Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate AZOBR_RS14130 AZOBR_RS14130 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5JFV8 (347 letters) >FitnessBrowser__azobra:AZOBR_RS14130 Length = 371 Score = 174 bits (442), Expect = 2e-48 Identities = 132/366 (36%), Positives = 200/366 (54%), Gaps = 44/366 (12%) Query: 3 RVAVIPGDGIGPEVIDGAVRVLKAVTGR--VRFEYYEG--GVDVFQECGSPIREEDLEEI 58 ++ +PGDGIGPEV+ RV+ + + V F+ EG G G P+++E L + Sbjct: 6 KLLFLPGDGIGPEVMRQVRRVIDWLDRKRNVTFDVTEGLVGGAAIDAYGVPLKDETLADA 65 Query: 59 RRSDAVLFGATTTP-FDLPGYRSL-----ILTLRKELGLYANLR-------------IIP 99 +DAV+ GA P +D P + +L+LRKEL L+ANLR + Sbjct: 66 LAADAVMLGAVGGPKWDNPTDYTKRPEAGLLSLRKELNLFANLRPAVVFDALVDASTLKA 125 Query: 100 DLRTGREIVIVRENSEGLYFG----IGAVVNG--RAVDVRLITREGAERIARFAVEQAKA 153 D+ G +I+IVRE + G+YFG I + NG R V+ ++ T R+AR A E A+ Sbjct: 126 DVIKGLDILIVRELTGGVYFGEPRGITDIGNGERRGVNTQVYTTSEIRRVARVAFELARK 185 Query: 154 RGSFITFVHKANVLTGDKFFRRIVREVAGEE--GVEVRDAIIDSFTIKLVRNPWEHGVIL 211 RG+ + + KANV+ +R+ V ++ EE V + D+ ++L++NP + VI+ Sbjct: 186 RGNKLHSMEKANVMESGLLWRQEVTKLHQEEFSDVTLEHMYADNGAMQLLKNPKQFDVIV 245 Query: 212 SENLFGDILSDLATVHAGSIGIVPSGNYG------DGIALFEPVHGSAPDIAGKGIANPI 265 ++NLFGDILSD A + GS+G++PS + G AL+EPVHGSAPDIAG+ +ANP Sbjct: 246 TDNLFGDILSDEAAMMTGSLGMLPSASLGAPDANGQRKALYEPVHGSAPDIAGRDLANPC 305 Query: 266 GAILSGAMLLDY---LGLDGSLIRAAVRGYVVNGELTPDM--GGRARTEDVVRG--IIGE 318 +LS AM L Y + + ++ AV+ + G T D+ G AR V G I+ E Sbjct: 306 ATLLSFAMCLRYSFNMDEEAKMLEKAVQNVLSGGMRTADIMAPGMARCSTTVMGDSILRE 365 Query: 319 IEDLLS 324 ++ L S Sbjct: 366 LDKLAS 371 Lambda K H 0.321 0.143 0.411 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: 329 Number of extensions: 24 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: 347 Length of database: 371 Length adjustment: 29 Effective length of query: 318 Effective length of database: 342 Effective search space: 108756 Effective search space used: 108756 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 (21.8 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