Query psy7546
Match_columns 150
No_of_seqs 110 out of 1362
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 21:08:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7546.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7546hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2191|consensus 99.9 6E-24 1.3E-28 164.0 14.0 131 9-150 26-163 (402)
2 KOG2190|consensus 99.9 2.4E-21 5.2E-26 159.4 11.4 119 18-150 40-169 (485)
3 KOG1676|consensus 99.9 2.2E-21 4.8E-26 159.3 10.7 117 19-150 228-349 (600)
4 KOG1676|consensus 99.8 8.6E-20 1.9E-24 150.0 12.6 122 18-150 136-261 (600)
5 KOG2192|consensus 99.8 3.1E-19 6.8E-24 135.0 8.7 109 19-150 46-154 (390)
6 KOG2193|consensus 99.8 1.7E-19 3.7E-24 143.4 4.9 117 15-150 405-524 (584)
7 KOG2190|consensus 99.7 3.5E-17 7.7E-22 134.9 12.2 131 20-150 137-287 (485)
8 KOG2193|consensus 99.7 4.7E-17 1E-21 129.6 5.4 113 18-150 196-311 (584)
9 KOG2192|consensus 99.7 3.5E-16 7.7E-21 118.5 8.5 75 16-90 118-195 (390)
10 cd02396 PCBP_like_KH K homolog 99.7 2.9E-16 6.3E-21 96.8 6.5 61 22-82 1-64 (65)
11 KOG2191|consensus 99.6 5.2E-15 1.1E-19 114.8 8.2 129 22-150 133-275 (402)
12 cd02394 vigilin_like_KH K homo 99.6 1.1E-14 2.4E-19 88.7 6.0 60 23-82 2-61 (62)
13 PF00013 KH_1: KH domain syndr 99.5 9.6E-15 2.1E-19 88.4 4.1 60 22-82 1-60 (60)
14 TIGR03665 arCOG04150 arCOG0415 99.5 6.3E-14 1.4E-18 101.9 6.2 104 25-150 2-120 (172)
15 PRK13763 putative RNA-processi 99.5 1.8E-13 3.8E-18 100.2 7.6 108 21-150 3-126 (180)
16 cd00105 KH-I K homology RNA-bi 99.5 3.7E-13 7.9E-18 82.1 7.5 61 22-82 1-63 (64)
17 cd02393 PNPase_KH Polynucleoti 99.5 4.9E-13 1.1E-17 81.3 7.6 58 21-82 2-60 (61)
18 smart00322 KH K homology RNA-b 99.3 2E-11 4.4E-16 74.4 8.6 67 20-86 2-68 (69)
19 PF13014 KH_3: KH domain 99.3 8.5E-12 1.9E-16 70.6 5.1 40 31-70 1-43 (43)
20 KOG2279|consensus 98.9 7.9E-10 1.7E-14 91.0 3.5 107 17-150 64-171 (608)
21 cd02395 SF1_like-KH Splicing f 98.8 5.9E-08 1.3E-12 66.6 8.1 59 30-88 15-95 (120)
22 PRK08406 transcription elongat 98.7 1.6E-08 3.5E-13 71.2 4.8 98 21-149 32-129 (140)
23 KOG2113|consensus 98.6 3.2E-08 6.9E-13 76.9 4.5 122 19-149 24-145 (394)
24 cd02393 PNPase_KH Polynucleoti 98.6 8.4E-08 1.8E-12 58.2 3.7 32 119-150 2-33 (61)
25 TIGR03665 arCOG04150 arCOG0415 98.5 1.3E-07 2.8E-12 68.8 5.2 53 31-88 99-151 (172)
26 cd02396 PCBP_like_KH K homolog 98.5 6.7E-08 1.5E-12 59.2 2.6 31 120-150 1-31 (65)
27 PRK13763 putative RNA-processi 98.5 3.1E-07 6.7E-12 67.3 5.9 53 31-88 105-157 (180)
28 TIGR01952 nusA_arch NusA famil 98.4 4E-07 8.6E-12 64.1 3.5 97 22-149 34-130 (141)
29 KOG2208|consensus 98.3 1.2E-06 2.6E-11 76.5 7.0 105 20-149 346-450 (753)
30 PF00013 KH_1: KH domain syndr 98.3 8.3E-08 1.8E-12 57.7 -0.2 31 120-150 1-31 (60)
31 cd00105 KH-I K homology RNA-bi 98.3 7.9E-07 1.7E-11 53.7 3.1 30 121-150 2-31 (64)
32 cd02394 vigilin_like_KH K homo 98.3 4.1E-07 8.8E-12 55.0 1.8 30 121-150 2-31 (62)
33 KOG0336|consensus 98.3 2.3E-06 5.1E-11 69.5 6.4 74 16-90 42-115 (629)
34 PF13014 KH_3: KH domain 98.2 1.5E-06 3.2E-11 48.9 2.3 22 129-150 1-22 (43)
35 TIGR02696 pppGpp_PNP guanosine 97.9 3E-05 6.5E-10 67.1 7.4 64 20-87 577-641 (719)
36 smart00322 KH K homology RNA-b 97.9 1.3E-05 2.9E-10 48.2 3.8 32 119-150 3-34 (69)
37 COG1094 Predicted RNA-binding 97.9 1.8E-05 3.9E-10 58.1 4.3 112 19-150 6-133 (194)
38 TIGR03591 polynuc_phos polyrib 97.9 3E-05 6.5E-10 67.4 6.1 66 18-87 548-614 (684)
39 COG0195 NusA Transcription elo 97.8 1.2E-05 2.7E-10 59.2 2.8 93 25-149 80-172 (190)
40 KOG0119|consensus 97.8 8.7E-05 1.9E-09 61.2 7.9 70 20-89 137-231 (554)
41 KOG2279|consensus 97.8 2.7E-05 5.9E-10 64.8 4.7 133 18-150 137-327 (608)
42 cd02134 NusA_KH NusA_K homolog 97.7 8.6E-05 1.9E-09 44.8 4.5 37 20-56 24-60 (61)
43 KOG2814|consensus 97.6 9.7E-05 2.1E-09 58.2 5.1 70 21-90 57-127 (345)
44 KOG1588|consensus 97.6 0.0001 2.3E-09 56.4 4.6 42 16-57 87-134 (259)
45 COG1094 Predicted RNA-binding 97.5 0.00031 6.8E-09 51.7 5.9 53 31-88 112-164 (194)
46 TIGR02696 pppGpp_PNP guanosine 97.2 0.00096 2.1E-08 58.0 6.4 35 116-150 575-609 (719)
47 cd02134 NusA_KH NusA_K homolog 97.1 0.0007 1.5E-08 40.8 3.7 32 118-149 24-55 (61)
48 PRK12327 nusA transcription el 97.1 0.00045 9.7E-09 55.8 3.7 88 30-149 245-333 (362)
49 COG5176 MSL5 Splicing factor ( 97.1 0.0015 3.2E-08 48.6 5.8 40 19-58 146-191 (269)
50 PRK00468 hypothetical protein; 97.1 0.0008 1.7E-08 42.3 3.6 35 16-50 25-59 (75)
51 TIGR03591 polynuc_phos polyrib 97.1 0.0008 1.7E-08 58.6 4.8 34 117-150 549-582 (684)
52 TIGR01953 NusA transcription t 97.1 0.00057 1.2E-08 54.8 3.5 106 12-149 224-331 (341)
53 PRK04163 exosome complex RNA-b 97.0 0.0019 4.2E-08 49.2 6.1 59 23-85 147-206 (235)
54 PLN00207 polyribonucleotide nu 97.0 0.00074 1.6E-08 60.0 4.3 65 19-87 683-749 (891)
55 TIGR03319 YmdA_YtgF conserved 97.0 0.0028 6.1E-08 53.6 7.1 49 19-70 202-251 (514)
56 PRK00468 hypothetical protein; 97.0 0.00074 1.6E-08 42.5 2.8 32 116-147 27-58 (75)
57 PRK12704 phosphodiesterase; Pr 97.0 0.0028 6E-08 53.7 7.0 49 19-70 208-257 (520)
58 PRK12328 nusA transcription el 97.0 0.00054 1.2E-08 55.4 2.6 87 30-149 251-338 (374)
59 PRK02821 hypothetical protein; 97.0 0.00081 1.8E-08 42.5 2.8 32 117-148 29-60 (77)
60 PRK00106 hypothetical protein; 96.9 0.0034 7.4E-08 53.2 7.3 50 18-70 222-272 (535)
61 COG1185 Pnp Polyribonucleotide 96.9 0.0021 4.5E-08 55.3 5.9 65 20-88 551-616 (692)
62 PRK02821 hypothetical protein; 96.9 0.0012 2.7E-08 41.7 3.4 36 17-52 27-62 (77)
63 PRK12329 nusA transcription el 96.9 0.00074 1.6E-08 55.6 2.9 88 30-149 277-365 (449)
64 COG1837 Predicted RNA-binding 96.9 0.0016 3.4E-08 41.0 3.7 32 18-49 27-58 (76)
65 PRK09202 nusA transcription el 96.8 0.0007 1.5E-08 56.5 2.3 87 30-149 245-332 (470)
66 PRK01064 hypothetical protein; 96.8 0.002 4.4E-08 40.8 3.8 35 16-50 25-59 (78)
67 PRK01064 hypothetical protein; 96.8 0.0016 3.6E-08 41.2 3.3 33 116-148 27-59 (78)
68 COG1837 Predicted RNA-binding 96.6 0.003 6.6E-08 39.7 3.3 32 116-147 27-58 (76)
69 PRK08406 transcription elongat 96.4 0.0042 9E-08 43.8 3.3 39 19-57 97-135 (140)
70 PRK11824 polynucleotide phosph 96.3 0.0042 9.1E-08 54.3 3.6 63 21-87 554-617 (693)
71 PLN00207 polyribonucleotide nu 96.3 0.0051 1.1E-07 54.9 4.0 35 116-150 682-716 (891)
72 KOG2208|consensus 96.2 0.0032 7E-08 55.4 2.8 103 18-149 637-739 (753)
73 cd02414 jag_KH jag_K homology 96.1 0.005 1.1E-07 38.7 2.5 35 21-55 24-58 (77)
74 PF13083 KH_4: KH domain; PDB: 95.9 0.0045 9.7E-08 38.5 1.4 35 18-52 26-60 (73)
75 cd02410 archeal_CPSF_KH The ar 95.6 0.032 7E-07 39.4 5.1 86 36-149 21-106 (145)
76 cd02409 KH-II KH-II (K homolo 95.6 0.027 5.8E-07 33.6 4.3 35 20-54 24-58 (68)
77 KOG0336|consensus 95.4 0.0085 1.9E-07 49.3 1.8 37 113-149 41-77 (629)
78 PF13083 KH_4: KH domain; PDB: 95.3 0.0044 9.4E-08 38.5 -0.2 33 116-148 26-58 (73)
79 PRK12705 hypothetical protein; 95.2 0.03 6.5E-07 47.3 4.5 42 19-60 196-238 (508)
80 COG1097 RRP4 RNA-binding prote 95.2 0.088 1.9E-06 40.1 6.5 46 25-74 150-195 (239)
81 COG1782 Predicted metal-depend 95.2 0.042 9.2E-07 46.2 5.2 88 34-149 42-129 (637)
82 PF13184 KH_5: NusA-like KH do 95.2 0.015 3.2E-07 36.0 2.0 37 23-59 5-47 (69)
83 PRK06418 transcription elongat 95.0 0.031 6.7E-07 40.4 3.5 35 24-59 64-98 (166)
84 KOG4369|consensus 94.9 0.014 3E-07 53.3 1.8 65 18-82 1337-1404(2131)
85 PRK11824 polynucleotide phosph 94.8 0.025 5.4E-07 49.6 3.0 34 117-150 552-585 (693)
86 PF07650 KH_2: KH domain syndr 94.8 0.015 3.3E-07 36.4 1.2 35 21-55 25-59 (78)
87 TIGR03319 YmdA_YtgF conserved 94.6 0.059 1.3E-06 45.7 4.8 34 117-150 202-236 (514)
88 PRK00106 hypothetical protein; 94.5 0.073 1.6E-06 45.3 5.0 34 117-150 223-257 (535)
89 PRK12704 phosphodiesterase; Pr 94.5 0.067 1.4E-06 45.4 4.7 34 117-150 208-242 (520)
90 cd02409 KH-II KH-II (K homolo 94.4 0.064 1.4E-06 31.9 3.5 31 119-149 25-55 (68)
91 cd02414 jag_KH jag_K homology 94.3 0.063 1.4E-06 33.7 3.3 30 119-148 24-53 (77)
92 PF07650 KH_2: KH domain syndr 94.3 0.014 3E-07 36.6 0.2 30 119-148 25-54 (78)
93 KOG3273|consensus 94.0 0.024 5.2E-07 42.1 1.0 54 30-88 178-231 (252)
94 cd02413 40S_S3_KH K homology R 93.9 0.099 2.1E-06 33.3 3.6 34 23-56 32-65 (81)
95 TIGR01952 nusA_arch NusA famil 93.6 0.059 1.3E-06 38.0 2.5 40 18-57 97-136 (141)
96 COG1185 Pnp Polyribonucleotide 93.5 0.1 2.3E-06 45.2 4.1 34 117-150 550-583 (692)
97 COG0195 NusA Transcription elo 93.4 0.091 2E-06 38.9 3.2 38 22-59 143-180 (190)
98 KOG1588|consensus 93.3 0.096 2.1E-06 40.3 3.3 34 117-150 90-129 (259)
99 KOG0119|consensus 93.2 0.067 1.5E-06 44.6 2.4 33 118-150 137-175 (554)
100 PRK12705 hypothetical protein; 93.1 0.16 3.5E-06 43.0 4.6 34 117-150 196-230 (508)
101 PF14611 SLS: Mitochondrial in 92.9 1.8 3.9E-05 32.1 9.7 64 23-89 28-91 (210)
102 COG5176 MSL5 Splicing factor ( 92.8 0.099 2.1E-06 39.1 2.6 34 117-150 146-185 (269)
103 KOG1067|consensus 92.5 0.22 4.7E-06 42.6 4.6 69 15-88 591-660 (760)
104 COG1855 ATPase (PilT family) [ 92.2 0.092 2E-06 43.9 2.0 37 23-59 488-524 (604)
105 TIGR03675 arCOG00543 arCOG0054 92.1 0.3 6.5E-06 42.5 5.2 87 35-149 37-123 (630)
106 PRK12328 nusA transcription el 92.0 0.19 4E-06 40.9 3.5 41 18-58 305-345 (374)
107 KOG2113|consensus 91.8 0.2 4.4E-06 39.7 3.4 59 17-76 111-169 (394)
108 TIGR01953 NusA transcription t 91.8 0.2 4.4E-06 40.3 3.5 40 19-58 299-338 (341)
109 cd02412 30S_S3_KH K homology R 91.6 0.21 4.5E-06 33.6 2.9 30 23-52 63-92 (109)
110 KOG2874|consensus 91.5 0.46 1E-05 37.2 5.0 50 34-88 162-211 (356)
111 cd02413 40S_S3_KH K homology R 91.4 0.3 6.4E-06 31.1 3.3 29 119-147 30-58 (81)
112 cd02411 archeal_30S_S3_KH K ho 91.4 0.29 6.2E-06 31.3 3.3 28 23-50 40-67 (85)
113 PRK09202 nusA transcription el 91.1 0.19 4.1E-06 42.2 2.8 38 21-58 302-339 (470)
114 PRK12327 nusA transcription el 90.8 0.3 6.5E-06 39.7 3.6 41 18-58 300-340 (362)
115 PRK13764 ATPase; Provisional 90.7 0.19 4.1E-06 43.4 2.5 37 22-58 482-518 (602)
116 COG0092 RpsC Ribosomal protein 89.8 0.38 8.3E-06 36.6 3.2 30 20-49 50-79 (233)
117 PRK12329 nusA transcription el 89.2 0.38 8.3E-06 40.0 3.0 41 18-58 332-372 (449)
118 cd02410 archeal_CPSF_KH The ar 89.1 0.73 1.6E-05 32.6 4.0 37 24-60 79-115 (145)
119 PRK04163 exosome complex RNA-b 88.7 0.2 4.4E-06 38.2 1.0 30 121-150 147-176 (235)
120 PF13184 KH_5: NusA-like KH do 88.2 0.29 6.3E-06 30.2 1.3 29 120-148 4-37 (69)
121 KOG1067|consensus 88.1 0.46 1E-05 40.7 2.8 35 116-150 594-628 (760)
122 cd02411 archeal_30S_S3_KH K ho 87.8 0.73 1.6E-05 29.4 3.1 27 121-147 40-66 (85)
123 cd02412 30S_S3_KH K homology R 87.8 0.53 1.1E-05 31.5 2.5 28 120-147 62-89 (109)
124 TIGR00436 era GTP-binding prot 87.4 0.48 1E-05 36.5 2.4 30 119-148 221-251 (270)
125 PRK00089 era GTPase Era; Revie 85.6 0.7 1.5E-05 35.8 2.5 30 119-148 226-256 (292)
126 COG1159 Era GTPase [General fu 85.2 0.66 1.4E-05 36.6 2.2 29 119-147 229-258 (298)
127 COG0092 RpsC Ribosomal protein 85.2 1 2.3E-05 34.3 3.2 30 118-147 50-79 (233)
128 TIGR00436 era GTP-binding prot 85.2 1.4 3.1E-05 33.9 4.0 29 21-49 221-250 (270)
129 PRK15494 era GTPase Era; Provi 84.7 0.78 1.7E-05 36.8 2.5 29 119-147 273-302 (339)
130 PRK06418 transcription elongat 83.8 1.4 3E-05 31.9 3.2 29 120-149 62-90 (166)
131 PTZ00084 40S ribosomal protein 83.8 2.2 4.8E-05 32.3 4.4 30 23-52 46-75 (220)
132 COG1847 Jag Predicted RNA-bind 82.6 0.74 1.6E-05 34.4 1.4 39 18-56 88-126 (208)
133 COG5166 Uncharacterized conser 82.5 1.8 4E-05 36.7 3.8 31 119-149 449-479 (657)
134 PRK00089 era GTPase Era; Revie 81.9 2.3 4.9E-05 33.0 4.0 36 21-56 226-270 (292)
135 PRK15494 era GTPase Era; Provi 81.5 2.3 5E-05 34.1 4.0 29 21-49 273-302 (339)
136 CHL00048 rps3 ribosomal protei 81.5 3.2 6.9E-05 31.3 4.5 29 22-50 67-95 (214)
137 KOG1423|consensus 81.0 1.8 3.9E-05 34.7 3.1 34 18-51 325-359 (379)
138 TIGR01008 rpsC_E_A ribosomal p 80.9 2.3 5E-05 31.6 3.5 30 22-51 39-68 (195)
139 PRK04191 rps3p 30S ribosomal p 80.0 2.5 5.4E-05 31.7 3.5 30 23-52 42-71 (207)
140 COG1855 ATPase (PilT family) [ 79.3 0.94 2E-05 38.1 1.1 31 119-149 486-516 (604)
141 COG1159 Era GTPase [General fu 77.7 4 8.7E-05 32.3 4.1 29 20-48 228-257 (298)
142 PRK13764 ATPase; Provisional 77.0 1.5 3.2E-05 38.1 1.7 32 118-149 480-511 (602)
143 KOG2814|consensus 74.2 1 2.2E-05 36.0 -0.0 32 118-149 56-87 (345)
144 COG1847 Jag Predicted RNA-bind 72.0 3.5 7.6E-05 30.9 2.4 31 118-148 90-120 (208)
145 TIGR03675 arCOG00543 arCOG0054 71.8 5.2 0.00011 35.0 3.8 38 23-60 95-132 (630)
146 COG1782 Predicted metal-depend 71.6 5.5 0.00012 34.0 3.6 39 22-60 100-138 (637)
147 PRK04191 rps3p 30S ribosomal p 70.6 5.6 0.00012 29.8 3.3 27 121-147 42-68 (207)
148 TIGR01008 rpsC_E_A ribosomal p 69.4 6.8 0.00015 29.1 3.5 29 119-147 38-66 (195)
149 TIGR01009 rpsC_bact ribosomal 68.2 6.7 0.00015 29.5 3.2 28 23-50 64-91 (211)
150 COG1097 RRP4 RNA-binding prote 67.5 5 0.00011 30.8 2.4 28 122-149 149-176 (239)
151 PTZ00084 40S ribosomal protein 66.5 7.1 0.00015 29.6 3.1 28 120-147 45-72 (220)
152 CHL00048 rps3 ribosomal protei 66.3 8.5 0.00018 29.0 3.5 29 119-147 66-94 (214)
153 KOG1423|consensus 63.1 10 0.00022 30.6 3.5 32 117-148 326-358 (379)
154 COG1702 PhoH Phosphate starvat 62.9 33 0.00072 27.8 6.4 53 26-83 20-72 (348)
155 KOG4369|consensus 58.8 3.4 7.3E-05 38.7 0.2 31 120-150 1341-1371(2131)
156 PRK00310 rpsC 30S ribosomal pr 57.7 12 0.00026 28.6 3.0 28 23-50 64-91 (232)
157 COG5166 Uncharacterized conser 56.2 11 0.00023 32.3 2.7 70 21-90 449-526 (657)
158 TIGR01009 rpsC_bact ribosomal 53.6 15 0.00033 27.5 2.9 27 121-147 64-90 (211)
159 COG0331 FabD (acyl-carrier-pro 51.9 38 0.00082 27.0 5.0 56 30-86 131-188 (310)
160 cd07049 BMC_EutL_repeat1 ethan 48.5 61 0.0013 21.6 4.8 42 48-89 47-100 (103)
161 COG4010 Uncharacterized protei 48.4 71 0.0015 22.7 5.3 43 41-87 126-168 (170)
162 PF09869 DUF2096: Uncharacteri 41.8 95 0.0021 22.5 5.3 58 18-86 110-167 (169)
163 PF09186 DUF1949: Domain of un 41.2 23 0.0005 19.8 1.8 42 2-50 12-53 (56)
164 PRK00310 rpsC 30S ribosomal pr 39.0 31 0.00068 26.3 2.7 28 120-147 63-90 (232)
165 PF02749 QRPTase_N: Quinolinat 38.9 1E+02 0.0022 19.4 6.1 50 39-88 32-86 (88)
166 cd07055 BMC_like_2 Bacterial M 34.3 97 0.0021 18.6 3.7 23 62-84 37-59 (61)
167 PRK15468 carboxysome structura 31.7 90 0.002 21.0 3.6 27 64-90 75-101 (111)
168 TIGR03667 Rv3369 PPOX class pr 25.8 2.1E+02 0.0046 19.2 5.6 54 21-74 31-84 (130)
169 PF02196 RBD: Raf-like Ras-bin 24.4 98 0.0021 18.8 2.7 26 22-47 2-27 (71)
170 PF00936 BMC: BMC domain; Int 20.9 2.1E+02 0.0046 17.4 3.9 43 46-88 21-64 (75)
171 PF02080 TrkA_C: TrkA-C domain 20.2 1.4E+02 0.003 17.3 2.7 41 40-80 14-68 (71)
No 1
>KOG2191|consensus
Probab=99.92 E-value=6e-24 Score=164.02 Aligned_cols=131 Identities=34% Similarity=0.464 Sum_probs=108.6
Q ss_pred ccCCCCCCCCC-ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC----CC-CCceEEEecChHHHHHHHHHH
Q psy7546 9 SNFKRFRGGPN-DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC----PG-PERILTIFAELENGLKVIEEV 82 (150)
Q Consensus 9 ~~~~~~~~~~~-~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~----~~-~ervv~I~G~~~~v~~A~~~i 82 (150)
...+|.....+ .+.+++|||+..+|.||||+|++|.+||++|||+|+++++ |+ +||+|.|+|+.+++......|
T Consensus 26 ~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI 105 (402)
T KOG2191|consen 26 GSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFI 105 (402)
T ss_pred cccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHH
Confidence 34555555544 4999999999999999999999999999999999999975 45 999999999999999999999
Q ss_pred HHHHHHhhhhcCCCCCC-CCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 83 LPALDEIRQKYGKGRGG-EDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 83 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.+++.+.++........ .+.. .+....+++++|++.+|.||||+|++||.+++++||
T Consensus 106 ~dKire~p~~~~k~v~~~~pqt-----------~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga 163 (402)
T KOG2191|consen 106 ADKIREKPQAVAKPVDILQPQT-----------PDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGA 163 (402)
T ss_pred HHHHHHhHHhhcCCccccCCCC-----------ccccceeEEeccCCcccceecCCcchHHHHHHhhCc
Confidence 99999988665442111 1110 134456999999999999999999999999999986
No 2
>KOG2190|consensus
Probab=99.86 E-value=2.4e-21 Score=159.41 Aligned_cols=119 Identities=31% Similarity=0.504 Sum_probs=99.8
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--CCCCceEEEec---------ChHHHHHHHHHHHHHH
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--PGPERILTIFA---------ELENGLKVIEEVLPAL 86 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~~~ervv~I~G---------~~~~v~~A~~~i~~~~ 86 (150)
+...++||||+..++|.||||+|..||+|+.+|.++|++.+. +++||+++|+| ..+++.+|..+|...+
T Consensus 40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKL 119 (485)
T ss_pred CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcc
Confidence 455668999999999999999999999999999998888875 36999999999 9999999999999988
Q ss_pred HHhhhhcCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 87 DEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
+++.....++ + ......+.+++|+||.+++|+||||+|+.||+|+++|||
T Consensus 120 ~~d~~~~~d~-------------~-~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA 169 (485)
T KOG2190|consen 120 EEDDEAAEDN-------------G-EDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGA 169 (485)
T ss_pred cccccccccC-------------C-ccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCc
Confidence 7543322221 0 011123689999999999999999999999999999997
No 3
>KOG1676|consensus
Probab=99.86 E-value=2.2e-21 Score=159.30 Aligned_cols=117 Identities=26% Similarity=0.412 Sum_probs=97.6
Q ss_pred CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC---CCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCC
Q psy7546 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC---PGPERILTIFAELENGLKVIEEVLPALDEIRQKYGK 95 (150)
Q Consensus 19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~---~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~ 95 (150)
...++++.||.+.||.||||+|++||+|+.+||++|+|... ++.||.+.|.|+++.+++|...|.+++.+.......
T Consensus 228 ~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~ 307 (600)
T KOG1676|consen 228 GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGG 307 (600)
T ss_pred ccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCC
Confidence 34599999999999999999999999999999999999743 369999999999999999998888888876432110
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCce--EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 96 GRGGEDGGDGYNGGGVGGLGKDDY--DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.-+ .+..-. .+.+.||++.+|+||||+|++||.|.++|||
T Consensus 308 -------~~~--------~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA 349 (600)
T KOG1676|consen 308 -------GMG--------GGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGA 349 (600)
T ss_pred -------CcC--------CCCccceeeEEEeccccccccccCCCccchhhhcccCCc
Confidence 000 111222 7889999999999999999999999999998
No 4
>KOG1676|consensus
Probab=99.83 E-value=8.6e-20 Score=150.03 Aligned_cols=122 Identities=27% Similarity=0.385 Sum_probs=98.8
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC----CCCceEEEecChHHHHHHHHHHHHHHHHhhhhc
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP----GPERILTIFAELENGLKVIEEVLPALDEIRQKY 93 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~----~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~ 93 (150)
+.+++.+|+||++.+|+||||+|++||+||+.+||++.+..+. ...+-+.|+|+++.++.|..++.+.|.+.....
T Consensus 136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~ 215 (600)
T KOG1676|consen 136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEV 215 (600)
T ss_pred ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCC
Confidence 4678999999999999999999999999999999999987653 367889999999999999999999999732111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 94 GKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
. .+. ..+.. ......+.++.||.+.||.||||+|++||+|+.+|||
T Consensus 216 ~-g~~-----~~~g~-----~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~ 261 (600)
T KOG1676|consen 216 P-GSG-----GHAGV-----RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGA 261 (600)
T ss_pred C-ccc-----cccCc-----CccccceeEEeccccceeeEEecCchHHHHHhhccCc
Confidence 0 000 00000 0123348999999999999999999999999999997
No 5
>KOG2192|consensus
Probab=99.79 E-value=3.1e-19 Score=135.03 Aligned_cols=109 Identities=52% Similarity=0.830 Sum_probs=98.6
Q ss_pred CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCC
Q psy7546 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRG 98 (150)
Q Consensus 19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~ 98 (150)
..+.+++|+.+..+|+||||+|++||.|+.+.+|+|++++++.++|+++|+.+.+.+-+-+..|+..+++.++
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f~------- 118 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGFQ------- 118 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCC-------
Confidence 4589999999999999999999999999999999999999999999999999999988888888888887442
Q ss_pred CCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 99 GEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
...+..++|+|.++++|.|||++|++||+|++.+.|
T Consensus 119 ----------------~~~pce~rllihqs~ag~iigrngskikelrekcsa 154 (390)
T KOG2192|consen 119 ----------------LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSA 154 (390)
T ss_pred ----------------CCCchhhhhhhhhhhccceecccchhHHHHHHhhhh
Confidence 246678999999999999999999999999998765
No 6
>KOG2193|consensus
Probab=99.78 E-value=1.7e-19 Score=143.37 Aligned_cols=117 Identities=28% Similarity=0.449 Sum_probs=102.1
Q ss_pred CCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--C-CCCceEEEecChHHHHHHHHHHHHHHHHhhh
Q psy7546 15 RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--P-GPERILTIFAELENGLKVIEEVLPALDEIRQ 91 (150)
Q Consensus 15 ~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~ 91 (150)
-..++...++|.||...+|+||||+|.+||+|-.++||.|+|... + ..+|+|+|+|+++..++|...|..++.+...
T Consensus 405 hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf 484 (584)
T KOG2193|consen 405 HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF 484 (584)
T ss_pred hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc
Confidence 344577889999999999999999999999999999999999754 3 4899999999999999999999999988643
Q ss_pred hcCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 92 KYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..+. +.-.....+.||++.+|.||||||.++++|+..|+|
T Consensus 485 ~~Pk-------------------eevklethirVPs~~aGRvIGKGGktVnELQnlt~A 524 (584)
T KOG2193|consen 485 FLPK-------------------EEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSA 524 (584)
T ss_pred CCch-------------------hhheeeeeeeccchhhhhhhccccccHHHHhccccc
Confidence 2221 235567889999999999999999999999999997
No 7
>KOG2190|consensus
Probab=99.73 E-value=3.5e-17 Score=134.90 Aligned_cols=131 Identities=32% Similarity=0.430 Sum_probs=101.4
Q ss_pred ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--C-CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcC--
Q psy7546 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--P-GPERILTIFAELENGLKVIEEVLPALDEIRQKYG-- 94 (150)
Q Consensus 20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~-- 94 (150)
++++||+||++++|.||||+|..||+|+++|||+|++... | +++|.|+|.|.++.+.+|+..|+..|.+......
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~ 216 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPP 216 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCC
Confidence 6899999999999999999999999999999999999976 4 7999999999999999999999999999652211
Q ss_pred CCC---CCC--C-CC---CCCCC------CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 95 KGR---GGE--D-GG---DGYNG------GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 95 ~~~---~~~--~-~~---~~~~~------~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..+ |-+ + .. +.... +......+.+..+++.+|.+.++.|+|++|..|+.++..+|+
T Consensus 217 ~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~ 287 (485)
T KOG2190|consen 217 LVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGA 287 (485)
T ss_pred CCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCC
Confidence 111 111 0 00 00000 000111124456788999999999999999999999999986
No 8
>KOG2193|consensus
Probab=99.67 E-value=4.7e-17 Score=129.60 Aligned_cols=113 Identities=23% Similarity=0.445 Sum_probs=100.1
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C--CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcC
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P--GPERILTIFAELENGLKVIEEVLPALDEIRQKYG 94 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~ 94 (150)
.-.+.+|++||...+|.||||.|++||.|.+.|-|+|-|-.- + ..|++++|.++++...+|+.+|++.+........
T Consensus 196 ~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k 275 (584)
T KOG2193|consen 196 LKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDK 275 (584)
T ss_pred ccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhhccc
Confidence 457899999999999999999999999999999999988742 2 3899999999999999999999999988664332
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 95 KGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
. ..++..+++.-+.++|.+|||.|++||+|.+.||.
T Consensus 276 ~--------------------~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgT 311 (584)
T KOG2193|consen 276 V--------------------AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGT 311 (584)
T ss_pred h--------------------hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCC
Confidence 2 36678889999999999999999999999999984
No 9
>KOG2192|consensus
Probab=99.66 E-value=3.5e-16 Score=118.54 Aligned_cols=75 Identities=31% Similarity=0.478 Sum_probs=67.7
Q ss_pred CCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC--C-CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC--P-GPERILTIFAELENGLKVIEEVLPALDEIR 90 (150)
Q Consensus 16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~--~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~ 90 (150)
..++.+.+||||+.+.+|.|||++|..||.|++++.+++++-.. | +++|+|.+.|.+.+|..++..|++.+.+.+
T Consensus 118 ~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~p 195 (390)
T KOG2192|consen 118 QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESP 195 (390)
T ss_pred CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCC
Confidence 34677999999999999999999999999999999999988643 4 699999999999999999999999998843
No 10
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.66 E-value=2.9e-16 Score=96.76 Aligned_cols=61 Identities=39% Similarity=0.585 Sum_probs=56.8
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC---CCCceEEEecChHHHHHHHHHH
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP---GPERILTIFAELENGLKVIEEV 82 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~---~~ervv~I~G~~~~v~~A~~~i 82 (150)
+++|+||.+.+|.|||++|++|++|+++|||+|++.+.. .++|+|+|.|+++++.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 479999999999999999999999999999999998753 5899999999999999999876
No 11
>KOG2191|consensus
Probab=99.58 E-value=5.2e-15 Score=114.79 Aligned_cols=129 Identities=22% Similarity=0.270 Sum_probs=96.7
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C----CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCC
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P----GPERILTIFAELENGLKVIEEVLPALDEIRQKYGKG 96 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~----~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~ 96 (150)
.+++++|++.+|.||||+|++||.++|++||+|++++. + ..||+|++.|.+++..+|+.+|+.++.++++.....
T Consensus 133 qikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scl 212 (402)
T KOG2191|consen 133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCL 212 (402)
T ss_pred eeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCccccee
Confidence 38999999999999999999999999999999999943 2 389999999999999999999999999988654321
Q ss_pred --CCCCC--CCCCCCCCCCC-----CCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 97 --RGGED--GGDGYNGGGVG-----GLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 97 --~~~~~--~~~~~~~~~~~-----~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
+|... +.-++++.+.+ ...+.......-++..+.|..-|.+|.+.-.+-..+|+
T Consensus 213 n~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~ 275 (402)
T KOG2191|consen 213 NISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGA 275 (402)
T ss_pred ccchhcccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeeccccc
Confidence 22221 11223322221 11223345567788889999999988887777666653
No 12
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.55 E-value=1.1e-14 Score=88.66 Aligned_cols=60 Identities=30% Similarity=0.400 Sum_probs=56.5
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHH
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEV 82 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i 82 (150)
.+|.||.+.+|.|||++|++|++|+++|||+|.+++...+++.|+|+|+.+++..|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHh
Confidence 578999999999999999999999999999999998777899999999999999998776
No 13
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.53 E-value=9.6e-15 Score=88.41 Aligned_cols=60 Identities=30% Similarity=0.460 Sum_probs=55.0
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHH
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEV 82 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i 82 (150)
|.+|.||.+.+|.|||++|.+|++|+++|||+|++++.+ .+..|+|.|+++++.+|..+|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC-CcEEEEEEeCHHHHHHHHhhC
Confidence 678999999999999999999999999999999999774 445999999999999998765
No 14
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.48 E-value=6.3e-14 Score=101.90 Aligned_cols=104 Identities=21% Similarity=0.276 Sum_probs=76.5
Q ss_pred EEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEE---ecChHHHHHHHHHHHHHHHHh-hhh-cCCCCCC
Q psy7546 25 LLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI---FAELENGLKVIEEVLPALDEI-RQK-YGKGRGG 99 (150)
Q Consensus 25 l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I---~G~~~~v~~A~~~i~~~~~~~-~~~-~~~~~~~ 99 (150)
|.||.+.+|.|||++|++|+.|+++||++|.+.+. +..|.| +++++++.+|...|....... +.. ....
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~--- 75 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE---TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLL--- 75 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC---CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhc---
Confidence 56899999999999999999999999999999974 245777 789999999998877644421 100 0000
Q ss_pred CCCCCCCCCCCCCCCCCCceEEE-EEEec---------CceeEEeecCCchHHHHHHhhCC
Q psy7546 100 EDGGDGYNGGGVGGLGKDDYDIR-LIVHQ---------SQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~-l~vp~---------~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
...++.. +.|+. ..+|.|||++|++++.|++.|||
T Consensus 76 ----------------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~ 120 (172)
T TIGR03665 76 ----------------DDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGV 120 (172)
T ss_pred ----------------CCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCC
Confidence 0111111 22222 36899999999999999999996
No 15
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.47 E-value=1.8e-13 Score=100.22 Aligned_cols=108 Identities=19% Similarity=0.210 Sum_probs=79.2
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEE----ecChHHHHHHHHHHHHHHHHh-hhh-cC
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTI----FAELENGLKVIEEVLPALDEI-RQK-YG 94 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I----~G~~~~v~~A~~~i~~~~~~~-~~~-~~ 94 (150)
....+.||.+.+|.|||++|++|+.|+++||++|++.+. +..|.| +++++.+.+|..+|....... +.. ..
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~~ 79 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALR 79 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC---CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHH
Confidence 567899999999999999999999999999999999975 356677 489999999998877655420 100 00
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCceEEEE-EE---------ecCceeEEeecCCchHHHHHHhhCC
Q psy7546 95 KGRGGEDGGDGYNGGGVGGLGKDDYDIRL-IV---------HQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~v---------p~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.. ...+...+ .+ ....+|.|||++|++++.|++.||+
T Consensus 80 l~-------------------gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~ 126 (180)
T PRK13763 80 LL-------------------DDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGV 126 (180)
T ss_pred Hh-------------------CCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCc
Confidence 00 01111111 01 1136899999999999999999986
No 16
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.46 E-value=3.7e-13 Score=82.08 Aligned_cols=61 Identities=39% Similarity=0.610 Sum_probs=55.7
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHH
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEV 82 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i 82 (150)
+.+|.||...++.|||++|++|++|+++|||+|.+++.. .+++.|.|.|+.+++..|..+|
T Consensus 1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 368999999999999999999999999999999999764 5889999999999999988765
No 17
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.45 E-value=4.9e-13 Score=81.31 Aligned_cols=58 Identities=22% Similarity=0.313 Sum_probs=52.3
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecC-hHHHHHHHHHH
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAE-LENGLKVIEEV 82 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~-~~~v~~A~~~i 82 (150)
.+..|.||.+.+|.|||++|++|++|+++|||+|.+++ ++.|.|.|+ ++++..|..+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~----~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC----CCEEEEEeCCHHHHHHHHHHh
Confidence 45678999999999999999999999999999999987 467999998 88999888765
No 18
>smart00322 KH K homology RNA-binding domain.
Probab=99.31 E-value=2e-11 Score=74.40 Aligned_cols=67 Identities=33% Similarity=0.540 Sum_probs=60.6
Q ss_pred ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHH
Q psy7546 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPAL 86 (150)
Q Consensus 20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~ 86 (150)
..+.++.||...+|.+||++|.+|++|++.||++|.+.........+.|.|+.+++..|...|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 4678999999999999999999999999999999999876667899999999999999988887654
No 19
>PF13014 KH_3: KH domain
Probab=99.28 E-value=8.5e-12 Score=70.56 Aligned_cols=40 Identities=38% Similarity=0.664 Sum_probs=36.6
Q ss_pred ccceEecCCchHHHHHHHHhCCeEEecC---CCCCCceEEEec
Q psy7546 31 VAGSVIGKGGSNIARLRNDFKASVTVPD---CPGPERILTIFA 70 (150)
Q Consensus 31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~---~~~~ervv~I~G 70 (150)
++|.|||++|.+|++|+++|||+|+|++ .++++|.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 4799999999999999999999999998 336899999987
No 20
>KOG2279|consensus
Probab=98.91 E-value=7.9e-10 Score=91.04 Aligned_cols=107 Identities=29% Similarity=0.431 Sum_probs=96.6
Q ss_pred CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-CCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCC
Q psy7546 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-GPERILTIFAELENGLKVIEEVLPALDEIRQKYGK 95 (150)
Q Consensus 17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~ 95 (150)
.++++..+++||...|-+++|+.|.+|+.|++.++++|.+.... +.++.-.+.|.+..+..|...++.++.+
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~------- 136 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE------- 136 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc-------
Confidence 35788999999999999999999999999999999999998765 5788888888999999999999988886
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 96 GRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..++...+.+|...++.++|++|.++..++.-++|
T Consensus 137 --------------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~a 171 (608)
T KOG2279|consen 137 --------------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGA 171 (608)
T ss_pred --------------------CCcccccccchhhhcccccccchhhhcchhccccc
Confidence 46677889999999999999999999999988876
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=98.76 E-value=5.9e-08 Score=66.59 Aligned_cols=59 Identities=20% Similarity=0.282 Sum_probs=46.7
Q ss_pred CccceEecCCchHHHHHHHHhCCeEEecCCCC-------------------CCceEEEecCh---HHHHHHHHHHHHHHH
Q psy7546 30 RVAGSVIGKGGSNIARLRNDFKASVTVPDCPG-------------------PERILTIFAEL---ENGLKVIEEVLPALD 87 (150)
Q Consensus 30 ~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~-------------------~ervv~I~G~~---~~v~~A~~~i~~~~~ 87 (150)
+.+|.|||++|.++|+|+++|||+|.|.+..| ..--|.|+++. +.+.+|+.+|...+.
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 56899999999999999999999999986421 11457777755 788888888777766
Q ss_pred H
Q psy7546 88 E 88 (150)
Q Consensus 88 ~ 88 (150)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 22
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.73 E-value=1.6e-08 Score=71.15 Aligned_cols=98 Identities=19% Similarity=0.264 Sum_probs=67.8
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCC
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGE 100 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~ 100 (150)
-.+.++|+...+|+.||++|++|+.|++..|-+|.+-+.. +... ..+.+.+....-..-..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s------------~d~~---~fI~n~l~Pa~V~~v~I---- 92 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS------------DDPE---EFIKNIFAPAAVRSVTI---- 92 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC------------CCHH---HHHHHHcCCCEEEEEEE----
Confidence 4567889999999999999999999999999988887642 1111 12222222110000000
Q ss_pred CCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 101 DGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
..........+.|+....|..|||+|.+++.++..+|
T Consensus 93 ------------~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~ 129 (140)
T PRK08406 93 ------------KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAK 129 (140)
T ss_pred ------------EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhC
Confidence 0012345677889999999999999999999998876
No 23
>KOG2113|consensus
Probab=98.65 E-value=3.2e-08 Score=76.91 Aligned_cols=122 Identities=19% Similarity=0.294 Sum_probs=91.2
Q ss_pred CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCC
Q psy7546 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRG 98 (150)
Q Consensus 19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~ 98 (150)
+.++..+-+|..+++.+.|++|.+||.|+.+|..+|+-+..+ .|-++.++|..++++.|..+|-..-+....... ..+
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~-eePiF~vTg~~edv~~aRrei~saaeH~~l~~~-s~s 101 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG-EEPIFPVTGRHEDVRRARREIPSAAEHFGLIRA-SRS 101 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC-CCCcceeccCchhHHHHhhcCccccceeeeeee-ccc
Confidence 889999999999999999999999999999999999877554 557899999999999998777654443211100 001
Q ss_pred CCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 99 GEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
+..+.+.+ ..+...+...-+|...+|+|.|..|++|+.+++.+.
T Consensus 102 ~Sgg~~~~-------s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tn 145 (394)
T KOG2113|consen 102 FSGGTNGA-------SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTN 145 (394)
T ss_pred ccCCCccc-------cccCCCceeeeccceeeeeccccccCccchheeccc
Confidence 11111111 113455667788999999999999999999998653
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=98.55 E-value=8.4e-08 Score=58.16 Aligned_cols=32 Identities=19% Similarity=0.282 Sum_probs=29.8
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
....+.||.+++|+|||++|++|++|+++|||
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~ 33 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGV 33 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCC
Confidence 46779999999999999999999999999996
No 25
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.55 E-value=1.3e-07 Score=68.84 Aligned_cols=53 Identities=19% Similarity=0.286 Sum_probs=48.9
Q ss_pred ccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546 31 VAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE 88 (150)
Q Consensus 31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~ 88 (150)
..|.|||++|++++.|++.|||+|.+++ +.|.|.|+++++..|...|..++..
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~-----~~v~i~G~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG-----KTVGIIGDPEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC-----CEEEEECCHHHHHHHHHHHHHHHcC
Confidence 6899999999999999999999999986 5699999999999999999888854
No 26
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=98.52 E-value=6.7e-08 Score=59.22 Aligned_cols=31 Identities=58% Similarity=0.909 Sum_probs=29.4
Q ss_pred EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
+.++.||++.+|+|||++|++|++|++.|||
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga 31 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGA 31 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCC
Confidence 3689999999999999999999999999997
No 27
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.49 E-value=3.1e-07 Score=67.29 Aligned_cols=53 Identities=17% Similarity=0.244 Sum_probs=47.7
Q ss_pred ccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546 31 VAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE 88 (150)
Q Consensus 31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~ 88 (150)
.+|.|||++|++++.|++.|||+|.+++. .|.|.|+++++..|...|...+..
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-----~v~i~G~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-----TVAIIGDPEQVEIAREAIEMLIEG 157 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-----EEEEEeCHHHHHHHHHHHHHHHcC
Confidence 68999999999999999999999999864 388999999999999888887754
No 28
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=98.36 E-value=4e-07 Score=64.09 Aligned_cols=97 Identities=24% Similarity=0.294 Sum_probs=65.8
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCC
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGED 101 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~ 101 (150)
-+=|+|....+|..||++|.+|+.|++..|-+|.+-+.. ++... .+.+.+. |.....-.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys------------~D~~~---fI~N~l~-----PA~V~~V~- 92 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS------------ENLEE---FVANKLA-----PAEVKNVT- 92 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC------------CCHHH---HHHHcCC-----CceEEEEE-
Confidence 556888999999999999999999999999888886642 11111 1111111 11000000
Q ss_pred CCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 102 GGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 102 ~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
....+......+.||.+..+..|||+|.+++...+.+|
T Consensus 93 ----------i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~ 130 (141)
T TIGR01952 93 ----------VSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAK 130 (141)
T ss_pred ----------EEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhc
Confidence 00002345677889999999999999999999988876
No 29
>KOG2208|consensus
Probab=98.35 E-value=1.2e-06 Score=76.55 Aligned_cols=105 Identities=21% Similarity=0.274 Sum_probs=93.9
Q ss_pred ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCC
Q psy7546 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGG 99 (150)
Q Consensus 20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~ 99 (150)
.+...+-+-...+..++||+|.++.++++++.+.+.+....+++..+.++|...++.+|...+...+.+...
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-------- 417 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIAEILN-------- 417 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHHhhhc--------
Confidence 366777888899999999999999999999999999999777889999999999999999999999888652
Q ss_pred CCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 100 EDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
......+.+|...+..+||.+|+.|+.|...+|
T Consensus 418 -----------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~ 450 (753)
T KOG2208|consen 418 -----------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHG 450 (753)
T ss_pred -----------------ccccceeecCccchhhhhccccccHHHHHhhcC
Confidence 245666899999999999999999999999876
No 30
>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=98.34 E-value=8.3e-08 Score=57.70 Aligned_cols=31 Identities=39% Similarity=0.537 Sum_probs=29.5
Q ss_pred EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
|.++.||.+++|+|||++|++|++|+++|||
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~ 31 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGV 31 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTS
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCe
Confidence 5789999999999999999999999999986
No 31
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.27 E-value=7.9e-07 Score=53.72 Aligned_cols=30 Identities=50% Similarity=0.756 Sum_probs=28.3
Q ss_pred EEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.++.||..++++|||++|++|++|++.||+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~ 31 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGA 31 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCC
Confidence 578999999999999999999999999985
No 32
>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=98.27 E-value=4.1e-07 Score=55.01 Aligned_cols=30 Identities=20% Similarity=0.350 Sum_probs=28.4
Q ss_pred EEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..+.||.+++++|||++|++|++|++.||+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~ 31 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGV 31 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCC
Confidence 578999999999999999999999999986
No 33
>KOG0336|consensus
Probab=98.27 E-value=2.3e-06 Score=69.46 Aligned_cols=74 Identities=30% Similarity=0.432 Sum_probs=61.1
Q ss_pred CCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR 90 (150)
Q Consensus 16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~ 90 (150)
.+.++.+++|.+-+..||.|||++|.+||+||.+|+++|++..+. .+-.|+|.|...--.+|.+.|-..+..+.
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~-~e~kv~ifg~~~m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD-LEVKVTIFGINHMRKKAKASIDRGQDKDE 115 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC-ceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence 346788999999999999999999999999999999999999875 56678899987776677666655555443
No 34
>PF13014 KH_3: KH domain
Probab=98.15 E-value=1.5e-06 Score=48.87 Aligned_cols=22 Identities=55% Similarity=0.844 Sum_probs=20.8
Q ss_pred ceeEEeecCCchHHHHHHhhCC
Q psy7546 129 QAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 129 ~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
++|+|||++|++|++|+++|||
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~ 22 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGA 22 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCc
Confidence 5899999999999999999997
No 35
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.95 E-value=3e-05 Score=67.14 Aligned_cols=64 Identities=19% Similarity=0.223 Sum_probs=53.4
Q ss_pred ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD 87 (150)
Q Consensus 20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~ 87 (150)
.-...|.||.+++|.|||+||.+||.|+++||++|.+.+. ..|.|.+ +.+.+.+|+.+|.....
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~----G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD----GTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC----cEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 4567788999999999999999999999999999999984 4677766 56677788877766665
No 36
>smart00322 KH K homology RNA-binding domain.
Probab=97.94 E-value=1.3e-05 Score=48.17 Aligned_cols=32 Identities=31% Similarity=0.643 Sum_probs=29.8
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.+.++.||...+|++||++|++|++|++.||+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~ 34 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGV 34 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCC
Confidence 56789999999999999999999999999985
No 37
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.88 E-value=1.8e-05 Score=58.14 Aligned_cols=112 Identities=20% Similarity=0.227 Sum_probs=72.5
Q ss_pred CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-----ChHHHHHHHHHHHHHHHHhhhhc
Q psy7546 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-----ELENGLKVIEEVLPALDEIRQKY 93 (150)
Q Consensus 19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-----~~~~v~~A~~~i~~~~~~~~~~~ 93 (150)
....+.+.||.+.++.+||+.|++.+.|.+.+++++.++... ..|.|.. +|..+.+|...+ .++..-++..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~---~~V~i~~~~~t~Dp~~~~ka~d~V-kAIgrGF~pe 81 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKT---GSVTIRTTRKTEDPLALLKARDVV-KAIGRGFPPE 81 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCC---CeEEEEecCCCCChHHHHHHHHHH-HHHhcCCCHH
Confidence 445677999999999999999999999999999999998653 4555543 456666666333 3333211100
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCceEEEE------EE-e----cCceeEEeecCCchHHHHHHhhCC
Q psy7546 94 GKGRGGEDGGDGYNGGGVGGLGKDDYDIRL------IV-H----QSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l------~v-p----~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.... .- .....+.+ .- + ....|.|||++|.+-+.|++.||+
T Consensus 82 ~A~~---------------LL-~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~ 133 (194)
T COG1094 82 KALK---------------LL-EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGV 133 (194)
T ss_pred HHHH---------------Hh-cCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCC
Confidence 0000 00 01111111 11 1 124699999999999999999985
No 38
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.86 E-value=3e-05 Score=67.36 Aligned_cols=66 Identities=20% Similarity=0.168 Sum_probs=52.2
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD 87 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~ 87 (150)
--.-...+.||.+.+|.|||+||.+||.|+++|||+|.+.+. -.|.|.+ ..+.+.+|...|.....
T Consensus 548 ~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd----G~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 548 YAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD----GTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred cCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC----eEEEEEECcHHHHHHHHHHHHhhhc
Confidence 345677788999999999999999999999999999999874 3455544 56667777766665543
No 39
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.84 E-value=1.2e-05 Score=59.24 Aligned_cols=93 Identities=20% Similarity=0.245 Sum_probs=62.0
Q ss_pred EEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCC
Q psy7546 25 LLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGD 104 (150)
Q Consensus 25 l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~ 104 (150)
+.+-.+.+|..||++|.+|+.|+++.|-+|.+-... ++....+ .+.+. +.....-
T Consensus 80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s------------~d~~~fI---~nal~-----Pa~v~~V----- 134 (190)
T COG0195 80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS------------EDPAEFI---KNALA-----PAEVLSV----- 134 (190)
T ss_pred eecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC------------CCHHHHH---HHhcC-----cceEeEE-----
Confidence 444457899999999999999999999888776542 1122222 22222 1100000
Q ss_pred CCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 105 GYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.-...+.....+.||.+..+.+|||+|.+++.+.+.||
T Consensus 135 -------~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg 172 (190)
T COG0195 135 -------NIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTG 172 (190)
T ss_pred -------EEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhC
Confidence 00000122788889999999999999999999999987
No 40
>KOG0119|consensus
Probab=97.84 E-value=8.7e-05 Score=61.17 Aligned_cols=70 Identities=21% Similarity=0.269 Sum_probs=52.5
Q ss_pred ceEEEEEeeC------CccceEecCCchHHHHHHHHhCCeEEecCC----------------C-C-CCceEEEec-ChHH
Q psy7546 20 DVELRLLIPS------RVAGSVIGKGGSNIARLRNDFKASVTVPDC----------------P-G-PERILTIFA-ELEN 74 (150)
Q Consensus 20 ~~~~~l~vp~------~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~----------------~-~-~ervv~I~G-~~~~ 74 (150)
.++-++.||- +.||+|||..|.+.|+|+++|||+|.|-.. + . .+--|.|++ +-+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 5677888885 459999999999999999999999999531 1 1 122366665 4566
Q ss_pred HHHHHHHHHHHHHHh
Q psy7546 75 GLKVIEEVLPALDEI 89 (150)
Q Consensus 75 v~~A~~~i~~~~~~~ 89 (150)
|.+|++.|..++...
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 888888887777763
No 41
>KOG2279|consensus
Probab=97.81 E-value=2.7e-05 Score=64.80 Aligned_cols=133 Identities=18% Similarity=0.212 Sum_probs=93.7
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC--CCCceEEEecChHHHHHHHHHHHHHHHHhhhhc--
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP--GPERILTIFAELENGLKVIEEVLPALDEIRQKY-- 93 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~--~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~-- 93 (150)
...+...+.+|...++.++|++|+++..++.-++++|.+..+. +..++..|.+..+....|..++...++++....
T Consensus 137 ~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~ 216 (608)
T KOG2279|consen 137 NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKR 216 (608)
T ss_pred CCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhh
Confidence 3456777889999999999999999999999999999999874 578999999988888778877777766543211
Q ss_pred ---------CC----CCCCC----------------------CCCCCCCCCCC-------------------CCCCCCce
Q psy7546 94 ---------GK----GRGGE----------------------DGGDGYNGGGV-------------------GGLGKDDY 119 (150)
Q Consensus 94 ---------~~----~~~~~----------------------~~~~~~~~~~~-------------------~~~~~~~~ 119 (150)
+. +..+. ++.+..+..+. ........
T Consensus 217 ~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~ 296 (608)
T KOG2279|consen 217 IAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALA 296 (608)
T ss_pred chhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccc
Confidence 00 00000 00000000000 01112334
Q ss_pred EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
...+.+|...+|.+||+.|++++.+...|++
T Consensus 297 i~e~e~p~~lsg~lig~~gey~s~yssasn~ 327 (608)
T KOG2279|consen 297 IPEMEMPEILSGDLIGHAGEYLSVYSSASNH 327 (608)
T ss_pred cceeecCcccccchhhhhhhhhhhhhhccCc
Confidence 4678899999999999999999999998874
No 42
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=97.70 E-value=8.6e-05 Score=44.85 Aligned_cols=37 Identities=24% Similarity=0.498 Sum_probs=34.0
Q ss_pred ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEe
Q psy7546 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV 56 (150)
Q Consensus 20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i 56 (150)
.....+.||.+.+|.+|||+|.+|+.+++.+|-+|.+
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4788899999999999999999999999999988765
No 43
>KOG2814|consensus
Probab=97.63 E-value=9.7e-05 Score=58.19 Aligned_cols=70 Identities=21% Similarity=0.310 Sum_probs=58.9
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC-CCCceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-GPERILTIFAELENGLKVIEEVLPALDEIR 90 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~-~~ervv~I~G~~~~v~~A~~~i~~~~~~~~ 90 (150)
...-+.+++...|+|||++|.+-++|+++|+++|.++... ..+.++.+.+..+.|.+|...|...+...-
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 4556889999999999999999999999999999999876 355566666788889999888888877654
No 44
>KOG1588|consensus
Probab=97.59 E-value=0.0001 Score=56.35 Aligned_cols=42 Identities=21% Similarity=0.589 Sum_probs=36.3
Q ss_pred CCCCceEEEEEeeCC------ccceEecCCchHHHHHHHHhCCeEEec
Q psy7546 16 GGPNDVELRLLIPSR------VAGSVIGKGGSNIARLRNDFKASVTVP 57 (150)
Q Consensus 16 ~~~~~~~~~l~vp~~------~vg~IIGk~G~~Ik~l~~~tg~~I~i~ 57 (150)
..+-.++.+++||-. .||.|+|++|.++|+|+++|||+|-|-
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 334567788999965 599999999999999999999999995
No 45
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.49 E-value=0.00031 Score=51.68 Aligned_cols=53 Identities=17% Similarity=0.211 Sum_probs=48.0
Q ss_pred ccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546 31 VAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE 88 (150)
Q Consensus 31 ~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~ 88 (150)
..|.|||++|.+-+.|++-|||+|.+.+.. |.|-|.++++.-|...|..++..
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~t-----VaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGKT-----VAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCcE-----EEEecChhhhHHHHHHHHHHHcC
Confidence 368999999999999999999999999864 99999999999999888888764
No 46
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.20 E-value=0.00096 Score=58.05 Aligned_cols=35 Identities=23% Similarity=0.317 Sum_probs=32.1
Q ss_pred CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..+....+.||.+.+|.|||+||.+||.|+++|||
T Consensus 575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~ 609 (719)
T TIGR02696 575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGA 609 (719)
T ss_pred CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCC
Confidence 35677889999999999999999999999999996
No 47
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=97.14 E-value=0.0007 Score=40.82 Aligned_cols=32 Identities=28% Similarity=0.514 Sum_probs=29.5
Q ss_pred ceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.....+.||...+|.+|||+|.+|+.+++.+|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~ 55 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLG 55 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence 46888999999999999999999999998876
No 48
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.14 E-value=0.00045 Score=55.82 Aligned_cols=88 Identities=18% Similarity=0.236 Sum_probs=59.3
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546 30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG 108 (150)
Q Consensus 30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 (150)
+-+|+.||++|.+|+.+.++. |-+|.+-... ++... .|.+.+.- .....-
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s------------~d~~~---fi~nal~P-----a~v~~v--------- 295 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS------------EDPAE---FVANALSP-----AKVVSV--------- 295 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcC------------CCHHH---HHHHhCCC-----ceEEEE---------
Confidence 569999999999999999998 7888776542 11111 22222211 000000
Q ss_pred CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
...........+.||.+..+..|||+|.+++.....||
T Consensus 296 ---~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~ 333 (362)
T PRK12327 296 ---EVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTG 333 (362)
T ss_pred ---EEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHC
Confidence 00002335788999999999999999999999999887
No 49
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.10 E-value=0.0015 Score=48.62 Aligned_cols=40 Identities=23% Similarity=0.446 Sum_probs=33.8
Q ss_pred CceEEEEEeeC------CccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546 19 NDVELRLLIPS------RVAGSVIGKGGSNIARLRNDFKASVTVPD 58 (150)
Q Consensus 19 ~~~~~~l~vp~------~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~ 58 (150)
..++-++.||- +.||++||+.|.+.|+|++.|+|+|-|-.
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 34566777774 56999999999999999999999999864
No 50
>PRK00468 hypothetical protein; Provisional
Probab=97.08 E-value=0.0008 Score=42.34 Aligned_cols=35 Identities=31% Similarity=0.420 Sum_probs=30.5
Q ss_pred CCCCceEEEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDF 50 (150)
Q Consensus 16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t 50 (150)
..++.+.+++.+..+-+|.||||+|.+|+.||.-.
T Consensus 25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred eCCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 34566889999999999999999999999999753
No 51
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.07 E-value=0.0008 Score=58.64 Aligned_cols=34 Identities=21% Similarity=0.323 Sum_probs=31.8
Q ss_pred CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.+...++.||.+.+|.|||++|++||+|+++|||
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~ 582 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGA 582 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCC
Confidence 5677889999999999999999999999999996
No 52
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.06 E-value=0.00057 Score=54.82 Aligned_cols=106 Identities=18% Similarity=0.251 Sum_probs=66.1
Q ss_pred CCCCCCCCceEEEEEeeC-CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546 12 KRFRGGPNDVELRLLIPS-RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEI 89 (150)
Q Consensus 12 ~~~~~~~~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~ 89 (150)
.|.++.-..+.+.-.-|. +-+|+.||++|.+|+.|.++. |-+|.+-... ++... .|.+.+.-
T Consensus 224 aR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s------------~d~~~---fi~nal~P- 287 (341)
T TIGR01953 224 AREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYS------------DDPAE---FIANALSP- 287 (341)
T ss_pred eeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhCCCeEEEEEcC------------CCHHH---HHHHhcCC-
Confidence 344443333333333333 569999999999999999998 7888776542 11111 12222211
Q ss_pred hhhcCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 90 RQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.....- .-.........+.||.+..+..|||+|.+++.....||
T Consensus 288 ----a~v~~v------------~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g 331 (341)
T TIGR01953 288 ----AKVISV------------EVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTG 331 (341)
T ss_pred ----ceEEEE------------EEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhC
Confidence 000000 00001335788999999999999999999999999988
No 53
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.04 E-value=0.0019 Score=49.20 Aligned_cols=59 Identities=24% Similarity=0.170 Sum_probs=46.9
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChH-HHHHHHHHHHHH
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELE-NGLKVIEEVLPA 85 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~-~v~~A~~~i~~~ 85 (150)
+.+.||.+.++.+||++|.+|+.|.+++++.|.+-.+ -.|.|.+... .+.+|...|...
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N----G~VwI~~~~~~~~~~a~~~I~~~ 206 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN----GRIWIKGPDEEDEEIAIEAIKKI 206 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC----cEEEEeeCCHHHHHHHHHHHHHH
Confidence 4578899999999999999999999999999999764 4688877665 555555444443
No 54
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.04 E-value=0.00074 Score=59.98 Aligned_cols=65 Identities=14% Similarity=0.153 Sum_probs=52.5
Q ss_pred CceEEEEEeeCCccceEecCCchHHHHHHHHhCCe-EEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKAS-VTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD 87 (150)
Q Consensus 19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~-I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~ 87 (150)
-.....|.||.++++.|||.||.+||.|+++||+. |.+.+. -.|.|.+ +.+.+.+|+..|.....
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd----g~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD----GTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC----eeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 45677889999999999999999999999999999 888874 3466655 56777778777666654
No 55
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.97 E-value=0.0028 Score=53.56 Aligned_cols=49 Identities=20% Similarity=0.386 Sum_probs=41.3
Q ss_pred CceEEEEEeeC-CccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec
Q psy7546 19 NDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70 (150)
Q Consensus 19 ~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G 70 (150)
+..+--+.+|+ +.-|.||||.|.|||.|+.-||+.+-|++.| ..|++++
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp---~~v~ls~ 251 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP---EAVILSG 251 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC---CeEEecC
Confidence 44555688898 5679999999999999999999999999976 5566776
No 56
>PRK00468 hypothetical protein; Provisional
Probab=96.97 E-value=0.00074 Score=42.49 Aligned_cols=32 Identities=28% Similarity=0.413 Sum_probs=28.6
Q ss_pred CCceEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
......++.+..+-+|.||||+|.+|+.|+..
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 35578899999999999999999999999865
No 57
>PRK12704 phosphodiesterase; Provisional
Probab=96.97 E-value=0.0028 Score=53.67 Aligned_cols=49 Identities=20% Similarity=0.386 Sum_probs=41.2
Q ss_pred CceEEEEEeeC-CccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec
Q psy7546 19 NDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70 (150)
Q Consensus 19 ~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G 70 (150)
+..+--+.+|+ +.-|.||||.|.|||.|+.-||+.+-|++.| .+|.++|
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp---~~v~ls~ 257 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP---EAVILSG 257 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC---CeEEEec
Confidence 44555677898 5689999999999999999999999999976 5666777
No 58
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.96 E-value=0.00054 Score=55.36 Aligned_cols=87 Identities=14% Similarity=0.153 Sum_probs=58.7
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546 30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG 108 (150)
Q Consensus 30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 (150)
+-+|+.||++|.+|+.|.++. |-+|.+-... ++... .|.+.+.- .....-.
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s------------~D~~~---fI~Nal~P-----a~V~~V~-------- 302 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS------------NVPEI---FIARALAP-----AIISSVK-------- 302 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC------------CCHHH---HHHHhCCC-----ceeeEEE--------
Confidence 559999999999999999998 7888776542 11111 12222211 0000000
Q ss_pred CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
-........+.||.+..+..|||+|.+++...+.||
T Consensus 303 -----i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtG 338 (374)
T PRK12328 303 -----IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTG 338 (374)
T ss_pred -----EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhC
Confidence 001335778899999999999999999999999988
No 59
>PRK02821 hypothetical protein; Provisional
Probab=96.95 E-value=0.00081 Score=42.51 Aligned_cols=32 Identities=28% Similarity=0.536 Sum_probs=28.4
Q ss_pred CceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546 117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t 148 (150)
......|.+..+-+|.||||+|.+|+.|+..-
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 45778999999999999999999999998753
No 60
>PRK00106 hypothetical protein; Provisional
Probab=96.94 E-value=0.0034 Score=53.17 Aligned_cols=50 Identities=22% Similarity=0.440 Sum_probs=41.8
Q ss_pred CCceEEEEEeeC-CccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec
Q psy7546 18 PNDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA 70 (150)
Q Consensus 18 ~~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G 70 (150)
.+..+--+.+|+ +.-|.||||.|.||+.|+.-||+.+-|++.| ..|+++|
T Consensus 222 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp---~~v~lS~ 272 (535)
T PRK00106 222 TEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP---EVVVLSG 272 (535)
T ss_pred hhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC---CeEEEeC
Confidence 345556688898 5679999999999999999999999999976 4566777
No 61
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.93 E-value=0.0021 Score=55.29 Aligned_cols=65 Identities=22% Similarity=0.223 Sum_probs=52.1
Q ss_pred ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecCh-HHHHHHHHHHHHHHHH
Q psy7546 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAEL-ENGLKVIEEVLPALDE 88 (150)
Q Consensus 20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~-~~v~~A~~~i~~~~~~ 88 (150)
+-...+-++.+.+..+||++|.+|+.|.++||++|.+.+.+ .|.|.++. +.+.+|+..|.....+
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG----tv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG----TVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC----cEEEEecchHHHHHHHHHHHHHHhh
Confidence 34566888999999999999999999999999999999643 46666654 6677777777766654
No 62
>PRK02821 hypothetical protein; Provisional
Probab=96.92 E-value=0.0012 Score=41.68 Aligned_cols=36 Identities=28% Similarity=0.411 Sum_probs=30.6
Q ss_pred CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKA 52 (150)
Q Consensus 17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~ 52 (150)
..+...+++.+..+-+|.||||+|.+|+.||.-..+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 345578999999999999999999999999976543
No 63
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.89 E-value=0.00074 Score=55.57 Aligned_cols=88 Identities=18% Similarity=0.229 Sum_probs=58.4
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546 30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG 108 (150)
Q Consensus 30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 (150)
+-+|+.||++|.+|+.|.++. |-+|.+-... ++... .|.+.+.- .......
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys------------~Dp~~---fI~NaLsP-----A~V~~V~-------- 328 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS------------PDPAT---YIANALSP-----ARVDEVR-------- 328 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC------------CCHHH---HHHHhcCC-----ceeeEEE--------
Confidence 559999999999999999998 7888776542 11111 12222211 0000000
Q ss_pred CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
-.........+.||.+..+..|||+|.+++.....||
T Consensus 329 ----i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg 365 (449)
T PRK12329 329 ----LVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTG 365 (449)
T ss_pred ----EEcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHC
Confidence 0001334678999999999999999999999999887
No 64
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.88 E-value=0.0016 Score=41.01 Aligned_cols=32 Identities=31% Similarity=0.482 Sum_probs=29.3
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHH
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRND 49 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~ 49 (150)
+....+++.+..+-+|.||||+|.+|+.|+.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 66788999999999999999999999999975
No 65
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.83 E-value=0.0007 Score=56.50 Aligned_cols=87 Identities=17% Similarity=0.290 Sum_probs=58.8
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCC
Q psy7546 30 RVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNG 108 (150)
Q Consensus 30 ~~vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 (150)
+-+|+.||++|.+|+.|.++. |-+|-+-... ++.. ..|.+.+.- .....-.
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s------------~d~~---~fi~nal~p-----a~v~~v~-------- 296 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS------------DDPA---QFIINALSP-----AEVSSVV-------- 296 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC------------CCHH---HHHHHhCCC-----CEEEEEE--------
Confidence 459999999999999999998 7888776542 1111 122222221 0000000
Q ss_pred CCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 109 ~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
-........+.||....+..|||+|.+++...+.||
T Consensus 297 -----~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g 332 (470)
T PRK09202 297 -----VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTG 332 (470)
T ss_pred -----EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHC
Confidence 001234788999999999999999999999999987
No 66
>PRK01064 hypothetical protein; Provisional
Probab=96.82 E-value=0.002 Score=40.82 Aligned_cols=35 Identities=26% Similarity=0.458 Sum_probs=30.6
Q ss_pred CCCCceEEEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDF 50 (150)
Q Consensus 16 ~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t 50 (150)
...+.+.+++.+...-.|.+|||+|.+|+.||.-.
T Consensus 25 ~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred eCCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 34577899999999999999999999999999753
No 67
>PRK01064 hypothetical protein; Provisional
Probab=96.80 E-value=0.0016 Score=41.23 Aligned_cols=33 Identities=33% Similarity=0.470 Sum_probs=29.1
Q ss_pred CCceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t 148 (150)
......++.+..+..|.+|||+|.+|+.|+...
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 466788899999999999999999999998753
No 68
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.57 E-value=0.003 Score=39.74 Aligned_cols=32 Identities=31% Similarity=0.494 Sum_probs=28.5
Q ss_pred CCceEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
+.....+|.+..+-+|.||||+|.+|+.|+..
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 45677899999999999999999999999864
No 69
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=96.35 E-value=0.0042 Score=43.75 Aligned_cols=39 Identities=26% Similarity=0.335 Sum_probs=33.5
Q ss_pred CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEec
Q psy7546 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP 57 (150)
Q Consensus 19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~ 57 (150)
+.-.+.+.|+.+..|.+|||+|.+++.++.-++-++.+.
T Consensus 97 ~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 97 GDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 345667789999999999999999999999999877664
No 70
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.27 E-value=0.0042 Score=54.33 Aligned_cols=63 Identities=22% Similarity=0.250 Sum_probs=48.3
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHH
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALD 87 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~ 87 (150)
-...+.||.+.++.+||+||.+||.|+++||++|.+.+. -.|.|.+ ..+.+.+|...|.....
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~----G~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD----GTVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC----ceEEEEcccHHHHHHHHHHHHHhcc
Confidence 445566799999999999999999999999998888653 3466655 45667777766665553
No 71
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.25 E-value=0.0051 Score=54.85 Aligned_cols=35 Identities=23% Similarity=0.316 Sum_probs=32.2
Q ss_pred CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..+....+.||.+.++.|||.||.+||.|.++||+
T Consensus 682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~ 716 (891)
T PLN00207 682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGV 716 (891)
T ss_pred cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCC
Confidence 35678889999999999999999999999999986
No 72
>KOG2208|consensus
Probab=96.25 E-value=0.0032 Score=55.44 Aligned_cols=103 Identities=20% Similarity=0.290 Sum_probs=73.8
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCC
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGR 97 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~ 97 (150)
....+.+..+|...+-.+.|.+|..+++++...+..+.+++.+...+.-. ..........++.+...+
T Consensus 637 ~~~~~~~~~i~~~~~~~~~~~~g~~~~~~t~~~~~~~~~~~~~~~~s~~~---~~~~~~~~~~e~~~~~~~--------- 704 (753)
T KOG2208|consen 637 SAYATTNTKIPDKFHRSIVGYRGHIIEEITSKFGVGGYFGDAPTEGSVNT---IHVSGEKMQSEIAKIALE--------- 704 (753)
T ss_pred ccccceeeecccccceeeecCCCcccccceeecCccceeCCCCCccccCc---chhhhhhhhhhhcccccc---------
Confidence 45566779999999999999999999999999999999998763211110 111111111111111111
Q ss_pred CCCCCCCCCCCCCCCCCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 98 GGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.....+..+.+|.++++.+||++|++++.+...++
T Consensus 705 -----------------~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~ 739 (753)
T KOG2208|consen 705 -----------------AKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFN 739 (753)
T ss_pred -----------------cccceeeEEeccHHHhhhccCCCCccHHHHHHHhc
Confidence 14667888999999999999999999999988875
No 73
>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=96.10 E-value=0.005 Score=38.73 Aligned_cols=35 Identities=20% Similarity=0.246 Sum_probs=27.3
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEE
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVT 55 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~ 55 (150)
-.+.+-+..+..|.+|||.|++++.||--++.-++
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 34556667788999999999999999976664443
No 74
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=95.86 E-value=0.0045 Score=38.47 Aligned_cols=35 Identities=26% Similarity=0.336 Sum_probs=29.6
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKA 52 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~ 52 (150)
.+...+.+-+..+..|.||||.|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 55677788889999999999999999999976543
No 75
>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=95.64 E-value=0.032 Score=39.35 Aligned_cols=86 Identities=21% Similarity=0.367 Sum_probs=57.2
Q ss_pred ecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCCCC
Q psy7546 36 IGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLG 115 (150)
Q Consensus 36 IGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (150)
+-..|..|++|-++.--+|.+-.+++ + ...-++|...|.+.+.+.... .+. .
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dps------~---l~~~e~A~~~I~~ivP~ea~i-----------~di--------~ 72 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDPS------V---LKPPEEAIKIILEIVPEEAGI-----------TDI--------Y 72 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCChh------h---cCCHHHHHHHHHHhCCCccCc-----------eee--------E
Confidence 33567888999988888888865431 0 011134665666655432100 000 1
Q ss_pred CCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.+..+-.+.|-...-|.+||++|.++++|..+||
T Consensus 73 Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tg 106 (145)
T cd02410 73 FDDDTGEVIIEAEKPGLVIGKGGSTLREITRETG 106 (145)
T ss_pred ecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhC
Confidence 2455677888899999999999999999999987
No 76
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=95.64 E-value=0.027 Score=33.63 Aligned_cols=35 Identities=29% Similarity=0.491 Sum_probs=28.1
Q ss_pred ceEEEEEeeCCccceEecCCchHHHHHHHHhCCeE
Q psy7546 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASV 54 (150)
Q Consensus 20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I 54 (150)
.....+.+.....|.+||++|.+++.++..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45556666666789999999999999999988554
No 77
>KOG0336|consensus
Probab=95.40 E-value=0.0085 Score=49.25 Aligned_cols=37 Identities=24% Similarity=0.615 Sum_probs=31.8
Q ss_pred CCCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 113 GLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 113 ~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
+.+..+...-+.+.+.++|.|||++|++|+.||..|.
T Consensus 41 aag~~e~plcf~iks~mvg~vigrggskik~iq~~tn 77 (629)
T KOG0336|consen 41 AAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTN 77 (629)
T ss_pred ccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccc
Confidence 3445677778889999999999999999999998875
No 78
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=95.27 E-value=0.0044 Score=38.52 Aligned_cols=33 Identities=27% Similarity=0.422 Sum_probs=28.8
Q ss_pred CCceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t 148 (150)
.......+.+..+..|.||||.|.+++.||...
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~ 58 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLV 58 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHH
Confidence 356678889999999999999999999998754
No 79
>PRK12705 hypothetical protein; Provisional
Probab=95.21 E-value=0.03 Score=47.28 Aligned_cols=42 Identities=26% Similarity=0.411 Sum_probs=35.9
Q ss_pred CceEEEEEeeC-CccceEecCCchHHHHHHHHhCCeEEecCCC
Q psy7546 19 NDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFKASVTVPDCP 60 (150)
Q Consensus 19 ~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~ 60 (150)
+..+--+.+|+ +.-|.||||.|.+||.++..||+.+-|++.|
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp 238 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP 238 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence 44455577887 5689999999999999999999999999876
No 80
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.18 E-value=0.088 Score=40.12 Aligned_cols=46 Identities=26% Similarity=0.291 Sum_probs=39.1
Q ss_pred EEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHH
Q psy7546 25 LLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELEN 74 (150)
Q Consensus 25 l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~ 74 (150)
+.||...|-.+||++|..++.|.++|+|+|-+-.+. .|.|.+..+.
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG----~IWV~~~~~~ 195 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG----RIWVDGENES 195 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC----EEEecCCCcc
Confidence 568888899999999999999999999999998753 5777776664
No 81
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=95.17 E-value=0.042 Score=46.19 Aligned_cols=88 Identities=22% Similarity=0.325 Sum_probs=61.7
Q ss_pred eEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCC
Q psy7546 34 SVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGG 113 (150)
Q Consensus 34 ~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 113 (150)
..+-+.|+.||+|-++.--+|.+-.+|+. ...-+.|...|.+.+.+...... .
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dPsv---------l~~~e~A~~~I~eivP~ea~i~~-----------i------- 94 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDPSV---------LKPPEEARKIILEIVPEEAGITD-----------I------- 94 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCchh---------cCCHHHHHHHHHHhCccccCcee-----------E-------
Confidence 35678899999999999999988766521 11224566666666544321110 0
Q ss_pred CCCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 114 LGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 114 ~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.....+-.+.|-...-|.+|||+|++.++|.++||
T Consensus 95 -~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tg 129 (637)
T COG1782 95 -YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETG 129 (637)
T ss_pred -EecCCCceEEEEecCCceEEecCchHHHHHHHHhC
Confidence 02445667889999999999999999999999987
No 82
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=95.17 E-value=0.015 Score=35.96 Aligned_cols=37 Identities=24% Similarity=0.447 Sum_probs=28.3
Q ss_pred EEEEeeCCc-----cceEecCCchHHHHHHHHh-CCeEEecCC
Q psy7546 23 LRLLIPSRV-----AGSVIGKGGSNIARLRNDF-KASVTVPDC 59 (150)
Q Consensus 23 ~~l~vp~~~-----vg~IIGk~G~~Ik~l~~~t-g~~I~i~~~ 59 (150)
..+.|-+.. +|..||++|.+|+.|.++. |-+|.+-+.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 345555555 9999999999999999999 899988654
No 83
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=95.00 E-value=0.031 Score=40.44 Aligned_cols=35 Identities=31% Similarity=0.344 Sum_probs=30.4
Q ss_pred EEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC
Q psy7546 24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC 59 (150)
Q Consensus 24 ~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~ 59 (150)
=|+|.... |..|||+|.++++|++..|-+|.+-+.
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 35666666 999999999999999999999999764
No 84
>KOG4369|consensus
Probab=94.91 E-value=0.014 Score=53.27 Aligned_cols=65 Identities=20% Similarity=0.139 Sum_probs=55.6
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC-C--CCCceEEEecChHHHHHHHHHH
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC-P--GPERILTIFAELENGLKVIEEV 82 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~-~--~~ervv~I~G~~~~v~~A~~~i 82 (150)
.+.-..++-+|......|||++|.+|..++.-||+.|.+.+- + -.||.+.+.|+++.+.-|...|
T Consensus 1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I 1404 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPI 1404 (2131)
T ss_pred CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccc
Confidence 455667788999999999999999999999999999999872 2 4899999999999998776433
No 85
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.77 E-value=0.025 Score=49.57 Aligned_cols=34 Identities=21% Similarity=0.318 Sum_probs=29.8
Q ss_pred CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.+....+.||.+.++.+||.||.+||.|.++||+
T Consensus 552 ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~ 585 (693)
T PRK11824 552 APRIETIKIPPDKIRDVIGPGGKTIREITEETGA 585 (693)
T ss_pred CchheeecCCHHHHHHHhcCCchhHHHHHHHHCC
Confidence 4455667789999999999999999999999986
No 86
>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=94.76 E-value=0.015 Score=36.43 Aligned_cols=35 Identities=31% Similarity=0.610 Sum_probs=29.2
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEE
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVT 55 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~ 55 (150)
....+.+...+.|.|||++|++|++|.++..-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 34568888999999999999999999987765553
No 87
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.62 E-value=0.059 Score=45.71 Aligned_cols=34 Identities=21% Similarity=0.291 Sum_probs=28.8
Q ss_pred CceEEEEEEecC-ceeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQS-QAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
......+.+|++ +.|.||||.|.+|+.+...||.
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgv 236 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGV 236 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCc
Confidence 445666789995 5699999999999999999984
No 88
>PRK00106 hypothetical protein; Provisional
Probab=94.48 E-value=0.073 Score=45.28 Aligned_cols=34 Identities=21% Similarity=0.323 Sum_probs=28.9
Q ss_pred CceEEEEEEecC-ceeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQS-QAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
......+.+|++ +.|.||||.|.+|+.+...||.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGv 257 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGI 257 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCc
Confidence 445666889995 5699999999999999999984
No 89
>PRK12704 phosphodiesterase; Provisional
Probab=94.45 E-value=0.067 Score=45.44 Aligned_cols=34 Identities=21% Similarity=0.291 Sum_probs=28.5
Q ss_pred CceEEEEEEecC-ceeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQS-QAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
......+.+|++ +.|.||||.|.+|+.+...||.
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgv 242 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGV 242 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCC
Confidence 445566788995 5699999999999999999984
No 90
>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=94.44 E-value=0.064 Score=31.92 Aligned_cols=31 Identities=32% Similarity=0.641 Sum_probs=24.4
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
....+.+.....|.+||++|.+++.++..++
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~ 55 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQ 55 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHH
Confidence 4455555555689999999999999998764
No 91
>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=94.27 E-value=0.063 Score=33.65 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=25.1
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t 148 (150)
....+.+..+..|.+|||.|.+++.||-.+
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~ 53 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLA 53 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHH
Confidence 356677888899999999999999998654
No 92
>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=94.26 E-value=0.014 Score=36.59 Aligned_cols=30 Identities=37% Similarity=0.722 Sum_probs=26.4
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t 148 (150)
....+.+..++.|.+||++|++|++|.+..
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~ 54 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREEL 54 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHH
Confidence 457788899999999999999999998764
No 93
>KOG3273|consensus
Probab=93.99 E-value=0.024 Score=42.11 Aligned_cols=54 Identities=20% Similarity=0.328 Sum_probs=49.2
Q ss_pred CccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546 30 RVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE 88 (150)
Q Consensus 30 ~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~ 88 (150)
..+|.|+||+|.+--.|++.|-++|.+.+.. +.|-|..+++.-|...+|.++--
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad~k-----IHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLADSK-----IHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecCce-----EEEeecchhhHHHHHhhHhhhcc
Confidence 4689999999999999999999999999864 89999999999999999998864
No 94
>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=93.86 E-value=0.099 Score=33.29 Aligned_cols=34 Identities=18% Similarity=0.325 Sum_probs=29.4
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCCeEEe
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV 56 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i 56 (150)
.++.+....-|.|||++|+.|++|+++..-...+
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 7788888899999999999999999887665555
No 95
>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=93.64 E-value=0.059 Score=37.97 Aligned_cols=40 Identities=28% Similarity=0.331 Sum_probs=33.9
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEec
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP 57 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~ 57 (150)
++.....+.||.+..+..|||+|.+++...+-++-++.+.
T Consensus 97 ~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 97 NGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 3456677889999999999999999999999998877554
No 96
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=93.46 E-value=0.1 Score=45.20 Aligned_cols=34 Identities=18% Similarity=0.280 Sum_probs=31.3
Q ss_pred CceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.+...++.++.+.++-+||++|++|++|.++|||
T Consensus 550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~ 583 (692)
T COG1185 550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGV 583 (692)
T ss_pred CCceEEEccCHHHHhhccCCcccchhhhhhhhCc
Confidence 5567789999999999999999999999999996
No 97
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=93.38 E-value=0.091 Score=38.86 Aligned_cols=38 Identities=18% Similarity=0.257 Sum_probs=35.1
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC 59 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~ 59 (150)
.+.+.||.++.+.+|||+|.+++...+-||-++.+...
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 78888999999999999999999999999999988653
No 98
>KOG1588|consensus
Probab=93.28 E-value=0.096 Score=40.35 Aligned_cols=34 Identities=21% Similarity=0.352 Sum_probs=29.1
Q ss_pred CceEEEEEEecC------ceeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQS------QAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~~------~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
...+.++.||-. +||.|+|..|.++|+|+++||.
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgC 129 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGC 129 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCC
Confidence 456777888765 7999999999999999999984
No 99
>KOG0119|consensus
Probab=93.19 E-value=0.067 Score=44.63 Aligned_cols=33 Identities=24% Similarity=0.316 Sum_probs=28.0
Q ss_pred ceEEEEEEec------CceeEEeecCCchHHHHHHhhCC
Q psy7546 118 DYDIRLIVHQ------SQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 118 ~~~~~l~vp~------~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..+-++.||. +++|+|||..|.+.|+|+++|||
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgA 175 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGA 175 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCC
Confidence 4556666665 47999999999999999999998
No 100
>PRK12705 hypothetical protein; Provisional
Probab=93.07 E-value=0.16 Score=42.98 Aligned_cols=34 Identities=21% Similarity=0.270 Sum_probs=28.0
Q ss_pred CceEEEEEEecCc-eeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQSQ-AGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~~~-~g~iIGk~G~~Ik~i~~~tGA 150 (150)
......+.+|++- .|.||||.|.+|+.+...||.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGv 230 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGV 230 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCC
Confidence 4445567788864 699999999999999999984
No 101
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=92.92 E-value=1.8 Score=32.10 Aligned_cols=64 Identities=14% Similarity=0.119 Sum_probs=50.9
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHh
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEI 89 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~ 89 (150)
+.+.++....-++...+|..++.|-...|++|.+... +..+.|+|+...+..+...|...+...
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~---~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS---ENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC---CcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 3444557788899999999999998888999999874 468999999888877766666666553
No 102
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=92.75 E-value=0.099 Score=39.14 Aligned_cols=34 Identities=24% Similarity=0.454 Sum_probs=27.1
Q ss_pred CceEEEEEEec------CceeEEeecCCchHHHHHHhhCC
Q psy7546 117 DDYDIRLIVHQ------SQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 117 ~~~~~~l~vp~------~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..++-++-||- .++|++||..|+++|+|++.|+|
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~a 185 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRA 185 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCC
Confidence 34455555553 47999999999999999999987
No 103
>KOG1067|consensus
Probab=92.52 E-value=0.22 Score=42.58 Aligned_cols=69 Identities=17% Similarity=0.157 Sum_probs=52.8
Q ss_pred CCCCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEec-ChHHHHHHHHHHHHHHHH
Q psy7546 15 RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIEEVLPALDE 88 (150)
Q Consensus 15 ~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G-~~~~v~~A~~~i~~~~~~ 88 (150)
......+...+.++.++...+||.+|...|+|+.+||+.-++++. .+.|.. +....++|.+.|...+..
T Consensus 591 ~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe~-----t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 591 DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDEG-----TFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeecCc-----eEEEEecCHHHHHHHHHHHHHHhcC
Confidence 344567788899999999999999999999999999976666654 255544 556677888777666554
No 104
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=92.22 E-value=0.092 Score=43.91 Aligned_cols=37 Identities=24% Similarity=0.451 Sum_probs=33.2
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC 59 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~ 59 (150)
..+.+|...++.+|||+|.+|++|.+..|.+|.+...
T Consensus 488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 4477899999999999999999999999999998653
No 105
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=92.12 E-value=0.3 Score=42.48 Aligned_cols=87 Identities=20% Similarity=0.331 Sum_probs=57.8
Q ss_pred EecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCCC
Q psy7546 35 VIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGL 114 (150)
Q Consensus 35 IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (150)
.+-..|..||+|-++.--+|.+-.+|+ + ...-++|...|.+.+.+.... .+.
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~~------~---~~~~~~~~~~i~~~~~~~~~~-----------~~~-------- 88 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDPS------V---LLPPEEAIEKIKEIVPEEAGI-----------TDI-------- 88 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecChh------h---cCCHHHHHHHHHHhCCCcCCc-----------eeE--------
Confidence 445677888999888888888865442 0 011134555555555432110 000
Q ss_pred CCCceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 115 GKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 115 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
-.+..+-.+.|-...-|.||||+|+++++|..+||
T Consensus 89 ~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~ 123 (630)
T TIGR03675 89 YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETG 123 (630)
T ss_pred EecCCCceEEEEEcCCeEEEecCcchHHHHHHHhC
Confidence 12455677889999999999999999999999987
No 106
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=91.96 E-value=0.19 Score=40.94 Aligned_cols=41 Identities=17% Similarity=0.151 Sum_probs=36.6
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD 58 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~ 58 (150)
++.-...+.||.++.++.|||+|.+++-..+-||.+|.|-.
T Consensus 305 ~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 305 EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 34457789999999999999999999999999999999964
No 107
>KOG2113|consensus
Probab=91.83 E-value=0.2 Score=39.69 Aligned_cols=59 Identities=20% Similarity=0.333 Sum_probs=48.9
Q ss_pred CCCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHH
Q psy7546 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGL 76 (150)
Q Consensus 17 ~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~ 76 (150)
.+...+...-+|-..+|+|.|.+|++|+.+|+.++..|.-.-. +.+.+..++|.++++.
T Consensus 111 ~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~-~~~~Vf~Vtg~~~nC~ 169 (394)
T KOG2113|consen 111 ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR-CGEPVFCVTGAPKNCV 169 (394)
T ss_pred ccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-CCCceEEEecCCcchh
Confidence 4666777788899999999999999999999999998876532 4678888999888833
No 108
>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=91.75 E-value=0.2 Score=40.32 Aligned_cols=40 Identities=20% Similarity=0.309 Sum_probs=36.1
Q ss_pred CceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD 58 (150)
Q Consensus 19 ~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~ 58 (150)
+.-.+.+.||.++.+..|||+|.+++-...-||.+|.+..
T Consensus 299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 4457889999999999999999999999999999998753
No 109
>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=91.60 E-value=0.21 Score=33.55 Aligned_cols=30 Identities=30% Similarity=0.617 Sum_probs=25.2
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKA 52 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~ 52 (150)
+++.+....-|.|||++|+.|++|++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 567777788899999999999999976543
No 110
>KOG2874|consensus
Probab=91.53 E-value=0.46 Score=37.16 Aligned_cols=50 Identities=16% Similarity=0.182 Sum_probs=41.8
Q ss_pred eEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546 34 SVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE 88 (150)
Q Consensus 34 ~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~~ 88 (150)
.+||.+|.++|.|+--|.|.|-+.... |.+.|+...+..+...+.+++.+
T Consensus 162 RLiGpng~TLKAlelLT~CYilVqG~T-----VsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 162 RLIGPNGSTLKALELLTNCYILVQGNT-----VSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HhcCCCchhHHHHHHHhhcEEEeeCcE-----EEeecCcchHHHHHHHHHHHHhc
Confidence 489999999999999999999998753 78888888887777666666654
No 111
>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=91.45 E-value=0.3 Score=31.09 Aligned_cols=29 Identities=21% Similarity=0.503 Sum_probs=25.2
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
..+++.|-...-|.+||++|+.|++|++.
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~ 58 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSL 58 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHH
Confidence 35778888889999999999999999764
No 112
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=91.43 E-value=0.29 Score=31.28 Aligned_cols=28 Identities=36% Similarity=0.573 Sum_probs=23.2
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDF 50 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~t 50 (150)
.++.+....-|.+||++|++|++|++..
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5566666788999999999999998764
No 113
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=91.08 E-value=0.19 Score=42.18 Aligned_cols=38 Identities=16% Similarity=0.216 Sum_probs=35.2
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD 58 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~ 58 (150)
-.+.+.||.++.+..|||+|.+++...+-||.+|.+..
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 47889999999999999999999999999999998864
No 114
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=90.76 E-value=0.3 Score=39.67 Aligned_cols=41 Identities=17% Similarity=0.225 Sum_probs=36.6
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD 58 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~ 58 (150)
++.-.+.+.||.++.++.|||+|.+++--..-||.+|.+..
T Consensus 300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 34457889999999999999999999999999999998864
No 115
>PRK13764 ATPase; Provisional
Probab=90.74 E-value=0.19 Score=43.44 Aligned_cols=37 Identities=24% Similarity=0.499 Sum_probs=33.3
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD 58 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~ 58 (150)
..-+.||...++.+|||+|.+|++|.+..|.+|.+-.
T Consensus 482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 4457899999999999999999999999999999864
No 116
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=89.77 E-value=0.38 Score=36.58 Aligned_cols=30 Identities=43% Similarity=0.606 Sum_probs=25.8
Q ss_pred ceEEEEEeeCCccceEecCCchHHHHHHHH
Q psy7546 20 DVELRLLIPSRVAGSVIGKGGSNIARLRND 49 (150)
Q Consensus 20 ~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~ 49 (150)
....++.|....-|.|||++|++|++|+++
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 446678888899999999999999998865
No 117
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=89.17 E-value=0.38 Score=39.98 Aligned_cols=41 Identities=22% Similarity=0.332 Sum_probs=36.5
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecC
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPD 58 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~ 58 (150)
++.-.+.+.||.++.++.|||+|.+++--..-||.+|.|..
T Consensus 332 ~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 332 PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 34456789999999999999999999999999999998865
No 118
>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=89.14 E-value=0.73 Score=32.58 Aligned_cols=37 Identities=30% Similarity=0.499 Sum_probs=32.0
Q ss_pred EEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC
Q psy7546 24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP 60 (150)
Q Consensus 24 ~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~ 60 (150)
++.|-...-|.+||++|.+++.|..+||-.-.+...|
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 4566678889999999999999999999988887664
No 119
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=88.66 E-value=0.2 Score=38.18 Aligned_cols=30 Identities=20% Similarity=0.328 Sum_probs=27.3
Q ss_pred EEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..+.||.++++.+||++|.+|+.|.+.|++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~ 176 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGC 176 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCc
Confidence 557899999999999999999999998874
No 120
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.18 E-value=0.29 Score=30.17 Aligned_cols=29 Identities=28% Similarity=0.602 Sum_probs=23.6
Q ss_pred EEEEEEecCc-----eeEEeecCCchHHHHHHhh
Q psy7546 120 DIRLIVHQSQ-----AGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 120 ~~~l~vp~~~-----~g~iIGk~G~~Ik~i~~~t 148 (150)
...+.|-+.. +|..||++|++|+.|.++.
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L 37 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEEL 37 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHT
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHh
Confidence 4556777776 8999999999999999886
No 121
>KOG1067|consensus
Probab=88.07 E-value=0.46 Score=40.67 Aligned_cols=35 Identities=26% Similarity=0.234 Sum_probs=32.2
Q ss_pred CCceEEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 116 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
..+....|.++++....+||.+|-..|.|+.+|||
T Consensus 594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGa 628 (760)
T KOG1067|consen 594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGA 628 (760)
T ss_pred cCceeeEEeecchhhheeecCccceeeeEeeeccc
Confidence 46678889999999999999999999999999996
No 122
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=87.78 E-value=0.73 Score=29.39 Aligned_cols=27 Identities=30% Similarity=0.719 Sum_probs=22.4
Q ss_pred EEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
.++.+-...-|.+||++|++|+++++.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~ 66 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEI 66 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHH
Confidence 556666688899999999999998764
No 123
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=87.77 E-value=0.53 Score=31.54 Aligned_cols=28 Identities=36% Similarity=0.717 Sum_probs=24.2
Q ss_pred EEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 120 DIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
.+++.+-...-|.|||+.|+.|++|++.
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~ 89 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKE 89 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHH
Confidence 4677788888899999999999999875
No 124
>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=87.37 E-value=0.48 Score=36.53 Aligned_cols=30 Identities=33% Similarity=0.376 Sum_probs=23.2
Q ss_pred eEEEEEEec-CceeEEeecCCchHHHHHHhh
Q psy7546 119 YDIRLIVHQ-SQAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 119 ~~~~l~vp~-~~~g~iIGk~G~~Ik~i~~~t 148 (150)
....+.|.. ++.+.|||++|++||+|....
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 455666754 467999999999999997653
No 125
>PRK00089 era GTPase Era; Reviewed
Probab=85.57 E-value=0.7 Score=35.85 Aligned_cols=30 Identities=37% Similarity=0.607 Sum_probs=22.5
Q ss_pred eEEEEEEe-cCceeEEeecCCchHHHHHHhh
Q psy7546 119 YDIRLIVH-QSQAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 119 ~~~~l~vp-~~~~g~iIGk~G~~Ik~i~~~t 148 (150)
+...+.|. .++.+.|||++|++||+|....
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 34455564 4467999999999999997653
No 126
>COG1159 Era GTPase [General function prediction only]
Probab=85.17 E-value=0.66 Score=36.62 Aligned_cols=29 Identities=34% Similarity=0.563 Sum_probs=22.2
Q ss_pred eEEEEEEecC-ceeEEeecCCchHHHHHHh
Q psy7546 119 YDIRLIVHQS-QAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 119 ~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~ 147 (150)
....+.|+.+ +-|.||||+|++||+|-..
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 3444666554 6899999999999999654
No 127
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=85.17 E-value=1 Score=34.26 Aligned_cols=30 Identities=33% Similarity=0.664 Sum_probs=25.8
Q ss_pred ceEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
+..+++.|-...=|.|||++|+.|++|+..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 456778888899999999999999998764
No 128
>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=85.16 E-value=1.4 Score=33.89 Aligned_cols=29 Identities=21% Similarity=0.275 Sum_probs=23.8
Q ss_pred eEEEEEeeC-CccceEecCCchHHHHHHHH
Q psy7546 21 VELRLLIPS-RVAGSVIGKGGSNIARLRND 49 (150)
Q Consensus 21 ~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~ 49 (150)
+...++|.. ++-+.|||++|+.||+|..+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 566678884 77899999999999998754
No 129
>PRK15494 era GTPase Era; Provisional
Probab=84.68 E-value=0.78 Score=36.77 Aligned_cols=29 Identities=31% Similarity=0.516 Sum_probs=22.6
Q ss_pred eEEEEEEecC-ceeEEeecCCchHHHHHHh
Q psy7546 119 YDIRLIVHQS-QAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 119 ~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~ 147 (150)
+...+.|..+ +.+.|||++|++||+|...
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 3455667554 6799999999999999765
No 130
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=83.79 E-value=1.4 Score=31.93 Aligned_cols=29 Identities=31% Similarity=0.408 Sum_probs=24.3
Q ss_pred EEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.+-++|.... |..|||+|++++.+++..|
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lg 90 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLG 90 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhC
Confidence 4556776666 9999999999999998766
No 131
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=83.78 E-value=2.2 Score=32.31 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=25.1
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKA 52 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~ 52 (150)
.++.+....-|.|||++|..|++|+++..-
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k 75 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQK 75 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHH
Confidence 667777788899999999999999877543
No 132
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=82.64 E-value=0.74 Score=34.45 Aligned_cols=39 Identities=21% Similarity=0.241 Sum_probs=30.7
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEe
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV 56 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i 56 (150)
.+.-.+.+-+..+..+.+||+.|.++..||--++..++-
T Consensus 88 ~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 88 EEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred ecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 344556666777779999999999999999887766655
No 133
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=82.52 E-value=1.8 Score=36.72 Aligned_cols=31 Identities=32% Similarity=0.450 Sum_probs=26.2
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
....+.||..++-.|||.||..|++.....+
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~ 479 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHA 479 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhh
Confidence 3566889999999999999999998876543
No 134
>PRK00089 era GTPase Era; Reviewed
Probab=81.95 E-value=2.3 Score=32.97 Aligned_cols=36 Identities=22% Similarity=0.525 Sum_probs=26.9
Q ss_pred eEEEEEee-CCccceEecCCchHHHHHHHH--------hCCeEEe
Q psy7546 21 VELRLLIP-SRVAGSVIGKGGSNIARLRND--------FKASVTV 56 (150)
Q Consensus 21 ~~~~l~vp-~~~vg~IIGk~G~~Ik~l~~~--------tg~~I~i 56 (150)
+...+.|. .++-+.|||++|+.||+|... .|++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 55567777 477899999999999988643 5655554
No 135
>PRK15494 era GTPase Era; Provisional
Probab=81.53 E-value=2.3 Score=34.05 Aligned_cols=29 Identities=17% Similarity=0.408 Sum_probs=23.5
Q ss_pred eEEEEEeeC-CccceEecCCchHHHHHHHH
Q psy7546 21 VELRLLIPS-RVAGSVIGKGGSNIARLRND 49 (150)
Q Consensus 21 ~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~ 49 (150)
+...++|.. ++-+.|||++|+.||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 556688885 77899999999999988643
No 136
>CHL00048 rps3 ribosomal protein S3
Probab=81.47 E-value=3.2 Score=31.30 Aligned_cols=29 Identities=17% Similarity=0.339 Sum_probs=24.6
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDF 50 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t 50 (150)
..++.+....-|.|||++|++|++|++..
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46677777788999999999999999775
No 137
>KOG1423|consensus
Probab=80.98 E-value=1.8 Score=34.71 Aligned_cols=34 Identities=21% Similarity=0.388 Sum_probs=27.6
Q ss_pred CCceEEEEEeeC-CccceEecCCchHHHHHHHHhC
Q psy7546 18 PNDVELRLLIPS-RVAGSVIGKGGSNIARLRNDFK 51 (150)
Q Consensus 18 ~~~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~~tg 51 (150)
...+..+++||. +..-+||||||..|++|-++.+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 346677899996 6788899999999999977654
No 138
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=80.93 E-value=2.3 Score=31.60 Aligned_cols=30 Identities=30% Similarity=0.581 Sum_probs=25.2
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhC
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFK 51 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg 51 (150)
..++.+....-|.|||++|..|++|+++..
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 367778888889999999999999987643
No 139
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=80.05 E-value=2.5 Score=31.68 Aligned_cols=30 Identities=37% Similarity=0.580 Sum_probs=24.3
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCC
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKA 52 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~ 52 (150)
.++.+....-|.+||++|++|+++++...-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 556666678899999999999999977543
No 140
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=79.32 E-value=0.94 Score=38.12 Aligned_cols=31 Identities=29% Similarity=0.425 Sum_probs=27.8
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
....+.||...++.+|||+|.+|++|....|
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klg 516 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLG 516 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhC
Confidence 3566889999999999999999999998876
No 141
>COG1159 Era GTPase [General function prediction only]
Probab=77.68 E-value=4 Score=32.28 Aligned_cols=29 Identities=21% Similarity=0.483 Sum_probs=22.7
Q ss_pred ceEEEEEeeC-CccceEecCCchHHHHHHH
Q psy7546 20 DVELRLLIPS-RVAGSVIGKGGSNIARLRN 48 (150)
Q Consensus 20 ~~~~~l~vp~-~~vg~IIGk~G~~Ik~l~~ 48 (150)
.+...+.|+. ++-|.||||+|+.||+|-.
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHH
Confidence 3444578884 7789999999999998753
No 142
>PRK13764 ATPase; Provisional
Probab=76.99 E-value=1.5 Score=38.11 Aligned_cols=32 Identities=28% Similarity=0.512 Sum_probs=28.1
Q ss_pred ceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.....+.||...++.+|||+|.+|++|.+..|
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~ 511 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLG 511 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhC
Confidence 34566789999999999999999999999876
No 143
>KOG2814|consensus
Probab=74.19 E-value=1 Score=36.03 Aligned_cols=32 Identities=31% Similarity=0.549 Sum_probs=28.9
Q ss_pred ceEEEEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
.....+.++++..|.|||++|.+-+.|+++|+
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq 87 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQ 87 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhc
Confidence 45667899999999999999999999999986
No 144
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=72.01 E-value=3.5 Score=30.89 Aligned_cols=31 Identities=23% Similarity=0.366 Sum_probs=25.8
Q ss_pred ceEEEEEEecCceeEEeecCCchHHHHHHhh
Q psy7546 118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 118 ~~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~t 148 (150)
..++.+.+..+..+.+||+.|.+++.||-.+
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~ 120 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLA 120 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHH
Confidence 3456677888889999999999999998664
No 145
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=71.81 E-value=5.2 Score=34.95 Aligned_cols=38 Identities=29% Similarity=0.446 Sum_probs=33.1
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP 60 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~ 60 (150)
=+++|-...-|+||||+|.+.+.|..+||-.-.+...|
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 34667778889999999999999999999988888765
No 146
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=71.60 E-value=5.5 Score=34.03 Aligned_cols=39 Identities=26% Similarity=0.447 Sum_probs=33.5
Q ss_pred EEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCC
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP 60 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~ 60 (150)
+=+++|-+.+-|++|||+|++.+.|..+||-.-.+...|
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 345778888899999999999999999999888887665
No 147
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=70.61 E-value=5.6 Score=29.79 Aligned_cols=27 Identities=33% Similarity=0.758 Sum_probs=22.4
Q ss_pred EEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
..+.+-...-|.+||++|++|+++++.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~ 68 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEI 68 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHH
Confidence 556666688899999999999999764
No 148
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=69.43 E-value=6.8 Score=29.11 Aligned_cols=29 Identities=31% Similarity=0.769 Sum_probs=24.4
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
..+++.+-...-|.+||++|..|++|++.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHH
Confidence 34777888888899999999999999764
No 149
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=68.20 E-value=6.7 Score=29.47 Aligned_cols=28 Identities=46% Similarity=0.757 Sum_probs=23.6
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDF 50 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~t 50 (150)
+++.+....-|.|||++|..+++|++..
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5677777778999999999999998654
No 150
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=67.54 E-value=5 Score=30.75 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=24.9
Q ss_pred EEEEecCceeEEeecCCchHHHHHHhhC
Q psy7546 122 RLIVHQSQAGCIIGKGGTKIKELRDTFD 149 (150)
Q Consensus 122 ~l~vp~~~~g~iIGk~G~~Ik~i~~~tG 149 (150)
-+.||+..+-.+||++|++++.+.+.|+
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~ 176 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTG 176 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcC
Confidence 3678999999999999999999988875
No 151
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=66.51 E-value=7.1 Score=29.59 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=23.7
Q ss_pred EEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 120 DIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
.+++.|-...-|.|||++|..|++|++.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~ 72 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSL 72 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHH
Confidence 4677777788899999999999999764
No 152
>CHL00048 rps3 ribosomal protein S3
Probab=66.28 E-value=8.5 Score=29.01 Aligned_cols=29 Identities=24% Similarity=0.287 Sum_probs=23.6
Q ss_pred eEEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 119 ~~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
..+++.|-...-|.|||++|..|++|++.
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~ 94 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQIN 94 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHH
Confidence 34667777777899999999999998764
No 153
>KOG1423|consensus
Probab=63.11 E-value=10 Score=30.56 Aligned_cols=32 Identities=25% Similarity=0.410 Sum_probs=25.3
Q ss_pred CceEEEEEEecC-ceeEEeecCCchHHHHHHhh
Q psy7546 117 DDYDIRLIVHQS-QAGCIIGKGGTKIKELRDTF 148 (150)
Q Consensus 117 ~~~~~~l~vp~~-~~g~iIGk~G~~Ik~i~~~t 148 (150)
-.+..++.+|-. +...+|||+|..|++|-++-
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 346677888765 56889999999999997653
No 154
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=62.90 E-value=33 Score=27.81 Aligned_cols=53 Identities=13% Similarity=0.072 Sum_probs=42.5
Q ss_pred EeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHH
Q psy7546 26 LIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVL 83 (150)
Q Consensus 26 ~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~ 83 (150)
+-+...+-.+.|..+.+++.|.+.+|+.|..... -+.+.|....+..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~-----~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVARGE-----AVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeCCc-----eEEEEechHHHHHHHHHHh
Confidence 3446778889999999999999999999988764 4888898767776765555
No 155
>KOG4369|consensus
Probab=58.80 E-value=3.4 Score=38.71 Aligned_cols=31 Identities=19% Similarity=0.157 Sum_probs=26.8
Q ss_pred EEEEEEecCceeEEeecCCchHHHHHHhhCC
Q psy7546 120 DIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150 (150)
Q Consensus 120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~tGA 150 (150)
.-++.+|.....+|||++|++|+.++..|||
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga 1371 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGA 1371 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccce
Confidence 4556788888999999999999999999986
No 156
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=57.69 E-value=12 Score=28.56 Aligned_cols=28 Identities=39% Similarity=0.709 Sum_probs=22.8
Q ss_pred EEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546 23 LRLLIPSRVAGSVIGKGGSNIARLRNDF 50 (150)
Q Consensus 23 ~~l~vp~~~vg~IIGk~G~~Ik~l~~~t 50 (150)
+++.+....-|.|||++|..+++|++..
T Consensus 64 i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 64 VRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred EEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 5566666677999999999999998765
No 157
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=56.23 E-value=11 Score=32.28 Aligned_cols=70 Identities=16% Similarity=0.157 Sum_probs=50.9
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCC---C-CC-CceEEEecChHHH---HHHHHHHHHHHHHhh
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDC---P-GP-ERILTIFAELENG---LKVIEEVLPALDEIR 90 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~---~-~~-ervv~I~G~~~~v---~~A~~~i~~~~~~~~ 90 (150)
..+.+.||...+-.|||-||..|.+.+.+.++.|++... + +. ..-|.|..+..++ .-+...+.+++.+..
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c 526 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQC 526 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhhhc
Confidence 345689999999999999999999999999999999743 1 21 1226676665553 345556666666554
No 158
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=53.64 E-value=15 Score=27.54 Aligned_cols=27 Identities=41% Similarity=0.840 Sum_probs=23.0
Q ss_pred EEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 121 ~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
+.+.+-...-|.|||+.|..|++|++.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~ 90 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKD 90 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHH
Confidence 667777777899999999999999764
No 159
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=51.93 E-value=38 Score=27.01 Aligned_cols=56 Identities=16% Similarity=0.142 Sum_probs=43.0
Q ss_pred CccceEecCCchHHHHHHHHhCCe--EEecCCCCCCceEEEecChHHHHHHHHHHHHHH
Q psy7546 30 RVAGSVIGKGGSNIARLRNDFKAS--VTVPDCPGPERILTIFAELENGLKVIEEVLPAL 86 (150)
Q Consensus 30 ~~vg~IIGk~G~~Ik~l~~~tg~~--I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~ 86 (150)
.-+..|+|-.-+.|.++.++.+-. |.+...+++ +-+.|+|.++.++++...+...-
T Consensus 131 g~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~N~~-~QiVIsG~~~ale~a~~~~~~~g 188 (310)
T COG0331 131 GGMAAVLGLDDEQVEKACEEAAQGTVVEIANYNSP-GQIVISGTKEALEKAAEILKEAG 188 (310)
T ss_pred ccHHHHcCCCHHHHHHHHHHhccCCeEEEeeeCCC-CcEEEECCHHHHHHHHHHHHHhh
Confidence 456778888999999999988764 666666655 78999999999998875544433
No 160
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=48.46 E-value=61 Score=21.60 Aligned_cols=42 Identities=7% Similarity=-0.027 Sum_probs=31.6
Q ss_pred HHhCCeEEecCCC-----------CCCceEEEec-ChHHHHHHHHHHHHHHHHh
Q psy7546 48 NDFKASVTVPDCP-----------GPERILTIFA-ELENGLKVIEEVLPALDEI 89 (150)
Q Consensus 48 ~~tg~~I~i~~~~-----------~~ervv~I~G-~~~~v~~A~~~i~~~~~~~ 89 (150)
+.+++.|-+.+.- +.+-++.|.| ++..|+.|+..+++.+++.
T Consensus 47 Kaa~vev~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 47 KAAEVEVVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred hhcCeEEEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 4567777777541 3555677999 9999999999888888763
No 161
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=48.35 E-value=71 Score=22.74 Aligned_cols=43 Identities=7% Similarity=0.219 Sum_probs=34.2
Q ss_pred hHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHHH
Q psy7546 41 SNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALD 87 (150)
Q Consensus 41 ~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~~ 87 (150)
+++..|.+..|+-|.+.+. .+|.|.|+.+.|.+|+.++-..+.
T Consensus 126 eRlqDi~E~hgvIiE~~E~----D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFEEY----DLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEeeec----cEEEEeccHHHHHHHHHHHHHHHh
Confidence 5667777778888888753 589999999999999988876543
No 162
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=41.78 E-value=95 Score=22.55 Aligned_cols=58 Identities=10% Similarity=0.119 Sum_probs=44.0
Q ss_pred CCceEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHHHHHHHHHHHHHH
Q psy7546 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPAL 86 (150)
Q Consensus 18 ~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~v~~A~~~i~~~~ 86 (150)
++..+.|+-+|....- +++..|.+-.|+-+.+.+ +..|.|.|..+.+.+|+.++....
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efee----~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEFEE----DDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEecC----CcEEEEeccHHHHHHHHHHHHHHh
Confidence 4556677777665432 677888888999998833 457999999999999998886553
No 163
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=41.24 E-value=23 Score=19.84 Aligned_cols=42 Identities=19% Similarity=0.084 Sum_probs=28.3
Q ss_pred hhhhhhcccCCCCCCCCCceEEEEEeeCCccceEecCCchHHHHHHHHh
Q psy7546 2 EFFIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDF 50 (150)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~t 50 (150)
+.++++....-......+.+.+.+.||.+.+- ...++|.+.|
T Consensus 12 ~~~l~~~~~~i~~~~y~~~V~~~v~v~~~~~~-------~f~~~l~~~t 53 (56)
T PF09186_consen 12 ERLLEQNGIEIVDEDYTDDVTLTVAVPEEEVE-------EFKAQLTDLT 53 (56)
T ss_dssp HHHHHHTTTEEEEEEECTTEEEEEEEECCCHH-------HHHHHHHHHT
T ss_pred HHHHHHCCCEEEcceecceEEEEEEECHHHHH-------HHHHHHHHHc
Confidence 45666665555566667889999999988765 3345555544
No 164
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=38.98 E-value=31 Score=26.30 Aligned_cols=28 Identities=36% Similarity=0.784 Sum_probs=22.7
Q ss_pred EEEEEEecCceeEEeecCCchHHHHHHh
Q psy7546 120 DIRLIVHQSQAGCIIGKGGTKIKELRDT 147 (150)
Q Consensus 120 ~~~l~vp~~~~g~iIGk~G~~Ik~i~~~ 147 (150)
.+.+.|-...-+.+||++|..|++|++.
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~ 90 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKE 90 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHH
Confidence 4566666677799999999999998764
No 165
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=38.92 E-value=1e+02 Score=19.43 Aligned_cols=50 Identities=16% Similarity=0.028 Sum_probs=39.8
Q ss_pred CchHHHHHHHHhCCeEEecCCC-----CCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546 39 GGSNIARLRNDFKASVTVPDCP-----GPERILTIFAELENGLKVIEEVLPALDE 88 (150)
Q Consensus 39 ~G~~Ik~l~~~tg~~I~i~~~~-----~~ervv~I~G~~~~v~~A~~~i~~~~~~ 88 (150)
|=..+.++=+..|+.+...... ..+.++.+.|+..++..+...+++.++.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 5567788888889888776332 4789999999999999998888888765
No 166
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=34.26 E-value=97 Score=18.59 Aligned_cols=23 Identities=22% Similarity=0.153 Sum_probs=17.5
Q ss_pred CCceEEEecChHHHHHHHHHHHH
Q psy7546 62 PERILTIFAELENGLKVIEEVLP 84 (150)
Q Consensus 62 ~ervv~I~G~~~~v~~A~~~i~~ 84 (150)
..-.+.|.|+..+|+.|+.++.+
T Consensus 37 ~~~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 37 HMITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred ceEEEEEEecHHHHHHHHHHHhh
Confidence 34456679999999999877654
No 167
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=31.71 E-value=90 Score=21.00 Aligned_cols=27 Identities=11% Similarity=0.254 Sum_probs=23.8
Q ss_pred ceEEEecChHHHHHHHHHHHHHHHHhh
Q psy7546 64 RILTIFAELENGLKVIEEVLPALDEIR 90 (150)
Q Consensus 64 rvv~I~G~~~~v~~A~~~i~~~~~~~~ 90 (150)
-.+.|+|+..+|+.|+.++.+.+.+..
T Consensus 75 GslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 75 GALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred eeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 348899999999999999999998865
No 168
>TIGR03667 Rv3369 PPOX class probable F420-dependent enzyme, Rv3369 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN.
Probab=25.81 E-value=2.1e+02 Score=19.21 Aligned_cols=54 Identities=9% Similarity=0.038 Sum_probs=34.8
Q ss_pred eEEEEEeeCCccceEecCCchHHHHHHHHhCCeEEecCCCCCCceEEEecChHH
Q psy7546 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELEN 74 (150)
Q Consensus 21 ~~~~l~vp~~~vg~IIGk~G~~Ik~l~~~tg~~I~i~~~~~~ervv~I~G~~~~ 74 (150)
.++.+......+=..-..++..+++|+..-.+.+.+.......+.+.|.|..+-
T Consensus 31 ~P~~~~~~d~~l~~~t~~~s~K~~~l~~np~Vsl~~~~~~~~~~~v~v~G~a~i 84 (130)
T TIGR03667 31 VPVWFLWDGTEFLIYSRPQAAKLRNIRRNPRVSLHLNSDGRGGDVVVFTGTAEV 84 (130)
T ss_pred EEEEEEEECCEEEEEeCCcCHHHHHHhhCCcEEEEEEcCCCCceEEEEEEEEEE
Confidence 333343334444445566678999999988888888764433466788887543
No 169
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=24.38 E-value=98 Score=18.79 Aligned_cols=26 Identities=19% Similarity=0.179 Sum_probs=18.3
Q ss_pred EEEEEeeCCccceEecCCchHHHHHH
Q psy7546 22 ELRLLIPSRVAGSVIGKGGSNIARLR 47 (150)
Q Consensus 22 ~~~l~vp~~~vg~IIGk~G~~Ik~l~ 47 (150)
+.++.+|+++.-.|.=|-|.+++..-
T Consensus 2 ~~~v~LP~~q~t~V~vrpg~ti~d~L 27 (71)
T PF02196_consen 2 TCRVHLPNGQRTVVQVRPGMTIRDAL 27 (71)
T ss_dssp EEEEEETTTEEEEEEE-TTSBHHHHH
T ss_pred eEEEECCCCCEEEEEEcCCCCHHHHH
Confidence 45777888887777778887776554
No 170
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=20.89 E-value=2.1e+02 Score=17.42 Aligned_cols=43 Identities=7% Similarity=0.023 Sum_probs=29.5
Q ss_pred HHHHhCCeEEecCCC-CCCceEEEecChHHHHHHHHHHHHHHHH
Q psy7546 46 LRNDFKASVTVPDCP-GPERILTIFAELENGLKVIEEVLPALDE 88 (150)
Q Consensus 46 l~~~tg~~I~i~~~~-~~ervv~I~G~~~~v~~A~~~i~~~~~~ 88 (150)
+-+..++.+.-.+.. +..-.+.++|+..+|+.|+....+...+
T Consensus 21 alKaa~V~l~~~~~~~~g~~~~~i~G~vs~V~~Av~a~~~~~~~ 64 (75)
T PF00936_consen 21 ALKAANVELVEIELICGGKVTVIITGDVSAVKAAVDAAEEAAGK 64 (75)
T ss_dssp HHHHSSEEEEEEEEESTTEEEEEEEESHHHHHHHHHHHHHHHHH
T ss_pred HhhcCCEEEEEEEecCCCeEEEEEEECHHHHHHHHHHHHHHHhh
Confidence 334445554333332 3566788999999999999888887776
No 171
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=20.17 E-value=1.4e+02 Score=17.31 Aligned_cols=41 Identities=17% Similarity=0.298 Sum_probs=27.6
Q ss_pred chHHHH--HHHHhCCeEEecC-C-----C------CCCceEEEecChHHHHHHHH
Q psy7546 40 GSNIAR--LRNDFKASVTVPD-C-----P------GPERILTIFAELENGLKVIE 80 (150)
Q Consensus 40 G~~Ik~--l~~~tg~~I~i~~-~-----~------~~ervv~I~G~~~~v~~A~~ 80 (150)
|.+++. +++.+++.|---. . | .....+.+.|+.+.+.++..
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~ 68 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFRE 68 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHH
Confidence 567888 8888888774421 1 1 24467888899999887654
Done!