Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate SMa1846 SMa1846 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5JFV8 (347 letters) >FitnessBrowser__Smeli:SMa1846 Length = 347 Score = 175 bits (444), Expect = 1e-48 Identities = 124/346 (35%), Positives = 180/346 (52%), Gaps = 29/346 (8%) Query: 2 YRVAVIPGDGIGPEVIDGAVRVLKAVTGRVRFEY----YEGGVDVFQECGSPIREEDLEE 57 Y +A+IPGDGIG +V D A +VL V F + ++E G+ + + +E Sbjct: 4 YSIALIPGDGIGQDVTDAAWQVLSTVARHSGFTLTGTSFPWSCAFYKETGAMMPADGIEA 63 Query: 58 IRRSDAVLFGATTTPFDLP---GYRSLILTLRKELGLYANLRII--------PDLRTGRE 106 +R DA+L G+ P ++P L+L +RK YAN+R P + + Sbjct: 64 LRPFDAILLGSVGWPAEVPDSISLHGLLLPIRKAFVQYANIRPHRLLSGVEGPLKASDFD 123 Query: 107 IVIVRENSEGLYFGIGAVVNGR-----AVDVRLITREGAERIARFAVEQAKARGSFITFV 161 I+ VREN+EG Y G G V+ AV+ + TR G ERI RFA EQA+ R + V Sbjct: 124 ILCVRENTEGEYSGAGGRVHQGTADEVAVETSIFTRAGVERILRFAFEQARQRRGKLASV 183 Query: 162 HKANVLTGDK-FFRRIVREVAGE-EGVEVRDAIIDSFTIKLVRNPWEHGVILSENLFGDI 219 K+N F+ + R++A E VEV ID+ ++V P V+++ NLFGDI Sbjct: 184 TKSNAQKHSMVFWDEVTRQLADEYPDVEVTSYHIDAMAARVVMAPESLDVVVASNLFGDI 243 Query: 220 LSDLATVHAGSIGIVPSGNYG---DGIALFEPVHGSAPDIAGKGIANPIGAILSGAMLLD 276 L+DL G +G S N ++FEPVHGSAPDIA GIANPI AI SGAM+L+ Sbjct: 244 LTDLGAAIQGGLGFAASANINPDRSAPSMFEPVHGSAPDIAHLGIANPIAAIWSGAMMLE 303 Query: 277 YLG--LDGSLIRAAVRGYVVNGELTPDMGGRARTEDVVRGIIGEIE 320 +LG +I AA+ + G T + G+ RT + ++ ++ Sbjct: 304 HLGEREAAGMIMAALERTTIRGIGT--VPGKDRTRSITAAVLAALD 347 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: 281 Number of extensions: 12 Number of successful extensions: 5 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: 347 Length adjustment: 29 Effective length of query: 318 Effective length of database: 318 Effective search space: 101124 Effective search space used: 101124 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