Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate AO353_28225 AO353_28225 tartrate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28225 Length = 359 Score = 202 bits (513), Expect = 1e-56 Identities = 128/356 (35%), Positives = 194/356 (54%), Gaps = 28/356 (7%) Query: 3 YRICLIEGDGIGHEVIPAARRVLE--ATGLPLEFVEAEAGW---ETFERRGTSVPEETVE 57 +RI I GDGIG EV+P RVLE A LE W + + G +P++ E Sbjct: 5 FRIAAIAGDGIGKEVLPEGLRVLEQAAKKWQLELSIEVLDWAHCDYYLEHGQMMPDDWFE 64 Query: 58 KILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAK-----SRPVPGSR 109 ++ A FGA P KVP +G++ RR D Y N+RP + P+ G + Sbjct: 65 QLKGFDAIYFGAVGWPD-KVPDHISLWGSLLKFRRDFDQYVNIRPVRLFPGVPCPLAGRK 123 Query: 110 PG-VDLVIVRENTEGLYVEQERRYLD-----VAIADAVISKKASERIGRAALRIAEGRPR 163 PG +D V++RENTEG Y + + + ++V +++ +RI + A +A+ RPR Sbjct: 124 PGDIDFVVIRENTEGEYSSVGGKMFEGTEHEFVLQESVFTRRGVDRILKFAFDLAQTRPR 183 Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTT 223 K L A K+N + ++ + + +A +P + +D + V++P+RFDV+V + Sbjct: 184 KRLTAATKSNGISISMPYWDERTALMAAQYPEITWDKQHIDILCARFVLQPDRFDVVVAS 243 Query: 224 NLLGDILSDLAAGLVGGLGLAPSGNIGDT---TAVFEPVHGSAPDIAGKGIANPTAAILS 280 NL GDILSDL G +G+APS N+ ++FEPVHGSAPDI G+ IANP A I S Sbjct: 244 NLFGDILSDLGPACAGTIGIAPSANLDPERRFPSLFEPVHGSAPDIYGQNIANPIAMIWS 303 Query: 281 AAMMLDYLGEKEAAKR-----VEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 A+MLD+LG + R + +A++ V+ GP TPDLGG +T+ +A+ + L Sbjct: 304 GALMLDFLGNGDERYRAAHDGILQAIERVIAEGPITPDLGGKGSTQDVGKAIADRL 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: 318 Number of extensions: 17 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: 359 Length adjustment: 29 Effective length of query: 305 Effective length of database: 330 Effective search space: 100650 Effective search space used: 100650 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 17 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