Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_012275611.1 SHAL_RS02455 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683 (865 letters) >NCBI__GCF_000019185.1:WP_012275611.1 Length = 865 Score = 1431 bits (3705), Expect = 0.0 Identities = 697/865 (80%), Positives = 783/865 (90%) Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60 MLE YRKHVAERA+EG+ PKPLDA Q+A LVEL+KNPPAGEE F+LDLL NR+PPGVDEA Sbjct: 1 MLEAYRKHVAERASEGVVPKPLDAQQVAQLVELVKNPPAGEEAFILDLLENRIPPGVDEA 60 Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 AYVKAGFL A+AK E SP+L+ ++A+ELLGTMQGGYNI PLI LD+ AP+A KALS Sbjct: 61 AYVKAGFLDAVAKCEIASPILSSQRAVELLGTMQGGYNIEPLIAQLDNDAQAPLAVKALS 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180 HTLLMFD+F+DV +K +AGN+YAKQV+ +WADA+WFL+RP LAEK+++TVFKV+GETNTD Sbjct: 121 HTLLMFDSFHDVVDKMQAGNDYAKQVVHAWADAKWFLSRPKLAEKISLTVFKVSGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240 DLSPAPDAWSRPDIPLHALAMLKNAR+GI PD+ GVVGPIK+IE+L+ KGFPL YVGDVV Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNARDGIVPDEAGVVGPIKEIESLKTKGFPLVYVGDVV 240 Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300 GTGSSRKSATNSVLWFMGDDIP+VPNKR GG CLGGKIAPIFFNTMEDAGALPIE+DVS Sbjct: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSK 300 Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360 + MGDVID+YPY+G V+ H T E+++ F LKTDVL+DEVRAGGRIPLIIGRGLT +ARE Sbjct: 301 MEMGDVIDIYPYEGIVKRHGTDEVISQFSLKTDVLMDEVRAGGRIPLIIGRGLTDRARET 360 Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420 L L S F + KDVA++ +GF+LAQKMVG+ACGV GIRPG YCEPKMTSVGSQDTTGPM Sbjct: 361 LNLEASTEFVRPKDVADTGKGFTLAQKMVGKACGVTGIRPGQYCEPKMTSVGSQDTTGPM 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 FSGR+LEIEGL LKVEQAFEL+DASA Sbjct: 541 QPGITLRDLVHAIPHKAIEMGLLTVEKKGKINAFSGRVLEIEGLEQLKVEQAFELSDASA 600 Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660 ERSAAGCTIKL+KEPIIEYLNSNIV+LKWMI+EGYGDRRT+ERRI M++WLA PEL+EA Sbjct: 601 ERSAAGCTIKLDKEPIIEYLNSNIVMLKWMISEGYGDRRTIERRITAMQEWLATPELMEA 660 Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720 D+DAEYA VI+IDL +IKEPILCAPNDPDDA LS+V KIDEVF+GSCMTNIGHFRA Sbjct: 661 DSDAEYAEVIEIDLNEIKEPILCAPNDPDDAILLSSVVNTKIDEVFVGSCMTNIGHFRAT 720 Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780 GK+LD LPTRLW+APPT+MD QLTEEGYY++FG+ GARIEIPGCSLCMGNQARVA Sbjct: 721 GKMLDKFASTLPTRLWIAPPTKMDRDQLTEEGYYAIFGRVGARIEIPGCSLCMGNQARVA 780 Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840 +GATVVSTSTRNFPNRLGTGANV+LASAELA+VAAL+G+LP+P+EYQTY ++D TA DT Sbjct: 781 EGATVVSTSTRNFPNRLGTGANVYLASAELASVAALLGRLPSPDEYQTYAKELDATAADT 840 Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865 YRYL+F++++ YT KAD VIFQTAV Sbjct: 841 YRYLSFDKIASYTAKADEVIFQTAV 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: 2136 Number of extensions: 75 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 24 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