Query psy8115
Match_columns 218
No_of_seqs 113 out of 943
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 18:59:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8115.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8115hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00084 40S ribosomal protein 100.0 1.9E-37 4.1E-42 270.4 15.6 129 78-206 3-131 (220)
2 COG0092 RpsC Ribosomal protein 100.0 2E-36 4.4E-41 265.3 15.2 122 81-207 16-137 (233)
3 TIGR01008 rpsC_E_A ribosomal p 100.0 2.6E-35 5.6E-40 252.9 15.1 122 83-206 2-123 (195)
4 PRK04191 rps3p 30S ribosomal p 100.0 4.9E-34 1.1E-38 246.4 15.9 124 81-206 2-125 (207)
5 CHL00048 rps3 ribosomal protei 100.0 4.8E-32 1E-36 235.3 15.8 137 70-207 16-154 (214)
6 TIGR01009 rpsC_bact ribosomal 100.0 1.1E-31 2.3E-36 232.5 14.6 135 65-206 10-146 (211)
7 PRK00310 rpsC 30S ribosomal pr 100.0 5E-31 1.1E-35 231.3 14.7 131 69-206 15-146 (232)
8 KOG3181|consensus 100.0 3E-28 6.4E-33 210.0 11.8 132 76-207 1-132 (244)
9 cd02413 40S_S3_KH K homology R 99.9 1.3E-21 2.8E-26 147.1 10.7 80 90-169 1-80 (81)
10 cd02412 30S_S3_KH K homology R 99.8 6.2E-21 1.4E-25 149.6 9.4 94 70-169 15-109 (109)
11 cd02411 archeal_30S_S3_KH K ho 99.8 5.9E-20 1.3E-24 138.1 9.7 84 83-168 2-85 (85)
12 PF07650 KH_2: KH domain syndr 99.6 2E-15 4.3E-20 110.5 7.2 77 95-171 1-78 (78)
13 cd02409 KH-II KH-II (K homolo 98.9 7.6E-09 1.7E-13 71.4 8.0 65 97-163 1-67 (68)
14 smart00322 KH K homology RNA-b 97.8 2.5E-05 5.3E-10 52.7 3.3 67 119-185 3-69 (69)
15 PF13083 KH_4: KH domain; PDB: 97.0 0.0011 2.4E-08 47.9 4.1 68 95-162 3-72 (73)
16 cd02414 jag_KH jag_K homology 97.0 0.0058 1.3E-07 44.9 7.9 56 98-153 2-58 (77)
17 PRK01064 hypothetical protein; 95.9 0.13 2.8E-06 38.8 9.6 54 112-165 21-76 (78)
18 PF00189 Ribosomal_S3_C: Ribos 95.8 0.012 2.5E-07 44.3 3.5 28 179-206 1-29 (85)
19 COG1847 Jag Predicted RNA-bind 95.0 0.13 2.8E-06 45.4 8.0 110 90-199 61-185 (208)
20 cd02410 archeal_CPSF_KH The ar 94.8 0.25 5.5E-06 41.4 9.0 86 97-196 55-141 (145)
21 cd02134 NusA_KH NusA_K homolog 94.7 0.073 1.6E-06 37.6 4.8 53 97-149 2-55 (61)
22 PRK02821 hypothetical protein; 94.6 0.62 1.3E-05 35.1 9.7 65 98-165 7-74 (77)
23 PRK08406 transcription elongat 94.1 0.085 1.8E-06 43.5 4.6 60 95-154 73-134 (140)
24 PRK00468 hypothetical protein; 93.3 1.1 2.4E-05 33.5 9.0 52 112-163 21-74 (75)
25 TIGR00436 era GTP-binding prot 92.8 0.86 1.9E-05 40.1 9.1 74 85-163 181-267 (270)
26 PRK15494 era GTPase Era; Provi 92.7 0.9 2E-05 41.8 9.4 99 60-163 203-319 (339)
27 COG1159 Era GTPase [General fu 92.5 1.2 2.5E-05 41.4 9.8 69 84-154 188-269 (298)
28 COG1837 Predicted RNA-binding 91.6 2.2 4.9E-05 32.2 8.8 47 117-163 26-74 (76)
29 COG1782 Predicted metal-depend 91.2 1.3 2.9E-05 44.2 9.1 78 95-189 80-157 (637)
30 PRK00089 era GTPase Era; Revie 89.8 2.7 5.8E-05 37.0 9.1 73 86-163 189-272 (292)
31 TIGR03675 arCOG00543 arCOG0054 88.3 3.7 8E-05 41.4 9.9 77 106-196 82-158 (630)
32 TIGR01952 nusA_arch NusA famil 86.8 1.1 2.4E-05 37.2 4.4 60 95-154 74-135 (141)
33 cd02393 PNPase_KH Polynucleoti 77.7 2.3 5.1E-05 29.8 2.6 29 120-148 3-31 (61)
34 PF13014 KH_3: KH domain 77.3 1.9 4.1E-05 27.9 1.9 16 131-146 3-18 (43)
35 PRK06418 transcription elongat 74.1 3.4 7.4E-05 35.3 3.2 55 95-150 34-91 (166)
36 cd00105 KH-I K homology RNA-bi 71.6 4.7 0.0001 27.2 2.8 27 122-148 3-29 (64)
37 cd02396 PCBP_like_KH K homolog 70.3 4 8.6E-05 28.6 2.3 27 121-147 2-28 (65)
38 PF13184 KH_5: NusA-like KH do 65.7 8.4 0.00018 28.1 3.3 38 118-161 2-44 (69)
39 PF00013 KH_1: KH domain syndr 65.7 2.3 5.1E-05 28.9 0.3 28 121-148 2-29 (60)
40 cd02394 vigilin_like_KH K homo 63.3 5.7 0.00012 27.1 2.0 27 122-148 3-29 (62)
41 COG1534 Predicted RNA-binding 55.9 39 0.00084 26.7 5.6 53 126-185 15-70 (97)
42 PRK09202 nusA transcription el 55.1 19 0.00041 35.3 4.6 53 95-147 278-330 (470)
43 PRK12327 nusA transcription el 51.3 74 0.0016 30.3 7.8 55 95-149 203-266 (362)
44 PRK08406 transcription elongat 51.0 24 0.00051 29.0 4.0 43 104-148 19-61 (140)
45 TIGR01953 NusA transcription t 51.0 70 0.0015 30.1 7.5 55 95-149 201-264 (341)
46 PF14698 ASL_C2: Argininosucci 50.9 11 0.00023 27.4 1.7 34 171-207 2-38 (70)
47 COG0195 NusA Transcription elo 48.3 53 0.0011 28.6 5.9 19 131-149 88-106 (190)
48 TIGR03665 arCOG04150 arCOG0415 47.2 14 0.00031 31.0 2.2 61 126-193 5-71 (172)
49 PRK13764 ATPase; Provisional 45.6 35 0.00077 34.6 4.9 51 95-148 460-510 (602)
50 PRK12328 nusA transcription el 45.0 91 0.002 30.0 7.3 55 95-149 209-272 (374)
51 PF14480 DNA_pol3_a_NI: DNA po 44.8 1.1E+02 0.0024 21.6 6.6 57 101-163 18-74 (76)
52 TIGR01952 nusA_arch NusA famil 44.7 27 0.00059 29.0 3.4 45 103-148 18-62 (141)
53 TIGR03112 6_pyr_pter_rel 6-pyr 44.6 1.1E+02 0.0023 24.2 6.7 64 120-189 28-91 (113)
54 PRK09509 fieF ferrous iron eff 44.1 74 0.0016 28.5 6.4 75 91-167 213-288 (299)
55 COG1942 Uncharacterized protei 43.1 38 0.00083 24.9 3.6 46 123-168 4-49 (69)
56 COG4604 CeuD ABC-type enteroch 42.9 1.1E+02 0.0023 28.0 7.0 62 119-182 18-79 (252)
57 COG0195 NusA Transcription elo 41.6 48 0.001 28.9 4.6 53 95-147 117-170 (190)
58 PLN02808 alpha-galactosidase 41.4 8.1 0.00018 37.0 -0.2 68 38-114 5-73 (386)
59 TIGR00253 RNA_bind_YhbY putati 41.3 89 0.0019 24.3 5.6 53 126-185 14-69 (95)
60 COG1855 ATPase (PilT family) [ 41.2 41 0.0009 33.9 4.5 52 93-148 463-515 (604)
61 PRK12327 nusA transcription el 41.0 43 0.00092 31.9 4.5 52 95-146 278-330 (362)
62 TIGR01953 NusA transcription t 40.5 42 0.00092 31.6 4.4 51 95-145 276-327 (341)
63 PRK12329 nusA transcription el 39.4 1.1E+02 0.0023 30.3 7.0 54 95-148 228-297 (449)
64 PRK09202 nusA transcription el 38.7 1.1E+02 0.0024 30.1 7.1 55 95-149 203-266 (470)
65 PRK13763 putative RNA-processi 37.4 74 0.0016 27.0 5.0 59 129-193 105-163 (180)
66 PRK12328 nusA transcription el 37.3 49 0.0011 31.8 4.3 51 95-145 284-334 (374)
67 PHA02754 hypothetical protein; 36.9 45 0.00098 24.5 3.1 34 177-211 4-37 (67)
68 PRK13916 plasmid segregation p 36.1 28 0.0006 27.3 2.0 35 61-111 17-51 (97)
69 KOG2192|consensus 35.9 16 0.00034 34.3 0.8 39 116-154 120-158 (390)
70 PF03780 Asp23: Asp23 family; 34.0 70 0.0015 23.9 3.9 54 107-166 45-107 (108)
71 KOG2191|consensus 33.8 68 0.0015 30.9 4.5 53 92-147 105-160 (402)
72 TIGR00013 taut 4-oxalocrotonat 33.7 68 0.0015 21.7 3.5 30 139-168 19-48 (63)
73 PRK10343 RNA-binding protein Y 33.7 1.3E+02 0.0028 23.6 5.4 53 126-185 16-71 (97)
74 PRK08384 thiamine biosynthesis 33.5 91 0.002 29.8 5.4 101 100-217 31-145 (381)
75 PRK13763 putative RNA-processi 33.3 52 0.0011 27.9 3.5 69 121-191 5-75 (180)
76 KOG1423|consensus 33.3 3.1E+02 0.0067 26.5 8.8 75 86-163 289-374 (379)
77 PHA03303 envelope glycoprotein 33.2 1.2E+02 0.0026 26.0 5.5 43 172-217 98-143 (159)
78 cd00554 MECDP_synthase MECDP_s 32.8 1.7E+02 0.0038 24.7 6.4 50 103-164 82-131 (153)
79 PRK14958 DNA polymerase III su 32.6 2.7E+02 0.0059 27.4 8.7 88 117-217 411-506 (509)
80 PF14552 Tautomerase_2: Tautom 32.5 36 0.00078 25.6 2.1 54 114-168 23-76 (82)
81 TIGR03665 arCOG04150 arCOG0415 31.6 70 0.0015 26.9 3.9 67 129-202 99-165 (172)
82 COG1302 Uncharacterized protei 30.3 3.2E+02 0.0068 22.6 7.7 60 105-170 49-118 (131)
83 cd00491 4Oxalocrotonate_Tautom 30.0 89 0.0019 20.6 3.5 32 137-168 16-47 (58)
84 PRK05090 hypothetical protein; 29.8 2.7E+02 0.0058 21.7 7.1 40 137-176 44-91 (95)
85 PRK12329 nusA transcription el 29.5 82 0.0018 31.1 4.5 52 95-146 310-362 (449)
86 PF12685 SpoIIIAH: SpoIIIAH-li 28.0 3.8E+02 0.0082 22.8 8.5 56 100-161 140-195 (196)
87 PRK02289 4-oxalocrotonate taut 27.7 1.2E+02 0.0027 20.7 4.0 29 140-168 20-48 (60)
88 PF01545 Cation_efflux: Cation 27.4 2.3E+02 0.005 24.4 6.6 74 91-165 205-280 (284)
89 TIGR03131 malonate_mdcH malona 27.2 2E+02 0.0044 25.2 6.3 42 157-198 211-252 (295)
90 COG1094 Predicted RNA-binding 27.2 1.5E+02 0.0032 26.2 5.2 59 130-194 113-171 (194)
91 PRK03094 hypothetical protein; 26.9 1.6E+02 0.0034 22.5 4.7 36 102-137 15-52 (80)
92 KOG2192|consensus 26.1 69 0.0015 30.2 3.2 64 120-183 316-384 (390)
93 PF11324 DUF3126: Protein of u 26.0 90 0.002 22.9 3.1 20 140-161 1-20 (63)
94 PRK00745 4-oxalocrotonate taut 25.7 1.2E+02 0.0027 20.3 3.7 29 140-168 20-48 (62)
95 KOG1676|consensus 25.5 45 0.00097 34.0 2.0 27 120-146 140-166 (600)
96 PF14389 Lzipper-MIP1: Leucine 25.2 68 0.0015 24.4 2.5 36 179-216 19-54 (88)
97 TIGR00342 thiazole biosynthesi 25.0 89 0.0019 29.3 3.8 107 96-217 22-137 (371)
98 PF08731 AFT: Transcription fa 24.6 1.4E+02 0.0029 24.3 4.2 32 94-127 5-36 (111)
99 cd00552 RaiA RaiA ("ribosome-a 24.3 2.8E+02 0.006 20.0 7.9 45 95-140 22-71 (93)
100 KOG2190|consensus 24.2 58 0.0013 32.2 2.5 27 121-147 45-71 (485)
101 COG1782 Predicted metal-depend 23.9 1.2E+02 0.0025 31.0 4.4 55 95-154 9-64 (637)
102 PRK08446 coproporphyrinogen II 23.6 5.3E+02 0.011 23.7 8.5 34 133-166 156-189 (350)
103 TIGR03675 arCOG00543 arCOG0054 23.5 1E+02 0.0022 31.3 4.0 53 95-152 3-56 (630)
104 PF02542 YgbB: YgbB family; I 22.8 2.1E+02 0.0046 24.3 5.3 50 103-164 83-132 (157)
105 TIGR00151 ispF 2C-methyl-D-ery 22.7 2.2E+02 0.0047 24.2 5.3 40 120-164 92-131 (155)
106 PF06069 PerC: PerC transcript 22.6 63 0.0014 25.1 1.9 23 177-199 3-25 (90)
107 COG0053 MMT1 Predicted Co/Zn/C 22.6 4E+02 0.0087 24.4 7.5 62 108-170 232-294 (304)
108 PRK00084 ispF 2-C-methyl-D-ery 22.3 2.2E+02 0.0047 24.3 5.2 40 120-164 95-134 (159)
109 PRK01565 thiamine biosynthesis 21.8 1.5E+02 0.0031 28.1 4.5 45 97-154 27-71 (394)
110 PF01985 CRS1_YhbY: CRS1 / Yhb 21.8 1.5E+02 0.0033 22.0 3.8 52 127-185 15-69 (84)
111 PF10118 Metal_hydrol: Predict 21.7 72 0.0016 28.5 2.4 24 78-101 45-68 (253)
112 PRK06418 transcription elongat 21.5 2.8E+02 0.0062 23.7 5.8 62 95-161 101-163 (166)
113 PF06857 ACP: Malonate decarbo 21.2 3.8E+02 0.0083 20.5 6.4 66 110-184 14-82 (87)
114 COG1129 MglA ABC-type sugar tr 21.0 2.7E+02 0.0059 27.8 6.4 95 118-213 24-141 (500)
115 TIGR03367 queuosine_QueD queuo 20.9 3.7E+02 0.0079 20.1 6.5 44 141-186 49-92 (92)
116 PF08664 YcbB: YcbB domain; I 20.7 42 0.00092 27.8 0.6 23 182-206 65-87 (134)
117 PRK01271 4-oxalocrotonate taut 20.6 1.5E+02 0.0032 22.0 3.5 29 140-168 21-49 (76)
118 COG0779 Uncharacterized protei 20.1 5.3E+02 0.012 21.7 8.3 74 95-174 9-87 (153)
No 1
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=1.9e-37 Score=270.35 Aligned_cols=129 Identities=66% Similarity=0.970 Sum_probs=126.5
Q ss_pred cchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCC
Q psy8115 78 LSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADG 157 (218)
Q Consensus 78 ~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~k 157 (218)
.|++.+++||+|++++++|||||.++|.++|||+|+|+|+++.++|+||+++||+|||++|+++++|++.|+++|+++++
T Consensus 3 ~~~~~~k~fi~~~~~~~~~re~l~k~~~~agis~ieI~Rt~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~~~~ 82 (220)
T PTZ00084 3 GQISKKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEG 82 (220)
T ss_pred cccchhhHHHHcchhhHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEECCCccEEcCCchHHHHHHHHHHHHhCCCCc
Confidence 56889999999999999999999999999999999999999999999999999999999999999999999999998889
Q ss_pred cEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115 158 AIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT 206 (218)
Q Consensus 158 kI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA 206 (218)
+|+|++.||++|++||.++|++||+|||+|++||||||+||+++|++||
T Consensus 83 ~i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGa 131 (220)
T PTZ00084 83 KVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGA 131 (220)
T ss_pred eEEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999999999999999999999999999999998
No 2
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-36 Score=265.26 Aligned_cols=122 Identities=29% Similarity=0.369 Sum_probs=117.0
Q ss_pred hhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEE
Q psy8115 81 CVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIE 160 (218)
Q Consensus 81 ~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~ 160 (218)
.+|.+++.+|. +|||||.++|.+||||+|+|+|++++++|+||++|||+|||++|++|++|+..|+++|+.+ ++.
T Consensus 16 ~~~~~~l~ed~---kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~--~v~ 90 (233)
T COG0092 16 KEYAKLLVEDL---KIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE--NVQ 90 (233)
T ss_pred ccchHHHHHHH---HHHHHHHHHHHhCCcceEEEEecCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC--Cce
Confidence 57888888887 9999999999999999999999999999999999999999999999999999999999963 788
Q ss_pred EEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115 161 LYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY 207 (218)
Q Consensus 161 I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~ 207 (218)
|+|.||++|++||+++|++||.|||+|++||||||+||+++|++||-
T Consensus 91 I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAk 137 (233)
T COG0092 91 INIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAK 137 (233)
T ss_pred EEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCCc
Confidence 99999999999999999999999999999999999999999999984
No 3
>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=100.00 E-value=2.6e-35 Score=252.95 Aligned_cols=122 Identities=41% Similarity=0.581 Sum_probs=118.4
Q ss_pred hhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEE
Q psy8115 83 SLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY 162 (218)
Q Consensus 83 ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~ 162 (218)
+++|++|++++.+|||||.++|.++|||+|+|+|+++.++|+||+++||++||++|+++++|++.|+++++. .+++|+
T Consensus 2 ~kkfi~~~~~~~~ire~l~k~~~~agis~ieI~r~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~--~~~~I~ 79 (195)
T TIGR01008 2 ERKFVAEGLKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL--ENPQID 79 (195)
T ss_pred cEehHhcchHHHHHHHHHHHHHHhCCeeEEEEEEcCCcEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC--CceEEE
Confidence 689999999999999999999999999999999999999999999999999999999999999999999975 368999
Q ss_pred EEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115 163 AEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT 206 (218)
Q Consensus 163 I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA 206 (218)
+.||++|++||.++|++||+|||+|++||||||+||+++|++||
T Consensus 80 v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGa 123 (195)
T TIGR01008 80 VEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGA 123 (195)
T ss_pred EEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999997
No 4
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=4.9e-34 Score=246.40 Aligned_cols=124 Identities=31% Similarity=0.468 Sum_probs=119.7
Q ss_pred hhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEE
Q psy8115 81 CVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIE 160 (218)
Q Consensus 81 ~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~ 160 (218)
..+++|++|++++.+||+||.+.|.+|||++|+|+|++++++|+||+++||++||++|+++++|+..|++.++. .++.
T Consensus 2 ~~~~~fi~~~~~~~~irefi~~~~~~AgIs~IeI~Rt~~~i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~~~--~~v~ 79 (207)
T PRK04191 2 AIEKKFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGL--ENPQ 79 (207)
T ss_pred chhhHHHHcchHHHHHHHHHHhhhhhcceeEEEEEEcCCcEEEEEEECCCCeEECCCchhHHHHHHHHHHHhCC--Ccee
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999975 3588
Q ss_pred EEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115 161 LYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT 206 (218)
Q Consensus 161 I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA 206 (218)
|++.||++|++||.++|++||+|||+|++||||||+||+++|++||
T Consensus 80 I~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~aga 125 (207)
T PRK04191 80 IDVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGA 125 (207)
T ss_pred EEEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCC
Confidence 8899999999999999999999999999999999999999999997
No 5
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=4.8e-32 Score=235.29 Aligned_cols=137 Identities=15% Similarity=0.109 Sum_probs=124.0
Q ss_pred hhhhcc-cccchhhhhhHHh-hhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHH
Q psy8115 70 NTIGVS-NSLSICVSLQFVA-DGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSV 147 (218)
Q Consensus 70 ~~~~~~-m~~~~~~ykkfV~-d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~ 147 (218)
..|.+. .+.. ++|+++|. |.+++.+|++||.+++.+|||++|+|+|+++.++|+||+++||.|||++|+++++|++.
T Consensus 16 ~~~~S~W~a~~-~~y~~~l~eD~~ir~~i~~~l~~~~~~agis~i~I~r~~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~ 94 (214)
T CHL00048 16 QKHHSLWFAQP-KNYSEGLQEDKKIRDCIKNYVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLLIERKGRGIEELQIN 94 (214)
T ss_pred CCCceEEecCh-hhhHHHHHHHHHHHHHHHHHHHhhhhhCCeeEEEEEEcCCeEEEEEEECCCceEECCCcHhHHHHHHH
Confidence 455433 5543 79999998 66677777777777789999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115 148 VQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY 207 (218)
Q Consensus 148 LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~ 207 (218)
|++.|++.++++.|++.||++|++||.++|++||+|||+|++|||||+++++++|++||-
T Consensus 95 L~k~~~~~~~~i~I~v~ev~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga~ 154 (214)
T CHL00048 95 LQKELNSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIK 154 (214)
T ss_pred HHHHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCCc
Confidence 999998777789999999999999999999999999999999999999999999999873
No 6
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=99.97 E-value=1.1e-31 Score=232.54 Aligned_cols=135 Identities=19% Similarity=0.280 Sum_probs=124.6
Q ss_pred HHH-Hhhhhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHH
Q psy8115 65 FRV-LVNTIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIR 142 (218)
Q Consensus 65 ~~~-~~~~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik 142 (218)
||. +...|.|. .++. ++|+++|.||. +|||||.++|.++||++|+|+|+++.++|+||+++|++|||++|++++
T Consensus 10 fRLGi~~~w~S~Wfa~~-k~Y~~~l~eD~---~IR~~i~k~~~~agis~IeI~rt~~~i~I~I~~~~pg~vIG~~g~~i~ 85 (211)
T TIGR01009 10 FRLGITKDWKSRWYANP-KEYAKLLHEDL---KIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKKGSEIE 85 (211)
T ss_pred cccccccCCceEEccCc-chhHHHHHHHH---HHHHHHHHHhhhCCcceEEEEEcCCceEEEEEeCCCcceeCCCchHHH
Confidence 344 33456444 6665 79999999999 999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115 143 ELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT 206 (218)
Q Consensus 143 ~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA 206 (218)
+|++.|++.|+ .++.|++.+|++|+++|.++|++||+|||+|++||||++++|+++|++||
T Consensus 86 ~l~~~l~~~~~---~~~~i~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~ 146 (211)
T TIGR01009 86 KLRKDLQKLTG---KEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGA 146 (211)
T ss_pred HHHHHHHHHhC---CceEEEEEEecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCC
Confidence 99999999996 46899999999999999999999999999999999999999999999986
No 7
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=99.97 E-value=5e-31 Score=231.30 Aligned_cols=131 Identities=20% Similarity=0.247 Sum_probs=122.5
Q ss_pred hhhhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHH
Q psy8115 69 VNTIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSV 147 (218)
Q Consensus 69 ~~~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~ 147 (218)
...|.|. .+.. ++|+++|.||. +||+||.++|.++||++|+|+|+++.++|+||+++|++|||++|+++++|++.
T Consensus 15 ~k~w~S~Wya~~-k~Y~~~L~eD~---~IRe~i~k~~~~agis~IeI~R~~~~i~I~I~~~rP~~iiG~~g~~i~~l~~~ 90 (232)
T PRK00310 15 IKDWDSRWYADK-KDYADLLHEDL---KIRKFLKKKLKKAGVSRIEIERPAKRVRVTIHTARPGIVIGKKGAEIEKLRKE 90 (232)
T ss_pred cCCCCCeEeCCc-chhHHHHHHHH---HHHHHHHHhHhhCceeEEEEEEcCCeEEEEEEECCCccccCCCcHHHHHHHHH
Confidence 3456544 6643 79999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115 148 VQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT 206 (218)
Q Consensus 148 LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA 206 (218)
|++.|+ +++.|++.||++|+++|.++|++||+|||+|++||||++++|+++|++||
T Consensus 91 L~~~~~---~~~~i~v~ev~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~ 146 (232)
T PRK00310 91 LEKLTG---KPVQINIVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGA 146 (232)
T ss_pred HHHHhC---CceEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCC
Confidence 999996 57899999999999999999999999999999999999999999999986
No 8
>KOG3181|consensus
Probab=99.95 E-value=3e-28 Score=210.02 Aligned_cols=132 Identities=73% Similarity=1.047 Sum_probs=128.9
Q ss_pred cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCC
Q psy8115 76 NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFA 155 (218)
Q Consensus 76 m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~ 155 (218)
|+.+|+..++|+.||+++++++|||.++|.+.|||++|++.||.+++|+|.+++|+.++|.+|.+|++|+..+||+|++.
T Consensus 1 ~a~~iSkkrkfv~dGvf~AELnef~treLaedGySgvEvRvtptr~eiIi~atrtq~vlGEkgrRirelt~lvqkRf~f~ 80 (244)
T KOG3181|consen 1 MALQISKKRKFVADGVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFP 80 (244)
T ss_pred CccccchhhhhhhcchhHHHHHHHHHHHHHhcCcCceEEEeeccceeEEEEecchhhhhhhcchhHHHHHHHHHHhcCCC
Confidence 46678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115 156 DGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY 207 (218)
Q Consensus 156 ~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~ 207 (218)
+..|++++++|.+.+|||..+|++|+++|-.++++||||+.+++.+|++||-
T Consensus 81 ~~svelyaEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgAk 132 (244)
T KOG3181|consen 81 EGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAK 132 (244)
T ss_pred CCcEEEehhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccCC
Confidence 9999999999999999999999999999999999999999999999999985
No 9
>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=99.87 E-value=1.3e-21 Score=147.08 Aligned_cols=80 Identities=83% Similarity=1.219 Sum_probs=76.9
Q ss_pred hhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCC
Q psy8115 90 GVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATR 169 (218)
Q Consensus 90 ~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP 169 (218)
++++++||+||.+++.+||||+|||+|++++++|+|||++||++||++|+++++|++.|++.|++++++|+|++++|.+.
T Consensus 1 ~~~~~~Ire~l~k~~~~agis~IeI~Rt~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~~i~v~~~~v~~~ 80 (81)
T cd02413 1 GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEGSVELYAEKVANR 80 (81)
T ss_pred CchhHHHHHHHHHHHHhCCeeeEEEEEcCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCCeEEEEEEEcccC
Confidence 35788999999999999999999999999999999999999999999999999999999999999999999999999875
No 10
>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=99.84 E-value=6.2e-21 Score=149.61 Aligned_cols=94 Identities=19% Similarity=0.301 Sum_probs=85.9
Q ss_pred hhhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHH
Q psy8115 70 NTIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 70 ~~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
..|.+. +|.. ++|++++.+|. +||+||.+.+.+|||++|+|+|+++.++|+||+++||+|||++|+++++|++.|
T Consensus 15 ~~~~s~W~~~~-~~y~~~l~ed~---~IR~yL~k~~~~agis~I~I~R~~~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 15 KDWDSRWYADK-KDYAELLHEDL---KIRKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred CCCcceEcCCc-hhhHHHHHhHH---HHHHHHHHHHhhCCccEEEEEEcCCCEEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 456444 7764 69999999999 999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCcEEEEEEEecCC
Q psy8115 149 QKRFKFADGAIELYAEKVATR 169 (218)
Q Consensus 149 qK~~~~~~kkI~I~I~EV~nP 169 (218)
++.+++ +++.|+|.||.+|
T Consensus 91 ~~~~~~--~~~~I~V~ev~~P 109 (109)
T cd02412 91 QKLLGN--KKVRINIVEVKKP 109 (109)
T ss_pred HHHhCC--CceEEEEEEecCC
Confidence 999864 5789999999998
No 11
>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=99.82 E-value=5.9e-20 Score=138.09 Aligned_cols=84 Identities=38% Similarity=0.649 Sum_probs=79.4
Q ss_pred hhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEE
Q psy8115 83 SLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY 162 (218)
Q Consensus 83 ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~ 162 (218)
+++|++|++++.+||+||.+.+..||||+|+|+|+++.++|+||+++||.+||++|+++++|+..|++.++. .++.|+
T Consensus 2 ~~~~~~~~~~~~~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~~~~--~~v~I~ 79 (85)
T cd02411 2 ERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGL--ENPQID 79 (85)
T ss_pred eEeHHhcchHHHHHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECCCCceECCCchhHHHHHHHHHHHhCC--CCceEE
Confidence 688999999999999999999999999999999999999999999999999999999999999999999974 478888
Q ss_pred EEEecC
Q psy8115 163 AEKVAT 168 (218)
Q Consensus 163 I~EV~n 168 (218)
|.||++
T Consensus 80 v~ev~~ 85 (85)
T cd02411 80 VQEVEN 85 (85)
T ss_pred EEEecC
Confidence 899875
No 12
>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=99.60 E-value=2e-15 Score=110.48 Aligned_cols=77 Identities=29% Similarity=0.434 Sum_probs=72.5
Q ss_pred HHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhC-CCCCcEEEEEEEecCCCc
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK-FADGAIELYAEKVATRGL 171 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~-~~~kkI~I~I~EV~nP~l 171 (218)
+|++||.+++..+|+++|+|+|+++.+.|++|+++|+++||++|+.+++|+..+++.+. +.+++|.+++.+|++|++
T Consensus 1 eI~~~l~~~~~~~~~~~i~I~r~~~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~~~~~~~V~l~v~~V~~~~~ 78 (78)
T PF07650_consen 1 EIRYFLFKEIKKAGISDIEIERTPDQIIIVIKASQPGIVIGKKGSNIKKIREELRKELEKLLNKKVFLNVVKVKKPWR 78 (78)
T ss_dssp HHHHHHHHHTTTTTEEEEEEEESSSEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHHHHCSSSEEEEEEEESSCGG
T ss_pred ChhhhHHhhhhhccCceEEEEEcCCeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHhhcCCCcEEEEEEEecCCCC
Confidence 68999999999999999999999999999999999999999999999999999999995 457889999999999974
No 13
>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=98.91 E-value=7.6e-09 Score=71.38 Aligned_cols=65 Identities=43% Similarity=0.641 Sum_probs=57.6
Q ss_pred HHHHHhhhccCCeeeeEEEecCCeEEEEEEecc--cceEeccCcccHHHHHHHHHHHhCCCCCcEEEEE
Q psy8115 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATR--TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA 163 (218)
Q Consensus 97 Refl~K~l~~AGIs~IEI~Rt~~~I~IiI~aar--PgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I 163 (218)
|+||.+.+..+|+++|+|+++++...+.+++.+ ||.+||++|+.++.|+..+++.+ .++++.|++
T Consensus 1 r~~l~~~~~~~~i~~i~i~~~~~~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~--~~~~~~i~v 67 (68)
T cd02409 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL--RKKRVKIDV 67 (68)
T ss_pred ChHHHHHHHHCCCCeEEEEEcCCcEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc--CCCceEEEE
Confidence 478888888899999999999888999999999 99999999999999999999988 356666654
No 14
>smart00322 KH K homology RNA-binding domain.
Probab=97.77 E-value=2.5e-05 Score=52.69 Aligned_cols=67 Identities=15% Similarity=0.174 Sum_probs=52.9
Q ss_pred CeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy8115 119 ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI 185 (218)
Q Consensus 119 ~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLE 185 (218)
..++|.|+...++.+||++|+.+++|++.....+...+..-...+..|..+..++...++.|..+++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 4578889999999999999999999999887666543322134557788888999999999988764
No 15
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=96.96 E-value=0.0011 Score=47.91 Aligned_cols=68 Identities=15% Similarity=0.175 Sum_probs=46.0
Q ss_pred HHHHHHHhhhccCCeeeeEEE--ecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEE
Q psy8115 95 ELDEFLTRELAEDGYSGVEIR--FTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY 162 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~--Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~ 162 (218)
.+++|+..-+...+=-.|++. .....+.+.+.....|.+||++|+.++.|+..++...+-...++.|.
T Consensus 3 ~l~~~l~~l~~~~~~v~v~~~~~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~v~ 72 (73)
T PF13083_consen 3 FLEDFLKNLVDKPMDVEVTIEIEEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAANKHGKRVRVE 72 (73)
T ss_dssp --HHHHHHHHHHTT--EEEEEEETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHHHT-SS-EEE
T ss_pred hHHHHHHHHhCCcCeEEEEEEEcCCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHHHhCCCEEEEe
Confidence 456666665533222224443 45779999999999999999999999999999988776545556553
No 16
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.96 E-value=0.0058 Score=44.89 Aligned_cols=56 Identities=20% Similarity=0.319 Sum_probs=46.6
Q ss_pred HHHHhhhccCCe-eeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhC
Q psy8115 98 EFLTRELAEDGY-SGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK 153 (218)
Q Consensus 98 efl~K~l~~AGI-s~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~ 153 (218)
+||.+-+...|+ +.|++....+.+.+.|....+|.+||++|+.++.|+..+...++
T Consensus 2 ~~L~~il~~mg~~~~v~~~~~~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 2 EFLEEVLELMGIEADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred hHHHHHHHHcCCCcEEEEEecCCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 466666666666 34777777889999999999999999999999999999888776
No 17
>PRK01064 hypothetical protein; Provisional
Probab=95.88 E-value=0.13 Score=38.80 Aligned_cols=54 Identities=9% Similarity=0.162 Sum_probs=41.6
Q ss_pred eEEEecCCeEEEEEEeccc--ceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEE
Q psy8115 112 VEIRFTPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK 165 (218)
Q Consensus 112 IEI~Rt~~~I~IiI~aarP--giVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~E 165 (218)
|+.......+.+.+++... |.+||++|+.++.++..+.......++++.+.|.+
T Consensus 21 V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~leI~~ 76 (78)
T PRK01064 21 IKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME 76 (78)
T ss_pred EEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhhCCCEEEEEEec
Confidence 4444445677777887766 78999999999999999988776656777776654
No 18
>PF00189 Ribosomal_S3_C: Ribosomal protein S3, C-terminal domain; InterPro: IPR001351 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S3 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S3 is known to be involved in the binding of initiator Met-tRNA. This family of ribosomal proteins includes S3 from bacteria, algae and plant chloroplast, cyanelle, archaebacteria, plant mitochondria, vertebrates, insects, Caenorhabditis elegans and yeast []. This entry is the C-terminal domain.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_C 2XZM_C 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C ....
Probab=95.75 E-value=0.012 Score=44.29 Aligned_cols=28 Identities=18% Similarity=0.074 Sum_probs=25.1
Q ss_pred HHHHHHHcChhHHHHHHHHHHHH-HHcCC
Q psy8115 179 SLRYKLIGGLAVRRYNSDVSLYC-LNCYT 206 (218)
Q Consensus 179 ~IA~QLEkRv~FRRAmK~AIr~a-mkaGA 206 (218)
+|+++||++.+|||+++++++.+ |++|+
T Consensus 1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~ 29 (85)
T PF00189_consen 1 FIAQKLEKRISFRRIIKKIIRRIMMNKGI 29 (85)
T ss_dssp HHHHHHHTTSTHHHHHHHHHHHHHHCTTS
T ss_pred ChHHHHhcCcHHHHHHHHHHHHHHhhccc
Confidence 58999999999999999999999 65555
No 19
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=94.96 E-value=0.13 Score=45.44 Aligned_cols=110 Identities=14% Similarity=0.151 Sum_probs=76.0
Q ss_pred hhHHHHHHHHHHhhhccCCee-eeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCC---CcEEEEEEE
Q psy8115 90 GVFRAELDEFLTRELAEDGYS-GVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFAD---GAIELYAEK 165 (218)
Q Consensus 90 ~iir~~IRefl~K~l~~AGIs-~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~---kkI~I~I~E 165 (218)
..+..++.+||..-+..-|++ .|.+......+.+.|....++.+||++|+.++.|+...+-.++... .+|.|++..
T Consensus 61 ~~~~~~~~~~L~ell~~m~~~~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~ 140 (208)
T COG1847 61 EKIAQEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGD 140 (208)
T ss_pred hHHHHHHHHHHHHHHHHhCCceEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhh
Confidence 345568899999888877765 4888888899999999999999999999999999988887665322 345555542
Q ss_pred ecC-CCcCHHHHHHHHHHHH-HcChh---------HHHHHHHHHH
Q psy8115 166 VAT-RGLCAIAQAESLRYKL-IGGLA---------VRRYNSDVSL 199 (218)
Q Consensus 166 V~n-P~l~A~llAe~IA~QL-EkRv~---------FRRAmK~AIr 199 (218)
=.. ..-.=..+|+.+|.|. +.+-+ =||.++.++.
T Consensus 141 yRerR~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~ 185 (208)
T COG1847 141 YRERRKETLIKLAERAAERVLETGRSVELEPMPPFERKIVHTALS 185 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHH
Confidence 221 1122244666666655 22221 3667777665
No 20
>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=94.84 E-value=0.25 Score=41.43 Aligned_cols=86 Identities=24% Similarity=0.280 Sum_probs=58.4
Q ss_pred HHHHHhhh-ccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHH
Q psy8115 97 DEFLTREL-AEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIA 175 (218)
Q Consensus 97 Refl~K~l-~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~l 175 (218)
++.+.+-. .+||+.+ |...++.=+|+|++.+||.+||++|..++++.. ..|. .-.| +..|=+.+..
T Consensus 55 ~~~I~~ivP~ea~i~d--i~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~----~tgW---~p~v----vRtpPi~S~t 121 (145)
T cd02410 55 IKIILEIVPEEAGITD--IYFDDDTGEVIIEAEKPGLVIGKGGSTLREITR----ETGW---APKV----VRTPPIQSRT 121 (145)
T ss_pred HHHHHHhCCCccCcee--eEecCCCcEEEEEEcCCeEEEecCchhHHHHHH----HhCC---eeEE----EecCCCCcHH
Confidence 34444433 2578865 455677789999999999999999988877665 4443 2333 6667677776
Q ss_pred HHHHHHHHHHcChhHHHHHHH
Q psy8115 176 QAESLRYKLIGGLAVRRYNSD 196 (218)
Q Consensus 176 lAe~IA~QLEkRv~FRRAmK~ 196 (218)
+ +.|++-|-+--.+|+-+-+
T Consensus 122 i-~~ir~~l~~~~~eR~~~L~ 141 (145)
T cd02410 122 V-KSIRRFLRREREERKEILK 141 (145)
T ss_pred H-HHHHHHHHHhHHHHHHHHH
Confidence 5 5666777666667765433
No 21
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=94.72 E-value=0.073 Score=37.62 Aligned_cols=53 Identities=15% Similarity=0.315 Sum_probs=43.0
Q ss_pred HHHHHhhhccCCeeeeEEEec-CCeEEEEEEecccceEeccCcccHHHHHHHHH
Q psy8115 97 DEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELTSVVQ 149 (218)
Q Consensus 97 Refl~K~l~~AGIs~IEI~Rt-~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~Lq 149 (218)
.+|+..-+.-+.+.+|++... .+...|.+....-+..||++|++++.+++.+.
T Consensus 2 ~~~i~n~~~p~~i~~V~~~~~~~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~ 55 (61)
T cd02134 2 AEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLG 55 (61)
T ss_pred HHHHHHhcCcccceEEEEecCCCcEEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence 357777777778888888655 47888888888889999999999999887665
No 22
>PRK02821 hypothetical protein; Provisional
Probab=94.55 E-value=0.62 Score=35.07 Aligned_cols=65 Identities=17% Similarity=0.228 Sum_probs=44.4
Q ss_pred HHHHhhhcc-CCeeeeEEEecCCeEEEEEEeccc--ceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEE
Q psy8115 98 EFLTRELAE-DGYSGVEIRFTPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK 165 (218)
Q Consensus 98 efl~K~l~~-AGIs~IEI~Rt~~~I~IiI~aarP--giVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~E 165 (218)
+|+-+.|-+ -.=-.|+.+.....+.+.|+++.- |.|||++|+.++.|+..+.-. .++++.+.|.+
T Consensus 7 ~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~leI~~ 74 (77)
T PRK02821 7 EHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI---GGRGVRVDVVD 74 (77)
T ss_pred HHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh---cCCeEEEEEEe
Confidence 445454432 112225555556677778887654 569999999999999999876 46788877665
No 23
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=94.10 E-value=0.085 Score=43.45 Aligned_cols=60 Identities=15% Similarity=0.321 Sum_probs=48.4
Q ss_pred HHHHHHHhhhccCCeeeeEEEecC--CeEEEEEEecccceEeccCcccHHHHHHHHHHHhCC
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTP--ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 154 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~--~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~ 154 (218)
...+|+.+-+..+++.+|+|.... ..+.|.+.-..-+..||++|+.++.++..+.+.|+.
T Consensus 73 d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 73 DPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred CHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 567889888999999999885443 345566666777889999999999999999887764
No 24
>PRK00468 hypothetical protein; Provisional
Probab=93.33 E-value=1.1 Score=33.48 Aligned_cols=52 Identities=13% Similarity=0.136 Sum_probs=37.3
Q ss_pred eEEEecCCeEEEEEEeccc--ceEeccCcccHHHHHHHHHHHhCCCCCcEEEEE
Q psy8115 112 VEIRFTPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYA 163 (218)
Q Consensus 112 IEI~Rt~~~I~IiI~aarP--giVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I 163 (218)
|+.+.....+.+.|+++.- |.|||++|+.++.|+..+.-.-...++++.+.|
T Consensus 21 V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~leI 74 (75)
T PRK00468 21 VNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVEI 74 (75)
T ss_pred EEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhcCCCEEEEEE
Confidence 4444555677777777654 569999999999999999865444456666543
No 25
>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=92.77 E-value=0.86 Score=40.06 Aligned_cols=74 Identities=18% Similarity=0.311 Sum_probs=46.9
Q ss_pred hHHhhhhHHHHHHHHHHhhhccCCeeeeEEEe---cC---CeEEEEEEecccc---eEeccCcccHHHH----HHHHHHH
Q psy8115 85 QFVADGVFRAELDEFLTRELAEDGYSGVEIRF---TP---ARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKR 151 (218)
Q Consensus 85 kfV~d~iir~~IRefl~K~l~~AGIs~IEI~R---t~---~~I~IiI~aarPg---iVIGrkG~~Ik~L----~~~LqK~ 151 (218)
+|....++|.++-+++..++..+= .|+|+. .+ ..|...|++.|+. +|||++|+.|+++ +..|++.
T Consensus 181 ~~~~~e~ire~~~~~~~~e~p~~~--~~~~~~~~~~~~~~~~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~ 258 (270)
T TIGR00436 181 RFKISEIIREKIIRYTKEEIPHSV--RVEIERKSFNEKGLLKIHALISVERESQKKIIIGKNGSMIKAIGIAARKDILEL 258 (270)
T ss_pred HHHHHHHHHHHHHHhcccccCceE--EEEEEEEEECCCCeEEEEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHH
Confidence 444555666666666666654432 233332 22 2577889998874 7999999999776 5667777
Q ss_pred hCCCCCcEEEEE
Q psy8115 152 FKFADGAIELYA 163 (218)
Q Consensus 152 ~~~~~kkI~I~I 163 (218)
|+ .+|.+.+
T Consensus 259 ~~---~~v~l~l 267 (270)
T TIGR00436 259 FD---CDVFLEL 267 (270)
T ss_pred hC---CCEEEEE
Confidence 76 5565543
No 26
>PRK15494 era GTPase Era; Provisional
Probab=92.65 E-value=0.9 Score=41.80 Aligned_cols=99 Identities=19% Similarity=0.307 Sum_probs=60.1
Q ss_pred cchhhHHHHhhhh--h--cccccchhh-hhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEec---C---CeEEEEEEec
Q psy8115 60 GFSVLFRVLVNTI--G--VSNSLSICV-SLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFT---P---ARTEIIIMAT 128 (218)
Q Consensus 60 ~~~~~~~~~~~~~--~--~~m~~~~~~-ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt---~---~~I~IiI~aa 128 (218)
|...+|..+.+.. + .+...++.+ -.+|+...++|.+|-+++..++..+ ..|+|+.- . ..|...||+.
T Consensus 203 gv~eL~~~L~~~l~~~~~~~~~~~~td~~~~~~~~eiiRe~~~~~~~~EiP~~--~~v~i~~~~~~~~~~~~i~~~i~v~ 280 (339)
T PRK15494 203 NIDGLLEYITSKAKISPWLYAEDDITDLPMRFIAAEITREQLFLNLQKELPYK--LTVQTEKWEDLKDKSVKINQVIVVS 280 (339)
T ss_pred CHHHHHHHHHHhCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHhhCCcccCce--EEEEEEEEEEcCCCeEEEEEEEEEC
Confidence 4556666665543 1 222222222 2355566677777777777776554 22444332 2 2477899998
Q ss_pred ccc---eEeccCcccHHHH----HHHHHHHhCCCCCcEEEEE
Q psy8115 129 RTQ---NVLGDKGRRIREL----TSVVQKRFKFADGAIELYA 163 (218)
Q Consensus 129 rPg---iVIGrkG~~Ik~L----~~~LqK~~~~~~kkI~I~I 163 (218)
|++ +|||++|+.|+++ +..|++.|+ .+|.+.+
T Consensus 281 ~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~---~~v~l~l 319 (339)
T PRK15494 281 RESYKTIILGKNGSKIKEIGAKSRMQMERFFG---FPVHLFL 319 (339)
T ss_pred CCCceeEEEcCCcHHHHHHHHHHHHHHHHHhC---CCeEEEE
Confidence 886 7999999999776 566777776 4554443
No 27
>COG1159 Era GTPase [General function prediction only]
Probab=92.46 E-value=1.2 Score=41.44 Aligned_cols=69 Identities=23% Similarity=0.347 Sum_probs=48.6
Q ss_pred hhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecC------CeEEEEEEeccc---ceEeccCcccHHHH----HHHHHH
Q psy8115 84 LQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTP------ARTEIIIMATRT---QNVLGDKGRRIREL----TSVVQK 150 (218)
Q Consensus 84 kkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~------~~I~IiI~aarP---giVIGrkG~~Ik~L----~~~LqK 150 (218)
-+|+.-.++|.++=.|+..++..+ ..|+|++.. ..|.-.|++.|- ++|||++|+.|+++ +.++++
T Consensus 188 ~rf~~aEiiREk~~~~l~eElPhs--v~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~ 265 (298)
T COG1159 188 ERFLAAEIIREKLLLLLREELPHS--VAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEK 265 (298)
T ss_pred HHHHHHHHHHHHHHHhcccccCce--EEEEEEEEEecCCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHH
Confidence 345666667777777777777654 447776642 256667888665 58999999999776 667888
Q ss_pred HhCC
Q psy8115 151 RFKF 154 (218)
Q Consensus 151 ~~~~ 154 (218)
.|+.
T Consensus 266 l~~~ 269 (298)
T COG1159 266 LLGC 269 (298)
T ss_pred HhCC
Confidence 8863
No 28
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=91.65 E-value=2.2 Score=32.15 Aligned_cols=47 Identities=13% Similarity=0.187 Sum_probs=33.5
Q ss_pred cCCeEEEEEEeccc--ceEeccCcccHHHHHHHHHHHhCCCCCcEEEEE
Q psy8115 117 TPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYA 163 (218)
Q Consensus 117 t~~~I~IiI~aarP--giVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I 163 (218)
....+.+.|+++.. |-|||++|+.++.|+..|.-.-.-.++++.|.+
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~~~~~~v~i~i 74 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGSKDSKRVVVEI 74 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHHHHHhcccCceEEEEEe
Confidence 35576666666654 569999999999999999865543345555544
No 29
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=91.15 E-value=1.3 Score=44.25 Aligned_cols=78 Identities=27% Similarity=0.335 Sum_probs=52.3
Q ss_pred HHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAI 174 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~ 174 (218)
.|+|.+.+ +|||++ |....+.=+|+|.+.+||++||+.|+..+++... .+.. -.| +..|-+...
T Consensus 80 ~I~eivP~---ea~i~~--i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~----tgW~---p~i----vR~PPi~S~ 143 (637)
T COG1782 80 IILEIVPE---EAGITD--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAE----TGWA---PKI----VRTPPIQSR 143 (637)
T ss_pred HHHHhCcc---ccCcee--EEecCCCceEEEEecCCceEEecCchHHHHHHHH----hCCc---cee----eecCCCchh
Confidence 44554443 688987 6667888899999999999999999887776653 3332 223 566767666
Q ss_pred HHHHHHHHHHHcChh
Q psy8115 175 AQAESLRYKLIGGLA 189 (218)
Q Consensus 175 llAe~IA~QLEkRv~ 189 (218)
.+ ++|+.-|.+-..
T Consensus 144 ti-~~ir~~l~~~~~ 157 (637)
T COG1782 144 TI-KSIREILRSERK 157 (637)
T ss_pred hH-HHHHHHHHHhHH
Confidence 65 344444444333
No 30
>PRK00089 era GTPase Era; Reviewed
Probab=89.81 E-value=2.7 Score=37.03 Aligned_cols=73 Identities=25% Similarity=0.342 Sum_probs=44.2
Q ss_pred HHhhhhHHHHHHHHHHhhhccCCeeeeEEEe----cCCeEEEEEEecccc---eEeccCcccHHHH----HHHHHHHhCC
Q psy8115 86 FVADGVFRAELDEFLTRELAEDGYSGVEIRF----TPARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKRFKF 154 (218)
Q Consensus 86 fV~d~iir~~IRefl~K~l~~AGIs~IEI~R----t~~~I~IiI~aarPg---iVIGrkG~~Ik~L----~~~LqK~~~~ 154 (218)
|....++|.++-+++.+++..+ ..|+|+. ....|...|++.++. +|||++|+.|+++ +..|++.|+
T Consensus 189 ~~~~EiiRe~~~~~l~~e~p~~--~~v~~~~~~~~~~~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~- 265 (292)
T PRK00089 189 FLAAEIIREKLLRLLGDELPYS--VAVEIEKFEERGLVRIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLG- 265 (292)
T ss_pred HHHHHHHHHHHHhhCCccCCce--EEEEEEEEEECCeEEEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhC-
Confidence 4444455555555555555433 1133321 223577789998885 7999999999776 456777776
Q ss_pred CCCcEEEEE
Q psy8115 155 ADGAIELYA 163 (218)
Q Consensus 155 ~~kkI~I~I 163 (218)
.+|.+.+
T Consensus 266 --~~v~l~l 272 (292)
T PRK00089 266 --KKVFLEL 272 (292)
T ss_pred --CCEEEEE
Confidence 4554443
No 31
>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=88.25 E-value=3.7 Score=41.42 Aligned_cols=77 Identities=25% Similarity=0.309 Sum_probs=53.2
Q ss_pred cCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy8115 106 EDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI 185 (218)
Q Consensus 106 ~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLE 185 (218)
+||+.+ |...++.=+|+|.+.+||.|||+.|..++++.. ..+. .-.| +..|-+....+ +.|+.-|-
T Consensus 82 ~~~~~~--~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~----~~~w---~~~~----~~~~~~~~~~~-~~~~~~~~ 147 (630)
T TIGR03675 82 EAGITD--IYFDDVTGEVIIEAEKPGLVIGKGGSTLREITA----ETGW---TPKV----VRTPPIESKTI-KNIREYLR 147 (630)
T ss_pred cCCcee--EEecCCCceEEEEEcCCeEEEecCcchHHHHHH----HhCC---eeeE----EecCCCCcHHH-HHHHHHHH
Confidence 588865 555777889999999999999999988877665 3443 2233 66777777765 45666665
Q ss_pred cChhHHHHHHH
Q psy8115 186 GGLAVRRYNSD 196 (218)
Q Consensus 186 kRv~FRRAmK~ 196 (218)
+--..|+-+-+
T Consensus 148 ~~~~~r~~~l~ 158 (630)
T TIGR03675 148 SESEERKEFLR 158 (630)
T ss_pred HhHHHHHHHHH
Confidence 55555554433
No 32
>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=86.84 E-value=1.1 Score=37.20 Aligned_cols=60 Identities=15% Similarity=0.283 Sum_probs=44.8
Q ss_pred HHHHHHHhhhccCCeeeeEEEecCC--eEEEEEEecccceEeccCcccHHHHHHHHHHHhCC
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTPA--RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 154 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~~--~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~ 154 (218)
-+.+|+.+.|.-|.+.+|.+.-... ...|.+.-..-+..||++|++++.....+...++.
T Consensus 74 D~~~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 74 NLEEFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred CHHHHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 5678888889999999998865322 34455555556789999999998888877766653
No 33
>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=77.74 E-value=2.3 Score=29.82 Aligned_cols=29 Identities=17% Similarity=0.392 Sum_probs=22.6
Q ss_pred eEEEEEEecccceEeccCcccHHHHHHHH
Q psy8115 120 RTEIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 120 ~I~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
...+.|-..+-+.+||++|+.+++|++.-
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~t 31 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEET 31 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHH
Confidence 34566677788899999999998877643
No 34
>PF13014 KH_3: KH domain
Probab=77.27 E-value=1.9 Score=27.90 Aligned_cols=16 Identities=25% Similarity=0.636 Sum_probs=14.2
Q ss_pred ceEeccCcccHHHHHH
Q psy8115 131 QNVLGDKGRRIRELTS 146 (218)
Q Consensus 131 giVIGrkG~~Ik~L~~ 146 (218)
+.|||++|..|++|++
T Consensus 3 g~iIG~~G~~I~~I~~ 18 (43)
T PF13014_consen 3 GRIIGKGGSTIKEIRE 18 (43)
T ss_pred CeEECCCChHHHHHHH
Confidence 6799999999998876
No 35
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=74.08 E-value=3.4 Score=35.31 Aligned_cols=55 Identities=15% Similarity=0.240 Sum_probs=36.4
Q ss_pred HHHHHHHhhhccCCeeeeEEEec---CCeEEEEEEecccceEeccCcccHHHHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFT---PARTEIIIMATRTQNVLGDKGRRIRELTSVVQK 150 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt---~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK 150 (218)
++-+-|-+...+..+++++..+. .+++-+.+..+. |..||++|+.+++|++.|-+
T Consensus 34 ~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk 91 (166)
T PRK06418 34 EVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGP-RIPIGKGGKIAKALSRKLGK 91 (166)
T ss_pred HHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCC-cccccccchHHHHHHHHhCC
Confidence 44444443323333444555444 578888888888 99999999999888776643
No 36
>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=71.62 E-value=4.7 Score=27.16 Aligned_cols=27 Identities=15% Similarity=0.445 Sum_probs=21.3
Q ss_pred EEEEEecccceEeccCcccHHHHHHHH
Q psy8115 122 EIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 122 ~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
+|.|-...-+.|||++|..+++|++.-
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s 29 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREET 29 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHH
Confidence 455566677889999999999988754
No 37
>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=70.26 E-value=4 Score=28.58 Aligned_cols=27 Identities=15% Similarity=0.486 Sum_probs=21.8
Q ss_pred EEEEEEecccceEeccCcccHHHHHHH
Q psy8115 121 TEIIIMATRTQNVLGDKGRRIRELTSV 147 (218)
Q Consensus 121 I~IiI~aarPgiVIGrkG~~Ik~L~~~ 147 (218)
+++.|-...-+.|||++|..+++|++.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~ 28 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREE 28 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHH
Confidence 456666677788999999999998874
No 38
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=65.68 E-value=8.4 Score=28.13 Aligned_cols=38 Identities=21% Similarity=0.460 Sum_probs=28.0
Q ss_pred CCeEEEEEEecc-----cceEeccCcccHHHHHHHHHHHhCCCCCcEEE
Q psy8115 118 PARTEIIIMATR-----TQNVLGDKGRRIRELTSVVQKRFKFADGAIEL 161 (218)
Q Consensus 118 ~~~I~IiI~aar-----PgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I 161 (218)
.+++.|.++... -|..+|.+|.+++.|.+.|. +.+|.|
T Consensus 2 G~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~------gekIdv 44 (69)
T PF13184_consen 2 GNRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELN------GEKIDV 44 (69)
T ss_dssp TTEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTT------T-EEEE
T ss_pred CceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhC------CCeEEE
Confidence 357788888877 57899999999999888764 356665
No 39
>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=65.67 E-value=2.3 Score=28.89 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=21.9
Q ss_pred EEEEEEecccceEeccCcccHHHHHHHH
Q psy8115 121 TEIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 121 I~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
.+|.|....-+.|||++|..+++|++.-
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t 29 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEET 29 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHH
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhc
Confidence 3566677777889999999998887644
No 40
>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=63.34 E-value=5.7 Score=27.10 Aligned_cols=27 Identities=26% Similarity=0.427 Sum_probs=20.2
Q ss_pred EEEEEecccceEeccCcccHHHHHHHH
Q psy8115 122 EIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 122 ~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
+|.|-...-+.|||++|+.+++|++.-
T Consensus 3 ~i~Vp~~~~~~iIG~~G~~i~~i~~~~ 29 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIMEET 29 (62)
T ss_pred EEEeCHHHhhhccCCCCCcHHHHHHHh
Confidence 344445566789999999999988744
No 41
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=55.86 E-value=39 Score=26.71 Aligned_cols=53 Identities=17% Similarity=0.154 Sum_probs=38.1
Q ss_pred EecccceEeccCccc---HHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy8115 126 MATRTQNVLGDKGRR---IRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI 185 (218)
Q Consensus 126 ~aarPgiVIGrkG~~---Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLE 185 (218)
|..+|-+.||++|-. |+++...|..+= -|.| .-..+-.-+-..+|+.|+.+..
T Consensus 15 h~l~piv~IGk~Glte~vi~Ei~~aL~~re-----LIKV--kvl~~~~edr~eia~~l~~~~~ 70 (97)
T COG1534 15 HHLKPIVQIGKNGLTEGVIKEIDRALEARE-----LIKV--KVLQNAREDKKEIAEALAEETG 70 (97)
T ss_pred ccCCceEEecCCccCHHHHHHHHHHHHhCC-----cEEE--EeeccchhhHHHHHHHHHHHhC
Confidence 677899999999843 688888887532 1333 3366666688999999988764
No 42
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=55.12 E-value=19 Score=35.33 Aligned_cols=53 Identities=13% Similarity=0.309 Sum_probs=43.8
Q ss_pred HHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSV 147 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~ 147 (218)
-..+|+.+.|.-|.+.+|.+......+.|.+....-+..||++|++++.....
T Consensus 278 d~~~fi~nal~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l 330 (470)
T PRK09202 278 DPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKL 330 (470)
T ss_pred CHHHHHHHhCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHH
Confidence 45678899999999999988776678888888888889999999999765543
No 43
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=51.35 E-value=74 Score=30.28 Aligned_cols=55 Identities=24% Similarity=0.340 Sum_probs=40.1
Q ss_pred HHHHHHHhhhccCCeeeeEE---Eec-CCeEEEEEEecccc-----eEeccCcccHHHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEI---RFT-PARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQ 149 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI---~Rt-~~~I~IiI~aarPg-----iVIGrkG~~Ik~L~~~Lq 149 (218)
++++.|..+..+-.=+-|+| -|- ..+++|-+++..|+ ..||.+|.+++.+.+.|.
T Consensus 203 ~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~ 266 (362)
T PRK12327 203 LVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELK 266 (362)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhC
Confidence 55666666666543333555 454 47999999998885 589999999999988773
No 44
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=51.04 E-value=24 Score=29.04 Aligned_cols=43 Identities=12% Similarity=0.222 Sum_probs=31.8
Q ss_pred hccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHH
Q psy8115 104 LAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 104 l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
+.++..-++.+ ..+++-+.+....-|..||++|++++.|++.+
T Consensus 19 ~t~~~~~dc~~--d~~~vi~vV~~~~vG~~IG~~G~rI~~i~e~l 61 (140)
T PRK08406 19 ITGATVKDCII--DDDRIIFVVKEGDMGLAIGKGGENVKRLEEKL 61 (140)
T ss_pred HhCCCceEEEE--eCCEEEEEEeCCCccccCCcCchHHHHHHHHh
Confidence 33444444433 23888888888899999999999999986655
No 45
>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=50.95 E-value=70 Score=30.15 Aligned_cols=55 Identities=25% Similarity=0.334 Sum_probs=39.9
Q ss_pred HHHHHHHhhhccCCeeeeEE---Eec-CCeEEEEEEecccc-----eEeccCcccHHHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEI---RFT-PARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQ 149 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI---~Rt-~~~I~IiI~aarPg-----iVIGrkG~~Ik~L~~~Lq 149 (218)
.+++.|..+..+-.=+-|+| -|- ..+++|-+++..|+ ..||.+|.+++.+.+.|.
T Consensus 201 ~v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ 264 (341)
T TIGR01953 201 FVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELN 264 (341)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhC
Confidence 55666666666542233555 455 47999999998885 589999999999888773
No 46
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=50.88 E-value=11 Score=27.43 Aligned_cols=34 Identities=18% Similarity=0.012 Sum_probs=23.1
Q ss_pred cCHHHHHHHHHHHHHcChhHHHHHHH---HHHHHHHcCCc
Q psy8115 171 LCAIAQAESLRYKLIGGLAVRRYNSD---VSLYCLNCYTY 207 (218)
Q Consensus 171 l~A~llAe~IA~QLEkRv~FRRAmK~---AIr~amkaGA~ 207 (218)
..|.=+|++|+.+ ++|||.|=+- ..+.+.+.|-.
T Consensus 2 ~~ATdlAD~LVr~---GipFR~AH~iVg~~V~~a~~~~~~ 38 (70)
T PF14698_consen 2 STATDLADYLVRK---GIPFREAHHIVGRLVRLAEEEGKP 38 (70)
T ss_dssp GGHHHHHHHHHHT---TS-HHHHHHHHHHHHHHHHHTTS-
T ss_pred ccHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHHcCCC
Confidence 4678899999887 9999988554 44455566643
No 47
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=48.33 E-value=53 Score=28.59 Aligned_cols=19 Identities=16% Similarity=0.538 Sum_probs=17.0
Q ss_pred ceEeccCcccHHHHHHHHH
Q psy8115 131 QNVLGDKGRRIRELTSVVQ 149 (218)
Q Consensus 131 giVIGrkG~~Ik~L~~~Lq 149 (218)
|..||++|++++.|.+.|.
T Consensus 88 G~~iG~~G~rvk~i~~eLg 106 (190)
T COG0195 88 GACIGKRGSRVKAVSEELG 106 (190)
T ss_pred hhhccCCChHHHHHHHHhC
Confidence 8899999999999888776
No 48
>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=47.23 E-value=14 Score=31.00 Aligned_cols=61 Identities=13% Similarity=0.218 Sum_probs=40.4
Q ss_pred EecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEE----EEe--cCCCcCHHHHHHHHHHHHHcChhHHHH
Q psy8115 126 MATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA----EKV--ATRGLCAIAQAESLRYKLIGGLAVRRY 193 (218)
Q Consensus 126 ~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I----~EV--~nP~l~A~llAe~IA~QLEkRv~FRRA 193 (218)
-..+-+.|||++|+.+++|.+.. +. +|+|+- ..| ..++.++..-|..+...|-...++..|
T Consensus 5 p~~kig~vIG~gG~~Ik~I~~~t----gv---~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A 71 (172)
T TIGR03665 5 PKDRIGVLIGKGGETKKEIEERT----GV---KLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKA 71 (172)
T ss_pred CHHHhhhHhCCchhHHHHHHHHh----Cc---EEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 34556789999999998877644 32 233321 134 557778888888888888776554433
No 49
>PRK13764 ATPase; Provisional
Probab=45.57 E-value=35 Score=34.57 Aligned_cols=51 Identities=22% Similarity=0.429 Sum_probs=31.8
Q ss_pred HHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
+|.+.+.+.+ .|...|++. ..+...|.+--.--+.+||++|++|++|.+.|
T Consensus 460 ~~~~~~~~~~--~~~~~~~~~-~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~ 510 (602)
T PRK13764 460 EIEREIKRYL--PGPVEVEVV-SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKL 510 (602)
T ss_pred HHHHHHHHhc--CCceEEEEe-cCCeEEEEEChhhhhHHhccCcchHHHHHHHh
Confidence 4455555544 456667776 34455554444444569999999998876643
No 50
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=45.03 E-value=91 Score=30.03 Aligned_cols=55 Identities=22% Similarity=0.294 Sum_probs=39.7
Q ss_pred HHHHHHHhhhccCCeeeeEE---Eec-CCeEEEEEEecccc-----eEeccCcccHHHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEI---RFT-PARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQ 149 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI---~Rt-~~~I~IiI~aarPg-----iVIGrkG~~Ik~L~~~Lq 149 (218)
.+++.|..+..+-.=+-|+| -|- ..++.|-+++.-|+ ..||.+|.+++.+.+.|.
T Consensus 209 ~v~~Lfe~EVPEI~dG~VeIk~IARepG~RtKVAV~S~d~~iDPvGacIG~~G~rI~~I~~eL~ 272 (374)
T PRK12328 209 FLEALLELEVPEIKDGEVIIIHSARIPGERAKVALFSNNPNIDPIGATVGVKGVRINAVSKELN 272 (374)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeccCcceeEEEEEcCCCCCChHHhhcCCCcchHHHHHHHhC
Confidence 45566666666542233555 455 47999999998886 589999999999888773
No 51
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=44.78 E-value=1.1e+02 Score=21.60 Aligned_cols=57 Identities=9% Similarity=0.123 Sum_probs=41.7
Q ss_pred HhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEE
Q psy8115 101 TRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA 163 (218)
Q Consensus 101 ~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I 163 (218)
...+.++.|.+|.+.+.....++.|....+ + .-..+..+.+.|++.|+. ..+|++.+
T Consensus 18 ~~~f~~~~I~kv~v~k~~~~w~f~l~~~~~--l---~~~~~~~~~~~l~~~F~~-ia~v~~~i 74 (76)
T PF14480_consen 18 NPLFEDAEIEKVTVHKKSRKWRFHLSSPHI--L---PFEVYQKFEEKLKKQFSH-IAKVELII 74 (76)
T ss_pred hhhhcccEEEEEEEEccCCEEEEEEEeCCc--C---CHHHHHHHHHHHHHHhCC-cCeEEEEE
Confidence 345567889999999999999887766543 3 235679999999999864 23666644
No 52
>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=44.70 E-value=27 Score=28.96 Aligned_cols=45 Identities=11% Similarity=0.258 Sum_probs=31.7
Q ss_pred hhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHH
Q psy8115 103 ELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 103 ~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
.+.++..-++.+.-.. ++-..+.....|..+|++|++++.|++.+
T Consensus 18 ~~t~~~~~dc~~d~~~-riifvV~~g~vG~~IG~~G~rIk~i~el~ 62 (141)
T TIGR01952 18 DMTGATVVDCLIDDRN-RVVFVVKEGEMGAAIGKGGENVKRLEELI 62 (141)
T ss_pred HHhCCceEEEEecCCc-EEEEEEcCCCccccCCCCchHHHHHHHhc
Confidence 3445656666553322 67777777888999999999999985443
No 53
>TIGR03112 6_pyr_pter_rel 6-pyruvoyl tetrahydropterin synthase-related domain. Members of this family are small proteins, or small domains of larger proteins, that occur in certain Firmicutes in the same regions as members of families TIGR03110 and TIGR03111. Members of TIGR03110 resemble exosortase, a proposed protein sorting transpeptidase (see TIGR02602). TIGR03111 represents a small clade among the group 2 glycosyltransferases. Members of the current protein family resemble eukaryotic known and prokaryotic predicted 6-pyruvoyl tetrahydropterin synthases.
Probab=44.63 E-value=1.1e+02 Score=24.25 Aligned_cols=64 Identities=9% Similarity=-0.003 Sum_probs=36.2
Q ss_pred eEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChh
Q psy8115 120 RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLA 189 (218)
Q Consensus 120 ~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~ 189 (218)
.++|+|.....|. | ....|++.|++.+.--+.+.-..+.+...-+-.|..+|.+|.++|...++
T Consensus 28 ~vev~v~g~~~g~-v-----Df~~lk~~l~~v~~~~DH~~LNdv~~f~~~~PTaEniA~~i~~~l~~~l~ 91 (113)
T TIGR03112 28 EITIFVIKKEDKF-I-----LFNDVEKKVEKYLKPYQNKYLNDLEPFDKINPTLENIGDYFFDEIKKLLK 91 (113)
T ss_pred EEEEEEEecCCeE-E-----EHHHHHHHHHHHHHcCCCceeccCCccCCCCCCHHHHHHHHHHHHHHhhc
Confidence 5666665544332 2 35666666655443212222223444432223899999999999987764
No 54
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=44.13 E-value=74 Score=28.53 Aligned_cols=75 Identities=13% Similarity=0.131 Sum_probs=45.7
Q ss_pred hHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceE-eccCcccHHHHHHHHHHHhCCCCCcEEEEEEEec
Q psy8115 91 VFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNV-LGDKGRRIRELTSVVQKRFKFADGAIELYAEKVA 167 (218)
Q Consensus 91 iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiV-IGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~ 167 (218)
....+|++-+.+.-.-.++.++.+.+......+.+|..-|+.. +.+-.+-.+++++.|++.++ .-.+.|.+++..
T Consensus 213 ~~~~~I~~~i~~~~~v~~v~~l~~~~~G~~~~v~v~i~v~~~~~~~e~h~i~~~ie~~l~~~~~--~~~v~ihveP~~ 288 (299)
T PRK09509 213 EERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQLHLEMEDNLPLVQAHMIADQVEQALLRRFP--GSDVIIHQDPCS 288 (299)
T ss_pred HHHHHHHHHHHhCCCCcCceeeeeEeeCCeEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHhCC--CCEEEEEeCCCC
Confidence 3445777777653233467778888877777888887666432 22212224667777777765 345777777643
No 55
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=43.05 E-value=38 Score=24.88 Aligned_cols=46 Identities=20% Similarity=0.117 Sum_probs=32.0
Q ss_pred EEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecC
Q psy8115 123 IIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVAT 168 (218)
Q Consensus 123 IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~n 168 (218)
|+|+..+.+.--+.|.+-++++++.+.+.+|..+..|.|-++||..
T Consensus 4 v~Ik~~~g~~~~~~K~~la~~vT~~~~~~lg~~~~~i~Viieev~~ 49 (69)
T COG1942 4 VNIKLFEGRLDEEQKAELAAEVTEVTVETLGKDPSAIHVIIEEVPP 49 (69)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHHhCCCcccEEEEEEecCh
Confidence 4555555322222234446899999999999877889998998875
No 56
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=42.88 E-value=1.1e+02 Score=27.96 Aligned_cols=62 Identities=16% Similarity=0.202 Sum_probs=50.1
Q ss_pred CeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHH
Q psy8115 119 ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRY 182 (218)
Q Consensus 119 ~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~ 182 (218)
+.+.+.|..++--.+||.+|++-..|-+.....++....+|.|.=.++.+ .+...+|+.|.-
T Consensus 18 ~~isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~d~G~i~i~g~~~~~--~~s~~LAk~lSI 79 (252)
T COG4604 18 DDVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKDSGEITIDGLELTS--TPSKELAKKLSI 79 (252)
T ss_pred ccceeeecCCceeEEECCCCccHHHHHHHHHHhccccCceEEEeeeeccc--CChHHHHHHHHH
Confidence 45666777777778999999999999999999998888888887777765 567778877753
No 57
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=41.62 E-value=48 Score=28.87 Aligned_cols=53 Identities=17% Similarity=0.289 Sum_probs=40.3
Q ss_pred HHHHHHHhhhccCCeeeeEEEec-CCeEEEEEEecccceEeccCcccHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELTSV 147 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt-~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~ 147 (218)
.+.+|+.+.|..|.+.+|.+.-. .....|.+.-..-+.+||++|++++...+.
T Consensus 117 d~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~L 170 (190)
T COG0195 117 DPAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQL 170 (190)
T ss_pred CHHHHHHHhcCcceEeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHH
Confidence 46788888888899999999874 225666666677778999999888665553
No 58
>PLN02808 alpha-galactosidase
Probab=41.38 E-value=8.1 Score=37.00 Aligned_cols=68 Identities=24% Similarity=0.316 Sum_probs=44.2
Q ss_pred CCCCCcceeeecCCceeecccc-cchhhHHHHhhhhhcccccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEE
Q psy8115 38 GVPTTPLTQTISNGATVRDSPL-GFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEI 114 (218)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI 114 (218)
|.||-.+|| |+.|+......- |....=+..-|+|. -|..-+.|.+++...+.++..-|+++||.-|.|
T Consensus 5 ~~~~~~~~~-~~~~~~~~~~~~ngla~tPpmGWnsW~--------~~~~~i~e~~i~~~a~~mv~~Gl~~~Gy~yv~i 73 (386)
T PLN02808 5 GAPTLTLTQ-ITDGFISRNLLDNGLGLTPQMGWNSWN--------HFQCNINETLIKQTADAMVSSGLAALGYKYINL 73 (386)
T ss_pred cchHHHHhh-hhhhhhhhhcccCcccCCCcceEEchH--------HHCCCCCHHHHHHHHHHHHHcchHHhCCEEEEE
Confidence 568877777 455544333221 22333345668883 344446788888888888888899999988777
No 59
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=41.35 E-value=89 Score=24.28 Aligned_cols=53 Identities=17% Similarity=0.159 Sum_probs=36.5
Q ss_pred EecccceEeccCccc---HHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy8115 126 MATRTQNVLGDKGRR---IRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI 185 (218)
Q Consensus 126 ~aarPgiVIGrkG~~---Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLE 185 (218)
|.-+|-+.||++|-. ++++.+.|.++= =|.|.+ .++-..+..-+|+.|+.+..
T Consensus 14 h~l~p~v~IGK~Glt~~vi~ei~~aL~~hE-----LIKVkv--l~~~~~~~~e~a~~i~~~~~ 69 (95)
T TIGR00253 14 HHLKPVVLVGKNGLTEGVIKEIEQALEHRE-----LIKVKV--ATEDREDKTLIAEALVKETG 69 (95)
T ss_pred CCCCCeEEECCCCCCHHHHHHHHHHHHhCC-----cEEEEe--cCCChhHHHHHHHHHHHHHC
Confidence 556788999999853 688888887532 233433 45555677778888887764
No 60
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=41.18 E-value=41 Score=33.86 Aligned_cols=52 Identities=23% Similarity=0.429 Sum_probs=32.9
Q ss_pred HHHHHHHHHhhhccCCeeeeEEEecC-CeEEEEEEecccceEeccCcccHHHHHHHH
Q psy8115 93 RAELDEFLTRELAEDGYSGVEIRFTP-ARTEIIIMATRTQNVLGDKGRRIRELTSVV 148 (218)
Q Consensus 93 r~~IRefl~K~l~~AGIs~IEI~Rt~-~~I~IiI~aarPgiVIGrkG~~Ik~L~~~L 148 (218)
..+|.+++.+.+.. +++++-.. ....|.+.-..-+.+||++|++|++|.+.|
T Consensus 463 ~~~i~~~i~r~~p~----~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~kl 515 (604)
T COG1855 463 EEEIEREIKRYLPG----DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKL 515 (604)
T ss_pred HHHHHHHHHHhCCC----CceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHh
Confidence 34566666666543 45555553 445555544455679999999998876543
No 61
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=41.02 E-value=43 Score=31.87 Aligned_cols=52 Identities=15% Similarity=0.268 Sum_probs=38.1
Q ss_pred HHHHHHHhhhccCCeeeeEEEec-CCeEEEEEEecccceEeccCcccHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELTS 146 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt-~~~I~IiI~aarPgiVIGrkG~~Ik~L~~ 146 (218)
-..+|+.+.|.-|.+.+|.|... .....|++--..-+..||++|++++--..
T Consensus 278 d~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~ 330 (362)
T PRK12327 278 DPAEFVANALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAAR 330 (362)
T ss_pred CHHHHHHHhCCCceEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHH
Confidence 45788999999999999987432 23555555556667899999999965443
No 62
>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=40.55 E-value=42 Score=31.57 Aligned_cols=51 Identities=18% Similarity=0.313 Sum_probs=38.3
Q ss_pred HHHHHHHhhhccCCeeeeEEEec-CCeEEEEEEecccceEeccCcccHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELT 145 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt-~~~I~IiI~aarPgiVIGrkG~~Ik~L~ 145 (218)
...+|+.+.|.-|.+.+|+|... .....|++--..-+..||++|++++.-.
T Consensus 276 d~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~ 327 (341)
T TIGR01953 276 DPAEFIANALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLAS 327 (341)
T ss_pred CHHHHHHHhcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHHH
Confidence 45788888899999999987433 3456666666667789999999996543
No 63
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=39.44 E-value=1.1e+02 Score=30.29 Aligned_cols=54 Identities=20% Similarity=0.262 Sum_probs=38.1
Q ss_pred HHHHHHHhhhccCCeeeeEE---Eec--------CCeEEEEEEecccc-----eEeccCcccHHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEI---RFT--------PARTEIIIMATRTQ-----NVLGDKGRRIRELTSVV 148 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI---~Rt--------~~~I~IiI~aarPg-----iVIGrkG~~Ik~L~~~L 148 (218)
.+++.|..+..+-.=+-|+| -|- ..+++|-+++.-|+ ..||.+|.+|+.+.+.|
T Consensus 228 lv~~Lfe~EVPEI~dG~VeIk~IAREa~~~~ripG~RtKVAV~S~d~~VDPvGacVG~kG~RI~~I~~eL 297 (449)
T PRK12329 228 LVVYLFENEVPEIEEGVVRIVAVAREANPPSRYVGPRTKIAVDTLERDVDPVGACIGARGSRIQAVVNEL 297 (449)
T ss_pred HHHHHHHhhCcccccCeEEEEEEEecCCCCCCCCcceeEEEEEcCCCCCChhhccCCCCcchHHHHHHHh
Confidence 44555566655432223444 554 47999999998885 58999999999998887
No 64
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=38.72 E-value=1.1e+02 Score=30.06 Aligned_cols=55 Identities=22% Similarity=0.394 Sum_probs=40.8
Q ss_pred HHHHHHHhhhccCCeeeeEE---EecC-CeEEEEEEecccc-----eEeccCcccHHHHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEI---RFTP-ARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQ 149 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI---~Rt~-~~I~IiI~aarPg-----iVIGrkG~~Ik~L~~~Lq 149 (218)
.+++.|..+..+-.=+-|+| -|-| .+.+|-+++.-|. ..||.+|.+|+.+.+.|.
T Consensus 203 ~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ 266 (470)
T PRK09202 203 FLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELG 266 (470)
T ss_pred HHHHHHHHhCcccccCeEEEEEEeecCcceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhC
Confidence 56667777766543333555 4554 7999999998875 589999999999988873
No 65
>PRK13763 putative RNA-processing protein; Provisional
Probab=37.41 E-value=74 Score=26.96 Aligned_cols=59 Identities=12% Similarity=0.135 Sum_probs=33.6
Q ss_pred ccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHH
Q psy8115 129 RTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRY 193 (218)
Q Consensus 129 rPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRA 193 (218)
.-|.+||++|+.++.|++.-.-.+.+.++.|.| . - +.+..-.|......|-++.+.-++
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i--~--G--~~~~~~~A~~~I~~li~g~~~~~~ 163 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAI--I--G--DPEQVEIAREAIEMLIEGAPHGTV 163 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEE--E--e--CHHHHHHHHHHHHHHHcCCCcHHH
Confidence 467899999988887766444333333333332 3 2 334555566655666655544433
No 66
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=37.32 E-value=49 Score=31.84 Aligned_cols=51 Identities=22% Similarity=0.341 Sum_probs=38.9
Q ss_pred HHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELT 145 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~ 145 (218)
-..+|+.+.|.-|.+.+|.+.-......|++--..-+..||++|++++.-.
T Consensus 284 D~~~fI~Nal~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~ 334 (374)
T PRK12328 284 VPEIFIARALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRLAS 334 (374)
T ss_pred CHHHHHHHhCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHHHH
Confidence 456888888988999999876444566666666667789999999986544
No 67
>PHA02754 hypothetical protein; Provisional
Probab=36.89 E-value=45 Score=24.48 Aligned_cols=34 Identities=12% Similarity=0.080 Sum_probs=23.9
Q ss_pred HHHHHHHHHcChhHHHHHHHHHHHHHHcCCccCCC
Q psy8115 177 AESLRYKLIGGLAVRRYNSDVSLYCLNCYTYADAP 211 (218)
Q Consensus 177 Ae~IA~QLEkRv~FRRAmK~AIr~amkaGA~~~~~ 211 (218)
|+.|...|- .-.|+++|++.-...-++|.|+|--
T Consensus 4 AeEi~k~i~-eK~Fke~MRelkD~LSe~GiYi~RI 37 (67)
T PHA02754 4 AEEIPKAIM-EKDFKEAMRELKDILSEAGIYIDRI 37 (67)
T ss_pred HHHHHHHHH-HhHHHHHHHHHHHHHhhCceEEEEE
Confidence 444444332 2369999999877888999999853
No 68
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=36.09 E-value=28 Score=27.29 Aligned_cols=35 Identities=29% Similarity=0.390 Sum_probs=24.3
Q ss_pred chhhHHHHhhhhhcccccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeee
Q psy8115 61 FSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSG 111 (218)
Q Consensus 61 ~~~~~~~~~~~~~~~m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~ 111 (218)
++++|.||+|. -+|-.-..||+-|.++..+.|.+.
T Consensus 17 ~~~iF~FL~~~----------------P~GT~~~~iR~~L~rYI~~~G~~~ 51 (97)
T PRK13916 17 YPQIFDFLENV----------------PRGTKTAHIREALRRYIEEIGENP 51 (97)
T ss_pred cHHHHHHHHHC----------------CCCCccHHHHHHHHHHHHhcCCCC
Confidence 68899999883 245555667777777766777664
No 69
>KOG2192|consensus
Probab=35.91 E-value=16 Score=34.30 Aligned_cols=39 Identities=23% Similarity=0.497 Sum_probs=32.6
Q ss_pred ecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCC
Q psy8115 116 FTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 154 (218)
Q Consensus 116 Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~ 154 (218)
+.|-.++.-||-...|.+||++|..|++|++.-.-+++.
T Consensus 120 ~~pce~rllihqs~ag~iigrngskikelrekcsarlki 158 (390)
T KOG2192|consen 120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKI 158 (390)
T ss_pred CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhh
Confidence 344456678899999999999999999999998887764
No 70
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=34.01 E-value=70 Score=23.92 Aligned_cols=54 Identities=13% Similarity=0.185 Sum_probs=34.2
Q ss_pred CCeeeeEEEec-CCeEEEEEEecccceEeccCcccH--------HHHHHHHHHHhCCCCCcEEEEEEEe
Q psy8115 107 DGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRI--------RELTSVVQKRFKFADGAIELYAEKV 166 (218)
Q Consensus 107 AGIs~IEI~Rt-~~~I~IiI~aarPgiVIGrkG~~I--------k~L~~~LqK~~~~~~kkI~I~I~EV 166 (218)
....+|.++.. ...+.|.++..-. -|..+ +++++.|++..++.-..|+|.+..|
T Consensus 45 ~~~~~v~v~~~~~~~i~v~l~v~v~------~g~~i~~v~~~iq~~V~~~v~~~tg~~v~~V~V~V~~v 107 (108)
T PF03780_consen 45 RPSKGVKVEVDEDGGITVDLHVVVE------YGVNIPEVAEEIQEKVKEAVEEMTGIEVSEVNVHVEDV 107 (108)
T ss_pred CCCCCeEEEEccCcceEEEEEEEEE------CCccHHHHHHHHHHHHHHHHHHHHCCeeEEEEEEEEec
Confidence 33455777766 6777776665321 23333 5666677777777667888888765
No 71
>KOG2191|consensus
Probab=33.77 E-value=68 Score=30.92 Aligned_cols=53 Identities=15% Similarity=0.228 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhhhccCCeeeeEEEecCCeE---EEEEEecccceEeccCcccHHHHHHH
Q psy8115 92 FRAELDEFLTRELAEDGYSGVEIRFTPART---EIIIMATRTQNVLGDKGRRIRELTSV 147 (218)
Q Consensus 92 ir~~IRefl~K~l~~AGIs~IEI~Rt~~~I---~IiI~aarPgiVIGrkG~~Ik~L~~~ 147 (218)
|-.+|||-... .+++.+|.=.++++++ +|.+=..--|.|||+.|..||.+++.
T Consensus 105 I~dKire~p~~---~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq 160 (402)
T KOG2191|consen 105 IADKIREKPQA---VAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160 (402)
T ss_pred HHHHHHHhHHh---hcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence 33345554332 2444445445566654 45555566688999999999988764
No 72
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=33.71 E-value=68 Score=21.66 Aligned_cols=30 Identities=10% Similarity=0.144 Sum_probs=24.4
Q ss_pred ccHHHHHHHHHHHhCCCCCcEEEEEEEecC
Q psy8115 139 RRIRELTSVVQKRFKFADGAIELYAEKVAT 168 (218)
Q Consensus 139 ~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~n 168 (218)
+-++.|.+.|...++.....+.|.+.++..
T Consensus 19 ~l~~~it~~l~~~lg~~~~~v~V~i~e~~~ 48 (63)
T TIGR00013 19 QLIEGVTEAMAETLGANLESIVVIIDEMPK 48 (63)
T ss_pred HHHHHHHHHHHHHhCCCcccEEEEEEEcCH
Confidence 346888889999999888889998888764
No 73
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=33.65 E-value=1.3e+02 Score=23.56 Aligned_cols=53 Identities=11% Similarity=0.117 Sum_probs=36.6
Q ss_pred EecccceEeccCccc---HHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy8115 126 MATRTQNVLGDKGRR---IRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI 185 (218)
Q Consensus 126 ~aarPgiVIGrkG~~---Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLE 185 (218)
|.-+|-+.||++|-. ++++.+.|...= =|.|.+ ..+-..+..-+|+.|+++..
T Consensus 16 h~l~Pvv~IGk~Glt~~vi~ei~~aL~~hE-----LIKvkv--~~~~~~~~~e~~~~i~~~~~ 71 (97)
T PRK10343 16 HPLKPVVLLGSNGLTEGVLAEIEQALEHHE-----LIKVKI--ATEDRETKTLIVEAIVRETG 71 (97)
T ss_pred CCCCCeEEECCCCCCHHHHHHHHHHHHHCC-----cEEEEe--cCCChhHHHHHHHHHHHHHC
Confidence 667888999999874 677777777532 234433 35555667888888888764
No 74
>PRK08384 thiamine biosynthesis protein ThiI; Provisional
Probab=33.52 E-value=91 Score=29.76 Aligned_cols=101 Identities=17% Similarity=0.181 Sum_probs=53.0
Q ss_pred HHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHH--HH
Q psy8115 100 LTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIA--QA 177 (218)
Q Consensus 100 l~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~l--lA 177 (218)
|.+.+.+.|+....+++..+++-|. +. ..+++.+.|++.||.. .+.. +.++ ++++++.. ++
T Consensus 31 i~~~l~~~~~~~~~v~~~~~ri~v~--~~-----------~~~~~~~~l~~vfGI~--~~s~-~~~~-~~~~~~i~~~~~ 93 (381)
T PRK08384 31 IREALVSEGIEFKKVEAKHGRILVK--TN-----------RAEEAVEVLTRVFGIV--SLSP-AMEI-DAELEKINRTAL 93 (381)
T ss_pred HHHHHHhcCCccceEEEECCEEEEE--cC-----------CHHHHHHHHhhCCCce--eEEE-EEEe-CCCHHHHHHHHH
Confidence 3444555665544566666777664 21 2234667899999863 2322 1223 24433322 22
Q ss_pred HHHHHHHHc----C----hhHHHHHHH----HHHHHHHcCCccCCCCCCCCC
Q psy8115 178 ESLRYKLIG----G----LAVRRYNSD----VSLYCLNCYTYADAPSTLPVD 217 (218)
Q Consensus 178 e~IA~QLEk----R----v~FRRAmK~----AIr~amkaGA~~~~~~~~~~~ 217 (218)
+.+.+.++. + +.-||+-|. ..+.+.+.||+.-....++||
T Consensus 94 ~~~~~~~~~~~~~~~tF~V~~rR~~k~f~~tS~ei~~~vG~~i~~~~~~~Vd 145 (381)
T PRK08384 94 KLFRRKKRELELEKPRFRVTARRITKEFPLKSPEIQAKVGEYILENEESEVD 145 (381)
T ss_pred HHHHHhhhcccccCCeEEEEEEeCCCCCCCChHHHHHHHHHHHHhcCCCCcc
Confidence 334443332 1 234565543 677888888887322247776
No 75
>PRK13763 putative RNA-processing protein; Provisional
Probab=33.29 E-value=52 Score=27.87 Aligned_cols=69 Identities=14% Similarity=0.231 Sum_probs=42.0
Q ss_pred EEEEEEecccceEeccCcccHHHHHHHHHHHhCCC--CCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHH
Q psy8115 121 TEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFA--DGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVR 191 (218)
Q Consensus 121 I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~--~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FR 191 (218)
..+.|-..+-+.|||++|+.++.|.+...-..... +..|.|.... .++.++..-|..+...|-.....-
T Consensus 5 ~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~--~~d~~~i~kA~~~I~ai~~gf~~e 75 (180)
T PRK13763 5 EYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD--GEDPLAVLKARDIVKAIGRGFSPE 75 (180)
T ss_pred EEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC--CCCHHHHHHHHHHHHHHhcCCCHH
Confidence 34455667778899999999988776442222111 1222221111 567788888888888777765433
No 76
>KOG1423|consensus
Probab=33.27 E-value=3.1e+02 Score=26.51 Aligned_cols=75 Identities=15% Similarity=0.253 Sum_probs=44.1
Q ss_pred HHhhhhHHHHHHHHHHhhhccCC---eeeeEEEec-CCeEEEEEEecccc---eEeccCcccHHHH----HHHHHHHhCC
Q psy8115 86 FVADGVFRAELDEFLTRELAEDG---YSGVEIRFT-PARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKRFKF 154 (218)
Q Consensus 86 fV~d~iir~~IRefl~K~l~~AG---Is~IEI~Rt-~~~I~IiI~aarPg---iVIGrkG~~Ik~L----~~~LqK~~~~ 154 (218)
++--+.+|++|-+++..+...+= +..=+-++. ...|++.+.+.++. ++||++|..|.+| .++|...|+
T Consensus 289 ~l~~e~VReklLd~~pqEVPY~lq~~i~~w~e~~~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL~~if~- 367 (379)
T KOG1423|consen 289 FLCSESVREKLLDHLPQEVPYNLQVRILSWKERPAGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDLEDIFQ- 367 (379)
T ss_pred HHHHHHHHHHHHhhCccccCcceEEEEEEeeecCCcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHHHHHhh-
Confidence 33444556666666555443321 111112222 34788888888876 6999999999665 456777775
Q ss_pred CCCcEEEEE
Q psy8115 155 ADGAIELYA 163 (218)
Q Consensus 155 ~~kkI~I~I 163 (218)
++|.+.+
T Consensus 368 --r~V~l~l 374 (379)
T KOG1423|consen 368 --RKVFLRL 374 (379)
T ss_pred --ceeeEEE
Confidence 5565543
No 77
>PHA03303 envelope glycoprotein L; Provisional
Probab=33.23 E-value=1.2e+02 Score=26.01 Aligned_cols=43 Identities=19% Similarity=-0.051 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHHH---cChhHHHHHHHHHHHHHHcCCccCCCCCCCCC
Q psy8115 172 CAIAQAESLRYKLI---GGLAVRRYNSDVSLYCLNCYTYADAPSTLPVD 217 (218)
Q Consensus 172 ~A~llAe~IA~QLE---kRv~FRRAmK~AIr~amkaGA~~~~~~~~~~~ 217 (218)
||-++++-+++.++ ..--+|+|..++++.|..+. -|+ ||-|++
T Consensus 98 NPf~~~~Glaedv~~~~~e~d~r~aL~~al~~al~sr--~d~-st~pp~ 143 (159)
T PHA03303 98 NPYVMLHGLANSIGEEEKEDDIRDALLDALSGALQDR--GDI-STDIPD 143 (159)
T ss_pred CHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHhcC--Ccc-ccCCCC
Confidence 34444444444444 44458999999999998543 333 555544
No 78
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=32.77 E-value=1.7e+02 Score=24.72 Aligned_cols=50 Identities=16% Similarity=0.254 Sum_probs=36.8
Q ss_pred hhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEE
Q psy8115 103 ELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAE 164 (218)
Q Consensus 103 ~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~ 164 (218)
.+.+.||.= ..+.++|-+.+|.+ +.-+.++++.|.+.++....+|.|+++
T Consensus 82 ~~~~~g~~i-------~niD~tii~e~PKi-----~p~~~~m~~~ls~~L~~~~~~V~iKat 131 (153)
T cd00554 82 LIREKGYEI-------VNIDITIIAERPKI-----SPYREAMRANLAELLGIPPSRVNIKAT 131 (153)
T ss_pred HHHHcCCEE-------EEEEEEEEecCCcc-----hHHHHHHHHHHHHHhCCCCceEEEEEe
Confidence 344566542 24667788888865 567899999999999987677887765
No 79
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=32.61 E-value=2.7e+02 Score=27.41 Aligned_cols=88 Identities=11% Similarity=0.135 Sum_probs=50.9
Q ss_pred cCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCC-CcCHHHHHHHHHHHHHcChhHHHHHH
Q psy8115 117 TPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATR-GLCAIAQAESLRYKLIGGLAVRRYNS 195 (218)
Q Consensus 117 t~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP-~l~A~llAe~IA~QLEkRv~FRRAmK 195 (218)
+.+.+.+.+....-... .....++|.+.|++.|| +.+.|.++ +..+ ..-|.-..+..+.+ ++. ..+
T Consensus 411 ~~~~i~L~L~~~~~~L~---~~~~~~~L~~ALs~~~G---~~i~L~I~-~g~~~~~TPa~~~~r~~~e--rq~----~A~ 477 (509)
T PRK14958 411 TDNRLYLMLNPKQKPLL---QQKHIERISEALSEHFN---RTITVKID-ISNHQTETPAALAQKKAQD--RQT----EAE 477 (509)
T ss_pred cCCEEEEEEChhhhhhc---CHHHHHHHHHHHHHHhC---CCeEEEEE-eCCCCCCCHHHHHHHHHHH--HHH----HHH
Confidence 44555554443332222 23457899999999997 44555554 3344 34555555555542 222 333
Q ss_pred HHHH-------HHHHcCCccCCCCCCCCC
Q psy8115 196 DVSL-------YCLNCYTYADAPSTLPVD 217 (218)
Q Consensus 196 ~AIr-------~amkaGA~~~~~~~~~~~ 217 (218)
.+|+ ...+-||-+|..|--|+|
T Consensus 478 ~~i~~Dp~Vq~l~~~F~A~l~~~SI~~~~ 506 (509)
T PRK14958 478 KRMMNDRQVQRIMQTFDATLVKESIVPHD 506 (509)
T ss_pred HHHhcCHHHHHHHHHCCCEEcCCceEeCC
Confidence 3333 344669999999988876
No 80
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=32.51 E-value=36 Score=25.57 Aligned_cols=54 Identities=11% Similarity=0.045 Sum_probs=31.7
Q ss_pred EEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecC
Q psy8115 114 IRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVAT 168 (218)
Q Consensus 114 I~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~n 168 (218)
+.|+.+.+-|.|.+..| .=...|.+=.+.|.+.|+..+|+....|.|.+.|...
T Consensus 23 ~~Rs~~~v~I~It~~~g-Rs~e~K~~ly~~l~~~L~~~~gi~p~Dv~I~l~e~~~ 76 (82)
T PF14552_consen 23 IDRSDDFVIIQITSGAG-RSTEQKKALYRALAERLAEKLGIRPEDVMIVLVENPR 76 (82)
T ss_dssp -TS-TT-EEEEEEECS----HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-G
T ss_pred CCCCCCEEEEEEEECCC-CCHHHHHHHHHHHHHHHHHHcCCCHHHEEEEEEECCc
Confidence 77888877777765442 2222233335788888988899888899999988764
No 81
>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=31.60 E-value=70 Score=26.87 Aligned_cols=67 Identities=10% Similarity=0.065 Sum_probs=37.0
Q ss_pred ccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHH
Q psy8115 129 RTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCL 202 (218)
Q Consensus 129 rPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~am 202 (218)
.-|.+||++|+.++.|+..=.-.+.+.++.|.| +-+ .+..-+|......|-+.-... +++.-|++.+
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~~v~i----~G~--~~~~~~A~~~i~~li~~~~~~-~vy~~l~~~~ 165 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGKTVGI----IGD--PEQVQIAREAIEMLIEGAPHG-TVYKFLERKR 165 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCCEEEE----ECC--HHHHHHHHHHHHHHHcCCCCh-hHHHHHHHHH
Confidence 568899999988877665333332222333332 223 345555565556565554433 4455565554
No 82
>COG1302 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.25 E-value=3.2e+02 Score=22.61 Aligned_cols=60 Identities=8% Similarity=0.142 Sum_probs=37.6
Q ss_pred ccCCeee-eEEEecCCe-EEEEEEecccceEeccCcccH--------HHHHHHHHHHhCCCCCcEEEEEEEecCCC
Q psy8115 105 AEDGYSG-VEIRFTPAR-TEIIIMATRTQNVLGDKGRRI--------RELTSVVQKRFKFADGAIELYAEKVATRG 170 (218)
Q Consensus 105 ~~AGIs~-IEI~Rt~~~-I~IiI~aarPgiVIGrkG~~I--------k~L~~~LqK~~~~~~kkI~I~I~EV~nP~ 170 (218)
.+.++++ |.++...+. +.|.+|+-- .=|..| +.+++.|+++.++.-..|+|++.-|.-+.
T Consensus 49 ~~~n~~kGV~Ve~~~~~~v~VDvyi~v------~YGv~IpeVa~~Iq~~V~~~v~~mtgl~v~~VNV~V~gV~~~k 118 (131)
T COG1302 49 GKENVTKGVKVEVGEDQSVAVDVYIIV------EYGVKIPEVAENIQERVKEEVENMTGLKVVEVNVHVVGVKVKK 118 (131)
T ss_pred CccccCCCeEEEecCCCcEEEEEEEEE------ecCCchHHHHHHHHHHHHHHHHHhhCCceEEEEEEEEEeEecC
Confidence 3455544 888885544 777776532 124444 55666667777776667888888776543
No 83
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=30.04 E-value=89 Score=20.59 Aligned_cols=32 Identities=16% Similarity=0.243 Sum_probs=25.1
Q ss_pred CcccHHHHHHHHHHHhCCCCCcEEEEEEEecC
Q psy8115 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVAT 168 (218)
Q Consensus 137 kG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~n 168 (218)
+.+-.+.|.+.+.+.++.....+.|.+.|+..
T Consensus 16 k~~l~~~i~~~l~~~~g~~~~~v~V~i~e~~~ 47 (58)
T cd00491 16 KRELIERVTEAVSEILGAPEATIVVIIDEMPK 47 (58)
T ss_pred HHHHHHHHHHHHHHHhCcCcccEEEEEEEeCc
Confidence 34446888888889998877889999988764
No 84
>PRK05090 hypothetical protein; Validated
Probab=29.82 E-value=2.7e+02 Score=21.67 Aligned_cols=40 Identities=13% Similarity=0.199 Sum_probs=28.1
Q ss_pred CcccHHHHHHHHHHHhCCCCCcEEE--------EEEEecCCCcCHHHH
Q psy8115 137 KGRRIRELTSVVQKRFKFADGAIEL--------YAEKVATRGLCAIAQ 176 (218)
Q Consensus 137 kG~~Ik~L~~~LqK~~~~~~kkI~I--------~I~EV~nP~l~A~ll 176 (218)
+|+-=++|...|.+.|+....+|+| ...+|..|.--+..+
T Consensus 44 eGkAN~ali~~LAk~l~v~ks~I~i~~G~tsr~K~v~I~~~~~~~~~~ 91 (95)
T PRK05090 44 DGQANAHLLKFLAKQFRVAKSQVVIEKGELGRHKQVRIINPQQIPPEI 91 (95)
T ss_pred CChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEcCcccChHhH
Confidence 4666699999999999987666655 455677775544433
No 85
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=29.48 E-value=82 Score=31.11 Aligned_cols=52 Identities=10% Similarity=0.248 Sum_probs=38.5
Q ss_pred HHHHHHHhhhccCCeeeeEEEec-CCeEEEEEEecccceEeccCcccHHHHHH
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELTS 146 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt-~~~I~IiI~aarPgiVIGrkG~~Ik~L~~ 146 (218)
-..+|+.+.|.-|.+.+|.|... .....|++.-..-+..||++|++++--..
T Consensus 310 Dp~~fI~NaLsPA~V~~V~i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~ 362 (449)
T PRK12329 310 DPATYIANALSPARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAAR 362 (449)
T ss_pred CHHHHHHHhcCCceeeEEEEEcCCCcEEEEEEChHhcchhhcCCChhHHHHHH
Confidence 45678888999999999987432 23556666666777899999999965443
No 86
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=27.96 E-value=3.8e+02 Score=22.79 Aligned_cols=56 Identities=11% Similarity=0.282 Sum_probs=39.6
Q ss_pred HHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEE
Q psy8115 100 LTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIEL 161 (218)
Q Consensus 100 l~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I 161 (218)
+...++..||.++-+.-..+.+.|++.+.. + ..+...+|.+.+.+.++....+|.|
T Consensus 140 iE~llkakGf~davv~~~~~~v~VvV~~~~----L--~~~~~~~I~diV~~~~~v~~~~I~V 195 (196)
T PF12685_consen 140 IENLLKAKGFEDAVVFIEDDSVDVVVKADK----L--SDAEAAQIIDIVMRETGVPAENISV 195 (196)
T ss_dssp HHHHHHTTS-SEEEEE-SSSEEEEEEE-S---------HHHHHHHHHHHHHHHC-STSEEEE
T ss_pred HHHHHHhCCCCceEEEeeCCEEEEEEeCCC----C--CHHHHHHHHHHHHHHhCCCcCeEEe
Confidence 344567789999999889999999988866 1 3456789999999999977667765
No 87
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=27.73 E-value=1.2e+02 Score=20.71 Aligned_cols=29 Identities=28% Similarity=0.367 Sum_probs=24.5
Q ss_pred cHHHHHHHHHHHhCCCCCcEEEEEEEecC
Q psy8115 140 RIRELTSVVQKRFKFADGAIELYAEKVAT 168 (218)
Q Consensus 140 ~Ik~L~~~LqK~~~~~~kkI~I~I~EV~n 168 (218)
-++.+.+.+.+.|+.....|.|.+.|+..
T Consensus 20 L~~~it~a~~~~~~~p~~~v~V~i~ev~~ 48 (60)
T PRK02289 20 LAREVTEVVSRIAKAPKEAIHVFINDMPE 48 (60)
T ss_pred HHHHHHHHHHHHhCcCcceEEEEEEEeCh
Confidence 35788888889999888899999999864
No 88
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=27.41 E-value=2.3e+02 Score=24.44 Aligned_cols=74 Identities=4% Similarity=0.012 Sum_probs=42.8
Q ss_pred hHHHHHHHHHHhhhccCCeeeeEEEecCC-eEEEEEEecccceE-eccCcccHHHHHHHHHHHhCCCCCcEEEEEEE
Q psy8115 91 VFRAELDEFLTRELAEDGYSGVEIRFTPA-RTEIIIMATRTQNV-LGDKGRRIRELTSVVQKRFKFADGAIELYAEK 165 (218)
Q Consensus 91 iir~~IRefl~K~l~~AGIs~IEI~Rt~~-~I~IiI~aarPgiV-IGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~E 165 (218)
....++++.+++.=.-..+.++.+.+... ...+.++...++.. +++.-+-.+++++.|++.++. -..+.|.++.
T Consensus 205 ~~~~~i~~~i~~~~~v~~v~~~~~~~~g~~~~~v~i~v~v~~~~~v~~~~~i~~~i~~~l~~~~~~-i~~v~I~~~p 280 (284)
T PF01545_consen 205 ELVEKIRRIIESVPGVIEVHDLRVWQVGRNKYVVEIHVQVDPDMSVEEAHEIRERIEKRLREKFPG-IYDVTIHIEP 280 (284)
T ss_dssp HHHHHHHHHHHHTSS-SEEEEEEEEEETT-EEEEEEEEEETTTSBHHHHHHHHHHHHHHHHHHSTT-CEEEEEEEEE
T ss_pred cchhHHHHhhccCCceEeccceEEEEecCCcEEEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCC-cEEEEEEEEe
Confidence 33457777776532234577788888776 88888887766544 222222357777777777742 1224454443
No 89
>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=27.23 E-value=2e+02 Score=25.18 Aligned_cols=42 Identities=7% Similarity=-0.110 Sum_probs=31.0
Q ss_pred CcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHH
Q psy8115 157 GAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVS 198 (218)
Q Consensus 157 kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AI 198 (218)
+++.+.-.--.++..++..+++++..||.+-+.|.++++.+.
T Consensus 211 ~~ip~~S~~~g~~~~~~~~~~~~~~~~l~~pV~~~~~i~~l~ 252 (295)
T TIGR03131 211 PRLPYLSGIDARLVRDAAQIRDDLARQIATPVDWHDCMQAAY 252 (295)
T ss_pred CCceEEECCCCeecCCHHHHHHHHHHHhcCCCcHHHHHHHHH
Confidence 445543333344556778899999999999999999988764
No 90
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=27.20 E-value=1.5e+02 Score=26.23 Aligned_cols=59 Identities=12% Similarity=0.189 Sum_probs=38.2
Q ss_pred cceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHH
Q psy8115 130 TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYN 194 (218)
Q Consensus 130 PgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAm 194 (218)
-|.|||++|+..+.+.+.-.-......+.|.| +-.| ...-+|+...+.|-++.+...+-
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVai----iG~~--~~v~iAr~AVemli~G~~h~~Vy 171 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVYGKTVAI----IGGF--EQVEIAREAVEMLINGAPHGKVY 171 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEeCcEEEE----ecCh--hhhHHHHHHHHHHHcCCCchhHH
Confidence 46899999987766655444333222344444 4443 56778899999999988865443
No 91
>PRK03094 hypothetical protein; Provisional
Probab=26.92 E-value=1.6e+02 Score=22.50 Aligned_cols=36 Identities=22% Similarity=0.424 Sum_probs=25.3
Q ss_pred hhhccCCeeeeEEEec--CCeEEEEEEecccceEeccC
Q psy8115 102 RELAEDGYSGVEIRFT--PARTEIIIMATRTQNVLGDK 137 (218)
Q Consensus 102 K~l~~AGIs~IEI~Rt--~~~I~IiI~aarPgiVIGrk 137 (218)
..|++.||.=+.+.-. ...+.-+++++....+.|-.
T Consensus 15 ~~L~~~GYeVv~l~~~~~~~~~Da~VitG~d~n~mgi~ 52 (80)
T PRK03094 15 QALKQKGYEVVQLRSEQDAQGCDCCVVTGQDSNVMGIA 52 (80)
T ss_pred HHHHHCCCEEEecCcccccCCcCEEEEeCCCcceeccc
Confidence 3445589998888532 35677888898888888743
No 92
>KOG2192|consensus
Probab=26.07 E-value=69 Score=30.17 Aligned_cols=64 Identities=11% Similarity=0.105 Sum_probs=41.2
Q ss_pred eEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCC-----cEEEEEEEecCCCcCHHHHHHHHHHH
Q psy8115 120 RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADG-----AIELYAEKVATRGLCAIAQAESLRYK 183 (218)
Q Consensus 120 ~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~k-----kI~I~I~EV~nP~l~A~llAe~IA~Q 183 (218)
..+|+|-.---|.|||+.|++|++++..+--...++++ .=.|.|.-.+.--.+|+.+-+.-+.|
T Consensus 316 TaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 316 TAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred eeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 45677777788899999999999999877655544321 11233454555555666655554444
No 93
>PF11324 DUF3126: Protein of unknown function (DUF3126); InterPro: IPR021473 This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=26.05 E-value=90 Score=22.89 Aligned_cols=20 Identities=20% Similarity=0.514 Sum_probs=16.0
Q ss_pred cHHHHHHHHHHHhCCCCCcEEE
Q psy8115 140 RIRELTSVVQKRFKFADGAIEL 161 (218)
Q Consensus 140 ~Ik~L~~~LqK~~~~~~kkI~I 161 (218)
+|++|+..|++.|+ ++.|.|
T Consensus 1 Ei~klq~yLr~~f~--n~~i~v 20 (63)
T PF11324_consen 1 EIKKLQAYLRRTFG--NPGITV 20 (63)
T ss_pred ChHHHHHHHHHHhC--CCceEE
Confidence 47899999999997 456665
No 94
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=25.70 E-value=1.2e+02 Score=20.33 Aligned_cols=29 Identities=14% Similarity=0.268 Sum_probs=24.2
Q ss_pred cHHHHHHHHHHHhCCCCCcEEEEEEEecC
Q psy8115 140 RIRELTSVVQKRFKFADGAIELYAEKVAT 168 (218)
Q Consensus 140 ~Ik~L~~~LqK~~~~~~kkI~I~I~EV~n 168 (218)
-.+.|.+.|.+.++.....+.|.+.|+..
T Consensus 20 l~~~it~~l~~~~~~p~~~v~V~i~e~~~ 48 (62)
T PRK00745 20 LVEEITRVTVETLGCPPESVDIIITDVKR 48 (62)
T ss_pred HHHHHHHHHHHHcCCChhHEEEEEEEcCh
Confidence 35888999999999888889999988764
No 95
>KOG1676|consensus
Probab=25.53 E-value=45 Score=33.98 Aligned_cols=27 Identities=30% Similarity=0.546 Sum_probs=23.8
Q ss_pred eEEEEEEecccceEeccCcccHHHHHH
Q psy8115 120 RTEIIIMATRTQNVLGDKGRRIRELTS 146 (218)
Q Consensus 120 ~I~IiI~aarPgiVIGrkG~~Ik~L~~ 146 (218)
..+|.|=+.|-|+|||++|..|++|++
T Consensus 140 tqeI~IPa~k~GlIIGKgGETikqlqe 166 (600)
T KOG1676|consen 140 TQEILIPANKCGLIIGKGGETIKQLQE 166 (600)
T ss_pred eeeeccCccceeeEeccCccHHHHHHh
Confidence 567788889999999999999999876
No 96
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=25.20 E-value=68 Score=24.37 Aligned_cols=36 Identities=22% Similarity=0.222 Sum_probs=24.7
Q ss_pred HHHHHHHcChhHHHHHHHHHHHHHHcCCccCCCCCCCC
Q psy8115 179 SLRYKLIGGLAVRRYNSDVSLYCLNCYTYADAPSTLPV 216 (218)
Q Consensus 179 ~IA~QLEkRv~FRRAmK~AIr~amkaGA~~~~~~~~~~ 216 (218)
.+-.||++-...|+|+..|+.. ..|+..+.|+++|-
T Consensus 19 ~Lq~~L~~E~~~r~aLe~al~~--~~~~~~~~~~~lp~ 54 (88)
T PF14389_consen 19 ELQKQLQEEQDLRRALEKALGR--SSGSLPSSPSSLPK 54 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHhCC--CCcccCCccccCCh
Confidence 3455666666677777666655 55777788888885
No 97
>TIGR00342 thiazole biosynthesis/tRNA modification protein ThiI. The protein product of the thiI gene is required for the synthesis of the thiazole moiety in thiamine biosynthesis. It also acts in the generation of 4-thiouridine in tRNA, and may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis.
Probab=25.00 E-value=89 Score=29.28 Aligned_cols=107 Identities=13% Similarity=0.027 Sum_probs=54.5
Q ss_pred HHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHH
Q psy8115 96 LDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIA 175 (218)
Q Consensus 96 IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~l 175 (218)
|.+-|.+.+.+.++. .++.+..+++-|.. . .....+++.+.|.+.||.. .+....+.++++++..
T Consensus 22 L~~ni~~~l~~~~~~-~~~~~~~~r~~v~~--~--------~~~~~~~~~~~l~~vfGi~----~~s~~~~~~~~~~~i~ 86 (371)
T TIGR00342 22 LKKNIKKALKKYEIL-RAVVYHFDRIVVIA--I--------DKEQRDALLDLLTKIPGIV----SFSPAFKCDLPFDEIH 86 (371)
T ss_pred HHHHHHHHHHhCCCC-ceEEEEcCEEEEEe--C--------CcccHHHHHHHHhcCCCcc----EEEEEEEECCCHHHHH
Confidence 333344445455543 56666667766542 1 1224556778899999862 3333445566665554
Q ss_pred HH-HHHHHHHHcChhH----HHHHHH----HHHHHHHcCCccCCCCCCCCC
Q psy8115 176 QA-ESLRYKLIGGLAV----RRYNSD----VSLYCLNCYTYADAPSTLPVD 217 (218)
Q Consensus 176 lA-e~IA~QLEkRv~F----RRAmK~----AIr~amkaGA~~~~~~~~~~~ 217 (218)
.| +.+...++.+-+| ||+-|. ..+...+.|+++-....++||
T Consensus 87 ~~~~~~~~~~~~~~tF~Vr~kR~~k~f~~~S~ei~r~~G~~i~~~~~~~Vd 137 (371)
T TIGR00342 87 ILLKALKQLRKEGKTFKVRTKRRGKDFPLNSVEVNKYVGGGIVEKIGLKVD 137 (371)
T ss_pred HHHHHHHHhhccCCcEEEEEEECCCCCCCChHHHHHHHHHHHHHHcCCccc
Confidence 33 3333333333233 333222 566666777766332225665
No 98
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=24.59 E-value=1.4e+02 Score=24.26 Aligned_cols=32 Identities=16% Similarity=0.366 Sum_probs=24.1
Q ss_pred HHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEe
Q psy8115 94 AELDEFLTRELAEDGYSGVEIRFTPARTEIIIMA 127 (218)
Q Consensus 94 ~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~a 127 (218)
.+|..||.+.+...||. |.|+|- |...|+-.+
T Consensus 5 ~~ikpwlq~~~~~~Gi~-iVIerS-d~~ki~FkC 36 (111)
T PF08731_consen 5 DEIKPWLQKIFYPQGIG-IVIERS-DKKKIVFKC 36 (111)
T ss_pred HHHHHHHHHHhhhcCce-EEEEec-CCceEEEEE
Confidence 47899999988899998 889995 445554343
No 99
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=24.30 E-value=2.8e+02 Score=20.00 Aligned_cols=45 Identities=13% Similarity=0.049 Sum_probs=23.4
Q ss_pred HHHHHHHhhhccCCeeeeEEEecC-----CeEEEEEEecccceEeccCccc
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTP-----ARTEIIIMATRTQNVLGDKGRR 140 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~-----~~I~IiI~aarPgiVIGrkG~~ 140 (218)
++.+ |.+.+....-..|.+.... ..++|.+++..+-++....+..
T Consensus 22 k~~k-l~r~~~~i~~~~V~l~~~~~~~~~~~v~i~v~~~g~~~~a~~~~~d 71 (93)
T cd00552 22 KLEK-LEKYFDRIISVDVVLSVEKNHGKRFKVEITIHLPGGVLRAEASAED 71 (93)
T ss_pred HHHH-HHHhcCCCceEEEEEEEecCCCCceEEEEEEEeCCCEEEEEEccCC
Confidence 3444 5555533333445555533 4677777776544555555544
No 100
>KOG2190|consensus
Probab=24.16 E-value=58 Score=32.18 Aligned_cols=27 Identities=11% Similarity=0.373 Sum_probs=24.6
Q ss_pred EEEEEEecccceEeccCcccHHHHHHH
Q psy8115 121 TEIIIMATRTQNVLGDKGRRIRELTSV 147 (218)
Q Consensus 121 I~IiI~aarPgiVIGrkG~~Ik~L~~~ 147 (218)
+++..++...|.+||++|..+++++..
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~ 71 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKE 71 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhc
Confidence 688999999999999999999999843
No 101
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=23.89 E-value=1.2e+02 Score=31.05 Aligned_cols=55 Identities=20% Similarity=0.346 Sum_probs=41.0
Q ss_pred HHHHHHHhhhc-cCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCC
Q psy8115 95 ELDEFLTRELA-EDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 154 (218)
Q Consensus 95 ~IRefl~K~l~-~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~ 154 (218)
+|++-+.+.+. ++.|.+|+. .+-++.||+-.|..+..+ |.-+++|-+.|+|+.-.
T Consensus 9 ei~~~i~~~~p~~~~It~vef----EGPelvvY~k~P~~~~~~-~dlik~lAk~lrKRI~i 64 (637)
T COG1782 9 EIRNKINEILPSDVKITDVEF----EGPELVVYTKNPELFAKD-GDLIKDLAKDLRKRIII 64 (637)
T ss_pred HHHHHHHHhCCCcCceEEEEe----cCCeEEEEecCHHHhccc-hhHHHHHHHHHhhceEe
Confidence 56666666665 467777766 467899999999887654 56789999999887653
No 102
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=23.60 E-value=5.3e+02 Score=23.71 Aligned_cols=34 Identities=6% Similarity=0.062 Sum_probs=25.3
Q ss_pred EeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEe
Q psy8115 133 VLGDKGRRIRELTSVVQKRFKFADGAIELYAEKV 166 (218)
Q Consensus 133 VIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV 166 (218)
+.|--|+..+.+++.|+....+....|.++...+
T Consensus 156 i~GlPgqt~~~~~~~l~~~~~l~~~~is~y~L~~ 189 (350)
T PRK08446 156 IYDTPLDNKKLLKEELKLAKELPINHLSAYSLTI 189 (350)
T ss_pred ecCCCCCCHHHHHHHHHHHHhcCCCEEEecccee
Confidence 4454578899999999988877667777766544
No 103
>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=23.48 E-value=1e+02 Score=31.35 Aligned_cols=53 Identities=23% Similarity=0.383 Sum_probs=38.5
Q ss_pred HHHHHHHhhhc-cCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHh
Q psy8115 95 ELDEFLTRELA-EDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRF 152 (218)
Q Consensus 95 ~IRefl~K~l~-~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~ 152 (218)
+|++-+.+.+. ++.|++||.+ +-+|.||+-.|..+... +.-+++|-+.|+|+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~e----gp~~~~~~~~~~~~~~~-~~~~~~~~~~~~~r~ 56 (630)
T TIGR03675 3 EIKEIINELLPKDIKITDVEFE----GPELVIYTKNPELFAKD-DDLVKELAKKLRKRI 56 (630)
T ss_pred HHHHHHHHhCCCCCeEEEEEEe----CCeEEEEeCCHHHhccc-hHHHHHHHHHhhceE
Confidence 34445555553 6789999885 57899999999987654 466788888887755
No 104
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=22.80 E-value=2.1e+02 Score=24.33 Aligned_cols=50 Identities=20% Similarity=0.256 Sum_probs=36.9
Q ss_pred hhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEE
Q psy8115 103 ELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAE 164 (218)
Q Consensus 103 ~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~ 164 (218)
.+.+.||.= ..+.++|-+.+|.+ +.-+.++++.|.+.++....+|+|++.
T Consensus 83 ~~~~~g~~i-------~niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~~~V~iKat 132 (157)
T PF02542_consen 83 LLREKGYRI-------VNIDITIIAERPKI-----SPYRPAMRENLAKLLGIPPDRVNIKAT 132 (157)
T ss_dssp HHHHTTEEE-------EEEEEEEESSSSTT-----GGGHHHHHHHHHHHHTS-GGGEEEEEE
T ss_pred HHHHcCcEE-------EEEEEEEEcCCCcc-----HHHHHHHHHHHHHHhCCCcceEEEEEe
Confidence 445577642 24667888888865 567899999999999987678888665
No 105
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=22.65 E-value=2.2e+02 Score=24.20 Aligned_cols=40 Identities=15% Similarity=0.209 Sum_probs=32.0
Q ss_pred eEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEE
Q psy8115 120 RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAE 164 (218)
Q Consensus 120 ~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~ 164 (218)
.+.++|-+.+|.+ +.-..++++.|.+.+++...+|+|++.
T Consensus 92 niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~~~V~iKat 131 (155)
T TIGR00151 92 NVDITIIAQRPKL-----LPHIPAMRENIAELLGIPLDSVNVKAT 131 (155)
T ss_pred EEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEEe
Confidence 4666778888865 567899999999999987677887665
No 106
>PF06069 PerC: PerC transcriptional activator; InterPro: IPR024684 This family includes PerC, which is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria []. It also includes a number of uncharacterised proteins, such as Orf40 from bacteriophage SfV.
Probab=22.60 E-value=63 Score=25.11 Aligned_cols=23 Identities=13% Similarity=-0.129 Sum_probs=19.3
Q ss_pred HHHHHHHHHcChhHHHHHHHHHH
Q psy8115 177 AESLRYKLIGGLAVRRYNSDVSL 199 (218)
Q Consensus 177 Ae~IA~QLEkRv~FRRAmK~AIr 199 (218)
-+.+|++||.+--||||...=++
T Consensus 3 ~d~~Ae~LE~kGl~RRAA~rW~e 25 (90)
T PF06069_consen 3 HDKKAEELEAKGLWRRAATRWLE 25 (90)
T ss_pred chHHHHHHHHcccHHHHHHHHHH
Confidence 37899999999999999876543
No 107
>COG0053 MMT1 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=22.57 E-value=4e+02 Score=24.36 Aligned_cols=62 Identities=13% Similarity=0.180 Sum_probs=41.1
Q ss_pred CeeeeEEEecCCeEEEEEEecccceEeccCccc-HHHHHHHHHHHhCCCCCcEEEEEEEecCCC
Q psy8115 108 GYSGVEIRFTPARTEIIIMATRTQNVLGDKGRR-IRELTSVVQKRFKFADGAIELYAEKVATRG 170 (218)
Q Consensus 108 GIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~-Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~ 170 (218)
|+.++..++.+..+.+.+|..-|..+=-.+.-+ .+++.+.|++.++. ...+.|++++..+.+
T Consensus 232 ~v~~lr~R~~G~~~~id~~i~v~~~ls~~eah~I~~~ie~~i~~~~~~-~~~v~IhveP~~~~~ 294 (304)
T COG0053 232 GVHDLRTRKSGSRIFIDVHIEVDPDLSLEEAHEIADEVEKRIKKEFPK-VADVTIHVEPLGEKE 294 (304)
T ss_pred eeecceeeeeCCeEEEEEEEEECCCCChHHHHHHHHHHHHHHHHhcCC-CceEEEEecCCcccc
Confidence 456677777789999999998886543333323 36777777777752 356777777655443
No 108
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=22.31 E-value=2.2e+02 Score=24.32 Aligned_cols=40 Identities=18% Similarity=0.309 Sum_probs=31.6
Q ss_pred eEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEE
Q psy8115 120 RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAE 164 (218)
Q Consensus 120 ~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~ 164 (218)
.+.++|-+.+|.+ +.-+.++++.|.+.++....+|.|+++
T Consensus 95 niD~tii~e~PKi-----~p~~~~m~~~la~~L~i~~~~V~iKat 134 (159)
T PRK00084 95 NVDITIIAQRPKM-----APHIEEMRANIAEDLGIPLDDVNVKAT 134 (159)
T ss_pred EEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEEe
Confidence 4566778888865 567899999999999987667777665
No 109
>PRK01565 thiamine biosynthesis protein ThiI; Provisional
Probab=21.81 E-value=1.5e+02 Score=28.10 Aligned_cols=45 Identities=18% Similarity=0.260 Sum_probs=28.3
Q ss_pred HHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCC
Q psy8115 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 154 (218)
Q Consensus 97 Refl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~ 154 (218)
.+-|.+.+...| .+.+++...++.|.. .+...+++.+.|++.||.
T Consensus 27 ~~ni~~~l~~~~--~~~~~~~~~r~~v~~-----------~~~~~~~~~~~l~~vfGI 71 (394)
T PRK01565 27 KRNIKKALKDLP--EVKVEAERDRMYIEL-----------NGEDYEEVIERLKKVFGI 71 (394)
T ss_pred HHHHHHHHHhcC--CeeEEEECCEEEEEe-----------CCcCHHHHHHHHhhCCCc
Confidence 333444455555 467777777776653 123456777889999986
No 110
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=21.79 E-value=1.5e+02 Score=21.96 Aligned_cols=52 Identities=17% Similarity=0.139 Sum_probs=28.8
Q ss_pred ecccceEeccCccc---HHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy8115 127 ATRTQNVLGDKGRR---IRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI 185 (218)
Q Consensus 127 aarPgiVIGrkG~~---Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLE 185 (218)
.-+|-+.||++|-. ++++.+.|++.= =|.|.+ ..++..+..-+|+.|+++..
T Consensus 15 ~l~p~v~IGk~Glt~~vi~~i~~~l~~~e-----LvKVk~--~~~~~~~~~~~~~~l~~~t~ 69 (84)
T PF01985_consen 15 HLKPVVQIGKNGLTDGVIEEIDDALEKHE-----LVKVKV--LGNCREDRKEIAEQLAEKTG 69 (84)
T ss_dssp TC--SEEE-TTSS-HHHHHHHHHHHHHHS-----EEEEEE--TT--HHHHHHHHHHHHHHHT
T ss_pred CCCCeEEECCCCCCHHHHHHHHHHHHhCC-----eeEEEE--ccCCHHHHHHHHHHHHHHhC
Confidence 45777889999863 577777777632 233433 44566666666666666543
No 111
>PF10118 Metal_hydrol: Predicted metal-dependent hydrolase; InterPro: IPR016516 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function
Probab=21.68 E-value=72 Score=28.49 Aligned_cols=24 Identities=21% Similarity=0.285 Sum_probs=20.6
Q ss_pred cchhhhhhHHhhhhHHHHHHHHHH
Q psy8115 78 LSICVSLQFVADGVFRAELDEFLT 101 (218)
Q Consensus 78 ~~~~~ykkfV~d~iir~~IRefl~ 101 (218)
++++.|...|+|...+.+|+.||.
T Consensus 45 ~svr~~~~~i~D~~L~~~i~~FIg 68 (253)
T PF10118_consen 45 RSVRRARPQIKDPELREEIKGFIG 68 (253)
T ss_pred HHHHHHHhhCCCHHHHHHHHHHHH
Confidence 455789999999999999999995
No 112
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=21.54 E-value=2.8e+02 Score=23.70 Aligned_cols=62 Identities=16% Similarity=0.207 Sum_probs=42.0
Q ss_pred HHHHHHHhhhccCCeeeeEEEecCCeEEEE-EEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEE
Q psy8115 95 ELDEFLTRELAEDGYSGVEIRFTPARTEII-IMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIEL 161 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI~Rt~~~I~Ii-I~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I 161 (218)
-+++|+.+-+.-|.+.++.+.-.+++...+ ++..+-.. ++-....+.+...+++..| +.+.+
T Consensus 101 d~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~Dk--~~l~~k~e~~~~v~~kltg---k~v~~ 163 (166)
T PRK06418 101 DIKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRDR--RRLPAKPELLESILSKITG---TEVKI 163 (166)
T ss_pred CHHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHHh--hcccccHHHHHHHHHHHHC---CcEEE
Confidence 367888888889999999998877764443 55543211 1114467888889998887 44554
No 113
>PF06857 ACP: Malonate decarboxylase delta subunit (MdcD); InterPro: IPR023439 This family consists of the acyl carrier protein found in malonate decarboxylase and citrate lyase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=21.24 E-value=3.8e+02 Score=20.48 Aligned_cols=66 Identities=20% Similarity=0.337 Sum_probs=37.7
Q ss_pred eeeEEEecC---CeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHH
Q psy8115 110 SGVEIRFTP---ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKL 184 (218)
Q Consensus 110 s~IEI~Rt~---~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QL 184 (218)
|+++|.-.| ..++|.|.+..-..+ |..++++-...-+.++..+-+|. +.+.+.-+-.+.-++...+
T Consensus 14 sD~~V~v~p~~~~gi~i~l~S~v~~~f----g~~i~~vi~~~l~~~~i~~~~v~-----i~D~GAld~vi~aRl~~A~ 82 (87)
T PF06857_consen 14 SDLEVTVEPAESGGIEIELESSVVKQF----GDQIRAVIRETLEELGIEDAKVE-----INDKGALDCVIRARLEQAL 82 (87)
T ss_pred CcEEEEEEeCCCCcEEEEEEchHHhhh----HHHHHHHHHHHHHhcCCCceEEE-----EEeCCCCHHHHHHHHHHHH
Confidence 456665554 489999888732222 77787777777777776443443 3344444444444444443
No 114
>COG1129 MglA ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]
Probab=21.00 E-value=2.7e+02 Score=27.84 Aligned_cols=95 Identities=19% Similarity=0.166 Sum_probs=60.0
Q ss_pred CCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEec-----------------CCCcCHHH-HHHH
Q psy8115 118 PARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVA-----------------TRGLCAIA-QAES 179 (218)
Q Consensus 118 ~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~-----------------nP~l~A~l-lAe~ 179 (218)
-+.+...|+.+.-..++|.+|++-.-|-+.|.-.+.-....|.++=.++. ++.+++.+ +||+
T Consensus 24 L~~v~l~v~~GEV~aL~GeNGAGKSTLmKiLsGv~~p~~G~I~~~G~~~~~~sp~~A~~~GI~~V~QEl~L~p~LsVaeN 103 (500)
T COG1129 24 LDGVSLTVRPGEVHALLGENGAGKSTLMKILSGVYPPDSGEILIDGKPVAFSSPRDALAAGIATVHQELSLVPNLSVAEN 103 (500)
T ss_pred eccceeEEeCceEEEEecCCCCCHHHHHHHHhCcccCCCceEEECCEEccCCCHHHHHhCCcEEEeechhccCCccHHHH
Confidence 46788888888888999999999988888877655533344544433332 33344443 7888
Q ss_pred HHHHHHc----ChhHHHHHHHHHHHHHH-cCCccCCCCC
Q psy8115 180 LRYKLIG----GLAVRRYNSDVSLYCLN-CYTYADAPST 213 (218)
Q Consensus 180 IA~QLEk----Rv~FRRAmK~AIr~amk-aGA~~~~~~~ 213 (218)
|-.-=|- ++=-|++|++.-+.+++ .|...| |.+
T Consensus 104 ifLgre~~~~~g~id~~~m~~~A~~~l~~lg~~~~-~~~ 141 (500)
T COG1129 104 IFLGREPTRRFGLIDRKAMRRRARELLARLGLDID-PDT 141 (500)
T ss_pred hhcccccccCCCccCHHHHHHHHHHHHHHcCCCCC-hhh
Confidence 8633221 12234777777777776 676644 443
No 115
>TIGR03367 queuosine_QueD queuosine biosynthesis protein QueD. Members of this protein family, closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes, are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr, His, Asp, and Asn in many species. This modification, although widespread, appears not to be important for viability. The queuosine precursor made by this enzyme may be converted instead to archeaosine as in some Archaea.
Probab=20.91 E-value=3.7e+02 Score=20.13 Aligned_cols=44 Identities=16% Similarity=0.093 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHc
Q psy8115 141 IRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIG 186 (218)
Q Consensus 141 Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEk 186 (218)
...|+..++.....-+.+.-..+.+..+| .+..+|.+|..+|.+
T Consensus 49 f~~lk~~~~~i~~~lDh~~Lne~~~~~~p--T~E~ia~~i~~~l~~ 92 (92)
T TIGR03367 49 FSDLKAIVKEVVDRLDHALLNDVPGLENP--TAENLARWIYDRLKA 92 (92)
T ss_pred HHHHHHHHHHHHHhCCCcEeeCCCCCCCC--CHHHHHHHHHHHHhC
Confidence 34555555443322234443333344455 889999999998863
No 116
>PF08664 YcbB: YcbB domain; InterPro: IPR013972 YcbB is a DNA-binding protein [].
Probab=20.70 E-value=42 Score=27.77 Aligned_cols=23 Identities=9% Similarity=-0.130 Sum_probs=17.1
Q ss_pred HHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115 182 YKLIGGLAVRRYNSDVSLYCLNCYT 206 (218)
Q Consensus 182 ~QLEkRv~FRRAmK~AIr~amkaGA 206 (218)
..+|+| .|||+++|+...-..|.
T Consensus 65 Ka~EQR--IRRai~~al~nlAsLGl 87 (134)
T PF08664_consen 65 KAIEQR--IRRAIKQALTNLASLGL 87 (134)
T ss_pred HHHHHH--HHHHHHHHHHHHHHhCC
Confidence 345666 48999999988777774
No 117
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=20.58 E-value=1.5e+02 Score=22.03 Aligned_cols=29 Identities=14% Similarity=0.328 Sum_probs=25.4
Q ss_pred cHHHHHHHHHHHhCCCCCcEEEEEEEecC
Q psy8115 140 RIRELTSVVQKRFKFADGAIELYAEKVAT 168 (218)
Q Consensus 140 ~Ik~L~~~LqK~~~~~~kkI~I~I~EV~n 168 (218)
-++++++.+.+.+|.....|.|.+++|..
T Consensus 21 La~~iT~a~~~~lg~~~e~v~V~I~ev~~ 49 (76)
T PRK01271 21 LAADITDVIIRHLNSKDSSISIALQQIQP 49 (76)
T ss_pred HHHHHHHHHHHHhCcCcceEEEEEEEcCH
Confidence 46899999999999988899999999875
No 118
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.15 E-value=5.3e+02 Score=21.72 Aligned_cols=74 Identities=14% Similarity=0.211 Sum_probs=47.5
Q ss_pred HHHHHHHhhhccCCeeeeEE--EecCCeEEEEEEecccceEeccCcccH---HHHHHHHHHHhCCCCCcEEEEEEEecCC
Q psy8115 95 ELDEFLTRELAEDGYSGVEI--RFTPARTEIIIMATRTQNVLGDKGRRI---RELTSVVQKRFKFADGAIELYAEKVATR 169 (218)
Q Consensus 95 ~IRefl~K~l~~AGIs~IEI--~Rt~~~I~IiI~aarPgiVIGrkG~~I---k~L~~~LqK~~~~~~kkI~I~I~EV~nP 169 (218)
+|.+.+..-+...|+.=+++ .+....-.+-|+.-+| +|-.+ .++...+.-.|..+++-..=|..||..|
T Consensus 9 ~v~~liep~~~~lG~ELv~ve~~~~~~~~~lrI~id~~------g~v~lddC~~vSr~is~~LD~edpi~~~Y~LEVSSP 82 (153)
T COG0779 9 KVTELIEPVVESLGFELVDVEFVKEGRDSVLRIYIDKE------GGVTLDDCADVSRAISALLDVEDPIEGAYFLEVSSP 82 (153)
T ss_pred HHHHHHHHhHhhcCcEEEEEEEEEcCCCcEEEEEeCCC------CCCCHHHHHHHHHHHHHHhccCCcccccEEEEeeCC
Confidence 56667776677788765444 4444345555566666 33344 5666777777765555455777899999
Q ss_pred CcCHH
Q psy8115 170 GLCAI 174 (218)
Q Consensus 170 ~l~A~ 174 (218)
+++-.
T Consensus 83 GldRp 87 (153)
T COG0779 83 GLDRP 87 (153)
T ss_pred CCCCC
Confidence 98743
Done!