Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF2253 HP15_2203 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683 (865 letters) >FitnessBrowser__Marino:GFF2253 Length = 864 Score = 1269 bits (3284), Expect = 0.0 Identities = 620/859 (72%), Positives = 720/859 (83%), Gaps = 4/859 (0%) Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60 MLE YR+HVAER A GI PKPL+A Q AALV+LLKNPPAGEE+ L+ LL NRVPPGVDEA Sbjct: 1 MLEAYREHVAEREALGIPPKPLNAEQTAALVDLLKNPPAGEEDTLVYLLENRVPPGVDEA 60 Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 AYVKA FL AI KGEA SPLL A++LLG MQGGYNI L+D LDD++LA +A + L Sbjct: 61 AYVKAAFLTAIVKGEASSPLLDKPTAVKLLGMMQGGYNIATLVDLLDDSELAELAGEQLK 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180 TLLMFD F DV+EK AGN A+ V++SWA+ EWF N+ + E + VFKVTGETNTD Sbjct: 121 RTLLMFDAFNDVKEKMDAGNPVARAVIESWANGEWFTNKKKVPESTKMVVFKVTGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240 DLSPAPDAWSRPDIPLHA A K R+G++P++PGV GP+ QI+ ++ KG P+A+VGDVV Sbjct: 181 DLSPAPDAWSRPDIPLHARAAYKMERDGLKPEEPGVTGPMSQIDEIKAKGLPVAFVGDVV 240 Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300 GTGSSRKSATNSVLWF GDDIP VPNKR GG+C+G K+APIFFNTMEDAGAL E V + Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPGVPNKRAGGVCIGNKVAPIFFNTMEDAGALVFEAPVDD 300 Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360 +NMGDVI++ PY G++ N E GE ++ F+ K+DV++DEV+AGGRIPLIIGRGLT KAR A Sbjct: 301 MNMGDVIEIRPYDGKILN-EAGETISEFKFKSDVILDEVQAGGRIPLIIGRGLTAKARTA 359 Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417 LG+ +D+FR KD +GF+LAQKMVG+ACG+ KG+RP YCEP MT+VGSQDTT Sbjct: 360 LGMGATDLFRLPKDPEAGTKGFTLAQKMVGKACGLEEGKGVRPNTYCEPHMTTVGSQDTT 419 Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477 GPMTRDELKDLACLGF ADLVMQSFCHTAAYPKPVDV HT+PDFI RGGVSLRPGDG Sbjct: 420 GPMTRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVEMQHTMPDFIRTRGGVSLRPGDG 479 Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537 +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFK Sbjct: 480 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 539 Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597 G+MQPGITLRDLVHAIPLY IKQG+LTVEKKGK N FSGRILEIEGL L VEQAFEL+D Sbjct: 540 GEMQPGITLRDLVHAIPLYGIKQGMLTVEKKGKINEFSGRILEIEGLEHLTVEQAFELSD 599 Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657 ASAERSAAGCTI L+++ + EYL SNI +L+WMIAEGYGD RTLERR Q ME+WLA+P+L Sbjct: 600 ASAERSAAGCTINLSEDSVAEYLRSNITMLRWMIAEGYGDPRTLERRAQQMEEWLADPKL 659 Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717 + AD DAEYA VI+IDLADIKEPI+C PNDPDDA+ LS V G+K+DEVFIGSCMTNIGHF Sbjct: 660 MRADKDAEYAHVIEIDLADIKEPIVCCPNDPDDAKFLSEVAGDKVDEVFIGSCMTNIGHF 719 Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777 RAAGKLL+ HKG L TRLW++PPT+MD AQL EEGY++ +G +G R E+PGCSLCMGNQA Sbjct: 720 RAAGKLLEQHKGPLSTRLWMSPPTKMDQAQLMEEGYFNTYGTAGVRTEMPGCSLCMGNQA 779 Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837 RVA +TV+STSTRNFPNRLG GANV+L SAELAAV A++GKLP+P EY Y ++ + Sbjct: 780 RVAPKSTVLSTSTRNFPNRLGDGANVYLTSAELAAVGAVLGKLPSPAEYMEYAKDLNSMS 839 Query: 838 VDTYRYLNFNQLSQYTEKA 856 + Y+YLNF+Q+ YT+KA Sbjct: 840 KEIYKYLNFDQMENYTKKA 858 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: 2088 Number of extensions: 72 Number of successful extensions: 3 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: 864 Length adjustment: 42 Effective length of query: 823 Effective length of database: 822 Effective search space: 676506 Effective search space used: 676506 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