Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate Synpcc7942_1505 Synpcc7942_1505 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__SynE:Synpcc7942_1505 Length = 365 Score = 201 bits (512), Expect = 2e-56 Identities = 149/364 (40%), Positives = 201/364 (55%), Gaps = 38/364 (10%) Query: 2 AYRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETVE 57 +YRI L+ GDGIG E++ +L A G L EF EA G + G +PE T+ Sbjct: 4 SYRITLLPGDGIGPEIMAVTVDILRAIGRQFDLNFEFEEALIGGSAIDATGEPLPEATLA 63 Query: 58 KILSCHATLFGAA------TSPTRKVP--GFFGAIRYLRRRLDLYANVRPAKSRP--VPG 107 + A L A + P + P G G LR L L+AN+RPA P V Sbjct: 64 TCRNSDAVLLAAIGGYKWDSLPRSQRPETGLLG----LRAGLGLFANLRPAAILPQLVDA 119 Query: 108 SR------PGVDLVIVRENTEGLYVEQ------ERRYLDVAIADAVISKKASERIGRAAL 155 S GVDL++VRE T G+Y + + + A V + +RIGR A Sbjct: 120 SSLKREVIEGVDLMVVRELTGGIYFGEPKGCFADEQGRQRAFNTMVYREDEIDRIGRVAF 179 Query: 156 RIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPE 215 IA R ++ + KANVL ++Q L+ D + + D+ V + + VDN AMQLV P+ Sbjct: 180 DIARKRGKRLCSV-DKANVLEVSQ-LWRDRMTLLGSDYADVELSHLYVDNAAMQLVRWPK 237 Query: 216 RFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIG-DTTAVFEPVHGSAPDIAGKGIANP 274 +FD IVT NL GDILSD+AA L G +G+ PS ++G + VFEPVHGSAPDIAG+ ANP Sbjct: 238 QFDTIVTGNLFGDILSDIAAMLTGSIGMLPSASLGAEGPGVFEPVHGSAPDIAGQDKANP 297 Query: 275 TAAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATT----EAFTEAVVE 329 A +LSAAMML Y L E EAA R+E AV+ VL++G RT DL + T + +A++ Sbjct: 298 LAQVLSAAMMLRYGLDEPEAAARIEAAVNQVLDQGYRTGDLYSEGMTLVGCKGMGDALLA 357 Query: 330 ALKS 333 AL+S Sbjct: 358 ALES 361 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: 306 Number of extensions: 13 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: 365 Length adjustment: 29 Effective length of query: 305 Effective length of database: 336 Effective search space: 102480 Effective search space used: 102480 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