Query 039298
Match_columns 197
No_of_seqs 158 out of 799
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 08:22:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039298hhsearch_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 7.5E-55 1.6E-59 354.9 18.2 144 38-195 5-149 (149)
2 PRK09607 rps11p 30S ribosomal 100.0 8.1E-51 1.8E-55 325.8 17.2 127 57-197 6-132 (132)
3 KOG0407 40S ribosomal protein 100.0 6.8E-48 1.5E-52 303.0 15.1 138 46-197 2-139 (139)
4 COG0100 RpsK Ribosomal protein 100.0 2.4E-47 5.3E-52 304.4 15.0 118 54-194 12-129 (129)
5 PRK05309 30S ribosomal protein 100.0 4.3E-45 9.2E-50 290.9 15.8 115 57-194 14-128 (128)
6 TIGR03628 arch_S11P archaeal r 100.0 9.3E-45 2E-49 284.6 15.7 113 60-186 2-114 (114)
7 PF00411 Ribosomal_S11: Riboso 100.0 8.7E-45 1.9E-49 281.4 13.3 110 61-193 1-110 (110)
8 TIGR03632 bact_S11 30S ribosom 100.0 5.1E-44 1.1E-48 276.9 14.8 108 61-191 1-108 (108)
9 CHL00041 rps11 ribosomal prote 100.0 1.2E-40 2.6E-45 261.2 15.3 108 56-186 9-116 (116)
10 KOG0408 Mitochondrial/chloropl 100.0 2.2E-37 4.8E-42 256.4 14.1 161 8-193 3-189 (190)
11 PTZ00090 40S ribosomal protein 100.0 7.9E-37 1.7E-41 261.8 14.6 109 62-194 120-233 (233)
12 cd00432 Ribosomal_L18_L5e Ribo 97.4 0.0036 7.8E-08 47.6 10.8 89 60-156 11-103 (103)
13 PF00861 Ribosomal_L18p: Ribos 97.0 0.016 3.4E-07 45.7 10.8 91 60-158 23-119 (119)
14 PRK05593 rplR 50S ribosomal pr 96.8 0.019 4.2E-07 45.5 10.5 93 57-157 21-116 (117)
15 TIGR00060 L18_bact ribosomal p 96.5 0.049 1.1E-06 43.2 10.8 87 60-157 24-113 (114)
16 CHL00139 rpl18 ribosomal prote 96.4 0.078 1.7E-06 41.6 10.8 91 60-157 15-108 (109)
17 PRK08569 rpl18p 50S ribosomal 96.0 0.16 3.4E-06 43.8 11.7 94 61-158 33-130 (193)
18 COG0256 RplR Ribosomal protein 95.1 0.4 8.6E-06 38.7 10.6 94 57-158 26-125 (125)
19 PTZ00032 60S ribosomal protein 90.2 1.7 3.8E-05 37.9 8.0 67 61-127 106-186 (211)
20 cd05313 NAD_bind_2_Glu_DH NAD( 63.1 17 0.00037 32.3 5.4 58 95-161 10-67 (254)
21 PLN02477 glutamate dehydrogena 56.3 31 0.00068 32.7 6.1 57 96-161 179-235 (410)
22 cd01076 NAD_bind_1_Glu_DH NAD( 54.0 35 0.00075 29.4 5.6 56 97-161 5-60 (227)
23 COG3981 Predicted acetyltransf 49.9 90 0.002 26.7 7.3 64 52-129 73-138 (174)
24 TIGR03694 exosort_acyl putativ 47.8 65 0.0014 27.9 6.4 46 102-161 153-198 (241)
25 PTZ00079 NADP-specific glutama 46.5 54 0.0012 31.8 6.1 57 96-161 210-266 (454)
26 PF13420 Acetyltransf_4: Acety 45.4 1.2E+02 0.0026 22.8 6.9 46 105-161 93-139 (155)
27 COG2099 CobK Precorrin-6x redu 42.5 34 0.00074 30.9 3.9 27 101-128 74-100 (257)
28 PF00583 Acetyltransf_1: Acety 42.5 1E+02 0.0022 20.5 5.8 41 106-157 43-83 (83)
29 PRK14030 glutamate dehydrogena 42.0 65 0.0014 31.1 5.9 65 97-170 202-274 (445)
30 PRK09414 glutamate dehydrogena 38.2 71 0.0015 30.7 5.5 57 96-161 205-261 (445)
31 PF05677 DUF818: Chlamydia CHL 37.1 2.3E+02 0.005 26.9 8.5 71 80-161 171-249 (365)
32 PRK14031 glutamate dehydrogena 35.4 96 0.0021 29.9 5.9 59 96-163 201-259 (444)
33 PTZ00069 60S ribosomal protein 34.6 3E+02 0.0064 25.5 8.6 58 61-120 49-112 (300)
34 COG1710 Uncharacterized protei 34.1 51 0.0011 27.0 3.3 59 108-174 64-129 (139)
35 PF00208 ELFV_dehydrog: Glutam 33.9 34 0.00074 29.9 2.5 70 97-174 5-82 (244)
36 KOG0747 Putative NAD+-dependen 33.5 1.1E+02 0.0024 28.6 5.8 72 100-178 153-229 (331)
37 PF13302 Acetyltransf_3: Acety 32.3 1.5E+02 0.0032 21.6 5.4 45 101-157 97-142 (142)
38 PRK13883 conjugal transfer pro 30.4 2.5E+02 0.0055 23.3 6.9 54 100-161 27-83 (151)
39 TIGR02382 wecD_rffC TDP-D-fuco 29.5 1.8E+02 0.0038 23.5 5.8 47 103-161 139-185 (191)
40 PRK13260 2,3-diketo-L-gulonate 29.1 4.6E+02 0.01 24.1 9.5 69 100-188 84-152 (332)
41 cd01469 vWA_integrins_alpha_su 28.9 1.5E+02 0.0032 23.8 5.3 100 57-162 38-139 (177)
42 COG0334 GdhA Glutamate dehydro 28.9 1.2E+02 0.0026 29.1 5.4 57 96-161 180-236 (411)
43 cd05211 NAD_bind_Glu_Leu_Phe_V 28.6 1.2E+02 0.0025 26.0 4.8 49 104-161 4-52 (217)
44 PRK10809 ribosomal-protein-S5- 27.5 2.6E+02 0.0056 22.2 6.5 47 103-161 119-166 (194)
45 cd05801 PGM_like3 This bacteri 26.6 3.9E+02 0.0086 25.6 8.5 57 100-161 36-93 (522)
46 TIGR00829 FRU PTS system, fruc 26.3 1.2E+02 0.0026 22.4 3.9 27 105-132 12-38 (85)
47 PRK07564 phosphoglucomutase; V 24.5 3.1E+02 0.0067 26.5 7.4 57 100-161 53-110 (543)
48 COG0027 PurT Formate-dependent 24.1 3E+02 0.0066 26.2 6.9 70 58-129 193-271 (394)
49 PRK10975 TDP-fucosamine acetyl 24.0 3.8E+02 0.0082 21.4 7.0 46 104-161 143-188 (194)
50 PF05673 DUF815: Protein of un 23.9 2.2E+02 0.0047 25.6 5.8 44 120-170 48-95 (249)
51 PRK10151 ribosomal-protein-L7/ 23.8 3.5E+02 0.0077 21.0 7.1 49 101-161 106-155 (179)
52 PRK00394 transcription factor; 23.5 2.3E+02 0.0051 23.7 5.7 49 72-124 38-86 (179)
53 TIGR03234 OH-pyruv-isom hydrox 23.5 2.4E+02 0.0051 23.6 5.8 42 111-161 17-58 (254)
54 COG4130 Predicted sugar epimer 23.4 2.4E+02 0.0051 25.6 5.8 48 111-161 20-68 (272)
55 cd04518 TBP_archaea archaeal T 22.5 2.1E+02 0.0045 24.0 5.2 50 71-124 38-87 (174)
56 PRK06920 dnaE DNA polymerase I 22.4 60 0.0013 34.7 2.3 45 107-184 323-367 (1107)
57 TIGR01575 rimI ribosomal-prote 21.8 3E+02 0.0065 19.4 6.3 46 104-161 71-116 (131)
58 PRK09491 rimI ribosomal-protei 21.6 3.5E+02 0.0076 20.2 7.7 49 101-161 77-125 (146)
59 PRK05673 dnaE DNA polymerase I 20.5 67 0.0015 34.4 2.2 45 107-184 338-382 (1135)
60 cd07996 WGR_MMR_like WGR domai 20.4 3E+02 0.0065 19.0 5.2 45 78-123 24-72 (74)
61 PRK07135 dnaE DNA polymerase I 20.1 68 0.0015 33.9 2.1 46 106-184 271-316 (973)
62 COG3916 LasI N-acyl-L-homoseri 20.0 4E+02 0.0087 23.4 6.5 46 101-161 118-163 (209)
No 1
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=100.00 E-value=7.5e-55 Score=354.88 Aligned_cols=144 Identities=85% Similarity=1.258 Sum_probs=136.9
Q ss_pred cccCccc-cccccCCcccCCceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHH
Q 039298 38 KNREPKE-ENVTLGPAVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTR 116 (197)
Q Consensus 38 k~k~~k~-e~islg~~~~e~~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k 116 (197)
+.|..|+ .+++++|++.++++.+||+||++|||||||||||++|++++|+|+|++|||++++|+||||||.||++++++
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~Gi~hI~as~NNTiItiTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k 84 (149)
T PTZ00129 5 ATKMSKKQEVATLGPNVAKGELVFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAAR 84 (149)
T ss_pred cccCCcceeeeecCCcccCCceeEEEEEEEcccCCeEEEEEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHHH
Confidence 3344444 377889988899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCCCCCCCCCCC
Q 039298 117 CKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRRGR 195 (197)
Q Consensus 117 ~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGcR~kK~RR~~ 195 (197)
|+++||+.|+|+|||+|||+++||||||++|||+|+++||+|.+| +|+||||||||||||+||+|
T Consensus 85 ~~~~Gi~~v~V~vr~~gg~~~kg~GpGr~~airaL~~~glkI~~I--------------~DvTPiPhNGcRppk~RR~r 149 (149)
T PTZ00129 85 CKELGINALHIKLRATGGVRTKTPGPGAQAALRALARAGLKIGRI--------------EDVTPIPTDSTRRKGGRRGR 149 (149)
T ss_pred HHHcCCeEEEEEEEecCCCCCCCCCCCHHHHHHHHHHCCCEEEEE--------------EecCCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999999999999999999999999 99999999999999999987
No 2
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=100.00 E-value=8.1e-51 Score=325.81 Aligned_cols=127 Identities=65% Similarity=1.061 Sum_probs=119.6
Q ss_pred ceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCC
Q 039298 57 EHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNK 136 (197)
Q Consensus 57 ~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~ 136 (197)
+.+.||+||++|||||||||||++|+++++|+|||+.+++++||+||||||.|||+++++|+++||+.|+|+|+|+|||+
T Consensus 6 ~~~~gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~ 85 (132)
T PRK09607 6 KEKWGIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNG 85 (132)
T ss_pred CceeeEEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCC
Confidence 45799999999999999999999998666677777676777779999999999999999999999999999999999999
Q ss_pred ccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCCCCCCCCCCCCC
Q 039298 137 TKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRRGRRL 197 (197)
Q Consensus 137 ~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGcR~kK~RR~~~~ 197 (197)
++-||+||++|||+|+++||+|.+| +|+||||||||||||+||+|||
T Consensus 86 ~~~~G~Gr~~airal~~~glkI~~I--------------~DvTpiPhNGCRp~K~RR~r~~ 132 (132)
T PRK09607 86 QKSPGPGAQAAIRALARAGLRIGRI--------------EDVTPIPHDGTRPPGGRRGRRV 132 (132)
T ss_pred CcCCCCcHHHHHHHHHHCCCEEEEE--------------EEcCCCCCCCCCCCCCCCCCCC
Confidence 9999999999999999999999999 9999999999999999999996
No 3
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.8e-48 Score=303.05 Aligned_cols=138 Identities=89% Similarity=1.350 Sum_probs=136.0
Q ss_pred ccccCCcccCCceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEE
Q 039298 46 NVTLGPAVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITAL 125 (197)
Q Consensus 46 ~islg~~~~e~~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l 125 (197)
+..||||+.|++.++|++||++|||+||||+||++|++++...+|||.+|.+|++++|||||+|||+++.+|+++||+.+
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 EEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCCCCCCCCCCCCC
Q 039298 126 HIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRRGRRL 197 (197)
Q Consensus 126 ~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGcR~kK~RR~~~~ 197 (197)
||++||+||+++|.||||.|+|||+|+++||+|++| +||||||.+.+|+|.+||+||+
T Consensus 82 h~klratgg~ktktpgpgaqsalralar~gmrigri--------------edvtpip~d~trrkggrrgrrl 139 (139)
T KOG0407|consen 82 HIKLRATGGTKTKTPGPGAQSALRALARSGMRIGRI--------------EDVTPIPSDSTRRKGGRRGRRL 139 (139)
T ss_pred EEEEEecCCcccCCCCccHHHHHHHHHHhcceeeee--------------cccccCCccchhhccCcccccC
Confidence 999999999999999999999999999999999999 9999999999999999999996
No 4
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-47 Score=304.39 Aligned_cols=118 Identities=49% Similarity=0.769 Sum_probs=113.9
Q ss_pred cCCceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeC
Q 039298 54 RDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATG 133 (197)
Q Consensus 54 ~e~~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~g 133 (197)
.++.+..|++||++||||||||+||++||+++|.|+|++|||+++ ++||||||+||+++++.++|+||+.|||+|
T Consensus 12 ~~~~i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~r-k~tpyAA~~aa~~aa~~a~e~Gi~~v~v~v---- 86 (129)
T COG0100 12 VKKNIADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSR-KSTPYAAQLAAEDAAKKAKEHGIKSVEVKV---- 86 (129)
T ss_pred eccccccceEEEEcccCCcEEEecCCCCCEEEEEecCCceEcCCC-CCCHHHHHHHHHHHHHHHHHhCccEEEEEE----
Confidence 334578899999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred CCCccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCCCCCCCCCC
Q 039298 134 GNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRRG 194 (197)
Q Consensus 134 g~~~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGcR~kK~RR~ 194 (197)
+|||||||+|+|+|+++|++|.+| +|+||||||||||||+||+
T Consensus 87 ----kgpG~GreaAiraL~~ag~~i~~I--------------~DvTPiphnG~Rppk~RR~ 129 (129)
T COG0100 87 ----KGPGPGREAAIRALAAAGLKITRI--------------EDVTPIPHNGCRPPKRRRV 129 (129)
T ss_pred ----ECCCCcHHHHHHHHHHccceEEEE--------------EEcCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999 9999999999999999985
No 5
>PRK05309 30S ribosomal protein S11; Validated
Probab=100.00 E-value=4.3e-45 Score=290.90 Aligned_cols=115 Identities=41% Similarity=0.665 Sum_probs=111.6
Q ss_pred ceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCC
Q 039298 57 EHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNK 136 (197)
Q Consensus 57 ~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~ 136 (197)
.+..||+||++|+|||||||||++|+++.|.|+|.+|||+.+ |+||||||+||++++++|+++||+.|+|++
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 477899999999999999999999999999999999999887 899999999999999999999999999999
Q ss_pred ccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCCCCCCCCCC
Q 039298 137 TKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRRG 194 (197)
Q Consensus 137 ~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGcR~kK~RR~ 194 (197)
+|+|+||+++|++|+++|++|.+| +|+||+|||||||||+||.
T Consensus 86 -kG~G~Gr~~air~L~~~glkI~~I--------------~D~TpiphNGcR~~K~RRv 128 (128)
T PRK05309 86 -KGPGSGRESAIRALQAAGLEVTSI--------------KDVTPIPHNGCRPPKRRRV 128 (128)
T ss_pred -ECCCCcHHHHHHHHHHCCCEEEEE--------------EEcCCCCCCCcCcCCCCCC
Confidence 999999999999999999999999 9999999999999999984
No 6
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=100.00 E-value=9.3e-45 Score=284.59 Aligned_cols=113 Identities=66% Similarity=1.067 Sum_probs=107.3
Q ss_pred eeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccC
Q 039298 60 FGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKT 139 (197)
Q Consensus 60 ~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG 139 (197)
+||+||++|||||||||||.+|+++++|+|+|+.+++++||+||||||.|||+++++|+++||+.|+|+|+|+|||++|.
T Consensus 2 ~gi~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~~ 81 (114)
T TIGR03628 2 WGIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKS 81 (114)
T ss_pred cEEEEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCCC
Confidence 79999999999999999999998766777777666667779999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCC
Q 039298 140 PGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDST 186 (197)
Q Consensus 140 ~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGc 186 (197)
|||||++|||+|+++||+|.+| +|+||+|||||
T Consensus 82 ~G~Gr~~air~l~~~glkI~~I--------------~DvTpiPhNGC 114 (114)
T TIGR03628 82 PGPGAQAAIRALARAGLRIGRI--------------EDVTPIPHDGT 114 (114)
T ss_pred CCCcHHHHHHHHHHCCCEEEEE--------------EEcCCCCCCCC
Confidence 9999999999999999999999 99999999999
No 7
>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=8.7e-45 Score=281.38 Aligned_cols=110 Identities=45% Similarity=0.741 Sum_probs=104.6
Q ss_pred eEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCC
Q 039298 61 GVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTP 140 (197)
Q Consensus 61 gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~ 140 (197)
||+||++|+|||||||||++|+++.|+|+|++|||+++ |+||||||++|++++++|+++||+.|+|+| +|+
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 79999999999999999999999999999999999999 999999999999999999999999999999 999
Q ss_pred CCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCCCCCCCCC
Q 039298 141 GPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRR 193 (197)
Q Consensus 141 G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGcR~kK~RR 193 (197)
|+||++++|+|+++|++|.+| +|+||+|||||||||+||
T Consensus 72 g~gr~~~lk~l~~~gl~I~~I--------------~D~T~iphnGcR~kK~RR 110 (110)
T PF00411_consen 72 GPGREAALKALKKSGLKIVSI--------------TDVTPIPHNGCRPKKKRR 110 (110)
T ss_dssp STTHHHHHHHHHHTTSEEEEE--------------EEETT--SSSS--TTTTT
T ss_pred CccHHHHHHHHHhcCCEEEEE--------------EeecCCCCCCCCCCCCCC
Confidence 999999999999999999999 999999999999999998
No 8
>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=5.1e-44 Score=276.91 Aligned_cols=108 Identities=41% Similarity=0.699 Sum_probs=105.6
Q ss_pred eEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCC
Q 039298 61 GVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTP 140 (197)
Q Consensus 61 gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~ 140 (197)
|++||++|+||||||+||++|+++.|.|+|.+|||+.+ |+||||||+||++++++++++||+.|+|++ +|+
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 68999999999999999999999999999999999998 899999999999999999999999999999 999
Q ss_pred CCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCCCCCCC
Q 039298 141 GPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGG 191 (197)
Q Consensus 141 G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGcR~kK~ 191 (197)
|+||+++||+|+++|++|.+| +|+||+|||||||||+
T Consensus 72 G~gr~~~ir~l~~~glkI~~I--------------~D~T~iphNGcR~~K~ 108 (108)
T TIGR03632 72 GAGRESAIRALQAAGLEVTSI--------------KDVTPIPHNGCRPPKR 108 (108)
T ss_pred CCcHHHHHHHHHHCCCEEEEE--------------EEcCCCCCCCcCCCCC
Confidence 999999999999999999999 9999999999999984
No 9
>CHL00041 rps11 ribosomal protein S11
Probab=100.00 E-value=1.2e-40 Score=261.23 Aligned_cols=108 Identities=38% Similarity=0.596 Sum_probs=105.3
Q ss_pred CceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCC
Q 039298 56 GEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGN 135 (197)
Q Consensus 56 ~~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~ 135 (197)
+++..|++||++|+|||||||||++|+++.|.|+|.+|||+.+ |+||||||+||++++++|+++||+.|+|++
T Consensus 9 ~~~~~gi~hI~~t~NNTiiTlTd~~G~~l~~~S~G~~gfKg~r-K~T~~Aa~~~a~~~~~~~~~~gi~~v~I~i------ 81 (116)
T CHL00041 9 RKIPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGAR-KGTPFAAQTAAENAIRTVIDQGMKRAEVMI------ 81 (116)
T ss_pred ccceeEEEEEEcccCCEEEEEEcCCCCEEEEEecCceeeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEE------
Confidence 4578999999999999999999999999999999999999998 899999999999999999999999999999
Q ss_pred CccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCC
Q 039298 136 KTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDST 186 (197)
Q Consensus 136 ~~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGc 186 (197)
+|+|+||+++||+|+++|++|.+| +|+||+|||||
T Consensus 82 --kG~G~Gr~~~ir~l~~~glkI~~I--------------~D~TpiphNGC 116 (116)
T CHL00041 82 --KGPGLGRDTALRAIRRSGLKLSSI--------------RDVTPMPHNGC 116 (116)
T ss_pred --ECCCCcHHHHHHHHHHCCCEEEEE--------------EEcCCCCCCCC
Confidence 999999999999999999999999 99999999999
No 10
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-37 Score=256.37 Aligned_cols=161 Identities=30% Similarity=0.461 Sum_probs=138.9
Q ss_pred hhhHhHhhhhccCCCcccCCcccccccccccccCccc---------c-----cc--ccC--C------cccCC--ceeee
Q 039298 8 LFRVFTFSFRLGTNPSLLNPSRVFAGMSRRKNREPKE---------E-----NV--TLG--P------AVRDG--EHVFG 61 (197)
Q Consensus 8 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~rk~k~~k~---------e-----~i--slg--~------~~~e~--~~~~g 61 (197)
+-++|....|.-+.|. +.++|++...++++...++ | .| .+. | +..++ ...+.
T Consensus 3 lr~~~s~~lRs~t~pa--q~~Rih~s~~ir~a~rq~~~~a~~q~~~egt~g~~i~t~I~r~p~aet~~r~~~g~~f~eiP 80 (190)
T KOG0408|consen 3 LRRLVSDLLRSCTQPA--QQNRIHASISIRDAHRQGTRIATGQVETEGTTGAGIATPINRRPGAETNTRSFSGKNFREIP 80 (190)
T ss_pred HHHHHHHHHHHhcchh--hhCceecccchhhHHHhhhhhhccceeecCCcccccccccccCCChhhhhcccCCccccccc
Confidence 4578888899999998 7778998888876654422 1 01 111 1 11122 24567
Q ss_pred EEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCC
Q 039298 62 VAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPG 141 (197)
Q Consensus 62 i~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G 141 (197)
|+||.+|+|||||||||.+|.++.|.|||.+|||+.| |+|++|||.||..++++++++|+..++|++ ||+|
T Consensus 81 i~hIraS~NNTivtVtd~kg~vi~~~ScgteGFrntr-kgT~iAaQtaavaa~~r~v~~G~~~vrV~V--------kGlG 151 (190)
T KOG0408|consen 81 IIHIRASFNNTIVTVTDVKGEVISWSSCGTEGFRNTR-KGTPIAAQTAAVAAIRRAVDQGMQTVRVRV--------KGLG 151 (190)
T ss_pred eEEEEecCCCeEEEEEccCCcEEEEeecccccccccc-cCCchhHHHHHHHHHHHHHHhcceEEEEEE--------ecCC
Confidence 9999999999999999999999999999999999999 899999999999999999999999999999 9999
Q ss_pred CChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCCCCCCCCCCC
Q 039298 142 PGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRR 193 (197)
Q Consensus 142 ~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhnGcR~kK~RR 193 (197)
|||.+|+++|.++|+.+.+| +|+||+|||||||+|.||
T Consensus 152 pGRmsa~kgl~m~Gl~vvsI--------------tD~Tp~~~ng~RPrK~Rr 189 (190)
T KOG0408|consen 152 PGRMSALKGLRMGGLLVVSI--------------TDNTPMPHNGCRPRKKRR 189 (190)
T ss_pred ccHHHHHhhhhhcceEEEEe--------------ecCCcCCCCCCCcccccc
Confidence 99999999999999999999 999999999999999998
No 11
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=7.9e-37 Score=261.82 Aligned_cols=109 Identities=20% Similarity=0.346 Sum_probs=103.3
Q ss_pred EEEEEccCCCeEEEEEcCCCCe--EEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccC
Q 039298 62 VAHIFASFNDTFIHVTDLSGRE--TLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKT 139 (197)
Q Consensus 62 i~hI~ss~NNTiitlTD~~G~~--~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG 139 (197)
.+-|++|+|||||||||..||+ +.|+|+|.+|||+.+ |+||||||.||++++++|+++||+.|+|+| +|
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 3458999999999999999995 999999999999988 999999999999999999999999999999 99
Q ss_pred CCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCC---CCCCCCCCCCC
Q 039298 140 PGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPT---DSTRRKGGRRG 194 (197)
Q Consensus 140 ~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPh---nGcR~kK~RR~ 194 (197)
+| |||+|||+|+.+|++|..| .|+||+|| |||||||+||+
T Consensus 191 pG-gREtALRaL~~~GLkIt~I--------------~DvTpiPHNG~NGCRPpKKRRV 233 (233)
T PTZ00090 191 IM-RVETVLQAFYANGLQVTQI--------------IHEPRLPKCGLNAVKPRKRRRV 233 (233)
T ss_pred CC-hHHHHHHHHHHCCCEEEEE--------------EECCCCCcCCCCCCCCCCCCCC
Confidence 99 6999999999999999999 99999999 55999999884
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=97.38 E-value=0.0036 Score=47.63 Aligned_cols=89 Identities=16% Similarity=0.128 Sum_probs=65.6
Q ss_pred eeEEEEEccCCCeEEEEEcCC-CCeEEEEeeccCcccCC-CCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCc
Q 039298 60 FGVAHIFASFNDTFIHVTDLS-GRETLVRITGGMKVKAD-RDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKT 137 (197)
Q Consensus 60 ~gi~hI~ss~NNTiitlTD~~-G~~~~~~SsG~~g~k~~-rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~ 137 (197)
...+.|+.|.+|....|.|.. +.++.+.|+-...+++. .....-.||+.+++.++++|++.|+..+.+-.
T Consensus 11 ~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D~-------- 82 (103)
T cd00432 11 RPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDR-------- 82 (103)
T ss_pred CCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeC--------
Confidence 456788899999999999998 66776667666666543 22566788999999999999999999877765
Q ss_pred cCCC-CCh-HHHHHHHHhCCc
Q 039298 138 KTPG-PGA-QSALRALARSGM 156 (197)
Q Consensus 138 KG~G-~Gr-~~alraL~~~Gl 156 (197)
.|.- -|| .+++.++...|+
T Consensus 83 ~~~~~~grv~a~~~~~r~~Gl 103 (103)
T cd00432 83 GGYRYHGRVKALAKGAREGGL 103 (103)
T ss_pred CCcccccHHHHHHHHHHHcCC
Confidence 3332 234 346667766664
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=96.95 E-value=0.016 Score=45.65 Aligned_cols=91 Identities=16% Similarity=0.111 Sum_probs=66.9
Q ss_pred eeEEEEEccCCCeEEEEEcCC-CCeEEEEeeccCcccCC---CCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCC
Q 039298 60 FGVAHIFASFNDTFIHVTDLS-GRETLVRITGGMKVKAD---RDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGN 135 (197)
Q Consensus 60 ~gi~hI~ss~NNTiitlTD~~-G~~~~~~SsG~~g~k~~---rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~ 135 (197)
...+-|+.|.+++.+.|.|.. +.++...|+-...+++. .....--||+.+++.++++|++.||..+.+-.
T Consensus 23 ~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~lla~ra~~~gi~~v~fdr------ 96 (119)
T PF00861_consen 23 RPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGELLAKRALEKGIAKVVFDR------ 96 (119)
T ss_dssp SEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHHHHHHHHHTTSSEEEECT------
T ss_pred CCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHHHHHHHHHcCCcEEEEcC------
Confidence 456778899999999997776 66666777777667652 21345778999999999999999998777765
Q ss_pred CccCCCCC-h-HHHHHHHHhCCcEE
Q 039298 136 KTKTPGPG-A-QSALRALARSGMKI 158 (197)
Q Consensus 136 ~~KG~G~G-r-~~alraL~~~GlkI 158 (197)
.|+-.+ | .+++.++...|++|
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 444443 3 45778888888875
No 14
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=96.84 E-value=0.019 Score=45.49 Aligned_cols=93 Identities=19% Similarity=0.159 Sum_probs=63.5
Q ss_pred ceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeec-cCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCC
Q 039298 57 EHVFGVAHIFASFNDTFIHVTDLSGRETLVRITG-GMKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGN 135 (197)
Q Consensus 57 ~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG-~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~ 135 (197)
......+.|+-|.+++.+.|.|..+..++...+. ...++.+-+...--||+.+++.++++|++.||+.+..--
T Consensus 21 ~~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~~~~n~~aa~~vG~~la~ra~~~gi~~vvfDr------ 94 (117)
T PRK05593 21 TAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGLKGGNKEAAKKVGKLIAERAKAKGIKQVVFDR------ 94 (117)
T ss_pred CCCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhccccCCCHHHHHHHHHHHHHHHHHCCCCEEEEcC------
Confidence 3345678899999999999998888866554443 333433322456778999999999999999999854432
Q ss_pred CccCCCC-Ch-HHHHHHHHhCCcE
Q 039298 136 KTKTPGP-GA-QSALRALARSGMK 157 (197)
Q Consensus 136 ~~KG~G~-Gr-~~alraL~~~Glk 157 (197)
.|+=+ || .+++.++..+||+
T Consensus 95 --g~~~yhGrV~a~a~~are~Gl~ 116 (117)
T PRK05593 95 --GGYKYHGRVKALADAAREAGLK 116 (117)
T ss_pred --CCCcccHHHHHHHHHHHHhCCC
Confidence 22222 23 3456677677775
No 15
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=96.55 E-value=0.049 Score=43.18 Aligned_cols=87 Identities=23% Similarity=0.163 Sum_probs=61.5
Q ss_pred eeEEEEEccCCCeEEEEEcCCCCeEEEEeecc-CcccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCcc
Q 039298 60 FGVAHIFASFNDTFIHVTDLSGRETLVRITGG-MKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTK 138 (197)
Q Consensus 60 ~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~-~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~K 138 (197)
...+.|+-|.+++.+.|.|..+..+++.++.. ..++ ....--||..+++.++++|++.||+.+..-- .
T Consensus 24 rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~---~~~n~~aA~~vG~~la~ra~~~gi~~vvfDr--------g 92 (114)
T TIGR00060 24 RPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK---YTGNKDAAKKVGKLVAERLKEKGIKDVVFDR--------G 92 (114)
T ss_pred CcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc---CCCCHHHHHHHHHHHHHHHHHCCCCEEEEeC--------C
Confidence 55788899999999999988877666555533 3343 2456778999999999999999999875443 2
Q ss_pred CCCC-Ch-HHHHHHHHhCCcE
Q 039298 139 TPGP-GA-QSALRALARSGMK 157 (197)
Q Consensus 139 G~G~-Gr-~~alraL~~~Glk 157 (197)
|+=. || +++..++...||+
T Consensus 93 g~~YhGrv~A~a~~aRe~Gl~ 113 (114)
T TIGR00060 93 GYKYHGRVAALAEAAREAGLN 113 (114)
T ss_pred CCcchHHHHHHHHHHHHhCCC
Confidence 3322 34 3355666667765
No 16
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=96.35 E-value=0.078 Score=41.59 Aligned_cols=91 Identities=21% Similarity=0.266 Sum_probs=61.0
Q ss_pred eeEEEEEccCCCeEEEEEc-CCCCeEEEEeeccCcccCC-CCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCc
Q 039298 60 FGVAHIFASFNDTFIHVTD-LSGRETLVRITGGMKVKAD-RDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKT 137 (197)
Q Consensus 60 ~gi~hI~ss~NNTiitlTD-~~G~~~~~~SsG~~g~k~~-rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~ 137 (197)
...+.|+-|.+++.+.|.| .+|+++.+.|+-...+++. .....--||+.+++.++++|++.||+.+..-- ||.+
T Consensus 15 rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~~vvfDr---gg~~- 90 (109)
T CHL00139 15 RPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKVVFDR---GGKL- 90 (109)
T ss_pred CCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEcC---CCCc-
Confidence 4467888999999997775 5677776666645444431 12355678899999999999999999765443 2222
Q ss_pred cCCCCCh-HHHHHHHHhCCcE
Q 039298 138 KTPGPGA-QSALRALARSGMK 157 (197)
Q Consensus 138 KG~G~Gr-~~alraL~~~Glk 157 (197)
++ || +++..++..+||+
T Consensus 91 --yh-GrV~a~a~~are~GL~ 108 (109)
T CHL00139 91 --YH-GRIKALAEAAREAGLQ 108 (109)
T ss_pred --cc-hHHHHHHHHHHHhCCC
Confidence 11 23 3466677777775
No 17
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=95.97 E-value=0.16 Score=43.81 Aligned_cols=94 Identities=16% Similarity=0.209 Sum_probs=62.2
Q ss_pred eEEEEEccCCCeEEEEE--cCCCCeEEEEeec-cCcccCC-CCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCC
Q 039298 61 GVAHIFASFNDTFIHVT--DLSGRETLVRITG-GMKVKAD-RDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNK 136 (197)
Q Consensus 61 gi~hI~ss~NNTiitlT--D~~G~~~~~~SsG-~~g~k~~-rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~ 136 (197)
.-+-|+-|.+++++.|. |..|..+++..+. ....++- .....--||++++..++++|++.||+.+.+-. ||.+
T Consensus 33 pRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~~~~N~~AAy~vG~llA~ral~kGi~~vvfDr---Gg~~ 109 (193)
T PRK08569 33 PRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKGDTGNTPAAYLTGLLAGKKALKAGVEEAVLDI---GLHR 109 (193)
T ss_pred CEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEec---CCcc
Confidence 45667889999999999 7777665554443 3333221 11355678899999999999999999866665 3333
Q ss_pred ccCCCCChHHHHHHHHhCCcEE
Q 039298 137 TKTPGPGAQSALRALARSGMKI 158 (197)
Q Consensus 137 ~KG~G~Gr~~alraL~~~GlkI 158 (197)
.. .|--=.+++++...+||+|
T Consensus 110 yh-~gGRV~A~akgArd~GL~f 130 (193)
T PRK08569 110 PT-KGSRVFAALKGAIDAGLEI 130 (193)
T ss_pred cc-CCccHHHHHHHHHHcCCcC
Confidence 21 1111345778888888764
No 18
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=95.12 E-value=0.4 Score=38.74 Aligned_cols=94 Identities=12% Similarity=0.042 Sum_probs=61.9
Q ss_pred ceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeecc-CcccC---CCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEee
Q 039298 57 EHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGG-MKVKA---DRDESSPYAAMLAAQDVSTRCKELGITALHIKLRAT 132 (197)
Q Consensus 57 ~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~-~g~k~---~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~ 132 (197)
......+-|+-|.++.++.+.|.+.+.+....|-- ..+++ ......-.||.++++.+++++++.||+.+.+-.
T Consensus 26 ~~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG~lia~ra~~kgi~~vVfdr--- 102 (125)
T COG0256 26 TSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFDR--- 102 (125)
T ss_pred CCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEcC---
Confidence 33345666778888999999988887666555532 11211 111244678999999999999999999888555
Q ss_pred CCCCccCCCCC-hH-HHHHHHHhCCcEE
Q 039298 133 GGNKTKTPGPG-AQ-SALRALARSGMKI 158 (197)
Q Consensus 133 gg~~~KG~G~G-r~-~alraL~~~GlkI 158 (197)
.|+=.| |- ++.++....||++
T Consensus 103 -----~g~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 103 -----GGYKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred -----CCCCcchHHHHHHHHHHHcCcCC
Confidence 555554 32 3445555667753
No 19
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=90.20 E-value=1.7 Score=37.93 Aligned_cols=67 Identities=10% Similarity=0.016 Sum_probs=48.3
Q ss_pred eEEEEEccCCCeEEEEEcCCC-CeEEEEeeccCcccCC-------------CCCCCHHHHHHHHHHHHHHHHHcCccEEE
Q 039298 61 GVAHIFASFNDTFIHVTDLSG-RETLVRITGGMKVKAD-------------RDESSPYAAMLAAQDVSTRCKELGITALH 126 (197)
Q Consensus 61 gi~hI~ss~NNTiitlTD~~G-~~~~~~SsG~~g~k~~-------------rrkst~~Aa~~aa~~v~~k~~elGi~~l~ 126 (197)
..+-|+-|.++..+.+.|... .++.+.|+=.-.+++. +..++--||..+++.++++|++.||+.|.
T Consensus 106 PRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI~kVv 185 (211)
T PTZ00032 106 PRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGISKVR 185 (211)
T ss_pred ceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCCCEEE
Confidence 467889999999999987754 5555444433334331 12567789999999999999999999654
Q ss_pred E
Q 039298 127 I 127 (197)
Q Consensus 127 V 127 (197)
.
T Consensus 186 F 186 (211)
T PTZ00032 186 F 186 (211)
T ss_pred E
Confidence 3
No 20
>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=63.08 E-value=17 Score=32.32 Aligned_cols=58 Identities=17% Similarity=0.202 Sum_probs=46.1
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 95 KADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 95 k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
-.+|...|-|....+++.+++.. ...++...|.| .|||---..+.+.|...|.+|+-|
T Consensus 10 s~gR~~aTg~Gv~~~~~~~~~~~-~~~l~g~~vaI--------qGfGnVG~~~a~~L~e~GakvvaV 67 (254)
T cd05313 10 SLIRPEATGYGLVYFVEEMLKDR-NETLKGKRVAI--------SGSGNVAQYAAEKLLELGAKVVTL 67 (254)
T ss_pred CCCCCchhHHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEE
Confidence 34566888888888877766655 45677789999 889987778888999999999977
No 21
>PLN02477 glutamate dehydrogenase
Probab=56.27 E-value=31 Score=32.71 Aligned_cols=57 Identities=14% Similarity=0.155 Sum_probs=43.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 96 ADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 96 ~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
.++...|-|....+++.+++.. ...++..+|-| .|||.=-..+.+.|...|.+|+-|
T Consensus 179 ~~r~~aTg~Gv~~~~~~~~~~~-g~~l~g~~VaI--------qGfGnVG~~~A~~L~e~GakVVaV 235 (410)
T PLN02477 179 LGREAATGRGVVFATEALLAEH-GKSIAGQTFVI--------QGFGNVGSWAAQLIHEKGGKIVAV 235 (410)
T ss_pred CCCCccchHHHHHHHHHHHHHc-CCCccCCEEEE--------ECCCHHHHHHHHHHHHcCCEEEEE
Confidence 3566788888888877776652 23466788999 888876666778999999999987
No 22
>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=54.03 E-value=35 Score=29.43 Aligned_cols=56 Identities=18% Similarity=0.317 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 97 DRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 97 ~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
++...|-|....+.+.+++... ..+...+|-| .|+|.=-..+.+.|.+.|.+|+.|
T Consensus 5 ~~~~~Tg~Gv~~~~~~~~~~~~-~~l~~~~v~I--------~G~G~VG~~~a~~L~~~g~~vv~v 60 (227)
T cd01076 5 GREEATGRGVAYATREALKKLG-IGLAGARVAI--------QGFGNVGSHAARFLHEAGAKVVAV 60 (227)
T ss_pred CCCccchHHHHHHHHHHHHhcC-CCccCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEE
Confidence 4557788877777776666543 4577888999 788865556778888899999977
No 23
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=49.93 E-value=90 Score=26.70 Aligned_cols=64 Identities=20% Similarity=0.373 Sum_probs=44.0
Q ss_pred cccCCceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCc--ccCCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEE
Q 039298 52 AVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMK--VKADRDESSPYAAMLAAQDVSTRCKELGITALHIKL 129 (197)
Q Consensus 52 ~~~e~~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g--~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~l 129 (197)
.+.+.....|+++|.-+.|+-+... .|..| ++... +.--||-++. ..+.++|+++||+.|-|..
T Consensus 73 ~v~~d~~ivG~i~lRh~Ln~~ll~~------------gGHIGY~VrPse-R~KGYA~emL-kl~L~~ar~lgi~~Vlvtc 138 (174)
T COG3981 73 AVDEDGQIVGFINLRHQLNDFLLEE------------GGHIGYSVRPSE-RRKGYAKEML-KLALEKARELGIKKVLVTC 138 (174)
T ss_pred EEecCCcEEEEEEeeeecchHHHhc------------CCcccceeChhh-hccCHHHHHH-HHHHHHHHHcCCCeEEEEe
Confidence 3345467789999999887765332 45555 34333 2335766644 5588999999999999999
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=47.80 E-value=65 Score=27.95 Aligned_cols=46 Identities=17% Similarity=0.171 Sum_probs=37.8
Q ss_pred CHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 102 SPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 102 t~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
.++.+......+.+.|.+.||+.+.... --...+.|.+.|+.+.+|
T Consensus 153 ~~~~~~~L~~~~~~~a~~~Gi~~~~~v~--------------~~~l~r~l~r~G~~~~~l 198 (241)
T TIGR03694 153 FPHIPLGLYLGLIALSSANGITHWYAIM--------------EPRLARLLSRFGIQFRQV 198 (241)
T ss_pred CchHHHHHHHHHHHHHHHCCCcEEEEEe--------------CHHHHHHHHHhCCceEEc
Confidence 3666776777788999999999998888 235778899999999998
No 25
>PTZ00079 NADP-specific glutamate dehydrogenase; Provisional
Probab=46.50 E-value=54 Score=31.76 Aligned_cols=57 Identities=19% Similarity=0.221 Sum_probs=45.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 96 ADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 96 ~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
.+|.+.|-|....+++.+.+.. ...++..+|.| .|+|--...+.+-|...|.+|+.+
T Consensus 210 ~~r~eATG~Gv~~~~~~~l~~~-~~~l~Gk~VaV--------qG~GnVg~~aa~~L~e~GakVVav 266 (454)
T PTZ00079 210 NIRPEATGYGLVYFVLEVLKKL-NDSLEGKTVVV--------SGSGNVAQYAVEKLLQLGAKVLTM 266 (454)
T ss_pred CCCCcccHHHHHHHHHHHHHHc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEE
Confidence 4567899999888888776654 44577789999 889987778888888999999977
No 26
>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=45.43 E-value=1.2e+02 Score=22.79 Aligned_cols=46 Identities=15% Similarity=0.201 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHH-HHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 105 AAMLAAQDVSTRC-KELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 105 Aa~~aa~~v~~k~-~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
.+..+.+.+.+.| .++|+..|.+.+. ..-..+++.+++.|+++...
T Consensus 93 ig~~l~~~l~~~af~~~~~~~i~~~v~-----------~~N~~~i~~~~~~GF~~~g~ 139 (155)
T PF13420_consen 93 IGRKLLDELIEYAFKELGIHKIYLEVF-----------SSNEKAINFYKKLGFEEEGE 139 (155)
T ss_dssp HHHHHHHHHHHHH-HHTT-CEEEEEEE-----------TT-HHHHHHHHHTTEEEEEE
T ss_pred HHHHHHHHHHHHhhhccCeEEEEEEEe-----------cCCHHHHHHHHhCCCEEEEE
Confidence 3445666777888 9999999999992 23667999999999998765
No 27
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=42.48 E-value=34 Score=30.88 Aligned_cols=27 Identities=37% Similarity=0.599 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHHHHHHHHHcCccEEEEE
Q 039298 101 SSPYAAMLAAQDVSTRCKELGITALHIK 128 (197)
Q Consensus 101 st~~Aa~~aa~~v~~k~~elGi~~l~V~ 128 (197)
+=||||+ +.+++++.|++.||..+...
T Consensus 74 THPyAa~-iS~Na~~aake~gipy~r~e 100 (257)
T COG2099 74 THPYAAR-ISQNAARAAKETGIPYLRLE 100 (257)
T ss_pred CChHHHH-HHHHHHHHHHHhCCcEEEEE
Confidence 5699999 55779999999999976654
No 28
>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=42.48 E-value=1e+02 Score=20.46 Aligned_cols=41 Identities=17% Similarity=0.285 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcE
Q 039298 106 AMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMK 157 (197)
Q Consensus 106 a~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~Glk 157 (197)
+...-+.+.+.|++.|++.+.+.+ .+....+++-+.+.|++
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 344456678888889999999998 46667788888887764
No 29
>PRK14030 glutamate dehydrogenase; Provisional
Probab=42.02 E-value=65 Score=31.06 Aligned_cols=65 Identities=18% Similarity=0.178 Sum_probs=48.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE--------eccccee
Q 039298 97 DRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI--------DLEGLLI 168 (197)
Q Consensus 97 ~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I--------~~~~~~~ 168 (197)
+|.+.|-|....+++.+++.. ...++..+|.| .|+|-=-..+.+.|...|.+|+-+ +.+|+.+
T Consensus 202 gr~~ATg~Gv~~~~~~~~~~~-g~~l~g~~vaI--------QGfGnVG~~aA~~L~e~GakvVavSD~~G~i~d~~Gld~ 272 (445)
T PRK14030 202 IRPEATGFGALYFVHQMLETK-GIDIKGKTVAI--------SGFGNVAWGAATKATELGAKVVTISGPDGYIYDPDGISG 272 (445)
T ss_pred CCCCccHHHHHHHHHHHHHHc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEEcCCceEECCCCCCH
Confidence 466789998888887776554 23466789999 888876667777888899999984 5566665
Q ss_pred cc
Q 039298 169 LG 170 (197)
Q Consensus 169 ~~ 170 (197)
-.
T Consensus 273 ~~ 274 (445)
T PRK14030 273 EK 274 (445)
T ss_pred HH
Confidence 43
No 30
>PRK09414 glutamate dehydrogenase; Provisional
Probab=38.17 E-value=71 Score=30.73 Aligned_cols=57 Identities=16% Similarity=0.144 Sum_probs=44.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 96 ADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 96 ~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
.++...|-|....+++.+++.. ...++..+|.| -|||-=-..+.+.|...|.+|+-|
T Consensus 205 ~gr~~aTg~Gv~~~~~~~~~~~-~~~l~g~rVaI--------qGfGnVG~~~A~~L~~~GakVVav 261 (445)
T PRK09414 205 LIRTEATGYGLVYFAEEMLKAR-GDSFEGKRVVV--------SGSGNVAIYAIEKAQQLGAKVVTC 261 (445)
T ss_pred CCCCCcccHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEE
Confidence 3566889888888877776654 44577889999 888876667778888999999988
No 31
>PF05677 DUF818: Chlamydia CHLPS protein (DUF818); InterPro: IPR008536 This family of unknown function includes several Chlamydia CHLPS proteins and Legionella SidB proteins.
Probab=37.06 E-value=2.3e+02 Score=26.91 Aligned_cols=71 Identities=17% Similarity=0.130 Sum_probs=49.8
Q ss_pred CCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHH--cCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhC---
Q 039298 80 SGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKE--LGITALHIKLRATGGNKTKTPGPGAQSALRALARS--- 154 (197)
Q Consensus 80 ~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~e--lGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~--- 154 (197)
..|++.+-.. |.|.-+|. .++.+-..+++.+.+..++ .|+++=+|.+ .|...|.-.+-.+|+..
T Consensus 171 ~aNvl~fNYp-GVg~S~G~--~s~~dLv~~~~a~v~yL~d~~~G~ka~~Ii~--------yG~SLGG~Vqa~AL~~~~~~ 239 (365)
T PF05677_consen 171 GANVLVFNYP-GVGSSTGP--PSRKDLVKDYQACVRYLRDEEQGPKAKNIIL--------YGHSLGGGVQAEALKKEVLK 239 (365)
T ss_pred CCcEEEECCC-ccccCCCC--CCHHHHHHHHHHHHHHHHhcccCCChheEEE--------eeccccHHHHHHHHHhcccc
Confidence 4455555444 34555555 5676667778888888875 8999999999 88888876655677664
Q ss_pred ---CcEEEEE
Q 039298 155 ---GMKIGRI 161 (197)
Q Consensus 155 ---GlkI~~I 161 (197)
|++-..|
T Consensus 240 ~~dgi~~~~i 249 (365)
T PF05677_consen 240 GSDGIRWFLI 249 (365)
T ss_pred cCCCeeEEEE
Confidence 5565666
No 32
>PRK14031 glutamate dehydrogenase; Provisional
Probab=35.39 E-value=96 Score=29.90 Aligned_cols=59 Identities=14% Similarity=0.076 Sum_probs=45.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEEec
Q 039298 96 ADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDL 163 (197)
Q Consensus 96 ~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I~~ 163 (197)
.++...|-|....+++.+++.. ...+....|.| .|+|.=...+.+.|...|-+|+-|-|
T Consensus 201 ~~r~~aTg~Gv~~~~~~~~~~~-g~~l~g~rVaV--------QGfGNVG~~aA~~L~e~GAkVVaVSD 259 (444)
T PRK14031 201 LIRPEATGYGNIYFLMEMLKTK-GTDLKGKVCLV--------SGSGNVAQYTAEKVLELGGKVVTMSD 259 (444)
T ss_pred CCCCcccHHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEEC
Confidence 4667889998888877776554 23467788999 88888777788888899999998743
No 33
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=34.63 E-value=3e+02 Score=25.54 Aligned_cols=58 Identities=10% Similarity=0.039 Sum_probs=42.2
Q ss_pred eEEEEEccCCCeEEEEE--cCCCCeEEEEeecc----CcccCCCCCCCHHHHHHHHHHHHHHHHHc
Q 039298 61 GVAHIFASFNDTFIHVT--DLSGRETLVRITGG----MKVKADRDESSPYAAMLAAQDVSTRCKEL 120 (197)
Q Consensus 61 gi~hI~ss~NNTiitlT--D~~G~~~~~~SsG~----~g~k~~rrkst~~Aa~~aa~~v~~k~~el 120 (197)
.-+-|..|..|+|+.++ ++.|..+++..... .|++.+. ...-||++++.-+++++.+.
T Consensus 49 ~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~k~gl--~N~~AAY~TGlL~arR~L~k 112 (300)
T PTZ00069 49 YRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGIPVGL--TNYAAAYATGLLLARRLLKK 112 (300)
T ss_pred ceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcCCCC--ccHHHHHHHHHHHHHHHHHh
Confidence 44556778889988774 67898887766554 5777776 33457788999899887765
No 34
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.06 E-value=51 Score=27.03 Aligned_cols=59 Identities=25% Similarity=0.425 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHH------HHHHHHhCCcEEEEE-ecccceecccccc
Q 039298 108 LAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQS------ALRALARSGMKIGRI-DLEGLLILGLYYI 174 (197)
Q Consensus 108 ~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~------alraL~~~GlkI~~I-~~~~~~~~~l~~~ 174 (197)
...+++.+...++||+.+-|++ ||-|.-|.. .++-+.+.|..-..| .+-|-+|.-+||+
T Consensus 64 k~skkvlkaleq~gI~vIPvk~--------KgrGrprkyd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~ 129 (139)
T COG1710 64 KVSKKVLKALEQMGIKVIPVKL--------KGRGRPRKYDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYL 129 (139)
T ss_pred HHHHHHHHHHHhCCceEeeeee--------cCCCCCcccchhHHHHHHHHHHcCCCHHHHHHhhCCchhhhHHH
Confidence 5677888888899999999999 664543332 667778888876555 1224444444443
No 35
>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=33.92 E-value=34 Score=29.87 Aligned_cols=70 Identities=23% Similarity=0.268 Sum_probs=48.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE--------eccccee
Q 039298 97 DRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI--------DLEGLLI 168 (197)
Q Consensus 97 ~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I--------~~~~~~~ 168 (197)
++...|-|....+.+.+.+......+...++.+ .|||.=-..+.+.|...|.+|.-| +.+|+.+
T Consensus 5 ~~~~aTg~GV~~~~~~~~~~~~~~~l~g~~v~I--------qGfG~VG~~~a~~l~~~Ga~vv~vsD~~G~i~~~~Gld~ 76 (244)
T PF00208_consen 5 GRSEATGYGVAYAIEAALEHLGGDSLEGKRVAI--------QGFGNVGSHAARFLAELGAKVVAVSDSSGAIYDPDGLDV 76 (244)
T ss_dssp TTTTHHHHHHHHHHHHHHHHTTCHSSTTCEEEE--------EESSHHHHHHHHHHHHTTEEEEEEEESSEEEEETTEEHH
T ss_pred CCCcchHHHHHHHHHHHHHHcCCCCcCCCEEEE--------ECCCHHHHHHHHHHHHcCCEEEEEecCceEEEcCCCchH
Confidence 455666676666666665552222366788999 788876667888898999999888 5566666
Q ss_pred cccccc
Q 039298 169 LGLYYI 174 (197)
Q Consensus 169 ~~l~~~ 174 (197)
-.|+.+
T Consensus 77 ~~l~~~ 82 (244)
T PF00208_consen 77 EELLRI 82 (244)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 555553
No 36
>KOG0747 consensus Putative NAD+-dependent epimerases [Carbohydrate transport and metabolism]
Probab=33.47 E-value=1.1e+02 Score=28.57 Aligned_cols=72 Identities=26% Similarity=0.351 Sum_probs=40.9
Q ss_pred CCCHHHHHHHH-HHHHHH-HHHcCccEEEEEEEeeCCCCccCCCCChHHHHH---HHHhCCcEEEEEecccceecccccc
Q 039298 100 ESSPYAAMLAA-QDVSTR-CKELGITALHIKLRATGGNKTKTPGPGAQSALR---ALARSGMKIGRIDLEGLLILGLYYI 174 (197)
Q Consensus 100 kst~~Aa~~aa-~~v~~k-~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alr---aL~~~GlkI~~I~~~~~~~~~l~~~ 174 (197)
-.+||||..|| +.+.+. -.+.|+..+.++. |..-||++-.+-.|- -|+.. .+-..|.-.|+...+-+|.
T Consensus 153 PtnpyAasKaAaE~~v~Sy~~sy~lpvv~~R~-----nnVYGP~q~~~klipkFi~l~~~-~~~~~i~g~g~~~rs~l~v 226 (331)
T KOG0747|consen 153 PTNPYAASKAAAEMLVRSYGRSYGLPVVTTRM-----NNVYGPNQYPEKLIPKFIKLAMR-GKEYPIHGDGLQTRSYLYV 226 (331)
T ss_pred CCCchHHHHHHHHHHHHHHhhccCCcEEEEec-----cCccCCCcChHHHhHHHHHHHHh-CCCcceecCcccceeeEeH
Confidence 36799996555 444443 3457888777777 333566665555554 22222 2223334556777766666
Q ss_pred cccc
Q 039298 175 SEDV 178 (197)
Q Consensus 175 ~~Dv 178 (197)
+|+
T Consensus 227 -eD~ 229 (331)
T KOG0747|consen 227 -EDV 229 (331)
T ss_pred -HHH
Confidence 665
No 37
>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=32.32 E-value=1.5e+02 Score=21.62 Aligned_cols=45 Identities=16% Similarity=0.256 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHHHH-HHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcE
Q 039298 101 SSPYAAMLAAQDVSTRC-KELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMK 157 (197)
Q Consensus 101 st~~Aa~~aa~~v~~k~-~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~Glk 157 (197)
+.-|+...+ ..+...+ .++|+..|...+ -+.-..+++.+.+.|++
T Consensus 97 g~G~~~~~~-~~~~~~~~~~~~~~~i~a~~-----------~~~N~~s~~~~~k~GF~ 142 (142)
T PF13302_consen 97 GKGYGTEAL-KLLLDWAFEELGLHRIIATV-----------MADNEASRRLLEKLGFE 142 (142)
T ss_dssp TSSHHHHHH-HHHHHHHHHTSTSSEEEEEE-----------ETT-HHHHHHHHHTT-E
T ss_pred hhhHHHHHH-HHHHHHHHhcCCcEEEEEEE-----------CcCCHHHHHHHHHcCCC
Confidence 445665544 4466666 689999999999 45677899999999875
No 38
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=30.45 E-value=2.5e+02 Score=23.33 Aligned_cols=54 Identities=20% Similarity=0.209 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHc-C--ccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 100 ESSPYAAMLAAQDVSTRCKEL-G--ITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 100 kst~~Aa~~aa~~v~~k~~el-G--i~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
.-|.-+++..|.|++++..++ + -+.+.++- ....+.-.+.+.+|+..|.-|..-
T Consensus 27 ~~s~~~a~~iA~D~v~qL~~~ypPA~Tt~~l~q--------~~~D~Fg~aL~~aLR~~GYaV~e~ 83 (151)
T PRK13883 27 QASAADQQKLATDAVQQLATLYPPAQTRFELQQ--------PTPDAFGQALVKALRDKGYALLEY 83 (151)
T ss_pred ccCHHHHHHHHHHHHHHHHHhCCCcceEEEEec--------CCCcHHHHHHHHHHHHcCeEEEec
Confidence 356677888888888888775 3 45555554 445566678999999999988764
No 39
>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=29.45 E-value=1.8e+02 Score=23.45 Aligned_cols=47 Identities=30% Similarity=0.355 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 103 PYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 103 ~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
-|+.+ +.+.+.+.|+++|+..|.+.+ ...-..+++-..+.|++....
T Consensus 139 G~G~~-ll~~~~~~a~~~g~~~I~l~v-----------~~~N~~A~~~Y~klGF~~~~~ 185 (191)
T TIGR02382 139 GIGAE-LMQTALNWCYARGLTRLRVAT-----------QMGNTAALRLYIRSGANIEST 185 (191)
T ss_pred CHHHH-HHHHHHHHHHHcCCCEEEEEe-----------CCCCHHHHHHHHHcCCccccc
Confidence 35544 445577777889999999998 344457888888999987654
No 40
>PRK13260 2,3-diketo-L-gulonate reductase; Provisional
Probab=29.11 E-value=4.6e+02 Score=24.15 Aligned_cols=69 Identities=10% Similarity=-0.037 Sum_probs=47.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccC
Q 039298 100 ESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVT 179 (197)
Q Consensus 100 kst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvT 179 (197)
---++++..|.+.+.++|++.|+-.|-|+= +..+|.....+.++. ..||=-...-| .+-+
T Consensus 84 g~G~~~~~~am~~aiekAr~~Gi~~v~vrn-------s~H~G~~g~y~~~aa-~~G~igi~~tn------------~~~~ 143 (332)
T PRK13260 84 AIGNLTAKKMMDRAIELARDHGIGLVALRN-------ANHWMRGGSYGWQAA-EKGYIGICWTN------------SIAV 143 (332)
T ss_pred CchHHHHHHHHHHHHHHHHHhCEEEEEEcC-------CCchhhHHHHHHHHH-HCCCEEEEEeC------------CCCe
Confidence 445889999999999999999999776654 367888777776665 46654333311 3334
Q ss_pred CCCCCCCCC
Q 039298 180 PIPTDSTRR 188 (197)
Q Consensus 180 piPhnGcR~ 188 (197)
-.|++|.+|
T Consensus 144 vaP~Gg~~~ 152 (332)
T PRK13260 144 MPPWGAKEC 152 (332)
T ss_pred eCCCCCCCC
Confidence 457887664
No 41
>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=28.95 E-value=1.5e+02 Score=23.80 Aligned_cols=100 Identities=12% Similarity=0.180 Sum_probs=53.4
Q ss_pred ceeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHH--HcCccEEEEEEEeeCC
Q 039298 57 EHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCK--ELGITALHIKLRATGG 134 (197)
Q Consensus 57 ~~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~--elGi~~l~V~lr~~gg 134 (197)
..-.|++. |++.-.+.+.++|.....-....-..+.+.++. ..+..|-..|.+.+..... ..+.+.+-|.+ |-|
T Consensus 38 ~~rvgvv~-fs~~~~~~~~l~~~~~~~~~~~~i~~~~~~~g~-T~~~~AL~~a~~~l~~~~~g~R~~~~kv~ill--TDG 113 (177)
T cd01469 38 KTQFGLVQ-YSESFRTEFTLNEYRTKEEPLSLVKHISQLLGL-TNTATAIQYVVTELFSESNGARKDATKVLVVI--TDG 113 (177)
T ss_pred CcEEEEEE-ECCceeEEEecCccCCHHHHHHHHHhCccCCCC-ccHHHHHHHHHHHhcCcccCCCCCCCeEEEEE--eCC
Confidence 34567765 566667777787755432111111123333333 3443333444444322111 12467778888 555
Q ss_pred CCccCCCCChHHHHHHHHhCCcEEEEEe
Q 039298 135 NKTKTPGPGAQSALRALARSGMKIGRID 162 (197)
Q Consensus 135 ~~~KG~G~Gr~~alraL~~~GlkI~~I~ 162 (197)
....+.-+ +.+++.+++.|+.|..|.
T Consensus 114 ~~~~~~~~--~~~~~~~k~~gv~v~~Vg 139 (177)
T cd01469 114 ESHDDPLL--KDVIPQAEREGIIRYAIG 139 (177)
T ss_pred CCCCcccc--HHHHHHHHHCCcEEEEEE
Confidence 54433333 568888999999988873
No 42
>COG0334 GdhA Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]
Probab=28.92 E-value=1.2e+02 Score=29.11 Aligned_cols=57 Identities=18% Similarity=0.243 Sum_probs=42.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 96 ADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 96 ~~rrkst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
.+|...|-|.....++.+ .+....++....|-+ .|+|---+.+.+-|...|-||+-+
T Consensus 180 ~~r~~aTg~Gv~~~~~~a-~~~~g~~l~G~rVaV--------QG~GNVg~~aa~~l~~~GAkvva~ 236 (411)
T COG0334 180 LGRSEATGYGVFYAIREA-LKALGDDLEGARVAV--------QGFGNVGQYAAEKLHELGAKVVAV 236 (411)
T ss_pred CCCCcccceehHHHHHHH-HHHcCCCcCCCEEEE--------ECccHHHHHHHHHHHHcCCEEEEE
Confidence 356678888877777733 333344578899999 888876666777776779999998
No 43
>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=28.57 E-value=1.2e+02 Score=26.04 Aligned_cols=49 Identities=16% Similarity=0.222 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 104 YAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 104 ~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
|....+.+.+++... ..+...+|-| -|||.--..+.+.|.+.|.+++-+
T Consensus 4 ~Gv~~~~~~~~~~~~-~~l~g~~vaI--------qGfGnVG~~~a~~L~~~G~~vV~v 52 (217)
T cd05211 4 YGVVVAMKAAMKHLG-DSLEGLTVAV--------QGLGNVGWGLAKKLAEEGGKVLAV 52 (217)
T ss_pred hHHHHHHHHHHHHcC-CCcCCCEEEE--------ECCCHHHHHHHHHHHHcCCEEEEE
Confidence 334444444433332 3566788999 888875667778888999998887
No 44
>PRK10809 ribosomal-protein-S5-alanine N-acetyltransferase; Provisional
Probab=27.46 E-value=2.6e+02 Score=22.16 Aligned_cols=47 Identities=15% Similarity=0.053 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHH-cCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 103 PYAAMLAAQDVSTRCKE-LGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 103 ~~Aa~~aa~~v~~k~~e-lGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
-||.. +.+.+.+.|.+ +|+..|.+.+ -+.-..+++.+.+.|++...+
T Consensus 119 G~~~e-a~~~ll~~~~~~l~l~~i~~~v-----------~~~N~~S~~l~ek~Gf~~~g~ 166 (194)
T PRK10809 119 GLMFE-ALQAAIRYMQRQQHMHRIMANY-----------MPHNKRSGDLLARLGFEKEGY 166 (194)
T ss_pred CHHHH-HHHHHHHHHHhcCCceEEEEEe-----------eCCCHHHHHHHHHCCCcEEee
Confidence 35444 44557777765 7999999999 345667889999999987554
No 45
>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=26.58 E-value=3.9e+02 Score=25.65 Aligned_cols=57 Identities=26% Similarity=0.282 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCcc-CCCCChHHHHHHHHhCCcEEEEE
Q 039298 100 ESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTK-TPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 100 kst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~K-G~G~Gr~~alraL~~~GlkI~~I 161 (197)
.-|++-++.+++.+++.+++.+... .|.| |--++ .-++-.+.++.+|...|+++...
T Consensus 36 ~lt~~~v~~i~~a~~~~l~~~~~~~-~VvV----g~D~R~~S~~~~~~~~~gL~s~Gi~V~~~ 93 (522)
T cd05801 36 SFNEAHILAISQAICDYRKSQGITG-PLFL----GKDTHALSEPAFISALEVLAANGVEVIIQ 93 (522)
T ss_pred chhHHHHHHHHHHHHHHHHhhCCCC-eEEE----EeCCCcCCHHHHHHHHHHHHHCCCEEEEe
Confidence 4789999999998888887655322 1444 11223 23455667779999999999976
No 46
>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=26.32 E-value=1.2e+02 Score=22.40 Aligned_cols=27 Identities=15% Similarity=0.350 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHcCccEEEEEEEee
Q 039298 105 AAMLAAQDVSTRCKELGITALHIKLRAT 132 (197)
Q Consensus 105 Aa~~aa~~v~~k~~elGi~~l~V~lr~~ 132 (197)
-+++||+.+.+.++++|+. +.|..+|.
T Consensus 12 ht~lAae~L~~aA~~~G~~-i~VE~qg~ 38 (85)
T TIGR00829 12 HTFMAAEALEKAAKKRGWE-VKVETQGS 38 (85)
T ss_pred HHHHHHHHHHHHHHHCCCe-EEEEecCC
Confidence 4678899999999999996 78888654
No 47
>PRK07564 phosphoglucomutase; Validated
Probab=24.48 E-value=3.1e+02 Score=26.54 Aligned_cols=57 Identities=25% Similarity=0.293 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCC-CChHHHHHHHHhCCcEEEEE
Q 039298 100 ESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 100 kst~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G-~Gr~~alraL~~~GlkI~~I 161 (197)
.-|+.-++.+++.+++..++.+... .|.| |--++-.+ .-+++++.+|+..|+++..+
T Consensus 53 ~lt~~~v~~i~~a~a~~~~~~~~~~-~VvV----G~D~R~~S~~~a~a~a~gL~s~Gi~V~~~ 110 (543)
T PRK07564 53 SFNENHILAIFQAICEYRGKQGITG-PLFV----GGDTHALSEPAIQSALEVLAANGVGVVIV 110 (543)
T ss_pred CcCHHHHHHHHHHHHHHHHhcCCCC-eEEE----EecCCcCCHHHHHHHHHHHHHCCCEEEEe
Confidence 4688999999998888876654322 2444 11122223 23678999999999999988
No 48
>COG0027 PurT Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]
Probab=24.14 E-value=3e+02 Score=26.23 Aligned_cols=70 Identities=21% Similarity=0.243 Sum_probs=43.2
Q ss_pred eeeeEEEEEccCCCeEEEEEcCCCCeEEEEeeccCcccCCCCCCCH-----HHHHHHHHHHHHHHHH----cCccEEEEE
Q 039298 58 HVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSP-----YAAMLAAQDVSTRCKE----LGITALHIK 128 (197)
Q Consensus 58 ~~~gi~hI~ss~NNTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~-----~Aa~~aa~~v~~k~~e----lGi~~l~V~ 128 (197)
++.+++ ...+-=|.+|+--.+|+..+|.--|.---.++-++|=- -.+...|+.++++..+ .|+-.|++.
T Consensus 193 IVE~fv--~fd~EiTlLtvr~~~~~~~Fc~PIGHrq~dgdY~ESWQP~~mS~~al~~A~~IA~~vt~aLGG~GiFGVElf 270 (394)
T COG0027 193 IVEEFV--KFDFEITLLTVRAVDGTGSFCAPIGHRQEDGDYRESWQPQEMSEAALEEAQSIAKRVTDALGGRGLFGVELF 270 (394)
T ss_pred EEEEEe--cceEEEEEEEEEEecCCCCcCCCcccccCCCChhcccCccccCHHHHHHHHHHHHHHHHhhcCccceeEEEE
Confidence 555554 45666788888888887655555555444444434321 2344455666666554 678889999
Q ss_pred E
Q 039298 129 L 129 (197)
Q Consensus 129 l 129 (197)
+
T Consensus 271 v 271 (394)
T COG0027 271 V 271 (394)
T ss_pred E
Confidence 8
No 49
>PRK10975 TDP-fucosamine acetyltransferase; Provisional
Probab=23.95 E-value=3.8e+02 Score=21.43 Aligned_cols=46 Identities=30% Similarity=0.389 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 104 YAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 104 ~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
++.. +.+.+.+.+.+.|++.+.+.+ -..-..+++.+.+.|++...+
T Consensus 143 ig~~-Ll~~~~~~a~~~g~~~i~l~v-----------~~~N~~a~~~yek~Gf~~~~~ 188 (194)
T PRK10975 143 IGAR-LMQAALNWCQARGLTRLRVAT-----------QMGNLAALRLYIRSGANIEST 188 (194)
T ss_pred HHHH-HHHHHHHHHHHcCCCEEEEEe-----------CCCcHHHHHHHHHCCCeEeEE
Confidence 4444 335566777889999988887 233457888899999997765
No 50
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=23.91 E-value=2.2e+02 Score=25.60 Aligned_cols=44 Identities=27% Similarity=0.380 Sum_probs=35.0
Q ss_pred cCccEEEEEEEeeCCCCccCCCCChHHHHHHHH----hCCcEEEEEecccceecc
Q 039298 120 LGITALHIKLRATGGNKTKTPGPGAQSALRALA----RSGMKIGRIDLEGLLILG 170 (197)
Q Consensus 120 lGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~----~~GlkI~~I~~~~~~~~~ 170 (197)
.|..+.+|-++|. -|.|+.+.+|+|. ..|++++.|+.+++..++
T Consensus 48 ~G~pannvLL~G~-------rGtGKSSlVkall~~y~~~GLRlIev~k~~L~~l~ 95 (249)
T PF05673_consen 48 QGLPANNVLLWGA-------RGTGKSSLVKALLNEYADQGLRLIEVSKEDLGDLP 95 (249)
T ss_pred cCCCCcceEEecC-------CCCCHHHHHHHHHHHHhhcCceEEEECHHHhccHH
Confidence 5899999999776 3677889999985 469999999777765554
No 51
>PRK10151 ribosomal-protein-L7/L12-serine acetyltransferase; Provisional
Probab=23.76 E-value=3.5e+02 Score=21.01 Aligned_cols=49 Identities=10% Similarity=0.062 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHHHH-HcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 101 SSPYAAMLAAQDVSTRCK-ELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 101 st~~Aa~~aa~~v~~k~~-elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
+--||.++ .+.+.+.+. ++|+..|.+.+ -.+-.++.+.+.+.|++...+
T Consensus 106 g~G~~tea-~~~l~~~~~~~~~~~ri~~~v-----------~~~N~~S~~v~ek~Gf~~~g~ 155 (179)
T PRK10151 106 GQGIISQA-LQALIHHYAQSGELRRFVIKC-----------RVDNPASNQVALRNGFTLEGC 155 (179)
T ss_pred CCcHHHHH-HHHHHHHHHhhCCccEEEEEE-----------cCCCHHHHHHHHHCCCEEEeE
Confidence 34566664 344556554 57899999888 345667889999999997655
No 52
>PRK00394 transcription factor; Reviewed
Probab=23.52 E-value=2.3e+02 Score=23.74 Aligned_cols=49 Identities=20% Similarity=0.185 Sum_probs=33.4
Q ss_pred eEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccE
Q 039298 72 TFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITA 124 (197)
Q Consensus 72 TiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~ 124 (197)
.++-+.||.- ....+++|-+-..+++ |.-.|..|++++++..+++|++.
T Consensus 38 li~Rl~~Pk~-t~lIf~sGKiv~tGa~---S~~~a~~a~~~~~~~l~~~g~~~ 86 (179)
T PRK00394 38 LVYRLEDPKI-AALIFRSGKVVCTGAK---SVEDLHEAVKIIIKKLKELGIKV 86 (179)
T ss_pred EEEEecCCce-EEEEEcCCcEEEEccC---CHHHHHHHHHHHHHHHHHcCCCc
Confidence 3444455544 3445677776666655 35578889999999999999765
No 53
>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=23.52 E-value=2.4e+02 Score=23.63 Aligned_cols=42 Identities=14% Similarity=0.099 Sum_probs=31.1
Q ss_pred HHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 111 QDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 111 ~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
+++.+.+.++|+..|++.. . .....+.+.+.+...|++|..+
T Consensus 17 ~e~~~~~~e~G~~~vEl~~--------~-~~~~~~~l~~~l~~~gl~v~~~ 58 (254)
T TIGR03234 17 LERFAAAAQAGFTGVEYLF--------P-YDWDAEALKARLAAAGLEQVLF 58 (254)
T ss_pred HHHHHHHHHcCCCEEEecC--------C-ccCCHHHHHHHHHHcCCeEEEE
Confidence 5577888899999999865 1 1234555666777899999887
No 54
>COG4130 Predicted sugar epimerase [Carbohydrate transport and metabolism]
Probab=23.37 E-value=2.4e+02 Score=25.58 Aligned_cols=48 Identities=21% Similarity=0.346 Sum_probs=34.6
Q ss_pred HHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHH-hCCcEEEEE
Q 039298 111 QDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALA-RSGMKIGRI 161 (197)
Q Consensus 111 ~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~-~~GlkI~~I 161 (197)
++...-|+++|++.|+|+=.=+++.-..|..+ +.+|+++ +.|+.|++|
T Consensus 20 ~affa~ak~lg~s~VeiRndl~~~~I~dg~p~---a~vka~Aek~Gl~IvSI 68 (272)
T COG4130 20 EAFFALAKRLGLSKVEIRNDLPSNAIADGTPA---AEVKALAEKAGLTIVSI 68 (272)
T ss_pred HHHHHHHHHcCcceeEEecCCCcccccCCCCH---HHHHHHHHHcCcEEEEe
Confidence 56777899999999998864333333344433 4688886 579999999
No 55
>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=22.48 E-value=2.1e+02 Score=23.95 Aligned_cols=50 Identities=18% Similarity=0.214 Sum_probs=33.1
Q ss_pred CeEEEEEcCCCCeEEEEeeccCcccCCCCCCCHHHHHHHHHHHHHHHHHcCccE
Q 039298 71 DTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKELGITA 124 (197)
Q Consensus 71 NTiitlTD~~G~~~~~~SsG~~g~k~~rrkst~~Aa~~aa~~v~~k~~elGi~~ 124 (197)
-.++-+.|++- ....+++|-+-..+.+ |.-.|..|++++++..+++|++.
T Consensus 38 gli~Rl~~Pk~-t~lIF~SGKiv~tGak---s~~~a~~a~~~~~~~L~~~g~~~ 87 (174)
T cd04518 38 GLVYRLEDPKI-AALIFRSGKMVCTGAK---SVEDLHRAVKEIIKKLKDYGIKV 87 (174)
T ss_pred EEEEEccCCcE-EEEEECCCeEEEEccC---CHHHHHHHHHHHHHHHHhcCCCc
Confidence 34444455544 3345666666665554 35678888999999999999664
No 56
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=22.35 E-value=60 Score=34.71 Aligned_cols=45 Identities=33% Similarity=0.409 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCC
Q 039298 107 MLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTD 184 (197)
Q Consensus 107 ~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhn 184 (197)
.++..++.+.|++.||. + ||||=+|--.|..- ...| +||-||+||
T Consensus 323 FLIV~D~i~~Ak~~gI~-----V-----------GPGRGSaAGSLVaY---~LgI--------------T~VDPl~y~ 367 (1107)
T PRK06920 323 FLIVWDFMKYAHENHIL-----T-----------GPGRGSAAGSLVSY---VLEI--------------TDIDPIEYD 367 (1107)
T ss_pred hHHHHHHHHHHHHCCCE-----e-----------CCCcchHHHHHHHH---HhCC--------------CccCccccC
Confidence 34556777778877764 3 66666666666432 2334 888999987
No 57
>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=21.75 E-value=3e+02 Score=19.43 Aligned_cols=46 Identities=13% Similarity=0.192 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 104 YAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 104 ~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
+|.++. +.+.+.+.+.|+..+.+.+ .+....+++-+.+.|+++...
T Consensus 71 ~g~~ll-~~~~~~~~~~~~~~i~~~~-----------~~~n~~~~~~y~~~Gf~~~~~ 116 (131)
T TIGR01575 71 IGRALL-RELIDEAKGRGVNEIFLEV-----------RVSNIAAQALYKKLGFNEIAI 116 (131)
T ss_pred HHHHHH-HHHHHHHHHcCCCeEEEEE-----------ecccHHHHHHHHHcCCCcccc
Confidence 444433 5566778888999888877 233456788889999987665
No 58
>PRK09491 rimI ribosomal-protein-alanine N-acetyltransferase; Provisional
Probab=21.62 E-value=3.5e+02 Score=20.19 Aligned_cols=49 Identities=12% Similarity=0.204 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 101 SSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 101 st~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
+.-||..+. +.+.+.+.+.|+..+.+.+ -.....+++.+.+.|++...+
T Consensus 77 g~G~g~~ll-~~~~~~~~~~~~~~~~~~~-----------~~~N~~a~~~y~k~Gf~~~~~ 125 (146)
T PRK09491 77 RQGLGRALL-EHLIDELEKRGVATLWLEV-----------RASNAAAIALYESLGFNEVTI 125 (146)
T ss_pred cCCHHHHHH-HHHHHHHHHCCCcEEEEEE-----------ccCCHHHHHHHHHcCCEEeee
Confidence 344555544 4566678889999888877 233467899999999997665
No 59
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=20.54 E-value=67 Score=34.41 Aligned_cols=45 Identities=29% Similarity=0.416 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCC
Q 039298 107 MLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTD 184 (197)
Q Consensus 107 ~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhn 184 (197)
.++..++.+.|++.||. + ||||=+|--.|..- ...| +||-||+||
T Consensus 338 FLIV~D~i~~Ak~~gI~-----v-----------GpGRGSaAGSLVaY---~LgI--------------T~vDPl~y~ 382 (1135)
T PRK05673 338 FLIVADFIQWAKDNGIP-----V-----------GPGRGSGAGSLVAY---ALGI--------------TDLDPLRFG 382 (1135)
T ss_pred HHHHHHHHHHHHHCCCe-----e-----------CCCCchHHHHHHHH---HhcC--------------CccCccccC
Confidence 45667888888888754 3 66666666666432 2334 888999986
No 60
>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=20.42 E-value=3e+02 Score=18.96 Aligned_cols=45 Identities=29% Similarity=0.281 Sum_probs=26.9
Q ss_pred cCCCCeEEEEeeccCcccCCCCC----CCHHHHHHHHHHHHHHHHHcCcc
Q 039298 78 DLSGRETLVRITGGMKVKADRDE----SSPYAAMLAAQDVSTRCKELGIT 123 (197)
Q Consensus 78 D~~G~~~~~~SsG~~g~k~~rrk----st~~Aa~~aa~~v~~k~~elGi~ 123 (197)
|+.|...++..-|-.|-.+.. + .++.+|+.+++++.+.....||.
T Consensus 24 ~lfg~~~v~~~wGRiG~~Gq~-~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 24 DLFGEWSLVRRWGRIGTKGQS-RTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred cCCCCEEEEEEECCCCCCCce-EEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 344555556666777743333 4 45566777777776666666764
No 61
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=20.07 E-value=68 Score=33.91 Aligned_cols=46 Identities=28% Similarity=0.382 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEEecccceeccccccccccCCCCCC
Q 039298 106 AMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTPIPTD 184 (197)
Q Consensus 106 a~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I~~~~~~~~~l~~~~~DvTpiPhn 184 (197)
+.++..++.+.|++.||. + ||||=+|--.|..- ...| +||-||+||
T Consensus 271 YFLIV~D~v~~Ak~~gI~-----v-----------GpGRGSaAGSLVaY---~LgI--------------T~VDPl~y~ 316 (973)
T PRK07135 271 YFLIIWDFIKWARKNKIS-----I-----------GPGRGSASGSLVSY---LLNI--------------TSVNPLKYD 316 (973)
T ss_pred hHHHHHHHHHHHHHCCce-----e-----------CCCCcchHHHHHHH---HhcC--------------CccCccccC
Confidence 346667888888888754 3 56665665555422 2334 888999986
No 62
>COG3916 LasI N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.04 E-value=4e+02 Score=23.43 Aligned_cols=46 Identities=28% Similarity=0.270 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHHHHHHcCccEEEEEEEeeCCCCccCCCCChHHHHHHHHhCCcEEEEE
Q 039298 101 SSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 161 (197)
Q Consensus 101 st~~Aa~~aa~~v~~k~~elGi~~l~V~lr~~gg~~~KG~G~Gr~~alraL~~~GlkI~~I 161 (197)
-++ |+...--.+.+.+...|++.|.... --...|-|.++|..+.+|
T Consensus 118 ~~~-a~~el~~g~ie~a~~~G~~~IvtVt--------------~~~meril~r~Gw~~~ri 163 (209)
T COG3916 118 VSP-AAYELFAGMIEYALARGITGIVTVT--------------DTGMERILRRAGWPLTRI 163 (209)
T ss_pred ccH-HHHHHHHHHHHHHHHcCCceEEEEE--------------chHHHHHHHHcCCCeEEc
Confidence 344 4554555588899999999998888 224678899999998888
Done!