Query 031952
Match_columns 150
No_of_seqs 107 out of 834
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 07:37:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031952.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031952hhsearch_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 1.4E-52 3.1E-57 323.2 18.2 137 12-148 13-149 (149)
2 PRK09607 rps11p 30S ribosomal 100.0 4.1E-50 8.9E-55 304.7 17.5 126 24-150 6-132 (132)
3 PRK05309 30S ribosomal protein 100.0 4E-47 8.6E-52 287.2 16.0 115 24-147 14-128 (128)
4 COG0100 RpsK Ribosomal protein 100.0 5.4E-47 1.2E-51 286.0 15.3 125 14-147 5-129 (129)
5 PF00411 Ribosomal_S11: Riboso 100.0 7.3E-47 1.6E-51 278.6 13.5 110 28-146 1-110 (110)
6 TIGR03632 bact_S11 30S ribosom 100.0 2.1E-45 4.5E-50 270.4 15.2 108 28-144 1-108 (108)
7 TIGR03628 arch_S11P archaeal r 100.0 3.8E-43 8.3E-48 260.9 16.1 112 27-139 2-114 (114)
8 CHL00041 rps11 ribosomal prote 100.0 3.2E-42 6.9E-47 256.5 15.6 112 19-139 5-116 (116)
9 PTZ00090 40S ribosomal protein 100.0 6.6E-40 1.4E-44 265.3 14.8 109 29-147 120-233 (233)
10 KOG0408 Mitochondrial/chloropl 100.0 1.7E-38 3.6E-43 248.2 13.3 114 25-147 77-190 (190)
11 KOG0407 40S ribosomal protein 100.0 4.3E-35 9.3E-40 217.3 14.9 138 13-150 2-139 (139)
12 cd00432 Ribosomal_L18_L5e Ribo 97.9 0.00023 5E-09 51.4 10.8 90 26-123 10-103 (103)
13 PF00861 Ribosomal_L18p: Ribos 97.7 0.0011 2.4E-08 49.4 11.0 92 26-125 22-119 (119)
14 PRK05593 rplR 50S ribosomal pr 97.6 0.00085 1.8E-08 50.2 10.2 94 24-124 21-116 (117)
15 PRK08569 rpl18p 50S ribosomal 97.6 0.0018 3.9E-08 52.4 12.2 104 28-146 33-142 (193)
16 TIGR00060 L18_bact ribosomal p 97.6 0.0017 3.8E-08 48.5 10.7 88 26-124 23-113 (114)
17 CHL00139 rpl18 ribosomal prote 97.4 0.003 6.5E-08 46.8 10.5 94 24-124 12-108 (109)
18 COG0256 RplR Ribosomal protein 96.8 0.025 5.4E-07 43.0 10.7 93 24-125 26-125 (125)
19 PTZ00032 60S ribosomal protein 94.8 0.21 4.6E-06 41.0 8.3 69 27-97 105-187 (211)
20 PTZ00069 60S ribosomal protein 84.6 11 0.00024 32.6 9.5 61 25-87 46-112 (300)
21 cd05313 NAD_bind_2_Glu_DH NAD( 69.0 13 0.00029 31.2 5.5 65 63-136 11-75 (254)
22 PF05677 DUF818: Chlamydia CHL 61.1 64 0.0014 28.7 8.4 78 47-135 171-256 (365)
23 COG0241 HisB Histidinol phosph 54.6 68 0.0015 25.7 7.0 59 79-144 38-108 (181)
24 TIGR03694 exosort_acyl putativ 47.5 60 0.0013 26.6 5.8 57 70-142 154-210 (241)
25 cd01076 NAD_bind_1_Glu_DH NAD( 46.8 52 0.0011 26.7 5.3 59 67-134 8-66 (227)
26 PLN02477 glutamate dehydrogena 45.9 62 0.0013 29.0 6.1 60 64-133 180-240 (410)
27 COG1433 Uncharacterized conser 45.0 62 0.0013 24.3 5.1 38 78-128 55-92 (121)
28 TIGR03234 OH-pyruv-isom hydrox 43.3 78 0.0017 25.2 5.8 43 78-129 17-59 (254)
29 cd05211 NAD_bind_Glu_Leu_Phe_V 40.0 68 0.0015 25.9 5.0 39 87-133 19-57 (217)
30 PF13420 Acetyltransf_4: Acety 40.0 1.4E+02 0.0029 21.3 6.7 45 73-128 94-139 (155)
31 PF02601 Exonuc_VII_L: Exonucl 39.4 91 0.002 26.1 5.9 54 72-127 56-112 (319)
32 COG2099 CobK Precorrin-6x redu 39.2 45 0.00097 28.3 3.9 26 68-94 74-99 (257)
33 PF00044 Gp_dh_N: Glyceraldehy 38.3 38 0.00082 26.1 3.1 29 105-133 6-35 (151)
34 PRK14030 glutamate dehydrogena 37.3 1E+02 0.0022 28.1 6.1 63 65-136 203-265 (445)
35 PRK01060 endonuclease IV; Prov 36.0 81 0.0017 25.4 4.9 55 78-137 15-75 (281)
36 PTZ00079 NADP-specific glutama 35.8 1.2E+02 0.0026 27.8 6.3 61 64-133 211-271 (454)
37 PRK14829 undecaprenyl pyrophos 35.7 1.8E+02 0.0039 24.2 7.0 61 70-135 40-114 (243)
38 TIGR00511 ribulose_e2b2 ribose 35.5 1.2E+02 0.0025 25.9 5.9 49 76-131 127-175 (301)
39 COG1570 XseA Exonuclease VII, 34.2 66 0.0014 29.4 4.4 54 72-127 177-230 (440)
40 PRK00394 transcription factor; 33.8 1.4E+02 0.003 23.6 5.8 51 37-91 36-86 (179)
41 PRK08535 translation initiatio 32.8 1.4E+02 0.003 25.4 6.0 50 76-132 132-181 (310)
42 PF01713 Smr: Smr domain; Int 32.6 1.5E+02 0.0033 19.7 7.1 64 70-137 8-74 (83)
43 PF13302 Acetyltransf_3: Acety 32.5 1.7E+02 0.0037 20.2 5.6 46 67-124 96-142 (142)
44 cd04516 TBP_eukaryotes eukaryo 32.0 1.3E+02 0.0027 23.8 5.2 49 38-90 38-86 (174)
45 PRK08335 translation initiatio 31.8 1.5E+02 0.0032 25.2 5.9 50 76-132 121-170 (275)
46 PF08901 DUF1847: Protein of u 31.7 99 0.0022 24.4 4.5 43 78-129 44-88 (157)
47 cd00652 TBP_TLF TATA box bindi 31.4 1.3E+02 0.0029 23.5 5.3 52 36-91 36-87 (174)
48 PRK07564 phosphoglucomutase; V 31.2 68 0.0015 29.3 4.1 78 51-135 38-119 (543)
49 PRK09989 hypothetical protein; 31.1 1.5E+02 0.0032 23.8 5.6 43 78-129 18-60 (258)
50 PF00583 Acetyltransf_1: Acety 31.0 1.4E+02 0.003 18.7 5.5 41 73-124 43-83 (83)
51 PRK13210 putative L-xylulose 5 30.9 1.5E+02 0.0033 23.7 5.7 52 77-129 18-72 (284)
52 cd04518 TBP_archaea archaeal T 30.9 1.4E+02 0.003 23.5 5.3 51 37-91 37-87 (174)
53 PRK07757 acetyltransferase; Pr 30.9 1.1E+02 0.0024 21.9 4.5 55 70-141 81-135 (152)
54 TIGR00542 hxl6Piso_put hexulos 30.6 1.3E+02 0.0028 24.4 5.3 51 78-129 19-72 (279)
55 PF00208 ELFV_dehydrog: Glutam 30.2 57 0.0012 26.9 3.1 59 67-133 8-66 (244)
56 PRK14031 glutamate dehydrogena 30.0 1.5E+02 0.0034 26.9 6.0 60 63-131 201-260 (444)
57 cd05801 PGM_like3 This bacteri 29.6 2.5E+02 0.0053 25.6 7.3 78 51-135 21-102 (522)
58 PRK09414 glutamate dehydrogena 29.6 1.3E+02 0.0028 27.3 5.5 59 65-132 207-265 (445)
59 PRK14834 undecaprenyl pyrophos 29.4 3.4E+02 0.0074 22.7 8.3 62 70-136 40-115 (249)
60 cd01469 vWA_integrins_alpha_su 28.3 1.1E+02 0.0024 23.1 4.3 100 25-130 39-140 (177)
61 COG1184 GCD2 Translation initi 28.2 2.1E+02 0.0046 24.8 6.3 50 76-132 131-180 (301)
62 PRK13209 L-xylulose 5-phosphat 27.4 1.7E+02 0.0037 23.6 5.4 51 78-129 24-77 (283)
63 PRK14840 undecaprenyl pyrophos 27.1 3.8E+02 0.0082 22.5 8.0 62 70-136 48-123 (250)
64 PTZ00349 dehydrodolichyl dipho 26.8 4.1E+02 0.0089 23.3 7.9 62 70-136 45-123 (322)
65 PRK14841 undecaprenyl pyrophos 26.4 3.7E+02 0.0081 22.2 7.9 62 70-136 29-104 (233)
66 PRK06371 translation initiatio 25.9 1.7E+02 0.0036 25.6 5.4 50 76-131 156-205 (329)
67 TIGR00512 salvage_mtnA S-methy 25.7 1.6E+02 0.0035 25.6 5.2 49 77-131 167-215 (331)
68 TIGR02382 wecD_rffC TDP-D-fuco 25.5 2.5E+02 0.0055 21.3 5.9 47 68-126 137-183 (191)
69 PLN00062 TATA-box-binding prot 25.5 1.9E+02 0.004 23.0 5.2 48 38-89 38-85 (179)
70 PF08444 Gly_acyl_tr_C: Aralky 25.4 2.6E+02 0.0056 20.0 6.1 71 42-125 2-77 (89)
71 PRK04266 fibrillarin; Provisio 25.3 2.6E+02 0.0057 22.6 6.1 66 70-137 152-217 (226)
72 COG3981 Predicted acetyltransf 25.3 3.4E+02 0.0074 21.8 6.6 39 56-96 98-138 (174)
73 PRK08334 translation initiatio 25.1 2.3E+02 0.005 25.1 6.1 51 76-132 179-229 (356)
74 PRK15425 gapA glyceraldehyde-3 25.0 87 0.0019 27.3 3.4 30 105-134 8-38 (331)
75 PRK09542 manB phosphomannomuta 24.8 2.3E+02 0.0049 25.1 6.1 63 67-136 13-76 (445)
76 TIGR01918 various_sel_PB selen 24.7 2.5E+02 0.0054 25.7 6.3 56 72-136 320-378 (431)
77 PLN02891 IMP cyclohydrolase 24.2 82 0.0018 29.6 3.2 42 78-136 36-77 (547)
78 TIGR00587 nfo apurinic endonuc 24.1 1.7E+02 0.0037 24.0 4.9 64 78-141 14-78 (274)
79 cd01853 Toc34_like Toc34-like 23.8 2.4E+02 0.0051 23.2 5.7 49 67-122 7-55 (249)
80 cd04517 TLF TBP-like factors ( 23.5 2.7E+02 0.0058 21.9 5.7 52 36-91 36-87 (174)
81 TIGR01575 rimI ribosomal-prote 23.5 2.4E+02 0.0051 18.9 6.2 49 70-130 70-118 (131)
82 PRK10646 ADP-binding protein; 23.3 3.4E+02 0.0073 21.0 6.1 44 69-123 10-54 (153)
83 COG3916 LasI N-acyl-L-homoseri 23.3 2.9E+02 0.0064 22.8 6.0 51 70-134 119-169 (209)
84 COG0057 GapA Glyceraldehyde-3- 23.3 1E+02 0.0022 27.2 3.5 30 105-134 7-38 (335)
85 cd07996 WGR_MMR_like WGR domai 23.2 2.2E+02 0.0048 18.5 5.1 43 47-90 26-72 (74)
86 PRK14831 undecaprenyl pyrophos 23.0 4.5E+02 0.0097 21.9 7.4 62 70-136 46-121 (249)
87 PRK00286 xseA exodeoxyribonucl 22.9 1.6E+02 0.0035 25.9 4.8 36 91-127 194-229 (438)
88 PRK09491 rimI ribosomal-protei 22.9 2.8E+02 0.0061 19.6 7.9 55 67-133 76-130 (146)
89 PRK05720 mtnA methylthioribose 22.8 2.5E+02 0.0054 24.6 5.9 49 77-131 167-215 (344)
90 TIGR00829 FRU PTS system, fruc 22.1 1.7E+02 0.0036 20.2 3.9 26 72-98 12-37 (85)
91 cd01421 IMPCH Inosine monophos 22.0 1.4E+02 0.003 24.1 3.9 42 78-136 14-55 (187)
92 PF01008 IF-2B: Initiation fac 21.9 2.4E+02 0.0051 23.0 5.4 48 77-131 120-167 (282)
93 PRK09997 hydroxypyruvate isome 21.8 2.9E+02 0.0063 22.0 5.8 42 78-128 18-59 (258)
94 COG2840 Uncharacterized protei 21.7 2.5E+02 0.0055 22.6 5.3 43 69-118 105-147 (184)
95 PRK09856 fructoselysine 3-epim 21.7 2.8E+02 0.0061 22.1 5.7 61 77-138 15-77 (275)
96 TIGR00524 eIF-2B_rel eIF-2B al 21.5 2.5E+02 0.0053 24.0 5.5 50 76-131 138-187 (303)
97 PRK14742 thrL thr operon leade 21.3 52 0.0011 18.5 0.9 15 35-49 11-25 (28)
98 TIGR01917 gly_red_sel_B glycin 21.1 3.9E+02 0.0085 24.4 6.8 56 72-136 320-378 (431)
99 PF03198 Glyco_hydro_72: Gluca 21.0 1.8E+02 0.0039 25.4 4.6 50 69-126 47-96 (314)
100 PF02878 PGM_PMM_I: Phosphoglu 20.8 2.4E+02 0.0051 20.5 4.7 61 68-135 18-80 (137)
101 KOG0747 Putative NAD+-dependen 20.4 1.7E+02 0.0037 25.8 4.2 39 67-112 153-193 (331)
102 PF01261 AP_endonuc_2: Xylose 20.4 85 0.0018 23.3 2.2 44 82-132 2-50 (213)
103 PRK14830 undecaprenyl pyrophos 20.3 5.1E+02 0.011 21.6 8.0 62 70-136 48-123 (251)
104 PRK14836 undecaprenyl pyrophos 20.3 4.2E+02 0.0092 22.2 6.5 62 70-136 40-115 (253)
105 COG1710 Uncharacterized protei 20.2 1.2E+02 0.0026 23.3 2.9 54 75-136 64-123 (139)
106 PRK07729 glyceraldehyde-3-phos 20.2 1.2E+02 0.0026 26.6 3.4 30 105-134 8-38 (343)
107 PF06300 Tsp45I: Tsp45I type I 20.1 26 0.00056 29.6 -0.7 19 4-22 107-125 (261)
No 1
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=100.00 E-value=1.4e-52 Score=323.22 Aligned_cols=137 Identities=88% Similarity=1.306 Sum_probs=131.4
Q ss_pred eeeecCCcccCCceeeeEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcE
Q 031952 12 ENVTLGPAVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITA 91 (150)
Q Consensus 12 ~~~~~~~~~~~~~~~~~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~ 91 (150)
.++.++|+..+..+..||+||++|+|||||||||+.|++++|+|||++|||+.++|+||||||.||++++++|.++||+.
T Consensus 13 ~~~~~~~~~~~~~~~~Gi~hI~as~NNTiItiTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~~ 92 (149)
T PTZ00129 13 EVATLGPNVAKGELVFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGINA 92 (149)
T ss_pred eeeecCCcccCCceeEEEEEEEcccCCeEEEEEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCeE
Confidence 34467777778889999999999999999999999999999999999999999989999999999999999999999999
Q ss_pred EEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCCCCCC
Q 031952 92 LHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGR 148 (150)
Q Consensus 92 v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~RR~~ 148 (150)
|+|+++|+||+.++|+|+||+++|++|+++||+|.+|+|+||||||||||||+||.|
T Consensus 93 v~V~vr~~gg~~~kg~GpGr~~airaL~~~glkI~~I~DvTPiPhNGcRppk~RR~r 149 (149)
T PTZ00129 93 LHIKLRATGGVRTKTPGPGAQAALRALARAGLKIGRIEDVTPIPTDSTRRKGGRRGR 149 (149)
T ss_pred EEEEEEecCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEecCCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999999999999999999999999999999999986
No 2
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=100.00 E-value=4.1e-50 Score=304.69 Aligned_cols=126 Identities=60% Similarity=0.963 Sum_probs=115.8
Q ss_pred ceeeeEEEEEccCCCeEEEEeCCCCC-eEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCC
Q 031952 24 EHVFGVAHIFASFNDTFIHVTDLSGR-ETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGN 102 (150)
Q Consensus 24 ~~~~~ilhI~~t~NNT~itlTD~~G~-~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~ 102 (150)
+.+.||+||++|+|||||||||++|+ ++.|+|+|.+||+ +++|+||||||.|||+++++|.++||+.|+|+++|+||+
T Consensus 6 ~~~~gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~k-g~kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn 84 (132)
T PRK09607 6 KEKWGIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKA-DRDESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGN 84 (132)
T ss_pred CceeeEEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeC-CCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCC
Confidence 34789999999999999999999997 5555555555555 555999999999999999999999999999999999999
Q ss_pred cccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCCCCCCCC
Q 031952 103 KTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGRRL 150 (150)
Q Consensus 103 ~~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~RR~~~~ 150 (150)
+.+-+|+||+++|++|+.+||+|.+|+|+||+|||||||||+||+|||
T Consensus 85 ~~~~~G~Gr~~airal~~~glkI~~I~DvTpiPhNGCRp~K~RR~r~~ 132 (132)
T PRK09607 85 GQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTRPPGGRRGRRV 132 (132)
T ss_pred CCcCCCCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999999999999999999999999996
No 3
>PRK05309 30S ribosomal protein S11; Validated
Probab=100.00 E-value=4e-47 Score=287.18 Aligned_cols=115 Identities=41% Similarity=0.669 Sum_probs=111.8
Q ss_pred ceeeeEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCc
Q 031952 24 EHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNK 103 (150)
Q Consensus 24 ~~~~~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~ 103 (150)
+++.|++||++|+|||||||||++|++++|+|||++||++.+ |+|+||||++|+.+++++.++||+.|+|++
T Consensus 14 ~~~~gi~hI~~t~NNTiitlTd~~G~~~~~~S~G~~gfKg~r-K~T~~Aa~~aa~~~~~~~~~~gi~~v~v~i------- 85 (128)
T PRK05309 14 NIPSGVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGSR-KSTPYAAQVAAEDAAKKAKEHGMKTVEVFV------- 85 (128)
T ss_pred ccceeEEEEEccCCCEEEEEEcCCCCEEEEEecCccEeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEE-------
Confidence 488999999999999999999999999999999999999887 899999999999999999999999999999
Q ss_pred ccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCCCCC
Q 031952 104 TKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRG 147 (150)
Q Consensus 104 ~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~RR~ 147 (150)
+|+|+||+++|++|+.+|++|.+|+|+||+|||||||||+||+
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 9999999999999999999999999999999999999999985
No 4
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.4e-47 Score=286.00 Aligned_cols=125 Identities=46% Similarity=0.711 Sum_probs=118.2
Q ss_pred eecCCcccCCceeeeEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEE
Q 031952 14 VTLGPAVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALH 93 (150)
Q Consensus 14 ~~~~~~~~~~~~~~~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~ 93 (150)
+........+++..|+.||++|+||||||+||++||++.|.|+|++|||+.+ ++||||||++|+.+++.++++|++.||
T Consensus 5 ~~~~~~~~~~~i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~r-k~tpyAA~~aa~~aa~~a~e~Gi~~v~ 83 (129)
T COG0100 5 KARKKKKVKKNIADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSR-KSTPYAAQLAAEDAAKKAKEHGIKSVE 83 (129)
T ss_pred cccccceeccccccceEEEEcccCCcEEEecCCCCCEEEEEecCCceEcCCC-CCCHHHHHHHHHHHHHHHHHhCccEEE
Confidence 3344555667789999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred EEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCCCCC
Q 031952 94 IKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRG 147 (150)
Q Consensus 94 V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~RR~ 147 (150)
|++ +|+|+||++++++|+.+|++|.+|.|+||||||||||||+||+
T Consensus 84 v~v--------kgpG~GreaAiraL~~ag~~i~~I~DvTPiphnG~Rppk~RR~ 129 (129)
T COG0100 84 VKV--------KGPGPGREAAIRALAAAGLKITRIEDVTPIPHNGCRPPKRRRV 129 (129)
T ss_pred EEE--------ECCCCcHHHHHHHHHHccceEEEEEEcCCCCCCCCCCCCCCCC
Confidence 999 9999999999999999999999999999999999999999985
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=7.3e-47 Score=278.59 Aligned_cols=110 Identities=45% Similarity=0.745 Sum_probs=104.3
Q ss_pred eEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCC
Q 031952 28 GVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTP 107 (150)
Q Consensus 28 ~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~ 107 (150)
||+||++|+||||+||||++|++++|+|+|++|||+++ |+|+|||+++++.++++|+++|++.|+|+| +|+
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 79999999999999999999999999999999999998 999999999999999999999999999999 999
Q ss_pred CCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCCCC
Q 031952 108 GPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRR 146 (150)
Q Consensus 108 G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~RR 146 (150)
|+||+++|++|+++|++|.+|+|+||+|||||||||+||
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
>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=2.1e-45 Score=270.45 Aligned_cols=108 Identities=41% Similarity=0.703 Sum_probs=105.4
Q ss_pred eEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCC
Q 031952 28 GVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTP 107 (150)
Q Consensus 28 ~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~ 107 (150)
|++||++|+||||||+||++|+++.|.|+|++||++.+ |+|+|||+.+|+.++++++++||+.|+|++ +|+
T Consensus 1 gi~hI~~s~NNT~itlTd~~g~~~~~~S~G~~gfkg~r-k~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~--------kG~ 71 (108)
T TIGR03632 1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSK-KSTPYAAQLAAEDAAKKAKEFGMKTVDVYV--------KGP 71 (108)
T ss_pred CEEEEEccCCCEEEEEEcCCCCEEEEEecCceeeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEE--------ECC
Confidence 68999999999999999999999999999999999887 999999999999999999999999999999 999
Q ss_pred CCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCC
Q 031952 108 GPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGG 144 (150)
Q Consensus 108 G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~ 144 (150)
|+||+++|++|+.+|++|.+|+|+||+|||||||||+
T Consensus 72 G~gr~~~ir~l~~~glkI~~I~D~T~iphNGcR~~K~ 108 (108)
T TIGR03632 72 GAGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKR 108 (108)
T ss_pred CCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCcCCCCC
Confidence 9999999999999999999999999999999999984
No 7
>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=3.8e-43 Score=260.93 Aligned_cols=112 Identities=61% Similarity=0.961 Sum_probs=103.6
Q ss_pred eeEEEEEccCCCeEEEEeCCCCCe-EEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCccc
Q 031952 27 FGVAHIFASFNDTFIHVTDLSGRE-TLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTK 105 (150)
Q Consensus 27 ~~ilhI~~t~NNT~itlTD~~G~~-~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~k 105 (150)
.|++||++|+||||||+||..|++ +.|+|+|++||+ +++|+||||||.|+|+++++|.++||+.|+|+++|.||++.|
T Consensus 2 ~gi~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~k-g~kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~ 80 (114)
T TIGR03628 2 WGIAHIYSSFNNTIITITDITGAETIARSSGGMVVKA-DRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQK 80 (114)
T ss_pred cEEEEEEccCCCeEEEEEcCCCCEEEEEecCcceEeC-CCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCC
Confidence 689999999999999999999975 555555555555 555999999999999999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCC
Q 031952 106 TPGPGAQSALRALARSGMKIGRIEDVTPIPTDST 139 (150)
Q Consensus 106 G~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGc 139 (150)
.+|+||+++|++|+++||+|.+|+|+||+|||||
T Consensus 81 ~~G~Gr~~air~l~~~glkI~~I~DvTpiPhNGC 114 (114)
T TIGR03628 81 SPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGT 114 (114)
T ss_pred CCCCcHHHHHHHHHHCCCEEEEEEEcCCCCCCCC
Confidence 9999999999999999999999999999999999
No 8
>CHL00041 rps11 ribosomal protein S11
Probab=100.00 E-value=3.2e-42 Score=256.48 Aligned_cols=112 Identities=37% Similarity=0.574 Sum_probs=107.2
Q ss_pred cccCCceeeeEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEe
Q 031952 19 AVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRA 98 (150)
Q Consensus 19 ~~~~~~~~~~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~ 98 (150)
.+..+++..|++||++|+|||||||||++|+++.|+|+|++||++.+ |+||||||++|++++++|+++|++.|+|++
T Consensus 5 ~~~~~~~~~gi~hI~~t~NNTiiTlTd~~G~~l~~~S~G~~gfKg~r-K~T~~Aa~~~a~~~~~~~~~~gi~~v~I~i-- 81 (116)
T CHL00041 5 RKSKRKIPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGAR-KGTPFAAQTAAENAIRTVIDQGMKRAEVMI-- 81 (116)
T ss_pred ccccccceeEEEEEEcccCCEEEEEEcCCCCEEEEEecCceeeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEE--
Confidence 33445689999999999999999999999999999999999999997 899999999999999999999999999999
Q ss_pred eCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCC
Q 031952 99 TGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDST 139 (150)
Q Consensus 99 ~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGc 139 (150)
+|+|+||+++|++|+++|++|.+|+|+||+|||||
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 99999999999999999999999999999999999
No 9
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=6.6e-40 Score=265.31 Aligned_cols=109 Identities=20% Similarity=0.350 Sum_probs=103.7
Q ss_pred EEEEEccCCCeEEEEeCCCCCe--EEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccC
Q 031952 29 VAHIFASFNDTFIHVTDLSGRE--TLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKT 106 (150)
Q Consensus 29 ilhI~~t~NNT~itlTD~~G~~--~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG 106 (150)
.+.|++|+||||+||||..||+ ++|+|||.+|||+.+ |+||||||.|||+++++|.++||+.|+|.+ +|
T Consensus 120 ~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGsK-KsTpfAAQ~aae~aakka~~~GIk~V~V~v--------KG 190 (233)
T PTZ00090 120 MLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKKL-QQSERCAYRIGENIAKKCRRLGIFAVDIKF--------RR 190 (233)
T ss_pred EEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccCc-cCCHHHHHHHHHHHHHHHHHcCCeEEEEEE--------eC
Confidence 4778999999999999999995 999999999999888 999999999999999999999999999999 99
Q ss_pred CCCChHHHHHHHHhCCCeEEEEEeccCCCC---CCCCCCCCCCC
Q 031952 107 PGPGAQSALRALARSGMKIGRIEDVTPIPT---DSTRRKGGRRG 147 (150)
Q Consensus 107 ~G~gr~~~lk~L~~~gl~I~~I~D~Tpiph---NGcR~kK~RR~ 147 (150)
+| +||++|++|+++||+|.+|.|+||+|| |||||||+||+
T Consensus 191 pG-gREtALRaL~~~GLkIt~I~DvTpiPHNG~NGCRPpKKRRV 233 (233)
T PTZ00090 191 IM-RVETVLQAFYANGLQVTQIIHEPRLPKCGLNAVKPRKRRRV 233 (233)
T ss_pred CC-hHHHHHHHHHHCCCEEEEEEECCCCCcCCCCCCCCCCCCCC
Confidence 99 699999999999999999999999999 55999999885
No 10
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-38 Score=248.24 Aligned_cols=114 Identities=32% Similarity=0.491 Sum_probs=110.5
Q ss_pred eeeeEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcc
Q 031952 25 HVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKT 104 (150)
Q Consensus 25 ~~~~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~ 104 (150)
...+|+||.+|+|||+||+||.+|.++.|.|||.+||++.+ |+|++|||.++..+++++.++|+..|+|.+
T Consensus 77 ~eiPi~hIraS~NNTivtVtd~kg~vi~~~ScgteGFrntr-kgT~iAaQtaavaa~~r~v~~G~~~vrV~V-------- 147 (190)
T KOG0408|consen 77 REIPIIHIRASFNNTIVTVTDVKGEVISWSSCGTEGFRNTR-KGTPIAAQTAAVAAIRRAVDQGMQTVRVRV-------- 147 (190)
T ss_pred cccceEEEEecCCCeEEEEEccCCcEEEEeecccccccccc-cCCchhHHHHHHHHHHHHHHhcceEEEEEE--------
Confidence 55679999999999999999999999999999999999998 899999999999999999999999999999
Q ss_pred cCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCCCCC
Q 031952 105 KTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRG 147 (150)
Q Consensus 105 kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~RR~ 147 (150)
||+|+||.+++++|...|+.|+||+|.||+|||||||+|+||.
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 9999999999999999999999999999999999999999984
No 11
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-35 Score=217.32 Aligned_cols=138 Identities=89% Similarity=1.348 Sum_probs=135.1
Q ss_pred eeecCCcccCCceeeeEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEE
Q 031952 13 NVTLGPAVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITAL 92 (150)
Q Consensus 13 ~~~~~~~~~~~~~~~~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v 92 (150)
++.|||+..+.+.++++.||++|+|+||+++||+.|...+....|++..|-.+..++||||.+||+.++.+|+++|++.+
T Consensus 2 ~~~lg~q~~e~~~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi~al 81 (139)
T KOG0407|consen 2 AVNLGPQVREGEQVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGITAL 81 (139)
T ss_pred cccccchhcccceeeeEEEEEeecccceEEEeccCCceEEEEecCCeEEecccccCChHHHHHHHHHHHHHHHhcCeeEE
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCCCCCCCC
Q 031952 93 HIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGRRL 150 (150)
Q Consensus 93 ~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~RR~~~~ 150 (150)
||+++++||++.|-+|||.+++|++|..+|++|-.|+|+||||-+..|.+..||+||+
T Consensus 82 h~klratgg~ktktpgpgaqsalralar~gmrigriedvtpip~d~trrkggrrgrrl 139 (139)
T KOG0407|consen 82 HIKLRATGGTKTKTPGPGAQSALRALARSGMRIGRIEDVTPIPSDSTRRKGGRRGRRL 139 (139)
T ss_pred EEEEEecCCcccCCCCccHHHHHHHHHHhcceeeeecccccCCccchhhccCcccccC
Confidence 9999999999999999999999999999999999999999999999999999999996
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=97.93 E-value=0.00023 Score=51.42 Aligned_cols=90 Identities=16% Similarity=0.125 Sum_probs=67.5
Q ss_pred eeeEEEEEccCCCeEEEEeCCC-CCeEEEEEeecCccccC-CCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCc
Q 031952 26 VFGVAHIFASFNDTFIHVTDLS-GRETLVRITGGMKVKAD-RDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNK 103 (150)
Q Consensus 26 ~~~ilhI~~t~NNT~itlTD~~-G~~~~~~SsG~~g~kk~-~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~ 103 (150)
..+.|.|+.|.+|++.++.|.. +.++.+.|+-...+++. .......||..+++.++++|.+.|+..+.+-.
T Consensus 10 ~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D~------- 82 (103)
T cd00432 10 ERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDR------- 82 (103)
T ss_pred CCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeC-------
Confidence 4578889999999999999998 66676666666666543 22567888999999999999999999986654
Q ss_pred ccCCC-CCh-HHHHHHHHhCCC
Q 031952 104 TKTPG-PGA-QSALRALARSGM 123 (150)
Q Consensus 104 ~kG~G-~gr-~~~lk~L~~~gl 123 (150)
.|+- -|| .+++.++...||
T Consensus 83 -~~~~~~grv~a~~~~~r~~Gl 103 (103)
T cd00432 83 -GGYRYHGRVKALAKGAREGGL 103 (103)
T ss_pred -CCcccccHHHHHHHHHHHcCC
Confidence 2222 234 557777777775
No 13
>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=97.66 E-value=0.0011 Score=49.40 Aligned_cols=92 Identities=17% Similarity=0.137 Sum_probs=67.7
Q ss_pred eeeEEEEEccCCCeEEEEeCCC-CCeEEEEEeecCccccC---CCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCC
Q 031952 26 VFGVAHIFASFNDTFIHVTDLS-GRETLVRITGGMKVKAD---RDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGG 101 (150)
Q Consensus 26 ~~~ilhI~~t~NNT~itlTD~~-G~~~~~~SsG~~g~kk~---~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g 101 (150)
..+.|.|+.|..++.+.+.|.. +.++...|+-...+++. .......||+.+++.+++.|.+.|+..|.+-.
T Consensus 22 ~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~lla~ra~~~gi~~v~fdr----- 96 (119)
T PF00861_consen 22 ERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGELLAKRALEKGIAKVVFDR----- 96 (119)
T ss_dssp SSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHHHHHHHHHTTSSEEEECT-----
T ss_pred CCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHHHHHHHHHcCCcEEEEcC-----
Confidence 4578888999999999998877 55666666666666642 11346788999999999999999998876554
Q ss_pred CcccCCCC-Ch-HHHHHHHHhCCCeE
Q 031952 102 NKTKTPGP-GA-QSALRALARSGMKI 125 (150)
Q Consensus 102 ~~~kG~G~-gr-~~~lk~L~~~gl~I 125 (150)
.|+-. || .+++.++...||+|
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 44333 34 56778888899875
No 14
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=97.65 E-value=0.00085 Score=50.22 Aligned_cols=94 Identities=23% Similarity=0.241 Sum_probs=65.0
Q ss_pred ceeeeEEEEEccCCCeEEEEeCCCCCeEEE-EEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCC
Q 031952 24 EHVFGVAHIFASFNDTFIHVTDLSGRETLV-RITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGN 102 (150)
Q Consensus 24 ~~~~~ilhI~~t~NNT~itlTD~~G~~~~~-~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~ 102 (150)
....+-|.|+.|.+++.+.+.|..+..++. .|+-...++.+-....-.||+.+++.++++|.+.|++.+ .|. .+|-
T Consensus 21 ~~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~~~~n~~aa~~vG~~la~ra~~~gi~~v--vfD-rg~~ 97 (117)
T PRK05593 21 TAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGLKGGNKEAAKKVGKLIAERAKAKGIKQV--VFD-RGGY 97 (117)
T ss_pred CCCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhccccCCCHHHHHHHHHHHHHHHHHCCCCEE--EEc-CCCC
Confidence 445678999999999999999888775443 333333343322256678899999999999999999996 553 1222
Q ss_pred cccCCCCCh-HHHHHHHHhCCCe
Q 031952 103 KTKTPGPGA-QSALRALARSGMK 124 (150)
Q Consensus 103 ~~kG~G~gr-~~~lk~L~~~gl~ 124 (150)
+.. || .+++.++..+||+
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 5567777778876
No 15
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=97.60 E-value=0.0018 Score=52.43 Aligned_cols=104 Identities=15% Similarity=0.211 Sum_probs=72.2
Q ss_pred eEEEEEccCCCeEEEEe--CCCCCeEE-EEEeecCcccc--CCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCC
Q 031952 28 GVAHIFASFNDTFIHVT--DLSGRETL-VRITGGMKVKA--DRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGN 102 (150)
Q Consensus 28 ~ilhI~~t~NNT~itlT--D~~G~~~~-~~SsG~~g~kk--~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~ 102 (150)
+-+.|+.|.+|+++.+. |..|..++ +.||-....++ .. ....-||+.++..++++|.+.|++.+.+-. ||.
T Consensus 33 pRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~~-~~N~~AAy~vG~llA~ral~kGi~~vvfDr---Gg~ 108 (193)
T PRK08569 33 PRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKGD-TGNTPAAYLTGLLAGKKALKAGVEEAVLDI---GLH 108 (193)
T ss_pred CEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccCC-CCCHHHHHHHHHHHHHHHHHCCCCEEEEec---CCc
Confidence 67888899999999999 67666544 33433333322 22 456778999999999999999999875544 222
Q ss_pred cccCCCCCh-HHHHHHHHhCCCeEEEEEeccCCCCCCCCCCCCCC
Q 031952 103 KTKTPGPGA-QSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRR 146 (150)
Q Consensus 103 ~~kG~G~gr-~~~lk~L~~~gl~I~~I~D~TpiphNGcR~kK~RR 146 (150)
+.. .| || .+++++...+||+ +||+-.|.|.--|
T Consensus 109 ~yh-~g-GRV~A~akgArd~GL~---------fPh~~~~~p~~~r 142 (193)
T PRK08569 109 RPT-KG-SRVFAALKGAIDAGLE---------IPHGEEVLPDEDR 142 (193)
T ss_pred ccc-CC-ccHHHHHHHHHHcCCc---------CCCCCCcCCCccc
Confidence 222 01 34 6678888889997 5998888776444
No 16
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=97.56 E-value=0.0017 Score=48.48 Aligned_cols=88 Identities=23% Similarity=0.186 Sum_probs=62.8
Q ss_pred eeeEEEEEccCCCeEEEEeCCCCCeEEEEEee-cCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcc
Q 031952 26 VFGVAHIFASFNDTFIHVTDLSGRETLVRITG-GMKVKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKT 104 (150)
Q Consensus 26 ~~~ilhI~~t~NNT~itlTD~~G~~~~~~SsG-~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~ 104 (150)
..+-|.|+.|.+++.+.+.|..+..+++++|. ...+. . ...-.||..+++.++++|.+.|+..| .|. .
T Consensus 23 ~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~--~-~~n~~aA~~vG~~la~ra~~~gi~~v--vfD-r----- 91 (114)
T TIGR00060 23 NRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK--Y-TGNKDAAKKVGKLVAERLKEKGIKDV--VFD-R----- 91 (114)
T ss_pred CCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc--C-CCCHHHHHHHHHHHHHHHHHCCCCEE--EEe-C-----
Confidence 46789999999999999998877755444443 33343 2 46678899999999999999999998 453 1
Q ss_pred cCCCC-Ch-HHHHHHHHhCCCe
Q 031952 105 KTPGP-GA-QSALRALARSGMK 124 (150)
Q Consensus 105 kG~G~-gr-~~~lk~L~~~gl~ 124 (150)
.|+=. || .++..++...||+
T Consensus 92 gg~~YhGrv~A~a~~aRe~Gl~ 113 (114)
T TIGR00060 92 GGYKYHGRVAALAEAAREAGLN 113 (114)
T ss_pred CCCcchHHHHHHHHHHHHhCCC
Confidence 23222 34 4456667777875
No 17
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=97.43 E-value=0.003 Score=46.77 Aligned_cols=94 Identities=20% Similarity=0.262 Sum_probs=64.0
Q ss_pred ceeeeEEEEEccCCCeEEEEeC-CCCCeEEEEEeecCccccC-CCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCC
Q 031952 24 EHVFGVAHIFASFNDTFIHVTD-LSGRETLVRITGGMKVKAD-RDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGG 101 (150)
Q Consensus 24 ~~~~~ilhI~~t~NNT~itlTD-~~G~~~~~~SsG~~g~kk~-~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g 101 (150)
....+-|.|+.|.+++.+.+.| .+|.++.+.|+-...+++. .....-.||+.+++.++++|.+.|+..| .|. .+|
T Consensus 12 ~~~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~~v--vfD-rgg 88 (109)
T CHL00139 12 TAERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKV--VFD-RGG 88 (109)
T ss_pred CCCCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEE--EEc-CCC
Confidence 3345678999999999998886 4577776666544444331 1145577899999999999999999987 443 122
Q ss_pred CcccCCCCCh-HHHHHHHHhCCCe
Q 031952 102 NKTKTPGPGA-QSALRALARSGMK 124 (150)
Q Consensus 102 ~~~kG~G~gr-~~~lk~L~~~gl~ 124 (150)
.+ ++ || +++..++..+||+
T Consensus 89 ~~---yh-GrV~a~a~~are~GL~ 108 (109)
T CHL00139 89 KL---YH-GRIKALAEAAREAGLQ 108 (109)
T ss_pred Cc---cc-hHHHHHHHHHHHhCCC
Confidence 22 11 24 5566777778875
No 18
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=96.85 E-value=0.025 Score=42.98 Aligned_cols=93 Identities=13% Similarity=0.086 Sum_probs=63.1
Q ss_pred ceeeeEEEEEccCCCeEEEEeCCCCCeEEEEEe-ecCccc----cCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEe
Q 031952 24 EHVFGVAHIFASFNDTFIHVTDLSGRETLVRIT-GGMKVK----ADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRA 98 (150)
Q Consensus 24 ~~~~~ilhI~~t~NNT~itlTD~~G~~~~~~Ss-G~~g~k----k~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~ 98 (150)
....+-|.|+-|.+|+++.+.|...+.....+| =..-+. +.. .+...||..+++.+++++.+.|++.+.+=.
T Consensus 26 ~~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~-~~N~~aA~~vG~lia~ra~~kgi~~vVfdr-- 102 (125)
T COG0256 26 TSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGG-GGNTEAAYLVGKLIAERALAKGIEEVVFDR-- 102 (125)
T ss_pred CCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCC-CCCHHHHHHHHHHHHHHHHHcCCcEEEEcC--
Confidence 344567778888999999999988665443333 222221 112 345778999999999999999999987444
Q ss_pred eCCCcccCCCC-Ch-HHHHHHHHhCCCeE
Q 031952 99 TGGNKTKTPGP-GA-QSALRALARSGMKI 125 (150)
Q Consensus 99 ~~g~~~kG~G~-gr-~~~lk~L~~~gl~I 125 (150)
.|+=+ || .++.++...+||++
T Consensus 103 ------~g~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 103 ------GGYKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred ------CCCCcchHHHHHHHHHHHcCcCC
Confidence 44444 34 44566667778764
No 19
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=94.82 E-value=0.21 Score=40.97 Aligned_cols=69 Identities=10% Similarity=0.022 Sum_probs=50.8
Q ss_pred eeEEEEEccCCCeEEEEeCCC-CCeEEEEEeecCccccC-------------CCCCCHHHHHHHHHHHHHHHHHcCCcEE
Q 031952 27 FGVAHIFASFNDTFIHVTDLS-GRETLVRITGGMKVKAD-------------RDESSPYAAMLAAQDVSQRCKELGITAL 92 (150)
Q Consensus 27 ~~ilhI~~t~NNT~itlTD~~-G~~~~~~SsG~~g~kk~-------------~rK~t~~Aa~~aa~~i~~~~~~~gi~~v 92 (150)
.+-|.|+-|.+++.+++.|.. |.++.+.|+-.-.++.. ...++-.||..+++.++++|.+.||+.|
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 457888899999999999875 55555444433333321 1256789999999999999999999987
Q ss_pred EEEEE
Q 031952 93 HIKLR 97 (150)
Q Consensus 93 ~V~~~ 97 (150)
.|.
T Consensus 185 --vFD 187 (211)
T PTZ00032 185 --RFD 187 (211)
T ss_pred --EEe
Confidence 564
No 20
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=84.63 E-value=11 Score=32.57 Aligned_cols=61 Identities=10% Similarity=0.005 Sum_probs=44.2
Q ss_pred eeeeEEEEEccCCCeEEEEeC--CCCCeEEEEEee----cCccccCCCCCCHHHHHHHHHHHHHHHHHc
Q 031952 25 HVFGVAHIFASFNDTFIHVTD--LSGRETLVRITG----GMKVKADRDESSPYAAMLAAQDVSQRCKEL 87 (150)
Q Consensus 25 ~~~~ilhI~~t~NNT~itlTD--~~G~~~~~~SsG----~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~ 87 (150)
.+..-+.|..|..|+++.++. +.|..++++... -.|++.+. ...-||+.++.-+++++...
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--TNYAAAYATGLLLARRLLKK 112 (300)
T ss_pred CCCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcCCCC--ccHHHHHHHHHHHHHHHHHh
Confidence 455678889999999998874 668876655433 25677665 44667888999899887765
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=69.00 E-value=13 Score=31.16 Aligned_cols=65 Identities=17% Similarity=0.177 Sum_probs=46.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCC
Q 031952 63 ADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 136 (150)
Q Consensus 63 k~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tpiph 136 (150)
.+|...|-+....+.+.+++.. +..++...|.+ .|||.-=..+.+.|...|.+|+.|.|.+-.-|
T Consensus 11 ~gR~~aTg~Gv~~~~~~~~~~~-~~~l~g~~vaI--------qGfGnVG~~~a~~L~e~GakvvaVsD~~G~i~ 75 (254)
T cd05313 11 LIRPEATGYGLVYFVEEMLKDR-NETLKGKRVAI--------SGSGNVAQYAAEKLLELGAKVVTLSDSKGYVY 75 (254)
T ss_pred CCCCchhHHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEECCCceEE
Confidence 3444677777666666666555 45566788999 89997555666888889999999999654333
No 22
>PF05677 DUF818: Chlamydia CHLPS protein (DUF818); InterPro: IPR008536 This family of unknown function includes several Chlamydia CHLPS proteins and Legionella SidB proteins.
Probab=61.05 E-value=64 Score=28.74 Aligned_cols=78 Identities=17% Similarity=0.127 Sum_probs=56.2
Q ss_pred CCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHH--cCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhC---
Q 031952 47 SGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKE--LGITALHIKLRATGGNKTKTPGPGAQSALRALARS--- 121 (150)
Q Consensus 47 ~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~--~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~--- 121 (150)
..|++.+-..| +|+-++. .++.+-..+++.+.+.+++ .|++.=+|.+ .|...|--.+=.+|++.
T Consensus 171 ~aNvl~fNYpG-Vg~S~G~--~s~~dLv~~~~a~v~yL~d~~~G~ka~~Ii~--------yG~SLGG~Vqa~AL~~~~~~ 239 (365)
T PF05677_consen 171 GANVLVFNYPG-VGSSTGP--PSRKDLVKDYQACVRYLRDEEQGPKAKNIIL--------YGHSLGGGVQAEALKKEVLK 239 (365)
T ss_pred CCcEEEECCCc-cccCCCC--CCHHHHHHHHHHHHHHHHhcccCCChheEEE--------eeccccHHHHHHHHHhcccc
Confidence 34666655555 5777666 5677777888999999985 7898889999 66666655544567653
Q ss_pred ---CCeEEEEEeccCCC
Q 031952 122 ---GMKIGRIEDVTPIP 135 (150)
Q Consensus 122 ---gl~I~~I~D~Tpip 135 (150)
|++-..|.|.|+-.
T Consensus 240 ~~dgi~~~~ikDRsfss 256 (365)
T PF05677_consen 240 GSDGIRWFLIKDRSFSS 256 (365)
T ss_pred cCCCeeEEEEecCCcch
Confidence 67888999998743
No 23
>COG0241 HisB Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]
Probab=54.63 E-value=68 Score=25.66 Aligned_cols=59 Identities=20% Similarity=0.244 Sum_probs=36.5
Q ss_pred HHHHHHHHcCCcEEEEEEEeeCCCcccCCCCCh--HH--------HHHHHHhCCCeEEEEEeccCCCC--CCCCCCCC
Q 031952 79 DVSQRCKELGITALHIKLRATGGNKTKTPGPGA--QS--------ALRALARSGMKIGRIEDVTPIPT--DSTRRKGG 144 (150)
Q Consensus 79 ~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr--~~--------~lk~L~~~gl~I~~I~D~Tpiph--NGcR~kK~ 144 (150)
.+..++.+.||.-|.|.-+ .|+|.|- +. .+..|++.|++|..|.=---.|- ..||+||.
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 3455667889998877764 5666543 22 33445667876666554433343 58999874
No 24
>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=47.52 E-value=60 Score=26.60 Aligned_cols=57 Identities=18% Similarity=0.207 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRK 142 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~k 142 (150)
++.+......+.+.|...|++.+.... --...+.|...|+.+..|-+ |..|+|.|.|
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 555666677889999999999998887 33577888999999988886 5567787643
No 25
>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=46.82 E-value=52 Score=26.74 Aligned_cols=59 Identities=17% Similarity=0.276 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCC
Q 031952 67 ESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPI 134 (150)
Q Consensus 67 K~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tpi 134 (150)
..|.|-...+.+.+++... ..+....|.+ .|||.==..+.+.|...|.+|+.|.|..-.
T Consensus 8 ~~Tg~Gv~~~~~~~~~~~~-~~l~~~~v~I--------~G~G~VG~~~a~~L~~~g~~vv~v~D~~g~ 66 (227)
T cd01076 8 EATGRGVAYATREALKKLG-IGLAGARVAI--------QGFGNVGSHAARFLHEAGAKVVAVSDSDGT 66 (227)
T ss_pred ccchHHHHHHHHHHHHhcC-CCccCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEECCCCe
Confidence 5666666666665555442 4577788889 788863344446788889999999998543
No 26
>PLN02477 glutamate dehydrogenase
Probab=45.94 E-value=62 Score=28.99 Aligned_cols=60 Identities=18% Similarity=0.283 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEeccC
Q 031952 64 DRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDVTP 133 (150)
Q Consensus 64 ~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~-gr~~~lk~L~~~gl~I~~I~D~Tp 133 (150)
++...|-+-...+++.+++. ....++...|-+ .|||. |+.++ +.|...|.+|+.|.|..-
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 44467777776666666655 223456678899 88996 55554 788889999999999863
No 27
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=44.97 E-value=62 Score=24.28 Aligned_cols=38 Identities=21% Similarity=0.325 Sum_probs=26.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 128 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I 128 (150)
..+++.+.+.|+..| .. .++|++- +..|++.|++|...
T Consensus 55 ~~~a~~l~~~gvdvv--i~--------~~iG~~a---~~~l~~~GIkv~~~ 92 (121)
T COG1433 55 IRIAELLVDEGVDVV--IA--------SNIGPNA---YNALKAAGIKVYVA 92 (121)
T ss_pred HHHHHHHHHcCCCEE--EE--------CccCHHH---HHHHHHcCcEEEec
Confidence 456667788898866 44 6677754 45577788887654
No 28
>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=43.30 E-value=78 Score=25.18 Aligned_cols=43 Identities=14% Similarity=0.098 Sum_probs=33.2
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 129 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~ 129 (150)
+.+++.+.++|+..|++.. . +....+.+.+.|...|++|..+.
T Consensus 17 ~e~~~~~~e~G~~~vEl~~--------~-~~~~~~~l~~~l~~~gl~v~~~~ 59 (254)
T TIGR03234 17 LERFAAAAQAGFTGVEYLF--------P-YDWDAEALKARLAAAGLEQVLFN 59 (254)
T ss_pred HHHHHHHHHcCCCEEEecC--------C-ccCCHHHHHHHHHHcCCeEEEEe
Confidence 5677788899999999866 1 23456667777888999999885
No 29
>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=40.01 E-value=68 Score=25.94 Aligned_cols=39 Identities=18% Similarity=0.193 Sum_probs=30.0
Q ss_pred cCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccC
Q 031952 87 LGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTP 133 (150)
Q Consensus 87 ~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tp 133 (150)
..+....|-+ .|||.==..+.+.|...|.+++.|.|...
T Consensus 19 ~~l~g~~vaI--------qGfGnVG~~~a~~L~~~G~~vV~vsD~~g 57 (217)
T cd05211 19 DSLEGLTVAV--------QGLGNVGWGLAKKLAEEGGKVLAVSDPDG 57 (217)
T ss_pred CCcCCCEEEE--------ECCCHHHHHHHHHHHHcCCEEEEEEcCCC
Confidence 3566678889 78886334555778888999999999876
No 30
>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=39.99 E-value=1.4e+02 Score=21.29 Aligned_cols=45 Identities=16% Similarity=0.225 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHH-HHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 031952 73 AMLAAQDVSQRC-KELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 128 (150)
Q Consensus 73 a~~aa~~i~~~~-~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I 128 (150)
+..+...+.+.| .++|+..|.+.+- ..-..+++.+++.|+++...
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 445667788888 9999999999882 23677889899999986543
No 31
>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=39.36 E-value=91 Score=26.10 Aligned_cols=54 Identities=22% Similarity=0.233 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHcC---CcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 031952 72 AAMLAAQDVSQRCKELG---ITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 127 (150)
Q Consensus 72 Aa~~aa~~i~~~~~~~g---i~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~ 127 (150)
|+..++. .++.+.+.+ --.|.|..|| ||+..-=+-.+-+.+.+++..+.+.|++
T Consensus 56 A~~~I~~-al~~~~~~~~~~~~Dviii~RG-GGs~eDL~~FN~e~varai~~~~~Pvis 112 (319)
T PF02601_consen 56 AAASIVS-ALRKANEMGQADDFDVIIIIRG-GGSIEDLWAFNDEEVARAIAASPIPVIS 112 (319)
T ss_pred hHHHHHH-HHHHHHhccccccccEEEEecC-CCChHHhcccChHHHHHHHHhCCCCEEE
Confidence 3444433 333444444 2236667765 6666666778999999999999888754
No 32
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=39.15 E-value=45 Score=28.33 Aligned_cols=26 Identities=38% Similarity=0.629 Sum_probs=21.8
Q ss_pred CCHHHHHHHHHHHHHHHHHcCCcEEEE
Q 031952 68 SSPYAAMLAAQDVSQRCKELGITALHI 94 (150)
Q Consensus 68 ~t~~Aa~~aa~~i~~~~~~~gi~~v~V 94 (150)
+-||||+ +.+++++-|++.|+..+..
T Consensus 74 THPyAa~-iS~Na~~aake~gipy~r~ 99 (257)
T COG2099 74 THPYAAR-ISQNAARAAKETGIPYLRL 99 (257)
T ss_pred CChHHHH-HHHHHHHHHHHhCCcEEEE
Confidence 4599888 5688999999999998853
No 33
>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=38.26 E-value=38 Score=26.09 Aligned_cols=29 Identities=24% Similarity=0.323 Sum_probs=21.8
Q ss_pred cCCCC-ChHHHHHHHHhCCCeEEEEEeccC
Q 031952 105 KTPGP-GAQSALRALARSGMKIGRIEDVTP 133 (150)
Q Consensus 105 kG~G~-gr~~~lk~L~~~gl~I~~I~D~Tp 133 (150)
+|||. ||..+-.++.+..++|+-|.|..+
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 88885 666654445567899999999873
No 34
>PRK14030 glutamate dehydrogenase; Provisional
Probab=37.27 E-value=1e+02 Score=28.07 Aligned_cols=63 Identities=16% Similarity=0.149 Sum_probs=43.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCC
Q 031952 65 RDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 136 (150)
Q Consensus 65 ~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tpiph 136 (150)
+...|-|-...+++.+++.. ...++...|.+ .|||.==..+.+.|...|-+|+.|.|.+--=+
T Consensus 203 r~~ATg~Gv~~~~~~~~~~~-g~~l~g~~vaI--------QGfGnVG~~aA~~L~e~GakvVavSD~~G~i~ 265 (445)
T PRK14030 203 RPEATGFGALYFVHQMLETK-GIDIKGKTVAI--------SGFGNVAWGAATKATELGAKVVTISGPDGYIY 265 (445)
T ss_pred CCCccHHHHHHHHHHHHHHc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEEcCCceEE
Confidence 44577777777776666544 23466788899 88986344444667889999999988765433
No 35
>PRK01060 endonuclease IV; Provisional
Probab=35.99 E-value=81 Score=25.44 Aligned_cols=55 Identities=15% Similarity=0.105 Sum_probs=32.3
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCCh------HHHHHHHHhCCCeEEEEEeccCCCCC
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGA------QSALRALARSGMKIGRIEDVTPIPTD 137 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr------~~~lk~L~~~gl~I~~I~D~TpiphN 137 (150)
+.+++.+.++|+..|++.+..+ ..+-... +.+-+.+...|+.+..+.=-.|.+.|
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 5677889999999999988322 1111111 22334566789987544333344433
No 36
>PTZ00079 NADP-specific glutamate dehydrogenase; Provisional
Probab=35.76 E-value=1.2e+02 Score=27.80 Aligned_cols=61 Identities=20% Similarity=0.229 Sum_probs=45.4
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccC
Q 031952 64 DRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTP 133 (150)
Q Consensus 64 ~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tp 133 (150)
.+...|-|-...+++.+++.. ...++...|.+ .|+|.=-..+.+.|...|-+|+.|.|..-
T Consensus 211 ~r~eATG~Gv~~~~~~~l~~~-~~~l~Gk~VaV--------qG~GnVg~~aa~~L~e~GakVVavSD~~G 271 (454)
T PTZ00079 211 IRPEATGYGLVYFVLEVLKKL-NDSLEGKTVVV--------SGSGNVAQYAVEKLLQLGAKVLTMSDSDG 271 (454)
T ss_pred CCCcccHHHHHHHHHHHHHHc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEEcCCC
Confidence 444678888877777776554 44567778899 88987555555667889999999999883
No 37
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=35.66 E-value=1.8e+02 Score=24.16 Aligned_cols=61 Identities=13% Similarity=0.031 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChH------HHH--------HHHHhCCCeEEEEEeccCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQ------SAL--------RALARSGMKIGRIEDVTPIP 135 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~------~~l--------k~L~~~gl~I~~I~D~Tpip 135 (150)
..++..+...+.+.|.++|++.|.|+.=-+ -.|..-.+ .++ ..+...|++|.-|-|...+|
T Consensus 40 H~~G~~~l~~iv~~c~~~gI~~vTvYaFS~-----eN~kR~~~Ev~~lm~L~~~~l~~~~~~~~~~~iri~~iG~~~~Lp 114 (243)
T PRK14829 40 HKAGEPVLFDVVAGAIEAGVPYLSLYTFST-----ENWKRSPDEVRFLMGFSRDVIHRRREQMDEWGVRVRWSGRRPRLW 114 (243)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEeeecc-----hhhCCCHHHHHHHHHHHHHHHHHHHHHHHHcCcEEEEEechhhCC
Confidence 445566667888899999999999987211 22332222 111 12345689999999999888
No 38
>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=35.53 E-value=1.2e+02 Score=25.89 Aligned_cols=49 Identities=24% Similarity=0.287 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 031952 76 AAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 131 (150)
Q Consensus 76 aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~ 131 (150)
+++.++..|.+.|.+ ++|++--+ +-.+.|+..+ +.|.+.|+.+..|.|.
T Consensus 127 tv~~~l~~a~~~~~~-f~V~v~Es-----rP~~~G~~~a-~~L~~~gI~vtlI~Ds 175 (301)
T TIGR00511 127 AALSVIKTAFEQGKD-IEVIATET-----RPRKQGHITA-KELRDYGIPVTLIVDS 175 (301)
T ss_pred HHHHHHHHHHHcCCc-EEEEEecC-----CCcchHHHHH-HHHHHCCCCEEEEehh
Confidence 455666777666644 56666322 5566787665 6788999999999985
No 39
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=34.21 E-value=66 Score=29.35 Aligned_cols=54 Identities=22% Similarity=0.188 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 031952 72 AAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 127 (150)
Q Consensus 72 Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~ 127 (150)
|+..+++ +++.+.+.+--.|-|.-|| ||+-.--+..+-|.+.+++..+.+.|+|
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 3444443 4445666664445555554 6677777889999999999999988765
No 40
>PRK00394 transcription factor; Reviewed
Probab=33.80 E-value=1.4e+02 Score=23.59 Aligned_cols=51 Identities=20% Similarity=0.182 Sum_probs=36.8
Q ss_pred CCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcE
Q 031952 37 NDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITA 91 (150)
Q Consensus 37 NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~ 91 (150)
.-.++-+.|+.- .+.-++||-+--.+++ + ...+..|++++++.++++|+..
T Consensus 36 pgli~Rl~~Pk~-t~lIf~sGKiv~tGa~--S-~~~a~~a~~~~~~~l~~~g~~~ 86 (179)
T PRK00394 36 PGLVYRLEDPKI-AALIFRSGKVVCTGAK--S-VEDLHEAVKIIIKKLKELGIKV 86 (179)
T ss_pred ceEEEEecCCce-EEEEEcCCcEEEEccC--C-HHHHHHHHHHHHHHHHHcCCCc
Confidence 345566666665 4556888887777665 3 5567888899999999999754
No 41
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=32.77 E-value=1.4e+02 Score=25.45 Aligned_cols=50 Identities=26% Similarity=0.346 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEecc
Q 031952 76 AAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 132 (150)
Q Consensus 76 aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~T 132 (150)
+++.++..|.+.|-+ ++|++--+ +-.+.|+..+ +.|.+.|+.+..|.|..
T Consensus 132 tv~~~l~~A~~~~k~-~~V~v~Es-----rP~~~G~~~a-~~L~~~GI~vtlI~Dsa 181 (310)
T PRK08535 132 AALSVIKTAHEQGKD-IEVIATET-----RPRNQGHITA-KELAEYGIPVTLIVDSA 181 (310)
T ss_pred HHHHHHHHHHHCCCe-EEEEEecC-----CchhhHHHHH-HHHHHCCCCEEEEehhH
Confidence 556666777776644 56666322 5556786665 67888999999999853
No 42
>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=32.64 E-value=1.5e+02 Score=19.65 Aligned_cols=64 Identities=20% Similarity=0.255 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCC---CeEEEEEeccCCCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSG---MKIGRIEDVTPIPTD 137 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~g---l~I~~I~D~TpiphN 137 (150)
...|..+.+.....+.+.++..+.|.- |.|-... -|.=+.++...|.. + -.|..+.+..|-+.|
T Consensus 8 ~~eA~~~l~~~l~~~~~~~~~~~~II~-G~G~hS~--~g~Lk~~V~~~L~~-~~~~~~v~~~~~~~~~~g~ 74 (83)
T PF01713_consen 8 VEEALRALEEFLDEARQRGIRELRIIT-GKGNHSK--GGVLKRAVRRWLEE-GYQYEEVLAYRDAEPEDGN 74 (83)
T ss_dssp HHHHHHHHHHHHHHHHHTTHSEEEEE---STCTCC--TSHHHHHHHHHHHH-THCCTTEEEEEE--CCCTG
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEe-ccCCCCC--CCcHHHHHHHHHHh-hhccchhheeeecCCCCCC
Confidence 345666778888899999999998766 3211111 12235666666755 4 347777777666654
No 43
>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=32.49 E-value=1.7e+02 Score=20.18 Aligned_cols=46 Identities=15% Similarity=0.260 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHHHH-HHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCe
Q 031952 67 ESSPYAAMLAAQDVSQRC-KELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMK 124 (150)
Q Consensus 67 K~t~~Aa~~aa~~i~~~~-~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~ 124 (150)
.+.-|+...+ ..+...+ .++|+..|...+ -..-.++++.+.+.|++
T Consensus 96 ~g~G~~~~~~-~~~~~~~~~~~~~~~i~a~~-----------~~~N~~s~~~~~k~GF~ 142 (142)
T PF13302_consen 96 RGKGYGTEAL-KLLLDWAFEELGLHRIIATV-----------MADNEASRRLLEKLGFE 142 (142)
T ss_dssp TTSSHHHHHH-HHHHHHHHHTSTSSEEEEEE-----------ETT-HHHHHHHHHTT-E
T ss_pred HhhhHHHHHH-HHHHHHHHhcCCcEEEEEEE-----------CcCCHHHHHHHHHcCCC
Confidence 3456765544 4566666 789999999999 35567888888888864
No 44
>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=31.98 E-value=1.3e+02 Score=23.78 Aligned_cols=49 Identities=18% Similarity=0.293 Sum_probs=34.3
Q ss_pred CeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCc
Q 031952 38 DTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGIT 90 (150)
Q Consensus 38 NT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~ 90 (150)
-.++-+.|+.- ++.-++||-+-..+++ + ...+..|++++++.++++|++
T Consensus 38 gli~Rl~~Pk~-t~lIF~SGKiviTGak--s-~e~a~~a~~~i~~~L~~~g~~ 86 (174)
T cd04516 38 AVIMRIREPKT-TALIFSSGKMVCTGAK--S-EDDSKLAARKYARIIQKLGFP 86 (174)
T ss_pred EEEEEeCCCcE-EEEEECCCeEEEEecC--C-HHHHHHHHHHHHHHHHHcCCC
Confidence 34455556655 3556888877777665 3 556777889999999999864
No 45
>PRK08335 translation initiation factor IF-2B subunit alpha; Validated
Probab=31.82 E-value=1.5e+02 Score=25.18 Aligned_cols=50 Identities=18% Similarity=0.226 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEecc
Q 031952 76 AAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 132 (150)
Q Consensus 76 aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~T 132 (150)
++..++..+.+.|.. ++|++--+ +-...|+.. .+.|...|+.+..|.|..
T Consensus 121 tv~~~l~~A~~~gk~-~~V~v~Es-----rP~~qG~~l-a~eL~~~GI~vtlI~Dsa 170 (275)
T PRK08335 121 AVLEILKTAKRKGKR-FKVILTES-----APDYEGLAL-ANELEFLGIEFEVITDAQ 170 (275)
T ss_pred HHHHHHHHHHHcCCc-eEEEEecC-----CCchhHHHH-HHHHHHCCCCEEEEeccH
Confidence 556667777777743 55566332 566788887 688999999999999964
No 46
>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=31.74 E-value=99 Score=24.44 Aligned_cols=43 Identities=14% Similarity=0.300 Sum_probs=34.4
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHH--HHHHHHhCCCeEEEEE
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQS--ALRALARSGMKIGRIE 129 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~--~lk~L~~~gl~I~~I~ 129 (150)
+.+++.|+.+|++.|=|-+ =+|.-+++ +-+.|...|+.+.|+.
T Consensus 44 eEiieFak~mgykkiGiAf---------CiGL~~EA~~~~~iL~~~gFev~sV~ 88 (157)
T PF08901_consen 44 EEIIEFAKRMGYKKIGIAF---------CIGLRKEARILAKILEANGFEVYSVC 88 (157)
T ss_pred HHHHHHHHHcCCCeeeehh---------hHhHHHHHHHHHHHHHHCCCEEEEEE
Confidence 6688899999999998877 46776665 5567778999999875
No 47
>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=31.40 E-value=1.3e+02 Score=23.51 Aligned_cols=52 Identities=21% Similarity=0.336 Sum_probs=37.2
Q ss_pred CCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcE
Q 031952 36 FNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITA 91 (150)
Q Consensus 36 ~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~ 91 (150)
++-.++-+.|++. .+.-+++|-+--.+++ + ...+..+++.+++.++++|++.
T Consensus 36 fpgli~R~~~P~~-t~lIf~sGKivitGak--s-~~~~~~a~~~~~~~L~~~g~~~ 87 (174)
T cd00652 36 FPGVIMRLREPKT-TALIFSSGKMVITGAK--S-EEDAKLAARKYARILQKLGFPV 87 (174)
T ss_pred cceEEEEcCCCcE-EEEEECCCEEEEEecC--C-HHHHHHHHHHHHHHHHHcCCCc
Confidence 3445566666666 4556888877777664 3 5667788899999999999765
No 48
>PRK07564 phosphoglucomutase; Validated
Probab=31.18 E-value=68 Score=29.33 Aligned_cols=78 Identities=21% Similarity=0.226 Sum_probs=47.8
Q ss_pred EEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCC-cEEEEEEEeeCCCcccCCC-CChHHHHHHHHhCCCeEEEE
Q 031952 51 TLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGI-TALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRI 128 (150)
Q Consensus 51 ~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi-~~v~V~~~~~~g~~~kG~G-~gr~~~lk~L~~~gl~I~~I 128 (150)
+.+-++|--|.-+.. .-|+.-++.++..+++.+.+.+. ..|.|-... +-.+ .-.+++..+|...|++|..+
T Consensus 38 ~~FGT~GiRg~~~~~-~lt~~~v~~i~~a~a~~~~~~~~~~~VvVG~D~------R~~S~~~a~a~a~gL~s~Gi~V~~~ 110 (543)
T PRK07564 38 VKFGTSGHRGSSLQP-SFNENHILAIFQAICEYRGKQGITGPLFVGGDT------HALSEPAIQSALEVLAANGVGVVIV 110 (543)
T ss_pred CCCcccccccccCCC-CcCHHHHHHHHHHHHHHHHhcCCCCeEEEEecC------CcCCHHHHHHHHHHHHHCCCEEEEe
Confidence 334455544433222 46888888888888888766543 224333321 2222 23567888999999999999
Q ss_pred Ee--ccCCC
Q 031952 129 ED--VTPIP 135 (150)
Q Consensus 129 ~D--~Tpip 135 (150)
.| .+|.|
T Consensus 111 ~~~g~~pTP 119 (543)
T PRK07564 111 GRGGYTPTP 119 (543)
T ss_pred CCCCcCCch
Confidence 76 55655
No 49
>PRK09989 hypothetical protein; Provisional
Probab=31.05 E-value=1.5e+02 Score=23.80 Aligned_cols=43 Identities=7% Similarity=0.127 Sum_probs=31.7
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 129 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~ 129 (150)
+..++.+.++||+.|++.. + .+...+-+.+.|...||++..+.
T Consensus 18 ~~~l~~~~~~Gfd~VEl~~--~-------~~~~~~~~~~~l~~~Gl~v~~~~ 60 (258)
T PRK09989 18 IERFAAARKAGFDAVEFLF--P-------YDYSTLQIQKQLEQNHLTLALFN 60 (258)
T ss_pred HHHHHHHHHcCCCEEEECC--c-------ccCCHHHHHHHHHHcCCcEEEec
Confidence 4567788899999999854 1 23445566677888999998775
No 50
>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=31.00 E-value=1.4e+02 Score=18.67 Aligned_cols=41 Identities=17% Similarity=0.300 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCe
Q 031952 73 AMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMK 124 (150)
Q Consensus 73 a~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~ 124 (150)
+....+.+.+.+++.|+..|.+.+ .+....+++.+.+.|++
T Consensus 43 g~~L~~~~~~~~~~~g~~~i~~~~-----------~~~n~~~~~~~~k~Gf~ 83 (83)
T PF00583_consen 43 GSKLLQAAEEWARKRGIKRIYLDV-----------SPDNPAARRFYEKLGFE 83 (83)
T ss_dssp HHHHHHHHHHHHHHTTESEEEEEE-----------ETTGHHHHHHHHHTTEE
T ss_pred chhhhhhhhhhHHhcCccEEEEEE-----------eCCCHHHHHHHHHcCCC
Confidence 444556788888889999999988 45566777777776653
No 51
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=30.93 E-value=1.5e+02 Score=23.68 Aligned_cols=52 Identities=15% Similarity=0.215 Sum_probs=32.8
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeeCCCccc--CCCCC-hHHHHHHHHhCCCeEEEEE
Q 031952 77 AQDVSQRCKELGITALHIKLRATGGNKTK--TPGPG-AQSALRALARSGMKIGRIE 129 (150)
Q Consensus 77 a~~i~~~~~~~gi~~v~V~~~~~~g~~~k--G~G~g-r~~~lk~L~~~gl~I~~I~ 129 (150)
-+.+++.+.++|+..|++.+.... .... ++... ...+-+.|...||.|.++.
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 366788899999999999873110 0001 11222 3445556788899999874
No 52
>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=30.89 E-value=1.4e+02 Score=23.55 Aligned_cols=51 Identities=18% Similarity=0.214 Sum_probs=36.5
Q ss_pred CCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcE
Q 031952 37 NDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITA 91 (150)
Q Consensus 37 NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~ 91 (150)
+-.++-+.|++- ..+-++||-+-..+++ + ...+..+++++++.++++|++.
T Consensus 37 pgli~Rl~~Pk~-t~lIF~SGKiv~tGak--s-~~~a~~a~~~~~~~L~~~g~~~ 87 (174)
T cd04518 37 PGLVYRLEDPKI-AALIFRSGKMVCTGAK--S-VEDLHRAVKEIIKKLKDYGIKV 87 (174)
T ss_pred cEEEEEccCCcE-EEEEECCCeEEEEccC--C-HHHHHHHHHHHHHHHHhcCCCc
Confidence 345666666665 3456788877777665 3 5667888899999999999653
No 53
>PRK07757 acetyltransferase; Provisional
Probab=30.89 E-value=1.1e+02 Score=21.88 Aligned_cols=55 Identities=13% Similarity=0.130 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCCCCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRR 141 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphNGcR~ 141 (150)
-++.... ..+.+.+.+.|+..+.+.. . ..+-..+.|+....-.|..+--+|+|+.
T Consensus 81 Glg~~Ll-~~l~~~a~~~g~~~i~~~~--------~--------~~~~Y~k~GF~~~~~~~~~~~~~~~~~~ 135 (152)
T PRK07757 81 GIGRMLV-EACLEEARELGVKRVFALT--------Y--------QPEFFEKLGFREVDKEALPQKVWADCIK 135 (152)
T ss_pred CHHHHHH-HHHHHHHHhCCCCeEEEEe--------C--------cHHHHHHCCCEEcccccCChhHHhcCcc
Confidence 4544433 4566677788998876555 1 1255677899998888888888899974
No 54
>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=30.63 E-value=1.3e+02 Score=24.35 Aligned_cols=51 Identities=14% Similarity=0.214 Sum_probs=31.5
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCC--CCC-hHHHHHHHHhCCCeEEEEE
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTP--GPG-AQSALRALARSGMKIGRIE 129 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~--G~g-r~~~lk~L~~~gl~I~~I~ 129 (150)
+.+++.+.++||..|+|-+... ..+.... ... .+.+.+.|.+.|++|.++.
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 5677888899999999977210 0000011 122 2334556788899999884
No 55
>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=30.19 E-value=57 Score=26.89 Aligned_cols=59 Identities=19% Similarity=0.221 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccC
Q 031952 67 ESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTP 133 (150)
Q Consensus 67 K~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tp 133 (150)
..|.|....+.+.+++.+....+....|.+ .|||.==..+.+.|...|.+|+-|.|.+.
T Consensus 8 ~aTg~GV~~~~~~~~~~~~~~~l~g~~v~I--------qGfG~VG~~~a~~l~~~Ga~vv~vsD~~G 66 (244)
T PF00208_consen 8 EATGYGVAYAIEAALEHLGGDSLEGKRVAI--------QGFGNVGSHAARFLAELGAKVVAVSDSSG 66 (244)
T ss_dssp THHHHHHHHHHHHHHHHTTCHSSTTCEEEE--------EESSHHHHHHHHHHHHTTEEEEEEEESSE
T ss_pred cchHHHHHHHHHHHHHHcCCCCcCCCEEEE--------ECCCHHHHHHHHHHHHcCCEEEEEecCce
Confidence 455555555555555542222355678889 78886445556778888999999999763
No 56
>PRK14031 glutamate dehydrogenase; Provisional
Probab=30.05 E-value=1.5e+02 Score=26.88 Aligned_cols=60 Identities=15% Similarity=0.123 Sum_probs=42.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 031952 63 ADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 131 (150)
Q Consensus 63 k~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~ 131 (150)
.++...|-|-...+++.+++.. ...++...|.+ .|||.=-..+.+.|...|-+|+.|.|.
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 3445677777766666666544 33466778899 788874455567788899999999993
No 57
>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=29.58 E-value=2.5e+02 Score=25.56 Aligned_cols=78 Identities=21% Similarity=0.235 Sum_probs=48.3
Q ss_pred EEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCC-cEEEEEEEeeCCCccc-CCCCChHHHHHHHHhCCCeEEEE
Q 031952 51 TLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGI-TALHIKLRATGGNKTK-TPGPGAQSALRALARSGMKIGRI 128 (150)
Q Consensus 51 ~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi-~~v~V~~~~~~g~~~k-G~G~gr~~~lk~L~~~gl~I~~I 128 (150)
+.+-++|--|.-+.. .-|++-++.++..+++.+.+.+. ..|.|=... + .-++-.+.++.+|...|++|...
T Consensus 21 ~~FGT~GiRG~~g~~-~lt~~~v~~i~~a~~~~l~~~~~~~~VvVg~D~------R~~S~~~~~~~~~gL~s~Gi~V~~~ 93 (522)
T cd05801 21 VAFGTSGHRGSSLKG-SFNEAHILAISQAICDYRKSQGITGPLFLGKDT------HALSEPAFISALEVLAANGVEVIIQ 93 (522)
T ss_pred eeEEcccccCccCCC-chhHHHHHHHHHHHHHHHHhhCCCCeEEEEeCC------CcCCHHHHHHHHHHHHHCCCEEEEe
Confidence 444555544432222 46888899999988888876543 234443321 2 12344566678999999999987
Q ss_pred Ee--ccCCC
Q 031952 129 ED--VTPIP 135 (150)
Q Consensus 129 ~D--~Tpip 135 (150)
.| .+|.|
T Consensus 94 ~~~g~~pTP 102 (522)
T cd05801 94 QNDGYTPTP 102 (522)
T ss_pred CCCCCCCch
Confidence 76 45555
No 58
>PRK09414 glutamate dehydrogenase; Provisional
Probab=29.57 E-value=1.3e+02 Score=27.33 Aligned_cols=59 Identities=17% Similarity=0.205 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEecc
Q 031952 65 RDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 132 (150)
Q Consensus 65 ~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~T 132 (150)
+...|-+-...+++.+++.. ...++...|.+ .|||.==..+.+.|...|.+|+.|.|.+
T Consensus 207 r~~aTg~Gv~~~~~~~~~~~-~~~l~g~rVaI--------qGfGnVG~~~A~~L~~~GakVVavsDs~ 265 (445)
T PRK09414 207 RTEATGYGLVYFAEEMLKAR-GDSFEGKRVVV--------SGSGNVAIYAIEKAQQLGAKVVTCSDSS 265 (445)
T ss_pred CCCcccHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEEcCC
Confidence 44677777776766666554 44567788899 8898644445577888999999999954
No 59
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=29.39 E-value=3.4e+02 Score=22.71 Aligned_cols=62 Identities=23% Similarity=0.251 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHH--H------------HHHHHhCCCeEEEEEeccCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQS--A------------LRALARSGMKIGRIEDVTPIP 135 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~--~------------lk~L~~~gl~I~~I~D~Tpip 135 (150)
..++....+.+...|.++|++.|.|+.=-+ ..|..-.+- . +..+...|++|..|-|...+|
T Consensus 40 H~~G~~~l~~i~~~c~~lgI~~lTvYaFS~-----eN~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~iri~viGd~~~Lp 114 (249)
T PRK14834 40 HRAGVEALRRVVRAAGELGIGYLTLFAFSS-----ENWSRPASEVSDLFGLLRLFIRRDLAELHRNGVRVRVIGERAGLE 114 (249)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEEEec-----cccCCCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEcChhhCC
Confidence 444555667889999999999999998322 444433311 1 112345689999999999888
Q ss_pred C
Q 031952 136 T 136 (150)
Q Consensus 136 h 136 (150)
-
T Consensus 115 ~ 115 (249)
T PRK14834 115 A 115 (249)
T ss_pred H
Confidence 4
No 60
>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.
Probab=28.26 E-value=1.1e+02 Score=23.12 Aligned_cols=100 Identities=12% Similarity=0.155 Sum_probs=50.1
Q ss_pred eeeeEEEEEccCCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHH--HHcCCcEEEEEEEeeCCC
Q 031952 25 HVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRC--KELGITALHIKLRATGGN 102 (150)
Q Consensus 25 ~~~~ilhI~~t~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~--~~~gi~~v~V~~~~~~g~ 102 (150)
...+++. +++.-.+.+.++|.....-+...-..+.+..+. ..+..|-..+.+.+.... ...+.+.+.|.+ +.|.
T Consensus 39 ~rvgvv~-fs~~~~~~~~l~~~~~~~~~~~~i~~~~~~~g~-T~~~~AL~~a~~~l~~~~~g~R~~~~kv~ill--TDG~ 114 (177)
T cd01469 39 TQFGLVQ-YSESFRTEFTLNEYRTKEEPLSLVKHISQLLGL-TNTATAIQYVVTELFSESNGARKDATKVLVVI--TDGE 114 (177)
T ss_pred cEEEEEE-ECCceeEEEecCccCCHHHHHHHHHhCccCCCC-ccHHHHHHHHHHHhcCcccCCCCCCCeEEEEE--eCCC
Confidence 4455555 455557777787755421100111122333333 344444444433332111 112467777888 4444
Q ss_pred cccCCCCChHHHHHHHHhCCCeEEEEEe
Q 031952 103 KTKTPGPGAQSALRALARSGMKIGRIED 130 (150)
Q Consensus 103 ~~kG~G~gr~~~lk~L~~~gl~I~~I~D 130 (150)
...+.-. +.+++.++..|+.|..|.=
T Consensus 115 ~~~~~~~--~~~~~~~k~~gv~v~~Vgv 140 (177)
T cd01469 115 SHDDPLL--KDVIPQAEREGIIRYAIGV 140 (177)
T ss_pred CCCcccc--HHHHHHHHHCCcEEEEEEe
Confidence 4333222 5678889989998877654
No 61
>COG1184 GCD2 Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Probab=28.22 E-value=2.1e+02 Score=24.81 Aligned_cols=50 Identities=20% Similarity=0.360 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEecc
Q 031952 76 AAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 132 (150)
Q Consensus 76 aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~T 132 (150)
++..+...|.+.|-+ +.|++-- ++--+.|+..+ +.|.++|+.+.-|.|..
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 345566666666666 5555522 24556677776 88999999999999864
No 62
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=27.44 E-value=1.7e+02 Score=23.58 Aligned_cols=51 Identities=10% Similarity=0.179 Sum_probs=30.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCC---hHHHHHHHHhCCCeEEEEE
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPG---AQSALRALARSGMKIGRIE 129 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~g---r~~~lk~L~~~gl~I~~I~ 129 (150)
+..++.+.++|+..|++.+.... ......+.. .+.+-+.+...|++|.++.
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 45667788999999999872110 000111212 2334555678899998875
No 63
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional
Probab=27.12 E-value=3.8e+02 Score=22.50 Aligned_cols=62 Identities=16% Similarity=0.270 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHH---HH-----------HHHhCCCeEEEEEeccCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSA---LR-----------ALARSGMKIGRIEDVTPIP 135 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~---lk-----------~L~~~gl~I~~I~D~Tpip 135 (150)
..+...+.+.+.+.|.++|++.|.|+.=-+ -.|....+=+ +. .+...|++|.-|-|...+|
T Consensus 48 H~~G~~~l~~v~~~c~~~GIk~lTvYaFS~-----EN~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~irvr~iGd~~~Lp 122 (250)
T PRK14840 48 HYYGAKSLPQIVDTALHLGIEVLTLFAFST-----ENFSRSKEEVAELFSLFNSQLDSQLPYLHENEIRLRCIGDLSKLP 122 (250)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEeChhhCC
Confidence 445566678889999999999999987322 4444333211 11 1234689999999999888
Q ss_pred C
Q 031952 136 T 136 (150)
Q Consensus 136 h 136 (150)
-
T Consensus 123 ~ 123 (250)
T PRK14840 123 Q 123 (250)
T ss_pred H
Confidence 4
No 64
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=26.77 E-value=4.1e+02 Score=23.30 Aligned_cols=62 Identities=15% Similarity=0.173 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHH-----------------HHHHHhCCCeEEEEEecc
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSA-----------------LRALARSGMKIGRIEDVT 132 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~-----------------lk~L~~~gl~I~~I~D~T 132 (150)
-.++..+...+.+.|.++|++.|.|+.=-+ -.|..-.+=+ ..-|...|++|.-|-|..
T Consensus 45 H~~G~~~l~~il~~c~~lGIk~lTlYAFSt-----ENwkRp~~EV~~Lm~L~~~~l~~~~~~~~~l~~~~irirviGd~~ 119 (322)
T PTZ00349 45 HFMGSKALIQIIEICIKLKIKILSVFSFSL-----LNYNRSPEEIHFLFYLNLLILINEDFFFKFIKDNKIKIKIIGNLS 119 (322)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhhCCCHHHHHHHHHHHHHHHHHhhhhHHHHHHCCCEEEEEeChh
Confidence 344555667888999999999999987222 3333222211 123345689999999999
Q ss_pred CCCC
Q 031952 133 PIPT 136 (150)
Q Consensus 133 piph 136 (150)
.+|-
T Consensus 120 ~Lp~ 123 (322)
T PTZ00349 120 YIND 123 (322)
T ss_pred hCCH
Confidence 8884
No 65
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=26.38 E-value=3.7e+02 Score=22.21 Aligned_cols=62 Identities=15% Similarity=0.117 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHH---HHH-----------HHHhCCCeEEEEEeccCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQS---ALR-----------ALARSGMKIGRIEDVTPIP 135 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~---~lk-----------~L~~~gl~I~~I~D~Tpip 135 (150)
..++..+...+.+.|.++|++.|.|+.=-+ ..|..-.+= .+. .+...|++|.-|-|...+|
T Consensus 29 H~~G~~~l~~i~~~~~~lgIk~lTvYaFS~-----eN~~R~~~Ev~~Lm~L~~~~l~~~~~~~~~~~irvr~iG~~~~Lp 103 (233)
T PRK14841 29 HQRGAEVLHNTVKWSLELGIKYLTAFSFST-----ENWKRPKEEVEFLMDLFVQMIDREMELLRRERVRVRILGRKEGLP 103 (233)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEeeeH-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHcCcEEEEEeChhhCC
Confidence 445566667888999999999999987222 334322211 111 2335689999999999888
Q ss_pred C
Q 031952 136 T 136 (150)
Q Consensus 136 h 136 (150)
-
T Consensus 104 ~ 104 (233)
T PRK14841 104 E 104 (233)
T ss_pred H
Confidence 4
No 66
>PRK06371 translation initiation factor IF-2B subunit alpha; Provisional
Probab=25.94 E-value=1.7e+02 Score=25.60 Aligned_cols=50 Identities=20% Similarity=0.203 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 031952 76 AAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 131 (150)
Q Consensus 76 aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~ 131 (150)
++..+++.|.+.|-+ ++|++-- ++-.+.|..-.-+.|...|+.+..|.|.
T Consensus 156 Tal~~l~~A~~~gk~-f~V~v~E-----sRP~~qG~rlta~eL~~~GI~vtlI~Ds 205 (329)
T PRK06371 156 TALAPIRIAHRNGKN-IFVFVDE-----TRPRLQGARLTAWELAQEGIDHAIIADN 205 (329)
T ss_pred hHHHHHHHHHHcCCe-eEEEECC-----CCCcchHHHHHHHHHHHCCCCEEEEccc
Confidence 455667777777755 7777732 2566777665457799999999999985
No 67
>TIGR00512 salvage_mtnA S-methyl-5-thioribose-1-phosphate isomerase. The delineation of this family was based 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. This clade is now recognized to include the methionine salvage pathway enzyme MtnA.
Probab=25.68 E-value=1.6e+02 Score=25.64 Aligned_cols=49 Identities=24% Similarity=0.246 Sum_probs=33.6
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 031952 77 AQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 131 (150)
Q Consensus 77 a~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~ 131 (150)
+..+++.+.+.|. .++|++-- ++-.+.|..-..+.|...|+.+..|.|.
T Consensus 167 al~~l~~A~~~g~-~~~V~v~E-----srP~~qG~rlta~~L~~~GI~vtlI~Ds 215 (331)
T TIGR00512 167 ALGVIRSAHEKGR-LEHVYADE-----TRPRLQGARLTAWELVQEGIPATLITDS 215 (331)
T ss_pred HHHHHHHHHHcCC-ceEEEECC-----CCchhhHHHHHHHHHHHCCCCEEEEccc
Confidence 3456667777774 46666632 2555677655457799999999999994
No 68
>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=25.50 E-value=2.5e+02 Score=21.26 Aligned_cols=47 Identities=32% Similarity=0.376 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEE
Q 031952 68 SSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 126 (150)
Q Consensus 68 ~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~ 126 (150)
+.-++.. +.+.+.+.+.++|+..|.+.+ ...-..+++...+.|++..
T Consensus 137 GkG~G~~-ll~~~~~~a~~~g~~~I~l~v-----------~~~N~~A~~~Y~klGF~~~ 183 (191)
T TIGR02382 137 SRGIGAE-LMQTALNWCYARGLTRLRVAT-----------QMGNTAALRLYIRSGANIE 183 (191)
T ss_pred CCCHHHH-HHHHHHHHHHHcCCCEEEEEe-----------CCCCHHHHHHHHHcCCccc
Confidence 4446444 446677788899999999888 2334577787888888754
No 69
>PLN00062 TATA-box-binding protein; Provisional
Probab=25.46 E-value=1.9e+02 Score=22.98 Aligned_cols=48 Identities=19% Similarity=0.309 Sum_probs=33.4
Q ss_pred CeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCC
Q 031952 38 DTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGI 89 (150)
Q Consensus 38 NT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi 89 (150)
-.++-+.|++- +++-++||-+-..+++ + ...+..|++++++.++++|+
T Consensus 38 gli~Rl~~Pk~-t~lIF~SGKiviTGak--s-~e~a~~a~~~~~~~L~~lg~ 85 (179)
T PLN00062 38 AVIMRIREPKT-TALIFASGKMVCTGAK--S-EHDSKLAARKYARIIQKLGF 85 (179)
T ss_pred EEEEEeCCCcE-EEEEECCCeEEEEecC--C-HHHHHHHHHHHHHHHHHcCC
Confidence 34444556554 3556788877777664 3 55677788999999999997
No 70
>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=25.36 E-value=2.6e+02 Score=19.96 Aligned_cols=71 Identities=13% Similarity=0.120 Sum_probs=43.4
Q ss_pred EEeCCCCCeEEEEE---eecCc--cccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHH
Q 031952 42 HVTDLSGRETLVRI---TGGMK--VKADRDESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALR 116 (150)
Q Consensus 42 tlTD~~G~~~~~~S---sG~~g--~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk 116 (150)
.|.|++|+.+.|.- +|.++ |.=-.=++.-++.+ ++...++.+.++|+.. -.++ -...++..|
T Consensus 2 CllgpeG~PVSW~lmdqtge~rmgyTlPeyR~~G~~~~-v~~~~~~~L~~~g~P~-Y~hv-----------~~~N~~~~r 68 (89)
T PF08444_consen 2 CLLGPEGNPVSWSLMDQTGEMRMGYTLPEYRGQGLMSQ-VMYHLAQYLHKLGFPF-YGHV-----------DEDNEASQR 68 (89)
T ss_pred cccCCCCCEeEEEEecccccccccccCHhHhcCCHHHH-HHHHHHHHHHHCCCCe-Eeeh-----------HhccHHHHH
Confidence 57899999876543 44333 32111123345444 5567899999999973 3333 244677888
Q ss_pred HHHhCCCeE
Q 031952 117 ALARSGMKI 125 (150)
Q Consensus 117 ~L~~~gl~I 125 (150)
.+..-|..+
T Consensus 69 ~~~~lg~~~ 77 (89)
T PF08444_consen 69 LSKSLGFIF 77 (89)
T ss_pred HHHHCCCee
Confidence 888777543
No 71
>PRK04266 fibrillarin; Provisional
Probab=25.30 E-value=2.6e+02 Score=22.58 Aligned_cols=66 Identities=29% Similarity=0.369 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 137 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~TpiphN 137 (150)
+.....+.+.+.+.++.-|.-.|.|..+.. ++.+....-.+..++.|..+|+++....|.+|...|
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 333333444555555555655555555211 111111111123568889999999999999887543
No 72
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=25.30 E-value=3.4e+02 Score=21.79 Aligned_cols=39 Identities=18% Similarity=0.335 Sum_probs=28.3
Q ss_pred eecCcc--ccCCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEEE
Q 031952 56 TGGMKV--KADRDESSPYAAMLAAQDVSQRCKELGITALHIKL 96 (150)
Q Consensus 56 sG~~g~--kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~ 96 (150)
+|..|| .... +.--||-+.. ..+.++|+++|++.|-|..
T Consensus 98 gGHIGY~VrPse-R~KGYA~emL-kl~L~~ar~lgi~~Vlvtc 138 (174)
T COG3981 98 GGHIGYSVRPSE-RRKGYAKEML-KLALEKARELGIKKVLVTC 138 (174)
T ss_pred CCcccceeChhh-hccCHHHHHH-HHHHHHHHHcCCCeEEEEe
Confidence 666675 2333 2335766544 7788999999999999999
No 73
>PRK08334 translation initiation factor IF-2B subunit beta; Validated
Probab=25.13 E-value=2.3e+02 Score=25.06 Aligned_cols=51 Identities=16% Similarity=0.117 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEecc
Q 031952 76 AAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 132 (150)
Q Consensus 76 aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~T 132 (150)
++..++..+.+.|. .++|++. -++-...|....-..|...|+.+..|.|..
T Consensus 179 Tal~vi~~A~~~gk-~~~V~v~-----EtRP~~qG~rlta~eL~~~GI~vtlI~Dsa 229 (356)
T PRK08334 179 TVGAVLRVMHKDGT-LKLLWVD-----ETRPVLQGARLSAWEYHYDGIPLKLISDNM 229 (356)
T ss_pred hHHHHHHHHHHcCC-eEEEEEC-----CCCchhhHHHHHHHHHHHCCCCEEEEehhH
Confidence 55667777777784 5677773 235567777665577999999999999963
No 74
>PRK15425 gapA glyceraldehyde-3-phosphate dehydrogenase A; Provisional
Probab=24.95 E-value=87 Score=27.31 Aligned_cols=30 Identities=27% Similarity=0.272 Sum_probs=21.2
Q ss_pred cCCCCChHHHHHHH-HhCCCeEEEEEeccCC
Q 031952 105 KTPGPGAQSALRAL-ARSGMKIGRIEDVTPI 134 (150)
Q Consensus 105 kG~G~gr~~~lk~L-~~~gl~I~~I~D~Tpi 134 (150)
+|||.==..++|++ ...+++|+-|-|.+..
T Consensus 8 nGfGRIGr~~~r~~~~~~~~~vvaiNd~~~~ 38 (331)
T PRK15425 8 NGFGRIGRIVFRAAQKRSDIEIVAINDLLDA 38 (331)
T ss_pred EeeChHHHHHHHHHHHCCCCEEEEEecCCCH
Confidence 88886334555664 4568999999997753
No 75
>PRK09542 manB phosphomannomutase/phosphoglucomutase; Reviewed
Probab=24.81 E-value=2.3e+02 Score=25.07 Aligned_cols=63 Identities=11% Similarity=0.108 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCC-CChHHHHHHHHhCCCeEEEEEeccCCCC
Q 031952 67 ESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRIEDVTPIPT 136 (150)
Q Consensus 67 K~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G-~gr~~~lk~L~~~gl~I~~I~D~Tpiph 136 (150)
.-||.-+..++..++..+.+.+-..|.|--.. +-.+ .-..+++.+|...|++|..+ +.+|.|-
T Consensus 13 ~lt~~~v~~l~~a~~~~l~~~~~~~VvVg~D~------R~~s~~l~~a~~~gL~s~G~~V~~l-g~~pTP~ 76 (445)
T PRK09542 13 QIDEDLVRDVGAAFARLMRAEGATTVVIGHDM------RDSSPELAAAFAEGVTAQGLDVVRI-GLASTDQ 76 (445)
T ss_pred CcCHHHHHHHHHHHHHHHHHcCCCeEEEEeCC------CCCHHHHHHHHHHHHHHCCCEEEEe-CCCCCHH
Confidence 46888888888888888765543444333311 2222 12467888899999999988 6888774
No 76
>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=24.66 E-value=2.5e+02 Score=25.65 Aligned_cols=56 Identities=20% Similarity=0.304 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCC-h--HHHHHHHHhCCCeEEEEEeccCCCC
Q 031952 72 AAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPG-A--QSALRALARSGMKIGRIEDVTPIPT 136 (150)
Q Consensus 72 Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~g-r--~~~lk~L~~~gl~I~~I~D~Tpiph 136 (150)
.+...+..|++++++-|+..|.+.= .=|-- | -...|.|.++||.++.|..+|||..
T Consensus 320 ~a~~~g~eIa~~Lk~dgVDAVILTs---------tCgtC~r~~a~m~keiE~~GiPvv~~~~~~pis~ 378 (431)
T TIGR01918 320 ESKQFAKEFVVELKQGGVDAVILTS---------TUGTCTRCGATMVKEIERAGIPVVHMCTVIPIAL 378 (431)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEcC---------CCCcchhHHHHHHHHHHHcCCCEEEEeecccHhh
Confidence 3457888899999999999885542 22322 2 3456889999999999999999864
No 77
>PLN02891 IMP cyclohydrolase
Probab=24.16 E-value=82 Score=29.56 Aligned_cols=42 Identities=29% Similarity=0.487 Sum_probs=32.2
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCC
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 136 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tpiph 136 (150)
+.+++.+.++|+.-| = | | |- -+.|+.+|+++..|.|+|..|.
T Consensus 36 ~~fAk~L~~~gveIi---S--T------g-GT-----ak~L~e~Gi~v~~Vsd~TgfPE 77 (547)
T PLN02891 36 ALLANGLQELGYTIV---S--T------G-GT-----ASALEAAGVSVTKVEELTNFPE 77 (547)
T ss_pred HHHHHHHHHCCCEEE---E--c------c-hH-----HHHHHHcCCceeeHHhccCCch
Confidence 457778888887633 2 2 2 22 5889999999999999999997
No 78
>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=24.14 E-value=1.7e+02 Score=23.98 Aligned_cols=64 Identities=16% Similarity=0.056 Sum_probs=38.5
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHH-HHHHhCCCeEEEEEeccCCCCCCCCC
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSAL-RALARSGMKIGRIEDVTPIPTDSTRR 141 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~l-k~L~~~gl~I~~I~D~TpiphNGcR~ 141 (150)
..+.+.+.++|+..++|..+.+.+-..+-+.......+ +.+...++.+..|.--.|.+.|-|=|
T Consensus 14 ~~a~~~~~~~G~~~~qif~~~P~~w~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Hapy~iNlas~ 78 (274)
T TIGR00587 14 QAAYNRAAEIGATAFMFFLKSPRWWRRPMLEEEVIDWFKAALETNKNLSQIVLVHAPYLINLASP 78 (274)
T ss_pred HHHHHHHHHhCCCEEEEEecCccccCCCCCCHHHHHHHHHHHHHcCCCCcceeccCCeeeecCCC
Confidence 34667788999999999996553333332233333344 34566677654455556666676644
No 79
>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts). This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.
Probab=23.80 E-value=2.4e+02 Score=23.18 Aligned_cols=49 Identities=22% Similarity=0.182 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCC
Q 031952 67 ESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSG 122 (150)
Q Consensus 67 K~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~g 122 (150)
...+.||+..+..+..+..+..-..+.|.+=|. .|.|+-+++.+|....
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IllvG~-------tGvGKSSliNaLlg~~ 55 (249)
T cd01853 7 QFFPDAAQTKALELEAKGKEELDFSLTILVLGK-------TGVGKSSTINSIFGER 55 (249)
T ss_pred ccCcHHHHHHHHHHHHHhhhhccCCeEEEEECC-------CCCcHHHHHHHHhCCC
Confidence 466889999998888888887777788888553 6889999999998653
No 80
>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=23.53 E-value=2.7e+02 Score=21.86 Aligned_cols=52 Identities=15% Similarity=0.239 Sum_probs=36.6
Q ss_pred CCCeEEEEeCCCCCeEEEEEeecCccccCCCCCCHHHHHHHHHHHHHHHHHcCCcE
Q 031952 36 FNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGITA 91 (150)
Q Consensus 36 ~NNT~itlTD~~G~~~~~~SsG~~g~kk~~rK~t~~Aa~~aa~~i~~~~~~~gi~~ 91 (150)
++-.++-+.|++= ...-|++|-+--.+++ + ...+..+++.+++.++++|++.
T Consensus 36 fpgli~R~~~Pk~-t~lIF~sGKiviTGak--s-~~~~~~a~~~~~~~l~~~g~~~ 87 (174)
T cd04517 36 YPKVTMRLREPRA-TASVWSSGKITITGAT--S-EEEAKQAARRAARLLQKLGFKV 87 (174)
T ss_pred CCEEEEEecCCcE-EEEEECCCeEEEEccC--C-HHHHHHHHHHHHHHHHHcCCCc
Confidence 4445566666644 3456888888877665 3 5567778899999999998765
No 81
>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=23.48 E-value=2.4e+02 Score=18.91 Aligned_cols=49 Identities=10% Similarity=0.141 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 130 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D 130 (150)
-+|.+ +...+.+.+.+.|+..+.+.+ ......+++.+++.|+++....+
T Consensus 70 G~g~~-ll~~~~~~~~~~~~~~i~~~~-----------~~~n~~~~~~y~~~Gf~~~~~~~ 118 (131)
T TIGR01575 70 GIGRA-LLRELIDEAKGRGVNEIFLEV-----------RVSNIAAQALYKKLGFNEIAIRR 118 (131)
T ss_pred CHHHH-HHHHHHHHHHHcCCCeEEEEE-----------ecccHHHHHHHHHcCCCcccccc
Confidence 35444 445677778888998888777 23345567888889998765543
No 82
>PRK10646 ADP-binding protein; Provisional
Probab=23.34 E-value=3.4e+02 Score=21.00 Aligned_cols=44 Identities=20% Similarity=0.298 Sum_probs=29.5
Q ss_pred CHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhC-CC
Q 031952 69 SPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARS-GM 123 (150)
Q Consensus 69 t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~-gl 123 (150)
++.+.+..|+.+++.+.. | -.|.+.|. +|.|+.++.|+|.++ |+
T Consensus 10 s~~~t~~l~~~la~~l~~-g---~vi~L~Gd-------LGaGKTtf~rgl~~~Lg~ 54 (153)
T PRK10646 10 DEQATLDLGARVAKACDG-A---TVIYLYGD-------LGAGKTTFSRGFLQALGH 54 (153)
T ss_pred CHHHHHHHHHHHHHhCCC-C---cEEEEECC-------CCCCHHHHHHHHHHHcCC
Confidence 456666777777765532 2 23677443 999999999999764 54
No 83
>COG3916 LasI N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.29 E-value=2.9e+02 Score=22.78 Aligned_cols=51 Identities=24% Similarity=0.177 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPI 134 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tpi 134 (150)
+.|+......+++.+...|++.|.... --...+.|..+|+.+..|-+...+
T Consensus 119 ~~a~~el~~g~ie~a~~~G~~~IvtVt--------------~~~meril~r~Gw~~~riG~~~~i 169 (209)
T COG3916 119 SPAAYELFAGMIEYALARGITGIVTVT--------------DTGMERILRRAGWPLTRIGPPLTI 169 (209)
T ss_pred cHHHHHHHHHHHHHHHHcCCceEEEEE--------------chHHHHHHHHcCCCeEEcCCceee
Confidence 345666666789999999999998877 224578888999988887765544
No 84
>COG0057 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]
Probab=23.27 E-value=1e+02 Score=27.17 Aligned_cols=30 Identities=30% Similarity=0.333 Sum_probs=21.5
Q ss_pred cCCCC-ChHHHHHHHHhC-CCeEEEEEeccCC
Q 031952 105 KTPGP-GAQSALRALARS-GMKIGRIEDVTPI 134 (150)
Q Consensus 105 kG~G~-gr~~~lk~L~~~-gl~I~~I~D~Tpi 134 (150)
+|||. ||..+-..+.+. .++|+-|.|.|+.
T Consensus 7 NGfGrIGR~v~ra~~~~~~dieVVaInd~t~~ 38 (335)
T COG0057 7 NGFGRIGRLVARAALERDGDIEVVAINDLTDP 38 (335)
T ss_pred ecCcHHHHHHHHHHHhCCCCeEEEEEecCCCH
Confidence 89995 776664444445 4999999997653
No 85
>cd07996 WGR_MMR_like WGR domain of molybdate metabolism regulator and related proteins. The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.
Probab=23.17 E-value=2.2e+02 Score=18.46 Aligned_cols=43 Identities=26% Similarity=0.240 Sum_probs=25.8
Q ss_pred CCCeEEEEEeecCccccCCCC----CCHHHHHHHHHHHHHHHHHcCCc
Q 031952 47 SGRETLVRITGGMKVKADRDE----SSPYAAMLAAQDVSQRCKELGIT 90 (150)
Q Consensus 47 ~G~~~~~~SsG~~g~kk~~rK----~t~~Aa~~aa~~i~~~~~~~gi~ 90 (150)
.|....+..-|-+|-.+.. + .++.+|..+++++.+.-...||.
T Consensus 26 fg~~~v~~~wGRiG~~Gq~-~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 26 FGEWSLVRRWGRIGTKGQS-RTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred CCCEEEEEEECCCCCCCce-EEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 3444445555666644333 3 35566777777777776677775
No 86
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=23.00 E-value=4.5e+02 Score=21.94 Aligned_cols=62 Identities=23% Similarity=0.320 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChH---HHH-----------HHHHhCCCeEEEEEeccCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQ---SAL-----------RALARSGMKIGRIEDVTPIP 135 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~---~~l-----------k~L~~~gl~I~~I~D~Tpip 135 (150)
..++..+...+...|.++|++.|.|+.=-+ ..|....+ ..+ ..+...|++|.-|-|.+.+|
T Consensus 46 H~~G~~~l~~i~~~c~~~GI~~vT~yaFS~-----eN~kR~~~Ev~~Lm~L~~~~l~~~~~~~~~~~iri~~iG~~~~Lp 120 (249)
T PRK14831 46 HRRGVDALKDLLRCCKDWGIGALTAYAFST-----ENWSRPLEEVNFLMTLFERVLRRELEELMEENVRIRFVGDLDPLP 120 (249)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEeecch-----hhhCcCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEechhhCC
Confidence 344555667788899999999999998111 22332221 111 12345689999999999888
Q ss_pred C
Q 031952 136 T 136 (150)
Q Consensus 136 h 136 (150)
-
T Consensus 121 ~ 121 (249)
T PRK14831 121 K 121 (249)
T ss_pred H
Confidence 4
No 87
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=22.94 E-value=1.6e+02 Score=25.89 Aligned_cols=36 Identities=22% Similarity=0.221 Sum_probs=26.3
Q ss_pred EEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 031952 91 ALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 127 (150)
Q Consensus 91 ~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~ 127 (150)
.|.|..|| ||+..-=+-.+-+.+.+++..+.+.|++
T Consensus 194 Dviii~RG-GGS~eDL~~Fn~e~v~~ai~~~~~Pvis 229 (438)
T PRK00286 194 DVLIVARG-GGSLEDLWAFNDEAVARAIAASRIPVIS 229 (438)
T ss_pred CEEEEecC-CCCHHHhhccCcHHHHHHHHcCCCCEEE
Confidence 56666755 5665555667889999999988887654
No 88
>PRK09491 rimI ribosomal-protein-alanine N-acetyltransferase; Provisional
Probab=22.88 E-value=2.8e+02 Score=19.57 Aligned_cols=55 Identities=9% Similarity=0.123 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccC
Q 031952 67 ESSPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTP 133 (150)
Q Consensus 67 K~t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tp 133 (150)
++.-+|.. +.+.+.+.+.+.|+..+.+.+ -.....+++.+.+.|++.........
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 34456544 445667778888998887776 23347788989999998777665543
No 89
>PRK05720 mtnA methylthioribose-1-phosphate isomerase; Reviewed
Probab=22.79 E-value=2.5e+02 Score=24.58 Aligned_cols=49 Identities=27% Similarity=0.308 Sum_probs=34.4
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 031952 77 AQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 131 (150)
Q Consensus 77 a~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~ 131 (150)
+..+++.+.+.|.+ ++|++--+ +-...|..-.-+.|...|+.+..|.|.
T Consensus 167 al~~i~~A~~~gk~-~~V~v~Es-----RP~~qG~~lta~eL~~~GI~vtlI~Ds 215 (344)
T PRK05720 167 ALAPIYAAKEKGID-IHVYADET-----RPRLQGARLTAWELYQAGIDVTVITDN 215 (344)
T ss_pred HHHHHHHHHHcCCc-eEEEEcCC-----CChhhhHHHHHHHHHHCCCCEEEEccc
Confidence 44566666666655 66666332 566778755557799999999999995
No 90
>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=22.11 E-value=1.7e+02 Score=20.24 Aligned_cols=26 Identities=15% Similarity=0.362 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEEe
Q 031952 72 AAMLAAQDVSQRCKELGITALHIKLRA 98 (150)
Q Consensus 72 Aa~~aa~~i~~~~~~~gi~~v~V~~~~ 98 (150)
.++++++.+.+.++++|+. +.|..+|
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 4678889999999999997 7778854
No 91
>cd01421 IMPCH Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. This is the final step in de novo purine production.
Probab=22.04 E-value=1.4e+02 Score=24.13 Aligned_cols=42 Identities=24% Similarity=0.472 Sum_probs=32.4
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEeccCCCC
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 136 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~Tpiph 136 (150)
..+++++.++|++-+ +| .| + -+.|+..|+.+..|.+.|..|.
T Consensus 14 ~~lAk~L~~lGf~I~-----AT-----~G------T-Ak~L~e~GI~v~~V~k~TgfpE 55 (187)
T cd01421 14 VEFAKELVELGVEIL-----ST-----GG------T-AKFLKEAGIPVTDVSDITGFPE 55 (187)
T ss_pred HHHHHHHHHCCCEEE-----Ec-----cH------H-HHHHHHcCCeEEEhhhccCCcH
Confidence 467888889998743 22 22 2 4789999999999999999986
No 92
>PF01008 IF-2B: Initiation factor 2 subunit family; InterPro: IPR000649 Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. The eukaryotic translation initiation factor EIF-2B is a complex made up of five different subunits, alpha, beta, gamma, delta and epsilon, and catalyses the exchange of EIF-2-bound GDP for GTP. This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes; related proteins from archaebacteria and IF-2 from prokaryotes and also contains a subfamily of proteins in eukaryotes, archaeae (e.g. Pyrococcus furiosus), or eubacteria such as Bacillus subtilis and Thermotoga maritima. Many of these proteins were initially annotated as putative translation initiation factors despite the fact that there is no evidence for the requirement of an IF2 recycling factor in prokaryotic translation initiation. Recently, one of these proteins from B. subtilis has been functionally characterised as a 5-methylthioribose-1-phosphate isomerase (MTNA) []. This enzyme participates in the methionine salvage pathway catalysing the isomerisation of 5-methylthioribose-1-phosphate to 5-methylthioribulose-1-phosphate []. The methionine salvage pathway leads to the synthesis of methionine from methylthioadenosine, the end product of the spermidine and spermine anabolism in many species.; GO: 0044237 cellular metabolic process; PDB: 1VB5_A 1T5O_D 3A11_E 3VM6_C 1W2W_A 1T9K_A 3ECS_B 2YRF_A 2YVK_B 2A0U_A ....
Probab=21.95 E-value=2.4e+02 Score=23.03 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=29.2
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 031952 77 AQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 131 (150)
Q Consensus 77 a~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~ 131 (150)
.+.++..|.+.| +.++|++-.. +-.+.|++.+ +.|...|+.+..|.|.
T Consensus 120 v~~~l~~a~~~~-~~~~V~v~es-----~P~~eG~~~a-~~L~~~gi~v~~i~d~ 167 (282)
T PF01008_consen 120 VERFLLSAKKKG-KKFRVIVLES-----RPYNEGRLMA-KELAEAGIPVTLIPDS 167 (282)
T ss_dssp HHHHHHHHHHTT-EEEEEEEE-------TTTTHHHTHH-HHHHHTT-EEEEE-GG
T ss_pred HHHHHHHHHHcC-CeEEEEEccC-----CcchhhhhHH-HHhhhcceeEEEEech
Confidence 345555676666 4566666322 4455666655 7788899999999885
No 93
>PRK09997 hydroxypyruvate isomerase; Provisional
Probab=21.78 E-value=2.9e+02 Score=22.03 Aligned_cols=42 Identities=7% Similarity=0.046 Sum_probs=30.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 031952 78 QDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 128 (150)
Q Consensus 78 ~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I 128 (150)
+..++.+.+.||..|++.. -++..-+.+.+.|...||++...
T Consensus 18 ~~~l~~~a~~Gf~~VEl~~---------~~~~~~~~~~~~l~~~gl~~~~~ 59 (258)
T PRK09997 18 LARFEKAAQCGFRGVEFMF---------PYDYDIEELKQVLASNKLEHTLH 59 (258)
T ss_pred HHHHHHHHHhCCCEEEEcC---------CCCCCHHHHHHHHHHcCCcEEEE
Confidence 4567788899999999844 12345666777788899998763
No 94
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.73 E-value=2.5e+02 Score=22.59 Aligned_cols=43 Identities=14% Similarity=0.192 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHH
Q 031952 69 SPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRAL 118 (150)
Q Consensus 69 t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L 118 (150)
|..-|+.+-..++..|.+.|+.+|.|+= | ||..+|...+||..
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 4555666777788899999999998877 2 44446667777753
No 95
>PRK09856 fructoselysine 3-epimerase; Provisional
Probab=21.67 E-value=2.8e+02 Score=22.10 Aligned_cols=61 Identities=13% Similarity=0.035 Sum_probs=33.6
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEec-cCCCCCC
Q 031952 77 AQDVSQRCKELGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDV-TPIPTDS 138 (150)
Q Consensus 77 a~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~-gr~~~lk~L~~~gl~I~~I~D~-TpiphNG 138 (150)
.+..++.+.++|+..|++...-+ -.....+.. ..+.+-+.+...|++|.++.-. ...|+|.
T Consensus 15 l~~~l~~~~~~G~~~vEl~~~~~-~~~~~~~~~~~~~~l~~~~~~~gl~v~s~~~~~~~~~~~~ 77 (275)
T PRK09856 15 IEHAFRDASELGYDGIEIWGGRP-HAFAPDLKAGGIKQIKALAQTYQMPIIGYTPETNGYPYNM 77 (275)
T ss_pred HHHHHHHHHHcCCCEEEEccCCc-cccccccCchHHHHHHHHHHHcCCeEEEecCcccCcCccc
Confidence 36678888999999999854100 000001111 1233444566789999887532 2344543
No 96
>TIGR00524 eIF-2B_rel eIF-2B alpha/beta/delta-related uncharacterized proteins. This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins.
Probab=21.53 E-value=2.5e+02 Score=24.01 Aligned_cols=50 Identities=20% Similarity=0.256 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 031952 76 AAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 131 (150)
Q Consensus 76 aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~~I~D~ 131 (150)
+++.+++.|.+.|.+ .+|++-- ++-.+.|.....+.|...|+.+..|.|.
T Consensus 138 tv~~~l~~A~~~g~~-~~V~v~E-----srP~~~G~~~~a~~L~~~gI~vtlI~Ds 187 (303)
T TIGR00524 138 TALGVIRSAWEDGKR-IRVIACE-----TRPRNQGSRLTAWELMQDGIDVTLITDS 187 (303)
T ss_pred hHHHHHHHHHHcCCc-eEEEECC-----CCCccchHHHHHHHHHHCCCCEEEEChh
Confidence 445566677677754 5566622 2566778334447799999999999884
No 97
>PRK14742 thrL thr operon leader peptide; Provisional
Probab=21.26 E-value=52 Score=18.53 Aligned_cols=15 Identities=40% Similarity=0.565 Sum_probs=11.9
Q ss_pred cCCCeEEEEeCCCCC
Q 031952 35 SFNDTFIHVTDLSGR 49 (150)
Q Consensus 35 t~NNT~itlTD~~G~ 49 (150)
+.+-||||-|+..|+
T Consensus 11 ~l~ttiittt~ttg~ 25 (28)
T PRK14742 11 SLNTTIITTTETTGY 25 (28)
T ss_pred EeEEEEEEEEEeccc
Confidence 466789999988775
No 98
>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=21.08 E-value=3.9e+02 Score=24.42 Aligned_cols=56 Identities=23% Similarity=0.344 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCC-h--HHHHHHHHhCCCeEEEEEeccCCCC
Q 031952 72 AAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPG-A--QSALRALARSGMKIGRIEDVTPIPT 136 (150)
Q Consensus 72 Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~g-r--~~~lk~L~~~gl~I~~I~D~Tpiph 136 (150)
.++..+..|++++++-|+..|.+.= .=|-- | -...|.|.++||.++.|..+|||..
T Consensus 320 ~a~~~g~eIa~~Lk~dgVDAvILts---------tCgtCtrcga~m~keiE~~GIPvV~i~~~~pI~~ 378 (431)
T TIGR01917 320 NSKQFAKEFSKELLAAGVDAVILTS---------TUGTCTRCGATMVKEIERAGIPVVHICTVTPIAL 378 (431)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEcC---------CCCcchhHHHHHHHHHHHcCCCEEEEeechhHHH
Confidence 3556788899999999999885542 22322 2 3466889999999999999999853
No 99
>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=20.99 E-value=1.8e+02 Score=25.41 Aligned_cols=50 Identities=24% Similarity=0.321 Sum_probs=32.9
Q ss_pred CHHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHHHHHHHHhCCCeEE
Q 031952 69 SPYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 126 (150)
Q Consensus 69 t~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~~lk~L~~~gl~I~ 126 (150)
-|.|-..+.+.=+..+++||+..|+|+- =-+-..-+.++++|..+||-++
T Consensus 47 DPLad~~~C~rDi~~l~~LgiNtIRVY~--------vdp~~nHd~CM~~~~~aGIYvi 96 (314)
T PF03198_consen 47 DPLADPEACKRDIPLLKELGINTIRVYS--------VDPSKNHDECMSAFADAGIYVI 96 (314)
T ss_dssp -GGG-HHHHHHHHHHHHHHT-SEEEES-----------TTS--HHHHHHHHHTT-EEE
T ss_pred CcccCHHHHHHhHHHHHHcCCCEEEEEE--------eCCCCCHHHHHHHHHhCCCEEE
Confidence 3565555667677788999999999887 3345567889999999997653
No 100
>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=20.80 E-value=2.4e+02 Score=20.52 Aligned_cols=61 Identities=20% Similarity=0.189 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHHHHHHHHc-CCcEEEEEEEeeCCCcccCCC-CChHHHHHHHHhCCCeEEEEEeccCCC
Q 031952 68 SSPYAAMLAAQDVSQRCKEL-GITALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRIEDVTPIP 135 (150)
Q Consensus 68 ~t~~Aa~~aa~~i~~~~~~~-gi~~v~V~~~~~~g~~~kG~G-~gr~~~lk~L~~~gl~I~~I~D~Tpip 135 (150)
-||..+..++..++..+.+. .-..|.|=... +-.+ .-.+++..+|...|++|..+. .+|.|
T Consensus 18 lt~~~~~~~~~a~~~~~~~~~~~~~VvVg~D~------R~~s~~~~~~~~~~l~~~G~~V~~~g-~~~tP 80 (137)
T PF02878_consen 18 LTPEFAARLAQAFASYLKEKGNGSRVVVGRDT------RPSSPMLAKALAAGLRANGVDVIDIG-LVPTP 80 (137)
T ss_dssp BSHHHHHHHHHHHHHHHHHTTTSSEEEEEE-S------STTHHHHHHHHHHHHHHTTEEEEEEE-EB-HH
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCeEEEEEcc------cCCHHHHHHHHHHHHhhccccccccc-ccCcH
Confidence 68999999999999888775 33445444421 2222 234677788889999998776 55544
No 101
>KOG0747 consensus Putative NAD+-dependent epimerases [Carbohydrate transport and metabolism]
Probab=20.45 E-value=1.7e+02 Score=25.75 Aligned_cols=39 Identities=23% Similarity=0.456 Sum_probs=25.6
Q ss_pred CCCHHHHHHHH-HHHHHHH-HHcCCcEEEEEEEeeCCCcccCCCCChH
Q 031952 67 ESSPYAAMLAA-QDVSQRC-KELGITALHIKLRATGGNKTKTPGPGAQ 112 (150)
Q Consensus 67 K~t~~Aa~~aa-~~i~~~~-~~~gi~~v~V~~~~~~g~~~kG~G~gr~ 112 (150)
=.+||||..|| |.+.+.. .++|+..+.++.. .-.||++.
T Consensus 153 PtnpyAasKaAaE~~v~Sy~~sy~lpvv~~R~n-------nVYGP~q~ 193 (331)
T KOG0747|consen 153 PTNPYAASKAAAEMLVRSYGRSYGLPVVTTRMN-------NVYGPNQY 193 (331)
T ss_pred CCCchHHHHHHHHHHHHHHhhccCCcEEEEecc-------CccCCCcC
Confidence 35799996665 5544443 5678888888883 22677663
No 102
>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=20.41 E-value=85 Score=23.31 Aligned_cols=44 Identities=20% Similarity=0.305 Sum_probs=29.0
Q ss_pred HHHHHcCCcEEEEEEEeeCCCcccCCCCC-----hHHHHHHHHhCCCeEEEEEecc
Q 031952 82 QRCKELGITALHIKLRATGGNKTKTPGPG-----AQSALRALARSGMKIGRIEDVT 132 (150)
Q Consensus 82 ~~~~~~gi~~v~V~~~~~~g~~~kG~G~g-----r~~~lk~L~~~gl~I~~I~D~T 132 (150)
+.+.++|+..|++.+. ...... .+.+.+.+.+.|++|.++.=.+
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 4677889999888883 222222 4566677788899887766433
No 103
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.29 E-value=5.1e+02 Score=21.60 Aligned_cols=62 Identities=19% Similarity=0.276 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChH---HHHH-----------HHHhCCCeEEEEEeccCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQ---SALR-----------ALARSGMKIGRIEDVTPIP 135 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~---~~lk-----------~L~~~gl~I~~I~D~Tpip 135 (150)
..++......+.+-|.++|++.|.|+.=-+ ..|..-.+ ..+. .+...|++|.-|-|...+|
T Consensus 48 h~~G~~~l~~~l~~c~~~GI~~vTvYaFS~-----eN~~R~~~Ev~~Lm~l~~~~l~~~~~~~~~~~iri~viG~~~~Lp 122 (251)
T PRK14830 48 HKAGMDTVKKITKAASELGVKVLTLYAFST-----ENWKRPKDEVKFLMNLPVEFLDKFVPELIENNVKVNVIGDTDRLP 122 (251)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEEEeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcChhhCC
Confidence 444555668889999999999999987322 44544332 2221 1234689999999999888
Q ss_pred C
Q 031952 136 T 136 (150)
Q Consensus 136 h 136 (150)
-
T Consensus 123 ~ 123 (251)
T PRK14830 123 E 123 (251)
T ss_pred H
Confidence 3
No 104
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.27 E-value=4.2e+02 Score=22.16 Aligned_cols=62 Identities=21% Similarity=0.244 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHH---HHH-----------HHHhCCCeEEEEEeccCCC
Q 031952 70 PYAAMLAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQS---ALR-----------ALARSGMKIGRIEDVTPIP 135 (150)
Q Consensus 70 ~~Aa~~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~---~lk-----------~L~~~gl~I~~I~D~Tpip 135 (150)
..+...+...+.+.|.++|++.|.|+.= ....|..-.+- .+. -+...|++|.-|-|.+++|
T Consensus 40 H~~G~~~~~~iv~~c~~~gI~~lTvYaF-----S~eN~~R~~~EV~~Lm~l~~~~l~~~~~~~~~~~irv~viG~~~~Lp 114 (253)
T PRK14836 40 HRAGVRAVRRTIEFCLEKGIEMLTLFAF-----SSENWLRPADEVSALMELFLKALDREVDKLHRNGIRVRFIGDRSRLS 114 (253)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEehhHh-----hhhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEeccccCC
Confidence 3444556678888999999999998862 12444433331 111 1234689999999999988
Q ss_pred C
Q 031952 136 T 136 (150)
Q Consensus 136 h 136 (150)
-
T Consensus 115 ~ 115 (253)
T PRK14836 115 P 115 (253)
T ss_pred H
Confidence 4
No 105
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.21 E-value=1.2e+02 Score=23.27 Aligned_cols=54 Identities=24% Similarity=0.376 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEeeCCCcccCCCCChHH------HHHHHHhCCCeEEEEEeccCCCC
Q 031952 75 LAAQDVSQRCKELGITALHIKLRATGGNKTKTPGPGAQS------ALRALARSGMKIGRIEDVTPIPT 136 (150)
Q Consensus 75 ~aa~~i~~~~~~~gi~~v~V~~~~~~g~~~kG~G~gr~~------~lk~L~~~gl~I~~I~D~Tpiph 136 (150)
....++.+.+.+.|++.+-|.+ ||-|.-|.. .++-+...|..-..|...+.||.
T Consensus 64 k~skkvlkaleq~gI~vIPvk~--------KgrGrprkyd~~t~~~i~emlr~gk~preIsk~lGIpi 123 (139)
T COG1710 64 KVSKKVLKALEQMGIKVIPVKL--------KGRGRPRKYDRNTLLRIREMLRNGKTPREISKDLGIPI 123 (139)
T ss_pred HHHHHHHHHHHhCCceEeeeee--------cCCCCCcccchhHHHHHHHHHHcCCCHHHHHHhhCCch
Confidence 5667888888999999999999 775554433 45555667776666666666664
No 106
>PRK07729 glyceraldehyde-3-phosphate dehydrogenase; Validated
Probab=20.18 E-value=1.2e+02 Score=26.59 Aligned_cols=30 Identities=20% Similarity=0.180 Sum_probs=21.4
Q ss_pred cCCCCChHHHHHHH-HhCCCeEEEEEeccCC
Q 031952 105 KTPGPGAQSALRAL-ARSGMKIGRIEDVTPI 134 (150)
Q Consensus 105 kG~G~gr~~~lk~L-~~~gl~I~~I~D~Tpi 134 (150)
+|||.-=..++|++ ....++|+-|-|.+.+
T Consensus 8 NGfGRIGR~~~r~~~~~~~~~vvaINd~~~~ 38 (343)
T PRK07729 8 NGFGRIGRMVFRKAIKESAFEIVAINASYPS 38 (343)
T ss_pred ECcChHHHHHHHHHhhcCCcEEEEecCCCCH
Confidence 89997334556664 4567999999997653
No 107
>PF06300 Tsp45I: Tsp45I type II restriction enzyme; InterPro: IPR010443 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases such as Tsp45I, which recognises the DNA sequence 5' GTSAC, cleaving prior to G-1 [].
Probab=20.07 E-value=26 Score=29.63 Aligned_cols=19 Identities=42% Similarity=0.761 Sum_probs=16.8
Q ss_pred CCCCCccceeeecCCcccC
Q 031952 4 RKTREPKEENVTLGPAVRD 22 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~ 22 (150)
+++-||||-|+||||-|+.
T Consensus 107 ek~t~PkEtNRQIGPlFk~ 125 (261)
T PF06300_consen 107 EKCTEPKETNRQIGPLFKN 125 (261)
T ss_pred HHcCCCchhcchhhHHHHH
Confidence 5778999999999999874
Done!