Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate 5209348 Shew_1822 aconitate hydratase (RefSeq)
Query= curated2:Q9WZ24 (417 letters) >FitnessBrowser__PV4:5209348 Length = 862 Score = 117 bits (293), Expect = 1e-30 Identities = 111/344 (32%), Positives = 156/344 (45%), Gaps = 48/344 (13%) Query: 114 DLVVGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVWFRVPESIKVTLRGKFKDLVTAK 173 D +VG DSHT ALG A GVG + L + R+P+ + V L GK + +TA Sbjct: 194 DTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRPSYMRLPDIVGVELTGKRQSGITAT 253 Query: 174 DLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEAGGKTGLFPVDEITIA 233 D+VL L L + +EF G G ++++ R TISNM E G G+F +D+ TI Sbjct: 254 DIVLALTEFLRQEKVVSAYLEFFGEGAADLTLGDRATISNMTPEFGASAGMFYIDQQTID 313 Query: 234 YERERGIEVEE------------MYPD--EDAKYVREVEMDLSELEPQVAYPFLPSNAKD 279 Y G + E+ ++ D +DA+Y R + DLS + +A P P Sbjct: 314 YLTITGRDSEQVKLVENYAKTTGLWADSLKDAEYERVLTFDLSSVVRNIAGPSNPHRRVA 373 Query: 280 VSEAEKERIK--IDQ------------AVIGSCTNGRIEDLRLAAQILK------GRTVS 319 SE + I ++Q A I SCTN +AA +L G Sbjct: 374 TSELASQGIAGVVEQDDKLMPDGAVIIAAITSCTNTSNPRNVIAAGLLAKKANELGLVRK 433 Query: 320 PDVRCIIIPGSQKVYKQALKE-GLIDIFIDAGCAVSTPTCGPCLG--GHMGVLAEGEV-- 374 P V+ PGS KV + LK+ GL+ G + C C G G + + + EV Sbjct: 434 PWVKTSFAPGS-KVAELYLKDAGLLPELEQLGFGIVGFACTTCNGMSGALDPVIQQEVID 492 Query: 375 ------AISTTNRNFVGRMGHPNSK-VFLASPAVAAASAIKGYI 411 A+ + NRNF GR+ HP +K FLASP + A AI G I Sbjct: 493 RDLYATAVLSGNRNFDGRI-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: 716 Number of extensions: 39 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 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