Align Aconitate isomerase; AI; EC 5.3.3.7 (uncharacterized)
to candidate H281DRAFT_02738 H281DRAFT_02738 molybdate transport system substrate-binding protein
Query= curated2:A0A0A1H8I4 (262 letters) >FitnessBrowser__Burk376:H281DRAFT_02738 Length = 262 Score = 184 bits (466), Expect = 2e-51 Identities = 99/251 (39%), Positives = 150/251 (59%), Gaps = 1/251 (0%) Query: 9 ALGALLLASTPLLAAQPVTTLTVLSSGGIMGTIREVAPAYEKATGVKLDIAAAPSMGDTP 68 AL A LL+ + A + VL++G + RE+ P YE+ TG L I+ PS G + Sbjct: 12 ALSAALLSGALISTAVHAADVHVLATGALSAAFRELGPGYERQTGNHLIISWGPSYGTSA 71 Query: 69 QAIPNRLARNEPADVVLMVGSALDKLVASGQVAKDSRVDLGQSFIAMAVRQGAPKPDISN 128 A+P R+ E DV LM+ ALD+ ++ G+ D+R DL S I +AV+ G PKPD+S Sbjct: 72 DALPMRIRNGEAMDVCLMIRPALDEQISQGKFLPDTRTDLVASRIGVAVQAGMPKPDVST 131 Query: 129 MDAFKQTLEKAQSVAYSDSASGVYLSRILFPRMQLDKSFMAKARMIPA-EPVGAVVARGE 187 +D + L A+SVA+S+ ASG Y++ LFPR+ + A++ I E VG + RG+ Sbjct: 132 VDKLRNALLTAKSVAFSEGASGTYITGTLFPRLGIAHQMNARSVQIKGKELVGTAIERGD 191 Query: 188 AQLGFQQLSELKAVPGIDIVGLIPDQAQKMTLYSGAMVSKSQHPEAARALLQYLASKDAA 247 A+LG QQ+SEL+A+ GI VG +P++ QK ++ S A+ + +Q E A AL+ YL + A+ Sbjct: 192 AELGLQQISELRAIQGIQYVGPLPEEVQKASVVSAAVSTSAQEREGAAALISYLKTPAAS 251 Query: 248 KAIEDSGLKPV 258 E +GL P+ Sbjct: 252 AVFEKTGLDPI 262 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: 132 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: 262 Length adjustment: 25 Effective length of query: 237 Effective length of database: 237 Effective search space: 56169 Effective search space used: 56169 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 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