Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_057509301.1 ABB28_RS14490 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_001431535.1:WP_057509301.1 Length = 527 Score = 388 bits (997), Expect = e-112 Identities = 226/522 (43%), Positives = 323/522 (61%), Gaps = 27/522 (5%) Query: 22 PTYVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMI 81 P +RI DTTLRDGEQSPG +M+ QKL AR L +LGVD+IE GFP +S+ D A+ MI Sbjct: 11 PPRIRIFDTTLRDGEQSPGCSMSPQQKLVMARALDELGVDVIETGFPASSQSDREAMTMI 70 Query: 82 AEEVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRK 141 EV PV+ +SRC DI T+ +L A PRL F++TSP+H E+KLR Sbjct: 71 GREVQR--------PVLAVLSRCLAADIETSVRSLDSAAHPRLHVFLSTSPLHREHKLRM 122 Query: 142 SKDQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTV 201 +++QVLE+ R V ARS D++F AEDA R++ ++L ++ I AGATT+ +PDTV Sbjct: 123 TREQVLESVRKHVALARSY-IDDVEFSAEDATRTELDYLIEVSRVAIAAGATTINLPDTV 181 Query: 202 GIAMPFE----YGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVT 257 G P E + ++IA + A+ G E I + HCHNDLGLA AN++ GARQ+E T Sbjct: 182 GFTTPEEIRAMFQQVIAGV-ADVSGAERVIFSAHCHNDLGLAVANSLAAIEGGARQVECT 240 Query: 258 INGIGERAGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKA 317 +NGIGERAGN + EE+ MAL R T INT+ I+ TS+++++ G+ +Q +KA Sbjct: 241 VNGIGERAGNCAVEEIAMALKVR--QAFYDQDTAINTQRIVSTSQLLQRLVGMPVQRNKA 298 Query: 318 LVGANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEE 377 +VGANAF HESGIHQ GML+HRGTYEI+ PED+G S +VLG+ SGR A+ RL Sbjct: 299 IVGANAFAHESGIHQHGMLRHRGTYEIMRPEDVGWEDS---QMVLGRHSGRAAVEARLRA 355 Query: 378 LGYKLKDTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVG 437 LG+ L++ E++ VF QFK++ E+++ +TD+DL+ L+ A + ++L + T VG Sbjct: 356 LGFWLEEEELKLVFEQFKSLCEQQRVVTDSDLQTLMQGGASTQG--YRLASM--TISDVG 411 Query: 438 F-STATVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATA 496 + A V+L DG+ + G GPVD+ + A++ +L Y + ++ G DA Sbjct: 412 SRANALVELSDPDGNRVAETAQGDGPVDALFGALSSATGVSLQLDSYQVHSVGIGADARG 471 Query: 497 TTSVEISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNMLR 538 ++ + GD VF GTG D++ +S A+L N +LR Sbjct: 472 EANLSVRSGD---EVFEGTGTSRDIIEASALAWLDVANRLLR 510 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: 605 Number of extensions: 25 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: 527 Length adjustment: 35 Effective length of query: 505 Effective length of database: 492 Effective search space: 248460 Effective search space used: 248460 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