Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 5210998 Shew_3424 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq)
Query= BRENDA::P36683 (865 letters) >FitnessBrowser__PV4:5210998 Length = 865 Score = 1438 bits (3723), Expect = 0.0 Identities = 704/865 (81%), Positives = 785/865 (90%) Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60 MLE YRKHVAERAAEG+ PKPLDA+Q+A L+EL+KNPPAGEEEF+LDLL NR+PPGVDEA Sbjct: 1 MLEAYRKHVAERAAEGVVPKPLDAHQVAELIELVKNPPAGEEEFILDLLENRIPPGVDEA 60 Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 AYVKAGFL A+AKGEA SP+L+ +A+ELLGTMQGGYNI PLI LD+ AP+A KALS Sbjct: 61 AYVKAGFLDAVAKGEATSPILSAARAVELLGTMQGGYNIEPLIAQLDNDVQAPLAVKALS 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180 +TLLMFD ++DV EK +AGN +AKQV++SWA+AEWFL+RP LA+K+T+TVFKVTGETNTD Sbjct: 121 NTLLMFDAYHDVVEKMQAGNAHAKQVVESWANAEWFLSRPKLADKVTLTVFKVTGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240 DLSPAPDAWSRPDIPLHALAMLKNAR+GI PD+ GV GPI +IEAL+QKG PL YVGDVV Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNARDGIVPDEAGVKGPINEIEALKQKGHPLVYVGDVV 240 Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300 GTGSSRKSATNSVLWFMGDDIP VPNKR GG CLGGKIAPIFFNTMEDAGALPIE+DVS Sbjct: 241 GTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSK 300 Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360 +NMGDVID+YPY+G V+ H + E+++ F+LKTDVL+DEVRAGGRIPLIIGRGLT +ARE Sbjct: 301 MNMGDVIDIYPYEGVVKLHGSDEVISEFKLKTDVLLDEVRAGGRIPLIIGRGLTDRARET 360 Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420 LGLP SDVF + +DVA+S +G++LAQKMVG+ACGV G+RPG YCEPKMTSVGSQDTTGPM Sbjct: 361 LGLPASDVFVRPQDVADSGKGYTLAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPM 420 Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480 TRDELKDLACLGFSADL MQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH Sbjct: 421 TRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480 Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES+LVRFKG+M Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEM 540 Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600 QPGITLRDLVHAIP AI+ GLLTVEKKGK N FSGRILEIEGL LKVEQAFEL+DASA Sbjct: 541 QPGITLRDLVHAIPHKAIEMGLLTVEKKGKINAFSGRILEIEGLEKLKVEQAFELSDASA 600 Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660 ERSAAGCTIKL+KEPIIEYLNSNIV+LKWMIAEGYGDRRT+ERRI ME+WLANPEL+ A Sbjct: 601 ERSAAGCTIKLDKEPIIEYLNSNIVMLKWMIAEGYGDRRTIERRIAAMEEWLANPELMAA 660 Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720 DADAEYA VI+IDL +IKEPILCAPNDPDDA LS V+ +IDEVF+GSCMTNIGHFRA Sbjct: 661 DADAEYAEVIEIDLNEIKEPILCAPNDPDDAVLLSQVKDTQIDEVFVGSCMTNIGHFRAT 720 Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780 GK+LD LPTRLW+APPT+MD QLTEEGYY++FG+ GARIEIPGCSLCMGNQARVA Sbjct: 721 GKMLDKFAKTLPTRLWIAPPTKMDRDQLTEEGYYAIFGRVGARIEIPGCSLCMGNQARVA 780 Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840 +GATVVSTSTRNFPNRLGTGANV+LASAELAAVAAL+G+LP+ EEYQ Y ++D TA DT Sbjct: 781 EGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPSVEEYQEYAKEIDATAADT 840 Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865 YRYLNF+Q+ YT+KA VIFQ+AV Sbjct: 841 YRYLNFDQIDSYTQKAGEVIFQSAV 865 Lambda K H 0.317 0.136 0.400 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 2167 Number of extensions: 77 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 865 Length of database: 865 Length adjustment: 42 Effective length of query: 823 Effective length of database: 823 Effective search space: 677329 Effective search space used: 677329 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory