Align Aconitate isomerase; AI; EC 5.3.3.7 (uncharacterized)
to candidate WP_028312319.1 H566_RS0116655 molybdate ABC transporter substrate-binding protein
Query= curated2:A0A0A1H8I4 (262 letters) >NCBI__GCF_000482785.1:WP_028312319.1 Length = 276 Score = 216 bits (549), Expect = 5e-61 Identities = 115/252 (45%), Positives = 163/252 (64%) Query: 10 LGALLLASTPLLAAQPVTTLTVLSSGGIMGTIREVAPAYEKATGVKLDIAAAPSMGDTPQ 69 +GA L AS L + V++SG +E+ PA+E+ TG + A S G Sbjct: 25 VGATLAASALLACQALAADINVMTSGAFTAAYKELVPAFERDTGHAIHSAYGASQGGAAD 84 Query: 70 AIPNRLARNEPADVVLMVGSALDKLVASGQVAKDSRVDLGQSFIAMAVRQGAPKPDISNM 129 +IP+RL R EPADVV+M ALD LV +G+V S VDL +S I M VR GAP+PDIS + Sbjct: 85 SIPSRLDRGEPADVVIMARPALDALVKAGKVVPGSEVDLVRSSIGMVVRAGAPRPDISTV 144 Query: 130 DAFKQTLEKAQSVAYSDSASGVYLSRILFPRMQLDKSFMAKARMIPAEPVGAVVARGEAQ 189 +A K+TL A+SVAYS SASG YLS LFP++ + ++ K + I + V A+VARGEA+ Sbjct: 145 EALKKTLLAAKSVAYSASASGTYLSTELFPKLGVAEAIAPKLQRIESARVAAIVARGEAE 204 Query: 190 LGFQQLSELKAVPGIDIVGLIPDQAQKMTLYSGAMVSKSQHPEAARALLQYLASKDAAKA 249 +GFQQ+SEL VPG+D VG++P+ AQ+ T +S + + ++ PE +AL++Y S AA Sbjct: 205 IGFQQVSELLPVPGVDFVGVLPEGAQRATFFSAGITTTARAPEEGKALIRYFGSPAAAPV 264 Query: 250 IEDSGLKPVPAQ 261 IE +GL+ +PA+ Sbjct: 265 IERTGLEALPAR 276 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: 189 Number of extensions: 7 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: 262 Length of database: 276 Length adjustment: 25 Effective length of query: 237 Effective length of database: 251 Effective search space: 59487 Effective search space used: 59487 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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