Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_004511698.1 GMET_RS13850 aconitate hydratase
Query= SwissProt::Q9ZNE0 (418 letters) >NCBI__GCF_000012925.1:WP_004511698.1 Length = 648 Score = 198 bits (504), Expect = 3e-55 Identities = 150/427 (35%), Positives = 211/427 (49%), Gaps = 26/427 (6%) Query: 1 MGQTLAEKIL-SHKVGRPVRAGELVVVEVDQVMVVDSIAGSFFKRLEYLEATPRYPERVS 59 MG+ LA KIL +H ++ G + +++D ++ D+ + LE +RV Sbjct: 1 MGKNLATKILEAHLAKGELKPGTEIALKIDHALLQDATG-----TMAMLEFIAMGVDRVK 55 Query: 60 I-----VIDHVAPAANLEVAKAQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWV 114 + IDH + A + +R GI V G GV HQV +E PG Sbjct: 56 VELAAQYIDHNLLQTDNRNADDHIFLMTAAQRFGIHVSKPGNGVSHQVHLER-FGVPGKT 114 Query: 115 VVGSDSHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGRLPKGVTAKDA 174 ++G+DSH+T+ + G G D++LA A L P+ V G L V+AKD Sbjct: 115 MLGADSHTTSAAGLSMIAIGAGGLDVSLAMAGHPFHLPCPKIWGVKLTGELQPWVSAKDV 174 Query: 175 ALEMVRLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVVPSG----E 230 LEM+R T +G +E + G L+ +R + N+ E GA V PS E Sbjct: 175 ILEMLRRHTVKGGVGKIIEYYG-PGVATLSATDRAIIGNMGAELGATTS-VFPSDHRTRE 232 Query: 231 ILEMY-RVPDW--LYPDPDARYAKEVEIDLSALTPRVSVPFYVDNVHEVAQVKGKRVDQV 287 LE R W L DPDA Y + EIDL+ + P ++ P DNV VA ++G +VDQV Sbjct: 233 FLEAQGRGQLWQELAADPDATYDEYEEIDLATVEPLIARPSSPDNVVRVADIEGLKVDQV 292 Query: 288 FIGTCTNGRIEDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATI 347 +G+ N DL +L GR++AP + V P S QVLE A G ++ LL AGA I Sbjct: 293 LVGSSANSAFRDLMTVCRILDGRRIAPHLSFNVNPGSRQVLENVADQGGIMMLLLAGAQI 352 Query: 348 GTPGCGPCMGRHMGVLAPG--EVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYL 405 PGC C+G MG APG +V + T RNF GR G + +YL SP AAA+ + G + Sbjct: 353 HQPGCLGCIG--MG-QAPGTNQVSLRTFPRNFPGRSGTKNDLVYLCSPETAAAAGLFGVV 409 Query: 406 TTPEELE 412 T P +LE Sbjct: 410 TDPRKLE 416 Lambda K H 0.318 0.135 0.393 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: 599 Number of extensions: 38 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: 418 Length of database: 648 Length adjustment: 35 Effective length of query: 383 Effective length of database: 613 Effective search space: 234779 Effective search space used: 234779 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 Apr 10 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