Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_043745065.1 AMB_RS17765 2-isopropylmalate synthase
Query= BRENDA::D0VY45 (540 letters) >NCBI__GCF_000009985.1:WP_043745065.1 Length = 514 Score = 418 bits (1074), Expect = e-121 Identities = 231/513 (45%), Positives = 325/513 (63%), Gaps = 17/513 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 V I DTTLRDGEQSPGA+M +K+ A L ++GVD+IEAGFP AS DF AV+ +A+ Sbjct: 6 VIIFDTTLRDGEQSPGASMNLEEKVRIALVLEEMGVDVIEAGFPIASNGDFEAVEAVAKA 65 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 V V I G++R + DI EA++ A R R+ TF++TSP+HM+YKL+ + Sbjct: 66 VKTSV--------ICGLARATKGDIERCAEAIRPAARGRIHTFLSTSPLHMKYKLQMEPE 117 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 +VLE V +AR L D+++ AED +R++ +FL + I AGA T+ IPDTVG A Sbjct: 118 KVLEKVAESVAYARKL-TDDVEWSAEDGSRTEHDFLCRCVEAAIAAGARTINIPDTVGYA 176 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 +P EY LIA + P I+ A+++ HCHNDLGLA AN++ GARQ+E T+NG+GER Sbjct: 177 VPDEYAALIAMLINRVPNIDKAVLSVHCHNDLGLAVANSLAAVGKGARQIECTVNGLGER 236 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGNA+ EE+VMAL R D+L TGI T +I + S++V +G +QP+KA+VG NAF Sbjct: 237 AGNAAMEEIVMALRTRP-DLL-PFKTGIKTENITRASRLVSTITGFVVQPNKAIVGKNAF 294 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 HESGIHQDG+LKH TYEI++PE +GL RS +V+GK SGR A + +L+ELGY+L D Sbjct: 295 AHESGIHQDGVLKHAQTYEIMTPESVGLHRS---NLVMGKHSGRAAFKAKLKELGYELGD 351 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATVK 444 +E F +FK +A++KK + D D+ ALV + KL L+V CGT + Sbjct: 352 NAIEDAFTRFKDLADRKKDVFDEDIVALVDDAVVRGNDRVKLVSLEVLCGTKHQPPSATL 411 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 S+DG + + G GPVD+ + AI + A+L Y + A+T+G DA A +V + Sbjct: 412 ELSVDGEVKGVRATGDGPVDATFNAIKALFPHEARLQLYQVSAVTQGTDAQAEVTVRL-- 469 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNML 537 + + +G G TD +V+S AY++ALN +L Sbjct: 470 -EEDGKTVNGQGAETDTLVASARAYVNALNKLL 501 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: 639 Number of extensions: 25 Number of successful extensions: 6 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 09 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