Query 003997
Match_columns 780
No_of_seqs 252 out of 777
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 15:43:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003997.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003997hhsearch_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 1.9E-57 4.1E-62 492.0 38.1 209 66-276 13-254 (554)
2 COG5176 MSL5 Splicing factor ( 100.0 4.3E-39 9.3E-44 321.3 10.9 175 83-261 58-241 (269)
3 cd02395 SF1_like-KH Splicing f 99.9 4.3E-28 9.2E-33 225.7 10.1 110 168-277 1-118 (120)
4 KOG1588 RNA-binding protein Sa 99.9 3.8E-27 8.1E-32 242.4 12.0 143 135-277 54-211 (259)
5 TIGR02696 pppGpp_PNP guanosine 99.3 5.9E-12 1.3E-16 145.8 11.6 95 135-260 548-642 (719)
6 PLN00207 polyribonucleotide nu 99.3 7E-12 1.5E-16 147.7 7.8 100 135-265 654-755 (891)
7 TIGR03591 polynuc_phos polyrib 99.2 2.1E-11 4.6E-16 141.2 9.7 99 135-264 520-619 (684)
8 cd02393 PNPase_KH Polynucleoti 99.2 9.1E-11 2E-15 97.6 7.8 59 168-255 3-61 (61)
9 COG1185 Pnp Polyribonucleotide 99.1 9.5E-11 2E-15 134.3 8.4 100 135-265 521-621 (692)
10 PRK11824 polynucleotide phosph 99.0 2.7E-10 6E-15 132.3 7.5 99 135-264 523-622 (693)
11 cd00105 KH-I K homology RNA-bi 98.7 4.2E-08 9E-13 79.4 7.9 63 169-255 2-64 (64)
12 PF00013 KH_1: KH domain syndr 98.7 1.4E-08 2.9E-13 82.7 4.8 59 169-254 2-60 (60)
13 cd02394 vigilin_like_KH K homo 98.7 3.1E-08 6.7E-13 81.1 6.1 61 169-255 2-62 (62)
14 PRK13763 putative RNA-processi 98.6 6.3E-08 1.4E-12 96.2 6.5 67 168-262 4-73 (180)
15 smart00322 KH K homology RNA-b 98.6 2.6E-07 5.7E-12 73.3 8.4 65 168-258 4-68 (69)
16 cd02396 PCBP_like_KH K homolog 98.5 4.8E-07 1E-11 75.5 7.8 63 169-254 2-64 (65)
17 TIGR03665 arCOG04150 arCOG0415 98.5 1.5E-07 3.3E-12 92.8 5.0 62 171-261 2-66 (172)
18 KOG1067 Predicted RNA-binding 98.4 3.1E-07 6.8E-12 103.9 7.5 98 135-264 566-664 (760)
19 KOG1960 Predicted RNA-binding 98.3 1.4E-05 3.1E-10 88.0 16.3 91 169-267 212-302 (531)
20 TIGR03665 arCOG04150 arCOG0415 98.2 2.4E-06 5.2E-11 84.4 5.9 54 183-261 99-152 (172)
21 PF13014 KH_3: KH domain 98.1 4E-06 8.7E-11 65.0 5.3 28 183-210 1-28 (43)
22 PRK13763 putative RNA-processi 98.1 4.2E-06 9.2E-11 83.3 6.3 54 183-261 105-158 (180)
23 KOG1676 K-homology type RNA bi 98.0 3.4E-05 7.3E-10 88.3 12.3 74 167-262 139-212 (600)
24 KOG1676 K-homology type RNA bi 98.0 2.8E-05 6E-10 89.0 10.7 74 168-265 231-305 (600)
25 KOG2191 RNA-binding protein NO 97.9 7E-05 1.5E-09 81.2 11.0 126 135-280 95-225 (402)
26 PRK04163 exosome complex RNA-b 97.9 1.6E-05 3.5E-10 82.1 5.9 66 169-263 147-212 (235)
27 COG1094 Predicted RNA-binding 97.5 0.00021 4.6E-09 72.8 6.5 56 183-263 112-167 (194)
28 KOG2190 PolyC-binding proteins 96.6 0.0077 1.7E-07 68.9 9.6 103 135-260 105-208 (485)
29 PRK12704 phosphodiesterase; Pr 96.6 0.0081 1.7E-07 69.1 9.6 74 161-261 204-277 (520)
30 KOG2814 Transcription coactiva 96.6 0.0024 5.2E-08 69.6 5.0 62 182-262 66-127 (345)
31 PRK00106 hypothetical protein; 96.5 0.01 2.2E-07 68.6 9.7 77 161-264 219-295 (535)
32 TIGR03319 YmdA_YtgF conserved 96.5 0.0093 2E-07 68.5 9.4 74 161-261 198-271 (514)
33 KOG2191 RNA-binding protein NO 96.5 0.0084 1.8E-07 65.7 8.2 78 168-266 40-117 (402)
34 KOG0119 Splicing factor 1/bran 96.5 0.033 7.2E-07 63.6 13.0 73 8-95 30-104 (554)
35 KOG1960 Predicted RNA-binding 96.4 0.0037 8E-08 69.7 5.1 82 186-274 308-389 (531)
36 KOG2193 IGF-II mRNA-binding pr 96.3 0.0031 6.8E-08 70.6 3.4 75 169-266 201-275 (584)
37 KOG2193 IGF-II mRNA-binding pr 95.6 0.0091 2E-07 67.0 3.3 67 180-261 287-353 (584)
38 PRK12705 hypothetical protein; 94.6 0.073 1.6E-06 61.5 7.0 40 167-211 198-237 (508)
39 COG1094 Predicted RNA-binding 93.7 0.19 4.1E-06 51.8 7.1 65 168-260 9-77 (194)
40 KOG2874 rRNA processing protei 92.9 0.13 2.9E-06 55.6 4.9 27 185-211 161-187 (356)
41 cd02134 NusA_KH NusA_K homolog 92.2 0.24 5.1E-06 41.7 4.5 37 167-209 25-61 (61)
42 COG1097 RRP4 RNA-binding prote 91.8 0.3 6.5E-06 51.8 5.7 38 169-212 148-185 (239)
43 KOG2192 PolyC-binding hnRNP-K 89.1 0.38 8.2E-06 52.1 3.7 72 168-262 124-195 (390)
44 KOG2190 PolyC-binding proteins 89.0 0.94 2E-05 52.4 7.1 70 169-262 45-123 (485)
45 COG1855 ATPase (PilT family) [ 87.9 0.75 1.6E-05 53.2 5.3 63 143-213 464-526 (604)
46 KOG2192 PolyC-binding hnRNP-K 87.3 1.4 3.1E-05 47.8 6.7 67 168-260 316-384 (390)
47 PF13184 KH_5: NusA-like KH do 87.2 0.3 6.5E-06 42.6 1.3 41 170-211 6-47 (69)
48 KOG0633 Histidinol phosphate a 86.7 1.6 3.6E-05 47.6 6.7 102 123-257 270-374 (375)
49 KOG0336 ATP-dependent RNA heli 86.7 0.71 1.5E-05 52.8 4.1 60 182-262 56-115 (629)
50 COG1702 PhoH Phosphate starvat 78.8 3.1 6.8E-05 46.5 5.2 56 182-262 24-81 (348)
51 PRK08406 transcription elongat 76.7 2.9 6.4E-05 40.9 3.9 30 182-211 41-70 (140)
52 PF09981 DUF2218: Uncharacteri 76.5 3.9 8.5E-05 37.2 4.4 65 192-260 11-77 (89)
53 PRK13764 ATPase; Provisional 76.4 2.4 5.3E-05 50.3 3.8 39 168-212 482-520 (602)
54 cd02409 KH-II KH-II (K homolo 76.3 2.1 4.5E-05 34.6 2.3 24 183-206 35-58 (68)
55 PF14611 SLS: Mitochondrial in 64.0 18 0.00038 36.7 6.3 61 183-266 36-96 (210)
56 KOG2113 Predicted RNA binding 63.0 4.6 0.0001 44.9 2.1 55 181-256 34-88 (394)
57 COG0195 NusA Transcription elo 61.8 6 0.00013 40.8 2.6 33 180-212 83-115 (190)
58 KOG3273 Predicted RNA-binding 58.7 5.8 0.00013 41.9 1.8 29 183-211 179-207 (252)
59 cd02414 jag_KH jag_K homology 58.4 12 0.00026 32.7 3.5 27 183-209 34-60 (77)
60 KOG2208 Vigilin [Lipid transpo 58.4 9.9 0.00021 46.4 4.0 62 183-260 357-418 (753)
61 PRK12327 nusA transcription el 57.5 9.4 0.0002 42.9 3.3 42 169-211 233-275 (362)
62 TIGR01952 nusA_arch NusA famil 57.5 8.6 0.00019 38.0 2.7 30 182-211 42-71 (141)
63 TIGR01953 NusA transcription t 57.0 10 0.00022 42.2 3.5 42 169-211 231-273 (341)
64 KOG0334 RNA helicase [RNA proc 55.5 5.1 0.00011 49.9 1.0 84 172-267 901-984 (997)
65 PRK12329 nusA transcription el 55.3 18 0.00038 42.0 5.1 43 168-211 264-307 (449)
66 PRK09986 DNA-binding transcrip 54.4 18 0.00039 37.0 4.5 20 192-211 39-58 (294)
67 KOG4849 mRNA cleavage factor I 53.7 3E+02 0.0066 31.8 13.9 14 762-775 354-367 (498)
68 KOG2279 Kinase anchor protein 53.6 8.8 0.00019 45.3 2.4 40 168-213 69-108 (608)
69 PF13083 KH_4: KH domain; PDB: 53.4 5.2 0.00011 34.3 0.5 30 168-203 30-59 (73)
70 PRK08406 transcription elongat 52.9 11 0.00023 37.1 2.5 36 168-209 100-135 (140)
71 cd02410 archeal_CPSF_KH The ar 51.1 42 0.00091 33.8 6.3 28 182-209 85-112 (145)
72 PRK12328 nusA transcription el 49.1 12 0.00026 42.5 2.4 42 169-211 239-281 (374)
73 KOG2113 Predicted RNA binding 48.7 10 0.00023 42.2 1.9 56 181-256 123-179 (394)
74 TIGR00707 argD acetylornithine 45.7 1.6E+02 0.0034 31.6 10.1 23 236-258 354-379 (379)
75 TIGR01825 gly_Cac_T_rel pyrido 45.6 1.5E+02 0.0033 31.8 10.0 62 182-260 314-381 (385)
76 PF08303 tRNA_lig_kinase: tRNA 45.5 64 0.0014 33.2 6.7 56 137-211 65-120 (168)
77 PRK06418 transcription elongat 44.8 17 0.00036 37.1 2.5 30 182-212 70-99 (166)
78 PRK00089 era GTPase Era; Revie 43.3 51 0.0011 34.6 5.9 66 139-209 193-271 (292)
79 PRK15494 era GTPase Era; Provi 42.0 61 0.0013 35.6 6.5 68 138-210 237-319 (339)
80 PRK11242 DNA-binding transcrip 41.9 39 0.00084 34.6 4.7 19 193-211 34-52 (296)
81 COG0081 RplA Ribosomal protein 41.8 34 0.00075 36.6 4.4 44 168-211 112-167 (228)
82 PRK09202 nusA transcription el 41.3 20 0.00044 41.6 2.8 41 169-210 233-274 (470)
83 TIGR01169 rplA_bact ribosomal 41.2 27 0.00059 36.8 3.5 37 175-211 116-164 (227)
84 PRK11716 DNA-binding transcrip 40.5 39 0.00084 33.7 4.3 19 193-211 10-28 (269)
85 PRK13392 5-aminolevulinate syn 40.2 2.1E+02 0.0046 31.5 10.3 25 236-260 370-397 (410)
86 PRK10837 putative DNA-binding 39.5 41 0.0009 34.3 4.5 19 193-211 36-54 (290)
87 PRK01170 phosphopantetheine ad 39.3 1.8E+02 0.0038 32.7 9.5 84 183-271 86-191 (322)
88 PRK09906 DNA-binding transcrip 38.7 42 0.00091 34.5 4.4 21 192-212 33-53 (296)
89 PRK03601 transcriptional regul 37.5 44 0.00095 34.5 4.3 19 193-211 34-52 (275)
90 PF15188 CCDC-167: Coiled-coil 37.4 63 0.0014 30.0 4.8 42 86-150 12-53 (85)
91 PRK15421 DNA-binding transcrip 36.9 46 0.00099 35.4 4.5 20 192-211 34-53 (317)
92 PRK06107 aspartate aminotransf 36.2 2.3E+02 0.005 31.2 9.8 26 236-261 375-401 (402)
93 PLN02397 aspartate transaminas 35.9 2.4E+02 0.0051 31.7 10.0 81 135-259 338-420 (423)
94 PRK02821 hypothetical protein; 35.1 20 0.00044 32.3 1.3 23 182-204 40-62 (77)
95 PRK00468 hypothetical protein; 34.7 21 0.00046 31.9 1.3 20 182-201 39-58 (75)
96 KOG2208 Vigilin [Lipid transpo 34.1 26 0.00056 43.0 2.3 37 168-210 710-746 (753)
97 PRK11013 DNA-binding transcrip 33.9 38 0.00083 35.4 3.3 20 193-212 37-56 (309)
98 PRK09791 putative DNA-binding 33.4 63 0.0014 33.5 4.7 20 193-212 38-57 (302)
99 TIGR00436 era GTP-binding prot 33.3 97 0.0021 32.5 6.1 67 138-209 185-266 (270)
100 COG1847 Jag Predicted RNA-bind 33.2 92 0.002 33.1 5.8 27 184-210 102-128 (208)
101 PRK10094 DNA-binding transcrip 32.7 59 0.0013 34.3 4.4 19 193-211 35-53 (308)
102 COG0026 PurK Phosphoribosylami 32.6 70 0.0015 36.6 5.2 50 194-257 318-367 (375)
103 KOG4165 Gamma-glutamyl phospha 32.0 51 0.0011 37.5 3.9 27 182-211 190-218 (433)
104 PRK11151 DNA-binding transcrip 31.9 59 0.0013 33.7 4.3 19 193-211 34-52 (305)
105 PRK14322 glmM phosphoglucosami 31.8 3.2E+02 0.007 30.9 10.3 26 234-259 403-428 (429)
106 TIGR03812 tyr_de_CO2_Arch tyro 31.3 2.7E+02 0.0058 29.7 9.1 22 236-257 351-373 (373)
107 PRK01064 hypothetical protein; 31.3 30 0.00065 31.3 1.7 21 183-203 40-60 (78)
108 PRK12328 nusA transcription el 30.8 56 0.0012 37.3 4.1 79 127-213 260-348 (374)
109 PRK11074 putative DNA-binding 30.7 73 0.0016 33.2 4.7 19 193-211 35-53 (300)
110 PRK12680 transcriptional regul 30.6 57 0.0012 35.0 4.0 21 193-213 35-55 (327)
111 PRK02936 argD acetylornithine 30.5 2.9E+02 0.0063 29.9 9.3 23 236-258 352-377 (377)
112 TIGR03418 chol_sulf_TF putativ 29.7 41 0.0009 34.5 2.7 19 193-211 34-52 (291)
113 COG0014 ProA Gamma-glutamyl ph 29.4 81 0.0018 36.5 5.0 31 182-212 195-226 (417)
114 TIGR02424 TF_pcaQ pca operon t 29.0 64 0.0014 33.3 3.9 20 193-212 36-55 (300)
115 PRK09064 5-aminolevulinate syn 28.7 4.4E+02 0.0095 28.9 10.4 28 236-263 370-400 (407)
116 PRK02047 hypothetical protein; 28.1 2.5E+02 0.0053 25.9 7.0 63 177-256 12-83 (91)
117 TIGR02036 dsdC D-serine deamin 28.0 73 0.0016 33.3 4.2 20 193-212 41-60 (302)
118 PRK10887 glmM phosphoglucosami 28.0 2.4E+02 0.0053 32.0 8.5 27 234-260 415-441 (443)
119 COG1837 Predicted RNA-binding 28.0 32 0.0007 31.1 1.3 18 183-200 40-57 (76)
120 TIGR03675 arCOG00543 arCOG0054 27.3 1.1E+02 0.0024 36.9 5.9 60 145-210 71-130 (630)
121 TIGR01953 NusA transcription t 27.3 62 0.0013 36.3 3.6 77 127-211 252-339 (341)
122 cd00652 TBP_TLF TATA box bindi 27.2 3.6E+02 0.0079 27.4 8.8 63 91-153 15-84 (174)
123 PRK08175 aminotransferase; Val 26.8 3.5E+02 0.0077 29.6 9.3 24 236-259 364-388 (395)
124 PRK05424 rplA 50S ribosomal pr 26.8 73 0.0016 33.8 3.9 43 169-211 111-165 (230)
125 PF00126 HTH_1: Bacterial regu 26.8 47 0.001 27.4 2.0 20 193-212 32-51 (60)
126 PRK00394 transcription factor; 26.8 3.4E+02 0.0073 27.9 8.5 64 92-155 15-85 (179)
127 PRK07179 hypothetical protein; 26.5 5.1E+02 0.011 28.5 10.5 27 236-262 371-400 (407)
128 PRK10341 DNA-binding transcrip 26.4 85 0.0018 33.0 4.3 21 192-212 39-59 (312)
129 PRK12329 nusA transcription el 26.0 33 0.00072 39.9 1.3 77 127-211 286-373 (449)
130 PRK10086 DNA-binding transcrip 25.9 69 0.0015 33.7 3.6 21 192-212 46-66 (311)
131 cd04517 TLF TBP-like factors ( 25.9 3.8E+02 0.0083 27.4 8.6 62 91-153 16-84 (174)
132 PRK15092 DNA-binding transcrip 25.7 80 0.0017 33.6 4.0 21 192-212 43-63 (310)
133 PRK11139 DNA-binding transcrip 25.5 74 0.0016 32.9 3.6 19 193-211 39-57 (297)
134 COG3967 DltE Short-chain dehyd 25.4 54 0.0012 35.3 2.6 56 200-263 2-58 (245)
135 PRK04073 rocD ornithine--oxo-a 24.4 4.4E+02 0.0095 29.0 9.5 23 236-258 370-395 (396)
136 KOG4369 RTK signaling protein 24.2 1.2E+02 0.0025 39.7 5.4 79 169-271 1342-1421(2131)
137 PRK10082 cell density-dependen 24.2 72 0.0016 33.3 3.3 19 193-211 44-62 (303)
138 TIGR03339 phn_lysR aminoethylp 24.1 1.2E+02 0.0026 30.5 4.7 19 193-211 30-48 (279)
139 KOG1478 3-keto sterol reductas 24.0 84 0.0018 34.9 3.8 32 228-259 26-57 (341)
140 PRK07682 hypothetical protein; 24.0 5.2E+02 0.011 28.0 9.8 26 236-261 351-377 (378)
141 PRK09801 transcriptional activ 24.0 77 0.0017 33.5 3.5 20 193-212 39-58 (310)
142 PTZ00225 60S ribosomal protein 24.0 1.1E+02 0.0025 32.1 4.7 28 184-211 117-157 (214)
143 PF00381 PTS-HPr: PTS HPr comp 23.8 98 0.0021 27.2 3.6 59 195-258 22-81 (84)
144 PRK13393 5-aminolevulinate syn 23.6 6.9E+02 0.015 27.6 10.8 26 236-261 369-397 (406)
145 PRK11482 putative DNA-binding 23.5 68 0.0015 34.1 3.0 20 193-212 62-81 (317)
146 COG0079 HisC Histidinol-phosph 23.4 5.5E+02 0.012 28.8 10.0 86 135-259 265-353 (356)
147 PRK14997 LysR family transcrip 23.4 1E+02 0.0023 31.8 4.3 20 193-212 35-54 (301)
148 KOG1423 Ras-like GTPase ERA [C 23.3 1.4E+02 0.0031 33.9 5.4 64 135-203 289-359 (379)
149 CHL00129 rpl1 ribosomal protei 23.2 81 0.0018 33.5 3.4 72 170-260 112-198 (229)
150 COG0436 Aspartate/tyrosine/aro 22.9 4.7E+02 0.01 29.5 9.5 26 235-260 365-391 (393)
151 KOG1924 RhoA GTPase effector D 22.8 3.4E+02 0.0074 34.4 8.7 7 375-381 436-442 (1102)
152 KOG2335 tRNA-dihydrouridine sy 22.6 92 0.002 35.5 3.9 39 228-266 69-107 (358)
153 PF00408 PGM_PMM_IV: Phosphogl 22.6 1.3E+02 0.0028 25.8 4.0 25 235-259 49-73 (73)
154 PRK06019 phosphoribosylaminoim 22.5 2E+02 0.0043 31.8 6.4 48 195-256 319-366 (372)
155 COG0583 LysR Transcriptional r 22.5 95 0.0021 31.1 3.6 21 192-212 33-53 (297)
156 PRK13520 L-tyrosine decarboxyl 22.5 4.9E+02 0.011 27.7 9.1 24 236-259 344-370 (371)
157 TIGR03538 DapC_gpp succinyldia 22.4 4.7E+02 0.01 28.6 9.2 24 235-258 369-393 (393)
158 COG1159 Era GTPase [General fu 22.2 1.9E+02 0.0041 32.3 6.1 70 135-209 190-274 (298)
159 PF00639 Rotamase: PPIC-type P 22.2 36 0.00079 30.3 0.6 42 236-277 1-43 (95)
160 PF03420 Peptidase_U9: Prohead 22.0 1.6E+02 0.0035 31.5 5.2 76 135-216 59-147 (213)
161 PRK13348 chromosome replicatio 22.0 82 0.0018 32.5 3.2 21 193-213 35-55 (294)
162 PRK05387 histidinol-phosphate 22.0 7E+02 0.015 26.5 10.2 24 236-259 329-352 (353)
163 PRK06939 2-amino-3-ketobutyrat 22.0 7E+02 0.015 26.8 10.2 19 242-260 375-393 (397)
164 PF04795 PAPA-1: PAPA-1-like c 22.0 1.3E+02 0.0029 27.6 4.1 61 135-195 18-80 (89)
165 PRK11062 nhaR transcriptional 21.6 99 0.0021 32.2 3.7 20 193-212 37-56 (296)
166 PRK12682 transcriptional regul 21.4 99 0.0021 32.3 3.7 20 193-212 35-55 (309)
167 CHL00180 rbcR LysR transcripti 21.2 1.2E+02 0.0027 31.6 4.3 19 193-211 38-56 (305)
168 cd04518 TBP_archaea archaeal T 21.1 4.4E+02 0.0096 27.0 8.0 63 91-153 15-84 (174)
169 KOG2279 Kinase anchor protein 20.9 51 0.0011 39.3 1.5 31 182-212 149-179 (608)
170 PRK02627 acetylornithine amino 20.5 5.1E+02 0.011 28.0 8.9 24 236-259 367-393 (396)
171 TIGR01142 purT phosphoribosylg 20.4 2.9E+02 0.0062 30.1 7.0 25 234-258 353-377 (380)
172 PHA00431 internal virion prote 20.4 1.8E+02 0.0039 35.6 5.7 32 96-152 120-151 (746)
No 1
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=1.9e-57 Score=491.98 Aligned_cols=209 Identities=31% Similarity=0.491 Sum_probs=181.7
Q ss_pred cccccCCCCCCCCC-----c--------------hhhhhhhHHHHHHHHHHHHHHHhhCCCccCCCCCCCCCCCCCCCCC
Q 003997 66 KVVRKTKWGPDLSL-----D--------------ASVKRGRALAYQTRVDQIVQQLESGSLEAEENQVPEVAAQNADQKS 126 (780)
Q Consensus 66 ~rkRKSRWgpdl~~-----d--------------~~v~~~~a~A~QlRIeeIt~KL~tg~l~~~~~e~s~SP~P~p~yds 126 (780)
.|+|+|||..|... + -..++.++|++++||||||+||+++|+.++..+..+||+|+++||.
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 35569999988542 1 1124567899999999999999999998888888899999999999
Q ss_pred CCCchhHH----HHHHHHHHHHHHHHHHHhCCCCCCCCCCCCC-ccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHH
Q 003997 127 PNPQVDRE----LECLELEKQEVIGEILKLNPSYRTPPDYKPL-LKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKE 201 (780)
Q Consensus 127 ~GkR~NTr----RekLEeER~~IIeemlKliP~fRPPsDYkP~-~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeE 201 (780)
.|+|+||| |++||+||++||++|+|+||.||+|.|||+. ++.+|||||+|||||||||||||||||+|+|+||+|
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 99999994 8999999999999999999999999999999 578999999999999999999999999999999999
Q ss_pred hCCeEEEeCCccCCCcchhcccCCCC-ccCCCCceEEEEEecCHHHHHHHHHHHHhcccc---cccchhh-----hcccc
Q 003997 202 TRTVIKVYGTKADTGEKVEISTSDAN-VQSTYEEFHISISADSYEKVDAATDLIELLVTS---VSGSLAA-----ISTST 272 (780)
Q Consensus 202 TGAKI~IRGKGS~k~~K~E~~~~Dg~-~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~p---Vevg~~a-----~~~~~ 272 (780)
|||||.||||||+||+|. +..|.. ...++|+|||+|+||++|+|++|+++||+||.+ +-++..+ +++++
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 999999999999999883 334566 777999999999999999999999999999996 3333333 34446
Q ss_pred cccc
Q 003997 273 LVSG 276 (780)
Q Consensus 273 ~v~g 276 (780)
+.+|
T Consensus 251 ~lNg 254 (554)
T KOG0119|consen 251 RLNG 254 (554)
T ss_pred HhCC
Confidence 6666
No 2
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=100.00 E-value=4.3e-39 Score=321.29 Aligned_cols=175 Identities=25% Similarity=0.339 Sum_probs=157.6
Q ss_pred hhhhhHHHHHH--HHHHHHHHHhhCCCccCCCCCCCCCCCCCCCCCCCCchhHH----HHHHHHHHHHHHHHHHHhCCCC
Q 003997 83 VKRGRALAYQT--RVDQIVQQLESGSLEAEENQVPEVAAQNADQKSPNPQVDRE----LECLELEKQEVIGEILKLNPSY 156 (780)
Q Consensus 83 v~~~~a~A~Ql--RIeeIt~KL~tg~l~~~~~e~s~SP~P~p~yds~GkR~NTr----RekLEeER~~IIeemlKliP~f 156 (780)
+++++.|.||+ |++||+.||+++|.+....+ .+||+|.+.||..|+|+||+ ++||||||+.|++..+|++|.|
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 46788999998 99999999999999877654 35777778999999999994 8999999999999999999999
Q ss_pred CCCCCCCCCcc-EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCC--ccCCCC
Q 003997 157 RTPPDYKPLLK-EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDAN--VQSTYE 233 (780)
Q Consensus 157 RPPsDYkP~~k-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~--~~~~~E 233 (780)
++|.||+...| +.|||||+++||++|||||||||||.|+|+||+.|+|||.|||+||+|++|. .+|.. .....+
T Consensus 137 v~p~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~---ssd~p~~~~N~e~ 213 (269)
T COG5176 137 VLPNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKI---SSDTPESLKNAEA 213 (269)
T ss_pred cCCccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcc---cccCchhhhhhHH
Confidence 99999997764 7999999999999999999999999999999999999999999999998886 34433 456788
Q ss_pred ceEEEEEecCHHHHHHHHHHHHhccccc
Q 003997 234 EFHISISADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 234 pLHVlIsAd~~EkVdkAvelIE~LL~pV 261 (780)
+|||+|++|+++++.++++.|.++|.+.
T Consensus 214 ~lhcLI~adsedki~~~ik~~~n~I~~a 241 (269)
T COG5176 214 VLHCLIEADSEDKICRLIKSQLNAIREA 241 (269)
T ss_pred hHHHHhhcchhhhHHHHHHHHHHHHHHH
Confidence 9999999999999999999999988763
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=4.3e-28 Score=225.74 Aligned_cols=110 Identities=34% Similarity=0.496 Sum_probs=96.5
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecC--HH
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADS--YE 245 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~--~E 245 (780)
++|||||+|+||+|||||+||||||+|+|+||+||||||.|||+||++++++|....+..+++++|+|||+|+|++ .+
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 3799999999999999999999999999999999999999999999999998876555558999999999999999 99
Q ss_pred HHHHHHHHHHhcccccccc------hhhhccccccccc
Q 003997 246 KVDAATDLIELLVTSVSGS------LAAISTSTLVSGE 277 (780)
Q Consensus 246 kVdkAvelIE~LL~pVevg------~~a~~~~~~v~g~ 277 (780)
++++|+++|+.||.++..+ ..-..+++.++|.
T Consensus 81 ~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt 118 (120)
T cd02395 81 ALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGT 118 (120)
T ss_pred HHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhccc
Confidence 9999999999999988765 1234444666653
No 4
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=99.94 E-value=3.8e-27 Score=242.39 Aligned_cols=143 Identities=26% Similarity=0.361 Sum_probs=112.5
Q ss_pred HHHHHHHHHHHHHHHHHh---CCCCCC-CCCC--CCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEE
Q 003997 135 LECLELEKQEVIGEILKL---NPSYRT-PPDY--KPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKV 208 (780)
Q Consensus 135 RekLEeER~~IIeemlKl---iP~fRP-PsDY--kP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~I 208 (780)
.+.|.+|+.++...+.+. ++.-.. ...| ++.+..+||+||+++||+|||||+||||||+|+|+||+||||||.|
T Consensus 54 ~rLL~~Ei~rv~~~~~~~~~~~~~~~~~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~I 133 (259)
T KOG1588|consen 54 ERLLDEEIERVQTSGRQHGSKEPEELPYADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMI 133 (259)
T ss_pred HHHHHHHHHHHHhhhhhccCCCchhcccccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEE
Confidence 455666666655555543 233222 0122 3445679999999999999999999999999999999999999999
Q ss_pred eCCccCCCcchhcc-cCCCCccCCCCceEEEEEecCH-----HHHHHHHHHHHhcccccccchhhhc---cccccccc
Q 003997 209 YGTKADTGEKVEIS-TSDANVQSTYEEFHISISADSY-----EKVDAATDLIELLVTSVSGSLAAIS---TSTLVSGE 277 (780)
Q Consensus 209 RGKGS~k~~K~E~~-~~Dg~~~~~~EpLHVlIsAd~~-----EkVdkAvelIE~LL~pVevg~~a~~---~~~~v~g~ 277 (780)
|||||+|+..+|.+ +.|..|+|.+|||||+|++... .+|.+|++.|++||.+++++...-+ +++..+|.
T Consensus 134 rGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~dk~~QL~ELa~lngt 211 (259)
T KOG1588|consen 134 RGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDEDKREQLRELAILNGT 211 (259)
T ss_pred ecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHhhcCCc
Confidence 99999999888764 5677899999999999998754 4888999999999999999876333 34666664
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=99.32 E-value=5.9e-12 Score=145.76 Aligned_cols=95 Identities=19% Similarity=0.285 Sum_probs=87.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccC
Q 003997 135 LECLELEKQEVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKAD 214 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRPPsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~ 214 (780)
.+..+++|.+|++.|.+.+..+...++|.|. +.++.|+. ++||.||||+|+|||.|++||||+|.|.++|
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--IITVKIPV------DKIGEVIGPKGKMINQIQDETGAEISIEDDG-- 617 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCccccccCCCe--eEEEEeCh------HHhhheeCCCcHhHHHHHHHHCCEEEEecCc--
Confidence 5677888999999999999988337888887 99999999 6999999999999999999999999999986
Q ss_pred CCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccc
Q 003997 215 TGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 215 k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~p 260 (780)
+|.|+|.|.+++++|+++|+.|+..
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=99.26 E-value=7e-12 Score=147.75 Aligned_cols=100 Identities=17% Similarity=0.256 Sum_probs=92.8
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCe-EEEeCCc
Q 003997 135 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTV-IKVYGTK 212 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRP-PsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAK-I~IRGKG 212 (780)
.+...++|.+|+++|.++++.+|. .++|.|. +.++.|+. ++||.||||+|+|||.|++|||++ |.|+++|
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 567788899999999999999998 8899987 99999999 699999999999999999999999 9999986
Q ss_pred cCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccccch
Q 003997 213 ADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSL 265 (780)
Q Consensus 213 S~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVevg~ 265 (780)
+|.|.+.|.+++++|+++|+.|+..+++|.
T Consensus 726 -----------------------~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~ 755 (891)
T PLN00207 726 -----------------------TVKITAKDLSSLEKSKAIISSLTMVPTVGD 755 (891)
T ss_pred -----------------------eEEEEeCCHHHHHHHHHHHHHHhcCcCCCc
Confidence 899999999999999999999998776653
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=99.23 E-value=2.1e-11 Score=141.23 Aligned_cols=99 Identities=21% Similarity=0.297 Sum_probs=90.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCcc
Q 003997 135 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRP-PsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS 213 (780)
.+...++|.+|++.|.+.+..++. .++|.|. ++++.||. ++||.||||+|+|||+|++||||+|.|.++|
T Consensus 520 l~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~--~~~~~I~~------~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG- 590 (684)
T TIGR03591 520 LEQAKEGRLHILGEMNKVISEPRAELSPYAPR--IETIKINP------DKIRDVIGPGGKVIREITEETGAKIDIEDDG- 590 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhccccccCCe--EEEEecCH------HHHHhhcCCCcHHHHHHHHHHCCEEEEecCe-
Confidence 566778899999999999999988 8899987 99999999 6999999999999999999999999999886
Q ss_pred CCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccccc
Q 003997 214 DTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGS 264 (780)
Q Consensus 214 ~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVevg 264 (780)
+|.|.+.+.+++++|+++|+.|+...++|
T Consensus 591 ----------------------~V~i~~~~~~~~~~a~~~I~~~~~~~~~G 619 (684)
T TIGR03591 591 ----------------------TVKIAASDGEAAEAAIKMIEGITAEPEVG 619 (684)
T ss_pred ----------------------EEEEEECcHHHHHHHHHHHHhhhcccccC
Confidence 89999999999999999999998765544
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=99.16 E-value=9.1e-11 Score=97.58 Aligned_cols=59 Identities=25% Similarity=0.374 Sum_probs=54.2
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 247 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkV 247 (780)
.+.|.||. +++|+|||++|.|+|+|+++|||+|.|..+| .|.|+|++.+++
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 67899998 5999999999999999999999999997643 599999999999
Q ss_pred HHHHHHHH
Q 003997 248 DAATDLIE 255 (780)
Q Consensus 248 dkAvelIE 255 (780)
++|+++|+
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=99.13 E-value=9.5e-11 Score=134.26 Aligned_cols=100 Identities=20% Similarity=0.217 Sum_probs=92.4
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCcc
Q 003997 135 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRP-PsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS 213 (780)
.+.+++.|.+||+.|.+.+...|. .+.|+|. ++.+.|++ ++|+.+|||+|+|+|.|.+||||||.|.++|
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr~els~~aPr--i~t~~i~~------dKI~dvIG~gGk~I~~I~eetg~~IdieddG- 591 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPRKELSPYAPR--IETIKIDP------DKIRDVIGPGGKTIKAITEETGVKIDIEDDG- 591 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhccCCc--eEEEccCH------HHHhhccCCcccchhhhhhhhCcEEEecCCC-
Confidence 456677899999999999999996 8889887 89999998 5999999999999999999999999999887
Q ss_pred CCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccccch
Q 003997 214 DTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSL 265 (780)
Q Consensus 214 ~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVevg~ 265 (780)
.|.|.+.+.+++++|+++|+.|+.++++|.
T Consensus 592 ----------------------tv~i~~s~~~~~~~ak~~I~~i~~e~evg~ 621 (692)
T COG1185 592 ----------------------TVKIAASDGESAKKAKERIEAITREVEVGE 621 (692)
T ss_pred ----------------------cEEEEecchHHHHHHHHHHHHHHhhccccc
Confidence 588999999999999999999999999884
No 10
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.04 E-value=2.7e-10 Score=132.27 Aligned_cols=99 Identities=21% Similarity=0.300 Sum_probs=89.5
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCcc
Q 003997 135 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRP-PsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS 213 (780)
.+..+++|.+|+++|.+.+..+|. .++|+|. +..+.|+. ++||.|||++|+|||.|++|||++|.|+++|
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 567778899999999999999998 8888886 77777776 6999999999999999999999999999886
Q ss_pred CCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccccc
Q 003997 214 DTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGS 264 (780)
Q Consensus 214 ~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVevg 264 (780)
+|.|++.+.+++++|+++|+.|+...++|
T Consensus 594 ----------------------~v~i~~~~~~~~~~a~~~I~~~~~~~~vG 622 (693)
T PRK11824 594 ----------------------TVKIAATDGEAAEAAKERIEGITAEPEVG 622 (693)
T ss_pred ----------------------eEEEEcccHHHHHHHHHHHHHhcccCcCC
Confidence 79999999999999999999999876654
No 11
>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=98.73 E-value=4.2e-08 Score=79.44 Aligned_cols=63 Identities=30% Similarity=0.410 Sum_probs=53.1
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 248 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVd 248 (780)
.+|+||. +++|+|||++|+++|+|+++|||+|.|...+. ..++-.|.|.|. .+.++
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 69999999999999999999999999998742 123347889987 78999
Q ss_pred HHHHHHH
Q 003997 249 AATDLIE 255 (780)
Q Consensus 249 kAvelIE 255 (780)
+|..+|+
T Consensus 58 ~a~~~i~ 64 (64)
T cd00105 58 KAKELIL 64 (64)
T ss_pred HHHHHhC
Confidence 9988874
No 12
>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=98.72 E-value=1.4e-08 Score=82.68 Aligned_cols=59 Identities=29% Similarity=0.445 Sum_probs=51.8
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 248 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVd 248 (780)
++|.||. +++|+|||.+|.++|+|+++|||+|.|..++ +.-.|.|+| +.+.|+
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 6999999999999999999999999997762 113799999 999999
Q ss_pred HHHHHH
Q 003997 249 AATDLI 254 (780)
Q Consensus 249 kAvelI 254 (780)
+|+++|
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 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=98.70 E-value=3.1e-08 Score=81.06 Aligned_cols=61 Identities=23% Similarity=0.311 Sum_probs=52.1
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 248 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVd 248 (780)
++|.||. .++|.|||++|+++|+|+++|||+|.|..... .+-.|.|+|. .++|+
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 59999999999999999999999999998741 1237999998 78999
Q ss_pred HHHHHHH
Q 003997 249 AATDLIE 255 (780)
Q Consensus 249 kAvelIE 255 (780)
+|+++|+
T Consensus 56 ~A~~~i~ 62 (62)
T cd02394 56 KAKEEIL 62 (62)
T ss_pred HHHHHhC
Confidence 9999874
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.61 E-value=6.3e-08 Score=96.18 Aligned_cols=67 Identities=21% Similarity=0.321 Sum_probs=59.6
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEE---ecCH
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISIS---ADSY 244 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIs---Ad~~ 244 (780)
+..+.||. +.||+|||++|+|+|.|+++|||+|.|..+. ..|.|. +.|.
T Consensus 4 ~~~i~IP~------~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~----------------------g~V~I~~~~~~d~ 55 (180)
T PRK13763 4 MEYVKIPK------DRIGVLIGKKGETKKEIEERTGVKLEIDSET----------------------GEVIIEPTDGEDP 55 (180)
T ss_pred eEEEEcCH------HHhhhHhccchhHHHHHHHHHCcEEEEECCC----------------------CeEEEEeCCCCCH
Confidence 56888998 6999999999999999999999999999871 168888 8899
Q ss_pred HHHHHHHHHHHhcccccc
Q 003997 245 EKVDAATDLIELLVTSVS 262 (780)
Q Consensus 245 EkVdkAvelIE~LL~pVe 262 (780)
+++++|+++|+.|+...+
T Consensus 56 ~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 56 LAVLKARDIVKAIGRGFS 73 (180)
T ss_pred HHHHHHHHHHHHHhcCCC
Confidence 999999999999998533
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=98.59 E-value=2.6e-07 Score=73.32 Aligned_cols=65 Identities=32% Similarity=0.438 Sum_probs=56.2
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 247 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkV 247 (780)
..+|+|+. +++|+|||.+|+++|+|+++|||+|.|.+.+. +.-.|.|.++ .+.+
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 69999999999999999999999999987642 1237889998 8999
Q ss_pred HHHHHHHHhcc
Q 003997 248 DAATDLIELLV 258 (780)
Q Consensus 248 dkAvelIE~LL 258 (780)
+.|.++|++++
T Consensus 58 ~~a~~~i~~~~ 68 (69)
T smart00322 58 EKAAELILEIL 68 (69)
T ss_pred HHHHHHHHHHh
Confidence 99999998876
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=98.49 E-value=4.8e-07 Score=75.52 Aligned_cols=63 Identities=27% Similarity=0.274 Sum_probs=50.8
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 248 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVd 248 (780)
.+++||. +++|+|||.+|.++|+|+++|||+|.|..... ..+.+--|.|+|+ .+.++
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 5789998 69999999999999999999999999976531 0112224778875 88999
Q ss_pred HHHHHH
Q 003997 249 AATDLI 254 (780)
Q Consensus 249 kAvelI 254 (780)
+|+++|
T Consensus 59 ~A~~~I 64 (65)
T cd02396 59 KALLLI 64 (65)
T ss_pred HHHHhh
Confidence 999987
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=98.47 E-value=1.5e-07 Score=92.78 Aligned_cols=62 Identities=19% Similarity=0.370 Sum_probs=55.1
Q ss_pred EEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCC-ccCCCcchhcccCCCCccCCCCceEEEE--EecCHHHH
Q 003997 171 VPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT-KADTGEKVEISTSDANVQSTYEEFHISI--SADSYEKV 247 (780)
Q Consensus 171 IyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGK-GS~k~~K~E~~~~Dg~~~~~~EpLHVlI--sAd~~EkV 247 (780)
|+||. ++||+|||++|+|+|+|+++|||+|.|..+ | .|.| .+.|.+++
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 699999999999999999999999999976 3 5788 78899999
Q ss_pred HHHHHHHHhccccc
Q 003997 248 DAATDLIELLVTSV 261 (780)
Q Consensus 248 dkAvelIE~LL~pV 261 (780)
++|+++|+.|+..+
T Consensus 53 ~kA~~~I~~i~~gf 66 (172)
T TIGR03665 53 MKAREVVKAIGRGF 66 (172)
T ss_pred HHHHHHHHHHHcCC
Confidence 99999999999853
No 18
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.45 E-value=3.1e-07 Score=103.94 Aligned_cols=98 Identities=18% Similarity=0.257 Sum_probs=84.9
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC-CCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCcc
Q 003997 135 LECLELEKQEVIGEILKLNPSYRT-PPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRP-PsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS 213 (780)
.+++.+.|.+||++|.|.++.+|. ..+|.|. .+.+.+.. .....||||+|...|+|+.|||+.-.| +.|
T Consensus 566 l~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~--~~tlkv~~------sk~~~lIGp~G~~~kki~~EtGai~~v-De~- 635 (760)
T KOG1067|consen 566 LQKAREARLQILDIMEKNINSPRGSDKEYSPV--LETLKVSP------SKRATLIGPGGVLKKKIEVETGAISQV-DEG- 635 (760)
T ss_pred HHhhhHHHHHHHHHHHhhcCCcccCccccCce--eeEEeecc------hhhheeecCccceeeeEeeeccceeee-cCc-
Confidence 678888999999999999999999 8899998 67777776 478899999999999999999943333 332
Q ss_pred CCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccccc
Q 003997 214 DTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGS 264 (780)
Q Consensus 214 ~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVevg 264 (780)
|+.|.|.+...+++|.+.|+.|+....++
T Consensus 636 ----------------------t~~i~A~~~~am~~Ak~~I~~i~~~~~~~ 664 (760)
T KOG1067|consen 636 ----------------------TFSIFAPTQAAMEEAKEFIDGIIKDDQVQ 664 (760)
T ss_pred ----------------------eEEEEecCHHHHHHHHHHHHHHhcCcccc
Confidence 99999999999999999999999886654
No 19
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.33 E-value=1.4e-05 Score=88.02 Aligned_cols=91 Identities=15% Similarity=-0.037 Sum_probs=80.9
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 248 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVd 248 (780)
.|++|++| .|.+|.-+..=|++..+|..+|.|+++++.||||+|+.-+-++ .++.+|+++|+|++.+.+.+.
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 47888887 7889999999999999999999999999999999986433222 677999999999999999999
Q ss_pred HHHHHHHhcccccccchhh
Q 003997 249 AATDLIELLVTSVSGSLAA 267 (780)
Q Consensus 249 kAvelIE~LL~pVevg~~a 267 (780)
+|+++|++|+..++.++--
T Consensus 284 ~A~r~~~nl~~~v~~~~sr 302 (531)
T KOG1960|consen 284 GAPRRKWNLEEKVYINLSR 302 (531)
T ss_pred cchhHHHhHHHHHHHHhhh
Confidence 9999999999999988764
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=98.18 E-value=2.4e-06 Score=84.40 Aligned_cols=54 Identities=31% Similarity=0.500 Sum_probs=49.6
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhccccc
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pV 261 (780)
.+|+|||++|+|+|.||+.|||+|.|.|+ .|.|.| +.+.++.|.++|+.||..-
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~------------------------~v~i~G-~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGK------------------------TVGIIG-DPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCC------------------------EEEEEC-CHHHHHHHHHHHHHHHcCC
Confidence 58999999999999999999999999874 689999 9999999999999999543
No 21
>PF13014 KH_3: KH domain
Probab=98.14 E-value=4e-06 Score=64.98 Aligned_cols=28 Identities=32% Similarity=0.502 Sum_probs=27.1
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEeC
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVIKVYG 210 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI~IRG 210 (780)
|+|+|||++|.|||+|++||||+|.|..
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 22
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.12 E-value=4.2e-06 Score=83.29 Aligned_cols=54 Identities=31% Similarity=0.504 Sum_probs=48.7
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhccccc
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pV 261 (780)
.+|+|||++|+|+|.||+.|||+|.|.++ .|.|.| +.+.++.|.+.|+.|+..-
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~------------------------~v~i~G-~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK------------------------TVAIIG-DPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC------------------------EEEEEe-CHHHHHHHHHHHHHHHcCC
Confidence 68999999999999999999999999865 477887 8999999999999999544
No 23
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.04 E-value=3.4e-05 Score=88.35 Aligned_cols=74 Identities=20% Similarity=0.312 Sum_probs=59.2
Q ss_pred cEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHH
Q 003997 167 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEK 246 (780)
Q Consensus 167 k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~Ek 246 (780)
...+|.||. |++|+|||-+|.|||.|++++|||+.+--+|+... +.+. -+.|++ |.++
T Consensus 139 ttqeI~IPa------~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~-------------~~~K--plritG-dp~~ 196 (600)
T KOG1676|consen 139 TTQEILIPA------NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT-------------GADK--PLRITG-DPDK 196 (600)
T ss_pred eeeeeccCc------cceeeEeccCccHHHHHHhhcCCceEEEecCCcCC-------------CCCC--ceeecC-CHHH
Confidence 467899998 79999999999999999999999998887764321 1222 345666 5789
Q ss_pred HHHHHHHHHhcccccc
Q 003997 247 VDAATDLIELLVTSVS 262 (780)
Q Consensus 247 VdkAvelIE~LL~pVe 262 (780)
|+.|++||.+||.+-.
T Consensus 197 ve~a~~lV~dil~e~~ 212 (600)
T KOG1676|consen 197 VEQAKQLVADILREED 212 (600)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 9999999999999633
No 24
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.00 E-value=2.8e-05 Score=89.01 Aligned_cols=74 Identities=19% Similarity=0.324 Sum_probs=58.5
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCce-EEEEEecCHHH
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEF-HISISADSYEK 246 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpL-HVlIsAd~~Ek 246 (780)
...|.||- +.||+|||=+|+|||+|+.|||+||.++-+.- -+. ++ -+.|.+ +.++
T Consensus 231 ~~~V~VPr------~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~---p~s--------------peR~~~IiG-~~d~ 286 (600)
T KOG1676|consen 231 TREVKVPR------SKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD---PSS--------------PERPAQIIG-TVDQ 286 (600)
T ss_pred eeEEeccc------cceeeEEecCchHHHHHhhccCceeEeecCCC---CCC--------------ccceeeeec-CHHH
Confidence 35666666 79999999999999999999999999986521 011 12 344555 6899
Q ss_pred HHHHHHHHHhcccccccch
Q 003997 247 VDAATDLIELLVTSVSGSL 265 (780)
Q Consensus 247 VdkAvelIE~LL~pVevg~ 265 (780)
|++|.+||++||...+.+-
T Consensus 287 ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 287 IEHAAELINEIIAEAEAGA 305 (600)
T ss_pred HHHHHHHHHHHHHHHhccC
Confidence 9999999999999988874
No 25
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.90 E-value=7e-05 Score=81.22 Aligned_cols=126 Identities=17% Similarity=0.245 Sum_probs=76.3
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCC-CCCc----cEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEe
Q 003997 135 LECLELEKQEVIGEILKLNPSYRTPPDY-KPLL----KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVY 209 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRPPsDY-kP~~----k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IR 209 (780)
.|.|..-...|.||+.+.--.--.+.|. .|.. |+.||.+|- .--|.|||.+|.|||.|+||+||-|.|.
T Consensus 95 ~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPN------stag~iigkggAtiK~~~Eqsga~iqis 168 (402)
T KOG2191|consen 95 VEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPN------STAGMIIGKGGATIKAIQEQSGAWIQIS 168 (402)
T ss_pred HHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccC------CcccceecCCcchHHHHHHhhCcceEec
Confidence 5566655556666665543222223333 3433 678999997 4679999999999999999999999998
Q ss_pred CCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccccchhhhcccccccccccc
Q 003997 210 GTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSLAAISTSTLVSGENVS 280 (780)
Q Consensus 210 GKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVevg~~a~~~~~~v~g~~~~ 280 (780)
-.. ..+ -..++--|.|+++-++.++++..++++|.++++-+..--.--+.|+|.+.|
T Consensus 169 Pqk---pt~-----------~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaN 225 (402)
T KOG2191|consen 169 PQK---PTG-----------ISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVAN 225 (402)
T ss_pred ccC---CCC-----------ccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccc
Confidence 421 111 012223444555444444444455567777766665433333777775543
No 26
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.90 E-value=1.6e-05 Score=82.05 Aligned_cols=66 Identities=20% Similarity=0.148 Sum_probs=59.1
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 248 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVd 248 (780)
..+.||. ++|++|||++|+++|.|.++|+|+|.|-..| +|+|+|.+.++++
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 5677787 6999999999999999999999999997765 8999999999999
Q ss_pred HHHHHHHhccccccc
Q 003997 249 AATDLIELLVTSVSG 263 (780)
Q Consensus 249 kAvelIE~LL~pVev 263 (780)
+|+++|++|-...+.
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=97.47 E-value=0.00021 Score=72.80 Aligned_cols=56 Identities=29% Similarity=0.542 Sum_probs=50.5
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccc
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVS 262 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVe 262 (780)
..|+|||.+|+|.+.||+-|||.|.|.|+ +|.|.| +.+.|+.|.+.|+.|+.-.+
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 46999999999999999999999999999 788888 58899999999999997655
Q ss_pred c
Q 003997 263 G 263 (780)
Q Consensus 263 v 263 (780)
.
T Consensus 167 h 167 (194)
T COG1094 167 H 167 (194)
T ss_pred c
Confidence 3
No 28
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.64 E-value=0.0077 Score=68.87 Aligned_cols=103 Identities=15% Similarity=0.111 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCCCCC-ccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCcc
Q 003997 135 LECLELEKQEVIGEILKLNPSYRTPPDYKPL-LKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRPPsDYkP~-~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS 213 (780)
.+.|.+.-..|+.+..+-+-.+..-...... ....++.||- +-+|-|||=+|+.||+|.++|||+|.|-++ .
T Consensus 105 ~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~------sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~ 177 (485)
T KOG2190|consen 105 TDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPS------SQVGSLIGKGGSLIKEIREETGAKIRVSSD-M 177 (485)
T ss_pred HHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEech------hheeeeeccCcHHHHHHHHhcCceEEecCC-C
Confidence 5666666566666554332222221101111 2357889998 799999999999999999999999999988 1
Q ss_pred CCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccc
Q 003997 214 DTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 214 ~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~p 260 (780)
. ....|.. |.|+| ..++|.+|+..|-.+|.+
T Consensus 178 --l------------P~ster~-V~IsG-~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 178 --L------------PNSTERA-VTISG-EPDAVKKALVQISSRLLE 208 (485)
T ss_pred --C------------Cccccee-EEEcC-chHHHHHHHHHHHHHHHh
Confidence 1 0111222 66766 578999999998888865
No 29
>PRK12704 phosphodiesterase; Provisional
Probab=96.61 E-value=0.0081 Score=69.08 Aligned_cols=74 Identities=22% Similarity=0.157 Sum_probs=57.8
Q ss_pred CCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEE
Q 003997 161 DYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISIS 240 (780)
Q Consensus 161 DYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIs 240 (780)
||.--..+..|.||-| ++-|+|||-.|.+||.||.-|||.|.|.+.- --|+|+
T Consensus 204 ~~~~e~~~~~v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iiddtp----------------------~~v~ls 256 (520)
T PRK12704 204 DHVAETTVSVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDDTP----------------------EAVILS 256 (520)
T ss_pred hhhhhhceeeeecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEcCCC----------------------CeEEEe
Confidence 4433334678889987 6889999999999999999999999999883 267888
Q ss_pred ecCHHHHHHHHHHHHhccccc
Q 003997 241 ADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 241 Ad~~EkVdkAvelIE~LL~pV 261 (780)
+-|...-+.|...++.|+.+.
T Consensus 257 ~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 257 GFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred cCChhhHHHHHHHHHHHHhcC
Confidence 877777667777776666543
No 30
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.60 E-value=0.0024 Score=69.64 Aligned_cols=62 Identities=32% Similarity=0.357 Sum_probs=54.1
Q ss_pred cceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhccccc
Q 003997 182 NFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pV 261 (780)
-|||-|||=+|+|.|+||+||+|+|.|==.+.. | -|+.|++-..+.|-+|.+.|..+|++.
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n---~----------------~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN---K----------------EEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCCCC---c----------------ceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 489999999999999999999999998655421 1 289999999999999999999999876
Q ss_pred c
Q 003997 262 S 262 (780)
Q Consensus 262 e 262 (780)
.
T Consensus 127 r 127 (345)
T KOG2814|consen 127 R 127 (345)
T ss_pred h
Confidence 5
No 31
>PRK00106 hypothetical protein; Provisional
Probab=96.54 E-value=0.01 Score=68.65 Aligned_cols=77 Identities=19% Similarity=0.153 Sum_probs=61.0
Q ss_pred CCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEE
Q 003997 161 DYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISIS 240 (780)
Q Consensus 161 DYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIs 240 (780)
||.--..+..|.+|-| ++-|+|||-.|.+||.+|.-|||.|.|.+.- --|.|+
T Consensus 219 ~~~~e~tvs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliiddtp----------------------~~v~lS 271 (535)
T PRK00106 219 EYVTEQTITTVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIIDDTP----------------------EVVVLS 271 (535)
T ss_pred hhhhhheeeeEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEcCCC----------------------CeEEEe
Confidence 4433334678899987 6889999999999999999999999999883 257888
Q ss_pred ecCHHHHHHHHHHHHhcccccccc
Q 003997 241 ADSYEKVDAATDLIELLVTSVSGS 264 (780)
Q Consensus 241 Ad~~EkVdkAvelIE~LL~pVevg 264 (780)
+-|.-.-+-|...++.|+.+-...
T Consensus 272 ~fdpvRReiAr~~le~Li~dgrIh 295 (535)
T PRK00106 272 GFDPIRREIARMTLESLIKDGRIH 295 (535)
T ss_pred CCChHHHHHHHHHHHHHHHcCCcC
Confidence 888887777777777777764433
No 32
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.54 E-value=0.0093 Score=68.49 Aligned_cols=74 Identities=20% Similarity=0.164 Sum_probs=57.5
Q ss_pred CCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEE
Q 003997 161 DYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISIS 240 (780)
Q Consensus 161 DYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIs 240 (780)
||.--..+..|.||-| ++-|+|||-.|.+||.||.-|||.|.|.+.- --|.|+
T Consensus 198 ~~~~e~~~~~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iiddtp----------------------~~v~ls 250 (514)
T TIGR03319 198 DHVAETTVSVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDDTP----------------------EAVILS 250 (514)
T ss_pred hhhhhheeeeEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEcCCC----------------------CeEEec
Confidence 4433334678899987 6889999999999999999999999999883 157778
Q ss_pred ecCHHHHHHHHHHHHhccccc
Q 003997 241 ADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 241 Ad~~EkVdkAvelIE~LL~pV 261 (780)
+-|.-.-+-|...++.||.+-
T Consensus 251 ~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 251 GFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred CCchHHHHHHHHHHHHHHHcC
Confidence 777766666666666666553
No 33
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.49 E-value=0.0084 Score=65.67 Aligned_cols=78 Identities=27% Similarity=0.278 Sum_probs=53.4
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 247 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkV 247 (780)
..||.||- +-.|.|||-+|.||.+||+||||+|.+--.. |. +.+- -+--|+|.+ +-|.|
T Consensus 40 ~ikvLips------~AaGsIIGKGG~ti~~lqk~tgariklSks~-------df------yPGT-TeRvcli~G-t~eai 98 (402)
T KOG2191|consen 40 FLKVLIPS------YAAGSIIGKGGQTIVQLQKETGARIKLSKSK-------DF------YPGT-TERVCLIQG-TVEAL 98 (402)
T ss_pred EEEEEeec------ccccceeccchHHHHHHHhccCcEEEecccc-------cc------CCCc-cceEEEEec-cHHHH
Confidence 68999998 6899999999999999999999999986221 11 1111 122677777 45566
Q ss_pred HHHHHHHHhcccccccchh
Q 003997 248 DAATDLIELLVTSVSGSLA 266 (780)
Q Consensus 248 dkAvelIE~LL~pVevg~~ 266 (780)
...++.|.+-|.+...+..
T Consensus 99 ~av~efI~dKire~p~~~~ 117 (402)
T KOG2191|consen 99 NAVHEFIADKIREKPQAVA 117 (402)
T ss_pred HHHHHHHHHHHHHhHHhhc
Confidence 6666666655555444333
No 34
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.48 E-value=0.033 Score=63.65 Aligned_cols=73 Identities=18% Similarity=0.008 Sum_probs=49.4
Q ss_pred CCCcccCCCCceeeecccccceecCCCCCCcccceeccCCCC--cccchhhhcCCCCCCCcccccCCCCCCCCCchhhhh
Q 003997 8 TPSTVSNAGPKISKFAAKSGFVIPKNKLSGSLVPVFKGAKKN--DAINEEEKASSNDDGKKVVRKTKWGPDLSLDASVKR 85 (780)
Q Consensus 8 ~~~~~~~~~~kiS~F~AKsGFvIPknkl~Gslv~~fr~~k~~--~a~~~e~~a~~~~~G~~rkRKSRWgpdl~~d~~v~~ 85 (780)
+-|..++..-|++|| ||+|.+||++++|..+|.-.++. .+.-+ -..-|+. |++++..+-+++.
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 9999888777766
Q ss_pred hhHHHHHHHH
Q 003997 86 GRALAYQTRV 95 (780)
Q Consensus 86 ~~a~A~QlRI 95 (780)
.|+.+++.|.
T Consensus 95 ~R~ntRe~R~ 104 (554)
T KOG0119|consen 95 KRLNTREQRA 104 (554)
T ss_pred cchhhHHHHH
Confidence 6666666544
No 35
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=96.43 E-value=0.0037 Score=69.65 Aligned_cols=82 Identities=24% Similarity=0.297 Sum_probs=70.1
Q ss_pred eeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccccch
Q 003997 186 LIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSL 265 (780)
Q Consensus 186 lIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVevg~ 265 (780)
.|.||-|.+.|.|+.|+-..+.|.|-||..-.- ...+..+|+.||.|...+..+|+.|+-+|+.+|.+|+..|
T Consensus 308 ~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p-------~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~~v~~qy 380 (531)
T KOG1960|consen 308 AIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEP-------STNRESDEPIHLCIMSHDPNAIQRAKVLCEDLIASVHQQY 380 (531)
T ss_pred ccccCCcccccccCCCCCcceeccCccceeecC-------CCCCCCCCCcccccccCChhhhhhhhhcccccCCcccccC
Confidence 467899999999999999999999999865211 1256789999999999999999999999999999999999
Q ss_pred hhhcccccc
Q 003997 266 AAISTSTLV 274 (780)
Q Consensus 266 ~a~~~~~~v 274 (780)
++|..-.+-
T Consensus 381 ~~~~~qp~~ 389 (531)
T KOG1960|consen 381 KAWKSQPKD 389 (531)
T ss_pred cccccCCCc
Confidence 998765443
No 36
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.25 E-value=0.0031 Score=70.58 Aligned_cols=75 Identities=17% Similarity=0.224 Sum_probs=54.0
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHH
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVD 248 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVd 248 (780)
.++.+|. .|+|.|||+.|.|||.|-+.|.|||++.-+- .++ .++..+.|+= +.|...
T Consensus 201 lR~lVpt------qyvgaIIGkeG~TIknItkqTqsriD~hrke----n~G----------aaek~itvh~---tpEg~s 257 (584)
T KOG2193|consen 201 LRLLVPT------QYVGAIIGKEGATIKNITKQTQSRIDVHRKE----NAG----------AAEKIITVHS---TPEGTS 257 (584)
T ss_pred eeeeecc------ceeEEEecCCCccccCcchhhhheeeeeecc----cCC----------cccCceEEec---CccchH
Confidence 4677777 4999999999999999999999999998762 111 1122344433 456778
Q ss_pred HHHHHHHhcccccccchh
Q 003997 249 AATDLIELLVTSVSGSLA 266 (780)
Q Consensus 249 kAvelIE~LL~pVevg~~ 266 (780)
+||++|-+|+..-.++.+
T Consensus 258 ~Ac~~ILeimqkEA~~~k 275 (584)
T KOG2193|consen 258 KACKMILEIMQKEAVDDK 275 (584)
T ss_pred HHHHHHHHHHHHhhhccc
Confidence 889998888876544433
No 37
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=95.56 E-value=0.0091 Score=67.04 Aligned_cols=67 Identities=22% Similarity=0.258 Sum_probs=47.3
Q ss_pred CCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhccc
Q 003997 180 GYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 180 ~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~ 259 (780)
..||+|+|||-.|.+||+||.+||+||.|---- |+ ...+-+-.+.|-| +-|.+.+|.++|-+-|+
T Consensus 287 HN~lvGRLIGKeGrnlKkIeq~TgTkITis~lq-------el-------s~ynpERTItVkG-siEac~~AE~eImkKlr 351 (584)
T KOG2193|consen 287 HNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQ-------EL-------SLYNPERTITVKG-SIEACVQAEAEIMKKLR 351 (584)
T ss_pred hcchhhhhhhhccccHHHHHhhcCCceeeeehh-------hh-------cccCccceEEecc-cHHHHHHHHHHHHHHHH
Confidence 459999999999999999999999999996421 11 1112234666777 66777777766666555
Q ss_pred cc
Q 003997 260 SV 261 (780)
Q Consensus 260 pV 261 (780)
+-
T Consensus 352 e~ 353 (584)
T KOG2193|consen 352 EC 353 (584)
T ss_pred HH
Confidence 43
No 38
>PRK12705 hypothetical protein; Provisional
Probab=94.60 E-value=0.073 Score=61.48 Aligned_cols=40 Identities=28% Similarity=0.366 Sum_probs=36.3
Q ss_pred cEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCC
Q 003997 167 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 167 k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGK 211 (780)
.+..|.+|-| +.-|+|||-.|.+||.+|..||+.|.|.+.
T Consensus 198 tvs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 198 SVSVVPIPSD-----AMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred eeeeeecCCh-----HhhccccCccchhHHHHHHhhCCceEecCC
Confidence 4568888876 688999999999999999999999999987
No 39
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=93.66 E-value=0.19 Score=51.83 Aligned_cols=65 Identities=17% Similarity=0.330 Sum_probs=49.9
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEec----C
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISAD----S 243 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd----~ 243 (780)
.+.+.||. +-+|.|||..|++-|.||+.+||+|.|..+.. .|.|... |
T Consensus 9 ~~~v~iPk------~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~----------------------~V~i~~~~~t~D 60 (194)
T COG1094 9 SEAVKIPK------DRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTG----------------------SVTIRTTRKTED 60 (194)
T ss_pred eeeeecCc------hhheeeecccccchHHHHhhcCeEEEEECCCC----------------------eEEEEecCCCCC
Confidence 46788888 48999999999999999999999999998831 3444433 5
Q ss_pred HHHHHHHHHHHHhcccc
Q 003997 244 YEKVDAATDLIELLVTS 260 (780)
Q Consensus 244 ~EkVdkAvelIE~LL~p 260 (780)
.-++.+|.++|+.|=.-
T Consensus 61 p~~~~ka~d~VkAIgrG 77 (194)
T COG1094 61 PLALLKARDVVKAIGRG 77 (194)
T ss_pred hHHHHHHHHHHHHHhcC
Confidence 66777777777765443
No 40
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=92.91 E-value=0.13 Score=55.59 Aligned_cols=27 Identities=37% Similarity=0.415 Sum_probs=25.9
Q ss_pred eeeecCCchhHHHHHHHhCCeEEEeCC
Q 003997 185 GLIFGPASDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 185 GlIIGPrGnTiKrLEeETGAKI~IRGK 211 (780)
-+||||.|.|||.||--|.|-|.|.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~ 187 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN 187 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc
Confidence 589999999999999999999999997
No 41
>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=92.15 E-value=0.24 Score=41.69 Aligned_cols=37 Identities=27% Similarity=0.334 Sum_probs=32.1
Q ss_pred cEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEe
Q 003997 167 KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVY 209 (780)
Q Consensus 167 k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IR 209 (780)
...+|+++. +-+|+.||.+|.++|.+++.+|.+|.|.
T Consensus 25 ~~~~v~V~~------~~~~~aIGk~G~nI~~~~~l~~~~I~v~ 61 (61)
T cd02134 25 KRARVVVPD------DQLGLAIGKGGQNVRLASKLLGEKIDIV 61 (61)
T ss_pred cEEEEEECc------ccceeeECCCCHHHHHHHHHHCCCeEEC
Confidence 356777777 5789999999999999999999999873
No 42
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=91.77 E-value=0.3 Score=51.81 Aligned_cols=38 Identities=21% Similarity=0.221 Sum_probs=33.4
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCc
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKG 212 (780)
.-|.|+. .++-++||.+|..+|.|.++|+|+|.|=-.|
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 5667776 6899999999999999999999999997665
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=89.10 E-value=0.38 Score=52.06 Aligned_cols=72 Identities=17% Similarity=0.255 Sum_probs=54.0
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 247 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkV 247 (780)
+.++.|=+ ...|.|||=+|.-||+|.|.+-|++.|--.-.- ...| .|+|++-..+.|
T Consensus 124 e~rllihq------s~ag~iigrngskikelrekcsarlkift~c~p-------~std----------rv~l~~g~~k~v 180 (390)
T KOG2192|consen 124 ELRLLIHQ------SLAGGIIGRNGSKIKELREKCSARLKIFTECCP-------HSTD----------RVVLIGGKPKRV 180 (390)
T ss_pred hhhhhhhh------hhccceecccchhHHHHHHhhhhhhhhhhccCC-------CCcc----------eEEEecCCcchH
Confidence 45666666 588999999999999999999888877644210 0011 688888888888
Q ss_pred HHHHHHHHhcccccc
Q 003997 248 DAATDLIELLVTSVS 262 (780)
Q Consensus 248 dkAvelIE~LL~pVe 262 (780)
-.++++|-++|.+.-
T Consensus 181 ~~~i~~il~~i~e~p 195 (390)
T KOG2192|consen 181 VECIKIILDLISESP 195 (390)
T ss_pred HHHHHHHHHHhhcCC
Confidence 888888888887643
No 44
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=89.02 E-value=0.94 Score=52.36 Aligned_cols=70 Identities=26% Similarity=0.271 Sum_probs=50.8
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCC-ccCCCcchhcccCCCCccCCCCceEEEEEe------
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT-KADTGEKVEISTSDANVQSTYEEFHISISA------ 241 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGK-GS~k~~K~E~~~~Dg~~~~~~EpLHVlIsA------ 241 (780)
.+|..+.+ .+|.|||=.|.++|+|.+||++||.|... +.. .+--|.|++
T Consensus 45 ~RlL~~~k------evG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c------------------~eRIiti~g~~~~~~ 100 (485)
T KOG2190|consen 45 YRLLCHVK------EVGSIIGKKGDIVKKIRKETESKIRVNESLPGC------------------PERIITITGNRVELN 100 (485)
T ss_pred EEEEeccc------cceeEEccCcHHHHHHhhcccccceeecCCCCC------------------CcceEEEeccccccc
Confidence 47777775 79999999999999999999999999876 211 111233333
Q ss_pred --cCHHHHHHHHHHHHhcccccc
Q 003997 242 --DSYEKVDAATDLIELLVTSVS 262 (780)
Q Consensus 242 --d~~EkVdkAvelIE~LL~pVe 262 (780)
...++|.+|.++|-..+.+.+
T Consensus 101 ~~~~~~al~ka~~~iv~~~~~d~ 123 (485)
T KOG2190|consen 101 LSPATDALFKAFDMIVFKLEEDD 123 (485)
T ss_pred CCchHHHHHHHHHHHhhcccccc
Confidence 366888888888877655333
No 45
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.94 E-value=0.75 Score=53.20 Aligned_cols=63 Identities=24% Similarity=0.303 Sum_probs=45.4
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCcc
Q 003997 143 QEVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 143 ~~IIeemlKliP~fRPPsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS 213 (780)
.+|.+++.+.+|. +.-.++.- .....|+||.+ +|+.+||-+|+.|++||+..|.||.|+-.+.
T Consensus 464 ~~i~~~i~r~~p~-~~eVe~~g-d~~avv~vpe~------~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 464 EEIEREIKRYLPG-DVEVEVVG-DGRAVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred HHHHHHHHHhCCC-CceEEEec-CCeEEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 3455666677765 11111210 12467888874 8999999999999999999999999998753
No 46
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=87.30 E-value=1.4 Score=47.78 Aligned_cols=67 Identities=25% Similarity=0.374 Sum_probs=53.5
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCC--ccCCCcchhcccCCCCccCCCCceEEEEEecCHH
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT--KADTGEKVEISTSDANVQSTYEEFHISISADSYE 245 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGK--GS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~E 245 (780)
...|.||. ++-|-|||-+|.-||+|..|+||.|.|..- |+ |+--+.|++ +++
T Consensus 316 TaQvtip~------dlggsiigkggqri~~ir~esGA~IkidepleGs-------------------edrIitItG-Tqd 369 (390)
T KOG2192|consen 316 TAQVTIPK------DLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGS-------------------EDRIITITG-TQD 369 (390)
T ss_pred eeeEeccc------ccCcceecccchhhhhhhhccCceEEecCcCCCC-------------------CceEEEEec-cHH
Confidence 35788998 589999999999999999999999999874 32 222444555 788
Q ss_pred HHHHHHHHHHhcccc
Q 003997 246 KVDAATDLIELLVTS 260 (780)
Q Consensus 246 kVdkAvelIE~LL~p 260 (780)
.++.|--|+++.++.
T Consensus 370 QIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 370 QIQNAQYLLQNSVKQ 384 (390)
T ss_pred HHhhHHHHHHHHHHh
Confidence 999998888887763
No 47
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.17 E-value=0.3 Score=42.55 Aligned_cols=41 Identities=20% Similarity=0.223 Sum_probs=29.1
Q ss_pred EEEcCCCCCCCCcceeeeecCCchhHHHHHHHh-CCeEEEeCC
Q 003997 170 VVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 211 (780)
Q Consensus 170 KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGK 211 (780)
||-+-.. .+++|-+|..||.+|..+|.|++|. |-||.|=.-
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 4444433 3789999999999999999999999 777766554
No 48
>KOG0633 consensus Histidinol phosphate aminotransferase [Amino acid transport and metabolism]
Probab=86.68 E-value=1.6 Score=47.62 Aligned_cols=102 Identities=15% Similarity=0.143 Sum_probs=61.1
Q ss_pred CCCCCCCchhHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcce-eeeec-CCchhHH-HHH
Q 003997 123 DQKSPNPQVDRELECLELEKQEVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFL-GLIFG-PASDTQK-RLE 199 (780)
Q Consensus 123 ~yds~GkR~NTrRekLEeER~~IIeemlKliP~fRPPsDYkP~~k~~KIyIPvkeyP~~NFI-GlIIG-PrGnTiK-rLE 199 (780)
..+++|+...+.|+.+.+||.+|+.++.++. .. .||- =+- +-||| -+|.| -.|.--| -.|
T Consensus 270 ls~~n~kkme~~rdaiv~er~RL~keLt~v~-~~---~~~~---------gg~----daNFiLi~v~~~~n~~akkly~q 332 (375)
T KOG0633|consen 270 LSDSNGKKMEDVRDAIVRERERLFKELTEVP-FL---NDYP---------GGS----DANFILIEVTGGDNGMAKKLYKQ 332 (375)
T ss_pred cCcccchHHHHHHHHHHHHHHHHHHHhhcCc-cc---cCCC---------Ccc----cccEEEEEEcCCCcHHHHHHHHH
Confidence 3566888888889999999999999876652 11 1110 011 34665 23332 2232222 234
Q ss_pred HHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhc
Q 003997 200 KETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELL 257 (780)
Q Consensus 200 eETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~L 257 (780)
..|.-++.+|=+|+..+.| ..+.|++-++|.-+.-++.++..
T Consensus 333 ~at~~gVvVRfrgse~~c~----------------G~lRitvGt~EentvL~k~~K~~ 374 (375)
T KOG0633|consen 333 DATKMGVVVRFRGSEEGCK----------------GYLRITVGTPEENTVLMKCLKQF 374 (375)
T ss_pred HHHhcceEEEEcCCccccc----------------eeEEEEcCCcccchHHHHHHHhh
Confidence 4466667777777543333 37889988887666666666554
No 49
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=86.65 E-value=0.71 Score=52.78 Aligned_cols=60 Identities=18% Similarity=0.219 Sum_probs=43.3
Q ss_pred cceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhccccc
Q 003997 182 NFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pV 261 (780)
++||.+||=+|..||+||..|+++|.|---. -...|.|.|.+.- -.+|.+.|+.+++..
T Consensus 56 ~mvg~vigrggskik~iq~~tnt~iqii~~~--------------------~e~kv~ifg~~~m-~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 56 EMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD--------------------LEVKVTIFGINHM-RKKAKASIDRGQDKD 114 (629)
T ss_pred hhhheeeccCcchhhhhhcccceeEEEeccC--------------------ceeEEEEechHHH-HHHHHhhHhhhhhhh
Confidence 7999999999999999999999999986431 1135667776542 244556666666544
Q ss_pred c
Q 003997 262 S 262 (780)
Q Consensus 262 e 262 (780)
+
T Consensus 115 e 115 (629)
T KOG0336|consen 115 E 115 (629)
T ss_pred h
Confidence 3
No 50
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=78.83 E-value=3.1 Score=46.49 Aligned_cols=56 Identities=29% Similarity=0.307 Sum_probs=46.3
Q ss_pred cceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHH--hccc
Q 003997 182 NFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIE--LLVT 259 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE--~LL~ 259 (780)
|-+-.|+||.|..++.||+.+|++|.-||. ++.|.++.. .++.|..+++ .++.
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 8888888887 5555
Q ss_pred ccc
Q 003997 260 SVS 262 (780)
Q Consensus 260 pVe 262 (780)
...
T Consensus 79 ~~~ 81 (348)
T COG1702 79 EVR 81 (348)
T ss_pred HHh
Confidence 433
No 51
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=76.69 E-value=2.9 Score=40.90 Aligned_cols=30 Identities=27% Similarity=0.380 Sum_probs=27.6
Q ss_pred cceeeeecCCchhHHHHHHHhCCeEEEeCC
Q 003997 182 NFLGLIFGPASDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGAKI~IRGK 211 (780)
+.+|+.||.+|..+|.|+++.|-||.|=.-
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 52
>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=76.51 E-value=3.9 Score=37.20 Aligned_cols=65 Identities=14% Similarity=0.105 Sum_probs=49.1
Q ss_pred chhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCC--ccCCCCceEEEEEecCHHHHHHHHHHHHhcccc
Q 003997 192 SDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDAN--VQSTYEEFHISISADSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 192 GnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~--~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~p 260 (780)
..++|+|.+-.+-||.++-.+. ++.+....|. ....++-|++.|+|+|.+.|++....|..-|.-
T Consensus 11 ~ryl~qLc~Hf~hk~~v~~d~~----~g~i~f~~G~~~l~a~~~~L~l~vea~~~~~L~~~~~vv~~HL~r 77 (89)
T PF09981_consen 11 SRYLKQLCKHFAHKFEVEWDED----SGRITFPFGTCTLSAEPDALTLRVEAPDAEALARLEDVVARHLER 77 (89)
T ss_dssp HHHHHHHHHHTTTSSEEEE-SS----EEEEE-SSS-EEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCceEEcCC----ceEEEeCCEEEEEEeCCCeEEEEEEeCCHHHHHHHHHHHHHHHHH
Confidence 4689999999999999998752 2334444555 555778899999999999999999888876654
No 53
>PRK13764 ATPase; Provisional
Probab=76.39 E-value=2.4 Score=50.29 Aligned_cols=39 Identities=28% Similarity=0.325 Sum_probs=35.6
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCc
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKG 212 (780)
...|||+.+ .|+.+||-+|++|++||+..|.+|.||-..
T Consensus 482 ~~~v~~~~~------~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 482 KAVVYVPEK------DIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred eEEEEEChh------hhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 568999985 889999999999999999999999999874
No 54
>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=76.29 E-value=2.1 Score=34.55 Aligned_cols=24 Identities=21% Similarity=0.396 Sum_probs=21.3
Q ss_pred ceeeeecCCchhHHHHHHHhCCeE
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVI 206 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI 206 (780)
-.|++||-+|.+++.|+..++-.+
T Consensus 35 ~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 35 QPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CCceEECCCCccHHHHHHHHHHHc
Confidence 379999999999999999998554
No 55
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=64.05 E-value=18 Score=36.69 Aligned_cols=61 Identities=11% Similarity=0.115 Sum_probs=48.4
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccccc
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVS 262 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVe 262 (780)
.+=+|+..+|..++.|-...||||.+.-.- -.+.|+| +...++.+.+.|+++|..+.
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 567899999999999988889999997551 1688888 67788888888888887655
Q ss_pred cchh
Q 003997 263 GSLA 266 (780)
Q Consensus 263 vg~~ 266 (780)
...-
T Consensus 93 ~~~i 96 (210)
T PF14611_consen 93 TEEI 96 (210)
T ss_pred EEEE
Confidence 5433
No 56
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=63.01 E-value=4.6 Score=44.85 Aligned_cols=55 Identities=25% Similarity=0.155 Sum_probs=40.1
Q ss_pred CcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHh
Q 003997 181 YNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIEL 256 (780)
Q Consensus 181 ~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~ 256 (780)
+.|+++|.|++|.+||.|+.+|...|.---+|- | -+++..--.|.|+.|.+.|+.
T Consensus 34 s~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e-------------------e--PiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 34 SEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE-------------------E--PIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred cccceeecccCccccchhhhhhcceeccCCCCC-------------------C--CcceeccCchhHHHHhhcCcc
Confidence 469999999999999999999998776443430 1 234434445678888887765
No 57
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=61.78 E-value=6 Score=40.85 Aligned_cols=33 Identities=18% Similarity=0.166 Sum_probs=29.6
Q ss_pred CCcceeeeecCCchhHHHHHHHhCCeEEEeCCc
Q 003997 180 GYNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 180 ~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKG 212 (780)
+.+-+|..||.+|..+|.|.+|.|-||.|=.-.
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
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=58.66 E-value=5.8 Score=41.86 Aligned_cols=29 Identities=31% Similarity=0.353 Sum_probs=27.7
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEeCC
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI~IRGK 211 (780)
-||+|+|-+|+|--.||+-|.++|.|-+.
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad~ 207 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLADS 207 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecCc
Confidence 58999999999999999999999999887
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=58.44 E-value=12 Score=32.72 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=22.3
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEe
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVIKVY 209 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI~IR 209 (780)
-.|+|||-+|+|++.||-=++.-+.-+
T Consensus 34 ~~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 34 DIGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCCeEECCCCccHHHHHHHHHHHHhhc
Confidence 579999999999999998877555444
No 60
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=58.42 E-value=9.9 Score=46.42 Aligned_cols=62 Identities=15% Similarity=0.268 Sum_probs=46.2
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhcccc
Q 003997 183 FLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~p 260 (780)
+..-|+|.+|..+.+|++++.|+|.++-.|+..... --.++.+.++++++...+.+++|+..
T Consensus 357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v----------------~~~~~~~~~~ka~~~v~~~~~ei~n~ 418 (753)
T KOG2208|consen 357 ELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKV----------------VITGVSANDEKAVEDVEKIIAEILNS 418 (753)
T ss_pred hhhhhcCCCCccHHHHHHhhhhceecccccCCCCCe----------------EEeccccchhHHHHHHHHHHHhhhcc
Confidence 677899999999999999999999999977532111 12234566777777777777777773
No 61
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=57.53 E-value=9.4 Score=42.93 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=34.7
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHh-CCeEEEeCC
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 211 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGK 211 (780)
.||-+=-. .+++|-+|..||++|..++.|.+|. |-||.|=.-
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 46655443 4899999999999999999999999 888888653
No 62
>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=57.51 E-value=8.6 Score=38.02 Aligned_cols=30 Identities=23% Similarity=0.318 Sum_probs=27.5
Q ss_pred cceeeeecCCchhHHHHHHHhCCeEEEeCC
Q 003997 182 NFLGLIFGPASDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGAKI~IRGK 211 (780)
+-+|+.||.+|..+|.|++..|-||.|=.-
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVey 71 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIEY 71 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEEc
Confidence 589999999999999999999999998773
No 63
>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=57.01 E-value=10 Score=42.22 Aligned_cols=42 Identities=14% Similarity=0.233 Sum_probs=35.0
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHh-CCeEEEeCC
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 211 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGK 211 (780)
.||-+=-. .+++|-+|..||.+|..++.|.+|. |-||.|=.-
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 46665544 5899999999999999999999999 888887654
No 64
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=55.52 E-value=5.1 Score=49.95 Aligned_cols=84 Identities=13% Similarity=0.100 Sum_probs=60.9
Q ss_pred EcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHH
Q 003997 172 PIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAAT 251 (780)
Q Consensus 172 yIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAv 251 (780)
-...++||-. .-+++.+= .++.+|.+.++|-|.+||+=-- .+|. -...++-||.+|.+.++..|++|+
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-ARWRVTYK--EALLRISEPTAAGITTRGKFNP-PGKE--------PKPGERKLYLLVEGPDELSVQRAI 968 (997)
T ss_pred eccccccchh-cceeeech--hhhhhccCccccceeeccccCC-CCCC--------CCCcchhhhhhhhcchhHHHHHHH
Confidence 3445667743 44555543 3499999999999999998311 0010 123566799999999999999999
Q ss_pred HHHHhcccccccchhh
Q 003997 252 DLIELLVTSVSGSLAA 267 (780)
Q Consensus 252 elIE~LL~pVevg~~a 267 (780)
+.++.+|.+...+...
T Consensus 969 ~e~~r~l~e~~~~~~~ 984 (997)
T KOG0334|consen 969 EELERLLEEEVVNLFS 984 (997)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999998877766654
No 65
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=55.35 E-value=18 Score=42.01 Aligned_cols=43 Identities=12% Similarity=0.102 Sum_probs=35.2
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHh-CCeEEEeCC
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 211 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGK 211 (780)
..||-|=.. .+++|-||..||.+|..||.|.+|. |-||.|=.=
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 356655543 4799999999999999999999999 888888653
No 66
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=54.44 E-value=18 Score=36.97 Aligned_cols=20 Identities=25% Similarity=0.150 Sum_probs=18.0
Q ss_pred chhHHHHHHHhCCeEEEeCC
Q 003997 192 SDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 192 GnTiKrLEeETGAKI~IRGK 211 (780)
.+.||+||++.|+++-+|..
T Consensus 39 S~~i~~LE~~lg~~Lf~R~~ 58 (294)
T PRK09986 39 SIHIKELEDQLGTPLFIRHS 58 (294)
T ss_pred HHHHHHHHHHhCCeeEeeCC
Confidence 45799999999999999985
No 67
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=53.71 E-value=3e+02 Score=31.75 Aligned_cols=14 Identities=36% Similarity=0.676 Sum_probs=11.1
Q ss_pred CCCCCChhHHHHhh
Q 003997 762 RKPENDPEYEDLMA 775 (780)
Q Consensus 762 ~k~e~dpeyedlma 775 (780)
+-+-.|.||||+|.
T Consensus 354 ~~plSeAEFEdiM~ 367 (498)
T KOG4849|consen 354 MFPLSEAEFEDIMT 367 (498)
T ss_pred CccchHHHHHHHHh
Confidence 44567899999996
No 68
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=53.58 E-value=8.8 Score=45.33 Aligned_cols=40 Identities=25% Similarity=0.339 Sum_probs=36.0
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCcc
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS 213 (780)
..++.+++ .++-+|||=.|.++|.|++.|++||.++.+-+
T Consensus 69 ~~e~Vv~~------e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~ 108 (608)
T KOG2279|consen 69 EIEMVVPQ------EAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV 108 (608)
T ss_pred eeeEeecc------cceeeeeccccCCcchhhcccccceecCcccC
Confidence 46888888 49999999999999999999999999998854
No 69
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=53.39 E-value=5.2 Score=34.29 Aligned_cols=30 Identities=23% Similarity=0.187 Sum_probs=23.0
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhC
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETR 203 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETG 203 (780)
...+.|.. +-.|+|||-+|+|++.||--.+
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 70
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=52.92 E-value=11 Score=37.08 Aligned_cols=36 Identities=14% Similarity=0.182 Sum_probs=29.4
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEe
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVY 209 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IR 209 (780)
...++|+. +-+|++||-+|.|+|.+++-+|-+|.|.
T Consensus 100 ~~~V~V~~------~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 100 VAYVEVAP------EDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EEEEEECc------cccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 34555665 3679999999999999999999888774
No 71
>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=51.13 E-value=42 Score=33.79 Aligned_cols=28 Identities=29% Similarity=0.375 Sum_probs=24.6
Q ss_pred cceeeeecCCchhHHHHHHHhCCeEEEe
Q 003997 182 NFLGLIFGPASDTQKRLEKETRTVIKVY 209 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGAKI~IR 209 (780)
.+-|++||-+|.|+++|-++||-+-.|.
T Consensus 85 eKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 85 EKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred cCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 3679999999999999999999776664
No 72
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=49.12 E-value=12 Score=42.48 Aligned_cols=42 Identities=19% Similarity=0.165 Sum_probs=34.7
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHh-CCeEEEeCC
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYGT 211 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRGK 211 (780)
.||-|=- ..+++|-||..||.+|..++.|.+|. |-||.|=.-
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 4665544 34799999999999999999999999 888887653
No 73
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=48.74 E-value=10 Score=42.23 Aligned_cols=56 Identities=27% Similarity=0.289 Sum_probs=40.4
Q ss_pred CcceeeeecCCchhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHH-HHHHh
Q 003997 181 YNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAAT-DLIEL 256 (780)
Q Consensus 181 ~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAv-elIE~ 256 (780)
+-.+|+|.||.|+|+|+||+.++.-|.--.+-+ |+ -.+|++.+...+++|- +.||.
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~-------------------~~-Vf~Vtg~~~nC~kra~s~eie~ 179 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVRCG-------------------EP-VFCVTGAPKNCVKRARSCEIEQ 179 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeeccCC-------------------Cc-eEEEecCCcchhhhccccchhh
Confidence 469999999999999999999998887666521 11 2346666666666665 55544
No 74
>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=45.75 E-value=1.6e+02 Score=31.62 Aligned_cols=23 Identities=17% Similarity=0.206 Sum_probs=19.2
Q ss_pred EEEEE---ecCHHHHHHHHHHHHhcc
Q 003997 236 HISIS---ADSYEKVDAATDLIELLV 258 (780)
Q Consensus 236 HVlIs---Ad~~EkVdkAvelIE~LL 258 (780)
++.|+ ..+.|.++++++.|+++|
T Consensus 354 ~lRi~~~~~~t~~~i~~~~~~l~~~~ 379 (379)
T TIGR00707 354 VLRFLPPLIITKEEIDEAVSALEEAI 379 (379)
T ss_pred EEEEECCCcCCHHHHHHHHHHHHHhC
Confidence 56776 578999999999999875
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=45.62 E-value=1.5e+02 Score=31.80 Aligned_cols=62 Identities=18% Similarity=0.143 Sum_probs=36.7
Q ss_pred cceeeeecCC---chhHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEE---ecCHHHHHHHHHHHH
Q 003997 182 NFLGLIFGPA---SDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISIS---ADSYEKVDAATDLIE 255 (780)
Q Consensus 182 NFIGlIIGPr---GnTiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIs---Ad~~EkVdkAvelIE 255 (780)
++++.+++.. ....++|.++ | |.|++.+.....+ ...+|.|+ ..++|.|+++++.|+
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 5677776643 2234566665 5 4556543211000 11255554 479999999999999
Q ss_pred hcccc
Q 003997 256 LLVTS 260 (780)
Q Consensus 256 ~LL~p 260 (780)
++++.
T Consensus 377 ~~~~~ 381 (385)
T TIGR01825 377 KVGKE 381 (385)
T ss_pred HHHHH
Confidence 98853
No 76
>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=45.48 E-value=64 Score=33.19 Aligned_cols=56 Identities=18% Similarity=0.377 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCC
Q 003997 137 CLELEKQEVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 137 kLEeER~~IIeemlKliP~fRPPsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGK 211 (780)
-+..||.+|++.+.++.+.|.+ |.- ++.||++-.-... .+.+|.+-|--+|.=||+
T Consensus 65 h~~reR~ql~~~~~~~~~~yl~---~~~---------------~~r~VaL~fv~~~-~~~~i~~it~~RV~~RGD 120 (168)
T PF08303_consen 65 HQKRERKQLFEDVSQLKPDYLP---YDT---------------NVRFVALNFVHDD-DLDEIRRITQDRVLARGD 120 (168)
T ss_pred chHHHHHHHHHHHHHhcccccc---cCC---------------CeEEEEEEccCCC-CHHHHHHHHHHHHHhcCc
Confidence 4678999999999998876653 211 2235555554444 567777777777777776
No 77
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=44.77 E-value=17 Score=37.07 Aligned_cols=30 Identities=13% Similarity=0.199 Sum_probs=26.8
Q ss_pred cceeeeecCCchhHHHHHHHhCCeEEEeCCc
Q 003997 182 NFLGLIFGPASDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGAKI~IRGKG 212 (780)
.. |+-||.+|.++|+|++..|-+|.|=+..
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 9999999999999999999999887753
No 78
>PRK00089 era GTPase Era; Reviewed
Probab=43.33 E-value=51 Score=34.63 Aligned_cols=66 Identities=17% Similarity=0.240 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHhCCCCCC--CCCCCC--Ccc-EEEEEcCCCCCCCCcceeeeecCCchhHHHH--------HHHhCCe
Q 003997 139 ELEKQEVIGEILKLNPSYRT--PPDYKP--LLK-EAVVPIPVKEYPGYNFLGLIFGPASDTQKRL--------EKETRTV 205 (780)
Q Consensus 139 EeER~~IIeemlKliP~fRP--PsDYkP--~~k-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrL--------EeETGAK 205 (780)
|--|..|+..+.+-+|.-.. ..+|.. ..+ ...||+..+ .-.+.|||-+|++||+| |+-+|||
T Consensus 193 EiiRe~~~~~l~~e~p~~~~v~~~~~~~~~~~~i~~~i~v~~~-----~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~ 267 (292)
T PRK00089 193 EIIREKLLRLLGDELPYSVAVEIEKFEERGLVRIEATIYVERD-----SQKGIIIGKGGAMLKKIGTEARKDIEKLLGKK 267 (292)
T ss_pred HHHHHHHHhhCCccCCceEEEEEEEEEECCeEEEEEEEEEccC-----CceeEEEeCCcHHHHHHHHHHHHHHHHHhCCC
Confidence 33377777777776665322 112211 112 246666665 44789999999999865 5567777
Q ss_pred EEEe
Q 003997 206 IKVY 209 (780)
Q Consensus 206 I~IR 209 (780)
|.++
T Consensus 268 v~l~ 271 (292)
T PRK00089 268 VFLE 271 (292)
T ss_pred EEEE
Confidence 7665
No 79
>PRK15494 era GTPase Era; Provisional
Probab=41.96 E-value=61 Score=35.64 Aligned_cols=68 Identities=16% Similarity=0.291 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHhCCCCCC--CCCCCCC----cc-EEEEEcCCCCCCCCcceeeeecCCchhHHHH--------HHHh
Q 003997 138 LELEKQEVIGEILKLNPSYRT--PPDYKPL----LK-EAVVPIPVKEYPGYNFLGLIFGPASDTQKRL--------EKET 202 (780)
Q Consensus 138 LEeER~~IIeemlKliP~fRP--PsDYkP~----~k-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrL--------EeET 202 (780)
.|-=|.+|+..+-+=+|.-.. ...|+-. .+ ...||+.-+ .--|.|||-+|++||+| |+-.
T Consensus 237 ~eiiRe~~~~~~~~EiP~~~~v~i~~~~~~~~~~~~i~~~i~v~~~-----sqk~iiiG~~g~~ik~i~~~ar~~le~~~ 311 (339)
T PRK15494 237 AEITREQLFLNLQKELPYKLTVQTEKWEDLKDKSVKINQVIVVSRE-----SYKTIILGKNGSKIKEIGAKSRMQMERFF 311 (339)
T ss_pred HHHHHHHHHhhCCcccCceEEEEEEEEEEcCCCeEEEEEEEEECCC-----CceeEEEcCCcHHHHHHHHHHHHHHHHHh
Confidence 444577777777776665333 2223211 11 257777765 45789999999999864 6667
Q ss_pred CCeEEEeC
Q 003997 203 RTVIKVYG 210 (780)
Q Consensus 203 GAKI~IRG 210 (780)
||||.++=
T Consensus 312 ~~~v~l~l 319 (339)
T PRK15494 312 GFPVHLFL 319 (339)
T ss_pred CCCeEEEE
Confidence 77777653
No 80
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=41.94 E-value=39 Score=34.58 Aligned_cols=19 Identities=11% Similarity=0.046 Sum_probs=17.3
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
+.||+||++.|+++-+|++
T Consensus 34 ~~i~~LE~~lg~~Lf~R~~ 52 (296)
T PRK11242 34 QQIRQLEESLGVQLFDRSG 52 (296)
T ss_pred HHHHHHHHHhCCeeEeEcC
Confidence 5699999999999999974
No 81
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=41.84 E-value=34 Score=36.59 Aligned_cols=44 Identities=16% Similarity=0.167 Sum_probs=31.7
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchh-----------HHHHHHHhCC-eEEEeCC
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDT-----------QKRLEKETRT-VIKVYGT 211 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnT-----------iKrLEeETGA-KI~IRGK 211 (780)
.+.++.-.+-.+.+-.+|.||||||.. +..+.+|... +|.+|=+
T Consensus 112 fD~~IAtpdmM~~v~~LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K~g~v~~R~d 167 (228)
T COG0081 112 FDVFIATPDMMPLVGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRAD 167 (228)
T ss_pred CCEEEECchHHHHHHHHhhhcCCCCCCCCCCCCCCCcCHHHHHHHHhcCcEEEEEC
Confidence 456666677777788899999999963 4556666655 6666665
No 82
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=41.26 E-value=20 Score=41.61 Aligned_cols=41 Identities=15% Similarity=0.191 Sum_probs=34.3
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHh-CCeEEEeC
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKET-RTVIKVYG 210 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeET-GAKI~IRG 210 (780)
.||-|=- ..++++-||..||.+|..++.|.+|. |-||.|=.
T Consensus 233 aKvAV~s-~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 274 (470)
T PRK09202 233 AKIAVKS-NDPRIDPVGACVGMRGSRIQAISNELGGEKIDIIL 274 (470)
T ss_pred eEEEEEc-CCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEE
Confidence 4665543 45899999999999999999999999 88888765
No 83
>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=41.25 E-value=27 Score=36.82 Aligned_cols=37 Identities=16% Similarity=0.211 Sum_probs=24.7
Q ss_pred CCCCCCCcceeeeecCCc-----------hhHHHHHHHhCC-eEEEeCC
Q 003997 175 VKEYPGYNFLGLIFGPAS-----------DTQKRLEKETRT-VIKVYGT 211 (780)
Q Consensus 175 vkeyP~~NFIGlIIGPrG-----------nTiKrLEeETGA-KI~IRGK 211 (780)
.+-.+.+..+|+|||||| ..+..+.++... +|.+|-+
T Consensus 116 ~~~m~~l~~Lg~iLGPrGlMP~~k~gtv~~di~~~I~~~k~g~v~~r~~ 164 (227)
T TIGR01169 116 PDMMRVVGKLGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEFRAD 164 (227)
T ss_pred HHHHHHHHHhccccccccCCCCCCCCCccccHHHHHHHHHcCcEEEEeC
Confidence 344455667899999996 346666666643 5666644
No 84
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=40.45 E-value=39 Score=33.72 Aligned_cols=19 Identities=26% Similarity=0.247 Sum_probs=17.0
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
..||+||++.|+++-+|..
T Consensus 10 ~~I~~LE~~lg~~Lf~R~~ 28 (269)
T PRK11716 10 RQIQRLEEELGQPLFVRDN 28 (269)
T ss_pred HHHHHHHHHhCCeeEEecC
Confidence 4689999999999999975
No 85
>PRK13392 5-aminolevulinate synthase; Provisional
Probab=40.23 E-value=2.1e+02 Score=31.49 Aligned_cols=25 Identities=16% Similarity=0.227 Sum_probs=19.9
Q ss_pred EEEEE---ecCHHHHHHHHHHHHhcccc
Q 003997 236 HISIS---ADSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 236 HVlIs---Ad~~EkVdkAvelIE~LL~p 260 (780)
++.|+ ..++|.+|++++.|+++++.
T Consensus 370 ~lRis~~~~~t~edid~l~~aL~~~~~~ 397 (410)
T PRK13392 370 RLRITPTPLHDDEDIDALVAALVAIWDR 397 (410)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence 56666 46889999999999998764
No 86
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=39.53 E-value=41 Score=34.28 Aligned_cols=19 Identities=11% Similarity=-0.115 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
+.||+||++.||++-+|..
T Consensus 36 ~~I~~LE~~lg~~Lf~R~~ 54 (290)
T PRK10837 36 AALTDLEGQLGVQLFDRVG 54 (290)
T ss_pred HHHHHHHHHhCCccEeecC
Confidence 4689999999999999975
No 87
>PRK01170 phosphopantetheine adenylyltransferase/unknown domain fusion protein; Provisional
Probab=39.30 E-value=1.8e+02 Score=32.71 Aligned_cols=84 Identities=15% Similarity=0.192 Sum_probs=51.2
Q ss_pred ceeeeecC----CchhHHHHHHHhCCe-EEEe-------CCc----cCCCcchhcccCCCCccCCCCceEEEEEecCHHH
Q 003997 183 FLGLIFGP----ASDTQKRLEKETRTV-IKVY-------GTK----ADTGEKVEISTSDANVQSTYEEFHISISADSYEK 246 (780)
Q Consensus 183 FIGlIIGP----rGnTiKrLEeETGAK-I~IR-------GKG----S~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~Ek 246 (780)
+=.+++++ ++.-|+++.+|-|.+ +.|. +.| |.+-.++|+. . .-....+++|.|-..|.-|
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 33456665 788999999999976 2222 222 1111222221 1 1123457999999999999
Q ss_pred HHHHHHHHHhc------ccccccchhhhccc
Q 003997 247 VDAATDLIELL------VTSVSGSLAAISTS 271 (780)
Q Consensus 247 VdkAvelIE~L------L~pVevg~~a~~~~ 271 (780)
++++.+.++.+ +..+++.++ ..+.
T Consensus 162 i~Av~~af~~~f~~~~~v~~v~v~Sg-~~QP 191 (322)
T PRK01170 162 INAVRRFFESLMKNFIVVKNIDYKLE-TQQP 191 (322)
T ss_pred HHHHHHHHHHhcCCCceEEEeeCCCC-CCCC
Confidence 98888877765 444555555 4444
No 88
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=38.75 E-value=42 Score=34.51 Aligned_cols=21 Identities=24% Similarity=0.191 Sum_probs=18.0
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003997 192 SDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 192 GnTiKrLEeETGAKI~IRGKG 212 (780)
.+.||+||++.||++-+|..+
T Consensus 33 Sr~i~~LE~~lg~~Lf~R~~~ 53 (296)
T PRK09906 33 SQQIKDLENCVGVPLLVRDKR 53 (296)
T ss_pred HHHHHHHHHHhCCeeeeeCCC
Confidence 356999999999999999653
No 89
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=37.51 E-value=44 Score=34.49 Aligned_cols=19 Identities=11% Similarity=-0.010 Sum_probs=16.9
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
+.||+||+|.|+++-+|..
T Consensus 34 ~~I~~LE~~lG~~LF~R~~ 52 (275)
T PRK03601 34 FRIRQLENQLGVNLFTRHR 52 (275)
T ss_pred HHHHHHHHHhCCceEEECC
Confidence 4589999999999999964
No 90
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=37.36 E-value=63 Score=29.95 Aligned_cols=42 Identities=19% Similarity=0.265 Sum_probs=29.0
Q ss_pred hhHHHHHHHHHHHHHHHhhCCCccCCCCCCCCCCCCCCCCCCCCchhHHHHHHHHHHHHHHHHHH
Q 003997 86 GRALAYQTRVDQIVQQLESGSLEAEENQVPEVAAQNADQKSPNPQVDRELECLELEKQEVIGEIL 150 (780)
Q Consensus 86 ~~a~A~QlRIeeIt~KL~tg~l~~~~~e~s~SP~P~p~yds~GkR~NTrRekLEeER~~IIeeml 150 (780)
.+...++-|||.|+++|+...+...+ |+.||+|...|.+.+.
T Consensus 12 ekl~~cr~~le~ve~rL~~~eLs~e~-----------------------R~~lE~E~~~l~~~l~ 53 (85)
T PF15188_consen 12 EKLAQCRRRLEAVESRLRRRELSPEA-----------------------RRSLEKELNELKEKLE 53 (85)
T ss_pred HHHHHHHHHHHHHHHHHcccCCChHH-----------------------HHHHHHHHHHHHHHhh
Confidence 34567788999999999977664321 5677777666655543
No 91
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=36.89 E-value=46 Score=35.40 Aligned_cols=20 Identities=20% Similarity=0.074 Sum_probs=17.4
Q ss_pred chhHHHHHHHhCCeEEEeCC
Q 003997 192 SDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 192 GnTiKrLEeETGAKI~IRGK 211 (780)
.+.||+||+|.|+++-+|..
T Consensus 34 S~~Ik~LE~~lg~~LF~R~~ 53 (317)
T PRK15421 34 SHQFSDLEQRLGFRLFVRKS 53 (317)
T ss_pred HHHHHHHHHHhCCEEEEecC
Confidence 35699999999999999964
No 92
>PRK06107 aspartate aminotransferase; Provisional
Probab=36.23 E-value=2.3e+02 Score=31.16 Aligned_cols=26 Identities=31% Similarity=0.346 Sum_probs=20.8
Q ss_pred EEEEE-ecCHHHHHHHHHHHHhccccc
Q 003997 236 HISIS-ADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 236 HVlIs-Ad~~EkVdkAvelIE~LL~pV 261 (780)
||.|+ +.+.|.+++|+++|.++|..+
T Consensus 375 ~iRis~~~~~e~l~~~l~~l~~~l~~~ 401 (402)
T PRK06107 375 YFRLSIATSLETLEEACARIERAVAAL 401 (402)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHHhc
Confidence 66664 567899999999999988643
No 93
>PLN02397 aspartate transaminase
Probab=35.92 E-value=2.4e+02 Score=31.70 Aligned_cols=81 Identities=16% Similarity=0.131 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCCC--CCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeCCc
Q 003997 135 LECLELEKQEVIGEILKLNPSYRTPPDYK--PLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRPPsDYk--P~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRGKG 212 (780)
|+.++++|..+++++.++. +.. .|. .+..-.-+++..+ ..-.++|-+|.|+-|. +.|
T Consensus 338 ~~~~~~rr~~l~~~L~~~~--~~~--~~~~~~p~gg~fl~~~l~---------------~~~~~~Ll~~~~V~v~--~~~ 396 (423)
T PLN02397 338 ADRIISMRQKLYDALEARG--SPG--DWSHITKQIGMFSFTGLN---------------KEQVDRMTKEYHIYMT--RDG 396 (423)
T ss_pred HHHHHHHHHHHHHHHHhcC--CCC--CCCcccCCceEEEecCCC---------------HHHHHHHHHhCCEEEC--CCC
Confidence 5566677777777776652 111 222 1111223333331 3456778888776663 221
Q ss_pred cCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhccc
Q 003997 213 ADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 213 S~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~ 259 (780)
.+.+++.+.++|+++++.|++.|+
T Consensus 397 -----------------------Ri~~~~~~~~~i~~~~~~i~~~~~ 420 (423)
T PLN02397 397 -----------------------RISMAGLSSKNVPYLADAIHAVVT 420 (423)
T ss_pred -----------------------eEEEeeCCHHHHHHHHHHHHHHHh
Confidence 577788999999999999999874
No 94
>PRK02821 hypothetical protein; Provisional
Probab=35.15 E-value=20 Score=32.29 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=18.9
Q ss_pred cceeeeecCCchhHHHHHHHhCC
Q 003997 182 NFLGLIFGPASDTQKRLEKETRT 204 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGA 204 (780)
.=+|+|||=+|.|+|.|..--.+
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHHH
Confidence 46899999999999988765443
No 95
>PRK00468 hypothetical protein; Provisional
Probab=34.65 E-value=21 Score=31.89 Aligned_cols=20 Identities=15% Similarity=0.283 Sum_probs=16.8
Q ss_pred cceeeeecCCchhHHHHHHH
Q 003997 182 NFLGLIFGPASDTQKRLEKE 201 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeE 201 (780)
+=+|+|||=+|.|++.|..-
T Consensus 39 ~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 39 EDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred hhCcceecCCChhHHHHHHH
Confidence 35799999999999988653
No 96
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=34.05 E-value=26 Score=42.96 Aligned_cols=37 Identities=27% Similarity=0.404 Sum_probs=32.2
Q ss_pred EEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeC
Q 003997 168 EAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYG 210 (780)
Q Consensus 168 ~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRG 210 (780)
..+++||. .+-+.||||+|.+++.+++|++|-|.+--
T Consensus 710 ~~~~~~p~------~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 710 TKEIEIPR------SLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred eeEEeccH------HHhhhccCCCCccHHHHHHHhccceecCC
Confidence 46788887 47789999999999999999999988755
No 97
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=33.93 E-value=38 Score=35.44 Aligned_cols=20 Identities=15% Similarity=-0.067 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
+-||+||++.|+++-+|..+
T Consensus 37 ~~Ik~LE~~lg~~Lf~R~~~ 56 (309)
T PRK11013 37 RELARFEKVIGLKLFERVRG 56 (309)
T ss_pred HHHHHHHHHhCceeeeecCC
Confidence 45899999999999999864
No 98
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=33.41 E-value=63 Score=33.53 Aligned_cols=20 Identities=15% Similarity=0.147 Sum_probs=17.7
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
+.||+||++.|+++-+|.++
T Consensus 38 ~~i~~LE~~lG~~LF~R~~r 57 (302)
T PRK09791 38 KSIQELEEGLAAQLFFRRSK 57 (302)
T ss_pred HHHHHHHHHhCCeEEEEcCC
Confidence 45899999999999999764
No 99
>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=33.31 E-value=97 Score=32.54 Aligned_cols=67 Identities=15% Similarity=0.117 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCC--CCCCC--C--Ccc-EEEEEcCCCCCCCCcceeeeecCCchhHHHH--------HHHh
Q 003997 138 LELEKQEVIGEILKLNPSYRT--PPDYK--P--LLK-EAVVPIPVKEYPGYNFLGLIFGPASDTQKRL--------EKET 202 (780)
Q Consensus 138 LEeER~~IIeemlKliP~fRP--PsDYk--P--~~k-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrL--------EeET 202 (780)
.|-=|.+|+..+.+-+|.-.. ..+|. + ..+ ...|++..+ .--|.|||-+|++||+| |+-.
T Consensus 185 ~e~ire~~~~~~~~e~p~~~~~~~~~~~~~~~~~~~i~~~i~v~~~-----s~k~iiig~~g~~ik~i~~~ar~~l~~~~ 259 (270)
T TIGR00436 185 SEIIREKIIRYTKEEIPHSVRVEIERKSFNEKGLLKIHALISVERE-----SQKKIIIGKNGSMIKAIGIAARKDILELF 259 (270)
T ss_pred HHHHHHHHHHhcccccCceEEEEEEEEEECCCCeEEEEEEEEECcC-----CceeEEEcCCcHHHHHHHHHHHHHHHHHh
Confidence 333366666666555554222 11221 1 111 245666654 45689999999999865 5556
Q ss_pred CCeEEEe
Q 003997 203 RTVIKVY 209 (780)
Q Consensus 203 GAKI~IR 209 (780)
||||.++
T Consensus 260 ~~~v~l~ 266 (270)
T TIGR00436 260 DCDVFLE 266 (270)
T ss_pred CCCEEEE
Confidence 7776653
No 100
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=33.21 E-value=92 Score=33.12 Aligned_cols=27 Identities=19% Similarity=0.261 Sum_probs=23.6
Q ss_pred eeeeecCCchhHHHHHHHhCCeEEEeC
Q 003997 184 LGLIFGPASDTQKRLEKETRTVIKVYG 210 (780)
Q Consensus 184 IGlIIGPrGnTiKrLEeETGAKI~IRG 210 (780)
+|+|||=+|+||+.||--+.+-+..++
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~~~ 128 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNKIG 128 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhhhc
Confidence 899999999999999999887666633
No 101
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=32.68 E-value=59 Score=34.30 Aligned_cols=19 Identities=26% Similarity=0.118 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
..||+||++.||++-+|.+
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~ 53 (308)
T PRK10094 35 YRIKLLEENTGVALFFRTT 53 (308)
T ss_pred HHHHHHHHHhCCEEEeeCC
Confidence 4689999999999999975
No 102
>COG0026 PurK Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism]
Probab=32.65 E-value=70 Score=36.57 Aligned_cols=50 Identities=10% Similarity=0.144 Sum_probs=37.0
Q ss_pred hHHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhc
Q 003997 194 TQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELL 257 (780)
Q Consensus 194 TiKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~L 257 (780)
..+.+-+.-+|+|-++||.-.+.+++ =.||.|.++|.+++...+.+|..+
T Consensus 318 ~~~~~l~~p~~~lH~YGK~e~R~gRK--------------mGHvn~~~~~~~~~~~~~~~l~~~ 367 (375)
T COG0026 318 DVKAVLALPGAHLHWYGKAEARPGRK--------------MGHVNVLGSDSDELEQLAALLPAK 367 (375)
T ss_pred hhHHHHhCCCCEEEEecCccCCCCCe--------------eeeEEeecCCHHHHHHHHHhhhhh
Confidence 46889999999999999963222221 159999999977777776666644
No 103
>KOG4165 consensus Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=32.00 E-value=51 Score=37.49 Aligned_cols=27 Identities=22% Similarity=0.635 Sum_probs=19.6
Q ss_pred cceeeeecCCchh--HHHHHHHhCCeEEEeCC
Q 003997 182 NFLGLIFGPASDT--QKRLEKETRTVIKVYGT 211 (780)
Q Consensus 182 NFIGlIIGPrGnT--iKrLEeETGAKI~IRGK 211 (780)
++|-+|| |||.+ .++|++.|. |=+-|.
T Consensus 190 ~~IDLvI-PRGSs~LVr~Ik~~tk--IPVLGH 218 (433)
T KOG4165|consen 190 DYIDLVI-PRGSSDLVRSIKDTTK--IPVLGH 218 (433)
T ss_pred hheeEEe-cCCcHHHHHHHhhccc--Cccccc
Confidence 5677777 88876 577777665 877776
No 104
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=31.92 E-value=59 Score=33.75 Aligned_cols=19 Identities=16% Similarity=0.212 Sum_probs=17.2
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
+.||+||++.||++-+|..
T Consensus 34 ~~i~~LE~~lg~~LF~R~~ 52 (305)
T PRK11151 34 GQIRKLEDELGVMLLERTS 52 (305)
T ss_pred HHHHHHHHHhCchheeeCC
Confidence 5799999999999999964
No 105
>PRK14322 glmM phosphoglucosamine mutase; Provisional
Probab=31.77 E-value=3.2e+02 Score=30.90 Aligned_cols=26 Identities=12% Similarity=0.285 Sum_probs=22.8
Q ss_pred ceEEEEEecCHHHHHHHHHHHHhccc
Q 003997 234 EFHISISADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 234 pLHVlIsAd~~EkVdkAvelIE~LL~ 259 (780)
-+||+++|+|++.+++-++.+..+|+
T Consensus 403 ~irv~~Ea~~~~~a~~l~~~~~~~l~ 428 (429)
T PRK14322 403 VVRITVEGKDREEIEKIVEEISRVLE 428 (429)
T ss_pred EEEEEEEECCHHHHHHHHHHHHHHHh
Confidence 38999999999999998888888774
No 106
>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=31.30 E-value=2.7e+02 Score=29.75 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=15.6
Q ss_pred EEEEEe-cCHHHHHHHHHHHHhc
Q 003997 236 HISISA-DSYEKVDAATDLIELL 257 (780)
Q Consensus 236 HVlIsA-d~~EkVdkAvelIE~L 257 (780)
+|.+.. .+++.+|+.++.|++|
T Consensus 351 Ris~~~~~t~edid~l~~~L~~~ 373 (373)
T TIGR03812 351 RIVVMPHVTREHIEEFLEDLKEI 373 (373)
T ss_pred EEEEECCCCHHHHHHHHHHHhhC
Confidence 333333 3889999999988864
No 107
>PRK01064 hypothetical protein; Provisional
Probab=31.28 E-value=30 Score=31.25 Aligned_cols=21 Identities=24% Similarity=0.229 Sum_probs=18.0
Q ss_pred ceeeeecCCchhHHHHHHHhC
Q 003997 183 FLGLIFGPASDTQKRLEKETR 203 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEeETG 203 (780)
=+|+|||=+|+|++.|..-..
T Consensus 40 D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 40 DIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred cceEEECCCCccHHHHHHHHH
Confidence 479999999999999987544
No 108
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=30.77 E-value=56 Score=37.31 Aligned_cols=79 Identities=13% Similarity=0.049 Sum_probs=50.5
Q ss_pred CCCchhHHHHHHHHHHHHHHH------HHHHh--CCCCCCCCCC--CCCccEEEEEcCCCCCCCCcceeeeecCCchhHH
Q 003997 127 PNPQVDRELECLELEKQEVIG------EILKL--NPSYRTPPDY--KPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQK 196 (780)
Q Consensus 127 ~GkR~NTrRekLEeER~~IIe------emlKl--iP~fRPPsDY--kP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiK 196 (780)
.|.|++.-.+.|..|+-+||+ ++.+- -|.- ..+. ..-.+...++++.+ -+++.||=+|.++|
T Consensus 260 ~G~rI~~I~~eL~gEkIDvI~~s~D~~~fI~Nal~Pa~--V~~V~i~~~~~~~~V~V~~~------qlslAIGk~GqNvr 331 (374)
T PRK12328 260 KGVRINAVSKELNGENIDCIEYSNVPEIFIARALAPAI--ISSVKIEEEEKKAIVTLLSD------QKSKAIGKNGINIR 331 (374)
T ss_pred CcchHHHHHHHhCCCeEEEEEcCCCHHHHHHHhCCCce--eeEEEEcCCCcEEEEEEChH------HhhhhhcCCChhHH
Confidence 456666656667666666553 22221 1111 0111 01123456677763 56999999999999
Q ss_pred HHHHHhCCeEEEeCCcc
Q 003997 197 RLEKETRTVIKVYGTKA 213 (780)
Q Consensus 197 rLEeETGAKI~IRGKGS 213 (780)
..-+-||+||.|+.-+|
T Consensus 332 LA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 332 LASMLTGYEIELNEIGS 348 (374)
T ss_pred HHHHHhCCEEEEEECCC
Confidence 99999999999999876
No 109
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=30.66 E-value=73 Score=33.19 Aligned_cols=19 Identities=16% Similarity=-0.038 Sum_probs=17.0
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
..||+||++.|+++-+|..
T Consensus 35 ~~I~~LE~~lg~~LF~R~~ 53 (300)
T PRK11074 35 YTVRQLEEWLAVPLFERRH 53 (300)
T ss_pred HHHHHHHHHhCCeeEEeCC
Confidence 4689999999999999964
No 110
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=30.62 E-value=57 Score=34.96 Aligned_cols=21 Identities=24% Similarity=0.245 Sum_probs=18.3
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q 003997 193 DTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKGS 213 (780)
+.||+||+|.||++-+|..+.
T Consensus 35 ~~I~~LE~~lG~~LF~R~~r~ 55 (327)
T PRK12680 35 KQLKQLEDELGFLLFVRKGRS 55 (327)
T ss_pred HHHHHHHHHhCCeEEEECCCc
Confidence 458999999999999998653
No 111
>PRK02936 argD acetylornithine aminotransferase; Provisional
Probab=30.46 E-value=2.9e+02 Score=29.88 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=18.2
Q ss_pred EEEEE---ecCHHHHHHHHHHHHhcc
Q 003997 236 HISIS---ADSYEKVDAATDLIELLV 258 (780)
Q Consensus 236 HVlIs---Ad~~EkVdkAvelIE~LL 258 (780)
++.|+ ..++|.|+++++.|+++|
T Consensus 352 ~lRi~p~~~~~~~~i~~~i~~l~~~~ 377 (377)
T PRK02936 352 VIRLLPPLVVTKEELDQAVYLLKKVL 377 (377)
T ss_pred EEEEECCcccCHHHHHHHHHHHHHhC
Confidence 45554 678999999999998765
No 112
>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=29.69 E-value=41 Score=34.46 Aligned_cols=19 Identities=37% Similarity=0.356 Sum_probs=16.9
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
+.||+||+|.||++-+|..
T Consensus 34 ~~Ik~LE~~lg~~LF~R~~ 52 (291)
T TIGR03418 34 QQVKRLEEELGTPLFERGH 52 (291)
T ss_pred HHHHHHHHHhCcHHhhcCC
Confidence 4689999999999999974
No 113
>COG0014 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=29.44 E-value=81 Score=36.51 Aligned_cols=31 Identities=10% Similarity=0.238 Sum_probs=20.5
Q ss_pred cceeeeecCCchh-HHHHHHHhCCeEEEeCCc
Q 003997 182 NFLGLIFGPASDT-QKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 182 NFIGlIIGPrGnT-iKrLEeETGAKI~IRGKG 212 (780)
.||-+||==||+. ++++.+++-+=+.-.|.|
T Consensus 195 ~yiD~iIPRGg~~Li~~v~~~a~vPVi~~~~G 226 (417)
T COG0014 195 GYIDLVIPRGGAGLIRRVVENATVPVIEHGVG 226 (417)
T ss_pred CceeEEEcCCcHHHHHHHHhCCcCCEEecCcc
Confidence 3566666444444 677888777777777776
No 114
>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=29.02 E-value=64 Score=33.28 Aligned_cols=20 Identities=20% Similarity=0.125 Sum_probs=17.9
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
..||+||++.|+++-+|..+
T Consensus 36 ~~I~~LE~~lg~~LF~R~~~ 55 (300)
T TIGR02424 36 KTLRELEEILGTPLFERDRR 55 (300)
T ss_pred HHHHHHHHHhCCeEEEEcCC
Confidence 46999999999999999764
No 115
>PRK09064 5-aminolevulinate synthase; Validated
Probab=28.74 E-value=4.4e+02 Score=28.93 Aligned_cols=28 Identities=11% Similarity=0.153 Sum_probs=21.4
Q ss_pred EEEEEec---CHHHHHHHHHHHHhccccccc
Q 003997 236 HISISAD---SYEKVDAATDLIELLVTSVSG 263 (780)
Q Consensus 236 HVlIsAd---~~EkVdkAvelIE~LL~pVev 263 (780)
++.|+-. +.|.++++++.|++++..+..
T Consensus 370 ~lRis~~~~~t~edi~~l~~~l~~~~~~~~~ 400 (407)
T PRK09064 370 RLRITPTPFHTDEMIDHLVEALVEVWARLGL 400 (407)
T ss_pred eEEEEeCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 4555544 889999999999999875543
No 116
>PRK02047 hypothetical protein; Provisional
Probab=28.05 E-value=2.5e+02 Score=25.91 Aligned_cols=63 Identities=22% Similarity=0.290 Sum_probs=41.1
Q ss_pred CCCCCcceeeeecCCch----hHHHHHHHhCCe-----EEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003997 177 EYPGYNFLGLIFGPASD----TQKRLEKETRTV-----IKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 247 (780)
Q Consensus 177 eyP~~NFIGlIIGPrGn----TiKrLEeETGAK-----I~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkV 247 (780)
+||- +|-=++||+.+. .+.+|.++..++ |.+|-. .+ | -+--+.|.|++.++|.+
T Consensus 12 efPc-~~~~KvIG~~~~~~~~~v~~iv~~~~~~~~~~~i~~k~S--s~----------G----kY~Svtv~v~v~s~eq~ 74 (91)
T PRK02047 12 EYPS-DFPIKVMGKAHPEFADTIFKVVSVHDPEFDLEKIEERPS--SG----------G----NYTGLTITVRATSREQL 74 (91)
T ss_pred cCCC-CCeEEEEEeCcHhHHHHHHHHHHHhCCCCccCceEEccC--CC----------C----eEEEEEEEEEECCHHHH
Confidence 4443 577799999995 456666666444 333332 11 1 23457899999999999
Q ss_pred HHHHHHHHh
Q 003997 248 DAATDLIEL 256 (780)
Q Consensus 248 dkAvelIE~ 256 (780)
++-.+.+..
T Consensus 75 ~~iY~~L~~ 83 (91)
T PRK02047 75 DNIYRALTG 83 (91)
T ss_pred HHHHHHHhh
Confidence 887776654
No 117
>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=27.99 E-value=73 Score=33.34 Aligned_cols=20 Identities=20% Similarity=0.210 Sum_probs=17.7
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
..||+||+|.|+++-+|...
T Consensus 41 ~~I~~LE~~lg~~Lf~R~~r 60 (302)
T TIGR02036 41 HRINQLEEELGIQLFVRSHR 60 (302)
T ss_pred HHHHHHHHHhCCceEEECCC
Confidence 45899999999999999864
No 118
>PRK10887 glmM phosphoglucosamine mutase; Provisional
Probab=27.97 E-value=2.4e+02 Score=32.03 Aligned_cols=27 Identities=15% Similarity=0.192 Sum_probs=23.4
Q ss_pred ceEEEEEecCHHHHHHHHHHHHhcccc
Q 003997 234 EFHISISADSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 234 pLHVlIsAd~~EkVdkAvelIE~LL~p 260 (780)
-+||+++|+|+|.+++-++.++.+|+.
T Consensus 415 ~iri~~Ea~s~e~a~~l~~~~~~~v~~ 441 (443)
T PRK10887 415 LIRVMVEGEDEAQVTALAERIADAVKA 441 (443)
T ss_pred EEEEEEeeCCHHHHHHHHHHHHHHHHh
Confidence 389999999999999998888888754
No 119
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=27.96 E-value=32 Score=31.13 Aligned_cols=18 Identities=17% Similarity=0.327 Sum_probs=15.9
Q ss_pred ceeeeecCCchhHHHHHH
Q 003997 183 FLGLIFGPASDTQKRLEK 200 (780)
Q Consensus 183 FIGlIIGPrGnTiKrLEe 200 (780)
=+|+|||=+|.|++.|..
T Consensus 40 D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 40 DMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred cccceecCCChhHHHHHH
Confidence 589999999999999854
No 120
>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=27.33 E-value=1.1e+02 Score=36.91 Aligned_cols=60 Identities=23% Similarity=0.155 Sum_probs=36.9
Q ss_pred HHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeC
Q 003997 145 VIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYG 210 (780)
Q Consensus 145 IIeemlKliP~fRPPsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRG 210 (780)
..+++.+++|.=--..|+.--.-.--|+|-. .+=|++||=+|.|+++|-++||-+-.|.-
T Consensus 71 ~~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~------~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 71 AIEKIKEIVPEEAGITDIYFDDVTGEVIIEA------EKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred HHHHHHHhCCCcCCceeEEecCCCceEEEEE------cCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 3455666665432222221111112444444 36799999999999999999997766643
No 121
>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=27.28 E-value=62 Score=36.29 Aligned_cols=77 Identities=21% Similarity=0.172 Sum_probs=49.2
Q ss_pred CCCchhHHHHHHHHHHHHHHH------HHHHh--CCCCCCCCCC---CCCccEEEEEcCCCCCCCCcceeeeecCCchhH
Q 003997 127 PNPQVDRELECLELEKQEVIG------EILKL--NPSYRTPPDY---KPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQ 195 (780)
Q Consensus 127 ~GkR~NTrRekLEeER~~IIe------emlKl--iP~fRPPsDY---kP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTi 195 (780)
.|.|+++-.+.|..|+-+||+ ++.+- -|.- ..+. ..-.+...++++. +-.++.||=+|.++
T Consensus 252 ~G~ri~~i~~el~ge~Idiv~~s~d~~~fi~nal~Pa~--v~~v~i~~~~~~~~~v~V~~------~~~~~aIGk~G~Nv 323 (341)
T TIGR01953 252 KGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAK--VISVEVLDEDKHSAEVVVPD------DQLSLAIGKGGQNV 323 (341)
T ss_pred CCchHHHHHHHhCCCeEEEEEcCCCHHHHHHHhcCCce--EEEEEEEcCCCcEEEEEECh------HHcchhhcCCChhH
Confidence 467777766777677766653 22221 1110 1111 1111345666676 35789999999999
Q ss_pred HHHHHHhCCeEEEeCC
Q 003997 196 KRLEKETRTVIKVYGT 211 (780)
Q Consensus 196 KrLEeETGAKI~IRGK 211 (780)
|..-+-||+||.|+-.
T Consensus 324 ~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 324 RLASKLTGWNIDVKTE 339 (341)
T ss_pred HHHHHHhCCEEEEEeC
Confidence 9999999999999853
No 122
>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=27.22 E-value=3.6e+02 Score=27.42 Aligned_cols=63 Identities=13% Similarity=0.014 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHhhCCCccCCCC----CCCCCCCCCCCCCCCCchhH--H-HHHHHHHHHHHHHHHHHhC
Q 003997 91 YQTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDR--E-LECLELEKQEVIGEILKLN 153 (780)
Q Consensus 91 ~QlRIeeIt~KL~tg~l~~~~~e----~s~SP~P~p~yds~GkR~NT--r-RekLEeER~~IIeemlKli 153 (780)
.++.|++|..+|+.-++++..-. |...|.-.-.--+.||-+=| + .+.+++..+++++.+.++.
T Consensus 15 ~~idL~~la~~~~n~~YePe~fpgli~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~L~~~g 84 (174)
T cd00652 15 CELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARILQKLG 84 (174)
T ss_pred CccCHHHHHhhCCCcEECCCccceEEEEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence 35678899888875555542211 11233322222245666655 4 7888888888888887776
No 123
>PRK08175 aminotransferase; Validated
Probab=26.84 E-value=3.5e+02 Score=29.63 Aligned_cols=24 Identities=13% Similarity=0.332 Sum_probs=19.9
Q ss_pred EEEEE-ecCHHHHHHHHHHHHhccc
Q 003997 236 HISIS-ADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 236 HVlIs-Ad~~EkVdkAvelIE~LL~ 259 (780)
|+.|+ +.+++.+++|+++|.++|.
T Consensus 364 ~lRis~~~~~~~~~~al~~l~~~l~ 388 (395)
T PRK08175 364 HVRFALIENRDRIRQAIRGIKAMFR 388 (395)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHH
Confidence 66665 4678999999999999986
No 124
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=26.82 E-value=73 Score=33.77 Aligned_cols=43 Identities=21% Similarity=0.191 Sum_probs=26.7
Q ss_pred EEEEcCCCCCCCCcceeeeecCCc-----------hhHHHHHHHhCC-eEEEeCC
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPAS-----------DTQKRLEKETRT-VIKVYGT 211 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrG-----------nTiKrLEeETGA-KI~IRGK 211 (780)
+.++--.+-.+.+..+|+|||||| ..+..+.++.-. +|.+|-+
T Consensus 111 d~~iat~~~m~~l~~Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k~g~v~~r~~ 165 (230)
T PRK05424 111 DVVIATPDMMGKVGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVD 165 (230)
T ss_pred CEEEECHHHHHHHHHhccccccccCCCCCCCCCcchhHHHHHHHHhcCcEEEEec
Confidence 344444444555667899999998 345666666643 5666643
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=26.81 E-value=47 Score=27.42 Aligned_cols=20 Identities=20% Similarity=0.145 Sum_probs=16.5
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
..||+||++.|+++.+|..+
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 45899999999999999764
No 126
>PRK00394 transcription factor; Reviewed
Probab=26.81 E-value=3.4e+02 Score=27.90 Aligned_cols=64 Identities=14% Similarity=0.102 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHhhCCCccCCCC----CCCCCCCCCCCCCCCCchhH--H-HHHHHHHHHHHHHHHHHhCCC
Q 003997 92 QTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDR--E-LECLELEKQEVIGEILKLNPS 155 (780)
Q Consensus 92 QlRIeeIt~KL~tg~l~~~~~e----~s~SP~P~p~yds~GkR~NT--r-RekLEeER~~IIeemlKliP~ 155 (780)
.+.|++|..+|+.-++++..-. |...|.-.-.--+.||-+=| + .+.+++...++++.+.+++=.
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 4577888888876555543211 11233322222345766655 4 788999999999988887633
No 127
>PRK07179 hypothetical protein; Provisional
Probab=26.55 E-value=5.1e+02 Score=28.53 Aligned_cols=27 Identities=15% Similarity=0.181 Sum_probs=20.9
Q ss_pred EEEEEec---CHHHHHHHHHHHHhcccccc
Q 003997 236 HISISAD---SYEKVDAATDLIELLVTSVS 262 (780)
Q Consensus 236 HVlIsAd---~~EkVdkAvelIE~LL~pVe 262 (780)
++.|+-. ++|.|+++++.|+++++...
T Consensus 371 ~lRis~~~~~t~edi~~~~~~l~~~~~~~~ 400 (407)
T PRK07179 371 LIRLSLNADLTASDLDRVLEVCREARDEVD 400 (407)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHhhC
Confidence 5555543 88999999999999987543
No 128
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=26.43 E-value=85 Score=32.95 Aligned_cols=21 Identities=14% Similarity=0.028 Sum_probs=18.2
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003997 192 SDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 192 GnTiKrLEeETGAKI~IRGKG 212 (780)
.+.||+||+|.|+++-+|...
T Consensus 39 S~~I~~LE~~lg~~LF~R~~r 59 (312)
T PRK10341 39 SKIINDIEDYFGVELIVRKNT 59 (312)
T ss_pred HHHHHHHHHHhCCeEEEEcCC
Confidence 356899999999999999864
No 129
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=25.98 E-value=33 Score=39.89 Aligned_cols=77 Identities=19% Similarity=0.234 Sum_probs=49.4
Q ss_pred CCCchhHHHHHHHHHHHHHHH------HHHHh--CCCCCCCCCC---CCCccEEEEEcCCCCCCCCcceeeeecCCchhH
Q 003997 127 PNPQVDRELECLELEKQEVIG------EILKL--NPSYRTPPDY---KPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQ 195 (780)
Q Consensus 127 ~GkR~NTrRekLEeER~~IIe------emlKl--iP~fRPPsDY---kP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTi 195 (780)
.|.|+++-++.|..||-.||+ ++++- -|.- ..+. .+-.+...|+|+. +-+++.||=+|.++
T Consensus 286 kG~RI~~I~~eL~gEkIDVI~ys~Dp~~fI~NaLsPA~--V~~V~i~~~~~k~a~V~V~~------~qlslAIGK~GqNv 357 (449)
T PRK12329 286 RGSRIQAVVNELRGEKIDVIRWSPDPATYIANALSPAR--VDEVRLVDPEGRHAHVLVPP------DQLSLAIGKEGQNV 357 (449)
T ss_pred CcchHHHHHHHhCCCeEEEEEcCCCHHHHHHHhcCCce--eeEEEEEcCCCcEEEEEECh------HhcchhhcCCChhH
Confidence 466777656677667666653 22221 1111 1111 0112345667776 46789999999999
Q ss_pred HHHHHHhCCeEEEeCC
Q 003997 196 KRLEKETRTVIKVYGT 211 (780)
Q Consensus 196 KrLEeETGAKI~IRGK 211 (780)
|.--+-||.+|.|+..
T Consensus 358 rLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 358 RLAARLTGWKIDIKDS 373 (449)
T ss_pred HHHHHHHCCEeccccH
Confidence 9999999999999875
No 130
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=25.93 E-value=69 Score=33.68 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=18.0
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003997 192 SDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 192 GnTiKrLEeETGAKI~IRGKG 212 (780)
.+.||+||+|.||++-.|...
T Consensus 46 S~~I~~LE~~lG~~LF~R~~r 66 (311)
T PRK10086 46 SHRINQLEEELGIKLFVRSHR 66 (311)
T ss_pred HHHHHHHHHHhCCeeEEEcCC
Confidence 346899999999999999753
No 131
>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=25.93 E-value=3.8e+02 Score=27.37 Aligned_cols=62 Identities=8% Similarity=-0.061 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhhCCCccCCCC----CCCCCCCCCCCCCCCCchhH--H-HHHHHHHHHHHHHHHHHhC
Q 003997 91 YQTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDR--E-LECLELEKQEVIGEILKLN 153 (780)
Q Consensus 91 ~QlRIeeIt~KL~tg~l~~~~~e----~s~SP~P~p~yds~GkR~NT--r-RekLEeER~~IIeemlKli 153 (780)
..+.|++|...|+.-++++ .-. |-..|.-.-.--++||-+=| + .+.+++...++++.+.+++
T Consensus 16 ~~idL~~la~~l~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l~~~g 84 (174)
T cd04517 16 CHIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLLQKLG 84 (174)
T ss_pred CcccHHHHHhhCCCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHHHcC
Confidence 3456788888887655555 321 11223211222245666555 4 7888888888888887775
No 132
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=25.71 E-value=80 Score=33.63 Aligned_cols=21 Identities=19% Similarity=0.158 Sum_probs=18.0
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003997 192 SDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 192 GnTiKrLEeETGAKI~IRGKG 212 (780)
.+.||+||++.||++-+|...
T Consensus 43 S~~I~~LE~~lG~~LF~R~~~ 63 (310)
T PRK15092 43 SQQMQRLEQLVGKELFARHGR 63 (310)
T ss_pred HHHHHHHHHHhCcceEEECCC
Confidence 356899999999999999753
No 133
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=25.52 E-value=74 Score=32.93 Aligned_cols=19 Identities=16% Similarity=-0.081 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
..||+||++.||++-+|.+
T Consensus 39 ~~i~~LE~~lg~~Lf~R~~ 57 (297)
T PRK11139 39 HQIKALEDFLGLKLFRRRN 57 (297)
T ss_pred HHHHHHHHHhCchheEecC
Confidence 4689999999999999975
No 134
>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=25.39 E-value=54 Score=35.31 Aligned_cols=56 Identities=18% Similarity=0.121 Sum_probs=39.6
Q ss_pred HHhCCeEEEeCCccCCCcchhccc-CCCCccCCCCceEEEEEecCHHHHHHHHHHHHhccccccc
Q 003997 200 KETRTVIKVYGTKADTGEKVEIST-SDANVQSTYEEFHISISADSYEKVDAATDLIELLVTSVSG 263 (780)
Q Consensus 200 eETGAKI~IRGKGS~k~~K~E~~~-~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVev 263 (780)
+-||-.|.|-|-+|+=+.+-..+. .-| =.|.|+|.++++|++|++.+-.|...|++
T Consensus 2 k~tgnTiLITGG~sGIGl~lak~f~elg--------N~VIi~gR~e~~L~e~~~~~p~~~t~v~D 58 (245)
T COG3967 2 KTTGNTILITGGASGIGLALAKRFLELG--------NTVIICGRNEERLAEAKAENPEIHTEVCD 58 (245)
T ss_pred cccCcEEEEeCCcchhhHHHHHHHHHhC--------CEEEEecCcHHHHHHHHhcCcchheeeec
Confidence 358899999998875443221111 011 27999999999999999988888777654
No 135
>PRK04073 rocD ornithine--oxo-acid transaminase; Provisional
Probab=24.42 E-value=4.4e+02 Score=29.05 Aligned_cols=23 Identities=22% Similarity=0.229 Sum_probs=19.5
Q ss_pred EEEEE---ecCHHHHHHHHHHHHhcc
Q 003997 236 HISIS---ADSYEKVDAATDLIELLV 258 (780)
Q Consensus 236 HVlIs---Ad~~EkVdkAvelIE~LL 258 (780)
+|.|+ ..++|.||++++.|+++|
T Consensus 370 ~iRi~p~l~~t~e~i~~~~~~l~~~l 395 (396)
T PRK04073 370 VIRFAPPLVITKEELDWAFEKIKAVL 395 (396)
T ss_pred EEEEECCcccCHHHHHHHHHHHHHHh
Confidence 56676 679999999999999876
No 136
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=24.23 E-value=1.2e+02 Score=39.69 Aligned_cols=79 Identities=14% Similarity=0.059 Sum_probs=58.0
Q ss_pred EEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhCCeEEEeC-CccCCCcchhcccCCCCccCCCCceEEEEEecCHHHH
Q 003997 169 AVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYG-TKADTGEKVEISTSDANVQSTYEEFHISISADSYEKV 247 (780)
Q Consensus 169 ~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETGAKI~IRG-KGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkV 247 (780)
.|+.||+ |-+-|+||=+|.|+..+.+.||+.|.|+- .++. ..| .+....-..+..
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 4777887 68999999999999999999999999976 3321 111 122222345678
Q ss_pred HHHHHHHHhcccccccchhhhccc
Q 003997 248 DAATDLIELLVTSVSGSLAAISTS 271 (780)
Q Consensus 248 dkAvelIE~LL~pVevg~~a~~~~ 271 (780)
..|..+|..+|.+.++...-.+..
T Consensus 1398 r~a~~~I~~~i~Dpdv~~~~~ssi 1421 (2131)
T KOG4369|consen 1398 RVATSPIGLPIIDPDVSSPSSSSI 1421 (2131)
T ss_pred hhhhccccceeecCCcCccccccc
Confidence 889999999999988887754444
No 137
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=24.21 E-value=72 Score=33.25 Aligned_cols=19 Identities=11% Similarity=-0.001 Sum_probs=17.2
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
+.||+||+|.|+++-.|..
T Consensus 44 ~~I~~LE~~lG~~Lf~R~~ 62 (303)
T PRK10082 44 RRIRALEQAIGVELFNRQV 62 (303)
T ss_pred HHHHHHHHHcCCEEEEecC
Confidence 4689999999999999985
No 138
>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=24.11 E-value=1.2e+02 Score=30.55 Aligned_cols=19 Identities=16% Similarity=0.142 Sum_probs=16.8
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
..||+||++.||++-+|.+
T Consensus 30 ~~i~~LE~~lg~~Lf~R~~ 48 (279)
T TIGR03339 30 DQVRKLEERYGVELFHRNG 48 (279)
T ss_pred HHHHHHHHHhCCccEEEcC
Confidence 4689999999999999964
No 139
>KOG1478 consensus 3-keto sterol reductase [Lipid transport and metabolism]
Probab=24.04 E-value=84 Score=34.94 Aligned_cols=32 Identities=6% Similarity=0.168 Sum_probs=27.5
Q ss_pred ccCCCCceEEEEEecCHHHHHHHHHHHHhccc
Q 003997 228 VQSTYEEFHISISADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 228 ~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~ 259 (780)
.+|+++-||+++++.+.+|++++|+.|+..--
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 44566779999999999999999999988765
No 140
>PRK07682 hypothetical protein; Validated
Probab=24.01 E-value=5.2e+02 Score=27.99 Aligned_cols=26 Identities=27% Similarity=0.300 Sum_probs=20.2
Q ss_pred EEEEE-ecCHHHHHHHHHHHHhccccc
Q 003997 236 HISIS-ADSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 236 HVlIs-Ad~~EkVdkAvelIE~LL~pV 261 (780)
||.|+ +.+.+.+++|++.|..+|+.+
T Consensus 351 ~iRis~~~~~~~l~~~l~~l~~~l~~~ 377 (378)
T PRK07682 351 FIRCSYATSLEQLQEAMKRMKRFVENK 377 (378)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhhc
Confidence 66664 346899999999999988643
No 141
>PRK09801 transcriptional activator TtdR; Provisional
Probab=23.98 E-value=77 Score=33.54 Aligned_cols=20 Identities=15% Similarity=0.115 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
..||+||+|.|+++-.|.+.
T Consensus 39 ~~I~~LE~~LG~~Lf~R~~r 58 (310)
T PRK09801 39 KRIQILENTLATTLLNRSAR 58 (310)
T ss_pred HHHHHHHHHhCCEeeeecCC
Confidence 56899999999999999864
No 142
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=23.97 E-value=1.1e+02 Score=32.09 Aligned_cols=28 Identities=21% Similarity=0.256 Sum_probs=20.3
Q ss_pred eeeeecCC-------------chhHHHHHHHhCCeEEEeCC
Q 003997 184 LGLIFGPA-------------SDTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 184 IGlIIGPr-------------GnTiKrLEeETGAKI~IRGK 211 (780)
||+||||+ ...++...+|..++|.+|=+
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 44467777788767776643
No 143
>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=23.79 E-value=98 Score=27.23 Aligned_cols=59 Identities=12% Similarity=0.111 Sum_probs=34.6
Q ss_pred HHHHHHHhCCeEEEeCCccCCCcchhcccCCCC-ccCCCCceEEEEEecCHHHHHHHHHHHHhcc
Q 003997 195 QKRLEKETRTVIKVYGTKADTGEKVEISTSDAN-VQSTYEEFHISISADSYEKVDAATDLIELLV 258 (780)
Q Consensus 195 iKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~-~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL 258 (780)
+-++-++++|+|.|+-++..-+.|+-..- .. .....+.++|.+.++|++. |++.|+++|
T Consensus 22 lv~~a~~~~~~i~i~~~~~~vdakSil~l--~~L~~~~G~~i~i~~~G~de~~---a~~~i~~~~ 81 (84)
T PF00381_consen 22 LVQIASKFDSDITIRKGGKTVDAKSILGL--MSLGAKKGDEIEIEAEGEDEEE---ALEAIAEFL 81 (84)
T ss_dssp HHHHHHTSSSEEEEEETTEEEETTSHHHH--HHHTBSTTEEEEEEEESTTHHH---HHHHHHHHH
T ss_pred HHHHHhhCCCEEEEEeCceeEecCCHHHH--hhhhcCCCCEEEEEEECcCHHH---HHHHHHHHH
Confidence 55678889999999966532222221100 00 2235667999999998854 344444443
No 144
>PRK13393 5-aminolevulinate synthase; Provisional
Probab=23.59 E-value=6.9e+02 Score=27.59 Aligned_cols=26 Identities=4% Similarity=0.190 Sum_probs=20.5
Q ss_pred EEEEEe---cCHHHHHHHHHHHHhccccc
Q 003997 236 HISISA---DSYEKVDAATDLIELLVTSV 261 (780)
Q Consensus 236 HVlIsA---d~~EkVdkAvelIE~LL~pV 261 (780)
+|.|+- .++|.+|++++.|++++...
T Consensus 369 ~iRis~~~~~t~edid~l~~~l~~~~~~~ 397 (406)
T PRK13393 369 RLRITPSPLHTDADIEHLVQALSEIWARL 397 (406)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHhc
Confidence 566655 38899999999999988654
No 145
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=23.55 E-value=68 Score=34.14 Aligned_cols=20 Identities=5% Similarity=0.001 Sum_probs=17.7
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
+.||+||++.|+++-+|.+.
T Consensus 62 ~~I~~LE~~lG~~LF~R~~r 81 (317)
T PRK11482 62 QSIQKLRVIFPDPLFIRKGQ 81 (317)
T ss_pred HHHHHHHHHhCCcceEecCC
Confidence 46999999999999999853
No 146
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=23.43 E-value=5.5e+02 Score=28.80 Aligned_cols=86 Identities=16% Similarity=0.192 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCccEEEEEcCCCCCCCCcceeeeecCCch---hHHHHHHHhCCeEEEeCC
Q 003997 135 LECLELEKQEVIGEILKLNPSYRTPPDYKPLLKEAVVPIPVKEYPGYNFLGLIFGPASD---TQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRPPsDYkP~~k~~KIyIPvkeyP~~NFIGlIIGPrGn---TiKrLEeETGAKI~IRGK 211 (780)
++++.+||.+|.+++.++. -++. +|- .-|||=.=.+- +. -.+.|.+. .|.||.-
T Consensus 265 ~~~~~~~r~rl~~~l~~~~-~~~v--------------~pS----~aNFvlv~~~~-~~~~~l~~~L~~~---giivR~~ 321 (356)
T COG0079 265 VERIREERERLYAALKALG-LFGV--------------FPS----QANFVLVRVPD-AEAAALAEALLKK---GILVRDC 321 (356)
T ss_pred HHHHHHHHHHHHHHHHhCC-CCee--------------cCC----CCcEEEEECCC-ccHHHHHHHHHHC---CEEEEeC
Confidence 7888888888888887765 2211 111 13666333322 34 34455444 6888877
Q ss_pred ccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHhccc
Q 003997 212 KADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 212 GS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~ 259 (780)
++ .+ ..+-|+.|+--+.|.-++-++.+++++.
T Consensus 322 ~~-~~---------------~~~~~lRitvgt~een~~ll~AL~~~~~ 353 (356)
T COG0079 322 SS-VG---------------LLPGYLRITVGTPEENDRLLAALREVLK 353 (356)
T ss_pred CC-CC---------------CCCCeEEEEeCCHHHHHHHHHHHHHHHh
Confidence 53 21 1234899998888777888888777764
No 147
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=23.42 E-value=1e+02 Score=31.82 Aligned_cols=20 Identities=15% Similarity=0.087 Sum_probs=17.6
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
..||+||++.|+++-+|.+.
T Consensus 35 ~~I~~LE~~lG~~LF~R~~r 54 (301)
T PRK14997 35 RRIAQLEERLGVRLIQRTTR 54 (301)
T ss_pred HHHHHHHHHhCCEeeeeccC
Confidence 45899999999999999863
No 148
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=23.31 E-value=1.4e+02 Score=33.94 Aligned_cols=64 Identities=13% Similarity=0.181 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC--CCCCCCCc-----cEEEEEcCCCCCCCCcceeeeecCCchhHHHHHHHhC
Q 003997 135 LECLELEKQEVIGEILKLNPSYRT--PPDYKPLL-----KEAVVPIPVKEYPGYNFLGLIFGPASDTQKRLEKETR 203 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRP--PsDYkP~~-----k~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrLEeETG 203 (780)
-..+|--|.+||+..-.-+|---- ..+|+-.. -+.+|..|.. ...-+|||++|+-|++|-++-+
T Consensus 289 ~l~~e~VReklLd~~pqEVPY~lq~~i~~w~e~~~g~l~I~~~v~~pK~-----s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 289 FLCSESVREKLLDHLPQEVPYNLQVRILSWKERPAGVLFIQVEVVCPKN-----SQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred HHHHHHHHHHHHhhCccccCcceEEEEEEeeecCCcEEEEEEEEEcCCC-----cceeEEEcCCCccHHHHHHHHH
Confidence 344555566666655444432111 33444221 1235555553 5667899999999999877644
No 149
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=23.18 E-value=81 Score=33.54 Aligned_cols=72 Identities=13% Similarity=0.160 Sum_probs=40.5
Q ss_pred EEEcCCCCCCCCcceeeeecCCch-----------hHHHHHHHhCC-eEEEeCCccCCCcchhcccCCCCccCCCCceEE
Q 003997 170 VVPIPVKEYPGYNFLGLIFGPASD-----------TQKRLEKETRT-VIKVYGTKADTGEKVEISTSDANVQSTYEEFHI 237 (780)
Q Consensus 170 KIyIPvkeyP~~NFIGlIIGPrGn-----------TiKrLEeETGA-KI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHV 237 (780)
.++--.+-.+.+..+|+||||||. .+..+.++... +|.+|-+. .--+||
T Consensus 112 ~~iAt~d~m~~l~kLgriLGprGlMP~pk~gTvt~di~~~V~~~k~G~v~~r~dk-------------------~g~i~~ 172 (229)
T CHL00129 112 LLIATPDMMPKLAKLGRVLGPRGLMPSPKSGTVTTDLASAINEFKKGKLEYRADK-------------------TGIVHV 172 (229)
T ss_pred EEEECHHHHHHHHHhcCcccccCCCCCCCCCCccccHHHHHHHHhcCcEEEEecC-------------------CcEEEE
Confidence 343344445556678999999964 35566666543 67777431 112577
Q ss_pred EEEe---cCHHHHHHHHHHHHhcccc
Q 003997 238 SISA---DSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 238 lIsA---d~~EkVdkAvelIE~LL~p 260 (780)
-|-- ++++-++.+..+|+.|+.-
T Consensus 173 ~VG~~~m~~~~l~eNi~a~l~~i~~~ 198 (229)
T CHL00129 173 LFGKSNFTEEDLLENLQAIYESIEQN 198 (229)
T ss_pred EEeCCCCCHHHHHHHHHHHHHHHHHh
Confidence 6642 3344455555555555553
No 150
>COG0436 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=22.93 E-value=4.7e+02 Score=29.52 Aligned_cols=26 Identities=19% Similarity=0.186 Sum_probs=21.0
Q ss_pred eEEEEE-ecCHHHHHHHHHHHHhcccc
Q 003997 235 FHISIS-ADSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 235 LHVlIs-Ad~~EkVdkAvelIE~LL~p 260 (780)
.||.|+ +.+.+.+++|+++|+.++..
T Consensus 365 ~~vRis~~~~~~~l~~a~~rl~~~~~~ 391 (393)
T COG0436 365 GYVRLSLATSEETLEEALRRLARFLAE 391 (393)
T ss_pred CeEEEEEecCHHHHHHHHHHHHHHHHh
Confidence 488875 55669999999999998754
No 151
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=22.82 E-value=3.4e+02 Score=34.36 Aligned_cols=7 Identities=29% Similarity=-0.026 Sum_probs=3.8
Q ss_pred CCCCCCC
Q 003997 375 VPPGPYM 381 (780)
Q Consensus 375 ~~~~~~m 381 (780)
|||.++|
T Consensus 436 vlHr~~~ 442 (1102)
T KOG1924|consen 436 VLHRTGM 442 (1102)
T ss_pred HHhcCCC
Confidence 4455555
No 152
>KOG2335 consensus tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=22.61 E-value=92 Score=35.48 Aligned_cols=39 Identities=8% Similarity=0.111 Sum_probs=35.5
Q ss_pred ccCCCCceEEEEEecCHHHHHHHHHHHHhcccccccchh
Q 003997 228 VQSTYEEFHISISADSYEKVDAATDLIELLVTSVSGSLA 266 (780)
Q Consensus 228 ~~~~~EpLHVlIsAd~~EkVdkAvelIE~LL~pVevg~~ 266 (780)
...+|.+|-|.|.|+|.+.+-+|+++|+.+.+.+..|++
T Consensus 69 t~~~D~PLIvQf~~ndp~~ll~Aa~lv~~y~D~idlNcG 107 (358)
T KOG2335|consen 69 TSPEDRPLIVQFGGNDPENLLKAARLVQPYCDGIDLNCG 107 (358)
T ss_pred cCCCCCceEEEEcCCCHHHHHHHHHHhhhhcCcccccCC
Confidence 446788999999999999999999999999999988876
No 153
>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=22.57 E-value=1.3e+02 Score=25.80 Aligned_cols=25 Identities=12% Similarity=0.239 Sum_probs=22.3
Q ss_pred eEEEEEecCHHHHHHHHHHHHhccc
Q 003997 235 FHISISADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 235 LHVlIsAd~~EkVdkAvelIE~LL~ 259 (780)
+.|++.|.+.+.+++.++.|.++|+
T Consensus 49 iRv~~Ea~~~~~~~~~~~~i~~~ik 73 (73)
T PF00408_consen 49 IRVYVEAPDEEELEEIAEEIAEAIK 73 (73)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred EEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 8999999999999999999888763
No 154
>PRK06019 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed
Probab=22.54 E-value=2e+02 Score=31.83 Aligned_cols=48 Identities=15% Similarity=0.162 Sum_probs=32.0
Q ss_pred HHHHHHHhCCeEEEeCCccCCCcchhcccCCCCccCCCCceEEEEEecCHHHHHHHHHHHHh
Q 003997 195 QKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQSTYEEFHISISADSYEKVDAATDLIEL 256 (780)
Q Consensus 195 iKrLEeETGAKI~IRGKGS~k~~K~E~~~~Dg~~~~~~EpLHVlIsAd~~EkVdkAvelIE~ 256 (780)
+..+.+..|+++.+.||...+.+.+ -.||.|.++|.+.+.+-++.+..
T Consensus 319 ~~~~~~~~~~~~~~ygk~~~~~~rk--------------~Ghv~~~~~~~~~~~~~~~~~~~ 366 (372)
T PRK06019 319 WDALLALPGAHLHLYGKAEARPGRK--------------MGHVTVLGDDVEALLAKLEALAP 366 (372)
T ss_pred HHHHhhCCCCEEEECCCCCCCCCCc--------------eEEEEeecCCHHHHHHHHHHHHh
Confidence 3445566899999999954332221 25999999988766655555443
No 155
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=22.49 E-value=95 Score=31.12 Aligned_cols=21 Identities=33% Similarity=0.257 Sum_probs=18.1
Q ss_pred chhHHHHHHHhCCeEEEeCCc
Q 003997 192 SDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 192 GnTiKrLEeETGAKI~IRGKG 212 (780)
...||+||++.|+++-+|..+
T Consensus 33 S~~I~~LE~~lg~~Lf~R~~~ 53 (297)
T COG0583 33 SRQIKRLEEELGVPLFERTTR 53 (297)
T ss_pred HHHHHHHHHHhCchheeecCC
Confidence 356999999999999999854
No 156
>PRK13520 L-tyrosine decarboxylase; Provisional
Probab=22.48 E-value=4.9e+02 Score=27.71 Aligned_cols=24 Identities=8% Similarity=0.117 Sum_probs=18.2
Q ss_pred EEEEEe---cCHHHHHHHHHHHHhccc
Q 003997 236 HISISA---DSYEKVDAATDLIELLVT 259 (780)
Q Consensus 236 HVlIsA---d~~EkVdkAvelIE~LL~ 259 (780)
++.|+- .++|.+++.++.++++++
T Consensus 344 ~iRis~~~~~t~edi~~~~~~l~~~~~ 370 (371)
T PRK13520 344 ALRIVCMPHVTREHIENFLEDLKEVKK 370 (371)
T ss_pred EEEEEEECCCCHHHHHHHHHHHHHHhh
Confidence 344543 588999999999998764
No 157
>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=22.36 E-value=4.7e+02 Score=28.60 Aligned_cols=24 Identities=17% Similarity=0.230 Sum_probs=19.8
Q ss_pred eEEEEE-ecCHHHHHHHHHHHHhcc
Q 003997 235 FHISIS-ADSYEKVDAATDLIELLV 258 (780)
Q Consensus 235 LHVlIs-Ad~~EkVdkAvelIE~LL 258 (780)
-|+.|+ +.+.+.+++|++.|.+++
T Consensus 369 ~~~Ris~~~~~~~l~~~l~~l~~~~ 393 (393)
T TIGR03538 369 GRVRIALVAPLEECVEAAERIRSFI 393 (393)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHhC
Confidence 378887 668999999999998754
No 158
>COG1159 Era GTPase [General function prediction only]
Probab=22.16 E-value=1.9e+02 Score=32.30 Aligned_cols=70 Identities=14% Similarity=0.175 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC--CCCCCCC-c---c-EEEEEcCCCCCCCCcceeeeecCCchhHHHH--------H
Q 003997 135 LECLELEKQEVIGEILKLNPSYRT--PPDYKPL-L---K-EAVVPIPVKEYPGYNFLGLIFGPASDTQKRL--------E 199 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRP--PsDYkP~-~---k-~~KIyIPvkeyP~~NFIGlIIGPrGnTiKrL--------E 199 (780)
....|-=|..|+...-+-+|.-.. ..+++.. . + ...|||.-+ .--|-|||-+|..||+| |
T Consensus 190 f~~aEiiREk~~~~l~eElPhsv~VeIe~~~~~~~~~~~I~a~I~Ver~-----sQK~IiIGk~G~~iK~IG~~AR~~ie 264 (298)
T COG1159 190 FLAAEIIREKLLLLLREELPHSVAVEIEEFEEREKGLLKIHATIYVERE-----SQKGIIIGKNGAMIKKIGTAARKDIE 264 (298)
T ss_pred HHHHHHHHHHHHHhcccccCceEEEEEEEEEecCCCeEEEEEEEEEecC-----CccceEECCCcHHHHHHHHHHHHHHH
Confidence 455566677777777776766433 2233332 1 2 246788876 45688999999999865 5
Q ss_pred HHhCCeEEEe
Q 003997 200 KETRTVIKVY 209 (780)
Q Consensus 200 eETGAKI~IR 209 (780)
+-.||||.+.
T Consensus 265 ~l~~~kV~L~ 274 (298)
T COG1159 265 KLLGCKVYLE 274 (298)
T ss_pred HHhCCceEEE
Confidence 5566766554
No 159
>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=22.16 E-value=36 Score=30.26 Aligned_cols=42 Identities=19% Similarity=0.152 Sum_probs=33.4
Q ss_pred EEEEEecC-HHHHHHHHHHHHhcccccccchhhhccccccccc
Q 003997 236 HISISADS-YEKVDAATDLIELLVTSVSGSLAAISTSTLVSGE 277 (780)
Q Consensus 236 HVlIsAd~-~EkVdkAvelIE~LL~pVevg~~a~~~~~~v~g~ 277 (780)
||+|..++ .+..+++.+.+++|+..+..+...|...++=+++
T Consensus 1 HIl~~~~~~~~~~~~~~~~a~~i~~~l~~g~~~F~~~A~~yS~ 43 (95)
T PF00639_consen 1 HILVKPPPSDEEKDAAKKKAEEIYEQLKKGEDSFAELAREYSE 43 (95)
T ss_dssp EEEEESTTSCCHHHHHHHHHHHHHHHHHTTSSSHHHHHHHHCS
T ss_pred CEEEECCCchhhHHHHHHHHHHHHHHHHhCchhHHHHHHHhCC
Confidence 88888765 7888999999999999998887767777665553
No 160
>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=22.05 E-value=1.6e+02 Score=31.47 Aligned_cols=76 Identities=21% Similarity=0.109 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCC---C----CCCCCC-ccEEEEEcCCCCCCCCcceee---eecCCchhHHHHHHHhC
Q 003997 135 LECLELEKQEVIGEILKLNPSYRT---P----PDYKPL-LKEAVVPIPVKEYPGYNFLGL---IFGPASDTQKRLEKETR 203 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRP---P----sDYkP~-~k~~KIyIPvkeyP~~NFIGl---IIGPrGnTiKrLEeETG 203 (780)
++-|++|=.+-+++.++..-.+-. | .|.... -++++++.-= -||+|+ |=+|.|+.+|.|.++ |
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 566666665556655555533322 1 111111 1578888753 378886 448999999999988 7
Q ss_pred Ce--EEEeCCccCCC
Q 003997 204 TV--IKVYGTKADTG 216 (780)
Q Consensus 204 AK--I~IRGKGS~k~ 216 (780)
.+ ++-||-|+.+.
T Consensus 133 ~~lGVSSRG~Gslk~ 147 (213)
T PF03420_consen 133 WKLGVSSRGLGSLKK 147 (213)
T ss_pred CccceecCCcccccc
Confidence 66 45577777653
No 161
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=22.02 E-value=82 Score=32.47 Aligned_cols=21 Identities=24% Similarity=0.238 Sum_probs=18.6
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q 003997 193 DTQKRLEKETRTVIKVYGTKA 213 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKGS 213 (780)
+.||+||++.|+++-+|++|.
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i 55 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPC 55 (294)
T ss_pred HHHHHHHHHhCceeeecCCCC
Confidence 568999999999999998754
No 162
>PRK05387 histidinol-phosphate aminotransferase; Provisional
Probab=22.01 E-value=7e+02 Score=26.53 Aligned_cols=24 Identities=17% Similarity=0.365 Sum_probs=19.9
Q ss_pred EEEEEecCHHHHHHHHHHHHhccc
Q 003997 236 HISISADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 236 HVlIsAd~~EkVdkAvelIE~LL~ 259 (780)
|+.|+--+.+.++++++.|++++.
T Consensus 329 ~iRis~~~~~~~~~~~~~L~~~~~ 352 (353)
T PRK05387 329 FLRITIGTDEEMEALVDALKEILA 352 (353)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHhh
Confidence 777776688999999999988764
No 163
>PRK06939 2-amino-3-ketobutyrate coenzyme A ligase; Provisional
Probab=21.98 E-value=7e+02 Score=26.79 Aligned_cols=19 Identities=26% Similarity=0.307 Sum_probs=16.8
Q ss_pred cCHHHHHHHHHHHHhcccc
Q 003997 242 DSYEKVDAATDLIELLVTS 260 (780)
Q Consensus 242 d~~EkVdkAvelIE~LL~p 260 (780)
.+++.|+++++.|+.++..
T Consensus 375 ~~~~~i~~~l~~L~~~~~~ 393 (397)
T PRK06939 375 HTKEQLDRAIDAFEKVGKE 393 (397)
T ss_pred CCHHHHHHHHHHHHHHHHH
Confidence 7899999999999998764
No 164
>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=21.96 E-value=1.3e+02 Score=27.58 Aligned_cols=61 Identities=16% Similarity=0.076 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCC--CCCccEEEEEcCCCCCCCCcceeeeecCCchhH
Q 003997 135 LECLELEKQEVIGEILKLNPSYRTPPDY--KPLLKEAVVPIPVKEYPGYNFLGLIFGPASDTQ 195 (780)
Q Consensus 135 RekLEeER~~IIeemlKliP~fRPPsDY--kP~~k~~KIyIPvkeyP~~NFIGlIIGPrGnTi 195 (780)
-+++|||..+-|+++++....-+.-.+- .-........=....+...++|--|.|+.|.+|
T Consensus 18 eKk~EEeK~eTInKLLkkqa~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~IR~v~~~~G~~v 80 (89)
T PF04795_consen 18 EKKLEEEKMETINKLLKKQATRKKREPKDKEGEEDSAQEKKRRAPKPNPPMIRWVSNKNGSRV 80 (89)
T ss_pred HHHHHHHHHHHHHHHHhhhccccccchhhhhhhhhccccccccccCCCCCEEEEEECCCceEE
Confidence 5799999999999999988622211000 000001111112234456689999998888764
No 165
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=21.58 E-value=99 Score=32.21 Aligned_cols=20 Identities=15% Similarity=0.067 Sum_probs=17.4
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q 003997 193 DTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGKG 212 (780)
.-||+||++.|+++-+|...
T Consensus 37 ~~I~~LE~~lg~~Lf~R~~r 56 (296)
T PRK11062 37 GQIKALEERLQGKLFKRKGR 56 (296)
T ss_pred HHHHHHHHHcCccceeecCC
Confidence 35899999999999999764
No 166
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=21.37 E-value=99 Score=32.35 Aligned_cols=20 Identities=20% Similarity=0.144 Sum_probs=17.4
Q ss_pred hhHHHHHHHhCCeEEEeC-Cc
Q 003997 193 DTQKRLEKETRTVIKVYG-TK 212 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRG-KG 212 (780)
..||+||++.||++-+|. +|
T Consensus 35 r~I~~LE~~lg~~LF~R~~~~ 55 (309)
T PRK12682 35 KAIIELEEELGIEIFIRHGKR 55 (309)
T ss_pred HHHHHHHHHhCCeeEEECCCC
Confidence 468999999999999996 44
No 167
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=21.24 E-value=1.2e+02 Score=31.57 Aligned_cols=19 Identities=21% Similarity=0.037 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEeCC
Q 003997 193 DTQKRLEKETRTVIKVYGT 211 (780)
Q Consensus 193 nTiKrLEeETGAKI~IRGK 211 (780)
+.||+||+|.||++-+|..
T Consensus 38 ~~i~~LE~~lg~~Lf~R~~ 56 (305)
T CHL00180 38 LQIKNLEKQLNIPLFDRSK 56 (305)
T ss_pred HHHHHHHHHhCCEEEEecC
Confidence 4589999999999999975
No 168
>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=21.06 E-value=4.4e+02 Score=26.98 Aligned_cols=63 Identities=13% Similarity=0.111 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHhhCCCccCCCC----CCCCCCCCCCCCCCCCchhH--H-HHHHHHHHHHHHHHHHHhC
Q 003997 91 YQTRVDQIVQQLESGSLEAEENQ----VPEVAAQNADQKSPNPQVDR--E-LECLELEKQEVIGEILKLN 153 (780)
Q Consensus 91 ~QlRIeeIt~KL~tg~l~~~~~e----~s~SP~P~p~yds~GkR~NT--r-RekLEeER~~IIeemlKli 153 (780)
.++.|++|...|+.-++++..-. |.+.|.-.-.--+.||-+=| + .+.+++.-.++++.+.+++
T Consensus 15 ~~ldL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~L~~~g 84 (174)
T cd04518 15 QELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKKLKDYG 84 (174)
T ss_pred CeecHHHHHhhCCCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHHhcC
Confidence 35678899888877666553211 11233322222345776666 4 7788888888888888776
No 169
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=20.86 E-value=51 Score=39.35 Aligned_cols=31 Identities=19% Similarity=0.252 Sum_probs=29.2
Q ss_pred cceeeeecCCchhHHHHHHHhCCeEEEeCCc
Q 003997 182 NFLGLIFGPASDTQKRLEKETRTVIKVYGTK 212 (780)
Q Consensus 182 NFIGlIIGPrGnTiKrLEeETGAKI~IRGKG 212 (780)
.-.++|+|-+|.|++.|++-++|||.+|-.|
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 170
>PRK02627 acetylornithine aminotransferase; Provisional
Probab=20.45 E-value=5.1e+02 Score=28.03 Aligned_cols=24 Identities=25% Similarity=0.302 Sum_probs=19.3
Q ss_pred EEEEE---ecCHHHHHHHHHHHHhccc
Q 003997 236 HISIS---ADSYEKVDAATDLIELLVT 259 (780)
Q Consensus 236 HVlIs---Ad~~EkVdkAvelIE~LL~ 259 (780)
++.|+ ..+++.++++++.|+++|+
T Consensus 367 ~lRi~~~~~~~~~~i~~~~~~l~~~l~ 393 (396)
T PRK02627 367 VLRLLPPLIISKEEIDEAVDRLEEVLK 393 (396)
T ss_pred EEEEECCcccCHHHHHHHHHHHHHHHH
Confidence 45554 6789999999999998875
No 171
>TIGR01142 purT phosphoribosylglycinamide formyltransferase 2. This enzyme is an alternative to PurN (TIGR00639)
Probab=20.42 E-value=2.9e+02 Score=30.10 Aligned_cols=25 Identities=16% Similarity=-0.023 Sum_probs=19.9
Q ss_pred ceEEEEEecCHHHHHHHHHHHHhcc
Q 003997 234 EFHISISADSYEKVDAATDLIELLV 258 (780)
Q Consensus 234 pLHVlIsAd~~EkVdkAvelIE~LL 258 (780)
-.||.+.+++.+.+++.++.+..+|
T Consensus 353 ~G~v~~~~~s~~~~~~~~~~~~~~i 377 (380)
T TIGR01142 353 LGVALATAKSVEAARERAEEVAHAV 377 (380)
T ss_pred CEEEEEecCCHHHHHHHHHHHHhhc
Confidence 3799999999988887777766555
No 172
>PHA00431 internal virion protein C
Probab=20.39 E-value=1.8e+02 Score=35.58 Aligned_cols=32 Identities=19% Similarity=0.322 Sum_probs=25.1
Q ss_pred HHHHHHHhhCCCccCCCCCCCCCCCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHh
Q 003997 96 DQIVQQLESGSLEAEENQVPEVAAQNADQKSPNPQVDRELECLELEKQEVIGEILKL 152 (780)
Q Consensus 96 eeIt~KL~tg~l~~~~~e~s~SP~P~p~yds~GkR~NTrRekLEeER~~IIeemlKl 152 (780)
|||.+||++|++. .|+.||+-||..|++-.+.
T Consensus 120 dev~~Ki~nGeFr-------------------------tRqemEEyRhsrL~e~aks 151 (746)
T PHA00431 120 DEVAQKIKNGEFR-------------------------TRQEMEEYRHSRLQESAKS 151 (746)
T ss_pred HHHHHHHhccCcc-------------------------cHHHHHHHHHHHHHHHHHH
Confidence 6788888888761 1689999999999877664
Done!