Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_019555815.1 F612_RS0100685 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000381085.1:WP_019555815.1 Length = 514 Score = 416 bits (1068), Expect = e-120 Identities = 239/513 (46%), Positives = 329/513 (64%), Gaps = 21/513 (4%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 + DTTLRDGEQSPGA+MT +K+ A+QL KL VD+IEAGFP AS+ DF +V +A V Sbjct: 7 VFDTTLRDGEQSPGASMTKEEKVRIAKQLEKLRVDVIEAGFPAASQGDFDSVHAVASAVK 66 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 I G++R E DI A EA+K A R+ TFIATSPIHME KLR + D+V Sbjct: 67 EST--------ICGLARAVENDIRKAGEAIKPANSGRIHTFIATSPIHMEKKLRMTPDEV 118 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 +E A VK AR D++F EDA RSD +FL ++ I AGATT+ IPDTVG +MP Sbjct: 119 VERAVWAVKRARDF-TDDVEFSPEDAGRSDVDFLCRVIEAAINAGATTINIPDTVGYSMP 177 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGERAG 266 ++G L ++ P + AI + HCHNDLGLA AN++ R GARQ+E T+NG+GERAG Sbjct: 178 HQFGSLFKELIERIPNSDKAIFSAHCHNDLGLAVANSLSAVRNGARQVECTLNGLGERAG 237 Query: 267 NASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFLH 326 N + EE+VMA+ R D+ + T INT+ IL S++V +G +QP+KA+VGANAF H Sbjct: 238 NTALEEMVMAIKTRQ-DVF-DVDTRINTKEILAASRLVSNITGFAVQPNKAIVGANAFAH 295 Query: 327 ESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLK-DT 385 ESGIHQDG+LKHR TYEI+ ED+G + +V+GK SGR A + RLEELG + + Sbjct: 296 ESGIHQDGVLKHRETYEIMRAEDVGWST---NKMVMGKHSGRNAFKTRLEELGMVFETEQ 352 Query: 386 EVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFN--EQPIWKLGDLQVTCGTVGFSTATV 443 E+ VF +FK +A++K I D DL++L+++ + E I++L L+V+ T S A V Sbjct: 353 ELNDVFVRFKELADRKHEIYDEDLQSLITDNSNQRVENEIYRLIALKVSTETGEASKAEV 412 Query: 444 KLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEIS 503 L+ ++G A + G G VD+ +KAI +VK A L Y++ +T G D+ TSV + Sbjct: 413 TLW-VEGKELYAMAEGGGVVDATFKAIESLVKSGASLELYSVSNVTNGTDSLGETSVRLE 471 Query: 504 RGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536 +G + +G G TD+V+SS AY++ALN + Sbjct: 472 KGGR---IANGQGSDTDIVLSSAKAYINALNKI 501 Lambda K H 0.318 0.134 0.390 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: 610 Number of extensions: 26 Number of successful extensions: 8 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: 540 Length of database: 514 Length adjustment: 35 Effective length of query: 505 Effective length of database: 479 Effective search space: 241895 Effective search space used: 241895 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 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