Query gi|254780881|ref|YP_003065294.1| Mrp protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 101 No_of_seqs 106 out of 1506 Neff 7.9 Searched_HMMs 39220 Date Mon May 30 01:21:16 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780881.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK11670 putative ATPase; Prov 99.8 1.6E-20 4.1E-25 136.5 10.0 99 3-101 11-113 (369) 2 TIGR02945 SUF_assoc FeS assemb 99.7 2.4E-17 6.2E-22 118.5 4.9 89 7-95 1-90 (96) 3 TIGR03406 FeS_long_SufT probab 99.7 1.2E-16 3.1E-21 114.6 6.7 91 3-93 72-167 (174) 4 pfam01883 DUF59 Domain of unkn 99.7 2.3E-16 6E-21 113.0 7.5 75 5-79 1-76 (76) 5 COG2151 PaaD Predicted metal-s 99.6 9.6E-16 2.4E-20 109.6 6.1 94 2-95 10-105 (111) 6 TIGR02159 PA_CoA_Oxy4 phenylac 98.9 6.1E-09 1.6E-13 71.3 6.7 73 16-88 1-75 (152) 7 TIGR03341 YhgI_GntY IscR-regul 89.9 0.94 2.4E-05 25.2 5.5 76 5-84 106-184 (190) 8 PRK11190 putative DNA uptake p 83.2 3.1 8E-05 22.2 5.2 76 5-84 107-186 (192) 9 pfam01106 NifU NifU-like domai 82.3 2.2 5.7E-05 23.1 4.1 62 10-75 2-65 (68) 10 TIGR01748 rhaA L-rhamnose isom 82.1 2.1 5.4E-05 23.2 3.9 71 8-78 18-91 (415) 11 pfam09650 PHA_gran_rgn Putativ 79.7 3 7.7E-05 22.3 4.0 45 25-69 42-86 (87) 12 TIGR02830 spore_III_AG stage I 79.7 3.2 8.3E-05 22.2 4.2 34 52-85 62-95 (193) 13 COG5133 Uncharacterized conser 78.8 6 0.00015 20.7 5.6 77 4-80 54-140 (181) 14 KOG3381 consensus 74.0 6 0.00015 20.6 4.3 77 5-81 35-121 (161) 15 TIGR01608 citD citrate lyase a 71.0 8.2 0.00021 19.9 4.4 46 34-80 19-66 (95) 16 cd00371 HMA Heavy-metal-associ 60.0 6.5 0.00017 20.4 2.1 26 58-83 12-37 (63) 17 TIGR02668 moaA_archaeal probab 57.4 18 0.00045 18.0 4.9 78 4-83 74-167 (324) 18 pfam00403 HMA Heavy-metal-asso 56.7 8.7 0.00022 19.7 2.3 26 57-82 11-36 (62) 19 TIGR01162 purE phosphoribosyla 48.5 25 0.00064 17.2 3.9 44 57-101 12-62 (159) 20 pfam03780 DUF322 Protein of un 47.6 26 0.00066 17.1 4.7 43 38-80 57-103 (108) 21 TIGR02052 MerP mercuric transp 46.7 9 0.00023 19.7 1.1 32 42-79 24-58 (92) 22 TIGR03123 one_C_unchar_1 proba 41.9 12 0.0003 19.0 1.1 47 38-84 18-64 (318) 23 pfam08921 DUF1904 Domain of un 41.8 32 0.00081 16.6 5.7 73 8-82 19-96 (107) 24 pfam04953 consensus 40.9 33 0.00084 16.5 4.1 38 42-80 28-66 (97) 25 cd00756 MoaE MoaE family. Memb 40.1 34 0.00087 16.4 4.8 67 9-78 3-69 (124) 26 TIGR02610 PHA_gran_rgn putativ 38.1 27 0.00069 17.0 2.4 47 22-68 42-88 (91) 27 COG4806 RhaA L-rhamnose isomer 37.3 38 0.00096 16.2 4.5 71 8-78 22-95 (419) 28 PRK11033 zntA zinc/cadmium/mer 37.2 25 0.00064 17.2 2.1 42 39-83 47-88 (739) 29 COG3965 Predicted Co/Zn/Cd cat 36.4 39 0.001 16.1 5.2 39 48-86 275-313 (314) 30 PRK13253 citrate lyase subunit 34.4 42 0.0011 15.9 5.3 41 38-80 26-66 (92) 31 TIGR00884 guaA_Cterm GMP synth 33.3 18 0.00046 17.9 0.9 30 55-84 284-313 (319) 32 TIGR02544 III_secr_YscJ type I 32.3 46 0.0012 15.7 4.5 67 9-84 75-142 (203) 33 PRK10671 copA copper exporting 29.9 50 0.0013 15.4 4.8 40 41-83 99-138 (834) 34 PRK10503 multidrug efflux syst 29.6 51 0.0013 15.4 6.7 18 60-77 169-186 (1040) 35 PRK05783 hypothetical protein; 27.1 57 0.0014 15.2 4.5 65 14-79 13-81 (84) 36 COG0041 PurE Phosphoribosylcar 27.0 57 0.0015 15.2 3.8 43 58-101 17-65 (162) 37 pfam01251 Ribosomal_S7e Riboso 26.6 58 0.0015 15.1 4.8 73 5-77 14-91 (189) 38 pfam01514 YscJ_FliF Secretory 25.7 60 0.0015 15.0 4.3 33 52-84 109-141 (206) 39 PRK00435 ef1B elongation facto 25.6 60 0.0015 15.0 2.5 68 3-80 16-85 (88) 40 TIGR00003 TIGR00003 copper ion 25.6 43 0.0011 15.8 1.8 27 57-83 13-39 (66) 41 TIGR01923 menE O-succinylbenzo 24.8 63 0.0016 14.9 2.5 32 58-89 403-434 (490) 42 PRK06156 hypothetical protein; 24.6 63 0.0016 14.9 4.9 59 18-79 369-427 (522) 43 cd04887 ACT_MalLac-Enz ACT_Mal 24.6 63 0.0016 14.9 4.2 51 20-77 22-72 (74) 44 pfam02391 MoaE MoaE protein. T 24.6 63 0.0016 14.9 4.7 68 8-78 10-77 (117) 45 TIGR02347 chap_CCT_zeta T-comp 23.6 66 0.0017 14.8 2.6 57 13-70 342-409 (548) 46 pfam09580 Spore_YhcN_YlaJ Spor 23.5 67 0.0017 14.8 5.1 42 36-77 88-130 (169) 47 pfam00873 ACR_tran AcrB/AcrD/A 22.8 69 0.0018 14.7 5.6 35 42-76 672-706 (1021) 48 KOG4656 consensus 22.4 70 0.0018 14.6 3.0 25 56-80 18-42 (247) 49 PRK10614 multidrug efflux syst 21.4 74 0.0019 14.5 6.6 19 59-77 159-177 (1025) 50 TIGR01054 rgy reverse gyrase; 21.1 53 0.0013 15.3 1.5 42 2-45 840-884 (1843) 51 PRK13614 lipoprotein LpqB; Pro 21.0 75 0.0019 14.5 4.9 48 32-79 238-288 (573) 52 COG2608 CopZ Copper chaperone 20.5 77 0.002 14.4 4.4 36 43-81 4-39 (71) 53 TIGR00855 L12 ribosomal protei 20.0 66 0.0017 14.8 1.8 18 1-18 1-18 (131) No 1 >PRK11670 putative ATPase; Provisional Probab=99.84 E-value=1.6e-20 Score=136.47 Aligned_cols=99 Identities=18% Similarity=0.292 Sum_probs=90.9 Q ss_pred CCCHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEC Q ss_conf 03589999998414187999762323870101336987999999672222068999999999985398534069999707 Q gi|254780881|r 3 QILKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTEN 82 (101) Q Consensus 3 ~~~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~ 82 (101) +-++++|+++|++|.||++++||+|+|||+++.++++++.|.|.++++.|+.+++++++++++|++++|++++++.++++ T Consensus 11 ~~l~~~v~~~L~~v~dP~~~~~iv~lg~v~~i~i~~~~v~i~l~l~~~~~~~~~~~~~~~~~~l~~~~~~~~v~~~~~~~ 90 (369) T PRK11670 11 EALRAMVAGTLANFQHPTLKHNLTTLKALHHVAWMDDTLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHN 90 (369) T ss_pred HHHHHHHHHHHHCCCCCCCCCCEECCCCEEEEEEECCEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEC T ss_conf 89999999998077798999880037970169997999999999688898879999999999998578974589999740 Q ss_pred CCC----CCCCCCCCCCEEEEEC Q ss_conf 898----7321569985588859 Q gi|254780881|r 83 KNP----PQQRNNLNVKKFVAVA 101 (101) Q Consensus 83 ~~~----~~~~~~~gvKnIIAVA 101 (101) ... +....++||||||||| T Consensus 91 ~~~~~~~~~~~~~~~v~~vIAVa 113 (369) T PRK11670 91 IATLKRVNNQPGVNGVKNIIAVS 113 (369) T ss_pred CCCCCCCCCCCCCCCCCEEEEEE T ss_conf 45645556678888868899998 No 2 >TIGR02945 SUF_assoc FeS assembly SUF system protein; InterPro: IPR014291 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry is a subset of the larger DUF59 family. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here are all found as part of the FeS assembly SUF system locus, in a subset of SUF-positive proteobacteria. . Probab=99.69 E-value=2.4e-17 Score=118.54 Aligned_cols=89 Identities=17% Similarity=0.194 Sum_probs=83.4 Q ss_pred HHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCC-CEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCC Q ss_conf 99999984141879997623238701013369-87999999672222068999999999985398534069999707898 Q gi|254780881|r 7 NQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVH-NTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKNP 85 (101) Q Consensus 7 ~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~-~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~~ 85 (101) ++|.++|++|.|||..-||++||+||.|+++| ++|+|.++|++|+||.+..+=..+++|+.+++||++|+|+||++++| T Consensus 1 ~~~i~alktVYDPEIPvnIYeLGLIY~i~i~Dd~~V~I~MTLTaPgCPvAgemP~~V~~aV~~v~GV~~v~VelvwdPPW 80 (96) T TIGR02945 1 EEVIEALKTVYDPEIPVNIYELGLIYKIEISDDRHVHIDMTLTAPGCPVAGEMPGWVEDAVGQVPGVSSVEVELVWDPPW 80 (96) T ss_pred CHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCCCCCCCCHHHHHHHHCCCCCCCEEEEEEEECCCC T ss_conf 92455420268998876610358675887658986788775178568422452268899733388985025776767866 Q ss_pred CCCCCCCCCC Q ss_conf 7321569985 Q gi|254780881|r 86 PQQRNNLNVK 95 (101) Q Consensus 86 ~~~~~~~gvK 95 (101) ...+.....| T Consensus 81 ~~~RMSdeAr 90 (96) T TIGR02945 81 DMDRMSDEAR 90 (96) T ss_pred CCCCCCHHHH T ss_conf 9233677899 No 3 >TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways. Probab=99.67 E-value=1.2e-16 Score=114.63 Aligned_cols=91 Identities=14% Similarity=0.115 Sum_probs=84.1 Q ss_pred CCCHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCC-----CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEE Q ss_conf 03589999998414187999762323870101336-----9879999996722220689999999999853985340699 Q gi|254780881|r 3 QILKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIV-----HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVV 77 (101) Q Consensus 3 ~~~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~-----~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V 77 (101) +..+++|+++|++|.|||.+-|||++|+|+++.++ +++|.|.+++++|+|++...|..++++++..++|+++|+| T Consensus 72 ~~~E~~vweaLk~V~DPEIpVnIVdLGLIY~v~i~~~~~~~~~V~I~MTLTapgCpmg~~i~~dv~~~v~~v~~v~~v~V 151 (174) T TIGR03406 72 EDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEV 151 (174) T ss_pred CHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCEEEE T ss_conf 42099999998415598887544863025799987647889779999960479998317999999999977999664999 Q ss_pred EEEECCCCCCCCCCCC Q ss_conf 9970789873215699 Q gi|254780881|r 78 TLTENKNPPQQRNNLN 93 (101) Q Consensus 78 ~lt~~~~~~~~~~~~g 93 (101) .++++++|.+...... T Consensus 152 elV~dPpW~~dmmSee 167 (174) T TIGR03406 152 ELVFDPPWSREMMSEA 167 (174) T ss_pred EEEECCCCCHHHCCHH T ss_conf 9998899893347799 No 4 >pfam01883 DUF59 Domain of unknown function DUF59. This family includes prokaryotic proteins of unknown function. The family also includes PhaH from Pseudomonas putida. PhaH forms a complex with PhaF, PhaG, and PhaI, which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid. So members of this family may all be components of ring hydroxylating complexes. Probab=99.66 E-value=2.3e-16 Score=113.01 Aligned_cols=75 Identities=21% Similarity=0.303 Sum_probs=71.8 Q ss_pred CHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCC-CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE Q ss_conf 589999998414187999762323870101336-987999999672222068999999999985398534069999 Q gi|254780881|r 5 LKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIV-HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL 79 (101) Q Consensus 5 ~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~-~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l 79 (101) ++++|+++|++|.||+++.||+++|+|+++.++ +|++.|.+++++++||..+.|.+++++++.+++|+++|+|.+ T Consensus 1 l~e~I~~aL~~V~DPEl~~~Iv~LGlI~~i~v~~~g~v~I~~~lT~~~CP~~~~i~~~i~~~l~~v~gv~~V~V~l 76 (76) T pfam01883 1 LKEAILEALKTVIDPELPVDIVDLGLVYEVDIDDDGNVKVKMTLTTPGCPLADLIALDVREALLELPGVEDVEVEL 76 (76) T ss_pred CHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEC T ss_conf 9789999982778999997800245368999857984999999589999837899999999998399940789979 No 5 >COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only] Probab=99.61 E-value=9.6e-16 Score=109.56 Aligned_cols=94 Identities=18% Similarity=0.223 Sum_probs=86.0 Q ss_pred CCCCHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCC--CEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE Q ss_conf 6035899999984141879997623238701013369--87999999672222068999999999985398534069999 Q gi|254780881|r 2 NQILKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVH--NTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL 79 (101) Q Consensus 2 s~~~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~--~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l 79 (101) ...++++|+++|++|.||+.+.||+++|+|+++.+++ +.+.|.+++++++|+..+.+..++++++..++|+++++|.+ T Consensus 10 ~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111) T COG2151 10 IKVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111) T ss_pred HHHHHHHHHHHHHCCCCCCCCEEEEEECCEEEEEEECCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEE T ss_conf 36669999998534779666603576310799997267746999995178888820788999999998468813079999 Q ss_pred EECCCCCCCCCCCCCC Q ss_conf 7078987321569985 Q gi|254780881|r 80 TENKNPPQQRNNLNVK 95 (101) Q Consensus 80 t~~~~~~~~~~~~gvK 95 (101) +++++|...+..+..| T Consensus 90 ~~~p~Wt~~~ms~ear 105 (111) T COG2151 90 TLSPPWTPDRMSEEAR 105 (111) T ss_pred EEECCCCHHHCCHHHH T ss_conf 9707966554389899 No 6 >TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit; InterPro: IPR011883 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA . . Probab=98.87 E-value=6.1e-09 Score=71.26 Aligned_cols=73 Identities=11% Similarity=0.132 Sum_probs=67.3 Q ss_pred CCCCCCC-CCHHHCCCCCCCCCCCCEEEEE-EEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCC Q ss_conf 4187999-7623238701013369879999-99672222068999999999985398534069999707898732 Q gi|254780881|r 16 LSIPGEK-NNIVEMQRLSEIFIVHNTVYLS-ITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKNPPQQ 88 (101) Q Consensus 16 v~dP~~~-~~iv~~g~V~~i~i~~~~v~i~-l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~~~~~ 88 (101) |-|||+. -.|++||||+++.++|+-++|. ++-+|.+|+..+.|+++|++||..+.+++.|+|.++-++.|.+. T Consensus 1 VPDPEiPv~s~~DLGmVR~V~v~g~G~~v~s~tPTySGCPA~~~i~~~i~~A~~~~GW~~~VeV~~~L~P~WTTd 75 (152) T TIGR02159 1 VPDPEIPVVSVTDLGMVREVEVDGEGVVVKSFTPTYSGCPALEVIRQDIRDALRALGWVEEVEVKTSLDPAWTTD 75 (152) T ss_pred CCCCCCCEEEEECCCEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCC T ss_conf 988887702211065343578647947988874587772368999999999997478975115887718987840 No 7 >TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization. Probab=89.90 E-value=0.94 Score=25.20 Aligned_cols=76 Identities=13% Similarity=0.166 Sum_probs=60.6 Q ss_pred CHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCC-CCEEEEEEEECHHHCHHHH-HHHHHHHHHHHC-CCCCCCEEEEEEE Q ss_conf 589999998414187999762323870101336-9879999996722220689-999999999853-9853406999970 Q gi|254780881|r 5 LKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIV-HNTVYLSITVPHTIAHQLQ-SLRSNAQQIIQN-IPTVKNAVVTLTE 81 (101) Q Consensus 5 ~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~-~~~v~i~l~l~~~~~~~~~-~l~~~i~~~l~~-i~gv~~v~V~lt~ 81 (101) ++++|..+|..=..|.+..+ -|-|+=+.++ ++.+.+.+.=....|++.. .|+.-++++|+. +|+|+.|. .+|- T Consensus 106 l~~~i~~vl~~ei~P~l~~h---GG~v~lv~i~~~~~v~~~~~G~C~gC~~s~~Tlk~gvE~~l~~~~Pei~~V~-d~td 181 (190) T TIGR03341 106 LEERINYVLQSEINPQLASH---GGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVR-DATD 181 (190) T ss_pred HHHHHHHHHHHHCCHHHHHC---CCEEEEEEEECCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEE-ECCC T ss_conf 99999999986029357636---9989999990797899995754899836899999999999998698753588-7657 Q ss_pred CCC Q ss_conf 789 Q gi|254780881|r 82 NKN 84 (101) Q Consensus 82 ~~~ 84 (101) |.. T Consensus 182 h~~ 184 (190) T TIGR03341 182 HTR 184 (190) T ss_pred CCC T ss_conf 888 No 8 >PRK11190 putative DNA uptake protein; Provisional Probab=83.23 E-value=3.1 Score=22.24 Aligned_cols=76 Identities=17% Similarity=0.166 Sum_probs=59.2 Q ss_pred CHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCC-CCCEEEEEEEECHHHCHHHH-HHHHHHHHHHH-CCCC-CCCEEEEEE Q ss_conf 58999999841418799976232387010133-69879999996722220689-99999999985-3985-340699997 Q gi|254780881|r 5 LKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFI-VHNTVYLSITVPHTIAHQLQ-SLRSNAQQIIQ-NIPT-VKNAVVTLT 80 (101) Q Consensus 5 ~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i-~~~~v~i~l~l~~~~~~~~~-~l~~~i~~~l~-~i~g-v~~v~V~lt 80 (101) ++++|...|.+=..|.+..+ -|.|+=+.+ ++|.+.+.+.=...+|++.. .|+.-++..|+ .+|| ++.| +.+| T Consensus 107 l~~~i~~vl~~~i~P~l~~h---GG~v~l~~i~~~~~~~~~~~G~C~gC~~~~~Tlk~gvE~~l~~~~P~ei~~V-~d~t 182 (192) T PRK11190 107 LMERVEYVLQSQINPQLAGH---GGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGV-RDLT 182 (192) T ss_pred HHHHHHHHHHHHCCHHHHHC---CCEEEEEEECCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCEE-EECC T ss_conf 99999999987319567637---9879999982798899996665789868899999999999998697867057-8766 Q ss_pred ECCC Q ss_conf 0789 Q gi|254780881|r 81 ENKN 84 (101) Q Consensus 81 ~~~~ 84 (101) -|.. T Consensus 183 dh~~ 186 (192) T PRK11190 183 EHQR 186 (192) T ss_pred CCCC T ss_conf 6788 No 9 >pfam01106 NifU NifU-like domain. This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown. Probab=82.29 E-value=2.2 Score=23.06 Aligned_cols=62 Identities=5% Similarity=0.017 Sum_probs=45.9 Q ss_pred HHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHH-HHHHHHHHHHHC-CCCCCCE Q ss_conf 99984141879997623238701013369879999996722220689-999999999853-9853406 Q gi|254780881|r 10 VDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQ-SLRSNAQQIIQN-IPTVKNA 75 (101) Q Consensus 10 ~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~-~l~~~i~~~l~~-i~gv~~v 75 (101) .++|.. .-|.+..| -|-++=+.++++.+.+.|.=.-..|+... .++..+++.|+. +|.+..| T Consensus 2 ~~~le~-IRP~l~~d---GGdvelv~v~~~~v~v~l~GaC~gC~~s~~Tlk~~Ie~~L~~~vpev~~V 65 (68) T pfam01106 2 EEVIDE-IRPMLQRD---GGDIELVDVDGDIVKVRLQGACGGCMSSTMTLKGGIERKLRERLGESLRV 65 (68) T ss_pred HHHHHH-HCHHHHHC---CCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEE T ss_conf 779987-56488855---99289999869999999812898981089999999999999878997669 No 10 >TIGR01748 rhaA L-rhamnose isomerase; InterPro: IPR009308 This family consists of several bacterial L-rhamnose isomerase proteins (5.3.1.14 from EC). This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including Escherichia coli, this is the first step in rhamnose catabolism. Sequential steps are catalyzed by rhamnulose kinase (rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to yield glycerone phosphate and (S)-lactaldehyde. ; GO: 0008740 L-rhamnose isomerase activity, 0030145 manganese ion binding, 0019299 rhamnose metabolic process. Probab=82.15 E-value=2.1 Score=23.19 Aligned_cols=71 Identities=11% Similarity=0.028 Sum_probs=48.2 Q ss_pred HHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEE--ECHHH-CHHHHHHHHHHHHHHHCCCCCCCEEEE Q ss_conf 999998414187999762323870101336987999999--67222-206899999999998539853406999 Q gi|254780881|r 8 QIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSIT--VPHTI-AHQLQSLRSNAQQIIQNIPTVKNAVVT 78 (101) Q Consensus 8 ~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~--l~~~~-~~~~~~l~~~i~~~l~~i~gv~~v~V~ 78 (101) +|.+||++..+=-..-==..-+=|++-...+|.++=.|. =+||+ +...++|+++.|+|++=|||-..++.- T Consensus 18 DvEeALr~L~~~piS~HCWQGDDv~GFenp~GeLtGGI~aTGNYPGkA~tp~eLR~DLEkA~sLIPGk~rlNLH 91 (415) T TIGR01748 18 DVEEALRQLEDVPISMHCWQGDDVEGFENPEGELTGGIDATGNYPGKARTPEELRRDLEKALSLIPGKHRLNLH 91 (415) T ss_pred CHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCEECCEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEE T ss_conf 67898864165865676314876454256886312561012588856689788889999997508898510115 No 11 >pfam09650 PHA_gran_rgn Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn). Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins found at the surface of PHA granules. These proteins have so far been found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria. Probab=79.71 E-value=3 Score=22.34 Aligned_cols=45 Identities=0% Similarity=0.118 Sum_probs=38.9 Q ss_pred HHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCC Q ss_conf 232387010133698799999967222206899999999998539 Q gi|254780881|r 25 IVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNI 69 (101) Q Consensus 25 iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i 69 (101) +--.|.-..+.+.++.+.+.+.|+.-..++...|+++|++.|-++ T Consensus 42 F~~~Gv~G~l~v~~~~v~v~i~Lg~ll~~fkg~Ie~eIe~~LD~~ 86 (87) T pfam09650 42 FKRSGVKGTLHVTEDKIRVDLKLGFLLSAFKGRIEQEIEKNLDKL 86 (87) T ss_pred EEECCCCEEEEECCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 971775469998277799999928888876768999999988721 No 12 >TIGR02830 spore_III_AG stage III sporulation protein AG; InterPro: IPR014195 This entry represents the stage III sporulation protein AG, which is encoded in a spore formation operon: spoIIIAABCDEFGH under the control of sigma G . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.. Probab=79.69 E-value=3.2 Score=22.16 Aligned_cols=34 Identities=12% Similarity=0.239 Sum_probs=28.5 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCC Q ss_conf 2068999999999985398534069999707898 Q gi|254780881|r 52 AHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKNP 85 (101) Q Consensus 52 ~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~~ 85 (101) ..+..++..+.+++|.+|.||.+|+|.++..... T Consensus 62 ~~yE~~~e~~Lk~~Le~I~GVg~V~V~vnL~~~e 95 (193) T TIGR02830 62 SDYEKEYENELKEILEKIEGVGDVTVMVNLDSSE 95 (193) T ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCC T ss_conf 9999999999999864203756148999965996 No 13 >COG5133 Uncharacterized conserved protein [Function unknown] Probab=78.76 E-value=6 Score=20.65 Aligned_cols=77 Identities=13% Similarity=0.141 Sum_probs=57.7 Q ss_pred CCHHHHHHHHHHCCCCCCCCCHHHCCCC--CCCCCCCC-------EEEEEEEECHHHCHHHHHHHHHHHHHHHC-CCCCC Q ss_conf 3589999998414187999762323870--10133698-------79999996722220689999999999853-98534 Q gi|254780881|r 4 ILKNQIVDSLKVLSIPGEKNNIVEMQRL--SEIFIVHN-------TVYLSITVPHTIAHQLQSLRSNAQQIIQN-IPTVK 73 (101) Q Consensus 4 ~~~~~I~~~L~~v~dP~~~~~iv~~g~V--~~i~i~~~-------~v~i~l~l~~~~~~~~~~l~~~i~~~l~~-i~gv~ 73 (101) ++.+.|.+.+..|.||+-...+-.++.| +++++.+| -|.+.++-+-|.|.+..-+.--|+-.|+. +|--- T Consensus 54 id~qeiydLia~I~DPEHPltL~QLsVV~lEdi~v~D~~~~n~i~~v~v~itPTIpHCSmatlIGLcIrvrleR~lpprF 133 (181) T COG5133 54 IDQQEIYDLIADIRDPEHPLTLEQLSVVSLEDISVPDGIAPNVIRCVKVVITPTIPHCSMATLIGLCIRVRLERHLPPRF 133 (181) T ss_pred CCHHHHHHHHHHCCCCCCCCCHHHCCEEEECCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHEEEEEHHCCCCCE T ss_conf 68899999998607988874076601352025534678887704789999635887206887764320332000379841 Q ss_pred CEEEEEE Q ss_conf 0699997 Q gi|254780881|r 74 NAVVTLT 80 (101) Q Consensus 74 ~v~V~lt 80 (101) .|+|.+. T Consensus 134 ~v~v~ik 140 (181) T COG5133 134 HVQVHIK 140 (181) T ss_pred EEEEEEE T ss_conf 6899981 No 14 >KOG3381 consensus Probab=74.01 E-value=6 Score=20.64 Aligned_cols=77 Identities=12% Similarity=0.108 Sum_probs=57.0 Q ss_pred CHHHHHHHHHHCCCCCCCCCHHHCCCCCC--CCCCC-------CEEEEEEEECHHHCHHHHHHHHHHHHHHH-CCCCCCC Q ss_conf 58999999841418799976232387010--13369-------87999999672222068999999999985-3985340 Q gi|254780881|r 5 LKNQIVDSLKVLSIPGEKNNIVEMQRLSE--IFIVH-------NTVYLSITVPHTIAHQLQSLRSNAQQIIQ-NIPTVKN 74 (101) Q Consensus 5 ~~~~I~~~L~~v~dP~~~~~iv~~g~V~~--i~i~~-------~~v~i~l~l~~~~~~~~~~l~~~i~~~l~-~i~gv~~ 74 (101) ..+.+.+.++.|.||+-...+-+++-|+. +++.+ ..|.+.++-+-|.|.+.--|---|+-.|. .+|---+ T Consensus 35 ~~~~~~dlir~I~DPEhP~TLeqL~VV~ee~v~V~d~~~~~~~s~V~i~ftPTipHCSmaTlIGLcIrVkl~RsLp~rfk 114 (161) T KOG3381 35 DAEEIFDLIRDIRDPEHPLTLEQLNVVSEEGVEVDDPNVGDEESYVRITFTPTIPHCSMATLIGLCIRVKLLRSLPPRFK 114 (161) T ss_pred HHHHHHHHHHCCCCCCCCCCHHHCCCEEECCEEEECCCCCCCCEEEEEEECCCCCCCHHHHHHHHEEEEEEEECCCCCEE T ss_conf 67899999861689888865887062422056764577788513899995368875227766422026655304887426 Q ss_pred EEEEEEE Q ss_conf 6999970 Q gi|254780881|r 75 AVVTLTE 81 (101) Q Consensus 75 v~V~lt~ 81 (101) +.|.++. T Consensus 115 vdV~I~~ 121 (161) T KOG3381 115 VDVYIKP 121 (161) T ss_pred EEEEECC T ss_conf 8999757 No 15 >TIGR01608 citD citrate lyase acyl carrier protein; InterPro: IPR006495 This group of sequences represent the acyl carrier protein (gamma subunit) of the holoenzyme citrate lyase (4.1.3.6 from EC) composed of alpha (2.8.3.10 from EC), beta (4.1.3.34 from EC), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The acyl carrier protein covalently binds the coenzyme of citrate lyase. The set contains an experimentally characterised member from Leuconostoc mesenteroides . The sequences come from a wide range of Gram-positive bacteria. For Gram-negative bacteria, it appears that only sequences from the gamma proteobacteria are included.. Probab=70.99 E-value=8.2 Score=19.90 Aligned_cols=46 Identities=15% Similarity=0.278 Sum_probs=34.5 Q ss_pred CCCCCC-EEEEEEEECHHH-CHHHHHHHHHHHHHHHCCCCCCCEEEEEE Q ss_conf 133698-799999967222-20689999999999853985340699997 Q gi|254780881|r 34 IFIVHN-TVYLSITVPHTI-AHQLQSLRSNAQQIIQNIPTVKNAVVTLT 80 (101) Q Consensus 34 i~i~~~-~v~i~l~l~~~~-~~~~~~l~~~i~~~l~~i~gv~~v~V~lt 80 (101) |.+..+ ..+|.|.+.+.= ..+...|+.-+++.|..+ ||+++.|.+. T Consensus 19 v~v~pa~~~Gi~~~l~S~VkkQFg~~I~~~vkeTL~~l-Gv~~a~v~v~ 66 (95) T TIGR01608 19 VSVEPAAQVGIEIDLSSSVKKQFGDEIEKVVKETLKEL-GVENAVVKVV 66 (95) T ss_pred EEECCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEEE T ss_conf 77324888847887520177775799999999989865-9443568872 No 16 >cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions. Probab=60.00 E-value=6.5 Score=20.44 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=21.0 Q ss_pred HHHHHHHHHHCCCCCCCEEEEEEECC Q ss_conf 99999999853985340699997078 Q gi|254780881|r 58 LRSNAQQIIQNIPTVKNAVVTLTENK 83 (101) Q Consensus 58 l~~~i~~~l~~i~gv~~v~V~lt~~~ 83 (101) =...++++|++++||.++.|.+..++ T Consensus 12 C~~~Ie~~l~~~~GV~~~~vn~~~~~ 37 (63) T cd00371 12 CVSKIEKALEKLPGVESVEVDLETGK 37 (63) T ss_pred HHHHHHHHHCCCCCCEEEEEECCCCE T ss_conf 99999999707999579999888999 No 17 >TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A; InterPro: IPR013485 This entry consists of archaeal proteins which are predicted to be functionally equivalent to MoaA (molybdenum cofactor biosynthesis protein A) from bacteria (see IPR013483 from INTERPRO).; GO: 0046872 metal ion binding, 0006777 Mo-molybdopterin cofactor biosynthetic process. Probab=57.36 E-value=18 Score=17.99 Aligned_cols=78 Identities=9% Similarity=0.153 Sum_probs=57.9 Q ss_pred CCHHHHHHHHHHCCCCCC-CCCHHHCCCC-----CCCCCCC-CEEEEEEEECHH---------HCHHHHHHHHHHHHHHH Q ss_conf 358999999841418799-9762323870-----1013369-879999996722---------22068999999999985 Q gi|254780881|r 4 ILKNQIVDSLKVLSIPGE-KNNIVEMQRL-----SEIFIVH-NTVYLSITVPHT---------IAHQLQSLRSNAQQIIQ 67 (101) Q Consensus 4 ~~~~~I~~~L~~v~dP~~-~~~iv~~g~V-----~~i~i~~-~~v~i~l~l~~~---------~~~~~~~l~~~i~~~l~ 67 (101) +++.+|.++.+.+++-.. .-++..-|.. +++.-.| ++|.|+|....+ .....+....-|++|+. T Consensus 74 lLR~D~~~Ii~~~~~~~~~~vSmTTNG~LL~~~A~~Lk~AGLdRVNVSLdtld~e~Y~kITG~~~~~~~~Vi~GI~~A~~ 153 (324) T TIGR02668 74 LLRKDLIEIIRRIKDYGIKDVSMTTNGILLEKLAKKLKEAGLDRVNVSLDTLDPEKYKKITGQSRDALDRVIEGIESAVD 153 (324) T ss_pred CHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHH T ss_conf 34566999998614675034420303144898999999828561312026788678886448998607899999999997 Q ss_pred CCCCCCCEEEEEEECC Q ss_conf 3985340699997078 Q gi|254780881|r 68 NIPTVKNAVVTLTENK 83 (101) Q Consensus 68 ~i~gv~~v~V~lt~~~ 83 (101) . |...|+++++.-+ T Consensus 154 ~--GL~PVKlN~Vvl~ 167 (324) T TIGR02668 154 A--GLTPVKLNMVVLK 167 (324) T ss_pred C--CCCCEEEEEEEEC T ss_conf 2--8981378888754 No 18 >pfam00403 HMA Heavy-metal-associated domain. Probab=56.67 E-value=8.7 Score=19.74 Aligned_cols=26 Identities=15% Similarity=0.333 Sum_probs=21.2 Q ss_pred HHHHHHHHHHHCCCCCCCEEEEEEEC Q ss_conf 99999999985398534069999707 Q gi|254780881|r 57 SLRSNAQQIIQNIPTVKNAVVTLTEN 82 (101) Q Consensus 57 ~l~~~i~~~l~~i~gv~~v~V~lt~~ 82 (101) .=...++++|.++|||.++.+.+..+ T Consensus 11 ~C~~~Ie~~l~~~~GV~~v~v~~~~~ 36 (62) T pfam00403 11 GCAKKVEKALSKLPGVSSVSVDLETG 36 (62) T ss_pred HHHHHHHHHHHCCCCCEEEEEECCCC T ss_conf 99999999985599954999987899 No 19 >TIGR01162 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain . The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex. Probab=48.48 E-value=25 Score=17.17 Aligned_cols=44 Identities=14% Similarity=0.240 Sum_probs=32.2 Q ss_pred HHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCC------CCCCC-CEEEEEC Q ss_conf 999999999853985340699997078987321------56998-5588859 Q gi|254780881|r 57 SLRSNAQQIIQNIPTVKNAVVTLTENKNPPQQR------NNLNV-KKFVAVA 101 (101) Q Consensus 57 ~l~~~i~~~l~~i~gv~~v~V~lt~~~~~~~~~------~~~gv-KnIIAVA 101 (101) ...+.+-+.|+.| ||.-.--+..+||+|..-. .-.|+ |=|||+| T Consensus 12 ~~m~~a~~~L~~f-gi~~e~~V~SAHRTP~~~~~ya~~a~~~G~P~ViIAgA 62 (159) T TIGR01162 12 ETMKKAAEILEEF-GIPYELRVVSAHRTPELMFEYAKEAEERGIPKVIIAGA 62 (159) T ss_pred HHHHHHHHHHHHC-CCCEEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEECC T ss_conf 8999999999855-99667898606778088999999998678997998403 No 20 >pfam03780 DUF322 Protein of unknown function (DUF322). This is a family of small proteins. It includes a protein identified as an alkaline shock protein so may be involved in stress response. Probab=47.62 E-value=26 Score=17.09 Aligned_cols=43 Identities=9% Similarity=0.222 Sum_probs=31.8 Q ss_pred CCEEEEE----EEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEE Q ss_conf 9879999----996722220689999999999853985340699997 Q gi|254780881|r 38 HNTVYLS----ITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLT 80 (101) Q Consensus 38 ~~~v~i~----l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt 80 (101) ++.+.++ +..+.+-....+.++..++++++.+.|++-..|.+. T Consensus 57 ~~~v~v~l~v~v~YG~~i~~v~~~iq~~V~~~v~~mtgl~V~~VnV~ 103 (108) T pfam03780 57 EGQVAIDLYVIVEYGVNIPEVAKNIQEKVKYAVENMTGLEVSEVNVH 103 (108) T ss_pred CCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCEEEEEEEE T ss_conf 98699999999977998899999999999999999879867899999 No 21 >TIGR02052 MerP mercuric transport protein periplasmic component; InterPro: IPR011795 This entry represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding . MerP is related to a larger family of metal binding proteins.; GO: 0015097 mercury ion transmembrane transporter activity, 0045340 mercury ion binding, 0015694 mercury ion transport, 0046689 response to mercury ion, 0042597 periplasmic space. Probab=46.66 E-value=9 Score=19.67 Aligned_cols=32 Identities=16% Similarity=0.283 Sum_probs=24.9 Q ss_pred EEEEEECHH---HCHHHHHHHHHHHHHHHCCCCCCCEEEEE Q ss_conf 999996722---22068999999999985398534069999 Q gi|254780881|r 42 YLSITVPHT---IAHQLQSLRSNAQQIIQNIPTVKNAVVTL 79 (101) Q Consensus 42 ~i~l~l~~~---~~~~~~~l~~~i~~~l~~i~gv~~v~V~l 79 (101) +|.|++|+- .||+- ++.||+++|||++++|.+ T Consensus 24 TVTL~vPgMtC~aCPiT------V~~AL~kVdGV~Kaev~f 58 (92) T TIGR02052 24 TVTLEVPGMTCAACPIT------VKTALKKVDGVEKAEVDF 58 (92) T ss_pred CEEEECCCCCCCCCCHH------HHHHCCCCCCCCCEEEEC T ss_conf 33530688866678501------774064388800000012 No 22 >TIGR03123 one_C_unchar_1 probable H4MPT-linked C1 transfer pathway protein. This protein family was identified, by the method of partial phylogenetic profiling, as related to the use of tetrahydromethanopterin (H4MPT) as a C-1 carrier. Characteristic markers of the H4MPT-linked C1 transfer pathway include formylmethanofuran dehydrogenase subunits, methenyltetrahydromethanopterin cyclohydrolase, etc. Tetrahydromethanopterin, a tetrahydrofolate analog, occurs in methanogenic archaea, bacterial methanotrophs, planctomycetes, and a few other lineages. Probab=41.95 E-value=12 Score=19.01 Aligned_cols=47 Identities=15% Similarity=0.153 Sum_probs=34.7 Q ss_pred CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCC Q ss_conf 98799999967222206899999999998539853406999970789 Q gi|254780881|r 38 HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKN 84 (101) Q Consensus 38 ~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~ 84 (101) +|.+.-.-..+.|-....+.|...+++....++....+-|.||.+-. T Consensus 18 ~g~i~~~~~~~~plWk~~~~L~~~l~~i~~~~~~~~~~avTMTgELa 64 (318) T TIGR03123 18 DGRIKEVHQLYCPLWKGNDKLAETLKEISQDLSSADNVAVTMTGELA 64 (318) T ss_pred CCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEHHHH T ss_conf 98688999851702178367899999999855831318999206576 No 23 >pfam08921 DUF1904 Domain of unknown function (DUF1904). This domain is found in a set of hypothetical bacterial proteins. Probab=41.83 E-value=32 Score=16.57 Aligned_cols=73 Identities=5% Similarity=0.129 Sum_probs=53.5 Q ss_pred HHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEE-----EEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEC Q ss_conf 99999841418799976232387010133698799-----9999672222068999999999985398534069999707 Q gi|254780881|r 8 QIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVY-----LSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTEN 82 (101) Q Consensus 8 ~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~-----i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~ 82 (101) .+.+.|..+. ..+++-+.+.++....+.+|.+. |.+.-=.-+.+..+.+.+-|.+.++.++|-.+|.|.++.= T Consensus 19 ~Li~eLa~i~--~~~~e~ftlE~i~s~~~~~G~~~~~ypfVEVlWF~R~qe~~d~vA~~It~~v~~~~~~~~V~V~F~~L 96 (107) T pfam08921 19 TLIEELADIC--KCPPEAFTLEWINSVFFRDGKIDDAYPFVEVLWFPRDQETQDLVAQIITEAVRAVNGLQDVAVIFTAL 96 (107) T ss_pred HHHHHHHHHH--CCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC T ss_conf 9999999997--79824489998336899737556773359999803898999999999999998438997399999964 No 24 >pfam04953 consensus Probab=40.93 E-value=33 Score=16.48 Aligned_cols=38 Identities=11% Similarity=0.156 Sum_probs=28.6 Q ss_pred EEEEEECHH-HCHHHHHHHHHHHHHHHCCCCCCCEEEEEE Q ss_conf 999996722-220689999999999853985340699997 Q gi|254780881|r 42 YLSITVPHT-IAHQLQSLRSNAQQIIQNIPTVKNAVVTLT 80 (101) Q Consensus 42 ~i~l~l~~~-~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt 80 (101) .+.+++.+. ...+-++|+.-+++.|..+ ||+++.|.+. T Consensus 28 gi~iel~S~V~kQFG~~Ir~~v~etL~~l-gV~~a~v~v~ 66 (97) T pfam04953 28 GIELELDSSVEKQFGDAIRQTIRETLAAY-GVTAAQVNVV 66 (97) T ss_pred CEEEEEEEHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEEE T ss_conf 56999977899997699999999999983-9734799997 No 25 >cd00756 MoaE MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for 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), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits. Probab=40.13 E-value=34 Score=16.41 Aligned_cols=67 Identities=7% Similarity=0.013 Sum_probs=44.5 Q ss_pred HHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEE Q ss_conf 9999841418799976232387010133698799999967222206899999999998539853406999 Q gi|254780881|r 9 IVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVT 78 (101) Q Consensus 9 I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~ 78 (101) +...+..+.+|+.|--..-.|.|++-. +|.-.-.|++.........+|++-++++.... ++..+.+. T Consensus 3 ~~~~~~~~~~~~~GAiv~F~G~VR~~~--~g~~v~~L~ye~y~~mA~k~l~~I~~~~~~k~-~i~~v~i~ 69 (124) T cd00756 3 LAELLAALRDPEAGAVVTFVGTVRDHD--EGKGVEALEYEAYPPMAEKELEEIAEEARERW-GLLRVAII 69 (124) T ss_pred HHHHHHHHCCCCCCEEEEEEEEECCCC--CCCCEEEEEEEEECHHHHHHHHHHHHHHHHCC-CCCEEEEE T ss_conf 899999726989986999999978899--99633179999600678999999999998507-87608999 No 26 >TIGR02610 PHA_gran_rgn putative polyhydroxyalkanoic acid system protein; InterPro: IPR013433 Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.. Probab=38.06 E-value=27 Score=16.95 Aligned_cols=47 Identities=4% Similarity=0.132 Sum_probs=40.5 Q ss_pred CCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHC Q ss_conf 97623238701013369879999996722220689999999999853 Q gi|254780881|r 22 KNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQN 68 (101) Q Consensus 22 ~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~ 68 (101) .-+|-=.|.=..|.+-+..|.|+++|..--..+...++.+|+++|-. T Consensus 42 tl~~aRsGv~Gav~~g~~~irv~~eLG~llSaM~g~iksEI~raLdk 88 (91) T TIGR02610 42 TLRIARSGVDGAVHLGEESIRVEVELGMLLSAMSGTIKSEIERALDK 88 (91) T ss_pred EEEEEECCCCCEEEECCCEEEEEEEECHHHHHCCCCCHHHHHHHHHH T ss_conf 66777516773364278416886310116530287536889999886 No 27 >COG4806 RhaA L-rhamnose isomerase [Carbohydrate transport and metabolism] Probab=37.27 E-value=38 Score=16.15 Aligned_cols=71 Identities=14% Similarity=0.073 Sum_probs=46.1 Q ss_pred HHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEE--ECHHH-CHHHHHHHHHHHHHHHCCCCCCCEEEE Q ss_conf 999998414187999762323870101336987999999--67222-206899999999998539853406999 Q gi|254780881|r 8 QIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSIT--VPHTI-AHQLQSLRSNAQQIIQNIPTVKNAVVT 78 (101) Q Consensus 8 ~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~--l~~~~-~~~~~~l~~~i~~~l~~i~gv~~v~V~ 78 (101) ++.++|++..+--..---..-+-|++.+..+|.++=.+. -+||+ +...++++++.+.||+-+||-..++.. T Consensus 22 Dve~AL~~L~~~piSmHCWQGDDv~GFe~~~GeLtGGI~~TGnYPGkA~t~~eLR~DLEkAlsLIPG~~rlNLH 95 (419) T COG4806 22 DVEEALRQLDRLPVSMHCWQGDDVSGFENPEGELTGGIQATGNYPGKARNAEELRADLEKALSLIPGPKRLNLH 95 (419) T ss_pred CHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCEEECCEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEE T ss_conf 69999988741862666405786556147887041554404778876699899999999987408896513236 No 28 >PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional Probab=37.24 E-value=25 Score=17.17 Aligned_cols=42 Identities=14% Similarity=0.146 Sum_probs=28.0 Q ss_pred CEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC Q ss_conf 879999996722220689999999999853985340699997078 Q gi|254780881|r 39 NTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENK 83 (101) Q Consensus 39 ~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~ 83 (101) +..+.+..+..-.|.. =...+|++|.++|||.+++|.++.++ T Consensus 47 ~~~~~~f~V~GM~Caa---Ca~~IE~~L~~~~GV~~a~Vn~at~~ 88 (739) T PRK11033 47 SGTRYSWKVSGMDCPS---CARKVENAVRQLAGVNQAQVLFATEK 88 (739) T ss_pred CCCEEEEEECCCCCHH---HHHHHHHHHHCCCCEEEEEEECCCCE T ss_conf 7867579977844699---99999998717979339999976878 No 29 >COG3965 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism] Probab=36.37 E-value=39 Score=16.07 Aligned_cols=39 Identities=10% Similarity=0.113 Sum_probs=31.7 Q ss_pred CHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCC Q ss_conf 722220689999999999853985340699997078987 Q gi|254780881|r 48 PHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKNPP 86 (101) Q Consensus 48 ~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~~~ 86 (101) +.-.-+.++++++++.++|...+-=.-+++.+|.+++|. T Consensus 275 ~ar~Ved~d~Irdei~~slg~~g~~rwltvsfT~D~kWa 313 (314) T COG3965 275 DARNVEDWDDIRDEIGQSLGSLGYERWLTVSFTRDEKWA 313 (314) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC T ss_conf 874633689999999888634786743899985330003 No 30 >PRK13253 citrate lyase subunit gamma; Provisional Probab=34.41 E-value=42 Score=15.89 Aligned_cols=41 Identities=12% Similarity=0.173 Sum_probs=31.0 Q ss_pred CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEE Q ss_conf 9879999996722220689999999999853985340699997 Q gi|254780881|r 38 HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLT 80 (101) Q Consensus 38 ~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt 80 (101) +|.+.+.|+-. ....+-++|+.-+++.|..+ ||+++.|.+. T Consensus 26 ~g~i~i~l~S~-V~kQFG~~Ir~~v~etL~~l-gV~~~~v~v~ 66 (92) T PRK13253 26 TQGIDIQLESS-VEKQFGDQIRAVILETLAKL-GVTNAQVNVD 66 (92) T ss_pred CCCEEEEEEEH-HHHHHHHHHHHHHHHHHHHC-CCCEEEEEEE T ss_conf 98379999678-99987799999999999972-9751699995 No 31 >TIGR00884 guaA_Cterm GMP synthase, C-terminal domain; InterPro: IPR001674 The amidotransferase family of enzymes utilises the ammonia derived from the hydrolysis of glutamine for a subsequent chemical reaction catalyzed by the same enzyme. The ammonia intermediate does not dissociate into solution during the chemical transformations . GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. The C-terminal domain is specific to the GMP synthases 6.3.5.2 from EC. In prokaryotes this domain mediates dimerisation. Eukaryotic GMP synthases are monomers. This domain in eukaryotes includes several large insertions that may form globular domains .; GO: 0003922 GMP synthase (glutamine-hydrolyzing) activity, 0005524 ATP binding, 0006164 purine nucleotide biosynthetic process, 0006177 GMP biosynthetic process. Probab=33.32 E-value=18 Score=17.95 Aligned_cols=30 Identities=20% Similarity=0.333 Sum_probs=14.5 Q ss_pred HHHHHHHHHHHHHCCCCCCCEEEEEEECCC Q ss_conf 899999999998539853406999970789 Q gi|254780881|r 55 LQSLRSNAQQIIQNIPTVKNAVVTLTENKN 84 (101) Q Consensus 55 ~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~ 84 (101) |+-|++=..+....+++|+.|-..+|+.++ T Consensus 284 yd~L~ris~RItnEv~~V~RVVYDITsKPP 313 (319) T TIGR00884 284 YDLLERISNRITNEVPGVNRVVYDITSKPP 313 (319) T ss_pred HHHHHHHHCCCCCCCCCCEEEEEEECCCCC T ss_conf 889988821100122884079985167349 No 32 >TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family; InterPro: IPR003282 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia. The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. One of the outer membrane protein subunit families, termed "K" here for nomenclature purposes, aids in the structural assembly of the invasion complex . It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.; GO: 0009306 protein secretion. Probab=32.30 E-value=46 Score=15.68 Aligned_cols=67 Identities=24% Similarity=0.310 Sum_probs=43.0 Q ss_pred HHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECH-HHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCC Q ss_conf 99998414187999762323870101336987999999672-22206899999999998539853406999970789 Q gi|254780881|r 9 IVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPH-TIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKN 84 (101) Q Consensus 9 I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~-~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~ 84 (101) -++.|+..-.|.-. ..-+.+++-.+|-|. -|. ..+.+.=.+.+++++.|+.++||-++.|.+..+.. T Consensus 75 A~~lL~~~GLP~~~-----~~~~~~~Fp~~gLvs----SP~eEraR~~ya~eQ~Le~tLs~IdGV~~ArVhVvlP~~ 142 (203) T TIGR02544 75 AVELLRQNGLPRQS-----FVNLGELFPKDGLVS----SPTEERARLLYAIEQELEQTLSQIDGVISARVHVVLPEN 142 (203) T ss_pred HHHHHHHCCCCCCC-----CCCHHHHCCCCCEEC----CHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCC T ss_conf 99999863888953-----236887513577034----869999999999999999986017926866799972167 No 33 >PRK10671 copA copper exporting ATPase; Provisional Probab=29.87 E-value=50 Score=15.45 Aligned_cols=40 Identities=20% Similarity=0.233 Sum_probs=28.7 Q ss_pred EEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC Q ss_conf 9999996722220689999999999853985340699997078 Q gi|254780881|r 41 VYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENK 83 (101) Q Consensus 41 v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~ 83 (101) -.+.|.+..-.|.. -...+|++|+++|||.+++|.+..++ T Consensus 99 ~~~~l~i~Gm~Caa---C~~~ie~~l~~~~GV~~a~Vn~~~~~ 138 (834) T PRK10671 99 DSQQLLLSGMSCAS---CVTRVQNALQSVPGVTQARVNLAERT 138 (834) T ss_pred CEEEEEECCCCHHH---HHHHHHHHHHCCCCEEEEEEECCCCE T ss_conf 55899987835288---89999999836979008999988883 No 34 >PRK10503 multidrug efflux system subunit MdtB; Provisional Probab=29.62 E-value=51 Score=15.42 Aligned_cols=18 Identities=17% Similarity=0.202 Sum_probs=7.4 Q ss_pred HHHHHHHHCCCCCCCEEE Q ss_conf 999999853985340699 Q gi|254780881|r 60 SNAQQIIQNIPTVKNAVV 77 (101) Q Consensus 60 ~~i~~~l~~i~gv~~v~V 77 (101) ..++..|+.+|||..|.+ T Consensus 169 ~~l~~~L~~i~GV~~V~i 186 (1040) T PRK10503 169 TRVAQKISQVSGVGLVTL 186 (1040) T ss_pred HHHHHHHHCCCCEEEEEE T ss_conf 999999847999179997 No 35 >PRK05783 hypothetical protein; Provisional Probab=27.10 E-value=57 Score=15.16 Aligned_cols=65 Identities=14% Similarity=0.090 Sum_probs=42.3 Q ss_pred HHCCCCCC---CCCHHHCCCCCCCCCC-CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE Q ss_conf 41418799---9762323870101336-987999999672222068999999999985398534069999 Q gi|254780881|r 14 KVLSIPGE---KNNIVEMQRLSEIFIV-HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL 79 (101) Q Consensus 14 ~~v~dP~~---~~~iv~~g~V~~i~i~-~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l 79 (101) .++.||+. .++++..|+-+-..+. |..+.|.++-+.+. ...+.....|.+....=|=|..++|.+ T Consensus 13 ~gi~DPeG~TI~~~L~~~g~~~v~~vR~GK~l~~~iea~s~e-eA~~~v~~ic~~lrL~NPvI~~~~i~v 81 (84) T PRK05783 13 DGIRDPEGETIQRYVLERMLGYSIEVRAGKCLVFRIEASSPE-EAQELALKLAKEMRLGNPIVHKIVVRV 81 (84) T ss_pred CCCCCCCHHHHHHHHHHHCCCCEEEEEEEEEEEEEEECCCHH-HHHHHHHHHHHHHHCCCCCEEEEEEEE T ss_conf 977596337999999985589648987104999999479989-999999999986203498528999999 No 36 >COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism] Probab=27.00 E-value=57 Score=15.15 Aligned_cols=43 Identities=21% Similarity=0.305 Sum_probs=29.9 Q ss_pred HHHHHHHHHHCCCCCCCEEEEEEECCCCCCC------CCCCCCCEEEEEC Q ss_conf 9999999985398534069999707898732------1569985588859 Q gi|254780881|r 58 LRSNAQQIIQNIPTVKNAVVTLTENKNPPQQ------RNNLNVKKFVAVA 101 (101) Q Consensus 58 l~~~i~~~l~~i~gv~~v~V~lt~~~~~~~~------~~~~gvKnIIAVA 101 (101) ..+.+-+.|..+ ||.-..-.+.+|+.|..- -.-.|+|-|||.| T Consensus 17 ~mk~Aa~~L~~f-gv~ye~~VvSAHRTPe~m~~ya~~a~~~g~~viIAgA 65 (162) T COG0041 17 TMKKAAEILEEF-GVPYEVRVVSAHRTPEKMFEYAEEAEERGVKVIIAGA 65 (162) T ss_pred HHHHHHHHHHHC-CCCEEEEEEECCCCHHHHHHHHHHHHHCCCEEEEECC T ss_conf 999999999984-9975999984467989999999999878975999657 No 37 >pfam01251 Ribosomal_S7e Ribosomal protein S7e. Probab=26.65 E-value=58 Score=15.12 Aligned_cols=73 Identities=16% Similarity=0.176 Sum_probs=50.8 Q ss_pred CHHHHHHHHHHCC--CCCCCCCHHHCCC--CCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHC-CCCCCCEEE Q ss_conf 5899999984141--8799976232387--01013369879999996722220689999999999853-985340699 Q gi|254780881|r 5 LKNQIVDSLKVLS--IPGEKNNIVEMQR--LSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQN-IPTVKNAVV 77 (101) Q Consensus 5 ~~~~I~~~L~~v~--dP~~~~~iv~~g~--V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~-i~gv~~v~V 77 (101) .+++|-++|-.+. .|++..++-++-. ++++++.+|.=.+.+.+|++....+..+....-..|+. +.|-.-+.| T Consensus 14 ~E~~Vaqal~dLE~~~~dLK~~Lr~L~i~~akEi~v~~gkKaivIfVP~p~lk~f~Kiq~rLvrELEKKfsgkhVv~i 91 (189) T pfam01251 14 LELSVAQALFDLESNSPDLKAELRDLQITSAKEIEVGGGKKAVVIFVPVPQLKAYRKIQQRLVRELEKKFSGKHVVFV 91 (189) T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHCEEEEEEEEEECCCCEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCEEEEE T ss_conf 999999999999827798987634028855699985699479999960799899999999999999864589879999 No 38 >pfam01514 YscJ_FliF Secretory protein of YscJ/FliF family. This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins. Probab=25.70 E-value=60 Score=15.01 Aligned_cols=33 Identities=18% Similarity=0.216 Sum_probs=26.1 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCC Q ss_conf 206899999999998539853406999970789 Q gi|254780881|r 52 AHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKN 84 (101) Q Consensus 52 ~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~ 84 (101) ......+..++++.|..++||.++.|.++-++. T Consensus 109 ~~~~rAle~eL~rtI~~i~gV~~ArVhl~lPe~ 141 (206) T pfam01514 109 ARLIYALEQELSRTLSQIDGVISARVHIVLPER 141 (206) T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCC T ss_conf 999999999999999727883067999967887 No 39 >PRK00435 ef1B elongation factor 1-beta; Validated Probab=25.62 E-value=60 Score=15.01 Aligned_cols=68 Identities=13% Similarity=0.191 Sum_probs=37.2 Q ss_pred CCCHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCC--EEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEE Q ss_conf 0358999999841418799976232387010133698--79999996722220689999999999853985340699997 Q gi|254780881|r 3 QILKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHN--TVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLT 80 (101) Q Consensus 3 ~~~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~--~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt 80 (101) +...+.+.+.++.....+.. .+.+..--+.=| .+.+.+..+- .+...+.+++++++++||.++.|.-. T Consensus 16 evDle~L~e~ik~~l~~~~~-----i~~~e~ePiAFGLkaL~v~vv~~D-----~eG~tD~~Ee~~~~iegV~sveV~~v 85 (88) T PRK00435 16 EVDLDELKEKIKEKLPEGYE-----INRIEEEPIAFGLKALKLYVIMPD-----EEGGTDPVEEAFAAVEGVESVEVEEV 85 (88) T ss_pred CCCHHHHHHHHHHHCCCCCE-----EEEEEEEEEECCCEEEEEEEEEEC-----CCCCCHHHHHHHHCCCCCCEEEEEEE T ss_conf 86999999999975758764-----746678845645232799999975-----88683799999854689657999988 No 40 >TIGR00003 TIGR00003 copper ion binding protein; InterPro: IPR006122 Proteins that transport heavy metals in micro-organisms and eukaryotes share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases . A conserved 30-residue domain has been found in a number of these heavy metal transport or detoxification proteins . The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. This sub-domain is found in copper-binding proteins. ; GO: 0005507 copper ion binding, 0006825 copper ion transport. Probab=25.58 E-value=43 Score=15.82 Aligned_cols=27 Identities=15% Similarity=0.241 Sum_probs=21.1 Q ss_pred HHHHHHHHHHHCCCCCCCEEEEEEECC Q ss_conf 999999999853985340699997078 Q gi|254780881|r 57 SLRSNAQQIIQNIPTVKNAVVTLTENK 83 (101) Q Consensus 57 ~l~~~i~~~l~~i~gv~~v~V~lt~~~ 83 (101) .=-+.||+.+..|+||+.+.|.|...+ T Consensus 13 HCV~~iE~~VGel~GVs~v~v~L~k~~ 39 (66) T TIGR00003 13 HCVDKIEKFVGELEGVSAVKVQLEKEK 39 (66) T ss_pred HHHHHHHHHCCEECCCEEEEEEEECCE T ss_conf 247765410470037306766763241 No 41 >TIGR01923 menE O-succinylbenzoate-CoA ligase; InterPro: IPR010192 This entry represents the enzyme O-succinylbenzoate-CoA ligase (MenE), which is involved in the fourth step of the menaquinone (vitamin K2) biosynthesis pathway. In bacteria, menaquinone is used during fumarate reduction in anaerobic respiration. In green sulphur bacteria and heliobacteria, menaquinones are thought to be used as a loosely bound secondary electron acceptor in the photosynthetic reaction centre. In cyanobacteria, the product of the menaquinone pathway is phylloquinone (2-methyl-3-phytyl-1,4-naphthoquinone), a molecule used exclusively as an electron transfer cofactor in Photosystem (PS) I. .; GO: 0008756 o-succinylbenzoate-CoA ligase activity, 0009234 menaquinone biosynthetic process. Probab=24.83 E-value=63 Score=14.92 Aligned_cols=32 Identities=19% Similarity=0.217 Sum_probs=26.7 Q ss_pred HHHHHHHHHHCCCCCCCEEEEEEECCCCCCCC Q ss_conf 99999999853985340699997078987321 Q gi|254780881|r 58 LRSNAQQIIQNIPTVKNAVVTLTENKNPPQQR 89 (101) Q Consensus 58 l~~~i~~~l~~i~gv~~v~V~lt~~~~~~~~~ 89 (101) --.+||+.|.++|+|..+-|.-..+.+|++.+ T Consensus 403 yP~EIE~v~~s~p~v~~a~vvp~~D~~wG~vP 434 (490) T TIGR01923 403 YPEEIEKVLYSHPGVQEAVVVPKPDAEWGQVP 434 (490) T ss_pred CHHHHHHHHHCCCCEEEEEEECCCCCCCCCCC T ss_conf 87999999853876268888478470017865 No 42 >PRK06156 hypothetical protein; Provisional Probab=24.62 E-value=63 Score=14.90 Aligned_cols=59 Identities=2% Similarity=-0.006 Sum_probs=38.4 Q ss_pred CCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE Q ss_conf 87999762323870101336987999999672222068999999999985398534069999 Q gi|254780881|r 18 IPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL 79 (101) Q Consensus 18 dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l 79 (101) |..+|.--+..|.+ ..+++...+.+.+-+|-....+.+..++.+++.....-..+.+.+ T Consensus 369 De~sG~LT~n~gii---~~~~~~~~l~iniRyPv~~~~e~l~~~i~~~l~~~~~~~~~~l~i 427 (522) T PRK06156 369 DDFMGPLTLSPTVV---KQTDKGTEVTVNLRRPVGKTPELLKGEIAEALAKWQAKHQVTLDI 427 (522) T ss_pred CCCCCCCEEEEEEE---EEECCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCEEEE T ss_conf 68876847986899---997988999999968898888999999999999878752836987 No 43 >cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains. Probab=24.62 E-value=63 Score=14.90 Aligned_cols=51 Identities=16% Similarity=0.154 Sum_probs=33.7 Q ss_pred CCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEE Q ss_conf 9997623238701013369879999996722220689999999999853985340699 Q gi|254780881|r 20 GEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVV 77 (101) Q Consensus 20 ~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V 77 (101) +.|-||.+...++. ..+....+++...+... ..+.+-++|+++||++-.+| T Consensus 22 ~~GGnI~~idvve~---~~~~~v~Ditv~~~d~~----h~~~Iv~al~~l~gV~V~~v 72 (74) T cd04887 22 EAGGDIGAIDLVEQ---GRDYTVRDITVDAPSEE----HAETIVAAVRALPEVKVLSV 72 (74) T ss_pred HCCCCEEEEEEEEE---CCCEEEEEEEEECCCHH----HHHHHHHHHHCCCCEEEEEE T ss_conf 76985677899994---49959999999869778----89999999961998599994 No 44 >pfam02391 MoaE MoaE protein. This family contains the MoaE protein that is involved in biosynthesis of molybdopterin. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins. Probab=24.59 E-value=63 Score=14.89 Aligned_cols=68 Identities=7% Similarity=0.029 Sum_probs=44.2 Q ss_pred HHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEE Q ss_conf 99999841418799976232387010133698799999967222206899999999998539853406999 Q gi|254780881|r 8 QIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVT 78 (101) Q Consensus 8 ~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~ 78 (101) ++...++.+.+|..|--..-.|.|++-. +|.-.-.|++..........++.-++++..+.+ +..+.+. T Consensus 10 d~~~~~~~~~~~~~GAiv~F~G~VR~~~--~g~~v~~L~ye~y~~mA~~~l~~I~~~a~~k~~-~~~v~i~ 77 (117) T pfam02391 10 DVDEVIEKVSEPSAGAIVTFVGTVRDHN--GGKRVSRLEYEAYPEMAEKELAEIVEEAREKWP-GIDVAVV 77 (117) T ss_pred CHHHHHHHHCCCCCCEEEEEEEEECCCC--CCCCEEEEEEEECHHHHHHHHHHHHHHHHHHCC-CCCEEEE T ss_conf 9899999821999988999999978899--998478999998228999999999999997579-8655899 No 45 >TIGR02347 chap_CCT_zeta T-complex protein 1, zeta subunit; InterPro: IPR012722 Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT zeta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding. Probab=23.61 E-value=66 Score=14.78 Aligned_cols=57 Identities=9% Similarity=0.066 Sum_probs=43.6 Q ss_pred HHHCCCCCCC-CCHHHCCCCCCCCCCCCEEE----------EEEEECHHHCHHHHHHHHHHHHHHHCCC Q ss_conf 8414187999-76232387010133698799----------9999672222068999999999985398 Q gi|254780881|r 13 LKVLSIPGEK-NNIVEMQRLSEIFIVHNTVY----------LSITVPHTIAHQLQSLRSNAQQIIQNIP 70 (101) Q Consensus 13 L~~v~dP~~~-~~iv~~g~V~~i~i~~~~v~----------i~l~l~~~~~~~~~~l~~~i~~~l~~i~ 70 (101) +-.|.| ... .++==+|+||+..+.+.+=+ ++|-+-.|......|+++.+++-|+++. T Consensus 342 ~NSv~d-L~Pfe~LG~AGlVYE~~~GEEKyTFiEe~~~PkScTiLIkGpn~~ti~QiKDAvRDGLRAv~ 409 (548) T TIGR02347 342 LNSVED-LTPFECLGWAGLVYETVIGEEKYTFIEEVKNPKSCTILIKGPNDHTIKQIKDAVRDGLRAVK 409 (548) T ss_pred CCCCCC-CCCHHHCCCCCEEEEEEECCCCCEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHH T ss_conf 374246-87311237652134135568500022103878616887328864467764676652257645 No 46 >pfam09580 Spore_YhcN_YlaJ Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ). This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain. Probab=23.50 E-value=67 Score=14.77 Aligned_cols=42 Identities=7% Similarity=0.296 Sum_probs=20.6 Q ss_pred CCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCC-CCCCCEEE Q ss_conf 3698799999967222206899999999998539-85340699 Q gi|254780881|r 36 IVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNI-PTVKNAVV 77 (101) Q Consensus 36 i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i-~gv~~v~V 77 (101) +.|..+.|.+.+........+.++++++++++.. |.+..|-| T Consensus 88 Vt~~~a~V~v~~~~~~~~~~~~ik~~V~~~v~~~~p~~~~VyV 130 (169) T pfam09580 88 VTGEEALVAVDLDNGERSLTEEIKKQVKKAVKSVDPRIYNVYV 130 (169) T ss_pred EECCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE T ss_conf 9899799999738864035899999999999840888656999 No 47 >pfam00873 ACR_tran AcrB/AcrD/AcrF family. Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer membrane channel TolC. The structure shows the AcrB forms a homotrimer. Probab=22.79 E-value=69 Score=14.69 Aligned_cols=35 Identities=11% Similarity=0.174 Sum_probs=15.0 Q ss_pred EEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 99999672222068999999999985398534069 Q gi|254780881|r 42 YLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAV 76 (101) Q Consensus 42 ~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~ 76 (101) .+.+.+..+.......+.+++++.|+++||+.+++ T Consensus 672 ~i~i~l~G~d~~~L~~~a~~v~~~L~~~~gv~~v~ 706 (1021) T pfam00873 672 DLQVKIFGDGLDALDEARNQILAALAQLPGLADVR 706 (1021) T ss_pred EEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEE T ss_conf 79999479999999999999999983599817875 No 48 >KOG4656 consensus Probab=22.43 E-value=70 Score=14.65 Aligned_cols=25 Identities=16% Similarity=0.347 Sum_probs=19.6 Q ss_pred HHHHHHHHHHHHCCCCCCCEEEEEE Q ss_conf 9999999999853985340699997 Q gi|254780881|r 56 QSLRSNAQQIIQNIPTVKNAVVTLT 80 (101) Q Consensus 56 ~~l~~~i~~~l~~i~gv~~v~V~lt 80 (101) +.-..+++..|+.++||++|+|.+. T Consensus 18 escvnavk~~L~~V~Gi~~vevdle 42 (247) T KOG4656 18 ESCVNAVKACLKGVPGINSVEVDLE 42 (247) T ss_pred HHHHHHHHHHHCCCCCCCEEEEEHH T ss_conf 7788999998606887104787710 No 49 >PRK10614 multidrug efflux system subunit MdtC; Provisional Probab=21.36 E-value=74 Score=14.52 Aligned_cols=19 Identities=26% Similarity=0.256 Sum_probs=8.8 Q ss_pred HHHHHHHHHCCCCCCCEEE Q ss_conf 9999999853985340699 Q gi|254780881|r 59 RSNAQQIIQNIPTVKNAVV 77 (101) Q Consensus 59 ~~~i~~~l~~i~gv~~v~V 77 (101) ...++..|+.+|||.+|.+ T Consensus 159 ~~~l~~~L~~i~GV~~V~~ 177 (1025) T PRK10614 159 STQLAQTIAQIDGVGDVDV 177 (1025) T ss_pred HHHHHHHHHCCCCCEEEEE T ss_conf 9999999857989269997 No 50 >TIGR01054 rgy reverse gyrase; InterPro: IPR005736 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=21.14 E-value=53 Score=15.34 Aligned_cols=42 Identities=17% Similarity=0.256 Sum_probs=25.4 Q ss_pred CCCCHHHHHHHHHHCC---CCCCCCCHHHCCCCCCCCCCCCEEEEEE Q ss_conf 6035899999984141---8799976232387010133698799999 Q gi|254780881|r 2 NQILKNQIVDSLKVLS---IPGEKNNIVEMQRLSEIFIVHNTVYLSI 45 (101) Q Consensus 2 s~~~~~~I~~~L~~v~---dP~~~~~iv~~g~V~~i~i~~~~v~i~l 45 (101) .|+|+.+|++||++.+ .=++..|+|.+..|+.| .|==|.|.| T Consensus 840 HEVT~rAi~eAl~s~rkGeel~vd~NLVkAQvVRRI--~DRWiGF~L 884 (1843) T TIGR01054 840 HEVTKRAILEALESPRKGEELSVDENLVKAQVVRRI--EDRWIGFTL 884 (1843) T ss_pred CCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEE--EEEEECEEE T ss_conf 562379999986087657501000231011588898--754003011 No 51 >PRK13614 lipoprotein LpqB; Provisional Probab=21.05 E-value=75 Score=14.48 Aligned_cols=48 Identities=17% Similarity=0.252 Sum_probs=37.8 Q ss_pred CCCCCCCCEEEEEEEEC---HHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE Q ss_conf 10133698799999967---2222068999999999985398534069999 Q gi|254780881|r 32 SEIFIVHNTVYLSITVP---HTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL 79 (101) Q Consensus 32 ~~i~i~~~~v~i~l~l~---~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l 79 (101) ..+.+.+|..++.|..+ .........|..++...|.+++++.+|++.. T Consensus 238 ~~V~v~~g~a~VdLs~~~~~~a~~~~r~~maaQL~~TL~~lp~V~~V~L~~ 288 (573) T PRK13614 238 ESVPVVSGTATVDLSAKELDPASAEDRQRMQQQLQLTLRAQPDVENVELRA 288 (573) T ss_pred CCEEECCCEEEEECCHHCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEE T ss_conf 745403884798524020465899999999999999985489612699998 No 52 >COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism] Probab=20.55 E-value=77 Score=14.42 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=25.7 Q ss_pred EEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEE Q ss_conf 999967222206899999999998539853406999970 Q gi|254780881|r 43 LSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTE 81 (101) Q Consensus 43 i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~ 81 (101) ..+.++.-.| ..=...++++|+.++|+.++.|.+.. T Consensus 4 ~~l~v~~MtC---~~C~~~V~~al~~v~gv~~v~v~l~~ 39 (71) T COG2608 4 TTLKVEGMTC---GHCVKTVEKALEEVDGVASVDVDLEK 39 (71) T ss_pred EEEEECCCCC---HHHHHHHHHHHHCCCCCEEEEEECCC T ss_conf 6997779294---89999999988438982399995221 No 53 >TIGR00855 L12 ribosomal protein L7/L12; InterPro: IPR000206 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family of large subunit ribosomal proteins is called the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain . The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=20.01 E-value=66 Score=14.79 Aligned_cols=18 Identities=39% Similarity=0.717 Sum_probs=14.7 Q ss_pred CCCCCHHHHHHHHHHCCC Q ss_conf 960358999999841418 Q gi|254780881|r 1 MNQILKNQIVDSLKVLSI 18 (101) Q Consensus 1 Ms~~~~~~I~~~L~~v~d 18 (101) |+.++.++|++.|+..+- T Consensus 1 Ma~l~~~~i~E~l~~~tv 18 (131) T TIGR00855 1 MAKLSKEQIIEALKSLTV 18 (131) T ss_pred CCCCCHHHHHHHHHCCCH T ss_conf 976658899999866803 Done!