Align Homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_012970814.1 ALVIN_RS07965 3-isopropylmalate dehydratase small subunit
Query= SwissProt::Q9ZND9 (163 letters) >NCBI__GCF_000025485.1:WP_012970814.1 Length = 212 Score = 52.8 bits (125), Expect = 4e-12 Identities = 39/124 (31%), Positives = 58/124 (46%), Gaps = 28/124 (22%) Query: 11 INTDDILPGKY---------APFMVGEDRFHLYAFAHLRPEFAKEVRP------------ 49 ++TD I+P ++ P++ E R+ H P+ RP Sbjct: 19 VDTDAIIPKQFLKSIKRSGFGPYLFDEWRY----LDHGEPDMDCTHRPRNTEFVLNDARY 74 Query: 50 --GDILVFGRNAGLGSSREYAPEALKRLGVRAIIAKSYARIFFRNLVNLGIVPFESE-EV 106 +IL+ N G GSSRE+AP AL G+R I+A S+A IFF N G++P + V Sbjct: 75 QSAEILLTRENFGCGSSREHAPWALTDFGIRVILAPSFADIFFNNCFKNGLLPIRLDAAV 134 Query: 107 VDAL 110 +D L Sbjct: 135 IDGL 138 Lambda K H 0.322 0.144 0.432 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: 74 Number of extensions: 3 Number of successful extensions: 1 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: 163 Length of database: 212 Length adjustment: 19 Effective length of query: 144 Effective length of database: 193 Effective search space: 27792 Effective search space used: 27792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 44 (21.6 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