Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate Ac3H11_375 Tartrate dehydrogenase (EC 1.1.1.93) @ Tartrate decarboxylase (EC 4.1.1.73) @ D-malic enzyme (EC 1.1.1.83)
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_375 Length = 364 Score = 228 bits (580), Expect = 2e-64 Identities = 142/361 (39%), Positives = 205/361 (56%), Gaps = 29/361 (8%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAE-AGWETFERRGTSVPEETVE 57 +RI ++ GDGIG EV+P RVL+ G+ L F + + W+ +E+ G +P+ E Sbjct: 4 HRIAVVAGDGIGKEVMPEGLRVLDVAARKFGIDLHFDHFDFSSWDYYEKHGKMLPDNWKE 63 Query: 58 KILSCHATLFGAATSPTRKVP--GFFGAIRYLRRRLDLYANVRPAKSRP---VPGSR--- 109 +I S A FGA P + +G++ RR D Y N+RPA+ P P R Sbjct: 64 QIGSHEAIYFGAVGWPEKIADHVSLWGSLLLFRREFDQYINLRPARLMPGVIAPVVRRDG 123 Query: 110 ----PG-VDLVIVRENTEGLYVEQERRYLD-----VAIADAVISKKASERIGRAALRIAE 159 PG +D++IVRENTEG Y R + + + + V+S+ +R+ + A +A+ Sbjct: 124 SPRLPGEIDMLIVRENTEGEYSSIGGRMYEGTPREIVMQETVMSRHGVDRVLKFAFDLAQ 183 Query: 160 GRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDV 219 RP+K L A K+N + +T + + V E+AK +P V V +D V RP+ FDV Sbjct: 184 SRPKKHLTSATKSNGIAITMPYWDERVAEMAKSYPDVKVDKFHIDILTAHFVQRPDFFDV 243 Query: 220 IVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDT---TAVFEPVHGSAPDIAGKGIANPTA 276 +V +NL GDILSDL G +G+APS N+ T ++FEPVHGSAPDIAG+GIANP Sbjct: 244 VVASNLFGDILSDLGPACTGTIGIAPSANLNPTRTMPSLFEPVHGSAPDIAGQGIANPIG 303 Query: 277 AILSAAMMLDYLGEKEAAKRVEKAVDLVLE---RGPRTPDLGGDATTEAFTEAVVEALKS 333 I AMMLD+LG + A V A++ VL+ GPRTPDLGG + T+ +A+ EAL + Sbjct: 304 QIWCGAMMLDFLGYRAAHDAVLAAIEAVLDPQSGGPRTPDLGGKSGTQDVGKAIAEALSA 363 Query: 334 L 334 + Sbjct: 364 V 364 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: 341 Number of extensions: 17 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: 334 Length of database: 364 Length adjustment: 29 Effective length of query: 305 Effective length of database: 335 Effective search space: 102175 Effective search space used: 102175 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