Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_019894549.1 A377_RS0102465 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000384235.1:WP_019894549.1 Length = 517 Score = 403 bits (1035), Expect = e-116 Identities = 240/516 (46%), Positives = 324/516 (62%), Gaps = 25/516 (4%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 I DTTLRDGEQSPGA+MT +K+ ARQL KL VD+IEAGFP AS+ DF AV+ +AE V Sbjct: 10 IFDTTLRDGEQSPGASMTREEKIRIARQLEKLRVDVIEAGFPAASQGDFEAVRSVAEAVR 69 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 + + G++R E DI A EA+ A+ R+ TFIATSPIHME KL+ + DQV Sbjct: 70 DSR--------VCGLARALENDIVRAGEAIAPAEAGRIHTFIATSPIHMEKKLKMTPDQV 121 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 +E A VK AR D++F EDA RSD +FL ++ I AGATT+ IPDTVG +P Sbjct: 122 VEQAVWAVKRARDF-TDDVEFSPEDAGRSDLDFLCRVIEAAIDAGATTINIPDTVGYNIP 180 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGERAG 266 ++G+ I + P + A+ + HCHNDLGLA AN++ + GARQ+E TING+GERAG Sbjct: 181 EQFGERIHQLLTRIPNSDKAVFSAHCHNDLGLAVANSLAAVQAGARQVECTINGLGERAG 240 Query: 267 NASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFLH 326 N + EEVVMA+ R D+ + T I+T IL S++V +G +QP+KA+VGANAF H Sbjct: 241 NTALEEVVMAVRTRQ-DVF-PVDTRIHTPEILAASRLVASITGFAVQPNKAIVGANAFAH 298 Query: 327 ESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLK-DT 385 ESGIHQDG+LKHR TYEI+ ED+G + +VLGK SGR A R+R LG + +T Sbjct: 299 ESGIHQDGVLKHRETYEIMRAEDVGWSM---NRMVLGKHSGRNAFRDRCLSLGIAFETET 355 Query: 386 EVEGVFWQFKAVAEKKKRITDTDLRALV----SNEAFNEQPIWKLGDLQVTCGTVGFSTA 441 E+ F FKA+A++K I D D++ALV S NEQ KL ++V T A Sbjct: 356 ELSEAFMSFKALADRKHEIYDEDIQALVTDNDSRRTENEQV--KLVSMRVQSETGESPMA 413 Query: 442 TVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVE 501 V L+ ++G A + G G VD+ +KAI IV A L Y++ +T G D+ TSV Sbjct: 414 QVTLW-LNGEEKQASAEGGGAVDATFKAIERIVDSGASLELYSVSNVTNGTDSLGETSVR 472 Query: 502 ISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 + +G + +G G TD+V++S AY++ALN ++ Sbjct: 473 MEKGGR---IVNGQGTDTDIVIASAKAYINALNKLM 505 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: 615 Number of extensions: 21 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: 517 Length adjustment: 35 Effective length of query: 505 Effective length of database: 482 Effective search space: 243410 Effective search space used: 243410 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