Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate PP_2336 PP_2336 aconitate hydratase 1
Query= curated2:A7MIC7 (466 letters) >FitnessBrowser__Putida:PP_2336 Length = 862 Score = 116 bits (290), Expect = 3e-30 Identities = 113/390 (28%), Positives = 170/390 (43%), Gaps = 50/390 (12%) Query: 99 DLNHPYQGIVH---------VMGPEQGITLPGMTIVCGDSHTATHGAFGALAFGIGTSEV 149 D+ P GI+H V+ ++G+ P T V DSHT A G +A G+G E Sbjct: 163 DVIQPGNGIMHQINLEKMSPVVHSDRGVAYPD-TCVGTDSHTPHVDALGVIAIGVGGLEA 221 Query: 150 EHVLATQTLKQGRAKTMKIEVNGRAAPGITAKDIVLAIIGKTGSAGGTGYVVEFCGDAIR 209 E+V+ + + + +E+ G+ AP ITA D+VLA+ G +EF G+ R Sbjct: 222 ENVMLGRASWMRLPEIVGVELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGAR 281 Query: 210 ALSMEGRMTLCNMAIEMGAKAGLVAPDETTFNYVKGRLHAPKGQDFDEAVAYWKT--LKT 267 AL++ R T+ NMA E GA A + A D+ T +Y+ RL + Q Y K L Sbjct: 282 ALTLGDRATISNMAPEYGATAAMFAIDQQTIDYL--RLTGREEQQVKLVETYAKATGLWA 339 Query: 268 DD--GAQFDAVVTLNAEEIAPQVTWGTNPGQVIAVSDAIPDPASFADPVERASAEKALAY 325 D GA ++ ++ + + + +NP +A SD A K +A Sbjct: 340 DSLGGAVYERTLSFDLSSVVRNMAGPSNPHARVATSDL---------------AAKGIAG 384 Query: 326 MGLKPGVPLTDVAIDKVFIGSCTN-SRIEDLRAAAEIAR-----GRKVAPGVQALVVPGS 379 + + D A+ I SCTN S ++ AA IAR G P V++ + PGS Sbjct: 385 SWEEVPGQMPDGAVIIAAITSCTNTSNPRNVIAAGLIARNANKLGLTRKPWVKSSLAPGS 444 Query: 380 GPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP-----------GERCASTS 428 V+ E GL+K + GF C+ C M+ L+P + Sbjct: 445 KAVQLYLEEAGLEKELEQLGFGIVAFACTTCNGMSG-ALDPVIQQEIIDRDLYATAVLSG 503 Query: 429 NRNFEGR-QGRGGRTHLVSPAMAAAAAVTG 457 NRNF+GR + L SP + A A+ G Sbjct: 504 NRNFDGRIHPYAKQAFLASPPLVVAYAIAG 533 Lambda K H 0.318 0.134 0.395 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: 926 Number of extensions: 51 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 466 Length of database: 862 Length adjustment: 38 Effective length of query: 428 Effective length of database: 824 Effective search space: 352672 Effective search space used: 352672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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