Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate RR42_RS21205 RR42_RS21205 2-isopropylmalate synthase
Query= SwissProt::P05342 (385 letters) >FitnessBrowser__Cup4G11:RR42_RS21205 Length = 565 Score = 82.4 bits (202), Expect = 3e-20 Identities = 92/346 (26%), Positives = 145/346 (41%), Gaps = 37/346 (10%) Query: 9 TTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEEREVMHAIAGLG---- 64 T LRDG Q+ N K+ L ++G+ ++E+ PS + + + + + Sbjct: 36 TDLRDGNQALIEPMNPQRKLRFFEQLVKIGLKQIEVAFPSASQTDFDFVRMLIEEDRIPD 95 Query: 65 -LSSRLLAWCR--LCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVA--- 118 ++ +L R L + + R +V L P++ R+ ++E+A Sbjct: 96 DVTIVVLTQAREDLIRRTIESVRGAARAVVHLYNPIAPAFRRIVFGASRE-EVKEIALEG 154 Query: 119 -RLVGEARMAGLEVCLGCEDA----SRADLEFVVQVGEVAQAA---GARR---LRFADTV 167 RL+ E E + S +L+F ++V + A G R L TV Sbjct: 155 TRLIKALTDGMPETAWSYEYSPETFSMTELDFSLEVCDAVSAIWQPGPTRPLILNLPTTV 214 Query: 168 GVMEPFGMLDRF----RFLSRRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGL 223 P D+ R L+RR D+ L VH H+D G A A AVM GA + + G Sbjct: 215 ECSTPNIFADQVEWMHRHLARRADIVLSVHPHNDRGTAVAAAELAVMAGADRVEGCLFGN 274 Query: 224 GERAGNAALEECVLALKNLHGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTH 283 GER GN L L L G+D G+D I + VE + V + VG VFT Sbjct: 275 GERTGNVDLVTLALNLYT-QGVDPGLDFSDIDEVRQCVEDCNQLPVHPRHPYVGDLVFTA 333 Query: 284 EAGIHVD----GLLKHRRN------YEGLNPDELGRSHSLVLGKHS 319 +G H D G +H+ + Y ++P +LGRS+ V+ +S Sbjct: 334 FSGSHQDAIRKGFAQHKADAIWEVPYLPIDPADLGRSYDAVIRVNS 379 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: 434 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 385 Length of database: 565 Length adjustment: 33 Effective length of query: 352 Effective length of database: 532 Effective search space: 187264 Effective search space used: 187264 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