Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_013643670.1 METBO_RS00320 2-isopropylmalate synthase
Query= BRENDA::Q58595 (518 letters) >NCBI__GCF_000191585.1:WP_013643670.1 Length = 505 Score = 610 bits (1573), Expect = e-179 Identities = 317/509 (62%), Positives = 395/509 (77%), Gaps = 9/509 (1%) Query: 11 IKKALENLNIPDRVYIFDTTLRDGEQTPGVSLTPEEKIDIAIKLDDLGVDVIEAGFPVSS 70 I+ + +N+PD V I DTTLRDGEQTPGV+LT +EKI IA KLD LGV+ +E GFP +S Sbjct: 3 IETVKQTMNLPDTVKILDTTLRDGEQTPGVALTVDEKIRIAKKLDKLGVNTMEVGFPAAS 62 Query: 71 LGEQEAIKKICSLNLDAEICGLARAVKKDIDVAIDCGVDRIHTFIATSPLHRKYKLKKSK 130 GE A K+I L LD+ +CGLAR ++ D+D AIDCGVD IHTFI TSPLHR+YKLK K Sbjct: 63 DGEVRATKEILKLELDSRVCGLARPLRVDLDAAIDCGVDYIHTFIGTSPLHREYKLKMDK 122 Query: 131 EEIIDIAVDAIEYIKEHGIRVEFSAEDATRTEIDYLIEVYKKAVDAGADIINVPDTVGVM 190 EEI++ +V+ +EYIK+HGI EFSAEDATRTE DYL EVY DAGAD INVPDTVGVM Sbjct: 123 EEILNKSVEGVEYIKDHGITAEFSAEDATRTEFDYLKEVYLAVEDAGADFINVPDTVGVM 182 Query: 191 IPRAMYYLINELKKEIKVPISVHCHNDFGLAVANSLAAVEAGAEQVHCTINGLGERGGNA 250 IP +M YLI ELKK +K PISVHCH+DFGLAVANSL+AVEAGA QVH TINGLGER GNA Sbjct: 183 IPSSMNYLITELKKILKTPISVHCHDDFGLAVANSLSAVEAGASQVHSTINGLGERAGNA 242 Query: 251 ALEEVVMSLMSIYGVKTNIKTQKLYEISQLVSKYTEIKVQPNKAIVGENAFAHESGIHAH 310 +LEEVVM+L S Y +KT+I T+ L + S+ VS+ T IK+ PNKAI+GENAFAHE+GIH H Sbjct: 243 SLEEVVMALTSQYNIKTSIDTKLLVDTSEFVSRITGIKMPPNKAIIGENAFAHEAGIHVH 302 Query: 311 GVLAHALTYEPIPPELVGQKRKIILGKHTGTHAIEAKLKELGIEVGKDINKDQFDEIVKR 370 GVL +A TYEPI PE+VG R+I+LGKHTG +AI+AKL E GIE +N+DQF + + Sbjct: 303 GVLQNAETYEPITPEMVGHTRRIVLGKHTGANAIKAKLDEYGIE----LNEDQFIRVFDQ 358 Query: 371 IKALGDKGKRVTDRDVEAIVEDVVGKLAKKDRVVELEQIAVMTGNRVIPTASVALKIEEE 430 +K LGDKGK VTD D++A+ E V+GK K+ +V+LE +VMTG+ V+PTA+V L I + Sbjct: 359 VKRLGDKGKCVTDADLKAMSETVLGKAHKE--IVKLEGFSVMTGDNVMPTATVKLDINGK 416 Query: 431 IKKSSAIGVGPVDAAVKAIQKAIGE--KIKLKEYHINAITGGTDALAEVIVTL-EGYGRE 487 +K ++ GVGPVDAA+ AIQ +GE I+LKEY+I AITGGT+ALAEV V + + G + Sbjct: 417 VKTAAKTGVGPVDAAINAIQSLVGETADIELKEYNIEAITGGTNALAEVFVIMGDKKGNK 476 Query: 488 ITTKAASEDIVRASVEAVIDGINKILAKR 516 T ++ ++D+V ASVEAV+D INKIL +R Sbjct: 477 ATGRSTTDDVVMASVEAVLDSINKILIER 505 Lambda K H 0.316 0.135 0.368 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: 774 Number of extensions: 31 Number of successful extensions: 5 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: 518 Length of database: 505 Length adjustment: 35 Effective length of query: 483 Effective length of database: 470 Effective search space: 227010 Effective search space used: 227010 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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