Align Lactate utilization protein A (characterized)
to candidate AZOBR_RS01615 AZOBR_RS01615 Fe-S oxidoreductase
Query= SwissProt::Q81GA5 (239 letters) >FitnessBrowser__azobra:AZOBR_RS01615 Length = 261 Score = 234 bits (596), Expect = 2e-66 Identities = 114/235 (48%), Positives = 152/235 (64%), Gaps = 1/235 (0%) Query: 2 KVTLFVTCLVDMFETNVGKATVEVLERLGCEIEFPEAQVCCGQPAYNSGHVEAAKEAMKH 61 +V LFVTCLVD++ VG A V++LE GC +E P +Q CCGQPA+N+G A++ + Sbjct: 9 RVGLFVTCLVDVYRPTVGFAAVKLLEDAGCTVEVPASQTCCGQPAFNAGDRATARDLARS 68 Query: 62 MIETFEDAEYIVTPSGSCATMFHE-YPHVFKDDPKWAKRAQKVADKTYEFTQFIVDVLKV 120 I FE +++V PSGSCA + YP + DDP WA RA+ ++ +T+E F+ DVL V Sbjct: 69 TIAAFEGFDHVVVPSGSCAGQIRKHYPELLADDPAWAARARHLSARTHELVSFLTDVLGV 128 Query: 121 TDVGASLPGIATIHKSCHMTRMLGVKEAPGILLSNVKGLTVRDLPNVQNCCGFGGTFSVK 180 TD GA G T H SC R LGVKE P LL+ V+GLT+ +LP + CCGFGGTF VK Sbjct: 129 TDTGARYDGTITYHDSCSGLRELGVKEQPRRLLAKVEGLTLNELPGAEVCCGFGGTFCVK 188 Query: 181 MTPISEQMVDEKVDSVMETGADYLIGADCGCLLNIGGRIERLGKEVKVMHIAEVL 235 IS +MV+ K + T AD L+ D GCLLN+ G+++R G V+V H+AEVL Sbjct: 189 YPDISNRMVEAKTADIAGTKADTLLAGDMGCLLNMAGKLKREGSAVRVRHVAEVL 243 Lambda K H 0.320 0.135 0.407 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: 220 Number of extensions: 9 Number of successful extensions: 3 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: 239 Length of database: 261 Length adjustment: 24 Effective length of query: 215 Effective length of database: 237 Effective search space: 50955 Effective search space used: 50955 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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