Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate 14219 b0073 3-isopropylmalate dehydrogenase (VIMSS)
Query= BRENDA::Q5JFV8 (347 letters) >FitnessBrowser__Keio:14219 Length = 363 Score = 184 bits (467), Expect = 3e-51 Identities = 133/344 (38%), Positives = 184/344 (53%), Gaps = 37/344 (10%) Query: 2 YRVAVIPGDGIGPEVIDGAVRVLKAVTGR----VRFEYYEGGVDVFQECGSPIREEDLEE 57 Y +AV+PGDGIGPEV+ A++VL AV R + +Y+ G G P+ +E Sbjct: 5 YHIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYDVGGAAIDNHGQPLPPATVEG 64 Query: 58 IRRSDAVLFGATTTPF------DLPGYRSLILTLRKELGLYANLR-------------II 98 ++DAVLFG+ P D R +L LRK L++NLR + Sbjct: 65 CEQADAVLFGSVGGPKWEHLPPDQQPERGALLPLRKHFKLFSNLRPAKLYQGLEAFCPLR 124 Query: 99 PDLRT-GREIVIVRENSEGLYFGI-----GAVVNGRAVDVRLITREGAERIARFAVEQAK 152 D+ G +I+ VRE + G+YFG G+ +A D + R ERIAR A E A+ Sbjct: 125 ADIAANGFDILCVRELTGGIYFGQPKGREGSGQYEKAFDTEVYHRFEIERIARIAFESAR 184 Query: 153 ARGSFITFVHKANVLTGDKFFRRIVREVAGE-EGVEVRDAIIDSFTIKLVRNPWEHGVIL 211 R +T + KANVL +R IV E+A E VE+ ID+ T++L+++P + V+L Sbjct: 185 KRRHKVTSIDKANVLQSSILWREIVNEIATEYPDVELAHMYIDNATMQLIKDPSQFDVLL 244 Query: 212 SENLFGDILSDLATVHAGSIGIVPSGNYGD-GIALFEPVHGSAPDIAGKGIANPIGAILS 270 NLFGDILSD + GS+G++PS + + G L+EP GSAPDIAGK IANPI ILS Sbjct: 245 CSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIAQILS 304 Query: 271 GAMLLDYLGLDGSLIRAAVRGYVVNGELTPDMGGRARTEDVVRG 314 A+LL Y LD A+ +N L + RT D+ RG Sbjct: 305 LALLLRY-SLDADDAACAIE-RAINRALEEGI----RTGDLARG 342 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: 311 Number of extensions: 19 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: 363 Length adjustment: 29 Effective length of query: 318 Effective length of database: 334 Effective search space: 106212 Effective search space used: 106212 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