Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_012969593.1 ALVIN_RS01770 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000025485.1:WP_012969593.1 Length = 516 Score = 419 bits (1076), Expect = e-121 Identities = 246/515 (47%), Positives = 328/515 (63%), Gaps = 24/515 (4%) Query: 27 ILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEEVG 86 I DTTLRDGEQSPGA+MT +K+ A+ L KL VD+IEAGFP AS DF AVK +AE V Sbjct: 9 IFDTTLRDGEQSPGASMTRDEKVRIAKALEKLRVDVIEAGFPIASPGDFEAVKAVAEAVK 68 Query: 87 NCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKDQV 146 + + G++R + DI A EALK+A R+ TFIATSPIHME KLR S DQV Sbjct: 69 DSR--------VCGLARALDADIDRAGEALKNANAGRIHTFIATSPIHMEKKLRMSPDQV 120 Query: 147 LETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIAMP 206 LE A VK AR+L D++F EDA RS+ +FL +I VI AGA TL IPDTVG +P Sbjct: 121 LEQAVYAVKRARNL-TDDVEFSPEDAGRSEIDFLCRILEAVIDAGARTLNIPDTVGYNIP 179 Query: 207 FEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGERAG 266 ++G LIA ++A P + AI + HCHNDLGLA AN++ R GARQ+E TING+GERAG Sbjct: 180 DQFGSLIATLRARIPNADKAIFSVHCHNDLGLAVANSLAAVRNGARQVECTINGLGERAG 239 Query: 267 NASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAFLH 326 NA+ EE+VM T R L T ++T I+ S++V +G +QP+KA+VGANAF H Sbjct: 240 NAALEEIVM--TVRTRQDLFDCDTRLDTTQIMNCSRLVSGITGFAVQPNKAVVGANAFAH 297 Query: 327 ESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKDTE 386 ESGIHQDG+LKHR TYEI+ +D+G + +VLGK SGR A R RL+ELG + E Sbjct: 298 ESGIHQDGVLKHRETYEIMRAQDVGWSE---NRMVLGKHSGRNAFRARLQELGVVMNSEE 354 Query: 387 -VEGVFWQFKAVAEKKKRITDTDLRALVSN---EAFNEQPIWKLGDLQVTCGTVGFSTAT 442 + F +FK +A+KK I D DL+ALV+ E NE+ KL ++V C G + + Sbjct: 355 DLNAAFARFKDLADKKHEIFDEDLQALVTETTLETANERV--KLVSMRV-CSETGETPSA 411 Query: 443 VKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEI 502 + ++DG + G GPVD+ +KAI +V+ + L Y++ AIT G DA +V + Sbjct: 412 ALVLAVDGQERSGTATGGGPVDATFKAIESLVQTGSTLKLYSVNAITSGTDAQGEVTVRL 471 Query: 503 SRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 +G + +G G TD++V+S AY++A N +L Sbjct: 472 EKGGR---IVNGQGADTDILVASAKAYINACNKIL 503 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: 633 Number of extensions: 24 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: 516 Length adjustment: 35 Effective length of query: 505 Effective length of database: 481 Effective search space: 242905 Effective search space used: 242905 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