Align Lactate utilization protein A (characterized)
to candidate BPHYT_RS26975 BPHYT_RS26975 Fe-S oxidoreductase
Query= SwissProt::O07020 (238 letters) >FitnessBrowser__BFirm:BPHYT_RS26975 Length = 247 Score = 157 bits (398), Expect = 1e-43 Identities = 92/247 (37%), Positives = 127/247 (51%), Gaps = 15/247 (6%) Query: 1 MKVSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMK 60 MKV+LF+ C +D F VG AT+ELLER G +VD+P+ Q CCGQP NSG +A + Sbjct: 1 MKVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER 60 Query: 61 RMIETFQDSEYVVSPSGSCTTMFREYPHLFQDDPKWADKAKKLADKTYELTDFIVNVLGV 120 F +Y+V PS SC RE+ + D+ KK+ YEL +F+ +V+G Sbjct: 61 VFARNFAGYDYIVGPSASCIHHVREHLTALEQ----TDEVKKVRANAYELVEFLHDVVGA 116 Query: 121 EDV-GATLHTKATLHTSCHMTRLL----------GVRKEPMKLLSHVKGLQFTELPGKHN 169 + A + LH SC R L +P LL VKG++F + Sbjct: 117 REFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDE 176 Query: 170 CCGFGGTFSVKMAQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRKDKNVKVM 229 CCGFGGTFSV +S +M +KV GAE ++ D CLM+ G R + + + Sbjct: 177 CCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFI 236 Query: 230 HIAEVLN 236 HIA+VLN Sbjct: 237 HIAQVLN 243 Lambda K H 0.321 0.136 0.411 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: 209 Number of extensions: 17 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: 238 Length of database: 247 Length adjustment: 23 Effective length of query: 215 Effective length of database: 224 Effective search space: 48160 Effective search space used: 48160 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 (21.9 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