Align Aconitate isomerase; AI; EC 5.3.3.7 (uncharacterized)
to candidate Ac3H11_1182 Hypothetical ABC transport system, periplasmic component
Query= curated2:A0A0A1H8I4 (262 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1182 Length = 233 Score = 135 bits (339), Expect = 1e-36 Identities = 92/236 (38%), Positives = 132/236 (55%), Gaps = 8/236 (3%) Query: 26 VTTLTVLSSGGIMGT---IREVAPAYEKATGVKLDIAAAPSMGDTPQAIPNRLARNEPAD 82 +TT T+L M T + ++ AY A+ + S+G A R+A E D Sbjct: 1 MTTATLLRGISSMATRQVLADLTAAYA-ASAAEAGTVQIESVGGVDAA--KRVAAGEVFD 57 Query: 83 VVLMVGSALDKLVASGQVAKDSRVDLGQSFIAMAVRQGAPKPDISNMDAFKQTLEKAQSV 142 VV++ A+DKL+A+G + S+VD S +A+AV GAP PD+S+ DA + A S+ Sbjct: 58 VVILASDAIDKLLAAGHLLPGSKVDWVHSGVAVAVPAGAPLPDLSSEDAVHSAVLAAPSI 117 Query: 143 AYSDSASGVYLSRILFPRMQLDKSFMAK-ARMIPAEPVGAVVARGEAQLGFQQLSELKAV 201 + S SGV L++ LF R + + + + P PVG++VA+GE LGFQQLSEL V Sbjct: 118 SLSTGPSGVALAK-LFERWGIAEQIAPRMVQAPPGVPVGSLVAKGEVALGFQQLSELLHV 176 Query: 202 PGIDIVGLIPDQAQKMTLYSGAMVSKSQHPEAARALLQYLASKDAAKAIEDSGLKP 257 GI IVG +P Q T +S + SQ +AAR+LL YLAS AA+A + G+ P Sbjct: 177 QGIQIVGPLPPAIQITTTFSAGVGVHSQQADAARSLLAYLASPAAAEAKQKQGMTP 232 Lambda K H 0.316 0.130 0.354 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: 142 Number of extensions: 6 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: 262 Length of database: 233 Length adjustment: 24 Effective length of query: 238 Effective length of database: 209 Effective search space: 49742 Effective search space used: 49742 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 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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