Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate WP_013431026.1 CALKRO_RS10670 aconitate hydratase
Query= curated2:O28084 (416 letters) >NCBI__GCF_000166775.1:WP_013431026.1 Length = 643 Score = 327 bits (837), Expect = 8e-94 Identities = 175/414 (42%), Positives = 247/414 (59%), Gaps = 2/414 (0%) Query: 1 MGKTIAEKILSEKS-KSDAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59 MG T+A+KI+ + K + G + IDQ QD T +A Q +G + R+ Sbjct: 1 MGLTVAQKIIKQHLVKGEMIPGKEIAIRIDQTLTQDSTGTMAYLQFEAMGIDRVKTKRSV 60 Query: 60 FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119 ++DH E ++D +I AKK G F+ PG GI HQ+ +ER+ PG +G+DS Sbjct: 61 AYIDHNTLQTGPENADDHLYIQTVAKKYGIYFSKPGNGICHQVHLERFAVPGQTLLGSDS 120 Query: 120 HTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIG 179 HT T GGIG + G G DVAVA+ G+ + +P+ +V L G L V AKD+IL+L+ Sbjct: 121 HTPTAGGIGMLAIGAGGLDVAVAMGGGEYYLIMPKIVKVNLKGKLQPWVSAKDIILELLR 180 Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239 L V G K E+ GE + +++ ER TI NM E GA IF SDE T +FL GRE Sbjct: 181 RLTVKGGVGKIFEYTGEGVKALSIPERATITNMGAELGATTSIFPSDEVTYEFLKAQGRE 240 Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299 DF E+ D DA+Y++EI +D+SSLVP+ + PH+ DNV +SE++G +V+QV IG+CTN Sbjct: 241 ADFVEILPDPDAQYDEEIEIDLSSLVPLAACPHSPDNVVPVSELKGIKVDQVAIGSCTNS 300 Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359 DL A+IL+G+ + E V L++ P S++V G + V AG +L CGPC Sbjct: 301 SYKDLMKVAKILEGKTIAEHVSLVISPGSKQVLNMLAQNGALASMVAAGARILECACGPC 360 Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPR 413 +G+ Q G + + T NRNF+GR G P+A+++L SP TAAASA+ GYI DPR Sbjct: 361 IGMGQAPRTGG-ISLRTFNRNFEGRSGTPSAKVYLVSPETAAASAITGYITDPR 413 Lambda K H 0.318 0.136 0.391 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: 653 Number of extensions: 30 Number of successful extensions: 2 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: 416 Length of database: 643 Length adjustment: 35 Effective length of query: 381 Effective length of database: 608 Effective search space: 231648 Effective search space used: 231648 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: 52 (24.6 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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