Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate HSERO_RS17185 HSERO_RS17185 2-isopropylmalate synthase
Query= SwissProt::P05342 (385 letters) >FitnessBrowser__HerbieS:HSERO_RS17185 Length = 567 Score = 77.0 bits (188), Expect = 1e-18 Identities = 92/360 (25%), Positives = 142/360 (39%), Gaps = 41/360 (11%) Query: 9 TTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEE----------EREVMH 58 T LRDG Q+ NA+ K+ L + G+ E+E+G PS + E + Sbjct: 37 TDLRDGNQALIEPMNAERKLRFFELLLKTGLKEIEVGFPSASQTDFDFVRKLIVENRIPD 96 Query: 59 AIAGLGLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVA 118 + + L+ R L A+ V + + P ++ + + Sbjct: 97 DVTIIVLTQSREELIRRTIESLEGAKKAIVHLYNSVAPAFRKIVFNMSREEIKNIAVTGT 156 Query: 119 RLVGEARMA--GLEVCL--GCEDASRADLEFVVQVGE-VAQAAGARR-----LRFADTVG 168 RLV E A G E E S +L+F ++ + V + GA L TV Sbjct: 157 RLVKELTDARPGTEWRFEYSPESFSTTELDFSKEICDAVCETWGASPERKVILNLPSTVE 216 Query: 169 VMEPFGMLDRFRFLSRRLDME----LEVHAHDDFGLATANTLAAVMGGATHINTTVNGLG 224 P D+ ++ R L + VH H+D G A A+ AVM GA + + G G Sbjct: 217 CATPNVYADQIEWMCRNLKDRASTIISVHPHNDRGTAVASAELAVMAGADRVEGCLFGNG 276 Query: 225 ERAGNAALEECVLALKNLHGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHE 284 ER GN L L L G++ G+D I + +VE + V + VG VFT Sbjct: 277 ERTGNVDLVTLALNLYT-QGVNPGLDFSDIDVVRQVVEECNQIPVHPRHPYVGDLVFTAF 335 Query: 285 AGIHVDGLLKHRRN----------YEGLNPDELGRSHSLVL------GKHSGAHMVRNTY 328 +G H D + K Y ++P +LGRS+ V+ GK A+++ Y Sbjct: 336 SGSHQDAIKKGFAKQQPDAIWEVPYLPIDPADLGRSYDAVIRVNSQSGKGGMAYLLEQEY 395 Lambda K H 0.320 0.135 0.396 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: 405 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 385 Length of database: 567 Length adjustment: 33 Effective length of query: 352 Effective length of database: 534 Effective search space: 187968 Effective search space used: 187968 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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