Query psy3230
Match_columns 151
No_of_seqs 109 out of 819
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 19:42:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3230hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00129 40S ribosomal protein 100.0 5.7E-55 1.2E-59 337.5 18.9 146 4-149 4-149 (149)
2 PRK09607 rps11p 30S ribosomal 100.0 2.6E-52 5.7E-57 317.5 17.7 127 25-151 6-132 (132)
3 COG0100 RpsK Ribosomal protein 100.0 1E-47 2.2E-52 290.8 15.4 119 21-148 11-129 (129)
4 PRK05309 30S ribosomal protein 100.0 1.8E-46 4E-51 284.2 16.3 113 26-148 15-128 (128)
5 PF00411 Ribosomal_S11: Riboso 100.0 2.6E-46 5.6E-51 276.3 13.3 110 29-147 1-110 (110)
6 TIGR03628 arch_S11P archaeal r 100.0 1.8E-45 3.9E-50 274.1 16.4 113 28-140 2-114 (114)
7 TIGR03632 bact_S11 30S ribosom 100.0 6.2E-45 1.4E-49 268.5 15.3 107 29-145 1-108 (108)
8 CHL00041 rps11 ribosomal prote 100.0 7E-42 1.5E-46 255.2 15.6 110 21-140 6-116 (116)
9 PTZ00090 40S ribosomal protein 100.0 1.4E-39 3.1E-44 264.1 15.0 109 30-148 120-233 (233)
10 KOG0407|consensus 100.0 7.7E-38 1.7E-42 232.7 15.2 137 15-151 3-139 (139)
11 KOG0408|consensus 100.0 4.4E-38 9.6E-43 246.6 13.1 115 24-148 75-190 (190)
12 cd00432 Ribosomal_L18_L5e Ribo 97.6 0.0013 2.8E-08 47.6 10.8 92 26-124 9-103 (103)
13 PRK08569 rpl18p 50S ribosomal 97.4 0.006 1.3E-07 49.6 12.6 106 28-148 32-143 (193)
14 PRK05593 rplR 50S ribosomal pr 97.4 0.0031 6.8E-08 47.3 10.2 94 25-125 21-116 (117)
15 TIGR00060 L18_bact ribosomal p 97.2 0.0067 1.4E-07 45.5 10.2 90 27-126 23-114 (114)
16 PF00861 Ribosomal_L18p: Ribos 97.1 0.0087 1.9E-07 44.7 9.8 93 26-126 21-119 (119)
17 CHL00139 rpl18 ribosomal prote 96.9 0.018 3.8E-07 42.8 10.3 94 25-125 12-108 (109)
18 COG0256 RplR Ribosomal protein 96.4 0.056 1.2E-06 41.2 10.1 93 24-126 25-125 (125)
19 PTZ00032 60S ribosomal protein 93.8 0.41 8.8E-06 39.5 7.9 69 28-96 105-187 (211)
20 PTZ00069 60S ribosomal protein 91.3 1.4 3.1E-05 38.1 8.3 61 26-88 46-112 (300)
21 cd05313 NAD_bind_2_Glu_DH NAD( 65.8 14 0.0003 31.1 5.1 62 65-135 12-73 (254)
22 COG3981 Predicted acetyltransf 61.1 56 0.0012 26.3 7.4 61 26-98 79-139 (174)
23 PRK00394 transcription factor; 56.8 46 0.001 26.4 6.3 52 37-92 35-86 (179)
24 cd00652 TBP_TLF TATA box bindi 55.8 41 0.00089 26.5 5.9 52 37-92 36-87 (174)
25 cd04516 TBP_eukaryotes eukaryo 55.4 45 0.00097 26.4 6.0 49 39-91 38-86 (174)
26 cd04518 TBP_archaea archaeal T 53.6 38 0.00082 26.8 5.4 52 37-92 36-87 (174)
27 COG2099 CobK Precorrin-6x redu 49.9 24 0.00051 30.1 3.8 27 69-96 74-100 (257)
28 cd04517 TLF TBP-like factors ( 49.7 59 0.0013 25.7 5.9 53 36-92 35-87 (174)
29 PF13420 Acetyltransf_4: Acety 48.4 98 0.0021 22.1 6.6 45 74-129 94-139 (155)
30 COG0241 HisB Histidinol phosph 48.3 86 0.0019 25.1 6.7 59 80-145 38-108 (181)
31 TIGR03694 exosort_acyl putativ 47.7 60 0.0013 26.6 5.9 57 71-143 154-210 (241)
32 PLN00062 TATA-box-binding prot 46.7 72 0.0016 25.4 6.0 49 38-90 37-85 (179)
33 TIGR03234 OH-pyruv-isom hydrox 46.7 59 0.0013 25.9 5.6 44 79-131 17-60 (254)
34 PF08901 DUF1847: Protein of u 45.9 41 0.00088 26.7 4.3 44 78-130 43-88 (157)
35 PF02601 Exonuc_VII_L: Exonucl 44.0 69 0.0015 26.9 5.8 47 81-128 63-112 (319)
36 PRK13260 2,3-diketo-L-gulonate 43.9 2.2E+02 0.0048 24.8 10.1 88 46-142 62-152 (332)
37 cd01076 NAD_bind_1_Glu_DH NAD( 43.4 55 0.0012 26.7 5.0 59 66-134 6-65 (227)
38 PF08444 Gly_acyl_tr_C: Aralky 43.3 1.2E+02 0.0026 21.8 6.1 70 43-126 2-77 (89)
39 PRK00539 atpC F0F1 ATP synthas 42.8 48 0.001 25.0 4.2 60 2-61 10-69 (133)
40 PLN02477 glutamate dehydrogena 42.1 67 0.0014 28.9 5.7 60 65-134 180-240 (410)
41 PF00044 Gp_dh_N: Glyceraldehy 41.0 34 0.00074 26.4 3.2 29 106-134 6-35 (151)
42 TIGR01216 ATP_synt_epsi ATP sy 40.7 47 0.001 24.7 3.9 60 2-61 8-67 (130)
43 PF00583 Acetyltransf_1: Acety 39.9 95 0.0021 19.5 5.4 42 71-124 41-82 (83)
44 PRK13450 atpC F0F1 ATP synthas 38.4 58 0.0013 24.4 4.1 60 2-61 10-69 (132)
45 PRK14829 undecaprenyl pyrophos 37.7 1.7E+02 0.0036 24.5 7.0 58 72-136 41-114 (243)
46 TIGR01575 rimI ribosomal-prote 36.3 1.4E+02 0.0029 20.2 6.2 48 72-131 71-118 (131)
47 PRK09989 hypothetical protein; 36.2 99 0.0021 24.8 5.4 43 79-130 18-60 (258)
48 PRK14742 thrL thr operon leade 36.1 22 0.00049 20.1 1.1 15 36-50 11-25 (28)
49 PRK01060 endonuclease IV; Prov 35.8 86 0.0019 25.3 5.0 55 79-138 15-75 (281)
50 PF01713 Smr: Smr domain; Int 35.1 1.4E+02 0.003 19.9 6.9 64 71-138 8-74 (83)
51 PF13302 Acetyltransf_3: Acety 34.4 1.4E+02 0.0031 20.6 5.5 46 68-125 96-142 (142)
52 cd05211 NAD_bind_Glu_Leu_Phe_V 34.2 91 0.002 25.2 4.9 38 88-134 19-57 (217)
53 PF05677 DUF818: Chlamydia CHL 34.2 3.2E+02 0.007 24.5 8.5 76 49-135 172-255 (365)
54 PRK00571 atpC F0F1 ATP synthas 34.0 78 0.0017 23.6 4.2 60 2-61 10-69 (135)
55 PTZ00079 NADP-specific glutama 33.7 1.1E+02 0.0023 28.1 5.7 62 65-135 211-272 (454)
56 PF02823 ATP-synt_DE_N: ATP sy 33.7 29 0.00062 23.4 1.6 61 3-63 8-69 (80)
57 PRK14743 thrL thr operon leade 33.3 27 0.00058 19.5 1.1 15 36-50 5-19 (26)
58 COG1570 XseA Exonuclease VII, 33.0 70 0.0015 29.3 4.3 54 73-128 177-230 (440)
59 COG1433 Uncharacterized conser 32.8 1.1E+02 0.0024 23.0 4.7 38 79-129 55-92 (121)
60 KOG3302|consensus 32.6 1.5E+02 0.0033 24.4 5.8 48 40-91 60-107 (200)
61 TIGR02382 wecD_rffC TDP-D-fuco 32.4 1.6E+02 0.0035 22.4 5.8 47 70-128 138-184 (191)
62 PRK14030 glutamate dehydrogena 32.3 1.2E+02 0.0025 27.8 5.7 62 66-137 203-265 (445)
63 COG2840 Uncharacterized protei 32.2 92 0.002 25.2 4.5 43 70-119 105-147 (184)
64 TIGR00829 FRU PTS system, fruc 32.0 95 0.0021 21.6 4.1 26 73-99 12-37 (85)
65 PRK13442 atpC F0F1 ATP synthas 31.3 92 0.002 21.7 3.9 60 2-61 12-71 (89)
66 PHA02773 hypothetical protein; 31.1 75 0.0016 23.4 3.5 75 5-96 9-87 (112)
67 PRK14831 undecaprenyl pyrophos 31.0 2.2E+02 0.0047 23.9 6.7 59 72-137 47-121 (249)
68 PRK07757 acetyltransferase; Pr 30.5 1.1E+02 0.0025 21.8 4.5 55 71-142 81-135 (152)
69 PLN00105 malate/L-lactate dehy 29.9 3.5E+02 0.0077 23.5 8.1 68 68-142 73-142 (330)
70 TIGR03175 AllD ureidoglycolate 29.8 3.9E+02 0.0084 23.5 10.6 67 68-142 84-152 (349)
71 PRK14834 undecaprenyl pyrophos 28.9 2.8E+02 0.0061 23.3 7.1 61 72-137 41-115 (249)
72 COG0334 GdhA Glutamate dehydro 28.9 1.2E+02 0.0026 27.5 5.1 64 65-138 181-245 (411)
73 TIGR03166 alt_F1F0_F1_eps alte 28.7 1.3E+02 0.0028 22.4 4.5 61 2-62 6-67 (122)
74 PRK09491 rimI ribosomal-protei 28.3 2.2E+02 0.0048 20.2 7.9 55 68-134 76-130 (146)
75 PRK13210 putative L-xylulose 5 28.3 1.7E+02 0.0037 23.5 5.6 52 78-130 18-72 (284)
76 TIGR00587 nfo apurinic endonuc 28.2 1.3E+02 0.0028 24.7 4.9 64 79-142 14-78 (274)
77 TIGR00542 hxl6Piso_put hexulos 27.1 1.5E+02 0.0033 24.0 5.1 51 79-130 19-72 (279)
78 PF08903 DUF1846: Domain of un 27.0 98 0.0021 28.6 4.2 45 70-120 113-190 (491)
79 PRK15425 gapA glyceraldehyde-3 27.0 76 0.0017 27.7 3.4 30 106-135 8-38 (331)
80 PRK09414 glutamate dehydrogena 26.8 1.3E+02 0.0029 27.3 5.1 58 66-133 207-265 (445)
81 COG2518 Pcm Protein-L-isoaspar 26.8 2.4E+02 0.0053 23.2 6.2 44 79-126 108-166 (209)
82 TIGR00511 ribulose_e2b2 ribose 26.6 1.9E+02 0.0041 24.6 5.8 49 77-132 127-175 (301)
83 PRK14736 atpC F0F1 ATP synthas 26.2 1E+02 0.0022 23.2 3.7 60 2-61 10-69 (133)
84 PRK13449 atpC F0F1 ATP synthas 25.6 1.5E+02 0.0033 20.6 4.2 63 2-64 10-74 (88)
85 PRK14031 glutamate dehydrogena 25.4 1.8E+02 0.0038 26.6 5.6 60 64-132 201-260 (444)
86 PRK10098 putative dehydrogenas 25.2 4.7E+02 0.01 22.9 10.7 88 46-142 66-158 (350)
87 PRK00286 xseA exodeoxyribonucl 24.9 1.3E+02 0.0029 26.5 4.7 42 85-128 188-229 (438)
88 COG1184 GCD2 Translation initi 24.5 2.6E+02 0.0055 24.4 6.2 50 77-133 131-180 (301)
89 COG4782 Uncharacterized protei 24.1 2.6E+02 0.0057 25.1 6.3 84 23-121 114-211 (377)
90 TIGR00715 precor6x_red precorr 23.9 1.3E+02 0.0027 25.2 4.1 27 69-96 73-99 (256)
91 PF00352 TBP: Transcription fa 23.2 2.5E+02 0.0054 19.1 5.2 35 52-89 52-86 (86)
92 PF03198 Glyco_hydro_72: Gluca 23.1 1.7E+02 0.0037 25.6 4.9 54 70-133 47-100 (314)
93 PF01121 CoaE: Dephospho-CoA k 23.0 1.9E+02 0.0041 22.6 4.8 22 107-128 8-29 (180)
94 COG0057 GapA Glyceraldehyde-3- 22.9 1.1E+02 0.0023 27.2 3.5 29 106-135 7-38 (335)
95 PRK08057 cobalt-precorrin-6x r 22.9 1E+02 0.0022 25.6 3.4 27 69-96 73-99 (248)
96 PRK08335 translation initiatio 22.8 2.6E+02 0.0056 23.8 5.8 50 77-133 121-170 (275)
97 PF01261 AP_endonuc_2: Xylose 22.8 79 0.0017 23.5 2.5 44 83-133 2-50 (213)
98 PRK14841 undecaprenyl pyrophos 22.6 4.3E+02 0.0093 21.9 7.0 59 72-137 30-104 (233)
99 PRK13209 L-xylulose 5-phosphat 22.6 2.2E+02 0.0049 22.9 5.3 51 79-130 24-77 (283)
100 PRK13663 hypothetical protein; 22.6 1.2E+02 0.0025 28.1 3.8 24 70-93 114-137 (493)
101 PRK04266 fibrillarin; Provisio 22.5 3.6E+02 0.0078 21.8 6.5 66 71-138 152-217 (226)
102 PRK13490 chemoreceptor glutami 22.5 2.3E+02 0.0051 22.1 5.2 59 69-128 62-130 (162)
103 TIGR01917 gly_red_sel_B glycin 22.5 3.7E+02 0.0081 24.6 7.0 55 73-136 320-377 (431)
104 PRK10240 undecaprenyl pyrophos 22.3 4.5E+02 0.0097 21.7 7.0 58 73-137 21-94 (229)
105 PF00208 ELFV_dehydrog: Glutam 22.3 69 0.0015 26.5 2.2 61 66-134 6-66 (244)
106 PRK10809 ribosomal-protein-S5- 22.2 3.4E+02 0.0075 20.3 6.8 48 71-130 119-167 (194)
107 PF02571 CbiJ: Precorrin-6x re 22.2 1.1E+02 0.0025 25.3 3.5 27 69-96 74-100 (249)
108 PRK14830 undecaprenyl pyrophos 21.9 4E+02 0.0087 22.3 6.7 61 72-137 49-123 (251)
109 PRK09997 hydroxypyruvate isome 21.8 2.4E+02 0.0052 22.6 5.3 42 79-129 18-59 (258)
110 TIGR02530 flg_new flagellar op 21.7 1E+02 0.0022 22.5 2.8 22 28-49 60-81 (96)
111 PRK10427 putative PTS system f 21.7 1.7E+02 0.0038 21.5 4.1 26 74-100 18-43 (114)
112 TIGR01918 various_sel_PB selen 21.6 3.5E+02 0.0075 24.8 6.6 55 74-137 321-378 (431)
113 PRK10975 TDP-fucosamine acetyl 21.6 3.6E+02 0.0079 20.4 7.1 47 71-129 142-188 (194)
114 PRK08535 translation initiatio 21.3 3E+02 0.0065 23.5 6.0 50 76-132 131-180 (310)
115 cd05801 PGM_like3 This bacteri 21.1 5.1E+02 0.011 23.5 7.8 77 55-136 23-102 (522)
116 PRK14837 undecaprenyl pyrophos 21.0 4.8E+02 0.011 21.7 7.0 62 71-137 32-107 (230)
117 PRK07729 glyceraldehyde-3-phos 20.9 1.1E+02 0.0025 26.8 3.4 30 106-135 8-38 (343)
118 PF15492 Nbas_N: Neuroblastoma 20.9 1.5E+02 0.0032 25.7 3.9 44 16-60 218-261 (282)
119 PRK08334 translation initiatio 20.8 2.4E+02 0.0051 25.1 5.3 50 77-132 179-228 (356)
120 PF03123 CAT_RBD: CAT RNA bind 20.3 95 0.0021 20.4 2.2 26 37-64 8-33 (59)
121 PF02878 PGM_PMM_I: Phosphoglu 20.1 82 0.0018 23.1 2.1 62 68-136 17-80 (137)
No 1
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=100.00 E-value=5.7e-55 Score=337.45 Aligned_cols=146 Identities=79% Similarity=1.211 Sum_probs=140.1
Q ss_pred CCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHH
Q psy3230 4 RKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAE 83 (151)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~ 83 (151)
.+++.+|++.+..++|++.++++..||+||++|+|||||||||++|++++|+|||+++||++++|+||||||.||+++++
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~Gi~hI~as~NNTiItiTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~ 83 (149)
T PTZ00129 4 KATKMSKKQEVATLGPNVAKGELVFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAA 83 (149)
T ss_pred ccccCCcceeeeecCCcccCCceeEEEEEEEcccCCeEEEEEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHH
Confidence 45778899999999999888999999999999999999999999999988888888999998779999999999999999
Q ss_pred HHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCCCC
Q psy3230 84 KCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRRGR 149 (151)
Q Consensus 84 k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~RR~~ 149 (151)
+|.++||+.|+|+|||+||++.+|+|+||+++|++|+++||+|.+|+|+||||||||||||+||.|
T Consensus 84 k~~~~Gi~~v~V~vr~~gg~~~kg~GpGr~~airaL~~~glkI~~I~DvTPiPhNGcRppk~RR~r 149 (149)
T PTZ00129 84 RCKELGINALHIKLRATGGVRTKTPGPGAQAALRALARAGLKIGRIEDVTPIPTDSTRRKGGRRGR 149 (149)
T ss_pred HHHHcCCeEEEEEEEecCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEecCCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999987
No 2
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=100.00 E-value=2.6e-52 Score=317.53 Aligned_cols=127 Identities=65% Similarity=1.060 Sum_probs=121.5
Q ss_pred ceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCc
Q psy3230 25 EDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNR 104 (151)
Q Consensus 25 ~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~ 104 (151)
+.+.||+||++|+|||||||||.+||.+++|+|||+.+|++++|+||||||.||++++++|+++||+.|+|+|+|.||++
T Consensus 6 ~~~~gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~ 85 (132)
T PRK09607 6 KEKWGIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNG 85 (132)
T ss_pred CceeeEEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCC
Confidence 35789999999999999999999998668999999877777889999999999999999999999999999999999999
Q ss_pred ccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCCCCCC
Q psy3230 105 TKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRRGRRL 151 (151)
Q Consensus 105 ~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~RR~~~~ 151 (151)
.+-+|+||+++|++|+++||+|.+|+|+||+|||||||||+||+|||
T Consensus 86 ~~~~G~Gr~~airal~~~glkI~~I~DvTpiPhNGCRp~K~RR~r~~ 132 (132)
T PRK09607 86 QKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTRPPGGRRGRRV 132 (132)
T ss_pred CcCCCCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCCCCCCCCCCCCC
Confidence 99999999999999999999999999999999999999999999997
No 3
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-47 Score=290.76 Aligned_cols=119 Identities=50% Similarity=0.735 Sum_probs=112.4
Q ss_pred eeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEec
Q psy3230 21 VKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRAT 100 (151)
Q Consensus 21 ~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~ 100 (151)
..+..+..|++||++|+||||||+||++||+++|.|||++|||+++ |+||||||.||+.+++.++++|++.|||+|
T Consensus 11 ~~~~~i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~r-k~tpyAA~~aa~~aa~~a~e~Gi~~v~v~v--- 86 (129)
T COG0100 11 KVKKNIADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSR-KSTPYAAQLAAEDAAKKAKEHGIKSVEVKV--- 86 (129)
T ss_pred eeccccccceEEEEcccCCcEEEecCCCCCEEEEEecCCceEcCCC-CCCHHHHHHHHHHHHHHHHHhCccEEEEEE---
Confidence 3444488999999999999999999999999888888889999987 999999999999999999999999999999
Q ss_pred CCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCCC
Q psy3230 101 GGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRRG 148 (151)
Q Consensus 101 ~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~RR~ 148 (151)
+|||+||++++++|+.+|++|.+|+|+||||||||||||+||+
T Consensus 87 -----kgpG~GreaAiraL~~ag~~i~~I~DvTPiphnG~Rppk~RR~ 129 (129)
T COG0100 87 -----KGPGPGREAAIRALAAAGLKITRIEDVTPIPHNGCRPPKRRRV 129 (129)
T ss_pred -----ECCCCcHHHHHHHHHHccceEEEEEEcCCCCCCCCCCCCCCCC
Confidence 7999999999999999999999999999999999999999985
No 4
>PRK05309 30S ribosomal protein S11; Validated
Probab=100.00 E-value=1.8e-46 Score=284.22 Aligned_cols=113 Identities=40% Similarity=0.634 Sum_probs=105.7
Q ss_pred eeeeEEEEEccCCCeEEEEEcCCCCEEEEEeccc-ceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCc
Q psy3230 26 DVFGVAHIFASFNDTFVHVTDLSGRETIARITGG-MKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNR 104 (151)
Q Consensus 26 ~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg-~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~ 104 (151)
+..|++||++|+|||||||||++|+++ +|+|+| +||++. +|+||||||++++.++++|+++||+.|+|++
T Consensus 15 ~~~gi~hI~~t~NNTiitlTd~~G~~~-~~~S~G~~gfKg~-rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~i------- 85 (128)
T PRK05309 15 IPSGVAHIHATFNNTIVTITDRQGNVI-SWASAGGLGFKGS-RKSTPYAAQVAAEDAAKKAKEHGMKTVEVFV------- 85 (128)
T ss_pred cceeEEEEEccCCCEEEEEEcCCCCEE-EEEecCccEeCCC-ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEE-------
Confidence 778999999999999999999999985 555555 688875 5999999999999999999999999999999
Q ss_pred ccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCCC
Q psy3230 105 TKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRRG 148 (151)
Q Consensus 105 ~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~RR~ 148 (151)
+|+|+||+++|++|+.+|++|.+|+|+||+|||||||||+||+
T Consensus 86 -kG~G~Gr~~air~L~~~glkI~~I~D~TpiphNGcR~~K~RRv 128 (128)
T PRK05309 86 -KGPGSGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKRRRV 128 (128)
T ss_pred -ECCCCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCcCcCCCCCC
Confidence 7999999999999999999999999999999999999999985
No 5
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 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 S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=100.00 E-value=2.6e-46 Score=276.27 Aligned_cols=110 Identities=45% Similarity=0.712 Sum_probs=101.0
Q ss_pred eEEEEEccCCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCC
Q psy3230 29 GVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTP 108 (151)
Q Consensus 29 gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~ 108 (151)
||+||++|+||||+||||.+|+++.|+|+|++|||+++ |+|+|||+++++.++++|+++||+.|+|+| +|+
T Consensus 1 giihI~~s~NNt~vtlTd~~G~~~~~~S~G~~gfK~~r-k~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i--------kG~ 71 (110)
T PF00411_consen 1 GIIHIKSSFNNTIVTLTDLKGNVLFWSSAGSLGFKGAR-KSTPYAAQQAAEKIAKKAKELGIKTVRVKI--------KGF 71 (110)
T ss_dssp EEEEEEEESSEEEEEEEETTSEEEEEEETTTSSTTTTC-GSSHHHHHHHHHHHHHHHHCTTEEEEEEEE--------ESS
T ss_pred CEEEEEecCCCEEEEEECCCCCEEEEEecccccccccc-ccCHHHHHHHHHHHHHHHHHcCCeEEEEEE--------cCC
Confidence 79999999999999999999999776666668999876 999999999999999999999999999999 799
Q ss_pred CCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCC
Q psy3230 109 GPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRR 147 (151)
Q Consensus 109 G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~RR 147 (151)
|+||+++|++|+++|++|.+|+|+||+|||||||||+||
T Consensus 72 g~gr~~~lk~l~~~gl~I~~I~D~T~iphnGcR~kK~RR 110 (110)
T PF00411_consen 72 GPGREAALKALKKSGLKIVSITDVTPIPHNGCRPKKKRR 110 (110)
T ss_dssp STTHHHHHHHHHHTTSEEEEEEEETT--SSSS--TTTTT
T ss_pred CccHHHHHHHHHhcCCEEEEEEeecCCCCCCCCCCCCCC
Confidence 999999999999999999999999999999999999998
No 6
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=100.00 E-value=1.8e-45 Score=274.09 Aligned_cols=113 Identities=67% Similarity=1.059 Sum_probs=109.4
Q ss_pred eeEEEEEccCCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccC
Q psy3230 28 FGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKT 107 (151)
Q Consensus 28 ~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG 107 (151)
.|++||++|+|||||||||.+|+++++|+|+|+.+|++++|+||||||.|+++++++|+++||+.|+|+++|.||++.|.
T Consensus 2 ~gi~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~~ 81 (114)
T TIGR03628 2 WGIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKS 81 (114)
T ss_pred cEEEEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCCC
Confidence 69999999999999999999998778999999877777889999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHhCCCeEEEEEecCCCCCCCC
Q psy3230 108 PGPGAQSALRALARSNMKIGRIEDVTPIPSDST 140 (151)
Q Consensus 108 ~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGC 140 (151)
+|+||+++||+|+++||+|.+|+|+||+|||||
T Consensus 82 ~G~Gr~~air~l~~~glkI~~I~DvTpiPhNGC 114 (114)
T TIGR03628 82 PGPGAQAAIRALARAGLRIGRIEDVTPIPHDGT 114 (114)
T ss_pred CCCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCC
Confidence 999999999999999999999999999999999
No 7
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=100.00 E-value=6.2e-45 Score=268.50 Aligned_cols=107 Identities=41% Similarity=0.695 Sum_probs=99.8
Q ss_pred eEEEEEccCCCeEEEEEcCCCCEEEEEeccc-ceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccC
Q psy3230 29 GVAHIFASFNDTFVHVTDLSGRETIARITGG-MKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKT 107 (151)
Q Consensus 29 gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg-~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG 107 (151)
|++||++|+||||||+||++|+++ +|+|+| +||++. +|+|+||||.++++++++++++||+.|+|++ +|
T Consensus 1 gi~hI~~s~NNT~itlTd~~g~~~-~~~S~G~~gfkg~-rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~--------kG 70 (108)
T TIGR03632 1 GVAHIHATFNNTIVTITDPQGNVL-SWASAGAVGFKGS-KKSTPYAAQLAAEDAAKKAKEFGMKTVDVYV--------KG 70 (108)
T ss_pred CEEEEEccCCCEEEEEEcCCCCEE-EEEecCceeeCCC-ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEE--------EC
Confidence 689999999999999999999985 455555 688876 5999999999999999999999999999999 79
Q ss_pred CCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCC
Q psy3230 108 PGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGG 145 (151)
Q Consensus 108 ~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~ 145 (151)
+|+||+++|++|+.+|++|.+|+|+||+|||||||||+
T Consensus 71 ~G~gr~~~ir~l~~~glkI~~I~D~T~iphNGcR~~K~ 108 (108)
T TIGR03632 71 PGAGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKR 108 (108)
T ss_pred CCCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCcCCCCC
Confidence 99999999999999999999999999999999999984
No 8
>CHL00041 rps11 ribosomal protein S11
Probab=100.00 E-value=7e-42 Score=255.22 Aligned_cols=110 Identities=36% Similarity=0.560 Sum_probs=100.8
Q ss_pred eeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEeccc-ceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEe
Q psy3230 21 VKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGG-MKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRA 99 (151)
Q Consensus 21 ~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg-~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~ 99 (151)
+..+....|++||++|+|||||||||++||++ +|+|+| +||++. +|+||||||+++++++++|+++||+.|+|++
T Consensus 6 ~~~~~~~~gi~hI~~t~NNTiiTlTd~~G~~l-~~~S~G~~gfKg~-rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~i-- 81 (116)
T CHL00041 6 KSKRKIPKGVIHIQASFNNTIVTVTDVRGRVI-SWSSAGACGFKGA-RKGTPFAAQTAAENAIRTVIDQGMKRAEVMI-- 81 (116)
T ss_pred cccccceeEEEEEEcccCCEEEEEEcCCCCEE-EEEecCceeeCCC-ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEE--
Confidence 33445889999999999999999999999985 555555 688886 5999999999999999999999999999999
Q ss_pred cCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCC
Q psy3230 100 TGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDST 140 (151)
Q Consensus 100 ~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGC 140 (151)
+|+|+||+++|++|+++|++|.+|+|+||+|||||
T Consensus 82 ------kG~G~Gr~~~ir~l~~~glkI~~I~D~TpiphNGC 116 (116)
T CHL00041 82 ------KGPGLGRDTALRAIRRSGLKLSSIRDVTPMPHNGC 116 (116)
T ss_pred ------ECCCCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCC
Confidence 79999999999999999999999999999999999
No 9
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=1.4e-39 Score=264.12 Aligned_cols=109 Identities=22% Similarity=0.325 Sum_probs=99.9
Q ss_pred EEEEEccCCCeEEEEEcCCCCE-EEEEeccc-ceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccC
Q psy3230 30 VAHIFASFNDTFVHVTDLSGRE-TIARITGG-MKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKT 107 (151)
Q Consensus 30 i~hI~~t~NNTiitlTD~~G~~-~~~~sSgg-~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG 107 (151)
.+-|++|+|||||||||..||+ +++|+|+| +|||+. +|+||||||.|+++++++|+++||+.|+|.| +|
T Consensus 120 ~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGs-KKsTpfAAQ~aae~aakka~~~GIk~V~V~v--------KG 190 (233)
T PTZ00090 120 MLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKK-LQQSERCAYRIGENIAKKCRRLGIFAVDIKF--------RR 190 (233)
T ss_pred EEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccC-ccCCHHHHHHHHHHHHHHHHHcCCeEEEEEE--------eC
Confidence 4678999999999999999997 46777776 688875 5999999999999999999999999999999 78
Q ss_pred CCCChHHHHHHHHhCCCeEEEEEecCCCCC---CCCCCCCCCCC
Q psy3230 108 PGPGAQSALRALARSNMKIGRIEDVTPIPS---DSTRRKGGRRG 148 (151)
Q Consensus 108 ~G~Gr~~~ik~L~~~gl~I~~I~D~Tpiph---NGCRpkK~RR~ 148 (151)
+| +||+||++|+++||+|.+|.|+||+|| |||||||+||+
T Consensus 191 pG-gREtALRaL~~~GLkIt~I~DvTpiPHNG~NGCRPpKKRRV 233 (233)
T PTZ00090 191 IM-RVETVLQAFYANGLQVTQIIHEPRLPKCGLNAVKPRKRRRV 233 (233)
T ss_pred CC-hHHHHHHHHHHCCCEEEEEEECCCCCcCCCCCCCCCCCCCC
Confidence 98 699999999999999999999999999 55999999885
No 10
>KOG0407|consensus
Probab=100.00 E-value=7.7e-38 Score=232.69 Aligned_cols=137 Identities=91% Similarity=1.338 Sum_probs=134.7
Q ss_pred EecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEE
Q psy3230 15 VSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITALH 94 (151)
Q Consensus 15 ~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~ 94 (151)
..|+||.++++.++|+.||++|||+||+++||..|..++...+|||..|..+..++||||++||++++.+|+++||+.+|
T Consensus 3 ~~lg~q~~e~~~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi~alh 82 (139)
T KOG0407|consen 3 VNLGPQVREGEQVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGITALH 82 (139)
T ss_pred ccccchhcccceeeeEEEEEeecccceEEEeccCCceEEEEecCCeEEecccccCChHHHHHHHHHHHHHHHhcCeeEEE
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCCCCCC
Q psy3230 95 IKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRRGRRL 151 (151)
Q Consensus 95 V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~RR~~~~ 151 (151)
|++|++||++.+-+|||.+++|++|.++|++|.+|+|+||||.+..|.|..||.||+
T Consensus 83 ~klratgg~ktktpgpgaqsalralar~gmrigriedvtpip~d~trrkggrrgrrl 139 (139)
T KOG0407|consen 83 IKLRATGGTKTKTPGPGAQSALRALARSGMRIGRIEDVTPIPSDSTRRKGGRRGRRL 139 (139)
T ss_pred EEEEecCCcccCCCCccHHHHHHHHHHhcceeeeecccccCCccchhhccCcccccC
Confidence 999999999999999999999999999999999999999999999999999999996
No 11
>KOG0408|consensus
Probab=100.00 E-value=4.4e-38 Score=246.58 Aligned_cols=115 Identities=31% Similarity=0.462 Sum_probs=107.0
Q ss_pred cceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccc-eeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCC
Q psy3230 24 GEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGM-KVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGG 102 (151)
Q Consensus 24 ~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~-g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g 102 (151)
...-.+|+||.+|+|||+||+||.+|.+ ++|+|||. ||++. ||+|++|||.++..+++++.++|++.|+|.+
T Consensus 75 ~f~eiPi~hIraS~NNTivtVtd~kg~v-i~~~ScgteGFrnt-rkgT~iAaQtaavaa~~r~v~~G~~~vrV~V----- 147 (190)
T KOG0408|consen 75 NFREIPIIHIRASFNNTIVTVTDVKGEV-ISWSSCGTEGFRNT-RKGTPIAAQTAAVAAIRRAVDQGMQTVRVRV----- 147 (190)
T ss_pred cccccceEEEEecCCCeEEEEEccCCcE-EEEeeccccccccc-ccCCchhHHHHHHHHHHHHHHhcceEEEEEE-----
Confidence 3355789999999999999999999986 67888885 88876 5999999999999999999999999999999
Q ss_pred CcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCCC
Q psy3230 103 NRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRRG 148 (151)
Q Consensus 103 ~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~RR~ 148 (151)
||+||||.+++++|...||.|+||+|.||+|||||||+|.||.
T Consensus 148 ---kGlGpGRmsa~kgl~m~Gl~vvsItD~Tp~~~ng~RPrK~Rrl 190 (190)
T KOG0408|consen 148 ---KGLGPGRMSALKGLRMGGLLVVSITDNTPMPHNGCRPRKKRRL 190 (190)
T ss_pred ---ecCCccHHHHHhhhhhcceEEEEeecCCcCCCCCCCccccccC
Confidence 7999999999999999999999999999999999999999984
No 12
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=97.64 E-value=0.0013 Score=47.62 Aligned_cols=92 Identities=17% Similarity=0.202 Sum_probs=64.1
Q ss_pred eeeeEEEEEccCCCeEEEEEcCCCCEEEEEecc-cceeecc-CCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCC
Q psy3230 26 DVFGVAHIFASFNDTFVHVTDLSGRETIARITG-GMKVKAD-RDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGN 103 (151)
Q Consensus 26 ~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSg-g~g~k~~-~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~ 103 (151)
...+.+.|+.|.+|++..+.|..+..+++..|. ...+++. .......||+.+++.++++|.+.|+..+.+-. +|.
T Consensus 9 ~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D~---~~~ 85 (103)
T cd00432 9 QERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDR---GGY 85 (103)
T ss_pred CCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeC---CCc
Confidence 356889999999999999999985444444444 3444432 12456678899999999999999999987775 122
Q ss_pred cccCCCCChH-HHHHHHHhCCC
Q psy3230 104 RTKTPGPGAQ-SALRALARSNM 124 (151)
Q Consensus 104 ~~kG~G~Gr~-~~ik~L~~~gl 124 (151)
+. -||- +++.++...||
T Consensus 86 ~~----~grv~a~~~~~r~~Gl 103 (103)
T cd00432 86 RY----HGRVKALAKGAREGGL 103 (103)
T ss_pred cc----ccHHHHHHHHHHHcCC
Confidence 21 2343 46677777664
No 13
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=97.39 E-value=0.006 Score=49.58 Aligned_cols=106 Identities=16% Similarity=0.184 Sum_probs=74.3
Q ss_pred eeEEEEEccCCCeEEEEE--cCCCCEEEEEecc-cceeec--cCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCC
Q psy3230 28 FGVAHIFASFNDTFVHVT--DLSGRETIARITG-GMKVKA--DRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGG 102 (151)
Q Consensus 28 ~gi~hI~~t~NNTiitlT--D~~G~~~~~~sSg-g~g~k~--~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g 102 (151)
.+.+.|+.|.+|+++.+. |..|..+++.+|. ....++ +. .+..-||+.++..++++|.+.|++.+.+-. ||
T Consensus 32 kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~~-~~N~~AAy~vG~llA~ral~kGi~~vvfDr---Gg 107 (193)
T PRK08569 32 KPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKGD-TGNTPAAYLTGLLAGKKALKAGVEEAVLDI---GL 107 (193)
T ss_pred CCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccCC-CCCHHHHHHHHHHHHHHHHHCCCCEEEEec---CC
Confidence 377888999999999999 7777766655554 333322 12 344568889999999999999999877665 22
Q ss_pred CcccCCCCCh-HHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCCC
Q psy3230 103 NRTKTPGPGA-QSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRRG 148 (151)
Q Consensus 103 ~~~kG~G~Gr-~~~ik~L~~~gl~I~~I~D~TpiphNGCRpkK~RR~ 148 (151)
.+..- | || .+++++....||+ +||+-.|.|---|.
T Consensus 108 ~~yh~-g-GRV~A~akgArd~GL~---------fPh~~~~~p~~~ri 143 (193)
T PRK08569 108 HRPTK-G-SRVFAALKGAIDAGLE---------IPHGEEVLPDEDRI 143 (193)
T ss_pred ccccC-C-ccHHHHHHHHHHcCCc---------CCCCCCcCCCcccc
Confidence 22220 1 34 4577888889987 59998888765554
No 14
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=97.37 E-value=0.0031 Score=47.30 Aligned_cols=94 Identities=21% Similarity=0.224 Sum_probs=65.3
Q ss_pred ceeeeEEEEEccCCCeEEEEEcCCCCEEEEEeccc-ceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCC
Q psy3230 25 EDVFGVAHIFASFNDTFVHVTDLSGRETIARITGG-MKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGN 103 (151)
Q Consensus 25 ~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg-~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~ 103 (151)
....+.+.|+.|.+++.+.|.|..+..+++.+|.- ..++.+-+...--||+.+++.++++|.+.||..+..-- +|.
T Consensus 21 ~~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~~~~n~~aa~~vG~~la~ra~~~gi~~vvfDr---g~~ 97 (117)
T PRK05593 21 TAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGLKGGNKEAAKKVGKLIAERAKAKGIKQVVFDR---GGY 97 (117)
T ss_pred CCCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhccccCCCHHHHHHHHHHHHHHHHHCCCCEEEEcC---CCC
Confidence 34567899999999999999998888665555543 33333222455678889999999999999999965442 222
Q ss_pred cccCCCCCh-HHHHHHHHhCCCe
Q psy3230 104 RTKTPGPGA-QSALRALARSNMK 125 (151)
Q Consensus 104 ~~kG~G~Gr-~~~ik~L~~~gl~ 125 (151)
... || .+++.++...||+
T Consensus 98 ~yh----GrV~a~a~~are~Gl~ 116 (117)
T PRK05593 98 KYH----GRVKALADAAREAGLK 116 (117)
T ss_pred ccc----HHHHHHHHHHHHhCCC
Confidence 221 23 3466777778876
No 15
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=97.20 E-value=0.0067 Score=45.47 Aligned_cols=90 Identities=23% Similarity=0.214 Sum_probs=64.1
Q ss_pred eeeEEEEEccCCCeEEEEEcCCCCEEEEEeccc-ceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcc
Q psy3230 27 VFGVAHIFASFNDTFVHVTDLSGRETIARITGG-MKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRT 105 (151)
Q Consensus 27 ~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg-~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~ 105 (151)
..+.+.|+.|.+++.+.+.|..+..+++.+|.- ..+. ..+.--||..+++.++++|.+.|++.|..-- +|...
T Consensus 23 ~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~---~~~n~~aA~~vG~~la~ra~~~gi~~vvfDr---gg~~Y 96 (114)
T TIGR00060 23 NRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK---YTGNKDAAKKVGKLVAERLKEKGIKDVVFDR---GGYKY 96 (114)
T ss_pred CCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc---CCCCHHHHHHHHHHHHHHHHHCCCCEEEEeC---CCCcc
Confidence 467899999999999999999887766665542 3443 2445678889999999999999999985542 23322
Q ss_pred cCCCCChHH-HHHHHHhCCCeE
Q psy3230 106 KTPGPGAQS-ALRALARSNMKI 126 (151)
Q Consensus 106 kG~G~Gr~~-~ik~L~~~gl~I 126 (151)
. ||-. +..++...||++
T Consensus 97 h----Grv~A~a~~aRe~Gl~F 114 (114)
T TIGR00060 97 H----GRVAALAEAAREAGLNF 114 (114)
T ss_pred h----HHHHHHHHHHHHhCCCC
Confidence 2 3433 556666778763
No 16
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 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 [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=97.06 E-value=0.0087 Score=44.66 Aligned_cols=93 Identities=15% Similarity=0.108 Sum_probs=63.8
Q ss_pred eeeeEEEEEccCCCeEEEEEcCCCCEEEEEec-ccceeecc---CCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecC
Q psy3230 26 DVFGVAHIFASFNDTFVHVTDLSGRETIARIT-GGMKVKAD---RDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATG 101 (151)
Q Consensus 26 ~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sS-gg~g~k~~---~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~ 101 (151)
...+.+.|+.|..++.+.|.|.....++...| -...+++. ......-||+.+++.+++.|.+.|+..|.+-.
T Consensus 21 ~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~lla~ra~~~gi~~v~fdr---- 96 (119)
T PF00861_consen 21 AERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGELLAKRALEKGIAKVVFDR---- 96 (119)
T ss_dssp TSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHHHHHHHHHTTSSEEEECT----
T ss_pred CCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHHHHHHHHHcCCcEEEEcC----
Confidence 44588899999999999998887544433333 34344431 11335668899999999999999998777664
Q ss_pred CCcccCCCC-Ch-HHHHHHHHhCCCeE
Q psy3230 102 GNRTKTPGP-GA-QSALRALARSNMKI 126 (151)
Q Consensus 102 g~~~kG~G~-Gr-~~~ik~L~~~gl~I 126 (151)
.|+-. || .+++.++...||+|
T Consensus 97 ----~~~~y~grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 97 ----GGYKYHGRVKALADGAREGGLEF 119 (119)
T ss_dssp ----STSSSSSHHHHHHHHHHHTTCB-
T ss_pred ----CCCcccHHHHHHHHHHHHcCCCC
Confidence 33332 34 34678888889875
No 17
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=96.94 E-value=0.018 Score=42.78 Aligned_cols=94 Identities=21% Similarity=0.247 Sum_probs=61.5
Q ss_pred ceeeeEEEEEccCCCeEEEEEcC-CCCEEEEEecccceeecc-CCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCC
Q psy3230 25 EDVFGVAHIFASFNDTFVHVTDL-SGRETIARITGGMKVKAD-RDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGG 102 (151)
Q Consensus 25 ~~~~gi~hI~~t~NNTiitlTD~-~G~~~~~~sSgg~g~k~~-~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g 102 (151)
....+.+.|+.|.+++.+.+.|. +|.++.+.||-...+++. .....--||+.+++.++++|.+.||..|..-- +|
T Consensus 12 ~~~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~~vvfDr---gg 88 (109)
T CHL00139 12 TAERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKVVFDR---GG 88 (109)
T ss_pred CCCCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEcC---CC
Confidence 34457899999999999988864 566654433333333321 11345568889999999999999999976552 22
Q ss_pred CcccCCCCCh-HHHHHHHHhCCCe
Q psy3230 103 NRTKTPGPGA-QSALRALARSNMK 125 (151)
Q Consensus 103 ~~~kG~G~Gr-~~~ik~L~~~gl~ 125 (151)
.... || .++..++...||+
T Consensus 89 ~~yh----GrV~a~a~~are~GL~ 108 (109)
T CHL00139 89 KLYH----GRIKALAEAAREAGLQ 108 (109)
T ss_pred Cccc----hHHHHHHHHHHHhCCC
Confidence 2211 33 3466677777876
No 18
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=96.42 E-value=0.056 Score=41.21 Aligned_cols=93 Identities=15% Similarity=0.090 Sum_probs=64.2
Q ss_pred cceeeeEEEEEccCCCeEEEEEcCCCCEEEEEeccc-ce-----eeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEE
Q psy3230 24 GEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGG-MK-----VKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKL 97 (151)
Q Consensus 24 ~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg-~g-----~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~v 97 (151)
+....+.+-|+-|.+|+++.+.|...+.++..+|.= .. .+++ .+.-.||..+++.+++++.+.|++.+.+=.
T Consensus 25 g~~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~--~~N~~aA~~vG~lia~ra~~kgi~~vVfdr 102 (125)
T COG0256 25 GTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGG--GGNTEAAYLVGKLIAERALAKGIEEVVFDR 102 (125)
T ss_pred cCCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCC--CCCHHHHHHHHHHHHHHHHHcCCcEEEEcC
Confidence 445567788888999999999999887766555532 11 2221 234567889999999999999999988544
Q ss_pred EecCCCcccCCCC-ChHH-HHHHHHhCCCeE
Q psy3230 98 RATGGNRTKTPGP-GAQS-ALRALARSNMKI 126 (151)
Q Consensus 98 r~~~g~~~kG~G~-Gr~~-~ik~L~~~gl~I 126 (151)
.|+=. ||-. +.++....||++
T Consensus 103 --------~g~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 103 --------GGYKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred --------CCCCcchHHHHHHHHHHHcCcCC
Confidence 34433 3433 455666678764
No 19
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=93.78 E-value=0.41 Score=39.46 Aligned_cols=69 Identities=12% Similarity=0.040 Sum_probs=50.6
Q ss_pred eeEEEEEccCCCeEEEEEcCCCCEEEEEecc-cceeecc-------------CCCCCHHHHHHHHHHHHHHHHHcCceEE
Q psy3230 28 FGVAHIFASFNDTFVHVTDLSGRETIARITG-GMKVKAD-------------RDEASPYAAMLAAQDVAEKCKTLGITAL 93 (151)
Q Consensus 28 ~gi~hI~~t~NNTiitlTD~~G~~~~~~sSg-g~g~k~~-------------~rK~t~~Aa~~aa~~~~~k~~~~gi~~v 93 (151)
.+.+-|+-|.+++.+++.|.....+++.+|. .-.+++. ...++-.||..+++.++++|.+.||+.|
T Consensus 105 rPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI~kV 184 (211)
T PTZ00032 105 RPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGISKV 184 (211)
T ss_pred cceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCCCEE
Confidence 4788899999999999998865454555543 2233221 1245678999999999999999999986
Q ss_pred EEE
Q psy3230 94 HIK 96 (151)
Q Consensus 94 ~V~ 96 (151)
..-
T Consensus 185 vFD 187 (211)
T PTZ00032 185 RFD 187 (211)
T ss_pred EEe
Confidence 654
No 20
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=91.25 E-value=1.4 Score=38.11 Aligned_cols=61 Identities=10% Similarity=0.003 Sum_probs=44.2
Q ss_pred eeeeEEEEEccCCCeEEEEE--cCCCCEEEEEeccc----ceeeccCCCCCHHHHHHHHHHHHHHHHHc
Q psy3230 26 DVFGVAHIFASFNDTFVHVT--DLSGRETIARITGG----MKVKADRDEASPYAAMLAAQDVAEKCKTL 88 (151)
Q Consensus 26 ~~~gi~hI~~t~NNTiitlT--D~~G~~~~~~sSgg----~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~ 88 (151)
.+...+.|..|..|+|+.++ ++.|..+++...+- .|.+.+. .+ .-||+.++.-+++.+...
T Consensus 46 spK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~k~gl-~N-~~AAY~TGlL~arR~L~k 112 (300)
T PTZ00069 46 SPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGIPVGL-TN-YAAAYATGLLLARRLLKK 112 (300)
T ss_pred CCCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcCCCC-cc-HHHHHHHHHHHHHHHHHh
Confidence 34577889999999999887 56688876666553 3777654 33 346788998888887764
No 21
>cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t
Probab=65.82 E-value=14 Score=31.10 Aligned_cols=62 Identities=18% Similarity=0.191 Sum_probs=43.6
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCC
Q psy3230 65 DRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPI 135 (151)
Q Consensus 65 ~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~Tpi 135 (151)
+|...|-|....+.+.+++.. +..++...|.| .|||.-=..+.+.|...|.+|+.|.|.+-.
T Consensus 12 gR~~aTg~Gv~~~~~~~~~~~-~~~l~g~~vaI--------qGfGnVG~~~a~~L~e~GakvvaVsD~~G~ 73 (254)
T cd05313 12 IRPEATGYGLVYFVEEMLKDR-NETLKGKRVAI--------SGSGNVAQYAAEKLLELGAKVVTLSDSKGY 73 (254)
T ss_pred CCCchhHHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEECCCce
Confidence 344667777766666665544 45666788888 588864445557788899999999995543
No 22
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=61.07 E-value=56 Score=26.30 Aligned_cols=61 Identities=21% Similarity=0.379 Sum_probs=39.4
Q ss_pred eeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEE
Q psy3230 26 DVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLR 98 (151)
Q Consensus 26 ~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr 98 (151)
...|+++|.-+.|+-+... -|+. |.+..-.. ++--||-++. ..+.++|+++||+.|-|...
T Consensus 79 ~ivG~i~lRh~Ln~~ll~~---gGHI-------GY~VrPse-R~KGYA~emL-kl~L~~ar~lgi~~Vlvtcd 139 (174)
T COG3981 79 QIVGFINLRHQLNDFLLEE---GGHI-------GYSVRPSE-RRKGYAKEML-KLALEKARELGIKKVLVTCD 139 (174)
T ss_pred cEEEEEEeeeecchHHHhc---CCcc-------cceeChhh-hccCHHHHHH-HHHHHHHHHcCCCeEEEEeC
Confidence 5678888877775543322 3332 22333333 3335877655 77889999999999999993
No 23
>PRK00394 transcription factor; Reviewed
Probab=56.78 E-value=46 Score=26.44 Aligned_cols=52 Identities=19% Similarity=0.168 Sum_probs=39.1
Q ss_pred CCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceE
Q psy3230 37 FNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITA 92 (151)
Q Consensus 37 ~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~ 92 (151)
+.-.++-+.|+.-. ++.|+||-+...+++ +...+..|++++++.++++|+..
T Consensus 35 fpgli~Rl~~Pk~t-~lIf~sGKiv~tGa~---S~~~a~~a~~~~~~~l~~~g~~~ 86 (179)
T PRK00394 35 FPGLVYRLEDPKIA-ALIFRSGKVVCTGAK---SVEDLHEAVKIIIKKLKELGIKV 86 (179)
T ss_pred CceEEEEecCCceE-EEEEcCCcEEEEccC---CHHHHHHHHHHHHHHHHHcCCCc
Confidence 34456777777764 466888888877754 56678889999999999999754
No 24
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=55.76 E-value=41 Score=26.49 Aligned_cols=52 Identities=21% Similarity=0.293 Sum_probs=39.2
Q ss_pred CCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceE
Q psy3230 37 FNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITA 92 (151)
Q Consensus 37 ~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~ 92 (151)
++-.++-+.|++.. ++-|+||-+-..+++ +...+..+++.+++.++++|+..
T Consensus 36 fpgli~R~~~P~~t-~lIf~sGKivitGak---s~~~~~~a~~~~~~~L~~~g~~~ 87 (174)
T cd00652 36 FPGVIMRLREPKTT-ALIFSSGKMVITGAK---SEEDAKLAARKYARILQKLGFPV 87 (174)
T ss_pred cceEEEEcCCCcEE-EEEECCCEEEEEecC---CHHHHHHHHHHHHHHHHHcCCCc
Confidence 45566677777774 456888888777754 56677788899999999999766
No 25
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=55.37 E-value=45 Score=26.42 Aligned_cols=49 Identities=18% Similarity=0.247 Sum_probs=35.6
Q ss_pred CeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCce
Q psy3230 39 DTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGIT 91 (151)
Q Consensus 39 NTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~ 91 (151)
-.++-+.|++-. ++-|+||-+...+++ +...+..|++++++.++++|++
T Consensus 38 gli~Rl~~Pk~t-~lIF~SGKiviTGak---s~e~a~~a~~~i~~~L~~~g~~ 86 (174)
T cd04516 38 AVIMRIREPKTT-ALIFSSGKMVCTGAK---SEDDSKLAARKYARIIQKLGFP 86 (174)
T ss_pred EEEEEeCCCcEE-EEEECCCeEEEEecC---CHHHHHHHHHHHHHHHHHcCCC
Confidence 445556676653 456888888777754 5667778889999999999864
No 26
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=53.58 E-value=38 Score=26.83 Aligned_cols=52 Identities=19% Similarity=0.202 Sum_probs=38.8
Q ss_pred CCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceE
Q psy3230 37 FNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITA 92 (151)
Q Consensus 37 ~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~ 92 (151)
++-.++-+.|++-.. +.++||-+...+++ +...+..|++++++.++++|++.
T Consensus 36 fpgli~Rl~~Pk~t~-lIF~SGKiv~tGak---s~~~a~~a~~~~~~~L~~~g~~~ 87 (174)
T cd04518 36 FPGLVYRLEDPKIAA-LIFRSGKMVCTGAK---SVEDLHRAVKEIIKKLKDYGIKV 87 (174)
T ss_pred CcEEEEEccCCcEEE-EEECCCeEEEEccC---CHHHHHHHHHHHHHHHHhcCCCc
Confidence 444667777777644 56888888777754 56778888999999999999754
No 27
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=49.86 E-value=24 Score=30.09 Aligned_cols=27 Identities=37% Similarity=0.569 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHHHHHHHHHcCceEEEEE
Q psy3230 69 ASPYAAMLAAQDVAEKCKTLGITALHIK 96 (151)
Q Consensus 69 ~t~~Aa~~aa~~~~~k~~~~gi~~v~V~ 96 (151)
+=|||++ +++++++-|++.|+..+...
T Consensus 74 THPyAa~-iS~Na~~aake~gipy~r~e 100 (257)
T COG2099 74 THPYAAR-ISQNAARAAKETGIPYLRLE 100 (257)
T ss_pred CChHHHH-HHHHHHHHHHHhCCcEEEEE
Confidence 4599997 66889999999999998865
No 28
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=49.73 E-value=59 Score=25.67 Aligned_cols=53 Identities=15% Similarity=0.203 Sum_probs=37.9
Q ss_pred cCCCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCceE
Q psy3230 36 SFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITA 92 (151)
Q Consensus 36 t~NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~ 92 (151)
-++-.++-+.|++=. .+.|+||-+...+++ +...+..+++.+++.++++|++.
T Consensus 35 ~fpgli~R~~~Pk~t-~lIF~sGKiviTGak---s~~~~~~a~~~~~~~l~~~g~~~ 87 (174)
T cd04517 35 RYPKVTMRLREPRAT-ASVWSSGKITITGAT---SEEEAKQAARRAARLLQKLGFKV 87 (174)
T ss_pred CCCEEEEEecCCcEE-EEEECCCeEEEEccC---CHHHHHHHHHHHHHHHHHcCCCc
Confidence 344556666776543 456888888778754 56667778899999999998765
No 29
>PF13420 Acetyltransf_4: Acetyltransferase (GNAT) domain; PDB: 3DR8_A 3DR6_A 2AE6_B 2JLM_C 2J8R_A 1YVO_B 2J8M_A 2J8N_A 2BL1_A 3IWG_A ....
Probab=48.43 E-value=98 Score=22.10 Aligned_cols=45 Identities=13% Similarity=0.171 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHH-HHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q psy3230 74 AMLAAQDVAEKC-KTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRI 129 (151)
Q Consensus 74 a~~aa~~~~~k~-~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I 129 (151)
+..+.+.+.+.| .++|+..|.+.+- ..-..+++.+++.|+++...
T Consensus 94 g~~l~~~l~~~af~~~~~~~i~~~v~-----------~~N~~~i~~~~~~GF~~~g~ 139 (155)
T PF13420_consen 94 GRKLLDELIEYAFKELGIHKIYLEVF-----------SSNEKAINFYKKLGFEEEGE 139 (155)
T ss_dssp HHHHHHHHHHHH-HHTT-CEEEEEEE-----------TT-HHHHHHHHHTTEEEEEE
T ss_pred HHHHHHHHHHHhhhccCeEEEEEEEe-----------cCCHHHHHHHHhCCCEEEEE
Confidence 445667788899 9999999999883 33677889899999976544
No 30
>COG0241 HisB Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]
Probab=48.29 E-value=86 Score=25.15 Aligned_cols=59 Identities=20% Similarity=0.187 Sum_probs=37.1
Q ss_pred HHHHHHHHcCceEEEEEEEecCCCcccCCCCChHH----------HHHHHHhCCCeEEEEEecCCCCC--CCCCCCCC
Q psy3230 80 DVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQS----------ALRALARSNMKIGRIEDVTPIPS--DSTRRKGG 145 (151)
Q Consensus 80 ~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~----------~ik~L~~~gl~I~~I~D~Tpiph--NGCRpkK~ 145 (151)
.+..+..+.||+-|.|.-+ .|+|.|-.+ .+..|...|++|..|.=---.|- ..||.||.
T Consensus 38 ~al~~l~~~gy~lVvvTNQ-------sGi~rgyf~~~~f~~~~~~m~~~l~~~gv~id~i~~Cph~p~~~c~cRKP~~ 108 (181)
T COG0241 38 PALLKLQRAGYKLVVVTNQ-------SGIGRGYFTEADFDKLHNKMLKILASQGVKIDGILYCPHHPEDNCDCRKPKP 108 (181)
T ss_pred HHHHHHHhCCCeEEEEECC-------CCccccCccHHHHHHHHHHHHHHHHHcCCccceEEECCCCCCCCCcccCCCh
Confidence 3455667899999998876 677776322 23345566776655554333333 57888874
No 31
>TIGR03694 exosort_acyl putative PEP-CTERM/exosortase system-associated acyltransferase. Members of this protein family are restricted to bacterial species with the PEP-CTERM/exosortase system predicted to act in exopolysaccharide-associated protein targeting. PSI-BLAST and CDD reveal relationships to the acyltransferase family that includes N-acyl-L-homoserine lactone synthetase. Several members of this family may be found in a single genome. These proteins likely contribute to chemical modifications in exopolysaccharide and biofilm structural material production.
Probab=47.65 E-value=60 Score=26.65 Aligned_cols=57 Identities=16% Similarity=0.181 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCC
Q psy3230 71 PYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRK 143 (151)
Q Consensus 71 ~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRpk 143 (151)
++.+......+++.|.+.||+.+.... --...+.|...|+.+..|-+ |..|+|.|.+
T Consensus 154 ~~~~~~L~~~~~~~a~~~Gi~~~~~v~--------------~~~l~r~l~r~G~~~~~lG~--~~~~~G~r~p 210 (241)
T TIGR03694 154 PHIPLGLYLGLIALSSANGITHWYAIM--------------EPRLARLLSRFGIQFRQVGP--PVDYHGLRAP 210 (241)
T ss_pred chHHHHHHHHHHHHHHHCCCcEEEEEe--------------CHHHHHHHHHhCCceEEcCC--CeeECcEecc
Confidence 556666777789999999999998887 23567888899999988875 5567787643
No 32
>PLN00062 TATA-box-binding protein; Provisional
Probab=46.67 E-value=72 Score=25.41 Aligned_cols=49 Identities=18% Similarity=0.255 Sum_probs=35.2
Q ss_pred CCeEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCc
Q psy3230 38 NDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGI 90 (151)
Q Consensus 38 NNTiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi 90 (151)
.-.++-+.|++-. ++.++||-+...+++ +...+..|++++++.++++|+
T Consensus 37 pgli~Rl~~Pk~t-~lIF~SGKiviTGak---s~e~a~~a~~~~~~~L~~lg~ 85 (179)
T PLN00062 37 AAVIMRIREPKTT-ALIFASGKMVCTGAK---SEHDSKLAARKYARIIQKLGF 85 (179)
T ss_pred cEEEEEeCCCcEE-EEEECCCeEEEEecC---CHHHHHHHHHHHHHHHHHcCC
Confidence 3445555666653 456888888777754 556777888999999999997
No 33
>TIGR03234 OH-pyruv-isom hydroxypyruvate isomerase. This enzyme interconverts tartronate semi-aldehyde (TSA, aka 2-hydroxy 3-oxopropionate) and hydroxypyruvate. The E. coli enzyme has been characterized and found to be specific for TSA, contain no cofactors, and have a rather high Km for hydroxypyruvate of 12.5 mM. The gene is ofter found in association with glyoxalate carboligase (which produces TSA), but has been shown to have no effect on growth on glyoxalate when knocked out. This is consistent with the fact that the gene for tartronate semialdehyde reductase (glxR) is also associated and may have primary responsibility for the catabolism of TSA.
Probab=46.66 E-value=59 Score=25.93 Aligned_cols=44 Identities=11% Similarity=0.018 Sum_probs=33.1
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIED 131 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D 131 (151)
+.+++.+.++||..|++.. -.....+.+.+.|...|++|..+..
T Consensus 17 ~e~~~~~~e~G~~~vEl~~---------~~~~~~~~l~~~l~~~gl~v~~~~~ 60 (254)
T TIGR03234 17 LERFAAAAQAGFTGVEYLF---------PYDWDAEALKARLAAAGLEQVLFNL 60 (254)
T ss_pred HHHHHHHHHcCCCEEEecC---------CccCCHHHHHHHHHHcCCeEEEEeC
Confidence 5577888899999999975 1234456666777789999998853
No 34
>PF08901 DUF1847: Protein of unknown function (DUF1847); InterPro: IPR014997 This group of proteins are functionally uncharacterised. They contain 4 N-terminal cysteines that may form a zinc-binding domain.
Probab=45.85 E-value=41 Score=26.69 Aligned_cols=44 Identities=14% Similarity=0.264 Sum_probs=35.6
Q ss_pred HHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHH--HHHHHHhCCCeEEEEE
Q psy3230 78 AQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQS--ALRALARSNMKIGRIE 130 (151)
Q Consensus 78 a~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~--~ik~L~~~gl~I~~I~ 130 (151)
.+.++++|+.+||+.|=|-+ =+|.-+|+ +-+.|...|+.+.|+.
T Consensus 43 veEiieFak~mgykkiGiAf---------CiGL~~EA~~~~~iL~~~gFev~sV~ 88 (157)
T PF08901_consen 43 VEEIIEFAKRMGYKKIGIAF---------CIGLRKEARILAKILEANGFEVYSVC 88 (157)
T ss_pred HHHHHHHHHHcCCCeeeehh---------hHhHHHHHHHHHHHHHHCCCEEEEEE
Confidence 36788999999999999887 56777776 4466778899998874
No 35
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=44.01 E-value=69 Score=26.90 Aligned_cols=47 Identities=21% Similarity=0.236 Sum_probs=33.3
Q ss_pred HHHHHHHcC---ceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q psy3230 81 VAEKCKTLG---ITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGR 128 (151)
Q Consensus 81 ~~~k~~~~g---i~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~ 128 (151)
+++.+.+.+ --.|.|..|| ||+..--+-.+-+.+.+++..+.+.|++
T Consensus 63 al~~~~~~~~~~~~Dviii~RG-GGs~eDL~~FN~e~varai~~~~~Pvis 112 (319)
T PF02601_consen 63 ALRKANEMGQADDFDVIIIIRG-GGSIEDLWAFNDEEVARAIAASPIPVIS 112 (319)
T ss_pred HHHHHHhccccccccEEEEecC-CCChHHhcccChHHHHHHHHhCCCCEEE
Confidence 334444444 2357777776 6776667778999999999999887654
No 36
>PRK13260 2,3-diketo-L-gulonate reductase; Provisional
Probab=43.86 E-value=2.2e+02 Score=24.80 Aligned_cols=88 Identities=10% Similarity=0.008 Sum_probs=58.1
Q ss_pred cCCCCEEEEEecccc-eeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCC
Q psy3230 46 DLSGRETIARITGGM-KVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNM 124 (151)
Q Consensus 46 D~~G~~~~~~sSgg~-g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl 124 (151)
|++.++.+-..++.+ ..-+ ..---++++..+.+.++++|++.|+-.|-|+= ++-+|..-..+.++. +.|+
T Consensus 62 ~~~~~~~v~~~~~a~a~~Dg-~~g~G~~~~~~am~~aiekAr~~Gi~~v~vrn-------s~H~G~~g~y~~~aa-~~G~ 132 (332)
T PRK13260 62 IPDAQPQRVTSLGAIEQWDA-QRAIGNLTAKKMMDRAIELARDHGIGLVALRN-------ANHWMRGGSYGWQAA-EKGY 132 (332)
T ss_pred CCCCCeEEEecCCcEEEEEC-CCCchHHHHHHHHHHHHHHHHHhCEEEEEEcC-------CCchhhHHHHHHHHH-HCCC
Confidence 444444333444444 3333 33556889999999999999999999988874 367888777776655 4566
Q ss_pred eEEEEEecCC--CCCCCCCC
Q psy3230 125 KIGRIEDVTP--IPSDSTRR 142 (151)
Q Consensus 125 ~I~~I~D~Tp--iphNGCRp 142 (151)
-=+..++..| .||+|-+|
T Consensus 133 igi~~tn~~~~vaP~Gg~~~ 152 (332)
T PRK13260 133 IGICWTNSIAVMPPWGAKEC 152 (332)
T ss_pred EEEEEeCCCCeeCCCCCCCC
Confidence 5445555444 57777654
No 37
>cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids
Probab=43.36 E-value=55 Score=26.68 Aligned_cols=59 Identities=22% Similarity=0.379 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCC
Q psy3230 66 RDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGP-GAQSALRALARSNMKIGRIEDVTP 134 (151)
Q Consensus 66 ~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~-Gr~~~ik~L~~~gl~I~~I~D~Tp 134 (151)
+...|-|....+.+.+++... ..+...+|.| .|||. |+..+ +.|...|.+|+.|.|..-
T Consensus 6 ~~~~Tg~Gv~~~~~~~~~~~~-~~l~~~~v~I--------~G~G~VG~~~a-~~L~~~g~~vv~v~D~~g 65 (227)
T cd01076 6 REEATGRGVAYATREALKKLG-IGLAGARVAI--------QGFGNVGSHAA-RFLHEAGAKVVAVSDSDG 65 (227)
T ss_pred CCccchHHHHHHHHHHHHhcC-CCccCCEEEE--------ECCCHHHHHHH-HHHHHCCCEEEEEECCCC
Confidence 335677766666565555432 4567788888 58885 56555 667788999999999853
No 38
>PF08444 Gly_acyl_tr_C: Aralkyl acyl-CoA:amino acid N-acyltransferase, C-terminal region; InterPro: IPR013652 This entry represents mammalian-specific glycine N-acyltransferase (also called aralkyl acyl-CoA:amino acid N-acyltransferase; 2.3.1.13 from EC). Mitochondrial acyltransferases catalyse the transfer of an acyl group from acyl-CoA to the N terminus of glycine to produce N-acylglycine. These enzymes can conjugate a multitude of substrates to form a variety of N-acylglycines. The CoA derivatives of a number of aliphatic and aromatic acids, but not phenylacetyl-CoA or (indol-3-yl)acetyl-CoA, can act as donor [, ].
Probab=43.28 E-value=1.2e+02 Score=21.75 Aligned_cols=70 Identities=11% Similarity=0.069 Sum_probs=43.6
Q ss_pred EEEcCCCCEEEEEe----ccc--ceeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHH
Q psy3230 43 HVTDLSGRETIARI----TGG--MKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSAL 116 (151)
Q Consensus 43 tlTD~~G~~~~~~s----Sgg--~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~i 116 (151)
.|.|++|+++ +|+ +|- +++.=-.=++--++.+ ++...++.+.++||.. -.++ -.-.+...
T Consensus 2 CllgpeG~PV-SW~lmdqtge~rmgyTlPeyR~~G~~~~-v~~~~~~~L~~~g~P~-Y~hv-----------~~~N~~~~ 67 (89)
T PF08444_consen 2 CLLGPEGNPV-SWSLMDQTGEMRMGYTLPEYRGQGLMSQ-VMYHLAQYLHKLGFPF-YGHV-----------DEDNEASQ 67 (89)
T ss_pred cccCCCCCEe-EEEEecccccccccccCHhHhcCCHHHH-HHHHHHHHHHHCCCCe-Eeeh-----------HhccHHHH
Confidence 5789999985 555 443 3443222233346555 5566889999999973 3333 23467788
Q ss_pred HHHHhCCCeE
Q psy3230 117 RALARSNMKI 126 (151)
Q Consensus 117 k~L~~~gl~I 126 (151)
|.+..-|..+
T Consensus 68 r~~~~lg~~~ 77 (89)
T PF08444_consen 68 RLSKSLGFIF 77 (89)
T ss_pred HHHHHCCCee
Confidence 8888777643
No 39
>PRK00539 atpC F0F1 ATP synthase subunit epsilon; Validated
Probab=42.76 E-value=48 Score=25.03 Aligned_cols=60 Identities=13% Similarity=0.079 Sum_probs=46.5
Q ss_pred CCCCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccce
Q psy3230 2 APRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMK 61 (151)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g 61 (151)
.|+...-+.+.+.+.+...-++=.+..+..-+-++...-.+.+...+|+......+||+.
T Consensus 10 TP~~~~~~~~v~~V~l~t~~G~~gIL~~Haplit~L~~G~~~i~~~~~~~~~~~v~gGf~ 69 (133)
T PRK00539 10 SPSGIKLDEKIISAQVKTTEGYAGLNRNRAPLIAAIQSHVCKITFADKTKRSAIIGAGLL 69 (133)
T ss_pred cCCCeEEeceEEEEEEecCccCceecCCCcceEeEecceEEEEEECCCcEEEEEEeeeEE
Confidence 577766667788888888888877888888888888888888987677644467788863
No 40
>PLN02477 glutamate dehydrogenase
Probab=42.11 E-value=67 Score=28.88 Aligned_cols=60 Identities=18% Similarity=0.264 Sum_probs=41.9
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCC
Q psy3230 65 DRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGP-GAQSALRALARSNMKIGRIEDVTP 134 (151)
Q Consensus 65 ~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~-Gr~~~ik~L~~~gl~I~~I~D~Tp 134 (151)
++...|-|....+++.+++. ....++-.+|-| .|||. |+.++ +.|...|.+|+.|.|..-
T Consensus 180 ~r~~aTg~Gv~~~~~~~~~~-~g~~l~g~~VaI--------qGfGnVG~~~A-~~L~e~GakVVaVsD~~G 240 (410)
T PLN02477 180 GREAATGRGVVFATEALLAE-HGKSIAGQTFVI--------QGFGNVGSWAA-QLIHEKGGKIVAVSDITG 240 (410)
T ss_pred CCCccchHHHHHHHHHHHHH-cCCCccCCEEEE--------ECCCHHHHHHH-HHHHHcCCEEEEEECCCC
Confidence 34466777666666655554 223456677888 58886 66655 778889999999999863
No 41
>PF00044 Gp_dh_N: Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; InterPro: IPR020828 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain []. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme []. GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis []. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself. GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins []. This entry represents the N-terminal domain which is a Rossmann NAD(P) binding fold.; GO: 0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 2G82_Q 1CER_R 1ZNQ_Q 3GPD_G 1U8F_R 3DOC_B 2YYY_A 1GPD_G 4GPD_1 2I5P_O ....
Probab=40.98 E-value=34 Score=26.40 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=21.9
Q ss_pred cCCCC-ChHHHHHHHHhCCCeEEEEEecCC
Q psy3230 106 KTPGP-GAQSALRALARSNMKIGRIEDVTP 134 (151)
Q Consensus 106 kG~G~-Gr~~~ik~L~~~gl~I~~I~D~Tp 134 (151)
+|||. ||..+--++.+..++|+-|.|..+
T Consensus 6 NGfGRIGR~v~r~~~~~~~~evvaInd~~~ 35 (151)
T PF00044_consen 6 NGFGRIGRLVLRAALDQPDIEVVAINDPAP 35 (151)
T ss_dssp ESTSHHHHHHHHHHHTSTTEEEEEEEESSS
T ss_pred ECCCcccHHHHHhhcccceEEEEEEecccc
Confidence 78896 666664445567899999999874
No 42
>TIGR01216 ATP_synt_epsi ATP synthase, F1 epsilon subunit (delta in mitochondria). This model describes one of the five types of subunits in the F1 part of F1/F0 ATP synthases. Members of this family are designated epsilon in bacterial and chloroplast systems but designated delta in mitochondria, where the counterpart of the bacterial delta subunit is designated OSCP. In a few cases (Propionigenium modestum, Acetobacterium woodii) scoring above the trusted cutoff and designated here as exceptions, Na+ replaces H+ for translocation.
Probab=40.70 E-value=47 Score=24.65 Aligned_cols=60 Identities=18% Similarity=0.155 Sum_probs=43.0
Q ss_pred CCCCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccce
Q psy3230 2 APRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMK 61 (151)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g 61 (151)
.|+...-..+.+++.+...-++=.+..++.-+-+....-++++.+.+|....+..+||+-
T Consensus 8 tP~~~~~~~~v~~v~~~t~~G~~giL~~H~p~i~~L~~G~v~i~~~~~~~~~~~v~gG~~ 67 (130)
T TIGR01216 8 TPEGEIYSGEVESVILPGSEGELGILPGHAPLITALKPGVVRIRKLGDDWEHIAVSGGFA 67 (130)
T ss_pred cCCceEEeeeEEEEEEECCcCCeeecCCChhhEeEecceEEEEEECCCCEEEEEEcCcEE
Confidence 576665556677777777766665777777777888888888887777665567788863
No 43
>PF00583 Acetyltransf_1: Acetyltransferase (GNAT) family; InterPro: IPR000182 The N-acetyltransferases (NAT) (EC 2.3.1.-) are enzymes that use acetyl coenzyme A (CoA) to transfer an acetyl group to a substrate, a reaction implicated in various functions from bacterial antibiotic resistance to mammalian circadian rhythm and chromatin remodeling. The Gcn5-related N-acetyltransferases (GNAT) catalyze the transfer of the acetyl from the CoA donor to a primary amine of the acceptor. The GNAT proteins share a domain composed of four conserved sequence motifs A-D [, ]. This GNAT domain is named after yeast GCN5 (from General Control Nonrepressed) and related histone acetyltransferases (HATs) like Hat1 and PCAF. HATs acetylate lysine residues of amino terminal histone tails, resulting in transcription activation. Another category of GNAT, the aminoglycoside N-acetyltransferases, confer antibiotic resistance by catalyzing the acetylation of amino groups in aminoglycoside antibiotics []. GNAT proteins can also have anabolic and catabolic functions in both prokaryotes and eukaryotes [, , , , ]. The acetyltransferase/GNAT domain forms a structurally conserved fold of 6 to 7 beta strands (B) and 4 helices (H) in the topology B1-H1-H2-B2-B3-B4-H3-B5-H4-B6, followed by a C-terminal strand which may be from the same monomer or contributed by another [, ]. Motifs D (B2-B3), A (B4-H3) and B (B5-H4) are collectively called the HAT core [, , ], while the N-terminal motif C (B1-H1) is less conserved. Some proteins known to contain a GNAT domain: Yeast GCN5 and Hat1, which are histone acetyltransferases (EC 2.3.1.48). Human PCAF, a histone acetyltransferase. Mammalian serotonin N-acetyltransferase (SNAT) or arylalkylamine NAT (AANAT), which acetylates serotonin into a circadian neurohormone that may participate in light-dark rhythms, and human mood and behavior. Mammalian glucosamine 6-phosphate N-acetyltransferase (GNA1) (EC 2.3.1.4). Escherichia coli rimI and rimJ, which acetylate the N-terminal alanine of ribosomal proteins S18 and S5, respectively (EC 2.3.1.128). Mycobacterium tuberculosis aminoglycoside 2'-N-acetyltransferase (aac), which acetylates the 2' hydroxyl or amino group of a broad spectrum of aminoglycoside antibiotics. Bacillus subtilis bltD and paiA, which acetylate spermine and spermidine. This entry represents the entire GNAT domain.; GO: 0008080 N-acetyltransferase activity, 0008152 metabolic process; PDB: 3T9Y_A 2R7H_B 2OZH_A 1Y9W_B 1VKC_B 2OH1_C 3R9E_B 3R9G_B 3R9F_A 3R96_A ....
Probab=39.90 E-value=95 Score=19.49 Aligned_cols=42 Identities=17% Similarity=0.231 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCC
Q psy3230 71 PYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNM 124 (151)
Q Consensus 71 ~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl 124 (151)
-++.. ..+.+.+.+++.|+..|.+.+ .+....+++.+.+.|+
T Consensus 41 Gig~~-L~~~~~~~~~~~g~~~i~~~~-----------~~~n~~~~~~~~k~Gf 82 (83)
T PF00583_consen 41 GIGSK-LLQAAEEWARKRGIKRIYLDV-----------SPDNPAARRFYEKLGF 82 (83)
T ss_dssp SHHHH-HHHHHHHHHHHTTESEEEEEE-----------ETTGHHHHHHHHHTTE
T ss_pred CCchh-hhhhhhhhHHhcCccEEEEEE-----------eCCCHHHHHHHHHcCC
Confidence 35444 456688888889999999998 4556677787777765
No 44
>PRK13450 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=38.35 E-value=58 Score=24.38 Aligned_cols=60 Identities=13% Similarity=0.045 Sum_probs=44.7
Q ss_pred CCCCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccce
Q psy3230 2 APRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMK 61 (151)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g 61 (151)
.|+...-..+.+.+.+...-++=.+..++..+-++...-.+++.+.+|.......+||+.
T Consensus 10 tP~~~~~~~~v~~V~~p~~~G~~GILp~H~p~it~L~~G~l~i~~~~~~~~~~~v~gGf~ 69 (132)
T PRK13450 10 TPEKNFYIGEVKEVITEGLDGDIAILPNHVPLITYLKPTITKIIDENGEKKKIFTSSGVL 69 (132)
T ss_pred cCCceEEeceEEEEEEECCccCceecCCCcccEeEEccEEEEEEECCCcEEEEEEcCeEE
Confidence 466554446666677777776666888888888999999999998888755567788864
No 45
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=37.68 E-value=1.7e+02 Score=24.46 Aligned_cols=58 Identities=10% Similarity=-0.022 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHH--------H--------HHHHhCCCeEEEEEecCCC
Q psy3230 72 YAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSA--------L--------RALARSNMKIGRIEDVTPI 135 (151)
Q Consensus 72 ~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~--------i--------k~L~~~gl~I~~I~D~Tpi 135 (151)
.++..+...+.+.|.++||+.|.|+.= .-=+..|... + ..+.+.|++|.-|-|...+
T Consensus 41 ~~G~~~l~~iv~~c~~~gI~~vTvYaF-------S~eN~kR~~~Ev~~lm~L~~~~l~~~~~~~~~~~iri~~iG~~~~L 113 (243)
T PRK14829 41 KAGEPVLFDVVAGAIEAGVPYLSLYTF-------STENWKRSPDEVRFLMGFSRDVIHRRREQMDEWGVRVRWSGRRPRL 113 (243)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEeee-------cchhhCCCHHHHHHHHHHHHHHHHHHHHHHHHcCcEEEEEechhhC
Confidence 455567788999999999999999971 1112223211 1 1234568999999999988
Q ss_pred C
Q psy3230 136 P 136 (151)
Q Consensus 136 p 136 (151)
|
T Consensus 114 p 114 (243)
T PRK14829 114 W 114 (243)
T ss_pred C
Confidence 8
No 46
>TIGR01575 rimI ribosomal-protein-alanine acetyltransferase. Members of this model belong to the GCN5-related N-acetyltransferase (GNAT) superfamily. This model covers prokarotes and the archaea. The seed contains a characterized accession for Gram negative E. coli. An untraceable characterized accession (PIR|S66013) for Gram positive B. subtilis scores well (205.0) in the full alignment. Characterized members are lacking in the archaea. Noise cutoff (72.4) was set to exclude M. loti paralog of rimI. Trusted cutoff (80.0) was set at next highest scoring member in the mini-database.
Probab=36.33 E-value=1.4e+02 Score=20.21 Aligned_cols=48 Identities=10% Similarity=0.174 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q psy3230 72 YAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIED 131 (151)
Q Consensus 72 ~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D 131 (151)
++.+ +.+.+.+.+.+.|+..+.+.+. +....+++.+++.|+++....+
T Consensus 71 ~g~~-ll~~~~~~~~~~~~~~i~~~~~-----------~~n~~~~~~y~~~Gf~~~~~~~ 118 (131)
T TIGR01575 71 IGRA-LLRELIDEAKGRGVNEIFLEVR-----------VSNIAAQALYKKLGFNEIAIRR 118 (131)
T ss_pred HHHH-HHHHHHHHHHHcCCCeEEEEEe-----------cccHHHHHHHHHcCCCcccccc
Confidence 5444 4466777888889998888772 3345677888889998766554
No 47
>PRK09989 hypothetical protein; Provisional
Probab=36.25 E-value=99 Score=24.85 Aligned_cols=43 Identities=7% Similarity=0.145 Sum_probs=31.5
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIE 130 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~ 130 (151)
+..++.+.++||+.|++.. -.+...+-+.+.|...||.+..+.
T Consensus 18 ~~~l~~~~~~Gfd~VEl~~---------~~~~~~~~~~~~l~~~Gl~v~~~~ 60 (258)
T PRK09989 18 IERFAAARKAGFDAVEFLF---------PYDYSTLQIQKQLEQNHLTLALFN 60 (258)
T ss_pred HHHHHHHHHcCCCEEEECC---------cccCCHHHHHHHHHHcCCcEEEec
Confidence 4567788899999999853 123445556677788999998875
No 48
>PRK14742 thrL thr operon leader peptide; Provisional
Probab=36.08 E-value=22 Score=20.11 Aligned_cols=15 Identities=33% Similarity=0.545 Sum_probs=12.5
Q ss_pred cCCCeEEEEEcCCCC
Q psy3230 36 SFNDTFVHVTDLSGR 50 (151)
Q Consensus 36 t~NNTiitlTD~~G~ 50 (151)
+.+-||||-||..|+
T Consensus 11 ~l~ttiittt~ttg~ 25 (28)
T PRK14742 11 SLNTTIITTTETTGY 25 (28)
T ss_pred EeEEEEEEEEEeccc
Confidence 467899999998886
No 49
>PRK01060 endonuclease IV; Provisional
Probab=35.78 E-value=86 Score=25.32 Aligned_cols=55 Identities=11% Similarity=0.051 Sum_probs=32.2
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCcccCCCCCh------HHHHHHHHhCCCeEEEEEecCCCCCC
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPGA------QSALRALARSNMKIGRIEDVTPIPSD 138 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr------~~~ik~L~~~gl~I~~I~D~TpiphN 138 (151)
+.+++.+.++|+..|++.+..+ ..+-... +.+-+.+...|+.+..+.=-.|.+.|
T Consensus 15 ~~~l~~~~~~G~d~vEl~~~~p-----~~~~~~~~~~~~~~~lk~~~~~~gl~~~~~~~h~~~~~n 75 (281)
T PRK01060 15 EGAVAEAAEIGANAFMIFTGNP-----QQWKRKPLEELNIEAFKAACEKYGISPEDILVHAPYLIN 75 (281)
T ss_pred HHHHHHHHHcCCCEEEEECCCC-----CCCcCCCCCHHHHHHHHHHHHHcCCCCCceEEecceEec
Confidence 5577889999999999998322 1111111 22334556779987544433444444
No 50
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=35.11 E-value=1.4e+02 Score=19.91 Aligned_cols=64 Identities=22% Similarity=0.278 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCC---CeEEEEEecCCCCCC
Q psy3230 71 PYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSN---MKIGRIEDVTPIPSD 138 (151)
Q Consensus 71 ~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~g---l~I~~I~D~TpiphN 138 (151)
...|..+.+..+..+.+.+++.+.|.- |.| +-++ -|.=+.++.+.|.. + -.|..+.+..|-+.|
T Consensus 8 ~~eA~~~l~~~l~~~~~~~~~~~~II~-G~G-~hS~-~g~Lk~~V~~~L~~-~~~~~~v~~~~~~~~~~g~ 74 (83)
T PF01713_consen 8 VEEALRALEEFLDEARQRGIRELRIIT-GKG-NHSK-GGVLKRAVRRWLEE-GYQYEEVLAYRDAEPEDGN 74 (83)
T ss_dssp HHHHHHHHHHHHHHHHHTTHSEEEEE---ST-CTCC-TSHHHHHHHHHHHH-THCCTTEEEEEE--CCCTG
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEe-ccC-CCCC-CCcHHHHHHHHHHh-hhccchhheeeecCCCCCC
Confidence 345666778888899999999999886 211 0000 12225566666754 3 356777777666554
No 51
>PF13302 Acetyltransf_3: Acetyltransferase (GNAT) domain; PDB: 3TTH_C 3JUW_A 2ZXV_A 2Z0Z_A 2VI7_B 3EG7_F 1YRE_C 3IGR_B 3FBU_A 2FCK_A ....
Probab=34.38 E-value=1.4e+02 Score=20.58 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHHH-HHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCe
Q psy3230 68 EASPYAAMLAAQDVAEKC-KTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMK 125 (151)
Q Consensus 68 K~t~~Aa~~aa~~~~~k~-~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~ 125 (151)
.+.-|+.. +...+.+.+ .++|+..|...+ -..-.++++.+.+.|++
T Consensus 96 ~g~G~~~~-~~~~~~~~~~~~~~~~~i~a~~-----------~~~N~~s~~~~~k~GF~ 142 (142)
T PF13302_consen 96 RGKGYGTE-ALKLLLDWAFEELGLHRIIATV-----------MADNEASRRLLEKLGFE 142 (142)
T ss_dssp TTSSHHHH-HHHHHHHHHHHTSTSSEEEEEE-----------ETT-HHHHHHHHHTT-E
T ss_pred HhhhHHHH-HHHHHHHHHHhcCCcEEEEEEE-----------CcCCHHHHHHHHHcCCC
Confidence 44567765 445577777 689999999998 35577888888888864
No 52
>cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral
Probab=34.22 E-value=91 Score=25.24 Aligned_cols=38 Identities=21% Similarity=0.230 Sum_probs=29.0
Q ss_pred cCceEEEEEEEecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCC
Q psy3230 88 LGITALHIKLRATGGNRTKTPGP-GAQSALRALARSNMKIGRIEDVTP 134 (151)
Q Consensus 88 ~gi~~v~V~vr~~~g~~~kG~G~-Gr~~~ik~L~~~gl~I~~I~D~Tp 134 (151)
..+...+|-| -|||. |+..+ +.|...|.+++.|.|...
T Consensus 19 ~~l~g~~vaI--------qGfGnVG~~~a-~~L~~~G~~vV~vsD~~g 57 (217)
T cd05211 19 DSLEGLTVAV--------QGLGNVGWGLA-KKLAEEGGKVLAVSDPDG 57 (217)
T ss_pred CCcCCCEEEE--------ECCCHHHHHHH-HHHHHcCCEEEEEEcCCC
Confidence 3556678888 58885 66555 678888999999999876
No 53
>PF05677 DUF818: Chlamydia CHLPS protein (DUF818); InterPro: IPR008536 This family of unknown function includes several Chlamydia CHLPS proteins and Legionella SidB proteins.
Probab=34.21 E-value=3.2e+02 Score=24.50 Aligned_cols=76 Identities=16% Similarity=0.056 Sum_probs=52.8
Q ss_pred CCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHH--cCceEEEEEEEecCCCcccCCCCChHHHHHHHHhC----
Q psy3230 49 GRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKT--LGITALHIKLRATGGNRTKTPGPGAQSALRALARS---- 122 (151)
Q Consensus 49 G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~--~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~---- 122 (151)
.|+ +.+-=-|+|+.+|. .++.+-..+++.+.+..++ .|++.=+|.+ .|...|--.+=.+|++.
T Consensus 172 aNv-l~fNYpGVg~S~G~--~s~~dLv~~~~a~v~yL~d~~~G~ka~~Ii~--------yG~SLGG~Vqa~AL~~~~~~~ 240 (365)
T PF05677_consen 172 ANV-LVFNYPGVGSSTGP--PSRKDLVKDYQACVRYLRDEEQGPKAKNIIL--------YGHSLGGGVQAEALKKEVLKG 240 (365)
T ss_pred CcE-EEECCCccccCCCC--CCHHHHHHHHHHHHHHHHhcccCCChheEEE--------eeccccHHHHHHHHHhccccc
Confidence 454 34444566776663 4676666677888999875 7999889998 46666655544566653
Q ss_pred --CCeEEEEEecCCC
Q psy3230 123 --NMKIGRIEDVTPI 135 (151)
Q Consensus 123 --gl~I~~I~D~Tpi 135 (151)
|++-..|.|.|+-
T Consensus 241 ~dgi~~~~ikDRsfs 255 (365)
T PF05677_consen 241 SDGIRWFLIKDRSFS 255 (365)
T ss_pred CCCeeEEEEecCCcc
Confidence 7888899999874
No 54
>PRK00571 atpC F0F1 ATP synthase subunit epsilon; Validated
Probab=34.00 E-value=78 Score=23.57 Aligned_cols=60 Identities=18% Similarity=0.192 Sum_probs=42.2
Q ss_pred CCCCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccce
Q psy3230 2 APRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMK 61 (151)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g 61 (151)
.|+......+.+.+.+...-++=.+..++.-+-++...-.+++.+.+|....+..+||+-
T Consensus 10 tP~~~~~~~~v~~v~~~~~~G~~gILp~H~p~it~L~~G~l~i~~~~~~~~~~~v~gG~~ 69 (135)
T PRK00571 10 SPEGLIYSGEVEEVVVPGTEGELGILPGHAPLLTALKPGVVRIKKDDGEEEVIAVSGGFL 69 (135)
T ss_pred cCCCcEEeeeEEEEEEEcCccCeeecCCCcceEEEeeceEEEEEECCCcEEEEEEccEEE
Confidence 466654445566667776666666777888888888889999998677654456688864
No 55
>PTZ00079 NADP-specific glutamate dehydrogenase; Provisional
Probab=33.70 E-value=1.1e+02 Score=28.12 Aligned_cols=62 Identities=21% Similarity=0.199 Sum_probs=43.9
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCC
Q psy3230 65 DRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPI 135 (151)
Q Consensus 65 ~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~Tpi 135 (151)
++...|-|....+++.+++.. ...++-.+|.| .|+|-=-..+.+.|...|-+|+.|.|..-.
T Consensus 211 ~r~eATG~Gv~~~~~~~l~~~-~~~l~Gk~VaV--------qG~GnVg~~aa~~L~e~GakVVavSD~~G~ 272 (454)
T PTZ00079 211 IRPEATGYGLVYFVLEVLKKL-NDSLEGKTVVV--------SGSGNVAQYAVEKLLQLGAKVLTMSDSDGY 272 (454)
T ss_pred CCCcccHHHHHHHHHHHHHHc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEEcCCCc
Confidence 345778887777767666544 44567778888 588864444446677889999999998843
No 56
>PF02823 ATP-synt_DE_N: ATP synthase, Delta/Epsilon chain, beta-sandwich domain; InterPro: IPR020546 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This family represents subunits called delta (in mitochondrial ATPase) or epsilon (in bacteria or chloroplast ATPase). The interaction site of subunit C of the F0 complex with the delta or epsilon subunit of the F1 complex may be important for connecting the rotor of F1 (gamma subunit) to the rotor of F0 (C subunit) []. In bacterial species, the delta subunit is the equivalent of the Oligomycin sensitive subunit (OSCP, IPR000711 from INTERPRO) in metazoans. The C-terminal domain of the epsilon subunit appears to act as an inhibitor of ATPase activity []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0045261 proton-transporting ATP synthase complex, catalytic core F(1); PDB: 2WSS_H 1E79_H 2JDI_H 2W6I_H 2W6H_H 2W6J_H 2CK3_H 2V7Q_H 1H8E_H 2XND_H ....
Probab=33.65 E-value=29 Score=23.43 Aligned_cols=61 Identities=21% Similarity=0.180 Sum_probs=42.4
Q ss_pred CCCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccc-eee
Q psy3230 3 PRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGM-KVK 63 (151)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~-g~k 63 (151)
|+....+.+.+.+.+...-++=.+..+..-+-+...+-.+.+.+.+|+...+..++|+ -+.
T Consensus 8 P~~~~~~~~v~~v~~~t~~G~~gIl~~H~p~i~~l~~G~~~i~~~~~~~~~~~v~~G~~~v~ 69 (80)
T PF02823_consen 8 PDGIFFEGEVESVVLPTTDGEFGILPNHAPFITALKPGELRIKDADGEEKKFAVSGGFLEVK 69 (80)
T ss_dssp SSSEEEEEEESEEEEEBSSSEEEEETTS-SEEEEEESEEEEEEESSSEEEEEEESSEEEEEE
T ss_pred CCceEEeeEEEEEEEECCCcChhhccCCchhheeccceEEEEEEcCCCEEEEEEcCEEEEEE
Confidence 4444444556666777766665566777777777888889999888887777788886 444
No 57
>PRK14743 thrL thr operon leader peptide; Provisional
Probab=33.26 E-value=27 Score=19.53 Aligned_cols=15 Identities=20% Similarity=0.253 Sum_probs=12.1
Q ss_pred cCCCeEEEEEcCCCC
Q psy3230 36 SFNDTFVHVTDLSGR 50 (151)
Q Consensus 36 t~NNTiitlTD~~G~ 50 (151)
+.+-|++|.|+..||
T Consensus 5 s~~ttiit~t~ttgn 19 (26)
T PRK14743 5 GMITTIITTTITTGN 19 (26)
T ss_pred eeEEEEEEEEEecCC
Confidence 456789999998886
No 58
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=32.95 E-value=70 Score=29.26 Aligned_cols=54 Identities=22% Similarity=0.189 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q psy3230 73 AAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGR 128 (151)
Q Consensus 73 Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~ 128 (151)
|+..+++ +++.+.+++--.|-|.-|| ||+-.--|..+-|.+.+++..+.+.|+|
T Consensus 177 A~~eIv~-aI~~an~~~~~DvlIVaRG-GGSiEDLW~FNdE~vaRAi~~s~iPvIS 230 (440)
T COG1570 177 AAEEIVE-AIERANQRGDVDVLIVARG-GGSIEDLWAFNDEIVARAIAASRIPVIS 230 (440)
T ss_pred cHHHHHH-HHHHhhccCCCCEEEEecC-cchHHHHhccChHHHHHHHHhCCCCeEe
Confidence 4444444 4456666665556666666 6677777889999999999999887765
No 59
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=32.75 E-value=1.1e+02 Score=23.02 Aligned_cols=38 Identities=24% Similarity=0.264 Sum_probs=24.9
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRI 129 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I 129 (151)
..+++.+.+.|+..|.+ .++|++.. ..|++.|++|...
T Consensus 55 ~~~a~~l~~~gvdvvi~----------~~iG~~a~---~~l~~~GIkv~~~ 92 (121)
T COG1433 55 IRIAELLVDEGVDVVIA----------SNIGPNAY---NALKAAGIKVYVA 92 (121)
T ss_pred HHHHHHHHHcCCCEEEE----------CccCHHHH---HHHHHcCcEEEec
Confidence 34566777888875544 36777544 4566788887654
No 60
>KOG3302|consensus
Probab=32.60 E-value=1.5e+02 Score=24.40 Aligned_cols=48 Identities=19% Similarity=0.234 Sum_probs=33.7
Q ss_pred eEEEEEcCCCCEEEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCce
Q psy3230 40 TFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGIT 91 (151)
Q Consensus 40 TiitlTD~~G~~~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~ 91 (151)
.|+-+..+.=.. +.|+||-+--.+++ +...|..++.++++-++.+|++
T Consensus 60 Vimrir~P~~ta-~I~ssGKi~ctgA~---se~~ar~aark~aRilqkLgf~ 107 (200)
T KOG3302|consen 60 VIMRIRSPRTTA-LIFSSGKIVCTGAK---SEDSARLAARKYARILQKLGFP 107 (200)
T ss_pred EEEEEcCCceEE-EEecCCcEEEeccC---CHHHHHHHHHHHHHHHHHcCCC
Confidence 455566665543 56888877656543 4566778888999999999875
No 61
>TIGR02382 wecD_rffC TDP-D-fucosamine acetyltransferase. This model represents the WecD protein (Formerly RffC) for the biosynthesis of enterobacterial common antigen (ECA), an outer leaflet, outer membrane glycolipid with a trisaccharide repeat unit. WecD is a member of the GNAT family of acetytransferases (pfam00583).
Probab=32.40 E-value=1.6e+02 Score=22.43 Aligned_cols=47 Identities=28% Similarity=0.314 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q psy3230 70 SPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGR 128 (151)
Q Consensus 70 t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~ 128 (151)
--++.+ +.+.+.+.|.++|+..|.+.+ ...-..+++...+.|++...
T Consensus 138 kG~G~~-ll~~~~~~a~~~g~~~I~l~v-----------~~~N~~A~~~Y~klGF~~~~ 184 (191)
T TIGR02382 138 RGIGAE-LMQTALNWCYARGLTRLRVAT-----------QMGNTAALRLYIRSGANIES 184 (191)
T ss_pred CCHHHH-HHHHHHHHHHHcCCCEEEEEe-----------CCCCHHHHHHHHHcCCcccc
Confidence 346554 446678888899999999998 34446788888888887543
No 62
>PRK14030 glutamate dehydrogenase; Provisional
Probab=32.26 E-value=1.2e+02 Score=27.76 Aligned_cols=62 Identities=16% Similarity=0.147 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCCCCC
Q psy3230 66 RDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGP-GAQSALRALARSNMKIGRIEDVTPIPS 137 (151)
Q Consensus 66 ~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~-Gr~~~ik~L~~~gl~I~~I~D~Tpiph 137 (151)
+...|-|....+++.+++.. ...++..+|.| .|||. |..++ +.|...|-+|+.|.|.+-.=+
T Consensus 203 r~~ATg~Gv~~~~~~~~~~~-g~~l~g~~vaI--------QGfGnVG~~aA-~~L~e~GakvVavSD~~G~i~ 265 (445)
T PRK14030 203 RPEATGFGALYFVHQMLETK-GIDIKGKTVAI--------SGFGNVAWGAA-TKATELGAKVVTISGPDGYIY 265 (445)
T ss_pred CCCccHHHHHHHHHHHHHHc-CCCcCCCEEEE--------ECCCHHHHHHH-HHHHHCCCEEEEEEcCCceEE
Confidence 44668887766666665544 23456678888 57885 55555 557788999999988765433
No 63
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.25 E-value=92 Score=25.17 Aligned_cols=43 Identities=12% Similarity=0.190 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHH
Q psy3230 70 SPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRAL 119 (151)
Q Consensus 70 t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L 119 (151)
|-.=|+.+-..++..|.+.|+.+|.|+= | ||-..|...+||..
T Consensus 105 tq~eAr~~L~~Fi~~a~~~~~rcv~Vih-G------kG~s~g~~~vLK~~ 147 (184)
T COG2840 105 TQEEARQELGAFIARARAEGLRCVLVIH-G------KGRSKGSKPVLKSQ 147 (184)
T ss_pred CHHHHHHHHHHHHHHHHHhCCcEEEEEe-C------CCcCCCCchhHHHH
Confidence 3344666667788899999999999985 1 33336667777653
No 64
>TIGR00829 FRU PTS system, fructose-specific, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several PTS components of unknown specificities. The fructose components of this family phosphorylate fructose on the 1-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIB domain of the fructose PTS transporters.
Probab=32.03 E-value=95 Score=21.58 Aligned_cols=26 Identities=15% Similarity=0.344 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHcCceEEEEEEEe
Q psy3230 73 AAMLAAQDVAEKCKTLGITALHIKLRA 99 (151)
Q Consensus 73 Aa~~aa~~~~~k~~~~gi~~v~V~vr~ 99 (151)
.+++|++.+.+.++++|+. +.|..+|
T Consensus 12 ht~lAae~L~~aA~~~G~~-i~VE~qg 37 (85)
T TIGR00829 12 HTFMAAEALEKAAKKRGWE-VKVETQG 37 (85)
T ss_pred HHHHHHHHHHHHHHHCCCe-EEEEecC
Confidence 3567888888889999997 7888864
No 65
>PRK13442 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=31.29 E-value=92 Score=21.73 Aligned_cols=60 Identities=17% Similarity=0.161 Sum_probs=42.2
Q ss_pred CCCCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccce
Q psy3230 2 APRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMK 61 (151)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g 61 (151)
.|+...-..+.+++.+...-++=.+..+..-+-+...--.+++.+.+|+......+||+-
T Consensus 12 tP~~~~~~~~v~~V~~p~~~G~~gILp~H~p~it~L~~G~l~i~~~~~~~~~~~v~gG~~ 71 (89)
T PRK13442 12 AADRPVWSGEATMVVARTTEGDIGILPGHEPLLGVLESGTVTVVTPGGERISAAVDGGFI 71 (89)
T ss_pred cCCccEEeceeEEEEEECCcCCcEecCCCcCeEEEEcceEEEEEECCCcEEEEEEccEEE
Confidence 466554445666677777766666777777777888888888887777765567788863
No 66
>PHA02773 hypothetical protein; Provisional
Probab=31.12 E-value=75 Score=23.39 Aligned_cols=75 Identities=25% Similarity=0.217 Sum_probs=39.0
Q ss_pred CCcccceeeEEecCceeecccee-eeEEEEEccCCCeEEEEEcCCCCE--EEEEecccc-eeeccCCCCCHHHHHHHHHH
Q psy3230 5 KGKVQKEEVLVSLGPQVKEGEDV-FGVAHIFASFNDTFVHVTDLSGRE--TIARITGGM-KVKADRDEASPYAAMLAAQD 80 (151)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~-~gi~hI~~t~NNTiitlTD~~G~~--~~~~sSgg~-g~k~~~rK~t~~Aa~~aa~~ 80 (151)
+++|-.+|.+++|+|.-++=-+. +-++- .|.+|.. .+..++|-+ -|++..++--.||. -
T Consensus 9 kvkems~e~qi~lr~kqkell~rffeiae------------~de~gdlciply~segdl~lfkkd~~~yq~f~y-----~ 71 (112)
T PHA02773 9 KVKEMSEEKQIKLRPKQKELLIRFFEIAE------------KDEDGDLCIPLYDSEGDLFLFKKDANKYQMFAY-----F 71 (112)
T ss_pred EhhhhchhhceeechhhHHHHHHHHHHhe------------ecCCCCEEEEeecCCCcEEEEeccchhhhhhHH-----H
Confidence 46667888999999975442211 12222 3444443 122233333 57766533222222 2
Q ss_pred HHHHHHHcCceEEEEE
Q psy3230 81 VAEKCKTLGITALHIK 96 (151)
Q Consensus 81 ~~~k~~~~gi~~v~V~ 96 (151)
-+..+.+.+|-++.|+
T Consensus 72 ri~rli~k~iffikvk 87 (112)
T PHA02773 72 RIKRLIDKNIFFIKIK 87 (112)
T ss_pred HHHHHHhcCeEEEEEE
Confidence 2345556788887765
No 67
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=31.04 E-value=2.2e+02 Score=23.90 Aligned_cols=59 Identities=25% Similarity=0.342 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHH-----HH-----------HHHHhCCCeEEEEEecCCC
Q psy3230 72 YAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQS-----AL-----------RALARSNMKIGRIEDVTPI 135 (151)
Q Consensus 72 ~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~-----~i-----------k~L~~~gl~I~~I~D~Tpi 135 (151)
.++..+...+.+.|.++|++.|.|+. ++-=+..|.. .+ ..+...|++|.-|-|.+.+
T Consensus 47 ~~G~~~l~~i~~~c~~~GI~~vT~ya-------FS~eN~kR~~~Ev~~Lm~L~~~~l~~~~~~~~~~~iri~~iG~~~~L 119 (249)
T PRK14831 47 RRGVDALKDLLRCCKDWGIGALTAYA-------FSTENWSRPLEEVNFLMTLFERVLRRELEELMEENVRIRFVGDLDPL 119 (249)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEee-------cchhhhCcCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEechhhC
Confidence 34555667788999999999999997 2212223332 11 1234568999999999888
Q ss_pred CC
Q psy3230 136 PS 137 (151)
Q Consensus 136 ph 137 (151)
|-
T Consensus 120 p~ 121 (249)
T PRK14831 120 PK 121 (249)
T ss_pred CH
Confidence 84
No 68
>PRK07757 acetyltransferase; Provisional
Probab=30.48 E-value=1.1e+02 Score=21.83 Aligned_cols=55 Identities=11% Similarity=0.095 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCC
Q psy3230 71 PYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRR 142 (151)
Q Consensus 71 ~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphNGCRp 142 (151)
-++..+. ..+.+.+.+.|+..+.+... ..+...+.|++...-.|..+--+|+|+.
T Consensus 81 Glg~~Ll-~~l~~~a~~~g~~~i~~~~~----------------~~~~Y~k~GF~~~~~~~~~~~~~~~~~~ 135 (152)
T PRK07757 81 GIGRMLV-EACLEEARELGVKRVFALTY----------------QPEFFEKLGFREVDKEALPQKVWADCIK 135 (152)
T ss_pred CHHHHHH-HHHHHHHHhCCCCeEEEEeC----------------cHHHHHHCCCEEcccccCChhHHhcCcc
Confidence 3555433 55667778889988866541 1355678899988888888888889873
No 69
>PLN00105 malate/L-lactate dehydrogenase; Provisional
Probab=29.90 E-value=3.5e+02 Score=23.50 Aligned_cols=68 Identities=13% Similarity=0.064 Sum_probs=48.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCC--CCCCCCCC
Q psy3230 68 EASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTP--IPSDSTRR 142 (151)
Q Consensus 68 K~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~Tp--iphNGCRp 142 (151)
---++++..+.+.++++|++.|+-.|.|+= -+.-+|..-..+.++. +.|+--+..++..| .||+|-+|
T Consensus 73 g~G~~~~~~am~~aiekAr~~Gi~~v~vrn------~S~H~G~~g~y~~~aa-~~Gligi~~tN~~~~vaP~GG~~~ 142 (330)
T PLN00105 73 NAGMLVLHHAMDMAIDKAKTHGVGIVGTCN------TSTSTGALGYYAEKVA-QQGLIGLVFANSPEFVAPAGGIEP 142 (330)
T ss_pred CccHHHHHHHHHHHHHHHHHhCEEEEEEeC------CcCCccchHHHHHHHH-HCCCeEEEEeCCCCeeCCCCCCCC
Confidence 446788999999999999999999888872 0146888777776655 46765555555444 57777554
No 70
>TIGR03175 AllD ureidoglycolate dehydrogenase. This enzyme converts ureidoglycolate to oxalureate in the non-urea-forming catabolism of allantoin (GenProp0687). The pathway has been characterized in E. coli and is observed in the genomes of Entercoccus faecalis and Bacillus licheniformis.
Probab=29.83 E-value=3.9e+02 Score=23.50 Aligned_cols=67 Identities=21% Similarity=0.192 Sum_probs=49.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCC--CCCCCCCC
Q psy3230 68 EASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTP--IPSDSTRR 142 (151)
Q Consensus 68 K~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~Tp--iphNGCRp 142 (151)
---++++..+.+.++++|++.|+-.|.|+= ++-+|..-..+.++.. .|+-=+..++..| .||+|-+|
T Consensus 84 g~G~~a~~~Am~~aiekAr~~Gi~~v~v~n-------s~H~G~~g~Y~~~aa~-~G~Igi~~tNs~~~vaP~GG~~~ 152 (349)
T TIGR03175 84 GAGQVAAKMAMEHAIEIAKKSGVAVVGISR-------MSHSGALSYFVRQAAE-QGMVALSMCQSDPMVVPFGGTDI 152 (349)
T ss_pred CchHHHHHHHHHHHHHHHHHhCEEEEEecC-------CCccccHHHHHHHHHH-CCCEEEEEeCCCCeeCCCCCCCC
Confidence 446789999999999999999999888874 3678887777877665 5665444544444 57777654
No 71
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=28.90 E-value=2.8e+02 Score=23.26 Aligned_cols=61 Identities=20% Similarity=0.206 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHH---H-----------HHHHHhCCCeEEEEEecCCCCC
Q psy3230 72 YAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQS---A-----------LRALARSNMKIGRIEDVTPIPS 137 (151)
Q Consensus 72 ~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~---~-----------ik~L~~~gl~I~~I~D~Tpiph 137 (151)
.++......+.+.|.++|++.|.|+.=-+ ..|..-.+- . +..+...|++|..|-|...+|-
T Consensus 41 ~~G~~~l~~i~~~c~~lgI~~lTvYaFS~-----eN~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~iri~viGd~~~Lp~ 115 (249)
T PRK14834 41 RAGVEALRRVVRAAGELGIGYLTLFAFSS-----ENWSRPASEVSDLFGLLRLFIRRDLAELHRNGVRVRVIGERAGLEA 115 (249)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEEEec-----cccCCCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEcChhhCCH
Confidence 34555668899999999999999997211 223322211 1 1123356899999999998884
No 72
>COG0334 GdhA Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]
Probab=28.89 E-value=1.2e+02 Score=27.53 Aligned_cols=64 Identities=22% Similarity=0.215 Sum_probs=41.9
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCCCCCC
Q psy3230 65 DRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGP-GAQSALRALARSNMKIGRIEDVTPIPSD 138 (151)
Q Consensus 65 ~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~-Gr~~~ik~L~~~gl~I~~I~D~TpiphN 138 (151)
++...|-|.....++ .+.+....+++-..|-| .|+|- |..++.+ |...|-+|+.+.|..-.=||
T Consensus 181 ~r~~aTg~Gv~~~~~-~a~~~~g~~l~G~rVaV--------QG~GNVg~~aa~~-l~~~GAkvva~sds~g~i~~ 245 (411)
T COG0334 181 GRSEATGYGVFYAIR-EALKALGDDLEGARVAV--------QGFGNVGQYAAEK-LHELGAKVVAVSDSKGGIYD 245 (411)
T ss_pred CCCcccceehHHHHH-HHHHHcCCCcCCCEEEE--------ECccHHHHHHHHH-HHHcCCEEEEEEcCCCceec
Confidence 344566666555555 33333344578888999 57775 6666655 54569999999998874443
No 73
>TIGR03166 alt_F1F0_F1_eps alternate F1F0 ATPase, F1 subunit epsilon. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 epsilon subunit of this apparent second ATP synthase.
Probab=28.68 E-value=1.3e+02 Score=22.36 Aligned_cols=61 Identities=11% Similarity=0.055 Sum_probs=44.3
Q ss_pred CCCCCccc-ceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEeccccee
Q psy3230 2 APRKGKVQ-KEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKV 62 (151)
Q Consensus 2 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g~ 62 (151)
+|+...-+ .+.+++.+...-++=.+..+.+-+-+...--.+.+.+.+|+...+..+||+-.
T Consensus 6 tP~~~~~~~~~v~~v~~~~~~G~~GILp~H~p~it~L~~G~l~i~~~~~~~~~~av~gGf~~ 67 (122)
T TIGR03166 6 TPFRVFLDKLPVTRIVAETESGSFGLLPGHVDCVAALVPGILIYETADGGEHYVAVDQGILV 67 (122)
T ss_pred CCCeeEEecCcEEEEEEEcCcCCeEEcCCCcCeEeEeccEEEEEEECCCcEEEEEEeeeEEE
Confidence 56665555 66777777777777667778888888888888888877776555567888643
No 74
>PRK09491 rimI ribosomal-protein-alanine N-acetyltransferase; Provisional
Probab=28.35 E-value=2.2e+02 Score=20.20 Aligned_cols=55 Identities=7% Similarity=0.099 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCC
Q psy3230 68 EASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTP 134 (151)
Q Consensus 68 K~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~Tp 134 (151)
++.-++.. +.+.+.+.+.+.|+..+.+.+ -.....+++.+.+.|++.........
T Consensus 76 rg~G~g~~-ll~~~~~~~~~~~~~~~~~~~-----------~~~N~~a~~~y~k~Gf~~~~~~~~~~ 130 (146)
T PRK09491 76 QRQGLGRA-LLEHLIDELEKRGVATLWLEV-----------RASNAAAIALYESLGFNEVTIRRNYY 130 (146)
T ss_pred ccCCHHHH-HHHHHHHHHHHCCCcEEEEEE-----------ccCCHHHHHHHHHcCCEEeeeeeccc
Confidence 34446554 445677778889999888877 23357788989999998877665553
No 75
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=28.26 E-value=1.7e+02 Score=23.45 Aligned_cols=52 Identities=13% Similarity=0.167 Sum_probs=32.4
Q ss_pred HHHHHHHHHHcCceEEEEEEEecCCCccc--CCCCC-hHHHHHHHHhCCCeEEEEE
Q psy3230 78 AQDVAEKCKTLGITALHIKLRATGGNRTK--TPGPG-AQSALRALARSNMKIGRIE 130 (151)
Q Consensus 78 a~~~~~k~~~~gi~~v~V~vr~~~g~~~k--G~G~G-r~~~ik~L~~~gl~I~~I~ 130 (151)
-+.+++.+.++|+..|++.+.... .... .+... ...+.+.|...||.|.++.
T Consensus 18 ~~e~~~~~~~~G~~~iEl~~~~~~-~~~~~~~~~~~~~~~l~~~l~~~Gl~i~~~~ 72 (284)
T PRK13210 18 WEERLVFAKELGFDFVEMSVDESD-ERLARLDWSKEERLSLVKAIYETGVRIPSMC 72 (284)
T ss_pred HHHHHHHHHHcCCCeEEEecCCcc-cccccccCCHHHHHHHHHHHHHcCCCceEEe
Confidence 366778889999999999863100 0001 11222 3335556778899999884
No 76
>TIGR00587 nfo apurinic endonuclease (APN1). All proteins in this family for which functions are known are 5' AP endonculeases that are used in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.17 E-value=1.3e+02 Score=24.73 Aligned_cols=64 Identities=14% Similarity=0.058 Sum_probs=38.8
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHH-HHHhCCCeEEEEEecCCCCCCCCCC
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALR-ALARSNMKIGRIEDVTPIPSDSTRR 142 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik-~L~~~gl~I~~I~D~TpiphNGCRp 142 (151)
..+.+.+.++|+..+.|.++.+.+...+-+.......++ .+...++.+..|.--.|++.|-|=|
T Consensus 14 ~~a~~~~~~~G~~~~qif~~~P~~w~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Hapy~iNlas~ 78 (274)
T TIGR00587 14 QAAYNRAAEIGATAFMFFLKSPRWWRRPMLEEEVIDWFKAALETNKNLSQIVLVHAPYLINLASP 78 (274)
T ss_pred HHHHHHHHHhCCCEEEEEecCccccCCCCCCHHHHHHHHHHHHHcCCCCcceeccCCeeeecCCC
Confidence 346678889999999999965533322222333333443 4556677655555556666676644
No 77
>TIGR00542 hxl6Piso_put hexulose-6-phosphate isomerase, putative. This family is conserved at better than 40 % identity among the four known examples from three species: Escherichia coli (SgbU and SgaU), Haemophilus influenzae, and Mycoplasma pneumoniae. The rarity of the family, high level of conservation, and proposed catabolic role suggests lateral transfer may be a part of the evolutionary history of this protein.
Probab=27.08 E-value=1.5e+02 Score=23.97 Aligned_cols=51 Identities=14% Similarity=0.190 Sum_probs=31.2
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCccc--CCCCCh-HHHHHHHHhCCCeEEEEE
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTK--TPGPGA-QSALRALARSNMKIGRIE 130 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~k--G~G~Gr-~~~ik~L~~~gl~I~~I~ 130 (151)
+.+.+.+.++||..|+|-+... ..+.. ++.... +.+.+.|.+.|++|.++.
T Consensus 19 ~e~l~~~~~~G~~~VEl~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~gl~i~~~~ 72 (279)
T TIGR00542 19 LERLQLAKTCGFDFVEMSVDET-DDRLSRLDWSREQRLALVNAIIETGVRIPSMC 72 (279)
T ss_pred HHHHHHHHHcCCCEEEEecCCc-cchhhccCCCHHHHHHHHHHHHHcCCCceeee
Confidence 5577888899999999987210 00000 111222 334455778899999885
No 78
>PF08903 DUF1846: Domain of unknown function (DUF1846); InterPro: IPR014999 This group of proteins are functionally uncharacterised. ; PDB: 3BH1_B.
Probab=27.03 E-value=98 Score=28.61 Aligned_cols=45 Identities=29% Similarity=0.453 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHHHHHHHcCceEEE--------------------------------EEEEecCCCcccCCCCChHH-HH
Q psy3230 70 SPYAAMLAAQDVAEKCKTLGITALH--------------------------------IKLRATGGNRTKTPGPGAQS-AL 116 (151)
Q Consensus 70 t~~Aa~~aa~~~~~k~~~~gi~~v~--------------------------------V~vr~~~g~~~kG~G~Gr~~-~i 116 (151)
|.|+.|-+|..+.+++..+||+.-. |.+.++ |+|.|+.+ +|
T Consensus 113 T~y~~q~~a~~F~~kLe~~gIkvy~Hy~i~GYP~dv~~IvSdeGyGkN~YIeTtrpLVVVTAP------GPGSGKlATCL 186 (491)
T PF08903_consen 113 TQYEGQPAADAFKNKLERLGIKVYRHYPIEGYPTDVDLIVSDEGYGKNDYIETTRPLVVVTAP------GPGSGKLATCL 186 (491)
T ss_dssp ECE-T-HHHHHHHHHHHTTT-EEEEEE--TTTTT-HHHHSSTTTGGGS-----SSSEEEEE-S------STTS-HHHHHH
T ss_pred EecCCCHHHHHHHHHHHHCCCcEEEecCcCCCCCCccceeCcccCCCCCceeccCCeEEEeCC------CCCccHHHHHH
Confidence 5677888889999999999997644 677664 77888876 77
Q ss_pred HHHH
Q psy3230 117 RALA 120 (151)
Q Consensus 117 k~L~ 120 (151)
..|-
T Consensus 187 SQlY 190 (491)
T PF08903_consen 187 SQLY 190 (491)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 7775
No 79
>PRK15425 gapA glyceraldehyde-3-phosphate dehydrogenase A; Provisional
Probab=26.96 E-value=76 Score=27.74 Aligned_cols=30 Identities=27% Similarity=0.297 Sum_probs=21.3
Q ss_pred cCCCCChHHHHHHHH-hCCCeEEEEEecCCC
Q psy3230 106 KTPGPGAQSALRALA-RSNMKIGRIEDVTPI 135 (151)
Q Consensus 106 kG~G~Gr~~~ik~L~-~~gl~I~~I~D~Tpi 135 (151)
+|||.==..++|++. ...++|+-|-|.+..
T Consensus 8 nGfGRIGr~~~r~~~~~~~~~vvaiNd~~~~ 38 (331)
T PRK15425 8 NGFGRIGRIVFRAAQKRSDIEIVAINDLLDA 38 (331)
T ss_pred EeeChHHHHHHHHHHHCCCCEEEEEecCCCH
Confidence 788863345567654 568999999997753
No 80
>PRK09414 glutamate dehydrogenase; Provisional
Probab=26.85 E-value=1.3e+02 Score=27.32 Aligned_cols=58 Identities=14% Similarity=0.171 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecC
Q psy3230 66 RDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGP-GAQSALRALARSNMKIGRIEDVT 133 (151)
Q Consensus 66 ~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~-Gr~~~ik~L~~~gl~I~~I~D~T 133 (151)
+...|-|....+++.+++.. ...++..+|.| .|||- |+.++ +.|...|.+|+.|.|.+
T Consensus 207 r~~aTg~Gv~~~~~~~~~~~-~~~l~g~rVaI--------qGfGnVG~~~A-~~L~~~GakVVavsDs~ 265 (445)
T PRK09414 207 RTEATGYGLVYFAEEMLKAR-GDSFEGKRVVV--------SGSGNVAIYAI-EKAQQLGAKVVTCSDSS 265 (445)
T ss_pred CCCcccHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHH-HHHHHCCCEEEEEEcCC
Confidence 44678887766666665543 44567788888 58885 55555 66778899999999954
No 81
>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=26.82 E-value=2.4e+02 Score=23.16 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=31.4
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCcccCCCCCh---------------HHHHHHHHhCCCeE
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPGA---------------QSALRALARSNMKI 126 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr---------------~~~ik~L~~~gl~I 126 (151)
+.+-+.+..+||..|+|+. |++.+|+-... ++.+..|+..|.-|
T Consensus 108 ~~A~~~L~~lg~~nV~v~~----gDG~~G~~~~aPyD~I~Vtaaa~~vP~~Ll~QL~~gGrlv 166 (209)
T COG2518 108 EQARRNLETLGYENVTVRH----GDGSKGWPEEAPYDRIIVTAAAPEVPEALLDQLKPGGRLV 166 (209)
T ss_pred HHHHHHHHHcCCCceEEEE----CCcccCCCCCCCcCEEEEeeccCCCCHHHHHhcccCCEEE
Confidence 4444556779998899988 78888876644 66788887666544
No 82
>TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=26.65 E-value=1.9e+02 Score=24.61 Aligned_cols=49 Identities=20% Similarity=0.227 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q psy3230 77 AAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDV 132 (151)
Q Consensus 77 aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~ 132 (151)
+++.++..|.+.|.+ ++|++-- ++-.+.|+..+ +.|.+.|+.+..|.|.
T Consensus 127 tv~~~l~~a~~~~~~-f~V~v~E-----srP~~~G~~~a-~~L~~~gI~vtlI~Ds 175 (301)
T TIGR00511 127 AALSVIKTAFEQGKD-IEVIATE-----TRPRKQGHITA-KELRDYGIPVTLIVDS 175 (301)
T ss_pred HHHHHHHHHHHcCCc-EEEEEec-----CCCcchHHHHH-HHHHHCCCCEEEEehh
Confidence 455566777666644 5666622 24456787666 6688899999999885
No 83
>PRK14736 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=26.23 E-value=1e+02 Score=23.24 Aligned_cols=60 Identities=20% Similarity=0.243 Sum_probs=43.3
Q ss_pred CCCCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccce
Q psy3230 2 APRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMK 61 (151)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~g 61 (151)
.|+...-+.+.+++.+...-++=.+..+..-+-++...-.+++.+.+|+......+||+-
T Consensus 10 TP~~~~~~~~v~~V~vp~~~G~~gILp~H~P~it~L~~G~l~i~~~~~~~~~~~v~gGf~ 69 (133)
T PRK14736 10 GPERTLYSGEVEAVQLPGSEGEMTVLPGHAPVLTTLKVGVITVTETTGNGKRIYVRGGFA 69 (133)
T ss_pred cCCccEEeeeeEEEEEecCccCeeEcCCChhhEeEecceEEEEEECCCcEEEEEEeceEE
Confidence 466665556677778877777666777777777888888888877677654567788863
No 84
>PRK13449 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=25.58 E-value=1.5e+02 Score=20.61 Aligned_cols=63 Identities=17% Similarity=0.208 Sum_probs=42.7
Q ss_pred CCCCCcccceeeEEecCceeeccceeeeEEEEEccCCCeEEEEEcCCCC-EEEEEecccc-eeec
Q psy3230 2 APRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGR-ETIARITGGM-KVKA 64 (151)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~-~~~~~sSgg~-g~k~ 64 (151)
+|+...-+.+.+.+.+...-++=.+..+.+-+-+....-.+.+.+.+++ ...+..+||+ -+.+
T Consensus 10 tP~~~~~~~~v~~V~~p~~~G~~gILp~H~p~it~L~~G~l~i~~~~~~~~~~~~v~gGf~~v~~ 74 (88)
T PRK13449 10 TPERLLRSGEVDMVVVPGTEGDFGVLAGHAPFMTTLREGEVTVYSSDGAAPEVFHVQGGFAEVNE 74 (88)
T ss_pred cCCceEEccEEEEEEEeCCccCeEEcCCCcceEEEeeceEEEEEECCCCeEEEEEEcceEEEEEC
Confidence 5666555566677777777766667777777778888888888865553 3345668886 4443
No 85
>PRK14031 glutamate dehydrogenase; Provisional
Probab=25.45 E-value=1.8e+02 Score=26.61 Aligned_cols=60 Identities=15% Similarity=0.099 Sum_probs=41.0
Q ss_pred ccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q psy3230 64 ADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDV 132 (151)
Q Consensus 64 ~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~ 132 (151)
.++...|-|....+++.+++.. ...++...|.| .|+|.=-..+.+.|...|-+|+-|.|.
T Consensus 201 ~~r~~aTg~Gv~~~~~~~~~~~-g~~l~g~rVaV--------QGfGNVG~~aA~~L~e~GAkVVaVSD~ 260 (444)
T PRK14031 201 LIRPEATGYGNIYFLMEMLKTK-GTDLKGKVCLV--------SGSGNVAQYTAEKVLELGGKVVTMSDS 260 (444)
T ss_pred CCCCcccHHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEECC
Confidence 3455678887766666565544 33466778888 578863344556677899999999993
No 86
>PRK10098 putative dehydrogenase; Provisional
Probab=25.19 E-value=4.7e+02 Score=22.94 Aligned_cols=88 Identities=14% Similarity=0.107 Sum_probs=57.7
Q ss_pred cCCCCEEEEEecccc-eeeccCCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCC
Q psy3230 46 DLSGRETIARITGGM-KVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNM 124 (151)
Q Consensus 46 D~~G~~~~~~sSgg~-g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl 124 (151)
|++.++.+...++.+ ..-. ..---.+++..+.+.++++|++.|+-.|-|+= ++-||.--..+.++. ..|+
T Consensus 66 ~~~~~~~v~~~~~a~~~vDg-~~g~G~~a~~~Am~~aie~Ar~~Gi~~v~vrn-------S~H~G~~g~y~~~aa-~~G~ 136 (350)
T PRK10098 66 QLNHHAKIVKDAGAVLTLDG-DRGFGQVVAHEAMALGIERARQHGICAVALRN-------SHHIGRIGHWAEQCA-AAGL 136 (350)
T ss_pred CCCCCeEEEecCCcEEEEEC-CCCccHHHHHHHHHHHHHHHHHhCEEEEEEec-------CCCccchHHHHHHHH-HCCC
Confidence 344444333334443 2332 22445788999999999999999999888874 377888778887755 4676
Q ss_pred eEEEEEe----cCCCCCCCCCC
Q psy3230 125 KIGRIED----VTPIPSDSTRR 142 (151)
Q Consensus 125 ~I~~I~D----~TpiphNGCRp 142 (151)
-=+..++ -+-.||+|-+|
T Consensus 137 igi~~tN~~s~~~vaP~Gg~~~ 158 (350)
T PRK10098 137 VSIHFVNVVGDPMVAPFHGRDS 158 (350)
T ss_pred EEEEEecCCCCceecCCCCCCC
Confidence 5445555 34578888654
No 87
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=24.92 E-value=1.3e+02 Score=26.51 Aligned_cols=42 Identities=21% Similarity=0.249 Sum_probs=30.1
Q ss_pred HHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q psy3230 85 CKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGR 128 (151)
Q Consensus 85 ~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~ 128 (151)
+.+.+ -.|.|..|| ||+-.--+-.+-+.+.+++..+.+.|++
T Consensus 188 ~~~~~-~Dviii~RG-GGS~eDL~~Fn~e~v~~ai~~~~~Pvis 229 (438)
T PRK00286 188 ANARG-EDVLIVARG-GGSLEDLWAFNDEAVARAIAASRIPVIS 229 (438)
T ss_pred hcCCC-CCEEEEecC-CCCHHHhhccCcHHHHHHHHcCCCCEEE
Confidence 33334 367788876 6666666777889999999988877654
No 88
>COG1184 GCD2 Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Probab=24.47 E-value=2.6e+02 Score=24.37 Aligned_cols=50 Identities=18% Similarity=0.307 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q psy3230 77 AAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVT 133 (151)
Q Consensus 77 aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~T 133 (151)
++..+...|.+.|-+ +.|++-- ++--+.|+..+ +.|.++|+...-|.|..
T Consensus 131 ~v~~~l~~A~~~~k~-~~V~VtE-----SRP~~eG~~~a-k~L~~~gI~~~~I~Dsa 180 (301)
T COG1184 131 TVLEVLKTAADRGKR-FKVIVTE-----SRPRGEGRIMA-KELRQSGIPVTVIVDSA 180 (301)
T ss_pred HHHHHHHHhhhcCCc-eEEEEEc-----CCCcchHHHHH-HHHHHcCCceEEEechH
Confidence 456677777777766 5555531 24445677776 88999999999998853
No 89
>COG4782 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.10 E-value=2.6e+02 Score=25.15 Aligned_cols=84 Identities=19% Similarity=0.247 Sum_probs=51.5
Q ss_pred ccceeeeEEEEEccCCCeEEE-------EEcCCCC----EEEEEecccc--eeeccCCCCCHHHHHHHHHHHHHH-HHHc
Q psy3230 23 EGEDVFGVAHIFASFNDTFVH-------VTDLSGR----ETIARITGGM--KVKADRDEASPYAAMLAAQDVAEK-CKTL 88 (151)
Q Consensus 23 ~~~~~~gi~hI~~t~NNTiit-------lTD~~G~----~~~~~sSgg~--g~k~~~rK~t~~Aa~~aa~~~~~k-~~~~ 88 (151)
.++.+...+|= +||+|.- +....|+ ++++|-|+|. +|--.+ .++.|+.-.. +.+++. +.+.
T Consensus 114 ~~k~vlvFvHG---fNntf~dav~R~aqI~~d~g~~~~pVvFSWPS~g~l~~Yn~Dr-eS~~~Sr~aL-e~~lr~La~~~ 188 (377)
T COG4782 114 SAKTVLVFVHG---FNNTFEDAVYRTAQIVHDSGNDGVPVVFSWPSRGSLLGYNYDR-ESTNYSRPAL-ERLLRYLATDK 188 (377)
T ss_pred CCCeEEEEEcc---cCCchhHHHHHHHHHHhhcCCCcceEEEEcCCCCeeeecccch-hhhhhhHHHH-HHHHHHHHhCC
Confidence 44455555553 6887642 2223333 3588989883 665553 7777866544 555555 4557
Q ss_pred CceEEEEEEEecCCCcccCCCCChHHHHHHHHh
Q psy3230 89 GITALHIKLRATGGNRTKTPGPGAQSALRALAR 121 (151)
Q Consensus 89 gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~ 121 (151)
..+.|+|.- + ..|-..+..+|++
T Consensus 189 ~~~~I~ilA--------H--SMGtwl~~e~LrQ 211 (377)
T COG4782 189 PVKRIYLLA--------H--SMGTWLLMEALRQ 211 (377)
T ss_pred CCceEEEEE--------e--cchHHHHHHHHHH
Confidence 799999987 3 4556666666654
No 90
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=23.92 E-value=1.3e+02 Score=25.18 Aligned_cols=27 Identities=30% Similarity=0.613 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHHHHHHHHcCceEEEEE
Q psy3230 69 ASPYAAMLAAQDVAEKCKTLGITALHIK 96 (151)
Q Consensus 69 ~t~~Aa~~aa~~~~~k~~~~gi~~v~V~ 96 (151)
+.|||++ +.+.+.+.|.++|+..+++.
T Consensus 73 tHPfA~~-is~~a~~a~~~~~ipylR~e 99 (256)
T TIGR00715 73 THPFAAQ-ITTNATAVCKELGIPYVRFE 99 (256)
T ss_pred CCHHHHH-HHHHHHHHHHHhCCcEEEEE
Confidence 5789875 66889999999999999885
No 91
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=23.16 E-value=2.5e+02 Score=19.09 Aligned_cols=35 Identities=17% Similarity=0.217 Sum_probs=24.0
Q ss_pred EEEEecccceeeccCCCCCHHHHHHHHHHHHHHHHHcC
Q psy3230 52 TIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLG 89 (151)
Q Consensus 52 ~~~~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~g 89 (151)
++.++||-+-..+++ ++-.+..|.+.+...++++|
T Consensus 52 ~~IF~sGki~itGak---s~~~~~~a~~~i~~~L~~~~ 86 (86)
T PF00352_consen 52 VLIFSSGKIVITGAK---SEEEAKKAIEKILPILQKLG 86 (86)
T ss_dssp EEEETTSEEEEEEES---SHHHHHHHHHHHHHHHHHTT
T ss_pred EEEEcCCEEEEEecC---CHHHHHHHHHHHHHHHHHcC
Confidence 455667766666643 45667778888888887765
No 92
>PF03198 Glyco_hydro_72: Glucanosyltransferase; InterPro: IPR004886 This family is a group of yeast glycolipid proteins anchored to the membrane. It includes Candida albicans (Yeast) pH-regulated protein, which is required for apical growth and plays a role in morphogenesis and Saccharomyces cerevisiae glycolipid anchored surface protein.; PDB: 2W61_A 2W62_A 2W63_A.
Probab=23.07 E-value=1.7e+02 Score=25.61 Aligned_cols=54 Identities=22% Similarity=0.320 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q psy3230 70 SPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVT 133 (151)
Q Consensus 70 t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~T 133 (151)
=|.|-..+.+.=+...++||+..|+|+- =-+-..-+.++++|..+|+.+ |.|+.
T Consensus 47 DPLad~~~C~rDi~~l~~LgiNtIRVY~--------vdp~~nHd~CM~~~~~aGIYv--i~Dl~ 100 (314)
T PF03198_consen 47 DPLADPEACKRDIPLLKELGINTIRVYS--------VDPSKNHDECMSAFADAGIYV--ILDLN 100 (314)
T ss_dssp -GGG-HHHHHHHHHHHHHHT-SEEEES-----------TTS--HHHHHHHHHTT-EE--EEES-
T ss_pred CcccCHHHHHHhHHHHHHcCCCEEEEEE--------eCCCCCHHHHHHHHHhCCCEE--EEecC
Confidence 3565555666677788999999999985 234557788999999999765 44543
No 93
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The crystal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases [].; GO: 0004140 dephospho-CoA kinase activity, 0005524 ATP binding, 0015937 coenzyme A biosynthetic process; PDB: 1VHL_A 1N3B_A 1VIY_A 1VHT_B 1T3H_B 1UF9_C 2F6R_A 2GRJ_D 2IF2_C 1JJV_A.
Probab=22.99 E-value=1.9e+02 Score=22.63 Aligned_cols=22 Identities=18% Similarity=0.237 Sum_probs=19.0
Q ss_pred CCCCChHHHHHHHHhCCCeEEE
Q psy3230 107 TPGPGAQSALRALARSNMKIGR 128 (151)
Q Consensus 107 G~G~Gr~~~ik~L~~~gl~I~~ 128 (151)
|+|.|+.++.+.|...|+.+.+
T Consensus 8 ~igsGKStv~~~l~~~G~~vid 29 (180)
T PF01121_consen 8 GIGSGKSTVSKILAELGFPVID 29 (180)
T ss_dssp STTSSHHHHHHHHHHTT-EEEE
T ss_pred CCcCCHHHHHHHHHHCCCCEEC
Confidence 7999999999999999988765
No 94
>COG0057 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]
Probab=22.89 E-value=1.1e+02 Score=27.17 Aligned_cols=29 Identities=31% Similarity=0.381 Sum_probs=21.2
Q ss_pred cCCCC-ChHHHHHHHH-hC-CCeEEEEEecCCC
Q psy3230 106 KTPGP-GAQSALRALA-RS-NMKIGRIEDVTPI 135 (151)
Q Consensus 106 kG~G~-Gr~~~ik~L~-~~-gl~I~~I~D~Tpi 135 (151)
+|||. ||..+ +++. +. .++|+-|.|.|+.
T Consensus 7 NGfGrIGR~v~-ra~~~~~~dieVVaInd~t~~ 38 (335)
T COG0057 7 NGFGRIGRLVA-RAALERDGDIEVVAINDLTDP 38 (335)
T ss_pred ecCcHHHHHHH-HHHHhCCCCeEEEEEecCCCH
Confidence 79996 67665 5555 45 4999999997653
No 95
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=22.87 E-value=1e+02 Score=25.59 Aligned_cols=27 Identities=37% Similarity=0.739 Sum_probs=22.7
Q ss_pred CCHHHHHHHHHHHHHHHHHcCceEEEEE
Q psy3230 69 ASPYAAMLAAQDVAEKCKTLGITALHIK 96 (151)
Q Consensus 69 ~t~~Aa~~aa~~~~~k~~~~gi~~v~V~ 96 (151)
+=|||++ +.+.+.+.|.++|+..+++.
T Consensus 73 THPfA~~-is~~a~~ac~~~~ipyiR~e 99 (248)
T PRK08057 73 THPYAAQ-ISANAAAACRALGIPYLRLE 99 (248)
T ss_pred CCccHHH-HHHHHHHHHHHhCCcEEEEe
Confidence 4589876 66889999999999999876
No 96
>PRK08335 translation initiation factor IF-2B subunit alpha; Validated
Probab=22.80 E-value=2.6e+02 Score=23.81 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q psy3230 77 AAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVT 133 (151)
Q Consensus 77 aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~T 133 (151)
++..++..+.+.|.. ++|++-- ++-...|+.. .+.|.+.|+.+..|.|..
T Consensus 121 tv~~~l~~A~~~gk~-~~V~v~E-----srP~~qG~~l-a~eL~~~GI~vtlI~Dsa 170 (275)
T PRK08335 121 AVLEILKTAKRKGKR-FKVILTE-----SAPDYEGLAL-ANELEFLGIEFEVITDAQ 170 (275)
T ss_pred HHHHHHHHHHHcCCc-eEEEEec-----CCCchhHHHH-HHHHHHCCCCEEEEeccH
Confidence 456666777777743 5555522 2456678888 688999999999999863
No 97
>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3.1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae []. ; PDB: 3KWS_B 3DX5_A 3CQH_B 3CQI_A 3CQK_A 3CQJ_B 2G0W_B 1DXI_A 2ZDS_D 3TVA_B ....
Probab=22.75 E-value=79 Score=23.52 Aligned_cols=44 Identities=18% Similarity=0.246 Sum_probs=28.0
Q ss_pred HHHHHcCceEEEEEEEecCCCcccCCCCC-----hHHHHHHHHhCCCeEEEEEecC
Q psy3230 83 EKCKTLGITALHIKLRATGGNRTKTPGPG-----AQSALRALARSNMKIGRIEDVT 133 (151)
Q Consensus 83 ~k~~~~gi~~v~V~vr~~~g~~~kG~G~G-----r~~~ik~L~~~gl~I~~I~D~T 133 (151)
+.+.++|+..|++.+. ...... .+.+.+.+.+.|++|.++.=.+
T Consensus 2 ~~~~~~G~~~vE~~~~-------~~~~~~~~~~~~~~~~~~~~~~gl~i~~~~~~~ 50 (213)
T PF01261_consen 2 EAAAEAGFDGVELRFD-------DGQPWDEKDDEAEELRRLLEDYGLKIASLHPPT 50 (213)
T ss_dssp HHHHHTTHSEEEEEHH-------HHSHHTHHHHHHHHHHHHHHHTTCEEEEEEEEE
T ss_pred hHHHHcCCCEEEEecC-------CCcccccchHHHHHHHHHHHHcCCeEEEEeccc
Confidence 4567788888888873 222222 4456666777888877765433
No 98
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=22.64 E-value=4.3e+02 Score=21.92 Aligned_cols=59 Identities=14% Similarity=0.107 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHH-----HH-----------HHHHhCCCeEEEEEecCCC
Q psy3230 72 YAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQS-----AL-----------RALARSNMKIGRIEDVTPI 135 (151)
Q Consensus 72 ~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~-----~i-----------k~L~~~gl~I~~I~D~Tpi 135 (151)
.++..+...+.+.|.++||+.|.|+. +.-=+..|.. .+ ..+...|++|.-|-|...+
T Consensus 30 ~~G~~~l~~i~~~~~~lgIk~lTvYa-------FS~eN~~R~~~Ev~~Lm~L~~~~l~~~~~~~~~~~irvr~iG~~~~L 102 (233)
T PRK14841 30 QRGAEVLHNTVKWSLELGIKYLTAFS-------FSTENWKRPKEEVEFLMDLFVQMIDREMELLRRERVRVRILGRKEGL 102 (233)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEe-------eeHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHcCcEEEEEeChhhC
Confidence 45566778889999999999999987 2332333411 11 1233568999999999888
Q ss_pred CC
Q psy3230 136 PS 137 (151)
Q Consensus 136 ph 137 (151)
|-
T Consensus 103 p~ 104 (233)
T PRK14841 103 PE 104 (233)
T ss_pred CH
Confidence 84
No 99
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=22.61 E-value=2.2e+02 Score=22.88 Aligned_cols=51 Identities=12% Similarity=0.178 Sum_probs=30.2
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCcccCCCCC---hHHHHHHHHhCCCeEEEEE
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPG---AQSALRALARSNMKIGRIE 130 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~G---r~~~ik~L~~~gl~I~~I~ 130 (151)
+..++.+.++|+..|++.+.... ......+.. .+.+-+.+...|+.|.++.
T Consensus 24 ~e~~~~~~~~G~~~iEl~~~~~~-~~~~~~~~~~~~~~~l~~~l~~~gl~i~~~~ 77 (283)
T PRK13209 24 LEKLAIAKTAGFDFVEMSVDESD-ERLARLDWSREQRLALVNALVETGFRVNSMC 77 (283)
T ss_pred HHHHHHHHHcCCCeEEEecCccc-cchhccCCCHHHHHHHHHHHHHcCCceeEEe
Confidence 44667788999999999873110 000111112 2234455667899998875
No 100
>PRK13663 hypothetical protein; Provisional
Probab=22.55 E-value=1.2e+02 Score=28.14 Aligned_cols=24 Identities=25% Similarity=0.401 Sum_probs=19.3
Q ss_pred CHHHHHHHHHHHHHHHHHcCceEE
Q psy3230 70 SPYAAMLAAQDVAEKCKTLGITAL 93 (151)
Q Consensus 70 t~~Aa~~aa~~~~~k~~~~gi~~v 93 (151)
|.|..|-+|..+.+++..+||+.-
T Consensus 114 Tqy~~qp~a~~F~~rLe~~GIkvy 137 (493)
T PRK13663 114 TQYDGQPAADAFRNRLERLGIKVY 137 (493)
T ss_pred EecCCChHHHHHHHHHHHCCCceE
Confidence 567778888889999999998753
No 101
>PRK04266 fibrillarin; Provisional
Probab=22.52 E-value=3.6e+02 Score=21.81 Aligned_cols=66 Identities=27% Similarity=0.315 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q psy3230 71 PYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSD 138 (151)
Q Consensus 71 ~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~TpiphN 138 (151)
|.....+.+.+.+.++.-|.=.|.|..+.. ++.+....-.+..++.|..+|+++....|.+|...|
T Consensus 152 p~~~~~~L~~~~r~LKpGG~lvI~v~~~~~--d~~~~~~~~~~~~~~~l~~aGF~~i~~~~l~p~~~~ 217 (226)
T PRK04266 152 PNQAEIAIDNAEFFLKDGGYLLLAIKARSI--DVTKDPKEIFKEEIRKLEEGGFEILEVVDLEPYHKD 217 (226)
T ss_pred hhHHHHHHHHHHHhcCCCcEEEEEEecccc--cCcCCHHHHHHHHHHHHHHcCCeEEEEEcCCCCcCC
Confidence 443333445555556656665555665210 111111111123568888999999999999887543
No 102
>PRK13490 chemoreceptor glutamine deamidase CheD; Provisional
Probab=22.49 E-value=2.3e+02 Score=22.11 Aligned_cols=59 Identities=19% Similarity=0.240 Sum_probs=39.7
Q ss_pred CCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccC-------CCC---ChHHHHHHHHhCCCeEEE
Q psy3230 69 ASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKT-------PGP---GAQSALRALARSNMKIGR 128 (151)
Q Consensus 69 ~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG-------~G~---Gr~~~ik~L~~~gl~I~~ 128 (151)
...||.. |.+.+++...++|...=++..+-.||-.+-. ++. +-+++.+.|.+.|+.|+.
T Consensus 62 ~~rY~d~-ai~~Li~~m~~~Ga~~~~l~aKifGGA~m~~~~~~~~~~~IG~rNv~~a~~~L~~~gI~i~a 130 (162)
T PRK13490 62 PMKFADL-AIPILIEKMEKLGANKRNLKAKIAGGASMFNFSDKSMVMDIGNRNGKAVKKKLKELSIPILA 130 (162)
T ss_pred CccCHHH-HHHHHHHHHHHcCCCHHHEEEEEEeCccccCCCCccccCChhHHHHHHHHHHHHHcCCcEEE
Confidence 3457664 6688999999999875444444466665432 233 446688888899998865
No 103
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=22.47 E-value=3.7e+02 Score=24.62 Aligned_cols=55 Identities=20% Similarity=0.334 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCC-h--HHHHHHHHhCCCeEEEEEecCCCC
Q psy3230 73 AAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPG-A--QSALRALARSNMKIGRIEDVTPIP 136 (151)
Q Consensus 73 Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~G-r--~~~ik~L~~~gl~I~~I~D~Tpip 136 (151)
.++..+..+++++++-|+..|.+. ..=|.- | -...|.|.+.|+.++.|..+|||.
T Consensus 320 ~a~~~g~eIa~~Lk~dgVDAvILt---------stCgtCtrcga~m~keiE~~GIPvV~i~~~~pI~ 377 (431)
T TIGR01917 320 NSKQFAKEFSKELLAAGVDAVILT---------STUGTCTRCGATMVKEIERAGIPVVHICTVTPIA 377 (431)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEc---------CCCCcchhHHHHHHHHHHHcCCCEEEEeechhHH
Confidence 345577889999999999988776 344443 2 236688999999999999999975
No 104
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=22.27 E-value=4.5e+02 Score=21.73 Aligned_cols=58 Identities=19% Similarity=0.217 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHH-----HHH-----------HHHhCCCeEEEEEecCCCC
Q psy3230 73 AAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQS-----ALR-----------ALARSNMKIGRIEDVTPIP 136 (151)
Q Consensus 73 Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~-----~ik-----------~L~~~gl~I~~I~D~Tpip 136 (151)
++......+.+.|.++|++.|.|+. +.-=+..|.. .+. .+...|++|.-|-|...+|
T Consensus 21 ~G~~~l~~i~~~c~~~GI~~lT~ya-------FS~eN~~R~~~Ev~~Lm~l~~~~l~~~~~~~~~~~i~vr~iG~~~~Lp 93 (229)
T PRK10240 21 AGAKSVRRAVSFAANNGIEALTLYA-------FSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFN 93 (229)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEe-------eehhhcCcCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEeChhhCC
Confidence 4455667888999999999999987 2322333321 111 1334588999999999888
Q ss_pred C
Q psy3230 137 S 137 (151)
Q Consensus 137 h 137 (151)
-
T Consensus 94 ~ 94 (229)
T PRK10240 94 S 94 (229)
T ss_pred H
Confidence 4
No 105
>PF00208 ELFV_dehydrog: Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; InterPro: IPR006096 Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction. Glutamate dehydrogenases (1.4.1.2 from EC, 1.4.1.3 from EC, and 1.4.1.4 from EC) (GluDH) are enzymes that catalyse the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate [, ]. GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction [] - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha- keto acids []. Leucine dehydrogenase (1.4.1.9 from EC) (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues []. Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle. Phenylalanine dehydrogenase (1.4.1.20 from EC) (PheDH) is na NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate []. Valine dehydrogenase (1.4.1.8 from EC) (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate []. This entry represents the C-terminal domain of these proteins.; GO: 0016491 oxidoreductase activity, 0006520 cellular amino acid metabolic process, 0055114 oxidation-reduction process; PDB: 1LEH_A 3AOG_D 3AOE_A 2YFQ_B 2YFH_B 1HRD_A 1K89_A 1AUP_A 1BGV_A 1B26_C ....
Probab=22.25 E-value=69 Score=26.46 Aligned_cols=61 Identities=21% Similarity=0.229 Sum_probs=36.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCC
Q psy3230 66 RDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTP 134 (151)
Q Consensus 66 ~rK~t~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~Tp 134 (151)
+...|-|....+.+.+++......+...+|.+ .|||.==..+.+.|...|.+|+-|.|.+.
T Consensus 6 ~~~aTg~GV~~~~~~~~~~~~~~~l~g~~v~I--------qGfG~VG~~~a~~l~~~Ga~vv~vsD~~G 66 (244)
T PF00208_consen 6 RSEATGYGVAYAIEAALEHLGGDSLEGKRVAI--------QGFGNVGSHAARFLAELGAKVVAVSDSSG 66 (244)
T ss_dssp TTTHHHHHHHHHHHHHHHHTTCHSSTTCEEEE--------EESSHHHHHHHHHHHHTTEEEEEEEESSE
T ss_pred CCcchHHHHHHHHHHHHHHcCCCCcCCCEEEE--------ECCCHHHHHHHHHHHHcCCEEEEEecCce
Confidence 33445555444545444442111255677888 47775333445668788999999999763
No 106
>PRK10809 ribosomal-protein-S5-alanine N-acetyltransferase; Provisional
Probab=22.20 E-value=3.4e+02 Score=20.31 Aligned_cols=48 Identities=13% Similarity=0.014 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHH-cCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q psy3230 71 PYAAMLAAQDVAEKCKT-LGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIE 130 (151)
Q Consensus 71 ~~Aa~~aa~~~~~k~~~-~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~ 130 (151)
-|+.. +...+.+.+.+ +|+..|.+.+ -..-..+++.+.+.|++...+.
T Consensus 119 G~~~e-a~~~ll~~~~~~l~l~~i~~~v-----------~~~N~~S~~l~ek~Gf~~~g~~ 167 (194)
T PRK10809 119 GLMFE-ALQAAIRYMQRQQHMHRIMANY-----------MPHNKRSGDLLARLGFEKEGYA 167 (194)
T ss_pred CHHHH-HHHHHHHHHHhcCCceEEEEEe-----------eCCCHHHHHHHHHCCCcEEeee
Confidence 46554 44667788765 7999999998 3556788888889999765543
No 107
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y [, ].; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process, 0055114 oxidation-reduction process
Probab=22.16 E-value=1.1e+02 Score=25.33 Aligned_cols=27 Identities=37% Similarity=0.704 Sum_probs=22.6
Q ss_pred CCHHHHHHHHHHHHHHHHHcCceEEEEE
Q psy3230 69 ASPYAAMLAAQDVAEKCKTLGITALHIK 96 (151)
Q Consensus 69 ~t~~Aa~~aa~~~~~k~~~~gi~~v~V~ 96 (151)
+=|||++ +.+++.+-|.++|+..+++.
T Consensus 74 THPfA~~-is~na~~a~~~~~ipylR~e 100 (249)
T PF02571_consen 74 THPFAAE-ISQNAIEACRELGIPYLRFE 100 (249)
T ss_pred CCchHHH-HHHHHHHHHhhcCcceEEEE
Confidence 4589775 66889999999999998876
No 108
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=21.86 E-value=4e+02 Score=22.30 Aligned_cols=61 Identities=20% Similarity=0.275 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChH---HHH-----------HHHHhCCCeEEEEEecCCCCC
Q psy3230 72 YAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQ---SAL-----------RALARSNMKIGRIEDVTPIPS 137 (151)
Q Consensus 72 ~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~---~~i-----------k~L~~~gl~I~~I~D~Tpiph 137 (151)
.++......+.+-|.++|++.|.|+.=-. ..|..-.+ ..+ ..+...|+.|.-|-|...+|-
T Consensus 49 ~~G~~~l~~~l~~c~~~GI~~vTvYaFS~-----eN~~R~~~Ev~~Lm~l~~~~l~~~~~~~~~~~iri~viG~~~~Lp~ 123 (251)
T PRK14830 49 KAGMDTVKKITKAASELGVKVLTLYAFST-----ENWKRPKDEVKFLMNLPVEFLDKFVPELIENNVKVNVIGDTDRLPE 123 (251)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEEEeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcChhhCCH
Confidence 34555678899999999999999987211 22333222 122 122346899999999998883
No 109
>PRK09997 hydroxypyruvate isomerase; Provisional
Probab=21.76 E-value=2.4e+02 Score=22.60 Aligned_cols=42 Identities=12% Similarity=0.071 Sum_probs=30.5
Q ss_pred HHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q psy3230 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRI 129 (151)
Q Consensus 79 ~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I 129 (151)
+..++.+.++||..|++.. -+...-+.+.+.|...||++...
T Consensus 18 ~~~l~~~a~~Gf~~VEl~~---------~~~~~~~~~~~~l~~~gl~~~~~ 59 (258)
T PRK09997 18 LARFEKAAQCGFRGVEFMF---------PYDYDIEELKQVLASNKLEHTLH 59 (258)
T ss_pred HHHHHHHHHhCCCEEEEcC---------CCCCCHHHHHHHHHHcCCcEEEE
Confidence 4467788899999999953 22345566667777899999763
No 110
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=21.74 E-value=1e+02 Score=22.49 Aligned_cols=22 Identities=18% Similarity=0.111 Sum_probs=18.4
Q ss_pred eeEEEEEccCCCeEEEEEcCCC
Q psy3230 28 FGVAHIFASFNDTFVHVTDLSG 49 (151)
Q Consensus 28 ~gi~hI~~t~NNTiitlTD~~G 49 (151)
....+|-+-.|+|+||..|...
T Consensus 60 ~d~AlVvsv~NrTVITAmd~~~ 81 (96)
T TIGR02530 60 NDAALVVSLKNRTVITAMDKDE 81 (96)
T ss_pred CCEEEEEEcCCCeEEEEeCchh
Confidence 4668888999999999998653
No 111
>PRK10427 putative PTS system fructose-like transporter subunit EIIB; Provisional
Probab=21.71 E-value=1.7e+02 Score=21.47 Aligned_cols=26 Identities=15% Similarity=0.311 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHcCceEEEEEEEec
Q psy3230 74 AMLAAQDVAEKCKTLGITALHIKLRAT 100 (151)
Q Consensus 74 a~~aa~~~~~k~~~~gi~~v~V~vr~~ 100 (151)
+++|++.+.+.++++|+. +.|..+|.
T Consensus 18 t~lAAeaL~kAA~~~G~~-i~VE~qg~ 43 (114)
T PRK10427 18 TYMAAERLEKLCQLEKWG-VKIETQGA 43 (114)
T ss_pred HHHHHHHHHHHHHHCCCe-EEEEecCC
Confidence 457788888889999997 88888653
No 112
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=21.61 E-value=3.5e+02 Score=24.82 Aligned_cols=55 Identities=18% Similarity=0.280 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCC-h--HHHHHHHHhCCCeEEEEEecCCCCC
Q psy3230 74 AMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPG-A--QSALRALARSNMKIGRIEDVTPIPS 137 (151)
Q Consensus 74 a~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~G-r--~~~ik~L~~~gl~I~~I~D~Tpiph 137 (151)
+...+..+++++++-|+..|.+. ..=|.- | -...|.|.+.|+.++.|..+|||..
T Consensus 321 a~~~g~eIa~~Lk~dgVDAVILT---------stCgtC~r~~a~m~keiE~~GiPvv~~~~~~pis~ 378 (431)
T TIGR01918 321 SKQFAKEFVVELKQGGVDAVILT---------STUGTCTRCGATMVKEIERAGIPVVHMCTVIPIAL 378 (431)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEc---------CCCCcchhHHHHHHHHHHHcCCCEEEEeecccHhh
Confidence 44677889999999999988776 233443 2 2356889999999999999999754
No 113
>PRK10975 TDP-fucosamine acetyltransferase; Provisional
Probab=21.59 E-value=3.6e+02 Score=20.38 Aligned_cols=47 Identities=28% Similarity=0.326 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q psy3230 71 PYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRI 129 (151)
Q Consensus 71 ~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I 129 (151)
-++.. +.+.+.+.+.+.|+..|.+.+ -..-..+++.+.+.|+....+
T Consensus 142 Gig~~-Ll~~~~~~a~~~g~~~i~l~v-----------~~~N~~a~~~yek~Gf~~~~~ 188 (194)
T PRK10975 142 GIGAR-LMQAALNWCQARGLTRLRVAT-----------QMGNLAALRLYIRSGANIEST 188 (194)
T ss_pred CHHHH-HHHHHHHHHHHcCCCEEEEEe-----------CCCcHHHHHHHHHCCCeEeEE
Confidence 35444 446677788889999998887 233457788888889876544
No 114
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=21.28 E-value=3e+02 Score=23.51 Aligned_cols=50 Identities=22% Similarity=0.269 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q psy3230 76 LAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDV 132 (151)
Q Consensus 76 ~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~ 132 (151)
.+++.++..|.+.|-+ ++|.+-- +.-.+.|+..+ +.|.+.|+.+.-|.|.
T Consensus 131 ~tv~~~l~~A~~~~k~-~~V~v~E-----srP~~~G~~~a-~~L~~~GI~vtlI~Ds 180 (310)
T PRK08535 131 SAALSVIKTAHEQGKD-IEVIATE-----TRPRNQGHITA-KELAEYGIPVTLIVDS 180 (310)
T ss_pred HHHHHHHHHHHHCCCe-EEEEEec-----CCchhhHHHHH-HHHHHCCCCEEEEehh
Confidence 3556666777766654 5566521 24455676665 6688899999999985
No 115
>cd05801 PGM_like3 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=21.14 E-value=5.1e+02 Score=23.54 Aligned_cols=77 Identities=21% Similarity=0.227 Sum_probs=45.8
Q ss_pred EecccceeeccCCCCCHHHHHHHHHHHHHHHHHcCc-eEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe--
Q psy3230 55 RITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGI-TALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIED-- 131 (151)
Q Consensus 55 ~sSgg~g~k~~~rK~t~~Aa~~aa~~~~~k~~~~gi-~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D-- 131 (151)
..++|+...-+...-|++-++.++.-+++.+.+.+- ..|.|=-.. -..-..-.+.++.+|...|++|....|
T Consensus 23 FGT~GiRG~~g~~~lt~~~v~~i~~a~~~~l~~~~~~~~VvVg~D~-----R~~S~~~~~~~~~gL~s~Gi~V~~~~~~g 97 (522)
T cd05801 23 FGTSGHRGSSLKGSFNEAHILAISQAICDYRKSQGITGPLFLGKDT-----HALSEPAFISALEVLAANGVEVIIQQNDG 97 (522)
T ss_pred EEcccccCccCCCchhHHHHHHHHHHHHHHHHhhCCCCeEEEEeCC-----CcCCHHHHHHHHHHHHHCCCEEEEeCCCC
Confidence 334455332222246888888888888888765543 224333211 011234445666889999999998766
Q ss_pred cCCCC
Q psy3230 132 VTPIP 136 (151)
Q Consensus 132 ~Tpip 136 (151)
.+|.|
T Consensus 98 ~~pTP 102 (522)
T cd05801 98 YTPTP 102 (522)
T ss_pred CCCch
Confidence 56666
No 116
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=21.02 E-value=4.8e+02 Score=21.66 Aligned_cols=62 Identities=16% Similarity=0.197 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChH---HHHH-----------HHHhCCCeEEEEEecCCCC
Q psy3230 71 PYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQ---SALR-----------ALARSNMKIGRIEDVTPIP 136 (151)
Q Consensus 71 ~~Aa~~aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~---~~ik-----------~L~~~gl~I~~I~D~Tpip 136 (151)
-.++..+...+.+.|.++|++.|.|+.=-+ ..|..-.+ ..+. .|...|+.|.-|-|...+|
T Consensus 32 H~~G~~~~~~i~~~c~~~GI~~lT~YaFS~-----EN~~Rp~~EV~~Lm~L~~~~l~~~~~~~~~~~irvr~iGd~~~Lp 106 (230)
T PRK14837 32 HKEGLKRAKEIVKHSLKLGIKYLSLYVFST-----ENWNRTDSEIEHLMFLIADYLSSEFNFYKKNNIKIIVSGDIESLS 106 (230)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEcChhhCC
Confidence 345566778899999999999999986211 22322221 1111 2234689999999999888
Q ss_pred C
Q psy3230 137 S 137 (151)
Q Consensus 137 h 137 (151)
-
T Consensus 107 ~ 107 (230)
T PRK14837 107 E 107 (230)
T ss_pred H
Confidence 4
No 117
>PRK07729 glyceraldehyde-3-phosphate dehydrogenase; Validated
Probab=20.93 E-value=1.1e+02 Score=26.83 Aligned_cols=30 Identities=20% Similarity=0.167 Sum_probs=21.7
Q ss_pred cCCCCChHHHHHHHH-hCCCeEEEEEecCCC
Q psy3230 106 KTPGPGAQSALRALA-RSNMKIGRIEDVTPI 135 (151)
Q Consensus 106 kG~G~Gr~~~ik~L~-~~gl~I~~I~D~Tpi 135 (151)
+|||.-=..++|++. ...++|+-|-|.+.+
T Consensus 8 NGfGRIGR~~~r~~~~~~~~~vvaINd~~~~ 38 (343)
T PRK07729 8 NGFGRIGRMVFRKAIKESAFEIVAINASYPS 38 (343)
T ss_pred ECcChHHHHHHHHHhhcCCcEEEEecCCCCH
Confidence 799974445667654 567999999997653
No 118
>PF15492 Nbas_N: Neuroblastoma-amplified sequence, N terminal
Probab=20.88 E-value=1.5e+02 Score=25.70 Aligned_cols=44 Identities=14% Similarity=0.194 Sum_probs=35.2
Q ss_pred ecCceeeccceeeeEEEEEccCCCeEEEEEcCCCCEEEEEecccc
Q psy3230 16 SLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGM 60 (151)
Q Consensus 16 ~~~~~~~~~~~~~gi~hI~~t~NNTiitlTD~~G~~~~~~sSgg~ 60 (151)
+++-..+++++..+|.-+..|+|++++..+...|...+ |.--++
T Consensus 218 ~~~~fs~~~~~~d~i~kmSlSPdg~~La~ih~sG~lsL-W~iPsL 261 (282)
T PF15492_consen 218 SFKFFSRQGQEQDGIFKMSLSPDGSLLACIHFSGSLSL-WEIPSL 261 (282)
T ss_pred ceeeeeccccCCCceEEEEECCCCCEEEEEEcCCeEEE-EecCcc
Confidence 44445778889999999999999999999999998754 554443
No 119
>PRK08334 translation initiation factor IF-2B subunit beta; Validated
Probab=20.84 E-value=2.4e+02 Score=25.08 Aligned_cols=50 Identities=14% Similarity=0.070 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHcCceEEEEEEEecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q psy3230 77 AAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDV 132 (151)
Q Consensus 77 aa~~~~~k~~~~gi~~v~V~vr~~~g~~~kG~G~Gr~~~ik~L~~~gl~I~~I~D~ 132 (151)
++..++..|.+.|. .++|++- -++-...|....-..|...|+.+..|.|.
T Consensus 179 Tal~vi~~A~~~gk-~~~V~v~-----EtRP~~qG~rlta~eL~~~GI~vtlI~Ds 228 (356)
T PRK08334 179 TVGAVLRVMHKDGT-LKLLWVD-----ETRPVLQGARLSAWEYHYDGIPLKLISDN 228 (356)
T ss_pred hHHHHHHHHHHcCC-eEEEEEC-----CCCchhhHHHHHHHHHHHCCCCEEEEehh
Confidence 45556677777784 5777762 22455677766556788999999999996
No 120
>PF03123 CAT_RBD: CAT RNA binding domain; InterPro: IPR004341 The CAT RNA-binding domain is found at the amino terminus of a family of transcriptional antiterminator proteins, the Co-AntiTerminator (CAT) domain. This domain forms a dimer in the crystal structure []. Transcriptional antiterminators of the BglG/SacY family are regulatory proteins that mediate the induction of sugar metabolizing operons in Gram-positive and Gram-negative bacteria. Upon activation, these proteins bind to specific targets in nascent mRNAs, thereby preventing abortive dissociation of the RNA polymerase from the DNA template [].; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1AUU_B 1TLV_A 1L1C_A 1H99_A 3RIO_A.
Probab=20.35 E-value=95 Score=20.42 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=15.4
Q ss_pred CCCeEEEEEcCCCCEEEEEecccceeec
Q psy3230 37 FNDTFVHVTDLSGRETIARITGGMKVKA 64 (151)
Q Consensus 37 ~NNTiitlTD~~G~~~~~~sSgg~g~k~ 64 (151)
.||.++ +.|.+|+.. ....-|+||.+
T Consensus 8 NNNvvl-~~~~~~~E~-Iv~GkGIGF~k 33 (59)
T PF03123_consen 8 NNNVVL-AKDDNGQEV-IVMGKGIGFGK 33 (59)
T ss_dssp ETTEEE-EE-CCSSEE-EEE-TTSSTT-
T ss_pred cCeEEE-EEeCCCCEE-EEEeecceecc
Confidence 456655 559999874 35556888865
No 121
>PF02878 PGM_PMM_I: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I; InterPro: IPR005844 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 3I3W_B 1WQA_C 1KFQ_B 1KFI_A 2Z0F_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=20.12 E-value=82 Score=23.08 Aligned_cols=62 Identities=19% Similarity=0.162 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHc-CceEEEEEEEecCCCcccCCC-CChHHHHHHHHhCCCeEEEEEecCCCC
Q psy3230 68 EASPYAAMLAAQDVAEKCKTL-GITALHIKLRATGGNRTKTPG-PGAQSALRALARSNMKIGRIEDVTPIP 136 (151)
Q Consensus 68 K~t~~Aa~~aa~~~~~k~~~~-gi~~v~V~vr~~~g~~~kG~G-~Gr~~~ik~L~~~gl~I~~I~D~Tpip 136 (151)
.-||..+..++..+++.+.+. .-..|.|=-.. +-.+ .-.+++..+|...|++|..+. .+|.|
T Consensus 17 ~lt~~~~~~~~~a~~~~~~~~~~~~~VvVg~D~------R~~s~~~~~~~~~~l~~~G~~V~~~g-~~~tP 80 (137)
T PF02878_consen 17 ELTPEFAARLAQAFASYLKEKGNGSRVVVGRDT------RPSSPMLAKALAAGLRANGVDVIDIG-LVPTP 80 (137)
T ss_dssp TBSHHHHHHHHHHHHHHHHHTTTSSEEEEEE-S------STTHHHHHHHHHHHHHHTTEEEEEEE-EB-HH
T ss_pred CCCHHHHHHHHHHHHHhhcccCCCCeEEEEEcc------cCCHHHHHHHHHHHHhhccccccccc-ccCcH
Confidence 368998888989888888774 33444444321 1111 235567788888999998776 55554
Done!