Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_084275692.1 B8779_RS06295 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_900176045.1:WP_084275692.1 Length = 356 Score = 235 bits (600), Expect = 1e-66 Identities = 153/348 (43%), Positives = 206/348 (59%), Gaps = 22/348 (6%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETVEK 58 Y + LI+GDGIG E+I A +VL+A G + + EA G + G +PEET+E Sbjct: 4 YTVALIKGDGIGPEIIDEAVKVLDAVSVKEGFEITYKEALLGGAAIDVTGEPIPEETIEI 63 Query: 59 ILSCHATLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPAK--------SRPV 105 S A LFGA P R G ++ LR+ L+++AN+RP S Sbjct: 64 AKSADAVLFGAIGGPQWDDLPRDKRPETGLLK-LRKALEVFANLRPVTVYDELVNASTLK 122 Query: 106 PGSRPGVDLVIVRENTEGLYVEQERRYL-DVAIADAVISKKASERIGRAALRIAEGRPRK 164 P G DL++VRE G+Y Q R Y D A V +K+ RI + IA R +K Sbjct: 123 PEVIQGTDLMVVRELIGGIYFGQPRAYEGDRAYNTMVYTKQEVYRIAKVGFEIAMKRNKK 182 Query: 165 TLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTN 224 + + KANVL ++Q L+ DTV EVAK++P V+V+ + VDN AMQLV P++FDVI+T N Sbjct: 183 LVSV-DKANVLEVSQ-LWRDTVNEVAKEYPEVSVEHMYVDNAAMQLVRDPKQFDVILTGN 240 Query: 225 LLGDILSDLAAGLVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMM 284 + GDILSD A+ L G +GL PS +IG+ ++EP+HGSAPDIAG+GIANP A I SAAMM Sbjct: 241 IFGDILSDEASMLSGSIGLLPSASIGEKYGLYEPIHGSAPDIAGQGIANPIATIASAAMM 300 Query: 285 LDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 L Y GE+ AAKR+E A+ VL+ G RT DL E T + + +L Sbjct: 301 LRYQFGEESAAKRIEDAIKRVLKEGYRTKDLSSFDAKEVVTTSEMGSL 348 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: 281 Number of extensions: 14 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: 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 Jul 25 2024. The underlying query database was built on Jul 25 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