Align Aconitate isomerase; AI; EC 5.3.3.7 (uncharacterized)
to candidate H281DRAFT_03337 H281DRAFT_03337 molybdate transport system substrate-binding protein
Query= curated2:A0A0A1H8I4 (262 letters) >FitnessBrowser__Burk376:H281DRAFT_03337 Length = 260 Score = 225 bits (573), Expect = 8e-64 Identities = 119/249 (47%), Positives = 160/249 (64%) Query: 12 ALLLASTPLLAAQPVTTLTVLSSGGIMGTIREVAPAYEKATGVKLDIAAAPSMGDTPQAI 71 A L+A++ A L V+SSGG + + P + TG LD A PSMG +P+AI Sbjct: 11 AALIATSAAAANVHAADLHVMSSGGFTAAYKVLGPKFSAETGNALDTALGPSMGKSPEAI 70 Query: 72 PNRLARNEPADVVLMVGSALDKLVASGQVAKDSRVDLGQSFIAMAVRQGAPKPDISNMDA 131 PNRL R EPAD V+MVG ALD L+ G+V SRV+L S I M VR+GA KPDIS++D Sbjct: 71 PNRLERGEPADAVIMVGYALDDLIQKGKVVPGSRVELADSRIGMVVREGAAKPDISSVDG 130 Query: 132 FKQTLEKAQSVAYSDSASGVYLSRILFPRMQLDKSFMAKARMIPAEPVGAVVARGEAQLG 191 +QTL A+S+AYSDSASGVY+ R LF ++ ++ AKA+MIP PV +VVA G+ ++G Sbjct: 131 LRQTLLHAKSIAYSDSASGVYIERELFKKLGIEDQVKAKAKMIPRIPVASVVANGDYEIG 190 Query: 192 FQQLSELKAVPGIDIVGLIPDQAQKMTLYSGAMVSKSQHPEAARALLQYLASKDAAKAIE 251 FQQ+SEL V G VG IP+ Q +T ++ + +QHP+ A+ALL YLAS ++ Sbjct: 191 FQQVSELLPVKGATFVGKIPESLQSVTRFAAGIPVSAQHPKEAKALLDYLASPGVQPEVK 250 Query: 252 DSGLKPVPA 260 +GL V A Sbjct: 251 STGLDTVSA 259 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: 187 Number of extensions: 2 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: 260 Length adjustment: 25 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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