Query psy1775
Match_columns 304
No_of_seqs 406 out of 1752
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 21:56:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1775.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1775hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0119|consensus 100.0 1.1E-51 2.3E-56 399.9 14.4 188 103-298 50-238 (554)
2 COG5176 MSL5 Splicing factor ( 100.0 1.7E-43 3.7E-48 311.7 10.9 178 117-299 71-249 (269)
3 KOG1588|consensus 100.0 2.2E-30 4.8E-35 236.6 11.7 135 160-299 52-197 (259)
4 cd02395 SF1_like-KH Splicing f 100.0 2.9E-29 6.3E-34 207.8 11.0 94 197-290 1-97 (120)
5 TIGR02696 pppGpp_PNP guanosine 99.6 8.8E-15 1.9E-19 151.3 10.3 112 158-298 541-654 (719)
6 COG1185 Pnp Polyribonucleotide 99.5 1.3E-14 2.9E-19 147.5 7.3 115 157-299 513-627 (692)
7 PLN00207 polyribonucleotide nu 99.5 5.1E-14 1.1E-18 148.5 7.0 113 157-297 646-759 (891)
8 TIGR03591 polynuc_phos polyrib 99.5 8.8E-14 1.9E-18 144.9 7.5 114 156-298 512-625 (684)
9 KOG0119|consensus 99.4 2.4E-13 5.3E-18 133.4 5.6 105 3-115 207-327 (554)
10 cd02393 PNPase_KH Polynucleoti 99.3 5.8E-12 1.3E-16 92.4 7.4 61 195-283 1-61 (61)
11 PRK11824 polynucleotide phosph 99.3 2.1E-12 4.5E-17 134.9 5.3 113 159-299 517-629 (693)
12 PF00013 KH_1: KH domain syndr 98.9 1.5E-09 3.1E-14 78.6 3.6 60 197-282 1-60 (60)
13 KOG1067|consensus 98.9 5.2E-09 1.1E-13 104.8 7.7 110 159-297 560-669 (760)
14 PRK13763 putative RNA-processi 98.8 4.7E-09 1E-13 92.9 5.7 75 196-298 3-88 (180)
15 cd00105 KH-I K homology RNA-bi 98.8 1.6E-08 3.5E-13 73.3 7.5 63 198-283 2-64 (64)
16 cd02394 vigilin_like_KH K homo 98.8 8E-09 1.7E-13 75.2 5.5 61 198-283 2-62 (62)
17 TIGR03665 arCOG04150 arCOG0415 98.7 7.9E-09 1.7E-13 90.8 4.4 71 200-298 2-82 (172)
18 COG5082 AIR1 Arginine methyltr 98.7 8.8E-09 1.9E-13 91.1 3.6 51 36-86 55-118 (190)
19 smart00322 KH K homology RNA-b 98.6 2.1E-07 4.5E-12 66.9 8.8 66 196-286 3-68 (69)
20 cd02396 PCBP_like_KH K homolog 98.6 1.8E-07 3.9E-12 69.1 7.7 63 198-282 2-64 (65)
21 PTZ00368 universal minicircle 98.5 6.8E-08 1.5E-12 82.5 2.8 44 42-85 78-122 (148)
22 PTZ00368 universal minicircle 98.4 3.4E-07 7.4E-12 78.1 4.2 46 41-86 27-72 (148)
23 TIGR03665 arCOG04150 arCOG0415 98.3 1E-06 2.2E-11 77.5 5.2 60 212-295 99-158 (172)
24 PF13014 KH_3: KH domain 98.3 2E-06 4.3E-11 58.4 5.2 28 212-239 1-28 (43)
25 KOG1960|consensus 98.2 1.4E-06 3.1E-11 84.4 4.0 86 197-289 211-296 (531)
26 PF00098 zf-CCHC: Zinc knuckle 98.2 1E-06 2.2E-11 49.5 1.6 16 68-83 2-17 (18)
27 PRK13763 putative RNA-processi 98.1 4E-06 8.6E-11 74.2 5.4 56 212-291 105-160 (180)
28 COG5082 AIR1 Arginine methyltr 98.0 2.5E-06 5.4E-11 75.7 2.6 43 42-87 98-141 (190)
29 PF00098 zf-CCHC: Zinc knuckle 98.0 2.9E-06 6.4E-11 47.6 1.7 18 42-59 1-18 (18)
30 KOG4400|consensus 98.0 3.1E-06 6.8E-11 78.8 2.8 43 42-88 144-186 (261)
31 PRK04163 exosome complex RNA-b 98.0 1.2E-05 2.6E-10 74.0 6.0 66 198-291 147-212 (235)
32 KOG1676|consensus 97.9 7.3E-05 1.6E-09 75.9 10.7 107 163-293 195-305 (600)
33 KOG1676|consensus 97.7 0.0002 4.3E-09 72.9 10.6 74 194-288 137-210 (600)
34 COG1094 Predicted RNA-binding 97.7 7.3E-05 1.6E-09 66.7 5.9 60 212-295 112-171 (194)
35 KOG4400|consensus 97.3 0.00013 2.9E-09 67.8 2.7 45 41-85 92-162 (261)
36 KOG2191|consensus 97.3 0.0022 4.8E-08 61.4 10.8 77 196-292 132-209 (402)
37 PF13696 zf-CCHC_2: Zinc knuck 97.1 0.00023 4.9E-09 45.7 1.0 22 66-87 8-29 (32)
38 KOG2190|consensus 96.9 0.0065 1.4E-07 61.6 10.1 102 162-288 105-208 (485)
39 KOG2193|consensus 96.7 0.0016 3.5E-08 64.1 4.1 72 198-291 201-272 (584)
40 PRK00106 hypothetical protein; 96.7 0.0093 2E-07 61.2 9.8 69 195-289 224-292 (535)
41 TIGR03319 YmdA_YtgF conserved 96.6 0.0096 2.1E-07 60.9 9.4 75 187-289 197-271 (514)
42 PRK12704 phosphodiesterase; Pr 96.6 0.012 2.6E-07 60.3 9.5 69 195-289 209-277 (520)
43 PF13696 zf-CCHC_2: Zinc knuck 96.1 0.0027 5.9E-08 40.7 1.2 21 40-60 7-27 (32)
44 KOG2193|consensus 95.9 0.0056 1.2E-07 60.5 3.2 67 209-289 287-353 (584)
45 KOG2191|consensus 95.9 0.033 7.1E-07 53.6 7.8 72 196-287 39-110 (402)
46 COG1094 Predicted RNA-binding 95.8 0.029 6.3E-07 50.3 6.9 64 195-286 7-75 (194)
47 KOG2814|consensus 95.8 0.014 3E-07 56.1 5.1 67 199-289 60-126 (345)
48 PF13917 zf-CCHC_3: Zinc knuck 95.7 0.0048 1E-07 42.1 1.2 17 42-58 5-21 (42)
49 PF13917 zf-CCHC_3: Zinc knuck 95.4 0.0079 1.7E-07 41.0 1.3 19 66-84 4-22 (42)
50 smart00343 ZnF_C2HC zinc finge 95.1 0.009 1.9E-07 36.1 0.8 18 68-85 1-18 (26)
51 KOG1960|consensus 94.9 0.03 6.5E-07 55.1 4.3 65 218-289 110-174 (531)
52 PRK12705 hypothetical protein; 94.8 0.076 1.6E-06 54.3 7.1 70 195-290 197-266 (508)
53 cd02134 NusA_KH NusA_K homolog 94.8 0.061 1.3E-06 39.2 4.6 36 196-237 25-60 (61)
54 smart00343 ZnF_C2HC zinc finge 94.6 0.016 3.4E-07 35.1 1.0 17 43-59 1-17 (26)
55 PF14787 zf-CCHC_5: GAG-polypr 94.6 0.023 5E-07 37.3 1.8 23 67-89 3-25 (36)
56 KOG0109|consensus 94.1 0.023 5.1E-07 53.8 1.5 25 66-90 160-184 (346)
57 PF15288 zf-CCHC_6: Zinc knuck 93.8 0.057 1.2E-06 36.4 2.4 22 67-88 2-25 (40)
58 KOG0336|consensus 92.6 0.15 3.3E-06 50.8 4.4 61 211-291 56-116 (629)
59 KOG2190|consensus 92.3 0.78 1.7E-05 46.8 9.3 79 188-289 35-122 (485)
60 KOG2874|consensus 91.4 0.13 2.8E-06 48.7 2.3 27 214-240 161-187 (356)
61 COG1097 RRP4 RNA-binding prote 91.3 0.44 9.5E-06 44.1 5.6 39 198-242 148-186 (239)
62 PF15288 zf-CCHC_6: Zinc knuck 90.5 0.14 3E-06 34.5 1.2 19 42-60 2-22 (40)
63 KOG2192|consensus 89.9 1.1 2.4E-05 42.3 6.9 67 197-288 316-384 (390)
64 COG1855 ATPase (PilT family) [ 89.7 0.67 1.5E-05 47.0 5.7 70 166-245 460-529 (604)
65 PF14392 zf-CCHC_4: Zinc knuck 89.6 0.12 2.6E-06 36.0 0.4 17 67-83 32-48 (49)
66 PF13184 KH_5: NusA-like KH do 88.9 0.2 4.3E-06 37.6 1.1 38 199-237 6-44 (69)
67 KOG2192|consensus 88.5 2 4.4E-05 40.6 7.6 38 196-239 48-85 (390)
68 PF14392 zf-CCHC_4: Zinc knuck 88.3 0.19 4E-06 35.1 0.6 19 41-59 31-49 (49)
69 COG5222 Uncharacterized conser 87.1 0.26 5.6E-06 47.0 1.0 22 66-87 176-197 (427)
70 KOG0109|consensus 84.8 0.36 7.9E-06 45.9 0.7 22 40-61 159-180 (346)
71 PRK08406 transcription elongat 84.0 1.4 3E-05 37.6 3.9 35 199-239 35-69 (140)
72 COG5222 Uncharacterized conser 83.0 0.53 1.1E-05 45.0 1.0 21 41-61 176-196 (427)
73 PF14787 zf-CCHC_5: GAG-polypr 82.5 0.89 1.9E-05 29.9 1.6 20 43-62 4-23 (36)
74 KOG0314|consensus 81.9 1.2 2.6E-05 44.8 3.1 45 43-87 135-179 (448)
75 cd02409 KH-II KH-II (K homolo 81.0 1.4 3E-05 31.2 2.4 23 213-235 36-58 (68)
76 KOG2113|consensus 73.5 3 6.5E-05 40.3 2.9 36 196-237 26-61 (394)
77 PRK08406 transcription elongat 71.3 3.9 8.5E-05 34.8 2.9 36 197-238 100-135 (140)
78 COG0195 NusA Transcription elo 71.1 3.5 7.6E-05 37.0 2.7 32 210-241 84-115 (190)
79 cd02414 jag_KH jag_K homology 70.3 5.3 0.00011 30.1 3.2 26 212-237 34-59 (77)
80 PRK13764 ATPase; Provisional 69.8 3.6 7.9E-05 43.1 2.9 40 197-242 482-521 (602)
81 KOG3116|consensus 68.9 1.1 2.5E-05 38.6 -0.9 21 42-62 28-48 (177)
82 TIGR01952 nusA_arch NusA famil 68.7 5.6 0.00012 34.0 3.3 28 212-239 43-70 (141)
83 KOG3116|consensus 67.6 1.6 3.6E-05 37.7 -0.1 24 64-87 25-48 (177)
84 PF12353 eIF3g: Eukaryotic tra 65.5 3 6.6E-05 35.0 1.0 21 65-86 105-125 (128)
85 PRK12327 nusA transcription el 65.1 6.6 0.00014 38.7 3.4 40 199-239 234-274 (362)
86 COG1702 PhoH Phosphate starvat 64.6 9.3 0.0002 37.4 4.3 55 211-289 24-80 (348)
87 KOG2279|consensus 62.9 6.2 0.00013 40.7 2.9 43 194-242 66-108 (608)
88 PRK06418 transcription elongat 62.1 6.4 0.00014 34.6 2.5 28 212-240 71-98 (166)
89 TIGR01953 NusA transcription t 61.8 8.5 0.00018 37.6 3.5 40 199-239 232-272 (341)
90 PF13083 KH_4: KH domain; PDB: 61.5 3.5 7.7E-05 30.6 0.7 30 197-232 30-59 (73)
91 KOG2113|consensus 61.2 8.2 0.00018 37.4 3.2 30 210-239 123-152 (394)
92 KOG3273|consensus 60.2 5.3 0.00011 36.3 1.6 60 212-295 179-238 (252)
93 KOG2208|consensus 59.1 6.8 0.00015 42.2 2.5 39 195-239 708-746 (753)
94 PRK00468 hypothetical protein; 55.2 7.3 0.00016 29.7 1.5 28 196-229 30-57 (75)
95 PRK02821 hypothetical protein; 54.9 7.4 0.00016 29.9 1.5 30 197-232 32-61 (77)
96 PRK12328 nusA transcription el 54.8 9.1 0.0002 37.9 2.4 40 199-239 240-280 (374)
97 PRK12329 nusA transcription el 53.7 11 0.00024 38.1 2.8 41 198-239 265-306 (449)
98 PRK04023 DNA polymerase II lar 53.5 31 0.00066 38.4 6.3 73 40-118 625-698 (1121)
99 PRK00089 era GTPase Era; Revie 51.8 79 0.0017 29.3 8.2 90 141-238 171-271 (292)
100 KOG2560|consensus 51.6 4.1 8.8E-05 41.2 -0.6 22 66-87 112-133 (529)
101 KOG2208|consensus 51.2 20 0.00043 38.7 4.4 33 212-244 357-389 (753)
102 PF14611 SLS: Mitochondrial in 50.8 47 0.001 29.5 6.2 90 169-289 2-91 (210)
103 KOG2044|consensus 50.3 5.8 0.00013 42.6 0.3 22 66-87 260-281 (931)
104 KOG2673|consensus 50.2 6.4 0.00014 39.7 0.6 20 44-63 131-150 (485)
105 COG1837 Predicted RNA-binding 49.2 10 0.00023 29.1 1.5 29 195-229 29-57 (76)
106 PRK01064 hypothetical protein; 47.2 26 0.00057 26.9 3.4 30 196-231 30-59 (78)
107 COG5179 TAF1 Transcription ini 46.0 12 0.00025 39.5 1.7 12 68-79 939-950 (968)
108 PF05191 ADK_lid: Adenylate ki 45.4 9.8 0.00021 24.9 0.7 27 43-74 3-29 (36)
109 PRK09202 nusA transcription el 45.2 17 0.00038 37.0 2.8 40 199-239 234-274 (470)
110 KOG0334|consensus 44.0 15 0.00032 40.7 2.1 81 199-290 899-979 (997)
111 PF07295 DUF1451: Protein of u 43.7 20 0.00043 30.8 2.5 61 3-75 79-139 (146)
112 KOG0107|consensus 41.8 20 0.00044 32.0 2.3 17 68-84 102-118 (195)
113 PRK12328 nusA transcription el 41.5 29 0.00063 34.4 3.6 43 196-244 308-350 (374)
114 KOG2044|consensus 40.8 13 0.00029 40.0 1.2 23 38-60 257-279 (931)
115 COG0347 GlnK Nitrogen regulato 38.9 80 0.0017 26.1 5.2 66 233-303 29-95 (112)
116 KOG3070|consensus 36.7 34 0.00074 31.7 3.1 42 41-85 173-218 (235)
117 PRK09986 DNA-binding transcrip 36.4 58 0.0013 29.5 4.6 21 222-242 40-60 (294)
118 COG1847 Jag Predicted RNA-bind 36.4 1.2E+02 0.0026 27.8 6.4 67 161-237 60-126 (208)
119 KOG2673|consensus 36.2 18 0.00039 36.6 1.3 21 67-87 129-149 (485)
120 cd02410 archeal_CPSF_KH The ar 34.2 45 0.00098 28.7 3.2 34 199-238 79-112 (145)
121 KOG3794|consensus 34.1 17 0.00036 36.2 0.6 23 65-87 123-147 (453)
122 PF12353 eIF3g: Eukaryotic tra 34.0 22 0.00048 29.8 1.3 20 41-61 106-125 (128)
123 TIGR00436 era GTP-binding prot 33.9 79 0.0017 29.1 5.1 38 195-237 220-265 (270)
124 KOG0107|consensus 33.1 21 0.00045 31.9 1.0 34 43-87 102-135 (195)
125 COG0484 DnaJ DnaJ-class molecu 32.0 24 0.00052 35.0 1.3 49 229-287 300-349 (371)
126 PRK14890 putative Zn-ribbon RN 31.4 20 0.00044 26.2 0.6 11 66-76 48-58 (59)
127 KOG4165|consensus 31.2 51 0.0011 32.4 3.4 25 212-239 191-217 (433)
128 KOG0341|consensus 30.8 29 0.00062 35.0 1.6 18 42-59 571-588 (610)
129 PRK14714 DNA polymerase II lar 30.4 86 0.0019 35.9 5.4 71 41-117 667-743 (1337)
130 TIGR01953 NusA transcription t 30.2 55 0.0012 32.0 3.5 38 196-239 301-338 (341)
131 KOG2560|consensus 29.4 14 0.00031 37.4 -0.7 20 42-61 113-132 (529)
132 PF09779 Ima1_N: Ima1 N-termin 29.2 46 0.00099 27.9 2.4 36 43-83 2-37 (131)
133 PF07650 KH_2: KH domain syndr 29.2 24 0.00052 26.3 0.7 24 212-235 35-58 (78)
134 PRK11242 DNA-binding transcrip 29.0 95 0.0021 28.1 4.7 20 222-241 34-53 (296)
135 TIGR03655 anti_R_Lar restricti 28.8 45 0.00098 23.3 2.0 36 42-78 2-38 (53)
136 COG0026 PurK Phosphoribosylami 28.3 1E+02 0.0023 30.5 5.0 53 223-288 318-370 (375)
137 PRK15494 era GTPase Era; Provi 28.3 1.1E+02 0.0023 29.6 5.1 40 195-239 272-319 (339)
138 cd04516 TBP_eukaryotes eukaryo 27.4 1.5E+02 0.0033 26.1 5.5 36 231-288 137-173 (174)
139 PF04795 PAPA-1: PAPA-1-like c 27.3 1.4E+02 0.0031 23.3 4.8 68 157-224 13-80 (89)
140 PF12773 DZR: Double zinc ribb 26.8 79 0.0017 21.3 2.9 13 38-50 9-21 (50)
141 TIGR02642 phage_xxxx uncharact 26.5 40 0.00087 30.2 1.7 31 41-80 99-129 (186)
142 smart00401 ZnF_GATA zinc finge 26.2 61 0.0013 22.7 2.3 32 41-75 3-34 (52)
143 COG3286 Uncharacterized protei 25.9 68 0.0015 29.1 3.0 57 224-302 19-76 (204)
144 PRK09906 DNA-binding transcrip 25.6 1.1E+02 0.0024 27.8 4.5 21 222-242 34-54 (296)
145 KOG0341|consensus 25.2 37 0.0008 34.2 1.3 22 65-86 569-590 (610)
146 PRK09202 nusA transcription el 25.0 69 0.0015 32.7 3.3 38 197-240 303-340 (470)
147 PRK11032 hypothetical protein; 24.6 52 0.0011 28.8 2.0 61 3-75 91-151 (160)
148 PF05741 zf-nanos: Nanos RNA b 24.5 35 0.00077 24.6 0.8 26 55-84 26-54 (55)
149 TIGR01952 nusA_arch NusA famil 24.4 71 0.0015 27.3 2.8 37 196-238 100-136 (141)
150 COG5179 TAF1 Transcription ini 24.2 33 0.0007 36.3 0.8 24 33-56 929-952 (968)
151 smart00778 Prim_Zn_Ribbon Zinc 24.1 76 0.0016 21.0 2.3 30 42-74 4-33 (37)
152 cd02412 30S_S3_KH K homology R 24.0 61 0.0013 26.1 2.2 22 212-233 71-92 (109)
153 TIGR02036 dsdC D-serine deamin 23.9 1.1E+02 0.0024 28.2 4.2 21 222-242 41-61 (302)
154 PRK04023 DNA polymerase II lar 23.7 56 0.0012 36.5 2.4 35 42-76 639-673 (1121)
155 COG0081 RplA Ribosomal protein 23.6 90 0.002 28.9 3.4 43 198-240 113-167 (228)
156 PF00126 HTH_1: Bacterial regu 23.5 71 0.0015 22.5 2.2 21 222-242 32-52 (60)
157 KOG1244|consensus 23.4 31 0.00067 32.9 0.4 15 40-54 245-259 (336)
158 PRK10094 DNA-binding transcrip 23.4 1.2E+02 0.0025 28.2 4.3 21 222-242 35-55 (308)
159 PF07282 OrfB_Zn_ribbon: Putat 22.9 51 0.0011 23.9 1.4 30 41-77 28-57 (69)
160 PF00408 PGM_PMM_IV: Phosphogl 22.8 1.3E+02 0.0028 22.0 3.7 25 263-287 49-73 (73)
161 PLN03119 putative ADP-ribosyla 22.8 87 0.0019 32.9 3.5 32 39-75 21-52 (648)
162 COG2888 Predicted Zn-ribbon RN 22.7 33 0.00071 25.2 0.3 10 67-76 51-60 (61)
163 PRK10837 putative DNA-binding 22.3 1.3E+02 0.0028 27.1 4.3 21 222-242 36-56 (290)
164 PF00352 TBP: Transcription fa 22.2 1.5E+02 0.0032 22.6 4.0 37 230-288 47-84 (86)
165 PF08271 TF_Zn_Ribbon: TFIIB z 22.0 37 0.0008 22.6 0.5 28 43-76 2-29 (43)
166 KOG2279|consensus 21.7 67 0.0014 33.5 2.4 58 178-239 276-333 (608)
167 PRK12327 nusA transcription el 21.4 1E+02 0.0022 30.4 3.6 39 196-240 303-341 (362)
168 KOG0703|consensus 21.4 1.6E+02 0.0035 28.2 4.7 61 36-115 20-85 (287)
169 COG1198 PriA Primosomal protei 21.0 1.3E+02 0.0028 32.5 4.5 74 206-288 631-714 (730)
170 PRK05424 rplA 50S ribosomal pr 20.8 1.6E+02 0.0034 27.2 4.5 22 200-221 113-134 (230)
171 PRK14291 chaperone protein Dna 20.7 62 0.0013 31.9 1.9 19 66-84 195-213 (382)
172 PRK09791 putative DNA-binding 20.5 1.8E+02 0.004 26.5 5.0 21 223-243 39-59 (302)
173 PRK03601 transcriptional regul 20.4 1.6E+02 0.0034 26.8 4.4 20 222-241 34-53 (275)
174 KOG0956|consensus 20.3 60 0.0013 34.8 1.8 29 40-76 116-144 (900)
175 PF00684 DnaJ_CXXCXGXG: DnaJ c 20.2 46 0.00099 24.3 0.7 47 38-84 12-61 (66)
No 1
>KOG0119|consensus
Probab=100.00 E-value=1.1e-51 Score=399.90 Aligned_cols=188 Identities=52% Similarity=0.855 Sum_probs=171.8
Q ss_pred hhHHHHHHHHHhCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHhCCC
Q psy1775 103 IDEEYMSLMAELGEGPPPDKRQRDNDSYRKNNTSGSLSPSPEPIYSSDGKRMNTREYRTRKKLEEERHDLIQKMFKVNPE 182 (304)
Q Consensus 103 ~d~EY~~lmaEL~~~~~e~tr~L~tG~~~~~~~~~~rsPsp~p~yd~~gkr~ntr~~r~~~~Le~er~~~i~~l~~~~p~ 182 (304)
.+.+.+.++-++ ++++|+|+++|++.+.+.++|||||+|+||+.|+|+||||+|++++||+||+++|++++++||.
T Consensus 50 eq~~~y~l~~~i----ee~t~kLrt~d~~~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~nP~ 125 (554)
T KOG0119|consen 50 EQKESYSLNLRI----EEITRKLRTGDVGVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLNPG 125 (554)
T ss_pred hhhhhhhHHHHH----HHhhhhhccccCCCCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhCcC
Confidence 344455555555 4589999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCC-CCCCCCCCC
Q psy1775 183 FKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKD-GQPLPGENE 261 (304)
Q Consensus 183 ~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~-g~~~~~~~e 261 (304)
|++|.||+++. +++.||||||++||+||||||||||||+|+|+||+||||||.|||||||||+| .+.+ .......+|
T Consensus 126 fkpP~DYk~p~-~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk-~~~~d~~~~~~~~e 203 (554)
T KOG0119|consen 126 FKPPADYKPPA-KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK-GRSDDLSYIPKENE 203 (554)
T ss_pred CCCCcccCccc-ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc-cCCccccccccccc
Confidence 99999999995 89999999999999999999999999999999999999999999999999999 5544 556788999
Q ss_pred CcEEEEEeCCHHHHHHHHHHHHhhhcCCCCCCCCCCc
Q psy1775 262 PLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGA 298 (304)
Q Consensus 262 ~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~~~~~~g~ 298 (304)
||||+|+|+|+|+|++|++.|++||.+. .+++|||
T Consensus 204 pLH~~Isadt~eki~~Ai~vienli~~a--v~~~e~~ 238 (554)
T KOG0119|consen 204 PLHCLISADTQEKIKKAIAVIENLIQSA--VSVPEGQ 238 (554)
T ss_pred ceeEEEecchHHHHHHHHHHHHHHHHhh--ccCcccc
Confidence 9999999999999999999999999985 3467774
No 2
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=100.00 E-value=1.7e-43 Score=311.65 Aligned_cols=178 Identities=39% Similarity=0.594 Sum_probs=162.3
Q ss_pred CCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcce
Q psy1775 117 GPPPDKRQRDNDSYRKNNTSGSLSPSPEPIYSSDGKRMNTREYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKV 196 (304)
Q Consensus 117 ~~~e~tr~L~tG~~~~~~~~~~rsPsp~p~yd~~gkr~ntr~~r~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~ 196 (304)
-+.+++.+|++++.+++ ..+.|||||||.||..|+|+|||++|++++|++||..|+++.++|.|.|.+|.||..| ++.
T Consensus 71 r~~eit~Klrt~d~Vp~-~re~Rspsppp~yd~~GrRlntre~ry~kkLeder~~l~era~k~lp~fv~p~dy~rp-sk~ 148 (269)
T COG5176 71 RPFEITEKLRTPDGVPS-KRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKERAQKILPRFVLPNDYIRP-SKY 148 (269)
T ss_pred cHhhhhhhhcCCCCCCc-hhhccCCCCCcchhHHhhhhhHHHHHHhhhhhHHHHHHHHHHHHhcCcccCCccccCc-ccc
Confidence 35679999999999886 4678999999999999999999999999999999999999999999999999999999 689
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCC-CCCCCCCcEEEEEeCCHHHH
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQP-LPGENEPLHAYVTAHNPENV 275 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~-~~~~~e~LHv~I~a~~~~~v 275 (304)
+.||||||++||+.||||+||||||.|+|+||+.|+|||.|||+||+|+++.. .+-.+ .-.+.++||+||++++++++
T Consensus 149 q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~s-sd~p~~~~N~e~~lhcLI~adsedki 227 (269)
T COG5176 149 QNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKIS-SDTPESLKNAEAVLHCLIEADSEDKI 227 (269)
T ss_pred cceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCccc-ccCchhhhhhHHhHHHHhhcchhhhH
Confidence 99999999999999999999999999999999999999999999999999843 12111 34678999999999999999
Q ss_pred HHHHHHHHhhhcCCCCCCCCCCcc
Q psy1775 276 KKAVDRLVCLVSARPRARFPPGAD 299 (304)
Q Consensus 276 ~~A~~~I~~ll~~~~~~~~~~g~~ 299 (304)
.+++..+.++|.+. .+.|+||.
T Consensus 228 ~~~ik~~~n~I~~a--~~~PeGqn 249 (269)
T COG5176 228 CRLIKSQLNAIREA--RRNPEGQN 249 (269)
T ss_pred HHHHHHHHHHHHHH--hcCCcccc
Confidence 99999999999886 67899974
No 3
>KOG1588|consensus
Probab=99.97 E-value=2.2e-30 Score=236.58 Aligned_cols=135 Identities=31% Similarity=0.552 Sum_probs=110.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCCC----CCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeE
Q psy1775 160 RTRKKLEEERHDLIQKMFKVNPEFKPP----PDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKI 235 (304)
Q Consensus 160 r~~~~Le~er~~~i~~l~~~~p~~~~P----~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI 235 (304)
.+...|.+|..++-..+.++....+.+ ..+....+++++||+||+++||+|||||+||||+|+|+|+||++|||||
T Consensus 52 ~~~rLL~~Ei~rv~~~~~~~~~~~~~~~~~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki 131 (259)
T KOG1588|consen 52 HAERLLDEEIERVQTSGRQHGSKEPEELPYADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKI 131 (259)
T ss_pred HHHHHHHHHHHHHHhhhhhccCCCchhcccccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeE
Confidence 455677888877777666542212211 3455667899999999999999999999999999999999999999999
Q ss_pred EEeCCccccCCCC-CCCCCCC-CCCCCCCcEEEEEeCCHH-----HHHHHHHHHHhhhcCCCCCCCCCCcc
Q psy1775 236 IIRGKGSVKEGKV-GRKDGQP-LPGENEPLHAYVTAHNPE-----NVKKAVDRLVCLVSARPRARFPPGAD 299 (304)
Q Consensus 236 ~IrG~Gs~~~~~~-~~~~g~~-~~~~~e~LHv~I~a~~~~-----~v~~A~~~I~~ll~~~~~~~~~~g~~ 299 (304)
.|||+||+||... +...+++ |+|+++||||+|++..+. .|.+|++.|++||.++ +|++|
T Consensus 132 ~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~-----~e~~d 197 (259)
T KOG1588|consen 132 MIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPD-----HEDED 197 (259)
T ss_pred EEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCC-----CCCch
Confidence 9999999999753 3445566 899999999999998753 5889999999999999 55555
No 4
>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=99.96 E-value=2.9e-29 Score=207.84 Aligned_cols=94 Identities=50% Similarity=0.773 Sum_probs=85.6
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCC-CCCCCCCCCCCCcEEEEEeCC--HH
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGR-KDGQPLPGENEPLHAYVTAHN--PE 273 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~-~~g~~~~~~~e~LHv~I~a~~--~~ 273 (304)
++|||||+++||+|||||+||||+|+|+|+||++|||+|.|||+||+++++.+. ..+..+++++|||||+|+|++ .+
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 469999999999999999999999999999999999999999999999987543 233447899999999999999 99
Q ss_pred HHHHHHHHHHhhhcCCC
Q psy1775 274 NVKKAVDRLVCLVSARP 290 (304)
Q Consensus 274 ~v~~A~~~I~~ll~~~~ 290 (304)
++++|+++|+.||.+..
T Consensus 81 ~~~~A~~~I~~ll~~~~ 97 (120)
T cd02395 81 ALAKAVEAIEELLKPAI 97 (120)
T ss_pred HHHHHHHHHHHHhccCC
Confidence 99999999999999763
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=99.56 E-value=8.8e-15 Score=151.32 Aligned_cols=112 Identities=21% Similarity=0.325 Sum_probs=106.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEE
Q psy1775 158 EYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237 (304)
Q Consensus 158 ~~r~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~I 237 (304)
...+.++|++++.++.+++..|...++.| ...++++|++.++.||++ +||.||||+|+|+|.|+++||++|.|
T Consensus 541 ~e~l~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi 613 (719)
T TIGR02696 541 ASVLASALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISI 613 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEE
Confidence 45789999999999999999999999999 889999999999999999 99999999999999999999999999
Q ss_pred eCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhc--CCCCCCCCCCc
Q psy1775 238 RGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVS--ARPRARFPPGA 298 (304)
Q Consensus 238 rG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~--~~~~~~~~~g~ 298 (304)
..+|. |.|+|.+.+++++|+++|+.|+. .+.+|++|+|.
T Consensus 614 ~d~G~----------------------V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~Gk 654 (719)
T TIGR02696 614 EDDGT----------------------VYIGAADGPSAEAARAMINAIANPTMPEVGERFLGT 654 (719)
T ss_pred ecCcE----------------------EEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEE
Confidence 99877 77999999999999999999999 58899999985
No 6
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.52 E-value=1.3e-14 Score=147.54 Aligned_cols=115 Identities=23% Similarity=0.353 Sum_probs=109.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEE
Q psy1775 157 REYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKII 236 (304)
Q Consensus 157 r~~r~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~ 236 (304)
..+-|+++|+|+|.+++|+|..|+.++..|+...++++|..+.+.|+++ .|+.+|||+|+|++.|.++||++|.
T Consensus 513 t~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~d------KI~dvIG~gGk~I~~I~eetg~~Id 586 (692)
T COG1185 513 TKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPD------KIRDVIGPGGKTIKAITEETGVKID 586 (692)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHH------HHhhccCCcccchhhhhhhhCcEEE
Confidence 3456999999999999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred EeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCCCCCCCCcc
Q psy1775 237 IRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGAD 299 (304)
Q Consensus 237 IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~~~~~~g~~ 299 (304)
|..+|+ |.|++.+.+.+.+|++.|+.++.+.++|.+|+|.-
T Consensus 587 ieddGt----------------------v~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V 627 (692)
T COG1185 587 IEDDGT----------------------VKIAASDGESAKKAKERIEAITREVEVGEVYEGTV 627 (692)
T ss_pred ecCCCc----------------------EEEEecchHHHHHHHHHHHHHHhhcccccEEEEEE
Confidence 999999 55999999999999999999999999999999864
No 7
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.47 E-value=5.1e-14 Score=148.46 Aligned_cols=113 Identities=15% Similarity=0.203 Sum_probs=107.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCe-E
Q psy1775 157 REYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAK-I 235 (304)
Q Consensus 157 r~~r~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~k-I 235 (304)
....|.++|++++.++.+++..|...++.|+...++++|++.++.||.+ +||.||||+|+|+|.|+++||++ |
T Consensus 646 s~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~------ki~~vIG~GGktIk~I~eetg~~~I 719 (891)
T PLN00207 646 TLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPE------KVNMIIGSGGKKVKSIIEETGVEAI 719 (891)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHH------HHHHHhcCCchhHHHHHHHHCCCcc
Confidence 4578999999999999999999999999999999999999999999998 99999999999999999999999 9
Q ss_pred EEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCCCCCCCC
Q psy1775 236 IIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPG 297 (304)
Q Consensus 236 ~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~~~~~~g 297 (304)
.|+.+|. |.|++.|.+++++|+++|+.|+..+.+|++|+|
T Consensus 720 di~ddg~----------------------V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~ 759 (891)
T PLN00207 720 DTQDDGT----------------------VKITAKDLSSLEKSKAIISSLTMVPTVGDIYRN 759 (891)
T ss_pred CcCCCee----------------------EEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEEC
Confidence 9999877 669999999999999999999999999999964
No 8
>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=99.46 E-value=8.8e-14 Score=144.85 Aligned_cols=114 Identities=22% Similarity=0.353 Sum_probs=107.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeE
Q psy1775 156 TREYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKI 235 (304)
Q Consensus 156 tr~~r~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI 235 (304)
+.++ +.++|++++.++.+++..|...++.|+...++++|++.++.||++ +||.||||+|+|+|.|+++|||+|
T Consensus 512 ~~~~-l~~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I 584 (684)
T TIGR03591 512 TREI-MEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPD------KIRDVIGPGGKVIREITEETGAKI 584 (684)
T ss_pred CHHH-HHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEE
Confidence 3444 899999999999999999999999999999999999999999999 999999999999999999999999
Q ss_pred EEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCCCCCCCCc
Q psy1775 236 IIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGA 298 (304)
Q Consensus 236 ~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~~~~~~g~ 298 (304)
.|..+|. |.|++.+.+.+++|.++|+.+.....+|++|+|+
T Consensus 585 ~i~ddG~----------------------V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~ 625 (684)
T TIGR03591 585 DIEDDGT----------------------VKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGK 625 (684)
T ss_pred EEecCeE----------------------EEEEECcHHHHHHHHHHHHhhhcccccCcEEEEE
Confidence 9998877 6699999999999999999999999999999986
No 9
>KOG0119|consensus
Probab=99.40 E-value=2.4e-13 Score=133.38 Aligned_cols=105 Identities=34% Similarity=0.631 Sum_probs=80.4
Q ss_pred cccccchHHHHHHHHhhc---------Ccccccccc-------cccCCccccCCCCCcccCCCCCcccCCCCCCCCCccc
Q psy1775 3 CDVTNFINYRLRKLAENC---------VPETWAFHP-------ILKKGTLRENEGPRCTNCGASDHKSWLCPDKPNITNS 66 (304)
Q Consensus 3 ~~~~~~~~~~~~~~a~~~---------~p~~~~~~~-------~~~nGtlr~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~ 66 (304)
|=||+.+.+++++++.|+ +|..+++.+ ..+|||+|++++..|.+||..||..++||........
T Consensus 207 ~~Isadt~eki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n 286 (554)
T KOG0119|consen 207 CLISADTQEKIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTN 286 (554)
T ss_pred EEEecchHHHHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCccccccccccCCCccccccCCcccccccc
Confidence 556777777777665542 444445444 4569999999999999999999999999997322222
Q ss_pred ccccccccccccccccCCCCCCCCCCCCCCcccchhhhHHHHHHHHHhC
Q psy1775 67 TLCSSCGGAGHIARDCREKRPGMGGPPANTHRNRAKIDEEYMSLMAELG 115 (304)
Q Consensus 67 ~~C~~CG~~GH~ardC~~~~~~~~g~~~~~~~~~a~~d~EY~~lmaEL~ 115 (304)
.|++||..||+++||+..... ...+.+.||+||.++|.||+
T Consensus 287 -~c~~cg~~gH~~~dc~~~~q~-------~~~~~~~~d~ey~~lm~e~~ 327 (554)
T KOG0119|consen 287 -VCKICGPLGHISIDCKVNDQQ-------MPMSSANFDREYASLMLELG 327 (554)
T ss_pred -cccccCCcccccccCCCcccc-------cchhhhccCHHHHhhhcccc
Confidence 899999999999999987322 22346789999999998886
No 10
>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=99.32 E-value=5.8e-12 Score=92.41 Aligned_cols=61 Identities=33% Similarity=0.528 Sum_probs=54.9
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHH
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPEN 274 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~ 274 (304)
|..+.+.||.+ ++|+|||++|+|+|.|+++|||+|.|...|. |.|+|.+.++
T Consensus 1 P~~~~i~Ip~~------~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~----------------------v~I~G~~~~~ 52 (61)
T cd02393 1 PRIETMKIPPD------KIRDVIGPGGKTIKKIIEETGVKIDIEDDGT----------------------VYIAASDKEA 52 (61)
T ss_pred CeEEEEEeChh------heeeeECCCchHHHHHHHHHCCEEEeCCCCE----------------------EEEEeCCHHH
Confidence 35789999998 9999999999999999999999999976443 8899999999
Q ss_pred HHHHHHHHH
Q psy1775 275 VKKAVDRLV 283 (304)
Q Consensus 275 v~~A~~~I~ 283 (304)
+++|+++|+
T Consensus 53 v~~A~~~I~ 61 (61)
T cd02393 53 AEKAKKMIE 61 (61)
T ss_pred HHHHHHHhC
Confidence 999999884
No 11
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.29 E-value=2.1e-12 Score=134.86 Aligned_cols=113 Identities=23% Similarity=0.348 Sum_probs=106.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEe
Q psy1775 159 YRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIR 238 (304)
Q Consensus 159 ~r~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~Ir 238 (304)
.-+.++|++++.++.+++..|...+..|+...++++++...+.||.+ .|+.+|||+|+|+|.|+++||++|.|+
T Consensus 517 ~~l~~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~------kI~~vIG~gg~~ik~I~~~~~~~idi~ 590 (693)
T PRK11824 517 EILEEALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPD------KIRDVIGPGGKTIREITEETGAKIDIE 590 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHH------HHHHHhcCCchhHHHHHHHHCCccccC
Confidence 34999999999999999999999999999999999999999999887 899999999999999999999999999
Q ss_pred CCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCCCCCCCCcc
Q psy1775 239 GKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGAD 299 (304)
Q Consensus 239 G~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~~~~~~g~~ 299 (304)
..|. |.|++.+.+++++|.++|+.++....+|++|+|.=
T Consensus 591 d~G~----------------------v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V 629 (693)
T PRK11824 591 DDGT----------------------VKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKV 629 (693)
T ss_pred CCce----------------------EEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEE
Confidence 8887 66999999999999999999999999999999863
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=98.88 E-value=1.5e-09 Score=78.63 Aligned_cols=60 Identities=32% Similarity=0.606 Sum_probs=52.0
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHH
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVK 276 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~ 276 (304)
+.+|.||.+ ++|+|||++|.++++|+++|||+|.|...+ +.-.|.|+| +.++|+
T Consensus 1 T~~i~vp~~------~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~-------------------~~~~v~I~G-~~~~v~ 54 (60)
T PF00013_consen 1 TERIEVPSS------LVGRIIGKKGSNIKEIEEETGVKIQIPDDD-------------------ERDIVTISG-SPEQVE 54 (60)
T ss_dssp EEEEEEEHH------HHHHHHTGGGHHHHHHHHHHTSEEEEESTT-------------------EEEEEEEEE-SHHHHH
T ss_pred CEEEEECHH------HcCEEECCCCCcHHHhhhhcCeEEEEcCCC-------------------CcEEEEEEe-CHHHHH
Confidence 357899987 999999999999999999999999997652 112488999 999999
Q ss_pred HHHHHH
Q psy1775 277 KAVDRL 282 (304)
Q Consensus 277 ~A~~~I 282 (304)
+|.++|
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
>KOG1067|consensus
Probab=98.86 E-value=5.2e-09 Score=104.78 Aligned_cols=110 Identities=17% Similarity=0.205 Sum_probs=98.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEe
Q psy1775 159 YRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIR 238 (304)
Q Consensus 159 ~r~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~Ir 238 (304)
.-+-++|++++..+.+||..|..++.+|+.+...+.|+.+.+.++.+ ....+|||+|...|+|+.||| .|.--
T Consensus 560 ~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~s------k~~~lIGp~G~~~kki~~EtG-ai~~v 632 (760)
T KOG1067|consen 560 KIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPS------KRATLIGPGGVLKKKIEVETG-AISQV 632 (760)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecch------hhheeecCccceeeeEeeecc-ceeee
Confidence 45778999999999999999999999999999999999999999998 789999999999999999999 44433
Q ss_pred CCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCCCCCCCC
Q psy1775 239 GKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPG 297 (304)
Q Consensus 239 G~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~~~~~~g 297 (304)
+.|. +-|.|.++..+++|.+.|..|+..+.+++++-|
T Consensus 633 De~t----------------------~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g 669 (760)
T KOG1067|consen 633 DEGT----------------------FSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFG 669 (760)
T ss_pred cCce----------------------EEEEecCHHHHHHHHHHHHHHhcCccccceEee
Confidence 4444 669999999999999999999999888776654
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.83 E-value=4.7e-09 Score=92.86 Aligned_cols=75 Identities=29% Similarity=0.392 Sum_probs=64.9
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCC-ccccCCCCCCCCCCCCCCCCCCcEEEEE---eCC
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK-GSVKEGKVGRKDGQPLPGENEPLHAYVT---AHN 271 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~-Gs~~~~~~~~~~g~~~~~~~e~LHv~I~---a~~ 271 (304)
....+.||.+ .+|.||||+|+|+|.|+++|||+|.|..+ |. |.|. +.|
T Consensus 3 ~~~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~----------------------V~I~~~~~~d 54 (180)
T PRK13763 3 MMEYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSETGE----------------------VIIEPTDGED 54 (180)
T ss_pred ceEEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECCCCe----------------------EEEEeCCCCC
Confidence 4578899998 99999999999999999999999999987 55 7798 899
Q ss_pred HHHHHHHHHHHHhhhc--CCC-----CCCCCCCc
Q psy1775 272 PENVKKAVDRLVCLVS--ARP-----RARFPPGA 298 (304)
Q Consensus 272 ~~~v~~A~~~I~~ll~--~~~-----~~~~~~g~ 298 (304)
++++++|.++|+.|+. +++ +++.|.|.
T Consensus 55 ~~~i~kA~~~I~ai~~gf~~e~A~~l~gd~y~~~ 88 (180)
T PRK13763 55 PLAVLKARDIVKAIGRGFSPEKALRLLDDDYVLE 88 (180)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHhCCCceEE
Confidence 9999999999999998 444 56666554
No 15
>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=98.83 E-value=1.6e-08 Score=73.33 Aligned_cols=63 Identities=38% Similarity=0.654 Sum_probs=52.4
Q ss_pred EEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHH
Q psy1775 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKK 277 (304)
Q Consensus 198 ~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~ 277 (304)
.+|.||.+ ++|.||||+|++++.|+++|||+|.|...++ ...+-.|.|+|. .+.+.+
T Consensus 2 ~~i~ip~~------~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~----------------~~~~~~v~i~G~-~~~v~~ 58 (64)
T cd00105 2 ERVLVPSS------LVGRIIGKGGSTIKEIREETGAKIKIPDSGS----------------GSEERIVTITGT-PEAVEK 58 (64)
T ss_pred EEEEEchh------hcceeECCCCHHHHHHHHHHCCEEEEcCCCC----------------CCCceEEEEEcC-HHHHHH
Confidence 57899997 9999999999999999999999999987543 123345888887 789999
Q ss_pred HHHHHH
Q psy1775 278 AVDRLV 283 (304)
Q Consensus 278 A~~~I~ 283 (304)
|..+|+
T Consensus 59 a~~~i~ 64 (64)
T cd00105 59 AKELIL 64 (64)
T ss_pred HHHHhC
Confidence 988763
No 16
>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=98.81 E-value=8e-09 Score=75.21 Aligned_cols=61 Identities=30% Similarity=0.538 Sum_probs=51.6
Q ss_pred EEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHH
Q psy1775 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKK 277 (304)
Q Consensus 198 ~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~ 277 (304)
..|.||.+ ++|.|||++|+++++|+++|||+|.|-...+ ..=.|.|+|. .++|.+
T Consensus 2 ~~i~Vp~~------~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~------------------~~~~v~I~G~-~~~v~~ 56 (62)
T cd02394 2 EEVEIPKK------LHRFIIGKKGSNIRKIMEETGVKIRFPDPGS------------------KSDTITITGP-KENVEK 56 (62)
T ss_pred eEEEeCHH------HhhhccCCCCCcHHHHHHHhCCEEEcCCCCC------------------CCCEEEEEcC-HHHHHH
Confidence 57889988 9999999999999999999999999987542 1123889998 789999
Q ss_pred HHHHHH
Q psy1775 278 AVDRLV 283 (304)
Q Consensus 278 A~~~I~ 283 (304)
|+++|.
T Consensus 57 A~~~i~ 62 (62)
T cd02394 57 AKEEIL 62 (62)
T ss_pred HHHHhC
Confidence 998873
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=98.75 E-value=7.9e-09 Score=90.78 Aligned_cols=71 Identities=30% Similarity=0.374 Sum_probs=59.9
Q ss_pred EEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCC-ccccCCCCCCCCCCCCCCCCCCcEEEE--EeCCHHHHH
Q psy1775 200 VMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK-GSVKEGKVGRKDGQPLPGENEPLHAYV--TAHNPENVK 276 (304)
Q Consensus 200 i~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~-Gs~~~~~~~~~~g~~~~~~~e~LHv~I--~a~~~~~v~ 276 (304)
+.||.+ .||.||||+|+|+|.|+++||++|.|..+ |. |.| .+.|++++.
T Consensus 2 i~Ip~~------kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~----------------------V~I~~~t~d~~~i~ 53 (172)
T TIGR03665 2 VKIPKD------RIGVLIGKGGETKKEIEERTGVKLDIDSETGE----------------------VKIEEEDEDPLAVM 53 (172)
T ss_pred ccCCHH------HhhhHhCCchhHHHHHHHHhCcEEEEEcCCce----------------------EEEecCCCCHHHHH
Confidence 467777 99999999999999999999999999876 54 668 788999999
Q ss_pred HHHHHHHhhhc--CCC-----CCCCCCCc
Q psy1775 277 KAVDRLVCLVS--ARP-----RARFPPGA 298 (304)
Q Consensus 277 ~A~~~I~~ll~--~~~-----~~~~~~g~ 298 (304)
+|.++|+.|.. +++ .++.|.+.
T Consensus 54 kA~~~I~~i~~gf~~e~A~~l~gd~y~~~ 82 (172)
T TIGR03665 54 KAREVVKAIGRGFSPEKALKLLDDDYMLE 82 (172)
T ss_pred HHHHHHHHHHcCCCHHHHHHhcCCcceEE
Confidence 99999999988 444 45555554
No 18
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.71 E-value=8.8e-09 Score=91.14 Aligned_cols=51 Identities=37% Similarity=0.857 Sum_probs=39.0
Q ss_pred cccCCCCCcccCCCCCcccCCCCC-----------CCC-CcccccccccccccccccccC-CCC
Q psy1775 36 LRENEGPRCTNCGASDHKSWLCPD-----------KPN-ITNSTLCSSCGGAGHIARDCR-EKR 86 (304)
Q Consensus 36 lr~~~~~~C~~Cg~~GH~~~~Cp~-----------~~~-~~~~~~C~~CG~~GH~ardC~-~~~ 86 (304)
....+++.||+||+.||.+++||. ..+ -...++|++||..||+++||. .+.
T Consensus 55 ~~~~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~ 118 (190)
T COG5082 55 AIREENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKD 118 (190)
T ss_pred cccccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccCcccc
Confidence 444567999999999999999991 110 012479999999999999994 443
No 19
>smart00322 KH K homology RNA-binding domain.
Probab=98.65 E-value=2.1e-07 Score=66.90 Aligned_cols=66 Identities=44% Similarity=0.655 Sum_probs=56.1
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHH
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENV 275 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v 275 (304)
....|.||.+ ++|.|||++|++++.|+++||++|.+...++ ..-.|.|.|+ .+.+
T Consensus 3 ~~~~i~i~~~------~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~------------------~~~~v~i~g~-~~~v 57 (69)
T smart00322 3 VTIEVLIPAD------KVGLIIGKGGSTIKKIEEETGVKIDIPEDGS------------------EERVVEITGP-PENV 57 (69)
T ss_pred eEEEEEEcch------hcceeECCCchHHHHHHHHHCCEEEECCCCC------------------CccEEEEEcC-HHHH
Confidence 4678999987 9999999999999999999999999976543 1234889888 8999
Q ss_pred HHHHHHHHhhh
Q psy1775 276 KKAVDRLVCLV 286 (304)
Q Consensus 276 ~~A~~~I~~ll 286 (304)
..|..+|.+.+
T Consensus 58 ~~a~~~i~~~~ 68 (69)
T smart00322 58 EKAAELILEIL 68 (69)
T ss_pred HHHHHHHHHHh
Confidence 99999998876
No 20
>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=98.62 E-value=1.8e-07 Score=69.06 Aligned_cols=63 Identities=30% Similarity=0.524 Sum_probs=50.3
Q ss_pred EEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHH
Q psy1775 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKK 277 (304)
Q Consensus 198 ~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~ 277 (304)
.++.||.+ .+|.|||.+|.++++|+++|||+|.|..... ...++ --|.|+|. .+++++
T Consensus 2 ~r~~ip~~------~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--------------~~~~~-r~v~I~G~-~~~v~~ 59 (65)
T cd02396 2 LRLLVPSS------QAGSIIGKGGSTIKEIREETGAKIRVSKSVL--------------PGSTE-RVVTISGK-PSAVQK 59 (65)
T ss_pred EEEEECHH------HcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--------------CCCCc-eEEEEEeC-HHHHHH
Confidence 58899998 9999999999999999999999999954332 01122 23777775 899999
Q ss_pred HHHHH
Q psy1775 278 AVDRL 282 (304)
Q Consensus 278 A~~~I 282 (304)
|.++|
T Consensus 60 A~~~I 64 (65)
T cd02396 60 ALLLI 64 (65)
T ss_pred HHHhh
Confidence 99987
No 21
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=98.49 E-value=6.8e-08 Score=82.47 Aligned_cols=44 Identities=41% Similarity=0.955 Sum_probs=34.0
Q ss_pred CCcccCCCCCcccCCCCCCCC-CcccccccccccccccccccCCC
Q psy1775 42 PRCTNCGASDHKSWLCPDKPN-ITNSTLCSSCGGAGHIARDCREK 85 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp~~~~-~~~~~~C~~CG~~GH~ardC~~~ 85 (304)
..||+|++.||++++|++... ......||+||+.||++++|++.
T Consensus 78 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA 122 (148)
T ss_pred cccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence 568899999999888888542 23346788888888888888875
No 22
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=98.37 E-value=3.4e-07 Score=78.14 Aligned_cols=46 Identities=35% Similarity=0.834 Sum_probs=28.5
Q ss_pred CCCcccCCCCCcccCCCCCCCCCcccccccccccccccccccCCCC
Q psy1775 41 GPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKR 86 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~GH~ardC~~~~ 86 (304)
...||+|++.||++++||..........|+.||..||++++||...
T Consensus 27 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~ 72 (148)
T PTZ00368 27 ARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAP 72 (148)
T ss_pred CccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcc
Confidence 4567777777777777766543223345666666666666666543
No 23
>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=98.28 E-value=1e-06 Score=77.51 Aligned_cols=60 Identities=28% Similarity=0.451 Sum_probs=51.5
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCC
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPR 291 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~ 291 (304)
.+|+|||++|.|++.||..|||+|.|-|+ .|.|+| +++.++.|.+.|+.||..-.-
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~-----------------------~v~i~G-~~~~~~~A~~~i~~li~~~~~ 154 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGK-----------------------TVGIIG-DPEQVQIAREAIEMLIEGAPH 154 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCC-----------------------EEEEEC-CHHHHHHHHHHHHHHHcCCCC
Confidence 58999999999999999999999999751 278999 899999999999999966544
Q ss_pred CCCC
Q psy1775 292 ARFP 295 (304)
Q Consensus 292 ~~~~ 295 (304)
+++|
T Consensus 155 ~~vy 158 (172)
T TIGR03665 155 GTVY 158 (172)
T ss_pred hhHH
Confidence 4433
No 24
>PF13014 KH_3: KH domain
Probab=98.26 E-value=2e-06 Score=58.42 Aligned_cols=28 Identities=50% Similarity=0.808 Sum_probs=26.9
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
|+|.|||++|.|+++|+++|||+|.|-.
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 6899999999999999999999999977
No 25
>KOG1960|consensus
Probab=98.17 E-value=1.4e-06 Score=84.43 Aligned_cols=86 Identities=20% Similarity=0.202 Sum_probs=76.0
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHH
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVK 276 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~ 276 (304)
.-|++|++| .|.+|.-+..=||+-.+|..+|.||++++.||||+|+. .+...| .+.+|||+++|++.+.+.+.
T Consensus 211 ~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~---iEP~~G---~EsnEPMYI~i~h~~~~g~~ 283 (531)
T KOG1960|consen 211 PNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGR---REPNEG---NESNEPMYIFSTHGNGNGEN 283 (531)
T ss_pred hhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccc---cCcccc---cccCCceeEEeecCCchhhc
Confidence 348899988 89999999999999999999999999999999999954 233344 36899999999999999999
Q ss_pred HHHHHHHhhhcCC
Q psy1775 277 KAVDRLVCLVSAR 289 (304)
Q Consensus 277 ~A~~~I~~ll~~~ 289 (304)
+|.++|.+|+...
T Consensus 284 ~A~r~~~nl~~~v 296 (531)
T KOG1960|consen 284 GAPRRKWNLEEKV 296 (531)
T ss_pred cchhHHHhHHHHH
Confidence 9999999998764
No 26
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.15 E-value=1e-06 Score=49.48 Aligned_cols=16 Identities=63% Similarity=1.333 Sum_probs=9.4
Q ss_pred cccccccccccccccC
Q psy1775 68 LCSSCGGAGHIARDCR 83 (304)
Q Consensus 68 ~C~~CG~~GH~ardC~ 83 (304)
.||+||+.||+++|||
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 4556666666666655
No 27
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.11 E-value=4e-06 Score=74.25 Aligned_cols=56 Identities=30% Similarity=0.510 Sum_probs=48.6
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCC
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPR 291 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~ 291 (304)
.+|+|||++|+|+|.||+.|||+|.|-++ .|.|.| +++.++.|.+.|+.|+..-.-
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-----------------------~v~i~G-~~~~~~~A~~~I~~li~g~~~ 160 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-----------------------TVAIIG-DPEQVEIAREAIEMLIEGAPH 160 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-----------------------EEEEEe-CHHHHHHHHHHHHHHHcCCCc
Confidence 68999999999999999999999999642 166887 899999999999999965433
No 28
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.03 E-value=2.5e-06 Score=75.68 Aligned_cols=43 Identities=33% Similarity=0.734 Sum_probs=35.3
Q ss_pred CCcccCCCCCcccCCC-CCCCCCcccccccccccccccccccCCCCC
Q psy1775 42 PRCTNCGASDHKSWLC-PDKPNITNSTLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~C-p~~~~~~~~~~C~~CG~~GH~ardC~~~~~ 87 (304)
..|++||+.||++++| |.+. ....|+.|...+|.+++||+...
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~~---~~~~C~~C~s~~H~s~~Cp~~~k 141 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSKD---QQKSCFDCNSTRHSSEDCPSIWK 141 (190)
T ss_pred cccccccccCccccccCcccc---cCcceeccCCCccccccCccccc
Confidence 6899999999999999 5543 34578888888888888887654
No 29
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.02 E-value=2.9e-06 Score=47.60 Aligned_cols=18 Identities=39% Similarity=0.972 Sum_probs=16.4
Q ss_pred CCcccCCCCCcccCCCCC
Q psy1775 42 PRCTNCGASDHKSWLCPD 59 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp~ 59 (304)
+.||+||+.||++++||+
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 369999999999999985
No 30
>KOG4400|consensus
Probab=98.01 E-value=3.1e-06 Score=78.75 Aligned_cols=43 Identities=37% Similarity=0.850 Sum_probs=36.7
Q ss_pred CCcccCCCCCcccCCCCCCCCCcccccccccccccccccccCCCCCC
Q psy1775 42 PRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRPG 88 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~GH~ardC~~~~~~ 88 (304)
..||+||+.||++.+||++ ....||.|+..||.++||+.....
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~----~~~~c~~c~~~~h~~~~C~~~~~~ 186 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN----KGGTCFRCGKVGHGSRDCPSKQKS 186 (261)
T ss_pred CccCCCCcCCcchhhCCCC----CCCccccCCCcceecccCCccccc
Confidence 4599999999999999975 247899999999999999988754
No 31
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.97 E-value=1.2e-05 Score=74.03 Aligned_cols=66 Identities=20% Similarity=0.350 Sum_probs=59.2
Q ss_pred EEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHH
Q psy1775 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKK 277 (304)
Q Consensus 198 ~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~ 277 (304)
..+.||.+ ++++||||+|.+++.|.++|+++|.|--.|. |+|+|.+.+.+++
T Consensus 147 ~~~~V~~~------~i~~lig~~g~~i~~l~~~~~~~I~ig~NG~----------------------VwI~~~~~~~~~~ 198 (235)
T PRK04163 147 TIVEIKPV------KVPRVIGKKGSMINMLKEETGCDIIVGQNGR----------------------IWIKGPDEEDEEI 198 (235)
T ss_pred EEEEECHH------HHHhhcCCCChhHhhhhhhhCcEEEEcCCcE----------------------EEEeeCCHHHHHH
Confidence 46778877 9999999999999999999999999966655 8899999999999
Q ss_pred HHHHHHhhhcCCCC
Q psy1775 278 AVDRLVCLVSARPR 291 (304)
Q Consensus 278 A~~~I~~ll~~~~~ 291 (304)
|++.|+.+-.+.+.
T Consensus 199 a~~~I~~~e~~~~~ 212 (235)
T PRK04163 199 AIEAIKKIEREAHT 212 (235)
T ss_pred HHHHHHHHHhhhhc
Confidence 99999998877655
No 32
>KOG1676|consensus
Probab=97.91 E-value=7.3e-05 Score=75.92 Aligned_cols=107 Identities=17% Similarity=0.275 Sum_probs=72.9
Q ss_pred HHHHHHHHHHHHHHHH-hCCCCCCCCCCCC-CCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCC
Q psy1775 163 KKLEEERHDLIQKMFK-VNPEFKPPPDYKP-PVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK 240 (304)
Q Consensus 163 ~~Le~er~~~i~~l~~-~~p~~~~P~~~~~-~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~ 240 (304)
++.|+++.-..++|.. -..++..-..+-. ...--...|.||-. .||.|||-+|.|||+|+.+||+||.++-+
T Consensus 195 ~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~------~VG~IIGkgGE~IKklq~etG~KIQfkpD 268 (600)
T KOG1676|consen 195 DKVEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRS------KVGIIIGKGGEMIKKLQNETGAKIQFKPD 268 (600)
T ss_pred HHHHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEecccc------ceeeEEecCchHHHHHhhccCceeEeecC
Confidence 4677777766666653 3333333222222 22222456677765 89999999999999999999999999753
Q ss_pred -ccccCCCCCCCCCCCCCCCCCCcE-EEEEeCCHHHHHHHHHHHHhhhcCCCCCC
Q psy1775 241 -GSVKEGKVGRKDGQPLPGENEPLH-AYVTAHNPENVKKAVDRLVCLVSARPRAR 293 (304)
Q Consensus 241 -Gs~~~~~~~~~~g~~~~~~~e~LH-v~I~a~~~~~v~~A~~~I~~ll~~~~~~~ 293 (304)
+. .-++. +.|.| +.+.+.+|.++|.+||.....+.
T Consensus 269 d~p-----------------~speR~~~IiG-~~d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 269 DDP-----------------SSPERPAQIIG-TVDQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred CCC-----------------CCccceeeeec-CHHHHHHHHHHHHHHHHHHhccC
Confidence 21 11122 33555 68899999999999999887763
No 33
>KOG1676|consensus
Probab=97.74 E-value=0.0002 Score=72.87 Aligned_cols=74 Identities=28% Similarity=0.667 Sum_probs=61.4
Q ss_pred cceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHH
Q psy1775 194 IKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPE 273 (304)
Q Consensus 194 ~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~ 273 (304)
...+..|.||.+ .+|+|||-+|.|+|.|+++||||+.+--+|+...+ .+.||. |++ |.+
T Consensus 137 ~~ttqeI~IPa~------k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~------------~~Kplr--itG-dp~ 195 (600)
T KOG1676|consen 137 VETTQEILIPAN------KCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG------------ADKPLR--ITG-DPD 195 (600)
T ss_pred cceeeeeccCcc------ceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC------------CCCcee--ecC-CHH
Confidence 356789999987 99999999999999999999999999888775433 233333 666 588
Q ss_pred HHHHHHHHHHhhhcC
Q psy1775 274 NVKKAVDRLVCLVSA 288 (304)
Q Consensus 274 ~v~~A~~~I~~ll~~ 288 (304)
+|+.|.++|.+||.+
T Consensus 196 ~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 196 KVEQAKQLVADILRE 210 (600)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999999996
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.69 E-value=7.3e-05 Score=66.71 Aligned_cols=60 Identities=27% Similarity=0.410 Sum_probs=53.4
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCC
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPR 291 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~ 291 (304)
..|+|||+.|+|.+.||+-|||.|+|.|+ +|.|.| +++.|+.|.+.|+.|+....-
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-----------------------tVaiiG-~~~~v~iAr~AVemli~G~~h 167 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-----------------------TVAIIG-GFEQVEIAREAVEMLINGAPH 167 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-----------------------EEEEec-ChhhhHHHHHHHHHHHcCCCc
Confidence 57999999999999999999999999984 266777 488999999999999999888
Q ss_pred CCCC
Q psy1775 292 ARFP 295 (304)
Q Consensus 292 ~~~~ 295 (304)
++||
T Consensus 168 ~~Vy 171 (194)
T COG1094 168 GKVY 171 (194)
T ss_pred hhHH
Confidence 7776
No 35
>KOG4400|consensus
Probab=97.31 E-value=0.00013 Score=67.82 Aligned_cols=45 Identities=38% Similarity=0.836 Sum_probs=33.0
Q ss_pred CCCcccCCCCCcccCCCCCCCCCc--------------------------ccccccccccccccccccCCC
Q psy1775 41 GPRCTNCGASDHKSWLCPDKPNIT--------------------------NSTLCSSCGGAGHIARDCREK 85 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~~~~~~--------------------------~~~~C~~CG~~GH~ardC~~~ 85 (304)
...|++|++.||+.++|+...... ..+.||+||+.||+..+|+++
T Consensus 92 ~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 92 AAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred chhhhhCCCCccchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCC
Confidence 456777777777777777632211 115699999999999999965
No 36
>KOG2191|consensus
Probab=97.31 E-value=0.0022 Score=61.41 Aligned_cols=77 Identities=23% Similarity=0.341 Sum_probs=51.4
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHH
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENV 275 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v 275 (304)
++.||.+|.. --|.|||++|.|+|.+++++||-|.|-- .++-+ -.+ ++- |.....+.|.+
T Consensus 132 kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisP---qkpt~---------~sL-qer-vvt~sge~e~~ 191 (402)
T KOG2191|consen 132 KQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISP---QKPTG---------ISL-QER-VVTVSGEPEQN 191 (402)
T ss_pred ceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecc---cCCCC---------ccc-eeE-EEEecCCHHHH
Confidence 5679999987 6799999999999999999999999973 11100 011 111 22334456777
Q ss_pred HHHHHHHHh-hhcCCCCC
Q psy1775 276 KKAVDRLVC-LVSARPRA 292 (304)
Q Consensus 276 ~~A~~~I~~-ll~~~~~~ 292 (304)
.+|+++|-+ |.+++.-+
T Consensus 192 ~~A~~~IL~Ki~eDpqs~ 209 (402)
T KOG2191|consen 192 MKAVSLILQKIQEDPQSG 209 (402)
T ss_pred HHHHHHHHHHhhcCCccc
Confidence 777776654 44444433
No 37
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.05 E-value=0.00023 Score=45.68 Aligned_cols=22 Identities=36% Similarity=0.998 Sum_probs=17.6
Q ss_pred cccccccccccccccccCCCCC
Q psy1775 66 STLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 66 ~~~C~~CG~~GH~ardC~~~~~ 87 (304)
+-.|++|++.||+.+|||.+.+
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~~P 29 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTNKP 29 (32)
T ss_pred CCEeecCCCCCccHhHCCCCCC
Confidence 3579999999999999998543
No 38
>KOG2190|consensus
Probab=96.87 E-value=0.0065 Score=61.63 Aligned_cols=102 Identities=25% Similarity=0.361 Sum_probs=71.9
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCCCC--CCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 162 RKKLEEERHDLIQKMFKVNPEFKPPPDYK--PPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 162 ~~~Le~er~~~i~~l~~~~p~~~~P~~~~--~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
.++|.++-..++..+..- .....|.. ...-+...++.||-. -+|-|||=+|+.||.|.++|||+|.|-+
T Consensus 105 ~~al~ka~~~iv~~~~~d---~~~~~d~~~~~~~~~v~~RLlVp~s------q~GslIGK~G~~Ik~Ire~TgA~I~v~~ 175 (485)
T KOG2190|consen 105 TDALFKAFDMIVFKLEED---DEAAEDNGEDASGPEVTCRLLVPSS------QVGSLIGKGGSLIKEIREETGAKIRVSS 175 (485)
T ss_pred HHHHHHHHHHHhhccccc---ccccccCCccccCCceEEEEEechh------heeeeeccCcHHHHHHHHhcCceEEecC
Confidence 456777777777765511 11111111 111146789999988 8999999999999999999999999988
Q ss_pred CccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcC
Q psy1775 240 KGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSA 288 (304)
Q Consensus 240 ~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~ 288 (304)
+ . .+.-.|.. |.|+| .+++|.+|+..|-.+|..
T Consensus 176 ~-~-------------lP~ster~-V~IsG-~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 176 D-M-------------LPNSTERA-VTISG-EPDAVKKALVQISSRLLE 208 (485)
T ss_pred C-C-------------CCccccee-EEEcC-chHHHHHHHHHHHHHHHh
Confidence 6 1 12223333 77766 488999999998888876
No 39
>KOG2193|consensus
Probab=96.70 E-value=0.0016 Score=64.10 Aligned_cols=72 Identities=24% Similarity=0.487 Sum_probs=53.7
Q ss_pred EEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHH
Q psy1775 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKK 277 (304)
Q Consensus 198 ~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~ 277 (304)
.++.+|.. |+|.||||.|.|||.|-+.|-|+|.+.-+-.. | ..+..+-| ..++|.--+
T Consensus 201 lR~lVptq------yvgaIIGkeG~TIknItkqTqsriD~hrken~---------G----aaek~itv---h~tpEg~s~ 258 (584)
T KOG2193|consen 201 LRLLVPTQ------YVGAIIGKEGATIKNITKQTQSRIDVHRKENA---------G----AAEKIITV---HSTPEGTSK 258 (584)
T ss_pred eeeeeccc------eeEEEecCCCccccCcchhhhheeeeeecccC---------C----cccCceEE---ecCccchHH
Confidence 47788887 99999999999999999999999999764210 1 11223333 235778889
Q ss_pred HHHHHHhhhcCCCC
Q psy1775 278 AVDRLVCLVSARPR 291 (304)
Q Consensus 278 A~~~I~~ll~~~~~ 291 (304)
|+++|-+|+....+
T Consensus 259 Ac~~ILeimqkEA~ 272 (584)
T KOG2193|consen 259 ACKMILEIMQKEAV 272 (584)
T ss_pred HHHHHHHHHHHhhh
Confidence 99999999876544
No 40
>PRK00106 hypothetical protein; Provisional
Probab=96.70 E-value=0.0093 Score=61.17 Aligned_cols=69 Identities=23% Similarity=0.392 Sum_probs=59.9
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHH
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPEN 274 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~ 274 (304)
..+..|.+|-|+ +-|+|||-.|.+++.+|.-||+.|.|...-. -|.||+.|+-.
T Consensus 224 ~tvs~v~lp~de-----mkGriIGreGrNir~~E~~tGvdliiddtp~---------------------~v~lS~fdpvR 277 (535)
T PRK00106 224 QTITTVHLPDDN-----MKGRIIGREGRNIRTLESLTGIDVIIDDTPE---------------------VVVLSGFDPIR 277 (535)
T ss_pred heeeeEEcCChH-----hhcceeCCCcchHHHHHHHhCceEEEcCCCC---------------------eEEEeCCChHH
Confidence 456789999985 7799999999999999999999999976432 38899999999
Q ss_pred HHHHHHHHHhhhcCC
Q psy1775 275 VKKAVDRLVCLVSAR 289 (304)
Q Consensus 275 v~~A~~~I~~ll~~~ 289 (304)
-+-|..-++.|+..+
T Consensus 278 ReiAr~~le~Li~dg 292 (535)
T PRK00106 278 REIARMTLESLIKDG 292 (535)
T ss_pred HHHHHHHHHHHHHcC
Confidence 999999999998864
No 41
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.64 E-value=0.0096 Score=60.89 Aligned_cols=75 Identities=24% Similarity=0.351 Sum_probs=61.8
Q ss_pred CCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEE
Q psy1775 187 PDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAY 266 (304)
Q Consensus 187 ~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~ 266 (304)
.+|..- ..+..|.+|-|+ +-|+|||-.|.++|.+|.-||+.|.|...-. -|.
T Consensus 197 ~~~~~e--~~~~~v~lp~d~-----~kgriigreGrnir~~e~~tgvd~iiddtp~---------------------~v~ 248 (514)
T TIGR03319 197 GDHVAE--TTVSVVNLPNDE-----MKGRIIGREGRNIRALETLTGVDLIIDDTPE---------------------AVI 248 (514)
T ss_pred chhhhh--heeeeEEcCChh-----hhccccCCCcchHHHHHHHhCceEEEcCCCC---------------------eEE
Confidence 344443 346788999985 7799999999999999999999999977522 288
Q ss_pred EEeCCHHHHHHHHHHHHhhhcCC
Q psy1775 267 VTAHNPENVKKAVDRLVCLVSAR 289 (304)
Q Consensus 267 I~a~~~~~v~~A~~~I~~ll~~~ 289 (304)
||+.|+-.-+-|..-++.||..+
T Consensus 249 ls~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 249 LSGFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred ecCCchHHHHHHHHHHHHHHHcC
Confidence 99999999888999999998764
No 42
>PRK12704 phosphodiesterase; Provisional
Probab=96.56 E-value=0.012 Score=60.31 Aligned_cols=69 Identities=26% Similarity=0.379 Sum_probs=58.7
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHH
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPEN 274 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~ 274 (304)
..+..|.+|-|+ +-|+|||-.|.++|.+|.-||+.|.|...-. -|+||+.|+-.
T Consensus 209 ~~~~~v~lp~d~-----mkgriigreGrnir~~e~~tgvd~iiddtp~---------------------~v~ls~~~~~r 262 (520)
T PRK12704 209 TTVSVVNLPNDE-----MKGRIIGREGRNIRALETLTGVDLIIDDTPE---------------------AVILSGFDPIR 262 (520)
T ss_pred hceeeeecCCch-----hhcceeCCCcchHHHHHHHhCCeEEEcCCCC---------------------eEEEecCChhh
Confidence 446688999985 7799999999999999999999999976522 38899999988
Q ss_pred HHHHHHHHHhhhcCC
Q psy1775 275 VKKAVDRLVCLVSAR 289 (304)
Q Consensus 275 v~~A~~~I~~ll~~~ 289 (304)
-+.|...++.|+...
T Consensus 263 re~a~~~l~~l~~dg 277 (520)
T PRK12704 263 REIARLALEKLVQDG 277 (520)
T ss_pred HHHHHHHHHHHHhcC
Confidence 888888888887754
No 43
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.09 E-value=0.0027 Score=40.73 Aligned_cols=21 Identities=33% Similarity=0.707 Sum_probs=18.6
Q ss_pred CCCCcccCCCCCcccCCCCCC
Q psy1775 40 EGPRCTNCGASDHKSWLCPDK 60 (304)
Q Consensus 40 ~~~~C~~Cg~~GH~~~~Cp~~ 60 (304)
.+..|+.|++.||+..+||..
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 347899999999999999984
No 44
>KOG2193|consensus
Probab=95.95 E-value=0.0056 Score=60.45 Aligned_cols=67 Identities=33% Similarity=0.371 Sum_probs=46.5
Q ss_pred CCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcC
Q psy1775 209 DINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSA 288 (304)
Q Consensus 209 ~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~ 288 (304)
--||+|+|||-.|.++|+|+.+||+||.|--= -| ....+-+--+.|-| +-|.+..|-++|..-|.+
T Consensus 287 HN~lvGRLIGKeGrnlKkIeq~TgTkITis~l---qe----------ls~ynpERTItVkG-siEac~~AE~eImkKlre 352 (584)
T KOG2193|consen 287 HNNLVGRLIGKEGRNLKKIEQDTGTKITISKL---QE----------LSLYNPERTITVKG-SIEACVQAEAEIMKKLRE 352 (584)
T ss_pred hcchhhhhhhhccccHHHHHhhcCCceeeeeh---hh----------hcccCccceEEecc-cHHHHHHHHHHHHHHHHH
Confidence 34799999999999999999999999999431 00 01112223355556 667777787777766655
Q ss_pred C
Q psy1775 289 R 289 (304)
Q Consensus 289 ~ 289 (304)
-
T Consensus 353 ~ 353 (584)
T KOG2193|consen 353 C 353 (584)
T ss_pred H
Confidence 4
No 45
>KOG2191|consensus
Probab=95.86 E-value=0.033 Score=53.62 Aligned_cols=72 Identities=26% Similarity=0.389 Sum_probs=49.6
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHH
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENV 275 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v 275 (304)
...||+||-- -.|-|||-+|.|+.+||++|||+|.+-= - + +.+++-.| =-|+|++. -+.|
T Consensus 39 y~ikvLips~------AaGsIIGKGG~ti~~lqk~tgariklSk-s--~---------dfyPGTTe-Rvcli~Gt-~eai 98 (402)
T KOG2191|consen 39 YFLKVLIPSY------AAGSIIGKGGQTIVQLQKETGARIKLSK-S--K---------DFYPGTTE-RVCLIQGT-VEAL 98 (402)
T ss_pred eEEEEEeecc------cccceeccchHHHHHHHhccCcEEEecc-c--c---------ccCCCccc-eEEEEecc-HHHH
Confidence 5679999986 7899999999999999999999999841 1 1 11222222 23677774 5566
Q ss_pred HHHHHHHHhhhc
Q psy1775 276 KKAVDRLVCLVS 287 (304)
Q Consensus 276 ~~A~~~I~~ll~ 287 (304)
-..++.|.+=|.
T Consensus 99 ~av~efI~dKir 110 (402)
T KOG2191|consen 99 NAVHEFIADKIR 110 (402)
T ss_pred HHHHHHHHHHHH
Confidence 666666555444
No 46
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=95.81 E-value=0.029 Score=50.26 Aligned_cols=64 Identities=38% Similarity=0.573 Sum_probs=53.4
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCC-ccccCCCCCCCCCCCCCCCCCCcEEEEEeC---
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK-GSVKEGKVGRKDGQPLPGENEPLHAYVTAH--- 270 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~-Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~--- 270 (304)
+..+.+.||.+ -+|-|||+.|.+.+.|++.++++|.|..+ |++ -|...
T Consensus 7 ~~~~~v~iPk~------R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V----------------------~i~~~~~t 58 (194)
T COG1094 7 KSSEAVKIPKD------RIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSV----------------------TIRTTRKT 58 (194)
T ss_pred cceeeeecCch------hheeeecccccchHHHHhhcCeEEEEECCCCeE----------------------EEEecCCC
Confidence 34577899998 89999999999999999999999999987 664 35544
Q ss_pred -CHHHHHHHHHHHHhhh
Q psy1775 271 -NPENVKKAVDRLVCLV 286 (304)
Q Consensus 271 -~~~~v~~A~~~I~~ll 286 (304)
|+-++-+|.+.|+.|=
T Consensus 59 ~Dp~~~~ka~d~VkAIg 75 (194)
T COG1094 59 EDPLALLKARDVVKAIG 75 (194)
T ss_pred CChHHHHHHHHHHHHHh
Confidence 7788888888888763
No 47
>KOG2814|consensus
Probab=95.80 E-value=0.014 Score=56.07 Aligned_cols=67 Identities=24% Similarity=0.450 Sum_probs=55.4
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHH
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKA 278 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A 278 (304)
.+.++.- |+|.|||-+|+|.|+||+||+|+|.+=-.+..+ =|+.|++-..+.|-+|
T Consensus 60 si~v~s~------~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~------------------~~i~i~~~~~~~V~~a 115 (345)
T KOG2814|consen 60 SILVRSS------FIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK------------------EEIKIIGISRNCVIQA 115 (345)
T ss_pred hhhhhHH------HhhhhhcccchHHHHHHHhhccceEccCCCCCc------------------ceEEEeehhHHHHHHH
Confidence 4455554 999999999999999999999999985443322 2588999999999999
Q ss_pred HHHHHhhhcCC
Q psy1775 279 VDRLVCLVSAR 289 (304)
Q Consensus 279 ~~~I~~ll~~~ 289 (304)
.+.|..+|...
T Consensus 116 ~~Ri~~~ids~ 126 (345)
T KOG2814|consen 116 LERIAKLIDSD 126 (345)
T ss_pred HHHHHHHHHhh
Confidence 99999999876
No 48
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.70 E-value=0.0048 Score=42.07 Aligned_cols=17 Identities=41% Similarity=1.130 Sum_probs=8.7
Q ss_pred CCcccCCCCCcccCCCC
Q psy1775 42 PRCTNCGASDHKSWLCP 58 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp 58 (304)
..|.+|++.||+.++|+
T Consensus 5 ~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 5 VRCQKCGQKGHWTYECP 21 (42)
T ss_pred CcCcccCCCCcchhhCC
Confidence 34555555555555555
No 49
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.37 E-value=0.0079 Score=41.03 Aligned_cols=19 Identities=32% Similarity=0.875 Sum_probs=17.6
Q ss_pred cccccccccccccccccCC
Q psy1775 66 STLCSSCGGAGHIARDCRE 84 (304)
Q Consensus 66 ~~~C~~CG~~GH~ardC~~ 84 (304)
...|.+|++.|||+-+|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 5789999999999999995
No 50
>smart00343 ZnF_C2HC zinc finger.
Probab=95.10 E-value=0.009 Score=36.12 Aligned_cols=18 Identities=56% Similarity=1.200 Sum_probs=15.4
Q ss_pred cccccccccccccccCCC
Q psy1775 68 LCSSCGGAGHIARDCREK 85 (304)
Q Consensus 68 ~C~~CG~~GH~ardC~~~ 85 (304)
.|+.||+.||++++|+..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 489999999999999844
No 51
>KOG1960|consensus
Probab=94.92 E-value=0.03 Score=55.10 Aligned_cols=65 Identities=22% Similarity=0.279 Sum_probs=53.0
Q ss_pred cCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCC
Q psy1775 218 GPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSAR 289 (304)
Q Consensus 218 GP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~ 289 (304)
=-||.|+-.|+++||+.|..||.=...|.+ .. -..+.||..+|.+.+.|-+++|++.|+-++..+
T Consensus 110 ~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~---~v----g~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~ 174 (531)
T KOG1960|consen 110 STRGTSYDHIEGITGTTSASRGSAPAPELP---PV----GSSEGPLVDHIPPSTAEITSKAIERIKGVFMQD 174 (531)
T ss_pred eccchhHHhhhhhccceeeccCCCCCccCC---CC----CCCCCcceeecCCccHHHHHHHHhhCccceeec
Confidence 348999999999999999999975544332 12 246789999999999999999999999776665
No 52
>PRK12705 hypothetical protein; Provisional
Probab=94.82 E-value=0.076 Score=54.27 Aligned_cols=70 Identities=26% Similarity=0.341 Sum_probs=57.3
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHH
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPEN 274 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~ 274 (304)
..+..|.+|-|+ +-|+|||-.|.+++.+|..||+.|.|...-. -|.|++.|+..
T Consensus 197 ~tvs~v~lp~de-----mkGriIGreGrNir~~E~~tGvdliiddtp~---------------------~V~ls~fdp~r 250 (508)
T PRK12705 197 LSVSVVPIPSDA-----MKGRIIGREGRNIRAFEGLTGVDLIIDDTPE---------------------AVVISSFNPIR 250 (508)
T ss_pred heeeeeecCChH-----hhccccCccchhHHHHHHhhCCceEecCCcc---------------------chhhcccCccc
Confidence 346688999885 7799999999999999999999999976422 16688888888
Q ss_pred HHHHHHHHHhhhcCCC
Q psy1775 275 VKKAVDRLVCLVSARP 290 (304)
Q Consensus 275 v~~A~~~I~~ll~~~~ 290 (304)
-+.|...++.||..+-
T Consensus 251 reia~~~l~~Li~dgr 266 (508)
T PRK12705 251 REIARLTLEKLLADGR 266 (508)
T ss_pred hHHHHHHHHHHHhcCC
Confidence 8888888888887763
No 53
>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=94.76 E-value=0.061 Score=39.19 Aligned_cols=36 Identities=36% Similarity=0.570 Sum_probs=32.1
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEE
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~I 237 (304)
....+++|.+ -+|+.||.+|.+++.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~------~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDD------QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcc------cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4568888887 78999999999999999999998876
No 54
>smart00343 ZnF_C2HC zinc finger.
Probab=94.65 E-value=0.016 Score=35.06 Aligned_cols=17 Identities=41% Similarity=1.040 Sum_probs=15.7
Q ss_pred CcccCCCCCcccCCCCC
Q psy1775 43 RCTNCGASDHKSWLCPD 59 (304)
Q Consensus 43 ~C~~Cg~~GH~~~~Cp~ 59 (304)
.|++||+.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 49999999999999985
No 55
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=94.58 E-value=0.023 Score=37.30 Aligned_cols=23 Identities=39% Similarity=0.702 Sum_probs=14.5
Q ss_pred ccccccccccccccccCCCCCCC
Q psy1775 67 TLCSSCGGAGHIARDCREKRPGM 89 (304)
Q Consensus 67 ~~C~~CG~~GH~ardC~~~~~~~ 89 (304)
..|.+||+..|||+||..+....
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d~~ 25 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTDVD 25 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCCCC
T ss_pred ccCcccCCCcchhhhhhhhhccc
Confidence 47999999999999999887543
No 56
>KOG0109|consensus
Probab=94.11 E-value=0.023 Score=53.79 Aligned_cols=25 Identities=32% Similarity=0.755 Sum_probs=21.3
Q ss_pred cccccccccccccccccCCCCCCCC
Q psy1775 66 STLCSSCGGAGHIARDCREKRPGMG 90 (304)
Q Consensus 66 ~~~C~~CG~~GH~ardC~~~~~~~~ 90 (304)
.-.||.||+.|||+++||..+.+..
T Consensus 160 q~~cyrcGkeghwskEcP~~~~~rv 184 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVDRTGRV 184 (346)
T ss_pred HHHheeccccccccccCCccCCCcc
Confidence 3579999999999999999886543
No 57
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=93.77 E-value=0.057 Score=36.40 Aligned_cols=22 Identities=27% Similarity=0.656 Sum_probs=17.1
Q ss_pred ccccccccccccc--cccCCCCCC
Q psy1775 67 TLCSSCGGAGHIA--RDCREKRPG 88 (304)
Q Consensus 67 ~~C~~CG~~GH~a--rdC~~~~~~ 88 (304)
++|..||..||++ +.||.....
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~ 25 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWS 25 (40)
T ss_pred ccccccccccccccCccCCCCCCC
Confidence 5788899999988 468887743
No 58
>KOG0336|consensus
Probab=92.57 E-value=0.15 Score=50.84 Aligned_cols=61 Identities=25% Similarity=0.265 Sum_probs=41.8
Q ss_pred cccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCC
Q psy1775 211 NFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARP 290 (304)
Q Consensus 211 NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~ 290 (304)
||||.+||=+|+.+|+||..|+++|.|----+ ..-|.|.|.+. --.+|...|..++...+
T Consensus 56 ~mvg~vigrggskik~iq~~tnt~iqii~~~~-------------------e~kv~ifg~~~-m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 56 EMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDL-------------------EVKVTIFGINH-MRKKAKASIDRGQDKDE 115 (629)
T ss_pred hhhheeeccCcchhhhhhcccceeEEEeccCc-------------------eeEEEEechHH-HHHHHHhhHhhhhhhhh
Confidence 49999999999999999999999999843211 11244555433 22456666666666554
Q ss_pred C
Q psy1775 291 R 291 (304)
Q Consensus 291 ~ 291 (304)
+
T Consensus 116 ~ 116 (629)
T KOG0336|consen 116 R 116 (629)
T ss_pred h
Confidence 3
No 59
>KOG2190|consensus
Probab=92.31 E-value=0.78 Score=46.80 Aligned_cols=79 Identities=23% Similarity=0.303 Sum_probs=54.7
Q ss_pred CCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCC-ccccCCCCCCCCCCCCCCCCCCcEEE
Q psy1775 188 DYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK-GSVKEGKVGRKDGQPLPGENEPLHAY 266 (304)
Q Consensus 188 ~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~-Gs~~~~~~~~~~g~~~~~~~e~LHv~ 266 (304)
++..|..-...++..+++ -+|.|||-.|.++|+|.++|.++|.|-.. +..-+ | =|.
T Consensus 35 ~~~~p~~t~~~RlL~~~k------evG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~e----R-------------Iit 91 (485)
T KOG2190|consen 35 ISTGPDETLTYRLLCHVK------EVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPE----R-------------IIT 91 (485)
T ss_pred ccCCCCCcceEEEEeccc------cceeEEccCcHHHHHHhhcccccceeecCCCCCCc----c-------------eEE
Confidence 334433334479999999 79999999999999999999999999765 22111 1 122
Q ss_pred EEe--------CCHHHHHHHHHHHHhhhcCC
Q psy1775 267 VTA--------HNPENVKKAVDRLVCLVSAR 289 (304)
Q Consensus 267 I~a--------~~~~~v~~A~~~I~~ll~~~ 289 (304)
|++ ...+++.+|..+|=..+.++
T Consensus 92 i~g~~~~~~~~~~~~al~ka~~~iv~~~~~d 122 (485)
T KOG2190|consen 92 ITGNRVELNLSPATDALFKAFDMIVFKLEED 122 (485)
T ss_pred EecccccccCCchHHHHHHHHHHHhhccccc
Confidence 333 26678888888776655533
No 60
>KOG2874|consensus
Probab=91.40 E-value=0.13 Score=48.65 Aligned_cols=27 Identities=44% Similarity=0.716 Sum_probs=25.4
Q ss_pred ceeecCCchhHHHHHHHhCCeEEEeCC
Q psy1775 214 GLLIGPRGNTLKSMEKDTGAKIIIRGK 240 (304)
Q Consensus 214 G~iiGP~G~t~K~ie~etg~kI~IrG~ 240 (304)
-+||||.|+|+|.||--|.|-|.+.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~ 187 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN 187 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc
Confidence 479999999999999999999999995
No 61
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=91.29 E-value=0.44 Score=44.14 Aligned_cols=39 Identities=33% Similarity=0.570 Sum_probs=33.3
Q ss_pred EEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCcc
Q psy1775 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 198 ~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs 242 (304)
.-|.||.- ++-++||.+|+.++.|.++|+|.|.|=-.|-
T Consensus 148 ~iv~i~p~------kVpRvig~~~sm~~~l~~~~~~~I~VG~NG~ 186 (239)
T COG1097 148 QIVKIPPS------KVPRVIGKKGSMLNMLKEKTGCEIIVGQNGR 186 (239)
T ss_pred EEEEEchh------hcceEecCCCcHHHHhhhhcCeEEEEecCCE
Confidence 45677765 8889999999999999999999999965555
No 62
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=90.48 E-value=0.14 Score=34.53 Aligned_cols=19 Identities=42% Similarity=0.821 Sum_probs=16.2
Q ss_pred CCcccCCCCCccc--CCCCCC
Q psy1775 42 PRCTNCGASDHKS--WLCPDK 60 (304)
Q Consensus 42 ~~C~~Cg~~GH~~--~~Cp~~ 60 (304)
.+|.+||..||.+ +.||-.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred ccccccccccccccCccCCCC
Confidence 5799999999997 678874
No 63
>KOG2192|consensus
Probab=89.87 E-value=1.1 Score=42.34 Aligned_cols=67 Identities=28% Similarity=0.435 Sum_probs=53.4
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeC--CccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHH
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRG--KGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPEN 274 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG--~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~ 274 (304)
+..|.||.| +-|-|||-+|.-+|+|-.|+||.|.|.. .|| ++--+.| --+++.
T Consensus 316 TaQvtip~d------lggsiigkggqri~~ir~esGA~IkidepleGs------------------edrIitI-tGTqdQ 370 (390)
T KOG2192|consen 316 TAQVTIPKD------LGGSIIGKGGQRIKQIRHESGASIKIDEPLEGS------------------EDRIITI-TGTQDQ 370 (390)
T ss_pred eeeEecccc------cCcceecccchhhhhhhhccCceEEecCcCCCC------------------CceEEEE-eccHHH
Confidence 567899999 8999999999999999999999999976 233 2222344 447889
Q ss_pred HHHHHHHHHhhhcC
Q psy1775 275 VKKAVDRLVCLVSA 288 (304)
Q Consensus 275 v~~A~~~I~~ll~~ 288 (304)
++.|-=+.++-+.+
T Consensus 371 IqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 371 IQNAQYLLQNSVKQ 384 (390)
T ss_pred HhhHHHHHHHHHHh
Confidence 99998888877664
No 64
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=89.68 E-value=0.67 Score=46.99 Aligned_cols=70 Identities=19% Similarity=0.306 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccC
Q psy1775 166 EEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKE 245 (304)
Q Consensus 166 e~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~ 245 (304)
..+-.++..++.++.|. ..--....+ -...|++|.+ +|+.+||-+|+.+++||+..|-+|.|+-.+.-.+
T Consensus 460 ~~a~~~i~~~i~r~~p~-~~eVe~~gd---~~avv~vpe~------~i~~vigk~g~~i~~ie~klgi~I~v~~~e~~~~ 529 (604)
T COG1855 460 KLAEEEIEREIKRYLPG-DVEVEVVGD---GRAVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE 529 (604)
T ss_pred HHHHHHHHHHHHHhCCC-CceEEEecC---CeEEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEcccccc
Confidence 34444555666777776 211222322 2357899988 8999999999999999999999999998766443
No 65
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=89.62 E-value=0.12 Score=36.01 Aligned_cols=17 Identities=35% Similarity=1.040 Sum_probs=10.2
Q ss_pred ccccccccccccccccC
Q psy1775 67 TLCSSCGGAGHIARDCR 83 (304)
Q Consensus 67 ~~C~~CG~~GH~ardC~ 83 (304)
..|+.||..||..++|+
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 34666666666666665
No 66
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.85 E-value=0.2 Score=37.64 Aligned_cols=38 Identities=34% Similarity=0.650 Sum_probs=27.9
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHh-CCeEEE
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDT-GAKIII 237 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~et-g~kI~I 237 (304)
|+.+-.. .|.++-+|..||++|..+|.|+++. |-+|.|
T Consensus 6 kvaV~~~-~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 6 KVAVKSG-DPNIDPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp EEEEEES-STTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred EEEEEcC-CCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence 3444333 3788999999999999999999999 777766
No 67
>KOG2192|consensus
Probab=88.48 E-value=2 Score=40.59 Aligned_cols=38 Identities=21% Similarity=0.466 Sum_probs=32.3
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
+..+|++-.+ -.|.|||-+|+++|+|..+.+|.|++-.
T Consensus 48 ~e~ril~~sk------~agavigkgg~nik~lr~d~na~v~vpd 85 (390)
T KOG2192|consen 48 VELRILLQSK------NAGAVIGKGGKNIKALRTDYNASVSVPD 85 (390)
T ss_pred eeEEEEEecc------cccceeccccccHHHHhhhccceeeccC
Confidence 4557777776 5699999999999999999999998844
No 68
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=88.28 E-value=0.19 Score=35.08 Aligned_cols=19 Identities=32% Similarity=0.711 Sum_probs=17.0
Q ss_pred CCCcccCCCCCcccCCCCC
Q psy1775 41 GPRCTNCGASDHKSWLCPD 59 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~ 59 (304)
...|++||..||...+||.
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 4679999999999999984
No 69
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.11 E-value=0.26 Score=47.02 Aligned_cols=22 Identities=27% Similarity=0.791 Sum_probs=19.1
Q ss_pred cccccccccccccccccCCCCC
Q psy1775 66 STLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 66 ~~~C~~CG~~GH~ardC~~~~~ 87 (304)
.-.||+||+.|||-+.||....
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred ceeEEecCCCCchhhcCCCCCC
Confidence 3579999999999999998763
No 70
>KOG0109|consensus
Probab=84.84 E-value=0.36 Score=45.94 Aligned_cols=22 Identities=32% Similarity=0.655 Sum_probs=19.1
Q ss_pred CCCCcccCCCCCcccCCCCCCC
Q psy1775 40 EGPRCTNCGASDHKSWLCPDKP 61 (304)
Q Consensus 40 ~~~~C~~Cg~~GH~~~~Cp~~~ 61 (304)
+...||.||+.||++.+||...
T Consensus 159 Dq~~cyrcGkeghwskEcP~~~ 180 (346)
T KOG0109|consen 159 DQSGCYRCGKEGHWSKECPVDR 180 (346)
T ss_pred CHHHheeccccccccccCCccC
Confidence 3467999999999999999854
No 71
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=83.97 E-value=1.4 Score=37.57 Aligned_cols=35 Identities=26% Similarity=0.449 Sum_probs=30.2
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
.+.++.. .+|..||++|+.+|.|++..|-+|.|=.
T Consensus 35 i~vV~~~------~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 35 IFVVKEG------DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred EEEEeCC------CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 5555654 7899999999999999999999999866
No 72
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.97 E-value=0.53 Score=44.98 Aligned_cols=21 Identities=33% Similarity=0.702 Sum_probs=18.7
Q ss_pred CCCcccCCCCCcccCCCCCCC
Q psy1775 41 GPRCTNCGASDHKSWLCPDKP 61 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~~~ 61 (304)
+..||+||+.||+..+||...
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~ 196 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQ 196 (427)
T ss_pred ceeEEecCCCCchhhcCCCCC
Confidence 577999999999999999853
No 73
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=82.51 E-value=0.89 Score=29.93 Aligned_cols=20 Identities=30% Similarity=0.624 Sum_probs=13.1
Q ss_pred CcccCCCCCcccCCCCCCCC
Q psy1775 43 RCTNCGASDHKSWLCPDKPN 62 (304)
Q Consensus 43 ~C~~Cg~~GH~~~~Cp~~~~ 62 (304)
.|++|++-.|++.+|..+..
T Consensus 4 ~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp C-TTTSSSCS-TTT---TCC
T ss_pred cCcccCCCcchhhhhhhhhc
Confidence 59999999999999988653
No 74
>KOG0314|consensus
Probab=81.89 E-value=1.2 Score=44.83 Aligned_cols=45 Identities=20% Similarity=0.431 Sum_probs=29.1
Q ss_pred CcccCCCCCcccCCCCCCCCCcccccccccccccccccccCCCCC
Q psy1775 43 RCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 43 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~GH~ardC~~~~~ 87 (304)
.|..|-..+|+..-|........+..|++|+..|||.+.|+....
T Consensus 135 ~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~~ 179 (448)
T KOG0314|consen 135 VCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVSG 179 (448)
T ss_pred eeeecccCccccccccccCCCCCCcceecCCCCCccceeccccCC
Confidence 344444444444444433222245789999999999999998763
No 75
>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=80.97 E-value=1.4 Score=31.21 Aligned_cols=23 Identities=26% Similarity=0.572 Sum_probs=20.6
Q ss_pred cceeecCCchhHHHHHHHhCCeE
Q psy1775 213 VGLLIGPRGNTLKSMEKDTGAKI 235 (304)
Q Consensus 213 iG~iiGP~G~t~K~ie~etg~kI 235 (304)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 59999999999999999998554
No 76
>KOG2113|consensus
Probab=73.45 E-value=3 Score=40.26 Aligned_cols=36 Identities=25% Similarity=0.486 Sum_probs=29.3
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEE
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~I 237 (304)
+.+.+.+|-+ |++.|.|++|.++|.|+.+|...|.-
T Consensus 26 vt~sv~vps~------~v~~ivg~qg~kikalr~KTqtyi~t 61 (394)
T KOG2113|consen 26 VTESVEVPSE------HVAEIVGRQGCKIKALRAKTQTYIKT 61 (394)
T ss_pred cceeeecCcc------cceeecccCccccchhhhhhcceecc
Confidence 4456666633 99999999999999999999987753
No 77
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=71.31 E-value=3.9 Score=34.82 Aligned_cols=36 Identities=17% Similarity=0.225 Sum_probs=30.0
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEe
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIR 238 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~Ir 238 (304)
...+.|+.+ -+|++||.+|.|++.++.-+|-.+.|.
T Consensus 100 ~~~V~V~~~------d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 100 VAYVEVAPE------DKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EEEEEECcc------ccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 446677776 579999999999999999999887663
No 78
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=71.09 E-value=3.5 Score=37.02 Aligned_cols=32 Identities=34% Similarity=0.515 Sum_probs=28.2
Q ss_pred CcccceeecCCchhHHHHHHHhCCeEEEeCCc
Q psy1775 210 INFVGLLIGPRGNTLKSMEKDTGAKIIIRGKG 241 (304)
Q Consensus 210 ~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~G 241 (304)
.+-+|..||++|..+|.|.++.|=+|.|=.-.
T Consensus 84 ~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s 115 (190)
T COG0195 84 IDPVGACIGKRGSRVKAVSEELGEKIDVVEWS 115 (190)
T ss_pred cCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence 45799999999999999999999889886643
No 79
>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=70.29 E-value=5.3 Score=30.14 Aligned_cols=26 Identities=35% Similarity=0.482 Sum_probs=21.4
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEE
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIII 237 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~I 237 (304)
-.|+|||-+|.|+..||-=++.-+.-
T Consensus 34 ~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 34 DIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred CCCeEECCCCccHHHHHHHHHHHHhh
Confidence 46999999999999999887754443
No 80
>PRK13764 ATPase; Provisional
Probab=69.83 E-value=3.6 Score=43.11 Aligned_cols=40 Identities=28% Similarity=0.445 Sum_probs=36.3
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCcc
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs 242 (304)
...||||.+ .|+.+||-+|+++++||+..|..|.||-...
T Consensus 482 ~~~v~~~~~------~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 482 KAVVYVPEK------DIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred eEEEEEChh------hhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 458999999 8899999999999999999999999998644
No 81
>KOG3116|consensus
Probab=68.91 E-value=1.1 Score=38.62 Aligned_cols=21 Identities=29% Similarity=0.745 Sum_probs=16.3
Q ss_pred CCcccCCCCCcccCCCCCCCC
Q psy1775 42 PRCTNCGASDHKSWLCPDKPN 62 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp~~~~ 62 (304)
.+|..|-+.||+.++|.+++.
T Consensus 28 ~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 28 ARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred hhHHHHHhhccceeeecCcee
Confidence 578888888888888877653
No 82
>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=68.73 E-value=5.6 Score=34.01 Aligned_cols=28 Identities=29% Similarity=0.405 Sum_probs=26.1
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
-+|..||++|..++.|++..|=+|.|=.
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 7899999999999999988999999876
No 83
>KOG3116|consensus
Probab=67.59 E-value=1.6 Score=37.66 Aligned_cols=24 Identities=38% Similarity=0.769 Sum_probs=21.4
Q ss_pred cccccccccccccccccccCCCCC
Q psy1775 64 TNSTLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 64 ~~~~~C~~CG~~GH~ardC~~~~~ 87 (304)
.+.+.|.+|-+.|||.-+|..++.
T Consensus 25 ~~~~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 25 GSSARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred ccchhHHHHHhhccceeeecCcee
Confidence 356899999999999999999885
No 84
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=65.53 E-value=3 Score=35.02 Aligned_cols=21 Identities=24% Similarity=0.561 Sum_probs=17.6
Q ss_pred ccccccccccccccccccCCCC
Q psy1775 65 NSTLCSSCGGAGHIARDCREKR 86 (304)
Q Consensus 65 ~~~~C~~CG~~GH~ardC~~~~ 86 (304)
..+.|..|+ ..||+..||.+.
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred ceEEeCCCC-CCcccccCCccc
Confidence 457899996 899999999764
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=65.06 E-value=6.6 Score=38.68 Aligned_cols=40 Identities=25% Similarity=0.586 Sum_probs=32.9
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHh-CCeEEEeC
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDT-GAKIIIRG 239 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~et-g~kI~IrG 239 (304)
||-+=. ..|+++-+|..||++|..++.|.++. |=+|.|=.
T Consensus 234 KVAV~s-~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 234 KIAVRS-NNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred EEEEEc-CCCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 444433 35899999999999999999999999 88888754
No 86
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=64.64 E-value=9.3 Score=37.40 Aligned_cols=55 Identities=27% Similarity=0.386 Sum_probs=43.5
Q ss_pred cccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHH--hhhcC
Q psy1775 211 NFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLV--CLVSA 288 (304)
Q Consensus 211 NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~--~ll~~ 288 (304)
|-+-.|.||.|..++.|++.+|+.|.-||.- +.|.+..+ .++.|...+. .++..
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~~-----------------------~~i~g~~~-~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGEA-----------------------VRIIGARP-LVDVATRVLLTLELLAE 79 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCce-----------------------EEEEechH-HHHHHHHHHhHHHHHHH
Confidence 4677889999999999999999999998852 45777655 7777777777 55555
Q ss_pred C
Q psy1775 289 R 289 (304)
Q Consensus 289 ~ 289 (304)
.
T Consensus 80 ~ 80 (348)
T COG1702 80 V 80 (348)
T ss_pred H
Confidence 4
No 87
>KOG2279|consensus
Probab=62.93 E-value=6.2 Score=40.71 Aligned_cols=43 Identities=33% Similarity=0.584 Sum_probs=39.1
Q ss_pred cceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCcc
Q psy1775 194 IKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 194 ~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs 242 (304)
.....++.+|++ |+-+++|-.|..+|.|.+.|++||.++-+-+
T Consensus 66 k~v~~e~Vv~~e------~vkli~gr~gsnik~l~~~t~aKi~L~~ed~ 108 (608)
T KOG2279|consen 66 KDIEIEMVVPQE------AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV 108 (608)
T ss_pred hheeeeEeeccc------ceeeeeccccCCcchhhcccccceecCcccC
Confidence 466778999999 9999999999999999999999999988755
No 88
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=62.14 E-value=6.4 Score=34.62 Aligned_cols=28 Identities=25% Similarity=0.395 Sum_probs=25.9
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEEeCC
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIIIRGK 240 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~IrG~ 240 (304)
. |+-||++|.++|+|++..|-+|.|=+.
T Consensus 71 d-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 71 P-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred C-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 5 999999999999999999999998774
No 89
>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=61.79 E-value=8.5 Score=37.59 Aligned_cols=40 Identities=30% Similarity=0.610 Sum_probs=33.1
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHh-CCeEEEeC
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDT-GAKIIIRG 239 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~et-g~kI~IrG 239 (304)
||-+=.. .|+++-+|..||++|..++.|.++. |=+|.|=.
T Consensus 232 KvAV~s~-~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 232 KIAVESN-DENIDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred EEEEEcC-CCCCCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 5544433 5899999999999999999999999 88888754
No 90
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=61.53 E-value=3.5 Score=30.60 Aligned_cols=30 Identities=30% Similarity=0.339 Sum_probs=23.5
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhC
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTG 232 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg 232 (304)
...+.|..+ -.|+|||-+|.|++.||-=.+
T Consensus 30 ~i~v~i~~e------d~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 30 TIVVNIDGE------DAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp EEEEEEESC------CCHHHCTTHHHHHHHHHHHHH
T ss_pred EEEEEECCC------ccceEECCCCeeHHHHHHHHH
Confidence 345666555 579999999999999987654
No 91
>KOG2113|consensus
Probab=61.24 E-value=8.2 Score=37.35 Aligned_cols=30 Identities=33% Similarity=0.607 Sum_probs=26.2
Q ss_pred CcccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 210 INFVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 210 ~NfiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
+-.+|+|.||.|+|+|++|+.++.-|.--.
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v 152 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPV 152 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeec
Confidence 448999999999999999999998887544
No 92
>KOG3273|consensus
Probab=60.15 E-value=5.3 Score=36.35 Aligned_cols=60 Identities=20% Similarity=0.326 Sum_probs=47.3
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCC
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPR 291 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~ 291 (304)
-||+|+|-+|+|--.||.-|.++|.+-+. . ++|-| +.+++.-|-..|=.||-.-..
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad~---------------------k--IHiLG-~~~niriAR~avcsLIlGspp 234 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLADS---------------------K--IHILG-AFQNIRIARDAVCSLILGSPP 234 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecCc---------------------e--EEEee-cchhhHHHHHhhHhhhccCCc
Confidence 58999999999999999999999999652 1 44545 467888888877777777666
Q ss_pred CCCC
Q psy1775 292 ARFP 295 (304)
Q Consensus 292 ~~~~ 295 (304)
|++|
T Consensus 235 gkVy 238 (252)
T KOG3273|consen 235 GKVY 238 (252)
T ss_pred hhHH
Confidence 6665
No 93
>KOG2208|consensus
Probab=59.10 E-value=6.8 Score=42.18 Aligned_cols=39 Identities=31% Similarity=0.668 Sum_probs=34.2
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
+....++||.+ |-+-||||+|.+++.++.++++-|.+--
T Consensus 708 ~~~~~~~~p~~------~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 708 LVTKEIEIPRS------LHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred ceeeEEeccHH------HhhhccCCCCccHHHHHHHhccceecCC
Confidence 45678999998 7899999999999999999999887643
No 94
>PRK00468 hypothetical protein; Provisional
Probab=55.22 E-value=7.3 Score=29.72 Aligned_cols=28 Identities=21% Similarity=0.375 Sum_probs=21.6
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHH
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEK 229 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~ 229 (304)
....+.+..+ =+|+|||=+|.|++.|-.
T Consensus 30 ~~~~l~v~~~------D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 30 VILELKVAPE------DMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred EEEEEEEChh------hCcceecCCChhHHHHHH
Confidence 3445666666 479999999999998854
No 95
>PRK02821 hypothetical protein; Provisional
Probab=54.94 E-value=7.4 Score=29.92 Aligned_cols=30 Identities=23% Similarity=0.318 Sum_probs=22.6
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhC
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTG 232 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg 232 (304)
...|++..+ =+|+|||=+|.|++.|-.--.
T Consensus 32 ~i~l~v~~~------D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 32 TLEVRVHPD------DLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred EEEEEEChh------hCcceeCCCCchHHHHHHHHH
Confidence 456666555 479999999999999865443
No 96
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=54.78 E-value=9.1 Score=37.86 Aligned_cols=40 Identities=25% Similarity=0.466 Sum_probs=32.6
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHh-CCeEEEeC
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDT-GAKIIIRG 239 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~et-g~kI~IrG 239 (304)
||-+=- ..|+++-+|..||++|..++.|.++. |=+|.|=.
T Consensus 240 KVAV~S-~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 240 KVALFS-NNPNIDPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred EEEEEc-CCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 444433 45899999999999999999999999 88887744
No 97
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=53.75 E-value=11 Score=38.11 Aligned_cols=41 Identities=27% Similarity=0.464 Sum_probs=33.7
Q ss_pred EEEEeCCCCCCCCcccceeecCCchhHHHHHHHh-CCeEEEeC
Q psy1775 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDT-GAKIIIRG 239 (304)
Q Consensus 198 ~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~et-g~kI~IrG 239 (304)
.||-+-.. .|+++-||..||++|..++.|.++. |=+|.|=.
T Consensus 265 tKVAV~S~-d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 265 TKIAVDTL-ERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred eEEEEEcC-CCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 35555443 4889999999999999999999999 88888754
No 98
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.55 E-value=31 Score=38.41 Aligned_cols=73 Identities=19% Similarity=0.349 Sum_probs=46.1
Q ss_pred CCCCcccCCCCCcccCCCCCCCCC-cccccccccccccccccccCCCCCCCCCCCCCCcccchhhhHHHHHHHHHhCCCC
Q psy1775 40 EGPRCTNCGASDHKSWLCPDKPNI-TNSTLCSSCGGAGHIARDCREKRPGMGGPPANTHRNRAKIDEEYMSLMAELGEGP 118 (304)
Q Consensus 40 ~~~~C~~Cg~~GH~~~~Cp~~~~~-~~~~~C~~CG~~GH~ardC~~~~~~~~g~~~~~~~~~a~~d~EY~~lmaEL~~~~ 118 (304)
....|..||..+ ....||.=... .....|..||..+.- ..||.-..... ......-.+...|.+.|..|+...
T Consensus 625 g~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~~~~-y~CPKCG~El~----~~s~~~i~l~~~~~~A~~~lg~~~ 698 (1121)
T PRK04023 625 GRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIEVEE-DECEKCGREPT----PYSKRKIDLKELYDRALENLGERK 698 (1121)
T ss_pred cCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCcCCC-CcCCCCCCCCC----ccceEEecHHHHHHHHHHHhCCcC
Confidence 457899999997 66788852211 223579999888764 34876443211 112233456788888888887643
No 99
>PRK00089 era GTPase Era; Reviewed
Probab=51.78 E-value=79 Score=29.25 Aligned_cols=90 Identities=21% Similarity=0.379 Sum_probs=49.3
Q ss_pred CCCCCCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCC--CCCCC-CCcceeEEEEeCCCCCCCCcccceee
Q psy1775 141 PSPEPIYSSDGKRMNTREYRTRKKLEEERHDLIQKMFKVNPEFKPP--PDYKP-PVIKVNDKVMIPQDEHPDINFVGLLI 217 (304)
Q Consensus 141 Psp~p~yd~~gkr~ntr~~r~~~~Le~er~~~i~~l~~~~p~~~~P--~~~~~-~~~~~~~ki~IP~~~~P~~NfiG~ii 217 (304)
|..|+.|+.+-..-.+.... ..|--|+.++..+.+=.|.-..- ..|.. ........|++.-+. -.+-||
T Consensus 171 ~~~~~~y~~~~~td~~~r~~---~~EiiRe~~~~~l~~e~p~~~~v~~~~~~~~~~~~i~~~i~v~~~~-----~k~i~i 242 (292)
T PRK00089 171 PEGPPYYPEDQITDRPERFL---AAEIIREKLLRLLGDELPYSVAVEIEKFEERGLVRIEATIYVERDS-----QKGIII 242 (292)
T ss_pred CCCCCCCCCCCCCCCCHHHH---HHHHHHHHHHhhCCccCCceEEEEEEEEEECCeEEEEEEEEEccCC-----ceeEEE
Confidence 33345666653322222222 33344666777665555531110 01110 123455677777764 469999
Q ss_pred cCCchhHHHH--------HHHhCCeEEEe
Q psy1775 218 GPRGNTLKSM--------EKDTGAKIIIR 238 (304)
Q Consensus 218 GP~G~t~K~i--------e~etg~kI~Ir 238 (304)
|-+|+++|+| |+-+|++|.+.
T Consensus 243 g~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 243 GKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred eCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 9999999987 55567777764
No 100
>KOG2560|consensus
Probab=51.57 E-value=4.1 Score=41.15 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=19.2
Q ss_pred cccccccccccccccccCCCCC
Q psy1775 66 STLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 66 ~~~C~~CG~~GH~ardC~~~~~ 87 (304)
...|-+||.+||-.+||..+..
T Consensus 112 KGACeNCGAmtHk~KDCmERPR 133 (529)
T KOG2560|consen 112 KGACENCGAMTHKVKDCMERPR 133 (529)
T ss_pred hhhhhhhhhhhcchHHHhhcch
Confidence 4679999999999999988764
No 101
>KOG2208|consensus
Probab=51.18 E-value=20 Score=38.74 Aligned_cols=33 Identities=21% Similarity=0.453 Sum_probs=29.9
Q ss_pred ccceeecCCchhHHHHHHHhCCeEEEeCCcccc
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVK 244 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~ 244 (304)
|..-++|..|..+.+|++++.|+|.++-.|+..
T Consensus 357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~ 389 (753)
T KOG2208|consen 357 ELKFVIGKKGANIEKIREESQVKIDLPKQGSNN 389 (753)
T ss_pred hhhhhcCCCCccHHHHHHhhhhceecccccCCC
Confidence 778899999999999999999999999877743
No 102
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=50.79 E-value=47 Score=29.50 Aligned_cols=90 Identities=14% Similarity=0.200 Sum_probs=57.4
Q ss_pred HHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCC
Q psy1775 169 RHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKV 248 (304)
Q Consensus 169 r~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~ 248 (304)
+..+++.++.-...+..... ......+ -|.++.. .+=+|+.++|..++.|-...||+|.+.-.-.
T Consensus 2 K~~l~~~Il~d~W~l~v~e~-v~~~g~l--~v~l~~~------~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~~------ 66 (210)
T PF14611_consen 2 KQKLAERILRDCWNLEVSEE-VDELGDL--DVWLQPD------EFFLLLTGNGRILENLAARNGAKIEVSRSEN------ 66 (210)
T ss_pred HHHHHHHHHHHhcCCcccce-eecccee--EEEecch------heeeeecCCchHHHHHHHhcCceEEEecCCc------
Confidence 34566777666666655322 2111111 2333433 5678999999999999788899999854211
Q ss_pred CCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCC
Q psy1775 249 GRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSAR 289 (304)
Q Consensus 249 ~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~ 289 (304)
.+.|+| +...++.+...|.+++...
T Consensus 67 ---------------~i~I~g-~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 67 ---------------RIRITG-TKSTAEYIEASINEILSNI 91 (210)
T ss_pred ---------------EEEEEc-cHHHHHHHHHHHHHHHhhc
Confidence 266888 5667777777777777543
No 103
>KOG2044|consensus
Probab=50.32 E-value=5.8 Score=42.64 Aligned_cols=22 Identities=41% Similarity=0.826 Sum_probs=18.8
Q ss_pred cccccccccccccccccCCCCC
Q psy1775 66 STLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 66 ~~~C~~CG~~GH~ardC~~~~~ 87 (304)
...|+.||+.||.++||.....
T Consensus 260 ~~~C~~cgq~gh~~~dc~g~~~ 281 (931)
T KOG2044|consen 260 PRRCFLCGQTGHEAKDCEGKPR 281 (931)
T ss_pred cccchhhcccCCcHhhcCCcCC
Confidence 3579999999999999987743
No 104
>KOG2673|consensus
Probab=50.25 E-value=6.4 Score=39.72 Aligned_cols=20 Identities=35% Similarity=0.808 Sum_probs=14.1
Q ss_pred cccCCCCCcccCCCCCCCCC
Q psy1775 44 CTNCGASDHKSWLCPDKPNI 63 (304)
Q Consensus 44 C~~Cg~~GH~~~~Cp~~~~~ 63 (304)
|||||..-|.-++||...++
T Consensus 131 CFNC~g~~hsLrdC~rp~d~ 150 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPFDF 150 (485)
T ss_pred ccccCCCCCccccCCCcccc
Confidence 67777777777777776543
No 105
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=49.23 E-value=10 Score=29.10 Aligned_cols=29 Identities=21% Similarity=0.462 Sum_probs=22.1
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHHHH
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEK 229 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~ 229 (304)
.....+.+-.+ =+|++||=+|.|++.|-.
T Consensus 29 ~~~~~l~v~~~------D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 29 TVTIELRVAPE------DMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred eEEEEEEECcc------cccceecCCChhHHHHHH
Confidence 44556666655 379999999999999854
No 106
>PRK01064 hypothetical protein; Provisional
Probab=47.25 E-value=26 Score=26.93 Aligned_cols=30 Identities=20% Similarity=0.386 Sum_probs=22.7
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHh
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDT 231 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~et 231 (304)
....+.+..+ =+|++||=+|.|++.|..-.
T Consensus 30 ~~~~l~v~~~------D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 30 IIYELTVAKP------DIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred EEEEEEECcc------cceEEECCCCccHHHHHHHH
Confidence 3445666655 46999999999999997643
No 107
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=45.97 E-value=12 Score=39.50 Aligned_cols=12 Identities=42% Similarity=1.204 Sum_probs=6.2
Q ss_pred cccccccccccc
Q psy1775 68 LCSSCGGAGHIA 79 (304)
Q Consensus 68 ~C~~CG~~GH~a 79 (304)
+|.+||+.||+-
T Consensus 939 ~C~nCGQvGHmk 950 (968)
T COG5179 939 TCGNCGQVGHMK 950 (968)
T ss_pred eccccccccccc
Confidence 455555555543
No 108
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=45.44 E-value=9.8 Score=24.91 Aligned_cols=27 Identities=33% Similarity=0.856 Sum_probs=21.0
Q ss_pred CcccCCCCCcccCCCCCCCCCccccccccccc
Q psy1775 43 RCTNCGASDHKSWLCPDKPNITNSTLCSSCGG 74 (304)
Q Consensus 43 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~ 74 (304)
.|-.||..-|...+=|.. ...|-.||+
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~-----~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKV-----EGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTTB--SS-----TTBCTTTTE
T ss_pred CcCCCCCccccccCCCCC-----CCccCCCCC
Confidence 589999999998887763 478999997
No 109
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=45.23 E-value=17 Score=37.00 Aligned_cols=40 Identities=30% Similarity=0.532 Sum_probs=32.9
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHh-CCeEEEeC
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDT-GAKIIIRG 239 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~et-g~kI~IrG 239 (304)
||-+- ...|.++-||..||++|+.++.|.++. |=+|.|=-
T Consensus 234 KvAV~-s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 274 (470)
T PRK09202 234 KIAVK-SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIIL 274 (470)
T ss_pred EEEEE-cCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEE
Confidence 44443 346889999999999999999999999 88888754
No 110
>KOG0334|consensus
Probab=44.04 E-value=15 Score=40.65 Aligned_cols=81 Identities=20% Similarity=0.209 Sum_probs=58.4
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHH
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKA 278 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A 278 (304)
.--.+.+++|- |.-+++.+-. ++.+|.+.+++-|.+||+=-- .|..-...+.-||.+|.+.++-.|++|
T Consensus 899 ~~~~~inD~Pq-~~r~~vt~~~--~L~~i~e~~~~~it~rg~f~~--------~gk~p~~gErklyl~ve~~~e~~vqra 967 (997)
T KOG0334|consen 899 EAELEINDFPQ-NARWRVTYKE--ALLRISEPTAAGITTRGKFNP--------PGKEPKPGERKLYLLVEGPDELSVQRA 967 (997)
T ss_pred eeeccccccch-hcceeeechh--hhhhccCccccceeeccccCC--------CCCCCCCcchhhhhhhhcchhHHHHHH
Confidence 34455567774 3555665543 499999999999999996321 111113457889999999999999999
Q ss_pred HHHHHhhhcCCC
Q psy1775 279 VDRLVCLVSARP 290 (304)
Q Consensus 279 ~~~I~~ll~~~~ 290 (304)
++.++.++....
T Consensus 968 ~~e~~r~l~e~~ 979 (997)
T KOG0334|consen 968 IEELERLLEEEV 979 (997)
T ss_pred HHHHHHHHHHHH
Confidence 999998776543
No 111
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=43.69 E-value=20 Score=30.85 Aligned_cols=61 Identities=21% Similarity=0.448 Sum_probs=40.2
Q ss_pred cccccchHHHHHHHHhhcCcccccccccccCCccccCCCCCcccCCCCCcccCCCCCCCCCcccccccccccc
Q psy1775 3 CDVTNFINYRLRKLAENCVPETWAFHPILKKGTLRENEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGA 75 (304)
Q Consensus 3 ~~~~~~~~~~~~~~a~~~~p~~~~~~~~~~nGtlr~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~ 75 (304)
.|||.-++-.+.+|+.= ... +.+-..|..-..+...|-+||..-|+.. |.. -..|.+||..
T Consensus 79 ~~ItDkTqvEw~el~~d----~~h-~g~Y~sGE~~g~G~l~C~~Cg~~~~~~~--~~~-----l~~Cp~C~~~ 139 (146)
T PF07295_consen 79 SSITDKTQVEWAELAQD----LEH-HGVYHSGEVVGPGTLVCENCGHEVELTH--PER-----LPPCPKCGHT 139 (146)
T ss_pred HhhhchhHHHHHHHHHH----HHh-cCCeecCcEecCceEecccCCCEEEecC--CCc-----CCCCCCCCCC
Confidence 46777777777666653 222 2345566666666778999998877764 432 3579999874
No 112
>KOG0107|consensus
Probab=41.78 E-value=20 Score=32.01 Aligned_cols=17 Identities=47% Similarity=1.351 Sum_probs=10.5
Q ss_pred cccccccccccccccCC
Q psy1775 68 LCSSCGGAGHIARDCRE 84 (304)
Q Consensus 68 ~C~~CG~~GH~ardC~~ 84 (304)
.|+.||..||+.+.|..
T Consensus 102 ~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 102 FCYRCGERGHIGRNCKD 118 (195)
T ss_pred ccccCCCcccccccccc
Confidence 36666666666666655
No 113
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=41.54 E-value=29 Score=34.39 Aligned_cols=43 Identities=23% Similarity=0.217 Sum_probs=37.1
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCCcccc
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVK 244 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~Gs~~ 244 (304)
....+++|.+ -.++.||-+|.+++.--+-||.+|.|+.-+|-.
T Consensus 308 ~~~~V~V~~~------qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~ 350 (374)
T PRK12328 308 KKAIVTLLSD------QKSKAIGKNGINIRLASMLTGYEIELNEIGSKE 350 (374)
T ss_pred cEEEEEEChH------HhhhhhcCCChhHHHHHHHhCCEEEEEECCCCc
Confidence 3557788887 458999999999999999999999999988843
No 114
>KOG2044|consensus
Probab=40.82 E-value=13 Score=40.01 Aligned_cols=23 Identities=35% Similarity=0.690 Sum_probs=19.3
Q ss_pred cCCCCCcccCCCCCcccCCCCCC
Q psy1775 38 ENEGPRCTNCGASDHKSWLCPDK 60 (304)
Q Consensus 38 ~~~~~~C~~Cg~~GH~~~~Cp~~ 60 (304)
.....+|+.||++||...+|.-.
T Consensus 257 P~~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 257 PNKPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CCCcccchhhcccCCcHhhcCCc
Confidence 34457899999999999999864
No 115
>COG0347 GlnK Nitrogen regulatory protein PII [Amino acid transport and metabolism]
Probab=38.91 E-value=80 Score=26.06 Aligned_cols=66 Identities=12% Similarity=0.172 Sum_probs=42.2
Q ss_pred CeEEEeCCccccCCCCCCCCCCCCCC-CCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCCCCCCCCcccccC
Q psy1775 233 AKIIIRGKGSVKEGKVGRKDGQPLPG-ENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGADFILN 303 (304)
Q Consensus 233 ~kI~IrG~Gs~~~~~~~~~~g~~~~~-~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~~~~~~g~~~~~~ 303 (304)
+...+.|+|..+. ..+...|..+.. ....+-+.|... .+.|+.+++.|.+.+.+ |.+-+|.=|+++
T Consensus 29 Tv~~V~G~G~Qkg-~~e~yrg~~~~~~~lpK~~ieIvV~-de~ve~vie~I~~~a~t---G~~GDGkIFV~~ 95 (112)
T COG0347 29 TVTEVKGRGRQKG-HTELYRGAEYEVDFLPKVKIEIVVS-DEDVDEVIEAIKKAART---GKIGDGKIFVSP 95 (112)
T ss_pred EEEeeeeecccCC-ccccccchhhhhhcccceEEEEEEC-hHHHHHHHHHHHHHHhc---CCCCCeEEEEEE
Confidence 4567888888662 222223333332 234455555554 88999999999999995 566788777753
No 116
>KOG3070|consensus
Probab=36.74 E-value=34 Score=31.71 Aligned_cols=42 Identities=31% Similarity=0.729 Sum_probs=29.7
Q ss_pred CCCcccCCCCCcccCC----CCCCCCCcccccccccccccccccccCCC
Q psy1775 41 GPRCTNCGASDHKSWL----CPDKPNITNSTLCSSCGGAGHIARDCREK 85 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~----Cp~~~~~~~~~~C~~CG~~GH~ardC~~~ 85 (304)
+..|+.|+..+|.... |--.. ..-.|+.|+..||.+.+|.+.
T Consensus 173 ~~~~~~~g~~~~~~~~~~r~~~g~r---~~~~~~~~~~~g~~~~~~~e~ 218 (235)
T KOG3070|consen 173 GVSGRACGGAGAAQRPPVRKCGGYR---PASLCYTCGEPGHVADGCEES 218 (235)
T ss_pred ccccccccccccccCCCCcccccCC---CcccccccCcccccccccccc
Confidence 4556888888865422 33221 235799999999999999986
No 117
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=36.42 E-value=58 Score=29.50 Aligned_cols=21 Identities=29% Similarity=0.455 Sum_probs=18.2
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q psy1775 222 NTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 222 ~t~K~ie~etg~kI~IrG~Gs 242 (304)
..||+||++.|+++.+|....
T Consensus 40 ~~i~~LE~~lg~~Lf~R~~r~ 60 (294)
T PRK09986 40 IHIKELEDQLGTPLFIRHSRS 60 (294)
T ss_pred HHHHHHHHHhCCeeEeeCCCc
Confidence 469999999999999998544
No 118
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=36.40 E-value=1.2e+02 Score=27.75 Aligned_cols=67 Identities=19% Similarity=0.142 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEE
Q psy1775 161 TRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237 (304)
Q Consensus 161 ~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~I 237 (304)
+.+..++.+.-|-+.+..|++...---+. ......+-|--+ | +|+|||-+|+|+..||--++.-+..
T Consensus 60 ~~~~~~~~~~~L~ell~~m~~~~~i~v~~----~~~~v~~~i~~~-----~-~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 60 IEKIAQEAKDYLEELLELMDFEVTITVSE----EGRRVVVSIEGE-----D-AGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred hhHHHHHHHHHHHHHHHHhCCceEEEEee----cCcEEEEEecCC-----c-hhhhhccCCcchHHHHHHHHHHhhh
Confidence 34444566666777778887754332111 123344555444 3 7999999999999999998877666
No 119
>KOG2673|consensus
Probab=36.24 E-value=18 Score=36.60 Aligned_cols=21 Identities=38% Similarity=0.792 Sum_probs=18.4
Q ss_pred ccccccccccccccccCCCCC
Q psy1775 67 TLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 67 ~~C~~CG~~GH~ardC~~~~~ 87 (304)
..||+||+.-|--+|||....
T Consensus 129 ~~CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 129 DPCFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred ccccccCCCCCccccCCCccc
Confidence 449999999999999998773
No 120
>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=34.18 E-value=45 Score=28.74 Aligned_cols=34 Identities=32% Similarity=0.546 Sum_probs=27.8
Q ss_pred EEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEe
Q psy1775 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIR 238 (304)
Q Consensus 199 ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~Ir 238 (304)
.|+|=.+ .-|++||-+|.|++.|-.+||=...|.
T Consensus 79 EV~Ieae------KPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 79 EVIIEAE------KPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred EEEEEEc------CCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 4555555 459999999999999999999777764
No 121
>KOG3794|consensus
Probab=34.11 E-value=17 Score=36.21 Aligned_cols=23 Identities=26% Similarity=0.517 Sum_probs=18.8
Q ss_pred cccccccccccccccc--ccCCCCC
Q psy1775 65 NSTLCSSCGGAGHIAR--DCREKRP 87 (304)
Q Consensus 65 ~~~~C~~CG~~GH~ar--dC~~~~~ 87 (304)
..+.|.+|+..||+.. +||-...
T Consensus 123 RNVrC~kChkwGH~n~DreCplf~~ 147 (453)
T KOG3794|consen 123 RNVRCLKCHKWGHINTDRECPLFGK 147 (453)
T ss_pred eeeeEEeecccccccCCccCcchhh
Confidence 4688999999999986 5987654
No 122
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=34.04 E-value=22 Score=29.79 Aligned_cols=20 Identities=35% Similarity=0.687 Sum_probs=17.0
Q ss_pred CCCcccCCCCCcccCCCCCCC
Q psy1775 41 GPRCTNCGASDHKSWLCPDKP 61 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~~~ 61 (304)
...|.+|+ -.|+...||.+.
T Consensus 106 ~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 106 KVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred eEEeCCCC-CCcccccCCccc
Confidence 46799997 789999999863
No 123
>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=33.86 E-value=79 Score=29.13 Aligned_cols=38 Identities=13% Similarity=0.378 Sum_probs=28.1
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHHH--------HHhCCeEEE
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSME--------KDTGAKIII 237 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie--------~etg~kI~I 237 (304)
+....|++..+. --|-|||.+|+++|+|. +-.|++|.+
T Consensus 220 ~i~~~i~v~~~s-----~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l 265 (270)
T TIGR00436 220 KIHALISVERES-----QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 (270)
T ss_pred EEEEEEEECcCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 455677888774 45899999999999874 445666654
No 124
>KOG0107|consensus
Probab=33.05 E-value=21 Score=31.94 Aligned_cols=34 Identities=26% Similarity=0.418 Sum_probs=26.4
Q ss_pred CcccCCCCCcccCCCCCCCCCcccccccccccccccccccCCCCC
Q psy1775 43 RCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRP 87 (304)
Q Consensus 43 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~GH~ardC~~~~~ 87 (304)
.|+.||+.||+.+.|.+ ||.| .+|..+.|.....
T Consensus 102 ~~~r~G~rg~~~r~~~~---------sy~r--~~r~~~rrrs~~r 135 (195)
T KOG0107|consen 102 FCYRCGERGHIGRNCKD---------SYSR--RSRSPRRRRSPSR 135 (195)
T ss_pred ccccCCCcccccccccc---------cccc--cCCCcccccCCCC
Confidence 49999999999999855 8777 5677777766543
No 125
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=32.02 E-value=24 Score=34.96 Aligned_cols=49 Identities=27% Similarity=0.355 Sum_probs=32.1
Q ss_pred HHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHH-HHHHHHHhhhc
Q psy1775 229 KDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVK-KAVDRLVCLVS 287 (304)
Q Consensus 229 ~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~-~A~~~I~~ll~ 287 (304)
.++|..+.|||+|--+-.. +-.-+|||.|....+..|. +..+++++|..
T Consensus 300 tq~G~~~rl~gkG~p~~~~----------~~~GDl~v~v~v~~P~~ls~~q~~lL~~~~~ 349 (371)
T COG0484 300 TQTGEVFRLRGKGMPKLRS----------GGRGDLYVRVKVETPKNLSDEQKELLEEFAK 349 (371)
T ss_pred CccCcEEEEcCCCccccCC----------CCcCCEEEEEEEEcCCCCCHHHHHHHHHHHH
Confidence 3459999999999743111 1236899999998887663 33444555554
No 126
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=31.39 E-value=20 Score=26.20 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=5.4
Q ss_pred ccccccccccc
Q psy1775 66 STLCSSCGGAG 76 (304)
Q Consensus 66 ~~~C~~CG~~G 76 (304)
.-.|-+||-.|
T Consensus 48 ~Y~CP~CGF~G 58 (59)
T PRK14890 48 PYTCPKCGFEG 58 (59)
T ss_pred ceECCCCCCcC
Confidence 34555555443
No 127
>KOG4165|consensus
Probab=31.20 E-value=51 Score=32.43 Aligned_cols=25 Identities=36% Similarity=0.808 Sum_probs=17.7
Q ss_pred ccceeecCCchh--HHHHHHHhCCeEEEeC
Q psy1775 212 FVGLLIGPRGNT--LKSMEKDTGAKIIIRG 239 (304)
Q Consensus 212 fiG~iiGP~G~t--~K~ie~etg~kI~IrG 239 (304)
+|-+|| |||++ ++.|++.|. |-+-|
T Consensus 191 ~IDLvI-PRGSs~LVr~Ik~~tk--IPVLG 217 (433)
T KOG4165|consen 191 YIDLVI-PRGSSDLVRSIKDTTK--IPVLG 217 (433)
T ss_pred heeEEe-cCCcHHHHHHHhhccc--Ccccc
Confidence 666666 88886 677777654 77766
No 128
>KOG0341|consensus
Probab=30.77 E-value=29 Score=35.00 Aligned_cols=18 Identities=33% Similarity=0.828 Sum_probs=10.9
Q ss_pred CCcccCCCCCcccCCCCC
Q psy1775 42 PRCTNCGASDHKSWLCPD 59 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp~ 59 (304)
..|.-||.-||+..+||.
T Consensus 571 kGCayCgGLGHRItdCPK 588 (610)
T KOG0341|consen 571 KGCAYCGGLGHRITDCPK 588 (610)
T ss_pred cccccccCCCcccccCch
Confidence 456666666666666664
No 129
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.43 E-value=86 Score=35.87 Aligned_cols=71 Identities=25% Similarity=0.516 Sum_probs=43.3
Q ss_pred CCCcccCCCCCcccCCCCCCCCC-ccccccccccccc----ccccccCCCCCCCCCCCCCC-cccchhhhHHHHHHHHHh
Q psy1775 41 GPRCTNCGASDHKSWLCPDKPNI-TNSTLCSSCGGAG----HIARDCREKRPGMGGPPANT-HRNRAKIDEEYMSLMAEL 114 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~~~~~-~~~~~C~~CG~~G----H~ardC~~~~~~~~g~~~~~-~~~~a~~d~EY~~lmaEL 114 (304)
..+|-+||...+. .-||.=... .....|..||..= +.+..||.=.. +..+ ....-.+...|.+.|..|
T Consensus 667 ~rkCPkCG~~t~~-~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGt-----plv~~~~~~i~~~~~~~~A~~~~ 740 (1337)
T PRK14714 667 RRRCPSCGTETYE-NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDV-----ELTPYQRRTINVKEEYRSALENV 740 (1337)
T ss_pred EEECCCCCCcccc-ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCC-----cccccceEEecHHHHHHHHHHHh
Confidence 3689999998765 488852211 1234799999852 22557885432 1111 122345678888888888
Q ss_pred CCC
Q psy1775 115 GEG 117 (304)
Q Consensus 115 ~~~ 117 (304)
+..
T Consensus 741 g~~ 743 (1337)
T PRK14714 741 GER 743 (1337)
T ss_pred Ccc
Confidence 754
No 130
>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=30.21 E-value=55 Score=32.01 Aligned_cols=38 Identities=29% Similarity=0.462 Sum_probs=33.2
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
....+++|.+ -.++.||-+|.+++.--+-||.+|.|+-
T Consensus 301 ~~~~v~V~~~------~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDD------QLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChH------HcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 3567888887 4689999999999999999999999974
No 131
>KOG2560|consensus
Probab=29.42 E-value=14 Score=37.39 Aligned_cols=20 Identities=45% Similarity=0.914 Sum_probs=17.6
Q ss_pred CCcccCCCCCcccCCCCCCC
Q psy1775 42 PRCTNCGASDHKSWLCPDKP 61 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp~~~ 61 (304)
..|.|||..||...+|-+++
T Consensus 113 GACeNCGAmtHk~KDCmERP 132 (529)
T KOG2560|consen 113 GACENCGAMTHKVKDCMERP 132 (529)
T ss_pred hhhhhhhhhhcchHHHhhcc
Confidence 56999999999999998754
No 132
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=29.23 E-value=46 Score=27.90 Aligned_cols=36 Identities=17% Similarity=0.384 Sum_probs=27.4
Q ss_pred CcccCCCCCcccCCCCCCCCCcccccccccccccccccccC
Q psy1775 43 RCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCR 83 (304)
Q Consensus 43 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~GH~ardC~ 83 (304)
.||.||+.....+..... .-.|-.|+..-++..|=-
T Consensus 2 ~C~fC~~~s~~~~~~~~~-----~w~C~~C~q~N~f~e~Gd 37 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNS-----NWTCPHCEQYNGFDEDGD 37 (131)
T ss_pred eeccCCCCCCCCCCCCCC-----eeECCCCCCccCccccCC
Confidence 699999988877765442 257999999988876643
No 133
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=29.21 E-value=24 Score=26.26 Aligned_cols=24 Identities=21% Similarity=0.580 Sum_probs=20.1
Q ss_pred ccceeecCCchhHHHHHHHhCCeE
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGAKI 235 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~kI 235 (304)
..|.+||-+|++++.|..+.+-.+
T Consensus 35 ~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 35 QPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CccHhHHhhhHHHHHHHHHHHHHH
Confidence 569999999999999988776444
No 134
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=29.01 E-value=95 Score=28.13 Aligned_cols=20 Identities=15% Similarity=0.408 Sum_probs=17.5
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q psy1775 222 NTLKSMEKDTGAKIIIRGKG 241 (304)
Q Consensus 222 ~t~K~ie~etg~kI~IrG~G 241 (304)
..|++||++.|+++.+|...
T Consensus 34 ~~i~~LE~~lg~~Lf~R~~~ 53 (296)
T PRK11242 34 QQIRQLEESLGVQLFDRSGR 53 (296)
T ss_pred HHHHHHHHHhCCeeEeEcCC
Confidence 46999999999999999743
No 135
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=28.78 E-value=45 Score=23.29 Aligned_cols=36 Identities=25% Similarity=0.486 Sum_probs=20.1
Q ss_pred CCcccCCCCCc-ccCCCCCCCCCccccccccccccccc
Q psy1775 42 PRCTNCGASDH-KSWLCPDKPNITNSTLCSSCGGAGHI 78 (304)
Q Consensus 42 ~~C~~Cg~~GH-~~~~Cp~~~~~~~~~~C~~CG~~GH~ 78 (304)
..|-.||.... +.+.-..... .....|..||..|..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~-~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDL-SHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCC-EEEEECCCCCCCccc
Confidence 46999999887 3321111111 112368888887754
No 136
>COG0026 PurK Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism]
Probab=28.30 E-value=1e+02 Score=30.55 Aligned_cols=53 Identities=23% Similarity=0.319 Sum_probs=40.6
Q ss_pred hHHHHHHHhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcC
Q psy1775 223 TLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSA 288 (304)
Q Consensus 223 t~K~ie~etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~ 288 (304)
..+.+-+..++++-..||.-.+.+ |+-| ||.|.++|.+.+..+...+......
T Consensus 318 ~~~~~l~~p~~~lH~YGK~e~R~g---RKmG----------Hvn~~~~~~~~~~~~~~~l~~~~~~ 370 (375)
T COG0026 318 DVKAVLALPGAHLHWYGKAEARPG---RKMG----------HVNVLGSDSDELEQLAALLPAKQLS 370 (375)
T ss_pred hhHHHHhCCCCEEEEecCccCCCC---Ceee----------eEEeecCCHHHHHHHHHhhhhhhcc
Confidence 468888999999999999765544 4555 8999999987777776666654443
No 137
>PRK15494 era GTPase Era; Provisional
Probab=28.28 E-value=1.1e+02 Score=29.61 Aligned_cols=40 Identities=18% Similarity=0.456 Sum_probs=30.4
Q ss_pred ceeEEEEeCCCCCCCCcccceeecCCchhHHHH--------HHHhCCeEEEeC
Q psy1775 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSM--------EKDTGAKIIIRG 239 (304)
Q Consensus 195 ~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~i--------e~etg~kI~IrG 239 (304)
.....||+.-+. --+-|||-+|.+||+| |+-.|+||.+.=
T Consensus 272 ~i~~~i~v~~~s-----qk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~l 319 (339)
T PRK15494 272 KINQVIVVSRES-----YKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLFL 319 (339)
T ss_pred EEEEEEEECCCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEEE
Confidence 345678888774 4589999999999987 555788877643
No 138
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=27.40 E-value=1.5e+02 Score=26.06 Aligned_cols=36 Identities=14% Similarity=0.205 Sum_probs=28.7
Q ss_pred hCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeC-CHHHHHHHHHHHHhhhcC
Q psy1775 231 TGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAH-NPENVKKAVDRLVCLVSA 288 (304)
Q Consensus 231 tg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~-~~~~v~~A~~~I~~ll~~ 288 (304)
+.+.+.|-..|. |.|+|- +++.+.+|++.|-.+|.+
T Consensus 137 pk~~~liF~sGk----------------------vvitGaks~~~~~~a~~~i~p~L~~ 173 (174)
T cd04516 137 PKIVLLIFVSGK----------------------IVLTGAKSREEIYQAFENIYPILLQ 173 (174)
T ss_pred CcEEEEEeCCCE----------------------EEEEecCCHHHHHHHHHHHHHHHhh
Confidence 447788887776 678854 888999999999988854
No 139
>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=27.30 E-value=1.4e+02 Score=23.26 Aligned_cols=68 Identities=19% Similarity=0.244 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhH
Q psy1775 157 REYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTL 224 (304)
Q Consensus 157 r~~r~~~~Le~er~~~i~~l~~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~ 224 (304)
|-.-..+++|+++..-|..|++-...-+....-............=+...++..++|--+.|+.|.+|
T Consensus 13 Rk~~~eKk~EEeK~eTInKLLkkqa~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~IR~v~~~~G~~v 80 (89)
T PF04795_consen 13 RKNQSEKKLEEEKMETINKLLKKQATRKKREPKDKEGEEDSAQEKKRRAPKPNPPMIRWVSNKNGSRV 80 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccccccchhhhhhhhhccccccccccCCCCCEEEEEECCCceEE
Confidence 34456678999999999999888773222111000000000111122234555679999999998875
No 140
>PF12773 DZR: Double zinc ribbon
Probab=26.76 E-value=79 Score=21.34 Aligned_cols=13 Identities=23% Similarity=0.846 Sum_probs=8.3
Q ss_pred cCCCCCcccCCCC
Q psy1775 38 ENEGPRCTNCGAS 50 (304)
Q Consensus 38 ~~~~~~C~~Cg~~ 50 (304)
+.+...|.+||..
T Consensus 9 ~~~~~fC~~CG~~ 21 (50)
T PF12773_consen 9 PDDAKFCPHCGTP 21 (50)
T ss_pred CccccCChhhcCC
Confidence 3445678888765
No 141
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=26.53 E-value=40 Score=30.20 Aligned_cols=31 Identities=19% Similarity=0.548 Sum_probs=22.2
Q ss_pred CCCcccCCCCCcccCCCCCCCCCccccccccccccccccc
Q psy1775 41 GPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIAR 80 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~GH~ar 80 (304)
...|..|+..|...... ..|..|++.|+...
T Consensus 99 ~~~C~~C~G~G~~i~~~---------~~C~~C~G~G~v~~ 129 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRRQ---------RECDTCAGTGRFRP 129 (186)
T ss_pred CCcCCCCCCeeEEecCC---------CCCCCCCCccEEee
Confidence 46788888888765432 25888999887664
No 142
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=26.16 E-value=61 Score=22.73 Aligned_cols=32 Identities=41% Similarity=0.947 Sum_probs=19.7
Q ss_pred CCCcccCCCCCcccCCCCCCCCCcccccccccccc
Q psy1775 41 GPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGA 75 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~ 75 (304)
...|.+|+......|-= .. ......|..||-.
T Consensus 3 ~~~C~~C~~~~T~~WR~--g~-~g~~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRR--GP-SGNKTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCcccc--CC-CCCCcEeecccHH
Confidence 36799999776665521 11 1123779999863
No 143
>COG3286 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.94 E-value=68 Score=29.06 Aligned_cols=57 Identities=23% Similarity=0.343 Sum_probs=40.1
Q ss_pred HHHHHHHh-CCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHHHHHHHHHHhhhcCCCCCCCCCCccccc
Q psy1775 224 LKSMEKDT-GAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGADFIL 302 (304)
Q Consensus 224 ~K~ie~et-g~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v~~A~~~I~~ll~~~~~~~~~~g~~~~~ 302 (304)
+++||.-- .|-|.++|+.+++ |.|.|. .+.|..|+..|.++.... ++..+.++.+.|
T Consensus 19 lE~lqr~~~~~~v~~~g~n~vk--------------------V~v~G~-~~eireair~irel~~~v-r~r~~~~~~~ly 76 (204)
T COG3286 19 LERLQRMVKDTYVEIRGKNRVK--------------------VNVFGT-KDEIREAIRAIRELHRRV-RRRLYPDRQGLY 76 (204)
T ss_pred HHHHHHhCcceEEEEccCceEE--------------------EEEecc-hHHHHHHHHHHHHHHHHH-HhhhccCccceE
Confidence 45555442 5888999986644 888887 888999999999988765 444455554443
No 144
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=25.62 E-value=1.1e+02 Score=27.83 Aligned_cols=21 Identities=24% Similarity=0.526 Sum_probs=18.2
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q psy1775 222 NTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 222 ~t~K~ie~etg~kI~IrG~Gs 242 (304)
..+|+||++.|+++.+|..+.
T Consensus 34 r~i~~LE~~lg~~Lf~R~~~~ 54 (296)
T PRK09906 34 QQIKDLENCVGVPLLVRDKRK 54 (296)
T ss_pred HHHHHHHHHhCCeeeeeCCCc
Confidence 469999999999999997554
No 145
>KOG0341|consensus
Probab=25.18 E-value=37 Score=34.23 Aligned_cols=22 Identities=36% Similarity=0.825 Sum_probs=18.7
Q ss_pred ccccccccccccccccccCCCC
Q psy1775 65 NSTLCSSCGGAGHIARDCREKR 86 (304)
Q Consensus 65 ~~~~C~~CG~~GH~ardC~~~~ 86 (304)
....|.-||+-||--.|||.-.
T Consensus 569 ~~kGCayCgGLGHRItdCPKle 590 (610)
T KOG0341|consen 569 GEKGCAYCGGLGHRITDCPKLE 590 (610)
T ss_pred CccccccccCCCcccccCchhh
Confidence 3468999999999999999643
No 146
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=24.99 E-value=69 Score=32.72 Aligned_cols=38 Identities=34% Similarity=0.486 Sum_probs=33.4
Q ss_pred eEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCC
Q psy1775 197 NDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK 240 (304)
Q Consensus 197 ~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~ 240 (304)
...|++|.+ -+++.||-+|.+++...+-||.+|.|.-.
T Consensus 303 ~~~v~V~~~------~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 303 SADVVVPDD------QLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEEEECcc------hHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 456788877 67999999999999999999999999873
No 147
>PRK11032 hypothetical protein; Provisional
Probab=24.59 E-value=52 Score=28.77 Aligned_cols=61 Identities=20% Similarity=0.359 Sum_probs=36.3
Q ss_pred cccccchHHHHHHHHhhcCcccccccccccCCccccCCCCCcccCCCCCcccCCCCCCCCCcccccccccccc
Q psy1775 3 CDVTNFINYRLRKLAENCVPETWAFHPILKKGTLRENEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGA 75 (304)
Q Consensus 3 ~~~~~~~~~~~~~~a~~~~p~~~~~~~~~~nGtlr~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~ 75 (304)
.|||.-++--.++++.= ... +.+-..|.+-.-++..|-+||..-|+.. |. .-..|.+||..
T Consensus 91 ~~ItDrTqvEw~el~~d----l~h-~g~Y~sGEvvg~G~LvC~~Cg~~~~~~~--p~-----~i~pCp~C~~~ 151 (160)
T PRK11032 91 ADITDKTQLEWREVFQD----LNH-HGVYHSGEVVGLGNLVCEKCHHHLAFYT--PE-----VLPLCPKCGHD 151 (160)
T ss_pred HHHHHHhHHHHHHHHHH----hhh-cCeeecceeeecceEEecCCCCEEEecC--CC-----cCCCCCCCCCC
Confidence 45666666655665552 111 2344456665566778999987766633 22 22569999874
No 148
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=24.55 E-value=35 Score=24.58 Aligned_cols=26 Identities=27% Similarity=0.710 Sum_probs=7.8
Q ss_pred CCCCCCCCCcccccccccccc---cccccccCC
Q psy1775 55 WLCPDKPNITNSTLCSSCGGA---GHIARDCRE 84 (304)
Q Consensus 55 ~~Cp~~~~~~~~~~C~~CG~~---GH~ardC~~ 84 (304)
..||--+ ...|-.||.. .|..+-||.
T Consensus 26 v~CPvLr----~y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 26 VTCPVLR----KYVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp B--TTGG----G---TTT---GGG---GGG-TT
T ss_pred EeCHHHh----cCcCCCCcCcCccccccccCcC
Confidence 3566632 3567777664 455556664
No 149
>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=24.43 E-value=71 Score=27.29 Aligned_cols=37 Identities=16% Similarity=0.130 Sum_probs=30.8
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEe
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIR 238 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~Ir 238 (304)
....+.||.+ -.|+.||-+|.+++...+-+|-++.|.
T Consensus 100 ~~a~V~V~~~------d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 100 KVAYVEVHPR------DKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EEEEEEEChh------hhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 4567788887 459999999999999999999887764
No 150
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=24.20 E-value=33 Score=36.35 Aligned_cols=24 Identities=33% Similarity=0.538 Sum_probs=17.1
Q ss_pred CCccccCCCCCcccCCCCCcccCC
Q psy1775 33 KGTLRENEGPRCTNCGASDHKSWL 56 (304)
Q Consensus 33 nGtlr~~~~~~C~~Cg~~GH~~~~ 56 (304)
+|.=|......|.+||+.||+..+
T Consensus 929 ~G~GRK~Ttr~C~nCGQvGHmkTN 952 (968)
T COG5179 929 AGKGRKNTTRTCGNCGQVGHMKTN 952 (968)
T ss_pred cCCCCCCcceeccccccccccccc
Confidence 343344446789999999999754
No 151
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=24.14 E-value=76 Score=20.95 Aligned_cols=30 Identities=37% Similarity=0.738 Sum_probs=19.7
Q ss_pred CCcccCCCCCcccCCCCCCCCCccccccccccc
Q psy1775 42 PRCTNCGASDHKSWLCPDKPNITNSTLCSSCGG 74 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~ 74 (304)
..|-.||...-++++=... ...-.|+.|+.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g---~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDG---RGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCC---CcCEEeCCCCC
Confidence 5699999888887432211 23467888864
No 152
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=24.04 E-value=61 Score=26.12 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=18.6
Q ss_pred ccceeecCCchhHHHHHHHhCC
Q psy1775 212 FVGLLIGPRGNTLKSMEKDTGA 233 (304)
Q Consensus 212 fiG~iiGP~G~t~K~ie~etg~ 233 (304)
+-|.|||-+|.+++.|++....
T Consensus 71 rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 71 RPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CCCcccCCchHHHHHHHHHHHH
Confidence 4599999999999999887543
No 153
>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=23.93 E-value=1.1e+02 Score=28.22 Aligned_cols=21 Identities=14% Similarity=0.521 Sum_probs=18.3
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q psy1775 222 NTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 222 ~t~K~ie~etg~kI~IrG~Gs 242 (304)
..|++||++.|+++.+|....
T Consensus 41 ~~I~~LE~~lg~~Lf~R~~r~ 61 (302)
T TIGR02036 41 HRINQLEEELGIQLFVRSHRK 61 (302)
T ss_pred HHHHHHHHHhCCceEEECCCc
Confidence 358999999999999999655
No 154
>PRK04023 DNA polymerase II large subunit; Validated
Probab=23.69 E-value=56 Score=36.48 Aligned_cols=35 Identities=26% Similarity=0.629 Sum_probs=26.3
Q ss_pred CCcccCCCCCcccCCCCCCCCCccccccccccccc
Q psy1775 42 PRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAG 76 (304)
Q Consensus 42 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~G 76 (304)
..|-+||......+.||.=........|-+||..-
T Consensus 639 frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El 673 (1121)
T PRK04023 639 RRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREP 673 (1121)
T ss_pred ccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCC
Confidence 67999999877888888743333446799998864
No 155
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=23.62 E-value=90 Score=28.90 Aligned_cols=43 Identities=21% Similarity=0.388 Sum_probs=27.8
Q ss_pred EEEEeCCCCCCCCcccceeecCCchh-----------HHHHHHHhCC-eEEEeCC
Q psy1775 198 DKVMIPQDEHPDINFVGLLIGPRGNT-----------LKSMEKDTGA-KIIIRGK 240 (304)
Q Consensus 198 ~ki~IP~~~~P~~NfiG~iiGP~G~t-----------~K~ie~etg~-kI~IrG~ 240 (304)
+.+.-..+-.|.+-.+|.+|||||.. +...-++.-. +|.+|-+
T Consensus 113 D~~IAtpdmM~~v~~LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K~g~v~~R~d 167 (228)
T COG0081 113 DVFIATPDMMPLVGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRAD 167 (228)
T ss_pred CEEEECchHHHHHHHHhhhcCCCCCCCCCCCCCCCcCHHHHHHHHhcCcEEEEEC
Confidence 45555666677777899999999963 3444455443 5555543
No 156
>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=23.45 E-value=71 Score=22.49 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=16.7
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q psy1775 222 NTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 222 ~t~K~ie~etg~kI~IrG~Gs 242 (304)
..+++||++.|+++.+|..+.
T Consensus 32 ~~i~~LE~~lg~~Lf~r~~~~ 52 (60)
T PF00126_consen 32 RQIKQLEEELGVPLFERSGRG 52 (60)
T ss_dssp HHHHHHHHHHTS-SEEECSSS
T ss_pred HHHHHHHHHhCCeEEEECCCC
Confidence 358999999999999996543
No 157
>KOG1244|consensus
Probab=23.42 E-value=31 Score=32.87 Aligned_cols=15 Identities=47% Similarity=0.884 Sum_probs=10.8
Q ss_pred CCCCcccCCCCCccc
Q psy1775 40 EGPRCTNCGASDHKS 54 (304)
Q Consensus 40 ~~~~C~~Cg~~GH~~ 54 (304)
+...|..||..||-+
T Consensus 245 elvscsdcgrsghps 259 (336)
T KOG1244|consen 245 ELVSCSDCGRSGHPS 259 (336)
T ss_pred hhcchhhcCCCCCcc
Confidence 456788888888843
No 158
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=23.37 E-value=1.2e+02 Score=28.24 Aligned_cols=21 Identities=29% Similarity=0.487 Sum_probs=17.9
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q psy1775 222 NTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 222 ~t~K~ie~etg~kI~IrG~Gs 242 (304)
..+|+||++.|+++.+|....
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r~ 55 (308)
T PRK10094 35 YRIKLLEENTGVALFFRTTRS 55 (308)
T ss_pred HHHHHHHHHhCCEEEeeCCCc
Confidence 358999999999999997544
No 159
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.93 E-value=51 Score=23.88 Aligned_cols=30 Identities=23% Similarity=0.569 Sum_probs=18.8
Q ss_pred CCCcccCCCCCcccCCCCCCCCCcccccccccccccc
Q psy1775 41 GPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGH 77 (304)
Q Consensus 41 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~GH 77 (304)
.+.|..||..... +.. ...-.|..||-..|
T Consensus 28 Sq~C~~CG~~~~~----~~~---~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----RRS---GRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCccccccc----ccc---cceEEcCCCCCEEC
Confidence 4789999765444 111 13467999987643
No 160
>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=22.84 E-value=1.3e+02 Score=22.01 Aligned_cols=25 Identities=16% Similarity=0.409 Sum_probs=21.5
Q ss_pred cEEEEEeCCHHHHHHHHHHHHhhhc
Q psy1775 263 LHAYVTAHNPENVKKAVDRLVCLVS 287 (304)
Q Consensus 263 LHv~I~a~~~~~v~~A~~~I~~ll~ 287 (304)
|-|++.|.+.+.+++..+.|..+|.
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 6799999999999998888887763
No 161
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=22.78 E-value=87 Score=32.89 Aligned_cols=32 Identities=25% Similarity=0.716 Sum_probs=20.7
Q ss_pred CCCCCcccCCCCCcccCCCCCCCCCcccccccccccc
Q psy1775 39 NEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGA 75 (304)
Q Consensus 39 ~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~ 75 (304)
.+|..|+.||..+ -.|.|-+- ..-.|..|.+.
T Consensus 21 PgNk~CADCgs~~-P~WASiNl----GIFICi~CSGI 52 (648)
T PLN03119 21 PPNRRCINCNSLG-PQYVCTTF----WTFVCMACSGI 52 (648)
T ss_pred cCCCccccCCCCC-CCceeecc----ceEEeccchhh
Confidence 3678999999865 44544431 23568888654
No 162
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=22.65 E-value=33 Score=25.23 Aligned_cols=10 Identities=40% Similarity=0.913 Sum_probs=4.8
Q ss_pred cccccccccc
Q psy1775 67 TLCSSCGGAG 76 (304)
Q Consensus 67 ~~C~~CG~~G 76 (304)
-+|-+||-.|
T Consensus 51 Y~Cp~CGF~G 60 (61)
T COG2888 51 YRCPKCGFEG 60 (61)
T ss_pred eECCCcCccC
Confidence 3455555443
No 163
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=22.34 E-value=1.3e+02 Score=27.11 Aligned_cols=21 Identities=19% Similarity=0.272 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeCCcc
Q psy1775 222 NTLKSMEKDTGAKIIIRGKGS 242 (304)
Q Consensus 222 ~t~K~ie~etg~kI~IrG~Gs 242 (304)
..||+||++.|+++.+|....
T Consensus 36 ~~I~~LE~~lg~~Lf~R~~r~ 56 (290)
T PRK10837 36 AALTDLEGQLGVQLFDRVGKR 56 (290)
T ss_pred HHHHHHHHHhCCccEeecCCe
Confidence 368999999999999997544
No 164
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=22.21 E-value=1.5e+02 Score=22.61 Aligned_cols=37 Identities=22% Similarity=0.457 Sum_probs=30.0
Q ss_pred HhCCeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEe-CCHHHHHHHHHHHHhhhcC
Q psy1775 230 DTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTA-HNPENVKKAVDRLVCLVSA 288 (304)
Q Consensus 230 etg~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a-~~~~~v~~A~~~I~~ll~~ 288 (304)
+..|.+.|--.|. +.|+| .+.+.++.|++.|-.+|..
T Consensus 47 ~p~~t~~IF~sGk----------------------i~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 47 NPKATVLIFSSGK----------------------IVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TTTEEEEEETTSE----------------------EEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred CCcEEEEEEcCCE----------------------EEEEecCCHHHHHHHHHHHHHHHHH
Confidence 3468888888777 66776 5999999999999988864
No 165
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=22.03 E-value=37 Score=22.60 Aligned_cols=28 Identities=29% Similarity=0.833 Sum_probs=16.6
Q ss_pred CcccCCCCCcccCCCCCCCCCccccccccccccc
Q psy1775 43 RCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAG 76 (304)
Q Consensus 43 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~G 76 (304)
.|-+||... +..+ +. .....|..||..-
T Consensus 2 ~Cp~Cg~~~-~~~D-~~----~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-PE----RGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSE-EEEE-TT----TTEEEETTT-BBE
T ss_pred CCcCCcCCc-eEEc-CC----CCeEECCCCCCEe
Confidence 478887755 5444 22 1346899998654
No 166
>KOG2279|consensus
Probab=21.73 E-value=67 Score=33.48 Aligned_cols=58 Identities=24% Similarity=0.343 Sum_probs=41.8
Q ss_pred HhCCCCCCCCCCCCCCcceeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeC
Q psy1775 178 KVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRG 239 (304)
Q Consensus 178 ~~~p~~~~P~~~~~~~~~~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG 239 (304)
+..+.|.+|.|-.-+ ..+-+.||.=+.|+. .+|+|||=.|.+++-+-..+|.++-|+-
T Consensus 276 sk~~s~~~~~d~s~~---k~~~l~i~e~e~p~~-lsg~lig~~gey~s~yssasn~~~hi~t 333 (608)
T KOG2279|consen 276 SKEGSWEKPSDDSFQ---KSEALAIPEMEMPEI-LSGDLIGHAGEYLSVYSSASNHPNHIWT 333 (608)
T ss_pred ecccccCCccccccc---cccccccceeecCcc-cccchhhhhhhhhhhhhhccCccceEEe
Confidence 456778888765433 123333333344443 7899999999999999999999999986
No 167
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=21.43 E-value=1e+02 Score=30.42 Aligned_cols=39 Identities=28% Similarity=0.423 Sum_probs=34.0
Q ss_pred eeEEEEeCCCCCCCCcccceeecCCchhHHHHHHHhCCeEEEeCC
Q psy1775 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK 240 (304)
Q Consensus 196 ~~~ki~IP~~~~P~~NfiG~iiGP~G~t~K~ie~etg~kI~IrG~ 240 (304)
....+++|.+ -.++.||-+|.+++.--+-||.+|.|...
T Consensus 303 ~~~~v~V~~~------~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 303 KAARVVVPDY------QLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred cEEEEEEChh------hcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 3567888887 57999999999999999999999999864
No 168
>KOG0703|consensus
Probab=21.36 E-value=1.6e+02 Score=28.22 Aligned_cols=61 Identities=28% Similarity=0.630 Sum_probs=38.2
Q ss_pred cccCCCCCcccCCCCCcccCCCCCCCCCcccccccccccc----c-ccccccCCCCCCCCCCCCCCcccchhhhHHHHHH
Q psy1775 36 LRENEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGA----G-HIARDCREKRPGMGGPPANTHRNRAKIDEEYMSL 110 (304)
Q Consensus 36 lr~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~----G-H~ardC~~~~~~~~g~~~~~~~~~a~~d~EY~~l 110 (304)
|+.-+|..|.-||.. +-.|.-=+ -.--.|-+|-+. | |+++- ....-..|..|...+
T Consensus 20 l~~~~N~~CADC~a~-~P~WaSwn----lGvFiC~~C~giHR~lg~hiSkV--------------kSv~LD~W~~eqv~~ 80 (287)
T KOG0703|consen 20 LREPDNKVCADCGAK-GPRWASWN----LGVFICLRCAGIHRSLGVHISKV--------------KSVTLDEWTDEQVDF 80 (287)
T ss_pred HcCcccCcccccCCC-CCCeEEee----cCeEEEeecccccccccchhhee--------------eeeeccccCHHHHHH
Confidence 455578999999876 33332111 122358887654 3 66642 112346799999999
Q ss_pred HHHhC
Q psy1775 111 MAELG 115 (304)
Q Consensus 111 maEL~ 115 (304)
|.++|
T Consensus 81 m~~~G 85 (287)
T KOG0703|consen 81 MISMG 85 (287)
T ss_pred HHHHc
Confidence 99998
No 169
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=21.01 E-value=1.3e+02 Score=32.53 Aligned_cols=74 Identities=11% Similarity=0.166 Sum_probs=46.3
Q ss_pred CCCCCcccceeecCCchhHHHHHHHhC----------CeEEEeCCccccCCCCCCCCCCCCCCCCCCcEEEEEeCCHHHH
Q psy1775 206 EHPDINFVGLLIGPRGNTLKSMEKDTG----------AKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENV 275 (304)
Q Consensus 206 ~~P~~NfiG~iiGP~G~t~K~ie~etg----------~kI~IrG~Gs~~~~~~~~~~g~~~~~~~e~LHv~I~a~~~~~v 275 (304)
.||-|.++-+|+....+.-+-++.-.. ..+.|.|-...--.+ -....-.+++|-+.+...+
T Consensus 631 ~~PPf~~l~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vlGP~~a~~~r---------~~~~yR~qiLl~~~~~~~L 701 (730)
T COG1198 631 GLPPFSRLAAVIASAKNEEKALEFARALRELLKEALPVDVEVLGPAPAPLAK---------LAGRYRYQILLKSPSRADL 701 (730)
T ss_pred CCCChhhheeeEecCCCHHHHHHHHHHHHHHHHhcccccceeeCCCcchhHH---------hCCceEEEEEEecCcHHHH
Confidence 677788888998888777665543322 224444432211000 0123445688899999999
Q ss_pred HHHHHHHHhhhcC
Q psy1775 276 KKAVDRLVCLVSA 288 (304)
Q Consensus 276 ~~A~~~I~~ll~~ 288 (304)
.++...+...+..
T Consensus 702 ~~~l~~~~~~~~~ 714 (730)
T COG1198 702 QKLLRAWLAVLPK 714 (730)
T ss_pred HHHHHHHHHHhcc
Confidence 9998887777665
No 170
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=20.84 E-value=1.6e+02 Score=27.16 Aligned_cols=22 Identities=32% Similarity=0.649 Sum_probs=15.3
Q ss_pred EEeCCCCCCCCcccceeecCCc
Q psy1775 200 VMIPQDEHPDINFVGLLIGPRG 221 (304)
Q Consensus 200 i~IP~~~~P~~NfiG~iiGP~G 221 (304)
+.--.+-.|.+..+|+++||+|
T Consensus 113 ~iat~~~m~~l~~Lg~iLGPrG 134 (230)
T PRK05424 113 VIATPDMMGKVGKLGRILGPRG 134 (230)
T ss_pred EEECHHHHHHHHHhcccccccc
Confidence 3334445555667899999987
No 171
>PRK14291 chaperone protein DnaJ; Provisional
Probab=20.69 E-value=62 Score=31.86 Aligned_cols=19 Identities=37% Similarity=1.017 Sum_probs=14.0
Q ss_pred cccccccccccccccccCC
Q psy1775 66 STLCSSCGGAGHIARDCRE 84 (304)
Q Consensus 66 ~~~C~~CG~~GH~ardC~~ 84 (304)
...|..|++.|-+...|+.
T Consensus 195 ~~~C~~C~G~G~~~~~C~~ 213 (382)
T PRK14291 195 SQTCPTCGGEGVLREPCSK 213 (382)
T ss_pred EecCCCCCCceEEccCCCC
Confidence 3579999999966556654
No 172
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=20.51 E-value=1.8e+02 Score=26.53 Aligned_cols=21 Identities=19% Similarity=0.447 Sum_probs=18.3
Q ss_pred hHHHHHHHhCCeEEEeCCccc
Q psy1775 223 TLKSMEKDTGAKIIIRGKGSV 243 (304)
Q Consensus 223 t~K~ie~etg~kI~IrG~Gs~ 243 (304)
.+|+||++.|+++..|..+.+
T Consensus 39 ~i~~LE~~lG~~LF~R~~r~~ 59 (302)
T PRK09791 39 SIQELEEGLAAQLFFRRSKGV 59 (302)
T ss_pred HHHHHHHHhCCeEEEEcCCCc
Confidence 689999999999999986553
No 173
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=20.44 E-value=1.6e+02 Score=26.80 Aligned_cols=20 Identities=15% Similarity=0.439 Sum_probs=17.2
Q ss_pred hhHHHHHHHhCCeEEEeCCc
Q psy1775 222 NTLKSMEKDTGAKIIIRGKG 241 (304)
Q Consensus 222 ~t~K~ie~etg~kI~IrG~G 241 (304)
..||+||++.|+++..|...
T Consensus 34 ~~I~~LE~~lG~~LF~R~~r 53 (275)
T PRK03601 34 FRIRQLENQLGVNLFTRHRN 53 (275)
T ss_pred HHHHHHHHHhCCceEEECCC
Confidence 36899999999999999743
No 174
>KOG0956|consensus
Probab=20.30 E-value=60 Score=34.78 Aligned_cols=29 Identities=17% Similarity=0.444 Sum_probs=18.4
Q ss_pred CCCCcccCCCCCcccCCCCCCCCCccccccccccccc
Q psy1775 40 EGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAG 76 (304)
Q Consensus 40 ~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~CG~~G 76 (304)
-+..||+|.+.|.-.+. ....|..|.+.|
T Consensus 116 fnKtCYIC~E~GrpnkA--------~~GACMtCNKs~ 144 (900)
T KOG0956|consen 116 FNKTCYICNEEGRPNKA--------AKGACMTCNKSG 144 (900)
T ss_pred hcceeeeecccCCcccc--------ccccceeccccc
Confidence 47889999988743221 345666666643
No 175
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=20.24 E-value=46 Score=24.27 Aligned_cols=47 Identities=21% Similarity=0.529 Sum_probs=27.0
Q ss_pred cCCCCCcccCCCCCcccCCCCCC-CCCcccccccccccccccc--cccCC
Q psy1775 38 ENEGPRCTNCGASDHKSWLCPDK-PNITNSTLCSSCGGAGHIA--RDCRE 84 (304)
Q Consensus 38 ~~~~~~C~~Cg~~GH~~~~Cp~~-~~~~~~~~C~~CG~~GH~a--rdC~~ 84 (304)
......|..|...|.....=... ..+.....|..|++.|.+. ..|+.
T Consensus 12 ~~~~~~C~~C~G~G~~~~~~~~~~~~~~~~~~C~~C~G~G~~i~~~~C~~ 61 (66)
T PF00684_consen 12 GKKPKTCPQCNGSGQVTRRQQTPGGVFQMQQTCPKCGGTGKIIEKDPCKT 61 (66)
T ss_dssp TTT-EE-TTSSSSSEEEEEEESSSTTEEEEEE-TTTSSSSEE-TSSB-SS
T ss_pred CCCCcCCcCCCCeeEEEEEEeCCCeEEEEEEECCCCcceeeEECCCCCCC
Confidence 33456799999988876543211 1112357899999999984 44653
Done!