Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_012383606.1 BIND_RS03045 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000019845.1:WP_012383606.1 Length = 532 Score = 400 bits (1029), Expect = e-116 Identities = 229/517 (44%), Positives = 319/517 (61%), Gaps = 18/517 (3%) Query: 21 NPTYVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKM 80 N + I DTTLRDGEQSPGA+M +K+E A L +GVD+IEAGFP S+ DF AV Sbjct: 20 NTEQIIIFDTTLRDGEQSPGASMNLDEKIEVAELLDAMGVDVIEAGFPVTSEGDFEAVSA 79 Query: 81 IAEEVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLR 140 I+ V + G++R +DI EAL+ A RPR+ FI+TSP+HM+YKL+ Sbjct: 80 ISRRVKRAS--------VAGLARAAARDIDRCAEALRDAVRPRMHVFISTSPLHMKYKLQ 131 Query: 141 KSKDQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDT 200 K +VL+ V AR+ DI++ AED R++ +FL + IKAGA T+ IPDT Sbjct: 132 KEPGEVLDMISTYVGRARNR-IDDIEWSAEDGTRTEIDFLCRCVEAAIKAGARTINIPDT 190 Query: 201 VGIAMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTING 260 VG +P EY L ++ P + AI + HCHNDLGLA ANT+ G + GARQ+E TING Sbjct: 191 VGYTIPEEYQALFETVRTRVPNSDQAIFSVHCHNDLGLAVANTLAGIKGGARQVECTING 250 Query: 261 IGERAGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVG 320 +GERAGNA+ EEVVMAL R D L H+ I+ R + + SK+V S +Q +KA+VG Sbjct: 251 LGERAGNAAMEEVVMALRVRA-DAL-AYHSNIDARMLTRASKLVSAVSSFPVQYNKAIVG 308 Query: 321 ANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGY 380 NAF HESGIHQDGMLK+ TYEI++PE +G+ ++ ++V+GK SGR A + +L+ELGY Sbjct: 309 RNAFAHESGIHQDGMLKNAQTYEIMTPESVGVHKT---SLVMGKHSGRHAFKEKLKELGY 365 Query: 381 KLKDTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFST 440 +L + +E F +FK +A++KK + D DL ALV +E + KL L V GT G + Sbjct: 366 ELGENALEEAFARFKDLADRKKIVYDEDLIALVDDEIIHAHDRIKLVALTVIAGTKGPQS 425 Query: 441 ATVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSV 500 A + L +IDG + G GP+D+ + A+ +V A L Y + A+T+G DA A SV Sbjct: 426 AALTL-TIDGVEQTHQATGNGPIDAIFNAVQALVPHGAVLELYQVHAVTKGTDAQAEVSV 484 Query: 501 EISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 +S + + G D +V+S AY++ALN ++ Sbjct: 485 RLSE---DGKTVTARGADPDTLVASAKAYIAALNKLV 518 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: 619 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: 532 Length adjustment: 35 Effective length of query: 505 Effective length of database: 497 Effective search space: 250985 Effective search space used: 250985 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