Align Aconitate isomerase; AI; EC 5.3.3.7 (uncharacterized)
to candidate WP_013091154.1 BC1002_RS16585 molybdenum ABC transporter substrate-binding protein
Query= curated2:A0A0A1H8I4 (262 letters) >NCBI__GCF_000092885.1:WP_013091154.1 Length = 238 Score = 144 bits (362), Expect = 2e-39 Identities = 89/230 (38%), Positives = 136/230 (59%), Gaps = 7/230 (3%) Query: 29 LTVLSSGGIMGTIREVAPAYEKATGVKLDIAAAPSMGDTPQAIPNRLARNEPADVVLMVG 88 +T +SS + E+A +YE+ TG + A S+G A R+ +E D+V++ Sbjct: 14 ITGISSMATRQVLAELAASYERRTGQSV---AIESVGGVDAA--RRVENDEVFDIVVLAA 68 Query: 89 SALDKLVASGQVAKDSRVDLGQSFIAMAVRQGAPKPDISNMDAFKQTLEKAQSVAYSDSA 148 A+++LV +G V SRV L +S IA+AV GA +PDI+ A + + A+S+ YS Sbjct: 69 DAIERLVVTGYVEAASRVGLARSGIAVAVAAGATQPDIATEAALRDAILGARSIGYSTGP 128 Query: 149 SGVYLSRILFPRMQLDKSFMAK-ARMIPAEPVGAVVARGEAQLGFQQLSELKAVPGIDIV 207 SG +L + LF R + ++ + P PVG +VARGE LGFQQ+SEL VPGID++ Sbjct: 129 SGTHLLK-LFERWGIAGQIASRIVKAPPGVPVGTLVARGEVALGFQQMSELIHVPGIDVL 187 Query: 208 GLIPDQAQKMTLYSGAMVSKSQHPEAARALLQYLASKDAAKAIEDSGLKP 257 G +P Q T ++ A+ + ++H EAARALL +LAS++A A +G+ P Sbjct: 188 GELPAAIQSTTTFTAAVCTAARHREAARALLTFLASREADGAKLQNGMLP 237 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: 118 Number of extensions: 4 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: 238 Length adjustment: 24 Effective length of query: 238 Effective length of database: 214 Effective search space: 50932 Effective search space used: 50932 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 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