Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate BWI76_RS10680 BWI76_RS10680 tartrate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Koxy:BWI76_RS10680 Length = 372 Score = 211 bits (536), Expect = 3e-59 Identities = 137/356 (38%), Positives = 203/356 (57%), Gaps = 30/356 (8%) Query: 4 RICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAE-AGWETFERRGTSVPEETVEK 58 RI I GDGIG EV+P RVL+A GL L F E A + + + G +P++ + Sbjct: 6 RIAAIPGDGIGKEVLPEGVRVLQAAAERWGLALSFEHFEWASCDYYAQHGAMMPDDWRAQ 65 Query: 59 ILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAK-----SRPVPGSRP 110 + + A FGA P VP +G++ RR D Y N+RP + P+ G +P Sbjct: 66 LQTFDAIYFGAVGWPDI-VPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQP 124 Query: 111 G-VDLVIVRENTEGLY------VEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPR 163 G +D +VRENTEG Y V + +V I ++V +++ +RI R A +A+ RPR Sbjct: 125 GDIDFYVVRENTEGEYSALGGHVNPGTEH-EVVIQESVFTRRGVDRILRYAFELAQSRPR 183 Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTT 223 +TL A K+N L ++ + V+ +A+++P V +D + V++PERFDV+V + Sbjct: 184 RTLTSATKSNGLAISMPFWDQRVEAMAQEYPEVKWDKQHIDILCARFVLQPERFDVVVGS 243 Query: 224 NLLGDILSDLAAGLVGGLGLAPSGNIG-DTT--AVFEPVHGSAPDIAGKGIANPTAAILS 280 NL GDILSDL G +G+APS N+ D T ++FE VHGSAPDI GK IANP A I + Sbjct: 244 NLFGDILSDLGPACTGTIGIAPSANLNPDRTFPSLFEAVHGSAPDIYGKNIANPIATIWA 303 Query: 281 AAMMLDYLGEKEAAKR-----VEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 AMMLD+LG +A + + A++ + GP+TPD+ G A+T+ EA+ +A+ Sbjct: 304 GAMMLDFLGNGDARYQAAHDGILAAIEQTIASGPKTPDMQGTASTQQVGEAICQAI 359 Lambda K H 0.319 0.137 0.391 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: 322 Number of extensions: 18 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: 334 Length of database: 372 Length adjustment: 29 Effective length of query: 305 Effective length of database: 343 Effective search space: 104615 Effective search space used: 104615 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 (21.7 bits) S2: 49 (23.5 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