Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_057508507.1 ABB28_RS10115 tartrate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_001431535.1:WP_057508507.1 Length = 356 Score = 222 bits (566), Expect = 1e-62 Identities = 137/354 (38%), Positives = 202/354 (57%), Gaps = 29/354 (8%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAE-AGWETFERRGTSVPEETVE 57 ++I +I GDGIG EV+P RVLEA L L+F + A + +++ G +P++ Sbjct: 5 FKIAVIPGDGIGQEVMPEGLRVLEAAARRFQLDLQFTHIDWASCDYYQQHGQMMPDDWKV 64 Query: 58 KILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAK-----SRPVPGSR 109 ++ A FGA P VP +G++ RR D Y N+RP + P+ G + Sbjct: 65 QLQDMDAIFFGAVGWPDT-VPDHVSLWGSLLKFRREFDQYINLRPVRLFEGVPCPLAGRK 123 Query: 110 PG-VDLVIVRENTEG--------LYVEQERRYLDVAIADAVISKKASERIGRAALRIAEG 160 PG +D ++VRENTEG +Y ER ++ I + V+S+ ++R+ + A +A+ Sbjct: 124 PGDIDFLVVRENTEGEYTNLGGIMYAGTER---EIVIQETVMSRHGADRVLKYAYELAQS 180 Query: 161 RPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVI 220 R R+ L +A K+N + ++ + V +P V V +D + V++P+RFDV+ Sbjct: 181 RTRRHLTVATKSNGIAISMPWWDGRADAVGAAYPEVTVDKQHIDILTARFVLQPQRFDVV 240 Query: 221 VTTNLLGDILSDLAAGLVGGLGLAPSGNIG---DTTAVFEPVHGSAPDIAGKGIANPTAA 277 V +NL GDILSDL G +GLAPS N+ D ++FEPVHGSAPDI G+GIANP A Sbjct: 241 VASNLFGDILSDLGPACTGTIGLAPSANLNPERDFPSLFEPVHGSAPDIFGQGIANPIAM 300 Query: 278 ILSAAMMLDYLGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 I S A+ML +LG +EA + A++ VL +GP TPDLGG ATT EAV A+ Sbjct: 301 IWSGALMLKFLGSEEAHDAIMAAIEGVLAQGPLTPDLGGKATTAQLGEAVAAAV 354 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: 304 Number of extensions: 16 Number of successful extensions: 5 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: 356 Length adjustment: 29 Effective length of query: 305 Effective length of database: 327 Effective search space: 99735 Effective search space used: 99735 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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