Query gi|254780245|ref|YP_003064658.1| 50S ribosomal protein L18 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 120 No_of_seqs 103 out of 1938 Neff 5.6 Searched_HMMs 39220 Date Tue May 24 05:18:53 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780245.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK05593 rplR 50S ribosomal pr 100.0 0 0 297.3 15.3 115 1-120 1-115 (115) 2 TIGR00060 L18_bact ribosomal p 100.0 0 0 294.3 12.8 117 4-120 1-118 (118) 3 CHL00139 rpl18 ribosomal prote 100.0 1.4E-45 0 291.9 12.4 109 11-120 1-109 (109) 4 pfam00861 Ribosomal_L18p Ribos 100.0 5.2E-43 0 275.8 15.0 117 3-120 1-119 (119) 5 COG0256 RplR Ribosomal protein 100.0 2E-40 5.6E-45 260.5 14.6 119 1-120 5-125 (125) 6 cd00432 Ribosomal_L18_L5e Ribo 100.0 1.9E-34 4.8E-39 225.1 12.4 96 23-118 8-103 (103) 7 PTZ00032 60S ribosomal protein 100.0 2.1E-32 5.3E-37 213.0 11.3 96 25-120 104-211 (211) 8 PRK08569 rpl18p 50S ribosomal 99.6 8.5E-15 2.2E-19 108.6 10.1 102 16-119 24-129 (193) 9 PTZ00069 60S ribosomal protein 99.2 4.4E-10 1.1E-14 80.7 11.2 95 25-119 47-173 (300) 10 KOG3333 consensus 98.6 4.2E-07 1.1E-11 63.0 8.7 93 27-120 61-154 (188) 11 PTZ00090 40S ribosomal protein 96.5 0.014 3.7E-07 36.1 7.2 91 24-119 97-188 (214) 12 PRK05309 30S ribosomal protein 96.5 0.063 1.6E-06 32.3 10.3 87 27-119 17-104 (126) 13 CHL00041 rps11 ribosomal prote 96.4 0.054 1.4E-06 32.7 9.9 87 27-119 14-101 (116) 14 pfam00411 Ribosomal_S11 Riboso 96.4 0.06 1.5E-06 32.4 9.8 84 29-119 3-88 (109) 15 TIGR03632 bact_S11 30S ribosom 96.2 0.1 2.6E-06 31.1 10.3 84 29-119 3-88 (108) 16 KOG0875 consensus 95.6 0.026 6.6E-07 34.6 4.9 68 25-92 47-117 (264) 17 PRK09607 rps11p 30S ribosomal 93.5 0.68 1.7E-05 26.2 9.3 89 28-119 8-103 (129) 18 TIGR03628 arch_S11P archaeal r 91.6 1.2 3.1E-05 24.7 10.0 89 28-119 4-99 (114) 19 COG0100 RpsK Ribosomal protein 87.5 2.5 6.5E-05 22.8 8.7 67 29-98 21-88 (129) 20 PTZ00129 40S ribosomal protein 87.2 2.7 6.8E-05 22.7 7.2 89 28-119 29-124 (150) 21 TIGR02360 pbenz_hydroxyl 4-hyd 81.9 2.3 6E-05 23.0 4.1 44 75-118 11-61 (393) 22 pfam02065 Melibiase Melibiase. 81.0 3.5 9E-05 22.0 4.7 41 80-120 62-120 (395) 23 COG3345 GalA Alpha-galactosida 76.6 5.2 0.00013 21.0 4.5 41 80-120 313-371 (687) 24 PRK00072 hemC porphobilinogen 68.5 11 0.00027 19.1 5.0 41 37-89 258-298 (300) 25 pfam03900 Porphobil_deamC Porp 68.1 11 0.00028 19.0 4.9 21 69-89 54-74 (74) 26 pfam07355 GRDB Glycine/sarcosi 67.6 11 0.00028 19.0 4.5 36 61-96 312-347 (349) 27 smart00812 Alpha_L_fucos Alpha 66.0 12 0.00031 18.8 4.9 42 79-120 84-144 (384) 28 TIGR02298 HpaD_Fe 3,4-dihydrox 60.8 6.1 0.00015 20.5 2.1 26 71-96 88-114 (343) 29 pfam01120 Alpha_L_fucos Alpha- 59.2 16 0.00041 18.0 5.0 45 76-120 92-155 (344) 30 cd06290 PBP1_LacI_like_9 Ligan 56.4 18 0.00046 17.8 5.6 45 76-120 101-148 (265) 31 pfam00875 DNA_photolyase DNA p 55.1 19 0.00048 17.6 4.7 44 77-120 76-120 (164) 32 cd01574 PBP1_LacI Ligand-bindi 50.0 23 0.00058 17.1 5.5 43 77-119 103-148 (264) 33 TIGR01035 hemA glutamyl-tRNA r 49.3 23 0.00059 17.1 3.6 46 71-120 190-237 (436) 34 cd06294 PBP1_ycjW_transcriptio 47.1 25 0.00065 16.9 5.9 45 76-120 108-155 (270) 35 cd01545 PBP1_SalR Ligand-bindi 47.0 25 0.00065 16.9 6.2 46 75-120 103-151 (270) 36 cd06271 PBP1_AglR_RafR_like Li 46.8 26 0.00065 16.8 5.7 45 76-120 106-153 (268) 37 KOG0104 consensus 46.6 26 0.00066 16.8 3.4 97 18-119 91-187 (902) 38 PRK05477 gatB aspartyl/glutamy 45.7 21 0.00054 17.3 2.9 63 37-104 12-87 (479) 39 cd06273 PBP1_GntR_like_1 This 43.4 29 0.00074 16.5 5.7 46 75-120 101-150 (268) 40 cd06274 PBP1_FruR Ligand bindi 42.9 29 0.00075 16.5 6.1 45 76-120 102-149 (264) 41 PRK07666 fabG 3-ketoacyl-(acyl 42.6 30 0.00076 16.4 3.9 43 73-119 14-56 (238) 42 cd06277 PBP1_LacI_like_1 Ligan 41.0 31 0.0008 16.3 5.8 45 76-120 104-151 (268) 43 cd06272 PBP1_hexuronate_repres 40.9 32 0.00081 16.3 5.8 46 75-120 96-144 (261) 44 cd06270 PBP1_GalS_like Ligand 40.2 32 0.00083 16.2 5.9 45 76-120 102-149 (268) 45 PRK05866 short chain dehydroge 39.3 33 0.00085 16.1 4.3 42 73-118 48-89 (290) 46 cd06275 PBP1_PurR Ligand-bindi 38.6 34 0.00088 16.1 5.8 45 76-120 103-150 (269) 47 TIGR03206 benzo_BadH 2-hydroxy 38.4 35 0.00088 16.1 3.9 43 73-119 11-53 (250) 48 PRK13381 peptidase T; Provisio 38.2 35 0.00089 16.0 4.5 24 77-100 39-62 (413) 49 PRK06181 short chain dehydroge 38.1 35 0.00089 16.0 4.5 40 74-117 10-49 (263) 50 PRK10703 DNA-binding transcrip 38.0 35 0.0009 16.0 5.6 47 74-120 162-211 (335) 51 pfam06370 DUF1069 Protein of u 36.4 19 0.00048 17.7 1.4 22 84-105 161-182 (206) 52 TIGR00666 PBP4 D-alanyl-D-alan 34.6 28 0.00071 16.6 2.1 20 100-119 76-97 (427) 53 cd00494 HMBS Hydroxymethylbila 32.9 43 0.0011 15.5 4.3 38 37-86 254-291 (292) 54 PRK05650 short chain dehydroge 32.9 43 0.0011 15.5 4.2 21 77-97 12-32 (270) 55 PRK10727 DNA-binding transcrip 32.8 43 0.0011 15.5 5.4 45 76-120 162-209 (342) 56 PRK10014 DNA-binding transcrip 32.6 43 0.0011 15.5 6.1 47 74-120 166-215 (342) 57 PRK08278 short chain dehydroge 32.4 43 0.0011 15.5 4.6 45 74-118 15-62 (273) 58 KOG0408 consensus 31.1 46 0.0012 15.3 7.7 89 25-119 78-167 (190) 59 PRK10423 transcriptional repre 30.2 47 0.0012 15.3 5.5 45 76-120 160-207 (327) 60 PRK07454 short chain dehydroge 29.2 49 0.0013 15.2 3.9 42 73-118 14-55 (241) 61 COG0299 PurN Folate-dependent 28.7 50 0.0013 15.1 4.2 37 81-119 42-81 (200) 62 PRK08277 D-mannonate oxidoredu 28.7 50 0.0013 15.1 4.0 41 74-118 19-59 (278) 63 cd06293 PBP1_LacI_like_11 Liga 28.5 51 0.0013 15.1 6.1 44 77-120 103-149 (269) 64 cd06298 PBP1_CcpA_like Ligand- 28.5 51 0.0013 15.1 5.9 45 76-120 102-150 (268) 65 PRK07775 short chain dehydroge 28.4 51 0.0013 15.1 4.4 41 73-117 18-58 (275) 66 PRK08243 4-hydroxybenzoate 3-m 28.4 51 0.0013 15.1 4.1 12 94-105 260-271 (392) 67 cd01543 PBP1_XylR Ligand-bindi 28.0 52 0.0013 15.0 6.0 46 75-120 94-141 (265) 68 PRK11041 DNA-binding transcrip 27.8 52 0.0013 15.0 6.1 45 76-120 170-217 (341) 69 PRK00819 RNA 2'-phosphotransfe 27.7 30 0.00078 16.4 1.3 22 98-119 93-114 (179) 70 PRK08862 short chain dehydroge 27.5 53 0.0013 15.0 3.6 17 72-88 117-133 (227) 71 pfam00289 CPSase_L_chain Carba 27.3 53 0.0014 15.0 3.2 49 69-120 53-101 (109) 72 cd06291 PBP1_Qymf_like Ligand 27.3 53 0.0014 15.0 5.9 45 76-120 98-146 (265) 73 cd06284 PBP1_LacI_like_6 Ligan 27.2 54 0.0014 14.9 5.9 45 76-120 101-148 (267) 74 cd06280 PBP1_LacI_like_4 Ligan 26.8 54 0.0014 14.9 6.0 46 75-120 100-147 (263) 75 PRK12857 putative aldolase; Re 26.7 55 0.0014 14.9 5.0 38 81-118 89-129 (284) 76 cd06285 PBP1_LacI_like_7 Ligan 26.7 55 0.0014 14.9 5.9 44 77-120 101-147 (265) 77 PRK07035 short chain dehydroge 26.6 55 0.0014 14.9 3.9 40 74-117 17-56 (252) 78 PRK08185 hypothetical protein; 26.4 55 0.0014 14.9 5.1 39 80-118 82-123 (283) 79 PRK12737 gatY tagatose-bisphos 26.4 55 0.0014 14.8 4.9 38 81-118 89-129 (284) 80 PRK07832 short chain dehydroge 26.3 55 0.0014 14.8 4.6 38 75-116 10-47 (272) 81 TIGR01830 3oxo_ACP_reduc 3-oxo 25.9 56 0.0014 14.8 4.9 44 73-119 6-49 (238) 82 PRK12827 short chain dehydroge 25.9 57 0.0014 14.8 5.1 46 73-118 14-59 (251) 83 PRK06457 pyruvate dehydrogenas 25.8 57 0.0015 14.8 4.9 16 97-114 424-439 (549) 84 PRK06139 short chain dehydroge 25.7 57 0.0015 14.8 5.0 42 73-118 14-55 (324) 85 PRK05653 fabG 3-ketoacyl-(acyl 25.0 59 0.0015 14.7 3.9 38 76-117 16-53 (246) 86 COG3669 Alpha-L-fucosidase [Ca 24.9 45 0.0012 15.4 1.8 40 81-120 59-117 (430) 87 pfam02776 TPP_enzyme_N Thiamin 24.8 59 0.0015 14.7 4.9 39 77-120 3-42 (172) 88 COG1908 FrhD Coenzyme F420-red 24.5 60 0.0015 14.6 2.8 39 81-119 45-93 (132) 89 PRK08945 short chain dehydroge 24.4 60 0.0015 14.6 4.2 27 69-95 124-150 (245) 90 TIGR02867 spore_II_P stage II 24.2 61 0.0016 14.6 2.5 20 75-94 40-60 (221) 91 COG4861 Uncharacterized protei 24.1 37 0.00095 15.9 1.2 48 69-118 144-192 (345) 92 cd01575 PBP1_GntR Ligand-bindi 24.0 61 0.0016 14.6 6.0 46 75-120 101-149 (268) 93 cd06267 PBP1_LacI_sugar_bindin 24.0 62 0.0016 14.6 5.6 45 76-120 102-149 (264) 94 PRK10401 DNA-binding transcrip 23.6 63 0.0016 14.5 5.3 44 77-120 163-209 (346) 95 PRK09526 lacI lac repressor; R 23.4 63 0.0016 14.5 5.4 44 76-119 167-213 (342) 96 COG0064 GatB Asp-tRNAAsn/Glu-t 22.9 65 0.0016 14.5 3.6 63 37-104 13-89 (483) 97 pfam02826 2-Hacid_dh_C D-isome 22.6 66 0.0017 14.4 3.1 24 76-99 46-69 (176) 98 PRK07102 short chain dehydroge 22.6 66 0.0017 14.4 4.3 26 70-95 107-132 (243) 99 KOG4691 consensus 22.5 48 0.0012 15.2 1.5 22 85-106 187-209 (227) 100 PRK06194 hypothetical protein; 22.2 67 0.0017 14.4 3.8 41 74-118 15-55 (301) 101 pfam12005 DUF3499 Protein of u 22.1 52 0.0013 15.0 1.6 46 73-118 40-89 (125) 102 TIGR01318 gltD_gamma_fam gluta 21.9 63 0.0016 14.5 2.0 23 76-98 153-175 (480) 103 COG0068 HypF Hydrogenase matur 21.7 68 0.0017 14.3 5.4 48 73-120 677-724 (750) 104 PRK07109 short chain dehydroge 21.6 69 0.0018 14.3 4.1 42 73-118 16-57 (338) 105 TIGR01235 pyruv_carbox pyruvat 21.5 69 0.0018 14.3 2.3 17 35-51 210-226 (1169) 106 COG1400 SEC65 Signal recogniti 21.3 61 0.0016 14.6 1.8 13 80-92 36-48 (93) 107 pfam01116 F_bP_aldolase Fructo 21.1 70 0.0018 14.2 5.0 38 81-118 87-127 (283) 108 PRK12738 kbaY tagatose-bisphos 21.1 71 0.0018 14.2 5.0 38 81-118 89-129 (286) 109 pfam03446 NAD_binding_2 NAD bi 21.0 71 0.0018 14.2 4.0 14 81-96 105-118 (163) 110 PRK06806 fructose-bisphosphate 21.0 71 0.0018 14.2 5.1 39 80-118 88-129 (281) 111 cd00947 TBP_aldolase_IIB Tagat 20.9 71 0.0018 14.2 5.0 38 81-118 84-124 (276) 112 cd07039 TPP_PYR_POX Pyrimidine 20.8 71 0.0018 14.2 4.9 39 77-120 2-41 (164) 113 cd06319 PBP1_ABC_sugar_binding 20.4 73 0.0019 14.1 6.3 52 68-119 101-157 (277) 114 KOG3396 consensus 20.4 73 0.0019 14.1 6.8 62 38-99 53-128 (150) 115 KOG1185 consensus 20.3 73 0.0019 14.1 4.3 38 78-120 17-54 (571) 116 pfam00532 Peripla_BP_1 family. 20.2 74 0.0019 14.1 5.4 45 76-120 106-154 (281) No 1 >PRK05593 rplR 50S ribosomal protein L18; Reviewed Probab=100.00 E-value=0 Score=297.25 Aligned_cols=115 Identities=49% Similarity=0.736 Sum_probs=109.9 Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHH Q ss_conf 98879999989987768750578788249999638709999996279759999850210000013468667899999999 Q gi|254780245|r 1 MATKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNL 80 (120) Q Consensus 1 m~~k~~~~~kR~~R~R~k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ 80 (120) ||+|++.+.||+.|+|+++.+++ ++|||+|||||+|||||||||.+++||||+||+|++++. ++|+++|..||++ T Consensus 1 ~~~K~~~r~rR~~RiR~ki~~t~-~rpRL~VfrSnkhiyaQiIDD~~~~tl~saST~~k~~~~----~~n~~~A~~vG~~ 75 (115) T PRK05593 1 KMDKKEARLRRAKRVRKKISGTA-ERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDLKA----GGNKEAAKKVGKL 75 (115) T ss_pred CCCHHHHHHHHHHHHHHHHHCCC-CCCEEEEEECCCEEEEEEEECCCCCEEEEEECCCHHHHC----CCCHHHHHHHHHH T ss_conf 98678999999999999972789-986799996088279999986999799997414244416----8849999999999 Q ss_pred HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999997799799983898631225999999999658789 Q gi|254780245|r 81 LVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 81 ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ||++++++||++|+||||||+|||||+||||++||+||+| T Consensus 76 ia~~a~~~~I~~v~FDR~g~~YHGrvkalAd~aRe~Gl~F 115 (115) T PRK05593 76 IAERAKAKGIKQVVFDRGGYKYHGRVKALADAAREAGLKF 115 (115) T ss_pred HHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCCC T ss_conf 9999998799889981899842239999999999848999 No 2 >TIGR00060 L18_bact ribosomal protein L18; InterPro: IPR004389 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 is the ribosomal protein L18 family. The archaebacterial and eukaryotic type rpL18 is not included in this family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=100.00 E-value=0 Score=294.25 Aligned_cols=117 Identities=48% Similarity=0.705 Sum_probs=112.0 Q ss_pred HHHHHHHHHHHHHHHHCCCC-CCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHH Q ss_conf 79999989987768750578-78824999963870999999627975999985021000001346866789999999999 Q gi|254780245|r 4 KKKVLARRISRIRRHLKSVS-RGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLV 82 (120) Q Consensus 4 k~~~~~kR~~R~R~k~k~~~-~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia 82 (120) ++..+.+|+.|++.||..+. ..+|||+|||||+|||||+|||.++.||+|+||+++++...+..++|.|+|+.||+++| T Consensus 1 ~~~~r~rR~~Ri~~kl~~~~~~~rprl~VfrS~~hiYAQvIDd~~~~tlas~Stl~~~l~~~~~~~~n~~~a~~vG~~~A 80 (118) T TIGR00060 1 KKSARLRRHKRIRKKLRGTGEANRPRLVVFRSNRHIYAQVIDDVKQVTLASASTLEKKLKEQLKSTGNKDAAKKVGKLVA 80 (118) T ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 91578899999999986214256836899861681789999858884787315566887765103789889999999999 Q ss_pred HHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99997799799983898631225999999999658789 Q gi|254780245|r 83 ERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 83 ~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ++++++||+.|+||||||+|||||+||||++||+||+| T Consensus 81 ~rl~~kgi~~vvFDR~G~~YHGrv~ALAeaaRE~Gl~f 118 (118) T TIGR00060 81 ERLIKKGINDVVFDRGGYKYHGRVAALAEAAREAGLNF 118 (118) T ss_pred HHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCC T ss_conf 99997277226852699622338999999999700359 No 3 >CHL00139 rpl18 ribosomal protein L18; Validated Probab=100.00 E-value=1.4e-45 Score=291.85 Aligned_cols=109 Identities=47% Similarity=0.759 Sum_probs=105.7 Q ss_pred HHHHHHHHHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCC Q ss_conf 99877687505787882499996387099999962797599998502100000134686678999999999999997799 Q gi|254780245|r 11 RISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGV 90 (120) Q Consensus 11 R~~R~R~k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI 90 (120) |++|+|+++++++ .+|||+|||||+|||||||||.+++||||+||++++++..++.++|+++|+.||++||++++++|| T Consensus 1 R~~RiR~ki~gt~-~rpRL~V~rSnkhiyaQiIDD~~g~tl~saST~~k~~~~~~~~~~n~e~A~~vG~~ia~~a~~~gI 79 (109) T CHL00139 1 KHRRLRKKIQGTA-ERPRLSVFRSNKHIYAQIIDDTNGKTLVSCSTLDPDVKSNLSIGSTCDASKLVGQKLAKKSLKKGI 79 (109) T ss_pred CCHHHHHHCCCCC-CCCEEEEEECCCEEEEEEEECCCCCEEEEEECCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC T ss_conf 9466662604899-988899997088189999987999899996233677765514786699999999999999998799 Q ss_pred CEEEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 799983898631225999999999658789 Q gi|254780245|r 91 KSVYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 91 ~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ++|+||||||+||||||||||++||+||+| T Consensus 80 ~~VvFDRggy~YHGrVkalAd~aRe~GLkF 109 (109) T CHL00139 80 TKVVFDRGGKLYHGRIKALAEAAREAGLQF 109 (109) T ss_pred CEEEECCCCCCCHHHHHHHHHHHHHCCCCC T ss_conf 999985899842219999999999848989 No 4 >pfam00861 Ribosomal_L18p Ribosomal L18p/L5e family. This family includes ribosomal proteins from the large subunit. This family includes L18 from bacteria and L5 from eukaryotes. It has been shown that the amino terminal 93 amino acids of the rat 60S ribosomal protein L5 are necessary and sufficient to bind 5S rRNA in vitro. Suggesting that the entire family has a function in rRNA binding. Probab=100.00 E-value=5.2e-43 Score=275.78 Aligned_cols=117 Identities=49% Similarity=0.682 Sum_probs=110.0 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCC--CCCCCCHHHHHHHHHH Q ss_conf 87999998998776875057878824999963870999999627975999985021000001--3468667899999999 Q gi|254780245|r 3 TKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSS--LKTGANIVAATAVGNL 80 (120) Q Consensus 3 ~k~~~~~kR~~R~R~k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~--~~~~~ni~aA~~vG~~ 80 (120) .|+..+.+|+.|+|+++.+++ .+|||+||+||+|||||||||..+.||+++||++++++.. ....+|+++|++||++ T Consensus 1 ~k~~~r~~r~~rir~k~~~~~-~rpRL~V~rSNkhiyaQiIdd~~~~tl~saSt~~k~lkk~~~k~~~~n~~aA~~vG~~ 79 (119) T pfam00861 1 GKRRRRRRKRLRVRRKLKGTA-ERPRLVVRRSNKHIYAQIIDDTKGGTLVSASTLSKELKKYGLKGGGNNTAAAYLVGLL 79 (119) T ss_pred CCHHHHHHHHHHHHHHHCCCC-CCCEEEEEEECCEEEEEEEECCCCCEEEEEECCCHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 927889999999997653899-9988999996894899999868998899997340567773444677649999999999 Q ss_pred HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999997799799983898631225999999999658789 Q gi|254780245|r 81 LVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 81 ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ||++++++||++|+||||||+|||||+||||++||+||+| T Consensus 80 ia~ka~~~gi~~v~fDR~g~~yhGrvka~A~~aRe~Gl~F 119 (119) T pfam00861 80 LAKRALKKGIAVVVFDRGGYTYHGRVFALAKGAREAGLNF 119 (119) T ss_pred HHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCC T ss_conf 9999998799889983899844599999999999838889 No 5 >COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=2e-40 Score=260.51 Aligned_cols=119 Identities=47% Similarity=0.699 Sum_probs=110.9 Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCC--CCCCCCCHHHHHHHH Q ss_conf 988799999899877687505787882499996387099999962797599998502100000--134686678999999 Q gi|254780245|r 1 MATKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRS--SLKTGANIVAATAVG 78 (120) Q Consensus 1 m~~k~~~~~kR~~R~R~k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~--~~~~~~ni~aA~~vG 78 (120) |+.++..+.||+.|+|.++.+. ..+|||+||+||+|||||||||..+.|++++||+++++.. +...++|+++|++|| T Consensus 5 ~~~rr~~~~kr~~r~R~kl~g~-~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG 83 (125) T COG0256 5 VKFRRRRRGKRAYRIRKKLLGT-SGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVG 83 (125) T ss_pred HHHHHHHHHHHHHHHHHHHCCC-CCCCEEEEEEECCCEEEEEEECCCCCEEEEEECCHHHHHHHCCCCCCCCHHHHHHHH T ss_conf 2557899876777777653068-999579999808938999997489966999871367776403257898789999999 Q ss_pred HHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 999999997799799983898631225999999999658789 Q gi|254780245|r 79 NLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 79 ~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) +++|++++++||++|+|||+||+|||||+|+||++||+||+| T Consensus 84 ~lia~ra~~kgi~~vVfdr~g~~yhgRV~Ala~~AreaGL~f 125 (125) T COG0256 84 KLIAERALAKGIEEVVFDRGGYKYHGRVAALADGAREAGLEF 125 (125) T ss_pred HHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCCC T ss_conf 999999998599589983898865119999999999729679 No 6 >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=100.00 E-value=1.9e-34 Score=225.05 Aligned_cols=96 Identities=51% Similarity=0.744 Sum_probs=93.1 Q ss_pred CCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCC Q ss_conf 87882499996387099999962797599998502100000134686678999999999999997799799983898631 Q gi|254780245|r 23 SRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLY 102 (120) Q Consensus 23 ~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FDR~g~~y 102 (120) ...+|||+||+||+|||||||||.+++||||+||+|+++++.+...+|+++|+.||++||++++++||++|+||||||+| T Consensus 8 ~~~~pRl~V~~Snk~i~aqiid~~~~~tl~sasT~~~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vvfDrg~~~y 87 (103) T cd00432 8 TQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYRY 87 (103) T ss_pred CCCCCEEEEEEECCEEEEEEEECCCCCEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCC T ss_conf 89998899998189389999985999599999714065531236886299999999999999998799889986799976 Q ss_pred HHHHHHHHHHHHHCCC Q ss_conf 2259999999996587 Q gi|254780245|r 103 CGRIAALADAVRKGGV 118 (120) Q Consensus 103 HGrvka~ad~~R~~Gl 118 (120) ||||+||||++||+|| T Consensus 88 hgrv~a~a~~~re~Gl 103 (103) T cd00432 88 HGRVKALAKGAREGGL 103 (103) T ss_pred CHHHHHHHHHHHHCCC T ss_conf 3799999999998589 No 7 >PTZ00032 60S ribosomal protein L18; Provisional Probab=99.98 E-value=2.1e-32 Score=212.96 Aligned_cols=96 Identities=30% Similarity=0.482 Sum_probs=90.0 Q ss_pred CCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCC------------CCCCCCHHHHHHHHHHHHHHHHHCCCCE Q ss_conf 8824999963870999999627975999985021000001------------3468667899999999999999779979 Q gi|254780245|r 25 GRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSS------------LKTGANIVAATAVGNLLVERAVKVGVKS 92 (120) Q Consensus 25 ~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~------------~~~~~ni~aA~~vG~~ia~r~~~~gI~~ 92 (120) .+|||.+.+||+||||.||||.+.++||..+|.++.+..- .+.++|++||+.||++||++|+++||++ T Consensus 104 R~pRl~iK~Tnn~iyAtIvDDy~r~vlCf~cs~~~~lS~I~Gty~~k~tnr~~nnGg~i~aA~eVGk~IakkA~~kGI~~ 183 (211) T PTZ00032 104 RRPRLTLKNTNNQMYATIVDDYTRYVLCFTCTNFKYLSHIFGTYPTKATNRVRNNGGTIKAAYELGKLIGRKALSKGISK 183 (211) T ss_pred CCCCEEEECCCCEEEEEEECCCCCEEEEEECCCCCHHHHHHCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHCCCCE T ss_conf 65306875267736787730200057999625882176663466666767375589765999999999999999879988 Q ss_pred EEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9983898631225999999999658789 Q gi|254780245|r 93 VYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 93 v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) |+||||||+|||||+||||+|||+||+| T Consensus 184 VvFDRggy~YHGRVkALAe~ARe~GL~F 211 (211) T PTZ00032 184 VRFDRAHYKYAGKVEALAEGARAVGLQF 211 (211) T ss_pred EEECCCCCCCCHHHHHHHHHHHHHCCCC T ss_conf 9987999732028999999999718899 No 8 >PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed Probab=99.60 E-value=8.5e-15 Score=108.57 Aligned_cols=102 Identities=29% Similarity=0.316 Sum_probs=90.4 Q ss_pred HHHHCCCCCCCCEEEEEEECCCEEEEEEE--CCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE Q ss_conf 68750578788249999638709999996--2797599998502100000134686678999999999999997799799 Q gi|254780245|r 16 RRHLKSVSRGRLRLSVCRSSKHIYGQIID--DSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV 93 (120) Q Consensus 16 R~k~k~~~~~~pRL~V~rSnkhiyAQiId--d~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v 93 (120) |.++ ...++|||+|.+||++|.+||+. ..++.|||||.|.|..-.++....+|++||++.|.++|.+++++|+++. T Consensus 24 R~~L--l~s~k~R~VVR~TN~~ii~Qiv~~~~~GD~v~~sa~s~eL~kyG~k~~~~N~pAaYltGlL~gkral~~G~~ea 101 (193) T PRK08569 24 RLKL--LLSGKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSKELAKYGWKGDTGNTPAAYLTGLLAGKKALKAGVEEA 101 (193) T ss_pred HHHH--HHCCCCEEEEEECCCCEEEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEE T ss_conf 9999--85699759999738847999998607898999997652375568478877208999989999999997497637 Q ss_pred EECCCCCCCH--HHHHHHHHHHHHCCCC Q ss_conf 9838986312--2599999999965878 Q gi|254780245|r 94 YFDRGKHLYC--GRIAALADAVRKGGVS 119 (120) Q Consensus 94 ~FDR~g~~yH--Grvka~ad~~R~~Gl~ 119 (120) ++|-|-.+.. +||.|...++-++||+ T Consensus 102 iLDiGL~~~t~G~rvfaalKGavDaGl~ 129 (193) T PRK08569 102 VLDIGLHRPTKGSRVFAALKGAVDAGLE 129 (193) T ss_pred EEECCCCCCCCCCCHHHHHHCCCCCCCC T ss_conf 9840566465562068866323245611 No 9 >PTZ00069 60S ribosomal protein L5; Provisional Probab=99.18 E-value=4.4e-10 Score=80.65 Aligned_cols=95 Identities=28% Similarity=0.251 Sum_probs=78.9 Q ss_pred CCCEEEEEEECCCEEEEEEE--CCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHC--------CCCE-- Q ss_conf 88249999638709999996--27975999985021000001346866789999999999999977--------9979-- Q gi|254780245|r 25 GRLRLSVCRSSKHIYGQIID--DSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKV--------GVKS-- 92 (120) Q Consensus 25 ~~pRL~V~rSnkhiyAQiId--d~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~--------gI~~-- 92 (120) -+|||+|.+||++|.+||+. ..++.|+|+|.|.|..--+......|.+||+..|.++|.+++++ |+++ T Consensus 47 pKyRlVVR~TN~~iicQiv~a~~~GD~v~~aA~s~EL~kyG~k~gltNyaAAY~TGlLlarR~L~kl~ld~~y~G~~e~~ 126 (300) T PTZ00069 47 PKYRLVVRITNKDIICQIVYAKIVGDKVVAAAYSHELPRFGIPVGLTNYAAAYATGLLLARRTLKKLKLADKFEGVKEAD 126 (300) T ss_pred CCCEEEEEEECCEEEEEEEEECCCCCEEEEEEECCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCC T ss_conf 87449999877828999998506898999985112042358878877408999989999999998606223315752145 Q ss_pred ------------------EEECCCCCCC--HHHHHHHHHHHHHCCCC Q ss_conf ------------------9983898631--22599999999965878 Q gi|254780245|r 93 ------------------VYFDRGKHLY--CGRIAALADAVRKGGVS 119 (120) Q Consensus 93 ------------------v~FDR~g~~y--HGrvka~ad~~R~~Gl~ 119 (120) +++|-|-.+= -.||.+...|+-++||. T Consensus 127 g~~~~v~e~~~~~~rpFka~LDvGL~rtTtG~RVFaaLKGAvDgGl~ 173 (300) T PTZ00069 127 GSYYAVDEEDDEERRPFKAILDVGLARTTTGNRVFGALKGAVDGGLA 173 (300) T ss_pred CCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHCCCCCCCC T ss_conf 75101222355787764799732544477653244532123357735 No 10 >KOG3333 consensus Probab=98.58 E-value=4.2e-07 Score=62.97 Aligned_cols=93 Identities=24% Similarity=0.420 Sum_probs=78.0 Q ss_pred CEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCC-CCHHH Q ss_conf 24999963870999999627975999985021000001346866789999999999999977997999838986-31225 Q gi|254780245|r 27 LRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKH-LYCGR 105 (120) Q Consensus 27 pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FDR~g~-~yHGr 105 (120) +||-|-+|-.|..+-+.+-+ +.|++||||.|..++..+.++.|+.|+..||..||.||++.||+..++.-... .--.. T Consensus 61 h~lev~~~~~hveg~v~H~~-~gvvvSAST~EwaIk~qLYst~dtsA~~niGRVLAqRCLqsGI~fm~~~~t~ea~~~s~ 139 (188) T KOG3333 61 HRLEVIRTQHHVEGLVEHQN-GGVVVSASTREWAIKKQLYSTRDTSACENIGRVLAQRCLQSGINFMVYQPTPEAAASSS 139 (188) T ss_pred EEEEEEECCCCEEEEEEEEC-CCEEEEECCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCEECCCCCHHHCCCHH T ss_conf 67887404641122356722-98899704551578987751463499887889999999982766332588834333158 Q ss_pred HHHHHHHHHHCCCCC Q ss_conf 999999999658789 Q gi|254780245|r 106 IAALADAVRKGGVSF 120 (120) Q Consensus 106 vka~ad~~R~~Gl~F 120 (120) .+-|-.++-|+|+-| T Consensus 140 ~q~l~~a~~e~Gv~l 154 (188) T KOG3333 140 MQRLQSAMTEGGVVL 154 (188) T ss_pred HHHHHHHHHHCCEEE T ss_conf 999999987488653 No 11 >PTZ00090 40S ribosomal protein S11; Provisional Probab=96.50 E-value=0.014 Score=36.12 Aligned_cols=91 Identities=18% Similarity=0.258 Sum_probs=64.7 Q ss_pred CCCCEEEEEEECCCEEEEEEECCCC-EEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCC Q ss_conf 7882499996387099999962797-599998502100000134686678999999999999997799799983898631 Q gi|254780245|r 24 RGRLRLSVCRSSKHIYGQIIDDSIG-HTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLY 102 (120) Q Consensus 24 ~~~pRL~V~rSnkhiyAQiIdd~~~-~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FDR~g~~y 102 (120) .++.++++.-|..+.+||+|+.... +|+...---.-.+...+- ..-.-|+.+|+.||++|+-.||..|-. .|+| T Consensus 97 td~F~~V~ttsKNNvhaqvvNkS~nyrTvfgsfAGnVG~~K~~q--q~~kcAyRIGeniAkKcrRLGif~vdv---kFRr 171 (214) T PTZ00090 97 TDRFMLVLTTSKNNVHAQLVNRSKNYKTVFGSFAGNVGFTKKLQ--QSERCAYRIGENIAKKCKRLGIFAVDV---KFRR 171 (214) T ss_pred CCEEEEEEECCCCCEEEEEEECCCCEEEEEEECCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHCEEEEEH---HHHH T ss_conf 76189999805774440110044440256531154210678876--300689999889999988728221104---6899 Q ss_pred HHHHHHHHHHHHHCCCC Q ss_conf 22599999999965878 Q gi|254780245|r 103 CGRIAALADAVRKGGVS 119 (120) Q Consensus 103 HGrvka~ad~~R~~Gl~ 119 (120) --||..+..+.-.+||+ T Consensus 172 imRve~vlqa~~a~~l~ 188 (214) T PTZ00090 172 IMRVETVLQAFYANGLQ 188 (214) T ss_pred HHHHHHHHHHHHHCCCC T ss_conf 99999999999973762 No 12 >PRK05309 30S ribosomal protein S11; Validated Probab=96.46 E-value=0.063 Score=32.31 Aligned_cols=87 Identities=23% Similarity=0.243 Sum_probs=65.6 Q ss_pred CEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHH Q ss_conf 2499996387099999962797599998502100000134686678999999999999997799799-983898631225 Q gi|254780245|r 27 LRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRGKHLYCGR 105 (120) Q Consensus 27 pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~g~~yHGr 105 (120) =-+.|+-|..|....|. |.+|.+|+..|+-...|++..+ +.--||..+++.+++++++.||..| ++=+|- = -|| T Consensus 17 GivhI~ss~NNTiitlT-D~~Gn~l~~~S~G~~gfKg~rK--~T~~Aa~~aa~~~~~~~~~~Gi~~v~V~ikG~-G-~GR 91 (126) T PRK05309 17 GVAHIHATFNNTIVTIT-DRQGNAISWASAGGSGFKGSRK--STPYAAQVAAEDAAKKAKEHGMKTVEVFVKGP-G-SGR 91 (126) T ss_pred EEEEEEECCCCEEEEEE-CCCCCEEEEEECCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-C-CCH T ss_conf 08999944798899998-3999999998077502588765--66669999999999999972971999999778-8-338 Q ss_pred HHHHHHHHHHCCCC Q ss_conf 99999999965878 Q gi|254780245|r 106 IAALADAVRKGGVS 119 (120) Q Consensus 106 vka~ad~~R~~Gl~ 119 (120) -.+ .-++...||+ T Consensus 92 ~~a-ir~L~~~gik 104 (126) T PRK05309 92 ESA-IRALQAAGLE 104 (126) T ss_pred HHH-HHHHHHCCCE T ss_conf 999-9999878988 No 13 >CHL00041 rps11 ribosomal protein S11 Probab=96.44 E-value=0.054 Score=32.69 Aligned_cols=87 Identities=18% Similarity=0.199 Sum_probs=66.1 Q ss_pred CEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHH Q ss_conf 2499996387099999962797599998502100000134686678999999999999997799799-983898631225 Q gi|254780245|r 27 LRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRGKHLYCGR 105 (120) Q Consensus 27 pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~g~~yHGr 105 (120) -.+.|+.|..|....+. |.+|.+++.+|+=...|++..+ ..--||..+++.+++++++.||+.| ++=+| .= .|| T Consensus 14 Gi~hI~~t~NNTiitlT-D~~Gn~l~~~S~G~~gfKg~rK--~T~~Aa~~aa~~~~~~a~~~Gi~~v~v~vkG-~G-~GR 88 (116) T CHL00041 14 GVIHIQASFNNTIVTVT-DVRGRVISWSSAGACGFKGRRK--GTPFAAQTAAENAIRTVIDQGMKRAEVMIKG-PG-LGR 88 (116) T ss_pred EEEEEEECCCCEEEEEE-CCCCCEEEEECCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHCCCEEEEEEEEC-CC-CCH T ss_conf 79999944798899998-4999999998077311588876--8988999999999999997398499999978-88-458 Q ss_pred HHHHHHHHHHCCCC Q ss_conf 99999999965878 Q gi|254780245|r 106 IAALADAVRKGGVS 119 (120) Q Consensus 106 vka~ad~~R~~Gl~ 119 (120) -.+ .-++...||+ T Consensus 89 ~~a-ik~l~~~glk 101 (116) T CHL00041 89 DTA-LRAIRRSGLK 101 (116) T ss_pred HHH-HHHHHHCCCE T ss_conf 999-9999878988 No 14 >pfam00411 Ribosomal_S11 Ribosomal protein S11. Probab=96.39 E-value=0.06 Score=32.43 Aligned_cols=84 Identities=21% Similarity=0.218 Sum_probs=61.9 Q ss_pred EEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CCCCHHHH Q ss_conf 99996387099999962797599998502100000134686678999999999999997799799-98389-86312259 Q gi|254780245|r 29 LSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG-KHLYCGRI 106 (120) Q Consensus 29 L~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~-g~~yHGrv 106 (120) +-|+-|..|....+- |..|.+++..|+-..-|++..+ +.-.||..+++.+++++++.||..| ++=+| |. ||- T Consensus 3 vhi~~t~NNTiitlT-D~~G~~l~~~S~G~~gfKg~rK--~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~G~---Gr~ 76 (109) T pfam00411 3 AHIQASFNNTIVTVT-DVIGRVVSWSSAGGCGFKGSRK--STPYAAQTAAENAAKIAKEQGIKALEVKIKGPGP---GRE 76 (109) T ss_pred EEEEECCCCEEEEEE-CCCCCEEEEEECCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCC---CHH T ss_conf 999925788899998-5998999999578765588876--8989999999999999998198599999988998---789 Q ss_pred HHHHHHHHHCCCC Q ss_conf 9999999965878 Q gi|254780245|r 107 AALADAVRKGGVS 119 (120) Q Consensus 107 ka~ad~~R~~Gl~ 119 (120) .+ ..++...||+ T Consensus 77 ~a-ir~l~~~gl~ 88 (109) T pfam00411 77 SA-LRALARSGLR 88 (109) T ss_pred HH-HHHHHHCCCE T ss_conf 99-9999877998 No 15 >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=96.23 E-value=0.1 Score=31.09 Aligned_cols=84 Identities=23% Similarity=0.265 Sum_probs=63.0 Q ss_pred EEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CCCCHHHH Q ss_conf 99996387099999962797599998502100000134686678999999999999997799799-98389-86312259 Q gi|254780245|r 29 LSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG-KHLYCGRI 106 (120) Q Consensus 29 L~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~-g~~yHGrv 106 (120) +-|+-|..|..+.|- |.+|.+++.+|+=...|++..+ +.--||..+++.+++++++.||+.| ++=+| |. ||- T Consensus 3 ~hI~~s~NNTiit~T-d~~Gn~~~~~S~G~~gfKg~rK--~T~~Aa~~aa~~~~~~~~~~gi~~v~V~ikG~G~---Gr~ 76 (108) T TIGR03632 3 AHIHATFNNTIVTIT-DPQGNVLSWASAGAVGFKGSKK--STPYAAQLAAEDAAKKAKEFGMKTVDVYVKGPGA---GRE 76 (108) T ss_pred EEEEECCCCEEEEEE-CCCCCEEEEEECCCEECCCCCC--CCHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCC---CHH T ss_conf 999935787899998-7999999999477333277655--8889999999999999997096199999968997---479 Q ss_pred HHHHHHHHHCCCC Q ss_conf 9999999965878 Q gi|254780245|r 107 AALADAVRKGGVS 119 (120) Q Consensus 107 ka~ad~~R~~Gl~ 119 (120) . +.-+++..||+ T Consensus 77 ~-air~l~~~glk 88 (108) T TIGR03632 77 S-AIRALQAAGLE 88 (108) T ss_pred H-HHHHHHHCCCE T ss_conf 9-99999988988 No 16 >KOG0875 consensus Probab=95.58 E-value=0.026 Score=34.59 Aligned_cols=68 Identities=25% Similarity=0.148 Sum_probs=54.3 Q ss_pred CCCEEEEEEECCCEEEEEEEC--CCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHC-CCCE Q ss_conf 882499996387099999962--7975999985021000001346866789999999999999977-9979 Q gi|254780245|r 25 GRLRLSVCRSSKHIYGQIIDD--SIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKV-GVKS 92 (120) Q Consensus 25 ~~pRL~V~rSnkhiyAQiIdd--~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~-gI~~ 92 (120) -++||.|..+|+.+.+||+.. +...+++++-+.|..-.+......|-.||...|-+||.++++. |..+ T Consensus 47 ~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elpkyg~~~GLtNyaAay~TglLLarR~l~~~gmD~ 117 (264) T KOG0875 47 PKYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELPKYGVKVGLTNYAAAYCTGLLLACRLLKRFGMDK 117 (264) T ss_pred CCEEEEEEEECHHHHHHHHHHEECCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 73389999824046888776321323999720133466555554640168887667899999998708610 No 17 >PRK09607 rps11p 30S ribosomal protein S11P; Reviewed Probab=93.50 E-value=0.68 Score=26.18 Aligned_cols=89 Identities=19% Similarity=0.038 Sum_probs=57.3 Q ss_pred EEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CC-CC-- Q ss_conf 499996387099999962797599998502100000134686678999999999999997799799-98389-86-31-- Q gi|254780245|r 28 RLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG-KH-LY-- 102 (120) Q Consensus 28 RL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~-g~-~y-- 102 (120) -+.|+-|-.|..+.|-|-....+++..|.-.-.+.+.. .+.--||..+++.+++++++.||+.| ++=+| |+ += T Consensus 8 ivhI~asfNNTivtvTD~~G~~~~~~ssgg~~~k~~~k--K~Tp~AAq~aae~~~~~a~~~Gi~~v~V~vkG~G~~~~k~ 85 (129) T PRK09607 8 IAHIYASFNNTIITITDLTGAETIAKVSGGMVVKADRD--EPSPYAAMQAAFRAAELAKDKGITGVHIKVRAPGGNGSKT 85 (129) T ss_pred EEEEEECCCCEEEEEECCCCCEEEEEECCCCEECCCCC--CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCC T ss_conf 99999368985999985999969999477630048887--6898999999999999999769858999998378777678 Q ss_pred --HHHHHHHHHHHHHCCCC Q ss_conf --22599999999965878 Q gi|254780245|r 103 --CGRIAALADAVRKGGVS 119 (120) Q Consensus 103 --HGrvka~ad~~R~~Gl~ 119 (120) -||-.|+ -++...||+ T Consensus 86 pGpGr~~ai-r~l~~~Gl~ 103 (129) T PRK09607 86 PGPGAQAAI-RALARAGLR 103 (129) T ss_pred CCCCHHHHH-HHHHHCCCE T ss_conf 884289999-999868978 No 18 >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=91.60 E-value=1.2 Score=24.67 Aligned_cols=89 Identities=18% Similarity=0.073 Sum_probs=56.6 Q ss_pred EEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CC----- Q ss_conf 499996387099999962797599998502100000134686678999999999999997799799-98389-86----- Q gi|254780245|r 28 RLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG-KH----- 100 (120) Q Consensus 28 RL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~-g~----- 100 (120) .+-|+-|-.|-...|-|.....+++..|.-.--+++.. .+.--||....+.+++++++.|+..| ++=|| |. T Consensus 4 i~hI~atfNNTiitvTD~~G~~~~~~ssgg~~~~~~~~--K~Tp~AAq~aae~~a~~~~~~Gi~~v~V~ikG~G~n~~~~ 81 (114) T TIGR03628 4 IAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRD--ESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKS 81 (114) T ss_pred EEEEECCCCCEEEEEECCCCCEEEEEECCCCEECCCCC--CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCC T ss_conf 99999168985999985999979999668746518887--7888999999999999999869849999999478787778 Q ss_pred CCHHHHHHHHHHHHHCCCC Q ss_conf 3122599999999965878 Q gi|254780245|r 101 LYCGRIAALADAVRKGGVS 119 (120) Q Consensus 101 ~yHGrvka~ad~~R~~Gl~ 119 (120) .=-||-.|+ -++...||+ T Consensus 82 pGpGresAi-ral~~~Gl~ 99 (114) T TIGR03628 82 PGPGAQAAI-RALARAGLR 99 (114) T ss_pred CCCCHHHHH-HHHHHCCCE T ss_conf 986289999-999868979 No 19 >COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis] Probab=87.54 E-value=2.5 Score=22.78 Aligned_cols=67 Identities=24% Similarity=0.193 Sum_probs=50.8 Q ss_pred EEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC Q ss_conf 99996387099999962797599998502100000134686678999999999999997799799-98389 Q gi|254780245|r 29 LSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG 98 (120) Q Consensus 29 L~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~ 98 (120) .-|+.|-.|-...+ .|..|.+++.+|+=..-|++.. .+.--||...++..++.+++.||+.| ++=+| T Consensus 21 ahI~asfNNTivti-tD~~Gn~i~wassG~~gfk~~r--k~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkg 88 (129) T COG0100 21 AHIHASFNNTIVTI-TDLTGNVIIWASSGGMGFKGSR--KSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKG 88 (129) T ss_pred EEEECCCCCCEEEE-CCCCCCEEEEEECCCCEECCCC--CCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEC T ss_conf 89972678858974-0789988999704762474788--88868999999999999997085479999968 No 20 >PTZ00129 40S ribosomal protein S14; Provisional Probab=87.24 E-value=2.7 Score=22.67 Aligned_cols=89 Identities=21% Similarity=0.163 Sum_probs=54.5 Q ss_pred EEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC--CCCCH- Q ss_conf 499996387099999962797599998502100000134686678999999999999997799799-98389--86312- Q gi|254780245|r 28 RLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRG--KHLYC- 103 (120) Q Consensus 28 RL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~--g~~yH- 103 (120) -.-|+=|-.|....|-|.....|+++ |+-...++.... .+.-=||....+..|+++++.||+.| +.=|+ |.+-+ T Consensus 29 vaHI~ASfNNTIVtvTD~~G~~t~~~-sSGg~~~k~~r~-ksTPyAAq~AAe~aa~~a~e~Gi~~v~V~vrg~Gg~~~k~ 106 (150) T PTZ00129 29 VAHVFASFNDTFIHITDLSGRETLVR-VTGGMKVKADRD-ESSPYAAMMAAQDAAARAKELGITAVHVKLRATGGTRSKT 106 (150) T ss_pred EEEEECCCCCEEEEEECCCCCEEEEE-ECCCCEEECCCC-CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCC T ss_conf 99998245871899873999989999-689726857877-7887999999999999999819818999998247876788 Q ss_pred ---HHHHHHHHHHHHCCCC Q ss_conf ---2599999999965878 Q gi|254780245|r 104 ---GRIAALADAVRKGGVS 119 (120) Q Consensus 104 ---Grvka~ad~~R~~Gl~ 119 (120) ||=.|+= ++...||+ T Consensus 107 PGpGresAIR-aL~~~Gl~ 124 (150) T PTZ00129 107 PGPGAQSALR-SLARSGLK 124 (150) T ss_pred CCCCHHHHHH-HHHHCCCE T ss_conf 9864667789-98747988 No 21 >TIGR02360 pbenz_hydroxyl 4-hydroxybenzoate 3-monooxygenase; InterPro: IPR012733 4-hydroxybenzoate 3-monooxygenase is a flavoprotein that converts its substrate to 3,4-dihydroxybenzoate, which subsequently enters the beta-ketioadipate pathway of aromatic degradation, using molecular oxygen and NADPH as shown below .4-hydroxybenzoate + NADPH + O(2) = 3,4-dihydroxybenzoate + NADP(+) + H(2)O 4-hydroxybenzoate is an intermediate in the degradation of lignin and other aromatic plant compounds, and this enzyme is found extensively in soil bacteria. This enzyme is a homodimer where each subunit is composed of three distinct domains: an N-terminal flavin-binding domain with a beta-alpha-beta fold, a small substrate-binding domain composed of a single alpha helix and beta-sheet, and a C-terminal helical domain . The active site is found at the interface of all three domains. Catalysis occurs by a two-step reaction. In the first step, flavin is reduced by NADPH. Subsequently, the reduced flavin is oxygenated to a hydroperoxide which transfers the hydroxyl group to the substrate, forming 3,4-dihydroxybenzoate.; GO: 0018659 4-hydroxybenzoate 3-monooxygenase activity, 0050660 FAD binding, 0043639 benzoate catabolic process. Probab=81.90 E-value=2.3 Score=22.99 Aligned_cols=44 Identities=36% Similarity=0.538 Sum_probs=34.0 Q ss_pred HHHHHHHHHHHHHCCCCEEEECCCCCCCH-HHHHH------HHHHHHHCCC Q ss_conf 99999999999977997999838986312-25999------9999996587 Q gi|254780245|r 75 TAVGNLLVERAVKVGVKSVYFDRGKHLYC-GRIAA------LADAVRKGGV 118 (120) Q Consensus 75 ~~vG~~ia~r~~~~gI~~v~FDR~g~~yH-Grvka------~ad~~R~~Gl 118 (120) -=-|-+|++.+.++||..|++.|-.-.|= |||.| ++|=++++|+ T Consensus 11 GPsGLLLGQLLh~~GId~viLEr~~~dYVlgRIRAGvLE~g~v~LL~~agv 61 (393) T TIGR02360 11 GPSGLLLGQLLHKAGIDTVILERKSRDYVLGRIRAGVLEQGTVDLLREAGV 61 (393) T ss_pred CHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 735789999998669858997235722343321012357899999987223 No 22 >pfam02065 Melibiase Melibiase. Probab=81.03 E-value=3.5 Score=21.95 Aligned_cols=41 Identities=27% Similarity=0.439 Sum_probs=35.3 Q ss_pred HHHHHHHHCCCCEEEECCCC------------------CCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999997799799983898------------------631225999999999658789 Q gi|254780245|r 80 LLVERAVKVGVKSVYFDRGK------------------HLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 80 ~ia~r~~~~gI~~v~FDR~g------------------~~yHGrvka~ad~~R~~Gl~F 120 (120) .||+.|.+.||+-+|.|-|= .+|-+=++.|+|.+++.|++| T Consensus 62 ~la~~Aa~lGvE~FVlDDGWFg~R~~D~~gLGDW~v~~~kfP~GL~~l~d~v~~~GM~F 120 (395) T pfam02065 62 DLADEAADLGIELFVLDDGWFGGRNDDNSSLGDWFVNEQKFPNGLKPLADHVHSLGMEF 120 (395) T ss_pred HHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHCCCCE T ss_conf 99999997398699981787789999887773816165005898799999999739843 No 23 >COG3345 GalA Alpha-galactosidase [Carbohydrate transport and metabolism] Probab=76.61 E-value=5.2 Score=20.95 Aligned_cols=41 Identities=29% Similarity=0.408 Sum_probs=34.9 Q ss_pred HHHHHHHHCCCCEEEECCCCC------------------CCHHHHHHHHHHHHHCCCCC Q ss_conf 999999977997999838986------------------31225999999999658789 Q gi|254780245|r 80 LLVERAVKVGVKSVYFDRGKH------------------LYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 80 ~ia~r~~~~gI~~v~FDR~g~------------------~yHGrvka~ad~~R~~Gl~F 120 (120) .+++.+++-|++-++.|-|-+ +|-+-|..++++++|+|++| T Consensus 313 e~vk~akk~gvE~FvlDDGwfg~rndd~~slGDWlv~seKfPsgiE~li~~I~e~Gl~f 371 (687) T COG3345 313 ENVKEAKKFGVELFVLDDGWFGGRNDDLKSLGDWLVNSEKFPSGIEELIEAIAENGLIF 371 (687) T ss_pred HHHHHHHHCCEEEEEECCCCCCCCCCCHHHHHCEECCHHHCCCCHHHHHHHHHHCCCCC T ss_conf 99998863682799973500156676312332114336435520899999999728764 No 24 >PRK00072 hemC porphobilinogen deaminase; Reviewed Probab=68.51 E-value=11 Score=19.09 Aligned_cols=41 Identities=22% Similarity=0.194 Sum_probs=28.5 Q ss_pred CEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCC Q ss_conf 09999996279759999850210000013468667899999999999999779 Q gi|254780245|r 37 HIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVG 89 (120) Q Consensus 37 hiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~g 89 (120) ++.+.+.+..+...+. .+ ..++++.|..+|..+|+.+++.| T Consensus 258 ~l~~~v~s~dG~~~i~-~~-----------~~g~~~~a~~lG~~la~~Ll~~G 298 (300) T PRK00072 258 HLRGLVGSPDGSRIIR-EE-----------RIGNGADAEALGIELAEELLAQG 298 (300) T ss_pred EEEEEEECCCCCEEEE-EE-----------EEECHHHHHHHHHHHHHHHHHCC T ss_conf 9999999899987999-99-----------98579999999999999999757 No 25 >pfam03900 Porphobil_deamC Porphobilinogen deaminase, C-terminal domain. Probab=68.12 E-value=11 Score=19.04 Aligned_cols=21 Identities=29% Similarity=0.434 Sum_probs=18.3 Q ss_pred CCHHHHHHHHHHHHHHHHHCC Q ss_conf 667899999999999999779 Q gi|254780245|r 69 ANIVAATAVGNLLVERAVKVG 89 (120) Q Consensus 69 ~ni~aA~~vG~~ia~r~~~~g 89 (120) ++++.|..+|..+|+.++++| T Consensus 54 g~~~~a~~lG~~lA~~Ll~~G 74 (74) T pfam03900 54 GDIEDAEELGKKLAEELLAQG 74 (74) T ss_pred ECHHHHHHHHHHHHHHHHHCC T ss_conf 858999999999999999683 No 26 >pfam07355 GRDB Glycine/sarcosine/betaine reductase selenoprotein B (GRDB). This family represents a conserved region approximately 350 residues long within the selenoprotein B component of the bacterial glycine, sarcosine and betaine reductase complexes. Probab=67.59 E-value=11 Score=19.00 Aligned_cols=36 Identities=17% Similarity=0.347 Sum_probs=29.1 Q ss_pred HCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEC Q ss_conf 000134686678999999999999997799799983 Q gi|254780245|r 61 LRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFD 96 (120) Q Consensus 61 ~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FD 96 (120) +......+..++.|+..|+.||+.+++.||..|.+- T Consensus 312 fytT~G~gT~v~~ak~fg~eia~~L~~~gVdAvILT 347 (349) T pfam07355 312 FYSTVGNGTSVANSKKFAKEIVKKLKEDGVDAVILT 347 (349) T ss_pred EEEECCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE T ss_conf 689527981089999999999999998499989970 No 27 >smart00812 Alpha_L_fucos Alpha-L-fucosidase. O-Glycosyl hydrolases (EC 3.2.1.-) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site PUBMED:. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Family 29 encompasses alpha-L-fucosidases, which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Deficiency of alpha-L-fucosidase results in the lysosomal storage disease fucosidosis. Probab=66.00 E-value=12 Score=18.78 Aligned_cols=42 Identities=31% Similarity=0.384 Sum_probs=30.2 Q ss_pred HHHHHHHHHCCCCEEEEC---CCCC--------CC-------H-HHHHHHHHHHHHCCCCC Q ss_conf 999999997799799983---8986--------31-------2-25999999999658789 Q gi|254780245|r 79 NLLVERAVKVGVKSVYFD---RGKH--------LY-------C-GRIAALADAVRKGGVSF 120 (120) Q Consensus 79 ~~ia~r~~~~gI~~v~FD---R~g~--------~y-------H-Grvka~ad~~R~~Gl~F 120 (120) +..|+.++++|-+=|+|- .-|| .| + --|++|++++|+.||+| T Consensus 84 ~~Wa~lak~AGaKY~V~TaKHHDGF~lwdS~~s~~n~~~~gpkrDiv~el~~A~rk~Glk~ 144 (384) T smart00812 84 EEWADLFKKAGAKYVVLTAKHHDGFCLWDSKYSNWNAVDTGPKRDLVGELADAVRKRGLKF 144 (384) T ss_pred HHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEE T ss_conf 9999999984995477521304774146788999866567887667999999998769769 No 28 >TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase; InterPro: IPR011984 This enzyme catalyses the ring-opening step in the degradation of 4-hydroxyphenylacetate .. Probab=60.80 E-value=6.1 Score=20.55 Aligned_cols=26 Identities=31% Similarity=0.378 Sum_probs=20.1 Q ss_pred HHHHHHHHHHHHHHHHHCCCCEE-EEC Q ss_conf 78999999999999997799799-983 Q gi|254780245|r 71 IVAATAVGNLLVERAVKVGVKSV-YFD 96 (120) Q Consensus 71 i~aA~~vG~~ia~r~~~~gI~~v-~FD 96 (120) -.+|---=+.|+++|+|.+|+.| ||| T Consensus 88 Rq~AidghkEi~~rakE~~VdTivVfD 114 (343) T TIGR02298 88 RQAAIDGHKEISRRAKEMGVDTIVVFD 114 (343) T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 289999988886431004686699963 No 29 >pfam01120 Alpha_L_fucos Alpha-L-fucosidase. Probab=59.24 E-value=16 Score=18.05 Aligned_cols=45 Identities=24% Similarity=0.229 Sum_probs=31.2 Q ss_pred HHHHHHHHHHHHCCCCEEEEC---CCCC---------------CCH-HHHHHHHHHHHHCCCCC Q ss_conf 999999999997799799983---8986---------------312-25999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFD---RGKH---------------LYC-GRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FD---R~g~---------------~yH-Grvka~ad~~R~~Gl~F 120 (120) .-.+..++.++++|-+-++|- .-|| .++ --|+.|++++|+.||+| T Consensus 92 fd~~~Wa~~ak~AGakY~vlTaKHHDGF~lwdS~~t~~n~~~~~~krDiv~el~~A~rk~Glk~ 155 (344) T pfam01120 92 FDADEWAKLAKAAGAKYVVLTTKHHDGFTMWDSKYSDWNSVDTGPKRDIVGELAKACRKNGIKF 155 (344) T ss_pred CCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEE T ss_conf 7999999999985996588613415775257788999877678999776999999999859867 No 30 >cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=56.35 E-value=18 Score=17.75 Aligned_cols=45 Identities=18% Similarity=0.275 Sum_probs=32.3 Q ss_pred HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999779979998389---8631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F 120 (120) ..|..+++.+.++|..++.|=.+ ..-.-.|...|-+++++.|+++ T Consensus 101 ~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~g~~~ 148 (265) T cd06290 101 QGGYLATQHLIDLGHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEV 148 (265) T ss_pred HHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999998299865560488787019999999999999869999 No 31 >pfam00875 DNA_photolyase DNA photolyase. This domain binds a light harvesting cofactor. Probab=55.07 E-value=19 Score=17.63 Aligned_cols=44 Identities=32% Similarity=0.521 Sum_probs=34.9 Q ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCH-HHHHHHHHHHHHCCCCC Q ss_conf 999999999977997999838986312-25999999999658789 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDRGKHLYC-GRIAALADAVRKGGVSF 120 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR~g~~yH-Grvka~ad~~R~~Gl~F 120 (120) ..+.|.+.+.+-+|+.|+|++.--.|. -|-.++.+.+.+.|++| T Consensus 76 ~~~~l~~l~~~~~i~~v~~n~~~~~~~~~rd~~v~~~l~~~~i~~ 120 (164) T pfam00875 76 PAEVLPELAKELGASAVYWNRDYEPYERRRDAAVKEALREAGIEV 120 (164) T ss_pred HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCEE T ss_conf 589999999967999999916789899999999999998547469 No 32 >cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b Probab=49.98 E-value=23 Score=17.14 Aligned_cols=43 Identities=16% Similarity=0.206 Sum_probs=32.4 Q ss_pred HHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCC Q ss_conf 999999999977997999838---9863122599999999965878 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~ 119 (120) .|..+++.+.++|.+++.|=- +..-...|...|-+++++.|+. T Consensus 103 ~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~G~~~al~~~~i~ 148 (264) T cd01574 103 GARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIA 148 (264) T ss_pred HHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHCCCC T ss_conf 9999999999849982732589977757999999999999986989 No 33 >TIGR01035 hemA glutamyl-tRNA reductase; InterPro: IPR000343 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway . The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin . The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) . This entry represents glutamyl-tRNA reductase (1.2.1.70 from EC), which reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway , . This enzyme required NADPH as a coenzyme.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process. Probab=49.33 E-value=23 Score=17.08 Aligned_cols=46 Identities=26% Similarity=0.397 Sum_probs=40.4 Q ss_pred HHHHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHHHHHHHHHHHH-CCCCC Q ss_conf 78999999999999997799799-9838986312259999999996-58789 Q gi|254780245|r 71 IVAATAVGNLLVERAVKVGVKSV-YFDRGKHLYCGRIAALADAVRK-GGVSF 120 (120) Q Consensus 71 i~aA~~vG~~ia~r~~~~gI~~v-~FDR~g~~yHGrvka~ad~~R~-~Gl~F 120 (120) +-.|-..|.|.|+-+..+||.+| +..|+-. |=..||+-+.+ .++.| T Consensus 190 liGAGeMg~Lva~~L~~~~v~~~~i~NRt~~----rA~~LA~e~~~P~~~~f 237 (436) T TIGR01035 190 LIGAGEMGELVAKHLREKGVGKVLIANRTYE----RAEKLAKELGGPEAVKF 237 (436) T ss_pred EEECCHHHHHHHHHHHHCCCCEEEEECCCHH----HHHHHHHHCCCCCCCCC T ss_conf 9827457999999996489528988556778----99999987078664544 No 34 >cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=47.05 E-value=25 Score=16.87 Aligned_cols=45 Identities=22% Similarity=0.321 Sum_probs=34.4 Q ss_pred HHHHHHHHHHHHCCCCEEEECCCC---CCCHHHHHHHHHHHHHCCCCC Q ss_conf 999999999997799799983898---631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRGK---HLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~g---~~yHGrvka~ad~~R~~Gl~F 120 (120) .-|..+++.+.+.|-.+|.|=.+. ....-|...|.+++++.|+.+ T Consensus 108 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~ 155 (270) T cd06294 108 QAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIPD 155 (270) T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999997699569998189986589999999999999869997 No 35 >cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind Probab=47.01 E-value=25 Score=16.86 Aligned_cols=46 Identities=17% Similarity=0.331 Sum_probs=34.6 Q ss_pred HHHHHHHHHHHHHCCCCEEEECCCCCCC---HHHHHHHHHHHHHCCCCC Q ss_conf 9999999999997799799983898631---225999999999658789 Q gi|254780245|r 75 TAVGNLLVERAVKVGVKSVYFDRGKHLY---CGRIAALADAVRKGGVSF 120 (120) Q Consensus 75 ~~vG~~ia~r~~~~gI~~v~FDR~g~~y---HGrvka~ad~~R~~Gl~F 120 (120) ...|..+++.+.++|-+++.|=.+.-.+ .-|.+.|-+++.+.|+.+ T Consensus 103 ~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~a~~~~gi~~ 151 (270) T cd01545 103 RAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPL 151 (270) T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 9999999999997499659993699777369999999999999839997 No 36 >cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso Probab=46.78 E-value=26 Score=16.84 Aligned_cols=45 Identities=18% Similarity=0.219 Sum_probs=34.1 Q ss_pred HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999779979998389---8631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F 120 (120) .-|..+++.+.++|-.+|.|=-+ ..-..-|...|.+++++.|+.+ T Consensus 106 ~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~ 153 (268) T cd06271 106 AAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPL 153 (268) T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999998598748754887546079999999999999839997 No 37 >KOG0104 consensus Probab=46.57 E-value=26 Score=16.83 Aligned_cols=97 Identities=16% Similarity=0.084 Sum_probs=57.9 Q ss_pred HHCCCCCCCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECC Q ss_conf 75057878824999963870999999627975999985021000001346866789999999999999977997999838 Q gi|254780245|r 18 HLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSVYFDR 97 (120) Q Consensus 18 k~k~~~~~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v~FDR 97 (120) .+-+.+-.-| ++.+.+.+|-+-++++|+.-.||+.--+.+-++.-+---.-...-|.. +|+-..+.-|+.+++-- T Consensus 91 ~llgk~~~~~-~v~ly~~~~p~~e~v~d~~rstV~F~i~d~~~ysvEellAMil~~a~~----~ae~~a~~~Ikd~ViTV 165 (902) T KOG0104 91 DLLGKSLDDP-TVDLYQKRFPFFELVEDPQRSTVVFKISDQEEYSVEELLAMILQYAKS----LAEEYAKQPIKDMVITV 165 (902) T ss_pred HHHCCCCCCC-HHHHHHHCCCCEEECCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH----HHHHHHHCCHHHEEEEC T ss_conf 8747645770-888987118763421367664378981785416799999999999999----99998736143269967 Q ss_pred CCCCCHHHHHHHHHHHHHCCCC Q ss_conf 9863122599999999965878 Q gi|254780245|r 98 GKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 98 ~g~~yHGrvka~ad~~R~~Gl~ 119 (120) .+|-=.--=.|+.++++=+||+ T Consensus 166 P~~F~qaeR~all~Aa~iagl~ 187 (902) T KOG0104 166 PPFFNQAERRALLQAAQIAGLN 187 (902) T ss_pred CCCCCHHHHHHHHHHHHHCCCH T ss_conf 8645889999999898862851 No 38 >PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated Probab=45.73 E-value=21 Score=17.32 Aligned_cols=63 Identities=17% Similarity=0.127 Sum_probs=30.9 Q ss_pred CEEEEEEECCCCEEEEEEEECCC------------HHCCCCCCCCCHHHHHHHHHHHHHHHHHCCC-CEEEECCCCCCCH Q ss_conf 09999996279759999850210------------0000134686678999999999999997799-7999838986312 Q gi|254780245|r 37 HIYGQIIDDSIGHTLVSASSLNE------------PLRSSLKTGANIVAATAVGNLLVERAVKVGV-KSVYFDRGKHLYC 103 (120) Q Consensus 37 hiyAQiIdd~~~~tl~saST~~k------------~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI-~~v~FDR~g~~yH 103 (120) -|++|+ +++.+-.|+++|... .+-+.++. -| +.|-..+-.+|..+ .-.| ..+.|||-.|-|. T Consensus 12 EiH~qL--~t~tKlF~~~~~~~~~~pNt~v~~v~~~~PG~lP~-lN-~~av~~ai~~a~al-~~~i~~~~~f~RK~YfYp 86 (479) T PRK05477 12 EVHVQL--NTKSKIFSGCSTEFGAEPNTNVCPVCLGLPGALPV-LN-KEAVEKAIKAGLAL-NCEIAKRSVFDRKNYFYP 86 (479) T ss_pred EEEEEE--CCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCC-CC-HHHHHHHHHHHHHC-CCCCCCCCEECCCCCCCC T ss_conf 998770--79968578999878999766638420068988776-69-99999999999983-986463315502346689 Q ss_pred H Q ss_conf 2 Q gi|254780245|r 104 G 104 (120) Q Consensus 104 G 104 (120) - T Consensus 87 D 87 (479) T PRK05477 87 D 87 (479) T ss_pred C T ss_conf 8 No 39 >cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational Probab=43.43 E-value=29 Score=16.53 Aligned_cols=46 Identities=17% Similarity=0.283 Sum_probs=34.2 Q ss_pred HHHHHHHHHHHHHCCCCEEEECCCCCC----CHHHHHHHHHHHHHCCCCC Q ss_conf 999999999999779979998389863----1225999999999658789 Q gi|254780245|r 75 TAVGNLLVERAVKVGVKSVYFDRGKHL----YCGRIAALADAVRKGGVSF 120 (120) Q Consensus 75 ~~vG~~ia~r~~~~gI~~v~FDR~g~~----yHGrvka~ad~~R~~Gl~F 120 (120) ..-|..+++.+.++|.+++.|=-+... ..-|...|.+++++.|+.. T Consensus 101 ~~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~~R~~gf~~al~~~~~~~ 150 (268) T cd06273 101 REAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALAEAGLEL 150 (268) T ss_pred HHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCC T ss_conf 99999999999872987479994687777789999999999999809998 No 40 >cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor Probab=42.91 E-value=29 Score=16.48 Aligned_cols=45 Identities=16% Similarity=0.137 Sum_probs=34.2 Q ss_pred HHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999999999977997999838---98631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F 120 (120) .-|..+++.+.++|-.+|.|=- +.....-|.+.|.+++++.|+.+ T Consensus 102 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~ 149 (264) T cd06274 102 DGAAELTRELLAAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLPV 149 (264) T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCC T ss_conf 999999999998599669997689877309999999999999779987 No 41 >PRK07666 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional Probab=42.55 E-value=30 Score=16.45 Aligned_cols=43 Identities=26% Similarity=0.375 Sum_probs=33.1 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCC Q ss_conf 99999999999999779979998389863122599999999965878 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~ 119 (120) ++.-+|+.+|+..-+.|.+-+..||... ++..+++.+++.|.+ T Consensus 14 as~GIG~aiA~~la~~Ga~V~l~~r~~~----~l~~~~~~i~~~g~~ 56 (238) T PRK07666 14 AGRGIGRAVAIALAKEGVNVGLLARSEE----NLKAVAKEVEAEGVK 56 (238) T ss_pred CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCCC T ss_conf 3778999999999987998999989999----999999999955992 No 42 >cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=41.05 E-value=31 Score=16.31 Aligned_cols=45 Identities=16% Similarity=0.212 Sum_probs=33.2 Q ss_pred HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999779979998389---8631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F 120 (120) ..|..+++.+.++|-..|.|=-+ ..-..-|...|.+++++.|+++ T Consensus 104 ~a~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~ 151 (268) T cd06277 104 SGAYAATEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKALLDHGIPF 151 (268) T ss_pred HHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999997099836997278888129999999999999859999 No 43 >cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor Probab=40.90 E-value=32 Score=16.29 Aligned_cols=46 Identities=15% Similarity=0.145 Sum_probs=35.5 Q ss_pred HHHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999977997999838---98631225999999999658789 Q gi|254780245|r 75 TAVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 75 ~~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ...|..+++.+.++|-..|.|=- ..+-..-|...|.++++++|+.+ T Consensus 96 ~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~gf~~al~~~g~~~ 144 (261) T cd06272 96 EKAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGISI 144 (261) T ss_pred HHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 9999999999998699828996698887359999999999999859985 No 44 >cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi Probab=40.19 E-value=32 Score=16.23 Aligned_cols=45 Identities=20% Similarity=0.303 Sum_probs=33.0 Q ss_pred HHHHHHHHHHHHCCCCEEEECCCC---CCCHHHHHHHHHHHHHCCCCC Q ss_conf 999999999997799799983898---631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRGK---HLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~g---~~yHGrvka~ad~~R~~Gl~F 120 (120) ..|..+++.+.++|-.++.|=-+. .-..-|...|-+++.++|+.+ T Consensus 102 ~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~ 149 (268) T cd06270 102 QGGYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIAL 149 (268) T ss_pred HHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999998399838984598888319999999999999859997 No 45 >PRK05866 short chain dehydrogenase; Provisional Probab=39.35 E-value=33 Score=16.15 Aligned_cols=42 Identities=26% Similarity=0.398 Sum_probs=32.0 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 9999999999999977997999838986312259999999996587 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl 118 (120) ++.=+|..+|+..-+.|-+-+..||+.. ++.++++.+.+.|- T Consensus 48 assGIG~aiA~~la~~Ga~Vvl~~R~~~----~l~~~~~~i~~~g~ 89 (290) T PRK05866 48 ASSGIGEAAAEKFARRGATVVAVARRKD----LLDAVADRITAAGG 89 (290) T ss_pred CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC T ss_conf 1309999999999986998999989999----99999999996499 No 46 >cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a Probab=38.56 E-value=34 Score=16.07 Aligned_cols=45 Identities=18% Similarity=0.233 Sum_probs=33.4 Q ss_pred HHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999999999977997999838---98631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ..|.++++.+.++|-.+++|=- +.+-..-|...|.+++.+.|++| T Consensus 103 ~~~~~a~~~Li~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~i~~ 150 (269) T cd06275 103 EGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPV 150 (269) T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999998299717755699777169999999999999859997 No 47 >TIGR03206 benzo_BadH 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase. Members of this protein family are the enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase. The enzymatic properties were confirmed experimentally in Rhodopseudomonas palustris; the enzyme is homotetrameric, and not sensitive to oxygen. This enzyme is part of proposed pathway for degradation of benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from the analogous in Thauera aromatica. It also may occur in degradation of the non-aromatic compound cyclohexane-1-carboxylate. Probab=38.44 E-value=35 Score=16.06 Aligned_cols=43 Identities=21% Similarity=0.338 Sum_probs=31.9 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCC Q ss_conf 99999999999999779979998389863122599999999965878 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~ 119 (120) ++.-+|..++++..+.|-+-+.+||+.. .+..+++.+++.|-+ T Consensus 11 ~s~GIG~aia~~la~~Ga~V~i~~r~~~----~~~~~~~~l~~~g~~ 53 (250) T TIGR03206 11 GGGGIGGATCRRFAEEGAKVAVFDLNRE----AAEKVAADIRAKGGN 53 (250) T ss_pred CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCCC T ss_conf 5768999999999987999999979889----999999999953992 No 48 >PRK13381 peptidase T; Provisional Probab=38.23 E-value=35 Score=16.04 Aligned_cols=24 Identities=17% Similarity=0.374 Sum_probs=8.3 Q ss_pred HHHHHHHHHHHCCCCEEEECCCCC Q ss_conf 999999999977997999838986 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDRGKH 100 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR~g~ 100 (120) +++.|++.+++.|++.|..|-.|| T Consensus 39 la~~L~~eL~~lGl~~v~~d~~g~ 62 (413) T PRK13381 39 LAKLLAKELRELGLEDIVIDEHAI 62 (413) T ss_pred HHHHHHHHHHHCCCEEEEECCCEE T ss_conf 999999999976993688669759 No 49 >PRK06181 short chain dehydrogenase; Provisional Probab=38.13 E-value=35 Score=16.03 Aligned_cols=40 Identities=28% Similarity=0.473 Sum_probs=18.8 Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC Q ss_conf 99999999999997799799983898631225999999999658 Q gi|254780245|r 74 ATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG 117 (120) Q Consensus 74 A~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G 117 (120) +.-+|..+|+..-+.|-+-+..||+.. ++.++++.+++.| T Consensus 10 ssGIG~a~A~~la~~Ga~vvl~~r~~~----~l~~~~~~l~~~g 49 (263) T PRK06181 10 SEGIGRALAVRLARAGARLVLAARNEE----RLASLAQELANYG 49 (263) T ss_pred CCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCC T ss_conf 019999999999987998999988999----9999999999549 No 50 >PRK10703 DNA-binding transcriptional repressor PurR; Provisional Probab=38.02 E-value=35 Score=16.02 Aligned_cols=47 Identities=19% Similarity=0.270 Sum_probs=36.0 Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999999999999779979998389---8631225999999999658789 Q gi|254780245|r 74 ATAVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 74 A~~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F 120 (120) ...-|.+.++.+.+.|-.+|.|=-+ ......|...|.+++++.|+.+ T Consensus 162 ~~~~~~~a~~~L~~~Ghr~Ia~i~~~~~~~~~~~R~~gf~~al~~~gl~~ 211 (335) T PRK10703 162 AFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKV 211 (335) T ss_pred HHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 79999999999997599869999588765217899999999999859998 No 51 >pfam06370 DUF1069 Protein of unknown function (DUF1069). This family consists of several Maize streak virus 21.7 kDa proteins. The function of this family is unknown. Probab=36.45 E-value=19 Score=17.65 Aligned_cols=22 Identities=32% Similarity=0.598 Sum_probs=18.0 Q ss_pred HHHHCCCCEEEECCCCCCCHHH Q ss_conf 9997799799983898631225 Q gi|254780245|r 84 RAVKVGVKSVYFDRGKHLYCGR 105 (120) Q Consensus 84 r~~~~gI~~v~FDR~g~~yHGr 105 (120) +....|+.+|.|.-||.+|||- T Consensus 161 rssgigvdevtyasggdryhgg 182 (206) T pfam06370 161 RSSGIGVDEVTYASGGDRYHGG 182 (206) T ss_pred ECCCCCCEEEEECCCCCCCCCC T ss_conf 4067661057761578624589 No 52 >TIGR00666 PBP4 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase; InterPro: IPR000667 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This family of serine peptidases belong to MEROPS peptidase family S13 (D-Ala-D-Ala carboxypeptidase C, clan SE). The predicted active site residues for members of this family and family S12 occur in the motif SXXK. D-Ala-D-Ala carboxypeptidase C is involved in the metabolism of cell components ; it is synthesised with a leader peptide to target it to the cell membrane . After cleavage of the leader peptide, the enzyme is retained in the membrane by a C-terminal anchor . There are three families of serine-type D-Ala-D-Ala peptidase (designated S11, S12 and S13), which are also known as low molecular weight penicillin-binding proteins . Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence similarity around their active sites to assume a distant evolutionary relationship to other clan members; members of the S13 family also bind penicillin and have D-amino-peptidase activity. Proteases of family S11 have exclusive D-Ala-D-Ala peptidase activity, while some members of S12 are C beta-lactamases . ; GO: 0004185 serine carboxypeptidase activity, 0006508 proteolysis. Probab=34.63 E-value=28 Score=16.61 Aligned_cols=20 Identities=35% Similarity=0.732 Sum_probs=13.2 Q ss_pred CCCHH--HHHHHHHHHHHCCCC Q ss_conf 63122--599999999965878 Q gi|254780245|r 100 HLYCG--RIAALADAVRKGGVS 119 (120) Q Consensus 100 ~~yHG--rvka~ad~~R~~Gl~ 119 (120) --||| |+..+++.++..|++ T Consensus 76 tWyhGaar~~~l~~~LK~~GV~ 97 (427) T TIGR00666 76 TWYHGAARLDKLVEELKKSGVK 97 (427) T ss_pred CCHHHHHHHHHHHHHHHHCCCC T ss_conf 2012478999999999864880 No 53 >cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses. Probab=32.91 E-value=43 Score=15.53 Aligned_cols=38 Identities=18% Similarity=0.210 Sum_probs=23.4 Q ss_pred CEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 09999996279759999850210000013468667899999999999999 Q gi|254780245|r 37 HIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAV 86 (120) Q Consensus 37 hiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~ 86 (120) ++.+.+.+..+...+. .+ -.++.+.|..+|..+|+.++ T Consensus 254 ~l~~~v~s~DG~~~~~-~~-----------~~g~~~~a~~lG~~lA~~Ll 291 (292) T cd00494 254 KLKGLVGSPDGKRLIE-GE-----------VRGNIEDAEELGKKLAEELL 291 (292) T ss_pred EEEEEEECCCCCEEEE-EE-----------EEECHHHHHHHHHHHHHHHH T ss_conf 9999999888987999-99-----------99778999999999999971 No 54 >PRK05650 short chain dehydrogenase; Provisional Probab=32.89 E-value=43 Score=15.53 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=6.9 Q ss_pred HHHHHHHHHHHCCCCEEEECC Q ss_conf 999999999977997999838 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDR 97 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR 97 (120) +|..+|+...+.|..-+..|| T Consensus 12 IG~alA~~la~~G~~V~l~~r 32 (270) T PRK05650 12 LGRAIALRWAREGWRLALADV 32 (270) T ss_pred HHHHHHHHHHHCCCEEEEEEC T ss_conf 999999999988998999979 No 55 >PRK10727 DNA-binding transcriptional regulator GalR; Provisional Probab=32.77 E-value=43 Score=15.51 Aligned_cols=45 Identities=13% Similarity=0.112 Sum_probs=35.0 Q ss_pred HHHHHHHHHHHHCCCCEEEECCCC---CCCHHHHHHHHHHHHHCCCCC Q ss_conf 999999999997799799983898---631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRGK---HLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~g---~~yHGrvka~ad~~R~~Gl~F 120 (120) .-|.+.++.+.+.|-.+|.|=-+. .-...|...|-+++++.||.+ T Consensus 162 ~~~~~a~~~L~~~Ghr~Ia~i~~~~~~~~~~~R~~g~~~al~~~gl~~ 209 (342) T PRK10727 162 YGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPA 209 (342) T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999997499759999689888359999999999999769999 No 56 >PRK10014 DNA-binding transcriptional repressor MalI; Provisional Probab=32.60 E-value=43 Score=15.50 Aligned_cols=47 Identities=21% Similarity=0.347 Sum_probs=35.6 Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCC--CCCCH-HHHHHHHHHHHHCCCCC Q ss_conf 9999999999999779979998389--86312-25999999999658789 Q gi|254780245|r 74 ATAVGNLLVERAVKVGVKSVYFDRG--KHLYC-GRIAALADAVRKGGVSF 120 (120) Q Consensus 74 A~~vG~~ia~r~~~~gI~~v~FDR~--g~~yH-Grvka~ad~~R~~Gl~F 120 (120) -...|..+++.+.+.|-..|.|=-+ ..... -|...|-+++++.|+.| T Consensus 166 ~~~~~~~a~~~L~~~Ghr~Ia~i~~~~~~~~~~~R~~gf~~al~~~~l~~ 215 (342) T PRK10014 166 NMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPF 215 (342) T ss_pred HHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 69999999999987599869999578886339999999999999769998 No 57 >PRK08278 short chain dehydrogenase; Provisional Probab=32.41 E-value=43 Score=15.48 Aligned_cols=45 Identities=20% Similarity=0.255 Sum_probs=26.5 Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCC---CCHHHHHHHHHHHHHCCC Q ss_conf 999999999999977997999838986---312259999999996587 Q gi|254780245|r 74 ATAVGNLLVERAVKVGVKSVYFDRGKH---LYCGRIAALADAVRKGGV 118 (120) Q Consensus 74 A~~vG~~ia~r~~~~gI~~v~FDR~g~---~yHGrvka~ad~~R~~Gl 118 (120) +.-+|..+|+++.+.|-+-+..+|+.. +..|.+.+.++.+++.|- T Consensus 15 s~GIG~aiA~~la~~Ga~Vvi~~r~~~~~~~l~~~~~~~a~e~~~~g~ 62 (273) T PRK08278 15 SRGIGLAIALRAARDGANIVIAAKTAEPHPKLPGTIHTAAAEIEAAGG 62 (273) T ss_pred CCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 659999999999987998999967722213345489999999997499 No 58 >KOG0408 consensus Probab=31.11 E-value=46 Score=15.35 Aligned_cols=89 Identities=26% Similarity=0.306 Sum_probs=63.1 Q ss_pred CCCEEEEEEECCCEEEEEEECCCCEEEEEEEECCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEE-EECCCCCCCH Q ss_conf 882499996387099999962797599998502100000134686678999999999999997799799-9838986312 Q gi|254780245|r 25 GRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAATAVGNLLVERAVKVGVKSV-YFDRGKHLYC 103 (120) Q Consensus 25 ~~pRL~V~rSnkhiyAQiIdd~~~~tl~saST~~k~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI~~v-~FDR~g~~yH 103 (120) +-|=..|.-|-.|-.+||. |..+.++...|---.-|+...+. .--||.-.|-..+.+++++|+..| +--+| +=- T Consensus 78 eiPi~hIraS~NNTivtVt-d~kg~vi~~~ScgteGFrntrkg--T~iAaQtaavaa~~r~v~~G~~~vrV~VkG--lGp 152 (190) T KOG0408 78 EIPIIHIRASFNNTIVTVT-DVKGEVISWSSCGTEGFRNTRKG--TPIAAQTAAVAAIRRAVDQGMQTVRVRVKG--LGP 152 (190) T ss_pred CCCEEEEEECCCCEEEEEE-CCCCCEEEEEECCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHCCEEEEEEEEC--CCC T ss_conf 0546899853787089998-06884898850242012356668--850677777899999997163699999845--886 Q ss_pred HHHHHHHHHHHHCCCC Q ss_conf 2599999999965878 Q gi|254780245|r 104 GRIAALADAVRKGGVS 119 (120) Q Consensus 104 Grvka~ad~~R~~Gl~ 119 (120) ||..|+ .+++-.||. T Consensus 153 GRmsa~-kgl~m~Gl~ 167 (190) T KOG0408 153 GRMSAL-KGLRMGGLL 167 (190) T ss_pred CHHHHH-HHHHHCCEE T ss_conf 478887-655215569 No 59 >PRK10423 transcriptional repressor RbsR; Provisional Probab=30.22 E-value=47 Score=15.26 Aligned_cols=45 Identities=18% Similarity=0.254 Sum_probs=34.2 Q ss_pred HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999779979998389---8631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F 120 (120) .-|.+.++.+.++|-..|.|=-+ .....-|...|-+++++.||.+ T Consensus 160 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~gf~~al~~~gl~~ 207 (327) T PRK10423 160 LGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNI 207 (327) T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999997599749996688766179999999999999859998 No 60 >PRK07454 short chain dehydrogenase; Provisional Probab=29.25 E-value=49 Score=15.16 Aligned_cols=42 Identities=26% Similarity=0.383 Sum_probs=24.9 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 9999999999999977997999838986312259999999996587 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl 118 (120) ++.-+|..+|++.-+.|.+-+..||... ++..+++.+++.|. T Consensus 14 as~GIG~a~A~~la~~G~~V~l~~R~~~----~l~~~~~e~~~~g~ 55 (241) T PRK07454 14 ASRGIGKATALAFAKAGWDLALVARSQD----ALEALAEELRSTGV 55 (241) T ss_pred CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC T ss_conf 5878999999999987998999989999----99999999996599 No 61 >COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism] Probab=28.66 E-value=50 Score=15.10 Aligned_cols=37 Identities=35% Similarity=0.478 Sum_probs=27.1 Q ss_pred HHHHHHHCCCCEEEECCCCCCCHHH---HHHHHHHHHHCCCC Q ss_conf 9999997799799983898631225---99999999965878 Q gi|254780245|r 81 LVERAVKVGVKSVYFDRGKHLYCGR---IAALADAVRKGGVS 119 (120) Q Consensus 81 ia~r~~~~gI~~v~FDR~g~~yHGr---vka~ad~~R~~Gl~ 119 (120) --++|.+.||..++||+..|. +| -.++++.+++.+.. T Consensus 42 ~lerA~~~gIpt~~~~~k~~~--~r~~~d~~l~~~l~~~~~d 81 (200) T COG0299 42 ALERAAKAGIPTVVLDRKEFP--SREAFDRALVEALDEYGPD 81 (200) T ss_pred HHHHHHHCCCCEEEECCCCCC--CHHHHHHHHHHHHHHCCCC T ss_conf 999999849988974445678--7789999999999852999 No 62 >PRK08277 D-mannonate oxidoreductase; Provisional Probab=28.65 E-value=50 Score=15.09 Aligned_cols=41 Identities=17% Similarity=0.434 Sum_probs=25.2 Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 999999999999977997999838986312259999999996587 Q gi|254780245|r 74 ATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118 (120) Q Consensus 74 A~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl 118 (120) +.-+|.-+|+...+.|-+-+..||+.. .+.++++.+++.|- T Consensus 19 s~GIG~aia~~la~~Ga~V~i~~~~~~----~~~~~~~~l~~~g~ 59 (278) T PRK08277 19 GGVLGGAMAKELARAGAKVAILDRNQE----KAEAVVEEIKANGG 59 (278) T ss_pred CCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC T ss_conf 748999999999987998999979889----99999999984599 No 63 >cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=28.53 E-value=51 Score=15.08 Aligned_cols=44 Identities=18% Similarity=0.243 Sum_probs=32.1 Q ss_pred HHHHHHHHHHHCCCCEEEECCCCC---CCHHHHHHHHHHHHHCCCCC Q ss_conf 999999999977997999838986---31225999999999658789 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDRGKH---LYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR~g~---~yHGrvka~ad~~R~~Gl~F 120 (120) -|+++++.+.+.|-.++.|=.+.. -..-|...|-+++++.|+.+ T Consensus 103 ~~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~G~~~a~~~~~~~~ 149 (269) T cd06293 103 GGRLATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIPE 149 (269) T ss_pred HHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 99999999998299838995488776339999999999999769999 No 64 >cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators. Probab=28.53 E-value=51 Score=15.08 Aligned_cols=45 Identities=22% Similarity=0.245 Sum_probs=32.6 Q ss_pred HHHHHHHHHHHHCCCCEEEECCCCCCC----HHHHHHHHHHHHHCCCCC Q ss_conf 999999999997799799983898631----225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRGKHLY----CGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~g~~y----HGrvka~ad~~R~~Gl~F 120 (120) .-|..+++.+.++|-.+|.|=-+.... .=|...|-+++.+.|+.+ T Consensus 102 ~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~gf~~a~~~~g~~~ 150 (268) T cd06298 102 KAAFEATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEALSEANIEF 150 (268) T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 9999999999972996699996787776259999999999999849997 No 65 >PRK07775 short chain dehydrogenase; Provisional Probab=28.37 E-value=51 Score=15.07 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=24.5 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC Q ss_conf 999999999999997799799983898631225999999999658 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG 117 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G 117 (120) ++.-+|..+|+++-+.|.+-+..+|... ++.++++.+++.| T Consensus 18 AssGIG~aiA~~la~~G~~V~l~~R~~e----~l~~~~~~l~~~g 58 (275) T PRK07775 18 ASSGIGAATAIELAAHGFPVALGARRVE----KCEEIVDKIRADG 58 (275) T ss_pred CCHHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCC T ss_conf 2359999999999987998999989899----9999999999649 No 66 >PRK08243 4-hydroxybenzoate 3-monooxygenase; Validated Probab=28.36 E-value=51 Score=15.06 Aligned_cols=12 Identities=0% Similarity=-0.144 Sum_probs=5.5 Q ss_pred EECCCCCCCHHH Q ss_conf 983898631225 Q gi|254780245|r 94 YFDRGKHLYCGR 105 (120) Q Consensus 94 ~FDR~g~~yHGr 105 (120) .|+++-+.+|.+ T Consensus 260 ~~~~sv~~lrs~ 271 (392) T PRK08243 260 SIEKSIAPLRSF 271 (392) T ss_pred EEEEEEEEHHHH T ss_conf 345666205655 No 67 >cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=27.98 E-value=52 Score=15.02 Aligned_cols=46 Identities=22% Similarity=0.313 Sum_probs=33.5 Q ss_pred HHHHHHHHHHHHHCCCCEEEECC--CCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999977997999838--98631225999999999658789 Q gi|254780245|r 75 TAVGNLLVERAVKVGVKSVYFDR--GKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 75 ~~vG~~ia~r~~~~gI~~v~FDR--~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ...|.+.++.+.+.|-..|.|=- ....-+-|...|.+++++.|+.+ T Consensus 94 ~~~~~~a~~~L~~~Ghr~I~~ig~~~~~~~~~R~~Gf~~al~~~g~~~ 141 (265) T cd01543 94 AAIGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYEC 141 (265) T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999999869974999899988069999999999999779997 No 68 >PRK11041 DNA-binding transcriptional regulator CytR; Provisional Probab=27.78 E-value=52 Score=15.00 Aligned_cols=45 Identities=20% Similarity=0.243 Sum_probs=34.7 Q ss_pred HHHHHHHHHHHHCCCCEEEECCC---CCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999779979998389---8631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRG---KHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~---g~~yHGrvka~ad~~R~~Gl~F 120 (120) .-|...++.+.+.|-..|.|=-+ ....+-|...|.++++++|+.+ T Consensus 170 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~G~~~al~~~gl~~ 217 (341) T PRK11041 170 TAAFEAVNYLYELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITV 217 (341) T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999997499769999689877689999999999999869999 No 69 >PRK00819 RNA 2'-phosphotransferase-like protein; Reviewed Probab=27.70 E-value=30 Score=16.39 Aligned_cols=22 Identities=23% Similarity=0.489 Sum_probs=16.8 Q ss_pred CCCCCHHHHHHHHHHHHHCCCC Q ss_conf 9863122599999999965878 Q gi|254780245|r 98 GKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 98 ~g~~yHGrvka~ad~~R~~Gl~ 119 (120) ..+.|||--..+.+.+++.||+ T Consensus 93 p~~lyHGT~~~~~~~I~~~GL~ 114 (179) T PRK00819 93 PQFLYHGTARRFLDSILEQGIK 114 (179) T ss_pred CCEEEECCCHHHHHHHHHHCCC T ss_conf 8666734579999999996687 No 70 >PRK08862 short chain dehydrogenase; Provisional Probab=27.49 E-value=53 Score=14.97 Aligned_cols=17 Identities=24% Similarity=0.208 Sum_probs=8.2 Q ss_pred HHHHHHHHHHHHHHHHC Q ss_conf 89999999999999977 Q gi|254780245|r 72 VAATAVGNLLVERAVKV 88 (120) Q Consensus 72 ~aA~~vG~~ia~r~~~~ 88 (120) .....+....+...++. T Consensus 117 ~~~~~~~~~~~~~m~~~ 133 (227) T PRK08862 117 STLFTYGQVAAERMRKR 133 (227) T ss_pred HHHHHHHHHHHHHHHHC T ss_conf 69999999999999966 No 71 >pfam00289 CPSase_L_chain Carbamoyl-phosphate synthase L chain, N-terminal domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. Probab=27.34 E-value=53 Score=14.95 Aligned_cols=49 Identities=18% Similarity=0.207 Sum_probs=39.4 Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 6678999999999999997799799983898631225999999999658789 Q gi|254780245|r 69 ANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 69 ~ni~aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) +....+++-.+.|-+-+.+.|+..|. +||-|----..||+.+.++|+.| T Consensus 53 ~~~~~~Yl~~~~Ii~ia~~~~~~aih---pGyGflsEn~~fa~~~~~~Gi~f 101 (109) T pfam00289 53 GPASESYLNIERILDIAEKEGADAIH---PGYGFLSENAEFAEACEKAGITF 101 (109) T ss_pred CCCCCCCCCHHHHHHHHHHHCCCEEE---CCCCCCCCCHHHHHHHHHCCCEE T ss_conf 98321113799999999981889687---79762335999999999888989 No 72 >cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription Probab=27.32 E-value=53 Score=14.95 Aligned_cols=45 Identities=20% Similarity=0.291 Sum_probs=33.3 Q ss_pred HHHHHHHHHHHHCCCCEEEECCCCC---C-CHHHHHHHHHHHHHCCCCC Q ss_conf 9999999999977997999838986---3-1225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRGKH---L-YCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~g~---~-yHGrvka~ad~~R~~Gl~F 120 (120) ..|.++++.+.+.|-.+|.|=-+.. - -+-|...|-+++++.|+.+ T Consensus 98 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~ 146 (265) T cd06291 98 EGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEV 146 (265) T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 9999999999973996499996688887489999999999999769996 No 73 >cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Probab=27.20 E-value=54 Score=14.94 Aligned_cols=45 Identities=18% Similarity=0.314 Sum_probs=31.1 Q ss_pred HHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999999999977997999838---98631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ..|+.+++.+.++|-.++.|=- +..-.-=|.+.|.+++++.|+.+ T Consensus 101 ~a~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~ 148 (267) T cd06284 101 AAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLPA 148 (267) T ss_pred HHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999997099769996288887259999999999999839985 No 74 >cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=26.81 E-value=54 Score=14.90 Aligned_cols=46 Identities=26% Similarity=0.235 Sum_probs=33.5 Q ss_pred HHHHHHHHHHHHHCCCCEEEEC--CCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999999999997799799983--898631225999999999658789 Q gi|254780245|r 75 TAVGNLLVERAVKVGVKSVYFD--RGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 75 ~~vG~~ia~r~~~~gI~~v~FD--R~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ..-|..+++.+.++|-.+|.|= ...+...-|...|.+++.+.|+.+ T Consensus 100 ~~~~~~a~~~L~~~Ghr~I~~l~g~~~~~~~~R~~Gf~~al~~~gi~~ 147 (263) T cd06280 100 RAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAP 147 (263) T ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCC T ss_conf 999999999998608966999938998439999999999999769997 No 75 >PRK12857 putative aldolase; Reviewed Probab=26.70 E-value=55 Score=14.89 Aligned_cols=38 Identities=21% Similarity=0.244 Sum_probs=30.0 Q ss_pred HHHHHHHCCCCEEEECCCCCCCH---HHHHHHHHHHHHCCC Q ss_conf 99999977997999838986312---259999999996587 Q gi|254780245|r 81 LVERAVKVGVKSVYFDRGKHLYC---GRIAALADAVRKGGV 118 (120) Q Consensus 81 ia~r~~~~gI~~v~FDR~g~~yH---Grvka~ad~~R~~Gl 118 (120) ..+++++.|.+.|.||-+.+.|. -..+.+++-++..|+ T Consensus 89 ~i~~ai~~Gf~SVM~DgS~l~~eeNi~~Tk~vv~~ah~~gv 129 (284) T PRK12857 89 QVMKCIRNGFTSVMIDGSKLPLEENIALTKKVVEIAHAVGV 129 (284) T ss_pred HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 99999980998799728989999999999999999987089 No 76 >cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=26.68 E-value=55 Score=14.88 Aligned_cols=44 Identities=18% Similarity=0.315 Sum_probs=32.1 Q ss_pred HHHHHHHHHHHCCCCEEEECCCCC---CCHHHHHHHHHHHHHCCCCC Q ss_conf 999999999977997999838986---31225999999999658789 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDRGKH---LYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR~g~---~yHGrvka~ad~~R~~Gl~F 120 (120) -|.++++.+.++|-.++.|=.+.. .-..|...|-+++.++|+.+ T Consensus 101 ~~~~~~~~Li~~G~~~i~~l~~~~~~~~~~~R~~Gf~~a~~~~~~~~ 147 (265) T cd06285 101 GGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEV 147 (265) T ss_pred HHHHHHHHHHHHCCCCEEECCCCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 99999999998388658754788777059999999999999869998 No 77 >PRK07035 short chain dehydrogenase; Provisional Probab=26.62 E-value=55 Score=14.88 Aligned_cols=40 Identities=20% Similarity=0.324 Sum_probs=20.4 Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC Q ss_conf 99999999999997799799983898631225999999999658 Q gi|254780245|r 74 ATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG 117 (120) Q Consensus 74 A~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G 117 (120) +.-+|..+|+.+.+.|-.-+..||... .+.++++.+++.| T Consensus 17 s~GIG~aia~~la~~Ga~V~i~~r~~~----~l~~~~~~i~~~g 56 (252) T PRK07035 17 SRGIGEAIAKLLAQQGAHVIVSSRKLD----GCQAVADAIVAAG 56 (252) T ss_pred CCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCC T ss_conf 749999999999987998999979889----9999999999649 No 78 >PRK08185 hypothetical protein; Provisional Probab=26.44 E-value=55 Score=14.86 Aligned_cols=39 Identities=28% Similarity=0.286 Sum_probs=30.2 Q ss_pred HHHHHHHHCCCCEEEECCCCCCCHH---HHHHHHHHHHHCCC Q ss_conf 9999999779979998389863122---59999999996587 Q gi|254780245|r 80 LLVERAVKVGVKSVYFDRGKHLYCG---RIAALADAVRKGGV 118 (120) Q Consensus 80 ~ia~r~~~~gI~~v~FDR~g~~yHG---rvka~ad~~R~~Gl 118 (120) ...+++.+.|.+.|.||-+.+.|.- +.+.+++-++..|+ T Consensus 82 e~~~~ai~~GFsSVM~DgS~lp~eeNi~~Tk~vv~~ah~~gv 123 (283) T PRK08185 82 EDVMRAIRCGFTSVMIDGSLLPYEENVALTKEVVELAHKVGV 123 (283) T ss_pred HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 999999982998798638989999999999999999986598 No 79 >PRK12737 gatY tagatose-bisphosphate aldolase; Reviewed Probab=26.37 E-value=55 Score=14.85 Aligned_cols=38 Identities=13% Similarity=0.280 Sum_probs=29.2 Q ss_pred HHHHHHHCCCCEEEECCCCCCCHH---HHHHHHHHHHHCCC Q ss_conf 999999779979998389863122---59999999996587 Q gi|254780245|r 81 LVERAVKVGVKSVYFDRGKHLYCG---RIAALADAVRKGGV 118 (120) Q Consensus 81 ia~r~~~~gI~~v~FDR~g~~yHG---rvka~ad~~R~~Gl 118 (120) ..++|++.|.+.|.||-+.+.|.- ..+.+++-++..|+ T Consensus 89 ~~~~ai~~GftSVM~DgS~lp~eeNi~~T~~vv~~Ah~~gv 129 (284) T PRK12737 89 DIKKKVRAGIRSVMIDGSHLSFEENIAIVKEVVEFCHRYDA 129 (284) T ss_pred HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 99999981998798709999999999999999998645288 No 80 >PRK07832 short chain dehydrogenase; Provisional Probab=26.35 E-value=55 Score=14.85 Aligned_cols=38 Identities=18% Similarity=0.212 Sum_probs=15.7 Q ss_pred HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHC Q ss_conf 999999999999779979998389863122599999999965 Q gi|254780245|r 75 TAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKG 116 (120) Q Consensus 75 ~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~ 116 (120) .=+|..+|....+.|..-+..||+.- .+.++++.++.. T Consensus 10 sGIG~a~A~~la~~Ga~v~l~~r~~~----~l~~~~~~l~~~ 47 (272) T PRK07832 10 SGIGRATALRLAAQGAELFLTDRDAD----GLAQTVADARAL 47 (272) T ss_pred HHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHC T ss_conf 19999999999988998999989889----999999999845 No 81 >TIGR01830 3oxo_ACP_reduc 3-oxoacyl-(acyl-carrier-protein) reductase; InterPro: IPR011284 This entry represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis found in many plant and bacterial species. This enzyme is involved in type II fatty acid biosynthesis, where the individual metabolic transformations are carried out by different enzymes rather than by a single enzyme as occurs in type I fatty acid biosynthesis . Structural studies show that the enzyme is a tetramer which forms a typical Rossman fold , . Unlike other members of the short-chain dehydrogenase/reductase superfamily, the enzyme undergoes a marked conformational change upon binding of the NADP(H)cofactor. This conformational change aligns the side chains of the catalytic triad at the active site in an active conformation and increases the affinity of the enzyme for its substrate.; GO: 0004316 3-oxoacyl-[acyl-carrier-protein] reductase activity, 0051287 NAD binding, 0006633 fatty acid biosynthetic process. Probab=25.94 E-value=56 Score=14.80 Aligned_cols=44 Identities=18% Similarity=0.295 Sum_probs=36.1 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCC Q ss_conf 99999999999999779979998389863122599999999965878 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~ 119 (120) |+.=||.-||+++-+.|.+=++-||+... .+.+++|.+++.|.+ T Consensus 6 asRGIG~AIA~~LA~~Ga~V~i~y~~~e~---~~~~~~~e~~~~G~~ 49 (238) T TIGR01830 6 ASRGIGRAIALKLAKEGAKVIITYRTSEE---GAEEVVEEIKELGVK 49 (238) T ss_pred CCCHHHHHHHHHHHHCCCEEEEECCCCHH---HHHHHHHHHHHCCCE T ss_conf 78616799999998679959996598257---888999999856975 No 82 >PRK12827 short chain dehydrogenase; Provisional Probab=25.92 E-value=57 Score=14.80 Aligned_cols=46 Identities=15% Similarity=0.166 Sum_probs=33.0 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 9999999999999977997999838986312259999999996587 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl 118 (120) ++.-+|..+|++..+.|-+-++.|+....-.-...++++.+++.|- T Consensus 14 as~GIG~aia~~la~~Ga~V~i~~~~~~~~~~~~~~~~~~~~~~g~ 59 (251) T PRK12827 14 GSGGLGRAIAVRLAADGADVIVLDIHPMRGRAEAEAVAALIEAAGG 59 (251) T ss_pred CCCHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHCCC T ss_conf 2558999999999987998999848885328999999999996498 No 83 >PRK06457 pyruvate dehydrogenase; Provisional Probab=25.75 E-value=57 Score=14.78 Aligned_cols=16 Identities=19% Similarity=0.243 Sum_probs=7.5 Q ss_pred CCCCCCHHHHHHHHHHHH Q ss_conf 898631225999999999 Q gi|254780245|r 97 RGKHLYCGRIAALADAVR 114 (120) Q Consensus 97 R~g~~yHGrvka~ad~~R 114 (120) =|++.|+ +.+|.-++| T Consensus 424 DGsf~m~--~~EL~Ta~r 439 (549) T PRK06457 424 DGGFAMT--MMELITAKK 439 (549) T ss_pred CCHHHCC--HHHHHHHHH T ss_conf 6077514--899999999 No 84 >PRK06139 short chain dehydrogenase; Provisional Probab=25.66 E-value=57 Score=14.77 Aligned_cols=42 Identities=21% Similarity=0.339 Sum_probs=29.8 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 9999999999999977997999838986312259999999996587 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl 118 (120) ++.=||..+|+..-+.|-.-|..||+.. .+.++++.+++.|- T Consensus 14 ASsGIG~aiA~~~A~~Ga~Vvl~~R~~~----~L~~~a~e~~~~G~ 55 (324) T PRK06139 14 ASSGIGRATAEAFARRGARLVLAARDEE----ALFEVAEECRALGA 55 (324) T ss_pred HHHHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC T ss_conf 2549999999999987998999989999----99999999995499 No 85 >PRK05653 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Validated Probab=24.99 E-value=59 Score=14.70 Aligned_cols=38 Identities=26% Similarity=0.490 Sum_probs=16.0 Q ss_pred HHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC Q ss_conf 999999999997799799983898631225999999999658 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG 117 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G 117 (120) -+|..+|+...+.|.+-+..||+.. ++..+.+.+.+.| T Consensus 16 GIG~a~a~~la~~G~~V~~~~r~~~----~l~~~~~~~~~~~ 53 (246) T PRK05653 16 GIGRAIALRLAADGARVVIYDSNEE----AAEALAEELRAAG 53 (246) T ss_pred HHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCC T ss_conf 8999999999987999999979999----9999999999659 No 86 >COG3669 Alpha-L-fucosidase [Carbohydrate transport and metabolism] Probab=24.90 E-value=45 Score=15.37 Aligned_cols=40 Identities=28% Similarity=0.353 Sum_probs=22.4 Q ss_pred HHHHHHHCCCCEEEEC---CCC-----CCCH-----------HHHHHHHHHHHHCCCCC Q ss_conf 9999997799799983---898-----6312-----------25999999999658789 Q gi|254780245|r 81 LVERAVKVGVKSVYFD---RGK-----HLYC-----------GRIAALADAVRKGGVSF 120 (120) Q Consensus 81 ia~r~~~~gI~~v~FD---R~g-----~~yH-----------Grvka~ad~~R~~Gl~F 120 (120) .|...|++|-+.|+.- .-| -.|| --|..+|.++|+.||-| T Consensus 59 War~fK~AGAKyvilvakHHDGFaLw~t~ys~wnsvk~GpKrDlVgela~Avr~qGL~F 117 (430) T COG3669 59 WARLFKEAGAKYVILVAKHHDGFALWPTDYSVWNSVKRGPKRDLVGELAKAVREQGLRF 117 (430) T ss_pred HHHHHHHCCCCEEEEEEEECCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEE T ss_conf 99999971884799865403770423665300015540775118999999999728715 No 87 >pfam02776 TPP_enzyme_N Thiamine pyrophosphate enzyme, N-terminal TPP binding domain. Probab=24.83 E-value=59 Score=14.68 Aligned_cols=39 Identities=31% Similarity=0.440 Sum_probs=25.7 Q ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHC-CCCC Q ss_conf 9999999999779979998389863122599999999965-8789 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKG-GVSF 120 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~-Gl~F 120 (120) .++.|++.+++.||+.|.-==|+ .+-.|.|++.+. |++| T Consensus 3 ~~~~i~~~L~~~Gv~~vFg~pG~-----~~~~l~~al~~~~~i~~ 42 (172) T pfam02776 3 GADALAEALKALGVDHVFGVPGG-----SILPLLDALAKSPGIRY 42 (172) T ss_pred HHHHHHHHHHHCCCCEEEEECCC-----CHHHHHHHHHHCCCCEE T ss_conf 89999999998799999996897-----77999999986799769 No 88 >COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion] Probab=24.51 E-value=60 Score=14.64 Aligned_cols=39 Identities=18% Similarity=0.311 Sum_probs=27.5 Q ss_pred HHHHHHHCCCC----------EEEECCCCCCCHHHHHHHHHHHHHCCCC Q ss_conf 99999977997----------9998389863122599999999965878 Q gi|254780245|r 81 LVERAVKVGVK----------SVYFDRGKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 81 ia~r~~~~gI~----------~v~FDR~g~~yHGrvka~ad~~R~~Gl~ 119 (120) +.-+|..+|++ ++.|++|.|+-.-|+..+.+.+-|-||+ T Consensus 45 fvl~Al~~GaDGV~v~GC~~geCHy~~GN~ka~rR~~~lke~l~elgie 93 (132) T COG1908 45 FVLKALRKGADGVLVAGCKIGECHYISGNYKAKRRMELLKELLKELGIE 93 (132) T ss_pred HHHHHHHCCCCEEEEECCCCCCEEEECCCHHHHHHHHHHHHHHHHHCCC T ss_conf 9999997389868993441561233016647999999999999994888 No 89 >PRK08945 short chain dehydrogenase; Provisional Probab=24.42 E-value=60 Score=14.63 Aligned_cols=27 Identities=22% Similarity=0.236 Sum_probs=13.7 Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 667899999999999999779979998 Q gi|254780245|r 69 ANIVAATAVGNLLVERAVKVGVKSVYF 95 (120) Q Consensus 69 ~ni~aA~~vG~~ia~r~~~~gI~~v~F 95 (120) .|..+...+-+.+....++.+--.|+| T Consensus 124 vNl~g~~~l~~~~~p~m~~~~~G~Ii~ 150 (245) T PRK08945 124 VNVNATFMLTQALLPLLLKSPAASLVF 150 (245) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEE T ss_conf 675999999999999998779978999 No 90 >TIGR02867 spore_II_P stage II sporulation protein P; InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation . SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, , , ), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers .. Probab=24.23 E-value=61 Score=14.61 Aligned_cols=20 Identities=25% Similarity=0.414 Sum_probs=16.5 Q ss_pred HHHHHHHHHHHHHC-CCCEEE Q ss_conf 99999999999977-997999 Q gi|254780245|r 75 TAVGNLLVERAVKV-GVKSVY 94 (120) Q Consensus 75 ~~vG~~ia~r~~~~-gI~~v~ 94 (120) ..||..|++.+-++ ||..++ T Consensus 40 ~~VG~~L~~~Le~~YGI~~~~ 60 (221) T TIGR02867 40 TKVGDRLAKELEEKYGIGAIH 60 (221) T ss_pred HHHHHHHHHHHHHHCCEEEEE T ss_conf 067889999999828945786 No 91 >COG4861 Uncharacterized protein conserved in bacteria [Function unknown] Probab=24.13 E-value=37 Score=15.87 Aligned_cols=48 Identities=19% Similarity=0.188 Sum_probs=25.0 Q ss_pred CCHHHHHHHHHHHHHHH-HHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 66789999999999999-977997999838986312259999999996587 Q gi|254780245|r 69 ANIVAATAVGNLLVERA-VKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118 (120) Q Consensus 69 ~ni~aA~~vG~~ia~r~-~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl 118 (120) -|-.+|..+|.+++.-. ...-+-+|.=-- ----|-++...|.+||.|+ T Consensus 144 ftp~raqv~~ALL~aP~lv~~P~REIAasA--gVsvGTa~~t~d~LrE~G~ 192 (345) T COG4861 144 FTPKRAQVVCALLDAPQLVDAPLREIAASA--GVSVGTAKETMDTLRETGF 192 (345) T ss_pred CCHHHHHHHHHHHCCHHHHCCHHHHHHHHC--CCEECHHHHHHHHHHHCCH T ss_conf 886788899997558877544588887640--5101108888999886010 No 92 >cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, Probab=24.04 E-value=61 Score=14.59 Aligned_cols=46 Identities=15% Similarity=0.243 Sum_probs=34.1 Q ss_pred HHHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999977997999838---98631225999999999658789 Q gi|254780245|r 75 TAVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 75 ~~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ...|...++.+.++|-.+|.|=- ......=|...|.+++.++|+.. T Consensus 101 ~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~G~~~al~~~g~~~ 149 (268) T cd01575 101 AEAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDP 149 (268) T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 9999999999997499769998489887369999999999999769898 No 93 >cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain. Probab=23.98 E-value=62 Score=14.58 Aligned_cols=45 Identities=20% Similarity=0.324 Sum_probs=31.6 Q ss_pred HHHHHHHHHHHHCCCCEEEECC---CCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999999999977997999838---98631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDR---GKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR---~g~~yHGrvka~ad~~R~~Gl~F 120 (120) ..|..+++.+.+.|.++|.|=. +..-..-|...|-+++.+.|+.+ T Consensus 102 ~a~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 149 (264) T cd06267 102 AGAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIPL 149 (264) T ss_pred HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 999999999987188856896389877069999999999999869998 No 94 >PRK10401 DNA-binding transcriptional regulator GalS; Provisional Probab=23.55 E-value=63 Score=14.53 Aligned_cols=44 Identities=14% Similarity=0.115 Sum_probs=33.4 Q ss_pred HHHHHHHHHHHCCCCEEEECCCCC---CCHHHHHHHHHHHHHCCCCC Q ss_conf 999999999977997999838986---31225999999999658789 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDRGKH---LYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR~g~---~yHGrvka~ad~~R~~Gl~F 120 (120) -|...++.+.+.|-..|.|=-+.. -..-|...|.+++++.||.+ T Consensus 163 g~~~a~~~L~~~GhrrI~~i~~~~~~~~~~~R~~G~~~al~~~gl~~ 209 (346) T PRK10401 163 GARMATRMLLNNGHQRIGYLSSSHGIEDDAMRKAGWLSALKEQGIIP 209 (346) T ss_pred HHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 99999999996299828999479887168999999999999849998 No 95 >PRK09526 lacI lac repressor; Reviewed Probab=23.44 E-value=63 Score=14.52 Aligned_cols=44 Identities=18% Similarity=0.118 Sum_probs=34.9 Q ss_pred HHHHHHHHHHHHCCCCEEEEC---CCCCCCHHHHHHHHHHHHHCCCC Q ss_conf 999999999997799799983---89863122599999999965878 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFD---RGKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FD---R~g~~yHGrvka~ad~~R~~Gl~ 119 (120) .-|.++++.+.++|-..+.|= ++..--+-|...|.+++++.|+. T Consensus 167 ~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~R~~Gf~~~~~~~~l~ 213 (342) T PRK09526 167 DGTRLGVEHLVELGHQQIALLAGPLSSVSARLRLAGWLEYLTRNQLS 213 (342) T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC T ss_conf 99999999999759975999958976600999999999999977989 No 96 >COG0064 GatB Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis] Probab=22.93 E-value=65 Score=14.46 Aligned_cols=63 Identities=17% Similarity=0.133 Sum_probs=33.0 Q ss_pred CEEEEEEECCCCEEEEEEEECCC-------------HHCCCCCCCCCHHHHHHHHHHHHHHHHHCCC-CEEEECCCCCCC Q ss_conf 09999996279759999850210-------------0000134686678999999999999997799-799983898631 Q gi|254780245|r 37 HIYGQIIDDSIGHTLVSASSLNE-------------PLRSSLKTGANIVAATAVGNLLVERAVKVGV-KSVYFDRGKHLY 102 (120) Q Consensus 37 hiyAQiIdd~~~~tl~saST~~k-------------~~~~~~~~~~ni~aA~~vG~~ia~r~~~~gI-~~v~FDR~g~~y 102 (120) -|++|+ ....+..|+++|.-- .+-+.++. -|. .|-..+-.+| .++...| ...+|||..|-| T Consensus 13 EvHvqL--~T~tKlFs~~~~~f~~a~PNtnv~pv~lglPGaLPv-lN~-~av~~ai~~~-lAL~~~i~~~~~FdRK~YFY 87 (483) T COG0064 13 EVHVQL--NTKTKLFSGCSTDFGGAEPNTNVCPVCLGLPGALPV-LNK-EAVEKAIKAG-LALNCEINEKSVFDRKNYFY 87 (483) T ss_pred EEEEEE--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCH-HHHHHHHHHH-HHHCCEECCCEECCCCCCCC T ss_conf 787786--157664678852126789977788500268987665-689-9999999964-53165625650316678899 Q ss_pred HH Q ss_conf 22 Q gi|254780245|r 103 CG 104 (120) Q Consensus 103 HG 104 (120) -- T Consensus 88 PD 89 (483) T COG0064 88 PD 89 (483) T ss_pred CC T ss_conf 98 No 97 >pfam02826 2-Hacid_dh_C D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain. This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389. Probab=22.61 E-value=66 Score=14.42 Aligned_cols=24 Identities=25% Similarity=0.462 Sum_probs=21.1 Q ss_pred HHHHHHHHHHHHCCCCEEEECCCC Q ss_conf 999999999997799799983898 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRGK 99 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~g 99 (120) .+|+.+|++++..|.+-++|||.. T Consensus 46 ~IG~~va~~l~~fg~~V~~~d~~~ 69 (176) T pfam02826 46 RIGRAVARRLKAFGMKVIAYDRYP 69 (176) T ss_pred HHHHHHHHHHHHHCCCEEEECCCC T ss_conf 999999999998398125437987 No 98 >PRK07102 short chain dehydrogenase; Provisional Probab=22.57 E-value=66 Score=14.41 Aligned_cols=26 Identities=23% Similarity=0.172 Sum_probs=11.8 Q ss_pred CHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 67899999999999999779979998 Q gi|254780245|r 70 NIVAATAVGNLLVERAVKVGVKSVYF 95 (120) Q Consensus 70 ni~aA~~vG~~ia~r~~~~gI~~v~F 95 (120) |.-+...+-..+.....+.+--.|++ T Consensus 107 N~~g~~~l~~~~~~~m~~~~~G~Iv~ 132 (243) T PRK07102 107 NFEGPIALLTLLANRFEARGSGTIVG 132 (243) T ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEE T ss_conf 98999999999999988723974999 No 99 >KOG4691 consensus Probab=22.52 E-value=48 Score=15.22 Aligned_cols=22 Identities=23% Similarity=0.181 Sum_probs=17.1 Q ss_pred HHH-CCCCEEEECCCCCCCHHHH Q ss_conf 997-7997999838986312259 Q gi|254780245|r 85 AVK-VGVKSVYFDRGKHLYCGRI 106 (120) Q Consensus 85 ~~~-~gI~~v~FDR~g~~yHGrv 106 (120) +++ -.+..+..||.|.+||||- T Consensus 187 AL~~p~~ynfAIdraGNky~vr~ 209 (227) T KOG4691 187 ALDSPKNYNFAIDRAGNKYVVRP 209 (227) T ss_pred HHCCCCCCCHHHCCCCCEEECCC T ss_conf 97386433233112677333677 No 100 >PRK06194 hypothetical protein; Provisional Probab=22.24 E-value=67 Score=14.37 Aligned_cols=41 Identities=20% Similarity=0.323 Sum_probs=23.8 Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 999999999999977997999838986312259999999996587 Q gi|254780245|r 74 ATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118 (120) Q Consensus 74 A~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl 118 (120) +.=+|..+|+++.+.|-+-|..||... .+...++.+++.|. T Consensus 15 ssGIG~a~A~~la~~Ga~Vvl~d~~~~----~l~~~~~~l~~~g~ 55 (301) T PRK06194 15 ASGFGREFARIGARLGMKLVLADVQQD----ALDRAVAELRAQGA 55 (301) T ss_pred CCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC T ss_conf 779999999999987998999979889----99999999984598 No 101 >pfam12005 DUF3499 Protein of unknown function (DUF3499). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length. Probab=22.10 E-value=52 Score=15.02 Aligned_cols=46 Identities=24% Similarity=0.178 Sum_probs=26.4 Q ss_pred HHHHHHHHHHHHHHH-CCCCEEEECCCC---CCCHHHHHHHHHHHHHCCC Q ss_conf 999999999999997-799799983898---6312259999999996587 Q gi|254780245|r 73 AATAVGNLLVERAVK-VGVKSVYFDRGK---HLYCGRIAALADAVRKGGV 118 (120) Q Consensus 73 aA~~vG~~ia~r~~~-~gI~~v~FDR~g---~~yHGrvka~ad~~R~~Gl 118 (120) -++-+-..-|+++.. .|-+-|-.+-.. -.=.--+-||||++||+|- T Consensus 40 h~yDLC~~Ha~rlTaP~GW~vvr~~~~~~~~~p~~dDL~ALAdAVREaar 89 (125) T pfam12005 40 HSYDLCEEHAERLTAPLGWEVVRLAGEFAPAEPDEDDLVALADAVREAAR 89 (125) T ss_pred CHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHCC T ss_conf 40465888986356888757786047777789777889999999987424 No 102 >TIGR01318 gltD_gamma_fam glutamate synthase, small subunit; InterPro: IPR006006 One pathway for the assimilation of ammonia and glutamate biosynthesis involves glutamate synthase (1.4.1.13 from EC) which transfers the amide group of glutamine to 2-oxoglutarate to yield two molecules of glutamate.2 L-glutamate + NADP^+ = L-glutamine + 2-oxoglutarate + NADPH + H^+. This model describes both glutatate synthase small subunit and closely related paralogs of unknown function from a number of gamma and alpha subdivision Proteobacteria, including Escherichia coli. ; GO: 0016639 oxidoreductase activity acting on the CH-NH2 group of donors NAD or NADP as acceptor, 0006537 glutamate biosynthetic process. Probab=21.93 E-value=63 Score=14.50 Aligned_cols=23 Identities=30% Similarity=0.453 Sum_probs=18.7 Q ss_pred HHHHHHHHHHHHCCCCEEEECCC Q ss_conf 99999999999779979998389 Q gi|254780245|r 76 AVGNLLVERAVKVGVKSVYFDRG 98 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~v~FDR~ 98 (120) =-|.-=|+.+.-.|++-+||||= T Consensus 153 PAGLaCAD~L~RaGV~v~VfDRh 175 (480) T TIGR01318 153 PAGLACADILARAGVQVVVFDRH 175 (480) T ss_pred CCHHHHHHHHHHCCCEEEEEECC T ss_conf 60257999875178559997477 No 103 >COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones] Probab=21.74 E-value=68 Score=14.31 Aligned_cols=48 Identities=29% Similarity=0.336 Sum_probs=34.6 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 999999999999997799799983898631225999999999658789 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) -|..+++++.+.++..||++|++-=|-+-=.=-++.+++.+-+.|++| T Consensus 677 la~~~~e~~~~~a~~~gi~~V~lsGGVf~N~~l~~~~~~~lk~~~f~~ 724 (750) T COG0068 677 LAEGFAELAVELAKKYGINKVVLSGGVFQNRLLLERLAKYLKKEGFRF 724 (750) T ss_pred HHHHHHHHHHHHHHHCCCCEEEEECCEEECHHHHHHHHHHHHHCCCEE T ss_conf 999999999999986594279972776414999999999997539267 No 104 >PRK07109 short chain dehydrogenase; Provisional Probab=21.63 E-value=69 Score=14.30 Aligned_cols=42 Identities=29% Similarity=0.456 Sum_probs=31.5 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 9999999999999977997999838986312259999999996587 Q gi|254780245|r 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118 (120) Q Consensus 73 aA~~vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl 118 (120) ++.-||..+|+..-+.|..-+..+|+.. .+.++++.+++.|- T Consensus 16 ASsGIGra~A~~fA~~Ga~Vvl~aR~~~----~L~~~a~e~~~~G~ 57 (338) T PRK07109 16 ASAGVGRATARAFARRGAKVVLLARGEE----GLEGLAAEIRAAGG 57 (338) T ss_pred CCCHHHHHHHHHHHHCCCEEEEEECCHH----HHHHHHHHHHHCCC T ss_conf 4349999999999987998999989999----99999999996398 No 105 >TIGR01235 pyruv_carbox pyruvate carboxylase; InterPro: IPR005930 In the postabsorptive state, blood glucose concentration is kept constant by a combination of glycogenolysis and gluconeogenesis. During prolonged fasting, when hepatic glycogen is exhausted, gluconeogenesis becomes the only source of plasma glucose. Gluconeogenesis (the production of new glucose molecules) occurs mainly in liver and, to a small extent, in kidneys. Pyruvate carboxylase (6.4.1.1 from EC), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate, thus playing a crucial role in gluconeogenesis.ATP + pyruvate + HCO3- = ADP + phosphate + oxaloacetate Most well characterised forms of active enzyme consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain.; GO: 0004736 pyruvate carboxylase activity, 0006094 gluconeogenesis, 0005737 cytoplasm. Probab=21.51 E-value=69 Score=14.28 Aligned_cols=17 Identities=35% Similarity=0.554 Sum_probs=13.0 Q ss_pred CCCEEEEEEECCCCEEE Q ss_conf 87099999962797599 Q gi|254780245|r 35 SKHIYGQIIDDSIGHTL 51 (120) Q Consensus 35 nkhiyAQiIdd~~~~tl 51 (120) -|||-+||+-|..|.++ T Consensus 210 pkHiEvQ~LGD~~GNVV 226 (1169) T TIGR01235 210 PKHIEVQLLGDKHGNVV 226 (1169) T ss_pred CCEEEEEEEECCCCCEE T ss_conf 82078987634889878 No 106 >COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion] Probab=21.31 E-value=61 Score=14.60 Aligned_cols=13 Identities=23% Similarity=0.383 Sum_probs=6.4 Q ss_pred HHHHHHHHCCCCE Q ss_conf 9999999779979 Q gi|254780245|r 80 LLVERAVKVGVKS 92 (120) Q Consensus 80 ~ia~r~~~~gI~~ 92 (120) .|++.+.+.|++- T Consensus 36 ei~~a~~~LGl~~ 48 (93) T COG1400 36 EIAEALRELGLKP 48 (93) T ss_pred HHHHHHHHCCCCE T ss_conf 9999999849974 No 107 >pfam01116 F_bP_aldolase Fructose-bisphosphate aldolase class-II. Probab=21.09 E-value=70 Score=14.23 Aligned_cols=38 Identities=18% Similarity=0.233 Sum_probs=26.4 Q ss_pred HHHHHHHCCCCEEEECCCCCCCHH---HHHHHHHHHHHCCC Q ss_conf 999999779979998389863122---59999999996587 Q gi|254780245|r 81 LVERAVKVGVKSVYFDRGKHLYCG---RIAALADAVRKGGV 118 (120) Q Consensus 81 ia~r~~~~gI~~v~FDR~g~~yHG---rvka~ad~~R~~Gl 118 (120) ..++|.+.|.+.|.||-+...|.- ..+.+++-+...|+ T Consensus 87 ~~~~ai~~GftSVM~DgS~l~~eeNi~~T~~vv~~Ah~~gv 127 (283) T pfam01116 87 GILEAIEAGFSSVMIDGSHLPFEENIAITKEVVEYAHARGV 127 (283) T ss_pred HHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 99999981998698638979999999999999999987398 No 108 >PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed Probab=21.06 E-value=71 Score=14.23 Aligned_cols=38 Identities=18% Similarity=0.319 Sum_probs=29.4 Q ss_pred HHHHHHHCCCCEEEECCCCCCCH---HHHHHHHHHHHHCCC Q ss_conf 99999977997999838986312---259999999996587 Q gi|254780245|r 81 LVERAVKVGVKSVYFDRGKHLYC---GRIAALADAVRKGGV 118 (120) Q Consensus 81 ia~r~~~~gI~~v~FDR~g~~yH---Grvka~ad~~R~~Gl 118 (120) ...+|.+.|.+.|.||-+.+.|. -+.+.+++-++..|+ T Consensus 89 ~i~~ai~~GftSVM~DgS~lp~eeNi~~Tk~vv~~Ah~~gv 129 (286) T PRK12738 89 DIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVDFCHSQDC 129 (286) T ss_pred HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 99999977998798738999999999999999999847399 No 109 >pfam03446 NAD_binding_2 NAD binding domain of 6-phosphogluconate dehydrogenase. The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold. Probab=21.01 E-value=71 Score=14.22 Aligned_cols=14 Identities=21% Similarity=0.631 Sum_probs=6.9 Q ss_pred HHHHHHHCCCCEEEEC Q ss_conf 9999997799799983 Q gi|254780245|r 81 LVERAVKVGVKSVYFD 96 (120) Q Consensus 81 ia~r~~~~gI~~v~FD 96 (120) +++++.++|+. ++| T Consensus 105 ~~~~~~~~g~~--~lD 118 (163) T pfam03446 105 LAKELKEKGIR--FLD 118 (163) T ss_pred HHHHHHHCCCC--CCC T ss_conf 99987530344--347 No 110 >PRK06806 fructose-bisphosphate aldolase; Provisional Probab=20.95 E-value=71 Score=14.21 Aligned_cols=39 Identities=18% Similarity=0.316 Sum_probs=30.4 Q ss_pred HHHHHHHHCCCCEEEECCCCCCCH---HHHHHHHHHHHHCCC Q ss_conf 999999977997999838986312---259999999996587 Q gi|254780245|r 80 LLVERAVKVGVKSVYFDRGKHLYC---GRIAALADAVRKGGV 118 (120) Q Consensus 80 ~ia~r~~~~gI~~v~FDR~g~~yH---Grvka~ad~~R~~Gl 118 (120) ...++|.+.|.+.|.||-+...|. -..+.++|-+...|+ T Consensus 88 e~i~~ai~~GfsSVM~DgS~l~~eeNi~~Tkevve~Ah~~gv 129 (281) T PRK06806 88 EKIKEALEIGFTSVMFDGSHYPLEENIQKTKEIVELAKQYGA 129 (281) T ss_pred HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 999999982998799609989999999999999999988598 No 111 >cd00947 TBP_aldolase_IIB Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures. Probab=20.93 E-value=71 Score=14.21 Aligned_cols=38 Identities=24% Similarity=0.420 Sum_probs=27.9 Q ss_pred HHHHHHHCCCCEEEECCCCCCCHH---HHHHHHHHHHHCCC Q ss_conf 999999779979998389863122---59999999996587 Q gi|254780245|r 81 LVERAVKVGVKSVYFDRGKHLYCG---RIAALADAVRKGGV 118 (120) Q Consensus 81 ia~r~~~~gI~~v~FDR~g~~yHG---rvka~ad~~R~~Gl 118 (120) ..+++.+.|.+.|.||-+.+.|.- ..+.+++-+...|+ T Consensus 84 ~i~~ai~~Gf~SVM~DgS~lp~eeNi~~T~~vv~~ah~~gv 124 (276) T cd00947 84 LIKRAIRAGFSSVMIDGSHLPFEENVAKTKEVVELAHAYGV 124 (276) T ss_pred HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 99999983998798528989999999999999999998198 No 112 >cd07039 TPP_PYR_POX Pyrimidine (PYR) binding domain of POX. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Lactobacillus plantarum POX is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of differ Probab=20.83 E-value=71 Score=14.20 Aligned_cols=39 Identities=41% Similarity=0.630 Sum_probs=25.0 Q ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCC-CCC Q ss_conf 99999999997799799983898631225999999999658-789 Q gi|254780245|r 77 VGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG-VSF 120 (120) Q Consensus 77 vG~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~G-l~F 120 (120) |++.|++.+.+.||+.|.-=-|+ .+-.|.|++.+.+ ++| T Consensus 2 va~~l~~~L~~~Gv~~vFg~pG~-----~~~~l~~al~~~~~i~~ 41 (164) T cd07039 2 VADVIVETLENWGVKRVYGIPGD-----SINGLMDALRREGKIEF 41 (164) T ss_pred HHHHHHHHHHHCCCCEEEEECCC-----CHHHHHHHHHHCCCCEE T ss_conf 89999999998799999991783-----57999999986599739 No 113 >cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=20.43 E-value=73 Score=14.15 Aligned_cols=52 Identities=17% Similarity=0.197 Sum_probs=36.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHCC--CCEEEEC---CCCCCCHHHHHHHHHHHHHCCCC Q ss_conf 8667899999999999999779--9799983---89863122599999999965878 Q gi|254780245|r 68 GANIVAATAVGNLLVERAVKVG--VKSVYFD---RGKHLYCGRIAALADAVRKGGVS 119 (120) Q Consensus 68 ~~ni~aA~~vG~~ia~r~~~~g--I~~v~FD---R~g~~yHGrvka~ad~~R~~Gl~ 119 (120) ..|.+++..+|+.+++.+...+ -.+|.+- .+..--.-|+..|-+++.+.|++ T Consensus 101 ~dn~~~g~~~g~~l~~~~~~~~~~~~~v~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~ 157 (277) T cd06319 101 SDNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCD 157 (277) T ss_pred EHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCC T ss_conf 235899999999999986764778866999965877623999999999999875997 No 114 >KOG3396 consensus Probab=20.40 E-value=73 Score=14.14 Aligned_cols=62 Identities=19% Similarity=0.341 Sum_probs=37.6 Q ss_pred EEEEEEECCCCEEEEEEEEC--CCHHCCCCCCCCCHH--------HHHHHHHHHH----HHHHHCCCCEEEECCCC Q ss_conf 99999962797599998502--100000134686678--------9999999999----99997799799983898 Q gi|254780245|r 38 IYGQIIDDSIGHTLVSASSL--NEPLRSSLKTGANIV--------AATAVGNLLV----ERAVKVGVKSVYFDRGK 99 (120) Q Consensus 38 iyAQiIdd~~~~tl~saST~--~k~~~~~~~~~~ni~--------aA~~vG~~ia----~r~~~~gI~~v~FDR~g 99 (120) .|.-+|.|.....++.+.|+ |+.|--.....+-+| .-+.+|+++- +.+++.|..++.+|+.. T Consensus 53 Y~i~Vied~~s~~vigtatL~IE~KfIh~~g~rGhiEDVVV~~~~rgk~LGkllv~~Lv~l~k~lgcYKi~LdC~~ 128 (150) T KOG3396 53 YYIVVIEDKESEKVIGTATLFIERKFIHGCGSRGHIEDVVVDSEYRGKQLGKLLVETLVDLAKSLGCYKIILDCDP 128 (150) T ss_pred EEEEEEEECCCCEEEEEEEEEEEHHHHHCCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCH T ss_conf 7999999678672788877777666665044457514798675451567869999999999874282799996362 No 115 >KOG1185 consensus Probab=20.25 E-value=73 Score=14.12 Aligned_cols=38 Identities=26% Similarity=0.339 Sum_probs=16.8 Q ss_pred HHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 9999999997799799983898631225999999999658789 Q gi|254780245|r 78 GNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 78 G~~ia~r~~~~gI~~v~FDR~g~~yHGrvka~ad~~R~~Gl~F 120 (120) |+++|+-++..||+.|.==-|+ -|-.+++++-..||+| T Consensus 17 ~~~vA~~Lk~~gVe~iFgiVGi-----pV~el~~aaqalGIk~ 54 (571) T KOG1185 17 GELVAAVLKAQGVEYIFGIVGI-----PVIELAVAAQALGIKF 54 (571) T ss_pred HHHHHHHHHHCCCEEEEEEECC-----CHHHHHHHHHHCCCEE T ss_conf 8999999997696299998162-----1079999999809868 No 116 >pfam00532 Peripla_BP_1 family. This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356). Probab=20.17 E-value=74 Score=14.11 Aligned_cols=45 Identities=13% Similarity=0.106 Sum_probs=31.5 Q ss_pred HHHHHHHHHHHHCCCCE-EEEC---CCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 99999999999779979-9983---898631225999999999658789 Q gi|254780245|r 76 AVGNLLVERAVKVGVKS-VYFD---RGKHLYCGRIAALADAVRKGGVSF 120 (120) Q Consensus 76 ~vG~~ia~r~~~~gI~~-v~FD---R~g~~yHGrvka~ad~~R~~Gl~F 120 (120) .-|...++.+.+.|-.+ +.|- .+..-..-|...|.+++++.|+.+ T Consensus 106 ~~~~~a~~~Li~~Ghrr~i~~~~~~~~~~~~~~R~~Gf~~al~~~g~~~ 154 (281) T pfam00532 106 QAGYESTQYLIAEGHKRPIAVMAGPASALTARERVQGFMAALAAAGREV 154 (281) T ss_pred HHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC T ss_conf 9999999999983897704773078765078999999999999759999 Done!