHHHHHhhcccc
Q 003989 248 VDAATDLIELLVTSV 262 (781)
Q Consensus 248 VdkAvelIE~LL~pv 262 (781)
-+.|...++.|+.+.
T Consensus 263 re~a~~~l~~l~~dg 277 (520)
T PRK12704 263 REIARLALEKLVQDG 277 (520)
T ss_pred HHHHHHHHHHHHhcC
Confidence 666666666666543
No 34
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.57 E-value=0.008 Score=69.05 Aligned_cols=74 Identities=20% Similarity=0.182 Sum_probs=56.2
Q ss_pred CCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEE
Q 003989 162 DYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISIS 241 (781)
Q Consensus 162 DYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIs 241 (781)
||.--..+..|.||-| ++-|+|||-.|.+||.||.-|||.|.|.+.-. -|.|+
T Consensus 198 ~~~~e~~~~~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iiddtp~----------------------~v~ls 250 (514)
T TIGR03319 198 DHVAETTVSVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDDTPE----------------------AVILS 250 (514)
T ss_pred hhhhhheeeeEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEcCCCC----------------------eEEec
Confidence 4433334678899987 68899999999999999999999999998831 46777
Q ss_pred ecCHHHHHHHHHHHHhhcccc
Q 003989 242 ADSYEKVDAATDLIELLVTSV 262 (781)
Q Consensus 242 AdteEkVdkAvelIE~LL~pv 262 (781)
+-|.-.-+-|...+++||.+-
T Consensus 251 ~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 251 GFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred CCchHHHHHHHHHHHHHHHcC
Confidence 777666666666666666553
No 35
>PRK00106 hypothetical protein; Provisional
Probab=96.49 E-value=0.01 Score=68.54 Aligned_cols=71 Identities=20% Similarity=0.163 Sum_probs=57.7
Q ss_pred cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHH
Q 003989 168 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEK 247 (781)
Q Consensus 168 K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEk 247 (781)
.+..|.||-| ++-|+|||-.|.+||.||.-|||.|.|.+.-. -|.|++-|.-+
T Consensus 225 tvs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliiddtp~----------------------~v~lS~fdpvR 277 (535)
T PRK00106 225 TITTVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIIDDTPE----------------------VVVLSGFDPIR 277 (535)
T ss_pred eeeeEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEcCCCC----------------------eEEEeCCChHH
Confidence 4678889987 68899999999999999999999999998841 57788888777
Q ss_pred HHHHHHHHHhhccccccc
Q 003989 248 VDAATDLIELLVTSVSGS 265 (781)
Q Consensus 248 VdkAvelIE~LL~pve~g 265 (781)
-+-|...+++|+.+--..
T Consensus 278 ReiAr~~le~Li~dgrIh 295 (535)
T PRK00106 278 REIARMTLESLIKDGRIH 295 (535)
T ss_pred HHHHHHHHHHHHHcCCcC
Confidence 777777777777664433
No 36
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.36 E-value=0.0028 Score=70.91 Aligned_cols=74 Identities=18% Similarity=0.253 Sum_probs=54.1
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 249 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVd 249 (781)
.++.+|.+ |+|.|||+.|.|||.|-+.|.|||++.-+- .+ |+ .+..+.|+ .+.|...
T Consensus 201 lR~lVptq------yvgaIIGkeG~TIknItkqTqsriD~hrke----n~-------Ga---aek~itvh---~tpEg~s 257 (584)
T KOG2193|consen 201 LRLLVPTQ------YVGAIIGKEGATIKNITKQTQSRIDVHRKE----NA-------GA---AEKIITVH---STPEGTS 257 (584)
T ss_pred eeeeeccc------eeEEEecCCCccccCcchhhhheeeeeecc----cC-------Cc---ccCceEEe---cCccchH
Confidence 46777774 999999999999999999999999998762 11 11 12233433 2557778
Q ss_pred HHHHHHHhhccccccch
Q 003989 250 AATDLIELLVTSVSGSL 266 (781)
Q Consensus 250 kAvelIE~LL~pve~g~ 266 (781)
+||++|-+|+....++.
T Consensus 258 ~Ac~~ILeimqkEA~~~ 274 (584)
T KOG2193|consen 258 KACKMILEIMQKEAVDD 274 (584)
T ss_pred HHHHHHHHHHHHhhhcc
Confidence 89999988887655443
No 37
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=95.19 E-value=0.02 Score=64.09 Aligned_cols=63 Identities=14% Similarity=0.038 Sum_probs=51.1
Q ss_pred CCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccc
Q 003989 191 PASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 191 PrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~p 261 (781)
-||.++..||+++|+.|..||+--..+.+. + -..+++|..+|.+.+.|-+++|+++|+.+++.
T Consensus 111 TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~-----v---g~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~ 173 (531)
T KOG1960|consen 111 TRGTSYDHIEGITGTTSASRGSAPAPELPP-----V---GSSEGPLVDHIPPSTAEITSKAIERIKGVFMQ 173 (531)
T ss_pred ccchhHHhhhhhccceeeccCCCCCccCCC-----C---CCCCCcceeecCCccHHHHHHHHhhCccceee
Confidence 589999999999999999999864333221 2 23577899999999999999999999955543
No 38
>PRK12705 hypothetical protein; Provisional
Probab=94.67 E-value=0.067 Score=61.78 Aligned_cols=41 Identities=27% Similarity=0.353 Sum_probs=36.5
Q ss_pred cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCc
Q 003989 168 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 168 K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkG 213 (781)
.+..|.+|-| ++-|+|||-.|.+||.||..||+.|.|.+.-
T Consensus 198 tvs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliiddtp 238 (508)
T PRK12705 198 SVSVVPIPSD-----AMKGRIIGREGRNIRAFEGLTGVDLIIDDTP 238 (508)
T ss_pred eeeeeecCCh-----HhhccccCccchhHHHHHHhhCCceEecCCc
Confidence 3567888876 6889999999999999999999999999873
No 39
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=93.42 E-value=0.23 Score=51.26 Aligned_cols=65 Identities=17% Similarity=0.321 Sum_probs=49.7
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEec----C
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISAD----S 244 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd----t 244 (781)
.+.|.||.+ -+|.|||..|++-|.||+.+||+|.|..+.. .|.|... |
T Consensus 9 ~~~v~iPk~------R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~----------------------~V~i~~~~~t~D 60 (194)
T COG1094 9 SEAVKIPKD------RIGVLIGKWGEVKKAIEEKTGVKLRIDSKTG----------------------SVTIRTTRKTED 60 (194)
T ss_pred eeeeecCch------hheeeecccccchHHHHhhcCeEEEEECCCC----------------------eEEEEecCCCCC
Confidence 467888885 8999999999999999999999999998831 2333333 5
Q ss_pred HHHHHHHHHHHHhhccc
Q 003989 245 YEKVDAATDLIELLVTS 261 (781)
Q Consensus 245 eEkVdkAvelIE~LL~p 261 (781)
.-++.+|.++|+.|=..
T Consensus 61 p~~~~ka~d~VkAIgrG 77 (194)
T COG1094 61 PLALLKARDVVKAIGRG 77 (194)
T ss_pred hHHHHHHHHHHHHHhcC
Confidence 66777777777765443
No 40
>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=92.82 E-value=0.18 Score=42.45 Aligned_cols=37 Identities=27% Similarity=0.319 Sum_probs=32.1
Q ss_pred cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEe
Q 003989 168 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVY 210 (781)
Q Consensus 168 K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IR 210 (781)
+..+|+++.+ -+|+.||.+|.++|.+++.+|.+|.|.
T Consensus 25 ~~~~v~V~~~------~~~~aIGk~G~nI~~~~~l~~~~I~v~ 61 (61)
T cd02134 25 KRARVVVPDD------QLGLAIGKGGQNVRLASKLLGEKIDIV 61 (61)
T ss_pred cEEEEEECcc------cceeeECCCCHHHHHHHHHHCCCeEEC
Confidence 3567788874 789999999999999999999999873
No 41
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=92.42 E-value=0.35 Score=52.33 Aligned_cols=70 Identities=24% Similarity=0.321 Sum_probs=55.4
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 248 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkV 248 (781)
...|.||.| +-|-|||-+|.-||+|..|+||.|.|..--. -.|+--+.|++ +++.+
T Consensus 316 TaQvtip~d------lggsiigkggqri~~ir~esGA~Ikideple-----------------GsedrIitItG-TqdQI 371 (390)
T KOG2192|consen 316 TAQVTIPKD------LGGSIIGKGGQRIKQIRHESGASIKIDEPLE-----------------GSEDRIITITG-TQDQI 371 (390)
T ss_pred eeeEecccc------cCcceecccchhhhhhhhccCceEEecCcCC-----------------CCCceEEEEec-cHHHH
Confidence 468899985 8999999999999999999999999987410 12333566666 78899
Q ss_pred HHHHHHHHhhcccc
Q 003989 249 DAATDLIELLVTSV 262 (781)
Q Consensus 249 dkAvelIE~LL~pv 262 (781)
+.|.-+.++.++.-
T Consensus 372 qnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 372 QNAQYLLQNSVKQY 385 (390)
T ss_pred hhHHHHHHHHHHhh
Confidence 99998888877643
No 42
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=92.18 E-value=0.2 Score=54.31 Aligned_cols=27 Identities=37% Similarity=0.415 Sum_probs=25.7
Q ss_pred ceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 186 GLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 186 GlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
-+||||.|.|||.||--|.|-|.+.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~ 187 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN 187 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc
Confidence 389999999999999999999999997
No 43
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=91.97 E-value=0.29 Score=51.98 Aligned_cols=38 Identities=21% Similarity=0.221 Sum_probs=33.1
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCc
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkG 213 (781)
.-|.|+. .++-++||.+|..+|.|.++|+|+|.|=-.|
T Consensus 148 ~iv~i~p------~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG 185 (239)
T COG1097 148 QIVKIPP------SKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG 185 (239)
T ss_pred EEEEEch------hhcceEecCCCcHHHHhhhhcCeEEEEecCC
Confidence 4667776 6899999999999999999999999996665
No 44
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=90.67 E-value=0.56 Score=54.17 Aligned_cols=68 Identities=26% Similarity=0.303 Sum_probs=50.3
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCC-ccCCCcchhcccCCCCccCCCCceEEEEEe------
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT-KADTGEKVEISTSDANVQSTYEEFHISISA------ 242 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk-GS~k~~K~E~~~~Dg~~~~~~EpLHVlIsA------ 242 (781)
.+|..+.+ .+|.|||-.|.++|+|.+||++||.|... +. +.+--|.|++
T Consensus 45 ~RlL~~~k------evG~IIGk~G~~vkkir~~t~s~i~i~~~~~~------------------c~eRIiti~g~~~~~~ 100 (485)
T KOG2190|consen 45 YRLLCHVK------EVGSIIGKKGDIVKKIRKETESKIRVNESLPG------------------CPERIITITGNRVELN 100 (485)
T ss_pred EEEEeccc------cceeEEccCcHHHHHHhhcccccceeecCCCC------------------CCcceEEEeccccccc
Confidence 47777876 79999999999999999999999999876 21 1122344444
Q ss_pred --cCHHHHHHHHHHHHhhccc
Q 003989 243 --DSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 243 --dteEkVdkAvelIE~LL~p 261 (781)
...++|.+|.++|=..+.+
T Consensus 101 ~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 101 LSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred CCchHHHHHHHHHHHhhcccc
Confidence 2567888888887766553
No 45
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=90.30 E-value=0.98 Score=49.02 Aligned_cols=38 Identities=18% Similarity=0.266 Sum_probs=32.7
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
+.+|.+--| -.|.|||-+|++||+|..|++|.|++-+.
T Consensus 49 e~ril~~sk------~agavigkgg~nik~lr~d~na~v~vpds 86 (390)
T KOG2192|consen 49 ELRILLQSK------NAGAVIGKGGKNIKALRTDYNASVSVPDS 86 (390)
T ss_pred eEEEEEecc------cccceeccccccHHHHhhhccceeeccCC
Confidence 456666665 56999999999999999999999999876
No 46
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=89.79 E-value=0.48 Score=54.68 Aligned_cols=62 Identities=24% Similarity=0.284 Sum_probs=44.4
Q ss_pred HHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCcc
Q 003989 145 EVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 214 (781)
Q Consensus 145 ~IIe~mlkliP~frPPsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS 214 (781)
+|.+++.+.+|. +.--++. -.....|+||.+ +|+.+||-+|+++++||+..|.||.|+-.+.
T Consensus 465 ~i~~~i~r~~p~-~~eVe~~-gd~~avv~vpe~------~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 465 EIEREIKRYLPG-DVEVEVV-GDGRAVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred HHHHHHHHhCCC-CceEEEe-cCCeEEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 345556666665 1111121 012467888885 8999999999999999999999999998753
No 47
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=88.85 E-value=0.52 Score=53.83 Aligned_cols=61 Identities=18% Similarity=0.213 Sum_probs=45.3
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhcccc
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSV 262 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pv 262 (781)
++||.+||-+|..||+||..|+++|.|---- -+..|.|.|.++ --.+|.+.|+.+++..
T Consensus 56 ~mvg~vigrggskik~iq~~tnt~iqii~~~--------------------~e~kv~ifg~~~-m~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 56 EMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD--------------------LEVKVTIFGINH-MRKKAKASIDRGQDKD 114 (629)
T ss_pred hhhheeeccCcchhhhhhcccceeEEEeccC--------------------ceeEEEEechHH-HHHHHHhhHhhhhhhh
Confidence 7999999999999999999999999986431 113566777554 3345666777777665
Q ss_pred cc
Q 003989 263 SG 264 (781)
Q Consensus 263 e~ 264 (781)
+.
T Consensus 115 e~ 116 (629)
T KOG0336|consen 115 ER 116 (629)
T ss_pred hh
Confidence 54
No 48
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=86.89 E-value=0.33 Score=42.30 Aligned_cols=41 Identities=20% Similarity=0.223 Sum_probs=29.2
Q ss_pred EEEcCCCCCCCCcccceeeCCCchhHHHHHHHh-CCeEEEeCC
Q 003989 171 VVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 212 (781)
Q Consensus 171 KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGk 212 (781)
||.+-.. .++++-+|..||.+|..+|.|++|. |-||.|=.-
T Consensus 6 kvaV~~~-~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 6 KVAVKSG-DPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEES-STTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred EEEEEcC-CCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 4444333 3788999999999999999999999 777776654
No 49
>PRK13764 ATPase; Provisional
Probab=83.62 E-value=1.2 Score=52.69 Aligned_cols=39 Identities=28% Similarity=0.325 Sum_probs=35.9
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCc
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkG 213 (781)
...||||.+ .|+.+||-+|++|++||+..|.+|.||-..
T Consensus 482 ~~~v~~~~~------~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 482 KAVVYVPEK------DIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred eEEEEEChh------hhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 568999986 889999999999999999999999999875
No 50
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=78.96 E-value=3.4 Score=46.26 Aligned_cols=58 Identities=28% Similarity=0.293 Sum_probs=47.6
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHH--hhcc
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIE--LLVT 260 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE--~LL~ 260 (781)
|-+-.|+||.|.+++.||+.+|++|.-||. ++.|+++.. .++.|.++++ .++.
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~------------------------~~~i~g~~~-~v~~A~~~l~~l~~~~ 78 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGE------------------------AVRIIGARP-LVDVATRVLLTLELLA 78 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCc------------------------eEEEEechH-HHHHHHHHHhHHHHHH
Confidence 677789999999999999999999999998 677888766 8888888888 5555
Q ss_pred ccccc
Q 003989 261 SVSGS 265 (781)
Q Consensus 261 pve~g 265 (781)
....+
T Consensus 79 ~~~~g 83 (348)
T COG1702 79 EVRRG 83 (348)
T ss_pred HHhcc
Confidence 54433
No 51
>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=78.28 E-value=1.8 Score=34.94 Aligned_cols=24 Identities=21% Similarity=0.396 Sum_probs=21.3
Q ss_pred ccceeeCCCchhHHHHHHHhCCeE
Q 003989 184 FLGLIFGPASDTQKRLEKETRTVI 207 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETGAKI 207 (781)
-.|++||.+|.+++.|+..++-.+
T Consensus 35 ~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 35 QPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CCceEECCCCccHHHHHHHHHHHc
Confidence 379999999999999999998554
No 52
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=75.90 E-value=3.3 Score=40.61 Aligned_cols=30 Identities=27% Similarity=0.380 Sum_probs=27.6
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
+.+|+.||.+|..+|.|+++.|-||.|=.-
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve~ 70 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVEY 70 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEEc
Confidence 589999999999999999999999998773
No 53
>PF09981 DUF2218: Uncharacterized protein conserved in bacteria (DUF2218); InterPro: IPR014543 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2JPI_A.
Probab=74.29 E-value=5.5 Score=36.30 Aligned_cols=67 Identities=13% Similarity=0.108 Sum_probs=50.4
Q ss_pred chhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCC--ccCCCCceEEEEEecCHHHHHHHHHHHHhhccccc
Q 003989 193 SDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDAN--VQSTYEEFHISISADSYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 193 GnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~--~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve 263 (781)
..++|+|++-.+-||.++-.+. +..+....|. ....++-|+|.|+|++.+.|++....|..-|.-..
T Consensus 11 ~ryl~qLc~Hf~hk~~v~~d~~----~g~i~f~~G~~~l~a~~~~L~l~vea~~~~~L~~~~~vv~~HL~rFa 79 (89)
T PF09981_consen 11 SRYLKQLCKHFAHKFEVEWDED----SGRITFPFGTCTLSAEPDALTLRVEAPDAEALARLEDVVARHLERFA 79 (89)
T ss_dssp HHHHHHHHHHTTTSSEEEE-SS----EEEEE-SSS-EEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHhcCCCceEEcCC----ceEEEeCCEEEEEEeCCCeEEEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence 4679999999999999997752 2334444554 55577889999999999999999998887776543
No 54
>KOG0633 consensus Histidinol phosphate aminotransferase [Amino acid transport and metabolism]
Probab=73.54 E-value=7.2 Score=42.88 Aligned_cols=100 Identities=15% Similarity=0.159 Sum_probs=57.0
Q ss_pred CCCCCccchHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcccc-eee-CCCchhHH-HHHH
Q 003989 125 KSPNPQVDREKLECLELEKQEVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLG-LIF-GPASDTQK-RLEK 201 (781)
Q Consensus 125 ds~GkRiNTR~rekLEeER~~IIe~mlkliP~frPPsDYkP~~K~~KIyIPvkeyP~~NFIG-lII-GPrGnTiK-rLEe 201 (781)
+++|+.+-+ +|+.+.+||.+|+.++.++. .. .||- =+- +-|||= +|. |-.|.--| -.|.
T Consensus 272 ~~n~kkme~-~rdaiv~er~RL~keLt~v~-~~---~~~~---------gg~----daNFiLi~v~~~~n~~akkly~q~ 333 (375)
T KOG0633|consen 272 DSNGKKMED-VRDAIVRERERLFKELTEVP-FL---NDYP---------GGS----DANFILIEVTGGDNGMAKKLYKQD 333 (375)
T ss_pred cccchHHHH-HHHHHHHHHHHHHHHhhcCc-cc---cCCC---------Ccc----cccEEEEEEcCCCcHHHHHHHHHH
Confidence 556666554 56888899999988876643 11 1110 011 335553 333 23333322 2355
Q ss_pred HhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhh
Q 003989 202 ETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELL 258 (781)
Q Consensus 202 ETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~L 258 (781)
.|.-++.+|=+|+..+.| ..+.|++-++|.-+.-++.++..
T Consensus 334 at~~gVvVRfrgse~~c~----------------G~lRitvGt~EentvL~k~~K~~ 374 (375)
T KOG0633|consen 334 ATKMGVVVRFRGSEEGCK----------------GYLRITVGTPEENTVLMKCLKQF 374 (375)
T ss_pred HHhcceEEEEcCCccccc----------------eeEEEEcCCcccchHHHHHHHhh
Confidence 567778888887643333 27889888887666666666553
No 55
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=68.81 E-value=3 Score=43.84 Aligned_cols=62 Identities=27% Similarity=0.329 Sum_probs=45.1
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhcccc
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSV 262 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pv 262 (781)
--||+|+|-+|+|--.||+-|.++|.|-+. .|+|-| ..+.+.-|...|-.||-
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad~------------------------kIHiLG-~~~niriAR~avcsLIl-- 230 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLADS------------------------KIHILG-AFQNIRIARDAVCSLIL-- 230 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecCc------------------------eEEEee-cchhhHHHHHhhHhhhc--
Confidence 369999999999999999999999999887 244444 45566666666555553
Q ss_pred ccchhhhcccccccc
Q 003989 263 SGSLAAISTSTLVSG 277 (781)
Q Consensus 263 e~g~~a~~~~~~v~g 277 (781)
.+..++|||
T Consensus 231 ------GsppgkVy~ 239 (252)
T KOG3273|consen 231 ------GSPPGKVYG 239 (252)
T ss_pred ------cCCchhHHH
Confidence 234466665
No 56
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=66.01 E-value=16 Score=36.90 Aligned_cols=59 Identities=12% Similarity=0.139 Sum_probs=47.8
Q ss_pred ccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccc
Q 003989 184 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve 263 (781)
.+=+|+..+|..++.|-...||||.+.-.- -.+.|+| ++..++.+.+.|++++..+.
T Consensus 36 ~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~----------------------~~i~I~g-~k~~~~~i~~~i~~~l~~i~ 92 (210)
T PF14611_consen 36 EFFLLLTGNGRILENLAARNGAKIEVSRSE----------------------NRIRITG-TKSTAEYIEASINEILSNIR 92 (210)
T ss_pred heeeeecCCchHHHHHHHhcCceEEEecCC----------------------cEEEEEc-cHHHHHHHHHHHHHHHhhcE
Confidence 567899999999999988889999997552 1688888 77788888888888887655
Q ss_pred cc
Q 003989 264 GS 265 (781)
Q Consensus 264 ~g 265 (781)
..
T Consensus 93 ~~ 94 (210)
T PF14611_consen 93 TE 94 (210)
T ss_pred EE
Confidence 44
No 57
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=63.97 E-value=5.5 Score=41.16 Aligned_cols=33 Identities=18% Similarity=0.166 Sum_probs=29.8
Q ss_pred CCcccceeeCCCchhHHHHHHHhCCeEEEeCCc
Q 003989 181 GYNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 181 ~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkG 213 (781)
+.+-+|..||.+|..+|.|.+|.|-||.|=.-.
T Consensus 83 ~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s 115 (190)
T COG0195 83 KIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS 115 (190)
T ss_pred CcCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence 458899999999999999999999999887764
No 58
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=62.33 E-value=5 Score=47.25 Aligned_cols=40 Identities=25% Similarity=0.341 Sum_probs=35.9
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCcc
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 214 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS 214 (781)
..++.++++ ++-+|||-.|.++|.|++.|++||.++.+-+
T Consensus 69 ~~e~Vv~~e------~vkli~gr~gsnik~l~~~t~aKi~L~~ed~ 108 (608)
T KOG2279|consen 69 EIEMVVPQE------AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV 108 (608)
T ss_pred eeeEeeccc------ceeeeeccccCCcchhhcccccceecCcccC
Confidence 467888885 9999999999999999999999999998854
No 59
>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=61.57 E-value=10 Score=33.16 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=22.0
Q ss_pred ccceeeCCCchhHHHHHHHhCCeEEEe
Q 003989 184 FLGLIFGPASDTQKRLEKETRTVIKVY 210 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETGAKI~IR 210 (781)
-.|+|||-+|+|++.||-=++.-+.-+
T Consensus 34 ~~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 34 DIGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCCeEECCCCccHHHHHHHHHHHHhhc
Confidence 579999999999999998877554443
No 60
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=61.46 E-value=10 Score=46.35 Aligned_cols=61 Identities=13% Similarity=0.261 Sum_probs=44.7
Q ss_pred ccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhcc
Q 003989 184 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~ 260 (781)
+..-|+|.+|.++.+|+++++|+|.++-.|+..... --.++.+.++.+++...+.+.+|+.
T Consensus 357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v----------------~~~~~~~~~~ka~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 357 ELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKV----------------VITGVSANDEKAVEDVEKIIAEILN 417 (753)
T ss_pred hhhhhcCCCCccHHHHHHhhhhceecccccCCCCCe----------------EEeccccchhHHHHHHHHHHHhhhc
Confidence 778899999999999999999999999977532100 1223445566677777777777776
No 61
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=60.43 E-value=3.7 Score=35.22 Aligned_cols=30 Identities=23% Similarity=0.187 Sum_probs=22.9
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhC
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETR 204 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETG 204 (781)
...+.|.. +-.|+|||-+|+|++.||-=.+
T Consensus 30 ~i~v~i~~------ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 30 TIVVNIDG------EDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp EEEEEEES------CCCHHHCTTHHHHHHHHHHHHH
T ss_pred EEEEEECC------CccceEECCCCeeHHHHHHHHH
Confidence 34555544 3589999999999999987655
No 62
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=58.90 E-value=14 Score=37.67 Aligned_cols=21 Identities=24% Similarity=0.186 Sum_probs=18.4
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003989 193 SDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 193 GnTiKrLEeETGAKI~IRGkG 213 (781)
.+.||+||++.|+++-+|..+
T Consensus 39 S~~i~~LE~~lg~~Lf~R~~r 59 (294)
T PRK09986 39 SIHIKELEDQLGTPLFIRHSR 59 (294)
T ss_pred HHHHHHHHHHhCCeeEeeCCC
Confidence 457999999999999999853
No 63
>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=58.88 E-value=8 Score=38.25 Aligned_cols=30 Identities=23% Similarity=0.318 Sum_probs=27.6
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
+-+|..||.+|..+|.|++..|-||.|=.-
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVey 71 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIEY 71 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEEc
Confidence 589999999999999999999999998874
No 64
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=57.99 E-value=6.1 Score=43.99 Aligned_cols=32 Identities=25% Similarity=0.208 Sum_probs=27.1
Q ss_pred CcccceeeCCCchhHHHHHHHhCCeEEEeCCc
Q 003989 182 YNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 182 ~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkG 213 (781)
+.|+++|.|++|.+||.|+.+|...|.---+|
T Consensus 34 s~~v~~ivg~qg~kikalr~KTqtyi~tPsr~ 65 (394)
T KOG2113|consen 34 SEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG 65 (394)
T ss_pred cccceeecccCccccchhhhhhcceeccCCCC
Confidence 36999999999999999999999877654443
No 65
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=57.24 E-value=10 Score=42.73 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=35.0
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHh-CCeEEEeCC
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 212 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGk 212 (781)
.||-+=-. .++++-+|..||++|..++.|.+|. |-||.|=.-
T Consensus 233 tKVAV~s~-~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~~ 275 (362)
T PRK12327 233 TKIAVRSN-NPNVDAKGACVGPKGQRVQNIVSELKGEKIDIIDW 275 (362)
T ss_pred eEEEEEcC-CCCCCchheeECCCChhHHHHHHHhCCCeEEEEEc
Confidence 56655443 4899999999999999999999999 888888654
No 66
>PRK00089 era GTPase Era; Reviewed
Probab=56.22 E-value=27 Score=36.65 Aligned_cols=69 Identities=16% Similarity=0.205 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHHHHhCCCCCC--CCCCCC--Ccc-EEEEEcCCCCCCCCcccceeeCCCchhHHHH--------HHHhC
Q 003989 138 CLELEKQEVIGEILKLNPSYRT--PPDYKP--LLK-EAVVPIPVKEYPGYNFLGLIFGPASDTQKRL--------EKETR 204 (781)
Q Consensus 138 kLEeER~~IIe~mlkliP~frP--PsDYkP--~~K-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrL--------EeETG 204 (781)
..|--|..|+..+.+-+|.-.. ..+|.. ..+ ...||+.-+ .-.+.|||-+|++||+| |+-+|
T Consensus 191 ~~EiiRe~~~~~l~~e~p~~~~v~~~~~~~~~~~~i~~~i~v~~~-----~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~ 265 (292)
T PRK00089 191 AAEIIREKLLRLLGDELPYSVAVEIEKFEERGLVRIEATIYVERD-----SQKGIIIGKGGAMLKKIGTEARKDIEKLLG 265 (292)
T ss_pred HHHHHHHHHHhhCCccCCceEEEEEEEEEECCeEEEEEEEEEccC-----CceeEEEeCCcHHHHHHHHHHHHHHHHHhC
Confidence 3444477777777776665422 222221 112 246677765 45789999999999964 66677
Q ss_pred CeEEEeC
Q 003989 205 TVIKVYG 211 (781)
Q Consensus 205 AKI~IRG 211 (781)
|||.++=
T Consensus 266 ~~v~l~l 272 (292)
T PRK00089 266 KKVFLEL 272 (292)
T ss_pred CCEEEEE
Confidence 8777653
No 67
>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=55.65 E-value=11 Score=42.00 Aligned_cols=42 Identities=14% Similarity=0.233 Sum_probs=35.2
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHh-CCeEEEeCC
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 212 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGk 212 (781)
.||-+=-. .++++-+|..||.+|..++.|.+|. |-||.|=.-
T Consensus 231 tKvAV~s~-~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~ 273 (341)
T TIGR01953 231 TKIAVESN-DENIDPVGACVGPKGSRIQAISKELNGEKIDIIEY 273 (341)
T ss_pred eEEEEEcC-CCCCCcceeeECCCCchHHHHHHHhCCCeEEEEEc
Confidence 56666544 4899999999999999999999999 888888654
No 68
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=55.51 E-value=9.3 Score=37.49 Aligned_cols=36 Identities=14% Similarity=0.185 Sum_probs=29.5
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEe
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVY 210 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IR 210 (781)
...++|+.+ -+|++||.+|.|+|.+++-+|-+|.|.
T Consensus 100 ~~~V~V~~~------d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 100 VAYVEVAPE------DKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EEEEEECcc------ccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 345566654 679999999999999999999888774
No 69
>PRK15494 era GTPase Era; Provisional
Probab=52.18 E-value=41 Score=36.93 Aligned_cols=69 Identities=16% Similarity=0.289 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHhCCCCCC--CCCCCCC----cc-EEEEEcCCCCCCCCcccceeeCCCchhHHH--------HHHH
Q 003989 138 CLELEKQEVIGEILKLNPSYRT--PPDYKPL----LK-EAVVPIPVKEYPGYNFLGLIFGPASDTQKR--------LEKE 202 (781)
Q Consensus 138 kLEeER~~IIe~mlkliP~frP--PsDYkP~----~K-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKr--------LEeE 202 (781)
..|--|.+|+..+-+-+|.-.. ...|+-. .+ ...||+.-+ .--|.|||-+|..||+ ||+-
T Consensus 236 ~~eiiRe~~~~~~~~EiP~~~~v~i~~~~~~~~~~~~i~~~i~v~~~-----sqk~iiiG~~g~~ik~i~~~ar~~le~~ 310 (339)
T PRK15494 236 AAEITREQLFLNLQKELPYKLTVQTEKWEDLKDKSVKINQVIVVSRE-----SYKTIILGKNGSKIKEIGAKSRMQMERF 310 (339)
T ss_pred HHHHHHHHHHhhCCcccCceEEEEEEEEEEcCCCeEEEEEEEEECCC-----CceeEEEcCCcHHHHHHHHHHHHHHHHH
Confidence 3455677777777777765433 2333321 11 257787776 4578999999999996 5666
Q ss_pred hCCeEEEeC
Q 003989 203 TRTVIKVYG 211 (781)
Q Consensus 203 TGAKI~IRG 211 (781)
+||||.++=
T Consensus 311 ~~~~v~l~l 319 (339)
T PRK15494 311 FGFPVHLFL 319 (339)
T ss_pred hCCCeEEEE
Confidence 788877653
No 70
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=49.68 E-value=7.6 Score=48.52 Aligned_cols=85 Identities=13% Similarity=0.088 Sum_probs=61.8
Q ss_pred EcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHH
Q 003989 173 PIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAAT 252 (781)
Q Consensus 173 yIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAv 252 (781)
-+..+++|-. .-+++.+-. ++.+|.+.++|-|.+||+=--. +|. -...++-||.+|.+.++-.|++|+
T Consensus 901 ~~~inD~Pq~-~r~~vt~~~--~L~~i~e~~~~~it~rg~f~~~-gk~--------p~~gErklyl~ve~~~e~~vqra~ 968 (997)
T KOG0334|consen 901 ELEINDFPQN-ARWRVTYKE--ALLRISEPTAAGITTRGKFNPP-GKE--------PKPGERKLYLLVEGPDELSVQRAI 968 (997)
T ss_pred eccccccchh-cceeeechh--hhhhccCccccceeeccccCCC-CCC--------CCCcchhhhhhhhcchhHHHHHHH
Confidence 3445667743 555665543 4999999999999999983211 110 123566799999999999999999
Q ss_pred HHHHhhccccccchhhh
Q 003989 253 DLIELLVTSVSGSLAAI 269 (781)
Q Consensus 253 elIE~LL~pve~g~~a~ 269 (781)
+.++.+|.+...+...+
T Consensus 969 ~e~~r~l~e~~~~~~~~ 985 (997)
T KOG0334|consen 969 EELERLLEEEVVNLFSS 985 (997)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 99999988877766553
No 71
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=49.08 E-value=3.9e+02 Score=30.93 Aligned_cols=15 Identities=33% Similarity=0.627 Sum_probs=11.5
Q ss_pred CCCCCCChhHHHHhh
Q 003989 762 ARKPENDPEYEDLMA 776 (781)
Q Consensus 762 ~~k~e~dpeyedlma 776 (781)
.+-+-.|.||||+|.
T Consensus 353 ~~~plSeAEFEdiM~ 367 (498)
T KOG4849|consen 353 QMFPLSEAEFEDIMT 367 (498)
T ss_pred CCccchHHHHHHHHh
Confidence 344567899999996
No 72
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=48.86 E-value=13 Score=42.28 Aligned_cols=42 Identities=19% Similarity=0.165 Sum_probs=34.8
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHh-CCeEEEeCC
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 212 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGk 212 (781)
.||-+=- ..++++-||..||.+|..++.|.+|. |-||.|=.-
T Consensus 239 tKVAV~S-~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~~ 281 (374)
T PRK12328 239 AKVALFS-NNPNIDPIGATVGVKGVRINAVSKELNGENIDCIEY 281 (374)
T ss_pred eEEEEEc-CCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEEEc
Confidence 5665544 34799999999999999999999999 888888653
No 73
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=47.83 E-value=14 Score=37.57 Aligned_cols=30 Identities=13% Similarity=0.199 Sum_probs=26.9
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeCCc
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRGkG 213 (781)
.. |+-||.+|.++|+|++..|-+|.|=+..
T Consensus 70 gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s 99 (166)
T PRK06418 70 GP-RIPIGKGGKIAKALSRKLGKKVRVVEKT 99 (166)
T ss_pred CC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence 35 9999999999999999999999988753
No 74
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=47.50 E-value=11 Score=43.56 Aligned_cols=43 Identities=12% Similarity=0.102 Sum_probs=35.5
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHh-CCeEEEeCC
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 212 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGk 212 (781)
..||-+=.. .++++-||..||.+|..||.|.+|. |-||.|=.=
T Consensus 264 RtKVAV~S~-d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~y 307 (449)
T PRK12329 264 RTKIAVDTL-ERDVDPVGACIGARGSRIQAVVNELRGEKIDVIRW 307 (449)
T ss_pred eeEEEEEcC-CCCCChhhccCCCCcchHHHHHHHhCCCeEEEEEc
Confidence 356665543 4799999999999999999999999 888888653
No 75
>TIGR01825 gly_Cac_T_rel pyridoxal phosphate-dependent acyltransferase, putative. This model represents an enzyme subfamily related to three known enzymes; it appears closest to glycine C-acteyltransferase, shows no overlap with it in species distribution, and may share that function. The three closely related enzymes are glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase), 5-aminolevulinic acid synthase, and 8-amino-7-oxononanoate synthase. All transfer the R-group (acetyl, succinyl, or 6-carboxyhexanoyl) from coenzyme A to an amino acid (Gly, Gly, Ala, respectively), with release of CO2 for the latter two reactions.
Probab=46.39 E-value=1.7e+02 Score=31.53 Aligned_cols=62 Identities=18% Similarity=0.143 Sum_probs=36.4
Q ss_pred cccceeeCCC---chhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEE---ecCHHHHHHHHHHHH
Q 003989 183 NFLGLIFGPA---SDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISIS---ADSYEKVDAATDLIE 256 (781)
Q Consensus 183 NFIGlIIGPr---GnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIs---AdteEkVdkAvelIE 256 (781)
++++.+++.. ....++|.++ | |.|++.+.....+ ...+|.|+ ..++|.|+++++.|+
T Consensus 314 ~~~~~~~~~~~~~~~~~~~L~~~-g--i~v~~~~~~~~~~--------------~~~~iRi~~~~~~~~e~i~~~~~~l~ 376 (385)
T TIGR01825 314 PITPVVIGDEKAAQEFSRRLFDE-G--IFAQSIVFPTVPR--------------GTARIRNIPTAEHTKDDLDQALDAYE 376 (385)
T ss_pred CEEEEEECCHHHHHHHHHHHHHC-C--cEEcccCCCCCCC--------------CCceEEEEEcCCCCHHHHHHHHHHHH
Confidence 5666666643 2334566665 5 5566543211000 11245554 479999999999999
Q ss_pred hhccc
Q 003989 257 LLVTS 261 (781)
Q Consensus 257 ~LL~p 261 (781)
++++.
T Consensus 377 ~~~~~ 381 (385)
T TIGR01825 377 KVGKE 381 (385)
T ss_pred HHHHH
Confidence 98853
No 76
>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=46.11 E-value=55 Score=34.35 Aligned_cols=68 Identities=15% Similarity=0.110 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHhCCCCCC--CCCCC--C--Ccc-EEEEEcCCCCCCCCcccceeeCCCchhHHHH--------HHH
Q 003989 138 CLELEKQEVIGEILKLNPSYRT--PPDYK--P--LLK-EAVVPIPVKEYPGYNFLGLIFGPASDTQKRL--------EKE 202 (781)
Q Consensus 138 kLEeER~~IIe~mlkliP~frP--PsDYk--P--~~K-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrL--------EeE 202 (781)
..|--|..|+..+.+-+|.-.. ...|. + ..+ ...|++..+ .--|.|||-+|.+||+| |+-
T Consensus 184 ~~e~ire~~~~~~~~e~p~~~~~~~~~~~~~~~~~~~i~~~i~v~~~-----s~k~iiig~~g~~ik~i~~~ar~~l~~~ 258 (270)
T TIGR00436 184 ISEIIREKIIRYTKEEIPHSVRVEIERKSFNEKGLLKIHALISVERE-----SQKKIIIGKNGSMIKAIGIAARKDILEL 258 (270)
T ss_pred HHHHHHHHHHHhcccccCceEEEEEEEEEECCCCeEEEEEEEEECcC-----CceeEEEcCCcHHHHHHHHHHHHHHHHH
Confidence 3445566666666665554322 22222 1 111 246666665 45689999999999965 555
Q ss_pred hCCeEEEe
Q 003989 203 TRTVIKVY 210 (781)
Q Consensus 203 TGAKI~IR 210 (781)
.||||.++
T Consensus 259 ~~~~v~l~ 266 (270)
T TIGR00436 259 FDCDVFLE 266 (270)
T ss_pred hCCCEEEE
Confidence 67777653
No 77
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=45.99 E-value=32 Score=35.17 Aligned_cols=19 Identities=11% Similarity=0.046 Sum_probs=17.3
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
+.||+||++.|+++-+|+.
T Consensus 34 ~~i~~LE~~lg~~Lf~R~~ 52 (296)
T PRK11242 34 QQIRQLEESLGVQLFDRSG 52 (296)
T ss_pred HHHHHHHHHhCCeeEeEcC
Confidence 5799999999999999974
No 78
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=45.90 E-value=11 Score=41.95 Aligned_cols=31 Identities=32% Similarity=0.449 Sum_probs=27.6
Q ss_pred CcccceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 182 YNFLGLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 182 ~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
+-.+|+|.|+.|+|+|+||+.++.-|.--.+
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 4699999999999999999999988876665
No 79
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=45.70 E-value=30 Score=34.49 Aligned_cols=19 Identities=26% Similarity=0.247 Sum_probs=17.0
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
..||+||+|.|+++-+|..
T Consensus 10 ~~I~~LE~~lg~~Lf~R~~ 28 (269)
T PRK11716 10 RQIQRLEEELGQPLFVRDN 28 (269)
T ss_pred HHHHHHHHHhCCeeEEecC
Confidence 4689999999999999975
No 80
>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=45.68 E-value=24 Score=35.44 Aligned_cols=29 Identities=28% Similarity=0.351 Sum_probs=25.1
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeC
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYG 211 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRG 211 (781)
..-|++||-+|.|+++|-++||-+-.|.-
T Consensus 85 eKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 85 EKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred cCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 36799999999999999999997776643
No 81
>PRK00468 hypothetical protein; Provisional
Probab=44.40 E-value=13 Score=33.30 Aligned_cols=18 Identities=17% Similarity=0.333 Sum_probs=15.9
Q ss_pred ccceeeCCCchhHHHHHH
Q 003989 184 FLGLIFGPASDTQKRLEK 201 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEe 201 (781)
=+|+|||-+|+|++.|..
T Consensus 40 D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 40 DMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred hCcceecCCChhHHHHHH
Confidence 579999999999998854
No 82
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=44.35 E-value=33 Score=35.01 Aligned_cols=20 Identities=15% Similarity=-0.056 Sum_probs=17.5
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
+.||+||++.||++-+|...
T Consensus 36 ~~I~~LE~~lg~~Lf~R~~r 55 (290)
T PRK10837 36 AALTDLEGQLGVQLFDRVGK 55 (290)
T ss_pred HHHHHHHHHhCCccEeecCC
Confidence 46999999999999999753
No 83
>PRK02821 hypothetical protein; Provisional
Probab=44.19 E-value=12 Score=33.61 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=18.2
Q ss_pred cccceeeCCCchhHHHHHHHhC
Q 003989 183 NFLGLIFGPASDTQKRLEKETR 204 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETG 204 (781)
.=+|+|||-+|+|++.|..--.
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHH
Confidence 4689999999999998865544
No 84
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=44.16 E-value=33 Score=35.32 Aligned_cols=21 Identities=24% Similarity=0.191 Sum_probs=18.1
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003989 193 SDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 193 GnTiKrLEeETGAKI~IRGkG 213 (781)
.+.||+||++.||++-+|..+
T Consensus 33 Sr~i~~LE~~lg~~Lf~R~~~ 53 (296)
T PRK09906 33 SQQIKDLENCVGVPLLVRDKR 53 (296)
T ss_pred HHHHHHHHHHhCCeeeeeCCC
Confidence 356999999999999999754
No 85
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=41.87 E-value=36 Score=36.16 Aligned_cols=19 Identities=16% Similarity=0.039 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
+.||+||+|.|+++-+|..
T Consensus 35 ~~Ik~LE~~lg~~LF~R~~ 53 (317)
T PRK15421 35 HQFSDLEQRLGFRLFVRKS 53 (317)
T ss_pred HHHHHHHHHhCCEEEEecC
Confidence 5699999999999999964
No 86
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=41.73 E-value=36 Score=35.12 Aligned_cols=19 Identities=11% Similarity=-0.010 Sum_probs=17.0
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
+.||+||+|.|+++-+|..
T Consensus 34 ~~I~~LE~~lG~~LF~R~~ 52 (275)
T PRK03601 34 FRIRQLENQLGVNLFTRHR 52 (275)
T ss_pred HHHHHHHHHhCCceEEECC
Confidence 4689999999999999965
No 87
>PRK13392 5-aminolevulinate synthase; Provisional
Probab=40.89 E-value=2.3e+02 Score=31.28 Aligned_cols=25 Identities=16% Similarity=0.227 Sum_probs=19.6
Q ss_pred EEEEE---ecCHHHHHHHHHHHHhhccc
Q 003989 237 HISIS---ADSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 237 HVlIs---AdteEkVdkAvelIE~LL~p 261 (781)
++.|+ ..++|.++++++.|+++++.
T Consensus 370 ~lRis~~~~~t~edid~l~~aL~~~~~~ 397 (410)
T PRK13392 370 RLRITPTPLHDDEDIDALVAALVAIWDR 397 (410)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence 45555 36889999999999998764
No 88
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=40.87 E-value=22 Score=41.42 Aligned_cols=42 Identities=14% Similarity=0.159 Sum_probs=34.8
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHh-CCeEEEeCC
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 212 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGk 212 (781)
.||-+=- ..++++-||..||.+|..++.|.+|. |-||.|=.-
T Consensus 233 aKvAV~s-~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~ 275 (470)
T PRK09202 233 AKIAVKS-NDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILW 275 (470)
T ss_pred eEEEEEc-CCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEEc
Confidence 4665543 45799999999999999999999999 888888653
No 89
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=40.82 E-value=35 Score=36.06 Aligned_cols=77 Identities=19% Similarity=0.225 Sum_probs=43.9
Q ss_pred EEEcCCCCCCCCcccceeeCCCc-----------hhHHHHHHHhCC-eEEEeCCccCCCcchhcccCCCCccCCCCceEE
Q 003989 171 VVPIPVKEYPGYNFLGLIFGPAS-----------DTQKRLEKETRT-VIKVYGTKADTGEKVEISTSDANVQSTYEEFHI 238 (781)
Q Consensus 171 KIyIPvkeyP~~NFIGlIIGPrG-----------nTiKrLEeETGA-KI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHV 238 (781)
.++--.+-.+.+..+|+|||||| ..+..+-++... +|.+|-+. ..-+||
T Consensus 111 ~~iat~~~m~~l~~Lg~iLGPrGlMP~~k~gtv~~di~~~I~~~k~g~v~~r~~k-------------------~g~i~~ 171 (227)
T TIGR01169 111 VVIATPDMMRVVGKLGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEFRADK-------------------AGNIHA 171 (227)
T ss_pred EEEECHHHHHHHHHhccccccccCCCCCCCCCccccHHHHHHHHHcCcEEEEeCC-------------------CCEEEE
Confidence 33333444566678899999996 346666666643 56666432 112466
Q ss_pred EEEe---cCHHHHHHHHHHHHhhccccccch
Q 003989 239 SISA---DSYEKVDAATDLIELLVTSVSGSL 266 (781)
Q Consensus 239 lIsA---dteEkVdkAvelIE~LL~pve~g~ 266 (781)
-|-- ++++-++....+|+.|...-..+.
T Consensus 172 ~VG~~~m~~e~i~eNi~a~l~~i~~~~p~~~ 202 (227)
T TIGR01169 172 SIGKVSFDSEKLKENLEALLDAIKKAKPSGA 202 (227)
T ss_pred EEecCCCCHHHHHHHHHHHHHHHHHhCcccc
Confidence 6642 234455556666666665444433
No 90
>TIGR00707 argD acetylornithine and succinylornithine aminotransferases. Members of this family may also act on ornithine, like ornithine aminotransferase (EC 2.6.1.13) (see MEDLINE:90337349) and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (EC 2.6.1.17, DapC, an enzyme of lysine biosynthesis) (see MEDLINE:99175097)
Probab=40.31 E-value=2.2e+02 Score=30.56 Aligned_cols=23 Identities=17% Similarity=0.206 Sum_probs=19.0
Q ss_pred EEEEE---ecCHHHHHHHHHHHHhhc
Q 003989 237 HISIS---ADSYEKVDAATDLIELLV 259 (781)
Q Consensus 237 HVlIs---AdteEkVdkAvelIE~LL 259 (781)
++.|+ ..++|.++++++.|+++|
T Consensus 354 ~lRi~~~~~~t~~~i~~~~~~l~~~~ 379 (379)
T TIGR00707 354 VLRFLPPLIITKEEIDEAVSALEEAI 379 (379)
T ss_pred EEEEECCCcCCHHHHHHHHHHHHHhC
Confidence 56666 578999999999999875
No 91
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=39.26 E-value=30 Score=36.27 Aligned_cols=20 Identities=15% Similarity=-0.067 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
+-||+||++.|+++-+|..+
T Consensus 37 ~~Ik~LE~~lg~~Lf~R~~~ 56 (309)
T PRK11013 37 RELARFEKVIGLKLFERVRG 56 (309)
T ss_pred HHHHHHHHHhCceeeeecCC
Confidence 45899999999999999865
No 92
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=38.71 E-value=20 Score=43.89 Aligned_cols=37 Identities=27% Similarity=0.397 Sum_probs=32.1
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeC
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYG 211 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRG 211 (781)
..+++||.+ |-+.|||++|.++|.++.|++|-|.+--
T Consensus 710 ~~~~~~p~~------~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 710 TKEIEIPRS------LHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred eeEEeccHH------HhhhccCCCCccHHHHHHHhccceecCC
Confidence 467788875 7899999999999999999999988755
No 93
>COG0026 PurK Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism]
Probab=38.44 E-value=50 Score=37.72 Aligned_cols=51 Identities=10% Similarity=0.125 Sum_probs=37.3
Q ss_pred hHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhc
Q 003989 195 TQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLV 259 (781)
Q Consensus 195 TiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL 259 (781)
..+.+-+.-+|+|.+.||.-.|.+.+ = .||.|.+++.+++...+.+|..+.
T Consensus 318 ~~~~~l~~p~~~lH~YGK~e~R~gRK-----m---------GHvn~~~~~~~~~~~~~~~l~~~~ 368 (375)
T COG0026 318 DVKAVLALPGAHLHWYGKAEARPGRK-----M---------GHVNVLGSDSDELEQLAALLPAKQ 368 (375)
T ss_pred hhHHHHhCCCCEEEEecCccCCCCCe-----e---------eeEEeecCCHHHHHHHHHhhhhhh
Confidence 46889999999999999964332221 1 399999999877777776666443
No 94
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=38.07 E-value=50 Score=34.22 Aligned_cols=20 Identities=15% Similarity=0.147 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
+.||+||++.|+++-+|.++
T Consensus 38 ~~i~~LE~~lG~~LF~R~~r 57 (302)
T PRK09791 38 KSIQELEEGLAAQLFFRRSK 57 (302)
T ss_pred HHHHHHHHHhCCeEEEEcCC
Confidence 46899999999999999765
No 95
>PRK01064 hypothetical protein; Provisional
Probab=37.83 E-value=20 Score=32.40 Aligned_cols=21 Identities=24% Similarity=0.229 Sum_probs=17.8
Q ss_pred ccceeeCCCchhHHHHHHHhC
Q 003989 184 FLGLIFGPASDTQKRLEKETR 204 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEeETG 204 (781)
=+|+|||-+|+|++.|..-..
T Consensus 40 D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 40 DIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred cceEEECCCCccHHHHHHHHH
Confidence 479999999999999877543
No 96
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=37.69 E-value=46 Score=35.10 Aligned_cols=20 Identities=25% Similarity=0.157 Sum_probs=17.5
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
..||+||++.||++-+|.+.
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r 54 (308)
T PRK10094 35 YRIKLLEENTGVALFFRTTR 54 (308)
T ss_pred HHHHHHHHHhCCEEEeeCCC
Confidence 46899999999999999753
No 97
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=37.42 E-value=19 Score=32.61 Aligned_cols=18 Identities=17% Similarity=0.327 Sum_probs=15.9
Q ss_pred ccceeeCCCchhHHHHHH
Q 003989 184 FLGLIFGPASDTQKRLEK 201 (781)
Q Consensus 184 FIGlIIGPrGnTiKrLEe 201 (781)
=+|+|||-+|.|++.|..
T Consensus 40 D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 40 DMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred cccceecCCChhHHHHHH
Confidence 589999999999999844
No 98
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=37.10 E-value=39 Score=38.52 Aligned_cols=41 Identities=15% Similarity=0.046 Sum_probs=35.1
Q ss_pred cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCcc
Q 003989 168 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 214 (781)
Q Consensus 168 K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS 214 (781)
+...++++.+ -+++.||-+|.++|..-+-||+||.|+.-+|
T Consensus 308 ~~~~V~V~~~------qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 308 KKAIVTLLSD------QKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred cEEEEEEChH------HhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 3456777764 5699999999999999999999999999876
No 99
>PRK01170 phosphopantetheine adenylyltransferase/unknown domain fusion protein; Provisional
Probab=36.38 E-value=2.3e+02 Score=31.90 Aligned_cols=80 Identities=16% Similarity=0.201 Sum_probs=48.9
Q ss_pred ccceeeCC----CchhHHHHHHHhCCe-EEEe-------CCc---c-CCCcchhcccCCCCccCCCCceEEEEEecCHHH
Q 003989 184 FLGLIFGP----ASDTQKRLEKETRTV-IKVY-------GTK---A-DTGEKVEISTSDANVQSTYEEFHISISADSYEK 247 (781)
Q Consensus 184 FIGlIIGP----rGnTiKrLEeETGAK-I~IR-------GkG---S-~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEk 247 (781)
+=.+++++ ++.-|+++-+|-|.+ +.|. +.| | .+=.++|+. . .-....+++|.|-..|..|
T Consensus 86 ~d~IVVS~ET~~~~~~IN~~R~e~Gl~pleIv~I~~v~~~d~~~iSSTrIr~~eid---~-~g~~~~~~~V~VGS~NPvK 161 (322)
T PRK01170 86 YEIIVVSPETYQRALKINEIRIKNGLPPLKIVRVPYVLAEDLFPISSTRIINGEID---G-NGKRLKPLKINISTTNPAK 161 (322)
T ss_pred CCEEEEeccccccHHHHHHHHHHCCCCceEEEEEEeEEcCCCCcccHHHHhhhhcc---c-cCCcCCCcEEEEeCCChHH
Confidence 33455555 788899999999976 2222 222 1 111122221 1 1123457999999999999
Q ss_pred HHHHHHHHHhh------ccccccchh
Q 003989 248 VDAATDLIELL------VTSVSGSLA 267 (781)
Q Consensus 248 VdkAvelIE~L------L~pve~g~~ 267 (781)
+++..+..+.+ +..+++.++
T Consensus 162 i~Av~~af~~~f~~~~~v~~v~v~Sg 187 (322)
T PRK01170 162 INAVRRFFESLMKNFIVVKNIDYKLE 187 (322)
T ss_pred HHHHHHHHHHhcCCCceEEEeeCCCC
Confidence 99888877775 444555555
No 100
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=35.99 E-value=49 Score=34.36 Aligned_cols=19 Identities=16% Similarity=0.212 Sum_probs=17.2
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
+.||+||++.||++-+|..
T Consensus 34 ~~i~~LE~~lg~~LF~R~~ 52 (305)
T PRK11151 34 GQIRKLEDELGVMLLERTS 52 (305)
T ss_pred HHHHHHHHHhCchheeeCC
Confidence 5799999999999999964
No 101
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=35.39 E-value=57 Score=33.93 Aligned_cols=19 Identities=16% Similarity=-0.038 Sum_probs=17.0
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
..||+||++.|+++-+|..
T Consensus 35 ~~I~~LE~~lg~~LF~R~~ 53 (300)
T PRK11074 35 YTVRQLEEWLAVPLFERRH 53 (300)
T ss_pred HHHHHHHHHhCCeeEEeCC
Confidence 4689999999999999964
No 102
>PLN02397 aspartate transaminase
Probab=35.36 E-value=2.6e+02 Score=31.36 Aligned_cols=42 Identities=26% Similarity=0.294 Sum_probs=32.0
Q ss_pred hhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhcc
Q 003989 194 DTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~ 260 (781)
+-.++|-+|.|+-|. +.| .+.+++.+.++|+++++.|+++|+
T Consensus 379 ~~~~~Ll~~~~V~v~--~~~-----------------------Ri~~~~~~~~~i~~~~~~i~~~~~ 420 (423)
T PLN02397 379 EQVDRMTKEYHIYMT--RDG-----------------------RISMAGLSSKNVPYLADAIHAVVT 420 (423)
T ss_pred HHHHHHHHhCCEEEC--CCC-----------------------eEEEeeCCHHHHHHHHHHHHHHHh
Confidence 456778788776553 221 577888999999999999999874
No 103
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=35.21 E-value=1.2e+02 Score=34.52 Aligned_cols=65 Identities=12% Similarity=0.184 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCC--CCCCCCCc-----cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhC
Q 003989 135 KLECLELEKQEVIGEILKLNPSYRT--PPDYKPLL-----KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETR 204 (781)
Q Consensus 135 ~rekLEeER~~IIe~mlkliP~frP--PsDYkP~~-----K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETG 204 (781)
+--.+|--|.+||+..-.-+|---- ..+|+-.. -+.+|..|.. ...-+|||++|+-|++|-++-+
T Consensus 288 e~l~~e~VReklLd~~pqEVPY~lq~~i~~w~e~~~g~l~I~~~v~~pK~-----s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 288 EFLCSESVREKLLDHLPQEVPYNLQVRILSWKERPAGVLFIQVEVVCPKN-----SQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred HHHHHHHHHHHHHhhCccccCcceEEEEEEeeecCCcEEEEEEEEEcCCC-----cceeEEEcCCCccHHHHHHHHH
Confidence 3445666677777765444432111 34454321 1245555553 5667999999999998866543
No 104
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=34.88 E-value=32 Score=35.30 Aligned_cols=19 Identities=37% Similarity=0.356 Sum_probs=17.0
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
+.||+||+|.||++-+|..
T Consensus 34 ~~Ik~LE~~lg~~LF~R~~ 52 (291)
T TIGR03418 34 QQVKRLEEELGTPLFERGH 52 (291)
T ss_pred HHHHHHHHHhCcHHhhcCC
Confidence 4689999999999999974
No 105
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=34.80 E-value=47 Score=35.63 Aligned_cols=21 Identities=24% Similarity=0.245 Sum_probs=18.4
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q 003989 194 DTQKRLEKETRTVIKVYGTKA 214 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkGS 214 (781)
+.||+||+|.||++-+|..+.
T Consensus 35 ~~I~~LE~~lG~~LF~R~~r~ 55 (327)
T PRK12680 35 KQLKQLEDELGFLLFVRKGRS 55 (327)
T ss_pred HHHHHHHHHhCCeEEEECCCc
Confidence 468999999999999998753
No 106
>COG1159 Era GTPase [General function prediction only]
Probab=34.46 E-value=90 Score=34.77 Aligned_cols=69 Identities=14% Similarity=0.168 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCC--CCCCCCC-c---c-EEEEEcCCCCCCCCcccceeeCCCchhHHHH--------HH
Q 003989 137 ECLELEKQEVIGEILKLNPSYRT--PPDYKPL-L---K-EAVVPIPVKEYPGYNFLGLIFGPASDTQKRL--------EK 201 (781)
Q Consensus 137 ekLEeER~~IIe~mlkliP~frP--PsDYkP~-~---K-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrL--------Ee 201 (781)
...|--|..|+..+-+-.|.-.. ..+++.. . + ...||+.-+ .--|-|||-+|..||+| |+
T Consensus 191 ~~aEiiREk~~~~l~eElPhsv~VeIe~~~~~~~~~~~I~a~I~Ver~-----sQK~IiIGk~G~~iK~IG~~AR~~ie~ 265 (298)
T COG1159 191 LAAEIIREKLLLLLREELPHSVAVEIEEFEEREKGLLKIHATIYVERE-----SQKGIIIGKNGAMIKKIGTAARKDIEK 265 (298)
T ss_pred HHHHHHHHHHHHhcccccCceEEEEEEEEEecCCCeEEEEEEEEEecC-----CccceEECCCcHHHHHHHHHHHHHHHH
Confidence 45666777777777777776543 3344432 1 2 246888876 45688999999999965 55
Q ss_pred HhCCeEEEe
Q 003989 202 ETRTVIKVY 210 (781)
Q Consensus 202 ETGAKI~IR 210 (781)
-.||||.+.
T Consensus 266 l~~~kV~L~ 274 (298)
T COG1159 266 LLGCKVYLE 274 (298)
T ss_pred HhCCceEEE
Confidence 567776654
No 107
>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=34.18 E-value=1.8e+02 Score=29.72 Aligned_cols=62 Identities=8% Similarity=-0.057 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHhcCCCcccCCC----CCCCCCCCCCCCCCCCccch--HHHHHHHHHHHHHHHHHHHhC
Q 003989 92 QTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDR--EKLECLELEKQEVIGEILKLN 154 (781)
Q Consensus 92 Q~RieEItrkL~sg~le~~~~e----~s~SPpP~p~yds~GkRiNT--R~rekLEeER~~IIe~mlkli 154 (781)
++.|++|...|+.=++++ .-. |-..|.-.-.--++||=+=| +..+.+++...++++.+.+++
T Consensus 17 ~idL~~la~~l~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l~~~g 84 (174)
T cd04517 17 HIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLLQKLG 84 (174)
T ss_pred cccHHHHHhhCCCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHHHcC
Confidence 456788888887666665 322 11122211111456776656 346778888888888877765
No 108
>COG0014 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=34.12 E-value=63 Score=37.35 Aligned_cols=55 Identities=16% Similarity=0.225 Sum_probs=34.7
Q ss_pred cccceeeCCCchh-HHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhcc
Q 003989 183 NFLGLIFGPASDT-QKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 183 NFIGlIIGPrGnT-iKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~ 260 (781)
.||-+||=-||+. ++++.+++-+=+.-.|.| -|+|.-|....+|+|+++|.+-=.
T Consensus 195 ~yiD~iIPRGg~~Li~~v~~~a~vPVi~~~~G-----------------------~CHiyvd~~ADld~A~~ii~nAKt 250 (417)
T COG0014 195 GYIDLVIPRGGAGLIRRVVENATVPVIEHGVG-----------------------NCHIYVDESADLDKALKIIVNAKT 250 (417)
T ss_pred CceeEEEcCCcHHHHHHHHhCCcCCEEecCcc-----------------------eEEEEecccCCHHHHHHHHHcccC
Confidence 3566777555554 677777777777777776 344444555667777777655433
No 109
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=33.53 E-value=62 Score=41.91 Aligned_cols=79 Identities=14% Similarity=0.059 Sum_probs=58.1
Q ss_pred EEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeC-CccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYG-TKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 248 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRG-kGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkV 248 (781)
.|+.||+ |-+-|+||-+|.|+..+-+.||+.|.|.- .++. ..| .+....-..+..
T Consensus 1342 ~k~~~P~------~a~SRVig~ggsnVna~r~~tga~ielekmq~~N---qae---------------rs~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1342 GKGDGPL------YASSRVIGDGGSNVNAARLGTGALIELEKMQPDN---QAE---------------RSKAPKGRPPSQ 1397 (2131)
T ss_pred cccccch------hhhhhhhccCcchhhhHhhccceEEehhhcCCcc---chh---------------hhcccCCCChhh
Confidence 4777777 68999999999999999999999999876 2211 111 122222345688
Q ss_pred HHHHHHHHhhccccccchhhhccc
Q 003989 249 DAATDLIELLVTSVSGSLAAISTS 272 (781)
Q Consensus 249 dkAvelIE~LL~pve~g~~a~~~~ 272 (781)
..|..+|..+|.+.++.....+..
T Consensus 1398 r~a~~~I~~~i~Dpdv~~~~~ssi 1421 (2131)
T KOG4369|consen 1398 RVATSPIGLPIIDPDVSSPSSSSI 1421 (2131)
T ss_pred hhhhccccceeecCCcCccccccc
Confidence 889999999999999887754444
No 110
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=33.29 E-value=52 Score=33.94 Aligned_cols=20 Identities=20% Similarity=0.125 Sum_probs=17.9
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
..||+||++.|+++-+|..+
T Consensus 36 ~~I~~LE~~lg~~LF~R~~~ 55 (300)
T TIGR02424 36 KTLRELEEILGTPLFERDRR 55 (300)
T ss_pred HHHHHHHHHhCCeEEEEcCC
Confidence 46999999999999999765
No 111
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=33.27 E-value=96 Score=32.98 Aligned_cols=26 Identities=15% Similarity=0.187 Sum_probs=22.9
Q ss_pred cceeeCCCchhHHHHHHHhCCeEEEe
Q 003989 185 LGLIFGPASDTQKRLEKETRTVIKVY 210 (781)
Q Consensus 185 IGlIIGPrGnTiKrLEeETGAKI~IR 210 (781)
+|+|||-+|+|++.||--++.-+..+
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~~ 127 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNKI 127 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhhh
Confidence 89999999999999999988666653
No 112
>PF09692 Arb1: Argonaute siRNA chaperone (ARC) complex subunit Arb1; InterPro: IPR018606 Arb1 is required for histone H3 Lys9 (H3-K9) methylation, heterochromatin, assembly and siRNA generation in fission yeast [].
Probab=32.74 E-value=1.5e+02 Score=34.06 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=18.2
Q ss_pred EEecCHHHHHHHHHHHHhhcc
Q 003989 240 ISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 240 IsAdteEkVdkAvelIE~LL~ 260 (781)
+++.+++.++.|+..|++.|.
T Consensus 139 ~~g~~~~~~~~a~~vI~NFL~ 159 (396)
T PF09692_consen 139 LTGESEEQMKLATDVIRNFLN 159 (396)
T ss_pred hcCCcHHHHHHHHHHHHHHHH
Confidence 467899999999999999775
No 113
>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=32.73 E-value=2e+02 Score=29.28 Aligned_cols=63 Identities=13% Similarity=0.006 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHhcCCCcccCCC----CCCCCCCCCCCCCCCCccchH--HHHHHHHHHHHHHHHHHHhC
Q 003989 92 QTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDRE--KLECLELEKQEVIGEILKLN 154 (781)
Q Consensus 92 Q~RieEItrkL~sg~le~~~~e----~s~SPpP~p~yds~GkRiNTR--~rekLEeER~~IIe~mlkli 154 (781)
++.|++|..+|+.=++++..-. |...|.-.-.--+.||=+=|. ..+.+++..+++++.+.++.
T Consensus 16 ~idL~~la~~~~n~~YePe~fpgli~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~L~~~g 84 (174)
T cd00652 16 ELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARILQKLG 84 (174)
T ss_pred ccCHHHHHhhCCCcEECCCccceEEEEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence 5678889888876555553321 112222222224567766663 46778888888888887776
No 114
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=32.53 E-value=58 Score=34.09 Aligned_cols=20 Identities=20% Similarity=0.210 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
..||+||+|.|+++-+|...
T Consensus 41 ~~I~~LE~~lg~~Lf~R~~r 60 (302)
T TIGR02036 41 HRINQLEEELGIQLFVRSHR 60 (302)
T ss_pred HHHHHHHHHhCCceEEECCC
Confidence 45899999999999999864
No 115
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=32.33 E-value=57 Score=35.02 Aligned_cols=77 Identities=18% Similarity=0.241 Sum_probs=47.2
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchh-----------HHHHHHHhCC-eEEEeCCccCCCcchhcccCCCCccCCCCce
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDT-----------QKRLEKETRT-VIKVYGTKADTGEKVEISTSDANVQSTYEEF 236 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnT-----------iKrLEeETGA-KI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpL 236 (781)
.+.++.-.|-.+.+-.+|.||||||.. +..+-+|... +|.+|=+.. --+
T Consensus 112 fD~~IAtpdmM~~v~~LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K~g~v~~R~dk~-------------------g~i 172 (228)
T COG0081 112 FDVFIATPDMMPLVGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRADKA-------------------GVI 172 (228)
T ss_pred CCEEEECchHHHHHHHHhhhcCCCCCCCCCCCCCCCcCHHHHHHHHhcCcEEEEECCC-------------------ceE
Confidence 466666777788888899999999963 4555566554 666665531 125
Q ss_pred EEEEEe---cCHHHHHHHHHHHHhhcccccc
Q 003989 237 HISISA---DSYEKVDAATDLIELLVTSVSG 264 (781)
Q Consensus 237 HVlIsA---dteEkVdkAvelIE~LL~pve~ 264 (781)
|+.|=- ++++-++.+..+++.|..-...
T Consensus 173 h~~iGk~sf~~e~L~eNi~a~l~~i~~~~p~ 203 (228)
T COG0081 173 HVPIGKVSFDDEKLAENIEALLNAIVKAKPA 203 (228)
T ss_pred EEEecCCCCCHHHHHHHHHHHHHHHHHhCcC
Confidence 777743 2334445555555555544443
No 116
>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=32.17 E-value=45 Score=37.35 Aligned_cols=39 Identities=26% Similarity=0.210 Sum_probs=32.8
Q ss_pred cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 168 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 168 K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
+...++++.+ -.++.||-+|.++|..-+-||+||.|+-.
T Consensus 301 ~~~~v~V~~~------~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 301 HSAEVVVPDD------QLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred cEEEEEEChH------HcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 3456677764 57899999999999999999999999854
No 117
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=30.71 E-value=68 Score=33.66 Aligned_cols=21 Identities=14% Similarity=0.028 Sum_probs=18.3
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003989 193 SDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 193 GnTiKrLEeETGAKI~IRGkG 213 (781)
.+.||+||+|.|+++-+|...
T Consensus 39 S~~I~~LE~~lg~~LF~R~~r 59 (312)
T PRK10341 39 SKIINDIEDYFGVELIVRKNT 59 (312)
T ss_pred HHHHHHHHHHhCCeEEEEcCC
Confidence 356999999999999999864
No 118
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=30.54 E-value=61 Score=34.49 Aligned_cols=21 Identities=19% Similarity=0.158 Sum_probs=18.1
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003989 193 SDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 193 GnTiKrLEeETGAKI~IRGkG 213 (781)
.+.||+||++.||++.+|...
T Consensus 43 S~~I~~LE~~lG~~LF~R~~~ 63 (310)
T PRK15092 43 SQQMQRLEQLVGKELFARHGR 63 (310)
T ss_pred HHHHHHHHHHhCcceEEECCC
Confidence 356999999999999999763
No 119
>PF03420 Peptidase_U9: Prohead core protein protease This family belongs to family U9 of the peptidase classification.; InterPro: IPR005082 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belongs to MEROPS peptidase family U9 (phage prohead processing peptidase family, clan U-), which play a role in the head assembly of Bacteriophage T4. The pathway of bacteriophage T4 head assembly begins with the formation of a prohead bound to the bacterial cell membrane which is later converted to the mature, DNA-containing head. During maturation, all but one of the prohead proteins are proteolytically processed by a phage-coded protease which is formed by autocatalytic cleavage of the product of gene 21 (gp21). Protease gp21 has been tentatively located in the centre of the prohead core [].
Probab=30.44 E-value=59 Score=34.57 Aligned_cols=76 Identities=20% Similarity=0.072 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-------CCCCCCC-ccEEEEEcCCCCCCCCcccce---eeCCCchhHHHHHHHhC
Q 003989 136 LECLELEKQEVIGEILKLNPSYRT-------PPDYKPL-LKEAVVPIPVKEYPGYNFLGL---IFGPASDTQKRLEKETR 204 (781)
Q Consensus 136 rekLEeER~~IIe~mlkliP~frP-------PsDYkP~-~K~~KIyIPvkeyP~~NFIGl---IIGPrGnTiKrLEeETG 204 (781)
++-|++|=.+-+++.++..-.+-. --|.... -++++++.-= -||+|+ |=+|.|+.+|.|.++ |
T Consensus 59 k~vl~reV~~Y~~e~V~t~rAlGEL~HP~~~~vd~~~vsh~I~~l~weG-----~n~~G~a~vL~t~~G~~l~aLi~a-G 132 (213)
T PF03420_consen 59 KSVLEREVQRYIEEQVKTGRALGELNHPDRPNVDPDRVSHKIESLWWEG-----DNVMGRARVLETPMGDILAALIDA-G 132 (213)
T ss_pred HHHHHHHHHHHHHHHHhccceeeEcCCCCCCCCCHHHhhhheeEEEEeC-----CeeEEEEEEcCCcchHHHHHHHHc-C
Confidence 455666655555555555544322 1111111 2578888754 489984 458999999999988 7
Q ss_pred Ce--EEEeCCccCCC
Q 003989 205 TV--IKVYGTKADTG 217 (781)
Q Consensus 205 AK--I~IRGkGS~k~ 217 (781)
.+ ++-||-|+++.
T Consensus 133 ~~lGVSSRG~Gslk~ 147 (213)
T PF03420_consen 133 WKLGVSSRGLGSLKK 147 (213)
T ss_pred CccceecCCcccccc
Confidence 66 45567777654
No 120
>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=30.32 E-value=2.2e+02 Score=29.46 Aligned_cols=55 Identities=18% Similarity=0.391 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 139 LELEKQEVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 139 LEeER~~IIe~mlkliP~frPPsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
+..||.+|++.+.++.+.|.+ |. -++.||++-.-... .+.+|.+-|--+|.=||+
T Consensus 66 ~~reR~ql~~~~~~~~~~yl~---~~---------------~~~r~VaL~fv~~~-~~~~i~~it~~RV~~RGD 120 (168)
T PF08303_consen 66 QKRERKQLFEDVSQLKPDYLP---YD---------------TNVRFVALNFVHDD-DLDEIRRITQDRVLARGD 120 (168)
T ss_pred hHHHHHHHHHHHHHhcccccc---cC---------------CCeEEEEEEccCCC-CHHHHHHHHHHHHHhcCc
Confidence 567889999999888866653 11 12235555444444 566666667667766776
No 121
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=29.79 E-value=59 Score=33.66 Aligned_cols=20 Identities=15% Similarity=-0.032 Sum_probs=17.5
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
..||+||++.||++.+|...
T Consensus 39 ~~i~~LE~~lg~~Lf~R~~r 58 (297)
T PRK11139 39 HQIKALEDFLGLKLFRRRNR 58 (297)
T ss_pred HHHHHHHHHhCchheEecCC
Confidence 46999999999999999753
No 122
>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=29.75 E-value=46 Score=40.00 Aligned_cols=29 Identities=28% Similarity=0.314 Sum_probs=25.1
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeC
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYG 211 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRG 211 (781)
.+=|++||-+|.|+++|-++||-+-.|.-
T Consensus 102 ~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 102 EKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred cCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 36799999999999999999997766654
No 123
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=29.63 E-value=57 Score=34.28 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=18.2
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003989 193 SDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 193 GnTiKrLEeETGAKI~IRGkG 213 (781)
.+.||+||+|.||++-.|...
T Consensus 46 S~~I~~LE~~lG~~LF~R~~r 66 (311)
T PRK10086 46 SHRINQLEEELGIKLFVRSHR 66 (311)
T ss_pred HHHHHHHHHHhCCeeEEEcCC
Confidence 356999999999999999764
No 124
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=29.18 E-value=28 Score=41.39 Aligned_cols=31 Identities=19% Similarity=0.252 Sum_probs=29.1
Q ss_pred cccceeeCCCchhHHHHHHHhCCeEEEeCCc
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI~IRGkG 213 (781)
.-.++|+|-+|.|++.|++-+++||.++-.|
T Consensus 149 r~~~~i~grgget~~si~~ss~aki~~d~ng 179 (608)
T KOG2279|consen 149 RSVGRIIGRGGETIRSICKSSGAKITCDKNG 179 (608)
T ss_pred hhcccccccchhhhcchhccccccccccccc
Confidence 5789999999999999999999999999886
No 125
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=29.03 E-value=41 Score=27.75 Aligned_cols=20 Identities=20% Similarity=0.145 Sum_probs=16.6
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
..||+||++.|+++.+|..+
T Consensus 32 ~~i~~LE~~lg~~Lf~r~~~ 51 (60)
T PF00126_consen 32 RQIKQLEEELGVPLFERSGR 51 (60)
T ss_dssp HHHHHHHHHHTS-SEEECSS
T ss_pred HHHHHHHHHhCCeEEEECCC
Confidence 46899999999999999764
No 126
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=28.75 E-value=95 Score=26.62 Aligned_cols=26 Identities=12% Similarity=0.245 Sum_probs=22.9
Q ss_pred ceEEEEEecCHHHHHHHHHHHHhhcc
Q 003989 235 EFHISISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 235 pLHVlIsAdteEkVdkAvelIE~LL~ 260 (781)
-+.|++.|.+.+.+++.++.|.++|+
T Consensus 48 ~iRv~~Ea~~~~~~~~~~~~i~~~ik 73 (73)
T PF00408_consen 48 KIRVYVEAPDEEELEEIAEEIAEAIK 73 (73)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred eEEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 38999999999999999999988764
No 127
>PRK09801 transcriptional activator TtdR; Provisional
Probab=28.72 E-value=59 Score=34.40 Aligned_cols=20 Identities=15% Similarity=0.115 Sum_probs=17.9
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
..||+||+|.|+++-+|.+.
T Consensus 39 ~~I~~LE~~LG~~Lf~R~~r 58 (310)
T PRK09801 39 KRIQILENTLATTLLNRSAR 58 (310)
T ss_pred HHHHHHHHHhCCEeeeecCC
Confidence 56999999999999999864
No 128
>PRK06107 aspartate aminotransferase; Provisional
Probab=28.54 E-value=4.5e+02 Score=28.98 Aligned_cols=26 Identities=31% Similarity=0.346 Sum_probs=20.6
Q ss_pred EEEEE-ecCHHHHHHHHHHHHhhcccc
Q 003989 237 HISIS-ADSYEKVDAATDLIELLVTSV 262 (781)
Q Consensus 237 HVlIs-AdteEkVdkAvelIE~LL~pv 262 (781)
||.|+ +.++|.+++|+++|.++|..+
T Consensus 375 ~iRis~~~~~e~l~~~l~~l~~~l~~~ 401 (402)
T PRK06107 375 YFRLSIATSLETLEEACARIERAVAAL 401 (402)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHHhc
Confidence 66664 567899999999999988653
No 129
>COG3967 DltE Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane]
Probab=28.39 E-value=44 Score=35.95 Aligned_cols=57 Identities=18% Similarity=0.113 Sum_probs=40.5
Q ss_pred HHhCCeEEEeCCccCCCcchhccc-CCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccccc
Q 003989 201 KETRTVIKVYGTKADTGEKVEIST-SDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGS 265 (781)
Q Consensus 201 eETGAKI~IRGkGS~k~~K~E~~~-~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve~g 265 (781)
+-||-.|.|-|-+|+=+.+-..+. .-| =.|.|+|.++++|+++++.+-.|...+++-
T Consensus 2 k~tgnTiLITGG~sGIGl~lak~f~elg--------N~VIi~gR~e~~L~e~~~~~p~~~t~v~Dv 59 (245)
T COG3967 2 KTTGNTILITGGASGIGLALAKRFLELG--------NTVIICGRNEERLAEAKAENPEIHTEVCDV 59 (245)
T ss_pred cccCcEEEEeCCcchhhHHHHHHHHHhC--------CEEEEecCcHHHHHHHHhcCcchheeeecc
Confidence 358899999998876443321111 111 279999999999999999988888776653
No 130
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=28.36 E-value=58 Score=33.96 Aligned_cols=20 Identities=10% Similarity=0.001 Sum_probs=17.6
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
+.||+||+|.|+++-.|...
T Consensus 44 ~~I~~LE~~lG~~Lf~R~~r 63 (303)
T PRK10082 44 RRIRALEQAIGVELFNRQVT 63 (303)
T ss_pred HHHHHHHHHcCCEEEEecCC
Confidence 46999999999999999853
No 131
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, 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=28.22 E-value=2.2e+02 Score=29.20 Aligned_cols=63 Identities=13% Similarity=0.110 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHhcCCCcccCCC----CCCCCCCCCCCCCCCCccchH--HHHHHHHHHHHHHHHHHHhC
Q 003989 92 QTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDRE--KLECLELEKQEVIGEILKLN 154 (781)
Q Consensus 92 Q~RieEItrkL~sg~le~~~~e----~s~SPpP~p~yds~GkRiNTR--~rekLEeER~~IIe~mlkli 154 (781)
++.|++|...|+.-++++..-. |...|.-.-.--+.||=+=|. ..+.+.+.-.++++.+.+++
T Consensus 16 ~ldL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~L~~~g 84 (174)
T cd04518 16 ELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKKLKDYG 84 (174)
T ss_pred eecHHHHHhhCCCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHHhcC
Confidence 5678899888877666654321 112222222224567776663 45677777777888777776
No 132
>TIGR03812 tyr_de_CO2_Arch tyrosine decarboxylase MnfA. Members of this protein family are the archaeal form, MnfA, of tyrosine decarboxylase, and are involved in methanofuran biosynthesis. Members show clear homology to the Enterococcus form, Tdc, that is involved in tyrosine decarboxylation for resistance to acidic conditions.
Probab=28.06 E-value=3.5e+02 Score=28.88 Aligned_cols=23 Identities=9% Similarity=0.198 Sum_probs=16.0
Q ss_pred eEEEEEe-cCHHHHHHHHHHHHhh
Q 003989 236 FHISISA-DSYEKVDAATDLIELL 258 (781)
Q Consensus 236 LHVlIsA-dteEkVdkAvelIE~L 258 (781)
++|.+.. .++|.+++.++.|++|
T Consensus 350 iRis~~~~~t~edid~l~~~L~~~ 373 (373)
T TIGR03812 350 LRIVVMPHVTREHIEEFLEDLKEI 373 (373)
T ss_pred EEEEEECCCCHHHHHHHHHHHhhC
Confidence 3444443 3889999999888764
No 133
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=28.02 E-value=96 Score=31.24 Aligned_cols=19 Identities=16% Similarity=0.142 Sum_probs=16.9
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
..||+||++.||++.+|..
T Consensus 30 ~~i~~LE~~lg~~Lf~R~~ 48 (279)
T TIGR03339 30 DQVRKLEERYGVELFHRNG 48 (279)
T ss_pred HHHHHHHHHhCCccEEEcC
Confidence 4689999999999999964
No 134
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=27.93 E-value=53 Score=34.94 Aligned_cols=20 Identities=5% Similarity=0.001 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
+.||+||++.|+++-+|.+.
T Consensus 62 ~~I~~LE~~lG~~LF~R~~r 81 (317)
T PRK11482 62 QSIQKLRVIFPDPLFIRKGQ 81 (317)
T ss_pred HHHHHHHHHhCCcceEecCC
Confidence 56999999999999999864
No 135
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=27.45 E-value=83 Score=32.55 Aligned_cols=20 Identities=15% Similarity=0.087 Sum_probs=17.6
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
..||+||++.|+++-+|.+.
T Consensus 35 ~~I~~LE~~lG~~LF~R~~r 54 (301)
T PRK14997 35 RRIAQLEERLGVRLIQRTTR 54 (301)
T ss_pred HHHHHHHHHhCCEeeeeccC
Confidence 46899999999999999863
No 136
>PLN00062 TATA-box-binding protein; Provisional
Probab=26.69 E-value=3.2e+02 Score=28.18 Aligned_cols=140 Identities=17% Similarity=0.133 Sum_probs=74.3
Q ss_pred HHHHHHHHHHHHhcCCCcccCCC----CCCCCCCCCCCCCCCCccch--HHHHHHHHHHHHHHHHHHHhCCCCCCCCCCC
Q 003989 91 YQTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDR--EKLECLELEKQEVIGEILKLNPSYRTPPDYK 164 (781)
Q Consensus 91 ~Q~RieEItrkL~sg~le~~~~e----~s~SPpP~p~yds~GkRiNT--R~rekLEeER~~IIe~mlkliP~frPPsDYk 164 (781)
.++.|++|..+++.=++++..-. |-..|.-.-.--+.||=+=| +..+.+++...++++.+.+++=..+ ..+|+
T Consensus 15 ~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L~~lg~~~~-~~~f~ 93 (179)
T PLN00062 15 CKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARIIQKLGFPAK-FKDFK 93 (179)
T ss_pred CcccHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHHHcCCCcC-CCccE
Confidence 35678899888876455544321 11223222222466777666 3467777788888877777653222 13443
Q ss_pred CCccEEEEEcCCC--------------CCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCcc
Q 003989 165 PLLKEAVVPIPVK--------------EYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQ 230 (781)
Q Consensus 165 P~~K~~KIyIPvk--------------eyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~ 230 (781)
-..-..+..++.+ +|----|=|+|.=- .+..|++.|-..|
T Consensus 94 v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~---------~~pk~~~liF~sG----------------- 147 (179)
T PLN00062 94 IQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRM---------KQPKIVLLIFVSG----------------- 147 (179)
T ss_pred EEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEe---------CCCcEEEEEeCCC-----------------
Confidence 2111222222221 01000122332211 1234555555554
Q ss_pred CCCCceEEEEE-ecCHHHHHHHHHHHHhhccccc
Q 003989 231 STYEEFHISIS-ADSYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 231 ~~~EpLHVlIs-AdteEkVdkAvelIE~LL~pve 263 (781)
.|.|+ |.++|.+++|++.|..+|....
T Consensus 148 ------kvvitGaks~~~~~~ai~~i~p~L~~~~ 175 (179)
T PLN00062 148 ------KIVITGAKVREEIYTAFENIYPVLTEFR 175 (179)
T ss_pred ------EEEEEecCCHHHHHHHHHHHHHHHHHhc
Confidence 57777 4568999999999999987654
No 137
>PRK08175 aminotransferase; Validated
Probab=26.41 E-value=4.1e+02 Score=29.16 Aligned_cols=25 Identities=12% Similarity=0.333 Sum_probs=20.1
Q ss_pred EEEEE-ecCHHHHHHHHHHHHhhccc
Q 003989 237 HISIS-ADSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 237 HVlIs-AdteEkVdkAvelIE~LL~p 261 (781)
|+.|+ +.+++.+++|+++|.++|..
T Consensus 364 ~lRis~~~~~~~~~~al~~l~~~l~~ 389 (395)
T PRK08175 364 HVRFALIENRDRIRQAIRGIKAMFRA 389 (395)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHHh
Confidence 55554 46789999999999999963
No 138
>PRK06019 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed
Probab=26.38 E-value=1.5e+02 Score=32.74 Aligned_cols=48 Identities=15% Similarity=0.162 Sum_probs=31.8
Q ss_pred HHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHh
Q 003989 196 QKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIEL 257 (781)
Q Consensus 196 iKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~ 257 (781)
+..+.+..|+++.+.||...+.+.+ -.||.|.+++.+.+.+-++.+..
T Consensus 319 ~~~~~~~~~~~~~~ygk~~~~~~rk--------------~Ghv~~~~~~~~~~~~~~~~~~~ 366 (372)
T PRK06019 319 WDALLALPGAHLHLYGKAEARPGRK--------------MGHVTVLGDDVEALLAKLEALAP 366 (372)
T ss_pred HHHHhhCCCCEEEECCCCCCCCCCc--------------eEEEEeecCCHHHHHHHHHHHHh
Confidence 3445556899999999954333221 14999999998766655555444
No 139
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=26.37 E-value=76 Score=31.81 Aligned_cols=21 Identities=33% Similarity=0.257 Sum_probs=18.2
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003989 193 SDTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 193 GnTiKrLEeETGAKI~IRGkG 213 (781)
...||+||++.|+++-+|..+
T Consensus 33 S~~I~~LE~~lg~~Lf~R~~~ 53 (297)
T COG0583 33 SRQIKRLEEELGVPLFERTTR 53 (297)
T ss_pred HHHHHHHHHHhCchheeecCC
Confidence 356999999999999999854
No 140
>KOG4165 consensus Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=26.14 E-value=74 Score=36.28 Aligned_cols=66 Identities=18% Similarity=0.350 Sum_probs=37.5
Q ss_pred cccceeeCCCchh--HHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhcc
Q 003989 183 NFLGLIFGPASDT--QKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 183 NFIGlIIGPrGnT--iKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~ 260 (781)
++|-+|| |||.+ ++.|++.|. |=+-|.- +.-.|||| |....+++|.+++..--.
T Consensus 190 ~~IDLvI-PRGSs~LVr~Ik~~tk--IPVLGHA-------------------~GichvYv--d~dad~~kA~riv~DaK~ 245 (433)
T KOG4165|consen 190 DYIDLVI-PRGSSDLVRSIKDTTK--IPVLGHA-------------------EGICHVYV--DKDADLDKAKRIVRDAKC 245 (433)
T ss_pred hheeEEe-cCCcHHHHHHHhhccc--Ccccccc-------------------cceeEEEe--ccccCHHHHHHHHhcccC
Confidence 4677777 78866 577777654 7777762 11125554 445556666665554444
Q ss_pred ccccchhhhccc
Q 003989 261 SVSGSLAAISTS 272 (781)
Q Consensus 261 pve~g~~a~~~~ 272 (781)
+.-..+.|.+++
T Consensus 246 dYPAaCNAmETL 257 (433)
T KOG4165|consen 246 DYPAACNAMETL 257 (433)
T ss_pred CCchhhhhHHHH
Confidence 444444444443
No 141
>PRK05387 histidinol-phosphate aminotransferase; Provisional
Probab=25.64 E-value=6e+02 Score=27.04 Aligned_cols=24 Identities=17% Similarity=0.365 Sum_probs=19.5
Q ss_pred EEEEEecCHHHHHHHHHHHHhhcc
Q 003989 237 HISISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 237 HVlIsAdteEkVdkAvelIE~LL~ 260 (781)
|+.|+--+.+.++++++.|++++.
T Consensus 329 ~iRis~~~~~~~~~~~~~L~~~~~ 352 (353)
T PRK05387 329 FLRITIGTDEEMEALVDALKEILA 352 (353)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHhh
Confidence 677766688999999999988764
No 142
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=25.53 E-value=78 Score=33.00 Aligned_cols=20 Identities=15% Similarity=0.067 Sum_probs=17.5
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
.-||+||++.|+++-+|...
T Consensus 37 ~~I~~LE~~lg~~Lf~R~~r 56 (296)
T PRK11062 37 GQIKALEERLQGKLFKRKGR 56 (296)
T ss_pred HHHHHHHHHcCccceeecCC
Confidence 35899999999999999864
No 143
>PRK02936 argD acetylornithine aminotransferase; Provisional
Probab=25.18 E-value=4.5e+02 Score=28.49 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=17.9
Q ss_pred EEEEE---ecCHHHHHHHHHHHHhhc
Q 003989 237 HISIS---ADSYEKVDAATDLIELLV 259 (781)
Q Consensus 237 HVlIs---AdteEkVdkAvelIE~LL 259 (781)
++.|+ ..++|.++++++.|+++|
T Consensus 352 ~lRi~p~~~~~~~~i~~~i~~l~~~~ 377 (377)
T PRK02936 352 VIRLLPPLVVTKEELDQAVYLLKKVL 377 (377)
T ss_pred EEEEECCcccCHHHHHHHHHHHHHhC
Confidence 44444 578999999999998765
No 144
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=25.06 E-value=70 Score=32.97 Aligned_cols=21 Identities=24% Similarity=0.238 Sum_probs=18.6
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q 003989 194 DTQKRLEKETRTVIKVYGTKA 214 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkGS 214 (781)
+.||+||++.|+++-+|++|.
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i 55 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPC 55 (294)
T ss_pred HHHHHHHHHhCceeeecCCCC
Confidence 569999999999999998753
No 145
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=24.79 E-value=1e+02 Score=32.23 Aligned_cols=19 Identities=21% Similarity=0.037 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
+.||+||+|.||++-+|..
T Consensus 38 ~~i~~LE~~lg~~Lf~R~~ 56 (305)
T CHL00180 38 LQIKNLEKQLNIPLFDRSK 56 (305)
T ss_pred HHHHHHHHHhCCEEEEecC
Confidence 4589999999999999975
No 146
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=24.77 E-value=82 Score=32.97 Aligned_cols=19 Identities=21% Similarity=0.083 Sum_probs=16.9
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
..||+||++.||++-+|..
T Consensus 35 r~I~~LE~~lg~~LF~R~~ 53 (309)
T PRK12682 35 KAIIELEEELGIEIFIRHG 53 (309)
T ss_pred HHHHHHHHHhCCeeEEECC
Confidence 4699999999999999964
No 147
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=24.34 E-value=1.4e+02 Score=31.78 Aligned_cols=78 Identities=19% Similarity=0.196 Sum_probs=44.0
Q ss_pred EEEEcCCCCCCCCcccceeeCCCc-----------hhHHHHHHHhCC-eEEEeCCccCCCcchhcccCCCCccCCCCceE
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPAS-----------DTQKRLEKETRT-VIKVYGTKADTGEKVEISTSDANVQSTYEEFH 237 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrG-----------nTiKrLEeETGA-KI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLH 237 (781)
+.++--.+-.+.+..+|+|||||| ..+..+-++.-. +|.+|-+. +.-+|
T Consensus 111 d~~iat~~~m~~l~~Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k~g~v~~r~~k-------------------~g~i~ 171 (230)
T PRK05424 111 DVVIATPDMMGKVGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVDK-------------------AGIIH 171 (230)
T ss_pred CEEEECHHHHHHHHHhccccccccCCCCCCCCCcchhHHHHHHHHhcCcEEEEecC-------------------CCEEE
Confidence 444444455566677999999998 345566666643 56666431 11256
Q ss_pred EEEEe---cCHHHHHHHHHHHHhhccccccch
Q 003989 238 ISISA---DSYEKVDAATDLIELLVTSVSGSL 266 (781)
Q Consensus 238 VlIsA---dteEkVdkAvelIE~LL~pve~g~ 266 (781)
|-|-- ++++-++.+...++.|..--..++
T Consensus 172 ~~IG~~~m~~e~i~eNi~a~l~~i~~~~p~~~ 203 (230)
T PRK05424 172 APIGKVSFDAEKLKENLKALIDAIKKAKPATA 203 (230)
T ss_pred EEEeCCCCCHHHHHHHHHHHHHHHHHhCcccc
Confidence 66643 234455555556666655444433
No 148
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=24.09 E-value=1.3e+02 Score=28.02 Aligned_cols=42 Identities=19% Similarity=0.262 Sum_probs=30.0
Q ss_pred hhHHHHHHHHHHHHHHHhcCCCcccCCCCCCCCCCCCCCCCCCCccchHHHHHHHHHHHHHHHHHH
Q 003989 86 GRALAYQTRVDQIVQQLESGSLEAEENQVPEVAAQNADQKSPNPQVDREKLECLELEKQEVIGEIL 151 (781)
Q Consensus 86 ~ra~a~Q~RieEItrkL~sg~le~~~~e~s~SPpP~p~yds~GkRiNTR~rekLEeER~~IIe~ml 151 (781)
.+.-.++-|||.|+++|+.-.+... .|+.||+|...|-+.+.
T Consensus 12 ekl~~cr~~le~ve~rL~~~eLs~e------------------------~R~~lE~E~~~l~~~l~ 53 (85)
T PF15188_consen 12 EKLAQCRRRLEAVESRLRRRELSPE------------------------ARRSLEKELNELKEKLE 53 (85)
T ss_pred HHHHHHHHHHHHHHHHHcccCCChH------------------------HHHHHHHHHHHHHHHhh
Confidence 3566788899999999987766421 35778888777666544
No 149
>PRK13520 L-tyrosine decarboxylase; Provisional
Probab=23.97 E-value=5.1e+02 Score=27.59 Aligned_cols=18 Identities=6% Similarity=0.058 Sum_probs=15.5
Q ss_pred cCHHHHHHHHHHHHhhcc
Q 003989 243 DSYEKVDAATDLIELLVT 260 (781)
Q Consensus 243 dteEkVdkAvelIE~LL~ 260 (781)
.++|.+++.++.++++++
T Consensus 353 ~t~edi~~~~~~l~~~~~ 370 (371)
T PRK13520 353 VTREHIENFLEDLKEVKK 370 (371)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 588999999999998764
No 150
>PF00381 PTS-HPr: PTS HPr component phosphorylation site; InterPro: IPR005698 The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. The overall architecture of the HPr domain has been described as an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. Regulatory phosphorylation at the conserved Ser residue does not appear to induce large structural changes to the HPr domain, in particular in the region of the active site [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TXE_A 1QR5_A 1RZR_S 2NZU_L 2OEN_L 2NZV_L 1Y51_B 1Y4Y_A 1Y50_A 2HPR_A ....
Probab=23.94 E-value=1e+02 Score=27.19 Aligned_cols=60 Identities=12% Similarity=0.108 Sum_probs=35.4
Q ss_pred HHHHHHHhCCeEEEeCCccCCCcchhcccCCCC-ccCCCCceEEEEEecCHHHHHHHHHHHHhhcc
Q 003989 196 QKRLEKETRTVIKVYGTKADTGEKVEISTSDAN-VQSTYEEFHISISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 196 iKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~-~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~ 260 (781)
+-++-++++|+|.|+-++..-+.|.-..- .. .....+.++|.+.|+|++. |++.|+++|+
T Consensus 22 lv~~a~~~~~~i~i~~~~~~vdakSil~l--~~L~~~~G~~i~i~~~G~de~~---a~~~i~~~~~ 82 (84)
T PF00381_consen 22 LVQIASKFDSDITIRKGGKTVDAKSILGL--MSLGAKKGDEIEIEAEGEDEEE---ALEAIAEFLE 82 (84)
T ss_dssp HHHHHHTSSSEEEEEETTEEEETTSHHHH--HHHTBSTTEEEEEEEESTTHHH---HHHHHHHHHH
T ss_pred HHHHHhhCCCEEEEEeCceeEecCCHHHH--hhhhcCCCCEEEEEEECcCHHH---HHHHHHHHHh
Confidence 45677889999999966532222221100 01 2335667999999998854 4444555443
No 151
>KOG2335 consensus tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=23.54 E-value=87 Score=35.68 Aligned_cols=70 Identities=11% Similarity=0.089 Sum_probs=47.5
Q ss_pred HHHHHHHhCCeEEEe----CCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccccccchh
Q 003989 196 QKRLEKETRTVIKVY----GTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSLA 267 (781)
Q Consensus 196 iKrLEeETGAKI~IR----GkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~pve~g~~ 267 (781)
-|+|.+.+||.|.-- -+--++.+|.. ..+-..-.+|.+|-|.|.|+|.+.+-+|+++|+.+.+.+..|++
T Consensus 34 fR~L~R~y~~~l~yTpMi~a~~fv~~ek~r--~~~~st~~~D~PLIvQf~~ndp~~ll~Aa~lv~~y~D~idlNcG 107 (358)
T KOG2335|consen 34 FRRLVRLYGADLLYTPMIHAKTFVHSEKYR--DSELSTSPEDRPLIVQFGGNDPENLLKAARLVQPYCDGIDLNCG 107 (358)
T ss_pred HHHHHHHhCCceEechHHHHHHHhcCccch--hhhcccCCCCCceEEEEcCCCHHHHHHHHHHhhhhcCcccccCC
Confidence 466777777766422 12111111211 11222345788999999999999999999999999999998876
No 152
>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=23.50 E-value=27 Score=30.16 Aligned_cols=25 Identities=20% Similarity=0.440 Sum_probs=21.0
Q ss_pred cccceeeCCCchhHHHHHHHhCCeE
Q 003989 183 NFLGLIFGPASDTQKRLEKETRTVI 207 (781)
Q Consensus 183 NFIGlIIGPrGnTiKrLEeETGAKI 207 (781)
...|.|||-+|.++|+|.++.+-++
T Consensus 34 ~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 34 SQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4779999999999999988876444
No 153
>PRK10632 transcriptional regulator; Provisional
Probab=23.21 E-value=93 Score=32.71 Aligned_cols=20 Identities=25% Similarity=0.288 Sum_probs=17.7
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
..||+||++.||++-+|...
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r 54 (309)
T PRK10632 35 QTVSKLEDELQVKLLNRSTR 54 (309)
T ss_pred HHHHHHHHHhCCeeecccCC
Confidence 45899999999999999864
No 154
>PRK09064 5-aminolevulinate synthase; Validated
Probab=23.20 E-value=6.6e+02 Score=27.59 Aligned_cols=27 Identities=11% Similarity=0.213 Sum_probs=20.5
Q ss_pred EEEEEec---CHHHHHHHHHHHHhhccccc
Q 003989 237 HISISAD---SYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 237 HVlIsAd---teEkVdkAvelIE~LL~pve 263 (781)
++.|+-. ++|.++++++.|++++....
T Consensus 370 ~lRis~~~~~t~edi~~l~~~l~~~~~~~~ 399 (407)
T PRK09064 370 RLRITPTPFHTDEMIDHLVEALVEVWARLG 399 (407)
T ss_pred eEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 3455543 89999999999999987543
No 155
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=22.81 E-value=85 Score=33.14 Aligned_cols=20 Identities=25% Similarity=0.215 Sum_probs=17.4
Q ss_pred hhHHHHHHHhCCeEEEeC-Cc
Q 003989 194 DTQKRLEKETRTVIKVYG-TK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRG-kG 213 (781)
+.||+||++.|+++.+|. +|
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r~ 55 (309)
T PRK12683 35 KQIKDLEDELGVEIFIRRGKR 55 (309)
T ss_pred HHHHHHHHHhCCeeEeeCCCC
Confidence 469999999999999995 44
No 156
>PRK02047 hypothetical protein; Provisional
Probab=22.64 E-value=2.5e+02 Score=25.83 Aligned_cols=59 Identities=19% Similarity=0.201 Sum_probs=38.6
Q ss_pred cccceeeCCCch----hHHHHHHHhCCe-----EEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHH
Q 003989 183 NFLGLIFGPASD----TQKRLEKETRTV-----IKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATD 253 (781)
Q Consensus 183 NFIGlIIGPrGn----TiKrLEeETGAK-----I~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAve 253 (781)
+|-=++||+.+. .+.+|.++..++ |.+|-. .+ | -+--+.|.|.+.++|.+++--+
T Consensus 16 ~~~~KvIG~~~~~~~~~v~~iv~~~~~~~~~~~i~~k~S--s~----------G----kY~Svtv~v~v~s~eq~~~iY~ 79 (91)
T PRK02047 16 DFPIKVMGKAHPEFADTIFKVVSVHDPEFDLEKIEERPS--SG----------G----NYTGLTITVRATSREQLDNIYR 79 (91)
T ss_pred CCeEEEEEeCcHhHHHHHHHHHHHhCCCCccCceEEccC--CC----------C----eEEEEEEEEEECCHHHHHHHHH
Confidence 477799999995 456666666444 333332 11 1 2344789999999999887776
Q ss_pred HHHh
Q 003989 254 LIEL 257 (781)
Q Consensus 254 lIE~ 257 (781)
.+..
T Consensus 80 ~L~~ 83 (91)
T PRK02047 80 ALTG 83 (91)
T ss_pred HHhh
Confidence 6544
No 157
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=22.57 E-value=86 Score=35.52 Aligned_cols=39 Identities=23% Similarity=0.222 Sum_probs=33.7
Q ss_pred cEEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 168 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 168 K~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
+...|+++.+ -.++.||-+|.++|.--+-||++|.|+..
T Consensus 303 ~~~~v~V~~~------~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 303 KAARVVVPDY------QLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred cEEEEEEChh------hcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 4566777764 67999999999999999999999999976
No 158
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=22.56 E-value=69 Score=32.97 Aligned_cols=20 Identities=20% Similarity=0.120 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003989 194 DTQKRLEKETRTVIKVYGTK 213 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkG 213 (781)
+-||+||++.|+++-+|++|
T Consensus 34 ~~I~~LE~~lg~~Lf~R~r~ 53 (292)
T TIGR03298 34 QRIKALEERLGQPLLVRTQP 53 (292)
T ss_pred HHHHHHHHHhCchheecCCC
Confidence 35899999999999999865
No 159
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=22.32 E-value=92 Score=33.32 Aligned_cols=19 Identities=21% Similarity=0.101 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003989 194 DTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGk 212 (781)
..||+||++.|+++-+|..
T Consensus 35 ~~I~~LE~~lG~~LF~R~~ 53 (324)
T PRK12681 35 KQVRMLEDELGIQIFARSG 53 (324)
T ss_pred HHHHHHHHHhCCEeEEECC
Confidence 5699999999999999964
No 160
>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=22.30 E-value=3.8e+02 Score=27.43 Aligned_cols=137 Identities=15% Similarity=0.127 Sum_probs=72.4
Q ss_pred HHHHHHHHHHHhcCCCcccCCC----CCCCCCCCCCCCCCCCccch--HHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCC
Q 003989 92 QTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDR--EKLECLELEKQEVIGEILKLNPSYRTPPDYKP 165 (781)
Q Consensus 92 Q~RieEItrkL~sg~le~~~~e----~s~SPpP~p~yds~GkRiNT--R~rekLEeER~~IIe~mlkliP~frPPsDYkP 165 (781)
++.|++|..+|+.=++++..-. |...|.-.-.--+.||=+=| +..+.+++...++++.+.++.=..+ ..+|+-
T Consensus 16 ~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L~~~g~~~~-~~~~~v 94 (174)
T cd04516 16 KLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARIIQKLGFPAK-FTDFKI 94 (174)
T ss_pred eecHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHHHcCCCCC-CCceEE
Confidence 5678888888866555543311 12222222122456776666 3456777788888887777652222 134431
Q ss_pred CccEEEEEcCCC--------------CCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccC
Q 003989 166 LLKEAVVPIPVK--------------EYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQS 231 (781)
Q Consensus 166 ~~K~~KIyIPvk--------------eyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~ 231 (781)
..-..+..++.+ +|----|=|++.=.. +..+++.|-..|
T Consensus 95 ~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~---------~pk~~~liF~sG------------------ 147 (174)
T cd04516 95 QNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMV---------KPKIVLLIFVSG------------------ 147 (174)
T ss_pred EEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEec---------CCcEEEEEeCCC------------------
Confidence 111122222221 010001223332111 134556666655
Q ss_pred CCCceEEEEEe-cCHHHHHHHHHHHHhhccc
Q 003989 232 TYEEFHISISA-DSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 232 ~~EpLHVlIsA-dteEkVdkAvelIE~LL~p 261 (781)
.|.|+| .++|.+++|++.|-.+|.+
T Consensus 148 -----kvvitGaks~~~~~~a~~~i~p~L~~ 173 (174)
T cd04516 148 -----KIVLTGAKSREEIYQAFENIYPILLQ 173 (174)
T ss_pred -----EEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 577885 5889999999999988864
No 161
>PF04795 PAPA-1: PAPA-1-like conserved region; InterPro: IPR006880 This is a group of proteins with a conserved C-terminal region which is found in PAPA-1, a PAP-1 binding protein, Q9C086 from SWISSPROT.
Probab=22.21 E-value=1.1e+02 Score=28.19 Aligned_cols=60 Identities=17% Similarity=0.092 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCCCCC--CCCccEEEEEcCCCCCCCCcccceeeCCCchhH
Q 003989 137 ECLELEKQEVIGEILKLNPSYRTPPDY--KPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQ 196 (781)
Q Consensus 137 ekLEeER~~IIe~mlkliP~frPPsDY--kP~~K~~KIyIPvkeyP~~NFIGlIIGPrGnTi 196 (781)
+++|||..+-|+++++....-+.-.+- .-........=....+...++|-.|.|+.|.+|
T Consensus 19 Kk~EEeK~eTInKLLkkqa~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~IR~v~~~~G~~v 80 (89)
T PF04795_consen 19 KKLEEEKMETINKLLKKQATRKKREPKDKEGEEDSAQEKKRRAPKPNPPMIRWVSNKNGSRV 80 (89)
T ss_pred HHHHHHHHHHHHHHHhhhccccccchhhhhhhhhccccccccccCCCCCEEEEEECCCceEE
Confidence 579999999999999988622221100 000001111112223556689999998888754
No 162
>PRK00394 transcription factor; Reviewed
Probab=22.14 E-value=2.8e+02 Score=28.52 Aligned_cols=65 Identities=14% Similarity=0.101 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHhcCCCcccCCC----CCCCCCCCCCCCCCCCccch--HHHHHHHHHHHHHHHHHHHhCCC
Q 003989 92 QTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDR--EKLECLELEKQEVIGEILKLNPS 156 (781)
Q Consensus 92 Q~RieEItrkL~sg~le~~~~e----~s~SPpP~p~yds~GkRiNT--R~rekLEeER~~IIe~mlkliP~ 156 (781)
.+.|++|..+|+.-++++..-. |...|.-.-.--+.||=+=| +..+.+.+...++++.+.++.=.
T Consensus 15 ~ldL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~S~~~a~~a~~~~~~~l~~~g~~ 85 (179)
T PRK00394 15 ELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKSVEDLHEAVKIIIKKLKELGIK 85 (179)
T ss_pred CcCHHHHHhhCCCceeCcccCceEEEEecCCceEEEEEcCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCC
Confidence 4578888888876555554321 11222222222456776666 44678888888898888887633
No 163
>PRK07179 hypothetical protein; Provisional
Probab=22.03 E-value=8e+02 Score=27.07 Aligned_cols=27 Identities=15% Similarity=0.105 Sum_probs=20.6
Q ss_pred EEEEEe---cCHHHHHHHHHHHHhhccccc
Q 003989 237 HISISA---DSYEKVDAATDLIELLVTSVS 263 (781)
Q Consensus 237 HVlIsA---dteEkVdkAvelIE~LL~pve 263 (781)
++.|+- .++|.++++++.|+++++..+
T Consensus 371 ~lRis~~~~~t~edi~~~~~~l~~~~~~~~ 400 (407)
T PRK07179 371 LIRLSLNADLTASDLDRVLEVCREARDEVD 400 (407)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHhhC
Confidence 444543 388999999999999988644
No 164
>PRK13393 5-aminolevulinate synthase; Provisional
Probab=22.00 E-value=8.3e+02 Score=26.98 Aligned_cols=26 Identities=4% Similarity=0.190 Sum_probs=20.2
Q ss_pred EEEEEe---cCHHHHHHHHHHHHhhcccc
Q 003989 237 HISISA---DSYEKVDAATDLIELLVTSV 262 (781)
Q Consensus 237 HVlIsA---dteEkVdkAvelIE~LL~pv 262 (781)
+|.|+- .++|.+|+.++.|++++...
T Consensus 369 ~iRis~~~~~t~edid~l~~~l~~~~~~~ 397 (406)
T PRK13393 369 RLRITPSPLHTDADIEHLVQALSEIWARL 397 (406)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHhc
Confidence 455554 38899999999999998654
No 165
>PF00639 Rotamase: PPIC-type PPIASE domain; InterPro: IPR000297 Peptidylprolyl isomerase (5.2.1.8 from EC) is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides []. It has been reported in bacteria and eukayotes. Synonyms for proteins with this domain are: Peptidylprolyl isomerase, Peptidyl-prolyl cis-trans isomerase, PPIase, rotamase, cyclophilin, FKBP65.; GO: 0016853 isomerase activity; PDB: 2JZV_A 2PV3_B 1M5Y_A 2PV2_B 2PV1_A 1JNS_A 1JNT_A 3KAB_A 2ZR6_A 2XPB_A ....
Probab=21.72 E-value=43 Score=29.81 Aligned_cols=41 Identities=17% Similarity=0.127 Sum_probs=32.6
Q ss_pred EEEEEecC-HHHHHHHHHHHHhhccccccchhhhcccccccc
Q 003989 237 HISISADS-YEKVDAATDLIELLVTSVSGSLAAISTSTLVSG 277 (781)
Q Consensus 237 HVlIsAdt-eEkVdkAvelIE~LL~pve~g~~a~~~~~~v~g 277 (781)
||+|..++ .+..+++.+.+++|+..+..|...+.+.++-++
T Consensus 1 HIl~~~~~~~~~~~~~~~~a~~i~~~l~~g~~~F~~~A~~yS 42 (95)
T PF00639_consen 1 HILVKPPPSDEEKDAAKKKAEEIYEQLKKGEDSFAELAREYS 42 (95)
T ss_dssp EEEEESTTSCCHHHHHHHHHHHHHHHHHTTSSSHHHHHHHHC
T ss_pred CEEEECCCchhhHHHHHHHHHHHHHHHHhCchhHHHHHHHhC
Confidence 88888765 788899999999999999998776666655554
No 166
>KOG1478 consensus 3-keto sterol reductase [Lipid transport and metabolism]
Probab=21.67 E-value=1e+02 Score=34.38 Aligned_cols=32 Identities=6% Similarity=0.168 Sum_probs=27.0
Q ss_pred ccCCCCceEEEEEecCHHHHHHHHHHHHhhcc
Q 003989 229 VQSTYEEFHISISADSYEKVDAATDLIELLVT 260 (781)
Q Consensus 229 ~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~ 260 (781)
.+++++-||+.+++.+.+|++++|+.|+..--
T Consensus 26 ~~De~~~ltl~ltcR~~~kae~vc~~lk~f~p 57 (341)
T KOG1478|consen 26 EDDENVRLTLCLTCRNMSKAEAVCAALKAFHP 57 (341)
T ss_pred ccCCceeEEEEEEeCChhHHHHHHHHHHHhCC
Confidence 34566679999999999999999999987655
No 167
>PRK07682 hypothetical protein; Validated
Probab=21.51 E-value=6.6e+02 Score=27.23 Aligned_cols=26 Identities=27% Similarity=0.300 Sum_probs=20.1
Q ss_pred EEEEE-ecCHHHHHHHHHHHHhhcccc
Q 003989 237 HISIS-ADSYEKVDAATDLIELLVTSV 262 (781)
Q Consensus 237 HVlIs-AdteEkVdkAvelIE~LL~pv 262 (781)
||.|+ +.+.+.+++|++.|+++++.+
T Consensus 351 ~iRis~~~~~~~l~~~l~~l~~~l~~~ 377 (378)
T PRK07682 351 FIRCSYATSLEQLQEAMKRMKRFVENK 377 (378)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhc
Confidence 55554 346899999999999988654
No 168
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=21.42 E-value=1.3e+02 Score=26.73 Aligned_cols=37 Identities=16% Similarity=0.316 Sum_probs=29.7
Q ss_pred HhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEe-cCHHHHHHHHHHHHhhccc
Q 003989 202 ETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISA-DSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 202 ETGAKI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsA-dteEkVdkAvelIE~LL~p 261 (781)
+.+|.+.|--.| .|.|+| .++|.+++|++.|..+|..
T Consensus 47 ~p~~t~~IF~sG-----------------------ki~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 47 NPKATVLIFSSG-----------------------KIVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TTTEEEEEETTS-----------------------EEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred CCcEEEEEEcCC-----------------------EEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 346788888776 577876 5999999999999998864
No 169
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=21.00 E-value=6.6e+02 Score=28.17 Aligned_cols=86 Identities=16% Similarity=0.202 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcccceeeCCCch---hHHHHHHHhCCeEEEeC
Q 003989 136 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASD---TQKRLEKETRTVIKVYG 211 (781)
Q Consensus 136 rekLEeER~~IIe~mlkliP~frP-PsDYkP~~K~~KIyIPvkeyP~~NFIGlIIGPrGn---TiKrLEeETGAKI~IRG 211 (781)
++++.+||.+|.+++.++. -++. |++ -|||=.=.+- +. -.+.|.+. .|.||.
T Consensus 265 ~~~~~~~r~rl~~~l~~~~-~~~v~pS~-------------------aNFvlv~~~~-~~~~~l~~~L~~~---giivR~ 320 (356)
T COG0079 265 VERIREERERLYAALKALG-LFGVFPSQ-------------------ANFVLVRVPD-AEAAALAEALLKK---GILVRD 320 (356)
T ss_pred HHHHHHHHHHHHHHHHhCC-CCeecCCC-------------------CcEEEEECCC-ccHHHHHHHHHHC---CEEEEe
Confidence 5667788888888877765 3311 111 3565333332 33 34445443 688888
Q ss_pred CccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhhccc
Q 003989 212 TKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 212 kGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAdteEkVdkAvelIE~LL~p 261 (781)
-++ .+ ..+-|+.|+--+.|.-++-++.+++++..
T Consensus 321 ~~~-~~---------------~~~~~lRitvgt~een~~ll~AL~~~~~~ 354 (356)
T COG0079 321 CSS-VG---------------LLPGYLRITVGTPEENDRLLAALREVLKG 354 (356)
T ss_pred CCC-CC---------------CCCCeEEEEeCCHHHHHHHHHHHHHHHhc
Confidence 753 21 12238999988877778888777777653
No 170
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=20.97 E-value=84 Score=36.77 Aligned_cols=38 Identities=24% Similarity=0.227 Sum_probs=32.6
Q ss_pred EEEEEcCCCCCCCCcccceeeCCCchhHHHHHHHhCCeEEEeCC
Q 003989 169 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 169 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGk 212 (781)
...|+++. +-+++-||-+|.++|...+-||++|.|...
T Consensus 303 ~~~v~V~~------~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 303 SADVVVPD------DQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEEEECc------chHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 45666666 377999999999999999999999999874
No 171
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=20.78 E-value=1.2e+02 Score=32.37 Aligned_cols=79 Identities=11% Similarity=0.147 Sum_probs=45.3
Q ss_pred EEEEcCCCCCCCCcccceeeCCCch-----------hHHHHHHHhCC-eEEEeCCccCCCcchhcccCCCCccCCCCceE
Q 003989 170 AVVPIPVKEYPGYNFLGLIFGPASD-----------TQKRLEKETRT-VIKVYGTKADTGEKVEISTSDANVQSTYEEFH 237 (781)
Q Consensus 170 ~KIyIPvkeyP~~NFIGlIIGPrGn-----------TiKrLEeETGA-KI~IRGkGS~k~~K~E~~~~Dg~~~~~~EpLH 237 (781)
+.++--.+-.+.+..+|+||||||. .+..+-++... +|.+|-+. .--+|
T Consensus 111 d~~iAt~d~m~~l~kLgriLGprGlMP~pk~gTvt~di~~~V~~~k~G~v~~r~dk-------------------~g~i~ 171 (229)
T CHL00129 111 DLLIATPDMMPKLAKLGRVLGPRGLMPSPKSGTVTTDLASAINEFKKGKLEYRADK-------------------TGIVH 171 (229)
T ss_pred CEEEECHHHHHHHHHhcCcccccCCCCCCCCCCccccHHHHHHHHhcCcEEEEecC-------------------CcEEE
Confidence 3444444555666678999999963 35555566543 66776431 11256
Q ss_pred EEEEe---cCHHHHHHHHHHHHhhccccccchh
Q 003989 238 ISISA---DSYEKVDAATDLIELLVTSVSGSLA 267 (781)
Q Consensus 238 VlIsA---dteEkVdkAvelIE~LL~pve~g~~ 267 (781)
|-|-- ++++-++.+..+|+.|+..-..+..
T Consensus 172 ~~VG~~~m~~~~l~eNi~a~l~~i~~~~p~~~k 204 (229)
T CHL00129 172 VLFGKSNFTEEDLLENLQAIYESIEQNRPSGVK 204 (229)
T ss_pred EEEeCCCCCHHHHHHHHHHHHHHHHHhCccccc
Confidence 66632 3455556666666666665444433
No 172
>PRK06939 2-amino-3-ketobutyrate coenzyme A ligase; Provisional
Probab=20.65 E-value=8.8e+02 Score=26.03 Aligned_cols=20 Identities=25% Similarity=0.322 Sum_probs=17.3
Q ss_pred cCHHHHHHHHHHHHhhcccc
Q 003989 243 DSYEKVDAATDLIELLVTSV 262 (781)
Q Consensus 243 dteEkVdkAvelIE~LL~pv 262 (781)
.++|.++++++.|++++...
T Consensus 375 ~~~~~i~~~l~~L~~~~~~~ 394 (397)
T PRK06939 375 HTKEQLDRAIDAFEKVGKEL 394 (397)
T ss_pred CCHHHHHHHHHHHHHHHHHh
Confidence 78999999999999987643
No 173
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=20.64 E-value=89 Score=32.44 Aligned_cols=21 Identities=24% Similarity=0.226 Sum_probs=18.6
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q 003989 194 DTQKRLEKETRTVIKVYGTKA 214 (781)
Q Consensus 194 nTiKrLEeETGAKI~IRGkGS 214 (781)
..||+||++.|+++-.|++|-
T Consensus 35 ~~I~~LE~~lg~~LF~R~~~~ 55 (294)
T PRK03635 35 QRIKALEERVGQVLLVRTQPC 55 (294)
T ss_pred HHHHHHHHHhCceeeecCCCC
Confidence 469999999999999998754
No 174
>PRK07324 transaminase; Validated
Probab=20.62 E-value=4.9e+02 Score=28.48 Aligned_cols=25 Identities=12% Similarity=0.220 Sum_probs=20.4
Q ss_pred EEEEE-ecCHHHHHHHHHHHHhhccc
Q 003989 237 HISIS-ADSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 237 HVlIs-AdteEkVdkAvelIE~LL~p 261 (781)
|+.|+ +.++|.+++|+++|+++|..
T Consensus 345 ~iRis~~~~~~~l~~~l~rl~~~l~~ 370 (373)
T PRK07324 345 HVRIGYCCDTETLKKGLKKLSEFLRE 370 (373)
T ss_pred eEEEEecCCHHHHHHHHHHHHHHHHh
Confidence 66665 55789999999999998864
No 175
>COG0436 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=20.58 E-value=1e+03 Score=26.90 Aligned_cols=26 Identities=19% Similarity=0.186 Sum_probs=20.9
Q ss_pred eEEEEE-ecCHHHHHHHHHHHHhhccc
Q 003989 236 FHISIS-ADSYEKVDAATDLIELLVTS 261 (781)
Q Consensus 236 LHVlIs-AdteEkVdkAvelIE~LL~p 261 (781)
-||.|+ +.+.|.+++|+++|++++..
T Consensus 365 ~~vRis~~~~~~~l~~a~~rl~~~~~~ 391 (393)
T COG0436 365 GYVRLSLATSEETLEEALRRLARFLAE 391 (393)
T ss_pred CeEEEEEecCHHHHHHHHHHHHHHHHh
Confidence 378865 55669999999999998864
No 176
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=20.55 E-value=1.6e+02 Score=31.14 Aligned_cols=28 Identities=21% Similarity=0.256 Sum_probs=20.2
Q ss_pred cceeeCCC-------------chhHHHHHHHhCCeEEEeCC
Q 003989 185 LGLIFGPA-------------SDTQKRLEKETRTVIKVYGT 212 (781)
Q Consensus 185 IGlIIGPr-------------GnTiKrLEeETGAKI~IRGk 212 (781)
+|+||||+ ...++...+|+.++|.+|=+
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~ 157 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLK 157 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEec
Confidence 69999998 44567777777766666643
No 177
>TIGR03538 DapC_gpp succinyldiaminopimelate transaminase. This family of succinyldiaminopimelate transaminases (DapC) includes the experimentally characterized enzyme from Bordatella pertussis. The majority of genes in this family are proximal to genes encoding components of the lysine biosynthesis via diaminopimelate pathway (GenProp0125).
Probab=20.25 E-value=5.9e+02 Score=27.87 Aligned_cols=23 Identities=17% Similarity=0.315 Sum_probs=19.1
Q ss_pred EEEEE-ecCHHHHHHHHHHHHhhc
Q 003989 237 HISIS-ADSYEKVDAATDLIELLV 259 (781)
Q Consensus 237 HVlIs-AdteEkVdkAvelIE~LL 259 (781)
||.|+ +.+++.+++|++.|++++
T Consensus 370 ~~Ris~~~~~~~l~~~l~~l~~~~ 393 (393)
T TIGR03538 370 RVRIALVAPLEECVEAAERIRSFI 393 (393)
T ss_pred EEEEEecCCHHHHHHHHHHHHHhC
Confidence 77777 668999999999998754
Done!