Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_012675437.1 PERMA_RS04545 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000021565.1:WP_012675437.1 Length = 514 Score = 439 bits (1129), Expect = e-127 Identities = 246/512 (48%), Positives = 333/512 (65%), Gaps = 18/512 (3%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 I DTTLRDGEQ+PG +MT +K+ A+QL KLGVD+IEAGF AS+ DF AV IAE + Sbjct: 6 IFDTTLRDGEQAPGFSMTVEEKVTMAKQLEKLGVDVIEAGFAAASEGDFQAVNAIAETIK 65 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 + + ++R DI A EAL A+R R+ TFIATSPIHM+YKL+ + +QV Sbjct: 66 DST--------VCSLARSLHSDIEKAGEALAPAERKRIHTFIATSPIHMQYKLKMTPEQV 117 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 LE A + VKFAR+ D++F AEDA RS+++FL+++F VI AGA T+ +PDTVG AMP Sbjct: 118 LERAVDAVKFARNF-TDDVEFSAEDAFRSERDFLFKVFEAVIDAGAKTINVPDTVGYAMP 176 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGERAG 266 E+G+LI DI N P I+ A+++ HCHNDLGLA AN++ + GARQ VTINGIGERAG Sbjct: 177 EEFGQLIEDIINNVPNIDKAVISVHCHNDLGLAVANSLSAIKKGARQAHVTINGIGERAG 236 Query: 267 NASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFLH 326 NA+ EEVVM++ R D ++T INT+ I KTS+++ + +G +QP+KA+VG NAF H Sbjct: 237 NAALEEVVMSIKVRH-DYFKDVYTEINTKEIYKTSRLLCRITGSFVQPNKAIVGDNAFAH 295 Query: 327 ESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYK-LKDT 385 E+GIHQ G+L HR TYEI+ ED+G+ S IVLGK SGR A + RLEELGY+ L + Sbjct: 296 EAGIHQHGVLAHRETYEIMRAEDVGVPAS---KIVLGKHSGRHAFKTRLEELGYRNLSEE 352 Query: 386 EVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATVKL 445 EV+ +F +FKA+A+KKK + D D+ AL+ +E F KL V G ++TVK+ Sbjct: 353 EVDKLFRKFKALADKKKEVFDEDIEALIFDELFRTYEEVKLVYFHVLSGNSAIPSSTVKI 412 Query: 446 FSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISRG 505 DG A + G GP+DSA KAI + +L Y++ +++ G DA + Sbjct: 413 -EKDGKEITATACGDGPIDSALKAIEKALGMTGRLKDYSIRSLSAGKDAMGEVRTVV--- 468 Query: 506 DTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 D SG G TD++ +SV AYL A N + Sbjct: 469 DFEGTTVSGKGTSTDIIEASVKAYLDAYNRYI 500 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: 645 Number of extensions: 30 Number of successful extensions: 7 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