Query gi|254781063|ref|YP_003065476.1| hypothetical protein CLIBASIA_04825 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 129 No_of_seqs 105 out of 1277 Neff 5.8 Searched_HMMs 39220 Date Mon May 30 04:44:03 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781063.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR02945 SUF_assoc FeS assemb 100.0 4.4E-40 1.1E-44 261.8 8.8 96 34-129 1-96 (96) 2 TIGR03406 FeS_long_SufT probab 100.0 4.8E-37 1.2E-41 243.5 13.5 120 9-128 48-174 (174) 3 COG2151 PaaD Predicted metal-s 100.0 9.5E-32 2.4E-36 211.7 12.4 105 25-129 6-111 (111) 4 TIGR02159 PA_CoA_Oxy4 phenylac 99.9 2.2E-25 5.6E-30 173.5 8.7 86 43-129 1-88 (152) 5 pfam01883 DUF59 Domain of unkn 99.9 6.5E-23 1.7E-27 158.6 8.9 76 32-107 1-76 (76) 6 PRK11670 putative ATPase; Prov 99.6 2E-15 5E-20 113.7 11.2 87 25-112 6-92 (369) 7 KOG3381 consensus 98.2 3.7E-06 9.4E-11 58.0 6.1 106 1-108 4-120 (161) 8 COG5133 Uncharacterized conser 96.9 0.0015 3.9E-08 42.3 4.8 78 31-108 54-140 (181) 9 TIGR03341 YhgI_GntY IscR-regul 94.2 0.3 7.7E-06 28.5 7.2 73 29-104 103-177 (190) 10 PRK11190 putative DNA uptake p 88.8 2.2 5.5E-05 23.4 6.7 73 29-104 104-179 (192) 11 TIGR02052 MerP mercuric transp 84.7 0.43 1.1E-05 27.6 1.3 28 75-108 32-59 (92) 12 COG0694 Thioredoxin-like prote 74.0 8.1 0.00021 19.9 7.0 74 29-105 7-83 (93) 13 pfam01106 NifU NifU-like domai 69.6 10 0.00026 19.3 6.2 61 38-103 3-65 (68) 14 TIGR02187 GlrX_arch Glutaredox 66.8 6.2 0.00016 20.6 3.0 30 64-93 146-175 (237) 15 TIGR00411 redox_disulf_1 redox 65.9 2.5 6.3E-05 23.0 0.9 33 70-102 4-36 (82) 16 PRK10503 multidrug efflux syst 61.8 15 0.00037 18.4 7.3 32 73-104 677-708 (1040) 17 pfam07350 DUF1479 Protein of u 50.9 22 0.00057 17.3 3.8 91 38-128 309-408 (408) 18 pfam09650 PHA_gran_rgn Putativ 50.6 23 0.00057 17.3 3.8 69 27-96 12-85 (87) 19 pfam00873 ACR_tran AcrB/AcrD/A 50.3 23 0.00058 17.2 7.2 37 69-105 671-707 (1021) 20 cd02973 TRX_GRX_like Thioredox 49.0 22 0.00057 17.3 3.4 39 68-109 2-40 (67) 21 TIGR02830 spore_III_AG stage I 46.0 27 0.00068 16.8 3.8 28 83-110 65-92 (193) 22 cd00371 HMA Heavy-metal-associ 41.9 22 0.00057 17.3 2.5 34 87-120 13-53 (63) 23 pfam00403 HMA Heavy-metal-asso 40.5 27 0.00069 16.8 2.7 23 86-108 12-34 (62) 24 COG2608 CopZ Copper chaperone 39.4 30 0.00075 16.5 2.8 35 71-108 4-38 (71) 25 PRK00435 ef1B elongation facto 37.9 36 0.00091 16.1 6.3 72 24-108 14-85 (88) 26 PRK10775 cell division protein 37.4 35 0.00089 16.1 2.9 23 87-109 93-115 (274) 27 KOG4656 consensus 35.1 40 0.001 15.8 3.9 24 84-107 18-41 (247) 28 pfam03612 EIIBC-GUT_N Sorbitol 35.0 18 0.00045 17.9 1.1 75 30-109 36-120 (182) 29 cd00958 DhnA Class I fructose- 33.2 42 0.0011 15.6 3.1 89 35-125 22-115 (235) 30 TIGR01608 citD citrate lyase a 31.9 45 0.0011 15.5 4.7 48 61-109 19-67 (95) 31 pfam05768 DUF836 Glutaredoxin- 29.5 49 0.0013 15.2 3.2 40 73-113 3-42 (76) 32 PRK07226 fructose-bisphosphate 28.6 45 0.0012 15.4 2.3 89 35-125 40-132 (266) 33 TIGR00003 TIGR00003 copper ion 27.1 38 0.00097 15.9 1.7 22 87-108 15-36 (66) 34 pfam09129 Chol_subst-bind Chol 25.6 58 0.0015 14.8 3.8 43 72-114 222-264 (321) 35 PRK08744 consensus 25.5 58 0.0015 14.8 4.6 72 35-114 1123-1195(1195) 36 COG3963 Phospholipid N-methylt 24.9 46 0.0012 15.4 1.8 25 36-60 36-60 (194) 37 COG3732 SrlE Phosphotransferas 24.3 51 0.0013 15.1 1.9 61 45-110 61-122 (328) 38 pfam03780 DUF322 Protein of un 23.6 63 0.0016 14.6 6.2 45 63-107 54-102 (108) 39 pfam08478 POTRA_1 POTRA domain 23.6 63 0.0016 14.6 3.1 31 79-109 26-56 (67) 40 pfam02700 PurS Phosphoribosylf 23.6 63 0.0016 14.6 3.5 53 52-108 25-79 (80) 41 TIGR02794 tolA_full protein To 23.5 63 0.0016 14.6 5.1 68 28-98 354-426 (452) 42 cd03026 AhpF_NTD_C TRX-GRX-lik 23.1 64 0.0016 14.5 2.8 28 63-90 10-37 (89) 43 TIGR02346 chap_CCT_theta T-com 23.0 65 0.0017 14.5 2.8 71 35-107 325-406 (554) 44 COG4492 PheB ACT domain-contai 22.4 67 0.0017 14.4 2.9 47 55-106 101-147 (150) 45 PRK10555 aminoglycoside/multid 22.4 67 0.0017 14.4 8.0 78 27-106 98-178 (1037) 46 TIGR00904 mreB cell shape dete 20.7 53 0.0014 15.0 1.4 28 30-58 261-288 (337) 47 PRK05783 hypothetical protein; 20.7 72 0.0018 14.2 3.0 65 42-108 14-82 (84) 48 pfam02084 Bindin Bindin. 20.5 31 0.00078 16.4 0.2 39 29-67 96-140 (239) No 1 >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=100.00 E-value=4.4e-40 Score=261.75 Aligned_cols=96 Identities=61% Similarity=1.145 Sum_probs=94.5 Q ss_pred HHHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCC Q ss_conf 99999972088888998433204013215603996999999658988517899999999997099866169999977889 Q gi|254781063|r 34 NDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITFDPPW 113 (129) Q Consensus 34 ~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~~~p~W 113 (129) ++|.+|||+|||||||+||+||||||+|.|.++|+|+|.||||+|+||.++.|...|++|+..++||++|+|+++|+||| 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 CCCCCCHHHHHHCCCC Q ss_conf 8330698999960799 Q gi|254781063|r 114 TPDLMSEEAQIATGYY 129 (129) Q Consensus 114 ~~~~is~~~r~~lG~~ 129 (129) +++|||++||++|||| T Consensus 81 ~~~RMSdeArL~Lg~~ 96 (96) T TIGR02945 81 DMDRMSDEARLELGMF 96 (96) T ss_pred CCCCCCHHHHHHCCCC T ss_conf 9233677899841579 No 2 >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=100.00 E-value=4.8e-37 Score=243.51 Aligned_cols=120 Identities=40% Similarity=0.700 Sum_probs=107.0 Q ss_pred CCCCCCCCCCCCCCCC---CCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEE----CCCEEEEEEEECCCCCC Q ss_conf 3210000268988778---8565358999999997208888899843320401321560----39969999996589885 Q gi|254781063|r 9 ENNIADKIALSPESTI---PPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVE----NDYMVKILMTLTAPGCP 81 (129) Q Consensus 9 ~~~~~d~~~~~~~~~~---~~~~~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~----~~g~V~V~l~lT~~~CP 81 (129) ....+|+++..+.... ...+....+++||++||+|+|||||+|||||||||++.++ +++.|.|.||||+|||| T Consensus 48 ~g~DaDAlG~~~~~~~~~~~~~~~~~~E~~vweaLk~V~DPEIpVnIVdLGLIY~v~i~~~~~~~~~V~I~MTLTapgCp 127 (174) T TIGR03406 48 DGKDADALGKEPPPPLDLPENADGEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCG 127 (174) T ss_pred CCCCHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCCCC T ss_conf 57486661899776556788888742099999998415598887544863025799987647889779999960479998 Q ss_pred HHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCCHHHHHHCCC Q ss_conf 17899999999997099866169999977889833069899996079 Q gi|254781063|r 82 VAGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSEEAQIATGY 128 (129) Q Consensus 82 ~~~~i~~~i~~al~~~~gv~~V~V~~~~~p~W~~~~is~~~r~~lG~ 128 (129) +++.|.++++++++.++||.+|+|+++|+|||+++|||++||++||+ T Consensus 128 mg~~i~~dv~~~v~~v~~v~~v~VelV~dPpW~~dmmSeeakl~LGm 174 (174) T TIGR03406 128 MGPVLVEDVEDKVLAVPNVDEVEVELVFDPPWSREMMSEAAKLELGM 174 (174) T ss_pred CCHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCHHHCCHHHHHHCCC T ss_conf 31799999999997799966499999988998933477999987389 No 3 >COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only] Probab=99.98 E-value=9.5e-32 Score=211.69 Aligned_cols=105 Identities=49% Similarity=0.835 Sum_probs=99.3 Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEEC-CCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEE Q ss_conf 85653589999999972088888998433204013215603-99699999965898851789999999999709986616 Q gi|254781063|r 25 PPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVEN-DYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGV 103 (129) Q Consensus 25 ~~~~~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~-~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V 103 (129) .......+.++|+++|++|+|||+|+|||+|||||++.+++ +|.++|.|+||++|||+++.|.++++++++.++|++++ T Consensus 6 ~~~~~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v 85 (111) T COG2151 6 EEEAIKVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDV 85 (111) T ss_pred CCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCEEEEEEECCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEE T ss_conf 12123666999999853477966660357631079999726774699999517888882078899999999846881307 Q ss_pred EEEEEECCCCCCCCCCHHHHHHCCCC Q ss_conf 99999778898330698999960799 Q gi|254781063|r 104 EVSITFDPPWTPDLMSEEAQIATGYY 129 (129) Q Consensus 104 ~V~~~~~p~W~~~~is~~~r~~lG~~ 129 (129) +|+++|+|||+++|||++||.++|++ T Consensus 86 ~V~l~~~p~Wt~~~ms~ear~~~g~~ 111 (111) T COG2151 86 EVELTLSPPWTPDRMSEEARRALGIT 111 (111) T ss_pred EEEEEEECCCCHHHCCHHHHHHHCCC T ss_conf 99999707966554389899862789 No 4 >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=99.92 E-value=2.2e-25 Score=173.45 Aligned_cols=86 Identities=34% Similarity=0.602 Sum_probs=81.0 Q ss_pred CCCCCCC-CCEEEECCEEEEEEECCCEEEEE-EEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCCH Q ss_conf 8888899-84332040132156039969999-996589885178999999999970998661699999778898330698 Q gi|254781063|r 43 VYDPEIP-CDIFELGLIYKIDVENDYMVKIL-MTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSE 120 (129) Q Consensus 43 V~DPEl~-v~IvdLGlV~~i~i~~~g~V~V~-l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~~~p~W~~~~is~ 120 (129) |.||||| ++|+|||||++|+++++| +.|. ||+||+|||+.++|.++|++||+++.++..|+|++..+|+||.|+|+| T Consensus 1 VPDPEiPv~s~~DLGmVR~V~v~g~G-~~v~s~tPTySGCPA~~~i~~~i~~A~~~~GW~~~VeV~~~L~P~WTTdwITe 79 (152) T TIGR02159 1 VPDPEIPVVSVTDLGMVREVEVDGEG-VVVKSFTPTYSGCPALEVIRQDIRDALRALGWVEEVEVKTSLDPAWTTDWITE 79 (152) T ss_pred CCCCCCCEEEEECCCEEEEEEECCCC-EEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCC T ss_conf 98888770221106534357864794-79888745877723689999999999974789751158877189878400270 Q ss_pred HHHHHCCCC Q ss_conf 999960799 Q gi|254781063|r 121 EAQIATGYY 129 (129) Q Consensus 121 ~~r~~lG~~ 129 (129) +||.+|--| T Consensus 80 ~are~Lr~y 88 (152) T TIGR02159 80 DAREKLREY 88 (152) T ss_pred HHHHHHHHC T ss_conf 036888850 No 5 >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=99.89 E-value=6.5e-23 Score=158.63 Aligned_cols=76 Identities=45% Similarity=0.804 Sum_probs=72.9 Q ss_pred HHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 9999999972088888998433204013215603996999999658988517899999999997099866169999 Q gi|254781063|r 32 ISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSI 107 (129) Q Consensus 32 l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~ 107 (129) ++++|+++|++|+|||+|+|||+|||||+++++++|.|+|.|+||+++||+++.|.+++++++++++||.+|+|++ 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 6 >PRK11670 putative ATPase; Provisional Probab=99.65 E-value=2e-15 Score=113.71 Aligned_cols=87 Identities=8% Similarity=0.133 Sum_probs=80.3 Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEE Q ss_conf 85653589999999972088888998433204013215603996999999658988517899999999997099866169 Q gi|254781063|r 25 PPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVE 104 (129) Q Consensus 25 ~~~~~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~ 104 (129) .+..++.++++|+++|++|.||+++.|||+||||+++.++ ++.|.|.+++|+++||..+.|.+++++++++++|+.+|+ T Consensus 6 ~~~~~~~l~~~v~~~L~~v~dP~~~~~iv~lg~v~~i~i~-~~~v~i~l~l~~~~~~~~~~~~~~~~~~l~~~~~~~~v~ 84 (369) T PRK11670 6 QAKSPEALRAMVAGTLANFQHPTLKHNLTTLKALHHVAWM-DDTLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAID 84 (369) T ss_pred CCCCCHHHHHHHHHHHHCCCCCCCCCCEECCCCEEEEEEE-CCEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEE T ss_conf 7888189999999998077798999880037970169997-999999999688898879999999999998578974589 Q ss_pred EEEEECCC Q ss_conf 99997788 Q gi|254781063|r 105 VSITFDPP 112 (129) Q Consensus 105 V~~~~~p~ 112 (129) |.++.+.. T Consensus 85 ~~~~~~~~ 92 (369) T PRK11670 85 WKLSHNIA 92 (369) T ss_pred EEEEECCC T ss_conf 99974045 No 7 >KOG3381 consensus Probab=98.21 E-value=3.7e-06 Score=58.00 Aligned_cols=106 Identities=24% Similarity=0.338 Sum_probs=74.0 Q ss_pred CCCCCCCCCCC--CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEE------CC--CEEE Q ss_conf 98887986321--00002689887788565358999999997208888899843320401321560------39--9699 Q gi|254781063|r 1 MKQKNPDTENN--IADKIALSPESTIPPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVE------ND--YMVK 70 (129) Q Consensus 1 ~~~~~P~~~~~--~~d~~~~~~~~~~~~~~~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~------~~--g~V~ 70 (129) |.++||.-+.. ...+...+.+....+ .....+.+.+.++.+.|||-|.++-+|+.|+.-.|+ ++ ..|+ T Consensus 4 l~N~np~v~~~~~~~~r~~~s~~d~~~~--~~~~~~~~~dlir~I~DPEhP~TLeqL~VV~ee~v~V~d~~~~~~~s~V~ 81 (161) T KOG3381 4 LQNENPLVYPTRSRERRVTASEEDELLP--DSEDAEEIFDLIRDIRDPEHPLTLEQLNVVSEEGVEVDDPNVGDEESYVR 81 (161) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHCCCCCCCCCCHHHCCCEEECCEEEECCCCCCCCEEEE T ss_conf 4348962024445441025556664458--60367899999861689888865887062422056764577788513899 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHH-HCCCCCCEEEEEEE Q ss_conf 999965898851789999999999-70998661699999 Q gi|254781063|r 71 ILMTLTAPGCPVAGDMPKWIENAV-GAVEGISGVEVSIT 108 (129) Q Consensus 71 V~l~lT~~~CP~~~~i~~~i~~al-~~~~gv~~V~V~~~ 108 (129) |.+|+|.|+|.++..|---|+-+| +.++.-..|.|.++ T Consensus 82 i~ftPTipHCSmaTlIGLcIrVkl~RsLp~rfkvdV~I~ 120 (161) T KOG3381 82 ITFTPTIPHCSMATLIGLCIRVKLLRSLPPRFKVDVYIK 120 (161) T ss_pred EEECCCCCCCHHHHHHHHEEEEEEEECCCCCEEEEEEEC T ss_conf 995368875227766422026655304887426899975 No 8 >COG5133 Uncharacterized conserved protein [Function unknown] Probab=96.94 E-value=0.0015 Score=42.30 Aligned_cols=78 Identities=24% Similarity=0.309 Sum_probs=60.6 Q ss_pred HHHHHHHHHHHCCCCCCCCCCEEEECCEEE--EEEEC----C--CEEEEEEEECCCCCCHHHHHHHHHHHHHHCC-CCCC Q ss_conf 899999999720888889984332040132--15603----9--9699999965898851789999999999709-9866 Q gi|254781063|r 31 RISNDIIAALKTVYDPEIPCDIFELGLIYK--IDVEN----D--YMVKILMTLTAPGCPVAGDMPKWIENAVGAV-EGIS 101 (129) Q Consensus 31 ~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~--i~i~~----~--g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~-~gv~ 101 (129) ...++|++.++.+.|||-|.++-.||.|.- |.+.+ + .-|+|.+++|.|.|.++..|---|+..+++. +.-. 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 EEEEEEE Q ss_conf 1699999 Q gi|254781063|r 102 GVEVSIT 108 (129) Q Consensus 102 ~V~V~~~ 108 (129) .|.|.+. T Consensus 134 ~v~v~ik 140 (181) T COG5133 134 HVQVHIK 140 (181) T ss_pred EEEEEEE T ss_conf 6899981 No 9 >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=94.15 E-value=0.3 Score=28.51 Aligned_cols=73 Identities=14% Similarity=0.278 Sum_probs=57.3 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHH-HHHHHHHHHHHC-CCCCCEEE Q ss_conf 35899999999720888889984332040132156039969999996589885178-999999999970-99866169 Q gi|254781063|r 29 LERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAG-DMPKWIENAVGA-VEGISGVE 104 (129) Q Consensus 29 ~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~-~i~~~i~~al~~-~~gv~~V~ 104 (129) ..+++++|.+.|..=+-|-|.- +=|-|.=+.|+++|.|.+.|.=.+.+||+.. -|+..|+++|+. +|++..|. T Consensus 103 d~~l~~~i~~vl~~ei~P~l~~---hGG~v~lv~i~~~~~v~~~~~G~C~gC~~s~~Tlk~gvE~~l~~~~Pei~~V~ 177 (190) T TIGR03341 103 DAPLEERINYVLQSEINPQLAS---HGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVR 177 (190) T ss_pred CCCHHHHHHHHHHHHCCHHHHH---CCCEEEEEEEECCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEE T ss_conf 7689999999998602935763---69989999990797899995754899836899999999999998698753588 No 10 >PRK11190 putative DNA uptake protein; Provisional Probab=88.79 E-value=2.2 Score=23.36 Aligned_cols=73 Identities=15% Similarity=0.300 Sum_probs=55.2 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHH-HHHHHHHHHH-HCCCC-CCEEE Q ss_conf 35899999999720888889984332040132156039969999996589885178-9999999999-70998-66169 Q gi|254781063|r 29 LERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAG-DMPKWIENAV-GAVEG-ISGVE 104 (129) Q Consensus 29 ~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~-~i~~~i~~al-~~~~g-v~~V~ 104 (129) ..+++++|...|.+=+-|-|..+ =|-|.=+.|.++|.+.|.|.=.+.|||+.. -++..|+..| +.+|| ++.|. T Consensus 104 d~~l~~~i~~vl~~~i~P~l~~h---GG~v~l~~i~~~~~~~~~~~G~C~gC~~~~~Tlk~gvE~~l~~~~P~ei~~V~ 179 (192) T PRK11190 104 DAPLMERVEYVLQSQINPQLAGH---GGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVR 179 (192) T ss_pred CCCHHHHHHHHHHHHCCHHHHHC---CCEEEEEEECCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCEEE T ss_conf 75599999999987319567637---98799999827988999966657898688999999999999986978670578 No 11 >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=84.68 E-value=0.43 Score=27.56 Aligned_cols=28 Identities=29% Similarity=0.720 Sum_probs=21.7 Q ss_pred ECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEE Q ss_conf 6589885178999999999970998661699999 Q gi|254781063|r 75 LTAPGCPVAGDMPKWIENAVGAVEGISGVEVSIT 108 (129) Q Consensus 75 lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~ 108 (129) +|+..||.. |+.||.+++||..++|.+- T Consensus 32 MtC~aCPiT------V~~AL~kVdGV~Kaev~f~ 59 (92) T TIGR02052 32 MTCAACPIT------VKTALKKVDGVEKAEVDFK 59 (92) T ss_pred CCCCCCCHH------HHHHCCCCCCCCCEEEECC T ss_conf 866678501------7740643888000000121 No 12 >COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones] Probab=74.05 E-value=8.1 Score=19.91 Aligned_cols=74 Identities=16% Similarity=0.273 Sum_probs=50.1 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEEC-CCEEEEEEEECCCCCCHHH-HHHHHHHHHHHCC-CCCCEEEE Q ss_conf 3589999999972088888998433204013215603-9969999996589885178-9999999999709-98661699 Q gi|254781063|r 29 LERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVEN-DYMVKILMTLTAPGCPVAG-DMPKWIENAVGAV-EGISGVEV 105 (129) Q Consensus 29 ~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~-~g~V~V~l~lT~~~CP~~~-~i~~~i~~al~~~-~gv~~V~V 105 (129) ...+.++|.++|.+=+-|-+-. |=|=|.=+.+++ +|.|.+.+-=.+.+||... .++..|++.|+.. +++..|.. T Consensus 7 ~~~~~e~v~~~l~~~irP~l~~---dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~ 83 (93) T COG0694 7 DAELLERVEEVLDEKIRPQLAM---DGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQ 83 (93) T ss_pred CHHHHHHHHHHHHHCCCCEEEE---CCCEEEEEEEECCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEE T ss_conf 2899999999998445710210---4980899987568986999967757899662899999999999966886516997 No 13 >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=69.57 E-value=10 Score=19.29 Aligned_cols=61 Identities=20% Similarity=0.235 Sum_probs=38.3 Q ss_pred HHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHHH-HHHHHHHHHH-CCCCCCEE Q ss_conf 997208888899843320401321560399699999965898851789-9999999997-09986616 Q gi|254781063|r 38 AALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGD-MPKWIENAVG-AVEGISGV 103 (129) Q Consensus 38 eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~-i~~~i~~al~-~~~gv~~V 103 (129) ++|.. +-|-+.. |=|-|.=+.++ ++.|.|.|.=.+.+||+... +..-|++.|+ .++.+..| T Consensus 3 ~~le~-IRP~l~~---dGGdvelv~v~-~~~v~v~l~GaC~gC~~s~~Tlk~~Ie~~L~~~vpev~~V 65 (68) T pfam01106 3 EVIDE-IRPMLQR---DGGDIELVDVD-GDIVKVRLQGACGGCMSSTMTLKGGIERKLRERLGESLRV 65 (68) T ss_pred HHHHH-HCHHHHH---CCCCEEEEEEE-CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEE T ss_conf 79987-5648885---59928999986-9999999812898981089999999999999878997669 No 14 >TIGR02187 GlrX_arch Glutaredoxin-like domain protein; InterPro: IPR011903 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different.. Probab=66.77 E-value=6.2 Score=20.62 Aligned_cols=30 Identities=27% Similarity=0.359 Sum_probs=23.7 Q ss_pred ECCCEEEEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 039969999996589885178999999999 Q gi|254781063|r 64 ENDYMVKILMTLTAPGCPVAGDMPKWIENA 93 (129) Q Consensus 64 ~~~g~V~V~l~lT~~~CP~~~~i~~~i~~a 93 (129) +..=.+.|-+|+|+|=||.+-.|+...--+ T Consensus 146 ~~~v~I~vfVTPtCPYCP~AV~mAH~fA~~ 175 (237) T TIGR02187 146 DEPVRIEVFVTPTCPYCPRAVLMAHKFALA 175 (237) T ss_pred CCCEEEEEEEECCCCCHHHHHHHHHHHHHH T ss_conf 983599999856899725799999999983 No 15 >TIGR00411 redox_disulf_1 redox-active disulfide protein 1; InterPro: IPR004502 This group of proteins includes thioredoxins, glutaredoxins, protein-disulphide isomerases, and others, some of which have several such domains. The sequence of proteins in this group at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although overall the sequence seems closer to thioredoxins. Proteins may be involved in a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis. Probab=65.92 E-value=2.5 Score=23.02 Aligned_cols=33 Identities=18% Similarity=0.375 Sum_probs=19.7 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCE Q ss_conf 999996589885178999999999970998661 Q gi|254781063|r 70 KILMTLTAPGCPVAGDMPKWIENAVGAVEGISG 102 (129) Q Consensus 70 ~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~ 102 (129) ++-=-+|+|.||.+....+++.......-.+.. T Consensus 4 ~lFTSPtCPyCP~A~~VV~~vakE~gd~~~v~~ 36 (82) T TIGR00411 4 ELFTSPTCPYCPKAEKVVEEVAKEEGDLVEVEK 36 (82) T ss_pred EEECCCCCCCCCCHHHHHHHHHCCCCCEEEEEE T ss_conf 551188768885436889887405897343222 No 16 >PRK10503 multidrug efflux system subunit MdtB; Provisional Probab=61.83 E-value=15 Score=18.38 Aligned_cols=32 Identities=19% Similarity=0.158 Sum_probs=12.5 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHCCCCCCEEE Q ss_conf 99658988517899999999997099866169 Q gi|254781063|r 73 MTLTAPGCPVAGDMPKWIENAVGAVEGISGVE 104 (129) Q Consensus 73 l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~ 104 (129) +.+..+.--....+.+++++++++.+|+.+|+ T Consensus 677 i~l~g~d~~~L~~~a~~l~~~L~~~~gv~~V~ 708 (1040) T PRK10503 677 FTLQATSLDALSTWVPKLMNKLQQLPQLSDVS 708 (1040) T ss_pred EEEECCCHHHHHHHHHHHHHHHHCCCCCEEEE T ss_conf 99947999999999999999986599935632 No 17 >pfam07350 DUF1479 Protein of unknown function (DUF1479). This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length. Members of this family are often known as YbiU. The function of this family is unknown. Probab=50.91 E-value=22 Score=17.28 Aligned_cols=91 Identities=19% Similarity=0.183 Sum_probs=56.5 Q ss_pred HHHHCCCCCCCC-CCEEEECCEEEEEEE--CCCEEEEEEEECCCCCCH-HHHHHHHHHHHHHCCCC--CCEEE--EEEEE Q ss_conf 997208888899-843320401321560--399699999965898851-78999999999970998--66169--99997 Q gi|254781063|r 38 AALKTVYDPEIP-CDIFELGLIYKIDVE--NDYMVKILMTLTAPGCPV-AGDMPKWIENAVGAVEG--ISGVE--VSITF 109 (129) Q Consensus 38 eaL~~V~DPEl~-v~IvdLGlV~~i~i~--~~g~V~V~l~lT~~~CP~-~~~i~~~i~~al~~~~g--v~~V~--V~~~~ 109 (129) +.|-.|.+=+=| .-.-..-+|..|.-. +++.-.|...+.+|.|+. ..++..+-+..++..++ ...-. -+..| T Consensus 309 ~~mv~iP~v~pGD~V~WHcD~iH~V~~~h~g~~~ssV~Yipa~Pl~~~N~~Yl~~Qr~aFl~G~~ppDF~~~~~~gE~~~ 388 (408) T pfam07350 309 ETMVSIPDVEPGDYVFWHCDLIHAVDPEHNGKGDSSVMYIPAAPLCETNAAYLARQREAFLRGSPPPDFPSDGGGGESEF 388 (408) T ss_pred CCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC T ss_conf 25333788799986787677544446556888866048851698847899999999999866999888887899754476 Q ss_pred CCCCCCCCCCHH-HHHHCCC Q ss_conf 788983306989-9996079 Q gi|254781063|r 110 DPPWTPDLMSEE-AQIATGY 128 (129) Q Consensus 110 ~p~W~~~~is~~-~r~~lG~ 128 (129) .--.+.+.+++. ||.+||+ T Consensus 389 ~gr~~~~dl~~~~G~ramGl 408 (408) T pfam07350 389 AGRATPEDLTEHGGLRAMGL 408 (408) T ss_pred CCCCCHHHHCCHHHHHHCCC T ss_conf 89889667211002653088 No 18 >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=50.63 E-value=23 Score=17.25 Aligned_cols=69 Identities=13% Similarity=0.166 Sum_probs=48.8 Q ss_pred CCHHHHHHHHHHHHHCCCCCCCC-----CCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHC Q ss_conf 65358999999997208888899-----84332040132156039969999996589885178999999999970 Q gi|254781063|r 27 EDLERISNDIIAALKTVYDPEIP-----CDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGA 96 (129) Q Consensus 27 ~~~~~l~~~V~eaL~~V~DPEl~-----v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~ 96 (129) .......+++.+.|+.-++=+.- +++--.|.--.+.++ ++.|.+.+.|..-.-|+...|.++|.+.|.. T Consensus 12 ~~ar~~ae~la~~l~~~~g~~~~w~gd~l~F~~~Gv~G~l~v~-~~~v~v~i~Lg~ll~~fkg~Ie~eIe~~LD~ 85 (87) T pfam09650 12 DQARAAAEKLAEKLAEEYGLECEWEGDTLSFKRSGVKGTLHVT-EDKIRVDLKLGFLLSAFKGRIEQEIEKNLDK 85 (87) T ss_pred HHHHHHHHHHHHHHHHHHCCEEEEECCEEEEEECCCCEEEEEC-CCEEEEEEECHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999859751883689999717754699982-7779999992888887676899999998872 No 19 >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=50.33 E-value=23 Score=17.23 Aligned_cols=37 Identities=14% Similarity=0.224 Sum_probs=20.7 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEE Q ss_conf 9999996589885178999999999970998661699 Q gi|254781063|r 69 VKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEV 105 (129) Q Consensus 69 V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V 105 (129) ..|.+.+..+.--....+++++++.+++.+|+.+++- T Consensus 671 ~~i~i~l~G~d~~~L~~~a~~v~~~L~~~~gv~~v~~ 707 (1021) T pfam00873 671 SDLQVKIFGDGLDALDEARNQILAALAQLPGLADVRP 707 (1021) T ss_pred EEEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 2799994799999999999999999835998178754 No 20 >cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri Probab=48.95 E-value=22 Score=17.26 Aligned_cols=39 Identities=21% Similarity=0.252 Sum_probs=26.3 Q ss_pred EEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEE Q ss_conf 699999965898851789999999999709986616999997 Q gi|254781063|r 68 MVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITF 109 (129) Q Consensus 68 ~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~~ 109 (129) ++++-++||.|.||..-...+.+. +. -+.+..--|+... T Consensus 2 ~i~vfvS~sCp~CP~~v~~~~~~a--~~-n~~I~~~~id~~~ 40 (67) T cd02973 2 NIEVFVSPTCPYCPDAVQAANRIA--AL-NPNISAEMIDAAE 40 (67) T ss_pred EEEEEECCCCCCCHHHHHHHHHHH--HH-CCCEEEEEEECCC T ss_conf 699997699999789999999999--76-8980899999954 No 21 >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=45.96 E-value=27 Score=16.81 Aligned_cols=28 Identities=18% Similarity=0.413 Sum_probs=22.9 Q ss_pred HHHHHHHHHHHHHCCCCCCEEEEEEEEC Q ss_conf 7899999999997099866169999977 Q gi|254781063|r 83 AGDMPKWIENAVGAVEGISGVEVSITFD 110 (129) Q Consensus 83 ~~~i~~~i~~al~~~~gv~~V~V~~~~~ 110 (129) -..+..+-++.|..+.||.+|.|.+.+. T Consensus 65 E~~~e~~Lk~~Le~I~GVg~V~V~vnL~ 92 (193) T TIGR02830 65 EKEYENELKEILEKIEGVGDVTVMVNLD 92 (193) T ss_pred HHHHHHHHHHHHHHHCCCCEEEEEEEEC T ss_conf 9999999999864203756148999965 No 22 >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=41.94 E-value=22 Score=17.27 Aligned_cols=34 Identities=32% Similarity=0.582 Sum_probs=24.1 Q ss_pred HHHHHHHHHCCCCCCEEEEE-------EEECCCCCCCCCCH Q ss_conf 99999999709986616999-------99778898330698 Q gi|254781063|r 87 PKWIENAVGAVEGISGVEVS-------ITFDPPWTPDLMSE 120 (129) Q Consensus 87 ~~~i~~al~~~~gv~~V~V~-------~~~~p~W~~~~is~ 120 (129) +..|+++|++++||.+++|+ +.|++.++++.+-. T Consensus 13 ~~~Ie~~l~~~~GV~~~~vn~~~~~v~V~~~~~~~~~~i~~ 53 (63) T cd00371 13 VSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLE 53 (63) T ss_pred HHHHHHHHCCCCCCEEEEEECCCCEEEEEECCCCCHHHHHH T ss_conf 99999997079995799998889999999899999999999 No 23 >pfam00403 HMA Heavy-metal-associated domain. Probab=40.46 E-value=27 Score=16.77 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=18.4 Q ss_pred HHHHHHHHHHCCCCCCEEEEEEE Q ss_conf 99999999970998661699999 Q gi|254781063|r 86 MPKWIENAVGAVEGISGVEVSIT 108 (129) Q Consensus 86 i~~~i~~al~~~~gv~~V~V~~~ 108 (129) -...|+++|.+++||.++.|++. T Consensus 12 C~~~Ie~~l~~~~GV~~v~v~~~ 34 (62) T pfam00403 12 CAKKVEKALSKLPGVSSVSVDLE 34 (62) T ss_pred HHHHHHHHHHCCCCCEEEEEECC T ss_conf 99999999855999549999878 No 24 >COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism] Probab=39.40 E-value=30 Score=16.54 Aligned_cols=35 Identities=23% Similarity=0.448 Sum_probs=25.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEE Q ss_conf 99996589885178999999999970998661699999 Q gi|254781063|r 71 ILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSIT 108 (129) Q Consensus 71 V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~ 108 (129) ..+......|... ...++++|..++||.+|+|++. T Consensus 4 ~~l~v~~MtC~~C---~~~V~~al~~v~gv~~v~v~l~ 38 (71) T COG2608 4 TTLKVEGMTCGHC---VKTVEKALEEVDGVASVDVDLE 38 (71) T ss_pred EEEEECCCCCHHH---HHHHHHHHHCCCCCEEEEEECC T ss_conf 6997779294899---9999998843898239999522 No 25 >PRK00435 ef1B elongation factor 1-beta; Validated Probab=37.93 E-value=36 Score=16.06 Aligned_cols=72 Identities=24% Similarity=0.307 Sum_probs=43.3 Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEE Q ss_conf 88565358999999997208888899843320401321560399699999965898851789999999999709986616 Q gi|254781063|r 24 IPPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGV 103 (129) Q Consensus 24 ~~~~~~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V 103 (129) .+..+.+.++++|.+.|..-+ . ++-+..--+ .-|...+.+....+. .....+.+..++.++.||.++ T Consensus 14 s~evDle~L~e~ik~~l~~~~------~---i~~~e~ePi-AFGLkaL~v~vv~~D---~eG~tD~~Ee~~~~iegV~sv 80 (88) T PRK00435 14 SPEVDLDELKEKIKEKLPEGY------E---INRIEEEPI-AFGLKALKLYVIMPD---EEGGTDPVEEAFAAVEGVESV 80 (88) T ss_pred CCCCCHHHHHHHHHHHCCCCC------E---EEEEEEEEE-ECCCEEEEEEEEEEC---CCCCCHHHHHHHHCCCCCCEE T ss_conf 988699999999997575876------4---746678845-645232799999975---886837999998546896579 Q ss_pred EEEEE Q ss_conf 99999 Q gi|254781063|r 104 EVSIT 108 (129) Q Consensus 104 ~V~~~ 108 (129) +|.-+ T Consensus 81 eV~~v 85 (88) T PRK00435 81 EVEEV 85 (88) T ss_pred EEEEE T ss_conf 99988 No 26 >PRK10775 cell division protein FtsQ; Provisional Probab=37.39 E-value=35 Score=16.10 Aligned_cols=23 Identities=17% Similarity=0.202 Sum_probs=16.8 Q ss_pred HHHHHHHHHCCCCCCEEEEEEEE Q ss_conf 99999999709986616999997 Q gi|254781063|r 87 PKWIENAVGAVEGISGVEVSITF 109 (129) Q Consensus 87 ~~~i~~al~~~~gv~~V~V~~~~ 109 (129) .++++++++++|+|.+|.|+-.| T Consensus 93 l~~iq~~le~lPWV~~asVRR~W 115 (274) T PRK10775 93 VNIIQQQIERLPWIKQVSVRKQW 115 (274) T ss_pred HHHHHHHHHHCCCEEEEEEEEEC T ss_conf 99999999849993378899848 No 27 >KOG4656 consensus Probab=35.10 E-value=40 Score=15.78 Aligned_cols=24 Identities=25% Similarity=0.396 Sum_probs=13.5 Q ss_pred HHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 899999999997099866169999 Q gi|254781063|r 84 GDMPKWIENAVGAVEGISGVEVSI 107 (129) Q Consensus 84 ~~i~~~i~~al~~~~gv~~V~V~~ 107 (129) +.-..+++.+|+.++|+.+|+|.+ T Consensus 18 escvnavk~~L~~V~Gi~~vevdl 41 (247) T KOG4656 18 ESCVNAVKACLKGVPGINSVEVDL 41 (247) T ss_pred HHHHHHHHHHHCCCCCCCEEEEEH T ss_conf 778899999860688710478771 No 28 >pfam03612 EIIBC-GUT_N Sorbitol phosphotransferase enzyme II N-terminus. Probab=35.04 E-value=18 Score=17.89 Aligned_cols=75 Identities=16% Similarity=0.165 Sum_probs=53.0 Q ss_pred HHHHHHHHHHH---------HCCCCCCCCCCEEEECCEEEEEEEC-CCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCC Q ss_conf 58999999997---------2088888998433204013215603-9969999996589885178999999999970998 Q gi|254781063|r 30 ERISNDIIAAL---------KTVYDPEIPCDIFELGLIYKIDVEN-DYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEG 99 (129) Q Consensus 30 ~~l~~~V~eaL---------~~V~DPEl~v~IvdLGlV~~i~i~~-~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~g 99 (129) .++.++|-+.. ..+.|-|+..-|+|.|---++-+-. .+.-+|.+.+|.+.-|++..|.++|-- .+ T Consensus 36 ~~i~~kiaeltG~e~vdgFk~~~p~eei~~~viDCGGTlRcGiYPkk~IpTini~ptg~sGPLA~~I~ediyV-----S~ 110 (182) T pfam03612 36 PPVVDKIAELTGAEAVDGFKTSIPDEEIALVVIDCGGTLRCGLYPKKRIPTINVLPTGKSGPLAKFITEDIYV-----SG 110 (182) T ss_pred CHHHHHHHHHHCCEECCCCCCCCCHHHEEEEEECCCCEEEECCCCCCCCCEEEECCCCCCCHHHHHHCCCCEE-----EE T ss_conf 8799999997698033670689983786999990687057423345788627632489985066662026447-----40 Q ss_pred CCEEEEEEEE Q ss_conf 6616999997 Q gi|254781063|r 100 ISGVEVSITF 109 (129) Q Consensus 100 v~~V~V~~~~ 109 (129) |..-.|++.. T Consensus 111 V~~~~I~l~d 120 (182) T pfam03612 111 VTPEQISLVD 120 (182) T ss_pred CCHHHEEECC T ss_conf 3677868825 No 29 >cd00958 DhnA Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs) found in bacteria and archaea. Catalysis of the enzymes proceeds via a Schiff-base mechanism like other class I aldolases, although this subfamily is clearly divergent based on sequence similarity to other class I and class II (metal dependent) aldolase subfamilies. Probab=33.25 E-value=42 Score=15.60 Aligned_cols=89 Identities=16% Similarity=0.157 Sum_probs=59.4 Q ss_pred HHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCC--C---CHHHHHHHHHHHHHHCCCCCCEEEEEEEE Q ss_conf 999997208888899843320401321560399699999965898--8---51789999999999709986616999997 Q gi|254781063|r 35 DIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPG--C---PVAGDMPKWIENAVGAVEGISGVEVSITF 109 (129) Q Consensus 35 ~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~--C---P~~~~i~~~i~~al~~~~gv~~V~V~~~~ 109 (129) .....++.+.+....-=+...|+++...-.-.+.+.+.+.++... . +....+.-.+++|++- |...|.+.+-| T Consensus 22 d~~~~i~~~~~~g~dai~~~~G~~~~~~~~~~~~~~li~~ls~~t~~~~~~~~~~~l~~sVeeAvrl--GAdaV~~~v~~ 99 (235) T cd00958 22 DPEETVKLAAEGGADAVALTKGIARAYGREYAGDIPLIVKLNGSTSLSPKDDNDKVLVASVEDAVRL--GADAVGVTVYV 99 (235) T ss_pred CHHHHHHHHHHCCCCEEEECHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCHHHHHCCHHHHHHC--CCCEEEEEEEC T ss_conf 9899999998649999998888997515321578766999646764578885177665169999835--55679999868 Q ss_pred CCCCCCCCCCHHHHHH Q ss_conf 7889833069899996 Q gi|254781063|r 110 DPPWTPDLMSEEAQIA 125 (129) Q Consensus 110 ~p~W~~~~is~~~r~~ 125 (129) --+-..+|+.+-+|.. T Consensus 100 Gs~~E~~~l~~l~~v~ 115 (235) T cd00958 100 GSEEEREMLEELARVA 115 (235) T ss_pred CCCHHHHHHHHHHHHH T ss_conf 9816899999999999 No 30 >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=31.89 E-value=45 Score=15.46 Aligned_cols=48 Identities=17% Similarity=0.264 Sum_probs=32.9 Q ss_pred EEEECCCEEEEEEEECCCCC-CHHHHHHHHHHHHHHCCCCCCEEEEEEEE Q ss_conf 15603996999999658988-51789999999999709986616999997 Q gi|254781063|r 61 IDVENDYMVKILMTLTAPGC-PVAGDMPKWIENAVGAVEGISGVEVSITF 109 (129) Q Consensus 61 i~i~~~g~V~V~l~lT~~~C-P~~~~i~~~i~~al~~~~gv~~V~V~~~~ 109 (129) |.+++..+.-|.+-|++.=. =++..|.+-|++.|..+ ||+++.|+++. T Consensus 19 v~v~pa~~~Gi~~~l~S~VkkQFg~~I~~~vkeTL~~l-Gv~~a~v~v~D 67 (95) T TIGR01608 19 VSVEPAAQVGIEIDLSSSVKKQFGDEIEKVVKETLKEL-GVENAVVKVVD 67 (95) T ss_pred EEECCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEEEC T ss_conf 77324888847887520177775799999999989865-94435688724 No 31 >pfam05768 DUF836 Glutaredoxin-like domain (DUF836). These proteins are related to the pfam00462 family. Probab=29.51 E-value=49 Score=15.22 Aligned_cols=40 Identities=18% Similarity=0.244 Sum_probs=25.1 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCC Q ss_conf 99658988517899999999997099866169999977889 Q gi|254781063|r 73 MTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITFDPPW 113 (129) Q Consensus 73 l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~~~p~W 113 (129) .-.|.++|++.+....-+...... .++.=..|++.-++.| T Consensus 3 ~Ly~r~gChLCe~a~~~L~~~~~~-~~~~~~~vdI~~d~~L 42 (76) T pfam05768 3 TLYGKPGCHLCEGAKEVLAELEAA-LGFDLERIDIDDDEEL 42 (76) T ss_pred EEEECCCCCHHHHHHHHHHHHHHC-CCCEEEEEECCCCHHH T ss_conf 999189957389999999987534-5955999988899899 No 32 >PRK07226 fructose-bisphosphate aldolase; Provisional Probab=28.65 E-value=45 Score=15.42 Aligned_cols=89 Identities=17% Similarity=0.224 Sum_probs=56.7 Q ss_pred HHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCC--C--CHHHHHHHHHHHHHHCCCCCCEEEEEEEEC Q ss_conf 999997208888899843320401321560399699999965898--8--517899999999997099866169999977 Q gi|254781063|r 35 DIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPG--C--PVAGDMPKWIENAVGAVEGISGVEVSITFD 110 (129) Q Consensus 35 ~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~--C--P~~~~i~~~i~~al~~~~gv~~V~V~~~~~ 110 (129) .....++.+.+-...-=+..+|+++...-.-.+.+-+.+.++... . +....+...+++|++ -|...|.+.+-|- T Consensus 40 d~~~~i~~~~~~g~dai~~~~G~~~~~~~~~~~~~~lil~l~~~t~~~~~~~~~~~~~sVeeAvr--lGAdaV~~~v~~G 117 (266) T PRK07226 40 DMRETVNKVAEGGADAVLMHKGLARHGHRGYGRDVGLIVHLSASTSLSPDPNDKVLVGTVEDAIK--LGADAVSVHVNVG 117 (266) T ss_pred CHHHHHHHHHHCCCCEEEECHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCHHEEECCHHHHHH--CCCCEEEEEEECC T ss_conf 99999999986399999967677864352215788749994377314788640101214999985--5877899985479 Q ss_pred CCCCCCCCCHHHHHH Q ss_conf 889833069899996 Q gi|254781063|r 111 PPWTPDLMSEEAQIA 125 (129) Q Consensus 111 p~W~~~~is~~~r~~ 125 (129) -+-..+++.+-++.. T Consensus 118 s~~E~~~l~~l~~l~ 132 (266) T PRK07226 118 SETEAEMLEDLGRIA 132 (266) T ss_pred CCCHHHHHHHHHHHH T ss_conf 983799999999999 No 33 >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=27.08 E-value=38 Score=15.88 Aligned_cols=22 Identities=41% Similarity=0.607 Sum_probs=19.1 Q ss_pred HHHHHHHHHCCCCCCEEEEEEE Q ss_conf 9999999970998661699999 Q gi|254781063|r 87 PKWIENAVGAVEGISGVEVSIT 108 (129) Q Consensus 87 ~~~i~~al~~~~gv~~V~V~~~ 108 (129) .+.|+.++.+++||..|.|++. T Consensus 15 V~~iE~~VGel~GVs~v~v~L~ 36 (66) T TIGR00003 15 VDKIEKFVGELEGVSAVKVQLE 36 (66) T ss_pred HHHHHHHCCEECCCEEEEEEEE T ss_conf 7765410470037306766763 No 34 >pfam09129 Chol_subst-bind Cholesterol oxidase, substrate-binding. The substrate-binding domain found in Cholesterol oxidase is composed of an eight-stranded mixed beta-pleated sheet and six alpha-helices. This domain is positioned over the isoalloxazine ring system of the FAD cofactor bound by FAD_binding_4 (PF:PF01565) and forms the roof of the active site cavity, allowing for catalysis of oxidation and isomerisation of cholesterol to cholest-4-en-3-one. Probab=25.62 E-value=58 Score=14.80 Aligned_cols=43 Identities=19% Similarity=0.224 Sum_probs=32.9 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCC Q ss_conf 9996589885178999999999970998661699999778898 Q gi|254781063|r 72 LMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITFDPPWT 114 (129) Q Consensus 72 ~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~~~p~W~ 114 (129) .=.||-||-|.+..+-.++++-+.+...-....|+.-|+.-|. T Consensus 222 ldiLtlPGTp~a~~FyrEiEqwm~~~y~g~yAtvRpEWSKGWa 264 (321) T pfam09129 222 LDILGVPGTPGANEFYREMEQWMRSHYSGDYATFRPEWSKGWG 264 (321) T ss_pred EEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCC T ss_conf 5323688984577899999999983257876336312035644 No 35 >PRK08744 consensus Probab=25.45 E-value=58 Score=14.78 Aligned_cols=72 Identities=11% Similarity=0.248 Sum_probs=42.3 Q ss_pred HHHHHHHCCCCCCC-CCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCC Q ss_conf 99999720888889-98433204013215603996999999658988517899999999997099866169999977889 Q gi|254781063|r 35 DIIAALKTVYDPEI-PCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITFDPPW 113 (129) Q Consensus 35 ~V~eaL~~V~DPEl-~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~~~p~W 113 (129) ..++.|+.+..|.- |..=|.+.+++... .+.+...+.|..... -...++...+|++++|+.+ |++.++||| T Consensus 1123 ~~~~~l~~~l~~~~~g~~~v~~~~~~~~~---~~~~~~~l~l~~~~~---v~~~~~l~~~l~~~~g~~~--v~~~y~~~~ 1194 (1195) T PRK08744 1123 QAWSRIDALLAKHRPGKTPLRLDLLLRSP---SGGVAGMLDLNGSHS---VRIDQQLMDSLRADPAVRT--LKVKYSPPW 1194 (1195) T ss_pred HHHHHHHHHHHHCCCCCCCEEEEEEEECC---CCCEEEEEECCCCCC---CCCCHHHHHHHHHCCCCCE--EEEEECCCC T ss_conf 58999999998338999864899999627---887579997388575---3789999999985328552--899848999 Q ss_pred C Q ss_conf 8 Q gi|254781063|r 114 T 114 (129) Q Consensus 114 ~ 114 (129) . T Consensus 1195 ~ 1195 (1195) T PRK08744 1195 A 1195 (1195) T ss_pred C T ss_conf 9 No 36 >COG3963 Phospholipid N-methyltransferase [Lipid metabolism] Probab=24.88 E-value=46 Score=15.37 Aligned_cols=25 Identities=28% Similarity=0.367 Sum_probs=19.5 Q ss_pred HHHHHHCCCCCCCCCCEEEECCEEE Q ss_conf 9999720888889984332040132 Q gi|254781063|r 36 IIAALKTVYDPEIPCDIFELGLIYK 60 (129) Q Consensus 36 V~eaL~~V~DPEl~v~IvdLGlV~~ 60 (129) .-+++..++|||-|..|.|||==.+ T Consensus 36 lA~~M~s~I~pesglpVlElGPGTG 60 (194) T COG3963 36 LARKMASVIDPESGLPVLELGPGTG 60 (194) T ss_pred HHHHHHHCCCCCCCCEEEEECCCCC T ss_conf 9999984348445976477769866 No 37 >COG3732 SrlE Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism] Probab=24.34 E-value=51 Score=15.10 Aligned_cols=61 Identities=20% Similarity=0.239 Sum_probs=47.0 Q ss_pred CCCCCCCEEEECCEEEEEEEC-CCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEEC Q ss_conf 888998433204013215603-996999999658988517899999999997099866169999977 Q gi|254781063|r 45 DPEIPCDIFELGLIYKIDVEN-DYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITFD 110 (129) Q Consensus 45 DPEl~v~IvdLGlV~~i~i~~-~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~~~ 110 (129) +-|+..-++|.|---++-+-. .+.-+|.+.+|.+.-|+++.|.+|+- +.||+.-++.++-. T Consensus 61 e~ei~~vvidCgGt~RcGvYP~kripTini~~t~~sGPLaq~I~Ediy-----VSgVk~~~i~l~d~ 122 (328) T COG3732 61 EEEIGCVVIDCGGTLRCGVYPKKRIPTINILPTGKSGPLAQFIVEDIY-----VSGVKPENITLVDG 122 (328) T ss_pred CCEEEEEEEECCCEEEECCCCCCCCCEEEECCCCCCCCHHHHHHHHCE-----ECCCCHHHEEEECC T ss_conf 642689999058704632434467862662358888607887644301-----10356788587247 No 38 >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=23.56 E-value=63 Score=14.56 Aligned_cols=45 Identities=24% Similarity=0.308 Sum_probs=29.5 Q ss_pred EECCCEEEEEEEECC-CCCC---HHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 603996999999658-9885---17899999999997099866169999 Q gi|254781063|r 63 VENDYMVKILMTLTA-PGCP---VAGDMPKWIENAVGAVEGISGVEVSI 107 (129) Q Consensus 63 i~~~g~V~V~l~lT~-~~CP---~~~~i~~~i~~al~~~~gv~~V~V~~ 107 (129) +++++.+.|++.+.. .|+| .+..+++.++.+++...|++-.+|++ T Consensus 54 ~~~~~~v~v~l~v~v~YG~~i~~v~~~iq~~V~~~v~~mtgl~V~~VnV 102 (108) T pfam03780 54 VGEEGQVAIDLYVIVEYGVNIPEVAKNIQEKVKYAVENMTGLEVSEVNV 102 (108) T ss_pred ECCCCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCEEEEEEE T ss_conf 8679869999999997799889999999999999999987986789999 No 39 >pfam08478 POTRA_1 POTRA domain, FtsQ-type. FtsQ/DivIB bacterial division proteins (pfam03799) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts. Probab=23.55 E-value=63 Score=14.56 Aligned_cols=31 Identities=16% Similarity=0.110 Sum_probs=23.7 Q ss_pred CCCHHHHHHHHHHHHHHCCCCCCEEEEEEEE Q ss_conf 8851789999999999709986616999997 Q gi|254781063|r 79 GCPVAGDMPKWIENAVGAVEGISGVEVSITF 109 (129) Q Consensus 79 ~CP~~~~i~~~i~~al~~~~gv~~V~V~~~~ 109 (129) +-++...=.+++++.+++.++|.+|.|+-.| T Consensus 26 ~~~~~~i~~~~i~~~l~~~p~I~~a~V~r~~ 56 (67) T pfam08478 26 GTSFFSVDLNAIEDRLEKLPWIKSASVRRQW 56 (67) T ss_pred CCCEEEECHHHHHHHHHCCCCEEEEEEEEEC T ss_conf 9927999899999987478872699999977 No 40 >pfam02700 PurS Phosphoribosylformylglycinamidine (FGAM) synthase. This family forms a component of the de novo purine biosynthesis pathway. Probab=23.55 E-value=63 Score=14.56 Aligned_cols=53 Identities=17% Similarity=0.147 Sum_probs=33.9 Q ss_pred EEEECC--EEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEE Q ss_conf 332040--132156039969999996589885178999999999970998661699999 Q gi|254781063|r 52 IFELGL--IYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSIT 108 (129) Q Consensus 52 IvdLGl--V~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~~~ 108 (129) +..||+ |.++++ |. .+.+++-....-.+....+++-+.|.+-+=+.+.++++. T Consensus 25 L~~lG~~~v~~vr~---GK-~iel~i~~~~~e~a~~~v~~~c~~lLaNpVIE~y~i~i~ 79 (80) T pfam02700 25 LHRLGYEGVEDVRI---GK-YIELTLEAEDEEEAEEQVEEMCDKLLANPVIEDYRIELE 79 (80) T ss_pred HHHCCCCCCCEEEE---EE-EEEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEE T ss_conf 98648644222774---12-999998689989999999999998638875466999997 No 41 >TIGR02794 tolA_full protein TolA; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.. Probab=23.54 E-value=63 Score=14.56 Aligned_cols=68 Identities=18% Similarity=0.230 Sum_probs=42.1 Q ss_pred CHHHHHHHHHHHHHC---CCCCCCCCCEEEECCEEEEEEECCCEEEEEE--EECCCCCCHHHHHHHHHHHHHHCCC Q ss_conf 535899999999720---8888899843320401321560399699999--9658988517899999999997099 Q gi|254781063|r 28 DLERISNDIIAALKT---VYDPEIPCDIFELGLIYKIDVENDYMVKILM--TLTAPGCPVAGDMPKWIENAVGAVE 98 (129) Q Consensus 28 ~~~~l~~~V~eaL~~---V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l--~lT~~~CP~~~~i~~~i~~al~~~~ 98 (129) +.+.....|...... ++++. +.-.+=-+..|++..||.|.|.= .-.++|||+=..+.+.+..+|.... T Consensus 354 e~~~Y~~~~~~~i~~~~~~~~~~---s~~g~~c~~~i~l~pdG~~~~~~~r~~~~sG~PYd~~~c~Aa~~AV~~~~ 426 (452) T TIGR02794 354 EVDKYAAIIKQAIQQNKNLYDDP---SFRGKTCTVRIRLAPDGTVTLLSARVTKSSGAPYDPALCQAALAAVAKAA 426 (452) T ss_pred HHHHHHHHHHHHHHHHHCCCCCH---HCCCCEEEEEEEECCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHC T ss_conf 78899999999988642356731---01798899988874898578853167536888998677699999999827 No 42 >cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain. Probab=23.10 E-value=64 Score=14.51 Aligned_cols=28 Identities=11% Similarity=0.265 Sum_probs=20.0 Q ss_pred EECCCEEEEEEEECCCCCCHHHHHHHHH Q ss_conf 6039969999996589885178999999 Q gi|254781063|r 63 VENDYMVKILMTLTAPGCPVAGDMPKWI 90 (129) Q Consensus 63 i~~~g~V~V~l~lT~~~CP~~~~i~~~i 90 (129) ++..-++++-++||++.||-.-+..+.+ T Consensus 10 i~~~~~i~vfVSlsC~~CP~vV~a~~~~ 37 (89) T cd03026 10 LNGPINFETYVSLSCHNCPDVVQALNLM 37 (89) T ss_pred CCCCEEEEEEECCCCCCCHHHHHHHHHH T ss_conf 6997689999828999978999999999 No 43 >TIGR02346 chap_CCT_theta T-complex protein 1, theta subunit; InterPro: IPR012721 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 theta 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=23.00 E-value=65 Score=14.49 Aligned_cols=71 Identities=14% Similarity=0.148 Sum_probs=50.3 Q ss_pred HHHHHHHCCCCCCCCC-CEEEECCEEEEEEECCCEEEEEEEECCCC--C--------CHHHHHHHHHHHHHHCCCCCCEE Q ss_conf 9999972088888998-43320401321560399699999965898--8--------51789999999999709986616 Q gi|254781063|r 35 DIIAALKTVYDPEIPC-DIFELGLIYKIDVENDYMVKILMTLTAPG--C--------PVAGDMPKWIENAVGAVEGISGV 103 (129) Q Consensus 35 ~V~eaL~~V~DPEl~v-~IvdLGlV~~i~i~~~g~V~V~l~lT~~~--C--------P~~~~i~~~i~~al~~~~gv~~V 103 (129) ++=..+....=|-|+. +--|||.|..|.+.+=|..+|++.=---. | .+.+-+-+||+||+. +||..+ T Consensus 325 RlCk~~gA~~l~rL~~P~PEe~G~vds~~v~EIG~~~VTvf~~e~~di~~~~TIiLRGsT~N~LDDiERAiD--DGVN~~ 402 (554) T TIGR02346 325 RLCKTVGATPLARLGAPQPEELGYVDSVYVSEIGGQKVTVFKQENGDISKISTIILRGSTKNLLDDIERAID--DGVNVI 402 (554) T ss_pred HHHHHHCCCCCCCCCCCCHHHCCCEEEEEEEEECCCEEEEEEEECCCCCCCCCEEECCCCCCHHHHHHHHHH--CCHHHH T ss_conf 999880777735183458226442007999998584889997303775432116752300001344444430--431210 Q ss_pred EEEE Q ss_conf 9999 Q gi|254781063|r 104 EVSI 107 (129) Q Consensus 104 ~V~~ 107 (129) +.-+ T Consensus 403 K~L~ 406 (554) T TIGR02346 403 KALV 406 (554) T ss_pred HEEE T ss_conf 1000 No 44 >COG4492 PheB ACT domain-containing protein [General function prediction only] Probab=22.36 E-value=67 Score=14.42 Aligned_cols=47 Identities=17% Similarity=0.217 Sum_probs=32.1 Q ss_pred ECCEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEE Q ss_conf 0401321560399699999965898851789999999999709986616999 Q gi|254781063|r 55 LGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVS 106 (129) Q Consensus 55 LGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al~~~~gv~~V~V~ 106 (129) |-....+-+ +|.+.+++.+-++ ..+.=.+.+-.+++.+.+|..|++- T Consensus 101 LTI~Q~ipl--~g~Anvtlsi~~s---sm~~~V~~ii~kl~k~e~V~kVeiv 147 (150) T COG4492 101 LTIHQTIPL--QGRANVTLSIDTS---SMEKDVDKIIEKLRKVEGVEKVEIV 147 (150) T ss_pred EEEECCCCC--CCEEEEEEEEECH---HHHHHHHHHHHHHHCCCCEEEEEEE T ss_conf 998604443--7642589999713---3242299999998521554689985 No 45 >PRK10555 aminoglycoside/multidrug efflux system; Provisional Probab=22.35 E-value=67 Score=14.42 Aligned_cols=78 Identities=13% Similarity=0.262 Sum_probs=40.8 Q ss_pred CCHHHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEECCCEEEEEEEECCCCCC---HHHHHHHHHHHHHHCCCCCCEE Q ss_conf 6535899999999720888889984332040132156039969999996589885---1789999999999709986616 Q gi|254781063|r 27 EDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCP---VAGDMPKWIENAVGAVEGISGV 103 (129) Q Consensus 27 ~~~~~l~~~V~eaL~~V~DPEl~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP---~~~~i~~~i~~al~~~~gv~~V 103 (129) .+.+...++|++++.++. +.+|-++-+-+... ....+.....+.+..+...-. +.+.++++++..++.++||.+| T Consensus 98 ~d~~~a~~~v~~~v~~~~-~~LP~~~~~p~i~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~L~~v~GV~~V 175 (1037) T PRK10555 98 TDPDEAVQQVQNQLQSAM-RKLPQAVQNQGVTV-RKTGDTNILTIAFVSTDGSMDKQDIADYVASNIQDPLSRVNGVGDI 175 (1037) T ss_pred CCHHHHHHHHHHHHHHHH-HCCCCCCCCCCCEE-CCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE T ss_conf 998999999999999888-53997546786441-1468740799999917999799999999999999997369993698 Q ss_pred EEE Q ss_conf 999 Q gi|254781063|r 104 EVS 106 (129) Q Consensus 104 ~V~ 106 (129) ++. T Consensus 176 ~~~ 178 (1037) T PRK10555 176 DAY 178 (1037) T ss_pred EEC T ss_conf 733 No 46 >TIGR00904 mreB cell shape determining protein, MreB/Mrl family; InterPro: IPR004753 Bacterial cell shape varies greatly between species, and characteristic morphologies are used for identification purposes. In addition to individual cell shape, the way in which groups of cells are arranged is also typical of some bacterial species, especially Gram-positive coccoids. For many years, it was believed that micro-organisms with other than spheroidal cell shapes maintained morphology by means of their external cell walls. Recently, however, studies of the Gram-positive rod Bacillus subtilis have revealed two related genes that are essential for the integrity of cell morphogenesis . Termed mreB and mbl, the gene products localise close to the cell surface, forming filamentous helical structures. Many homologues have been found in diverse bacterial groups, suggesting a common ancestor . The crystal structure of MreB from Thermotoga maritima has been resolved using X-ray crystallography . It consists of 19 beta-strands and 15 alpha- helices, and shows remarkable structural similarity to eukaryotic actin. MreB crystals also contain proto-filaments, with individual proteins assembling into polymers like F-actin, in the same orientation. It is hypothesised therefore, that MreB was the forerunner of actin in early eukaryotes .; GO: 0000902 cell morphogenesis. Probab=20.73 E-value=53 Score=15.00 Aligned_cols=28 Identities=29% Similarity=0.605 Sum_probs=20.5 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCEEEECCE Q ss_conf 58999999997208888899843320401 Q gi|254781063|r 30 ERISNDIIAALKTVYDPEIPCDIFELGLI 58 (129) Q Consensus 30 ~~l~~~V~eaL~~V~DPEl~v~IvdLGlV 58 (129) ...-+.|+-+|..+ -|||.-||+|=|+| T Consensus 261 ~~IV~aVk~tLE~t-PPELA~DIveRGiV 288 (337) T TIGR00904 261 NQIVEAVKSTLEKT-PPELAADIVERGIV 288 (337) T ss_pred HHHHHHHHHHHHCC-CCCHHHHHHHCCEE T ss_conf 89999999875168-87046577646937 No 47 >PRK05783 hypothetical protein; Provisional Probab=20.66 E-value=72 Score=14.20 Aligned_cols=65 Identities=17% Similarity=0.171 Sum_probs=37.4 Q ss_pred CCCCCCC---CCCEEEECCEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHH-HCCCCCCEEEEEEE Q ss_conf 0888889---9843320401321560399699999965898851789999999999-70998661699999 Q gi|254781063|r 42 TVYDPEI---PCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAV-GAVEGISGVEVSIT 108 (129) Q Consensus 42 ~V~DPEl---~v~IvdLGlV~~i~i~~~g~V~V~l~lT~~~CP~~~~i~~~i~~al-~~~~gv~~V~V~~~ 108 (129) .|.|||= ..+++.+|+-+-..+-. |.. +.+++....---+....+++-..+ ..-|-|+.+.|++. T Consensus 14 gi~DPeG~TI~~~L~~~g~~~v~~vR~-GK~-l~~~iea~s~eeA~~~v~~ic~~lrL~NPvI~~~~i~v~ 82 (84) T PRK05783 14 GIRDPEGETIQRYVLERMLGYSIEVRA-GKC-LVFRIEASSPEEAQELALKLAKEMRLGNPIVHKIVVRVE 82 (84) T ss_pred CCCCCCHHHHHHHHHHHCCCCEEEEEE-EEE-EEEEEECCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEE T ss_conf 775963379999999855896489871-049-999994799899999999999862034985289999996 No 48 >pfam02084 Bindin Bindin. Probab=20.52 E-value=31 Score=16.44 Aligned_cols=39 Identities=28% Similarity=0.549 Sum_probs=24.0 Q ss_pred HHHHHHHHHHHHHCCCCC---CCCCCE---EEECCEEEEEEECCC Q ss_conf 358999999997208888---899843---320401321560399 Q gi|254781063|r 29 LERISNDIIAALKTVYDP---EIPCDI---FELGLIYKIDVENDY 67 (129) Q Consensus 29 ~~~l~~~V~eaL~~V~DP---El~v~I---vdLGlV~~i~i~~~g 67 (129) ...+..+|++.+|.|.-- +||||| +||||.-+--....+ T Consensus 96 etTIsAkvm~~IKAVLGATKIDLPVDINDPYDLGLLLRHLRHHSN 140 (239) T pfam02084 96 DTTISADVMEKIKAVLGATKIDLPVDINDPYDLGLLLRHLRHHSN 140 (239) T ss_pred CCEEEHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 753509999989998575434674436873367899999887777 Done!