Query gi|254780244|ref|YP_003064657.1| 30S ribosomal protein S5 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 199
No_of_seqs 117 out of 919
Neff 5.0
Searched_HMMs 39220
Date Tue May 24 06:50:31 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780244.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01021 rpsE_bact ribosomal 100.0 0 0 442.8 13.9 157 19-175 1-157 (157)
2 COG0098 RpsE Ribosomal protein 100.0 0 0 402.7 15.2 166 13-178 15-180 (181)
3 PRK00550 rpsE 30S ribosomal pr 100.0 0 0 388.6 16.5 154 19-173 3-156 (156)
4 PRK04044 rps5p 30S ribosomal p 100.0 0 0 342.8 13.2 149 14-162 43-201 (211)
5 TIGR01020 rpsE_arch ribosomal 100.0 0 0 337.6 11.3 149 14-162 44-207 (220)
6 CHL00138 rps5 ribosomal protei 100.0 0 0 311.4 12.8 127 15-141 13-139 (139)
7 PTZ00070 40S ribosomal protein 100.0 2.8E-45 0 296.9 10.7 146 21-166 83-239 (261)
8 KOG2646 consensus 100.0 2.4E-41 0 272.4 5.9 170 16-185 176-348 (396)
9 KOG0877 consensus 100.0 1.5E-30 3.8E-35 206.6 9.1 144 19-162 48-199 (213)
10 pfam03719 Ribosomal_S5_C Ribos 99.9 3.3E-26 8.5E-31 180.1 8.0 74 97-170 1-74 (74)
11 pfam00333 Ribosomal_S5 Ribosom 99.9 5.8E-24 1.5E-28 166.4 6.9 67 21-87 1-67 (67)
12 TIGR00479 rumA 23S rRNA (uraci 83.8 2.2 5.6E-05 22.7 4.5 82 64-152 321-407 (434)
13 COG1710 Uncharacterized protei 74.8 6.1 0.00015 20.0 4.5 73 102-176 50-126 (139)
14 PRK13186 lpxC UDP-3-O-[3-hydro 53.8 8.7 0.00022 19.1 1.9 81 22-112 53-150 (299)
15 cd00308 enolase_like Enolase-s 52.0 19 0.00049 16.9 3.5 101 37-158 17-119 (229)
16 pfam03331 LpxC UDP-3-O-acyl N- 51.6 9.9 0.00025 18.7 1.9 49 56-112 98-149 (276)
17 COG2265 TrmA SAM-dependent met 49.9 21 0.00053 16.7 4.7 98 53-157 303-410 (432)
18 PRK13188 bifunctional UDP-3-O- 45.9 14 0.00035 17.9 1.9 16 59-74 103-118 (465)
19 pfam12327 FtsZ_C FtsZ family, 42.2 21 0.00054 16.7 2.4 22 54-75 2-24 (97)
20 PRK13846 putative glycerol-3-p 42.2 28 0.0007 16.0 3.7 40 129-168 273-314 (316)
21 TIGR00182 plsX fatty acid/phos 40.0 18 0.00045 17.2 1.7 46 129-176 291-336 (344)
22 TIGR02406 ectoine_EctA L-2,4-d 40.0 30 0.00076 15.8 3.1 54 106-160 72-129 (162)
23 PRK05463 hypothetical protein; 39.0 31 0.00079 15.7 3.1 84 53-143 110-214 (264)
24 pfam02624 YcaO YcaO-like famil 37.5 33 0.00083 15.6 5.7 50 35-84 181-231 (332)
25 PHA02448 hypothetical protein 36.4 24 0.0006 16.4 1.9 40 38-82 69-108 (192)
26 PRK05331 putative glycerol-3-p 36.4 34 0.00087 15.4 2.7 29 129-157 288-316 (317)
27 cd03315 MLE_like Muconate lact 35.9 35 0.00088 15.4 5.2 108 37-157 17-127 (265)
28 PRK00094 gpsA NAD(P)H-dependen 31.7 27 0.00068 16.1 1.5 57 122-183 231-289 (325)
29 pfam07286 DUF1445 Protein of u 31.2 39 0.001 15.1 2.3 80 57-143 1-101 (143)
30 TIGR03247 glucar-dehydr glucar 30.4 33 0.00083 15.6 1.8 44 41-87 30-73 (441)
31 PRK13187 UDP-3-O-[3-hydroxymyr 30.1 31 0.00078 15.7 1.7 18 58-75 113-130 (305)
32 PRK12371 ribonuclease III; Rev 30.0 43 0.0011 14.8 4.1 40 39-82 190-229 (235)
33 cd00048 DSRM Double-stranded R 29.5 44 0.0011 14.8 5.3 43 36-82 26-68 (68)
34 COG0131 HisB Imidazoleglycerol 29.4 44 0.0011 14.7 7.5 92 65-157 70-173 (195)
35 pfam02504 FA_synthesis Fatty a 28.4 43 0.0011 14.8 2.2 30 129-158 285-314 (322)
36 PRK11568 hypothetical protein; 27.4 42 0.0011 14.9 2.0 42 112-156 75-121 (204)
37 TIGR02087 LEUD_arch 3-isopropy 26.9 29 0.00074 15.9 1.1 35 115-149 58-96 (159)
38 KOG4328 consensus 25.9 51 0.0013 14.4 2.2 34 26-60 175-215 (498)
39 cd01684 Tet_like_IV EF-G_domai 25.7 52 0.0013 14.3 4.5 42 99-156 23-64 (115)
40 smart00358 DSRM Double-strande 25.4 52 0.0013 14.3 4.8 40 39-82 27-66 (67)
41 pfam02294 7kD_DNA_binding 7kD 24.9 42 0.0011 14.9 1.6 45 23-71 10-54 (62)
42 PRK12439 NAD(P)H-dependent gly 23.8 25 0.00064 16.3 0.3 44 123-171 236-281 (340)
43 TIGR01237 D1pyr5carbox2 delta- 23.2 56 0.0014 14.1 2.0 36 92-133 191-226 (518)
44 TIGR02173 cyt_kin_arch cytidyl 22.6 59 0.0015 14.0 4.9 48 106-177 2-49 (173)
45 cd01680 EFG_like_IV Elongation 22.5 60 0.0015 14.0 4.1 21 98-118 22-42 (116)
46 pfam03302 VSP Giardia variant- 21.8 62 0.0016 13.9 2.5 13 44-59 374-386 (397)
47 COG0371 GldA Glycerol dehydrog 21.1 33 0.00084 15.5 0.4 84 52-140 84-176 (360)
48 TIGR01284 alt_nitrog_alph nitr 21.1 36 0.00092 15.3 0.6 47 122-169 227-276 (468)
49 pfam01989 DUF126 Protein of un 20.7 64 0.0016 13.8 1.8 58 93-153 18-75 (83)
50 TIGR02326 transamin_PhnW 2-ami 20.4 54 0.0014 14.2 1.4 25 137-161 234-261 (366)
51 PRK05920 aromatic acid decarbo 20.0 31 0.00078 15.7 0.1 100 42-141 93-201 (205)
No 1
>TIGR01021 rpsE_bact ribosomal protein S5; InterPro: IPR005712 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 of 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 chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=442.78 Aligned_cols=157 Identities=52% Similarity=0.875 Sum_probs=154.5
Q ss_pred CCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCCCCCEECC
Q ss_conf 11602100002244401278738467999998089983899704744247899999999963012522016687620011
Q gi|254780244|r 19 DNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGV 98 (199)
Q Consensus 19 ~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~TI~h~v~ 98 (199)
+++|+|+||+||||||||||||+|||+|||||||++|+||||+|||.||+.||+||+.+|+|||+.||++++.||||||.
T Consensus 1 ~~~l~Ervv~vnRvsKVVKGGRrfsF~ALvVVGd~~G~VG~G~GKA~EV~~AI~Ka~~~A~Knl~~Vp~~~~~tI~H~V~ 80 (157)
T TIGR01021 1 ESELEERVVAVNRVSKVVKGGRRFSFSALVVVGDKKGRVGFGFGKAKEVPDAIKKAVEDAKKNLIKVPLVKGNTIPHEVI 80 (157)
T ss_pred CCCCEEEEEEEEEEEEEEECCCCEEEEEEEEEECCCCEEEEEEEEHHHHHHHHHHHHHHHHHCEEEEEEECCCEEECCEE
T ss_conf 96615688986027876428940368999997178743788650120047899886875312517888608974502148
Q ss_pred CCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHH
Q ss_conf 03376799996367544850304899999980944100454689888899999999995069989999861997989
Q gi|254780244|r 99 GRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSL 175 (199)
Q Consensus 99 gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~i~~ 175 (199)
|+|++++|+|+||++|||||||+++|+|||||||+||+||++||+||+|+++|||+||.+|++|++||..||+++.|
T Consensus 81 G~~~aa~vllkPA~~GTGvIAGGa~RavlE~AGv~DIlaK~LGSnNP~N~vrAt~~AL~~l~~~~~vA~~Rg~~v~e 157 (157)
T TIGR01021 81 GKSGAAKVLLKPASPGTGVIAGGAVRAVLELAGVKDILAKSLGSNNPINVVRATFDALLKLKSPEDVAEERGKSVEE 157 (157)
T ss_pred EEECCEEEEEECCCCCCCEEECCCHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCC
T ss_conf 87778289986589989579477457887753841256651568774689999999997236967999845886679
No 2
>COG0098 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=402.68 Aligned_cols=166 Identities=51% Similarity=0.816 Sum_probs=160.3
Q ss_pred HHHCCCCCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCCC
Q ss_conf 21000011602100002244401278738467999998089983899704744247899999999963012522016687
Q gi|254780244|r 13 QNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRT 92 (199)
Q Consensus 13 ~~~~~~~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~T 92 (199)
...+...++|.|+||+|+||+|||+|||++||+|||||||+||+||||+|||.|++.||+||++.|++||++||++++||
T Consensus 15 ~~~e~~~~~l~e~vv~inrV~K~~kgGRr~~F~alvVVGd~~G~VG~G~GKA~EV~~AIrKAi~~Ak~nii~V~~~~~~T 94 (181)
T COG0098 15 PIKEPEVDELLEKVVDINRVSKVVKGGRRFRFSALVVVGDRNGRVGFGIGKAKEVPEAIRKAIEDAKKNIIEVPRGNGHT 94 (181)
T ss_pred CCCCHHHHHCCCCCEEEEEEEEEECCCEEEEEEEEEEEECCCCEEEEEECCHHHHHHHHHHHHHHHHHCEEEEECCCCCE
T ss_conf 76770665303001588977775137517889999999679980712003023568999999999984769985479964
Q ss_pred CCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCC
Q ss_conf 62001103376799996367544850304899999980944100454689888899999999995069989999861997
Q gi|254780244|r 93 LHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172 (199)
Q Consensus 93 I~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~ 172 (199)
|||++.|+||+++|+|+|||+||||+||+++|+|||||||+|||+|++||+||+|+++|||+||.++++|+++|..||+.
T Consensus 95 iph~v~Gk~g~~~V~L~PA~~GtGiiAGg~~r~vlelAGi~Dv~tks~GS~n~~N~vrAt~~aL~~~~~p~~ia~~Rg~~ 174 (181)
T COG0098 95 IPHEVIGKHGAVKVLLKPAPEGTGIIAGGAVRAVLELAGIKDVLAKSLGSRNPINVVRATFDALKKLRTPEDVAAKRGKK 174 (181)
T ss_pred EEEEEEEEECCEEEEEEECCCCCEEEECCHHHHHHHHCCCHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCC
T ss_conf 62687888784899998789985488473789999982800411102678984489999999999756999999871996
Q ss_pred HHHHHH
Q ss_conf 989445
Q gi|254780244|r 173 HSLLQA 178 (199)
Q Consensus 173 i~~~~~ 178 (199)
+.++..
T Consensus 175 ~~~~~~ 180 (181)
T COG0098 175 VEDILG 180 (181)
T ss_pred CHHHHC
T ss_conf 065315
No 3
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=100.00 E-value=0 Score=388.60 Aligned_cols=154 Identities=57% Similarity=0.926 Sum_probs=151.5
Q ss_pred CCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCCCCCEECC
Q ss_conf 11602100002244401278738467999998089983899704744247899999999963012522016687620011
Q gi|254780244|r 19 DNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGV 98 (199)
Q Consensus 19 ~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~TI~h~v~ 98 (199)
++||+|+||+|+||+|||++||++||+|||+|||+||+||||+|||.|+++||+||.++|++||++||++ ++||||+++
T Consensus 3 ~~~~~e~vi~i~rv~k~tkgGr~~~f~alvvvGn~nG~vG~G~gKa~ev~~Ai~kA~~~Ak~nl~~V~~~-~~Tiph~v~ 81 (156)
T PRK00550 3 EDELEEKLVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRKAVEAAKKNMIKVPLV-GGTIPHEVK 81 (156)
T ss_pred CCCCEEEEEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHHHCEEEEEEC-CCEEEEEEE
T ss_conf 6560126898862347864983577899999987998297756607668999999999997378999913-998988898
Q ss_pred CCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCH
Q ss_conf 033767999963675448503048999999809441004546898888999999999950699899998619979
Q gi|254780244|r 99 GRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKH 173 (199)
Q Consensus 99 gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~i 173 (199)
+||++++|+|+|||+|+||+||+.++.||+|+||+||++|++||+||+|+++|||+||++|+||+|+|+.||+++
T Consensus 82 gk~~~~kV~l~Pap~G~Gl~a~~~~r~vl~laGI~d~~~K~~Gs~n~~NvvkA~~~aL~~~~t~~~iA~~rG~~~ 156 (156)
T PRK00550 82 GKHGAAKVLLKPASEGTGVIAGGAMRAVLELAGVHDVLAKSLGSNNPINVVRATFDALKKLRTPEEVAAKRGKSV 156 (156)
T ss_pred EEECCEEEEEEECCCCCCEECCHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCC
T ss_conf 898638999996799955783879999999759160576716899788999999999981899999999848989
No 4
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed
Probab=100.00 E-value=0 Score=342.77 Aligned_cols=149 Identities=30% Similarity=0.456 Sum_probs=140.8
Q ss_pred HHCCCCCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCC----
Q ss_conf 1000011602100002244401278738467999998089983899704744247899999999963012522016----
Q gi|254780244|r 14 NREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLD---- 89 (199)
Q Consensus 14 ~~~~~~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~---- 89 (199)
..|.--++|+|+||+|+||||||++||++||+|+|+|||+||+||+|.|||+||+.||+||+..|++||++|++.+
T Consensus 43 IvD~llp~L~deVl~I~~VqK~T~~Grr~rF~AlVvVGd~~G~VGlG~gkakEV~~AI~KA~~~AK~nli~V~rg~GsW~ 122 (211)
T PRK04044 43 IVDALLPDLEDEVLDINMVQRMTDSGRRVRFRVVVVVGNRDGYVGVGQGKAKQVGPAIRKAIRNAKLNIIKVRRGCGSWE 122 (211)
T ss_pred HHHHHCCCCHHHEEEEEEEEEEEECCCCEEEEEEEEEECCCCCEEECCCCCCCHHHHHHHHHHHHHHCEEEEECCCCCCC
T ss_conf 89887053233348875567875078513689999984589837433432431188999999999866089750467544
Q ss_pred -----CCCCCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCC-CCHHHHHHHHHHHHHCCCCH
Q ss_conf -----68762001103376799996367544850304899999980944100454689-88889999999999506998
Q gi|254780244|r 90 -----GRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGS-SNPHNVIRATFEVLRSQSHP 162 (199)
Q Consensus 90 -----~~TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS-~N~~NvvkAt~~AL~~~~t~ 162 (199)
+|||||++.|||||++|+|+|||+|+||+|++.++.||++|||+||++|++|| +|++|+++|||+||+++.++
T Consensus 123 ~~~~~~hTIp~~v~Gk~gS~~V~L~PAp~GtGivAg~~~k~vLelAGI~Dv~tks~GsTrn~~N~akATf~AL~~~~~~ 201 (211)
T PRK04044 123 CGCGEPHSVPFKVEGKSGSVRVTLKPAPRGLGLVAGDVAKKVLELAGIKDVWTRTFGETRTTVNFAKATFNALKNTNKV 201 (211)
T ss_pred CCCCCCCCCCEEEEEEECCEEEEEEECCCCCEEEECCHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf 5668887401689989786899999779997378182899999973813134423457897114999999999986477
No 5
>TIGR01020 rpsE_arch ribosomal protein S5; InterPro: IPR005711 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 of 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 model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=337.59 Aligned_cols=149 Identities=29% Similarity=0.422 Sum_probs=141.6
Q ss_pred HHCCCC-CCC---E-EEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECC
Q ss_conf 100001-160---2-10000224440127873846799999808998389970474424789999999996301252201
Q gi|254780244|r 14 NREERD-NSI---V-DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLL 88 (199)
Q Consensus 14 ~~~~~~-~~l---~-ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~ 88 (199)
.-|.-- ++| + |+||+|+-|||||+.||+.+|||+|||||+|||||+|.|||+||..||+||+.+||+|+|+|.|.
T Consensus 44 IvD~LLGP~L~aren~eVldv~lVQrmt~sGRrtrFra~vvVGn~dGYVGlG~gkA~eV~~AIrKAI~~AKlnIi~VrRG 123 (220)
T TIGR01020 44 IVDALLGPDLNARENEEVLDVSLVQRMTDSGRRTRFRATVVVGNRDGYVGLGKGKAKEVAPAIRKAINNAKLNIIPVRRG 123 (220)
T ss_pred HHHEECCCCCCCCCCCCEEEEECCEEECCCCCEEEEEEEEEEECCCCCEEECCCCCCHHHHHHHHHHHHCCCCEEEEECC
T ss_conf 41101088878755652023313164234686043489999857898176234631003468999997247143566405
Q ss_pred CC---------CCCCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECC-CCCHHHHHHHHHHHHHC
Q ss_conf 66---------876200110337679999636754485030489999998094410045468-98888999999999950
Q gi|254780244|r 89 DG---------RTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIG-SSNPHNVIRATFEVLRS 158 (199)
Q Consensus 89 ~~---------~TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~G-S~N~~NvvkAt~~AL~~ 158 (199)
|| ||||+.|.||+||++|.|.|||+|+||+|++..+.||+||||+|||+++.| ++|.+|+|||||+||++
T Consensus 124 CGsWec~cG~pHsvPfkV~Gk~GSV~V~LiPAP~G~GLVaGDV~K~~L~LAGI~DVWt~T~G~T~Tt~NFAkAtF~Al~~ 203 (220)
T TIGR01020 124 CGSWECGCGRPHSVPFKVSGKSGSVRVRLIPAPKGVGLVAGDVAKKVLRLAGIKDVWTQTRGETRTTVNFAKATFEALKK 203 (220)
T ss_pred CCCCCCCCCCCCCCCEEEEECCCEEEEEEECCCCCCEEEECCHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHHHHHHHH
T ss_conf 67634657888533456500000489998749996238874644688774596235404556022330388999999987
Q ss_pred CCCH
Q ss_conf 6998
Q gi|254780244|r 159 QSHP 162 (199)
Q Consensus 159 ~~t~ 162 (199)
+.+.
T Consensus 204 t~~~ 207 (220)
T TIGR01020 204 TYSF 207 (220)
T ss_pred HHCC
T ss_conf 4212
No 6
>CHL00138 rps5 ribosomal protein S5; Validated
Probab=100.00 E-value=0 Score=311.38 Aligned_cols=127 Identities=39% Similarity=0.692 Sum_probs=124.2
Q ss_pred HCCCCCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCCCCC
Q ss_conf 00001160210000224440127873846799999808998389970474424789999999996301252201668762
Q gi|254780244|r 15 REERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLH 94 (199)
Q Consensus 15 ~~~~~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~TI~ 94 (199)
...++++|+|+||+|+||||||++||++||+|||+|||+||+||||.|||.|+++||+||..+|++||++||++++||||
T Consensus 13 ~~~~~~~~~e~vi~i~rV~k~tkgGr~~~f~alVvVGn~~G~vG~G~gKa~ev~~AI~KA~~~Akknl~~V~~~~~~TIp 92 (139)
T CHL00138 13 LIEQENKWEERVIQIKRVSKVVKGGKKLSFRAIVVIGNENGWVGVGVGKASDVQGAVKKAVTDAKKNIINIPLTKSNSIP 92 (139)
T ss_pred CHHHCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEEEEEECCHHHHHHHHHHHHHHHCEEEEECCCCCEEE
T ss_conf 20130573068898985543622893667999999977999798878853419999999999996269999812896488
Q ss_pred EECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECC
Q ss_conf 00110337679999636754485030489999998094410045468
Q gi|254780244|r 95 HDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIG 141 (199)
Q Consensus 95 h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~G 141 (199)
|++.+||++++|+|+|||+|+||+||+.++.||+|+||+|+++|++|
T Consensus 93 h~v~gk~gs~~V~l~Pap~G~Gliag~~ir~ilelaGIkDv~~K~~G 139 (139)
T CHL00138 93 HNITGIFGAAKVILRPSAPGSGVIAGGSIRTVLELAGIKNILAKQLG 139 (139)
T ss_pred EEEEEEECCEEEEEEECCCCCCEECCHHHHHHHHHCCCCEEEEECCC
T ss_conf 99999986389999989999868858099999997695305466259
No 7
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=100.00 E-value=2.8e-45 Score=296.94 Aligned_cols=146 Identities=32% Similarity=0.428 Sum_probs=137.4
Q ss_pred CCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECC-------CCCCC
Q ss_conf 60210000224440127873846799999808998389970474424789999999996301252201-------66876
Q gi|254780244|r 21 SIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLL-------DGRTL 93 (199)
Q Consensus 21 ~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~-------~~~TI 93 (199)
+|+|+||+|+.|||||+.||+++|+|+|+|||+||+||+|.||++||++||++|+..||+|+++|.+. +.|||
T Consensus 83 ~LkdEVl~I~~VQKqT~aGqrtrFka~VvVGd~nG~VGlG~~kskEV~~AIrkAi~~AKlniipVrrG~W~~~~g~pHTV 162 (261)
T PTZ00070 83 QLKDEVMKIVPVQKQTSAGQRTRFKAFVVVGDGNGHIGLGAKVAKEVALAIRGAMIAAKLNLVPVRRGYWGNKIGEPHTV 162 (261)
T ss_pred CHHHHHHHHHHHEECCCCCCEEEEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCC
T ss_conf 01556421142101012575257899999726888515551211014788999999753255455324446788999854
Q ss_pred CEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCC-CCHHHHHHHHHHHHHCCC---CHHHHH
Q ss_conf 2001103376799996367544850304899999980944100454689-888899999999995069---989999
Q gi|254780244|r 94 HHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGS-SNPHNVIRATFEVLRSQS---HPRDVA 166 (199)
Q Consensus 94 ~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS-~N~~NvvkAt~~AL~~~~---t~~~iA 166 (199)
||.++|+|||++|.|.|||+|+||++++.++.+|++|||+|||+++.|+ ++..|+++|||+||++-. ||+...
T Consensus 163 P~kVtGk~GSv~V~L~PAPrGtGiVag~v~KklL~lAGI~Dv~T~s~G~T~T~~NfaKATf~Al~kTYs~lTPdlW~ 239 (261)
T PTZ00070 163 PMKVTGKCGSVRVRLVPAPRGTGIVAAPTPKKILEFAGVEDVYTSSRGKTRTRGNFIMATFYALKKTYGFLTPDLWA 239 (261)
T ss_pred CEEEEEEECCEEEEEEECCCCCEEEECHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHC
T ss_conf 34889886737899876799961674608689998636440553067656320248999999999876164966622
No 8
>KOG2646 consensus
Probab=100.00 E-value=2.4e-41 Score=272.37 Aligned_cols=170 Identities=25% Similarity=0.303 Sum_probs=157.7
Q ss_pred CCCCCCCEEEEEEE--CCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCC-CHHHHHHHHHHHHHHCEEEEECCCCCC
Q ss_conf 00011602100002--244401278738467999998089983899704744-247899999999963012522016687
Q gi|254780244|r 16 EERDNSIVDRIVAI--NRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAR-EVPEAVRKATEAAKRNMISVSLLDGRT 92 (199)
Q Consensus 16 ~~~~~~l~ekvi~v--~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~-ev~~Ai~KA~~~Akknli~V~~~~~~T 92 (199)
.+...+|+++.+.+ +||..|++.|++-||++||||||+||.+|||+||+. +...|+.+|+..|.+||.+||+|+++|
T Consensus 176 ~~n~~Dfe~r~l~lvrr~~~~~~r~Gki~s~~~LVvvGn~nGaaG~~eGKa~~~~s~A~~ka~~rAv~~l~~ieRyE~rT 255 (396)
T KOG2646 176 GMNYLDFELRHLELVRRRVENQNRKGKIASMYALVVVGNGNGAAGLGEGKAADPNSPAIYKAIGRAVRNLGYIERYERRT 255 (396)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEECCCCCEEECCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 78800266778888876533002212001479999980587531002354767667889988888876327600103720
Q ss_pred CCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCC
Q ss_conf 62001103376799996367544850304899999980944100454689888899999999995069989999861997
Q gi|254780244|r 93 LHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172 (199)
Q Consensus 93 I~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~ 172 (199)
|++++.-+|..+++.|+.+|+|+|+.||+.+..||+++||+|+++|++||+|-+|+++|+|+||..|+|++|+|..+|++
T Consensus 256 iygDi~~r~~~~~l~mk~rp~GfGLrcn~il~kIC~~~GIKDis~kv~GsrN~m~i~k~~~e~l~~qet~qqlA~rkG~h 335 (396)
T KOG2646 256 IYGDIDDRFHEVRLDMKSRPDGFGLRCNPILIKICECAGIKDISGKVKGSRNEMNITKAAFEALALQETHQQLAYRKGLH 335 (396)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf 01431256666656665188865450058999999984630001124023007789999999876433267778745974
Q ss_pred HHHHHHHHHHCCC
Q ss_conf 9894454431245
Q gi|254780244|r 173 HSLLQARRVVSSK 185 (199)
Q Consensus 173 i~~~~~~~~~~~~ 185 (199)
++|+..+..++..
T Consensus 336 vVdVr~e~~~~t~ 348 (396)
T KOG2646 336 VVDVRGEVYRLTG 348 (396)
T ss_pred EEEECCCEEECCC
T ss_conf 8983251322354
No 9
>KOG0877 consensus
Probab=99.97 E-value=1.5e-30 Score=206.60 Aligned_cols=144 Identities=24% Similarity=0.353 Sum_probs=133.9
Q ss_pred CCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECC-------CCC
Q ss_conf 1160210000224440127873846799999808998389970474424789999999996301252201-------668
Q gi|254780244|r 19 DNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLL-------DGR 91 (199)
Q Consensus 19 ~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~-------~~~ 91 (199)
...|.|+||.|.+|+|||++|++.+|.|+|++||.||+||+|+.+++|+..||+.|+..|+.++++|++. ..|
T Consensus 48 g~slkdeVLkImpVqKqtrAGQrtRfKAfVaigD~~ghVGlgvk~sKeva~airgaiilaklsivpvrrgyw~~~~g~pH 127 (213)
T KOG0877 48 GASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPH 127 (213)
T ss_pred CCCHHHHHHEEEEECCCCCCCCCCCEEEEEEEEECCCCCCEEEEEHHHHHHHHHHHHHHHHEEEEEEECCCCCCCCCCCC
T ss_conf 63067665403330010234553304799997203683322123147889988677764330664432033334358875
Q ss_pred CCCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCH-HHHHHHHHHHHHCCCCH
Q ss_conf 762001103376799996367544850304899999980944100454689888-89999999999506998
Q gi|254780244|r 92 TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNP-HNVIRATFEVLRSQSHP 162 (199)
Q Consensus 92 TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~-~NvvkAt~~AL~~~~t~ 162 (199)
|+|.++.|+|+++.|.+.|+|+|+||++.+..+.+|+++||.|+++...|+++. -|.++|+|.|++...+.
T Consensus 128 t~~~kvtg~~~svlv~l~papRgtGivs~p~~kkll~mAGi~d~~t~~~G~t~tl~n~~ka~~~a~~~ty~~ 199 (213)
T KOG0877 128 TVPCKVTGDCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSY 199 (213)
T ss_pred CCCCCCCCCCCCCEEEEEECCCCCCEEECCCHHHHHHHCCCCCCCHHHCCCCHHHCHHHHHHHHHHHHHHHH
T ss_conf 566764566785338875169878545065017899863642001010366311010899999998866520
No 10
>pfam03719 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain.
Probab=99.93 E-value=3.3e-26 Score=180.11 Aligned_cols=74 Identities=53% Similarity=0.855 Sum_probs=72.8
Q ss_pred CCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf 11033767999963675448503048999999809441004546898888999999999950699899998619
Q gi|254780244|r 97 GVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRG 170 (199)
Q Consensus 97 v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG 170 (199)
|.|||++++|+|+|||+|+||+||+.++.|||++||+|+++|++||+|++|+++|||+||++|+|++++|+.||
T Consensus 1 V~gk~gs~~V~l~PAp~GtGiia~~~vr~il~~aGikDi~sK~~Gs~n~~N~~kAt~~AL~~~~t~~~ia~~rG 74 (74)
T pfam03719 1 VTGKFGAVKVLLKPAPPGTGIIAGGAVRAVLELAGIKDVLAKSLGSRNPINVVKATFDALKKLRTPEEVAALRG 74 (74)
T ss_pred CEEEECCEEEEEEECCCCCEEEECCHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCC
T ss_conf 97898128999998899972880809999999839264034537889778899999999990799999998639
No 11
>pfam00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain.
Probab=99.90 E-value=5.8e-24 Score=166.44 Aligned_cols=67 Identities=48% Similarity=0.785 Sum_probs=65.9
Q ss_pred CCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEEC
Q ss_conf 6021000022444012787384679999980899838997047442478999999999630125220
Q gi|254780244|r 21 SIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSL 87 (199)
Q Consensus 21 ~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~ 87 (199)
||+|+||+|+||||||++||++||+|||+|||+||+||||+|||.|+++||+||.++|++||++|||
T Consensus 1 ~~~e~vv~i~rV~k~t~~Gr~~~f~alvvVGn~~G~vG~G~gKa~ev~~Ai~KA~~~Ak~nmi~VpR 67 (67)
T pfam00333 1 DLEEKVLVINRVQKVTKGGRRFSFRALVVVGDKNGHVGLGEGKAKEVPGAIRKAIEDAKLNLIEVPR 67 (67)
T ss_pred CCHHEEEEEEEEEEEECCCCCEEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHCCEECCC
T ss_conf 9402489998664782588611589999997799839774664361899999999999867667789
No 12
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA; InterPro: IPR001566 This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from Escherichia coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA .; GO: 0003723 RNA binding, 0008173 RNA methyltransferase activity, 0006396 RNA processing.
Probab=83.80 E-value=2.2 Score=22.72 Aligned_cols=82 Identities=26% Similarity=0.342 Sum_probs=65.2
Q ss_pred CCC-HHHHHHHHHHHHHHC-EEEEECCCC---CCCCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEE
Q ss_conf 442-478999999999630-125220166---876200110337679999636754485030489999998094410045
Q gi|254780244|r 64 ARE-VPEAVRKATEAAKRN-MISVSLLDG---RTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAK 138 (199)
Q Consensus 64 a~e-v~~Ai~KA~~~Akkn-li~V~~~~~---~TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK 138 (199)
|-| ++++|++|.++|++| |-.|+.+.+ +.||.--..++..=+|+|=|...|= |...+++|+++=-.+=+|.
T Consensus 321 G~E~v~e~v~~a~~NAe~Ng~~N~~F~~g~~E~~~p~~~~e~~~~D~~llDPPR~GC---a~~~L~~I~~~kP~rivYV- 396 (434)
T TIGR00479 321 GVEVVPESVEDAKRNAELNGIANVEFLAGTLETVLPKQPWEGISPDVVLLDPPRKGC---AAEVLRTIIKLKPKRIVYV- 396 (434)
T ss_pred EEECCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCC---HHHHHHHHHHCCCEEEEEE-
T ss_conf 871437678999888886035320133312321101442226778988888889874---5899998862077059998-
Q ss_pred ECCCCCHHHHHHHH
Q ss_conf 46898888999999
Q gi|254780244|r 139 SIGSSNPHNVIRAT 152 (199)
Q Consensus 139 ~~GS~N~~NvvkAt 152 (199)
|.||-.+||=.
T Consensus 397 ---SCNP~TLARDl 407 (434)
T TIGR00479 397 ---SCNPATLARDL 407 (434)
T ss_pred ---ECCCHHHHHHH
T ss_conf ---44853479999
No 13
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=74.85 E-value=6.1 Score=20.02 Aligned_cols=73 Identities=22% Similarity=0.259 Sum_probs=48.2
Q ss_pred CCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCH----HHHHHHHHHHHHCCCCHHHHHHHCCCCHHHH
Q ss_conf 76799996367544850304899999980944100454689888----8999999999950699899998619979894
Q gi|254780244|r 102 GAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNP----HNVIRATFEVLRSQSHPRDVANRRGIKHSLL 176 (199)
Q Consensus 102 g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~----~NvvkAt~~AL~~~~t~~~iA~~RG~~i~~~ 176 (199)
..+++.-.|. -.==..+..+..-|+-+||+.+-.|..|.--| .|..--.-+.|.+-++|.+|+..-|+.+--+
T Consensus 50 ~~vK~Ig~P~--s~y~k~skkvlkaleq~gI~vIPvk~KgrGrprkyd~~t~~~i~emlr~gk~preIsk~lGIpirTv 126 (139)
T COG1710 50 PNVKVIGCPP--SLYPKVSKKVLKALEQMGIKVIPVKLKGRGRPRKYDRNTLLRIREMLRNGKTPREISKDLGIPIRTV 126 (139)
T ss_pred CCCCEECCCC--HHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH
T ss_conf 9851634881--1326789999988986895686553047899754345489999999984998778888609862206
No 14
>PRK13186 lpxC UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=53.79 E-value=8.7 Score=19.07 Aligned_cols=81 Identities=16% Similarity=0.123 Sum_probs=34.1
Q ss_pred CEEEEEEECCCCEECCCCEEEEE--------------EEEEEECCCCCCEEEEECCCCCHHHHHHHHHHH---HHHCEEE
Q ss_conf 02100002244401278738467--------------999998089983899704744247899999999---9630125
Q gi|254780244|r 22 IVDRIVAINRVSTALPGGRRFAF--------------SVLVVVGDTKSKVGFAHSTAREVPEAVRKATEA---AKRNMIS 84 (199)
Q Consensus 22 l~ekvi~v~RV~k~tkgGr~~sf--------------~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~---Akknli~ 84 (199)
..+.|.+..|-|....+|...+- .+++-+ |+ --+=+-=|.|.+...||++|-.. +.+..+.
T Consensus 53 ~~~~V~~t~~~T~L~~~g~~V~TVEHLLAAL~glgIDN~~Iei-dg-~EvPIlDGSA~~fv~~i~~aGi~~q~~~r~~~~ 130 (299)
T PRK13186 53 RADNVGDTRLCTTLGNGGVRVSTVEHLMAALAGLGIDNAIIEV-DG-PEVPIMDGSAAPFVFLIQSAGIVEQNAPKKFIR 130 (299)
T ss_pred EHHHCCCCCCCCEEECCCEEEEEHHHHHHHHHHCCCCEEEEEE-CC-CCCCCCCCCHHHHHHHHHHCCCEECCCCCCEEE
T ss_conf 7410567776378805984997499999999857874189996-88-627601586699999987448450467420489
Q ss_pred EECCCCCCCCEECCCCCCCEEEEEEECC
Q ss_conf 2201668762001103376799996367
Q gi|254780244|r 85 VSLLDGRTLHHDGVGRHGAGKVIMRSAM 112 (199)
Q Consensus 85 V~~~~~~TI~h~v~gk~g~~kV~l~Pap 112 (199)
|-.++..+.+...+.+.|..
T Consensus 131 --------I~~~i~v~~~~~~i~~~P~~ 150 (299)
T PRK13186 131 --------IKKPVRVEDGDKFAELLPYD 150 (299)
T ss_pred --------ECCEEEEEECCEEEEEECCC
T ss_conf --------57709999699999993799
No 15
>cd00308 enolase_like Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase.
Probab=51.99 E-value=19 Score=16.94 Aligned_cols=101 Identities=20% Similarity=0.183 Sum_probs=55.0
Q ss_pred CCCEEEEE-EEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCCCCCEECCCCCCCEEEEEEECCCCC
Q ss_conf 78738467-99999808998389970474424789999999996301252201668762001103376799996367544
Q gi|254780244|r 37 PGGRRFAF-SVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGT 115 (199)
Q Consensus 37 kgGr~~sf-~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~TI~h~v~gk~g~~kV~l~Pap~G~ 115 (199)
..|....+ ..+|.+=..+|.+|||. +.+||+=|.+++.-....+|+++- +-|++. .+|....
T Consensus 17 ~~~~~~~~~~~~V~l~td~G~~G~Ge-----a~said~AlwDl~gK~~~~Pv~~l------lgG~~~-~~v~~y~----- 79 (229)
T cd00308 17 AGGTADTNDTVLVKLTTDSGVVGWGE-----VISGIDMALWDLAAKALGVPLAEL------LGGGSR-DRVPAYG----- 79 (229)
T ss_pred CCEEEEECEEEEEEEEECCCCEEEEH-----HHHHHHHHHHHHHHHHCCCCHHHH------HCCCCC-CCCCCCH-----
T ss_conf 47899822179999998999967426-----999999999989798859969998------088445-7775506-----
Q ss_pred CCCCCHHHHHHHHHHCCC-CCCEEECCCCCHHHHHHHHHHHHHC
Q ss_conf 850304899999980944-1004546898888999999999950
Q gi|254780244|r 116 GVIAGGAIRAVCEVLGMH-DVVAKSIGSSNPHNVIRATFEVLRS 158 (199)
Q Consensus 116 Gi~a~~~vr~il~laGI~-dv~aK~~GS~N~~NvvkAt~~AL~~ 158 (199)
.-..++.+-+..|=. ++..-..+.=+ ..-+..+.+.|..
T Consensus 80 ---s~~~v~~ir~~~G~~~~l~vDaN~~~~-~~~A~~~~~~l~~ 119 (229)
T cd00308 80 ---SIERVRAVREAFGPDARLAVDANGAWT-PKEAIRLIRALEK 119 (229)
T ss_pred ---HHHHHHHHHHHCCCCCEEEEECCCCCC-HHHHHHHHHHHHH
T ss_conf ---999999999966999869998999999-9999999998521
No 16
>pfam03331 LpxC UDP-3-O-acyl N-acetylglycosamine deacetylase. The enzymes in this family catalyse the second step in the biosynthetic pathway for lipid A.
Probab=51.59 E-value=9.9 Score=18.71 Aligned_cols=49 Identities=10% Similarity=0.087 Sum_probs=20.6
Q ss_pred CEEEEECCCCCHHHHHHHHHHHH---HHCEEEEECCCCCCCCEECCCCCCCEEEEEEECC
Q ss_conf 38997047442478999999999---6301252201668762001103376799996367
Q gi|254780244|r 56 KVGFAHSTAREVPEAVRKATEAA---KRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAM 112 (199)
Q Consensus 56 ~vG~G~GKa~ev~~Ai~KA~~~A---kknli~V~~~~~~TI~h~v~gk~g~~kV~l~Pap 112 (199)
-+=+-=|.|.+...+|++|-... .+..+. |..++....+.+.+.+.|..
T Consensus 98 EvPIlDGSa~~fv~~i~~aGi~eq~~~r~~~~--------i~~~v~v~~~~~~i~~~P~~ 149 (276)
T pfam03331 98 EIPIMDGSALPFVELIDQAGIKEQEAAKKIIR--------IKEPVYVQDGDKFLAAFPSD 149 (276)
T ss_pred CCCCCCCCHHHHHHHHHHCCCCCCCCCCCEEE--------ECCCEEEEECCEEEEEECCC
T ss_conf 88833787899999999709876677541478--------55608999899999997689
No 17
>COG2265 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=49.92 E-value=21 Score=16.74 Aligned_cols=98 Identities=21% Similarity=0.238 Sum_probs=56.2
Q ss_pred CCCCEEEEECC------CCC-HHHHHHHHHHHHHHCEEE-EECCCCC--CCCEECCCCCCCEEEEEEECCCCCCCCCCHH
Q ss_conf 99838997047------442-478999999999630125-2201668--7620011033767999963675448503048
Q gi|254780244|r 53 TKSKVGFAHST------ARE-VPEAVRKATEAAKRNMIS-VSLLDGR--TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGA 122 (199)
Q Consensus 53 ~~G~vG~G~GK------a~e-v~~Ai~KA~~~Akknli~-V~~~~~~--TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~ 122 (199)
|.|.+|+..++ |-| +++|+..|..+|+.|=+. +....+. .+.-...--+.-..|++-|-..|- ....
T Consensus 303 GvG~f~l~lA~~~~~V~gvEi~~~aV~~A~~NA~~n~i~N~~f~~~~ae~~~~~~~~~~~~d~VvvDPPR~G~---~~~~ 379 (432)
T COG2265 303 GVGTFGLPLAKRVKKVHGVEISPEAVEAAQENAAANGIDNVEFIAGDAEEFTPAWWEGYKPDVVVVDPPRAGA---DREV 379 (432)
T ss_pred CCCHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHCCCCCCCEEEECCCCCCC---CHHH
T ss_conf 8870135531246579999648999999999999739887799958688886510025799989989999999---9899
Q ss_pred HHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHH
Q ss_conf 99999980944100454689888899999999995
Q gi|254780244|r 123 IRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLR 157 (199)
Q Consensus 123 vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~ 157 (199)
++.++++.=.+=++. |.||...++-.-.-..
T Consensus 380 lk~l~~~~p~~IvYV----SCNP~TlaRDl~~L~~ 410 (432)
T COG2265 380 LKQLAKLKPKRIVYV----SCNPATLARDLAILAS 410 (432)
T ss_pred HHHHHHCCCCCEEEE----ECCHHHHHHHHHHHHH
T ss_conf 999985589868999----7687888989999985
No 18
>PRK13188 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed
Probab=45.95 E-value=14 Score=17.85 Aligned_cols=16 Identities=19% Similarity=0.302 Sum_probs=7.5
Q ss_pred EEECCCCCHHHHHHHH
Q ss_conf 9704744247899999
Q gi|254780244|r 59 FAHSTAREVPEAVRKA 74 (199)
Q Consensus 59 ~G~GKa~ev~~Ai~KA 74 (199)
+-=|.|.+...||++|
T Consensus 103 IlDGSA~~Fv~~I~~a 118 (465)
T PRK13188 103 IMDGSSMPFVEAIERA 118 (465)
T ss_pred CCCCCHHHHHHHHHHH
T ss_conf 5378789999999972
No 19
>pfam12327 FtsZ_C FtsZ family, C-terminal domain. This family includes the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea.
Probab=42.22 E-value=21 Score=16.69 Aligned_cols=22 Identities=18% Similarity=0.283 Sum_probs=14.1
Q ss_pred CCCEEEEECCCCC-HHHHHHHHH
Q ss_conf 9838997047442-478999999
Q gi|254780244|r 54 KSKVGFAHSTARE-VPEAVRKAT 75 (199)
Q Consensus 54 ~G~vG~G~GKa~e-v~~Ai~KA~ 75 (199)
.-++|+|.+++.+ +..|+++|+
T Consensus 2 ~A~iGiG~a~G~~ra~~Av~~Al 24 (97)
T pfam12327 2 VAMMGTGEASGEDRAEEAAEAAI 24 (97)
T ss_pred EEEEEEEEECCCCHHHHHHHHHH
T ss_conf 69999899779869999999998
No 20
>PRK13846 putative glycerol-3-phosphate acyltransferase PlsX; Provisional
Probab=42.17 E-value=28 Score=16.01 Aligned_cols=40 Identities=15% Similarity=0.178 Sum_probs=28.6
Q ss_pred HHCCCCCCEEECCCCCHHHHHHHHHHHHHCC--CCHHHHHHH
Q ss_conf 8094410045468988889999999999506--998999986
Q gi|254780244|r 129 VLGMHDVVAKSIGSSNPHNVIRATFEVLRSQ--SHPRDVANR 168 (199)
Q Consensus 129 laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~--~t~~~iA~~ 168 (199)
|.|+.-+..|.+||+++..+..|...|.... .-.+.|++.
T Consensus 273 LLGl~Givvk~HGsS~~~a~~nAI~~a~~~~~~~v~~kI~~~ 314 (316)
T PRK13846 273 VCGLSKLVIKCHGKACGTSLFGGISGSIDLARARVCSRILSR 314 (316)
T ss_pred EEECCCCEEECCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_conf 870784389758999989999999999999996778999986
No 21
>TIGR00182 plsX fatty acid/phospholipid synthesis protein PlsX; InterPro: IPR003664 The plsX gene is part of the bacterial fab gene cluster which encodes several key fatty acid biosynthetic enzymes . The plsX gene encodes a poorly understood enzyme of phospholipid metabolism .; GO: 0003824 catalytic activity, 0006633 fatty acid biosynthetic process.
Probab=40.00 E-value=18 Score=17.20 Aligned_cols=46 Identities=28% Similarity=0.346 Sum_probs=33.7
Q ss_pred HHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHH
Q ss_conf 809441004546898888999999999950699899998619979894
Q gi|254780244|r 129 VLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLL 176 (199)
Q Consensus 129 laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~i~~~ 176 (199)
|+|++-..-|+|||.|.-.+..|...|-..+++ ||+.+=-..+.++
T Consensus 291 L~Gl~~~viksHGss~~~a~~~AIrqA~~av~~--qv~~~I~~~~~~~ 336 (344)
T TIGR00182 291 LLGLNKLVIKSHGSSDSRAIFSAIRQAKEAVKS--QVINRIKSSLESL 336 (344)
T ss_pred EECCCCEEEEECCCCCHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
T ss_conf 761473178723741035799999999999987--7999999988640
No 22
>TIGR02406 ectoine_EctA L-2,4-diaminobutyric acid acetyltransferase; InterPro: IPR012772 This enzyme family is the EctA of ectoine biosynthesis. Ectoine is a compatible solute, analogous to trehalose, betaines, etc., found often in halotolerant organisms. EctA is L-2,4-diaminobutyric acid acetyltransferase, also called DABA acetyltransferase.; GO: 0008415 acyltransferase activity, 0019491 ectoine biosynthetic process.
Probab=39.97 E-value=30 Score=15.80 Aligned_cols=54 Identities=24% Similarity=0.326 Sum_probs=44.0
Q ss_pred EEEEECCCCCCCCCCHHHHHHHHHHCCCCCCE---EECCCCCHHHHH-HHHHHHHHCCC
Q ss_conf 99963675448503048999999809441004---546898888999-99999995069
Q gi|254780244|r 106 VIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVA---KSIGSSNPHNVI-RATFEVLRSQS 160 (199)
Q Consensus 106 V~l~Pap~G~Gi~a~~~vr~il~laGI~dv~a---K~~GS~N~~Nvv-kAt~~AL~~~~ 160 (199)
|=+-|+.+|+|| |.+.+-.||+--...++.. -+.-+=+|=|-+ +|+|++|-+-+
T Consensus 72 VAV~~~~RG~GL-A~rll~all~R~~~~~v~~~I~~~EtTiTPdN~AS~aLF~~La~~~ 129 (162)
T TIGR02406 72 VAVDPKARGKGL-ASRLLEALLERVALERVRHCIQAVETTITPDNEASRALFKKLARRR 129 (162)
T ss_pred EEECCCCCCCHH-HHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHC
T ss_conf 542713143168-9999999761033313798210466210766668999999876542
No 23
>PRK05463 hypothetical protein; Provisional
Probab=39.01 E-value=31 Score=15.70 Aligned_cols=84 Identities=23% Similarity=0.315 Sum_probs=59.6
Q ss_pred CCCCEEEEECCCCCHHHHHHHHHHHHHHCE---EEEECCCCCCCCEECCCCCCCEE-EEEEECCC---------------
Q ss_conf 998389970474424789999999996301---25220166876200110337679-99963675---------------
Q gi|254780244|r 53 TKSKVGFAHSTAREVPEAVRKATEAAKRNM---ISVSLLDGRTLHHDGVGRHGAGK-VIMRSAMA--------------- 113 (199)
Q Consensus 53 ~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl---i~V~~~~~~TI~h~v~gk~g~~k-V~l~Pap~--------------- 113 (199)
..-+|+|-+|.+=.+..|+.+|-.-- +|+ ..|+.|. .+|+..-.|.|.+.- |-|+|-|+
T Consensus 110 ~dD~V~FliGCSFSFE~aL~~aGip~-rhi~~~~nVpMY~-Tni~c~~aG~F~g~mVVSMRP~~~~~v~~a~~iT~~~p~ 187 (264)
T PRK05463 110 RDDLVTFLIGCSFSFEEALLEAGIPV-RHIEEGRNVPMYR-TNIACRPAGRFSGPMVVSMRPIPAADAIRAVQITSRFPA 187 (264)
T ss_pred CCCEEEEEEECCCCHHHHHHHCCCCC-CCCCCCCCCCEEE-CCCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCC
T ss_conf 44758998406414899999879985-3356898447075-587764677766873787403798998899967632765
Q ss_pred --CCCCCCCHHHHHHHHHHCCCCCCEEECCCC
Q ss_conf --448503048999999809441004546898
Q gi|254780244|r 114 --GTGVIAGGAIRAVCEVLGMHDVVAKSIGSS 143 (199)
Q Consensus 114 --G~Gi~a~~~vr~il~laGI~dv~aK~~GS~ 143 (199)
|.-|..|.+ +.+||+|+..--+|-.
T Consensus 188 ~HGaPihiGdP-----~~iGI~Dl~~PD~Gd~ 214 (264)
T PRK05463 188 VHGAPVHIGDP-----AAIGIADLARPDFGDA 214 (264)
T ss_pred CCCCCEECCCH-----HHCCCCCCCCCCCCCC
T ss_conf 57884131886-----5627455789999997
No 24
>pfam02624 YcaO YcaO-like family.
Probab=37.54 E-value=33 Score=15.56 Aligned_cols=50 Identities=8% Similarity=-0.064 Sum_probs=38.4
Q ss_pred ECCCCEEEEEEEEEEEC-CCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEE
Q ss_conf 12787384679999980-899838997047442478999999999630125
Q gi|254780244|r 35 ALPGGRRFAFSVLVVVG-DTKSKVGFAHSTAREVPEAVRKATEAAKRNMIS 84 (199)
Q Consensus 35 ~tkgGr~~sf~alvvvG-n~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~ 84 (199)
.|-...+..|.|++.-- ...+.+-+|.|.+.+...|+.||+..|.+....
T Consensus 181 ~t~d~giPvv~a~~~~~~~~~~~~~~G~ga~~d~~~A~~rAl~Ea~q~~~~ 231 (332)
T pfam02624 181 ATLDLGIPVVAAVLDDTDPDPGLLVAGFGAHLDPEIALERALTEAAQSRLT 231 (332)
T ss_pred CCCCCCCEEEEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 578989648999997578998546999657999999999999999988898
No 25
>PHA02448 hypothetical protein
Probab=36.38 E-value=24 Score=16.43 Aligned_cols=40 Identities=28% Similarity=0.555 Sum_probs=29.1
Q ss_pred CCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCE
Q ss_conf 873846799999808998389970474424789999999996301
Q gi|254780244|r 38 GGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNM 82 (199)
Q Consensus 38 gGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl 82 (199)
||--.+..+. | --..|||..-+++.+.|++.|+-+|.+|-
T Consensus 69 gGlWIrLTvc---g--vTR~GYG~~qG~~~~d~vK~aIGdAlRnA 108 (192)
T PHA02448 69 GGLWIRLTLC---G--VTRIGYGDAGGKKGPNAVKEAIGDALRNA 108 (192)
T ss_pred CCEEEEEEEE---C--CEECCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 9668999972---1--00002467666763158899988999998
No 26
>PRK05331 putative glycerol-3-phosphate acyltransferase PlsX; Provisional
Probab=36.36 E-value=34 Score=15.45 Aligned_cols=29 Identities=31% Similarity=0.462 Sum_probs=22.2
Q ss_pred HHCCCCCCEEECCCCCHHHHHHHHHHHHH
Q ss_conf 80944100454689888899999999995
Q gi|254780244|r 129 VLGMHDVVAKSIGSSNPHNVIRATFEVLR 157 (199)
Q Consensus 129 laGI~dv~aK~~GS~N~~NvvkAt~~AL~ 157 (199)
+.|+.-+..|++||+++..+..|...|..
T Consensus 288 lLGl~g~vik~HG~S~~~a~~~AI~~A~~ 316 (317)
T PRK05331 288 LLGLNGIVIKSHGSSDAKAFKNAIRQAVE 316 (317)
T ss_pred EECCCCCEEECCCCCCHHHHHHHHHHHHH
T ss_conf 97488228981789998999999999974
No 27
>cd03315 MLE_like Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and residues that can function as general acid/base catalysts, a Lys-X-Lys motif and another conserved lysine. Despite these conserved residues, the members of the MLE subgroup, like muconate lactonizing enzyme, o-succinylbenzoate synthase (OSBS) and N-acylamino acid racemase (NAAAR), catalyze different reactions.
Probab=35.89 E-value=35 Score=15.40 Aligned_cols=108 Identities=19% Similarity=0.099 Sum_probs=56.8
Q ss_pred CCCEEEEE-EEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCCCCCEECCCCCC-CEEEEEEECCCC
Q ss_conf 78738467-9999980899838997047442478999999999630125220166876200110337-679999636754
Q gi|254780244|r 37 PGGRRFAF-SVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHG-AGKVIMRSAMAG 114 (199)
Q Consensus 37 kgGr~~sf-~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~TI~h~v~gk~g-~~kV~l~Pap~G 114 (199)
..|..... ..+|-|=+.+|.+|+|.+ ...||+=|.++..-...-+|+++ +.|.+. ...+... -+.+
T Consensus 17 ~~~~~~~~~~~~v~v~~~~G~~G~GE~----a~said~AlwDl~gK~~~~Pv~~-------LlGg~~~~i~~~~~-~~~~ 84 (265)
T cd03315 17 ASGTLTTADHVLLRLHTDDGLVGWAEA----TKAAVDMALWDLWGKRLGVPVYL-------LLGGYRDRVRVAHM-LGLG 84 (265)
T ss_pred CCEEEEEEEEEEEEEEECCCCEEEEEC----HHHHHHHHHHHHHHHHCCCCHHH-------HCCCCCCCEEEEEE-CCCC
T ss_conf 489999868999999979989898624----88999999999999981988999-------72999997699997-7999
Q ss_pred CCCCCCHHHHHHHHHHCCCCCCEEECCC-CCHHHHHHHHHHHHH
Q ss_conf 4850304899999980944100454689-888899999999995
Q gi|254780244|r 115 TGVIAGGAIRAVCEVLGMHDVVAKSIGS-SNPHNVIRATFEVLR 157 (199)
Q Consensus 115 ~Gi~a~~~vr~il~laGI~dv~aK~~GS-~N~~NvvkAt~~AL~ 157 (199)
+-=-....++...+ .|++-+..|+-.. ..-+..+++.-+++-
T Consensus 85 ~~~~~~~~~~~~~~-~G~~~~Kikvg~~~~~d~~~v~~ir~~~g 127 (265)
T cd03315 85 EPAEVAEEARRALE-AGFRTFKLKVGRDPARDVAVVAALREAVG 127 (265)
T ss_pred CHHHHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHHHCC
T ss_conf 99999999999997-59998999768985999999999998729
No 28
>PRK00094 gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated
Probab=31.68 E-value=27 Score=16.11 Aligned_cols=57 Identities=14% Similarity=0.099 Sum_probs=31.6
Q ss_pred HHHHHHHHHCCCCCCEEECC--CCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf 89999998094410045468--988889999999999506998999986199798944544312
Q gi|254780244|r 122 AIRAVCEVLGMHDVVAKSIG--SSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQARRVVS 183 (199)
Q Consensus 122 ~vr~il~laGI~dv~aK~~G--S~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~i~~~~~~~~~~ 183 (199)
...+++.++|+=|+..-..+ |||.. +=..|-+-.+++++.+..|..+.=+...+.+|
T Consensus 231 ~~~T~~glaG~GDL~lTc~s~~SRN~~-----~G~~lg~g~~~~~~~~~~~~~~EG~~t~~~v~ 289 (325)
T PRK00094 231 NPETFLGLAGLGDLILTCTSPLSRNRR-----FGLALGQGKSLEDALEEIGQVAEGVRTAKAVY 289 (325)
T ss_pred CCCCCCCCCCHHHHHHHCCCCCCCCHH-----HHHHHHCCCCHHHHHHHCCCEECHHHHHHHHH
T ss_conf 834422563076325333788997289-----99999579999999997599701299999999
No 29
>pfam07286 DUF1445 Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
Probab=31.20 E-value=39 Score=15.08 Aligned_cols=80 Identities=23% Similarity=0.319 Sum_probs=54.1
Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHCE---EEEECCCCCCCCEECCCCCCCE-EEEEEECCC-----------------CC
Q ss_conf 89970474424789999999996301---2522016687620011033767-999963675-----------------44
Q gi|254780244|r 57 VGFAHSTAREVPEAVRKATEAAKRNM---ISVSLLDGRTLHHDGVGRHGAG-KVIMRSAMA-----------------GT 115 (199)
Q Consensus 57 vG~G~GKa~ev~~Ai~KA~~~Akknl---i~V~~~~~~TI~h~v~gk~g~~-kV~l~Pap~-----------------G~ 115 (199)
|.|-+|.+-.+..|+.+|-..- +|+ ..|+.|. .+|+..-.|.|.+. -|-|||-|+ |.
T Consensus 1 V~F~iGCSFSFE~aL~~aGip~-rhi~~~~nV~MY~-Tni~~~~aG~F~g~mVVSMRp~~~~~~~~a~~iT~~fp~~HGa 78 (143)
T pfam07286 1 VAFLIGCSFSFEEALLAAGIPV-RHIEEGRNVPMYR-TNIPCRPAGPFSGPMVVSMRPIPADDVIRAVQITSRFPAVHGA 78 (143)
T ss_pred CEEEEECCCCHHHHHHHCCCCC-CCCCCCCCCCEEE-CCCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCCCCC
T ss_conf 9799755305899999879985-3323586668386-5865535677567547874038989988999676238554787
Q ss_pred CCCCCHHHHHHHHHHCCCCCCEEECCCC
Q ss_conf 8503048999999809441004546898
Q gi|254780244|r 116 GVIAGGAIRAVCEVLGMHDVVAKSIGSS 143 (199)
Q Consensus 116 Gi~a~~~vr~il~laGI~dv~aK~~GS~ 143 (199)
-|..|.+ +.+||+|+..--+|..
T Consensus 79 PihiGdP-----~~iGI~Dl~~PD~Gd~ 101 (143)
T pfam07286 79 PVHIGDP-----ALIGIKDLSKPDFGDA 101 (143)
T ss_pred CEEECCH-----HHCCCCCCCCCCCCCC
T ss_conf 3240897-----6728444689989987
No 30
>TIGR03247 glucar-dehydr glucarate dehydratase. Glucarate dehydratase converts D-glucarate (and L-idarate, a stereoisomer) to 5-dehydro-4-deoxyglucarate which is subsequently acted on by GarL, tartronate semialdehyde reductase and glycerate kinase (, GenProp0716). The E. coli enzyme has been well-characterized.
Probab=30.41 E-value=33 Score=15.56 Aligned_cols=44 Identities=20% Similarity=0.343 Sum_probs=30.8
Q ss_pred EEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEEC
Q ss_conf 84679999980899838997047442478999999999630125220
Q gi|254780244|r 41 RFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSL 87 (199)
Q Consensus 41 ~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~ 87 (199)
-+-.|.+|++=+-.|.+|+|...+.+ ++.++.++++--++-.+.
T Consensus 30 p~f~R~Iv~l~~~~G~~GvGE~~Gg~---~~~~~L~~~~~~vvG~~v 73 (441)
T TIGR03247 30 PFFTRNIVILTDSSGNTGVGEVPGGE---KIRATLEDARPLVVGKPL 73 (441)
T ss_pred CCEEEEEEEEEECCCCEEECCCCCCH---HHHHHHHHHHHHHCCCCH
T ss_conf 85367899999789975420288978---999999997888568977
No 31
>PRK13187 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=30.13 E-value=31 Score=15.72 Aligned_cols=18 Identities=17% Similarity=0.182 Sum_probs=10.1
Q ss_pred EEEECCCCCHHHHHHHHH
Q ss_conf 997047442478999999
Q gi|254780244|r 58 GFAHSTAREVPEAVRKAT 75 (199)
Q Consensus 58 G~G~GKa~ev~~Ai~KA~ 75 (199)
=+-=|.|.+...+|++|-
T Consensus 113 PIlDGSa~~fv~~i~~aG 130 (305)
T PRK13187 113 PILDGSATPWVDAIRACG 130 (305)
T ss_pred CCCCCCHHHHHHHHHHCC
T ss_conf 713686299999987448
No 32
>PRK12371 ribonuclease III; Reviewed
Probab=29.98 E-value=43 Score=14.81 Aligned_cols=40 Identities=20% Similarity=0.040 Sum_probs=27.0
Q ss_pred CEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCE
Q ss_conf 73846799999808998389970474424789999999996301
Q gi|254780244|r 39 GRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNM 82 (199)
Q Consensus 39 Gr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl 82 (199)
.....|.+-|.+++.. +|.|.|..-..|=+.|..+|.+.+
T Consensus 190 ~h~~~F~v~v~i~~~~----~~~G~G~SKK~AEq~AA~~aL~k~ 229 (235)
T PRK12371 190 DHDPLFTVEVEVKGFA----PETGEGRSKRIAEQVAAEKMLERE 229 (235)
T ss_pred CCCCEEEEEEEECCEE----EEEEEECCHHHHHHHHHHHHHHHH
T ss_conf 9898089999999968----899870899999999999999985
No 33
>cd00048 DSRM Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
Probab=29.52 E-value=44 Score=14.76 Aligned_cols=43 Identities=28% Similarity=0.215 Sum_probs=29.8
Q ss_pred CCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCE
Q ss_conf 27873846799999808998389970474424789999999996301
Q gi|254780244|r 36 LPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNM 82 (199)
Q Consensus 36 tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl 82 (199)
........|.+-|.+++ .-++.|.+..-..|-+.|...|.+.|
T Consensus 26 ~g~~h~~~F~~~v~i~~----~~~~~g~g~sKK~Aeq~AA~~aL~~L 68 (68)
T cd00048 26 EGPDHAPRFTVEVTVGG----KITGEGEGSSKKEAKQNAAEAALRKL 68 (68)
T ss_pred CCCCCCCEEEEEEEECC----EEEECCCCCCHHHHHHHHHHHHHHHC
T ss_conf 08987734999999999----88615777769999999999999849
No 34
>COG0131 HisB Imidazoleglycerol-phosphate dehydratase [Amino acid transport and metabolism]
Probab=29.36 E-value=44 Score=14.74 Aligned_cols=92 Identities=14% Similarity=0.098 Sum_probs=59.1
Q ss_pred CCHHHHHHHHHHHHHHCEEEEECCCCCCCC---------EECCCCCCCEEEEEEECCCCCCC---CCCHHHHHHHHHHCC
Q ss_conf 424789999999996301252201668762---------00110337679999636754485---030489999998094
Q gi|254780244|r 65 REVPEAVRKATEAAKRNMISVSLLDGRTLH---------HDGVGRHGAGKVIMRSAMAGTGV---IAGGAIRAVCEVLGM 132 (199)
Q Consensus 65 ~ev~~Ai~KA~~~Akknli~V~~~~~~TI~---------h~v~gk~g~~kV~l~Pap~G~Gi---~a~~~vr~il~laGI 132 (199)
-|+..|+-.|+.+|.-+-.-|.||-+..|| -|+.|+-.-+.=.=.+.+..-++ ....-.++++.-+||
T Consensus 70 ED~gIaLGqAl~~AlGdk~GI~Rfg~~~vPMDEaL~~~~vDlSGRp~lv~~~~f~~~~vG~~~te~v~hFf~sla~~a~i 149 (195)
T COG0131 70 EDTGIALGQALKEALGDKRGIRRFGSAYVPMDEALARVAVDLSGRPYLVFNAEFTREKVGDFDTELVEHFFRSLANNAGI 149 (195)
T ss_pred HHHHHHHHHHHHHHHCCCCCCEECCCCCCCCHHHHHEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 88998999999998564215311155424626543105785389825999455373411786545399999999974675
Q ss_pred CCCCEEECCCCCHHHHHHHHHHHHH
Q ss_conf 4100454689888899999999995
Q gi|254780244|r 133 HDVVAKSIGSSNPHNVIRATFEVLR 157 (199)
Q Consensus 133 ~dv~aK~~GS~N~~NvvkAt~~AL~ 157 (199)
. +...++.-.|++..+-|.|+|+-
T Consensus 150 t-lHi~~~~G~N~HH~iEa~FKA~a 173 (195)
T COG0131 150 T-LHLSVLYGKNDHHIIEALFKAFA 173 (195)
T ss_pred E-EEEEECCCCCHHHHHHHHHHHHH
T ss_conf 7-99995258870899999999999
No 35
>pfam02504 FA_synthesis Fatty acid synthesis protein. The plsX gene is part of the bacterial fab gene cluster which encodes several key fatty acid biosynthetic enzymes. The exact function of the plsX protein in fatty acid synthesis is unknown.
Probab=28.41 E-value=43 Score=14.82 Aligned_cols=30 Identities=27% Similarity=0.430 Sum_probs=22.7
Q ss_pred HHCCCCCCEEECCCCCHHHHHHHHHHHHHC
Q ss_conf 809441004546898888999999999950
Q gi|254780244|r 129 VLGMHDVVAKSIGSSNPHNVIRATFEVLRS 158 (199)
Q Consensus 129 laGI~dv~aK~~GS~N~~NvvkAt~~AL~~ 158 (199)
+.|+.-+..|.+||+++..+..|...|...
T Consensus 285 llGl~g~vvk~HG~S~~~a~~naI~~a~~~ 314 (322)
T pfam02504 285 LLGLSGLVIKSHGSADKTAIFAAIRQAIEL 314 (322)
T ss_pred EECCCCCEEECCCCCCHHHHHHHHHHHHHH
T ss_conf 975884389757999989999999999999
No 36
>PRK11568 hypothetical protein; Provisional
Probab=27.37 E-value=42 Score=14.87 Aligned_cols=42 Identities=24% Similarity=0.240 Sum_probs=29.6
Q ss_pred CCCCCCCCCHHHHHHHHHHCCCCCCE---EECCCC--CHHHHHHHHHHHH
Q ss_conf 75448503048999999809441004---546898--8889999999999
Q gi|254780244|r 112 MAGTGVIAGGAIRAVCEVLGMHDVVA---KSIGSS--NPHNVIRATFEVL 156 (199)
Q Consensus 112 p~G~Gi~a~~~vr~il~laGI~dv~a---K~~GS~--N~~NvvkAt~~AL 156 (199)
|.|| ||.++..+|+-.++.|+.+ +-+|=. -.--++||.-.|.
T Consensus 75 PsGT---AG~PiL~vL~~~~l~nv~vVVtRYFGGikLG~GGLvRAY~~aa 121 (204)
T PRK11568 75 PAGT---AGKPMLAQLMGSGVGEITAVVVRYYGGILLGTGGLVKAYGGGV 121 (204)
T ss_pred CCCC---CCHHHHHHHHHCCCCCEEEEEEEEECCEEECCCHHHHHHHHHH
T ss_conf 0899---9505899996389976999999975667706526789999999
No 37
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis. The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=26.94 E-value=29 Score=15.87 Aligned_cols=35 Identities=20% Similarity=0.178 Sum_probs=22.0
Q ss_pred CCCCCCHHH-HHHHHHHCCCCCCEEECC---CCCHHHHH
Q ss_conf 485030489-999998094410045468---98888999
Q gi|254780244|r 115 TGVIAGGAI-RAVCEVLGMHDVVAKSIG---SSNPHNVI 149 (199)
Q Consensus 115 ~Gi~a~~~v-r~il~laGI~dv~aK~~G---S~N~~Nvv 149 (199)
||+=.++-. --=|+.|||.=|-|+|++ =||.+|+=
T Consensus 58 FGcGSSREQA~~ALK~aGv~aviA~SFARIFYRNAIN~G 96 (159)
T TIGR02087 58 FGCGSSREQAALALKAAGVAAVIAESFARIFYRNAINIG 96 (159)
T ss_pred CCCCCCHHHHHHHHHHCCEEEEEEEECCCHHHHHHHHCC
T ss_conf 477887788999997479048985201660103233325
No 38
>KOG4328 consensus
Probab=25.95 E-value=51 Score=14.40 Aligned_cols=34 Identities=29% Similarity=0.319 Sum_probs=23.9
Q ss_pred EEEECCCCEECCCCEEEEEE-------EEEEECCCCCCEEEE
Q ss_conf 00022444012787384679-------999980899838997
Q gi|254780244|r 26 IVAINRVSTALPGGRRFAFS-------VLVVVGDTKSKVGFA 60 (199)
Q Consensus 26 vi~v~RV~k~tkgGr~~sf~-------alvvvGn~~G~vG~G 60 (199)
.+.+--|.|+| -||+++.. -||++||..|.||+=
T Consensus 175 ~~~~~~v~kv~-~~Rit~l~fHPt~~~~lva~GdK~G~VG~W 215 (498)
T KOG4328 175 DYRILNVAKVT-DRRITSLAFHPTENRKLVAVGDKGGQVGLW 215 (498)
T ss_pred CCEECCEEEEC-CCCEEEEEECCCCCCEEEEECCCCCCEEEE
T ss_conf 10003156740-562578886356861189971577727787
No 39
>cd01684 Tet_like_IV EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit the accommodation of aminoacyl-tRNA into ribosomal A site and therefore prevent the addition of new amino acids to the growing polypeptide. RPPs Tet(M) confer tetracycline resistance by releasing tetracycline from the ribosome and thereby freeing the ribosome from inhibitory effects of the drug, such that aa-tRNA can bind to the A site and protein synthesis can continue.
Probab=25.66 E-value=52 Score=14.34 Aligned_cols=42 Identities=14% Similarity=0.054 Sum_probs=27.1
Q ss_pred CCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHH
Q ss_conf 0337679999636754485030489999998094410045468988889999999999
Q gi|254780244|r 99 GRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVL 156 (199)
Q Consensus 99 gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL 156 (199)
+.|+-+.+.+.|.|+|.|+.-- .++.|-.=|-..+.|+-+++
T Consensus 23 ~~fa~V~l~veP~~~g~G~~F~----------------~~i~gg~iP~~f~~ave~Gv 64 (115)
T cd01684 23 PFWATVGLRVEPLPRGSGLQYE----------------SEVSLGSLPRSFQNAVEETV 64 (115)
T ss_pred CCCEEEEEEEEECCCCCCCEEE----------------EEEECCCCCHHHHHHHHHHH
T ss_conf 8316999999889999988898----------------87608847988999999999
No 40
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=25.38 E-value=52 Score=14.30 Aligned_cols=40 Identities=33% Similarity=0.363 Sum_probs=27.5
Q ss_pred CEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCE
Q ss_conf 73846799999808998389970474424789999999996301
Q gi|254780244|r 39 GRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNM 82 (199)
Q Consensus 39 Gr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl 82 (199)
.....|.+-|.+++. .+|.| .+..-..|-+.|...|.+.|
T Consensus 27 ~h~~~F~~~v~i~g~--~~~~g--~g~sKK~Ae~~AA~~al~~L 66 (67)
T smart00358 27 DHAPRFTVTVKVGGE--YTGEG--EGSSKKEAKQRAAEAALRSL 66 (67)
T ss_pred CCCCEEEEEEEECCE--EEECC--CCCCHHHHHHHHHHHHHHHH
T ss_conf 978479999999999--98435--78999999999999999973
No 41
>pfam02294 7kD_DNA_binding 7kD DNA-binding domain. This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.
Probab=24.92 E-value=42 Score=14.88 Aligned_cols=45 Identities=18% Similarity=0.394 Sum_probs=34.2
Q ss_pred EEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHH
Q ss_conf 2100002244401278738467999998089983899704744247899
Q gi|254780244|r 23 VDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAV 71 (199)
Q Consensus 23 ~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai 71 (199)
+|.-++|+.+-|+.+-|+..||.. -|++|.-|-|--.-+|.|--+
T Consensus 10 ee~evdiskikkvwrvgkmisfty----ddg~gktgrgavsekdapkel 54 (62)
T pfam02294 10 EEKEVDISKIKKVWRVGKMISFTY----DDGGGKTGRGAVSEKDAPKEL 54 (62)
T ss_pred CCEEECHHHHHHHHHHCCEEEEEE----ECCCCCCCCCCCCCCCCHHHH
T ss_conf 300421999888981212479987----169984465520555276999
No 42
>PRK12439 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional
Probab=23.79 E-value=25 Score=16.25 Aligned_cols=44 Identities=16% Similarity=0.155 Sum_probs=23.0
Q ss_pred HHHHHHHHCCCCCCEEECC--CCCHHHHHHHHHHHHHCCCCHHHHHHHCCC
Q ss_conf 9999998094410045468--988889999999999506998999986199
Q gi|254780244|r 123 IRAVCEVLGMHDVVAKSIG--SSNPHNVIRATFEVLRSQSHPRDVANRRGI 171 (199)
Q Consensus 123 vr~il~laGI~dv~aK~~G--S~N~~NvvkAt~~AL~~~~t~~~iA~~RG~ 171 (199)
..++..++|+=|+..-..+ ||| +.+=..|-+-++.+++.+..+.
T Consensus 236 ~~T~~GLaG~GDLilTc~s~~SRN-----~~~G~~lg~G~~~~~~~~~~~~ 281 (340)
T PRK12439 236 RETFPGLAGLGDLIVTCTSQRSRN-----RHVGEQLGAGKPIDEIIASMNQ 281 (340)
T ss_pred CCCCCCCCCHHHHHEECCCCCCCH-----HHHHHHHHCCCCHHHHHHHCCC
T ss_conf 666555536542240246899821-----7999998489989999986699
No 43
>TIGR01237 D1pyr5carbox2 delta-1-pyrroline-5-carboxylate dehydrogenase, putative; InterPro: IPR005932 The delta(1)-pyrroline-5-carboxylate synthetase (1.5.1.12 from EC) a mitochondrial inner membrane, ATP- and NADPH-dependent, bifunctional enzyme, catalyzes the reduction of glutamate to delta1-pyrroline-5-carboxylate, a critical step in the de novo biosynthesis of proline and ornithine. It is the rate-limiting enzyme in proline biosynthesis and is subject to feedback inhibition by proline. 1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase.; GO: 0003842 1-pyrroline-5-carboxylate dehydrogenase activity, 0006561 proline biosynthetic process.
Probab=23.24 E-value=56 Score=14.12 Aligned_cols=36 Identities=28% Similarity=0.302 Sum_probs=24.7
Q ss_pred CCCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf 762001103376799996367544850304899999980944
Q gi|254780244|r 92 TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMH 133 (199)
Q Consensus 92 TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~ 133 (199)
|+--=|.|.| |.|+||.. ++|||+.. -.||+-+|+=
T Consensus 191 tvApiVtGNc----vvlKPAe~-~~vIAak~-veiL~eaGlP 226 (518)
T TIGR01237 191 TVAPIVTGNC----VVLKPAEA-ATVIAAKI-VEILEEAGLP 226 (518)
T ss_pred HHHHHHHCCE----EEECCCCC-CHHHHHHH-HHHHHHCCCC
T ss_conf 7867761880----58716776-21589999-9999964789
No 44
>TIGR02173 cyt_kin_arch cytidylate kinase, putative; InterPro: IPR011892 Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by IPR003136 from INTERPRO.; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=22.59 E-value=59 Score=13.97 Aligned_cols=48 Identities=21% Similarity=0.324 Sum_probs=36.7
Q ss_pred EEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHH
Q ss_conf 999636754485030489999998094410045468988889999999999506998999986199798944
Q gi|254780244|r 106 VIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQ 177 (199)
Q Consensus 106 V~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~i~~~~ 177 (199)
+....-|||+| -.-..+.+.+-.|++.|++= ...|+|+.+|+.+.|..
T Consensus 2 ~I~ISGpPGSG--ktTvA~~lA~~Lsl~~iSaG----------------------~iRelA~~~Gldl~E~~ 49 (173)
T TIGR02173 2 IITISGPPGSG--KTTVAKILAEKLSLKLISAG----------------------DIRELAEKMGLDLAESK 49 (173)
T ss_pred EEEEECCCCCC--HHHHHHHHHHHCCCCEECCC----------------------HHHHHHHHCCCCHHHHH
T ss_conf 78873589686--47899999986398312020----------------------07889864298877734
No 45
>cd01680 EFG_like_IV Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm.
Probab=22.51 E-value=60 Score=13.96 Aligned_cols=21 Identities=19% Similarity=0.243 Sum_probs=15.4
Q ss_pred CCCCCCEEEEEEECCCCCCCC
Q ss_conf 103376799996367544850
Q gi|254780244|r 98 VGRHGAGKVIMRSAMAGTGVI 118 (199)
Q Consensus 98 ~gk~g~~kV~l~Pap~G~Gi~ 118 (199)
.+.|+-+.+.+.|.++|.|+.
T Consensus 22 ~~q~a~V~l~veP~~~g~g~~ 42 (116)
T cd01680 22 KPQFGEVTLRVEPLERGSGVR 42 (116)
T ss_pred CCCEEEEEEEEEECCCCCCCE
T ss_conf 984789999999898898748
No 46
>pfam03302 VSP Giardia variant-specific surface protein.
Probab=21.77 E-value=62 Score=13.87 Aligned_cols=13 Identities=54% Similarity=0.979 Sum_probs=5.3
Q ss_pred EEEEEEECCCCCCEEE
Q ss_conf 7999998089983899
Q gi|254780244|r 44 FSVLVVVGDTKSKVGF 59 (199)
Q Consensus 44 f~alvvvGn~~G~vG~ 59 (199)
..|+|||| |+|||
T Consensus 374 vavv~vvg---glvgf 386 (397)
T pfam03302 374 VAVVIVVG---GLVGF 386 (397)
T ss_pred EEEEEEEC---CEEEE
T ss_conf 89999955---41487
No 47
>COG0371 GldA Glycerol dehydrogenase and related enzymes [Energy production and conversion]
Probab=21.10 E-value=33 Score=15.54 Aligned_cols=84 Identities=18% Similarity=0.150 Sum_probs=50.2
Q ss_pred CCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCC-CCCEE-CCCCCCCE--EEEEEECCCC-----CCCCCCHH
Q ss_conf 8998389970474424789999999996301252201668-76200-11033767--9999636754-----48503048
Q gi|254780244|r 52 DTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGR-TLHHD-GVGRHGAG--KVIMRSAMAG-----TGVIAGGA 122 (199)
Q Consensus 52 n~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~-TI~h~-v~gk~g~~--kV~l~Pap~G-----~Gi~a~~~ 122 (199)
+-.-.+|+|=||.-|+.-+. ..+-..-++.||---.+ -++.+ ..-.+... +....+.+|- +-+++..+
T Consensus 84 ~~d~vIGVGGGk~iD~aK~~---A~~~~~pfIsvPT~AS~Da~~Sp~aSv~~~~~g~~~~~~~~~P~~vivD~evI~~AP 160 (360)
T COG0371 84 GADVVIGVGGGKTIDTAKAA---AYRLGLPFISVPTIASTDAITSPVASVIYNGKGDKYSFLAKAPDAVIVDTEVIAAAP 160 (360)
T ss_pred CCCEEEEECCCHHHHHHHHH---HHHCCCCEEECCCCCCCCCCCCCCEEEEECCCCCEEEEECCCCCEEEECHHHHHHCH
T ss_conf 99989995681899999999---998199979805764445556886346876988345566589847997289997696
Q ss_pred HHHHHHHHCCCCCCEEEC
Q ss_conf 999999809441004546
Q gi|254780244|r 123 IRAVCEVLGMHDVVAKSI 140 (199)
Q Consensus 123 vr~il~laGI~dv~aK~~ 140 (199)
.|- -.+||=|+.+|.+
T Consensus 161 ~r~--L~AGiGD~lakw~ 176 (360)
T COG0371 161 RRL--LAAGIGDALAKWT 176 (360)
T ss_pred HHH--HHHCCHHHHHHHH
T ss_conf 999--9714027665379
No 48
>TIGR01284 alt_nitrog_alph nitrogenase alpha chain; InterPro: IPR005974 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene. Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I. This model represents the alpha chains of various forms of the nitrogen-fixing enzyme nitrogenase: vanadium-iron, iron-iron, and molybdenum-iron. Most examples of NifD, the molybdenum-iron type nitrogenase alpha chain, are excluded from this model and described instead by equivalog model IPR005972 from INTERPRO.; GO: 0016163 nitrogenase activity, 0051536 iron-sulfur cluster binding, 0009399 nitrogen fixation.
Probab=21.08 E-value=36 Score=15.30 Aligned_cols=47 Identities=19% Similarity=0.298 Sum_probs=25.8
Q ss_pred HHHHHHHHHCCCCCCEEECC--CCC-HHHHHHHHHHHHHCCCCHHHHHHHC
Q ss_conf 89999998094410045468--988-8899999999995069989999861
Q gi|254780244|r 122 AIRAVCEVLGMHDVVAKSIG--SSN-PHNVIRATFEVLRSQSHPRDVANRR 169 (199)
Q Consensus 122 ~vr~il~laGI~dv~aK~~G--S~N-~~NvvkAt~~AL~~~~t~~~iA~~R 169 (199)
.+..-++-+||+=+ +...| |.. .--+=+|-++-|..+||.+-||+.-
T Consensus 227 vl~~Yf~rmGI~Vl-stFTGng~yD~lr~MHrA~Lnvv~CaRSa~YIa~eL 276 (468)
T TIGR01284 227 VLKKYFERMGIQVL-STFTGNGSYDELRAMHRAKLNVVECARSAEYIANEL 276 (468)
T ss_pred HHHHHHHHCCCEEE-EEECCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf 99999986394588-763588870566777664030432111057999986
No 49
>pfam01989 DUF126 Protein of unknown function DUF126. This archaebacterial protein family has no known function.
Probab=20.72 E-value=64 Score=13.79 Aligned_cols=58 Identities=19% Similarity=0.163 Sum_probs=32.0
Q ss_pred CCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHH
Q ss_conf 6200110337679999636754485030489999998094410045468988889999999
Q gi|254780244|r 93 LHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATF 153 (199)
Q Consensus 93 I~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~ 153 (199)
-.|++.|+.-+-||++.|..+|+- ++..+.--|...|.-- .+=++...+++-..=|.+
T Consensus 18 ~~Hpl~G~si~gkILv~p~~kGSt--~gs~vL~~l~~~g~aP-~AiI~~~~d~I~~~Gaiv 75 (83)
T pfam01989 18 PGHPLYGQSIAGKILVFPGGKGST--VGSYVLYELAKNGTAP-AAIVFEEAEPILALGAIV 75 (83)
T ss_pred CCCCCCCCCCCCEEEEEECCCCCC--HHHHHHHHHHHCCCCC-HHHHHCCCCHHHHHHHHH
T ss_conf 799767972457299975898764--6899999999869997-412224855578788998
No 50
>TIGR02326 transamin_PhnW 2-aminoethylphosphonate--pyruvate transaminase; InterPro: IPR012703 Phosphonates are a class of organophosphorus compounds, characterised by a stable C-P bond, which are found in a variety of biologically produced molecules including antiobiotics, lipids, proteins and polysaccharides . The functions of these molecules include phosphorus storage, cell communication, host recognition and chemical warfare. 2-Aminoethylphosphonate (AEP), the most common naturally occurring phosphonate, is an important precursor used in the biosynthesis of phosphonolipids, phosphonoproteins, and phosphonoglycans. This entry represents 2-aminoethylphosphonate-pyruvate transaminase (AEPT)(2.6.1.37 from EC) which catalyses the interconversion of AEP and phosphonoacetaldehyde (P-Ald), coupled with the interconversion of pryuvate and L-alanine. In some bacterial species this is the first step in an AEP degradation pathway which allows them to utilise this compound as a source of carbon, nitrogen and phosphorus. Phosphonoacetaldeyhde hydrolase, often encoded by an adjacent gene, then converts P-Ald to acetaldehyde and phosphate.Species with this pathway generally have an identified phosphonate ABC transporter but do not also have the multisubunit C-P lyase complex as found in Escherichia coli. The crystal structure of AEPT from Salmonella typhimurium has been studied to 2.2 A resolution . The protein is a homodimer where each subunit is composed of two domains, large and small. The large domain forms an alpha-beta complex characteristic of the aspartate transaminase family, while the small domain is comosed of highly twisted beta strands. The active site contains a pyridoxal 5'-phosphate cofactor and is found at the domain interface, being composed of residues from both subunits..
Probab=20.40 E-value=54 Score=14.21 Aligned_cols=25 Identities=24% Similarity=0.320 Sum_probs=18.1
Q ss_pred EEECC---CCCHHHHHHHHHHHHHCCCC
Q ss_conf 45468---98888999999999950699
Q gi|254780244|r 137 AKSIG---SSNPHNVIRATFEVLRSQSH 161 (199)
Q Consensus 137 aK~~G---S~N~~NvvkAt~~AL~~~~t 161 (199)
.+..| -+.|-.+|.|+.+||.+++.
T Consensus 234 ~~~~GkWRFTsPTHvV~Af~qAL~el~~ 261 (366)
T TIGR02326 234 EKQHGKWRFTSPTHVVHAFAQALLELEK 261 (366)
T ss_pred HCCCCCEEECCCHHHHHHHHHHHHHHHH
T ss_conf 4489962217726899999999999984
No 51
>PRK05920 aromatic acid decarboxylase; Validated
Probab=20.05 E-value=31 Score=15.72 Aligned_cols=100 Identities=15% Similarity=0.215 Sum_probs=68.1
Q ss_pred EEEEEEEEEC-CCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCC-CCCCEECCCCCCCEEEEEEECCCCCCC--
Q ss_conf 4679999980-899838997047442478999999999630125220166-876200110337679999636754485--
Q gi|254780244|r 42 FAFSVLVVVG-DTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDG-RTLHHDGVGRHGAGKVIMRSAMAGTGV-- 117 (199)
Q Consensus 42 ~sf~alvvvG-n~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~-~TI~h~v~gk~g~~kV~l~Pap~G~Gi-- 117 (199)
|.+.+++|+= ..+-+..++.|-+.+..+=-..-..+-++.|+-+||.-. ++|+-+---+-.-.-+.|.|+.|||=-
T Consensus 93 ~~~dgMvV~PCSm~TLa~IA~G~sdnLi~RaAdV~LKErR~LVlvpREtPls~iHLeNMlkls~~GaiI~P~~P~FY~~P 172 (205)
T PRK05920 93 FATDGMVIAPCSMGTLAAIAHGLSDNLIERAADVVLKERRKLILVPRETPLSLIHLENMLKLAEAGAVILPAIPAFYHKP 172 (205)
T ss_pred CCCCCEEEECCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEECCCCCCCCCC
T ss_conf 66583699415287899987346455899999999985681799976889768999999999988998947982002799
Q ss_pred -----CCCHHHHHHHHHHCCCCCCEEECC
Q ss_conf -----030489999998094410045468
Q gi|254780244|r 118 -----IAGGAIRAVCEVLGMHDVVAKSIG 141 (199)
Q Consensus 118 -----~a~~~vr~il~laGI~dv~aK~~G 141 (199)
.....+-.+|.++||.+-..+-++
T Consensus 173 ~tiedlvdfvvgrvLD~lgi~~~l~~RW~ 201 (205)
T PRK05920 173 QTIDDLVDFVVARILDLLGIDHDLIKRWG 201 (205)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 98999999999999986599877777889
Done!