Query psy8224
Match_columns 766
No_of_seqs 569 out of 2613
Neff 7.4
Searched_HMMs 46136
Date Fri Aug 16 21:52:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8224.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8224hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1094 Predicted RNA-binding 100.0 3.7E-51 8.1E-56 394.7 15.3 170 30-200 8-177 (194)
2 KOG3273|consensus 100.0 3.4E-49 7.5E-54 374.2 11.3 186 16-201 56-245 (252)
3 KOG2874|consensus 100.0 1.4E-40 3.1E-45 330.2 7.9 204 16-226 40-246 (356)
4 PRK13763 putative RNA-processi 100.0 2E-35 4.3E-40 292.4 15.5 167 30-199 3-169 (180)
5 TIGR03665 arCOG04150 arCOG0415 100.0 1.3E-35 2.8E-40 291.9 14.0 164 33-200 1-164 (172)
6 KOG2084|consensus 99.6 3.1E-15 6.8E-20 171.4 16.7 123 615-739 197-330 (482)
7 KOG1676|consensus 99.3 1.4E-11 3.1E-16 136.6 11.8 150 29-188 138-301 (600)
8 KOG2193|consensus 99.1 2.2E-10 4.8E-15 121.3 9.3 134 30-185 411-562 (584)
9 PF00856 SET: SET domain; Int 99.0 1.1E-10 2.3E-15 112.5 4.0 51 615-665 110-162 (162)
10 PF00856 SET: SET domain; Int 99.0 2.2E-10 4.8E-15 110.3 5.1 51 550-601 109-162 (162)
11 smart00317 SET SET (Su(var)3-9 99.0 3.9E-10 8.5E-15 103.1 3.9 48 617-664 67-116 (116)
12 KOG1676|consensus 98.9 3.7E-09 8E-14 117.7 8.6 146 30-195 230-397 (600)
13 PRK00106 hypothetical protein; 98.5 1.1E-07 2.4E-12 108.5 6.0 63 126-191 230-296 (535)
14 TIGR03319 YmdA_YtgF conserved 98.5 1.2E-07 2.5E-12 109.0 6.1 64 126-192 209-276 (514)
15 PF01753 zf-MYND: MYND finger; 98.5 1.9E-08 4.1E-13 73.2 -0.6 37 317-353 1-37 (37)
16 PRK12704 phosphodiesterase; Pr 98.3 5.3E-07 1.1E-11 103.8 6.3 62 126-190 215-280 (520)
17 KOG2191|consensus 98.3 6.6E-06 1.4E-10 85.7 13.6 169 30-212 39-229 (402)
18 cd02393 PNPase_KH Polynucleoti 98.2 2.1E-06 4.6E-11 69.8 4.9 49 134-182 11-61 (61)
19 KOG2193|consensus 98.1 3.9E-06 8.5E-11 89.7 7.0 129 31-179 200-344 (584)
20 PF00013 KH_1: KH domain syndr 98.1 2.9E-06 6.4E-11 68.6 4.6 48 134-181 9-60 (60)
21 cd02395 SF1_like-KH Splicing f 98.1 6.5E-06 1.4E-10 76.2 6.5 58 134-191 15-99 (120)
22 cd02394 vigilin_like_KH K homo 98.1 5.7E-06 1.2E-10 67.4 5.3 48 134-181 9-61 (62)
23 smart00317 SET SET (Su(var)3-9 97.9 3.6E-06 7.8E-11 76.7 1.7 45 556-600 70-116 (116)
24 cd02393 PNPase_KH Polynucleoti 97.9 2.4E-05 5.1E-10 63.7 6.2 59 31-94 3-61 (61)
25 cd00105 KH-I K homology RNA-bi 97.9 2.3E-05 5E-10 64.0 5.6 48 134-181 9-63 (64)
26 smart00322 KH K homology RNA-b 97.9 3E-05 6.5E-10 63.5 6.2 52 134-185 12-68 (69)
27 PRK12705 hypothetical protein; 97.8 1.4E-05 3E-10 91.0 4.0 62 126-190 203-268 (508)
28 KOG2589|consensus 97.8 1.9E-05 4.1E-10 83.5 4.0 59 624-694 197-256 (453)
29 cd02396 PCBP_like_KH K homolog 97.7 4.9E-05 1.1E-09 62.6 5.3 48 134-181 9-64 (65)
30 KOG1710|consensus 97.7 2.6E-06 5.5E-11 87.4 -3.2 43 314-356 319-362 (396)
31 KOG2190|consensus 97.7 0.0003 6.5E-09 80.1 11.7 147 30-189 43-210 (485)
32 COG2940 Proteins containing SE 97.5 5.7E-05 1.2E-09 87.0 3.2 74 621-694 403-478 (480)
33 PRK13763 putative RNA-processi 97.5 0.00017 3.7E-09 71.9 5.9 65 40-111 105-169 (180)
34 PF13014 KH_3: KH domain 97.4 0.00016 3.5E-09 54.3 4.0 27 136-162 2-28 (43)
35 PF00013 KH_1: KH domain syndr 97.4 0.00028 6.2E-09 57.0 5.1 58 31-93 1-60 (60)
36 TIGR03665 arCOG04150 arCOG0415 97.2 0.00048 1E-08 68.2 5.7 58 134-191 7-69 (172)
37 KOG1080|consensus 97.2 0.00032 6.9E-09 85.3 4.3 46 623-668 939-986 (1005)
38 KOG4442|consensus 97.2 0.00034 7.5E-09 80.1 4.3 48 624-671 194-243 (729)
39 cd02394 vigilin_like_KH K homo 97.2 0.00084 1.8E-08 54.6 5.5 57 32-93 2-61 (62)
40 cd02396 PCBP_like_KH K homolog 97.1 0.00095 2E-08 55.0 5.4 58 31-93 1-64 (65)
41 cd00105 KH-I K homology RNA-bi 96.9 0.0019 4.1E-08 52.5 5.8 57 32-93 2-63 (64)
42 KOG4442|consensus 96.9 0.0008 1.7E-08 77.2 4.6 44 337-382 105-148 (729)
43 KOG2589|consensus 96.9 0.0007 1.5E-08 72.0 3.6 78 559-638 196-277 (453)
44 KOG2190|consensus 96.5 0.0063 1.4E-07 69.5 7.5 150 30-184 138-322 (485)
45 PF01753 zf-MYND: MYND finger; 96.4 0.00019 4.2E-09 52.1 -3.2 26 418-443 9-37 (37)
46 KOG1083|consensus 96.4 0.0015 3.2E-08 77.6 2.0 105 560-665 1169-1294(1306)
47 TIGR02696 pppGpp_PNP guanosine 96.3 0.0094 2E-07 70.5 8.0 70 29-103 577-646 (719)
48 cd02395 SF1_like-KH Splicing f 96.2 0.015 3.3E-07 53.9 7.3 68 32-103 2-99 (120)
49 smart00322 KH K homology RNA-b 96.2 0.017 3.6E-07 46.9 6.9 62 30-96 3-67 (69)
50 KOG1082|consensus 96.1 0.0035 7.7E-08 69.7 3.2 44 626-669 275-324 (364)
51 TIGR02696 pppGpp_PNP guanosine 95.9 0.014 3E-07 69.2 6.5 66 134-199 587-656 (719)
52 PRK08406 transcription elongat 95.8 0.017 3.7E-07 55.1 5.9 104 30-161 32-135 (140)
53 PRK02821 hypothetical protein; 95.8 0.007 1.5E-07 51.4 2.6 31 134-167 40-70 (77)
54 TIGR03591 polynuc_phos polyrib 95.6 0.018 3.8E-07 69.2 6.1 66 134-199 560-627 (684)
55 KOG1588|consensus 95.4 0.011 2.5E-07 61.0 3.1 29 135-163 108-136 (259)
56 KOG1337|consensus 95.2 0.016 3.5E-07 66.8 4.1 64 615-685 228-291 (472)
57 KOG0119|consensus 95.2 0.031 6.7E-07 62.1 6.0 94 96-199 122-243 (554)
58 PRK00468 hypothetical protein; 95.0 0.024 5.1E-07 48.0 3.4 32 135-166 40-71 (75)
59 KOG3612|consensus 94.9 0.0053 1.1E-07 68.7 -1.2 98 254-356 469-567 (588)
60 TIGR03591 polynuc_phos polyrib 94.7 0.058 1.2E-06 64.8 6.9 64 30-98 551-614 (684)
61 COG1837 Predicted RNA-binding 94.7 0.027 5.9E-07 47.5 2.9 20 136-155 41-60 (76)
62 COG1185 Pnp Polyribonucleotide 94.4 0.065 1.4E-06 62.3 6.2 68 30-102 552-619 (692)
63 KOG2084|consensus 94.3 0.041 8.8E-07 63.1 4.2 114 173-291 258-377 (482)
64 KOG1141|consensus 94.2 0.025 5.5E-07 65.8 2.3 58 624-689 1190-1253(1262)
65 KOG1085|consensus 93.8 0.037 8E-07 57.3 2.4 46 624-669 334-381 (392)
66 PRK01064 hypothetical protein; 93.3 0.036 7.9E-07 47.2 1.1 33 135-167 40-72 (78)
67 PLN00207 polyribonucleotide nu 93.2 0.09 1.9E-06 63.9 4.7 61 134-194 694-757 (891)
68 KOG1080|consensus 93.1 0.04 8.7E-07 67.6 1.6 43 559-601 939-983 (1005)
69 PF13083 KH_4: KH domain; PDB: 92.8 0.0097 2.1E-07 50.2 -3.0 30 136-165 40-69 (73)
70 KOG2192|consensus 92.6 0.4 8.6E-06 49.3 7.5 137 31-188 49-194 (390)
71 cd02134 NusA_KH NusA_K homolog 92.3 0.1 2.2E-06 42.4 2.4 27 134-160 34-60 (61)
72 PF13824 zf-Mss51: Zinc-finger 92.2 0.026 5.7E-07 44.3 -1.1 43 317-359 2-48 (55)
73 KOG2061|consensus 92.0 0.12 2.7E-06 55.9 3.3 48 314-361 136-184 (362)
74 PRK04163 exosome complex RNA-b 91.8 0.24 5.2E-06 51.6 5.2 57 134-190 154-212 (235)
75 COG1185 Pnp Polyribonucleotide 91.6 0.23 5E-06 58.0 5.1 67 134-200 561-629 (692)
76 TIGR01952 nusA_arch NusA famil 91.3 0.47 1E-05 45.3 6.1 100 32-161 35-136 (141)
77 PRK11824 polynucleotide phosph 91.1 0.23 4.9E-06 59.9 4.7 65 135-199 564-630 (693)
78 PF13014 KH_3: KH domain 90.9 0.23 4.9E-06 37.1 2.9 35 41-75 2-42 (43)
79 COG5176 MSL5 Splicing factor ( 90.9 0.18 3.9E-06 50.1 2.8 31 134-164 163-193 (269)
80 KOG1079|consensus 90.6 0.25 5.5E-06 57.0 4.1 43 625-667 667-711 (739)
81 PLN00207 polyribonucleotide nu 90.5 0.31 6.8E-06 59.3 5.1 65 29-98 684-749 (891)
82 KOG2192|consensus 89.1 0.55 1.2E-05 48.3 4.8 53 134-186 324-383 (390)
83 KOG2191|consensus 88.9 1 2.2E-05 48.1 6.6 60 31-95 133-200 (402)
84 KOG2279|consensus 88.7 0.36 7.8E-06 54.6 3.4 108 30-163 68-178 (608)
85 COG1094 Predicted RNA-binding 88.0 0.96 2.1E-05 45.1 5.5 61 134-194 17-84 (194)
86 PRK04163 exosome complex RNA-b 87.9 1.1 2.4E-05 46.7 6.4 64 30-98 145-208 (235)
87 COG0195 NusA Transcription elo 87.6 0.72 1.6E-05 46.3 4.5 103 32-164 78-181 (190)
88 cd02414 jag_KH jag_K homology 87.2 0.29 6.2E-06 41.7 1.2 26 136-161 35-60 (77)
89 PF14611 SLS: Mitochondrial in 87.0 12 0.00026 38.2 13.3 137 31-192 27-170 (210)
90 COG2940 Proteins containing SE 87.0 0.27 5.8E-06 56.9 1.2 50 559-608 405-456 (480)
91 KOG2814|consensus 86.8 0.85 1.9E-05 48.8 4.7 66 134-199 66-140 (345)
92 COG1847 Jag Predicted RNA-bind 86.6 0.49 1.1E-05 47.6 2.7 53 136-188 102-164 (208)
93 KOG1710|consensus 86.0 0.15 3.3E-06 53.2 -1.3 29 418-446 331-362 (396)
94 KOG1337|consensus 85.9 0.52 1.1E-05 54.4 2.8 77 525-602 197-278 (472)
95 PLN03158 methionine aminopepti 84.7 0.29 6.3E-06 54.9 0.1 40 312-351 7-53 (396)
96 cd02409 KH-II KH-II (K homolo 84.1 0.6 1.3E-05 37.8 1.7 23 136-158 36-58 (68)
97 KOG0336|consensus 83.8 1.3 2.8E-05 48.7 4.5 53 136-188 58-114 (629)
98 KOG1338|consensus 83.1 0.33 7.1E-06 52.9 -0.4 132 524-666 173-317 (466)
99 PRK11824 polynucleotide phosph 81.2 1.5 3.2E-05 53.1 4.1 64 30-98 554-617 (693)
100 KOG1082|consensus 75.9 1.3 2.8E-05 49.4 1.4 45 559-603 272-322 (364)
101 PF04438 zf-HIT: HIT zinc fing 74.6 0.94 2E-05 31.3 -0.1 27 315-342 3-29 (30)
102 PF13824 zf-Mss51: Zinc-finger 73.5 1.2 2.7E-05 35.1 0.3 33 418-450 14-49 (55)
103 KOG1085|consensus 72.0 1.5 3.3E-05 45.8 0.7 44 560-603 334-379 (392)
104 KOG1067|consensus 70.8 2.9 6.3E-05 47.7 2.6 60 135-194 607-668 (760)
105 KOG2857|consensus 70.8 1.6 3.4E-05 40.9 0.4 38 396-446 6-45 (157)
106 KOG1081|consensus 65.3 2.8 6.1E-05 48.1 1.1 54 615-668 362-418 (463)
107 KOG1141|consensus 64.8 4.5 9.7E-05 48.1 2.5 44 559-602 1189-1238(1262)
108 COG1097 RRP4 RNA-binding prote 64.0 12 0.00025 38.9 5.1 53 136-188 157-211 (239)
109 PF07650 KH_2: KH domain syndr 61.7 1.1 2.3E-05 38.1 -2.4 34 134-167 34-68 (78)
110 COG5176 MSL5 Splicing factor ( 61.3 14 0.0003 37.2 4.8 79 17-98 133-220 (269)
111 COG1159 Era GTPase [General fu 60.4 12 0.00026 40.0 4.6 58 103-160 198-273 (298)
112 KOG0119|consensus 57.6 28 0.00061 39.5 7.0 81 16-97 122-228 (554)
113 PRK12328 nusA transcription el 56.6 25 0.00055 39.0 6.5 94 39-161 251-344 (374)
114 KOG1083|consensus 55.8 6.2 0.00014 48.3 1.7 42 559-601 1250-1294(1306)
115 TIGR00436 era GTP-binding prot 55.6 26 0.00056 37.1 6.3 27 134-160 231-265 (270)
116 KOG1338|consensus 55.0 9.3 0.0002 42.1 2.7 54 612-667 207-261 (466)
117 KOG1067|consensus 54.5 11 0.00023 43.4 3.2 62 30-97 597-658 (760)
118 COG1702 PhoH Phosphate starvat 54.4 24 0.00051 38.7 5.7 49 136-184 26-74 (348)
119 PRK15494 era GTPase Era; Provi 52.3 26 0.00055 38.7 5.8 27 134-160 283-317 (339)
120 TIGR01953 NusA transcription t 52.1 28 0.00062 38.4 6.0 93 40-162 244-338 (341)
121 KOG2113|consensus 51.1 9.8 0.00021 40.5 2.1 124 29-160 25-150 (394)
122 KOG3362|consensus 49.3 6.1 0.00013 37.3 0.3 34 314-348 118-151 (156)
123 PRK12329 nusA transcription el 49.0 29 0.00063 39.3 5.5 94 39-162 277-372 (449)
124 PRK12327 nusA transcription el 48.9 34 0.00073 38.1 6.0 95 39-163 245-341 (362)
125 KOG4317|consensus 48.7 9.3 0.0002 40.6 1.5 22 418-439 19-40 (383)
126 PRK09202 nusA transcription el 48.7 29 0.00063 40.0 5.6 93 41-162 247-339 (470)
127 PRK08406 transcription elongat 47.4 14 0.00031 35.2 2.5 46 135-190 42-87 (140)
128 PF04810 zf-Sec23_Sec24: Sec23 44.1 6.9 0.00015 28.8 -0.2 30 197-226 3-33 (40)
129 KOG2814|consensus 43.5 18 0.0004 39.0 2.7 93 17-113 40-143 (345)
130 cd02134 NusA_KH NusA_K homolog 41.1 27 0.00058 28.2 2.8 36 30-65 25-60 (61)
131 COG1855 ATPase (PilT family) [ 39.5 44 0.00096 38.0 5.0 28 134-161 495-522 (604)
132 cd02410 archeal_CPSF_KH The ar 39.4 47 0.001 31.8 4.5 85 49-161 25-112 (145)
133 PF10058 DUF2296: Predicted in 37.7 30 0.00065 27.4 2.5 44 181-226 5-53 (54)
134 PRK12704 phosphodiesterase; Pr 37.0 81 0.0018 37.0 7.0 63 30-96 210-273 (520)
135 PF07282 OrfB_Zn_ribbon: Putat 36.9 31 0.00067 28.3 2.6 41 191-234 23-63 (69)
136 TIGR00112 proC pyrroline-5-car 36.6 33 0.00072 35.8 3.5 98 50-154 125-224 (245)
137 PF13184 KH_5: NusA-like KH do 36.4 25 0.00055 29.2 2.0 33 134-172 17-49 (69)
138 PRK01343 zinc-binding protein; 35.0 32 0.00069 27.6 2.2 31 313-348 8-38 (57)
139 TIGR01952 nusA_arch NusA famil 33.8 33 0.00072 32.8 2.6 26 135-160 43-68 (141)
140 PRK00106 hypothetical protein; 33.8 98 0.0021 36.3 6.9 61 30-94 225-286 (535)
141 PF14949 ARF7EP_C: ARF7 effect 33.6 18 0.00038 32.7 0.7 25 418-442 74-101 (103)
142 PRK00089 era GTPase Era; Revie 33.4 79 0.0017 33.7 5.8 27 134-160 236-270 (292)
143 COG1855 ATPase (PilT family) [ 33.4 30 0.00065 39.2 2.5 40 30-69 486-525 (604)
144 cd03031 GRX_GRX_like Glutaredo 32.7 2.4E+02 0.0051 27.2 8.3 66 156-224 62-140 (147)
145 TIGR03319 YmdA_YtgF conserved 32.5 1E+02 0.0022 36.1 6.9 62 30-95 204-266 (514)
146 KOG2857|consensus 32.4 21 0.00046 33.7 1.0 38 315-357 6-46 (157)
147 TIGR02059 swm_rep_I cyanobacte 32.4 89 0.0019 28.0 4.7 69 592-668 29-99 (101)
148 KOG2593|consensus 32.3 46 0.001 37.3 3.7 51 195-245 127-188 (436)
149 PRK06418 transcription elongat 32.2 35 0.00077 33.6 2.5 46 137-195 72-117 (166)
150 PHA00626 hypothetical protein 31.9 38 0.00082 26.9 2.1 36 197-232 1-38 (59)
151 PRK00398 rpoP DNA-directed RNA 31.6 30 0.00064 26.2 1.5 28 687-715 5-32 (46)
152 COG1998 RPS31 Ribosomal protei 31.5 24 0.00052 27.3 0.9 29 195-227 18-47 (51)
153 PRK13764 ATPase; Provisional 31.3 76 0.0016 37.8 5.5 28 134-161 490-517 (602)
154 PF09889 DUF2116: Uncharacteri 31.1 14 0.0003 29.8 -0.4 31 314-350 3-33 (59)
155 PRK04223 rpl22p 50S ribosomal 30.8 56 0.0012 31.7 3.6 28 82-110 23-50 (153)
156 PF02150 RNA_POL_M_15KD: RNA p 30.2 15 0.00034 26.2 -0.2 31 198-230 3-33 (35)
157 COG1675 TFA1 Transcription ini 29.8 78 0.0017 31.5 4.5 41 672-715 102-143 (176)
158 KOG1079|consensus 29.3 36 0.00077 40.2 2.3 43 559-601 665-709 (739)
159 KOG2208|consensus 29.2 1.5E+02 0.0033 36.4 7.7 107 30-161 347-457 (753)
160 smart00778 Prim_Zn_Ribbon Zinc 29.1 41 0.0009 24.5 1.8 29 197-225 4-33 (37)
161 KOG4369|consensus 28.6 31 0.00066 43.1 1.7 59 128-186 1343-1409(2131)
162 COG3024 Uncharacterized protei 28.4 22 0.00047 29.0 0.3 9 427-435 27-35 (65)
163 PF01927 Mut7-C: Mut7-C RNAse 28.4 1.2E+02 0.0026 29.1 5.5 84 134-227 39-134 (147)
164 TIGR01038 L22_arch ribosomal p 27.2 74 0.0016 30.8 3.7 28 82-110 19-46 (150)
165 PF00403 HMA: Heavy-metal-asso 27.0 1.7E+02 0.0037 23.0 5.4 36 50-85 15-51 (62)
166 PF14748 P5CR_dimer: Pyrroline 27.0 23 0.0005 32.1 0.2 61 89-154 24-85 (107)
167 cd02412 30S_S3_KH K homology R 26.9 37 0.00081 30.9 1.6 22 136-157 72-93 (109)
168 PF07754 DUF1610: Domain of un 26.3 52 0.0011 21.6 1.7 24 398-426 1-24 (24)
169 COG1997 RPL43A Ribosomal prote 26.3 34 0.00074 29.7 1.2 57 163-230 5-66 (89)
170 PF09846 DUF2073: Uncharacteri 26.1 67 0.0015 28.8 2.9 43 118-179 52-94 (104)
171 PF12855 Ecl1: Life-span regul 25.8 23 0.00051 26.6 0.1 31 315-348 7-37 (43)
172 PF11513 TA0956: Thermoplasma 24.5 1.2E+02 0.0025 26.7 4.0 39 232-270 23-61 (110)
173 COG1781 PyrI Aspartate carbamo 24.3 53 0.0011 31.6 2.1 65 158-234 76-152 (153)
174 smart00661 RPOL9 RNA polymeras 24.0 49 0.0011 25.4 1.6 29 199-228 3-31 (52)
175 COG1782 Predicted metal-depend 23.8 72 0.0016 36.7 3.3 29 134-162 108-136 (637)
176 PF04723 GRDA: Glycine reducta 22.5 52 0.0011 31.1 1.7 43 159-203 2-44 (150)
177 PF14369 zf-RING_3: zinc-finge 21.5 60 0.0013 23.3 1.4 27 688-715 5-32 (35)
178 KOG2461|consensus 21.2 70 0.0015 36.1 2.7 27 643-669 121-147 (396)
179 cd02413 40S_S3_KH K homology R 21.1 44 0.00096 28.7 0.9 27 134-160 39-65 (81)
180 KOG2113|consensus 21.0 62 0.0013 34.7 2.0 52 132-183 33-88 (394)
181 PF03604 DNA_RNApol_7kD: DNA d 20.9 77 0.0017 22.3 1.8 27 687-715 2-28 (32)
182 TIGR00373 conserved hypothetic 20.8 77 0.0017 30.9 2.6 60 672-739 98-158 (158)
183 PF13453 zf-TFIIB: Transcripti 20.8 47 0.001 24.4 0.9 39 198-237 1-40 (41)
184 KOG2279|consensus 20.8 53 0.0011 37.9 1.6 58 135-192 78-141 (608)
185 PF14803 Nudix_N_2: Nudix N-te 20.6 53 0.0011 23.4 1.0 28 199-226 3-31 (34)
186 PRK06266 transcription initiat 20.6 72 0.0016 31.8 2.4 62 672-741 106-168 (178)
187 smart00874 B5 tRNA synthetase 20.1 1E+02 0.0022 25.2 2.9 66 32-100 2-69 (71)
188 PF08666 SAF: SAF domain; Int 20.1 61 0.0013 25.7 1.5 16 647-662 3-18 (63)
No 1
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=100.00 E-value=3.7e-51 Score=394.68 Aligned_cols=170 Identities=36% Similarity=0.573 Sum_probs=166.4
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhc
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALL 109 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll 109 (766)
+++.|+||++|+++|||+||+++++|++.++++++||+++|+|+|+++..|.||++++||+|+|+||+|||+||+|++||
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL 87 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLL 87 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHh
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchhhHHHHHHHHHHhhcCCC
Q psy8224 110 RLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSP 189 (766)
Q Consensus 110 ~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~~l~~ar~~i~~~~~~~~ 189 (766)
+ ||++||+|||++++.++++|++|++|||||++|+|+++||++|||+|+|||+||+|||+|+++++||+||+||++|++
T Consensus 88 ~-d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 88 E-DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGKTVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred c-CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCcEEEEecChhhhHHHHHHHHHHHcCCC
Confidence 8 699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Ccccccceeec
Q psy8224 190 PNKVYGGILCS 200 (766)
Q Consensus 190 p~~~~s~l~c~ 200 (766)
|++||.+|+..
T Consensus 167 h~~Vy~fLer~ 177 (194)
T COG1094 167 HGKVYKFLERK 177 (194)
T ss_pred chhHHHHHHHH
Confidence 99999998874
No 2
>KOG3273|consensus
Probab=100.00 E-value=3.4e-49 Score=374.24 Aligned_cols=186 Identities=67% Similarity=1.089 Sum_probs=179.6
Q ss_pred CCCCCCccccCCCC----ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHH
Q psy8224 16 AKAQEPAVKKAKHV----DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAAD 91 (766)
Q Consensus 16 ~~~~~~~~~~~~~~----~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~ 91 (766)
.+|.|+|..+.+.. ++|+|+||++|+..|+..|.+||.||+++++++|+||.+.++|+++++..|+||.+++|+.|
T Consensus 56 ~~~~~~p~~a~~~~~~k~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~ad 135 (252)
T KOG3273|consen 56 PKPTFAPLKAKRKRGGKIETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGAD 135 (252)
T ss_pred CCCCCCCccccccccCccceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccceeEeecCCCCCChHHHHHHHH
Confidence 55677787777763 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCChhhHHhhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcch
Q psy8224 92 FVKAFVYGFDVDDALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSY 171 (766)
Q Consensus 92 ~i~ai~~gf~~~~a~~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~ 171 (766)
||+||..||+++||++||+.||+|+|.|+|+||+.++++|++|++|||+|++|+|+.+||+.|.++|+|+|.+|||+|.|
T Consensus 136 fv~Af~lGF~i~DAiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad~kIHiLG~~ 215 (252)
T KOG3273|consen 136 FVRAFILGFDIDDAIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLADSKIHILGAF 215 (252)
T ss_pred HHHHHHhCCcchhHHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecCceEEEeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHhhcCCCCcccccceeecc
Q psy8224 172 QNVQVALKALSNLILGSPPNKVYGGILCSR 201 (766)
Q Consensus 172 ~~l~~ar~~i~~~~~~~~p~~~~s~l~c~~ 201 (766)
+++++||.+||.+|.|++|++||+.|+...
T Consensus 216 ~niriAR~avcsLIlGsppgkVy~~LR~va 245 (252)
T KOG3273|consen 216 QNIRIARDAVCSLILGSPPGKVYGNLRNVA 245 (252)
T ss_pred hhhHHHHHhhHhhhccCCchhHHHHHHHHH
Confidence 999999999999999999999999998754
No 3
>KOG2874|consensus
Probab=100.00 E-value=1.4e-40 Score=330.19 Aligned_cols=204 Identities=15% Similarity=0.250 Sum_probs=192.6
Q ss_pred CCCCCCccccCCCC---ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHH
Q psy8224 16 AKAQEPAVKKAKHV---DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADF 92 (766)
Q Consensus 16 ~~~~~~~~~~~~~~---~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~ 92 (766)
..+.|.+++++++. ++|.+.||+||+.||++.|+.|.+.| ..+++...+|+.+|+|+|.|+.+|+|||+|+||+||
T Consensus 40 ki~~Fs~edn~~g~~EeSSfatlFPKYREkYlke~wp~v~raL-~e~~i~c~lDL~egsm~V~TtRkT~DPyIiikArdl 118 (356)
T KOG2874|consen 40 KIEKFSKEDNPHGFLEESSFATLFPKYREKYLKECWPLVERAL-DEHHIKCVLDLVEGSMTVKTTRKTRDPYIIIKARDL 118 (356)
T ss_pred cccccCcccCccchhhhhhHHhhhHHHHHHHHHHHHHHHHHHH-HhcCcceEEeeccceeEEeecccccCceeeeeHHHH
Confidence 78899999999996 89999999999999999999997766 689999999999999999999999999999999999
Q ss_pred HHHHHcCCChhhHHhhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchh
Q psy8224 93 VKAFVYGFDVDDALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQ 172 (766)
Q Consensus 93 i~ai~~gf~~~~a~~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~ 172 (766)
|++++||+++++|+++|+ |+++||||+|..++++++.|+ +++.|+||++|.|+++||.+|+|||.|+|+||++||+|.
T Consensus 119 IKLlaRsVp~eqAvkiLq-Dev~CdiIkIgn~V~nkerFv-KRRqRLiGpng~TLKAlelLT~CYilVqG~TVsaiGpfk 196 (356)
T KOG2874|consen 119 IKLLARSVPFEQAVKILQ-DEVACDIIKIGNLVRNKERFV-KRRQRLIGPNGSTLKALELLTNCYILVQGNTVSAIGPFK 196 (356)
T ss_pred HHHHHcCCCHHHHHHHHh-hccceeeeehhhhhccHHHHH-HHHHHhcCCCchhHHHHHHHhhcEEEeeCcEEEeecCcc
Confidence 999999999999999999 999999999999999998888 779999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhcCCCCcccccceeecccCCceecCCCCCCCCCcccCCCCCc
Q psy8224 173 NVQVALKALSNLILGSPPNKVYGGILCSRCRHHVISTNPLDNLAKWKCIMCSHT 226 (766)
Q Consensus 173 ~l~~ar~~i~~~~~~~~p~~~~s~l~c~~c~g~~l~~~pl~~~~~W~C~~C~~~ 226 (766)
+|+.+|+++.+||.+.||..+...|.-. ..|..||...+.+|.-..-.++
T Consensus 197 Glkevr~IV~DcM~NiHPiY~IK~LmiK----Rel~kd~~l~ne~W~rfLP~fk 246 (356)
T KOG2874|consen 197 GLKEVRKIVEDCMKNIHPIYNIKTLMIK----RELAKDPELANEDWSRFLPQFK 246 (356)
T ss_pred hHHHHHHHHHHHHhccchHHHHHHHHHH----HHhhcChhhccccHHHHhHHhh
Confidence 9999999999999999999988888874 6899999999999987654443
No 4
>PRK13763 putative RNA-processing protein; Provisional
Probab=100.00 E-value=2e-35 Score=292.45 Aligned_cols=167 Identities=29% Similarity=0.414 Sum_probs=161.4
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhc
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALL 109 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll 109 (766)
.+.+++||++|+++|||.||++++.|++++|++|+||.++|.|.|.|++ +.||.+++||+++|+||++||+||+|++++
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~ 81 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLL 81 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHh
Confidence 4678999999999999999999999999999999999999999999988 899999999999999999999999999999
Q ss_pred ccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchhhHHHHHHHHHHhhcCCC
Q psy8224 110 RLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSP 189 (766)
Q Consensus 110 ~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~~l~~ar~~i~~~~~~~~ 189 (766)
. |++++++|+|.++ .+++++++|++|||||++|+|+++||++|||+|.|++++|+|+|++++++.|+++|+++++|+.
T Consensus 82 g-d~y~~~Vi~i~~~-~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i~G~~~~~~~A~~~I~~li~g~~ 159 (180)
T PRK13763 82 D-DDYVLEVIDLSDY-GDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAP 159 (180)
T ss_pred C-CCceEEEEEhhhc-cCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence 8 8899999999999 5778999999999999999999999999999999999999999999999999999999999999
Q ss_pred Ccccccceee
Q psy8224 190 PNKVYGGILC 199 (766)
Q Consensus 190 p~~~~s~l~c 199 (766)
|+++|+.|+-
T Consensus 160 ~~~~~~~l~~ 169 (180)
T PRK13763 160 HGTVYKFLER 169 (180)
T ss_pred cHHHHHHHHH
Confidence 9999998875
No 5
>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=100.00 E-value=1.3e-35 Score=291.93 Aligned_cols=164 Identities=30% Similarity=0.441 Sum_probs=157.4
Q ss_pred EEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhcccc
Q psy8224 33 KVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALLRLD 112 (766)
Q Consensus 33 ~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll~~d 112 (766)
++.||++|++.|||+||++++.|++++|++|+||.++|.|.|+ ..++||++++||++||+||++||+|++|++++. |
T Consensus 1 ~i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~--~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~g-d 77 (172)
T TIGR03665 1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIE--EEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD-D 77 (172)
T ss_pred CccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEe--cCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcC-C
Confidence 3789999999999999999999999999999999999999997 567999999999999999999999999999998 8
Q ss_pred cceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchhhHHHHHHHHHHhhcCCCCcc
Q psy8224 113 NLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSPPNK 192 (766)
Q Consensus 113 ~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~~l~~ar~~i~~~~~~~~p~~ 192 (766)
++++++|+|.++ ..++++++|++|||||++|+|+++||++|||+|+|+|++|+|+|++++++.||++|++|++|+.|++
T Consensus 78 ~y~~~Vi~I~~~-~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~~~v~i~G~~~~~~~A~~~i~~li~~~~~~~ 156 (172)
T TIGR03665 78 DYMLEVIDLKEY-GKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGT 156 (172)
T ss_pred cceEEEEEhhhc-cCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcCCEEEEECCHHHHHHHHHHHHHHHcCCCChh
Confidence 899999999999 5677999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccceeec
Q psy8224 193 VYGGILCS 200 (766)
Q Consensus 193 ~~s~l~c~ 200 (766)
+|++|+..
T Consensus 157 vy~~l~~~ 164 (172)
T TIGR03665 157 VYKFLERK 164 (172)
T ss_pred HHHHHHHH
Confidence 99999764
No 6
>KOG2084|consensus
Probab=99.63 E-value=3.1e-15 Score=171.39 Aligned_cols=123 Identities=30% Similarity=0.564 Sum_probs=95.8
Q ss_pred ccchhhhhhhcccCCCCCCCeEEEEEeCCeEEEEEEecccCCCC-eEEeecCCCCCCHHHHHHHHhCCCCcEEeccCCCC
Q psy8224 615 RMSKWIYMKTAMLSHNCKPNTKHVIVNEDFSLQLIALVNIRKGD-IISTTYTQPFWGTMDRRLHLRMSKCFDCTCDRCKD 693 (766)
Q Consensus 615 ~i~~glyp~~s~~NHsC~PN~~~~~~~~g~~l~vra~r~I~~Ge-eI~isY~~~~~~~~~Rr~~L~~~y~F~C~C~rC~~ 693 (766)
..+.|+||..+++||||.||+...| ++....+++...+.+++ +|+++|++..+++..|+..|+..|.|.|.|+||.+
T Consensus 197 ~~~~~l~~~~~~~~hsC~pn~~~~~--~~~~~~~~~~~~~~~~~~~l~~~y~~~~~~~~~r~~~l~~~~~f~c~c~rc~d 274 (482)
T KOG2084|consen 197 FLGRGLFPGSSLFNHSCFPNISVIF--DGRGLALLVPAGIDAGEEELTISYTDPLLSTASRQKQLRQSKLFSCQCPRCLD 274 (482)
T ss_pred cceeeecccchhcccCCCCCeEEEE--CCceeEEEeecccCCCCCEEEEeecccccCHHHHHHHHhhccceeeecCCCCC
Confidence 3567788888888888888888666 46777888888888887 99999999999999999999999999999999999
Q ss_pred CCcccccccccccccc-cccceeccc-------cchhHHHHHH--HHHHHHHHHHh
Q psy8224 694 PTELETYLGKSFCLVY-CEIRSLASL-------VSLDNCEEAM--RYLAESTEIIK 739 (766)
Q Consensus 694 ~~e~~~~~~~~~C~~~-C~~~~~~~~-------~~~~~c~~~~--~~~~~~~~~~~ 739 (766)
|++.+++..+++|-.. |.+.+.... ..+..|.... .++....+...
T Consensus 275 ~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~ 330 (482)
T KOG2084|consen 275 PTELGTFLSSLRCENCTCGGLLGTSFLDKEDLQWPCTECALVRLKAYVVESREELQ 330 (482)
T ss_pred CCccccchhhhhhcCCCCCCccCCCcccccCCCccccccccchhHHHHHHHHHHHH
Confidence 9999999999999885 555444322 2345555554 44444444444
No 7
>KOG1676|consensus
Probab=99.29 E-value=1.4e-11 Score=136.61 Aligned_cols=150 Identities=15% Similarity=0.203 Sum_probs=114.9
Q ss_pred CceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeE--EEEeCCCCCCHHHHHHHHHHHHHHHc-CCC---h
Q psy8224 29 VDMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNV--EIRLSPETEDISNLQKAADFVKAFVY-GFD---V 102 (766)
Q Consensus 29 ~~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v--~i~~~~~t~d~~~~~ka~~~i~ai~~-gf~---~ 102 (766)
..+.+|.||.+|+|+|||+.|++++.|.+++++++.+.-+.... ..++-+.|.||+.+.+|+.+|.-|.+ ++. .
T Consensus 138 ~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g 217 (600)
T KOG1676|consen 138 ETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPG 217 (600)
T ss_pred ceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCc
Confidence 47899999999999999999999999999999999886544422 24555667899999999999999987 221 1
Q ss_pred hhHHhhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEe--------CceEEEEcchhhH
Q psy8224 103 DDALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA--------DSKIHVLGSYQNV 174 (766)
Q Consensus 103 ~~a~~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~--------~~~v~iiG~~~~l 174 (766)
+. --...++.--..++|+ |-+ -.+|-||||+|+|+|-|++-||+||.+. ++++.|||+.++|
T Consensus 218 ~~--~~~g~~~g~~~~~~V~-VPr-------~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~i 287 (600)
T KOG1676|consen 218 SG--GHAGVRGGGSATREVK-VPR-------SKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQI 287 (600)
T ss_pred cc--cccCcCccccceeEEe-ccc-------cceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHH
Confidence 10 1111122222233333 112 3499999999999999999999999994 4679999999999
Q ss_pred HHHHHHHHHhhcCC
Q psy8224 175 QVALKALSNLILGS 188 (766)
Q Consensus 175 ~~ar~~i~~~~~~~ 188 (766)
..|.+.|..++...
T Consensus 288 e~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 288 EHAAELINEIIAEA 301 (600)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998543
No 8
>KOG2193|consensus
Probab=99.10 E-value=2.2e-10 Score=121.31 Aligned_cols=134 Identities=19% Similarity=0.295 Sum_probs=104.1
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEE------cccCeEEEEeCCCCCCHHHHHHHHHHHHHHHc---CC
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFN------LKSRNVEIRLSPETEDISNLQKAADFVKAFVY---GF 100 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~------~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~---gf 100 (766)
++..+.||..-+|+|||+.|.-++.|.+..|.+|.|. .+++.|+|. ++|.+.+||+--|..-.. .|
T Consensus 411 e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViIt-----GppeaqfKAQgrifgKikEenf~ 485 (584)
T KOG2193|consen 411 EQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIIT-----GPPEAQFKAQGRIFGKIKEENFF 485 (584)
T ss_pred hheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEec-----CChHHHHhhhhhhhhhhhhhccC
Confidence 6788999999999999999999999999999999994 456666665 599999999977743211 33
Q ss_pred ChhhHHhhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeC--------c-eEEEEcch
Q psy8224 101 DVDDALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIAD--------S-KIHVLGSY 171 (766)
Q Consensus 101 ~~~~a~~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~--------~-~v~iiG~~ 171 (766)
.|.+-++| + .. | +..+++.||||||||+|.+.++++|++.++|.. . -|-|||.|
T Consensus 486 ~Pkeevkl-e-th-------i--------rVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhf 548 (584)
T KOG2193|consen 486 LPKEEVKL-E-TH-------I--------RVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHF 548 (584)
T ss_pred Cchhhhee-e-ee-------e--------eccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechh
Confidence 44443333 2 11 1 234588999999999999999999999999942 1 28899999
Q ss_pred hhHHHHHHHHHHhh
Q psy8224 172 QNVQVALKALSNLI 185 (766)
Q Consensus 172 ~~l~~ar~~i~~~~ 185 (766)
..-..|.+-|..+.
T Consensus 549 yatq~aQrki~~iv 562 (584)
T KOG2193|consen 549 YATQNAQRKIAHIV 562 (584)
T ss_pred hcchHHHHHHHHHH
Confidence 98887777666665
No 9
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=99.05 E-value=1.1e-10 Score=112.50 Aligned_cols=51 Identities=29% Similarity=0.416 Sum_probs=45.2
Q ss_pred ccchhhhhhhcccCCCCCCCeEEEEE--eCCeEEEEEEecccCCCCeEEeecC
Q psy8224 615 RMSKWIYMKTAMLSHNCKPNTKHVIV--NEDFSLQLIALVNIRKGDIISTTYT 665 (766)
Q Consensus 615 ~i~~glyp~~s~~NHsC~PN~~~~~~--~~g~~l~vra~r~I~~GeeI~isY~ 665 (766)
..+.++||.++++||||.||+.+.+. ..+..+.++|.|+|++|||||+||+
T Consensus 110 ~~~~~l~p~~d~~NHsc~pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 110 RDGIALYPFADMLNHSCDPNCEVSFDFDGDGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp EEEEEEETGGGGSEEESSTSEEEEEEEETTTTEEEEEESS-B-TTSBEEEEST
T ss_pred ccccccCcHhHheccccccccceeeEeecccceEEEEECCccCCCCEEEEEEC
Confidence 45789999999999999999999996 3579999999999999999999997
No 10
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=99.02 E-value=2.2e-10 Score=110.28 Aligned_cols=51 Identities=27% Similarity=0.384 Sum_probs=45.1
Q ss_pred ceeEEEeecccccccccccCCceeeeec---CccchhhhhhhcccCCCeeeeccc
Q psy8224 550 KIKIRGIYMKTAMLSHNCKPNTKHVIVN---EDFSLQLIALVNICKGDIISTTYT 601 (766)
Q Consensus 550 ~~~~~gLyp~~SllNHSC~PN~~~~f~~---~~~~l~~~A~r~I~~GeeI~~sY~ 601 (766)
...+.+|||.++++||||.||+...| + .+..+.++|.++|++||||+++||
T Consensus 109 ~~~~~~l~p~~d~~NHsc~pn~~~~~-~~~~~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 109 DRDGIALYPFADMLNHSCDPNCEVSF-DFDGDGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp EEEEEEEETGGGGSEEESSTSEEEEE-EEETTTTEEEEEESS-B-TTSBEEEEST
T ss_pred cccccccCcHhHheccccccccceee-EeecccceEEEEECCccCCCCEEEEEEC
Confidence 56789999999999999999999999 5 567899999999999999999997
No 11
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=98.96 E-value=3.9e-10 Score=103.11 Aligned_cols=48 Identities=21% Similarity=0.451 Sum_probs=41.4
Q ss_pred chhhhhhhcccCCCCCCCeEEEEEeCCe--EEEEEEecccCCCCeEEeec
Q psy8224 617 SKWIYMKTAMLSHNCKPNTKHVIVNEDF--SLQLIALVNIRKGDIISTTY 664 (766)
Q Consensus 617 ~~glyp~~s~~NHsC~PN~~~~~~~~g~--~l~vra~r~I~~GeeI~isY 664 (766)
+..++|.++++||||.||+...+...++ .+.++|+|+|++||||+++|
T Consensus 67 ~~~~~~~~~~iNHsc~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 67 ARRKGNIARFINHSCEPNCELLFVEVNGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred CCccCcHHHeeCCCCCCCEEEEEEEECCCcEEEEEECCCcCCCCEEeecC
Confidence 3336899999999999999998854333 69999999999999999999
No 12
>KOG1676|consensus
Probab=98.88 E-value=3.7e-09 Score=117.75 Aligned_cols=146 Identities=18% Similarity=0.310 Sum_probs=118.0
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEE------cccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChh
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFN------LKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVD 103 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~------~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~ 103 (766)
+++.|+||...+|.|||+.|+++++|...+|++|+|- +.++.+.|.+ .+.-|.+|..+|++|..+..--
T Consensus 230 ~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG-----~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 230 ATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIG-----TVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred ceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeec-----CHHHHHHHHHHHHHHHHHHhcc
Confidence 6999999999999999999999999999999999994 3466788876 7789999999999997644322
Q ss_pred h-------HHhhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEe---------CceEEE
Q psy8224 104 D-------ALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA---------DSKIHV 167 (766)
Q Consensus 104 ~-------a~~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~---------~~~v~i 167 (766)
. +-.++. .|.+. ... -..|.||||+|+|+|.|+.-||+++-+. .+|+.|
T Consensus 305 ~~~~~~~G~P~~~~-------~fy~~---VPa-----~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~I 369 (600)
T KOG1676|consen 305 AGGGMGGGAPGLVA-------QFYMK---VPA-----DKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVI 369 (600)
T ss_pred CCCCcCCCCcccee-------eEEEe---ccc-----cccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEE
Confidence 1 111211 11111 111 3389999999999999999999999883 578999
Q ss_pred EcchhhHHHHHHHHHHhhcCCCCccccc
Q psy8224 168 LGSYQNVQVALKALSNLILGSPPNKVYG 195 (766)
Q Consensus 168 iG~~~~l~~ar~~i~~~~~~~~p~~~~s 195 (766)
-|+..+|..||+.|..-+.+..+.+-|.
T Consensus 370 rG~~~QIdhAk~LIr~kvg~~~~n~~~~ 397 (600)
T KOG1676|consen 370 RGDKRQIDHAKQLIRDKVGDIAPNTPYP 397 (600)
T ss_pred ecCcccchHHHHHHHHHhcccCCCCCCC
Confidence 9999999999999999999888877665
No 13
>PRK00106 hypothetical protein; Provisional
Probab=98.51 E-value=1.1e-07 Score=108.47 Aligned_cols=63 Identities=30% Similarity=0.525 Sum_probs=56.4
Q ss_pred ccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCce-EEEEcchhhHH--HHHHHHHHhh-cCCCCc
Q psy8224 126 TLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSK-IHVLGSYQNVQ--VALKALSNLI-LGSPPN 191 (766)
Q Consensus 126 ~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~-v~iiG~~~~l~--~ar~~i~~~~-~~~~p~ 191 (766)
.++++.| +|||||++|+++|++|.+||+.|.|+|+. +.++.+|++++ +||.++++++ +|..|+
T Consensus 230 ~lp~dem---kGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li~dgrIhp 296 (535)
T PRK00106 230 HLPDDNM---KGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLIKDGRIHP 296 (535)
T ss_pred EcCChHh---hcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHHHcCCcCH
Confidence 4556777 99999999999999999999999999988 77799999998 9999999999 777653
No 14
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=98.50 E-value=1.2e-07 Score=109.02 Aligned_cols=64 Identities=30% Similarity=0.495 Sum_probs=57.2
Q ss_pred ccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCce-EEEEcchhhHH--HHHHHHHHhh-cCCCCcc
Q psy8224 126 TLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSK-IHVLGSYQNVQ--VALKALSNLI-LGSPPNK 192 (766)
Q Consensus 126 ~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~-v~iiG~~~~l~--~ar~~i~~~~-~~~~p~~ 192 (766)
.++.+.| +|||||++|+++|++|.+||+.|.|+|+. +.++.+|++++ +||.+++.++ +|..|+.
T Consensus 209 ~lp~d~~---kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrihp~ 276 (514)
T TIGR03319 209 NLPNDEM---KGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIHPA 276 (514)
T ss_pred EcCChhh---hccccCCCcchHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCCHH
Confidence 4556777 99999999999999999999999999988 78899999997 9999999999 7776643
No 15
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=98.48 E-value=1.9e-08 Score=73.17 Aligned_cols=37 Identities=41% Similarity=0.998 Sum_probs=32.9
Q ss_pred ccccCCcccCCCCCCCCcccCCchhhccccccccCCC
Q psy8224 317 CEVCKVAASLKCGGCNQVFYCSKSHQKQHWKEHKPGC 353 (766)
Q Consensus 317 C~~C~~~~~~~C~~C~~v~YCs~~cq~~~w~~Hk~~C 353 (766)
|..|+..+..+|++|+.++|||++||+.||..|+.+|
T Consensus 1 C~~C~~~~~~~C~~C~~~~YCs~~Cq~~~w~~Hk~~C 37 (37)
T PF01753_consen 1 CAVCGKPALKRCSRCKSVYYCSEECQRADWPYHKFEC 37 (37)
T ss_dssp -TTTSSCSSEEETTTSSSEESSHHHHHHHHHHHCCTH
T ss_pred CcCCCCCcCCcCCCCCCEEecCHHHHHHHHHHHhhhC
Confidence 6788888777999999999999999999997799876
No 16
>PRK12704 phosphodiesterase; Provisional
Probab=98.34 E-value=5.3e-07 Score=103.78 Aligned_cols=62 Identities=27% Similarity=0.507 Sum_probs=55.8
Q ss_pred ccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCce-EEEEcchhhHH--HHHHHHHHhh-cCCCC
Q psy8224 126 TLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSK-IHVLGSYQNVQ--VALKALSNLI-LGSPP 190 (766)
Q Consensus 126 ~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~-v~iiG~~~~l~--~ar~~i~~~~-~~~~p 190 (766)
.++.+.| +|||||++|+++|++|.+||+.|.|+|+. +.++..|++++ +|+.+++.++ +|..|
T Consensus 215 ~lp~d~m---kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~ 280 (520)
T PRK12704 215 NLPNDEM---KGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLVQDGRIH 280 (520)
T ss_pred ecCCchh---hcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHHhcCCcC
Confidence 4556777 99999999999999999999999999987 88899999999 9999999999 66544
No 17
>KOG2191|consensus
Probab=98.34 E-value=6.6e-06 Score=85.70 Aligned_cols=169 Identities=17% Similarity=0.178 Sum_probs=110.2
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEc-------ccCeEE-EEeCCCCCCHHHHHHHHHHHHHHHcCCC
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNL-------KSRNVE-IRLSPETEDISNLQKAADFVKAFVYGFD 101 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~-------~~~~v~-i~~~~~t~d~~~~~ka~~~i~ai~~gf~ 101 (766)
-..+|.||.+-.|.|||+.|+++..|++.+|.+|+|-- .+..|- |.+ ...+|+...+||..-.|.-+
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~G-----t~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQG-----TVEALNAVHEFIADKIREKP 113 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEec-----cHHHHHHHHHHHHHHHHHhH
Confidence 35689999999999999999999999999999999952 133343 443 67888888888887666443
Q ss_pred hhhHH--hhcccccceeeeee-eccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEe----------CceEEEE
Q psy8224 102 VDDAL--ALLRLDNLFIESFE-IKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA----------DSKIHVL 168 (766)
Q Consensus 102 ~~~a~--~ll~~d~~~~~~~~-i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~----------~~~v~ii 168 (766)
-..+- .+|+ . -.-|-+. |+=++.+ --.|.||||+|-|+|+|.+-+|+.|.|+ +.-|.+.
T Consensus 114 ~~~~k~v~~~~-p-qt~~r~kqikivvPN------stag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~s 185 (402)
T KOG2191|consen 114 QAVAKPVDILQ-P-QTPDRIKQIKIVVPN------STAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVS 185 (402)
T ss_pred HhhcCCccccC-C-CCccccceeEEeccC------CcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEec
Confidence 22222 1110 0 0000011 1112222 1269999999999999999999999997 3448899
Q ss_pred cchhhHH-HHHHHHHHhhcCCCCcccccceeecccCCceecCCCC
Q psy8224 169 GSYQNVQ-VALKALSNLILGSPPNKVYGGILCSRCRHHVISTNPL 212 (766)
Q Consensus 169 G~~~~l~-~ar~~i~~~~~~~~p~~~~s~l~c~~c~g~~l~~~pl 212 (766)
|++++.. .+..++..+.+--++++-...-. ..=.|.+.-.+|.
T Consensus 186 ge~e~~~~A~~~IL~Ki~eDpqs~scln~sy-a~vsGpvaNsnPt 229 (402)
T KOG2191|consen 186 GEPEQNMKAVSLILQKIQEDPQSGSCLNISY-ANVSGPVANSNPT 229 (402)
T ss_pred CCHHHHHHHHHHHHHHhhcCCcccceeccch-hcccCcccccCCC
Confidence 9999755 55556666666555555222000 1112456666665
No 18
>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=98.19 E-value=2.1e-06 Score=69.80 Aligned_cols=49 Identities=27% Similarity=0.319 Sum_probs=44.2
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC-ceEEEEcc-hhhHHHHHHHHH
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD-SKIHVLGS-YQNVQVALKALS 182 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~-~~v~iiG~-~~~l~~ar~~i~ 182 (766)
..+|+|||++|+|++.|++.|||+|.|.+ .+|.|.|+ .+.++.|+..|+
T Consensus 11 ~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 11 DKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred hheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHHHhC
Confidence 45899999999999999999999999975 66999998 789999998763
No 19
>KOG2193|consensus
Probab=98.14 E-value=3.9e-06 Score=89.66 Aligned_cols=129 Identities=22% Similarity=0.272 Sum_probs=94.2
Q ss_pred eEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEc------ccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhh
Q psy8224 31 MRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNL------KSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDD 104 (766)
Q Consensus 31 ~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~------~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~ 104 (766)
-..+.||..-+|+|||+.|.+++.|-+.+..+|.+-- .++.|+|-+ .|..--+|-.+|-.|+-.-
T Consensus 200 PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~-----tpEg~s~Ac~~ILeimqkE---- 270 (584)
T KOG2193|consen 200 PLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHS-----TPEGTSKACKMILEIMQKE---- 270 (584)
T ss_pred ceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEec-----CccchHHHHHHHHHHHHHh----
Confidence 3468899999999999999999999999999988842 357788887 4456677877777666422
Q ss_pred HHhhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEe----------CceEEEEcchhhH
Q psy8224 105 ALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA----------DSKIHVLGSYQNV 174 (766)
Q Consensus 105 a~~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~----------~~~v~iiG~~~~l 174 (766)
|. +|++. +-+. ++.+-.+ ...||+|||.|+++|-||.-|||+|.|- ++||.+-|+.+..
T Consensus 271 A~----~~k~~-~e~p---Lk~lAHN---~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac 339 (584)
T KOG2193|consen 271 AV----DDKVA-EEIP---LKILAHN---NLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEAC 339 (584)
T ss_pred hh----ccchh-hhcc---hhhhhhc---chhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHH
Confidence 21 12221 1111 2222223 3499999999999999999999999983 6899999988865
Q ss_pred HHHHH
Q psy8224 175 QVALK 179 (766)
Q Consensus 175 ~~ar~ 179 (766)
-.|..
T Consensus 340 ~~AE~ 344 (584)
T KOG2193|consen 340 VQAEA 344 (584)
T ss_pred HHHHH
Confidence 44433
No 20
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.13 E-value=2.9e-06 Score=68.64 Aligned_cols=48 Identities=33% Similarity=0.458 Sum_probs=44.5
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC----ceEEEEcchhhHHHHHHHH
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD----SKIHVLGSYQNVQVALKAL 181 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~----~~v~iiG~~~~l~~ar~~i 181 (766)
...|+|||++|++++.||..|||.|.|.+ ..|.|.|+.+++..|++.|
T Consensus 9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence 56999999999999999999999999997 4899999999999999875
No 21
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.09 E-value=6.5e-06 Score=76.19 Aligned_cols=58 Identities=19% Similarity=0.282 Sum_probs=51.9
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeCc------------------------eEEEEcch---hhHHHHHHHHHHhhc
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIADS------------------------KIHVLGSY---QNVQVALKALSNLIL 186 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~~------------------------~v~iiG~~---~~l~~ar~~i~~~~~ 186 (766)
..+|||||++|+|+|.||..|||+|.|.|+ +|.|.|.- +.+..|++.|+.++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 349999999999999999999999999986 58999876 789999999999998
Q ss_pred CCCCc
Q psy8224 187 GSPPN 191 (766)
Q Consensus 187 ~~~p~ 191 (766)
-.++.
T Consensus 95 ~~~~~ 99 (120)
T cd02395 95 PAIEG 99 (120)
T ss_pred cCCCc
Confidence 66664
No 22
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.08 E-value=5.7e-06 Score=67.43 Aligned_cols=48 Identities=25% Similarity=0.307 Sum_probs=44.3
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC-----ceEEEEcchhhHHHHHHHH
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD-----SKIHVLGSYQNVQVALKAL 181 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~-----~~v~iiG~~~~l~~ar~~i 181 (766)
...|+|||++|.+++.|+..|||+|.|.+ +.|.|.|+.+++..|+..|
T Consensus 9 ~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 9 KLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred HHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHh
Confidence 55899999999999999999999999976 6799999999999998875
No 23
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=97.93 E-value=3.6e-06 Score=76.69 Aligned_cols=45 Identities=22% Similarity=0.424 Sum_probs=38.1
Q ss_pred eecccccccccccCCceeeeecCcc--chhhhhhhcccCCCeeeecc
Q psy8224 556 IYMKTAMLSHNCKPNTKHVIVNEDF--SLQLIALVNICKGDIISTTY 600 (766)
Q Consensus 556 Lyp~~SllNHSC~PN~~~~f~~~~~--~l~~~A~r~I~~GeeI~~sY 600 (766)
++|.++++||||.||+...+...+. .+.++|+|+|++||||+++|
T Consensus 70 ~~~~~~~iNHsc~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 70 KGNIARFINHSCEPNCELLFVEVNGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred cCcHHHeeCCCCCCCEEEEEEEECCCcEEEEEECCCcCCCCEEeecC
Confidence 6788999999999999877632222 48899999999999999988
No 24
>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=97.92 E-value=2.4e-05 Score=63.66 Aligned_cols=59 Identities=15% Similarity=0.219 Sum_probs=53.5
Q ss_pred eEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHH
Q psy8224 31 MRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVK 94 (766)
Q Consensus 31 ~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ 94 (766)
+..+.||+++++.|+|+.|++++.|++.+|++|.|+. ++.|.|.+ .|+.++.+|+++|.
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-~g~v~I~G----~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-DGTVYIAA----SDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-CCEEEEEe----CCHHHHHHHHHHhC
Confidence 4679999999999999999999999999999999987 68999998 46889999998873
No 25
>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=97.88 E-value=2.3e-05 Score=63.98 Aligned_cols=48 Identities=31% Similarity=0.477 Sum_probs=43.5
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC-------ceEEEEcchhhHHHHHHHH
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD-------SKIHVLGSYQNVQVALKAL 181 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~-------~~v~iiG~~~~l~~ar~~i 181 (766)
...|+|||++|.+++.|+..|||.|.|.. ..|.|.|+.+++..|+..+
T Consensus 9 ~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 9 SLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred hhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 45899999999999999999999999976 5599999999999998875
No 26
>smart00322 KH K homology RNA-binding domain.
Probab=97.87 E-value=3e-05 Score=63.47 Aligned_cols=52 Identities=29% Similarity=0.459 Sum_probs=47.8
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC-----ceEEEEcchhhHHHHHHHHHHhh
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD-----SKIHVLGSYQNVQVALKALSNLI 185 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~-----~~v~iiG~~~~l~~ar~~i~~~~ 185 (766)
...|++||++|.+++.|+..||++|.+.+ ..|.|.|+.++++.|+.++...+
T Consensus 12 ~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 12 DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred hhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 45899999999999999999999999987 77999999999999999998765
No 27
>PRK12705 hypothetical protein; Provisional
Probab=97.81 E-value=1.4e-05 Score=91.05 Aligned_cols=62 Identities=26% Similarity=0.475 Sum_probs=53.7
Q ss_pred ccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCce-EEEEcchhhHH--HHHHHHHHhh-cCCCC
Q psy8224 126 TLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSK-IHVLGSYQNVQ--VALKALSNLI-LGSPP 190 (766)
Q Consensus 126 ~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~-v~iiG~~~~l~--~ar~~i~~~~-~~~~p 190 (766)
.++.+.| +|||||++|+++|++|.+||+.|.|+|.. +.++..|++++ +|+.+++.++ .|..|
T Consensus 203 ~lp~dem---kGriIGreGrNir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li~dgri~ 268 (508)
T PRK12705 203 PIPSDAM---KGRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLADGRIH 268 (508)
T ss_pred ecCChHh---hccccCccchhHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHHhcCCCC
Confidence 4556777 99999999999999999999999999977 66688899877 9999999999 56543
No 28
>KOG2589|consensus
Probab=97.77 E-value=1.9e-05 Score=83.53 Aligned_cols=59 Identities=29% Similarity=0.613 Sum_probs=50.6
Q ss_pred hcccCCCCCCCeEEEEEeCC-eEEEEEEecccCCCCeEEeecCCCCCCHHHHHHHHhCCCCcEEeccCCCCC
Q psy8224 624 TAMLSHNCKPNTKHVIVNED-FSLQLIALVNIRKGDIISTTYTQPFWGTMDRRLHLRMSKCFDCTCDRCKDP 694 (766)
Q Consensus 624 ~s~~NHsC~PN~~~~~~~~g-~~l~vra~r~I~~GeeI~isY~~~~~~~~~Rr~~L~~~y~F~C~C~rC~~~ 694 (766)
++++||.|.||+..+- .| ..+.|+++|||++|||||.=|+..+.+. ..-.|.|.-|...
T Consensus 197 aafINHDCrpnCkFvs--~g~~tacvkvlRDIePGeEITcFYgs~fFG~----------~N~~CeC~TCER~ 256 (453)
T KOG2589|consen 197 AAFINHDCRPNCKFVS--TGRDTACVKVLRDIEPGEEITCFYGSGFFGE----------NNEECECVTCERR 256 (453)
T ss_pred HHhhcCCCCCCceeec--CCCceeeeehhhcCCCCceeEEeecccccCC----------CCceeEEeecccc
Confidence 5689999999997665 45 7999999999999999999999988875 2457999999865
No 29
>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=97.74 E-value=4.9e-05 Score=62.61 Aligned_cols=48 Identities=29% Similarity=0.395 Sum_probs=43.1
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC--------ceEEEEcchhhHHHHHHHH
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD--------SKIHVLGSYQNVQVALKAL 181 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~--------~~v~iiG~~~~l~~ar~~i 181 (766)
..+|+|||++|.+++.|+..|||+|.|.. +.|.|.|+.++++.|+..|
T Consensus 9 ~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 9 SQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 55999999999999999999999999964 3489999999999998765
No 30
>KOG1710|consensus
Probab=97.72 E-value=2.6e-06 Score=87.43 Aligned_cols=43 Identities=35% Similarity=0.742 Sum_probs=39.7
Q ss_pred CCcccccCCc-ccCCCCCCCCcccCCchhhccccccccCCCccc
Q psy8224 314 SGKCEVCKVA-ASLKCGGCNQVFYCSKSHQKQHWKEHKPGCAKY 356 (766)
Q Consensus 314 ~~~C~~C~~~-~~~~C~~C~~v~YCs~~cq~~~w~~Hk~~C~~l 356 (766)
-+.|..||++ +.++|++|+++.||+++||+.||-.||..|+.+
T Consensus 319 ~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~hWf~HKK~C~~L 362 (396)
T KOG1710|consen 319 CQFCSTCGHPGAKKRCSQCKAVAYCDQECQKFHWFIHKKVCSFL 362 (396)
T ss_pred cccccccCCCCccchhhhhHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 3679999998 578899999999999999999999999999877
No 31
>KOG2190|consensus
Probab=97.65 E-value=0.0003 Score=80.06 Aligned_cols=147 Identities=21% Similarity=0.228 Sum_probs=104.6
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcc-----cCeEEEEeC----CCCCCHHHHHHHHHHHHHHHcCC
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLK-----SRNVEIRLS----PETEDISNLQKAADFVKAFVYGF 100 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~-----~~~v~i~~~----~~t~d~~~~~ka~~~i~ai~~gf 100 (766)
.++.+..|-..+|-+||+.|+++++|...++.+++|+.. ++-|+|.++ ...+.-.++.||.++|-.. |
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~---~ 119 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFK---L 119 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhc---c
Confidence 568899999999999999999999999888888888654 566666651 0011336788888887432 2
Q ss_pred ChhhHHhhcccccce-eee---eeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCc--------eEEEE
Q psy8224 101 DVDDALALLRLDNLF-IES---FEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADS--------KIHVL 168 (766)
Q Consensus 101 ~~~~a~~ll~~d~~~-~~~---~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~--------~v~ii 168 (766)
. ++.... +|.- .+. +.++=++. +-..|=||||+|+.+|.|.+.||++|.|.++ .|-|-
T Consensus 120 ~-~d~~~~---~d~~~~~~~~~v~~RLlVp------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~Is 189 (485)
T KOG2190|consen 120 E-EDDEAA---EDNGEDASGPEVTCRLLVP------SSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTIS 189 (485)
T ss_pred c-cccccc---ccCCccccCCceEEEEEec------hhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEc
Confidence 2 010000 1110 000 11222221 2458999999999999999999999999764 49999
Q ss_pred cchhhHHHHHHHHHHhhcCCC
Q psy8224 169 GSYQNVQVALKALSNLILGSP 189 (766)
Q Consensus 169 G~~~~l~~ar~~i~~~~~~~~ 189 (766)
|..+.++.|-..|+.+++...
T Consensus 190 G~~~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 190 GEPDAVKKALVQISSRLLENP 210 (485)
T ss_pred CchHHHHHHHHHHHHHHHhcC
Confidence 999999999999999997743
No 32
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=97.49 E-value=5.7e-05 Score=87.00 Aligned_cols=74 Identities=19% Similarity=0.397 Sum_probs=61.4
Q ss_pred hhhhcccCCCCCCCeEEEEEeCC--eEEEEEEecccCCCCeEEeecCCCCCCHHHHHHHHhCCCCcEEeccCCCCC
Q psy8224 621 YMKTAMLSHNCKPNTKHVIVNED--FSLQLIALVNIRKGDIISTTYTQPFWGTMDRRLHLRMSKCFDCTCDRCKDP 694 (766)
Q Consensus 621 yp~~s~~NHsC~PN~~~~~~~~g--~~l~vra~r~I~~GeeI~isY~~~~~~~~~Rr~~L~~~y~F~C~C~rC~~~ 694 (766)
-..+.++||||.||+........ ..+..+|++||.+||||+..|....+....+...+...+...|.|.+|...
T Consensus 403 g~~~r~~nHS~~pN~~~~~~~~~g~~~~~~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 478 (480)
T COG2940 403 GDVARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHT 478 (480)
T ss_pred ccccceeecCCCCCcceecccccccceeeecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCCC
Confidence 34567899999999998875433 489999999999999999999998886655566777788899999999764
No 33
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.47 E-value=0.00017 Score=71.88 Aligned_cols=65 Identities=15% Similarity=0.076 Sum_probs=60.3
Q ss_pred cchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhccc
Q psy8224 40 RYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALLRL 111 (766)
Q Consensus 40 r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll~~ 111 (766)
+.|.|||+.|++++.|++.+|++|.|+. +.|.|.+ ||..+..|++.|.+|.+|+.++.++++|++
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~--~~v~i~G-----~~~~~~~A~~~I~~li~g~~~~~~~~~l~~ 169 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG--KTVAIIG-----DPEQVEIAREAIEMLIEGAPHGTVYKFLER 169 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC--CEEEEEe-----CHHHHHHHHHHHHHHHcCCCcHHHHHHHHH
Confidence 7899999999999999999999999985 4588775 999999999999999999999999999983
No 34
>PF13014 KH_3: KH domain
Probab=97.44 E-value=0.00016 Score=54.34 Aligned_cols=27 Identities=41% Similarity=0.613 Sum_probs=25.8
Q ss_pred hccccCCCCcHHHHHHHhhCceEEEeC
Q psy8224 136 IGRLAGKGGRTKFTIENITKTRIVIAD 162 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~I~v~~ 162 (766)
.|+|||++|.+++.|+..|||+|.|..
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECC
Confidence 689999999999999999999999976
No 35
>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=97.39 E-value=0.00028 Score=56.96 Aligned_cols=58 Identities=16% Similarity=0.181 Sum_probs=52.0
Q ss_pred eEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcc--cCeEEEEeCCCCCCHHHHHHHHHHH
Q psy8224 31 MRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLK--SRNVEIRLSPETEDISNLQKAADFV 93 (766)
Q Consensus 31 ~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~--~~~v~i~~~~~t~d~~~~~ka~~~i 93 (766)
|..+.||...+++|+|+.|..++.|++.++++|.++.. ...|.|.+ ++..+.+|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G-----~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-----SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-----SHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-----CHHHHHHHHhhC
Confidence 56899999999999999999999999999999999765 45788887 889999999876
No 36
>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=97.22 E-value=0.00048 Score=68.23 Aligned_cols=58 Identities=29% Similarity=0.360 Sum_probs=51.5
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeCc--eEEE---EcchhhHHHHHHHHHHhhcCCCCc
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIADS--KIHV---LGSYQNVQVALKALSNLILGSPPN 191 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~~--~v~i---iG~~~~l~~ar~~i~~~~~~~~p~ 191 (766)
..+|.|||++|+|++.||..||++|.|.++ +|.| -++.+.+..|+++|..+.+|-+|.
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e 69 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE 69 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH
Confidence 459999999999999999999999999975 6777 577889999999999999986654
No 37
>KOG1080|consensus
Probab=97.15 E-value=0.00032 Score=85.30 Aligned_cols=46 Identities=22% Similarity=0.449 Sum_probs=38.7
Q ss_pred hhcccCCCCCCCeEEEE--EeCCeEEEEEEecccCCCCeEEeecCCCC
Q psy8224 623 KTAMLSHNCKPNTKHVI--VNEDFSLQLIALVNIRKGDIISTTYTQPF 668 (766)
Q Consensus 623 ~~s~~NHsC~PN~~~~~--~~~g~~l~vra~r~I~~GeeI~isY~~~~ 668 (766)
++.+|||||.|||.... ++...++++.|.|+|.+|||||-.|--..
T Consensus 939 iAr~InHsC~PNCyakvi~V~g~~~IvIyakr~I~~~EElTYDYkF~~ 986 (1005)
T KOG1080|consen 939 IARFINHSCNPNCYAKVITVEGDKRIVIYSKRDIAAGEELTYDYKFPT 986 (1005)
T ss_pred hhheeecccCCCceeeEEEecCeeEEEEEEecccccCceeeeeccccc
Confidence 57799999999996655 44558999999999999999999996544
No 38
>KOG4442|consensus
Probab=97.15 E-value=0.00034 Score=80.06 Aligned_cols=48 Identities=23% Similarity=0.491 Sum_probs=38.2
Q ss_pred hcccCCCCCCCeEEE-E-EeCCeEEEEEEecccCCCCeEEeecCCCCCCH
Q psy8224 624 TAMLSHNCKPNTKHV-I-VNEDFSLQLIALVNIRKGDIISTTYTQPFWGT 671 (766)
Q Consensus 624 ~s~~NHsC~PN~~~~-~-~~~g~~l~vra~r~I~~GeeI~isY~~~~~~~ 671 (766)
+-++||||+||+..- | +++-.+|=+.|.|+|++|||||.-|--...+.
T Consensus 194 aRFiNHSC~PNa~~~KWtV~~~lRvGiFakk~I~~GEEITFDYqf~rYGr 243 (729)
T KOG4442|consen 194 ARFINHSCDPNAEVQKWTVPDELRVGIFAKKVIKPGEEITFDYQFDRYGR 243 (729)
T ss_pred HHhhcCCCCCCceeeeeeeCCeeEEEEeEecccCCCceeeEecccccccc
Confidence 347899999999432 3 34457888999999999999999998766654
No 39
>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=97.15 E-value=0.00084 Score=54.57 Aligned_cols=57 Identities=19% Similarity=0.206 Sum_probs=51.4
Q ss_pred EEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcc---cCeEEEEeCCCCCCHHHHHHHHHHH
Q psy8224 32 RKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLK---SRNVEIRLSPETEDISNLQKAADFV 93 (766)
Q Consensus 32 ~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~---~~~v~i~~~~~t~d~~~~~ka~~~i 93 (766)
.++.||+...+.|+|..|..++.|++.+|++|.+... ++.|+|.+ ++.++.+|.++|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G-----~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITG-----PKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEc-----CHHHHHHHHHHh
Confidence 5789999999999999999999999999999999864 78999998 478888988876
No 40
>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=97.10 E-value=0.00095 Score=54.96 Aligned_cols=58 Identities=22% Similarity=0.205 Sum_probs=50.9
Q ss_pred eEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEccc------CeEEEEeCCCCCCHHHHHHHHHHH
Q psy8224 31 MRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKS------RNVEIRLSPETEDISNLQKAADFV 93 (766)
Q Consensus 31 ~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~------~~v~i~~~~~t~d~~~~~ka~~~i 93 (766)
+.++.||...++.|+|++|...+.|.+.+|++|.+.... +.|+|.+ ++..+.+|..+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G-----~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISG-----KPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEe-----CHHHHHHHHHhh
Confidence 468999999999999999999999999999999997543 5777877 788999998876
No 41
>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=96.94 E-value=0.0019 Score=52.52 Aligned_cols=57 Identities=19% Similarity=0.213 Sum_probs=50.2
Q ss_pred EEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcc-----cCeEEEEeCCCCCCHHHHHHHHHHH
Q psy8224 32 RKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLK-----SRNVEIRLSPETEDISNLQKAADFV 93 (766)
Q Consensus 32 ~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~-----~~~v~i~~~~~t~d~~~~~ka~~~i 93 (766)
..+.||.+.+++|+|..|...+.|++.+++.|.|... .+.|.|.+ ++..+.+|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G-----~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITG-----TPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEc-----CHHHHHHHHHHh
Confidence 5789999999999999999999999999999999864 56778887 478888888876
No 42
>KOG4442|consensus
Probab=96.93 E-value=0.0008 Score=77.16 Aligned_cols=44 Identities=30% Similarity=0.456 Sum_probs=36.9
Q ss_pred CCchhhccccccccCCCccccccccccccccccccccccCCceEee
Q psy8224 337 CSKSHQKQHWKEHKPGCAKYKVVRNDILGRHMVATKDIREGEIILE 382 (766)
Q Consensus 337 Cs~~cq~~~w~~Hk~~C~~l~v~~s~~~GR~lvA~r~~~~ge~Il~ 382 (766)
|+..|+.+..+. .++..++++..+.+|.|+.|..+|++|+.|++
T Consensus 105 cg~~C~NQRFQk--kqyA~vevF~Te~KG~GLRA~~dI~~g~FI~E 148 (729)
T KOG4442|consen 105 CGVYCKNQRFQK--KQYAKVEVFLTEKKGCGLRAEEDIPKGQFILE 148 (729)
T ss_pred ccccccchhhhh--hccCceeEEEecCcccceeeccccCCCcEEee
Confidence 667788765554 45778888899999999999999999999988
No 43
>KOG2589|consensus
Probab=96.90 E-value=0.0007 Score=71.97 Aligned_cols=78 Identities=23% Similarity=0.353 Sum_probs=58.7
Q ss_pred ccccccccccCCceeeeecCccchhhhhhhcccCCCeeeecccCCCCCcccc----ccccccchhhhhhhcccCCCCCCC
Q psy8224 559 KTAMLSHNCKPNTKHVIVNEDFSLQLIALVNICKGDIISTTYTQPFWGTMDR----RLHLRMSKWIYMKTAMLSHNCKPN 634 (766)
Q Consensus 559 ~~SllNHSC~PN~~~~f~~~~~~l~~~A~r~I~~GeeI~~sY~~~~~~~~~r----~~~~~i~~glyp~~s~~NHsC~PN 634 (766)
-++.+||+|.||+..+- .+.+..-|+++|+|.+||||+.-|+..|+|.... ..-.+.|.|-|-.. .=+-||.|-
T Consensus 196 PaafINHDCrpnCkFvs-~g~~tacvkvlRDIePGeEITcFYgs~fFG~~N~~CeC~TCER~g~gaFk~~-~g~~s~~p~ 273 (453)
T KOG2589|consen 196 PAAFINHDCRPNCKFVS-TGRDTACVKVLRDIEPGEEITCFYGSGFFGENNEECECVTCERRGTGAFKKL-AGLPSCSPK 273 (453)
T ss_pred cHHhhcCCCCCCceeec-CCCceeeeehhhcCCCCceeEEeecccccCCCCceeEEeecccccccchhhc-cCCCCCCCc
Confidence 45789999999998765 4547899999999999999999999999998432 34556666666544 346677776
Q ss_pred eEEE
Q psy8224 635 TKHV 638 (766)
Q Consensus 635 ~~~~ 638 (766)
...-
T Consensus 274 ~s~k 277 (453)
T KOG2589|consen 274 ISSK 277 (453)
T ss_pred cccc
Confidence 5433
No 44
>KOG2190|consensus
Probab=96.46 E-value=0.0063 Score=69.50 Aligned_cols=150 Identities=19% Similarity=0.167 Sum_probs=99.5
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEc------ccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC--
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNL------KSRNVEIRLSPETEDISNLQKAADFVKAFVYGFD-- 101 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~------~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~-- 101 (766)
-+..+.||...+|.|||+.|++++.|.+.++++|++-. .++.|+|.+ .+.++.+|--.|-.+.+-+.
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG-----~~~av~~al~~Is~~L~~~~~~ 212 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISG-----EPDAVKKALVQISSRLLENPPR 212 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcC-----chHHHHHHHHHHHHHHHhcCCc
Confidence 36789999999999999999999999999999999953 477788876 88999999988888877632
Q ss_pred ---hhhHHhhccc-----ccceeeeeeec-------cccccc-----cchhhhhhccccCCCCcHHHHHHHhhCceEEEe
Q psy8224 102 ---VDDALALLRL-----DNLFIESFEIK-------DVKTLK-----GDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA 161 (766)
Q Consensus 102 ---~~~a~~ll~~-----d~~~~~~~~i~-------~~~~~~-----~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~ 161 (766)
+-.+-.-.+- ..+.....--. ..+... --...-.+++|||++|-..+++++.||+-|.|.
T Consensus 213 ~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~ 292 (485)
T KOG2190|consen 213 SPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVG 292 (485)
T ss_pred CCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEec
Confidence 2222222110 00100000000 000000 011234689999999999999999999999998
Q ss_pred CceE---EEEcchhhHH----HHHHHHHHh
Q psy8224 162 DSKI---HVLGSYQNVQ----VALKALSNL 184 (766)
Q Consensus 162 ~~~v---~iiG~~~~l~----~ar~~i~~~ 184 (766)
+... ..+...+..+ .|.+++-..
T Consensus 293 ~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~ 322 (485)
T KOG2190|consen 293 DSRTDRIVTISARENPEDRYSMAQEALLLV 322 (485)
T ss_pred cccCcceeeeccccCcccccccchhhhhhc
Confidence 7542 3444444333 555555333
No 45
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=96.43 E-value=0.00019 Score=52.07 Aligned_cols=26 Identities=35% Similarity=0.900 Sum_probs=22.6
Q ss_pred cccCCCCCc-cccCccCC--CCCCcHhhh
Q psy8224 418 FYKCSDCGW-PLCAPRCK--SLPSHQKEC 443 (766)
Q Consensus 418 ~~~C~~C~~-~yCS~~C~--~~~~H~~EC 443 (766)
+.+|++|+. .|||++|+ +|..|+.+|
T Consensus 9 ~~~C~~C~~~~YCs~~Cq~~~w~~Hk~~C 37 (37)
T PF01753_consen 9 LKRCSRCKSVYYCSEECQRADWPYHKFEC 37 (37)
T ss_dssp SEEETTTSSSEESSHHHHHHHHHHHCCTH
T ss_pred CCcCCCCCCEEecCHHHHHHHHHHHhhhC
Confidence 459999998 99999998 488898887
No 46
>KOG1083|consensus
Probab=96.39 E-value=0.0015 Score=77.63 Aligned_cols=105 Identities=21% Similarity=0.313 Sum_probs=72.6
Q ss_pred cccccccccCCceeeeecCccchhhhhhhcccCCCeeeecccCC-----CCCc------ccc-ccccccchhhhh-----
Q psy8224 560 TAMLSHNCKPNTKHVIVNEDFSLQLIALVNICKGDIISTTYTQP-----FWGT------MDR-RLHLRMSKWIYM----- 622 (766)
Q Consensus 560 ~SllNHSC~PN~~~~f~~~~~~l~~~A~r~I~~GeeI~~sY~~~-----~~~~------~~r-~~~~~i~~glyp----- 622 (766)
..|.-|.|.|-..+.| ++..-..+++..+|+.|+-|+.--|.. |-.. +++ ...+.+..+.++
T Consensus 1169 qrm~r~e~cp~L~v~~-gp~~G~~v~tk~PikagtfI~EYvGeVit~ke~e~~mmtl~~~d~~~~cL~I~p~l~id~~R~ 1247 (1306)
T KOG1083|consen 1169 QRMQRHEECPPLEVFR-GPKKGWGVRTKEPIKAGTFIMEYVGEVITEKEFEPRMMTLYHNDDDHYCLVIDPGLFIDIPRM 1247 (1306)
T ss_pred HHhhhhccCCCcceec-cCCCCccccccccccccchHHHHHHHHHHHHhhcccccccCCCCCcccccccCccccCChhhc
Confidence 5677888888888888 877778899999999998886433331 1111 111 122333333332
Q ss_pred --hhcccCCCCCCCeEEE-E-EeCCeEEEEEEecccCCCCeEEeecC
Q psy8224 623 --KTAMLSHNCKPNTKHV-I-VNEDFSLQLIALVNIRKGDIISTTYT 665 (766)
Q Consensus 623 --~~s~~NHsC~PN~~~~-~-~~~g~~l~vra~r~I~~GeeI~isY~ 665 (766)
.+-++||||.||+... | ++.-.++-|.|+|||.+||||+.-|=
T Consensus 1248 ~n~~RfinhscKPNc~~qkwSVNG~~Rv~L~A~rDi~kGEELtYDYN 1294 (1306)
T KOG1083|consen 1248 GNGARFINHSCKPNCEMQKWSVNGEYRVGLFALRDLPKGEELTYDYN 1294 (1306)
T ss_pred cccccccccccCCCCccccccccceeeeeeeecCCCCCCceEEEecc
Confidence 3457799999999544 3 34348999999999999999999874
No 47
>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=96.30 E-value=0.0094 Score=70.53 Aligned_cols=70 Identities=14% Similarity=0.134 Sum_probs=62.9
Q ss_pred CceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChh
Q psy8224 29 VDMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVD 103 (766)
Q Consensus 29 ~~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~ 103 (766)
+-+..+.||+++++.|||..|++++.|.+.+|++|.|+- +|.|.|.. .|...+.+|+++|+.|...|.|+
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-~G~V~I~a----~d~~~~~~A~~~I~~i~~~~~~~ 646 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-DGTVYIGA----ADGPSAEAARAMINAIANPTMPE 646 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-CcEEEEEe----CCHHHHHHHHHHHHHhhCcCcCC
Confidence 367889999999999999999999999999999999995 79999987 58899999999999998865443
No 48
>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=96.22 E-value=0.015 Score=53.93 Aligned_cols=68 Identities=16% Similarity=0.111 Sum_probs=55.2
Q ss_pred EEEecCCC------cchhhhccCcccHHHHHHhcCcEEEEEccc----------------------CeEEEEeCCCCCC-
Q psy8224 32 RKVPVPNH------RYGPLKENWMKIFTPIVEHLKLQVRFNLKS----------------------RNVEIRLSPETED- 82 (766)
Q Consensus 32 ~~i~iP~~------r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~----------------------~~v~i~~~~~t~d- 82 (766)
.+|.||.+ .+|.|+|..|++.+.|++.+|++|.|.-+. +.|.|.. .+
T Consensus 2 ~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a----~~~ 77 (120)
T cd02395 2 EKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITA----ETP 77 (120)
T ss_pred CEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEe----CCc
Confidence 46677764 569999999999999999999999998542 7788887 45
Q ss_pred -HHHHHHHHHHHHHHHcCCChh
Q psy8224 83 -ISNLQKAADFVKAFVYGFDVD 103 (766)
Q Consensus 83 -~~~~~ka~~~i~ai~~gf~~~ 103 (766)
..++.+|..+|..+...+.++
T Consensus 78 ~~e~~~~A~~~I~~ll~~~~~~ 99 (120)
T cd02395 78 PEEALAKAVEAIEELLKPAIEG 99 (120)
T ss_pred HHHHHHHHHHHHHHHhccCCCc
Confidence 689999999999887755443
No 49
>smart00322 KH K homology RNA-binding domain.
Probab=96.22 E-value=0.017 Score=46.92 Aligned_cols=62 Identities=21% Similarity=0.227 Sum_probs=53.5
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcc---cCeEEEEeCCCCCCHHHHHHHHHHHHHH
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLK---SRNVEIRLSPETEDISNLQKAADFVKAF 96 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~---~~~v~i~~~~~t~d~~~~~ka~~~i~ai 96 (766)
.+..+.||.++.+.++|+.|...+.|++.++++|.+... ...|.|.+ ++..+..|+++|...
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g-----~~~~v~~a~~~i~~~ 67 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITG-----PPENVEKAAELILEI 67 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEc-----CHHHHHHHHHHHHHH
Confidence 357899999999999999999999999999999998764 37778887 578999999988754
No 50
>KOG1082|consensus
Probab=96.13 E-value=0.0035 Score=69.65 Aligned_cols=44 Identities=25% Similarity=0.532 Sum_probs=37.5
Q ss_pred ccCCCCCCCeEEEEEeCC------eEEEEEEecccCCCCeEEeecCCCCC
Q psy8224 626 MLSHNCKPNTKHVIVNED------FSLQLIALVNIRKGDIISTTYTQPFW 669 (766)
Q Consensus 626 ~~NHsC~PN~~~~~~~~g------~~l~vra~r~I~~GeeI~isY~~~~~ 669 (766)
++||||.||+.+..+..+ .++.+.|+++|++|+|||.-|+....
T Consensus 275 finHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~~~ 324 (364)
T KOG1082|consen 275 FINHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKAYK 324 (364)
T ss_pred cccCCCCccceeeeeeecCCccchheeeeeeccccCCCcccchhhccccc
Confidence 689999999988875322 47899999999999999999997754
No 51
>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=95.87 E-value=0.014 Score=69.22 Aligned_cols=66 Identities=17% Similarity=0.237 Sum_probs=53.7
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC-ceEEEEcch-hhHHHHHHHHHHhhcC--CCCcccccceee
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD-SKIHVLGSY-QNVQVALKALSNLILG--SPPNKVYGGILC 199 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~-~~v~iiG~~-~~l~~ar~~i~~~~~~--~~p~~~~s~l~c 199 (766)
..+|.|||+||+|+|.|+..||+.|.|.+ .+|.|.|.- +.++.|+..|..+... -+.|.+|..-..
T Consensus 587 ~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~ 656 (719)
T TIGR02696 587 DKIGEVIGPKGKMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVV 656 (719)
T ss_pred HHhhheeCCCcHhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEE
Confidence 45999999999999999999999999976 568888754 5899999999999985 344666654443
No 52
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=95.82 E-value=0.017 Score=55.12 Aligned_cols=104 Identities=14% Similarity=0.103 Sum_probs=67.7
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhc
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALL 109 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll 109 (766)
++..+.|++..+|..+|++|+..+.|.+..|-+|++ -. -+.|| +.||+.+.....+.+.. +.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdV---------ve--~s~d~------~~fI~n~l~Pa~V~~v~-I~ 93 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIEL---------VE--YSDDP------EEFIKNIFAPAAVRSVT-IK 93 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEE---------EE--cCCCH------HHHHHHHcCCCEEEEEE-EE
Confidence 566778899999999999999999998887755543 22 12344 66777664444433221 11
Q ss_pred ccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEe
Q psy8224 110 RLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA 161 (766)
Q Consensus 110 ~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~ 161 (766)
+.++-- ++.+. + . ..-.|+.|||+|++++.++.++|-++-|.
T Consensus 94 ~~~~~~--~~~V~--V-~-----~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 94 KKNGDK--VAYVE--V-A-----PEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred ecCCcE--EEEEE--E-C-----ccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 111100 01110 1 1 14489999999999999999999998764
No 53
>PRK02821 hypothetical protein; Provisional
Probab=95.75 E-value=0.007 Score=51.39 Aligned_cols=31 Identities=23% Similarity=0.551 Sum_probs=24.8
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeCceEEE
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIADSKIHV 167 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~i 167 (766)
.=+||||||+|+|.+||-.+-.+- .|+.|.+
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~l 70 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVAAI---GGRGVRV 70 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHHHh---cCCeEEE
Confidence 348999999999999999876654 6676654
No 54
>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=95.58 E-value=0.018 Score=69.16 Aligned_cols=66 Identities=23% Similarity=0.373 Sum_probs=53.9
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC-ceEEEEcc-hhhHHHHHHHHHHhhcCCCCcccccceee
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD-SKIHVLGS-YQNVQVALKALSNLILGSPPNKVYGGILC 199 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~-~~v~iiG~-~~~l~~ar~~i~~~~~~~~p~~~~s~l~c 199 (766)
-.+|+|||+||+|+|.|+..||+.|.|.+ .+|.|.+. -..+..|++.|..+..-...|.+|....-
T Consensus 560 ~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~ 627 (684)
T TIGR03591 560 DKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVV 627 (684)
T ss_pred HHHHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEE
Confidence 44999999999999999999999999974 66888764 45788999999999876666776655443
No 55
>KOG1588|consensus
Probab=95.38 E-value=0.011 Score=60.97 Aligned_cols=29 Identities=28% Similarity=0.445 Sum_probs=27.4
Q ss_pred hhccccCCCCcHHHHHHHhhCceEEEeCc
Q psy8224 135 AIGRLAGKGGRTKFTIENITKTRIVIADS 163 (766)
Q Consensus 135 ~~griiG~~G~t~~~ie~~t~~~I~v~~~ 163 (766)
-+|||+|+.|.|.|.||+-|||+|.|-|+
T Consensus 108 FVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 108 FVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred cccccccCCcchHHHHHHHHCCeEEEecC
Confidence 48999999999999999999999999886
No 56
>KOG1337|consensus
Probab=95.24 E-value=0.016 Score=66.83 Aligned_cols=64 Identities=16% Similarity=0.142 Sum_probs=51.0
Q ss_pred ccchhhhhhhcccCCCCCCCeEEEEEeCCeEEEEEEecccCCCCeEEeecCCCCCCHHHHHHHHhCCCCcE
Q psy8224 615 RMSKWIYMKTAMLSHNCKPNTKHVIVNEDFSLQLIALVNIRKGDIISTTYTQPFWGTMDRRLHLRMSKCFD 685 (766)
Q Consensus 615 ~i~~glyp~~s~~NHsC~PN~~~~~~~~g~~l~vra~r~I~~GeeI~isY~~~~~~~~~Rr~~L~~~y~F~ 685 (766)
....++.|..-++||+|.+....+.. .+..+.+.+.++|.+||||+|+|++. + ...|...|+|.
T Consensus 228 ~~~~~L~P~~D~~NH~~~~~~~~~~~-~d~~~~l~~~~~v~~geevfi~YG~~--~----N~eLL~~YGFv 291 (472)
T KOG1337|consen 228 DDNEALAPLIDLLNHSPEVIKAGYNQ-EDEAVELVAERDVSAGEEVFINYGPK--S----NAELLLHYGFV 291 (472)
T ss_pred CcchhhhhhHHhhccCchhccccccC-CCCcEEEEEeeeecCCCeEEEecCCC--c----hHHHHHhcCCC
Confidence 44567899999999999994444442 34589999999999999999999983 3 35566789997
No 57
>KOG0119|consensus
Probab=95.23 E-value=0.031 Score=62.07 Aligned_cols=94 Identities=20% Similarity=0.306 Sum_probs=61.3
Q ss_pred HHcCCChhhH---HhhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCce--------
Q psy8224 96 FVYGFDVDDA---LALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSK-------- 164 (766)
Q Consensus 96 i~~gf~~~~a---~~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~-------- 164 (766)
+.-||.+-.- ..++. |.+|+ +++++-.. .-+|.|||..|.|.|.||..||++|.|-|+.
T Consensus 122 ~nP~fkpP~DYk~p~~~~-~Kv~I---Pvke~Pd~------NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~ 191 (554)
T KOG0119|consen 122 LNPGFKPPADYKPPAKLH-DKVYI---PVKEFPDI------NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGR 191 (554)
T ss_pred hCcCCCCCcccCcccccc-cceec---chhhcCCc------ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccC
Confidence 3447744332 22445 67775 34444322 2389999999999999999999999998721
Q ss_pred ---------------EEEEcc-hhhHHHHHHHHHHhhcC-CCCcccccceee
Q psy8224 165 ---------------IHVLGS-YQNVQVALKALSNLILG-SPPNKVYGGILC 199 (766)
Q Consensus 165 ---------------v~iiG~-~~~l~~ar~~i~~~~~~-~~p~~~~s~l~c 199 (766)
.-|.++ ++.|+.|-..|+.+|.- ..-.+.-..|+.
T Consensus 192 ~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av~~~e~~n~l~~ 243 (554)
T KOG0119|consen 192 SDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAVSVPEGQNDLKR 243 (554)
T ss_pred CcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhccCccccccccH
Confidence 334333 45799999999999964 344444444444
No 58
>PRK00468 hypothetical protein; Provisional
Probab=95.01 E-value=0.024 Score=48.03 Aligned_cols=32 Identities=22% Similarity=0.484 Sum_probs=22.4
Q ss_pred hhccccCCCCcHHHHHHHhhCceEEEeCceEE
Q psy8224 135 AIGRLAGKGGRTKFTIENITKTRIVIADSKIH 166 (766)
Q Consensus 135 ~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~ 166 (766)
=+||||||+|+|.++|-.+-.+-=.=.|++|.
T Consensus 40 D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~ 71 (75)
T PRK00468 40 DMGKVIGKQGRIAKAIRTVVKAAAIKENKRVV 71 (75)
T ss_pred hCcceecCCChhHHHHHHHHHHHHhcCCCEEE
Confidence 37999999999999998865443222344433
No 59
>KOG3612|consensus
Probab=94.86 E-value=0.0053 Score=68.67 Aligned_cols=98 Identities=20% Similarity=0.355 Sum_probs=65.6
Q ss_pred HHHHHHHHhccccccCCCChhHH-HHHHHHHHHhhhhccccccccccccccccccccccCCCCcccccCCcccCCCCCCC
Q psy8224 254 LEMFLDKFQAQDSVLHDQNQHIV-QAKLALLQIYETSVEDQKCQLNVDDQKCQLNVDKKMDSGKCEVCKVAASLKCGGCN 332 (766)
Q Consensus 254 ~e~~l~k~~~~~~~l~p~~~~~~-~~k~~l~~~yg~~ll~e~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~C~~C~ 332 (766)
+|..=.++...-..++-|-.+.+ +-+..|-+.....+.++.-.|. .+-+-.++..-+..=|..|..++.+.| |-
T Consensus 469 ~e~~q~~~~~~l~~~~~~~~~em~~~r~tlE~k~~~n~~e~~kkl~---~~~qr~l~etKkKQWC~nC~~EAiy~C--CW 543 (588)
T KOG3612|consen 469 FEELQQTSRRELPVPLRNFELEMAEMRKTLEQKHAENIKEEIKKLA---EEHQRALAETKKKQWCYNCLDEAIYHC--CW 543 (588)
T ss_pred HHHHHHHHhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHhhhHHHHHHh--hc
Confidence 33333444433223455555555 4445666677766666544332 222334444566788999999998888 88
Q ss_pred CcccCCchhhccccccccCCCccc
Q psy8224 333 QVFYCSKSHQKQHWKEHKPGCAKY 356 (766)
Q Consensus 333 ~v~YCs~~cq~~~w~~Hk~~C~~l 356 (766)
...|||-+||+.||+.|+..|..-
T Consensus 544 NTSYCsveCQQ~HW~~H~ksCrrk 567 (588)
T KOG3612|consen 544 NTSYCSVECQQGHWPEHRKSCRRK 567 (588)
T ss_pred cccccCcchhhccchhHhhhhccc
Confidence 999999999999999999999654
No 60
>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=94.69 E-value=0.058 Score=64.82 Aligned_cols=64 Identities=11% Similarity=0.134 Sum_probs=58.5
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVY 98 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~ 98 (766)
-+..+.||+++++.|||..|++++.|.+.+|++|.|+- +|.|.|.. .|...+.+|..+|+.+..
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-dG~V~i~~----~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-DGTVKIAA----SDGEAAEAAIKMIEGITA 614 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-CeEEEEEE----CcHHHHHHHHHHHHhhhc
Confidence 56889999999999999999999999999999999985 79999987 477899999999998854
No 61
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.67 E-value=0.027 Score=47.52 Aligned_cols=20 Identities=35% Similarity=0.630 Sum_probs=17.8
Q ss_pred hccccCCCCcHHHHHHHhhC
Q psy8224 136 IGRLAGKGGRTKFTIENITK 155 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~ 155 (766)
+||+|||+|+|++||-.+-.
T Consensus 41 ~GkvIGk~GRti~AIRTll~ 60 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTLLS 60 (76)
T ss_pred ccceecCCChhHHHHHHHHH
Confidence 89999999999999988643
No 62
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=94.43 E-value=0.065 Score=62.35 Aligned_cols=68 Identities=15% Similarity=0.201 Sum_probs=61.9
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCh
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDV 102 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~ 102 (766)
....+.||++.++-+||+.|++++.|.+.+|++|.|+ ++|+|.|-+ .|...+.+|++.|..|.+.+.+
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-ddGtv~i~~----s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-DDGTVKIAA----SDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-CCCcEEEEe----cchHHHHHHHHHHHHHHhhccc
Confidence 5678999999999999999999999999999999999 899999998 4778999999999999865543
No 63
>KOG2084|consensus
Probab=94.26 E-value=0.041 Score=63.11 Aligned_cols=114 Identities=15% Similarity=0.201 Sum_probs=84.7
Q ss_pred hHHHHHHHHHHhhcCCCCc---ccccceeecccC--CceecCCCCCCCCCcccCCCCCcccHHHHHHHHHHHHHHHhccc
Q psy8224 173 NVQVALKALSNLILGSPPN---KVYGGILCSRCR--HHVISTNPLDNLAKWKCIMCSHTLTAKQIAMGNDSIKSELAGLD 247 (766)
Q Consensus 173 ~l~~ar~~i~~~~~~~~p~---~~~s~l~c~~c~--g~~l~~~pl~~~~~W~C~~C~~~~~~~~v~~~~~~~~~e~~~~~ 247 (766)
.++..+.+-|.|-+|.+|. ++++.++|..|. +.+.+..+...+..|.|..|.......+|.........+ ..+
T Consensus 258 ~l~~~~~f~c~c~rc~d~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~--~~~ 335 (482)
T KOG2084|consen 258 QLRQSKLFSCQCPRCLDPTELGTFLSSLRCENCTCGGLLGTSFLDKEDLQWPCTECALVRLKAYVVESREELQNE--LLD 335 (482)
T ss_pred HHhhccceeeecCCCCCCCccccchhhhhhcCCCCCCccCCCcccccCCCccccccccchhHHHHHHHHHHHHhh--ccc
Confidence 5666667888899999884 489999997764 446666665578899999999999999999999988877 222
Q ss_pred C-CChhhHHHHHHHHhccccccCCCChhHHHHHHHHHHHhhhhcc
Q psy8224 248 K-TEPTGLEMFLDKFQAQDSVLHDQNQHIVQAKLALLQIYETSVE 291 (766)
Q Consensus 248 ~-~~~~~~e~~l~k~~~~~~~l~p~~~~~~~~k~~l~~~yg~~ll 291 (766)
. .+....|.++.+.. .+.+++|+.....+..+..+++....
T Consensus 336 ~~~~~~~~e~l~~~~~---~~~~~~~~~~~~~~~~~~~il~~~~~ 377 (482)
T KOG2084|consen 336 AFSDLLIEELLLLRQE---SLELPNDFEVLLLKLHLLFILGSLLG 377 (482)
T ss_pred cCChhhhHHHHHHHHH---hhhCcchHHHHHHHHHHHHHHHHHHh
Confidence 2 23333444555554 78999999999888777777766553
No 64
>KOG1141|consensus
Probab=94.22 E-value=0.025 Score=65.83 Aligned_cols=58 Identities=21% Similarity=0.399 Sum_probs=41.0
Q ss_pred hcccCCCCCCCeEEE--EEe-CC---eEEEEEEecccCCCCeEEeecCCCCCCHHHHHHHHhCCCCcEEecc
Q psy8224 624 TAMLSHNCKPNTKHV--IVN-ED---FSLQLIALVNIRKGDIISTTYTQPFWGTMDRRLHLRMSKCFDCTCD 689 (766)
Q Consensus 624 ~s~~NHsC~PN~~~~--~~~-~g---~~l~vra~r~I~~GeeI~isY~~~~~~~~~Rr~~L~~~y~F~C~C~ 689 (766)
.-++||||+||+.+. |++ ++ .-+.+.|.+-|++|.|||.-|....-..+ ..-..|+|-
T Consensus 1190 GRfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~g~v~--------~keL~C~CG 1253 (1262)
T KOG1141|consen 1190 GRFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQGQVA--------TKELTCHCG 1253 (1262)
T ss_pred hhhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccccccc--------cceEEEecC
Confidence 346899999998654 443 12 23566778899999999999987654442 345778874
No 65
>KOG1085|consensus
Probab=93.82 E-value=0.037 Score=57.32 Aligned_cols=46 Identities=22% Similarity=0.300 Sum_probs=39.4
Q ss_pred hcccCCCCCCCeEEEEE--eCCeEEEEEEecccCCCCeEEeecCCCCC
Q psy8224 624 TAMLSHNCKPNTKHVIV--NEDFSLQLIALVNIRKGDIISTTYTQPFW 669 (766)
Q Consensus 624 ~s~~NHsC~PN~~~~~~--~~g~~l~vra~r~I~~GeeI~isY~~~~~ 669 (766)
.-|||||=.+|+....+ +...++++.|.|+|.+||||+.-|+|...
T Consensus 334 GRLINHS~~gNl~TKvv~Idg~pHLiLvA~rdIa~GEELlYDYGDRSk 381 (392)
T KOG1085|consen 334 GRLINHSVRGNLKTKVVEIDGSPHLILVARRDIAQGEELLYDYGDRSK 381 (392)
T ss_pred hhhhcccccCcceeeEEEecCCceEEEEeccccccchhhhhhccccch
Confidence 45899999999977664 44579999999999999999999998754
No 66
>PRK01064 hypothetical protein; Provisional
Probab=93.30 E-value=0.036 Score=47.23 Aligned_cols=33 Identities=27% Similarity=0.423 Sum_probs=25.0
Q ss_pred hhccccCCCCcHHHHHHHhhCceEEEeCceEEE
Q psy8224 135 AIGRLAGKGGRTKFTIENITKTRIVIADSKIHV 167 (766)
Q Consensus 135 ~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~i 167 (766)
-+||+|||+|+|+++|..+.++--.-.+++|.+
T Consensus 40 D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~l 72 (78)
T PRK01064 40 DIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSL 72 (78)
T ss_pred cceEEECCCCccHHHHHHHHHHHHhhCCCEEEE
Confidence 379999999999999999866544445555443
No 67
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=93.23 E-value=0.09 Score=63.89 Aligned_cols=61 Identities=16% Similarity=0.292 Sum_probs=53.2
Q ss_pred hhhccccCCCCcHHHHHHHhhCce-EEEeC-ceEEEEcch-hhHHHHHHHHHHhhcCCCCcccc
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTR-IVIAD-SKIHVLGSY-QNVQVALKALSNLILGSPPNKVY 194 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~-I~v~~-~~v~iiG~~-~~l~~ar~~i~~~~~~~~p~~~~ 194 (766)
..+|.|||+||+|+|.|+.-||+. |.|.+ .+|.|.|.- +.++.|+..|..+..--.-|.+|
T Consensus 694 ~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy 757 (891)
T PLN00207 694 EKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIY 757 (891)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEE
Confidence 459999999999999999999999 98865 569998854 58999999999999866678888
No 68
>KOG1080|consensus
Probab=93.11 E-value=0.04 Score=67.58 Aligned_cols=43 Identities=21% Similarity=0.467 Sum_probs=35.6
Q ss_pred ccccccccccCCceeee--ecCccchhhhhhhcccCCCeeeeccc
Q psy8224 559 KTAMLSHNCKPNTKHVI--VNEDFSLQLIALVNICKGDIISTTYT 601 (766)
Q Consensus 559 ~~SllNHSC~PN~~~~f--~~~~~~l~~~A~r~I~~GeeI~~sY~ 601 (766)
.+.++||||.|||..-. +++...+++.|.|+|.+||||+..|.
T Consensus 939 iAr~InHsC~PNCyakvi~V~g~~~IvIyakr~I~~~EElTYDYk 983 (1005)
T KOG1080|consen 939 IARFINHSCNPNCYAKVITVEGDKRIVIYSKRDIAAGEELTYDYK 983 (1005)
T ss_pred hhheeecccCCCceeeEEEecCeeEEEEEEecccccCceeeeecc
Confidence 57899999999996322 25555799999999999999999986
No 69
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.84 E-value=0.0097 Score=50.16 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=23.3
Q ss_pred hccccCCCCcHHHHHHHhhCceEEEeCceE
Q psy8224 136 IGRLAGKGGRTKFTIENITKTRIVIADSKI 165 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~I~v~~~~v 165 (766)
.||+|||+|+|+.+||.+++..+.-+++.+
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~ 69 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNAAANKHGKRV 69 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHHHHHHT-SS-
T ss_pred cceEECCCCeeHHHHHHHHHHHHHhCCCEE
Confidence 799999999999999999877654444433
No 70
>KOG2192|consensus
Probab=92.58 E-value=0.4 Score=49.33 Aligned_cols=137 Identities=16% Similarity=0.245 Sum_probs=87.3
Q ss_pred eEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEE-cccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhc
Q psy8224 31 MRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFN-LKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALL 109 (766)
Q Consensus 31 ~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~-~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll 109 (766)
...|.+-..--|+++|+.|+-++.|...++..|.+- +.+-.-.+.-+.+.+....| -+++|--+-.||+..+--+|
T Consensus 49 e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~i--lk~iip~lee~f~~~~pce~- 125 (390)
T KOG2192|consen 49 ELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEI--LKKIIPTLEEGFQLPSPCEL- 125 (390)
T ss_pred eEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHH--HHHHhhhhhhCCCCCCchhh-
Confidence 345777888899999999999999999999999984 33222222222222222223 34777777777764443222
Q ss_pred ccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeC-------ceEEEE-cchhhHHHHHHHH
Q psy8224 110 RLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIAD-------SKIHVL-GSYQNVQVALKAL 181 (766)
Q Consensus 110 ~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~-------~~v~ii-G~~~~l~~ar~~i 181 (766)
+ -++ |- ..-|-|||++|.-+|.+-+...+++.|.- ..|.|+ |...++-..-+.|
T Consensus 126 r------------lli-----hq-s~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~i 187 (390)
T KOG2192|consen 126 R------------LLI-----HQ-SLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKII 187 (390)
T ss_pred h------------hhh-----hh-hhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHH
Confidence 1 111 11 34799999999999999999999988851 235555 4555655555555
Q ss_pred HHhhcCC
Q psy8224 182 SNLILGS 188 (766)
Q Consensus 182 ~~~~~~~ 188 (766)
.+++.-+
T Consensus 188 l~~i~e~ 194 (390)
T KOG2192|consen 188 LDLISES 194 (390)
T ss_pred HHHhhcC
Confidence 5555433
No 71
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=92.31 E-value=0.1 Score=42.39 Aligned_cols=27 Identities=26% Similarity=0.394 Sum_probs=24.6
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEE
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVI 160 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v 160 (766)
.-+|+.|||+|++++.++.++|-+|-|
T Consensus 34 ~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 34 DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 448999999999999999999988876
No 72
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=92.16 E-value=0.026 Score=44.33 Aligned_cols=43 Identities=30% Similarity=0.754 Sum_probs=36.6
Q ss_pred ccccCC----cccCCCCCCCCcccCCchhhccccccccCCCcccccc
Q psy8224 317 CEVCKV----AASLKCGGCNQVFYCSKSHQKQHWKEHKPGCAKYKVV 359 (766)
Q Consensus 317 C~~C~~----~~~~~C~~C~~v~YCs~~cq~~~w~~Hk~~C~~l~v~ 359 (766)
|.+|.+ +....|+.|....|||+++-..|.+.|+..|..++.+
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~D~e~H~~~c~~LRqv 48 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIPTHCSEEHWEDDYEEHRQLCERLRQV 48 (55)
T ss_pred CCCCccccccccCCcCCCCCCcCccCHHHHHHhHHHHHHHHHHHHHh
Confidence 677777 5677899999999999999999988899899877653
No 73
>KOG2061|consensus
Probab=91.95 E-value=0.12 Score=55.86 Aligned_cols=48 Identities=33% Similarity=0.778 Sum_probs=43.2
Q ss_pred CCcccccCCcccCCCCCCCCcccCCchhhcccccc-ccCCCcccccccc
Q psy8224 314 SGKCEVCKVAASLKCGGCNQVFYCSKSHQKQHWKE-HKPGCAKYKVVRN 361 (766)
Q Consensus 314 ~~~C~~C~~~~~~~C~~C~~v~YCs~~cq~~~w~~-Hk~~C~~l~v~~s 361 (766)
...|..|+..+...|++|+...|||..||..||.. |+.+|....+...
T Consensus 136 ~~~~~~~~~~a~~~~~~~~~a~~~S~~~q~~d~~~~~~~a~aq~~~~~~ 184 (362)
T KOG2061|consen 136 ADLCGSCGCSAPAACSPCKAAAYCSKKHQSLDWPKGHKDACAQPSTLGE 184 (362)
T ss_pred cchhccCcccCcccccccchhhhcCchhhcccccccccccccCcccccc
Confidence 47899999999999999999999999999999999 9999988766543
No 74
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=91.80 E-value=0.24 Score=51.65 Aligned_cols=57 Identities=18% Similarity=0.328 Sum_probs=48.8
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC-ceEEEEcchh-hHHHHHHHHHHhhcCCCC
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD-SKIHVLGSYQ-NVQVALKALSNLILGSPP 190 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~-~~v~iiG~~~-~l~~ar~~i~~~~~~~~p 190 (766)
..++|+||++|++++.|...|++.|.|.. ..|.|-|... .+..|+++|.++-+-.|-
T Consensus 154 ~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 154 VKVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred HHHHhhcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 44899999999999999999999999986 4588888876 788999999998865543
No 75
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=91.58 E-value=0.23 Score=57.97 Aligned_cols=67 Identities=22% Similarity=0.331 Sum_probs=58.3
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEe-CceEEEEcch-hhHHHHHHHHHHhhcCCCCcccccceeec
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIA-DSKIHVLGSY-QNVQVALKALSNLILGSPPNKVYGGILCS 200 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~-~~~v~iiG~~-~~l~~ar~~i~~~~~~~~p~~~~s~l~c~ 200 (766)
-.++-+||++|+++++|-..||+.|.|. +.||.|-++. +.++.||+.|.++.+-..-+.+|....-.
T Consensus 561 dKI~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~r 629 (692)
T COG1185 561 DKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVR 629 (692)
T ss_pred HHHhhccCCcccchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEE
Confidence 3478899999999999999999999997 4779998888 57999999999999888888888766553
No 76
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=91.27 E-value=0.47 Score=45.30 Aligned_cols=100 Identities=15% Similarity=0.156 Sum_probs=63.8
Q ss_pred EEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhh--c
Q psy8224 32 RKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALAL--L 109 (766)
Q Consensus 32 ~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~l--l 109 (766)
--..|.+..+|..+|++|...+.|.+..|-+|++ -. -+.||. +||+. -|+|.+-..+ .
T Consensus 35 iifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV---------Ve--ys~D~~------~fI~N---~l~PA~V~~V~i~ 94 (141)
T TIGR01952 35 VVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL---------IE--YSENLE------EFVAN---KLAPAEVKNVTVS 94 (141)
T ss_pred EEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE---------EE--cCCCHH------HHHHH---cCCCceEEEEEEE
Confidence 3456777899999999999999998877755544 21 235764 34433 3555443333 1
Q ss_pred ccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEe
Q psy8224 110 RLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA 161 (766)
Q Consensus 110 ~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~ 161 (766)
+.++-.. ..+.-. .+-+|+.|||+|++.+-...++|-++-|.
T Consensus 95 ~~~~~~~-----a~V~V~-----~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 95 EFNGKKV-----AYVEVH-----PRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred cCCCCEE-----EEEEEC-----hhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 1111110 001011 25589999999999999999999888654
No 77
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=91.13 E-value=0.23 Score=59.95 Aligned_cols=65 Identities=20% Similarity=0.339 Sum_probs=54.6
Q ss_pred hhccccCCCCcHHHHHHHhhCceEEEeC-ceEEEEc-chhhHHHHHHHHHHhhcCCCCcccccceee
Q psy8224 135 AIGRLAGKGGRTKFTIENITKTRIVIAD-SKIHVLG-SYQNVQVALKALSNLILGSPPNKVYGGILC 199 (766)
Q Consensus 135 ~~griiG~~G~t~~~ie~~t~~~I~v~~-~~v~iiG-~~~~l~~ar~~i~~~~~~~~p~~~~s~l~c 199 (766)
.+|.+||+||+|++.|+..||+.|.+.+ .+|.|.+ +.+.++.|++.|..+..-...|.+|....-
T Consensus 564 kI~~vIG~gg~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~ 630 (693)
T PRK11824 564 KIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVV 630 (693)
T ss_pred HHHHHhcCCchhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEE
Confidence 4899999999999999999999999974 6788888 455899999999999987677776655444
No 78
>PF13014 KH_3: KH domain
Probab=90.93 E-value=0.23 Score=37.12 Aligned_cols=35 Identities=17% Similarity=0.143 Sum_probs=29.8
Q ss_pred chhhhccCcccHHHHHHhcCcEEEEEc------ccCeEEEE
Q psy8224 41 YGPLKENWMKIFTPIVEHLKLQVRFNL------KSRNVEIR 75 (766)
Q Consensus 41 ~~~l~~~~~~i~~~i~~~~~~~i~i~~------~~~~v~i~ 75 (766)
+++|||+.|..++.|++.++++|.|.. .++.|+|+
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~ 42 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTIT 42 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEE
Confidence 578999999999999999999999976 45555554
No 79
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=90.89 E-value=0.18 Score=50.06 Aligned_cols=31 Identities=32% Similarity=0.475 Sum_probs=27.9
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeCce
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIADSK 164 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~~~ 164 (766)
.-+|-|||+.|.|.+.+|..|+++|.|-|+-
T Consensus 163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 3489999999999999999999999998753
No 80
>KOG1079|consensus
Probab=90.57 E-value=0.25 Score=57.04 Aligned_cols=43 Identities=21% Similarity=0.348 Sum_probs=36.1
Q ss_pred cccCCCCCCCeEE--EEEeCCeEEEEEEecccCCCCeEEeecCCC
Q psy8224 625 AMLSHNCKPNTKH--VIVNEDFSLQLIALVNIRKGDIISTTYTQP 667 (766)
Q Consensus 625 s~~NHsC~PN~~~--~~~~~g~~l~vra~r~I~~GeeI~isY~~~ 667 (766)
-++|||=.||+.. ++++..+++-++|.|.|.+|||||..|...
T Consensus 667 rFANHS~nPNCYAkvm~V~GdhRIGifAkRaIeagEELffDYrYs 711 (739)
T KOG1079|consen 667 RFANHSFNPNCYAKVMMVAGDHRIGIFAKRAIEAGEELFFDYRYS 711 (739)
T ss_pred hhccCCCCCCcEEEEEEecCCcceeeeehhhcccCceeeeeeccC
Confidence 3679999999954 335656899999999999999999999764
No 81
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=90.54 E-value=0.31 Score=59.35 Aligned_cols=65 Identities=15% Similarity=0.197 Sum_probs=58.8
Q ss_pred CceEEEecCCCcchhhhccCcccHHHHHHhcCcE-EEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Q psy8224 29 VDMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQ-VRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVY 98 (766)
Q Consensus 29 ~~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~-i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~ 98 (766)
+-+..+.||+++++.|||..|++++.|.+.+|++ |.++- +|.|.|-. .|...+.+|+++|+.+..
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-dg~V~I~a----~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-DGTVKITA----KDLSSLEKSKAIISSLTM 749 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-CeeEEEEe----CCHHHHHHHHHHHHHHhc
Confidence 3678899999999999999999999999999999 88875 69999887 578899999999998875
No 82
>KOG2192|consensus
Probab=89.12 E-value=0.55 Score=48.30 Aligned_cols=53 Identities=26% Similarity=0.334 Sum_probs=47.8
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC-------ceEEEEcchhhHHHHHHHHHHhhc
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD-------SKIHVLGSYQNVQVALKALSNLIL 186 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~-------~~v~iiG~~~~l~~ar~~i~~~~~ 186 (766)
-.-|-||||+|+-++.|-.-+|+.|.|.. .-+.|-|+.++|..|.+....|.+
T Consensus 324 dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vk 383 (390)
T KOG2192|consen 324 DLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVK 383 (390)
T ss_pred ccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHH
Confidence 45789999999999999999999999964 558899999999999999988875
No 83
>KOG2191|consensus
Probab=88.92 E-value=1 Score=48.06 Aligned_cols=60 Identities=20% Similarity=0.190 Sum_probs=52.6
Q ss_pred eEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEE--------cccCeEEEEeCCCCCCHHHHHHHHHHHHH
Q psy8224 31 MRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFN--------LKSRNVEIRLSPETEDISNLQKAADFVKA 95 (766)
Q Consensus 31 ~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~--------~~~~~v~i~~~~~t~d~~~~~ka~~~i~a 95 (766)
..+|.+|...-+.+||+.|.+++.|.|+++..|+|- +.++.|+|.. +|...+||.++|-+
T Consensus 133 qikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sg-----e~e~~~~A~~~IL~ 200 (402)
T KOG2191|consen 133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSG-----EPEQNMKAVSLILQ 200 (402)
T ss_pred eeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecC-----CHHHHHHHHHHHHH
Confidence 368999999999999999999999999999999985 4566666665 89999999999965
No 84
>KOG2279|consensus
Probab=88.67 E-value=0.36 Score=54.62 Aligned_cols=108 Identities=14% Similarity=0.120 Sum_probs=73.9
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEccc---CeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHH
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKS---RNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDAL 106 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~---~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~ 106 (766)
-.-++.||..-+..++|+-|.-+++|.+.++.++.++.++ ..+.+... -|..+-+|+..+-.
T Consensus 68 v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~----~p~~v~~a~a~~~~----------- 132 (608)
T KOG2279|consen 68 IEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISG----FPVQVCKAKAAIHQ----------- 132 (608)
T ss_pred eeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhcc----CCCCCChHHHHHHH-----------
Confidence 4567899999999999999999999999999999886432 22222221 12222233322221
Q ss_pred hhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCc
Q psy8224 107 ALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADS 163 (766)
Q Consensus 107 ~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~ 163 (766)
++++.. .+.......+|..|||+|++|.|.+.|+..++++|.+..+
T Consensus 133 ~~~~~~-----------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n 178 (608)
T KOG2279|consen 133 ILTENT-----------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN 178 (608)
T ss_pred HHhcCC-----------cccccccchhhhcccccccchhhhcchhcccccccccccc
Confidence 222211 1223334566999999999999999999999999999754
No 85
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=87.97 E-value=0.96 Score=45.12 Aligned_cols=61 Identities=26% Similarity=0.341 Sum_probs=52.1
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeCc--eEEEEcc---hh--hHHHHHHHHHHhhcCCCCcccc
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIADS--KIHVLGS---YQ--NVQVALKALSNLILGSPPNKVY 194 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~~--~v~iiG~---~~--~l~~ar~~i~~~~~~~~p~~~~ 194 (766)
.+.|=+||+.|.+++.||..+++.|.|+.+ +|.|..+ .+ .+..|+++|..+-+|=+|..-+
T Consensus 17 ~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~ 84 (194)
T COG1094 17 DRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKAL 84 (194)
T ss_pred hhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHH
Confidence 568999999999999999999999999865 4888766 34 4669999999999999997643
No 86
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=87.88 E-value=1.1 Score=46.68 Aligned_cols=64 Identities=9% Similarity=-0.002 Sum_probs=57.6
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVY 98 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~ 98 (766)
.-+.+.||++.++-|+|..+.+.+.|.+.++++|.+.. +|.|-|.+ .++..+.+|..+|+.+.+
T Consensus 145 ~G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-NG~VwI~~----~~~~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 145 GGTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-NGRIWIKG----PDEEDEEIAIEAIKKIER 208 (235)
T ss_pred CCEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-CcEEEEee----CCHHHHHHHHHHHHHHHh
Confidence 35779999999999999999999999999999999876 59999998 588899999999998865
No 87
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=87.62 E-value=0.72 Score=46.31 Aligned_cols=103 Identities=16% Similarity=0.119 Sum_probs=64.1
Q ss_pred EEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhccc
Q psy8224 32 RKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALLRL 111 (766)
Q Consensus 32 ~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll~~ 111 (766)
....+-.+-+|..+|+||...+.|.+.+|=+|++ |.- ..||..+ +.+|++ |.+-+.+.-.
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV--------Ve~---s~d~~~f-----I~nal~----Pa~v~~V~~~ 137 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV--------VEW---SEDPAEF-----IKNALA----PAEVLSVNIK 137 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEE--------EEe---CCCHHHH-----HHHhcC----cceEeEEEEE
Confidence 4444556778999999999999999999843332 121 2466432 233332 3333333211
Q ss_pred c-cceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCce
Q psy8224 112 D-NLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSK 164 (766)
Q Consensus 112 d-~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~ 164 (766)
+ |-- ...+ ....+.+++.|||+|++.+.+..+||-+|-|..-.
T Consensus 138 ~~d~~-----~~~v-----~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~~ 181 (190)
T COG0195 138 EDDGH-----VAIV-----VVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETIS 181 (190)
T ss_pred eCCCc-----EEEE-----EECHHHHhhccCcccHHHHHHHHHhCCEEEEEehh
Confidence 1 110 0111 01125689999999999999999999999987543
No 88
>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=87.17 E-value=0.29 Score=41.69 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=23.0
Q ss_pred hccccCCCCcHHHHHHHhhCceEEEe
Q psy8224 136 IGRLAGKGGRTKFTIENITKTRIVIA 161 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~I~v~ 161 (766)
.|++|||+|+|+.|||-+++..+.-.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHHhhc
Confidence 69999999999999999998776643
No 89
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=87.03 E-value=12 Score=38.16 Aligned_cols=137 Identities=9% Similarity=0.036 Sum_probs=93.1
Q ss_pred eEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhcc
Q psy8224 31 MRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALLR 110 (766)
Q Consensus 31 ~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll~ 110 (766)
...|.+++.-+-.|-...+.+.+.|....|.+|.+....+.|.|++++ ..+.-+.+-|.-+.
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~~~i~I~g~k-----~~~~~i~~~i~~~l------------- 88 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRSENRIRITGTK-----STAEYIEASINEIL------------- 88 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecCCcEEEEEccH-----HHHHHHHHHHHHHH-------------
Confidence 345666677777888888899899988899999999999999999833 34444444444332
Q ss_pred cccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCce--EEEEc-----chhhHHHHHHHHHH
Q psy8224 111 LDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSK--IHVLG-----SYQNVQVALKALSN 183 (766)
Q Consensus 111 ~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~--v~iiG-----~~~~l~~ar~~i~~ 183 (766)
..+.-+.|++..+...- - ....+ --....+..|+.+|+|+|...++. +.|.+ ..+.+..|++.+.-
T Consensus 89 -~~i~~~~i~l~~~~~~~---~-~~~~~--~~~~~~l~~i~~~t~~~ie~~~~~~~~~i~~~~~~~~~~~~~~a~RlL~~ 161 (210)
T PF14611_consen 89 -SNIRTEEIDLSPIISKH---S-EKKNS--QFTPDLLEEIQKLTNVYIEKNPDGNKLKISWLASPENEKRADRAKRLLLW 161 (210)
T ss_pred -hhcEEEEEecchhhhhh---c-ccccc--cccHHHHHHHHHHHcEEEEECCCCCeEEEEEEeeccccchHHHHHHHHHH
Confidence 23555667777653211 0 00111 113668899999999999987654 44443 44579999999998
Q ss_pred hhcCCCCcc
Q psy8224 184 LILGSPPNK 192 (766)
Q Consensus 184 ~~~~~~p~~ 192 (766)
.....++.+
T Consensus 162 a~~~~~~~~ 170 (210)
T PF14611_consen 162 ALDYNPHSQ 170 (210)
T ss_pred hccCCcccc
Confidence 886555544
No 90
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=86.99 E-value=0.27 Score=56.89 Aligned_cols=50 Identities=18% Similarity=0.434 Sum_probs=40.2
Q ss_pred ccccccccccCCceeeeecCc--cchhhhhhhcccCCCeeeecccCCCCCcc
Q psy8224 559 KTAMLSHNCKPNTKHVIVNED--FSLQLIALVNICKGDIISTTYTQPFWGTM 608 (766)
Q Consensus 559 ~~SllNHSC~PN~~~~f~~~~--~~l~~~A~r~I~~GeeI~~sY~~~~~~~~ 608 (766)
.+.++||||.||+....+... ..+...|+++|.+||||+..|...++...
T Consensus 405 ~~r~~nHS~~pN~~~~~~~~~g~~~~~~~~~rDI~~geEl~~dy~~~~~~~~ 456 (480)
T COG2940 405 VARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPSLEDNR 456 (480)
T ss_pred ccceeecCCCCCcceecccccccceeeecccccchhhhhhccccccccccch
Confidence 456899999999987753332 36778999999999999999998776654
No 91
>KOG2814|consensus
Probab=86.85 E-value=0.85 Score=48.80 Aligned_cols=66 Identities=30% Similarity=0.399 Sum_probs=50.0
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEe-----CceEEEEcc-hhhHHHHHHHHHHhhc---CCCCcccccceee
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIA-----DSKIHVLGS-YQNVQVALKALSNLIL---GSPPNKVYGGILC 199 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~-----~~~v~iiG~-~~~l~~ar~~i~~~~~---~~~p~~~~s~l~c 199 (766)
-..|-|||++|+|++-||+-|+|+|.+. ...|.|+|- .+.+..|.+-|.-+|. -+-|.++|=++-+
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p~thflal~l 140 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDRKSFPITHFLALPL 140 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhhhcCchhhhhhhhc
Confidence 4589999999999999999999999994 223555544 4578888888888873 2567777755555
No 92
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=86.64 E-value=0.49 Score=47.60 Aligned_cols=53 Identities=23% Similarity=0.433 Sum_probs=40.2
Q ss_pred hccccCCCCcHHHHHHHhhCceEEEeCce---EEE-Ecchhh------HHHHHHHHHHhhcCC
Q psy8224 136 IGRLAGKGGRTKFTIENITKTRIVIADSK---IHV-LGSYQN------VQVALKALSNLILGS 188 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~I~v~~~~---v~i-iG~~~~------l~~ar~~i~~~~~~~ 188 (766)
.||+||++|+|..+||.+++.++.-.+.+ |.+ +|.|.. +++|.++-.+..+..
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV~~tg 164 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRERRKETLIKLAERAAERVLETG 164 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhhHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 79999999999999999999998875433 555 777762 556777666665433
No 93
>KOG1710|consensus
Probab=85.97 E-value=0.15 Score=53.19 Aligned_cols=29 Identities=28% Similarity=0.714 Sum_probs=26.7
Q ss_pred cccCCCCCc-cccCccCC--CCCCcHhhhhhh
Q psy8224 418 FYKCSDCGW-PLCAPRCK--SLPSHQKECKLM 446 (766)
Q Consensus 418 ~~~C~~C~~-~yCS~~C~--~~~~H~~EC~~l 446 (766)
..+|+.|+. .||+++|| +|-.|+.-|+.+
T Consensus 331 ~KrCs~CKav~YCdqeCQk~hWf~HKK~C~~L 362 (396)
T KOG1710|consen 331 KKRCSQCKAVAYCDQECQKFHWFIHKKVCSFL 362 (396)
T ss_pred cchhhhhHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 579999997 99999998 499999999988
No 94
>KOG1337|consensus
Probab=85.92 E-value=0.52 Score=54.43 Aligned_cols=77 Identities=14% Similarity=0.142 Sum_probs=54.4
Q ss_pred CCHHHHHHHHhhhccccccccccC-----CceeEEEeecccccccccccCCceeeeecCccchhhhhhhcccCCCeeeec
Q psy8224 525 VSEETILRIAGILDTNAFDIRRSV-----GKIKIRGIYMKTAMLSHNCKPNTKHVIVNEDFSLQLIALVNICKGDIISTT 599 (766)
Q Consensus 525 ~s~~~i~~i~~~l~~Naf~i~~~~-----~~~~~~gLyp~~SllNHSC~PN~~~~f~~~~~~l~~~A~r~I~~GeeI~~s 599 (766)
++.+.+....+++...+|...... ......+|.|..-++||++.+...-.+ ..+..+.+++.+++.+|+||+++
T Consensus 197 ~~~~~~~w~~~~~~sr~~~~~~~~~~~~~~~~~~~~L~P~~D~~NH~~~~~~~~~~-~~d~~~~l~~~~~v~~geevfi~ 275 (472)
T KOG1337|consen 197 FTFSAFKWAYSIVNSRAFYLPSLQRLTAGDPDDNEALAPLIDLLNHSPEVIKAGYN-QEDEAVELVAERDVSAGEEVFIN 275 (472)
T ss_pred cchHHHHHHHHHHhhhhhccccccccccCCCCcchhhhhhHHhhccCchhcccccc-CCCCcEEEEEeeeecCCCeEEEe
Confidence 344455556666666666554331 223446789999999999998443333 33337889999999999999999
Q ss_pred ccC
Q psy8224 600 YTQ 602 (766)
Q Consensus 600 Y~~ 602 (766)
||+
T Consensus 276 YG~ 278 (472)
T KOG1337|consen 276 YGP 278 (472)
T ss_pred cCC
Confidence 998
No 95
>PLN03158 methionine aminopeptidase; Provisional
Probab=84.74 E-value=0.29 Score=54.93 Aligned_cols=40 Identities=30% Similarity=0.687 Sum_probs=34.7
Q ss_pred CCCCcccccCCcccCCCCCCCC-------cccCCchhhccccccccC
Q psy8224 312 MDSGKCEVCKVAASLKCGGCNQ-------VFYCSKSHQKQHWKEHKP 351 (766)
Q Consensus 312 ~~~~~C~~C~~~~~~~C~~C~~-------v~YCs~~cq~~~w~~Hk~ 351 (766)
..+..|..|++++...|+.|.. .+|||.+|-+..|+.||.
T Consensus 7 ~~~~~c~~c~~~a~l~Cp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~ 53 (396)
T PLN03158 7 TSPLACARCSKPAHLQCPKCLELKLPREGASFCSQDCFKAAWSSHKS 53 (396)
T ss_pred CCcccccCCCCcccccCccchhcCCCCCCceeECHHHHHHHHHHHHH
Confidence 3456799999999999999974 789999999999999875
No 96
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=84.05 E-value=0.6 Score=37.85 Aligned_cols=23 Identities=17% Similarity=0.355 Sum_probs=21.3
Q ss_pred hccccCCCCcHHHHHHHhhCceE
Q psy8224 136 IGRLAGKGGRTKFTIENITKTRI 158 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~I 158 (766)
.|++||++|+++++|+.+++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 79999999999999999999665
No 97
>KOG0336|consensus
Probab=83.83 E-value=1.3 Score=48.71 Aligned_cols=53 Identities=26% Similarity=0.357 Sum_probs=45.1
Q ss_pred hccccCCCCcHHHHHHHhhCceEEEeC----ceEEEEcchhhHHHHHHHHHHhhcCC
Q psy8224 136 IGRLAGKGGRTKFTIENITKTRIVIAD----SKIHVLGSYQNVQVALKALSNLILGS 188 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~I~v~~----~~v~iiG~~~~l~~ar~~i~~~~~~~ 188 (766)
+|-+||++|..++-||+-|+|+|.|.. -.|.|.|.-.--+.|+.+|...++-.
T Consensus 58 vg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 58 VGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQDKD 114 (629)
T ss_pred hheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhhhhh
Confidence 999999999999999999999999863 45888888777778888888877433
No 98
>KOG1338|consensus
Probab=83.13 E-value=0.33 Score=52.91 Aligned_cols=132 Identities=17% Similarity=0.096 Sum_probs=77.7
Q ss_pred CCCHHHHHHHHhhhccccccccccC----------CceeEEEeeccccccccccc-CCceeeeecCccchhhhhhhcccC
Q psy8224 524 DVSEETILRIAGILDTNAFDIRRSV----------GKIKIRGIYMKTAMLSHNCK-PNTKHVIVNEDFSLQLIALVNICK 592 (766)
Q Consensus 524 ~~s~~~i~~i~~~l~~Naf~i~~~~----------~~~~~~gLyp~~SllNHSC~-PN~~~~f~~~~~~l~~~A~r~I~~ 592 (766)
.++-+.++.+.+++..-+|.+.... -...+-..-|.+-++||.-. -|+...+ +++.+.|+|.|+|.+
T Consensus 173 ~~slEdF~y~~Al~laysfdve~~~s~~~~eee~e~e~ngk~m~p~ad~lNhd~~k~nanl~y--~~NcL~mva~r~iek 250 (466)
T KOG1338|consen 173 RPSLEDFMYAYALGLAYSFDVEFLLSLDNLEEESEIECNGKLMTPIADFLNHDGLKANANLRY--EDNCLEMVADRNIEK 250 (466)
T ss_pred ccCHHHHHHHHHHHHHHheeeehhcchhhhhhhhccccCcccccchhhhhccchhhcccceec--cCcceeeeecCCCCC
Confidence 3555666666666555555554321 12445567789999999875 5666665 556889999999999
Q ss_pred CCeeeecccCCCCCccccccccccchhhhhhhcccCC--CCCCCeEEEEEeCCeEEEEEEecccCCCCeEEeecCC
Q psy8224 593 GDIISTTYTQPFWGTMDRRLHLRMSKWIYMKTAMLSH--NCKPNTKHVIVNEDFSLQLIALVNIRKGDIISTTYTQ 666 (766)
Q Consensus 593 GeeI~~sY~~~~~~~~~r~~~~~i~~glyp~~s~~NH--sC~PN~~~~~~~~g~~l~vra~r~I~~GeeI~isY~~ 666 (766)
|++|.-+|+-.-.+ ....+.+..+..-+++. -|.-++...+ +.....++++.|.| |.++..+|+.
T Consensus 251 gdev~n~dg~~p~~------l~~l~ka~c~gihm~~g~~~l~niv~~l~-D~~~d~tm~~~R~i--l~ql~nt~te 317 (466)
T KOG1338|consen 251 GDEVDNSDGLKPMG------LLKLTKALCVGIHMVWGILKLYNIVQILM-DVPNDDTMRNMRLI--LLQLHNTRTE 317 (466)
T ss_pred ccccccccccCcch------hhhhhhhccceeeeecceeecchHHHHHh-cCCCcchHHHHHHH--HHHhccchhh
Confidence 99999999732111 12233333333222221 1111221222 22456778888888 6666666653
No 99
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=81.19 E-value=1.5 Score=53.09 Aligned_cols=64 Identities=13% Similarity=0.146 Sum_probs=56.0
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHc
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVY 98 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~ 98 (766)
-...+.||+++++.+||..|++++.|.+.+|.+|.++. +|.|.|.. .|...+.+|+++|+.+..
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d-~G~v~i~~----~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-DGTVKIAA----TDGEAAEAAKERIEGITA 617 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-CceEEEEc----ccHHHHHHHHHHHHHhcc
Confidence 45677889999999999999999999999999887754 69998886 477899999999998874
No 100
>KOG1082|consensus
Probab=75.92 E-value=1.3 Score=49.40 Aligned_cols=45 Identities=24% Similarity=0.498 Sum_probs=34.0
Q ss_pred ccccccccccCCceeeeecCc------cchhhhhhhcccCCCeeeecccCC
Q psy8224 559 KTAMLSHNCKPNTKHVIVNED------FSLQLIALVNICKGDIISTTYTQP 603 (766)
Q Consensus 559 ~~SllNHSC~PN~~~~f~~~~------~~l~~~A~r~I~~GeeI~~sY~~~ 603 (766)
.+-++||||.||.....+-.+ -++.+.|+++|.+|+|.+.-|+..
T Consensus 272 v~RfinHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~ 322 (364)
T KOG1082|consen 272 VARFINHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKA 322 (364)
T ss_pred ccccccCCCCccceeeeeeecCCccchheeeeeeccccCCCcccchhhccc
Confidence 455899999999875443211 134577889999999999999975
No 101
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=74.57 E-value=0.94 Score=31.25 Aligned_cols=27 Identities=33% Similarity=0.751 Sum_probs=20.9
Q ss_pred CcccccCCcccCCCCCCCCcccCCchhh
Q psy8224 315 GKCEVCKVAASLKCGGCNQVFYCSKSHQ 342 (766)
Q Consensus 315 ~~C~~C~~~~~~~C~~C~~v~YCs~~cq 342 (766)
..|..|+..+..+|++|. ..|||-+|-
T Consensus 3 ~~C~vC~~~~kY~Cp~C~-~~~CSl~C~ 29 (30)
T PF04438_consen 3 KLCSVCGNPAKYRCPRCG-ARYCSLACY 29 (30)
T ss_dssp EEETSSSSEESEE-TTT---EESSHHHH
T ss_pred CCCccCcCCCEEECCCcC-CceeCcEeE
Confidence 469999998899999997 559999885
No 102
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=73.46 E-value=1.2 Score=35.14 Aligned_cols=33 Identities=21% Similarity=0.642 Sum_probs=27.4
Q ss_pred cccCCCCCc-cccCccCCC--CCCcHhhhhhhhhcc
Q psy8224 418 FYKCSDCGW-PLCAPRCKS--LPSHQKECKLMKDNQ 450 (766)
Q Consensus 418 ~~~C~~C~~-~yCS~~C~~--~~~H~~EC~~l~~~~ 450 (766)
.+.|+.|++ .|||++=+. ...|+.-|..|+...
T Consensus 14 ~~~Cp~cGipthcS~ehw~~D~e~H~~~c~~LRqvN 49 (55)
T PF13824_consen 14 NFECPDCGIPTHCSEEHWEDDYEEHRQLCERLRQVN 49 (55)
T ss_pred CCcCCCCCCcCccCHHHHHHhHHHHHHHHHHHHHhc
Confidence 678999999 799999863 378999999998743
No 103
>KOG1085|consensus
Probab=71.96 E-value=1.5 Score=45.78 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=35.9
Q ss_pred cccccccccCCcee--eeecCccchhhhhhhcccCCCeeeecccCC
Q psy8224 560 TAMLSHNCKPNTKH--VIVNEDFSLQLIALVNICKGDIISTTYTQP 603 (766)
Q Consensus 560 ~SllNHSC~PN~~~--~f~~~~~~l~~~A~r~I~~GeeI~~sY~~~ 603 (766)
+-|+|||-.+|+.. +-++..-+++++|.++|..|||+..-||+.
T Consensus 334 GRLINHS~~gNl~TKvv~Idg~pHLiLvA~rdIa~GEELlYDYGDR 379 (392)
T KOG1085|consen 334 GRLINHSVRGNLKTKVVEIDGSPHLILVARRDIAQGEELLYDYGDR 379 (392)
T ss_pred hhhhcccccCcceeeEEEecCCceEEEEeccccccchhhhhhcccc
Confidence 35899999999753 222666689999999999999999999984
No 104
>KOG1067|consensus
Probab=70.83 E-value=2.9 Score=47.73 Aligned_cols=60 Identities=18% Similarity=0.211 Sum_probs=49.9
Q ss_pred hhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchh-hHHHHHHHHHHhh-cCCCCcccc
Q psy8224 135 AIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQ-NVQVALKALSNLI-LGSPPNKVY 194 (766)
Q Consensus 135 ~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~-~l~~ar~~i~~~~-~~~~p~~~~ 194 (766)
.+.-+||++|..+|-||.-||+.-.|++.|+.|+..-. .+..||++|..++ +-+.+.-++
T Consensus 607 k~~~lIGp~G~~~kki~~EtGai~~vDe~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~ 668 (760)
T KOG1067|consen 607 KRATLIGPGGVLKKKIEVETGAISQVDEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEF 668 (760)
T ss_pred hhheeecCccceeeeEeeeccceeeecCceEEEEecCHHHHHHHHHHHHHHhcCccccceEe
Confidence 36789999999999999999999999999999988765 6889999999988 434443333
No 105
>KOG2857|consensus
Probab=70.77 E-value=1.6 Score=40.93 Aligned_cols=38 Identities=29% Similarity=0.778 Sum_probs=26.2
Q ss_pred CCcccccCCCCCCCcccCCCCCcccCCCCCccccCccCCCCCCcHh--hhhhh
Q psy8224 396 PLCLGCHRTLKPTSMEENEPLSFYKCSDCGWPLCAPRCKSLPSHQK--ECKLM 446 (766)
Q Consensus 396 ~~C~~C~~~~~~~~~~~~~~~~~~~C~~C~~~yCS~~C~~~~~H~~--EC~~l 446 (766)
..|.-|.+... -++|+.|..+|||--|. ..|+. +|.--
T Consensus 6 ~tC~ic~e~~~-----------KYKCpkC~vPYCSl~Cf--KiHk~tPq~~~v 45 (157)
T KOG2857|consen 6 TTCVICLESEI-----------KYKCPKCSVPYCSLPCF--KIHKSTPQCETV 45 (157)
T ss_pred eeehhhhcchh-----------hccCCCCCCccccchhh--hhccCCcccccc
Confidence 45677766432 57899999999999995 34443 55443
No 106
>KOG1081|consensus
Probab=65.27 E-value=2.8 Score=48.11 Aligned_cols=54 Identities=22% Similarity=0.299 Sum_probs=41.0
Q ss_pred ccchhhhhhhc-ccCCCCCCCeEEEE--EeCCeEEEEEEecccCCCCeEEeecCCCC
Q psy8224 615 RMSKWIYMKTA-MLSHNCKPNTKHVI--VNEDFSLQLIALVNIRKGDIISTTYTQPF 668 (766)
Q Consensus 615 ~i~~glyp~~s-~~NHsC~PN~~~~~--~~~g~~l~vra~r~I~~GeeI~isY~~~~ 668 (766)
.+..+.++..+ +.||||.||+.-.- .....++.+.|.+.|++|+|++.+|.-.-
T Consensus 362 ~id~~~~~n~sr~~nh~~~~~v~~~k~~~~~~t~~~~~a~~~i~~g~e~t~~~n~~~ 418 (463)
T KOG1081|consen 362 IIDAGPKGNYSRFLNHSCQPNVETEKWQVIGDTRVGLFAPRQIEAGEELTFNYNGNC 418 (463)
T ss_pred ccccccccchhhhhcccCCCceeechhheecccccccccccccccchhhhheeeccc
Confidence 45566677655 66999999995442 11347889999999999999999998543
No 107
>KOG1141|consensus
Probab=64.79 E-value=4.5 Score=48.09 Aligned_cols=44 Identities=23% Similarity=0.459 Sum_probs=30.7
Q ss_pred ccccccccccCCce--eeeecC-ccc---hhhhhhhcccCCCeeeecccC
Q psy8224 559 KTAMLSHNCKPNTK--HVIVNE-DFS---LQLIALVNICKGDIISTTYTQ 602 (766)
Q Consensus 559 ~~SllNHSC~PN~~--~~f~~~-~~~---l~~~A~r~I~~GeeI~~sY~~ 602 (766)
.+-.+||||.||.. ++|++- +-+ +-+.+.+.|++|.|+++-|+=
T Consensus 1189 lGRfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Y 1238 (1262)
T KOG1141|consen 1189 LGRFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQY 1238 (1262)
T ss_pred hhhhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccc
Confidence 45679999999975 455331 112 334556899999999998863
No 108
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=64.02 E-value=12 Score=38.87 Aligned_cols=53 Identities=21% Similarity=0.362 Sum_probs=43.0
Q ss_pred hccccCCCCcHHHHHHHhhCceEEEeC-ceEEEEcchhh-HHHHHHHHHHhhcCC
Q psy8224 136 IGRLAGKGGRTKFTIENITKTRIVIAD-SKIHVLGSYQN-VQVALKALSNLILGS 188 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~I~v~~-~~v~iiG~~~~-l~~ar~~i~~~~~~~ 188 (766)
+=|+||++|...+.+...|+|+|.|.- ..|.+-|.-+. -.+|-.+|.+|-+-+
T Consensus 157 VpRvig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~ea 211 (239)
T COG1097 157 VPRVIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIEREA 211 (239)
T ss_pred cceEecCCCcHHHHhhhhcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhhhh
Confidence 457999999999999999999999964 56888888884 557777777766544
No 109
>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=61.71 E-value=1.1 Score=38.09 Aligned_cols=34 Identities=18% Similarity=0.294 Sum_probs=25.6
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEE-EeCceEEE
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIV-IADSKIHV 167 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~-v~~~~v~i 167 (766)
...|.+||++|++++.|....+-.+. +.++.|.+
T Consensus 34 ~~~~ivIGk~G~~ik~i~~~~~k~l~~~~~~~V~l 68 (78)
T PF07650_consen 34 SQPGIVIGKKGSNIKKIREELRKELEKLLNKKVFL 68 (78)
T ss_dssp SSHHHHHTGGGHHHHHHHHHHHHHHHHHCSSSEEE
T ss_pred CCccHhHHhhhHHHHHHHHHHHHHHhhcCCCcEEE
Confidence 45899999999999999887776663 44554443
No 110
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=61.26 E-value=14 Score=37.15 Aligned_cols=79 Identities=9% Similarity=0.047 Sum_probs=54.6
Q ss_pred CCCCCccccCCCC--ceEEEecC------CCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCC-CCHHHHH
Q psy8224 17 KAQEPAVKKAKHV--DMRKVPVP------NHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPET-EDISNLQ 87 (766)
Q Consensus 17 ~~~~~~~~~~~~~--~~~~i~iP------~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t-~d~~~~~ 87 (766)
-|.|-+.+.-..+ .+-+|.|| .+-+|.|||.-|.+.+.+++.++++|-|--. |+|. -+... +.|..+.
T Consensus 133 lp~fv~p~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~-gsvK--egk~ssd~p~~~~ 209 (269)
T COG5176 133 LPRFVLPNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS-GSVK--EGKISSDTPESLK 209 (269)
T ss_pred cCcccCCccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc-cccc--cCcccccCchhhh
Confidence 4666554433332 45566666 3568999999999999999999999998642 4442 22222 3488999
Q ss_pred HHHHHHHHHHc
Q psy8224 88 KAADFVKAFVY 98 (766)
Q Consensus 88 ka~~~i~ai~~ 98 (766)
.|.+.+..+..
T Consensus 210 N~e~~lhcLI~ 220 (269)
T COG5176 210 NAEAVLHCLIE 220 (269)
T ss_pred hhHHhHHHHhh
Confidence 99988876643
No 111
>COG1159 Era GTPase [General function prediction only]
Probab=60.39 E-value=12 Score=40.04 Aligned_cols=58 Identities=21% Similarity=0.280 Sum_probs=38.0
Q ss_pred hhHHhhcccccceeeeeeeccccccccc----------hhhhhhccccCCCCcHHHH--------HHHhhCceEEE
Q psy8224 103 DDALALLRLDNLFIESFEIKDVKTLKGD----------HLSRAIGRLAGKGGRTKFT--------IENITKTRIVI 160 (766)
Q Consensus 103 ~~a~~ll~~d~~~~~~~~i~~~~~~~~~----------~~~r~~griiG~~G~t~~~--------ie~~t~~~I~v 160 (766)
|+++..+++|=-+.-.++|.++..++++ .-...+|-|||++|..+|. ||.+-+++|.+
T Consensus 198 Ek~~~~l~eElPhsv~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 198 EKLLLLLREELPHSVAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred HHHHHhcccccCceEEEEEEEEEecCCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 8899999855555555666666543222 1125689999999987665 46666666554
No 112
>KOG0119|consensus
Probab=57.61 E-value=28 Score=39.51 Aligned_cols=81 Identities=14% Similarity=0.096 Sum_probs=55.1
Q ss_pred CCCCCCccccCCCC--ceEEEecCC------CcchhhhccCcccHHHHHHhcCcEEEEEcccCeEE---EEeC-----C-
Q psy8224 16 AKAQEPAVKKAKHV--DMRKVPVPN------HRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVE---IRLS-----P- 78 (766)
Q Consensus 16 ~~~~~~~~~~~~~~--~~~~i~iP~------~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~---i~~~-----~- 78 (766)
..|.|+|...-... -..+|+||- +-+|.|||--|.+.+.||+.+|++|.|--+ |+|. .++. .
T Consensus 122 ~nP~fkpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGk-gSvkEgk~~~~d~~~~~~ 200 (554)
T KOG0119|consen 122 LNPGFKPPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGK-GSVKEGKGRSDDLSYIPK 200 (554)
T ss_pred hCcCCCCCcccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecc-ccccccccCCcccccccc
Confidence 57888876554433 556777775 468999999999999999999999999642 2221 0100 0
Q ss_pred ---------CCCCHHHHHHHHHHHHHHH
Q psy8224 79 ---------ETEDISNLQKAADFVKAFV 97 (766)
Q Consensus 79 ---------~t~d~~~~~ka~~~i~ai~ 97 (766)
..++-..|.||..+|+.|.
T Consensus 201 ~~epLH~~Isadt~eki~~Ai~vienli 228 (554)
T KOG0119|consen 201 ENEPLHCLISADTQEKIKKAIAVIENLI 228 (554)
T ss_pred cccceeEEEecchHHHHHHHHHHHHHHH
Confidence 0124456888888888775
No 113
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=56.58 E-value=25 Score=39.03 Aligned_cols=94 Identities=10% Similarity=-0.013 Sum_probs=58.0
Q ss_pred CcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhcccccceeee
Q psy8224 39 HRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALLRLDNLFIES 118 (766)
Q Consensus 39 ~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll~~d~~~~~~ 118 (766)
+=+|+.+|..|.-.+.|.+.++ ...|.|-. -..||.. || ..-++|.+...+.-+++-- .
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~--------gEkIDvI~--~s~D~~~------fI---~Nal~Pa~V~~V~i~~~~~--~ 309 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELN--------GENIDCIE--YSNVPEI------FI---ARALAPAIISSVKIEEEEK--K 309 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhC--------CCeEEEEE--cCCCHHH------HH---HHhCCCceeeEEEEcCCCc--E
Confidence 4478899999999999988773 34555443 1245533 32 2334555543331112211 1
Q ss_pred eeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEe
Q psy8224 119 FEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA 161 (766)
Q Consensus 119 ~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~ 161 (766)
+.+ ++. . ...++-||++|++.+-.-.+||.+|-|.
T Consensus 310 ~~V--~V~-~-----~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 310 AIV--TLL-S-----DQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred EEE--EEC-h-----HHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 111 111 1 3478999999999999999999999885
No 114
>KOG1083|consensus
Probab=55.78 E-value=6.2 Score=48.29 Aligned_cols=42 Identities=29% Similarity=0.650 Sum_probs=32.6
Q ss_pred ccccccccccCCcee---eeecCccchhhhhhhcccCCCeeeeccc
Q psy8224 559 KTAMLSHNCKPNTKH---VIVNEDFSLQLIALVNICKGDIISTTYT 601 (766)
Q Consensus 559 ~~SllNHSC~PN~~~---~f~~~~~~l~~~A~r~I~~GeeI~~sY~ 601 (766)
.+-..||+|.||+.. .. ++.-++.|.|+|+|.+||||+.-|.
T Consensus 1250 ~~RfinhscKPNc~~qkwSV-NG~~Rv~L~A~rDi~kGEELtYDYN 1294 (1306)
T KOG1083|consen 1250 GARFINHSCKPNCEMQKWSV-NGEYRVGLFALRDLPKGEELTYDYN 1294 (1306)
T ss_pred cccccccccCCCCccccccc-cceeeeeeeecCCCCCCceEEEecc
Confidence 445679999999853 22 4444688999999999999988775
No 115
>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=55.56 E-value=26 Score=37.12 Aligned_cols=27 Identities=15% Similarity=0.194 Sum_probs=20.4
Q ss_pred hhhccccCCCCcHHHHH--------HHhhCceEEE
Q psy8224 134 RAIGRLAGKGGRTKFTI--------ENITKTRIVI 160 (766)
Q Consensus 134 r~~griiG~~G~t~~~i--------e~~t~~~I~v 160 (766)
+.+|-|||++|+++|.| |.+.|++|.+
T Consensus 231 s~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l 265 (270)
T TIGR00436 231 SQKKIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 (270)
T ss_pred CceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 67899999999987765 5566666544
No 116
>KOG1338|consensus
Probab=54.96 E-value=9.3 Score=42.11 Aligned_cols=54 Identities=24% Similarity=0.196 Sum_probs=42.3
Q ss_pred cccccchhhhhhhcccCCCCC-CCeEEEEEeCCeEEEEEEecccCCCCeEEeecCCC
Q psy8224 612 LHLRMSKWIYMKTAMLSHNCK-PNTKHVIVNEDFSLQLIALVNIRKGDIISTTYTQP 667 (766)
Q Consensus 612 ~~~~i~~glyp~~s~~NHsC~-PN~~~~~~~~g~~l~vra~r~I~~GeeI~isY~~~ 667 (766)
.....|...-|.+.++||.=. -|+...+ +..-+.+.|.|+|++|+|++.+|+..
T Consensus 207 e~e~ngk~m~p~ad~lNhd~~k~nanl~y--~~NcL~mva~r~iekgdev~n~dg~~ 261 (466)
T KOG1338|consen 207 EIECNGKLMTPIADFLNHDGLKANANLRY--EDNCLEMVADRNIEKGDEVDNSDGLK 261 (466)
T ss_pred ccccCcccccchhhhhccchhhcccceec--cCcceeeeecCCCCCccccccccccC
Confidence 345667788899999999654 4554444 35778999999999999999999743
No 117
>KOG1067|consensus
Probab=54.54 E-value=11 Score=43.40 Aligned_cols=62 Identities=10% Similarity=0.095 Sum_probs=53.1
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHH
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFV 97 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~ 97 (766)
-.-.++||+....-|||..|..++.|+..+|....+| ++++.|-. .++.+..+|++||.-|.
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD--e~t~~i~A----~~~~am~~Ak~~I~~i~ 658 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD--EGTFSIFA----PTQAAMEEAKEFIDGII 658 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeeec--CceEEEEe----cCHHHHHHHHHHHHHHh
Confidence 3456789999999999999999999999999777676 67887775 58899999999998775
No 118
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=54.44 E-value=24 Score=38.66 Aligned_cols=49 Identities=22% Similarity=0.247 Sum_probs=44.7
Q ss_pred hccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchhhHHHHHHHHHHh
Q psy8224 136 IGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALKALSNL 184 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~~l~~ar~~i~~~ 184 (766)
...+.|..|..++.||...|+.|..-|+.+.|+|....+..|+..+..+
T Consensus 26 ~~~l~G~~~~~l~l~e~~~gv~i~~rG~~~~i~g~~~~v~~A~~~l~~l 74 (348)
T COG1702 26 LVALFGPTDTNLSLLEIALGVSIVARGEAVRIIGARPLVDVATRVLLTL 74 (348)
T ss_pred hhhhcCCCCccHHHHHHHhCcEEEeCCceEEEEechHHHHHHHHHHhHH
Confidence 5678999999999999999999999999999999988888888888743
No 119
>PRK15494 era GTPase Era; Provisional
Probab=52.27 E-value=26 Score=38.69 Aligned_cols=27 Identities=15% Similarity=0.122 Sum_probs=21.3
Q ss_pred hhhccccCCCCcHHHH--------HHHhhCceEEE
Q psy8224 134 RAIGRLAGKGGRTKFT--------IENITKTRIVI 160 (766)
Q Consensus 134 r~~griiG~~G~t~~~--------ie~~t~~~I~v 160 (766)
+.+|-|||++|+++|. ||.+.|++|.+
T Consensus 283 sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 283 SYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred CceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 6789999999998765 57777777665
No 120
>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=52.06 E-value=28 Score=38.37 Aligned_cols=93 Identities=17% Similarity=0.237 Sum_probs=58.4
Q ss_pred cchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhh--cccccceee
Q psy8224 40 RYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALAL--LRLDNLFIE 117 (766)
Q Consensus 40 r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~l--l~~d~~~~~ 117 (766)
=+|+.+|..|.-.+.|.+.++ ...|+|-. -..||.. || ..-++|.+...+ ++ ++--
T Consensus 244 pvga~vG~~G~ri~~i~~el~--------ge~Idiv~--~s~d~~~------fi---~nal~Pa~v~~v~i~~-~~~~-- 301 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELN--------GEKIDIIE--YSDDPAE------FI---ANALSPAKVISVEVLD-EDKH-- 301 (341)
T ss_pred cceeeECCCCchHHHHHHHhC--------CCeEEEEE--cCCCHHH------HH---HHhcCCceEEEEEEEc-CCCc--
Confidence 468889999999999988773 34555443 1246633 22 233556554443 23 2211
Q ss_pred eeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeC
Q psy8224 118 SFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIAD 162 (766)
Q Consensus 118 ~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~ 162 (766)
.+.+ ++ ++ ...+.-|||+|++.+-.-.+||.+|-|..
T Consensus 302 ~~~v--~V--~~----~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 302 SAEV--VV--PD----DQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEE--EE--Ch----HHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 1111 11 11 34788999999999999999999998864
No 121
>KOG2113|consensus
Probab=51.15 E-value=9.8 Score=40.49 Aligned_cols=124 Identities=14% Similarity=0.071 Sum_probs=86.5
Q ss_pred CceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEcccC-eEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHh
Q psy8224 29 VDMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSR-NVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALA 107 (766)
Q Consensus 29 ~~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~-~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ 107 (766)
.-+..+.||..-++.+-|..|-.++.|..++...|.--+..+ -|.+.+ .-+..+.+||.=|.+-+.-|..-.|..
T Consensus 25 nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vT----g~~edv~~aRrei~saaeH~~l~~~s~ 100 (394)
T KOG2113|consen 25 NVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVT----GRHEDVRRARREIPSAAEHFGLIRASR 100 (394)
T ss_pred ccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceec----cCchhHHHHhhcCccccceeeeeeecc
Confidence 367889999777888888888888889888888886654332 333333 456788889888877666666666665
Q ss_pred hcccccce-eeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEE
Q psy8224 108 LLRLDNLF-IESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVI 160 (766)
Q Consensus 108 ll~~d~~~-~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v 160 (766)
-+-.+-.- -+.-+....+... + |++|-+.|+.|.+++.|+..|+++|.-
T Consensus 101 s~Sgg~~~~s~s~qt~sy~svP---~-rvvglvv~~~~~ti~~iqq~tnt~I~T 150 (394)
T KOG2113|consen 101 SFSGGTNGASASGQTTSYVSVP---L-RVVGLVVGPKGATIKRIQQFTNTYIAT 150 (394)
T ss_pred cccCCCccccccCCCceeeecc---c-eeeeeccccccCccchheecccceEee
Confidence 55422211 1233344443333 3 889999999999999999999999963
No 122
>KOG3362|consensus
Probab=49.33 E-value=6.1 Score=37.28 Aligned_cols=34 Identities=29% Similarity=0.601 Sum_probs=29.4
Q ss_pred CCcccccCCcccCCCCCCCCcccCCchhhcccccc
Q psy8224 314 SGKCEVCKVAASLKCGGCNQVFYCSKSHQKQHWKE 348 (766)
Q Consensus 314 ~~~C~~C~~~~~~~C~~C~~v~YCs~~cq~~~w~~ 348 (766)
-+.|.+||-.+..+|..|. ..|||..|.+.|.+.
T Consensus 118 r~fCaVCG~~S~ysC~~CG-~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 118 RKFCAVCGYDSKYSCVNCG-TKYCSVRCLKTHNET 151 (156)
T ss_pred chhhhhcCCCchhHHHhcC-Cceeechhhhhcccc
Confidence 4679999988999999997 679999999988664
No 123
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=49.05 E-value=29 Score=39.32 Aligned_cols=94 Identities=12% Similarity=0.128 Sum_probs=59.7
Q ss_pred CcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhh--ccccccee
Q psy8224 39 HRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALAL--LRLDNLFI 116 (766)
Q Consensus 39 ~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~l--l~~d~~~~ 116 (766)
+=+|+.+|..|.-++.|.+.++ ...|.|-. -..||.. || ..-++|.+...+ .+ ++--.
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~--------gEkIDVI~--ys~Dp~~------fI---~NaLsPA~V~~V~i~~-~~~k~ 336 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELR--------GEKIDVIR--WSPDPAT------YI---ANALSPARVDEVRLVD-PEGRH 336 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhC--------CCeEEEEE--cCCCHHH------HH---HHhcCCceeeEEEEEc-CCCcE
Confidence 4478999999999999988773 34555443 1245532 32 334566554443 23 22111
Q ss_pred eeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeC
Q psy8224 117 ESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIAD 162 (766)
Q Consensus 117 ~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~ 162 (766)
+.+ ++. . ..+++-|||+|++.+-.-.+||-+|-|..
T Consensus 337 --a~V--~V~-~-----~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 337 --AHV--LVP-P-----DQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred --EEE--EEC-h-----HhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 111 111 1 34788999999999999999999998865
No 124
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=48.86 E-value=34 Score=38.09 Aligned_cols=95 Identities=18% Similarity=0.168 Sum_probs=59.1
Q ss_pred CcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhh--ccccccee
Q psy8224 39 HRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALAL--LRLDNLFI 116 (766)
Q Consensus 39 ~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~l--l~~d~~~~ 116 (766)
+=+|+.+|..|.-.+.|.+.++ ...|+|-. -..||.. || ..-++|.....+ .+ ++--
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~--------gekIdiv~--~s~d~~~------fi---~nal~Pa~v~~v~i~~-~~~~- 303 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELK--------GEKIDIID--WSEDPAE------FV---ANALSPAKVVSVEVDD-EEEK- 303 (362)
T ss_pred CchheeECCCChhHHHHHHHhC--------CCeEEEEE--cCCCHHH------HH---HHhCCCceEEEEEEEc-CCCc-
Confidence 3478899999999999988773 34555443 1245532 33 233556554443 12 2211
Q ss_pred eeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCc
Q psy8224 117 ESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADS 163 (766)
Q Consensus 117 ~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~ 163 (766)
.+.+ ++. . ..+++-|||+|++.+-.-.+||.+|-|...
T Consensus 304 -~~~v--~V~-~-----~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 304 -AARV--VVP-D-----YQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred -EEEE--EEC-h-----hhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0111 111 1 447899999999999999999999988643
No 125
>KOG4317|consensus
Probab=48.70 E-value=9.3 Score=40.64 Aligned_cols=22 Identities=27% Similarity=0.738 Sum_probs=17.8
Q ss_pred cccCCCCCccccCccCCCCCCc
Q psy8224 418 FYKCSDCGWPLCAPRCKSLPSH 439 (766)
Q Consensus 418 ~~~C~~C~~~yCS~~C~~~~~H 439 (766)
.+.||+|..+|||-.|-....|
T Consensus 19 ~YtCPRCn~~YCsl~CYr~h~~ 40 (383)
T KOG4317|consen 19 EYTCPRCNLLYCSLKCYRNHKH 40 (383)
T ss_pred cccCCCCCccceeeeeecCCCc
Confidence 5899999999999999643333
No 126
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=48.70 E-value=29 Score=39.99 Aligned_cols=93 Identities=16% Similarity=0.187 Sum_probs=56.9
Q ss_pred chhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHHhhcccccceeeeee
Q psy8224 41 YGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALLRLDNLFIESFE 120 (766)
Q Consensus 41 ~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~~ll~~d~~~~~~~~ 120 (766)
+|+.+|..|.-++.|.+.++ ...|.|-. -..||... +.+| ++|.....+.-+++- ..+.
T Consensus 247 vga~vG~~G~ri~~i~~el~--------ge~Idiv~--~s~d~~~f-----i~na----l~pa~v~~v~~~~~~--~~~~ 305 (470)
T PRK09202 247 VGACVGMRGSRIQAISNELG--------GEKIDIIL--WSDDPAQF-----IINA----LSPAEVSSVVVDEDE--HSAD 305 (470)
T ss_pred hHccCCCCCchHHHHHHHhC--------CCeEEEEE--cCCCHHHH-----HHHh----CCCCEEEEEEEeCCC--CEEE
Confidence 68889999999999988773 44555543 12355322 2233 444443333211221 1111
Q ss_pred eccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeC
Q psy8224 121 IKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIAD 162 (766)
Q Consensus 121 i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~ 162 (766)
+ ++.. ...+.-|||+|++.+-...+||.+|-|..
T Consensus 306 v--~V~~------~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 306 V--VVPD------DQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred E--EECc------chHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 1 1111 34788999999999999999999998865
No 127
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=47.39 E-value=14 Score=35.23 Aligned_cols=46 Identities=17% Similarity=0.230 Sum_probs=31.7
Q ss_pred hhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchhhHHHHHHHHHHhhcCCCC
Q psy8224 135 AIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSPP 190 (766)
Q Consensus 135 ~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~~l~~ar~~i~~~~~~~~p 190 (766)
..|..||++|+.+++|+++.|-+|-|-. -.+ ..+.++...+.....
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve-------~s~---d~~~fI~n~l~Pa~V 87 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE-------YSD---DPEEFIKNIFAPAAV 87 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE-------cCC---CHHHHHHHHcCCCEE
Confidence 4899999999999999999986665533 212 345566665554433
No 128
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=44.15 E-value=6.9 Score=28.82 Aligned_cols=30 Identities=27% Similarity=0.707 Sum_probs=17.7
Q ss_pred eeecccCCceecCCCCCC-CCCcccCCCCCc
Q psy8224 197 ILCSRCRHHVISTNPLDN-LAKWKCIMCSHT 226 (766)
Q Consensus 197 l~c~~c~g~~l~~~pl~~-~~~W~C~~C~~~ 226 (766)
++|.+|.+.+=|--..+. ...|.|.-|++.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 688999888766666554 468999999875
No 129
>KOG2814|consensus
Probab=43.54 E-value=18 Score=39.01 Aligned_cols=93 Identities=13% Similarity=0.048 Sum_probs=65.3
Q ss_pred CCCCCccccCCCC----ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEE---cccCeEEEEeCCCCCCHHHHHHH
Q psy8224 17 KAQEPAVKKAKHV----DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFN---LKSRNVEIRLSPETEDISNLQKA 89 (766)
Q Consensus 17 ~~~~~~~~~~~~~----~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~---~~~~~v~i~~~~~t~d~~~~~ka 89 (766)
.+.+.+.+..++. .+.++.+++--++-|||+.|.+.+.|++.++++|.+- ...+.|.|.. ..-..+++|
T Consensus 40 d~p~~~~dv~~~~~~~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~----~~~~~V~~a 115 (345)
T KOG2814|consen 40 DMPGDTVDVEDDAGAKDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIG----ISRNCVIQA 115 (345)
T ss_pred cCCCChHHhhhccccccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEee----hhHHHHHHH
Confidence 3445555444443 5678999999999999999999999999999999884 3345666655 455677777
Q ss_pred HH----HHHHHHcCCChhhHHhhccccc
Q psy8224 90 AD----FVKAFVYGFDVDDALALLRLDN 113 (766)
Q Consensus 90 ~~----~i~ai~~gf~~~~a~~ll~~d~ 113 (766)
.+ +|.-..+.|++-.=++++-+++
T Consensus 116 ~~Ri~~~ids~r~s~p~thflal~lne~ 143 (345)
T KOG2814|consen 116 LERIAKLIDSDRKSFPITHFLALPLNEH 143 (345)
T ss_pred HHHHHHHHHhhhhcCchhhhhhhhcchH
Confidence 64 3334455777776666654333
No 130
>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=41.14 E-value=27 Score=28.21 Aligned_cols=36 Identities=14% Similarity=0.098 Sum_probs=32.2
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEE
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRF 65 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i 65 (766)
....+.||++-++..+|+.|...+.+.+.++-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 568899999999999999999999999999876654
No 131
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=39.47 E-value=44 Score=37.97 Aligned_cols=28 Identities=29% Similarity=0.434 Sum_probs=26.0
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEe
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIA 161 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~ 161 (766)
..++.+|||+|+.++-||+..|.+|-|.
T Consensus 495 ~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 495 KYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred HHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 4589999999999999999999999885
No 132
>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=39.43 E-value=47 Score=31.84 Aligned_cols=85 Identities=21% Similarity=0.329 Sum_probs=52.3
Q ss_pred cccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHH---HHHHHHHHHHHcCCChhhHHhhcccccceeeeeeecccc
Q psy8224 49 MKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNL---QKAADFVKAFVYGFDVDDALALLRLDNLFIESFEIKDVK 125 (766)
Q Consensus 49 ~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~---~ka~~~i~ai~~gf~~~~a~~ll~~d~~~~~~~~i~~~~ 125 (766)
+++.+.|.+..+ +.|.|++ ||..+ ..|+++|+.+. |++|- + .|+++|- +..+|.
T Consensus 25 ~dli~~lAk~lr---------KRIvvR~-----dps~l~~~e~A~~~I~~iv----P~ea~-i---~di~Fd~-~tGEV~ 81 (145)
T cd02410 25 GDLVKDLAKDLR---------KRIVIRP-----DPSVLKPPEEAIKIILEIV----PEEAG-I---TDIYFDD-DTGEVI 81 (145)
T ss_pred cHHHHHHHHHHh---------ceEEEcC-----ChhhcCCHHHHHHHHHHhC----CCccC-c---eeeEecC-CCcEEE
Confidence 456666665443 4556676 66555 46777777653 33332 1 3455431 122222
Q ss_pred ccccchhhhhhccccCCCCcHHHHHHHhhCceEEEe
Q psy8224 126 TLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA 161 (766)
Q Consensus 126 ~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~ 161 (766)
- . ...-|++||++|.+.+.|-.-||=.-.|.
T Consensus 82 I----e-aeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 82 I----E-AEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred E----E-EcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 1 1 14479999999999999999999888774
No 133
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=37.66 E-value=30 Score=27.38 Aligned_cols=44 Identities=18% Similarity=0.502 Sum_probs=29.3
Q ss_pred HHHhhcCCCC--cccccceeecccC--Cceec-CCCCCCCCCcccCCCCCc
Q psy8224 181 LSNLILGSPP--NKVYGGILCSRCR--HHVIS-TNPLDNLAKWKCIMCSHT 226 (766)
Q Consensus 181 i~~~~~~~~p--~~~~s~l~c~~c~--g~~l~-~~pl~~~~~W~C~~C~~~ 226 (766)
|-+.+-|.+| .+.-.+|-|.+|. .++.| .++. .-.|.|-.|++.
T Consensus 5 i~d~L~G~d~~~~~~r~aLIC~~C~~hNGla~~~~~~--~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 5 ILDVLLGDDPTSPSNRYALICSKCFSHNGLAPKEEFE--EIQYRCPYCGAL 53 (54)
T ss_pred HHHHHhCCCCccccCceeEECcccchhhcccccccCC--ceEEEcCCCCCc
Confidence 3455667777 4467789999995 34443 3332 458999999863
No 134
>PRK12704 phosphodiesterase; Provisional
Probab=37.04 E-value=81 Score=36.97 Aligned_cols=63 Identities=11% Similarity=0.016 Sum_probs=51.1
Q ss_pred ceEEEecCC-CcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHH
Q psy8224 30 DMRKVPVPN-HRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAF 96 (766)
Q Consensus 30 ~~~~i~iP~-~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai 96 (766)
....|.+|. +--|-|||+-|.-++.++..+|+.|-||-.-..|.|.+ .||+-=.-|+.-+..+
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~----~~~~rre~a~~~l~~l 273 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSG----FDPIRREIARLALEKL 273 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEec----CChhhHHHHHHHHHHH
Confidence 566799999 55689999999999999999999999998777777765 6887766676666544
No 135
>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=36.88 E-value=31 Score=28.32 Aligned_cols=41 Identities=20% Similarity=0.409 Sum_probs=28.6
Q ss_pred cccccceeecccCCceecCCCCCCCCCcccCCCCCcccHHHHHH
Q psy8224 191 NKVYGGILCSRCRHHVISTNPLDNLAKWKCIMCSHTLTAKQIAM 234 (766)
Q Consensus 191 ~~~~s~l~c~~c~g~~l~~~pl~~~~~W~C~~C~~~~~~~~v~~ 234 (766)
.+.|++..|+.|....-. ++ ....|.|..|+++..++.+..
T Consensus 23 ~~~~TSq~C~~CG~~~~~--~~-~~r~~~C~~Cg~~~~rD~naA 63 (69)
T PF07282_consen 23 DEAYTSQTCPRCGHRNKK--RR-SGRVFTCPNCGFEMDRDVNAA 63 (69)
T ss_pred CCCCCccCccCccccccc--cc-ccceEEcCCCCCEECcHHHHH
Confidence 346799999999644322 22 245799999999988776543
No 136
>TIGR00112 proC pyrroline-5-carboxylate reductase. This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs.
Probab=36.65 E-value=33 Score=35.84 Aligned_cols=98 Identities=10% Similarity=0.086 Sum_probs=64.8
Q ss_pred ccHHHHHHhcCcEEEEEcccCeEEEEeCCC-CCCHHHHHHHHHHHH-HHHcCCChhhHHhhcccccceeeeeeecccccc
Q psy8224 50 KIFTPIVEHLKLQVRFNLKSRNVEIRLSPE-TEDISNLQKAADFVK-AFVYGFDVDDALALLRLDNLFIESFEIKDVKTL 127 (766)
Q Consensus 50 ~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~-t~d~~~~~ka~~~i~-ai~~gf~~~~a~~ll~~d~~~~~~~~i~~~~~~ 127 (766)
+..+.|.+..|..+.++ +..+..-+.-- ...++...=++.+++ ++..|+++++|.++.. + .+.- -..+...
T Consensus 125 ~~v~~lf~~~G~~~~v~--E~~~~~~talsgsgPA~~~~~~~al~~~~v~~Gl~~~~A~~lv~-~-~~~G---~a~l~~~ 197 (245)
T TIGR00112 125 ALVLALFKAVGEVVELP--EALMDAVTALSGSGPAYVFLFIEALADAGVKQGLPRELALELAA-Q-TVKG---AAKLLEE 197 (245)
T ss_pred HHHHHHHHhCCCEEEEC--HHHcchHHhhccCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHHH-H-HHHH---HHHHHHh
Confidence 55678889999999997 44555333211 223333334445554 5678999999999985 2 2211 1112223
Q ss_pred ccchhhhhhccccCCCCcHHHHHHHhh
Q psy8224 128 KGDHLSRAIGRLAGKGGRTKFTIENIT 154 (766)
Q Consensus 128 ~~~~~~r~~griiG~~G~t~~~ie~~t 154 (766)
++.++...+.++.-+||-|...|+.+-
T Consensus 198 ~~~~~~~l~~~v~spgGtT~~gl~~Le 224 (245)
T TIGR00112 198 SGEHPALLKDQVTSPGGTTIAGLAVLE 224 (245)
T ss_pred cCCCHHHHHHcCCCCcHHHHHHHHHHH
Confidence 456888899999999999999999874
No 137
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=36.41 E-value=25 Score=29.24 Aligned_cols=33 Identities=24% Similarity=0.286 Sum_probs=22.4
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchh
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQ 172 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~ 172 (766)
-.+|..||++|+.+++|++..+ |..|-++.-.+
T Consensus 17 d~vG~~iG~~G~rik~i~~~L~------gekIdvV~~s~ 49 (69)
T PF13184_consen 17 DPVGACIGKKGSRIKAISEELN------GEKIDVVEYSD 49 (69)
T ss_dssp -HHHHHH-CCCCCHHHHHHHTT------T-EEEEEE--S
T ss_pred CcceecCccccHHHHHHHHHhC------CCeEEEEEcCC
Confidence 5699999999999999999994 44444444444
No 138
>PRK01343 zinc-binding protein; Provisional
Probab=34.96 E-value=32 Score=27.58 Aligned_cols=31 Identities=13% Similarity=0.356 Sum_probs=23.6
Q ss_pred CCCcccccCCcccCCCCCCCCcccCCchhhcccccc
Q psy8224 313 DSGKCEVCKVAASLKCGGCNQVFYCSKSHQKQHWKE 348 (766)
Q Consensus 313 ~~~~C~~C~~~~~~~C~~C~~v~YCs~~cq~~~w~~ 348 (766)
....|..|+++... ..+.|||+.|+..|.-.
T Consensus 8 p~~~CP~C~k~~~~-----~~rPFCS~RC~~iDLg~ 38 (57)
T PRK01343 8 PTRPCPECGKPSTR-----EAYPFCSERCRDIDLNR 38 (57)
T ss_pred CCCcCCCCCCcCcC-----CCCcccCHHHhhhhHHH
Confidence 45679999987542 46799999999988643
No 139
>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=33.81 E-value=33 Score=32.81 Aligned_cols=26 Identities=27% Similarity=0.493 Sum_probs=22.6
Q ss_pred hhccccCCCCcHHHHHHHhhCceEEE
Q psy8224 135 AIGRLAGKGGRTKFTIENITKTRIVI 160 (766)
Q Consensus 135 ~~griiG~~G~t~~~ie~~t~~~I~v 160 (766)
-.|..||++|+.+++|+++.|=+|-|
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdV 68 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIEL 68 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEE
Confidence 48999999999999999999866654
No 140
>PRK00106 hypothetical protein; Provisional
Probab=33.77 E-value=98 Score=36.33 Aligned_cols=61 Identities=11% Similarity=0.032 Sum_probs=51.8
Q ss_pred ceEEEecCC-CcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHH
Q psy8224 30 DMRKVPVPN-HRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVK 94 (766)
Q Consensus 30 ~~~~i~iP~-~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ 94 (766)
....|.+|+ +--|-|||+-|.-++.++..+|+.|-||-.-..|.|.+ .||+-=.-|+--+.
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~----fdpvRReiAr~~le 286 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSG----FDPIRREIARMTLE 286 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeC----CChHHHHHHHHHHH
Confidence 566799999 55689999999999999999999999998888888876 89987776765554
No 141
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=33.61 E-value=18 Score=32.67 Aligned_cols=25 Identities=32% Similarity=0.843 Sum_probs=19.3
Q ss_pred cccCCCCCccccCccCC---CCCCcHhh
Q psy8224 418 FYKCSDCGWPLCAPRCK---SLPSHQKE 442 (766)
Q Consensus 418 ~~~C~~C~~~yCS~~C~---~~~~H~~E 442 (766)
.++|+.|+..-|+.+|+ .|.|-+.|
T Consensus 74 ~~PC~~C~S~KCG~~CR~nRkw~ye~ie 101 (103)
T PF14949_consen 74 HYPCPKCGSRKCGPECRCNRKWVYESIE 101 (103)
T ss_pred cccCCCCCCCccChhhCcCCceeeeeee
Confidence 57899999999999996 36665544
No 142
>PRK00089 era GTPase Era; Reviewed
Probab=33.42 E-value=79 Score=33.73 Aligned_cols=27 Identities=26% Similarity=0.468 Sum_probs=21.0
Q ss_pred hhhccccCCCCcHHHH--------HHHhhCceEEE
Q psy8224 134 RAIGRLAGKGGRTKFT--------IENITKTRIVI 160 (766)
Q Consensus 134 r~~griiG~~G~t~~~--------ie~~t~~~I~v 160 (766)
..++-|||++|++++. ||.+.|++|.+
T Consensus 236 ~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 236 SQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred CceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 5689999999998775 46677776655
No 143
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=33.39 E-value=30 Score=39.25 Aligned_cols=40 Identities=15% Similarity=0.093 Sum_probs=35.8
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEccc
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKS 69 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~ 69 (766)
..--|.||.+.++.++|+.|.-.+.|++++|++|++-..+
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 4567999999999999999999999999999999986543
No 144
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=32.72 E-value=2.4e+02 Score=27.24 Aligned_cols=66 Identities=21% Similarity=0.324 Sum_probs=37.2
Q ss_pred ceEEEeCceEEEEcchhhHHHHHH--HHHHhhcCCC---Ccc------cccceeecccCCc--eecCCCCCCCCCcccCC
Q psy8224 156 TRIVIADSKIHVLGSYQNVQVALK--ALSNLILGSP---PNK------VYGGILCSRCRHH--VISTNPLDNLAKWKCIM 222 (766)
Q Consensus 156 ~~I~v~~~~v~iiG~~~~l~~ar~--~i~~~~~~~~---p~~------~~s~l~c~~c~g~--~l~~~pl~~~~~W~C~~ 222 (766)
=.|.|.|+ .||..+.+....+ -+..++.+.+ ++. -+.++-|..|.|. +...+......-.+|..
T Consensus 62 PqVFI~G~---~IGG~del~~L~e~G~L~~lL~~~~~~~~~~~C~~Cgg~rfv~C~~C~Gs~k~~~~~~~~~~~~~rC~~ 138 (147)
T cd03031 62 PRVFVDGR---YLGGAEEVLRLNESGELRKLLKGIRARAGGGVCEGCGGARFVPCSECNGSCKVFAENATAAGGFLRCPE 138 (147)
T ss_pred CEEEECCE---EEecHHHHHHHHHcCCHHHHHhhcccccCCCCCCCCCCcCeEECCCCCCcceEEeccCcccccEEECCC
Confidence 35777775 4567776553322 1222222221 211 4778889999874 55555333345678988
Q ss_pred CC
Q psy8224 223 CS 224 (766)
Q Consensus 223 C~ 224 (766)
|+
T Consensus 139 Cn 140 (147)
T cd03031 139 CN 140 (147)
T ss_pred CC
Confidence 87
No 145
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=32.50 E-value=1e+02 Score=36.08 Aligned_cols=62 Identities=11% Similarity=0.015 Sum_probs=51.8
Q ss_pred ceEEEecCC-CcchhhhccCcccHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHH
Q psy8224 30 DMRKVPVPN-HRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKA 95 (766)
Q Consensus 30 ~~~~i~iP~-~r~~~l~~~~~~i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~a 95 (766)
....|.+|. +--|-|||+-|.-++.++..+|+.|-||-.-..|.|.+ .||+-=.-|+--+.-
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~----fdp~rreia~~~l~~ 266 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSG----FDPVRREIARMALEK 266 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCCeEEecC----CchHHHHHHHHHHHH
Confidence 566799999 55689999999999999999999999998888888876 799877767655543
No 146
>KOG2857|consensus
Probab=32.45 E-value=21 Score=33.67 Aligned_cols=38 Identities=34% Similarity=0.766 Sum_probs=29.0
Q ss_pred CcccccCCcc-cCCCCCCCCcccCCchhhccccccccC--CCcccc
Q psy8224 315 GKCEVCKVAA-SLKCGGCNQVFYCSKSHQKQHWKEHKP--GCAKYK 357 (766)
Q Consensus 315 ~~C~~C~~~~-~~~C~~C~~v~YCs~~cq~~~w~~Hk~--~C~~l~ 357 (766)
..|..|.... ..+|+.|. +.|||-.| |+.|+. +|....
T Consensus 6 ~tC~ic~e~~~KYKCpkC~-vPYCSl~C----fKiHk~tPq~~~ve 46 (157)
T KOG2857|consen 6 TTCVICLESEIKYKCPKCS-VPYCSLPC----FKIHKSTPQCETVE 46 (157)
T ss_pred eeehhhhcchhhccCCCCC-Cccccchh----hhhccCCccccccC
Confidence 4688888764 88999995 89999999 455555 676554
No 147
>TIGR02059 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803.
Probab=32.38 E-value=89 Score=28.02 Aligned_cols=69 Identities=17% Similarity=0.333 Sum_probs=40.3
Q ss_pred CCCeeeecccCCCCCccccccccccchhhhhhhcccCCCCCCCeEEEE-Ee-CCeEEEEEEecccCCCCeEEeecCCCC
Q psy8224 592 KGDIISTTYTQPFWGTMDRRLHLRMSKWIYMKTAMLSHNCKPNTKHVI-VN-EDFSLQLIALVNIRKGDIISTTYTQPF 668 (766)
Q Consensus 592 ~GeeI~~sY~~~~~~~~~r~~~~~i~~glyp~~s~~NHsC~PN~~~~~-~~-~g~~l~vra~r~I~~GeeI~isY~~~~ 668 (766)
.|.+|...|-..+.... .+.+...+|.-+. |- .||...-. ++ ....+++.-.++|..|++++++|.++.
T Consensus 29 nG~~lVLtY~e~L~~~t---~~~p~~~~FtVtV---nG--~~n~Vt~VsV~~s~ktVTLTL~~~V~~Gq~VTVsYt~ps 99 (101)
T TIGR02059 29 NGNLLVLTFNEPLADIT---NHAPTRDQFAVTV---NG--APNTVTSVSLGGSNTTITLTLAQVVEDGDEVTLSYTKNS 99 (101)
T ss_pred cCCEEEEEechhcCccc---cCCCCCCcEEEEe---CC--cEeeEEEEEEcCcccEEEEEecccccCCCEEEEEeeCCC
Confidence 46777777766533111 1122233333221 22 44443333 21 224899999999999999999999875
No 148
>KOG2593|consensus
Probab=32.33 E-value=46 Score=37.33 Aligned_cols=51 Identities=22% Similarity=0.526 Sum_probs=31.3
Q ss_pred cceeecccCCc--eecCCCC-CC-CCCcccCCCCCc-------ccHHHHHHHHHHHHHHHhc
Q psy8224 195 GGILCSRCRHH--VISTNPL-DN-LAKWKCIMCSHT-------LTAKQIAMGNDSIKSELAG 245 (766)
Q Consensus 195 s~l~c~~c~g~--~l~~~pl-~~-~~~W~C~~C~~~-------~~~~~v~~~~~~~~~e~~~ 245 (766)
..-+|+.|... .|--+-| +. ++..+|..|+.. ++..++...+.++..+++.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~~~~Q~~p 188 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKLPSKESRTALNRLMEQLEP 188 (436)
T ss_pred ccccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccCchHHHHHHHHHHHHHHHH
Confidence 34478999633 3333322 22 578999999976 4566666666666665444
No 149
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=32.16 E-value=35 Score=33.56 Aligned_cols=46 Identities=20% Similarity=0.346 Sum_probs=32.4
Q ss_pred ccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchhhHHHHHHHHHHhhcCCCCccccc
Q psy8224 137 GRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSPPNKVYG 195 (766)
Q Consensus 137 griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~~l~~ar~~i~~~~~~~~p~~~~s 195 (766)
|.-||++|++++.+++..|-+|-|-+ ..+. .+.++..++. |..+.+
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE-------~s~d---~~~fl~Nl~~---PA~V~g 117 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVE-------KTND---IKKLAVQLLS---PARVLG 117 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEE-------cCCC---HHHHHHhcCC---CcEEEE
Confidence 88999999999999999987776643 2222 4566666654 444544
No 150
>PHA00626 hypothetical protein
Probab=31.93 E-value=38 Score=26.90 Aligned_cols=36 Identities=14% Similarity=0.353 Sum_probs=23.5
Q ss_pred eeecccCCceecCCC--CCCCCCcccCCCCCcccHHHH
Q psy8224 197 ILCSRCRHHVISTNP--LDNLAKWKCIMCSHTLTAKQI 232 (766)
Q Consensus 197 l~c~~c~g~~l~~~p--l~~~~~W~C~~C~~~~~~~~v 232 (766)
+.|++|.-..+.... -.+...+.|..|++..+.+..
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeechhhh
Confidence 357888643222222 134568999999999998765
No 151
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.64 E-value=30 Score=26.18 Aligned_cols=28 Identities=36% Similarity=0.688 Sum_probs=21.2
Q ss_pred eccCCCCCCccccccccccccccccccee
Q psy8224 687 TCDRCKDPTELETYLGKSFCLVYCEIRSL 715 (766)
Q Consensus 687 ~C~rC~~~~e~~~~~~~~~C~~~C~~~~~ 715 (766)
.|+.|-..-+.+.....++||. |+..+.
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~-CG~~~~ 32 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPY-CGYRIL 32 (46)
T ss_pred ECCCCCCEEEECCCCCceECCC-CCCeEE
Confidence 5888887766665555899999 987665
No 152
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=31.54 E-value=24 Score=27.27 Aligned_cols=29 Identities=28% Similarity=0.708 Sum_probs=20.4
Q ss_pred cceeecccC-CceecCCCCCCCCCcccCCCCCcc
Q psy8224 195 GGILCSRCR-HHVISTNPLDNLAKWKCIMCSHTL 227 (766)
Q Consensus 195 s~l~c~~c~-g~~l~~~pl~~~~~W~C~~C~~~~ 227 (766)
..-.|++|. |..++.. .| .|.|-+|+++.
T Consensus 18 k~~~CPrCG~gvfmA~H-~d---R~~CGkCgyTe 47 (51)
T COG1998 18 KNRFCPRCGPGVFMADH-KD---RWACGKCGYTE 47 (51)
T ss_pred ccccCCCCCCcchhhhc-Cc---eeEeccccceE
Confidence 345689997 4455544 33 89999999874
No 153
>PRK13764 ATPase; Provisional
Probab=31.29 E-value=76 Score=37.84 Aligned_cols=28 Identities=29% Similarity=0.421 Sum_probs=26.0
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEe
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIA 161 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~ 161 (766)
+-++.+|||+|+.++.||+..|.+|-|.
T Consensus 490 ~~~~~~~~k~~~~~~~~~~~~~~~i~v~ 517 (602)
T PRK13764 490 KDIPKVIGKGGKRIKKIEKKLGIDIDVR 517 (602)
T ss_pred hhhhHHhccCcchHHHHHHHhCCceEEE
Confidence 5589999999999999999999999985
No 154
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=31.08 E-value=14 Score=29.84 Aligned_cols=31 Identities=23% Similarity=0.451 Sum_probs=23.3
Q ss_pred CCcccccCCcccCCCCCCCCcccCCchhhcccccccc
Q psy8224 314 SGKCEVCKVAASLKCGGCNQVFYCSKSHQKQHWKEHK 350 (766)
Q Consensus 314 ~~~C~~C~~~~~~~C~~C~~v~YCs~~cq~~~w~~Hk 350 (766)
..+|..||.+-.. ...|||++|++.-++.++
T Consensus 3 HkHC~~CG~~Ip~------~~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 3 HKHCPVCGKPIPP------DESFCSPKCREEYRKRQK 33 (59)
T ss_pred CCcCCcCCCcCCc------chhhhCHHHHHHHHHHHH
Confidence 4689999987542 477999999988766544
No 155
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=30.80 E-value=56 Score=31.74 Aligned_cols=28 Identities=18% Similarity=0.290 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHHHHcCCChhhHHhhcc
Q psy8224 82 DISNLQKAADFVKAFVYGFDVDDALALLR 110 (766)
Q Consensus 82 d~~~~~ka~~~i~ai~~gf~~~~a~~ll~ 110 (766)
-..+..|++.+..+| ||-++++|+.+|+
T Consensus 23 ~rvS~kk~r~va~~I-RG~~v~~A~~~L~ 50 (153)
T PRK04223 23 LPISPKHSVEIAREI-RGMKLDEAKAYLE 50 (153)
T ss_pred CccChHHHHHHHHHH-cCCcHHHHHHHHH
Confidence 345677888888765 7888888888887
No 156
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=30.22 E-value=15 Score=26.21 Aligned_cols=31 Identities=13% Similarity=0.426 Sum_probs=20.1
Q ss_pred eecccCCceecCCCCCCCCCcccCCCCCcccHH
Q psy8224 198 LCSRCRHHVISTNPLDNLAKWKCIMCSHTLTAK 230 (766)
Q Consensus 198 ~c~~c~g~~l~~~pl~~~~~W~C~~C~~~~~~~ 230 (766)
-|+.|...++|..-..... .|..|++...+.
T Consensus 3 FCp~C~nlL~p~~~~~~~~--~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRV--ACRTCGYEEPIS 33 (35)
T ss_dssp BETTTTSBEEEEEETTTTE--EESSSS-EEE-S
T ss_pred eCCCCCccceEcCCCccCc--CCCCCCCccCCC
Confidence 3888988877766443222 699999987653
No 157
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.79 E-value=78 Score=31.50 Aligned_cols=41 Identities=10% Similarity=0.125 Sum_probs=30.9
Q ss_pred HHHHHHHhCCCCcEEeccCCCCCCccc-cccccccccccccccee
Q psy8224 672 MDRRLHLRMSKCFDCTCDRCKDPTELE-TYLGKSFCLVYCEIRSL 715 (766)
Q Consensus 672 ~~Rr~~L~~~y~F~C~C~rC~~~~e~~-~~~~~~~C~~~C~~~~~ 715 (766)
..+.+...++-+|.| +.|..+-.++ .+...|.||. |+..+.
T Consensus 102 k~~le~~~~~~~y~C--~~~~~r~sfdeA~~~~F~Cp~-Cg~~L~ 143 (176)
T COG1675 102 KRKLEKETENNYYVC--PNCHVKYSFDEAMELGFTCPK-CGEDLE 143 (176)
T ss_pred HHHHHhhccCCceeC--CCCCCcccHHHHHHhCCCCCC-CCchhh
Confidence 445566778889999 8888776554 5677899999 977653
No 158
>KOG1079|consensus
Probab=29.30 E-value=36 Score=40.18 Aligned_cols=43 Identities=23% Similarity=0.342 Sum_probs=33.2
Q ss_pred ccccccccccCCce--eeeecCccchhhhhhhcccCCCeeeeccc
Q psy8224 559 KTAMLSHNCKPNTK--HVIVNEDFSLQLIALVNICKGDIISTTYT 601 (766)
Q Consensus 559 ~~SllNHSC~PN~~--~~f~~~~~~l~~~A~r~I~~GeeI~~sY~ 601 (766)
.+-+.|||-.||+. ..++.+.-++-+.|.|.|.+|||+++-|.
T Consensus 665 k~rFANHS~nPNCYAkvm~V~GdhRIGifAkRaIeagEELffDYr 709 (739)
T KOG1079|consen 665 KIRFANHSFNPNCYAKVMMVAGDHRIGIFAKRAIEAGEELFFDYR 709 (739)
T ss_pred hhhhccCCCCCCcEEEEEEecCCcceeeeehhhcccCceeeeeec
Confidence 55678999999985 23323444688999999999999998664
No 159
>KOG2208|consensus
Probab=29.21 E-value=1.5e+02 Score=36.44 Aligned_cols=107 Identities=16% Similarity=0.108 Sum_probs=73.2
Q ss_pred ceEEEecCCCcchhhhccCcccHHHHHHhcCcEEEEEc---ccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChhhHH
Q psy8224 30 DMRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNL---KSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDAL 106 (766)
Q Consensus 30 ~~~~i~iP~~r~~~l~~~~~~i~~~i~~~~~~~i~i~~---~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf~~~~a~ 106 (766)
.-.++.|-+.-..+++|+.+.-.+.|++.+.+.+.+-. ..+.|.+.. .-..+.+|.+.|.-+..++
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~-----~~~~~~ka~~~v~~~~~ei------ 415 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITG-----VSANDEKAVEDVEKIIAEI------ 415 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEec-----cccchhHHHHHHHHHHHhh------
Confidence 34567788888999999998867889999998887743 344555543 4567788888887654332
Q ss_pred hhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhhC-ceEEEe
Q psy8224 107 ALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITK-TRIVIA 161 (766)
Q Consensus 107 ~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~-~~I~v~ 161 (766)
+.. ..-+.+.|. ++-..||||.+|+.+.+|..-+| ..|.-+
T Consensus 416 --~n~--~~~~~~~iP----------~k~~~~iig~~g~~i~~I~~k~~~v~i~f~ 457 (753)
T KOG2208|consen 416 --LNS--IVKEEVQIP----------TKSHKRIIGTKGALINYIMGKHGGVHIKFQ 457 (753)
T ss_pred --hcc--cccceeecC----------ccchhhhhccccccHHHHHhhcCcEEEecC
Confidence 110 111111222 24588999999999999999999 555443
No 160
>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=29.14 E-value=41 Score=24.46 Aligned_cols=29 Identities=21% Similarity=0.542 Sum_probs=19.4
Q ss_pred eeecccCCc-eecCCCCCCCCCcccCCCCC
Q psy8224 197 ILCSRCRHH-VISTNPLDNLAKWKCIMCSH 225 (766)
Q Consensus 197 l~c~~c~g~-~l~~~pl~~~~~W~C~~C~~ 225 (766)
.-|+.|.|. -...+-.+..+.|.|..|+.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 357888654 22244455678999999964
No 161
>KOG4369|consensus
Probab=28.64 E-value=31 Score=43.07 Aligned_cols=59 Identities=24% Similarity=0.206 Sum_probs=49.4
Q ss_pred ccchhhhhhccccCCCCcHHHHHHHhhCceEEEe--------CceEEEEcchhhHHHHHHHHHHhhc
Q psy8224 128 KGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIA--------DSKIHVLGSYQNVQVALKALSNLIL 186 (766)
Q Consensus 128 ~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~--------~~~v~iiG~~~~l~~ar~~i~~~~~ 186 (766)
+++-.--+..|+||++|.++.++-..||+.|-|. ++++.+-|..+..|+|...|--.|.
T Consensus 1343 k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~ 1409 (2131)
T KOG4369|consen 1343 KGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPII 1409 (2131)
T ss_pred ccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceee
Confidence 4444446789999999999999999999999984 2479999999999999888877663
No 162
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.42 E-value=22 Score=28.98 Aligned_cols=9 Identities=56% Similarity=1.438 Sum_probs=7.7
Q ss_pred cccCccCCC
Q psy8224 427 PLCAPRCKS 435 (766)
Q Consensus 427 ~yCS~~C~~ 435 (766)
+|||+.|+.
T Consensus 27 PFCSkRCkl 35 (65)
T COG3024 27 PFCSKRCKL 35 (65)
T ss_pred cchhHhhhh
Confidence 699999973
No 163
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=28.37 E-value=1.2e+02 Score=29.11 Aligned_cols=84 Identities=14% Similarity=0.228 Sum_probs=45.3
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchhhHHHHHHHHHHhhcCCCCcccccceeecccCCceecCCCC-
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSPPNKVYGGILCSRCRHHVISTNPL- 212 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~~l~~ar~~i~~~~~~~~p~~~~s~l~c~~c~g~~l~~~pl- 212 (766)
+.-||||=...+.....-...+. +.++.+-+..+..++.+...--...+... .-+|..|.|.+.+..+.
T Consensus 39 ~~e~RillTrd~~l~~~~~~~~~--------~~li~~~~~~~QL~ev~~~~~l~~~~~~~--~sRC~~CN~~L~~v~~~~ 108 (147)
T PF01927_consen 39 REEGRILLTRDRDLLKRRRVSGG--------VILIRSDDPEEQLREVLERFGLKLRLDPI--FSRCPKCNGPLRPVSKEE 108 (147)
T ss_pred hhCCeEEEECCHHHHHHhhccCC--------EEEEcCCCHHHHHHHHHHHcCCccccCCC--CCccCCCCcEeeechhhc
Confidence 34477775555433322222222 23344444455556666655332223222 45899998876555443
Q ss_pred -----------CCCCCcccCCCCCcc
Q psy8224 213 -----------DNLAKWKCIMCSHTL 227 (766)
Q Consensus 213 -----------~~~~~W~C~~C~~~~ 227 (766)
..+.-|.|..|++..
T Consensus 109 v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 109 VKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred cccccCccccccCCeEEECCCCCCEe
Confidence 224579999999874
No 164
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=27.21 E-value=74 Score=30.82 Aligned_cols=28 Identities=21% Similarity=0.318 Sum_probs=22.5
Q ss_pred CHHHHHHHHHHHHHHHcCCChhhHHhhcc
Q psy8224 82 DISNLQKAADFVKAFVYGFDVDDALALLR 110 (766)
Q Consensus 82 d~~~~~ka~~~i~ai~~gf~~~~a~~ll~ 110 (766)
-..+..|++.++.+| ||-++++|+..|+
T Consensus 19 ~riS~kk~r~va~~I-rG~~v~~A~~~L~ 46 (150)
T TIGR01038 19 LRVSFKNARETARAI-RGMELDKARKYLE 46 (150)
T ss_pred CcccHHHHHHHHHHH-cCCcHHHHHHHHH
Confidence 346778888888866 7999999999987
No 165
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=27.02 E-value=1.7e+02 Score=22.98 Aligned_cols=36 Identities=17% Similarity=0.402 Sum_probs=25.6
Q ss_pred ccHHHHHHhcCc-EEEEEcccCeEEEEeCCCCCCHHH
Q psy8224 50 KIFTPIVEHLKL-QVRFNLKSRNVEIRLSPETEDISN 85 (766)
Q Consensus 50 ~i~~~i~~~~~~-~i~i~~~~~~v~i~~~~~t~d~~~ 85 (766)
.|.+.|...-|+ .+.+|..++.|+|.......++..
T Consensus 15 ~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~ 51 (62)
T PF00403_consen 15 KVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEK 51 (62)
T ss_dssp HHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHH
T ss_pred HHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHH
Confidence 455667777776 599999999999998544333433
No 166
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=27.00 E-value=23 Score=32.11 Aligned_cols=61 Identities=18% Similarity=0.245 Sum_probs=38.9
Q ss_pred HHHHHH-HHHcCCChhhHHhhcccccceeeeeeeccccccccchhhhhhccccCCCCcHHHHHHHhh
Q psy8224 89 AADFVK-AFVYGFDVDDALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENIT 154 (766)
Q Consensus 89 a~~~i~-ai~~gf~~~~a~~ll~~d~~~~~~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t 154 (766)
+..+++ ++..|++.++|.++.- . .+. --..+....+.+++..+.++.-+||-|.+.|+.+-
T Consensus 24 ~eal~~a~v~~Gl~~~~A~~lv~-~-t~~---G~a~ll~~~~~~~~~l~~~v~tPgG~T~~gl~~L~ 85 (107)
T PF14748_consen 24 IEALADAAVAQGLPREEARKLVA-Q-TFI---GAAKLLEESGRSPAELRDEVTTPGGTTIAGLEVLE 85 (107)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHH-H-HHH---HHHHHHHHCSS-HHHHHHHHS-TTSHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHH-H-HHH---HHHHHHHccCCCHHHHhhhccCCCCcHHHHHHHHH
Confidence 334444 4567999999999975 2 221 11222233456888999999999999999999875
No 167
>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=26.86 E-value=37 Score=30.88 Aligned_cols=22 Identities=18% Similarity=0.164 Sum_probs=18.4
Q ss_pred hccccCCCCcHHHHHHHhhCce
Q psy8224 136 IGRLAGKGGRTKFTIENITKTR 157 (766)
Q Consensus 136 ~griiG~~G~t~~~ie~~t~~~ 157 (766)
-|+|||++|++++.|+......
T Consensus 72 Pg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 72 PGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred CCcccCCchHHHHHHHHHHHHH
Confidence 6999999999999988765544
No 168
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=26.35 E-value=52 Score=21.61 Aligned_cols=24 Identities=29% Similarity=0.966 Sum_probs=15.2
Q ss_pred cccccCCCCCCCcccCCCCCcccCCCCCc
Q psy8224 398 CLGCHRTLKPTSMEENEPLSFYKCSDCGW 426 (766)
Q Consensus 398 C~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 426 (766)
|..|...+.+.. ....+.||.|++
T Consensus 1 C~sC~~~i~~r~-----~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPRE-----QAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcc-----cCceEeCCCCCC
Confidence 566766665432 134789999974
No 169
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.32 E-value=34 Score=29.71 Aligned_cols=57 Identities=16% Similarity=0.428 Sum_probs=33.4
Q ss_pred ceEEEEcchhh-----HHHHHHHHHHhhcCCCCcccccceeecccCCceecCCCCCCCCCcccCCCCCcccHH
Q psy8224 163 SKIHVLGSYQN-----VQVALKALSNLILGSPPNKVYGGILCSRCRHHVISTNPLDNLAKWKCIMCSHTLTAK 230 (766)
Q Consensus 163 ~~v~iiG~~~~-----l~~ar~~i~~~~~~~~p~~~~s~l~c~~c~g~~l~~~pl~~~~~W~C~~C~~~~~~~ 230 (766)
+.|.+-|.|-. |+.-...|+.-++ ..-.|+.|.-..+--- ..+-|.|.+|+++.-+.
T Consensus 5 kkvG~aGrfGpRYG~~~Rrrv~~ie~~~~--------~~~~Cp~C~~~~VkR~---a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 5 KKVGIAGRFGPRYGSKLRRRVKEIEAQQR--------AKHVCPFCGRTTVKRI---ATGIWKCRKCGAKFAGG 66 (89)
T ss_pred ceeccCcccccccchHHHHHHHHHHHHHh--------cCCcCCCCCCcceeee---ccCeEEcCCCCCeeccc
Confidence 45777777752 4444444444433 3336888864422222 24689999999986543
No 170
>PF09846 DUF2073: Uncharacterized protein conserved in archaea (DUF2073); InterPro: IPR012017 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.08 E-value=67 Score=28.81 Aligned_cols=43 Identities=26% Similarity=0.419 Sum_probs=26.8
Q ss_pred eeeeccccccccchhhhhhccccCCCCcHHHHHHHhhCceEEEeCceEEEEcchhhHHHHHH
Q psy8224 118 SFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALK 179 (766)
Q Consensus 118 ~~~i~~~~~~~~~~~~r~~griiG~~G~t~~~ie~~t~~~I~v~~~~v~iiG~~~~l~~ar~ 179 (766)
-|+|..+-... .=+-..|||.|++.. ....|||+.++++..|+
T Consensus 52 GIEiesyp~~~--~~~~f~~rl~gk~~~-----------------~rlTVIGPAn~mktlkK 94 (104)
T PF09846_consen 52 GIEIESYPSKE--ADKSFLGRLLGKKSR-----------------ERLTVIGPANQMKTLKK 94 (104)
T ss_pred ceEEEecCccc--ccccHHHHHhCCCCC-----------------CCeEEEccHHHHHHHhc
Confidence 45665553222 111336888888742 25788999999987664
No 171
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=25.84 E-value=23 Score=26.64 Aligned_cols=31 Identities=19% Similarity=0.407 Sum_probs=22.3
Q ss_pred CcccccCCcccCCCCCCCCcccCCchhhcccccc
Q psy8224 315 GKCEVCKVAASLKCGGCNQVFYCSKSHQKQHWKE 348 (766)
Q Consensus 315 ~~C~~C~~~~~~~C~~C~~v~YCs~~cq~~~w~~ 348 (766)
..|-.|.+.-.. .-...-|||++|+..|+..
T Consensus 7 ~yC~~Cdk~~~~---~~~~~lYCSe~Cr~~D~~~ 37 (43)
T PF12855_consen 7 DYCIVCDKQIDP---PDDGSLYCSEECRLKDQEK 37 (43)
T ss_pred hHHHHhhccccC---CCCCccccCHHHHhHhhhc
Confidence 457777765322 2356789999999999876
No 172
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=24.54 E-value=1.2e+02 Score=26.70 Aligned_cols=39 Identities=15% Similarity=0.269 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHhcccCCChhhHHHHHHHHhccccccCC
Q psy8224 232 IAMGNDSIKSELAGLDKTEPTGLEMFLDKFQAQDSVLHD 270 (766)
Q Consensus 232 v~~~~~~~~~e~~~~~~~~~~~~e~~l~k~~~~~~~l~p 270 (766)
+.+.++.+.+-++-++.++.+.++.|+.+|+.++.+.+.
T Consensus 23 mdkFldSf~el~dv~~~~d~DelmdFIsryARTDEImPE 61 (110)
T PF11513_consen 23 MDKFLDSFKELIDVITSPDIDELMDFISRYARTDEIMPE 61 (110)
T ss_dssp HHHHHHHHHHHHHHTTS--CCHHHHHHHHH---S---TT
T ss_pred HHHHHHHHHHHHhhhccccHHHHHHHHHHhhcccccCCC
Confidence 456778888877778878888899999999977544443
No 173
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=24.32 E-value=53 Score=31.60 Aligned_cols=65 Identities=20% Similarity=0.558 Sum_probs=44.4
Q ss_pred EEEeCceEEEEcchhhHHHHHHHHHHhhcCCCCcccccceee--cccC-C--------c-eecCCCCCCCCCcccCCCCC
Q psy8224 158 IVIADSKIHVLGSYQNVQVALKALSNLILGSPPNKVYGGILC--SRCR-H--------H-VISTNPLDNLAKWKCIMCSH 225 (766)
Q Consensus 158 I~v~~~~v~iiG~~~~l~~ar~~i~~~~~~~~p~~~~s~l~c--~~c~-g--------~-~l~~~pl~~~~~W~C~~C~~ 225 (766)
+.=.+-||.||-+|+=++-. +=..|.++.+.|+| +.|- . + ++..+|+ ..+|.=|+.
T Consensus 76 liaP~ATvNiI~ny~VveK~--------~v~lP~~i~gvlkCpN~nCITn~e~pv~s~F~~~~~~~~----~lrC~YCe~ 143 (153)
T COG1781 76 LIAPNATVNIIRNYEVVEKF--------KVKLPEEIEGVLRCPNPNCITNAEEPVESKFYVVSKEPL----ALRCKYCEK 143 (153)
T ss_pred eeCCCCEEEEeeceEEEEee--------ccCCChhhccEEEcCCCCcccCCCccCCccEEEEecCCc----EEEEEecCc
Confidence 34456789999888743321 23568888999999 4472 1 1 4444553 699999999
Q ss_pred cccHHHHHH
Q psy8224 226 TLTAKQIAM 234 (766)
Q Consensus 226 ~~~~~~v~~ 234 (766)
+++.++|..
T Consensus 144 ~~~~~~v~~ 152 (153)
T COG1781 144 TFSEDEVLE 152 (153)
T ss_pred Eechhhhhc
Confidence 999888753
No 174
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.01 E-value=49 Score=25.37 Aligned_cols=29 Identities=17% Similarity=0.526 Sum_probs=18.6
Q ss_pred ecccCCceecCCCCCCCCCcccCCCCCccc
Q psy8224 199 CSRCRHHVISTNPLDNLAKWKCIMCSHTLT 228 (766)
Q Consensus 199 c~~c~g~~l~~~pl~~~~~W~C~~C~~~~~ 228 (766)
|+.|+..+.+.. ++....|.|..|++...
T Consensus 3 Cp~Cg~~l~~~~-~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 3 CPKCGNMLIPKE-GKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCcccccc-CCCCCEEECCcCCCeEE
Confidence 777865444443 33334799999998744
No 175
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=23.75 E-value=72 Score=36.69 Aligned_cols=29 Identities=31% Similarity=0.263 Sum_probs=25.0
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEEeC
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVIAD 162 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v~~ 162 (766)
+.-|.+|||+|+|.+.|-..||=.=.|.-
T Consensus 108 ~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 108 KKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred cCCceEEecCchHHHHHHHHhCCcceeee
Confidence 44789999999999999999998777653
No 176
>PF04723 GRDA: Glycine reductase complex selenoprotein A; InterPro: IPR006812 Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP []. A member of this family may also exist in Treponema denticola [].; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=22.51 E-value=52 Score=31.08 Aligned_cols=43 Identities=14% Similarity=0.375 Sum_probs=35.8
Q ss_pred EEeCceEEEEcchhhHHHHHHHHHHhhcCCCCcccccceeecccC
Q psy8224 159 VIADSKIHVLGSYQNVQVALKALSNLILGSPPNKVYGGILCSRCR 203 (766)
Q Consensus 159 ~v~~~~v~iiG~~~~l~~ar~~i~~~~~~~~p~~~~s~l~c~~c~ 203 (766)
.+.||+|.|||..++|- -.+++.|++...-.-+||+-.|--|+
T Consensus 2 ~l~gkKviiiGdRDGiP--gpAie~c~~~~gaevvfs~TeCFVct 44 (150)
T PF04723_consen 2 ILEGKKVIIIGDRDGIP--GPAIEECVKTAGAEVVFSSTECFVCT 44 (150)
T ss_pred ccCCcEEEEEecCCCCC--cHHHHHHHHhcCceEEEEeeeEEEec
Confidence 36799999999999875 35788999888766689999998885
No 177
>PF14369 zf-RING_3: zinc-finger
Probab=21.45 E-value=60 Score=23.25 Aligned_cols=27 Identities=15% Similarity=0.379 Sum_probs=15.0
Q ss_pred ccCCCCCCccccccc-cccccccccccee
Q psy8224 688 CDRCKDPTELETYLG-KSFCLVYCEIRSL 715 (766)
Q Consensus 688 C~rC~~~~e~~~~~~-~~~C~~~C~~~~~ 715 (766)
|-.|...-....... ...||. |.+|++
T Consensus 5 Ch~C~~~V~~~~~~~~~~~CP~-C~~gFv 32 (35)
T PF14369_consen 5 CHQCNRFVRIAPSPDSDVACPR-CHGGFV 32 (35)
T ss_pred CccCCCEeEeCcCCCCCcCCcC-CCCcEe
Confidence 456655333221222 235999 999886
No 178
>KOG2461|consensus
Probab=21.16 E-value=70 Score=36.09 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=24.6
Q ss_pred CeEEEEEEecccCCCCeEEeecCCCCC
Q psy8224 643 DFSLQLIALVNIRKGDIISTTYTQPFW 669 (766)
Q Consensus 643 g~~l~vra~r~I~~GeeI~isY~~~~~ 669 (766)
|..+..+|+|+|++|+||.+=|++.+.
T Consensus 121 ~~~Ifyrt~r~I~p~eELlVWY~~e~~ 147 (396)
T KOG2461|consen 121 GENIFYRTIRDIRPNEELLVWYGSEYA 147 (396)
T ss_pred cCceEEEecccCCCCCeEEEEeccchH
Confidence 689999999999999999999998653
No 179
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=21.12 E-value=44 Score=28.74 Aligned_cols=27 Identities=15% Similarity=0.290 Sum_probs=19.6
Q ss_pred hhhccccCCCCcHHHHHHHhhCceEEE
Q psy8224 134 RAIGRLAGKGGRTKFTIENITKTRIVI 160 (766)
Q Consensus 134 r~~griiG~~G~t~~~ie~~t~~~I~v 160 (766)
..-|.|||++|++++.|.....-..-+
T Consensus 39 arPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 39 TRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CCCceEECCCchhHHHHHHHHHHHhCC
Confidence 346999999999999887755443333
No 180
>KOG2113|consensus
Probab=21.02 E-value=62 Score=34.73 Aligned_cols=52 Identities=19% Similarity=0.277 Sum_probs=42.8
Q ss_pred hhhhhccccCCCCcHHHHHHHhhCceEEEe----CceEEEEcchhhHHHHHHHHHH
Q psy8224 132 LSRAIGRLAGKGGRTKFTIENITKTRIVIA----DSKIHVLGSYQNVQVALKALSN 183 (766)
Q Consensus 132 ~~r~~griiG~~G~t~~~ie~~t~~~I~v~----~~~v~iiG~~~~l~~ar~~i~~ 183 (766)
.++.++-|.|++|-++++|...|++||+-- +-+.-+-|.++.++.||+=|..
T Consensus 33 ps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 33 PSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCcc
Confidence 367899999999999999999999999863 2235568999999999985543
No 181
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.86 E-value=77 Score=22.30 Aligned_cols=27 Identities=30% Similarity=0.488 Sum_probs=18.9
Q ss_pred eccCCCCCCccccccccccccccccccee
Q psy8224 687 TCDRCKDPTELETYLGKSFCLVYCEIRSL 715 (766)
Q Consensus 687 ~C~rC~~~~e~~~~~~~~~C~~~C~~~~~ 715 (766)
.|..|-.+.++. ....++|+. |+..++
T Consensus 2 ~C~~Cg~~~~~~-~~~~irC~~-CG~RIl 28 (32)
T PF03604_consen 2 ICGECGAEVELK-PGDPIRCPE-CGHRIL 28 (32)
T ss_dssp BESSSSSSE-BS-TSSTSSBSS-SS-SEE
T ss_pred CCCcCCCeeEcC-CCCcEECCc-CCCeEE
Confidence 377898887755 566899999 987654
No 182
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=20.83 E-value=77 Score=30.90 Aligned_cols=60 Identities=15% Similarity=0.130 Sum_probs=0.0
Q ss_pred HHHHHHHhCCCCcEEeccCCCCCCccccccc-ccccccccccceeccccchhHHHHHHHHHHHHHHHHh
Q psy8224 672 MDRRLHLRMSKCFDCTCDRCKDPTELETYLG-KSFCLVYCEIRSLASLVSLDNCEEAMRYLAESTEIIK 739 (766)
Q Consensus 672 ~~Rr~~L~~~y~F~C~C~rC~~~~e~~~~~~-~~~C~~~C~~~~~~~~~~~~~c~~~~~~~~~~~~~~~ 739 (766)
..|.+.-.+.-+|.| ++|.........++ .|.||. |++.+. ...-...+..|++.++.+.
T Consensus 98 k~~l~~e~~~~~Y~C--p~c~~r~tf~eA~~~~F~Cp~-Cg~~L~-----~~dn~~~i~~l~~~i~~l~ 158 (158)
T TIGR00373 98 REKLEFETNNMFFIC--PNMCVRFTFNEAMELNFTCPR-CGAMLD-----YLDNSEAIEKLEEQIKFLK 158 (158)
T ss_pred HHHHhhccCCCeEEC--CCCCcEeeHHHHHHcCCcCCC-CCCEee-----eccCHHHHHHHHHHHHhhC
No 183
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.81 E-value=47 Score=24.41 Aligned_cols=39 Identities=18% Similarity=0.359 Sum_probs=25.1
Q ss_pred eecccCCceecCCCCCCCCCcccCCCCCc-ccHHHHHHHHH
Q psy8224 198 LCSRCRHHVISTNPLDNLAKWKCIMCSHT-LTAKQIAMGND 237 (766)
Q Consensus 198 ~c~~c~g~~l~~~pl~~~~~W~C~~C~~~-~~~~~v~~~~~ 237 (766)
+|++|...+.+. .+..-.-+.|.+|+.. +++.+..++++
T Consensus 1 ~CP~C~~~l~~~-~~~~~~id~C~~C~G~W~d~~el~~~~e 40 (41)
T PF13453_consen 1 KCPRCGTELEPV-RLGDVEIDVCPSCGGIWFDAGELEKLLE 40 (41)
T ss_pred CcCCCCcccceE-EECCEEEEECCCCCeEEccHHHHHHHHh
Confidence 478886432222 2233456889999966 78888877765
No 184
>KOG2279|consensus
Probab=20.79 E-value=53 Score=37.94 Aligned_cols=58 Identities=16% Similarity=0.229 Sum_probs=47.5
Q ss_pred hhccccCCCCcHHHHHHHhhCceEEEeCce-----EEEEc-chhhHHHHHHHHHHhhcCCCCcc
Q psy8224 135 AIGRLAGKGGRTKFTIENITKTRIVIADSK-----IHVLG-SYQNVQVALKALSNLILGSPPNK 192 (766)
Q Consensus 135 ~~griiG~~G~t~~~ie~~t~~~I~v~~~~-----v~iiG-~~~~l~~ar~~i~~~~~~~~p~~ 192 (766)
.+--|||+.|.+++.|+..|+.+|++.+.+ +-++| -..++.-|+.+++..+....|-+
T Consensus 78 ~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pvk 141 (608)
T KOG2279|consen 78 AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTENTPVS 141 (608)
T ss_pred ceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhcCCccc
Confidence 466799999999999999999999997544 55555 55689999999999887777744
No 185
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=20.60 E-value=53 Score=23.42 Aligned_cols=28 Identities=18% Similarity=0.460 Sum_probs=14.6
Q ss_pred ecccCCce-ecCCCCCCCCCcccCCCCCc
Q psy8224 199 CSRCRHHV-ISTNPLDNLAKWKCIMCSHT 226 (766)
Q Consensus 199 c~~c~g~~-l~~~pl~~~~~W~C~~C~~~ 226 (766)
|+.|.+.+ +..-+.|....|.|..|++.
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred cccccChhhhhcCCCCCccceECCCCCCE
Confidence 78898763 33333455668999999864
No 186
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.59 E-value=72 Score=31.79 Aligned_cols=62 Identities=15% Similarity=0.164 Sum_probs=0.0
Q ss_pred HHHHHHHhCCCCcEEeccCCCCCCccccccc-ccccccccccceeccccchhHHHHHHHHHHHHHHHHhcc
Q psy8224 672 MDRRLHLRMSKCFDCTCDRCKDPTELETYLG-KSFCLVYCEIRSLASLVSLDNCEEAMRYLAESTEIIKTE 741 (766)
Q Consensus 672 ~~Rr~~L~~~y~F~C~C~rC~~~~e~~~~~~-~~~C~~~C~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~ 741 (766)
.+|.+.-.+.-+|.| ++|.........++ .|.||. |++.+. -..-...+..|++.++.+..+
T Consensus 106 k~~l~~e~~~~~Y~C--p~C~~rytf~eA~~~~F~Cp~-Cg~~L~-----~~dn~~~~~~l~~~I~~l~~~ 168 (178)
T PRK06266 106 KEQLEEEENNMFFFC--PNCHIRFTFDEAMEYGFRCPQ-CGEMLE-----EYDNSELIKELKEQIKELEEE 168 (178)
T ss_pred HHHhhhccCCCEEEC--CCCCcEEeHHHHhhcCCcCCC-CCCCCe-----ecccHHHHHHHHHHHHHHHHH
No 187
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=20.14 E-value=1e+02 Score=25.19 Aligned_cols=66 Identities=14% Similarity=0.215 Sum_probs=46.4
Q ss_pred EEEecCCCcchhhhccCcc--cHHHHHHhcCcEEEEEcccCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCC
Q psy8224 32 RKVPVPNHRYGPLKENWMK--IFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGF 100 (766)
Q Consensus 32 ~~i~iP~~r~~~l~~~~~~--i~~~i~~~~~~~i~i~~~~~~v~i~~~~~t~d~~~~~ka~~~i~ai~~gf 100 (766)
..+.++..++.-+.|..-. -...+.+++|..+..+..++.+.|... ++= ..++...|+|.-|+|++
T Consensus 2 ~~i~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~~~~~~~~~~v~~P--~~R-~Di~~~~DliEei~r~~ 69 (71)
T smart00874 2 RTITLRRERINRLLGLDLSAEEIEEILKRLGFEVEVSGDDDTLEVTVP--SYR-FDILIEADLIEEVARIY 69 (71)
T ss_pred cEEEecHHHHHHHHCCCCCHHHHHHHHHHCCCeEEecCCCCeEEEECC--CCc-cccCcccHHHHHHHHHh
Confidence 4678888899888886542 235566889998876544566776642 222 47888999999888854
No 188
>PF08666 SAF: SAF domain; InterPro: IPR013974 This entry includes a range of different proteins, such as antifreeze proteins, flagellar FlgA proteins, and CpaB pilus proteins. ; PDB: 1C89_A 3NLA_A 3RDN_A 1C8A_A 3FRN_A 1WVO_A 3K3S_H 3G8R_B 1XUU_A 1XUZ_A ....
Probab=20.07 E-value=61 Score=25.66 Aligned_cols=16 Identities=25% Similarity=0.486 Sum_probs=11.7
Q ss_pred EEEEecccCCCCeEEe
Q psy8224 647 QLIALVNIRKGDIIST 662 (766)
Q Consensus 647 ~vra~r~I~~GeeI~i 662 (766)
++.|.++|++|+.|+-
T Consensus 3 vvVA~~di~~G~~i~~ 18 (63)
T PF08666_consen 3 VVVAARDIPAGTVITA 18 (63)
T ss_dssp EEEESSTB-TT-BECT
T ss_pred EEEEeCccCCCCEEcc
Confidence 5789999999999853
Done!