Query gi|254780187|ref|YP_003064600.1| 30S ribosomal protein S4 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 206 No_of_seqs 159 out of 1658 Neff 5.4 Searched_HMMs 39220 Date Mon May 23 13:10:36 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780187.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01017 rpsD_bact ribosomal 100.0 0 0 583.5 15.1 204 3-206 1-217 (217) 2 PRK05327 rpsD 30S ribosomal pr 100.0 0 0 538.9 18.7 201 1-206 1-201 (201) 3 PRK12565 30S ribosomal protein 100.0 0 0 531.5 19.2 196 1-206 1-197 (197) 4 CHL00113 rps4 ribosomal protei 100.0 0 0 531.6 18.8 198 1-206 1-199 (201) 5 COG0522 RpsD Ribosomal protein 100.0 0 0 427.3 14.5 202 1-206 1-205 (205) 6 pfam00163 Ribosomal_S4 Ribosom 99.9 2.9E-28 7.3E-33 204.0 6.5 91 2-93 1-94 (94) 7 KOG3301 consensus 99.8 3.9E-21 9.9E-26 157.8 3.9 130 1-136 1-139 (183) 8 TIGR01018 rpsD_arch ribosomal 99.7 2.5E-18 6.4E-23 139.5 3.5 57 91-147 109-167 (170) 9 PRK04051 rps4p 30S ribosomal p 99.7 1.8E-16 4.6E-21 127.5 7.5 60 90-149 99-160 (177) 10 PTZ00155 40S ribosomal protein 99.6 1.6E-15 4E-20 121.5 5.8 59 90-148 103-163 (188) 11 smart00363 S4 S4 RNA-binding d 99.2 1.2E-11 3.1E-16 96.2 4.9 54 94-147 1-54 (60) 12 pfam01479 S4 S4 domain. The S4 99.2 8.7E-12 2.2E-16 97.1 3.6 48 94-141 1-48 (48) 13 cd00165 S4 S4/Hsp/ tRNA synthe 99.1 6.1E-11 1.6E-15 91.6 4.8 56 94-149 1-56 (70) 14 COG1189 Predicted rRNA methyla 98.5 2.4E-07 6E-12 68.4 5.4 52 94-145 3-54 (245) 15 COG1188 Ribosome-associated he 98.4 3.3E-07 8.3E-12 67.5 4.1 58 91-149 6-63 (100) 16 TIGR00478 tly hemolysin A; Int 98.3 5.3E-07 1.4E-11 66.1 4.2 54 95-148 1-54 (240) 17 TIGR03069 PS_II_S4 photosystem 98.3 9.2E-07 2.3E-11 64.6 4.9 55 93-148 183-237 (257) 18 PRK10348 ribosome-associated h 98.2 1.4E-06 3.7E-11 63.3 3.7 53 93-146 8-60 (133) 19 PRK10839 16S rRNA pseudouridyl 98.2 3.3E-06 8.4E-11 61.0 5.3 53 94-147 1-53 (231) 20 COG2302 Uncharacterized conser 98.1 4.4E-06 1.1E-10 60.1 4.9 54 94-148 181-234 (257) 21 PRK11180 rluD 23S rRNA pseudou 97.8 5E-05 1.3E-09 53.3 5.2 53 94-146 18-70 (325) 22 PRK11025 23S rRNA pseudouridyl 97.6 0.00012 3.2E-09 50.7 5.3 50 94-144 20-69 (317) 23 KOG4655 consensus 97.6 1.9E-05 4.9E-10 56.0 0.6 71 88-158 101-173 (181) 24 COG0564 RluA Pseudouridylate s 97.5 0.00042 1.1E-08 47.3 7.1 53 91-145 10-62 (289) 25 PRK10475 23S rRNA pseudouridin 97.5 0.0002 5E-09 49.4 5.1 51 94-146 7-57 (290) 26 COG1187 RsuA 16S rRNA uridine- 97.1 0.0013 3.4E-08 44.1 5.5 53 93-146 2-55 (248) 27 PRK13354 tyrosyl-tRNA syntheta 96.7 0.0038 9.7E-08 41.1 5.3 100 49-148 291-396 (405) 28 PRK10700 23S rRNA pseudouridyl 96.6 0.005 1.3E-07 40.4 5.6 53 93-146 2-55 (291) 29 PRK11507 hypothetical protein; 96.5 0.0044 1.1E-07 40.7 4.7 52 95-146 13-64 (70) 30 TIGR02988 YaaA_near_RecF S4 do 96.4 0.0057 1.4E-07 40.0 4.8 50 96-145 11-60 (60) 31 PRK04313 30S ribosomal protein 96.4 0.004 1E-07 40.9 3.7 44 102-145 47-90 (237) 32 PTZ00223 40S ribosomal protein 96.4 0.0039 1E-07 41.0 3.7 44 102-145 48-91 (273) 33 PTZ00118 40S ribosomal protein 96.2 0.0056 1.4E-07 40.0 3.8 44 102-145 51-94 (262) 34 COG2501 S4-like RNA binding pr 96.2 0.013 3.3E-07 37.7 5.4 51 96-146 14-64 (73) 35 TIGR00005 rluA_subfam pseudour 95.8 0.02 5E-07 36.5 5.1 87 93-184 5-95 (337) 36 PRK05912 tyrosyl-tRNA syntheta 95.7 0.013 3.4E-07 37.6 3.9 89 48-141 286-382 (402) 37 COG1471 RPS4A Ribosomal protei 95.4 0.016 4.1E-07 37.0 3.4 44 102-145 50-93 (241) 38 COG0162 TyrS Tyrosyl-tRNA synt 93.9 0.37 9.6E-06 28.2 7.4 86 49-135 288-377 (401) 39 TIGR01687 moaD_arch MoaD famil 80.6 1 2.6E-05 25.3 1.9 60 81-145 24-88 (93) 40 cd00754 MoaD MoaD family. Memb 79.0 4 0.0001 21.5 4.5 52 81-145 24-75 (80) 41 KOG0378 consensus 67.3 3.3 8.3E-05 22.1 1.7 43 102-144 51-93 (263) 42 TIGR01647 ATPase-IIIA_H plasma 67.0 3.9 9.8E-05 21.6 2.0 65 113-178 95-163 (835) 43 pfam00498 FHA FHA domain. The 66.1 6.4 0.00016 20.2 3.0 26 118-143 41-66 (67) 44 pfam02597 ThiS ThiS family. Th 64.6 5.8 0.00015 20.4 2.6 28 118-145 36-65 (70) 45 KOG2623 consensus 63.8 7.6 0.00019 19.7 3.0 39 98-136 403-441 (467) 46 pfam00122 E1-E2_ATPase E1-E2 A 61.6 4.7 0.00012 21.0 1.6 52 119-178 36-87 (222) 47 cd01668 TGS_RelA_SpoT TGS_RelA 61.2 7 0.00018 19.9 2.5 23 121-144 37-59 (60) 48 KOG1919 consensus 58.5 15 0.00039 17.7 4.9 46 96-143 47-92 (371) 49 pfam02824 TGS TGS domain. The 55.9 10 0.00027 18.8 2.6 23 120-143 36-58 (60) 50 TIGR01344 malate_syn_A malate 55.4 7.5 0.00019 19.7 1.8 35 107-141 441-476 (522) 51 cd01616 TGS The TGS domain, na 53.6 11 0.00028 18.7 2.4 22 121-143 37-58 (60) 52 TIGR00398 metG methionyl-tRNA 52.5 6.5 0.00017 20.1 1.1 33 109-141 327-361 (573) 53 TIGR01832 kduD 2-deoxy-D-gluco 50.8 6.7 0.00017 20.1 1.0 69 101-173 113-192 (249) 54 TIGR02375 pseudoazurin pseudoa 47.9 23 0.00058 16.6 4.2 25 126-150 12-37 (123) 55 cd01089 PA2G4-like Related to 47.2 15 0.00037 17.9 2.2 25 120-144 62-92 (228) 56 PRK06488 sulfur carrier protei 46.8 19 0.00048 17.2 2.7 41 95-144 16-59 (65) 57 PRK05659 sulfur carrier protei 45.0 19 0.00047 17.2 2.5 23 121-143 34-59 (66) 58 cd00060 FHA Forkhead associate 44.8 24 0.00062 16.4 3.0 16 166-181 56-71 (102) 59 COG0474 MgtA Cation transport 44.0 14 0.00035 18.0 1.7 81 90-179 108-195 (917) 60 pfam07828 PA-IL PA-IL-like pro 43.4 14 0.00034 18.1 1.6 28 119-146 4-31 (121) 61 cd00430 PLPDE_III_AR Type III 42.5 22 0.00057 16.6 2.6 30 96-125 125-156 (367) 62 PRK11930 putative bifunctional 42.0 21 0.00055 16.8 2.4 30 96-125 586-617 (824) 63 COG2104 ThiS Sulfur transfer p 41.2 24 0.00062 16.4 2.6 23 121-143 36-61 (68) 64 PRK09940 transcriptional regul 39.2 31 0.00079 15.7 3.0 28 58-86 219-246 (253) 65 cd00565 ThiS ThiS (ThiaminS) i 39.0 26 0.00067 16.2 2.5 23 121-143 33-58 (65) 66 cd03190 GST_C_ECM4_like GST_C 38.2 28 0.0007 16.1 2.5 26 86-111 9-34 (142) 67 cd06826 PLPDE_III_AR2 Type III 37.5 30 0.00078 15.8 2.6 27 100-126 130-160 (365) 68 PRK07440 hypothetical protein; 37.4 33 0.00084 15.6 2.9 23 121-143 38-63 (70) 69 cd06827 PLPDE_III_AR_proteobac 37.2 30 0.00076 15.8 2.5 29 97-125 122-152 (354) 70 TIGR01683 thiS thiamine biosyn 36.7 34 0.00086 15.5 2.9 23 121-143 33-58 (65) 71 TIGR00691 spoT_relA RelA/SpoT 35.2 36 0.00091 15.3 3.0 24 104-127 573-596 (741) 72 PRK08053 sulfur carrier protei 34.2 37 0.00094 15.2 2.7 24 121-144 34-60 (66) 73 TIGR01266 fum_ac_acetase fumar 34.0 27 0.00069 16.1 1.9 36 97-141 330-365 (436) 74 PRK11033 zntA zinc/cadmium/mer 32.1 40 0.001 15.0 4.7 64 108-179 227-294 (739) 75 pfam02563 Poly_export Polysacc 31.3 29 0.00075 15.9 1.7 17 128-144 7-23 (83) 76 smart00736 CADG Dystroglycan-t 29.3 40 0.001 15.0 2.1 23 161-185 41-63 (97) 77 PRK13340 alanine racemase; Rev 29.1 45 0.0011 14.7 2.4 27 99-125 167-197 (404) 78 TIGR01523 ATPase-IID_K-Na pota 29.1 37 0.00095 15.2 1.9 40 106-145 106-146 (1001) 79 KOG0202 consensus 28.3 38 0.00097 15.2 1.9 67 107-180 104-171 (972) 80 pfam02042 RWP-RK RWP-RK domain 28.0 10 0.00027 18.8 -1.1 13 10-22 34-46 (52) 81 PRK06944 sulfur carrier protei 27.8 47 0.0012 14.5 2.4 23 121-143 33-58 (65) 82 pfam00842 Ala_racemase_C Alani 27.1 48 0.0012 14.5 2.5 42 104-147 40-95 (125) 83 COG4043 Preprotein translocase 26.9 38 0.00098 15.1 1.7 41 101-144 3-43 (111) 84 PRK10517 magnesium-transportin 26.4 28 0.00072 16.0 0.9 48 124-178 170-217 (900) 85 COG0787 Alr Alanine racemase [ 26.1 50 0.0013 14.4 2.8 12 96-107 128-139 (360) 86 PRK09393 ftrA transcriptional 26.1 51 0.0013 14.4 2.3 57 58-118 238-306 (320) 87 KOG3312 consensus 25.5 38 0.00098 15.1 1.5 20 97-116 156-175 (186) 88 cd01669 TGS_Ygr210_C TGS_Ygr21 25.4 35 0.00089 15.4 1.3 22 122-144 54-75 (76) 89 PRK00053 alr alanine racemase; 25.4 52 0.0013 14.3 2.5 12 96-107 124-135 (360) 90 PRK07696 sulfur carrier protei 24.9 53 0.0014 14.2 2.8 23 121-143 35-60 (67) 91 PRK03646 dadX alanine racemase 24.5 54 0.0014 14.2 2.5 30 96-125 123-154 (355) 92 PRK00133 metG methionyl-tRNA s 24.3 42 0.0011 14.9 1.5 18 113-130 313-330 (666) 93 KOG4383 consensus 23.4 57 0.0014 14.0 2.3 29 122-150 161-189 (1354) 94 TIGR02299 HpaE 5-carboxymethyl 23.3 32 0.00081 15.7 0.7 32 92-140 262-293 (494) 95 PRK06083 sulfur carrier protei 22.3 59 0.0015 13.9 2.4 23 121-143 37-62 (69) 96 TIGR02170 thyX thymidylate syn 21.4 52 0.0013 14.3 1.5 21 107-127 87-108 (259) 97 TIGR01517 ATPase-IIB_Ca calciu 21.3 62 0.0016 13.8 2.9 26 120-145 160-185 (885) 98 pfam07299 FBP Fibronectin-bind 21.2 61 0.0016 13.8 1.8 24 61-84 81-104 (208) 99 pfam12331 DUF3636 Protein of u 21.1 63 0.0016 13.7 2.4 39 82-120 98-142 (155) 100 pfam10614 Tafi-CsgF Curli prod 20.9 64 0.0016 13.7 6.1 48 82-144 67-123 (142) 101 TIGR01940 nqrE NADH:ubiquinone 20.8 64 0.0016 13.7 2.1 20 87-112 94-113 (203) 102 TIGR01828 pyru_phos_dikin pyru 20.7 64 0.0016 13.7 2.2 23 123-145 501-525 (920) 103 pfam09285 Elong-fact-P_C Elong 20.7 64 0.0016 13.7 2.4 26 120-146 24-49 (56) 104 TIGR03164 UHCUDC OHCU decarbox 20.2 54 0.0014 14.2 1.4 21 79-99 114-134 (157) 105 TIGR01838 PHA_synth_I poly(R)- 20.2 66 0.0017 13.6 1.8 38 108-145 394-437 (541) No 1 >TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 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 , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=100.00 E-value=0 Score=583.48 Aligned_cols=204 Identities=45% Similarity=0.788 Sum_probs=192.4 Q ss_pred CCCCCEEEEEEECCCCCCCC--CCCCHHC---CC--CCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 64487123520058888888--8770001---36--899877654-4334135899999988485551565479999999 Q gi|254780187|r 3 KRESSKHKIDRRIGENLWGR--PKSPVNT---RS--YGPGLHGQR-RKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIF 74 (206) Q Consensus 3 r~~gpk~K~~RrlG~~l~~~--~k~~~~~---r~--~~pGqhg~~-r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~ 74 (206) ||+||++|+|||||++|||+ .+....+ |+ |||||||++ ++.|.||||+||+||||||++||.|+||||++|| T Consensus 1 Ry~Gp~~k~~RRlG~~l~g~~~~~~~~~K~k~r~~~~~PGQHG~~~r~~K~SdYg~QL~EKQKl~~~YG~i~EkQfr~~f 80 (217) T TIGR01017 1 RYTGPKFKLSRRLGVSLFGKSGSRKLLLKGKIRPFLYPPGQHGQRFRRKKLSDYGLQLQEKQKLKFMYGMITEKQFRKYF 80 (217) T ss_pred CCCCCCCEEEHEECCEECCCCCCCCHHHHCCCCCCCCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHH T ss_conf 94255401100002101368776551120120114688887641104667764567789989998625974413778899 Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHH-- Q ss_conf 875303344302689999988888998621212478878876249787888894135348338847886110022699-- Q gi|254780187|r 75 KEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLAS-- 152 (206) Q Consensus 75 ~~A~~~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~-- 152 (206) ++|.+.+|+||++||.+||+||||||||||||+||++|||||+||||+|||++||||||+|+|||+|+|+||+++.+. T Consensus 81 ~~A~~~~GntGe~LL~~LE~RLDNvVYRlGfA~Tr~~ARQLVsHGhi~vNGk~VdIPSy~v~~Gd~i~ikEk~~~~~~sn 160 (217) T TIGR01017 81 KEAKKLKGNTGENLLELLESRLDNVVYRLGFAPTRRAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLSN 160 (217) T ss_pred HHHHCCCCHHHHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHCCEEEECCEEECCCEEEECCCCEEEEEECCCCCCHHH T ss_conf 99843787278999998611001010212712007876356408807879818522406707998899810320353567 Q ss_pred HHHHHHHC--CCCCCCEEEECCCCCEEEEEECCCCCC-CCCCCCCCCCCEEEEEECC Q ss_conf 99877521--689996278812431899996788421-1246753466316775049 Q gi|254780187|r 153 VLEASQLA--ERDVPEYISVNHDNMVATFVRIPSSLK-DVPYPVIMQPNLVVEFYSR 206 (206) Q Consensus 153 i~~~~~~~--~~~~P~wLevd~~~l~g~v~~~P~r~e-~i~~p~~ine~LVVEyYSR 206 (206) |.++++.. .+.+|+|||||.++|.|+|++.|+.++ +.++|+.+||+|||||||| T Consensus 161 i~~~~E~~~~~~~~P~~Le~d~~~~~G~~~~~Pe~~qir~~l~~~ine~lvvE~YSk 217 (217) T TIGR01017 161 IKENLELAGIQRNIPSWLEVDKDKLEGKVLRVPELDQIRSELPLPINEQLVVEYYSK 217 (217) T ss_pred HHHHHHHCCCCCCCCCEEEEECCCCEEEEEECCCCCCCCCCCCCCCEEEEEEEEECC T ss_conf 888765200023678636776575079998778721112003536405788665059 No 2 >PRK05327 rpsD 30S ribosomal protein S4; Validated Probab=100.00 E-value=0 Score=538.92 Aligned_cols=201 Identities=51% Similarity=0.871 Sum_probs=193.8 Q ss_pred CCCCCCCEEEEEEECCCCCCCCCCCCHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHC Q ss_conf 97644871235200588888888770001368998776544334135899999988485551565479999999875303 Q gi|254780187|r 1 MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRS 80 (206) Q Consensus 1 M~r~~gpk~K~~RrlG~~l~~~~k~~~~~r~~~pGqhg~~r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~~~ 80 (206) ||||+||++|+|||||++||+++++++++|++||||||++++ |.|+||+||+||||+||+|| ++||||++||++|.++ T Consensus 1 MsRy~GPk~Ki~RRlG~~l~g~~k~~~~rr~~~PGqhG~~r~-k~S~Yg~qL~eKQK~r~~Yg-~~EkQ~~~~~~~A~r~ 78 (201) T PRK05327 1 MARYTGPKCKLSRRLGTDLFGKSKDKLEKRPYPPGQHGQRRK-KLSDYGLQLREKQKLKRIYG-VLEKQFRNYFKEAARR 78 (201) T ss_pred CCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHC T ss_conf 986447686730107999788887713368999998887877-65389999999999999829-7799999999998526 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHC Q ss_conf 34430268999998888899862121247887887624978788889413534833884788611002269999877521 Q gi|254780187|r 81 RGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLA 160 (206) Q Consensus 81 ~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~ 160 (206) +|+||++||++||+||||+|||+|||+|+++|||||+||||+|||++||||||+|+|||+|+++++++++..+.++.+.. T Consensus 79 ~G~Tg~~Ll~lLE~RLD~vv~r~g~a~t~~~ARQ~v~Hghi~vNg~~v~ips~~~k~gd~i~vkeks~~~~~v~~~~~~~ 158 (201) T PRK05327 79 KGNTGENLLQLLERRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREKSKKLPRIKEALELA 158 (201) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHEEEEEEEEECCEEECCCCEECCCCCEEEECCCCCCHHHHHHHHHHC T ss_conf 99689999999999988999871410588886200644059989998357874738999999770002459999999705 Q ss_pred CCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC Q ss_conf 6899962788124318999967884211246753466316775049 Q gi|254780187|r 161 ERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206 (206) Q Consensus 161 ~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR 206 (206) .+.+|+||++|.++++|++++.|++ +| +|+.+||+|||||||| T Consensus 159 ~~~~P~wL~~d~~~l~g~v~~~P~r-~~--i~~~vne~LVVEyYSr 201 (201) T PRK05327 159 ERGVPSWLEVDKDKLEGTFKRLPER-SE--IPAPINEQLIVELYSR 201 (201) T ss_pred CCCCCCEEEEECCCCEEEEEECCCH-HH--CCCCCCCCEEEEEECC T ss_conf 8999985897566788999843687-88--8977772379986149 No 3 >PRK12565 30S ribosomal protein S4; Provisional Probab=100.00 E-value=0 Score=531.46 Aligned_cols=196 Identities=39% Similarity=0.661 Sum_probs=186.1 Q ss_pred CCCCCCCEEEEEEECCCCCCCCCCCCHHCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 97644871235200588888888770001368998776544-33413589999998848555156547999999987530 Q gi|254780187|r 1 MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRR-KSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADR 79 (206) Q Consensus 1 M~r~~gpk~K~~RrlG~~l~~~~k~~~~~r~~~pGqhg~~r-~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~~ 79 (206) ||||+||++|+|||+|++||++++ +++|||||+.+ ++|.|+||+||+||||+||+|| ++|+||++||++|.+ T Consensus 1 MaRy~GPk~K~~RRlG~~l~g~~k------~~~pGqhg~~r~r~K~S~Yg~qL~EKQKlr~~YG-v~EkQfr~y~~~A~r 73 (197) T PRK12565 1 MARMRGPRFKLSRRLGVNIYGHPK------AMKRAQHGNSRERKKLSEYGIQLLEKQKLRAYYG-VLEKQFRRYVKKAMK 73 (197) T ss_pred CCCCCCCHHHHHHCCCCCCCCCCC------CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHH T ss_conf 987458774531016897679998------8799877757788876779999999999999849-888999999999985 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHH Q ss_conf 33443026899999888889986212124788788762497878888941353483388478861100226999987752 Q gi|254780187|r 80 SRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQL 159 (206) Q Consensus 80 ~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~ 159 (206) ++|+||++||++||+||||||||+|||+|+++|||||+||||+|||++||||||+|+|||+|+++++++++..+.++.+. T Consensus 74 ~~G~Tg~~Ll~lLE~RLDnvv~R~gfa~t~~~ARQlV~Hghi~vng~kVdIPSy~vk~GDvI~vkeks~~~~~v~~~~~~ 153 (197) T PRK12565 74 SKEVTGEVLLQLLECRLDNVVYRIGFASSIRQARQMVNHGHILVNGKKVNIPSYEVKVGDEITLREKSRKNEEFAENFLD 153 (197) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCEEEECHHHCCHHHHHHHHHH T ss_conf 48977999999999866677113441057999866740788897998955887670699999973322133899999972 Q ss_pred CCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC Q ss_conf 16899962788124318999967884211246753466316775049 Q gi|254780187|r 160 AERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206 (206) Q Consensus 160 ~~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR 206 (206) .....|+||++|.++++|++++.|++ +| +|+.+||+|||||||| T Consensus 154 ~~~~~p~wL~~d~~~~~g~v~~~P~r-~~--i~~~ine~lVVEyYSr 197 (197) T PRK12565 154 LRLFSLPYIEKDEDKFSGRLIRLPER-EE--IPIEVNEQLVVELYSK 197 (197) T ss_pred CCCCCCCEEEEECCCCEEEEEECCCH-HH--CCCCCCCCEEEEECCC T ss_conf 68899983887577788999934078-88--8998761479885479 No 4 >CHL00113 rps4 ribosomal protein S4; Reviewed Probab=100.00 E-value=0 Score=531.60 Aligned_cols=198 Identities=35% Similarity=0.524 Sum_probs=185.5 Q ss_pred CCCCCCCEEEEEEECCCCCCCCCCCCHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHC Q ss_conf 97644871235200588888888770001368998776544334135899999988485551565479999999875303 Q gi|254780187|r 1 MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRS 80 (206) Q Consensus 1 M~r~~gpk~K~~RrlG~~l~~~~k~~~~~r~~~pGqhg~~r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~~~ 80 (206) ||||+||++|+|||||...+.+.|++ +|+++|||||++ +|.|+||+||+||||+||+|| |+||||++||++|.++ T Consensus 1 MaRy~GP~~K~~RRlG~l~g~~~k~~--kr~~~pGqhg~~--rK~S~Yg~qL~EKQKlr~~YG-v~EkQfr~y~~~A~r~ 75 (201) T CHL00113 1 MSRYRGPRLKKIRRLGALPGLTSKRP--KRGSDLGNQSRS--GKKSQYRIRLEEKQKLRFNYG-LTERQLLKYVRIARKA 75 (201) T ss_pred CCCCCCCHHHEECCCCCCCCCCCCCC--CCCCCCCCCCCC--CCCCHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHC T ss_conf 98655767550215888856675443--689999878888--840689999999999999808-5499999999999865 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHC Q ss_conf 34430268999998888899862121247887887624978788889413534833884788611002269999877521 Q gi|254780187|r 81 RGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLA 160 (206) Q Consensus 81 ~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~ 160 (206) +|+||+|||++||+||||||||+|||+|+++|||||+||||+|||++||||||+|+|||+|++++++++...+.++++.. T Consensus 76 ~G~Tg~~Ll~lLE~RLDnvVyRlGfA~Tr~~ARQlV~HgHi~VNgkkVnIPSy~vk~GDvI~v~~ks~~~~~v~~~~~~~ 155 (201) T CHL00113 76 KGSTGQVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPRDIITIKDKQKSRALIQNNLDSS 155 (201) T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHEEECCEEEECCEEECCCCEEEECCCEEEECCCCCCHHHHHHHHHHC T ss_conf 89689999999999999999870540588876105846629989989337875842799899753444458999999731 Q ss_pred -CCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC Q ss_conf -6899962788124318999967884211246753466316775049 Q gi|254780187|r 161 -ERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206 (206) Q Consensus 161 -~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR 206 (206) ...+|+||++|.++++|++++.|++ +| +|+.+||+|||||||| T Consensus 156 ~~~~~p~wl~~d~~~~~g~v~~~P~r-~~--i~~~i~e~LIVE~YSr 199 (201) T CHL00113 156 KLEELPNHLTFHKFQLKGLVNQIIDR-KW--VGLKINELLVVEYYSR 199 (201) T ss_pred CCCCCCCCEEEECCCCEEEEEECCCH-HH--CCCCCCCCEEEEEECC T ss_conf 55799980186554588999606876-77--8977764579998067 No 5 >COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=427.33 Aligned_cols=202 Identities=44% Similarity=0.704 Sum_probs=188.7 Q ss_pred CCCCCCCEEEEEEECCCCCCCCCCC-CHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 9764487123520058888888877-000136899877654433413589999998848555156547999999987530 Q gi|254780187|r 1 MSKRESSKHKIDRRIGENLWGRPKS-PVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADR 79 (206) Q Consensus 1 M~r~~gpk~K~~RrlG~~l~~~~k~-~~~~r~~~pGqhg~~r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~~ 79 (206) |+||.||+.|++||+|.++|++... ...+++++|||||+.+.++.|+||.||+||||++++|| +.|+||+++|.+|.. T Consensus 1 M~r~~~~~~K~~rr~g~~~~~~~~~~~~~~~~~~pGqhk~~~~~k~s~yg~qL~ekqkl~~~yg-~~ekqf~~~l~~a~~ 79 (205) T COG0522 1 MARYPGPKKKLSRRLGFNPWLKERLCKERKLPYKPGQHGQERWKKLSDYGLQLREKQKLRAFYG-VLEKQFRRYLKEAGR 79 (205) T ss_pred CCCCCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHC T ss_conf 9987673204210068776777778877612788564621677799999999999777652023-779999999999705 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHH Q ss_conf 33443026899999888889986212124788788762497878888941353483388478861100226999987752 Q gi|254780187|r 80 SRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQL 159 (206) Q Consensus 80 ~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~ 159 (206) .+|+|+.+++.+||+||||+|||+|||+|+.+|||||+||||.|||++||||||+|++||+|+|++++++...+..+.+. T Consensus 80 l~g~~~~~~~~~LErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~~~~~~~~~ 159 (205) T COG0522 80 LKGVTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALEL 159 (205) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEEECCCCEEEEECCCCCHHHHHHHHHH T ss_conf 57708889999999887899998404135999998840662899999952673796377788752034542555554653 Q ss_pred C--CCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC Q ss_conf 1--6899962788124318999967884211246753466316775049 Q gi|254780187|r 160 A--ERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206 (206) Q Consensus 160 ~--~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR 206 (206) + ...+|+|+++|.+++.|++.+.|++.+ +|..+||+|||||||| T Consensus 160 ~~~~~~~~~~~e~d~~~~~~~~~~~p~~~~---~~~~~~e~~ive~ys~ 205 (205) T COG0522 160 AAQRGIPPAWLEVDEEKLEGTFKRLPERSD---LPAPINEQLIVEFYSK 205 (205) T ss_pred HHHCCCCHHHHHCCHHHHCEEEEECCCCCC---CCCCCCHHEEEEEECC T ss_conf 310147604542453330033100784001---6888781048851329 No 6 >pfam00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain. This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices. Probab=99.95 E-value=2.9e-28 Score=204.04 Aligned_cols=91 Identities=32% Similarity=0.448 Sum_probs=84.3 Q ss_pred CCCCCCEEEEEEECCCCCCCCCCC-CHHCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH Q ss_conf 764487123520058888888877-00013689987765443--341358999999884855515654799999998753 Q gi|254780187|r 2 SKRESSKHKIDRRIGENLWGRPKS-PVNTRSYGPGLHGQRRK--SKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEAD 78 (206) Q Consensus 2 ~r~~gpk~K~~RrlG~~l~~~~k~-~~~~r~~~pGqhg~~r~--~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~ 78 (206) |||+||++|+|||+|+++|++.+. ...+.+++|||||+.++ +|+|+||+||.||||+||+|| |+|+||++||++|. T Consensus 1 aRy~GP~~K~~RR~g~~~~~~~~~~~~~~~~~~pg~hg~~~~~~rk~S~Yg~qL~EKQklr~~YG-l~ErQfr~y~~~A~ 79 (94) T pfam00163 1 SRYRGPTLKLPRRLGELPRLTAKTKLAGEYGLRPGQHGWRVKKGRRLSRYLLRLDEKQKLRFFYG-LLERQLRRYGVLAK 79 (94) T ss_pred CCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC-HHHHHHHHHHHHHH T ss_conf 96657554431789998677677767676778999865344576526189887864307999805-30999999999997 Q ss_pred HCCCCCCHHHHHHHH Q ss_conf 033443026899999 Q gi|254780187|r 79 RSRGDTSHNLISFLE 93 (206) Q Consensus 79 ~~~g~t~~~ll~~LE 93 (206) +++|+||+||+++|| T Consensus 80 k~~G~TG~~Ll~lLE 94 (94) T pfam00163 80 KLDGSLGLNLLDLLE 94 (94) T ss_pred CCCCCHHHHHHHHHC T ss_conf 479877999999809 No 7 >KOG3301 consensus Probab=99.82 E-value=3.9e-21 Score=157.79 Aligned_cols=130 Identities=18% Similarity=0.171 Sum_probs=104.3 Q ss_pred CCCCCCCE--EEEEEECCCCCCCCCCCCHHCCCCCCCCCCCCCCCCHHHHHHH----HHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 97644871--2352005888888887700013689987765443341358999----99988485551565479999999 Q gi|254780187|r 1 MSKRESSK--HKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQ----LRAKQKMKKYYGDISEKKFRSIF 74 (206) Q Consensus 1 M~r~~gpk--~K~~RrlG~~l~~~~k~~~~~r~~~pGqhg~~r~~k~S~yg~q----L~eKQKlr~~YG~~~ekq~~~~~ 74 (206) |.+|.+|+ |+..|..++.-.-...-..+++-.. ...+.-+-+.|+.+ +.++|++ |.|+ ..+.++.+|- T Consensus 1 ~k~y~~PRrpfek~Rld~elkl~g~yglknk~elw----r~~~~l~K~r~aaR~ll~~k~p~rl-f~g~-allrrLvr~g 74 (183) T KOG3301 1 SKTYKTPRRPFEKERLDAELKLVGEYGLKNKRELW----RVSRSLSKIRYAARELLDEKDPKRL-FEGN-ALLRRLVRYG 74 (183) T ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHH----HHHHHHHHHHHHHHHHHCCCCHHHH-HCCH-HHHHHHHHHH T ss_conf 98557898708888887660123212654305999----9999999999999986401267777-4000-8999999985 Q ss_pred HHH---HHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEEC Q ss_conf 875---30334430268999998888899862121247887887624978788889413534833 Q gi|254780187|r 75 KEA---DRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCK 136 (206) Q Consensus 75 ~~A---~~~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k 136 (206) ..+ .+..++++..+..+||+|||++||++|+|.|+.+||++|.|+||.|++++||||||+|+ T Consensus 75 ~l~e~~~Kldyvl~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vr 139 (183) T KOG3301 75 VLDERKNKLDYVLALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVR 139 (183) T ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCEEEECCCEEEE T ss_conf 32012343137799899999999999999998665442788987427607615757624654566 No 8 >TIGR01018 rpsD_arch ribosomal protein S4; InterPro: IPR005710 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 , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This model finds eukaryotic ribosomal protein S9 as well as eukaryotic and archaeal ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=99.72 E-value=2.5e-18 Score=139.55 Aligned_cols=57 Identities=40% Similarity=0.614 Sum_probs=52.9 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCC--CEEEECCHH Q ss_conf 999888889986212124788788762497878888941353483388--478861100 Q gi|254780187|r 91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEG--DVIEVKQKS 147 (206) Q Consensus 91 ~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~g--d~I~~~~ks 147 (206) .||+||+++||+.|+|.|+.||||||.||||-|||++||+|||+|+.+ |.|++...| T Consensus 109 ~LERRLQT~Vyk~GLArTi~~ARqLi~hGHI~v~Gr~v~~Psy~V~~e~e~kI~fa~~S 167 (170) T TIGR01018 109 VLERRLQTLVYKKGLARTIKQARQLIVHGHIAVDGRRVTSPSYIVRREEEDKIDFARSS 167 (170) T ss_pred HHHHHHHHHHHHHHHCCCHHHCCEEEEECEEEECCEEEECCCEEEECCCCCCCCCCCCC T ss_conf 55345678999863022632343023203388768477358616746554421205688 No 9 >PRK04051 rps4p 30S ribosomal protein S4; Validated Probab=99.67 E-value=1.8e-16 Score=127.52 Aligned_cols=60 Identities=40% Similarity=0.520 Sum_probs=56.4 Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCC--CEEEECCHHHH Q ss_conf 9999888889986212124788788762497878888941353483388--47886110022 Q gi|254780187|r 90 SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEG--DVIEVKQKSKQ 149 (206) Q Consensus 90 ~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~g--d~I~~~~ksk~ 149 (206) .+||+|||++|||+|||+|+.+|||||.||||.|||++|++|||+|+.. |.|++.+.|+- T Consensus 99 ~~l~RRL~~vv~r~~~a~si~~Ar~lI~hgHi~V~~~~v~~Ps~~V~r~~Ed~I~~~~~S~i 160 (177) T PRK04051 99 DILERRLQTIVYRKGLARTPKQARQLIVHGHIAVNGRRVTSPGYLVSREEEDKIDYYPTSPL 160 (177) T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCEEEEECCCCCEEECCCCCC T ss_conf 99996888999880566889999999747828999999536865886556685463179977 No 10 >PTZ00155 40S ribosomal protein S9; Provisional Probab=99.59 E-value=1.6e-15 Score=121.46 Aligned_cols=59 Identities=27% Similarity=0.428 Sum_probs=54.7 Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCC--CEEEECCHHH Q ss_conf 9999888889986212124788788762497878888941353483388--4788611002 Q gi|254780187|r 90 SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEG--DVIEVKQKSK 148 (206) Q Consensus 90 ~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~g--d~I~~~~ksk 148 (206) .+||+||+++||++|||.|+.+|||||.||||.|||++||+|||+|..+ |.|++.+.|- T Consensus 103 ~~l~RRLqt~v~~~glA~si~~Ar~lI~hgHI~V~~~~V~~Ps~lV~r~~Ed~I~~~~~Sp 163 (188) T PTZ00155 103 DILERRLQTKVFKLGLAKSVHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIAFALTSP 163 (188) T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHEECCEEEECCEEECCCCEEEEECCCCCEEEECCCC T ss_conf 8998767689998601158898888834462889998953774588605446445436898 No 11 >smart00363 S4 S4 RNA-binding domain. Probab=99.22 E-value=1.2e-11 Score=96.21 Aligned_cols=54 Identities=39% Similarity=0.576 Sum_probs=51.6 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHH Q ss_conf 888889986212124788788762497878888941353483388478861100 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKS 147 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ks 147 (206) +|||.++.++||+.|+.+|+++|.||+|.|||++++.|||.|++||.|++..+. T Consensus 1 ~RLD~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I~~~~~~ 54 (60) T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKE 54 (60) T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECCCC T ss_conf 978899998387047999999998491798999947898898999999998850 No 12 >pfam01479 S4 S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA. Probab=99.21 E-value=8.7e-12 Score=97.13 Aligned_cols=48 Identities=46% Similarity=0.652 Sum_probs=46.8 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEE Q ss_conf 888889986212124788788762497878888941353483388478 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVI 141 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I 141 (206) +|||.+++++||++|+.+|+++|.||+|.|||++++.|||.|++||+| T Consensus 1 ~RLd~~l~~~~~~~Sr~~a~~~I~~G~V~VNg~~v~~~~~~v~~gD~i 48 (48) T pfam01479 1 MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI 48 (48) T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCCC T ss_conf 966799998676148999999998897798999957898688992999 No 13 >cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes. Probab=99.13 E-value=6.1e-11 Score=91.65 Aligned_cols=56 Identities=50% Similarity=0.711 Sum_probs=52.5 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHH Q ss_conf 88888998621212478878876249787888894135348338847886110022 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQ 149 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~ 149 (206) +|||.++.++|++.|+.+|+++|.||+|.|||+.++.||+.|++||.|++.+.... T Consensus 1 ~RLd~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~gd~i~i~~~~~~ 56 (70) T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIE 56 (70) T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEECCCCCC T ss_conf 94889998748715899999999819389899995888889899999998787788 No 14 >COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Probab=98.49 E-value=2.4e-07 Score=68.40 Aligned_cols=52 Identities=31% Similarity=0.345 Sum_probs=50.8 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 8888899862121247887887624978788889413534833884788611 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) +|||..+++.|++.||..|+-+|..|.|.|||.+|+.||+.|+.++.|++.+ T Consensus 3 ~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~ 54 (245) T COG1189 3 MRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKG 54 (245) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECC T ss_conf 2389999973533209999999876857889999427652458986378756 No 15 >COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] Probab=98.38 E-value=3.3e-07 Score=67.48 Aligned_cols=58 Identities=26% Similarity=0.391 Sum_probs=53.5 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHH Q ss_conf 99988888998621212478878876249787888894135348338847886110022 Q gi|254780187|r 91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQ 149 (206) Q Consensus 91 ~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~ 149 (206) -.++|||-.|.-++|..|+.-|.-+|.-|+|.|||..+ .||..|++||+|+|+-..+. T Consensus 6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~ 63 (100) T COG1188 6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKE 63 (100) T ss_pred CCCEEHHHHHHHHHHHHHHHHHHHHHHCCEEEECCEEC-CCCCCCCCCCEEEEEECCCE T ss_conf 65165678887887742289999998779698999675-65561477989999957818 No 16 >TIGR00478 tly hemolysin A; InterPro: IPR004538 Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. The mechanism of action is not well defined. Hemolysin A is induced by sodium ribonucleate, and is produced by pathogenic bacterial strains. Hemolysin A from Treponema hyodysenteriae causes swine dysentry.; GO: 0003723 RNA binding, 0019836 hemolysis by symbiont of host red blood cells. Probab=98.34 E-value=5.3e-07 Score=66.11 Aligned_cols=54 Identities=26% Similarity=0.316 Sum_probs=51.5 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHH Q ss_conf 888899862121247887887624978788889413534833884788611002 Q gi|254780187|r 95 RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148 (206) Q Consensus 95 RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk 148 (206) |||++|++-||+.||..|..+|.-|.|.||+++|+.||..|+..+.|++.+... T Consensus 1 RLD~lLv~rgl~~sR~~Ak~lI~kG~V~VN~~~v~KP~~~v~~~~~i~l~~~~~ 54 (240) T TIGR00478 1 RLDILLVKRGLVESREKAKRLILKGEVLVNKKKVDKPSALVDKDAKIELVQNPL 54 (240) T ss_pred CCHHHHHHHCHHHHHHHHHHHHHCCCEEECCEEECCCCCEECCCCCEEEECCCC T ss_conf 903677650114578999999873945555765208860441676034414777 No 17 >TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium. Probab=98.31 E-value=9.2e-07 Score=64.57 Aligned_cols=55 Identities=22% Similarity=0.244 Sum_probs=50.4 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHH Q ss_conf 98888899862121247887887624978788889413534833884788611002 Q gi|254780187|r 93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148 (206) Q Consensus 93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk 148 (206) -.|||+|+= ++|--||..|.++|..|.|.||++.++.|||.|++||+||++-.-+ T Consensus 183 SlRLDavvs-~~~~~SRska~~lI~~g~V~vN~~~v~~~s~~v~~gDiiSvRG~GR 237 (257) T TIGR03069 183 SLRIDAIAS-AGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGKGR 237 (257) T ss_pred CCCHHHHHH-HHHCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEEECCCE T ss_conf 213899999-8866579999999884968989999057875668999999906717 No 18 >PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Probab=98.19 E-value=1.4e-06 Score=63.30 Aligned_cols=53 Identities=26% Similarity=0.338 Sum_probs=49.7 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH Q ss_conf 988888998621212478878876249787888894135348338847886110 Q gi|254780187|r 93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146 (206) Q Consensus 93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k 146 (206) .+|||--|+-+.|+.|+..|-+.|.-|||.|||.. ..||..|++||+|+|+.. T Consensus 8 k~RiDkwLW~aRffKTRslA~~a~~~G~V~vnG~~-~Kps~~V~~GD~l~i~~~ 60 (133) T PRK10348 8 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQG 60 (133) T ss_pred CEEEHHHHHHHEEHHHHHHHHHHHHCCCEEECCEE-CCCCCCCCCCCEEEEEEC T ss_conf 05402003152010009999999987988989988-688887689999999869 No 19 >PRK10839 16S rRNA pseudouridylate synthase A; Provisional Probab=98.18 E-value=3.3e-06 Score=60.98 Aligned_cols=53 Identities=17% Similarity=0.180 Sum_probs=49.6 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHH Q ss_conf 888889986212124788788762497878888941353483388478861100 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKS 147 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ks 147 (206) +||+-++-.+|+| ||.+|..||..|.|.|||+.|+.|++.|.++|.|.+..+. T Consensus 1 mRL~K~La~~g~~-SRR~ae~lI~~GrV~VNg~~v~~~~~~V~~~~~v~vdg~~ 53 (231) T PRK10839 1 MRLDKFIAQQLGV-SRAIAGREIRGNRVTVDGEIVKNAAFKLLPEHDVAYDGNP 53 (231) T ss_pred CCHHHHHHHCCCC-CHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCE T ss_conf 9378999887895-6999999998797999999914588084999869991958 No 20 >COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Probab=98.11 E-value=4.4e-06 Score=60.15 Aligned_cols=54 Identities=30% Similarity=0.452 Sum_probs=49.1 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHH Q ss_conf 8888899862121247887887624978788889413534833884788611002 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk 148 (206) .|||.++=- +|--||..|.|+|..|.|.||.+.|+.+||.|..||.||++-.-+ T Consensus 181 lRLD~vis~-~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~GR 234 (257) T COG2302 181 LRLDVVISE-GFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGR 234 (257) T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHCCCEEEEEEEECCCCCEECCCCEEEEECCCC T ss_conf 407999998-876559999998773732771299126663322498999840451 No 21 >PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Probab=97.76 E-value=5e-05 Score=53.32 Aligned_cols=53 Identities=19% Similarity=0.271 Sum_probs=46.9 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH Q ss_conf 88888998621212478878876249787888894135348338847886110 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k 146 (206) .|||..+-+.-=..|+...+++|..|.|.|||++++.|++.|+.||+|++... T Consensus 18 ~RLD~fL~~~~~~~srs~i~k~ir~g~I~VNgk~v~k~~~~v~~GD~I~i~~~ 70 (325) T PRK11180 18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAE 70 (325) T ss_pred CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCCEEEECCC T ss_conf 73999999757888999999999869889999994782127889999998168 No 22 >PRK11025 23S rRNA pseudouridylate synthase C; Provisional Probab=97.60 E-value=0.00012 Score=50.73 Aligned_cols=50 Identities=16% Similarity=0.232 Sum_probs=43.5 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEEC Q ss_conf 888889986212124788788762497878888941353483388478861 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVK 144 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~ 144 (206) +|||..+-..=-.-|+...+.+|..|.|.|||+++ .|||.|+.||+|++. T Consensus 20 ~RLD~fL~~~l~~~srs~i~klir~g~V~VNg~~v-k~~~~l~~GD~I~i~ 69 (317) T PRK11025 20 QRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIP 69 (317) T ss_pred CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEC-CCCCCCCCCCEEEEC T ss_conf 75999999756626999999999869989999995-710465799999988 No 23 >KOG4655 consensus Probab=97.56 E-value=1.9e-05 Score=56.00 Aligned_cols=71 Identities=25% Similarity=0.309 Sum_probs=62.6 Q ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEEC--CCCEEEECCHHHHHHHHHHHHH Q ss_conf 8999998888899862121247887887624978788889413534833--8847886110022699998775 Q gi|254780187|r 88 LISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCK--EGDVIEVKQKSKQLASVLEASQ 158 (206) Q Consensus 88 ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k--~gd~I~~~~ksk~~~~i~~~~~ 158 (206) --+++++||-.|..++++|.|...|--+|.||||.|.-+.|+-|+|+|. ..|.|+.-+.||....+.+-++ T Consensus 101 vssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SKIKr~v~~yn~ 173 (181) T KOG4655 101 VSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSKIKRKVLEYND 173 (181) T ss_pred HHHHHHHCCCEEEEECHHHHHHHHHHHHHHCCCEEECCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 6777630465133402001669999999981853517800047257742226656424226889999998648 No 24 >COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Probab=97.52 E-value=0.00042 Score=47.30 Aligned_cols=53 Identities=26% Similarity=0.368 Sum_probs=47.0 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 9998888899862121247887887624978788889413534833884788611 Q gi|254780187|r 91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 91 ~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) .-.+|||..+-.+.- .|+.....++..|.|.|||++++ +++.+++||+|++.. T Consensus 10 ~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~ 62 (289) T COG0564 10 EAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPL 62 (289) T ss_pred HCCCCHHHHHHHHCC-CCHHHHHHHHHCCCEEECCEECC-CCEEECCCCEEEEEC T ss_conf 135479999987257-47999999988898899999835-871608999999535 No 25 >PRK10475 23S rRNA pseudouridine synthase F; Provisional Probab=97.49 E-value=0.0002 Score=49.43 Aligned_cols=51 Identities=22% Similarity=0.442 Sum_probs=46.3 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH Q ss_conf 88888998621212478878876249787888894135348338847886110 Q gi|254780187|r 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146 (206) Q Consensus 94 ~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k 146 (206) .||+-+|=++|+| |+.+|-+||..|.|.|||+.++ ++..|.++|.|.+..+ T Consensus 7 ~RL~K~LA~~G~~-SRReAe~lI~~GrV~VNGk~v~-~g~~V~~~D~V~vdg~ 57 (290) T PRK10475 7 TRLNKYISESGIC-SRREADRYIEQGNVFINGKRAT-IGDQVKPGDVVKVNGQ 57 (290) T ss_pred CHHHHHHHHCCCC-HHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCE T ss_conf 1499999877783-5999999998597898999957-9888699998999998 No 26 >COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Probab=97.08 E-value=0.0013 Score=44.09 Aligned_cols=53 Identities=26% Similarity=0.385 Sum_probs=47.7 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCC-EEEECCH Q ss_conf 98888899862121247887887624978788889413534833884-7886110 Q gi|254780187|r 93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGD-VIEVKQK 146 (206) Q Consensus 93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd-~I~~~~k 146 (206) .+|||-++-++|+| |+.+|.+||..|.|.|||+.++.+...+.+++ +|.+..+ T Consensus 2 ~~RL~K~La~~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~ 55 (248) T COG1187 2 SMRLNKFLAEAGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGK 55 (248) T ss_pred CCCHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEEECCCCEEECCCCCEEEECCE T ss_conf 52068999874777-8899999997398788999922477672798768998998 No 27 >PRK13354 tyrosyl-tRNA synthetase; Provisional Probab=96.70 E-value=0.0038 Score=41.11 Aligned_cols=100 Identities=16% Similarity=0.234 Sum_probs=61.9 Q ss_pred HHHHHHHHHHHHHHCCCC----HHHHHHHHHHHHHCCCCCCHHHHHHH--HHHHHHHHHHHCCCCCHHHHHHHHHCCCEE Q ss_conf 999999884855515654----79999999875303344302689999--988888998621212478878876249787 Q gi|254780187|r 49 GLQLRAKQKMKKYYGDIS----EKKFRSIFKEADRSRGDTSHNLISFL--ESRLDTIVYRAKFVPTIFAARQFVNHRHVL 122 (206) Q Consensus 49 g~qL~eKQKlr~~YG~~~----ekq~~~~~~~A~~~~g~t~~~ll~~L--E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~ 122 (206) +....+..-.+.+||.-. ++.|..+|....-......-.+.... ..-|-.++..+|+++|..+||.+|..|-|. T Consensus 291 aKk~LA~Eit~lvHG~e~a~~A~~~~~~lF~~~~l~e~ip~~~~~~~~~~~~~l~dlLv~~gl~~SksEARRlI~qGgV~ 370 (405) T PRK13354 291 AKMILAEEITRFYHGEEALLAAEEIFKALFQAGEIPQEIPEIPTIQSSKETKNIVDLLVDLGLAPSKREARRLINNGAVK 370 (405) T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEE T ss_conf 99999999999836999999999999999678998000875410001257888999999839867889999999859989 Q ss_pred ECCEEEECCCEEECCCCEEEECCHHH Q ss_conf 88889413534833884788611002 Q gi|254780187|r 123 VNGRSVNIGSYRCKEGDVIEVKQKSK 148 (206) Q Consensus 123 vng~~v~~ps~~~k~gd~I~~~~ksk 148 (206) |||.+|+-|.+.+.++|.+-++-..| T Consensus 371 INgekV~D~~~~l~~~~~llLr~GKK 396 (405) T PRK13354 371 INGEKVTDVGTDVTVENSLIIQVGKK 396 (405) T ss_pred ECCEEECCCCCCCCCCCCEEEEECCC T ss_conf 89999328876446899489982681 No 28 >PRK10700 23S rRNA pseudouridylate synthase B; Provisional Probab=96.64 E-value=0.005 Score=40.36 Aligned_cols=53 Identities=17% Similarity=0.283 Sum_probs=42.3 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCE-EECCCCEEEECCH Q ss_conf 98888899862121247887887624978788889413534-8338847886110 Q gi|254780187|r 93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY-RCKEGDVIEVKQK 146 (206) Q Consensus 93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~-~~k~gd~I~~~~k 146 (206) +.|||-++-++|+| |+.+|.++|.-|.|.|||++++.... .+.++|.|.+..+ T Consensus 2 ~eRL~K~LA~~G~~-SRReae~lI~~GrV~VNG~v~~lg~~v~~~~~~~V~vDG~ 55 (291) T PRK10700 2 SEKLQKVLARAGHG-SRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGH 55 (291) T ss_pred HHHHHHHHHHCCCC-HHHHHHHHHHCCEEEECCEECCCCCEECCCCCCEEEECCE T ss_conf 17999999987894-3999999998694998999955688265899988999999 No 29 >PRK11507 hypothetical protein; Provisional Probab=96.52 E-value=0.0044 Score=40.69 Aligned_cols=52 Identities=12% Similarity=0.115 Sum_probs=48.1 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH Q ss_conf 8888998621212478878876249787888894135348338847886110 Q gi|254780187|r 95 RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146 (206) Q Consensus 95 RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k 146 (206) .|+.++--.|++.|=-+|..+|.-|.|.|||..-+.-...+..||+|++... T Consensus 13 eL~~lLK~~glv~sGg~AK~~Ia~G~V~VnGevEtRKr~Ki~~GdvV~f~g~ 64 (70) T PRK11507 13 ELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH 64 (70) T ss_pred EHHHHHHHCCCCCCCHHHHHHEECCEEEECCEEEEEEEEEEECCCEEEECCE T ss_conf 0888884717204658778654187689999996331025108999999999 No 30 >TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330 This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members that are not near recF are found instead near dnaA and/or dnaN, the usual neighbours of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.. Probab=96.44 E-value=0.0057 Score=39.98 Aligned_cols=50 Identities=28% Similarity=0.357 Sum_probs=46.1 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 88899862121247887887624978788889413534833884788611 Q gi|254780187|r 96 LDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 96 LD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) ||-+|=-+|.+.|=-+|.+++.-+.|+|||+.-+.-+--|.+||+|+|.+ T Consensus 11 LgQlLK~~~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~~ 60 (60) T TIGR02988 11 LGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIPD 60 (60) T ss_pred HHHHHHHHHHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEECC T ss_conf 76786688562282578898706955547844045887004896688269 No 31 >PRK04313 30S ribosomal protein S4e; Validated Probab=96.37 E-value=0.004 Score=40.93 Aligned_cols=44 Identities=25% Similarity=0.305 Sum_probs=41.3 Q ss_pred HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 62121247887887624978788889413534833884788611 Q gi|254780187|r 102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) ++++|.|..+|+.++..|.|+|||+...-+.|.+-.-|+||+-+ T Consensus 47 ~L~~a~t~rEak~Il~~~~V~VDG~vr~d~~~pvGlmDVisi~~ 90 (237) T PRK04313 47 VLGYADTAREARKIISEGKVLVDGRVRKDYKFPVGLMDVISIPE 90 (237) T ss_pred HHHHHCCHHHHHHHHHCCEEEECCEEEECCCCCCCEEEEEEECC T ss_conf 77250448899998648859989999603788754167998647 No 32 >PTZ00223 40S ribosomal protein S4; Provisional Probab=96.37 E-value=0.0039 Score=41.00 Aligned_cols=44 Identities=25% Similarity=0.357 Sum_probs=41.5 Q ss_pred HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 62121247887887624978788889413534833884788611 Q gi|254780187|r 102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) ++++|.|..+|+.++..|+|+|||++.+-+.|.+-.-||||+-. T Consensus 48 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~k 91 (273) T PTZ00223 48 RLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK 91 (273) T ss_pred HHCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECC T ss_conf 64521657999999877937977999655899885789999857 No 33 >PTZ00118 40S ribosomal protein S4; Provisional Probab=96.21 E-value=0.0056 Score=40.03 Aligned_cols=44 Identities=23% Similarity=0.259 Sum_probs=41.4 Q ss_pred HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 62121247887887624978788889413534833884788611 Q gi|254780187|r 102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) ++++|.|..+|+.++..|+|+|||+..+-+.|.+-.-|+||+-. T Consensus 51 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~k 94 (262) T PTZ00118 51 RLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTK 94 (262) T ss_pred HHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECC T ss_conf 64522658999999867908889999534899874678999856 No 34 >COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Probab=96.16 E-value=0.013 Score=37.68 Aligned_cols=51 Identities=24% Similarity=0.363 Sum_probs=46.0 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCH Q ss_conf 888998621212478878876249787888894135348338847886110 Q gi|254780187|r 96 LDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146 (206) Q Consensus 96 LD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~k 146 (206) |+-++--+|+..|=-+|.++++-|.|+|||..-|.-.-.+..||+|++.+. T Consensus 14 L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~ 64 (73) T COG2501 14 LGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQ 64 (73) T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCEEEECCEEECCCCCEEECCCEEEECCE T ss_conf 999998749505747888998779189888663016776016989998997 No 35 >TIGR00005 rluA_subfam pseudouridine synthase, RluA family; InterPro: IPR006225 This is the RluD subfamily of pseudouridine synthases. In Escherichia coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917. RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homologue from E. coli outside this family, TruC (Q46918 from SWISSPROT), modifies uracil-65 in transfer RNAs to pseudouridine. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis. Probab=95.82 E-value=0.02 Score=36.46 Aligned_cols=87 Identities=20% Similarity=0.275 Sum_probs=60.2 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEEC-CEEEECCCEEECCCCEEE-ECCHHHHHHHHHHHHHHCCCCCCC--EE Q ss_conf 98888899862121247887887624978788-889413534833884788-611002269999877521689996--27 Q gi|254780187|r 93 ESRLDTIVYRAKFVPTIFAARQFVNHRHVLVN-GRSVNIGSYRCKEGDVIE-VKQKSKQLASVLEASQLAERDVPE--YI 168 (206) Q Consensus 93 E~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vn-g~~v~~ps~~~k~gd~I~-~~~ksk~~~~i~~~~~~~~~~~P~--wL 168 (206) -.|||.++-..=--.|+....++|.+|.|.|| ++....+++.++.||.|+ |.=..... ..+......|. -| T Consensus 5 g~Rld~~L~~~l~~~sr~~~~~~i~~G~V~vN~~~~~~~~~~~~~~g~~~~~v~~~~~~~-----~~~~~~~~~p~~l~l 79 (337) T TIGR00005 5 GQRLDDFLASLLPDLSRSRIQKLIENGQVKVNKGKVTANPKLKIKDGDRITPVRVPEEQE-----ELEVPVQDIPADLKL 79 (337) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHCCCEEECCCCCCCCCCEEECCCCEEECEECCCCCC-----CCCCCCCCCCCCCCC T ss_conf 026999999983678888999998749689637642567430523874660100146433-----235766567342211 Q ss_pred EECCCCCEEEEEECCC Q ss_conf 8812431899996788 Q gi|254780187|r 169 SVNHDNMVATFVRIPS 184 (206) Q Consensus 169 evd~~~l~g~v~~~P~ 184 (206) ++=++.=...++.-|. T Consensus 80 ~IlfEDe~i~vinKP~ 95 (337) T TIGR00005 80 DILFEDEDILVINKPS 95 (337) T ss_pred EEEEECCCEEEEECCC T ss_conf 3787508389997898 No 36 >PRK05912 tyrosyl-tRNA synthetase; Validated Probab=95.73 E-value=0.013 Score=37.59 Aligned_cols=89 Identities=22% Similarity=0.335 Sum_probs=56.5 Q ss_pred HHHHHHHHHHHHHHHCCC----CHHHHHHHHHHHHHCCCCCCHHHH----HHHHHHHHHHHHHHCCCCCHHHHHHHHHCC Q ss_conf 899999988485551565----479999999875303344302689----999988888998621212478878876249 Q gi|254780187|r 48 FGLQLRAKQKMKKYYGDI----SEKKFRSIFKEADRSRGDTSHNLI----SFLESRLDTIVYRAKFVPTIFAARQFVNHR 119 (206) Q Consensus 48 yg~qL~eKQKlr~~YG~~----~ekq~~~~~~~A~~~~g~t~~~ll----~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg 119 (206) .+....+..-.+.++|.= .++.+..+|.. +...+.+- .--+..+=.++..+|+++|..+||.+|..| T Consensus 286 ~aqk~LA~Evt~lvHGe~~a~~A~~~~~~lF~~-----~~~~~dlp~~~~~~~~~~i~dlLv~~gl~~SksEARRlI~qG 360 (402) T PRK05912 286 EAKKVLAEEITALFHGEEAAEAAEEAFEALFLK-----GLIPDDLPEVELDEAGIGLVDLLVEAGLVPSKSEARRLIQQG 360 (402) T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC-----CCCCCCCCEEEECCCCCCHHHHHHHCCCCCCHHHHHHHHHCC T ss_conf 589999999999855999999999999999658-----998234885770689988999999868867889999999819 Q ss_pred CEEECCEEEECCCEEECCCCEE Q ss_conf 7878888941353483388478 Q gi|254780187|r 120 HVLVNGRSVNIGSYRCKEGDVI 141 (206) Q Consensus 120 ~i~vng~~v~~ps~~~k~gd~I 141 (206) -|.|||.+|+-|.+.+...|.+ T Consensus 361 gV~IN~~kI~D~~~~l~~~~l~ 382 (402) T PRK05912 361 AVKINGEKVSDPDYVFTEADLL 382 (402) T ss_pred CEEECCEEECCCCCCCCHHHCC T ss_conf 9898999964955422787805 No 37 >COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Probab=95.42 E-value=0.016 Score=37.04 Aligned_cols=44 Identities=23% Similarity=0.297 Sum_probs=40.4 Q ss_pred HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 62121247887887624978788889413534833884788611 Q gi|254780187|r 102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) .|++|.+..+||-+++.|+|+|||+...-.-|.|-.-|+|++-+ T Consensus 50 ~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~ 93 (241) T COG1471 50 YLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPK 93 (241) T ss_pred HHHHCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECC T ss_conf 87762234889998766957988898013557840689999768 No 38 >COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Probab=93.92 E-value=0.37 Score=28.17 Aligned_cols=86 Identities=26% Similarity=0.341 Sum_probs=53.1 Q ss_pred HHHHHHHHHHHHHHCCC----CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEEC Q ss_conf 99999988485551565----47999999987530334430268999998888899862121247887887624978788 Q gi|254780187|r 49 GLQLRAKQKMKKYYGDI----SEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVN 124 (206) Q Consensus 49 g~qL~eKQKlr~~YG~~----~ekq~~~~~~~A~~~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vn 124 (206) ...+.++-..+..||.= .+..+.+.|... ......-..|-..++..+=..+.-+|+++|+.+||.+|..|-+.+| T Consensus 288 ~k~~LA~e~~~~~hG~~~a~~a~~~~~~~F~~g-~~~~l~~~dlk~~~~~~~~~~lv~~~L~psr~earr~i~~g~v~in 366 (401) T COG0162 288 AKKLLAKEVTKLVHGEEAAEAAEEEFEKLFSEG-LPENLPPADLKQKLEDGLVDLLVDAGLAPSRSEARRLIQQGGVKIN 366 (401) T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEC T ss_conf 999887786675258899999999999998457-8354897998554167799999984461129999752315877888 Q ss_pred CEEEECCCEEE Q ss_conf 88941353483 Q gi|254780187|r 125 GRSVNIGSYRC 135 (206) Q Consensus 125 g~~v~~ps~~~ 135 (206) |.+|.-..+.+ T Consensus 367 ~~~v~d~~~~~ 377 (401) T COG0162 367 GEKVEDENYVL 377 (401) T ss_pred CEECCCCCCCH T ss_conf 87525634221 No 39 >TIGR01687 moaD_arch MoaD family protein; InterPro: IPR010038 Members of this family appear to be archaeal and bacterial (proteobacteria and Thermus) versions of MoaD, subunit 1 of molybdopterin converting factor.. Probab=80.63 E-value=1 Score=25.33 Aligned_cols=60 Identities=30% Similarity=0.374 Sum_probs=41.2 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH-HHHHHHCCCEEECCE-EEEC---CCEEECCCCEEEECC Q ss_conf 3443026899999888889986212124788-788762497878888-9413---534833884788611 Q gi|254780187|r 81 RGDTSHNLISFLESRLDTIVYRAKFVPTIFA-ARQFVNHRHVLVNGR-SVNI---GSYRCKEGDVIEVKQ 145 (206) Q Consensus 81 ~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~-Arq~v~hg~i~vng~-~v~~---ps~~~k~gd~I~~~~ 145 (206) .|.|...||+.|-+|--.. |..=+.. --..+..=.|+|||+ =|+. -++.||-||+|+|=| T Consensus 24 ~g~tv~dll~~l~~~Yp~~-----~~e~~~et~~~~~~~v~ilvNGran~~~l~GL~~~LkdGD~vai~P 88 (93) T TIGR01687 24 DGKTVGDLLEELSSRYPKE-----FSELFKETGLGLVPNVIILVNGRANVDWLEGLETELKDGDVVAIFP 88 (93) T ss_pred CCCCHHHHHHHHHHHCCHH-----HHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCEEEEEC T ss_conf 9980799899988615655-----6665147788764657898516414322036575232787567506 No 40 >cd00754 MoaD MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group. Probab=79.05 E-value=4 Score=21.47 Aligned_cols=52 Identities=25% Similarity=0.383 Sum_probs=37.3 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 34430268999998888899862121247887887624978788889413534833884788611 Q gi|254780187|r 81 RGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 81 ~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) .+.|...|+..|..+-... .-.+-.+-.+.||++.++ .+..++.||.|.+=| T Consensus 24 ~~~Tv~~L~~~L~~~~~~~------------~~~~~~~~~iavN~~~~~-~~~~l~~gdEva~~P 75 (80) T cd00754 24 EGATVGELLDALEARYPGL------------LEELLARVRIAVNGEYVR-LDTPLKDGDEVAIIP 75 (80) T ss_pred CCCCHHHHHHHHHHHCCHH------------HHHHHHCEEEEECCEECC-CCCCCCCCCEEEEEC T ss_conf 9988999999999878176------------764310409988879836-771569999999979 No 41 >KOG0378 consensus Probab=67.25 E-value=3.3 Score=22.07 Aligned_cols=43 Identities=21% Similarity=0.315 Sum_probs=38.3 Q ss_pred HHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEEC Q ss_conf 6212124788788762497878888941353483388478861 Q gi|254780187|r 102 RAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVK 144 (206) Q Consensus 102 r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~ 144 (206) |+.+|.+-..+.|+....+|.|||+.-+-++|..---|+|++- T Consensus 51 ~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mDvisie 93 (263) T KOG0378 51 RLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMDVISIE 93 (263) T ss_pred HHHHHHCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEEEEEEC T ss_conf 5555304108889887766530545641666765203688720 No 42 >TIGR01647 ATPase-IIIA_H plasma-membrane proton-efflux P-type ATPase; InterPro: IPR006534 These sequences represent the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast . ; GO: 0016887 ATPase activity, 0015992 proton transport, 0016021 integral to membrane. Probab=66.98 E-value=3.9 Score=21.61 Aligned_cols=65 Identities=18% Similarity=0.249 Sum_probs=43.3 Q ss_pred HHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHH---HHHHHHHHHHHC-CCCCCCEEEECCCCCEEE Q ss_conf 887624978788889413534833884788611002---269999877521-689996278812431899 Q gi|254780187|r 113 RQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK---QLASVLEASQLA-ERDVPEYISVNHDNMVAT 178 (206) Q Consensus 113 rq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk---~~~~i~~~~~~~-~~~~P~wLevd~~~l~g~ 178 (206) .-|...-.|.=+|+=+++||-.|=|||+|.++-..= +...+....+.. +. ---||+||...|+|. T Consensus 95 ~~Lap~A~V~RDG~W~~~~A~~LVPGDvv~l~~GdivPAD~~l~~g~~qhPfdh-eevy~~vDqaALTGE 163 (835) T TIGR01647 95 QSLAPKAKVLRDGKWQEIPAKELVPGDVVRLKLGDIVPADCRLFEGDPQHPFDH-EEVYIKVDQAALTGE 163 (835) T ss_pred HHCCCCEEEEECCEEEECCCCCCCCCCEEEEECCCEEECCCEEECCCCCCCCCC-CCCCEEEECHHHCCC T ss_conf 627885099778867761502279763898720764012406725777888764-534337622110477 No 43 >pfam00498 FHA FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif. Probab=66.10 E-value=6.4 Score=20.18 Aligned_cols=26 Identities=35% Similarity=0.562 Sum_probs=18.6 Q ss_pred CCCEEECCEEEECCCEEECCCCEEEE Q ss_conf 49787888894135348338847886 Q gi|254780187|r 118 HRHVLVNGRSVNIGSYRCKEGDVIEV 143 (206) Q Consensus 118 hg~i~vng~~v~~ps~~~k~gd~I~~ 143 (206) -.-..|||+++..-.+.|++||+|.+ T Consensus 41 ~nGt~vNg~~i~~~~~~L~~GD~i~i 66 (67) T pfam00498 41 TNGTFVNGQRLGPEPVRLKDGDVIRL 66 (67) T ss_pred CCCEEECCEECCCCCEECCCCCEEEE T ss_conf 86859999996788769999999984 No 44 >pfam02597 ThiS ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end. Probab=64.57 E-value=5.8 Score=20.44 Aligned_cols=28 Identities=29% Similarity=0.338 Sum_probs=22.4 Q ss_pred CCCEEECCEEEECC--CEEECCCCEEEECC Q ss_conf 49787888894135--34833884788611 Q gi|254780187|r 118 HRHVLVNGRSVNIG--SYRCKEGDVIEVKQ 145 (206) Q Consensus 118 hg~i~vng~~v~~p--s~~~k~gd~I~~~~ 145 (206) .=.|.|||..|... ++.|+.||.|++-+ T Consensus 36 ~v~v~vN~~~v~~~~~~~~L~~gD~v~ivp 65 (70) T pfam02597 36 RVAVAVNGEIVPRSQADTPLKDGDEVAIIP 65 (70) T ss_pred CEEEEECCEECCCCCCCCCCCCCCEEEEEC T ss_conf 889999999867856776779999999978 No 45 >KOG2623 consensus Probab=63.80 E-value=7.6 Score=19.67 Aligned_cols=39 Identities=21% Similarity=0.203 Sum_probs=33.2 Q ss_pred HHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEEC Q ss_conf 899862121247887887624978788889413534833 Q gi|254780187|r 98 TIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCK 136 (206) Q Consensus 98 ~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k 136 (206) -.+..++.++|...||.+|..|-|.||+++|..+|-.+- T Consensus 403 ~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~es~~~~ 441 (467) T KOG2623 403 DLLRKASRFPSGKEARRMIQQGGVSLNHEKVRDESVSIA 441 (467) T ss_pred HHHHHHHCCCCCHHHHHHHHCCCEEECCCCCCCCHHHCC T ss_conf 999874037885889999871656666730367002014 No 46 >pfam00122 E1-E2_ATPase E1-E2 ATPase. Probab=61.58 E-value=4.7 Score=21.03 Aligned_cols=52 Identities=17% Similarity=0.253 Sum_probs=34.8 Q ss_pred CCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEE Q ss_conf 978788889413534833884788611002269999877521689996278812431899 Q gi|254780187|r 119 RHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVAT 178 (206) Q Consensus 119 g~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~~~P~wLevd~~~l~g~ 178 (206) -.|.-||+...+|+-.+.+||+|.+++..+--.-. .-+-.-+++|...++|. T Consensus 36 ~~V~rdG~~~~v~~~~l~~GDiv~v~~G~~IPaDg--------~vi~g~~~vdes~lTGE 87 (222) T pfam00122 36 VTVIRDGKEEEIPADELVVGDIVLLKPGDRVPADG--------RIIEGSLEVDESALTGE 87 (222) T ss_pred EEEEECCEEEEEEHHHCCCCCEEEECCCCEEECCC--------EEECCCEEEEEHHHCCC T ss_conf 89998999999888997889999989999962174--------57518389972220686 No 47 >cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown. Probab=61.16 E-value=7 Score=19.92 Aligned_cols=23 Identities=39% Similarity=0.512 Sum_probs=18.5 Q ss_pred EEECCEEEECCCEEECCCCEEEEC Q ss_conf 878888941353483388478861 Q gi|254780187|r 121 VLVNGRSVNIGSYRCKEGDVIEVK 144 (206) Q Consensus 121 i~vng~~v~~ps~~~k~gd~I~~~ 144 (206) ..|||+.+. .++.++.||+|++- T Consensus 37 a~vNg~~~~-l~~~L~~GD~VeIi 59 (60) T cd01668 37 AKVNGKLVP-LSTVLKDGDIVEII 59 (60) T ss_pred EEECCEECC-CCCCCCCCCEEEEE T ss_conf 999999989-87682899999987 No 48 >KOG1919 consensus Probab=58.54 E-value=15 Score=17.69 Aligned_cols=46 Identities=26% Similarity=0.253 Sum_probs=34.6 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEE Q ss_conf 888998621212478878876249787888894135348338847886 Q gi|254780187|r 96 LDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEV 143 (206) Q Consensus 96 LD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~ 143 (206) +|.++.+.. +....-.+..|.+|-+.|||..+. .++.++.||+|.. T Consensus 47 ~~~~~~ef~-~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~ 92 (371) T KOG1919 47 VDVFVSEFR-LRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCH 92 (371) T ss_pred HHHHHHHHH-CCCHHHHHHHHHCCCEEECCEEEE-EEEEECCCCEEEE T ss_conf 799989875-371576665653686588858600-4787125888877 No 49 >pfam02824 TGS TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Probab=55.88 E-value=10 Score=18.80 Aligned_cols=23 Identities=35% Similarity=0.498 Sum_probs=17.6 Q ss_pred CEEECCEEEECCCEEECCCCEEEE Q ss_conf 787888894135348338847886 Q gi|254780187|r 120 HVLVNGRSVNIGSYRCKEGDVIEV 143 (206) Q Consensus 120 ~i~vng~~v~~ps~~~k~gd~I~~ 143 (206) ...|||+.++ +++.++.||+|++ T Consensus 36 ~A~VnG~~v~-l~~~L~~gd~V~I 58 (60) T pfam02824 36 GAKVNGQRVG-LDHVLEDGDVVEI 58 (60) T ss_pred EEEECCEECC-CCCCCCCCCEEEE T ss_conf 7899988876-2112489999998 No 50 >TIGR01344 malate_syn_A malate synthase A; InterPro: IPR006252 These sequences represent plant malate synthase and one of two bacterial forms, designated malate synthase A. This enzyme and isocitrate lyase are the two characteristic enzymes of the glyoxylate shunt. The shunt enables the cell to use acetyl-CoA to generate increased levels of TCA cycle intermediates for biosynthetic pathways such as gluconeogenesis.; GO: 0004474 malate synthase activity, 0006097 glyoxylate cycle. Probab=55.37 E-value=7.5 Score=19.72 Aligned_cols=35 Identities=23% Similarity=0.251 Sum_probs=26.3 Q ss_pred CCHHHHHHHHHCCCEEEC-CEEEECCCEEECCCCEE Q ss_conf 247887887624978788-88941353483388478 Q gi|254780187|r 107 PTIFAARQFVNHRHVLVN-GRSVNIGSYRCKEGDVI 141 (206) Q Consensus 107 ~t~~~Arq~v~hg~i~vn-g~~v~~ps~~~k~gd~I 141 (206) -||.|-=|+|.||-++=| |.+||--=+.=--++.+ T Consensus 441 ISR~Q~WQWi~~G~~L~dtG~~VT~eL~r~~l~~E~ 476 (522) T TIGR01344 441 ISRAQIWQWIKHGVVLEDTGRKVTPELFRDLLKEEM 476 (522) T ss_pred HHHHHHHHHHHCCCCEECCCCEECHHHHHHHHHHHH T ss_conf 877579999980851114775006789999999889 No 51 >cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Probab=53.61 E-value=11 Score=18.70 Aligned_cols=22 Identities=41% Similarity=0.738 Sum_probs=16.8 Q ss_pred EEECCEEEECCCEEECCCCEEEE Q ss_conf 87888894135348338847886 Q gi|254780187|r 121 VLVNGRSVNIGSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~~ps~~~k~gd~I~~ 143 (206) ..|||+.++ .|+.|+.||+|+| T Consensus 37 a~Vng~~~~-l~~~L~~gd~V~I 58 (60) T cd01616 37 ALVNGQLVD-LSYTLQDGDTVSI 58 (60) T ss_pred EEECCEECC-CCCCCCCCCEEEE T ss_conf 999999965-1669999999999 No 52 >TIGR00398 metG methionyl-tRNA synthetase; InterPro: IPR002304 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Methionyl-tRNA synthetase (6.1.1.10 from EC) is an alpha 2 dimer that belongs to class Ia. In some species (archaea, eubacteria and eukaryota) a coding sequence, similar to the C-term end of MetRS, is present as an independent gene which is a tRNA binding domain as a dimer. In eubacteria, MetRS can also be splitted in two sub-classes corresponding to the presence of one or two CXXC domain specific to zinc binding. The crystal structures of a number of methionyl-tRNA synthases are known , , .; GO: 0000166 nucleotide binding, 0004825 methionine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006431 methionyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=52.53 E-value=6.5 Score=20.14 Aligned_cols=33 Identities=15% Similarity=0.182 Sum_probs=22.9 Q ss_pred HHHHHHHHHCCCEEECCEEEEC-CCEEECCCC-EE Q ss_conf 7887887624978788889413-534833884-78 Q gi|254780187|r 109 IFAARQFVNHRHVLVNGRSVNI-GSYRCKEGD-VI 141 (206) Q Consensus 109 ~~~Arq~v~hg~i~vng~~v~~-ps~~~k~gd-~I 141 (206) ..--.|+++||++.++|.++.. -+.-|.|-| .| T Consensus 327 ~~lP~q~~~hGyl~~eG~KMSKS~G~vv~~~~~~~ 361 (573) T TIGR00398 327 LPLPTQVFAHGYLTVEGQKMSKSLGNVVDPEDDLL 361 (573) T ss_pred HHHHHHHEEEEEEEECCEEECCCCCCEECHHHHHH T ss_conf 02121324301688478443232475323217876 No 53 >TIGR01832 kduD 2-deoxy-D-gluconate 3-dehydrogenase; InterPro: IPR011286 This entry describes 2-deoxy-D-gluconate 3-dehydrogenase (also called 2-keto-3-deoxygluconate oxidoreductase), a member of the family of short-chain-alcohol dehydrogenases (IPR002198 from INTERPRO). This protein has been characterised in Erwinia chrysanthemi as an enzyme of pectin degradation .; GO: 0008678 2-deoxy-D-gluconate 3-dehydrogenase activity, 0051287 NAD binding. Probab=50.83 E-value=6.7 Score=20.06 Aligned_cols=69 Identities=28% Similarity=0.413 Sum_probs=42.4 Q ss_pred HHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEEC--CHHHHHHH-HH--HHHHHCCC------CCCCEEE Q ss_conf 86212124788788762497878888941353483388478861--10022699-99--87752168------9996278 Q gi|254780187|r 101 YRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVK--QKSKQLAS-VL--EASQLAER------DVPEYIS 169 (206) Q Consensus 101 ~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~--~ksk~~~~-i~--~~~~~~~~------~~P~wLe 169 (206) ...=|.-|...|||++..|+ .||+|||.|.+==-|=+ .|- .-||.-.. +. -+.|-+.. -.|.|++ T Consensus 113 lk~vF~l~q~~a~~~l~~G~---~GkiiNIAS~LSFQGGi-rVPsYTASK~~v~GlTk~lAnEWa~~ginVNAIAPGY~~ 188 (249) T TIGR01832 113 LKSVFFLTQAAAKQFLKQGR---GGKIINIASLLSFQGGI-RVPSYTASKHGVAGLTKLLANEWAAKGINVNAIAPGYME 188 (249) T ss_pred HHHHHHHHHHHHHHHHHCCC---CCCEEEEHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCC T ss_conf 89999999999999996489---95057514234422675-512466667777778999998998738815311588766 Q ss_pred ECCC Q ss_conf 8124 Q gi|254780187|r 170 VNHD 173 (206) Q Consensus 170 vd~~ 173 (206) .|.. T Consensus 189 T~NT 192 (249) T TIGR01832 189 TNNT 192 (249) T ss_pred CCCC T ss_conf 4551 No 54 >TIGR02375 pseudoazurin pseudoazurin; InterPro: IPR012745 Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related to plastocyanins. Several examples of pseudoazurin are encoded by a neighbouring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (IPR012746 from INTERPRO) of the same species.; GO: 0005507 copper ion binding. Probab=47.86 E-value=23 Score=16.60 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=19.2 Q ss_pred EEEECCCE-EECCCCEEEECCHHHHH Q ss_conf 89413534-83388478861100226 Q gi|254780187|r 126 RSVNIGSY-RCKEGDVIEVKQKSKQL 150 (206) Q Consensus 126 ~~v~~ps~-~~k~gd~I~~~~ksk~~ 150 (206) ..|.=|+| ++.|||.|++-+..|.+ T Consensus 12 ~MVFEPA~i~a~pGDtv~FvPtDKGH 37 (123) T TIGR02375 12 AMVFEPAYIKAAPGDTVTFVPTDKGH 37 (123) T ss_pred EEEECCCEEEECCCCEEEEECCCCCC T ss_conf 77617633665389768775288876 No 55 >cd01089 PA2G4-like Related to aminopepdidase M, this family contains proliferation-associated protein 2G4. Family members have been implicated in cell cycle control. Probab=47.16 E-value=15 Score=17.87 Aligned_cols=25 Identities=28% Similarity=0.508 Sum_probs=19.6 Q ss_pred CEEECCEEEE-CC-----CEEECCCCEEEEC Q ss_conf 7878888941-35-----3483388478861 Q gi|254780187|r 120 HVLVNGRSVN-IG-----SYRCKEGDVIEVK 144 (206) Q Consensus 120 ~i~vng~~v~-~p-----s~~~k~gd~I~~~ 144 (206) -+.||...+- || ++.++.||+|++. T Consensus 62 CiSvNe~v~HGiP~~~~~~~~L~~GDiV~iD 92 (228) T cd01089 62 CISVNNCVCHFSPLKSDATYTLKDGDVVKID 92 (228) T ss_pred EECCCCEEECCCCCCCCCCCCCCCCCEEEEE T ss_conf 7502544456899988887354689989997 No 56 >PRK06488 sulfur carrier protein ThiS; Validated Probab=46.78 E-value=19 Score=17.16 Aligned_cols=41 Identities=24% Similarity=0.340 Sum_probs=27.7 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEE---CCCEEECCCCEEEEC Q ss_conf 88889986212124788788762497878888941---353483388478861 Q gi|254780187|r 95 RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVN---IGSYRCKEGDVIEVK 144 (206) Q Consensus 95 RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~---~ps~~~k~gd~I~~~ 144 (206) -|+.++-.+|+..... -+-|||..|- ..++.++.||.|++- T Consensus 16 tl~~Ll~elg~~~~~v---------AvAvN~~~Vpr~~~~~~~L~eGDriEIv 59 (65) T PRK06488 16 TLALLLAELGYEGNWL---------ATAVNGELVHSEARAQFVLHEGDRIEIL 59 (65) T ss_pred HHHHHHHHCCCCCCCE---------EEEECCEEECHHHHCCCCCCCCCEEEEE T ss_conf 8999999729888808---------9998999874245054517999999996 No 57 >PRK05659 sulfur carrier protein ThiS; Validated Probab=44.99 E-value=19 Score=17.17 Aligned_cols=23 Identities=48% Similarity=0.618 Sum_probs=13.2 Q ss_pred EEECCEEEEC---CCEEECCCCEEEE Q ss_conf 8788889413---5348338847886 Q gi|254780187|r 121 VLVNGRSVNI---GSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~~---ps~~~k~gd~I~~ 143 (206) |-||+.+|.. +++.|+.||.|++ T Consensus 34 VevN~~ivpr~~~~~~~L~egD~iEI 59 (66) T PRK05659 34 VEVNGEIVPRSQHASTALREGDVVEI 59 (66) T ss_pred EEECCEECCHHHHCCCCCCCCCEEEE T ss_conf 99899881778957265899999999 No 58 >cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation). Probab=44.84 E-value=24 Score=16.43 Aligned_cols=16 Identities=19% Similarity=0.301 Sum_probs=9.7 Q ss_pred CEEEECCCCCEEEEEE Q ss_conf 6278812431899996 Q gi|254780187|r 166 EYISVNHDNMVATFVR 181 (206) Q Consensus 166 ~wLevd~~~l~g~v~~ 181 (206) .|.-.|.....|+++. T Consensus 56 ~~~~~d~~S~nGt~vn 71 (102) T cd00060 56 GVVLIDLGSTNGTFVN 71 (102) T ss_pred EEEEEECCCCCCEEEC T ss_conf 6999989987468999 No 59 >COG0474 MgtA Cation transport ATPase [Inorganic ion transport and metabolism] Probab=44.03 E-value=14 Score=18.05 Aligned_cols=81 Identities=17% Similarity=0.230 Sum_probs=47.0 Q ss_pred HHHHHHHHHHHHHHCCCC------CHHHHHHHH-HCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCC Q ss_conf 999988888998621212------478878876-2497878888941353483388478861100226999987752168 Q gi|254780187|r 90 SFLESRLDTIVYRAKFVP------TIFAARQFV-NHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAER 162 (206) Q Consensus 90 ~~LE~RLD~~v~r~g~a~------t~~~Arq~v-~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~ 162 (206) ..+=..+-|.++. |.. +..+-+++. .+-+|.-||+.+.+|+-.|-|||+|.+.....- +. -..+.+ T Consensus 108 ~I~~~i~~n~~~g--~~qe~~a~~~l~~lk~~~~~~~~V~R~g~~~~i~a~eLVpGDiV~l~~gd~v-PA---D~rLl~- 180 (917) T COG0474 108 VILLVVVINALLG--FVQEYRAEKALEALKKMSSPKAKVLRDGKFVEIPASELVPGDIVLLEAGDVV-PA---DLRLLE- 180 (917) T ss_pred HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHCCCCCEEEEECCCEEEEEHHHCCCCCEEEECCCCCC-CC---CEEEEE- T ss_conf 2688999998888--8776624899999984187855999779489974888666887998159971-58---777885- Q ss_pred CCCCEEEECCCCCEEEE Q ss_conf 99962788124318999 Q gi|254780187|r 163 DVPEYISVNHDNMVATF 179 (206) Q Consensus 163 ~~P~wLevd~~~l~g~v 179 (206) . +-|.||.+.|+|.= T Consensus 181 -~-~~l~VdEs~LTGES 195 (917) T COG0474 181 -S-SDLEVDESALTGES 195 (917) T ss_pred -C-CCCEEECHHCCCCC T ss_conf -4-77678931136776 No 60 >pfam07828 PA-IL PA-IL-like protein. The members of this family are similar to the galactophilic lectin-1 expressed by P. aeruginosa ((PA-IL). Lectins recognising specific carbohydrates found on the surface of host cells are known to be involved in the initiation of infections by this organism. The protein is thought to be organized into an extensive network of beta-sheets, as is the case with many other lectins. Probab=43.45 E-value=14 Score=18.07 Aligned_cols=28 Identities=25% Similarity=0.265 Sum_probs=21.4 Q ss_pred CCEEECCEEEECCCEEECCCCEEEECCH Q ss_conf 9787888894135348338847886110 Q gi|254780187|r 119 RHVLVNGRSVNIGSYRCKEGDVIEVKQK 146 (206) Q Consensus 119 g~i~vng~~v~~ps~~~k~gd~I~~~~k 146 (206) |-|..|..-=...+..+++||+||+-.+ T Consensus 4 G~VpAnae~gq~Tglilk~GD~IsivA~ 31 (121) T pfam07828 4 GEVLANAEAGKSTGIILKPGDTISIVAA 31 (121) T ss_pred CCCCCHHHCCCCCEEEECCCCEEEEEEE T ss_conf 6455400059952068627989988561 No 61 >cd00430 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with activ Probab=42.50 E-value=22 Score=16.64 Aligned_cols=30 Identities=20% Similarity=0.150 Sum_probs=12.5 Q ss_pred HHHHHHHHCCCCC--HHHHHHHHHCCCEEECC Q ss_conf 8889986212124--78878876249787888 Q gi|254780187|r 96 LDTIVYRAKFVPT--IFAARQFVNHRHVLVNG 125 (206) Q Consensus 96 LD~~v~r~g~a~t--~~~Arq~v~hg~i~vng 125 (206) +|+=.-|+||.+. ...++.+-.+.++.+-| T Consensus 125 iDTGM~RlG~~~~e~~~~~~~l~~~~~l~~~g 156 (367) T cd00430 125 IDTGMGRLGFRPEEAEELLEALKALPGLELEG 156 (367) T ss_pred EECCCCCCCCCHHHHHHHHHHHHHCCCCEEEE T ss_conf 80688757889799999999998689961889 No 62 >PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional Probab=42.05 E-value=21 Score=16.77 Aligned_cols=30 Identities=23% Similarity=0.278 Sum_probs=13.9 Q ss_pred HHHHHHHHCCCCC--HHHHHHHHHCCCEEECC Q ss_conf 8889986212124--78878876249787888 Q gi|254780187|r 96 LDTIVYRAKFVPT--IFAARQFVNHRHVLVNG 125 (206) Q Consensus 96 LD~~v~r~g~a~t--~~~Arq~v~hg~i~vng 125 (206) +|+=.-|+||.+. ...++.+-...++.+-| T Consensus 586 iDTGM~RlGf~~~e~~~l~~~l~~~~~l~~~g 617 (824) T PRK11930 586 IDTGMHRLGFEPEDIPELIERLKKQSAVIVRS 617 (824) T ss_pred ECCCCCCCCCCHHHHHHHHHHHHHCCCCCEEE T ss_conf 75999978599899999999998289985536 No 63 >COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism] Probab=41.16 E-value=24 Score=16.40 Aligned_cols=23 Identities=52% Similarity=0.537 Sum_probs=9.6 Q ss_pred EEECCEEEEC---CCEEECCCCEEEE Q ss_conf 8788889413---5348338847886 Q gi|254780187|r 121 VLVNGRSVNI---GSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~~---ps~~~k~gd~I~~ 143 (206) +.|||..|-. ..+.|+.||.|++ T Consensus 36 v~vNg~iVpr~~~~~~~l~~gD~iev 61 (68) T COG2104 36 VAVNGEIVPRSQWADTILKEGDRIEV 61 (68) T ss_pred EEECCEECCCHHHHHCCCCCCCEEEE T ss_conf 99889982504632013158998999 No 64 >PRK09940 transcriptional regulator YdeO; Provisional Probab=39.20 E-value=31 Score=15.74 Aligned_cols=28 Identities=18% Similarity=0.326 Sum_probs=11.8 Q ss_pred HHHHHCCCCHHHHHHHHHHHHHCCCCCCH Q ss_conf 85551565479999999875303344302 Q gi|254780187|r 58 MKKYYGDISEKKFRSIFKEADRSRGDTSH 86 (206) Q Consensus 58 lr~~YG~~~ekq~~~~~~~A~~~~g~t~~ 86 (206) .|.+|| ++-+||...++.-.+..-+||. T Consensus 219 FK~~fG-iTP~qy~~~~r~q~~~~~~~~~ 246 (253) T PRK09940 219 FRKHFG-NSPKRVSKEYRCQRHTGMNTGN 246 (253) T ss_pred HHHHHC-CCCHHHHHHHHHHHHCCCCCCC T ss_conf 998819-7918999999999863766564 No 65 >cd00565 ThiS ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity. Probab=39.00 E-value=26 Score=16.20 Aligned_cols=23 Identities=43% Similarity=0.525 Sum_probs=8.9 Q ss_pred EEECCEEEEC---CCEEECCCCEEEE Q ss_conf 8788889413---5348338847886 Q gi|254780187|r 121 VLVNGRSVNI---GSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~~---ps~~~k~gd~I~~ 143 (206) |.+||..|.. .++.++.||.|++ T Consensus 33 V~~N~~ivpk~~~~~~~l~~gD~iEi 58 (65) T cd00565 33 VEVNGEIVPRSEWADTELQEGDRIEI 58 (65) T ss_pred EEECCEECCHHHCCCCCCCCCCEEEE T ss_conf 99999980878928100899899999 No 66 >cd03190 GST_C_ECM4_like GST_C family, ECM4-like subfamily; composed of predominantly uncharacterized and taxonomically diverse proteins with similarity to the translation product of the Saccharomyces cerevisiae gene ECM4. ECM4, a gene of unknown function, is involved in cell surface biosynthesis and architecture. S. cerevisiae ECM4 mutants show increased amounts of the cell wall hexose, N-acetylglucosamine. More recently, global gene expression analysis shows that ECM4 is upregulated during genotoxic conditions and together with the expression profiles of 18 other genes could potentially differentiate between genotoxic and cytotoxic insults in yeast. Probab=38.16 E-value=28 Score=16.06 Aligned_cols=26 Identities=27% Similarity=0.382 Sum_probs=15.9 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHH Q ss_conf 26899999888889986212124788 Q gi|254780187|r 86 HNLISFLESRLDTIVYRAKFVPTIFA 111 (206) Q Consensus 86 ~~ll~~LE~RLD~~v~r~g~a~t~~~ 111 (206) +.+-..+-.-+-|-|||+|||.|-.+ T Consensus 9 d~~n~~iy~~iNnGVYk~GFA~tQ~a 34 (142) T cd03190 9 DELNEWIYDNINNGVYKAGFATTQEA 34 (142) T ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHH T ss_conf 99999998866506525366799999 No 67 >cd06826 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2. This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Probab=37.48 E-value=30 Score=15.79 Aligned_cols=27 Identities=11% Similarity=0.015 Sum_probs=15.0 Q ss_pred HHHHCCCCC----HHHHHHHHHCCCEEECCE Q ss_conf 986212124----788788762497878888 Q gi|254780187|r 100 VYRAKFVPT----IFAARQFVNHRHVLVNGR 126 (206) Q Consensus 100 v~r~g~a~t----~~~Arq~v~hg~i~vng~ 126 (206) .-|+||..+ ...+.++....++.+.|- T Consensus 130 M~RlG~~~~~~~~~~~~~~~~~~~~l~i~Gi 160 (365) T cd06826 130 MSRNGLELSTAQGKEDAVAIATLPNLKIVGI 160 (365) T ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCCCEEEE T ss_conf 7757867340789999999973899857999 No 68 >PRK07440 hypothetical protein; Provisional Probab=37.40 E-value=33 Score=15.56 Aligned_cols=23 Identities=26% Similarity=0.406 Sum_probs=8.8 Q ss_pred EEECCEEEEC---CCEEECCCCEEEE Q ss_conf 8788889413---5348338847886 Q gi|254780187|r 121 VLVNGRSVNI---GSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~~---ps~~~k~gd~I~~ 143 (206) |-+|+.++.. ++..++.||.|++ T Consensus 38 VE~N~~Iv~r~~~~~~~l~~gD~iEI 63 (70) T PRK07440 38 VEYNGEILHRQFWEQTQVQPGDRLEI 63 (70) T ss_pred EEECCEEECHHHCCCEECCCCCEEEE T ss_conf 99688670867707106799999999 No 69 >cd06827 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases. This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Probab=37.18 E-value=30 Score=15.85 Aligned_cols=29 Identities=21% Similarity=0.122 Sum_probs=13.8 Q ss_pred HHHHHHHCCCCCH--HHHHHHHHCCCEEECC Q ss_conf 8899862121247--8878876249787888 Q gi|254780187|r 97 DTIVYRAKFVPTI--FAARQFVNHRHVLVNG 125 (206) Q Consensus 97 D~~v~r~g~a~t~--~~Arq~v~hg~i~vng 125 (206) |+=.-|+||.+.- ..+.++-.+.++.+-| T Consensus 122 DTGM~RlG~~~~e~~~~~~~l~~~~~l~~~g 152 (354) T cd06827 122 DSGMHRLGFSPEEYAAAYQRLKASPNVASIV 152 (354) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCCCCEEE T ss_conf 5788857899899999999998589985689 No 70 >TIGR01683 thiS thiamine biosynthesis protein ThiS; InterPro: IPR010035 This entry identifies the ThiS family, which are thiamine-biosynthesis proteins related to MoaD (IPR010034 from INTERPRO). MoaD is a molybdenum cofactor biosynthesis protein. Both ThiS and MoaD proteins are involved in sulphur transfer.. Probab=36.74 E-value=34 Score=15.50 Aligned_cols=23 Identities=48% Similarity=0.499 Sum_probs=12.4 Q ss_pred EEECCEEEE---CCCEEECCCCEEEE Q ss_conf 878888941---35348338847886 Q gi|254780187|r 121 VLVNGRSVN---IGSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~---~ps~~~k~gd~I~~ 143 (206) |-||+.+|. -+++.|+.||.|+| T Consensus 33 ve~N~~ivp~~~w~~~~l~~gD~iEi 58 (65) T TIGR01683 33 VEVNGEIVPRSEWEDTILKEGDRIEI 58 (65) T ss_pred EEECCEEECCCCCCCEEECCCCEEEE T ss_conf 98698340834567510158985889 No 71 >TIGR00691 spoT_relA RelA/SpoT family protein; InterPro: IPR004811 The functions of Escherichia coli RelA and SpoT differ somewhat. RelA (2.7.6.5 from EC) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (3.1.7.2 from EC) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears responsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species. ; GO: 0015969 guanosine tetraphosphate metabolic process. Probab=35.24 E-value=36 Score=15.35 Aligned_cols=24 Identities=13% Similarity=-0.057 Sum_probs=12.7 Q ss_pred CCCCCHHHHHHHHHCCCEEECCEE Q ss_conf 121247887887624978788889 Q gi|254780187|r 104 KFVPTIFAARQFVNHRHVLVNGRS 127 (206) Q Consensus 104 g~a~t~~~Arq~v~hg~i~vng~~ 127 (206) -.|+.+++-+.+=.++++.++|-- T Consensus 573 ~~a~~p~~~~~~~~~~~~~i~g~~ 596 (741) T TIGR00691 573 FPAVNPRRPKVTENSSFVSIEGIE 596 (741) T ss_pred CCCCCCCCCHHHCCCCEEECCCCC T ss_conf 456788874000566412316755 No 72 >PRK08053 sulfur carrier protein ThiS; Provisional Probab=34.22 E-value=37 Score=15.24 Aligned_cols=24 Identities=21% Similarity=0.234 Sum_probs=18.2 Q ss_pred EEECCEEEE---CCCEEECCCCEEEEC Q ss_conf 878888941---353483388478861 Q gi|254780187|r 121 VLVNGRSVN---IGSYRCKEGDVIEVK 144 (206) Q Consensus 121 i~vng~~v~---~ps~~~k~gd~I~~~ 144 (206) |-||+.+|- -+++.|+.||.|++- T Consensus 34 vAiN~~vVPRs~W~~~~L~egD~I~i~ 60 (66) T PRK08053 34 LAINQQIVPREQWAQHIVQDGDQILLF 60 (66) T ss_pred EEECCEEECHHHCCCCCCCCCCEEEEE T ss_conf 998897855788665316899999999 No 73 >TIGR01266 fum_ac_acetase fumarylacetoacetase; InterPro: IPR005959 Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation . This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders , . The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole . FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures .; GO: 0004334 fumarylacetoacetase activity, 0009072 aromatic amino acid family metabolic process. Probab=34.05 E-value=27 Score=16.11 Aligned_cols=36 Identities=25% Similarity=0.526 Sum_probs=31.8 Q ss_pred HHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEE Q ss_conf 889986212124788788762497878888941353483388478 Q gi|254780187|r 97 DTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVI 141 (206) Q Consensus 97 D~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I 141 (206) +.+|.|++|-.=.+.-.|++.|- +||| ..|++||.. T Consensus 330 ~~~~~~sN~k~lywt~~Q~laHH--~vnG-------CnL~~GDLl 365 (436) T TIGR01266 330 PQVICRSNFKHLYWTLAQMLAHH--SVNG-------CNLRPGDLL 365 (436) T ss_pred CHHHHHHHHHHHHHHHHHHHHCC--EECC-------CCCCCCCEE T ss_conf 11444543266787686452011--0016-------768767501 No 74 >PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional Probab=32.10 E-value=40 Score=15.02 Aligned_cols=64 Identities=14% Similarity=0.171 Sum_probs=40.2 Q ss_pred CHHHHHHHHH----CCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEEE Q ss_conf 4788788762----49787888894135348338847886110022699998775216899962788124318999 Q gi|254780187|r 108 TIFAARQFVN----HRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATF 179 (206) Q Consensus 108 t~~~Arq~v~----hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~~~P~wLevd~~~l~g~v 179 (206) +..+.+.|.. .-.+.-||....+|.-.|++||+|.+++..+-= +-.. -+-...++|...++|.- T Consensus 227 a~~ai~~L~~l~P~~A~virdG~~~~Vp~~~l~~GDiV~V~~Ge~IP--aDG~------vv~G~s~vDES~LTGES 294 (739) T PRK11033 227 ARQGVSALMALVPETATRLRDGEREEVAINSLRPGDVIEVAPGGRLP--ADGK------LLSPFASFDESALTGES 294 (739) T ss_pred HHHHHHHHHHCCCCEEEEEECCEEEEEEHHHCCCCCEEEECCCCEEE--CCEE------EECCEEEEECCCCCCCC T ss_conf 99999998736999789998997999878997999999988999842--2279------97056888846869998 No 75 >pfam02563 Poly_export Polysaccharide biosynthesis/export protein. This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export. Probab=31.31 E-value=29 Score=15.88 Aligned_cols=17 Identities=29% Similarity=0.538 Sum_probs=13.9 Q ss_pred EECCCEEECCCCEEEEC Q ss_conf 41353483388478861 Q gi|254780187|r 128 VNIGSYRCKEGDVIEVK 144 (206) Q Consensus 128 v~~ps~~~k~gd~I~~~ 144 (206) ..-+.|.+.|||+|++. T Consensus 7 ~~~~~Y~lgpGD~l~i~ 23 (83) T pfam02563 7 AASPDYRLGPGDVLRIT 23 (83) T ss_pred CCCCCCEECCCCEEEEE T ss_conf 79998888799999999 No 76 >smart00736 CADG Dystroglycan-type cadherin-like domains. Cadherin-homologous domains present in metazoan dystroglycans and alpha/epsilon sarcoglycans, yeast Axl2p and in a very large protein from magnetotactic bacteria. Likely to bind calcium ions. Probab=29.27 E-value=40 Score=14.99 Aligned_cols=23 Identities=22% Similarity=0.538 Sum_probs=16.1 Q ss_pred CCCCCCEEEECCCCCEEEEEECCCC Q ss_conf 6899962788124318999967884 Q gi|254780187|r 161 ERDVPEYISVNHDNMVATFVRIPSS 185 (206) Q Consensus 161 ~~~~P~wLevd~~~l~g~v~~~P~r 185 (206) ...+|+||.+|... +++...|.. T Consensus 41 ~~~LPsWl~fd~~t--~~l~G~P~~ 63 (97) T smart00736 41 GSALPSWLSFDSDT--GTLSGTPTN 63 (97) T ss_pred CCCCCCCEEEECCC--CEEEECCCC T ss_conf 99899747990457--889964584 No 77 >PRK13340 alanine racemase; Reviewed Probab=29.15 E-value=45 Score=14.70 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=15.8 Q ss_pred HHHHHCCCCC----HHHHHHHHHCCCEEECC Q ss_conf 9986212124----78878876249787888 Q gi|254780187|r 99 IVYRAKFVPT----IFAARQFVNHRHVLVNG 125 (206) Q Consensus 99 ~v~r~g~a~t----~~~Arq~v~hg~i~vng 125 (206) =.-|+||-++ ...+.++..+.++.+-| T Consensus 167 GM~RlG~~~~~~~~~~~~~~i~~~~~l~v~G 197 (404) T PRK13340 167 GMGRNGLDPSTFRGAWEAVRIATLPSLGIVG 197 (404) T ss_pred CCCCCCCCCHHHHHHHHHHHHHHCCCCCEEE T ss_conf 8666798810289999999996089977789 No 78 >TIGR01523 ATPase-IID_K-Na potassium/sodium efflux P-type ATPase, fungal-type; InterPro: IPR006414 Initially described as a calcium efflux ATPase , more recent work has shown that the Schizosaccharomyces pombe CTA3 gene is in fact a potassium ion efflux pump . These sequences form the clade which represents the fungal P-type ATPases which are responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies. This group of ATPases has been classified by phylogentic analysis as type IID . ; GO: 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0006812 cation transport, 0016021 integral to membrane. Probab=29.07 E-value=37 Score=15.21 Aligned_cols=40 Identities=25% Similarity=0.287 Sum_probs=34.3 Q ss_pred CCCHHHHHHHHH-CCCEEECCEEEECCCEEECCCCEEEECC Q ss_conf 124788788762-4978788889413534833884788611 Q gi|254780187|r 106 VPTIFAARQFVN-HRHVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 106 a~t~~~Arq~v~-hg~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) .+|+..-|.|-+ .-||.-|||.-+|-|..|-|||++-++- T Consensus 106 ~KTM~SL~~L~SP~AHV~R~~K~~~I~S~~~VPGD~~~~K~ 146 (1001) T TIGR01523 106 EKTMDSLKTLASPNAHVIRSSKSDAIDSKLLVPGDVVLLKV 146 (1001) T ss_pred HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCEEEEEE T ss_conf 45788865315886246517754432453227876799830 No 79 >KOG0202 consensus Probab=28.29 E-value=38 Score=15.16 Aligned_cols=67 Identities=22% Similarity=0.306 Sum_probs=46.3 Q ss_pred CCHHHHHHHHHC-CCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEEEE Q ss_conf 247887887624-97878888941353483388478861100226999987752168999627881243189999 Q gi|254780187|r 107 PTIFAARQFVNH-RHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFV 180 (206) Q Consensus 107 ~t~~~Arq~v~h-g~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~~~P~wLevd~~~l~g~v~ 180 (206) +|+.+-+.++.+ +|++-+|+.-.+++..+-|||++.++-.-+-=+ -+.+.+ .-+ |++|...|+|.-. T Consensus 104 kalEaLk~l~p~~~~V~R~gk~~~i~A~eLVPGDiV~l~vGDkVPA----DlRl~e--~~s-l~iDeS~LTGEs~ 171 (972) T KOG0202 104 KALEALKELVPPMAHVLRSGKLQHILARELVPGDIVELKVGDKIPA----DLRLIE--AKS-LRIDESSLTGESE 171 (972) T ss_pred HHHHHHHHCCCCCCEEEECCCCCCCCHHCCCCCCEEEEECCCCCCC----CEEEEE--EEE-EEEECCCCCCCCC T ss_conf 8999998508964169844860340341068887899951880553----015876--430-0441121257764 No 80 >pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development. Probab=27.97 E-value=10 Score=18.80 Aligned_cols=13 Identities=38% Similarity=0.692 Sum_probs=6.3 Q ss_pred EEEEECCCCCCCC Q ss_conf 3520058888888 Q gi|254780187|r 10 KIDRRIGENLWGR 22 (206) Q Consensus 10 K~~RrlG~~l~~~ 22 (206) |+||++|+.=|+. T Consensus 34 k~CR~~gI~RWP~ 46 (52) T pfam02042 34 KICRQLGIPRWPH 46 (52) T ss_pred HHHHHCCCCCCCH T ss_conf 9999879987857 No 81 >PRK06944 sulfur carrier protein ThiS; Provisional Probab=27.78 E-value=47 Score=14.55 Aligned_cols=23 Identities=30% Similarity=0.408 Sum_probs=15.5 Q ss_pred EEECCEEEEC---CCEEECCCCEEEE Q ss_conf 8788889413---5348338847886 Q gi|254780187|r 121 VLVNGRSVNI---GSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~~---ps~~~k~gd~I~~ 143 (206) +-||+..|-. ..+.|+.||.|++ T Consensus 33 VavN~~~VPRs~~~~~~L~~GD~iei 58 (65) T PRK06944 33 VAVNGNFVARTQHAARALAAGDRLDL 58 (65) T ss_pred EEECCEEECHHHHHHCCCCCCCEEEE T ss_conf 99847980314533312789999999 No 82 >pfam00842 Ala_racemase_C Alanine racemase, C-terminal domain. Probab=27.14 E-value=48 Score=14.47 Aligned_cols=42 Identities=21% Similarity=0.320 Sum_probs=25.4 Q ss_pred CCCCCHHHHHHHHHCCCEEECCEEE-------------ECCC-EEECCCCEEEECCHH Q ss_conf 1212478878876249787888894-------------1353-483388478861100 Q gi|254780187|r 104 KFVPTIFAARQFVNHRHVLVNGRSV-------------NIGS-YRCKEGDVIEVKQKS 147 (206) Q Consensus 104 g~a~t~~~Arq~v~hg~i~vng~~v-------------~~ps-~~~k~gd~I~~~~ks 147 (206) |+|--.+ |.+=+.+++++||++. +++. -.+++||.+++=-.. T Consensus 40 GYaDG~~--r~~~~~~~v~i~g~~~pivGrIsMD~~~idv~~~~~~~~Gd~V~l~G~~ 95 (125) T pfam00842 40 GYADGYP--RALSNRGYVLINGKRAPIVGRVSMDQTMVDVTDIPDVKVGDEVTLFGPQ 95 (125) T ss_pred CCCCCCC--CCCCCCCEEEECCEEEEEECEECCCEEEEECCCCCCCCCCCEEEEECCC T ss_conf 2335735--2067985899899993010726122589955688777789899998999 No 83 >COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport] Probab=26.89 E-value=38 Score=15.14 Aligned_cols=41 Identities=15% Similarity=0.110 Sum_probs=30.9 Q ss_pred HHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEEC Q ss_conf 86212124788788762497878888941353483388478861 Q gi|254780187|r 101 YRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVK 144 (206) Q Consensus 101 ~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~ 144 (206) +++|+.. .-=.+|-.|.=.|-++.-+----.++|||.|.+. T Consensus 3 ~~mgL~e---eylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~ 43 (111) T COG4043 3 HRMGLRE---EYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFN 43 (111) T ss_pred EEECHHH---HHHHHHHCCCCEEEEEECCHHHCCCCCCCEEEEC T ss_conf 3300378---8999987044368999557766278989989983 No 84 >PRK10517 magnesium-transporting ATPase MgtA; Provisional Probab=26.35 E-value=28 Score=15.99 Aligned_cols=48 Identities=10% Similarity=0.170 Sum_probs=29.8 Q ss_pred CCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEE Q ss_conf 8889413534833884788611002269999877521689996278812431899 Q gi|254780187|r 124 NGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVAT 178 (206) Q Consensus 124 ng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~~~~~P~wLevd~~~l~g~ 178 (206) +|+.+.||+-.|-|||+|.+++..+-=+-. ...+ -.-|.+|.+.|+|. T Consensus 170 ~~~~~eIpa~eLVpGDIV~L~~Gd~VPAD~----rlie---~~~l~VDES~LTGE 217 (900) T PRK10517 170 ENGWLELPIDQLVPGDIIKLAAGDMIPADL----RILQ---ARDLFVAQASLTGE 217 (900) T ss_pred CCEEEEEEHHHCCCCCEEEECCCCEEECCE----EEEE---ECCCEEEECCCCCC T ss_conf 873789778988989789999999994128----9997---16877870123478 No 85 >COG0787 Alr Alanine racemase [Cell envelope biogenesis, outer membrane] Probab=26.13 E-value=50 Score=14.36 Aligned_cols=12 Identities=33% Similarity=0.437 Sum_probs=6.6 Q ss_pred HHHHHHHHCCCC Q ss_conf 888998621212 Q gi|254780187|r 96 LDTIVYRAKFVP 107 (206) Q Consensus 96 LD~~v~r~g~a~ 107 (206) +|+=.-|+||.+ T Consensus 128 iDTGM~RlG~~~ 139 (360) T COG0787 128 IDTGMNRLGLRP 139 (360) T ss_pred ECCCCCCCCCCH T ss_conf 778987579884 No 86 >PRK09393 ftrA transcriptional activator FtrA; Provisional Probab=26.09 E-value=51 Score=14.35 Aligned_cols=57 Identities=19% Similarity=0.211 Sum_probs=35.2 Q ss_pred HHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHH---------HH---HHHHHHHHHHHCCCCCHHHHHHHHHC Q ss_conf 855515654799999998753033443026899---------99---98888899862121247887887624 Q gi|254780187|r 58 MKKYYGDISEKKFRSIFKEADRSRGDTSHNLIS---------FL---ESRLDTIVYRAKFVPTIFAARQFVNH 118 (206) Q Consensus 58 lr~~YG~~~ekq~~~~~~~A~~~~g~t~~~ll~---------~L---E~RLD~~v~r~g~a~t~~~Arq~v~h 118 (206) +--.-| ++++||.+.|+++.. .|-..++. +| +.-++.|-++.||...-...|.+-.+ T Consensus 238 lA~~~~-~S~R~l~R~Fk~~~G---~tp~~y~~~~Rl~~Ar~lL~~t~~si~~IA~~~Gf~~~s~F~r~Fk~~ 306 (320) T PRK09393 238 LAARAA-MSPRTFLRRFEAATG---MTPAEWLLRERLARARDLLESSALSIAQIAARAGFGSEESLRHHFRRR 306 (320) T ss_pred HHHHHC-CCHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 999978-798799989978869---699999999999999999876899999999995899999999999998 No 87 >KOG3312 consensus Probab=25.54 E-value=38 Score=15.13 Aligned_cols=20 Identities=25% Similarity=0.154 Sum_probs=14.0 Q ss_pred HHHHHHHCCCCCHHHHHHHH Q ss_conf 88998621212478878876 Q gi|254780187|r 97 DTIVYRAKFVPTIFAARQFV 116 (206) Q Consensus 97 D~~v~r~g~a~t~~~Arq~v 116 (206) .|+---+|||||+.+|+|-. T Consensus 156 qNlQK~LGfaPsRaaa~q~~ 175 (186) T KOG3312 156 QNLQKILGFAPSRAAAKQGG 175 (186) T ss_pred HHHHHHHCCCCCHHHHHCCC T ss_conf 98999967698566761678 No 88 >cd01669 TGS_Ygr210_C TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Probab=25.38 E-value=35 Score=15.39 Aligned_cols=22 Identities=36% Similarity=0.545 Sum_probs=16.2 Q ss_pred EECCEEEECCCEEECCCCEEEEC Q ss_conf 78888941353483388478861 Q gi|254780187|r 122 LVNGRSVNIGSYRCKEGDVIEVK 144 (206) Q Consensus 122 ~vng~~v~~ps~~~k~gd~I~~~ 144 (206) .+||++|- ..|.++-||+|+|- T Consensus 54 a~~~r~v~-~d~~L~~gDvi~Iv 75 (76) T cd01669 54 ARTGRRVG-EDYELKHRDVIKIV 75 (76) T ss_pred EECCCCCC-CCCCCCCCCEEEEE T ss_conf 00587858-87284799999980 No 89 >PRK00053 alr alanine racemase; Reviewed Probab=25.36 E-value=52 Score=14.27 Aligned_cols=12 Identities=33% Similarity=0.335 Sum_probs=5.8 Q ss_pred HHHHHHHHCCCC Q ss_conf 888998621212 Q gi|254780187|r 96 LDTIVYRAKFVP 107 (206) Q Consensus 96 LD~~v~r~g~a~ 107 (206) +|+=.-|+||-+ T Consensus 124 iDTGM~RlG~~~ 135 (360) T PRK00053 124 VDTGMHRLGVRP 135 (360) T ss_pred ECCCCCCCCCCH T ss_conf 858987478887 No 90 >PRK07696 sulfur carrier protein ThiS; Provisional Probab=24.89 E-value=53 Score=14.21 Aligned_cols=23 Identities=26% Similarity=0.244 Sum_probs=10.2 Q ss_pred EEECCEEEE---CCCEEECCCCEEEE Q ss_conf 878888941---35348338847886 Q gi|254780187|r 121 VLVNGRSVN---IGSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~---~ps~~~k~gd~I~~ 143 (206) |-+|+.+|. .+++.++.||.|++ T Consensus 35 VE~N~eIvpr~~~~~~~L~~GD~iEI 60 (67) T PRK07696 35 VERNKDILQKDDHTDTSVFDGDQIEI 60 (67) T ss_pred EEECCEECCHHHHCCEECCCCCEEEE T ss_conf 99798575768809447799999999 No 91 >PRK03646 dadX alanine racemase; Reviewed Probab=24.54 E-value=54 Score=14.17 Aligned_cols=30 Identities=17% Similarity=0.059 Sum_probs=18.6 Q ss_pred HHHHHHHHCCCCCH--HHHHHHHHCCCEEECC Q ss_conf 88899862121247--8878876249787888 Q gi|254780187|r 96 LDTIVYRAKFVPTI--FAARQFVNHRHVLVNG 125 (206) Q Consensus 96 LD~~v~r~g~a~t~--~~Arq~v~hg~i~vng 125 (206) +|+=.-|+||.+.- ...+++...+++.+-| T Consensus 123 iDTGM~RlG~~~~e~~~~~~~l~~~~~l~~~g 154 (355) T PRK03646 123 VNSGMNRLGFQPERVQTVWQQLRAMGNVGEMT 154 (355) T ss_pred EECCCCCCCCCHHHHHHHHHHHHHCCCCCEEE T ss_conf 90798778988578999999998489987589 No 92 >PRK00133 metG methionyl-tRNA synthetase; Reviewed Probab=24.28 E-value=42 Score=14.89 Aligned_cols=18 Identities=17% Similarity=0.309 Sum_probs=12.3 Q ss_pred HHHHHCCCEEECCEEEEC Q ss_conf 887624978788889413 Q gi|254780187|r 113 RQFVNHRHVLVNGRSVNI 130 (206) Q Consensus 113 rq~v~hg~i~vng~~v~~ 130 (206) .++..||++.++|+++.. T Consensus 313 ~~v~~hg~l~~~G~KmSK 330 (666) T PRK00133 313 TNVFAHGFLTVEGAKMSK 330 (666) T ss_pred CCCCCCCCEEECCEEEEC T ss_conf 612114648778806001 No 93 >KOG4383 consensus Probab=23.37 E-value=57 Score=14.03 Aligned_cols=29 Identities=17% Similarity=0.362 Sum_probs=24.0 Q ss_pred EECCEEEECCCEEECCCCEEEECCHHHHH Q ss_conf 78888941353483388478861100226 Q gi|254780187|r 122 LVNGRSVNIGSYRCKEGDVIEVKQKSKQL 150 (206) Q Consensus 122 ~vng~~v~~ps~~~k~gd~I~~~~ksk~~ 150 (206) .-+|..++.|-..+-.||+|++++..... T Consensus 161 fRDGhlm~lP~~LLVeGDiIa~RPGQeaf 189 (1354) T KOG4383 161 FRDGHLMELPRILLVEGDIIAFRPGQEAF 189 (1354) T ss_pred HCCCEEEECCEEEEEECCEEEECCCCCCC T ss_conf 51671440542688853478765886255 No 94 >TIGR02299 HpaE 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase; InterPro: IPR011985 This entry represents the dehydrogenase responsible for the conversion of 5-carboxymethyl-2-hydroxymuconate semialdehyde to 5-carboxymethyl-2-hydroxymuconate (a tricarboxylic acid). This is the step in the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate following the oxidative opening of the aromatic ring .. Probab=23.27 E-value=32 Score=15.66 Aligned_cols=32 Identities=25% Similarity=0.336 Sum_probs=25.9 Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCE Q ss_conf 9988888998621212478878876249787888894135348338847 Q gi|254780187|r 92 LESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDV 140 (206) Q Consensus 92 LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~ 140 (206) |||=||.+||- -+..||+++|-.|-++=...+ T Consensus 262 LeRALDAvvF~-----------------IfS~NGeRCTasSRLL~~~sI 293 (494) T TIGR02299 262 LERALDAVVFM-----------------IFSFNGERCTASSRLLVQESI 293 (494) T ss_pred HHHHHHHHHHH-----------------HHHCCCCCCCCCHHHHHHHCC T ss_conf 44688899988-----------------760687501200134555042 No 95 >PRK06083 sulfur carrier protein ThiS; Provisional Probab=22.33 E-value=59 Score=13.89 Aligned_cols=23 Identities=30% Similarity=0.345 Sum_probs=13.9 Q ss_pred EEECCEEEEC---CCEEECCCCEEEE Q ss_conf 8788889413---5348338847886 Q gi|254780187|r 121 VLVNGRSVNI---GSYRCKEGDVIEV 143 (206) Q Consensus 121 i~vng~~v~~---ps~~~k~gd~I~~ 143 (206) |-||+.+|-. +++.|+.||.|++ T Consensus 37 vaiN~~iVPRs~W~~~~l~~gD~Iei 62 (69) T PRK06083 37 FAINNQVVPRSEWQSTVLSEGDAISL 62 (69) T ss_pred EEECCEEECHHHCCCCCCCCCCEEEE T ss_conf 99778384356716045899999999 No 96 >TIGR02170 thyX thymidylate synthase, flavin-dependent; InterPro: IPR003669 Thymidylate (dTMP) is an essential DNA precursor. There are two pathways for thymidylate synthesis, each utilising a different thymidylate synthase enzyme: ThyA (2.1.1.45 from EC) and ThyX (2.1.1.148 from EC) . Both enzymes convert dUMP to dTMP, but there is no sequence identity between the two enzymes, and their mechanisms of action differ . Only ThyX uses FAD as cofactor. This entry represents the flavin-dependent enzyme ThyX, which is a homotetramer bound to four FAD molecules. Under oxygen-limiting conditions, thyX can complement a thyA mutation .; GO: 0050660 FAD binding, 0050797 thymidylate synthase (FAD) activity, 0006231 dTMP biosynthetic process. Probab=21.43 E-value=52 Score=14.27 Aligned_cols=21 Identities=29% Similarity=0.218 Sum_probs=18.3 Q ss_pred CCHHHHHHHHHCCCE-EECCEE Q ss_conf 247887887624978-788889 Q gi|254780187|r 107 PTIFAARQFVNHRHV-LVNGRS 127 (206) Q Consensus 107 ~t~~~Arq~v~hg~i-~vng~~ 127 (206) -||..++|++.|.|. ..|-.- T Consensus 87 ~sr~~~~Q~~RHR~~~S~~~~S 108 (259) T TIGR02170 87 ASRSVAAQLVRHRIAFSYSVQS 108 (259) T ss_pred HHHHHHHHHHCCEEEEEEEECC T ss_conf 3189999882063767773001 No 97 >TIGR01517 ATPase-IIB_Ca calcium-translocating P-type ATPase, PMCA-type; InterPro: IPR006408 This family describes the P-type ATPase responsible for translocating calcium ions across the plasma membrane of eukaryotes , out of the cell. In some organisms, this type of pump may also be found in vacuolar membranes . In humans and mice, at least, there are multiple isoforms of the PMCA pump with overlapping but not redundant functions. Accordingly, there are no human diseases linked to PMCA defects, although alterations of PMCA function do elicit physiological effects . The calcium P-type ATPases have been characterised as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump .; GO: 0005388 calcium-transporting ATPase activity, 0005509 calcium ion binding, 0005524 ATP binding, 0015085 calcium ion transmembrane transporter activity, 0006816 calcium ion transport, 0016020 membrane. Probab=21.33 E-value=62 Score=13.76 Aligned_cols=26 Identities=19% Similarity=0.429 Sum_probs=22.5 Q ss_pred CEEECCEEEECCCEEECCCCEEEECC Q ss_conf 78788889413534833884788611 Q gi|254780187|r 120 HVLVNGRSVNIGSYRCKEGDVIEVKQ 145 (206) Q Consensus 120 ~i~vng~~v~~ps~~~k~gd~I~~~~ 145 (206) .+.=||+.+.|+=+.+.+||+|++.- T Consensus 160 ~VIRgG~~~~Isi~d~~VGDi~sL~~ 185 (885) T TIGR01517 160 KVIRGGQEIQISIHDVVVGDIVSLST 185 (885) T ss_pred EEEECCEEEEEEEEEEEECCEEEEEE T ss_conf 99787927898446888611899841 No 98 >pfam07299 FBP Fibronectin-binding protein (FBP). This family consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species. Probab=21.19 E-value=61 Score=13.82 Aligned_cols=24 Identities=4% Similarity=0.285 Sum_probs=19.0 Q ss_pred HHCCCCHHHHHHHHHHHHHCCCCC Q ss_conf 515654799999998753033443 Q gi|254780187|r 61 YYGDISEKKFRSIFKEADRSRGDT 84 (206) Q Consensus 61 ~YG~~~ekq~~~~~~~A~~~~g~t 84 (206) -.-.++++|+.++|+++++.+-.. T Consensus 81 pF~~~s~~ql~KLF~K~KKLK~P~ 104 (208) T pfam07299 81 PFPSPTTQQLKKLFRKVKKLKIPN 104 (208) T ss_pred CCCCCCHHHHHHHHHHHHCCCCCC T ss_conf 889999899999825535027998 No 99 >pfam12331 DUF3636 Protein of unknown function (DUF3636). This domain family is found in eukaryotes, and is approximately 160 amino acids in length. Probab=21.08 E-value=63 Score=13.73 Aligned_cols=39 Identities=15% Similarity=0.316 Sum_probs=32.5 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCHH------HHHHHHHCCC Q ss_conf 44302689999988888998621212478------8788762497 Q gi|254780187|r 82 GDTSHNLISFLESRLDTIVYRAKFVPTIF------AARQFVNHRH 120 (206) Q Consensus 82 g~t~~~ll~~LE~RLD~~v~r~g~a~t~~------~Arq~v~hg~ 120 (206) |...-.-.+.++.||..+-+=..||.+-+ ++.|+.+|-- T Consensus 98 g~~p~t~~~i~~lRleal~~Lt~~a~s~~~p~~~~g~~~lAshp~ 142 (155) T pfam12331 98 GEAPYTPDEICELRLEALSFLTSFAFSPYDPSQNHGGSALASHPT 142 (155) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCH T ss_conf 889986899999999999999999617888320067889970813 No 100 >pfam10614 Tafi-CsgF Curli production assembly/transport component CsgF. Fimbriae are cell-surface protein polymers, of eg. E coli and Salmonella spp, that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), that differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae (Tafi) are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous m Probab=20.90 E-value=64 Score=13.71 Aligned_cols=48 Identities=13% Similarity=0.219 Sum_probs=33.3 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHC---------CCEEECCEEEECCCEEECCCCEEEEC Q ss_conf 4430268999998888899862121247887887624---------97878888941353483388478861 Q gi|254780187|r 82 GDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNH---------RHVLVNGRSVNIGSYRCKEGDVIEVK 144 (206) Q Consensus 82 g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~h---------g~i~vng~~v~~ps~~~k~gd~I~~~ 144 (206) ..+.+.|+..||+|+=+-+ +||++.- |-+.+.|-.|.+ ++.+|-|.+. T Consensus 67 nt~l~~F~~nLesriya~L-----------S~ql~d~~FGe~~~~sGt~~~~g~~I~~----~~~~~~i~lt 123 (142) T pfam10614 67 NSQLDIFAQQLQSQLLSAL-----------ASQITTAIFGENPQESGTFSFGGTTISF----ARSDGQLQLT 123 (142) T ss_pred CCHHHHHHHHHHHHHHHHH-----------HHHHHHHHCCCCCCCCEEEEECCEEEEE----EECCCEEEEE T ss_conf 5489999999999999999-----------9999875616888885079989989999----9889989999 No 101 >TIGR01940 nqrE NADH:ubiquinone oxidoreductase, Na(+)-translocating, E subunit; InterPro: IPR010967 NADH can be oxidized by the respiratory chain of bacteria via NADH:quinone oxidoreductases that belong to three distinct enzyme families: NDH-1, NDH-2, and NQR. The NQR-type enzymes are sodium-motive NADH:quinone oxidoreductases consisting of six subunits (NqrA-F) and several cofactors: FAD, 2 FMN, a 2Fe-2S cluster and riboflavin. The NADH:quinone oxidoreductase activity of these enzymes is stimulated by sodium ions and is coupled with pumping of Na+ but not H+. Subunits NqrA, NqrC and NqrF represent the three major subunits of the NQR complex, which are alpha, gamma and beta, respectively. Subunits NqrB, NqrD and NqrE are very hydrophobic polypeptides that were found to co-localise with the alpha subunit . This entry represents the NqrE subunit.; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=20.77 E-value=64 Score=13.69 Aligned_cols=20 Identities=35% Similarity=0.778 Sum_probs=16.4 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 68999998888899862121247887 Q gi|254780187|r 87 NLISFLESRLDTIVYRAKFVPTIFAA 112 (206) Q Consensus 87 ~ll~~LE~RLD~~v~r~g~a~t~~~A 112 (206) .|.|+||+=|| .|.|+.+.| T Consensus 94 AlvQilEm~le------rF~p~LY~a 113 (203) T TIGR01940 94 ALVQILEMVLE------RFSPSLYNA 113 (203) T ss_pred HHHHHHHHHHH------HCCHHHHHH T ss_conf 99999999998------306778988 No 102 >TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase; InterPro: IPR010121 Pyruvate phosphate dikinase (PPDK, or pyruvate orthophosphate dikinase) is found in plants, bacteria and archaea. The amino acid sequence identity between bacterial and plant enzymes is high, and they are similar in sequence to other PEP-utilizing enzymes. PPDK catalyses the reversible conversion of ATP and pyruvate to AMP and PEP (phosphoenolpyruvate). In bacteria such as Clostridium symbiosum, PPDK uses Mg2+ and NH4+ ions as cofactors . The enzyme has three domains: the N- and C-terminal domains each have an active site centre that catalyses a different step in the reaction, and the middle domain has a carrier histidine residue that moves between the two active centres. In plants, PPDK is localised predominantly in chloroplast stroma where it catalyses the rate-limiting step in the C4 photosynthetic pathway, namely the synthesis of PEP, which acts as the primary CO2 acceptor in C4 photosynthesis . PPDK activity in C4 plants is strictly regulated by light, its activity decreasing in darkness. This response is regulated by phosphorylation and dephosphorylation of the enzyme using ADP; such regulation is not seen in the bacterial form of the enzyme. PPDK is also found in C3 plants, but it is not known to have a photosynthetic role .; GO: 0050242 pyruvate phosphate dikinase activity. Probab=20.70 E-value=64 Score=13.68 Aligned_cols=23 Identities=30% Similarity=0.559 Sum_probs=18.1 Q ss_pred ECCEEEECC--CEEECCCCEEEECC Q ss_conf 888894135--34833884788611 Q gi|254780187|r 123 VNGRSVNIG--SYRCKEGDVIEVKQ 145 (206) Q Consensus 123 vng~~v~~p--s~~~k~gd~I~~~~ 145 (206) ...|...++ +..++.||+|||.= T Consensus 501 ~~~k~~~~g~Gg~~~~EGD~isiDG 525 (920) T TIGR01828 501 EEKKTLTIGGGGRVIKEGDIISIDG 525 (920) T ss_pred CCCCEEEECCCCCEEECCEEEEEEC T ss_conf 1048788888894774343799708 No 103 >pfam09285 Elong-fact-P_C Elongation factor P, C-terminal. Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology. Probab=20.66 E-value=64 Score=13.68 Aligned_cols=26 Identities=27% Similarity=0.510 Sum_probs=19.1 Q ss_pred CEEECCEEEECCCEEECCCCEEEECCH Q ss_conf 787888894135348338847886110 Q gi|254780187|r 120 HVLVNGRSVNIGSYRCKEGDVIEVKQK 146 (206) Q Consensus 120 ~i~vng~~v~~ps~~~k~gd~I~~~~k 146 (206) -++-||-.|..|.| ++.||.|.+... T Consensus 24 A~letG~~i~VP~F-I~~Gd~I~VdT~ 49 (56) T pfam09285 24 ATLETGAEVQVPLF-IEEGEKIKVDTR 49 (56) T ss_pred EEECCCCEEECCCC-CCCCCEEEEECC T ss_conf 89838989983874-048999999899 No 104 >TIGR03164 UHCUDC OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. Probab=20.17 E-value=54 Score=14.16 Aligned_cols=21 Identities=24% Similarity=0.502 Sum_probs=16.9 Q ss_pred HCCCCCCHHHHHHHHHHHHHH Q ss_conf 033443026899999888889 Q gi|254780187|r 79 RSRGDTSHNLISFLESRLDTI 99 (206) Q Consensus 79 ~~~g~t~~~ll~~LE~RLD~~ 99 (206) -.+|.+.+.+|..|++||+|- T Consensus 114 ~v~g~~~~~IL~~l~~Rl~n~ 134 (157) T TIGR03164 114 AVKGKTKQSILAAFEARLNND 134 (157) T ss_pred EECCCCHHHHHHHHHHHHCCC T ss_conf 538989999999999997699 No 105 >TIGR01838 PHA_synth_I poly(R)-hydroxyalkanoic acid synthase, class I; InterPro: IPR010963 This entry represents the class I subfamily of poly(R)-hydroxyalkanoate synthases, which polymerises hydroxyacyl-CoAs with three to five carbons in the hydroxyacyl backbone into aliphatic esters termed poly(R)-hydroxyalkanoic acids. These polymers accumulate as carbon and energy storage inclusions in many species and can amount to 90 percent of the dry weight of the cell.; GO: 0008415 acyltransferase activity, 0042619 poly-hydroxybutyrate biosynthetic process, 0005737 cytoplasm. Probab=20.17 E-value=66 Score=13.61 Aligned_cols=38 Identities=21% Similarity=0.316 Sum_probs=27.8 Q ss_pred CHHHHHHHHHCCCEEECCEE-----EECCCEEEC-CCCEEEECC Q ss_conf 47887887624978788889-----413534833-884788611 Q gi|254780187|r 108 TIFAARQFVNHRHVLVNGRS-----VNIGSYRCK-EGDVIEVKQ 145 (206) Q Consensus 108 t~~~Arq~v~hg~i~vng~~-----v~~ps~~~k-~gd~I~~~~ 145 (206) ..+..-+|++.|.+.|+|.+ |++|+|.+. .-|-|..=. T Consensus 394 ~lYl~N~L~~~g~l~~~G~~lDL~~vk~P~y~~at~eDHIApW~ 437 (541) T TIGR01838 394 NLYLQNELVSKGKLEVGGVRLDLSKVKVPVYIIATKEDHIAPWQ 437 (541) T ss_pred HHHHHCCCCCCCCEEECCEEEECCCCCCCEEEEECCCCCCCCCH T ss_conf 53010111168854873246203424312457613444345827 Done!