Align Aconitate isomerase; AI; EC 5.3.3.7 (uncharacterized)
to candidate WP_108401383.1 B9Z44_RS00285 molybdate ABC transporter substrate-binding protein
Query= curated2:A0A0A1H8I4 (262 letters) >NCBI__GCF_003063475.1:WP_108401383.1 Length = 263 Score = 190 bits (483), Expect = 2e-53 Identities = 104/258 (40%), Positives = 157/258 (60%), Gaps = 4/258 (1%) Query: 4 RLPTLALGALLLASTPLLAAQPVTTLTVLSSGGIMGTIREVAPAYEKATGVKLDIAAAPS 63 RL + +G L A+ AA+ + V++SG +++ P +EK TG K+ A S Sbjct: 10 RLLLVGVGLFLAAAQIAQAAE----IRVITSGAFTEAYKQLVPEFEKQTGHKVISAFGAS 65 Query: 64 MGDTPQAIPNRLARNEPADVVLMVGSALDKLVASGQVAKDSRVDLGQSFIAMAVRQGAPK 123 +G+ P AIP R +R E D++++ L+ ++ G V + SRVDL +S I AVR+G PK Sbjct: 66 VGNAPDAIPTRFSRGEKFDLIILSDGGLEAMIKKGNVIQGSRVDLVRSQIGAAVRKGTPK 125 Query: 124 PDISNMDAFKQTLEKAQSVAYSDSASGVYLSRILFPRMQLDKSFMAKARMIPAEPVGAVV 183 PDIS + A KQTL A+S+AYS SASG YLS LFP++ + + A+ I +E VGAVV Sbjct: 126 PDISTVAALKQTLLNAKSIAYSASASGTYLSTELFPKLGVAEQLKDTAKKIMSERVGAVV 185 Query: 184 ARGEAQLGFQQLSELKAVPGIDIVGLIPDQAQKMTLYSGAMVSKSQHPEAARALLQYLAS 243 ARG+A+LGFQQ+SEL +D +G +P+ Q+ +S +V S + A+ L+++ S Sbjct: 186 ARGDAELGFQQVSELIYFKELDFIGTLPESVQQTIFFSAGLVEGSTEQDTAKQLIKFFQS 245 Query: 244 KDAAKAIEDSGLKPVPAQ 261 + A+ I +GL PV A+ Sbjct: 246 PEVAETIRQTGLDPVAAR 263 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: 159 Number of extensions: 8 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: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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