Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate PP_2336 PP_2336 aconitate hydratase 1
Query= curated2:Q9WZ24 (417 letters) >FitnessBrowser__Putida:PP_2336 Length = 862 Score = 118 bits (295), Expect = 8e-31 Identities = 108/343 (31%), Positives = 146/343 (42%), Gaps = 46/343 (13%) Query: 114 DLVVGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVWFRVPESIKVTLRGKFKDLVTAK 173 D VG DSHT ALG A GVG + L W R+PE + V L GK +TA Sbjct: 194 DTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPEIVGVELTGKLAPNITAT 253 Query: 174 DLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEAGGKTGLFPVDEITIA 233 DLVL L L +EF G G + +++ R TISNMA E G +F +D+ TI Sbjct: 254 DLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGATAAMFAIDQQTID 313 Query: 234 YERERGIEVEEMYPDE--------------DAKYVREVEMDLSELEPQVAYPFLPSNAKD 279 Y R G E +++ E A Y R + DLS + +A P P Sbjct: 314 YLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVRNMAGPSNPHARVA 373 Query: 280 VSEAEKERI--------------KIDQAVIGSCTNGRIEDLRLAAQILK------GRTVS 319 S+ + I + A I SCTN +AA ++ G T Sbjct: 374 TSDLAAKGIAGSWEEVPGQMPDGAVIIAAITSCTNTSNPRNVIAAGLIARNANKLGLTRK 433 Query: 320 PDVRCIIIPGSQKVYKQALKEGLIDIFIDAGCAVSTPTCGPCLG--GHMGVLAEGEV--- 374 P V+ + PGS+ V + GL G + C C G G + + + E+ Sbjct: 434 PWVKSSLAPGSKAVQLYLEEAGLEKELEQLGFGIVAFACTTCNGMSGALDPVIQQEIIDR 493 Query: 375 -----AISTTNRNFVGRMGHPNSK-VFLASPAVAAASAIKGYI 411 A+ + NRNF GR+ HP +K FLASP + A AI G I Sbjct: 494 DLYATAVLSGNRNFDGRI-HPYAKQAFLASPPLVVAYAIAGTI 535 Lambda K H 0.318 0.138 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: 728 Number of extensions: 33 Number of successful extensions: 3 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: 417 Length of database: 862 Length adjustment: 37 Effective length of query: 380 Effective length of database: 825 Effective search space: 313500 Effective search space used: 313500 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: 53 (25.0 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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