Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_011385541.1 AMB_RS16020 tartrate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_000009985.1:WP_011385541.1 Length = 358 Score = 204 bits (519), Expect = 3e-57 Identities = 136/354 (38%), Positives = 193/354 (54%), Gaps = 25/354 (7%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEAT-----GLPLEFVEAEAGWETFERRGTSVPEETVE 57 ++I I DGIG EV+ A VL+ G L + G + +++ GT +PE E Sbjct: 4 FKIAAIPADGIGKEVVAAGLEVLDVLAKRDGGFRLNIETFDWGSDYYKKHGTMMPENGRE 63 Query: 58 KILSCHATLFGAATSPTRKVPG---FFGAIRYLRRRLDLYANVRPAK-----SRPVPGSR 109 + A FGA +P VP +G + + D YANVRP + P+ G Sbjct: 64 TLKQFDAIYFGAVGAPD--VPDHVTLWGLRLNICQPFDQYANVRPTRILPGIKSPLAGVG 121 Query: 110 PGV-DLVIVRENTEGLYVEQERRYL-----DVAIADAVISKKASERIGRAALRIAEGRPR 163 P + + VIVREN+EG Y Q R +VA A+ ++ RI R A ++A+ RPR Sbjct: 122 PRLLNWVIVRENSEGEYAGQGGRSHRGFPEEVATEVAIFTRAGVTRIMRFAFKLAQSRPR 181 Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTT 223 K L + K+N ++ + EVA +FP V ++VD M++ ++PE D IV T Sbjct: 182 KLLTVVTKSNAQRHGMVMWDEIAAEVAGEFPDVTWDKMLVDAMTMRMTLKPETLDTIVAT 241 Query: 224 NLLGDILSDLAAGLVGGLGLAPSGNIGDT---TAVFEPVHGSAPDIAGKGIANPTAAILS 280 NL DILSDLAA L G LG+AP+ N+ ++FEP+HGSA DI GKGIANP + Sbjct: 242 NLHADILSDLAAALAGSLGIAPTANLNPERKFPSMFEPIHGSAFDITGKGIANPIGTFWT 301 Query: 281 AAMMLDYLGEKEAAKRVEKAVDLVLERG-PRTPDLGGDATTEAFTEAVVEALKS 333 A MMLD+LGE A+ R+ +A++ V TPDLGG ATT T+AV+ A+++ Sbjct: 302 ACMMLDHLGETAASARLMRAIERVTANPLLHTPDLGGKATTRIVTDAVIAAIEA 355 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: 288 Number of extensions: 21 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: 358 Length adjustment: 29 Effective length of query: 305 Effective length of database: 329 Effective search space: 100345 Effective search space used: 100345 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