Align Homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_052669763.1 NITAL_RS17280 aconitate hydratase
Query= SwissProt::Q9ZND9 (163 letters) >NCBI__GCF_000969705.1:WP_052669763.1 Length = 670 Score = 75.9 bits (185), Expect = 1e-18 Identities = 57/172 (33%), Positives = 85/172 (49%), Gaps = 23/172 (13%) Query: 8 GDQINTDDILPGKYA--PFMVGEDRFHLYAFAHLRPEFAKEV-------RPGDILVFGRN 58 GD ++TD+IL A P+ +AF + P + G ++V GRN Sbjct: 483 GDDVSTDEILRAGAAVLPYRSNIPEIARFAFDVIDPTYHDRAVAIQEAGGAGHVVVGGRN 542 Query: 59 AGLGSSREYAPEALKRLGVRAIIAKSYARIFFRNLVNLGIVP--FESEEVVDALEDGDEV 116 G GSSRE+A A + +G+RA + SYARI ++NL N G++P F E DAL GD + Sbjct: 543 YGQGSSREHAALAPRHVGLRATLVVSYARIHWQNLANFGVLPLRFADERDRDALAQGDRL 602 Query: 117 ELD-----LESGV-------LTRGEERFALRPPPPFLLEALKEGSLLDYYKK 156 L L+SG LT+G A+ P +E ++ G ++ Y K+ Sbjct: 603 RLTGLHAALDSGSGEVTVENLTQGTTITAVHDLSPRQVERIRSGGVIRYMKE 654 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: 216 Number of extensions: 9 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: 670 Length adjustment: 28 Effective length of query: 135 Effective length of database: 642 Effective search space: 86670 Effective search space used: 86670 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: 48 (23.1 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