Query psy2768
Match_columns 96
No_of_seqs 150 out of 1047
Neff 7.8
Searched_HMMs 46136
Date Sat Aug 17 00:39:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2768.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2768hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02396 PCBP_like_KH K homolog 99.8 3.5E-18 7.6E-23 98.1 7.0 63 25-87 1-65 (65)
2 PF00013 KH_1: KH domain syndr 99.7 5.4E-17 1.2E-21 91.4 5.9 60 25-86 1-60 (60)
3 cd02394 vigilin_like_KH K homo 99.7 5.5E-17 1.2E-21 92.0 5.9 61 26-87 2-62 (62)
4 cd02393 PNPase_KH Polynucleoti 99.7 1.3E-16 2.7E-21 90.8 7.3 60 23-87 1-61 (61)
5 cd00105 KH-I K homology RNA-bi 99.6 2.6E-15 5.5E-20 84.9 7.6 62 26-87 2-64 (64)
6 KOG1676|consensus 99.6 2.8E-15 6E-20 114.5 9.7 92 2-93 200-301 (600)
7 KOG2190|consensus 99.6 6.7E-15 1.5E-19 111.8 9.2 90 2-91 111-207 (485)
8 KOG2191|consensus 99.5 8.6E-14 1.9E-18 100.8 10.1 90 3-92 102-204 (402)
9 KOG2193|consensus 99.5 1.4E-14 3.1E-19 107.7 5.4 91 2-92 471-564 (584)
10 KOG2191|consensus 99.5 1E-13 2.3E-18 100.4 8.5 72 21-92 36-111 (402)
11 smart00322 KH K homology RNA-b 99.5 4.6E-13 9.9E-18 75.4 8.9 67 23-90 2-68 (69)
12 PF13014 KH_3: KH domain 99.4 2.4E-13 5.3E-18 72.0 5.3 41 34-74 1-43 (43)
13 KOG2192|consensus 99.4 1.7E-12 3.7E-17 92.4 7.7 73 20-92 311-384 (390)
14 TIGR02696 pppGpp_PNP guanosine 99.3 3.9E-11 8.4E-16 94.6 9.6 85 2-91 554-641 (719)
15 KOG2192|consensus 99.2 8.2E-12 1.8E-16 88.9 4.5 77 19-95 118-196 (390)
16 KOG1676|consensus 99.2 2.9E-11 6.2E-16 92.8 7.1 74 19-92 134-210 (600)
17 KOG2193|consensus 99.2 1E-11 2.2E-16 92.7 3.2 75 21-95 196-272 (584)
18 PRK13763 putative RNA-processi 99.2 6.1E-11 1.3E-15 80.2 6.3 65 23-91 2-70 (180)
19 TIGR03665 arCOG04150 arCOG0415 99.2 3.1E-11 6.8E-16 81.1 4.9 61 28-92 2-65 (172)
20 TIGR03591 polynuc_phos polyrib 99.1 1.6E-10 3.5E-15 91.2 8.0 88 2-94 526-617 (684)
21 TIGR03665 arCOG04150 arCOG0415 99.1 1.6E-10 3.6E-15 77.6 6.3 55 33-93 98-152 (172)
22 cd02395 SF1_like-KH Splicing f 99.1 4.3E-10 9.3E-15 71.7 7.3 62 32-93 14-96 (120)
23 PRK13763 putative RNA-processi 99.1 4.8E-10 1E-14 75.9 6.6 55 33-93 104-158 (180)
24 PLN00207 polyribonucleotide nu 99.1 3.5E-10 7.6E-15 90.9 6.8 89 2-95 660-753 (891)
25 COG1185 Pnp Polyribonucleotide 99.0 1E-09 2.3E-14 85.7 6.7 89 2-95 527-619 (692)
26 PRK11824 polynucleotide phosph 98.8 7E-09 1.5E-13 82.1 5.9 88 2-94 529-620 (693)
27 KOG2190|consensus 98.8 7.7E-09 1.7E-13 79.0 5.4 72 21-92 335-409 (485)
28 KOG0336|consensus 98.8 7.8E-09 1.7E-13 77.8 3.8 72 19-92 42-113 (629)
29 COG1094 Predicted RNA-binding 98.5 7.3E-07 1.6E-11 60.9 6.5 54 34-93 112-165 (194)
30 KOG0119|consensus 98.4 6.7E-07 1.5E-11 68.1 6.2 71 22-92 136-230 (554)
31 KOG2814|consensus 98.4 4E-07 8.6E-12 66.4 4.2 70 23-92 56-125 (345)
32 PRK04163 exosome complex RNA-b 98.3 1.9E-06 4.2E-11 60.5 5.1 64 26-94 147-211 (235)
33 KOG1067|consensus 98.3 2.7E-06 5.8E-11 66.1 6.2 87 2-94 572-662 (760)
34 TIGR03319 YmdA_YtgF conserved 98.1 1.9E-05 4.2E-10 61.0 8.7 69 23-95 203-273 (514)
35 PRK00106 hypothetical protein; 98.1 3.6E-05 7.9E-10 59.7 9.1 70 22-95 223-294 (535)
36 PRK12704 phosphodiesterase; Pr 98.1 3.5E-05 7.5E-10 59.7 8.7 66 23-92 209-276 (520)
37 cd02134 NusA_KH NusA_K homolog 98.0 1.3E-05 2.8E-10 45.2 4.3 37 23-59 24-60 (61)
38 KOG1588|consensus 98.0 1.4E-05 3E-10 56.7 4.8 73 19-91 87-190 (259)
39 PRK12705 hypothetical protein; 97.9 4.2E-05 9.1E-10 59.1 6.6 70 23-96 197-268 (508)
40 KOG2279|consensus 97.9 1.1E-05 2.5E-10 62.2 3.1 72 19-90 63-134 (608)
41 COG5176 MSL5 Splicing factor ( 97.7 5.3E-05 1.2E-09 52.6 4.0 72 19-92 143-221 (269)
42 KOG3273|consensus 97.7 1.9E-05 4E-10 54.5 1.3 56 32-93 177-233 (252)
43 PRK00468 hypothetical protein; 97.6 6.8E-05 1.5E-09 44.1 3.4 35 19-53 25-59 (75)
44 KOG2113|consensus 97.6 4.2E-05 9.1E-10 55.9 2.8 68 19-88 21-88 (394)
45 PRK02821 hypothetical protein; 97.5 0.00011 2.4E-09 43.5 3.1 36 20-55 27-62 (77)
46 COG1837 Predicted RNA-binding 97.5 0.00015 3.2E-09 42.8 3.4 34 19-52 25-58 (76)
47 PRK01064 hypothetical protein; 97.4 0.00027 5.8E-09 41.9 3.6 35 19-53 25-59 (78)
48 KOG4369|consensus 97.3 6E-05 1.3E-09 62.9 0.6 73 24-96 1340-1414(2131)
49 KOG2279|consensus 97.3 0.00018 4E-09 55.7 2.5 71 21-91 137-208 (608)
50 COG1094 Predicted RNA-binding 97.0 0.0033 7.1E-08 43.2 6.6 65 22-90 6-75 (194)
51 PRK08406 transcription elongat 97.0 0.0012 2.7E-08 43.0 4.2 37 24-60 32-68 (140)
52 PRK08406 transcription elongat 96.8 0.0013 2.7E-08 43.0 3.0 39 23-61 98-136 (140)
53 COG1097 RRP4 RNA-binding prote 96.7 0.0039 8.4E-08 44.0 5.0 58 27-89 149-207 (239)
54 PF13083 KH_4: KH domain; PDB: 96.7 0.0011 2.5E-08 38.2 2.0 35 21-55 26-60 (73)
55 KOG2208|consensus 96.6 0.0034 7.3E-08 50.8 4.4 69 22-91 345-413 (753)
56 cd02409 KH-II KH-II (K homolo 96.5 0.006 1.3E-07 33.7 4.0 35 23-57 24-58 (68)
57 TIGR01952 nusA_arch NusA famil 96.3 0.0048 1E-07 40.4 3.4 35 25-59 34-68 (141)
58 KOG2874|consensus 96.2 0.012 2.6E-07 42.8 4.9 51 36-92 161-211 (356)
59 PF14611 SLS: Mitochondrial in 96.1 0.11 2.4E-06 35.5 9.4 65 24-92 26-90 (210)
60 PF07650 KH_2: KH domain syndr 96.1 0.0044 9.6E-08 36.0 2.1 35 24-58 25-59 (78)
61 PF13184 KH_5: NusA-like KH do 96.1 0.0055 1.2E-07 35.4 2.3 36 26-61 5-46 (69)
62 cd02414 jag_KH jag_K homology 95.7 0.014 3E-07 34.1 3.0 34 25-58 25-58 (77)
63 TIGR01952 nusA_arch NusA famil 95.5 0.012 2.5E-07 38.6 2.5 39 23-61 99-137 (141)
64 TIGR01953 NusA transcription t 95.3 0.019 4.2E-07 42.5 3.3 38 24-61 301-338 (341)
65 COG0195 NusA Transcription elo 95.2 0.02 4.4E-07 39.2 3.0 37 25-61 143-179 (190)
66 PRK13764 ATPase; Provisional 95.1 0.018 3.8E-07 45.7 2.6 39 23-61 480-518 (602)
67 PRK12328 nusA transcription el 95.1 0.025 5.5E-07 42.4 3.3 38 24-61 308-345 (374)
68 COG1855 ATPase (PilT family) [ 95.1 0.016 3.4E-07 44.9 2.2 38 24-61 486-523 (604)
69 PRK06418 transcription elongat 94.9 0.038 8.3E-07 37.1 3.5 36 25-61 62-97 (166)
70 cd02413 40S_S3_KH K homology R 94.7 0.053 1.2E-06 32.2 3.4 37 24-60 30-66 (81)
71 PRK09202 nusA transcription el 94.4 0.038 8.3E-07 42.6 2.9 38 24-61 302-339 (470)
72 cd02410 archeal_CPSF_KH The ar 94.3 0.07 1.5E-06 35.1 3.6 39 25-63 77-115 (145)
73 PRK12327 nusA transcription el 94.3 0.052 1.1E-06 40.6 3.3 40 23-62 302-341 (362)
74 KOG2208|consensus 94.2 0.11 2.3E-06 42.4 5.1 65 23-88 419-484 (753)
75 TIGR00436 era GTP-binding prot 93.8 0.16 3.5E-06 35.9 5.0 30 23-52 220-250 (270)
76 cd02412 30S_S3_KH K homology R 93.4 0.1 2.2E-06 32.5 3.0 30 26-55 63-92 (109)
77 cd02411 archeal_30S_S3_KH K ho 93.4 0.12 2.6E-06 30.7 3.2 28 26-53 40-67 (85)
78 PRK12329 nusA transcription el 93.4 0.078 1.7E-06 40.7 2.9 38 24-61 335-372 (449)
79 PRK15494 era GTPase Era; Provi 93.0 0.22 4.8E-06 36.6 4.8 37 23-59 272-317 (339)
80 COG0195 NusA Transcription elo 93.0 0.13 2.8E-06 35.3 3.2 37 25-61 77-113 (190)
81 COG0092 RpsC Ribosomal protein 91.4 0.21 4.6E-06 35.3 2.8 30 23-52 50-79 (233)
82 COG1159 Era GTPase [General fu 91.3 0.54 1.2E-05 34.4 4.9 31 21-51 226-257 (298)
83 KOG1423|consensus 89.3 0.65 1.4E-05 34.6 4.0 35 19-53 323-358 (379)
84 PRK00089 era GTPase Era; Revie 89.0 0.68 1.5E-05 32.9 3.9 36 24-59 226-270 (292)
85 COG5166 Uncharacterized conser 87.2 0.44 9.5E-06 37.5 2.1 70 22-91 447-523 (657)
86 PRK12327 nusA transcription el 87.0 0.63 1.4E-05 34.9 2.7 28 33-60 245-273 (362)
87 TIGR03675 arCOG00543 arCOG0054 86.9 0.84 1.8E-05 36.5 3.5 40 24-63 93-132 (630)
88 COG1782 Predicted metal-depend 86.5 0.91 2E-05 35.8 3.4 38 25-62 100-137 (637)
89 TIGR01953 NusA transcription t 85.8 0.82 1.8E-05 34.0 2.8 29 33-61 243-272 (341)
90 KOG2113|consensus 85.6 0.6 1.3E-05 34.7 1.9 67 20-88 111-179 (394)
91 TIGR01008 rpsC_E_A ribosomal p 84.4 1.5 3.2E-05 30.2 3.4 30 24-53 38-67 (195)
92 COG1847 Jag Predicted RNA-bind 84.3 0.86 1.9E-05 31.7 2.2 38 22-59 89-126 (208)
93 PRK04191 rps3p 30S ribosomal p 84.1 1.5 3.2E-05 30.4 3.3 30 26-55 42-71 (207)
94 PRK12329 nusA transcription el 84.1 0.87 1.9E-05 35.1 2.3 28 33-60 277-305 (449)
95 PTZ00084 40S ribosomal protein 83.6 1.6 3.4E-05 30.7 3.3 30 25-54 45-74 (220)
96 PRK12328 nusA transcription el 83.5 0.82 1.8E-05 34.5 2.0 28 33-60 251-279 (374)
97 CHL00048 rps3 ribosomal protei 82.7 1.9 4.1E-05 30.0 3.4 30 24-53 66-95 (214)
98 PRK09202 nusA transcription el 82.3 1.1 2.4E-05 34.8 2.3 28 33-60 245-273 (470)
99 COG1702 PhoH Phosphate starvat 81.3 5 0.00011 30.1 5.3 50 32-87 23-72 (348)
100 TIGR01009 rpsC_bact ribosomal 75.0 4.1 8.9E-05 28.3 3.2 28 26-53 64-91 (211)
101 KOG4369|consensus 72.4 2.7 5.9E-05 36.6 2.0 69 25-93 782-851 (2131)
102 PRK00310 rpsC 30S ribosomal pr 65.1 8.3 0.00018 27.2 3.0 28 26-53 64-91 (232)
103 COG4010 Uncharacterized protei 60.5 41 0.00089 22.4 5.4 42 44-90 126-167 (170)
104 PF07837 FTCD_N: Formiminotran 53.0 62 0.0014 22.0 5.5 46 40-85 12-62 (178)
105 PF09869 DUF2096: Uncharacteri 47.8 86 0.0019 21.2 5.9 57 21-89 110-166 (169)
106 COG1117 PstB ABC-type phosphat 46.9 14 0.00031 26.3 1.7 36 19-54 19-54 (253)
107 cd07055 BMC_like_2 Bacterial M 45.4 42 0.00092 18.9 3.2 37 51-88 21-59 (61)
108 PF00675 Peptidase_M16: Insuli 45.0 51 0.0011 20.5 4.0 50 44-95 51-100 (149)
109 COG0331 FabD (acyl-carrier-pro 43.5 61 0.0013 23.8 4.6 54 34-89 132-187 (310)
110 TIGR02024 FtcD glutamate formi 42.5 1.4E+02 0.003 22.1 6.4 46 40-85 14-64 (298)
111 PF00352 TBP: Transcription fa 42.4 56 0.0012 19.0 3.6 34 54-92 49-84 (86)
112 PF00472 RF-1: RF-1 domain; I 42.4 28 0.00061 21.6 2.4 46 40-91 23-71 (113)
113 PRK04021 hypothetical protein; 42.0 78 0.0017 19.1 4.6 57 22-83 32-90 (92)
114 PRK15468 carboxysome structura 41.8 49 0.0011 20.8 3.4 36 54-92 64-99 (111)
115 PF00936 BMC: BMC domain; Int 40.1 72 0.0016 18.2 3.8 45 47-91 19-63 (75)
116 PF03958 Secretin_N: Bacterial 38.1 47 0.001 18.6 2.8 33 53-89 44-76 (82)
117 cd03710 BipA_TypA_C BipA_TypA_ 37.6 18 0.00038 20.7 0.9 32 22-60 2-33 (79)
118 PF02749 QRPTase_N: Quinolinat 36.4 90 0.002 18.2 5.9 66 22-91 16-85 (88)
119 COG4604 CeuD ABC-type enteroch 34.7 34 0.00075 24.3 2.1 27 25-51 19-45 (252)
120 PF10369 ALS_ss_C: Small subun 34.2 93 0.002 17.7 4.9 43 43-88 16-58 (75)
121 TIGR00237 xseA exodeoxyribonuc 34.2 1.6E+02 0.0035 22.5 5.8 77 2-88 103-184 (432)
122 PF02080 TrkA_C: TrkA-C domain 33.0 84 0.0018 16.9 3.6 43 43-85 14-69 (71)
123 cd07049 BMC_EutL_repeat1 ethan 31.6 1.3E+02 0.0029 18.7 4.2 44 50-93 46-100 (103)
124 COG1120 FepC ABC-type cobalami 30.1 45 0.00098 24.0 2.1 29 23-51 18-46 (258)
125 cd03709 lepA_C lepA_C: This fa 29.4 23 0.0005 20.3 0.5 32 22-60 2-33 (80)
126 COG5328 Uncharacterized protei 29.2 1.2E+02 0.0027 19.7 3.8 40 4-43 33-73 (160)
127 cd07046 BMC_PduU-EutS 1,2-prop 29.2 1.1E+02 0.0023 19.2 3.5 56 34-92 39-98 (110)
128 PF01253 SUI1: Translation ini 29.1 1.2E+02 0.0026 17.5 4.4 35 45-80 36-71 (83)
129 TIGR03131 malonate_mdcH malona 28.4 2.1E+02 0.0046 20.1 5.9 48 37-88 125-172 (295)
130 smart00877 BMC Bacterial micro 27.6 1.3E+02 0.0027 17.2 5.2 45 47-91 18-62 (75)
131 cd04871 ACT_PSP_2 ACT domains 27.1 96 0.0021 17.9 2.9 57 35-91 17-74 (84)
132 cd07557 trimeric_dUTPase Trime 26.3 68 0.0015 18.5 2.2 27 23-49 25-51 (92)
133 CHL00100 ilvH acetohydroxyacid 25.9 2.1E+02 0.0046 19.2 5.7 44 42-88 97-140 (174)
134 COG1135 AbcC ABC-type metal io 25.3 1.4E+02 0.003 22.5 4.0 27 25-51 24-50 (339)
135 PRK11895 ilvH acetolactate syn 24.6 2.2E+02 0.0047 18.9 5.8 42 43-88 98-140 (161)
136 PRK12415 fructose 1,6-bisphosp 24.5 2.2E+02 0.0047 21.3 4.8 42 43-85 168-221 (322)
137 TIGR00119 acolac_sm acetolacta 23.8 2.2E+02 0.0049 18.7 5.6 43 42-88 96-139 (157)
138 cd08072 MPN_archaeal Mov34/MPN 23.3 34 0.00074 21.2 0.4 15 29-43 16-30 (117)
139 cd07045 BMC_CcmK_like Carbon d 23.2 1.7E+02 0.0037 17.1 5.2 43 50-92 21-63 (84)
140 COG3840 ThiQ ABC-type thiamine 23.1 1.1E+02 0.0025 21.5 3.0 31 20-50 12-42 (231)
141 PF13710 ACT_5: ACT domain; PD 22.7 87 0.0019 17.1 2.0 29 63-91 31-59 (63)
142 PF09383 NIL: NIL domain; Int 22.7 1.5E+02 0.0033 16.4 6.5 57 26-88 5-68 (76)
143 PF09840 DUF2067: Uncharacteri 22.3 2.3E+02 0.0051 19.3 4.4 26 66-91 34-59 (190)
144 PRK12388 fructose-1,6-bisphosp 21.8 2.7E+02 0.0058 20.9 4.9 41 44-85 168-220 (321)
145 COG0505 CarA Carbamoylphosphat 21.7 1.3E+02 0.0029 22.9 3.3 53 40-93 188-250 (368)
146 COG4674 Uncharacterized ABC-ty 21.3 77 0.0017 22.6 1.9 27 23-49 21-47 (249)
147 cd08068 MPN_BRCC36 Mov34/MPN/P 21.1 1.5E+02 0.0032 21.2 3.4 58 30-90 22-82 (244)
148 PRK09256 hypothetical protein; 20.7 1.3E+02 0.0027 19.5 2.7 51 40-92 24-97 (138)
149 PF03320 FBPase_glpX: Bacteria 20.4 3E+02 0.0065 20.5 4.9 41 44-85 168-220 (309)
150 cd00652 TBP_TLF TATA box bindi 20.4 2E+02 0.0043 19.2 3.7 26 67-92 147-174 (174)
151 cd04096 eEF2_snRNP_like_C eEF2 20.1 47 0.001 18.8 0.6 32 22-60 2-33 (80)
152 cd01516 FBPase_glpX Bacterial 20.0 2.9E+02 0.0064 20.5 4.7 41 44-85 168-220 (309)
153 PRK09479 glpX fructose 1,6-bis 20.0 3E+02 0.0065 20.6 4.8 41 44-85 171-223 (319)
No 1
>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=99.76 E-value=3.5e-18 Score=98.06 Aligned_cols=63 Identities=41% Similarity=0.603 Sum_probs=58.4
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC--CCCceEEEEEcCHHHHHHHHHHHh
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF--NEEETNVHIVGSFFSVQETLKGCP 87 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~--~~~~~~v~I~G~~~~v~~A~~~I~ 87 (96)
+++|.||.+.+|+|||++|++|++|+++|||+|.+.+.. +..++.|+|.|+++++..|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 468999999999999999999999999999999999854 578899999999999999999874
No 2
>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=99.69 E-value=5.4e-17 Score=91.42 Aligned_cols=60 Identities=43% Similarity=0.617 Sum_probs=55.5
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHH
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGC 86 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I 86 (96)
|.++.||.+++|+|||++|++|++|+++|||+|++++. + .+..|+|.|+++++..|+++|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-C-CcEEEEEEeCHHHHHHHHhhC
Confidence 67899999999999999999999999999999999976 3 456999999999999999886
No 3
>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=99.69 E-value=5.5e-17 Score=91.95 Aligned_cols=61 Identities=26% Similarity=0.408 Sum_probs=56.4
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHh
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCP 87 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 87 (96)
.++.||.+++|+|||++|++|++|+++|||+|.+++.. ..++.|+|+|+++++..|+.+|.
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999999865 56799999999999999998873
No 4
>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=99.69 E-value=1.3e-16 Score=90.75 Aligned_cols=60 Identities=20% Similarity=0.366 Sum_probs=55.0
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHHHHHHHHHHh
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFSVQETLKGCP 87 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~v~~A~~~I~ 87 (96)
+.+..+.||.+++|+||||||++|++|+++|||+|++++ ++.|.|+|+ +++++.|+.+|.
T Consensus 1 P~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred CeEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----CCEEEEEeCCHHHHHHHHHHhC
Confidence 356789999999999999999999999999999999997 468999998 899999998874
No 5
>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=99.63 E-value=2.6e-15 Score=84.94 Aligned_cols=62 Identities=42% Similarity=0.608 Sum_probs=56.5
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC-CCCceEEEEEcCHHHHHHHHHHHh
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQETLKGCP 87 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-~~~~~~v~I~G~~~~v~~A~~~I~ 87 (96)
.++.||.+++|.|||++|++|++|+++|||+|.|+... +..++.|.|.|+.+++..|+.+|.
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999999853 356899999999999999998873
No 6
>KOG1676|consensus
Probab=99.62 E-value=2.8e-15 Score=114.55 Aligned_cols=92 Identities=29% Similarity=0.407 Sum_probs=79.2
Q ss_pred hHHHHHHHHHHhcccC--------CCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCCCceEEE
Q psy2768 2 AQYLIFEKMREEGLFA--------GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNEEETNVH 71 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~--------~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~~~~v~ 71 (96)
|..|+.|-|+|+.-.. +......+.++.||.+.||.||||+|++||.|+.+||+||+|..+ +.+.||.+.
T Consensus 200 a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~ 279 (600)
T KOG1676|consen 200 AKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQ 279 (600)
T ss_pred HHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceee
Confidence 6788999999764211 144556699999999999999999999999999999999999774 457899999
Q ss_pred EEcCHHHHHHHHHHHhHHhcCC
Q psy2768 72 IVGSFFSVQETLKGCPNIVDQP 93 (96)
Q Consensus 72 I~G~~~~v~~A~~~I~~~i~~~ 93 (96)
|.|+++.|+.|.++|.++|+..
T Consensus 280 IiG~~d~ie~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 280 IIGTVDQIEHAAELINEIIAEA 301 (600)
T ss_pred eecCHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999998753
No 7
>KOG2190|consensus
Probab=99.59 E-value=6.7e-15 Score=111.80 Aligned_cols=90 Identities=33% Similarity=0.435 Sum_probs=73.4
Q ss_pred hHHHHHHHHHHhcc--cCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCCCceEEEEEc
Q psy2768 2 AQYLIFEKMREEGL--FAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNEEETNVHIVG 74 (96)
Q Consensus 2 A~~~I~~k~~e~~~--~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~~~~v~I~G 74 (96)
|+.+|..+.+++.. ..+ .....++++|.||.+++|.||||+|+.||+|+++|||+|.+... |.+++|.|+|.|
T Consensus 111 a~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG 190 (485)
T KOG2190|consen 111 AFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISG 190 (485)
T ss_pred HHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcC
Confidence 45556665553332 111 22235899999999999999999999999999999999999885 888999999999
Q ss_pred CHHHHHHHHHHHhHHhc
Q psy2768 75 SFFSVQETLKGCPNIVD 91 (96)
Q Consensus 75 ~~~~v~~A~~~I~~~i~ 91 (96)
.+++|.+|+..|...|.
T Consensus 191 ~~~av~~al~~Is~~L~ 207 (485)
T KOG2190|consen 191 EPDAVKKALVQISSRLL 207 (485)
T ss_pred chHHHHHHHHHHHHHHH
Confidence 99999999999999443
No 8
>KOG2191|consensus
Probab=99.53 E-value=8.6e-14 Score=100.81 Aligned_cols=90 Identities=24% Similarity=0.357 Sum_probs=73.3
Q ss_pred HHHHHHHHHHhcccC---C------CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CC---CCCceE
Q psy2768 3 QYLIFEKMREEGLFA---G------ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SF---NEEETN 69 (96)
Q Consensus 3 ~~~I~~k~~e~~~~~---~------~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~---~~~~~~ 69 (96)
..+|+||++|..-.. . ..+....+++.+|++.+|.||||||++||.+++++||+|+|.. .| +..+|+
T Consensus 102 ~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqerv 181 (402)
T KOG2191|consen 102 HEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERV 181 (402)
T ss_pred HHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEE
Confidence 568999999975311 1 1122245899999999999999999999999999999999984 33 358999
Q ss_pred EEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 70 VHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 70 v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
|++.|.+++..+|..+|.+.+.+
T Consensus 182 vt~sge~e~~~~A~~~IL~Ki~e 204 (402)
T KOG2191|consen 182 VTVSGEPEQNMKAVSLILQKIQE 204 (402)
T ss_pred EEecCCHHHHHHHHHHHHHHhhc
Confidence 99999999999999999985443
No 9
>KOG2193|consensus
Probab=99.52 E-value=1.4e-14 Score=107.70 Aligned_cols=91 Identities=41% Similarity=0.672 Sum_probs=82.9
Q ss_pred hHHHHHHHHHHhcccCCCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCC-CceEEEEEcCHHH
Q psy2768 2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNE-EETNVHIVGSFFS 78 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~-~~~~v~I~G~~~~ 78 (96)
||.+||.|+.|+++..+++...+...+.||.+.+|++|||||.++++|+.-|++.+.||++ |++ +...|.|.|+..+
T Consensus 471 AQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfya 550 (584)
T KOG2193|consen 471 AQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYA 550 (584)
T ss_pred hhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhc
Confidence 7899999999999988888899999999999999999999999999999999999999994 444 4466889999999
Q ss_pred HHHHHHHHhHHhcC
Q psy2768 79 VQETLKGCPNIVDQ 92 (96)
Q Consensus 79 v~~A~~~I~~~i~~ 92 (96)
...|...|.+++.+
T Consensus 551 tq~aQrki~~iv~q 564 (584)
T KOG2193|consen 551 TQNAQRKIAHIVNQ 564 (584)
T ss_pred chHHHHHHHHHHHH
Confidence 99999999998764
No 10
>KOG2191|consensus
Probab=99.50 E-value=1e-13 Score=100.38 Aligned_cols=72 Identities=29% Similarity=0.452 Sum_probs=67.0
Q ss_pred CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC----CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS----FNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
+..+.++++||+..+|.||||||++|.++|++|||+|++.+. |+++||+|.|.|+.+.+......|.+.|++
T Consensus 36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire 111 (402)
T KOG2191|consen 36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIRE 111 (402)
T ss_pred CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence 345999999999999999999999999999999999999983 889999999999999999999999997765
No 11
>smart00322 KH K homology RNA-binding domain.
Probab=99.49 E-value=4.6e-13 Score=75.35 Aligned_cols=67 Identities=34% Similarity=0.584 Sum_probs=60.5
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIV 90 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i 90 (96)
..+.++.||.+.+|.+||++|++|++|++.||++|.++.... ....+.|.|+++++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC-CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 467899999999999999999999999999999999987433 4688999999999999999998865
No 12
>PF13014 KH_3: KH domain
Probab=99.45 E-value=2.4e-13 Score=71.99 Aligned_cols=41 Identities=44% Similarity=0.770 Sum_probs=37.5
Q ss_pred ccceeeccchhHHHHHHHHhCCeEEecC--CCCCCceEEEEEc
Q psy2768 34 QVGRIIGKGGQNVRELQRSTGSMIKLPN--SFNEEETNVHIVG 74 (96)
Q Consensus 34 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~--~~~~~~~~v~I~G 74 (96)
++|+|||++|++|++|+++|||+|+|++ .++..++.|+|+|
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 5899999999999999999999999999 4566889999987
No 13
>KOG2192|consensus
Probab=99.39 E-value=1.7e-12 Score=92.36 Aligned_cols=73 Identities=27% Similarity=0.405 Sum_probs=67.3
Q ss_pred CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SFNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
+.+..+..+.||++.-|.||||||..|++|+.++|+.|+++. ..++.+|.++|+|+.++++.|+.+++..+++
T Consensus 311 GGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 311 GGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred CCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 456778899999999999999999999999999999999999 5677899999999999999999999987764
No 14
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.26 E-value=3.9e-11 Score=94.64 Aligned_cols=85 Identities=21% Similarity=0.266 Sum_probs=75.0
Q ss_pred hHHHHHHHHHHhcccC--CCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHH
Q psy2768 2 AQYLIFEKMREEGLFA--GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFS 78 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~--~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~ 78 (96)
|...|++.|++....+ .+...+....+.||.+.+|.+||+||.+||+|+++||++|+|.+ +..|.|.+. .++
T Consensus 554 g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----~G~V~I~a~d~~~ 628 (719)
T TIGR02696 554 ARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----DGTVYIGAADGPS 628 (719)
T ss_pred HHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----CcEEEEEeCCHHH
Confidence 4567899999875433 36778999999999999999999999999999999999999997 688999884 599
Q ss_pred HHHHHHHHhHHhc
Q psy2768 79 VQETLKGCPNIVD 91 (96)
Q Consensus 79 v~~A~~~I~~~i~ 91 (96)
.++|+.+|..++.
T Consensus 629 ~~~A~~~I~~i~~ 641 (719)
T TIGR02696 629 AEAARAMINAIAN 641 (719)
T ss_pred HHHHHHHHHHhhC
Confidence 9999999999887
No 15
>KOG2192|consensus
Probab=99.24 E-value=8.2e-12 Score=88.90 Aligned_cols=77 Identities=22% Similarity=0.315 Sum_probs=70.7
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC--CCCCCceEEEEEcCHHHHHHHHHHHhHHhcCCCC
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN--SFNEEETNVHIVGSFFSVQETLKGCPNIVDQPSI 95 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~ 95 (96)
....+..+++.|.++.+|.||||.|++||+|++++.++++|.. +|..++|+|.+.|.+..|..+++.|.+++.+.++
T Consensus 118 ~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pi 196 (390)
T KOG2192|consen 118 QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPI 196 (390)
T ss_pred CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCc
Confidence 4456789999999999999999999999999999999999987 6889999999999999999999999998887654
No 16
>KOG1676|consensus
Probab=99.23 E-value=2.9e-11 Score=92.84 Aligned_cols=74 Identities=26% Similarity=0.457 Sum_probs=66.1
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC---CCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
......+.++.||.+.+|.||||||.+||.|++.|||++.+-++. ....+.+.|+|++++|+.|+.++.++|++
T Consensus 134 q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 134 QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILRE 210 (600)
T ss_pred CCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHh
Confidence 335678999999999999999999999999999999999987742 23678999999999999999999999985
No 17
>KOG2193|consensus
Probab=99.20 E-value=1e-11 Score=92.72 Aligned_cols=75 Identities=21% Similarity=0.334 Sum_probs=67.9
Q ss_pred CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCCCceEEEEEcCHHHHHHHHHHHhHHhcCCCC
Q psy2768 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNEEETNVHIVGSFFSVQETLKGCPNIVDQPSI 95 (96)
Q Consensus 21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~ 95 (96)
...+.+++.||..++|.||||.|++||+|-+.|.|+|+|-+. .+..|+.++|-|++++..+|+++|.+++.+..+
T Consensus 196 ~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~ 272 (584)
T KOG2193|consen 196 LKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAV 272 (584)
T ss_pred ccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence 347889999999999999999999999999999999999883 466899999999999999999999998876544
No 18
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.18 E-value=6.1e-11 Score=80.20 Aligned_cols=65 Identities=20% Similarity=0.320 Sum_probs=58.7
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEE----cCHHHHHHHHHHHhHHhc
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIV----GSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~i~ 91 (96)
.....+.||.+.+|.|||++|.+|+.|+++||++|++... +..|.|. ++++++.+|+.+|..+..
T Consensus 2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE----TGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC----CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 3567899999999999999999999999999999999973 3778885 899999999999999876
No 19
>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=99.18 E-value=3.1e-11 Score=81.07 Aligned_cols=61 Identities=23% Similarity=0.424 Sum_probs=55.0
Q ss_pred EEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEE---EcCHHHHHHHHHHHhHHhcC
Q psy2768 28 LVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHI---VGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 28 ~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I---~G~~~~v~~A~~~I~~~i~~ 92 (96)
+.||.+.+|.+||+||++|+.|+++||++|++.+. +..|.| .++++++.+|+.+|..+...
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~----~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE----TGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC----CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 57999999999999999999999999999999973 367888 78999999999999997763
No 20
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.15 E-value=1.6e-10 Score=91.17 Aligned_cols=88 Identities=18% Similarity=0.278 Sum_probs=74.8
Q ss_pred hHHHHHHHHHHhcccC---CCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHH
Q psy2768 2 AQYLIFEKMREEGLFA---GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFF 77 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~---~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~ 77 (96)
+...|++.|++....+ .+...+...++.||.+.+|.|||+||++||.|+++|||+|+|.+ +..|.|.+ +.+
T Consensus 526 ~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----dG~V~i~~~~~~ 600 (684)
T TIGR03591 526 GRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----DGTVKIAASDGE 600 (684)
T ss_pred HHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----CeEEEEEECcHH
Confidence 3467888888875433 37788999999999999999999999999999999999999987 57888877 459
Q ss_pred HHHHHHHHHhHHhcCCC
Q psy2768 78 SVQETLKGCPNIVDQPS 94 (96)
Q Consensus 78 ~v~~A~~~I~~~i~~~~ 94 (96)
.+.+|+.+|..+...+.
T Consensus 601 ~~~~a~~~I~~~~~~~~ 617 (684)
T TIGR03591 601 AAEAAIKMIEGITAEPE 617 (684)
T ss_pred HHHHHHHHHHhhhcccc
Confidence 99999999999876544
No 21
>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=99.13 E-value=1.6e-10 Score=77.58 Aligned_cols=55 Identities=29% Similarity=0.414 Sum_probs=50.5
Q ss_pred CccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768 33 SQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQP 93 (96)
Q Consensus 33 ~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~ 93 (96)
..+|+|||++|++++.|+..|||+|.|++ ..|.|.|++++++.|+..|+++++..
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~------~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG------KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 36899999999999999999999999984 67999999999999999999988653
No 22
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.11 E-value=4.3e-10 Score=71.73 Aligned_cols=62 Identities=19% Similarity=0.348 Sum_probs=51.2
Q ss_pred cCccceeeccchhHHHHHHHHhCCeEEecCCCC------------------CCceEEEEEcC---HHHHHHHHHHHhHHh
Q psy2768 32 SSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN------------------EEETNVHIVGS---FFSVQETLKGCPNIV 90 (96)
Q Consensus 32 ~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~------------------~~~~~v~I~G~---~~~v~~A~~~I~~~i 90 (96)
-+++|.|||++|+++|+|+++|||+|.|..... ...--|.|+++ .+++.+|+.+|..++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 367899999999999999999999999987410 11256888885 499999999999988
Q ss_pred cCC
Q psy2768 91 DQP 93 (96)
Q Consensus 91 ~~~ 93 (96)
...
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 754
No 23
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.07 E-value=4.8e-10 Score=75.86 Aligned_cols=55 Identities=27% Similarity=0.402 Sum_probs=49.8
Q ss_pred CccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768 33 SQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQP 93 (96)
Q Consensus 33 ~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~ 93 (96)
..+|+|||++|++++.|++.|||+|.|++ ..|.|.|+++++..|...|+.+++..
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~------~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG------KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 36899999999999999999999999985 34889999999999999999988653
No 24
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.07 E-value=3.5e-10 Score=90.95 Aligned_cols=89 Identities=20% Similarity=0.296 Sum_probs=78.2
Q ss_pred hHHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCe-EEecCCCCCCceEEEEEcC-H
Q psy2768 2 AQYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSM-IKLPNSFNEEETNVHIVGS-F 76 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~-I~i~~~~~~~~~~v~I~G~-~ 76 (96)
|...|++.|++.+..+. +...+....+.||.+.+|.|||.||.+||+|+++||++ |++.+ +..|.|.+. .
T Consensus 660 g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-----dg~V~I~a~d~ 734 (891)
T PLN00207 660 GRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-----DGTVKITAKDL 734 (891)
T ss_pred HHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----CeeEEEEeCCH
Confidence 45679999999876543 78889999999999999999999999999999999999 99987 688999984 5
Q ss_pred HHHHHHHHHHhHHhcCCCC
Q psy2768 77 FSVQETLKGCPNIVDQPSI 95 (96)
Q Consensus 77 ~~v~~A~~~I~~~i~~~~~ 95 (96)
+++++|+.+|..+...+.+
T Consensus 735 ~~i~~A~~~I~~l~~~~~v 753 (891)
T PLN00207 735 SSLEKSKAIISSLTMVPTV 753 (891)
T ss_pred HHHHHHHHHHHHHhcCcCC
Confidence 9999999999998776543
No 25
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.00 E-value=1e-09 Score=85.75 Aligned_cols=89 Identities=18% Similarity=0.249 Sum_probs=79.5
Q ss_pred hHHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCH-H
Q psy2768 2 AQYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSF-F 77 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~-~ 77 (96)
|..+|++.|.+.+..+. +...+...++.|+.+.++-+||+||++|++|.++||++|++.+ +..|.|.++. +
T Consensus 527 aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied-----dGtv~i~~s~~~ 601 (692)
T COG1185 527 ARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED-----DGTVKIAASDGE 601 (692)
T ss_pred HHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC-----CCcEEEEecchH
Confidence 56789999999876543 6777889999999999999999999999999999999999995 5789999876 9
Q ss_pred HHHHHHHHHhHHhcCCCC
Q psy2768 78 SVQETLKGCPNIVDQPSI 95 (96)
Q Consensus 78 ~v~~A~~~I~~~i~~~~~ 95 (96)
.+..|+..|..+++++++
T Consensus 602 ~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 602 SAKKAKERIEAITREVEV 619 (692)
T ss_pred HHHHHHHHHHHHHhhccc
Confidence 999999999999988765
No 26
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.82 E-value=7e-09 Score=82.12 Aligned_cols=88 Identities=20% Similarity=0.344 Sum_probs=74.9
Q ss_pred hHHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HH
Q psy2768 2 AQYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FF 77 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~ 77 (96)
|...|+++|.+....+. +...+....+.||.+.++.+||+||.+||+|.++||++|++.+ +..|.|++. .+
T Consensus 529 g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d-----~G~v~i~~~~~~ 603 (693)
T PRK11824 529 GRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-----DGTVKIAATDGE 603 (693)
T ss_pred HHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-----CceEEEEcccHH
Confidence 45789999999865443 5667888899999999999999999999999999999999875 588999885 59
Q ss_pred HHHHHHHHHhHHhcCCC
Q psy2768 78 SVQETLKGCPNIVDQPS 94 (96)
Q Consensus 78 ~v~~A~~~I~~~i~~~~ 94 (96)
.+++|+.+|..+...+.
T Consensus 604 ~~~~a~~~I~~~~~~~~ 620 (693)
T PRK11824 604 AAEAAKERIEGITAEPE 620 (693)
T ss_pred HHHHHHHHHHHhcccCc
Confidence 99999999999876643
No 27
>KOG2190|consensus
Probab=98.81 E-value=7.7e-09 Score=79.03 Aligned_cols=72 Identities=29% Similarity=0.367 Sum_probs=65.0
Q ss_pred CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC---CCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
...++.++.||++++|++|||+|++|.+|++.|||.|.|.+.+ ...++.++|+|...+...+..++...+..
T Consensus 335 ~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~ 409 (485)
T KOG2190|consen 335 TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSA 409 (485)
T ss_pred cceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhccccccc
Confidence 6678999999999999999999999999999999999999854 66899999999999999999988665544
No 28
>KOG0336|consensus
Probab=98.75 E-value=7.8e-09 Score=77.84 Aligned_cols=72 Identities=22% Similarity=0.340 Sum_probs=64.1
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
.+...+++.|.+.+++||.+||+||++|+.||..|+++|++.++. .+..|+|.|....-.+|+..|...++.
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~--~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD--LEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC--ceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 566788999999999999999999999999999999999999853 478899999999999999988876543
No 29
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.45 E-value=7.3e-07 Score=60.88 Aligned_cols=54 Identities=28% Similarity=0.477 Sum_probs=50.0
Q ss_pred ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768 34 QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQP 93 (96)
Q Consensus 34 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~ 93 (96)
..|+|||++|.+-+-|++-|||.|.|.. ..|.|.|.++++..|+..|..+++..
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g------~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG------KTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC------cEEEEecChhhhHHHHHHHHHHHcCC
Confidence 4699999999999999999999999995 78999999999999999999988764
No 30
>KOG0119|consensus
Probab=98.42 E-value=6.7e-07 Score=68.10 Aligned_cols=71 Identities=24% Similarity=0.389 Sum_probs=57.4
Q ss_pred ceeEEEEEeec------CccceeeccchhHHHHHHHHhCCeEEecCC----------------CCC-CceEEEEEcCH-H
Q psy2768 22 VRLTIELVVPS------SQVGRIIGKGGQNVRELQRSTGSMIKLPNS----------------FNE-EETNVHIVGSF-F 77 (96)
Q Consensus 22 ~~~~~~~~ip~------~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----------------~~~-~~~~v~I~G~~-~ 77 (96)
..++-++.||. ++||.|||..|.+.|+|+++|||+|.|... ++. .+--|.|+++. +
T Consensus 136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~e 215 (554)
T KOG0119|consen 136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQE 215 (554)
T ss_pred cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHH
Confidence 36777888885 689999999999999999999999999651 111 22347788755 9
Q ss_pred HHHHHHHHHhHHhcC
Q psy2768 78 SVQETLKGCPNIVDQ 92 (96)
Q Consensus 78 ~v~~A~~~I~~~i~~ 92 (96)
.|++|+++|+.+|.+
T Consensus 216 ki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 216 KIKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999998876
No 31
>KOG2814|consensus
Probab=98.39 E-value=4e-07 Score=66.39 Aligned_cols=70 Identities=27% Similarity=0.345 Sum_probs=59.2
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
.++..+.++++..|.|||+.|.+-+.|+++|+|+|.+|.+....+.+..+.+..++|.+|...|..++.+
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 5788899999999999999999999999999999999985544344444445779999999999998765
No 32
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.26 E-value=1.9e-06 Score=60.47 Aligned_cols=64 Identities=20% Similarity=0.273 Sum_probs=56.7
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCH-HHHHHHHHHHhHHhcCCC
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSF-FSVQETLKGCPNIVDQPS 94 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~-~~v~~A~~~I~~~i~~~~ 94 (96)
..+.||.++++++||++|.+|+.|.+.|+++|.+.. +..|.|.++. +++..|+.+|+.+-++++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----NGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 458999999999999999999999999999999986 5889999865 799999999998876654
No 33
>KOG1067|consensus
Probab=98.25 E-value=2.7e-06 Score=66.11 Aligned_cols=87 Identities=18% Similarity=0.238 Sum_probs=74.1
Q ss_pred hHHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHH
Q psy2768 2 AQYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFF 77 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~ 77 (96)
|...|++.|.+.+..+. +...++...+.++.+.+..+||++|-..|+|+.+||+.-.++ +..++|.. ++.
T Consensus 572 ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD------e~t~~i~A~~~~ 645 (760)
T KOG1067|consen 572 ARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD------EGTFSIFAPTQA 645 (760)
T ss_pred HHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec------CceEEEEecCHH
Confidence 56789999999876443 677899999999999999999999999999999999766666 46777776 569
Q ss_pred HHHHHHHHHhHHhcCCC
Q psy2768 78 SVQETLKGCPNIVDQPS 94 (96)
Q Consensus 78 ~v~~A~~~I~~~i~~~~ 94 (96)
+.++|+..|..++..+.
T Consensus 646 am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 646 AMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred HHHHHHHHHHHHhcCcc
Confidence 99999999999876654
No 34
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=98.13 E-value=1.9e-05 Score=60.98 Aligned_cols=69 Identities=22% Similarity=0.341 Sum_probs=56.7
Q ss_pred eeEEEEEeecC-ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcCCCC
Q psy2768 23 RLTIELVVPSS-QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQPSI 95 (96)
Q Consensus 23 ~~~~~~~ip~~-~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~~ 95 (96)
..+-.+.+|++ +-|+||||.|.+||-++.-||+.+-|++.| ..|+++| +|---+-|...+..++.+.-|
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp----~~v~ls~fdp~rreia~~~l~~li~dgri 273 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP----EAVILSGFDPVRREIARMALEKLIQDGRI 273 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC----CeEEecCCchHHHHHHHHHHHHHHHcCCC
Confidence 45556889985 559999999999999999999999999854 5677888 677778888888888876543
No 35
>PRK00106 hypothetical protein; Provisional
Probab=98.07 E-value=3.6e-05 Score=59.74 Aligned_cols=70 Identities=21% Similarity=0.331 Sum_probs=57.6
Q ss_pred ceeEEEEEeec-CccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcCCCC
Q psy2768 22 VRLTIELVVPS-SQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQPSI 95 (96)
Q Consensus 22 ~~~~~~~~ip~-~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~~ 95 (96)
...+-.+.+|+ ++-|+||||.|.+|+-++.-||+.+-|++.| ..|.++| +|---+-|...+..++.+.-|
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp----~~v~lS~fdpvRReiAr~~le~Li~dgrI 294 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP----EVVVLSGFDPIRREIARMTLESLIKDGRI 294 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC----CeEEEeCCChHHHHHHHHHHHHHHHcCCc
Confidence 35556688998 4559999999999999999999999999855 5677888 678888888888888876543
No 36
>PRK12704 phosphodiesterase; Provisional
Probab=98.05 E-value=3.5e-05 Score=59.69 Aligned_cols=66 Identities=23% Similarity=0.347 Sum_probs=52.9
Q ss_pred eeEEEEEeecC-ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcC
Q psy2768 23 RLTIELVVPSS-QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 23 ~~~~~~~ip~~-~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~ 92 (96)
..+-.+.+|++ +-|+||||.|.+||-++.-||+.|-|++.| ..|.++| +|-.-+.|...+..++.+
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp----~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP----EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC----CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 45556889984 559999999999999999999999999854 5677888 566666777777776654
No 37
>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=98.01 E-value=1.3e-05 Score=45.24 Aligned_cols=37 Identities=43% Similarity=0.656 Sum_probs=34.4
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEe
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i 59 (96)
.....+.||.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4688899999999999999999999999999988876
No 38
>KOG1588|consensus
Probab=97.97 E-value=1.4e-05 Score=56.75 Aligned_cols=73 Identities=22% Similarity=0.332 Sum_probs=53.3
Q ss_pred CCCceeEEEEEeecC------ccceeeccchhHHHHHHHHhCCeEEecCC---------------CC------CCceEEE
Q psy2768 19 ADEVRLTIELVVPSS------QVGRIIGKGGQNVRELQRSTGSMIKLPNS---------------FN------EEETNVH 71 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~------~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---------------~~------~~~~~v~ 71 (96)
......+.++.||-. +||+|+|+.|.++|+|+++|||+|.|... |+ .=.-.|.
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe 166 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIE 166 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEE
Confidence 455678888999965 89999999999999999999999999541 11 1123355
Q ss_pred EEcCHHH----HHHHHHHHhHHhc
Q psy2768 72 IVGSFFS----VQETLKGCPNIVD 91 (96)
Q Consensus 72 I~G~~~~----v~~A~~~I~~~i~ 91 (96)
..+++.- +..|+..|..+|.
T Consensus 167 ~~~p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 167 TEAPPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred EeCCHHHHHHHHHHHHHHHHHhcC
Confidence 5666633 4467888887653
No 39
>PRK12705 hypothetical protein; Provisional
Probab=97.90 E-value=4.2e-05 Score=59.08 Aligned_cols=70 Identities=21% Similarity=0.305 Sum_probs=56.1
Q ss_pred eeEEEEEeecCcc-ceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcCCCCC
Q psy2768 23 RLTIELVVPSSQV-GRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQPSID 96 (96)
Q Consensus 23 ~~~~~~~ip~~~v-g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~~~ 96 (96)
...-.+.+|++-+ |+||||.|.+||.++..||+.+.|++.| ..|.+.+ +|.--+.|...+..++..+.++
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp----~~V~ls~fdp~rreia~~~l~~Li~dgri~ 268 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP----EAVVISSFNPIRREIARLTLEKLLADGRIH 268 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc----cchhhcccCccchHHHHHHHHHHHhcCCCC
Confidence 4455678887555 9999999999999999999999999865 4466766 5677788888888888777653
No 40
>KOG2279|consensus
Probab=97.86 E-value=1.1e-05 Score=62.19 Aligned_cols=72 Identities=29% Similarity=0.423 Sum_probs=62.5
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIV 90 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i 90 (96)
+....+..++.+|...+-.++||+|++|+.++..|+++|.+.+..-..++.-.+.|.+.++..|...+..++
T Consensus 63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~ 134 (608)
T KOG2279|consen 63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQIL 134 (608)
T ss_pred CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHH
Confidence 445678899999999999999999999999999999999999865555677777778999999999888843
No 41
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.70 E-value=5.3e-05 Score=52.62 Aligned_cols=72 Identities=18% Similarity=0.257 Sum_probs=48.2
Q ss_pred CCCceeEEEEEee------cCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhc
Q psy2768 19 ADEVRLTIELVVP------SSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVD 91 (96)
Q Consensus 19 ~~~~~~~~~~~ip------~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~ 91 (96)
.....++-.+.|| .+++|.|||+.|++.|++++.|+|+|.|..... .....+.. ++++...|-.-+.-++.
T Consensus 143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs--vKegk~ssd~p~~~~N~e~~lhcLI~ 220 (269)
T COG5176 143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS--VKEGKISSDTPESLKNAEAVLHCLIE 220 (269)
T ss_pred cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccc--cccCcccccCchhhhhhHHhHHHHhh
Confidence 3445666777777 468999999999999999999999999976321 12233333 24455555554544444
Q ss_pred C
Q psy2768 92 Q 92 (96)
Q Consensus 92 ~ 92 (96)
.
T Consensus 221 a 221 (269)
T COG5176 221 A 221 (269)
T ss_pred c
Confidence 3
No 42
>KOG3273|consensus
Probab=97.66 E-value=1.9e-05 Score=54.54 Aligned_cols=56 Identities=29% Similarity=0.567 Sum_probs=50.2
Q ss_pred cCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHH-hcCC
Q psy2768 32 SSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNI-VDQP 93 (96)
Q Consensus 32 ~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~-i~~~ 93 (96)
+..+|+|+||+|.+---|++.|.++|.+.+ ..++|-|..+++..|...|+.+ +-+|
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------~kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------SKIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC------ceEEEeecchhhHHHHHhhHhhhccCC
Confidence 457899999999999999999999999994 7899999999999999999994 5444
No 43
>PRK00468 hypothetical protein; Provisional
Probab=97.64 E-value=6.8e-05 Score=44.13 Aligned_cols=35 Identities=26% Similarity=0.526 Sum_probs=30.1
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRST 53 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t 53 (96)
..+....+++.+..+-+|++|||+|.+++.|+.--
T Consensus 25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred eCCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 34556889999999999999999999999998643
No 44
>KOG2113|consensus
Probab=97.63 E-value=4.2e-05 Score=55.85 Aligned_cols=68 Identities=25% Similarity=0.387 Sum_probs=59.6
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
+....++..+.+|..+++.+.|++|.+||.++.+|.++|+-|..+. +-.+.++|.++.|..|++.|..
T Consensus 21 ~~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--ePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 21 SIGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--EPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CCCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--CCcceeccCchhHHHHhhcCcc
Confidence 3347889999999999999999999999999999999999887543 4778899999999999988765
No 45
>PRK02821 hypothetical protein; Provisional
Probab=97.52 E-value=0.00011 Score=43.48 Aligned_cols=36 Identities=25% Similarity=0.544 Sum_probs=30.3
Q ss_pred CCceeEEEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGS 55 (96)
Q Consensus 20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~ 55 (96)
......+.+.+.++-+|++|||+|.+++.|+.--.+
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 344578999999999999999999999999876543
No 46
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=97.49 E-value=0.00015 Score=42.79 Aligned_cols=34 Identities=32% Similarity=0.617 Sum_probs=30.2
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHH
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRS 52 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~ 52 (96)
..+....+++.+.++-+|.+|||+|.+++-|+.-
T Consensus 25 ~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 25 EGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 3467889999999999999999999999999853
No 47
>PRK01064 hypothetical protein; Provisional
Probab=97.38 E-value=0.00027 Score=41.91 Aligned_cols=35 Identities=26% Similarity=0.537 Sum_probs=30.8
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRST 53 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t 53 (96)
.+...+.+++.+..+..|++|||+|++++.|+.-.
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 44667889999999999999999999999998753
No 48
>KOG4369|consensus
Probab=97.34 E-value=6e-05 Score=62.87 Aligned_cols=73 Identities=23% Similarity=0.215 Sum_probs=63.4
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CC-CCCceEEEEEcCHHHHHHHHHHHhHHhcCCCCC
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SF-NEEETNVHIVGSFFSVQETLKGCPNIVDQPSID 96 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~-~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~~ 96 (96)
-...+.+|.....++||+||.+++.++.-||+-|.+.+ .+ +..||.+.+.|.++++..|-..|.-.+-+|.+|
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv~ 1414 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDVS 1414 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCcC
Confidence 34567889999999999999999999999999999988 33 357899999999999999999998877777654
No 49
>KOG2279|consensus
Probab=97.27 E-value=0.00018 Score=55.70 Aligned_cols=71 Identities=27% Similarity=0.371 Sum_probs=58.8
Q ss_pred CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC-CCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-~~~~~~v~I~G~~~~v~~A~~~I~~~i~ 91 (96)
..++...+.+|...+++++||+|.++++++..++++|.++.+. ....+...|.|...-...|+.++.+.++
T Consensus 137 ~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~ 208 (608)
T KOG2279|consen 137 NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVS 208 (608)
T ss_pred CCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhcccc
Confidence 3578888999999999999999999999999999999999863 2345667777777777788888877544
No 50
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.04 E-value=0.0033 Score=43.15 Aligned_cols=65 Identities=17% Similarity=0.301 Sum_probs=54.2
Q ss_pred ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-----CHHHHHHHHHHHhHHh
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-----SFFSVQETLKGCPNIV 90 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-----~~~~v~~A~~~I~~~i 90 (96)
...+..+.||....+.+||+.|...+.|.+.+++++.++.. +..|.|.. +|-.+.+|...|+.+=
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg 75 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK----TGSVTIRTTRKTEDPLALLKARDVVKAIG 75 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC----CCeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence 34566789999999999999999999999999999999974 45566643 5788999999888763
No 51
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.01 E-value=0.0012 Score=43.02 Aligned_cols=37 Identities=41% Similarity=0.604 Sum_probs=33.5
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEec
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP 60 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~ 60 (96)
-.+-|.|+...+|+.||++|++|+.|++..|-+|.|-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 4567888999999999999999999999999999983
No 52
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=96.82 E-value=0.0013 Score=43.01 Aligned_cols=39 Identities=18% Similarity=0.280 Sum_probs=34.5
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
.....+.||.+..|..|||+|++++.++.-++-.+.|.+
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~~ 136 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDD 136 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCeE
Confidence 456778899999999999999999999999999887753
No 53
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.71 E-value=0.0039 Score=44.05 Aligned_cols=58 Identities=24% Similarity=0.349 Sum_probs=45.4
Q ss_pred EEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHH-HHHHHHHHHhHH
Q psy2768 27 ELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFF-SVQETLKGCPNI 89 (96)
Q Consensus 27 ~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~-~v~~A~~~I~~~ 89 (96)
-+.||...+.++||++|+.++-+.+.|+|+|-|-. +..|-+.|..+ ....|...|..+
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----NG~IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----NGRIWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----CCEEEecCCCcchHHHHHHHHHHH
Confidence 46899999999999999999999999999999987 45666666654 344444444444
No 54
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=96.71 E-value=0.0011 Score=38.22 Aligned_cols=35 Identities=31% Similarity=0.433 Sum_probs=29.2
Q ss_pred CceeEEEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGS 55 (96)
Q Consensus 21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~ 55 (96)
.....+.+.+..+..|.+|||.|.+++.||--.+.
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 44567778889999999999999999999976543
No 55
>KOG2208|consensus
Probab=96.58 E-value=0.0034 Score=50.79 Aligned_cols=69 Identities=19% Similarity=0.315 Sum_probs=60.2
Q ss_pred ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~ 91 (96)
+.....+.+-......++||+|.++.+|++++.|.+.++. .++.+..+.++|....+.+|...++....
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~-~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ 413 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK-QGSNNKKVVITGVSANDEKAVEDVEKIIA 413 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc-ccCCCCCeEEeccccchhHHHHHHHHHHH
Confidence 3477888899999999999999999999999999999998 34557889999999999999988887543
No 56
>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=96.51 E-value=0.006 Score=33.75 Aligned_cols=35 Identities=43% Similarity=0.681 Sum_probs=28.4
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeE
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMI 57 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I 57 (96)
.....+.+.....|.+||++|.+++.++..++-.+
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 57
>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=96.34 E-value=0.0048 Score=40.39 Aligned_cols=35 Identities=40% Similarity=0.716 Sum_probs=33.1
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEe
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i 59 (96)
.+-|.|....+|+.||++|++|+.+++..|-+|.+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV 68 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL 68 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE
Confidence 77789999999999999999999999999999988
No 58
>KOG2874|consensus
Probab=96.19 E-value=0.012 Score=42.76 Aligned_cols=51 Identities=24% Similarity=0.401 Sum_probs=45.5
Q ss_pred ceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 36 GRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 36 g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
-++||..|++++.|+--|.|.|-|.. ..|.+.|...++..+...+.+.+.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 57999999999999999999999995 5688889999999999888886654
No 59
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.14 E-value=0.11 Score=35.50 Aligned_cols=65 Identities=14% Similarity=0.239 Sum_probs=55.2
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
-.+.+..+....-.+...+|..++++-...||+|.+... +..+.|+|+...+..+...|.+++.+
T Consensus 26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----~~~i~I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----ENRIRITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----CcEEEEEccHHHHHHHHHHHHHHHhh
Confidence 344555568888999999999999998888999999873 57899999999999999999988754
No 60
>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=96.11 E-value=0.0044 Score=36.04 Aligned_cols=35 Identities=29% Similarity=0.501 Sum_probs=29.6
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEE
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK 58 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~ 58 (96)
....+.+..+.-|.+||++|++|++|....+-.+.
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 45678889999999999999999999887766554
No 61
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=96.06 E-value=0.0055 Score=35.38 Aligned_cols=36 Identities=28% Similarity=0.517 Sum_probs=28.3
Q ss_pred EEEEeecCc-----cceeeccchhHHHHHHHHh-CCeEEecC
Q psy2768 26 IELVVPSSQ-----VGRIIGKGGQNVRELQRST-GSMIKLPN 61 (96)
Q Consensus 26 ~~~~ip~~~-----vg~iIGkgG~~Ik~i~~~t-g~~I~i~~ 61 (96)
..+.|.+.. +|..||++|.+|+.|.++. |-+|++-.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 345566666 8999999999999999999 99998865
No 62
>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=95.71 E-value=0.014 Score=34.07 Aligned_cols=34 Identities=26% Similarity=0.532 Sum_probs=27.2
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEE
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK 58 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~ 58 (96)
.+.+.+..+..|.+|||.|.++..||--++.-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 3556677788999999999999999987764443
No 63
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=95.54 E-value=0.012 Score=38.58 Aligned_cols=39 Identities=21% Similarity=0.322 Sum_probs=34.5
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
.....+.||.+..|..|||+|.+++-..+-++-+++|.+
T Consensus 99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~~ 137 (141)
T TIGR01952 99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDD 137 (141)
T ss_pred CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCeE
Confidence 456778899999999999999999999999998887763
No 64
>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=95.31 E-value=0.019 Score=42.51 Aligned_cols=38 Identities=45% Similarity=0.612 Sum_probs=35.6
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
....+.||.+..+..|||+|.+++--.+-||.+|+|..
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 56889999999999999999999999999999999975
No 65
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=95.25 E-value=0.02 Score=39.20 Aligned_cols=37 Identities=43% Similarity=0.575 Sum_probs=35.0
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
...+.||.+..+..|||+|.+++-..+-||-+++|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6778899999999999999999999999999999976
No 66
>PRK13764 ATPase; Provisional
Probab=95.10 E-value=0.018 Score=45.68 Aligned_cols=39 Identities=23% Similarity=0.534 Sum_probs=35.6
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
.-...+.||...++.+|||+|.+|++|.+..|..|.|..
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 445678999999999999999999999999999999976
No 67
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.07 E-value=0.025 Score=42.42 Aligned_cols=38 Identities=32% Similarity=0.344 Sum_probs=35.7
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
....+.||.+..+..|||+|.+++--.+-||.+|+|..
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 46788999999999999999999999999999999977
No 68
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=95.06 E-value=0.016 Score=44.95 Aligned_cols=38 Identities=26% Similarity=0.545 Sum_probs=34.7
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
-...+.+|...++.+|||+|.+|++|++..|-+|.|..
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 34668899999999999999999999999999999976
No 69
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=94.90 E-value=0.038 Score=37.11 Aligned_cols=36 Identities=31% Similarity=0.492 Sum_probs=30.3
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
.+-|.|.... |.-|||+|.+++.+++..|-+|.+-.
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 3446666667 99999999999999999999998843
No 70
>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=94.66 E-value=0.053 Score=32.16 Aligned_cols=37 Identities=19% Similarity=0.504 Sum_probs=29.7
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEec
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP 60 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~ 60 (96)
...++.|-...-|.+||++|+.|++|++.-.....++
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 3467788888889999999999999988766555554
No 71
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.41 E-value=0.038 Score=42.62 Aligned_cols=38 Identities=39% Similarity=0.550 Sum_probs=35.7
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
-...+.||....+.-|||+|.+++-..+-||.+|.|-.
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 47789999999999999999999999999999999976
No 72
>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=94.33 E-value=0.07 Score=35.11 Aligned_cols=39 Identities=36% Similarity=0.572 Sum_probs=32.8
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF 63 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~ 63 (96)
+-++.|-.+.-|.+||++|.++++|..+||-+-.|-+.|
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 345667777889999999999999999999888887643
No 73
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.30 E-value=0.052 Score=40.59 Aligned_cols=40 Identities=38% Similarity=0.473 Sum_probs=36.5
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~ 62 (96)
.....+.||.+..+..|||+|.+++--.+-||.+|+|...
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 3568899999999999999999999999999999999763
No 74
>KOG2208|consensus
Probab=94.20 E-value=0.11 Score=42.38 Aligned_cols=65 Identities=25% Similarity=0.315 Sum_probs=47.9
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHHhC-CeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTG-SMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg-~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
.....+.+|...+.++||.+|+.|+.|..++| ..|..++. ......+++.|....+..++.+...
T Consensus 419 ~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-~~~~~~~~~~~~~~dv~~~~~~~~~ 484 (753)
T KOG2208|consen 419 IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-NNSSDMVTIRGISKDVEKSVSLLKA 484 (753)
T ss_pred cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-CcccccceEeccccccchhHHHHHh
Confidence 56777999999999999999999999999999 55555543 2334556777766666655544443
No 75
>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=93.82 E-value=0.16 Score=35.86 Aligned_cols=30 Identities=27% Similarity=0.393 Sum_probs=23.3
Q ss_pred eeEEEEEee-cCccceeeccchhHHHHHHHH
Q psy2768 23 RLTIELVVP-SSQVGRIIGKGGQNVRELQRS 52 (96)
Q Consensus 23 ~~~~~~~ip-~~~vg~iIGkgG~~Ik~i~~~ 52 (96)
.+...+.|+ .++-+.|||++|+.||+|...
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 466777787 455599999999999887644
No 76
>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=93.43 E-value=0.1 Score=32.48 Aligned_cols=30 Identities=27% Similarity=0.572 Sum_probs=24.5
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGS 55 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~ 55 (96)
+++.+-...-|.+||+.|++|++|++....
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 566777777899999999999999876543
No 77
>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=93.42 E-value=0.12 Score=30.70 Aligned_cols=28 Identities=32% Similarity=0.684 Sum_probs=22.1
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHh
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRST 53 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~t 53 (96)
.++.+-...-|.+||++|++|+++++.-
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 4455555778999999999999887754
No 78
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.39 E-value=0.078 Score=40.68 Aligned_cols=38 Identities=39% Similarity=0.531 Sum_probs=35.5
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
....+.||.+..+..|||+|.+++--..-||.+|.|..
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 45689999999999999999999999999999999976
No 79
>PRK15494 era GTPase Era; Provisional
Probab=93.04 E-value=0.22 Score=36.61 Aligned_cols=37 Identities=30% Similarity=0.468 Sum_probs=26.6
Q ss_pred eeEEEEEeec-CccceeeccchhHHHHHH--------HHhCCeEEe
Q psy2768 23 RLTIELVVPS-SQVGRIIGKGGQNVRELQ--------RSTGSMIKL 59 (96)
Q Consensus 23 ~~~~~~~ip~-~~vg~iIGkgG~~Ik~i~--------~~tg~~I~i 59 (96)
.+...+.|+. ++-+.|||++|+.||+|. +-.|++|.+
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 3567778874 455999999999998764 445665554
No 80
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=92.97 E-value=0.13 Score=35.31 Aligned_cols=37 Identities=30% Similarity=0.464 Sum_probs=30.9
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~ 61 (96)
...+.+-...+|..||++|++++.+.++.|-+|.|-.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe 113 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE 113 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE
Confidence 3455556777899999999999999999999998833
No 81
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=91.43 E-value=0.21 Score=35.28 Aligned_cols=30 Identities=23% Similarity=0.504 Sum_probs=25.4
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHHH
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRS 52 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~ 52 (96)
+...++.|....-|.+||++|+.|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 566778888888999999999999887654
No 82
>COG1159 Era GTPase [General function prediction only]
Probab=91.29 E-value=0.54 Score=34.41 Aligned_cols=31 Identities=29% Similarity=0.497 Sum_probs=22.8
Q ss_pred CceeEEEEEeec-CccceeeccchhHHHHHHH
Q psy2768 21 EVRLTIELVVPS-SQVGRIIGKGGQNVRELQR 51 (96)
Q Consensus 21 ~~~~~~~~~ip~-~~vg~iIGkgG~~Ik~i~~ 51 (96)
.-.+...+.|+. ++=|.||||+|++||+|-.
T Consensus 226 ~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 226 LLKIHATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred eEEEEEEEEEecCCccceEECCCcHHHHHHHH
Confidence 335555677774 5559999999999987643
No 83
>KOG1423|consensus
Probab=89.30 E-value=0.65 Score=34.60 Aligned_cols=35 Identities=29% Similarity=0.562 Sum_probs=26.9
Q ss_pred CCCceeEEEEEeecC-ccceeeccchhHHHHHHHHh
Q psy2768 19 ADEVRLTIELVVPSS-QVGRIIGKGGQNVRELQRST 53 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~-~vg~iIGkgG~~Ik~i~~~t 53 (96)
.+.-.+..++.+|.. ....||||||..|++|-.+-
T Consensus 323 ~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 323 AGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred CcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 334567788999954 55778999999999986654
No 84
>PRK00089 era GTPase Era; Reviewed
Probab=89.00 E-value=0.68 Score=32.86 Aligned_cols=36 Identities=33% Similarity=0.545 Sum_probs=25.8
Q ss_pred eEEEEEee-cCccceeeccchhHHHHHH--------HHhCCeEEe
Q psy2768 24 LTIELVVP-SSQVGRIIGKGGQNVRELQ--------RSTGSMIKL 59 (96)
Q Consensus 24 ~~~~~~ip-~~~vg~iIGkgG~~Ik~i~--------~~tg~~I~i 59 (96)
+...+.|. .++-+.|||++|+.||+|. +-+|++|.+
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 55667776 4556999999999998765 445665554
No 85
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=87.20 E-value=0.44 Score=37.50 Aligned_cols=70 Identities=20% Similarity=0.143 Sum_probs=49.0
Q ss_pred ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC---CCC-CceEEEEEcCH---HHHHHHHHHHhHHhc
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS---FNE-EETNVHIVGSF---FSVQETLKGCPNIVD 91 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---~~~-~~~~v~I~G~~---~~v~~A~~~I~~~i~ 91 (96)
=+....|.||.+.+-.|||.||..|++.....++.|++... +.+ -...|.|..+. +++.-++.-..+++.
T Consensus 447 Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~ 523 (657)
T COG5166 447 FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK 523 (657)
T ss_pred CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHh
Confidence 35667899999999999999999999999999999998762 211 22336665543 344445444444443
No 86
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=86.96 E-value=0.63 Score=34.90 Aligned_cols=28 Identities=25% Similarity=0.442 Sum_probs=24.9
Q ss_pred CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768 33 SQVGRIIGKGGQNVRELQRST-GSMIKLP 60 (96)
Q Consensus 33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~ 60 (96)
+-+|+.||++|++|+.|.++. |-+|+|-
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv 273 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDII 273 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEE
Confidence 457999999999999998888 8999883
No 87
>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=86.86 E-value=0.84 Score=36.52 Aligned_cols=40 Identities=33% Similarity=0.529 Sum_probs=33.9
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF 63 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~ 63 (96)
.+-++.|-...-|.+|||+|.+.++|-.+||-+-.|-+.|
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 3446677888899999999999999999999888887643
No 88
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=86.47 E-value=0.91 Score=35.84 Aligned_cols=38 Identities=34% Similarity=0.581 Sum_probs=32.2
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~ 62 (96)
+-++.|-...-|.+|||+|++.++|..+||-.-.|-+.
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 34567888888999999999999999999987777663
No 89
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=85.76 E-value=0.82 Score=34.01 Aligned_cols=29 Identities=21% Similarity=0.505 Sum_probs=25.3
Q ss_pred CccceeeccchhHHHHHHHHh-CCeEEecC
Q psy2768 33 SQVGRIIGKGGQNVRELQRST-GSMIKLPN 61 (96)
Q Consensus 33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~~ 61 (96)
+-+|+.||++|++|+.|.++. |-+|+|-.
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 457999999999999999888 89998833
No 90
>KOG2113|consensus
Probab=85.57 E-value=0.6 Score=34.65 Aligned_cols=67 Identities=21% Similarity=0.255 Sum_probs=52.7
Q ss_pred CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHH-HHHHH-HHHhH
Q psy2768 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFS-VQETL-KGCPN 88 (96)
Q Consensus 20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~-v~~A~-~~I~~ 88 (96)
.....+....+|-..+|.+.|..|++|+.+|+.++..|.-+-. ..+-+..++|.+.. +++|. ..|+.
T Consensus 111 ~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--~~~~Vf~Vtg~~~nC~kra~s~eie~ 179 (394)
T KOG2113|consen 111 ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--CGEPVFCVTGAPKNCVKRARSCEIEQ 179 (394)
T ss_pred ccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--CCCceEEEecCCcchhhhccccchhh
Confidence 3556778889999999999999999999999999999877653 23577888898866 66665 44443
No 91
>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=84.41 E-value=1.5 Score=30.24 Aligned_cols=30 Identities=30% Similarity=0.657 Sum_probs=24.1
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRST 53 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t 53 (96)
...++.|....-|.+||++|+.|++|++.-
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 346677777778999999999999887654
No 92
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=84.29 E-value=0.86 Score=31.72 Aligned_cols=38 Identities=21% Similarity=0.357 Sum_probs=31.3
Q ss_pred ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEe
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i 59 (96)
....+.+.+-.+..|.+||+.|.++..||--+...++-
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 45566778888889999999999999999888765554
No 93
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=84.14 E-value=1.5 Score=30.38 Aligned_cols=30 Identities=30% Similarity=0.616 Sum_probs=23.0
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGS 55 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~ 55 (96)
.++.|-...-|.+||++|++|+++++.-.-
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 445555577899999999999988776543
No 94
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=84.09 E-value=0.87 Score=35.11 Aligned_cols=28 Identities=25% Similarity=0.455 Sum_probs=24.9
Q ss_pred CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768 33 SQVGRIIGKGGQNVRELQRST-GSMIKLP 60 (96)
Q Consensus 33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~ 60 (96)
+-+|+.||++|++|+.|.++. |-+|+|-
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI 305 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVI 305 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEE
Confidence 457999999999999998888 8999983
No 95
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=83.65 E-value=1.6 Score=30.70 Aligned_cols=30 Identities=20% Similarity=0.506 Sum_probs=23.8
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhC
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTG 54 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg 54 (96)
..++.|-...-|.+||++|..|++|++.-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 366677777789999999999998876543
No 96
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=83.53 E-value=0.82 Score=34.47 Aligned_cols=28 Identities=18% Similarity=0.395 Sum_probs=24.9
Q ss_pred CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768 33 SQVGRIIGKGGQNVRELQRST-GSMIKLP 60 (96)
Q Consensus 33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~ 60 (96)
+-+|+.||++|++|+.|.++- |-+|+|-
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI 279 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCI 279 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEE
Confidence 457999999999999998888 8999983
No 97
>CHL00048 rps3 ribosomal protein S3
Probab=82.70 E-value=1.9 Score=30.04 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=24.2
Q ss_pred eEEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768 24 LTIELVVPSSQVGRIIGKGGQNVRELQRST 53 (96)
Q Consensus 24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t 53 (96)
...++.|-...-|.+||++|.+|++|++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 346667777778999999999999987765
No 98
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=82.31 E-value=1.1 Score=34.75 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=24.7
Q ss_pred CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768 33 SQVGRIIGKGGQNVRELQRST-GSMIKLP 60 (96)
Q Consensus 33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~ 60 (96)
+-+|+.||++|++|+.|.++. |-+|.|-
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv 273 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDII 273 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEE
Confidence 347999999999999999888 8999983
No 99
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=81.34 E-value=5 Score=30.06 Aligned_cols=50 Identities=18% Similarity=0.181 Sum_probs=43.5
Q ss_pred cCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHh
Q psy2768 32 SSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCP 87 (96)
Q Consensus 32 ~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 87 (96)
.+.+-.+.|..|.+++.+.+..|+.|.... ..++|.|+...+..|...+.
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVARG------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeCC------ceEEEEechHHHHHHHHHHh
Confidence 556678889999999999999999998874 77899999778888888777
No 100
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=75.02 E-value=4.1 Score=28.30 Aligned_cols=28 Identities=25% Similarity=0.599 Sum_probs=22.6
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHh
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRST 53 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~t 53 (96)
+++.+-...-|.+||++|+.+++|++.-
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 5566777777999999999999987544
No 101
>KOG4369|consensus
Probab=72.39 E-value=2.7 Score=36.56 Aligned_cols=69 Identities=10% Similarity=-0.064 Sum_probs=55.4
Q ss_pred EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQP 93 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~ 93 (96)
.++...+..++.+|++.++..++-++.-+++.+.|... ..+.++.+++.|.-..-.-+..++....+++
T Consensus 782 niehrdkkgf~plImaatagh~tvV~~llk~ha~veaQsdrtkdt~lSlacsggr~~vvelLl~~ganke 851 (2131)
T KOG4369|consen 782 NIEHRDKKGFVPLIMAATAGHITVVQDLLKAHADVEAQSDRTKDTMLSLACSGGRTRVVELLLNAGANKE 851 (2131)
T ss_pred cccccccccchhhhhhcccCchHHHHHHHhhhhhhhhhcccccCceEEEecCCCcchHHHHHHHhhcccc
Confidence 45678899999999999999999999999999999884 3457889999887766666666666555544
No 102
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=65.06 E-value=8.3 Score=27.19 Aligned_cols=28 Identities=21% Similarity=0.580 Sum_probs=21.8
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHh
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRST 53 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~t 53 (96)
+.+.|-...-|.+||++|..+++|++.-
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 4555556667999999999999887654
No 103
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=60.55 E-value=41 Score=22.42 Aligned_cols=42 Identities=19% Similarity=0.295 Sum_probs=34.8
Q ss_pred hHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768 44 QNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIV 90 (96)
Q Consensus 44 ~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i 90 (96)
..+.+|.+..|+=|.+.. ...|.|.|+.+.|.+|++.+..+-
T Consensus 126 eRlqDi~E~hgvIiE~~E-----~D~V~i~Gd~drVk~aLke~~~~w 167 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE-----YDLVAIYGDSDRVKKALKEIGSFW 167 (170)
T ss_pred HHHHHHHHhhheeEEeee-----ccEEEEeccHHHHHHHHHHHHHHH
Confidence 467788888888888874 468999999999999999987753
No 104
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=52.99 E-value=62 Score=22.03 Aligned_cols=46 Identities=11% Similarity=0.205 Sum_probs=31.4
Q ss_pred ccchhHHHHHHHHhC----CeE-EecCCCCCCceEEEEEcCHHHHHHHHHH
Q psy2768 40 GKGGQNVRELQRSTG----SMI-KLPNSFNEEETNVHIVGSFFSVQETLKG 85 (96)
Q Consensus 40 GkgG~~Ik~i~~~tg----~~I-~i~~~~~~~~~~v~I~G~~~~v~~A~~~ 85 (96)
||.-..|..|.+..- +++ ++..+++.+...+|+.|.++.+..|.-.
T Consensus 12 gR~~~~ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~vG~p~~v~~a~~~ 62 (178)
T PF07837_consen 12 GRDKEVIEAIAKAARNVPGVKLLDVFSDADYNRSVITLVGEPEAVAEAAFA 62 (178)
T ss_dssp SSSHHHHHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEEE-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEeeChHHHHHHHHH
Confidence 777778888866543 333 4555566777889999999888777633
No 105
>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=47.78 E-value=86 Score=21.23 Aligned_cols=57 Identities=16% Similarity=0.219 Sum_probs=42.6
Q ss_pred CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHH
Q psy2768 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNI 89 (96)
Q Consensus 21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 89 (96)
...-+.++.+|....- ..+.+|.+-.|+=+.+.. +..|.|.|..+.|..|++-+..+
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efee-----~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEFEE-----DDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEecC-----CcEEEEeccHHHHHHHHHHHHHH
Confidence 3344556666655432 477889999999888843 56799999999999999988765
No 106
>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=46.86 E-value=14 Score=26.34 Aligned_cols=36 Identities=25% Similarity=0.366 Sum_probs=28.5
Q ss_pred CCCceeEEEEEeecCccceeeccchhHHHHHHHHhC
Q psy2768 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTG 54 (96)
Q Consensus 19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg 54 (96)
+......+.+.||...+-++||+.|+...-+-+..+
T Consensus 19 ~~~aL~~i~l~i~~~~VTAlIGPSGcGKST~LR~lN 54 (253)
T COG1117 19 DKHALKDINLDIPKNKVTALIGPSGCGKSTLLRCLN 54 (253)
T ss_pred chhhhccCceeccCCceEEEECCCCcCHHHHHHHHH
Confidence 455667788999999999999999998766655443
No 107
>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=45.43 E-value=42 Score=18.87 Aligned_cols=37 Identities=11% Similarity=0.112 Sum_probs=23.8
Q ss_pred HHhCCeEEecCCCCCC--ceEEEEEcCHHHHHHHHHHHhH
Q psy2768 51 RSTGSMIKLPNSFNEE--ETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 51 ~~tg~~I~i~~~~~~~--~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
+.+++.+ ++.-.+.+ --.+.|+|...+|+.|++.+++
T Consensus 21 Kaa~V~i-~d~f~gCPq~~~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 21 KASGVFV-SDIFGSCPQHMITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred hccCeEE-EEecCCCCCceEEEEEEecHHHHHHHHHHHhh
Confidence 3445555 44422221 2346689999999999988865
No 108
>PF00675 Peptidase_M16: Insulinase (Peptidase family M16) This is family M16 in the peptidase classification. ; InterPro: IPR011765 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. The majority of the sequences in this entry are metallopeptidases and non-peptidase homologs belong to MEROPS peptidase family M16 (clan ME), subfamilies M16A, M16B and M16C; they include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The proteins classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3P7L_A 3P7O_A 3TUV_A 3GO9_A 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B ....
Probab=45.02 E-value=51 Score=20.51 Aligned_cols=50 Identities=16% Similarity=0.151 Sum_probs=39.8
Q ss_pred hHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCCCC
Q psy2768 44 QNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQPSI 95 (96)
Q Consensus 44 ~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~ 95 (96)
..+.+..+..|+.+...-.. ....+.+.+..+....++.++.+.+.+|..
T Consensus 51 ~~l~~~l~~~G~~~~~~t~~--d~t~~~~~~~~~~~~~~l~~l~~~~~~P~f 100 (149)
T PF00675_consen 51 DELQEELESLGASFNASTSR--DSTSYSASVLSEDLEKALELLADMLFNPSF 100 (149)
T ss_dssp HHHHHHHHHTTCEEEEEEES--SEEEEEEEEEGGGHHHHHHHHHHHHHSBGG
T ss_pred hhhHHHhhhhccccceEecc--cceEEEEEEecccchhHHHHHHHHHhCCCC
Confidence 56777778889988766432 346788899999999999999999888764
No 109
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=43.54 E-value=61 Score=23.83 Aligned_cols=54 Identities=9% Similarity=0.148 Sum_probs=41.3
Q ss_pred ccceeeccchhHHHHHHHHhCCe--EEecCCCCCCceEEEEEcCHHHHHHHHHHHhHH
Q psy2768 34 QVGRIIGKGGQNVRELQRSTGSM--IKLPNSFNEEETNVHIVGSFFSVQETLKGCPNI 89 (96)
Q Consensus 34 ~vg~iIGkgG~~Ik~i~~~tg~~--I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 89 (96)
....++|-.-..+.++-++.+-. +.+.+.. .++.+.|+|+++++++|.....+.
T Consensus 132 ~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~N--~~~QiVIsG~~~ale~a~~~~~~~ 187 (310)
T COG0331 132 GMAAVLGLDDEQVEKACEEAAQGTVVEIANYN--SPGQIVISGTKEALEKAAEILKEA 187 (310)
T ss_pred cHHHHcCCCHHHHHHHHHHhccCCeEEEeeeC--CCCcEEEECCHHHHHHHHHHHHHh
Confidence 44677788888999998888754 5555432 248899999999999999887764
No 110
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=42.49 E-value=1.4e+02 Score=22.09 Aligned_cols=46 Identities=9% Similarity=0.146 Sum_probs=31.9
Q ss_pred ccchhHHHHHHHHh----CCeE-EecCCCCCCceEEEEEcCHHHHHHHHHH
Q psy2768 40 GKGGQNVRELQRST----GSMI-KLPNSFNEEETNVHIVGSFFSVQETLKG 85 (96)
Q Consensus 40 GkgG~~Ik~i~~~t----g~~I-~i~~~~~~~~~~v~I~G~~~~v~~A~~~ 85 (96)
||.=..|..|.+.. |+++ ++..+.+.+...+|+.|.++.+..|.-.
T Consensus 14 GR~~~vie~I~~a~~~~~gv~lld~~~D~d~NRsv~Tlvg~pe~v~eaa~~ 64 (298)
T TIGR02024 14 GRNKEVIEKIVDAIIKTDNVKLLDVDMDPDHNRSVITFVGEPECVVNAALK 64 (298)
T ss_pred CCCHHHHHHHHHHHhcCCCcEEEeCCCCCCCCceEEEEecChHHHHHHHHH
Confidence 67777777775544 4444 4454566677889999999988877633
No 111
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=42.42 E-value=56 Score=18.99 Aligned_cols=34 Identities=12% Similarity=0.166 Sum_probs=26.1
Q ss_pred CCeEEecCCCCCCceEEEEEc--CHHHHHHHHHHHhHHhcC
Q psy2768 54 GSMIKLPNSFNEEETNVHIVG--SFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 54 g~~I~i~~~~~~~~~~v~I~G--~~~~v~~A~~~I~~~i~~ 92 (96)
.+.+.|-. ...+.|+| +.+....|...+..+|++
T Consensus 49 ~~t~~IF~-----sGki~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 49 KATVLIFS-----SGKIVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TEEEEEET-----TSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred cEEEEEEc-----CCEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 56666664 47788888 569999999999887764
No 112
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=42.41 E-value=28 Score=21.60 Aligned_cols=46 Identities=22% Similarity=0.242 Sum_probs=29.7
Q ss_pred ccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC--H-HHHHHHHHHHhHHhc
Q psy2768 40 GKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS--F-FSVQETLKGCPNIVD 91 (96)
Q Consensus 40 GkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~--~-~~v~~A~~~I~~~i~ 91 (96)
|+||.+++... |.+++.... . .-.|....+ . .+...|+..+...|.
T Consensus 23 GpGGQ~VNk~~--s~V~l~h~p--t--gi~v~~~~~Rsq~~Nr~~A~~~L~~~l~ 71 (113)
T PF00472_consen 23 GPGGQNVNKTN--SKVRLRHIP--T--GIVVKCQESRSQHQNREDALEKLREKLD 71 (113)
T ss_dssp SSSSCHHHSSS--EEEEEEETT--T--TEEEEEESSSSHHHHHHHHHHHHHHHHH
T ss_pred CCCCCcccccC--CEEEEEEec--c--cEEEEEcccCCHHHHHHHHHHHHHHHHH
Confidence 99999998643 556665552 1 244444443 2 778888888887654
No 113
>PRK04021 hypothetical protein; Reviewed
Probab=41.97 E-value=78 Score=19.09 Aligned_cols=57 Identities=21% Similarity=0.383 Sum_probs=39.4
Q ss_pred ceeEEEEEeecCccceeeccch-hHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHH
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGG-QNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETL 83 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG-~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~ 83 (96)
..+.+++.-|... |+.- +-++-|-+..|+.|.|-....+....+.|.| +++.+...+
T Consensus 32 ~~lkv~v~apP~~-----GkAN~ali~~LAk~l~~~I~I~~G~~sr~K~v~i~g~~~e~l~~~L 90 (92)
T PRK04021 32 GRLKVKIKAPPVK-----GKANKELVKFFSKLLGAEVEIIRGETSREKDLLVKGISLEEVKKKL 90 (92)
T ss_pred CEEEEEEecCCCC-----ChHHHHHHHHHHHHhCCCEEEEecCCcCceEEEEecCCHHHHHHHh
Confidence 3456666666543 4443 4457778888999999876666788899998 677776554
No 114
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=41.75 E-value=49 Score=20.81 Aligned_cols=36 Identities=19% Similarity=0.138 Sum_probs=26.7
Q ss_pred CCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 54 GSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 54 g~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
++.|-+-+. -...+.|+|.-.+|+.|++.+.+.+++
T Consensus 64 ~V~igF~DR---FsGslvitGdvs~Ve~Al~~V~~~l~~ 99 (111)
T PRK15468 64 DVHIGFLDR---FSGALVIYGSVGAVEEALSQTVSGLGR 99 (111)
T ss_pred CcEEeeeec---cceeEEEEccHHHHHHHHHHHHHHHHh
Confidence 455544431 246789999999999999999887654
No 115
>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=40.15 E-value=72 Score=18.18 Aligned_cols=45 Identities=9% Similarity=0.090 Sum_probs=29.9
Q ss_pred HHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768 47 RELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 47 k~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~ 91 (96)
...-+.+++++.--+......-.+.|+|+..+|+.|.....+...
T Consensus 19 D~alKaa~V~l~~~~~~~~g~~~~~i~G~vs~V~~Av~a~~~~~~ 63 (75)
T PF00936_consen 19 DAALKAANVELVEIELICGGKVTVIITGDVSAVKAAVDAAEEAAG 63 (75)
T ss_dssp HHHHHHSSEEEEEEEEESTTEEEEEEEESHHHHHHHHHHHHHHHH
T ss_pred HHHhhcCCEEEEEEEecCCCeEEEEEEECHHHHHHHHHHHHHHHh
Confidence 344555566553333222346778999999999999988877543
No 116
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=38.07 E-value=47 Score=18.58 Aligned_cols=33 Identities=6% Similarity=0.059 Sum_probs=24.2
Q ss_pred hCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHH
Q psy2768 53 TGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNI 89 (96)
Q Consensus 53 tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 89 (96)
.+.+|..+.. ...+.+.|+++.+.....+|..+
T Consensus 44 ~~~~i~~d~~----tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 44 SSGRIVADER----TNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEECT----TTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEECC----CCEEEEEeCHHHHHHHHHHHHHH
Confidence 3445655542 35678889999999999988875
No 117
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=37.59 E-value=18 Score=20.71 Aligned_cols=32 Identities=19% Similarity=0.424 Sum_probs=21.5
Q ss_pred ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEec
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP 60 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~ 60 (96)
+-..+++.+|.+.+|.| +..|.+.-|.-..+.
T Consensus 2 Pi~~v~I~~P~~~~g~V-------~~~l~~rrg~i~~~~ 33 (79)
T cd03710 2 PIEELTIDVPEEYSGAV-------IEKLGKRKGEMVDME 33 (79)
T ss_pred CEEEEEEEeCchhhHHH-------HHHHHhCCCEEEccE
Confidence 45678899999998775 556665555444444
No 118
>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=36.38 E-value=90 Score=18.18 Aligned_cols=66 Identities=12% Similarity=0.127 Sum_probs=46.9
Q ss_pred ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCC----CCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN----EEETNVHIVGSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~----~~~~~v~I~G~~~~v~~A~~~I~~~i~ 91 (96)
...+..+....+ |.+ -|=.-..++-+..|+++...-.++ ..+..+++.|+..++..|-+.+.+++.
T Consensus 16 ~~~~a~i~are~--gV~--aG~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 16 KTGTATIIARED--GVL--AGLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SEEEEEEEESSS--EEE---SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CEEEEEEEeCCC--EEE--ECHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 355555555554 333 255677888888898888765433 367899999999999999999988765
No 119
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=34.67 E-value=34 Score=24.31 Aligned_cols=27 Identities=26% Similarity=0.468 Sum_probs=22.3
Q ss_pred EEEEEeecCccceeeccchhHHHHHHH
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQR 51 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~ 51 (96)
.+.+.+|...+-++||++|+....+-.
T Consensus 19 ~isl~i~~g~iTs~IGPNGAGKSTLLS 45 (252)
T COG4604 19 DVSLDIPKGGITSIIGPNGAGKSTLLS 45 (252)
T ss_pred cceeeecCCceeEEECCCCccHHHHHH
Confidence 456889999999999999988766643
No 120
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=34.23 E-value=93 Score=17.73 Aligned_cols=43 Identities=9% Similarity=0.047 Sum_probs=31.4
Q ss_pred hhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768 43 GQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 43 G~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
-..|.+|-+.++++|.=-.. ..-.+.++|+++.+.....++..
T Consensus 16 r~ei~~l~~~f~a~ivd~~~---~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVSP---DSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEET---TEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHHhCCEEEEECC---CEEEEEEcCCHHHHHHHHHHhhh
Confidence 45788899999998843321 25778999999999998888765
No 121
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=34.19 E-value=1.6e+02 Score=22.51 Aligned_cols=77 Identities=22% Similarity=0.207 Sum_probs=47.3
Q ss_pred hHHHHHHHHHHhcccCCCCCceeEEEEEeecCccceeeccchhHHHHHHHHhC-----CeEEecCCCCCCceEEEEEcCH
Q psy2768 2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTG-----SMIKLPNSFNEEETNVHIVGSF 76 (96)
Q Consensus 2 A~~~I~~k~~e~~~~~~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg-----~~I~i~~~~~~~~~~v~I~G~~ 76 (96)
++..+-.|+.+|.++..+... .+.-....+|.|-++.|+-++++..... ++|.+-+ ..|.=.+.+
T Consensus 103 ~~~~lk~~L~~eGlfd~~~k~----~lP~~p~~i~vits~~~aa~~D~~~~~~~r~p~~~~~~~~------~~vQG~~a~ 172 (432)
T TIGR00237 103 AYEQLKEKLAAEGLFDQEYKK----PLPHFPKRVGVITSQTGAALADILHILKRRDPSLKVVIYP------TLVQGEGAV 172 (432)
T ss_pred HHHHHHHHHHHCCCCCchhcC----CCCCCCCEEEEEeCCccHHHHHHHHHHHhhCCCceEEEec------ccccCccHH
Confidence 456677788888775432222 2233456789999999999988876532 4444443 122222345
Q ss_pred HHHHHHHHHHhH
Q psy2768 77 FSVQETLKGCPN 88 (96)
Q Consensus 77 ~~v~~A~~~I~~ 88 (96)
.++..|+..+..
T Consensus 173 ~~i~~al~~~~~ 184 (432)
T TIGR00237 173 QSIVESIELANT 184 (432)
T ss_pred HHHHHHHHHhhc
Confidence 778888776654
No 122
>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=33.02 E-value=84 Score=16.86 Aligned_cols=43 Identities=16% Similarity=0.178 Sum_probs=28.9
Q ss_pred hhHHHH--HHHHhCCeEEe-cC-------CCC---CCceEEEEEcCHHHHHHHHHH
Q psy2768 43 GQNVRE--LQRSTGSMIKL-PN-------SFN---EEETNVHIVGSFFSVQETLKG 85 (96)
Q Consensus 43 G~~Ik~--i~~~tg~~I~i-~~-------~~~---~~~~~v~I~G~~~~v~~A~~~ 85 (96)
|.++++ +++.+++.|-- .+ .++ .....+.+.|+++.+.++.+.
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~ 69 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFREL 69 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHh
Confidence 457888 77777887733 22 122 245678899999999888765
No 123
>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=31.62 E-value=1.3e+02 Score=18.66 Aligned_cols=44 Identities=16% Similarity=0.225 Sum_probs=31.4
Q ss_pred HHHhCCeEEecCCC-------C---CCceEEEEEc-CHHHHHHHHHHHhHHhcCC
Q psy2768 50 QRSTGSMIKLPNSF-------N---EEETNVHIVG-SFFSVQETLKGCPNIVDQP 93 (96)
Q Consensus 50 ~~~tg~~I~i~~~~-------~---~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~ 93 (96)
-+.++++|-+++.- . +.+-.+.|.| ++.+|+.|++.+.+.+++.
T Consensus 46 tKaa~vev~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 46 TKAAEVEVVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred hhhcCeEEEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 45677888777631 0 2233455899 8899999999999987764
No 124
>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]
Probab=30.11 E-value=45 Score=23.95 Aligned_cols=29 Identities=17% Similarity=0.406 Sum_probs=24.0
Q ss_pred eeEEEEEeecCccceeeccchhHHHHHHH
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVRELQR 51 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~ 51 (96)
--.+.|.+|...+-.|||++|+....+-+
T Consensus 18 l~~ls~~i~~G~i~~iiGpNG~GKSTLLk 46 (258)
T COG1120 18 LDDLSFSIPKGEITGILGPNGSGKSTLLK 46 (258)
T ss_pred EecceEEecCCcEEEEECCCCCCHHHHHH
Confidence 34567999999999999999998776644
No 125
>cd03709 lepA_C lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in initiation factor 2 (IF2), and in EF-Tu and EF-G (factors required for translation in Escherichia coli). Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including S. cerevisiae GUF1) originated within the bacterial LepA family. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=29.37 E-value=23 Score=20.32 Aligned_cols=32 Identities=19% Similarity=0.290 Sum_probs=21.3
Q ss_pred ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEec
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP 60 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~ 60 (96)
+-..+++.+|.+.+|.| +..|...-|.-+.+.
T Consensus 2 Pi~~v~i~vP~e~~G~V-------~~~l~~rrG~i~~~~ 33 (80)
T cd03709 2 PFVKATIITPSEYLGAI-------MELCQERRGVQKDME 33 (80)
T ss_pred CEEEEEEEeCHHhhHHH-------HHHHHHhCCEEeccE
Confidence 45678899999988775 556665555444444
No 126
>COG5328 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.23 E-value=1.2e+02 Score=19.71 Aligned_cols=40 Identities=18% Similarity=0.281 Sum_probs=28.9
Q ss_pred HHHHHHHHHhcccC-CCCCceeEEEEEeecCccceeeccch
Q psy2768 4 YLIFEKMREEGLFA-GADEVRLTIELVVPSSQVGRIIGKGG 43 (96)
Q Consensus 4 ~~I~~k~~e~~~~~-~~~~~~~~~~~~ip~~~vg~iIGkgG 43 (96)
.-|||.++|..+.+ +.+..++.+++..-....-.-|-+.|
T Consensus 33 VAIFDLiEeN~FeP~~~~~GPYrl~lSL~e~rLvF~i~~e~ 73 (160)
T COG5328 33 VAIFDLIEENSFEPVGHGGGPYRLKLSLVEARLVFAIAREG 73 (160)
T ss_pred hHHHHHhhccccccCCCCCCCeEEEeeeeeeeeeeEeeccC
Confidence 45999999887754 36778898888776666655566555
No 127
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=29.23 E-value=1.1e+02 Score=19.16 Aligned_cols=56 Identities=11% Similarity=0.119 Sum_probs=35.1
Q ss_pred ccceeeccchhH-HH---HHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 34 QVGRIIGKGGQN-VR---ELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 34 ~vg~iIGkgG~~-Ik---~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
.+|.+-..+-.. |. .--+..++.+-.- +. ....+.++|+..+|+.|+....+.+++
T Consensus 39 alGile~~~~~~~i~AaD~A~KaA~Vel~~~--~~-~~g~vii~GdvsaV~aAl~a~~~~~~~ 98 (110)
T cd07046 39 AIGILTITPSEAAIIAADIATKAADVEIGFL--DR-FSGALVITGDVSEVESALEAVVDYLRE 98 (110)
T ss_pred eEEEEEecCHHHHHHHHHHHHhhcCeEEEEE--eC-CeEEEEEEECHHHHHHHHHHHHHHHhh
Confidence 566666665542 32 3334445554222 11 245788999999999999988887665
No 128
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=29.08 E-value=1.2e+02 Score=17.46 Aligned_cols=35 Identities=11% Similarity=0.167 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCeEEecCCCCCCceEEEEEcCH-HHHH
Q psy2768 45 NVRELQRSTGSMIKLPNSFNEEETNVHIVGSF-FSVQ 80 (96)
Q Consensus 45 ~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~-~~v~ 80 (96)
-.++++...+|.-.|...++. ...|.|.|+. +.+.
T Consensus 36 lak~lkk~~ac~~sv~~~~~k-~~~I~iQGd~~~~i~ 71 (83)
T PF01253_consen 36 LAKELKKKFACGGSVTKDPGK-GEEIQIQGDHRDEIK 71 (83)
T ss_dssp HHHHHHHHHTS-EEEEE-TTT-SSEEEEESS-HHHHH
T ss_pred HHHHHHHhccCceEEeecCCC-CCEEEECCcHHHHHH
Confidence 447888999999988776533 6789999987 4443
No 129
>TIGR03131 malonate_mdcH malonate decarboxylase, epsilon subunit. Members of this protein family are the epsilon subunit of malonate decarboxylase. This subunit has malonyl-CoA/dephospho-CoA acyltransferase activity. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. The epsilon subunit is closely related to the malonyl CoA-acyl carrier protein (ACP) transacylase family described by TIGR00128, but acts on an ACP subunit of malonate decarboxylase that has an unusual coenzyme A derivative as its prothetic group.
Probab=28.43 E-value=2.1e+02 Score=20.06 Aligned_cols=48 Identities=19% Similarity=0.219 Sum_probs=33.7
Q ss_pred eeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768 37 RIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 37 ~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
.+.|-....+.++-.++++.|-..+. .+.++|.|+++.+......+..
T Consensus 125 av~~~~~~~~~~~l~~~~v~ia~~Ns----p~~~visG~~~~l~~l~~~l~~ 172 (295)
T TIGR03131 125 AVLGLDLAAVEALIAKHGVYLAIINA----PDQVVIAGSRAALRAVAELARA 172 (295)
T ss_pred EEeCCCHHHHHHHHHHcCEEEEEEcC----CCCEEEECCHHHHHHHHHHHHh
Confidence 34566667777777766655544432 4779999999999988877654
No 130
>smart00877 BMC Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
Probab=27.57 E-value=1.3e+02 Score=17.16 Aligned_cols=45 Identities=11% Similarity=0.119 Sum_probs=29.3
Q ss_pred HHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768 47 RELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 47 k~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~ 91 (96)
...-+..++++---+........+.++|+..+|+.|.....+..+
T Consensus 18 D~a~KaA~V~l~~~~~~~~g~~~~~v~Gdvs~V~~Av~a~~~~~~ 62 (75)
T smart00877 18 DAALKAANVELVGYESIGGGKVTVIITGDVAAVRAAVEAGLEAAE 62 (75)
T ss_pred HHHhhhcCcEEEEEEecCCCEEEEEEEEcHHHHHHHHHHHHHHHh
Confidence 344455555554333322345778899999999999887777543
No 131
>cd04871 ACT_PSP_2 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains
Probab=27.05 E-value=96 Score=17.94 Aligned_cols=57 Identities=12% Similarity=0.225 Sum_probs=29.6
Q ss_pred cceeeccchhHHHHHHHHhCCeE-EecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768 35 VGRIIGKGGQNVRELQRSTGSMI-KLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 35 vg~iIGkgG~~Ik~i~~~tg~~I-~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~ 91 (96)
+..++...|-+|-.|++.+|-.- .-...+...--.+.+.|++.....-+..+.++-+
T Consensus 17 Vs~~lA~~~~NI~~I~~l~~~~~~~~~~~~~~~~~e~~v~~~~~~~~~lr~~L~~la~ 74 (84)
T cd04871 17 VTRVVADQGLNIDRIRRLSGRVPLEEQDDSPKACVEFSVRGQPADLEALRAALLELAS 74 (84)
T ss_pred HHHHHHHcCCCHHHHHHhhccccccccCCCCcEEEEEEEeCCCCCHHHHHHHHHHHhc
Confidence 34456667889999988665432 2211111122356667766444444444444433
No 132
>cd07557 trimeric_dUTPase Trimeric dUTP diphosphatases. Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.
Probab=26.34 E-value=68 Score=18.47 Aligned_cols=27 Identities=11% Similarity=0.222 Sum_probs=21.3
Q ss_pred eeEEEEEeecCccceeeccchhHHHHH
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVREL 49 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i 49 (96)
+...++.+|...++.+.+|++-..+.+
T Consensus 25 ~t~~~i~~p~~~~~~i~~RSs~~~~Gi 51 (92)
T cd07557 25 PTGEAIELPEGYVGLVFPRSSLARKGI 51 (92)
T ss_pred EEeEEEEcCCCeEEEEEcCchhhcCCE
Confidence 455678999999999999998655444
No 133
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=25.89 E-value=2.1e+02 Score=19.23 Aligned_cols=44 Identities=7% Similarity=-0.032 Sum_probs=34.1
Q ss_pred chhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768 42 GGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 42 gG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
.-..+.++-+.++++|.=-.. ..-.+.++|+++.+.....++..
T Consensus 97 ~r~ei~~~~~~f~a~ivdv~~---~~~~ie~tG~~~ki~a~~~~l~~ 140 (174)
T CHL00100 97 TRPEILEIAQIFRAKVVDLSE---ESLILEVTGDPGKIVAIEQLLEK 140 (174)
T ss_pred CHHHHHHHHHHhCCEEEEecC---CEEEEEEcCCHHHHHHHHHHhhh
Confidence 456788999999999843321 24778899999999998888776
No 134
>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=25.31 E-value=1.4e+02 Score=22.48 Aligned_cols=27 Identities=30% Similarity=0.495 Sum_probs=21.9
Q ss_pred EEEEEeecCccceeeccchhHHHHHHH
Q psy2768 25 TIELVVPSSQVGRIIGKGGQNVRELQR 51 (96)
Q Consensus 25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~ 51 (96)
.+.+.|+.-.+=.|||+.|+....+-+
T Consensus 24 ~vsL~I~~GeI~GIIG~SGAGKSTLiR 50 (339)
T COG1135 24 DVSLEIPKGEIFGIIGYSGAGKSTLLR 50 (339)
T ss_pred cceEEEcCCcEEEEEcCCCCcHHHHHH
Confidence 378999999999999999987655543
No 135
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=24.61 E-value=2.2e+02 Score=18.90 Aligned_cols=42 Identities=10% Similarity=0.077 Sum_probs=33.7
Q ss_pred hhHHHHHHHHhCCeEE-ecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768 43 GQNVRELQRSTGSMIK-LPNSFNEEETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 43 G~~Ik~i~~~tg~~I~-i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
-..+-+|-+.++++|- +.. ..-.+.++|+++.+..-+.++..
T Consensus 98 r~~i~~i~~~f~a~ivdv~~----~~~~iE~tG~~~ki~~~~~~l~~ 140 (161)
T PRK11895 98 RAEILRLADIFRAKIVDVTP----ESLTIEVTGDSDKIDAFIDLLRP 140 (161)
T ss_pred HHHHHHHHHHhCCEEEEecC----CEEEEEEeCCHHHHHHHHHHhhh
Confidence 4578999999999984 543 35778999999999988888766
No 136
>PRK12415 fructose 1,6-bisphosphatase II; Reviewed
Probab=24.52 E-value=2.2e+02 Score=21.33 Aligned_cols=42 Identities=17% Similarity=0.066 Sum_probs=29.7
Q ss_pred hhHHHHHHHHhCCeEEecCC-----------CCC-CceEEEEEcCHHHHHHHHHH
Q psy2768 43 GQNVRELQRSTGSMIKLPNS-----------FNE-EETNVHIVGSFFSVQETLKG 85 (96)
Q Consensus 43 G~~Ik~i~~~tg~~I~i~~~-----------~~~-~~~~v~I~G~~~~v~~A~~~ 85 (96)
-.-|++||+ +|++|+.-.+ +++ -+-.+-|-|.|+.|-.|..+
T Consensus 168 ~~lI~eir~-~Gari~Li~DGDV~~ai~~~~~~~~vD~~~GiGGaPEGVlaAaAl 221 (322)
T PRK12415 168 QDIIDRVRA-KGARVKLFGDGDVGASIATALPGTGIDLFVGIGGAPEGVISAAAL 221 (322)
T ss_pred HHHHHHHHH-cCCeEEEeccccHHHHHHHhCCCCCeeEEEEcCCChHHHHHHHHH
Confidence 356788865 9999998663 222 34455677899999888754
No 137
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=23.78 E-value=2.2e+02 Score=18.74 Aligned_cols=43 Identities=14% Similarity=0.139 Sum_probs=34.2
Q ss_pred chhHHHHHHHHhCCeEE-ecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768 42 GGQNVRELQRSTGSMIK-LPNSFNEEETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 42 gG~~Ik~i~~~tg~~I~-i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
.-..|.+|-+.++++|. +.. +.-.+.++|+++.+..-..++..
T Consensus 96 ~r~~i~~i~~~f~a~ivdv~~----~~~~ie~tG~~~ki~~~~~~l~~ 139 (157)
T TIGR00119 96 GRDEIIRLTNIFRGRIVDVSP----DSYTVEVTGDSDKIDAFLELLRP 139 (157)
T ss_pred CHHHHHHHHHHhCCEEEEecC----CEEEEEEcCCHHHHHHHHHHhhh
Confidence 44678999999999984 543 24678899999999998888776
No 138
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=23.28 E-value=34 Score=21.24 Aligned_cols=15 Identities=27% Similarity=0.410 Sum_probs=12.7
Q ss_pred EeecCccceeeccch
Q psy2768 29 VVPSSQVGRIIGKGG 43 (96)
Q Consensus 29 ~ip~~~vg~iIGkgG 43 (96)
.-|.+.+|.|+|+.+
T Consensus 16 ~~P~E~CGlL~G~~~ 30 (117)
T cd08072 16 SHPNEFAALLRGKDG 30 (117)
T ss_pred cCCceEEEEEEeecc
Confidence 358889999999887
No 139
>cd07045 BMC_CcmK_like Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). Potential functional differences between the two types are not yet fully understood. In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carbox
Probab=23.21 E-value=1.7e+02 Score=17.13 Aligned_cols=43 Identities=9% Similarity=0.136 Sum_probs=28.1
Q ss_pred HHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768 50 QRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 50 ~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~ 92 (96)
-+..++++---+......-.+.++|+..+|+.|.....+..++
T Consensus 21 lKaA~V~l~~~~~~~~gk~~vii~GdvsaV~~Av~a~~~~~~~ 63 (84)
T cd07045 21 LKAANVTLVGYEKVGGGLVTVKITGDVAAVKAAVEAGAAAAER 63 (84)
T ss_pred hhhCCeEEEEEEecCCcEEEEEEEEcHHHHHHHHHHHHHHHhc
Confidence 3444555543333334467788999999999999877765443
No 140
>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]
Probab=23.06 E-value=1.1e+02 Score=21.47 Aligned_cols=31 Identities=23% Similarity=0.490 Sum_probs=26.1
Q ss_pred CCceeEEEEEeecCccceeeccchhHHHHHH
Q psy2768 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQ 50 (96)
Q Consensus 20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~ 50 (96)
+.-++...+.||...+-+|+|..|+....+-
T Consensus 12 ~~~~~~fdl~v~~ge~vAi~GpSGaGKSTLL 42 (231)
T COG3840 12 GHLPMRFDLTVPAGEIVAILGPSGAGKSTLL 42 (231)
T ss_pred CcceEEEEEeecCCcEEEEECCCCccHHHHH
Confidence 4567889999999999999999998776554
No 141
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=22.74 E-value=87 Score=17.14 Aligned_cols=29 Identities=10% Similarity=0.183 Sum_probs=20.5
Q ss_pred CCCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768 63 FNEEETNVHIVGSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 63 ~~~~~~~v~I~G~~~~v~~A~~~I~~~i~ 91 (96)
++...-.+++.|+.+.+....+++.++++
T Consensus 31 ~~~~riti~v~~~~~~i~~l~~Ql~Klid 59 (63)
T PF13710_consen 31 PGISRITIVVSGDDREIEQLVKQLEKLID 59 (63)
T ss_dssp TTEEEEEEEEES-CCHHHHHHHHHHCSTT
T ss_pred CCEEEEEEEEeeCchhHHHHHHHHhccCC
Confidence 44455667788988888888888887654
No 142
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=22.72 E-value=1.5e+02 Score=16.41 Aligned_cols=57 Identities=9% Similarity=0.084 Sum_probs=39.3
Q ss_pred EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-----CC--CCceEEEEEcCHHHHHHHHHHHhH
Q psy2768 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-----FN--EEETNVHIVGSFFSVQETLKGCPN 88 (96)
Q Consensus 26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-----~~--~~~~~v~I~G~~~~v~~A~~~I~~ 88 (96)
+++..+.+. ....-|.++.+++|..++|-.. .+ -..-.+.+.|+.+++++|+..+.+
T Consensus 5 ~~l~f~g~~------~~~piis~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~g~~~~~~~a~~~L~~ 68 (76)
T PF09383_consen 5 VRLTFTGNS------AQEPIISQLIREFGVDVNILHGNIEEIQGTPFGILILELPGDDEEIEKAIAYLRE 68 (76)
T ss_dssp EEEEEESCS------SSSCHHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHH
T ss_pred EEEEEcCCC------cCchHHHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEECCHHHHHHHHHHHHH
Confidence 445555443 3456789999999999998662 12 234567789999999999988876
No 143
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=22.25 E-value=2.3e+02 Score=19.32 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=22.2
Q ss_pred CceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768 66 EETNVHIVGSFFSVQETLKGCPNIVD 91 (96)
Q Consensus 66 ~~~~v~I~G~~~~v~~A~~~I~~~i~ 91 (96)
+.-.|.+.|++..+..|...|.+++.
T Consensus 34 n~l~I~i~G~~~eike~~~~Ik~~~~ 59 (190)
T PF09840_consen 34 NSLKIEIQGYEKEIKEAIRRIKELVR 59 (190)
T ss_pred CEEEEEEecChHHHHHHHHHHHHHHH
Confidence 35679999999999999999988764
No 144
>PRK12388 fructose-1,6-bisphosphatase II-like protein; Reviewed
Probab=21.82 E-value=2.7e+02 Score=20.86 Aligned_cols=41 Identities=12% Similarity=0.009 Sum_probs=28.8
Q ss_pred hHHHHHHHHhCCeEEecCC-----------CCC-CceEEEEEcCHHHHHHHHHH
Q psy2768 44 QNVRELQRSTGSMIKLPNS-----------FNE-EETNVHIVGSFFSVQETLKG 85 (96)
Q Consensus 44 ~~Ik~i~~~tg~~I~i~~~-----------~~~-~~~~v~I~G~~~~v~~A~~~ 85 (96)
.-|++||+ +|++|+.-.+ |++ -+-.+-|-|.|+.|-.|..+
T Consensus 168 ~lI~eiR~-~GarI~Li~DGDVa~ai~~~~~~s~vD~~~GiGGAPEGVlaAaAl 220 (321)
T PRK12388 168 AAIEEATQ-LGVKVFALPDGDVAASVLTCWQDNPYDVMYTIGGAPEGVISACAV 220 (321)
T ss_pred HHHHHHHH-cCCeEEEeccccHHHHHHHhCCCCCeeEEEEcCCChHHHHHHHHH
Confidence 56788865 9999998663 222 34445567899999888753
No 145
>COG0505 CarA Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]
Probab=21.68 E-value=1.3e+02 Score=22.87 Aligned_cols=53 Identities=11% Similarity=0.139 Sum_probs=36.2
Q ss_pred ccchhHHHHHHHHhCCeEEecCCCC--------CCceEEEEE--cCHHHHHHHHHHHhHHhcCC
Q psy2768 40 GKGGQNVRELQRSTGSMIKLPNSFN--------EEETNVHIV--GSFFSVQETLKGCPNIVDQP 93 (96)
Q Consensus 40 GkgG~~Ik~i~~~tg~~I~i~~~~~--------~~~~~v~I~--G~~~~v~~A~~~I~~~i~~~ 93 (96)
|-.-..++.+.+ -||++.|-.... ..+.++.-- |.|+.+..|+..|.++++..
T Consensus 188 GvK~nIlr~L~~-rg~~vtVVP~~t~~eeIl~~~pDGiflSNGPGDP~~~~~~i~~ik~l~~~~ 250 (368)
T COG0505 188 GVKRNILRELVK-RGCRVTVVPADTSAEEILALNPDGIFLSNGPGDPAPLDYAIETIKELLGTK 250 (368)
T ss_pred CccHHHHHHHHH-CCCeEEEEcCCCCHHHHHhhCCCEEEEeCCCCChhHHHHHHHHHHHHhccC
Confidence 555667777754 799998855221 123333332 68999999999999988764
No 146
>COG4674 Uncharacterized ABC-type transport system, ATPase component [General function prediction only]
Probab=21.31 E-value=77 Score=22.57 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=21.3
Q ss_pred eeEEEEEeecCccceeeccchhHHHHH
Q psy2768 23 RLTIELVVPSSQVGRIIGKGGQNVREL 49 (96)
Q Consensus 23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i 49 (96)
--.+.|.|+.-...++||++|+....+
T Consensus 21 ln~ls~~v~~Gelr~lIGpNGAGKTT~ 47 (249)
T COG4674 21 LNDLSFSVDPGELRVLIGPNGAGKTTL 47 (249)
T ss_pred eeeeEEEecCCeEEEEECCCCCCceee
Confidence 345678899999999999999875433
No 147
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=21.13 E-value=1.5e+02 Score=21.19 Aligned_cols=58 Identities=7% Similarity=0.077 Sum_probs=32.8
Q ss_pred eecCccceeeccchhHHHHHHHHhCCeEEecC---CCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN---SFNEEETNVHIVGSFFSVQETLKGCPNIV 90 (96)
Q Consensus 30 ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~---~~~~~~~~v~I~G~~~~v~~A~~~I~~~i 90 (96)
-|.+.+|.++|+-+.. + ....+..+.+.. ......+.....=+|+...+|...+.++.
T Consensus 22 ~P~EvCGLL~G~~~~~-~--~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~~~~ 82 (244)
T cd08068 22 EKEEVMGLLIGEIEVS-K--KGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAERLT 82 (244)
T ss_pred CCcceeEEEEeecccc-c--ccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHHHHH
Confidence 5778899999985421 1 122233444322 11222344555668888888877776643
No 148
>PRK09256 hypothetical protein; Provisional
Probab=20.69 E-value=1.3e+02 Score=19.55 Aligned_cols=51 Identities=20% Similarity=0.287 Sum_probs=30.5
Q ss_pred ccchhHHHHHHHHhCCeEEecCC----C--------------CCCceEEEEEc----CH-HHHHHHHHHHhHHhcC
Q psy2768 40 GKGGQNVRELQRSTGSMIKLPNS----F--------------NEEETNVHIVG----SF-FSVQETLKGCPNIVDQ 92 (96)
Q Consensus 40 GkgG~~Ik~i~~~tg~~I~i~~~----~--------------~~~~~~v~I~G----~~-~~v~~A~~~I~~~i~~ 92 (96)
|+||.+++... |.+++.++-. | -..+..+.|.- +. .+...|+..+.++|.+
T Consensus 24 GPGGQ~VNKt~--SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~ 97 (138)
T PRK09256 24 GPGGQNVNKVS--TAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALERLVALIRE 97 (138)
T ss_pred CCCcccccccc--eeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHHHHHHHHHH
Confidence 99999998764 6667664321 1 01123333332 33 6788888888887654
No 149
>PF03320 FBPase_glpX: Bacterial fructose-1,6-bisphosphatase, glpX-encoded; InterPro: IPR004464 Gluconeogenesis is an important metabolic pathway, which produces glucose from noncarbohydrate precursors such as organic acids, fatty acids, amino acids, or glycerol. Fructose-1,6-bisphosphatase, a key enzyme of gluconeogenesis, is found in all organisms, and five different classes of these enzymes have been identified. This entry represents the class 2 fructose-1,6-bisphosphatases, which include GlpX and YggF of Escherichia coli (strain K12), which show different catalytic properties. The crystal structure of GlpX has been determined in a free state and in the complex with a substrate (fructose 1,6-bisphosphate) or inhibitor (phosphate). The crystal structure of the ligand-free GlpX revealed a compact, globular shape with two alpha/beta-sandwich domains. The core fold of GlpX is structurally similar to that of Li+-sensitive phosphatases suggesting that they have a common evolutionary origin and catalytic mechanism. The structure of the GlpX complex with fructose 1,6-bisphosphate revealed that the active site is located between two domains and accommodates several conserved residues coordinating two metal ions and the substrate. A third metal ion is bound to phosphate 6 of the substrate. Inorganic phosphate strongly inhibited activity of both GlpX and YggF, and the crystal structure of the GlpX complex with phosphate demonstrated that the inhibitor molecule binds to the active site. Alanine replacement mutagenesis of GlpX identifies 12 conserved residues important for activity and suggested that Thr(90) is the primary catalytic residue []. A number of the proteins in this entry, particularly those from algae are bi functional and can catalyzes the hydrolysis of fructose 1,6-bisphosphate and sedoheptulose 1,7-bisphosphate to fructose 6-phosphate and sedoheptulose 7-phosphate, respectively. ; GO: 0006071 glycerol metabolic process; PDB: 3RPL_C 3ROJ_A 3D1R_A 2R8T_A 3BIH_A 3BIG_A 1NI9_A.
Probab=20.41 E-value=3e+02 Score=20.48 Aligned_cols=41 Identities=17% Similarity=0.154 Sum_probs=29.1
Q ss_pred hHHHHHHHHhCCeEEecCC-----------CC-CCceEEEEEcCHHHHHHHHHH
Q psy2768 44 QNVRELQRSTGSMIKLPNS-----------FN-EEETNVHIVGSFFSVQETLKG 85 (96)
Q Consensus 44 ~~Ik~i~~~tg~~I~i~~~-----------~~-~~~~~v~I~G~~~~v~~A~~~ 85 (96)
.-|++|++ +|++|+.-.+ ++ .-+-.+-|-|.|+.|-.|..+
T Consensus 168 ~lI~eiR~-~Garv~Li~DGDVa~ai~~~~~~sgvD~~~GiGGAPEGVlaAaAl 220 (309)
T PF03320_consen 168 ELIEEIRE-AGARVKLISDGDVAGAIATALPDSGVDMLMGIGGAPEGVLAAAAL 220 (309)
T ss_dssp HHHHHHHH-CT-EEEEESS-HHHHHHHTTCCTSS-SEEEEEEEHHHHHHHHHHH
T ss_pred HHHHHHHH-cCCeEEEeCcCcHHHHHHHhcCCCCccEEEECCCCcHHHHHHHHH
Confidence 46788865 9999998663 33 245667788999999888754
No 150
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=20.39 E-value=2e+02 Score=19.19 Aligned_cols=26 Identities=15% Similarity=0.213 Sum_probs=20.5
Q ss_pred ceEEEEEcC--HHHHHHHHHHHhHHhcC
Q psy2768 67 ETNVHIVGS--FFSVQETLKGCPNIVDQ 92 (96)
Q Consensus 67 ~~~v~I~G~--~~~v~~A~~~I~~~i~~ 92 (96)
...|.|+|. .+.+..|.+.|..+|.+
T Consensus 147 sGkvvitGaks~~~~~~a~~~i~~~L~~ 174 (174)
T cd00652 147 SGKIVITGAKSREDIYEAVEKIYPILKE 174 (174)
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHhC
Confidence 467888885 48899999999887753
No 151
>cd04096 eEF2_snRNP_like_C eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=20.12 E-value=47 Score=18.78 Aligned_cols=32 Identities=16% Similarity=0.373 Sum_probs=20.4
Q ss_pred ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEec
Q psy2768 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP 60 (96)
Q Consensus 22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~ 60 (96)
+-..+++.+|.+.+|.| +..|.+.-|.-+...
T Consensus 2 Pi~~~~I~~p~~~~g~V-------~~~l~~rrg~i~~~~ 33 (80)
T cd04096 2 PIYLVEIQCPEDALGKV-------YSVLSKRRGHVLSEE 33 (80)
T ss_pred CEEEEEEEEcHHHhhHH-------HHhhhhCeeEEeEEe
Confidence 45678899999988764 455554444444433
No 152
>cd01516 FBPase_glpX Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core structure around the active site is well preserved. In E. coli, FBPase II is part of the glp regulon, which mediates growth on glycerol or sn-glycerol 3-phosphate as the sole carbon source.
Probab=20.04 E-value=2.9e+02 Score=20.53 Aligned_cols=41 Identities=20% Similarity=0.130 Sum_probs=28.6
Q ss_pred hHHHHHHHHhCCeEEecCC-----------CCC-CceEEEEEcCHHHHHHHHHH
Q psy2768 44 QNVRELQRSTGSMIKLPNS-----------FNE-EETNVHIVGSFFSVQETLKG 85 (96)
Q Consensus 44 ~~Ik~i~~~tg~~I~i~~~-----------~~~-~~~~v~I~G~~~~v~~A~~~ 85 (96)
.-|++||+ +|++|+.-.+ +++ -+-.+-|-|.|+.|-.|..+
T Consensus 168 ~lI~eiR~-~Gari~Li~DGDV~~ai~~~~~~s~vD~~~GiGGaPEGVlaAaAl 220 (309)
T cd01516 168 ALIEEIRE-AGARIKLIPDGDVAAAIATALPGSGVDVLMGIGGAPEGVLAAAAL 220 (309)
T ss_pred HHHHHHHH-cCCeEEEeccccHHHHHHHhCCCCCeeEEEECCCChHHHHHHHHH
Confidence 46788865 9999998663 222 34445566899999888754
No 153
>PRK09479 glpX fructose 1,6-bisphosphatase II; Reviewed
Probab=20.02 E-value=3e+02 Score=20.58 Aligned_cols=41 Identities=17% Similarity=0.146 Sum_probs=29.0
Q ss_pred hHHHHHHHHhCCeEEecCC-----------CC-CCceEEEEEcCHHHHHHHHHH
Q psy2768 44 QNVRELQRSTGSMIKLPNS-----------FN-EEETNVHIVGSFFSVQETLKG 85 (96)
Q Consensus 44 ~~Ik~i~~~tg~~I~i~~~-----------~~-~~~~~v~I~G~~~~v~~A~~~ 85 (96)
.-|++||+ +|++|+.-.+ |+ .-+-.+-|-|.|+.|-.|..+
T Consensus 171 ~lI~eiR~-~Gari~Li~DGDVa~ai~~~~~~s~vD~~~GiGGaPEGVlaAaAl 223 (319)
T PRK09479 171 ELIAEIRE-AGARVKLISDGDVAGAIATAFPDTGVDILMGIGGAPEGVLAAAAL 223 (319)
T ss_pred HHHHHHHH-cCCeEEEeccccHHHHHHHhcCCCCeeEEEEcCcChHHHHHHHHH
Confidence 56788865 9999998663 22 234455577899999888754
Done!